From: hansonr Date: Thu, 23 Jul 2015 15:10:13 +0000 (+0100) Subject: JAL-1807 test X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;p=jalviewjs.git JAL-1807 test --- diff --git a/bin/.gitignore b/bin/.gitignore new file mode 100644 index 0000000..77d60bf --- /dev/null +++ b/bin/.gitignore @@ -0,0 +1,9 @@ +/MCview/ +/awt2swing/ +/com/ +/fr/ +/jalview/ +/javajs/ +/netscape/ +/org/ +/swingjs/ diff --git a/bin/MCview/Atom.js b/bin/MCview/Atom.js index 1f4c66f..ff57b47 100644 --- a/bin/MCview/Atom.js +++ b/bin/MCview/Atom.js @@ -1,55 +1,55 @@ -Clazz.declarePackage ("MCview"); -Clazz.load (["java.awt.Color"], "MCview.Atom", ["java.lang.Float"], function () { -c$ = Clazz.decorateAsClass (function () { -this.x = 0; -this.y = 0; -this.z = 0; -this.number = 0; -this.name = null; -this.resName = null; -this.resNumber = 0; -this.insCode = ' '; -this.resNumIns = null; -this.type = 0; -this.color = null; -this.chain = null; -this.alignmentMapping = -1; -this.atomIndex = 0; -this.occupancy = 0; -this.tfactor = 0; -this.isSelected = false; -Clazz.instantialize (this, arguments); -}, MCview, "Atom"); -Clazz.prepareFields (c$, function () { -this.color = java.awt.Color.lightGray; -}); -Clazz.makeConstructor (c$, -function (str) { -this.atomIndex = Integer.parseInt (str.substring (6, 11).trim ()); -this.name = str.substring (12, 15).trim (); -this.resName = str.substring (17, 20); -this.chain = str.substring (21, 22); -this.resNumber = Integer.parseInt (str.substring (22, 26).trim ()); -this.resNumIns = str.substring (22, 27).trim (); -this.insCode = str.substring (26, 27).charAt (0); -this.x = ( new Float (str.substring (30, 38).trim ()).floatValue ()); -this.y = ( new Float (str.substring (38, 46).trim ()).floatValue ()); -this.z = ( new Float (str.substring (47, 55).trim ()).floatValue ()); -var tm = str.substring (54, 60).trim (); -if (tm.length > 0) { -this.occupancy = ( new Float (tm)).floatValue (); -} else { -this.occupancy = 1; -}tm = str.substring (60, 66).trim (); -if (tm.length > 0) { -this.tfactor = ( new Float (tm).floatValue ()); -} else { -this.tfactor = 1; -}}, "~S"); -Clazz.makeConstructor (c$, -function (x, y, z) { -this.x = x; -this.y = y; -this.z = z; -}, "~N,~N,~N"); -}); +Clazz.declarePackage ("MCview"); +Clazz.load (["java.awt.Color"], "MCview.Atom", ["java.lang.Float"], function () { +c$ = Clazz.decorateAsClass (function () { +this.x = 0; +this.y = 0; +this.z = 0; +this.number = 0; +this.name = null; +this.resName = null; +this.resNumber = 0; +this.insCode = ' '; +this.resNumIns = null; +this.type = 0; +this.color = null; +this.chain = null; +this.alignmentMapping = -1; +this.atomIndex = 0; +this.occupancy = 0; +this.tfactor = 0; +this.isSelected = false; +Clazz.instantialize (this, arguments); +}, MCview, "Atom"); +Clazz.prepareFields (c$, function () { +this.color = java.awt.Color.lightGray; +}); +Clazz.makeConstructor (c$, +function (str) { +this.atomIndex = Integer.parseInt (str.substring (6, 11).trim ()); +this.name = str.substring (12, 15).trim (); +this.resName = str.substring (17, 20); +this.chain = str.substring (21, 22); +this.resNumber = Integer.parseInt (str.substring (22, 26).trim ()); +this.resNumIns = str.substring (22, 27).trim (); +this.insCode = str.substring (26, 27).charAt (0); +this.x = ( new Float (str.substring (30, 38).trim ()).floatValue ()); +this.y = ( new Float (str.substring (38, 46).trim ()).floatValue ()); +this.z = ( new Float (str.substring (47, 55).trim ()).floatValue ()); +var tm = str.substring (54, 60).trim (); +if (tm.length > 0) { +this.occupancy = ( new Float (tm)).floatValue (); +} else { +this.occupancy = 1; +}tm = str.substring (60, 66).trim (); +if (tm.length > 0) { +this.tfactor = ( new Float (tm).floatValue ()); +} else { +this.tfactor = 1; +}}, "~S"); +Clazz.makeConstructor (c$, +function (x, y, z) { +this.x = x; +this.y = y; +this.z = z; +}, "~N,~N,~N"); +}); diff --git a/bin/MCview/Bond.js b/bin/MCview/Bond.js index 539e323..9aaba45 100644 --- a/bin/MCview/Bond.js +++ b/bin/MCview/Bond.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("MCview"); -Clazz.load (["java.awt.Color"], "MCview.Bond", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.start = null; -this.end = null; -this.startCol = null; -this.endCol = null; -this.at1 = null; -this.at2 = null; -Clazz.instantialize (this, arguments); -}, MCview, "Bond"); -Clazz.prepareFields (c$, function () { -this.startCol = java.awt.Color.lightGray; -this.endCol = java.awt.Color.lightGray; -}); -Clazz.makeConstructor (c$, -function (at1, at2) { -this.start = Clazz.newFloatArray (-1, [at1.x, at1.y, at1.z]); -this.end = Clazz.newFloatArray (-1, [at2.x, at2.y, at2.z]); -this.startCol = at1.color; -this.endCol = at2.color; -this.at1 = at1; -this.at2 = at2; -}, "MCview.Atom,MCview.Atom"); -Clazz.defineMethod (c$, "translate", -function (x, y, z) { -this.start[0] = this.start[0] + x; -this.end[0] = this.end[0] + x; -this.start[1] = this.start[1] + y; -this.end[1] = this.end[1] + y; -this.start[2] = this.start[2] + z; -this.end[2] = this.end[2] + z; -}, "~N,~N,~N"); -}); +Clazz.declarePackage ("MCview"); +Clazz.load (["java.awt.Color"], "MCview.Bond", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.start = null; +this.end = null; +this.startCol = null; +this.endCol = null; +this.at1 = null; +this.at2 = null; +Clazz.instantialize (this, arguments); +}, MCview, "Bond"); +Clazz.prepareFields (c$, function () { +this.startCol = java.awt.Color.lightGray; +this.endCol = java.awt.Color.lightGray; +}); +Clazz.makeConstructor (c$, +function (at1, at2) { +this.start = Clazz.newFloatArray (-1, [at1.x, at1.y, at1.z]); +this.end = Clazz.newFloatArray (-1, [at2.x, at2.y, at2.z]); +this.startCol = at1.color; +this.endCol = at2.color; +this.at1 = at1; +this.at2 = at2; +}, "MCview.Atom,MCview.Atom"); +Clazz.defineMethod (c$, "translate", +function (x, y, z) { +this.start[0] = this.start[0] + x; +this.end[0] = this.end[0] + x; +this.start[1] = this.start[1] + y; +this.end[1] = this.end[1] + y; +this.start[2] = this.start[2] + z; +this.end[2] = this.end[2] + z; +}, "~N,~N,~N"); +}); diff --git a/bin/MCview/PDBChain.class b/bin/MCview/PDBChain.class index 3e017ed..8244cf6 100644 Binary files a/bin/MCview/PDBChain.class and b/bin/MCview/PDBChain.class differ diff --git a/bin/MCview/PDBChain.js b/bin/MCview/PDBChain.js index b58d3dd..727e98e 100644 --- a/bin/MCview/PDBChain.js +++ b/bin/MCview/PDBChain.js @@ -1,286 +1,286 @@ -Clazz.declarePackage ("MCview"); -Clazz.load (["java.util.Vector"], "MCview.PDBChain", ["MCview.Bond", "$.Residue", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.Sequence", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "java.awt.Color", "java.lang.StringBuilder"], function () { -c$ = Clazz.decorateAsClass (function () { -this.id = null; -this.bonds = null; -this.atoms = null; -this.residues = null; -this.offset = 0; -this.sequence = null; -this.shadow = null; -this.isNa = false; -this.isVisible = true; -this.pdbstart = 0; -this.pdbend = 0; -this.seqstart = 0; -this.seqend = 0; -this.pdbid = ""; -this.newline = null; -this.shadowMap = null; -Clazz.instantialize (this, arguments); -}, MCview, "PDBChain"); -Clazz.prepareFields (c$, function () { -this.bonds = new java.util.Vector (); -this.atoms = new java.util.Vector (); -this.residues = new java.util.Vector (); -this.newline = System.getProperty ("line.separator"); -}); -Clazz.makeConstructor (c$, -function (pdbid, id) { -this.pdbid = pdbid.toLowerCase (); -this.id = id; -}, "~S,~S"); -Clazz.defineMethod (c$, "setNewlineString", -function (nl) { -this.newline = nl; -}, "~S"); -Clazz.defineMethod (c$, "getNewlineString", -function () { -return this.newline; -}); -Clazz.defineMethod (c$, "print", -function () { -var tmp = new StringBuilder (256); -for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { -tmp.append (b.at1.resName).append (" ").append (b.at1.resNumber).append (" ").append (this.offset).append (this.newline); -} -return tmp.toString (); -}); -Clazz.defineMethod (c$, "makeExactMapping", -function (as, s1) { -var pdbpos = as.getSeq2Start () - 2; -var alignpos = s1.getStart () + as.getSeq1Start () - 3; -for (var atom, $atom = this.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { -atom.alignmentMapping = -1; -} -for (var i = 0; i < as.astr1.length; i++) { -if (as.astr1.charAt (i) != '-') { -alignpos++; -}if (as.astr2.charAt (i) != '-') { -pdbpos++; -}if (as.astr1.charAt (i) == as.astr2.charAt (i)) { -var res = this.residues.elementAt (pdbpos); -for (var atom, $atom = res.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { -atom.alignmentMapping = alignpos; -} -}} -}, "jalview.analysis.AlignSeq,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "transferRESNUMFeatures", -function (seq, status) { -var sq = seq; -while (sq != null && sq.getDatasetSequence () != null) { -sq = sq.getDatasetSequence (); -if (sq === this.sequence) { -return null; -}} -if (status == null) { -status = "IEA:jalview"; -}var features = this.sequence.getSequenceFeatures (); -for (var i = 0; i < features.length; i++) { -if (features[i].getFeatureGroup ().equals (this.pdbid)) { -var tx = new jalview.datamodel.SequenceFeature (features[i]); -tx.setBegin (1 + this.residues.elementAt (tx.getBegin () - this.offset).atoms.elementAt (0).alignmentMapping); -tx.setEnd (1 + this.residues.elementAt (tx.getEnd () - this.offset).atoms.elementAt (0).alignmentMapping); -tx.setStatus (status + ((tx.getStatus () == null || tx.getStatus ().length == 0) ? "" : ":" + tx.getStatus ())); -if (tx.begin != 0 && tx.end != 0) { -sq.addSequenceFeature (tx); -}}} -return features; -}, "jalview.datamodel.SequenceI,~S"); -Clazz.defineMethod (c$, "makeCaBondList", -function () { -var na = false; -var numNa = 0; -for (var i = 0; i < (this.residues.size () - 1); i++) { -var tmpres = this.residues.elementAt (i); -var tmpres2 = this.residues.elementAt (i + 1); -var at1 = tmpres.findAtom ("CA"); -var at2 = tmpres2.findAtom ("CA"); -na = false; -if ((at1 == null) && (at2 == null)) { -na = true; -at1 = tmpres.findAtom ("P"); -at2 = tmpres2.findAtom ("P"); -}if ((at1 != null) && (at2 != null)) { -if (at1.chain.equals (at2.chain)) { -if (na) { -numNa++; -}this.makeBond (at1, at2); -}} else { -System.out.println ("not found " + i); -}} -if (this.residues.size () > 0 && (Clazz.doubleToInt (numNa / (this.residues.size () - 1)) > 0.99)) { -this.isNa = true; -}}); -Clazz.defineMethod (c$, "makeBond", -function (at1, at2) { -this.bonds.addElement ( new MCview.Bond (at1, at2)); -}, "MCview.Atom,MCview.Atom"); -Clazz.defineMethod (c$, "makeResidueList", -function (visibleChainAnnotation) { -var count = 0; -var symbol; -var deoxyn = false; -var nucleotide = false; -var seq = new StringBuilder (256); -var resFeatures = new java.util.Vector (); -var resAnnotation = new java.util.Vector (); -var i; -var iSize = this.atoms.size () - 1; -var resNumber = -1; -for (i = 0; i <= iSize; i++) { -var tmp = this.atoms.elementAt (i); -resNumber = tmp.resNumber; -var res = resNumber; -if (i == 0) { -this.offset = resNumber; -}var resAtoms = new java.util.Vector (); -while ((resNumber == res) && (i < this.atoms.size ())) { -resAtoms.add (this.atoms.elementAt (i)); -i++; -if (i < this.atoms.size ()) { -resNumber = this.atoms.elementAt (i).resNumber; -} else { -resNumber++; -}} -i--; -this.residues.addElement ( new MCview.Residue (resAtoms, resNumber - 1, count)); -var tmpres = this.residues.lastElement (); -var tmpat = tmpres.atoms.get (0); -var sf = new jalview.datamodel.SequenceFeature ("RESNUM", tmpat.resName + ":" + tmpat.resNumIns + " " + this.pdbid + this.id, "", this.offset + count, this.offset + count, this.pdbid); -resFeatures.addElement (sf); -resAnnotation.addElement ( new jalview.datamodel.Annotation (tmpat.tfactor)); -if ((symbol = jalview.schemes.ResidueProperties.getAA3Hash ().get (tmpat.resName)) == null) { -var nucname = tmpat.resName.trim (); -deoxyn = nucname.length == 2 && jalview.schemes.ResidueProperties.aaIndex[nucname.charCodeAt (0)] == jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)]; -if (tmpat.name.equalsIgnoreCase ("CA") || jalview.schemes.ResidueProperties.nucleotideIndex[nucname.charCodeAt ((deoxyn ? 1 : 0))] == -1) { -seq.append ("X"); -} else { -nucleotide = true; -seq.append (nucname.charAt ((deoxyn ? 1 : 0))); -}} else { -if (nucleotide) { -System.err.println ("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); -}seq.append (jalview.schemes.ResidueProperties.aa[(symbol).intValue ()]); -}count++; -} -if (this.id.length < 1) { -this.id = " "; -}this.isNa = nucleotide; -this.sequence = new jalview.datamodel.Sequence (this.id, seq.toString (), this.offset, resNumber - 1); -for (i = 0, iSize = resFeatures.size (); i < iSize; i++) { -this.sequence.addSequenceFeature (resFeatures.elementAt (i)); -resFeatures.setElementAt (null, i); -} -if (visibleChainAnnotation) { -var annots = new Array (resAnnotation.size ()); -var max = 0; -for (i = 0, iSize = annots.length; i < iSize; i++) { -annots[i] = resAnnotation.elementAt (i); -if (annots[i].value > max) { -max = annots[i].value; -}resAnnotation.setElementAt (null, i); -} -var tfactorann = new jalview.datamodel.AlignmentAnnotation ("Temperature Factor", "Temperature Factor for " + this.pdbid + this.id, annots, 0, max, 2); -tfactorann.setSequenceRef (this.sequence); -this.sequence.addAlignmentAnnotation (tfactorann); -}}, "~B"); -Clazz.defineMethod (c$, "setChargeColours", -function () { -for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { -if (b.at1 != null && b.at2 != null) { -b.startCol = MCview.PDBChain.getChargeColour (b.at1.resName); -b.endCol = MCview.PDBChain.getChargeColour (b.at2.resName); -} else { -b.startCol = java.awt.Color.gray; -b.endCol = java.awt.Color.gray; -}} -}); -c$.getChargeColour = Clazz.defineMethod (c$, "getChargeColour", -function (resName) { -var result = java.awt.Color.lightGray; -if ("ASP".equals (resName) || "GLU".equals (resName)) { -result = java.awt.Color.red; -} else if ("LYS".equals (resName) || "ARG".equals (resName)) { -result = java.awt.Color.blue; -} else if ("CYS".equals (resName)) { -result = java.awt.Color.yellow; -}return result; -}, "~S"); -Clazz.defineMethod (c$, "setChainColours", -function (cs) { -var index; -for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { -try { -index = jalview.schemes.ResidueProperties.aa3Hash.get (b.at1.resName).intValue (); -b.startCol = cs.findColour (jalview.schemes.ResidueProperties.aa[index].charAt (0)); -index = jalview.schemes.ResidueProperties.aa3Hash.get (b.at2.resName).intValue (); -b.endCol = cs.findColour (jalview.schemes.ResidueProperties.aa[index].charAt (0)); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -b.startCol = java.awt.Color.gray; -b.endCol = java.awt.Color.gray; -} else { -throw e; -} -} -} -}, "jalview.schemes.ColourSchemeI"); -Clazz.defineMethod (c$, "setChainColours", -function (col) { -for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { -b.startCol = col; -b.endCol = col; -} -}, "java.awt.Color"); -Clazz.defineMethod (c$, "transferResidueAnnotation", -function (mapping, sqmpping) { -var sq = mapping.getSequence (); -var dsq = sq; -if (sq != null) { -while (dsq.getDatasetSequence () != null) { -dsq = dsq.getDatasetSequence (); -} -if (this.shadow != null && this.shadow.getAnnotation () != null) { -for (var ana, $ana = 0, $$ana = this.shadow.getAnnotation (); $ana < $$ana.length && ((ana = $$ana[$ana]) || true); $ana++) { -var transfer = sq.getAlignmentAnnotations (ana.getCalcId (), ana.label); -if (transfer == null || transfer.size () == 0) { -ana = new jalview.datamodel.AlignmentAnnotation (ana); -ana.liftOver (this.sequence, this.shadowMap); -ana.liftOver (dsq, sqmpping); -dsq.addAlignmentAnnotation (ana); -} else { -continue; -}} -} else { -if (this.sequence != null && this.sequence.getAnnotation () != null) { -for (var ana, $ana = 0, $$ana = this.sequence.getAnnotation (); $ana < $$ana.length && ((ana = $$ana[$ana]) || true); $ana++) { -var transfer = sq.getAlignmentAnnotations (ana.getCalcId (), ana.label); -if (transfer == null || transfer.size () == 0) { -ana = new jalview.datamodel.AlignmentAnnotation (ana); -ana.liftOver (dsq, sqmpping); -} else { -continue; -}} -}}if (false) { -var min = -1; -var max = 0; -var an = new Array (sq.getEnd () - sq.getStart () + 1); -for (var i = sq.getStart (), j = sq.getEnd (), k = 0; i <= j; i++, k++) { -var prn = mapping.getPDBResNum (k + 1); -an[k] = new jalview.datamodel.Annotation (prn); -if (min == -1) { -min = k; -max = k; -} else { -if (min > k) { -min = k; -} else if (max < k) { -max = k; -}}} -sq.addAlignmentAnnotation ( new jalview.datamodel.AlignmentAnnotation ("PDB.RESNUM", "PDB Residue Numbering for " + this.pdbid + ":" + this.id, an, min, max, 2)); -}}}, "jalview.structure.StructureMapping,jalview.datamodel.Mapping"); -Clazz.defineStatics (c$, -"PDBFILEFEATURE", "PDBFile", -"IEASTATUS", "IEA:jalview"); -}); +Clazz.declarePackage ("MCview"); +Clazz.load (["java.util.Vector"], "MCview.PDBChain", ["MCview.Bond", "$.Residue", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.Sequence", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "java.awt.Color", "java.lang.StringBuilder"], function () { +c$ = Clazz.decorateAsClass (function () { +this.id = null; +this.bonds = null; +this.atoms = null; +this.residues = null; +this.offset = 0; +this.sequence = null; +this.shadow = null; +this.isNa = false; +this.isVisible = true; +this.pdbstart = 0; +this.pdbend = 0; +this.seqstart = 0; +this.seqend = 0; +this.pdbid = ""; +this.newline = null; +this.shadowMap = null; +Clazz.instantialize (this, arguments); +}, MCview, "PDBChain"); +Clazz.prepareFields (c$, function () { +this.bonds = new java.util.Vector (); +this.atoms = new java.util.Vector (); +this.residues = new java.util.Vector (); +this.newline = System.getProperty ("line.separator"); +}); +Clazz.makeConstructor (c$, +function (pdbid, id) { +this.pdbid = pdbid.toLowerCase (); +this.id = id; +}, "~S,~S"); +Clazz.defineMethod (c$, "setNewlineString", +function (nl) { +this.newline = nl; +}, "~S"); +Clazz.defineMethod (c$, "getNewlineString", +function () { +return this.newline; +}); +Clazz.defineMethod (c$, "print", +function () { +var tmp = new StringBuilder (256); +for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { +tmp.append (b.at1.resName).append (" ").append (b.at1.resNumber).append (" ").append (this.offset).append (this.newline); +} +return tmp.toString (); +}); +Clazz.defineMethod (c$, "makeExactMapping", +function (as, s1) { +var pdbpos = as.getSeq2Start () - 2; +var alignpos = s1.getStart () + as.getSeq1Start () - 3; +for (var atom, $atom = this.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { +atom.alignmentMapping = -1; +} +for (var i = 0; i < as.astr1.length; i++) { +if (as.astr1.charAt (i) != '-') { +alignpos++; +}if (as.astr2.charAt (i) != '-') { +pdbpos++; +}if (as.astr1.charAt (i) == as.astr2.charAt (i)) { +var res = this.residues.elementAt (pdbpos); +for (var atom, $atom = res.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { +atom.alignmentMapping = alignpos; +} +}} +}, "jalview.analysis.AlignSeq,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "transferRESNUMFeatures", +function (seq, status) { +var sq = seq; +while (sq != null && sq.getDatasetSequence () != null) { +sq = sq.getDatasetSequence (); +if (sq === this.sequence) { +return null; +}} +if (status == null) { +status = "IEA:jalview"; +}var features = this.sequence.getSequenceFeatures (); +for (var i = 0; i < features.length; i++) { +if (features[i].getFeatureGroup ().equals (this.pdbid)) { +var tx = new jalview.datamodel.SequenceFeature (features[i]); +tx.setBegin (1 + this.residues.elementAt (tx.getBegin () - this.offset).atoms.elementAt (0).alignmentMapping); +tx.setEnd (1 + this.residues.elementAt (tx.getEnd () - this.offset).atoms.elementAt (0).alignmentMapping); +tx.setStatus (status + ((tx.getStatus () == null || tx.getStatus ().length == 0) ? "" : ":" + tx.getStatus ())); +if (tx.begin != 0 && tx.end != 0) { +sq.addSequenceFeature (tx); +}}} +return features; +}, "jalview.datamodel.SequenceI,~S"); +Clazz.defineMethod (c$, "makeCaBondList", +function () { +var na = false; +var numNa = 0; +for (var i = 0; i < (this.residues.size () - 1); i++) { +var tmpres = this.residues.elementAt (i); +var tmpres2 = this.residues.elementAt (i + 1); +var at1 = tmpres.findAtom ("CA"); +var at2 = tmpres2.findAtom ("CA"); +na = false; +if ((at1 == null) && (at2 == null)) { +na = true; +at1 = tmpres.findAtom ("P"); +at2 = tmpres2.findAtom ("P"); +}if ((at1 != null) && (at2 != null)) { +if (at1.chain.equals (at2.chain)) { +if (na) { +numNa++; +}this.makeBond (at1, at2); +}} else { +System.out.println ("not found " + i); +}} +if (this.residues.size () > 0 && (Clazz.doubleToInt (numNa / (this.residues.size () - 1)) > 0.99)) { +this.isNa = true; +}}); +Clazz.defineMethod (c$, "makeBond", +function (at1, at2) { +this.bonds.addElement ( new MCview.Bond (at1, at2)); +}, "MCview.Atom,MCview.Atom"); +Clazz.defineMethod (c$, "makeResidueList", +function (visibleChainAnnotation) { +var count = 0; +var symbol; +var deoxyn = false; +var nucleotide = false; +var seq = new StringBuilder (256); +var resFeatures = new java.util.Vector (); +var resAnnotation = new java.util.Vector (); +var i; +var iSize = this.atoms.size () - 1; +var resNumber = -1; +for (i = 0; i <= iSize; i++) { +var tmp = this.atoms.elementAt (i); +resNumber = tmp.resNumber; +var res = resNumber; +if (i == 0) { +this.offset = resNumber; +}var resAtoms = new java.util.Vector (); +while ((resNumber == res) && (i < this.atoms.size ())) { +resAtoms.add (this.atoms.elementAt (i)); +i++; +if (i < this.atoms.size ()) { +resNumber = this.atoms.elementAt (i).resNumber; +} else { +resNumber++; +}} +i--; +this.residues.addElement ( new MCview.Residue (resAtoms, resNumber - 1, count)); +var tmpres = this.residues.lastElement (); +var tmpat = tmpres.atoms.get (0); +var sf = new jalview.datamodel.SequenceFeature ("RESNUM", tmpat.resName + ":" + tmpat.resNumIns + " " + this.pdbid + this.id, "", this.offset + count, this.offset + count, this.pdbid); +resFeatures.addElement (sf); +resAnnotation.addElement ( new jalview.datamodel.Annotation (tmpat.tfactor)); +if ((symbol = jalview.schemes.ResidueProperties.getAA3Hash ().get (tmpat.resName)) == null) { +var nucname = tmpat.resName.trim (); +deoxyn = nucname.length == 2 && jalview.schemes.ResidueProperties.aaIndex[nucname.charCodeAt (0)] == jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)]; +if (tmpat.name.equalsIgnoreCase ("CA") || jalview.schemes.ResidueProperties.nucleotideIndex[nucname.charCodeAt ((deoxyn ? 1 : 0))] == -1) { +seq.append ("X"); +} else { +nucleotide = true; +seq.append (nucname.charAt ((deoxyn ? 1 : 0))); +}} else { +if (nucleotide) { +System.err.println ("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); +}seq.append (jalview.schemes.ResidueProperties.aa[(symbol).intValue ()]); +}count++; +} +if (this.id.length < 1) { +this.id = " "; +}this.isNa = nucleotide; +this.sequence = new jalview.datamodel.Sequence (this.id, seq.toString (), this.offset, resNumber - 1); +for (i = 0, iSize = resFeatures.size (); i < iSize; i++) { +this.sequence.addSequenceFeature (resFeatures.elementAt (i)); +resFeatures.setElementAt (null, i); +} +if (visibleChainAnnotation) { +var annots = new Array (resAnnotation.size ()); +var max = 0; +for (i = 0, iSize = annots.length; i < iSize; i++) { +annots[i] = resAnnotation.elementAt (i); +if (annots[i].value > max) { +max = annots[i].value; +}resAnnotation.setElementAt (null, i); +} +var tfactorann = new jalview.datamodel.AlignmentAnnotation ("Temperature Factor", "Temperature Factor for " + this.pdbid + this.id, annots, 0, max, 2); +tfactorann.setSequenceRef (this.sequence); +this.sequence.addAlignmentAnnotation (tfactorann); +}}, "~B"); +Clazz.defineMethod (c$, "setChargeColours", +function () { +for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { +if (b.at1 != null && b.at2 != null) { +b.startCol = MCview.PDBChain.getChargeColour (b.at1.resName); +b.endCol = MCview.PDBChain.getChargeColour (b.at2.resName); +} else { +b.startCol = java.awt.Color.gray; +b.endCol = java.awt.Color.gray; +}} +}); +c$.getChargeColour = Clazz.defineMethod (c$, "getChargeColour", +function (resName) { +var result = java.awt.Color.lightGray; +if ("ASP".equals (resName) || "GLU".equals (resName)) { +result = java.awt.Color.red; +} else if ("LYS".equals (resName) || "ARG".equals (resName)) { +result = java.awt.Color.blue; +} else if ("CYS".equals (resName)) { +result = java.awt.Color.yellow; +}return result; +}, "~S"); +Clazz.defineMethod (c$, "setChainColours", +function (cs) { +var index; +for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { +try { +index = jalview.schemes.ResidueProperties.aa3Hash.get (b.at1.resName).intValue (); +b.startCol = cs.findColour (jalview.schemes.ResidueProperties.aa[index].charAt (0)); +index = jalview.schemes.ResidueProperties.aa3Hash.get (b.at2.resName).intValue (); +b.endCol = cs.findColour (jalview.schemes.ResidueProperties.aa[index].charAt (0)); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +b.startCol = java.awt.Color.gray; +b.endCol = java.awt.Color.gray; +} else { +throw e; +} +} +} +}, "jalview.schemes.ColourSchemeI"); +Clazz.defineMethod (c$, "setChainColours", +function (col) { +for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) { +b.startCol = col; +b.endCol = col; +} +}, "java.awt.Color"); +Clazz.defineMethod (c$, "transferResidueAnnotation", +function (mapping, sqmpping) { +var sq = mapping.getSequence (); +var dsq = sq; +if (sq != null) { +while (dsq.getDatasetSequence () != null) { +dsq = dsq.getDatasetSequence (); +} +if (this.shadow != null && this.shadow.getAnnotation () != null) { +for (var ana, $ana = 0, $$ana = this.shadow.getAnnotation (); $ana < $$ana.length && ((ana = $$ana[$ana]) || true); $ana++) { +var transfer = sq.getAlignmentAnnotations (ana.getCalcId (), ana.label); +if (transfer == null || transfer.size () == 0) { +ana = new jalview.datamodel.AlignmentAnnotation (ana); +ana.liftOver (this.sequence, this.shadowMap); +ana.liftOver (dsq, sqmpping); +dsq.addAlignmentAnnotation (ana); +} else { +continue; +}} +} else { +if (this.sequence != null && this.sequence.getAnnotation () != null) { +for (var ana, $ana = 0, $$ana = this.sequence.getAnnotation (); $ana < $$ana.length && ((ana = $$ana[$ana]) || true); $ana++) { +var transfer = sq.getAlignmentAnnotations (ana.getCalcId (), ana.label); +if (transfer == null || transfer.size () == 0) { +ana = new jalview.datamodel.AlignmentAnnotation (ana); +ana.liftOver (dsq, sqmpping); +} else { +continue; +}} +}}if (false) { +var min = -1; +var max = 0; +var an = new Array (sq.getEnd () - sq.getStart () + 1); +for (var i = sq.getStart (), j = sq.getEnd (), k = 0; i <= j; i++, k++) { +var prn = mapping.getPDBResNum (k + 1); +an[k] = new jalview.datamodel.Annotation (prn); +if (min == -1) { +min = k; +max = k; +} else { +if (min > k) { +min = k; +} else if (max < k) { +max = k; +}}} +sq.addAlignmentAnnotation ( new jalview.datamodel.AlignmentAnnotation ("PDB.RESNUM", "PDB Residue Numbering for " + this.pdbid + ":" + this.id, an, min, max, 2)); +}}}, "jalview.structure.StructureMapping,jalview.datamodel.Mapping"); +Clazz.defineStatics (c$, +"PDBFILEFEATURE", "PDBFile", +"IEASTATUS", "IEA:jalview"); +}); diff --git a/bin/MCview/PDBfile.class b/bin/MCview/PDBfile.class index 251deb7..a9bf874 100644 Binary files a/bin/MCview/PDBfile.class and b/bin/MCview/PDBfile.class differ diff --git a/bin/MCview/PDBfile.js b/bin/MCview/PDBfile.js index dfc40cc..c6af5ca 100644 --- a/bin/MCview/PDBfile.js +++ b/bin/MCview/PDBfile.js @@ -1,320 +1,320 @@ -Clazz.declarePackage ("MCview"); -Clazz.load (["jalview.io.AlignFile"], "MCview.PDBfile", ["MCview.Atom", "$.PDBChain", "jalview.analysis.AlignSeq", "jalview.datamodel.Alignment", "$.AlignmentI", "$.PDBEntry", "jalview.io.FileParse", "jalview.util.MessageManager", "java.awt.Color", "java.io.IOException", "java.util.ArrayList", "$.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.chains = null; -this.id = null; -this.visibleChainAnnotation = false; -this.$predictSecondaryStructure = true; -this.externalSecondaryStructure = false; -Clazz.instantialize (this, arguments); -}, MCview, "PDBfile", jalview.io.AlignFile); -Clazz.makeConstructor (c$, -function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr) { -Clazz.superConstructor (this, MCview.PDBfile); -this.visibleChainAnnotation = addAlignmentAnnotations; -this.$predictSecondaryStructure = predictSecondaryStructure; -this.externalSecondaryStructure = externalSecStr; -}, "~B,~B,~B"); -Clazz.makeConstructor (c$, -function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr, file, protocol) { -Clazz.superConstructor (this, MCview.PDBfile, [false, file, protocol]); -this.visibleChainAnnotation = addAlignmentAnnotations; -this.$predictSecondaryStructure = predictSecondaryStructure; -this.externalSecondaryStructure = externalSecStr; -this.doParse (); -}, "~B,~B,~B,~S,~S"); -Clazz.makeConstructor (c$, -function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr, source) { -Clazz.superConstructor (this, MCview.PDBfile, [false, source]); -this.visibleChainAnnotation = addAlignmentAnnotations; -this.$predictSecondaryStructure = predictSecondaryStructure; -this.externalSecondaryStructure = externalSecStr; -this.doParse (); -}, "~B,~B,~B,jalview.io.FileParse"); -Clazz.overrideMethod (c$, "print", -function () { -return null; -}); -Clazz.overrideMethod (c$, "parse", -function () { -this.id = this.safeName (this.getDataName ()); -this.chains = new java.util.Vector (); -var rna = new java.util.ArrayList (); -var prot = new java.util.ArrayList (); -var tmpchain; -var line = null; -var modelFlag = false; -var terFlag = false; -var lastID = ""; -var indexx = 0; -var atomnam = null; -try { -while ((line = this.nextLine ()) != null) { -if (line.indexOf ("HEADER") == 0) { -if (line.length > 62) { -var tid; -if (line.length > 67) { -tid = line.substring (62, 67).trim (); -} else { -tid = line.substring (62).trim (); -}if (tid.length > 0) { -this.id = tid; -}continue; -}}if (line.indexOf ("SEQRES") == 0) { -}if (line.indexOf ("MODEL") == 0) { -modelFlag = true; -}if (line.indexOf ("TER") == 0) { -terFlag = true; -}if (modelFlag && line.indexOf ("ENDMDL") == 0) { -break; -}if (line.indexOf ("ATOM") == 0 || (line.indexOf ("HETATM") == 0 && !terFlag)) { -terFlag = false; -atomnam = line.substring (12, 15).trim (); -if (!atomnam.equals ("CA") && !atomnam.equals ("P")) { -continue; -}var tmpatom = new MCview.Atom (line); -tmpchain = this.findChain (tmpatom.chain); -if (tmpchain != null) { -if (tmpatom.resNumIns.trim ().equals (lastID)) { -continue; -}tmpchain.atoms.addElement (tmpatom); -} else { -tmpchain = new MCview.PDBChain (this.id, tmpatom.chain); -this.chains.addElement (tmpchain); -tmpchain.atoms.addElement (tmpatom); -}lastID = tmpatom.resNumIns.trim (); -}this.index++; -} -this.makeResidueList (); -this.makeCaBondList (); -if (this.id == null) { -this.id = this.inFile.getName (); -}for (var chain, $chain = this.chains.iterator (); $chain.hasNext () && ((chain = $chain.next ()) || true);) { -var chainseq = this.postProcessChain (chain); -if (MCview.PDBfile.isRNA (chainseq)) { -rna.add (chainseq); -} else { -prot.add (chainseq); -}} -if (this.$predictSecondaryStructure) { -this.predictSecondaryStructure (rna, prot); -}} catch (e$$) { -if (Clazz.exceptionOf (e$$, OutOfMemoryError)) { -var er = e$$; -{ -System.out.println ("OUT OF MEMORY LOADING PDB FILE"); -throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.outofmemory_loading_pdb_file")); -} -} else if (Clazz.exceptionOf (e$$, NumberFormatException)) { -var ex = e$$; -{ -if (line != null) { -System.err.println ("Couldn't read number from line:"); -System.err.println (line); -}} -} else { -throw e$$; -} -} -this.markCalcIds (); -}); -Clazz.defineMethod (c$, "predictSecondaryStructure", -function (rnaSequences, proteinSequences) { -if (this.externalSecondaryStructure && rnaSequences.size () > 0) { -try { -this.processPdbFileWithAnnotate3d (rnaSequences); -} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -System.err.println ("Exceptions when dealing with RNA in pdb file"); -x.printStackTrace (); -} else { -throw x; -} -} -}if (proteinSequences.size () > 0) { -try { -this.processPdbFileWithJmol (proteinSequences); -} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -System.err.println ("Exceptions from Jmol when processing data in pdb file"); -x.printStackTrace (); -} else { -throw x; -} -} -}}, "java.util.List,java.util.List"); -Clazz.defineMethod (c$, "postProcessChain", -function (chain) { -var dataset = chain.sequence; -dataset.setName (this.id + "|" + dataset.getName ()); -var entry = new jalview.datamodel.PDBEntry (); -entry.setId (this.id); -entry.setType (jalview.datamodel.PDBEntry.Type.PDB); -entry.setProperty ( new java.util.Hashtable ()); -if (chain.id != null) { -entry.setChainCode (String.valueOf (chain.id)); -}if (this.inFile != null) { -entry.setFile (this.inFile.getAbsolutePath ()); -} else { -entry.setFile (this.getDataName ()); -}dataset.addPDBId (entry); -var chainseq = dataset.deriveSequence (); -this.seqs.addElement (chainseq); -var chainannot = chainseq.getAnnotation (); -if (chainannot != null && this.visibleChainAnnotation) { -for (var ai = 0; ai < chainannot.length; ai++) { -chainannot[ai].visible = this.visibleChainAnnotation; -this.annotations.addElement (chainannot[ai]); -} -}return chainseq; -}, "MCview.PDBChain"); -c$.isCalcIdHandled = Clazz.defineMethod (c$, "isCalcIdHandled", -function (calcId) { -return calcId != null && (MCview.PDBfile.CALC_ID_PREFIX.equals (calcId)); -}, "~S"); -c$.isCalcIdForFile = Clazz.defineMethod (c$, "isCalcIdForFile", -function (alan, pdbFile) { -return alan.getCalcId () != null && MCview.PDBfile.CALC_ID_PREFIX.equals (alan.getCalcId ()) && pdbFile.equals (alan.getProperty ("PDBID")); -}, "jalview.datamodel.AlignmentAnnotation,~S"); -c$.relocateCalcId = Clazz.defineMethod (c$, "relocateCalcId", -function (calcId, alreadyLoadedPDB) { -var s = MCview.PDBfile.CALC_ID_PREFIX.length; -var end = calcId.indexOf (MCview.PDBfile.CALC_ID_PREFIX, s); -var between = calcId.substring (s, end - 1); -return MCview.PDBfile.CALC_ID_PREFIX + alreadyLoadedPDB.get (between) + ":" + calcId.substring (end); -}, "~S,java.util.Hashtable"); -Clazz.defineMethod (c$, "markCalcIds", -($fz = function () { -for (var sq, $sq = this.seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -if (sq.getAnnotation () != null) { -for (var aa, $aa = 0, $$aa = sq.getAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { -var oldId = aa.getCalcId (); -if (oldId == null) { -oldId = ""; -}aa.setCalcId (MCview.PDBfile.CALC_ID_PREFIX); -aa.setProperty ("PDBID", this.id); -aa.setProperty ("oldCalcId", oldId); -} -}} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "processPdbFileWithJmol", -($fz = function (prot) { -try { -var cl = Class.forName ("jalview.ext.jmol.PDBFileWithJmol"); -if (cl != null) { -var constructor = cl.getConstructor ( Clazz.newArray (-1, [jalview.io.FileParse])); -var args = Clazz.newArray (-1, [ new jalview.io.FileParse (this.getDataName (), this.type)]); -var jmf = constructor.newInstance (args); -var al = new jalview.datamodel.Alignment (cl.getMethod ("getSeqsAsArray", Clazz.newArray (-1, [])).invoke (jmf, [])); -cl.getMethod ("addAnnotations", Clazz.newArray (-1, [jalview.datamodel.AlignmentI])).invoke (jmf, [al]); -for (var sq, $sq = al.getSequences ().iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -if (sq.getDatasetSequence () != null) { -sq.getDatasetSequence ().getPDBId ().clear (); -} else { -sq.getPDBId ().clear (); -}} -this.replaceAndUpdateChains (prot, al, "pep", false); -}} catch (q) { -if (Clazz.exceptionOf (q, ClassNotFoundException)) { -} else { -throw q; -} -} -}, $fz.isPrivate = true, $fz), "java.util.List"); -Clazz.defineMethod (c$, "replaceAndUpdateChains", -($fz = function (prot, al, pep, b) { -var replaced = jalview.analysis.AlignSeq.replaceMatchingSeqsWith (this.seqs, this.annotations, prot, al, pep, false); -for (var ch, $ch = this.chains.iterator (); $ch.hasNext () && ((ch = $ch.next ()) || true);) { -var p = 0; -for (var sq, $sq = replaced.get (0).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -p++; -if (sq === ch.sequence || sq.getDatasetSequence () === ch.sequence) { -p = -p; -break; -}} -if (p < 0) { -p = -p - 1; -ch.shadow = replaced.get (1).get (p); -ch.shadowMap = (replaced.get (2).get (p)).getMappingFromS1 (false); -}} -}, $fz.isPrivate = true, $fz), "java.util.List,jalview.datamodel.AlignmentI,~S,~B"); -Clazz.defineMethod (c$, "processPdbFileWithAnnotate3d", -($fz = function (rna) { -try { -var cl = Class.forName ("jalview.ws.jws1.Annotate3D"); -if (cl != null) { -var annotate3d = cl.getConstructor ( Clazz.newArray (-1, [])).newInstance ( Clazz.newArray (-1, [])); -var al = (cl.getMethod ("getRNAMLFor", Clazz.newArray (-1, [jalview.io.FileParse])).invoke (annotate3d, Clazz.newArray (-1, [ new jalview.io.FileParse (this.getDataName (), this.type)]))); -for (var sq, $sq = al.getSequences ().iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -if (sq.getDatasetSequence () != null) { -if (sq.getDatasetSequence ().getPDBId () != null) { -sq.getDatasetSequence ().getPDBId ().clear (); -}} else { -if (sq.getPDBId () != null) { -sq.getPDBId ().clear (); -}}} -this.replaceAndUpdateChains (rna, al, "dna", false); -}} catch (x) { -if (Clazz.exceptionOf (x, ClassNotFoundException)) { -} else { -throw x; -} -} -;}, $fz.isPrivate = true, $fz), "java.util.List"); -Clazz.defineMethod (c$, "safeName", -($fz = function (dataName) { -var p = 0; -while ((p = dataName.indexOf ("/")) > -1 && p < dataName.length) { -dataName = dataName.substring (p + 1); -} -return dataName; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "makeResidueList", -function () { -for (var i = 0; i < this.chains.size (); i++) { -this.chains.elementAt (i).makeResidueList (this.visibleChainAnnotation); -} -}); -Clazz.defineMethod (c$, "makeCaBondList", -function () { -for (var i = 0; i < this.chains.size (); i++) { -this.chains.elementAt (i).makeCaBondList (); -} -}); -Clazz.defineMethod (c$, "findChain", -function (id) { -for (var i = 0; i < this.chains.size (); i++) { -if (this.chains.elementAt (i).id.equals (id)) { -return this.chains.elementAt (i); -}} -return null; -}, "~S"); -Clazz.defineMethod (c$, "setChargeColours", -function () { -for (var i = 0; i < this.chains.size (); i++) { -this.chains.elementAt (i).setChargeColours (); -} -}); -Clazz.defineMethod (c$, "setColours", -function (cs) { -for (var i = 0; i < this.chains.size (); i++) { -this.chains.elementAt (i).setChainColours (cs); -} -}, "jalview.schemes.ColourSchemeI"); -Clazz.defineMethod (c$, "setChainColours", -function () { -for (var i = 0; i < this.chains.size (); i++) { -this.chains.elementAt (i).setChainColours (java.awt.Color.getHSBColor (1.0 / i, .4, 1.0)); -} -}); -c$.isRNA = Clazz.defineMethod (c$, "isRNA", -function (seq) { -for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) { -if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U')) { -return false; -}} -return true; -}, "jalview.datamodel.SequenceI"); -Clazz.defineStatics (c$, -"CALC_ID_PREFIX", "JalviewPDB"); -}); +Clazz.declarePackage ("MCview"); +Clazz.load (["jalview.io.AlignFile"], "MCview.PDBfile", ["MCview.Atom", "$.PDBChain", "jalview.analysis.AlignSeq", "jalview.datamodel.Alignment", "$.AlignmentI", "$.PDBEntry", "jalview.io.FileParse", "jalview.util.MessageManager", "java.awt.Color", "java.io.IOException", "java.util.ArrayList", "$.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.chains = null; +this.id = null; +this.visibleChainAnnotation = false; +this.$predictSecondaryStructure = true; +this.externalSecondaryStructure = false; +Clazz.instantialize (this, arguments); +}, MCview, "PDBfile", jalview.io.AlignFile); +Clazz.makeConstructor (c$, +function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr) { +Clazz.superConstructor (this, MCview.PDBfile); +this.visibleChainAnnotation = addAlignmentAnnotations; +this.$predictSecondaryStructure = predictSecondaryStructure; +this.externalSecondaryStructure = externalSecStr; +}, "~B,~B,~B"); +Clazz.makeConstructor (c$, +function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr, file, protocol) { +Clazz.superConstructor (this, MCview.PDBfile, [false, file, protocol]); +this.visibleChainAnnotation = addAlignmentAnnotations; +this.$predictSecondaryStructure = predictSecondaryStructure; +this.externalSecondaryStructure = externalSecStr; +this.doParse (); +}, "~B,~B,~B,~S,~S"); +Clazz.makeConstructor (c$, +function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr, source) { +Clazz.superConstructor (this, MCview.PDBfile, [false, source]); +this.visibleChainAnnotation = addAlignmentAnnotations; +this.$predictSecondaryStructure = predictSecondaryStructure; +this.externalSecondaryStructure = externalSecStr; +this.doParse (); +}, "~B,~B,~B,jalview.io.FileParse"); +Clazz.overrideMethod (c$, "print", +function () { +return null; +}); +Clazz.overrideMethod (c$, "parse", +function () { +this.id = this.safeName (this.getDataName ()); +this.chains = new java.util.Vector (); +var rna = new java.util.ArrayList (); +var prot = new java.util.ArrayList (); +var tmpchain; +var line = null; +var modelFlag = false; +var terFlag = false; +var lastID = ""; +var indexx = 0; +var atomnam = null; +try { +while ((line = this.nextLine ()) != null) { +if (line.indexOf ("HEADER") == 0) { +if (line.length > 62) { +var tid; +if (line.length > 67) { +tid = line.substring (62, 67).trim (); +} else { +tid = line.substring (62).trim (); +}if (tid.length > 0) { +this.id = tid; +}continue; +}}if (line.indexOf ("SEQRES") == 0) { +}if (line.indexOf ("MODEL") == 0) { +modelFlag = true; +}if (line.indexOf ("TER") == 0) { +terFlag = true; +}if (modelFlag && line.indexOf ("ENDMDL") == 0) { +break; +}if (line.indexOf ("ATOM") == 0 || (line.indexOf ("HETATM") == 0 && !terFlag)) { +terFlag = false; +atomnam = line.substring (12, 15).trim (); +if (!atomnam.equals ("CA") && !atomnam.equals ("P")) { +continue; +}var tmpatom = new MCview.Atom (line); +tmpchain = this.findChain (tmpatom.chain); +if (tmpchain != null) { +if (tmpatom.resNumIns.trim ().equals (lastID)) { +continue; +}tmpchain.atoms.addElement (tmpatom); +} else { +tmpchain = new MCview.PDBChain (this.id, tmpatom.chain); +this.chains.addElement (tmpchain); +tmpchain.atoms.addElement (tmpatom); +}lastID = tmpatom.resNumIns.trim (); +}this.index++; +} +this.makeResidueList (); +this.makeCaBondList (); +if (this.id == null) { +this.id = this.inFile.getName (); +}for (var chain, $chain = this.chains.iterator (); $chain.hasNext () && ((chain = $chain.next ()) || true);) { +var chainseq = this.postProcessChain (chain); +if (MCview.PDBfile.isRNA (chainseq)) { +rna.add (chainseq); +} else { +prot.add (chainseq); +}} +if (this.$predictSecondaryStructure) { +this.predictSecondaryStructure (rna, prot); +}} catch (e$$) { +if (Clazz.exceptionOf (e$$, OutOfMemoryError)) { +var er = e$$; +{ +System.out.println ("OUT OF MEMORY LOADING PDB FILE"); +throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.outofmemory_loading_pdb_file")); +} +} else if (Clazz.exceptionOf (e$$, NumberFormatException)) { +var ex = e$$; +{ +if (line != null) { +System.err.println ("Couldn't read number from line:"); +System.err.println (line); +}} +} else { +throw e$$; +} +} +this.markCalcIds (); +}); +Clazz.defineMethod (c$, "predictSecondaryStructure", +function (rnaSequences, proteinSequences) { +if (this.externalSecondaryStructure && rnaSequences.size () > 0) { +try { +this.processPdbFileWithAnnotate3d (rnaSequences); +} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +System.err.println ("Exceptions when dealing with RNA in pdb file"); +x.printStackTrace (); +} else { +throw x; +} +} +}if (proteinSequences.size () > 0) { +try { +this.processPdbFileWithJmol (proteinSequences); +} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +System.err.println ("Exceptions from Jmol when processing data in pdb file"); +x.printStackTrace (); +} else { +throw x; +} +} +}}, "java.util.List,java.util.List"); +Clazz.defineMethod (c$, "postProcessChain", +function (chain) { +var dataset = chain.sequence; +dataset.setName (this.id + "|" + dataset.getName ()); +var entry = new jalview.datamodel.PDBEntry (); +entry.setId (this.id); +entry.setType (jalview.datamodel.PDBEntry.Type.PDB); +entry.setProperty ( new java.util.Hashtable ()); +if (chain.id != null) { +entry.setChainCode (String.valueOf (chain.id)); +}if (this.inFile != null) { +entry.setFile (this.inFile.getAbsolutePath ()); +} else { +entry.setFile (this.getDataName ()); +}dataset.addPDBId (entry); +var chainseq = dataset.deriveSequence (); +this.seqs.addElement (chainseq); +var chainannot = chainseq.getAnnotation (); +if (chainannot != null && this.visibleChainAnnotation) { +for (var ai = 0; ai < chainannot.length; ai++) { +chainannot[ai].visible = this.visibleChainAnnotation; +this.annotations.addElement (chainannot[ai]); +} +}return chainseq; +}, "MCview.PDBChain"); +c$.isCalcIdHandled = Clazz.defineMethod (c$, "isCalcIdHandled", +function (calcId) { +return calcId != null && (MCview.PDBfile.CALC_ID_PREFIX.equals (calcId)); +}, "~S"); +c$.isCalcIdForFile = Clazz.defineMethod (c$, "isCalcIdForFile", +function (alan, pdbFile) { +return alan.getCalcId () != null && MCview.PDBfile.CALC_ID_PREFIX.equals (alan.getCalcId ()) && pdbFile.equals (alan.getProperty ("PDBID")); +}, "jalview.datamodel.AlignmentAnnotation,~S"); +c$.relocateCalcId = Clazz.defineMethod (c$, "relocateCalcId", +function (calcId, alreadyLoadedPDB) { +var s = MCview.PDBfile.CALC_ID_PREFIX.length; +var end = calcId.indexOf (MCview.PDBfile.CALC_ID_PREFIX, s); +var between = calcId.substring (s, end - 1); +return MCview.PDBfile.CALC_ID_PREFIX + alreadyLoadedPDB.get (between) + ":" + calcId.substring (end); +}, "~S,java.util.Hashtable"); +Clazz.defineMethod (c$, "markCalcIds", +($fz = function () { +for (var sq, $sq = this.seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +if (sq.getAnnotation () != null) { +for (var aa, $aa = 0, $$aa = sq.getAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { +var oldId = aa.getCalcId (); +if (oldId == null) { +oldId = ""; +}aa.setCalcId (MCview.PDBfile.CALC_ID_PREFIX); +aa.setProperty ("PDBID", this.id); +aa.setProperty ("oldCalcId", oldId); +} +}} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "processPdbFileWithJmol", +($fz = function (prot) { +try { +var cl = Class.forName ("jalview.ext.jmol.PDBFileWithJmol"); +if (cl != null) { +var constructor = cl.getConstructor ( Clazz.newArray (-1, [jalview.io.FileParse])); +var args = Clazz.newArray (-1, [ new jalview.io.FileParse (this.getDataName (), this.type)]); +var jmf = constructor.newInstance (args); +var al = new jalview.datamodel.Alignment (cl.getMethod ("getSeqsAsArray", Clazz.newArray (-1, [])).invoke (jmf, [])); +cl.getMethod ("addAnnotations", Clazz.newArray (-1, [jalview.datamodel.AlignmentI])).invoke (jmf, [al]); +for (var sq, $sq = al.getSequences ().iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +if (sq.getDatasetSequence () != null) { +sq.getDatasetSequence ().getPDBId ().clear (); +} else { +sq.getPDBId ().clear (); +}} +this.replaceAndUpdateChains (prot, al, "pep", false); +}} catch (q) { +if (Clazz.exceptionOf (q, ClassNotFoundException)) { +} else { +throw q; +} +} +}, $fz.isPrivate = true, $fz), "java.util.List"); +Clazz.defineMethod (c$, "replaceAndUpdateChains", +($fz = function (prot, al, pep, b) { +var replaced = jalview.analysis.AlignSeq.replaceMatchingSeqsWith (this.seqs, this.annotations, prot, al, pep, false); +for (var ch, $ch = this.chains.iterator (); $ch.hasNext () && ((ch = $ch.next ()) || true);) { +var p = 0; +for (var sq, $sq = replaced.get (0).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +p++; +if (sq === ch.sequence || sq.getDatasetSequence () === ch.sequence) { +p = -p; +break; +}} +if (p < 0) { +p = -p - 1; +ch.shadow = replaced.get (1).get (p); +ch.shadowMap = (replaced.get (2).get (p)).getMappingFromS1 (false); +}} +}, $fz.isPrivate = true, $fz), "java.util.List,jalview.datamodel.AlignmentI,~S,~B"); +Clazz.defineMethod (c$, "processPdbFileWithAnnotate3d", +($fz = function (rna) { +try { +var cl = Class.forName ("jalview.ws.jws1.Annotate3D"); +if (cl != null) { +var annotate3d = cl.getConstructor ( Clazz.newArray (-1, [])).newInstance ( Clazz.newArray (-1, [])); +var al = (cl.getMethod ("getRNAMLFor", Clazz.newArray (-1, [jalview.io.FileParse])).invoke (annotate3d, Clazz.newArray (-1, [ new jalview.io.FileParse (this.getDataName (), this.type)]))); +for (var sq, $sq = al.getSequences ().iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +if (sq.getDatasetSequence () != null) { +if (sq.getDatasetSequence ().getPDBId () != null) { +sq.getDatasetSequence ().getPDBId ().clear (); +}} else { +if (sq.getPDBId () != null) { +sq.getPDBId ().clear (); +}}} +this.replaceAndUpdateChains (rna, al, "dna", false); +}} catch (x) { +if (Clazz.exceptionOf (x, ClassNotFoundException)) { +} else { +throw x; +} +} +;}, $fz.isPrivate = true, $fz), "java.util.List"); +Clazz.defineMethod (c$, "safeName", +($fz = function (dataName) { +var p = 0; +while ((p = dataName.indexOf ("/")) > -1 && p < dataName.length) { +dataName = dataName.substring (p + 1); +} +return dataName; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "makeResidueList", +function () { +for (var i = 0; i < this.chains.size (); i++) { +this.chains.elementAt (i).makeResidueList (this.visibleChainAnnotation); +} +}); +Clazz.defineMethod (c$, "makeCaBondList", +function () { +for (var i = 0; i < this.chains.size (); i++) { +this.chains.elementAt (i).makeCaBondList (); +} +}); +Clazz.defineMethod (c$, "findChain", +function (id) { +for (var i = 0; i < this.chains.size (); i++) { +if (this.chains.elementAt (i).id.equals (id)) { +return this.chains.elementAt (i); +}} +return null; +}, "~S"); +Clazz.defineMethod (c$, "setChargeColours", +function () { +for (var i = 0; i < this.chains.size (); i++) { +this.chains.elementAt (i).setChargeColours (); +} +}); +Clazz.defineMethod (c$, "setColours", +function (cs) { +for (var i = 0; i < this.chains.size (); i++) { +this.chains.elementAt (i).setChainColours (cs); +} +}, "jalview.schemes.ColourSchemeI"); +Clazz.defineMethod (c$, "setChainColours", +function () { +for (var i = 0; i < this.chains.size (); i++) { +this.chains.elementAt (i).setChainColours (java.awt.Color.getHSBColor (1.0 / i, .4, 1.0)); +} +}); +c$.isRNA = Clazz.defineMethod (c$, "isRNA", +function (seq) { +for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) { +if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U')) { +return false; +}} +return true; +}, "jalview.datamodel.SequenceI"); +Clazz.defineStatics (c$, +"CALC_ID_PREFIX", "JalviewPDB"); +}); diff --git a/bin/MCview/Residue.js b/bin/MCview/Residue.js index 93e2930..6cb43ed 100644 --- a/bin/MCview/Residue.js +++ b/bin/MCview/Residue.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("MCview"); -c$ = Clazz.decorateAsClass (function () { -this.atoms = null; -this.number = 0; -this.count = 0; -Clazz.instantialize (this, arguments); -}, MCview, "Residue"); -Clazz.makeConstructor (c$, -function (resAtoms, number, count) { -this.atoms = resAtoms; -this.number = number; -this.count = count; -}, "java.util.Vector,~N,~N"); -Clazz.defineMethod (c$, "findAtom", -function (name) { -for (var atom, $atom = this.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { -if (atom.name.equals (name)) { -return atom; -}} -return null; -}, "~S"); +Clazz.declarePackage ("MCview"); +c$ = Clazz.decorateAsClass (function () { +this.atoms = null; +this.number = 0; +this.count = 0; +Clazz.instantialize (this, arguments); +}, MCview, "Residue"); +Clazz.makeConstructor (c$, +function (resAtoms, number, count) { +this.atoms = resAtoms; +this.number = number; +this.count = count; +}, "java.util.Vector,~N,~N"); +Clazz.defineMethod (c$, "findAtom", +function (name) { +for (var atom, $atom = this.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { +if (atom.name.equals (name)) { +return atom; +}} +return null; +}, "~S"); diff --git a/bin/awt2swing/Button.js b/bin/awt2swing/Button.js index b25baa7..80ce87e 100644 --- a/bin/awt2swing/Button.js +++ b/bin/awt2swing/Button.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JButton"], "awt2swing.Button", null, function () { -c$ = Clazz.declareType (awt2swing, "Button", javax.swing.JButton); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JButton"], "awt2swing.Button", null, function () { +c$ = Clazz.declareType (awt2swing, "Button", javax.swing.JButton); +}); diff --git a/bin/awt2swing/Canvas.js b/bin/awt2swing/Canvas.js index df3f0b9..cf449b4 100644 --- a/bin/awt2swing/Canvas.js +++ b/bin/awt2swing/Canvas.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["awt2swing.Panel"], "awt2swing.Canvas", null, function () { -c$ = Clazz.declareType (awt2swing, "Canvas", awt2swing.Panel); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["awt2swing.Panel"], "awt2swing.Canvas", null, function () { +c$ = Clazz.declareType (awt2swing, "Canvas", awt2swing.Panel); +}); diff --git a/bin/awt2swing/Checkbox.js b/bin/awt2swing/Checkbox.js index cd50679..cfc477c 100644 --- a/bin/awt2swing/Checkbox.js +++ b/bin/awt2swing/Checkbox.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JCheckBox"], "awt2swing.Checkbox", null, function () { -c$ = Clazz.declareType (awt2swing, "Checkbox", javax.swing.JCheckBox); -Clazz.defineMethod (c$, "getState", -function () { -return this.isSelected (); -}); -Clazz.defineMethod (c$, "setState", -function (b) { -this.setSelected (b); -}, "~B"); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JCheckBox"], "awt2swing.Checkbox", null, function () { +c$ = Clazz.declareType (awt2swing, "Checkbox", javax.swing.JCheckBox); +Clazz.defineMethod (c$, "getState", +function () { +return this.isSelected (); +}); +Clazz.defineMethod (c$, "setState", +function (b) { +this.setSelected (b); +}, "~B"); +}); diff --git a/bin/awt2swing/CheckboxMenuItem.js b/bin/awt2swing/CheckboxMenuItem.js index 782c150..9364af7 100644 --- a/bin/awt2swing/CheckboxMenuItem.js +++ b/bin/awt2swing/CheckboxMenuItem.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JCheckBoxMenuItem"], "awt2swing.CheckboxMenuItem", null, function () { -c$ = Clazz.declareType (awt2swing, "CheckboxMenuItem", javax.swing.JCheckBoxMenuItem); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, awt2swing.CheckboxMenuItem, []); -}); -Clazz.overrideMethod (c$, "getState", -function () { -return this.isSelected (); -}); -Clazz.overrideMethod (c$, "setState", -function (tf) { -this.setSelected (tf); -}, "~B"); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JCheckBoxMenuItem"], "awt2swing.CheckboxMenuItem", null, function () { +c$ = Clazz.declareType (awt2swing, "CheckboxMenuItem", javax.swing.JCheckBoxMenuItem); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, awt2swing.CheckboxMenuItem, []); +}); +Clazz.overrideMethod (c$, "getState", +function () { +return this.isSelected (); +}); +Clazz.overrideMethod (c$, "setState", +function (tf) { +this.setSelected (tf); +}, "~B"); +}); diff --git a/bin/awt2swing/Choice.js b/bin/awt2swing/Choice.js index a4208b1..0eb2843 100644 --- a/bin/awt2swing/Choice.js +++ b/bin/awt2swing/Choice.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JComboBox"], "awt2swing.Choice", null, function () { -c$ = Clazz.declareType (awt2swing, "Choice", javax.swing.JComboBox); -Clazz.defineMethod (c$, "select", -function (key) { -this.setSelectedItem (key); -}, "~O"); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JComboBox"], "awt2swing.Choice", null, function () { +c$ = Clazz.declareType (awt2swing, "Choice", javax.swing.JComboBox); +Clazz.defineMethod (c$, "select", +function (key) { +this.setSelectedItem (key); +}, "~O"); +}); diff --git a/bin/awt2swing/Frame.js b/bin/awt2swing/Frame.js index 027d871..a4e228b 100644 --- a/bin/awt2swing/Frame.js +++ b/bin/awt2swing/Frame.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JFrame"], "awt2swing.Frame", null, function () { -c$ = Clazz.declareType (awt2swing, "Frame", javax.swing.JFrame); -Clazz.defineMethod (c$, "remove", -function (i) { -{ -this.removeInt(i); -}}, "~N"); -Clazz.defineMethod (c$, "setMenuBar", -function (m) { -this.setJMenuBar (m); -}, "awt2swing.MenuBar"); -Clazz.defineMethod (c$, "unsetMenuBar", -function () { -this.setJMenuBar (null); -}); -Clazz.defineMethod (c$, "getMenubar", -function () { -return this.getJMenuBar (); -}); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JFrame"], "awt2swing.Frame", null, function () { +c$ = Clazz.declareType (awt2swing, "Frame", javax.swing.JFrame); +Clazz.defineMethod (c$, "remove", +function (i) { +{ +this.removeInt(i); +}}, "~N"); +Clazz.defineMethod (c$, "setMenuBar", +function (m) { +this.setJMenuBar (m); +}, "awt2swing.MenuBar"); +Clazz.defineMethod (c$, "unsetMenuBar", +function () { +this.setJMenuBar (null); +}); +Clazz.defineMethod (c$, "getMenubar", +function () { +return this.getJMenuBar (); +}); +}); diff --git a/bin/awt2swing/Label.js b/bin/awt2swing/Label.js index 380eaf6..713f8b3 100644 --- a/bin/awt2swing/Label.js +++ b/bin/awt2swing/Label.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JLabel"], "awt2swing.Label", null, function () { -c$ = Clazz.declareType (awt2swing, "Label", javax.swing.JLabel); -Clazz.defineMethod (c$, "setAlignment", -function (alignment) { -this.setAlignmentX (alignment); -}, "~N"); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JLabel"], "awt2swing.Label", null, function () { +c$ = Clazz.declareType (awt2swing, "Label", javax.swing.JLabel); +Clazz.defineMethod (c$, "setAlignment", +function (alignment) { +this.setAlignmentX (alignment); +}, "~N"); +}); diff --git a/bin/awt2swing/Menu.js b/bin/awt2swing/Menu.js index da1b846..867b6ab 100644 --- a/bin/awt2swing/Menu.js +++ b/bin/awt2swing/Menu.js @@ -1,14 +1,14 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JMenu"], "awt2swing.Menu", null, function () { -c$ = Clazz.declareType (awt2swing, "Menu", javax.swing.JMenu); -Clazz.makeConstructor (c$, -function (title) { -Clazz.superConstructor (this, awt2swing.Menu, [title]); -title = null; -}, "~S"); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, awt2swing.Menu); -var s = null; -}); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JMenu"], "awt2swing.Menu", null, function () { +c$ = Clazz.declareType (awt2swing, "Menu", javax.swing.JMenu); +Clazz.makeConstructor (c$, +function (title) { +Clazz.superConstructor (this, awt2swing.Menu, [title]); +title = null; +}, "~S"); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, awt2swing.Menu); +var s = null; +}); +}); diff --git a/bin/awt2swing/MenuBar.js b/bin/awt2swing/MenuBar.js index 4865fdd..3b43191 100644 --- a/bin/awt2swing/MenuBar.js +++ b/bin/awt2swing/MenuBar.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JMenuBar"], "awt2swing.MenuBar", null, function () { -c$ = Clazz.declareType (awt2swing, "MenuBar", javax.swing.JMenuBar); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JMenuBar"], "awt2swing.MenuBar", null, function () { +c$ = Clazz.declareType (awt2swing, "MenuBar", javax.swing.JMenuBar); +}); diff --git a/bin/awt2swing/MenuItem.js b/bin/awt2swing/MenuItem.js index d20f729..f610760 100644 --- a/bin/awt2swing/MenuItem.js +++ b/bin/awt2swing/MenuItem.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JMenuItem"], "awt2swing.MenuItem", null, function () { -c$ = Clazz.declareType (awt2swing, "MenuItem", javax.swing.JMenuItem); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JMenuItem"], "awt2swing.MenuItem", null, function () { +c$ = Clazz.declareType (awt2swing, "MenuItem", javax.swing.JMenuItem); +}); diff --git a/bin/awt2swing/Panel.js b/bin/awt2swing/Panel.js index 5e33047..b6061d0 100644 --- a/bin/awt2swing/Panel.js +++ b/bin/awt2swing/Panel.js @@ -1,9 +1,9 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JPanel"], "awt2swing.Panel", null, function () { -c$ = Clazz.declareType (awt2swing, "Panel", javax.swing.JPanel); -Clazz.defineMethod (c$, "setName", -function (name) { -System.out.println (name); -Clazz.superCall (this, awt2swing.Panel, "setName", [name]); -}, "~S"); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JPanel"], "awt2swing.Panel", null, function () { +c$ = Clazz.declareType (awt2swing, "Panel", javax.swing.JPanel); +Clazz.defineMethod (c$, "setName", +function (name) { +System.out.println (name); +Clazz.superCall (this, awt2swing.Panel, "setName", [name]); +}, "~S"); +}); diff --git a/bin/awt2swing/PopupMenu.js b/bin/awt2swing/PopupMenu.js index 007642a..4af0e16 100644 --- a/bin/awt2swing/PopupMenu.js +++ b/bin/awt2swing/PopupMenu.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JPopupMenu"], "awt2swing.PopupMenu", null, function () { -c$ = Clazz.declareType (awt2swing, "PopupMenu", javax.swing.JPopupMenu); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JPopupMenu"], "awt2swing.PopupMenu", null, function () { +c$ = Clazz.declareType (awt2swing, "PopupMenu", javax.swing.JPopupMenu); +}); diff --git a/bin/awt2swing/ScrollPane.js b/bin/awt2swing/ScrollPane.js index 2ea1cea..3ba78cf 100644 --- a/bin/awt2swing/ScrollPane.js +++ b/bin/awt2swing/ScrollPane.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JScrollPane"], "awt2swing.ScrollPane", null, function () { -c$ = Clazz.declareType (awt2swing, "ScrollPane", javax.swing.JScrollPane); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JScrollPane"], "awt2swing.ScrollPane", null, function () { +c$ = Clazz.declareType (awt2swing, "ScrollPane", javax.swing.JScrollPane); +}); diff --git a/bin/awt2swing/Scrollbar.js b/bin/awt2swing/Scrollbar.js index b68bd0c..3859a96 100644 --- a/bin/awt2swing/Scrollbar.js +++ b/bin/awt2swing/Scrollbar.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JScrollBar"], "awt2swing.Scrollbar", null, function () { -c$ = Clazz.declareType (awt2swing, "Scrollbar", javax.swing.JScrollBar); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JScrollBar"], "awt2swing.Scrollbar", null, function () { +c$ = Clazz.declareType (awt2swing, "Scrollbar", javax.swing.JScrollBar); +}); diff --git a/bin/awt2swing/TextArea.js b/bin/awt2swing/TextArea.js index 3aec891..4358c37 100644 --- a/bin/awt2swing/TextArea.js +++ b/bin/awt2swing/TextArea.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JTextArea"], "awt2swing.TextArea", null, function () { -c$ = Clazz.declareType (awt2swing, "TextArea", javax.swing.JTextArea); -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JTextArea"], "awt2swing.TextArea", null, function () { +c$ = Clazz.declareType (awt2swing, "TextArea", javax.swing.JTextArea); +}); diff --git a/bin/awt2swing/TextField.js b/bin/awt2swing/TextField.js index e8c1558..ef48b75 100644 --- a/bin/awt2swing/TextField.js +++ b/bin/awt2swing/TextField.js @@ -1,23 +1,23 @@ -Clazz.declarePackage ("awt2swing"); -Clazz.load (["javax.swing.JTextField"], "awt2swing.TextField", ["java.awt.event.TextEvent", "javax.swing.event.DocumentListener"], function () { -c$ = Clazz.declareType (awt2swing, "TextField", javax.swing.JTextField); -Clazz.defineMethod (c$, "addTextListener", -function (textListener) { -this.getDocument ().addDocumentListener (((Clazz.isClassDefined ("awt2swing.TextField$1") ? 0 : awt2swing.TextField.$TextField$1$ ()), Clazz.innerTypeInstance (awt2swing.TextField$1, this, Clazz.cloneFinals ("textListener", textListener)))); -}, "java.awt.event.TextListener"); -c$.$TextField$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (awt2swing, "TextField$1", null, javax.swing.event.DocumentListener); -Clazz.overrideMethod (c$, "insertUpdate", -function (e) { -}, "javax.swing.event.DocumentEvent"); -Clazz.overrideMethod (c$, "removeUpdate", -function (e) { -}, "javax.swing.event.DocumentEvent"); -Clazz.overrideMethod (c$, "changedUpdate", -function (e) { -this.f$.textListener.textValueChanged ( new java.awt.event.TextEvent (this, 0)); -}, "javax.swing.event.DocumentEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("awt2swing"); +Clazz.load (["javax.swing.JTextField"], "awt2swing.TextField", ["java.awt.event.TextEvent", "javax.swing.event.DocumentListener"], function () { +c$ = Clazz.declareType (awt2swing, "TextField", javax.swing.JTextField); +Clazz.defineMethod (c$, "addTextListener", +function (textListener) { +this.getDocument ().addDocumentListener (((Clazz.isClassDefined ("awt2swing.TextField$1") ? 0 : awt2swing.TextField.$TextField$1$ ()), Clazz.innerTypeInstance (awt2swing.TextField$1, this, Clazz.cloneFinals ("textListener", textListener)))); +}, "java.awt.event.TextListener"); +c$.$TextField$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (awt2swing, "TextField$1", null, javax.swing.event.DocumentListener); +Clazz.overrideMethod (c$, "insertUpdate", +function (e) { +}, "javax.swing.event.DocumentEvent"); +Clazz.overrideMethod (c$, "removeUpdate", +function (e) { +}, "javax.swing.event.DocumentEvent"); +Clazz.overrideMethod (c$, "changedUpdate", +function (e) { +this.f$.textListener.textValueChanged ( new java.awt.event.TextEvent (this, 0)); +}, "javax.swing.event.DocumentEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/com/stevesoft/pat/AmpersandRule.js b/bin/com/stevesoft/pat/AmpersandRule.js index ac1ce77..6d1f622 100644 --- a/bin/com/stevesoft/pat/AmpersandRule.js +++ b/bin/com/stevesoft/pat/AmpersandRule.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.AmpersandRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "AmpersandRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.AmpersandRule, []); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -sb.append (res.stringMatched ()); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return "$&"; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.AmpersandRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "AmpersandRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.AmpersandRule, []); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +sb.append (res.stringMatched ()); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return "$&"; +}); +}); diff --git a/bin/com/stevesoft/pat/Any.js b/bin/com/stevesoft/pat/Any.js index f129d92..503de21 100644 --- a/bin/com/stevesoft/pat/Any.js +++ b/bin/com/stevesoft/pat/Any.js @@ -1,30 +1,30 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Any", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "Any", com.stevesoft.pat.Pattern); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (pos < pt.src.length ()) { -if (pt.dotDoesntMatchCR) { -if (pt.src.charAt (pos) != '\n') { -return this.nextMatch (pos + 1, pt); -}} else { -return this.nextMatch (pos + 1, pt); -}}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -return "." + this.nextString (); -}); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.Any (); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Any", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "Any", com.stevesoft.pat.Pattern); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (pos < pt.src.length ()) { +if (pt.dotDoesntMatchCR) { +if (pt.src.charAt (pos) != '\n') { +return this.nextMatch (pos + 1, pt); +}} else { +return this.nextMatch (pos + 1, pt); +}}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +return "." + this.nextString (); +}); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.Any (); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/BackG.js b/bin/com/stevesoft/pat/BackG.js index 28d17cd..a9d07b7 100644 --- a/bin/com/stevesoft/pat/BackG.js +++ b/bin/com/stevesoft/pat/BackG.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.BackG", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.c = '\0'; -this.altc = '\0'; -this.altc2 = '\0'; -this.mask = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "BackG", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.BackG, []); -}); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -return pos == pt.lastPos ? this.nextMatch (pos, pt) : -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -return "\\G" + this.nextString (); -}); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.BackG (); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.BackG", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.c = '\0'; +this.altc = '\0'; +this.altc2 = '\0'; +this.mask = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "BackG", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.BackG, []); +}); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +return pos == pt.lastPos ? this.nextMatch (pos, pt) : -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +return "\\G" + this.nextString (); +}); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.BackG (); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/BackMatch.js b/bin/com/stevesoft/pat/BackMatch.js index 018cdda..f3a2ea9 100644 --- a/bin/com/stevesoft/pat/BackMatch.js +++ b/bin/com/stevesoft/pat/BackMatch.js @@ -1,36 +1,36 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.BackMatch", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.id = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "BackMatch", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (id) { -Clazz.superConstructor (this, com.stevesoft.pat.BackMatch, []); -this.id = id; -}, "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -return "\\" + (this.id) + this.nextString (); -}); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, p) { -var i1 = p.marks[this.id]; -var i2 = p.marks[this.id + p.nMarks]; -var imax = i2 - i1; -if (i1 < 0 || imax < 0 || pos + imax > p.src.length ()) { -return -1; -}var ns = p.src.length () - pos; -if (imax < ns) { -ns = imax; -}for (var i = 0; i < ns; i++) { -if (p.src.charAt (i + i1) != p.src.charAt (pos + i)) { -return -1; -}} -return this.nextMatch (pos + imax, p); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.BackMatch (this.id); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.BackMatch", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.id = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "BackMatch", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (id) { +Clazz.superConstructor (this, com.stevesoft.pat.BackMatch, []); +this.id = id; +}, "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +return "\\" + (this.id) + this.nextString (); +}); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, p) { +var i1 = p.marks[this.id]; +var i2 = p.marks[this.id + p.nMarks]; +var imax = i2 - i1; +if (i1 < 0 || imax < 0 || pos + imax > p.src.length ()) { +return -1; +}var ns = p.src.length () - pos; +if (imax < ns) { +ns = imax; +}for (var i = 0; i < ns; i++) { +if (p.src.charAt (i + i1) != p.src.charAt (pos + i)) { +return -1; +}} +return this.nextMatch (pos + imax, p); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.BackMatch (this.id); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/BackRefRule.js b/bin/com/stevesoft/pat/BackRefRule.js index d6a1e2e..f744c08 100644 --- a/bin/com/stevesoft/pat/BackRefRule.js +++ b/bin/com/stevesoft/pat/BackRefRule.js @@ -1,25 +1,25 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.BackRefRule", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.n = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "BackRefRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function (n) { -Clazz.superConstructor (this, com.stevesoft.pat.BackRefRule, []); -this.n = n; -}, "~N"); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -var x = res.stringMatchedI (this.n); -sb.append (x == null ? "" : x); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return "$" + this.n; -}); -Clazz.overrideMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.BackRefRule (this.n); -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.BackRefRule", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.n = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "BackRefRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function (n) { +Clazz.superConstructor (this, com.stevesoft.pat.BackRefRule, []); +this.n = n; +}, "~N"); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +var x = res.stringMatchedI (this.n); +sb.append (x == null ? "" : x); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return "$" + this.n; +}); +Clazz.overrideMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.BackRefRule (this.n); +}); +}); diff --git a/bin/com/stevesoft/pat/Backup.js b/bin/com/stevesoft/pat/Backup.js index f155142..3063b71 100644 --- a/bin/com/stevesoft/pat/Backup.js +++ b/bin/com/stevesoft/pat/Backup.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Backup", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.bk = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Backup", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (ii) { -Clazz.superConstructor (this, com.stevesoft.pat.Backup, []); -this.bk = ii; -}, "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -return "(?" + (this.bk < 0 ? ">" + (-this.bk) : "<" + this.bk) + ")" + this.nextString (); -}); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (pos < this.bk) { -return -1; -}return this.nextMatch (pos - this.bk, pt); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (-this.bk); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (-this.bk); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.Backup (this.bk); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Backup", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.bk = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Backup", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (ii) { +Clazz.superConstructor (this, com.stevesoft.pat.Backup, []); +this.bk = ii; +}, "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +return "(?" + (this.bk < 0 ? ">" + (-this.bk) : "<" + this.bk) + ")" + this.nextString (); +}); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (pos < this.bk) { +return -1; +}return this.nextMatch (pos - this.bk, pt); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (-this.bk); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (-this.bk); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.Backup (this.bk); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/BasicStringBufferLike.js b/bin/com/stevesoft/pat/BasicStringBufferLike.js index f4df37f..c492d08 100644 --- a/bin/com/stevesoft/pat/BasicStringBufferLike.js +++ b/bin/com/stevesoft/pat/BasicStringBufferLike.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.declareInterface (com.stevesoft.pat, "BasicStringBufferLike"); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.declareInterface (com.stevesoft.pat, "BasicStringBufferLike"); diff --git a/bin/com/stevesoft/pat/Bits.js b/bin/com/stevesoft/pat/Bits.js index ec8b74c..61bb0fd 100644 --- a/bin/com/stevesoft/pat/Bits.js +++ b/bin/com/stevesoft/pat/Bits.js @@ -1,2958 +1,2958 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -c$ = Clazz.decorateAsClass (function () { -this.carray = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Bits"); -Clazz.makeConstructor (c$, -function (carray) { -this.carray = carray; -}, "~A"); -Clazz.defineMethod (c$, "get", -function (i) { -return ((this.carray[i >> 4]).charCodeAt (0) & (1 << (i & 15))) != 0; -}, "~N"); -Clazz.defineMethod (c$, "set", -function (i, b) { -if (b) { -this.carray[i >> 4] = String.fromCharCode ((this.carray[i >> 4]).charCodeAt (0) | ((String.fromCharCode (1)).charCodeAt (0) << (i & 15))); -} else { -this.carray[i >> 4] = String.fromCharCode ((this.carray[i >> 4]).charCodeAt (0) & (String.fromCharCode (~(1 << (i & 15)))).charCodeAt (0)); -}}, "~N,~B"); -c$.upper_f = Clazz.defineMethod (c$, "upper_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.upper = new com.stevesoft.pat.Bits (data); -data[4] = String.fromCharCode (0xfffe); -data[5] = String.fromCharCode (0x07ff); -data[12] = String.fromCharCode (0xffff); -data[13] = String.fromCharCode (0x7f7f); -data[16] = String.fromCharCode (0x5555); -data[17] = String.fromCharCode (0x5555); -data[18] = String.fromCharCode (0x5555); -data[19] = String.fromCharCode (0xaa55); -data[20] = String.fromCharCode (0x54aa); -data[21] = String.fromCharCode (0x5555); -data[22] = String.fromCharCode (0x5555); -data[23] = String.fromCharCode (0x2b55); -data[24] = String.fromCharCode (0xced6); -data[25] = String.fromCharCode (0xb1db); -data[26] = String.fromCharCode (0xd2d5); -data[27] = String.fromCharCode (0x11ae); -data[28] = String.fromCharCode (0xa490); -data[29] = String.fromCharCode (0x4aaa); -data[30] = String.fromCharCode (0x5555); -data[31] = String.fromCharCode (0x5412); -data[32] = String.fromCharCode (0x5555); -data[33] = 'U'; -data[56] = String.fromCharCode (0xd740); -data[57] = String.fromCharCode (0xfffe); -data[58] = String.fromCharCode (0x0ffb); -data[61] = String.fromCharCode (0x541c); -data[62] = String.fromCharCode (0x5555); -data[64] = String.fromCharCode (0xdffe); -data[65] = String.fromCharCode (0xffff); -data[66] = String.fromCharCode (0xffff); -data[70] = String.fromCharCode (0x5555); -data[71] = String.fromCharCode (0x5555); -data[72] = String.fromCharCode (0x0001); -data[73] = String.fromCharCode (0x5555); -data[74] = String.fromCharCode (0x5555); -data[75] = String.fromCharCode (0x5555); -data[76] = String.fromCharCode (0x088a); -data[77] = String.fromCharCode (0x5555); -data[78] = String.fromCharCode (0x4555); -data[79] = String.fromCharCode (0x0115); -data[83] = String.fromCharCode (0xfffe); -data[84] = String.fromCharCode (0xffff); -data[85] = String.fromCharCode (0x007f); -data[266] = String.fromCharCode (0xffff); -data[267] = String.fromCharCode (0xffff); -data[268] = String.fromCharCode (0x003f); -data[480] = String.fromCharCode (0x5555); -data[481] = String.fromCharCode (0x5555); -data[482] = String.fromCharCode (0x5555); -data[483] = String.fromCharCode (0x5555); -data[484] = String.fromCharCode (0x5555); -data[485] = String.fromCharCode (0x5555); -data[486] = String.fromCharCode (0x5555); -data[487] = String.fromCharCode (0x5555); -data[488] = String.fromCharCode (0x5555); -data[489] = String.fromCharCode (0x0015); -data[490] = String.fromCharCode (0x5555); -data[491] = String.fromCharCode (0x5555); -data[492] = String.fromCharCode (0x5555); -data[493] = String.fromCharCode (0x5555); -data[494] = String.fromCharCode (0x5555); -data[495] = String.fromCharCode (0x0155); -data[496] = String.fromCharCode (0xff00); -data[497] = String.fromCharCode (0x3f00); -data[498] = String.fromCharCode (0xff00); -data[499] = String.fromCharCode (0xff00); -data[500] = String.fromCharCode (0x3f00); -data[501] = String.fromCharCode (0xaa00); -data[502] = String.fromCharCode (0xff00); -data[504] = String.fromCharCode (0xff00); -data[505] = String.fromCharCode (0xff00); -data[506] = String.fromCharCode (0xff00); -data[507] = String.fromCharCode (0x5f00); -data[508] = String.fromCharCode (0x1f00); -data[509] = String.fromCharCode (0x0f00); -data[510] = String.fromCharCode (0x1f00); -data[511] = String.fromCharCode (0x1f00); -data[528] = String.fromCharCode (0x3884); -data[529] = String.fromCharCode (0x3f27); -data[530] = String.fromCharCode (0x3d50); -data[531] = String.fromCharCode (0x000b); -data[4082] = String.fromCharCode (0xfffe); -data[4083] = String.fromCharCode (0x07ff); -data[4100] = String.fromCharCode (0xfffe); -data[4101] = String.fromCharCode (0x07ff); -data[4108] = String.fromCharCode (0xffff); -data[4109] = String.fromCharCode (0x7f7f); -data[4112] = String.fromCharCode (0x5555); -data[4113] = String.fromCharCode (0x5555); -data[4114] = String.fromCharCode (0x5555); -data[4115] = String.fromCharCode (0xaa55); -data[4116] = String.fromCharCode (0x54aa); -data[4117] = String.fromCharCode (0x5555); -data[4118] = String.fromCharCode (0x5555); -data[4119] = String.fromCharCode (0x2b55); -data[4120] = String.fromCharCode (0xced6); -data[4121] = String.fromCharCode (0xb1db); -data[4122] = String.fromCharCode (0xd2d5); -data[4123] = String.fromCharCode (0x11ae); -data[4124] = String.fromCharCode (0xa490); -data[4125] = String.fromCharCode (0x4aaa); -data[4126] = String.fromCharCode (0x5555); -data[4127] = String.fromCharCode (0x5412); -data[4128] = String.fromCharCode (0x5555); -data[4129] = 'U'; -data[4152] = String.fromCharCode (0xd740); -data[4153] = String.fromCharCode (0xfffe); -data[4154] = String.fromCharCode (0x0ffb); -data[4157] = String.fromCharCode (0x541c); -data[4158] = 'U'; -}); -c$.lower_f = Clazz.defineMethod (c$, "lower_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.lower = new com.stevesoft.pat.Bits (data); -data[6] = String.fromCharCode (0xfffe); -data[7] = String.fromCharCode (0x07ff); -data[10] = String.fromCharCode (0x0400); -data[11] = String.fromCharCode (0x0420); -data[13] = String.fromCharCode (0x8000); -data[14] = String.fromCharCode (0xffff); -data[15] = String.fromCharCode (0xff7f); -data[16] = String.fromCharCode (0xaaaa); -data[17] = String.fromCharCode (0xaaaa); -data[18] = String.fromCharCode (0xaaaa); -data[19] = String.fromCharCode (0x55aa); -data[20] = String.fromCharCode (0xab55); -data[21] = String.fromCharCode (0xaaaa); -data[22] = String.fromCharCode (0xaaaa); -data[23] = String.fromCharCode (0xd4aa); -data[24] = String.fromCharCode (0x3129); -data[25] = String.fromCharCode (0x4e24); -data[26] = String.fromCharCode (0x292a); -data[27] = String.fromCharCode (0x2651); -data[28] = String.fromCharCode (0x5240); -data[29] = String.fromCharCode (0xb555); -data[30] = String.fromCharCode (0xaaaa); -data[31] = String.fromCharCode (0xa829); -data[32] = String.fromCharCode (0xaaaa); -data[33] = String.fromCharCode (0x00aa); -data[37] = String.fromCharCode (0xffff); -data[38] = String.fromCharCode (0xffff); -data[39] = String.fromCharCode (0xffff); -data[40] = String.fromCharCode (0xffff); -data[41] = String.fromCharCode (0xffff); -data[42] = String.fromCharCode (0x01ff); -data[57] = String.fromCharCode (0x0001); -data[58] = String.fromCharCode (0xf000); -data[59] = String.fromCharCode (0xffff); -data[60] = String.fromCharCode (0x7fff); -data[61] = 'c'; -data[62] = String.fromCharCode (0xaaa8); -data[63] = String.fromCharCode (0x0007); -data[67] = String.fromCharCode (0xffff); -data[68] = String.fromCharCode (0xffff); -data[69] = String.fromCharCode (0xdffe); -data[70] = String.fromCharCode (0xaaaa); -data[71] = String.fromCharCode (0xaaaa); -data[72] = String.fromCharCode (0x0002); -data[73] = String.fromCharCode (0xaaaa); -data[74] = String.fromCharCode (0xaaaa); -data[75] = String.fromCharCode (0xaaaa); -data[76] = String.fromCharCode (0x1114); -data[77] = String.fromCharCode (0xaaaa); -data[78] = String.fromCharCode (0x8aaa); -data[79] = String.fromCharCode (0x022a); -data[86] = String.fromCharCode (0xfffe); -data[87] = String.fromCharCode (0xffff); -data[88] = String.fromCharCode (0x00ff); -data[269] = String.fromCharCode (0xffff); -data[270] = String.fromCharCode (0xffff); -data[271] = String.fromCharCode (0x007f); -data[480] = String.fromCharCode (0xaaaa); -data[481] = String.fromCharCode (0xaaaa); -data[482] = String.fromCharCode (0xaaaa); -data[483] = String.fromCharCode (0xaaaa); -data[484] = String.fromCharCode (0xaaaa); -data[485] = String.fromCharCode (0xaaaa); -data[486] = String.fromCharCode (0xaaaa); -data[487] = String.fromCharCode (0xaaaa); -data[488] = String.fromCharCode (0xaaaa); -data[489] = String.fromCharCode (0x0fea); -data[490] = String.fromCharCode (0xaaaa); -data[491] = String.fromCharCode (0xaaaa); -data[492] = String.fromCharCode (0xaaaa); -data[493] = String.fromCharCode (0xaaaa); -data[494] = String.fromCharCode (0xaaaa); -data[495] = String.fromCharCode (0x02aa); -data[496] = String.fromCharCode (0x00ff); -data[497] = String.fromCharCode (0x003f); -data[498] = String.fromCharCode (0x00ff); -data[499] = String.fromCharCode (0x00ff); -data[500] = String.fromCharCode (0x003f); -data[501] = String.fromCharCode (0x00ff); -data[502] = String.fromCharCode (0x00ff); -data[503] = String.fromCharCode (0x3fff); -data[504] = String.fromCharCode (0x00ff); -data[505] = String.fromCharCode (0x00ff); -data[506] = String.fromCharCode (0x00ff); -data[507] = String.fromCharCode (0x00df); -data[508] = String.fromCharCode (0x00dc); -data[509] = String.fromCharCode (0x00cf); -data[510] = String.fromCharCode (0x00ff); -data[511] = String.fromCharCode (0x00dc); -data[519] = String.fromCharCode (0x8000); -data[528] = String.fromCharCode (0xc400); -data[529] = String.fromCharCode (0x0008); -data[530] = String.fromCharCode (0xc000); -data[531] = String.fromCharCode (0x0010); -data[4016] = String.fromCharCode (0x007f); -data[4017] = String.fromCharCode (0x00f8); -data[4084] = String.fromCharCode (0xfffe); -data[4085] = String.fromCharCode (0x07ff); -data[4102] = String.fromCharCode (0xfffe); -data[4103] = String.fromCharCode (0x07ff); -data[4106] = String.fromCharCode (0x0400); -data[4107] = String.fromCharCode (0x0420); -data[4109] = String.fromCharCode (0x8000); -data[4110] = String.fromCharCode (0xffff); -data[4111] = String.fromCharCode (0xff7f); -data[4112] = String.fromCharCode (0xaaaa); -data[4113] = String.fromCharCode (0xaaaa); -data[4114] = String.fromCharCode (0xaaaa); -data[4115] = String.fromCharCode (0x55aa); -data[4116] = String.fromCharCode (0xab55); -data[4117] = String.fromCharCode (0xaaaa); -data[4118] = String.fromCharCode (0xaaaa); -data[4119] = String.fromCharCode (0xd4aa); -data[4120] = String.fromCharCode (0x3129); -data[4121] = String.fromCharCode (0x4e24); -data[4122] = String.fromCharCode (0x292a); -data[4123] = String.fromCharCode (0x2651); -data[4124] = String.fromCharCode (0x5240); -data[4125] = String.fromCharCode (0xb555); -data[4126] = String.fromCharCode (0xaaaa); -data[4127] = String.fromCharCode (0xa829); -data[4128] = String.fromCharCode (0xaaaa); -data[4129] = String.fromCharCode (0x00aa); -data[4133] = String.fromCharCode (0xffff); -data[4134] = String.fromCharCode (0xffff); -data[4135] = String.fromCharCode (0xffff); -data[4136] = String.fromCharCode (0xffff); -data[4137] = String.fromCharCode (0xffff); -data[4138] = String.fromCharCode (0x01ff); -data[4153] = String.fromCharCode (0x0001); -data[4154] = String.fromCharCode (0xf000); -data[4155] = String.fromCharCode (0xffff); -data[4156] = String.fromCharCode (0x7fff); -data[4157] = 'c'; -data[4158] = String.fromCharCode (0x00a8); -}); -c$.title_f = Clazz.defineMethod (c$, "title_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.title = new com.stevesoft.pat.Bits (data); -data[6] = String.fromCharCode (0xfffe); -data[7] = String.fromCharCode (0x07ff); -data[10] = String.fromCharCode (0x0400); -data[11] = String.fromCharCode (0x0420); -data[13] = String.fromCharCode (0x8000); -data[14] = String.fromCharCode (0xffff); -data[15] = String.fromCharCode (0xff7f); -data[16] = String.fromCharCode (0xaaaa); -data[17] = String.fromCharCode (0xaaaa); -data[18] = String.fromCharCode (0xaaaa); -data[19] = String.fromCharCode (0x55aa); -data[20] = String.fromCharCode (0xab55); -data[21] = String.fromCharCode (0xaaaa); -data[22] = String.fromCharCode (0xaaaa); -data[23] = String.fromCharCode (0xd4aa); -data[24] = String.fromCharCode (0x3129); -data[25] = String.fromCharCode (0x4e24); -data[26] = String.fromCharCode (0x292a); -data[27] = String.fromCharCode (0x2651); -data[28] = String.fromCharCode (0x5240); -data[29] = String.fromCharCode (0xb555); -data[30] = String.fromCharCode (0xaaaa); -data[31] = String.fromCharCode (0xa829); -data[32] = String.fromCharCode (0xaaaa); -data[33] = String.fromCharCode (0x00aa); -data[37] = String.fromCharCode (0xffff); -data[38] = String.fromCharCode (0xffff); -data[39] = String.fromCharCode (0xffff); -data[40] = String.fromCharCode (0xffff); -data[41] = String.fromCharCode (0xffff); -data[42] = String.fromCharCode (0x01ff); -data[57] = String.fromCharCode (0x0001); -data[58] = String.fromCharCode (0xf000); -data[59] = String.fromCharCode (0xffff); -data[60] = String.fromCharCode (0x7fff); -data[61] = 'c'; -data[62] = String.fromCharCode (0xaaa8); -data[63] = String.fromCharCode (0x0007); -data[67] = String.fromCharCode (0xffff); -data[68] = String.fromCharCode (0xffff); -data[69] = String.fromCharCode (0xdffe); -data[70] = String.fromCharCode (0xaaaa); -data[71] = String.fromCharCode (0xaaaa); -data[72] = String.fromCharCode (0x0002); -data[73] = String.fromCharCode (0xaaaa); -data[74] = String.fromCharCode (0xaaaa); -data[75] = String.fromCharCode (0xaaaa); -data[76] = String.fromCharCode (0x1114); -data[77] = String.fromCharCode (0xaaaa); -data[78] = String.fromCharCode (0x8aaa); -data[79] = String.fromCharCode (0x022a); -data[86] = String.fromCharCode (0xfffe); -data[87] = String.fromCharCode (0xffff); -data[88] = String.fromCharCode (0x00ff); -data[269] = String.fromCharCode (0xffff); -data[270] = String.fromCharCode (0xffff); -data[271] = String.fromCharCode (0x007f); -data[480] = String.fromCharCode (0xaaaa); -data[481] = String.fromCharCode (0xaaaa); -data[482] = String.fromCharCode (0xaaaa); -data[483] = String.fromCharCode (0xaaaa); -data[484] = String.fromCharCode (0xaaaa); -data[485] = String.fromCharCode (0xaaaa); -data[486] = String.fromCharCode (0xaaaa); -data[487] = String.fromCharCode (0xaaaa); -data[488] = String.fromCharCode (0xaaaa); -data[489] = String.fromCharCode (0x0fea); -data[490] = String.fromCharCode (0xaaaa); -data[491] = String.fromCharCode (0xaaaa); -data[492] = String.fromCharCode (0xaaaa); -data[493] = String.fromCharCode (0xaaaa); -data[494] = String.fromCharCode (0xaaaa); -data[495] = String.fromCharCode (0x02aa); -data[496] = String.fromCharCode (0x00ff); -data[497] = String.fromCharCode (0x003f); -data[498] = String.fromCharCode (0x00ff); -data[499] = String.fromCharCode (0x00ff); -data[500] = String.fromCharCode (0x003f); -data[501] = String.fromCharCode (0x00ff); -data[502] = String.fromCharCode (0x00ff); -data[503] = String.fromCharCode (0x3fff); -data[504] = String.fromCharCode (0x00ff); -data[505] = String.fromCharCode (0x00ff); -data[506] = String.fromCharCode (0x00ff); -data[507] = String.fromCharCode (0x00df); -data[508] = String.fromCharCode (0x00dc); -data[509] = String.fromCharCode (0x00cf); -data[510] = String.fromCharCode (0x00ff); -data[511] = String.fromCharCode (0x00dc); -data[519] = String.fromCharCode (0x8000); -data[528] = String.fromCharCode (0xc400); -data[529] = String.fromCharCode (0x0008); -data[530] = String.fromCharCode (0xc000); -data[531] = String.fromCharCode (0x0010); -data[4016] = String.fromCharCode (0x007f); -data[4017] = String.fromCharCode (0x00f8); -data[4084] = String.fromCharCode (0xfffe); -data[4085] = String.fromCharCode (0x07ff); -data[4102] = String.fromCharCode (0xfffe); -data[4103] = String.fromCharCode (0x07ff); -data[4106] = String.fromCharCode (0x0400); -data[4107] = String.fromCharCode (0x0420); -data[4109] = String.fromCharCode (0x8000); -data[4110] = String.fromCharCode (0xffff); -data[4111] = String.fromCharCode (0xff7f); -data[4112] = String.fromCharCode (0xaaaa); -data[4113] = String.fromCharCode (0xaaaa); -data[4114] = String.fromCharCode (0xaaaa); -data[4115] = String.fromCharCode (0x55aa); -data[4116] = String.fromCharCode (0xab55); -data[4117] = String.fromCharCode (0xaaaa); -data[4118] = String.fromCharCode (0xaaaa); -data[4119] = String.fromCharCode (0xd4aa); -data[4120] = String.fromCharCode (0x3129); -data[4121] = String.fromCharCode (0x4e24); -data[4122] = String.fromCharCode (0x292a); -data[4123] = String.fromCharCode (0x2651); -data[4124] = String.fromCharCode (0x5240); -data[4125] = String.fromCharCode (0xb555); -data[4126] = String.fromCharCode (0xaaaa); -data[4127] = String.fromCharCode (0xa829); -data[4128] = String.fromCharCode (0xaaaa); -data[4129] = String.fromCharCode (0x00aa); -data[4133] = String.fromCharCode (0xffff); -data[4134] = String.fromCharCode (0xffff); -data[4135] = String.fromCharCode (0xffff); -data[4136] = String.fromCharCode (0xffff); -data[4137] = String.fromCharCode (0xffff); -data[4138] = String.fromCharCode (0x01ff); -data[4153] = String.fromCharCode (0x0001); -data[4154] = String.fromCharCode (0xf000); -data[4155] = String.fromCharCode (0xffff); -data[4156] = String.fromCharCode (0x7fff); -data[4157] = 'c'; -data[4158] = String.fromCharCode (0x00a8); -}); -c$.currency_f = Clazz.defineMethod (c$, "currency_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.currency = new com.stevesoft.pat.Bits (data); -data[2] = String.fromCharCode (0x0010); -data[10] = String.fromCharCode (0x003c); -data[159] = String.fromCharCode (0x000c); -data[227] = String.fromCharCode (0x8000); -data[522] = String.fromCharCode (0x1fff); -data[4070] = String.fromCharCode (0x0200); -data[4080] = String.fromCharCode (0x0010); -data[4094] = 'c'; -data[4098] = String.fromCharCode (0x0010); -data[4106] = String.fromCharCode (0x003c); -}); -c$.decimal_digit_f = Clazz.defineMethod (c$, "decimal_digit_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.decimal_digit = new com.stevesoft.pat.Bits (data); -data[3] = String.fromCharCode (0x03ff); -data[102] = String.fromCharCode (0x03ff); -data[111] = String.fromCharCode (0x03ff); -data[150] = String.fromCharCode (0xffc0); -data[158] = String.fromCharCode (0xffc0); -data[166] = String.fromCharCode (0xffc0); -data[174] = String.fromCharCode (0xffc0); -data[182] = String.fromCharCode (0xffc0); -data[190] = String.fromCharCode (0xff80); -data[198] = String.fromCharCode (0xffc0); -data[206] = String.fromCharCode (0xffc0); -data[214] = String.fromCharCode (0xffc0); -data[229] = String.fromCharCode (0x03ff); -data[237] = String.fromCharCode (0x03ff); -data[242] = String.fromCharCode (0x03ff); -data[4081] = String.fromCharCode (0x03ff); -data[4099] = String.fromCharCode (0x03ff); -}); -c$.math_f = Clazz.defineMethod (c$, "math_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.math = new com.stevesoft.pat.Bits (data); -data[2] = String.fromCharCode (0x0800); -data[3] = String.fromCharCode (0x7000); -data[7] = String.fromCharCode (0x5000); -data[10] = String.fromCharCode (0x1000); -data[11] = String.fromCharCode (0x0002); -data[13] = String.fromCharCode (0x0080); -data[15] = String.fromCharCode (0x0080); -data[516] = String.fromCharCode (0x0010); -data[519] = String.fromCharCode (0x1c00); -data[520] = String.fromCharCode (0x1c00); -data[537] = String.fromCharCode (0x001f); -data[541] = String.fromCharCode (0x0014); -data[544] = String.fromCharCode (0xffff); -data[545] = String.fromCharCode (0xffff); -data[546] = String.fromCharCode (0xffff); -data[547] = String.fromCharCode (0xffff); -data[548] = String.fromCharCode (0xffff); -data[549] = String.fromCharCode (0xffff); -data[550] = String.fromCharCode (0xffff); -data[551] = String.fromCharCode (0xffff); -data[552] = String.fromCharCode (0xffff); -data[553] = String.fromCharCode (0xffff); -data[554] = String.fromCharCode (0xffff); -data[555] = String.fromCharCode (0xffff); -data[556] = String.fromCharCode (0xffff); -data[557] = String.fromCharCode (0xffff); -data[558] = String.fromCharCode (0xffff); -data[559] = String.fromCharCode (0x0003); -data[560] = String.fromCharCode (0x0f00); -data[562] = String.fromCharCode (0x0003); -data[4018] = String.fromCharCode (0x0200); -data[4070] = 't'; -data[4080] = String.fromCharCode (0x0800); -data[4081] = String.fromCharCode (0x7000); -data[4085] = String.fromCharCode (0x5000); -data[4094] = String.fromCharCode (0x1f04); -data[4098] = String.fromCharCode (0x0800); -data[4099] = String.fromCharCode (0x7000); -data[4103] = String.fromCharCode (0x5000); -data[4106] = String.fromCharCode (0x1000); -data[4107] = String.fromCharCode (0x0002); -data[4109] = String.fromCharCode (0x0080); -data[4111] = String.fromCharCode (0x0080); -}); -c$.letter_f = Clazz.defineMethod (c$, "letter_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.letter = new com.stevesoft.pat.Bits (data); -data[4] = String.fromCharCode (0xfffe); -data[5] = String.fromCharCode (0x07ff); -data[6] = String.fromCharCode (0xfffe); -data[7] = String.fromCharCode (0x07ff); -data[10] = String.fromCharCode (0x0400); -data[11] = String.fromCharCode (0x0420); -data[12] = String.fromCharCode (0xffff); -data[13] = String.fromCharCode (0xff7f); -data[14] = String.fromCharCode (0xffff); -data[15] = String.fromCharCode (0xff7f); -data[16] = String.fromCharCode (0xffff); -data[17] = String.fromCharCode (0xffff); -data[18] = String.fromCharCode (0xffff); -data[19] = String.fromCharCode (0xffff); -data[20] = String.fromCharCode (0xffff); -data[21] = String.fromCharCode (0xffff); -data[22] = String.fromCharCode (0xffff); -data[23] = String.fromCharCode (0xffff); -data[24] = String.fromCharCode (0xffff); -data[25] = String.fromCharCode (0xffff); -data[26] = String.fromCharCode (0xffff); -data[27] = String.fromCharCode (0xffff); -data[28] = String.fromCharCode (0xffff); -data[29] = String.fromCharCode (0xffff); -data[30] = String.fromCharCode (0xffff); -data[31] = String.fromCharCode (0xfc3f); -data[32] = String.fromCharCode (0xffff); -data[33] = String.fromCharCode (0x00ff); -data[37] = String.fromCharCode (0xffff); -data[38] = String.fromCharCode (0xffff); -data[39] = String.fromCharCode (0xffff); -data[40] = String.fromCharCode (0xffff); -data[41] = String.fromCharCode (0xffff); -data[42] = String.fromCharCode (0x01ff); -data[43] = String.fromCharCode (0xf9ff); -data[44] = String.fromCharCode (0x0003); -data[45] = String.fromCharCode (0x0003); -data[46] = String.fromCharCode (0x001f); -data[55] = String.fromCharCode (0x0400); -data[56] = String.fromCharCode (0xd740); -data[57] = String.fromCharCode (0xffff); -data[58] = String.fromCharCode (0xfffb); -data[59] = String.fromCharCode (0xffff); -data[60] = String.fromCharCode (0x7fff); -data[61] = String.fromCharCode (0x547f); -data[62] = String.fromCharCode (0xfffd); -data[63] = String.fromCharCode (0x000f); -data[64] = String.fromCharCode (0xdffe); -data[65] = String.fromCharCode (0xffff); -data[66] = String.fromCharCode (0xffff); -data[67] = String.fromCharCode (0xffff); -data[68] = String.fromCharCode (0xffff); -data[69] = String.fromCharCode (0xdffe); -data[70] = String.fromCharCode (0xffff); -data[71] = String.fromCharCode (0xffff); -data[72] = String.fromCharCode (0x0003); -data[73] = String.fromCharCode (0xffff); -data[74] = String.fromCharCode (0xffff); -data[75] = String.fromCharCode (0xffff); -data[76] = String.fromCharCode (0x199f); -data[77] = String.fromCharCode (0xffff); -data[78] = String.fromCharCode (0xcfff); -data[79] = String.fromCharCode (0x033f); -data[83] = String.fromCharCode (0xfffe); -data[84] = String.fromCharCode (0xffff); -data[85] = String.fromCharCode (0x027f); -data[86] = String.fromCharCode (0xfffe); -data[87] = String.fromCharCode (0xffff); -data[88] = String.fromCharCode (0x00ff); -data[93] = String.fromCharCode (0xffff); -data[94] = String.fromCharCode (0x07ff); -data[95] = String.fromCharCode (0x0007); -data[98] = String.fromCharCode (0xfffe); -data[99] = String.fromCharCode (0x07ff); -data[100] = String.fromCharCode (0x07ff); -data[103] = String.fromCharCode (0xfffe); -data[104] = String.fromCharCode (0xffff); -data[105] = String.fromCharCode (0xffff); -data[106] = String.fromCharCode (0xffff); -data[107] = String.fromCharCode (0x7cff); -data[108] = String.fromCharCode (0x7fff); -data[109] = String.fromCharCode (0x002f); -data[110] = String.fromCharCode (0x0060); -data[144] = String.fromCharCode (0xffe0); -data[145] = String.fromCharCode (0xffff); -data[146] = String.fromCharCode (0xffff); -data[147] = String.fromCharCode (0x23ff); -data[149] = String.fromCharCode (0xff00); -data[150] = String.fromCharCode (0x0003); -data[152] = String.fromCharCode (0x9fe0); -data[153] = String.fromCharCode (0xfff9); -data[154] = String.fromCharCode (0xfdff); -data[155] = String.fromCharCode (0x03c5); -data[157] = String.fromCharCode (0xb000); -data[158] = String.fromCharCode (0x0003); -data[159] = String.fromCharCode (0x0003); -data[160] = String.fromCharCode (0x87e0); -data[161] = String.fromCharCode (0xfff9); -data[162] = String.fromCharCode (0xfdff); -data[163] = String.fromCharCode (0x036d); -data[165] = String.fromCharCode (0x5e00); -data[167] = String.fromCharCode (0x001c); -data[168] = String.fromCharCode (0xafe0); -data[169] = String.fromCharCode (0xfffb); -data[170] = String.fromCharCode (0xfdff); -data[171] = String.fromCharCode (0x23ed); -data[174] = String.fromCharCode (0x0001); -data[176] = String.fromCharCode (0x9fe0); -data[177] = String.fromCharCode (0xfff9); -data[178] = String.fromCharCode (0xfdff); -data[179] = String.fromCharCode (0x23cd); -data[181] = String.fromCharCode (0xb000); -data[182] = String.fromCharCode (0x0003); -data[184] = String.fromCharCode (0xc7e0); -data[185] = String.fromCharCode (0xd63d); -data[186] = String.fromCharCode (0xc718); -data[187] = String.fromCharCode (0x03bf); -data[192] = String.fromCharCode (0xdfe0); -data[193] = String.fromCharCode (0xfffd); -data[194] = String.fromCharCode (0xfdff); -data[195] = String.fromCharCode (0x03ef); -data[198] = String.fromCharCode (0x0003); -data[200] = String.fromCharCode (0xdfe0); -data[201] = String.fromCharCode (0xfffd); -data[202] = String.fromCharCode (0xfdff); -data[203] = String.fromCharCode (0x03ef); -data[205] = String.fromCharCode (0x4000); -data[206] = String.fromCharCode (0x0003); -data[208] = String.fromCharCode (0xdfe0); -data[209] = String.fromCharCode (0xfffd); -data[210] = String.fromCharCode (0xfdff); -data[211] = String.fromCharCode (0x03ff); -data[214] = String.fromCharCode (0x0003); -data[224] = String.fromCharCode (0xfffe); -data[225] = String.fromCharCode (0xffff); -data[226] = String.fromCharCode (0x7fff); -data[227] = String.fromCharCode (0x000d); -data[228] = String.fromCharCode (0x007f); -data[232] = String.fromCharCode (0x2596); -data[233] = String.fromCharCode (0xfef0); -data[234] = String.fromCharCode (0x6cae); -data[235] = String.fromCharCode (0x200d); -data[236] = String.fromCharCode (0x005f); -data[237] = String.fromCharCode (0x3000); -data[244] = String.fromCharCode (0xfeff); -data[245] = String.fromCharCode (0xffff); -data[246] = String.fromCharCode (0x03ff); -data[266] = String.fromCharCode (0xffff); -data[267] = String.fromCharCode (0xffff); -data[268] = String.fromCharCode (0x003f); -data[269] = String.fromCharCode (0xffff); -data[270] = String.fromCharCode (0xffff); -data[271] = String.fromCharCode (0x007f); -data[272] = String.fromCharCode (0xffff); -data[273] = String.fromCharCode (0xffff); -data[274] = String.fromCharCode (0xffff); -data[275] = String.fromCharCode (0xffff); -data[276] = String.fromCharCode (0xffff); -data[277] = String.fromCharCode (0x83ff); -data[278] = String.fromCharCode (0xffff); -data[279] = String.fromCharCode (0xffff); -data[280] = String.fromCharCode (0xffff); -data[281] = String.fromCharCode (0xffff); -data[282] = String.fromCharCode (0xff07); -data[283] = String.fromCharCode (0xffff); -data[284] = String.fromCharCode (0xffff); -data[285] = String.fromCharCode (0xffff); -data[286] = String.fromCharCode (0xffff); -data[287] = String.fromCharCode (0x03ff); -data[480] = String.fromCharCode (0xffff); -data[481] = String.fromCharCode (0xffff); -data[482] = String.fromCharCode (0xffff); -data[483] = String.fromCharCode (0xffff); -data[484] = String.fromCharCode (0xffff); -data[485] = String.fromCharCode (0xffff); -data[486] = String.fromCharCode (0xffff); -data[487] = String.fromCharCode (0xffff); -data[488] = String.fromCharCode (0xffff); -data[489] = String.fromCharCode (0x0fff); -data[490] = String.fromCharCode (0xffff); -data[491] = String.fromCharCode (0xffff); -data[492] = String.fromCharCode (0xffff); -data[493] = String.fromCharCode (0xffff); -data[494] = String.fromCharCode (0xffff); -data[495] = String.fromCharCode (0x03ff); -data[496] = String.fromCharCode (0xffff); -data[497] = String.fromCharCode (0x3f3f); -data[498] = String.fromCharCode (0xffff); -data[499] = String.fromCharCode (0xffff); -data[500] = String.fromCharCode (0x3f3f); -data[501] = String.fromCharCode (0xaaff); -data[502] = String.fromCharCode (0xffff); -data[503] = String.fromCharCode (0x3fff); -data[504] = String.fromCharCode (0xffff); -data[505] = String.fromCharCode (0xffff); -data[506] = String.fromCharCode (0xffff); -data[507] = String.fromCharCode (0x5fdf); -data[508] = String.fromCharCode (0x1fdc); -data[509] = String.fromCharCode (0x0fcf); -data[510] = String.fromCharCode (0x1fff); -data[511] = String.fromCharCode (0x1fdc); -data[519] = String.fromCharCode (0x8000); -data[528] = String.fromCharCode (0xfc84); -data[529] = String.fromCharCode (0x3f2f); -data[530] = String.fromCharCode (0xfd50); -data[531] = String.fromCharCode (0x01fb); -data[768] = String.fromCharCode (0x0020); -data[771] = String.fromCharCode (0x003e); -data[772] = String.fromCharCode (0xfffe); -data[773] = String.fromCharCode (0xffff); -data[774] = String.fromCharCode (0xffff); -data[775] = String.fromCharCode (0xffff); -data[776] = String.fromCharCode (0xffff); -data[777] = String.fromCharCode (0x781f); -data[778] = String.fromCharCode (0xfffe); -data[779] = String.fromCharCode (0xffff); -data[780] = String.fromCharCode (0xffff); -data[781] = String.fromCharCode (0xffff); -data[782] = String.fromCharCode (0xffff); -data[783] = String.fromCharCode (0x77ff); -data[784] = String.fromCharCode (0xffe0); -data[785] = String.fromCharCode (0xffff); -data[786] = String.fromCharCode (0x1fff); -data[787] = String.fromCharCode (0xfffe); -data[788] = String.fromCharCode (0xffff); -data[789] = String.fromCharCode (0xffff); -data[790] = String.fromCharCode (0xffff); -data[791] = String.fromCharCode (0xffff); -data[792] = String.fromCharCode (0x7fff); -data[1248] = String.fromCharCode (0xffff); -data[1249] = String.fromCharCode (0xffff); -data[1250] = String.fromCharCode (0xffff); -data[1251] = String.fromCharCode (0xffff); -data[1252] = String.fromCharCode (0xffff); -data[1253] = String.fromCharCode (0xffff); -data[1254] = String.fromCharCode (0xffff); -data[1255] = String.fromCharCode (0xffff); -data[1256] = String.fromCharCode (0xffff); -data[1257] = String.fromCharCode (0xffff); -data[1258] = String.fromCharCode (0xffff); -data[1259] = String.fromCharCode (0xffff); -data[1260] = String.fromCharCode (0xffff); -data[1261] = String.fromCharCode (0xffff); -data[1262] = String.fromCharCode (0xffff); -data[1263] = String.fromCharCode (0xffff); -data[1264] = String.fromCharCode (0xffff); -data[1265] = String.fromCharCode (0xffff); -data[1266] = String.fromCharCode (0xffff); -data[1267] = String.fromCharCode (0xffff); -data[1268] = String.fromCharCode (0xffff); -data[1269] = String.fromCharCode (0xffff); -data[1270] = String.fromCharCode (0xffff); -data[1271] = String.fromCharCode (0xffff); -data[1272] = String.fromCharCode (0xffff); -data[1273] = String.fromCharCode (0xffff); -data[1274] = String.fromCharCode (0xffff); -data[1275] = String.fromCharCode (0xffff); -data[1276] = String.fromCharCode (0xffff); -data[1277] = String.fromCharCode (0xffff); -data[1278] = String.fromCharCode (0xffff); -data[1279] = String.fromCharCode (0xffff); -data[1280] = String.fromCharCode (0xffff); -data[1281] = String.fromCharCode (0xffff); -data[1282] = String.fromCharCode (0xffff); -data[1283] = String.fromCharCode (0xffff); -data[1284] = String.fromCharCode (0xffff); -data[1285] = String.fromCharCode (0xffff); -data[1286] = String.fromCharCode (0xffff); -data[1287] = String.fromCharCode (0xffff); -data[1288] = String.fromCharCode (0xffff); -data[1289] = String.fromCharCode (0xffff); -data[1290] = String.fromCharCode (0xffff); -data[1291] = String.fromCharCode (0xffff); -data[1292] = String.fromCharCode (0xffff); -data[1293] = String.fromCharCode (0xffff); -data[1294] = String.fromCharCode (0xffff); -data[1295] = String.fromCharCode (0xffff); -data[1296] = String.fromCharCode (0xffff); -data[1297] = String.fromCharCode (0xffff); -data[1298] = String.fromCharCode (0xffff); -data[1299] = String.fromCharCode (0xffff); -data[1300] = String.fromCharCode (0xffff); -data[1301] = String.fromCharCode (0xffff); -data[1302] = String.fromCharCode (0xffff); -data[1303] = String.fromCharCode (0xffff); -data[1304] = String.fromCharCode (0xffff); -data[1305] = String.fromCharCode (0xffff); -data[1306] = String.fromCharCode (0xffff); -data[1307] = String.fromCharCode (0xffff); -data[1308] = String.fromCharCode (0xffff); -data[1309] = String.fromCharCode (0xffff); -data[1310] = String.fromCharCode (0xffff); -data[1311] = String.fromCharCode (0xffff); -data[1312] = String.fromCharCode (0xffff); -data[1313] = String.fromCharCode (0xffff); -data[1314] = String.fromCharCode (0xffff); -data[1315] = String.fromCharCode (0xffff); -data[1316] = String.fromCharCode (0xffff); -data[1317] = String.fromCharCode (0xffff); -data[1318] = String.fromCharCode (0xffff); -data[1319] = String.fromCharCode (0xffff); -data[1320] = String.fromCharCode (0xffff); -data[1321] = String.fromCharCode (0xffff); -data[1322] = String.fromCharCode (0xffff); -data[1323] = String.fromCharCode (0xffff); -data[1324] = String.fromCharCode (0xffff); -data[1325] = String.fromCharCode (0xffff); -data[1326] = String.fromCharCode (0xffff); -data[1327] = String.fromCharCode (0xffff); -data[1328] = String.fromCharCode (0xffff); -data[1329] = String.fromCharCode (0xffff); -data[1330] = String.fromCharCode (0xffff); -data[1331] = String.fromCharCode (0xffff); -data[1332] = String.fromCharCode (0xffff); -data[1333] = String.fromCharCode (0xffff); -data[1334] = String.fromCharCode (0xffff); -data[1335] = String.fromCharCode (0xffff); -data[1336] = String.fromCharCode (0xffff); -data[1337] = String.fromCharCode (0xffff); -data[1338] = String.fromCharCode (0xffff); -data[1339] = String.fromCharCode (0xffff); -data[1340] = String.fromCharCode (0xffff); -data[1341] = String.fromCharCode (0xffff); -data[1342] = String.fromCharCode (0xffff); -data[1343] = String.fromCharCode (0xffff); -data[1344] = String.fromCharCode (0xffff); -data[1345] = String.fromCharCode (0xffff); -data[1346] = String.fromCharCode (0xffff); -data[1347] = String.fromCharCode (0xffff); -data[1348] = String.fromCharCode (0xffff); -data[1349] = String.fromCharCode (0xffff); -data[1350] = String.fromCharCode (0xffff); -data[1351] = String.fromCharCode (0xffff); -data[1352] = String.fromCharCode (0xffff); -data[1353] = String.fromCharCode (0xffff); -data[1354] = String.fromCharCode (0xffff); -data[1355] = String.fromCharCode (0xffff); -data[1356] = String.fromCharCode (0xffff); -data[1357] = String.fromCharCode (0xffff); -data[1358] = String.fromCharCode (0xffff); -data[1359] = String.fromCharCode (0xffff); -data[1360] = String.fromCharCode (0xffff); -data[1361] = String.fromCharCode (0xffff); -data[1362] = String.fromCharCode (0xffff); -data[1363] = String.fromCharCode (0xffff); -data[1364] = String.fromCharCode (0xffff); -data[1365] = String.fromCharCode (0xffff); -data[1366] = String.fromCharCode (0xffff); -data[1367] = String.fromCharCode (0xffff); -data[1368] = String.fromCharCode (0xffff); -data[1369] = String.fromCharCode (0xffff); -data[1370] = String.fromCharCode (0xffff); -data[1371] = String.fromCharCode (0xffff); -data[1372] = String.fromCharCode (0xffff); -data[1373] = String.fromCharCode (0xffff); -data[1374] = String.fromCharCode (0xffff); -data[1375] = String.fromCharCode (0xffff); -data[1376] = String.fromCharCode (0xffff); -data[1377] = String.fromCharCode (0xffff); -data[1378] = String.fromCharCode (0xffff); -data[1379] = String.fromCharCode (0xffff); -data[1380] = String.fromCharCode (0xffff); -data[1381] = String.fromCharCode (0xffff); -data[1382] = String.fromCharCode (0xffff); -data[1383] = String.fromCharCode (0xffff); -data[1384] = String.fromCharCode (0xffff); -data[1385] = String.fromCharCode (0xffff); -data[1386] = String.fromCharCode (0xffff); -data[1387] = String.fromCharCode (0xffff); -data[1388] = String.fromCharCode (0xffff); -data[1389] = String.fromCharCode (0xffff); -data[1390] = String.fromCharCode (0xffff); -data[1391] = String.fromCharCode (0xffff); -data[1392] = String.fromCharCode (0xffff); -data[1393] = String.fromCharCode (0xffff); -data[1394] = String.fromCharCode (0xffff); -data[1395] = String.fromCharCode (0xffff); -data[1396] = String.fromCharCode (0xffff); -data[1397] = String.fromCharCode (0xffff); -data[1398] = String.fromCharCode (0xffff); -data[1399] = String.fromCharCode (0xffff); -data[1400] = String.fromCharCode (0xffff); -data[1401] = String.fromCharCode (0xffff); -data[1402] = String.fromCharCode (0xffff); -data[1403] = String.fromCharCode (0xffff); -data[1404] = String.fromCharCode (0xffff); -data[1405] = String.fromCharCode (0xffff); -data[1406] = String.fromCharCode (0xffff); -data[1407] = String.fromCharCode (0xffff); -data[1408] = String.fromCharCode (0xffff); -data[1409] = String.fromCharCode (0xffff); -data[1410] = String.fromCharCode (0xffff); -data[1411] = String.fromCharCode (0xffff); -data[1412] = String.fromCharCode (0xffff); -data[1413] = String.fromCharCode (0xffff); -data[1414] = String.fromCharCode (0xffff); -data[1415] = String.fromCharCode (0xffff); -data[1416] = String.fromCharCode (0xffff); -data[1417] = String.fromCharCode (0xffff); -data[1418] = String.fromCharCode (0xffff); -data[1419] = String.fromCharCode (0xffff); -data[1420] = String.fromCharCode (0xffff); -data[1421] = String.fromCharCode (0xffff); -data[1422] = String.fromCharCode (0xffff); -data[1423] = String.fromCharCode (0xffff); -data[1424] = String.fromCharCode (0xffff); -data[1425] = String.fromCharCode (0xffff); -data[1426] = String.fromCharCode (0xffff); -data[1427] = String.fromCharCode (0xffff); -data[1428] = String.fromCharCode (0xffff); -data[1429] = String.fromCharCode (0xffff); -data[1430] = String.fromCharCode (0xffff); -data[1431] = String.fromCharCode (0xffff); -data[1432] = String.fromCharCode (0xffff); -data[1433] = String.fromCharCode (0xffff); -data[1434] = String.fromCharCode (0xffff); -data[1435] = String.fromCharCode (0xffff); -data[1436] = String.fromCharCode (0xffff); -data[1437] = String.fromCharCode (0xffff); -data[1438] = String.fromCharCode (0xffff); -data[1439] = String.fromCharCode (0xffff); -data[1440] = String.fromCharCode (0xffff); -data[1441] = String.fromCharCode (0xffff); -data[1442] = String.fromCharCode (0xffff); -data[1443] = String.fromCharCode (0xffff); -data[1444] = String.fromCharCode (0xffff); -data[1445] = String.fromCharCode (0xffff); -data[1446] = String.fromCharCode (0xffff); -data[1447] = String.fromCharCode (0xffff); -data[1448] = String.fromCharCode (0xffff); -data[1449] = String.fromCharCode (0xffff); -data[1450] = String.fromCharCode (0xffff); -data[1451] = String.fromCharCode (0xffff); -data[1452] = String.fromCharCode (0xffff); -data[1453] = String.fromCharCode (0xffff); -data[1454] = String.fromCharCode (0xffff); -data[1455] = String.fromCharCode (0xffff); -data[1456] = String.fromCharCode (0xffff); -data[1457] = String.fromCharCode (0xffff); -data[1458] = String.fromCharCode (0xffff); -data[1459] = String.fromCharCode (0xffff); -data[1460] = String.fromCharCode (0xffff); -data[1461] = String.fromCharCode (0xffff); -data[1462] = String.fromCharCode (0xffff); -data[1463] = String.fromCharCode (0xffff); -data[1464] = String.fromCharCode (0xffff); -data[1465] = String.fromCharCode (0xffff); -data[1466] = String.fromCharCode (0xffff); -data[1467] = String.fromCharCode (0xffff); -data[1468] = String.fromCharCode (0xffff); -data[1469] = String.fromCharCode (0xffff); -data[1470] = String.fromCharCode (0xffff); -data[1471] = String.fromCharCode (0xffff); -data[1472] = String.fromCharCode (0xffff); -data[1473] = String.fromCharCode (0xffff); -data[1474] = String.fromCharCode (0xffff); -data[1475] = String.fromCharCode (0xffff); -data[1476] = String.fromCharCode (0xffff); -data[1477] = String.fromCharCode (0xffff); -data[1478] = String.fromCharCode (0xffff); -data[1479] = String.fromCharCode (0xffff); -data[1480] = String.fromCharCode (0xffff); -data[1481] = String.fromCharCode (0xffff); -data[1482] = String.fromCharCode (0xffff); -data[1483] = String.fromCharCode (0xffff); -data[1484] = String.fromCharCode (0xffff); -data[1485] = String.fromCharCode (0xffff); -data[1486] = String.fromCharCode (0xffff); -data[1487] = String.fromCharCode (0xffff); -data[1488] = String.fromCharCode (0xffff); -data[1489] = String.fromCharCode (0xffff); -data[1490] = String.fromCharCode (0xffff); -data[1491] = String.fromCharCode (0xffff); -data[1492] = String.fromCharCode (0xffff); -data[1493] = String.fromCharCode (0xffff); -data[1494] = String.fromCharCode (0xffff); -data[1495] = String.fromCharCode (0xffff); -data[1496] = String.fromCharCode (0xffff); -data[1497] = String.fromCharCode (0xffff); -data[1498] = String.fromCharCode (0xffff); -data[1499] = String.fromCharCode (0xffff); -data[1500] = String.fromCharCode (0xffff); -data[1501] = String.fromCharCode (0xffff); -data[1502] = String.fromCharCode (0xffff); -data[1503] = String.fromCharCode (0xffff); -data[1504] = String.fromCharCode (0xffff); -data[1505] = String.fromCharCode (0xffff); -data[1506] = String.fromCharCode (0xffff); -data[1507] = String.fromCharCode (0xffff); -data[1508] = String.fromCharCode (0xffff); -data[1509] = String.fromCharCode (0xffff); -data[1510] = String.fromCharCode (0xffff); -data[1511] = String.fromCharCode (0xffff); -data[1512] = String.fromCharCode (0xffff); -data[1513] = String.fromCharCode (0xffff); -data[1514] = String.fromCharCode (0xffff); -data[1515] = String.fromCharCode (0xffff); -data[1516] = String.fromCharCode (0xffff); -data[1517] = String.fromCharCode (0xffff); -data[1518] = String.fromCharCode (0xffff); -data[1519] = String.fromCharCode (0xffff); -data[1520] = String.fromCharCode (0xffff); -data[1521] = String.fromCharCode (0xffff); -data[1522] = String.fromCharCode (0xffff); -data[1523] = String.fromCharCode (0xffff); -data[1524] = String.fromCharCode (0xffff); -data[1525] = String.fromCharCode (0xffff); -data[1526] = String.fromCharCode (0xffff); -data[1527] = String.fromCharCode (0xffff); -data[1528] = String.fromCharCode (0xffff); -data[1529] = String.fromCharCode (0xffff); -data[1530] = String.fromCharCode (0xffff); -data[1531] = String.fromCharCode (0xffff); -data[1532] = String.fromCharCode (0xffff); -data[1533] = String.fromCharCode (0xffff); -data[1534] = String.fromCharCode (0xffff); -data[1535] = String.fromCharCode (0xffff); -data[1536] = String.fromCharCode (0xffff); -data[1537] = String.fromCharCode (0xffff); -data[1538] = String.fromCharCode (0xffff); -data[1539] = String.fromCharCode (0xffff); -data[1540] = String.fromCharCode (0xffff); -data[1541] = String.fromCharCode (0xffff); -data[1542] = String.fromCharCode (0xffff); -data[1543] = String.fromCharCode (0xffff); -data[1544] = String.fromCharCode (0xffff); -data[1545] = String.fromCharCode (0xffff); -data[1546] = String.fromCharCode (0xffff); -data[1547] = String.fromCharCode (0xffff); -data[1548] = String.fromCharCode (0xffff); -data[1549] = String.fromCharCode (0xffff); -data[1550] = String.fromCharCode (0xffff); -data[1551] = String.fromCharCode (0xffff); -data[1552] = String.fromCharCode (0xffff); -data[1553] = String.fromCharCode (0xffff); -data[1554] = String.fromCharCode (0xffff); -data[1555] = String.fromCharCode (0xffff); -data[1556] = String.fromCharCode (0xffff); -data[1557] = String.fromCharCode (0xffff); -data[1558] = String.fromCharCode (0xffff); -data[1559] = String.fromCharCode (0xffff); -data[1560] = String.fromCharCode (0xffff); -data[1561] = String.fromCharCode (0xffff); -data[1562] = String.fromCharCode (0xffff); -data[1563] = String.fromCharCode (0xffff); -data[1564] = String.fromCharCode (0xffff); -data[1565] = String.fromCharCode (0xffff); -data[1566] = String.fromCharCode (0xffff); -data[1567] = String.fromCharCode (0xffff); -data[1568] = String.fromCharCode (0xffff); -data[1569] = String.fromCharCode (0xffff); -data[1570] = String.fromCharCode (0xffff); -data[1571] = String.fromCharCode (0xffff); -data[1572] = String.fromCharCode (0xffff); -data[1573] = String.fromCharCode (0xffff); -data[1574] = String.fromCharCode (0xffff); -data[1575] = String.fromCharCode (0xffff); -data[1576] = String.fromCharCode (0xffff); -data[1577] = String.fromCharCode (0xffff); -data[1578] = String.fromCharCode (0xffff); -data[1579] = String.fromCharCode (0xffff); -data[1580] = String.fromCharCode (0xffff); -data[1581] = String.fromCharCode (0xffff); -data[1582] = String.fromCharCode (0xffff); -data[1583] = String.fromCharCode (0xffff); -data[1584] = String.fromCharCode (0xffff); -data[1585] = String.fromCharCode (0xffff); -data[1586] = String.fromCharCode (0xffff); -data[1587] = String.fromCharCode (0xffff); -data[1588] = String.fromCharCode (0xffff); -data[1589] = String.fromCharCode (0xffff); -data[1590] = String.fromCharCode (0xffff); -data[1591] = String.fromCharCode (0xffff); -data[1592] = String.fromCharCode (0xffff); -data[1593] = String.fromCharCode (0xffff); -data[1594] = String.fromCharCode (0xffff); -data[1595] = String.fromCharCode (0xffff); -data[1596] = String.fromCharCode (0xffff); -data[1597] = String.fromCharCode (0xffff); -data[1598] = String.fromCharCode (0xffff); -data[1599] = String.fromCharCode (0xffff); -data[1600] = String.fromCharCode (0xffff); -data[1601] = String.fromCharCode (0xffff); -data[1602] = String.fromCharCode (0xffff); -data[1603] = String.fromCharCode (0xffff); -data[1604] = String.fromCharCode (0xffff); -data[1605] = String.fromCharCode (0xffff); -data[1606] = String.fromCharCode (0xffff); -data[1607] = String.fromCharCode (0xffff); -data[1608] = String.fromCharCode (0xffff); -data[1609] = String.fromCharCode (0xffff); -data[1610] = String.fromCharCode (0xffff); -data[1611] = String.fromCharCode (0xffff); -data[1612] = String.fromCharCode (0xffff); -data[1613] = String.fromCharCode (0xffff); -data[1614] = String.fromCharCode (0xffff); -data[1615] = String.fromCharCode (0xffff); -data[1616] = String.fromCharCode (0xffff); -data[1617] = String.fromCharCode (0xffff); -data[1618] = String.fromCharCode (0xffff); -data[1619] = String.fromCharCode (0xffff); -data[1620] = String.fromCharCode (0xffff); -data[1621] = String.fromCharCode (0xffff); -data[1622] = String.fromCharCode (0xffff); -data[1623] = String.fromCharCode (0xffff); -data[1624] = String.fromCharCode (0xffff); -data[1625] = String.fromCharCode (0xffff); -data[1626] = String.fromCharCode (0xffff); -data[1627] = String.fromCharCode (0xffff); -data[1628] = String.fromCharCode (0xffff); -data[1629] = String.fromCharCode (0xffff); -data[1630] = String.fromCharCode (0xffff); -data[1631] = String.fromCharCode (0xffff); -data[1632] = String.fromCharCode (0xffff); -data[1633] = String.fromCharCode (0xffff); -data[1634] = String.fromCharCode (0xffff); -data[1635] = String.fromCharCode (0xffff); -data[1636] = String.fromCharCode (0xffff); -data[1637] = String.fromCharCode (0xffff); -data[1638] = String.fromCharCode (0xffff); -data[1639] = String.fromCharCode (0xffff); -data[1640] = String.fromCharCode (0xffff); -data[1641] = String.fromCharCode (0xffff); -data[1642] = String.fromCharCode (0xffff); -data[1643] = String.fromCharCode (0xffff); -data[1644] = String.fromCharCode (0xffff); -data[1645] = String.fromCharCode (0xffff); -data[1646] = String.fromCharCode (0xffff); -data[1647] = String.fromCharCode (0xffff); -data[1648] = String.fromCharCode (0xffff); -data[1649] = String.fromCharCode (0xffff); -data[1650] = String.fromCharCode (0xffff); -data[1651] = String.fromCharCode (0xffff); -data[1652] = String.fromCharCode (0xffff); -data[1653] = String.fromCharCode (0xffff); -data[1654] = String.fromCharCode (0xffff); -data[1655] = String.fromCharCode (0xffff); -data[1656] = String.fromCharCode (0xffff); -data[1657] = String.fromCharCode (0xffff); -data[1658] = String.fromCharCode (0xffff); -data[1659] = String.fromCharCode (0xffff); -data[1660] = String.fromCharCode (0xffff); -data[1661] = String.fromCharCode (0xffff); -data[1662] = String.fromCharCode (0xffff); -data[1663] = String.fromCharCode (0xffff); -data[1664] = String.fromCharCode (0xffff); -data[1665] = String.fromCharCode (0xffff); -data[1666] = String.fromCharCode (0xffff); -data[1667] = String.fromCharCode (0xffff); -data[1668] = String.fromCharCode (0xffff); -data[1669] = String.fromCharCode (0xffff); -data[1670] = String.fromCharCode (0xffff); -data[1671] = String.fromCharCode (0xffff); -data[1672] = String.fromCharCode (0xffff); -data[1673] = String.fromCharCode (0xffff); -data[1674] = String.fromCharCode (0xffff); -data[1675] = String.fromCharCode (0xffff); -data[1676] = String.fromCharCode (0xffff); -data[1677] = String.fromCharCode (0xffff); -data[1678] = String.fromCharCode (0xffff); -data[1679] = String.fromCharCode (0xffff); -data[1680] = String.fromCharCode (0xffff); -data[1681] = String.fromCharCode (0xffff); -data[1682] = String.fromCharCode (0xffff); -data[1683] = String.fromCharCode (0xffff); -data[1684] = String.fromCharCode (0xffff); -data[1685] = String.fromCharCode (0xffff); -data[1686] = String.fromCharCode (0xffff); -data[1687] = String.fromCharCode (0xffff); -data[1688] = String.fromCharCode (0xffff); -data[1689] = String.fromCharCode (0xffff); -data[1690] = String.fromCharCode (0xffff); -data[1691] = String.fromCharCode (0xffff); -data[1692] = String.fromCharCode (0xffff); -data[1693] = String.fromCharCode (0xffff); -data[1694] = String.fromCharCode (0xffff); -data[1695] = String.fromCharCode (0xffff); -data[1696] = String.fromCharCode (0xffff); -data[1697] = String.fromCharCode (0xffff); -data[1698] = String.fromCharCode (0xffff); -data[1699] = String.fromCharCode (0xffff); -data[1700] = String.fromCharCode (0xffff); -data[1701] = String.fromCharCode (0xffff); -data[1702] = String.fromCharCode (0xffff); -data[1703] = String.fromCharCode (0xffff); -data[1704] = String.fromCharCode (0xffff); -data[1705] = String.fromCharCode (0xffff); -data[1706] = String.fromCharCode (0xffff); -data[1707] = String.fromCharCode (0xffff); -data[1708] = String.fromCharCode (0xffff); -data[1709] = String.fromCharCode (0xffff); -data[1710] = String.fromCharCode (0xffff); -data[1711] = String.fromCharCode (0xffff); -data[1712] = String.fromCharCode (0xffff); -data[1713] = String.fromCharCode (0xffff); -data[1714] = String.fromCharCode (0xffff); -data[1715] = String.fromCharCode (0xffff); -data[1716] = String.fromCharCode (0xffff); -data[1717] = String.fromCharCode (0xffff); -data[1718] = String.fromCharCode (0xffff); -data[1719] = String.fromCharCode (0xffff); -data[1720] = String.fromCharCode (0xffff); -data[1721] = String.fromCharCode (0xffff); -data[1722] = String.fromCharCode (0xffff); -data[1723] = String.fromCharCode (0xffff); -data[1724] = String.fromCharCode (0xffff); -data[1725] = String.fromCharCode (0xffff); -data[1726] = String.fromCharCode (0xffff); -data[1727] = String.fromCharCode (0xffff); -data[1728] = String.fromCharCode (0xffff); -data[1729] = String.fromCharCode (0xffff); -data[1730] = String.fromCharCode (0xffff); -data[1731] = String.fromCharCode (0xffff); -data[1732] = String.fromCharCode (0xffff); -data[1733] = String.fromCharCode (0xffff); -data[1734] = String.fromCharCode (0xffff); -data[1735] = String.fromCharCode (0xffff); -data[1736] = String.fromCharCode (0xffff); -data[1737] = String.fromCharCode (0xffff); -data[1738] = String.fromCharCode (0xffff); -data[1739] = String.fromCharCode (0xffff); -data[1740] = String.fromCharCode (0xffff); -data[1741] = String.fromCharCode (0xffff); -data[1742] = String.fromCharCode (0xffff); -data[1743] = String.fromCharCode (0xffff); -data[1744] = String.fromCharCode (0xffff); -data[1745] = String.fromCharCode (0xffff); -data[1746] = String.fromCharCode (0xffff); -data[1747] = String.fromCharCode (0xffff); -data[1748] = String.fromCharCode (0xffff); -data[1749] = String.fromCharCode (0xffff); -data[1750] = String.fromCharCode (0xffff); -data[1751] = String.fromCharCode (0xffff); -data[1752] = String.fromCharCode (0xffff); -data[1753] = String.fromCharCode (0xffff); -data[1754] = String.fromCharCode (0xffff); -data[1755] = String.fromCharCode (0xffff); -data[1756] = String.fromCharCode (0xffff); -data[1757] = String.fromCharCode (0xffff); -data[1758] = String.fromCharCode (0xffff); -data[1759] = String.fromCharCode (0xffff); -data[1760] = String.fromCharCode (0xffff); -data[1761] = String.fromCharCode (0xffff); -data[1762] = String.fromCharCode (0xffff); -data[1763] = String.fromCharCode (0xffff); -data[1764] = String.fromCharCode (0xffff); -data[1765] = String.fromCharCode (0xffff); -data[1766] = String.fromCharCode (0xffff); -data[1767] = String.fromCharCode (0xffff); -data[1768] = String.fromCharCode (0xffff); -data[1769] = String.fromCharCode (0xffff); -data[1770] = String.fromCharCode (0xffff); -data[1771] = String.fromCharCode (0xffff); -data[1772] = String.fromCharCode (0xffff); -data[1773] = String.fromCharCode (0xffff); -data[1774] = String.fromCharCode (0xffff); -data[1775] = String.fromCharCode (0xffff); -data[1776] = String.fromCharCode (0xffff); -data[1777] = String.fromCharCode (0xffff); -data[1778] = String.fromCharCode (0xffff); -data[1779] = String.fromCharCode (0xffff); -data[1780] = String.fromCharCode (0xffff); -data[1781] = String.fromCharCode (0xffff); -data[1782] = String.fromCharCode (0xffff); -data[1783] = String.fromCharCode (0xffff); -data[1784] = String.fromCharCode (0xffff); -data[1785] = String.fromCharCode (0xffff); -data[1786] = String.fromCharCode (0xffff); -data[1787] = String.fromCharCode (0xffff); -data[1788] = String.fromCharCode (0xffff); -data[1789] = String.fromCharCode (0xffff); -data[1790] = String.fromCharCode (0xffff); -data[1791] = String.fromCharCode (0xffff); -data[1792] = String.fromCharCode (0xffff); -data[1793] = String.fromCharCode (0xffff); -data[1794] = String.fromCharCode (0xffff); -data[1795] = String.fromCharCode (0xffff); -data[1796] = String.fromCharCode (0xffff); -data[1797] = String.fromCharCode (0xffff); -data[1798] = String.fromCharCode (0xffff); -data[1799] = String.fromCharCode (0xffff); -data[1800] = String.fromCharCode (0xffff); -data[1801] = String.fromCharCode (0xffff); -data[1802] = String.fromCharCode (0xffff); -data[1803] = String.fromCharCode (0xffff); -data[1804] = String.fromCharCode (0xffff); -data[1805] = String.fromCharCode (0xffff); -data[1806] = String.fromCharCode (0xffff); -data[1807] = String.fromCharCode (0xffff); -data[1808] = String.fromCharCode (0xffff); -data[1809] = String.fromCharCode (0xffff); -data[1810] = String.fromCharCode (0xffff); -data[1811] = String.fromCharCode (0xffff); -data[1812] = String.fromCharCode (0xffff); -data[1813] = String.fromCharCode (0xffff); -data[1814] = String.fromCharCode (0xffff); -data[1815] = String.fromCharCode (0xffff); -data[1816] = String.fromCharCode (0xffff); -data[1817] = String.fromCharCode (0xffff); -data[1818] = String.fromCharCode (0xffff); -data[1819] = String.fromCharCode (0xffff); -data[1820] = String.fromCharCode (0xffff); -data[1821] = String.fromCharCode (0xffff); -data[1822] = String.fromCharCode (0xffff); -data[1823] = String.fromCharCode (0xffff); -data[1824] = String.fromCharCode (0xffff); -data[1825] = String.fromCharCode (0xffff); -data[1826] = String.fromCharCode (0xffff); -data[1827] = String.fromCharCode (0xffff); -data[1828] = String.fromCharCode (0xffff); -data[1829] = String.fromCharCode (0xffff); -data[1830] = String.fromCharCode (0xffff); -data[1831] = String.fromCharCode (0xffff); -data[1832] = String.fromCharCode (0xffff); -data[1833] = String.fromCharCode (0xffff); -data[1834] = String.fromCharCode (0xffff); -data[1835] = String.fromCharCode (0xffff); -data[1836] = String.fromCharCode (0xffff); -data[1837] = String.fromCharCode (0xffff); -data[1838] = String.fromCharCode (0xffff); -data[1839] = String.fromCharCode (0xffff); -data[1840] = String.fromCharCode (0xffff); -data[1841] = String.fromCharCode (0xffff); -data[1842] = String.fromCharCode (0xffff); -data[1843] = String.fromCharCode (0xffff); -data[1844] = String.fromCharCode (0xffff); -data[1845] = String.fromCharCode (0xffff); -data[1846] = String.fromCharCode (0xffff); -data[1847] = String.fromCharCode (0xffff); -data[1848] = String.fromCharCode (0xffff); -data[1849] = String.fromCharCode (0xffff); -data[1850] = String.fromCharCode (0xffff); -data[1851] = String.fromCharCode (0xffff); -data[1852] = String.fromCharCode (0xffff); -data[1853] = String.fromCharCode (0xffff); -data[1854] = String.fromCharCode (0xffff); -data[1855] = String.fromCharCode (0xffff); -data[1856] = String.fromCharCode (0xffff); -data[1857] = String.fromCharCode (0xffff); -data[1858] = String.fromCharCode (0xffff); -data[1859] = String.fromCharCode (0xffff); -data[1860] = String.fromCharCode (0xffff); -data[1861] = String.fromCharCode (0xffff); -data[1862] = String.fromCharCode (0xffff); -data[1863] = String.fromCharCode (0xffff); -data[1864] = String.fromCharCode (0xffff); -data[1865] = String.fromCharCode (0xffff); -data[1866] = String.fromCharCode (0xffff); -data[1867] = String.fromCharCode (0xffff); -data[1868] = String.fromCharCode (0xffff); -data[1869] = String.fromCharCode (0xffff); -data[1870] = String.fromCharCode (0xffff); -data[1871] = String.fromCharCode (0xffff); -data[1872] = String.fromCharCode (0xffff); -data[1873] = String.fromCharCode (0xffff); -data[1874] = String.fromCharCode (0xffff); -data[1875] = String.fromCharCode (0xffff); -data[1876] = String.fromCharCode (0xffff); -data[1877] = String.fromCharCode (0xffff); -data[1878] = String.fromCharCode (0xffff); -data[1879] = String.fromCharCode (0xffff); -data[1880] = String.fromCharCode (0xffff); -data[1881] = String.fromCharCode (0xffff); -data[1882] = String.fromCharCode (0xffff); -data[1883] = String.fromCharCode (0xffff); -data[1884] = String.fromCharCode (0xffff); -data[1885] = String.fromCharCode (0xffff); -data[1886] = String.fromCharCode (0xffff); -data[1887] = String.fromCharCode (0xffff); -data[1888] = String.fromCharCode (0xffff); -data[1889] = String.fromCharCode (0xffff); -data[1890] = String.fromCharCode (0xffff); -data[1891] = String.fromCharCode (0xffff); -data[1892] = String.fromCharCode (0xffff); -data[1893] = String.fromCharCode (0xffff); -data[1894] = String.fromCharCode (0xffff); -data[1895] = String.fromCharCode (0xffff); -data[1896] = String.fromCharCode (0xffff); -data[1897] = String.fromCharCode (0xffff); -data[1898] = String.fromCharCode (0xffff); -data[1899] = String.fromCharCode (0xffff); -data[1900] = String.fromCharCode (0xffff); -data[1901] = String.fromCharCode (0xffff); -data[1902] = String.fromCharCode (0xffff); -data[1903] = String.fromCharCode (0xffff); -data[1904] = String.fromCharCode (0xffff); -data[1905] = String.fromCharCode (0xffff); -data[1906] = String.fromCharCode (0xffff); -data[1907] = String.fromCharCode (0xffff); -data[1908] = String.fromCharCode (0xffff); -data[1909] = String.fromCharCode (0xffff); -data[1910] = String.fromCharCode (0xffff); -data[1911] = String.fromCharCode (0xffff); -data[1912] = String.fromCharCode (0xffff); -data[1913] = String.fromCharCode (0xffff); -data[1914] = String.fromCharCode (0xffff); -data[1915] = String.fromCharCode (0xffff); -data[1916] = String.fromCharCode (0xffff); -data[1917] = String.fromCharCode (0xffff); -data[1918] = String.fromCharCode (0xffff); -data[1919] = String.fromCharCode (0xffff); -data[1920] = String.fromCharCode (0xffff); -data[1921] = String.fromCharCode (0xffff); -data[1922] = String.fromCharCode (0xffff); -data[1923] = String.fromCharCode (0xffff); -data[1924] = String.fromCharCode (0xffff); -data[1925] = String.fromCharCode (0xffff); -data[1926] = String.fromCharCode (0xffff); -data[1927] = String.fromCharCode (0xffff); -data[1928] = String.fromCharCode (0xffff); -data[1929] = String.fromCharCode (0xffff); -data[1930] = String.fromCharCode (0xffff); -data[1931] = String.fromCharCode (0xffff); -data[1932] = String.fromCharCode (0xffff); -data[1933] = String.fromCharCode (0xffff); -data[1934] = String.fromCharCode (0xffff); -data[1935] = String.fromCharCode (0xffff); -data[1936] = String.fromCharCode (0xffff); -data[1937] = String.fromCharCode (0xffff); -data[1938] = String.fromCharCode (0xffff); -data[1939] = String.fromCharCode (0xffff); -data[1940] = String.fromCharCode (0xffff); -data[1941] = String.fromCharCode (0xffff); -data[1942] = String.fromCharCode (0xffff); -data[1943] = String.fromCharCode (0xffff); -data[1944] = String.fromCharCode (0xffff); -data[1945] = String.fromCharCode (0xffff); -data[1946] = String.fromCharCode (0xffff); -data[1947] = String.fromCharCode (0xffff); -data[1948] = String.fromCharCode (0xffff); -data[1949] = String.fromCharCode (0xffff); -data[1950] = String.fromCharCode (0xffff); -data[1951] = String.fromCharCode (0xffff); -data[1952] = String.fromCharCode (0xffff); -data[1953] = String.fromCharCode (0xffff); -data[1954] = String.fromCharCode (0xffff); -data[1955] = String.fromCharCode (0xffff); -data[1956] = String.fromCharCode (0xffff); -data[1957] = String.fromCharCode (0xffff); -data[1958] = String.fromCharCode (0xffff); -data[1959] = String.fromCharCode (0xffff); -data[1960] = String.fromCharCode (0xffff); -data[1961] = String.fromCharCode (0xffff); -data[1962] = String.fromCharCode (0xffff); -data[1963] = String.fromCharCode (0xffff); -data[1964] = String.fromCharCode (0xffff); -data[1965] = String.fromCharCode (0xffff); -data[1966] = String.fromCharCode (0xffff); -data[1967] = String.fromCharCode (0xffff); -data[1968] = String.fromCharCode (0xffff); -data[1969] = String.fromCharCode (0xffff); -data[1970] = String.fromCharCode (0xffff); -data[1971] = String.fromCharCode (0xffff); -data[1972] = String.fromCharCode (0xffff); -data[1973] = String.fromCharCode (0xffff); -data[1974] = String.fromCharCode (0xffff); -data[1975] = String.fromCharCode (0xffff); -data[1976] = String.fromCharCode (0xffff); -data[1977] = String.fromCharCode (0xffff); -data[1978] = String.fromCharCode (0xffff); -data[1979] = String.fromCharCode (0xffff); -data[1980] = String.fromCharCode (0xffff); -data[1981] = String.fromCharCode (0xffff); -data[1982] = String.fromCharCode (0xffff); -data[1983] = String.fromCharCode (0xffff); -data[1984] = String.fromCharCode (0xffff); -data[1985] = String.fromCharCode (0xffff); -data[1986] = String.fromCharCode (0xffff); -data[1987] = String.fromCharCode (0xffff); -data[1988] = String.fromCharCode (0xffff); -data[1989] = String.fromCharCode (0xffff); -data[1990] = String.fromCharCode (0xffff); -data[1991] = String.fromCharCode (0xffff); -data[1992] = String.fromCharCode (0xffff); -data[1993] = String.fromCharCode (0xffff); -data[1994] = String.fromCharCode (0xffff); -data[1995] = String.fromCharCode (0xffff); -data[1996] = String.fromCharCode (0xffff); -data[1997] = String.fromCharCode (0xffff); -data[1998] = String.fromCharCode (0xffff); -data[1999] = String.fromCharCode (0xffff); -data[2000] = String.fromCharCode (0xffff); -data[2001] = String.fromCharCode (0xffff); -data[2002] = String.fromCharCode (0xffff); -data[2003] = String.fromCharCode (0xffff); -data[2004] = String.fromCharCode (0xffff); -data[2005] = String.fromCharCode (0xffff); -data[2006] = String.fromCharCode (0xffff); -data[2007] = String.fromCharCode (0xffff); -data[2008] = String.fromCharCode (0xffff); -data[2009] = String.fromCharCode (0xffff); -data[2010] = String.fromCharCode (0xffff); -data[2011] = String.fromCharCode (0xffff); -data[2012] = String.fromCharCode (0xffff); -data[2013] = String.fromCharCode (0xffff); -data[2014] = String.fromCharCode (0xffff); -data[2015] = String.fromCharCode (0xffff); -data[2016] = String.fromCharCode (0xffff); -data[2017] = String.fromCharCode (0xffff); -data[2018] = String.fromCharCode (0xffff); -data[2019] = String.fromCharCode (0xffff); -data[2020] = String.fromCharCode (0xffff); -data[2021] = String.fromCharCode (0xffff); -data[2022] = String.fromCharCode (0xffff); -data[2023] = String.fromCharCode (0xffff); -data[2024] = String.fromCharCode (0xffff); -data[2025] = String.fromCharCode (0xffff); -data[2026] = String.fromCharCode (0xffff); -data[2027] = String.fromCharCode (0xffff); -data[2028] = String.fromCharCode (0xffff); -data[2029] = String.fromCharCode (0xffff); -data[2030] = String.fromCharCode (0xffff); -data[2031] = String.fromCharCode (0xffff); -data[2032] = String.fromCharCode (0xffff); -data[2033] = String.fromCharCode (0xffff); -data[2034] = String.fromCharCode (0xffff); -data[2035] = String.fromCharCode (0xffff); -data[2036] = String.fromCharCode (0xffff); -data[2037] = String.fromCharCode (0xffff); -data[2038] = String.fromCharCode (0xffff); -data[2039] = String.fromCharCode (0xffff); -data[2040] = String.fromCharCode (0xffff); -data[2041] = String.fromCharCode (0xffff); -data[2042] = String.fromCharCode (0xffff); -data[2043] = String.fromCharCode (0xffff); -data[2044] = String.fromCharCode (0xffff); -data[2045] = String.fromCharCode (0xffff); -data[2046] = String.fromCharCode (0xffff); -data[2047] = String.fromCharCode (0xffff); -data[2048] = String.fromCharCode (0xffff); -data[2049] = String.fromCharCode (0xffff); -data[2050] = String.fromCharCode (0xffff); -data[2051] = String.fromCharCode (0xffff); -data[2052] = String.fromCharCode (0xffff); -data[2053] = String.fromCharCode (0xffff); -data[2054] = String.fromCharCode (0xffff); -data[2055] = String.fromCharCode (0xffff); -data[2056] = String.fromCharCode (0xffff); -data[2057] = String.fromCharCode (0xffff); -data[2058] = String.fromCharCode (0xffff); -data[2059] = String.fromCharCode (0xffff); -data[2060] = String.fromCharCode (0xffff); -data[2061] = String.fromCharCode (0xffff); -data[2062] = String.fromCharCode (0xffff); -data[2063] = String.fromCharCode (0xffff); -data[2064] = String.fromCharCode (0xffff); -data[2065] = String.fromCharCode (0xffff); -data[2066] = String.fromCharCode (0xffff); -data[2067] = String.fromCharCode (0xffff); -data[2068] = String.fromCharCode (0xffff); -data[2069] = String.fromCharCode (0xffff); -data[2070] = String.fromCharCode (0xffff); -data[2071] = String.fromCharCode (0xffff); -data[2072] = String.fromCharCode (0xffff); -data[2073] = String.fromCharCode (0xffff); -data[2074] = String.fromCharCode (0xffff); -data[2075] = String.fromCharCode (0xffff); -data[2076] = String.fromCharCode (0xffff); -data[2077] = String.fromCharCode (0xffff); -data[2078] = String.fromCharCode (0xffff); -data[2079] = String.fromCharCode (0xffff); -data[2080] = String.fromCharCode (0xffff); -data[2081] = String.fromCharCode (0xffff); -data[2082] = String.fromCharCode (0xffff); -data[2083] = String.fromCharCode (0xffff); -data[2084] = String.fromCharCode (0xffff); -data[2085] = String.fromCharCode (0xffff); -data[2086] = String.fromCharCode (0xffff); -data[2087] = String.fromCharCode (0xffff); -data[2088] = String.fromCharCode (0xffff); -data[2089] = String.fromCharCode (0xffff); -data[2090] = String.fromCharCode (0xffff); -data[2091] = String.fromCharCode (0xffff); -data[2092] = String.fromCharCode (0xffff); -data[2093] = String.fromCharCode (0xffff); -data[2094] = String.fromCharCode (0xffff); -data[2095] = String.fromCharCode (0xffff); -data[2096] = String.fromCharCode (0xffff); -data[2097] = String.fromCharCode (0xffff); -data[2098] = String.fromCharCode (0xffff); -data[2099] = String.fromCharCode (0xffff); -data[2100] = String.fromCharCode (0xffff); -data[2101] = String.fromCharCode (0xffff); -data[2102] = String.fromCharCode (0xffff); -data[2103] = String.fromCharCode (0xffff); -data[2104] = String.fromCharCode (0xffff); -data[2105] = String.fromCharCode (0xffff); -data[2106] = String.fromCharCode (0xffff); -data[2107] = String.fromCharCode (0xffff); -data[2108] = String.fromCharCode (0xffff); -data[2109] = String.fromCharCode (0xffff); -data[2110] = String.fromCharCode (0xffff); -data[2111] = String.fromCharCode (0xffff); -data[2112] = String.fromCharCode (0xffff); -data[2113] = String.fromCharCode (0xffff); -data[2114] = String.fromCharCode (0xffff); -data[2115] = String.fromCharCode (0xffff); -data[2116] = String.fromCharCode (0xffff); -data[2117] = String.fromCharCode (0xffff); -data[2118] = String.fromCharCode (0xffff); -data[2119] = String.fromCharCode (0xffff); -data[2120] = String.fromCharCode (0xffff); -data[2121] = String.fromCharCode (0xffff); -data[2122] = String.fromCharCode (0xffff); -data[2123] = String.fromCharCode (0xffff); -data[2124] = String.fromCharCode (0xffff); -data[2125] = String.fromCharCode (0xffff); -data[2126] = String.fromCharCode (0xffff); -data[2127] = String.fromCharCode (0xffff); -data[2128] = String.fromCharCode (0xffff); -data[2129] = String.fromCharCode (0xffff); -data[2130] = String.fromCharCode (0xffff); -data[2131] = String.fromCharCode (0xffff); -data[2132] = String.fromCharCode (0xffff); -data[2133] = String.fromCharCode (0xffff); -data[2134] = String.fromCharCode (0xffff); -data[2135] = String.fromCharCode (0xffff); -data[2136] = String.fromCharCode (0xffff); -data[2137] = String.fromCharCode (0xffff); -data[2138] = String.fromCharCode (0xffff); -data[2139] = String.fromCharCode (0xffff); -data[2140] = String.fromCharCode (0xffff); -data[2141] = String.fromCharCode (0xffff); -data[2142] = String.fromCharCode (0xffff); -data[2143] = String.fromCharCode (0xffff); -data[2144] = String.fromCharCode (0xffff); -data[2145] = String.fromCharCode (0xffff); -data[2146] = String.fromCharCode (0xffff); -data[2147] = String.fromCharCode (0xffff); -data[2148] = String.fromCharCode (0xffff); -data[2149] = String.fromCharCode (0xffff); -data[2150] = String.fromCharCode (0xffff); -data[2151] = String.fromCharCode (0xffff); -data[2152] = String.fromCharCode (0xffff); -data[2153] = String.fromCharCode (0xffff); -data[2154] = String.fromCharCode (0xffff); -data[2155] = String.fromCharCode (0xffff); -data[2156] = String.fromCharCode (0xffff); -data[2157] = String.fromCharCode (0xffff); -data[2158] = String.fromCharCode (0xffff); -data[2159] = String.fromCharCode (0xffff); -data[2160] = String.fromCharCode (0xffff); -data[2161] = String.fromCharCode (0xffff); -data[2162] = String.fromCharCode (0xffff); -data[2163] = String.fromCharCode (0xffff); -data[2164] = String.fromCharCode (0xffff); -data[2165] = String.fromCharCode (0xffff); -data[2166] = String.fromCharCode (0xffff); -data[2167] = String.fromCharCode (0xffff); -data[2168] = String.fromCharCode (0xffff); -data[2169] = String.fromCharCode (0xffff); -data[2170] = String.fromCharCode (0xffff); -data[2171] = String.fromCharCode (0xffff); -data[2172] = String.fromCharCode (0xffff); -data[2173] = String.fromCharCode (0xffff); -data[2174] = String.fromCharCode (0xffff); -data[2175] = String.fromCharCode (0xffff); -data[2176] = String.fromCharCode (0xffff); -data[2177] = String.fromCharCode (0xffff); -data[2178] = String.fromCharCode (0xffff); -data[2179] = String.fromCharCode (0xffff); -data[2180] = String.fromCharCode (0xffff); -data[2181] = String.fromCharCode (0xffff); -data[2182] = String.fromCharCode (0xffff); -data[2183] = String.fromCharCode (0xffff); -data[2184] = String.fromCharCode (0xffff); -data[2185] = String.fromCharCode (0xffff); -data[2186] = String.fromCharCode (0xffff); -data[2187] = String.fromCharCode (0xffff); -data[2188] = String.fromCharCode (0xffff); -data[2189] = String.fromCharCode (0xffff); -data[2190] = String.fromCharCode (0xffff); -data[2191] = String.fromCharCode (0xffff); -data[2192] = String.fromCharCode (0xffff); -data[2193] = String.fromCharCode (0xffff); -data[2194] = String.fromCharCode (0xffff); -data[2195] = String.fromCharCode (0xffff); -data[2196] = String.fromCharCode (0xffff); -data[2197] = String.fromCharCode (0xffff); -data[2198] = String.fromCharCode (0xffff); -data[2199] = String.fromCharCode (0xffff); -data[2200] = String.fromCharCode (0xffff); -data[2201] = String.fromCharCode (0xffff); -data[2202] = String.fromCharCode (0xffff); -data[2203] = String.fromCharCode (0xffff); -data[2204] = String.fromCharCode (0xffff); -data[2205] = String.fromCharCode (0xffff); -data[2206] = String.fromCharCode (0xffff); -data[2207] = String.fromCharCode (0xffff); -data[2208] = String.fromCharCode (0xffff); -data[2209] = String.fromCharCode (0xffff); -data[2210] = String.fromCharCode (0xffff); -data[2211] = String.fromCharCode (0xffff); -data[2212] = String.fromCharCode (0xffff); -data[2213] = String.fromCharCode (0xffff); -data[2214] = String.fromCharCode (0xffff); -data[2215] = String.fromCharCode (0xffff); -data[2216] = String.fromCharCode (0xffff); -data[2217] = String.fromCharCode (0xffff); -data[2218] = String.fromCharCode (0xffff); -data[2219] = String.fromCharCode (0xffff); -data[2220] = String.fromCharCode (0xffff); -data[2221] = String.fromCharCode (0xffff); -data[2222] = String.fromCharCode (0xffff); -data[2223] = String.fromCharCode (0xffff); -data[2224] = String.fromCharCode (0xffff); -data[2225] = String.fromCharCode (0xffff); -data[2226] = String.fromCharCode (0xffff); -data[2227] = String.fromCharCode (0xffff); -data[2228] = String.fromCharCode (0xffff); -data[2229] = String.fromCharCode (0xffff); -data[2230] = String.fromCharCode (0xffff); -data[2231] = String.fromCharCode (0xffff); -data[2232] = String.fromCharCode (0xffff); -data[2233] = String.fromCharCode (0xffff); -data[2234] = String.fromCharCode (0xffff); -data[2235] = String.fromCharCode (0xffff); -data[2236] = String.fromCharCode (0xffff); -data[2237] = String.fromCharCode (0xffff); -data[2238] = String.fromCharCode (0xffff); -data[2239] = String.fromCharCode (0xffff); -data[2240] = String.fromCharCode (0xffff); -data[2241] = String.fromCharCode (0xffff); -data[2242] = String.fromCharCode (0xffff); -data[2243] = String.fromCharCode (0xffff); -data[2244] = String.fromCharCode (0xffff); -data[2245] = String.fromCharCode (0xffff); -data[2246] = String.fromCharCode (0xffff); -data[2247] = String.fromCharCode (0xffff); -data[2248] = String.fromCharCode (0xffff); -data[2249] = String.fromCharCode (0xffff); -data[2250] = String.fromCharCode (0xffff); -data[2251] = String.fromCharCode (0xffff); -data[2252] = String.fromCharCode (0xffff); -data[2253] = String.fromCharCode (0xffff); -data[2254] = String.fromCharCode (0xffff); -data[2255] = String.fromCharCode (0xffff); -data[2256] = String.fromCharCode (0xffff); -data[2257] = String.fromCharCode (0xffff); -data[2258] = String.fromCharCode (0xffff); -data[2259] = String.fromCharCode (0xffff); -data[2260] = String.fromCharCode (0xffff); -data[2261] = String.fromCharCode (0xffff); -data[2262] = String.fromCharCode (0xffff); -data[2263] = String.fromCharCode (0xffff); -data[2264] = String.fromCharCode (0xffff); -data[2265] = String.fromCharCode (0xffff); -data[2266] = String.fromCharCode (0xffff); -data[2267] = String.fromCharCode (0xffff); -data[2268] = String.fromCharCode (0xffff); -data[2269] = String.fromCharCode (0xffff); -data[2270] = String.fromCharCode (0xffff); -data[2271] = String.fromCharCode (0xffff); -data[2272] = String.fromCharCode (0xffff); -data[2273] = String.fromCharCode (0xffff); -data[2274] = String.fromCharCode (0xffff); -data[2275] = String.fromCharCode (0xffff); -data[2276] = String.fromCharCode (0xffff); -data[2277] = String.fromCharCode (0xffff); -data[2278] = String.fromCharCode (0xffff); -data[2279] = String.fromCharCode (0xffff); -data[2280] = String.fromCharCode (0xffff); -data[2281] = String.fromCharCode (0xffff); -data[2282] = String.fromCharCode (0xffff); -data[2283] = String.fromCharCode (0xffff); -data[2284] = String.fromCharCode (0xffff); -data[2285] = String.fromCharCode (0xffff); -data[2286] = String.fromCharCode (0xffff); -data[2287] = String.fromCharCode (0xffff); -data[2288] = String.fromCharCode (0xffff); -data[2289] = String.fromCharCode (0xffff); -data[2290] = String.fromCharCode (0xffff); -data[2291] = String.fromCharCode (0xffff); -data[2292] = String.fromCharCode (0xffff); -data[2293] = String.fromCharCode (0xffff); -data[2294] = String.fromCharCode (0xffff); -data[2295] = String.fromCharCode (0xffff); -data[2296] = String.fromCharCode (0xffff); -data[2297] = String.fromCharCode (0xffff); -data[2298] = String.fromCharCode (0xffff); -data[2299] = String.fromCharCode (0xffff); -data[2300] = String.fromCharCode (0xffff); -data[2301] = String.fromCharCode (0xffff); -data[2302] = String.fromCharCode (0xffff); -data[2303] = String.fromCharCode (0xffff); -data[2304] = String.fromCharCode (0xffff); -data[2305] = String.fromCharCode (0xffff); -data[2306] = String.fromCharCode (0xffff); -data[2307] = String.fromCharCode (0xffff); -data[2308] = String.fromCharCode (0xffff); -data[2309] = String.fromCharCode (0xffff); -data[2310] = String.fromCharCode (0xffff); -data[2311] = String.fromCharCode (0xffff); -data[2312] = String.fromCharCode (0xffff); -data[2313] = String.fromCharCode (0xffff); -data[2314] = String.fromCharCode (0xffff); -data[2315] = String.fromCharCode (0xffff); -data[2316] = String.fromCharCode (0xffff); -data[2317] = String.fromCharCode (0xffff); -data[2318] = String.fromCharCode (0xffff); -data[2319] = String.fromCharCode (0xffff); -data[2320] = String.fromCharCode (0xffff); -data[2321] = String.fromCharCode (0xffff); -data[2322] = String.fromCharCode (0xffff); -data[2323] = String.fromCharCode (0xffff); -data[2324] = String.fromCharCode (0xffff); -data[2325] = String.fromCharCode (0xffff); -data[2326] = String.fromCharCode (0xffff); -data[2327] = String.fromCharCode (0xffff); -data[2328] = String.fromCharCode (0xffff); -data[2329] = String.fromCharCode (0xffff); -data[2330] = String.fromCharCode (0xffff); -data[2331] = String.fromCharCode (0xffff); -data[2332] = String.fromCharCode (0xffff); -data[2333] = String.fromCharCode (0xffff); -data[2334] = String.fromCharCode (0xffff); -data[2335] = String.fromCharCode (0xffff); -data[2336] = String.fromCharCode (0xffff); -data[2337] = String.fromCharCode (0xffff); -data[2338] = String.fromCharCode (0xffff); -data[2339] = String.fromCharCode (0xffff); -data[2340] = String.fromCharCode (0xffff); -data[2341] = String.fromCharCode (0xffff); -data[2342] = String.fromCharCode (0xffff); -data[2343] = String.fromCharCode (0xffff); -data[2344] = String.fromCharCode (0xffff); -data[2345] = String.fromCharCode (0xffff); -data[2346] = String.fromCharCode (0xffff); -data[2347] = String.fromCharCode (0xffff); -data[2348] = String.fromCharCode (0xffff); -data[2349] = String.fromCharCode (0xffff); -data[2350] = String.fromCharCode (0xffff); -data[2351] = String.fromCharCode (0xffff); -data[2352] = String.fromCharCode (0xffff); -data[2353] = String.fromCharCode (0xffff); -data[2354] = String.fromCharCode (0xffff); -data[2355] = String.fromCharCode (0xffff); -data[2356] = String.fromCharCode (0xffff); -data[2357] = String.fromCharCode (0xffff); -data[2358] = String.fromCharCode (0xffff); -data[2359] = String.fromCharCode (0xffff); -data[2360] = String.fromCharCode (0xffff); -data[2361] = String.fromCharCode (0xffff); -data[2362] = String.fromCharCode (0xffff); -data[2363] = String.fromCharCode (0xffff); -data[2364] = String.fromCharCode (0xffff); -data[2365] = String.fromCharCode (0xffff); -data[2366] = String.fromCharCode (0xffff); -data[2367] = String.fromCharCode (0xffff); -data[2368] = String.fromCharCode (0xffff); -data[2369] = String.fromCharCode (0xffff); -data[2370] = String.fromCharCode (0xffff); -data[2371] = String.fromCharCode (0xffff); -data[2372] = String.fromCharCode (0xffff); -data[2373] = String.fromCharCode (0xffff); -data[2374] = String.fromCharCode (0xffff); -data[2375] = String.fromCharCode (0xffff); -data[2376] = String.fromCharCode (0xffff); -data[2377] = String.fromCharCode (0xffff); -data[2378] = String.fromCharCode (0xffff); -data[2379] = String.fromCharCode (0xffff); -data[2380] = String.fromCharCode (0xffff); -data[2381] = String.fromCharCode (0xffff); -data[2382] = String.fromCharCode (0xffff); -data[2383] = String.fromCharCode (0xffff); -data[2384] = String.fromCharCode (0xffff); -data[2385] = String.fromCharCode (0xffff); -data[2386] = String.fromCharCode (0xffff); -data[2387] = String.fromCharCode (0xffff); -data[2388] = String.fromCharCode (0xffff); -data[2389] = String.fromCharCode (0xffff); -data[2390] = String.fromCharCode (0xffff); -data[2391] = String.fromCharCode (0xffff); -data[2392] = String.fromCharCode (0xffff); -data[2393] = String.fromCharCode (0xffff); -data[2394] = String.fromCharCode (0xffff); -data[2395] = String.fromCharCode (0xffff); -data[2396] = String.fromCharCode (0xffff); -data[2397] = String.fromCharCode (0xffff); -data[2398] = String.fromCharCode (0xffff); -data[2399] = String.fromCharCode (0xffff); -data[2400] = String.fromCharCode (0xffff); -data[2401] = String.fromCharCode (0xffff); -data[2402] = String.fromCharCode (0xffff); -data[2403] = String.fromCharCode (0xffff); -data[2404] = String.fromCharCode (0xffff); -data[2405] = String.fromCharCode (0xffff); -data[2406] = String.fromCharCode (0xffff); -data[2407] = String.fromCharCode (0xffff); -data[2408] = String.fromCharCode (0xffff); -data[2409] = String.fromCharCode (0xffff); -data[2410] = String.fromCharCode (0xffff); -data[2411] = String.fromCharCode (0xffff); -data[2412] = String.fromCharCode (0xffff); -data[2413] = String.fromCharCode (0xffff); -data[2414] = String.fromCharCode (0xffff); -data[2415] = String.fromCharCode (0xffff); -data[2416] = String.fromCharCode (0xffff); -data[2417] = String.fromCharCode (0xffff); -data[2418] = String.fromCharCode (0xffff); -data[2419] = String.fromCharCode (0xffff); -data[2420] = String.fromCharCode (0xffff); -data[2421] = String.fromCharCode (0xffff); -data[2422] = String.fromCharCode (0xffff); -data[2423] = String.fromCharCode (0xffff); -data[2424] = String.fromCharCode (0xffff); -data[2425] = String.fromCharCode (0xffff); -data[2426] = String.fromCharCode (0xffff); -data[2427] = String.fromCharCode (0xffff); -data[2428] = String.fromCharCode (0xffff); -data[2429] = String.fromCharCode (0xffff); -data[2430] = String.fromCharCode (0xffff); -data[2431] = String.fromCharCode (0xffff); -data[2432] = String.fromCharCode (0xffff); -data[2433] = String.fromCharCode (0xffff); -data[2434] = String.fromCharCode (0xffff); -data[2435] = String.fromCharCode (0xffff); -data[2436] = String.fromCharCode (0xffff); -data[2437] = String.fromCharCode (0xffff); -data[2438] = String.fromCharCode (0xffff); -data[2439] = String.fromCharCode (0xffff); -data[2440] = String.fromCharCode (0xffff); -data[2441] = String.fromCharCode (0xffff); -data[2442] = String.fromCharCode (0xffff); -data[2443] = String.fromCharCode (0xffff); -data[2444] = String.fromCharCode (0xffff); -data[2445] = String.fromCharCode (0xffff); -data[2446] = String.fromCharCode (0xffff); -data[2447] = String.fromCharCode (0xffff); -data[2448] = String.fromCharCode (0xffff); -data[2449] = String.fromCharCode (0xffff); -data[2450] = String.fromCharCode (0xffff); -data[2451] = String.fromCharCode (0xffff); -data[2452] = String.fromCharCode (0xffff); -data[2453] = String.fromCharCode (0xffff); -data[2454] = String.fromCharCode (0xffff); -data[2455] = String.fromCharCode (0xffff); -data[2456] = String.fromCharCode (0xffff); -data[2457] = String.fromCharCode (0xffff); -data[2458] = String.fromCharCode (0xffff); -data[2459] = String.fromCharCode (0xffff); -data[2460] = String.fromCharCode (0xffff); -data[2461] = String.fromCharCode (0xffff); -data[2462] = String.fromCharCode (0xffff); -data[2463] = String.fromCharCode (0xffff); -data[2464] = String.fromCharCode (0xffff); -data[2465] = String.fromCharCode (0xffff); -data[2466] = String.fromCharCode (0xffff); -data[2467] = String.fromCharCode (0xffff); -data[2468] = String.fromCharCode (0xffff); -data[2469] = String.fromCharCode (0xffff); -data[2470] = String.fromCharCode (0xffff); -data[2471] = String.fromCharCode (0xffff); -data[2472] = String.fromCharCode (0xffff); -data[2473] = String.fromCharCode (0xffff); -data[2474] = String.fromCharCode (0xffff); -data[2475] = String.fromCharCode (0xffff); -data[2476] = String.fromCharCode (0xffff); -data[2477] = String.fromCharCode (0xffff); -data[2478] = String.fromCharCode (0xffff); -data[2479] = String.fromCharCode (0xffff); -data[2480] = String.fromCharCode (0xffff); -data[2481] = String.fromCharCode (0xffff); -data[2482] = String.fromCharCode (0xffff); -data[2483] = String.fromCharCode (0xffff); -data[2484] = String.fromCharCode (0xffff); -data[2485] = String.fromCharCode (0xffff); -data[2486] = String.fromCharCode (0xffff); -data[2487] = String.fromCharCode (0xffff); -data[2488] = String.fromCharCode (0xffff); -data[2489] = String.fromCharCode (0xffff); -data[2490] = String.fromCharCode (0xffff); -data[2491] = String.fromCharCode (0xffff); -data[2492] = String.fromCharCode (0xffff); -data[2493] = String.fromCharCode (0xffff); -data[2494] = String.fromCharCode (0xffff); -data[2495] = String.fromCharCode (0xffff); -data[2496] = String.fromCharCode (0xffff); -data[2497] = String.fromCharCode (0xffff); -data[2498] = String.fromCharCode (0xffff); -data[2499] = String.fromCharCode (0xffff); -data[2500] = String.fromCharCode (0xffff); -data[2501] = String.fromCharCode (0xffff); -data[2502] = String.fromCharCode (0xffff); -data[2503] = String.fromCharCode (0xffff); -data[2504] = String.fromCharCode (0xffff); -data[2505] = String.fromCharCode (0xffff); -data[2506] = String.fromCharCode (0xffff); -data[2507] = String.fromCharCode (0xffff); -data[2508] = String.fromCharCode (0xffff); -data[2509] = String.fromCharCode (0xffff); -data[2510] = String.fromCharCode (0xffff); -data[2511] = String.fromCharCode (0xffff); -data[2512] = String.fromCharCode (0xffff); -data[2513] = String.fromCharCode (0xffff); -data[2514] = String.fromCharCode (0xffff); -data[2515] = String.fromCharCode (0xffff); -data[2516] = String.fromCharCode (0xffff); -data[2517] = String.fromCharCode (0xffff); -data[2518] = String.fromCharCode (0xffff); -data[2519] = String.fromCharCode (0xffff); -data[2520] = String.fromCharCode (0xffff); -data[2521] = String.fromCharCode (0xffff); -data[2522] = String.fromCharCode (0xffff); -data[2523] = String.fromCharCode (0xffff); -data[2524] = String.fromCharCode (0xffff); -data[2525] = String.fromCharCode (0xffff); -data[2526] = String.fromCharCode (0xffff); -data[2527] = String.fromCharCode (0xffff); -data[2528] = String.fromCharCode (0xffff); -data[2529] = String.fromCharCode (0xffff); -data[2530] = String.fromCharCode (0xffff); -data[2531] = String.fromCharCode (0xffff); -data[2532] = String.fromCharCode (0xffff); -data[2533] = String.fromCharCode (0xffff); -data[2534] = String.fromCharCode (0xffff); -data[2535] = String.fromCharCode (0xffff); -data[2536] = String.fromCharCode (0xffff); -data[2537] = String.fromCharCode (0xffff); -data[2538] = String.fromCharCode (0xffff); -data[2539] = String.fromCharCode (0xffff); -data[2540] = String.fromCharCode (0xffff); -data[2541] = String.fromCharCode (0xffff); -data[2542] = String.fromCharCode (0xffff); -data[2543] = String.fromCharCode (0xffff); -data[2544] = String.fromCharCode (0xffff); -data[2545] = String.fromCharCode (0xffff); -data[2546] = String.fromCharCode (0xffff); -data[2547] = String.fromCharCode (0xffff); -data[2548] = String.fromCharCode (0xffff); -data[2549] = String.fromCharCode (0xffff); -data[2550] = String.fromCharCode (0xffff); -data[2551] = String.fromCharCode (0xffff); -data[2552] = String.fromCharCode (0xffff); -data[2553] = String.fromCharCode (0xffff); -data[2554] = String.fromCharCode (0x003f); -data[2752] = String.fromCharCode (0xffff); -data[2753] = String.fromCharCode (0xffff); -data[2754] = String.fromCharCode (0xffff); -data[2755] = String.fromCharCode (0xffff); -data[2756] = String.fromCharCode (0xffff); -data[2757] = String.fromCharCode (0xffff); -data[2758] = String.fromCharCode (0xffff); -data[2759] = String.fromCharCode (0xffff); -data[2760] = String.fromCharCode (0xffff); -data[2761] = String.fromCharCode (0xffff); -data[2762] = String.fromCharCode (0xffff); -data[2763] = String.fromCharCode (0xffff); -data[2764] = String.fromCharCode (0xffff); -data[2765] = String.fromCharCode (0xffff); -data[2766] = String.fromCharCode (0xffff); -data[2767] = String.fromCharCode (0xffff); -data[2768] = String.fromCharCode (0xffff); -data[2769] = String.fromCharCode (0xffff); -data[2770] = String.fromCharCode (0xffff); -data[2771] = String.fromCharCode (0xffff); -data[2772] = String.fromCharCode (0xffff); -data[2773] = String.fromCharCode (0xffff); -data[2774] = String.fromCharCode (0xffff); -data[2775] = String.fromCharCode (0xffff); -data[2776] = String.fromCharCode (0xffff); -data[2777] = String.fromCharCode (0xffff); -data[2778] = String.fromCharCode (0xffff); -data[2779] = String.fromCharCode (0xffff); -data[2780] = String.fromCharCode (0xffff); -data[2781] = String.fromCharCode (0xffff); -data[2782] = String.fromCharCode (0xffff); -data[2783] = String.fromCharCode (0xffff); -data[2784] = String.fromCharCode (0xffff); -data[2785] = String.fromCharCode (0xffff); -data[2786] = String.fromCharCode (0xffff); -data[2787] = String.fromCharCode (0xffff); -data[2788] = String.fromCharCode (0xffff); -data[2789] = String.fromCharCode (0xffff); -data[2790] = String.fromCharCode (0xffff); -data[2791] = String.fromCharCode (0xffff); -data[2792] = String.fromCharCode (0xffff); -data[2793] = String.fromCharCode (0xffff); -data[2794] = String.fromCharCode (0xffff); -data[2795] = String.fromCharCode (0xffff); -data[2796] = String.fromCharCode (0xffff); -data[2797] = String.fromCharCode (0xffff); -data[2798] = String.fromCharCode (0xffff); -data[2799] = String.fromCharCode (0xffff); -data[2800] = String.fromCharCode (0xffff); -data[2801] = String.fromCharCode (0xffff); -data[2802] = String.fromCharCode (0xffff); -data[2803] = String.fromCharCode (0xffff); -data[2804] = String.fromCharCode (0xffff); -data[2805] = String.fromCharCode (0xffff); -data[2806] = String.fromCharCode (0xffff); -data[2807] = String.fromCharCode (0xffff); -data[2808] = String.fromCharCode (0xffff); -data[2809] = String.fromCharCode (0xffff); -data[2810] = String.fromCharCode (0xffff); -data[2811] = String.fromCharCode (0xffff); -data[2812] = String.fromCharCode (0xffff); -data[2813] = String.fromCharCode (0xffff); -data[2814] = String.fromCharCode (0xffff); -data[2815] = String.fromCharCode (0xffff); -data[2816] = String.fromCharCode (0xffff); -data[2817] = String.fromCharCode (0xffff); -data[2818] = String.fromCharCode (0xffff); -data[2819] = String.fromCharCode (0xffff); -data[2820] = String.fromCharCode (0xffff); -data[2821] = String.fromCharCode (0xffff); -data[2822] = String.fromCharCode (0xffff); -data[2823] = String.fromCharCode (0xffff); -data[2824] = String.fromCharCode (0xffff); -data[2825] = String.fromCharCode (0xffff); -data[2826] = String.fromCharCode (0xffff); -data[2827] = String.fromCharCode (0xffff); -data[2828] = String.fromCharCode (0xffff); -data[2829] = String.fromCharCode (0xffff); -data[2830] = String.fromCharCode (0xffff); -data[2831] = String.fromCharCode (0xffff); -data[2832] = String.fromCharCode (0xffff); -data[2833] = String.fromCharCode (0xffff); -data[2834] = String.fromCharCode (0xffff); -data[2835] = String.fromCharCode (0xffff); -data[2836] = String.fromCharCode (0xffff); -data[2837] = String.fromCharCode (0xffff); -data[2838] = String.fromCharCode (0xffff); -data[2839] = String.fromCharCode (0xffff); -data[2840] = String.fromCharCode (0xffff); -data[2841] = String.fromCharCode (0xffff); -data[2842] = String.fromCharCode (0xffff); -data[2843] = String.fromCharCode (0xffff); -data[2844] = String.fromCharCode (0xffff); -data[2845] = String.fromCharCode (0xffff); -data[2846] = String.fromCharCode (0xffff); -data[2847] = String.fromCharCode (0xffff); -data[2848] = String.fromCharCode (0xffff); -data[2849] = String.fromCharCode (0xffff); -data[2850] = String.fromCharCode (0xffff); -data[2851] = String.fromCharCode (0xffff); -data[2852] = String.fromCharCode (0xffff); -data[2853] = String.fromCharCode (0xffff); -data[2854] = String.fromCharCode (0xffff); -data[2855] = String.fromCharCode (0xffff); -data[2856] = String.fromCharCode (0xffff); -data[2857] = String.fromCharCode (0xffff); -data[2858] = String.fromCharCode (0xffff); -data[2859] = String.fromCharCode (0xffff); -data[2860] = String.fromCharCode (0xffff); -data[2861] = String.fromCharCode (0xffff); -data[2862] = String.fromCharCode (0xffff); -data[2863] = String.fromCharCode (0xffff); -data[2864] = String.fromCharCode (0xffff); -data[2865] = String.fromCharCode (0xffff); -data[2866] = String.fromCharCode (0xffff); -data[2867] = String.fromCharCode (0xffff); -data[2868] = String.fromCharCode (0xffff); -data[2869] = String.fromCharCode (0xffff); -data[2870] = String.fromCharCode (0xffff); -data[2871] = String.fromCharCode (0xffff); -data[2872] = String.fromCharCode (0xffff); -data[2873] = String.fromCharCode (0xffff); -data[2874] = String.fromCharCode (0xffff); -data[2875] = String.fromCharCode (0xffff); -data[2876] = String.fromCharCode (0xffff); -data[2877] = String.fromCharCode (0xffff); -data[2878] = String.fromCharCode (0xffff); -data[2879] = String.fromCharCode (0xffff); -data[2880] = String.fromCharCode (0xffff); -data[2881] = String.fromCharCode (0xffff); -data[2882] = String.fromCharCode (0xffff); -data[2883] = String.fromCharCode (0xffff); -data[2884] = String.fromCharCode (0xffff); -data[2885] = String.fromCharCode (0xffff); -data[2886] = String.fromCharCode (0xffff); -data[2887] = String.fromCharCode (0xffff); -data[2888] = String.fromCharCode (0xffff); -data[2889] = String.fromCharCode (0xffff); -data[2890] = String.fromCharCode (0xffff); -data[2891] = String.fromCharCode (0xffff); -data[2892] = String.fromCharCode (0xffff); -data[2893] = String.fromCharCode (0xffff); -data[2894] = String.fromCharCode (0xffff); -data[2895] = String.fromCharCode (0xffff); -data[2896] = String.fromCharCode (0xffff); -data[2897] = String.fromCharCode (0xffff); -data[2898] = String.fromCharCode (0xffff); -data[2899] = String.fromCharCode (0xffff); -data[2900] = String.fromCharCode (0xffff); -data[2901] = String.fromCharCode (0xffff); -data[2902] = String.fromCharCode (0xffff); -data[2903] = String.fromCharCode (0xffff); -data[2904] = String.fromCharCode (0xffff); -data[2905] = String.fromCharCode (0xffff); -data[2906] = String.fromCharCode (0xffff); -data[2907] = String.fromCharCode (0xffff); -data[2908] = String.fromCharCode (0xffff); -data[2909] = String.fromCharCode (0xffff); -data[2910] = String.fromCharCode (0xffff); -data[2911] = String.fromCharCode (0xffff); -data[2912] = String.fromCharCode (0xffff); -data[2913] = String.fromCharCode (0xffff); -data[2914] = String.fromCharCode (0xffff); -data[2915] = String.fromCharCode (0xffff); -data[2916] = String.fromCharCode (0xffff); -data[2917] = String.fromCharCode (0xffff); -data[2918] = String.fromCharCode (0xffff); -data[2919] = String.fromCharCode (0xffff); -data[2920] = String.fromCharCode (0xffff); -data[2921] = String.fromCharCode (0xffff); -data[2922] = String.fromCharCode (0xffff); -data[2923] = String.fromCharCode (0xffff); -data[2924] = String.fromCharCode (0xffff); -data[2925] = String.fromCharCode (0xffff); -data[2926] = String.fromCharCode (0xffff); -data[2927] = String.fromCharCode (0xffff); -data[2928] = String.fromCharCode (0xffff); -data[2929] = String.fromCharCode (0xffff); -data[2930] = String.fromCharCode (0xffff); -data[2931] = String.fromCharCode (0xffff); -data[2932] = String.fromCharCode (0xffff); -data[2933] = String.fromCharCode (0xffff); -data[2934] = String.fromCharCode (0xffff); -data[2935] = String.fromCharCode (0xffff); -data[2936] = String.fromCharCode (0xffff); -data[2937] = String.fromCharCode (0xffff); -data[2938] = String.fromCharCode (0xffff); -data[2939] = String.fromCharCode (0xffff); -data[2940] = String.fromCharCode (0xffff); -data[2941] = String.fromCharCode (0xffff); -data[2942] = String.fromCharCode (0xffff); -data[2943] = String.fromCharCode (0xffff); -data[2944] = String.fromCharCode (0xffff); -data[2945] = String.fromCharCode (0xffff); -data[2946] = String.fromCharCode (0xffff); -data[2947] = String.fromCharCode (0xffff); -data[2948] = String.fromCharCode (0xffff); -data[2949] = String.fromCharCode (0xffff); -data[2950] = String.fromCharCode (0xffff); -data[2951] = String.fromCharCode (0xffff); -data[2952] = String.fromCharCode (0xffff); -data[2953] = String.fromCharCode (0xffff); -data[2954] = String.fromCharCode (0xffff); -data[2955] = String.fromCharCode (0xffff); -data[2956] = String.fromCharCode (0xffff); -data[2957] = String.fromCharCode (0xffff); -data[2958] = String.fromCharCode (0xffff); -data[2959] = String.fromCharCode (0xffff); -data[2960] = String.fromCharCode (0xffff); -data[2961] = String.fromCharCode (0xffff); -data[2962] = String.fromCharCode (0xffff); -data[2963] = String.fromCharCode (0xffff); -data[2964] = String.fromCharCode (0xffff); -data[2965] = String.fromCharCode (0xffff); -data[2966] = String.fromCharCode (0xffff); -data[2967] = String.fromCharCode (0xffff); -data[2968] = String.fromCharCode (0xffff); -data[2969] = String.fromCharCode (0xffff); -data[2970] = String.fromCharCode (0xffff); -data[2971] = String.fromCharCode (0xffff); -data[2972] = String.fromCharCode (0xffff); -data[2973] = String.fromCharCode (0xffff); -data[2974] = String.fromCharCode (0xffff); -data[2975] = String.fromCharCode (0xffff); -data[2976] = String.fromCharCode (0xffff); -data[2977] = String.fromCharCode (0xffff); -data[2978] = String.fromCharCode (0xffff); -data[2979] = String.fromCharCode (0xffff); -data[2980] = String.fromCharCode (0xffff); -data[2981] = String.fromCharCode (0xffff); -data[2982] = String.fromCharCode (0xffff); -data[2983] = String.fromCharCode (0xffff); -data[2984] = String.fromCharCode (0xffff); -data[2985] = String.fromCharCode (0xffff); -data[2986] = String.fromCharCode (0xffff); -data[2987] = String.fromCharCode (0xffff); -data[2988] = String.fromCharCode (0xffff); -data[2989] = String.fromCharCode (0xffff); -data[2990] = String.fromCharCode (0xffff); -data[2991] = String.fromCharCode (0xffff); -data[2992] = String.fromCharCode (0xffff); -data[2993] = String.fromCharCode (0xffff); -data[2994] = String.fromCharCode (0xffff); -data[2995] = String.fromCharCode (0xffff); -data[2996] = String.fromCharCode (0xffff); -data[2997] = String.fromCharCode (0xffff); -data[2998] = String.fromCharCode (0xffff); -data[2999] = String.fromCharCode (0xffff); -data[3000] = String.fromCharCode (0xffff); -data[3001] = String.fromCharCode (0xffff); -data[3002] = String.fromCharCode (0xffff); -data[3003] = String.fromCharCode (0xffff); -data[3004] = String.fromCharCode (0xffff); -data[3005] = String.fromCharCode (0xffff); -data[3006] = String.fromCharCode (0xffff); -data[3007] = String.fromCharCode (0xffff); -data[3008] = String.fromCharCode (0xffff); -data[3009] = String.fromCharCode (0xffff); -data[3010] = String.fromCharCode (0xffff); -data[3011] = String.fromCharCode (0xffff); -data[3012] = String.fromCharCode (0xffff); -data[3013] = String.fromCharCode (0xffff); -data[3014] = String.fromCharCode (0xffff); -data[3015] = String.fromCharCode (0xffff); -data[3016] = String.fromCharCode (0xffff); -data[3017] = String.fromCharCode (0xffff); -data[3018] = String.fromCharCode (0xffff); -data[3019] = String.fromCharCode (0xffff); -data[3020] = String.fromCharCode (0xffff); -data[3021] = String.fromCharCode (0xffff); -data[3022] = String.fromCharCode (0xffff); -data[3023] = String.fromCharCode (0xffff); -data[3024] = String.fromCharCode (0xffff); -data[3025] = String.fromCharCode (0xffff); -data[3026] = String.fromCharCode (0xffff); -data[3027] = String.fromCharCode (0xffff); -data[3028] = String.fromCharCode (0xffff); -data[3029] = String.fromCharCode (0xffff); -data[3030] = String.fromCharCode (0xffff); -data[3031] = String.fromCharCode (0xffff); -data[3032] = String.fromCharCode (0xffff); -data[3033] = String.fromCharCode (0xffff); -data[3034] = String.fromCharCode (0xffff); -data[3035] = String.fromCharCode (0xffff); -data[3036] = String.fromCharCode (0xffff); -data[3037] = String.fromCharCode (0xffff); -data[3038] = String.fromCharCode (0xffff); -data[3039] = String.fromCharCode (0xffff); -data[3040] = String.fromCharCode (0xffff); -data[3041] = String.fromCharCode (0xffff); -data[3042] = String.fromCharCode (0xffff); -data[3043] = String.fromCharCode (0xffff); -data[3044] = String.fromCharCode (0xffff); -data[3045] = String.fromCharCode (0xffff); -data[3046] = String.fromCharCode (0xffff); -data[3047] = String.fromCharCode (0xffff); -data[3048] = String.fromCharCode (0xffff); -data[3049] = String.fromCharCode (0xffff); -data[3050] = String.fromCharCode (0xffff); -data[3051] = String.fromCharCode (0xffff); -data[3052] = String.fromCharCode (0xffff); -data[3053] = String.fromCharCode (0xffff); -data[3054] = String.fromCharCode (0xffff); -data[3055] = String.fromCharCode (0xffff); -data[3056] = String.fromCharCode (0xffff); -data[3057] = String.fromCharCode (0xffff); -data[3058] = String.fromCharCode (0xffff); -data[3059] = String.fromCharCode (0xffff); -data[3060] = String.fromCharCode (0xffff); -data[3061] = String.fromCharCode (0xffff); -data[3062] = String.fromCharCode (0xffff); -data[3063] = String.fromCharCode (0xffff); -data[3064] = String.fromCharCode (0xffff); -data[3065] = String.fromCharCode (0xffff); -data[3066] = String.fromCharCode (0xffff); -data[3067] = String.fromCharCode (0xffff); -data[3068] = String.fromCharCode (0xffff); -data[3069] = String.fromCharCode (0xffff); -data[3070] = String.fromCharCode (0xffff); -data[3071] = String.fromCharCode (0xffff); -data[3072] = String.fromCharCode (0xffff); -data[3073] = String.fromCharCode (0xffff); -data[3074] = String.fromCharCode (0xffff); -data[3075] = String.fromCharCode (0xffff); -data[3076] = String.fromCharCode (0xffff); -data[3077] = String.fromCharCode (0xffff); -data[3078] = String.fromCharCode (0xffff); -data[3079] = String.fromCharCode (0xffff); -data[3080] = String.fromCharCode (0xffff); -data[3081] = String.fromCharCode (0xffff); -data[3082] = String.fromCharCode (0xffff); -data[3083] = String.fromCharCode (0xffff); -data[3084] = String.fromCharCode (0xffff); -data[3085] = String.fromCharCode (0xffff); -data[3086] = String.fromCharCode (0xffff); -data[3087] = String.fromCharCode (0xffff); -data[3088] = String.fromCharCode (0xffff); -data[3089] = String.fromCharCode (0xffff); -data[3090] = String.fromCharCode (0xffff); -data[3091] = String.fromCharCode (0xffff); -data[3092] = String.fromCharCode (0xffff); -data[3093] = String.fromCharCode (0xffff); -data[3094] = String.fromCharCode (0xffff); -data[3095] = String.fromCharCode (0xffff); -data[3096] = String.fromCharCode (0xffff); -data[3097] = String.fromCharCode (0xffff); -data[3098] = String.fromCharCode (0xffff); -data[3099] = String.fromCharCode (0xffff); -data[3100] = String.fromCharCode (0xffff); -data[3101] = String.fromCharCode (0xffff); -data[3102] = String.fromCharCode (0xffff); -data[3103] = String.fromCharCode (0xffff); -data[3104] = String.fromCharCode (0xffff); -data[3105] = String.fromCharCode (0xffff); -data[3106] = String.fromCharCode (0xffff); -data[3107] = String.fromCharCode (0xffff); -data[3108] = String.fromCharCode (0xffff); -data[3109] = String.fromCharCode (0xffff); -data[3110] = String.fromCharCode (0xffff); -data[3111] = String.fromCharCode (0xffff); -data[3112] = String.fromCharCode (0xffff); -data[3113] = String.fromCharCode (0xffff); -data[3114] = String.fromCharCode (0xffff); -data[3115] = String.fromCharCode (0xffff); -data[3116] = String.fromCharCode (0xffff); -data[3117] = String.fromCharCode (0xffff); -data[3118] = String.fromCharCode (0xffff); -data[3119] = String.fromCharCode (0xffff); -data[3120] = String.fromCharCode (0xffff); -data[3121] = String.fromCharCode (0xffff); -data[3122] = String.fromCharCode (0xffff); -data[3123] = String.fromCharCode (0xffff); -data[3124] = String.fromCharCode (0xffff); -data[3125] = String.fromCharCode (0xffff); -data[3126] = String.fromCharCode (0xffff); -data[3127] = String.fromCharCode (0xffff); -data[3128] = String.fromCharCode (0xffff); -data[3129] = String.fromCharCode (0xffff); -data[3130] = String.fromCharCode (0xffff); -data[3131] = String.fromCharCode (0xffff); -data[3132] = String.fromCharCode (0xffff); -data[3133] = String.fromCharCode (0xffff); -data[3134] = String.fromCharCode (0xffff); -data[3135] = String.fromCharCode (0xffff); -data[3136] = String.fromCharCode (0xffff); -data[3137] = String.fromCharCode (0xffff); -data[3138] = String.fromCharCode (0xffff); -data[3139] = String.fromCharCode (0xffff); -data[3140] = String.fromCharCode (0xffff); -data[3141] = String.fromCharCode (0xffff); -data[3142] = String.fromCharCode (0xffff); -data[3143] = String.fromCharCode (0xffff); -data[3144] = String.fromCharCode (0xffff); -data[3145] = String.fromCharCode (0xffff); -data[3146] = String.fromCharCode (0xffff); -data[3147] = String.fromCharCode (0xffff); -data[3148] = String.fromCharCode (0xffff); -data[3149] = String.fromCharCode (0xffff); -data[3150] = String.fromCharCode (0xffff); -data[3151] = String.fromCharCode (0xffff); -data[3152] = String.fromCharCode (0xffff); -data[3153] = String.fromCharCode (0xffff); -data[3154] = String.fromCharCode (0xffff); -data[3155] = String.fromCharCode (0xffff); -data[3156] = String.fromCharCode (0xffff); -data[3157] = String.fromCharCode (0xffff); -data[3158] = String.fromCharCode (0xffff); -data[3159] = String.fromCharCode (0xffff); -data[3160] = String.fromCharCode (0xffff); -data[3161] = String.fromCharCode (0xffff); -data[3162] = String.fromCharCode (0xffff); -data[3163] = String.fromCharCode (0xffff); -data[3164] = String.fromCharCode (0xffff); -data[3165] = String.fromCharCode (0xffff); -data[3166] = String.fromCharCode (0xffff); -data[3167] = String.fromCharCode (0xffff); -data[3168] = String.fromCharCode (0xffff); -data[3169] = String.fromCharCode (0xffff); -data[3170] = String.fromCharCode (0xffff); -data[3171] = String.fromCharCode (0xffff); -data[3172] = String.fromCharCode (0xffff); -data[3173] = String.fromCharCode (0xffff); -data[3174] = String.fromCharCode (0xffff); -data[3175] = String.fromCharCode (0xffff); -data[3176] = String.fromCharCode (0xffff); -data[3177] = String.fromCharCode (0xffff); -data[3178] = String.fromCharCode (0xffff); -data[3179] = String.fromCharCode (0xffff); -data[3180] = String.fromCharCode (0xffff); -data[3181] = String.fromCharCode (0xffff); -data[3182] = String.fromCharCode (0xffff); -data[3183] = String.fromCharCode (0xffff); -data[3184] = String.fromCharCode (0xffff); -data[3185] = String.fromCharCode (0xffff); -data[3186] = String.fromCharCode (0xffff); -data[3187] = String.fromCharCode (0xffff); -data[3188] = String.fromCharCode (0xffff); -data[3189] = String.fromCharCode (0xffff); -data[3190] = String.fromCharCode (0xffff); -data[3191] = String.fromCharCode (0xffff); -data[3192] = String.fromCharCode (0xffff); -data[3193] = String.fromCharCode (0xffff); -data[3194] = String.fromCharCode (0xffff); -data[3195] = String.fromCharCode (0xffff); -data[3196] = String.fromCharCode (0xffff); -data[3197] = String.fromCharCode (0xffff); -data[3198] = String.fromCharCode (0xffff); -data[3199] = String.fromCharCode (0xffff); -data[3200] = String.fromCharCode (0xffff); -data[3201] = String.fromCharCode (0xffff); -data[3202] = String.fromCharCode (0xffff); -data[3203] = String.fromCharCode (0xffff); -data[3204] = String.fromCharCode (0xffff); -data[3205] = String.fromCharCode (0xffff); -data[3206] = String.fromCharCode (0xffff); -data[3207] = String.fromCharCode (0xffff); -data[3208] = String.fromCharCode (0xffff); -data[3209] = String.fromCharCode (0xffff); -data[3210] = String.fromCharCode (0xffff); -data[3211] = String.fromCharCode (0xffff); -data[3212] = String.fromCharCode (0xffff); -data[3213] = String.fromCharCode (0xffff); -data[3214] = String.fromCharCode (0xffff); -data[3215] = String.fromCharCode (0xffff); -data[3216] = String.fromCharCode (0xffff); -data[3217] = String.fromCharCode (0xffff); -data[3218] = String.fromCharCode (0xffff); -data[3219] = String.fromCharCode (0xffff); -data[3220] = String.fromCharCode (0xffff); -data[3221] = String.fromCharCode (0xffff); -data[3222] = String.fromCharCode (0xffff); -data[3223] = String.fromCharCode (0xffff); -data[3224] = String.fromCharCode (0xffff); -data[3225] = String.fromCharCode (0xffff); -data[3226] = String.fromCharCode (0xffff); -data[3227] = String.fromCharCode (0xffff); -data[3228] = String.fromCharCode (0xffff); -data[3229] = String.fromCharCode (0xffff); -data[3230] = String.fromCharCode (0xffff); -data[3231] = String.fromCharCode (0xffff); -data[3232] = String.fromCharCode (0xffff); -data[3233] = String.fromCharCode (0xffff); -data[3234] = String.fromCharCode (0xffff); -data[3235] = String.fromCharCode (0xffff); -data[3236] = String.fromCharCode (0xffff); -data[3237] = String.fromCharCode (0xffff); -data[3238] = String.fromCharCode (0xffff); -data[3239] = String.fromCharCode (0xffff); -data[3240] = String.fromCharCode (0xffff); -data[3241] = String.fromCharCode (0xffff); -data[3242] = String.fromCharCode (0xffff); -data[3243] = String.fromCharCode (0xffff); -data[3244] = String.fromCharCode (0xffff); -data[3245] = String.fromCharCode (0xffff); -data[3246] = String.fromCharCode (0xffff); -data[3247] = String.fromCharCode (0xffff); -data[3248] = String.fromCharCode (0xffff); -data[3249] = String.fromCharCode (0xffff); -data[3250] = String.fromCharCode (0xffff); -data[3251] = String.fromCharCode (0xffff); -data[3252] = String.fromCharCode (0xffff); -data[3253] = String.fromCharCode (0xffff); -data[3254] = String.fromCharCode (0xffff); -data[3255] = String.fromCharCode (0xffff); -data[3256] = String.fromCharCode (0xffff); -data[3257] = String.fromCharCode (0xffff); -data[3258] = String.fromCharCode (0xffff); -data[3259] = String.fromCharCode (0xffff); -data[3260] = String.fromCharCode (0xffff); -data[3261] = String.fromCharCode (0xffff); -data[3262] = String.fromCharCode (0xffff); -data[3263] = String.fromCharCode (0xffff); -data[3264] = String.fromCharCode (0xffff); -data[3265] = String.fromCharCode (0xffff); -data[3266] = String.fromCharCode (0xffff); -data[3267] = String.fromCharCode (0xffff); -data[3268] = String.fromCharCode (0xffff); -data[3269] = String.fromCharCode (0xffff); -data[3270] = String.fromCharCode (0xffff); -data[3271] = String.fromCharCode (0xffff); -data[3272] = String.fromCharCode (0xffff); -data[3273] = String.fromCharCode (0xffff); -data[3274] = String.fromCharCode (0xffff); -data[3275] = String.fromCharCode (0xffff); -data[3276] = String.fromCharCode (0xffff); -data[3277] = String.fromCharCode (0xffff); -data[3278] = String.fromCharCode (0xffff); -data[3279] = String.fromCharCode (0xffff); -data[3280] = String.fromCharCode (0xffff); -data[3281] = String.fromCharCode (0xffff); -data[3282] = String.fromCharCode (0xffff); -data[3283] = String.fromCharCode (0xffff); -data[3284] = String.fromCharCode (0xffff); -data[3285] = String.fromCharCode (0xffff); -data[3286] = String.fromCharCode (0xffff); -data[3287] = String.fromCharCode (0xffff); -data[3288] = String.fromCharCode (0xffff); -data[3289] = String.fromCharCode (0xffff); -data[3290] = String.fromCharCode (0xffff); -data[3291] = String.fromCharCode (0xffff); -data[3292] = String.fromCharCode (0xffff); -data[3293] = String.fromCharCode (0xffff); -data[3294] = String.fromCharCode (0xffff); -data[3295] = String.fromCharCode (0xffff); -data[3296] = String.fromCharCode (0xffff); -data[3297] = String.fromCharCode (0xffff); -data[3298] = String.fromCharCode (0xffff); -data[3299] = String.fromCharCode (0xffff); -data[3300] = String.fromCharCode (0xffff); -data[3301] = String.fromCharCode (0xffff); -data[3302] = String.fromCharCode (0xffff); -data[3303] = String.fromCharCode (0xffff); -data[3304] = String.fromCharCode (0xffff); -data[3305] = String.fromCharCode (0xffff); -data[3306] = String.fromCharCode (0xffff); -data[3307] = String.fromCharCode (0xffff); -data[3308] = String.fromCharCode (0xffff); -data[3309] = String.fromCharCode (0xffff); -data[3310] = String.fromCharCode (0xffff); -data[3311] = String.fromCharCode (0xffff); -data[3312] = String.fromCharCode (0xffff); -data[3313] = String.fromCharCode (0xffff); -data[3314] = String.fromCharCode (0xffff); -data[3315] = String.fromCharCode (0xffff); -data[3316] = String.fromCharCode (0xffff); -data[3317] = String.fromCharCode (0xffff); -data[3318] = String.fromCharCode (0xffff); -data[3319] = String.fromCharCode (0xffff); -data[3320] = String.fromCharCode (0xffff); -data[3321] = String.fromCharCode (0xffff); -data[3322] = String.fromCharCode (0xffff); -data[3323] = String.fromCharCode (0xffff); -data[3324] = String.fromCharCode (0xffff); -data[3325] = String.fromCharCode (0xffff); -data[3326] = String.fromCharCode (0xffff); -data[3327] = String.fromCharCode (0xffff); -data[3328] = String.fromCharCode (0xffff); -data[3329] = String.fromCharCode (0xffff); -data[3330] = String.fromCharCode (0xffff); -data[3331] = String.fromCharCode (0xffff); -data[3332] = String.fromCharCode (0xffff); -data[3333] = String.fromCharCode (0xffff); -data[3334] = String.fromCharCode (0xffff); -data[3335] = String.fromCharCode (0xffff); -data[3336] = String.fromCharCode (0xffff); -data[3337] = String.fromCharCode (0xffff); -data[3338] = String.fromCharCode (0xffff); -data[3339] = String.fromCharCode (0xffff); -data[3340] = String.fromCharCode (0xffff); -data[3341] = String.fromCharCode (0xffff); -data[3342] = String.fromCharCode (0xffff); -data[3343] = String.fromCharCode (0xffff); -data[3344] = String.fromCharCode (0xffff); -data[3345] = String.fromCharCode (0xffff); -data[3346] = String.fromCharCode (0xffff); -data[3347] = String.fromCharCode (0xffff); -data[3348] = String.fromCharCode (0xffff); -data[3349] = String.fromCharCode (0xffff); -data[3350] = String.fromCharCode (0xffff); -data[3351] = String.fromCharCode (0xffff); -data[3352] = String.fromCharCode (0xffff); -data[3353] = String.fromCharCode (0xffff); -data[3354] = String.fromCharCode (0xffff); -data[3355] = String.fromCharCode (0xffff); -data[3356] = String.fromCharCode (0xffff); -data[3357] = String.fromCharCode (0xffff); -data[3358] = String.fromCharCode (0xffff); -data[3359] = String.fromCharCode (0xffff); -data[3360] = String.fromCharCode (0xffff); -data[3361] = String.fromCharCode (0xffff); -data[3362] = String.fromCharCode (0xffff); -data[3363] = String.fromCharCode (0xffff); -data[3364] = String.fromCharCode (0xffff); -data[3365] = String.fromCharCode (0xffff); -data[3366] = String.fromCharCode (0xffff); -data[3367] = String.fromCharCode (0xffff); -data[3368] = String.fromCharCode (0xffff); -data[3369] = String.fromCharCode (0xffff); -data[3370] = String.fromCharCode (0xffff); -data[3371] = String.fromCharCode (0xffff); -data[3372] = String.fromCharCode (0xffff); -data[3373] = String.fromCharCode (0xffff); -data[3374] = String.fromCharCode (0xffff); -data[3375] = String.fromCharCode (0xffff); -data[3376] = String.fromCharCode (0xffff); -data[3377] = String.fromCharCode (0xffff); -data[3378] = String.fromCharCode (0xffff); -data[3379] = String.fromCharCode (0xffff); -data[3380] = String.fromCharCode (0xffff); -data[3381] = String.fromCharCode (0xffff); -data[3382] = String.fromCharCode (0xffff); -data[3383] = String.fromCharCode (0xffff); -data[3384] = String.fromCharCode (0xffff); -data[3385] = String.fromCharCode (0xffff); -data[3386] = String.fromCharCode (0xffff); -data[3387] = String.fromCharCode (0xffff); -data[3388] = String.fromCharCode (0xffff); -data[3389] = String.fromCharCode (0xffff); -data[3390] = String.fromCharCode (0xffff); -data[3391] = String.fromCharCode (0xffff); -data[3392] = String.fromCharCode (0xffff); -data[3393] = String.fromCharCode (0xffff); -data[3394] = String.fromCharCode (0xffff); -data[3395] = String.fromCharCode (0xffff); -data[3396] = String.fromCharCode (0xffff); -data[3397] = String.fromCharCode (0xffff); -data[3398] = String.fromCharCode (0xffff); -data[3399] = String.fromCharCode (0xffff); -data[3400] = String.fromCharCode (0xffff); -data[3401] = String.fromCharCode (0xffff); -data[3402] = String.fromCharCode (0xffff); -data[3403] = String.fromCharCode (0xffff); -data[3404] = String.fromCharCode (0xffff); -data[3405] = String.fromCharCode (0xffff); -data[3406] = String.fromCharCode (0xffff); -data[3407] = String.fromCharCode (0xffff); -data[3408] = String.fromCharCode (0xffff); -data[3409] = String.fromCharCode (0xffff); -data[3410] = String.fromCharCode (0xffff); -data[3411] = String.fromCharCode (0xffff); -data[3412] = String.fromCharCode (0xffff); -data[3413] = String.fromCharCode (0xffff); -data[3414] = String.fromCharCode (0xffff); -data[3415] = String.fromCharCode (0xffff); -data[3416] = String.fromCharCode (0xffff); -data[3417] = String.fromCharCode (0xffff); -data[3418] = String.fromCharCode (0xffff); -data[3419] = String.fromCharCode (0xffff); -data[3420] = String.fromCharCode (0xffff); -data[3421] = String.fromCharCode (0xffff); -data[3422] = String.fromCharCode (0xffff); -data[3423] = String.fromCharCode (0xffff); -data[3424] = String.fromCharCode (0xffff); -data[3425] = String.fromCharCode (0xffff); -data[3426] = String.fromCharCode (0xffff); -data[3427] = String.fromCharCode (0xffff); -data[3428] = String.fromCharCode (0xffff); -data[3429] = String.fromCharCode (0xffff); -data[3430] = String.fromCharCode (0xffff); -data[3431] = String.fromCharCode (0xffff); -data[3432] = String.fromCharCode (0xffff); -data[3433] = String.fromCharCode (0xffff); -data[3434] = String.fromCharCode (0xffff); -data[3435] = String.fromCharCode (0xffff); -data[3436] = String.fromCharCode (0xffff); -data[3437] = String.fromCharCode (0xffff); -data[3438] = String.fromCharCode (0xffff); -data[3439] = String.fromCharCode (0xffff); -data[3440] = String.fromCharCode (0xffff); -data[3441] = String.fromCharCode (0xffff); -data[3442] = String.fromCharCode (0xffff); -data[3443] = String.fromCharCode (0xffff); -data[3444] = String.fromCharCode (0xffff); -data[3445] = String.fromCharCode (0xffff); -data[3446] = String.fromCharCode (0xffff); -data[3447] = String.fromCharCode (0xffff); -data[3448] = String.fromCharCode (0xffff); -data[3449] = String.fromCharCode (0xffff); -data[3450] = String.fromCharCode (0x000f); -data[3984] = String.fromCharCode (0xffff); -data[3985] = String.fromCharCode (0xffff); -data[3986] = String.fromCharCode (0xffff); -data[3987] = String.fromCharCode (0xffff); -data[3988] = String.fromCharCode (0xffff); -data[3989] = String.fromCharCode (0xffff); -data[3990] = String.fromCharCode (0xffff); -data[3991] = String.fromCharCode (0xffff); -data[3992] = String.fromCharCode (0xffff); -data[3993] = String.fromCharCode (0xffff); -data[3994] = String.fromCharCode (0xffff); -data[3995] = String.fromCharCode (0xffff); -data[3996] = String.fromCharCode (0xffff); -data[3997] = String.fromCharCode (0xffff); -data[3998] = String.fromCharCode (0xffff); -data[3999] = String.fromCharCode (0xffff); -data[4000] = String.fromCharCode (0xffff); -data[4001] = String.fromCharCode (0xffff); -data[4002] = String.fromCharCode (0x3fff); -data[4016] = String.fromCharCode (0x007f); -data[4017] = String.fromCharCode (0x80f8); -data[4018] = String.fromCharCode (0xfdff); -data[4019] = String.fromCharCode (0x5f7f); -data[4020] = String.fromCharCode (0xffdb); -data[4021] = String.fromCharCode (0xffff); -data[4022] = String.fromCharCode (0xffff); -data[4023] = String.fromCharCode (0xffff); -data[4024] = String.fromCharCode (0xffff); -data[4025] = String.fromCharCode (0xffff); -data[4026] = String.fromCharCode (0xffff); -data[4027] = String.fromCharCode (0x0003); -data[4029] = String.fromCharCode (0xfff8); -data[4030] = String.fromCharCode (0xffff); -data[4031] = String.fromCharCode (0xffff); -data[4032] = String.fromCharCode (0xffff); -data[4033] = String.fromCharCode (0xffff); -data[4034] = String.fromCharCode (0xffff); -data[4035] = String.fromCharCode (0xffff); -data[4036] = String.fromCharCode (0xffff); -data[4037] = String.fromCharCode (0xffff); -data[4038] = String.fromCharCode (0xffff); -data[4039] = String.fromCharCode (0xffff); -data[4040] = String.fromCharCode (0xffff); -data[4041] = String.fromCharCode (0xffff); -data[4042] = String.fromCharCode (0xffff); -data[4043] = String.fromCharCode (0xffff); -data[4044] = String.fromCharCode (0xffff); -data[4045] = String.fromCharCode (0xffff); -data[4046] = String.fromCharCode (0xffff); -data[4047] = String.fromCharCode (0xffff); -data[4048] = String.fromCharCode (0xffff); -data[4049] = String.fromCharCode (0xffff); -data[4050] = String.fromCharCode (0xffff); -data[4051] = String.fromCharCode (0x3fff); -data[4053] = String.fromCharCode (0xffff); -data[4054] = String.fromCharCode (0xffff); -data[4055] = String.fromCharCode (0xffff); -data[4056] = String.fromCharCode (0xffff); -data[4057] = String.fromCharCode (0xfffc); -data[4058] = String.fromCharCode (0xffff); -data[4059] = String.fromCharCode (0xffff); -data[4060] = String.fromCharCode (0x00ff); -data[4063] = String.fromCharCode (0x0fff); -data[4071] = String.fromCharCode (0xffd7); -data[4072] = String.fromCharCode (0xffff); -data[4073] = String.fromCharCode (0xffff); -data[4074] = String.fromCharCode (0xffff); -data[4075] = String.fromCharCode (0xffff); -data[4076] = String.fromCharCode (0xffff); -data[4077] = String.fromCharCode (0xffff); -data[4078] = String.fromCharCode (0xffff); -data[4079] = String.fromCharCode (0x1fff); -data[4082] = String.fromCharCode (0xfffe); -data[4083] = String.fromCharCode (0x07ff); -data[4084] = String.fromCharCode (0xfffe); -data[4085] = String.fromCharCode (0x07ff); -data[4086] = String.fromCharCode (0xffc0); -data[4087] = String.fromCharCode (0xffff); -data[4088] = String.fromCharCode (0xffff); -data[4089] = String.fromCharCode (0xffff); -data[4090] = String.fromCharCode (0xffff); -data[4091] = String.fromCharCode (0x7fff); -data[4092] = String.fromCharCode (0xfcfc); -data[4093] = String.fromCharCode (0x1cfc); -data[4100] = String.fromCharCode (0xfffe); -data[4101] = String.fromCharCode (0x07ff); -data[4102] = String.fromCharCode (0xfffe); -data[4103] = String.fromCharCode (0x07ff); -data[4106] = String.fromCharCode (0x0400); -data[4107] = String.fromCharCode (0x0420); -data[4108] = String.fromCharCode (0xffff); -data[4109] = String.fromCharCode (0xff7f); -data[4110] = String.fromCharCode (0xffff); -data[4111] = String.fromCharCode (0xff7f); -data[4112] = String.fromCharCode (0xffff); -data[4113] = String.fromCharCode (0xffff); -data[4114] = String.fromCharCode (0xffff); -data[4115] = String.fromCharCode (0xffff); -data[4116] = String.fromCharCode (0xffff); -data[4117] = String.fromCharCode (0xffff); -data[4118] = String.fromCharCode (0xffff); -data[4119] = String.fromCharCode (0xffff); -data[4120] = String.fromCharCode (0xffff); -data[4121] = String.fromCharCode (0xffff); -data[4122] = String.fromCharCode (0xffff); -data[4123] = String.fromCharCode (0xffff); -data[4124] = String.fromCharCode (0xffff); -data[4125] = String.fromCharCode (0xffff); -data[4126] = String.fromCharCode (0xffff); -data[4127] = String.fromCharCode (0xfc3f); -data[4128] = String.fromCharCode (0xffff); -data[4129] = String.fromCharCode (0x00ff); -data[4133] = String.fromCharCode (0xffff); -data[4134] = String.fromCharCode (0xffff); -data[4135] = String.fromCharCode (0xffff); -data[4136] = String.fromCharCode (0xffff); -data[4137] = String.fromCharCode (0xffff); -data[4138] = String.fromCharCode (0x01ff); -data[4139] = String.fromCharCode (0xf9ff); -data[4140] = String.fromCharCode (0x0003); -data[4141] = String.fromCharCode (0x0003); -data[4142] = String.fromCharCode (0x001f); -data[4151] = String.fromCharCode (0x0400); -data[4152] = String.fromCharCode (0xd740); -data[4153] = String.fromCharCode (0xffff); -data[4154] = String.fromCharCode (0xfffb); -data[4155] = String.fromCharCode (0xffff); -data[4156] = String.fromCharCode (0x7fff); -data[4157] = String.fromCharCode (0x547f); -data[4158] = String.fromCharCode (0x00fd); -}); -c$.white_f = Clazz.defineMethod (c$, "white_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.white = new com.stevesoft.pat.Bits (data); -data[0] = String.fromCharCode (0x3e00); -data[1] = String.fromCharCode (0xf000); -data[2] = String.fromCharCode (0x0001); -data[512] = String.fromCharCode (0x0fff); -data[514] = String.fromCharCode (0x0300); -data[768] = String.fromCharCode (0x0001); -data[4096] = String.fromCharCode (0x3e00); -data[4097] = String.fromCharCode (0xf000); -data[4098] = String.fromCharCode (0x0001); -}); -c$.punct_f = Clazz.defineMethod (c$, "punct_f", -function () { -var data = Clazz.newCharArray (4159, '\0'); -com.stevesoft.pat.Bits.punct = new com.stevesoft.pat.Bits (data); -data[2] = String.fromCharCode (0xf7ee); -data[3] = String.fromCharCode (0x8c00); -data[4] = String.fromCharCode (0x0001); -data[5] = String.fromCharCode (0xb800); -data[7] = String.fromCharCode (0x2800); -data[10] = String.fromCharCode (0x2802); -data[11] = String.fromCharCode (0x8880); -data[55] = String.fromCharCode (0x4030); -data[56] = String.fromCharCode (0x0080); -data[85] = String.fromCharCode (0xfc00); -data[88] = String.fromCharCode (0x0200); -data[91] = String.fromCharCode (0x4000); -data[92] = String.fromCharCode (0x0009); -data[95] = String.fromCharCode (0x0018); -data[96] = String.fromCharCode (0x1000); -data[97] = String.fromCharCode (0x8800); -data[102] = String.fromCharCode (0x3c00); -data[109] = String.fromCharCode (0x0010); -data[150] = '0'; -data[151] = String.fromCharCode (0x0001); -data[226] = String.fromCharCode (0x8000); -data[229] = String.fromCharCode (0x0c00); -data[234] = String.fromCharCode (0x8000); -data[240] = String.fromCharCode (0xfff0); -data[241] = String.fromCharCode (0x0007); -data[243] = String.fromCharCode (0x3c00); -data[248] = String.fromCharCode (0x0020); -data[271] = String.fromCharCode (0x0800); -data[513] = String.fromCharCode (0xffff); -data[514] = String.fromCharCode (0x00ff); -data[515] = String.fromCharCode (0xffff); -data[516] = 'o'; -data[519] = String.fromCharCode (0x6000); -data[520] = String.fromCharCode (0x6000); -data[562] = String.fromCharCode (0x0600); -data[768] = String.fromCharCode (0xff4e); -data[769] = String.fromCharCode (0xfff3); -data[771] = String.fromCharCode (0x0001); -data[783] = String.fromCharCode (0x0800); -data[4051] = String.fromCharCode (0xc000); -data[4067] = String.fromCharCode (0xffff); -data[4068] = String.fromCharCode (0xfe1f); -data[4069] = String.fromCharCode (0xfff7); -data[4070] = String.fromCharCode (0x0d0b); -data[4080] = String.fromCharCode (0xf7ee); -data[4081] = String.fromCharCode (0x8c00); -data[4082] = String.fromCharCode (0x0001); -data[4083] = String.fromCharCode (0xb800); -data[4085] = String.fromCharCode (0x2800); -data[4086] = String.fromCharCode (0x003e); -data[4098] = String.fromCharCode (0xf7ee); -data[4099] = String.fromCharCode (0x8c00); -data[4100] = String.fromCharCode (0x0001); -data[4101] = String.fromCharCode (0xb800); -data[4103] = String.fromCharCode (0x2800); -data[4106] = String.fromCharCode (0x2802); -data[4107] = String.fromCharCode (0x8880); -data[4151] = String.fromCharCode (0x4030); -data[4152] = String.fromCharCode (0x0080); -}); -Clazz.defineStatics (c$, -"upper", null, -"lower", null, -"title", null, -"currency", null, -"decimal_digit", null, -"math", null, -"letter", null, -"white", null, -"punct", null); +Clazz.declarePackage ("com.stevesoft.pat"); +c$ = Clazz.decorateAsClass (function () { +this.carray = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Bits"); +Clazz.makeConstructor (c$, +function (carray) { +this.carray = carray; +}, "~A"); +Clazz.defineMethod (c$, "get", +function (i) { +return ((this.carray[i >> 4]).charCodeAt (0) & (1 << (i & 15))) != 0; +}, "~N"); +Clazz.defineMethod (c$, "set", +function (i, b) { +if (b) { +this.carray[i >> 4] = String.fromCharCode ((this.carray[i >> 4]).charCodeAt (0) | ((String.fromCharCode (1)).charCodeAt (0) << (i & 15))); +} else { +this.carray[i >> 4] = String.fromCharCode ((this.carray[i >> 4]).charCodeAt (0) & (String.fromCharCode (~(1 << (i & 15)))).charCodeAt (0)); +}}, "~N,~B"); +c$.upper_f = Clazz.defineMethod (c$, "upper_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.upper = new com.stevesoft.pat.Bits (data); +data[4] = String.fromCharCode (0xfffe); +data[5] = String.fromCharCode (0x07ff); +data[12] = String.fromCharCode (0xffff); +data[13] = String.fromCharCode (0x7f7f); +data[16] = String.fromCharCode (0x5555); +data[17] = String.fromCharCode (0x5555); +data[18] = String.fromCharCode (0x5555); +data[19] = String.fromCharCode (0xaa55); +data[20] = String.fromCharCode (0x54aa); +data[21] = String.fromCharCode (0x5555); +data[22] = String.fromCharCode (0x5555); +data[23] = String.fromCharCode (0x2b55); +data[24] = String.fromCharCode (0xced6); +data[25] = String.fromCharCode (0xb1db); +data[26] = String.fromCharCode (0xd2d5); +data[27] = String.fromCharCode (0x11ae); +data[28] = String.fromCharCode (0xa490); +data[29] = String.fromCharCode (0x4aaa); +data[30] = String.fromCharCode (0x5555); +data[31] = String.fromCharCode (0x5412); +data[32] = String.fromCharCode (0x5555); +data[33] = 'U'; +data[56] = String.fromCharCode (0xd740); +data[57] = String.fromCharCode (0xfffe); +data[58] = String.fromCharCode (0x0ffb); +data[61] = String.fromCharCode (0x541c); +data[62] = String.fromCharCode (0x5555); +data[64] = String.fromCharCode (0xdffe); +data[65] = String.fromCharCode (0xffff); +data[66] = String.fromCharCode (0xffff); +data[70] = String.fromCharCode (0x5555); +data[71] = String.fromCharCode (0x5555); +data[72] = String.fromCharCode (0x0001); +data[73] = String.fromCharCode (0x5555); +data[74] = String.fromCharCode (0x5555); +data[75] = String.fromCharCode (0x5555); +data[76] = String.fromCharCode (0x088a); +data[77] = String.fromCharCode (0x5555); +data[78] = String.fromCharCode (0x4555); +data[79] = String.fromCharCode (0x0115); +data[83] = String.fromCharCode (0xfffe); +data[84] = String.fromCharCode (0xffff); +data[85] = String.fromCharCode (0x007f); +data[266] = String.fromCharCode (0xffff); +data[267] = String.fromCharCode (0xffff); +data[268] = String.fromCharCode (0x003f); +data[480] = String.fromCharCode (0x5555); +data[481] = String.fromCharCode (0x5555); +data[482] = String.fromCharCode (0x5555); +data[483] = String.fromCharCode (0x5555); +data[484] = String.fromCharCode (0x5555); +data[485] = String.fromCharCode (0x5555); +data[486] = String.fromCharCode (0x5555); +data[487] = String.fromCharCode (0x5555); +data[488] = String.fromCharCode (0x5555); +data[489] = String.fromCharCode (0x0015); +data[490] = String.fromCharCode (0x5555); +data[491] = String.fromCharCode (0x5555); +data[492] = String.fromCharCode (0x5555); +data[493] = String.fromCharCode (0x5555); +data[494] = String.fromCharCode (0x5555); +data[495] = String.fromCharCode (0x0155); +data[496] = String.fromCharCode (0xff00); +data[497] = String.fromCharCode (0x3f00); +data[498] = String.fromCharCode (0xff00); +data[499] = String.fromCharCode (0xff00); +data[500] = String.fromCharCode (0x3f00); +data[501] = String.fromCharCode (0xaa00); +data[502] = String.fromCharCode (0xff00); +data[504] = String.fromCharCode (0xff00); +data[505] = String.fromCharCode (0xff00); +data[506] = String.fromCharCode (0xff00); +data[507] = String.fromCharCode (0x5f00); +data[508] = String.fromCharCode (0x1f00); +data[509] = String.fromCharCode (0x0f00); +data[510] = String.fromCharCode (0x1f00); +data[511] = String.fromCharCode (0x1f00); +data[528] = String.fromCharCode (0x3884); +data[529] = String.fromCharCode (0x3f27); +data[530] = String.fromCharCode (0x3d50); +data[531] = String.fromCharCode (0x000b); +data[4082] = String.fromCharCode (0xfffe); +data[4083] = String.fromCharCode (0x07ff); +data[4100] = String.fromCharCode (0xfffe); +data[4101] = String.fromCharCode (0x07ff); +data[4108] = String.fromCharCode (0xffff); +data[4109] = String.fromCharCode (0x7f7f); +data[4112] = String.fromCharCode (0x5555); +data[4113] = String.fromCharCode (0x5555); +data[4114] = String.fromCharCode (0x5555); +data[4115] = String.fromCharCode (0xaa55); +data[4116] = String.fromCharCode (0x54aa); +data[4117] = String.fromCharCode (0x5555); +data[4118] = String.fromCharCode (0x5555); +data[4119] = String.fromCharCode (0x2b55); +data[4120] = String.fromCharCode (0xced6); +data[4121] = String.fromCharCode (0xb1db); +data[4122] = String.fromCharCode (0xd2d5); +data[4123] = String.fromCharCode (0x11ae); +data[4124] = String.fromCharCode (0xa490); +data[4125] = String.fromCharCode (0x4aaa); +data[4126] = String.fromCharCode (0x5555); +data[4127] = String.fromCharCode (0x5412); +data[4128] = String.fromCharCode (0x5555); +data[4129] = 'U'; +data[4152] = String.fromCharCode (0xd740); +data[4153] = String.fromCharCode (0xfffe); +data[4154] = String.fromCharCode (0x0ffb); +data[4157] = String.fromCharCode (0x541c); +data[4158] = 'U'; +}); +c$.lower_f = Clazz.defineMethod (c$, "lower_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.lower = new com.stevesoft.pat.Bits (data); +data[6] = String.fromCharCode (0xfffe); +data[7] = String.fromCharCode (0x07ff); +data[10] = String.fromCharCode (0x0400); +data[11] = String.fromCharCode (0x0420); +data[13] = String.fromCharCode (0x8000); +data[14] = String.fromCharCode (0xffff); +data[15] = String.fromCharCode (0xff7f); +data[16] = String.fromCharCode (0xaaaa); +data[17] = String.fromCharCode (0xaaaa); +data[18] = String.fromCharCode (0xaaaa); +data[19] = String.fromCharCode (0x55aa); +data[20] = String.fromCharCode (0xab55); +data[21] = String.fromCharCode (0xaaaa); +data[22] = String.fromCharCode (0xaaaa); +data[23] = String.fromCharCode (0xd4aa); +data[24] = String.fromCharCode (0x3129); +data[25] = String.fromCharCode (0x4e24); +data[26] = String.fromCharCode (0x292a); +data[27] = String.fromCharCode (0x2651); +data[28] = String.fromCharCode (0x5240); +data[29] = String.fromCharCode (0xb555); +data[30] = String.fromCharCode (0xaaaa); +data[31] = String.fromCharCode (0xa829); +data[32] = String.fromCharCode (0xaaaa); +data[33] = String.fromCharCode (0x00aa); +data[37] = String.fromCharCode (0xffff); +data[38] = String.fromCharCode (0xffff); +data[39] = String.fromCharCode (0xffff); +data[40] = String.fromCharCode (0xffff); +data[41] = String.fromCharCode (0xffff); +data[42] = String.fromCharCode (0x01ff); +data[57] = String.fromCharCode (0x0001); +data[58] = String.fromCharCode (0xf000); +data[59] = String.fromCharCode (0xffff); +data[60] = String.fromCharCode (0x7fff); +data[61] = 'c'; +data[62] = String.fromCharCode (0xaaa8); +data[63] = String.fromCharCode (0x0007); +data[67] = String.fromCharCode (0xffff); +data[68] = String.fromCharCode (0xffff); +data[69] = String.fromCharCode (0xdffe); +data[70] = String.fromCharCode (0xaaaa); +data[71] = String.fromCharCode (0xaaaa); +data[72] = String.fromCharCode (0x0002); +data[73] = String.fromCharCode (0xaaaa); +data[74] = String.fromCharCode (0xaaaa); +data[75] = String.fromCharCode (0xaaaa); +data[76] = String.fromCharCode (0x1114); +data[77] = String.fromCharCode (0xaaaa); +data[78] = String.fromCharCode (0x8aaa); +data[79] = String.fromCharCode (0x022a); +data[86] = String.fromCharCode (0xfffe); +data[87] = String.fromCharCode (0xffff); +data[88] = String.fromCharCode (0x00ff); +data[269] = String.fromCharCode (0xffff); +data[270] = String.fromCharCode (0xffff); +data[271] = String.fromCharCode (0x007f); +data[480] = String.fromCharCode (0xaaaa); +data[481] = String.fromCharCode (0xaaaa); +data[482] = String.fromCharCode (0xaaaa); +data[483] = String.fromCharCode (0xaaaa); +data[484] = String.fromCharCode (0xaaaa); +data[485] = String.fromCharCode (0xaaaa); +data[486] = String.fromCharCode (0xaaaa); +data[487] = String.fromCharCode (0xaaaa); +data[488] = String.fromCharCode (0xaaaa); +data[489] = String.fromCharCode (0x0fea); +data[490] = String.fromCharCode (0xaaaa); +data[491] = String.fromCharCode (0xaaaa); +data[492] = String.fromCharCode (0xaaaa); +data[493] = String.fromCharCode (0xaaaa); +data[494] = String.fromCharCode (0xaaaa); +data[495] = String.fromCharCode (0x02aa); +data[496] = String.fromCharCode (0x00ff); +data[497] = String.fromCharCode (0x003f); +data[498] = String.fromCharCode (0x00ff); +data[499] = String.fromCharCode (0x00ff); +data[500] = String.fromCharCode (0x003f); +data[501] = String.fromCharCode (0x00ff); +data[502] = String.fromCharCode (0x00ff); +data[503] = String.fromCharCode (0x3fff); +data[504] = String.fromCharCode (0x00ff); +data[505] = String.fromCharCode (0x00ff); +data[506] = String.fromCharCode (0x00ff); +data[507] = String.fromCharCode (0x00df); +data[508] = String.fromCharCode (0x00dc); +data[509] = String.fromCharCode (0x00cf); +data[510] = String.fromCharCode (0x00ff); +data[511] = String.fromCharCode (0x00dc); +data[519] = String.fromCharCode (0x8000); +data[528] = String.fromCharCode (0xc400); +data[529] = String.fromCharCode (0x0008); +data[530] = String.fromCharCode (0xc000); +data[531] = String.fromCharCode (0x0010); +data[4016] = String.fromCharCode (0x007f); +data[4017] = String.fromCharCode (0x00f8); +data[4084] = String.fromCharCode (0xfffe); +data[4085] = String.fromCharCode (0x07ff); +data[4102] = String.fromCharCode (0xfffe); +data[4103] = String.fromCharCode (0x07ff); +data[4106] = String.fromCharCode (0x0400); +data[4107] = String.fromCharCode (0x0420); +data[4109] = String.fromCharCode (0x8000); +data[4110] = String.fromCharCode (0xffff); +data[4111] = String.fromCharCode (0xff7f); +data[4112] = String.fromCharCode (0xaaaa); +data[4113] = String.fromCharCode (0xaaaa); +data[4114] = String.fromCharCode (0xaaaa); +data[4115] = String.fromCharCode (0x55aa); +data[4116] = String.fromCharCode (0xab55); +data[4117] = String.fromCharCode (0xaaaa); +data[4118] = String.fromCharCode (0xaaaa); +data[4119] = String.fromCharCode (0xd4aa); +data[4120] = String.fromCharCode (0x3129); +data[4121] = String.fromCharCode (0x4e24); +data[4122] = String.fromCharCode (0x292a); +data[4123] = String.fromCharCode (0x2651); +data[4124] = String.fromCharCode (0x5240); +data[4125] = String.fromCharCode (0xb555); +data[4126] = String.fromCharCode (0xaaaa); +data[4127] = String.fromCharCode (0xa829); +data[4128] = String.fromCharCode (0xaaaa); +data[4129] = String.fromCharCode (0x00aa); +data[4133] = String.fromCharCode (0xffff); +data[4134] = String.fromCharCode (0xffff); +data[4135] = String.fromCharCode (0xffff); +data[4136] = String.fromCharCode (0xffff); +data[4137] = String.fromCharCode (0xffff); +data[4138] = String.fromCharCode (0x01ff); +data[4153] = String.fromCharCode (0x0001); +data[4154] = String.fromCharCode (0xf000); +data[4155] = String.fromCharCode (0xffff); +data[4156] = String.fromCharCode (0x7fff); +data[4157] = 'c'; +data[4158] = String.fromCharCode (0x00a8); +}); +c$.title_f = Clazz.defineMethod (c$, "title_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.title = new com.stevesoft.pat.Bits (data); +data[6] = String.fromCharCode (0xfffe); +data[7] = String.fromCharCode (0x07ff); +data[10] = String.fromCharCode (0x0400); +data[11] = String.fromCharCode (0x0420); +data[13] = String.fromCharCode (0x8000); +data[14] = String.fromCharCode (0xffff); +data[15] = String.fromCharCode (0xff7f); +data[16] = String.fromCharCode (0xaaaa); +data[17] = String.fromCharCode (0xaaaa); +data[18] = String.fromCharCode (0xaaaa); +data[19] = String.fromCharCode (0x55aa); +data[20] = String.fromCharCode (0xab55); +data[21] = String.fromCharCode (0xaaaa); +data[22] = String.fromCharCode (0xaaaa); +data[23] = String.fromCharCode (0xd4aa); +data[24] = String.fromCharCode (0x3129); +data[25] = String.fromCharCode (0x4e24); +data[26] = String.fromCharCode (0x292a); +data[27] = String.fromCharCode (0x2651); +data[28] = String.fromCharCode (0x5240); +data[29] = String.fromCharCode (0xb555); +data[30] = String.fromCharCode (0xaaaa); +data[31] = String.fromCharCode (0xa829); +data[32] = String.fromCharCode (0xaaaa); +data[33] = String.fromCharCode (0x00aa); +data[37] = String.fromCharCode (0xffff); +data[38] = String.fromCharCode (0xffff); +data[39] = String.fromCharCode (0xffff); +data[40] = String.fromCharCode (0xffff); +data[41] = String.fromCharCode (0xffff); +data[42] = String.fromCharCode (0x01ff); +data[57] = String.fromCharCode (0x0001); +data[58] = String.fromCharCode (0xf000); +data[59] = String.fromCharCode (0xffff); +data[60] = String.fromCharCode (0x7fff); +data[61] = 'c'; +data[62] = String.fromCharCode (0xaaa8); +data[63] = String.fromCharCode (0x0007); +data[67] = String.fromCharCode (0xffff); +data[68] = String.fromCharCode (0xffff); +data[69] = String.fromCharCode (0xdffe); +data[70] = String.fromCharCode (0xaaaa); +data[71] = String.fromCharCode (0xaaaa); +data[72] = String.fromCharCode (0x0002); +data[73] = String.fromCharCode (0xaaaa); +data[74] = String.fromCharCode (0xaaaa); +data[75] = String.fromCharCode (0xaaaa); +data[76] = String.fromCharCode (0x1114); +data[77] = String.fromCharCode (0xaaaa); +data[78] = String.fromCharCode (0x8aaa); +data[79] = String.fromCharCode (0x022a); +data[86] = String.fromCharCode (0xfffe); +data[87] = String.fromCharCode (0xffff); +data[88] = String.fromCharCode (0x00ff); +data[269] = String.fromCharCode (0xffff); +data[270] = String.fromCharCode (0xffff); +data[271] = String.fromCharCode (0x007f); +data[480] = String.fromCharCode (0xaaaa); +data[481] = String.fromCharCode (0xaaaa); +data[482] = String.fromCharCode (0xaaaa); +data[483] = String.fromCharCode (0xaaaa); +data[484] = String.fromCharCode (0xaaaa); +data[485] = String.fromCharCode (0xaaaa); +data[486] = String.fromCharCode (0xaaaa); +data[487] = String.fromCharCode (0xaaaa); +data[488] = String.fromCharCode (0xaaaa); +data[489] = String.fromCharCode (0x0fea); +data[490] = String.fromCharCode (0xaaaa); +data[491] = String.fromCharCode (0xaaaa); +data[492] = String.fromCharCode (0xaaaa); +data[493] = String.fromCharCode (0xaaaa); +data[494] = String.fromCharCode (0xaaaa); +data[495] = String.fromCharCode (0x02aa); +data[496] = String.fromCharCode (0x00ff); +data[497] = String.fromCharCode (0x003f); +data[498] = String.fromCharCode (0x00ff); +data[499] = String.fromCharCode (0x00ff); +data[500] = String.fromCharCode (0x003f); +data[501] = String.fromCharCode (0x00ff); +data[502] = String.fromCharCode (0x00ff); +data[503] = String.fromCharCode (0x3fff); +data[504] = String.fromCharCode (0x00ff); +data[505] = String.fromCharCode (0x00ff); +data[506] = String.fromCharCode (0x00ff); +data[507] = String.fromCharCode (0x00df); +data[508] = String.fromCharCode (0x00dc); +data[509] = String.fromCharCode (0x00cf); +data[510] = String.fromCharCode (0x00ff); +data[511] = String.fromCharCode (0x00dc); +data[519] = String.fromCharCode (0x8000); +data[528] = String.fromCharCode (0xc400); +data[529] = String.fromCharCode (0x0008); +data[530] = String.fromCharCode (0xc000); +data[531] = String.fromCharCode (0x0010); +data[4016] = String.fromCharCode (0x007f); +data[4017] = String.fromCharCode (0x00f8); +data[4084] = String.fromCharCode (0xfffe); +data[4085] = String.fromCharCode (0x07ff); +data[4102] = String.fromCharCode (0xfffe); +data[4103] = String.fromCharCode (0x07ff); +data[4106] = String.fromCharCode (0x0400); +data[4107] = String.fromCharCode (0x0420); +data[4109] = String.fromCharCode (0x8000); +data[4110] = String.fromCharCode (0xffff); +data[4111] = String.fromCharCode (0xff7f); +data[4112] = String.fromCharCode (0xaaaa); +data[4113] = String.fromCharCode (0xaaaa); +data[4114] = String.fromCharCode (0xaaaa); +data[4115] = String.fromCharCode (0x55aa); +data[4116] = String.fromCharCode (0xab55); +data[4117] = String.fromCharCode (0xaaaa); +data[4118] = String.fromCharCode (0xaaaa); +data[4119] = String.fromCharCode (0xd4aa); +data[4120] = String.fromCharCode (0x3129); +data[4121] = String.fromCharCode (0x4e24); +data[4122] = String.fromCharCode (0x292a); +data[4123] = String.fromCharCode (0x2651); +data[4124] = String.fromCharCode (0x5240); +data[4125] = String.fromCharCode (0xb555); +data[4126] = String.fromCharCode (0xaaaa); +data[4127] = String.fromCharCode (0xa829); +data[4128] = String.fromCharCode (0xaaaa); +data[4129] = String.fromCharCode (0x00aa); +data[4133] = String.fromCharCode (0xffff); +data[4134] = String.fromCharCode (0xffff); +data[4135] = String.fromCharCode (0xffff); +data[4136] = String.fromCharCode (0xffff); +data[4137] = String.fromCharCode (0xffff); +data[4138] = String.fromCharCode (0x01ff); +data[4153] = String.fromCharCode (0x0001); +data[4154] = String.fromCharCode (0xf000); +data[4155] = String.fromCharCode (0xffff); +data[4156] = String.fromCharCode (0x7fff); +data[4157] = 'c'; +data[4158] = String.fromCharCode (0x00a8); +}); +c$.currency_f = Clazz.defineMethod (c$, "currency_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.currency = new com.stevesoft.pat.Bits (data); +data[2] = String.fromCharCode (0x0010); +data[10] = String.fromCharCode (0x003c); +data[159] = String.fromCharCode (0x000c); +data[227] = String.fromCharCode (0x8000); +data[522] = String.fromCharCode (0x1fff); +data[4070] = String.fromCharCode (0x0200); +data[4080] = String.fromCharCode (0x0010); +data[4094] = 'c'; +data[4098] = String.fromCharCode (0x0010); +data[4106] = String.fromCharCode (0x003c); +}); +c$.decimal_digit_f = Clazz.defineMethod (c$, "decimal_digit_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.decimal_digit = new com.stevesoft.pat.Bits (data); +data[3] = String.fromCharCode (0x03ff); +data[102] = String.fromCharCode (0x03ff); +data[111] = String.fromCharCode (0x03ff); +data[150] = String.fromCharCode (0xffc0); +data[158] = String.fromCharCode (0xffc0); +data[166] = String.fromCharCode (0xffc0); +data[174] = String.fromCharCode (0xffc0); +data[182] = String.fromCharCode (0xffc0); +data[190] = String.fromCharCode (0xff80); +data[198] = String.fromCharCode (0xffc0); +data[206] = String.fromCharCode (0xffc0); +data[214] = String.fromCharCode (0xffc0); +data[229] = String.fromCharCode (0x03ff); +data[237] = String.fromCharCode (0x03ff); +data[242] = String.fromCharCode (0x03ff); +data[4081] = String.fromCharCode (0x03ff); +data[4099] = String.fromCharCode (0x03ff); +}); +c$.math_f = Clazz.defineMethod (c$, "math_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.math = new com.stevesoft.pat.Bits (data); +data[2] = String.fromCharCode (0x0800); +data[3] = String.fromCharCode (0x7000); +data[7] = String.fromCharCode (0x5000); +data[10] = String.fromCharCode (0x1000); +data[11] = String.fromCharCode (0x0002); +data[13] = String.fromCharCode (0x0080); +data[15] = String.fromCharCode (0x0080); +data[516] = String.fromCharCode (0x0010); +data[519] = String.fromCharCode (0x1c00); +data[520] = String.fromCharCode (0x1c00); +data[537] = String.fromCharCode (0x001f); +data[541] = String.fromCharCode (0x0014); +data[544] = String.fromCharCode (0xffff); +data[545] = String.fromCharCode (0xffff); +data[546] = String.fromCharCode (0xffff); +data[547] = String.fromCharCode (0xffff); +data[548] = String.fromCharCode (0xffff); +data[549] = String.fromCharCode (0xffff); +data[550] = String.fromCharCode (0xffff); +data[551] = String.fromCharCode (0xffff); +data[552] = String.fromCharCode (0xffff); +data[553] = String.fromCharCode (0xffff); +data[554] = String.fromCharCode (0xffff); +data[555] = String.fromCharCode (0xffff); +data[556] = String.fromCharCode (0xffff); +data[557] = String.fromCharCode (0xffff); +data[558] = String.fromCharCode (0xffff); +data[559] = String.fromCharCode (0x0003); +data[560] = String.fromCharCode (0x0f00); +data[562] = String.fromCharCode (0x0003); +data[4018] = String.fromCharCode (0x0200); +data[4070] = 't'; +data[4080] = String.fromCharCode (0x0800); +data[4081] = String.fromCharCode (0x7000); +data[4085] = String.fromCharCode (0x5000); +data[4094] = String.fromCharCode (0x1f04); +data[4098] = String.fromCharCode (0x0800); +data[4099] = String.fromCharCode (0x7000); +data[4103] = String.fromCharCode (0x5000); +data[4106] = String.fromCharCode (0x1000); +data[4107] = String.fromCharCode (0x0002); +data[4109] = String.fromCharCode (0x0080); +data[4111] = String.fromCharCode (0x0080); +}); +c$.letter_f = Clazz.defineMethod (c$, "letter_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.letter = new com.stevesoft.pat.Bits (data); +data[4] = String.fromCharCode (0xfffe); +data[5] = String.fromCharCode (0x07ff); +data[6] = String.fromCharCode (0xfffe); +data[7] = String.fromCharCode (0x07ff); +data[10] = String.fromCharCode (0x0400); +data[11] = String.fromCharCode (0x0420); +data[12] = String.fromCharCode (0xffff); +data[13] = String.fromCharCode (0xff7f); +data[14] = String.fromCharCode (0xffff); +data[15] = String.fromCharCode (0xff7f); +data[16] = String.fromCharCode (0xffff); +data[17] = String.fromCharCode (0xffff); +data[18] = String.fromCharCode (0xffff); +data[19] = String.fromCharCode (0xffff); +data[20] = String.fromCharCode (0xffff); +data[21] = String.fromCharCode (0xffff); +data[22] = String.fromCharCode (0xffff); +data[23] = String.fromCharCode (0xffff); +data[24] = String.fromCharCode (0xffff); +data[25] = String.fromCharCode (0xffff); +data[26] = String.fromCharCode (0xffff); +data[27] = String.fromCharCode (0xffff); +data[28] = String.fromCharCode (0xffff); +data[29] = String.fromCharCode (0xffff); +data[30] = String.fromCharCode (0xffff); +data[31] = String.fromCharCode (0xfc3f); +data[32] = String.fromCharCode (0xffff); +data[33] = String.fromCharCode (0x00ff); +data[37] = String.fromCharCode (0xffff); +data[38] = String.fromCharCode (0xffff); +data[39] = String.fromCharCode (0xffff); +data[40] = String.fromCharCode (0xffff); +data[41] = String.fromCharCode (0xffff); +data[42] = String.fromCharCode (0x01ff); +data[43] = String.fromCharCode (0xf9ff); +data[44] = String.fromCharCode (0x0003); +data[45] = String.fromCharCode (0x0003); +data[46] = String.fromCharCode (0x001f); +data[55] = String.fromCharCode (0x0400); +data[56] = String.fromCharCode (0xd740); +data[57] = String.fromCharCode (0xffff); +data[58] = String.fromCharCode (0xfffb); +data[59] = String.fromCharCode (0xffff); +data[60] = String.fromCharCode (0x7fff); +data[61] = String.fromCharCode (0x547f); +data[62] = String.fromCharCode (0xfffd); +data[63] = String.fromCharCode (0x000f); +data[64] = String.fromCharCode (0xdffe); +data[65] = String.fromCharCode (0xffff); +data[66] = String.fromCharCode (0xffff); +data[67] = String.fromCharCode (0xffff); +data[68] = String.fromCharCode (0xffff); +data[69] = String.fromCharCode (0xdffe); +data[70] = String.fromCharCode (0xffff); +data[71] = String.fromCharCode (0xffff); +data[72] = String.fromCharCode (0x0003); +data[73] = String.fromCharCode (0xffff); +data[74] = String.fromCharCode (0xffff); +data[75] = String.fromCharCode (0xffff); +data[76] = String.fromCharCode (0x199f); +data[77] = String.fromCharCode (0xffff); +data[78] = String.fromCharCode (0xcfff); +data[79] = String.fromCharCode (0x033f); +data[83] = String.fromCharCode (0xfffe); +data[84] = String.fromCharCode (0xffff); +data[85] = String.fromCharCode (0x027f); +data[86] = String.fromCharCode (0xfffe); +data[87] = String.fromCharCode (0xffff); +data[88] = String.fromCharCode (0x00ff); +data[93] = String.fromCharCode (0xffff); +data[94] = String.fromCharCode (0x07ff); +data[95] = String.fromCharCode (0x0007); +data[98] = String.fromCharCode (0xfffe); +data[99] = String.fromCharCode (0x07ff); +data[100] = String.fromCharCode (0x07ff); +data[103] = String.fromCharCode (0xfffe); +data[104] = String.fromCharCode (0xffff); +data[105] = String.fromCharCode (0xffff); +data[106] = String.fromCharCode (0xffff); +data[107] = String.fromCharCode (0x7cff); +data[108] = String.fromCharCode (0x7fff); +data[109] = String.fromCharCode (0x002f); +data[110] = String.fromCharCode (0x0060); +data[144] = String.fromCharCode (0xffe0); +data[145] = String.fromCharCode (0xffff); +data[146] = String.fromCharCode (0xffff); +data[147] = String.fromCharCode (0x23ff); +data[149] = String.fromCharCode (0xff00); +data[150] = String.fromCharCode (0x0003); +data[152] = String.fromCharCode (0x9fe0); +data[153] = String.fromCharCode (0xfff9); +data[154] = String.fromCharCode (0xfdff); +data[155] = String.fromCharCode (0x03c5); +data[157] = String.fromCharCode (0xb000); +data[158] = String.fromCharCode (0x0003); +data[159] = String.fromCharCode (0x0003); +data[160] = String.fromCharCode (0x87e0); +data[161] = String.fromCharCode (0xfff9); +data[162] = String.fromCharCode (0xfdff); +data[163] = String.fromCharCode (0x036d); +data[165] = String.fromCharCode (0x5e00); +data[167] = String.fromCharCode (0x001c); +data[168] = String.fromCharCode (0xafe0); +data[169] = String.fromCharCode (0xfffb); +data[170] = String.fromCharCode (0xfdff); +data[171] = String.fromCharCode (0x23ed); +data[174] = String.fromCharCode (0x0001); +data[176] = String.fromCharCode (0x9fe0); +data[177] = String.fromCharCode (0xfff9); +data[178] = String.fromCharCode (0xfdff); +data[179] = String.fromCharCode (0x23cd); +data[181] = String.fromCharCode (0xb000); +data[182] = String.fromCharCode (0x0003); +data[184] = String.fromCharCode (0xc7e0); +data[185] = String.fromCharCode (0xd63d); +data[186] = String.fromCharCode (0xc718); +data[187] = String.fromCharCode (0x03bf); +data[192] = String.fromCharCode (0xdfe0); +data[193] = String.fromCharCode (0xfffd); +data[194] = String.fromCharCode (0xfdff); +data[195] = String.fromCharCode (0x03ef); +data[198] = String.fromCharCode (0x0003); +data[200] = String.fromCharCode (0xdfe0); +data[201] = String.fromCharCode (0xfffd); +data[202] = String.fromCharCode (0xfdff); +data[203] = String.fromCharCode (0x03ef); +data[205] = String.fromCharCode (0x4000); +data[206] = String.fromCharCode (0x0003); +data[208] = String.fromCharCode (0xdfe0); +data[209] = String.fromCharCode (0xfffd); +data[210] = String.fromCharCode (0xfdff); +data[211] = String.fromCharCode (0x03ff); +data[214] = String.fromCharCode (0x0003); +data[224] = String.fromCharCode (0xfffe); +data[225] = String.fromCharCode (0xffff); +data[226] = String.fromCharCode (0x7fff); +data[227] = String.fromCharCode (0x000d); +data[228] = String.fromCharCode (0x007f); +data[232] = String.fromCharCode (0x2596); +data[233] = String.fromCharCode (0xfef0); +data[234] = String.fromCharCode (0x6cae); +data[235] = String.fromCharCode (0x200d); +data[236] = String.fromCharCode (0x005f); +data[237] = String.fromCharCode (0x3000); +data[244] = String.fromCharCode (0xfeff); +data[245] = String.fromCharCode (0xffff); +data[246] = String.fromCharCode (0x03ff); +data[266] = String.fromCharCode (0xffff); +data[267] = String.fromCharCode (0xffff); +data[268] = String.fromCharCode (0x003f); +data[269] = String.fromCharCode (0xffff); +data[270] = String.fromCharCode (0xffff); +data[271] = String.fromCharCode (0x007f); +data[272] = String.fromCharCode (0xffff); +data[273] = String.fromCharCode (0xffff); +data[274] = String.fromCharCode (0xffff); +data[275] = String.fromCharCode (0xffff); +data[276] = String.fromCharCode (0xffff); +data[277] = String.fromCharCode (0x83ff); +data[278] = String.fromCharCode (0xffff); +data[279] = String.fromCharCode (0xffff); +data[280] = String.fromCharCode (0xffff); +data[281] = String.fromCharCode (0xffff); +data[282] = String.fromCharCode (0xff07); +data[283] = String.fromCharCode (0xffff); +data[284] = String.fromCharCode (0xffff); +data[285] = String.fromCharCode (0xffff); +data[286] = String.fromCharCode (0xffff); +data[287] = String.fromCharCode (0x03ff); +data[480] = String.fromCharCode (0xffff); +data[481] = String.fromCharCode (0xffff); +data[482] = String.fromCharCode (0xffff); +data[483] = String.fromCharCode (0xffff); +data[484] = String.fromCharCode (0xffff); +data[485] = String.fromCharCode (0xffff); +data[486] = String.fromCharCode (0xffff); +data[487] = String.fromCharCode (0xffff); +data[488] = String.fromCharCode (0xffff); +data[489] = String.fromCharCode (0x0fff); +data[490] = String.fromCharCode (0xffff); +data[491] = String.fromCharCode (0xffff); +data[492] = String.fromCharCode (0xffff); +data[493] = String.fromCharCode (0xffff); +data[494] = String.fromCharCode (0xffff); +data[495] = String.fromCharCode (0x03ff); +data[496] = String.fromCharCode (0xffff); +data[497] = String.fromCharCode (0x3f3f); +data[498] = String.fromCharCode (0xffff); +data[499] = String.fromCharCode (0xffff); +data[500] = String.fromCharCode (0x3f3f); +data[501] = String.fromCharCode (0xaaff); +data[502] = String.fromCharCode (0xffff); +data[503] = String.fromCharCode (0x3fff); +data[504] = String.fromCharCode (0xffff); +data[505] = String.fromCharCode (0xffff); +data[506] = String.fromCharCode (0xffff); +data[507] = String.fromCharCode (0x5fdf); +data[508] = String.fromCharCode (0x1fdc); +data[509] = String.fromCharCode (0x0fcf); +data[510] = String.fromCharCode (0x1fff); +data[511] = String.fromCharCode (0x1fdc); +data[519] = String.fromCharCode (0x8000); +data[528] = String.fromCharCode (0xfc84); +data[529] = String.fromCharCode (0x3f2f); +data[530] = String.fromCharCode (0xfd50); +data[531] = String.fromCharCode (0x01fb); +data[768] = String.fromCharCode (0x0020); +data[771] = String.fromCharCode (0x003e); +data[772] = String.fromCharCode (0xfffe); +data[773] = String.fromCharCode (0xffff); +data[774] = String.fromCharCode (0xffff); +data[775] = String.fromCharCode (0xffff); +data[776] = String.fromCharCode (0xffff); +data[777] = String.fromCharCode (0x781f); +data[778] = String.fromCharCode (0xfffe); +data[779] = String.fromCharCode (0xffff); +data[780] = String.fromCharCode (0xffff); +data[781] = String.fromCharCode (0xffff); +data[782] = String.fromCharCode (0xffff); +data[783] = String.fromCharCode (0x77ff); +data[784] = String.fromCharCode (0xffe0); +data[785] = String.fromCharCode (0xffff); +data[786] = String.fromCharCode (0x1fff); +data[787] = String.fromCharCode (0xfffe); +data[788] = String.fromCharCode (0xffff); +data[789] = String.fromCharCode (0xffff); +data[790] = String.fromCharCode (0xffff); +data[791] = String.fromCharCode (0xffff); +data[792] = String.fromCharCode (0x7fff); +data[1248] = String.fromCharCode (0xffff); +data[1249] = String.fromCharCode (0xffff); +data[1250] = String.fromCharCode (0xffff); +data[1251] = String.fromCharCode (0xffff); +data[1252] = String.fromCharCode (0xffff); +data[1253] = String.fromCharCode (0xffff); +data[1254] = String.fromCharCode (0xffff); +data[1255] = String.fromCharCode (0xffff); +data[1256] = String.fromCharCode (0xffff); +data[1257] = String.fromCharCode (0xffff); +data[1258] = String.fromCharCode (0xffff); +data[1259] = String.fromCharCode (0xffff); +data[1260] = String.fromCharCode (0xffff); +data[1261] = String.fromCharCode (0xffff); +data[1262] = String.fromCharCode (0xffff); +data[1263] = String.fromCharCode (0xffff); +data[1264] = String.fromCharCode (0xffff); +data[1265] = String.fromCharCode (0xffff); +data[1266] = String.fromCharCode (0xffff); +data[1267] = String.fromCharCode (0xffff); +data[1268] = String.fromCharCode (0xffff); +data[1269] = String.fromCharCode (0xffff); +data[1270] = String.fromCharCode (0xffff); +data[1271] = String.fromCharCode (0xffff); +data[1272] = String.fromCharCode (0xffff); +data[1273] = String.fromCharCode (0xffff); +data[1274] = String.fromCharCode (0xffff); +data[1275] = String.fromCharCode (0xffff); +data[1276] = String.fromCharCode (0xffff); +data[1277] = String.fromCharCode (0xffff); +data[1278] = String.fromCharCode (0xffff); +data[1279] = String.fromCharCode (0xffff); +data[1280] = String.fromCharCode (0xffff); +data[1281] = String.fromCharCode (0xffff); +data[1282] = String.fromCharCode (0xffff); +data[1283] = String.fromCharCode (0xffff); +data[1284] = String.fromCharCode (0xffff); +data[1285] = String.fromCharCode (0xffff); +data[1286] = String.fromCharCode (0xffff); +data[1287] = String.fromCharCode (0xffff); +data[1288] = String.fromCharCode (0xffff); +data[1289] = String.fromCharCode (0xffff); +data[1290] = String.fromCharCode (0xffff); +data[1291] = String.fromCharCode (0xffff); +data[1292] = String.fromCharCode (0xffff); +data[1293] = String.fromCharCode (0xffff); +data[1294] = String.fromCharCode (0xffff); +data[1295] = String.fromCharCode (0xffff); +data[1296] = String.fromCharCode (0xffff); +data[1297] = String.fromCharCode (0xffff); +data[1298] = String.fromCharCode (0xffff); +data[1299] = String.fromCharCode (0xffff); +data[1300] = String.fromCharCode (0xffff); +data[1301] = String.fromCharCode (0xffff); +data[1302] = String.fromCharCode (0xffff); +data[1303] = String.fromCharCode (0xffff); +data[1304] = String.fromCharCode (0xffff); +data[1305] = String.fromCharCode (0xffff); +data[1306] = String.fromCharCode (0xffff); +data[1307] = String.fromCharCode (0xffff); +data[1308] = String.fromCharCode (0xffff); +data[1309] = String.fromCharCode (0xffff); +data[1310] = String.fromCharCode (0xffff); +data[1311] = String.fromCharCode (0xffff); +data[1312] = String.fromCharCode (0xffff); +data[1313] = String.fromCharCode (0xffff); +data[1314] = String.fromCharCode (0xffff); +data[1315] = String.fromCharCode (0xffff); +data[1316] = String.fromCharCode (0xffff); +data[1317] = String.fromCharCode (0xffff); +data[1318] = String.fromCharCode (0xffff); +data[1319] = String.fromCharCode (0xffff); +data[1320] = String.fromCharCode (0xffff); +data[1321] = String.fromCharCode (0xffff); +data[1322] = String.fromCharCode (0xffff); +data[1323] = String.fromCharCode (0xffff); +data[1324] = String.fromCharCode (0xffff); +data[1325] = String.fromCharCode (0xffff); +data[1326] = String.fromCharCode (0xffff); +data[1327] = String.fromCharCode (0xffff); +data[1328] = String.fromCharCode (0xffff); +data[1329] = String.fromCharCode (0xffff); +data[1330] = String.fromCharCode (0xffff); +data[1331] = String.fromCharCode (0xffff); +data[1332] = String.fromCharCode (0xffff); +data[1333] = String.fromCharCode (0xffff); +data[1334] = String.fromCharCode (0xffff); +data[1335] = String.fromCharCode (0xffff); +data[1336] = String.fromCharCode (0xffff); +data[1337] = String.fromCharCode (0xffff); +data[1338] = String.fromCharCode (0xffff); +data[1339] = String.fromCharCode (0xffff); +data[1340] = String.fromCharCode (0xffff); +data[1341] = String.fromCharCode (0xffff); +data[1342] = String.fromCharCode (0xffff); +data[1343] = String.fromCharCode (0xffff); +data[1344] = String.fromCharCode (0xffff); +data[1345] = String.fromCharCode (0xffff); +data[1346] = String.fromCharCode (0xffff); +data[1347] = String.fromCharCode (0xffff); +data[1348] = String.fromCharCode (0xffff); +data[1349] = String.fromCharCode (0xffff); +data[1350] = String.fromCharCode (0xffff); +data[1351] = String.fromCharCode (0xffff); +data[1352] = String.fromCharCode (0xffff); +data[1353] = String.fromCharCode (0xffff); +data[1354] = String.fromCharCode (0xffff); +data[1355] = String.fromCharCode (0xffff); +data[1356] = String.fromCharCode (0xffff); +data[1357] = String.fromCharCode (0xffff); +data[1358] = String.fromCharCode (0xffff); +data[1359] = String.fromCharCode (0xffff); +data[1360] = String.fromCharCode (0xffff); +data[1361] = String.fromCharCode (0xffff); +data[1362] = String.fromCharCode (0xffff); +data[1363] = String.fromCharCode (0xffff); +data[1364] = String.fromCharCode (0xffff); +data[1365] = String.fromCharCode (0xffff); +data[1366] = String.fromCharCode (0xffff); +data[1367] = String.fromCharCode (0xffff); +data[1368] = String.fromCharCode (0xffff); +data[1369] = String.fromCharCode (0xffff); +data[1370] = String.fromCharCode (0xffff); +data[1371] = String.fromCharCode (0xffff); +data[1372] = String.fromCharCode (0xffff); +data[1373] = String.fromCharCode (0xffff); +data[1374] = String.fromCharCode (0xffff); +data[1375] = String.fromCharCode (0xffff); +data[1376] = String.fromCharCode (0xffff); +data[1377] = String.fromCharCode (0xffff); +data[1378] = String.fromCharCode (0xffff); +data[1379] = String.fromCharCode (0xffff); +data[1380] = String.fromCharCode (0xffff); +data[1381] = String.fromCharCode (0xffff); +data[1382] = String.fromCharCode (0xffff); +data[1383] = String.fromCharCode (0xffff); +data[1384] = String.fromCharCode (0xffff); +data[1385] = String.fromCharCode (0xffff); +data[1386] = String.fromCharCode (0xffff); +data[1387] = String.fromCharCode (0xffff); +data[1388] = String.fromCharCode (0xffff); +data[1389] = String.fromCharCode (0xffff); +data[1390] = String.fromCharCode (0xffff); +data[1391] = String.fromCharCode (0xffff); +data[1392] = String.fromCharCode (0xffff); +data[1393] = String.fromCharCode (0xffff); +data[1394] = String.fromCharCode (0xffff); +data[1395] = String.fromCharCode (0xffff); +data[1396] = String.fromCharCode (0xffff); +data[1397] = String.fromCharCode (0xffff); +data[1398] = String.fromCharCode (0xffff); +data[1399] = String.fromCharCode (0xffff); +data[1400] = String.fromCharCode (0xffff); +data[1401] = String.fromCharCode (0xffff); +data[1402] = String.fromCharCode (0xffff); +data[1403] = String.fromCharCode (0xffff); +data[1404] = String.fromCharCode (0xffff); +data[1405] = String.fromCharCode (0xffff); +data[1406] = String.fromCharCode (0xffff); +data[1407] = String.fromCharCode (0xffff); +data[1408] = String.fromCharCode (0xffff); +data[1409] = String.fromCharCode (0xffff); +data[1410] = String.fromCharCode (0xffff); +data[1411] = String.fromCharCode (0xffff); +data[1412] = String.fromCharCode (0xffff); +data[1413] = String.fromCharCode (0xffff); +data[1414] = String.fromCharCode (0xffff); +data[1415] = String.fromCharCode (0xffff); +data[1416] = String.fromCharCode (0xffff); +data[1417] = String.fromCharCode (0xffff); +data[1418] = String.fromCharCode (0xffff); +data[1419] = String.fromCharCode (0xffff); +data[1420] = String.fromCharCode (0xffff); +data[1421] = String.fromCharCode (0xffff); +data[1422] = String.fromCharCode (0xffff); +data[1423] = String.fromCharCode (0xffff); +data[1424] = String.fromCharCode (0xffff); +data[1425] = String.fromCharCode (0xffff); +data[1426] = String.fromCharCode (0xffff); +data[1427] = String.fromCharCode (0xffff); +data[1428] = String.fromCharCode (0xffff); +data[1429] = String.fromCharCode (0xffff); +data[1430] = String.fromCharCode (0xffff); +data[1431] = String.fromCharCode (0xffff); +data[1432] = String.fromCharCode (0xffff); +data[1433] = String.fromCharCode (0xffff); +data[1434] = String.fromCharCode (0xffff); +data[1435] = String.fromCharCode (0xffff); +data[1436] = String.fromCharCode (0xffff); +data[1437] = String.fromCharCode (0xffff); +data[1438] = String.fromCharCode (0xffff); +data[1439] = String.fromCharCode (0xffff); +data[1440] = String.fromCharCode (0xffff); +data[1441] = String.fromCharCode (0xffff); +data[1442] = String.fromCharCode (0xffff); +data[1443] = String.fromCharCode (0xffff); +data[1444] = String.fromCharCode (0xffff); +data[1445] = String.fromCharCode (0xffff); +data[1446] = String.fromCharCode (0xffff); +data[1447] = String.fromCharCode (0xffff); +data[1448] = String.fromCharCode (0xffff); +data[1449] = String.fromCharCode (0xffff); +data[1450] = String.fromCharCode (0xffff); +data[1451] = String.fromCharCode (0xffff); +data[1452] = String.fromCharCode (0xffff); +data[1453] = String.fromCharCode (0xffff); +data[1454] = String.fromCharCode (0xffff); +data[1455] = String.fromCharCode (0xffff); +data[1456] = String.fromCharCode (0xffff); +data[1457] = String.fromCharCode (0xffff); +data[1458] = String.fromCharCode (0xffff); +data[1459] = String.fromCharCode (0xffff); +data[1460] = String.fromCharCode (0xffff); +data[1461] = String.fromCharCode (0xffff); +data[1462] = String.fromCharCode (0xffff); +data[1463] = String.fromCharCode (0xffff); +data[1464] = String.fromCharCode (0xffff); +data[1465] = String.fromCharCode (0xffff); +data[1466] = String.fromCharCode (0xffff); +data[1467] = String.fromCharCode (0xffff); +data[1468] = String.fromCharCode (0xffff); +data[1469] = String.fromCharCode (0xffff); +data[1470] = String.fromCharCode (0xffff); +data[1471] = String.fromCharCode (0xffff); +data[1472] = String.fromCharCode (0xffff); +data[1473] = String.fromCharCode (0xffff); +data[1474] = String.fromCharCode (0xffff); +data[1475] = String.fromCharCode (0xffff); +data[1476] = String.fromCharCode (0xffff); +data[1477] = String.fromCharCode (0xffff); +data[1478] = String.fromCharCode (0xffff); +data[1479] = String.fromCharCode (0xffff); +data[1480] = String.fromCharCode (0xffff); +data[1481] = String.fromCharCode (0xffff); +data[1482] = String.fromCharCode (0xffff); +data[1483] = String.fromCharCode (0xffff); +data[1484] = String.fromCharCode (0xffff); +data[1485] = String.fromCharCode (0xffff); +data[1486] = String.fromCharCode (0xffff); +data[1487] = String.fromCharCode (0xffff); +data[1488] = String.fromCharCode (0xffff); +data[1489] = String.fromCharCode (0xffff); +data[1490] = String.fromCharCode (0xffff); +data[1491] = String.fromCharCode (0xffff); +data[1492] = String.fromCharCode (0xffff); +data[1493] = String.fromCharCode (0xffff); +data[1494] = String.fromCharCode (0xffff); +data[1495] = String.fromCharCode (0xffff); +data[1496] = String.fromCharCode (0xffff); +data[1497] = String.fromCharCode (0xffff); +data[1498] = String.fromCharCode (0xffff); +data[1499] = String.fromCharCode (0xffff); +data[1500] = String.fromCharCode (0xffff); +data[1501] = String.fromCharCode (0xffff); +data[1502] = String.fromCharCode (0xffff); +data[1503] = String.fromCharCode (0xffff); +data[1504] = String.fromCharCode (0xffff); +data[1505] = String.fromCharCode (0xffff); +data[1506] = String.fromCharCode (0xffff); +data[1507] = String.fromCharCode (0xffff); +data[1508] = String.fromCharCode (0xffff); +data[1509] = String.fromCharCode (0xffff); +data[1510] = String.fromCharCode (0xffff); +data[1511] = String.fromCharCode (0xffff); +data[1512] = String.fromCharCode (0xffff); +data[1513] = String.fromCharCode (0xffff); +data[1514] = String.fromCharCode (0xffff); +data[1515] = String.fromCharCode (0xffff); +data[1516] = String.fromCharCode (0xffff); +data[1517] = String.fromCharCode (0xffff); +data[1518] = String.fromCharCode (0xffff); +data[1519] = String.fromCharCode (0xffff); +data[1520] = String.fromCharCode (0xffff); +data[1521] = String.fromCharCode (0xffff); +data[1522] = String.fromCharCode (0xffff); +data[1523] = String.fromCharCode (0xffff); +data[1524] = String.fromCharCode (0xffff); +data[1525] = String.fromCharCode (0xffff); +data[1526] = String.fromCharCode (0xffff); +data[1527] = String.fromCharCode (0xffff); +data[1528] = String.fromCharCode (0xffff); +data[1529] = String.fromCharCode (0xffff); +data[1530] = String.fromCharCode (0xffff); +data[1531] = String.fromCharCode (0xffff); +data[1532] = String.fromCharCode (0xffff); +data[1533] = String.fromCharCode (0xffff); +data[1534] = String.fromCharCode (0xffff); +data[1535] = String.fromCharCode (0xffff); +data[1536] = String.fromCharCode (0xffff); +data[1537] = String.fromCharCode (0xffff); +data[1538] = String.fromCharCode (0xffff); +data[1539] = String.fromCharCode (0xffff); +data[1540] = String.fromCharCode (0xffff); +data[1541] = String.fromCharCode (0xffff); +data[1542] = String.fromCharCode (0xffff); +data[1543] = String.fromCharCode (0xffff); +data[1544] = String.fromCharCode (0xffff); +data[1545] = String.fromCharCode (0xffff); +data[1546] = String.fromCharCode (0xffff); +data[1547] = String.fromCharCode (0xffff); +data[1548] = String.fromCharCode (0xffff); +data[1549] = String.fromCharCode (0xffff); +data[1550] = String.fromCharCode (0xffff); +data[1551] = String.fromCharCode (0xffff); +data[1552] = String.fromCharCode (0xffff); +data[1553] = String.fromCharCode (0xffff); +data[1554] = String.fromCharCode (0xffff); +data[1555] = String.fromCharCode (0xffff); +data[1556] = String.fromCharCode (0xffff); +data[1557] = String.fromCharCode (0xffff); +data[1558] = String.fromCharCode (0xffff); +data[1559] = String.fromCharCode (0xffff); +data[1560] = String.fromCharCode (0xffff); +data[1561] = String.fromCharCode (0xffff); +data[1562] = String.fromCharCode (0xffff); +data[1563] = String.fromCharCode (0xffff); +data[1564] = String.fromCharCode (0xffff); +data[1565] = String.fromCharCode (0xffff); +data[1566] = String.fromCharCode (0xffff); +data[1567] = String.fromCharCode (0xffff); +data[1568] = String.fromCharCode (0xffff); +data[1569] = String.fromCharCode (0xffff); +data[1570] = String.fromCharCode (0xffff); +data[1571] = String.fromCharCode (0xffff); +data[1572] = String.fromCharCode (0xffff); +data[1573] = String.fromCharCode (0xffff); +data[1574] = String.fromCharCode (0xffff); +data[1575] = String.fromCharCode (0xffff); +data[1576] = String.fromCharCode (0xffff); +data[1577] = String.fromCharCode (0xffff); +data[1578] = String.fromCharCode (0xffff); +data[1579] = String.fromCharCode (0xffff); +data[1580] = String.fromCharCode (0xffff); +data[1581] = String.fromCharCode (0xffff); +data[1582] = String.fromCharCode (0xffff); +data[1583] = String.fromCharCode (0xffff); +data[1584] = String.fromCharCode (0xffff); +data[1585] = String.fromCharCode (0xffff); +data[1586] = String.fromCharCode (0xffff); +data[1587] = String.fromCharCode (0xffff); +data[1588] = String.fromCharCode (0xffff); +data[1589] = String.fromCharCode (0xffff); +data[1590] = String.fromCharCode (0xffff); +data[1591] = String.fromCharCode (0xffff); +data[1592] = String.fromCharCode (0xffff); +data[1593] = String.fromCharCode (0xffff); +data[1594] = String.fromCharCode (0xffff); +data[1595] = String.fromCharCode (0xffff); +data[1596] = String.fromCharCode (0xffff); +data[1597] = String.fromCharCode (0xffff); +data[1598] = String.fromCharCode (0xffff); +data[1599] = String.fromCharCode (0xffff); +data[1600] = String.fromCharCode (0xffff); +data[1601] = String.fromCharCode (0xffff); +data[1602] = String.fromCharCode (0xffff); +data[1603] = String.fromCharCode (0xffff); +data[1604] = String.fromCharCode (0xffff); +data[1605] = String.fromCharCode (0xffff); +data[1606] = String.fromCharCode (0xffff); +data[1607] = String.fromCharCode (0xffff); +data[1608] = String.fromCharCode (0xffff); +data[1609] = String.fromCharCode (0xffff); +data[1610] = String.fromCharCode (0xffff); +data[1611] = String.fromCharCode (0xffff); +data[1612] = String.fromCharCode (0xffff); +data[1613] = String.fromCharCode (0xffff); +data[1614] = String.fromCharCode (0xffff); +data[1615] = String.fromCharCode (0xffff); +data[1616] = String.fromCharCode (0xffff); +data[1617] = String.fromCharCode (0xffff); +data[1618] = String.fromCharCode (0xffff); +data[1619] = String.fromCharCode (0xffff); +data[1620] = String.fromCharCode (0xffff); +data[1621] = String.fromCharCode (0xffff); +data[1622] = String.fromCharCode (0xffff); +data[1623] = String.fromCharCode (0xffff); +data[1624] = String.fromCharCode (0xffff); +data[1625] = String.fromCharCode (0xffff); +data[1626] = String.fromCharCode (0xffff); +data[1627] = String.fromCharCode (0xffff); +data[1628] = String.fromCharCode (0xffff); +data[1629] = String.fromCharCode (0xffff); +data[1630] = String.fromCharCode (0xffff); +data[1631] = String.fromCharCode (0xffff); +data[1632] = String.fromCharCode (0xffff); +data[1633] = String.fromCharCode (0xffff); +data[1634] = String.fromCharCode (0xffff); +data[1635] = String.fromCharCode (0xffff); +data[1636] = String.fromCharCode (0xffff); +data[1637] = String.fromCharCode (0xffff); +data[1638] = String.fromCharCode (0xffff); +data[1639] = String.fromCharCode (0xffff); +data[1640] = String.fromCharCode (0xffff); +data[1641] = String.fromCharCode (0xffff); +data[1642] = String.fromCharCode (0xffff); +data[1643] = String.fromCharCode (0xffff); +data[1644] = String.fromCharCode (0xffff); +data[1645] = String.fromCharCode (0xffff); +data[1646] = String.fromCharCode (0xffff); +data[1647] = String.fromCharCode (0xffff); +data[1648] = String.fromCharCode (0xffff); +data[1649] = String.fromCharCode (0xffff); +data[1650] = String.fromCharCode (0xffff); +data[1651] = String.fromCharCode (0xffff); +data[1652] = String.fromCharCode (0xffff); +data[1653] = String.fromCharCode (0xffff); +data[1654] = String.fromCharCode (0xffff); +data[1655] = String.fromCharCode (0xffff); +data[1656] = String.fromCharCode (0xffff); +data[1657] = String.fromCharCode (0xffff); +data[1658] = String.fromCharCode (0xffff); +data[1659] = String.fromCharCode (0xffff); +data[1660] = String.fromCharCode (0xffff); +data[1661] = String.fromCharCode (0xffff); +data[1662] = String.fromCharCode (0xffff); +data[1663] = String.fromCharCode (0xffff); +data[1664] = String.fromCharCode (0xffff); +data[1665] = String.fromCharCode (0xffff); +data[1666] = String.fromCharCode (0xffff); +data[1667] = String.fromCharCode (0xffff); +data[1668] = String.fromCharCode (0xffff); +data[1669] = String.fromCharCode (0xffff); +data[1670] = String.fromCharCode (0xffff); +data[1671] = String.fromCharCode (0xffff); +data[1672] = String.fromCharCode (0xffff); +data[1673] = String.fromCharCode (0xffff); +data[1674] = String.fromCharCode (0xffff); +data[1675] = String.fromCharCode (0xffff); +data[1676] = String.fromCharCode (0xffff); +data[1677] = String.fromCharCode (0xffff); +data[1678] = String.fromCharCode (0xffff); +data[1679] = String.fromCharCode (0xffff); +data[1680] = String.fromCharCode (0xffff); +data[1681] = String.fromCharCode (0xffff); +data[1682] = String.fromCharCode (0xffff); +data[1683] = String.fromCharCode (0xffff); +data[1684] = String.fromCharCode (0xffff); +data[1685] = String.fromCharCode (0xffff); +data[1686] = String.fromCharCode (0xffff); +data[1687] = String.fromCharCode (0xffff); +data[1688] = String.fromCharCode (0xffff); +data[1689] = String.fromCharCode (0xffff); +data[1690] = String.fromCharCode (0xffff); +data[1691] = String.fromCharCode (0xffff); +data[1692] = String.fromCharCode (0xffff); +data[1693] = String.fromCharCode (0xffff); +data[1694] = String.fromCharCode (0xffff); +data[1695] = String.fromCharCode (0xffff); +data[1696] = String.fromCharCode (0xffff); +data[1697] = String.fromCharCode (0xffff); +data[1698] = String.fromCharCode (0xffff); +data[1699] = String.fromCharCode (0xffff); +data[1700] = String.fromCharCode (0xffff); +data[1701] = String.fromCharCode (0xffff); +data[1702] = String.fromCharCode (0xffff); +data[1703] = String.fromCharCode (0xffff); +data[1704] = String.fromCharCode (0xffff); +data[1705] = String.fromCharCode (0xffff); +data[1706] = String.fromCharCode (0xffff); +data[1707] = String.fromCharCode (0xffff); +data[1708] = String.fromCharCode (0xffff); +data[1709] = String.fromCharCode (0xffff); +data[1710] = String.fromCharCode (0xffff); +data[1711] = String.fromCharCode (0xffff); +data[1712] = String.fromCharCode (0xffff); +data[1713] = String.fromCharCode (0xffff); +data[1714] = String.fromCharCode (0xffff); +data[1715] = String.fromCharCode (0xffff); +data[1716] = String.fromCharCode (0xffff); +data[1717] = String.fromCharCode (0xffff); +data[1718] = String.fromCharCode (0xffff); +data[1719] = String.fromCharCode (0xffff); +data[1720] = String.fromCharCode (0xffff); +data[1721] = String.fromCharCode (0xffff); +data[1722] = String.fromCharCode (0xffff); +data[1723] = String.fromCharCode (0xffff); +data[1724] = String.fromCharCode (0xffff); +data[1725] = String.fromCharCode (0xffff); +data[1726] = String.fromCharCode (0xffff); +data[1727] = String.fromCharCode (0xffff); +data[1728] = String.fromCharCode (0xffff); +data[1729] = String.fromCharCode (0xffff); +data[1730] = String.fromCharCode (0xffff); +data[1731] = String.fromCharCode (0xffff); +data[1732] = String.fromCharCode (0xffff); +data[1733] = String.fromCharCode (0xffff); +data[1734] = String.fromCharCode (0xffff); +data[1735] = String.fromCharCode (0xffff); +data[1736] = String.fromCharCode (0xffff); +data[1737] = String.fromCharCode (0xffff); +data[1738] = String.fromCharCode (0xffff); +data[1739] = String.fromCharCode (0xffff); +data[1740] = String.fromCharCode (0xffff); +data[1741] = String.fromCharCode (0xffff); +data[1742] = String.fromCharCode (0xffff); +data[1743] = String.fromCharCode (0xffff); +data[1744] = String.fromCharCode (0xffff); +data[1745] = String.fromCharCode (0xffff); +data[1746] = String.fromCharCode (0xffff); +data[1747] = String.fromCharCode (0xffff); +data[1748] = String.fromCharCode (0xffff); +data[1749] = String.fromCharCode (0xffff); +data[1750] = String.fromCharCode (0xffff); +data[1751] = String.fromCharCode (0xffff); +data[1752] = String.fromCharCode (0xffff); +data[1753] = String.fromCharCode (0xffff); +data[1754] = String.fromCharCode (0xffff); +data[1755] = String.fromCharCode (0xffff); +data[1756] = String.fromCharCode (0xffff); +data[1757] = String.fromCharCode (0xffff); +data[1758] = String.fromCharCode (0xffff); +data[1759] = String.fromCharCode (0xffff); +data[1760] = String.fromCharCode (0xffff); +data[1761] = String.fromCharCode (0xffff); +data[1762] = String.fromCharCode (0xffff); +data[1763] = String.fromCharCode (0xffff); +data[1764] = String.fromCharCode (0xffff); +data[1765] = String.fromCharCode (0xffff); +data[1766] = String.fromCharCode (0xffff); +data[1767] = String.fromCharCode (0xffff); +data[1768] = String.fromCharCode (0xffff); +data[1769] = String.fromCharCode (0xffff); +data[1770] = String.fromCharCode (0xffff); +data[1771] = String.fromCharCode (0xffff); +data[1772] = String.fromCharCode (0xffff); +data[1773] = String.fromCharCode (0xffff); +data[1774] = String.fromCharCode (0xffff); +data[1775] = String.fromCharCode (0xffff); +data[1776] = String.fromCharCode (0xffff); +data[1777] = String.fromCharCode (0xffff); +data[1778] = String.fromCharCode (0xffff); +data[1779] = String.fromCharCode (0xffff); +data[1780] = String.fromCharCode (0xffff); +data[1781] = String.fromCharCode (0xffff); +data[1782] = String.fromCharCode (0xffff); +data[1783] = String.fromCharCode (0xffff); +data[1784] = String.fromCharCode (0xffff); +data[1785] = String.fromCharCode (0xffff); +data[1786] = String.fromCharCode (0xffff); +data[1787] = String.fromCharCode (0xffff); +data[1788] = String.fromCharCode (0xffff); +data[1789] = String.fromCharCode (0xffff); +data[1790] = String.fromCharCode (0xffff); +data[1791] = String.fromCharCode (0xffff); +data[1792] = String.fromCharCode (0xffff); +data[1793] = String.fromCharCode (0xffff); +data[1794] = String.fromCharCode (0xffff); +data[1795] = String.fromCharCode (0xffff); +data[1796] = String.fromCharCode (0xffff); +data[1797] = String.fromCharCode (0xffff); +data[1798] = String.fromCharCode (0xffff); +data[1799] = String.fromCharCode (0xffff); +data[1800] = String.fromCharCode (0xffff); +data[1801] = String.fromCharCode (0xffff); +data[1802] = String.fromCharCode (0xffff); +data[1803] = String.fromCharCode (0xffff); +data[1804] = String.fromCharCode (0xffff); +data[1805] = String.fromCharCode (0xffff); +data[1806] = String.fromCharCode (0xffff); +data[1807] = String.fromCharCode (0xffff); +data[1808] = String.fromCharCode (0xffff); +data[1809] = String.fromCharCode (0xffff); +data[1810] = String.fromCharCode (0xffff); +data[1811] = String.fromCharCode (0xffff); +data[1812] = String.fromCharCode (0xffff); +data[1813] = String.fromCharCode (0xffff); +data[1814] = String.fromCharCode (0xffff); +data[1815] = String.fromCharCode (0xffff); +data[1816] = String.fromCharCode (0xffff); +data[1817] = String.fromCharCode (0xffff); +data[1818] = String.fromCharCode (0xffff); +data[1819] = String.fromCharCode (0xffff); +data[1820] = String.fromCharCode (0xffff); +data[1821] = String.fromCharCode (0xffff); +data[1822] = String.fromCharCode (0xffff); +data[1823] = String.fromCharCode (0xffff); +data[1824] = String.fromCharCode (0xffff); +data[1825] = String.fromCharCode (0xffff); +data[1826] = String.fromCharCode (0xffff); +data[1827] = String.fromCharCode (0xffff); +data[1828] = String.fromCharCode (0xffff); +data[1829] = String.fromCharCode (0xffff); +data[1830] = String.fromCharCode (0xffff); +data[1831] = String.fromCharCode (0xffff); +data[1832] = String.fromCharCode (0xffff); +data[1833] = String.fromCharCode (0xffff); +data[1834] = String.fromCharCode (0xffff); +data[1835] = String.fromCharCode (0xffff); +data[1836] = String.fromCharCode (0xffff); +data[1837] = String.fromCharCode (0xffff); +data[1838] = String.fromCharCode (0xffff); +data[1839] = String.fromCharCode (0xffff); +data[1840] = String.fromCharCode (0xffff); +data[1841] = String.fromCharCode (0xffff); +data[1842] = String.fromCharCode (0xffff); +data[1843] = String.fromCharCode (0xffff); +data[1844] = String.fromCharCode (0xffff); +data[1845] = String.fromCharCode (0xffff); +data[1846] = String.fromCharCode (0xffff); +data[1847] = String.fromCharCode (0xffff); +data[1848] = String.fromCharCode (0xffff); +data[1849] = String.fromCharCode (0xffff); +data[1850] = String.fromCharCode (0xffff); +data[1851] = String.fromCharCode (0xffff); +data[1852] = String.fromCharCode (0xffff); +data[1853] = String.fromCharCode (0xffff); +data[1854] = String.fromCharCode (0xffff); +data[1855] = String.fromCharCode (0xffff); +data[1856] = String.fromCharCode (0xffff); +data[1857] = String.fromCharCode (0xffff); +data[1858] = String.fromCharCode (0xffff); +data[1859] = String.fromCharCode (0xffff); +data[1860] = String.fromCharCode (0xffff); +data[1861] = String.fromCharCode (0xffff); +data[1862] = String.fromCharCode (0xffff); +data[1863] = String.fromCharCode (0xffff); +data[1864] = String.fromCharCode (0xffff); +data[1865] = String.fromCharCode (0xffff); +data[1866] = String.fromCharCode (0xffff); +data[1867] = String.fromCharCode (0xffff); +data[1868] = String.fromCharCode (0xffff); +data[1869] = String.fromCharCode (0xffff); +data[1870] = String.fromCharCode (0xffff); +data[1871] = String.fromCharCode (0xffff); +data[1872] = String.fromCharCode (0xffff); +data[1873] = String.fromCharCode (0xffff); +data[1874] = String.fromCharCode (0xffff); +data[1875] = String.fromCharCode (0xffff); +data[1876] = String.fromCharCode (0xffff); +data[1877] = String.fromCharCode (0xffff); +data[1878] = String.fromCharCode (0xffff); +data[1879] = String.fromCharCode (0xffff); +data[1880] = String.fromCharCode (0xffff); +data[1881] = String.fromCharCode (0xffff); +data[1882] = String.fromCharCode (0xffff); +data[1883] = String.fromCharCode (0xffff); +data[1884] = String.fromCharCode (0xffff); +data[1885] = String.fromCharCode (0xffff); +data[1886] = String.fromCharCode (0xffff); +data[1887] = String.fromCharCode (0xffff); +data[1888] = String.fromCharCode (0xffff); +data[1889] = String.fromCharCode (0xffff); +data[1890] = String.fromCharCode (0xffff); +data[1891] = String.fromCharCode (0xffff); +data[1892] = String.fromCharCode (0xffff); +data[1893] = String.fromCharCode (0xffff); +data[1894] = String.fromCharCode (0xffff); +data[1895] = String.fromCharCode (0xffff); +data[1896] = String.fromCharCode (0xffff); +data[1897] = String.fromCharCode (0xffff); +data[1898] = String.fromCharCode (0xffff); +data[1899] = String.fromCharCode (0xffff); +data[1900] = String.fromCharCode (0xffff); +data[1901] = String.fromCharCode (0xffff); +data[1902] = String.fromCharCode (0xffff); +data[1903] = String.fromCharCode (0xffff); +data[1904] = String.fromCharCode (0xffff); +data[1905] = String.fromCharCode (0xffff); +data[1906] = String.fromCharCode (0xffff); +data[1907] = String.fromCharCode (0xffff); +data[1908] = String.fromCharCode (0xffff); +data[1909] = String.fromCharCode (0xffff); +data[1910] = String.fromCharCode (0xffff); +data[1911] = String.fromCharCode (0xffff); +data[1912] = String.fromCharCode (0xffff); +data[1913] = String.fromCharCode (0xffff); +data[1914] = String.fromCharCode (0xffff); +data[1915] = String.fromCharCode (0xffff); +data[1916] = String.fromCharCode (0xffff); +data[1917] = String.fromCharCode (0xffff); +data[1918] = String.fromCharCode (0xffff); +data[1919] = String.fromCharCode (0xffff); +data[1920] = String.fromCharCode (0xffff); +data[1921] = String.fromCharCode (0xffff); +data[1922] = String.fromCharCode (0xffff); +data[1923] = String.fromCharCode (0xffff); +data[1924] = String.fromCharCode (0xffff); +data[1925] = String.fromCharCode (0xffff); +data[1926] = String.fromCharCode (0xffff); +data[1927] = String.fromCharCode (0xffff); +data[1928] = String.fromCharCode (0xffff); +data[1929] = String.fromCharCode (0xffff); +data[1930] = String.fromCharCode (0xffff); +data[1931] = String.fromCharCode (0xffff); +data[1932] = String.fromCharCode (0xffff); +data[1933] = String.fromCharCode (0xffff); +data[1934] = String.fromCharCode (0xffff); +data[1935] = String.fromCharCode (0xffff); +data[1936] = String.fromCharCode (0xffff); +data[1937] = String.fromCharCode (0xffff); +data[1938] = String.fromCharCode (0xffff); +data[1939] = String.fromCharCode (0xffff); +data[1940] = String.fromCharCode (0xffff); +data[1941] = String.fromCharCode (0xffff); +data[1942] = String.fromCharCode (0xffff); +data[1943] = String.fromCharCode (0xffff); +data[1944] = String.fromCharCode (0xffff); +data[1945] = String.fromCharCode (0xffff); +data[1946] = String.fromCharCode (0xffff); +data[1947] = String.fromCharCode (0xffff); +data[1948] = String.fromCharCode (0xffff); +data[1949] = String.fromCharCode (0xffff); +data[1950] = String.fromCharCode (0xffff); +data[1951] = String.fromCharCode (0xffff); +data[1952] = String.fromCharCode (0xffff); +data[1953] = String.fromCharCode (0xffff); +data[1954] = String.fromCharCode (0xffff); +data[1955] = String.fromCharCode (0xffff); +data[1956] = String.fromCharCode (0xffff); +data[1957] = String.fromCharCode (0xffff); +data[1958] = String.fromCharCode (0xffff); +data[1959] = String.fromCharCode (0xffff); +data[1960] = String.fromCharCode (0xffff); +data[1961] = String.fromCharCode (0xffff); +data[1962] = String.fromCharCode (0xffff); +data[1963] = String.fromCharCode (0xffff); +data[1964] = String.fromCharCode (0xffff); +data[1965] = String.fromCharCode (0xffff); +data[1966] = String.fromCharCode (0xffff); +data[1967] = String.fromCharCode (0xffff); +data[1968] = String.fromCharCode (0xffff); +data[1969] = String.fromCharCode (0xffff); +data[1970] = String.fromCharCode (0xffff); +data[1971] = String.fromCharCode (0xffff); +data[1972] = String.fromCharCode (0xffff); +data[1973] = String.fromCharCode (0xffff); +data[1974] = String.fromCharCode (0xffff); +data[1975] = String.fromCharCode (0xffff); +data[1976] = String.fromCharCode (0xffff); +data[1977] = String.fromCharCode (0xffff); +data[1978] = String.fromCharCode (0xffff); +data[1979] = String.fromCharCode (0xffff); +data[1980] = String.fromCharCode (0xffff); +data[1981] = String.fromCharCode (0xffff); +data[1982] = String.fromCharCode (0xffff); +data[1983] = String.fromCharCode (0xffff); +data[1984] = String.fromCharCode (0xffff); +data[1985] = String.fromCharCode (0xffff); +data[1986] = String.fromCharCode (0xffff); +data[1987] = String.fromCharCode (0xffff); +data[1988] = String.fromCharCode (0xffff); +data[1989] = String.fromCharCode (0xffff); +data[1990] = String.fromCharCode (0xffff); +data[1991] = String.fromCharCode (0xffff); +data[1992] = String.fromCharCode (0xffff); +data[1993] = String.fromCharCode (0xffff); +data[1994] = String.fromCharCode (0xffff); +data[1995] = String.fromCharCode (0xffff); +data[1996] = String.fromCharCode (0xffff); +data[1997] = String.fromCharCode (0xffff); +data[1998] = String.fromCharCode (0xffff); +data[1999] = String.fromCharCode (0xffff); +data[2000] = String.fromCharCode (0xffff); +data[2001] = String.fromCharCode (0xffff); +data[2002] = String.fromCharCode (0xffff); +data[2003] = String.fromCharCode (0xffff); +data[2004] = String.fromCharCode (0xffff); +data[2005] = String.fromCharCode (0xffff); +data[2006] = String.fromCharCode (0xffff); +data[2007] = String.fromCharCode (0xffff); +data[2008] = String.fromCharCode (0xffff); +data[2009] = String.fromCharCode (0xffff); +data[2010] = String.fromCharCode (0xffff); +data[2011] = String.fromCharCode (0xffff); +data[2012] = String.fromCharCode (0xffff); +data[2013] = String.fromCharCode (0xffff); +data[2014] = String.fromCharCode (0xffff); +data[2015] = String.fromCharCode (0xffff); +data[2016] = String.fromCharCode (0xffff); +data[2017] = String.fromCharCode (0xffff); +data[2018] = String.fromCharCode (0xffff); +data[2019] = String.fromCharCode (0xffff); +data[2020] = String.fromCharCode (0xffff); +data[2021] = String.fromCharCode (0xffff); +data[2022] = String.fromCharCode (0xffff); +data[2023] = String.fromCharCode (0xffff); +data[2024] = String.fromCharCode (0xffff); +data[2025] = String.fromCharCode (0xffff); +data[2026] = String.fromCharCode (0xffff); +data[2027] = String.fromCharCode (0xffff); +data[2028] = String.fromCharCode (0xffff); +data[2029] = String.fromCharCode (0xffff); +data[2030] = String.fromCharCode (0xffff); +data[2031] = String.fromCharCode (0xffff); +data[2032] = String.fromCharCode (0xffff); +data[2033] = String.fromCharCode (0xffff); +data[2034] = String.fromCharCode (0xffff); +data[2035] = String.fromCharCode (0xffff); +data[2036] = String.fromCharCode (0xffff); +data[2037] = String.fromCharCode (0xffff); +data[2038] = String.fromCharCode (0xffff); +data[2039] = String.fromCharCode (0xffff); +data[2040] = String.fromCharCode (0xffff); +data[2041] = String.fromCharCode (0xffff); +data[2042] = String.fromCharCode (0xffff); +data[2043] = String.fromCharCode (0xffff); +data[2044] = String.fromCharCode (0xffff); +data[2045] = String.fromCharCode (0xffff); +data[2046] = String.fromCharCode (0xffff); +data[2047] = String.fromCharCode (0xffff); +data[2048] = String.fromCharCode (0xffff); +data[2049] = String.fromCharCode (0xffff); +data[2050] = String.fromCharCode (0xffff); +data[2051] = String.fromCharCode (0xffff); +data[2052] = String.fromCharCode (0xffff); +data[2053] = String.fromCharCode (0xffff); +data[2054] = String.fromCharCode (0xffff); +data[2055] = String.fromCharCode (0xffff); +data[2056] = String.fromCharCode (0xffff); +data[2057] = String.fromCharCode (0xffff); +data[2058] = String.fromCharCode (0xffff); +data[2059] = String.fromCharCode (0xffff); +data[2060] = String.fromCharCode (0xffff); +data[2061] = String.fromCharCode (0xffff); +data[2062] = String.fromCharCode (0xffff); +data[2063] = String.fromCharCode (0xffff); +data[2064] = String.fromCharCode (0xffff); +data[2065] = String.fromCharCode (0xffff); +data[2066] = String.fromCharCode (0xffff); +data[2067] = String.fromCharCode (0xffff); +data[2068] = String.fromCharCode (0xffff); +data[2069] = String.fromCharCode (0xffff); +data[2070] = String.fromCharCode (0xffff); +data[2071] = String.fromCharCode (0xffff); +data[2072] = String.fromCharCode (0xffff); +data[2073] = String.fromCharCode (0xffff); +data[2074] = String.fromCharCode (0xffff); +data[2075] = String.fromCharCode (0xffff); +data[2076] = String.fromCharCode (0xffff); +data[2077] = String.fromCharCode (0xffff); +data[2078] = String.fromCharCode (0xffff); +data[2079] = String.fromCharCode (0xffff); +data[2080] = String.fromCharCode (0xffff); +data[2081] = String.fromCharCode (0xffff); +data[2082] = String.fromCharCode (0xffff); +data[2083] = String.fromCharCode (0xffff); +data[2084] = String.fromCharCode (0xffff); +data[2085] = String.fromCharCode (0xffff); +data[2086] = String.fromCharCode (0xffff); +data[2087] = String.fromCharCode (0xffff); +data[2088] = String.fromCharCode (0xffff); +data[2089] = String.fromCharCode (0xffff); +data[2090] = String.fromCharCode (0xffff); +data[2091] = String.fromCharCode (0xffff); +data[2092] = String.fromCharCode (0xffff); +data[2093] = String.fromCharCode (0xffff); +data[2094] = String.fromCharCode (0xffff); +data[2095] = String.fromCharCode (0xffff); +data[2096] = String.fromCharCode (0xffff); +data[2097] = String.fromCharCode (0xffff); +data[2098] = String.fromCharCode (0xffff); +data[2099] = String.fromCharCode (0xffff); +data[2100] = String.fromCharCode (0xffff); +data[2101] = String.fromCharCode (0xffff); +data[2102] = String.fromCharCode (0xffff); +data[2103] = String.fromCharCode (0xffff); +data[2104] = String.fromCharCode (0xffff); +data[2105] = String.fromCharCode (0xffff); +data[2106] = String.fromCharCode (0xffff); +data[2107] = String.fromCharCode (0xffff); +data[2108] = String.fromCharCode (0xffff); +data[2109] = String.fromCharCode (0xffff); +data[2110] = String.fromCharCode (0xffff); +data[2111] = String.fromCharCode (0xffff); +data[2112] = String.fromCharCode (0xffff); +data[2113] = String.fromCharCode (0xffff); +data[2114] = String.fromCharCode (0xffff); +data[2115] = String.fromCharCode (0xffff); +data[2116] = String.fromCharCode (0xffff); +data[2117] = String.fromCharCode (0xffff); +data[2118] = String.fromCharCode (0xffff); +data[2119] = String.fromCharCode (0xffff); +data[2120] = String.fromCharCode (0xffff); +data[2121] = String.fromCharCode (0xffff); +data[2122] = String.fromCharCode (0xffff); +data[2123] = String.fromCharCode (0xffff); +data[2124] = String.fromCharCode (0xffff); +data[2125] = String.fromCharCode (0xffff); +data[2126] = String.fromCharCode (0xffff); +data[2127] = String.fromCharCode (0xffff); +data[2128] = String.fromCharCode (0xffff); +data[2129] = String.fromCharCode (0xffff); +data[2130] = String.fromCharCode (0xffff); +data[2131] = String.fromCharCode (0xffff); +data[2132] = String.fromCharCode (0xffff); +data[2133] = String.fromCharCode (0xffff); +data[2134] = String.fromCharCode (0xffff); +data[2135] = String.fromCharCode (0xffff); +data[2136] = String.fromCharCode (0xffff); +data[2137] = String.fromCharCode (0xffff); +data[2138] = String.fromCharCode (0xffff); +data[2139] = String.fromCharCode (0xffff); +data[2140] = String.fromCharCode (0xffff); +data[2141] = String.fromCharCode (0xffff); +data[2142] = String.fromCharCode (0xffff); +data[2143] = String.fromCharCode (0xffff); +data[2144] = String.fromCharCode (0xffff); +data[2145] = String.fromCharCode (0xffff); +data[2146] = String.fromCharCode (0xffff); +data[2147] = String.fromCharCode (0xffff); +data[2148] = String.fromCharCode (0xffff); +data[2149] = String.fromCharCode (0xffff); +data[2150] = String.fromCharCode (0xffff); +data[2151] = String.fromCharCode (0xffff); +data[2152] = String.fromCharCode (0xffff); +data[2153] = String.fromCharCode (0xffff); +data[2154] = String.fromCharCode (0xffff); +data[2155] = String.fromCharCode (0xffff); +data[2156] = String.fromCharCode (0xffff); +data[2157] = String.fromCharCode (0xffff); +data[2158] = String.fromCharCode (0xffff); +data[2159] = String.fromCharCode (0xffff); +data[2160] = String.fromCharCode (0xffff); +data[2161] = String.fromCharCode (0xffff); +data[2162] = String.fromCharCode (0xffff); +data[2163] = String.fromCharCode (0xffff); +data[2164] = String.fromCharCode (0xffff); +data[2165] = String.fromCharCode (0xffff); +data[2166] = String.fromCharCode (0xffff); +data[2167] = String.fromCharCode (0xffff); +data[2168] = String.fromCharCode (0xffff); +data[2169] = String.fromCharCode (0xffff); +data[2170] = String.fromCharCode (0xffff); +data[2171] = String.fromCharCode (0xffff); +data[2172] = String.fromCharCode (0xffff); +data[2173] = String.fromCharCode (0xffff); +data[2174] = String.fromCharCode (0xffff); +data[2175] = String.fromCharCode (0xffff); +data[2176] = String.fromCharCode (0xffff); +data[2177] = String.fromCharCode (0xffff); +data[2178] = String.fromCharCode (0xffff); +data[2179] = String.fromCharCode (0xffff); +data[2180] = String.fromCharCode (0xffff); +data[2181] = String.fromCharCode (0xffff); +data[2182] = String.fromCharCode (0xffff); +data[2183] = String.fromCharCode (0xffff); +data[2184] = String.fromCharCode (0xffff); +data[2185] = String.fromCharCode (0xffff); +data[2186] = String.fromCharCode (0xffff); +data[2187] = String.fromCharCode (0xffff); +data[2188] = String.fromCharCode (0xffff); +data[2189] = String.fromCharCode (0xffff); +data[2190] = String.fromCharCode (0xffff); +data[2191] = String.fromCharCode (0xffff); +data[2192] = String.fromCharCode (0xffff); +data[2193] = String.fromCharCode (0xffff); +data[2194] = String.fromCharCode (0xffff); +data[2195] = String.fromCharCode (0xffff); +data[2196] = String.fromCharCode (0xffff); +data[2197] = String.fromCharCode (0xffff); +data[2198] = String.fromCharCode (0xffff); +data[2199] = String.fromCharCode (0xffff); +data[2200] = String.fromCharCode (0xffff); +data[2201] = String.fromCharCode (0xffff); +data[2202] = String.fromCharCode (0xffff); +data[2203] = String.fromCharCode (0xffff); +data[2204] = String.fromCharCode (0xffff); +data[2205] = String.fromCharCode (0xffff); +data[2206] = String.fromCharCode (0xffff); +data[2207] = String.fromCharCode (0xffff); +data[2208] = String.fromCharCode (0xffff); +data[2209] = String.fromCharCode (0xffff); +data[2210] = String.fromCharCode (0xffff); +data[2211] = String.fromCharCode (0xffff); +data[2212] = String.fromCharCode (0xffff); +data[2213] = String.fromCharCode (0xffff); +data[2214] = String.fromCharCode (0xffff); +data[2215] = String.fromCharCode (0xffff); +data[2216] = String.fromCharCode (0xffff); +data[2217] = String.fromCharCode (0xffff); +data[2218] = String.fromCharCode (0xffff); +data[2219] = String.fromCharCode (0xffff); +data[2220] = String.fromCharCode (0xffff); +data[2221] = String.fromCharCode (0xffff); +data[2222] = String.fromCharCode (0xffff); +data[2223] = String.fromCharCode (0xffff); +data[2224] = String.fromCharCode (0xffff); +data[2225] = String.fromCharCode (0xffff); +data[2226] = String.fromCharCode (0xffff); +data[2227] = String.fromCharCode (0xffff); +data[2228] = String.fromCharCode (0xffff); +data[2229] = String.fromCharCode (0xffff); +data[2230] = String.fromCharCode (0xffff); +data[2231] = String.fromCharCode (0xffff); +data[2232] = String.fromCharCode (0xffff); +data[2233] = String.fromCharCode (0xffff); +data[2234] = String.fromCharCode (0xffff); +data[2235] = String.fromCharCode (0xffff); +data[2236] = String.fromCharCode (0xffff); +data[2237] = String.fromCharCode (0xffff); +data[2238] = String.fromCharCode (0xffff); +data[2239] = String.fromCharCode (0xffff); +data[2240] = String.fromCharCode (0xffff); +data[2241] = String.fromCharCode (0xffff); +data[2242] = String.fromCharCode (0xffff); +data[2243] = String.fromCharCode (0xffff); +data[2244] = String.fromCharCode (0xffff); +data[2245] = String.fromCharCode (0xffff); +data[2246] = String.fromCharCode (0xffff); +data[2247] = String.fromCharCode (0xffff); +data[2248] = String.fromCharCode (0xffff); +data[2249] = String.fromCharCode (0xffff); +data[2250] = String.fromCharCode (0xffff); +data[2251] = String.fromCharCode (0xffff); +data[2252] = String.fromCharCode (0xffff); +data[2253] = String.fromCharCode (0xffff); +data[2254] = String.fromCharCode (0xffff); +data[2255] = String.fromCharCode (0xffff); +data[2256] = String.fromCharCode (0xffff); +data[2257] = String.fromCharCode (0xffff); +data[2258] = String.fromCharCode (0xffff); +data[2259] = String.fromCharCode (0xffff); +data[2260] = String.fromCharCode (0xffff); +data[2261] = String.fromCharCode (0xffff); +data[2262] = String.fromCharCode (0xffff); +data[2263] = String.fromCharCode (0xffff); +data[2264] = String.fromCharCode (0xffff); +data[2265] = String.fromCharCode (0xffff); +data[2266] = String.fromCharCode (0xffff); +data[2267] = String.fromCharCode (0xffff); +data[2268] = String.fromCharCode (0xffff); +data[2269] = String.fromCharCode (0xffff); +data[2270] = String.fromCharCode (0xffff); +data[2271] = String.fromCharCode (0xffff); +data[2272] = String.fromCharCode (0xffff); +data[2273] = String.fromCharCode (0xffff); +data[2274] = String.fromCharCode (0xffff); +data[2275] = String.fromCharCode (0xffff); +data[2276] = String.fromCharCode (0xffff); +data[2277] = String.fromCharCode (0xffff); +data[2278] = String.fromCharCode (0xffff); +data[2279] = String.fromCharCode (0xffff); +data[2280] = String.fromCharCode (0xffff); +data[2281] = String.fromCharCode (0xffff); +data[2282] = String.fromCharCode (0xffff); +data[2283] = String.fromCharCode (0xffff); +data[2284] = String.fromCharCode (0xffff); +data[2285] = String.fromCharCode (0xffff); +data[2286] = String.fromCharCode (0xffff); +data[2287] = String.fromCharCode (0xffff); +data[2288] = String.fromCharCode (0xffff); +data[2289] = String.fromCharCode (0xffff); +data[2290] = String.fromCharCode (0xffff); +data[2291] = String.fromCharCode (0xffff); +data[2292] = String.fromCharCode (0xffff); +data[2293] = String.fromCharCode (0xffff); +data[2294] = String.fromCharCode (0xffff); +data[2295] = String.fromCharCode (0xffff); +data[2296] = String.fromCharCode (0xffff); +data[2297] = String.fromCharCode (0xffff); +data[2298] = String.fromCharCode (0xffff); +data[2299] = String.fromCharCode (0xffff); +data[2300] = String.fromCharCode (0xffff); +data[2301] = String.fromCharCode (0xffff); +data[2302] = String.fromCharCode (0xffff); +data[2303] = String.fromCharCode (0xffff); +data[2304] = String.fromCharCode (0xffff); +data[2305] = String.fromCharCode (0xffff); +data[2306] = String.fromCharCode (0xffff); +data[2307] = String.fromCharCode (0xffff); +data[2308] = String.fromCharCode (0xffff); +data[2309] = String.fromCharCode (0xffff); +data[2310] = String.fromCharCode (0xffff); +data[2311] = String.fromCharCode (0xffff); +data[2312] = String.fromCharCode (0xffff); +data[2313] = String.fromCharCode (0xffff); +data[2314] = String.fromCharCode (0xffff); +data[2315] = String.fromCharCode (0xffff); +data[2316] = String.fromCharCode (0xffff); +data[2317] = String.fromCharCode (0xffff); +data[2318] = String.fromCharCode (0xffff); +data[2319] = String.fromCharCode (0xffff); +data[2320] = String.fromCharCode (0xffff); +data[2321] = String.fromCharCode (0xffff); +data[2322] = String.fromCharCode (0xffff); +data[2323] = String.fromCharCode (0xffff); +data[2324] = String.fromCharCode (0xffff); +data[2325] = String.fromCharCode (0xffff); +data[2326] = String.fromCharCode (0xffff); +data[2327] = String.fromCharCode (0xffff); +data[2328] = String.fromCharCode (0xffff); +data[2329] = String.fromCharCode (0xffff); +data[2330] = String.fromCharCode (0xffff); +data[2331] = String.fromCharCode (0xffff); +data[2332] = String.fromCharCode (0xffff); +data[2333] = String.fromCharCode (0xffff); +data[2334] = String.fromCharCode (0xffff); +data[2335] = String.fromCharCode (0xffff); +data[2336] = String.fromCharCode (0xffff); +data[2337] = String.fromCharCode (0xffff); +data[2338] = String.fromCharCode (0xffff); +data[2339] = String.fromCharCode (0xffff); +data[2340] = String.fromCharCode (0xffff); +data[2341] = String.fromCharCode (0xffff); +data[2342] = String.fromCharCode (0xffff); +data[2343] = String.fromCharCode (0xffff); +data[2344] = String.fromCharCode (0xffff); +data[2345] = String.fromCharCode (0xffff); +data[2346] = String.fromCharCode (0xffff); +data[2347] = String.fromCharCode (0xffff); +data[2348] = String.fromCharCode (0xffff); +data[2349] = String.fromCharCode (0xffff); +data[2350] = String.fromCharCode (0xffff); +data[2351] = String.fromCharCode (0xffff); +data[2352] = String.fromCharCode (0xffff); +data[2353] = String.fromCharCode (0xffff); +data[2354] = String.fromCharCode (0xffff); +data[2355] = String.fromCharCode (0xffff); +data[2356] = String.fromCharCode (0xffff); +data[2357] = String.fromCharCode (0xffff); +data[2358] = String.fromCharCode (0xffff); +data[2359] = String.fromCharCode (0xffff); +data[2360] = String.fromCharCode (0xffff); +data[2361] = String.fromCharCode (0xffff); +data[2362] = String.fromCharCode (0xffff); +data[2363] = String.fromCharCode (0xffff); +data[2364] = String.fromCharCode (0xffff); +data[2365] = String.fromCharCode (0xffff); +data[2366] = String.fromCharCode (0xffff); +data[2367] = String.fromCharCode (0xffff); +data[2368] = String.fromCharCode (0xffff); +data[2369] = String.fromCharCode (0xffff); +data[2370] = String.fromCharCode (0xffff); +data[2371] = String.fromCharCode (0xffff); +data[2372] = String.fromCharCode (0xffff); +data[2373] = String.fromCharCode (0xffff); +data[2374] = String.fromCharCode (0xffff); +data[2375] = String.fromCharCode (0xffff); +data[2376] = String.fromCharCode (0xffff); +data[2377] = String.fromCharCode (0xffff); +data[2378] = String.fromCharCode (0xffff); +data[2379] = String.fromCharCode (0xffff); +data[2380] = String.fromCharCode (0xffff); +data[2381] = String.fromCharCode (0xffff); +data[2382] = String.fromCharCode (0xffff); +data[2383] = String.fromCharCode (0xffff); +data[2384] = String.fromCharCode (0xffff); +data[2385] = String.fromCharCode (0xffff); +data[2386] = String.fromCharCode (0xffff); +data[2387] = String.fromCharCode (0xffff); +data[2388] = String.fromCharCode (0xffff); +data[2389] = String.fromCharCode (0xffff); +data[2390] = String.fromCharCode (0xffff); +data[2391] = String.fromCharCode (0xffff); +data[2392] = String.fromCharCode (0xffff); +data[2393] = String.fromCharCode (0xffff); +data[2394] = String.fromCharCode (0xffff); +data[2395] = String.fromCharCode (0xffff); +data[2396] = String.fromCharCode (0xffff); +data[2397] = String.fromCharCode (0xffff); +data[2398] = String.fromCharCode (0xffff); +data[2399] = String.fromCharCode (0xffff); +data[2400] = String.fromCharCode (0xffff); +data[2401] = String.fromCharCode (0xffff); +data[2402] = String.fromCharCode (0xffff); +data[2403] = String.fromCharCode (0xffff); +data[2404] = String.fromCharCode (0xffff); +data[2405] = String.fromCharCode (0xffff); +data[2406] = String.fromCharCode (0xffff); +data[2407] = String.fromCharCode (0xffff); +data[2408] = String.fromCharCode (0xffff); +data[2409] = String.fromCharCode (0xffff); +data[2410] = String.fromCharCode (0xffff); +data[2411] = String.fromCharCode (0xffff); +data[2412] = String.fromCharCode (0xffff); +data[2413] = String.fromCharCode (0xffff); +data[2414] = String.fromCharCode (0xffff); +data[2415] = String.fromCharCode (0xffff); +data[2416] = String.fromCharCode (0xffff); +data[2417] = String.fromCharCode (0xffff); +data[2418] = String.fromCharCode (0xffff); +data[2419] = String.fromCharCode (0xffff); +data[2420] = String.fromCharCode (0xffff); +data[2421] = String.fromCharCode (0xffff); +data[2422] = String.fromCharCode (0xffff); +data[2423] = String.fromCharCode (0xffff); +data[2424] = String.fromCharCode (0xffff); +data[2425] = String.fromCharCode (0xffff); +data[2426] = String.fromCharCode (0xffff); +data[2427] = String.fromCharCode (0xffff); +data[2428] = String.fromCharCode (0xffff); +data[2429] = String.fromCharCode (0xffff); +data[2430] = String.fromCharCode (0xffff); +data[2431] = String.fromCharCode (0xffff); +data[2432] = String.fromCharCode (0xffff); +data[2433] = String.fromCharCode (0xffff); +data[2434] = String.fromCharCode (0xffff); +data[2435] = String.fromCharCode (0xffff); +data[2436] = String.fromCharCode (0xffff); +data[2437] = String.fromCharCode (0xffff); +data[2438] = String.fromCharCode (0xffff); +data[2439] = String.fromCharCode (0xffff); +data[2440] = String.fromCharCode (0xffff); +data[2441] = String.fromCharCode (0xffff); +data[2442] = String.fromCharCode (0xffff); +data[2443] = String.fromCharCode (0xffff); +data[2444] = String.fromCharCode (0xffff); +data[2445] = String.fromCharCode (0xffff); +data[2446] = String.fromCharCode (0xffff); +data[2447] = String.fromCharCode (0xffff); +data[2448] = String.fromCharCode (0xffff); +data[2449] = String.fromCharCode (0xffff); +data[2450] = String.fromCharCode (0xffff); +data[2451] = String.fromCharCode (0xffff); +data[2452] = String.fromCharCode (0xffff); +data[2453] = String.fromCharCode (0xffff); +data[2454] = String.fromCharCode (0xffff); +data[2455] = String.fromCharCode (0xffff); +data[2456] = String.fromCharCode (0xffff); +data[2457] = String.fromCharCode (0xffff); +data[2458] = String.fromCharCode (0xffff); +data[2459] = String.fromCharCode (0xffff); +data[2460] = String.fromCharCode (0xffff); +data[2461] = String.fromCharCode (0xffff); +data[2462] = String.fromCharCode (0xffff); +data[2463] = String.fromCharCode (0xffff); +data[2464] = String.fromCharCode (0xffff); +data[2465] = String.fromCharCode (0xffff); +data[2466] = String.fromCharCode (0xffff); +data[2467] = String.fromCharCode (0xffff); +data[2468] = String.fromCharCode (0xffff); +data[2469] = String.fromCharCode (0xffff); +data[2470] = String.fromCharCode (0xffff); +data[2471] = String.fromCharCode (0xffff); +data[2472] = String.fromCharCode (0xffff); +data[2473] = String.fromCharCode (0xffff); +data[2474] = String.fromCharCode (0xffff); +data[2475] = String.fromCharCode (0xffff); +data[2476] = String.fromCharCode (0xffff); +data[2477] = String.fromCharCode (0xffff); +data[2478] = String.fromCharCode (0xffff); +data[2479] = String.fromCharCode (0xffff); +data[2480] = String.fromCharCode (0xffff); +data[2481] = String.fromCharCode (0xffff); +data[2482] = String.fromCharCode (0xffff); +data[2483] = String.fromCharCode (0xffff); +data[2484] = String.fromCharCode (0xffff); +data[2485] = String.fromCharCode (0xffff); +data[2486] = String.fromCharCode (0xffff); +data[2487] = String.fromCharCode (0xffff); +data[2488] = String.fromCharCode (0xffff); +data[2489] = String.fromCharCode (0xffff); +data[2490] = String.fromCharCode (0xffff); +data[2491] = String.fromCharCode (0xffff); +data[2492] = String.fromCharCode (0xffff); +data[2493] = String.fromCharCode (0xffff); +data[2494] = String.fromCharCode (0xffff); +data[2495] = String.fromCharCode (0xffff); +data[2496] = String.fromCharCode (0xffff); +data[2497] = String.fromCharCode (0xffff); +data[2498] = String.fromCharCode (0xffff); +data[2499] = String.fromCharCode (0xffff); +data[2500] = String.fromCharCode (0xffff); +data[2501] = String.fromCharCode (0xffff); +data[2502] = String.fromCharCode (0xffff); +data[2503] = String.fromCharCode (0xffff); +data[2504] = String.fromCharCode (0xffff); +data[2505] = String.fromCharCode (0xffff); +data[2506] = String.fromCharCode (0xffff); +data[2507] = String.fromCharCode (0xffff); +data[2508] = String.fromCharCode (0xffff); +data[2509] = String.fromCharCode (0xffff); +data[2510] = String.fromCharCode (0xffff); +data[2511] = String.fromCharCode (0xffff); +data[2512] = String.fromCharCode (0xffff); +data[2513] = String.fromCharCode (0xffff); +data[2514] = String.fromCharCode (0xffff); +data[2515] = String.fromCharCode (0xffff); +data[2516] = String.fromCharCode (0xffff); +data[2517] = String.fromCharCode (0xffff); +data[2518] = String.fromCharCode (0xffff); +data[2519] = String.fromCharCode (0xffff); +data[2520] = String.fromCharCode (0xffff); +data[2521] = String.fromCharCode (0xffff); +data[2522] = String.fromCharCode (0xffff); +data[2523] = String.fromCharCode (0xffff); +data[2524] = String.fromCharCode (0xffff); +data[2525] = String.fromCharCode (0xffff); +data[2526] = String.fromCharCode (0xffff); +data[2527] = String.fromCharCode (0xffff); +data[2528] = String.fromCharCode (0xffff); +data[2529] = String.fromCharCode (0xffff); +data[2530] = String.fromCharCode (0xffff); +data[2531] = String.fromCharCode (0xffff); +data[2532] = String.fromCharCode (0xffff); +data[2533] = String.fromCharCode (0xffff); +data[2534] = String.fromCharCode (0xffff); +data[2535] = String.fromCharCode (0xffff); +data[2536] = String.fromCharCode (0xffff); +data[2537] = String.fromCharCode (0xffff); +data[2538] = String.fromCharCode (0xffff); +data[2539] = String.fromCharCode (0xffff); +data[2540] = String.fromCharCode (0xffff); +data[2541] = String.fromCharCode (0xffff); +data[2542] = String.fromCharCode (0xffff); +data[2543] = String.fromCharCode (0xffff); +data[2544] = String.fromCharCode (0xffff); +data[2545] = String.fromCharCode (0xffff); +data[2546] = String.fromCharCode (0xffff); +data[2547] = String.fromCharCode (0xffff); +data[2548] = String.fromCharCode (0xffff); +data[2549] = String.fromCharCode (0xffff); +data[2550] = String.fromCharCode (0xffff); +data[2551] = String.fromCharCode (0xffff); +data[2552] = String.fromCharCode (0xffff); +data[2553] = String.fromCharCode (0xffff); +data[2554] = String.fromCharCode (0x003f); +data[2752] = String.fromCharCode (0xffff); +data[2753] = String.fromCharCode (0xffff); +data[2754] = String.fromCharCode (0xffff); +data[2755] = String.fromCharCode (0xffff); +data[2756] = String.fromCharCode (0xffff); +data[2757] = String.fromCharCode (0xffff); +data[2758] = String.fromCharCode (0xffff); +data[2759] = String.fromCharCode (0xffff); +data[2760] = String.fromCharCode (0xffff); +data[2761] = String.fromCharCode (0xffff); +data[2762] = String.fromCharCode (0xffff); +data[2763] = String.fromCharCode (0xffff); +data[2764] = String.fromCharCode (0xffff); +data[2765] = String.fromCharCode (0xffff); +data[2766] = String.fromCharCode (0xffff); +data[2767] = String.fromCharCode (0xffff); +data[2768] = String.fromCharCode (0xffff); +data[2769] = String.fromCharCode (0xffff); +data[2770] = String.fromCharCode (0xffff); +data[2771] = String.fromCharCode (0xffff); +data[2772] = String.fromCharCode (0xffff); +data[2773] = String.fromCharCode (0xffff); +data[2774] = String.fromCharCode (0xffff); +data[2775] = String.fromCharCode (0xffff); +data[2776] = String.fromCharCode (0xffff); +data[2777] = String.fromCharCode (0xffff); +data[2778] = String.fromCharCode (0xffff); +data[2779] = String.fromCharCode (0xffff); +data[2780] = String.fromCharCode (0xffff); +data[2781] = String.fromCharCode (0xffff); +data[2782] = String.fromCharCode (0xffff); +data[2783] = String.fromCharCode (0xffff); +data[2784] = String.fromCharCode (0xffff); +data[2785] = String.fromCharCode (0xffff); +data[2786] = String.fromCharCode (0xffff); +data[2787] = String.fromCharCode (0xffff); +data[2788] = String.fromCharCode (0xffff); +data[2789] = String.fromCharCode (0xffff); +data[2790] = String.fromCharCode (0xffff); +data[2791] = String.fromCharCode (0xffff); +data[2792] = String.fromCharCode (0xffff); +data[2793] = String.fromCharCode (0xffff); +data[2794] = String.fromCharCode (0xffff); +data[2795] = String.fromCharCode (0xffff); +data[2796] = String.fromCharCode (0xffff); +data[2797] = String.fromCharCode (0xffff); +data[2798] = String.fromCharCode (0xffff); +data[2799] = String.fromCharCode (0xffff); +data[2800] = String.fromCharCode (0xffff); +data[2801] = String.fromCharCode (0xffff); +data[2802] = String.fromCharCode (0xffff); +data[2803] = String.fromCharCode (0xffff); +data[2804] = String.fromCharCode (0xffff); +data[2805] = String.fromCharCode (0xffff); +data[2806] = String.fromCharCode (0xffff); +data[2807] = String.fromCharCode (0xffff); +data[2808] = String.fromCharCode (0xffff); +data[2809] = String.fromCharCode (0xffff); +data[2810] = String.fromCharCode (0xffff); +data[2811] = String.fromCharCode (0xffff); +data[2812] = String.fromCharCode (0xffff); +data[2813] = String.fromCharCode (0xffff); +data[2814] = String.fromCharCode (0xffff); +data[2815] = String.fromCharCode (0xffff); +data[2816] = String.fromCharCode (0xffff); +data[2817] = String.fromCharCode (0xffff); +data[2818] = String.fromCharCode (0xffff); +data[2819] = String.fromCharCode (0xffff); +data[2820] = String.fromCharCode (0xffff); +data[2821] = String.fromCharCode (0xffff); +data[2822] = String.fromCharCode (0xffff); +data[2823] = String.fromCharCode (0xffff); +data[2824] = String.fromCharCode (0xffff); +data[2825] = String.fromCharCode (0xffff); +data[2826] = String.fromCharCode (0xffff); +data[2827] = String.fromCharCode (0xffff); +data[2828] = String.fromCharCode (0xffff); +data[2829] = String.fromCharCode (0xffff); +data[2830] = String.fromCharCode (0xffff); +data[2831] = String.fromCharCode (0xffff); +data[2832] = String.fromCharCode (0xffff); +data[2833] = String.fromCharCode (0xffff); +data[2834] = String.fromCharCode (0xffff); +data[2835] = String.fromCharCode (0xffff); +data[2836] = String.fromCharCode (0xffff); +data[2837] = String.fromCharCode (0xffff); +data[2838] = String.fromCharCode (0xffff); +data[2839] = String.fromCharCode (0xffff); +data[2840] = String.fromCharCode (0xffff); +data[2841] = String.fromCharCode (0xffff); +data[2842] = String.fromCharCode (0xffff); +data[2843] = String.fromCharCode (0xffff); +data[2844] = String.fromCharCode (0xffff); +data[2845] = String.fromCharCode (0xffff); +data[2846] = String.fromCharCode (0xffff); +data[2847] = String.fromCharCode (0xffff); +data[2848] = String.fromCharCode (0xffff); +data[2849] = String.fromCharCode (0xffff); +data[2850] = String.fromCharCode (0xffff); +data[2851] = String.fromCharCode (0xffff); +data[2852] = String.fromCharCode (0xffff); +data[2853] = String.fromCharCode (0xffff); +data[2854] = String.fromCharCode (0xffff); +data[2855] = String.fromCharCode (0xffff); +data[2856] = String.fromCharCode (0xffff); +data[2857] = String.fromCharCode (0xffff); +data[2858] = String.fromCharCode (0xffff); +data[2859] = String.fromCharCode (0xffff); +data[2860] = String.fromCharCode (0xffff); +data[2861] = String.fromCharCode (0xffff); +data[2862] = String.fromCharCode (0xffff); +data[2863] = String.fromCharCode (0xffff); +data[2864] = String.fromCharCode (0xffff); +data[2865] = String.fromCharCode (0xffff); +data[2866] = String.fromCharCode (0xffff); +data[2867] = String.fromCharCode (0xffff); +data[2868] = String.fromCharCode (0xffff); +data[2869] = String.fromCharCode (0xffff); +data[2870] = String.fromCharCode (0xffff); +data[2871] = String.fromCharCode (0xffff); +data[2872] = String.fromCharCode (0xffff); +data[2873] = String.fromCharCode (0xffff); +data[2874] = String.fromCharCode (0xffff); +data[2875] = String.fromCharCode (0xffff); +data[2876] = String.fromCharCode (0xffff); +data[2877] = String.fromCharCode (0xffff); +data[2878] = String.fromCharCode (0xffff); +data[2879] = String.fromCharCode (0xffff); +data[2880] = String.fromCharCode (0xffff); +data[2881] = String.fromCharCode (0xffff); +data[2882] = String.fromCharCode (0xffff); +data[2883] = String.fromCharCode (0xffff); +data[2884] = String.fromCharCode (0xffff); +data[2885] = String.fromCharCode (0xffff); +data[2886] = String.fromCharCode (0xffff); +data[2887] = String.fromCharCode (0xffff); +data[2888] = String.fromCharCode (0xffff); +data[2889] = String.fromCharCode (0xffff); +data[2890] = String.fromCharCode (0xffff); +data[2891] = String.fromCharCode (0xffff); +data[2892] = String.fromCharCode (0xffff); +data[2893] = String.fromCharCode (0xffff); +data[2894] = String.fromCharCode (0xffff); +data[2895] = String.fromCharCode (0xffff); +data[2896] = String.fromCharCode (0xffff); +data[2897] = String.fromCharCode (0xffff); +data[2898] = String.fromCharCode (0xffff); +data[2899] = String.fromCharCode (0xffff); +data[2900] = String.fromCharCode (0xffff); +data[2901] = String.fromCharCode (0xffff); +data[2902] = String.fromCharCode (0xffff); +data[2903] = String.fromCharCode (0xffff); +data[2904] = String.fromCharCode (0xffff); +data[2905] = String.fromCharCode (0xffff); +data[2906] = String.fromCharCode (0xffff); +data[2907] = String.fromCharCode (0xffff); +data[2908] = String.fromCharCode (0xffff); +data[2909] = String.fromCharCode (0xffff); +data[2910] = String.fromCharCode (0xffff); +data[2911] = String.fromCharCode (0xffff); +data[2912] = String.fromCharCode (0xffff); +data[2913] = String.fromCharCode (0xffff); +data[2914] = String.fromCharCode (0xffff); +data[2915] = String.fromCharCode (0xffff); +data[2916] = String.fromCharCode (0xffff); +data[2917] = String.fromCharCode (0xffff); +data[2918] = String.fromCharCode (0xffff); +data[2919] = String.fromCharCode (0xffff); +data[2920] = String.fromCharCode (0xffff); +data[2921] = String.fromCharCode (0xffff); +data[2922] = String.fromCharCode (0xffff); +data[2923] = String.fromCharCode (0xffff); +data[2924] = String.fromCharCode (0xffff); +data[2925] = String.fromCharCode (0xffff); +data[2926] = String.fromCharCode (0xffff); +data[2927] = String.fromCharCode (0xffff); +data[2928] = String.fromCharCode (0xffff); +data[2929] = String.fromCharCode (0xffff); +data[2930] = String.fromCharCode (0xffff); +data[2931] = String.fromCharCode (0xffff); +data[2932] = String.fromCharCode (0xffff); +data[2933] = String.fromCharCode (0xffff); +data[2934] = String.fromCharCode (0xffff); +data[2935] = String.fromCharCode (0xffff); +data[2936] = String.fromCharCode (0xffff); +data[2937] = String.fromCharCode (0xffff); +data[2938] = String.fromCharCode (0xffff); +data[2939] = String.fromCharCode (0xffff); +data[2940] = String.fromCharCode (0xffff); +data[2941] = String.fromCharCode (0xffff); +data[2942] = String.fromCharCode (0xffff); +data[2943] = String.fromCharCode (0xffff); +data[2944] = String.fromCharCode (0xffff); +data[2945] = String.fromCharCode (0xffff); +data[2946] = String.fromCharCode (0xffff); +data[2947] = String.fromCharCode (0xffff); +data[2948] = String.fromCharCode (0xffff); +data[2949] = String.fromCharCode (0xffff); +data[2950] = String.fromCharCode (0xffff); +data[2951] = String.fromCharCode (0xffff); +data[2952] = String.fromCharCode (0xffff); +data[2953] = String.fromCharCode (0xffff); +data[2954] = String.fromCharCode (0xffff); +data[2955] = String.fromCharCode (0xffff); +data[2956] = String.fromCharCode (0xffff); +data[2957] = String.fromCharCode (0xffff); +data[2958] = String.fromCharCode (0xffff); +data[2959] = String.fromCharCode (0xffff); +data[2960] = String.fromCharCode (0xffff); +data[2961] = String.fromCharCode (0xffff); +data[2962] = String.fromCharCode (0xffff); +data[2963] = String.fromCharCode (0xffff); +data[2964] = String.fromCharCode (0xffff); +data[2965] = String.fromCharCode (0xffff); +data[2966] = String.fromCharCode (0xffff); +data[2967] = String.fromCharCode (0xffff); +data[2968] = String.fromCharCode (0xffff); +data[2969] = String.fromCharCode (0xffff); +data[2970] = String.fromCharCode (0xffff); +data[2971] = String.fromCharCode (0xffff); +data[2972] = String.fromCharCode (0xffff); +data[2973] = String.fromCharCode (0xffff); +data[2974] = String.fromCharCode (0xffff); +data[2975] = String.fromCharCode (0xffff); +data[2976] = String.fromCharCode (0xffff); +data[2977] = String.fromCharCode (0xffff); +data[2978] = String.fromCharCode (0xffff); +data[2979] = String.fromCharCode (0xffff); +data[2980] = String.fromCharCode (0xffff); +data[2981] = String.fromCharCode (0xffff); +data[2982] = String.fromCharCode (0xffff); +data[2983] = String.fromCharCode (0xffff); +data[2984] = String.fromCharCode (0xffff); +data[2985] = String.fromCharCode (0xffff); +data[2986] = String.fromCharCode (0xffff); +data[2987] = String.fromCharCode (0xffff); +data[2988] = String.fromCharCode (0xffff); +data[2989] = String.fromCharCode (0xffff); +data[2990] = String.fromCharCode (0xffff); +data[2991] = String.fromCharCode (0xffff); +data[2992] = String.fromCharCode (0xffff); +data[2993] = String.fromCharCode (0xffff); +data[2994] = String.fromCharCode (0xffff); +data[2995] = String.fromCharCode (0xffff); +data[2996] = String.fromCharCode (0xffff); +data[2997] = String.fromCharCode (0xffff); +data[2998] = String.fromCharCode (0xffff); +data[2999] = String.fromCharCode (0xffff); +data[3000] = String.fromCharCode (0xffff); +data[3001] = String.fromCharCode (0xffff); +data[3002] = String.fromCharCode (0xffff); +data[3003] = String.fromCharCode (0xffff); +data[3004] = String.fromCharCode (0xffff); +data[3005] = String.fromCharCode (0xffff); +data[3006] = String.fromCharCode (0xffff); +data[3007] = String.fromCharCode (0xffff); +data[3008] = String.fromCharCode (0xffff); +data[3009] = String.fromCharCode (0xffff); +data[3010] = String.fromCharCode (0xffff); +data[3011] = String.fromCharCode (0xffff); +data[3012] = String.fromCharCode (0xffff); +data[3013] = String.fromCharCode (0xffff); +data[3014] = String.fromCharCode (0xffff); +data[3015] = String.fromCharCode (0xffff); +data[3016] = String.fromCharCode (0xffff); +data[3017] = String.fromCharCode (0xffff); +data[3018] = String.fromCharCode (0xffff); +data[3019] = String.fromCharCode (0xffff); +data[3020] = String.fromCharCode (0xffff); +data[3021] = String.fromCharCode (0xffff); +data[3022] = String.fromCharCode (0xffff); +data[3023] = String.fromCharCode (0xffff); +data[3024] = String.fromCharCode (0xffff); +data[3025] = String.fromCharCode (0xffff); +data[3026] = String.fromCharCode (0xffff); +data[3027] = String.fromCharCode (0xffff); +data[3028] = String.fromCharCode (0xffff); +data[3029] = String.fromCharCode (0xffff); +data[3030] = String.fromCharCode (0xffff); +data[3031] = String.fromCharCode (0xffff); +data[3032] = String.fromCharCode (0xffff); +data[3033] = String.fromCharCode (0xffff); +data[3034] = String.fromCharCode (0xffff); +data[3035] = String.fromCharCode (0xffff); +data[3036] = String.fromCharCode (0xffff); +data[3037] = String.fromCharCode (0xffff); +data[3038] = String.fromCharCode (0xffff); +data[3039] = String.fromCharCode (0xffff); +data[3040] = String.fromCharCode (0xffff); +data[3041] = String.fromCharCode (0xffff); +data[3042] = String.fromCharCode (0xffff); +data[3043] = String.fromCharCode (0xffff); +data[3044] = String.fromCharCode (0xffff); +data[3045] = String.fromCharCode (0xffff); +data[3046] = String.fromCharCode (0xffff); +data[3047] = String.fromCharCode (0xffff); +data[3048] = String.fromCharCode (0xffff); +data[3049] = String.fromCharCode (0xffff); +data[3050] = String.fromCharCode (0xffff); +data[3051] = String.fromCharCode (0xffff); +data[3052] = String.fromCharCode (0xffff); +data[3053] = String.fromCharCode (0xffff); +data[3054] = String.fromCharCode (0xffff); +data[3055] = String.fromCharCode (0xffff); +data[3056] = String.fromCharCode (0xffff); +data[3057] = String.fromCharCode (0xffff); +data[3058] = String.fromCharCode (0xffff); +data[3059] = String.fromCharCode (0xffff); +data[3060] = String.fromCharCode (0xffff); +data[3061] = String.fromCharCode (0xffff); +data[3062] = String.fromCharCode (0xffff); +data[3063] = String.fromCharCode (0xffff); +data[3064] = String.fromCharCode (0xffff); +data[3065] = String.fromCharCode (0xffff); +data[3066] = String.fromCharCode (0xffff); +data[3067] = String.fromCharCode (0xffff); +data[3068] = String.fromCharCode (0xffff); +data[3069] = String.fromCharCode (0xffff); +data[3070] = String.fromCharCode (0xffff); +data[3071] = String.fromCharCode (0xffff); +data[3072] = String.fromCharCode (0xffff); +data[3073] = String.fromCharCode (0xffff); +data[3074] = String.fromCharCode (0xffff); +data[3075] = String.fromCharCode (0xffff); +data[3076] = String.fromCharCode (0xffff); +data[3077] = String.fromCharCode (0xffff); +data[3078] = String.fromCharCode (0xffff); +data[3079] = String.fromCharCode (0xffff); +data[3080] = String.fromCharCode (0xffff); +data[3081] = String.fromCharCode (0xffff); +data[3082] = String.fromCharCode (0xffff); +data[3083] = String.fromCharCode (0xffff); +data[3084] = String.fromCharCode (0xffff); +data[3085] = String.fromCharCode (0xffff); +data[3086] = String.fromCharCode (0xffff); +data[3087] = String.fromCharCode (0xffff); +data[3088] = String.fromCharCode (0xffff); +data[3089] = String.fromCharCode (0xffff); +data[3090] = String.fromCharCode (0xffff); +data[3091] = String.fromCharCode (0xffff); +data[3092] = String.fromCharCode (0xffff); +data[3093] = String.fromCharCode (0xffff); +data[3094] = String.fromCharCode (0xffff); +data[3095] = String.fromCharCode (0xffff); +data[3096] = String.fromCharCode (0xffff); +data[3097] = String.fromCharCode (0xffff); +data[3098] = String.fromCharCode (0xffff); +data[3099] = String.fromCharCode (0xffff); +data[3100] = String.fromCharCode (0xffff); +data[3101] = String.fromCharCode (0xffff); +data[3102] = String.fromCharCode (0xffff); +data[3103] = String.fromCharCode (0xffff); +data[3104] = String.fromCharCode (0xffff); +data[3105] = String.fromCharCode (0xffff); +data[3106] = String.fromCharCode (0xffff); +data[3107] = String.fromCharCode (0xffff); +data[3108] = String.fromCharCode (0xffff); +data[3109] = String.fromCharCode (0xffff); +data[3110] = String.fromCharCode (0xffff); +data[3111] = String.fromCharCode (0xffff); +data[3112] = String.fromCharCode (0xffff); +data[3113] = String.fromCharCode (0xffff); +data[3114] = String.fromCharCode (0xffff); +data[3115] = String.fromCharCode (0xffff); +data[3116] = String.fromCharCode (0xffff); +data[3117] = String.fromCharCode (0xffff); +data[3118] = String.fromCharCode (0xffff); +data[3119] = String.fromCharCode (0xffff); +data[3120] = String.fromCharCode (0xffff); +data[3121] = String.fromCharCode (0xffff); +data[3122] = String.fromCharCode (0xffff); +data[3123] = String.fromCharCode (0xffff); +data[3124] = String.fromCharCode (0xffff); +data[3125] = String.fromCharCode (0xffff); +data[3126] = String.fromCharCode (0xffff); +data[3127] = String.fromCharCode (0xffff); +data[3128] = String.fromCharCode (0xffff); +data[3129] = String.fromCharCode (0xffff); +data[3130] = String.fromCharCode (0xffff); +data[3131] = String.fromCharCode (0xffff); +data[3132] = String.fromCharCode (0xffff); +data[3133] = String.fromCharCode (0xffff); +data[3134] = String.fromCharCode (0xffff); +data[3135] = String.fromCharCode (0xffff); +data[3136] = String.fromCharCode (0xffff); +data[3137] = String.fromCharCode (0xffff); +data[3138] = String.fromCharCode (0xffff); +data[3139] = String.fromCharCode (0xffff); +data[3140] = String.fromCharCode (0xffff); +data[3141] = String.fromCharCode (0xffff); +data[3142] = String.fromCharCode (0xffff); +data[3143] = String.fromCharCode (0xffff); +data[3144] = String.fromCharCode (0xffff); +data[3145] = String.fromCharCode (0xffff); +data[3146] = String.fromCharCode (0xffff); +data[3147] = String.fromCharCode (0xffff); +data[3148] = String.fromCharCode (0xffff); +data[3149] = String.fromCharCode (0xffff); +data[3150] = String.fromCharCode (0xffff); +data[3151] = String.fromCharCode (0xffff); +data[3152] = String.fromCharCode (0xffff); +data[3153] = String.fromCharCode (0xffff); +data[3154] = String.fromCharCode (0xffff); +data[3155] = String.fromCharCode (0xffff); +data[3156] = String.fromCharCode (0xffff); +data[3157] = String.fromCharCode (0xffff); +data[3158] = String.fromCharCode (0xffff); +data[3159] = String.fromCharCode (0xffff); +data[3160] = String.fromCharCode (0xffff); +data[3161] = String.fromCharCode (0xffff); +data[3162] = String.fromCharCode (0xffff); +data[3163] = String.fromCharCode (0xffff); +data[3164] = String.fromCharCode (0xffff); +data[3165] = String.fromCharCode (0xffff); +data[3166] = String.fromCharCode (0xffff); +data[3167] = String.fromCharCode (0xffff); +data[3168] = String.fromCharCode (0xffff); +data[3169] = String.fromCharCode (0xffff); +data[3170] = String.fromCharCode (0xffff); +data[3171] = String.fromCharCode (0xffff); +data[3172] = String.fromCharCode (0xffff); +data[3173] = String.fromCharCode (0xffff); +data[3174] = String.fromCharCode (0xffff); +data[3175] = String.fromCharCode (0xffff); +data[3176] = String.fromCharCode (0xffff); +data[3177] = String.fromCharCode (0xffff); +data[3178] = String.fromCharCode (0xffff); +data[3179] = String.fromCharCode (0xffff); +data[3180] = String.fromCharCode (0xffff); +data[3181] = String.fromCharCode (0xffff); +data[3182] = String.fromCharCode (0xffff); +data[3183] = String.fromCharCode (0xffff); +data[3184] = String.fromCharCode (0xffff); +data[3185] = String.fromCharCode (0xffff); +data[3186] = String.fromCharCode (0xffff); +data[3187] = String.fromCharCode (0xffff); +data[3188] = String.fromCharCode (0xffff); +data[3189] = String.fromCharCode (0xffff); +data[3190] = String.fromCharCode (0xffff); +data[3191] = String.fromCharCode (0xffff); +data[3192] = String.fromCharCode (0xffff); +data[3193] = String.fromCharCode (0xffff); +data[3194] = String.fromCharCode (0xffff); +data[3195] = String.fromCharCode (0xffff); +data[3196] = String.fromCharCode (0xffff); +data[3197] = String.fromCharCode (0xffff); +data[3198] = String.fromCharCode (0xffff); +data[3199] = String.fromCharCode (0xffff); +data[3200] = String.fromCharCode (0xffff); +data[3201] = String.fromCharCode (0xffff); +data[3202] = String.fromCharCode (0xffff); +data[3203] = String.fromCharCode (0xffff); +data[3204] = String.fromCharCode (0xffff); +data[3205] = String.fromCharCode (0xffff); +data[3206] = String.fromCharCode (0xffff); +data[3207] = String.fromCharCode (0xffff); +data[3208] = String.fromCharCode (0xffff); +data[3209] = String.fromCharCode (0xffff); +data[3210] = String.fromCharCode (0xffff); +data[3211] = String.fromCharCode (0xffff); +data[3212] = String.fromCharCode (0xffff); +data[3213] = String.fromCharCode (0xffff); +data[3214] = String.fromCharCode (0xffff); +data[3215] = String.fromCharCode (0xffff); +data[3216] = String.fromCharCode (0xffff); +data[3217] = String.fromCharCode (0xffff); +data[3218] = String.fromCharCode (0xffff); +data[3219] = String.fromCharCode (0xffff); +data[3220] = String.fromCharCode (0xffff); +data[3221] = String.fromCharCode (0xffff); +data[3222] = String.fromCharCode (0xffff); +data[3223] = String.fromCharCode (0xffff); +data[3224] = String.fromCharCode (0xffff); +data[3225] = String.fromCharCode (0xffff); +data[3226] = String.fromCharCode (0xffff); +data[3227] = String.fromCharCode (0xffff); +data[3228] = String.fromCharCode (0xffff); +data[3229] = String.fromCharCode (0xffff); +data[3230] = String.fromCharCode (0xffff); +data[3231] = String.fromCharCode (0xffff); +data[3232] = String.fromCharCode (0xffff); +data[3233] = String.fromCharCode (0xffff); +data[3234] = String.fromCharCode (0xffff); +data[3235] = String.fromCharCode (0xffff); +data[3236] = String.fromCharCode (0xffff); +data[3237] = String.fromCharCode (0xffff); +data[3238] = String.fromCharCode (0xffff); +data[3239] = String.fromCharCode (0xffff); +data[3240] = String.fromCharCode (0xffff); +data[3241] = String.fromCharCode (0xffff); +data[3242] = String.fromCharCode (0xffff); +data[3243] = String.fromCharCode (0xffff); +data[3244] = String.fromCharCode (0xffff); +data[3245] = String.fromCharCode (0xffff); +data[3246] = String.fromCharCode (0xffff); +data[3247] = String.fromCharCode (0xffff); +data[3248] = String.fromCharCode (0xffff); +data[3249] = String.fromCharCode (0xffff); +data[3250] = String.fromCharCode (0xffff); +data[3251] = String.fromCharCode (0xffff); +data[3252] = String.fromCharCode (0xffff); +data[3253] = String.fromCharCode (0xffff); +data[3254] = String.fromCharCode (0xffff); +data[3255] = String.fromCharCode (0xffff); +data[3256] = String.fromCharCode (0xffff); +data[3257] = String.fromCharCode (0xffff); +data[3258] = String.fromCharCode (0xffff); +data[3259] = String.fromCharCode (0xffff); +data[3260] = String.fromCharCode (0xffff); +data[3261] = String.fromCharCode (0xffff); +data[3262] = String.fromCharCode (0xffff); +data[3263] = String.fromCharCode (0xffff); +data[3264] = String.fromCharCode (0xffff); +data[3265] = String.fromCharCode (0xffff); +data[3266] = String.fromCharCode (0xffff); +data[3267] = String.fromCharCode (0xffff); +data[3268] = String.fromCharCode (0xffff); +data[3269] = String.fromCharCode (0xffff); +data[3270] = String.fromCharCode (0xffff); +data[3271] = String.fromCharCode (0xffff); +data[3272] = String.fromCharCode (0xffff); +data[3273] = String.fromCharCode (0xffff); +data[3274] = String.fromCharCode (0xffff); +data[3275] = String.fromCharCode (0xffff); +data[3276] = String.fromCharCode (0xffff); +data[3277] = String.fromCharCode (0xffff); +data[3278] = String.fromCharCode (0xffff); +data[3279] = String.fromCharCode (0xffff); +data[3280] = String.fromCharCode (0xffff); +data[3281] = String.fromCharCode (0xffff); +data[3282] = String.fromCharCode (0xffff); +data[3283] = String.fromCharCode (0xffff); +data[3284] = String.fromCharCode (0xffff); +data[3285] = String.fromCharCode (0xffff); +data[3286] = String.fromCharCode (0xffff); +data[3287] = String.fromCharCode (0xffff); +data[3288] = String.fromCharCode (0xffff); +data[3289] = String.fromCharCode (0xffff); +data[3290] = String.fromCharCode (0xffff); +data[3291] = String.fromCharCode (0xffff); +data[3292] = String.fromCharCode (0xffff); +data[3293] = String.fromCharCode (0xffff); +data[3294] = String.fromCharCode (0xffff); +data[3295] = String.fromCharCode (0xffff); +data[3296] = String.fromCharCode (0xffff); +data[3297] = String.fromCharCode (0xffff); +data[3298] = String.fromCharCode (0xffff); +data[3299] = String.fromCharCode (0xffff); +data[3300] = String.fromCharCode (0xffff); +data[3301] = String.fromCharCode (0xffff); +data[3302] = String.fromCharCode (0xffff); +data[3303] = String.fromCharCode (0xffff); +data[3304] = String.fromCharCode (0xffff); +data[3305] = String.fromCharCode (0xffff); +data[3306] = String.fromCharCode (0xffff); +data[3307] = String.fromCharCode (0xffff); +data[3308] = String.fromCharCode (0xffff); +data[3309] = String.fromCharCode (0xffff); +data[3310] = String.fromCharCode (0xffff); +data[3311] = String.fromCharCode (0xffff); +data[3312] = String.fromCharCode (0xffff); +data[3313] = String.fromCharCode (0xffff); +data[3314] = String.fromCharCode (0xffff); +data[3315] = String.fromCharCode (0xffff); +data[3316] = String.fromCharCode (0xffff); +data[3317] = String.fromCharCode (0xffff); +data[3318] = String.fromCharCode (0xffff); +data[3319] = String.fromCharCode (0xffff); +data[3320] = String.fromCharCode (0xffff); +data[3321] = String.fromCharCode (0xffff); +data[3322] = String.fromCharCode (0xffff); +data[3323] = String.fromCharCode (0xffff); +data[3324] = String.fromCharCode (0xffff); +data[3325] = String.fromCharCode (0xffff); +data[3326] = String.fromCharCode (0xffff); +data[3327] = String.fromCharCode (0xffff); +data[3328] = String.fromCharCode (0xffff); +data[3329] = String.fromCharCode (0xffff); +data[3330] = String.fromCharCode (0xffff); +data[3331] = String.fromCharCode (0xffff); +data[3332] = String.fromCharCode (0xffff); +data[3333] = String.fromCharCode (0xffff); +data[3334] = String.fromCharCode (0xffff); +data[3335] = String.fromCharCode (0xffff); +data[3336] = String.fromCharCode (0xffff); +data[3337] = String.fromCharCode (0xffff); +data[3338] = String.fromCharCode (0xffff); +data[3339] = String.fromCharCode (0xffff); +data[3340] = String.fromCharCode (0xffff); +data[3341] = String.fromCharCode (0xffff); +data[3342] = String.fromCharCode (0xffff); +data[3343] = String.fromCharCode (0xffff); +data[3344] = String.fromCharCode (0xffff); +data[3345] = String.fromCharCode (0xffff); +data[3346] = String.fromCharCode (0xffff); +data[3347] = String.fromCharCode (0xffff); +data[3348] = String.fromCharCode (0xffff); +data[3349] = String.fromCharCode (0xffff); +data[3350] = String.fromCharCode (0xffff); +data[3351] = String.fromCharCode (0xffff); +data[3352] = String.fromCharCode (0xffff); +data[3353] = String.fromCharCode (0xffff); +data[3354] = String.fromCharCode (0xffff); +data[3355] = String.fromCharCode (0xffff); +data[3356] = String.fromCharCode (0xffff); +data[3357] = String.fromCharCode (0xffff); +data[3358] = String.fromCharCode (0xffff); +data[3359] = String.fromCharCode (0xffff); +data[3360] = String.fromCharCode (0xffff); +data[3361] = String.fromCharCode (0xffff); +data[3362] = String.fromCharCode (0xffff); +data[3363] = String.fromCharCode (0xffff); +data[3364] = String.fromCharCode (0xffff); +data[3365] = String.fromCharCode (0xffff); +data[3366] = String.fromCharCode (0xffff); +data[3367] = String.fromCharCode (0xffff); +data[3368] = String.fromCharCode (0xffff); +data[3369] = String.fromCharCode (0xffff); +data[3370] = String.fromCharCode (0xffff); +data[3371] = String.fromCharCode (0xffff); +data[3372] = String.fromCharCode (0xffff); +data[3373] = String.fromCharCode (0xffff); +data[3374] = String.fromCharCode (0xffff); +data[3375] = String.fromCharCode (0xffff); +data[3376] = String.fromCharCode (0xffff); +data[3377] = String.fromCharCode (0xffff); +data[3378] = String.fromCharCode (0xffff); +data[3379] = String.fromCharCode (0xffff); +data[3380] = String.fromCharCode (0xffff); +data[3381] = String.fromCharCode (0xffff); +data[3382] = String.fromCharCode (0xffff); +data[3383] = String.fromCharCode (0xffff); +data[3384] = String.fromCharCode (0xffff); +data[3385] = String.fromCharCode (0xffff); +data[3386] = String.fromCharCode (0xffff); +data[3387] = String.fromCharCode (0xffff); +data[3388] = String.fromCharCode (0xffff); +data[3389] = String.fromCharCode (0xffff); +data[3390] = String.fromCharCode (0xffff); +data[3391] = String.fromCharCode (0xffff); +data[3392] = String.fromCharCode (0xffff); +data[3393] = String.fromCharCode (0xffff); +data[3394] = String.fromCharCode (0xffff); +data[3395] = String.fromCharCode (0xffff); +data[3396] = String.fromCharCode (0xffff); +data[3397] = String.fromCharCode (0xffff); +data[3398] = String.fromCharCode (0xffff); +data[3399] = String.fromCharCode (0xffff); +data[3400] = String.fromCharCode (0xffff); +data[3401] = String.fromCharCode (0xffff); +data[3402] = String.fromCharCode (0xffff); +data[3403] = String.fromCharCode (0xffff); +data[3404] = String.fromCharCode (0xffff); +data[3405] = String.fromCharCode (0xffff); +data[3406] = String.fromCharCode (0xffff); +data[3407] = String.fromCharCode (0xffff); +data[3408] = String.fromCharCode (0xffff); +data[3409] = String.fromCharCode (0xffff); +data[3410] = String.fromCharCode (0xffff); +data[3411] = String.fromCharCode (0xffff); +data[3412] = String.fromCharCode (0xffff); +data[3413] = String.fromCharCode (0xffff); +data[3414] = String.fromCharCode (0xffff); +data[3415] = String.fromCharCode (0xffff); +data[3416] = String.fromCharCode (0xffff); +data[3417] = String.fromCharCode (0xffff); +data[3418] = String.fromCharCode (0xffff); +data[3419] = String.fromCharCode (0xffff); +data[3420] = String.fromCharCode (0xffff); +data[3421] = String.fromCharCode (0xffff); +data[3422] = String.fromCharCode (0xffff); +data[3423] = String.fromCharCode (0xffff); +data[3424] = String.fromCharCode (0xffff); +data[3425] = String.fromCharCode (0xffff); +data[3426] = String.fromCharCode (0xffff); +data[3427] = String.fromCharCode (0xffff); +data[3428] = String.fromCharCode (0xffff); +data[3429] = String.fromCharCode (0xffff); +data[3430] = String.fromCharCode (0xffff); +data[3431] = String.fromCharCode (0xffff); +data[3432] = String.fromCharCode (0xffff); +data[3433] = String.fromCharCode (0xffff); +data[3434] = String.fromCharCode (0xffff); +data[3435] = String.fromCharCode (0xffff); +data[3436] = String.fromCharCode (0xffff); +data[3437] = String.fromCharCode (0xffff); +data[3438] = String.fromCharCode (0xffff); +data[3439] = String.fromCharCode (0xffff); +data[3440] = String.fromCharCode (0xffff); +data[3441] = String.fromCharCode (0xffff); +data[3442] = String.fromCharCode (0xffff); +data[3443] = String.fromCharCode (0xffff); +data[3444] = String.fromCharCode (0xffff); +data[3445] = String.fromCharCode (0xffff); +data[3446] = String.fromCharCode (0xffff); +data[3447] = String.fromCharCode (0xffff); +data[3448] = String.fromCharCode (0xffff); +data[3449] = String.fromCharCode (0xffff); +data[3450] = String.fromCharCode (0x000f); +data[3984] = String.fromCharCode (0xffff); +data[3985] = String.fromCharCode (0xffff); +data[3986] = String.fromCharCode (0xffff); +data[3987] = String.fromCharCode (0xffff); +data[3988] = String.fromCharCode (0xffff); +data[3989] = String.fromCharCode (0xffff); +data[3990] = String.fromCharCode (0xffff); +data[3991] = String.fromCharCode (0xffff); +data[3992] = String.fromCharCode (0xffff); +data[3993] = String.fromCharCode (0xffff); +data[3994] = String.fromCharCode (0xffff); +data[3995] = String.fromCharCode (0xffff); +data[3996] = String.fromCharCode (0xffff); +data[3997] = String.fromCharCode (0xffff); +data[3998] = String.fromCharCode (0xffff); +data[3999] = String.fromCharCode (0xffff); +data[4000] = String.fromCharCode (0xffff); +data[4001] = String.fromCharCode (0xffff); +data[4002] = String.fromCharCode (0x3fff); +data[4016] = String.fromCharCode (0x007f); +data[4017] = String.fromCharCode (0x80f8); +data[4018] = String.fromCharCode (0xfdff); +data[4019] = String.fromCharCode (0x5f7f); +data[4020] = String.fromCharCode (0xffdb); +data[4021] = String.fromCharCode (0xffff); +data[4022] = String.fromCharCode (0xffff); +data[4023] = String.fromCharCode (0xffff); +data[4024] = String.fromCharCode (0xffff); +data[4025] = String.fromCharCode (0xffff); +data[4026] = String.fromCharCode (0xffff); +data[4027] = String.fromCharCode (0x0003); +data[4029] = String.fromCharCode (0xfff8); +data[4030] = String.fromCharCode (0xffff); +data[4031] = String.fromCharCode (0xffff); +data[4032] = String.fromCharCode (0xffff); +data[4033] = String.fromCharCode (0xffff); +data[4034] = String.fromCharCode (0xffff); +data[4035] = String.fromCharCode (0xffff); +data[4036] = String.fromCharCode (0xffff); +data[4037] = String.fromCharCode (0xffff); +data[4038] = String.fromCharCode (0xffff); +data[4039] = String.fromCharCode (0xffff); +data[4040] = String.fromCharCode (0xffff); +data[4041] = String.fromCharCode (0xffff); +data[4042] = String.fromCharCode (0xffff); +data[4043] = String.fromCharCode (0xffff); +data[4044] = String.fromCharCode (0xffff); +data[4045] = String.fromCharCode (0xffff); +data[4046] = String.fromCharCode (0xffff); +data[4047] = String.fromCharCode (0xffff); +data[4048] = String.fromCharCode (0xffff); +data[4049] = String.fromCharCode (0xffff); +data[4050] = String.fromCharCode (0xffff); +data[4051] = String.fromCharCode (0x3fff); +data[4053] = String.fromCharCode (0xffff); +data[4054] = String.fromCharCode (0xffff); +data[4055] = String.fromCharCode (0xffff); +data[4056] = String.fromCharCode (0xffff); +data[4057] = String.fromCharCode (0xfffc); +data[4058] = String.fromCharCode (0xffff); +data[4059] = String.fromCharCode (0xffff); +data[4060] = String.fromCharCode (0x00ff); +data[4063] = String.fromCharCode (0x0fff); +data[4071] = String.fromCharCode (0xffd7); +data[4072] = String.fromCharCode (0xffff); +data[4073] = String.fromCharCode (0xffff); +data[4074] = String.fromCharCode (0xffff); +data[4075] = String.fromCharCode (0xffff); +data[4076] = String.fromCharCode (0xffff); +data[4077] = String.fromCharCode (0xffff); +data[4078] = String.fromCharCode (0xffff); +data[4079] = String.fromCharCode (0x1fff); +data[4082] = String.fromCharCode (0xfffe); +data[4083] = String.fromCharCode (0x07ff); +data[4084] = String.fromCharCode (0xfffe); +data[4085] = String.fromCharCode (0x07ff); +data[4086] = String.fromCharCode (0xffc0); +data[4087] = String.fromCharCode (0xffff); +data[4088] = String.fromCharCode (0xffff); +data[4089] = String.fromCharCode (0xffff); +data[4090] = String.fromCharCode (0xffff); +data[4091] = String.fromCharCode (0x7fff); +data[4092] = String.fromCharCode (0xfcfc); +data[4093] = String.fromCharCode (0x1cfc); +data[4100] = String.fromCharCode (0xfffe); +data[4101] = String.fromCharCode (0x07ff); +data[4102] = String.fromCharCode (0xfffe); +data[4103] = String.fromCharCode (0x07ff); +data[4106] = String.fromCharCode (0x0400); +data[4107] = String.fromCharCode (0x0420); +data[4108] = String.fromCharCode (0xffff); +data[4109] = String.fromCharCode (0xff7f); +data[4110] = String.fromCharCode (0xffff); +data[4111] = String.fromCharCode (0xff7f); +data[4112] = String.fromCharCode (0xffff); +data[4113] = String.fromCharCode (0xffff); +data[4114] = String.fromCharCode (0xffff); +data[4115] = String.fromCharCode (0xffff); +data[4116] = String.fromCharCode (0xffff); +data[4117] = String.fromCharCode (0xffff); +data[4118] = String.fromCharCode (0xffff); +data[4119] = String.fromCharCode (0xffff); +data[4120] = String.fromCharCode (0xffff); +data[4121] = String.fromCharCode (0xffff); +data[4122] = String.fromCharCode (0xffff); +data[4123] = String.fromCharCode (0xffff); +data[4124] = String.fromCharCode (0xffff); +data[4125] = String.fromCharCode (0xffff); +data[4126] = String.fromCharCode (0xffff); +data[4127] = String.fromCharCode (0xfc3f); +data[4128] = String.fromCharCode (0xffff); +data[4129] = String.fromCharCode (0x00ff); +data[4133] = String.fromCharCode (0xffff); +data[4134] = String.fromCharCode (0xffff); +data[4135] = String.fromCharCode (0xffff); +data[4136] = String.fromCharCode (0xffff); +data[4137] = String.fromCharCode (0xffff); +data[4138] = String.fromCharCode (0x01ff); +data[4139] = String.fromCharCode (0xf9ff); +data[4140] = String.fromCharCode (0x0003); +data[4141] = String.fromCharCode (0x0003); +data[4142] = String.fromCharCode (0x001f); +data[4151] = String.fromCharCode (0x0400); +data[4152] = String.fromCharCode (0xd740); +data[4153] = String.fromCharCode (0xffff); +data[4154] = String.fromCharCode (0xfffb); +data[4155] = String.fromCharCode (0xffff); +data[4156] = String.fromCharCode (0x7fff); +data[4157] = String.fromCharCode (0x547f); +data[4158] = String.fromCharCode (0x00fd); +}); +c$.white_f = Clazz.defineMethod (c$, "white_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.white = new com.stevesoft.pat.Bits (data); +data[0] = String.fromCharCode (0x3e00); +data[1] = String.fromCharCode (0xf000); +data[2] = String.fromCharCode (0x0001); +data[512] = String.fromCharCode (0x0fff); +data[514] = String.fromCharCode (0x0300); +data[768] = String.fromCharCode (0x0001); +data[4096] = String.fromCharCode (0x3e00); +data[4097] = String.fromCharCode (0xf000); +data[4098] = String.fromCharCode (0x0001); +}); +c$.punct_f = Clazz.defineMethod (c$, "punct_f", +function () { +var data = Clazz.newCharArray (4159, '\0'); +com.stevesoft.pat.Bits.punct = new com.stevesoft.pat.Bits (data); +data[2] = String.fromCharCode (0xf7ee); +data[3] = String.fromCharCode (0x8c00); +data[4] = String.fromCharCode (0x0001); +data[5] = String.fromCharCode (0xb800); +data[7] = String.fromCharCode (0x2800); +data[10] = String.fromCharCode (0x2802); +data[11] = String.fromCharCode (0x8880); +data[55] = String.fromCharCode (0x4030); +data[56] = String.fromCharCode (0x0080); +data[85] = String.fromCharCode (0xfc00); +data[88] = String.fromCharCode (0x0200); +data[91] = String.fromCharCode (0x4000); +data[92] = String.fromCharCode (0x0009); +data[95] = String.fromCharCode (0x0018); +data[96] = String.fromCharCode (0x1000); +data[97] = String.fromCharCode (0x8800); +data[102] = String.fromCharCode (0x3c00); +data[109] = String.fromCharCode (0x0010); +data[150] = '0'; +data[151] = String.fromCharCode (0x0001); +data[226] = String.fromCharCode (0x8000); +data[229] = String.fromCharCode (0x0c00); +data[234] = String.fromCharCode (0x8000); +data[240] = String.fromCharCode (0xfff0); +data[241] = String.fromCharCode (0x0007); +data[243] = String.fromCharCode (0x3c00); +data[248] = String.fromCharCode (0x0020); +data[271] = String.fromCharCode (0x0800); +data[513] = String.fromCharCode (0xffff); +data[514] = String.fromCharCode (0x00ff); +data[515] = String.fromCharCode (0xffff); +data[516] = 'o'; +data[519] = String.fromCharCode (0x6000); +data[520] = String.fromCharCode (0x6000); +data[562] = String.fromCharCode (0x0600); +data[768] = String.fromCharCode (0xff4e); +data[769] = String.fromCharCode (0xfff3); +data[771] = String.fromCharCode (0x0001); +data[783] = String.fromCharCode (0x0800); +data[4051] = String.fromCharCode (0xc000); +data[4067] = String.fromCharCode (0xffff); +data[4068] = String.fromCharCode (0xfe1f); +data[4069] = String.fromCharCode (0xfff7); +data[4070] = String.fromCharCode (0x0d0b); +data[4080] = String.fromCharCode (0xf7ee); +data[4081] = String.fromCharCode (0x8c00); +data[4082] = String.fromCharCode (0x0001); +data[4083] = String.fromCharCode (0xb800); +data[4085] = String.fromCharCode (0x2800); +data[4086] = String.fromCharCode (0x003e); +data[4098] = String.fromCharCode (0xf7ee); +data[4099] = String.fromCharCode (0x8c00); +data[4100] = String.fromCharCode (0x0001); +data[4101] = String.fromCharCode (0xb800); +data[4103] = String.fromCharCode (0x2800); +data[4106] = String.fromCharCode (0x2802); +data[4107] = String.fromCharCode (0x8880); +data[4151] = String.fromCharCode (0x4030); +data[4152] = String.fromCharCode (0x0080); +}); +Clazz.defineStatics (c$, +"upper", null, +"lower", null, +"title", null, +"currency", null, +"decimal_digit", null, +"math", null, +"letter", null, +"white", null, +"punct", null); diff --git a/bin/com/stevesoft/pat/Boundary.js b/bin/com/stevesoft/pat/Boundary.js index 58bb19c..9eaff99 100644 --- a/bin/com/stevesoft/pat/Boundary.js +++ b/bin/com/stevesoft/pat/Boundary.js @@ -1,52 +1,52 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Boundary", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "Boundary", com.stevesoft.pat.Pattern); -Clazz.overrideMethod (c$, "toString", -function () { -return "\\b" + this.nextString (); -}); -Clazz.defineMethod (c$, "isAChar", -function (c) { -if (c >= 'a' && c <= 'z') { -return true; -}if (c >= 'A' && c <= 'Z') { -return true; -}if (c >= '0' && c <= '9') { -return true; -}if (c == '_') { -return true; -}return false; -}, "~S"); -Clazz.defineMethod (c$, "matchLeft", -function (pos, pt) { -if (pos <= 0) { -return true; -}if (this.isAChar (pt.src.charAt (pos)) && this.isAChar (pt.src.charAt (pos - 1))) { -return false; -}return true; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "matchRight", -function (pos, pt) { -if (pos < 0) { -return false; -}if (pos + 1 >= pt.src.length ()) { -return true; -}if (this.isAChar (pt.src.charAt (pos)) && this.isAChar (pt.src.charAt (pos + 1))) { -return false; -}return true; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (this.matchRight (pos - 1, pt) || this.matchLeft (pos, pt)) { -return this.nextMatch (pos, pt); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.Boundary (); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Boundary", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "Boundary", com.stevesoft.pat.Pattern); +Clazz.overrideMethod (c$, "toString", +function () { +return "\\b" + this.nextString (); +}); +Clazz.defineMethod (c$, "isAChar", +function (c) { +if (c >= 'a' && c <= 'z') { +return true; +}if (c >= 'A' && c <= 'Z') { +return true; +}if (c >= '0' && c <= '9') { +return true; +}if (c == '_') { +return true; +}return false; +}, "~S"); +Clazz.defineMethod (c$, "matchLeft", +function (pos, pt) { +if (pos <= 0) { +return true; +}if (this.isAChar (pt.src.charAt (pos)) && this.isAChar (pt.src.charAt (pos - 1))) { +return false; +}return true; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "matchRight", +function (pos, pt) { +if (pos < 0) { +return false; +}if (pos + 1 >= pt.src.length ()) { +return true; +}if (this.isAChar (pt.src.charAt (pos)) && this.isAChar (pt.src.charAt (pos + 1))) { +return false; +}return true; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (this.matchRight (pos - 1, pt) || this.matchLeft (pos, pt)) { +return this.nextMatch (pos, pt); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.Boundary (); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/Bracket.js b/bin/com/stevesoft/pat/Bracket.js index 26a2303..064ec34 100644 --- a/bin/com/stevesoft/pat/Bracket.js +++ b/bin/com/stevesoft/pat/Bracket.js @@ -1,60 +1,60 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Or"], "com.stevesoft.pat.Bracket", ["com.stevesoft.pat.patInt", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.neg = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Bracket", com.stevesoft.pat.Or); -Clazz.makeConstructor (c$, -function (n) { -Clazz.superConstructor (this, com.stevesoft.pat.Bracket, []); -this.neg = n; -}, "~B"); -Clazz.overrideMethod (c$, "leftForm", -function () { -if (this.neg) { -return "[^"; -} else { -return "["; -}}); -Clazz.overrideMethod (c$, "rightForm", -function () { -return "]"; -}); -Clazz.overrideMethod (c$, "sepForm", -function () { -return ""; -}); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -if (pos >= pt.src.length ()) { -return -1; -}var r = Clazz.superCall (this, com.stevesoft.pat.Bracket, "matchInternal", [pos, pt]); -if ((this.neg && r < 0) || (!this.neg && r >= 0)) { -return this.nextMatch (pos + 1, pt); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "addOr", -function (p) { -this.pv = null; -this.v.addElement (p); -p.setParent (null); -return this; -}, "com.stevesoft.pat.Pattern"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -var b = new com.stevesoft.pat.Bracket (this.neg); -b.v = new java.util.Vector (); -for (var i = 0; i < this.v.size (); i++) { -b.v.addElement ((this.v.elementAt (i)).clone1 (h)); -} -return b; -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Or"], "com.stevesoft.pat.Bracket", ["com.stevesoft.pat.patInt", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.neg = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Bracket", com.stevesoft.pat.Or); +Clazz.makeConstructor (c$, +function (n) { +Clazz.superConstructor (this, com.stevesoft.pat.Bracket, []); +this.neg = n; +}, "~B"); +Clazz.overrideMethod (c$, "leftForm", +function () { +if (this.neg) { +return "[^"; +} else { +return "["; +}}); +Clazz.overrideMethod (c$, "rightForm", +function () { +return "]"; +}); +Clazz.overrideMethod (c$, "sepForm", +function () { +return ""; +}); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +if (pos >= pt.src.length ()) { +return -1; +}var r = Clazz.superCall (this, com.stevesoft.pat.Bracket, "matchInternal", [pos, pt]); +if ((this.neg && r < 0) || (!this.neg && r >= 0)) { +return this.nextMatch (pos + 1, pt); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "addOr", +function (p) { +this.pv = null; +this.v.addElement (p); +p.setParent (null); +return this; +}, "com.stevesoft.pat.Pattern"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +var b = new com.stevesoft.pat.Bracket (this.neg); +b.v = new java.util.Vector (); +for (var i = 0; i < this.v.size (); i++) { +b.v.addElement ((this.v.elementAt (i)).clone1 (h)); +} +return b; +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/CaseMgr.js b/bin/com/stevesoft/pat/CaseMgr.js index e35645b..30fe2ec 100644 --- a/bin/com/stevesoft/pat/CaseMgr.js +++ b/bin/com/stevesoft/pat/CaseMgr.js @@ -1,94 +1,94 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.CaseMgr", ["java.lang.Character"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "CaseMgr"); -c$.toUpperCaseC = Clazz.defineMethod (c$, "toUpperCaseC", -function (c) { -return Character.toUpperCase (c); -}, "~S"); -c$.toLowerCaseC = Clazz.defineMethod (c$, "toLowerCaseC", -function (c) { -return Character.toLowerCase (c); -}, "~S"); -c$.toUpperCase = Clazz.defineMethod (c$, "toUpperCase", -function (s) { -return s.toUpperCase (); -}, "~S"); -c$.toLowerCase = Clazz.defineMethod (c$, "toLowerCase", -function (s) { -return s.toLowerCase (); -}, "~S"); -c$.toTitleCaseC = Clazz.defineMethod (c$, "toTitleCaseC", -function (c) { -return Character.toUpperCase (c); -}, "~S"); -c$.regionMatchesLike = Clazz.defineMethod (c$, "regionMatchesLike", -function (s1, ign, i1, s2, i2, i3) { -var itot = i2 + i3; -if (itot > s2.length () || i1 + i3 > s1.length ()) { -return false; -}if (!ign) { -for (var i = i2; i < itot; i++) { -if (s2.charAt (i) != s1.charAt (i1++)) { -return false; -}} -} else { -for (var i = i2; i < itot; i++) { -if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { -return false; -}} -}return true; -}, "com.stevesoft.pat.StringLike,~B,~N,com.stevesoft.pat.StringLike,~N,~N"); -c$.regionMatches = Clazz.defineMethod (c$, "regionMatches", -function (s1, ign, i1, s2, i2, i3) { -var itot = i2 + i3; -if (itot > s2.length () || i1 + i3 > s1.length) { -return false; -}if (!ign) { -for (var i = i2; i < itot; i++) { -if (s2.charAt (i) != s1.charAt (i1++)) { -return false; -}} -} else { -for (var i = i2; i < itot; i++) { -if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { -return false; -}} -}return true; -}, "~S,~B,~N,com.stevesoft.pat.StringLike,~N,~N"); -c$.regionMatchesLike2 = Clazz.defineMethod (c$, "regionMatchesLike2", -function (s1, ign, i1, s2, i2, i3) { -var itot = i2 + i3; -if (itot > s2.length || i1 + i3 > s1.length ()) { -return false; -}if (!ign) { -for (var i = i2; i < itot; i++) { -if (s2.charAt (i) != s1.charAt (i1++)) { -return false; -}} -} else { -for (var i = i2; i < itot; i++) { -if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { -return false; -}} -}return true; -}, "com.stevesoft.pat.StringLike,~B,~N,~S,~N,~N"); -c$.regionMatches2 = Clazz.defineMethod (c$, "regionMatches2", -function (s1, ign, i1, s2, i2, i3) { -var itot = i2 + i3; -if (itot > s2.length || i1 + i3 > s1.length) { -return false; -}if (!ign) { -for (var i = i2; i < itot; i++) { -if (s2.charAt (i) != s1.charAt (i1++)) { -return false; -}} -} else { -for (var i = i2; i < itot; i++) { -if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { -return false; -}} -}return true; -}, "~S,~B,~N,~S,~N,~N"); -Clazz.defineStatics (c$, -"java_1_0", false); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.CaseMgr", ["java.lang.Character"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "CaseMgr"); +c$.toUpperCaseC = Clazz.defineMethod (c$, "toUpperCaseC", +function (c) { +return Character.toUpperCase (c); +}, "~S"); +c$.toLowerCaseC = Clazz.defineMethod (c$, "toLowerCaseC", +function (c) { +return Character.toLowerCase (c); +}, "~S"); +c$.toUpperCase = Clazz.defineMethod (c$, "toUpperCase", +function (s) { +return s.toUpperCase (); +}, "~S"); +c$.toLowerCase = Clazz.defineMethod (c$, "toLowerCase", +function (s) { +return s.toLowerCase (); +}, "~S"); +c$.toTitleCaseC = Clazz.defineMethod (c$, "toTitleCaseC", +function (c) { +return Character.toUpperCase (c); +}, "~S"); +c$.regionMatchesLike = Clazz.defineMethod (c$, "regionMatchesLike", +function (s1, ign, i1, s2, i2, i3) { +var itot = i2 + i3; +if (itot > s2.length () || i1 + i3 > s1.length ()) { +return false; +}if (!ign) { +for (var i = i2; i < itot; i++) { +if (s2.charAt (i) != s1.charAt (i1++)) { +return false; +}} +} else { +for (var i = i2; i < itot; i++) { +if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { +return false; +}} +}return true; +}, "com.stevesoft.pat.StringLike,~B,~N,com.stevesoft.pat.StringLike,~N,~N"); +c$.regionMatches = Clazz.defineMethod (c$, "regionMatches", +function (s1, ign, i1, s2, i2, i3) { +var itot = i2 + i3; +if (itot > s2.length () || i1 + i3 > s1.length) { +return false; +}if (!ign) { +for (var i = i2; i < itot; i++) { +if (s2.charAt (i) != s1.charAt (i1++)) { +return false; +}} +} else { +for (var i = i2; i < itot; i++) { +if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { +return false; +}} +}return true; +}, "~S,~B,~N,com.stevesoft.pat.StringLike,~N,~N"); +c$.regionMatchesLike2 = Clazz.defineMethod (c$, "regionMatchesLike2", +function (s1, ign, i1, s2, i2, i3) { +var itot = i2 + i3; +if (itot > s2.length || i1 + i3 > s1.length ()) { +return false; +}if (!ign) { +for (var i = i2; i < itot; i++) { +if (s2.charAt (i) != s1.charAt (i1++)) { +return false; +}} +} else { +for (var i = i2; i < itot; i++) { +if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { +return false; +}} +}return true; +}, "com.stevesoft.pat.StringLike,~B,~N,~S,~N,~N"); +c$.regionMatches2 = Clazz.defineMethod (c$, "regionMatches2", +function (s1, ign, i1, s2, i2, i3) { +var itot = i2 + i3; +if (itot > s2.length || i1 + i3 > s1.length) { +return false; +}if (!ign) { +for (var i = i2; i < itot; i++) { +if (s2.charAt (i) != s1.charAt (i1++)) { +return false; +}} +} else { +for (var i = i2; i < itot; i++) { +if (com.stevesoft.pat.CaseMgr.toLowerCaseC (s2.charAt (i)) != com.stevesoft.pat.CaseMgr.toLowerCaseC (s1.charAt (i1++))) { +return false; +}} +}return true; +}, "~S,~B,~N,~S,~N,~N"); +Clazz.defineStatics (c$, +"java_1_0", false); +}); diff --git a/bin/com/stevesoft/pat/ChangeRule.js b/bin/com/stevesoft/pat/ChangeRule.js index 1a6f683..3edb0ff 100644 --- a/bin/com/stevesoft/pat/ChangeRule.js +++ b/bin/com/stevesoft/pat/ChangeRule.js @@ -1,35 +1,35 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.ChangeRule", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.NewRule = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "ChangeRule", com.stevesoft.pat.SpecialRule); -Clazz.makeConstructor (c$, -function (c) { -Clazz.superConstructor (this, com.stevesoft.pat.ChangeRule, []); -this.NewRule = c.NewRule; -}, "com.stevesoft.pat.ChangeRule"); -Clazz.makeConstructor (c$, -function (nm, rr) { -Clazz.superConstructor (this, com.stevesoft.pat.ChangeRule, []); -this.name = nm; -this.NewRule = rr; -}, "~S,com.stevesoft.pat.Regex"); -Clazz.makeConstructor (c$, -function (nm, tr) { -Clazz.superConstructor (this, com.stevesoft.pat.ChangeRule, []); -this.name = nm; -this.NewRule = tr.rp; -}, "~S,com.stevesoft.pat.Transformer"); -Clazz.overrideMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.ChangeRule (this); -}); -Clazz.overrideMethod (c$, "toString1", -function () { -return "${=" + this.name + "}"; -}); -Clazz.overrideMethod (c$, "apply", -function (sb, rr) { -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.ChangeRule", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.NewRule = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "ChangeRule", com.stevesoft.pat.SpecialRule); +Clazz.makeConstructor (c$, +function (c) { +Clazz.superConstructor (this, com.stevesoft.pat.ChangeRule, []); +this.NewRule = c.NewRule; +}, "com.stevesoft.pat.ChangeRule"); +Clazz.makeConstructor (c$, +function (nm, rr) { +Clazz.superConstructor (this, com.stevesoft.pat.ChangeRule, []); +this.name = nm; +this.NewRule = rr; +}, "~S,com.stevesoft.pat.Regex"); +Clazz.makeConstructor (c$, +function (nm, tr) { +Clazz.superConstructor (this, com.stevesoft.pat.ChangeRule, []); +this.name = nm; +this.NewRule = tr.rp; +}, "~S,com.stevesoft.pat.Transformer"); +Clazz.overrideMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.ChangeRule (this); +}); +Clazz.overrideMethod (c$, "toString1", +function () { +return "${=" + this.name + "}"; +}); +Clazz.overrideMethod (c$, "apply", +function (sb, rr) { +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +}); diff --git a/bin/com/stevesoft/pat/CodeRule.js b/bin/com/stevesoft/pat/CodeRule.js index 85a0917..92c00f3 100644 --- a/bin/com/stevesoft/pat/CodeRule.js +++ b/bin/com/stevesoft/pat/CodeRule.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.CodeRule", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.c = 'E'; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "CodeRule", com.stevesoft.pat.SpecialRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.CodeRule, []); -}); -Clazz.makeConstructor (c$, -function (c) { -Clazz.superConstructor (this, com.stevesoft.pat.CodeRule, []); -this.c = c; -}, "~S"); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -sb.setMode (this.c); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return "\\" + this.c; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.CodeRule", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.c = 'E'; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "CodeRule", com.stevesoft.pat.SpecialRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.CodeRule, []); +}); +Clazz.makeConstructor (c$, +function (c) { +Clazz.superConstructor (this, com.stevesoft.pat.CodeRule, []); +this.c = c; +}, "~S"); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +sb.setMode (this.c); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return "\\" + this.c; +}); +}); diff --git a/bin/com/stevesoft/pat/Ctrl.js b/bin/com/stevesoft/pat/Ctrl.js index 9a42c67..43250ce 100644 --- a/bin/com/stevesoft/pat/Ctrl.js +++ b/bin/com/stevesoft/pat/Ctrl.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -c$ = Clazz.declareType (com.stevesoft.pat, "Ctrl"); -Clazz.defineStatics (c$, -"cmap", Clazz.newCharArray (-1, [String.fromCharCode (64), 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', String.fromCharCode (91), String.fromCharCode (92), String.fromCharCode (93), String.fromCharCode (94), String.fromCharCode (95), String.fromCharCode (96), 'a', 'a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', String.fromCharCode (123), String.fromCharCode (124), String.fromCharCode (125), String.fromCharCode (126), String.fromCharCode (127), String.fromCharCode (0), String.fromCharCode (1), String.fromCharCode (2), String.fromCharCode (3), String.fromCharCode (4), String.fromCharCode (5), String.fromCharCode (6), String.fromCharCode (7), String.fromCharCode (8), String.fromCharCode (9), String.fromCharCode (10), String.fromCharCode (11), String.fromCharCode (12), String.fromCharCode (13), String.fromCharCode (14), String.fromCharCode (15), String.fromCharCode (16), String.fromCharCode (17), String.fromCharCode (18), String.fromCharCode (19), String.fromCharCode (20), String.fromCharCode (21), String.fromCharCode (22), String.fromCharCode (23), String.fromCharCode (24), String.fromCharCode (25), String.fromCharCode (26), String.fromCharCode (27), String.fromCharCode (27), String.fromCharCode (29), String.fromCharCode (30), String.fromCharCode (31), String.fromCharCode (32), String.fromCharCode (1), String.fromCharCode (2), String.fromCharCode (3), String.fromCharCode (4), String.fromCharCode (5), String.fromCharCode (6), String.fromCharCode (7), String.fromCharCode (8), String.fromCharCode (9), String.fromCharCode (10), String.fromCharCode (11), String.fromCharCode (12), String.fromCharCode (13), String.fromCharCode (14), String.fromCharCode (15), String.fromCharCode (16), String.fromCharCode (17), String.fromCharCode (18), String.fromCharCode (19), String.fromCharCode (20), String.fromCharCode (21), String.fromCharCode (22), String.fromCharCode (23), String.fromCharCode (24), String.fromCharCode (25), String.fromCharCode (26), String.fromCharCode (59), String.fromCharCode (60), String.fromCharCode (61), String.fromCharCode (62), String.fromCharCode (63), String.fromCharCode (192), String.fromCharCode (193), String.fromCharCode (194), String.fromCharCode (195), String.fromCharCode (196), String.fromCharCode (197), String.fromCharCode (198), String.fromCharCode (199), String.fromCharCode (200), String.fromCharCode (201), String.fromCharCode (202), String.fromCharCode (203), String.fromCharCode (204), String.fromCharCode (205), String.fromCharCode (206), String.fromCharCode (207), String.fromCharCode (208), String.fromCharCode (209), String.fromCharCode (210), String.fromCharCode (211), String.fromCharCode (212), String.fromCharCode (213), String.fromCharCode (214), String.fromCharCode (215), String.fromCharCode (216), String.fromCharCode (217), String.fromCharCode (218), String.fromCharCode (219), String.fromCharCode (220), String.fromCharCode (221), String.fromCharCode (222), String.fromCharCode (223), String.fromCharCode (224), String.fromCharCode (225), String.fromCharCode (226), String.fromCharCode (227), String.fromCharCode (228), String.fromCharCode (229), String.fromCharCode (230), String.fromCharCode (231), String.fromCharCode (232), String.fromCharCode (233), String.fromCharCode (234), String.fromCharCode (235), String.fromCharCode (236), String.fromCharCode (237), String.fromCharCode (238), String.fromCharCode (239), String.fromCharCode (240), String.fromCharCode (241), String.fromCharCode (242), String.fromCharCode (243), String.fromCharCode (244), String.fromCharCode (245), String.fromCharCode (246), String.fromCharCode (247), String.fromCharCode (248), String.fromCharCode (249), String.fromCharCode (250), String.fromCharCode (251), String.fromCharCode (252), String.fromCharCode (253), String.fromCharCode (254), String.fromCharCode (255), String.fromCharCode (128), String.fromCharCode (129), String.fromCharCode (130), String.fromCharCode (131), String.fromCharCode (132), String.fromCharCode (133), String.fromCharCode (134), String.fromCharCode (135), String.fromCharCode (136), String.fromCharCode (137), String.fromCharCode (138), String.fromCharCode (139), String.fromCharCode (140), String.fromCharCode (141), String.fromCharCode (142), String.fromCharCode (143), String.fromCharCode (144), String.fromCharCode (145), String.fromCharCode (146), String.fromCharCode (147), String.fromCharCode (148), String.fromCharCode (149), String.fromCharCode (150), String.fromCharCode (151), String.fromCharCode (152), String.fromCharCode (153), String.fromCharCode (154), String.fromCharCode (155), String.fromCharCode (156), String.fromCharCode (157), String.fromCharCode (158), String.fromCharCode (159), String.fromCharCode (160), String.fromCharCode (161), String.fromCharCode (162), String.fromCharCode (163), String.fromCharCode (164), String.fromCharCode (165), String.fromCharCode (166), String.fromCharCode (167), String.fromCharCode (168), String.fromCharCode (169), String.fromCharCode (170), String.fromCharCode (171), String.fromCharCode (172), String.fromCharCode (173), String.fromCharCode (174), String.fromCharCode (175), String.fromCharCode (176), String.fromCharCode (177), String.fromCharCode (178), String.fromCharCode (179), String.fromCharCode (180), String.fromCharCode (181), String.fromCharCode (182), String.fromCharCode (183), String.fromCharCode (184), String.fromCharCode (185), String.fromCharCode (186), String.fromCharCode (187), String.fromCharCode (188), String.fromCharCode (189), String.fromCharCode (190), String.fromCharCode (191)])); +Clazz.declarePackage ("com.stevesoft.pat"); +c$ = Clazz.declareType (com.stevesoft.pat, "Ctrl"); +Clazz.defineStatics (c$, +"cmap", Clazz.newCharArray (-1, [String.fromCharCode (64), 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', String.fromCharCode (91), String.fromCharCode (92), String.fromCharCode (93), String.fromCharCode (94), String.fromCharCode (95), String.fromCharCode (96), 'a', 'a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', String.fromCharCode (123), String.fromCharCode (124), String.fromCharCode (125), String.fromCharCode (126), String.fromCharCode (127), String.fromCharCode (0), String.fromCharCode (1), String.fromCharCode (2), String.fromCharCode (3), String.fromCharCode (4), String.fromCharCode (5), String.fromCharCode (6), String.fromCharCode (7), String.fromCharCode (8), String.fromCharCode (9), String.fromCharCode (10), String.fromCharCode (11), String.fromCharCode (12), String.fromCharCode (13), String.fromCharCode (14), String.fromCharCode (15), String.fromCharCode (16), String.fromCharCode (17), String.fromCharCode (18), String.fromCharCode (19), String.fromCharCode (20), String.fromCharCode (21), String.fromCharCode (22), String.fromCharCode (23), String.fromCharCode (24), String.fromCharCode (25), String.fromCharCode (26), String.fromCharCode (27), String.fromCharCode (27), String.fromCharCode (29), String.fromCharCode (30), String.fromCharCode (31), String.fromCharCode (32), String.fromCharCode (1), String.fromCharCode (2), String.fromCharCode (3), String.fromCharCode (4), String.fromCharCode (5), String.fromCharCode (6), String.fromCharCode (7), String.fromCharCode (8), String.fromCharCode (9), String.fromCharCode (10), String.fromCharCode (11), String.fromCharCode (12), String.fromCharCode (13), String.fromCharCode (14), String.fromCharCode (15), String.fromCharCode (16), String.fromCharCode (17), String.fromCharCode (18), String.fromCharCode (19), String.fromCharCode (20), String.fromCharCode (21), String.fromCharCode (22), String.fromCharCode (23), String.fromCharCode (24), String.fromCharCode (25), String.fromCharCode (26), String.fromCharCode (59), String.fromCharCode (60), String.fromCharCode (61), String.fromCharCode (62), String.fromCharCode (63), String.fromCharCode (192), String.fromCharCode (193), String.fromCharCode (194), String.fromCharCode (195), String.fromCharCode (196), String.fromCharCode (197), String.fromCharCode (198), String.fromCharCode (199), String.fromCharCode (200), String.fromCharCode (201), String.fromCharCode (202), String.fromCharCode (203), String.fromCharCode (204), String.fromCharCode (205), String.fromCharCode (206), String.fromCharCode (207), String.fromCharCode (208), String.fromCharCode (209), String.fromCharCode (210), String.fromCharCode (211), String.fromCharCode (212), String.fromCharCode (213), String.fromCharCode (214), String.fromCharCode (215), String.fromCharCode (216), String.fromCharCode (217), String.fromCharCode (218), String.fromCharCode (219), String.fromCharCode (220), String.fromCharCode (221), String.fromCharCode (222), String.fromCharCode (223), String.fromCharCode (224), String.fromCharCode (225), String.fromCharCode (226), String.fromCharCode (227), String.fromCharCode (228), String.fromCharCode (229), String.fromCharCode (230), String.fromCharCode (231), String.fromCharCode (232), String.fromCharCode (233), String.fromCharCode (234), String.fromCharCode (235), String.fromCharCode (236), String.fromCharCode (237), String.fromCharCode (238), String.fromCharCode (239), String.fromCharCode (240), String.fromCharCode (241), String.fromCharCode (242), String.fromCharCode (243), String.fromCharCode (244), String.fromCharCode (245), String.fromCharCode (246), String.fromCharCode (247), String.fromCharCode (248), String.fromCharCode (249), String.fromCharCode (250), String.fromCharCode (251), String.fromCharCode (252), String.fromCharCode (253), String.fromCharCode (254), String.fromCharCode (255), String.fromCharCode (128), String.fromCharCode (129), String.fromCharCode (130), String.fromCharCode (131), String.fromCharCode (132), String.fromCharCode (133), String.fromCharCode (134), String.fromCharCode (135), String.fromCharCode (136), String.fromCharCode (137), String.fromCharCode (138), String.fromCharCode (139), String.fromCharCode (140), String.fromCharCode (141), String.fromCharCode (142), String.fromCharCode (143), String.fromCharCode (144), String.fromCharCode (145), String.fromCharCode (146), String.fromCharCode (147), String.fromCharCode (148), String.fromCharCode (149), String.fromCharCode (150), String.fromCharCode (151), String.fromCharCode (152), String.fromCharCode (153), String.fromCharCode (154), String.fromCharCode (155), String.fromCharCode (156), String.fromCharCode (157), String.fromCharCode (158), String.fromCharCode (159), String.fromCharCode (160), String.fromCharCode (161), String.fromCharCode (162), String.fromCharCode (163), String.fromCharCode (164), String.fromCharCode (165), String.fromCharCode (166), String.fromCharCode (167), String.fromCharCode (168), String.fromCharCode (169), String.fromCharCode (170), String.fromCharCode (171), String.fromCharCode (172), String.fromCharCode (173), String.fromCharCode (174), String.fromCharCode (175), String.fromCharCode (176), String.fromCharCode (177), String.fromCharCode (178), String.fromCharCode (179), String.fromCharCode (180), String.fromCharCode (181), String.fromCharCode (182), String.fromCharCode (183), String.fromCharCode (184), String.fromCharCode (185), String.fromCharCode (186), String.fromCharCode (187), String.fromCharCode (188), String.fromCharCode (189), String.fromCharCode (190), String.fromCharCode (191)])); diff --git a/bin/com/stevesoft/pat/Custom.js b/bin/com/stevesoft/pat/Custom.js index 4e0fa72..44fa656 100644 --- a/bin/com/stevesoft/pat/Custom.js +++ b/bin/com/stevesoft/pat/Custom.js @@ -1,41 +1,41 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.Custom", ["com.stevesoft.pat.Regex"], function () { -c$ = Clazz.decorateAsClass (function () { -this.select = null; -this.v = null; -this.start = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Custom", com.stevesoft.pat.PatternSub); -Clazz.makeConstructor (c$, -function (s) { -Clazz.superConstructor (this, com.stevesoft.pat.Custom, []); -this.select = s; -this.v = com.stevesoft.pat.Regex.validators.get (s); -}, "~S"); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -this.start = pos; -return this.sub.matchInternal (pos, pt); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -var a = this.v.argsave == null ? "" : ":" + this.v.argsave; -return "(??" + this.select + a + ")" + this.nextString (); -}); -Clazz.overrideMethod (c$, "minChars", -function () { -return this.v.minChars (); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return this.v.maxChars (); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -var c = new com.stevesoft.pat.Custom (this.select); -h.put (c, c); -h.put (this, c); -c.sub = this.sub.clone (h); -return c; -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.Custom", ["com.stevesoft.pat.Regex"], function () { +c$ = Clazz.decorateAsClass (function () { +this.select = null; +this.v = null; +this.start = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Custom", com.stevesoft.pat.PatternSub); +Clazz.makeConstructor (c$, +function (s) { +Clazz.superConstructor (this, com.stevesoft.pat.Custom, []); +this.select = s; +this.v = com.stevesoft.pat.Regex.validators.get (s); +}, "~S"); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +this.start = pos; +return this.sub.matchInternal (pos, pt); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +var a = this.v.argsave == null ? "" : ":" + this.v.argsave; +return "(??" + this.select + a + ")" + this.nextString (); +}); +Clazz.overrideMethod (c$, "minChars", +function () { +return this.v.minChars (); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return this.v.maxChars (); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +var c = new com.stevesoft.pat.Custom (this.select); +h.put (c, c); +h.put (this, c); +c.sub = this.sub.clone (h); +return c; +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/CustomEndpoint.js b/bin/com/stevesoft/pat/CustomEndpoint.js index f5cb0ed..800608f 100644 --- a/bin/com/stevesoft/pat/CustomEndpoint.js +++ b/bin/com/stevesoft/pat/CustomEndpoint.js @@ -1,27 +1,27 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.CustomEndpoint", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.c = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "CustomEndpoint", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (cm) { -Clazz.superConstructor (this, com.stevesoft.pat.CustomEndpoint, []); -this.c = cm; -}, "com.stevesoft.pat.Custom"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -var npos = this.c.v.validate (pt.src, this.c.start, pos); -if (npos >= 0) { -return this.nextMatch (npos, pt); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -return ""; -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.CustomEndpoint (this.c.clone (h)); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.CustomEndpoint", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.c = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "CustomEndpoint", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (cm) { +Clazz.superConstructor (this, com.stevesoft.pat.CustomEndpoint, []); +this.c = cm; +}, "com.stevesoft.pat.Custom"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +var npos = this.c.v.validate (pt.src, this.c.start, pos); +if (npos >= 0) { +return this.nextMatch (npos, pt); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +return ""; +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.CustomEndpoint (this.c.clone (h)); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/DirFileRegex.js b/bin/com/stevesoft/pat/DirFileRegex.js index 0a2470f..b078e11 100644 --- a/bin/com/stevesoft/pat/DirFileRegex.js +++ b/bin/com/stevesoft/pat/DirFileRegex.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.FileRegex"], "com.stevesoft.pat.DirFileRegex", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "DirFileRegex", com.stevesoft.pat.FileRegex); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.FileRegex"], "com.stevesoft.pat.DirFileRegex", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "DirFileRegex", com.stevesoft.pat.FileRegex); +}); diff --git a/bin/com/stevesoft/pat/DotMulti.class b/bin/com/stevesoft/pat/DotMulti.class index 3ec04e2..25dfe0a 100644 Binary files a/bin/com/stevesoft/pat/DotMulti.class and b/bin/com/stevesoft/pat/DotMulti.class differ diff --git a/bin/com/stevesoft/pat/DotMulti.js b/bin/com/stevesoft/pat/DotMulti.js index 3584af1..172397b 100644 --- a/bin/com/stevesoft/pat/DotMulti.js +++ b/bin/com/stevesoft/pat/DotMulti.js @@ -1,129 +1,129 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.DotMulti", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.fewestMatches = null; -this.mostMatches = null; -this.matchFewest = false; -this.src = null; -this.srclength = 0; -this.dotDoesntMatchCR = true; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "DotMulti", com.stevesoft.pat.PatternSub); -Clazz.overrideMethod (c$, "minChars", -function () { -return this.fewestMatches; -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return this.mostMatches; -}); -Clazz.makeConstructor (c$, -function (a, b) { -Clazz.superConstructor (this, com.stevesoft.pat.DotMulti, []); -this.fewestMatches = a; -this.mostMatches = b; -}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt"); -Clazz.overrideMethod (c$, "toString", -function () { -return ".{" + this.fewestMatches + "," + this.mostMatches + "}" + (this.matchFewest ? "?" : "") + "(?# <= dot multi)" + this.nextString (); -}); -Clazz.defineMethod (c$, "submatchInternal", -function (pos, pt) { -if (pos < this.srclength) { -if (this.dotDoesntMatchCR) { -if (this.src.charAt (pos) != '\n') { -return 1 + pos; -}} else { -return 1 + pos; -}}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -var m = -1; -var i = pos; -this.src = pt.src; -this.srclength = this.src.length (); -this.dotDoesntMatchCR = pt.dotDoesntMatchCR; -if (this.matchFewest) { -var nMatches = 0; -while (this.fewestMatches.intValue () > nMatches) { -i = this.submatchInternal (i, pt); -if (i < 0) { -return -1; -}nMatches++; -} -if (i < 0) { -return -1; -}var ii = this.nextMatch (i, pt); -if (ii >= 0) { -return ii; -}if (!this.mostMatches.finite ()) { -while (i >= 0) { -i = this.submatchInternal (i, pt); -if (i < 0) { -return -1; -}ii = this.nextMatch (i, pt); -if (ii >= 0) { -return ii; -}} -} else { -while (i > 0) { -i = this.submatchInternal (i, pt); -if (i < 0) { -return -1; -}nMatches++; -if (nMatches > this.mostMatches.intValue ()) { -return -1; -}ii = this.nextMatch (i, pt); -if (ii >= 0) { -return ii; -}} -}return -1; -}var nMatches = 0; -while (this.fewestMatches.intValue () > nMatches) { -i = this.submatchInternal (i, pt); -if (i >= 0) { -nMatches++; -} else { -return -1; -}} -m = i; -if (this.mostMatches.finite ()) { -while (nMatches < this.mostMatches.intValue ()) { -i = this.submatchInternal (i, pt); -if (i >= 0) { -m = i; -nMatches++; -} else { -break; -}} -} else { -while (true) { -i = this.submatchInternal (i, pt); -if (i >= 0) { -m = i; -nMatches++; -} else { -break; -}} -}while (m >= pos) { -var r = this.nextMatch (m, pt); -if (r >= 0) { -return r; -}m -= 1; -nMatches--; -if (nMatches < this.fewestMatches.intValue ()) { -return -1; -}} -return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -var dm = new com.stevesoft.pat.DotMulti (this.fewestMatches, this.mostMatches); -dm.matchFewest = this.matchFewest; -return dm; -}, "java.util.Hashtable"); -Clazz.defineStatics (c$, -"step", 1, -"idcount", 1); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.DotMulti", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.fewestMatches = null; +this.mostMatches = null; +this.matchFewest = false; +this.src = null; +this.srclength = 0; +this.dotDoesntMatchCR = true; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "DotMulti", com.stevesoft.pat.PatternSub); +Clazz.overrideMethod (c$, "minChars", +function () { +return this.fewestMatches; +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return this.mostMatches; +}); +Clazz.makeConstructor (c$, +function (a, b) { +Clazz.superConstructor (this, com.stevesoft.pat.DotMulti, []); +this.fewestMatches = a; +this.mostMatches = b; +}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt"); +Clazz.overrideMethod (c$, "toString", +function () { +return ".{" + this.fewestMatches + "," + this.mostMatches + "}" + (this.matchFewest ? "?" : "") + "(?# <= dot multi)" + this.nextString (); +}); +Clazz.defineMethod (c$, "submatchInternal", +function (pos, pt) { +if (pos < this.srclength) { +if (this.dotDoesntMatchCR) { +if (this.src.charAt (pos) != '\n') { +return 1 + pos; +}} else { +return 1 + pos; +}}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +var m = -1; +var i = pos; +this.src = pt.src; +this.srclength = this.src.length (); +this.dotDoesntMatchCR = pt.dotDoesntMatchCR; +if (this.matchFewest) { +var nMatches = 0; +while (this.fewestMatches.intValue () > nMatches) { +i = this.submatchInternal (i, pt); +if (i < 0) { +return -1; +}nMatches++; +} +if (i < 0) { +return -1; +}var ii = this.nextMatch (i, pt); +if (ii >= 0) { +return ii; +}if (!this.mostMatches.finite ()) { +while (i >= 0) { +i = this.submatchInternal (i, pt); +if (i < 0) { +return -1; +}ii = this.nextMatch (i, pt); +if (ii >= 0) { +return ii; +}} +} else { +while (i > 0) { +i = this.submatchInternal (i, pt); +if (i < 0) { +return -1; +}nMatches++; +if (nMatches > this.mostMatches.intValue ()) { +return -1; +}ii = this.nextMatch (i, pt); +if (ii >= 0) { +return ii; +}} +}return -1; +}var nMatches = 0; +while (this.fewestMatches.intValue () > nMatches) { +i = this.submatchInternal (i, pt); +if (i >= 0) { +nMatches++; +} else { +return -1; +}} +m = i; +if (this.mostMatches.finite ()) { +while (nMatches < this.mostMatches.intValue ()) { +i = this.submatchInternal (i, pt); +if (i >= 0) { +m = i; +nMatches++; +} else { +break; +}} +} else { +while (true) { +i = this.submatchInternal (i, pt); +if (i >= 0) { +m = i; +nMatches++; +} else { +break; +}} +}while (m >= pos) { +var r = this.nextMatch (m, pt); +if (r >= 0) { +return r; +}m -= 1; +nMatches--; +if (nMatches < this.fewestMatches.intValue ()) { +return -1; +}} +return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +var dm = new com.stevesoft.pat.DotMulti (this.fewestMatches, this.mostMatches); +dm.matchFewest = this.matchFewest; +return dm; +}, "java.util.Hashtable"); +Clazz.defineStatics (c$, +"step", 1, +"idcount", 1); +}); diff --git a/bin/com/stevesoft/pat/End.js b/bin/com/stevesoft/pat/End.js index b332682..3df399f 100644 --- a/bin/com/stevesoft/pat/End.js +++ b/bin/com/stevesoft/pat/End.js @@ -1,38 +1,38 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.End", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.retIsEnd = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "End", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (b) { -Clazz.superConstructor (this, com.stevesoft.pat.End, []); -this.retIsEnd = b; -}, "~B"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (this.retIsEnd && pt.mFlag && pos < pt.src.length ()) { -if (pt.src.charAt (pos) == '\n') { -return this.nextMatch (pos, pt); -}}if (pt.src.length () == pos) { -return this.nextMatch (pos, pt); -} else if (pos < pt.src.length ()) { -pt.src.charAt (pos); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -if (this.retIsEnd) { -return "$"; -} else { -return "\\Z"; -}}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.End (this.retIsEnd); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.End", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.retIsEnd = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "End", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (b) { +Clazz.superConstructor (this, com.stevesoft.pat.End, []); +this.retIsEnd = b; +}, "~B"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (this.retIsEnd && pt.mFlag && pos < pt.src.length ()) { +if (pt.src.charAt (pos) == '\n') { +return this.nextMatch (pos, pt); +}}if (pt.src.length () == pos) { +return this.nextMatch (pos, pt); +} else if (pos < pt.src.length ()) { +pt.src.charAt (pos); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +if (this.retIsEnd) { +return "$"; +} else { +return "\\Z"; +}}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.End (this.retIsEnd); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/FastBracket.js b/bin/com/stevesoft/pat/FastBracket.js index 0e7d38a..d26c009 100644 --- a/bin/com/stevesoft/pat/FastBracket.js +++ b/bin/com/stevesoft/pat/FastBracket.js @@ -1,156 +1,156 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Bracket"], "com.stevesoft.pat.FastBracket", ["com.stevesoft.pat.Range", "$.oneChar", "java.util.BitSet", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.$min = 0; -this.$max = 0; -this.bs = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "FastBracket", com.stevesoft.pat.Bracket); -c$.process = Clazz.defineMethod (c$, "process", -function (b, ignc) { -var v = b.v; -b.pv = null; -try { -var nv = v; -if (ignc) { -nv = new java.util.Vector (); -for (var i = 0; i < v.size (); i++) { -var p = v.elementAt (i); -nv.addElement (p); -if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar)) { -var oc = p; -nv.addElement ( new com.stevesoft.pat.oneChar (oc.altc)); -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Range)) { -var ra = p; -nv.addElement ( new com.stevesoft.pat.Range (ra.altlo, ra.althi)); -}} -}v = nv; -for (var i = 0; i < v.size () - 1; i++) { -for (var j = 0; j < v.size () - 1; j++) { -var c1 = com.stevesoft.pat.FastBracket.getl (v.elementAt (j)); -var c2 = com.stevesoft.pat.FastBracket.getl (v.elementAt (j + 1)); -if (c2 < c1) { -var o = v.elementAt (j); -v.setElementAt (v.elementAt (j + 1), j); -v.setElementAt (o, j + 1); -}} -} -nv = new java.util.Vector (); -var p = v.elementAt (0); -nv.addElement (p); -for (var i = 1; i < v.size (); i++) { -if ((com.stevesoft.pat.FastBracket.geth (p)).charCodeAt (0) + 1 >= (com.stevesoft.pat.FastBracket.getl (v.elementAt (i))).charCodeAt (0)) { -var p2 = v.elementAt (i); -var lo = com.stevesoft.pat.FastBracket.min (com.stevesoft.pat.FastBracket.getl (p), com.stevesoft.pat.FastBracket.getl (p2)); -var hi = com.stevesoft.pat.FastBracket.max (com.stevesoft.pat.FastBracket.geth (p), com.stevesoft.pat.FastBracket.geth (p2)); -nv.setElementAt (p = com.stevesoft.pat.FastBracket.mkelem (lo, hi), nv.size () - 1); -} else { -p = v.elementAt (i); -nv.addElement (p); -}} -b.v = v = nv; -} catch (e) { -if (Clazz.exceptionOf (e, com.stevesoft.pat.RegSyntax)) { -e.printStackTrace (); -} else { -throw e; -} -} -var negv = com.stevesoft.pat.FastBracket.neg (v); -if (v.size () == 1) { -return b; -}if (negv.size () == 1) { -b.v = negv; -b.neg = !b.neg; -return b; -}var fb = com.stevesoft.pat.FastBracket.newbrack (v, b.neg); -if (fb == null) { -fb = com.stevesoft.pat.FastBracket.newbrack (negv, !b.neg); -}if (fb != null) { -fb.parent = b.parent; -fb.next = b.next; -return fb; -}return b; -}, "com.stevesoft.pat.Bracket,~B"); -c$.newbrack = Clazz.defineMethod (c$, "newbrack", -function (v, neg) { -var fb = new com.stevesoft.pat.FastBracket (neg); -fb.v = v; -if (v.size () == 0) { -return null; -}fb.$min = (com.stevesoft.pat.FastBracket.getl (v.elementAt (0))).charCodeAt (0); -fb.$max = (com.stevesoft.pat.FastBracket.geth (v.elementAt (v.size () - 1))).charCodeAt (0); -if (fb.$max - fb.$min <= 256) { -fb.bs = new java.util.BitSet (fb.$max - fb.$min + 1); -for (var i = 0; i < v.size (); i++) { -var o = v.elementAt (i); -var min0 = (com.stevesoft.pat.FastBracket.getl (o)).charCodeAt (0) - fb.$min; -var max0 = (com.stevesoft.pat.FastBracket.geth (o)).charCodeAt (0) - fb.$min; -for (var j = min0; j <= max0; j++) { -fb.bs.set (j); -} -} -return fb; -}return null; -}, "java.util.Vector,~B"); -c$.neg = Clazz.defineMethod (c$, "neg", -function (v) { -try { -var nv = new java.util.Vector (); -if (v.size () == 0) { -nv.addElement ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (65535))); -return nv; -}var p0 = (com.stevesoft.pat.FastBracket.getl (v.elementAt (0))).charCodeAt (0); -if (p0 != 0) { -nv.addElement (com.stevesoft.pat.FastBracket.mkelem (String.fromCharCode (0), String.fromCharCode (p0 - 1))); -}for (var i = 0; i < v.size () - 1; i++) { -var hi = (com.stevesoft.pat.FastBracket.getl (v.elementAt (i + 1))).charCodeAt (0) - 1; -var lo = (com.stevesoft.pat.FastBracket.geth (v.elementAt (i))).charCodeAt (0) + 1; -nv.addElement (com.stevesoft.pat.FastBracket.mkelem (String.fromCharCode (lo), String.fromCharCode (hi))); -} -var pN = (com.stevesoft.pat.FastBracket.geth (v.lastElement ())).charCodeAt (0); -if (pN != 65535) { -nv.addElement (com.stevesoft.pat.FastBracket.mkelem (String.fromCharCode (pN + 1), String.fromCharCode (65535))); -}return nv; -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -return null; -} else { -throw rs; -} -} -}, "java.util.Vector"); -c$.mkelem = Clazz.defineMethod (c$, "mkelem", -function (lo, hi) { -return lo == hi ? ( new com.stevesoft.pat.oneChar (lo)) : ( new com.stevesoft.pat.Range (lo, hi)); -}, "~S,~S"); -c$.min = Clazz.defineMethod (c$, "min", -function (a, b) { -return a < b ? a : b; -}, "~S,~S"); -c$.max = Clazz.defineMethod (c$, "max", -function (a, b) { -return a > b ? a : b; -}, "~S,~S"); -c$.getl = Clazz.defineMethod (c$, "getl", -function (o) { -var p = o; -if (Clazz.instanceOf (p, com.stevesoft.pat.Range)) { -return (p).lo; -}return (p).c; -}, "~O"); -c$.geth = Clazz.defineMethod (c$, "geth", -function (o) { -var p = o; -if (Clazz.instanceOf (p, com.stevesoft.pat.Range)) { -return (p).hi; -}return (p).c; -}, "~O"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (pos >= pt.src.length () || this.Masked (pos, pt)) { -return -1; -}var c = pt.src.charAt (pos); -return ( new Boolean (this.neg ^ (c.charCodeAt (0) >= this.$min && c.charCodeAt (0) <= this.$max && this.bs.get (c.charCodeAt (0) - this.$min))).valueOf ()) ? this.nextMatch (pos + 1, pt) : -1; -}, "~N,com.stevesoft.pat.Pthings"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Bracket"], "com.stevesoft.pat.FastBracket", ["com.stevesoft.pat.Range", "$.oneChar", "java.util.BitSet", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.$min = 0; +this.$max = 0; +this.bs = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "FastBracket", com.stevesoft.pat.Bracket); +c$.process = Clazz.defineMethod (c$, "process", +function (b, ignc) { +var v = b.v; +b.pv = null; +try { +var nv = v; +if (ignc) { +nv = new java.util.Vector (); +for (var i = 0; i < v.size (); i++) { +var p = v.elementAt (i); +nv.addElement (p); +if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar)) { +var oc = p; +nv.addElement ( new com.stevesoft.pat.oneChar (oc.altc)); +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Range)) { +var ra = p; +nv.addElement ( new com.stevesoft.pat.Range (ra.altlo, ra.althi)); +}} +}v = nv; +for (var i = 0; i < v.size () - 1; i++) { +for (var j = 0; j < v.size () - 1; j++) { +var c1 = com.stevesoft.pat.FastBracket.getl (v.elementAt (j)); +var c2 = com.stevesoft.pat.FastBracket.getl (v.elementAt (j + 1)); +if (c2 < c1) { +var o = v.elementAt (j); +v.setElementAt (v.elementAt (j + 1), j); +v.setElementAt (o, j + 1); +}} +} +nv = new java.util.Vector (); +var p = v.elementAt (0); +nv.addElement (p); +for (var i = 1; i < v.size (); i++) { +if ((com.stevesoft.pat.FastBracket.geth (p)).charCodeAt (0) + 1 >= (com.stevesoft.pat.FastBracket.getl (v.elementAt (i))).charCodeAt (0)) { +var p2 = v.elementAt (i); +var lo = com.stevesoft.pat.FastBracket.min (com.stevesoft.pat.FastBracket.getl (p), com.stevesoft.pat.FastBracket.getl (p2)); +var hi = com.stevesoft.pat.FastBracket.max (com.stevesoft.pat.FastBracket.geth (p), com.stevesoft.pat.FastBracket.geth (p2)); +nv.setElementAt (p = com.stevesoft.pat.FastBracket.mkelem (lo, hi), nv.size () - 1); +} else { +p = v.elementAt (i); +nv.addElement (p); +}} +b.v = v = nv; +} catch (e) { +if (Clazz.exceptionOf (e, com.stevesoft.pat.RegSyntax)) { +e.printStackTrace (); +} else { +throw e; +} +} +var negv = com.stevesoft.pat.FastBracket.neg (v); +if (v.size () == 1) { +return b; +}if (negv.size () == 1) { +b.v = negv; +b.neg = !b.neg; +return b; +}var fb = com.stevesoft.pat.FastBracket.newbrack (v, b.neg); +if (fb == null) { +fb = com.stevesoft.pat.FastBracket.newbrack (negv, !b.neg); +}if (fb != null) { +fb.parent = b.parent; +fb.next = b.next; +return fb; +}return b; +}, "com.stevesoft.pat.Bracket,~B"); +c$.newbrack = Clazz.defineMethod (c$, "newbrack", +function (v, neg) { +var fb = new com.stevesoft.pat.FastBracket (neg); +fb.v = v; +if (v.size () == 0) { +return null; +}fb.$min = (com.stevesoft.pat.FastBracket.getl (v.elementAt (0))).charCodeAt (0); +fb.$max = (com.stevesoft.pat.FastBracket.geth (v.elementAt (v.size () - 1))).charCodeAt (0); +if (fb.$max - fb.$min <= 256) { +fb.bs = new java.util.BitSet (fb.$max - fb.$min + 1); +for (var i = 0; i < v.size (); i++) { +var o = v.elementAt (i); +var min0 = (com.stevesoft.pat.FastBracket.getl (o)).charCodeAt (0) - fb.$min; +var max0 = (com.stevesoft.pat.FastBracket.geth (o)).charCodeAt (0) - fb.$min; +for (var j = min0; j <= max0; j++) { +fb.bs.set (j); +} +} +return fb; +}return null; +}, "java.util.Vector,~B"); +c$.neg = Clazz.defineMethod (c$, "neg", +function (v) { +try { +var nv = new java.util.Vector (); +if (v.size () == 0) { +nv.addElement ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (65535))); +return nv; +}var p0 = (com.stevesoft.pat.FastBracket.getl (v.elementAt (0))).charCodeAt (0); +if (p0 != 0) { +nv.addElement (com.stevesoft.pat.FastBracket.mkelem (String.fromCharCode (0), String.fromCharCode (p0 - 1))); +}for (var i = 0; i < v.size () - 1; i++) { +var hi = (com.stevesoft.pat.FastBracket.getl (v.elementAt (i + 1))).charCodeAt (0) - 1; +var lo = (com.stevesoft.pat.FastBracket.geth (v.elementAt (i))).charCodeAt (0) + 1; +nv.addElement (com.stevesoft.pat.FastBracket.mkelem (String.fromCharCode (lo), String.fromCharCode (hi))); +} +var pN = (com.stevesoft.pat.FastBracket.geth (v.lastElement ())).charCodeAt (0); +if (pN != 65535) { +nv.addElement (com.stevesoft.pat.FastBracket.mkelem (String.fromCharCode (pN + 1), String.fromCharCode (65535))); +}return nv; +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +return null; +} else { +throw rs; +} +} +}, "java.util.Vector"); +c$.mkelem = Clazz.defineMethod (c$, "mkelem", +function (lo, hi) { +return lo == hi ? ( new com.stevesoft.pat.oneChar (lo)) : ( new com.stevesoft.pat.Range (lo, hi)); +}, "~S,~S"); +c$.min = Clazz.defineMethod (c$, "min", +function (a, b) { +return a < b ? a : b; +}, "~S,~S"); +c$.max = Clazz.defineMethod (c$, "max", +function (a, b) { +return a > b ? a : b; +}, "~S,~S"); +c$.getl = Clazz.defineMethod (c$, "getl", +function (o) { +var p = o; +if (Clazz.instanceOf (p, com.stevesoft.pat.Range)) { +return (p).lo; +}return (p).c; +}, "~O"); +c$.geth = Clazz.defineMethod (c$, "geth", +function (o) { +var p = o; +if (Clazz.instanceOf (p, com.stevesoft.pat.Range)) { +return (p).hi; +}return (p).c; +}, "~O"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (pos >= pt.src.length () || this.Masked (pos, pt)) { +return -1; +}var c = pt.src.charAt (pos); +return ( new Boolean (this.neg ^ (c.charCodeAt (0) >= this.$min && c.charCodeAt (0) <= this.$max && this.bs.get (c.charCodeAt (0) - this.$min))).valueOf ()) ? this.nextMatch (pos + 1, pt) : -1; +}, "~N,com.stevesoft.pat.Pthings"); +}); diff --git a/bin/com/stevesoft/pat/FastMulti.class b/bin/com/stevesoft/pat/FastMulti.class index 9de4ac6..5baa014 100644 Binary files a/bin/com/stevesoft/pat/FastMulti.class and b/bin/com/stevesoft/pat/FastMulti.class differ diff --git a/bin/com/stevesoft/pat/FastMulti.js b/bin/com/stevesoft/pat/FastMulti.js index 898aa9e..16ffec1 100644 --- a/bin/com/stevesoft/pat/FastMulti.js +++ b/bin/com/stevesoft/pat/FastMulti.js @@ -1,108 +1,108 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.FastMulti", ["com.stevesoft.pat.RegSyntaxError", "$.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fewestMatches = null; -this.mostMatches = null; -this.matchFewest = false; -this.step = -1; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "FastMulti", com.stevesoft.pat.PatternSub); -Clazz.overrideMethod (c$, "minChars", -function () { -return this.sub.countMinChars ().mul (this.fewestMatches); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return this.sub.countMaxChars ().mul (this.mostMatches); -}); -Clazz.makeConstructor (c$, -function (a, b, p) { -Clazz.superConstructor (this, com.stevesoft.pat.FastMulti, []); -if (p == null) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Null length pattern followed by *, +, or other Multi."); -}this.fewestMatches = a; -this.mostMatches = b; -this.sub = p; -this.step = p.countMinChars ().intValue (); -this.sub.setParent (null); -}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "toString", -function () { -return this.sub.toString () + "{" + this.fewestMatches + "," + this.mostMatches + "}" + (this.matchFewest ? "?" : "") + "(?# <= fast multi)" + this.nextString (); -}); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -var m = -1; -var i = pos; -var endstr = pt.src.length () - this.step; -var matches = new com.stevesoft.pat.patInt (0); -if (this.matchFewest) { -if (this.fewestMatches.lessEq (matches)) { -var ii = this.nextMatch (i, pt); -if (ii >= 0) { -return ii; -}}while (i >= 0 && i <= endstr) { -i = this.sub.matchInternal (i, pt); -if (i >= 0) { -matches.inc (); -if (this.fewestMatches.lessEq (matches)) { -var ii = this.nextMatch (i, pt); -if (ii >= 0) { -return ii; -}}if (matches.equals (this.mostMatches)) { -return -1; -}}} -return -1; -}var nMatches = 0; -while (this.fewestMatches.intValue () > nMatches) { -i = this.sub.matchInternal (i, pt); -if (i >= 0) { -nMatches++; -} else { -return -1; -}} -m = i; -if (this.mostMatches.finite ()) { -while (nMatches < this.mostMatches.intValue ()) { -i = this.sub.matchInternal (i, pt); -if (i >= 0) { -m = i; -nMatches++; -} else { -break; -}} -} else { -while (true) { -i = this.sub.matchInternal (i, pt); -if (i >= 0) { -m = i; -nMatches++; -} else { -break; -}} -}while (m >= pos) { -var r = this.nextMatch (m, pt); -if (r >= 0) { -return r; -}m -= this.step; -nMatches--; -if (nMatches < this.fewestMatches.intValue ()) { -return -1; -}} -return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -try { -var fm = new com.stevesoft.pat.FastMulti (this.fewestMatches, this.mostMatches, this.sub.clone (h)); -fm.matchFewest = this.matchFewest; -return fm; -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -return null; -} else { -throw rs; -} -} -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.FastMulti", ["com.stevesoft.pat.RegSyntaxError", "$.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fewestMatches = null; +this.mostMatches = null; +this.matchFewest = false; +this.step = -1; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "FastMulti", com.stevesoft.pat.PatternSub); +Clazz.overrideMethod (c$, "minChars", +function () { +return this.sub.countMinChars ().mul (this.fewestMatches); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return this.sub.countMaxChars ().mul (this.mostMatches); +}); +Clazz.makeConstructor (c$, +function (a, b, p) { +Clazz.superConstructor (this, com.stevesoft.pat.FastMulti, []); +if (p == null) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Null length pattern followed by *, +, or other Multi."); +}this.fewestMatches = a; +this.mostMatches = b; +this.sub = p; +this.step = p.countMinChars ().intValue (); +this.sub.setParent (null); +}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "toString", +function () { +return this.sub.toString () + "{" + this.fewestMatches + "," + this.mostMatches + "}" + (this.matchFewest ? "?" : "") + "(?# <= fast multi)" + this.nextString (); +}); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +var m = -1; +var i = pos; +var endstr = pt.src.length () - this.step; +var matches = new com.stevesoft.pat.patInt (0); +if (this.matchFewest) { +if (this.fewestMatches.lessEq (matches)) { +var ii = this.nextMatch (i, pt); +if (ii >= 0) { +return ii; +}}while (i >= 0 && i <= endstr) { +i = this.sub.matchInternal (i, pt); +if (i >= 0) { +matches.inc (); +if (this.fewestMatches.lessEq (matches)) { +var ii = this.nextMatch (i, pt); +if (ii >= 0) { +return ii; +}}if (matches.equals (this.mostMatches)) { +return -1; +}}} +return -1; +}var nMatches = 0; +while (this.fewestMatches.intValue () > nMatches) { +i = this.sub.matchInternal (i, pt); +if (i >= 0) { +nMatches++; +} else { +return -1; +}} +m = i; +if (this.mostMatches.finite ()) { +while (nMatches < this.mostMatches.intValue ()) { +i = this.sub.matchInternal (i, pt); +if (i >= 0) { +m = i; +nMatches++; +} else { +break; +}} +} else { +while (true) { +i = this.sub.matchInternal (i, pt); +if (i >= 0) { +m = i; +nMatches++; +} else { +break; +}} +}while (m >= pos) { +var r = this.nextMatch (m, pt); +if (r >= 0) { +return r; +}m -= this.step; +nMatches--; +if (nMatches < this.fewestMatches.intValue ()) { +return -1; +}} +return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +try { +var fm = new com.stevesoft.pat.FastMulti (this.fewestMatches, this.mostMatches, this.sub.clone (h)); +fm.matchFewest = this.matchFewest; +return fm; +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +return null; +} else { +throw rs; +} +} +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/FileRegex.js b/bin/com/stevesoft/pat/FileRegex.js index ca23839..8327c7c 100644 --- a/bin/com/stevesoft/pat/FileRegex.js +++ b/bin/com/stevesoft/pat/FileRegex.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Regex"], "com.stevesoft.pat.FileRegex", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "FileRegex", com.stevesoft.pat.Regex); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Regex"], "com.stevesoft.pat.FileRegex", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "FileRegex", com.stevesoft.pat.Regex); +}); diff --git a/bin/com/stevesoft/pat/Group.js b/bin/com/stevesoft/pat/Group.js index a9ebd1b..89fdd10 100644 --- a/bin/com/stevesoft/pat/Group.js +++ b/bin/com/stevesoft/pat/Group.js @@ -1,48 +1,48 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Group", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.op = '\0'; -this.cl = '\0'; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Group", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (opi, cli) { -Clazz.superConstructor (this, com.stevesoft.pat.Group, []); -this.op = opi; -this.cl = cli; -}, "~S,~S"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -var i; -var count = 1; -if (pos < pt.src.length ()) { -if (!this.Masked (pos, pt) && pt.src.charAt (pos) != this.op) { -return -1; -}}for (i = pos + 1; i < pt.src.length (); i++) { -var c = pt.src.charAt (i); -var b = !this.Masked (i, pt); -if (b && c == '\\') { -i++; -} else { -if (b && c == this.cl) { -count--; -}if (count == 0) { -return this.nextMatch (i + 1, pt); -}if (b && c == this.op) { -count++; -}}} -return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -return "(?@" + this.op + this.cl + ")" + this.nextString (); -}); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (2); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.Group (this.op, this.cl); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Group", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.op = '\0'; +this.cl = '\0'; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Group", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (opi, cli) { +Clazz.superConstructor (this, com.stevesoft.pat.Group, []); +this.op = opi; +this.cl = cli; +}, "~S,~S"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +var i; +var count = 1; +if (pos < pt.src.length ()) { +if (!this.Masked (pos, pt) && pt.src.charAt (pos) != this.op) { +return -1; +}}for (i = pos + 1; i < pt.src.length (); i++) { +var c = pt.src.charAt (i); +var b = !this.Masked (i, pt); +if (b && c == '\\') { +i++; +} else { +if (b && c == this.cl) { +count--; +}if (count == 0) { +return this.nextMatch (i + 1, pt); +}if (b && c == this.op) { +count++; +}}} +return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +return "(?@" + this.op + this.cl + ")" + this.nextString (); +}); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (2); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.Group (this.op, this.cl); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/LeftRule.js b/bin/com/stevesoft/pat/LeftRule.js index f70f50c..df5c04a 100644 --- a/bin/com/stevesoft/pat/LeftRule.js +++ b/bin/com/stevesoft/pat/LeftRule.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.LeftRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "LeftRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.LeftRule, []); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -sb.append (res.left ()); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return "$`"; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.LeftRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "LeftRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.LeftRule, []); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +sb.append (res.left ()); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return "$`"; +}); +}); diff --git a/bin/com/stevesoft/pat/MessageManager.js b/bin/com/stevesoft/pat/MessageManager.js index 801e5de..23502c3 100644 --- a/bin/com/stevesoft/pat/MessageManager.js +++ b/bin/com/stevesoft/pat/MessageManager.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -c$ = Clazz.declareType (com.stevesoft.pat, "MessageManager"); -c$.getString = Clazz.defineMethod (c$, "getString", -function (string) { -return string; -}, "~S"); -c$.formatMessage = Clazz.defineMethod (c$, "formatMessage", -function (s, fields) { -for (var i = 0; i < fields.length; i++) s += " " + fields[i]; - -return s; -}, "~S,~A"); +Clazz.declarePackage ("com.stevesoft.pat"); +c$ = Clazz.declareType (com.stevesoft.pat, "MessageManager"); +c$.getString = Clazz.defineMethod (c$, "getString", +function (string) { +return string; +}, "~S"); +c$.formatMessage = Clazz.defineMethod (c$, "formatMessage", +function (s, fields) { +for (var i = 0; i < fields.length; i++) s += " " + fields[i]; + +return s; +}, "~S,~A"); diff --git a/bin/com/stevesoft/pat/Multi.js b/bin/com/stevesoft/pat/Multi.js index e98b4ff..e759c95 100644 --- a/bin/com/stevesoft/pat/Multi.js +++ b/bin/com/stevesoft/pat/Multi.js @@ -1,62 +1,62 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.Multi", ["com.stevesoft.pat.Multi_stage2"], function () { -c$ = Clazz.decorateAsClass (function () { -this.a = null; -this.b = null; -this.p = null; -this.st2 = null; -this.matchFewest = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Multi", com.stevesoft.pat.PatternSub); -Clazz.overrideMethod (c$, "minChars", -function () { -return this.a.mul (this.p.countMinChars ()); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return this.b.mul (this.p.countMaxChars ()); -}); -Clazz.makeConstructor (c$, -function (a, b, p) { -Clazz.superConstructor (this, com.stevesoft.pat.Multi, []); -this.a = a; -this.b = b; -this.p = p; -this.st2 = new com.stevesoft.pat.Multi_stage2 (a, b, p); -this.st2.parent = this; -this.sub = this.st2.sub; -}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); -Clazz.overrideMethod (c$, "toString", -function () { -this.st2.matchFewest = this.matchFewest; -return this.st2.toString (); -}); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -try { -this.st2 = new com.stevesoft.pat.Multi_stage2 (this.a, this.b, this.p); -} catch (r__) { -if (Clazz.exceptionOf (r__, com.stevesoft.pat.RegSyntax)) { -} else { -throw r__; -} -} -this.st2.matchFewest = this.matchFewest; -this.st2.parent = this; -return this.st2.matchInternal (pos, pt); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -try { -var m = new com.stevesoft.pat.Multi (this.a, this.b, (this.p).clone (h)); -m.matchFewest = this.matchFewest; -return m; -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -return null; -} else { -throw rs; -} -} -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.Multi", ["com.stevesoft.pat.Multi_stage2"], function () { +c$ = Clazz.decorateAsClass (function () { +this.a = null; +this.b = null; +this.p = null; +this.st2 = null; +this.matchFewest = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Multi", com.stevesoft.pat.PatternSub); +Clazz.overrideMethod (c$, "minChars", +function () { +return this.a.mul (this.p.countMinChars ()); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return this.b.mul (this.p.countMaxChars ()); +}); +Clazz.makeConstructor (c$, +function (a, b, p) { +Clazz.superConstructor (this, com.stevesoft.pat.Multi, []); +this.a = a; +this.b = b; +this.p = p; +this.st2 = new com.stevesoft.pat.Multi_stage2 (a, b, p); +this.st2.parent = this; +this.sub = this.st2.sub; +}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); +Clazz.overrideMethod (c$, "toString", +function () { +this.st2.matchFewest = this.matchFewest; +return this.st2.toString (); +}); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +try { +this.st2 = new com.stevesoft.pat.Multi_stage2 (this.a, this.b, this.p); +} catch (r__) { +if (Clazz.exceptionOf (r__, com.stevesoft.pat.RegSyntax)) { +} else { +throw r__; +} +} +this.st2.matchFewest = this.matchFewest; +this.st2.parent = this; +return this.st2.matchInternal (pos, pt); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +try { +var m = new com.stevesoft.pat.Multi (this.a, this.b, (this.p).clone (h)); +m.matchFewest = this.matchFewest; +return m; +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +return null; +} else { +throw rs; +} +} +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/MultiMin.js b/bin/com/stevesoft/pat/MultiMin.js index f536031..e749758 100644 --- a/bin/com/stevesoft/pat/MultiMin.js +++ b/bin/com/stevesoft/pat/MultiMin.js @@ -1,9 +1,9 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Multi"], "com.stevesoft.pat.MultiMin", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "MultiMin", com.stevesoft.pat.Multi); -Clazz.makeConstructor (c$, -function (i1, i2, p) { -Clazz.superConstructor (this, com.stevesoft.pat.MultiMin, [i1, i2, p]); -this.matchFewest = true; -}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Multi"], "com.stevesoft.pat.MultiMin", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "MultiMin", com.stevesoft.pat.Multi); +Clazz.makeConstructor (c$, +function (i1, i2, p) { +Clazz.superConstructor (this, com.stevesoft.pat.MultiMin, [i1, i2, p]); +this.matchFewest = true; +}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); +}); diff --git a/bin/com/stevesoft/pat/Multi_stage2.js b/bin/com/stevesoft/pat/Multi_stage2.js index 1d291ab..6d4f8fc 100644 --- a/bin/com/stevesoft/pat/Multi_stage2.js +++ b/bin/com/stevesoft/pat/Multi_stage2.js @@ -1,95 +1,95 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.Multi_stage2", ["com.stevesoft.pat.RegSyntaxError", "$.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.nextRet = null; -this.count = null; -this.matchMin = null; -this.matchMax = null; -this.matchFewest = false; -this.pos_old = -1; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Multi_stage2", com.stevesoft.pat.PatternSub); -Clazz.defineMethod (c$, "toString", -function () { -var ret = ""; -ret += this.sub.toString (); -ret += "{" + this.matchMin + "," + this.matchMax + "}"; -if (this.matchFewest) { -ret += "?"; -}ret += this.parent.nextString (); -return ret; -}); -Clazz.makeConstructor (c$, -function (a, b, p) { -Clazz.superConstructor (this, com.stevesoft.pat.Multi_stage2, []); -if (p == null) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Multiple match of Null pattern requested."); -}this.sub = p; -this.nextRet = this; -this.sub.setParent (this); -this.matchMin = a; -this.matchMax = b; -this.count = new com.stevesoft.pat.patInt (0); -if (!a.lessEq (b)) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Bad Multi Args: " + a + ">" + b); -}var i = new com.stevesoft.pat.patInt (-1); -if (a.lessEq (i)) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Bad Multi Args: " + a + "< 0"); -}}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "getNext", -function () { -return this.nextRet; -}); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -this.sub.setParent (this); -var canUse = -1; -if (this.pos_old >= 0 && pos == this.pos_old) { -return -1; -}this.pos_old = pos; -if (this.matchMin.lessEq (this.count)) { -canUse = pos; -}if (!this.count.lessEq (this.matchMax) || pos > pt.src.length ()) { -return -1; -}if ((this.matchFewest || this.count.equals (this.matchMax)) && canUse >= 0) { -var n = Clazz.superCall (this, com.stevesoft.pat.Multi_stage2, "getNext", []); -if (n == null) { -return canUse; -}var ret = this.testMatch (n, pos, pt); -if (ret >= 0) { -return ret; -} else { -canUse = -1; -}}this.count.inc (); -try { -if (this.count.lessEq (this.matchMax)) { -var r = this.testMatch (this.sub, pos, pt); -if (r >= 0) { -return r; -}}} finally { -this.count.dec (); -} -if (!this.matchFewest && canUse >= 0) { -var n = Clazz.superCall (this, com.stevesoft.pat.Multi_stage2, "getNext", []); -if (n == null) { -return canUse; -}var ret = this.testMatch (n, pos, pt); -return ret; -} else { -return canUse; -}}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -try { -var m = new com.stevesoft.pat.Multi_stage2 (this.matchMin, this.matchMax, this.sub.clone (h)); -m.matchFewest = this.matchFewest; -return m; -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -return null; -} else { -throw rs; -} -} -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.PatternSub"], "com.stevesoft.pat.Multi_stage2", ["com.stevesoft.pat.RegSyntaxError", "$.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.nextRet = null; +this.count = null; +this.matchMin = null; +this.matchMax = null; +this.matchFewest = false; +this.pos_old = -1; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Multi_stage2", com.stevesoft.pat.PatternSub); +Clazz.defineMethod (c$, "toString", +function () { +var ret = ""; +ret += this.sub.toString (); +ret += "{" + this.matchMin + "," + this.matchMax + "}"; +if (this.matchFewest) { +ret += "?"; +}ret += this.parent.nextString (); +return ret; +}); +Clazz.makeConstructor (c$, +function (a, b, p) { +Clazz.superConstructor (this, com.stevesoft.pat.Multi_stage2, []); +if (p == null) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Multiple match of Null pattern requested."); +}this.sub = p; +this.nextRet = this; +this.sub.setParent (this); +this.matchMin = a; +this.matchMax = b; +this.count = new com.stevesoft.pat.patInt (0); +if (!a.lessEq (b)) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Bad Multi Args: " + a + ">" + b); +}var i = new com.stevesoft.pat.patInt (-1); +if (a.lessEq (i)) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Bad Multi Args: " + a + "< 0"); +}}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "getNext", +function () { +return this.nextRet; +}); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +this.sub.setParent (this); +var canUse = -1; +if (this.pos_old >= 0 && pos == this.pos_old) { +return -1; +}this.pos_old = pos; +if (this.matchMin.lessEq (this.count)) { +canUse = pos; +}if (!this.count.lessEq (this.matchMax) || pos > pt.src.length ()) { +return -1; +}if ((this.matchFewest || this.count.equals (this.matchMax)) && canUse >= 0) { +var n = Clazz.superCall (this, com.stevesoft.pat.Multi_stage2, "getNext", []); +if (n == null) { +return canUse; +}var ret = this.testMatch (n, pos, pt); +if (ret >= 0) { +return ret; +} else { +canUse = -1; +}}this.count.inc (); +try { +if (this.count.lessEq (this.matchMax)) { +var r = this.testMatch (this.sub, pos, pt); +if (r >= 0) { +return r; +}}} finally { +this.count.dec (); +} +if (!this.matchFewest && canUse >= 0) { +var n = Clazz.superCall (this, com.stevesoft.pat.Multi_stage2, "getNext", []); +if (n == null) { +return canUse; +}var ret = this.testMatch (n, pos, pt); +return ret; +} else { +return canUse; +}}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +try { +var m = new com.stevesoft.pat.Multi_stage2 (this.matchMin, this.matchMax, this.sub.clone (h)); +m.matchFewest = this.matchFewest; +return m; +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +return null; +} else { +throw rs; +} +} +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/NoPattern.js b/bin/com/stevesoft/pat/NoPattern.js index ec7438b..394e032 100644 --- a/bin/com/stevesoft/pat/NoPattern.js +++ b/bin/com/stevesoft/pat/NoPattern.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.NoPattern", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "NoPattern", com.stevesoft.pat.Pattern); -Clazz.overrideMethod (c$, "toString", -function () { -return "(?e=#)[^#d#D]"; -}); -Clazz.overrideMethod (c$, "matchInternal", -function (i, p) { -return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.NoPattern (); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.NoPattern", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "NoPattern", com.stevesoft.pat.Pattern); +Clazz.overrideMethod (c$, "toString", +function () { +return "(?e=#)[^#d#D]"; +}); +Clazz.overrideMethod (c$, "matchInternal", +function (i, p) { +return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.NoPattern (); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/NonDirFileRegex.js b/bin/com/stevesoft/pat/NonDirFileRegex.js index 59811e9..eb3a57d 100644 --- a/bin/com/stevesoft/pat/NonDirFileRegex.js +++ b/bin/com/stevesoft/pat/NonDirFileRegex.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.FileRegex"], "com.stevesoft.pat.NonDirFileRegex", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "NonDirFileRegex", com.stevesoft.pat.FileRegex); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.FileRegex"], "com.stevesoft.pat.NonDirFileRegex", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "NonDirFileRegex", com.stevesoft.pat.FileRegex); +}); diff --git a/bin/com/stevesoft/pat/NotImplementedError.js b/bin/com/stevesoft/pat/NotImplementedError.js index 45dd68f..4c44ef5 100644 --- a/bin/com/stevesoft/pat/NotImplementedError.js +++ b/bin/com/stevesoft/pat/NotImplementedError.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.lang.Error"], "com.stevesoft.pat.NotImplementedError", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "NotImplementedError", Error); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.lang.Error"], "com.stevesoft.pat.NotImplementedError", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "NotImplementedError", Error); +}); diff --git a/bin/com/stevesoft/pat/NullPattern.js b/bin/com/stevesoft/pat/NullPattern.js index 2198789..a8eda32 100644 --- a/bin/com/stevesoft/pat/NullPattern.js +++ b/bin/com/stevesoft/pat/NullPattern.js @@ -1,20 +1,20 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.NullPattern", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "NullPattern", com.stevesoft.pat.Pattern); -Clazz.overrideMethod (c$, "toString", -function () { -return this.nextString (); -}); -Clazz.overrideMethod (c$, "matchInternal", -function (p, pt) { -return this.nextMatch (p, pt); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.NullPattern (); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.NullPattern", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "NullPattern", com.stevesoft.pat.Pattern); +Clazz.overrideMethod (c$, "toString", +function () { +return this.nextString (); +}); +Clazz.overrideMethod (c$, "matchInternal", +function (p, pt) { +return this.nextMatch (p, pt); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.NullPattern (); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/NullRule.js b/bin/com/stevesoft/pat/NullRule.js index f6a1485..f781239 100644 --- a/bin/com/stevesoft/pat/NullRule.js +++ b/bin/com/stevesoft/pat/NullRule.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.NullRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "NullRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.NullRule, []); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return ""; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.NullRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "NullRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.NullRule, []); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return ""; +}); +}); diff --git a/bin/com/stevesoft/pat/Or.js b/bin/com/stevesoft/pat/Or.js index 1ca2671..9255825 100644 --- a/bin/com/stevesoft/pat/Or.js +++ b/bin/com/stevesoft/pat/Or.js @@ -1,92 +1,92 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Or", ["com.stevesoft.pat.patInt", "java.lang.StringBuffer", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.v = null; -this.pv = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Or", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.Or, []); -this.v = new java.util.Vector (); -}); -Clazz.defineMethod (c$, "leftForm", -function () { -return "(?:"; -}); -Clazz.defineMethod (c$, "rightForm", -function () { -return ")"; -}); -Clazz.defineMethod (c$, "sepForm", -function () { -return "|"; -}); -Clazz.defineMethod (c$, "addOr", -function (p) { -this.pv = null; -this.v.addElement (p); -p.setParent (this); -return this; -}, "com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "toString", -function () { -var i; -var sb = new StringBuffer (); -sb.append (this.leftForm ()); -if (this.v.size () > 0) { -sb.append ((this.v.elementAt (0)).toString ()); -}for (i = 1; i < this.v.size (); i++) { -sb.append (this.sepForm ()); -sb.append ((this.v.elementAt (i)).toString ()); -} -sb.append (this.rightForm ()); -sb.append (this.nextString ()); -return sb.toString (); -}); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -if (this.pv == null) { -this.pv = new Array (this.v.size ()); -this.v.copyInto (this.pv); -}for (var i = 0; i < this.v.size (); i++) { -var p = this.pv[i]; -var r = p.matchInternal (pos, pt); -if (r >= 0) { -return r; -}} -return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "minChars", -function () { -if (this.v.size () == 0) { -return new com.stevesoft.pat.patInt (0); -}var m = (this.v.elementAt (0)).countMinChars (); -for (var i = 1; i < this.v.size (); i++) { -var p = this.v.elementAt (i); -m.mineq (p.countMinChars ()); -} -return m; -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -if (this.v.size () == 0) { -return new com.stevesoft.pat.patInt (0); -}var m = (this.v.elementAt (0)).countMaxChars (); -for (var i = 1; i < this.v.size (); i++) { -var p = this.v.elementAt (i); -m.maxeq (p.countMaxChars ()); -} -return m; -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -var o = new com.stevesoft.pat.Or (); -h.put (this, o); -h.put (o, o); -for (var i = 0; i < this.v.size (); i++) { -o.v.addElement ((this.v.elementAt (i)).clone (h)); -} -return o; -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Or", ["com.stevesoft.pat.patInt", "java.lang.StringBuffer", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.v = null; +this.pv = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Or", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.Or, []); +this.v = new java.util.Vector (); +}); +Clazz.defineMethod (c$, "leftForm", +function () { +return "(?:"; +}); +Clazz.defineMethod (c$, "rightForm", +function () { +return ")"; +}); +Clazz.defineMethod (c$, "sepForm", +function () { +return "|"; +}); +Clazz.defineMethod (c$, "addOr", +function (p) { +this.pv = null; +this.v.addElement (p); +p.setParent (this); +return this; +}, "com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "toString", +function () { +var i; +var sb = new StringBuffer (); +sb.append (this.leftForm ()); +if (this.v.size () > 0) { +sb.append ((this.v.elementAt (0)).toString ()); +}for (i = 1; i < this.v.size (); i++) { +sb.append (this.sepForm ()); +sb.append ((this.v.elementAt (i)).toString ()); +} +sb.append (this.rightForm ()); +sb.append (this.nextString ()); +return sb.toString (); +}); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +if (this.pv == null) { +this.pv = new Array (this.v.size ()); +this.v.copyInto (this.pv); +}for (var i = 0; i < this.v.size (); i++) { +var p = this.pv[i]; +var r = p.matchInternal (pos, pt); +if (r >= 0) { +return r; +}} +return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "minChars", +function () { +if (this.v.size () == 0) { +return new com.stevesoft.pat.patInt (0); +}var m = (this.v.elementAt (0)).countMinChars (); +for (var i = 1; i < this.v.size (); i++) { +var p = this.v.elementAt (i); +m.mineq (p.countMinChars ()); +} +return m; +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +if (this.v.size () == 0) { +return new com.stevesoft.pat.patInt (0); +}var m = (this.v.elementAt (0)).countMaxChars (); +for (var i = 1; i < this.v.size (); i++) { +var p = this.v.elementAt (i); +m.maxeq (p.countMaxChars ()); +} +return m; +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +var o = new com.stevesoft.pat.Or (); +h.put (this, o); +h.put (o, o); +for (var i = 0; i < this.v.size (); i++) { +o.v.addElement ((this.v.elementAt (i)).clone (h)); +} +return o; +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/OrMark.js b/bin/com/stevesoft/pat/OrMark.js index bf47fca..7590a74 100644 --- a/bin/com/stevesoft/pat/OrMark.js +++ b/bin/com/stevesoft/pat/OrMark.js @@ -1,54 +1,54 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Or", "$.SubMark"], "com.stevesoft.pat.OrMark", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.sm = null; -this.id = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "OrMark", com.stevesoft.pat.Or); -Clazz.prepareFields (c$, function () { -this.sm = new com.stevesoft.pat.SubMark (); -}); -Clazz.makeConstructor (c$, -function (i) { -Clazz.superConstructor (this, com.stevesoft.pat.OrMark, []); -this.sm.om = this; -this.id = i; -}, "~N"); -Clazz.overrideMethod (c$, "leftForm", -function () { -return "("; -}); -Clazz.defineMethod (c$, "getNext", -function () { -return this.sm; -}); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -this.sm.next = Clazz.superCall (this, com.stevesoft.pat.OrMark, "getNext", []); -if (pt.marks == null) { -var n2 = 2 * pt.nMarks + 2; -pt.marks = Clazz.newIntArray (n2, 0); -for (var i = 0; i < n2; i++) { -pt.marks[i] = -1; -} -}pt.marks[this.id] = pos; -var ret = Clazz.superCall (this, com.stevesoft.pat.OrMark, "matchInternal", [pos, pt]); -if (ret < 0) { -pt.marks[this.id] = -1; -} else if (pt.marks[this.id] > pt.marks[this.id + pt.nMarks]) { -var swap = pt.marks[this.id]; -pt.marks[this.id] = pt.marks[this.id + pt.nMarks] + 1; -pt.marks[this.id + pt.nMarks] = swap + 1; -}return ret; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -var om = new com.stevesoft.pat.OrMark (this.id); -h.put (om, om); -h.put (this, om); -for (var i = 0; i < this.v.size (); i++) { -om.v.addElement ((this.v.elementAt (i)).clone (h)); -} -return om; -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Or", "$.SubMark"], "com.stevesoft.pat.OrMark", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.sm = null; +this.id = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "OrMark", com.stevesoft.pat.Or); +Clazz.prepareFields (c$, function () { +this.sm = new com.stevesoft.pat.SubMark (); +}); +Clazz.makeConstructor (c$, +function (i) { +Clazz.superConstructor (this, com.stevesoft.pat.OrMark, []); +this.sm.om = this; +this.id = i; +}, "~N"); +Clazz.overrideMethod (c$, "leftForm", +function () { +return "("; +}); +Clazz.defineMethod (c$, "getNext", +function () { +return this.sm; +}); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +this.sm.next = Clazz.superCall (this, com.stevesoft.pat.OrMark, "getNext", []); +if (pt.marks == null) { +var n2 = 2 * pt.nMarks + 2; +pt.marks = Clazz.newIntArray (n2, 0); +for (var i = 0; i < n2; i++) { +pt.marks[i] = -1; +} +}pt.marks[this.id] = pos; +var ret = Clazz.superCall (this, com.stevesoft.pat.OrMark, "matchInternal", [pos, pt]); +if (ret < 0) { +pt.marks[this.id] = -1; +} else if (pt.marks[this.id] > pt.marks[this.id + pt.nMarks]) { +var swap = pt.marks[this.id]; +pt.marks[this.id] = pt.marks[this.id + pt.nMarks] + 1; +pt.marks[this.id + pt.nMarks] = swap + 1; +}return ret; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +var om = new com.stevesoft.pat.OrMark (this.id); +h.put (om, om); +h.put (this, om); +for (var i = 0; i < this.v.size (); i++) { +om.v.addElement ((this.v.elementAt (i)).clone (h)); +} +return om; +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/PartialBuffer.js b/bin/com/stevesoft/pat/PartialBuffer.js index 8490ff2..02fc0e3 100644 --- a/bin/com/stevesoft/pat/PartialBuffer.js +++ b/bin/com/stevesoft/pat/PartialBuffer.js @@ -1,50 +1,50 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.StringLike"], "com.stevesoft.pat.PartialBuffer", ["java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.off = 0; -this.allowOverRun = true; -this.overRun = false; -this.sb = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "PartialBuffer", null, com.stevesoft.pat.StringLike); -Clazz.makeConstructor (c$, -function (sb) { -this.sb = sb; -}, "StringBuffer"); -Clazz.overrideMethod (c$, "charAt", -function (n) { -n += this.off; -if (n == this.sb.length ()) { -this.overRun = true; -return String.fromCharCode (0); -}return this.sb.charAt (n); -}, "~N"); -Clazz.overrideMethod (c$, "length", -function () { -return this.allowOverRun ? this.sb.length () + 1 : this.sb.length (); -}); -Clazz.overrideMethod (c$, "indexOf", -function (c) { -for (var i = 0; i < this.sb.length (); i++) { -if (this.sb.charAt (i) == c) { -return i; -}} -return -1; -}, "~S"); -Clazz.overrideMethod (c$, "unwrap", -function () { -return this.sb; -}); -Clazz.overrideMethod (c$, "substring", -function (i1, i2) { -var sb = new StringBuffer (i2 - i1); -for (var i = i1; i < i2; i++) { -sb.append (this.charAt (i)); -} -return sb.toString (); -}, "~N,~N"); -Clazz.overrideMethod (c$, "newStringBufferLike", -function () { -return null; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.StringLike"], "com.stevesoft.pat.PartialBuffer", ["java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.off = 0; +this.allowOverRun = true; +this.overRun = false; +this.sb = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "PartialBuffer", null, com.stevesoft.pat.StringLike); +Clazz.makeConstructor (c$, +function (sb) { +this.sb = sb; +}, "StringBuffer"); +Clazz.overrideMethod (c$, "charAt", +function (n) { +n += this.off; +if (n == this.sb.length ()) { +this.overRun = true; +return String.fromCharCode (0); +}return this.sb.charAt (n); +}, "~N"); +Clazz.overrideMethod (c$, "length", +function () { +return this.allowOverRun ? this.sb.length () + 1 : this.sb.length (); +}); +Clazz.overrideMethod (c$, "indexOf", +function (c) { +for (var i = 0; i < this.sb.length (); i++) { +if (this.sb.charAt (i) == c) { +return i; +}} +return -1; +}, "~S"); +Clazz.overrideMethod (c$, "unwrap", +function () { +return this.sb; +}); +Clazz.overrideMethod (c$, "substring", +function (i1, i2) { +var sb = new StringBuffer (i2 - i1); +for (var i = i1; i < i2; i++) { +sb.append (this.charAt (i)); +} +return sb.toString (); +}, "~N,~N"); +Clazz.overrideMethod (c$, "newStringBufferLike", +function () { +return null; +}); +}); diff --git a/bin/com/stevesoft/pat/Pattern.js b/bin/com/stevesoft/pat/Pattern.js index a4dc10b..a3dddd4 100644 --- a/bin/com/stevesoft/pat/Pattern.js +++ b/bin/com/stevesoft/pat/Pattern.js @@ -1,153 +1,153 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.Pattern", ["com.stevesoft.pat.MessageManager", "$.patInf", "$.patInt", "java.lang.Error", "$.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.next = null; -this.parent = null; -this.mfrom = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Pattern"); -Clazz.defineMethod (c$, "getNext", -function () { -return this.next != null ? this.next : (this.parent == null ? null : this.parent.getNext ()); -}); -Clazz.defineMethod (c$, "setParent", -function (p) { -if (this.next != null) { -this.next.setParent (p); -} else { -this.parent = p; -}}, "com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "nextMatch", -function (i, pt) { -var p = this.getNext (); -return p == null ? i : p.matchInternal (i, pt); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "nextString", -function () { -if (this.next == null) { -return ""; -}return this.next.toString (); -}); -c$.inString = Clazz.defineMethod (c$, "inString", -function (c, s) { -var i; -for (i = 0; i < s.length; i++) { -if (s.charAt (i) == c) { -return true; -}} -return false; -}, "~S,~S"); -c$.protect = Clazz.defineMethod (c$, "protect", -function (s, PROTECT_THESE, esc) { -var i; -var sb = new StringBuffer (); -var p = PROTECT_THESE + esc; -for (i = 0; i < s.length; i++) { -var c = s.charAt (i); -if (com.stevesoft.pat.Pattern.inString (c, p)) { -sb.append (esc); -}sb.append (c); -} -return sb.toString (); -}, "~S,~S,~S"); -Clazz.defineMethod (c$, "match", -function (s, pt) { -return this.matchAt (s, 0, pt); -}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "matchAt", -function (s, i, pt) { -pt.src = s; -var r = this.matchInternal (i, pt); -if (r < 0) { -return -1; -}this.mfrom = r < i ? r + 1 : i; -return r < i ? i - r - 1 : r - i; -}, "com.stevesoft.pat.StringLike,~N,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "Masked", -function (i, pt) { -return pt.cbits == null ? false : pt.cbits.get (i); -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "add", -function (p) { -if (this.next == null) { -if (p == null) { -return this; -}this.next = p; -p.parent = this.parent; -this.parent = null; -} else { -this.next.add (p); -}return this; -}, "com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.defineMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInf (); -}); -Clazz.defineMethod (c$, "countMinChars", -function () { -var p = this; -var sum = new com.stevesoft.pat.patInt (0); -while (p != null) { -sum.pluseq (p.minChars ()); -p = p.next; -} -return sum; -}); -Clazz.defineMethod (c$, "countMaxChars", -function () { -var p = this; -var sum = new com.stevesoft.pat.patInt (0); -while (p != null) { -sum.pluseq (p.maxChars ()); -p = p.next; -} -return sum; -}); -Clazz.defineMethod (c$, "testMatch", -function (p, pos, pt) { -var tab = null; -if (pt.marks != null) { -try { -tab = Clazz.newIntArray (pt.marks.length, 0); -for (var i = 0; i < tab.length; i++) { -tab[i] = pt.marks[i]; -} -} catch (t) { -} -}var ret = p.matchInternal (pos, pt); -if (ret < 0) { -pt.marks = tab; -}return ret; -}, "com.stevesoft.pat.Pattern,~N,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "clone1", -function (h) { -throw new Error (com.stevesoft.pat.MessageManager.formatMessage ("error.no_such_method_as_clone1_for", Clazz.newArray (-1, [this.getClass ().getName ()]))); -}, "java.util.Hashtable"); -Clazz.defineMethod (c$, "clone", -function (h) { -var p = h.get (this); -if (p != null) { -return p; -}p = this.clone1 (h); -if (p == null) { -throw new Error (com.stevesoft.pat.MessageManager.getString ("error.null_from_clone1")); -}h.put (this, p); -h.put (p, p); -if (this.next != null) { -p.next = this.next.clone (h); -}if (this.parent != null) { -p.parent = this.parent.clone (h); -}return p; -}, "java.util.Hashtable"); -Clazz.overrideMethod (c$, "equals", -function (o) { -return o === this; -}, "~O"); -Clazz.defineStatics (c$, -"ESC", '\\', -"PROTECT_THESE", "[]{}(),$,-\"^."); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.Pattern", ["com.stevesoft.pat.MessageManager", "$.patInf", "$.patInt", "java.lang.Error", "$.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.next = null; +this.parent = null; +this.mfrom = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Pattern"); +Clazz.defineMethod (c$, "getNext", +function () { +return this.next != null ? this.next : (this.parent == null ? null : this.parent.getNext ()); +}); +Clazz.defineMethod (c$, "setParent", +function (p) { +if (this.next != null) { +this.next.setParent (p); +} else { +this.parent = p; +}}, "com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "nextMatch", +function (i, pt) { +var p = this.getNext (); +return p == null ? i : p.matchInternal (i, pt); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "nextString", +function () { +if (this.next == null) { +return ""; +}return this.next.toString (); +}); +c$.inString = Clazz.defineMethod (c$, "inString", +function (c, s) { +var i; +for (i = 0; i < s.length; i++) { +if (s.charAt (i) == c) { +return true; +}} +return false; +}, "~S,~S"); +c$.protect = Clazz.defineMethod (c$, "protect", +function (s, PROTECT_THESE, esc) { +var i; +var sb = new StringBuffer (); +var p = PROTECT_THESE + esc; +for (i = 0; i < s.length; i++) { +var c = s.charAt (i); +if (com.stevesoft.pat.Pattern.inString (c, p)) { +sb.append (esc); +}sb.append (c); +} +return sb.toString (); +}, "~S,~S,~S"); +Clazz.defineMethod (c$, "match", +function (s, pt) { +return this.matchAt (s, 0, pt); +}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "matchAt", +function (s, i, pt) { +pt.src = s; +var r = this.matchInternal (i, pt); +if (r < 0) { +return -1; +}this.mfrom = r < i ? r + 1 : i; +return r < i ? i - r - 1 : r - i; +}, "com.stevesoft.pat.StringLike,~N,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "Masked", +function (i, pt) { +return pt.cbits == null ? false : pt.cbits.get (i); +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "add", +function (p) { +if (this.next == null) { +if (p == null) { +return this; +}this.next = p; +p.parent = this.parent; +this.parent = null; +} else { +this.next.add (p); +}return this; +}, "com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.defineMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInf (); +}); +Clazz.defineMethod (c$, "countMinChars", +function () { +var p = this; +var sum = new com.stevesoft.pat.patInt (0); +while (p != null) { +sum.pluseq (p.minChars ()); +p = p.next; +} +return sum; +}); +Clazz.defineMethod (c$, "countMaxChars", +function () { +var p = this; +var sum = new com.stevesoft.pat.patInt (0); +while (p != null) { +sum.pluseq (p.maxChars ()); +p = p.next; +} +return sum; +}); +Clazz.defineMethod (c$, "testMatch", +function (p, pos, pt) { +var tab = null; +if (pt.marks != null) { +try { +tab = Clazz.newIntArray (pt.marks.length, 0); +for (var i = 0; i < tab.length; i++) { +tab[i] = pt.marks[i]; +} +} catch (t) { +} +}var ret = p.matchInternal (pos, pt); +if (ret < 0) { +pt.marks = tab; +}return ret; +}, "com.stevesoft.pat.Pattern,~N,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "clone1", +function (h) { +throw new Error (com.stevesoft.pat.MessageManager.formatMessage ("error.no_such_method_as_clone1_for", Clazz.newArray (-1, [this.getClass ().getName ()]))); +}, "java.util.Hashtable"); +Clazz.defineMethod (c$, "clone", +function (h) { +var p = h.get (this); +if (p != null) { +return p; +}p = this.clone1 (h); +if (p == null) { +throw new Error (com.stevesoft.pat.MessageManager.getString ("error.null_from_clone1")); +}h.put (this, p); +h.put (p, p); +if (this.next != null) { +p.next = this.next.clone (h); +}if (this.parent != null) { +p.parent = this.parent.clone (h); +}return p; +}, "java.util.Hashtable"); +Clazz.overrideMethod (c$, "equals", +function (o) { +return o === this; +}, "~O"); +Clazz.defineStatics (c$, +"ESC", '\\', +"PROTECT_THESE", "[]{}(),$,-\"^."); +}); diff --git a/bin/com/stevesoft/pat/PatternSub.js b/bin/com/stevesoft/pat/PatternSub.js index 2199b2b..835661a 100644 --- a/bin/com/stevesoft/pat/PatternSub.js +++ b/bin/com/stevesoft/pat/PatternSub.js @@ -1,7 +1,7 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.PatternSub", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.sub = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "PatternSub", com.stevesoft.pat.Pattern); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.PatternSub", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.sub = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "PatternSub", com.stevesoft.pat.Pattern); +}); diff --git a/bin/com/stevesoft/pat/PopRule.js b/bin/com/stevesoft/pat/PopRule.js index d983d19..92af006 100644 --- a/bin/com/stevesoft/pat/PopRule.js +++ b/bin/com/stevesoft/pat/PopRule.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.PopRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "PopRule", com.stevesoft.pat.SpecialRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.PopRule, []); -}); -Clazz.overrideMethod (c$, "toString1", -function () { -return "${POP}"; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.PopRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "PopRule", com.stevesoft.pat.SpecialRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.PopRule, []); +}); +Clazz.overrideMethod (c$, "toString1", +function () { +return "${POP}"; +}); +}); diff --git a/bin/com/stevesoft/pat/Prop.js b/bin/com/stevesoft/pat/Prop.js index 7f99d0e..5dbb6db 100644 --- a/bin/com/stevesoft/pat/Prop.js +++ b/bin/com/stevesoft/pat/Prop.js @@ -1,40 +1,40 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.Prop", ["com.stevesoft.pat.Bits"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "Prop"); -c$.isDecimalDigit = Clazz.defineMethod (c$, "isDecimalDigit", -function (c) { -if (com.stevesoft.pat.Bits.decimal_digit == null) { -com.stevesoft.pat.Bits.decimal_digit_f (); -}return com.stevesoft.pat.Bits.decimal_digit.get (c.charCodeAt (0)); -}, "~S"); -c$.isAlphabetic = Clazz.defineMethod (c$, "isAlphabetic", -function (c) { -if (com.stevesoft.pat.Bits.letter == null) { -com.stevesoft.pat.Bits.letter_f (); -}return com.stevesoft.pat.Bits.letter.get (c.charCodeAt (0)); -}, "~S"); -c$.isMath = Clazz.defineMethod (c$, "isMath", -function (c) { -if (com.stevesoft.pat.Bits.math == null) { -com.stevesoft.pat.Bits.math_f (); -}return com.stevesoft.pat.Bits.math.get (c.charCodeAt (0)); -}, "~S"); -c$.isCurrency = Clazz.defineMethod (c$, "isCurrency", -function (c) { -if (com.stevesoft.pat.Bits.currency == null) { -com.stevesoft.pat.Bits.currency_f (); -}return com.stevesoft.pat.Bits.currency.get (c.charCodeAt (0)); -}, "~S"); -c$.isWhite = Clazz.defineMethod (c$, "isWhite", -function (c) { -if (com.stevesoft.pat.Bits.white == null) { -com.stevesoft.pat.Bits.white_f (); -}return com.stevesoft.pat.Bits.white.get (c.charCodeAt (0)); -}, "~S"); -c$.isPunct = Clazz.defineMethod (c$, "isPunct", -function (c) { -if (com.stevesoft.pat.Bits.punct == null) { -com.stevesoft.pat.Bits.punct_f (); -}return com.stevesoft.pat.Bits.punct.get (c.charCodeAt (0)); -}, "~S"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.Prop", ["com.stevesoft.pat.Bits"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "Prop"); +c$.isDecimalDigit = Clazz.defineMethod (c$, "isDecimalDigit", +function (c) { +if (com.stevesoft.pat.Bits.decimal_digit == null) { +com.stevesoft.pat.Bits.decimal_digit_f (); +}return com.stevesoft.pat.Bits.decimal_digit.get (c.charCodeAt (0)); +}, "~S"); +c$.isAlphabetic = Clazz.defineMethod (c$, "isAlphabetic", +function (c) { +if (com.stevesoft.pat.Bits.letter == null) { +com.stevesoft.pat.Bits.letter_f (); +}return com.stevesoft.pat.Bits.letter.get (c.charCodeAt (0)); +}, "~S"); +c$.isMath = Clazz.defineMethod (c$, "isMath", +function (c) { +if (com.stevesoft.pat.Bits.math == null) { +com.stevesoft.pat.Bits.math_f (); +}return com.stevesoft.pat.Bits.math.get (c.charCodeAt (0)); +}, "~S"); +c$.isCurrency = Clazz.defineMethod (c$, "isCurrency", +function (c) { +if (com.stevesoft.pat.Bits.currency == null) { +com.stevesoft.pat.Bits.currency_f (); +}return com.stevesoft.pat.Bits.currency.get (c.charCodeAt (0)); +}, "~S"); +c$.isWhite = Clazz.defineMethod (c$, "isWhite", +function (c) { +if (com.stevesoft.pat.Bits.white == null) { +com.stevesoft.pat.Bits.white_f (); +}return com.stevesoft.pat.Bits.white.get (c.charCodeAt (0)); +}, "~S"); +c$.isPunct = Clazz.defineMethod (c$, "isPunct", +function (c) { +if (com.stevesoft.pat.Bits.punct == null) { +com.stevesoft.pat.Bits.punct_f (); +}return com.stevesoft.pat.Bits.punct.get (c.charCodeAt (0)); +}, "~S"); +}); diff --git a/bin/com/stevesoft/pat/Pthings.js b/bin/com/stevesoft/pat/Pthings.js index 179ec6b..8969d4f 100644 --- a/bin/com/stevesoft/pat/Pthings.js +++ b/bin/com/stevesoft/pat/Pthings.js @@ -1,13 +1,13 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -c$ = Clazz.decorateAsClass (function () { -this.src = null; -this.ignoreCase = false; -this.mFlag = false; -this.cbits = null; -this.marks = null; -this.nMarks = 0; -this.dotDoesntMatchCR = false; -this.no_check = false; -this.lastPos = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Pthings"); +Clazz.declarePackage ("com.stevesoft.pat"); +c$ = Clazz.decorateAsClass (function () { +this.src = null; +this.ignoreCase = false; +this.mFlag = false; +this.cbits = null; +this.marks = null; +this.nMarks = 0; +this.dotDoesntMatchCR = false; +this.no_check = false; +this.lastPos = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Pthings"); diff --git a/bin/com/stevesoft/pat/PushRule.js b/bin/com/stevesoft/pat/PushRule.js index bac59ef..fd7d64e 100644 --- a/bin/com/stevesoft/pat/PushRule.js +++ b/bin/com/stevesoft/pat/PushRule.js @@ -1,35 +1,35 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.PushRule", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.NewRule = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "PushRule", com.stevesoft.pat.SpecialRule); -Clazz.makeConstructor (c$, -function (p) { -Clazz.superConstructor (this, com.stevesoft.pat.PushRule, []); -this.NewRule = p.NewRule; -}, "com.stevesoft.pat.PushRule"); -Clazz.makeConstructor (c$, -function (nm, rr) { -Clazz.superConstructor (this, com.stevesoft.pat.PushRule, []); -this.name = nm; -this.NewRule = rr; -}, "~S,com.stevesoft.pat.Regex"); -Clazz.makeConstructor (c$, -function (nm, tr) { -Clazz.superConstructor (this, com.stevesoft.pat.PushRule, []); -this.name = nm; -this.NewRule = tr.rp; -}, "~S,com.stevesoft.pat.Transformer"); -Clazz.overrideMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.PushRule (this); -}); -Clazz.defineMethod (c$, "String1", -function () { -return "${+" + this.name + "}"; -}); -Clazz.overrideMethod (c$, "apply", -function (sbl, rr) { -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.PushRule", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.NewRule = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "PushRule", com.stevesoft.pat.SpecialRule); +Clazz.makeConstructor (c$, +function (p) { +Clazz.superConstructor (this, com.stevesoft.pat.PushRule, []); +this.NewRule = p.NewRule; +}, "com.stevesoft.pat.PushRule"); +Clazz.makeConstructor (c$, +function (nm, rr) { +Clazz.superConstructor (this, com.stevesoft.pat.PushRule, []); +this.name = nm; +this.NewRule = rr; +}, "~S,com.stevesoft.pat.Regex"); +Clazz.makeConstructor (c$, +function (nm, tr) { +Clazz.superConstructor (this, com.stevesoft.pat.PushRule, []); +this.name = nm; +this.NewRule = tr.rp; +}, "~S,com.stevesoft.pat.Transformer"); +Clazz.overrideMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.PushRule (this); +}); +Clazz.defineMethod (c$, "String1", +function () { +return "${+" + this.name + "}"; +}); +Clazz.overrideMethod (c$, "apply", +function (sbl, rr) { +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +}); diff --git a/bin/com/stevesoft/pat/RBuffer.js b/bin/com/stevesoft/pat/RBuffer.js index 529f8a2..27970cf 100644 --- a/bin/com/stevesoft/pat/RBuffer.js +++ b/bin/com/stevesoft/pat/RBuffer.js @@ -1,32 +1,32 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.RBuffer", ["java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.done = false; -this.sb = null; -this.pos = 0; -this.epos = 0; -this.next = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RBuffer"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (sb) { -this.sb = sb; -}, "StringBuffer"); -Clazz.overrideMethod (c$, "toString", -function () { -return "sb=" + this.sb.toString ().$replace ('\n', ' ') + " pos=" + this.pos + " epos=" + this.epos + " sb.length()=" + this.sb.length () + "\n" + this.sp (this.pos + 3) + "^" + this.sp (this.epos - this.pos - 1) + "^"; -}); -Clazz.defineMethod (c$, "sp", -function (n) { -if (n <= 0) { -return ""; -}var sb = new StringBuffer (n); -for (var i = 0; i < n; i++) { -sb.append (' '); -} -return sb.toString (); -}, "~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.RBuffer", ["java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.done = false; +this.sb = null; +this.pos = 0; +this.epos = 0; +this.next = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RBuffer"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (sb) { +this.sb = sb; +}, "StringBuffer"); +Clazz.overrideMethod (c$, "toString", +function () { +return "sb=" + this.sb.toString ().$replace ('\n', ' ') + " pos=" + this.pos + " epos=" + this.epos + " sb.length()=" + this.sb.length () + "\n" + this.sp (this.pos + 3) + "^" + this.sp (this.epos - this.pos - 1) + "^"; +}); +Clazz.defineMethod (c$, "sp", +function (n) { +if (n <= 0) { +return ""; +}var sb = new StringBuffer (n); +for (var i = 0; i < n; i++) { +sb.append (' '); +} +return sb.toString (); +}, "~N"); +}); diff --git a/bin/com/stevesoft/pat/Range.js b/bin/com/stevesoft/pat/Range.js index cb007c4..8294a31 100644 --- a/bin/com/stevesoft/pat/Range.js +++ b/bin/com/stevesoft/pat/Range.js @@ -1,65 +1,65 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern", "$.RegSyntax"], ["com.stevesoft.pat.BadRangeArgs", "$.Range"], ["com.stevesoft.pat.RegSyntaxError", "$.oneChar", "$.patInt"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "BadRangeArgs", com.stevesoft.pat.RegSyntax); -c$ = Clazz.decorateAsClass (function () { -this.lo = '\0'; -this.hi = '\0'; -this.altlo = '\0'; -this.althi = '\0'; -this.printBrackets = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Range", com.stevesoft.pat.Pattern); -Clazz.overrideMethod (c$, "toString", -function () { -var s = com.stevesoft.pat.Pattern.protect ("" + this.lo, "[]{}(),$,-\"^.", '\\') + "-" + com.stevesoft.pat.Pattern.protect ("" + this.hi, "[]{}(),$,-\"^.", '\\'); -if (!this.printBrackets) { -return s; -}return "[" + s + "]"; -}); -Clazz.makeConstructor (c$, -function (loi, hii) { -Clazz.superConstructor (this, com.stevesoft.pat.Range, []); -this.lo = loi; -this.hi = hii; -var o = null; -if (this.lo >= this.hi) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Badly formed []'s : " + this.lo + " >= " + this.hi); -}o = new com.stevesoft.pat.oneChar (this.lo); -this.altlo = o.altc; -o = new com.stevesoft.pat.oneChar (this.hi); -this.althi = o.altc; -}, "~S,~S"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (pos >= pt.src.length ()) { -return -1; -}if (this.Masked (pos, pt)) { -return -1; -}var c = pt.src.charAt (pos); -if (this.lo <= c && c <= this.hi || (pt.ignoreCase && (this.altlo <= c && c <= this.althi))) { -return this.nextMatch (pos + 1, pt); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -try { -var r = new com.stevesoft.pat.Range (this.lo, this.hi); -r.printBrackets = this.printBrackets; -return r; -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -return null; -} else { -throw rs; -} -} -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern", "$.RegSyntax"], ["com.stevesoft.pat.BadRangeArgs", "$.Range"], ["com.stevesoft.pat.RegSyntaxError", "$.oneChar", "$.patInt"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "BadRangeArgs", com.stevesoft.pat.RegSyntax); +c$ = Clazz.decorateAsClass (function () { +this.lo = '\0'; +this.hi = '\0'; +this.altlo = '\0'; +this.althi = '\0'; +this.printBrackets = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Range", com.stevesoft.pat.Pattern); +Clazz.overrideMethod (c$, "toString", +function () { +var s = com.stevesoft.pat.Pattern.protect ("" + this.lo, "[]{}(),$,-\"^.", '\\') + "-" + com.stevesoft.pat.Pattern.protect ("" + this.hi, "[]{}(),$,-\"^.", '\\'); +if (!this.printBrackets) { +return s; +}return "[" + s + "]"; +}); +Clazz.makeConstructor (c$, +function (loi, hii) { +Clazz.superConstructor (this, com.stevesoft.pat.Range, []); +this.lo = loi; +this.hi = hii; +var o = null; +if (this.lo >= this.hi) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Badly formed []'s : " + this.lo + " >= " + this.hi); +}o = new com.stevesoft.pat.oneChar (this.lo); +this.altlo = o.altc; +o = new com.stevesoft.pat.oneChar (this.hi); +this.althi = o.altc; +}, "~S,~S"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (pos >= pt.src.length ()) { +return -1; +}if (this.Masked (pos, pt)) { +return -1; +}var c = pt.src.charAt (pos); +if (this.lo <= c && c <= this.hi || (pt.ignoreCase && (this.altlo <= c && c <= this.althi))) { +return this.nextMatch (pos + 1, pt); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +try { +var r = new com.stevesoft.pat.Range (this.lo, this.hi); +r.printBrackets = this.printBrackets; +return r; +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +return null; +} else { +throw rs; +} +} +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/RegOpt.class b/bin/com/stevesoft/pat/RegOpt.class index b62aeb0..96c50d7 100644 Binary files a/bin/com/stevesoft/pat/RegOpt.class and b/bin/com/stevesoft/pat/RegOpt.class differ diff --git a/bin/com/stevesoft/pat/RegOpt.js b/bin/com/stevesoft/pat/RegOpt.js index ed70432..54e0ed8 100644 --- a/bin/com/stevesoft/pat/RegOpt.js +++ b/bin/com/stevesoft/pat/RegOpt.js @@ -1,254 +1,254 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern", "$.oneChar", "java.util.Hashtable", "$.Vector"], ["com.stevesoft.pat.Branch", "$.RegOpt", "$.FastChar"], ["com.stevesoft.pat.Any", "$.Bracket", "$.Custom", "$.FastBracket", "$.FastMulti", "$.Multi", "$.NullPattern", "$.Or", "$.Range", "$.UniValidator", "$.patInt", "java.lang.Character", "$.StringBuffer"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "FastChar", com.stevesoft.pat.oneChar); -Clazz.overrideMethod (c$, "matchInternal", -function (p, pt) { -return (p < pt.src.length () && pt.src.charAt (p) == this.c) ? this.nextMatch (p + 1, pt) : -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.FastChar (this.c); -}, "java.util.Hashtable"); -c$ = Clazz.decorateAsClass (function () { -this.h = null; -this.keys = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Branch", com.stevesoft.pat.Pattern); -Clazz.prepareFields (c$, function () { -this.h = new java.util.Hashtable (); -this.keys = new java.util.Vector (); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.Branch, []); -}); -Clazz.overrideMethod (c$, "clone1", -function (x) { -var b = new com.stevesoft.pat.Branch (); -b.keys = this.keys.clone (); -x.put (this, b); -x.put (b, b); -for (var i = 0; i < this.keys.size (); i++) { -var p = this.h.get (this.keys.elementAt (i)); -b.h.put (this.keys.elementAt (i), p.clone (x)); -} -return b; -}, "java.util.Hashtable"); -Clazz.defineMethod (c$, "reduce", -function (ignoreCase, dontMinQ) { -if (this.h.size () == 1) { -var e = this.h.keys (); -var c = e.nextElement (); -var oc; -if (ignoreCase || dontMinQ) { -oc = new com.stevesoft.pat.oneChar (c.charValue ()); -} else { -oc = new com.stevesoft.pat.FastChar (c.charValue ()); -}oc.next = this.h.get (c); -oc.add (this.next); -return oc; -} else if (this.h.size () == 0) { -return null; -}return this; -}, "~B,~B"); -Clazz.defineMethod (c$, "maxChars", -function () { -var e = this.h.keys (); -var count = new com.stevesoft.pat.patInt (0); -while (e.hasMoreElements ()) { -var key = e.nextElement (); -var pa = this.h.get (key); -var pi = pa.maxChars (); -pi.inc (); -count.maxeq (pi); -} -return count; -}); -Clazz.defineMethod (c$, "minChars", -function () { -var e = this.h.keys (); -var count = new com.stevesoft.pat.patInt (0); -while (e.hasMoreElements ()) { -var key = e.nextElement (); -var pa = this.h.get (key); -var pi = pa.minChars (); -pi.inc (); -count.mineq (pi); -} -return count; -}); -Clazz.defineMethod (c$, "addc", -function (o, ignoreCase, dontMinQ) { -var n = o.next; -if (n == null) { -n = new com.stevesoft.pat.NullPattern (); -} else { -n = com.stevesoft.pat.RegOpt.opt (n, ignoreCase, dontMinQ); -}n.setParent (this); -this.set ( new Character (o.c), n, ignoreCase, dontMinQ); -if (ignoreCase) { -if (o.c != o.altc) { -this.set ( new Character (o.altc), n, ignoreCase, dontMinQ); -}if (o.c != o.altc2 && o.altc != o.altc2) { -this.set ( new Character (o.altc2), n, ignoreCase, dontMinQ); -}}}, "com.stevesoft.pat.oneChar,~B,~B"); -Clazz.defineMethod (c$, "set", -function (c, n, igc, dontMinQ) { -var p = this.h.get (c); -this.next = null; -if (p == null) { -if (Clazz.instanceOf (n, com.stevesoft.pat.Or)) { -var np = new com.stevesoft.pat.NullPattern (); -np.add (n); -this.h.put (c, np); -} else { -this.h.put (c, n); -}this.keys.addElement (c); -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or)) { -(p).addOr (n); -} else if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar) && Clazz.instanceOf (n, com.stevesoft.pat.oneChar) && (p).c != (n).c) { -var b = new com.stevesoft.pat.Branch (); -b.addc (p, igc, dontMinQ); -b.addc (n, igc, dontMinQ); -this.h.put (c, b); -b.setParent (this); -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Branch) && Clazz.instanceOf (n, com.stevesoft.pat.oneChar)) { -(p).addc (n, igc, dontMinQ); -n.setParent (p); -} else { -var o = new com.stevesoft.pat.Or (); -o.setParent (this); -if (Clazz.instanceOf (p, com.stevesoft.pat.NullPattern) && p.parent == null && p.next != null) { -o.addOr (p.next); -} else { -o.addOr (p); -}o.addOr (n); -var optpat = com.stevesoft.pat.RegOpt.opt (o, igc, dontMinQ); -this.h.put (c, optpat); -optpat.setParent (this); -}}, "Character,com.stevesoft.pat.Pattern,~B,~B"); -Clazz.overrideMethod (c$, "toString", -function () { -var sb = new StringBuffer (); -sb.append ("(?:(?#branch)"); -for (var i = 0; i < this.keys.size (); i++) { -var c = this.keys.elementAt (i); -sb.append (c); -sb.append (this.h.get (c)); -if (i + 1 < this.keys.size ()) { -sb.append ("|"); -}} -sb.append (")"); -sb.append (this.nextString ()); -return sb.toString (); -}); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -if (pos >= pt.src.length ()) { -return -1; -}var n = this.h.get ( new Character (pt.src.charAt (pos))); -if (n == null) { -return -1; -}if (pt.cbits != null && pt.cbits.get (pos)) { -return -1; -}return n.matchInternal (pos + 1, pt); -}, "~N,com.stevesoft.pat.Pthings"); -c$ = Clazz.declareType (com.stevesoft.pat, "RegOpt"); -c$.opt = Clazz.defineMethod (c$, "opt", -function (p, ignoreCase, dontMinQ) { -if (p == null) { -return p; -}if (Clazz.instanceOf (p, com.stevesoft.pat.Bracket)) { -var b = p; -p = com.stevesoft.pat.FastBracket.process (b, ignoreCase); -p.next = b.next; -p.parent = b.parent; -} else if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar) && !ignoreCase && !dontMinQ) { -var o = p; -p = new com.stevesoft.pat.FastChar (o.c); -p.next = o.next; -p.parent = o.parent; -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or) && (p).leftForm ().equals ("(?:") && (p).v.size () == 1) { -var o = p; -p = o.v.elementAt (0); -p.setParent (null); -p = com.stevesoft.pat.RegOpt.opt (p, ignoreCase, dontMinQ); -p.add (o.next); -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or)) { -var o = p; -o.pv = null; -var v = o.v; -o.v = new java.util.Vector (); -var b = new com.stevesoft.pat.Branch (); -b.parent = o.parent; -for (var i = 0; i < v.size (); i++) { -var pp = v.elementAt (i); -if (Clazz.instanceOf (pp, com.stevesoft.pat.oneChar) && (b.h.size () >= 1 || (i + 1 < v.size () && Clazz.instanceOf (v.elementAt (i + 1), com.stevesoft.pat.oneChar)))) { -b.addc (pp, ignoreCase, dontMinQ); -} else { -if (b.keys.size () > 0) { -var p2 = b.reduce (ignoreCase, dontMinQ); -if (p2 != null) { -o.addOr (p2); -b = new com.stevesoft.pat.Branch (); -b.parent = o.parent; -}}o.addOr (com.stevesoft.pat.RegOpt.opt (pp, ignoreCase, dontMinQ)); -}} -if (b.keys.size () > 0) { -var p2 = b.reduce (ignoreCase, dontMinQ); -if (p2 != null) { -o.addOr (p2); -}}if (o.v.size () == 1 && o.leftForm ().equals ("(?:")) { -p = o.v.elementAt (0); -p.setParent (null); -p = com.stevesoft.pat.RegOpt.opt (p, ignoreCase, dontMinQ); -p.add (o.next); -}} else if (Clazz.instanceOf (p, com.stevesoft.pat.FastMulti)) { -var ps = p; -ps.sub = com.stevesoft.pat.RegOpt.opt (ps.sub, ignoreCase, dontMinQ); -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Multi) && com.stevesoft.pat.RegOpt.safe4fm ((p).sub)) { -var m = p; -var fm = null; -try { -fm = new com.stevesoft.pat.FastMulti (m.a, m.b, com.stevesoft.pat.RegOpt.opt (m.sub, ignoreCase, dontMinQ)); -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -} else { -throw rs; -} -} -fm.parent = m.parent; -fm.matchFewest = m.matchFewest; -fm.next = m.next; -p = fm; -}if (p.next != null) { -p.next = com.stevesoft.pat.RegOpt.opt (p.next, ignoreCase, dontMinQ); -}return p; -}, "com.stevesoft.pat.Pattern,~B,~B"); -c$.safe4fm = Clazz.defineMethod (c$, "safe4fm", -function (x) { -while (x != null) { -if (Clazz.instanceOf (x, com.stevesoft.pat.Bracket)) { -;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Range)) { -;} else if (Clazz.instanceOf (x, com.stevesoft.pat.oneChar)) { -;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Any)) { -;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Custom) && Clazz.instanceOf ((x).v, com.stevesoft.pat.UniValidator)) { -;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Or)) { -var o = x; -if (!o.leftForm ().equals ("(?:")) { -return false; -}var lo = o.countMinChars (); -var hi = o.countMaxChars (); -if (!lo.equals (hi)) { -return false; -}for (var i = 0; i < o.v.size (); i++) { -if (!com.stevesoft.pat.RegOpt.safe4fm (o.v.elementAt (i))) { -return false; -}} -} else { -return false; -}x = x.next; -} -return true; -}, "com.stevesoft.pat.Pattern"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern", "$.oneChar", "java.util.Hashtable", "$.Vector"], ["com.stevesoft.pat.Branch", "$.RegOpt", "$.FastChar"], ["com.stevesoft.pat.Any", "$.Bracket", "$.Custom", "$.FastBracket", "$.FastMulti", "$.Multi", "$.NullPattern", "$.Or", "$.Range", "$.UniValidator", "$.patInt", "java.lang.Character", "$.StringBuffer"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "FastChar", com.stevesoft.pat.oneChar); +Clazz.overrideMethod (c$, "matchInternal", +function (p, pt) { +return (p < pt.src.length () && pt.src.charAt (p) == this.c) ? this.nextMatch (p + 1, pt) : -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.FastChar (this.c); +}, "java.util.Hashtable"); +c$ = Clazz.decorateAsClass (function () { +this.h = null; +this.keys = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Branch", com.stevesoft.pat.Pattern); +Clazz.prepareFields (c$, function () { +this.h = new java.util.Hashtable (); +this.keys = new java.util.Vector (); +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.Branch, []); +}); +Clazz.overrideMethod (c$, "clone1", +function (x) { +var b = new com.stevesoft.pat.Branch (); +b.keys = this.keys.clone (); +x.put (this, b); +x.put (b, b); +for (var i = 0; i < this.keys.size (); i++) { +var p = this.h.get (this.keys.elementAt (i)); +b.h.put (this.keys.elementAt (i), p.clone (x)); +} +return b; +}, "java.util.Hashtable"); +Clazz.defineMethod (c$, "reduce", +function (ignoreCase, dontMinQ) { +if (this.h.size () == 1) { +var e = this.h.keys (); +var c = e.nextElement (); +var oc; +if (ignoreCase || dontMinQ) { +oc = new com.stevesoft.pat.oneChar (c.charValue ()); +} else { +oc = new com.stevesoft.pat.FastChar (c.charValue ()); +}oc.next = this.h.get (c); +oc.add (this.next); +return oc; +} else if (this.h.size () == 0) { +return null; +}return this; +}, "~B,~B"); +Clazz.defineMethod (c$, "maxChars", +function () { +var e = this.h.keys (); +var count = new com.stevesoft.pat.patInt (0); +while (e.hasMoreElements ()) { +var key = e.nextElement (); +var pa = this.h.get (key); +var pi = pa.maxChars (); +pi.inc (); +count.maxeq (pi); +} +return count; +}); +Clazz.defineMethod (c$, "minChars", +function () { +var e = this.h.keys (); +var count = new com.stevesoft.pat.patInt (0); +while (e.hasMoreElements ()) { +var key = e.nextElement (); +var pa = this.h.get (key); +var pi = pa.minChars (); +pi.inc (); +count.mineq (pi); +} +return count; +}); +Clazz.defineMethod (c$, "addc", +function (o, ignoreCase, dontMinQ) { +var n = o.next; +if (n == null) { +n = new com.stevesoft.pat.NullPattern (); +} else { +n = com.stevesoft.pat.RegOpt.opt (n, ignoreCase, dontMinQ); +}n.setParent (this); +this.set ( new Character (o.c), n, ignoreCase, dontMinQ); +if (ignoreCase) { +if (o.c != o.altc) { +this.set ( new Character (o.altc), n, ignoreCase, dontMinQ); +}if (o.c != o.altc2 && o.altc != o.altc2) { +this.set ( new Character (o.altc2), n, ignoreCase, dontMinQ); +}}}, "com.stevesoft.pat.oneChar,~B,~B"); +Clazz.defineMethod (c$, "set", +function (c, n, igc, dontMinQ) { +var p = this.h.get (c); +this.next = null; +if (p == null) { +if (Clazz.instanceOf (n, com.stevesoft.pat.Or)) { +var np = new com.stevesoft.pat.NullPattern (); +np.add (n); +this.h.put (c, np); +} else { +this.h.put (c, n); +}this.keys.addElement (c); +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or)) { +(p).addOr (n); +} else if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar) && Clazz.instanceOf (n, com.stevesoft.pat.oneChar) && (p).c != (n).c) { +var b = new com.stevesoft.pat.Branch (); +b.addc (p, igc, dontMinQ); +b.addc (n, igc, dontMinQ); +this.h.put (c, b); +b.setParent (this); +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Branch) && Clazz.instanceOf (n, com.stevesoft.pat.oneChar)) { +(p).addc (n, igc, dontMinQ); +n.setParent (p); +} else { +var o = new com.stevesoft.pat.Or (); +o.setParent (this); +if (Clazz.instanceOf (p, com.stevesoft.pat.NullPattern) && p.parent == null && p.next != null) { +o.addOr (p.next); +} else { +o.addOr (p); +}o.addOr (n); +var optpat = com.stevesoft.pat.RegOpt.opt (o, igc, dontMinQ); +this.h.put (c, optpat); +optpat.setParent (this); +}}, "Character,com.stevesoft.pat.Pattern,~B,~B"); +Clazz.overrideMethod (c$, "toString", +function () { +var sb = new StringBuffer (); +sb.append ("(?:(?#branch)"); +for (var i = 0; i < this.keys.size (); i++) { +var c = this.keys.elementAt (i); +sb.append (c); +sb.append (this.h.get (c)); +if (i + 1 < this.keys.size ()) { +sb.append ("|"); +}} +sb.append (")"); +sb.append (this.nextString ()); +return sb.toString (); +}); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +if (pos >= pt.src.length ()) { +return -1; +}var n = this.h.get ( new Character (pt.src.charAt (pos))); +if (n == null) { +return -1; +}if (pt.cbits != null && pt.cbits.get (pos)) { +return -1; +}return n.matchInternal (pos + 1, pt); +}, "~N,com.stevesoft.pat.Pthings"); +c$ = Clazz.declareType (com.stevesoft.pat, "RegOpt"); +c$.opt = Clazz.defineMethod (c$, "opt", +function (p, ignoreCase, dontMinQ) { +if (p == null) { +return p; +}if (Clazz.instanceOf (p, com.stevesoft.pat.Bracket)) { +var b = p; +p = com.stevesoft.pat.FastBracket.process (b, ignoreCase); +p.next = b.next; +p.parent = b.parent; +} else if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar) && !ignoreCase && !dontMinQ) { +var o = p; +p = new com.stevesoft.pat.FastChar (o.c); +p.next = o.next; +p.parent = o.parent; +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or) && (p).leftForm ().equals ("(?:") && (p).v.size () == 1) { +var o = p; +p = o.v.elementAt (0); +p.setParent (null); +p = com.stevesoft.pat.RegOpt.opt (p, ignoreCase, dontMinQ); +p.add (o.next); +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or)) { +var o = p; +o.pv = null; +var v = o.v; +o.v = new java.util.Vector (); +var b = new com.stevesoft.pat.Branch (); +b.parent = o.parent; +for (var i = 0; i < v.size (); i++) { +var pp = v.elementAt (i); +if (Clazz.instanceOf (pp, com.stevesoft.pat.oneChar) && (b.h.size () >= 1 || (i + 1 < v.size () && Clazz.instanceOf (v.elementAt (i + 1), com.stevesoft.pat.oneChar)))) { +b.addc (pp, ignoreCase, dontMinQ); +} else { +if (b.keys.size () > 0) { +var p2 = b.reduce (ignoreCase, dontMinQ); +if (p2 != null) { +o.addOr (p2); +b = new com.stevesoft.pat.Branch (); +b.parent = o.parent; +}}o.addOr (com.stevesoft.pat.RegOpt.opt (pp, ignoreCase, dontMinQ)); +}} +if (b.keys.size () > 0) { +var p2 = b.reduce (ignoreCase, dontMinQ); +if (p2 != null) { +o.addOr (p2); +}}if (o.v.size () == 1 && o.leftForm ().equals ("(?:")) { +p = o.v.elementAt (0); +p.setParent (null); +p = com.stevesoft.pat.RegOpt.opt (p, ignoreCase, dontMinQ); +p.add (o.next); +}} else if (Clazz.instanceOf (p, com.stevesoft.pat.FastMulti)) { +var ps = p; +ps.sub = com.stevesoft.pat.RegOpt.opt (ps.sub, ignoreCase, dontMinQ); +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Multi) && com.stevesoft.pat.RegOpt.safe4fm ((p).sub)) { +var m = p; +var fm = null; +try { +fm = new com.stevesoft.pat.FastMulti (m.a, m.b, com.stevesoft.pat.RegOpt.opt (m.sub, ignoreCase, dontMinQ)); +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +} else { +throw rs; +} +} +fm.parent = m.parent; +fm.matchFewest = m.matchFewest; +fm.next = m.next; +p = fm; +}if (p.next != null) { +p.next = com.stevesoft.pat.RegOpt.opt (p.next, ignoreCase, dontMinQ); +}return p; +}, "com.stevesoft.pat.Pattern,~B,~B"); +c$.safe4fm = Clazz.defineMethod (c$, "safe4fm", +function (x) { +while (x != null) { +if (Clazz.instanceOf (x, com.stevesoft.pat.Bracket)) { +;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Range)) { +;} else if (Clazz.instanceOf (x, com.stevesoft.pat.oneChar)) { +;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Any)) { +;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Custom) && Clazz.instanceOf ((x).v, com.stevesoft.pat.UniValidator)) { +;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Or)) { +var o = x; +if (!o.leftForm ().equals ("(?:")) { +return false; +}var lo = o.countMinChars (); +var hi = o.countMaxChars (); +if (!lo.equals (hi)) { +return false; +}for (var i = 0; i < o.v.size (); i++) { +if (!com.stevesoft.pat.RegOpt.safe4fm (o.v.elementAt (i))) { +return false; +}} +} else { +return false; +}x = x.next; +} +return true; +}, "com.stevesoft.pat.Pattern"); +}); diff --git a/bin/com/stevesoft/pat/RegRes.js b/bin/com/stevesoft/pat/RegRes.js index ec4def1..9a31c29 100644 --- a/bin/com/stevesoft/pat/RegRes.js +++ b/bin/com/stevesoft/pat/RegRes.js @@ -1,155 +1,155 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.RegRes", ["java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.marks = null; -this.didMatch_ = false; -this.src = null; -this.charsMatched_ = 0; -this.matchFrom_ = 0; -this.numSubs_ = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RegRes"); -Clazz.defineMethod (c$, "getString", -function () { -return this.src.toString (); -}); -Clazz.defineMethod (c$, "getStringLike", -function () { -return this.src; -}); -Clazz.overrideMethod (c$, "toString", -function () { -var sb = new StringBuffer (); -sb.append ("match=" + this.matchedFrom () + ":" + this.charsMatched ()); -if (!this.didMatch ()) { -return sb.toString (); -}for (var i = 0; i < this.numSubs (); i++) { -var n = i + 1; -sb.append (" sub(" + n + ")=" + this.matchedFromI (n) + ":" + this.charsMatchedI (n)); -} -return sb.toString (); -}); -Clazz.defineMethod (c$, "copyOutOf", -function (r) { -if (r.marks == null) { -this.marks = null; -} else { -try { -this.marks = Clazz.newIntArray (r.marks.length, 0); -for (var i = 0; i < this.marks.length; i++) { -this.marks[i] = r.marks[i]; -} -} catch (t) { -} -}this.didMatch_ = r.didMatch_; -this.src = r.src; -this.charsMatched_ = r.charsMatched_; -this.matchFrom_ = r.matchFrom_; -this.numSubs_ = r.numSubs_; -}, "com.stevesoft.pat.RegRes"); -Clazz.defineMethod (c$, "equals", -function (r) { -if (this.charsMatched_ != r.charsMatched_ || this.matchFrom_ != r.matchFrom_ || this.didMatch_ != r.didMatch_ || this.numSubs_ != r.numSubs_ || !this.src.unwrap ().equals (r.src.unwrap ())) { -return false; -}if (this.marks == null && r.marks != null) { -return false; -}if (this.marks != null && r.marks == null) { -return false; -}for (var i = 1; i <= this.numSubs_; i++) { -if (this.matchedFromI (i) != r.matchedFromI (i)) { -return false; -} else if (this.charsMatchedI (i) != r.charsMatchedI (i)) { -return false; -}} -return true; -}, "com.stevesoft.pat.RegRes"); -Clazz.defineMethod (c$, "stringMatched", -function () { -var mf = this.matchedFrom (); -var cm = this.charsMatched (); -return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf, mf + cm); -}); -Clazz.defineMethod (c$, "matchedFromI", -function (i) { -if (this.marks == null || i > this.numSubs_) { -return -1; -}return this.marks[i]; -}, "~N"); -Clazz.defineMethod (c$, "charsMatchedI", -function (i) { -if (this.marks == null || i > this.numSubs_ || !this.didMatch_) { -return -1; -}var mf = this.matchedFromI (i); -return mf < 0 ? -1 : this.marks[i + this.numSubs_] - this.matchedFromI (i); -}, "~N"); -Clazz.defineMethod (c$, "matchedToI", -function (i) { -if (this.marks == null || i > this.numSubs_ || !this.didMatch_) { -return -1; -}return this.marks[i + this.numSubs_]; -}, "~N"); -Clazz.defineMethod (c$, "stringMatchedI", -function (i) { -var mf = this.matchedFromI (i); -var cm = this.charsMatchedI (i); -return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf, mf + cm); -}, "~N"); -Clazz.defineMethod (c$, "left", -function () { -var mf = this.matchedFrom (); -return !this.didMatch_ || (mf < 0) ? null : this.src.substring (0, mf); -}); -Clazz.defineMethod (c$, "leftI", -function (i) { -var mf = this.matchedFromI (i); -return !this.didMatch_ || (mf < 0) ? null : this.src.substring (0, mf); -}, "~N"); -Clazz.defineMethod (c$, "right", -function () { -var mf = this.matchedFrom (); -var cm = this.charsMatched (); -return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf + cm, this.src.length ()); -}); -Clazz.defineMethod (c$, "rightI", -function (i) { -var mf = this.matchedFromI (i); -var cm = this.charsMatchedI (i); -return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf + cm, this.src.length ()); -}, "~N"); -Clazz.defineMethod (c$, "matchedFrom", -function () { -return !this.didMatch_ ? -1 : this.matchFrom_; -}); -Clazz.defineMethod (c$, "charsMatched", -function () { -return !this.didMatch_ || this.matchFrom_ < 0 ? -1 : this.charsMatched_; -}); -Clazz.defineMethod (c$, "matchedTo", -function () { -return !this.didMatch_ ? -1 : this.matchFrom_ + this.charsMatched_; -}); -Clazz.defineMethod (c$, "numSubs", -function () { -return this.numSubs_; -}); -Clazz.defineMethod (c$, "didMatch", -function () { -return this.didMatch_; -}); -Clazz.defineMethod (c$, "matchFrom", -function () { -return this.matchedFrom (); -}); -Clazz.defineMethod (c$, "substring", -function () { -return this.stringMatched (); -}); -Clazz.defineMethod (c$, "matchFromI", -function (i) { -return this.matchedFromI (i); -}, "~N"); -Clazz.defineMethod (c$, "substringI", -function (i) { -return this.stringMatchedI (i); -}, "~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.RegRes", ["java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.marks = null; +this.didMatch_ = false; +this.src = null; +this.charsMatched_ = 0; +this.matchFrom_ = 0; +this.numSubs_ = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RegRes"); +Clazz.defineMethod (c$, "getString", +function () { +return this.src.toString (); +}); +Clazz.defineMethod (c$, "getStringLike", +function () { +return this.src; +}); +Clazz.overrideMethod (c$, "toString", +function () { +var sb = new StringBuffer (); +sb.append ("match=" + this.matchedFrom () + ":" + this.charsMatched ()); +if (!this.didMatch ()) { +return sb.toString (); +}for (var i = 0; i < this.numSubs (); i++) { +var n = i + 1; +sb.append (" sub(" + n + ")=" + this.matchedFromI (n) + ":" + this.charsMatchedI (n)); +} +return sb.toString (); +}); +Clazz.defineMethod (c$, "copyOutOf", +function (r) { +if (r.marks == null) { +this.marks = null; +} else { +try { +this.marks = Clazz.newIntArray (r.marks.length, 0); +for (var i = 0; i < this.marks.length; i++) { +this.marks[i] = r.marks[i]; +} +} catch (t) { +} +}this.didMatch_ = r.didMatch_; +this.src = r.src; +this.charsMatched_ = r.charsMatched_; +this.matchFrom_ = r.matchFrom_; +this.numSubs_ = r.numSubs_; +}, "com.stevesoft.pat.RegRes"); +Clazz.defineMethod (c$, "equals", +function (r) { +if (this.charsMatched_ != r.charsMatched_ || this.matchFrom_ != r.matchFrom_ || this.didMatch_ != r.didMatch_ || this.numSubs_ != r.numSubs_ || !this.src.unwrap ().equals (r.src.unwrap ())) { +return false; +}if (this.marks == null && r.marks != null) { +return false; +}if (this.marks != null && r.marks == null) { +return false; +}for (var i = 1; i <= this.numSubs_; i++) { +if (this.matchedFromI (i) != r.matchedFromI (i)) { +return false; +} else if (this.charsMatchedI (i) != r.charsMatchedI (i)) { +return false; +}} +return true; +}, "com.stevesoft.pat.RegRes"); +Clazz.defineMethod (c$, "stringMatched", +function () { +var mf = this.matchedFrom (); +var cm = this.charsMatched (); +return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf, mf + cm); +}); +Clazz.defineMethod (c$, "matchedFromI", +function (i) { +if (this.marks == null || i > this.numSubs_) { +return -1; +}return this.marks[i]; +}, "~N"); +Clazz.defineMethod (c$, "charsMatchedI", +function (i) { +if (this.marks == null || i > this.numSubs_ || !this.didMatch_) { +return -1; +}var mf = this.matchedFromI (i); +return mf < 0 ? -1 : this.marks[i + this.numSubs_] - this.matchedFromI (i); +}, "~N"); +Clazz.defineMethod (c$, "matchedToI", +function (i) { +if (this.marks == null || i > this.numSubs_ || !this.didMatch_) { +return -1; +}return this.marks[i + this.numSubs_]; +}, "~N"); +Clazz.defineMethod (c$, "stringMatchedI", +function (i) { +var mf = this.matchedFromI (i); +var cm = this.charsMatchedI (i); +return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf, mf + cm); +}, "~N"); +Clazz.defineMethod (c$, "left", +function () { +var mf = this.matchedFrom (); +return !this.didMatch_ || (mf < 0) ? null : this.src.substring (0, mf); +}); +Clazz.defineMethod (c$, "leftI", +function (i) { +var mf = this.matchedFromI (i); +return !this.didMatch_ || (mf < 0) ? null : this.src.substring (0, mf); +}, "~N"); +Clazz.defineMethod (c$, "right", +function () { +var mf = this.matchedFrom (); +var cm = this.charsMatched (); +return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf + cm, this.src.length ()); +}); +Clazz.defineMethod (c$, "rightI", +function (i) { +var mf = this.matchedFromI (i); +var cm = this.charsMatchedI (i); +return !this.didMatch_ || mf < 0 || cm < 0 ? null : this.src.substring (mf + cm, this.src.length ()); +}, "~N"); +Clazz.defineMethod (c$, "matchedFrom", +function () { +return !this.didMatch_ ? -1 : this.matchFrom_; +}); +Clazz.defineMethod (c$, "charsMatched", +function () { +return !this.didMatch_ || this.matchFrom_ < 0 ? -1 : this.charsMatched_; +}); +Clazz.defineMethod (c$, "matchedTo", +function () { +return !this.didMatch_ ? -1 : this.matchFrom_ + this.charsMatched_; +}); +Clazz.defineMethod (c$, "numSubs", +function () { +return this.numSubs_; +}); +Clazz.defineMethod (c$, "didMatch", +function () { +return this.didMatch_; +}); +Clazz.defineMethod (c$, "matchFrom", +function () { +return this.matchedFrom (); +}); +Clazz.defineMethod (c$, "substring", +function () { +return this.stringMatched (); +}); +Clazz.defineMethod (c$, "matchFromI", +function (i) { +return this.matchedFromI (i); +}, "~N"); +Clazz.defineMethod (c$, "substringI", +function (i) { +return this.stringMatchedI (i); +}, "~N"); +}); diff --git a/bin/com/stevesoft/pat/RegSyntax.js b/bin/com/stevesoft/pat/RegSyntax.js index 9275c48..8a6e621 100644 --- a/bin/com/stevesoft/pat/RegSyntax.js +++ b/bin/com/stevesoft/pat/RegSyntax.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.lang.Exception"], "com.stevesoft.pat.RegSyntax", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "RegSyntax", Exception); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.RegSyntax, []); -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.lang.Exception"], "com.stevesoft.pat.RegSyntax", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "RegSyntax", Exception); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.RegSyntax, []); +}); +}); diff --git a/bin/com/stevesoft/pat/RegSyntaxError.js b/bin/com/stevesoft/pat/RegSyntaxError.js index 5a81c21..3a127a5 100644 --- a/bin/com/stevesoft/pat/RegSyntaxError.js +++ b/bin/com/stevesoft/pat/RegSyntaxError.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.lang.Error"], "com.stevesoft.pat.RegSyntaxError", ["com.stevesoft.pat.RegSyntax"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "RegSyntaxError", Error); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.RegSyntaxError, []); -}); -c$.endItAll = Clazz.defineMethod (c$, "endItAll", -function (s) { -if (com.stevesoft.pat.RegSyntaxError.RegSyntaxErrorEnabled) { -throw new com.stevesoft.pat.RegSyntaxError (s); -}throw new com.stevesoft.pat.RegSyntax (s); -}, "~S"); -Clazz.defineStatics (c$, -"RegSyntaxErrorEnabled", false); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.lang.Error"], "com.stevesoft.pat.RegSyntaxError", ["com.stevesoft.pat.RegSyntax"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "RegSyntaxError", Error); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.RegSyntaxError, []); +}); +c$.endItAll = Clazz.defineMethod (c$, "endItAll", +function (s) { +if (com.stevesoft.pat.RegSyntaxError.RegSyntaxErrorEnabled) { +throw new com.stevesoft.pat.RegSyntaxError (s); +}throw new com.stevesoft.pat.RegSyntax (s); +}, "~S"); +Clazz.defineStatics (c$, +"RegSyntaxErrorEnabled", false); +}); diff --git a/bin/com/stevesoft/pat/Regex.class b/bin/com/stevesoft/pat/Regex.class index 89553f0..14f6f05 100644 Binary files a/bin/com/stevesoft/pat/Regex.class and b/bin/com/stevesoft/pat/Regex.class differ diff --git a/bin/com/stevesoft/pat/Regex.js b/bin/com/stevesoft/pat/Regex.js index d05b95e..893eaa7 100644 --- a/bin/com/stevesoft/pat/Regex.js +++ b/bin/com/stevesoft/pat/Regex.js @@ -1,1026 +1,1026 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.RegRes", "$.UniValidator", "jalview.jsdev.api.RegExpInterface", "com.stevesoft.pat.NoPattern", "$.Pthings", "$.patInt", "java.util.Hashtable"], ["com.stevesoft.pat.UnicodeW", "$.UnicodeCurrency", "$.UnicodeAlpha", "$.UnicodeUpper", "$.NUnicodeCurrency", "$.NUnicodeW", "$.NUnicodeAlpha", "$.UnicodeMath", "$.UnicodeWhite", "$.UnicodeDigit", "$.NUnicodeMath", "$.Regex", "$.NUnicodeDigit", "$.NUnicodeWhite", "$.NUnicodePunct", "$.UnicodePunct", "$.UnicodeLower"], ["com.stevesoft.pat.Any", "$.BackG", "$.BackMatch", "$.Backup", "$.Boundary", "$.Bracket", "$.CaseMgr", "$.Ctrl", "$.Custom", "$.CustomEndpoint", "$.DotMulti", "$.End", "$.FastMulti", "$.Group", "$.MessageManager", "$.Multi", "$.NullPattern", "$.Or", "$.OrMark", "$.Prop", "$.Range", "$.RegOpt", "$.RegSyntax", "$.RegSyntaxError", "$.ReplaceRule", "$.Replacer", "$.Rthings", "$.Skip", "$.Skipped", "$.Start", "$.StrPos", "$.lookAhead", "$.oneChar", "$.parsePerl", "$.patInf", "com.stevesoft.pat.wrap.StringWrap", "java.lang.NullPointerException", "$.StringBuffer", "java.util.BitSet"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodePunct", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && com.stevesoft.pat.Prop.isPunct (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeWhite", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && com.stevesoft.pat.Prop.isWhite (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodePunct", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && !com.stevesoft.pat.Prop.isPunct (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeWhite", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && !com.stevesoft.pat.Prop.isWhite (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeW", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -if (from >= s.length ()) { -return -1; -}var c = s.charAt (from); -return (com.stevesoft.pat.Prop.isAlphabetic (c) || com.stevesoft.pat.Prop.isDecimalDigit (c) || c == '_') ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeW", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -if (from >= s.length ()) { -return -1; -}var c = s.charAt (from); -return !(com.stevesoft.pat.Prop.isAlphabetic (c) || com.stevesoft.pat.Prop.isDecimalDigit (c) || c == '_') ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeDigit", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && com.stevesoft.pat.Prop.isDecimalDigit (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeDigit", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && !com.stevesoft.pat.Prop.isDecimalDigit (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeMath", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && com.stevesoft.pat.Prop.isMath (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeMath", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && !com.stevesoft.pat.Prop.isMath (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeCurrency", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && com.stevesoft.pat.Prop.isCurrency (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeCurrency", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && !com.stevesoft.pat.Prop.isCurrency (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeAlpha", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && com.stevesoft.pat.Prop.isAlphabetic (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeAlpha", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && !com.stevesoft.pat.Prop.isAlphabetic (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeUpper", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && this.isUpper (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "isUpper", -function (c) { -return c == com.stevesoft.pat.CaseMgr.toUpperCaseC (c) && c != com.stevesoft.pat.CaseMgr.toLowerCaseC (c); -}, "~S"); -c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeLower", com.stevesoft.pat.UniValidator); -Clazz.overrideMethod (c$, "validate", -function (s, from, to) { -return from < s.length () && this.isLower (s.charAt (from)) ? to : -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "isLower", -function (c) { -return c != com.stevesoft.pat.CaseMgr.toUpperCaseC (c) && c == com.stevesoft.pat.CaseMgr.toLowerCaseC (c); -}, "~S"); -c$ = Clazz.decorateAsClass (function () { -this.thePattern = null; -this.minMatch = null; -this.rep = null; -this.dontMatchInQuotes = false; -this.ignoreCase = false; -this.repr = null; -this.esc = '\\'; -this.pt = null; -this.gFlags = null; -this.gFlagto = 0; -this.gFlag = false; -this.sFlag = false; -this.mFlag = false; -this.p = null; -this.or = null; -this.skipper = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Regex", com.stevesoft.pat.RegRes, [jalview.jsdev.api.RegExpInterface, Cloneable]); -Clazz.prepareFields (c$, function () { -this.thePattern = com.stevesoft.pat.Regex.none; -this.minMatch = new com.stevesoft.pat.patInt (0); -this.pt = new com.stevesoft.pat.Pthings (); -}); -Clazz.makeConstructor (c$, -function (s, strRp) { -Clazz.superConstructor (this, com.stevesoft.pat.Regex, []); -try { -if (s != null) this.compile (s); -if (strRp.length > 0) this.rep = com.stevesoft.pat.ReplaceRule.perlCode (strRp); -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -} else { -throw rs; -} -} -}, "~S,~S"); -Clazz.overrideMethod (c$, "clone", -function () { -return new com.stevesoft.pat.Regex (null, "").cloneFrom (this); -}); -Clazz.defineMethod (c$, "cloneFrom", -function (r) { -this.copyOutOf (r); -this.dontMatchInQuotes = r.dontMatchInQuotes; -this.esc = r.esc; -this.ignoreCase = r.ignoreCase; -this.gFlag = r.gFlag; -if (r.rep == null) { -this.rep = null; -} else { -this.rep = r.rep.clone (); -}this.thePattern = r.thePattern.clone ( new java.util.Hashtable ()); -this.minMatch = r.minMatch; -this.skipper = r.skipper; -return this; -}, "com.stevesoft.pat.Regex"); -Clazz.defineMethod (c$, "setDontMatchInQuotes", -function (b) { -this.dontMatchInQuotes = b; -}, "~B"); -Clazz.defineMethod (c$, "getDontMatchInQuotes", -function () { -return this.dontMatchInQuotes; -}); -Clazz.overrideMethod (c$, "setIgnoreCase", -function (b) { -this.ignoreCase = b; -}, "~B"); -Clazz.defineMethod (c$, "getIgnoreCase", -function () { -return this.ignoreCase; -}); -c$.setDefaultMFlag = Clazz.defineMethod (c$, "setDefaultMFlag", -function (mFlag) { -com.stevesoft.pat.Regex.defaultMFlag = mFlag; -}, "~B"); -c$.getDefaultMFlag = Clazz.defineMethod (c$, "getDefaultMFlag", -function () { -return com.stevesoft.pat.Regex.defaultMFlag; -}); -Clazz.defineMethod (c$, "setReplaceRuleStr", -function (rp) { -this.rep = com.stevesoft.pat.ReplaceRule.perlCode (rp); -this.repr = null; -}, "~S"); -Clazz.defineMethod (c$, "setReplaceRule", -function (rp) { -this.rep = rp; -}, "com.stevesoft.pat.ReplaceRule"); -c$.isDefined = Clazz.defineMethod (c$, "isDefined", -function (nm) { -return com.stevesoft.pat.Regex.validators.get (nm) != null; -}, "~S"); -c$.undefine = Clazz.defineMethod (c$, "undefine", -function (nm) { -com.stevesoft.pat.Regex.validators.remove (nm); -}, "~S"); -c$.defineV = Clazz.defineMethod (c$, "defineV", -function (nm, pat, v) { -v.pattern = pat; -com.stevesoft.pat.Regex.validators.put (nm, v); -}, "~S,~S,com.stevesoft.pat.Validator"); -c$.define = Clazz.defineMethod (c$, "define", -function (nm, pat) { -com.stevesoft.pat.Regex.validators.put (nm, pat); -}, "~S,~S"); -Clazz.defineMethod (c$, "getReplaceRule", -function () { -return this.rep; -}); -Clazz.defineMethod (c$, "_getReplacer", -function () { -return this.repr == null ? this.repr = new com.stevesoft.pat.Replacer () : this.repr; -}); -Clazz.defineMethod (c$, "getReplacer", -function () { -if (this.repr == null) { -this.repr = new com.stevesoft.pat.Replacer (); -}this.repr.rh.me = this; -this.repr.rh.prev = null; -return this.repr; -}); -Clazz.defineMethod (c$, "replaceFirst", -function (s) { -return this._getReplacer ().replaceFirstRegion (s, this, 0, s.length).toString (); -}, "~S"); -Clazz.defineMethod (c$, "replaceFirstFrom", -function (s, pos) { -return this._getReplacer ().replaceFirstRegion (s, this, pos, s.length).toString (); -}, "~S,~N"); -Clazz.defineMethod (c$, "replaceFirstRegion", -function (s, start, end) { -return this._getReplacer ().replaceFirstRegion (s, this, start, end).toString (); -}, "~S,~N,~N"); -Clazz.overrideMethod (c$, "replaceAll", -function (s) { -return this._getReplacer ().replaceAllRegion (s, this, 0, s.length).toString (); -}, "~S"); -Clazz.defineMethod (c$, "replaceAllLike", -function (s) { -return this._getReplacer ().replaceAllRegion (s, this, 0, s.length ()); -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "replaceAllFrom", -function (s, pos) { -return this._getReplacer ().replaceAllRegion (s, this, pos, s.length).toString (); -}, "~S,~N"); -Clazz.defineMethod (c$, "replaceAllRegion", -function (s, start, end) { -return this._getReplacer ().replaceAllRegion (s, this, start, end).toString (); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "compile", -function (prepat) { -var postpat = com.stevesoft.pat.parsePerl.codify (prepat, true); -var pat = postpat == null ? prepat : postpat; -this.minMatch = null; -this.ignoreCase = false; -this.dontMatchInQuotes = false; -var mk = new com.stevesoft.pat.Rthings (this); -var offset = mk.val; -var newpat = pat; -this.thePattern = com.stevesoft.pat.Regex.none; -this.p = null; -this.or = null; -this.minMatch = new com.stevesoft.pat.patInt (0); -var sp = new com.stevesoft.pat.StrPos (pat, 0); -if (sp.incMatch ("(?e=")) { -var newEsc = sp.c; -sp.inc (); -if (sp.match (')')) { -newpat = com.stevesoft.pat.Regex.reEscape (pat.substring (6), newEsc, '\\'); -}} else if (this.esc != '\\') { -newpat = com.stevesoft.pat.Regex.reEscape (pat, this.esc, '\\'); -}this.thePattern = this._compile (newpat, mk); -this.numSubs_ = mk.val - offset; -mk.set (this); -}, "~S"); -Clazz.defineMethod (c$, "equals", -function (o) { -if (Clazz.instanceOf (o, com.stevesoft.pat.Regex)) { -if (this.toString ().equals (o.toString ())) { -return Clazz.superCall (this, com.stevesoft.pat.Regex, "equals", [o]); -} else { -return false; -}} else { -return Clazz.superCall (this, com.stevesoft.pat.Regex, "equals", [o]); -}}, "~O"); -Clazz.defineMethod (c$, "prep", -function (s) { -this.pt.lastPos = this.matchedTo (); -if (this.pt.lastPos < 0) { -this.pt.lastPos = 0; -}if ((s == null ? null : s.unwrap ()) !== (this.src == null ? null : s.unwrap ())) { -this.pt.lastPos = 0; -}this.src = s; -this.pt.dotDoesntMatchCR = com.stevesoft.pat.Regex.dotDoesntMatchCR && (!this.sFlag); -this.pt.mFlag = ( new Boolean (this.mFlag | com.stevesoft.pat.Regex.defaultMFlag).valueOf ()); -this.pt.ignoreCase = this.ignoreCase; -this.pt.no_check = false; -if (this.pt.marks != null) { -for (var i = 0; i < this.pt.marks.length; i++) { -this.pt.marks[i] = -1; -} -}this.pt.marks = null; -this.pt.nMarks = this.numSubs_; -this.pt.src = s; -if (this.dontMatchInQuotes) { -com.stevesoft.pat.Regex.setCbits (s, this.pt); -} else { -this.pt.cbits = null; -}return this.pt; -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "matchAt", -function (s, start_pos) { -return this._search (s, start_pos, start_pos); -}, "~S,~N"); -Clazz.defineMethod (c$, "matchAtLike", -function (s, start_pos) { -return this._searchLike (s, start_pos, start_pos); -}, "com.stevesoft.pat.StringLike,~N"); -Clazz.overrideMethod (c$, "search", -function (s) { -if (s == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_given_to_regex_search")); -}return this._search (s, 0, s.length); -}, "~S"); -Clazz.defineMethod (c$, "searchLike", -function (sl) { -if (sl == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search")); -}return this._searchLike (sl, 0, sl.length ()); -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "reverseSearch", -function (s) { -if (s == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_given_to_regex_reverse_search")); -}return this._reverseSearch (s, 0, s.length); -}, "~S"); -Clazz.defineMethod (c$, "reverseSearchLike", -function (sl) { -if (sl == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_reverse_search")); -}return this._reverseSearchLike (sl, 0, sl.length ()); -}, "com.stevesoft.pat.StringLike"); -Clazz.overrideMethod (c$, "searchFrom", -function (s, start) { -if (s == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search_from")); -}return this._search (s, start, s.length); -}, "~S,~N"); -Clazz.defineMethod (c$, "searchFromLike", -function (s, start) { -if (s == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search_from")); -}return this._searchLike (s, start, s.length ()); -}, "com.stevesoft.pat.StringLike,~N"); -Clazz.defineMethod (c$, "searchRegion", -function (s, start, end) { -if (s == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search_region")); -}return this._search (s, start, end); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "setGFlag", -function (b) { -this.gFlag = b; -}, "~B"); -Clazz.defineMethod (c$, "getGFlag", -function () { -return this.gFlag; -}); -Clazz.defineMethod (c$, "getSFlag", -function () { -return this.sFlag; -}); -Clazz.defineMethod (c$, "getMFlag", -function () { -return this.mFlag; -}); -Clazz.defineMethod (c$, "_search", -function (s, start, end) { -return this._searchLike ( new com.stevesoft.pat.wrap.StringWrap (s), start, end); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "_searchLike", -function (s, start, end) { -if (this.gFlag && this.gFlagto > 0 && this.gFlags != null && s.unwrap () === this.gFlags.unwrap ()) { -start = this.gFlagto; -}this.gFlags = null; -var pt = this.prep (s); -var up = (this.minMatch == null ? end : end - this.minMatch.i); -if (up < start && end >= start) { -up = start; -}if (this.skipper == null) { -for (var i = start; i <= up; i++) { -this.charsMatched_ = this.thePattern.matchAt (s, i, pt); -if (this.charsMatched_ >= 0) { -this.matchFrom_ = this.thePattern.mfrom; -this.marks = pt.marks; -this.gFlagto = this.matchFrom_ + this.charsMatched_; -this.gFlags = s; -return this.didMatch_ = true; -}} -} else { -pt.no_check = true; -for (var i = start; i <= up; i++) { -i = this.skipper.find (this.src, i, up); -if (i < 0) { -this.charsMatched_ = this.matchFrom_ = -1; -return this.didMatch_ = false; -}this.charsMatched_ = this.thePattern.matchAt (s, i, pt); -if (this.charsMatched_ >= 0) { -this.matchFrom_ = this.thePattern.mfrom; -this.marks = pt.marks; -this.gFlagto = this.matchFrom_ + this.charsMatched_; -this.gFlags = s; -return this.didMatch_ = true; -}} -}return this.didMatch_ = false; -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "_reverseSearch", -function (s, start, end) { -return this._reverseSearchLike ( new com.stevesoft.pat.wrap.StringWrap (s), start, end); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "_reverseSearchLike", -function (s, start, end) { -if (this.gFlag && this.gFlagto > 0 && s.unwrap () === this.gFlags.unwrap ()) { -end = this.gFlagto; -}this.gFlags = null; -var pt = this.prep (s); -for (var i = end; i >= start; i--) { -this.charsMatched_ = this.thePattern.matchAt (s, i, pt); -if (this.charsMatched_ >= 0) { -this.matchFrom_ = this.thePattern.mfrom; -this.marks = pt.marks; -this.gFlagto = this.matchFrom_ - 1; -this.gFlags = s; -return this.didMatch_ = true; -}} -return this.didMatch_ = false; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$.setCbits = Clazz.defineMethod (c$, "setCbits", -function (s, pt) { -if (s === com.stevesoft.pat.Regex.lasts) { -pt.cbits = com.stevesoft.pat.Regex.lastbs; -return; -}var bs = new java.util.BitSet (s.length ()); -var qc = ' '; -var setBit = false; -for (var i = 0; i < s.length (); i++) { -if (setBit) { -bs.set (i); -}var c = s.charAt (i); -if (!setBit && c == '"') { -qc = c; -setBit = true; -bs.set (i); -} else if (!setBit && c == '\'') { -qc = c; -setBit = true; -bs.set (i); -} else if (setBit && c == qc) { -setBit = false; -} else if (setBit && c == '\\' && i + 1 < s.length ()) { -i++; -if (setBit) { -bs.set (i); -}}} -pt.cbits = com.stevesoft.pat.Regex.lastbs = bs; -com.stevesoft.pat.Regex.lasts = s; -}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "add", -function (p2) { -if (this.p == null) { -this.p = p2; -} else { -this.p.add (p2); -p2 = this.p; -}}, "com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "compileSP", -function (sp, mk) { -if (sp.match ('[')) { -sp.inc (); -this.add (this.matchBracket (sp)); -} else if (sp.match ('|')) { -if (this.or == null) { -this.or = new com.stevesoft.pat.Or (); -}if (this.p == null) { -this.p = new com.stevesoft.pat.NullPattern (); -}this.or.addOr (this.p); -this.p = null; -} else if (sp.incMatch ("(?<")) { -var i = sp.getPatInt (); -if (i == null) { -com.stevesoft.pat.RegSyntaxError.endItAll ("No int after (?<"); -}this.add ( new com.stevesoft.pat.Backup (i.intValue ())); -if (!sp.match (')')) { -com.stevesoft.pat.RegSyntaxError.endItAll ("No ) after (?<"); -}} else if (sp.incMatch ("(?>")) { -var i = sp.getPatInt (); -if (i == null) { -com.stevesoft.pat.RegSyntaxError.endItAll ("No int after (?>"); -}this.add ( new com.stevesoft.pat.Backup (-i.intValue ())); -if (!sp.match (')')) { -com.stevesoft.pat.RegSyntaxError.endItAll ("No ) after (?<"); -}} else if (sp.incMatch ("(?@")) { -var op = sp.c; -sp.inc (); -var cl = sp.c; -sp.inc (); -if (!sp.match (')')) { -com.stevesoft.pat.RegSyntaxError.endItAll ("(?@ does not have closing paren"); -}this.add ( new com.stevesoft.pat.Group (op, cl)); -} else if (sp.incMatch ("(?#")) { -while (!sp.match (')')) { -sp.inc (); -} -} else if (sp.dontMatch && sp.c == 'w') { -var b = new com.stevesoft.pat.Bracket (false); -b.addOr ( new com.stevesoft.pat.Range ('a', 'z')); -b.addOr ( new com.stevesoft.pat.Range ('A', 'Z')); -b.addOr ( new com.stevesoft.pat.Range ('0', '9')); -b.addOr ( new com.stevesoft.pat.oneChar ('_')); -this.add (b); -} else if (sp.dontMatch && sp.c == 'G') { -this.add ( new com.stevesoft.pat.BackG ()); -} else if (sp.dontMatch && sp.c == 's') { -var b = new com.stevesoft.pat.Bracket (false); -b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (32))); -b.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (8), String.fromCharCode (10))); -b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (13))); -this.add (b); -} else if (sp.dontMatch && sp.c == 'd') { -var digit = new com.stevesoft.pat.Range ('0', '9'); -digit.printBrackets = true; -this.add (digit); -} else if (sp.dontMatch && sp.c == 'W') { -var b = new com.stevesoft.pat.Bracket (true); -b.addOr ( new com.stevesoft.pat.Range ('a', 'z')); -b.addOr ( new com.stevesoft.pat.Range ('A', 'Z')); -b.addOr ( new com.stevesoft.pat.Range ('0', '9')); -b.addOr ( new com.stevesoft.pat.oneChar ('_')); -this.add (b); -} else if (sp.dontMatch && sp.c == 'S') { -var b = new com.stevesoft.pat.Bracket (true); -b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (32))); -b.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (8), String.fromCharCode (10))); -b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (13))); -this.add (b); -} else if (sp.dontMatch && sp.c == 'D') { -var b = new com.stevesoft.pat.Bracket (true); -b.addOr ( new com.stevesoft.pat.Range ('0', '9')); -this.add (b); -} else if (sp.dontMatch && sp.c == 'B') { -var r = new com.stevesoft.pat.Regex (null, ""); -r._compile ("(?!\\b)", mk); -this.add (r.thePattern); -} else if (this.isOctalString (sp)) { -var d = sp.c.charCodeAt (0) - 48; -sp.inc (); -d = 8 * d + sp.c.charCodeAt (0) - 48; -var sp2 = new com.stevesoft.pat.StrPos (sp); -sp2.inc (); -if (this.isOctalDigit (sp2, false)) { -sp.inc (); -d = 8 * d + sp.c.charCodeAt (0) - 48; -}this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); -} else if (sp.dontMatch && sp.c >= '1' && sp.c <= '9') { -var iv = sp.c.charCodeAt (0) - 48; -var s2 = new com.stevesoft.pat.StrPos (sp); -s2.inc (); -if (!s2.dontMatch && s2.c >= '0' && s2.c <= '9') { -iv = 10 * iv + (s2.c.charCodeAt (0) - 48); -sp.inc (); -}this.add ( new com.stevesoft.pat.BackMatch (iv)); -} else if (sp.dontMatch && sp.c == 'b') { -this.add ( new com.stevesoft.pat.Boundary ()); -} else if (sp.match ('\b')) { -this.add ( new com.stevesoft.pat.Boundary ()); -} else if (sp.match ('$')) { -this.add ( new com.stevesoft.pat.End (true)); -} else if (sp.dontMatch && sp.c == 'Z') { -this.add ( new com.stevesoft.pat.End (false)); -} else if (sp.match ('.')) { -this.add ( new com.stevesoft.pat.Any ()); -} else if (sp.incMatch ("(??")) { -var sb = new StringBuffer (); -var sb2 = new StringBuffer (); -while (!sp.match (')') && !sp.match (':')) { -sb.append (sp.c); -sp.inc (); -} -if (sp.incMatch (":")) { -while (!sp.match (')')) { -sb2.append (sp.c); -sp.inc (); -} -}var sbs = sb.toString (); -if (Clazz.instanceOf (com.stevesoft.pat.Regex.validators.get (sbs), String)) { -var pat = com.stevesoft.pat.Regex.validators.get (sbs); -var r = new com.stevesoft.pat.Regex (null, ""); -var rth = new com.stevesoft.pat.Rthings (this); -rth.noBackRefs = true; -r._compile (pat, rth); -this.add (r.thePattern); -} else { -var cm = new com.stevesoft.pat.Custom (sb.toString ()); -if (cm.v != null) { -var v2 = cm.v.arg (sb2.toString ()); -if (v2 != null) { -v2.argsave = sb2.toString (); -var p = cm.v.pattern; -cm.v = v2; -v2.pattern = p; -}var r = new com.stevesoft.pat.Regex (null, ""); -var rth = new com.stevesoft.pat.Rthings (this); -rth.noBackRefs = true; -r._compile (cm.v.pattern, rth); -cm.sub = r.thePattern; -cm.sub.add ( new com.stevesoft.pat.CustomEndpoint (cm)); -cm.sub.setParent (cm); -this.add (cm); -}}} else if (sp.match ('(')) { -mk.parenLevel++; -var r = new com.stevesoft.pat.Regex (null, ""); -sp.inc (); -if (sp.incMatch ("?:")) { -r.or = new com.stevesoft.pat.Or (); -} else if (sp.incMatch ("?=")) { -r.or = new com.stevesoft.pat.lookAhead (false); -} else if (sp.incMatch ("?!")) { -r.or = new com.stevesoft.pat.lookAhead (true); -} else if (sp.match ('?')) { -sp.inc (); -do { -if (sp.c == 'i') { -mk.ignoreCase = true; -}if (sp.c == 'Q') { -mk.dontMatchInQuotes = true; -}if (sp.c == 'o') { -mk.optimizeMe = true; -}if (sp.c == 'g') { -mk.gFlag = true; -}if (sp.c == 's') { -mk.sFlag = true; -}if (sp.c == 'm') { -mk.mFlag = true; -}sp.inc (); -} while (!sp.match (')') && !sp.$eos); -r = null; -mk.parenLevel--; -if (sp.$eos) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Unclosed ()"); -}} else { -r.or = mk.noBackRefs ? new com.stevesoft.pat.Or () : new com.stevesoft.pat.OrMark (mk.val++); -}if (r != null) { -this.add (r._compileSP (sp, mk)); -}} else if (sp.match ('^')) { -this.add ( new com.stevesoft.pat.Start (true)); -} else if (sp.dontMatch && sp.c == 'A') { -this.add ( new com.stevesoft.pat.Start (false)); -} else if (sp.match ('*')) { -this.addMulti ( new com.stevesoft.pat.patInt (0), new com.stevesoft.pat.patInf ()); -} else if (sp.match ('+')) { -this.addMulti ( new com.stevesoft.pat.patInt (1), new com.stevesoft.pat.patInf ()); -} else if (sp.match ('?')) { -this.addMulti ( new com.stevesoft.pat.patInt (0), new com.stevesoft.pat.patInt (1)); -} else if (sp.match ('{')) { -var bad = false; -var sp2 = new com.stevesoft.pat.StrPos (sp); -sp.inc (); -var i1 = sp.getPatInt (); -var i2 = null; -if (sp.match ('}')) { -i2 = i1; -} else { -if (!sp.match (',')) { -bad = true; -}sp.inc (); -if (sp.match ('}')) { -i2 = new com.stevesoft.pat.patInf (); -} else { -i2 = sp.getPatInt (); -}}if (i1 == null || i2 == null) { -bad = true; -}if (bad) { -sp.dup (sp2); -this.add ( new com.stevesoft.pat.oneChar (sp.c)); -} else { -this.addMulti (i1, i2); -}} else if (sp.escMatch ('x') && this.next2Hex (sp)) { -sp.inc (); -var d = this.getHexDigit (sp); -sp.inc (); -d = 16 * d + this.getHexDigit (sp); -this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); -} else if (sp.escMatch ('c')) { -sp.inc (); -if (sp.c.charCodeAt (0) < com.stevesoft.pat.Ctrl.cmap.length) { -this.add ( new com.stevesoft.pat.oneChar (com.stevesoft.pat.Ctrl.cmap[sp.c.charCodeAt (0)])); -} else { -this.add ( new com.stevesoft.pat.oneChar (sp.c)); -}} else if (sp.escMatch ('f')) { -this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (12))); -} else if (sp.escMatch ('a')) { -this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (7))); -} else if (sp.escMatch ('t')) { -this.add ( new com.stevesoft.pat.oneChar ('\t')); -} else if (sp.escMatch ('n')) { -this.add ( new com.stevesoft.pat.oneChar ('\n')); -} else if (sp.escMatch ('r')) { -this.add ( new com.stevesoft.pat.oneChar ('\r')); -} else if (sp.escMatch ('b')) { -this.add ( new com.stevesoft.pat.oneChar ('\b')); -} else if (sp.escMatch ('e')) { -this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (27))); -} else { -this.add ( new com.stevesoft.pat.oneChar (sp.c)); -if (sp.match (')')) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Unmatched right paren in pattern"); -}}}, "com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings"); -Clazz.defineMethod (c$, "_compile", -($fz = function (pat, mk) { -this.minMatch = null; -this.sFlag = this.mFlag = this.ignoreCase = this.gFlag = false; -var sp = new com.stevesoft.pat.StrPos (pat, 0); -this.thePattern = this._compileSP (sp, mk); -this.pt.marks = null; -return this.thePattern; -}, $fz.isPrivate = true, $fz), "~S,com.stevesoft.pat.Rthings"); -Clazz.defineMethod (c$, "_compileSP", -function (sp, mk) { -while (!(sp.$eos || (this.or != null && sp.match (')')))) { -this.compileSP (sp, mk); -sp.inc (); -} -if (sp.match (')')) { -mk.parenLevel--; -} else if (sp.$eos && mk.parenLevel != 0) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Unclosed Parenthesis! lvl=" + mk.parenLevel); -}if (this.or != null) { -if (this.p == null) { -this.p = new com.stevesoft.pat.NullPattern (); -}this.or.addOr (this.p); -return this.or; -}return this.p == null ? new com.stevesoft.pat.NullPattern () : this.p; -}, "com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings"); -Clazz.defineMethod (c$, "addMulti", -function (i1, i2) { -var last; -var last2; -for (last = this.p; last != null && last.next != null; last = last.next) { -;} -if (last == null || last === this.p) { -last2 = null; -} else { -for (last2 = this.p; last2.next !== last; last2 = last2.next) { -;} -}if (Clazz.instanceOf (last, com.stevesoft.pat.Multi) && i1.intValue () == 0 && i2.intValue () == 1) { -(last).matchFewest = true; -} else if (Clazz.instanceOf (last, com.stevesoft.pat.FastMulti) && i1.intValue () == 0 && i2.intValue () == 1) { -(last).matchFewest = true; -} else if (Clazz.instanceOf (last, com.stevesoft.pat.DotMulti) && i1.intValue () == 0 && i2.intValue () == 1) { -(last).matchFewest = true; -} else if (Clazz.instanceOf (last, com.stevesoft.pat.Multi) || Clazz.instanceOf (last, com.stevesoft.pat.DotMulti) || Clazz.instanceOf (last, com.stevesoft.pat.FastMulti)) { -throw new com.stevesoft.pat.RegSyntax ("Syntax error."); -} else if (last2 == null) { -this.p = com.stevesoft.pat.Regex.mkMulti (i1, i2, this.p); -} else { -last2.next = com.stevesoft.pat.Regex.mkMulti (i1, i2, last); -}}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt"); -c$.mkMulti = Clazz.defineMethod (c$, "mkMulti", -function (lo, hi, p) { -if (Clazz.instanceOf (p, com.stevesoft.pat.Any) && p.next == null) { -return new com.stevesoft.pat.DotMulti (lo, hi); -}return com.stevesoft.pat.RegOpt.safe4fm (p) ? new com.stevesoft.pat.FastMulti (lo, hi, p) : new com.stevesoft.pat.Multi (lo, hi, p); -}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); -Clazz.defineMethod (c$, "matchBracket", -function (sp) { -var ret; -if (sp.match ('^')) { -ret = new com.stevesoft.pat.Bracket (true); -sp.inc (); -} else { -ret = new com.stevesoft.pat.Bracket (false); -}if (sp.match (']')) { -com.stevesoft.pat.RegSyntaxError.endItAll ("Unmatched []"); -}while (!sp.$eos && !sp.match (']')) { -var s1 = new com.stevesoft.pat.StrPos (sp); -s1.inc (); -var s1_ = new com.stevesoft.pat.StrPos (s1); -s1_.inc (); -if (s1.match ('-') && !s1_.match (']')) { -var s2 = new com.stevesoft.pat.StrPos (s1); -s2.inc (); -if (!s2.$eos) { -ret.addOr ( new com.stevesoft.pat.Range (sp.c, s2.c)); -}sp.inc (); -sp.inc (); -} else if (sp.escMatch ('Q')) { -sp.inc (); -while (!sp.escMatch ('E')) { -ret.addOr ( new com.stevesoft.pat.oneChar (sp.c)); -sp.inc (); -} -} else if (sp.escMatch ('d')) { -ret.addOr ( new com.stevesoft.pat.Range ('0', '9')); -} else if (sp.escMatch ('s')) { -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (32))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (8), String.fromCharCode (10))); -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (13))); -} else if (sp.escMatch ('w')) { -ret.addOr ( new com.stevesoft.pat.Range ('a', 'z')); -ret.addOr ( new com.stevesoft.pat.Range ('A', 'Z')); -ret.addOr ( new com.stevesoft.pat.Range ('0', '9')); -ret.addOr ( new com.stevesoft.pat.oneChar ('_')); -} else if (sp.escMatch ('D')) { -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (47))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (58), String.fromCharCode (65535))); -} else if (sp.escMatch ('S')) { -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (7))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (11), String.fromCharCode (12))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (14), String.fromCharCode (31))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (33), String.fromCharCode (65535))); -} else if (sp.escMatch ('W')) { -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (64))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (91), String.fromCharCode (94))); -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (96))); -ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (123), String.fromCharCode (65535))); -} else if (sp.escMatch ('x') && this.next2Hex (sp)) { -sp.inc (); -var d = this.getHexDigit (sp); -sp.inc (); -d = 16 * d + this.getHexDigit (sp); -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); -} else if (sp.escMatch ('a')) { -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (7))); -} else if (sp.escMatch ('f')) { -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (12))); -} else if (sp.escMatch ('e')) { -ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (27))); -} else if (sp.escMatch ('n')) { -ret.addOr ( new com.stevesoft.pat.oneChar ('\n')); -} else if (sp.escMatch ('t')) { -ret.addOr ( new com.stevesoft.pat.oneChar ('\t')); -} else if (sp.escMatch ('r')) { -ret.addOr ( new com.stevesoft.pat.oneChar ('\r')); -} else if (sp.escMatch ('c')) { -sp.inc (); -if (sp.c.charCodeAt (0) < com.stevesoft.pat.Ctrl.cmap.length) { -ret.addOr ( new com.stevesoft.pat.oneChar (com.stevesoft.pat.Ctrl.cmap[sp.c.charCodeAt (0)])); -} else { -ret.addOr ( new com.stevesoft.pat.oneChar (sp.c)); -}} else if (this.isOctalString (sp)) { -var d = sp.c.charCodeAt (0) - 48; -sp.inc (); -d = 8 * d + sp.c.charCodeAt (0) - 48; -var sp2 = new com.stevesoft.pat.StrPos (sp); -sp2.inc (); -if (this.isOctalDigit (sp2, false)) { -sp.inc (); -d = 8 * d + sp.c.charCodeAt (0) - 48; -}ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); -} else { -ret.addOr ( new com.stevesoft.pat.oneChar (sp.c)); -}sp.inc (); -} -return ret; -}, "com.stevesoft.pat.StrPos"); -Clazz.overrideMethod (c$, "toString", -function () { -{ -var sb = new StringBuffer (); -if (this.esc != '\\') { -sb.append ("(?e="); -sb.append (this.esc); -sb.append (")"); -}if (this.gFlag || this.mFlag || !com.stevesoft.pat.Regex.dotDoesntMatchCR || this.sFlag || this.ignoreCase || this.dontMatchInQuotes || this.optimized ()) { -sb.append ("(?"); -if (this.ignoreCase) { -sb.append ("i"); -}if (this.mFlag) { -sb.append ("m"); -}if (this.sFlag || !com.stevesoft.pat.Regex.dotDoesntMatchCR) { -sb.append ("s"); -}if (this.dontMatchInQuotes) { -sb.append ("Q"); -}if (this.optimized ()) { -sb.append ("o"); -}if (this.gFlag) { -sb.append ("g"); -}sb.append (")"); -}var patstr = this.thePattern.toString (); -if (this.esc != '\\') { -patstr = com.stevesoft.pat.Regex.reEscape (patstr, '\\', this.esc); -}sb.append (patstr); -return sb.toString (); -}}); -c$.reEscape = Clazz.defineMethod (c$, "reEscape", -function (s, oldEsc, newEsc) { -if (oldEsc == newEsc) { -return s; -}var i; -var sb = new StringBuffer (); -for (i = 0; i < s.length; i++) { -if (s.charAt (i) == oldEsc && i + 1 < s.length) { -if (s.charAt (i + 1) == oldEsc) { -sb.append (oldEsc); -} else { -sb.append (newEsc); -sb.append (s.charAt (i + 1)); -}i++; -} else if (s.charAt (i) == newEsc) { -sb.append (newEsc); -sb.append (newEsc); -} else { -sb.append (s.charAt (i)); -}} -return sb.toString (); -}, "~S,~S,~S"); -Clazz.defineMethod (c$, "accept", -function (dir, s) { -return this.search (s); -}, "java.io.File,~S"); -c$.version = Clazz.defineMethod (c$, "version", -function () { -return "lgpl release 1.5.3"; -}); -Clazz.defineMethod (c$, "optimize", -function () { -if (this.optimized () || this.thePattern == null) { -return; -}this.minMatch = new com.stevesoft.pat.patInt (0); -this.thePattern = com.stevesoft.pat.RegOpt.opt (this.thePattern, this.ignoreCase, this.dontMatchInQuotes); -this.skipper = com.stevesoft.pat.Skip.findSkipRegex (this); -return; -}); -Clazz.defineMethod (c$, "optimized", -function () { -return this.minMatch != null; -}); -c$.perlCode = Clazz.defineMethod (c$, "perlCode", -function (s) { -return com.stevesoft.pat.parsePerl.parse (s); -}, "~S"); -Clazz.defineMethod (c$, "isLiteral", -function () { -var x = this.thePattern; -while (x != null) { -if (Clazz.instanceOf (x, com.stevesoft.pat.oneChar)) { -;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Skipped)) { -;} else { -return false; -}x = x.next; -} -return true; -}); -Clazz.defineMethod (c$, "countMinChars", -function () { -return this.thePattern.countMinChars (); -}); -Clazz.defineMethod (c$, "countMaxChars", -function () { -return this.thePattern.countMaxChars (); -}); -Clazz.defineMethod (c$, "isHexDigit", -function (sp) { -var r = !sp.$eos && !sp.dontMatch && ((sp.c >= '0' && sp.c <= '9') || (sp.c >= 'a' && sp.c <= 'f') || (sp.c >= 'A' && sp.c <= 'F')); -return r; -}, "com.stevesoft.pat.StrPos"); -Clazz.defineMethod (c$, "isOctalDigit", -function (sp, first) { -var r = !sp.$eos && !( new Boolean (first ^ sp.dontMatch).valueOf ()) && sp.c >= '0' && sp.c <= '7'; -return r; -}, "com.stevesoft.pat.StrPos,~B"); -Clazz.defineMethod (c$, "getHexDigit", -function (sp) { -if (sp.c >= '0' && sp.c <= '9') { -return sp.c.charCodeAt (0) - 48; -}if (sp.c >= 'a' && sp.c <= 'f') { -return sp.c.charCodeAt (0) - 97 + 10; -}return sp.c.charCodeAt (0) - 65 + 10; -}, "com.stevesoft.pat.StrPos"); -Clazz.defineMethod (c$, "next2Hex", -function (sp) { -var sp2 = new com.stevesoft.pat.StrPos (sp); -sp2.inc (); -if (!this.isHexDigit (sp2)) { -return false; -}sp2.inc (); -if (!this.isHexDigit (sp2)) { -return false; -}return true; -}, "com.stevesoft.pat.StrPos"); -Clazz.defineMethod (c$, "isOctalString", -function (sp) { -if (!this.isOctalDigit (sp, true)) { -return false; -}var sp2 = new com.stevesoft.pat.StrPos (sp); -sp2.inc (); -if (!this.isOctalDigit (sp2, false)) { -return false; -}return true; -}, "com.stevesoft.pat.StrPos"); -Clazz.defineStatics (c$, -"BackRefOffset", 1); -c$.none = c$.prototype.none = new com.stevesoft.pat.NoPattern (); -c$.validators = c$.prototype.validators = new java.util.Hashtable (); -{ -com.stevesoft.pat.Regex.defineV ("p", "(?>1)", new com.stevesoft.pat.UnicodePunct ()); -com.stevesoft.pat.Regex.defineV ("P", "(?>1)", new com.stevesoft.pat.NUnicodePunct ()); -com.stevesoft.pat.Regex.defineV ("s", "(?>1)", new com.stevesoft.pat.UnicodeWhite ()); -com.stevesoft.pat.Regex.defineV ("S", "(?>1)", new com.stevesoft.pat.NUnicodeWhite ()); -com.stevesoft.pat.Regex.defineV ("w", "(?>1)", new com.stevesoft.pat.UnicodeW ()); -com.stevesoft.pat.Regex.defineV ("W", "(?>1)", new com.stevesoft.pat.NUnicodeW ()); -com.stevesoft.pat.Regex.defineV ("d", "(?>1)", new com.stevesoft.pat.UnicodeDigit ()); -com.stevesoft.pat.Regex.defineV ("D", "(?>1)", new com.stevesoft.pat.NUnicodeDigit ()); -com.stevesoft.pat.Regex.defineV ("m", "(?>1)", new com.stevesoft.pat.UnicodeMath ()); -com.stevesoft.pat.Regex.defineV ("M", "(?>1)", new com.stevesoft.pat.NUnicodeMath ()); -com.stevesoft.pat.Regex.defineV ("c", "(?>1)", new com.stevesoft.pat.UnicodeCurrency ()); -com.stevesoft.pat.Regex.defineV ("C", "(?>1)", new com.stevesoft.pat.NUnicodeCurrency ()); -com.stevesoft.pat.Regex.defineV ("a", "(?>1)", new com.stevesoft.pat.UnicodeAlpha ()); -com.stevesoft.pat.Regex.defineV ("A", "(?>1)", new com.stevesoft.pat.NUnicodeAlpha ()); -com.stevesoft.pat.Regex.defineV ("uc", "(?>1)", new com.stevesoft.pat.UnicodeUpper ()); -com.stevesoft.pat.Regex.defineV ("lc", "(?>1)", new com.stevesoft.pat.UnicodeLower ()); -}Clazz.defineStatics (c$, -"defaultMFlag", false, -"dotDoesntMatchCR", true, -"lasts", null, -"lastbs", null, -"back_slash", '\\'); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.RegRes", "$.UniValidator", "jalview.jsdev.api.RegExpInterface", "com.stevesoft.pat.NoPattern", "$.Pthings", "$.patInt", "java.util.Hashtable"], ["com.stevesoft.pat.UnicodeW", "$.UnicodeCurrency", "$.UnicodeAlpha", "$.UnicodeUpper", "$.NUnicodeCurrency", "$.NUnicodeW", "$.NUnicodeAlpha", "$.UnicodeMath", "$.UnicodeWhite", "$.UnicodeDigit", "$.NUnicodeMath", "$.Regex", "$.NUnicodeDigit", "$.NUnicodeWhite", "$.NUnicodePunct", "$.UnicodePunct", "$.UnicodeLower"], ["com.stevesoft.pat.Any", "$.BackG", "$.BackMatch", "$.Backup", "$.Boundary", "$.Bracket", "$.CaseMgr", "$.Ctrl", "$.Custom", "$.CustomEndpoint", "$.DotMulti", "$.End", "$.FastMulti", "$.Group", "$.MessageManager", "$.Multi", "$.NullPattern", "$.Or", "$.OrMark", "$.Prop", "$.Range", "$.RegOpt", "$.RegSyntax", "$.RegSyntaxError", "$.ReplaceRule", "$.Replacer", "$.Rthings", "$.Skip", "$.Skipped", "$.Start", "$.StrPos", "$.lookAhead", "$.oneChar", "$.parsePerl", "$.patInf", "com.stevesoft.pat.wrap.StringWrap", "java.lang.NullPointerException", "$.StringBuffer", "java.util.BitSet"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodePunct", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && com.stevesoft.pat.Prop.isPunct (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeWhite", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && com.stevesoft.pat.Prop.isWhite (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodePunct", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && !com.stevesoft.pat.Prop.isPunct (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeWhite", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && !com.stevesoft.pat.Prop.isWhite (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeW", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +if (from >= s.length ()) { +return -1; +}var c = s.charAt (from); +return (com.stevesoft.pat.Prop.isAlphabetic (c) || com.stevesoft.pat.Prop.isDecimalDigit (c) || c == '_') ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeW", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +if (from >= s.length ()) { +return -1; +}var c = s.charAt (from); +return !(com.stevesoft.pat.Prop.isAlphabetic (c) || com.stevesoft.pat.Prop.isDecimalDigit (c) || c == '_') ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeDigit", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && com.stevesoft.pat.Prop.isDecimalDigit (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeDigit", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && !com.stevesoft.pat.Prop.isDecimalDigit (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeMath", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && com.stevesoft.pat.Prop.isMath (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeMath", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && !com.stevesoft.pat.Prop.isMath (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeCurrency", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && com.stevesoft.pat.Prop.isCurrency (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeCurrency", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && !com.stevesoft.pat.Prop.isCurrency (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeAlpha", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && com.stevesoft.pat.Prop.isAlphabetic (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "NUnicodeAlpha", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && !com.stevesoft.pat.Prop.isAlphabetic (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeUpper", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && this.isUpper (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "isUpper", +function (c) { +return c == com.stevesoft.pat.CaseMgr.toUpperCaseC (c) && c != com.stevesoft.pat.CaseMgr.toLowerCaseC (c); +}, "~S"); +c$ = Clazz.declareType (com.stevesoft.pat, "UnicodeLower", com.stevesoft.pat.UniValidator); +Clazz.overrideMethod (c$, "validate", +function (s, from, to) { +return from < s.length () && this.isLower (s.charAt (from)) ? to : -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "isLower", +function (c) { +return c != com.stevesoft.pat.CaseMgr.toUpperCaseC (c) && c == com.stevesoft.pat.CaseMgr.toLowerCaseC (c); +}, "~S"); +c$ = Clazz.decorateAsClass (function () { +this.thePattern = null; +this.minMatch = null; +this.rep = null; +this.dontMatchInQuotes = false; +this.ignoreCase = false; +this.repr = null; +this.esc = '\\'; +this.pt = null; +this.gFlags = null; +this.gFlagto = 0; +this.gFlag = false; +this.sFlag = false; +this.mFlag = false; +this.p = null; +this.or = null; +this.skipper = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Regex", com.stevesoft.pat.RegRes, [jalview.jsdev.api.RegExpInterface, Cloneable]); +Clazz.prepareFields (c$, function () { +this.thePattern = com.stevesoft.pat.Regex.none; +this.minMatch = new com.stevesoft.pat.patInt (0); +this.pt = new com.stevesoft.pat.Pthings (); +}); +Clazz.makeConstructor (c$, +function (s, strRp) { +Clazz.superConstructor (this, com.stevesoft.pat.Regex, []); +try { +if (s != null) this.compile (s); +if (strRp.length > 0) this.rep = com.stevesoft.pat.ReplaceRule.perlCode (strRp); +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +} else { +throw rs; +} +} +}, "~S,~S"); +Clazz.overrideMethod (c$, "clone", +function () { +return new com.stevesoft.pat.Regex (null, "").cloneFrom (this); +}); +Clazz.defineMethod (c$, "cloneFrom", +function (r) { +this.copyOutOf (r); +this.dontMatchInQuotes = r.dontMatchInQuotes; +this.esc = r.esc; +this.ignoreCase = r.ignoreCase; +this.gFlag = r.gFlag; +if (r.rep == null) { +this.rep = null; +} else { +this.rep = r.rep.clone (); +}this.thePattern = r.thePattern.clone ( new java.util.Hashtable ()); +this.minMatch = r.minMatch; +this.skipper = r.skipper; +return this; +}, "com.stevesoft.pat.Regex"); +Clazz.defineMethod (c$, "setDontMatchInQuotes", +function (b) { +this.dontMatchInQuotes = b; +}, "~B"); +Clazz.defineMethod (c$, "getDontMatchInQuotes", +function () { +return this.dontMatchInQuotes; +}); +Clazz.overrideMethod (c$, "setIgnoreCase", +function (b) { +this.ignoreCase = b; +}, "~B"); +Clazz.defineMethod (c$, "getIgnoreCase", +function () { +return this.ignoreCase; +}); +c$.setDefaultMFlag = Clazz.defineMethod (c$, "setDefaultMFlag", +function (mFlag) { +com.stevesoft.pat.Regex.defaultMFlag = mFlag; +}, "~B"); +c$.getDefaultMFlag = Clazz.defineMethod (c$, "getDefaultMFlag", +function () { +return com.stevesoft.pat.Regex.defaultMFlag; +}); +Clazz.defineMethod (c$, "setReplaceRuleStr", +function (rp) { +this.rep = com.stevesoft.pat.ReplaceRule.perlCode (rp); +this.repr = null; +}, "~S"); +Clazz.defineMethod (c$, "setReplaceRule", +function (rp) { +this.rep = rp; +}, "com.stevesoft.pat.ReplaceRule"); +c$.isDefined = Clazz.defineMethod (c$, "isDefined", +function (nm) { +return com.stevesoft.pat.Regex.validators.get (nm) != null; +}, "~S"); +c$.undefine = Clazz.defineMethod (c$, "undefine", +function (nm) { +com.stevesoft.pat.Regex.validators.remove (nm); +}, "~S"); +c$.defineV = Clazz.defineMethod (c$, "defineV", +function (nm, pat, v) { +v.pattern = pat; +com.stevesoft.pat.Regex.validators.put (nm, v); +}, "~S,~S,com.stevesoft.pat.Validator"); +c$.define = Clazz.defineMethod (c$, "define", +function (nm, pat) { +com.stevesoft.pat.Regex.validators.put (nm, pat); +}, "~S,~S"); +Clazz.defineMethod (c$, "getReplaceRule", +function () { +return this.rep; +}); +Clazz.defineMethod (c$, "_getReplacer", +function () { +return this.repr == null ? this.repr = new com.stevesoft.pat.Replacer () : this.repr; +}); +Clazz.defineMethod (c$, "getReplacer", +function () { +if (this.repr == null) { +this.repr = new com.stevesoft.pat.Replacer (); +}this.repr.rh.me = this; +this.repr.rh.prev = null; +return this.repr; +}); +Clazz.defineMethod (c$, "replaceFirst", +function (s) { +return this._getReplacer ().replaceFirstRegion (s, this, 0, s.length).toString (); +}, "~S"); +Clazz.defineMethod (c$, "replaceFirstFrom", +function (s, pos) { +return this._getReplacer ().replaceFirstRegion (s, this, pos, s.length).toString (); +}, "~S,~N"); +Clazz.defineMethod (c$, "replaceFirstRegion", +function (s, start, end) { +return this._getReplacer ().replaceFirstRegion (s, this, start, end).toString (); +}, "~S,~N,~N"); +Clazz.overrideMethod (c$, "replaceAll", +function (s) { +return this._getReplacer ().replaceAllRegion (s, this, 0, s.length).toString (); +}, "~S"); +Clazz.defineMethod (c$, "replaceAllLike", +function (s) { +return this._getReplacer ().replaceAllRegion (s, this, 0, s.length ()); +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "replaceAllFrom", +function (s, pos) { +return this._getReplacer ().replaceAllRegion (s, this, pos, s.length).toString (); +}, "~S,~N"); +Clazz.defineMethod (c$, "replaceAllRegion", +function (s, start, end) { +return this._getReplacer ().replaceAllRegion (s, this, start, end).toString (); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "compile", +function (prepat) { +var postpat = com.stevesoft.pat.parsePerl.codify (prepat, true); +var pat = postpat == null ? prepat : postpat; +this.minMatch = null; +this.ignoreCase = false; +this.dontMatchInQuotes = false; +var mk = new com.stevesoft.pat.Rthings (this); +var offset = mk.val; +var newpat = pat; +this.thePattern = com.stevesoft.pat.Regex.none; +this.p = null; +this.or = null; +this.minMatch = new com.stevesoft.pat.patInt (0); +var sp = new com.stevesoft.pat.StrPos (pat, 0); +if (sp.incMatch ("(?e=")) { +var newEsc = sp.c; +sp.inc (); +if (sp.match (')')) { +newpat = com.stevesoft.pat.Regex.reEscape (pat.substring (6), newEsc, '\\'); +}} else if (this.esc != '\\') { +newpat = com.stevesoft.pat.Regex.reEscape (pat, this.esc, '\\'); +}this.thePattern = this._compile (newpat, mk); +this.numSubs_ = mk.val - offset; +mk.set (this); +}, "~S"); +Clazz.defineMethod (c$, "equals", +function (o) { +if (Clazz.instanceOf (o, com.stevesoft.pat.Regex)) { +if (this.toString ().equals (o.toString ())) { +return Clazz.superCall (this, com.stevesoft.pat.Regex, "equals", [o]); +} else { +return false; +}} else { +return Clazz.superCall (this, com.stevesoft.pat.Regex, "equals", [o]); +}}, "~O"); +Clazz.defineMethod (c$, "prep", +function (s) { +this.pt.lastPos = this.matchedTo (); +if (this.pt.lastPos < 0) { +this.pt.lastPos = 0; +}if ((s == null ? null : s.unwrap ()) !== (this.src == null ? null : s.unwrap ())) { +this.pt.lastPos = 0; +}this.src = s; +this.pt.dotDoesntMatchCR = com.stevesoft.pat.Regex.dotDoesntMatchCR && (!this.sFlag); +this.pt.mFlag = ( new Boolean (this.mFlag | com.stevesoft.pat.Regex.defaultMFlag).valueOf ()); +this.pt.ignoreCase = this.ignoreCase; +this.pt.no_check = false; +if (this.pt.marks != null) { +for (var i = 0; i < this.pt.marks.length; i++) { +this.pt.marks[i] = -1; +} +}this.pt.marks = null; +this.pt.nMarks = this.numSubs_; +this.pt.src = s; +if (this.dontMatchInQuotes) { +com.stevesoft.pat.Regex.setCbits (s, this.pt); +} else { +this.pt.cbits = null; +}return this.pt; +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "matchAt", +function (s, start_pos) { +return this._search (s, start_pos, start_pos); +}, "~S,~N"); +Clazz.defineMethod (c$, "matchAtLike", +function (s, start_pos) { +return this._searchLike (s, start_pos, start_pos); +}, "com.stevesoft.pat.StringLike,~N"); +Clazz.overrideMethod (c$, "search", +function (s) { +if (s == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_given_to_regex_search")); +}return this._search (s, 0, s.length); +}, "~S"); +Clazz.defineMethod (c$, "searchLike", +function (sl) { +if (sl == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search")); +}return this._searchLike (sl, 0, sl.length ()); +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "reverseSearch", +function (s) { +if (s == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_given_to_regex_reverse_search")); +}return this._reverseSearch (s, 0, s.length); +}, "~S"); +Clazz.defineMethod (c$, "reverseSearchLike", +function (sl) { +if (sl == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_reverse_search")); +}return this._reverseSearchLike (sl, 0, sl.length ()); +}, "com.stevesoft.pat.StringLike"); +Clazz.overrideMethod (c$, "searchFrom", +function (s, start) { +if (s == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search_from")); +}return this._search (s, start, s.length); +}, "~S,~N"); +Clazz.defineMethod (c$, "searchFromLike", +function (s, start) { +if (s == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search_from")); +}return this._searchLike (s, start, s.length ()); +}, "com.stevesoft.pat.StringLike,~N"); +Clazz.defineMethod (c$, "searchRegion", +function (s, start, end) { +if (s == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.null_string_like_given_to_regex_search_region")); +}return this._search (s, start, end); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "setGFlag", +function (b) { +this.gFlag = b; +}, "~B"); +Clazz.defineMethod (c$, "getGFlag", +function () { +return this.gFlag; +}); +Clazz.defineMethod (c$, "getSFlag", +function () { +return this.sFlag; +}); +Clazz.defineMethod (c$, "getMFlag", +function () { +return this.mFlag; +}); +Clazz.defineMethod (c$, "_search", +function (s, start, end) { +return this._searchLike ( new com.stevesoft.pat.wrap.StringWrap (s), start, end); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "_searchLike", +function (s, start, end) { +if (this.gFlag && this.gFlagto > 0 && this.gFlags != null && s.unwrap () === this.gFlags.unwrap ()) { +start = this.gFlagto; +}this.gFlags = null; +var pt = this.prep (s); +var up = (this.minMatch == null ? end : end - this.minMatch.i); +if (up < start && end >= start) { +up = start; +}if (this.skipper == null) { +for (var i = start; i <= up; i++) { +this.charsMatched_ = this.thePattern.matchAt (s, i, pt); +if (this.charsMatched_ >= 0) { +this.matchFrom_ = this.thePattern.mfrom; +this.marks = pt.marks; +this.gFlagto = this.matchFrom_ + this.charsMatched_; +this.gFlags = s; +return this.didMatch_ = true; +}} +} else { +pt.no_check = true; +for (var i = start; i <= up; i++) { +i = this.skipper.find (this.src, i, up); +if (i < 0) { +this.charsMatched_ = this.matchFrom_ = -1; +return this.didMatch_ = false; +}this.charsMatched_ = this.thePattern.matchAt (s, i, pt); +if (this.charsMatched_ >= 0) { +this.matchFrom_ = this.thePattern.mfrom; +this.marks = pt.marks; +this.gFlagto = this.matchFrom_ + this.charsMatched_; +this.gFlags = s; +return this.didMatch_ = true; +}} +}return this.didMatch_ = false; +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "_reverseSearch", +function (s, start, end) { +return this._reverseSearchLike ( new com.stevesoft.pat.wrap.StringWrap (s), start, end); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "_reverseSearchLike", +function (s, start, end) { +if (this.gFlag && this.gFlagto > 0 && s.unwrap () === this.gFlags.unwrap ()) { +end = this.gFlagto; +}this.gFlags = null; +var pt = this.prep (s); +for (var i = end; i >= start; i--) { +this.charsMatched_ = this.thePattern.matchAt (s, i, pt); +if (this.charsMatched_ >= 0) { +this.matchFrom_ = this.thePattern.mfrom; +this.marks = pt.marks; +this.gFlagto = this.matchFrom_ - 1; +this.gFlags = s; +return this.didMatch_ = true; +}} +return this.didMatch_ = false; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$.setCbits = Clazz.defineMethod (c$, "setCbits", +function (s, pt) { +if (s === com.stevesoft.pat.Regex.lasts) { +pt.cbits = com.stevesoft.pat.Regex.lastbs; +return; +}var bs = new java.util.BitSet (s.length ()); +var qc = ' '; +var setBit = false; +for (var i = 0; i < s.length (); i++) { +if (setBit) { +bs.set (i); +}var c = s.charAt (i); +if (!setBit && c == '"') { +qc = c; +setBit = true; +bs.set (i); +} else if (!setBit && c == '\'') { +qc = c; +setBit = true; +bs.set (i); +} else if (setBit && c == qc) { +setBit = false; +} else if (setBit && c == '\\' && i + 1 < s.length ()) { +i++; +if (setBit) { +bs.set (i); +}}} +pt.cbits = com.stevesoft.pat.Regex.lastbs = bs; +com.stevesoft.pat.Regex.lasts = s; +}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "add", +function (p2) { +if (this.p == null) { +this.p = p2; +} else { +this.p.add (p2); +p2 = this.p; +}}, "com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "compileSP", +function (sp, mk) { +if (sp.match ('[')) { +sp.inc (); +this.add (this.matchBracket (sp)); +} else if (sp.match ('|')) { +if (this.or == null) { +this.or = new com.stevesoft.pat.Or (); +}if (this.p == null) { +this.p = new com.stevesoft.pat.NullPattern (); +}this.or.addOr (this.p); +this.p = null; +} else if (sp.incMatch ("(?<")) { +var i = sp.getPatInt (); +if (i == null) { +com.stevesoft.pat.RegSyntaxError.endItAll ("No int after (?<"); +}this.add ( new com.stevesoft.pat.Backup (i.intValue ())); +if (!sp.match (')')) { +com.stevesoft.pat.RegSyntaxError.endItAll ("No ) after (?<"); +}} else if (sp.incMatch ("(?>")) { +var i = sp.getPatInt (); +if (i == null) { +com.stevesoft.pat.RegSyntaxError.endItAll ("No int after (?>"); +}this.add ( new com.stevesoft.pat.Backup (-i.intValue ())); +if (!sp.match (')')) { +com.stevesoft.pat.RegSyntaxError.endItAll ("No ) after (?<"); +}} else if (sp.incMatch ("(?@")) { +var op = sp.c; +sp.inc (); +var cl = sp.c; +sp.inc (); +if (!sp.match (')')) { +com.stevesoft.pat.RegSyntaxError.endItAll ("(?@ does not have closing paren"); +}this.add ( new com.stevesoft.pat.Group (op, cl)); +} else if (sp.incMatch ("(?#")) { +while (!sp.match (')')) { +sp.inc (); +} +} else if (sp.dontMatch && sp.c == 'w') { +var b = new com.stevesoft.pat.Bracket (false); +b.addOr ( new com.stevesoft.pat.Range ('a', 'z')); +b.addOr ( new com.stevesoft.pat.Range ('A', 'Z')); +b.addOr ( new com.stevesoft.pat.Range ('0', '9')); +b.addOr ( new com.stevesoft.pat.oneChar ('_')); +this.add (b); +} else if (sp.dontMatch && sp.c == 'G') { +this.add ( new com.stevesoft.pat.BackG ()); +} else if (sp.dontMatch && sp.c == 's') { +var b = new com.stevesoft.pat.Bracket (false); +b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (32))); +b.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (8), String.fromCharCode (10))); +b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (13))); +this.add (b); +} else if (sp.dontMatch && sp.c == 'd') { +var digit = new com.stevesoft.pat.Range ('0', '9'); +digit.printBrackets = true; +this.add (digit); +} else if (sp.dontMatch && sp.c == 'W') { +var b = new com.stevesoft.pat.Bracket (true); +b.addOr ( new com.stevesoft.pat.Range ('a', 'z')); +b.addOr ( new com.stevesoft.pat.Range ('A', 'Z')); +b.addOr ( new com.stevesoft.pat.Range ('0', '9')); +b.addOr ( new com.stevesoft.pat.oneChar ('_')); +this.add (b); +} else if (sp.dontMatch && sp.c == 'S') { +var b = new com.stevesoft.pat.Bracket (true); +b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (32))); +b.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (8), String.fromCharCode (10))); +b.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (13))); +this.add (b); +} else if (sp.dontMatch && sp.c == 'D') { +var b = new com.stevesoft.pat.Bracket (true); +b.addOr ( new com.stevesoft.pat.Range ('0', '9')); +this.add (b); +} else if (sp.dontMatch && sp.c == 'B') { +var r = new com.stevesoft.pat.Regex (null, ""); +r._compile ("(?!\\b)", mk); +this.add (r.thePattern); +} else if (this.isOctalString (sp)) { +var d = sp.c.charCodeAt (0) - 48; +sp.inc (); +d = 8 * d + sp.c.charCodeAt (0) - 48; +var sp2 = new com.stevesoft.pat.StrPos (sp); +sp2.inc (); +if (this.isOctalDigit (sp2, false)) { +sp.inc (); +d = 8 * d + sp.c.charCodeAt (0) - 48; +}this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); +} else if (sp.dontMatch && sp.c >= '1' && sp.c <= '9') { +var iv = sp.c.charCodeAt (0) - 48; +var s2 = new com.stevesoft.pat.StrPos (sp); +s2.inc (); +if (!s2.dontMatch && s2.c >= '0' && s2.c <= '9') { +iv = 10 * iv + (s2.c.charCodeAt (0) - 48); +sp.inc (); +}this.add ( new com.stevesoft.pat.BackMatch (iv)); +} else if (sp.dontMatch && sp.c == 'b') { +this.add ( new com.stevesoft.pat.Boundary ()); +} else if (sp.match ('\b')) { +this.add ( new com.stevesoft.pat.Boundary ()); +} else if (sp.match ('$')) { +this.add ( new com.stevesoft.pat.End (true)); +} else if (sp.dontMatch && sp.c == 'Z') { +this.add ( new com.stevesoft.pat.End (false)); +} else if (sp.match ('.')) { +this.add ( new com.stevesoft.pat.Any ()); +} else if (sp.incMatch ("(??")) { +var sb = new StringBuffer (); +var sb2 = new StringBuffer (); +while (!sp.match (')') && !sp.match (':')) { +sb.append (sp.c); +sp.inc (); +} +if (sp.incMatch (":")) { +while (!sp.match (')')) { +sb2.append (sp.c); +sp.inc (); +} +}var sbs = sb.toString (); +if (Clazz.instanceOf (com.stevesoft.pat.Regex.validators.get (sbs), String)) { +var pat = com.stevesoft.pat.Regex.validators.get (sbs); +var r = new com.stevesoft.pat.Regex (null, ""); +var rth = new com.stevesoft.pat.Rthings (this); +rth.noBackRefs = true; +r._compile (pat, rth); +this.add (r.thePattern); +} else { +var cm = new com.stevesoft.pat.Custom (sb.toString ()); +if (cm.v != null) { +var v2 = cm.v.arg (sb2.toString ()); +if (v2 != null) { +v2.argsave = sb2.toString (); +var p = cm.v.pattern; +cm.v = v2; +v2.pattern = p; +}var r = new com.stevesoft.pat.Regex (null, ""); +var rth = new com.stevesoft.pat.Rthings (this); +rth.noBackRefs = true; +r._compile (cm.v.pattern, rth); +cm.sub = r.thePattern; +cm.sub.add ( new com.stevesoft.pat.CustomEndpoint (cm)); +cm.sub.setParent (cm); +this.add (cm); +}}} else if (sp.match ('(')) { +mk.parenLevel++; +var r = new com.stevesoft.pat.Regex (null, ""); +sp.inc (); +if (sp.incMatch ("?:")) { +r.or = new com.stevesoft.pat.Or (); +} else if (sp.incMatch ("?=")) { +r.or = new com.stevesoft.pat.lookAhead (false); +} else if (sp.incMatch ("?!")) { +r.or = new com.stevesoft.pat.lookAhead (true); +} else if (sp.match ('?')) { +sp.inc (); +do { +if (sp.c == 'i') { +mk.ignoreCase = true; +}if (sp.c == 'Q') { +mk.dontMatchInQuotes = true; +}if (sp.c == 'o') { +mk.optimizeMe = true; +}if (sp.c == 'g') { +mk.gFlag = true; +}if (sp.c == 's') { +mk.sFlag = true; +}if (sp.c == 'm') { +mk.mFlag = true; +}sp.inc (); +} while (!sp.match (')') && !sp.$eos); +r = null; +mk.parenLevel--; +if (sp.$eos) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Unclosed ()"); +}} else { +r.or = mk.noBackRefs ? new com.stevesoft.pat.Or () : new com.stevesoft.pat.OrMark (mk.val++); +}if (r != null) { +this.add (r._compileSP (sp, mk)); +}} else if (sp.match ('^')) { +this.add ( new com.stevesoft.pat.Start (true)); +} else if (sp.dontMatch && sp.c == 'A') { +this.add ( new com.stevesoft.pat.Start (false)); +} else if (sp.match ('*')) { +this.addMulti ( new com.stevesoft.pat.patInt (0), new com.stevesoft.pat.patInf ()); +} else if (sp.match ('+')) { +this.addMulti ( new com.stevesoft.pat.patInt (1), new com.stevesoft.pat.patInf ()); +} else if (sp.match ('?')) { +this.addMulti ( new com.stevesoft.pat.patInt (0), new com.stevesoft.pat.patInt (1)); +} else if (sp.match ('{')) { +var bad = false; +var sp2 = new com.stevesoft.pat.StrPos (sp); +sp.inc (); +var i1 = sp.getPatInt (); +var i2 = null; +if (sp.match ('}')) { +i2 = i1; +} else { +if (!sp.match (',')) { +bad = true; +}sp.inc (); +if (sp.match ('}')) { +i2 = new com.stevesoft.pat.patInf (); +} else { +i2 = sp.getPatInt (); +}}if (i1 == null || i2 == null) { +bad = true; +}if (bad) { +sp.dup (sp2); +this.add ( new com.stevesoft.pat.oneChar (sp.c)); +} else { +this.addMulti (i1, i2); +}} else if (sp.escMatch ('x') && this.next2Hex (sp)) { +sp.inc (); +var d = this.getHexDigit (sp); +sp.inc (); +d = 16 * d + this.getHexDigit (sp); +this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); +} else if (sp.escMatch ('c')) { +sp.inc (); +if (sp.c.charCodeAt (0) < com.stevesoft.pat.Ctrl.cmap.length) { +this.add ( new com.stevesoft.pat.oneChar (com.stevesoft.pat.Ctrl.cmap[sp.c.charCodeAt (0)])); +} else { +this.add ( new com.stevesoft.pat.oneChar (sp.c)); +}} else if (sp.escMatch ('f')) { +this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (12))); +} else if (sp.escMatch ('a')) { +this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (7))); +} else if (sp.escMatch ('t')) { +this.add ( new com.stevesoft.pat.oneChar ('\t')); +} else if (sp.escMatch ('n')) { +this.add ( new com.stevesoft.pat.oneChar ('\n')); +} else if (sp.escMatch ('r')) { +this.add ( new com.stevesoft.pat.oneChar ('\r')); +} else if (sp.escMatch ('b')) { +this.add ( new com.stevesoft.pat.oneChar ('\b')); +} else if (sp.escMatch ('e')) { +this.add ( new com.stevesoft.pat.oneChar (String.fromCharCode (27))); +} else { +this.add ( new com.stevesoft.pat.oneChar (sp.c)); +if (sp.match (')')) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Unmatched right paren in pattern"); +}}}, "com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings"); +Clazz.defineMethod (c$, "_compile", +($fz = function (pat, mk) { +this.minMatch = null; +this.sFlag = this.mFlag = this.ignoreCase = this.gFlag = false; +var sp = new com.stevesoft.pat.StrPos (pat, 0); +this.thePattern = this._compileSP (sp, mk); +this.pt.marks = null; +return this.thePattern; +}, $fz.isPrivate = true, $fz), "~S,com.stevesoft.pat.Rthings"); +Clazz.defineMethod (c$, "_compileSP", +function (sp, mk) { +while (!(sp.$eos || (this.or != null && sp.match (')')))) { +this.compileSP (sp, mk); +sp.inc (); +} +if (sp.match (')')) { +mk.parenLevel--; +} else if (sp.$eos && mk.parenLevel != 0) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Unclosed Parenthesis! lvl=" + mk.parenLevel); +}if (this.or != null) { +if (this.p == null) { +this.p = new com.stevesoft.pat.NullPattern (); +}this.or.addOr (this.p); +return this.or; +}return this.p == null ? new com.stevesoft.pat.NullPattern () : this.p; +}, "com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings"); +Clazz.defineMethod (c$, "addMulti", +function (i1, i2) { +var last; +var last2; +for (last = this.p; last != null && last.next != null; last = last.next) { +;} +if (last == null || last === this.p) { +last2 = null; +} else { +for (last2 = this.p; last2.next !== last; last2 = last2.next) { +;} +}if (Clazz.instanceOf (last, com.stevesoft.pat.Multi) && i1.intValue () == 0 && i2.intValue () == 1) { +(last).matchFewest = true; +} else if (Clazz.instanceOf (last, com.stevesoft.pat.FastMulti) && i1.intValue () == 0 && i2.intValue () == 1) { +(last).matchFewest = true; +} else if (Clazz.instanceOf (last, com.stevesoft.pat.DotMulti) && i1.intValue () == 0 && i2.intValue () == 1) { +(last).matchFewest = true; +} else if (Clazz.instanceOf (last, com.stevesoft.pat.Multi) || Clazz.instanceOf (last, com.stevesoft.pat.DotMulti) || Clazz.instanceOf (last, com.stevesoft.pat.FastMulti)) { +throw new com.stevesoft.pat.RegSyntax ("Syntax error."); +} else if (last2 == null) { +this.p = com.stevesoft.pat.Regex.mkMulti (i1, i2, this.p); +} else { +last2.next = com.stevesoft.pat.Regex.mkMulti (i1, i2, last); +}}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt"); +c$.mkMulti = Clazz.defineMethod (c$, "mkMulti", +function (lo, hi, p) { +if (Clazz.instanceOf (p, com.stevesoft.pat.Any) && p.next == null) { +return new com.stevesoft.pat.DotMulti (lo, hi); +}return com.stevesoft.pat.RegOpt.safe4fm (p) ? new com.stevesoft.pat.FastMulti (lo, hi, p) : new com.stevesoft.pat.Multi (lo, hi, p); +}, "com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern"); +Clazz.defineMethod (c$, "matchBracket", +function (sp) { +var ret; +if (sp.match ('^')) { +ret = new com.stevesoft.pat.Bracket (true); +sp.inc (); +} else { +ret = new com.stevesoft.pat.Bracket (false); +}if (sp.match (']')) { +com.stevesoft.pat.RegSyntaxError.endItAll ("Unmatched []"); +}while (!sp.$eos && !sp.match (']')) { +var s1 = new com.stevesoft.pat.StrPos (sp); +s1.inc (); +var s1_ = new com.stevesoft.pat.StrPos (s1); +s1_.inc (); +if (s1.match ('-') && !s1_.match (']')) { +var s2 = new com.stevesoft.pat.StrPos (s1); +s2.inc (); +if (!s2.$eos) { +ret.addOr ( new com.stevesoft.pat.Range (sp.c, s2.c)); +}sp.inc (); +sp.inc (); +} else if (sp.escMatch ('Q')) { +sp.inc (); +while (!sp.escMatch ('E')) { +ret.addOr ( new com.stevesoft.pat.oneChar (sp.c)); +sp.inc (); +} +} else if (sp.escMatch ('d')) { +ret.addOr ( new com.stevesoft.pat.Range ('0', '9')); +} else if (sp.escMatch ('s')) { +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (32))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (8), String.fromCharCode (10))); +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (13))); +} else if (sp.escMatch ('w')) { +ret.addOr ( new com.stevesoft.pat.Range ('a', 'z')); +ret.addOr ( new com.stevesoft.pat.Range ('A', 'Z')); +ret.addOr ( new com.stevesoft.pat.Range ('0', '9')); +ret.addOr ( new com.stevesoft.pat.oneChar ('_')); +} else if (sp.escMatch ('D')) { +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (47))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (58), String.fromCharCode (65535))); +} else if (sp.escMatch ('S')) { +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (7))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (11), String.fromCharCode (12))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (14), String.fromCharCode (31))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (33), String.fromCharCode (65535))); +} else if (sp.escMatch ('W')) { +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (0), String.fromCharCode (64))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (91), String.fromCharCode (94))); +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (96))); +ret.addOr ( new com.stevesoft.pat.Range (String.fromCharCode (123), String.fromCharCode (65535))); +} else if (sp.escMatch ('x') && this.next2Hex (sp)) { +sp.inc (); +var d = this.getHexDigit (sp); +sp.inc (); +d = 16 * d + this.getHexDigit (sp); +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); +} else if (sp.escMatch ('a')) { +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (7))); +} else if (sp.escMatch ('f')) { +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (12))); +} else if (sp.escMatch ('e')) { +ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (27))); +} else if (sp.escMatch ('n')) { +ret.addOr ( new com.stevesoft.pat.oneChar ('\n')); +} else if (sp.escMatch ('t')) { +ret.addOr ( new com.stevesoft.pat.oneChar ('\t')); +} else if (sp.escMatch ('r')) { +ret.addOr ( new com.stevesoft.pat.oneChar ('\r')); +} else if (sp.escMatch ('c')) { +sp.inc (); +if (sp.c.charCodeAt (0) < com.stevesoft.pat.Ctrl.cmap.length) { +ret.addOr ( new com.stevesoft.pat.oneChar (com.stevesoft.pat.Ctrl.cmap[sp.c.charCodeAt (0)])); +} else { +ret.addOr ( new com.stevesoft.pat.oneChar (sp.c)); +}} else if (this.isOctalString (sp)) { +var d = sp.c.charCodeAt (0) - 48; +sp.inc (); +d = 8 * d + sp.c.charCodeAt (0) - 48; +var sp2 = new com.stevesoft.pat.StrPos (sp); +sp2.inc (); +if (this.isOctalDigit (sp2, false)) { +sp.inc (); +d = 8 * d + sp.c.charCodeAt (0) - 48; +}ret.addOr ( new com.stevesoft.pat.oneChar (String.fromCharCode (d))); +} else { +ret.addOr ( new com.stevesoft.pat.oneChar (sp.c)); +}sp.inc (); +} +return ret; +}, "com.stevesoft.pat.StrPos"); +Clazz.overrideMethod (c$, "toString", +function () { +{ +var sb = new StringBuffer (); +if (this.esc != '\\') { +sb.append ("(?e="); +sb.append (this.esc); +sb.append (")"); +}if (this.gFlag || this.mFlag || !com.stevesoft.pat.Regex.dotDoesntMatchCR || this.sFlag || this.ignoreCase || this.dontMatchInQuotes || this.optimized ()) { +sb.append ("(?"); +if (this.ignoreCase) { +sb.append ("i"); +}if (this.mFlag) { +sb.append ("m"); +}if (this.sFlag || !com.stevesoft.pat.Regex.dotDoesntMatchCR) { +sb.append ("s"); +}if (this.dontMatchInQuotes) { +sb.append ("Q"); +}if (this.optimized ()) { +sb.append ("o"); +}if (this.gFlag) { +sb.append ("g"); +}sb.append (")"); +}var patstr = this.thePattern.toString (); +if (this.esc != '\\') { +patstr = com.stevesoft.pat.Regex.reEscape (patstr, '\\', this.esc); +}sb.append (patstr); +return sb.toString (); +}}); +c$.reEscape = Clazz.defineMethod (c$, "reEscape", +function (s, oldEsc, newEsc) { +if (oldEsc == newEsc) { +return s; +}var i; +var sb = new StringBuffer (); +for (i = 0; i < s.length; i++) { +if (s.charAt (i) == oldEsc && i + 1 < s.length) { +if (s.charAt (i + 1) == oldEsc) { +sb.append (oldEsc); +} else { +sb.append (newEsc); +sb.append (s.charAt (i + 1)); +}i++; +} else if (s.charAt (i) == newEsc) { +sb.append (newEsc); +sb.append (newEsc); +} else { +sb.append (s.charAt (i)); +}} +return sb.toString (); +}, "~S,~S,~S"); +Clazz.defineMethod (c$, "accept", +function (dir, s) { +return this.search (s); +}, "java.io.File,~S"); +c$.version = Clazz.defineMethod (c$, "version", +function () { +return "lgpl release 1.5.3"; +}); +Clazz.defineMethod (c$, "optimize", +function () { +if (this.optimized () || this.thePattern == null) { +return; +}this.minMatch = new com.stevesoft.pat.patInt (0); +this.thePattern = com.stevesoft.pat.RegOpt.opt (this.thePattern, this.ignoreCase, this.dontMatchInQuotes); +this.skipper = com.stevesoft.pat.Skip.findSkipRegex (this); +return; +}); +Clazz.defineMethod (c$, "optimized", +function () { +return this.minMatch != null; +}); +c$.perlCode = Clazz.defineMethod (c$, "perlCode", +function (s) { +return com.stevesoft.pat.parsePerl.parse (s); +}, "~S"); +Clazz.defineMethod (c$, "isLiteral", +function () { +var x = this.thePattern; +while (x != null) { +if (Clazz.instanceOf (x, com.stevesoft.pat.oneChar)) { +;} else if (Clazz.instanceOf (x, com.stevesoft.pat.Skipped)) { +;} else { +return false; +}x = x.next; +} +return true; +}); +Clazz.defineMethod (c$, "countMinChars", +function () { +return this.thePattern.countMinChars (); +}); +Clazz.defineMethod (c$, "countMaxChars", +function () { +return this.thePattern.countMaxChars (); +}); +Clazz.defineMethod (c$, "isHexDigit", +function (sp) { +var r = !sp.$eos && !sp.dontMatch && ((sp.c >= '0' && sp.c <= '9') || (sp.c >= 'a' && sp.c <= 'f') || (sp.c >= 'A' && sp.c <= 'F')); +return r; +}, "com.stevesoft.pat.StrPos"); +Clazz.defineMethod (c$, "isOctalDigit", +function (sp, first) { +var r = !sp.$eos && !( new Boolean (first ^ sp.dontMatch).valueOf ()) && sp.c >= '0' && sp.c <= '7'; +return r; +}, "com.stevesoft.pat.StrPos,~B"); +Clazz.defineMethod (c$, "getHexDigit", +function (sp) { +if (sp.c >= '0' && sp.c <= '9') { +return sp.c.charCodeAt (0) - 48; +}if (sp.c >= 'a' && sp.c <= 'f') { +return sp.c.charCodeAt (0) - 97 + 10; +}return sp.c.charCodeAt (0) - 65 + 10; +}, "com.stevesoft.pat.StrPos"); +Clazz.defineMethod (c$, "next2Hex", +function (sp) { +var sp2 = new com.stevesoft.pat.StrPos (sp); +sp2.inc (); +if (!this.isHexDigit (sp2)) { +return false; +}sp2.inc (); +if (!this.isHexDigit (sp2)) { +return false; +}return true; +}, "com.stevesoft.pat.StrPos"); +Clazz.defineMethod (c$, "isOctalString", +function (sp) { +if (!this.isOctalDigit (sp, true)) { +return false; +}var sp2 = new com.stevesoft.pat.StrPos (sp); +sp2.inc (); +if (!this.isOctalDigit (sp2, false)) { +return false; +}return true; +}, "com.stevesoft.pat.StrPos"); +Clazz.defineStatics (c$, +"BackRefOffset", 1); +c$.none = c$.prototype.none = new com.stevesoft.pat.NoPattern (); +c$.validators = c$.prototype.validators = new java.util.Hashtable (); +{ +com.stevesoft.pat.Regex.defineV ("p", "(?>1)", new com.stevesoft.pat.UnicodePunct ()); +com.stevesoft.pat.Regex.defineV ("P", "(?>1)", new com.stevesoft.pat.NUnicodePunct ()); +com.stevesoft.pat.Regex.defineV ("s", "(?>1)", new com.stevesoft.pat.UnicodeWhite ()); +com.stevesoft.pat.Regex.defineV ("S", "(?>1)", new com.stevesoft.pat.NUnicodeWhite ()); +com.stevesoft.pat.Regex.defineV ("w", "(?>1)", new com.stevesoft.pat.UnicodeW ()); +com.stevesoft.pat.Regex.defineV ("W", "(?>1)", new com.stevesoft.pat.NUnicodeW ()); +com.stevesoft.pat.Regex.defineV ("d", "(?>1)", new com.stevesoft.pat.UnicodeDigit ()); +com.stevesoft.pat.Regex.defineV ("D", "(?>1)", new com.stevesoft.pat.NUnicodeDigit ()); +com.stevesoft.pat.Regex.defineV ("m", "(?>1)", new com.stevesoft.pat.UnicodeMath ()); +com.stevesoft.pat.Regex.defineV ("M", "(?>1)", new com.stevesoft.pat.NUnicodeMath ()); +com.stevesoft.pat.Regex.defineV ("c", "(?>1)", new com.stevesoft.pat.UnicodeCurrency ()); +com.stevesoft.pat.Regex.defineV ("C", "(?>1)", new com.stevesoft.pat.NUnicodeCurrency ()); +com.stevesoft.pat.Regex.defineV ("a", "(?>1)", new com.stevesoft.pat.UnicodeAlpha ()); +com.stevesoft.pat.Regex.defineV ("A", "(?>1)", new com.stevesoft.pat.NUnicodeAlpha ()); +com.stevesoft.pat.Regex.defineV ("uc", "(?>1)", new com.stevesoft.pat.UnicodeUpper ()); +com.stevesoft.pat.Regex.defineV ("lc", "(?>1)", new com.stevesoft.pat.UnicodeLower ()); +}Clazz.defineStatics (c$, +"defaultMFlag", false, +"dotDoesntMatchCR", true, +"lasts", null, +"lastbs", null, +"back_slash", '\\'); +}); diff --git a/bin/com/stevesoft/pat/RegexReader.class b/bin/com/stevesoft/pat/RegexReader.class index 2639d15..613abb5 100644 Binary files a/bin/com/stevesoft/pat/RegexReader.class and b/bin/com/stevesoft/pat/RegexReader.class differ diff --git a/bin/com/stevesoft/pat/RegexReader.js b/bin/com/stevesoft/pat/RegexReader.js index 301d8e7..d767d80 100644 --- a/bin/com/stevesoft/pat/RegexReader.js +++ b/bin/com/stevesoft/pat/RegexReader.js @@ -1,164 +1,164 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.io.Reader", "com.stevesoft.pat.PartialBuffer", "$.RBuffer", "java.lang.StringBuffer"], "com.stevesoft.pat.RegexReader", ["com.stevesoft.pat.StringBufferLike", "com.stevesoft.pat.wrap.StringBufferWrap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.rb = null; -this.wrap = null; -this.moreToRead = true; -this.r = null; -this.rp = null; -this.nmax = 2048; -this.max_lines = 2; -this.EOLchar = '\n'; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RegexReader", java.io.Reader); -Clazz.prepareFields (c$, function () { -this.rb = new com.stevesoft.pat.RBuffer ( new StringBuffer ()); -this.wrap = new com.stevesoft.pat.PartialBuffer (this.rb.sb); -}); -Clazz.makeConstructor (c$, -function (rex, r) { -Clazz.superConstructor (this, com.stevesoft.pat.RegexReader, []); -this.r = r; -this.rp = rex.getReplacer (); -}, "com.stevesoft.pat.Regex,java.io.Reader"); -Clazz.makeConstructor (c$, -function (tex, r) { -Clazz.superConstructor (this, com.stevesoft.pat.RegexReader, []); -this.r = r; -this.rp = tex.getReplacer (); -}, "com.stevesoft.pat.Transformer,java.io.Reader"); -Clazz.defineMethod (c$, "reset", -function () { -this.r.reset (); -this.rb = new com.stevesoft.pat.RBuffer ( new StringBuffer ()); -this.wrap = new com.stevesoft.pat.PartialBuffer (this.rb.sb); -this.moreToRead = true; -}); -Clazz.defineMethod (c$, "readData", -function () { -var c; -var n = 0; -while ((c = this.r.read ()) != -1) { -this.rb.sb.append (String.fromCharCode (c)); -if (n++ > this.nmax) { -break; -}} -if (c == -1 && n == 0) { -this.moreToRead = false; -this.wrap.allowOverRun = false; -}}); -Clazz.defineMethod (c$, "getMoreData", -function () { -while (this.rb.pos >= this.rb.epos) { -this.wrap.overRun = false; -if (this.rb.next != null) { -this.rb = this.rb.next; -} else if (this.rb.done) { -break; -} else if (this.rb.epos >= this.rb.sb.length () && this.rb.epos > this.nmax) { -this.rb.pos = 1; -this.rb.epos = 1; -this.rb.sb.setLength (1); -this.readData (); -} else if (this.rb.epos >= this.rb.sb.length () && this.moreToRead) { -this.readData (); -} else if (this.rp.getRegex ().matchAtLike (this.wrap, this.rb.epos)) { -if (this.wrap.overRun) { -this.readData (); -} else { -var sbw = new com.stevesoft.pat.wrap.StringBufferWrap (); -var sbl = new com.stevesoft.pat.StringBufferLike (sbw); -var rex = this.rp.getRegex (); -var npos = rex.matchedTo (); -this.rp.setBuffer (sbl); -this.rp.setSource (this.wrap); -this.rp.setPos (npos); -this.rp.apply (rex, rex.getReplaceRule ()); -var opos = this.rb.epos; -var rb2 = new com.stevesoft.pat.RBuffer (sbw.unwrap ()); -rb2.epos = rb2.sb.length (); -var rb3 = new com.stevesoft.pat.RBuffer (this.rb.sb); -this.rb.next = rb2; -rb2.next = rb3; -if (npos == opos) { -rb3.epos = npos + 1; -if (rb3.epos > rb3.sb.length ()) { -if (this.rb.pos >= this.rb.epos) { -this.rb = this.rb.next; -}rb3.pos = rb3.epos = 0; -rb3.done = true; -}rb3.pos = npos; -} else { -rb3.pos = rb3.epos = npos; -}}} else { -if (this.wrap.overRun) { -this.readData (); -} else if (this.rb.epos < this.rb.sb.length ()) { -this.rb.epos++; -} else { -break; -}}} -}); -Clazz.defineMethod (c$, "read", -function () { -if (this.rb.pos >= this.rb.epos) { -this.getMoreData (); -if (this.rb.pos >= this.rb.epos) { -return -1; -}}return this.rb.sb.charAt (this.rb.pos++); -}); -Clazz.defineMethod (c$, "read", -function (buf, off, len) { -var c = -1; -var end = off + len; -for (var i = off; i < end; i++) { -c = this.read (); -if (c < 0) { -if (i == off) { -return -1; -}return i - off; -}buf[i] = String.fromCharCode (c); -} -return len; -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "close", -function () { -this.r.close (); -}); -Clazz.overrideMethod (c$, "markSupported", -function () { -return false; -}); -Clazz.defineMethod (c$, "getBufferSize", -function () { -return this.nmax; -}); -Clazz.defineMethod (c$, "setBufferSize", -function (n) { -this.nmax = n; -}, "~N"); -Clazz.defineMethod (c$, "getMaxLines", -function () { -return this.max_lines; -}); -Clazz.defineMethod (c$, "setMaxLines", -function (ml) { -this.max_lines = ml; -}, "~N"); -Clazz.defineMethod (c$, "getEOLchar", -function () { -return this.EOLchar; -}); -Clazz.defineMethod (c$, "setEOLchar", -function (c) { -this.EOLchar = c; -}, "~S"); -Clazz.overrideMethod (c$, "skip", -function (d) { -var n = 0; -while (n < d && this.read () != -1) { -n++; -} -return n; -}, "~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.io.Reader", "com.stevesoft.pat.PartialBuffer", "$.RBuffer", "java.lang.StringBuffer"], "com.stevesoft.pat.RegexReader", ["com.stevesoft.pat.StringBufferLike", "com.stevesoft.pat.wrap.StringBufferWrap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.rb = null; +this.wrap = null; +this.moreToRead = true; +this.r = null; +this.rp = null; +this.nmax = 2048; +this.max_lines = 2; +this.EOLchar = '\n'; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RegexReader", java.io.Reader); +Clazz.prepareFields (c$, function () { +this.rb = new com.stevesoft.pat.RBuffer ( new StringBuffer ()); +this.wrap = new com.stevesoft.pat.PartialBuffer (this.rb.sb); +}); +Clazz.makeConstructor (c$, +function (rex, r) { +Clazz.superConstructor (this, com.stevesoft.pat.RegexReader, []); +this.r = r; +this.rp = rex.getReplacer (); +}, "com.stevesoft.pat.Regex,java.io.Reader"); +Clazz.makeConstructor (c$, +function (tex, r) { +Clazz.superConstructor (this, com.stevesoft.pat.RegexReader, []); +this.r = r; +this.rp = tex.getReplacer (); +}, "com.stevesoft.pat.Transformer,java.io.Reader"); +Clazz.defineMethod (c$, "reset", +function () { +this.r.reset (); +this.rb = new com.stevesoft.pat.RBuffer ( new StringBuffer ()); +this.wrap = new com.stevesoft.pat.PartialBuffer (this.rb.sb); +this.moreToRead = true; +}); +Clazz.defineMethod (c$, "readData", +function () { +var c; +var n = 0; +while ((c = this.r.read ()) != -1) { +this.rb.sb.append (String.fromCharCode (c)); +if (n++ > this.nmax) { +break; +}} +if (c == -1 && n == 0) { +this.moreToRead = false; +this.wrap.allowOverRun = false; +}}); +Clazz.defineMethod (c$, "getMoreData", +function () { +while (this.rb.pos >= this.rb.epos) { +this.wrap.overRun = false; +if (this.rb.next != null) { +this.rb = this.rb.next; +} else if (this.rb.done) { +break; +} else if (this.rb.epos >= this.rb.sb.length () && this.rb.epos > this.nmax) { +this.rb.pos = 1; +this.rb.epos = 1; +this.rb.sb.setLength (1); +this.readData (); +} else if (this.rb.epos >= this.rb.sb.length () && this.moreToRead) { +this.readData (); +} else if (this.rp.getRegex ().matchAtLike (this.wrap, this.rb.epos)) { +if (this.wrap.overRun) { +this.readData (); +} else { +var sbw = new com.stevesoft.pat.wrap.StringBufferWrap (); +var sbl = new com.stevesoft.pat.StringBufferLike (sbw); +var rex = this.rp.getRegex (); +var npos = rex.matchedTo (); +this.rp.setBuffer (sbl); +this.rp.setSource (this.wrap); +this.rp.setPos (npos); +this.rp.apply (rex, rex.getReplaceRule ()); +var opos = this.rb.epos; +var rb2 = new com.stevesoft.pat.RBuffer (sbw.unwrap ()); +rb2.epos = rb2.sb.length (); +var rb3 = new com.stevesoft.pat.RBuffer (this.rb.sb); +this.rb.next = rb2; +rb2.next = rb3; +if (npos == opos) { +rb3.epos = npos + 1; +if (rb3.epos > rb3.sb.length ()) { +if (this.rb.pos >= this.rb.epos) { +this.rb = this.rb.next; +}rb3.pos = rb3.epos = 0; +rb3.done = true; +}rb3.pos = npos; +} else { +rb3.pos = rb3.epos = npos; +}}} else { +if (this.wrap.overRun) { +this.readData (); +} else if (this.rb.epos < this.rb.sb.length ()) { +this.rb.epos++; +} else { +break; +}}} +}); +Clazz.defineMethod (c$, "read", +function () { +if (this.rb.pos >= this.rb.epos) { +this.getMoreData (); +if (this.rb.pos >= this.rb.epos) { +return -1; +}}return this.rb.sb.charAt (this.rb.pos++); +}); +Clazz.defineMethod (c$, "read", +function (buf, off, len) { +var c = -1; +var end = off + len; +for (var i = off; i < end; i++) { +c = this.read (); +if (c < 0) { +if (i == off) { +return -1; +}return i - off; +}buf[i] = String.fromCharCode (c); +} +return len; +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "close", +function () { +this.r.close (); +}); +Clazz.overrideMethod (c$, "markSupported", +function () { +return false; +}); +Clazz.defineMethod (c$, "getBufferSize", +function () { +return this.nmax; +}); +Clazz.defineMethod (c$, "setBufferSize", +function (n) { +this.nmax = n; +}, "~N"); +Clazz.defineMethod (c$, "getMaxLines", +function () { +return this.max_lines; +}); +Clazz.defineMethod (c$, "setMaxLines", +function (ml) { +this.max_lines = ml; +}, "~N"); +Clazz.defineMethod (c$, "getEOLchar", +function () { +return this.EOLchar; +}); +Clazz.defineMethod (c$, "setEOLchar", +function (c) { +this.EOLchar = c; +}, "~S"); +Clazz.overrideMethod (c$, "skip", +function (d) { +var n = 0; +while (n < d && this.read () != -1) { +n++; +} +return n; +}, "~N"); +}); diff --git a/bin/com/stevesoft/pat/RegexTokenizer.js b/bin/com/stevesoft/pat/RegexTokenizer.js index 08cc754..c5774f3 100644 --- a/bin/com/stevesoft/pat/RegexTokenizer.js +++ b/bin/com/stevesoft/pat/RegexTokenizer.js @@ -1,104 +1,104 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.util.Enumeration", "$.Vector"], "com.stevesoft.pat.RegexTokenizer", ["com.stevesoft.pat.Regex"], function () { -c$ = Clazz.decorateAsClass (function () { -this.toParse = null; -this.r = null; -this.count = 0; -this.v = null; -this.vi = null; -this.pos = 0; -this.offset = 1; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RegexTokenizer", null, java.util.Enumeration); -Clazz.prepareFields (c$, function () { -this.v = new java.util.Vector (); -this.vi = new java.util.Vector (); -}); -Clazz.defineMethod (c$, "getMore", -function () { -var s = this.r.right (); -if (this.r.searchFrom (this.toParse, this.pos)) { -this.v.addElement (this.r.left ().substring (this.pos)); -this.vi.addElement ( new Integer (this.r.matchFrom () + this.r.charsMatched ())); -for (var i = 0; i < this.r.numSubs (); i++) { -if (this.r.substring () != null) { -this.v.addElement (this.r.substringI (i + this.offset)); -this.vi.addElement ( new Integer (this.r.matchFromI (i + this.offset) + this.r.charsMatchedI (i + this.offset))); -}} -this.pos = this.r.matchFrom () + this.r.charsMatched (); -} else if (s != null) { -this.v.addElement (s); -}}); -Clazz.makeConstructor (c$, -function (txt, ptrn) { -this.toParse = txt; -this.r = new com.stevesoft.pat.Regex (ptrn, ""); -this.offset = com.stevesoft.pat.Regex.BackRefOffset; -this.getMore (); -}, "~S,~S"); -Clazz.makeConstructor (c$, -function (txt, r) { -this.toParse = txt; -this.r = r; -this.offset = com.stevesoft.pat.Regex.BackRefOffset; -this.getMore (); -}, "~S,com.stevesoft.pat.Regex"); -Clazz.overrideMethod (c$, "nextElement", -function () { -if (this.count >= this.v.size ()) { -this.getMore (); -}return this.v.elementAt (this.count++); -}); -Clazz.defineMethod (c$, "nextToken", -function () { -return this.nextElement (); -}); -Clazz.defineMethod (c$, "nextToken", -function (newpat) { -try { -this.r.compile (newpat); -} catch (r_) { -if (Clazz.exceptionOf (r_, com.stevesoft.pat.RegSyntax)) { -} else { -throw r_; -} -} -return this.nextToken (this.r); -}, "~S"); -Clazz.defineMethod (c$, "nextToken", -function (nr) { -this.r = nr; -if (this.vi.size () > this.count) { -this.pos = (this.vi.elementAt (this.count)).intValue (); -this.v.setSize (this.count); -this.vi.setSize (this.count); -}this.getMore (); -return this.nextToken (); -}, "com.stevesoft.pat.Regex"); -Clazz.overrideMethod (c$, "hasMoreElements", -function () { -if (this.count >= this.v.size ()) { -this.getMore (); -}return this.count < this.v.size (); -}); -Clazz.defineMethod (c$, "hasMoreTokens", -function () { -return this.hasMoreElements (); -}); -Clazz.defineMethod (c$, "countTokens", -function () { -var _count = this.count; -while (this.hasMoreTokens ()) { -this.nextToken (); -} -this.count = _count; -return this.v.size () - this.count; -}); -Clazz.defineMethod (c$, "allTokens", -function () { -this.countTokens (); -var ret = new Array (this.v.size ()); -this.v.copyInto (ret); -return ret; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.util.Enumeration", "$.Vector"], "com.stevesoft.pat.RegexTokenizer", ["com.stevesoft.pat.Regex"], function () { +c$ = Clazz.decorateAsClass (function () { +this.toParse = null; +this.r = null; +this.count = 0; +this.v = null; +this.vi = null; +this.pos = 0; +this.offset = 1; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RegexTokenizer", null, java.util.Enumeration); +Clazz.prepareFields (c$, function () { +this.v = new java.util.Vector (); +this.vi = new java.util.Vector (); +}); +Clazz.defineMethod (c$, "getMore", +function () { +var s = this.r.right (); +if (this.r.searchFrom (this.toParse, this.pos)) { +this.v.addElement (this.r.left ().substring (this.pos)); +this.vi.addElement ( new Integer (this.r.matchFrom () + this.r.charsMatched ())); +for (var i = 0; i < this.r.numSubs (); i++) { +if (this.r.substring () != null) { +this.v.addElement (this.r.substringI (i + this.offset)); +this.vi.addElement ( new Integer (this.r.matchFromI (i + this.offset) + this.r.charsMatchedI (i + this.offset))); +}} +this.pos = this.r.matchFrom () + this.r.charsMatched (); +} else if (s != null) { +this.v.addElement (s); +}}); +Clazz.makeConstructor (c$, +function (txt, ptrn) { +this.toParse = txt; +this.r = new com.stevesoft.pat.Regex (ptrn, ""); +this.offset = com.stevesoft.pat.Regex.BackRefOffset; +this.getMore (); +}, "~S,~S"); +Clazz.makeConstructor (c$, +function (txt, r) { +this.toParse = txt; +this.r = r; +this.offset = com.stevesoft.pat.Regex.BackRefOffset; +this.getMore (); +}, "~S,com.stevesoft.pat.Regex"); +Clazz.overrideMethod (c$, "nextElement", +function () { +if (this.count >= this.v.size ()) { +this.getMore (); +}return this.v.elementAt (this.count++); +}); +Clazz.defineMethod (c$, "nextToken", +function () { +return this.nextElement (); +}); +Clazz.defineMethod (c$, "nextToken", +function (newpat) { +try { +this.r.compile (newpat); +} catch (r_) { +if (Clazz.exceptionOf (r_, com.stevesoft.pat.RegSyntax)) { +} else { +throw r_; +} +} +return this.nextToken (this.r); +}, "~S"); +Clazz.defineMethod (c$, "nextToken", +function (nr) { +this.r = nr; +if (this.vi.size () > this.count) { +this.pos = (this.vi.elementAt (this.count)).intValue (); +this.v.setSize (this.count); +this.vi.setSize (this.count); +}this.getMore (); +return this.nextToken (); +}, "com.stevesoft.pat.Regex"); +Clazz.overrideMethod (c$, "hasMoreElements", +function () { +if (this.count >= this.v.size ()) { +this.getMore (); +}return this.count < this.v.size (); +}); +Clazz.defineMethod (c$, "hasMoreTokens", +function () { +return this.hasMoreElements (); +}); +Clazz.defineMethod (c$, "countTokens", +function () { +var _count = this.count; +while (this.hasMoreTokens ()) { +this.nextToken (); +} +this.count = _count; +return this.v.size () - this.count; +}); +Clazz.defineMethod (c$, "allTokens", +function () { +this.countTokens (); +var ret = new Array (this.v.size ()); +this.v.copyInto (ret); +return ret; +}); +}); diff --git a/bin/com/stevesoft/pat/RegexWriter.class b/bin/com/stevesoft/pat/RegexWriter.class index 36bb465..e4e7fdd 100644 Binary files a/bin/com/stevesoft/pat/RegexWriter.class and b/bin/com/stevesoft/pat/RegexWriter.class differ diff --git a/bin/com/stevesoft/pat/RegexWriter.js b/bin/com/stevesoft/pat/RegexWriter.js index 817515b..f1be88e 100644 --- a/bin/com/stevesoft/pat/RegexWriter.js +++ b/bin/com/stevesoft/pat/RegexWriter.js @@ -1,134 +1,134 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.io.Writer", "com.stevesoft.pat.PartialBuffer", "java.lang.StringBuffer"], "com.stevesoft.pat.RegexWriter", ["com.stevesoft.pat.StringBufferLike", "com.stevesoft.pat.wrap.WriterWrap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.repr = null; -this.w = null; -this.ww = null; -this.sb = null; -this.wrap = null; -this.pos = 0; -this.epos = 0; -this.interval = 128; -this.bufferSize = 2048; -this.EOLchar = '\n'; -this.max_lines = 2; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RegexWriter", java.io.Writer); -Clazz.prepareFields (c$, function () { -this.sb = new StringBuffer (); -this.wrap = new com.stevesoft.pat.PartialBuffer (this.sb); -}); -Clazz.makeConstructor (c$, -function (t, w) { -Clazz.superConstructor (this, com.stevesoft.pat.RegexWriter, []); -this.w = w; -this.ww = new com.stevesoft.pat.wrap.WriterWrap (w); -this.repr = t.getReplacer (); -this.repr.setBuffer ( new com.stevesoft.pat.StringBufferLike (this.ww)); -this.repr.setSource (this.wrap); -}, "com.stevesoft.pat.Transformer,java.io.Writer"); -Clazz.makeConstructor (c$, -function (r, w) { -Clazz.superConstructor (this, com.stevesoft.pat.RegexWriter, []); -this.w = w; -this.ww = new com.stevesoft.pat.wrap.WriterWrap (w); -this.repr = r.getReplacer (); -this.repr.setBuffer ( new com.stevesoft.pat.StringBufferLike (this.ww)); -this.repr.setSource (this.wrap); -}, "com.stevesoft.pat.Regex,java.io.Writer"); -Clazz.defineMethod (c$, "getEOLchar", -function () { -return this.EOLchar; -}); -Clazz.defineMethod (c$, "setEOLchar", -function (c) { -this.EOLchar = c; -}, "~S"); -Clazz.defineMethod (c$, "getMaxLines", -function () { -return this.max_lines; -}); -Clazz.defineMethod (c$, "setMaxLines", -function (ml) { -this.max_lines = ml; -}, "~N"); -Clazz.defineMethod (c$, "write", -function () { -var rex = this.repr.getRegex (); -var eposOld = this.epos; -if (rex.matchAtLike (this.wrap, this.epos) && !this.wrap.overRun) { -while (this.pos < this.epos) { -this.w.write (this.sb.charCodeAt (this.pos++)); -} -var to = rex.matchedTo (); -this.repr.setPos (to); -this.repr.apply (rex, rex.getReplaceRule ()); -this.epos = this.pos = to; -if (this.epos == eposOld && this.epos < this.sb.length ()) { -this.epos++; -}} else if (!this.wrap.overRun && this.epos < this.sb.length ()) { -this.epos++; -}while (this.pos < this.epos) { -this.w.write (this.sb.charCodeAt (this.pos++)); -} -if (this.epos == this.sb.length ()) { -this.sb.setLength (1); -this.pos = this.epos = 1; -} else if (this.pos > this.bufferSize) { -for (var i = this.bufferSize; i < this.sb.length (); i++) { -this.sb.setCharAt (i - this.bufferSize, this.sb.charAt (i)); -} -this.pos -= this.bufferSize; -this.epos -= this.bufferSize; -this.sb.setLength (this.sb.length () - this.bufferSize); -}}); -Clazz.defineMethod (c$, "write", -function (ca, b, n) { -var m = b + n; -for (var i = b; i < m; i++) { -this.sb.append (ca[i]); -if (this.sb.length () % this.interval == this.interval - 1) { -this.wrap.overRun = false; -while (this.epos + this.interval < this.sb.length () && !this.wrap.overRun) { -this.write (); -} -}} -}, "~A,~N,~N"); -Clazz.overrideMethod (c$, "flush", -function () { -}); -Clazz.defineMethod (c$, "close", -function () { -this.wrap.allowOverRun = false; -this.wrap.overRun = false; -while (this.epos < this.sb.length ()) { -this.write (); -} -this.write (); -this.w.close (); -}); -Clazz.defineMethod (c$, "length", -function () { -return this.sb.length (); -}); -Clazz.defineMethod (c$, "charAt", -function (i) { -return this.sb.charAt (i); -}, "~N"); -Clazz.defineMethod (c$, "setInterval", -function (i) { -this.interval = i; -}, "~N"); -Clazz.defineMethod (c$, "getInterval", -function () { -return this.interval; -}); -Clazz.defineMethod (c$, "getBufferSize", -function () { -return this.bufferSize; -}); -Clazz.defineMethod (c$, "setBufferSize", -function (i) { -this.bufferSize = i; -}, "~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.io.Writer", "com.stevesoft.pat.PartialBuffer", "java.lang.StringBuffer"], "com.stevesoft.pat.RegexWriter", ["com.stevesoft.pat.StringBufferLike", "com.stevesoft.pat.wrap.WriterWrap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.repr = null; +this.w = null; +this.ww = null; +this.sb = null; +this.wrap = null; +this.pos = 0; +this.epos = 0; +this.interval = 128; +this.bufferSize = 2048; +this.EOLchar = '\n'; +this.max_lines = 2; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RegexWriter", java.io.Writer); +Clazz.prepareFields (c$, function () { +this.sb = new StringBuffer (); +this.wrap = new com.stevesoft.pat.PartialBuffer (this.sb); +}); +Clazz.makeConstructor (c$, +function (t, w) { +Clazz.superConstructor (this, com.stevesoft.pat.RegexWriter, []); +this.w = w; +this.ww = new com.stevesoft.pat.wrap.WriterWrap (w); +this.repr = t.getReplacer (); +this.repr.setBuffer ( new com.stevesoft.pat.StringBufferLike (this.ww)); +this.repr.setSource (this.wrap); +}, "com.stevesoft.pat.Transformer,java.io.Writer"); +Clazz.makeConstructor (c$, +function (r, w) { +Clazz.superConstructor (this, com.stevesoft.pat.RegexWriter, []); +this.w = w; +this.ww = new com.stevesoft.pat.wrap.WriterWrap (w); +this.repr = r.getReplacer (); +this.repr.setBuffer ( new com.stevesoft.pat.StringBufferLike (this.ww)); +this.repr.setSource (this.wrap); +}, "com.stevesoft.pat.Regex,java.io.Writer"); +Clazz.defineMethod (c$, "getEOLchar", +function () { +return this.EOLchar; +}); +Clazz.defineMethod (c$, "setEOLchar", +function (c) { +this.EOLchar = c; +}, "~S"); +Clazz.defineMethod (c$, "getMaxLines", +function () { +return this.max_lines; +}); +Clazz.defineMethod (c$, "setMaxLines", +function (ml) { +this.max_lines = ml; +}, "~N"); +Clazz.defineMethod (c$, "write", +function () { +var rex = this.repr.getRegex (); +var eposOld = this.epos; +if (rex.matchAtLike (this.wrap, this.epos) && !this.wrap.overRun) { +while (this.pos < this.epos) { +this.w.write (this.sb.charCodeAt (this.pos++)); +} +var to = rex.matchedTo (); +this.repr.setPos (to); +this.repr.apply (rex, rex.getReplaceRule ()); +this.epos = this.pos = to; +if (this.epos == eposOld && this.epos < this.sb.length ()) { +this.epos++; +}} else if (!this.wrap.overRun && this.epos < this.sb.length ()) { +this.epos++; +}while (this.pos < this.epos) { +this.w.write (this.sb.charCodeAt (this.pos++)); +} +if (this.epos == this.sb.length ()) { +this.sb.setLength (1); +this.pos = this.epos = 1; +} else if (this.pos > this.bufferSize) { +for (var i = this.bufferSize; i < this.sb.length (); i++) { +this.sb.setCharAt (i - this.bufferSize, this.sb.charAt (i)); +} +this.pos -= this.bufferSize; +this.epos -= this.bufferSize; +this.sb.setLength (this.sb.length () - this.bufferSize); +}}); +Clazz.defineMethod (c$, "write", +function (ca, b, n) { +var m = b + n; +for (var i = b; i < m; i++) { +this.sb.append (ca[i]); +if (this.sb.length () % this.interval == this.interval - 1) { +this.wrap.overRun = false; +while (this.epos + this.interval < this.sb.length () && !this.wrap.overRun) { +this.write (); +} +}} +}, "~A,~N,~N"); +Clazz.overrideMethod (c$, "flush", +function () { +}); +Clazz.defineMethod (c$, "close", +function () { +this.wrap.allowOverRun = false; +this.wrap.overRun = false; +while (this.epos < this.sb.length ()) { +this.write (); +} +this.write (); +this.w.close (); +}); +Clazz.defineMethod (c$, "length", +function () { +return this.sb.length (); +}); +Clazz.defineMethod (c$, "charAt", +function (i) { +return this.sb.charAt (i); +}, "~N"); +Clazz.defineMethod (c$, "setInterval", +function (i) { +this.interval = i; +}, "~N"); +Clazz.defineMethod (c$, "getInterval", +function () { +return this.interval; +}); +Clazz.defineMethod (c$, "getBufferSize", +function () { +return this.bufferSize; +}); +Clazz.defineMethod (c$, "setBufferSize", +function (i) { +this.bufferSize = i; +}, "~N"); +}); diff --git a/bin/com/stevesoft/pat/ReplaceRule.class b/bin/com/stevesoft/pat/ReplaceRule.class index 02e0aca..07dc4de 100644 Binary files a/bin/com/stevesoft/pat/ReplaceRule.class and b/bin/com/stevesoft/pat/ReplaceRule.class differ diff --git a/bin/com/stevesoft/pat/ReplaceRule.js b/bin/com/stevesoft/pat/ReplaceRule.js index 795545b..7485c5f 100644 --- a/bin/com/stevesoft/pat/ReplaceRule.js +++ b/bin/com/stevesoft/pat/ReplaceRule.js @@ -1,203 +1,203 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["java.util.Hashtable"], "com.stevesoft.pat.ReplaceRule", ["com.stevesoft.pat.Ctrl", "$.Regex", "$.Transformer", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.next = null; -this.name = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "ReplaceRule"); -Clazz.prepareFields (c$, function () { -this.name = this.getClass ().getName (); -}); -Clazz.defineMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.RuleHolder (this); -}); -Clazz.overrideMethod (c$, "clone", -function () { -var x = this.clone1 (); -var xsav = x; -var y = this; -while (y.next != null) { -x.next = y.next.clone1 (); -x.name = y.name; -x = x.next; -y = y.next; -} -return xsav; -}); -c$.add = Clazz.defineMethod (c$, "add", -function (head, adding) { -if (head == null) { -return head = adding; -}head.addRule (adding); -return head; -}, "com.stevesoft.pat.ReplaceRule,com.stevesoft.pat.ReplaceRule"); -Clazz.defineMethod (c$, "add", -function (adding) { -return com.stevesoft.pat.ReplaceRule.add (this, adding); -}, "com.stevesoft.pat.ReplaceRule"); -Clazz.defineMethod (c$, "addRule", -function (r) { -if (this.next == null) { -this.next = r; -} else { -this.next.addRule (r); -}}, "com.stevesoft.pat.ReplaceRule"); -c$.getv = Clazz.defineMethod (c$, "getv", -($fz = function () { -if (com.stevesoft.pat.ReplaceRule.getvar != null) { -return com.stevesoft.pat.ReplaceRule.getvar.clone (); -}com.stevesoft.pat.ReplaceRule.getvar = new com.stevesoft.pat.Regex ("(?:\\\\(\\d+)|\\$(?:(\\d+)|(\\w+)|([&\'`])|\\{(?:(\\d+)|([^\n}\\\\]+))})|\\\\([nrbtaef])|\\\\c([\u0000-\uffff])|\\\\x([A-Fa-f0-9]{2})|\\\\([\u0000-\uffff]))", ""); -com.stevesoft.pat.ReplaceRule.getvar.optimize (); -return com.stevesoft.pat.ReplaceRule.getvar; -}, $fz.isPrivate = true, $fz)); -c$.perlCode = Clazz.defineMethod (c$, "perlCode", -function (s) { -try { -var mf = 0; -var mt = 0; -var gv = com.stevesoft.pat.ReplaceRule.getv (); -var head = null; -var tmp = null; -while (gv.searchFrom (s, mt)) { -var off = com.stevesoft.pat.Regex.BackRefOffset - 1; -mf = gv.matchedFrom (); -if (mf > mt) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule (s.substring (mt, mf))); -}var $var = null; -if (($var = gv.stringMatchedI (1 + off)) != null || ($var = gv.stringMatchedI (2 + off)) != null || ($var = gv.stringMatchedI (5 + off)) != null) { -var d = 0; -for (var i = 0; i < $var.length; i++) { -d = 8 * d + ($var.charCodeAt (i) - 48); -} -if ($var.length == 1) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.BackRefRule (d)); -} else { -head = new com.stevesoft.pat.StringRule ("" + String.fromCharCode (d)); -}} else if (($var = gv.stringMatchedI (10 + off)) != null) { -if ("QELlUu".indexOf ($var) >= 0) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.CodeRule ($var.charAt (0))); -} else { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ($var)); -}} else if (($var = gv.stringMatchedI (3 + off)) != null || ($var = gv.stringMatchedI (4 + off)) != null || ($var = gv.stringMatchedI (6 + off)) != null) { -var arg = ""; -var pc; -if ((pc = $var.indexOf (':')) > 0) { -arg = $var.substring (pc + 1); -$var = $var.substring (0, pc); -}if ($var.equals ("&") || $var.equals ("MATCH")) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.AmpersandRule ()); -} else if ($var.equals ("`") || $var.equals ("PREMATCH")) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.LeftRule ()); -} else if ($var.equals ("'") || $var.equals ("POSTMATCH")) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.RightRule ()); -} else if ($var.equals ("WANT_MORE_TEXT")) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.WantMoreTextReplaceRule ()); -} else if ($var.equals ("POP")) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.PopRule ()); -} else if ($var.startsWith ("+") && (tmp = com.stevesoft.pat.ReplaceRule.defs.get ($var.substring (1))) != null) { -if (Clazz.instanceOf (tmp, com.stevesoft.pat.Regex)) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.PushRule ($var.substring (1), tmp)); -} else if (Clazz.instanceOf (tmp, com.stevesoft.pat.Transformer)) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.PushRule ($var.substring (1), tmp)); -} else { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("${" + $var + "}")); -}} else if ($var.startsWith ("=") && (tmp = com.stevesoft.pat.ReplaceRule.defs.get ($var.substring (1))) != null) { -if (Clazz.instanceOf (tmp, com.stevesoft.pat.Regex)) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.ChangeRule ($var.substring (1), tmp)); -} else if (Clazz.instanceOf (tmp, com.stevesoft.pat.Transformer)) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.ChangeRule ($var.substring (1), tmp)); -} else { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("${" + $var + "}")); -}} else if ((tmp = com.stevesoft.pat.ReplaceRule.defs.get ($var)) != null) { -if (Clazz.instanceOf (tmp, com.stevesoft.pat.ReplaceRule)) { -var alt = (tmp).arg (arg); -if (alt == null) { -alt = (tmp); -}head = com.stevesoft.pat.ReplaceRule.add (head, (alt.clone ())); -}} else { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("${" + $var + "}")); -}} else if (($var = gv.stringMatchedI (7 + off)) != null) { -var c = $var.charAt (0); -if (c == 'n') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\n")); -} else if (c == 't') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\t")); -} else if (c == 'r') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\r")); -} else if (c == 'b') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\r")); -} else if (c == 'a') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\u0007")); -} else if (c == 'e') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\u001b")); -} else if (c == 'f') { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\f")); -}} else if (($var = gv.stringMatchedI (8 + off)) != null) { -var c = $var.charAt (0); -if (c.charCodeAt (0) < com.stevesoft.pat.Ctrl.cmap.length) { -c = com.stevesoft.pat.Ctrl.cmap[c.charCodeAt (0)]; -}head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("" + c)); -} else if (($var = gv.stringMatchedI (9 + off)) != null) { -var d = 16 * com.stevesoft.pat.ReplaceRule.getHexDigit ($var.charAt (0)) + com.stevesoft.pat.ReplaceRule.getHexDigit ($var.charAt (1)); -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("" + String.fromCharCode (d))); -}mt = gv.matchedTo (); -} -if (mt <= s.length) { -head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule (s.substring (mt))); -}return head; -} finally { -} -}, "~S"); -c$.isDefined = Clazz.defineMethod (c$, "isDefined", -function (s) { -return com.stevesoft.pat.ReplaceRule.defs.get (s) != null; -}, "~S"); -c$.define = Clazz.defineMethod (c$, "define", -function (s, r) { -com.stevesoft.pat.ReplaceRule.defs.put (s, r); -}, "~S,com.stevesoft.pat.Regex"); -c$.define = Clazz.defineMethod (c$, "define", -function (s, r) { -com.stevesoft.pat.ReplaceRule.defs.put (s, r); -r.name = s; -}, "~S,com.stevesoft.pat.ReplaceRule"); -c$.define = Clazz.defineMethod (c$, "define", -function (s, t) { -com.stevesoft.pat.ReplaceRule.defs.put (s, t); -}, "~S,com.stevesoft.pat.Transformer"); -c$.undefine = Clazz.defineMethod (c$, "undefine", -function (s) { -com.stevesoft.pat.ReplaceRule.defs.remove (s); -}, "~S"); -Clazz.defineMethod (c$, "toString1", -function () { -return "${" + this.name + "}"; -}); -Clazz.overrideMethod (c$, "toString", -function () { -var sb = new StringBuffer (); -sb.append (this.toString1 ()); -var rr = this.next; -while (rr != null) { -sb.append (rr.toString1 ()); -rr = rr.next; -} -return sb.toString (); -}); -Clazz.defineMethod (c$, "arg", -function (s) { -return null; -}, "~S"); -c$.getHexDigit = Clazz.defineMethod (c$, "getHexDigit", -function (c) { -if (c >= '0' && c <= '9') { -return c.charCodeAt (0) - 48; -}if (c >= 'a' && c <= 'f') { -return c.charCodeAt (0) - 97 + 10; -}return c.charCodeAt (0) - 65 + 10; -}, "~S"); -Clazz.defineStatics (c$, -"getvar", null); -c$.defs = c$.prototype.defs = new java.util.Hashtable (); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["java.util.Hashtable"], "com.stevesoft.pat.ReplaceRule", ["com.stevesoft.pat.Ctrl", "$.Regex", "$.Transformer", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.next = null; +this.name = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "ReplaceRule"); +Clazz.prepareFields (c$, function () { +this.name = this.getClass ().getName (); +}); +Clazz.defineMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.RuleHolder (this); +}); +Clazz.overrideMethod (c$, "clone", +function () { +var x = this.clone1 (); +var xsav = x; +var y = this; +while (y.next != null) { +x.next = y.next.clone1 (); +x.name = y.name; +x = x.next; +y = y.next; +} +return xsav; +}); +c$.add = Clazz.defineMethod (c$, "add", +function (head, adding) { +if (head == null) { +return head = adding; +}head.addRule (adding); +return head; +}, "com.stevesoft.pat.ReplaceRule,com.stevesoft.pat.ReplaceRule"); +Clazz.defineMethod (c$, "add", +function (adding) { +return com.stevesoft.pat.ReplaceRule.add (this, adding); +}, "com.stevesoft.pat.ReplaceRule"); +Clazz.defineMethod (c$, "addRule", +function (r) { +if (this.next == null) { +this.next = r; +} else { +this.next.addRule (r); +}}, "com.stevesoft.pat.ReplaceRule"); +c$.getv = Clazz.defineMethod (c$, "getv", +($fz = function () { +if (com.stevesoft.pat.ReplaceRule.getvar != null) { +return com.stevesoft.pat.ReplaceRule.getvar.clone (); +}com.stevesoft.pat.ReplaceRule.getvar = new com.stevesoft.pat.Regex ("(?:\\\\(\\d+)|\\$(?:(\\d+)|(\\w+)|([&\'`])|\\{(?:(\\d+)|([^\n}\\\\]+))})|\\\\([nrbtaef])|\\\\c([\u0000-\uffff])|\\\\x([A-Fa-f0-9]{2})|\\\\([\u0000-\uffff]))", ""); +com.stevesoft.pat.ReplaceRule.getvar.optimize (); +return com.stevesoft.pat.ReplaceRule.getvar; +}, $fz.isPrivate = true, $fz)); +c$.perlCode = Clazz.defineMethod (c$, "perlCode", +function (s) { +try { +var mf = 0; +var mt = 0; +var gv = com.stevesoft.pat.ReplaceRule.getv (); +var head = null; +var tmp = null; +while (gv.searchFrom (s, mt)) { +var off = com.stevesoft.pat.Regex.BackRefOffset - 1; +mf = gv.matchedFrom (); +if (mf > mt) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule (s.substring (mt, mf))); +}var $var = null; +if (($var = gv.stringMatchedI (1 + off)) != null || ($var = gv.stringMatchedI (2 + off)) != null || ($var = gv.stringMatchedI (5 + off)) != null) { +var d = 0; +for (var i = 0; i < $var.length; i++) { +d = 8 * d + ($var.charCodeAt (i) - 48); +} +if ($var.length == 1) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.BackRefRule (d)); +} else { +head = new com.stevesoft.pat.StringRule ("" + String.fromCharCode (d)); +}} else if (($var = gv.stringMatchedI (10 + off)) != null) { +if ("QELlUu".indexOf ($var) >= 0) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.CodeRule ($var.charAt (0))); +} else { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ($var)); +}} else if (($var = gv.stringMatchedI (3 + off)) != null || ($var = gv.stringMatchedI (4 + off)) != null || ($var = gv.stringMatchedI (6 + off)) != null) { +var arg = ""; +var pc; +if ((pc = $var.indexOf (':')) > 0) { +arg = $var.substring (pc + 1); +$var = $var.substring (0, pc); +}if ($var.equals ("&") || $var.equals ("MATCH")) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.AmpersandRule ()); +} else if ($var.equals ("`") || $var.equals ("PREMATCH")) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.LeftRule ()); +} else if ($var.equals ("'") || $var.equals ("POSTMATCH")) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.RightRule ()); +} else if ($var.equals ("WANT_MORE_TEXT")) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.WantMoreTextReplaceRule ()); +} else if ($var.equals ("POP")) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.PopRule ()); +} else if ($var.startsWith ("+") && (tmp = com.stevesoft.pat.ReplaceRule.defs.get ($var.substring (1))) != null) { +if (Clazz.instanceOf (tmp, com.stevesoft.pat.Regex)) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.PushRule ($var.substring (1), tmp)); +} else if (Clazz.instanceOf (tmp, com.stevesoft.pat.Transformer)) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.PushRule ($var.substring (1), tmp)); +} else { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("${" + $var + "}")); +}} else if ($var.startsWith ("=") && (tmp = com.stevesoft.pat.ReplaceRule.defs.get ($var.substring (1))) != null) { +if (Clazz.instanceOf (tmp, com.stevesoft.pat.Regex)) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.ChangeRule ($var.substring (1), tmp)); +} else if (Clazz.instanceOf (tmp, com.stevesoft.pat.Transformer)) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.ChangeRule ($var.substring (1), tmp)); +} else { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("${" + $var + "}")); +}} else if ((tmp = com.stevesoft.pat.ReplaceRule.defs.get ($var)) != null) { +if (Clazz.instanceOf (tmp, com.stevesoft.pat.ReplaceRule)) { +var alt = (tmp).arg (arg); +if (alt == null) { +alt = (tmp); +}head = com.stevesoft.pat.ReplaceRule.add (head, (alt.clone ())); +}} else { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("${" + $var + "}")); +}} else if (($var = gv.stringMatchedI (7 + off)) != null) { +var c = $var.charAt (0); +if (c == 'n') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\n")); +} else if (c == 't') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\t")); +} else if (c == 'r') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\r")); +} else if (c == 'b') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\r")); +} else if (c == 'a') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\u0007")); +} else if (c == 'e') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\u001b")); +} else if (c == 'f') { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("\f")); +}} else if (($var = gv.stringMatchedI (8 + off)) != null) { +var c = $var.charAt (0); +if (c.charCodeAt (0) < com.stevesoft.pat.Ctrl.cmap.length) { +c = com.stevesoft.pat.Ctrl.cmap[c.charCodeAt (0)]; +}head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("" + c)); +} else if (($var = gv.stringMatchedI (9 + off)) != null) { +var d = 16 * com.stevesoft.pat.ReplaceRule.getHexDigit ($var.charAt (0)) + com.stevesoft.pat.ReplaceRule.getHexDigit ($var.charAt (1)); +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule ("" + String.fromCharCode (d))); +}mt = gv.matchedTo (); +} +if (mt <= s.length) { +head = com.stevesoft.pat.ReplaceRule.add (head, new com.stevesoft.pat.StringRule (s.substring (mt))); +}return head; +} finally { +} +}, "~S"); +c$.isDefined = Clazz.defineMethod (c$, "isDefined", +function (s) { +return com.stevesoft.pat.ReplaceRule.defs.get (s) != null; +}, "~S"); +c$.define = Clazz.defineMethod (c$, "define", +function (s, r) { +com.stevesoft.pat.ReplaceRule.defs.put (s, r); +}, "~S,com.stevesoft.pat.Regex"); +c$.define = Clazz.defineMethod (c$, "define", +function (s, r) { +com.stevesoft.pat.ReplaceRule.defs.put (s, r); +r.name = s; +}, "~S,com.stevesoft.pat.ReplaceRule"); +c$.define = Clazz.defineMethod (c$, "define", +function (s, t) { +com.stevesoft.pat.ReplaceRule.defs.put (s, t); +}, "~S,com.stevesoft.pat.Transformer"); +c$.undefine = Clazz.defineMethod (c$, "undefine", +function (s) { +com.stevesoft.pat.ReplaceRule.defs.remove (s); +}, "~S"); +Clazz.defineMethod (c$, "toString1", +function () { +return "${" + this.name + "}"; +}); +Clazz.overrideMethod (c$, "toString", +function () { +var sb = new StringBuffer (); +sb.append (this.toString1 ()); +var rr = this.next; +while (rr != null) { +sb.append (rr.toString1 ()); +rr = rr.next; +} +return sb.toString (); +}); +Clazz.defineMethod (c$, "arg", +function (s) { +return null; +}, "~S"); +c$.getHexDigit = Clazz.defineMethod (c$, "getHexDigit", +function (c) { +if (c >= '0' && c <= '9') { +return c.charCodeAt (0) - 48; +}if (c >= 'a' && c <= 'f') { +return c.charCodeAt (0) - 97 + 10; +}return c.charCodeAt (0) - 65 + 10; +}, "~S"); +Clazz.defineStatics (c$, +"getvar", null); +c$.defs = c$.prototype.defs = new java.util.Hashtable (); +}); diff --git a/bin/com/stevesoft/pat/Replacer.class b/bin/com/stevesoft/pat/Replacer.class index 331ff3b..813f56f 100644 Binary files a/bin/com/stevesoft/pat/Replacer.class and b/bin/com/stevesoft/pat/Replacer.class differ diff --git a/bin/com/stevesoft/pat/Replacer.js b/bin/com/stevesoft/pat/Replacer.js index 847b11c..996de92 100644 --- a/bin/com/stevesoft/pat/Replacer.js +++ b/bin/com/stevesoft/pat/Replacer.js @@ -1,230 +1,230 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, ["com.stevesoft.pat.RegHolder", "$.Replacer", "$.CodeVal"], ["com.stevesoft.pat.AmpersandRule", "$.ChangeRule", "$.MessageManager", "$.PopRule", "$.PushRule", "$.RuleHolder", "$.SpecialRule", "$.StringBufferLike", "$.WantMoreTextReplaceRule", "com.stevesoft.pat.wrap.StringWrap", "java.lang.NullPointerException"], function () { -c$ = Clazz.decorateAsClass (function () { -this.me = null; -this.prev = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RegHolder"); -c$ = Clazz.decorateAsClass (function () { -this.pos = 0; -this.code = '\0'; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "CodeVal"); -Clazz.makeConstructor (c$, -function (p, c) { -this.pos = p; -this.code = c; -}, "~N,~S"); -Clazz.overrideMethod (c$, "toString", -function () { -return "(" + this.pos + "," + this.code + ")"; -}); -c$ = Clazz.decorateAsClass (function () { -this.first = false; -this.rh = null; -this.sb = null; -this.src = null; -this.pos = 0; -this.want_more_text = false; -this.want_more_text_enable = false; -this.$lastMatchedTo = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Replacer"); -Clazz.prepareFields (c$, function () { -this.rh = new com.stevesoft.pat.RegHolder (); -}); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "replaceFirstRegion", -function (s, r, start, end) { -return this.replaceFirstRegion ( new com.stevesoft.pat.wrap.StringWrap (s), r, start, end); -}, "~S,com.stevesoft.pat.Regex,~N,~N"); -Clazz.defineMethod (c$, "replaceFirstRegion", -function (s, r, start, end) { -this.first = true; -this.rh.me = r; -this.rh.prev = null; -return this.dorep (s, start, end); -}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Regex,~N,~N"); -Clazz.defineMethod (c$, "replaceFirst", -function (s) { -return this.replaceFirstRegion (s, 0, s.length ()); -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "replaceFirstFrom", -function (s, start) { -return this.replaceFirstRegion (s, start, s.length ()); -}, "com.stevesoft.pat.StringLike,~N"); -Clazz.defineMethod (c$, "replaceFirstRegion", -function (s, start, end) { -this.first = true; -return this.dorep (s, start, end); -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "replaceAllRegion", -function (s, r, start, end) { -return this.replaceAllRegion ( new com.stevesoft.pat.wrap.StringWrap (s), r, start, end); -}, "~S,com.stevesoft.pat.Regex,~N,~N"); -Clazz.defineMethod (c$, "replaceAllRegion", -function (s, r, start, end) { -this.first = false; -this.rh.me = r; -this.rh.prev = null; -return this.dorep (s, start, end); -}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Regex,~N,~N"); -Clazz.defineMethod (c$, "replaceAll", -function (s) { -return this.replaceAllRegion (s, 0, s.length ()); -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "replaceAllFrom", -function (s, start) { -return this.replaceAllRegion (s, start, s.length ()); -}, "com.stevesoft.pat.StringLike,~N"); -Clazz.defineMethod (c$, "replaceAllRegion", -function (s, start, end) { -this.first = false; -return this.dorep (s, start, end); -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "replaceAll", -function (s) { -return this.replaceAllRegion ( new com.stevesoft.pat.wrap.StringWrap (s), 0, s.length).toString (); -}, "~S"); -Clazz.defineMethod (c$, "replaceAllFrom", -function (s, start) { -return this.replaceAllRegion ( new com.stevesoft.pat.wrap.StringWrap (s), start, s.length).toString (); -}, "~S,~N"); -Clazz.defineMethod (c$, "replaceAllRegion", -function (s, start, end) { -this.first = false; -return this.dorep ( new com.stevesoft.pat.wrap.StringWrap (s), start, end).toString (); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "isSpecial", -function (x) { -while (x != null) { -if (Clazz.instanceOf (x, com.stevesoft.pat.SpecialRule) || (Clazz.instanceOf (x, com.stevesoft.pat.RuleHolder) && Clazz.instanceOf ((x).held, com.stevesoft.pat.SpecialRule))) { -return true; -}x = x.next; -} -return false; -}, "com.stevesoft.pat.ReplaceRule"); -Clazz.defineMethod (c$, "apply1", -function (rr) { -rr.charsMatched_++; -this.apply (rr, null); -rr.charsMatched_--; -}, "com.stevesoft.pat.RegRes"); -Clazz.defineMethod (c$, "dorep", -function (s, start, end) { -var ret = s; -this.want_more_text = false; -this.$lastMatchedTo = 0; -if (this.rh.me == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.replace_null_regex_pointer")); -}if (this.rh.me._searchLike (s, start, end)) { -var rmn = this.rh.me.matchedTo (); -if (this.rh.me.charsMatched () == 0 && !this.isSpecial (this.rh.me.getReplaceRule ())) { -this.apply1 (this.rh.me); -rmn++; -}this.apply (this.rh.me); -if (!this.first) { -for (var i = rmn; !this.want_more_text && this.rh.me._searchLike (s, i, end); i = rmn) { -rmn = this.rh.me.matchedTo (); -if (this.rh.me.charsMatched () == 0) { -if (!this.isSpecial (this.rh.me.getReplaceRule ())) { -this.apply1 (this.rh.me); -}rmn++; -}this.apply (this.rh.me); -} -}ret = this.finish (); -ret = ret == null ? s : ret; -}return ret; -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "apply", -function (r, rp) { -if (rp == null || (rp.next == null && Clazz.instanceOf (rp, com.stevesoft.pat.AmpersandRule))) { -return; -}if (r.didMatch ()) { -if (this.src == null) { -this.src = r.getStringLike (); -}if (this.sb == null) { -this.sb = new com.stevesoft.pat.StringBufferLike (this.src.newStringBufferLike ()); -}var rmf = r.matchedFrom (); -for (var ii = this.pos; ii < rmf; ii++) { -this.sb.appendC (this.src.charAt (ii)); -} -for (var x = rp; x != null; x = x.next) { -x.apply (this.sb, r); -if (Clazz.instanceOf (x, com.stevesoft.pat.SpecialRule)) { -if (Clazz.instanceOf (x, com.stevesoft.pat.WantMoreTextReplaceRule) && this.want_more_text_enable) { -this.want_more_text = true; -} else if (Clazz.instanceOf (x, com.stevesoft.pat.PushRule)) { -var rh2 = new com.stevesoft.pat.RegHolder (); -rh2.me = (x).NewRule; -rh2.prev = this.rh; -this.rh = rh2; -} else if (Clazz.instanceOf (x, com.stevesoft.pat.PopRule)) { -if (this.rh.prev != null) { -this.rh = this.rh.prev; -}} else if (Clazz.instanceOf (x, com.stevesoft.pat.ChangeRule)) { -this.rh.me = (x).NewRule; -}}} -if (!this.want_more_text) { -this.pos = r.matchedTo (); -}}}, "com.stevesoft.pat.RegRes,com.stevesoft.pat.ReplaceRule"); -Clazz.defineMethod (c$, "WantMoreText", -function () { -return this.want_more_text; -}); -Clazz.defineMethod (c$, "apply", -function (r) { -this.apply (r, r.getReplaceRule ()); -}, "com.stevesoft.pat.Regex"); -Clazz.defineMethod (c$, "finish", -function () { -if (this.src == null) { -return null; -}var s_end = this.src.length (); -for (var ii = this.pos; ii < s_end; ii++) { -this.sb.appendC (this.src.charAt (ii)); -} -this.src = null; -this.$lastMatchedTo = this.pos; -this.pos = 0; -var retstr = this.sb.toStringLike (); -this.sb = null; -return retstr; -}); -Clazz.overrideMethod (c$, "clone", -function () { -var r = new com.stevesoft.pat.Replacer (); -r.first = this.first; -r.src = this.src; -r.sb = this.sb; -r.pos = this.pos; -r.$lastMatchedTo = this.$lastMatchedTo; -r.want_more_text = this.want_more_text; -r.want_more_text_enable = this.want_more_text_enable; -r.rh.me = this.rh.me; -r.rh.prev = this.rh.prev; -return r; -}); -Clazz.defineMethod (c$, "lastMatchedTo", -function () { -return this.$lastMatchedTo; -}); -Clazz.defineMethod (c$, "getRegex", -function () { -return this.rh.me; -}); -Clazz.defineMethod (c$, "setSource", -function (sl) { -this.src = sl; -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "setBuffer", -function (sbl) { -this.sb = sbl; -}, "com.stevesoft.pat.StringBufferLike"); -Clazz.defineMethod (c$, "setPos", -function (pos) { -this.pos = pos; -}, "~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, ["com.stevesoft.pat.RegHolder", "$.Replacer", "$.CodeVal"], ["com.stevesoft.pat.AmpersandRule", "$.ChangeRule", "$.MessageManager", "$.PopRule", "$.PushRule", "$.RuleHolder", "$.SpecialRule", "$.StringBufferLike", "$.WantMoreTextReplaceRule", "com.stevesoft.pat.wrap.StringWrap", "java.lang.NullPointerException"], function () { +c$ = Clazz.decorateAsClass (function () { +this.me = null; +this.prev = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RegHolder"); +c$ = Clazz.decorateAsClass (function () { +this.pos = 0; +this.code = '\0'; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "CodeVal"); +Clazz.makeConstructor (c$, +function (p, c) { +this.pos = p; +this.code = c; +}, "~N,~S"); +Clazz.overrideMethod (c$, "toString", +function () { +return "(" + this.pos + "," + this.code + ")"; +}); +c$ = Clazz.decorateAsClass (function () { +this.first = false; +this.rh = null; +this.sb = null; +this.src = null; +this.pos = 0; +this.want_more_text = false; +this.want_more_text_enable = false; +this.$lastMatchedTo = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Replacer"); +Clazz.prepareFields (c$, function () { +this.rh = new com.stevesoft.pat.RegHolder (); +}); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "replaceFirstRegion", +function (s, r, start, end) { +return this.replaceFirstRegion ( new com.stevesoft.pat.wrap.StringWrap (s), r, start, end); +}, "~S,com.stevesoft.pat.Regex,~N,~N"); +Clazz.defineMethod (c$, "replaceFirstRegion", +function (s, r, start, end) { +this.first = true; +this.rh.me = r; +this.rh.prev = null; +return this.dorep (s, start, end); +}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Regex,~N,~N"); +Clazz.defineMethod (c$, "replaceFirst", +function (s) { +return this.replaceFirstRegion (s, 0, s.length ()); +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "replaceFirstFrom", +function (s, start) { +return this.replaceFirstRegion (s, start, s.length ()); +}, "com.stevesoft.pat.StringLike,~N"); +Clazz.defineMethod (c$, "replaceFirstRegion", +function (s, start, end) { +this.first = true; +return this.dorep (s, start, end); +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "replaceAllRegion", +function (s, r, start, end) { +return this.replaceAllRegion ( new com.stevesoft.pat.wrap.StringWrap (s), r, start, end); +}, "~S,com.stevesoft.pat.Regex,~N,~N"); +Clazz.defineMethod (c$, "replaceAllRegion", +function (s, r, start, end) { +this.first = false; +this.rh.me = r; +this.rh.prev = null; +return this.dorep (s, start, end); +}, "com.stevesoft.pat.StringLike,com.stevesoft.pat.Regex,~N,~N"); +Clazz.defineMethod (c$, "replaceAll", +function (s) { +return this.replaceAllRegion (s, 0, s.length ()); +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "replaceAllFrom", +function (s, start) { +return this.replaceAllRegion (s, start, s.length ()); +}, "com.stevesoft.pat.StringLike,~N"); +Clazz.defineMethod (c$, "replaceAllRegion", +function (s, start, end) { +this.first = false; +return this.dorep (s, start, end); +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "replaceAll", +function (s) { +return this.replaceAllRegion ( new com.stevesoft.pat.wrap.StringWrap (s), 0, s.length).toString (); +}, "~S"); +Clazz.defineMethod (c$, "replaceAllFrom", +function (s, start) { +return this.replaceAllRegion ( new com.stevesoft.pat.wrap.StringWrap (s), start, s.length).toString (); +}, "~S,~N"); +Clazz.defineMethod (c$, "replaceAllRegion", +function (s, start, end) { +this.first = false; +return this.dorep ( new com.stevesoft.pat.wrap.StringWrap (s), start, end).toString (); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "isSpecial", +function (x) { +while (x != null) { +if (Clazz.instanceOf (x, com.stevesoft.pat.SpecialRule) || (Clazz.instanceOf (x, com.stevesoft.pat.RuleHolder) && Clazz.instanceOf ((x).held, com.stevesoft.pat.SpecialRule))) { +return true; +}x = x.next; +} +return false; +}, "com.stevesoft.pat.ReplaceRule"); +Clazz.defineMethod (c$, "apply1", +function (rr) { +rr.charsMatched_++; +this.apply (rr, null); +rr.charsMatched_--; +}, "com.stevesoft.pat.RegRes"); +Clazz.defineMethod (c$, "dorep", +function (s, start, end) { +var ret = s; +this.want_more_text = false; +this.$lastMatchedTo = 0; +if (this.rh.me == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.getString ("exception.replace_null_regex_pointer")); +}if (this.rh.me._searchLike (s, start, end)) { +var rmn = this.rh.me.matchedTo (); +if (this.rh.me.charsMatched () == 0 && !this.isSpecial (this.rh.me.getReplaceRule ())) { +this.apply1 (this.rh.me); +rmn++; +}this.apply (this.rh.me); +if (!this.first) { +for (var i = rmn; !this.want_more_text && this.rh.me._searchLike (s, i, end); i = rmn) { +rmn = this.rh.me.matchedTo (); +if (this.rh.me.charsMatched () == 0) { +if (!this.isSpecial (this.rh.me.getReplaceRule ())) { +this.apply1 (this.rh.me); +}rmn++; +}this.apply (this.rh.me); +} +}ret = this.finish (); +ret = ret == null ? s : ret; +}return ret; +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "apply", +function (r, rp) { +if (rp == null || (rp.next == null && Clazz.instanceOf (rp, com.stevesoft.pat.AmpersandRule))) { +return; +}if (r.didMatch ()) { +if (this.src == null) { +this.src = r.getStringLike (); +}if (this.sb == null) { +this.sb = new com.stevesoft.pat.StringBufferLike (this.src.newStringBufferLike ()); +}var rmf = r.matchedFrom (); +for (var ii = this.pos; ii < rmf; ii++) { +this.sb.appendC (this.src.charAt (ii)); +} +for (var x = rp; x != null; x = x.next) { +x.apply (this.sb, r); +if (Clazz.instanceOf (x, com.stevesoft.pat.SpecialRule)) { +if (Clazz.instanceOf (x, com.stevesoft.pat.WantMoreTextReplaceRule) && this.want_more_text_enable) { +this.want_more_text = true; +} else if (Clazz.instanceOf (x, com.stevesoft.pat.PushRule)) { +var rh2 = new com.stevesoft.pat.RegHolder (); +rh2.me = (x).NewRule; +rh2.prev = this.rh; +this.rh = rh2; +} else if (Clazz.instanceOf (x, com.stevesoft.pat.PopRule)) { +if (this.rh.prev != null) { +this.rh = this.rh.prev; +}} else if (Clazz.instanceOf (x, com.stevesoft.pat.ChangeRule)) { +this.rh.me = (x).NewRule; +}}} +if (!this.want_more_text) { +this.pos = r.matchedTo (); +}}}, "com.stevesoft.pat.RegRes,com.stevesoft.pat.ReplaceRule"); +Clazz.defineMethod (c$, "WantMoreText", +function () { +return this.want_more_text; +}); +Clazz.defineMethod (c$, "apply", +function (r) { +this.apply (r, r.getReplaceRule ()); +}, "com.stevesoft.pat.Regex"); +Clazz.defineMethod (c$, "finish", +function () { +if (this.src == null) { +return null; +}var s_end = this.src.length (); +for (var ii = this.pos; ii < s_end; ii++) { +this.sb.appendC (this.src.charAt (ii)); +} +this.src = null; +this.$lastMatchedTo = this.pos; +this.pos = 0; +var retstr = this.sb.toStringLike (); +this.sb = null; +return retstr; +}); +Clazz.overrideMethod (c$, "clone", +function () { +var r = new com.stevesoft.pat.Replacer (); +r.first = this.first; +r.src = this.src; +r.sb = this.sb; +r.pos = this.pos; +r.$lastMatchedTo = this.$lastMatchedTo; +r.want_more_text = this.want_more_text; +r.want_more_text_enable = this.want_more_text_enable; +r.rh.me = this.rh.me; +r.rh.prev = this.rh.prev; +return r; +}); +Clazz.defineMethod (c$, "lastMatchedTo", +function () { +return this.$lastMatchedTo; +}); +Clazz.defineMethod (c$, "getRegex", +function () { +return this.rh.me; +}); +Clazz.defineMethod (c$, "setSource", +function (sl) { +this.src = sl; +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "setBuffer", +function (sbl) { +this.sb = sbl; +}, "com.stevesoft.pat.StringBufferLike"); +Clazz.defineMethod (c$, "setPos", +function (pos) { +this.pos = pos; +}, "~N"); +}); diff --git a/bin/com/stevesoft/pat/RightRule.js b/bin/com/stevesoft/pat/RightRule.js index 60fa08d..ab453dd 100644 --- a/bin/com/stevesoft/pat/RightRule.js +++ b/bin/com/stevesoft/pat/RightRule.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.RightRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "RightRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.RightRule, []); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -sb.append (res.right ()); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return "$'"; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.RightRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "RightRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.RightRule, []); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +sb.append (res.right ()); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return "$'"; +}); +}); diff --git a/bin/com/stevesoft/pat/Rthings.js b/bin/com/stevesoft/pat/Rthings.js index c9c902e..66f9c83 100644 --- a/bin/com/stevesoft/pat/Rthings.js +++ b/bin/com/stevesoft/pat/Rthings.js @@ -1,35 +1,35 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Regex"], "com.stevesoft.pat.Rthings", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.val = 0; -this.ignoreCase = false; -this.dontMatchInQuotes = false; -this.optimizeMe = false; -this.noBackRefs = false; -this.parenLevel = 0; -this.gFlag = false; -this.mFlag = false; -this.sFlag = false; -this.p = null; -this.o = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Rthings"); -Clazz.prepareFields (c$, function () { -this.val = com.stevesoft.pat.Regex.BackRefOffset; -}); -Clazz.makeConstructor (c$, -function (r) { -this.ignoreCase = r.ignoreCase; -this.dontMatchInQuotes = r.dontMatchInQuotes; -}, "com.stevesoft.pat.Regex"); -Clazz.defineMethod (c$, "set", -function (r) { -r.gFlag = this.gFlag; -r.mFlag = this.mFlag; -r.sFlag = this.sFlag; -r.ignoreCase = this.ignoreCase; -r.dontMatchInQuotes = this.dontMatchInQuotes; -if (this.optimizeMe) { -r.optimize (); -}}, "com.stevesoft.pat.Regex"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Regex"], "com.stevesoft.pat.Rthings", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.val = 0; +this.ignoreCase = false; +this.dontMatchInQuotes = false; +this.optimizeMe = false; +this.noBackRefs = false; +this.parenLevel = 0; +this.gFlag = false; +this.mFlag = false; +this.sFlag = false; +this.p = null; +this.o = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Rthings"); +Clazz.prepareFields (c$, function () { +this.val = com.stevesoft.pat.Regex.BackRefOffset; +}); +Clazz.makeConstructor (c$, +function (r) { +this.ignoreCase = r.ignoreCase; +this.dontMatchInQuotes = r.dontMatchInQuotes; +}, "com.stevesoft.pat.Regex"); +Clazz.defineMethod (c$, "set", +function (r) { +r.gFlag = this.gFlag; +r.mFlag = this.mFlag; +r.sFlag = this.sFlag; +r.ignoreCase = this.ignoreCase; +r.dontMatchInQuotes = this.dontMatchInQuotes; +if (this.optimizeMe) { +r.optimize (); +}}, "com.stevesoft.pat.Regex"); +}); diff --git a/bin/com/stevesoft/pat/RuleHolder.js b/bin/com/stevesoft/pat/RuleHolder.js index a628201..6924899 100644 --- a/bin/com/stevesoft/pat/RuleHolder.js +++ b/bin/com/stevesoft/pat/RuleHolder.js @@ -1,32 +1,32 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.RuleHolder", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.held = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "RuleHolder", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.RuleHolder, []); -}); -Clazz.makeConstructor (c$, -function (h) { -Clazz.superConstructor (this, com.stevesoft.pat.RuleHolder, []); -this.held = h; -}, "com.stevesoft.pat.ReplaceRule"); -Clazz.overrideMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.RuleHolder (this.held); -}); -Clazz.defineMethod (c$, "toString1", -function () { -return this.held.toString1 (); -}); -Clazz.defineMethod (c$, "apply", -function (sb, rr) { -this.held.apply (sb, rr); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.defineMethod (c$, "arg", -function (s) { -return new com.stevesoft.pat.RuleHolder (this.held.arg (s)); -}, "~S"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.RuleHolder", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.held = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "RuleHolder", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.RuleHolder, []); +}); +Clazz.makeConstructor (c$, +function (h) { +Clazz.superConstructor (this, com.stevesoft.pat.RuleHolder, []); +this.held = h; +}, "com.stevesoft.pat.ReplaceRule"); +Clazz.overrideMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.RuleHolder (this.held); +}); +Clazz.defineMethod (c$, "toString1", +function () { +return this.held.toString1 (); +}); +Clazz.defineMethod (c$, "apply", +function (sb, rr) { +this.held.apply (sb, rr); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.defineMethod (c$, "arg", +function (s) { +return new com.stevesoft.pat.RuleHolder (this.held.arg (s)); +}, "~S"); +}); diff --git a/bin/com/stevesoft/pat/Skip.js b/bin/com/stevesoft/pat/Skip.js index bdf02e4..6dd2756 100644 --- a/bin/com/stevesoft/pat/Skip.js +++ b/bin/com/stevesoft/pat/Skip.js @@ -1,108 +1,108 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.Skip", ["com.stevesoft.pat.CaseMgr", "$.Or", "$.Skipped", "$.oneChar", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.src = null; -this.c = 0; -this.mask = 0; -this.$offset = 0; -this.ign = false; -this.m1 = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Skip"); -c$.mkmask = Clazz.defineMethod (c$, "mkmask", -function (c) { -var x = String.fromCharCode (c); -return ~((com.stevesoft.pat.CaseMgr.toUpperCaseC (x)).charCodeAt (0) | (com.stevesoft.pat.CaseMgr.toLowerCaseC (x)).charCodeAt (0) | (com.stevesoft.pat.CaseMgr.toTitleCaseC (x)).charCodeAt (0)); -}, "~N"); -c$.string = Clazz.defineMethod (c$, "string", -function (r) { -return r.skipper == null ? null : r.skipper.src; -}, "com.stevesoft.pat.Regex"); -c$.offset = Clazz.defineMethod (c$, "offset", -function (r) { -return r.skipper == null ? -1 : r.skipper.$offset; -}, "com.stevesoft.pat.Regex"); -Clazz.makeConstructor (c$, -function (s, ign, o) { -this.src = s; -this.c = s.charCodeAt (0); -if (ign) { -this.mask = com.stevesoft.pat.Skip.mkmask (this.c); -} else { -this.mask = 0; -}this.$offset = o; -this.ign = ign; -this.m1 = (s.length == 1); -}, "~S,~B,~N"); -Clazz.defineMethod (c$, "find", -function (s) { -return this.find (s, 0, s.length ()); -}, "com.stevesoft.pat.StringLike"); -c$.min = Clazz.defineMethod (c$, "min", -function (a, b) { -return a < b ? a : b; -}, "~N,~N"); -Clazz.defineMethod (c$, "find", -function (s, start, end) { -if (start > end) { -return -1; -}start += this.$offset; -var vend = com.stevesoft.pat.Skip.min (s.length () - 1, end + this.$offset); -if (this.mask != this.c) { -for (var i = start; i <= vend; i++) { -if (0 == (s.charCodeAt (i) & this.mask)) { -if (this.m1 || com.stevesoft.pat.CaseMgr.regionMatchesLike2 (s, this.ign, i, this.src, 0, this.src.length)) { -return i - this.$offset; -}}} -} else { -for (var i = start; i <= vend; i++) { -if (this.c == s.charCodeAt (i)) { -if (this.m1 || com.stevesoft.pat.CaseMgr.regionMatchesLike2 (s, this.ign, i, this.src, 0, this.src.length)) { -return i - this.$offset; -}}} -}return -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -c$.findSkipRegex = Clazz.defineMethod (c$, "findSkipRegex", -function (r) { -return com.stevesoft.pat.Skip.findSkip (r.thePattern, r.ignoreCase, !r.dontMatchInQuotes); -}, "com.stevesoft.pat.Regex"); -c$.findSkip = Clazz.defineMethod (c$, "findSkip", -function (p, ignoreCase, trnc) { -var sb = new StringBuffer (); -var subsk = null; -var offset = 0; -var skipc = -1; -var skipoff = 0; -for (; p != null; p = p.next) { -if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar)) { -skipc = ((p).c).charCodeAt (0); -skipoff = offset; -}if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar) && Clazz.instanceOf (p.next, com.stevesoft.pat.oneChar)) { -var psav = p; -sb.append ((p).c); -while (Clazz.instanceOf (p.next, com.stevesoft.pat.oneChar)) { -sb.append ((p.next).c); -p = p.next; -} -var st = sb.toString (); -var sk = null; -if (st.length > 2) { -sk = new com.stevesoft.pat.SkipBMH (st, ignoreCase, offset); -} else { -sk = new com.stevesoft.pat.Skip2 (st, ignoreCase, offset); -}if (trnc && st.length > 2) { -psav.next = new com.stevesoft.pat.Skipped (st.substring (1)); -psav.next.next = p.next; -psav.next.parent = p.parent; -}return sk; -} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or) && (p).v.size () == 1 && !(p).leftForm ().equals ("(?!") && null != (subsk = com.stevesoft.pat.Skip.findSkip ((p).v.elementAt (0), ignoreCase, trnc))) { -subsk.$offset += offset; -return subsk; -} else if (p.minChars ().equals (p.maxChars ())) { -offset += p.minChars ().intValue (); -} else { -return skipc < 0 ? null : new com.stevesoft.pat.Skip ("" + String.fromCharCode (skipc), ignoreCase, skipoff); -}} -return null; -}, "com.stevesoft.pat.Pattern,~B,~B"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.Skip", ["com.stevesoft.pat.CaseMgr", "$.Or", "$.Skipped", "$.oneChar", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.src = null; +this.c = 0; +this.mask = 0; +this.$offset = 0; +this.ign = false; +this.m1 = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Skip"); +c$.mkmask = Clazz.defineMethod (c$, "mkmask", +function (c) { +var x = String.fromCharCode (c); +return ~((com.stevesoft.pat.CaseMgr.toUpperCaseC (x)).charCodeAt (0) | (com.stevesoft.pat.CaseMgr.toLowerCaseC (x)).charCodeAt (0) | (com.stevesoft.pat.CaseMgr.toTitleCaseC (x)).charCodeAt (0)); +}, "~N"); +c$.string = Clazz.defineMethod (c$, "string", +function (r) { +return r.skipper == null ? null : r.skipper.src; +}, "com.stevesoft.pat.Regex"); +c$.offset = Clazz.defineMethod (c$, "offset", +function (r) { +return r.skipper == null ? -1 : r.skipper.$offset; +}, "com.stevesoft.pat.Regex"); +Clazz.makeConstructor (c$, +function (s, ign, o) { +this.src = s; +this.c = s.charCodeAt (0); +if (ign) { +this.mask = com.stevesoft.pat.Skip.mkmask (this.c); +} else { +this.mask = 0; +}this.$offset = o; +this.ign = ign; +this.m1 = (s.length == 1); +}, "~S,~B,~N"); +Clazz.defineMethod (c$, "find", +function (s) { +return this.find (s, 0, s.length ()); +}, "com.stevesoft.pat.StringLike"); +c$.min = Clazz.defineMethod (c$, "min", +function (a, b) { +return a < b ? a : b; +}, "~N,~N"); +Clazz.defineMethod (c$, "find", +function (s, start, end) { +if (start > end) { +return -1; +}start += this.$offset; +var vend = com.stevesoft.pat.Skip.min (s.length () - 1, end + this.$offset); +if (this.mask != this.c) { +for (var i = start; i <= vend; i++) { +if (0 == (s.charCodeAt (i) & this.mask)) { +if (this.m1 || com.stevesoft.pat.CaseMgr.regionMatchesLike2 (s, this.ign, i, this.src, 0, this.src.length)) { +return i - this.$offset; +}}} +} else { +for (var i = start; i <= vend; i++) { +if (this.c == s.charCodeAt (i)) { +if (this.m1 || com.stevesoft.pat.CaseMgr.regionMatchesLike2 (s, this.ign, i, this.src, 0, this.src.length)) { +return i - this.$offset; +}}} +}return -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +c$.findSkipRegex = Clazz.defineMethod (c$, "findSkipRegex", +function (r) { +return com.stevesoft.pat.Skip.findSkip (r.thePattern, r.ignoreCase, !r.dontMatchInQuotes); +}, "com.stevesoft.pat.Regex"); +c$.findSkip = Clazz.defineMethod (c$, "findSkip", +function (p, ignoreCase, trnc) { +var sb = new StringBuffer (); +var subsk = null; +var offset = 0; +var skipc = -1; +var skipoff = 0; +for (; p != null; p = p.next) { +if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar)) { +skipc = ((p).c).charCodeAt (0); +skipoff = offset; +}if (Clazz.instanceOf (p, com.stevesoft.pat.oneChar) && Clazz.instanceOf (p.next, com.stevesoft.pat.oneChar)) { +var psav = p; +sb.append ((p).c); +while (Clazz.instanceOf (p.next, com.stevesoft.pat.oneChar)) { +sb.append ((p.next).c); +p = p.next; +} +var st = sb.toString (); +var sk = null; +if (st.length > 2) { +sk = new com.stevesoft.pat.SkipBMH (st, ignoreCase, offset); +} else { +sk = new com.stevesoft.pat.Skip2 (st, ignoreCase, offset); +}if (trnc && st.length > 2) { +psav.next = new com.stevesoft.pat.Skipped (st.substring (1)); +psav.next.next = p.next; +psav.next.parent = p.parent; +}return sk; +} else if (Clazz.instanceOf (p, com.stevesoft.pat.Or) && (p).v.size () == 1 && !(p).leftForm ().equals ("(?!") && null != (subsk = com.stevesoft.pat.Skip.findSkip ((p).v.elementAt (0), ignoreCase, trnc))) { +subsk.$offset += offset; +return subsk; +} else if (p.minChars ().equals (p.maxChars ())) { +offset += p.minChars ().intValue (); +} else { +return skipc < 0 ? null : new com.stevesoft.pat.Skip ("" + String.fromCharCode (skipc), ignoreCase, skipoff); +}} +return null; +}, "com.stevesoft.pat.Pattern,~B,~B"); +}); diff --git a/bin/com/stevesoft/pat/Skip2.js b/bin/com/stevesoft/pat/Skip2.js index c06b56e..e69b45e 100644 --- a/bin/com/stevesoft/pat/Skip2.js +++ b/bin/com/stevesoft/pat/Skip2.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Skip"], "com.stevesoft.pat.Skip2", ["com.stevesoft.pat.CaseMgr"], function () { -c$ = Clazz.decorateAsClass (function () { -this.c1 = 0; -this.mask1 = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Skip2", com.stevesoft.pat.Skip); -Clazz.makeConstructor (c$, -function (s, ign, offset) { -Clazz.superConstructor (this, com.stevesoft.pat.Skip2, [s, ign, offset]); -this.c1 = s.charCodeAt (1); -this.m1 = 2 == s.length; -if (ign) { -this.mask1 = com.stevesoft.pat.Skip.mkmask (this.c1); -} else { -this.mask1 = 0; -}}, "~S,~B,~N"); -Clazz.defineMethod (c$, "find", -function (s, start, end) { -if (start > end) { -return -1; -}start += this.$offset; -var vend = com.stevesoft.pat.Skip.min (s.length () - 2, end + this.$offset); -for (var i = start; i <= vend; i++) { -if (0 == (s.charCodeAt (i) & this.mask) && 0 == (s.charCodeAt (i + 1) & this.mask1)) { -if (this.m1 || com.stevesoft.pat.CaseMgr.regionMatchesLike2 (s, this.ign, i, this.src, 0, this.src.length)) { -return i - this.$offset; -}}} -return -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Skip"], "com.stevesoft.pat.Skip2", ["com.stevesoft.pat.CaseMgr"], function () { +c$ = Clazz.decorateAsClass (function () { +this.c1 = 0; +this.mask1 = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Skip2", com.stevesoft.pat.Skip); +Clazz.makeConstructor (c$, +function (s, ign, offset) { +Clazz.superConstructor (this, com.stevesoft.pat.Skip2, [s, ign, offset]); +this.c1 = s.charCodeAt (1); +this.m1 = 2 == s.length; +if (ign) { +this.mask1 = com.stevesoft.pat.Skip.mkmask (this.c1); +} else { +this.mask1 = 0; +}}, "~S,~B,~N"); +Clazz.defineMethod (c$, "find", +function (s, start, end) { +if (start > end) { +return -1; +}start += this.$offset; +var vend = com.stevesoft.pat.Skip.min (s.length () - 2, end + this.$offset); +for (var i = start; i <= vend; i++) { +if (0 == (s.charCodeAt (i) & this.mask) && 0 == (s.charCodeAt (i + 1) & this.mask1)) { +if (this.m1 || com.stevesoft.pat.CaseMgr.regionMatchesLike2 (s, this.ign, i, this.src, 0, this.src.length)) { +return i - this.$offset; +}}} +return -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +}); diff --git a/bin/com/stevesoft/pat/SkipBMH.js b/bin/com/stevesoft/pat/SkipBMH.js index 9ea4116..ac81e43 100644 --- a/bin/com/stevesoft/pat/SkipBMH.js +++ b/bin/com/stevesoft/pat/SkipBMH.js @@ -1,154 +1,154 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Skip"], "com.stevesoft.pat.SkipBMH", ["com.stevesoft.pat.CaseMgr", "com.stevesoft.pat.wrap.StringWrap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.MAX_CHAR = 64; -this.skip = null; -this.sm1 = 0; -this.jump_ahead = 0; -this.uc = '\0'; -this.lc = '\0'; -this.tc = '\0'; -this.x = '\0'; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "SkipBMH", com.stevesoft.pat.Skip); -Clazz.prepareFields (c$, function () { -this.skip = Clazz.newCharArray (64, '\0'); -}); -Clazz.defineMethod (c$, "exact", -function (c) { -return (this.ign && this.anyc (c)) || c == this.x; -}, "~S"); -Clazz.defineMethod (c$, "anyc", -function (c) { -return c == this.uc || c == this.lc || c == this.tc; -}, "~S"); -Clazz.makeConstructor (c$, -function (pt, ign) { -this.construct (pt, ign, 0); -}, "~S,~B"); -Clazz.makeConstructor (c$, -function (pt) { -this.construct (pt, false, 0); -}, "~S"); -Clazz.makeConstructor (c$, -function (pt, ign, offset) { -Clazz.superConstructor (this, com.stevesoft.pat.SkipBMH, [pt, ign, offset]); -for (var k = 0; k < 64; k++) { -this.skip[k] = String.fromCharCode (this.src.length); -} -this.sm1 = this.src.length - 1; -this.x = this.src.charAt (this.sm1); -this.uc = com.stevesoft.pat.CaseMgr.toUpperCaseC (this.x); -this.lc = com.stevesoft.pat.CaseMgr.toLowerCaseC (this.x); -this.tc = com.stevesoft.pat.CaseMgr.toTitleCaseC (this.x); -for (var k = 0; k < this.src.length - 1; k++) { -var x_ = this.src.charAt (k); -if (ign) { -var uc_ = com.stevesoft.pat.CaseMgr.toUpperCaseC (x_); -var lc_ = com.stevesoft.pat.CaseMgr.toLowerCaseC (x_); -var tc_ = com.stevesoft.pat.CaseMgr.toTitleCaseC (x_); -this.skip[uc_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); -this.skip[lc_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); -this.skip[tc_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); -} else { -this.skip[x_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); -}} -this.jump_ahead = this.src.length - 1; -for (var k = 0; k < this.src.length - 1; k++) { -var y = this.src.charAt (this.sm1 - k - 1); -if (this.exact (y)) { -this.jump_ahead = k; -break; -}} -}, "~S,~B,~N"); -Clazz.defineMethod (c$, "searchRegion", -function (s, start, end) { -return this.find (s, start, end); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "searchFrom", -function (s, start) { -return this.find (s, start, s.length); -}, "~S,~N"); -Clazz.defineMethod (c$, "search", -function (s) { -return this.find (s, 0, s.length); -}, "~S"); -Clazz.defineMethod (c$, "find", -function (s, start, end) { -start += this.$offset + this.sm1; -var vend = com.stevesoft.pat.Skip.min (s.length - 1, end + this.sm1 + this.$offset); -var k; -var vend1 = vend - this.jump_ahead; -if (this.ign) { -for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.anyc (s.charAt (k))) { -if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -}} -for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.anyc (s.charAt (k))) { -if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -if (k > vend) { -return -1; -}}} -} else { -for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.x == s.charAt (k)) { -if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, false, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -}} -for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.x == s.charAt (k)) { -if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, false, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -if (k > vend) { -return -1; -}}} -}return -1; -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "find", -function (s, start, end) { -if (Clazz.instanceOf (s, com.stevesoft.pat.wrap.StringWrap)) { -return this.find (s.toString (), start, end); -}start += this.$offset + this.sm1; -var vend = com.stevesoft.pat.Skip.min (s.length () - 1, end + this.sm1 + this.$offset); -var k; -var vend1 = vend - this.jump_ahead; -if (this.ign) { -for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.anyc (s.charAt (k))) { -if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -}} -for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.anyc (s.charAt (k))) { -if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -if (k > vend) { -return -1; -}}} -} else { -for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.x == s.charAt (k)) { -if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, false, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -}} -for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { -if (this.x == s.charAt (k)) { -if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, false, 0, s, k - this.sm1, this.sm1)) { -return k - this.sm1 - this.$offset; -}k += this.jump_ahead; -if (k > vend) { -return -1; -}}} -}return -1; -}, "com.stevesoft.pat.StringLike,~N,~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Skip"], "com.stevesoft.pat.SkipBMH", ["com.stevesoft.pat.CaseMgr", "com.stevesoft.pat.wrap.StringWrap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.MAX_CHAR = 64; +this.skip = null; +this.sm1 = 0; +this.jump_ahead = 0; +this.uc = '\0'; +this.lc = '\0'; +this.tc = '\0'; +this.x = '\0'; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "SkipBMH", com.stevesoft.pat.Skip); +Clazz.prepareFields (c$, function () { +this.skip = Clazz.newCharArray (64, '\0'); +}); +Clazz.defineMethod (c$, "exact", +function (c) { +return (this.ign && this.anyc (c)) || c == this.x; +}, "~S"); +Clazz.defineMethod (c$, "anyc", +function (c) { +return c == this.uc || c == this.lc || c == this.tc; +}, "~S"); +Clazz.makeConstructor (c$, +function (pt, ign) { +this.construct (pt, ign, 0); +}, "~S,~B"); +Clazz.makeConstructor (c$, +function (pt) { +this.construct (pt, false, 0); +}, "~S"); +Clazz.makeConstructor (c$, +function (pt, ign, offset) { +Clazz.superConstructor (this, com.stevesoft.pat.SkipBMH, [pt, ign, offset]); +for (var k = 0; k < 64; k++) { +this.skip[k] = String.fromCharCode (this.src.length); +} +this.sm1 = this.src.length - 1; +this.x = this.src.charAt (this.sm1); +this.uc = com.stevesoft.pat.CaseMgr.toUpperCaseC (this.x); +this.lc = com.stevesoft.pat.CaseMgr.toLowerCaseC (this.x); +this.tc = com.stevesoft.pat.CaseMgr.toTitleCaseC (this.x); +for (var k = 0; k < this.src.length - 1; k++) { +var x_ = this.src.charAt (k); +if (ign) { +var uc_ = com.stevesoft.pat.CaseMgr.toUpperCaseC (x_); +var lc_ = com.stevesoft.pat.CaseMgr.toLowerCaseC (x_); +var tc_ = com.stevesoft.pat.CaseMgr.toTitleCaseC (x_); +this.skip[uc_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); +this.skip[lc_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); +this.skip[tc_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); +} else { +this.skip[x_.charCodeAt (0) & (63)] = String.fromCharCode (this.src.length - k - 1); +}} +this.jump_ahead = this.src.length - 1; +for (var k = 0; k < this.src.length - 1; k++) { +var y = this.src.charAt (this.sm1 - k - 1); +if (this.exact (y)) { +this.jump_ahead = k; +break; +}} +}, "~S,~B,~N"); +Clazz.defineMethod (c$, "searchRegion", +function (s, start, end) { +return this.find (s, start, end); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "searchFrom", +function (s, start) { +return this.find (s, start, s.length); +}, "~S,~N"); +Clazz.defineMethod (c$, "search", +function (s) { +return this.find (s, 0, s.length); +}, "~S"); +Clazz.defineMethod (c$, "find", +function (s, start, end) { +start += this.$offset + this.sm1; +var vend = com.stevesoft.pat.Skip.min (s.length - 1, end + this.sm1 + this.$offset); +var k; +var vend1 = vend - this.jump_ahead; +if (this.ign) { +for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.anyc (s.charAt (k))) { +if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +}} +for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.anyc (s.charAt (k))) { +if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +if (k > vend) { +return -1; +}}} +} else { +for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.x == s.charAt (k)) { +if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, false, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +}} +for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.x == s.charAt (k)) { +if (com.stevesoft.pat.CaseMgr.regionMatches2 (this.src, false, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +if (k > vend) { +return -1; +}}} +}return -1; +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "find", +function (s, start, end) { +if (Clazz.instanceOf (s, com.stevesoft.pat.wrap.StringWrap)) { +return this.find (s.toString (), start, end); +}start += this.$offset + this.sm1; +var vend = com.stevesoft.pat.Skip.min (s.length () - 1, end + this.sm1 + this.$offset); +var k; +var vend1 = vend - this.jump_ahead; +if (this.ign) { +for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.anyc (s.charAt (k))) { +if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +}} +for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.anyc (s.charAt (k))) { +if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, this.ign, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +if (k > vend) { +return -1; +}}} +} else { +for (k = start; k <= vend1; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.x == s.charAt (k)) { +if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, false, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +}} +for (; k <= vend; k += (this.skip[s.charCodeAt (k) & (63)]).charCodeAt (0)) { +if (this.x == s.charAt (k)) { +if (com.stevesoft.pat.CaseMgr.regionMatches (this.src, false, 0, s, k - this.sm1, this.sm1)) { +return k - this.sm1 - this.$offset; +}k += this.jump_ahead; +if (k > vend) { +return -1; +}}} +}return -1; +}, "com.stevesoft.pat.StringLike,~N,~N"); +}); diff --git a/bin/com/stevesoft/pat/Skipped.js b/bin/com/stevesoft/pat/Skipped.js index 07c5ca9..8f6f1d3 100644 --- a/bin/com/stevesoft/pat/Skipped.js +++ b/bin/com/stevesoft/pat/Skipped.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Skipped", ["com.stevesoft.pat.CaseMgr", "$.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.s = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Skipped", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (s) { -Clazz.superConstructor (this, com.stevesoft.pat.Skipped, []); -this.s = s; -}, "~S"); -Clazz.overrideMethod (c$, "toString", -function () { -return this.s + this.nextString (); -}); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (pt.no_check || com.stevesoft.pat.CaseMgr.regionMatches (this.s, pt.ignoreCase, 0, pt.src, pos, this.s.length)) { -return this.nextMatch (pos + this.s.length, pt); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (this.s.length); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (this.s.length); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.Skipped (this.s); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Skipped", ["com.stevesoft.pat.CaseMgr", "$.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.s = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Skipped", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (s) { +Clazz.superConstructor (this, com.stevesoft.pat.Skipped, []); +this.s = s; +}, "~S"); +Clazz.overrideMethod (c$, "toString", +function () { +return this.s + this.nextString (); +}); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (pt.no_check || com.stevesoft.pat.CaseMgr.regionMatches (this.s, pt.ignoreCase, 0, pt.src, pos, this.s.length)) { +return this.nextMatch (pos + this.s.length, pt); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (this.s.length); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (this.s.length); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.Skipped (this.s); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/SpecialRule.js b/bin/com/stevesoft/pat/SpecialRule.js index 13dfbe5..aed49a6 100644 --- a/bin/com/stevesoft/pat/SpecialRule.js +++ b/bin/com/stevesoft/pat/SpecialRule.js @@ -1,11 +1,11 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.SpecialRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "SpecialRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.SpecialRule, []); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, rr) { -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.SpecialRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "SpecialRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.SpecialRule, []); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, rr) { +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +}); diff --git a/bin/com/stevesoft/pat/Start.js b/bin/com/stevesoft/pat/Start.js index 56168b1..1ef02d7 100644 --- a/bin/com/stevesoft/pat/Start.js +++ b/bin/com/stevesoft/pat/Start.js @@ -1,35 +1,35 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Start", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.retIsStart = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Start", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (b) { -Clazz.superConstructor (this, com.stevesoft.pat.Start, []); -this.retIsStart = b; -}, "~B"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -if (this.retIsStart && pt.mFlag && pos > 0 && pt.src.charAt (pos - 1) == '\n') { -return this.nextMatch (pos, pt); -}if (pos == 0) { -return this.nextMatch (pos, pt); -}return -1; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -if (this.retIsStart) { -return "^" + this.nextString (); -} else { -return "\\A" + this.nextString (); -}}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.Start (this.retIsStart); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.Start", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.retIsStart = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Start", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (b) { +Clazz.superConstructor (this, com.stevesoft.pat.Start, []); +this.retIsStart = b; +}, "~B"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +if (this.retIsStart && pt.mFlag && pos > 0 && pt.src.charAt (pos - 1) == '\n') { +return this.nextMatch (pos, pt); +}if (pos == 0) { +return this.nextMatch (pos, pt); +}return -1; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +if (this.retIsStart) { +return "^" + this.nextString (); +} else { +return "\\A" + this.nextString (); +}}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.Start (this.retIsStart); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/StrPos.class b/bin/com/stevesoft/pat/StrPos.class index 249075c..cc761f6 100644 Binary files a/bin/com/stevesoft/pat/StrPos.class and b/bin/com/stevesoft/pat/StrPos.class differ diff --git a/bin/com/stevesoft/pat/StrPos.js b/bin/com/stevesoft/pat/StrPos.js index fb1baf4..366f46b 100644 --- a/bin/com/stevesoft/pat/StrPos.js +++ b/bin/com/stevesoft/pat/StrPos.js @@ -1,109 +1,109 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.StrPos", ["com.stevesoft.pat.patInf", "$.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.s = null; -this.$pos = 0; -this.esc = '\\'; -this.c = '\0'; -this.dontMatch = false; -this.$eos = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "StrPos"); -Clazz.defineMethod (c$, "pos", -function () { -return this.$pos; -}); -Clazz.defineMethod (c$, "thisChar", -function () { -return this.c; -}); -Clazz.defineMethod (c$, "eos", -function () { -return this.$eos; -}); -Clazz.makeConstructor (c$, -function (sp) { -this.dup (sp); -}, "com.stevesoft.pat.StrPos"); -Clazz.defineMethod (c$, "dup", -function (sp) { -this.s = sp.s; -this.$pos = sp.$pos; -this.c = sp.c; -this.dontMatch = sp.dontMatch; -this.$eos = sp.$eos; -}, "com.stevesoft.pat.StrPos"); -Clazz.makeConstructor (c$, -function (s, pos) { -this.s = s; -this.$pos = pos - 1; -this.inc (); -}, "~S,~N"); -Clazz.defineMethod (c$, "inc", -function () { -this.$pos++; -if (this.$pos >= this.s.length) { -this.$eos = true; -return this; -}this.$eos = false; -this.c = this.s.charAt (this.$pos); -if (this.c == this.esc && this.$pos + 1 < this.s.length) { -this.$pos++; -this.c = this.s.charAt (this.$pos); -if (this.c != this.esc) { -this.dontMatch = true; -} else { -this.dontMatch = false; -}} else { -this.dontMatch = false; -}return this; -}); -Clazz.defineMethod (c$, "match", -function (ch) { -if (this.dontMatch || this.$eos) { -return false; -}return this.c == ch; -}, "~S"); -Clazz.defineMethod (c$, "escMatch", -function (ch) { -if (!this.dontMatch || this.$eos) { -return false; -}return this.c == ch; -}, "~S"); -Clazz.defineMethod (c$, "escaped", -function () { -return this.dontMatch; -}); -Clazz.defineMethod (c$, "incMatch", -function (st) { -var sp = new com.stevesoft.pat.StrPos (this); -var i; -for (i = 0; i < st.length; i++) { -if (!sp.match (st.charAt (i))) { -return false; -}sp.inc (); -} -this.dup (sp); -return true; -}, "~S"); -Clazz.defineMethod (c$, "getPatInt", -function () { -if (this.incMatch ("inf")) { -return new com.stevesoft.pat.patInf (); -}var i; -var cnt = 0; -var sp = new com.stevesoft.pat.StrPos (this); -for (i = 0; !sp.$eos && sp.c >= '0' && sp.c <= '9'; i++) { -cnt = 10 * cnt + sp.c.charCodeAt (0) - 48; -sp.inc (); -} -if (i == 0) { -return null; -}this.dup (sp); -return new com.stevesoft.pat.patInt (cnt); -}); -Clazz.defineMethod (c$, "getString", -function () { -return this.s; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.StrPos", ["com.stevesoft.pat.patInf", "$.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.s = null; +this.$pos = 0; +this.esc = '\\'; +this.c = '\0'; +this.dontMatch = false; +this.$eos = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "StrPos"); +Clazz.defineMethod (c$, "pos", +function () { +return this.$pos; +}); +Clazz.defineMethod (c$, "thisChar", +function () { +return this.c; +}); +Clazz.defineMethod (c$, "eos", +function () { +return this.$eos; +}); +Clazz.makeConstructor (c$, +function (sp) { +this.dup (sp); +}, "com.stevesoft.pat.StrPos"); +Clazz.defineMethod (c$, "dup", +function (sp) { +this.s = sp.s; +this.$pos = sp.$pos; +this.c = sp.c; +this.dontMatch = sp.dontMatch; +this.$eos = sp.$eos; +}, "com.stevesoft.pat.StrPos"); +Clazz.makeConstructor (c$, +function (s, pos) { +this.s = s; +this.$pos = pos - 1; +this.inc (); +}, "~S,~N"); +Clazz.defineMethod (c$, "inc", +function () { +this.$pos++; +if (this.$pos >= this.s.length) { +this.$eos = true; +return this; +}this.$eos = false; +this.c = this.s.charAt (this.$pos); +if (this.c == this.esc && this.$pos + 1 < this.s.length) { +this.$pos++; +this.c = this.s.charAt (this.$pos); +if (this.c != this.esc) { +this.dontMatch = true; +} else { +this.dontMatch = false; +}} else { +this.dontMatch = false; +}return this; +}); +Clazz.defineMethod (c$, "match", +function (ch) { +if (this.dontMatch || this.$eos) { +return false; +}return this.c == ch; +}, "~S"); +Clazz.defineMethod (c$, "escMatch", +function (ch) { +if (!this.dontMatch || this.$eos) { +return false; +}return this.c == ch; +}, "~S"); +Clazz.defineMethod (c$, "escaped", +function () { +return this.dontMatch; +}); +Clazz.defineMethod (c$, "incMatch", +function (st) { +var sp = new com.stevesoft.pat.StrPos (this); +var i; +for (i = 0; i < st.length; i++) { +if (!sp.match (st.charAt (i))) { +return false; +}sp.inc (); +} +this.dup (sp); +return true; +}, "~S"); +Clazz.defineMethod (c$, "getPatInt", +function () { +if (this.incMatch ("inf")) { +return new com.stevesoft.pat.patInf (); +}var i; +var cnt = 0; +var sp = new com.stevesoft.pat.StrPos (this); +for (i = 0; !sp.$eos && sp.c >= '0' && sp.c <= '9'; i++) { +cnt = 10 * cnt + sp.c.charCodeAt (0) - 48; +sp.inc (); +} +if (i == 0) { +return null; +}this.dup (sp); +return new com.stevesoft.pat.patInt (cnt); +}); +Clazz.defineMethod (c$, "getString", +function () { +return this.s; +}); +}); diff --git a/bin/com/stevesoft/pat/StringBufferLike.class b/bin/com/stevesoft/pat/StringBufferLike.class index 6426a06..0bfeef2 100644 Binary files a/bin/com/stevesoft/pat/StringBufferLike.class and b/bin/com/stevesoft/pat/StringBufferLike.class differ diff --git a/bin/com/stevesoft/pat/StringBufferLike.js b/bin/com/stevesoft/pat/StringBufferLike.js index 2455329..fd5b6c3 100644 --- a/bin/com/stevesoft/pat/StringBufferLike.js +++ b/bin/com/stevesoft/pat/StringBufferLike.js @@ -1,62 +1,62 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.BasicStringBufferLike"], "com.stevesoft.pat.StringBufferLike", ["com.stevesoft.pat.CaseMgr"], function () { -c$ = Clazz.decorateAsClass (function () { -this.sbl = null; -this.mode = 'E'; -this.altMode = ' '; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "StringBufferLike", null, com.stevesoft.pat.BasicStringBufferLike); -Clazz.makeConstructor (c$, -function (sbl) { -this.sbl = sbl; -}, "com.stevesoft.pat.BasicStringBufferLike"); -Clazz.defineMethod (c$, "toStringLike", -function () { -return this.sbl.toStringLike (); -}); -Clazz.defineMethod (c$, "toString", -function () { -return this.sbl.toString (); -}); -Clazz.defineMethod (c$, "appendC", -function (c) { -switch (this.mode) { -case 'u': -this.mode = this.altMode; -this.altMode = ' '; -case 'U': -this.sbl.appendC (com.stevesoft.pat.CaseMgr.toUpperCaseC (c)); -break; -case 'l': -this.mode = this.altMode; -this.altMode = ' '; -case 'L': -this.sbl.appendC (com.stevesoft.pat.CaseMgr.toLowerCaseC (c)); -break; -case 'Q': -if ((c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z') || (c >= '0' && c <= '9')) { -;} else { -this.sbl.appendC ('\\'); -}default: -this.sbl.appendC (c); -break; -} -}, "~S"); -Clazz.overrideMethod (c$, "append", -function (s) { -for (var i = 0; i < s.length; i++) { -this.appendC (s.charAt (i)); -} -}, "~S"); -Clazz.defineMethod (c$, "setMode", -function (c) { -if (c == 'u' || c == 'l') { -if (this.altMode == ' ') { -this.altMode = this.mode; -}}this.mode = c; -}, "~S"); -Clazz.defineMethod (c$, "unwrap", -function () { -return this.sbl.unwrap (); -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.BasicStringBufferLike"], "com.stevesoft.pat.StringBufferLike", ["com.stevesoft.pat.CaseMgr"], function () { +c$ = Clazz.decorateAsClass (function () { +this.sbl = null; +this.mode = 'E'; +this.altMode = ' '; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "StringBufferLike", null, com.stevesoft.pat.BasicStringBufferLike); +Clazz.makeConstructor (c$, +function (sbl) { +this.sbl = sbl; +}, "com.stevesoft.pat.BasicStringBufferLike"); +Clazz.defineMethod (c$, "toStringLike", +function () { +return this.sbl.toStringLike (); +}); +Clazz.defineMethod (c$, "toString", +function () { +return this.sbl.toString (); +}); +Clazz.defineMethod (c$, "appendC", +function (c) { +switch (this.mode) { +case 'u': +this.mode = this.altMode; +this.altMode = ' '; +case 'U': +this.sbl.appendC (com.stevesoft.pat.CaseMgr.toUpperCaseC (c)); +break; +case 'l': +this.mode = this.altMode; +this.altMode = ' '; +case 'L': +this.sbl.appendC (com.stevesoft.pat.CaseMgr.toLowerCaseC (c)); +break; +case 'Q': +if ((c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z') || (c >= '0' && c <= '9')) { +;} else { +this.sbl.appendC ('\\'); +}default: +this.sbl.appendC (c); +break; +} +}, "~S"); +Clazz.overrideMethod (c$, "append", +function (s) { +for (var i = 0; i < s.length; i++) { +this.appendC (s.charAt (i)); +} +}, "~S"); +Clazz.defineMethod (c$, "setMode", +function (c) { +if (c == 'u' || c == 'l') { +if (this.altMode == ' ') { +this.altMode = this.mode; +}}this.mode = c; +}, "~S"); +Clazz.defineMethod (c$, "unwrap", +function () { +return this.sbl.unwrap (); +}); +}); diff --git a/bin/com/stevesoft/pat/StringLike.js b/bin/com/stevesoft/pat/StringLike.js index c677532..12b2dc9 100644 --- a/bin/com/stevesoft/pat/StringLike.js +++ b/bin/com/stevesoft/pat/StringLike.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.declareInterface (com.stevesoft.pat, "StringLike"); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.declareInterface (com.stevesoft.pat, "StringLike"); diff --git a/bin/com/stevesoft/pat/StringRule.js b/bin/com/stevesoft/pat/StringRule.js index aea8a98..1c04a68 100644 --- a/bin/com/stevesoft/pat/StringRule.js +++ b/bin/com/stevesoft/pat/StringRule.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.StringRule", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.s = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "StringRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function (s) { -Clazz.superConstructor (this, com.stevesoft.pat.StringRule, []); -this.s = s; -}, "~S"); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -sb.append (this.s); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return this.s; -}); -Clazz.overrideMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.StringRule (this.s); -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule"], "com.stevesoft.pat.StringRule", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.s = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "StringRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function (s) { +Clazz.superConstructor (this, com.stevesoft.pat.StringRule, []); +this.s = s; +}, "~S"); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +sb.append (this.s); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return this.s; +}); +Clazz.overrideMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.StringRule (this.s); +}); +}); diff --git a/bin/com/stevesoft/pat/SubMark.js b/bin/com/stevesoft/pat/SubMark.js index 0ea6b3a..9e1b5b8 100644 --- a/bin/com/stevesoft/pat/SubMark.js +++ b/bin/com/stevesoft/pat/SubMark.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.SubMark", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.end_pos = 0; -this.start_pos = 0; -this.om = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "SubMark", com.stevesoft.pat.Pattern); -Clazz.overrideMethod (c$, "toString", -function () { -return ""; -}); -Clazz.overrideMethod (c$, "matchInternal", -function (i, pt) { -pt.marks[this.om.id + pt.nMarks] = i; -var ret = this.nextMatch (i, pt); -if (ret < 0) { -pt.marks[this.om.id + pt.nMarks] = -1; -}return ret; -}, "~N,com.stevesoft.pat.Pthings"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.SubMark", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.end_pos = 0; +this.start_pos = 0; +this.om = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "SubMark", com.stevesoft.pat.Pattern); +Clazz.overrideMethod (c$, "toString", +function () { +return ""; +}); +Clazz.overrideMethod (c$, "matchInternal", +function (i, pt) { +pt.marks[this.om.id + pt.nMarks] = i; +var ret = this.nextMatch (i, pt); +if (ret < 0) { +pt.marks[this.om.id + pt.nMarks] = -1; +}return ret; +}, "~N,com.stevesoft.pat.Pthings"); +}); diff --git a/bin/com/stevesoft/pat/TransPat.js b/bin/com/stevesoft/pat/TransPat.js index ec296f1..65f32a1 100644 --- a/bin/com/stevesoft/pat/TransPat.js +++ b/bin/com/stevesoft/pat/TransPat.js @@ -1,35 +1,35 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.TransPat", ["com.stevesoft.pat.Regex"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ra = null; -this.ra_len = 0; -this.pn = -1; -this.lastMatchedTo = -1; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "TransPat", com.stevesoft.pat.Pattern); -Clazz.prepareFields (c$, function () { -this.ra = new Array (10); -}); -Clazz.overrideMethod (c$, "toString", -function () { -return "(?#TransPat)"; -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.TransPat, []); -}); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -for (var i = 0; i < this.ra_len; i++) { -pt.ignoreCase = this.ra[i].ignoreCase; -pt.mFlag = this.ra[i].mFlag; -pt.dotDoesntMatchCR = com.stevesoft.pat.Regex.dotDoesntMatchCR; -var r = this.ra[i].thePattern.matchInternal (pos, pt); -if (r >= 0) { -this.pn = i; -return r; -}} -this.pn = -1; -return -1; -}, "~N,com.stevesoft.pat.Pthings"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.TransPat", ["com.stevesoft.pat.Regex"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ra = null; +this.ra_len = 0; +this.pn = -1; +this.lastMatchedTo = -1; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "TransPat", com.stevesoft.pat.Pattern); +Clazz.prepareFields (c$, function () { +this.ra = new Array (10); +}); +Clazz.overrideMethod (c$, "toString", +function () { +return "(?#TransPat)"; +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.TransPat, []); +}); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +for (var i = 0; i < this.ra_len; i++) { +pt.ignoreCase = this.ra[i].ignoreCase; +pt.mFlag = this.ra[i].mFlag; +pt.dotDoesntMatchCR = com.stevesoft.pat.Regex.dotDoesntMatchCR; +var r = this.ra[i].thePattern.matchInternal (pos, pt); +if (r >= 0) { +this.pn = i; +return r; +}} +this.pn = -1; +return -1; +}, "~N,com.stevesoft.pat.Pthings"); +}); diff --git a/bin/com/stevesoft/pat/Transformer.js b/bin/com/stevesoft/pat/Transformer.js index 3d169f9..25ef39f 100644 --- a/bin/com/stevesoft/pat/Transformer.js +++ b/bin/com/stevesoft/pat/Transformer.js @@ -1,130 +1,130 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.ReplaceRule", "$.Replacer"], ["com.stevesoft.pat.Transformer", "$.TransRepRule"], ["com.stevesoft.pat.MessageManager", "$.Regex", "$.TransPat", "com.stevesoft.pat.wrap.StringWrap", "java.lang.ArrayIndexOutOfBoundsException", "$.NullPointerException"], function () { -c$ = Clazz.decorateAsClass (function () { -this.t = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "TransRepRule", com.stevesoft.pat.ReplaceRule); -Clazz.makeConstructor (c$, -function (t) { -Clazz.superConstructor (this, com.stevesoft.pat.TransRepRule, []); -this.t = t; -}, "com.stevesoft.pat.Transformer"); -Clazz.overrideMethod (c$, "toString1", -function () { -return ""; -}); -Clazz.overrideMethod (c$, "clone1", -function () { -return new com.stevesoft.pat.TransRepRule (this.t); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, rr) { -this.next = this.t.tp.ra[this.t.tp.pn].getReplaceRule (); -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -c$ = Clazz.decorateAsClass (function () { -this.tp = null; -this.rp = null; -this.auto_optimize = false; -this.repr = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Transformer"); -Clazz.prepareFields (c$, function () { -this.repr = new com.stevesoft.pat.Replacer (); -}); -Clazz.defineMethod (c$, "getReplacer", -function () { -return this.rp.getReplacer (); -}); -Clazz.makeConstructor (c$, -function (auto) { -this.rp = new com.stevesoft.pat.Regex (null, ""); -this.auto_optimize = auto; -this.tp = new com.stevesoft.pat.TransPat (); -this.rp.setReplaceRule ( new com.stevesoft.pat.TransRepRule (this)); -this.rp.thePattern = this.tp; -}, "~B"); -Clazz.defineMethod (c$, "add", -function (r) { -if (this.auto_optimize) { -r.optimize (); -}this.tp.ra[this.tp.ra_len++] = r; -if (this.tp.ra.length == this.tp.ra_len) { -var ra2 = new Array (this.tp.ra_len + 10); -for (var i = 0; i < this.tp.ra_len; i++) { -ra2[i] = this.tp.ra[i]; -} -this.tp.ra = ra2; -}this.rp.numSubs_ = r.numSubs_ > this.rp.numSubs_ ? r.numSubs_ : this.rp.numSubs_; -}, "com.stevesoft.pat.Regex"); -Clazz.defineMethod (c$, "patterns", -function () { -return this.tp.ra_len; -}); -Clazz.defineMethod (c$, "getRegexAt", -function (i) { -if (i >= this.tp.ra_len) { -throw new ArrayIndexOutOfBoundsException ("i=" + i + ">=" + this.patterns ()); -}if (i < 0) { -throw new ArrayIndexOutOfBoundsException ("i=" + i + "< 0"); -}return this.tp.ra[i]; -}, "~N"); -Clazz.defineMethod (c$, "setRegexAt", -function (rx, i) { -if (i >= this.tp.ra_len) { -throw new ArrayIndexOutOfBoundsException ("i=" + i + ">=" + this.patterns ()); -}if (i < 0) { -throw new ArrayIndexOutOfBoundsException ("i=" + i + "< 0"); -}this.tp.ra[i] = rx; -}, "com.stevesoft.pat.Regex,~N"); -Clazz.defineMethod (c$, "add", -function (rs) { -var r = com.stevesoft.pat.Regex.perlCode (rs); -if (r == null) { -throw new NullPointerException (com.stevesoft.pat.MessageManager.formatMessage ("exception.bad_pattern_to_regex_perl_code", Clazz.newArray (-1, [rs]))); -}this.add (r); -}, "~S"); -Clazz.defineMethod (c$, "add", -function (array) { -for (var i = 0; i < array.length; i++) { -this.add (array[i]); -} -}, "~A"); -Clazz.defineMethod (c$, "replaceAll", -function (s) { -return this.dorep (s, 0, s.length); -}, "~S"); -Clazz.defineMethod (c$, "replaceAll", -function (s) { -return this.dorep (s, 0, s.length ()); -}, "com.stevesoft.pat.StringLike"); -Clazz.defineMethod (c$, "replaceAllFrom", -function (s, start) { -return this.dorep (s, start, s.length); -}, "~S,~N"); -Clazz.defineMethod (c$, "replaceAllRegion", -function (s, start, end) { -return this.dorep (s, start, end); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "dorep", -function (s, start, end) { -var tfmd = this.repr.replaceAllRegion (s, this.rp, start, end); -this.tp.lastMatchedTo = this.repr.$lastMatchedTo; -return tfmd; -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "dorep", -function (s, start, end) { -return this.dorep ( new com.stevesoft.pat.wrap.StringWrap (s), start, end).toString (); -}, "~S,~N,~N"); -Clazz.defineMethod (c$, "replaceFirst", -function (s) { -return this.dorep (s, 0, s.length); -}, "~S"); -Clazz.defineMethod (c$, "replaceFirstFrom", -function (s, start) { -return this.dorep (s, start, s.length); -}, "~S,~N"); -Clazz.defineMethod (c$, "replaceFirstRegion", -function (s, start, end) { -return this.dorep (s, start, end); -}, "~S,~N,~N"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.ReplaceRule", "$.Replacer"], ["com.stevesoft.pat.Transformer", "$.TransRepRule"], ["com.stevesoft.pat.MessageManager", "$.Regex", "$.TransPat", "com.stevesoft.pat.wrap.StringWrap", "java.lang.ArrayIndexOutOfBoundsException", "$.NullPointerException"], function () { +c$ = Clazz.decorateAsClass (function () { +this.t = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "TransRepRule", com.stevesoft.pat.ReplaceRule); +Clazz.makeConstructor (c$, +function (t) { +Clazz.superConstructor (this, com.stevesoft.pat.TransRepRule, []); +this.t = t; +}, "com.stevesoft.pat.Transformer"); +Clazz.overrideMethod (c$, "toString1", +function () { +return ""; +}); +Clazz.overrideMethod (c$, "clone1", +function () { +return new com.stevesoft.pat.TransRepRule (this.t); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, rr) { +this.next = this.t.tp.ra[this.t.tp.pn].getReplaceRule (); +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +c$ = Clazz.decorateAsClass (function () { +this.tp = null; +this.rp = null; +this.auto_optimize = false; +this.repr = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Transformer"); +Clazz.prepareFields (c$, function () { +this.repr = new com.stevesoft.pat.Replacer (); +}); +Clazz.defineMethod (c$, "getReplacer", +function () { +return this.rp.getReplacer (); +}); +Clazz.makeConstructor (c$, +function (auto) { +this.rp = new com.stevesoft.pat.Regex (null, ""); +this.auto_optimize = auto; +this.tp = new com.stevesoft.pat.TransPat (); +this.rp.setReplaceRule ( new com.stevesoft.pat.TransRepRule (this)); +this.rp.thePattern = this.tp; +}, "~B"); +Clazz.defineMethod (c$, "add", +function (r) { +if (this.auto_optimize) { +r.optimize (); +}this.tp.ra[this.tp.ra_len++] = r; +if (this.tp.ra.length == this.tp.ra_len) { +var ra2 = new Array (this.tp.ra_len + 10); +for (var i = 0; i < this.tp.ra_len; i++) { +ra2[i] = this.tp.ra[i]; +} +this.tp.ra = ra2; +}this.rp.numSubs_ = r.numSubs_ > this.rp.numSubs_ ? r.numSubs_ : this.rp.numSubs_; +}, "com.stevesoft.pat.Regex"); +Clazz.defineMethod (c$, "patterns", +function () { +return this.tp.ra_len; +}); +Clazz.defineMethod (c$, "getRegexAt", +function (i) { +if (i >= this.tp.ra_len) { +throw new ArrayIndexOutOfBoundsException ("i=" + i + ">=" + this.patterns ()); +}if (i < 0) { +throw new ArrayIndexOutOfBoundsException ("i=" + i + "< 0"); +}return this.tp.ra[i]; +}, "~N"); +Clazz.defineMethod (c$, "setRegexAt", +function (rx, i) { +if (i >= this.tp.ra_len) { +throw new ArrayIndexOutOfBoundsException ("i=" + i + ">=" + this.patterns ()); +}if (i < 0) { +throw new ArrayIndexOutOfBoundsException ("i=" + i + "< 0"); +}this.tp.ra[i] = rx; +}, "com.stevesoft.pat.Regex,~N"); +Clazz.defineMethod (c$, "add", +function (rs) { +var r = com.stevesoft.pat.Regex.perlCode (rs); +if (r == null) { +throw new NullPointerException (com.stevesoft.pat.MessageManager.formatMessage ("exception.bad_pattern_to_regex_perl_code", Clazz.newArray (-1, [rs]))); +}this.add (r); +}, "~S"); +Clazz.defineMethod (c$, "add", +function (array) { +for (var i = 0; i < array.length; i++) { +this.add (array[i]); +} +}, "~A"); +Clazz.defineMethod (c$, "replaceAll", +function (s) { +return this.dorep (s, 0, s.length); +}, "~S"); +Clazz.defineMethod (c$, "replaceAll", +function (s) { +return this.dorep (s, 0, s.length ()); +}, "com.stevesoft.pat.StringLike"); +Clazz.defineMethod (c$, "replaceAllFrom", +function (s, start) { +return this.dorep (s, start, s.length); +}, "~S,~N"); +Clazz.defineMethod (c$, "replaceAllRegion", +function (s, start, end) { +return this.dorep (s, start, end); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "dorep", +function (s, start, end) { +var tfmd = this.repr.replaceAllRegion (s, this.rp, start, end); +this.tp.lastMatchedTo = this.repr.$lastMatchedTo; +return tfmd; +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "dorep", +function (s, start, end) { +return this.dorep ( new com.stevesoft.pat.wrap.StringWrap (s), start, end).toString (); +}, "~S,~N,~N"); +Clazz.defineMethod (c$, "replaceFirst", +function (s) { +return this.dorep (s, 0, s.length); +}, "~S"); +Clazz.defineMethod (c$, "replaceFirstFrom", +function (s, start) { +return this.dorep (s, start, s.length); +}, "~S,~N"); +Clazz.defineMethod (c$, "replaceFirstRegion", +function (s, start, end) { +return this.dorep (s, start, end); +}, "~S,~N,~N"); +}); diff --git a/bin/com/stevesoft/pat/UniValidator.js b/bin/com/stevesoft/pat/UniValidator.js index e1731a4..18aa516 100644 --- a/bin/com/stevesoft/pat/UniValidator.js +++ b/bin/com/stevesoft/pat/UniValidator.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Validator"], "com.stevesoft.pat.UniValidator", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "UniValidator", com.stevesoft.pat.Validator); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Validator"], "com.stevesoft.pat.UniValidator", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "UniValidator", com.stevesoft.pat.Validator); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +}); diff --git a/bin/com/stevesoft/pat/Util.js b/bin/com/stevesoft/pat/Util.js index 6573d7b..3058320 100644 --- a/bin/com/stevesoft/pat/Util.js +++ b/bin/com/stevesoft/pat/Util.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -c$ = Clazz.declareType (com.stevesoft.pat, "Util"); +Clazz.declarePackage ("com.stevesoft.pat"); +c$ = Clazz.declareType (com.stevesoft.pat, "Util"); diff --git a/bin/com/stevesoft/pat/Validator.js b/bin/com/stevesoft/pat/Validator.js index c929431..e364969 100644 --- a/bin/com/stevesoft/pat/Validator.js +++ b/bin/com/stevesoft/pat/Validator.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.Validator", ["com.stevesoft.pat.patInf", "$.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.argsave = null; -this.pattern = "."; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "Validator"); -Clazz.defineMethod (c$, "validate", -function (src, start, end) { -return end; -}, "com.stevesoft.pat.StringLike,~N,~N"); -Clazz.defineMethod (c$, "arg", -function (s) { -return null; -}, "~S"); -Clazz.defineMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.defineMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInf (); -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.Validator", ["com.stevesoft.pat.patInf", "$.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.argsave = null; +this.pattern = "."; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "Validator"); +Clazz.defineMethod (c$, "validate", +function (src, start, end) { +return end; +}, "com.stevesoft.pat.StringLike,~N,~N"); +Clazz.defineMethod (c$, "arg", +function (s) { +return null; +}, "~S"); +Clazz.defineMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.defineMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInf (); +}); +}); diff --git a/bin/com/stevesoft/pat/WantMoreTextReplaceRule.js b/bin/com/stevesoft/pat/WantMoreTextReplaceRule.js index e305e86..b572563 100644 --- a/bin/com/stevesoft/pat/WantMoreTextReplaceRule.js +++ b/bin/com/stevesoft/pat/WantMoreTextReplaceRule.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.WantMoreTextReplaceRule", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "WantMoreTextReplaceRule", com.stevesoft.pat.SpecialRule); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.WantMoreTextReplaceRule, []); -}); -Clazz.overrideMethod (c$, "apply", -function (sb, res) { -}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); -Clazz.overrideMethod (c$, "toString1", -function () { -return "${WANT_MORE_TEXT}"; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.SpecialRule"], "com.stevesoft.pat.WantMoreTextReplaceRule", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "WantMoreTextReplaceRule", com.stevesoft.pat.SpecialRule); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.WantMoreTextReplaceRule, []); +}); +Clazz.overrideMethod (c$, "apply", +function (sb, res) { +}, "com.stevesoft.pat.StringBufferLike,com.stevesoft.pat.RegRes"); +Clazz.overrideMethod (c$, "toString1", +function () { +return "${WANT_MORE_TEXT}"; +}); +}); diff --git a/bin/com/stevesoft/pat/lookAhead.js b/bin/com/stevesoft/pat/lookAhead.js index 05e888d..6b9fe88 100644 --- a/bin/com/stevesoft/pat/lookAhead.js +++ b/bin/com/stevesoft/pat/lookAhead.js @@ -1,62 +1,62 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Or"], "com.stevesoft.pat.lookAhead", ["com.stevesoft.pat.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.reverse = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "lookAhead", com.stevesoft.pat.Or); -Clazz.makeConstructor (c$, -function (b) { -Clazz.superConstructor (this, com.stevesoft.pat.lookAhead, []); -this.reverse = b; -}, "~B"); -Clazz.defineMethod (c$, "getNext", -function () { -return null; -}); -Clazz.overrideMethod (c$, "nextMatch", -function (pos, pt) { -var p = Clazz.superCall (this, com.stevesoft.pat.lookAhead, "getNext", []); -if (p != null) { -return p.matchInternal (pos, pt); -} else { -return pos; -}}, "~N,com.stevesoft.pat.Pthings"); -Clazz.defineMethod (c$, "matchInternal", -function (pos, pt) { -if (Clazz.superCall (this, com.stevesoft.pat.lookAhead, "matchInternal", [pos, pt]) >= 0) { -if (this.reverse) { -return -1; -} else { -return this.nextMatch (pos, pt); -}} else { -if (this.reverse) { -return this.nextMatch (pos, pt); -} else { -return -1; -}}}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "leftForm", -function () { -if (this.reverse) { -return "(?!"; -} else { -return "(?="; -}}); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (0); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -var la = new com.stevesoft.pat.lookAhead (this.reverse); -h.put (this, la); -h.put (la, la); -for (var i = 0; i < this.v.size (); i++) { -la.v.addElement ((this.v.elementAt (i)).clone (h)); -} -return la; -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Or"], "com.stevesoft.pat.lookAhead", ["com.stevesoft.pat.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.reverse = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "lookAhead", com.stevesoft.pat.Or); +Clazz.makeConstructor (c$, +function (b) { +Clazz.superConstructor (this, com.stevesoft.pat.lookAhead, []); +this.reverse = b; +}, "~B"); +Clazz.defineMethod (c$, "getNext", +function () { +return null; +}); +Clazz.overrideMethod (c$, "nextMatch", +function (pos, pt) { +var p = Clazz.superCall (this, com.stevesoft.pat.lookAhead, "getNext", []); +if (p != null) { +return p.matchInternal (pos, pt); +} else { +return pos; +}}, "~N,com.stevesoft.pat.Pthings"); +Clazz.defineMethod (c$, "matchInternal", +function (pos, pt) { +if (Clazz.superCall (this, com.stevesoft.pat.lookAhead, "matchInternal", [pos, pt]) >= 0) { +if (this.reverse) { +return -1; +} else { +return this.nextMatch (pos, pt); +}} else { +if (this.reverse) { +return this.nextMatch (pos, pt); +} else { +return -1; +}}}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "leftForm", +function () { +if (this.reverse) { +return "(?!"; +} else { +return "(?="; +}}); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (0); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +var la = new com.stevesoft.pat.lookAhead (this.reverse); +h.put (this, la); +h.put (la, la); +for (var i = 0; i < this.v.size (); i++) { +la.v.addElement ((this.v.elementAt (i)).clone (h)); +} +return la; +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/oneChar.js b/bin/com/stevesoft/pat/oneChar.js index 3dac704..1fbc400 100644 --- a/bin/com/stevesoft/pat/oneChar.js +++ b/bin/com/stevesoft/pat/oneChar.js @@ -1,55 +1,55 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.oneChar", ["com.stevesoft.pat.CaseMgr", "$.patInt"], function () { -c$ = Clazz.decorateAsClass (function () { -this.c = '\0'; -this.altc = '\0'; -this.altc2 = '\0'; -this.mask = 0; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "oneChar", com.stevesoft.pat.Pattern); -Clazz.makeConstructor (c$, -function (ci) { -Clazz.superConstructor (this, com.stevesoft.pat.oneChar, []); -this.c = ci; -var cu; -var cl; -var ct; -cu = com.stevesoft.pat.CaseMgr.toUpperCaseC (this.c); -cl = com.stevesoft.pat.CaseMgr.toLowerCaseC (this.c); -ct = com.stevesoft.pat.CaseMgr.toTitleCaseC (this.c); -if (this.c == cu) { -this.altc = cl; -this.altc2 = ct; -} else if (this.c == cl) { -this.altc = cu; -this.altc2 = ct; -} else { -this.altc = cl; -this.altc2 = cu; -}this.mask = this.c.charCodeAt (0) & this.altc.charCodeAt (0) & this.altc2.charCodeAt (0); -}, "~S"); -Clazz.overrideMethod (c$, "matchInternal", -function (pos, pt) { -var p; -var ret = -1; -if (pos < pt.src.length () && !this.Masked (pos, pt) && ((p = pt.src.charAt (pos)) == this.c || (pt.ignoreCase && (p == this.altc || p == this.altc2)))) { -ret = this.nextMatch (pos + 1, pt); -}return ret; -}, "~N,com.stevesoft.pat.Pthings"); -Clazz.overrideMethod (c$, "toString", -function () { -return com.stevesoft.pat.Pattern.protect ("" + this.c, "[]{}(),$,-\"^.", '\\') + this.nextString (); -}); -Clazz.overrideMethod (c$, "minChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "maxChars", -function () { -return new com.stevesoft.pat.patInt (1); -}); -Clazz.overrideMethod (c$, "clone1", -function (h) { -return new com.stevesoft.pat.oneChar (this.c); -}, "java.util.Hashtable"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.Pattern"], "com.stevesoft.pat.oneChar", ["com.stevesoft.pat.CaseMgr", "$.patInt"], function () { +c$ = Clazz.decorateAsClass (function () { +this.c = '\0'; +this.altc = '\0'; +this.altc2 = '\0'; +this.mask = 0; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "oneChar", com.stevesoft.pat.Pattern); +Clazz.makeConstructor (c$, +function (ci) { +Clazz.superConstructor (this, com.stevesoft.pat.oneChar, []); +this.c = ci; +var cu; +var cl; +var ct; +cu = com.stevesoft.pat.CaseMgr.toUpperCaseC (this.c); +cl = com.stevesoft.pat.CaseMgr.toLowerCaseC (this.c); +ct = com.stevesoft.pat.CaseMgr.toTitleCaseC (this.c); +if (this.c == cu) { +this.altc = cl; +this.altc2 = ct; +} else if (this.c == cl) { +this.altc = cu; +this.altc2 = ct; +} else { +this.altc = cl; +this.altc2 = cu; +}this.mask = this.c.charCodeAt (0) & this.altc.charCodeAt (0) & this.altc2.charCodeAt (0); +}, "~S"); +Clazz.overrideMethod (c$, "matchInternal", +function (pos, pt) { +var p; +var ret = -1; +if (pos < pt.src.length () && !this.Masked (pos, pt) && ((p = pt.src.charAt (pos)) == this.c || (pt.ignoreCase && (p == this.altc || p == this.altc2)))) { +ret = this.nextMatch (pos + 1, pt); +}return ret; +}, "~N,com.stevesoft.pat.Pthings"); +Clazz.overrideMethod (c$, "toString", +function () { +return com.stevesoft.pat.Pattern.protect ("" + this.c, "[]{}(),$,-\"^.", '\\') + this.nextString (); +}); +Clazz.overrideMethod (c$, "minChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "maxChars", +function () { +return new com.stevesoft.pat.patInt (1); +}); +Clazz.overrideMethod (c$, "clone1", +function (h) { +return new com.stevesoft.pat.oneChar (this.c); +}, "java.util.Hashtable"); +}); diff --git a/bin/com/stevesoft/pat/package.js b/bin/com/stevesoft/pat/package.js index c28d225..1c96a94 100644 --- a/bin/com/stevesoft/pat/package.js +++ b/bin/com/stevesoft/pat/package.js @@ -1,34 +1,34 @@ -var path = ClazzLoader.getClasspathFor ("com.stevesoft.pat.package"); -path = path.substring (0, path.lastIndexOf ("package.js")); -ClazzLoader.jarClasspath (path + "Transformer.js", [ -"com.stevesoft.pat.Transformer", -"$.TransRepRule"]); -ClazzLoader.jarClasspath (path + "Replacer.js", [ -"com.stevesoft.pat.RegHolder", -"$.Replacer", -"$.CodeVal"]); -ClazzLoader.jarClasspath (path + "Regex.js", [ -"com.stevesoft.pat.UnicodeW", -"$.UnicodeCurrency", -"$.UnicodeAlpha", -"$.UnicodeUpper", -"$.NUnicodeCurrency", -"$.NUnicodeW", -"$.NUnicodeAlpha", -"$.UnicodeMath", -"$.UnicodeWhite", -"$.UnicodeDigit", -"$.NUnicodeMath", -"$.Regex", -"$.NUnicodeDigit", -"$.NUnicodeWhite", -"$.NUnicodePunct", -"$.UnicodePunct", -"$.UnicodeLower"]); -ClazzLoader.jarClasspath (path + "RegOpt.js", [ -"com.stevesoft.pat.Branch", -"$.RegOpt", -"$.FastChar"]); -ClazzLoader.jarClasspath (path + "Range.js", [ -"com.stevesoft.pat.BadRangeArgs", -"$.Range"]); +var path = ClazzLoader.getClasspathFor ("com.stevesoft.pat.package"); +path = path.substring (0, path.lastIndexOf ("package.js")); +ClazzLoader.jarClasspath (path + "Range.js", [ +"com.stevesoft.pat.BadRangeArgs", +"$.Range"]); +ClazzLoader.jarClasspath (path + "RegOpt.js", [ +"com.stevesoft.pat.Branch", +"$.RegOpt", +"$.FastChar"]); +ClazzLoader.jarClasspath (path + "Regex.js", [ +"com.stevesoft.pat.UnicodeW", +"$.UnicodeCurrency", +"$.UnicodeAlpha", +"$.UnicodeUpper", +"$.NUnicodeCurrency", +"$.NUnicodeW", +"$.NUnicodeAlpha", +"$.UnicodeMath", +"$.UnicodeWhite", +"$.UnicodeDigit", +"$.NUnicodeMath", +"$.Regex", +"$.NUnicodeDigit", +"$.NUnicodeWhite", +"$.NUnicodePunct", +"$.UnicodePunct", +"$.UnicodeLower"]); +ClazzLoader.jarClasspath (path + "Replacer.js", [ +"com.stevesoft.pat.RegHolder", +"$.Replacer", +"$.CodeVal"]); +ClazzLoader.jarClasspath (path + "Transformer.js", [ +"com.stevesoft.pat.Transformer", +"$.TransRepRule"]); diff --git a/bin/com/stevesoft/pat/parsePerl.class b/bin/com/stevesoft/pat/parsePerl.class index 09045a1..6c525dc 100644 Binary files a/bin/com/stevesoft/pat/parsePerl.class and b/bin/com/stevesoft/pat/parsePerl.class differ diff --git a/bin/com/stevesoft/pat/parsePerl.js b/bin/com/stevesoft/pat/parsePerl.js index 005236e..d34fbd4 100644 --- a/bin/com/stevesoft/pat/parsePerl.js +++ b/bin/com/stevesoft/pat/parsePerl.js @@ -1,267 +1,267 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (null, "com.stevesoft.pat.parsePerl", ["com.stevesoft.pat.CaseMgr", "$.Prop", "$.RegSyntaxError", "$.Regex", "$.ReplaceRule", "$.StringRule", "java.lang.StringBuffer"], function () { -c$ = Clazz.declareType (com.stevesoft.pat, "parsePerl"); -c$.close = Clazz.defineMethod (c$, "close", -function (c) { -if (c == '<') { -return '>'; -}if (c == '[') { -return ']'; -}if (c == '(') { -return ')'; -}if (c == '{') { -return '}'; -}return c; -}, "~S"); -c$.codify = Clazz.defineMethod (c$, "codify", -function (s, keepbs) { -return com.stevesoft.pat.parsePerl.codifyRange (s, 0, s.length, keepbs); -}, "~S,~B"); -c$.codifyRange = Clazz.defineMethod (c$, "codifyRange", -function (s, i0, iN, keepbs) { -var sb = new StringBuffer (); -var ucmode = false; -var lcmode = false; -var litmode = false; -var uc1 = false; -var lc1 = false; -var modified = false; -for (var i = i0; i < iN; i++) { -var c = s.charAt (i); -var mf = true; -var app = true; -if (c == '\\') { -app = false; -i++; -if (i < s.length) { -var c2 = s.charAt (i); -switch (c2) { -case 'Q': -litmode = true; -break; -case 'U': -ucmode = true; -break; -case 'L': -lcmode = true; -break; -case 'u': -uc1 = true; -break; -case 'l': -lc1 = true; -break; -case 'E': -uc1 = lc1 = ucmode = lcmode = litmode = false; -break; -default: -if (keepbs) { -sb.append ('\\'); -}c = c2; -if (keepbs) { -mf = false; -}app = true; -break; -} -modified = new Boolean (modified | mf).valueOf (); -}}if (app) { -if (lc1) { -c = com.stevesoft.pat.parsePerl.lc (c); -lc1 = false; -} else if (uc1) { -c = com.stevesoft.pat.parsePerl.uc (c); -uc1 = false; -} else if (ucmode) { -c = com.stevesoft.pat.parsePerl.uc (c); -} else if (lcmode) { -c = com.stevesoft.pat.parsePerl.lc (c); -}if (litmode && com.stevesoft.pat.parsePerl.needbs (c)) { -sb.append ('\\'); -}sb.append (c); -}} -return modified ? sb.toString () : s; -}, "~S,~N,~N,~B"); -c$.uc = Clazz.defineMethod (c$, "uc", -function (c) { -return com.stevesoft.pat.CaseMgr.toUpperCaseC (c); -}, "~S"); -c$.lc = Clazz.defineMethod (c$, "lc", -function (c) { -return com.stevesoft.pat.CaseMgr.toLowerCaseC (c); -}, "~S"); -c$.needbs = Clazz.defineMethod (c$, "needbs", -function (c) { -if (c >= 'a' && c <= 'z') { -return false; -}if (c >= 'A' && c <= 'Z') { -return false; -}if (c >= '0' && c <= '9') { -return false; -}if (c == '_') { -return false; -}return true; -}, "~S"); -c$.parse = Clazz.defineMethod (c$, "parse", -function (s) { -var igncase = false; -var optim = false; -var gFlag = false; -var sFlag = false; -var mFlag = false; -var xFlag = false; -var s1 = new StringBuffer (); -var s2 = new StringBuffer (); -var i = 0; -var count = 0; -var mode; -var delim = '/'; -var cdelim = '/'; -if (s.length >= 3 && s.charAt (0) == 's') { -mode = 's'; -delim = s.charAt (1); -cdelim = com.stevesoft.pat.parsePerl.close (delim); -i = 2; -} else if (s.length >= 2 && s.charAt (0) == 'm') { -mode = 'm'; -delim = s.charAt (1); -cdelim = com.stevesoft.pat.parsePerl.close (delim); -i = 2; -} else if (s.length >= 1 && s.charAt (0) == '/') { -mode = 'm'; -i = 1; -} else { -try { -com.stevesoft.pat.RegSyntaxError.endItAll ("Regex.perlCode should be of the form s/// or m// or //"); -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -} else { -throw rs; -} -} -return null; -}for (; i < s.length; i++) { -if (s.charAt (i) == '\\') { -s1.append ('\\'); -i++; -} else if (s.charAt (i) == cdelim && count == 0) { -i++; -break; -} else if (s.charAt (i) == delim && cdelim != delim) { -count++; -} else if (s.charAt (i) == cdelim && cdelim != delim) { -count--; -}s1.append (s.charAt (i)); -} -if (mode == 's' && cdelim != delim) { -while (i < s.length && com.stevesoft.pat.Prop.isWhite (s.charAt (i))) { -i++; -} -if (i >= s.length) { -try { -com.stevesoft.pat.RegSyntaxError.endItAll ("" + mode + delim + " needs " + cdelim); -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -} else { -throw rs; -} -} -return null; -}cdelim = com.stevesoft.pat.parsePerl.close (delim = s.charAt (i)); -i++; -}count = 0; -if (mode == 's') { -for (; i < s.length; i++) { -if (s.charAt (i) == '\\') { -s2.append ('\\'); -i++; -} else if (s.charAt (i) == cdelim && count == 0) { -i++; -break; -} else if (s.charAt (i) == delim && cdelim != delim) { -count++; -} else if (s.charAt (i) == cdelim && cdelim != delim) { -count--; -}s2.append (s.charAt (i)); -} -}for (; i < s.length; i++) { -var c = s.charAt (i); -switch (c) { -case 'x': -xFlag = true; -break; -case 'i': -igncase = true; -break; -case 'o': -optim = true; -break; -case 's': -sFlag = true; -break; -case 'm': -mFlag = true; -break; -case 'g': -gFlag = true; -break; -default: -try { -com.stevesoft.pat.RegSyntaxError.endItAll ("Illegal flag to pattern: " + c); -} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -} else { -throw rs; -} -} -return null; -} -} -var r = new com.stevesoft.pat.Regex (null, ""); -try { -var pat = s1.toString (); -var reprul = s2.toString (); -if (xFlag) { -pat = com.stevesoft.pat.parsePerl.strip (pat); -reprul = com.stevesoft.pat.parsePerl.strip (reprul); -}r.compile (pat); -r.ignoreCase = new Boolean (r.ignoreCase | igncase).valueOf (); -r.gFlag = new Boolean (r.gFlag | gFlag).valueOf (); -r.sFlag = new Boolean (r.sFlag | sFlag).valueOf (); -r.mFlag = new Boolean (r.mFlag | mFlag).valueOf (); -if (optim) { -r.optimize (); -}if (delim == '\'') { -r.setReplaceRule ( new com.stevesoft.pat.StringRule (reprul)); -} else { -r.setReplaceRule (com.stevesoft.pat.ReplaceRule.perlCode (reprul)); -}} catch (rs) { -if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { -r = null; -} else { -throw rs; -} -} -return r; -}, "~S"); -c$.strip = Clazz.defineMethod (c$, "strip", -function (s) { -var sb = new StringBuffer (); -for (var i = 0; i < s.length; i++) { -var c = s.charAt (i); -if (com.stevesoft.pat.Prop.isWhite (c)) { -;} else if (c == '#') { -i++; -while (i < s.length) { -if (s.charAt (i) == '\n') { -break; -}i++; -} -} else if (c == '\\') { -sb.append (c); -sb.append (s.charAt (++i)); -} else { -sb.append (c); -}} -return sb.toString (); -}, "~S"); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (null, "com.stevesoft.pat.parsePerl", ["com.stevesoft.pat.CaseMgr", "$.Prop", "$.RegSyntaxError", "$.Regex", "$.ReplaceRule", "$.StringRule", "java.lang.StringBuffer"], function () { +c$ = Clazz.declareType (com.stevesoft.pat, "parsePerl"); +c$.close = Clazz.defineMethod (c$, "close", +function (c) { +if (c == '<') { +return '>'; +}if (c == '[') { +return ']'; +}if (c == '(') { +return ')'; +}if (c == '{') { +return '}'; +}return c; +}, "~S"); +c$.codify = Clazz.defineMethod (c$, "codify", +function (s, keepbs) { +return com.stevesoft.pat.parsePerl.codifyRange (s, 0, s.length, keepbs); +}, "~S,~B"); +c$.codifyRange = Clazz.defineMethod (c$, "codifyRange", +function (s, i0, iN, keepbs) { +var sb = new StringBuffer (); +var ucmode = false; +var lcmode = false; +var litmode = false; +var uc1 = false; +var lc1 = false; +var modified = false; +for (var i = i0; i < iN; i++) { +var c = s.charAt (i); +var mf = true; +var app = true; +if (c == '\\') { +app = false; +i++; +if (i < s.length) { +var c2 = s.charAt (i); +switch (c2) { +case 'Q': +litmode = true; +break; +case 'U': +ucmode = true; +break; +case 'L': +lcmode = true; +break; +case 'u': +uc1 = true; +break; +case 'l': +lc1 = true; +break; +case 'E': +uc1 = lc1 = ucmode = lcmode = litmode = false; +break; +default: +if (keepbs) { +sb.append ('\\'); +}c = c2; +if (keepbs) { +mf = false; +}app = true; +break; +} +modified = new Boolean (modified | mf).valueOf (); +}}if (app) { +if (lc1) { +c = com.stevesoft.pat.parsePerl.lc (c); +lc1 = false; +} else if (uc1) { +c = com.stevesoft.pat.parsePerl.uc (c); +uc1 = false; +} else if (ucmode) { +c = com.stevesoft.pat.parsePerl.uc (c); +} else if (lcmode) { +c = com.stevesoft.pat.parsePerl.lc (c); +}if (litmode && com.stevesoft.pat.parsePerl.needbs (c)) { +sb.append ('\\'); +}sb.append (c); +}} +return modified ? sb.toString () : s; +}, "~S,~N,~N,~B"); +c$.uc = Clazz.defineMethod (c$, "uc", +function (c) { +return com.stevesoft.pat.CaseMgr.toUpperCaseC (c); +}, "~S"); +c$.lc = Clazz.defineMethod (c$, "lc", +function (c) { +return com.stevesoft.pat.CaseMgr.toLowerCaseC (c); +}, "~S"); +c$.needbs = Clazz.defineMethod (c$, "needbs", +function (c) { +if (c >= 'a' && c <= 'z') { +return false; +}if (c >= 'A' && c <= 'Z') { +return false; +}if (c >= '0' && c <= '9') { +return false; +}if (c == '_') { +return false; +}return true; +}, "~S"); +c$.parse = Clazz.defineMethod (c$, "parse", +function (s) { +var igncase = false; +var optim = false; +var gFlag = false; +var sFlag = false; +var mFlag = false; +var xFlag = false; +var s1 = new StringBuffer (); +var s2 = new StringBuffer (); +var i = 0; +var count = 0; +var mode; +var delim = '/'; +var cdelim = '/'; +if (s.length >= 3 && s.charAt (0) == 's') { +mode = 's'; +delim = s.charAt (1); +cdelim = com.stevesoft.pat.parsePerl.close (delim); +i = 2; +} else if (s.length >= 2 && s.charAt (0) == 'm') { +mode = 'm'; +delim = s.charAt (1); +cdelim = com.stevesoft.pat.parsePerl.close (delim); +i = 2; +} else if (s.length >= 1 && s.charAt (0) == '/') { +mode = 'm'; +i = 1; +} else { +try { +com.stevesoft.pat.RegSyntaxError.endItAll ("Regex.perlCode should be of the form s/// or m// or //"); +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +} else { +throw rs; +} +} +return null; +}for (; i < s.length; i++) { +if (s.charAt (i) == '\\') { +s1.append ('\\'); +i++; +} else if (s.charAt (i) == cdelim && count == 0) { +i++; +break; +} else if (s.charAt (i) == delim && cdelim != delim) { +count++; +} else if (s.charAt (i) == cdelim && cdelim != delim) { +count--; +}s1.append (s.charAt (i)); +} +if (mode == 's' && cdelim != delim) { +while (i < s.length && com.stevesoft.pat.Prop.isWhite (s.charAt (i))) { +i++; +} +if (i >= s.length) { +try { +com.stevesoft.pat.RegSyntaxError.endItAll ("" + mode + delim + " needs " + cdelim); +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +} else { +throw rs; +} +} +return null; +}cdelim = com.stevesoft.pat.parsePerl.close (delim = s.charAt (i)); +i++; +}count = 0; +if (mode == 's') { +for (; i < s.length; i++) { +if (s.charAt (i) == '\\') { +s2.append ('\\'); +i++; +} else if (s.charAt (i) == cdelim && count == 0) { +i++; +break; +} else if (s.charAt (i) == delim && cdelim != delim) { +count++; +} else if (s.charAt (i) == cdelim && cdelim != delim) { +count--; +}s2.append (s.charAt (i)); +} +}for (; i < s.length; i++) { +var c = s.charAt (i); +switch (c) { +case 'x': +xFlag = true; +break; +case 'i': +igncase = true; +break; +case 'o': +optim = true; +break; +case 's': +sFlag = true; +break; +case 'm': +mFlag = true; +break; +case 'g': +gFlag = true; +break; +default: +try { +com.stevesoft.pat.RegSyntaxError.endItAll ("Illegal flag to pattern: " + c); +} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +} else { +throw rs; +} +} +return null; +} +} +var r = new com.stevesoft.pat.Regex (null, ""); +try { +var pat = s1.toString (); +var reprul = s2.toString (); +if (xFlag) { +pat = com.stevesoft.pat.parsePerl.strip (pat); +reprul = com.stevesoft.pat.parsePerl.strip (reprul); +}r.compile (pat); +r.ignoreCase = new Boolean (r.ignoreCase | igncase).valueOf (); +r.gFlag = new Boolean (r.gFlag | gFlag).valueOf (); +r.sFlag = new Boolean (r.sFlag | sFlag).valueOf (); +r.mFlag = new Boolean (r.mFlag | mFlag).valueOf (); +if (optim) { +r.optimize (); +}if (delim == '\'') { +r.setReplaceRule ( new com.stevesoft.pat.StringRule (reprul)); +} else { +r.setReplaceRule (com.stevesoft.pat.ReplaceRule.perlCode (reprul)); +}} catch (rs) { +if (Clazz.exceptionOf (rs, com.stevesoft.pat.RegSyntax)) { +r = null; +} else { +throw rs; +} +} +return r; +}, "~S"); +c$.strip = Clazz.defineMethod (c$, "strip", +function (s) { +var sb = new StringBuffer (); +for (var i = 0; i < s.length; i++) { +var c = s.charAt (i); +if (com.stevesoft.pat.Prop.isWhite (c)) { +;} else if (c == '#') { +i++; +while (i < s.length) { +if (s.charAt (i) == '\n') { +break; +}i++; +} +} else if (c == '\\') { +sb.append (c); +sb.append (s.charAt (++i)); +} else { +sb.append (c); +}} +return sb.toString (); +}, "~S"); +}); diff --git a/bin/com/stevesoft/pat/patInf.js b/bin/com/stevesoft/pat/patInf.js index daf7087..1e11499 100644 --- a/bin/com/stevesoft/pat/patInf.js +++ b/bin/com/stevesoft/pat/patInf.js @@ -1,9 +1,9 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -Clazz.load (["com.stevesoft.pat.patInt"], "com.stevesoft.pat.patInf", null, function () { -c$ = Clazz.declareType (com.stevesoft.pat, "patInf", com.stevesoft.pat.patInt); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, com.stevesoft.pat.patInf, []); -this.inf = true; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat"); +Clazz.load (["com.stevesoft.pat.patInt"], "com.stevesoft.pat.patInf", null, function () { +c$ = Clazz.declareType (com.stevesoft.pat, "patInf", com.stevesoft.pat.patInt); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, com.stevesoft.pat.patInf, []); +this.inf = true; +}); +}); diff --git a/bin/com/stevesoft/pat/patInt.js b/bin/com/stevesoft/pat/patInt.js index 2d65e56..b7226f7 100644 --- a/bin/com/stevesoft/pat/patInt.js +++ b/bin/com/stevesoft/pat/patInt.js @@ -1,94 +1,94 @@ -Clazz.declarePackage ("com.stevesoft.pat"); -c$ = Clazz.decorateAsClass (function () { -this.i = 0; -this.inf = false; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat, "patInt"); -Clazz.makeConstructor (c$, -function () { -this.i = 0; -this.inf = false; -}); -Clazz.makeConstructor (c$, -function (init) { -this.i = init; -this.inf = false; -}, "~N"); -Clazz.makeConstructor (c$, -function (p) { -this.i = p.i; -this.inf = p.inf; -}, "com.stevesoft.pat.patInt"); -Clazz.defineMethod (c$, "setInf", -function (b) { -this.inf = b; -if (b) { -this.i = 2147483647; -}}, "~B"); -Clazz.defineMethod (c$, "inc", -function () { -if (!this.inf) { -this.i++; -}}); -Clazz.defineMethod (c$, "dec", -function () { -if (!this.inf) { -this.i--; -}}); -Clazz.defineMethod (c$, "lessEq", -function (j) { -return !this.inf && (j.inf || this.i <= j.i); -}, "com.stevesoft.pat.patInt"); -Clazz.defineMethod (c$, "equals", -function (j) { -return !j.inf && !this.inf && this.i == j.i; -}, "com.stevesoft.pat.patInt"); -Clazz.overrideMethod (c$, "toString", -function () { -if (this.inf) { -return ""; -} else { -return "" + this.i; -}}); -Clazz.defineMethod (c$, "pluseq", -function (p) { -if (this.inf || p.inf) { -this.setInf (true); -} else { -this.i += p.i; -}return this; -}, "com.stevesoft.pat.patInt"); -Clazz.defineMethod (c$, "mul", -function (p) { -if (this.inf || p.inf) { -return new com.stevesoft.pat.patInf (); -}return new com.stevesoft.pat.patInt (this.i * p.i); -}, "com.stevesoft.pat.patInt"); -Clazz.defineMethod (c$, "mineq", -function (p) { -if (p.inf) { -return this; -}if (this.inf) { -this.i = p.i; -} else if (p.i < this.i) { -this.i = p.i; -}this.setInf (false); -return this; -}, "com.stevesoft.pat.patInt"); -Clazz.defineMethod (c$, "maxeq", -function (p) { -if (this.inf || p.inf) { -this.setInf (true); -return this; -}if (p.i > this.i) { -this.i = p.i; -}return this; -}, "com.stevesoft.pat.patInt"); -Clazz.defineMethod (c$, "finite", -function () { -return !this.inf; -}); -Clazz.defineMethod (c$, "intValue", -function () { -return this.inf ? 2147483647 : this.i; -}); +Clazz.declarePackage ("com.stevesoft.pat"); +c$ = Clazz.decorateAsClass (function () { +this.i = 0; +this.inf = false; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat, "patInt"); +Clazz.makeConstructor (c$, +function () { +this.i = 0; +this.inf = false; +}); +Clazz.makeConstructor (c$, +function (init) { +this.i = init; +this.inf = false; +}, "~N"); +Clazz.makeConstructor (c$, +function (p) { +this.i = p.i; +this.inf = p.inf; +}, "com.stevesoft.pat.patInt"); +Clazz.defineMethod (c$, "setInf", +function (b) { +this.inf = b; +if (b) { +this.i = 2147483647; +}}, "~B"); +Clazz.defineMethod (c$, "inc", +function () { +if (!this.inf) { +this.i++; +}}); +Clazz.defineMethod (c$, "dec", +function () { +if (!this.inf) { +this.i--; +}}); +Clazz.defineMethod (c$, "lessEq", +function (j) { +return !this.inf && (j.inf || this.i <= j.i); +}, "com.stevesoft.pat.patInt"); +Clazz.defineMethod (c$, "equals", +function (j) { +return !j.inf && !this.inf && this.i == j.i; +}, "com.stevesoft.pat.patInt"); +Clazz.overrideMethod (c$, "toString", +function () { +if (this.inf) { +return ""; +} else { +return "" + this.i; +}}); +Clazz.defineMethod (c$, "pluseq", +function (p) { +if (this.inf || p.inf) { +this.setInf (true); +} else { +this.i += p.i; +}return this; +}, "com.stevesoft.pat.patInt"); +Clazz.defineMethod (c$, "mul", +function (p) { +if (this.inf || p.inf) { +return new com.stevesoft.pat.patInf (); +}return new com.stevesoft.pat.patInt (this.i * p.i); +}, "com.stevesoft.pat.patInt"); +Clazz.defineMethod (c$, "mineq", +function (p) { +if (p.inf) { +return this; +}if (this.inf) { +this.i = p.i; +} else if (p.i < this.i) { +this.i = p.i; +}this.setInf (false); +return this; +}, "com.stevesoft.pat.patInt"); +Clazz.defineMethod (c$, "maxeq", +function (p) { +if (this.inf || p.inf) { +this.setInf (true); +return this; +}if (p.i > this.i) { +this.i = p.i; +}return this; +}, "com.stevesoft.pat.patInt"); +Clazz.defineMethod (c$, "finite", +function () { +return !this.inf; +}); +Clazz.defineMethod (c$, "intValue", +function () { +return this.inf ? 2147483647 : this.i; +}); diff --git a/bin/com/stevesoft/pat/wrap/CharArrayBufferWrap.js b/bin/com/stevesoft/pat/wrap/CharArrayBufferWrap.js index cfade25..ce61261 100644 --- a/bin/com/stevesoft/pat/wrap/CharArrayBufferWrap.js +++ b/bin/com/stevesoft/pat/wrap/CharArrayBufferWrap.js @@ -1,38 +1,38 @@ -Clazz.declarePackage ("com.stevesoft.pat.wrap"); -Clazz.load (["com.stevesoft.pat.BasicStringBufferLike", "java.lang.StringBuffer"], "com.stevesoft.pat.wrap.CharArrayBufferWrap", ["com.stevesoft.pat.wrap.CharArrayWrap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.sb = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat.wrap, "CharArrayBufferWrap", null, com.stevesoft.pat.BasicStringBufferLike); -Clazz.prepareFields (c$, function () { -this.sb = new StringBuffer (); -}); -Clazz.overrideMethod (c$, "appendC", -function (c) { -this.sb.append (c); -}, "~S"); -Clazz.overrideMethod (c$, "append", -function (s) { -this.sb.append (s); -}, "~S"); -Clazz.overrideMethod (c$, "toStringLike", -function () { -var ca = Clazz.newCharArray (this.sb.length (), '\0'); -for (var i = 0; i < ca.length; i++) { -ca[i] = this.sb.charAt (i); -} -return new com.stevesoft.pat.wrap.CharArrayWrap (ca); -}); -Clazz.defineMethod (c$, "length", -function () { -return this.sb.length (); -}); -Clazz.overrideMethod (c$, "toString", -function () { -return this.sb.toString (); -}); -Clazz.overrideMethod (c$, "unwrap", -function () { -return this.sb; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat.wrap"); +Clazz.load (["com.stevesoft.pat.BasicStringBufferLike", "java.lang.StringBuffer"], "com.stevesoft.pat.wrap.CharArrayBufferWrap", ["com.stevesoft.pat.wrap.CharArrayWrap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.sb = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat.wrap, "CharArrayBufferWrap", null, com.stevesoft.pat.BasicStringBufferLike); +Clazz.prepareFields (c$, function () { +this.sb = new StringBuffer (); +}); +Clazz.overrideMethod (c$, "appendC", +function (c) { +this.sb.append (c); +}, "~S"); +Clazz.overrideMethod (c$, "append", +function (s) { +this.sb.append (s); +}, "~S"); +Clazz.overrideMethod (c$, "toStringLike", +function () { +var ca = Clazz.newCharArray (this.sb.length (), '\0'); +for (var i = 0; i < ca.length; i++) { +ca[i] = this.sb.charAt (i); +} +return new com.stevesoft.pat.wrap.CharArrayWrap (ca); +}); +Clazz.defineMethod (c$, "length", +function () { +return this.sb.length (); +}); +Clazz.overrideMethod (c$, "toString", +function () { +return this.sb.toString (); +}); +Clazz.overrideMethod (c$, "unwrap", +function () { +return this.sb; +}); +}); diff --git a/bin/com/stevesoft/pat/wrap/CharArrayWrap.js b/bin/com/stevesoft/pat/wrap/CharArrayWrap.js index 374d1dd..679bede 100644 --- a/bin/com/stevesoft/pat/wrap/CharArrayWrap.js +++ b/bin/com/stevesoft/pat/wrap/CharArrayWrap.js @@ -1,51 +1,51 @@ -Clazz.declarePackage ("com.stevesoft.pat.wrap"); -Clazz.load (["com.stevesoft.pat.StringLike"], "com.stevesoft.pat.wrap.CharArrayWrap", ["com.stevesoft.pat.wrap.CharArrayBufferWrap", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ca = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat.wrap, "CharArrayWrap", null, com.stevesoft.pat.StringLike); -Clazz.defineMethod (c$, "getCharArray", -function () { -return this.ca; -}); -Clazz.makeConstructor (c$, -function (ca) { -this.ca = ca; -}, "~A"); -Clazz.overrideMethod (c$, "toString", -function () { -return String.instantialize (this.ca); -}); -Clazz.overrideMethod (c$, "charAt", -function (i) { -return this.ca[i]; -}, "~N"); -Clazz.overrideMethod (c$, "length", -function () { -return this.ca.length; -}); -Clazz.overrideMethod (c$, "substring", -function (i1, i2) { -var sb = new StringBuffer (); -for (var i = i1; i < i2; i++) { -sb.append (this.ca[i]); -} -return sb.toString (); -}, "~N,~N"); -Clazz.overrideMethod (c$, "unwrap", -function () { -return this.ca; -}); -Clazz.overrideMethod (c$, "newStringBufferLike", -function () { -return new com.stevesoft.pat.wrap.CharArrayBufferWrap (); -}); -Clazz.overrideMethod (c$, "indexOf", -function (c) { -for (var i = 0; i < this.ca.length; i++) { -if (this.ca[i] == c) { -return i; -}} -return -1; -}, "~S"); -}); +Clazz.declarePackage ("com.stevesoft.pat.wrap"); +Clazz.load (["com.stevesoft.pat.StringLike"], "com.stevesoft.pat.wrap.CharArrayWrap", ["com.stevesoft.pat.wrap.CharArrayBufferWrap", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ca = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat.wrap, "CharArrayWrap", null, com.stevesoft.pat.StringLike); +Clazz.defineMethod (c$, "getCharArray", +function () { +return this.ca; +}); +Clazz.makeConstructor (c$, +function (ca) { +this.ca = ca; +}, "~A"); +Clazz.overrideMethod (c$, "toString", +function () { +return String.instantialize (this.ca); +}); +Clazz.overrideMethod (c$, "charAt", +function (i) { +return this.ca[i]; +}, "~N"); +Clazz.overrideMethod (c$, "length", +function () { +return this.ca.length; +}); +Clazz.overrideMethod (c$, "substring", +function (i1, i2) { +var sb = new StringBuffer (); +for (var i = i1; i < i2; i++) { +sb.append (this.ca[i]); +} +return sb.toString (); +}, "~N,~N"); +Clazz.overrideMethod (c$, "unwrap", +function () { +return this.ca; +}); +Clazz.overrideMethod (c$, "newStringBufferLike", +function () { +return new com.stevesoft.pat.wrap.CharArrayBufferWrap (); +}); +Clazz.overrideMethod (c$, "indexOf", +function (c) { +for (var i = 0; i < this.ca.length; i++) { +if (this.ca[i] == c) { +return i; +}} +return -1; +}, "~S"); +}); diff --git a/bin/com/stevesoft/pat/wrap/RandomAccessFileWrap.js b/bin/com/stevesoft/pat/wrap/RandomAccessFileWrap.js index a2b42c5..3b115fe 100644 --- a/bin/com/stevesoft/pat/wrap/RandomAccessFileWrap.js +++ b/bin/com/stevesoft/pat/wrap/RandomAccessFileWrap.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("com.stevesoft.pat.wrap"); -c$ = Clazz.declareType (com.stevesoft.pat.wrap, "RandomAccessFileWrap"); +Clazz.declarePackage ("com.stevesoft.pat.wrap"); +c$ = Clazz.declareType (com.stevesoft.pat.wrap, "RandomAccessFileWrap"); diff --git a/bin/com/stevesoft/pat/wrap/StringBufferWrap.js b/bin/com/stevesoft/pat/wrap/StringBufferWrap.js index 811c548..ea57230 100644 --- a/bin/com/stevesoft/pat/wrap/StringBufferWrap.js +++ b/bin/com/stevesoft/pat/wrap/StringBufferWrap.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("com.stevesoft.pat.wrap"); -Clazz.load (["com.stevesoft.pat.BasicStringBufferLike", "java.lang.StringBuffer"], "com.stevesoft.pat.wrap.StringBufferWrap", ["com.stevesoft.pat.wrap.StringWrap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.sb = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat.wrap, "StringBufferWrap", null, com.stevesoft.pat.BasicStringBufferLike); -Clazz.prepareFields (c$, function () { -this.sb = new StringBuffer (); -}); -Clazz.overrideMethod (c$, "appendC", -function (c) { -this.sb.append (c); -}, "~S"); -Clazz.overrideMethod (c$, "append", -function (s) { -this.sb.append (s); -}, "~S"); -Clazz.defineMethod (c$, "length", -function () { -return this.sb.length (); -}); -Clazz.overrideMethod (c$, "toString", -function () { -return this.sb.toString (); -}); -Clazz.overrideMethod (c$, "toStringLike", -function () { -return new com.stevesoft.pat.wrap.StringWrap (this.sb.toString ()); -}); -Clazz.overrideMethod (c$, "unwrap", -function () { -return this.sb; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat.wrap"); +Clazz.load (["com.stevesoft.pat.BasicStringBufferLike", "java.lang.StringBuffer"], "com.stevesoft.pat.wrap.StringBufferWrap", ["com.stevesoft.pat.wrap.StringWrap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.sb = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat.wrap, "StringBufferWrap", null, com.stevesoft.pat.BasicStringBufferLike); +Clazz.prepareFields (c$, function () { +this.sb = new StringBuffer (); +}); +Clazz.overrideMethod (c$, "appendC", +function (c) { +this.sb.append (c); +}, "~S"); +Clazz.overrideMethod (c$, "append", +function (s) { +this.sb.append (s); +}, "~S"); +Clazz.defineMethod (c$, "length", +function () { +return this.sb.length (); +}); +Clazz.overrideMethod (c$, "toString", +function () { +return this.sb.toString (); +}); +Clazz.overrideMethod (c$, "toStringLike", +function () { +return new com.stevesoft.pat.wrap.StringWrap (this.sb.toString ()); +}); +Clazz.overrideMethod (c$, "unwrap", +function () { +return this.sb; +}); +}); diff --git a/bin/com/stevesoft/pat/wrap/StringWrap.js b/bin/com/stevesoft/pat/wrap/StringWrap.js index d8e9dfe..a468b0d 100644 --- a/bin/com/stevesoft/pat/wrap/StringWrap.js +++ b/bin/com/stevesoft/pat/wrap/StringWrap.js @@ -1,39 +1,39 @@ -Clazz.declarePackage ("com.stevesoft.pat.wrap"); -Clazz.load (["com.stevesoft.pat.StringLike"], "com.stevesoft.pat.wrap.StringWrap", ["com.stevesoft.pat.wrap.StringBufferWrap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.s = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat.wrap, "StringWrap", null, com.stevesoft.pat.StringLike); -Clazz.makeConstructor (c$, -function (s) { -this.s = s; -}, "~S"); -Clazz.overrideMethod (c$, "toString", -function () { -return this.s; -}); -Clazz.overrideMethod (c$, "charAt", -function (i) { -return this.s.charAt (i); -}, "~N"); -Clazz.overrideMethod (c$, "length", -function () { -return this.s.length; -}); -Clazz.overrideMethod (c$, "substring", -function (i1, i2) { -return this.s.substring (i1, i2); -}, "~N,~N"); -Clazz.overrideMethod (c$, "unwrap", -function () { -return this.s; -}); -Clazz.overrideMethod (c$, "newStringBufferLike", -function () { -return new com.stevesoft.pat.wrap.StringBufferWrap (); -}); -Clazz.overrideMethod (c$, "indexOf", -function (c) { -return this.s.indexOf (c); -}, "~S"); -}); +Clazz.declarePackage ("com.stevesoft.pat.wrap"); +Clazz.load (["com.stevesoft.pat.StringLike"], "com.stevesoft.pat.wrap.StringWrap", ["com.stevesoft.pat.wrap.StringBufferWrap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.s = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat.wrap, "StringWrap", null, com.stevesoft.pat.StringLike); +Clazz.makeConstructor (c$, +function (s) { +this.s = s; +}, "~S"); +Clazz.overrideMethod (c$, "toString", +function () { +return this.s; +}); +Clazz.overrideMethod (c$, "charAt", +function (i) { +return this.s.charAt (i); +}, "~N"); +Clazz.overrideMethod (c$, "length", +function () { +return this.s.length; +}); +Clazz.overrideMethod (c$, "substring", +function (i1, i2) { +return this.s.substring (i1, i2); +}, "~N,~N"); +Clazz.overrideMethod (c$, "unwrap", +function () { +return this.s; +}); +Clazz.overrideMethod (c$, "newStringBufferLike", +function () { +return new com.stevesoft.pat.wrap.StringBufferWrap (); +}); +Clazz.overrideMethod (c$, "indexOf", +function (c) { +return this.s.indexOf (c); +}, "~S"); +}); diff --git a/bin/com/stevesoft/pat/wrap/WriterWrap.js b/bin/com/stevesoft/pat/wrap/WriterWrap.js index 4c80649..9eff73c 100644 --- a/bin/com/stevesoft/pat/wrap/WriterWrap.js +++ b/bin/com/stevesoft/pat/wrap/WriterWrap.js @@ -1,41 +1,41 @@ -Clazz.declarePackage ("com.stevesoft.pat.wrap"); -Clazz.load (["com.stevesoft.pat.BasicStringBufferLike"], "com.stevesoft.pat.wrap.WriterWrap", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.w = null; -Clazz.instantialize (this, arguments); -}, com.stevesoft.pat.wrap, "WriterWrap", null, com.stevesoft.pat.BasicStringBufferLike); -Clazz.makeConstructor (c$, -function (w) { -this.w = w; -}, "java.io.Writer"); -Clazz.overrideMethod (c$, "appendC", -function (c) { -try { -this.w.write ((c).charCodeAt (0)); -} catch (ioe) { -if (Clazz.exceptionOf (ioe, java.io.IOException)) { -} else { -throw ioe; -} -} -}, "~S"); -Clazz.overrideMethod (c$, "append", -function (s) { -try { -this.w.write (s); -} catch (ioe) { -if (Clazz.exceptionOf (ioe, java.io.IOException)) { -} else { -throw ioe; -} -} -}, "~S"); -Clazz.overrideMethod (c$, "toStringLike", -function () { -return null; -}); -Clazz.overrideMethod (c$, "unwrap", -function () { -return this.w; -}); -}); +Clazz.declarePackage ("com.stevesoft.pat.wrap"); +Clazz.load (["com.stevesoft.pat.BasicStringBufferLike"], "com.stevesoft.pat.wrap.WriterWrap", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.w = null; +Clazz.instantialize (this, arguments); +}, com.stevesoft.pat.wrap, "WriterWrap", null, com.stevesoft.pat.BasicStringBufferLike); +Clazz.makeConstructor (c$, +function (w) { +this.w = w; +}, "java.io.Writer"); +Clazz.overrideMethod (c$, "appendC", +function (c) { +try { +this.w.write ((c).charCodeAt (0)); +} catch (ioe) { +if (Clazz.exceptionOf (ioe, java.io.IOException)) { +} else { +throw ioe; +} +} +}, "~S"); +Clazz.overrideMethod (c$, "append", +function (s) { +try { +this.w.write (s); +} catch (ioe) { +if (Clazz.exceptionOf (ioe, java.io.IOException)) { +} else { +throw ioe; +} +} +}, "~S"); +Clazz.overrideMethod (c$, "toStringLike", +function () { +return null; +}); +Clazz.overrideMethod (c$, "unwrap", +function () { +return this.w; +}); +}); diff --git a/bin/fr/orsay/lri/varna/models/rna/RNA.js b/bin/fr/orsay/lri/varna/models/rna/RNA.js index 18df75b..c762cf3 100644 --- a/bin/fr/orsay/lri/varna/models/rna/RNA.js +++ b/bin/fr/orsay/lri/varna/models/rna/RNA.js @@ -1,10 +1,10 @@ -Clazz.declarePackage ("fr.orsay.lri.varna.models.rna"); -c$ = Clazz.declareType (fr.orsay.lri.varna.models.rna, "RNA"); -Clazz.defineMethod (c$, "getSize", -function () { -return 0; -}); -Clazz.defineMethod (c$, "getStructDBN", -function (b) { -return null; -}, "~B"); +Clazz.declarePackage ("fr.orsay.lri.varna.models.rna"); +c$ = Clazz.declareType (fr.orsay.lri.varna.models.rna, "RNA"); +Clazz.defineMethod (c$, "getSize", +function () { +return 0; +}); +Clazz.defineMethod (c$, "getStructDBN", +function (b) { +return null; +}, "~B"); diff --git a/bin/jalview/analysis/AAFrequency.class b/bin/jalview/analysis/AAFrequency.class index 4b1e306..89830d7 100644 Binary files a/bin/jalview/analysis/AAFrequency.class and b/bin/jalview/analysis/AAFrequency.class differ diff --git a/bin/jalview/analysis/AAFrequency.js b/bin/jalview/analysis/AAFrequency.js index 8e3d4c5..a7a69d1 100644 --- a/bin/jalview/analysis/AAFrequency.js +++ b/bin/jalview/analysis/AAFrequency.js @@ -1,308 +1,308 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.AAFrequency", ["jalview.analysis.CodingUtils", "jalview.datamodel.Annotation", "jalview.util.Format", "$.MappingUtils", "$.QuickSort", "java.lang.Float", "$.StringBuilder", "java.util.Arrays", "$.Hashtable"], function () { -c$ = Clazz.declareType (jalview.analysis, "AAFrequency"); -c$.calculate = Clazz.defineMethod (c$, "calculate", -function (list, start, end) { -return jalview.analysis.AAFrequency.calculate (list, start, end, false); -}, "java.util.List,~N,~N"); -c$.calculate = Clazz.defineMethod (c$, "calculate", -function (sequences, start, end, profile) { -var seqs = new Array (sequences.size ()); -var width = 0; -{ -for (var i = 0; i < sequences.size (); i++) { -seqs[i] = sequences.get (i); -if (seqs[i].getLength () > width) { -width = seqs[i].getLength (); -}} -var reply = new Array (width); -if (end >= width) { -end = width; -}jalview.analysis.AAFrequency.calculate (seqs, start, end, reply, profile); -return reply; -}}, "java.util.List,~N,~N,~B"); -c$.calculate = Clazz.defineMethod (c$, "calculate", -function (sequences, start, end, result, profile) { -var residueHash; -var maxCount; -var nongap; -var i; -var j; -var v; -var jSize = sequences.length; -var maxResidue; -var c = '-'; -var percentage; -var values = Clazz.newIntArray (255, 0); -var seq; -for (i = start; i < end; i++) { -residueHash = new java.util.Hashtable (); -maxCount = 0; -maxResidue = ""; -nongap = 0; -values = Clazz.newIntArray (255, 0); -for (j = 0; j < jSize; j++) { -if (sequences[j] == null) { -System.err.println ("WARNING: Consensus skipping null sequence - possible race condition."); -continue; -}seq = sequences[j].getSequence (); -if (seq.length > i) { -c = seq[i]; -if (c == '.' || c == ' ') { -c = '-'; -}if (c == '-') { -values['-'.charCodeAt (0)]++; -continue; -} else if ('a' <= c && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) + -32); -}nongap++; -values[c.charCodeAt (0)]++; -} else { -values['-'.charCodeAt (0)]++; -}} -if (jSize == 1) { -maxResidue = String.valueOf (c); -maxCount = 1; -} else { -for (v = 65; v <= 90; v++) { -if (values[v] < 1 || values[v] < maxCount) { -continue; -}if (values[v] > maxCount) { -maxResidue = jalview.analysis.AAFrequency.CHARS[v - 65]; -} else if (values[v] == maxCount) { -maxResidue += jalview.analysis.AAFrequency.CHARS[v - 65]; -}maxCount = values[v]; -} -}if (maxResidue.length == 0) { -maxResidue = "-"; -}if (profile) { -residueHash.put ("P", Clazz.newArray (-1, [values, Clazz.newIntArray (-1, [jSize, nongap])])); -}residueHash.put ("C", new Integer (maxCount)); -residueHash.put ("R", maxResidue); -percentage = (maxCount * 100) / jSize; -residueHash.put ("G", new Float (percentage)); -if (nongap > 0) { -percentage = (maxCount * 100) / nongap; -}residueHash.put ("N", new Float (percentage)); -result[i] = residueHash; -} -}, "~A,~N,~N,~A,~B"); -c$.completeConsensus = Clazz.defineMethod (c$, "completeConsensus", -function (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, nseq) { -jalview.analysis.AAFrequency.completeConsensus (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); -}, "jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~N"); -c$.completeConsensus = Clazz.defineMethod (c$, "completeConsensus", -function (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, alphabet, nseq) { -if (consensus == null || consensus.annotations == null || consensus.annotations.length < width) { -return; -}var fmt = jalview.analysis.AAFrequency.getPercentageFormat (nseq); -for (var i = iStart; i < width; i++) { -var hci; -if (i >= hconsensus.length || ((hci = hconsensus[i]) == null)) { -consensus.annotations[i] = null; -continue; -}var fv = hci.get (ignoreGapsInConsensusCalculation ? "N" : "G"); -if (fv == null) { -consensus.annotations[i] = null; -continue; -}var value = fv.floatValue (); -var maxRes = hci.get ("R").toString (); -var mouseOver = new StringBuilder (64); -if (maxRes.length > 1) { -mouseOver.append ("[").append (maxRes).append ("] "); -maxRes = "+"; -} else { -mouseOver.append (hci.get ("R") + " "); -}var profile = hci.get ("P"); -if (profile != null && includeAllConsSymbols) { -var sequenceCount = profile[1][0]; -var nonGappedCount = profile[1][1]; -var normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount : sequenceCount; -mouseOver.setLength (0); -if (alphabet != null) { -for (var c = 0; c < alphabet.length; c++) { -var tval = profile[0][alphabet[c].charCodeAt (0)] * 100 / normalisedBy; -mouseOver.append (((c == 0) ? "" : "; ")).append (alphabet[c]).append (" ").append (((fmt != null) ? fmt.formDouble (tval) : (Clazz.floatToInt (tval)))).append ("%"); -} -} else { -var ca = Clazz.newCharArray (profile[0].length, '\0'); -var vl = Clazz.newFloatArray (profile[0].length, 0); -for (var c = 0; c < ca.length; c++) { -ca[c] = String.fromCharCode (c); -vl[c] = profile[0][c]; -} -jalview.util.QuickSort.sortFloatChar (vl, ca); -for (var p = 0, c = ca.length - 1; profile[0][ca[c].charCodeAt (0)] > 0; c--) { -var residue = ca[c]; -if (residue != '-') { -var tval = profile[0][residue.charCodeAt (0)] * 100 / normalisedBy; -mouseOver.append ((((p == 0) ? "" : "; "))).append (residue).append (" ").append (((fmt != null) ? fmt.formDouble (tval) : (Clazz.floatToInt (tval)))).append ("%"); -p++; -}} -}} else { -mouseOver.append ((((fmt != null) ? fmt.formDouble (value) : (Clazz.floatToInt (value))))).append ("%"); -}consensus.annotations[i] = new jalview.datamodel.Annotation (maxRes, mouseOver.toString (), ' ', value); -} -}, "jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~A,~N"); -c$.getPercentageFormat = Clazz.defineMethod (c$, "getPercentageFormat", -function (nseq) { -var scale = 0; -while (nseq >= 10) { -scale++; -nseq /= 10; -} -return scale <= 1 ? null : new jalview.util.Format ("%3." + (scale - 1) + "f"); -}, "~N"); -c$.extractProfile = Clazz.defineMethod (c$, "extractProfile", -function (hconsensus, ignoreGaps) { -var rtnval = Clazz.newIntArray (64, 0); -var profile = hconsensus.get ("P"); -if (profile == null) { -return null; -}var ca = Clazz.newCharArray (profile[0].length, '\0'); -var vl = Clazz.newFloatArray (profile[0].length, 0); -for (var c = 0; c < ca.length; c++) { -ca[c] = String.fromCharCode (c); -vl[c] = profile[0][c]; -} -jalview.util.QuickSort.sortFloatChar (vl, ca); -var nextArrayPos = 2; -var totalPercentage = 0; -var distinctValuesCount = 0; -var divisor = profile[1][ignoreGaps ? 1 : 0]; -for (var c = ca.length - 1; profile[0][ca[c].charCodeAt (0)] > 0; c--) { -if (ca[c] != '-') { -rtnval[nextArrayPos++] = (ca[c]).charCodeAt (0); -var percentage = Clazz.floatToInt (profile[0][ca[c].charCodeAt (0)] * 100 / divisor); -rtnval[nextArrayPos++] = percentage; -totalPercentage += percentage; -distinctValuesCount++; -}} -rtnval[0] = distinctValuesCount; -rtnval[1] = totalPercentage; -var result = Clazz.newIntArray (rtnval.length + 1, 0); -result[0] = 0; -System.arraycopy (rtnval, 0, result, 1, rtnval.length); -return result; -}, "java.util.Hashtable,~B"); -c$.extractCdnaProfile = Clazz.defineMethod (c$, "extractCdnaProfile", -function (hashtable, ignoreGaps) { -var codonCounts = hashtable.get ("P"); -var sortedCounts = Clazz.newIntArray (codonCounts.length - 2, 0); -System.arraycopy (codonCounts, 2, sortedCounts, 0, codonCounts.length - 2); -var result = Clazz.newIntArray (3 + 2 * sortedCounts.length, 0); -result[0] = 2; -var codons = Clazz.newCharArray (sortedCounts.length, '\0'); -for (var i = 0; i < codons.length; i++) { -codons[i] = String.fromCharCode (i); -} -jalview.util.QuickSort.sortIntChar (sortedCounts, codons); -var totalPercentage = 0; -var distinctValuesCount = 0; -var j = 3; -var divisor = ignoreGaps ? codonCounts[1] : codonCounts[0]; -for (var i = codons.length - 1; i >= 0; i--) { -var codonCount = sortedCounts[i]; -if (codonCount == 0) { -break; -}distinctValuesCount++; -result[j++] = (codons[i]).charCodeAt (0); -var percentage = Clazz.doubleToInt (codonCount * 100 / divisor); -result[j++] = percentage; -totalPercentage += percentage; -} -result[2] = totalPercentage; -result[1] = distinctValuesCount; -return java.util.Arrays.copyOfRange (result, 0, j); -}, "java.util.Hashtable,~B"); -c$.calculateCdna = Clazz.defineMethod (c$, "calculateCdna", -function (alignment, mappings, hconsensus, col0, col1) { -var gapCharacter = alignment.getGapCharacter (); -for (var col = col0; col < col1; col++) { -var columnHash = new java.util.Hashtable (); -var codonCounts = Clazz.newIntArray (66, 0); -codonCounts[0] = alignment.getSequences ().size (); -var ungappedCount = 0; -for (var seq, $seq = alignment.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -if (seq.getCharAt (col) == gapCharacter) { -continue; -}var codon = jalview.util.MappingUtils.findCodonFor (seq, col, mappings); -var codonEncoded = jalview.analysis.CodingUtils.encodeCodon (codon); -if (codonEncoded >= 0) { -codonCounts[codonEncoded + 2]++; -ungappedCount++; -}} -codonCounts[1] = ungappedCount; -columnHash.put ("P", codonCounts); -hconsensus[col] = columnHash; -} -}, "jalview.datamodel.AlignmentI,java.util.Set,~A,~N,~N"); -c$.completeCdnaConsensus = Clazz.defineMethod (c$, "completeCdnaConsensus", -function (consensusAnnotation, consensusData, showProfileLogo, nseqs) { -if (consensusAnnotation == null || consensusAnnotation.annotations == null || consensusAnnotation.annotations.length < consensusData.length) { -return; -}consensusAnnotation.scaleColLabel = true; -for (var col = 0; col < consensusData.length; col++) { -var hci = consensusData[col]; -if (hci == null) { -continue; -}var codonCounts = hci.get ("P"); -var totalCount = 0; -var codons = Clazz.newCharArray (codonCounts.length - 2, '\0'); -for (var j = 2; j < codonCounts.length; j++) { -var codonCount = codonCounts[j]; -codons[j - 2] = String.fromCharCode (j - 2); -totalCount += codonCount; -} -var sortedCodonCounts = Clazz.newIntArray (codonCounts.length - 2, 0); -System.arraycopy (codonCounts, 2, sortedCodonCounts, 0, codonCounts.length - 2); -jalview.util.QuickSort.sortIntChar (sortedCodonCounts, codons); -var modalCodonEncoded = (codons[codons.length - 1]).charCodeAt (0); -var modalCodonCount = sortedCodonCounts[codons.length - 1]; -var modalCodon = String.valueOf (jalview.analysis.CodingUtils.decodeCodon (modalCodonEncoded)); -if (sortedCodonCounts.length > 1 && sortedCodonCounts[codons.length - 2] == modalCodonEncoded) { -modalCodon = "+"; -}var pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100 / totalCount; -var mouseOver = new StringBuilder (32); -var samePercent = new StringBuilder (); -var percent = null; -var lastPercent = null; -var fmt = jalview.analysis.AAFrequency.getPercentageFormat (nseqs); -for (var j = codons.length - 1; j >= 0; j--) { -var codonCount = sortedCodonCounts[j]; -if (codonCount == 0) { -if (samePercent.length () > 0) { -mouseOver.append (samePercent).append (": ").append (percent).append ("% "); -}break; -}var codonEncoded = (codons[j]).charCodeAt (0); -var pct = Clazz.doubleToInt (codonCount * 100 / totalCount); -var codon = String.valueOf (jalview.analysis.CodingUtils.decodeCodon (codonEncoded)); -percent = fmt == null ? Integer.toString (pct) : fmt.formLong (pct); -if (showProfileLogo || codonCount == modalCodonCount) { -if (percent.equals (lastPercent) && j > 0) { -samePercent.append (samePercent.length () == 0 ? "" : ", "); -samePercent.append (codon); -} else { -if (samePercent.length () > 0) { -mouseOver.append (samePercent).append (": ").append (lastPercent).append ("% "); -}samePercent.setLength (0); -samePercent.append (codon); -}lastPercent = percent; -}} -consensusAnnotation.annotations[col] = new jalview.datamodel.Annotation (modalCodon, mouseOver.toString (), ' ', pid); -} -}, "jalview.datamodel.AlignmentAnnotation,~A,~B,~N"); -Clazz.defineStatics (c$, -"TO_UPPER_CASE", -32, -"MAXCOUNT", "C", -"MAXRESIDUE", "R", -"PID_GAPS", "G", -"PID_NOGAPS", "N", -"PROFILE", "P", -"ENCODED_CHARS", "E"); -c$.CHARS = c$.prototype.CHARS = new Array (26); -{ -for (var c = 'A'; c <= 'Z'; c = String.fromCharCode (c.charCodeAt (0) + 1)) { -jalview.analysis.AAFrequency.CHARS[c.charCodeAt (0) - 65] = String.valueOf (c); -} -}}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.AAFrequency", ["jalview.analysis.CodingUtils", "jalview.datamodel.Annotation", "jalview.util.Format", "$.MappingUtils", "$.QuickSort", "java.lang.Float", "$.StringBuilder", "java.util.Arrays", "$.Hashtable"], function () { +c$ = Clazz.declareType (jalview.analysis, "AAFrequency"); +c$.calculate = Clazz.defineMethod (c$, "calculate", +function (list, start, end) { +return jalview.analysis.AAFrequency.calculate (list, start, end, false); +}, "java.util.List,~N,~N"); +c$.calculate = Clazz.defineMethod (c$, "calculate", +function (sequences, start, end, profile) { +var seqs = new Array (sequences.size ()); +var width = 0; +{ +for (var i = 0; i < sequences.size (); i++) { +seqs[i] = sequences.get (i); +if (seqs[i].getLength () > width) { +width = seqs[i].getLength (); +}} +var reply = new Array (width); +if (end >= width) { +end = width; +}jalview.analysis.AAFrequency.calculate (seqs, start, end, reply, profile); +return reply; +}}, "java.util.List,~N,~N,~B"); +c$.calculate = Clazz.defineMethod (c$, "calculate", +function (sequences, start, end, result, profile) { +var residueHash; +var maxCount; +var nongap; +var i; +var j; +var v; +var jSize = sequences.length; +var maxResidue; +var c = '-'; +var percentage; +var values = Clazz.newIntArray (255, 0); +var seq; +for (i = start; i < end; i++) { +residueHash = new java.util.Hashtable (); +maxCount = 0; +maxResidue = ""; +nongap = 0; +values = Clazz.newIntArray (255, 0); +for (j = 0; j < jSize; j++) { +if (sequences[j] == null) { +System.err.println ("WARNING: Consensus skipping null sequence - possible race condition."); +continue; +}seq = sequences[j].getSequence (); +if (seq.length > i) { +c = seq[i]; +if (c == '.' || c == ' ') { +c = '-'; +}if (c == '-') { +values['-'.charCodeAt (0)]++; +continue; +} else if ('a' <= c && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) + -32); +}nongap++; +values[c.charCodeAt (0)]++; +} else { +values['-'.charCodeAt (0)]++; +}} +if (jSize == 1) { +maxResidue = String.valueOf (c); +maxCount = 1; +} else { +for (v = 65; v <= 90; v++) { +if (values[v] < 1 || values[v] < maxCount) { +continue; +}if (values[v] > maxCount) { +maxResidue = jalview.analysis.AAFrequency.CHARS[v - 65]; +} else if (values[v] == maxCount) { +maxResidue += jalview.analysis.AAFrequency.CHARS[v - 65]; +}maxCount = values[v]; +} +}if (maxResidue.length == 0) { +maxResidue = "-"; +}if (profile) { +residueHash.put ("P", Clazz.newArray (-1, [values, Clazz.newIntArray (-1, [jSize, nongap])])); +}residueHash.put ("C", new Integer (maxCount)); +residueHash.put ("R", maxResidue); +percentage = (maxCount * 100) / jSize; +residueHash.put ("G", new Float (percentage)); +if (nongap > 0) { +percentage = (maxCount * 100) / nongap; +}residueHash.put ("N", new Float (percentage)); +result[i] = residueHash; +} +}, "~A,~N,~N,~A,~B"); +c$.completeConsensus = Clazz.defineMethod (c$, "completeConsensus", +function (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, nseq) { +jalview.analysis.AAFrequency.completeConsensus (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); +}, "jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~N"); +c$.completeConsensus = Clazz.defineMethod (c$, "completeConsensus", +function (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, alphabet, nseq) { +if (consensus == null || consensus.annotations == null || consensus.annotations.length < width) { +return; +}var fmt = jalview.analysis.AAFrequency.getPercentageFormat (nseq); +for (var i = iStart; i < width; i++) { +var hci; +if (i >= hconsensus.length || ((hci = hconsensus[i]) == null)) { +consensus.annotations[i] = null; +continue; +}var fv = hci.get (ignoreGapsInConsensusCalculation ? "N" : "G"); +if (fv == null) { +consensus.annotations[i] = null; +continue; +}var value = fv.floatValue (); +var maxRes = hci.get ("R").toString (); +var mouseOver = new StringBuilder (64); +if (maxRes.length > 1) { +mouseOver.append ("[").append (maxRes).append ("] "); +maxRes = "+"; +} else { +mouseOver.append (hci.get ("R") + " "); +}var profile = hci.get ("P"); +if (profile != null && includeAllConsSymbols) { +var sequenceCount = profile[1][0]; +var nonGappedCount = profile[1][1]; +var normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount : sequenceCount; +mouseOver.setLength (0); +if (alphabet != null) { +for (var c = 0; c < alphabet.length; c++) { +var tval = profile[0][alphabet[c].charCodeAt (0)] * 100 / normalisedBy; +mouseOver.append (((c == 0) ? "" : "; ")).append (alphabet[c]).append (" ").append (((fmt != null) ? fmt.formDouble (tval) : (Clazz.floatToInt (tval)))).append ("%"); +} +} else { +var ca = Clazz.newCharArray (profile[0].length, '\0'); +var vl = Clazz.newFloatArray (profile[0].length, 0); +for (var c = 0; c < ca.length; c++) { +ca[c] = String.fromCharCode (c); +vl[c] = profile[0][c]; +} +jalview.util.QuickSort.sortFloatChar (vl, ca); +for (var p = 0, c = ca.length - 1; profile[0][ca[c].charCodeAt (0)] > 0; c--) { +var residue = ca[c]; +if (residue != '-') { +var tval = profile[0][residue.charCodeAt (0)] * 100 / normalisedBy; +mouseOver.append ((((p == 0) ? "" : "; "))).append (residue).append (" ").append (((fmt != null) ? fmt.formDouble (tval) : (Clazz.floatToInt (tval)))).append ("%"); +p++; +}} +}} else { +mouseOver.append ((((fmt != null) ? fmt.formDouble (value) : (Clazz.floatToInt (value))))).append ("%"); +}consensus.annotations[i] = new jalview.datamodel.Annotation (maxRes, mouseOver.toString (), ' ', value); +} +}, "jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~A,~N"); +c$.getPercentageFormat = Clazz.defineMethod (c$, "getPercentageFormat", +function (nseq) { +var scale = 0; +while (nseq >= 10) { +scale++; +nseq /= 10; +} +return scale <= 1 ? null : new jalview.util.Format ("%3." + (scale - 1) + "f"); +}, "~N"); +c$.extractProfile = Clazz.defineMethod (c$, "extractProfile", +function (hconsensus, ignoreGaps) { +var rtnval = Clazz.newIntArray (64, 0); +var profile = hconsensus.get ("P"); +if (profile == null) { +return null; +}var ca = Clazz.newCharArray (profile[0].length, '\0'); +var vl = Clazz.newFloatArray (profile[0].length, 0); +for (var c = 0; c < ca.length; c++) { +ca[c] = String.fromCharCode (c); +vl[c] = profile[0][c]; +} +jalview.util.QuickSort.sortFloatChar (vl, ca); +var nextArrayPos = 2; +var totalPercentage = 0; +var distinctValuesCount = 0; +var divisor = profile[1][ignoreGaps ? 1 : 0]; +for (var c = ca.length - 1; profile[0][ca[c].charCodeAt (0)] > 0; c--) { +if (ca[c] != '-') { +rtnval[nextArrayPos++] = (ca[c]).charCodeAt (0); +var percentage = Clazz.floatToInt (profile[0][ca[c].charCodeAt (0)] * 100 / divisor); +rtnval[nextArrayPos++] = percentage; +totalPercentage += percentage; +distinctValuesCount++; +}} +rtnval[0] = distinctValuesCount; +rtnval[1] = totalPercentage; +var result = Clazz.newIntArray (rtnval.length + 1, 0); +result[0] = 0; +System.arraycopy (rtnval, 0, result, 1, rtnval.length); +return result; +}, "java.util.Hashtable,~B"); +c$.extractCdnaProfile = Clazz.defineMethod (c$, "extractCdnaProfile", +function (hashtable, ignoreGaps) { +var codonCounts = hashtable.get ("P"); +var sortedCounts = Clazz.newIntArray (codonCounts.length - 2, 0); +System.arraycopy (codonCounts, 2, sortedCounts, 0, codonCounts.length - 2); +var result = Clazz.newIntArray (3 + 2 * sortedCounts.length, 0); +result[0] = 2; +var codons = Clazz.newCharArray (sortedCounts.length, '\0'); +for (var i = 0; i < codons.length; i++) { +codons[i] = String.fromCharCode (i); +} +jalview.util.QuickSort.sortIntChar (sortedCounts, codons); +var totalPercentage = 0; +var distinctValuesCount = 0; +var j = 3; +var divisor = ignoreGaps ? codonCounts[1] : codonCounts[0]; +for (var i = codons.length - 1; i >= 0; i--) { +var codonCount = sortedCounts[i]; +if (codonCount == 0) { +break; +}distinctValuesCount++; +result[j++] = (codons[i]).charCodeAt (0); +var percentage = Clazz.doubleToInt (codonCount * 100 / divisor); +result[j++] = percentage; +totalPercentage += percentage; +} +result[2] = totalPercentage; +result[1] = distinctValuesCount; +return java.util.Arrays.copyOfRange (result, 0, j); +}, "java.util.Hashtable,~B"); +c$.calculateCdna = Clazz.defineMethod (c$, "calculateCdna", +function (alignment, mappings, hconsensus, col0, col1) { +var gapCharacter = alignment.getGapCharacter (); +for (var col = col0; col < col1; col++) { +var columnHash = new java.util.Hashtable (); +var codonCounts = Clazz.newIntArray (66, 0); +codonCounts[0] = alignment.getSequences ().size (); +var ungappedCount = 0; +for (var seq, $seq = alignment.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +if (seq.getCharAt (col) == gapCharacter) { +continue; +}var codon = jalview.util.MappingUtils.findCodonFor (seq, col, mappings); +var codonEncoded = jalview.analysis.CodingUtils.encodeCodon (codon); +if (codonEncoded >= 0) { +codonCounts[codonEncoded + 2]++; +ungappedCount++; +}} +codonCounts[1] = ungappedCount; +columnHash.put ("P", codonCounts); +hconsensus[col] = columnHash; +} +}, "jalview.datamodel.AlignmentI,java.util.Set,~A,~N,~N"); +c$.completeCdnaConsensus = Clazz.defineMethod (c$, "completeCdnaConsensus", +function (consensusAnnotation, consensusData, showProfileLogo, nseqs) { +if (consensusAnnotation == null || consensusAnnotation.annotations == null || consensusAnnotation.annotations.length < consensusData.length) { +return; +}consensusAnnotation.scaleColLabel = true; +for (var col = 0; col < consensusData.length; col++) { +var hci = consensusData[col]; +if (hci == null) { +continue; +}var codonCounts = hci.get ("P"); +var totalCount = 0; +var codons = Clazz.newCharArray (codonCounts.length - 2, '\0'); +for (var j = 2; j < codonCounts.length; j++) { +var codonCount = codonCounts[j]; +codons[j - 2] = String.fromCharCode (j - 2); +totalCount += codonCount; +} +var sortedCodonCounts = Clazz.newIntArray (codonCounts.length - 2, 0); +System.arraycopy (codonCounts, 2, sortedCodonCounts, 0, codonCounts.length - 2); +jalview.util.QuickSort.sortIntChar (sortedCodonCounts, codons); +var modalCodonEncoded = (codons[codons.length - 1]).charCodeAt (0); +var modalCodonCount = sortedCodonCounts[codons.length - 1]; +var modalCodon = String.valueOf (jalview.analysis.CodingUtils.decodeCodon (modalCodonEncoded)); +if (sortedCodonCounts.length > 1 && sortedCodonCounts[codons.length - 2] == modalCodonEncoded) { +modalCodon = "+"; +}var pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100 / totalCount; +var mouseOver = new StringBuilder (32); +var samePercent = new StringBuilder (); +var percent = null; +var lastPercent = null; +var fmt = jalview.analysis.AAFrequency.getPercentageFormat (nseqs); +for (var j = codons.length - 1; j >= 0; j--) { +var codonCount = sortedCodonCounts[j]; +if (codonCount == 0) { +if (samePercent.length () > 0) { +mouseOver.append (samePercent).append (": ").append (percent).append ("% "); +}break; +}var codonEncoded = (codons[j]).charCodeAt (0); +var pct = Clazz.doubleToInt (codonCount * 100 / totalCount); +var codon = String.valueOf (jalview.analysis.CodingUtils.decodeCodon (codonEncoded)); +percent = fmt == null ? Integer.toString (pct) : fmt.formLong (pct); +if (showProfileLogo || codonCount == modalCodonCount) { +if (percent.equals (lastPercent) && j > 0) { +samePercent.append (samePercent.length () == 0 ? "" : ", "); +samePercent.append (codon); +} else { +if (samePercent.length () > 0) { +mouseOver.append (samePercent).append (": ").append (lastPercent).append ("% "); +}samePercent.setLength (0); +samePercent.append (codon); +}lastPercent = percent; +}} +consensusAnnotation.annotations[col] = new jalview.datamodel.Annotation (modalCodon, mouseOver.toString (), ' ', pid); +} +}, "jalview.datamodel.AlignmentAnnotation,~A,~B,~N"); +Clazz.defineStatics (c$, +"TO_UPPER_CASE", -32, +"MAXCOUNT", "C", +"MAXRESIDUE", "R", +"PID_GAPS", "G", +"PID_NOGAPS", "N", +"PROFILE", "P", +"ENCODED_CHARS", "E"); +c$.CHARS = c$.prototype.CHARS = new Array (26); +{ +for (var c = 'A'; c <= 'Z'; c = String.fromCharCode (c.charCodeAt (0) + 1)) { +jalview.analysis.AAFrequency.CHARS[c.charCodeAt (0) - 65] = String.valueOf (c); +} +}}); diff --git a/bin/jalview/analysis/AlignSeq.class b/bin/jalview/analysis/AlignSeq.class index 7d2744f..b5cdebf 100644 Binary files a/bin/jalview/analysis/AlignSeq.class and b/bin/jalview/analysis/AlignSeq.class differ diff --git a/bin/jalview/analysis/AlignSeq.js b/bin/jalview/analysis/AlignSeq.js index 38f84c2..31dcb24 100644 --- a/bin/jalview/analysis/AlignSeq.js +++ b/bin/jalview/analysis/AlignSeq.js @@ -1,586 +1,586 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["jalview.schemes.ResidueProperties", "java.lang.StringBuffer"], "jalview.analysis.AlignSeq", ["jalview.datamodel.Mapping", "$.Sequence", "jalview.util.Comparison", "$.Format", "$.MapList", "$.MessageManager", "java.awt.Color", "java.lang.Error", "$.StringBuilder", "java.util.ArrayList", "$.Arrays", "$.StringTokenizer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.score = null; -this.E = null; -this.F = null; -this.traceback = null; -this.seq1 = null; -this.seq2 = null; -this.s1 = null; -this.s2 = null; -this.s1str = null; -this.s2str = null; -this.maxi = 0; -this.maxj = 0; -this.aseq1 = null; -this.aseq2 = null; -this.astr1 = ""; -this.astr2 = ""; -this.seq1start = 0; -this.seq1end = 0; -this.seq2start = 0; -this.seq2end = 0; -this.count = 0; -this.maxscore = 0; -this.pid = 0; -this.prev = 0; -this.gapOpen = 120; -this.gapExtend = 20; -this.lookup = null; -this.intToStr = null; -this.defInt = 23; -this.output = null; -this.type = null; -this.charToInt = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "AlignSeq"); -Clazz.prepareFields (c$, function () { -this.lookup = jalview.schemes.ResidueProperties.getBLOSUM62 (); -this.intToStr = jalview.analysis.AlignSeq.pep; -this.output = new StringBuffer (); -}); -Clazz.makeConstructor (c$, -function (s1, s2, type) { -this.SeqInit (s1, s1.getSequenceAsString (), s2, s2.getSequenceAsString (), type); -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S"); -Clazz.makeConstructor (c$, -function (s1, string1, s2, string2, type) { -this.SeqInit (s1, string1.toUpperCase (), s2, string2.toUpperCase (), type); -}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S"); -Clazz.defineMethod (c$, "getMaxScore", -function () { -return this.maxscore; -}); -Clazz.defineMethod (c$, "getSeq2Start", -function () { -return this.seq2start; -}); -Clazz.defineMethod (c$, "getSeq2End", -function () { -return this.seq2end; -}); -Clazz.defineMethod (c$, "getSeq1Start", -function () { -return this.seq1start; -}); -Clazz.defineMethod (c$, "getSeq1End", -function () { -return this.seq1end; -}); -Clazz.defineMethod (c$, "getOutput", -function () { -return this.output.toString (); -}); -Clazz.defineMethod (c$, "getAStr1", -function () { -return this.astr1; -}); -Clazz.defineMethod (c$, "getAStr2", -function () { -return this.astr2; -}); -Clazz.defineMethod (c$, "getASeq1", -function () { -return this.aseq1; -}); -Clazz.defineMethod (c$, "getASeq2", -function () { -return this.aseq2; -}); -Clazz.defineMethod (c$, "getS1", -function () { -return this.s1; -}); -Clazz.defineMethod (c$, "getS2", -function () { -return this.s2; -}); -Clazz.defineMethod (c$, "getAlignedSeq1", -function () { -var alSeq1 = new jalview.datamodel.Sequence (this.s1.getName (), this.getAStr1 ()); -alSeq1.setStart (this.s1.getStart () + this.getSeq1Start () - 1); -alSeq1.setEnd (this.s1.getStart () + this.getSeq1End () - 1); -alSeq1.setDatasetSequence (this.s1.getDatasetSequence () == null ? this.s1 : this.s1.getDatasetSequence ()); -return alSeq1; -}); -Clazz.defineMethod (c$, "getAlignedSeq2", -function () { -var alSeq2 = new jalview.datamodel.Sequence (this.s2.getName (), this.getAStr2 ()); -alSeq2.setStart (this.s2.getStart () + this.getSeq2Start () - 1); -alSeq2.setEnd (this.s2.getStart () + this.getSeq2End () - 1); -alSeq2.setDatasetSequence (this.s2.getDatasetSequence () == null ? this.s2 : this.s2.getDatasetSequence ()); -return alSeq2; -}); -Clazz.defineMethod (c$, "SeqInit", -function (s1, string1, s2, string2, type) { -this.s1 = s1; -this.s2 = s2; -this.setDefaultParams (type); -this.SeqInit (string1, string2); -}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S"); -Clazz.defineMethod (c$, "SeqInit", -function (s1, string1, s2, string2, scoreMatrix) { -this.s1 = s1; -this.s2 = s2; -this.setType (scoreMatrix.isDNA () ? "dna" : "pep"); -this.lookup = scoreMatrix.getMatrix (); -}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,jalview.schemes.ScoreMatrix"); -Clazz.defineMethod (c$, "SeqInit", -($fz = function (string1, string2) { -this.s1str = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, string1); -this.s2str = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, string2); -if (this.s1str.length == 0 || this.s2str.length == 0) { -this.output.append ("ALL GAPS: " + (this.s1str.length == 0 ? this.s1.getName () : " ") + (this.s2str.length == 0 ? this.s2.getName () : "")); -return; -}this.seq1 = Clazz.newIntArray (this.s1str.length, 0); -this.seq2 = Clazz.newIntArray (this.s2str.length, 0); -this.score = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); -this.E = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); -this.F = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); -this.traceback = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); -this.seq1 = this.stringToInt (this.s1str, this.type); -this.seq2 = this.stringToInt (this.s2str, this.type); -}, $fz.isPrivate = true, $fz), "~S,~S"); -Clazz.defineMethod (c$, "setDefaultParams", -($fz = function (type) { -this.setType (type); -if (type.equals ("pep")) { -this.lookup = jalview.schemes.ResidueProperties.getDefaultPeptideMatrix (); -} else if (type.equals ("dna")) { -this.lookup = jalview.schemes.ResidueProperties.getDefaultDnaMatrix (); -}}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "setType", -($fz = function (type2) { -this.type = type2; -if (this.type.equals ("pep")) { -this.intToStr = jalview.analysis.AlignSeq.pep; -this.charToInt = jalview.schemes.ResidueProperties.aaIndex; -this.defInt = 23; -} else if (this.type.equals ("dna")) { -this.intToStr = jalview.analysis.AlignSeq.dna; -this.charToInt = jalview.schemes.ResidueProperties.nucleotideIndex; -this.defInt = 10; -} else { -this.output.append ("Wrong type = dna or pep only"); -throw new Error (jalview.util.MessageManager.formatMessage ("error.unknown_type_dna_or_pep", Clazz.newArray (-1, [type2]))); -}}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "traceAlignment", -function () { -var max = -9999; -for (var i = 0; i < this.seq1.length; i++) { -if (this.score[i][this.seq2.length - 1] > max) { -max = this.score[i][this.seq2.length - 1]; -this.maxi = i; -this.maxj = this.seq2.length - 1; -}} -for (var j = 0; j < this.seq2.length; j++) { -if (this.score[this.seq1.length - 1][j] > max) { -max = this.score[this.seq1.length - 1][j]; -this.maxi = this.seq1.length - 1; -this.maxj = j; -}} -var i = this.maxi; -var j = this.maxj; -var trace; -this.maxscore = Clazz.doubleToInt (this.score[i][j] / 10); -this.seq1end = this.maxi + 1; -this.seq2end = this.maxj + 1; -this.aseq1 = Clazz.newIntArray (this.seq1.length + this.seq2.length, 0); -this.aseq2 = Clazz.newIntArray (this.seq1.length + this.seq2.length, 0); -this.count = (this.seq1.length + this.seq2.length) - 1; -while ((i > 0) && (j > 0)) { -if ((this.aseq1[this.count] != this.defInt) && (i >= 0)) { -this.aseq1[this.count] = this.seq1[i]; -this.astr1 = this.s1str.charAt (i) + this.astr1; -}if ((this.aseq2[this.count] != this.defInt) && (j > 0)) { -this.aseq2[this.count] = this.seq2[j]; -this.astr2 = this.s2str.charAt (j) + this.astr2; -}trace = this.findTrace (i, j); -if (trace == 0) { -i--; -j--; -} else if (trace == 1) { -j--; -this.aseq1[this.count] = this.defInt; -this.astr1 = "-" + this.astr1.substring (1); -} else if (trace == -1) { -i--; -this.aseq2[this.count] = this.defInt; -this.astr2 = "-" + this.astr2.substring (1); -}this.count--; -} -this.seq1start = i + 1; -this.seq2start = j + 1; -if (this.aseq1[this.count] != this.defInt) { -this.aseq1[this.count] = this.seq1[i]; -this.astr1 = this.s1str.charAt (i) + this.astr1; -}if (this.aseq2[this.count] != this.defInt) { -this.aseq2[this.count] = this.seq2[j]; -this.astr2 = this.s2str.charAt (j) + this.astr2; -}}); -Clazz.defineMethod (c$, "printAlignment", -function (os) { -var s1id = this.s1.getName (); -var s2id = this.s2.getName (); -var maxid = this.s1.getName ().length; -if (this.s2.getName ().length > maxid) { -maxid = this.s2.getName ().length; -}if (maxid > 30) { -maxid = 30; -if (this.s1.getName ().length > maxid) { -s1id = this.s1.getName ().substring (0, 30); -}if (this.s2.getName ().length > maxid) { -s2id = this.s2.getName ().substring (0, 30); -}}var len = 72 - maxid - 1; -var nochunks = (Clazz.doubleToInt ((this.aseq1.length - this.count) / len)) + 1; -this.pid = 0; -this.output.append ("Score = ").append (this.score[this.maxi][this.maxj]).append (jalview.analysis.AlignSeq.NEWLINE); -this.output.append ("Length of alignment = ").append (String.valueOf (this.aseq1.length - this.count)).append (jalview.analysis.AlignSeq.NEWLINE); -this.output.append ("Sequence "); -this.output.append ( new jalview.util.Format ("%" + maxid + "s").form (this.s1.getName ())); -this.output.append (" : ").append (String.valueOf (this.s1.getStart ())).append (" - ").append (String.valueOf (this.s1.getEnd ())); -this.output.append (" (Sequence length = ").append (String.valueOf (this.s1str.length)).append (")").append (jalview.analysis.AlignSeq.NEWLINE); -this.output.append ("Sequence "); -this.output.append ( new jalview.util.Format ("%" + maxid + "s").form (this.s2.getName ())); -this.output.append (" : ").append (String.valueOf (this.s2.getStart ())).append (" - ").append (String.valueOf (this.s2.getEnd ())); -this.output.append (" (Sequence length = ").append (String.valueOf (this.s2str.length)).append (")").append (jalview.analysis.AlignSeq.NEWLINE).append (jalview.analysis.AlignSeq.NEWLINE); -for (var j = 0; j < nochunks; j++) { -this.output.append ( new jalview.util.Format ("%" + (maxid) + "s").form (s1id)).append (" "); -for (var i = 0; i < len; i++) { -if ((i + (j * len)) < this.astr1.length) { -this.output.append (this.astr1.charAt (i + (j * len))); -}} -this.output.append (jalview.analysis.AlignSeq.NEWLINE); -this.output.append ( new jalview.util.Format ("%" + (maxid) + "s").form (" ")).append (" "); -for (var i = 0; i < len; i++) { -if ((i + (j * len)) < this.astr1.length) { -if (this.astr1.charAt (i + (j * len)) == this.astr2.charAt (i + (j * len)) && !jalview.util.Comparison.isGap (this.astr1.charAt (i + (j * len)))) { -this.pid++; -this.output.append ("|"); -} else if (this.type.equals ("pep")) { -if (jalview.schemes.ResidueProperties.getPAM250 (this.astr1.charAt (i + (j * len)), this.astr2.charAt (i + (j * len))) > 0) { -this.output.append ("."); -} else { -this.output.append (" "); -}} else { -this.output.append (" "); -}}} -this.output = this.output.append (jalview.analysis.AlignSeq.NEWLINE); -this.output = this.output.append ( new jalview.util.Format ("%" + (maxid) + "s").form (s2id)).append (" "); -for (var i = 0; i < len; i++) { -if ((i + (j * len)) < this.astr2.length) { -this.output.append (this.astr2.charAt (i + (j * len))); -}} -this.output.append (jalview.analysis.AlignSeq.NEWLINE).append (jalview.analysis.AlignSeq.NEWLINE); -} -this.pid = this.pid / (this.aseq1.length - this.count) * 100; -this.output = this.output.append ( new jalview.util.Format ("Percentage ID = %2.2f\n\n").formDouble (this.pid)); -try { -os.print (this.output.toString ()); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}, "java.io.PrintStream"); -Clazz.defineMethod (c$, "printScoreMatrix", -function (mat) { -var n = this.seq1.length; -var m = this.seq2.length; -for (var i = 0; i < n; i++) { -if (i == 0) { -jalview.util.Format.print (System.out, "%8s", this.s2str.substring (0, 1)); -for (var jj = 1; jj < m; jj++) { -jalview.util.Format.print (System.out, "%5s", this.s2str.substring (jj, jj + 1)); -} -System.out.println (); -}for (var j = 0; j < m; j++) { -if (j == 0) { -jalview.util.Format.print (System.out, "%3s", this.s1str.substring (i, i + 1)); -}jalview.util.Format.printLong (System.out, "%3d ", Clazz.doubleToInt (mat[i][j] / 10)); -} -System.out.println (); -} -}, "~A"); -Clazz.defineMethod (c$, "findTrace", -function (i, j) { -var t = 0; -var max = this.score[i - 1][j - 1] + (this.lookup[this.seq1[i]][this.seq2[j]] * 10); -if (this.F[i][j] > max) { -max = this.F[i][j]; -t = -1; -} else if (this.F[i][j] == max) { -if (this.prev == -1) { -max = this.F[i][j]; -t = -1; -}}if (this.E[i][j] >= max) { -max = this.E[i][j]; -t = 1; -} else if (this.E[i][j] == max) { -if (this.prev == 1) { -max = this.E[i][j]; -t = 1; -}}this.prev = t; -return t; -}, "~N,~N"); -Clazz.defineMethod (c$, "calcScoreMatrix", -function () { -var n = this.seq1.length; -var m = this.seq2.length; -this.score[0][0] = this.lookup[this.seq1[0]][this.seq2[0]] * 10; -this.E[0][0] = -this.gapExtend; -this.F[0][0] = 0; -for (var j = 1; j < m; j++) { -this.E[0][j] = this.max (this.score[0][j - 1] - this.gapOpen, this.E[0][j - 1] - this.gapExtend); -this.F[0][j] = -this.gapExtend; -this.score[0][j] = this.max (this.lookup[this.seq1[0]][this.seq2[j]] * 10, -this.gapOpen, -this.gapExtend); -this.traceback[0][j] = 1; -} -for (var i = 1; i < n; i++) { -this.E[i][0] = -this.gapOpen; -this.F[i][0] = this.max (this.score[i - 1][0] - this.gapOpen, this.F[i - 1][0] - this.gapExtend); -this.score[i][0] = this.max (this.lookup[this.seq1[i]][this.seq2[0]] * 10, this.E[i][0], this.F[i][0]); -this.traceback[i][0] = -1; -} -for (var i = 1; i < n; i++) { -for (var j = 1; j < m; j++) { -this.E[i][j] = this.max (this.score[i][j - 1] - this.gapOpen, this.E[i][j - 1] - this.gapExtend); -this.F[i][j] = this.max (this.score[i - 1][j] - this.gapOpen, this.F[i - 1][j] - this.gapExtend); -this.score[i][j] = this.max (this.score[i - 1][j - 1] + (this.lookup[this.seq1[i]][this.seq2[j]] * 10), this.E[i][j], this.F[i][j]); -this.traceback[i][j] = this.findTrace (i, j); -} -} -}); -c$.extractGaps = Clazz.defineMethod (c$, "extractGaps", -function (gapChars, seq) { -if (gapChars == null || seq == null) { -return null; -}var str = new java.util.StringTokenizer (seq, gapChars); -var newString = new StringBuilder (seq.length); -while (str.hasMoreTokens ()) { -newString.append (str.nextToken ()); -} -return newString.toString (); -}, "~S,~S"); -Clazz.defineMethod (c$, "max", -function (i1, i2, i3) { -var max = i1; -if (i2 > i1) { -max = i2; -}if (i3 > max) { -max = i3; -}return max; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "max", -function (i1, i2) { -var max = i1; -if (i2 > i1) { -max = i2; -}return max; -}, "~N,~N"); -Clazz.defineMethod (c$, "stringToInt", -function (s, type) { -var seq1 = Clazz.newIntArray (s.length, 0); -for (var i = 0; i < s.length; i++) { -var c = s.charAt (i); -if ('a' <= c && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) - (32)); -}try { -seq1[i] = this.charToInt[c.charCodeAt (0)]; -if (seq1[i] < 0 || seq1[i] > this.defInt) { -seq1[i] = this.defInt; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -seq1[i] = this.defInt; -} else { -throw e; -} -} -} -return seq1; -}, "~S,~S"); -c$.displayMatrix = Clazz.defineMethod (c$, "displayMatrix", -function (g, mat, n, m, psize) { -var max = -1000; -var min = 1000; -for (var i = 0; i < n; i++) { -for (var j = 0; j < m; j++) { -if (mat[i][j] >= max) { -max = mat[i][j]; -}if (mat[i][j] <= min) { -min = mat[i][j]; -}} -} -System.out.println (max + " " + min); -for (var i = 0; i < n; i++) { -for (var j = 0; j < m; j++) { -var x = psize * i; -var y = psize * j; -var score = (mat[i][j] - min) / (max - min); -g.setColor ( new java.awt.Color (score, 0, 0)); -g.fillRect (x, y, psize, psize); -} -} -}, "java.awt.Graphics,~A,~N,~N,~N"); -c$.doGlobalNWAlignment = Clazz.defineMethod (c$, "doGlobalNWAlignment", -function (s1, s2, type) { -var as = new jalview.analysis.AlignSeq (s1, s2, type); -as.calcScoreMatrix (); -as.traceAlignment (); -return as; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S"); -Clazz.defineMethod (c$, "getMappingFromS1", -function (allowmismatch) { -var as1 = new java.util.ArrayList (); -var as2 = new java.util.ArrayList (); -var pdbpos = this.s2.getStart () + this.getSeq2Start () - 2; -var alignpos = this.s1.getStart () + this.getSeq1Start () - 2; -var lp2 = pdbpos - 3; -var lp1 = alignpos - 3; -var lastmatch = false; -for (var i = 0; i < this.astr1.length; i++) { -var c1 = this.astr1.charAt (i); -var c2 = this.astr2.charAt (i); -if (c1 != '-') { -alignpos++; -}if (c2 != '-') { -pdbpos++; -}if (allowmismatch || c1 == c2) { -if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos) { -as1.add (Integer.$valueOf (alignpos)); -as2.add (Integer.$valueOf (pdbpos)); -}lastmatch = true; -lp1 = alignpos; -lp2 = pdbpos; -} else { -if (lastmatch) { -as1.add (Integer.$valueOf (lp1)); -as2.add (Integer.$valueOf (lp2)); -}lastmatch = false; -}} -var mapseq1 = Clazz.newIntArray (as1.size () + (lastmatch ? 1 : 0), 0); -var mapseq2 = Clazz.newIntArray (as2.size () + (lastmatch ? 1 : 0), 0); -var i = 0; -for (var ip, $ip = as1.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { -mapseq1[i++] = (ip).intValue (); -} -;i = 0; -for (var ip, $ip = as2.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { -mapseq2[i++] = (ip).intValue (); -} -;if (lastmatch) { -mapseq1[mapseq1.length - 1] = alignpos; -mapseq2[mapseq2.length - 1] = pdbpos; -}var map = new jalview.util.MapList (mapseq1, mapseq2, 1, 1); -var mapping = new jalview.datamodel.Mapping (map); -mapping.setTo (this.s2); -return mapping; -}, "~B"); -c$.replaceMatchingSeqsWith = Clazz.defineMethod (c$, "replaceMatchingSeqsWith", -function (seqs, annotations, ochains, al, dnaOrProtein, removeOldAnnots) { -var orig = new java.util.ArrayList (); -var repl = new java.util.ArrayList (); -var aligs = new java.util.ArrayList (); -if (al != null && al.getHeight () > 0) { -var matches = new java.util.ArrayList (); -var aligns = new java.util.ArrayList (); -for (var sq, $sq = ochains.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -var bestm = null; -var bestaseq = null; -var bestscore = 0; -for (var msq, $msq = al.getSequences ().iterator (); $msq.hasNext () && ((msq = $msq.next ()) || true);) { -var aseq = jalview.analysis.AlignSeq.doGlobalNWAlignment (msq, sq, dnaOrProtein); -if (bestm == null || aseq.getMaxScore () > bestscore) { -bestscore = aseq.getMaxScore (); -bestaseq = aseq; -bestm = msq; -}} -System.out.println ("Best Score for " + (matches.size () + 1) + " :" + bestscore); -matches.add (bestm); -aligns.add (bestaseq); -al.deleteSequence (bestm); -} -for (var p = 0, pSize = seqs.size (); p < pSize; p++) { -var sq; -var sp = seqs.get (p); -var q; -if ((q = ochains.indexOf (sp)) > -1) { -seqs.set (p, sq = matches.get (q)); -orig.add (sp); -repl.add (sq); -sq.setName (sp.getName ()); -sq.setDescription (sp.getDescription ()); -var sp2sq; -sq.transferAnnotation (sp, sp2sq = aligns.get (q).getMappingFromS1 (false)); -aligs.add (aligns.get (q)); -var inspos = -1; -for (var ap = 0; ap < annotations.size (); ) { -if (annotations.get (ap).sequenceRef === sp) { -if (inspos == -1) { -inspos = ap; -}if (removeOldAnnots) { -annotations.remove (ap); -} else { -var alan = annotations.remove (ap); -alan.liftOver (sq, sp2sq); -alan.setSequenceRef (sq); -sq.addAlignmentAnnotation (alan); -}} else { -ap++; -}} -if (sq.getAnnotation () != null && sq.getAnnotation ().length > 0) { -annotations.addAll (inspos == -1 ? annotations.size () : inspos, java.util.Arrays.asList (sq.getAnnotation ())); -}}} -}return java.util.Arrays.asList ([orig, repl, aligs]); -}, "java.util.List,java.util.List,java.util.List,jalview.datamodel.AlignmentI,~S,~B"); -c$.computeRedundancyMatrix = Clazz.defineMethod (c$, "computeRedundancyMatrix", -function (originalSequences, omitHidden, start, end, ungapped) { -var height = originalSequences.length; -var redundancy = Clazz.newFloatArray (height, 0); -var lngth = Clazz.newIntArray (height, 0); -for (var i = 0; i < height; i++) { -redundancy[i] = 0; -lngth[i] = -1; -} -var pid; -var seqi; -var seqj; -for (var i = 0; i < height; i++) { -for (var j = 0; j < i; j++) { -if (i == j) { -continue; -}if (omitHidden == null) { -seqi = originalSequences[i].getSequenceAsString (start, end); -seqj = originalSequences[j].getSequenceAsString (start, end); -} else { -seqi = omitHidden[i]; -seqj = omitHidden[j]; -}if (lngth[i] == -1) { -var ug = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, seqi); -lngth[i] = ug.length; -if (ungapped) { -seqi = ug; -}}if (lngth[j] == -1) { -var ug = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, seqj); -lngth[j] = ug.length; -if (ungapped) { -seqj = ug; -}}pid = jalview.util.Comparison.PID (seqi, seqj); -if (lngth[j] < lngth[i]) { -redundancy[j] = Math.max (pid, redundancy[j]); -} else { -redundancy[i] = Math.max (pid, redundancy[i]); -}} -} -return redundancy; -}, "~A,~A,~N,~N,~B"); -Clazz.defineStatics (c$, -"PEP", "pep", -"DNA", "dna"); -c$.NEWLINE = c$.prototype.NEWLINE = System.lineSeparator (); -Clazz.defineStatics (c$, -"dna", Clazz.newArray (-1, ["A", "C", "G", "T", "-"]), -"pep", Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"])); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["jalview.schemes.ResidueProperties", "java.lang.StringBuffer"], "jalview.analysis.AlignSeq", ["jalview.datamodel.Mapping", "$.Sequence", "jalview.util.Comparison", "$.Format", "$.MapList", "$.MessageManager", "java.awt.Color", "java.lang.Error", "$.StringBuilder", "java.util.ArrayList", "$.Arrays", "$.StringTokenizer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.score = null; +this.E = null; +this.F = null; +this.traceback = null; +this.seq1 = null; +this.seq2 = null; +this.s1 = null; +this.s2 = null; +this.s1str = null; +this.s2str = null; +this.maxi = 0; +this.maxj = 0; +this.aseq1 = null; +this.aseq2 = null; +this.astr1 = ""; +this.astr2 = ""; +this.seq1start = 0; +this.seq1end = 0; +this.seq2start = 0; +this.seq2end = 0; +this.count = 0; +this.maxscore = 0; +this.pid = 0; +this.prev = 0; +this.gapOpen = 120; +this.gapExtend = 20; +this.lookup = null; +this.intToStr = null; +this.defInt = 23; +this.output = null; +this.type = null; +this.charToInt = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "AlignSeq"); +Clazz.prepareFields (c$, function () { +this.lookup = jalview.schemes.ResidueProperties.getBLOSUM62 (); +this.intToStr = jalview.analysis.AlignSeq.pep; +this.output = new StringBuffer (); +}); +Clazz.makeConstructor (c$, +function (s1, s2, type) { +this.SeqInit (s1, s1.getSequenceAsString (), s2, s2.getSequenceAsString (), type); +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S"); +Clazz.makeConstructor (c$, +function (s1, string1, s2, string2, type) { +this.SeqInit (s1, string1.toUpperCase (), s2, string2.toUpperCase (), type); +}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S"); +Clazz.defineMethod (c$, "getMaxScore", +function () { +return this.maxscore; +}); +Clazz.defineMethod (c$, "getSeq2Start", +function () { +return this.seq2start; +}); +Clazz.defineMethod (c$, "getSeq2End", +function () { +return this.seq2end; +}); +Clazz.defineMethod (c$, "getSeq1Start", +function () { +return this.seq1start; +}); +Clazz.defineMethod (c$, "getSeq1End", +function () { +return this.seq1end; +}); +Clazz.defineMethod (c$, "getOutput", +function () { +return this.output.toString (); +}); +Clazz.defineMethod (c$, "getAStr1", +function () { +return this.astr1; +}); +Clazz.defineMethod (c$, "getAStr2", +function () { +return this.astr2; +}); +Clazz.defineMethod (c$, "getASeq1", +function () { +return this.aseq1; +}); +Clazz.defineMethod (c$, "getASeq2", +function () { +return this.aseq2; +}); +Clazz.defineMethod (c$, "getS1", +function () { +return this.s1; +}); +Clazz.defineMethod (c$, "getS2", +function () { +return this.s2; +}); +Clazz.defineMethod (c$, "getAlignedSeq1", +function () { +var alSeq1 = new jalview.datamodel.Sequence (this.s1.getName (), this.getAStr1 ()); +alSeq1.setStart (this.s1.getStart () + this.getSeq1Start () - 1); +alSeq1.setEnd (this.s1.getStart () + this.getSeq1End () - 1); +alSeq1.setDatasetSequence (this.s1.getDatasetSequence () == null ? this.s1 : this.s1.getDatasetSequence ()); +return alSeq1; +}); +Clazz.defineMethod (c$, "getAlignedSeq2", +function () { +var alSeq2 = new jalview.datamodel.Sequence (this.s2.getName (), this.getAStr2 ()); +alSeq2.setStart (this.s2.getStart () + this.getSeq2Start () - 1); +alSeq2.setEnd (this.s2.getStart () + this.getSeq2End () - 1); +alSeq2.setDatasetSequence (this.s2.getDatasetSequence () == null ? this.s2 : this.s2.getDatasetSequence ()); +return alSeq2; +}); +Clazz.defineMethod (c$, "SeqInit", +function (s1, string1, s2, string2, type) { +this.s1 = s1; +this.s2 = s2; +this.setDefaultParams (type); +this.SeqInit (string1, string2); +}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S"); +Clazz.defineMethod (c$, "SeqInit", +function (s1, string1, s2, string2, scoreMatrix) { +this.s1 = s1; +this.s2 = s2; +this.setType (scoreMatrix.isDNA () ? "dna" : "pep"); +this.lookup = scoreMatrix.getMatrix (); +}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,jalview.schemes.ScoreMatrix"); +Clazz.defineMethod (c$, "SeqInit", +($fz = function (string1, string2) { +this.s1str = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, string1); +this.s2str = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, string2); +if (this.s1str.length == 0 || this.s2str.length == 0) { +this.output.append ("ALL GAPS: " + (this.s1str.length == 0 ? this.s1.getName () : " ") + (this.s2str.length == 0 ? this.s2.getName () : "")); +return; +}this.seq1 = Clazz.newIntArray (this.s1str.length, 0); +this.seq2 = Clazz.newIntArray (this.s2str.length, 0); +this.score = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); +this.E = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); +this.F = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); +this.traceback = Clazz.newIntArray (this.s1str.length, this.s2str.length, 0); +this.seq1 = this.stringToInt (this.s1str, this.type); +this.seq2 = this.stringToInt (this.s2str, this.type); +}, $fz.isPrivate = true, $fz), "~S,~S"); +Clazz.defineMethod (c$, "setDefaultParams", +($fz = function (type) { +this.setType (type); +if (type.equals ("pep")) { +this.lookup = jalview.schemes.ResidueProperties.getDefaultPeptideMatrix (); +} else if (type.equals ("dna")) { +this.lookup = jalview.schemes.ResidueProperties.getDefaultDnaMatrix (); +}}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "setType", +($fz = function (type2) { +this.type = type2; +if (this.type.equals ("pep")) { +this.intToStr = jalview.analysis.AlignSeq.pep; +this.charToInt = jalview.schemes.ResidueProperties.aaIndex; +this.defInt = 23; +} else if (this.type.equals ("dna")) { +this.intToStr = jalview.analysis.AlignSeq.dna; +this.charToInt = jalview.schemes.ResidueProperties.nucleotideIndex; +this.defInt = 10; +} else { +this.output.append ("Wrong type = dna or pep only"); +throw new Error (jalview.util.MessageManager.formatMessage ("error.unknown_type_dna_or_pep", Clazz.newArray (-1, [type2]))); +}}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "traceAlignment", +function () { +var max = -9999; +for (var i = 0; i < this.seq1.length; i++) { +if (this.score[i][this.seq2.length - 1] > max) { +max = this.score[i][this.seq2.length - 1]; +this.maxi = i; +this.maxj = this.seq2.length - 1; +}} +for (var j = 0; j < this.seq2.length; j++) { +if (this.score[this.seq1.length - 1][j] > max) { +max = this.score[this.seq1.length - 1][j]; +this.maxi = this.seq1.length - 1; +this.maxj = j; +}} +var i = this.maxi; +var j = this.maxj; +var trace; +this.maxscore = Clazz.doubleToInt (this.score[i][j] / 10); +this.seq1end = this.maxi + 1; +this.seq2end = this.maxj + 1; +this.aseq1 = Clazz.newIntArray (this.seq1.length + this.seq2.length, 0); +this.aseq2 = Clazz.newIntArray (this.seq1.length + this.seq2.length, 0); +this.count = (this.seq1.length + this.seq2.length) - 1; +while ((i > 0) && (j > 0)) { +if ((this.aseq1[this.count] != this.defInt) && (i >= 0)) { +this.aseq1[this.count] = this.seq1[i]; +this.astr1 = this.s1str.charAt (i) + this.astr1; +}if ((this.aseq2[this.count] != this.defInt) && (j > 0)) { +this.aseq2[this.count] = this.seq2[j]; +this.astr2 = this.s2str.charAt (j) + this.astr2; +}trace = this.findTrace (i, j); +if (trace == 0) { +i--; +j--; +} else if (trace == 1) { +j--; +this.aseq1[this.count] = this.defInt; +this.astr1 = "-" + this.astr1.substring (1); +} else if (trace == -1) { +i--; +this.aseq2[this.count] = this.defInt; +this.astr2 = "-" + this.astr2.substring (1); +}this.count--; +} +this.seq1start = i + 1; +this.seq2start = j + 1; +if (this.aseq1[this.count] != this.defInt) { +this.aseq1[this.count] = this.seq1[i]; +this.astr1 = this.s1str.charAt (i) + this.astr1; +}if (this.aseq2[this.count] != this.defInt) { +this.aseq2[this.count] = this.seq2[j]; +this.astr2 = this.s2str.charAt (j) + this.astr2; +}}); +Clazz.defineMethod (c$, "printAlignment", +function (os) { +var s1id = this.s1.getName (); +var s2id = this.s2.getName (); +var maxid = this.s1.getName ().length; +if (this.s2.getName ().length > maxid) { +maxid = this.s2.getName ().length; +}if (maxid > 30) { +maxid = 30; +if (this.s1.getName ().length > maxid) { +s1id = this.s1.getName ().substring (0, 30); +}if (this.s2.getName ().length > maxid) { +s2id = this.s2.getName ().substring (0, 30); +}}var len = 72 - maxid - 1; +var nochunks = (Clazz.doubleToInt ((this.aseq1.length - this.count) / len)) + 1; +this.pid = 0; +this.output.append ("Score = ").append ("" + this.score[this.maxi][this.maxj]).append (jalview.analysis.AlignSeq.NEWLINE); +this.output.append ("Length of alignment = ").append (String.valueOf (this.aseq1.length - this.count)).append (jalview.analysis.AlignSeq.NEWLINE); +this.output.append ("Sequence "); +this.output.append ( new jalview.util.Format ("%" + maxid + "s").form (this.s1.getName ())); +this.output.append (" : ").append (String.valueOf (this.s1.getStart ())).append (" - ").append (String.valueOf (this.s1.getEnd ())); +this.output.append (" (Sequence length = ").append (String.valueOf (this.s1str.length)).append (")").append (jalview.analysis.AlignSeq.NEWLINE); +this.output.append ("Sequence "); +this.output.append ( new jalview.util.Format ("%" + maxid + "s").form (this.s2.getName ())); +this.output.append (" : ").append (String.valueOf (this.s2.getStart ())).append (" - ").append (String.valueOf (this.s2.getEnd ())); +this.output.append (" (Sequence length = ").append (String.valueOf (this.s2str.length)).append (")").append (jalview.analysis.AlignSeq.NEWLINE).append (jalview.analysis.AlignSeq.NEWLINE); +for (var j = 0; j < nochunks; j++) { +this.output.append ( new jalview.util.Format ("%" + (maxid) + "s").form (s1id)).append (" "); +for (var i = 0; i < len; i++) { +if ((i + (j * len)) < this.astr1.length) { +this.output.append (this.astr1.charAt (i + (j * len))); +}} +this.output.append (jalview.analysis.AlignSeq.NEWLINE); +this.output.append ( new jalview.util.Format ("%" + (maxid) + "s").form (" ")).append (" "); +for (var i = 0; i < len; i++) { +if ((i + (j * len)) < this.astr1.length) { +if (this.astr1.charAt (i + (j * len)) == this.astr2.charAt (i + (j * len)) && !jalview.util.Comparison.isGap (this.astr1.charAt (i + (j * len)))) { +this.pid++; +this.output.append ("|"); +} else if (this.type.equals ("pep")) { +if (jalview.schemes.ResidueProperties.getPAM250 (this.astr1.charAt (i + (j * len)), this.astr2.charAt (i + (j * len))) > 0) { +this.output.append ("."); +} else { +this.output.append (" "); +}} else { +this.output.append (" "); +}}} +this.output = this.output.append (jalview.analysis.AlignSeq.NEWLINE); +this.output = this.output.append ( new jalview.util.Format ("%" + (maxid) + "s").form (s2id)).append (" "); +for (var i = 0; i < len; i++) { +if ((i + (j * len)) < this.astr2.length) { +this.output.append (this.astr2.charAt (i + (j * len))); +}} +this.output.append (jalview.analysis.AlignSeq.NEWLINE).append (jalview.analysis.AlignSeq.NEWLINE); +} +this.pid = this.pid / (this.aseq1.length - this.count) * 100; +this.output = this.output.append ( new jalview.util.Format ("Percentage ID = %2.2f\n\n").formDouble (this.pid)); +try { +os.print (this.output.toString ()); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}, "java.io.PrintStream"); +Clazz.defineMethod (c$, "printScoreMatrix", +function (mat) { +var n = this.seq1.length; +var m = this.seq2.length; +for (var i = 0; i < n; i++) { +if (i == 0) { +jalview.util.Format.print (System.out, "%8s", this.s2str.substring (0, 1)); +for (var jj = 1; jj < m; jj++) { +jalview.util.Format.print (System.out, "%5s", this.s2str.substring (jj, jj + 1)); +} +System.out.println (); +}for (var j = 0; j < m; j++) { +if (j == 0) { +jalview.util.Format.print (System.out, "%3s", this.s1str.substring (i, i + 1)); +}jalview.util.Format.printLong (System.out, "%3d ", Clazz.doubleToInt (mat[i][j] / 10)); +} +System.out.println (); +} +}, "~A"); +Clazz.defineMethod (c$, "findTrace", +function (i, j) { +var t = 0; +var max = this.score[i - 1][j - 1] + (this.lookup[this.seq1[i]][this.seq2[j]] * 10); +if (this.F[i][j] > max) { +max = this.F[i][j]; +t = -1; +} else if (this.F[i][j] == max) { +if (this.prev == -1) { +max = this.F[i][j]; +t = -1; +}}if (this.E[i][j] >= max) { +max = this.E[i][j]; +t = 1; +} else if (this.E[i][j] == max) { +if (this.prev == 1) { +max = this.E[i][j]; +t = 1; +}}this.prev = t; +return t; +}, "~N,~N"); +Clazz.defineMethod (c$, "calcScoreMatrix", +function () { +var n = this.seq1.length; +var m = this.seq2.length; +this.score[0][0] = this.lookup[this.seq1[0]][this.seq2[0]] * 10; +this.E[0][0] = -this.gapExtend; +this.F[0][0] = 0; +for (var j = 1; j < m; j++) { +this.E[0][j] = this.max (this.score[0][j - 1] - this.gapOpen, this.E[0][j - 1] - this.gapExtend); +this.F[0][j] = -this.gapExtend; +this.score[0][j] = this.max (this.lookup[this.seq1[0]][this.seq2[j]] * 10, -this.gapOpen, -this.gapExtend); +this.traceback[0][j] = 1; +} +for (var i = 1; i < n; i++) { +this.E[i][0] = -this.gapOpen; +this.F[i][0] = this.max (this.score[i - 1][0] - this.gapOpen, this.F[i - 1][0] - this.gapExtend); +this.score[i][0] = this.max (this.lookup[this.seq1[i]][this.seq2[0]] * 10, this.E[i][0], this.F[i][0]); +this.traceback[i][0] = -1; +} +for (var i = 1; i < n; i++) { +for (var j = 1; j < m; j++) { +this.E[i][j] = this.max (this.score[i][j - 1] - this.gapOpen, this.E[i][j - 1] - this.gapExtend); +this.F[i][j] = this.max (this.score[i - 1][j] - this.gapOpen, this.F[i - 1][j] - this.gapExtend); +this.score[i][j] = this.max (this.score[i - 1][j - 1] + (this.lookup[this.seq1[i]][this.seq2[j]] * 10), this.E[i][j], this.F[i][j]); +this.traceback[i][j] = this.findTrace (i, j); +} +} +}); +c$.extractGaps = Clazz.defineMethod (c$, "extractGaps", +function (gapChars, seq) { +if (gapChars == null || seq == null) { +return null; +}var str = new java.util.StringTokenizer (seq, gapChars); +var newString = new StringBuilder (seq.length); +while (str.hasMoreTokens ()) { +newString.append (str.nextToken ()); +} +return newString.toString (); +}, "~S,~S"); +Clazz.defineMethod (c$, "max", +function (i1, i2, i3) { +var max = i1; +if (i2 > i1) { +max = i2; +}if (i3 > max) { +max = i3; +}return max; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "max", +function (i1, i2) { +var max = i1; +if (i2 > i1) { +max = i2; +}return max; +}, "~N,~N"); +Clazz.defineMethod (c$, "stringToInt", +function (s, type) { +var seq1 = Clazz.newIntArray (s.length, 0); +for (var i = 0; i < s.length; i++) { +var c = s.charAt (i); +if ('a' <= c && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) - (32)); +}try { +seq1[i] = this.charToInt[c.charCodeAt (0)]; +if (seq1[i] < 0 || seq1[i] > this.defInt) { +seq1[i] = this.defInt; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +seq1[i] = this.defInt; +} else { +throw e; +} +} +} +return seq1; +}, "~S,~S"); +c$.displayMatrix = Clazz.defineMethod (c$, "displayMatrix", +function (g, mat, n, m, psize) { +var max = -1000; +var min = 1000; +for (var i = 0; i < n; i++) { +for (var j = 0; j < m; j++) { +if (mat[i][j] >= max) { +max = mat[i][j]; +}if (mat[i][j] <= min) { +min = mat[i][j]; +}} +} +System.out.println (max + " " + min); +for (var i = 0; i < n; i++) { +for (var j = 0; j < m; j++) { +var x = psize * i; +var y = psize * j; +var score = (mat[i][j] - min) / (max - min); +g.setColor ( new java.awt.Color (score, 0, 0)); +g.fillRect (x, y, psize, psize); +} +} +}, "java.awt.Graphics,~A,~N,~N,~N"); +c$.doGlobalNWAlignment = Clazz.defineMethod (c$, "doGlobalNWAlignment", +function (s1, s2, type) { +var as = new jalview.analysis.AlignSeq (s1, s2, type); +as.calcScoreMatrix (); +as.traceAlignment (); +return as; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S"); +Clazz.defineMethod (c$, "getMappingFromS1", +function (allowmismatch) { +var as1 = new java.util.ArrayList (); +var as2 = new java.util.ArrayList (); +var pdbpos = this.s2.getStart () + this.getSeq2Start () - 2; +var alignpos = this.s1.getStart () + this.getSeq1Start () - 2; +var lp2 = pdbpos - 3; +var lp1 = alignpos - 3; +var lastmatch = false; +for (var i = 0; i < this.astr1.length; i++) { +var c1 = this.astr1.charAt (i); +var c2 = this.astr2.charAt (i); +if (c1 != '-') { +alignpos++; +}if (c2 != '-') { +pdbpos++; +}if (allowmismatch || c1 == c2) { +if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos) { +as1.add (Integer.$valueOf (alignpos)); +as2.add (Integer.$valueOf (pdbpos)); +}lastmatch = true; +lp1 = alignpos; +lp2 = pdbpos; +} else { +if (lastmatch) { +as1.add (Integer.$valueOf (lp1)); +as2.add (Integer.$valueOf (lp2)); +}lastmatch = false; +}} +var mapseq1 = Clazz.newIntArray (as1.size () + (lastmatch ? 1 : 0), 0); +var mapseq2 = Clazz.newIntArray (as2.size () + (lastmatch ? 1 : 0), 0); +var i = 0; +for (var ip, $ip = as1.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { +mapseq1[i++] = (ip).intValue (); +} +;i = 0; +for (var ip, $ip = as2.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { +mapseq2[i++] = (ip).intValue (); +} +;if (lastmatch) { +mapseq1[mapseq1.length - 1] = alignpos; +mapseq2[mapseq2.length - 1] = pdbpos; +}var map = new jalview.util.MapList (mapseq1, mapseq2, 1, 1); +var mapping = new jalview.datamodel.Mapping (map); +mapping.setTo (this.s2); +return mapping; +}, "~B"); +c$.replaceMatchingSeqsWith = Clazz.defineMethod (c$, "replaceMatchingSeqsWith", +function (seqs, annotations, ochains, al, dnaOrProtein, removeOldAnnots) { +var orig = new java.util.ArrayList (); +var repl = new java.util.ArrayList (); +var aligs = new java.util.ArrayList (); +if (al != null && al.getHeight () > 0) { +var matches = new java.util.ArrayList (); +var aligns = new java.util.ArrayList (); +for (var sq, $sq = ochains.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +var bestm = null; +var bestaseq = null; +var bestscore = 0; +for (var msq, $msq = al.getSequences ().iterator (); $msq.hasNext () && ((msq = $msq.next ()) || true);) { +var aseq = jalview.analysis.AlignSeq.doGlobalNWAlignment (msq, sq, dnaOrProtein); +if (bestm == null || aseq.getMaxScore () > bestscore) { +bestscore = aseq.getMaxScore (); +bestaseq = aseq; +bestm = msq; +}} +System.out.println ("Best Score for " + (matches.size () + 1) + " :" + bestscore); +matches.add (bestm); +aligns.add (bestaseq); +al.deleteSequence (bestm); +} +for (var p = 0, pSize = seqs.size (); p < pSize; p++) { +var sq; +var sp = seqs.get (p); +var q; +if ((q = ochains.indexOf (sp)) > -1) { +seqs.set (p, sq = matches.get (q)); +orig.add (sp); +repl.add (sq); +sq.setName (sp.getName ()); +sq.setDescription (sp.getDescription ()); +var sp2sq; +sq.transferAnnotation (sp, sp2sq = aligns.get (q).getMappingFromS1 (false)); +aligs.add (aligns.get (q)); +var inspos = -1; +for (var ap = 0; ap < annotations.size (); ) { +if (annotations.get (ap).sequenceRef === sp) { +if (inspos == -1) { +inspos = ap; +}if (removeOldAnnots) { +annotations.remove (ap); +} else { +var alan = annotations.remove (ap); +alan.liftOver (sq, sp2sq); +alan.setSequenceRef (sq); +sq.addAlignmentAnnotation (alan); +}} else { +ap++; +}} +if (sq.getAnnotation () != null && sq.getAnnotation ().length > 0) { +annotations.addAll (inspos == -1 ? annotations.size () : inspos, java.util.Arrays.asList (sq.getAnnotation ())); +}}} +}return java.util.Arrays.asList ([orig, repl, aligs]); +}, "java.util.List,java.util.List,java.util.List,jalview.datamodel.AlignmentI,~S,~B"); +c$.computeRedundancyMatrix = Clazz.defineMethod (c$, "computeRedundancyMatrix", +function (originalSequences, omitHidden, start, end, ungapped) { +var height = originalSequences.length; +var redundancy = Clazz.newFloatArray (height, 0); +var lngth = Clazz.newIntArray (height, 0); +for (var i = 0; i < height; i++) { +redundancy[i] = 0; +lngth[i] = -1; +} +var pid; +var seqi; +var seqj; +for (var i = 0; i < height; i++) { +for (var j = 0; j < i; j++) { +if (i == j) { +continue; +}if (omitHidden == null) { +seqi = originalSequences[i].getSequenceAsString (start, end); +seqj = originalSequences[j].getSequenceAsString (start, end); +} else { +seqi = omitHidden[i]; +seqj = omitHidden[j]; +}if (lngth[i] == -1) { +var ug = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, seqi); +lngth[i] = ug.length; +if (ungapped) { +seqi = ug; +}}if (lngth[j] == -1) { +var ug = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, seqj); +lngth[j] = ug.length; +if (ungapped) { +seqj = ug; +}}pid = jalview.util.Comparison.PID (seqi, seqj); +if (lngth[j] < lngth[i]) { +redundancy[j] = Math.max (pid, redundancy[j]); +} else { +redundancy[i] = Math.max (pid, redundancy[i]); +}} +} +return redundancy; +}, "~A,~A,~N,~N,~B"); +Clazz.defineStatics (c$, +"PEP", "pep", +"DNA", "dna"); +c$.NEWLINE = c$.prototype.NEWLINE = System.lineSeparator (); +Clazz.defineStatics (c$, +"dna", Clazz.newArray (-1, ["A", "C", "G", "T", "-"]), +"pep", Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"])); +}); diff --git a/bin/jalview/analysis/AlignmentAnnotationUtils.class b/bin/jalview/analysis/AlignmentAnnotationUtils.class index 4d24030..a01673f 100644 Binary files a/bin/jalview/analysis/AlignmentAnnotationUtils.class and b/bin/jalview/analysis/AlignmentAnnotationUtils.class differ diff --git a/bin/jalview/analysis/AlignmentAnnotationUtils.js b/bin/jalview/analysis/AlignmentAnnotationUtils.js index f742aa9..9522f6e 100644 --- a/bin/jalview/analysis/AlignmentAnnotationUtils.js +++ b/bin/jalview/analysis/AlignmentAnnotationUtils.js @@ -1,73 +1,73 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.AlignmentAnnotationUtils", ["java.util.ArrayList", "$.Arrays", "$.BitSet", "$.Collections", "$.HashMap"], function () { -c$ = Clazz.declareType (jalview.analysis, "AlignmentAnnotationUtils"); -c$.getShownHiddenTypes = Clazz.defineMethod (c$, "getShownHiddenTypes", -function (shownTypes, hiddenTypes, annotations, forSequences) { -var visibleGraphGroups = jalview.analysis.AlignmentAnnotationUtils.getVisibleLineGraphGroups (annotations); -var groupLabels = new java.util.HashMap (); -var addedToShown = new java.util.ArrayList (); -var addedToHidden = new java.util.ArrayList (); -for (var aa, $aa = annotations.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { -if (aa.annotations == null) { -continue; -}if (forSequences != null && (aa.sequenceRef != null && forSequences.contains (aa.sequenceRef))) { -var calcId = aa.getCalcId (); -var labelAsList = new java.util.ArrayList (); -var displayLabel = aa.label; -labelAsList.add (displayLabel); -if (aa.graph == 2 && aa.graphGroup > -1) { -if (!groupLabels.containsKey (calcId)) { -groupLabels.put (calcId, new java.util.HashMap ()); -}var groupLabelsForCalcId = groupLabels.get (calcId); -if (groupLabelsForCalcId.containsKey (new Integer (aa.graphGroup))) { -if (!groupLabelsForCalcId.get (new Integer (aa.graphGroup)).contains (displayLabel)) { -groupLabelsForCalcId.get (new Integer (aa.graphGroup)).add (displayLabel); -}} else { -groupLabelsForCalcId.put (new Integer (aa.graphGroup), labelAsList); -}} else { -var rememberAs = calcId + "!" + displayLabel; -if (aa.visible && !addedToShown.contains (rememberAs)) { -if (!shownTypes.containsKey (calcId)) { -shownTypes.put (calcId, new java.util.ArrayList ()); -}shownTypes.get (calcId).add (labelAsList); -addedToShown.add (rememberAs); -} else { -if (!aa.visible && !addedToHidden.contains (rememberAs)) { -if (!hiddenTypes.containsKey (calcId)) { -hiddenTypes.put (calcId, new java.util.ArrayList ()); -}hiddenTypes.get (calcId).add (labelAsList); -addedToHidden.add (rememberAs); -}}}}} -for (var calcId, $calcId = groupLabels.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) { -for (var group, $group = groupLabels.get (calcId).keySet ().iterator (); $group.hasNext () && ((group = $group.next ()) || true);) { -var groupLabel = groupLabels.get (calcId).get (new Integer (group)); -java.util.Collections.sort (groupLabel); -if (visibleGraphGroups.get (group)) { -if (!shownTypes.containsKey (calcId)) { -shownTypes.put (calcId, new java.util.ArrayList ()); -}if (!shownTypes.get (calcId).contains (groupLabel)) { -shownTypes.get (calcId).add (groupLabel); -}} else { -if (!hiddenTypes.containsKey (calcId)) { -hiddenTypes.put (calcId, new java.util.ArrayList ()); -}if (!hiddenTypes.get (calcId).contains (groupLabel)) { -hiddenTypes.get (calcId).add (groupLabel); -}}} -} -}, "java.util.Map,java.util.Map,java.util.List,java.util.List"); -c$.getVisibleLineGraphGroups = Clazz.defineMethod (c$, "getVisibleLineGraphGroups", -function (annotations) { -var result = new java.util.BitSet (); -for (var ann, $ann = annotations.iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) { -if (ann.graph == 2 && ann.visible) { -var gg = ann.graphGroup; -if (gg > -1) { -result.set (gg); -}}} -return result; -}, "java.util.List"); -c$.asList = Clazz.defineMethod (c$, "asList", -function (anns) { -return (anns == null ? java.util.Collections.emptyList () : java.util.Arrays.asList (anns)); -}, "~A"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.AlignmentAnnotationUtils", ["java.util.ArrayList", "$.Arrays", "$.BitSet", "$.Collections", "$.HashMap"], function () { +c$ = Clazz.declareType (jalview.analysis, "AlignmentAnnotationUtils"); +c$.getShownHiddenTypes = Clazz.defineMethod (c$, "getShownHiddenTypes", +function (shownTypes, hiddenTypes, annotations, forSequences) { +var visibleGraphGroups = jalview.analysis.AlignmentAnnotationUtils.getVisibleLineGraphGroups (annotations); +var groupLabels = new java.util.HashMap (); +var addedToShown = new java.util.ArrayList (); +var addedToHidden = new java.util.ArrayList (); +for (var aa, $aa = annotations.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { +if (aa.annotations == null) { +continue; +}if (forSequences != null && (aa.sequenceRef != null && forSequences.contains (aa.sequenceRef))) { +var calcId = aa.getCalcId (); +var labelAsList = new java.util.ArrayList (); +var displayLabel = aa.label; +labelAsList.add (displayLabel); +if (aa.graph == 2 && aa.graphGroup > -1) { +if (!groupLabels.containsKey (calcId)) { +groupLabels.put (calcId, new java.util.HashMap ()); +}var groupLabelsForCalcId = groupLabels.get (calcId); +if (groupLabelsForCalcId.containsKey (new Integer (aa.graphGroup))) { +if (!groupLabelsForCalcId.get (new Integer (aa.graphGroup)).contains (displayLabel)) { +groupLabelsForCalcId.get (new Integer (aa.graphGroup)).add (displayLabel); +}} else { +groupLabelsForCalcId.put (new Integer (aa.graphGroup), labelAsList); +}} else { +var rememberAs = calcId + "!" + displayLabel; +if (aa.visible && !addedToShown.contains (rememberAs)) { +if (!shownTypes.containsKey (calcId)) { +shownTypes.put (calcId, new java.util.ArrayList ()); +}shownTypes.get (calcId).add (labelAsList); +addedToShown.add (rememberAs); +} else { +if (!aa.visible && !addedToHidden.contains (rememberAs)) { +if (!hiddenTypes.containsKey (calcId)) { +hiddenTypes.put (calcId, new java.util.ArrayList ()); +}hiddenTypes.get (calcId).add (labelAsList); +addedToHidden.add (rememberAs); +}}}}} +for (var calcId, $calcId = groupLabels.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) { +for (var group, $group = groupLabels.get (calcId).keySet ().iterator (); $group.hasNext () && ((group = $group.next ()) || true);) { +var groupLabel = groupLabels.get (calcId).get (new Integer (group)); +java.util.Collections.sort (groupLabel); +if (visibleGraphGroups.get (group)) { +if (!shownTypes.containsKey (calcId)) { +shownTypes.put (calcId, new java.util.ArrayList ()); +}if (!shownTypes.get (calcId).contains (groupLabel)) { +shownTypes.get (calcId).add (groupLabel); +}} else { +if (!hiddenTypes.containsKey (calcId)) { +hiddenTypes.put (calcId, new java.util.ArrayList ()); +}if (!hiddenTypes.get (calcId).contains (groupLabel)) { +hiddenTypes.get (calcId).add (groupLabel); +}}} +} +}, "java.util.Map,java.util.Map,java.util.List,java.util.List"); +c$.getVisibleLineGraphGroups = Clazz.defineMethod (c$, "getVisibleLineGraphGroups", +function (annotations) { +var result = new java.util.BitSet (); +for (var ann, $ann = annotations.iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) { +if (ann.graph == 2 && ann.visible) { +var gg = ann.graphGroup; +if (gg > -1) { +result.set (gg); +}}} +return result; +}, "java.util.List"); +c$.asList = Clazz.defineMethod (c$, "asList", +function (anns) { +return (anns == null ? java.util.Collections.emptyList () : java.util.Arrays.asList (anns)); +}, "~A"); +}); diff --git a/bin/jalview/analysis/AlignmentSorter.class b/bin/jalview/analysis/AlignmentSorter.class index ef50ded..012f2ee 100644 Binary files a/bin/jalview/analysis/AlignmentSorter.class and b/bin/jalview/analysis/AlignmentSorter.class differ diff --git a/bin/jalview/analysis/AlignmentSorter.js b/bin/jalview/analysis/AlignmentSorter.js index 4c0604a..bcf66d4 100644 --- a/bin/jalview/analysis/AlignmentSorter.js +++ b/bin/jalview/analysis/AlignmentSorter.js @@ -1,383 +1,383 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.AlignmentSorter", ["jalview.datamodel.SequenceI", "jalview.util.Comparison", "$.MessageManager", "$.QuickSort", "java.lang.Error", "$.Float", "$.StringBuffer", "java.util.ArrayList"], function () { -c$ = Clazz.declareType (jalview.analysis, "AlignmentSorter"); -c$.sortByPID = Clazz.defineMethod (c$, "sortByPID", -function (align, s, tosort) { -jalview.analysis.AlignmentSorter.sortByPID (align, s, tosort, 0, -1); -}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI,~A"); -c$.sortByPID = Clazz.defineMethod (c$, "sortByPID", -function (align, s, tosort, start, end) { -var nSeq = align.getHeight (); -var scores = Clazz.newFloatArray (nSeq, 0); -var seqs = new Array (nSeq); -for (var i = 0; i < nSeq; i++) { -scores[i] = jalview.util.Comparison.PID (align.getSequenceAt (i).getSequenceAsString (), s.getSequenceAsString ()); -seqs[i] = align.getSequenceAt (i); -} -jalview.util.QuickSort.sortFloatObject (scores, seqs); -jalview.analysis.AlignmentSorter.setReverseOrder (align, seqs); -}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI,~A,~N,~N"); -c$.setReverseOrder = Clazz.defineMethod (c$, "setReverseOrder", -($fz = function (align, seqs) { -var nSeq = seqs.length; -var len = 0; -if ((nSeq % 2) == 0) { -len = Clazz.doubleToInt (nSeq / 2); -} else { -len = Clazz.doubleToInt ((nSeq + 1) / 2); -}var asq; -{ -for (var i = 0; i < len; i++) { -asq.set (i, seqs[nSeq - i - 1]); -asq.set (nSeq - i - 1, seqs[i]); -} -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~A"); -c$.setOrder = Clazz.defineMethod (c$, "setOrder", -($fz = function (align, tmp) { -jalview.analysis.AlignmentSorter.setOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (tmp, align.getSequences ())); -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List"); -c$.setOrder = Clazz.defineMethod (c$, "setOrder", -function (align, seqs) { -var algn; -{ -var tmp = new java.util.ArrayList (); -for (var i = 0; i < seqs.length; i++) { -if (algn.contains (seqs[i])) { -tmp.add (seqs[i]); -}} -algn.clear (); -for (var i = 0; i < tmp.size (); i++) { -algn.add (tmp.get (i)); -} -}}, "jalview.datamodel.AlignmentI,~A"); -c$.sortByID = Clazz.defineMethod (c$, "sortByID", -function (align) { -var nSeq = align.getHeight (); -var ids = new Array (nSeq); -var seqs = new Array (nSeq); -for (var i = 0; i < nSeq; i++) { -ids[i] = align.getSequenceAt (i).getName (); -seqs[i] = align.getSequenceAt (i); -} -jalview.util.QuickSort.sort (ids, seqs); -if (jalview.analysis.AlignmentSorter.sortIdAscending) { -jalview.analysis.AlignmentSorter.setReverseOrder (align, seqs); -} else { -jalview.analysis.AlignmentSorter.setOrder (align, seqs); -}jalview.analysis.AlignmentSorter.sortIdAscending = !jalview.analysis.AlignmentSorter.sortIdAscending; -}, "jalview.datamodel.AlignmentI"); -c$.sortByLength = Clazz.defineMethod (c$, "sortByLength", -function (align) { -var nSeq = align.getHeight (); -var length = Clazz.newFloatArray (nSeq, 0); -var seqs = new Array (nSeq); -for (var i = 0; i < nSeq; i++) { -seqs[i] = align.getSequenceAt (i); -length[i] = (seqs[i].getEnd () - seqs[i].getStart ()); -} -jalview.util.QuickSort.sortFloatObject (length, seqs); -if (jalview.analysis.AlignmentSorter.sortLengthAscending) { -jalview.analysis.AlignmentSorter.setReverseOrder (align, seqs); -} else { -jalview.analysis.AlignmentSorter.setOrder (align, seqs); -}jalview.analysis.AlignmentSorter.sortLengthAscending = !jalview.analysis.AlignmentSorter.sortLengthAscending; -}, "jalview.datamodel.AlignmentI"); -c$.sortByGroup = Clazz.defineMethod (c$, "sortByGroup", -function (align) { -var groups = new java.util.ArrayList (); -if (groups.hashCode () != jalview.analysis.AlignmentSorter.lastGroupHash) { -jalview.analysis.AlignmentSorter.sortGroupAscending = true; -jalview.analysis.AlignmentSorter.lastGroupHash = groups.hashCode (); -} else { -jalview.analysis.AlignmentSorter.sortGroupAscending = !jalview.analysis.AlignmentSorter.sortGroupAscending; -}for (var sg, $sg = align.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -for (var j = 0; j < groups.size (); j++) { -var sg2 = groups.get (j); -if (sg.getSize () > sg2.getSize ()) { -groups.add (j, sg); -break; -}} -if (!groups.contains (sg)) { -groups.add (sg); -}} -var seqs = new java.util.ArrayList (); -for (var i = 0; i < groups.size (); i++) { -var sg = groups.get (i); -var orderedseqs = sg.getSequencesInOrder (align); -for (var j = 0; j < orderedseqs.length; j++) { -seqs.add (orderedseqs[j]); -} -} -if (jalview.analysis.AlignmentSorter.sortGroupAscending) { -jalview.analysis.AlignmentSorter.setOrder (align, seqs); -} else { -jalview.analysis.AlignmentSorter.setReverseOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (seqs, align.getSequences ())); -}}, "jalview.datamodel.AlignmentI"); -c$.vectorSubsetToArray = Clazz.defineMethod (c$, "vectorSubsetToArray", -($fz = function (tmp, mask) { -var seqs = new java.util.ArrayList (); -var i; -var idx; -var tmask = Clazz.newBooleanArray (mask.size (), false); -for (i = 0; i < mask.size (); i++) { -tmask[i] = true; -} -for (i = 0; i < tmp.size (); i++) { -var sq = tmp.get (i); -idx = mask.indexOf (sq); -if (idx > -1 && tmask[idx]) { -tmask[idx] = false; -seqs.add (sq); -}} -for (i = 0; i < tmask.length; i++) { -if (tmask[i]) { -seqs.add (mask.get (i)); -}} -return seqs.toArray ( new Array (seqs.size ())); -}, $fz.isPrivate = true, $fz), "java.util.List,java.util.List"); -c$.sortBy = Clazz.defineMethod (c$, "sortBy", -function (align, order) { -var tmp = order.getOrder (); -if (jalview.analysis.AlignmentSorter.lastOrder === order) { -jalview.analysis.AlignmentSorter.sortOrderAscending = !jalview.analysis.AlignmentSorter.sortOrderAscending; -} else { -jalview.analysis.AlignmentSorter.sortOrderAscending = true; -}if (jalview.analysis.AlignmentSorter.sortOrderAscending) { -jalview.analysis.AlignmentSorter.setOrder (align, tmp); -} else { -jalview.analysis.AlignmentSorter.setReverseOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (tmp, align.getSequences ())); -}}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentOrder"); -c$.getOrderByTree = Clazz.defineMethod (c$, "getOrderByTree", -($fz = function (align, tree) { -var nSeq = align.getHeight (); -var tmp = new java.util.ArrayList (); -tmp = jalview.analysis.AlignmentSorter._sortByTree (tree.getTopNode (), tmp, align.getSequences ()); -if (tmp.size () != nSeq) { -if (tmp.size () != nSeq) { -jalview.analysis.AlignmentSorter.addStrays (align, tmp); -}if (tmp.size () != nSeq) { -System.err.println ("WARNING: tmp.size()=" + tmp.size () + " != nseq=" + nSeq + " in getOrderByTree - tree contains sequences not in alignment"); -}}return tmp; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,jalview.analysis.NJTree"); -c$.sortByTree = Clazz.defineMethod (c$, "sortByTree", -function (align, tree) { -var tmp = jalview.analysis.AlignmentSorter.getOrderByTree (align, tree); -if (jalview.analysis.AlignmentSorter.lastTree !== tree) { -jalview.analysis.AlignmentSorter.sortTreeAscending = true; -jalview.analysis.AlignmentSorter.lastTree = tree; -} else { -jalview.analysis.AlignmentSorter.sortTreeAscending = !jalview.analysis.AlignmentSorter.sortTreeAscending; -}if (jalview.analysis.AlignmentSorter.sortTreeAscending) { -jalview.analysis.AlignmentSorter.setOrder (align, tmp); -} else { -jalview.analysis.AlignmentSorter.setReverseOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (tmp, align.getSequences ())); -}}, "jalview.datamodel.AlignmentI,jalview.analysis.NJTree"); -c$.addStrays = Clazz.defineMethod (c$, "addStrays", -($fz = function (align, tmp) { -var nSeq = align.getHeight (); -for (var i = 0; i < nSeq; i++) { -if (!tmp.contains (align.getSequenceAt (i))) { -tmp.add (align.getSequenceAt (i)); -}} -if (nSeq != tmp.size ()) { -System.err.println ("ERROR: Size still not right even after addStrays"); -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List"); -c$._sortByTree = Clazz.defineMethod (c$, "_sortByTree", -($fz = function (node, tmp, seqset) { -if (node == null) { -return tmp; -}var left = node.left (); -var right = node.right (); -if ((left == null) && (right == null)) { -if (!node.isPlaceholder () && (node.element () != null)) { -if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { -if (!tmp.contains (node.element ())) { -tmp.add (node.element ()); -}}}return tmp; -} else { -jalview.analysis.AlignmentSorter._sortByTree (left, tmp, seqset); -jalview.analysis.AlignmentSorter._sortByTree (right, tmp, seqset); -}return tmp; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode,java.util.List,java.util.List"); -c$.recoverOrder = Clazz.defineMethod (c$, "recoverOrder", -function (alignment) { -var ids = Clazz.newFloatArray (alignment.length, 0); -for (var i = 0; i < alignment.length; i++) { -ids[i] = ( new Float (alignment[i].getName ().substring (8))).floatValue (); -} -jalview.util.QuickSort.sortFloatObject (ids, alignment); -}, "~A"); -c$.sortByAnnotationScore = Clazz.defineMethod (c$, "sortByAnnotationScore", -function (scoreLabel, alignment) { -var seqs = alignment.getSequencesArray (); -var hasScore = Clazz.newBooleanArray (seqs.length, false); -var hasScores = 0; -var scores = Clazz.newDoubleArray (seqs.length, 0); -var min = 0; -var max = 0; -for (var i = 0; i < seqs.length; i++) { -var scoreAnn = seqs[i].getAnnotation (scoreLabel); -if (scoreAnn != null) { -hasScores++; -hasScore[i] = true; -scores[i] = scoreAnn[0].getScore (); -if (hasScores == 1) { -max = min = scores[i]; -} else { -if (max < scores[i]) { -max = scores[i]; -}if (min > scores[i]) { -min = scores[i]; -}}} else { -hasScore[i] = false; -}} -if (hasScores == 0) { -return; -}if (hasScores < seqs.length) { -for (var i = 0; i < seqs.length; i++) { -if (!hasScore[i]) { -scores[i] = (max + i + 1.0); -}} -}jalview.util.QuickSort.sortDouble (scores, seqs); -if (jalview.analysis.AlignmentSorter.lastSortByScore !== scoreLabel) { -jalview.analysis.AlignmentSorter.lastSortByScore = scoreLabel; -jalview.analysis.AlignmentSorter.setOrder (alignment, seqs); -} else { -jalview.analysis.AlignmentSorter.setReverseOrder (alignment, seqs); -}}, "~S,jalview.datamodel.AlignmentI"); -c$.sortByFeature = Clazz.defineMethod (c$, "sortByFeature", -function (featureLabel, groupLabel, start, stop, alignment, method) { -jalview.analysis.AlignmentSorter.sortByFeature (featureLabel == null ? null : Clazz.newArray (-1, [featureLabel]), groupLabel == null ? null : Clazz.newArray (-1, [groupLabel]), start, stop, alignment, method); -}, "~S,~S,~N,~N,jalview.datamodel.AlignmentI,~S"); -c$.containsIgnoreCase = Clazz.defineMethod (c$, "containsIgnoreCase", -($fz = function (lab, labs) { -if (labs == null) { -return true; -}if (lab == null) { -return false; -}for (var q = 0; q < labs.length; q++) { -if (labs[q] != null && lab.equalsIgnoreCase (labs[q])) { -return true; -}} -return false; -}, $fz.isPrivate = true, $fz), "~S,~A"); -c$.sortByFeature = Clazz.defineMethod (c$, "sortByFeature", -function (featureLabels, groupLabels, start, stop, alignment, method) { -if (method !== jalview.analysis.AlignmentSorter.FEATURE_SCORE && method !== jalview.analysis.AlignmentSorter.FEATURE_LABEL && method !== jalview.analysis.AlignmentSorter.FEATURE_DENSITY) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_sortbyfeature")); -}var ignoreScore = method !== jalview.analysis.AlignmentSorter.FEATURE_SCORE; -var scoreLabel = new StringBuffer (); -scoreLabel.append (start + stop + method); -for (var i = 0; featureLabels != null && i < featureLabels.length; i++) { -scoreLabel.append (featureLabels[i] == null ? "null" : featureLabels[i]); -} -for (var i = 0; groupLabels != null && i < groupLabels.length; i++) { -scoreLabel.append (groupLabels[i] == null ? "null" : groupLabels[i]); -} -var seqs = alignment.getSequencesArray (); -var hasScore = Clazz.newBooleanArray (seqs.length, false); -var hasScores = 0; -var scores = Clazz.newDoubleArray (seqs.length, 0); -var seqScores = Clazz.newIntArray (seqs.length, 0); -var feats = new Array (seqs.length); -var min = 0; -var max = 0; -for (var i = 0; i < seqs.length; i++) { -var sf = seqs[i].getSequenceFeatures (); -if (sf == null) { -sf = new Array (0); -} else { -var tmp = new Array (sf.length); -for (var s = 0; s < tmp.length; s++) { -tmp[s] = sf[s]; -} -sf = tmp; -}var sstart = (start == -1) ? start : seqs[i].findPosition (start); -var sstop = (stop == -1) ? stop : seqs[i].findPosition (stop); -seqScores[i] = 0; -scores[i] = 0.0; -var n = sf.length; -for (var f = 0; f < sf.length; f++) { -if ((sf[f].end < sstart || sf[f].begin > sstop) || (featureLabels != null && !jalview.analysis.AlignmentSorter.containsIgnoreCase (sf[f].type, featureLabels)) || (groupLabels != null && (sf[f].getFeatureGroup () != null && !jalview.analysis.AlignmentSorter.containsIgnoreCase (sf[f].getFeatureGroup (), groupLabels)))) { -sf[f] = null; -n--; -} else { -if (!ignoreScore && !Float.isNaN (sf[f].getScore ())) { -if (seqScores[i] == 0) { -hasScores++; -}seqScores[i]++; -hasScore[i] = true; -scores[i] += sf[f].getScore (); -}}} -var fs; -feats[i] = fs = new Array (n); -if (n > 0) { -n = 0; -for (var f = 0; f < sf.length; f++) { -if (sf[f] != null) { -(feats[i])[n++] = sf[f]; -}} -if (method === jalview.analysis.AlignmentSorter.FEATURE_LABEL) { -var labs = new Array (fs.length); -for (var l = 0; l < labs.length; l++) { -labs[l] = (fs[l].getDescription () != null ? fs[l].getDescription () : fs[l].getType ()); -} -jalview.util.QuickSort.sort (labs, (feats[i])); -}}if (hasScore[i]) { -scores[i] /= seqScores[i]; -if (hasScores == 1) { -max = min = scores[i]; -} else { -if (max < scores[i]) { -max = scores[i]; -}if (min > scores[i]) { -min = scores[i]; -}}}} -if (method === jalview.analysis.AlignmentSorter.FEATURE_SCORE) { -if (hasScores == 0) { -return; -}if (hasScores < seqs.length) { -for (var i = 0; i < seqs.length; i++) { -if (!hasScore[i]) { -scores[i] = (max + 1 + i); -} else { -var nf = (feats[i] == null) ? 0 : (feats[i]).length; -}} -}jalview.util.QuickSort.sortDouble (scores, seqs); -} else if (method === jalview.analysis.AlignmentSorter.FEATURE_DENSITY) { -var fr = 0.9 / (1.0 * seqs.length); -for (var i = 0; i < seqs.length; i++) { -var nf; -scores[i] = (0.05 + fr * i) + (nf = ((feats[i] == null) ? 0.0 : 1.0 * (feats[i]).length)); -} -jalview.util.QuickSort.sortDouble (scores, seqs); -} else { -if (method === jalview.analysis.AlignmentSorter.FEATURE_LABEL) { -throw new Error (jalview.util.MessageManager.getString ("error.not_yet_implemented")); -}}if (jalview.analysis.AlignmentSorter.lastSortByFeatureScore == null || !scoreLabel.toString ().equals (jalview.analysis.AlignmentSorter.lastSortByFeatureScore)) { -jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending = true; -} else { -jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending = !jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending; -}if (jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending) { -jalview.analysis.AlignmentSorter.setOrder (alignment, seqs); -} else { -jalview.analysis.AlignmentSorter.setReverseOrder (alignment, seqs); -}jalview.analysis.AlignmentSorter.lastSortByFeatureScore = scoreLabel.toString (); -}, "~A,~A,~N,~N,jalview.datamodel.AlignmentI,~S"); -Clazz.defineStatics (c$, -"sortIdAscending", true, -"lastGroupHash", 0, -"sortGroupAscending", true, -"lastOrder", null, -"sortOrderAscending", true, -"lastTree", null, -"sortTreeAscending", true, -"lastSortByScore", null, -"sortByScoreAscending", true, -"lastSortByFeatureScore", null, -"sortByFeatureScoreAscending", true, -"sortLengthAscending", false, -"FEATURE_SCORE", "average_score", -"FEATURE_LABEL", "text", -"FEATURE_DENSITY", "density"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.AlignmentSorter", ["jalview.datamodel.SequenceI", "jalview.util.Comparison", "$.MessageManager", "$.QuickSort", "java.lang.Error", "$.Float", "$.StringBuffer", "java.util.ArrayList"], function () { +c$ = Clazz.declareType (jalview.analysis, "AlignmentSorter"); +c$.sortByPID = Clazz.defineMethod (c$, "sortByPID", +function (align, s, tosort) { +jalview.analysis.AlignmentSorter.sortByPID (align, s, tosort, 0, -1); +}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI,~A"); +c$.sortByPID = Clazz.defineMethod (c$, "sortByPID", +function (align, s, tosort, start, end) { +var nSeq = align.getHeight (); +var scores = Clazz.newFloatArray (nSeq, 0); +var seqs = new Array (nSeq); +for (var i = 0; i < nSeq; i++) { +scores[i] = jalview.util.Comparison.PID (align.getSequenceAt (i).getSequenceAsString (), s.getSequenceAsString ()); +seqs[i] = align.getSequenceAt (i); +} +jalview.util.QuickSort.sortFloatObject (scores, seqs); +jalview.analysis.AlignmentSorter.setReverseOrder (align, seqs); +}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI,~A,~N,~N"); +c$.setReverseOrder = Clazz.defineMethod (c$, "setReverseOrder", +($fz = function (align, seqs) { +var nSeq = seqs.length; +var len = 0; +if ((nSeq % 2) == 0) { +len = Clazz.doubleToInt (nSeq / 2); +} else { +len = Clazz.doubleToInt ((nSeq + 1) / 2); +}var asq; +{ +for (var i = 0; i < len; i++) { +asq.set (i, seqs[nSeq - i - 1]); +asq.set (nSeq - i - 1, seqs[i]); +} +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~A"); +c$.setOrder = Clazz.defineMethod (c$, "setOrder", +($fz = function (align, tmp) { +jalview.analysis.AlignmentSorter.setOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (tmp, align.getSequences ())); +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List"); +c$.setOrder = Clazz.defineMethod (c$, "setOrder", +function (align, seqs) { +var algn; +{ +var tmp = new java.util.ArrayList (); +for (var i = 0; i < seqs.length; i++) { +if (algn.contains (seqs[i])) { +tmp.add (seqs[i]); +}} +algn.clear (); +for (var i = 0; i < tmp.size (); i++) { +algn.add (tmp.get (i)); +} +}}, "jalview.datamodel.AlignmentI,~A"); +c$.sortByID = Clazz.defineMethod (c$, "sortByID", +function (align) { +var nSeq = align.getHeight (); +var ids = new Array (nSeq); +var seqs = new Array (nSeq); +for (var i = 0; i < nSeq; i++) { +ids[i] = align.getSequenceAt (i).getName (); +seqs[i] = align.getSequenceAt (i); +} +jalview.util.QuickSort.sort (ids, seqs); +if (jalview.analysis.AlignmentSorter.sortIdAscending) { +jalview.analysis.AlignmentSorter.setReverseOrder (align, seqs); +} else { +jalview.analysis.AlignmentSorter.setOrder (align, seqs); +}jalview.analysis.AlignmentSorter.sortIdAscending = !jalview.analysis.AlignmentSorter.sortIdAscending; +}, "jalview.datamodel.AlignmentI"); +c$.sortByLength = Clazz.defineMethod (c$, "sortByLength", +function (align) { +var nSeq = align.getHeight (); +var length = Clazz.newFloatArray (nSeq, 0); +var seqs = new Array (nSeq); +for (var i = 0; i < nSeq; i++) { +seqs[i] = align.getSequenceAt (i); +length[i] = (seqs[i].getEnd () - seqs[i].getStart ()); +} +jalview.util.QuickSort.sortFloatObject (length, seqs); +if (jalview.analysis.AlignmentSorter.sortLengthAscending) { +jalview.analysis.AlignmentSorter.setReverseOrder (align, seqs); +} else { +jalview.analysis.AlignmentSorter.setOrder (align, seqs); +}jalview.analysis.AlignmentSorter.sortLengthAscending = !jalview.analysis.AlignmentSorter.sortLengthAscending; +}, "jalview.datamodel.AlignmentI"); +c$.sortByGroup = Clazz.defineMethod (c$, "sortByGroup", +function (align) { +var groups = new java.util.ArrayList (); +if (groups.hashCode () != jalview.analysis.AlignmentSorter.lastGroupHash) { +jalview.analysis.AlignmentSorter.sortGroupAscending = true; +jalview.analysis.AlignmentSorter.lastGroupHash = groups.hashCode (); +} else { +jalview.analysis.AlignmentSorter.sortGroupAscending = !jalview.analysis.AlignmentSorter.sortGroupAscending; +}for (var sg, $sg = align.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +for (var j = 0; j < groups.size (); j++) { +var sg2 = groups.get (j); +if (sg.getSize () > sg2.getSize ()) { +groups.add (j, sg); +break; +}} +if (!groups.contains (sg)) { +groups.add (sg); +}} +var seqs = new java.util.ArrayList (); +for (var i = 0; i < groups.size (); i++) { +var sg = groups.get (i); +var orderedseqs = sg.getSequencesInOrder (align); +for (var j = 0; j < orderedseqs.length; j++) { +seqs.add (orderedseqs[j]); +} +} +if (jalview.analysis.AlignmentSorter.sortGroupAscending) { +jalview.analysis.AlignmentSorter.setOrder (align, seqs); +} else { +jalview.analysis.AlignmentSorter.setReverseOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (seqs, align.getSequences ())); +}}, "jalview.datamodel.AlignmentI"); +c$.vectorSubsetToArray = Clazz.defineMethod (c$, "vectorSubsetToArray", +($fz = function (tmp, mask) { +var seqs = new java.util.ArrayList (); +var i; +var idx; +var tmask = Clazz.newBooleanArray (mask.size (), false); +for (i = 0; i < mask.size (); i++) { +tmask[i] = true; +} +for (i = 0; i < tmp.size (); i++) { +var sq = tmp.get (i); +idx = mask.indexOf (sq); +if (idx > -1 && tmask[idx]) { +tmask[idx] = false; +seqs.add (sq); +}} +for (i = 0; i < tmask.length; i++) { +if (tmask[i]) { +seqs.add (mask.get (i)); +}} +return seqs.toArray ( new Array (seqs.size ())); +}, $fz.isPrivate = true, $fz), "java.util.List,java.util.List"); +c$.sortBy = Clazz.defineMethod (c$, "sortBy", +function (align, order) { +var tmp = order.getOrder (); +if (jalview.analysis.AlignmentSorter.lastOrder === order) { +jalview.analysis.AlignmentSorter.sortOrderAscending = !jalview.analysis.AlignmentSorter.sortOrderAscending; +} else { +jalview.analysis.AlignmentSorter.sortOrderAscending = true; +}if (jalview.analysis.AlignmentSorter.sortOrderAscending) { +jalview.analysis.AlignmentSorter.setOrder (align, tmp); +} else { +jalview.analysis.AlignmentSorter.setReverseOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (tmp, align.getSequences ())); +}}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentOrder"); +c$.getOrderByTree = Clazz.defineMethod (c$, "getOrderByTree", +($fz = function (align, tree) { +var nSeq = align.getHeight (); +var tmp = new java.util.ArrayList (); +tmp = jalview.analysis.AlignmentSorter._sortByTree (tree.getTopNode (), tmp, align.getSequences ()); +if (tmp.size () != nSeq) { +if (tmp.size () != nSeq) { +jalview.analysis.AlignmentSorter.addStrays (align, tmp); +}if (tmp.size () != nSeq) { +System.err.println ("WARNING: tmp.size()=" + tmp.size () + " != nseq=" + nSeq + " in getOrderByTree - tree contains sequences not in alignment"); +}}return tmp; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,jalview.analysis.NJTree"); +c$.sortByTree = Clazz.defineMethod (c$, "sortByTree", +function (align, tree) { +var tmp = jalview.analysis.AlignmentSorter.getOrderByTree (align, tree); +if (jalview.analysis.AlignmentSorter.lastTree !== tree) { +jalview.analysis.AlignmentSorter.sortTreeAscending = true; +jalview.analysis.AlignmentSorter.lastTree = tree; +} else { +jalview.analysis.AlignmentSorter.sortTreeAscending = !jalview.analysis.AlignmentSorter.sortTreeAscending; +}if (jalview.analysis.AlignmentSorter.sortTreeAscending) { +jalview.analysis.AlignmentSorter.setOrder (align, tmp); +} else { +jalview.analysis.AlignmentSorter.setReverseOrder (align, jalview.analysis.AlignmentSorter.vectorSubsetToArray (tmp, align.getSequences ())); +}}, "jalview.datamodel.AlignmentI,jalview.analysis.NJTree"); +c$.addStrays = Clazz.defineMethod (c$, "addStrays", +($fz = function (align, tmp) { +var nSeq = align.getHeight (); +for (var i = 0; i < nSeq; i++) { +if (!tmp.contains (align.getSequenceAt (i))) { +tmp.add (align.getSequenceAt (i)); +}} +if (nSeq != tmp.size ()) { +System.err.println ("ERROR: Size still not right even after addStrays"); +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List"); +c$._sortByTree = Clazz.defineMethod (c$, "_sortByTree", +($fz = function (node, tmp, seqset) { +if (node == null) { +return tmp; +}var left = node.left (); +var right = node.right (); +if ((left == null) && (right == null)) { +if (!node.isPlaceholder () && (node.element () != null)) { +if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { +if (!tmp.contains (node.element ())) { +tmp.add (node.element ()); +}}}return tmp; +} else { +jalview.analysis.AlignmentSorter._sortByTree (left, tmp, seqset); +jalview.analysis.AlignmentSorter._sortByTree (right, tmp, seqset); +}return tmp; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode,java.util.List,java.util.List"); +c$.recoverOrder = Clazz.defineMethod (c$, "recoverOrder", +function (alignment) { +var ids = Clazz.newFloatArray (alignment.length, 0); +for (var i = 0; i < alignment.length; i++) { +ids[i] = ( new Float (alignment[i].getName ().substring (8))).floatValue (); +} +jalview.util.QuickSort.sortFloatObject (ids, alignment); +}, "~A"); +c$.sortByAnnotationScore = Clazz.defineMethod (c$, "sortByAnnotationScore", +function (scoreLabel, alignment) { +var seqs = alignment.getSequencesArray (); +var hasScore = Clazz.newBooleanArray (seqs.length, false); +var hasScores = 0; +var scores = Clazz.newDoubleArray (seqs.length, 0); +var min = 0; +var max = 0; +for (var i = 0; i < seqs.length; i++) { +var scoreAnn = seqs[i].getAnnotation (scoreLabel); +if (scoreAnn != null) { +hasScores++; +hasScore[i] = true; +scores[i] = scoreAnn[0].getScore (); +if (hasScores == 1) { +max = min = scores[i]; +} else { +if (max < scores[i]) { +max = scores[i]; +}if (min > scores[i]) { +min = scores[i]; +}}} else { +hasScore[i] = false; +}} +if (hasScores == 0) { +return; +}if (hasScores < seqs.length) { +for (var i = 0; i < seqs.length; i++) { +if (!hasScore[i]) { +scores[i] = (max + i + 1.0); +}} +}jalview.util.QuickSort.sortDouble (scores, seqs); +if (jalview.analysis.AlignmentSorter.lastSortByScore !== scoreLabel) { +jalview.analysis.AlignmentSorter.lastSortByScore = scoreLabel; +jalview.analysis.AlignmentSorter.setOrder (alignment, seqs); +} else { +jalview.analysis.AlignmentSorter.setReverseOrder (alignment, seqs); +}}, "~S,jalview.datamodel.AlignmentI"); +c$.sortByFeature = Clazz.defineMethod (c$, "sortByFeature", +function (featureLabel, groupLabel, start, stop, alignment, method) { +jalview.analysis.AlignmentSorter.sortByFeature (featureLabel == null ? null : Clazz.newArray (-1, [featureLabel]), groupLabel == null ? null : Clazz.newArray (-1, [groupLabel]), start, stop, alignment, method); +}, "~S,~S,~N,~N,jalview.datamodel.AlignmentI,~S"); +c$.containsIgnoreCase = Clazz.defineMethod (c$, "containsIgnoreCase", +($fz = function (lab, labs) { +if (labs == null) { +return true; +}if (lab == null) { +return false; +}for (var q = 0; q < labs.length; q++) { +if (labs[q] != null && lab.equalsIgnoreCase (labs[q])) { +return true; +}} +return false; +}, $fz.isPrivate = true, $fz), "~S,~A"); +c$.sortByFeature = Clazz.defineMethod (c$, "sortByFeature", +function (featureLabels, groupLabels, start, stop, alignment, method) { +if (method !== jalview.analysis.AlignmentSorter.FEATURE_SCORE && method !== jalview.analysis.AlignmentSorter.FEATURE_LABEL && method !== jalview.analysis.AlignmentSorter.FEATURE_DENSITY) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_sortbyfeature")); +}var ignoreScore = method !== jalview.analysis.AlignmentSorter.FEATURE_SCORE; +var scoreLabel = new StringBuffer (); +scoreLabel.append (start + stop + method); +for (var i = 0; featureLabels != null && i < featureLabels.length; i++) { +scoreLabel.append (featureLabels[i] == null ? "null" : featureLabels[i]); +} +for (var i = 0; groupLabels != null && i < groupLabels.length; i++) { +scoreLabel.append (groupLabels[i] == null ? "null" : groupLabels[i]); +} +var seqs = alignment.getSequencesArray (); +var hasScore = Clazz.newBooleanArray (seqs.length, false); +var hasScores = 0; +var scores = Clazz.newDoubleArray (seqs.length, 0); +var seqScores = Clazz.newIntArray (seqs.length, 0); +var feats = new Array (seqs.length); +var min = 0; +var max = 0; +for (var i = 0; i < seqs.length; i++) { +var sf = seqs[i].getSequenceFeatures (); +if (sf == null) { +sf = new Array (0); +} else { +var tmp = new Array (sf.length); +for (var s = 0; s < tmp.length; s++) { +tmp[s] = sf[s]; +} +sf = tmp; +}var sstart = (start == -1) ? start : seqs[i].findPosition (start); +var sstop = (stop == -1) ? stop : seqs[i].findPosition (stop); +seqScores[i] = 0; +scores[i] = 0.0; +var n = sf.length; +for (var f = 0; f < sf.length; f++) { +if ((sf[f].end < sstart || sf[f].begin > sstop) || (featureLabels != null && !jalview.analysis.AlignmentSorter.containsIgnoreCase (sf[f].type, featureLabels)) || (groupLabels != null && (sf[f].getFeatureGroup () != null && !jalview.analysis.AlignmentSorter.containsIgnoreCase (sf[f].getFeatureGroup (), groupLabels)))) { +sf[f] = null; +n--; +} else { +if (!ignoreScore && !Float.isNaN (sf[f].getScore ())) { +if (seqScores[i] == 0) { +hasScores++; +}seqScores[i]++; +hasScore[i] = true; +scores[i] += sf[f].getScore (); +}}} +var fs; +feats[i] = fs = new Array (n); +if (n > 0) { +n = 0; +for (var f = 0; f < sf.length; f++) { +if (sf[f] != null) { +(feats[i])[n++] = sf[f]; +}} +if (method === jalview.analysis.AlignmentSorter.FEATURE_LABEL) { +var labs = new Array (fs.length); +for (var l = 0; l < labs.length; l++) { +labs[l] = (fs[l].getDescription () != null ? fs[l].getDescription () : fs[l].getType ()); +} +jalview.util.QuickSort.sort (labs, (feats[i])); +}}if (hasScore[i]) { +scores[i] /= seqScores[i]; +if (hasScores == 1) { +max = min = scores[i]; +} else { +if (max < scores[i]) { +max = scores[i]; +}if (min > scores[i]) { +min = scores[i]; +}}}} +if (method === jalview.analysis.AlignmentSorter.FEATURE_SCORE) { +if (hasScores == 0) { +return; +}if (hasScores < seqs.length) { +for (var i = 0; i < seqs.length; i++) { +if (!hasScore[i]) { +scores[i] = (max + 1 + i); +} else { +var nf = (feats[i] == null) ? 0 : (feats[i]).length; +}} +}jalview.util.QuickSort.sortDouble (scores, seqs); +} else if (method === jalview.analysis.AlignmentSorter.FEATURE_DENSITY) { +var fr = 0.9 / (1.0 * seqs.length); +for (var i = 0; i < seqs.length; i++) { +var nf; +scores[i] = (0.05 + fr * i) + (nf = ((feats[i] == null) ? 0.0 : 1.0 * (feats[i]).length)); +} +jalview.util.QuickSort.sortDouble (scores, seqs); +} else { +if (method === jalview.analysis.AlignmentSorter.FEATURE_LABEL) { +throw new Error (jalview.util.MessageManager.getString ("error.not_yet_implemented")); +}}if (jalview.analysis.AlignmentSorter.lastSortByFeatureScore == null || !scoreLabel.toString ().equals (jalview.analysis.AlignmentSorter.lastSortByFeatureScore)) { +jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending = true; +} else { +jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending = !jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending; +}if (jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending) { +jalview.analysis.AlignmentSorter.setOrder (alignment, seqs); +} else { +jalview.analysis.AlignmentSorter.setReverseOrder (alignment, seqs); +}jalview.analysis.AlignmentSorter.lastSortByFeatureScore = scoreLabel.toString (); +}, "~A,~A,~N,~N,jalview.datamodel.AlignmentI,~S"); +Clazz.defineStatics (c$, +"sortIdAscending", true, +"lastGroupHash", 0, +"sortGroupAscending", true, +"lastOrder", null, +"sortOrderAscending", true, +"lastTree", null, +"sortTreeAscending", true, +"lastSortByScore", null, +"sortByScoreAscending", true, +"lastSortByFeatureScore", null, +"sortByFeatureScoreAscending", true, +"sortLengthAscending", false, +"FEATURE_SCORE", "average_score", +"FEATURE_LABEL", "text", +"FEATURE_DENSITY", "density"); +}); diff --git a/bin/jalview/analysis/AlignmentUtils.class b/bin/jalview/analysis/AlignmentUtils.class index c52a1d7..85e58d3 100644 Binary files a/bin/jalview/analysis/AlignmentUtils.class and b/bin/jalview/analysis/AlignmentUtils.class differ diff --git a/bin/jalview/analysis/AlignmentUtils.js b/bin/jalview/analysis/AlignmentUtils.js index 6af5e7a..2990b03 100644 --- a/bin/jalview/analysis/AlignmentUtils.js +++ b/bin/jalview/analysis/AlignmentUtils.js @@ -1,532 +1,532 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.AlignmentUtils", ["jalview.analysis.CodonComparator", "jalview.datamodel.AlignedCodonFrame", "$.Alignment", "$.AlignmentAnnotation", "$.DBRefEntry", "$.DBRefSource", "$.FeatureProperties", "$.SearchResults", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.DBRefUtils", "$.MapList", "$.MappingUtils", "java.lang.StringBuilder", "java.util.ArrayList", "$.Arrays", "$.HashMap", "$.HashSet", "$.LinkedHashMap", "$.LinkedHashSet", "$.TreeMap"], function () { -c$ = Clazz.declareType (jalview.analysis, "AlignmentUtils"); -c$.expandContext = Clazz.defineMethod (c$, "expandContext", -function (core, flankSize) { -var sq = new java.util.ArrayList (); -var maxoffset = 0; -for (var s, $s = core.getSequences ().iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { -var newSeq = s.deriveSequence (); -var newSeqStart = newSeq.getStart () - 1; -if (newSeqStart > maxoffset && newSeq.getDatasetSequence ().getStart () < s.getStart ()) { -maxoffset = newSeqStart; -}sq.add (newSeq); -} -if (flankSize > -1) { -maxoffset = Math.min (maxoffset, flankSize); -}for (var s, $s = sq.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { -var ds = s; -while (ds.getDatasetSequence () != null) { -ds = ds.getDatasetSequence (); -} -var s_end = s.findPosition (s.getStart () + s.getLength ()); -var ustream_ds = s.getStart () - ds.getStart (); -var dstream_ds = ds.getEnd () - s_end; -var offset = maxoffset - ustream_ds; -if (flankSize >= 0) { -if (flankSize < ustream_ds) { -offset = maxoffset - flankSize; -ustream_ds = flankSize; -}if (flankSize <= dstream_ds) { -dstream_ds = flankSize - 1; -}}var upstream = String.instantialize (ds.getSequence (s.getStart () - 1 - ustream_ds, s.getStart () - 1)).toLowerCase ().toCharArray (); -var downstream = String.instantialize (ds.getSequence (s_end - 1, s_end + dstream_ds)).toLowerCase ().toCharArray (); -var coreseq = s.getSequence (); -var nseq = Clazz.newCharArray (offset + upstream.length + downstream.length + coreseq.length, '\0'); -var c = core.getGapCharacter (); -var p = 0; -for (; p < offset; p++) { -nseq[p] = c; -} -System.arraycopy (upstream, 0, nseq, p, upstream.length); -System.arraycopy (coreseq, 0, nseq, p + upstream.length, coreseq.length); -System.arraycopy (downstream, 0, nseq, p + coreseq.length + upstream.length, downstream.length); -s.setSequence ( String.instantialize (nseq)); -s.setStart (s.getStart () - ustream_ds); -s.setEnd (s_end + downstream.length); -} -var newAl = new jalview.datamodel.Alignment (sq.toArray ( new Array (0))); -for (var s, $s = sq.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { -if (s.getAnnotation () != null) { -for (var aa, $aa = 0, $$aa = s.getAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { -aa.adjustForAlignment (); -newAl.addAnnotation (aa); -} -}} -newAl.setDataset (core.getDataset ()); -return newAl; -}, "jalview.datamodel.AlignmentI,~N"); -c$.getSequenceIndex = Clazz.defineMethod (c$, "getSequenceIndex", -function (al, seq) { -var result = -1; -var pos = 0; -for (var alSeq, $alSeq = al.getSequences ().iterator (); $alSeq.hasNext () && ((alSeq = $alSeq.next ()) || true);) { -if (alSeq === seq) { -result = pos; -break; -}pos++; -} -return result; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI"); -c$.getSequencesByName = Clazz.defineMethod (c$, "getSequencesByName", -function (al) { -var theMap = new java.util.LinkedHashMap (); -for (var seq, $seq = al.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -var name = seq.getName (); -if (name != null) { -var seqs = theMap.get (name); -if (seqs == null) { -seqs = new java.util.ArrayList (); -theMap.put (name, seqs); -}seqs.add (seq); -}} -return theMap; -}, "jalview.datamodel.AlignmentI"); -c$.mapProteinToCdna = Clazz.defineMethod (c$, "mapProteinToCdna", -function (proteinAlignment, cdnaAlignment) { -if (proteinAlignment == null || cdnaAlignment == null) { -return false; -}var mappedDna = new java.util.HashSet (); -var mappedProtein = new java.util.HashSet (); -var mappingPerformed = jalview.analysis.AlignmentUtils.mapProteinToCdna (proteinAlignment, cdnaAlignment, mappedDna, mappedProtein, true); -mappingPerformed = new Boolean (mappingPerformed | jalview.analysis.AlignmentUtils.mapProteinToCdna (proteinAlignment, cdnaAlignment, mappedDna, mappedProtein, false)).valueOf (); -return mappingPerformed; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); -c$.mapProteinToCdna = Clazz.defineMethod (c$, "mapProteinToCdna", -function (proteinAlignment, cdnaAlignment, mappedDna, mappedProtein, xrefsOnly) { -var mappingPerformed = false; -var thisSeqs = proteinAlignment.getSequences (); -for (var aaSeq, $aaSeq = thisSeqs.iterator (); $aaSeq.hasNext () && ((aaSeq = $aaSeq.next ()) || true);) { -var proteinMapped = false; -var acf = new jalview.datamodel.AlignedCodonFrame (); -for (var cdnaSeq, $cdnaSeq = cdnaAlignment.getSequences ().iterator (); $cdnaSeq.hasNext () && ((cdnaSeq = $cdnaSeq.next ()) || true);) { -if (xrefsOnly && !jalview.analysis.AlignmentUtils.haveCrossRef (aaSeq, cdnaSeq)) { -continue; -}if (!xrefsOnly && (mappedProtein.contains (aaSeq) || mappedDna.contains (cdnaSeq))) { -continue; -}if (!jalview.analysis.AlignmentUtils.mappingExists (proteinAlignment.getCodonFrames (), aaSeq.getDatasetSequence (), cdnaSeq.getDatasetSequence ())) { -var map = jalview.analysis.AlignmentUtils.mapProteinToCdna (aaSeq, cdnaSeq); -if (map != null) { -acf.addMap (cdnaSeq, aaSeq, map); -mappingPerformed = true; -proteinMapped = true; -mappedDna.add (cdnaSeq); -mappedProtein.add (aaSeq); -}}} -if (proteinMapped) { -proteinAlignment.addCodonFrame (acf); -}} -return mappingPerformed; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI,java.util.Set,java.util.Set,~B"); -c$.mappingExists = Clazz.defineMethod (c$, "mappingExists", -function (set, aaSeq, cdnaSeq) { -if (set != null) { -for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -if (cdnaSeq === acf.getDnaForAaSeq (aaSeq)) { -return true; -}} -}return false; -}, "java.util.Set,jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -c$.mapProteinToCdna = Clazz.defineMethod (c$, "mapProteinToCdna", -function (proteinSeq, cdnaSeq) { -var proteinDataset = proteinSeq.getDatasetSequence (); -var aaSeqChars = proteinDataset != null ? proteinDataset.getSequence () : proteinSeq.getSequence (); -var cdnaDataset = cdnaSeq.getDatasetSequence (); -var cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence () : cdnaSeq.getSequence (); -if (aaSeqChars == null || cdnaSeqChars == null) { -return null; -}var mappedLength = 3 * aaSeqChars.length; -var cdnaLength = cdnaSeqChars.length; -var cdnaStart = 1; -var cdnaEnd = cdnaLength; -var proteinStart = 1; -var proteinEnd = aaSeqChars.length; -if (cdnaLength != mappedLength && cdnaLength > 2) { -var lastCodon = String.valueOf (cdnaSeqChars, cdnaLength - 3, 3).toUpperCase (); -for (var stop, $stop = jalview.schemes.ResidueProperties.STOP.iterator (); $stop.hasNext () && ((stop = $stop.next ()) || true);) { -if (lastCodon.equals (stop)) { -cdnaEnd -= 3; -cdnaLength -= 3; -break; -}} -}if (cdnaLength != mappedLength && cdnaLength > 2 && String.valueOf (cdnaSeqChars, 0, 3).toUpperCase ().equals (jalview.schemes.ResidueProperties.START)) { -cdnaStart += 3; -cdnaLength -= 3; -}if (cdnaLength != mappedLength) { -return null; -}if (!jalview.analysis.AlignmentUtils.translatesAs (cdnaSeqChars, cdnaStart - 1, aaSeqChars)) { -return null; -}var map = new jalview.util.MapList ( Clazz.newIntArray (-1, [cdnaStart, cdnaEnd]), Clazz.newIntArray (-1, [1, proteinEnd]), 3, 1); -return map; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -c$.translatesAs = Clazz.defineMethod (c$, "translatesAs", -function (cdnaSeqChars, cdnaStart, aaSeqChars) { -var aaResidue = 0; -for (var i = cdnaStart; i < cdnaSeqChars.length - 2 && aaResidue < aaSeqChars.length; i += 3, aaResidue++) { -var codon = String.valueOf (cdnaSeqChars, i, 3); -var translated = jalview.schemes.ResidueProperties.codonTranslate (codon); -var aaRes = aaSeqChars[aaResidue]; -if ((translated == null || "STOP".equals (translated)) && aaRes == 'X') { -continue; -}if (translated == null || !(aaRes == translated.charAt (0))) { -return false; -}} -return (aaResidue == aaSeqChars.length); -}, "~A,~N,~A"); -c$.alignSequenceAs = Clazz.defineMethod (c$, "alignSequenceAs", -function (seq, al, gap, preserveMappedGaps, preserveUnmappedGaps) { -var mappings = al.getCodonFrame (seq); -if (mappings == null || mappings.isEmpty ()) { -return false; -}var alignFrom = null; -var mapping = null; -for (var mp, $mp = mappings.iterator (); $mp.hasNext () && ((mp = $mp.next ()) || true);) { -alignFrom = mp.findAlignedSequence (seq.getDatasetSequence (), al); -if (alignFrom != null) { -mapping = mp; -break; -}} -if (alignFrom == null) { -return false; -}jalview.analysis.AlignmentUtils.alignSequenceAs (seq, alignFrom, mapping, gap, al.getGapCharacter (), preserveMappedGaps, preserveUnmappedGaps); -return true; -}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,~S,~B,~B"); -c$.alignSequenceAs = Clazz.defineMethod (c$, "alignSequenceAs", -function (alignTo, alignFrom, mapping, myGap, sourceGap, preserveMappedGaps, preserveUnmappedGaps) { -var thisSeq = alignTo.getSequence (); -var thatAligned = alignFrom.getSequence (); -var thisAligned = new StringBuilder (2 * thisSeq.length); -var thisSeqPos = 0; -var sourceDsPos = 0; -var basesWritten = 0; -var myGapChar = myGap.charAt (0); -var ratio = myGap.length; -var sourceGapMappedLength = 0; -var inExon = false; -for (var sourceChar, $sourceChar = 0, $$sourceChar = thatAligned; $sourceChar < $$sourceChar.length && ((sourceChar = $$sourceChar[$sourceChar]) || true); $sourceChar++) { -if (sourceChar == sourceGap) { -sourceGapMappedLength += ratio; -continue; -}sourceDsPos++; -var mappedPos = mapping.getMappedRegion (alignTo, alignFrom, sourceDsPos); -if (mappedPos == null) { -System.err.println ("Can't align: no codon mapping to residue " + sourceDsPos + "(" + sourceChar + ")"); -return; -}var mappedCodonStart = mappedPos[0]; -var mappedCodonEnd = mappedPos[mappedPos.length - 1]; -var trailingCopiedGap = new StringBuilder (); -var intronLength = 0; -while (basesWritten < mappedCodonEnd && thisSeqPos < thisSeq.length) { -var c = thisSeq[thisSeqPos++]; -if (c != myGapChar) { -basesWritten++; -if (basesWritten < mappedCodonStart) { -if (preserveUnmappedGaps && trailingCopiedGap.length () > 0) { -thisAligned.append (trailingCopiedGap.toString ()); -intronLength += trailingCopiedGap.length (); -trailingCopiedGap = new StringBuilder (); -}intronLength++; -inExon = false; -} else { -var startOfCodon = basesWritten == mappedCodonStart; -var gapsToAdd = jalview.analysis.AlignmentUtils.calculateGapsToInsert (preserveMappedGaps, preserveUnmappedGaps, sourceGapMappedLength, inExon, trailingCopiedGap.length (), intronLength, startOfCodon); -for (var i = 0; i < gapsToAdd; i++) { -thisAligned.append (myGapChar); -} -sourceGapMappedLength = 0; -inExon = true; -}thisAligned.append (c); -trailingCopiedGap = new StringBuilder (); -} else { -if (inExon && preserveMappedGaps) { -trailingCopiedGap.append (myGapChar); -} else if (!inExon && preserveUnmappedGaps) { -trailingCopiedGap.append (myGapChar); -}}} -} -while (thisSeqPos < thisSeq.length) { -var c = thisSeq[thisSeqPos++]; -if (c != myGapChar || preserveUnmappedGaps) { -thisAligned.append (c); -}} -alignTo.setSequence ( String.instantialize (thisAligned)); -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,~S,~S,~B,~B"); -c$.calculateGapsToInsert = Clazz.defineMethod (c$, "calculateGapsToInsert", -function (preserveMappedGaps, preserveUnmappedGaps, sourceGapMappedLength, inExon, trailingGapLength, intronLength, startOfCodon) { -var gapsToAdd = 0; -if (startOfCodon) { -if (inExon && !preserveMappedGaps) { -trailingGapLength = 0; -}if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps)) { -trailingGapLength = 0; -}if (inExon) { -gapsToAdd = Math.max (sourceGapMappedLength, trailingGapLength); -} else { -if (intronLength + trailingGapLength <= sourceGapMappedLength) { -gapsToAdd = sourceGapMappedLength - intronLength; -} else { -gapsToAdd = Math.min (intronLength + trailingGapLength - sourceGapMappedLength, trailingGapLength); -}}} else { -if (!preserveMappedGaps) { -trailingGapLength = 0; -}gapsToAdd = Math.max (sourceGapMappedLength, trailingGapLength); -}return gapsToAdd; -}, "~B,~B,~N,~B,~N,~N,~B"); -c$.getAlignedTranslation = Clazz.defineMethod (c$, "getAlignedTranslation", -function (sequences, gapCharacter, mappings) { -var alignedSeqs = new java.util.ArrayList (); -for (var seq, $seq = sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -var mapped = jalview.analysis.AlignmentUtils.getAlignedTranslation (seq, gapCharacter, mappings); -alignedSeqs.addAll (mapped); -} -return alignedSeqs; -}, "java.util.List,~S,java.util.Set"); -c$.getAlignedTranslation = Clazz.defineMethod (c$, "getAlignedTranslation", -function (seq, gapCharacter, mappings) { -var result = new java.util.ArrayList (); -for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { -if (mapping.involvesSequence (seq)) { -var mapped = jalview.analysis.AlignmentUtils.getAlignedTranslation (seq, gapCharacter, mapping); -if (mapped != null) { -result.add (mapped); -}}} -return result; -}, "jalview.datamodel.SequenceI,~S,java.util.Set"); -c$.getAlignedTranslation = Clazz.defineMethod (c$, "getAlignedTranslation", -function (seq, gapCharacter, mapping) { -var gap = String.valueOf (gapCharacter); -var toDna = false; -var fromRatio = 1; -var mapTo = mapping.getDnaForAaSeq (seq); -if (mapTo != null) { -toDna = true; -gap = String.valueOf ( Clazz.newCharArray (-1, [gapCharacter, gapCharacter, gapCharacter])); -} else { -mapTo = mapping.getAaForDnaSeq (seq); -fromRatio = 3; -}var newseq = new StringBuilder (seq.getLength () * (toDna ? 3 : 1)); -var residueNo = 0; -var phrase = Clazz.newIntArray (fromRatio, 0); -var phraseOffset = 0; -var gapWidth = 0; -var first = true; -var alignedSeq = new jalview.datamodel.Sequence ("", ""); -for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) { -if (c == gapCharacter) { -gapWidth++; -if (gapWidth >= fromRatio) { -newseq.append (gap); -gapWidth = 0; -}} else { -phrase[phraseOffset++] = residueNo + 1; -if (phraseOffset == fromRatio) { -var sr = new jalview.datamodel.SearchResults (); -for (var pos, $pos = 0, $$pos = phrase; $pos < $$pos.length && ((pos = $$pos[$pos]) || true); $pos++) { -mapping.markMappedRegion (seq, pos, sr); -} -newseq.append (sr.toString ()); -if (first) { -first = false; -var mappedTo = sr.getResultSequence (0); -alignedSeq.setName (mappedTo.getName ()); -alignedSeq.setDescription (mappedTo.getDescription ()); -alignedSeq.setDatasetSequence (mappedTo); -}phraseOffset = 0; -}residueNo++; -}} -alignedSeq.setSequence (newseq.toString ()); -return alignedSeq; -}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame"); -c$.alignProteinAsDna = Clazz.defineMethod (c$, "alignProteinAsDna", -function (protein, dna) { -var mappings = protein.getCodonFrames (); -var alignedCodons = new java.util.TreeMap ( new jalview.analysis.CodonComparator ()); -for (var dnaSeq, $dnaSeq = dna.getSequences ().iterator (); $dnaSeq.hasNext () && ((dnaSeq = $dnaSeq.next ()) || true);) { -for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { -var seqMap = mapping.getMappingForSequence (dnaSeq); -var prot = mapping.findAlignedSequence (dnaSeq.getDatasetSequence (), protein); -if (prot != null) { -jalview.analysis.AlignmentUtils.addCodonPositions (dnaSeq, prot, protein.getGapCharacter (), seqMap, alignedCodons); -}} -} -return jalview.analysis.AlignmentUtils.alignProteinAs (protein, alignedCodons); -}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); -c$.alignProteinAs = Clazz.defineMethod (c$, "alignProteinAs", -function (protein, alignedCodons) { -var alignedWidth = alignedCodons.size (); -var gaps = Clazz.newCharArray (alignedWidth, '\0'); -java.util.Arrays.fill (gaps, protein.getGapCharacter ()); -var allGaps = String.valueOf (gaps); -for (var seq, $seq = protein.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -seq.setSequence (allGaps); -} -var column = 0; -for (var codon, $codon = alignedCodons.keySet ().iterator (); $codon.hasNext () && ((codon = $codon.next ()) || true);) { -var columnResidues = alignedCodons.get (codon); -for (var entry, $entry = columnResidues.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) { -entry.getKey ().getSequence ()[column] = entry.getValue ().charAt (0); -} -column++; -} -return 0; -}, "jalview.datamodel.AlignmentI,java.util.Map"); -c$.addCodonPositions = Clazz.defineMethod (c$, "addCodonPositions", -function (dna, protein, gapChar, seqMap, alignedCodons) { -var codons = seqMap.getCodonIterator (dna, gapChar); -while (codons.hasNext ()) { -var codon = codons.next (); -var seqProduct = alignedCodons.get (codon); -if (seqProduct == null) { -seqProduct = new java.util.HashMap (); -alignedCodons.put (codon, seqProduct); -}seqProduct.put (protein, codon.product); -} -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S,jalview.datamodel.Mapping,java.util.Map"); -c$.isMappable = Clazz.defineMethod (c$, "isMappable", -function (al1, al2) { -if (al1.isNucleotide () == al2.isNucleotide ()) { -return false; -}var dna = al1.isNucleotide () ? al1 : al2; -var protein = dna === al1 ? al2 : al1; -var mappings = protein.getCodonFrames (); -for (var dnaSeq, $dnaSeq = dna.getSequences ().iterator (); $dnaSeq.hasNext () && ((dnaSeq = $dnaSeq.next ()) || true);) { -for (var proteinSeq, $proteinSeq = protein.getSequences ().iterator (); $proteinSeq.hasNext () && ((proteinSeq = $proteinSeq.next ()) || true);) { -if (jalview.analysis.AlignmentUtils.isMappable (dnaSeq, proteinSeq, mappings)) { -return true; -}} -} -return false; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); -c$.isMappable = Clazz.defineMethod (c$, "isMappable", -function (dnaSeq, proteinSeq, mappings) { -var dnaDs = dnaSeq.getDatasetSequence () == null ? dnaSeq : dnaSeq.getDatasetSequence (); -var proteinDs = proteinSeq.getDatasetSequence () == null ? proteinSeq : proteinSeq.getDatasetSequence (); -for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { -if (proteinDs === mapping.getAaForDnaSeq (dnaDs)) { -return true; -}} -return jalview.analysis.AlignmentUtils.mapProteinToCdna (proteinDs, dnaDs) != null; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,java.util.Set"); -c$.findAddableReferenceAnnotations = Clazz.defineMethod (c$, "findAddableReferenceAnnotations", -function (sequenceScope, labelForCalcId, candidates, al) { -if (sequenceScope == null) { -return; -}for (var seq, $seq = sequenceScope.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -var dataset = seq.getDatasetSequence (); -if (dataset == null) { -continue; -}var datasetAnnotations = dataset.getAnnotation (); -if (datasetAnnotations == null) { -continue; -}var result = new java.util.ArrayList (); -for (var dsann, $dsann = 0, $$dsann = datasetAnnotations; $dsann < $$dsann.length && ((dsann = $$dsann[$dsann]) || true); $dsann++) { -var matchedAlignmentAnnotations = al.findAnnotations (seq, dsann.getCalcId (), dsann.label); -if (!matchedAlignmentAnnotations.iterator ().hasNext ()) { -result.add (dsann); -if (labelForCalcId != null) { -labelForCalcId.put (dsann.getCalcId (), dsann.label); -}}} -if (!result.isEmpty ()) { -candidates.put (seq, result); -}} -}, "java.util.List,java.util.Map,java.util.Map,jalview.datamodel.AlignmentI"); -c$.addReferenceAnnotations = Clazz.defineMethod (c$, "addReferenceAnnotations", -function (annotations, alignment, selectionGroup) { -for (var seq, $seq = annotations.keySet ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -for (var ann, $ann = annotations.get (seq).iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) { -var copyAnn = new jalview.datamodel.AlignmentAnnotation (ann); -var startRes = 0; -var endRes = ann.annotations.length; -if (selectionGroup != null) { -startRes = selectionGroup.getStartRes (); -endRes = selectionGroup.getEndRes (); -}copyAnn.restrict (startRes, endRes); -if (!seq.hasAnnotation (ann)) { -seq.addAlignmentAnnotation (copyAnn); -}copyAnn.adjustForAlignment (); -alignment.addAnnotation (copyAnn); -copyAnn.visible = true; -} -} -}, "java.util.Map,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); -c$.showOrHideSequenceAnnotations = Clazz.defineMethod (c$, "showOrHideSequenceAnnotations", -function (al, types, forSequences, anyType, doShow) { -for (var aa, $aa = 0, $$aa = al.getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { -if (anyType || types.contains (aa.label)) { -if ((aa.sequenceRef != null) && (forSequences == null || forSequences.contains (aa.sequenceRef))) { -aa.visible = doShow; -}}} -}, "jalview.datamodel.AlignmentI,java.util.Collection,java.util.List,~B,~B"); -c$.haveCrossRef = Clazz.defineMethod (c$, "haveCrossRef", -function (seq1, seq2) { -return jalview.analysis.AlignmentUtils.hasCrossRef (seq1, seq2) || jalview.analysis.AlignmentUtils.hasCrossRef (seq2, seq1); -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -c$.hasCrossRef = Clazz.defineMethod (c$, "hasCrossRef", -function (seq1, seq2) { -if (seq1 == null || seq2 == null) { -return false; -}var name = seq2.getName (); -var xrefs = seq1.getDBRef (); -if (xrefs != null) { -for (var xref, $xref = 0, $$xref = xrefs; $xref < $$xref.length && ((xref = $$xref[$xref]) || true); $xref++) { -var xrefName = xref.getSource () + "|" + xref.getAccessionId (); -if (xrefName.equalsIgnoreCase (name)) { -return true; -}} -}return false; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -c$.makeExonAlignment = Clazz.defineMethod (c$, "makeExonAlignment", -function (dna, mappings) { -var newMappings = new java.util.LinkedHashSet (); -var exonSequences = new java.util.ArrayList (); -for (var dnaSeq, $dnaSeq = 0, $$dnaSeq = dna; $dnaSeq < $$dnaSeq.length && ((dnaSeq = $$dnaSeq[$dnaSeq]) || true); $dnaSeq++) { -var ds = dnaSeq.getDatasetSequence (); -var seqMappings = jalview.util.MappingUtils.findMappingsForSequence (ds, mappings); -for (var acf, $acf = seqMappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -var newMapping = new jalview.datamodel.AlignedCodonFrame (); -var mappedExons = jalview.analysis.AlignmentUtils.makeExonSequences (ds, acf, newMapping); -if (!mappedExons.isEmpty ()) { -exonSequences.addAll (mappedExons); -newMappings.add (newMapping); -}} -} -var al = new jalview.datamodel.Alignment (exonSequences.toArray ( new Array (exonSequences.size ()))); -al.setDataset (null); -mappings.clear (); -mappings.addAll (newMappings); -return al; -}, "~A,java.util.Set"); -c$.makeExonSequences = Clazz.defineMethod (c$, "makeExonSequences", -function (dnaSeq, mapping, newMapping) { -var exonSequences = new java.util.ArrayList (); -var seqMappings = mapping.getMappingsForSequence (dnaSeq); -var dna = dnaSeq.getSequence (); -for (var seqMapping, $seqMapping = seqMappings.iterator (); $seqMapping.hasNext () && ((seqMapping = $seqMapping.next ()) || true);) { -var newSequence = new StringBuilder (dnaSeq.getLength ()); -var dnaExonRanges = seqMapping.getMap ().getFromRanges (); -for (var range, $range = dnaExonRanges.iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { -for (var pos = range[0]; pos <= range[1]; pos++) { -newSequence.append (dna[pos - 1]); -} -} -var exon = new jalview.datamodel.Sequence (dnaSeq.getName (), newSequence.toString ()); -var cdsAccId = jalview.datamodel.FeatureProperties.getCodingFeature (jalview.datamodel.DBRefSource.EMBL); -var cdsRefs = jalview.util.DBRefUtils.selectRefs (seqMapping.getTo ().getDBRef (), jalview.datamodel.DBRefSource.CODINGDBS); -if (cdsRefs != null) { -for (var cdsRef, $cdsRef = 0, $$cdsRef = cdsRefs; $cdsRef < $$cdsRef.length && ((cdsRef = $$cdsRef[$cdsRef]) || true); $cdsRef++) { -exon.addDBRef ( new jalview.datamodel.DBRefEntry (cdsRef)); -cdsAccId = cdsRef.getAccessionId (); -} -}exon.setName (exon.getName () + "|" + cdsAccId); -exon.createDatasetSequence (); -var exonRange = new java.util.ArrayList (); -exonRange.add ( Clazz.newIntArray (-1, [1, newSequence.length ()])); -var map = new jalview.util.MapList (exonRange, seqMapping.getMap ().getToRanges (), 3, 1); -newMapping.addMap (exon.getDatasetSequence (), seqMapping.getTo (), map); -var cdsToDnaMap = new jalview.util.MapList (dnaExonRanges, exonRange, 1, 1); -newMapping.addMap (dnaSeq, exon.getDatasetSequence (), cdsToDnaMap); -exonSequences.add (exon); -} -return exonSequences; -}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,jalview.datamodel.AlignedCodonFrame"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.AlignmentUtils", ["jalview.analysis.CodonComparator", "jalview.datamodel.AlignedCodonFrame", "$.Alignment", "$.AlignmentAnnotation", "$.DBRefEntry", "$.DBRefSource", "$.FeatureProperties", "$.SearchResults", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.DBRefUtils", "$.MapList", "$.MappingUtils", "java.lang.StringBuilder", "java.util.ArrayList", "$.Arrays", "$.HashMap", "$.HashSet", "$.LinkedHashMap", "$.LinkedHashSet", "$.TreeMap"], function () { +c$ = Clazz.declareType (jalview.analysis, "AlignmentUtils"); +c$.expandContext = Clazz.defineMethod (c$, "expandContext", +function (core, flankSize) { +var sq = new java.util.ArrayList (); +var maxoffset = 0; +for (var s, $s = core.getSequences ().iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { +var newSeq = s.deriveSequence (); +var newSeqStart = newSeq.getStart () - 1; +if (newSeqStart > maxoffset && newSeq.getDatasetSequence ().getStart () < s.getStart ()) { +maxoffset = newSeqStart; +}sq.add (newSeq); +} +if (flankSize > -1) { +maxoffset = Math.min (maxoffset, flankSize); +}for (var s, $s = sq.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { +var ds = s; +while (ds.getDatasetSequence () != null) { +ds = ds.getDatasetSequence (); +} +var s_end = s.findPosition (s.getStart () + s.getLength ()); +var ustream_ds = s.getStart () - ds.getStart (); +var dstream_ds = ds.getEnd () - s_end; +var offset = maxoffset - ustream_ds; +if (flankSize >= 0) { +if (flankSize < ustream_ds) { +offset = maxoffset - flankSize; +ustream_ds = flankSize; +}if (flankSize <= dstream_ds) { +dstream_ds = flankSize - 1; +}}var upstream = String.instantialize (ds.getSequence (s.getStart () - 1 - ustream_ds, s.getStart () - 1)).toLowerCase ().toCharArray (); +var downstream = String.instantialize (ds.getSequence (s_end - 1, s_end + dstream_ds)).toLowerCase ().toCharArray (); +var coreseq = s.getSequence (); +var nseq = Clazz.newCharArray (offset + upstream.length + downstream.length + coreseq.length, '\0'); +var c = core.getGapCharacter (); +var p = 0; +for (; p < offset; p++) { +nseq[p] = c; +} +System.arraycopy (upstream, 0, nseq, p, upstream.length); +System.arraycopy (coreseq, 0, nseq, p + upstream.length, coreseq.length); +System.arraycopy (downstream, 0, nseq, p + coreseq.length + upstream.length, downstream.length); +s.setSequence ( String.instantialize (nseq)); +s.setStart (s.getStart () - ustream_ds); +s.setEnd (s_end + downstream.length); +} +var newAl = new jalview.datamodel.Alignment (sq.toArray ( new Array (0))); +for (var s, $s = sq.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { +if (s.getAnnotation () != null) { +for (var aa, $aa = 0, $$aa = s.getAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { +aa.adjustForAlignment (); +newAl.addAnnotation (aa); +} +}} +newAl.setDataset (core.getDataset ()); +return newAl; +}, "jalview.datamodel.AlignmentI,~N"); +c$.getSequenceIndex = Clazz.defineMethod (c$, "getSequenceIndex", +function (al, seq) { +var result = -1; +var pos = 0; +for (var alSeq, $alSeq = al.getSequences ().iterator (); $alSeq.hasNext () && ((alSeq = $alSeq.next ()) || true);) { +if (alSeq === seq) { +result = pos; +break; +}pos++; +} +return result; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI"); +c$.getSequencesByName = Clazz.defineMethod (c$, "getSequencesByName", +function (al) { +var theMap = new java.util.LinkedHashMap (); +for (var seq, $seq = al.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +var name = seq.getName (); +if (name != null) { +var seqs = theMap.get (name); +if (seqs == null) { +seqs = new java.util.ArrayList (); +theMap.put (name, seqs); +}seqs.add (seq); +}} +return theMap; +}, "jalview.datamodel.AlignmentI"); +c$.mapProteinToCdna = Clazz.defineMethod (c$, "mapProteinToCdna", +function (proteinAlignment, cdnaAlignment) { +if (proteinAlignment == null || cdnaAlignment == null) { +return false; +}var mappedDna = new java.util.HashSet (); +var mappedProtein = new java.util.HashSet (); +var mappingPerformed = jalview.analysis.AlignmentUtils.mapProteinToCdna (proteinAlignment, cdnaAlignment, mappedDna, mappedProtein, true); +mappingPerformed = new Boolean (mappingPerformed | jalview.analysis.AlignmentUtils.mapProteinToCdna (proteinAlignment, cdnaAlignment, mappedDna, mappedProtein, false)).valueOf (); +return mappingPerformed; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); +c$.mapProteinToCdna = Clazz.defineMethod (c$, "mapProteinToCdna", +function (proteinAlignment, cdnaAlignment, mappedDna, mappedProtein, xrefsOnly) { +var mappingPerformed = false; +var thisSeqs = proteinAlignment.getSequences (); +for (var aaSeq, $aaSeq = thisSeqs.iterator (); $aaSeq.hasNext () && ((aaSeq = $aaSeq.next ()) || true);) { +var proteinMapped = false; +var acf = new jalview.datamodel.AlignedCodonFrame (); +for (var cdnaSeq, $cdnaSeq = cdnaAlignment.getSequences ().iterator (); $cdnaSeq.hasNext () && ((cdnaSeq = $cdnaSeq.next ()) || true);) { +if (xrefsOnly && !jalview.analysis.AlignmentUtils.haveCrossRef (aaSeq, cdnaSeq)) { +continue; +}if (!xrefsOnly && (mappedProtein.contains (aaSeq) || mappedDna.contains (cdnaSeq))) { +continue; +}if (!jalview.analysis.AlignmentUtils.mappingExists (proteinAlignment.getCodonFrames (), aaSeq.getDatasetSequence (), cdnaSeq.getDatasetSequence ())) { +var map = jalview.analysis.AlignmentUtils.mapProteinToCdna (aaSeq, cdnaSeq); +if (map != null) { +acf.addMap (cdnaSeq, aaSeq, map); +mappingPerformed = true; +proteinMapped = true; +mappedDna.add (cdnaSeq); +mappedProtein.add (aaSeq); +}}} +if (proteinMapped) { +proteinAlignment.addCodonFrame (acf); +}} +return mappingPerformed; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI,java.util.Set,java.util.Set,~B"); +c$.mappingExists = Clazz.defineMethod (c$, "mappingExists", +function (set, aaSeq, cdnaSeq) { +if (set != null) { +for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +if (cdnaSeq === acf.getDnaForAaSeq (aaSeq)) { +return true; +}} +}return false; +}, "java.util.Set,jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +c$.mapProteinToCdna = Clazz.defineMethod (c$, "mapProteinToCdna", +function (proteinSeq, cdnaSeq) { +var proteinDataset = proteinSeq.getDatasetSequence (); +var aaSeqChars = proteinDataset != null ? proteinDataset.getSequence () : proteinSeq.getSequence (); +var cdnaDataset = cdnaSeq.getDatasetSequence (); +var cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence () : cdnaSeq.getSequence (); +if (aaSeqChars == null || cdnaSeqChars == null) { +return null; +}var mappedLength = 3 * aaSeqChars.length; +var cdnaLength = cdnaSeqChars.length; +var cdnaStart = 1; +var cdnaEnd = cdnaLength; +var proteinStart = 1; +var proteinEnd = aaSeqChars.length; +if (cdnaLength != mappedLength && cdnaLength > 2) { +var lastCodon = String.valueOf (cdnaSeqChars, cdnaLength - 3, 3).toUpperCase (); +for (var stop, $stop = jalview.schemes.ResidueProperties.STOP.iterator (); $stop.hasNext () && ((stop = $stop.next ()) || true);) { +if (lastCodon.equals (stop)) { +cdnaEnd -= 3; +cdnaLength -= 3; +break; +}} +}if (cdnaLength != mappedLength && cdnaLength > 2 && String.valueOf (cdnaSeqChars, 0, 3).toUpperCase ().equals (jalview.schemes.ResidueProperties.START)) { +cdnaStart += 3; +cdnaLength -= 3; +}if (cdnaLength != mappedLength) { +return null; +}if (!jalview.analysis.AlignmentUtils.translatesAs (cdnaSeqChars, cdnaStart - 1, aaSeqChars)) { +return null; +}var map = new jalview.util.MapList ( Clazz.newIntArray (-1, [cdnaStart, cdnaEnd]), Clazz.newIntArray (-1, [1, proteinEnd]), 3, 1); +return map; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +c$.translatesAs = Clazz.defineMethod (c$, "translatesAs", +function (cdnaSeqChars, cdnaStart, aaSeqChars) { +var aaResidue = 0; +for (var i = cdnaStart; i < cdnaSeqChars.length - 2 && aaResidue < aaSeqChars.length; i += 3, aaResidue++) { +var codon = String.valueOf (cdnaSeqChars, i, 3); +var translated = jalview.schemes.ResidueProperties.codonTranslate (codon); +var aaRes = aaSeqChars[aaResidue]; +if ((translated == null || "STOP".equals (translated)) && aaRes == 'X') { +continue; +}if (translated == null || !(aaRes == translated.charAt (0))) { +return false; +}} +return (aaResidue == aaSeqChars.length); +}, "~A,~N,~A"); +c$.alignSequenceAs = Clazz.defineMethod (c$, "alignSequenceAs", +function (seq, al, gap, preserveMappedGaps, preserveUnmappedGaps) { +var mappings = al.getCodonFrame (seq); +if (mappings == null || mappings.isEmpty ()) { +return false; +}var alignFrom = null; +var mapping = null; +for (var mp, $mp = mappings.iterator (); $mp.hasNext () && ((mp = $mp.next ()) || true);) { +alignFrom = mp.findAlignedSequence (seq.getDatasetSequence (), al); +if (alignFrom != null) { +mapping = mp; +break; +}} +if (alignFrom == null) { +return false; +}jalview.analysis.AlignmentUtils.alignSequenceAs (seq, alignFrom, mapping, gap, al.getGapCharacter (), preserveMappedGaps, preserveUnmappedGaps); +return true; +}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,~S,~B,~B"); +c$.alignSequenceAs = Clazz.defineMethod (c$, "alignSequenceAs", +function (alignTo, alignFrom, mapping, myGap, sourceGap, preserveMappedGaps, preserveUnmappedGaps) { +var thisSeq = alignTo.getSequence (); +var thatAligned = alignFrom.getSequence (); +var thisAligned = new StringBuilder (2 * thisSeq.length); +var thisSeqPos = 0; +var sourceDsPos = 0; +var basesWritten = 0; +var myGapChar = myGap.charAt (0); +var ratio = myGap.length; +var sourceGapMappedLength = 0; +var inExon = false; +for (var sourceChar, $sourceChar = 0, $$sourceChar = thatAligned; $sourceChar < $$sourceChar.length && ((sourceChar = $$sourceChar[$sourceChar]) || true); $sourceChar++) { +if (sourceChar == sourceGap) { +sourceGapMappedLength += ratio; +continue; +}sourceDsPos++; +var mappedPos = mapping.getMappedRegion (alignTo, alignFrom, sourceDsPos); +if (mappedPos == null) { +System.err.println ("Can't align: no codon mapping to residue " + sourceDsPos + "(" + sourceChar + ")"); +return; +}var mappedCodonStart = mappedPos[0]; +var mappedCodonEnd = mappedPos[mappedPos.length - 1]; +var trailingCopiedGap = new StringBuilder (); +var intronLength = 0; +while (basesWritten < mappedCodonEnd && thisSeqPos < thisSeq.length) { +var c = thisSeq[thisSeqPos++]; +if (c != myGapChar) { +basesWritten++; +if (basesWritten < mappedCodonStart) { +if (preserveUnmappedGaps && trailingCopiedGap.length () > 0) { +thisAligned.append (trailingCopiedGap.toString ()); +intronLength += trailingCopiedGap.length (); +trailingCopiedGap = new StringBuilder (); +}intronLength++; +inExon = false; +} else { +var startOfCodon = basesWritten == mappedCodonStart; +var gapsToAdd = jalview.analysis.AlignmentUtils.calculateGapsToInsert (preserveMappedGaps, preserveUnmappedGaps, sourceGapMappedLength, inExon, trailingCopiedGap.length (), intronLength, startOfCodon); +for (var i = 0; i < gapsToAdd; i++) { +thisAligned.append (myGapChar); +} +sourceGapMappedLength = 0; +inExon = true; +}thisAligned.append (c); +trailingCopiedGap = new StringBuilder (); +} else { +if (inExon && preserveMappedGaps) { +trailingCopiedGap.append (myGapChar); +} else if (!inExon && preserveUnmappedGaps) { +trailingCopiedGap.append (myGapChar); +}}} +} +while (thisSeqPos < thisSeq.length) { +var c = thisSeq[thisSeqPos++]; +if (c != myGapChar || preserveUnmappedGaps) { +thisAligned.append (c); +}} +alignTo.setSequence ( String.instantialize (thisAligned)); +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,~S,~S,~B,~B"); +c$.calculateGapsToInsert = Clazz.defineMethod (c$, "calculateGapsToInsert", +function (preserveMappedGaps, preserveUnmappedGaps, sourceGapMappedLength, inExon, trailingGapLength, intronLength, startOfCodon) { +var gapsToAdd = 0; +if (startOfCodon) { +if (inExon && !preserveMappedGaps) { +trailingGapLength = 0; +}if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps)) { +trailingGapLength = 0; +}if (inExon) { +gapsToAdd = Math.max (sourceGapMappedLength, trailingGapLength); +} else { +if (intronLength + trailingGapLength <= sourceGapMappedLength) { +gapsToAdd = sourceGapMappedLength - intronLength; +} else { +gapsToAdd = Math.min (intronLength + trailingGapLength - sourceGapMappedLength, trailingGapLength); +}}} else { +if (!preserveMappedGaps) { +trailingGapLength = 0; +}gapsToAdd = Math.max (sourceGapMappedLength, trailingGapLength); +}return gapsToAdd; +}, "~B,~B,~N,~B,~N,~N,~B"); +c$.getAlignedTranslation = Clazz.defineMethod (c$, "getAlignedTranslation", +function (sequences, gapCharacter, mappings) { +var alignedSeqs = new java.util.ArrayList (); +for (var seq, $seq = sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +var mapped = jalview.analysis.AlignmentUtils.getAlignedTranslation (seq, gapCharacter, mappings); +alignedSeqs.addAll (mapped); +} +return alignedSeqs; +}, "java.util.List,~S,java.util.Set"); +c$.getAlignedTranslation = Clazz.defineMethod (c$, "getAlignedTranslation", +function (seq, gapCharacter, mappings) { +var result = new java.util.ArrayList (); +for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { +if (mapping.involvesSequence (seq)) { +var mapped = jalview.analysis.AlignmentUtils.getAlignedTranslation (seq, gapCharacter, mapping); +if (mapped != null) { +result.add (mapped); +}}} +return result; +}, "jalview.datamodel.SequenceI,~S,java.util.Set"); +c$.getAlignedTranslation = Clazz.defineMethod (c$, "getAlignedTranslation", +function (seq, gapCharacter, mapping) { +var gap = String.valueOf (gapCharacter); +var toDna = false; +var fromRatio = 1; +var mapTo = mapping.getDnaForAaSeq (seq); +if (mapTo != null) { +toDna = true; +gap = String.valueOf ( Clazz.newCharArray (-1, [gapCharacter, gapCharacter, gapCharacter])); +} else { +mapTo = mapping.getAaForDnaSeq (seq); +fromRatio = 3; +}var newseq = new StringBuilder (seq.getLength () * (toDna ? 3 : 1)); +var residueNo = 0; +var phrase = Clazz.newIntArray (fromRatio, 0); +var phraseOffset = 0; +var gapWidth = 0; +var first = true; +var alignedSeq = new jalview.datamodel.Sequence ("", ""); +for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) { +if (c == gapCharacter) { +gapWidth++; +if (gapWidth >= fromRatio) { +newseq.append (gap); +gapWidth = 0; +}} else { +phrase[phraseOffset++] = residueNo + 1; +if (phraseOffset == fromRatio) { +var sr = new jalview.datamodel.SearchResults (); +for (var pos, $pos = 0, $$pos = phrase; $pos < $$pos.length && ((pos = $$pos[$pos]) || true); $pos++) { +mapping.markMappedRegion (seq, pos, sr); +} +newseq.append (sr.toString ()); +if (first) { +first = false; +var mappedTo = sr.getResultSequence (0); +alignedSeq.setName (mappedTo.getName ()); +alignedSeq.setDescription (mappedTo.getDescription ()); +alignedSeq.setDatasetSequence (mappedTo); +}phraseOffset = 0; +}residueNo++; +}} +alignedSeq.setSequence (newseq.toString ()); +return alignedSeq; +}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame"); +c$.alignProteinAsDna = Clazz.defineMethod (c$, "alignProteinAsDna", +function (protein, dna) { +var mappings = protein.getCodonFrames (); +var alignedCodons = new java.util.TreeMap ( new jalview.analysis.CodonComparator ()); +for (var dnaSeq, $dnaSeq = dna.getSequences ().iterator (); $dnaSeq.hasNext () && ((dnaSeq = $dnaSeq.next ()) || true);) { +for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { +var seqMap = mapping.getMappingForSequence (dnaSeq); +var prot = mapping.findAlignedSequence (dnaSeq.getDatasetSequence (), protein); +if (prot != null) { +jalview.analysis.AlignmentUtils.addCodonPositions (dnaSeq, prot, protein.getGapCharacter (), seqMap, alignedCodons); +}} +} +return jalview.analysis.AlignmentUtils.alignProteinAs (protein, alignedCodons); +}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); +c$.alignProteinAs = Clazz.defineMethod (c$, "alignProteinAs", +function (protein, alignedCodons) { +var alignedWidth = alignedCodons.size (); +var gaps = Clazz.newCharArray (alignedWidth, '\0'); +java.util.Arrays.fill (gaps, protein.getGapCharacter ()); +var allGaps = String.valueOf (gaps); +for (var seq, $seq = protein.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +seq.setSequence (allGaps); +} +var column = 0; +for (var codon, $codon = alignedCodons.keySet ().iterator (); $codon.hasNext () && ((codon = $codon.next ()) || true);) { +var columnResidues = alignedCodons.get (codon); +for (var entry, $entry = columnResidues.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) { +entry.getKey ().getSequence ()[column] = entry.getValue ().charAt (0); +} +column++; +} +return 0; +}, "jalview.datamodel.AlignmentI,java.util.Map"); +c$.addCodonPositions = Clazz.defineMethod (c$, "addCodonPositions", +function (dna, protein, gapChar, seqMap, alignedCodons) { +var codons = seqMap.getCodonIterator (dna, gapChar); +while (codons.hasNext ()) { +var codon = codons.next (); +var seqProduct = alignedCodons.get (codon); +if (seqProduct == null) { +seqProduct = new java.util.HashMap (); +alignedCodons.put (codon, seqProduct); +}seqProduct.put (protein, codon.product); +} +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S,jalview.datamodel.Mapping,java.util.Map"); +c$.isMappable = Clazz.defineMethod (c$, "isMappable", +function (al1, al2) { +if (al1.isNucleotide () == al2.isNucleotide ()) { +return false; +}var dna = al1.isNucleotide () ? al1 : al2; +var protein = dna === al1 ? al2 : al1; +var mappings = protein.getCodonFrames (); +for (var dnaSeq, $dnaSeq = dna.getSequences ().iterator (); $dnaSeq.hasNext () && ((dnaSeq = $dnaSeq.next ()) || true);) { +for (var proteinSeq, $proteinSeq = protein.getSequences ().iterator (); $proteinSeq.hasNext () && ((proteinSeq = $proteinSeq.next ()) || true);) { +if (jalview.analysis.AlignmentUtils.isMappable (dnaSeq, proteinSeq, mappings)) { +return true; +}} +} +return false; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); +c$.isMappable = Clazz.defineMethod (c$, "isMappable", +function (dnaSeq, proteinSeq, mappings) { +var dnaDs = dnaSeq.getDatasetSequence () == null ? dnaSeq : dnaSeq.getDatasetSequence (); +var proteinDs = proteinSeq.getDatasetSequence () == null ? proteinSeq : proteinSeq.getDatasetSequence (); +for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { +if (proteinDs === mapping.getAaForDnaSeq (dnaDs)) { +return true; +}} +return jalview.analysis.AlignmentUtils.mapProteinToCdna (proteinDs, dnaDs) != null; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,java.util.Set"); +c$.findAddableReferenceAnnotations = Clazz.defineMethod (c$, "findAddableReferenceAnnotations", +function (sequenceScope, labelForCalcId, candidates, al) { +if (sequenceScope == null) { +return; +}for (var seq, $seq = sequenceScope.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +var dataset = seq.getDatasetSequence (); +if (dataset == null) { +continue; +}var datasetAnnotations = dataset.getAnnotation (); +if (datasetAnnotations == null) { +continue; +}var result = new java.util.ArrayList (); +for (var dsann, $dsann = 0, $$dsann = datasetAnnotations; $dsann < $$dsann.length && ((dsann = $$dsann[$dsann]) || true); $dsann++) { +var matchedAlignmentAnnotations = al.findAnnotations (seq, dsann.getCalcId (), dsann.label); +if (!matchedAlignmentAnnotations.iterator ().hasNext ()) { +result.add (dsann); +if (labelForCalcId != null) { +labelForCalcId.put (dsann.getCalcId (), dsann.label); +}}} +if (!result.isEmpty ()) { +candidates.put (seq, result); +}} +}, "java.util.List,java.util.Map,java.util.Map,jalview.datamodel.AlignmentI"); +c$.addReferenceAnnotations = Clazz.defineMethod (c$, "addReferenceAnnotations", +function (annotations, alignment, selectionGroup) { +for (var seq, $seq = annotations.keySet ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +for (var ann, $ann = annotations.get (seq).iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) { +var copyAnn = new jalview.datamodel.AlignmentAnnotation (ann); +var startRes = 0; +var endRes = ann.annotations.length; +if (selectionGroup != null) { +startRes = selectionGroup.getStartRes (); +endRes = selectionGroup.getEndRes (); +}copyAnn.restrict (startRes, endRes); +if (!seq.hasAnnotation (ann)) { +seq.addAlignmentAnnotation (copyAnn); +}copyAnn.adjustForAlignment (); +alignment.addAnnotation (copyAnn); +copyAnn.visible = true; +} +} +}, "java.util.Map,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); +c$.showOrHideSequenceAnnotations = Clazz.defineMethod (c$, "showOrHideSequenceAnnotations", +function (al, types, forSequences, anyType, doShow) { +for (var aa, $aa = 0, $$aa = al.getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { +if (anyType || types.contains (aa.label)) { +if ((aa.sequenceRef != null) && (forSequences == null || forSequences.contains (aa.sequenceRef))) { +aa.visible = doShow; +}}} +}, "jalview.datamodel.AlignmentI,java.util.Collection,java.util.List,~B,~B"); +c$.haveCrossRef = Clazz.defineMethod (c$, "haveCrossRef", +function (seq1, seq2) { +return jalview.analysis.AlignmentUtils.hasCrossRef (seq1, seq2) || jalview.analysis.AlignmentUtils.hasCrossRef (seq2, seq1); +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +c$.hasCrossRef = Clazz.defineMethod (c$, "hasCrossRef", +function (seq1, seq2) { +if (seq1 == null || seq2 == null) { +return false; +}var name = seq2.getName (); +var xrefs = seq1.getDBRef (); +if (xrefs != null) { +for (var xref, $xref = 0, $$xref = xrefs; $xref < $$xref.length && ((xref = $$xref[$xref]) || true); $xref++) { +var xrefName = xref.getSource () + "|" + xref.getAccessionId (); +if (xrefName.equalsIgnoreCase (name)) { +return true; +}} +}return false; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +c$.makeExonAlignment = Clazz.defineMethod (c$, "makeExonAlignment", +function (dna, mappings) { +var newMappings = new java.util.LinkedHashSet (); +var exonSequences = new java.util.ArrayList (); +for (var dnaSeq, $dnaSeq = 0, $$dnaSeq = dna; $dnaSeq < $$dnaSeq.length && ((dnaSeq = $$dnaSeq[$dnaSeq]) || true); $dnaSeq++) { +var ds = dnaSeq.getDatasetSequence (); +var seqMappings = jalview.util.MappingUtils.findMappingsForSequence (ds, mappings); +for (var acf, $acf = seqMappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +var newMapping = new jalview.datamodel.AlignedCodonFrame (); +var mappedExons = jalview.analysis.AlignmentUtils.makeExonSequences (ds, acf, newMapping); +if (!mappedExons.isEmpty ()) { +exonSequences.addAll (mappedExons); +newMappings.add (newMapping); +}} +} +var al = new jalview.datamodel.Alignment (exonSequences.toArray ( new Array (exonSequences.size ()))); +al.setDataset (null); +mappings.clear (); +mappings.addAll (newMappings); +return al; +}, "~A,java.util.Set"); +c$.makeExonSequences = Clazz.defineMethod (c$, "makeExonSequences", +function (dnaSeq, mapping, newMapping) { +var exonSequences = new java.util.ArrayList (); +var seqMappings = mapping.getMappingsForSequence (dnaSeq); +var dna = dnaSeq.getSequence (); +for (var seqMapping, $seqMapping = seqMappings.iterator (); $seqMapping.hasNext () && ((seqMapping = $seqMapping.next ()) || true);) { +var newSequence = new StringBuilder (dnaSeq.getLength ()); +var dnaExonRanges = seqMapping.getMap ().getFromRanges (); +for (var range, $range = dnaExonRanges.iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { +for (var pos = range[0]; pos <= range[1]; pos++) { +newSequence.append (dna[pos - 1]); +} +} +var exon = new jalview.datamodel.Sequence (dnaSeq.getName (), newSequence.toString ()); +var cdsAccId = jalview.datamodel.FeatureProperties.getCodingFeature (jalview.datamodel.DBRefSource.EMBL); +var cdsRefs = jalview.util.DBRefUtils.selectRefs (seqMapping.getTo ().getDBRef (), jalview.datamodel.DBRefSource.CODINGDBS); +if (cdsRefs != null) { +for (var cdsRef, $cdsRef = 0, $$cdsRef = cdsRefs; $cdsRef < $$cdsRef.length && ((cdsRef = $$cdsRef[$cdsRef]) || true); $cdsRef++) { +exon.addDBRef ( new jalview.datamodel.DBRefEntry (cdsRef)); +cdsAccId = cdsRef.getAccessionId (); +} +}exon.setName (exon.getName () + "|" + cdsAccId); +exon.createDatasetSequence (); +var exonRange = new java.util.ArrayList (); +exonRange.add ( Clazz.newIntArray (-1, [1, newSequence.length ()])); +var map = new jalview.util.MapList (exonRange, seqMapping.getMap ().getToRanges (), 3, 1); +newMapping.addMap (exon.getDatasetSequence (), seqMapping.getTo (), map); +var cdsToDnaMap = new jalview.util.MapList (dnaExonRanges, exonRange, 1, 1); +newMapping.addMap (dnaSeq, exon.getDatasetSequence (), cdsToDnaMap); +exonSequences.add (exon); +} +return exonSequences; +}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,jalview.datamodel.AlignedCodonFrame"); +}); diff --git a/bin/jalview/analysis/AnnotationSorter.js b/bin/jalview/analysis/AnnotationSorter.js index 2757955..b7d78cd 100644 --- a/bin/jalview/analysis/AnnotationSorter.js +++ b/bin/jalview/analysis/AnnotationSorter.js @@ -1,171 +1,171 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["java.lang.Enum", "java.util.HashMap"], "jalview.analysis.AnnotationSorter", ["jalview.analysis.AlignmentUtils", "java.lang.UnsupportedOperationException", "java.util.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.alignment = null; -this.showAutocalcAbove = false; -this.sequenceIndices = null; -this.bySequenceAndLabel = null; -this.byLabelAndSequence = null; -this.noSort = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "AnnotationSorter"); -Clazz.prepareFields (c$, function () { -this.sequenceIndices = new java.util.HashMap (); -this.bySequenceAndLabel = ((Clazz.isClassDefined ("jalview.analysis.AnnotationSorter$1") ? 0 : jalview.analysis.AnnotationSorter.$AnnotationSorter$1$ ()), Clazz.innerTypeInstance (jalview.analysis.AnnotationSorter$1, this, null)); -this.byLabelAndSequence = ((Clazz.isClassDefined ("jalview.analysis.AnnotationSorter$2") ? 0 : jalview.analysis.AnnotationSorter.$AnnotationSorter$2$ ()), Clazz.innerTypeInstance (jalview.analysis.AnnotationSorter$2, this, null)); -this.noSort = ((Clazz.isClassDefined ("jalview.analysis.AnnotationSorter$3") ? 0 : jalview.analysis.AnnotationSorter.$AnnotationSorter$3$ ()), Clazz.innerTypeInstance (jalview.analysis.AnnotationSorter$3, this, null)); -}); -Clazz.makeConstructor (c$, -function (alignmentI, showAutocalculatedAbove) { -this.alignment = alignmentI; -this.showAutocalcAbove = showAutocalculatedAbove; -}, "jalview.datamodel.AlignmentI,~B"); -Clazz.defineMethod (c$, "sort", -function (alignmentAnnotations, order) { -if (alignmentAnnotations == null) { -return; -}this.saveSequenceIndices (alignmentAnnotations); -var comparator = this.getComparator (order); -if (alignmentAnnotations != null) { -{ -java.util.Arrays.sort (alignmentAnnotations, comparator); -}}}, "~A,jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); -Clazz.defineMethod (c$, "saveSequenceIndices", -($fz = function (alignmentAnnotations) { -this.sequenceIndices.clear (); -for (var ann, $ann = 0, $$ann = alignmentAnnotations; $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { -var seq = ann.sequenceRef; -if (seq != null) { -var index = jalview.analysis.AlignmentUtils.getSequenceIndex (this.alignment, seq); -this.sequenceIndices.put (seq, new Integer (index)); -}} -}, $fz.isPrivate = true, $fz), "~A"); -Clazz.defineMethod (c$, "getComparator", -($fz = function (order) { -if (order == null) { -return this.noSort; -}switch (order) { -case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE: -return this.noSort; -case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL: -return this.bySequenceAndLabel; -case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE: -return this.byLabelAndSequence; -default: -throw new UnsupportedOperationException (order.toString ()); -} -}, $fz.isPrivate = true, $fz), "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); -Clazz.defineMethod (c$, "compareLabels", -($fz = function (o1, o2) { -if (o1 == null || o2 == null) { -return 0; -}var label1 = o1.label; -var label2 = o2.label; -if (label1 == null && label2 == null) { -return 0; -}if (label1 == null) { -return -1; -}if (label2 == null) { -return 1; -}return label1.toUpperCase ().compareTo (label2.toUpperCase ()); -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "compareSequences", -($fz = function (o1, o2) { -var seq1 = o1.sequenceRef; -var seq2 = o2.sequenceRef; -if (seq1 == null && seq2 == null) { -return 0; -}if (seq1 == null) { -return this.showAutocalcAbove ? -1 : 1; -}if (seq2 == null) { -return this.showAutocalcAbove ? 1 : -1; -}var index1 = (this.sequenceIndices.get (seq1)).intValue (); -var index2 = (this.sequenceIndices.get (seq2)).intValue (); -if (index1 == index2) { -return 0; -}if (index1 == -1) { -return -1; -}if (index2 == -1) { -return 1; -}return Integer.compare (index1, index2); -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); -c$.$AnnotationSorter$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.analysis, "AnnotationSorter$1", null, java.util.Comparator); -Clazz.overrideMethod (c$, "compare", -function (o1, o2) { -if (o1 == null && o2 == null) { -return 0; -}if (o1 == null) { -return -1; -}if (o2 == null) { -return 1; -}if (o1.sequenceRef == null && o2.sequenceRef == null) { -return 0; -}var sequenceOrder = this.b$["jalview.analysis.AnnotationSorter"].compareSequences (o1, o2); -return sequenceOrder == 0 ? this.b$["jalview.analysis.AnnotationSorter"].compareLabels (o1, o2) : sequenceOrder; -}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationSorter$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.analysis, "AnnotationSorter$2", null, java.util.Comparator); -Clazz.overrideMethod (c$, "compare", -function (o1, o2) { -if (o1 == null && o2 == null) { -return 0; -}if (o1 == null) { -return -1; -}if (o2 == null) { -return 1; -}if (o1.sequenceRef == null && o2.sequenceRef == null) { -return 0; -}if (o1.sequenceRef == null) { -return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? -1 : 1; -}if (o2.sequenceRef == null) { -return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? 1 : -1; -}var labelOrder = this.b$["jalview.analysis.AnnotationSorter"].compareLabels (o1, o2); -return labelOrder == 0 ? this.b$["jalview.analysis.AnnotationSorter"].compareSequences (o1, o2) : labelOrder; -}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationSorter$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.analysis, "AnnotationSorter$3", null, java.util.Comparator); -Clazz.overrideMethod (c$, "compare", -function (o1, o2) { -if (o1 != null && o2 != null) { -if (o1.sequenceRef == null && o2.sequenceRef != null) { -return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? -1 : 1; -}if (o1.sequenceRef != null && o2.sequenceRef == null) { -return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? 1 : -1; -}}return 0; -}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); -c$ = Clazz.p0p (); -}; -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.description = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis.AnnotationSorter, "SequenceAnnotationOrder", Enum); -Clazz.makeConstructor (c$, -($fz = function (a) { -this.description = a; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.overrideMethod (c$, "toString", -function () { -return this.description; -}); -c$.forDescription = Clazz.defineMethod (c$, "forDescription", -function (a) { -for (var order, $order = 0, $$order = jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.values (); $order < $$order.length && ((order = $$order[$order]) || true); $order++) { -if (order.toString ().equals (a)) { -return order; -}} -return null; -}, "~S"); -Clazz.defineEnumConstant (c$, "SEQUENCE_AND_LABEL", 0, ["Sequence"]); -Clazz.defineEnumConstant (c$, "LABEL_AND_SEQUENCE", 1, ["Label"]); -Clazz.defineEnumConstant (c$, "NONE", 2, ["No sort"]); -c$ = Clazz.p0p (); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["java.lang.Enum", "java.util.HashMap"], "jalview.analysis.AnnotationSorter", ["jalview.analysis.AlignmentUtils", "java.lang.UnsupportedOperationException", "java.util.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.alignment = null; +this.showAutocalcAbove = false; +this.sequenceIndices = null; +this.bySequenceAndLabel = null; +this.byLabelAndSequence = null; +this.noSort = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "AnnotationSorter"); +Clazz.prepareFields (c$, function () { +this.sequenceIndices = new java.util.HashMap (); +this.bySequenceAndLabel = ((Clazz.isClassDefined ("jalview.analysis.AnnotationSorter$1") ? 0 : jalview.analysis.AnnotationSorter.$AnnotationSorter$1$ ()), Clazz.innerTypeInstance (jalview.analysis.AnnotationSorter$1, this, null)); +this.byLabelAndSequence = ((Clazz.isClassDefined ("jalview.analysis.AnnotationSorter$2") ? 0 : jalview.analysis.AnnotationSorter.$AnnotationSorter$2$ ()), Clazz.innerTypeInstance (jalview.analysis.AnnotationSorter$2, this, null)); +this.noSort = ((Clazz.isClassDefined ("jalview.analysis.AnnotationSorter$3") ? 0 : jalview.analysis.AnnotationSorter.$AnnotationSorter$3$ ()), Clazz.innerTypeInstance (jalview.analysis.AnnotationSorter$3, this, null)); +}); +Clazz.makeConstructor (c$, +function (alignmentI, showAutocalculatedAbove) { +this.alignment = alignmentI; +this.showAutocalcAbove = showAutocalculatedAbove; +}, "jalview.datamodel.AlignmentI,~B"); +Clazz.defineMethod (c$, "sort", +function (alignmentAnnotations, order) { +if (alignmentAnnotations == null) { +return; +}this.saveSequenceIndices (alignmentAnnotations); +var comparator = this.getComparator (order); +if (alignmentAnnotations != null) { +{ +java.util.Arrays.sort (alignmentAnnotations, comparator); +}}}, "~A,jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); +Clazz.defineMethod (c$, "saveSequenceIndices", +($fz = function (alignmentAnnotations) { +this.sequenceIndices.clear (); +for (var ann, $ann = 0, $$ann = alignmentAnnotations; $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { +var seq = ann.sequenceRef; +if (seq != null) { +var index = jalview.analysis.AlignmentUtils.getSequenceIndex (this.alignment, seq); +this.sequenceIndices.put (seq, new Integer (index)); +}} +}, $fz.isPrivate = true, $fz), "~A"); +Clazz.defineMethod (c$, "getComparator", +($fz = function (order) { +if (order == null) { +return this.noSort; +}switch (order) { +case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE: +return this.noSort; +case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL: +return this.bySequenceAndLabel; +case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE: +return this.byLabelAndSequence; +default: +throw new UnsupportedOperationException (order.toString ()); +} +}, $fz.isPrivate = true, $fz), "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); +Clazz.defineMethod (c$, "compareLabels", +($fz = function (o1, o2) { +if (o1 == null || o2 == null) { +return 0; +}var label1 = o1.label; +var label2 = o2.label; +if (label1 == null && label2 == null) { +return 0; +}if (label1 == null) { +return -1; +}if (label2 == null) { +return 1; +}return label1.toUpperCase ().compareTo (label2.toUpperCase ()); +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "compareSequences", +($fz = function (o1, o2) { +var seq1 = o1.sequenceRef; +var seq2 = o2.sequenceRef; +if (seq1 == null && seq2 == null) { +return 0; +}if (seq1 == null) { +return this.showAutocalcAbove ? -1 : 1; +}if (seq2 == null) { +return this.showAutocalcAbove ? 1 : -1; +}var index1 = (this.sequenceIndices.get (seq1)).intValue (); +var index2 = (this.sequenceIndices.get (seq2)).intValue (); +if (index1 == index2) { +return 0; +}if (index1 == -1) { +return -1; +}if (index2 == -1) { +return 1; +}return Integer.compare (index1, index2); +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); +c$.$AnnotationSorter$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.analysis, "AnnotationSorter$1", null, java.util.Comparator); +Clazz.overrideMethod (c$, "compare", +function (o1, o2) { +if (o1 == null && o2 == null) { +return 0; +}if (o1 == null) { +return -1; +}if (o2 == null) { +return 1; +}if (o1.sequenceRef == null && o2.sequenceRef == null) { +return 0; +}var sequenceOrder = this.b$["jalview.analysis.AnnotationSorter"].compareSequences (o1, o2); +return sequenceOrder == 0 ? this.b$["jalview.analysis.AnnotationSorter"].compareLabels (o1, o2) : sequenceOrder; +}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationSorter$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.analysis, "AnnotationSorter$2", null, java.util.Comparator); +Clazz.overrideMethod (c$, "compare", +function (o1, o2) { +if (o1 == null && o2 == null) { +return 0; +}if (o1 == null) { +return -1; +}if (o2 == null) { +return 1; +}if (o1.sequenceRef == null && o2.sequenceRef == null) { +return 0; +}if (o1.sequenceRef == null) { +return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? -1 : 1; +}if (o2.sequenceRef == null) { +return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? 1 : -1; +}var labelOrder = this.b$["jalview.analysis.AnnotationSorter"].compareLabels (o1, o2); +return labelOrder == 0 ? this.b$["jalview.analysis.AnnotationSorter"].compareSequences (o1, o2) : labelOrder; +}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationSorter$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.analysis, "AnnotationSorter$3", null, java.util.Comparator); +Clazz.overrideMethod (c$, "compare", +function (o1, o2) { +if (o1 != null && o2 != null) { +if (o1.sequenceRef == null && o2.sequenceRef != null) { +return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? -1 : 1; +}if (o1.sequenceRef != null && o2.sequenceRef == null) { +return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove ? 1 : -1; +}}return 0; +}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation"); +c$ = Clazz.p0p (); +}; +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.description = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis.AnnotationSorter, "SequenceAnnotationOrder", Enum); +Clazz.makeConstructor (c$, +($fz = function (a) { +this.description = a; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.overrideMethod (c$, "toString", +function () { +return this.description; +}); +c$.forDescription = Clazz.defineMethod (c$, "forDescription", +function (a) { +for (var order, $order = 0, $$order = jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.values (); $order < $$order.length && ((order = $$order[$order]) || true); $order++) { +if (order.toString ().equals (a)) { +return order; +}} +return null; +}, "~S"); +Clazz.defineEnumConstant (c$, "SEQUENCE_AND_LABEL", 0, ["Sequence"]); +Clazz.defineEnumConstant (c$, "LABEL_AND_SEQUENCE", 1, ["Label"]); +Clazz.defineEnumConstant (c$, "NONE", 2, ["No sort"]); +c$ = Clazz.p0p (); +}); diff --git a/bin/jalview/analysis/CodingUtils.js b/bin/jalview/analysis/CodingUtils.js index 08fa0ce..69abb90 100644 --- a/bin/jalview/analysis/CodingUtils.js +++ b/bin/jalview/analysis/CodingUtils.js @@ -1,64 +1,64 @@ -Clazz.declarePackage ("jalview.analysis"); -c$ = Clazz.declareType (jalview.analysis, "CodingUtils"); -c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", -function (codon) { -if (codon == null) { -return -1; -}return jalview.analysis.CodingUtils.encodeCodon (codon[2]) + (jalview.analysis.CodingUtils.encodeCodon (codon[1]) << 2) + (jalview.analysis.CodingUtils.encodeCodon (codon[0]) << (4)); -}, "~A"); -c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", -function (c) { -var result = -2147483648; -switch (c) { -case 'A': -case 'a': -result = 0; -break; -case 'C': -case 'c': -result = 1; -break; -case 'G': -case 'g': -result = 2; -break; -case 'T': -case 't': -case 'U': -case 'u': -result = 3; -break; -} -return result; -}, "~S"); -c$.decodeCodon = Clazz.defineMethod (c$, "decodeCodon", -function (encoded) { -var result = Clazz.newCharArray (3, '\0'); -result[2] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3); -encoded = encoded >>> 2; -result[1] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3); -encoded = encoded >>> 2; -result[0] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3); -return result; -}, "~N"); -c$.decodeNucleotide = Clazz.defineMethod (c$, "decodeNucleotide", -function (i) { -var result = '0'; -switch (i) { -case 0: -result = 'A'; -break; -case 1: -result = 'C'; -break; -case 2: -result = 'G'; -break; -case 3: -result = 'T'; -break; -} -return result; -}, "~N"); -Clazz.defineStatics (c$, -"CODON_ENCODING_BITSHIFT", 2); +Clazz.declarePackage ("jalview.analysis"); +c$ = Clazz.declareType (jalview.analysis, "CodingUtils"); +c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", +function (codon) { +if (codon == null) { +return -1; +}return jalview.analysis.CodingUtils.encodeCodon (codon[2]) + (jalview.analysis.CodingUtils.encodeCodon (codon[1]) << 2) + (jalview.analysis.CodingUtils.encodeCodon (codon[0]) << (4)); +}, "~A"); +c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", +function (c) { +var result = -2147483648; +switch (c) { +case 'A': +case 'a': +result = 0; +break; +case 'C': +case 'c': +result = 1; +break; +case 'G': +case 'g': +result = 2; +break; +case 'T': +case 't': +case 'U': +case 'u': +result = 3; +break; +} +return result; +}, "~S"); +c$.decodeCodon = Clazz.defineMethod (c$, "decodeCodon", +function (encoded) { +var result = Clazz.newCharArray (3, '\0'); +result[2] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3); +encoded = encoded >>> 2; +result[1] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3); +encoded = encoded >>> 2; +result[0] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3); +return result; +}, "~N"); +c$.decodeNucleotide = Clazz.defineMethod (c$, "decodeNucleotide", +function (i) { +var result = '0'; +switch (i) { +case 0: +result = 'A'; +break; +case 1: +result = 'C'; +break; +case 2: +result = 'G'; +break; +case 3: +result = 'T'; +break; +} +return result; +}, "~N"); +Clazz.defineStatics (c$, +"CODON_ENCODING_BITSHIFT", 2); diff --git a/bin/jalview/analysis/CodonComparator.js b/bin/jalview/analysis/CodonComparator.js index 7c07b92..afa4c8d 100644 --- a/bin/jalview/analysis/CodonComparator.js +++ b/bin/jalview/analysis/CodonComparator.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("jalview.analysis"); -c$ = Clazz.declareType (jalview.analysis, "CodonComparator", null, java.util.Comparator); -Clazz.overrideMethod (c$, "compare", -function (ac1, ac2) { -if (ac1 == null || ac2 == null || ac1.equals (ac2)) { -return 0; -}if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3) { -return -1; -}if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3) { -return 1; -}if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1) { -return 1; -}if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1) { -return -1; -}if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3) { -return Integer.compare (ac1.pos2, ac2.pos2); -}var compareMiddles = Integer.compare (ac1.pos2, ac2.pos2); -if (compareMiddles != 0) { -return compareMiddles; -}return Integer.compare (ac1.pos1, ac2.pos1); -}, "jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon"); +Clazz.declarePackage ("jalview.analysis"); +c$ = Clazz.declareType (jalview.analysis, "CodonComparator", null, java.util.Comparator); +Clazz.overrideMethod (c$, "compare", +function (ac1, ac2) { +if (ac1 == null || ac2 == null || ac1.equals (ac2)) { +return 0; +}if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3) { +return -1; +}if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3) { +return 1; +}if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1) { +return 1; +}if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1) { +return -1; +}if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3) { +return Integer.compare (ac1.pos2, ac2.pos2); +}var compareMiddles = Integer.compare (ac1.pos2, ac2.pos2); +if (compareMiddles != 0) { +return compareMiddles; +}return Integer.compare (ac1.pos1, ac2.pos1); +}, "jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon"); diff --git a/bin/jalview/analysis/Conservation.class b/bin/jalview/analysis/Conservation.class index c48157a..91e2340 100644 Binary files a/bin/jalview/analysis/Conservation.class and b/bin/jalview/analysis/Conservation.class differ diff --git a/bin/jalview/analysis/Conservation.js b/bin/jalview/analysis/Conservation.js index 1a43b1a..aa95a73 100644 --- a/bin/jalview/analysis/Conservation.js +++ b/bin/jalview/analysis/Conservation.js @@ -1,371 +1,370 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.Conservation", ["jalview.datamodel.Annotation", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color", "java.lang.Character", "$.Double", "$.StringBuffer", "java.util.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.sequences = null; -this.start = 0; -this.end = 0; -this.seqNums = null; -this.maxLength = 0; -this.seqNumsChanged = false; -this.total = null; -this.canonicaliseAa = true; -this.quality = null; -this.qualityRange = null; -this.consString = ""; -this.consSequence = null; -this.propHash = null; -this.threshold = 0; -this.name = ""; -this.cons2 = null; -this.consSymbs = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "Conservation"); -Clazz.prepareFields (c$, function () { -this.qualityRange = new Array (2); -}); -Clazz.makeConstructor (c$, -function (name, propHash, threshold, sequences, start, end) { -this.name = name; -this.propHash = propHash; -this.threshold = threshold; -this.start = start; -this.end = end; -this.maxLength = end - start + 1; -var s; -var sSize = sequences.size (); -var sarray = new Array (sSize); -this.sequences = sarray; -try { -for (s = 0; s < sSize; s++) { -sarray[s] = sequences.get (s); -if (sarray[s].getLength () > this.maxLength) { -this.maxLength = sarray[s].getLength (); -}} -} catch (ex) { -if (Clazz.exceptionOf (ex, ArrayIndexOutOfBoundsException)) { -this.sequences = new Array (0); -this.maxLength = 0; -} else { -throw ex; -} -} -}, "~S,java.util.Hashtable,~N,java.util.List,~N,~N"); -Clazz.defineMethod (c$, "calcSeqNum", -($fz = function (i) { -var sq = null; -var sqnum = null; -var sSize = this.sequences.length; -if ((i > -1) && (i < sSize)) { -sq = this.sequences[i].getSequenceAsString (); -if (this.seqNums.size () <= i) { -this.seqNums.addElement ( Clazz.newIntArray (sq.length + 1, 0)); -}if (sq.hashCode () != (this.seqNums.elementAt (i))[0]) { -var j; -var len; -this.seqNumsChanged = true; -len = sq.length; -if (this.maxLength < len) { -this.maxLength = len; -}sqnum = Clazz.newIntArray (len + 1, 0); -sqnum[0] = sq.hashCode (); -for (j = 1; j <= len; j++) { -sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charCodeAt (j - 1)]; -} -this.seqNums.setElementAt (sqnum, i); -} else { -System.out.println ("SEQUENCE HAS BEEN DELETED!!!"); -}} else { -System.err.println ("ERROR: calcSeqNum called with out of range sequence index for Alignment\n"); -}}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "calculate", -function () { -var resultHash; -var ht; -var thresh; -var j; -var jSize = this.sequences.length; -var values; -var type; -var res = null; -var c; -var enumeration2; -this.total = new Array (this.maxLength); -for (var i = this.start; i <= this.end; i++) { -values = Clazz.newIntArray (255, 0); -for (j = 0; j < jSize; j++) { -if (this.sequences[j].getLength () > i) { -c = this.sequences[j].getCharAt (i); -if (this.canonicaliseAa) { -c = String.fromCharCode (jalview.schemes.ResidueProperties.aaIndex[this.sequences[j].getCharAt (i).charCodeAt (0)]); -if (c.charCodeAt (0) > 20) { -c = '-'; -} else { -c = jalview.schemes.ResidueProperties.aa[c.charCodeAt (0)].charAt (0); -}} else { -if (c == '.' || c == ' ') { -c = '-'; -}if (!this.canonicaliseAa && 'a' <= c && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) - (32)); -}}values[c.charCodeAt (0)]++; -} else { -values['-'.charCodeAt (0)]++; -}} -thresh = Clazz.doubleToInt ((this.threshold * (jSize)) / 100); -resultHash = new java.util.Hashtable (); -for (var v = '-'; v < 'Z'; v = String.fromCharCode (v.charCodeAt (0) + 1)) { -if (values[v.charCodeAt (0)] > thresh) { -res = String.valueOf (v); -enumeration2 = this.propHash.keys (); -while (enumeration2.hasMoreElements ()) { -type = enumeration2.nextElement (); -ht = this.propHash.get (type); -if (!resultHash.containsKey (type)) { -if (ht.containsKey (res)) { -resultHash.put (type, ht.get (res)); -} else { -resultHash.put (type, ht.get ("-")); -}} else if ((resultHash.get (type)).equals (ht.get (res)) == false) { -resultHash.put (type, new Integer (-1)); -}} -}} -if (this.total.length > 0) { -this.total[i - this.start] = resultHash; -}} -}); -Clazz.defineMethod (c$, "countConsNGaps", -function (j) { -var count = 0; -var cons = 0; -var nres = 0; -var r = Clazz.newIntArray (2, 0); -var f = '$'; -var i; -var iSize = this.sequences.length; -var c; -for (i = 0; i < iSize; i++) { -if (j >= this.sequences[i].getLength ()) { -count++; -continue; -}c = this.sequences[i].getCharAt (j); -if (jalview.util.Comparison.isGap ((c))) { -count++; -} else { -nres++; -if (nres == 1) { -f = c; -cons++; -} else if (f == c) { -cons++; -}}} -r[0] = (nres == cons) ? 1 : 0; -r[1] = count; -return r; -}, "~N"); -Clazz.defineMethod (c$, "verdict", -function (consflag, percentageGaps) { -var consString = new StringBuffer (); -var type; -var result; -var gapcons; -var totGaps; -var count; -var pgaps; -var resultHash; -var enumeration; -for (var i = 0; i < this.start; i++) { -consString.append ('-'); -} -this.consSymbs = new Array (this.end - this.start + 1); -for (var i = this.start; i <= this.end; i++) { -gapcons = this.countConsNGaps (i); -totGaps = gapcons[1]; -pgaps = (totGaps * 100) / this.sequences.length; -this.consSymbs[i - this.start] = String.instantialize (); -if (percentageGaps > pgaps) { -resultHash = this.total[i - this.start]; -count = 0; -enumeration = resultHash.keys (); -while (enumeration.hasMoreElements ()) { -type = enumeration.nextElement (); -result = resultHash.get (type); -if (consflag) { -if (result.intValue () == 1) { -this.consSymbs[i - this.start] = type + " " + this.consSymbs[i - this.start]; -count++; -}} else { -if (result.intValue () != -1) { -{ -if (result.intValue () == 0) { -this.consSymbs[i - this.start] = this.consSymbs[i - this.start] + " !" + type; -} else { -this.consSymbs[i - this.start] = type + " " + this.consSymbs[i - this.start]; -}}count++; -}}} -if (count < 10) { -{ -consString.append(""+count); -}} else { -consString.append ((gapcons[0] == 1) ? "*" : "+"); -}} else { -consString.append ('-'); -}} -this.consSequence = new jalview.datamodel.Sequence (this.name, consString.toString (), this.start, this.end); -}, "~B,~N"); -Clazz.defineMethod (c$, "getConsSequence", -function () { -return this.consSequence; -}); -Clazz.defineMethod (c$, "findQuality", -function () { -this.findQuality (0, this.maxLength - 1); -}); -Clazz.defineMethod (c$, "percentIdentity2", -($fz = function () { -this.seqNums = new java.util.Vector (); -var i = 0; -var iSize = this.sequences.length; -for (i = 0; i < iSize; i++) { -this.calcSeqNum (i); -} -if ((this.cons2 == null) || this.seqNumsChanged) { -this.cons2 = Clazz.newIntArray (this.maxLength, 24, 0); -for (var j = 0; j < 24; j++) { -for (i = 0; i < this.maxLength; i++) { -this.cons2[i][j] = 0; -} -} -var sqnum; -var j = 0; -while (j < this.sequences.length) { -sqnum = this.seqNums.elementAt (j); -for (i = 1; i < sqnum.length; i++) { -this.cons2[i - 1][sqnum[i]]++; -} -for (i = sqnum.length - 1; i < this.maxLength; i++) { -this.cons2[i][23]++; -} -j++; -} -}}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "findQuality", -function (start, end) { -this.quality = new java.util.Vector (); -var max = -10000; -var BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62 (); -this.percentIdentity2 (); -var size = this.seqNums.size (); -var lengths = Clazz.newIntArray (size, 0); -var tot; -var bigtot; -var sr; -var tmp; -var x; -var xx; -var l; -var j; -var i; -var ii; -var i2; -var k; -var seqNum; -for (l = 0; l < size; l++) { -lengths[l] = (this.seqNums.elementAt (l)).length - 1; -} -for (j = start; j <= end; j++) { -bigtot = 0; -x = Clazz.newDoubleArray (24, 0); -for (ii = 0; ii < 24; ii++) { -x[ii] = 0; -for (i2 = 0; i2 < 24; i2++) { -x[ii] += ((this.cons2[j][i2] * BLOSUM62[ii][i2]) + 4); -} -x[ii] /= size; -} -for (k = 0; k < size; k++) { -tot = 0; -xx = Clazz.newDoubleArray (24, 0); -seqNum = (j < lengths[k]) ? (this.seqNums.elementAt (k))[j + 1] : 23; -for (i = 0; i < 23; i++) { -sr = 0; -sr = BLOSUM62[i][seqNum] + 4; -xx[i] = x[i] - sr; -tot += (xx[i] * xx[i]); -} -bigtot += Math.sqrt (tot); -} -if (max < bigtot) { -max = bigtot; -}this.quality.addElement ( new Double (bigtot)); -} -var newmax = -10000; -for (j = start; j <= end; j++) { -tmp = (this.quality.elementAt (j)).doubleValue (); -tmp = ((max - tmp) * (size - this.cons2[j][23])) / size; -this.quality.setElementAt ( new Double (tmp), j); -if (tmp > newmax) { -newmax = tmp; -}} -this.qualityRange[0] = new Double (0); -this.qualityRange[1] = new Double (newmax); -}, "~N,~N"); -Clazz.defineMethod (c$, "completeAnnotations", -function (conservation, quality2, istart, alWidth) { -var sequence = this.getConsSequence ().getSequence (); -var minR; -var minG; -var minB; -var maxR; -var maxG; -var maxB; -minR = 0.3; -minG = 0.0; -minB = 0; -maxR = 1.0 - minR; -maxG = 0.9 - minG; -maxB = 0 - minB; -var min = 0; -var max = 11; -var qmin = 0; -var qmax = 0; -var c; -if (conservation.annotations != null && conservation.annotations.length < alWidth) { -conservation.annotations = new Array (alWidth); -}if (quality2 != null) { -quality2.graphMax = this.qualityRange[1].floatValue (); -if (quality2.annotations != null && quality2.annotations.length < alWidth) { -quality2.annotations = new Array (alWidth); -}qmin = this.qualityRange[0].floatValue (); -qmax = this.qualityRange[1].floatValue (); -}for (var i = 0; i < alWidth; i++) { -var value = 0; -c = sequence[i]; -if (Character.isDigit (c)) { -value = c.charCodeAt (0) - 48; -} else if (c == '*') { -value = 11; -} else if (c == '+') { -value = 10; -}var vprop = value - min; -vprop /= max; -conservation.annotations[i] = new jalview.datamodel.Annotation (String.valueOf (c), this.consSymbs[i - this.start], ' ', value, new java.awt.Color (minR + (maxR * vprop), minG + (maxG * vprop), minB + (maxB * vprop))); -if (quality2 != null) { -value = (this.quality.elementAt (i)).floatValue (); -vprop = value - qmin; -vprop /= qmax; -quality2.annotations[i] = new jalview.datamodel.Annotation (" ", String.valueOf (value), ' ', value, new java.awt.Color (minR + (maxR * vprop), minG + (maxG * vprop), minB + (maxB * vprop))); -}} -}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation,~N,~N"); -c$.calculateConservation = Clazz.defineMethod (c$, "calculateConservation", -function (name, consHash, threshold, seqs, start, end, posOrNeg, consPercGaps, calcQuality) { -var cons = new jalview.analysis.Conservation (name, consHash, threshold, seqs, start, end); -return jalview.analysis.Conservation.calculateConservation (cons, posOrNeg, consPercGaps, calcQuality); -}, "~S,java.util.Hashtable,~N,java.util.List,~N,~N,~B,~N,~B"); -c$.calculateConservation = Clazz.defineMethod (c$, "calculateConservation", -function (cons, b, consPercGaps, calcQuality) { -cons.calculate (); -cons.verdict (b, consPercGaps); -if (calcQuality) { -cons.findQuality (); -}return cons; -}, "jalview.analysis.Conservation,~B,~N,~B"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.Conservation", ["jalview.datamodel.Annotation", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color", "java.lang.Character", "$.Double", "$.StringBuffer", "java.util.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.sequences = null; +this.start = 0; +this.end = 0; +this.seqNums = null; +this.maxLength = 0; +this.seqNumsChanged = false; +this.total = null; +this.canonicaliseAa = true; +this.quality = null; +this.qualityRange = null; +this.consString = ""; +this.consSequence = null; +this.propHash = null; +this.threshold = 0; +this.name = ""; +this.cons2 = null; +this.consSymbs = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "Conservation"); +Clazz.prepareFields (c$, function () { +this.qualityRange = new Array (2); +}); +Clazz.makeConstructor (c$, +function (name, propHash, threshold, sequences, start, end) { +this.name = name; +this.propHash = propHash; +this.threshold = threshold; +this.start = start; +this.end = end; +this.maxLength = end - start + 1; +var s; +var sSize = sequences.size (); +var sarray = new Array (sSize); +this.sequences = sarray; +try { +for (s = 0; s < sSize; s++) { +sarray[s] = sequences.get (s); +if (sarray[s].getLength () > this.maxLength) { +this.maxLength = sarray[s].getLength (); +}} +} catch (ex) { +if (Clazz.exceptionOf (ex, ArrayIndexOutOfBoundsException)) { +this.sequences = new Array (0); +this.maxLength = 0; +} else { +throw ex; +} +} +}, "~S,java.util.Hashtable,~N,java.util.List,~N,~N"); +Clazz.defineMethod (c$, "calcSeqNum", +($fz = function (i) { +var sq = null; +var sqnum = null; +var sSize = this.sequences.length; +if ((i > -1) && (i < sSize)) { +sq = this.sequences[i].getSequenceAsString (); +if (this.seqNums.size () <= i) { +this.seqNums.addElement ( Clazz.newIntArray (sq.length + 1, 0)); +}if (sq.hashCode () != (this.seqNums.elementAt (i))[0]) { +var j; +var len; +this.seqNumsChanged = true; +len = sq.length; +if (this.maxLength < len) { +this.maxLength = len; +}sqnum = Clazz.newIntArray (len + 1, 0); +sqnum[0] = sq.hashCode (); +for (j = 1; j <= len; j++) { +sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charCodeAt (j - 1)]; +} +this.seqNums.setElementAt (sqnum, i); +} else { +System.out.println ("SEQUENCE HAS BEEN DELETED!!!"); +}} else { +System.err.println ("ERROR: calcSeqNum called with out of range sequence index for Alignment\n"); +}}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "calculate", +function () { +var resultHash; +var ht; +var thresh; +var j; +var jSize = this.sequences.length; +var values; +var type; +var res = null; +var c; +var enumeration2; +this.total = new Array (this.maxLength); +for (var i = this.start; i <= this.end; i++) { +values = Clazz.newIntArray (255, 0); +for (j = 0; j < jSize; j++) { +if (this.sequences[j].getLength () > i) { +c = this.sequences[j].getCharAt (i); +if (this.canonicaliseAa) { +c = String.fromCharCode (jalview.schemes.ResidueProperties.aaIndex[this.sequences[j].getCharAt (i).charCodeAt (0)]); +if (c.charCodeAt (0) > 20) { +c = '-'; +} else { +c = jalview.schemes.ResidueProperties.aa[c.charCodeAt (0)].charAt (0); +}} else { +if (c == '.' || c == ' ') { +c = '-'; +}if (!this.canonicaliseAa && 'a' <= c && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) - (32)); +}}values[c.charCodeAt (0)]++; +} else { +values['-'.charCodeAt (0)]++; +}} +thresh = Clazz.doubleToInt ((this.threshold * (jSize)) / 100); +resultHash = new java.util.Hashtable (); +for (var v = '-'; v < 'Z'; v = String.fromCharCode (v.charCodeAt (0) + 1)) { +if (values[v.charCodeAt (0)] > thresh) { +res = String.valueOf (v); +enumeration2 = this.propHash.keys (); +while (enumeration2.hasMoreElements ()) { +type = enumeration2.nextElement (); +ht = this.propHash.get (type); +if (!resultHash.containsKey (type)) { +if (ht.containsKey (res)) { +resultHash.put (type, ht.get (res)); +} else { +resultHash.put (type, ht.get ("-")); +}} else if ((resultHash.get (type)).equals (ht.get (res)) == false) { +resultHash.put (type, new Integer (-1)); +}} +}} +if (this.total.length > 0) { +this.total[i - this.start] = resultHash; +}} +}); +Clazz.defineMethod (c$, "countConsNGaps", +function (j) { +var count = 0; +var cons = 0; +var nres = 0; +var r = Clazz.newIntArray (2, 0); +var f = '$'; +var i; +var iSize = this.sequences.length; +var c; +for (i = 0; i < iSize; i++) { +if (j >= this.sequences[i].getLength ()) { +count++; +continue; +}c = this.sequences[i].getCharAt (j); +if (jalview.util.Comparison.isGap ((c))) { +count++; +} else { +nres++; +if (nres == 1) { +f = c; +cons++; +} else if (f == c) { +cons++; +}}} +r[0] = (nres == cons) ? 1 : 0; +r[1] = count; +return r; +}, "~N"); +Clazz.defineMethod (c$, "verdict", +function (consflag, percentageGaps) { +var consString = new StringBuffer (); +var type; +var result; +var gapcons; +var totGaps; +var count; +var pgaps; +var resultHash; +var enumeration; +for (var i = 0; i < this.start; i++) { +consString.append ('-'); +} +this.consSymbs = new Array (this.end - this.start + 1); +for (var i = this.start; i <= this.end; i++) { +gapcons = this.countConsNGaps (i); +totGaps = gapcons[1]; +pgaps = (totGaps * 100) / this.sequences.length; +this.consSymbs[i - this.start] = String.instantialize (); +if (percentageGaps > pgaps) { +resultHash = this.total[i - this.start]; +count = 0; +enumeration = resultHash.keys (); +while (enumeration.hasMoreElements ()) { +type = enumeration.nextElement (); +result = resultHash.get (type); +if (consflag) { +if (result.intValue () == 1) { +this.consSymbs[i - this.start] = type + " " + this.consSymbs[i - this.start]; +count++; +}} else { +if (result.intValue () != -1) { +{ +if (result.intValue () == 0) { +this.consSymbs[i - this.start] = this.consSymbs[i - this.start] + " !" + type; +} else { +this.consSymbs[i - this.start] = type + " " + this.consSymbs[i - this.start]; +}}count++; +}}} +if (count < 10) { +consString.append ("" + count); +} else { +consString.append ((gapcons[0] == 1) ? "*" : "+"); +}} else { +consString.append ('-'); +}} +this.consSequence = new jalview.datamodel.Sequence (this.name, consString.toString (), this.start, this.end); +}, "~B,~N"); +Clazz.defineMethod (c$, "getConsSequence", +function () { +return this.consSequence; +}); +Clazz.defineMethod (c$, "findQuality", +function () { +this.findQuality (0, this.maxLength - 1); +}); +Clazz.defineMethod (c$, "percentIdentity2", +($fz = function () { +this.seqNums = new java.util.Vector (); +var i = 0; +var iSize = this.sequences.length; +for (i = 0; i < iSize; i++) { +this.calcSeqNum (i); +} +if ((this.cons2 == null) || this.seqNumsChanged) { +this.cons2 = Clazz.newIntArray (this.maxLength, 24, 0); +for (var j = 0; j < 24; j++) { +for (i = 0; i < this.maxLength; i++) { +this.cons2[i][j] = 0; +} +} +var sqnum; +var j = 0; +while (j < this.sequences.length) { +sqnum = this.seqNums.elementAt (j); +for (i = 1; i < sqnum.length; i++) { +this.cons2[i - 1][sqnum[i]]++; +} +for (i = sqnum.length - 1; i < this.maxLength; i++) { +this.cons2[i][23]++; +} +j++; +} +}}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "findQuality", +function (start, end) { +this.quality = new java.util.Vector (); +var max = -10000; +var BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62 (); +this.percentIdentity2 (); +var size = this.seqNums.size (); +var lengths = Clazz.newIntArray (size, 0); +var tot; +var bigtot; +var sr; +var tmp; +var x; +var xx; +var l; +var j; +var i; +var ii; +var i2; +var k; +var seqNum; +for (l = 0; l < size; l++) { +lengths[l] = (this.seqNums.elementAt (l)).length - 1; +} +for (j = start; j <= end; j++) { +bigtot = 0; +x = Clazz.newDoubleArray (24, 0); +for (ii = 0; ii < 24; ii++) { +x[ii] = 0; +for (i2 = 0; i2 < 24; i2++) { +x[ii] += ((this.cons2[j][i2] * BLOSUM62[ii][i2]) + 4); +} +x[ii] /= size; +} +for (k = 0; k < size; k++) { +tot = 0; +xx = Clazz.newDoubleArray (24, 0); +seqNum = (j < lengths[k]) ? (this.seqNums.elementAt (k))[j + 1] : 23; +for (i = 0; i < 23; i++) { +sr = 0; +sr = BLOSUM62[i][seqNum] + 4; +xx[i] = x[i] - sr; +tot += (xx[i] * xx[i]); +} +bigtot += Math.sqrt (tot); +} +if (max < bigtot) { +max = bigtot; +}this.quality.addElement ( new Double (bigtot)); +} +var newmax = -10000; +for (j = start; j <= end; j++) { +tmp = (this.quality.elementAt (j)).doubleValue (); +tmp = ((max - tmp) * (size - this.cons2[j][23])) / size; +this.quality.setElementAt ( new Double (tmp), j); +if (tmp > newmax) { +newmax = tmp; +}} +this.qualityRange[0] = new Double (0); +this.qualityRange[1] = new Double (newmax); +}, "~N,~N"); +Clazz.defineMethod (c$, "completeAnnotations", +function (conservation, quality2, istart, alWidth) { +var sequence = this.getConsSequence ().getSequence (); +var minR; +var minG; +var minB; +var maxR; +var maxG; +var maxB; +minR = 0.3; +minG = 0.0; +minB = 0; +maxR = 1.0 - minR; +maxG = 0.9 - minG; +maxB = 0 - minB; +var min = 0; +var max = 11; +var qmin = 0; +var qmax = 0; +var c; +if (conservation.annotations != null && conservation.annotations.length < alWidth) { +conservation.annotations = new Array (alWidth); +}if (quality2 != null) { +quality2.graphMax = this.qualityRange[1].floatValue (); +if (quality2.annotations != null && quality2.annotations.length < alWidth) { +quality2.annotations = new Array (alWidth); +}qmin = this.qualityRange[0].floatValue (); +qmax = this.qualityRange[1].floatValue (); +}for (var i = 0; i < alWidth; i++) { +var value = 0; +c = sequence[i]; +if (Character.isDigit (c)) { +value = c.charCodeAt (0) - 48; +} else if (c == '*') { +value = 11; +} else if (c == '+') { +value = 10; +}var vprop = value - min; +vprop /= max; +conservation.annotations[i] = new jalview.datamodel.Annotation (String.valueOf (c), this.consSymbs[i - this.start], ' ', value, new java.awt.Color (minR + (maxR * vprop), minG + (maxG * vprop), minB + (maxB * vprop))); +if (quality2 != null) { +value = (this.quality.elementAt (i)).floatValue (); +vprop = value - qmin; +vprop /= qmax; +quality2.annotations[i] = new jalview.datamodel.Annotation (" ", String.valueOf (value), ' ', value, new java.awt.Color (minR + (maxR * vprop), minG + (maxG * vprop), minB + (maxB * vprop))); +}} +}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation,~N,~N"); +c$.calculateConservation = Clazz.defineMethod (c$, "calculateConservation", +function (name, consHash, threshold, seqs, start, end, posOrNeg, consPercGaps, calcQuality) { +var cons = new jalview.analysis.Conservation (name, consHash, threshold, seqs, start, end); +return jalview.analysis.Conservation.calculateConservation (cons, posOrNeg, consPercGaps, calcQuality); +}, "~S,java.util.Hashtable,~N,java.util.List,~N,~N,~B,~N,~B"); +c$.calculateConservation = Clazz.defineMethod (c$, "calculateConservation", +function (cons, b, consPercGaps, calcQuality) { +cons.calculate (); +cons.verdict (b, consPercGaps); +if (calcQuality) { +cons.findQuality (); +}return cons; +}, "jalview.analysis.Conservation,~B,~N,~B"); +}); diff --git a/bin/jalview/analysis/Dna.class b/bin/jalview/analysis/Dna.class index 3ae87d0..23cc7cb 100644 Binary files a/bin/jalview/analysis/Dna.class and b/bin/jalview/analysis/Dna.class differ diff --git a/bin/jalview/analysis/Dna.js b/bin/jalview/analysis/Dna.js index 68086a9..57c052f 100644 --- a/bin/jalview/analysis/Dna.js +++ b/bin/jalview/analysis/Dna.js @@ -1,327 +1,327 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["jalview.analysis.CodonComparator"], "jalview.analysis.Dna", ["jalview.datamodel.AlignedCodon", "$.AlignedCodonFrame", "$.Alignment", "$.AlignmentAnnotation", "$.Annotation", "$.DBRefSource", "$.FeatureProperties", "$.GraphLine", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.DBRefUtils", "$.MapList", "$.ShiftList", "java.lang.IllegalStateException", "$.StringBuilder", "java.util.ArrayList", "$.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.selection = null; -this.seqstring = null; -this.contigs = null; -this.gapChar = '\0'; -this.annotations = null; -this.dnaWidth = 0; -this.dataset = null; -this.aaWidth = 0; -this.alignedCodons = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "Dna"); -Clazz.makeConstructor (c$, -function (viewport, visibleContigs) { -this.selection = java.util.Arrays.asList (viewport.getSequenceSelection ()); -this.seqstring = viewport.getViewAsString (true); -this.contigs = visibleContigs; -this.gapChar = viewport.getGapCharacter (); -this.annotations = viewport.getAlignment ().getAlignmentAnnotation (); -this.dnaWidth = viewport.getAlignment ().getWidth (); -this.dataset = viewport.getAlignment ().getDataset (); -}, "jalview.api.AlignViewportI,~A"); -c$.compareCodonPos = Clazz.defineMethod (c$, "compareCodonPos", -function (ac1, ac2) { -return jalview.analysis.Dna.comparator.compare (ac1, ac2); -}, "jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon"); -Clazz.defineMethod (c$, "translateCdna", -function () { -var acf = new jalview.datamodel.AlignedCodonFrame (); -this.alignedCodons = new Array (this.dnaWidth); -var s; -var sSize = this.selection.size (); -var pepseqs = new java.util.ArrayList (); -for (s = 0; s < sSize; s++) { -var newseq = this.translateCodingRegion (this.selection.get (s), this.seqstring[s], acf, pepseqs); -if (newseq != null) { -pepseqs.add (newseq); -var ds = newseq; -if (this.dataset != null) { -while (ds.getDatasetSequence () != null) { -ds = ds.getDatasetSequence (); -} -this.dataset.addSequence (ds); -}}} -var newseqs = pepseqs.toArray ( new Array (pepseqs.size ())); -var al = new jalview.datamodel.Alignment (newseqs); -al.padGaps (); -al.setDataset (this.dataset); -this.translateAlignedAnnotations (al, acf); -al.addCodonFrame (acf); -return al; -}); -c$.canTranslate = Clazz.defineMethod (c$, "canTranslate", -function (selection, viscontigs) { -for (var gd = 0; gd < selection.length; gd++) { -var dna = selection[gd]; -var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS); -if (dnarefs != null) { -var mappedrefs = new java.util.ArrayList (); -var refs = dna.getDBRef (); -for (var d = 0; d < refs.length; d++) { -if (refs[d].getMap () != null && refs[d].getMap ().getMap () != null && refs[d].getMap ().getMap ().getFromRatio () == 3 && refs[d].getMap ().getMap ().getToRatio () == 1) { -mappedrefs.add (refs[d]); -}} -dnarefs = mappedrefs.toArray ( new Array (mappedrefs.size ())); -for (var d = 0; d < dnarefs.length; d++) { -var mp = dnarefs[d].getMap (); -if (mp != null) { -for (var vc = 0; vc < viscontigs.length; vc += 2) { -var mpr = mp.locateMappedRange (viscontigs[vc], viscontigs[vc + 1]); -if (mpr != null) { -return true; -}} -}} -}} -return false; -}, "~A,~A"); -Clazz.defineMethod (c$, "translateAlignedAnnotations", -function (al, acf) { -if (this.annotations != null) { -for (var annotation, $annotation = 0, $$annotation = this.annotations; $annotation < $$annotation.length && ((annotation = $$annotation[$annotation]) || true); $annotation++) { -if (annotation.autoCalculated || !annotation.visible || annotation.isRNA ()) { -continue; -}var aSize = this.aaWidth; -var anots = (annotation.annotations == null) ? null : new Array (aSize); -if (anots != null) { -for (var a = 0; a < aSize; a++) { -if (a < this.alignedCodons.length && this.alignedCodons[a] != null && this.alignedCodons[a].pos1 == (this.alignedCodons[a].pos3 - 2)) { -anots[a] = jalview.analysis.Dna.getCodonAnnotation (this.alignedCodons[a], annotation.annotations); -}} -}var aa = new jalview.datamodel.AlignmentAnnotation (annotation.label, annotation.description, anots); -aa.graph = annotation.graph; -aa.graphGroup = annotation.graphGroup; -aa.graphHeight = annotation.graphHeight; -if (annotation.getThreshold () != null) { -aa.setThreshold ( new jalview.datamodel.GraphLine (annotation.getThreshold ())); -}if (annotation.$hasScore) { -aa.setScore (annotation.getScore ()); -}var seqRef = annotation.sequenceRef; -if (seqRef != null) { -var aaSeq = acf.getAaForDnaSeq (seqRef); -if (aaSeq != null) { -aa.setSequenceRef (aaSeq); -aa.createSequenceMapping (aaSeq, aaSeq.getStart (), true); -aa.adjustForAlignment (); -aaSeq.addAlignmentAnnotation (aa); -}}al.addAnnotation (aa); -} -}}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignedCodonFrame"); -c$.getCodonAnnotation = Clazz.defineMethod (c$, "getCodonAnnotation", -($fz = function (is, annotations) { -var contrib = 0; -var annot = null; -for (var p = 1; p <= 3; p++) { -var dnaCol = is.getBaseColumn (p); -if (annotations[dnaCol] != null) { -if (annot == null) { -annot = new jalview.datamodel.Annotation (annotations[dnaCol]); -contrib = 1; -} else { -var cpy = new jalview.datamodel.Annotation (annotations[dnaCol]); -if (annot.colour == null) { -annot.colour = cpy.colour; -}if (annot.description == null || annot.description.length == 0) { -annot.description = cpy.description; -}if (annot.displayCharacter == null) { -annot.displayCharacter = cpy.displayCharacter; -}if (annot.secondaryStructure.charCodeAt (0) == 0) { -annot.secondaryStructure = cpy.secondaryStructure; -}annot.value += cpy.value; -contrib++; -}}} -if (contrib > 1) { -annot.value /= contrib; -}return annot; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignedCodon,~A"); -Clazz.defineMethod (c$, "translateCodingRegion", -function (selection, seqstring, acf, proteinSeqs) { -var skip = new java.util.ArrayList (); -var skipint = null; -var vismapping = new jalview.util.ShiftList (); -var vc; -var scontigs = Clazz.newIntArray (this.contigs.length, 0); -var npos = 0; -for (vc = 0; vc < this.contigs.length; vc += 2) { -if (vc == 0) { -vismapping.addShift (npos, this.contigs[vc]); -} else { -vismapping.addShift (npos, this.contigs[vc] - this.contigs[vc - 1] + 1); -}scontigs[vc] = this.contigs[vc]; -scontigs[vc + 1] = this.contigs[vc + 1]; -} -var protein = new StringBuilder (Clazz.doubleToInt (seqstring.length / 2)); -var seq = seqstring.$replace ('U', 'T').$replace ('u', 'T'); -var codon = Clazz.newCharArray (3, '\0'); -var cdp = Clazz.newIntArray (3, 0); -var rf = 0; -var lastnpos = 0; -var nend; -var aspos = 0; -var resSize = 0; -for (npos = 0, nend = seq.length; npos < nend; npos++) { -if (!jalview.util.Comparison.isGap (seq.charAt (npos))) { -cdp[rf] = npos; -codon[rf++] = seq.charAt (npos); -}if (rf == 3) { -var alignedCodon = new jalview.datamodel.AlignedCodon (cdp[0], cdp[1], cdp[2]); -var aa = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (codon)); -rf = 0; -var gapString = String.valueOf (this.gapChar); -if (aa == null) { -aa = gapString; -if (skipint == null) { -skipint = Clazz.newIntArray (-1, [alignedCodon.pos1, alignedCodon.pos3]); -}skipint[1] = alignedCodon.pos3; -} else { -if (skipint != null) { -skipint[0] = vismapping.shift (skipint[0]); -skipint[1] = vismapping.shift (skipint[1]); -for (vc = 0; vc < scontigs.length; ) { -if (scontigs[vc + 1] < skipint[0]) { -vc += 2; -continue; -}if (scontigs[vc] > skipint[1]) { -break; -}var t; -if (scontigs[vc] <= skipint[0]) { -if (skipint[0] == scontigs[vc]) { -if (scontigs[vc + 1] > skipint[1]) { -scontigs[vc] = skipint[1]; -vc += 2; -} else { -if (scontigs[vc + 1] == skipint[1]) { -t = Clazz.newIntArray (scontigs.length - 2, 0); -if (vc > 0) { -System.arraycopy (scontigs, 0, t, 0, vc - 1); -}if (vc + 2 < t.length) { -System.arraycopy (scontigs, vc + 2, t, vc, t.length - vc + 2); -}scontigs = t; -} else { -scontigs[vc + 1] = skipint[0] - 1; -vc += 2; -}}} else { -if (scontigs[vc + 1] < skipint[1]) { -scontigs[vc + 1] = skipint[0] - 1; -vc += 2; -} else { -t = Clazz.newIntArray (scontigs.length + 2, 0); -System.arraycopy (scontigs, 0, t, 0, vc + 1); -t[vc + 1] = skipint[0]; -t[vc + 2] = skipint[1]; -System.arraycopy (scontigs, vc + 1, t, vc + 3, scontigs.length - (vc + 1)); -scontigs = t; -vc += 4; -}}}} -skip.add (skipint); -skipint = null; -}if (aa.equals ("STOP")) { -aa = "X"; -}resSize++; -}var findpos = true; -while (findpos) { -var compareCodonPos = jalview.analysis.Dna.compareCodonPos (alignedCodon, this.alignedCodons[aspos]); -switch (compareCodonPos) { -case -1: -this.insertAAGap (aspos, proteinSeqs); -findpos = false; -break; -case 1: -aa = gapString + aa; -aspos++; -break; -case 0: -findpos = false; -} -} -protein.append (aa); -lastnpos = npos; -if (this.alignedCodons[aspos] == null) { -this.alignedCodons[aspos] = alignedCodon; -} else if (!this.alignedCodons[aspos].equals (alignedCodon)) { -throw new IllegalStateException ("Tried to coalign " + this.alignedCodons[aspos].toString () + " with " + alignedCodon.toString ()); -}if (aspos >= this.aaWidth) { -this.aaWidth = aspos; -}aspos++; -}} -if (resSize > 0) { -var newseq = new jalview.datamodel.Sequence (selection.getName (), protein.toString ()); -if (rf != 0) { -var errMsg = "trimming contigs for incomplete terminal codon."; -System.err.println ("trimming contigs for incomplete terminal codon."); -vc = scontigs.length - 1; -lastnpos = vismapping.shift (lastnpos); -while (vc >= 0 && scontigs[vc] > lastnpos) { -if (vc > 0 && scontigs[vc - 1] > lastnpos) { -vc -= 2; -} else { -scontigs[vc] = lastnpos; -}} -if (vc > 0 && (vc + 1) < scontigs.length) { -var t = Clazz.newIntArray (vc + 1, 0); -System.arraycopy (scontigs, 0, t, 0, vc + 1); -scontigs = t; -}if (vc <= 0) { -scontigs = null; -}}if (scontigs != null) { -npos = 0; -for (vc = 0; vc < scontigs.length; vc += 2) { -scontigs[vc] = selection.findPosition (scontigs[vc]); -scontigs[vc + 1] = selection.findPosition (scontigs[vc + 1]); -if (scontigs[vc + 1] == selection.getEnd ()) { -break; -}} -if ((vc + 2) < scontigs.length) { -var t = Clazz.newIntArray (vc + 2, 0); -System.arraycopy (scontigs, 0, t, 0, vc + 2); -scontigs = t; -}var map = new jalview.util.MapList (scontigs, Clazz.newIntArray (-1, [1, resSize]), 3, 1); -jalview.analysis.Dna.transferCodedFeatures (selection, newseq, map, null, null); -var rseq = newseq.deriveSequence (); -acf.addMap (selection, rseq, map); -return rseq; -}}return null; -}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame,java.util.List"); -Clazz.defineMethod (c$, "insertAAGap", -function (pos, proteinSeqs) { -this.aaWidth++; -for (var seq, $seq = proteinSeqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -seq.insertCharAt (pos, this.gapChar); -} -this.checkCodonFrameWidth (); -if (pos < this.aaWidth) { -this.aaWidth++; -System.arraycopy (this.alignedCodons, pos, this.alignedCodons, pos + 1, this.alignedCodons.length - pos - 1); -this.alignedCodons[pos] = null; -}}, "~N,java.util.List"); -Clazz.defineMethod (c$, "checkCodonFrameWidth", -function () { -if (this.alignedCodons[this.alignedCodons.length - 1] != null) { -var c = new Array (this.alignedCodons.length + 10); -System.arraycopy (this.alignedCodons, 0, c, 0, this.alignedCodons.length); -this.alignedCodons = c; -}}); -c$.transferCodedFeatures = Clazz.defineMethod (c$, "transferCodedFeatures", -($fz = function (dna, pep, map, featureTypes, featureGroups) { -var sfs = dna.getSequenceFeatures (); -var fgstate; -var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS); -if (dnarefs != null) { -for (var d = 0; d < dnarefs.length; d++) { -var mp = dnarefs[d].getMap (); -if (mp != null) { -}} -}if (sfs != null) { -for (var sf, $sf = 0, $$sf = sfs; $sf < $$sf.length && ((sf = $$sf[$sf]) || true); $sf++) { -fgstate = (featureGroups == null) ? null : featureGroups.get (sf.featureGroup); -if ((featureTypes == null || featureTypes.containsKey (sf.getType ())) && (fgstate == null || fgstate.booleanValue ())) { -if (jalview.datamodel.FeatureProperties.isCodingFeature (null, sf.getType ())) { -{ -}}}} -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList,java.util.Map,java.util.Map"); -Clazz.defineStatics (c$, -"STOP_X", "X"); -c$.comparator = c$.prototype.comparator = new jalview.analysis.CodonComparator (); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["jalview.analysis.CodonComparator"], "jalview.analysis.Dna", ["jalview.datamodel.AlignedCodon", "$.AlignedCodonFrame", "$.Alignment", "$.AlignmentAnnotation", "$.Annotation", "$.DBRefSource", "$.FeatureProperties", "$.GraphLine", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.DBRefUtils", "$.MapList", "$.ShiftList", "java.lang.IllegalStateException", "$.StringBuilder", "java.util.ArrayList", "$.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.selection = null; +this.seqstring = null; +this.contigs = null; +this.gapChar = '\0'; +this.annotations = null; +this.dnaWidth = 0; +this.dataset = null; +this.aaWidth = 0; +this.alignedCodons = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "Dna"); +Clazz.makeConstructor (c$, +function (viewport, visibleContigs) { +this.selection = java.util.Arrays.asList (viewport.getSequenceSelection ()); +this.seqstring = viewport.getViewAsString (true); +this.contigs = visibleContigs; +this.gapChar = viewport.getGapCharacter (); +this.annotations = viewport.getAlignment ().getAlignmentAnnotation (); +this.dnaWidth = viewport.getAlignment ().getWidth (); +this.dataset = viewport.getAlignment ().getDataset (); +}, "jalview.api.AlignViewportI,~A"); +c$.compareCodonPos = Clazz.defineMethod (c$, "compareCodonPos", +function (ac1, ac2) { +return jalview.analysis.Dna.comparator.compare (ac1, ac2); +}, "jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon"); +Clazz.defineMethod (c$, "translateCdna", +function () { +var acf = new jalview.datamodel.AlignedCodonFrame (); +this.alignedCodons = new Array (this.dnaWidth); +var s; +var sSize = this.selection.size (); +var pepseqs = new java.util.ArrayList (); +for (s = 0; s < sSize; s++) { +var newseq = this.translateCodingRegion (this.selection.get (s), this.seqstring[s], acf, pepseqs); +if (newseq != null) { +pepseqs.add (newseq); +var ds = newseq; +if (this.dataset != null) { +while (ds.getDatasetSequence () != null) { +ds = ds.getDatasetSequence (); +} +this.dataset.addSequence (ds); +}}} +var newseqs = pepseqs.toArray ( new Array (pepseqs.size ())); +var al = new jalview.datamodel.Alignment (newseqs); +al.padGaps (); +al.setDataset (this.dataset); +this.translateAlignedAnnotations (al, acf); +al.addCodonFrame (acf); +return al; +}); +c$.canTranslate = Clazz.defineMethod (c$, "canTranslate", +function (selection, viscontigs) { +for (var gd = 0; gd < selection.length; gd++) { +var dna = selection[gd]; +var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS); +if (dnarefs != null) { +var mappedrefs = new java.util.ArrayList (); +var refs = dna.getDBRef (); +for (var d = 0; d < refs.length; d++) { +if (refs[d].getMap () != null && refs[d].getMap ().getMap () != null && refs[d].getMap ().getMap ().getFromRatio () == 3 && refs[d].getMap ().getMap ().getToRatio () == 1) { +mappedrefs.add (refs[d]); +}} +dnarefs = mappedrefs.toArray ( new Array (mappedrefs.size ())); +for (var d = 0; d < dnarefs.length; d++) { +var mp = dnarefs[d].getMap (); +if (mp != null) { +for (var vc = 0; vc < viscontigs.length; vc += 2) { +var mpr = mp.locateMappedRange (viscontigs[vc], viscontigs[vc + 1]); +if (mpr != null) { +return true; +}} +}} +}} +return false; +}, "~A,~A"); +Clazz.defineMethod (c$, "translateAlignedAnnotations", +function (al, acf) { +if (this.annotations != null) { +for (var annotation, $annotation = 0, $$annotation = this.annotations; $annotation < $$annotation.length && ((annotation = $$annotation[$annotation]) || true); $annotation++) { +if (annotation.autoCalculated || !annotation.visible || annotation.isRNA ()) { +continue; +}var aSize = this.aaWidth; +var anots = (annotation.annotations == null) ? null : new Array (aSize); +if (anots != null) { +for (var a = 0; a < aSize; a++) { +if (a < this.alignedCodons.length && this.alignedCodons[a] != null && this.alignedCodons[a].pos1 == (this.alignedCodons[a].pos3 - 2)) { +anots[a] = jalview.analysis.Dna.getCodonAnnotation (this.alignedCodons[a], annotation.annotations); +}} +}var aa = new jalview.datamodel.AlignmentAnnotation (annotation.label, annotation.description, anots); +aa.graph = annotation.graph; +aa.graphGroup = annotation.graphGroup; +aa.graphHeight = annotation.graphHeight; +if (annotation.getThreshold () != null) { +aa.setThreshold ( new jalview.datamodel.GraphLine (annotation.getThreshold ())); +}if (annotation.$hasScore) { +aa.setScore (annotation.getScore ()); +}var seqRef = annotation.sequenceRef; +if (seqRef != null) { +var aaSeq = acf.getAaForDnaSeq (seqRef); +if (aaSeq != null) { +aa.setSequenceRef (aaSeq); +aa.createSequenceMapping (aaSeq, aaSeq.getStart (), true); +aa.adjustForAlignment (); +aaSeq.addAlignmentAnnotation (aa); +}}al.addAnnotation (aa); +} +}}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignedCodonFrame"); +c$.getCodonAnnotation = Clazz.defineMethod (c$, "getCodonAnnotation", +($fz = function (is, annotations) { +var contrib = 0; +var annot = null; +for (var p = 1; p <= 3; p++) { +var dnaCol = is.getBaseColumn (p); +if (annotations[dnaCol] != null) { +if (annot == null) { +annot = new jalview.datamodel.Annotation (annotations[dnaCol]); +contrib = 1; +} else { +var cpy = new jalview.datamodel.Annotation (annotations[dnaCol]); +if (annot.colour == null) { +annot.colour = cpy.colour; +}if (annot.description == null || annot.description.length == 0) { +annot.description = cpy.description; +}if (annot.displayCharacter == null) { +annot.displayCharacter = cpy.displayCharacter; +}if (annot.secondaryStructure.charCodeAt (0) == 0) { +annot.secondaryStructure = cpy.secondaryStructure; +}annot.value += cpy.value; +contrib++; +}}} +if (contrib > 1) { +annot.value /= contrib; +}return annot; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignedCodon,~A"); +Clazz.defineMethod (c$, "translateCodingRegion", +function (selection, seqstring, acf, proteinSeqs) { +var skip = new java.util.ArrayList (); +var skipint = null; +var vismapping = new jalview.util.ShiftList (); +var vc; +var scontigs = Clazz.newIntArray (this.contigs.length, 0); +var npos = 0; +for (vc = 0; vc < this.contigs.length; vc += 2) { +if (vc == 0) { +vismapping.addShift (npos, this.contigs[vc]); +} else { +vismapping.addShift (npos, this.contigs[vc] - this.contigs[vc - 1] + 1); +}scontigs[vc] = this.contigs[vc]; +scontigs[vc + 1] = this.contigs[vc + 1]; +} +var protein = new StringBuilder (Clazz.doubleToInt (seqstring.length / 2)); +var seq = seqstring.$replace ('U', 'T').$replace ('u', 'T'); +var codon = Clazz.newCharArray (3, '\0'); +var cdp = Clazz.newIntArray (3, 0); +var rf = 0; +var lastnpos = 0; +var nend; +var aspos = 0; +var resSize = 0; +for (npos = 0, nend = seq.length; npos < nend; npos++) { +if (!jalview.util.Comparison.isGap (seq.charAt (npos))) { +cdp[rf] = npos; +codon[rf++] = seq.charAt (npos); +}if (rf == 3) { +var alignedCodon = new jalview.datamodel.AlignedCodon (cdp[0], cdp[1], cdp[2]); +var aa = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (codon)); +rf = 0; +var gapString = String.valueOf (this.gapChar); +if (aa == null) { +aa = gapString; +if (skipint == null) { +skipint = Clazz.newIntArray (-1, [alignedCodon.pos1, alignedCodon.pos3]); +}skipint[1] = alignedCodon.pos3; +} else { +if (skipint != null) { +skipint[0] = vismapping.shift (skipint[0]); +skipint[1] = vismapping.shift (skipint[1]); +for (vc = 0; vc < scontigs.length; ) { +if (scontigs[vc + 1] < skipint[0]) { +vc += 2; +continue; +}if (scontigs[vc] > skipint[1]) { +break; +}var t; +if (scontigs[vc] <= skipint[0]) { +if (skipint[0] == scontigs[vc]) { +if (scontigs[vc + 1] > skipint[1]) { +scontigs[vc] = skipint[1]; +vc += 2; +} else { +if (scontigs[vc + 1] == skipint[1]) { +t = Clazz.newIntArray (scontigs.length - 2, 0); +if (vc > 0) { +System.arraycopy (scontigs, 0, t, 0, vc - 1); +}if (vc + 2 < t.length) { +System.arraycopy (scontigs, vc + 2, t, vc, t.length - vc + 2); +}scontigs = t; +} else { +scontigs[vc + 1] = skipint[0] - 1; +vc += 2; +}}} else { +if (scontigs[vc + 1] < skipint[1]) { +scontigs[vc + 1] = skipint[0] - 1; +vc += 2; +} else { +t = Clazz.newIntArray (scontigs.length + 2, 0); +System.arraycopy (scontigs, 0, t, 0, vc + 1); +t[vc + 1] = skipint[0]; +t[vc + 2] = skipint[1]; +System.arraycopy (scontigs, vc + 1, t, vc + 3, scontigs.length - (vc + 1)); +scontigs = t; +vc += 4; +}}}} +skip.add (skipint); +skipint = null; +}if (aa.equals ("STOP")) { +aa = "X"; +}resSize++; +}var findpos = true; +while (findpos) { +var compareCodonPos = jalview.analysis.Dna.compareCodonPos (alignedCodon, this.alignedCodons[aspos]); +switch (compareCodonPos) { +case -1: +this.insertAAGap (aspos, proteinSeqs); +findpos = false; +break; +case 1: +aa = gapString + aa; +aspos++; +break; +case 0: +findpos = false; +} +} +protein.append (aa); +lastnpos = npos; +if (this.alignedCodons[aspos] == null) { +this.alignedCodons[aspos] = alignedCodon; +} else if (!this.alignedCodons[aspos].equals (alignedCodon)) { +throw new IllegalStateException ("Tried to coalign " + this.alignedCodons[aspos].toString () + " with " + alignedCodon.toString ()); +}if (aspos >= this.aaWidth) { +this.aaWidth = aspos; +}aspos++; +}} +if (resSize > 0) { +var newseq = new jalview.datamodel.Sequence (selection.getName (), protein.toString ()); +if (rf != 0) { +var errMsg = "trimming contigs for incomplete terminal codon."; +System.err.println ("trimming contigs for incomplete terminal codon."); +vc = scontigs.length - 1; +lastnpos = vismapping.shift (lastnpos); +while (vc >= 0 && scontigs[vc] > lastnpos) { +if (vc > 0 && scontigs[vc - 1] > lastnpos) { +vc -= 2; +} else { +scontigs[vc] = lastnpos; +}} +if (vc > 0 && (vc + 1) < scontigs.length) { +var t = Clazz.newIntArray (vc + 1, 0); +System.arraycopy (scontigs, 0, t, 0, vc + 1); +scontigs = t; +}if (vc <= 0) { +scontigs = null; +}}if (scontigs != null) { +npos = 0; +for (vc = 0; vc < scontigs.length; vc += 2) { +scontigs[vc] = selection.findPosition (scontigs[vc]); +scontigs[vc + 1] = selection.findPosition (scontigs[vc + 1]); +if (scontigs[vc + 1] == selection.getEnd ()) { +break; +}} +if ((vc + 2) < scontigs.length) { +var t = Clazz.newIntArray (vc + 2, 0); +System.arraycopy (scontigs, 0, t, 0, vc + 2); +scontigs = t; +}var map = new jalview.util.MapList (scontigs, Clazz.newIntArray (-1, [1, resSize]), 3, 1); +jalview.analysis.Dna.transferCodedFeatures (selection, newseq, map, null, null); +var rseq = newseq.deriveSequence (); +acf.addMap (selection, rseq, map); +return rseq; +}}return null; +}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame,java.util.List"); +Clazz.defineMethod (c$, "insertAAGap", +function (pos, proteinSeqs) { +this.aaWidth++; +for (var seq, $seq = proteinSeqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +seq.insertCharAt (pos, this.gapChar); +} +this.checkCodonFrameWidth (); +if (pos < this.aaWidth) { +this.aaWidth++; +System.arraycopy (this.alignedCodons, pos, this.alignedCodons, pos + 1, this.alignedCodons.length - pos - 1); +this.alignedCodons[pos] = null; +}}, "~N,java.util.List"); +Clazz.defineMethod (c$, "checkCodonFrameWidth", +function () { +if (this.alignedCodons[this.alignedCodons.length - 1] != null) { +var c = new Array (this.alignedCodons.length + 10); +System.arraycopy (this.alignedCodons, 0, c, 0, this.alignedCodons.length); +this.alignedCodons = c; +}}); +c$.transferCodedFeatures = Clazz.defineMethod (c$, "transferCodedFeatures", +($fz = function (dna, pep, map, featureTypes, featureGroups) { +var sfs = dna.getSequenceFeatures (); +var fgstate; +var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS); +if (dnarefs != null) { +for (var d = 0; d < dnarefs.length; d++) { +var mp = dnarefs[d].getMap (); +if (mp != null) { +}} +}if (sfs != null) { +for (var sf, $sf = 0, $$sf = sfs; $sf < $$sf.length && ((sf = $$sf[$sf]) || true); $sf++) { +fgstate = (featureGroups == null) ? null : featureGroups.get (sf.featureGroup); +if ((featureTypes == null || featureTypes.containsKey (sf.getType ())) && (fgstate == null || fgstate.booleanValue ())) { +if (jalview.datamodel.FeatureProperties.isCodingFeature (null, sf.getType ())) { +{ +}}}} +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList,java.util.Map,java.util.Map"); +Clazz.defineStatics (c$, +"STOP_X", "X"); +c$.comparator = c$.prototype.comparator = new jalview.analysis.CodonComparator (); +}); diff --git a/bin/jalview/analysis/Finder.class b/bin/jalview/analysis/Finder.class index ec046f2..3648614 100644 Binary files a/bin/jalview/analysis/Finder.class and b/bin/jalview/analysis/Finder.class differ diff --git a/bin/jalview/analysis/Finder.js b/bin/jalview/analysis/Finder.js index cf1d8f9..5d20c2c 100644 --- a/bin/jalview/analysis/Finder.js +++ b/bin/jalview/analysis/Finder.js @@ -1,182 +1,182 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.Finder", ["jalview.datamodel.SearchResults", "jalview.jsdev.RegExp", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.searchResults = null; -this.alignment = null; -this.selection = null; -this.idMatch = null; -this.caseSensitive = false; -this.includeDescription = false; -this.findAll = false; -this.regex = null; -this.seqIndex = 0; -this.resIndex = -1; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "Finder"); -Clazz.makeConstructor (c$, -function (alignment, selection) { -this.alignment = alignment; -this.selection = selection; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); -Clazz.makeConstructor (c$, -function (alignment, selectionGroup, seqIndex, resIndex) { -this.construct (alignment, selectionGroup); -this.seqIndex = seqIndex; -this.resIndex = resIndex; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup,~N,~N"); -Clazz.defineMethod (c$, "find", -function (searchString) { -var hasResults = false; -if (!this.caseSensitive) { -searchString = searchString.toUpperCase (); -}this.regex = jalview.jsdev.RegExp.newRegex ([searchString]); -this.regex.setIgnoreCase (!this.caseSensitive); -this.searchResults = new jalview.datamodel.SearchResults (); -this.idMatch = new java.util.Vector (); -var seq; -var item = null; -var found = false; -var end = this.alignment.getHeight (); -if (this.selection != null) { -if ((this.selection.getSize () < 1) || ((this.selection.getEndRes () - this.selection.getStartRes ()) < 2)) { -this.selection = null; -}}while (!found && (this.seqIndex < end)) { -seq = this.alignment.getSequenceAt (this.seqIndex); -if ((this.selection != null && this.selection.getSize () > 0) && !this.selection.getSequences (null).contains (seq)) { -this.seqIndex++; -this.resIndex = -1; -continue; -}if (this.resIndex < 0) { -this.resIndex = 0; -try { -var res = Integer.parseInt (searchString); -if (seq.getEnd () >= res) { -this.searchResults.addResult (seq, res, res); -hasResults = true; -if (!this.findAll) { -found = true; -break; -}}} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -if (this.regex.search (seq.getName ())) { -this.idMatch.addElement (seq); -hasResults = true; -if (!this.findAll) { -found = true; -break; -}}if (this.isIncludeDescription () && seq.getDescription () != null && this.regex.search (seq.getDescription ())) { -this.idMatch.addElement (seq); -hasResults = true; -if (!this.findAll) { -found = true; -break; -}}}item = seq.getSequenceAsString (); -if ((this.selection != null) && (this.selection.getEndRes () < this.alignment.getWidth () - 1)) { -item = item.substring (0, this.selection.getEndRes () + 1); -}var noGapsSB = new StringBuffer (); -var insertCount = 0; -var spaces = new java.util.Vector (); -for (var j = 0; j < item.length; j++) { -if (!jalview.util.Comparison.isGap (item.charAt (j))) { -noGapsSB.append (item.charAt (j)); -spaces.addElement ( new Integer (insertCount)); -} else { -insertCount++; -}} -var noGaps = noGapsSB.toString (); -for (var r = this.resIndex; r < noGaps.length; r++) { -if (this.regex.searchFrom (noGaps, r)) { -this.resIndex = this.regex.matchedFrom (); -if ((this.selection != null && this.selection.getSize () > 0) && ((this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ())) < this.selection.getStartRes ())) { -continue; -}var sres = seq.findPosition (this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ())); -var eres = seq.findPosition (this.regex.matchedTo () - 1 + Integer.parseInt (spaces.elementAt (this.regex.matchedTo () - 1).toString ())); -this.searchResults.addResult (seq, sres, eres); -hasResults = true; -if (!this.findAll) { -found = true; -this.resIndex++; -break; -}r = this.resIndex; -} else { -break; -}} -if (!found) { -this.seqIndex++; -this.resIndex = -1; -}} -return hasResults; -}, "~S"); -Clazz.defineMethod (c$, "getAlignment", -function () { -return this.alignment; -}); -Clazz.defineMethod (c$, "setAlignment", -function (alignment) { -this.alignment = alignment; -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "isCaseSensitive", -function () { -return this.caseSensitive; -}); -Clazz.defineMethod (c$, "setCaseSensitive", -function (caseSensitive) { -this.caseSensitive = caseSensitive; -}, "~B"); -Clazz.defineMethod (c$, "isFindAll", -function () { -return this.findAll; -}); -Clazz.defineMethod (c$, "setFindAll", -function (findAll) { -this.findAll = findAll; -}, "~B"); -Clazz.defineMethod (c$, "getSelection", -function () { -return this.selection; -}); -Clazz.defineMethod (c$, "setSelection", -function (selection) { -this.selection = selection; -}, "jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "getIdMatch", -function () { -return this.idMatch; -}); -Clazz.defineMethod (c$, "getRegex", -function () { -return this.regex; -}); -Clazz.defineMethod (c$, "getSearchResults", -function () { -return this.searchResults; -}); -Clazz.defineMethod (c$, "getResIndex", -function () { -return this.resIndex; -}); -Clazz.defineMethod (c$, "setResIndex", -function (resIndex) { -this.resIndex = resIndex; -}, "~N"); -Clazz.defineMethod (c$, "getSeqIndex", -function () { -return this.seqIndex; -}); -Clazz.defineMethod (c$, "setSeqIndex", -function (seqIndex) { -this.seqIndex = seqIndex; -}, "~N"); -Clazz.defineMethod (c$, "isIncludeDescription", -function () { -return this.includeDescription; -}); -Clazz.defineMethod (c$, "setIncludeDescription", -function (includeDescription) { -this.includeDescription = includeDescription; -}, "~B"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.Finder", ["jalview.datamodel.SearchResults", "jalview.jsdev.RegExp", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.searchResults = null; +this.alignment = null; +this.selection = null; +this.idMatch = null; +this.caseSensitive = false; +this.includeDescription = false; +this.findAll = false; +this.regex = null; +this.seqIndex = 0; +this.resIndex = -1; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "Finder"); +Clazz.makeConstructor (c$, +function (alignment, selection) { +this.alignment = alignment; +this.selection = selection; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); +Clazz.makeConstructor (c$, +function (alignment, selectionGroup, seqIndex, resIndex) { +this.construct (alignment, selectionGroup); +this.seqIndex = seqIndex; +this.resIndex = resIndex; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup,~N,~N"); +Clazz.defineMethod (c$, "find", +function (searchString) { +var hasResults = false; +if (!this.caseSensitive) { +searchString = searchString.toUpperCase (); +}this.regex = jalview.jsdev.RegExp.newRegex ([searchString]); +this.regex.setIgnoreCase (!this.caseSensitive); +this.searchResults = new jalview.datamodel.SearchResults (); +this.idMatch = new java.util.Vector (); +var seq; +var item = null; +var found = false; +var end = this.alignment.getHeight (); +if (this.selection != null) { +if ((this.selection.getSize () < 1) || ((this.selection.getEndRes () - this.selection.getStartRes ()) < 2)) { +this.selection = null; +}}while (!found && (this.seqIndex < end)) { +seq = this.alignment.getSequenceAt (this.seqIndex); +if ((this.selection != null && this.selection.getSize () > 0) && !this.selection.getSequences (null).contains (seq)) { +this.seqIndex++; +this.resIndex = -1; +continue; +}if (this.resIndex < 0) { +this.resIndex = 0; +try { +var res = Integer.parseInt (searchString); +if (seq.getEnd () >= res) { +this.searchResults.addResult (seq, res, res); +hasResults = true; +if (!this.findAll) { +found = true; +break; +}}} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +if (this.regex.search (seq.getName ())) { +this.idMatch.addElement (seq); +hasResults = true; +if (!this.findAll) { +found = true; +break; +}}if (this.isIncludeDescription () && seq.getDescription () != null && this.regex.search (seq.getDescription ())) { +this.idMatch.addElement (seq); +hasResults = true; +if (!this.findAll) { +found = true; +break; +}}}item = seq.getSequenceAsString (); +if ((this.selection != null) && (this.selection.getEndRes () < this.alignment.getWidth () - 1)) { +item = item.substring (0, this.selection.getEndRes () + 1); +}var noGapsSB = new StringBuffer (); +var insertCount = 0; +var spaces = new java.util.Vector (); +for (var j = 0; j < item.length; j++) { +if (!jalview.util.Comparison.isGap (item.charAt (j))) { +noGapsSB.append (item.charAt (j)); +spaces.addElement ( new Integer (insertCount)); +} else { +insertCount++; +}} +var noGaps = noGapsSB.toString (); +for (var r = this.resIndex; r < noGaps.length; r++) { +if (this.regex.searchFrom (noGaps, r)) { +this.resIndex = this.regex.matchedFrom (); +if ((this.selection != null && this.selection.getSize () > 0) && ((this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ())) < this.selection.getStartRes ())) { +continue; +}var sres = seq.findPosition (this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ())); +var eres = seq.findPosition (this.regex.matchedTo () - 1 + Integer.parseInt (spaces.elementAt (this.regex.matchedTo () - 1).toString ())); +this.searchResults.addResult (seq, sres, eres); +hasResults = true; +if (!this.findAll) { +found = true; +this.resIndex++; +break; +}r = this.resIndex; +} else { +break; +}} +if (!found) { +this.seqIndex++; +this.resIndex = -1; +}} +return hasResults; +}, "~S"); +Clazz.defineMethod (c$, "getAlignment", +function () { +return this.alignment; +}); +Clazz.defineMethod (c$, "setAlignment", +function (alignment) { +this.alignment = alignment; +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "isCaseSensitive", +function () { +return this.caseSensitive; +}); +Clazz.defineMethod (c$, "setCaseSensitive", +function (caseSensitive) { +this.caseSensitive = caseSensitive; +}, "~B"); +Clazz.defineMethod (c$, "isFindAll", +function () { +return this.findAll; +}); +Clazz.defineMethod (c$, "setFindAll", +function (findAll) { +this.findAll = findAll; +}, "~B"); +Clazz.defineMethod (c$, "getSelection", +function () { +return this.selection; +}); +Clazz.defineMethod (c$, "setSelection", +function (selection) { +this.selection = selection; +}, "jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "getIdMatch", +function () { +return this.idMatch; +}); +Clazz.defineMethod (c$, "getRegex", +function () { +return this.regex; +}); +Clazz.defineMethod (c$, "getSearchResults", +function () { +return this.searchResults; +}); +Clazz.defineMethod (c$, "getResIndex", +function () { +return this.resIndex; +}); +Clazz.defineMethod (c$, "setResIndex", +function (resIndex) { +this.resIndex = resIndex; +}, "~N"); +Clazz.defineMethod (c$, "getSeqIndex", +function () { +return this.seqIndex; +}); +Clazz.defineMethod (c$, "setSeqIndex", +function (seqIndex) { +this.seqIndex = seqIndex; +}, "~N"); +Clazz.defineMethod (c$, "isIncludeDescription", +function () { +return this.includeDescription; +}); +Clazz.defineMethod (c$, "setIncludeDescription", +function (includeDescription) { +this.includeDescription = includeDescription; +}, "~B"); +}); diff --git a/bin/jalview/analysis/Grouping.js b/bin/jalview/analysis/Grouping.js index 60e2571..49d4004 100644 --- a/bin/jalview/analysis/Grouping.js +++ b/bin/jalview/analysis/Grouping.js @@ -1,88 +1,88 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.Grouping", ["jalview.datamodel.SequenceGroup", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () { -c$ = Clazz.declareType (jalview.analysis, "Grouping"); -c$.makeGroupsFrom = Clazz.defineMethod (c$, "makeGroupsFrom", -function (sequences, selectedChars, list) { -var gps = new java.util.HashMap (); -var width = 0; -var i; -var pgroup = new java.util.HashMap (); -if (list != null) { -for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -pgroup.put (sq.toString (), sg); -} -} -}for (i = 0; i < sequences.length; i++) { -var schar = selectedChars[i]; -var pgp = pgroup.get ((sequences[i]).toString ()); -if (pgp != null) { -schar = pgp.getName () + ":" + schar; -}var svec = gps.get (schar); -if (svec == null) { -svec = new java.util.ArrayList (); -gps.put (schar, svec); -}if (width < sequences[i].getLength ()) { -width = sequences[i].getLength (); -}svec.add (sequences[i]); -} -var groups = new Array (gps.size ()); -i = 0; -for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { -var group = new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1); -groups[i++] = group; -} -gps.clear (); -pgroup.clear (); -return groups; -}, "~A,~A,java.util.List"); -c$.makeGroupsFromCols = Clazz.defineMethod (c$, "makeGroupsFromCols", -function (sequences, cs, list) { -var gps = new java.util.HashMap (); -var pgroup = new java.util.HashMap (); -if (list != null) { -for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -pgroup.put (sq.toString (), sg); -} -} -}var spos = Clazz.newIntArray (cs.getSelected ().size (), 0); -var width = -1; -var i = 0; -for (var pos, $pos = cs.getSelected ().iterator (); $pos.hasNext () && ((pos = $pos.next ()) || true);) { -spos[i++] = pos.intValue (); -} -;for (i = 0; i < sequences.length; i++) { -var slen = sequences[i].getLength (); -if (width < slen) { -width = slen; -}var pgp = pgroup.get ((sequences[i]).toString ()); -var schar = new StringBuilder (); -if (pgp != null) { -schar.append (pgp.getName () + ":"); -}for (var p, $p = 0, $$p = spos; $p < $$p.length && ((p = $$p[$p]) || true); $p++) { -if (p >= slen) { -schar.append ("~"); -} else { -schar.append (sequences[i].getCharAt (p)); -}} -var svec = gps.get (schar.toString ()); -if (svec == null) { -svec = new java.util.ArrayList (); -gps.put (schar.toString (), svec); -}svec.add (sequences[i]); -} -var groups = new Array (gps.size ()); -i = 0; -for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { -var group = new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1); -groups[i++] = group; -} -gps.clear (); -pgroup.clear (); -return groups; -}, "~A,jalview.datamodel.ColumnSelection,java.util.List"); -c$.divideByFeature = Clazz.defineMethod (c$, "divideByFeature", -function (featureLabels, groupLabels, start, stop, sequences, exgroups, method) { -}, "~A,~A,~N,~N,~A,java.util.Vector,~S"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.Grouping", ["jalview.datamodel.SequenceGroup", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () { +c$ = Clazz.declareType (jalview.analysis, "Grouping"); +c$.makeGroupsFrom = Clazz.defineMethod (c$, "makeGroupsFrom", +function (sequences, selectedChars, list) { +var gps = new java.util.HashMap (); +var width = 0; +var i; +var pgroup = new java.util.HashMap (); +if (list != null) { +for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +pgroup.put (sq.toString (), sg); +} +} +}for (i = 0; i < sequences.length; i++) { +var schar = selectedChars[i]; +var pgp = pgroup.get ((sequences[i]).toString ()); +if (pgp != null) { +schar = pgp.getName () + ":" + schar; +}var svec = gps.get (schar); +if (svec == null) { +svec = new java.util.ArrayList (); +gps.put (schar, svec); +}if (width < sequences[i].getLength ()) { +width = sequences[i].getLength (); +}svec.add (sequences[i]); +} +var groups = new Array (gps.size ()); +i = 0; +for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { +var group = new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1); +groups[i++] = group; +} +gps.clear (); +pgroup.clear (); +return groups; +}, "~A,~A,java.util.List"); +c$.makeGroupsFromCols = Clazz.defineMethod (c$, "makeGroupsFromCols", +function (sequences, cs, list) { +var gps = new java.util.HashMap (); +var pgroup = new java.util.HashMap (); +if (list != null) { +for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +pgroup.put (sq.toString (), sg); +} +} +}var spos = Clazz.newIntArray (cs.getSelected ().size (), 0); +var width = -1; +var i = 0; +for (var pos, $pos = cs.getSelected ().iterator (); $pos.hasNext () && ((pos = $pos.next ()) || true);) { +spos[i++] = pos.intValue (); +} +;for (i = 0; i < sequences.length; i++) { +var slen = sequences[i].getLength (); +if (width < slen) { +width = slen; +}var pgp = pgroup.get ((sequences[i]).toString ()); +var schar = new StringBuilder (); +if (pgp != null) { +schar.append (pgp.getName () + ":"); +}for (var p, $p = 0, $$p = spos; $p < $$p.length && ((p = $$p[$p]) || true); $p++) { +if (p >= slen) { +schar.append ("~"); +} else { +schar.append (sequences[i].getCharAt (p)); +}} +var svec = gps.get (schar.toString ()); +if (svec == null) { +svec = new java.util.ArrayList (); +gps.put (schar.toString (), svec); +}svec.add (sequences[i]); +} +var groups = new Array (gps.size ()); +i = 0; +for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { +var group = new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1); +groups[i++] = group; +} +gps.clear (); +pgroup.clear (); +return groups; +}, "~A,jalview.datamodel.ColumnSelection,java.util.List"); +c$.divideByFeature = Clazz.defineMethod (c$, "divideByFeature", +function (featureLabels, groupLabels, start, stop, sequences, exgroups, method) { +}, "~A,~A,~N,~N,~A,java.util.Vector,~S"); +}); diff --git a/bin/jalview/analysis/NJTree.class b/bin/jalview/analysis/NJTree.class index d31a891..b64f07a 100644 Binary files a/bin/jalview/analysis/NJTree.class and b/bin/jalview/analysis/NJTree.class differ diff --git a/bin/jalview/analysis/NJTree.js b/bin/jalview/analysis/NJTree.js index 24a8fc5..8f3a367 100644 --- a/bin/jalview/analysis/NJTree.js +++ b/bin/jalview/analysis/NJTree.js @@ -1,577 +1,577 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["java.util.Vector"], ["jalview.analysis.Cluster", "$.NJTree"], ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.AlignmentView", "$.CigarArray", "$.NodeTransformI", "$.SeqCigar", "$.Sequence", "$.SequenceI", "$.SequenceNode", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.Format", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.$cluster = null; -this.sequence = null; -this.seqData = null; -this.done = null; -this.noseqs = 0; -this.noClus = 0; -this.distance = null; -this.mini = 0; -this.minj = 0; -this.ri = 0; -this.rj = 0; -this.groups = null; -this.maxdist = null; -this.top = null; -this.maxDistValue = 0; -this.maxheight = 0; -this.ycount = 0; -this.node = null; -this.type = null; -this.pwtype = null; -this.found = null; -this.leaves = null; -this.hasDistances = true; -this.hasBootstrap = false; -this.hasRootDistance = true; -this._lycount = 0; -this._lylimit = 0; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "NJTree"); -Clazz.prepareFields (c$, function () { -this.groups = new java.util.Vector (); -}); -Clazz.makeConstructor (c$, -function (seqs, odata, treefile) { -this.construct (seqs, treefile); -if (odata != null) { -this.seqData = odata; -}}, "~A,jalview.datamodel.AlignmentView,jalview.io.NewickFile"); -Clazz.makeConstructor (c$, -function (seqs, treefile) { -this.sequence = seqs; -this.top = treefile.getTree (); -this.hasDistances = treefile.HasDistances (); -this.hasBootstrap = treefile.HasBootstrap (); -this.hasRootDistance = treefile.HasRootDistance (); -this.maxheight = this.findHeight (this.top); -var algnIds = new jalview.analysis.SequenceIdMatcher (seqs); -var leaves = new java.util.Vector (); -this.findLeaves (this.top, leaves); -var i = 0; -var namesleft = seqs.length; -var j; -var nam; -var realnam; -var one2many = new java.util.Vector (); -var countOne2Many = 0; -while (i < leaves.size ()) { -j = leaves.elementAt (i++); -realnam = j.getName (); -nam = null; -if (namesleft > -1) { -nam = algnIds.findIdMatch (realnam); -}if (nam != null) { -j.setElement (nam); -if (one2many.contains (nam)) { -countOne2Many++; -} else { -one2many.addElement (nam); -namesleft--; -}} else { -j.setElement ( new jalview.datamodel.Sequence (realnam, "THISISAPLACEHLDER")); -j.setPlaceholder (true); -}} -}, "~A,jalview.io.NewickFile"); -Clazz.makeConstructor (c$, -function (sequence, seqData, type, pwtype, sm, start, end) { -this.sequence = sequence; -this.node = new java.util.Vector (); -this.type = type; -this.pwtype = pwtype; -if (seqData != null) { -this.seqData = seqData; -} else { -var seqs = new Array (sequence.length); -for (var i = 0; i < sequence.length; i++) { -seqs[i] = new jalview.datamodel.SeqCigar (sequence[i], start, end); -} -var sdata = new jalview.datamodel.CigarArray (seqs); -sdata.addOperation ('M', end - start + 1); -this.seqData = new jalview.datamodel.AlignmentView (sdata, start); -}if (!(type.equals ("NJ"))) { -type = "AV"; -}if (sm == null && !(pwtype.equals ("PID"))) { -if (jalview.schemes.ResidueProperties.getScoreMatrix (pwtype) == null) { -pwtype = "BLOSUM62"; -}}var i = 0; -this.done = Clazz.newIntArray (sequence.length, 0); -while ((i < sequence.length) && (sequence[i] != null)) { -this.done[i] = 0; -i++; -} -this.noseqs = i++; -this.distance = this.findDistances (sm); -this.makeLeaves (); -this.noClus = this.$cluster.size (); -this.cluster (); -}, "~A,jalview.datamodel.AlignmentView,~S,~S,jalview.api.analysis.ScoreModelI,~N,~N"); -Clazz.overrideMethod (c$, "toString", -function () { -var fout = new jalview.io.NewickFile (this.getTopNode ()); -return fout.print (this.isHasBootstrap (), this.isHasDistances (), this.isHasRootDistance ()); -}); -Clazz.defineMethod (c$, "UpdatePlaceHolders", -function (list) { -var leaves = new java.util.Vector (); -this.findLeaves (this.top, leaves); -var sz = leaves.size (); -var seqmatcher = null; -var i = 0; -while (i < sz) { -var leaf = leaves.elementAt (i++); -if (list.contains (leaf.element ())) { -leaf.setPlaceholder (false); -} else { -if (seqmatcher == null) { -var seqs = new Array (list.size ()); -for (var j = 0; j < seqs.length; j++) { -seqs[j] = list.get (j); -} -seqmatcher = new jalview.analysis.SequenceIdMatcher (seqs); -}var nam = seqmatcher.findIdMatch (leaf.getName ()); -if (nam != null) { -if (!leaf.isPlaceholder ()) { -}leaf.setPlaceholder (false); -leaf.setElement (nam); -} else { -if (!leaf.isPlaceholder ()) { -leaf.setElement ( new jalview.datamodel.Sequence (leaf.getName (), "THISISAPLACEHLDER")); -}leaf.setPlaceholder (true); -}}} -}, "java.util.List"); -Clazz.defineMethod (c$, "renameAssociatedNodes", -function () { -this.applyToNodes (((Clazz.isClassDefined ("jalview.analysis.NJTree$1") ? 0 : jalview.analysis.NJTree.$NJTree$1$ ()), Clazz.innerTypeInstance (jalview.analysis.NJTree$1, this, null))); -}); -Clazz.defineMethod (c$, "cluster", -function () { -while (this.noClus > 2) { -if (this.type.equals ("NJ")) { -this.findMinNJDistance (); -} else { -this.findMinDistance (); -}var c = this.joinClusters (this.mini, this.minj); -this.done[this.minj] = 1; -this.$cluster.setElementAt (null, this.minj); -this.$cluster.setElementAt (c, this.mini); -this.noClus--; -} -var onefound = false; -var one = -1; -var two = -1; -for (var i = 0; i < this.noseqs; i++) { -if (this.done[i] != 1) { -if (onefound == false) { -two = i; -onefound = true; -} else { -one = i; -}}} -this.joinClusters (one, two); -this.top = (this.node.elementAt (one)); -this.reCount (this.top); -this.findHeight (this.top); -this.findMaxDist (this.top); -}); -Clazz.defineMethod (c$, "joinClusters", -function (i, j) { -var dist = this.distance[i][j]; -var noi = (this.$cluster.elementAt (i)).value.length; -var noj = (this.$cluster.elementAt (j)).value.length; -var value = Clazz.newIntArray (noi + noj, 0); -for (var ii = 0; ii < noi; ii++) { -value[ii] = (this.$cluster.elementAt (i)).value[ii]; -} -for (var ii = noi; ii < (noi + noj); ii++) { -value[ii] = (this.$cluster.elementAt (j)).value[ii - noi]; -} -var c = new jalview.analysis.Cluster (value); -this.ri = this.findr (i, j); -this.rj = this.findr (j, i); -if (this.type.equals ("NJ")) { -this.findClusterNJDistance (i, j); -} else { -this.findClusterDistance (i, j); -}var sn = new jalview.datamodel.SequenceNode (); -sn.setLeft ((this.node.elementAt (i))); -sn.setRight ((this.node.elementAt (j))); -var tmpi = (this.node.elementAt (i)); -var tmpj = (this.node.elementAt (j)); -if (this.type.equals ("NJ")) { -this.findNewNJDistances (tmpi, tmpj, dist); -} else { -this.findNewDistances (tmpi, tmpj, dist); -}tmpi.setParent (sn); -tmpj.setParent (sn); -this.node.setElementAt (sn, i); -return c; -}, "~N,~N"); -Clazz.defineMethod (c$, "findNewNJDistances", -function (tmpi, tmpj, dist) { -tmpi.dist = ((dist + this.ri) - this.rj) / 2; -tmpj.dist = (dist - tmpi.dist); -if (tmpi.dist < 0) { -tmpi.dist = 0; -}if (tmpj.dist < 0) { -tmpj.dist = 0; -}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N"); -Clazz.defineMethod (c$, "findNewDistances", -function (tmpi, tmpj, dist) { -var ih = 0; -var jh = 0; -var sni = tmpi; -var snj = tmpj; -while (sni != null) { -ih = ih + sni.dist; -sni = sni.left (); -} -while (snj != null) { -jh = jh + snj.dist; -snj = snj.left (); -} -tmpi.dist = ((dist / 2) - ih); -tmpj.dist = ((dist / 2) - jh); -}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N"); -Clazz.defineMethod (c$, "findClusterDistance", -function (i, j) { -var noi = (this.$cluster.elementAt (i)).value.length; -var noj = (this.$cluster.elementAt (j)).value.length; -var newdist = Clazz.newFloatArray (this.noseqs, 0); -for (var l = 0; l < this.noseqs; l++) { -if ((l != i) && (l != j)) { -newdist[l] = ((this.distance[i][l] * noi) + (this.distance[j][l] * noj)) / (noi + noj); -} else { -newdist[l] = 0; -}} -for (var ii = 0; ii < this.noseqs; ii++) { -this.distance[i][ii] = newdist[ii]; -this.distance[ii][i] = newdist[ii]; -} -}, "~N,~N"); -Clazz.defineMethod (c$, "findClusterNJDistance", -function (i, j) { -var newdist = Clazz.newFloatArray (this.noseqs, 0); -for (var l = 0; l < this.noseqs; l++) { -if ((l != i) && (l != j)) { -newdist[l] = ((this.distance[i][l] + this.distance[j][l]) - this.distance[i][j]) / 2; -} else { -newdist[l] = 0; -}} -for (var ii = 0; ii < this.noseqs; ii++) { -this.distance[i][ii] = newdist[ii]; -this.distance[ii][i] = newdist[ii]; -} -}, "~N,~N"); -Clazz.defineMethod (c$, "findr", -function (i, j) { -var tmp = 1; -for (var k = 0; k < this.noseqs; k++) { -if ((k != i) && (k != j) && (this.done[k] != 1)) { -tmp = tmp + this.distance[i][k]; -}} -if (this.noClus > 2) { -tmp = tmp / (this.noClus - 2); -}return tmp; -}, "~N,~N"); -Clazz.defineMethod (c$, "findMinNJDistance", -function () { -var min = 100000; -for (var i = 0; i < (this.noseqs - 1); i++) { -for (var j = i + 1; j < this.noseqs; j++) { -if ((this.done[i] != 1) && (this.done[j] != 1)) { -var tmp = this.distance[i][j] - (this.findr (i, j) + this.findr (j, i)); -if (tmp < min) { -this.mini = i; -this.minj = j; -min = tmp; -}}} -} -return min; -}); -Clazz.defineMethod (c$, "findMinDistance", -function () { -var min = 100000; -for (var i = 0; i < (this.noseqs - 1); i++) { -for (var j = i + 1; j < this.noseqs; j++) { -if ((this.done[i] != 1) && (this.done[j] != 1)) { -if (this.distance[i][j] < min) { -this.mini = i; -this.minj = j; -min = this.distance[i][j]; -}}} -} -return min; -}); -Clazz.defineMethod (c$, "findDistances", -function (_pwmatrix) { -var distance = Clazz.newFloatArray (this.noseqs, this.noseqs, 0); -if (_pwmatrix == null) { -_pwmatrix = jalview.schemes.ResidueProperties.getScoreModel (this.pwtype); -if (_pwmatrix == null) { -_pwmatrix = jalview.schemes.ResidueProperties.getScoreMatrix ("BLOSUM62"); -}}distance = _pwmatrix.findDistances (this.seqData); -return distance; -}, "jalview.api.analysis.ScoreModelI"); -Clazz.defineMethod (c$, "makeLeaves", -function () { -this.$cluster = new java.util.Vector (); -for (var i = 0; i < this.noseqs; i++) { -var sn = new jalview.datamodel.SequenceNode (); -sn.setElement (this.sequence[i]); -sn.setName (this.sequence[i].getName ()); -this.node.addElement (sn); -var value = Clazz.newIntArray (1, 0); -value[0] = i; -var c = new jalview.analysis.Cluster (value); -this.$cluster.addElement (c); -} -}); -Clazz.defineMethod (c$, "findLeaves", -function (node, leaves) { -if (node == null) { -return leaves; -}if ((node.left () == null) && (node.right () == null)) { -leaves.addElement (node); -return leaves; -} else { -this.findLeaves (node.left (), leaves); -this.findLeaves (node.right (), leaves); -}return leaves; -}, "jalview.datamodel.SequenceNode,java.util.Vector"); -Clazz.defineMethod (c$, "findLeaf", -function (node, count) { -this.found = this._findLeaf (node, count); -return this.found; -}, "jalview.datamodel.SequenceNode,~N"); -Clazz.defineMethod (c$, "_findLeaf", -function (node, count) { -if (node == null) { -return null; -}if (node.ycount == count) { -this.found = node.element (); -return this.found; -} else { -this._findLeaf (node.left (), count); -this._findLeaf (node.right (), count); -}return this.found; -}, "jalview.datamodel.SequenceNode,~N"); -Clazz.defineMethod (c$, "printNode", -function (node) { -if (node == null) { -return; -}if ((node.left () == null) && (node.right () == null)) { -System.out.println ("Leaf = " + (node.element ()).getName ()); -System.out.println ("Dist " + node.dist); -System.out.println ("Boot " + node.getBootstrap ()); -} else { -System.out.println ("Dist " + node.dist); -this.printNode (node.left ()); -this.printNode (node.right ()); -}}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "findMaxDist", -function (node) { -if (node == null) { -return; -}if ((node.left () == null) && (node.right () == null)) { -var dist = node.dist; -if (dist > this.maxDistValue) { -this.maxdist = node; -this.maxDistValue = dist; -}} else { -this.findMaxDist (node.left ()); -this.findMaxDist (node.right ()); -}}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "getGroups", -function () { -return this.groups; -}); -Clazz.defineMethod (c$, "getMaxHeight", -function () { -return this.maxheight; -}); -Clazz.defineMethod (c$, "groupNodes", -function (node, threshold) { -if (node == null) { -return; -}if ((node.height / this.maxheight) > threshold) { -this.groups.addElement (node); -} else { -this.groupNodes (node.left (), threshold); -this.groupNodes (node.right (), threshold); -}}, "jalview.datamodel.SequenceNode,~N"); -Clazz.defineMethod (c$, "findHeight", -function (node) { -if (node == null) { -return this.maxheight; -}if ((node.left () == null) && (node.right () == null)) { -node.height = (node.parent ()).height + node.dist; -if (node.height > this.maxheight) { -return node.height; -} else { -return this.maxheight; -}} else { -if (node.parent () != null) { -node.height = (node.parent ()).height + node.dist; -} else { -this.maxheight = 0; -node.height = 0.0; -}this.maxheight = this.findHeight ((node.left ())); -this.maxheight = this.findHeight ((node.right ())); -}return this.maxheight; -}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "reRoot", -function () { -if (this.maxdist != null) { -this.ycount = 0; -var tmpdist = this.maxdist.dist; -var sn = new jalview.datamodel.SequenceNode (); -sn.setParent (null); -var snr = this.maxdist.parent (); -this.changeDirection (snr, this.maxdist); -System.out.println ("Printing reversed tree"); -this.printN (snr); -snr.dist = tmpdist / 2; -this.maxdist.dist = tmpdist / 2; -snr.setParent (sn); -this.maxdist.setParent (sn); -sn.setRight (snr); -sn.setLeft (this.maxdist); -this.top = sn; -this.ycount = 0; -this.reCount (this.top); -this.findHeight (this.top); -}return this.top; -}); -Clazz.defineMethod (c$, "hasOriginalSequenceData", -function () { -return this.seqData != null; -}); -Clazz.defineMethod (c$, "printOriginalSequenceData", -function (gapChar) { -if (this.seqData == null) { -return null; -}var sb = new StringBuffer (); -var seqdatas = this.seqData.getSequenceStrings (gapChar); -for (var i = 0; i < seqdatas.length; i++) { -sb.append ( new jalview.util.Format ("%-15s").form (this.sequence[i].getName ())); -sb.append (" " + seqdatas[i] + "\n"); -} -return sb.toString (); -}, "~S"); -Clazz.defineMethod (c$, "printN", -function (node) { -if (node == null) { -return; -}if ((node.left () != null) && (node.right () != null)) { -this.printN (node.left ()); -this.printN (node.right ()); -} else { -System.out.println (" name = " + (node.element ()).getName ()); -}System.out.println (" dist = " + node.dist + " " + node.count + " " + node.height); -}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "reCount", -function (node) { -this.ycount = 0; -this._lycount = 0; -this._reCount (node); -}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "_reCount", -function (node) { -if (node == null) { -return; -}this._lycount++; -if ((node.left () != null) && (node.right () != null)) { -this._reCount (node.left ()); -this._reCount (node.right ()); -var l = node.left (); -var r = node.right (); -node.count = l.count + r.count; -node.ycount = (l.ycount + r.ycount) / 2; -} else { -node.count = 1; -node.ycount = this.ycount++; -}this._lycount--; -}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "swapNodes", -function (node) { -if (node == null) { -return; -}var tmp = node.left (); -node.setLeft (node.right ()); -node.setRight (tmp); -}, "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "changeDirection", -function (node, dir) { -if (node == null) { -return; -}if (node.parent () !== this.top) { -this.changeDirection (node.parent (), node); -var tmp = node.parent (); -if (dir === node.left ()) { -node.setParent (dir); -node.setLeft (tmp); -} else if (dir === node.right ()) { -node.setParent (dir); -node.setRight (tmp); -}} else { -if (dir === node.left ()) { -node.setParent (node.left ()); -if (this.top.left () === node) { -node.setRight (this.top.right ()); -} else { -node.setRight (this.top.left ()); -}} else { -node.setParent (node.right ()); -if (this.top.left () === node) { -node.setLeft (this.top.right ()); -} else { -node.setLeft (this.top.left ()); -}}}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "getMaxDist", -function () { -return this.maxdist; -}); -Clazz.defineMethod (c$, "getTopNode", -function () { -return this.top; -}); -Clazz.defineMethod (c$, "isHasDistances", -function () { -return this.hasDistances; -}); -Clazz.defineMethod (c$, "isHasBootstrap", -function () { -return this.hasBootstrap; -}); -Clazz.defineMethod (c$, "isHasRootDistance", -function () { -return this.hasRootDistance; -}); -Clazz.defineMethod (c$, "applyToNodes", -function (nodeTransformI) { -for (var nodes = this.node.elements (); nodes.hasMoreElements (); nodeTransformI.transform (nodes.nextElement ())) { -;} -}, "jalview.datamodel.NodeTransformI"); -c$.$NJTree$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.analysis, "NJTree$1", null, jalview.datamodel.NodeTransformI); -Clazz.defineMethod (c$, "transform", -function (node) { -var el = node.element (); -if (el != null && Clazz.instanceOf (el, jalview.datamodel.SequenceI)) { -node.setName ((el).getName ()); -}}, "jalview.datamodel.BinaryNode"); -c$ = Clazz.p0p (); -}; -c$ = Clazz.decorateAsClass (function () { -this.value = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "Cluster"); -Clazz.makeConstructor (c$, -function (value) { -this.value = value; -}, "~A"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["java.util.Vector"], ["jalview.analysis.Cluster", "$.NJTree"], ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.AlignmentView", "$.CigarArray", "$.NodeTransformI", "$.SeqCigar", "$.Sequence", "$.SequenceI", "$.SequenceNode", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.Format", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.$cluster = null; +this.sequence = null; +this.seqData = null; +this.done = null; +this.noseqs = 0; +this.noClus = 0; +this.distance = null; +this.mini = 0; +this.minj = 0; +this.ri = 0; +this.rj = 0; +this.groups = null; +this.maxdist = null; +this.top = null; +this.maxDistValue = 0; +this.maxheight = 0; +this.ycount = 0; +this.node = null; +this.type = null; +this.pwtype = null; +this.found = null; +this.leaves = null; +this.hasDistances = true; +this.hasBootstrap = false; +this.hasRootDistance = true; +this._lycount = 0; +this._lylimit = 0; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "NJTree"); +Clazz.prepareFields (c$, function () { +this.groups = new java.util.Vector (); +}); +Clazz.makeConstructor (c$, +function (seqs, odata, treefile) { +this.construct (seqs, treefile); +if (odata != null) { +this.seqData = odata; +}}, "~A,jalview.datamodel.AlignmentView,jalview.io.NewickFile"); +Clazz.makeConstructor (c$, +function (seqs, treefile) { +this.sequence = seqs; +this.top = treefile.getTree (); +this.hasDistances = treefile.HasDistances (); +this.hasBootstrap = treefile.HasBootstrap (); +this.hasRootDistance = treefile.HasRootDistance (); +this.maxheight = this.findHeight (this.top); +var algnIds = new jalview.analysis.SequenceIdMatcher (seqs); +var leaves = new java.util.Vector (); +this.findLeaves (this.top, leaves); +var i = 0; +var namesleft = seqs.length; +var j; +var nam; +var realnam; +var one2many = new java.util.Vector (); +var countOne2Many = 0; +while (i < leaves.size ()) { +j = leaves.elementAt (i++); +realnam = j.getName (); +nam = null; +if (namesleft > -1) { +nam = algnIds.findIdMatch (realnam); +}if (nam != null) { +j.setElement (nam); +if (one2many.contains (nam)) { +countOne2Many++; +} else { +one2many.addElement (nam); +namesleft--; +}} else { +j.setElement ( new jalview.datamodel.Sequence (realnam, "THISISAPLACEHLDER")); +j.setPlaceholder (true); +}} +}, "~A,jalview.io.NewickFile"); +Clazz.makeConstructor (c$, +function (sequence, seqData, type, pwtype, sm, start, end) { +this.sequence = sequence; +this.node = new java.util.Vector (); +this.type = type; +this.pwtype = pwtype; +if (seqData != null) { +this.seqData = seqData; +} else { +var seqs = new Array (sequence.length); +for (var i = 0; i < sequence.length; i++) { +seqs[i] = new jalview.datamodel.SeqCigar (sequence[i], start, end); +} +var sdata = new jalview.datamodel.CigarArray (seqs); +sdata.addOperation ('M', end - start + 1); +this.seqData = new jalview.datamodel.AlignmentView (sdata, start); +}if (!(type.equals ("NJ"))) { +type = "AV"; +}if (sm == null && !(pwtype.equals ("PID"))) { +if (jalview.schemes.ResidueProperties.getScoreMatrix (pwtype) == null) { +pwtype = "BLOSUM62"; +}}var i = 0; +this.done = Clazz.newIntArray (sequence.length, 0); +while ((i < sequence.length) && (sequence[i] != null)) { +this.done[i] = 0; +i++; +} +this.noseqs = i++; +this.distance = this.findDistances (sm); +this.makeLeaves (); +this.noClus = this.$cluster.size (); +this.cluster (); +}, "~A,jalview.datamodel.AlignmentView,~S,~S,jalview.api.analysis.ScoreModelI,~N,~N"); +Clazz.overrideMethod (c$, "toString", +function () { +var fout = new jalview.io.NewickFile (this.getTopNode ()); +return fout.print (this.isHasBootstrap (), this.isHasDistances (), this.isHasRootDistance ()); +}); +Clazz.defineMethod (c$, "UpdatePlaceHolders", +function (list) { +var leaves = new java.util.Vector (); +this.findLeaves (this.top, leaves); +var sz = leaves.size (); +var seqmatcher = null; +var i = 0; +while (i < sz) { +var leaf = leaves.elementAt (i++); +if (list.contains (leaf.element ())) { +leaf.setPlaceholder (false); +} else { +if (seqmatcher == null) { +var seqs = new Array (list.size ()); +for (var j = 0; j < seqs.length; j++) { +seqs[j] = list.get (j); +} +seqmatcher = new jalview.analysis.SequenceIdMatcher (seqs); +}var nam = seqmatcher.findIdMatch (leaf.getName ()); +if (nam != null) { +if (!leaf.isPlaceholder ()) { +}leaf.setPlaceholder (false); +leaf.setElement (nam); +} else { +if (!leaf.isPlaceholder ()) { +leaf.setElement ( new jalview.datamodel.Sequence (leaf.getName (), "THISISAPLACEHLDER")); +}leaf.setPlaceholder (true); +}}} +}, "java.util.List"); +Clazz.defineMethod (c$, "renameAssociatedNodes", +function () { +this.applyToNodes (((Clazz.isClassDefined ("jalview.analysis.NJTree$1") ? 0 : jalview.analysis.NJTree.$NJTree$1$ ()), Clazz.innerTypeInstance (jalview.analysis.NJTree$1, this, null))); +}); +Clazz.defineMethod (c$, "cluster", +function () { +while (this.noClus > 2) { +if (this.type.equals ("NJ")) { +this.findMinNJDistance (); +} else { +this.findMinDistance (); +}var c = this.joinClusters (this.mini, this.minj); +this.done[this.minj] = 1; +this.$cluster.setElementAt (null, this.minj); +this.$cluster.setElementAt (c, this.mini); +this.noClus--; +} +var onefound = false; +var one = -1; +var two = -1; +for (var i = 0; i < this.noseqs; i++) { +if (this.done[i] != 1) { +if (onefound == false) { +two = i; +onefound = true; +} else { +one = i; +}}} +this.joinClusters (one, two); +this.top = (this.node.elementAt (one)); +this.reCount (this.top); +this.findHeight (this.top); +this.findMaxDist (this.top); +}); +Clazz.defineMethod (c$, "joinClusters", +function (i, j) { +var dist = this.distance[i][j]; +var noi = (this.$cluster.elementAt (i)).value.length; +var noj = (this.$cluster.elementAt (j)).value.length; +var value = Clazz.newIntArray (noi + noj, 0); +for (var ii = 0; ii < noi; ii++) { +value[ii] = (this.$cluster.elementAt (i)).value[ii]; +} +for (var ii = noi; ii < (noi + noj); ii++) { +value[ii] = (this.$cluster.elementAt (j)).value[ii - noi]; +} +var c = new jalview.analysis.Cluster (value); +this.ri = this.findr (i, j); +this.rj = this.findr (j, i); +if (this.type.equals ("NJ")) { +this.findClusterNJDistance (i, j); +} else { +this.findClusterDistance (i, j); +}var sn = new jalview.datamodel.SequenceNode (); +sn.setLeft ((this.node.elementAt (i))); +sn.setRight ((this.node.elementAt (j))); +var tmpi = (this.node.elementAt (i)); +var tmpj = (this.node.elementAt (j)); +if (this.type.equals ("NJ")) { +this.findNewNJDistances (tmpi, tmpj, dist); +} else { +this.findNewDistances (tmpi, tmpj, dist); +}tmpi.setParent (sn); +tmpj.setParent (sn); +this.node.setElementAt (sn, i); +return c; +}, "~N,~N"); +Clazz.defineMethod (c$, "findNewNJDistances", +function (tmpi, tmpj, dist) { +tmpi.dist = ((dist + this.ri) - this.rj) / 2; +tmpj.dist = (dist - tmpi.dist); +if (tmpi.dist < 0) { +tmpi.dist = 0; +}if (tmpj.dist < 0) { +tmpj.dist = 0; +}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N"); +Clazz.defineMethod (c$, "findNewDistances", +function (tmpi, tmpj, dist) { +var ih = 0; +var jh = 0; +var sni = tmpi; +var snj = tmpj; +while (sni != null) { +ih = ih + sni.dist; +sni = sni.left (); +} +while (snj != null) { +jh = jh + snj.dist; +snj = snj.left (); +} +tmpi.dist = ((dist / 2) - ih); +tmpj.dist = ((dist / 2) - jh); +}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N"); +Clazz.defineMethod (c$, "findClusterDistance", +function (i, j) { +var noi = (this.$cluster.elementAt (i)).value.length; +var noj = (this.$cluster.elementAt (j)).value.length; +var newdist = Clazz.newFloatArray (this.noseqs, 0); +for (var l = 0; l < this.noseqs; l++) { +if ((l != i) && (l != j)) { +newdist[l] = ((this.distance[i][l] * noi) + (this.distance[j][l] * noj)) / (noi + noj); +} else { +newdist[l] = 0; +}} +for (var ii = 0; ii < this.noseqs; ii++) { +this.distance[i][ii] = newdist[ii]; +this.distance[ii][i] = newdist[ii]; +} +}, "~N,~N"); +Clazz.defineMethod (c$, "findClusterNJDistance", +function (i, j) { +var newdist = Clazz.newFloatArray (this.noseqs, 0); +for (var l = 0; l < this.noseqs; l++) { +if ((l != i) && (l != j)) { +newdist[l] = ((this.distance[i][l] + this.distance[j][l]) - this.distance[i][j]) / 2; +} else { +newdist[l] = 0; +}} +for (var ii = 0; ii < this.noseqs; ii++) { +this.distance[i][ii] = newdist[ii]; +this.distance[ii][i] = newdist[ii]; +} +}, "~N,~N"); +Clazz.defineMethod (c$, "findr", +function (i, j) { +var tmp = 1; +for (var k = 0; k < this.noseqs; k++) { +if ((k != i) && (k != j) && (this.done[k] != 1)) { +tmp = tmp + this.distance[i][k]; +}} +if (this.noClus > 2) { +tmp = tmp / (this.noClus - 2); +}return tmp; +}, "~N,~N"); +Clazz.defineMethod (c$, "findMinNJDistance", +function () { +var min = 100000; +for (var i = 0; i < (this.noseqs - 1); i++) { +for (var j = i + 1; j < this.noseqs; j++) { +if ((this.done[i] != 1) && (this.done[j] != 1)) { +var tmp = this.distance[i][j] - (this.findr (i, j) + this.findr (j, i)); +if (tmp < min) { +this.mini = i; +this.minj = j; +min = tmp; +}}} +} +return min; +}); +Clazz.defineMethod (c$, "findMinDistance", +function () { +var min = 100000; +for (var i = 0; i < (this.noseqs - 1); i++) { +for (var j = i + 1; j < this.noseqs; j++) { +if ((this.done[i] != 1) && (this.done[j] != 1)) { +if (this.distance[i][j] < min) { +this.mini = i; +this.minj = j; +min = this.distance[i][j]; +}}} +} +return min; +}); +Clazz.defineMethod (c$, "findDistances", +function (_pwmatrix) { +var distance = Clazz.newFloatArray (this.noseqs, this.noseqs, 0); +if (_pwmatrix == null) { +_pwmatrix = jalview.schemes.ResidueProperties.getScoreModel (this.pwtype); +if (_pwmatrix == null) { +_pwmatrix = jalview.schemes.ResidueProperties.getScoreMatrix ("BLOSUM62"); +}}distance = _pwmatrix.findDistances (this.seqData); +return distance; +}, "jalview.api.analysis.ScoreModelI"); +Clazz.defineMethod (c$, "makeLeaves", +function () { +this.$cluster = new java.util.Vector (); +for (var i = 0; i < this.noseqs; i++) { +var sn = new jalview.datamodel.SequenceNode (); +sn.setElement (this.sequence[i]); +sn.setName (this.sequence[i].getName ()); +this.node.addElement (sn); +var value = Clazz.newIntArray (1, 0); +value[0] = i; +var c = new jalview.analysis.Cluster (value); +this.$cluster.addElement (c); +} +}); +Clazz.defineMethod (c$, "findLeaves", +function (node, leaves) { +if (node == null) { +return leaves; +}if ((node.left () == null) && (node.right () == null)) { +leaves.addElement (node); +return leaves; +} else { +this.findLeaves (node.left (), leaves); +this.findLeaves (node.right (), leaves); +}return leaves; +}, "jalview.datamodel.SequenceNode,java.util.Vector"); +Clazz.defineMethod (c$, "findLeaf", +function (node, count) { +this.found = this._findLeaf (node, count); +return this.found; +}, "jalview.datamodel.SequenceNode,~N"); +Clazz.defineMethod (c$, "_findLeaf", +function (node, count) { +if (node == null) { +return null; +}if (node.ycount == count) { +this.found = node.element (); +return this.found; +} else { +this._findLeaf (node.left (), count); +this._findLeaf (node.right (), count); +}return this.found; +}, "jalview.datamodel.SequenceNode,~N"); +Clazz.defineMethod (c$, "printNode", +function (node) { +if (node == null) { +return; +}if ((node.left () == null) && (node.right () == null)) { +System.out.println ("Leaf = " + (node.element ()).getName ()); +System.out.println ("Dist " + node.dist); +System.out.println ("Boot " + node.getBootstrap ()); +} else { +System.out.println ("Dist " + node.dist); +this.printNode (node.left ()); +this.printNode (node.right ()); +}}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "findMaxDist", +function (node) { +if (node == null) { +return; +}if ((node.left () == null) && (node.right () == null)) { +var dist = node.dist; +if (dist > this.maxDistValue) { +this.maxdist = node; +this.maxDistValue = dist; +}} else { +this.findMaxDist (node.left ()); +this.findMaxDist (node.right ()); +}}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "getGroups", +function () { +return this.groups; +}); +Clazz.defineMethod (c$, "getMaxHeight", +function () { +return this.maxheight; +}); +Clazz.defineMethod (c$, "groupNodes", +function (node, threshold) { +if (node == null) { +return; +}if ((node.height / this.maxheight) > threshold) { +this.groups.addElement (node); +} else { +this.groupNodes (node.left (), threshold); +this.groupNodes (node.right (), threshold); +}}, "jalview.datamodel.SequenceNode,~N"); +Clazz.defineMethod (c$, "findHeight", +function (node) { +if (node == null) { +return this.maxheight; +}if ((node.left () == null) && (node.right () == null)) { +node.height = (node.parent ()).height + node.dist; +if (node.height > this.maxheight) { +return node.height; +} else { +return this.maxheight; +}} else { +if (node.parent () != null) { +node.height = (node.parent ()).height + node.dist; +} else { +this.maxheight = 0; +node.height = 0.0; +}this.maxheight = this.findHeight ((node.left ())); +this.maxheight = this.findHeight ((node.right ())); +}return this.maxheight; +}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "reRoot", +function () { +if (this.maxdist != null) { +this.ycount = 0; +var tmpdist = this.maxdist.dist; +var sn = new jalview.datamodel.SequenceNode (); +sn.setParent (null); +var snr = this.maxdist.parent (); +this.changeDirection (snr, this.maxdist); +System.out.println ("Printing reversed tree"); +this.printN (snr); +snr.dist = tmpdist / 2; +this.maxdist.dist = tmpdist / 2; +snr.setParent (sn); +this.maxdist.setParent (sn); +sn.setRight (snr); +sn.setLeft (this.maxdist); +this.top = sn; +this.ycount = 0; +this.reCount (this.top); +this.findHeight (this.top); +}return this.top; +}); +Clazz.defineMethod (c$, "hasOriginalSequenceData", +function () { +return this.seqData != null; +}); +Clazz.defineMethod (c$, "printOriginalSequenceData", +function (gapChar) { +if (this.seqData == null) { +return null; +}var sb = new StringBuffer (); +var seqdatas = this.seqData.getSequenceStrings (gapChar); +for (var i = 0; i < seqdatas.length; i++) { +sb.append ( new jalview.util.Format ("%-15s").form (this.sequence[i].getName ())); +sb.append (" " + seqdatas[i] + "\n"); +} +return sb.toString (); +}, "~S"); +Clazz.defineMethod (c$, "printN", +function (node) { +if (node == null) { +return; +}if ((node.left () != null) && (node.right () != null)) { +this.printN (node.left ()); +this.printN (node.right ()); +} else { +System.out.println (" name = " + (node.element ()).getName ()); +}System.out.println (" dist = " + node.dist + " " + node.count + " " + node.height); +}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "reCount", +function (node) { +this.ycount = 0; +this._lycount = 0; +this._reCount (node); +}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "_reCount", +function (node) { +if (node == null) { +return; +}this._lycount++; +if ((node.left () != null) && (node.right () != null)) { +this._reCount (node.left ()); +this._reCount (node.right ()); +var l = node.left (); +var r = node.right (); +node.count = l.count + r.count; +node.ycount = (l.ycount + r.ycount) / 2; +} else { +node.count = 1; +node.ycount = this.ycount++; +}this._lycount--; +}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "swapNodes", +function (node) { +if (node == null) { +return; +}var tmp = node.left (); +node.setLeft (node.right ()); +node.setRight (tmp); +}, "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "changeDirection", +function (node, dir) { +if (node == null) { +return; +}if (node.parent () !== this.top) { +this.changeDirection (node.parent (), node); +var tmp = node.parent (); +if (dir === node.left ()) { +node.setParent (dir); +node.setLeft (tmp); +} else if (dir === node.right ()) { +node.setParent (dir); +node.setRight (tmp); +}} else { +if (dir === node.left ()) { +node.setParent (node.left ()); +if (this.top.left () === node) { +node.setRight (this.top.right ()); +} else { +node.setRight (this.top.left ()); +}} else { +node.setParent (node.right ()); +if (this.top.left () === node) { +node.setLeft (this.top.right ()); +} else { +node.setLeft (this.top.left ()); +}}}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "getMaxDist", +function () { +return this.maxdist; +}); +Clazz.defineMethod (c$, "getTopNode", +function () { +return this.top; +}); +Clazz.defineMethod (c$, "isHasDistances", +function () { +return this.hasDistances; +}); +Clazz.defineMethod (c$, "isHasBootstrap", +function () { +return this.hasBootstrap; +}); +Clazz.defineMethod (c$, "isHasRootDistance", +function () { +return this.hasRootDistance; +}); +Clazz.defineMethod (c$, "applyToNodes", +function (nodeTransformI) { +for (var nodes = this.node.elements (); nodes.hasMoreElements (); nodeTransformI.transform (nodes.nextElement ())) { +;} +}, "jalview.datamodel.NodeTransformI"); +c$.$NJTree$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.analysis, "NJTree$1", null, jalview.datamodel.NodeTransformI); +Clazz.defineMethod (c$, "transform", +function (node) { +var el = node.element (); +if (el != null && Clazz.instanceOf (el, jalview.datamodel.SequenceI)) { +node.setName ((el).getName ()); +}}, "jalview.datamodel.BinaryNode"); +c$ = Clazz.p0p (); +}; +c$ = Clazz.decorateAsClass (function () { +this.value = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "Cluster"); +Clazz.makeConstructor (c$, +function (value) { +this.value = value; +}, "~A"); +}); diff --git a/bin/jalview/analysis/PCA.js b/bin/jalview/analysis/PCA.js index c9e885c..5effde0 100644 --- a/bin/jalview/analysis/PCA.js +++ b/bin/jalview/analysis/PCA.js @@ -1,163 +1,163 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["java.lang.StringBuffer"], "jalview.analysis.PCA", ["jalview.datamodel.BinarySequence", "jalview.math.Matrix", "jalview.schemes.ResidueProperties"], function () { -c$ = Clazz.decorateAsClass (function () { -this.m = null; -this.symm = null; -this.m2 = null; -this.eigenvalue = null; -this.eigenvector = null; -this.details = null; -this.jvCalcMode = true; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "PCA", null, Runnable); -Clazz.prepareFields (c$, function () { -this.details = new StringBuffer (); -}); -Clazz.makeConstructor (c$, -function (s) { -this.construct (s, false); -}, "~A"); -Clazz.makeConstructor (c$, -function (s, nucleotides) { -this.construct (s, nucleotides, null); -}, "~A,~B"); -Clazz.makeConstructor (c$, -function (s, nucleotides, s_m) { -var bs = new Array (s.length); -var ii = 0; -while ((ii < s.length) && (s[ii] != null)) { -bs[ii] = new jalview.datamodel.BinarySequence (s[ii], nucleotides); -bs[ii].encode (); -ii++; -} -var bs2 = new Array (s.length); -ii = 0; -var smtrx = null; -var sm = s_m; -if (sm != null) { -smtrx = jalview.schemes.ResidueProperties.getScoreMatrix (sm); -}if (smtrx == null) { -smtrx = jalview.schemes.ResidueProperties.getScoreMatrix (sm = (nucleotides ? "DNA" : "BLOSUM62")); -}this.details.append ("PCA calculation using " + sm + " sequence similarity matrix\n========\n\n"); -while ((ii < s.length) && (s[ii] != null)) { -bs2[ii] = new jalview.datamodel.BinarySequence (s[ii], nucleotides); -if (smtrx != null) { -try { -bs2[ii].matrixEncode (smtrx); -} catch (x) { -if (Clazz.exceptionOf (x, jalview.datamodel.BinarySequence.InvalidSequenceTypeException)) { -this.details.append ("Unexpected mismatch of sequence type and score matrix. Calculation will not be valid!\n\n"); -} else { -throw x; -} -} -}ii++; -} -var count = 0; -while ((count < bs.length) && (bs[count] != null)) { -count++; -} -var seqmat = Clazz.newDoubleArray (count, bs[0].getDBinary ().length, 0); -var seqmat2 = Clazz.newDoubleArray (count, bs2[0].getDBinary ().length, 0); -var i = 0; -while (i < count) { -seqmat[i] = bs[i].getDBinary (); -seqmat2[i] = bs2[i].getDBinary (); -i++; -} -this.m = new jalview.math.Matrix (seqmat, count, bs[0].getDBinary ().length); -this.m2 = new jalview.math.Matrix (seqmat2, count, bs2[0].getDBinary ().length); -}, "~A,~B,~S"); -Clazz.defineMethod (c$, "getM", -function () { -return this.m; -}); -Clazz.defineMethod (c$, "getEigenvalue", -function (i) { -return this.eigenvector.d[i]; -}, "~N"); -Clazz.defineMethod (c$, "getComponents", -function (l, n, mm, factor) { -var out = Clazz.newFloatArray (this.m.rows, 3, 0); -for (var i = 0; i < this.m.rows; i++) { -out[i][0] = this.component (i, l) * factor; -out[i][1] = this.component (i, n) * factor; -out[i][2] = this.component (i, mm) * factor; -} -return out; -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "component", -function (n) { -var out = Clazz.newDoubleArray (this.m.rows, 0); -for (var i = 0; i < this.m.rows; i++) { -out[i] = this.component (i, n); -} -return out; -}, "~N"); -Clazz.defineMethod (c$, "component", -function (row, n) { -var out = 0.0; -for (var i = 0; i < this.symm.cols; i++) { -out += (this.symm.value[row][i] * this.eigenvector.value[i][n]); -} -return out / this.eigenvector.d[n]; -}, "~N,~N"); -Clazz.defineMethod (c$, "getDetails", -function () { -return this.details.toString (); -}); -Clazz.overrideMethod (c$, "run", -function () { -var ps = ((Clazz.isClassDefined ("jalview.analysis.PCA$1") ? 0 : jalview.analysis.PCA.$PCA$1$ ()), Clazz.innerTypeInstance (jalview.analysis.PCA$1, this, null, System.out)); -try { -this.details.append ("PCA Calculation Mode is " + (this.jvCalcMode ? "Jalview variant" : "Original SeqSpace") + "\n"); -var mt = this.m.transpose (); -this.details.append (" --- OrigT * Orig ---- \n"); -if (!this.jvCalcMode) { -this.eigenvector = mt.preMultiply (this.m); -} else { -this.eigenvector = mt.preMultiply (this.m2); -}this.eigenvector.print (ps); -this.symm = this.eigenvector.copy (); -this.eigenvector.tred (); -this.details.append (" ---Tridiag transform matrix ---\n"); -this.details.append (" --- D vector ---\n"); -this.eigenvector.printD (ps); -ps.println (); -this.details.append ("--- E vector ---\n"); -this.eigenvector.printE (ps); -ps.println (); -this.eigenvector.tqli (); -} catch (q) { -if (Clazz.exceptionOf (q, Exception)) { -q.printStackTrace (); -this.details.append ("\n*** Unexpected exception when performing PCA ***\n" + q.getLocalizedMessage ()); -this.details.append ("*** Matrices below may not be fully diagonalised. ***\n"); -} else { -throw q; -} -} -this.details.append (" --- New diagonalization matrix ---\n"); -this.eigenvector.print (ps); -this.details.append (" --- Eigenvalues ---\n"); -this.eigenvector.printD (ps); -ps.println (); -}); -Clazz.defineMethod (c$, "setJvCalcMode", -function (calcMode) { -this.jvCalcMode = calcMode; -}, "~B"); -c$.$PCA$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.analysis, "PCA$1", java.io.PrintStream); -Clazz.defineMethod (c$, "print", -function (x) { -this.b$["jalview.analysis.PCA"].details.append (x); -}, "~S"); -Clazz.defineMethod (c$, "println", -function () { -this.b$["jalview.analysis.PCA"].details.append ("\n"); -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["java.lang.StringBuffer"], "jalview.analysis.PCA", ["jalview.datamodel.BinarySequence", "jalview.math.Matrix", "jalview.schemes.ResidueProperties"], function () { +c$ = Clazz.decorateAsClass (function () { +this.m = null; +this.symm = null; +this.m2 = null; +this.eigenvalue = null; +this.eigenvector = null; +this.details = null; +this.jvCalcMode = true; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "PCA", null, Runnable); +Clazz.prepareFields (c$, function () { +this.details = new StringBuffer (); +}); +Clazz.makeConstructor (c$, +function (s) { +this.construct (s, false); +}, "~A"); +Clazz.makeConstructor (c$, +function (s, nucleotides) { +this.construct (s, nucleotides, null); +}, "~A,~B"); +Clazz.makeConstructor (c$, +function (s, nucleotides, s_m) { +var bs = new Array (s.length); +var ii = 0; +while ((ii < s.length) && (s[ii] != null)) { +bs[ii] = new jalview.datamodel.BinarySequence (s[ii], nucleotides); +bs[ii].encode (); +ii++; +} +var bs2 = new Array (s.length); +ii = 0; +var smtrx = null; +var sm = s_m; +if (sm != null) { +smtrx = jalview.schemes.ResidueProperties.getScoreMatrix (sm); +}if (smtrx == null) { +smtrx = jalview.schemes.ResidueProperties.getScoreMatrix (sm = (nucleotides ? "DNA" : "BLOSUM62")); +}this.details.append ("PCA calculation using " + sm + " sequence similarity matrix\n========\n\n"); +while ((ii < s.length) && (s[ii] != null)) { +bs2[ii] = new jalview.datamodel.BinarySequence (s[ii], nucleotides); +if (smtrx != null) { +try { +bs2[ii].matrixEncode (smtrx); +} catch (x) { +if (Clazz.exceptionOf (x, jalview.datamodel.BinarySequence.InvalidSequenceTypeException)) { +this.details.append ("Unexpected mismatch of sequence type and score matrix. Calculation will not be valid!\n\n"); +} else { +throw x; +} +} +}ii++; +} +var count = 0; +while ((count < bs.length) && (bs[count] != null)) { +count++; +} +var seqmat = Clazz.newDoubleArray (count, bs[0].getDBinary ().length, 0); +var seqmat2 = Clazz.newDoubleArray (count, bs2[0].getDBinary ().length, 0); +var i = 0; +while (i < count) { +seqmat[i] = bs[i].getDBinary (); +seqmat2[i] = bs2[i].getDBinary (); +i++; +} +this.m = new jalview.math.Matrix (seqmat, count, bs[0].getDBinary ().length); +this.m2 = new jalview.math.Matrix (seqmat2, count, bs2[0].getDBinary ().length); +}, "~A,~B,~S"); +Clazz.defineMethod (c$, "getM", +function () { +return this.m; +}); +Clazz.defineMethod (c$, "getEigenvalue", +function (i) { +return this.eigenvector.d[i]; +}, "~N"); +Clazz.defineMethod (c$, "getComponents", +function (l, n, mm, factor) { +var out = Clazz.newFloatArray (this.m.rows, 3, 0); +for (var i = 0; i < this.m.rows; i++) { +out[i][0] = this.component (i, l) * factor; +out[i][1] = this.component (i, n) * factor; +out[i][2] = this.component (i, mm) * factor; +} +return out; +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "component", +function (n) { +var out = Clazz.newDoubleArray (this.m.rows, 0); +for (var i = 0; i < this.m.rows; i++) { +out[i] = this.component (i, n); +} +return out; +}, "~N"); +Clazz.defineMethod (c$, "component", +function (row, n) { +var out = 0.0; +for (var i = 0; i < this.symm.cols; i++) { +out += (this.symm.value[row][i] * this.eigenvector.value[i][n]); +} +return out / this.eigenvector.d[n]; +}, "~N,~N"); +Clazz.defineMethod (c$, "getDetails", +function () { +return this.details.toString (); +}); +Clazz.overrideMethod (c$, "run", +function () { +var ps = ((Clazz.isClassDefined ("jalview.analysis.PCA$1") ? 0 : jalview.analysis.PCA.$PCA$1$ ()), Clazz.innerTypeInstance (jalview.analysis.PCA$1, this, null, System.out)); +try { +this.details.append ("PCA Calculation Mode is " + (this.jvCalcMode ? "Jalview variant" : "Original SeqSpace") + "\n"); +var mt = this.m.transpose (); +this.details.append (" --- OrigT * Orig ---- \n"); +if (!this.jvCalcMode) { +this.eigenvector = mt.preMultiply (this.m); +} else { +this.eigenvector = mt.preMultiply (this.m2); +}this.eigenvector.print (ps); +this.symm = this.eigenvector.copy (); +this.eigenvector.tred (); +this.details.append (" ---Tridiag transform matrix ---\n"); +this.details.append (" --- D vector ---\n"); +this.eigenvector.printD (ps); +ps.println (); +this.details.append ("--- E vector ---\n"); +this.eigenvector.printE (ps); +ps.println (); +this.eigenvector.tqli (); +} catch (q) { +if (Clazz.exceptionOf (q, Exception)) { +q.printStackTrace (); +this.details.append ("\n*** Unexpected exception when performing PCA ***\n" + q.getLocalizedMessage ()); +this.details.append ("*** Matrices below may not be fully diagonalised. ***\n"); +} else { +throw q; +} +} +this.details.append (" --- New diagonalization matrix ---\n"); +this.eigenvector.print (ps); +this.details.append (" --- Eigenvalues ---\n"); +this.eigenvector.printD (ps); +ps.println (); +}); +Clazz.defineMethod (c$, "setJvCalcMode", +function (calcMode) { +this.jvCalcMode = calcMode; +}, "~B"); +c$.$PCA$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.analysis, "PCA$1", java.io.PrintStream); +Clazz.defineMethod (c$, "print", +function (x) { +this.b$["jalview.analysis.PCA"].details.append (x); +}, "~S"); +Clazz.defineMethod (c$, "println", +function () { +this.b$["jalview.analysis.PCA"].details.append ("\n"); +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/analysis/ParseProperties.js b/bin/jalview/analysis/ParseProperties.js index d18979d..c117d07 100644 --- a/bin/jalview/analysis/ParseProperties.js +++ b/bin/jalview/analysis/ParseProperties.js @@ -1,75 +1,75 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.ParseProperties", ["jalview.datamodel.AlignmentAnnotation", "jalview.jsdev.RegExp", "java.lang.Double"], function () { -c$ = Clazz.decorateAsClass (function () { -this.al = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "ParseProperties"); -Clazz.makeConstructor (c$, -function (al) { -this.al = al; -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "getScoresFromDescription", -function (ScoreName, ScoreDescriptions, regex, repeat) { -return this.getScoresFromDescription ( Clazz.newArray (-1, [ScoreName]), Clazz.newArray (-1, [ScoreDescriptions]), regex, repeat); -}, "~S,~S,~S,~B"); -Clazz.defineMethod (c$, "getScoresFromDescription", -function (ScoreNames, ScoreDescriptions, regex, repeat) { -return this.getScoresFromDescription (this.al.getSequencesArray (), ScoreNames, ScoreDescriptions, regex, repeat); -}, "~A,~A,~S,~B"); -Clazz.defineMethod (c$, "getScoresFromDescription", -function (seqs, ScoreNames, ScoreDescriptions, regex, repeat) { -var count = 0; -var pattern = jalview.jsdev.RegExp.newRegex ([regex]); -if (pattern.numSubs () > ScoreNames.length) { -var onamelen = ScoreNames.length; -var tnames = new Array (pattern.numSubs () + 1); -System.arraycopy (ScoreNames, 0, tnames, 0, ScoreNames.length); -var base = tnames[ScoreNames.length - 1]; -ScoreNames = tnames; -var descrbase = ScoreDescriptions[onamelen - 1]; -if (descrbase == null) { -descrbase = "Score parsed from (" + regex + ")"; -}tnames = new Array (pattern.numSubs () + 1); -System.arraycopy (ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length); -ScoreDescriptions = tnames; -for (var i = onamelen; i < ScoreNames.length; i++) { -ScoreNames[i] = base + "_" + i; -ScoreDescriptions[i] = descrbase + " (column " + i + ")"; -} -}for (var i = 0; i < seqs.length; i++) { -var descr = seqs[i].getDescription (); -if (descr == null) { -continue; -}var pos = 0; -var added = false; -var reps = 0; -while ((repeat || pos == 0) && pattern.searchFrom (descr, pos)) { -pos = pattern.matchedTo (); -for (var cols = 0; cols < pattern.numSubs (); cols++) { -var sstring = pattern.stringMatchedI (cols + 1); -var score = NaN; -try { -score = new Double (sstring).doubleValue (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -continue; -} else { -throw e; -} -} -var an = new jalview.datamodel.AlignmentAnnotation (ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""), ScoreDescriptions[cols], null); -an.setScore (score); -System.out.println (seqs[i].getName () + " score: '" + ScoreNames[cols] + "' = " + score); -an.setSequenceRef (seqs[i]); -seqs[i].addAlignmentAnnotation (an); -this.al.addAnnotation (an); -added = true; -} -reps++; -} -if (added) { -count++; -}} -return count; -}, "~A,~A,~A,~S,~B"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.ParseProperties", ["jalview.datamodel.AlignmentAnnotation", "jalview.jsdev.RegExp", "java.lang.Double"], function () { +c$ = Clazz.decorateAsClass (function () { +this.al = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "ParseProperties"); +Clazz.makeConstructor (c$, +function (al) { +this.al = al; +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "getScoresFromDescription", +function (ScoreName, ScoreDescriptions, regex, repeat) { +return this.getScoresFromDescription ( Clazz.newArray (-1, [ScoreName]), Clazz.newArray (-1, [ScoreDescriptions]), regex, repeat); +}, "~S,~S,~S,~B"); +Clazz.defineMethod (c$, "getScoresFromDescription", +function (ScoreNames, ScoreDescriptions, regex, repeat) { +return this.getScoresFromDescription (this.al.getSequencesArray (), ScoreNames, ScoreDescriptions, regex, repeat); +}, "~A,~A,~S,~B"); +Clazz.defineMethod (c$, "getScoresFromDescription", +function (seqs, ScoreNames, ScoreDescriptions, regex, repeat) { +var count = 0; +var pattern = jalview.jsdev.RegExp.newRegex ([regex]); +if (pattern.numSubs () > ScoreNames.length) { +var onamelen = ScoreNames.length; +var tnames = new Array (pattern.numSubs () + 1); +System.arraycopy (ScoreNames, 0, tnames, 0, ScoreNames.length); +var base = tnames[ScoreNames.length - 1]; +ScoreNames = tnames; +var descrbase = ScoreDescriptions[onamelen - 1]; +if (descrbase == null) { +descrbase = "Score parsed from (" + regex + ")"; +}tnames = new Array (pattern.numSubs () + 1); +System.arraycopy (ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length); +ScoreDescriptions = tnames; +for (var i = onamelen; i < ScoreNames.length; i++) { +ScoreNames[i] = base + "_" + i; +ScoreDescriptions[i] = descrbase + " (column " + i + ")"; +} +}for (var i = 0; i < seqs.length; i++) { +var descr = seqs[i].getDescription (); +if (descr == null) { +continue; +}var pos = 0; +var added = false; +var reps = 0; +while ((repeat || pos == 0) && pattern.searchFrom (descr, pos)) { +pos = pattern.matchedTo (); +for (var cols = 0; cols < pattern.numSubs (); cols++) { +var sstring = pattern.stringMatchedI (cols + 1); +var score = NaN; +try { +score = new Double (sstring).doubleValue (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +continue; +} else { +throw e; +} +} +var an = new jalview.datamodel.AlignmentAnnotation (ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""), ScoreDescriptions[cols], null); +an.setScore (score); +System.out.println (seqs[i].getName () + " score: '" + ScoreNames[cols] + "' = " + score); +an.setSequenceRef (seqs[i]); +seqs[i].addAlignmentAnnotation (an); +this.al.addAnnotation (an); +added = true; +} +reps++; +} +if (added) { +count++; +}} +return count; +}, "~A,~A,~A,~S,~B"); +}); diff --git a/bin/jalview/analysis/Rna.js b/bin/jalview/analysis/Rna.js index 0ed5a63..4b23f2d 100644 --- a/bin/jalview/analysis/Rna.js +++ b/bin/jalview/analysis/Rna.js @@ -1,106 +1,106 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["java.util.Arrays", "$.HashSet", "$.Hashtable"], "jalview.analysis.Rna", ["jalview.analysis.SecStrConsensus", "$.WUSSParseException", "jalview.datamodel.SequenceFeature", "jalview.util.MessageManager", "java.lang.StringBuffer", "java.util.ArrayList", "$.Stack", "$.Vector"], function () { -c$ = Clazz.declareType (jalview.analysis, "Rna"); -c$.isOpeningParenthesis = Clazz.defineMethod (c$, "isOpeningParenthesis", -($fz = function (c) { -return jalview.analysis.Rna.openingParsSet.contains (new Character (c).charCodeAt (0)); -}, $fz.isPrivate = true, $fz), "~S"); -c$.isClosingParenthesis = Clazz.defineMethod (c$, "isClosingParenthesis", -($fz = function (c) { -return jalview.analysis.Rna.closingParsSet.contains (new Character (c).charCodeAt (0)); -}, $fz.isPrivate = true, $fz), "~S"); -c$.matchingOpeningParenthesis = Clazz.defineMethod (c$, "matchingOpeningParenthesis", -($fz = function (closingParenthesis) { -if (!jalview.analysis.Rna.isClosingParenthesis (closingParenthesis)) { -throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis", Clazz.newArray (-1, [ new StringBuffer (closingParenthesis.charCodeAt (0)).toString ()])), -1); -}return String.fromCharCode (jalview.analysis.Rna.closingToOpening.get (new Character (closingParenthesis).charCodeAt (0))); -}, $fz.isPrivate = true, $fz), "~S"); -c$.GetSimpleBPs = Clazz.defineMethod (c$, "GetSimpleBPs", -function (line) { -var stacks = new java.util.Hashtable (); -var pairs = new java.util.Vector (); -var i = 0; -while (i < line.length) { -var base = line.charAt (i); -if (jalview.analysis.Rna.isOpeningParenthesis (base)) { -if (!stacks.containsKey (new Character (base).charCodeAt (0))) { -stacks.put (new Character (base).charCodeAt (0), new java.util.Stack ()); -}stacks.get (new Character (base).charCodeAt (0)).push (new Integer (i)); -} else if (jalview.analysis.Rna.isClosingParenthesis (base)) { -var opening = jalview.analysis.Rna.matchingOpeningParenthesis (base); -if (!stacks.containsKey (new Character (opening).charCodeAt (0))) { -throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.mismatched_unseen_closing_char", Clazz.newArray (-1, [ new StringBuffer (base.charCodeAt (0)).toString ()])), i); -}var stack = stacks.get (new Character (opening).charCodeAt (0)); -if (stack.isEmpty ()) { -throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.mismatched_closing_char", Clazz.newArray (-1, [ new StringBuffer (base.charCodeAt (0)).toString ()])), i); -}var temp = (stack.pop ()).intValue (); -pairs.add ( new jalview.analysis.SecStrConsensus.SimpleBP (temp, i)); -}i++; -} -for (var opening, $opening = stacks.keySet ().iterator (); $opening.hasNext () && ((opening = $opening.next ()) || true);) { -var stack = stacks.get (new Character (opening).charCodeAt (0)); -if (!stack.empty ()) { -throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.mismatched_opening_char", Clazz.newArray (-1, [ new StringBuffer (opening.charCodeAt (0)).toString (), Integer.$valueOf ((stack.pop ()).intValue ()).toString ()])), i); -}} -return pairs; -}, "CharSequence"); -c$.GetBasePairs = Clazz.defineMethod (c$, "GetBasePairs", -function (line) { -var bps = jalview.analysis.Rna.GetSimpleBPs (line); -var outPairs = new Array (bps.size ()); -for (var p = 0; p < bps.size (); p++) { -var bp = bps.elementAt (p); -outPairs[p] = new jalview.datamodel.SequenceFeature ("RNA helix", "", "", bp.getBP5 (), bp.getBP3 (), ""); -} -return outPairs; -}, "CharSequence"); -c$.GetModeleBP = Clazz.defineMethod (c$, "GetModeleBP", -function (line) { -var bps = jalview.analysis.Rna.GetSimpleBPs (line); -return new java.util.ArrayList (bps); -}, "CharSequence"); -c$.HelixMap = Clazz.defineMethod (c$, "HelixMap", -function (pairs) { -var helix = 0; -var lastopen = 0; -var lastclose = 9999999; -var i = pairs.length; -var open; -var close; -var j; -var helices = new java.util.Hashtable (); -for (i = 0; i < pairs.length; i++) { -open = pairs[i].getBegin (); -close = pairs[i].getEnd (); -if (open > lastclose) { -helix++; -}j = pairs.length - 1; -while (j >= 0) { -var popen = pairs[j].getBegin (); -if ((popen < lastopen) && (popen > open)) { -if (helices.containsValue (new Integer (popen)) && (((helices.get (new Integer (popen)))).intValue () === helix)) { -continue; -} else { -helix++; -break; -}}j -= 1; -} -helices.put (new Integer (open), new Integer (helix)); -helices.put (new Integer (close), new Integer (helix)); -pairs[i].setFeatureGroup (Integer.toString (helix)); -lastopen = open; -lastclose = close; -} -}, "~A"); -c$.pairHash = c$.prototype.pairHash = new java.util.Hashtable (); -Clazz.defineStatics (c$, -"openingPars", Clazz.newArray (-1, [new Character ('('), new Character ('['), new Character ('{'), new Character ('<'), new Character ('A'), new Character ('B'), new Character ('C'), new Character ('D'), new Character ('E'), new Character ('F'), new Character ('G'), new Character ('H'), new Character ('I'), new Character ('J'), new Character ('K'), new Character ('L'), new Character ('M'), new Character ('N'), new Character ('O'), new Character ('P'), new Character ('Q'), new Character ('R'), new Character ('S'), new Character ('T'), new Character ('U'), new Character ('V'), new Character ('W'), new Character ('X'), new Character ('Y'), new Character ('Z')]), -"closingPars", Clazz.newArray (-1, [new Character (')'), new Character (']'), new Character ('}'), new Character ('>'), new Character ('a'), new Character ('b'), new Character ('c'), new Character ('d'), new Character ('e'), new Character ('f'), new Character ('g'), new Character ('h'), new Character ('i'), new Character ('j'), new Character ('k'), new Character ('l'), new Character ('m'), new Character ('n'), new Character ('o'), new Character ('p'), new Character ('q'), new Character ('r'), new Character ('s'), new Character ('t'), new Character ('u'), new Character ('v'), new Character ('w'), new Character ('x'), new Character ('y'), new Character ('z')])); -c$.openingParsSet = c$.prototype.openingParsSet = new java.util.HashSet (java.util.Arrays.asList (jalview.analysis.Rna.openingPars)); -c$.closingParsSet = c$.prototype.closingParsSet = new java.util.HashSet (java.util.Arrays.asList (jalview.analysis.Rna.closingPars)); -c$.closingToOpening = c$.prototype.closingToOpening = new java.util.Hashtable (); -{ -for (var i = 0; i < jalview.analysis.Rna.openingPars.length; i++) { -jalview.analysis.Rna.closingToOpening.put (jalview.analysis.Rna.closingPars[i], jalview.analysis.Rna.openingPars[i]); -} -}}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["java.util.Arrays", "$.HashSet", "$.Hashtable"], "jalview.analysis.Rna", ["jalview.analysis.SecStrConsensus", "$.WUSSParseException", "jalview.datamodel.SequenceFeature", "jalview.util.MessageManager", "java.lang.StringBuffer", "java.util.ArrayList", "$.Stack", "$.Vector"], function () { +c$ = Clazz.declareType (jalview.analysis, "Rna"); +c$.isOpeningParenthesis = Clazz.defineMethod (c$, "isOpeningParenthesis", +($fz = function (c) { +return jalview.analysis.Rna.openingParsSet.contains (new Character (c).charCodeAt (0)); +}, $fz.isPrivate = true, $fz), "~S"); +c$.isClosingParenthesis = Clazz.defineMethod (c$, "isClosingParenthesis", +($fz = function (c) { +return jalview.analysis.Rna.closingParsSet.contains (new Character (c).charCodeAt (0)); +}, $fz.isPrivate = true, $fz), "~S"); +c$.matchingOpeningParenthesis = Clazz.defineMethod (c$, "matchingOpeningParenthesis", +($fz = function (closingParenthesis) { +if (!jalview.analysis.Rna.isClosingParenthesis (closingParenthesis)) { +throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis", Clazz.newArray (-1, [ new StringBuffer (closingParenthesis.charCodeAt (0)).toString ()])), -1); +}return String.fromCharCode (jalview.analysis.Rna.closingToOpening.get (new Character (closingParenthesis).charCodeAt (0))); +}, $fz.isPrivate = true, $fz), "~S"); +c$.GetSimpleBPs = Clazz.defineMethod (c$, "GetSimpleBPs", +function (line) { +var stacks = new java.util.Hashtable (); +var pairs = new java.util.Vector (); +var i = 0; +while (i < line.length) { +var base = line.charAt (i); +if (jalview.analysis.Rna.isOpeningParenthesis (base)) { +if (!stacks.containsKey (new Character (base).charCodeAt (0))) { +stacks.put (new Character (base).charCodeAt (0), new java.util.Stack ()); +}stacks.get (new Character (base).charCodeAt (0)).push (new Integer (i)); +} else if (jalview.analysis.Rna.isClosingParenthesis (base)) { +var opening = jalview.analysis.Rna.matchingOpeningParenthesis (base); +if (!stacks.containsKey (new Character (opening).charCodeAt (0))) { +throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.mismatched_unseen_closing_char", Clazz.newArray (-1, [ new StringBuffer (base.charCodeAt (0)).toString ()])), i); +}var stack = stacks.get (new Character (opening).charCodeAt (0)); +if (stack.isEmpty ()) { +throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.mismatched_closing_char", Clazz.newArray (-1, [ new StringBuffer (base.charCodeAt (0)).toString ()])), i); +}var temp = (stack.pop ()).intValue (); +pairs.add ( new jalview.analysis.SecStrConsensus.SimpleBP (temp, i)); +}i++; +} +for (var opening, $opening = stacks.keySet ().iterator (); $opening.hasNext () && ((opening = $opening.next ()) || true);) { +var stack = stacks.get (new Character (opening).charCodeAt (0)); +if (!stack.empty ()) { +throw new jalview.analysis.WUSSParseException (jalview.util.MessageManager.formatMessage ("exception.mismatched_opening_char", Clazz.newArray (-1, [ new StringBuffer (opening.charCodeAt (0)).toString (), Integer.$valueOf ((stack.pop ()).intValue ()).toString ()])), i); +}} +return pairs; +}, "CharSequence"); +c$.GetBasePairs = Clazz.defineMethod (c$, "GetBasePairs", +function (line) { +var bps = jalview.analysis.Rna.GetSimpleBPs (line); +var outPairs = new Array (bps.size ()); +for (var p = 0; p < bps.size (); p++) { +var bp = bps.elementAt (p); +outPairs[p] = new jalview.datamodel.SequenceFeature ("RNA helix", "", "", bp.getBP5 (), bp.getBP3 (), ""); +} +return outPairs; +}, "CharSequence"); +c$.GetModeleBP = Clazz.defineMethod (c$, "GetModeleBP", +function (line) { +var bps = jalview.analysis.Rna.GetSimpleBPs (line); +return new java.util.ArrayList (bps); +}, "CharSequence"); +c$.HelixMap = Clazz.defineMethod (c$, "HelixMap", +function (pairs) { +var helix = 0; +var lastopen = 0; +var lastclose = 9999999; +var i = pairs.length; +var open; +var close; +var j; +var helices = new java.util.Hashtable (); +for (i = 0; i < pairs.length; i++) { +open = pairs[i].getBegin (); +close = pairs[i].getEnd (); +if (open > lastclose) { +helix++; +}j = pairs.length - 1; +while (j >= 0) { +var popen = pairs[j].getBegin (); +if ((popen < lastopen) && (popen > open)) { +if (helices.containsValue (new Integer (popen)) && (((helices.get (new Integer (popen)))).intValue () === helix)) { +continue; +} else { +helix++; +break; +}}j -= 1; +} +helices.put (new Integer (open), new Integer (helix)); +helices.put (new Integer (close), new Integer (helix)); +pairs[i].setFeatureGroup (Integer.toString (helix)); +lastopen = open; +lastclose = close; +} +}, "~A"); +c$.pairHash = c$.prototype.pairHash = new java.util.Hashtable (); +Clazz.defineStatics (c$, +"openingPars", Clazz.newArray (-1, [new Character ('('), new Character ('['), new Character ('{'), new Character ('<'), new Character ('A'), new Character ('B'), new Character ('C'), new Character ('D'), new Character ('E'), new Character ('F'), new Character ('G'), new Character ('H'), new Character ('I'), new Character ('J'), new Character ('K'), new Character ('L'), new Character ('M'), new Character ('N'), new Character ('O'), new Character ('P'), new Character ('Q'), new Character ('R'), new Character ('S'), new Character ('T'), new Character ('U'), new Character ('V'), new Character ('W'), new Character ('X'), new Character ('Y'), new Character ('Z')]), +"closingPars", Clazz.newArray (-1, [new Character (')'), new Character (']'), new Character ('}'), new Character ('>'), new Character ('a'), new Character ('b'), new Character ('c'), new Character ('d'), new Character ('e'), new Character ('f'), new Character ('g'), new Character ('h'), new Character ('i'), new Character ('j'), new Character ('k'), new Character ('l'), new Character ('m'), new Character ('n'), new Character ('o'), new Character ('p'), new Character ('q'), new Character ('r'), new Character ('s'), new Character ('t'), new Character ('u'), new Character ('v'), new Character ('w'), new Character ('x'), new Character ('y'), new Character ('z')])); +c$.openingParsSet = c$.prototype.openingParsSet = new java.util.HashSet (java.util.Arrays.asList (jalview.analysis.Rna.openingPars)); +c$.closingParsSet = c$.prototype.closingParsSet = new java.util.HashSet (java.util.Arrays.asList (jalview.analysis.Rna.closingPars)); +c$.closingToOpening = c$.prototype.closingToOpening = new java.util.Hashtable (); +{ +for (var i = 0; i < jalview.analysis.Rna.openingPars.length; i++) { +jalview.analysis.Rna.closingToOpening.put (jalview.analysis.Rna.closingPars[i], jalview.analysis.Rna.openingPars[i]); +} +}}); diff --git a/bin/jalview/analysis/SecStrConsensus.class b/bin/jalview/analysis/SecStrConsensus.class index d4b9f08..c7ac833 100644 Binary files a/bin/jalview/analysis/SecStrConsensus.class and b/bin/jalview/analysis/SecStrConsensus.class differ diff --git a/bin/jalview/analysis/SecStrConsensus.js b/bin/jalview/analysis/SecStrConsensus.js index 44e1009..f96678e 100644 --- a/bin/jalview/analysis/SecStrConsensus.js +++ b/bin/jalview/analysis/SecStrConsensus.js @@ -1,139 +1,139 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.SecStrConsensus", ["java.util.ArrayList", "$.Hashtable"], function () { -c$ = Clazz.declareType (jalview.analysis, "SecStrConsensus"); -c$.extractConsensus = Clazz.defineMethod (c$, "extractConsensus", -function (bps) { -var maxlength = 0; -for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) { -for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) { -maxlength = Math.max (1 + Math.max (bp.bp5, bp.bp3), maxlength); -} -} -var seq = new java.util.ArrayList (); -for (var i = 0; i < maxlength; i++) { -seq.add ( new java.util.Hashtable ()); -} -for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) { -for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) { -var i = bp.bp5; -var j = bp.bp3; -var h = seq.get (i); -if (!h.containsKey (new Integer (j))) { -h.put (new Integer (j), new Double (0.0)); -}h.put (new Integer (j), new Double ((h.get (new Integer (j))).doubleValue () + 1.)); -} -} -var mat = jalview.analysis.SecStrConsensus.fillMatrix (seq); -var res = jalview.analysis.SecStrConsensus.backtrack (mat, seq); -var finalres = Clazz.newIntArray (seq.size (), 0); -for (var i = 0; i < seq.size (); i++) { -finalres[i] = -1; -} -for (var bp, $bp = res.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) { -finalres[bp.bp5] = bp.bp3; -finalres[bp.bp3] = bp.bp5; -} -return finalres; -}, "java.util.ArrayList"); -c$.canBasePair = Clazz.defineMethod (c$, "canBasePair", -($fz = function (seq, i, k) { -return seq.get (i).containsKey (new Integer (k)); -}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N"); -c$.basePairScore = Clazz.defineMethod (c$, "basePairScore", -($fz = function (seq, i, k) { -return seq.get (i).get (new Integer (k)); -}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N"); -c$.fillMatrix = Clazz.defineMethod (c$, "fillMatrix", -($fz = function (seq) { -var n = seq.size (); -var tab = Clazz.newDoubleArray (n, n, 0); -for (var m = 1; m <= n; m++) { -for (var i = 0; i < n - m + 1; i++) { -var j = i + m - 1; -tab[i][j] = 0; -if (i < j) { -tab[i][j] = Math.max (tab[i][j], tab[i + 1][j]); -for (var k = i + 1; k <= j; k++) { -if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) { -var fact1 = 0; -if (k > i + 1) { -fact1 = tab[i + 1][k - 1]; -}var fact2 = 0; -if (k < j) { -fact2 = tab[k + 1][j]; -}tab[i][j] = Math.max (tab[i][j], jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2); -}} -}} -} -return tab; -}, $fz.isPrivate = true, $fz), "java.util.ArrayList"); -c$.backtrack = Clazz.defineMethod (c$, "backtrack", -($fz = function (tab, seq) { -return jalview.analysis.SecStrConsensus.backtrack (tab, seq, 0, seq.size () - 1); -}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList"); -c$.backtrack = Clazz.defineMethod (c$, "backtrack", -($fz = function (tab, seq, i, j) { -var result = new java.util.ArrayList (); -if (i < j) { -var indices = new java.util.ArrayList (); -indices.add (new Integer (-1)); -for (var k = i + 1; k <= j; k++) { -indices.add (new Integer (k)); -} -for (var k, $k = indices.iterator (); $k.hasNext () && ((k = $k.next ()) || true);) { -if (k == -1) { -if (tab[i][j] == tab[i + 1][j]) { -result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, j); -}} else { -if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) { -var fact1 = 0; -if (k > i + 1) { -fact1 = tab[i + 1][k - 1]; -}var fact2 = 0; -if (k < j) { -fact2 = tab[k + 1][j]; -}if (tab[i][j] == jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2) { -result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, k - 1); -result.addAll (jalview.analysis.SecStrConsensus.backtrack (tab, seq, k + 1, j)); -result.add ( new jalview.analysis.SecStrConsensus.SimpleBP (i, k)); -}}}} -} else if (i == j) { -} else { -}return result; -}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList,~N,~N"); -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.bp5 = 0; -this.bp3 = 0; -Clazz.instantialize (this, arguments); -}, jalview.analysis.SecStrConsensus, "SimpleBP"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (a, b) { -this.bp5 = a; -this.bp3 = b; -}, "~N,~N"); -Clazz.defineMethod (c$, "setBP5", -function (a) { -this.bp5 = a; -}, "~N"); -Clazz.defineMethod (c$, "setBP3", -function (a) { -this.bp3 = a; -}, "~N"); -Clazz.defineMethod (c$, "getBP5", -function () { -return this.bp5; -}); -Clazz.defineMethod (c$, "getBP3", -function () { -return this.bp3; -}); -Clazz.overrideMethod (c$, "toString", -function () { -return "(" + this.bp5 + "," + this.bp3 + ")"; -}); -c$ = Clazz.p0p (); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.SecStrConsensus", ["java.util.ArrayList", "$.Hashtable"], function () { +c$ = Clazz.declareType (jalview.analysis, "SecStrConsensus"); +c$.extractConsensus = Clazz.defineMethod (c$, "extractConsensus", +function (bps) { +var maxlength = 0; +for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) { +for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) { +maxlength = Math.max (1 + Math.max (bp.bp5, bp.bp3), maxlength); +} +} +var seq = new java.util.ArrayList (); +for (var i = 0; i < maxlength; i++) { +seq.add ( new java.util.Hashtable ()); +} +for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) { +for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) { +var i = bp.bp5; +var j = bp.bp3; +var h = seq.get (i); +if (!h.containsKey (new Integer (j))) { +h.put (new Integer (j), new Double (0.0)); +}h.put (new Integer (j), new Double ((h.get (new Integer (j))).doubleValue () + 1.)); +} +} +var mat = jalview.analysis.SecStrConsensus.fillMatrix (seq); +var res = jalview.analysis.SecStrConsensus.backtrack (mat, seq); +var finalres = Clazz.newIntArray (seq.size (), 0); +for (var i = 0; i < seq.size (); i++) { +finalres[i] = -1; +} +for (var bp, $bp = res.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) { +finalres[bp.bp5] = bp.bp3; +finalres[bp.bp3] = bp.bp5; +} +return finalres; +}, "java.util.ArrayList"); +c$.canBasePair = Clazz.defineMethod (c$, "canBasePair", +($fz = function (seq, i, k) { +return seq.get (i).containsKey (new Integer (k)); +}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N"); +c$.basePairScore = Clazz.defineMethod (c$, "basePairScore", +($fz = function (seq, i, k) { +return seq.get (i).get (new Integer (k)); +}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N"); +c$.fillMatrix = Clazz.defineMethod (c$, "fillMatrix", +($fz = function (seq) { +var n = seq.size (); +var tab = Clazz.newDoubleArray (n, n, 0); +for (var m = 1; m <= n; m++) { +for (var i = 0; i < n - m + 1; i++) { +var j = i + m - 1; +tab[i][j] = 0; +if (i < j) { +tab[i][j] = Math.max (tab[i][j], tab[i + 1][j]); +for (var k = i + 1; k <= j; k++) { +if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) { +var fact1 = 0; +if (k > i + 1) { +fact1 = tab[i + 1][k - 1]; +}var fact2 = 0; +if (k < j) { +fact2 = tab[k + 1][j]; +}tab[i][j] = Math.max (tab[i][j], jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2); +}} +}} +} +return tab; +}, $fz.isPrivate = true, $fz), "java.util.ArrayList"); +c$.backtrack = Clazz.defineMethod (c$, "backtrack", +($fz = function (tab, seq) { +return jalview.analysis.SecStrConsensus.backtrack (tab, seq, 0, seq.size () - 1); +}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList"); +c$.backtrack = Clazz.defineMethod (c$, "backtrack", +($fz = function (tab, seq, i, j) { +var result = new java.util.ArrayList (); +if (i < j) { +var indices = new java.util.ArrayList (); +indices.add (new Integer (-1)); +for (var k = i + 1; k <= j; k++) { +indices.add (new Integer (k)); +} +for (var k, $k = indices.iterator (); $k.hasNext () && ((k = $k.next ()) || true);) { +if (k == -1) { +if (tab[i][j] == tab[i + 1][j]) { +result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, j); +}} else { +if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) { +var fact1 = 0; +if (k > i + 1) { +fact1 = tab[i + 1][k - 1]; +}var fact2 = 0; +if (k < j) { +fact2 = tab[k + 1][j]; +}if (tab[i][j] == jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2) { +result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, k - 1); +result.addAll (jalview.analysis.SecStrConsensus.backtrack (tab, seq, k + 1, j)); +result.add ( new jalview.analysis.SecStrConsensus.SimpleBP (i, k)); +}}}} +} else if (i == j) { +} else { +}return result; +}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList,~N,~N"); +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.bp5 = 0; +this.bp3 = 0; +Clazz.instantialize (this, arguments); +}, jalview.analysis.SecStrConsensus, "SimpleBP"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (a, b) { +this.bp5 = a; +this.bp3 = b; +}, "~N,~N"); +Clazz.defineMethod (c$, "setBP5", +function (a) { +this.bp5 = a; +}, "~N"); +Clazz.defineMethod (c$, "setBP3", +function (a) { +this.bp3 = a; +}, "~N"); +Clazz.defineMethod (c$, "getBP5", +function () { +return this.bp5; +}); +Clazz.defineMethod (c$, "getBP3", +function () { +return this.bp3; +}); +Clazz.overrideMethod (c$, "toString", +function () { +return "(" + this.bp5 + "," + this.bp3 + ")"; +}); +c$ = Clazz.p0p (); +}); diff --git a/bin/jalview/analysis/SeqsetUtils.js b/bin/jalview/analysis/SeqsetUtils.js index a93fedd..f8914e1 100644 --- a/bin/jalview/analysis/SeqsetUtils.js +++ b/bin/jalview/analysis/SeqsetUtils.js @@ -1,124 +1,124 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.SeqsetUtils", ["jalview.analysis.AlignSeq", "$.SequenceIdMatcher", "jalview.datamodel.Sequence", "jalview.util.Comparison", "java.util.Hashtable", "$.Vector"], function () { -c$ = Clazz.declareType (jalview.analysis, "SeqsetUtils"); -c$.SeqCharacterHash = Clazz.defineMethod (c$, "SeqCharacterHash", -function (seq) { -var sqinfo = new java.util.Hashtable (); -sqinfo.put ("Name", seq.getName ()); -sqinfo.put ("Start", new Integer (seq.getStart ())); -sqinfo.put ("End", new Integer (seq.getEnd ())); -if (seq.getDescription () != null) { -sqinfo.put ("Description", seq.getDescription ()); -}var sfeat = new java.util.Vector (); -var sfarray = seq.getSequenceFeatures (); -if (sfarray != null && sfarray.length > 0) { -for (var i = 0; i < sfarray.length; i++) { -sfeat.addElement (sfarray[i]); -} -}sqinfo.put ("SeqFeatures", sfeat); -sqinfo.put ("PdbId", (seq.getPDBId () != null) ? seq.getPDBId () : new java.util.Vector ()); -sqinfo.put ("datasetSequence", (seq.getDatasetSequence () != null) ? seq.getDatasetSequence () : new jalview.datamodel.Sequence ("THISISAPLACEHOLDER", "")); -return sqinfo; -}, "jalview.datamodel.SequenceI"); -c$.SeqCharacterUnhash = Clazz.defineMethod (c$, "SeqCharacterUnhash", -function (sq, sqinfo) { -var namePresent = true; -if (sqinfo == null) { -return false; -}var oldname = sqinfo.get ("Name"); -var start = sqinfo.get ("Start"); -var end = sqinfo.get ("End"); -var sfeatures = sqinfo.get ("SeqFeatures"); -var pdbid = sqinfo.get ("PdbId"); -var description = sqinfo.get ("Description"); -var seqds = sqinfo.get ("datasetSequence"); -if (oldname == null) { -namePresent = false; -} else { -sq.setName (oldname); -}if (pdbid != null && pdbid.size () > 0) { -sq.setPDBId (pdbid); -}if ((start != null) && (end != null)) { -sq.setStart (start.intValue ()); -sq.setEnd (end.intValue ()); -}if ((sfeatures != null) && (sfeatures.size () > 0)) { -var sfarray = new Array (sfeatures.size ()); -for (var is = 0, isize = sfeatures.size (); is < isize; is++) { -sfarray[is] = sfeatures.elementAt (is); -} -sq.setSequenceFeatures (sfarray); -}if (description != null) { -sq.setDescription (description); -}if ((seqds != null) && !(seqds.getName ().equals ("THISISAPLACEHOLDER") && seqds.getLength () == 0)) { -sq.setDatasetSequence (seqds); -}return namePresent; -}, "jalview.datamodel.SequenceI,java.util.Hashtable"); -c$.unique_name = Clazz.defineMethod (c$, "unique_name", -function (i) { -return String.instantialize ("Sequence" + i); -}, "~N"); -c$.uniquify = Clazz.defineMethod (c$, "uniquify", -function (sequences, write_names) { -var map = new java.util.Hashtable (); -for (var i = 0; i < sequences.length; i++) { -var safename = jalview.analysis.SeqsetUtils.unique_name (i); -map.put (safename, jalview.analysis.SeqsetUtils.SeqCharacterHash (sequences[i])); -if (write_names) { -sequences[i].setName (safename); -}} -return map; -}, "~A,~B"); -c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", -function (map, sequences) { -return jalview.analysis.SeqsetUtils.deuniquify (map, sequences, true); -}, "java.util.Hashtable,~A"); -c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", -function (map, sequences, quiet) { -var matcher = new jalview.analysis.SequenceIdMatcher (sequences); -var msq = null; -var keys = map.keys (); -var unmatched = new java.util.Vector (); -for (var i = 0, j = sequences.length; i < j; i++) { -unmatched.addElement (sequences[i]); -} -while (keys.hasMoreElements ()) { -var key = keys.nextElement (); -if (Clazz.instanceOf (key, String)) { -if ((msq = matcher.findIdMatch (key)) != null) { -var sqinfo = map.get (key); -unmatched.removeElement (msq); -jalview.analysis.SeqsetUtils.SeqCharacterUnhash (msq, sqinfo); -} else { -if (!quiet) { -System.err.println ("Can't find '" + (key) + "' in uniquified alignment"); -}}}} -if (unmatched.size () > 0 && !quiet) { -System.err.println ("Did not find matches for :"); -for (var i = unmatched.elements (); i.hasMoreElements (); System.out.println ((i.nextElement ()).getName ())) { -;} -return false; -}return true; -}, "java.util.Hashtable,~A,~B"); -c$.getNonEmptySequenceSet = Clazz.defineMethod (c$, "getNonEmptySequenceSet", -function (sequences) { -var ungapped = Clazz.newBooleanArray (sequences.length, false); -var msflen = 0; -for (var i = 0, j = sequences.length; i < j; i++) { -var tempseq = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, sequences[i].getSequenceAsString ()); -if (tempseq.length == 0) { -ungapped[i] = false; -} else { -ungapped[i] = true; -msflen++; -}} -if (msflen == 0) { -return null; -}var mset = new Array (msflen); -for (var i = 0, j = sequences.length, k = 0; i < j; i++) { -if (ungapped[i]) { -mset[k++] = sequences[i]; -}} -ungapped = null; -return mset; -}, "~A"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.SeqsetUtils", ["jalview.analysis.AlignSeq", "$.SequenceIdMatcher", "jalview.datamodel.Sequence", "jalview.util.Comparison", "java.util.Hashtable", "$.Vector"], function () { +c$ = Clazz.declareType (jalview.analysis, "SeqsetUtils"); +c$.SeqCharacterHash = Clazz.defineMethod (c$, "SeqCharacterHash", +function (seq) { +var sqinfo = new java.util.Hashtable (); +sqinfo.put ("Name", seq.getName ()); +sqinfo.put ("Start", new Integer (seq.getStart ())); +sqinfo.put ("End", new Integer (seq.getEnd ())); +if (seq.getDescription () != null) { +sqinfo.put ("Description", seq.getDescription ()); +}var sfeat = new java.util.Vector (); +var sfarray = seq.getSequenceFeatures (); +if (sfarray != null && sfarray.length > 0) { +for (var i = 0; i < sfarray.length; i++) { +sfeat.addElement (sfarray[i]); +} +}sqinfo.put ("SeqFeatures", sfeat); +sqinfo.put ("PdbId", (seq.getPDBId () != null) ? seq.getPDBId () : new java.util.Vector ()); +sqinfo.put ("datasetSequence", (seq.getDatasetSequence () != null) ? seq.getDatasetSequence () : new jalview.datamodel.Sequence ("THISISAPLACEHOLDER", "")); +return sqinfo; +}, "jalview.datamodel.SequenceI"); +c$.SeqCharacterUnhash = Clazz.defineMethod (c$, "SeqCharacterUnhash", +function (sq, sqinfo) { +var namePresent = true; +if (sqinfo == null) { +return false; +}var oldname = sqinfo.get ("Name"); +var start = sqinfo.get ("Start"); +var end = sqinfo.get ("End"); +var sfeatures = sqinfo.get ("SeqFeatures"); +var pdbid = sqinfo.get ("PdbId"); +var description = sqinfo.get ("Description"); +var seqds = sqinfo.get ("datasetSequence"); +if (oldname == null) { +namePresent = false; +} else { +sq.setName (oldname); +}if (pdbid != null && pdbid.size () > 0) { +sq.setPDBId (pdbid); +}if ((start != null) && (end != null)) { +sq.setStart (start.intValue ()); +sq.setEnd (end.intValue ()); +}if ((sfeatures != null) && (sfeatures.size () > 0)) { +var sfarray = new Array (sfeatures.size ()); +for (var is = 0, isize = sfeatures.size (); is < isize; is++) { +sfarray[is] = sfeatures.elementAt (is); +} +sq.setSequenceFeatures (sfarray); +}if (description != null) { +sq.setDescription (description); +}if ((seqds != null) && !(seqds.getName ().equals ("THISISAPLACEHOLDER") && seqds.getLength () == 0)) { +sq.setDatasetSequence (seqds); +}return namePresent; +}, "jalview.datamodel.SequenceI,java.util.Hashtable"); +c$.unique_name = Clazz.defineMethod (c$, "unique_name", +function (i) { +return String.instantialize ("Sequence" + i); +}, "~N"); +c$.uniquify = Clazz.defineMethod (c$, "uniquify", +function (sequences, write_names) { +var map = new java.util.Hashtable (); +for (var i = 0; i < sequences.length; i++) { +var safename = jalview.analysis.SeqsetUtils.unique_name (i); +map.put (safename, jalview.analysis.SeqsetUtils.SeqCharacterHash (sequences[i])); +if (write_names) { +sequences[i].setName (safename); +}} +return map; +}, "~A,~B"); +c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", +function (map, sequences) { +return jalview.analysis.SeqsetUtils.deuniquify (map, sequences, true); +}, "java.util.Hashtable,~A"); +c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", +function (map, sequences, quiet) { +var matcher = new jalview.analysis.SequenceIdMatcher (sequences); +var msq = null; +var keys = map.keys (); +var unmatched = new java.util.Vector (); +for (var i = 0, j = sequences.length; i < j; i++) { +unmatched.addElement (sequences[i]); +} +while (keys.hasMoreElements ()) { +var key = keys.nextElement (); +if (Clazz.instanceOf (key, String)) { +if ((msq = matcher.findIdMatch (key)) != null) { +var sqinfo = map.get (key); +unmatched.removeElement (msq); +jalview.analysis.SeqsetUtils.SeqCharacterUnhash (msq, sqinfo); +} else { +if (!quiet) { +System.err.println ("Can't find '" + (key) + "' in uniquified alignment"); +}}}} +if (unmatched.size () > 0 && !quiet) { +System.err.println ("Did not find matches for :"); +for (var i = unmatched.elements (); i.hasMoreElements (); System.out.println ((i.nextElement ()).getName ())) { +;} +return false; +}return true; +}, "java.util.Hashtable,~A,~B"); +c$.getNonEmptySequenceSet = Clazz.defineMethod (c$, "getNonEmptySequenceSet", +function (sequences) { +var ungapped = Clazz.newBooleanArray (sequences.length, false); +var msflen = 0; +for (var i = 0, j = sequences.length; i < j; i++) { +var tempseq = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, sequences[i].getSequenceAsString ()); +if (tempseq.length == 0) { +ungapped[i] = false; +} else { +ungapped[i] = true; +msflen++; +}} +if (msflen == 0) { +return null; +}var mset = new Array (msflen); +for (var i = 0, j = sequences.length, k = 0; i < j; i++) { +if (ungapped[i]) { +mset[k++] = sequences[i]; +}} +ungapped = null; +return mset; +}, "~A"); +}); diff --git a/bin/jalview/analysis/SequenceIdMatcher$SeqIdName.class b/bin/jalview/analysis/SequenceIdMatcher$SeqIdName.class index 1735f8a..58766c1 100644 Binary files a/bin/jalview/analysis/SequenceIdMatcher$SeqIdName.class and b/bin/jalview/analysis/SequenceIdMatcher$SeqIdName.class differ diff --git a/bin/jalview/analysis/SequenceIdMatcher.js b/bin/jalview/analysis/SequenceIdMatcher.js index 6e94b5f..adb0a5a 100644 --- a/bin/jalview/analysis/SequenceIdMatcher.js +++ b/bin/jalview/analysis/SequenceIdMatcher.js @@ -1,167 +1,167 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.SequenceIdMatcher", ["java.util.ArrayList", "$.Arrays", "$.HashMap", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.names = null; -if (!Clazz.isClassDefined ("jalview.analysis.SequenceIdMatcher.SeqIdName")) { -jalview.analysis.SequenceIdMatcher.$SequenceIdMatcher$SeqIdName$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.analysis, "SequenceIdMatcher"); -Clazz.makeConstructor (c$, -function (seqs) { -this.names = new java.util.HashMap (); -this.addAll (seqs); -}, "java.util.List"); -Clazz.defineMethod (c$, "addAll", -function (seqs) { -for (var seq, $seq = seqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -this.names.put (Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seq.getDisplayId (true)), seq); -var dbseq = seq; -while (dbseq.getDatasetSequence () != null) { -dbseq = dbseq.getDatasetSequence (); -} -if (dbseq.getDBRef () != null) { -var dbr = dbseq.getDBRef (); -var sid = null; -for (var r = 0; r < dbr.length; r++) { -sid = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, dbr[r].getAccessionId ()); -if (!this.names.containsKey (sid)) { -this.names.put (sid, seq); -}} -}} -}, "java.util.List"); -Clazz.makeConstructor (c$, -function (sequences) { -this.construct (java.util.Arrays.asList (sequences)); -}, "~A"); -Clazz.defineMethod (c$, "pickbestMatch", -($fz = function (candName, matches) { -var st = this.pickbestMatches (candName, matches); -return st == null || st.size () == 0 ? null : st.get (0); -}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List"); -Clazz.defineMethod (c$, "pickbestMatches", -($fz = function (candName, matches) { -var best = new java.util.ArrayList (); -if (candName == null || matches == null || matches.size () == 0) { -return null; -}var match = matches.remove (0); -best.add (match); -this.names.put (Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, match.getName ()), match); -var matchlen = match.getName ().length; -var namlen = candName.id.length; -while (matches.size () > 0) { -var cand = matches.remove (0); -this.names.put (Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, cand.getName ()), cand); -var q; -var w; -var candlen = cand.getName ().length; -if ((q = Math.abs (matchlen - namlen)) > (w = Math.abs (candlen - namlen)) && candlen > matchlen) { -best.clear (); -match = cand; -matchlen = candlen; -best.add (match); -}if (q == w && candlen == matchlen) { -best.add (cand); -}} -if (best.size () == 0) { -return null; -};return best; -}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List"); -Clazz.defineMethod (c$, "findIdMatch", -function (seq) { -var nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seq.getName ()); -return this.findIdMatch (nam); -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "findIdMatch", -function (seqnam) { -var nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seqnam); -return this.findIdMatch (nam); -}, "~S"); -Clazz.defineMethod (c$, "findAllIdMatches", -function (seqnam) { -var nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seqnam); -var m = this.findAllIdMatches (nam); -if (m != null) { -return m.toArray ( new Array (m.size ())); -}return null; -}, "~S"); -Clazz.defineMethod (c$, "findIdMatch", -function (seqs) { -var namedseqs = null; -var i = 0; -var nam; -if (seqs.length > 0) { -namedseqs = new Array (seqs.length); -do { -nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seqs[i].getName ()); -if (this.names.containsKey (nam)) { -namedseqs[i] = this.findIdMatch (nam); -} else { -namedseqs[i] = null; -}} while (++i < seqs.length); -}return namedseqs; -}, "~A"); -Clazz.defineMethod (c$, "findIdMatch", -($fz = function (nam) { -var matches = new java.util.Vector (); -while (this.names.containsKey (nam)) { -matches.addElement (this.names.remove (nam)); -} -return this.pickbestMatch (nam, matches); -}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName"); -Clazz.defineMethod (c$, "findAllIdMatches", -($fz = function (nam) { -var matches = new java.util.ArrayList (); -while (this.names.containsKey (nam)) { -matches.add (this.names.remove (nam)); -} -var r = this.pickbestMatches (nam, matches); -return r; -}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName"); -c$.$SequenceIdMatcher$SeqIdName$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.id = null; -this.WORD_SEP = "~. |#\\/<>!\"\u00a4$%^*)}[@\',?_"; -Clazz.instantialize (this, arguments); -}, jalview.analysis.SequenceIdMatcher, "SeqIdName"); -Clazz.makeConstructor (c$, -function (a) { -if (a != null) { -this.id = String.instantialize (a); -} else { -this.id = ""; -}}, "~S"); -Clazz.overrideMethod (c$, "hashCode", -function () { -return ((this.id.length >= 4) ? this.id.substring (0, 4).hashCode () : this.id.hashCode ()); -}); -Clazz.defineMethod (c$, "equals", -function (a) { -if (a == null) { -return false; -}if (Clazz.instanceOf (a, jalview.analysis.SequenceIdMatcher.SeqIdName)) { -return this.equals (a); -} else { -if (Clazz.instanceOf (a, String)) { -return this.equals (a); -}}return false; -}, "~O"); -Clazz.defineMethod (c$, "equals", -function (a) { -if (this.id.length > a.id.length) { -return this.id.startsWith (a.id) ? (this.WORD_SEP.indexOf (this.id.charAt (a.id.length)) > -1) : false; -} else { -return a.id.startsWith (this.id) ? (a.id.equals (this.id) ? true : (this.WORD_SEP.indexOf (a.id.charAt (this.id.length)) > -1)) : false; -}}, "jalview.analysis.SequenceIdMatcher.SeqIdName"); -Clazz.defineMethod (c$, "equals", -function (a) { -if (this.id.length > a.length) { -return this.id.startsWith (a) ? (this.WORD_SEP.indexOf (this.id.charAt (a.length)) > -1) : false; -} else { -return a.startsWith (this.id) ? (a.equals (this.id) ? true : (this.WORD_SEP.indexOf (a.charAt (this.id.length)) > -1)) : false; -}}, "~S"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.SequenceIdMatcher", ["java.util.ArrayList", "$.Arrays", "$.HashMap", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.names = null; +if (!Clazz.isClassDefined ("jalview.analysis.SequenceIdMatcher.SeqIdName")) { +jalview.analysis.SequenceIdMatcher.$SequenceIdMatcher$SeqIdName$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.analysis, "SequenceIdMatcher"); +Clazz.makeConstructor (c$, +function (seqs) { +this.names = new java.util.HashMap (); +this.addAll (seqs); +}, "java.util.List"); +Clazz.defineMethod (c$, "addAll", +function (seqs) { +for (var seq, $seq = seqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +this.names.put (Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seq.getDisplayId (true)), seq); +var dbseq = seq; +while (dbseq.getDatasetSequence () != null) { +dbseq = dbseq.getDatasetSequence (); +} +if (dbseq.getDBRef () != null) { +var dbr = dbseq.getDBRef (); +var sid = null; +for (var r = 0; r < dbr.length; r++) { +sid = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, dbr[r].getAccessionId ()); +if (!this.names.containsKey (sid)) { +this.names.put (sid, seq); +}} +}} +}, "java.util.List"); +Clazz.makeConstructor (c$, +function (sequences) { +this.construct (java.util.Arrays.asList (sequences)); +}, "~A"); +Clazz.defineMethod (c$, "pickbestMatch", +($fz = function (candName, matches) { +var st = this.pickbestMatches (candName, matches); +return st == null || st.size () == 0 ? null : st.get (0); +}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List"); +Clazz.defineMethod (c$, "pickbestMatches", +($fz = function (candName, matches) { +var best = new java.util.ArrayList (); +if (candName == null || matches == null || matches.size () == 0) { +return null; +}var match = matches.remove (0); +best.add (match); +this.names.put (Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, match.getName ()), match); +var matchlen = match.getName ().length; +var namlen = candName.id.length; +while (matches.size () > 0) { +var cand = matches.remove (0); +this.names.put (Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, cand.getName ()), cand); +var q; +var w; +var candlen = cand.getName ().length; +if ((q = Math.abs (matchlen - namlen)) > (w = Math.abs (candlen - namlen)) && candlen > matchlen) { +best.clear (); +match = cand; +matchlen = candlen; +best.add (match); +}if (q == w && candlen == matchlen) { +best.add (cand); +}} +if (best.size () == 0) { +return null; +};return best; +}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List"); +Clazz.defineMethod (c$, "findIdMatch", +function (seq) { +var nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seq.getName ()); +return this.findIdMatch (nam); +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "findIdMatch", +function (seqnam) { +var nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seqnam); +return this.findIdMatch (nam); +}, "~S"); +Clazz.defineMethod (c$, "findAllIdMatches", +function (seqnam) { +var nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seqnam); +var m = this.findAllIdMatches (nam); +if (m != null) { +return m.toArray ( new Array (m.size ())); +}return null; +}, "~S"); +Clazz.defineMethod (c$, "findIdMatch", +function (seqs) { +var namedseqs = null; +var i = 0; +var nam; +if (seqs.length > 0) { +namedseqs = new Array (seqs.length); +do { +nam = Clazz.innerTypeInstance (jalview.analysis.SequenceIdMatcher.SeqIdName, this, null, seqs[i].getName ()); +if (this.names.containsKey (nam)) { +namedseqs[i] = this.findIdMatch (nam); +} else { +namedseqs[i] = null; +}} while (++i < seqs.length); +}return namedseqs; +}, "~A"); +Clazz.defineMethod (c$, "findIdMatch", +($fz = function (nam) { +var matches = new java.util.Vector (); +while (this.names.containsKey (nam)) { +matches.addElement (this.names.remove (nam)); +} +return this.pickbestMatch (nam, matches); +}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName"); +Clazz.defineMethod (c$, "findAllIdMatches", +($fz = function (nam) { +var matches = new java.util.ArrayList (); +while (this.names.containsKey (nam)) { +matches.add (this.names.remove (nam)); +} +var r = this.pickbestMatches (nam, matches); +return r; +}, $fz.isPrivate = true, $fz), "jalview.analysis.SequenceIdMatcher.SeqIdName"); +c$.$SequenceIdMatcher$SeqIdName$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.id = null; +this.WORD_SEP = "~. |#\\/<>!\"\u00a4$%^*)}[@\',?_"; +Clazz.instantialize (this, arguments); +}, jalview.analysis.SequenceIdMatcher, "SeqIdName"); +Clazz.makeConstructor (c$, +function (a) { +if (a != null) { +this.id = String.instantialize (a); +} else { +this.id = ""; +}}, "~S"); +Clazz.overrideMethod (c$, "hashCode", +function () { +return ((this.id.length >= 4) ? this.id.substring (0, 4).hashCode () : this.id.hashCode ()); +}); +Clazz.defineMethod (c$, "equals", +function (a) { +if (a == null) { +return false; +}if (Clazz.instanceOf (a, jalview.analysis.SequenceIdMatcher.SeqIdName)) { +return this.equals (a); +} else { +if (Clazz.instanceOf (a, String)) { +return this.equals (a); +}}return false; +}, "~O"); +Clazz.defineMethod (c$, "equals", +function (a) { +if (this.id.length > a.id.length) { +return this.id.startsWith (a.id) ? (this.WORD_SEP.indexOf (this.id.charAt (a.id.length)) > -1) : false; +} else { +return a.id.startsWith (this.id) ? (a.id.equals (this.id) ? true : (this.WORD_SEP.indexOf (a.id.charAt (this.id.length)) > -1)) : false; +}}, "jalview.analysis.SequenceIdMatcher.SeqIdName"); +Clazz.defineMethod (c$, "equals", +function (a) { +if (this.id.length > a.length) { +return this.id.startsWith (a) ? (this.WORD_SEP.indexOf (this.id.charAt (a.length)) > -1) : false; +} else { +return a.startsWith (this.id) ? (a.equals (this.id) ? true : (this.WORD_SEP.indexOf (a.charAt (this.id.length)) > -1)) : false; +}}, "~S"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/analysis/StructureFrequency.class b/bin/jalview/analysis/StructureFrequency.class index 8b6d9eb..f7f3fc4 100644 Binary files a/bin/jalview/analysis/StructureFrequency.class and b/bin/jalview/analysis/StructureFrequency.class differ diff --git a/bin/jalview/analysis/StructureFrequency.js b/bin/jalview/analysis/StructureFrequency.js index 6c90b65..83c8f02 100644 --- a/bin/jalview/analysis/StructureFrequency.js +++ b/bin/jalview/analysis/StructureFrequency.js @@ -1,260 +1,260 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (null, "jalview.analysis.StructureFrequency", ["jalview.datamodel.Annotation", "jalview.util.Format", "$.QuickSort", "java.lang.Float", "java.util.Hashtable", "javajs.util.AU"], function () { -c$ = Clazz.declareType (jalview.analysis, "StructureFrequency"); -c$.findPair = Clazz.defineMethod (c$, "findPair", -function (pairs, indice) { -for (var i = 0; i < pairs.length; i++) { -if (pairs[i].getBegin () == indice) { -return pairs[i].getEnd (); -}} -return -1; -}, "~A,~N"); -c$.calculate = Clazz.defineMethod (c$, "calculate", -function (sequences, start, end, result, profile, rnaStruc) { -var residueHash; -var maxResidue; -var struc = rnaStruc.getRNAStruc ().toCharArray (); -var rna = rnaStruc._rnasecstr; -var c; -var s; -var cEnd; -var count = 0; -var nonGap = 0; -var i; -var bpEnd = -1; -var j; -var jSize = sequences.length; -var values; -var pairs; -var percentage; -var wooble = true; -for (i = start; i < end; i++) { -residueHash = new java.util.Hashtable (); -maxResidue = "-"; -values = Clazz.newIntArray (255, 0); -pairs = Clazz.newIntArray (255, 255, 0); -bpEnd = -1; -if (i < struc.length) { -s = struc[i]; -} else { -s = '-'; -}if (s == '.' || s == ' ') { -s = '-'; -}if (s != '(' && s != '[') { -if (s == '-') { -values['-'.charCodeAt (0)]++; -}} else { -bpEnd = jalview.analysis.StructureFrequency.findPair (rna, i); -if (bpEnd > -1) { -for (j = 0; j < jSize; j++) { -if (sequences[j] == null) { -System.err.println ("WARNING: Consensus skipping null sequence - possible race condition."); -continue; -}c = sequences[j].getCharAt (i); -if (c == '.' || c == ' ') { -c = '-'; -}if (c == '-') { -values['-'.charCodeAt (0)]++; -continue; -}cEnd = sequences[j].getCharAt (bpEnd); -if (jalview.analysis.StructureFrequency.checkBpType (c, cEnd) == true) { -values['('.charCodeAt (0)]++; -maxResidue = "("; -wooble = true; -}if (jalview.analysis.StructureFrequency.checkBpType (c, cEnd) == false) { -wooble = false; -values['['.charCodeAt (0)]++; -maxResidue = "["; -}pairs[c.charCodeAt (0)][cEnd.charCodeAt (0)]++; -} -}}if (profile) { -residueHash.put ("P", Clazz.newArray (-1, [values, Clazz.newIntArray (-1, [jSize, (jSize - values['-'.charCodeAt (0)])])])); -residueHash.put ("B", pairs); -}if (wooble == true) { -count = values['('.charCodeAt (0)]; -}if (wooble == false) { -count = values['['.charCodeAt (0)]; -}residueHash.put ("C", new Integer (count)); -residueHash.put ("R", maxResidue); -percentage = (count * 100) / jSize; -residueHash.put ("G", new Float (percentage)); -if (result[i] == null) { -result[i] = residueHash; -}if (bpEnd > 0) { -values[')'.charCodeAt (0)] = values['('.charCodeAt (0)]; -values[']'.charCodeAt (0)] = values['['.charCodeAt (0)]; -values['('.charCodeAt (0)] = 0; -values['['.charCodeAt (0)] = 0; -residueHash = new java.util.Hashtable (); -if (wooble == true) { -maxResidue = ")"; -}if (wooble == false) { -maxResidue = "]"; -}if (profile) { -residueHash.put ("P", Clazz.newArray (-1, [values, Clazz.newIntArray (-1, [jSize, (jSize - values['-'.charCodeAt (0)])])])); -residueHash.put ("B", pairs); -}residueHash.put ("C", new Integer (count)); -residueHash.put ("R", maxResidue); -percentage = (count * 100) / jSize; -residueHash.put ("G", new Float (percentage)); -result[bpEnd] = residueHash; -}} -}, "~A,~N,~N,~A,~B,jalview.datamodel.AlignmentAnnotation"); -c$.checkBpType = Clazz.defineMethod (c$, "checkBpType", -function (up, down) { -if (up > 'Z') { -up = String.fromCharCode (up.charCodeAt (0) - 32); -}if (down > 'Z') { -down = String.fromCharCode (down.charCodeAt (0) - 32); -}switch (up) { -case 'A': -switch (down) { -case 'T': -return true; -case 'U': -return true; -} -break; -case 'C': -switch (down) { -case 'G': -return true; -} -break; -case 'T': -switch (down) { -case 'A': -return true; -case 'G': -return true; -} -break; -case 'G': -switch (down) { -case 'C': -return true; -case 'T': -return true; -case 'U': -return true; -} -break; -case 'U': -switch (down) { -case 'A': -return true; -case 'G': -return true; -} -break; -} -return false; -}, "~S,~S"); -c$.completeConsensus = Clazz.defineMethod (c$, "completeConsensus", -function (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, nseq) { -var tval; -var value; -if (consensus == null || consensus.annotations == null || consensus.annotations.length < width) { -return; -}var fmtstr = "%3.1f"; -var precision = 2; -while (nseq > 100) { -precision++; -nseq /= 10; -} -if (precision > 2) { -fmtstr = "%" + (2 + precision) + "." + precision + "f"; -}var fmt = new jalview.util.Format (fmtstr); -for (var i = iStart; i < width; i++) { -var hci; -if (i >= hconsensus.length || ((hci = hconsensus[i]) == null)) { -consensus.annotations[i] = null; -continue; -}value = 0; -var fv; -if (ignoreGapsInConsensusCalculation) { -fv = hci.get ("N"); -} else { -fv = hci.get ("G"); -}if (fv == null) { -consensus.annotations[i] = null; -continue; -}value = fv.floatValue (); -var maxRes = hci.get ("R").toString (); -var mouseOver = hci.get ("R") + " "; -if (maxRes.length > 1) { -mouseOver = "[" + maxRes + "] "; -maxRes = "+"; -}var profile = hci.get ("P"); -var pairs = hci.get ("B"); -if (pairs != null && includeAllConsSymbols) { -mouseOver = ""; -var ca = javajs.util.AU.newInt2 (625); -var vl = Clazz.newFloatArray (625, 0); -var x = 0; -for (var c = 65; c < 90; c++) { -for (var d = 65; d < 90; d++) { -ca[x] = Clazz.newIntArray (-1, [c, d]); -vl[x] = pairs[c][d]; -x++; -} -} -jalview.util.QuickSort.sortFloatObject (vl, ca); -var p = 0; -var divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; -for (var c = 624; c > 0; c--) { -if (vl[c] > 0) { -tval = (vl[c] * 100 / divisor); -mouseOver += ((p == 0) ? "" : "; ") + String.fromCharCode (ca[c][0]) + String.fromCharCode (ca[c][1]) + " " + fmt.formDouble (tval) + "%"; -p++; -}} -} else { -mouseOver += (fmt.formDouble (value) + "%"); -}consensus.annotations[i] = new jalview.datamodel.Annotation (maxRes, mouseOver, ' ', value); -} -}, "jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~N"); -c$.extractProfile = Clazz.defineMethod (c$, "extractProfile", -function (hconsensus, ignoreGapsInConsensusCalculation) { -var rtnval = Clazz.newIntArray (74, 0); -var profile = hconsensus.get ("P"); -var pairs = hconsensus.get ("B"); -if (profile == null) { -return null; -}var ca = javajs.util.AU.newInt2 (625); -var vl = Clazz.newFloatArray (625, 0); -var x = 0; -for (var c = 65; c < 90; c++) { -for (var d = 65; d < 90; d++) { -ca[x] = Clazz.newIntArray (-1, [c, d]); -vl[x] = pairs[c][d]; -x++; -} -} -jalview.util.QuickSort.sortFloatObject (vl, ca); -var valuesCount = 0; -rtnval[1] = 0; -var offset = 2; -var divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; -for (var c = 624; c > 0; c--) { -if (vl[c] > 0) { -rtnval[offset++] = ca[c][0]; -rtnval[offset++] = ca[c][1]; -rtnval[offset] = Clazz.floatToInt (vl[c] * 100 / divisor); -rtnval[1] += rtnval[offset++]; -valuesCount++; -}} -rtnval[0] = valuesCount; -var result = Clazz.newIntArray (rtnval.length + 1, 0); -result[0] = 1; -System.arraycopy (rtnval, 0, result, 1, rtnval.length); -return result; -}, "java.util.Hashtable,~B"); -Clazz.defineStatics (c$, -"STRUCTURE_PROFILE_LENGTH", 74, -"MAXCOUNT", "C", -"MAXRESIDUE", "R", -"PID_GAPS", "G", -"PID_NOGAPS", "N", -"PROFILE", "P", -"PAIRPROFILE", "B"); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (null, "jalview.analysis.StructureFrequency", ["jalview.datamodel.Annotation", "jalview.util.Format", "$.QuickSort", "java.lang.Float", "java.util.Hashtable", "javajs.util.AU"], function () { +c$ = Clazz.declareType (jalview.analysis, "StructureFrequency"); +c$.findPair = Clazz.defineMethod (c$, "findPair", +function (pairs, indice) { +for (var i = 0; i < pairs.length; i++) { +if (pairs[i].getBegin () == indice) { +return pairs[i].getEnd (); +}} +return -1; +}, "~A,~N"); +c$.calculate = Clazz.defineMethod (c$, "calculate", +function (sequences, start, end, result, profile, rnaStruc) { +var residueHash; +var maxResidue; +var struc = rnaStruc.getRNAStruc ().toCharArray (); +var rna = rnaStruc._rnasecstr; +var c; +var s; +var cEnd; +var count = 0; +var nonGap = 0; +var i; +var bpEnd = -1; +var j; +var jSize = sequences.length; +var values; +var pairs; +var percentage; +var wooble = true; +for (i = start; i < end; i++) { +residueHash = new java.util.Hashtable (); +maxResidue = "-"; +values = Clazz.newIntArray (255, 0); +pairs = Clazz.newIntArray (255, 255, 0); +bpEnd = -1; +if (i < struc.length) { +s = struc[i]; +} else { +s = '-'; +}if (s == '.' || s == ' ') { +s = '-'; +}if (s != '(' && s != '[') { +if (s == '-') { +values['-'.charCodeAt (0)]++; +}} else { +bpEnd = jalview.analysis.StructureFrequency.findPair (rna, i); +if (bpEnd > -1) { +for (j = 0; j < jSize; j++) { +if (sequences[j] == null) { +System.err.println ("WARNING: Consensus skipping null sequence - possible race condition."); +continue; +}c = sequences[j].getCharAt (i); +if (c == '.' || c == ' ') { +c = '-'; +}if (c == '-') { +values['-'.charCodeAt (0)]++; +continue; +}cEnd = sequences[j].getCharAt (bpEnd); +if (jalview.analysis.StructureFrequency.checkBpType (c, cEnd) == true) { +values['('.charCodeAt (0)]++; +maxResidue = "("; +wooble = true; +}if (jalview.analysis.StructureFrequency.checkBpType (c, cEnd) == false) { +wooble = false; +values['['.charCodeAt (0)]++; +maxResidue = "["; +}pairs[c.charCodeAt (0)][cEnd.charCodeAt (0)]++; +} +}}if (profile) { +residueHash.put ("P", Clazz.newArray (-1, [values, Clazz.newIntArray (-1, [jSize, (jSize - values['-'.charCodeAt (0)])])])); +residueHash.put ("B", pairs); +}if (wooble == true) { +count = values['('.charCodeAt (0)]; +}if (wooble == false) { +count = values['['.charCodeAt (0)]; +}residueHash.put ("C", new Integer (count)); +residueHash.put ("R", maxResidue); +percentage = (count * 100) / jSize; +residueHash.put ("G", new Float (percentage)); +if (result[i] == null) { +result[i] = residueHash; +}if (bpEnd > 0) { +values[')'.charCodeAt (0)] = values['('.charCodeAt (0)]; +values[']'.charCodeAt (0)] = values['['.charCodeAt (0)]; +values['('.charCodeAt (0)] = 0; +values['['.charCodeAt (0)] = 0; +residueHash = new java.util.Hashtable (); +if (wooble == true) { +maxResidue = ")"; +}if (wooble == false) { +maxResidue = "]"; +}if (profile) { +residueHash.put ("P", Clazz.newArray (-1, [values, Clazz.newIntArray (-1, [jSize, (jSize - values['-'.charCodeAt (0)])])])); +residueHash.put ("B", pairs); +}residueHash.put ("C", new Integer (count)); +residueHash.put ("R", maxResidue); +percentage = (count * 100) / jSize; +residueHash.put ("G", new Float (percentage)); +result[bpEnd] = residueHash; +}} +}, "~A,~N,~N,~A,~B,jalview.datamodel.AlignmentAnnotation"); +c$.checkBpType = Clazz.defineMethod (c$, "checkBpType", +function (up, down) { +if (up > 'Z') { +up = String.fromCharCode (up.charCodeAt (0) - 32); +}if (down > 'Z') { +down = String.fromCharCode (down.charCodeAt (0) - 32); +}switch (up) { +case 'A': +switch (down) { +case 'T': +return true; +case 'U': +return true; +} +break; +case 'C': +switch (down) { +case 'G': +return true; +} +break; +case 'T': +switch (down) { +case 'A': +return true; +case 'G': +return true; +} +break; +case 'G': +switch (down) { +case 'C': +return true; +case 'T': +return true; +case 'U': +return true; +} +break; +case 'U': +switch (down) { +case 'A': +return true; +case 'G': +return true; +} +break; +} +return false; +}, "~S,~S"); +c$.completeConsensus = Clazz.defineMethod (c$, "completeConsensus", +function (consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, nseq) { +var tval; +var value; +if (consensus == null || consensus.annotations == null || consensus.annotations.length < width) { +return; +}var fmtstr = "%3.1f"; +var precision = 2; +while (nseq > 100) { +precision++; +nseq /= 10; +} +if (precision > 2) { +fmtstr = "%" + (2 + precision) + "." + precision + "f"; +}var fmt = new jalview.util.Format (fmtstr); +for (var i = iStart; i < width; i++) { +var hci; +if (i >= hconsensus.length || ((hci = hconsensus[i]) == null)) { +consensus.annotations[i] = null; +continue; +}value = 0; +var fv; +if (ignoreGapsInConsensusCalculation) { +fv = hci.get ("N"); +} else { +fv = hci.get ("G"); +}if (fv == null) { +consensus.annotations[i] = null; +continue; +}value = fv.floatValue (); +var maxRes = hci.get ("R").toString (); +var mouseOver = hci.get ("R") + " "; +if (maxRes.length > 1) { +mouseOver = "[" + maxRes + "] "; +maxRes = "+"; +}var profile = hci.get ("P"); +var pairs = hci.get ("B"); +if (pairs != null && includeAllConsSymbols) { +mouseOver = ""; +var ca = javajs.util.AU.newInt2 (625); +var vl = Clazz.newFloatArray (625, 0); +var x = 0; +for (var c = 65; c < 90; c++) { +for (var d = 65; d < 90; d++) { +ca[x] = Clazz.newIntArray (-1, [c, d]); +vl[x] = pairs[c][d]; +x++; +} +} +jalview.util.QuickSort.sortFloatObject (vl, ca); +var p = 0; +var divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; +for (var c = 624; c > 0; c--) { +if (vl[c] > 0) { +tval = (vl[c] * 100 / divisor); +mouseOver += ((p == 0) ? "" : "; ") + String.fromCharCode (ca[c][0]) + String.fromCharCode (ca[c][1]) + " " + fmt.formDouble (tval) + "%"; +p++; +}} +} else { +mouseOver += (fmt.formDouble (value) + "%"); +}consensus.annotations[i] = new jalview.datamodel.Annotation (maxRes, mouseOver, ' ', value); +} +}, "jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~N"); +c$.extractProfile = Clazz.defineMethod (c$, "extractProfile", +function (hconsensus, ignoreGapsInConsensusCalculation) { +var rtnval = Clazz.newIntArray (74, 0); +var profile = hconsensus.get ("P"); +var pairs = hconsensus.get ("B"); +if (profile == null) { +return null; +}var ca = javajs.util.AU.newInt2 (625); +var vl = Clazz.newFloatArray (625, 0); +var x = 0; +for (var c = 65; c < 90; c++) { +for (var d = 65; d < 90; d++) { +ca[x] = Clazz.newIntArray (-1, [c, d]); +vl[x] = pairs[c][d]; +x++; +} +} +jalview.util.QuickSort.sortFloatObject (vl, ca); +var valuesCount = 0; +rtnval[1] = 0; +var offset = 2; +var divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; +for (var c = 624; c > 0; c--) { +if (vl[c] > 0) { +rtnval[offset++] = ca[c][0]; +rtnval[offset++] = ca[c][1]; +rtnval[offset] = Clazz.floatToInt (vl[c] * 100 / divisor); +rtnval[1] += rtnval[offset++]; +valuesCount++; +}} +rtnval[0] = valuesCount; +var result = Clazz.newIntArray (rtnval.length + 1, 0); +result[0] = 1; +System.arraycopy (rtnval, 0, result, 1, rtnval.length); +return result; +}, "java.util.Hashtable,~B"); +Clazz.defineStatics (c$, +"STRUCTURE_PROFILE_LENGTH", 74, +"MAXCOUNT", "C", +"MAXRESIDUE", "R", +"PID_GAPS", "G", +"PID_NOGAPS", "N", +"PROFILE", "P", +"PAIRPROFILE", "B"); +}); diff --git a/bin/jalview/analysis/WUSSParseException.js b/bin/jalview/analysis/WUSSParseException.js index 535f6ac..32861ff 100644 --- a/bin/jalview/analysis/WUSSParseException.js +++ b/bin/jalview/analysis/WUSSParseException.js @@ -1,20 +1,20 @@ -Clazz.declarePackage ("jalview.analysis"); -Clazz.load (["java.lang.Exception"], "jalview.analysis.WUSSParseException", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.problemPos = 0; -Clazz.instantialize (this, arguments); -}, jalview.analysis, "WUSSParseException", Exception); -Clazz.makeConstructor (c$, -function (problemPos) { -this.construct ("Invalid WUSS Notation", problemPos); -}, "~N"); -Clazz.makeConstructor (c$, -function (message, problemPos) { -Clazz.superConstructor (this, jalview.analysis.WUSSParseException, [message + " at or near position " + problemPos]); -this.problemPos = problemPos; -}, "~S,~N"); -Clazz.defineMethod (c$, "getProblemPos", -function () { -return this.problemPos; -}); -}); +Clazz.declarePackage ("jalview.analysis"); +Clazz.load (["java.lang.Exception"], "jalview.analysis.WUSSParseException", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.problemPos = 0; +Clazz.instantialize (this, arguments); +}, jalview.analysis, "WUSSParseException", Exception); +Clazz.makeConstructor (c$, +function (problemPos) { +this.construct ("Invalid WUSS Notation", problemPos); +}, "~N"); +Clazz.makeConstructor (c$, +function (message, problemPos) { +Clazz.superConstructor (this, jalview.analysis.WUSSParseException, [message + " at or near position " + problemPos]); +this.problemPos = problemPos; +}, "~S,~N"); +Clazz.defineMethod (c$, "getProblemPos", +function () { +return this.problemPos; +}); +}); diff --git a/bin/jalview/analysis/package.js b/bin/jalview/analysis/package.js index 45e0428..a23ac21 100644 --- a/bin/jalview/analysis/package.js +++ b/bin/jalview/analysis/package.js @@ -1,5 +1,5 @@ -var path = ClazzLoader.getClasspathFor ("jalview.analysis.package"); -path = path.substring (0, path.lastIndexOf ("package.js")); -ClazzLoader.jarClasspath (path + "NJTree.js", [ -"jalview.analysis.Cluster", -"$.NJTree"]); +var path = ClazzLoader.getClasspathFor ("jalview.analysis.package"); +path = path.substring (0, path.lastIndexOf ("package.js")); +ClazzLoader.jarClasspath (path + "NJTree.js", [ +"jalview.analysis.Cluster", +"$.NJTree"]); diff --git a/bin/jalview/analysis/scoremodels/FeatureScoreModel.js b/bin/jalview/analysis/scoremodels/FeatureScoreModel.js index 3e8e57d..7e483bd 100644 --- a/bin/jalview/analysis/scoremodels/FeatureScoreModel.js +++ b/bin/jalview/analysis/scoremodels/FeatureScoreModel.js @@ -1,86 +1,86 @@ -Clazz.declarePackage ("jalview.analysis.scoremodels"); -Clazz.load (["jalview.api.analysis.ScoreModelI", "$.ViewBasedAnalysisI"], "jalview.analysis.scoremodels.FeatureScoreModel", ["jalview.util.Comparison", "java.util.ArrayList", "$.Arrays", "$.Hashtable"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fr = null; -Clazz.instantialize (this, arguments); -}, jalview.analysis.scoremodels, "FeatureScoreModel", null, [jalview.api.analysis.ScoreModelI, jalview.api.analysis.ViewBasedAnalysisI]); -Clazz.overrideMethod (c$, "configureFromAlignmentView", -function (view) { -this.fr = view.cloneFeatureRenderer (); -return true; -}, "jalview.api.AlignmentViewPanel"); -Clazz.overrideMethod (c$, "findDistances", -function (seqData) { -var nofeats = 0; -var dft = java.util.Arrays.asList (this.fr.getDisplayedFeatureTypes ()); -if (dft != null) { -nofeats = dft.size (); -}var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray (); -var noseqs = sequenceString.length; -var cpwidth = seqData.getWidth (); -var distance = Clazz.newFloatArray (noseqs, noseqs, 0); -if (nofeats == 0) { -for (var d, $d = 0, $$d = distance; $d < $$d.length && ((d = $$d[$d]) || true); $d++) { -for (var i = 0; i < d.length; d[i++] = 0) { -;} -} -return distance; -}var max = 0; -for (var cpos = 0; cpos < cpwidth; cpos++) { -var sfap = new java.util.ArrayList (); -for (var i = 0; i < noseqs; i++) { -var types = new java.util.Hashtable (); -var sfs = this.fr.findFeaturesAtRes (sequenceString[i], sequenceString[i].findPosition (cpos)); -for (var sf, $sf = sfs.iterator (); $sf.hasNext () && ((sf = $sf.next ()) || true);) { -types.put (sf.getType (), sf); -} -sfap.add (types); -} -for (var i = 0; i < (noseqs - 1); i++) { -if (cpos == 0) { -distance[i][i] = 0; -}for (var j = i + 1; j < noseqs; j++) { -var sfcommon = 0; -var fi = sfap.get (i); -var fk; -var fj = sfap.get (j); -if (fi.size () > fj.size ()) { -fk = fj; -} else { -fk = fi; -fi = fj; -}for (var k, $k = fi.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) { -var sfj = fk.get (k); -if (sfj != null) { -sfcommon++; -}} -distance[i][j] += (fi.size () + fk.size () - 2 * sfcommon); -distance[j][i] += distance[i][j]; -} -} -} -for (var i = 0; i < noseqs; i++) { -for (var j = i + 1; j < noseqs; j++) { -distance[i][j] /= cpwidth; -distance[j][i] = distance[i][j]; -} -} -return distance; -}, "jalview.datamodel.AlignmentView"); -Clazz.overrideMethod (c$, "getName", -function () { -return "Sequence Feature Similarity"; -}); -Clazz.overrideMethod (c$, "isDNA", -function () { -return true; -}); -Clazz.overrideMethod (c$, "isProtein", -function () { -return true; -}); -Clazz.overrideMethod (c$, "toString", -function () { -return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column"; -}); -}); +Clazz.declarePackage ("jalview.analysis.scoremodels"); +Clazz.load (["jalview.api.analysis.ScoreModelI", "$.ViewBasedAnalysisI"], "jalview.analysis.scoremodels.FeatureScoreModel", ["jalview.util.Comparison", "java.util.ArrayList", "$.Arrays", "$.Hashtable"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fr = null; +Clazz.instantialize (this, arguments); +}, jalview.analysis.scoremodels, "FeatureScoreModel", null, [jalview.api.analysis.ScoreModelI, jalview.api.analysis.ViewBasedAnalysisI]); +Clazz.overrideMethod (c$, "configureFromAlignmentView", +function (view) { +this.fr = view.cloneFeatureRenderer (); +return true; +}, "jalview.api.AlignmentViewPanel"); +Clazz.overrideMethod (c$, "findDistances", +function (seqData) { +var nofeats = 0; +var dft = java.util.Arrays.asList (this.fr.getDisplayedFeatureTypes ()); +if (dft != null) { +nofeats = dft.size (); +}var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray (); +var noseqs = sequenceString.length; +var cpwidth = seqData.getWidth (); +var distance = Clazz.newFloatArray (noseqs, noseqs, 0); +if (nofeats == 0) { +for (var d, $d = 0, $$d = distance; $d < $$d.length && ((d = $$d[$d]) || true); $d++) { +for (var i = 0; i < d.length; d[i++] = 0) { +;} +} +return distance; +}var max = 0; +for (var cpos = 0; cpos < cpwidth; cpos++) { +var sfap = new java.util.ArrayList (); +for (var i = 0; i < noseqs; i++) { +var types = new java.util.Hashtable (); +var sfs = this.fr.findFeaturesAtRes (sequenceString[i], sequenceString[i].findPosition (cpos)); +for (var sf, $sf = sfs.iterator (); $sf.hasNext () && ((sf = $sf.next ()) || true);) { +types.put (sf.getType (), sf); +} +sfap.add (types); +} +for (var i = 0; i < (noseqs - 1); i++) { +if (cpos == 0) { +distance[i][i] = 0; +}for (var j = i + 1; j < noseqs; j++) { +var sfcommon = 0; +var fi = sfap.get (i); +var fk; +var fj = sfap.get (j); +if (fi.size () > fj.size ()) { +fk = fj; +} else { +fk = fi; +fi = fj; +}for (var k, $k = fi.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) { +var sfj = fk.get (k); +if (sfj != null) { +sfcommon++; +}} +distance[i][j] += (fi.size () + fk.size () - 2 * sfcommon); +distance[j][i] += distance[i][j]; +} +} +} +for (var i = 0; i < noseqs; i++) { +for (var j = i + 1; j < noseqs; j++) { +distance[i][j] /= cpwidth; +distance[j][i] = distance[i][j]; +} +} +return distance; +}, "jalview.datamodel.AlignmentView"); +Clazz.overrideMethod (c$, "getName", +function () { +return "Sequence Feature Similarity"; +}); +Clazz.overrideMethod (c$, "isDNA", +function () { +return true; +}); +Clazz.overrideMethod (c$, "isProtein", +function () { +return true; +}); +Clazz.overrideMethod (c$, "toString", +function () { +return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column"; +}); +}); diff --git a/bin/jalview/analysis/scoremodels/PIDScoreModel.js b/bin/jalview/analysis/scoremodels/PIDScoreModel.js index 0266c33..09c86e5 100644 --- a/bin/jalview/analysis/scoremodels/PIDScoreModel.js +++ b/bin/jalview/analysis/scoremodels/PIDScoreModel.js @@ -1,32 +1,32 @@ -Clazz.declarePackage ("jalview.analysis.scoremodels"); -Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PIDScoreModel", ["jalview.util.Comparison"], function () { -c$ = Clazz.declareType (jalview.analysis.scoremodels, "PIDScoreModel", null, jalview.api.analysis.ScoreModelI); -Clazz.overrideMethod (c$, "findDistances", -function (seqData) { -var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0)); -var noseqs = sequenceString.length; -var distance = Clazz.newFloatArray (noseqs, noseqs, 0); -for (var i = 0; i < (noseqs - 1); i++) { -for (var j = i; j < noseqs; j++) { -if (j == i) { -distance[i][i] = 0; -} else { -distance[i][j] = 100 - jalview.util.Comparison.PID (sequenceString[i], sequenceString[j]); -distance[j][i] = distance[i][j]; -}} -} -return distance; -}, "jalview.datamodel.AlignmentView"); -Clazz.overrideMethod (c$, "getName", -function () { -return "PID"; -}); -Clazz.overrideMethod (c$, "isDNA", -function () { -return true; -}); -Clazz.overrideMethod (c$, "isProtein", -function () { -return true; -}); -}); +Clazz.declarePackage ("jalview.analysis.scoremodels"); +Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PIDScoreModel", ["jalview.util.Comparison"], function () { +c$ = Clazz.declareType (jalview.analysis.scoremodels, "PIDScoreModel", null, jalview.api.analysis.ScoreModelI); +Clazz.overrideMethod (c$, "findDistances", +function (seqData) { +var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0)); +var noseqs = sequenceString.length; +var distance = Clazz.newFloatArray (noseqs, noseqs, 0); +for (var i = 0; i < (noseqs - 1); i++) { +for (var j = i; j < noseqs; j++) { +if (j == i) { +distance[i][i] = 0; +} else { +distance[i][j] = 100 - jalview.util.Comparison.PID (sequenceString[i], sequenceString[j]); +distance[j][i] = distance[i][j]; +}} +} +return distance; +}, "jalview.datamodel.AlignmentView"); +Clazz.overrideMethod (c$, "getName", +function () { +return "PID"; +}); +Clazz.overrideMethod (c$, "isDNA", +function () { +return true; +}); +Clazz.overrideMethod (c$, "isProtein", +function () { +return true; +}); +}); diff --git a/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js b/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js index 6cfe67a..4c1456f 100644 --- a/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js +++ b/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js @@ -1,39 +1,39 @@ -Clazz.declarePackage ("jalview.analysis.scoremodels"); -Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PairwiseSeqScoreModel", ["jalview.util.Comparison"], function () { -c$ = Clazz.declareType (jalview.analysis.scoremodels, "PairwiseSeqScoreModel", null, jalview.api.analysis.ScoreModelI); -Clazz.overrideMethod (c$, "findDistances", -function (seqData) { -var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0)); -var noseqs = sequenceString.length; -var distance = Clazz.newFloatArray (noseqs, noseqs, 0); -var maxscore = 0; -var end = sequenceString[0].length; -for (var i = 0; i < (noseqs - 1); i++) { -for (var j = i; j < noseqs; j++) { -var score = 0; -for (var k = 0; k < end; k++) { -try { -score += this.getPairwiseScore (sequenceString[i].charAt (k), sequenceString[j].charAt (k)); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("err creating " + this.getName () + " tree"); -ex.printStackTrace (); -} else { -throw ex; -} -} -} -distance[i][j] = score; -if (score > maxscore) { -maxscore = score; -}} -} -for (var i = 0; i < (noseqs - 1); i++) { -for (var j = i; j < noseqs; j++) { -distance[i][j] = maxscore - distance[i][j]; -distance[j][i] = distance[i][j]; -} -} -return distance; -}, "jalview.datamodel.AlignmentView"); -}); +Clazz.declarePackage ("jalview.analysis.scoremodels"); +Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PairwiseSeqScoreModel", ["jalview.util.Comparison"], function () { +c$ = Clazz.declareType (jalview.analysis.scoremodels, "PairwiseSeqScoreModel", null, jalview.api.analysis.ScoreModelI); +Clazz.overrideMethod (c$, "findDistances", +function (seqData) { +var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0)); +var noseqs = sequenceString.length; +var distance = Clazz.newFloatArray (noseqs, noseqs, 0); +var maxscore = 0; +var end = sequenceString[0].length; +for (var i = 0; i < (noseqs - 1); i++) { +for (var j = i; j < noseqs; j++) { +var score = 0; +for (var k = 0; k < end; k++) { +try { +score += this.getPairwiseScore (sequenceString[i].charAt (k), sequenceString[j].charAt (k)); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("err creating " + this.getName () + " tree"); +ex.printStackTrace (); +} else { +throw ex; +} +} +} +distance[i][j] = score; +if (score > maxscore) { +maxscore = score; +}} +} +for (var i = 0; i < (noseqs - 1); i++) { +for (var j = i; j < noseqs; j++) { +distance[i][j] = maxscore - distance[i][j]; +distance[j][i] = distance[i][j]; +} +} +return distance; +}, "jalview.datamodel.AlignmentView"); +}); diff --git a/bin/jalview/analysis/scoremodels/SWScoreModel.js b/bin/jalview/analysis/scoremodels/SWScoreModel.js index 06ef966..e2e0eef 100644 --- a/bin/jalview/analysis/scoremodels/SWScoreModel.js +++ b/bin/jalview/analysis/scoremodels/SWScoreModel.js @@ -1,45 +1,45 @@ -Clazz.declarePackage ("jalview.analysis.scoremodels"); -Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.SWScoreModel", ["jalview.analysis.AlignSeq", "jalview.util.Comparison"], function () { -c$ = Clazz.declareType (jalview.analysis.scoremodels, "SWScoreModel", null, jalview.api.analysis.ScoreModelI); -Clazz.overrideMethod (c$, "findDistances", -function (seqData) { -var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray (); -var noseqs = sequenceString.length; -var distance = Clazz.newFloatArray (noseqs, noseqs, 0); -var max = -1; -for (var i = 0; i < (noseqs - 1); i++) { -for (var j = i; j < noseqs; j++) { -var as = new jalview.analysis.AlignSeq (sequenceString[i], sequenceString[j], seqData.isNa () ? "dna" : "pep"); -as.calcScoreMatrix (); -as.traceAlignment (); -as.printAlignment (System.out); -distance[i][j] = as.maxscore; -if (max < distance[i][j]) { -max = distance[i][j]; -}} -} -for (var i = 0; i < (noseqs - 1); i++) { -for (var j = i; j < noseqs; j++) { -distance[i][j] = max - distance[i][j]; -distance[j][i] = distance[i][j]; -} -} -return distance; -}, "jalview.datamodel.AlignmentView"); -Clazz.overrideMethod (c$, "getName", -function () { -return "Smith Waterman Score"; -}); -Clazz.overrideMethod (c$, "isDNA", -function () { -return true; -}); -Clazz.overrideMethod (c$, "isProtein", -function () { -return true; -}); -Clazz.overrideMethod (c$, "toString", -function () { -return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix"; -}); -}); +Clazz.declarePackage ("jalview.analysis.scoremodels"); +Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.SWScoreModel", ["jalview.analysis.AlignSeq", "jalview.util.Comparison"], function () { +c$ = Clazz.declareType (jalview.analysis.scoremodels, "SWScoreModel", null, jalview.api.analysis.ScoreModelI); +Clazz.overrideMethod (c$, "findDistances", +function (seqData) { +var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray (); +var noseqs = sequenceString.length; +var distance = Clazz.newFloatArray (noseqs, noseqs, 0); +var max = -1; +for (var i = 0; i < (noseqs - 1); i++) { +for (var j = i; j < noseqs; j++) { +var as = new jalview.analysis.AlignSeq (sequenceString[i], sequenceString[j], seqData.isNa () ? "dna" : "pep"); +as.calcScoreMatrix (); +as.traceAlignment (); +as.printAlignment (System.out); +distance[i][j] = as.maxscore; +if (max < distance[i][j]) { +max = distance[i][j]; +}} +} +for (var i = 0; i < (noseqs - 1); i++) { +for (var j = i; j < noseqs; j++) { +distance[i][j] = max - distance[i][j]; +distance[j][i] = distance[i][j]; +} +} +return distance; +}, "jalview.datamodel.AlignmentView"); +Clazz.overrideMethod (c$, "getName", +function () { +return "Smith Waterman Score"; +}); +Clazz.overrideMethod (c$, "isDNA", +function () { +return true; +}); +Clazz.overrideMethod (c$, "isProtein", +function () { +return true; +}); +Clazz.overrideMethod (c$, "toString", +function () { +return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix"; +}); +}); diff --git a/bin/jalview/api/AlignCalcManagerI.js b/bin/jalview/api/AlignCalcManagerI.js index 47dd8f5..231cd97 100644 --- a/bin/jalview/api/AlignCalcManagerI.js +++ b/bin/jalview/api/AlignCalcManagerI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "AlignCalcManagerI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "AlignCalcManagerI"); diff --git a/bin/jalview/api/AlignCalcWorkerI.js b/bin/jalview/api/AlignCalcWorkerI.js index cf7fe41..77fffcc 100644 --- a/bin/jalview/api/AlignCalcWorkerI.js +++ b/bin/jalview/api/AlignCalcWorkerI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "AlignCalcWorkerI", Runnable); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "AlignCalcWorkerI", Runnable); diff --git a/bin/jalview/api/AlignExportSettingI.js b/bin/jalview/api/AlignExportSettingI.js index d26a509..512e454 100644 --- a/bin/jalview/api/AlignExportSettingI.js +++ b/bin/jalview/api/AlignExportSettingI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "AlignExportSettingI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "AlignExportSettingI"); diff --git a/bin/jalview/api/AlignViewControllerGuiI.js b/bin/jalview/api/AlignViewControllerGuiI.js index b132c71..8dd9d75 100644 --- a/bin/jalview/api/AlignViewControllerGuiI.js +++ b/bin/jalview/api/AlignViewControllerGuiI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "AlignViewControllerGuiI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "AlignViewControllerGuiI"); diff --git a/bin/jalview/api/AlignViewControllerI.js b/bin/jalview/api/AlignViewControllerI.js index 9851769..4dbfb00 100644 --- a/bin/jalview/api/AlignViewControllerI.js +++ b/bin/jalview/api/AlignViewControllerI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "AlignViewControllerI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "AlignViewControllerI"); diff --git a/bin/jalview/api/AlignViewportI.js b/bin/jalview/api/AlignViewportI.js index b8de508..c65c3f7 100644 --- a/bin/jalview/api/AlignViewportI.js +++ b/bin/jalview/api/AlignViewportI.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.load (["jalview.api.ViewStyleI"], "jalview.api.AlignViewportI", null, function () { -Clazz.declareInterface (jalview.api, "AlignViewportI", jalview.api.ViewStyleI); -}); +Clazz.declarePackage ("jalview.api"); +Clazz.load (["jalview.api.ViewStyleI"], "jalview.api.AlignViewportI", null, function () { +Clazz.declareInterface (jalview.api, "AlignViewportI", jalview.api.ViewStyleI); +}); diff --git a/bin/jalview/api/AlignmentViewPanel.js b/bin/jalview/api/AlignmentViewPanel.js index 1a1598e..5e0dc22 100644 --- a/bin/jalview/api/AlignmentViewPanel.js +++ b/bin/jalview/api/AlignmentViewPanel.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.load (["jalview.api.OOMHandlerI"], "jalview.api.AlignmentViewPanel", null, function () { -Clazz.declareInterface (jalview.api, "AlignmentViewPanel", jalview.api.OOMHandlerI); -}); +Clazz.declarePackage ("jalview.api"); +Clazz.load (["jalview.api.OOMHandlerI"], "jalview.api.AlignmentViewPanel", null, function () { +Clazz.declareInterface (jalview.api, "AlignmentViewPanel", jalview.api.OOMHandlerI); +}); diff --git a/bin/jalview/api/ComplexAlignFile.js b/bin/jalview/api/ComplexAlignFile.js index 7e6e24d..c15e9ab 100644 --- a/bin/jalview/api/ComplexAlignFile.js +++ b/bin/jalview/api/ComplexAlignFile.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "ComplexAlignFile"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "ComplexAlignFile"); diff --git a/bin/jalview/api/FeatureRenderer.js b/bin/jalview/api/FeatureRenderer.js index cce7fb2..e845bcd 100644 --- a/bin/jalview/api/FeatureRenderer.js +++ b/bin/jalview/api/FeatureRenderer.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "FeatureRenderer"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "FeatureRenderer"); diff --git a/bin/jalview/api/FeatureSettingsControllerI.js b/bin/jalview/api/FeatureSettingsControllerI.js index d7e477c..6785f01 100644 --- a/bin/jalview/api/FeatureSettingsControllerI.js +++ b/bin/jalview/api/FeatureSettingsControllerI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "FeatureSettingsControllerI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "FeatureSettingsControllerI"); diff --git a/bin/jalview/api/FeatureSettingsModelI.js b/bin/jalview/api/FeatureSettingsModelI.js index a01cd0e..0fded11 100644 --- a/bin/jalview/api/FeatureSettingsModelI.js +++ b/bin/jalview/api/FeatureSettingsModelI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "FeatureSettingsModelI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "FeatureSettingsModelI"); diff --git a/bin/jalview/api/FeaturesDisplayedI.js b/bin/jalview/api/FeaturesDisplayedI.js index c796711..331bf21 100644 --- a/bin/jalview/api/FeaturesDisplayedI.js +++ b/bin/jalview/api/FeaturesDisplayedI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "FeaturesDisplayedI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "FeaturesDisplayedI"); diff --git a/bin/jalview/api/OOMHandlerI.js b/bin/jalview/api/OOMHandlerI.js index 48ab467..1f61be8 100644 --- a/bin/jalview/api/OOMHandlerI.js +++ b/bin/jalview/api/OOMHandlerI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "OOMHandlerI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "OOMHandlerI"); diff --git a/bin/jalview/api/RotatableCanvasI.js b/bin/jalview/api/RotatableCanvasI.js index ccaa5b8..e582e4c 100644 --- a/bin/jalview/api/RotatableCanvasI.js +++ b/bin/jalview/api/RotatableCanvasI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "RotatableCanvasI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "RotatableCanvasI"); diff --git a/bin/jalview/api/SequenceRenderer.js b/bin/jalview/api/SequenceRenderer.js index ce4be46..247757d 100644 --- a/bin/jalview/api/SequenceRenderer.js +++ b/bin/jalview/api/SequenceRenderer.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "SequenceRenderer"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "SequenceRenderer"); diff --git a/bin/jalview/api/SequenceStructureBinding.js b/bin/jalview/api/SequenceStructureBinding.js index f1a45f3..4eee259 100644 --- a/bin/jalview/api/SequenceStructureBinding.js +++ b/bin/jalview/api/SequenceStructureBinding.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "SequenceStructureBinding"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "SequenceStructureBinding"); diff --git a/bin/jalview/api/SplitContainerI.js b/bin/jalview/api/SplitContainerI.js index 03965d8..eb0b347 100644 --- a/bin/jalview/api/SplitContainerI.js +++ b/bin/jalview/api/SplitContainerI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "SplitContainerI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "SplitContainerI"); diff --git a/bin/jalview/api/StructureSelectionManagerProvider.js b/bin/jalview/api/StructureSelectionManagerProvider.js index a051fb2..e65f1a5 100644 --- a/bin/jalview/api/StructureSelectionManagerProvider.js +++ b/bin/jalview/api/StructureSelectionManagerProvider.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "StructureSelectionManagerProvider"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "StructureSelectionManagerProvider"); diff --git a/bin/jalview/api/ViewStyleI.js b/bin/jalview/api/ViewStyleI.js index 9838149..ea7a773 100644 --- a/bin/jalview/api/ViewStyleI.js +++ b/bin/jalview/api/ViewStyleI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api"); -Clazz.declareInterface (jalview.api, "ViewStyleI"); +Clazz.declarePackage ("jalview.api"); +Clazz.declareInterface (jalview.api, "ViewStyleI"); diff --git a/bin/jalview/api/analysis/ScoreModelI.js b/bin/jalview/api/analysis/ScoreModelI.js index 56b0281..4b5c4fb 100644 --- a/bin/jalview/api/analysis/ScoreModelI.js +++ b/bin/jalview/api/analysis/ScoreModelI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api.analysis"); -Clazz.declareInterface (jalview.api.analysis, "ScoreModelI"); +Clazz.declarePackage ("jalview.api.analysis"); +Clazz.declareInterface (jalview.api.analysis, "ScoreModelI"); diff --git a/bin/jalview/api/analysis/ViewBasedAnalysisI.js b/bin/jalview/api/analysis/ViewBasedAnalysisI.js index bc5e92d..cbb8c8d 100644 --- a/bin/jalview/api/analysis/ViewBasedAnalysisI.js +++ b/bin/jalview/api/analysis/ViewBasedAnalysisI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api.analysis"); -Clazz.declareInterface (jalview.api.analysis, "ViewBasedAnalysisI"); +Clazz.declarePackage ("jalview.api.analysis"); +Clazz.declareInterface (jalview.api.analysis, "ViewBasedAnalysisI"); diff --git a/bin/jalview/api/structures/JalviewStructureDisplayI.js b/bin/jalview/api/structures/JalviewStructureDisplayI.js index 2512221..643feb8 100644 --- a/bin/jalview/api/structures/JalviewStructureDisplayI.js +++ b/bin/jalview/api/structures/JalviewStructureDisplayI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.api.structures"); -Clazz.declareInterface (jalview.api.structures, "JalviewStructureDisplayI"); +Clazz.declarePackage ("jalview.api.structures"); +Clazz.declareInterface (jalview.api.structures, "JalviewStructureDisplayI"); diff --git a/bin/jalview/appletgui/APopupMenu.class b/bin/jalview/appletgui/APopupMenu.class index a328b2c..0400004 100644 Binary files a/bin/jalview/appletgui/APopupMenu.class and b/bin/jalview/appletgui/APopupMenu.class differ diff --git a/bin/jalview/appletgui/APopupMenu.js b/bin/jalview/appletgui/APopupMenu.js index eac223b..1e89852 100644 --- a/bin/jalview/appletgui/APopupMenu.js +++ b/bin/jalview/appletgui/APopupMenu.js @@ -1,797 +1,797 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.PopupMenu", "java.awt.event.ActionListener", "$.ItemListener", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuItem", "jalview.util.MessageManager"], "jalview.appletgui.APopupMenu", ["awt2swing.Frame", "jalview.analysis.AAFrequency", "$.AlignmentAnnotationUtils", "$.AlignmentUtils", "$.Conservation", "jalview.appletgui.AppletJmol", "$.CutAndPasteTransfer", "$.EditNameDialog", "$.SliderPanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.ChangeCaseCommand", "$.EditCommand", "jalview.datamodel.SequenceFeature", "jalview.io.AppletFormatAdapter", "$.SequenceAnnotationReport", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "$.StrandColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.util.DBRefUtils", "$.UrlLink", "java.lang.StringBuffer", "$.StringBuilder", "java.util.Arrays", "$.Collections", "$.LinkedHashMap", "$.TreeMap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.groupMenu = null; -this.editGroupName = null; -this.clustalColour = null; -this.zappoColour = null; -this.taylorColour = null; -this.hydrophobicityColour = null; -this.helixColour = null; -this.strandColour = null; -this.turnColour = null; -this.buriedColour = null; -this.abovePIDColour = null; -this.userDefinedColour = null; -this.PIDColour = null; -this.BLOSUM62Colour = null; -this.noColourmenuItem = null; -this.conservationMenuItem = null; -this.ap = null; -this.unGroupMenuItem = null; -this.createGroupMenuItem = null; -this.nucleotideMenuItem = null; -this.colourMenu = null; -this.showBoxes = null; -this.showText = null; -this.showColourText = null; -this.displayNonconserved = null; -this.seqShowAnnotationsMenu = null; -this.seqHideAnnotationsMenu = null; -this.seqAddReferenceAnnotations = null; -this.groupShowAnnotationsMenu = null; -this.groupHideAnnotationsMenu = null; -this.groupAddReferenceAnnotations = null; -this.editMenu = null; -this.copy = null; -this.cut = null; -this.toUpper = null; -this.toLower = null; -this.toggleCase = null; -this.outputmenu = null; -this.seqMenu = null; -this.pdb = null; -this.hideSeqs = null; -this.repGroup = null; -this.sequenceName = null; -this.sequenceFeature = null; -this.editSequence = null; -this.sequenceDetails = null; -this.selSeqDetails = null; -this.makeReferenceSeq = null; -this.seq = null; -this.revealAll = null; -this.revealSeq = null; -this.revealSeq_index = -1; -this.menu1 = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "APopupMenu", awt2swing.PopupMenu, [java.awt.event.ActionListener, java.awt.event.ItemListener]); -Clazz.prepareFields (c$, function () { -this.groupMenu = new awt2swing.Menu (); -this.editGroupName = new awt2swing.MenuItem (); -this.clustalColour = new awt2swing.MenuItem (); -this.zappoColour = new awt2swing.MenuItem (); -this.taylorColour = new awt2swing.MenuItem (); -this.hydrophobicityColour = new awt2swing.MenuItem (); -this.helixColour = new awt2swing.MenuItem (); -this.strandColour = new awt2swing.MenuItem (); -this.turnColour = new awt2swing.MenuItem (); -this.buriedColour = new awt2swing.MenuItem (); -this.abovePIDColour = new awt2swing.CheckboxMenuItem (); -this.userDefinedColour = new awt2swing.MenuItem (); -this.PIDColour = new awt2swing.MenuItem (); -this.BLOSUM62Colour = new awt2swing.MenuItem (); -this.noColourmenuItem = new awt2swing.MenuItem (); -this.conservationMenuItem = new awt2swing.CheckboxMenuItem (); -this.unGroupMenuItem = new awt2swing.MenuItem (); -this.createGroupMenuItem = new awt2swing.MenuItem (); -this.nucleotideMenuItem = new awt2swing.MenuItem (); -this.colourMenu = new awt2swing.Menu (); -this.showBoxes = new awt2swing.CheckboxMenuItem (); -this.showText = new awt2swing.CheckboxMenuItem (); -this.showColourText = new awt2swing.CheckboxMenuItem (); -this.displayNonconserved = new awt2swing.CheckboxMenuItem (); -this.seqShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations")); -this.seqHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations")); -this.seqAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations")); -this.groupShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations")); -this.groupHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations")); -this.groupAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations")); -this.editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit")); -this.copy = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.copy")); -this.cut = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.cut")); -this.toUpper = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_upper_case")); -this.toLower = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_lower_case")); -this.toggleCase = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.toggle_case")); -this.outputmenu = new awt2swing.Menu (); -this.seqMenu = new awt2swing.Menu (); -this.pdb = new awt2swing.MenuItem (); -this.hideSeqs = new awt2swing.MenuItem (); -this.repGroup = new awt2swing.MenuItem (); -this.sequenceName = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_name_description")); -this.sequenceFeature = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.create_sequence_feature")); -this.editSequence = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_sequence")); -this.sequenceDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "..."); -this.selSeqDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "..."); -this.makeReferenceSeq = new awt2swing.MenuItem (); -this.revealAll = new awt2swing.MenuItem (); -this.revealSeq = new awt2swing.MenuItem (); -this.menu1 = new awt2swing.Menu (); -}); -Clazz.makeConstructor (c$, -function (apanel, seq, links) { -Clazz.superConstructor (this, jalview.appletgui.APopupMenu, []); -this.ap = apanel; -this.seq = seq; -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { -var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); -item.addActionListener (this); -this.outputmenu.add (item); -} -this.buildAnnotationSubmenus (); -var sg = this.ap.av.getSelectionGroup (); -if (sg != null && sg.getSize () > 0) { -this.editGroupName.setLabel (jalview.util.MessageManager.formatMessage ("label.name_param", Clazz.newArray (-1, [sg.getName ()]))); -this.showText.setState (sg.getDisplayText ()); -this.showColourText.setState (sg.getColourText ()); -this.showBoxes.setState (sg.getDisplayBoxes ()); -this.displayNonconserved.setState (sg.getShowNonconserved ()); -if (!this.ap.av.getAlignment ().getGroups ().contains (sg)) { -this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_new_group")); -this.groupMenu.remove (this.unGroupMenuItem); -} else { -this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_group")); -this.groupMenu.remove (this.createGroupMenuItem); -}} else { -this.remove (this.hideSeqs); -this.remove (this.groupMenu); -}if (links != null && links.size () > 0) { -var linkMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.link")); -for (var i = 0; i < links.size (); i++) { -var link = links.elementAt (i); -var urlLink = new jalview.util.UrlLink (link); -if (!urlLink.isValid ()) { -System.err.println (urlLink.getInvalidMessage ()); -continue; -}var target = urlLink.getTarget (); -var label = urlLink.getLabel (); -if (seq != null && urlLink.isDynamic ()) { -var dbr = jalview.util.DBRefUtils.selectRefs (seq.getDBRef (), Clazz.newArray (-1, [target])); -var id = seq.getName (); -var descr = seq.getDescription (); -if (descr != null && descr.length < 1) { -descr = null; -}if (dbr != null) { -for (var r = 0; r < dbr.length; r++) { -if (id != null && dbr[r].getAccessionId ().equals (id)) { -id = null; -}var urls = urlLink.makeUrls (dbr[r].getAccessionId (), true); -if (urls != null) { -for (var u = 0; u < urls.length; u += 2) { -this.addshowLink (linkMenu, label + "|" + urls[u], urls[u + 1]); -} -}} -}if (id != null) { -var urls = urlLink.makeUrls (id, true); -if (urls != null) { -for (var u = 0; u < urls.length; u += 2) { -this.addshowLink (linkMenu, label, urls[u + 1]); -} -}}if (descr != null && urlLink.getRegexReplace () != null) { -var urls = urlLink.makeUrls (descr, true); -if (urls != null) { -for (var u = 0; u < urls.length; u += 2) { -this.addshowLink (linkMenu, label, urls[u + 1]); -} -}}} else { -this.addshowLink (linkMenu, target, urlLink.getUrl_prefix ()); -}} -if (linkMenu.getItemCount () > 0) { -if (seq != null) { -this.seqMenu.add (linkMenu); -} else { -this.add (linkMenu); -}}}if (seq != null) { -this.seqMenu.setLabel (seq.getName ()); -if (seq === this.ap.av.getAlignment ().getSeqrep ()) { -this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.unmark_as_reference")); -} else { -this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.set_as_reference")); -}this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [seq.getName ()]))); -} else { -this.remove (this.seqMenu); -}if (!this.ap.av.hasHiddenRows ()) { -this.remove (this.revealAll); -this.remove (this.revealSeq); -} else { -var index = this.ap.av.getAlignment ().findIndex (seq); -if (this.ap.av.adjustForHiddenSeqs (index) - this.ap.av.adjustForHiddenSeqs (index - 1) > 1) { -this.revealSeq_index = index; -} else { -this.remove (this.revealSeq); -}}}, "jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceI,java.util.Vector"); -Clazz.defineMethod (c$, "buildAnnotationSubmenus", -($fz = function () { -var selectedSequence = (this.seq == null ? java.util.Collections.emptyList () : java.util.Arrays.asList ([this.seq])); -this.buildAnnotationTypesMenus (this.seqShowAnnotationsMenu, this.seqHideAnnotationsMenu, selectedSequence); -this.configureReferenceAnnotationsMenu (this.seqAddReferenceAnnotations, selectedSequence); -var selectedGroup = (this.ap.av.getSelectionGroup () == null ? java.util.Collections.emptyList () : this.ap.av.getSelectionGroup ().getSequences ()); -this.buildAnnotationTypesMenus (this.groupShowAnnotationsMenu, this.groupHideAnnotationsMenu, selectedGroup); -this.configureReferenceAnnotationsMenu (this.groupAddReferenceAnnotations, selectedGroup); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "configureReferenceAnnotationsMenu", -($fz = function (menuItem, forSequences) { -menuItem.setEnabled (false); -var tipEntries = new java.util.TreeMap (); -var candidates = new java.util.LinkedHashMap (); -var al = this.ap.av.getAlignment (); -jalview.analysis.AlignmentUtils.findAddableReferenceAnnotations (forSequences, tipEntries, candidates, al); -if (!candidates.isEmpty ()) { -var tooltip = new StringBuilder (64); -tooltip.append (jalview.util.MessageManager.getString ("label.add_annotations_for")); -menuItem.setEnabled (true); -menuItem.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$1") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$1, this, Clazz.cloneFinals ("candidates", candidates)))); -}}, $fz.isPrivate = true, $fz), "awt2swing.MenuItem,java.util.List"); -Clazz.defineMethod (c$, "addReferenceAnnotations_actionPerformed", -function (candidates) { -var selectionGroup = this.ap.av.getSelectionGroup (); -var alignment = this.ap.getAlignment (); -jalview.analysis.AlignmentUtils.addReferenceAnnotations (candidates, alignment, selectionGroup); -this.refresh (); -}, "java.util.Map"); -Clazz.defineMethod (c$, "addshowLink", -($fz = function (linkMenu, target, url) { -this.addshowLink (linkMenu, target, target, url); -}, $fz.isPrivate = true, $fz), "awt2swing.Menu,~S,~S"); -Clazz.defineMethod (c$, "addshowLink", -($fz = function (linkMenu, target, label, url) { -var item = new awt2swing.MenuItem (label); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$2") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$2, this, Clazz.cloneFinals ("url", url, "target", target)))); -linkMenu.add (item); -}, $fz.isPrivate = true, $fz), "awt2swing.Menu,~S,~S,~S"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -if (evt.getSource () === this.abovePIDColour) { -this.abovePIDColour_itemStateChanged (); -} else if (evt.getSource () === this.showColourText) { -this.showColourText_itemStateChanged (); -} else if (evt.getSource () === this.showText) { -this.showText_itemStateChanged (); -} else if (evt.getSource () === this.showBoxes) { -this.showBoxes_itemStateChanged (); -} else if (evt.getSource () === this.displayNonconserved) { -this.showNonconserved_itemStateChanged (); -}}, "java.awt.event.ItemEvent"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -var source = evt.getSource (); -if (source === this.clustalColour) { -this.clustalColour_actionPerformed (); -} else if (source === this.zappoColour) { -this.zappoColour_actionPerformed (); -} else if (source === this.taylorColour) { -this.taylorColour_actionPerformed (); -} else if (source === this.hydrophobicityColour) { -this.hydrophobicityColour_actionPerformed (); -} else if (source === this.helixColour) { -this.helixColour_actionPerformed (); -} else if (source === this.strandColour) { -this.strandColour_actionPerformed (); -} else if (source === this.turnColour) { -this.turnColour_actionPerformed (); -} else if (source === this.buriedColour) { -this.buriedColour_actionPerformed (); -} else if (source === this.nucleotideMenuItem) { -this.nucleotideMenuItem_actionPerformed (); -} else if (source === this.userDefinedColour) { -this.userDefinedColour_actionPerformed (); -} else if (source === this.PIDColour) { -this.PIDColour_actionPerformed (); -} else if (source === this.BLOSUM62Colour) { -this.BLOSUM62Colour_actionPerformed (); -} else if (source === this.noColourmenuItem) { -this.noColourmenuItem_actionPerformed (); -} else if (source === this.conservationMenuItem) { -this.conservationMenuItem_itemStateChanged (); -} else if (source === this.unGroupMenuItem) { -this.unGroupMenuItem_actionPerformed (); -} else if (source === this.createGroupMenuItem) { -this.createGroupMenuItem_actionPerformed (); -} else if (source === this.sequenceName) { -this.editName (); -} else if (source === this.makeReferenceSeq) { -this.makeReferenceSeq_actionPerformed (); -} else if (source === this.sequenceDetails) { -this.showSequenceDetails (); -} else if (source === this.selSeqDetails) { -this.showSequenceSelectionDetails (); -} else if (source === this.pdb) { -this.addPDB (); -} else if (source === this.hideSeqs) { -this.hideSequences (false); -} else if (source === this.repGroup) { -this.hideSequences (true); -} else if (source === this.revealSeq) { -this.ap.av.showSequence (this.revealSeq_index); -} else if (source === this.revealAll) { -this.ap.av.showAllHiddenSeqs (); -} else if (source === this.editGroupName) { -var dialog = new jalview.appletgui.EditNameDialog (this.getGroup ().getName (), this.getGroup ().getDescription (), " Group Name", "Group Description", this.ap.alignFrame, "Edit Group Name / Description", 500, 100, true); -if (dialog.accept) { -this.getGroup ().setName (dialog.getName ().$replace (' ', '_')); -this.getGroup ().setDescription (dialog.getDescription ()); -}} else if (source === this.copy) { -this.ap.alignFrame.copy_actionPerformed (); -} else if (source === this.cut) { -this.ap.alignFrame.cut_actionPerformed (); -} else if (source === this.editSequence) { -var sg = this.ap.av.getSelectionGroup (); -if (sg != null) { -if (this.seq == null) { -this.seq = sg.getSequenceAt (0); -}var dialog = new jalview.appletgui.EditNameDialog (this.seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1), null, "Edit Sequence ", null, this.ap.alignFrame, "Edit Sequence", 500, 100, true); -if (dialog.accept) { -var editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.edit_sequences"), jalview.commands.EditCommand.Action.REPLACE, dialog.getName ().$replace (' ', this.ap.av.getGapCharacter ()), sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), sg.getStartRes (), sg.getEndRes () + 1, this.ap.av.getAlignment ()); -this.ap.alignFrame.addHistoryItem (editCommand); -this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); -}}} else if (source === this.toUpper || source === this.toLower || source === this.toggleCase) { -var sg = this.ap.av.getSelectionGroup (); -if (sg != null) { -var startEnd = this.ap.av.getVisibleRegionBoundaries (sg.getStartRes (), sg.getEndRes () + 1); -var description; -var caseChange; -if (source === this.toggleCase) { -description = "Toggle Case"; -caseChange = jalview.commands.ChangeCaseCommand.TOGGLE_CASE; -} else if (source === this.toUpper) { -description = "To Upper Case"; -caseChange = jalview.commands.ChangeCaseCommand.TO_UPPER; -} else { -description = "To Lower Case"; -caseChange = jalview.commands.ChangeCaseCommand.TO_LOWER; -}var caseCommand = new jalview.commands.ChangeCaseCommand (description, sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), startEnd, caseChange); -this.ap.alignFrame.addHistoryItem (caseCommand); -this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); -}} else if (source === this.sequenceFeature) { -var sg = this.ap.av.getSelectionGroup (); -if (sg == null) { -return; -}var rsize = 0; -var gSize = sg.getSize (); -var rseqs; -var seqs = new Array (gSize); -var tfeatures; -var features = new Array (gSize); -for (var i = 0; i < gSize; i++) { -var start = sg.getSequenceAt (i).findPosition (sg.getStartRes ()); -var end = sg.findEndRes (sg.getSequenceAt (i)); -if (start <= end) { -seqs[rsize] = sg.getSequenceAt (i); -features[rsize] = new jalview.datamodel.SequenceFeature (null, null, null, start, end, "Jalview"); -rsize++; -}} -rseqs = new Array (rsize); -tfeatures = new Array (rsize); -System.arraycopy (seqs, 0, rseqs, 0, rsize); -System.arraycopy (features, 0, tfeatures, 0, rsize); -features = tfeatures; -seqs = rseqs; -if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) { -this.ap.alignFrame.sequenceFeatures.setState (true); -this.ap.av.setShowSequenceFeatures (true); -;this.ap.highlightSearchResults (null); -}} else { -this.outputText (evt); -}}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "outputText", -function (e) { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.selection_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500); -cap.setText ( new jalview.io.AppletFormatAdapter ().formatSequences (e.getActionCommand (), this.ap.av.getShowJVSuffix (), this.ap, true)); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "showSequenceSelectionDetails", -function () { -this.createSequenceDetailsReport (this.ap.av.getSequenceSelection ()); -}); -Clazz.defineMethod (c$, "showSequenceDetails", -function () { -this.createSequenceDetailsReport ( Clazz.newArray (-1, [this.seq])); -}); -Clazz.defineMethod (c$, "createSequenceDetailsReport", -function (sequences) { -var cap = new jalview.appletgui.CutAndPasteTransfer (false, this.ap.alignFrame); -var contents = new StringBuffer (); -for (var seq, $seq = 0, $$seq = sequences; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { -contents.append (jalview.util.MessageManager.formatMessage ("label.annotation_for_displayid", Clazz.newArray (-1, [seq.getDisplayId (true)]))); - new jalview.io.SequenceAnnotationReport (null).createSequenceAnnotationReport (contents, seq, true, true, false, (this.ap.seqPanel.seqCanvas.fr != null) ? this.ap.seqPanel.seqCanvas.fr.getMinMax () : null); -contents.append ("

"); -} -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, "Sequence Details for " + (sequences.length == 1 ? sequences[0].getDisplayId (true) : "Selection"), 600, 500); -cap.setText (jalview.util.MessageManager.formatMessage ("label.html_content", Clazz.newArray (-1, [contents.toString ()]))); -}, "~A"); -Clazz.defineMethod (c$, "editName", -function () { -var dialog = new jalview.appletgui.EditNameDialog (this.seq.getName (), this.seq.getDescription (), " Sequence Name", "Sequence Description", this.ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true); -if (dialog.accept) { -this.seq.setName (dialog.getName ()); -this.seq.setDescription (dialog.getDescription ()); -this.ap.paintAlignment (false); -}}); -Clazz.defineMethod (c$, "addPDB", -function () { -if (this.seq.getPDBId () != null) { -var entry = this.seq.getPDBId ().firstElement (); -if (this.ap.av.applet.jmolAvailable) { - new jalview.appletgui.AppletJmol (entry, Clazz.newArray (-1, [this.seq]), null, this.ap, jalview.io.AppletFormatAdapter.URL); -}} else { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame); -cap.setText (jalview.util.MessageManager.getString ("label.paste_pdb_file")); -cap.setPDBImport (this.seq); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.paste_pdb_file_for_sequence", Clazz.newArray (-1, [this.seq.getName ()])), 400, 300); -}}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.groupMenu.setLabel (jalview.util.MessageManager.getString ("label.selection")); -this.sequenceFeature.addActionListener (this); -this.editGroupName.addActionListener (this); -this.unGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_group")); -this.unGroupMenuItem.addActionListener (this); -this.createGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.create_group")); -this.createGroupMenuItem.addActionListener (this); -this.nucleotideMenuItem.setLabel (jalview.util.MessageManager.getString ("label.nucleotide")); -this.nucleotideMenuItem.addActionListener (this); -this.conservationMenuItem.addItemListener (this); -this.abovePIDColour.addItemListener (this); -this.colourMenu.setLabel (jalview.util.MessageManager.getString ("label.group_colour")); -this.showBoxes.setLabel (jalview.util.MessageManager.getString ("action.boxes")); -this.showBoxes.setState (true); -this.showBoxes.addItemListener (this); -this.sequenceName.addActionListener (this); -this.sequenceDetails.addActionListener (this); -this.selSeqDetails.addActionListener (this); -this.displayNonconserved.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed")); -this.displayNonconserved.setState (false); -this.displayNonconserved.addItemListener (this); -this.showText.setLabel (jalview.util.MessageManager.getString ("action.text")); -this.showText.addItemListener (this); -this.showColourText.setLabel (jalview.util.MessageManager.getString ("label.colour_text")); -this.showColourText.addItemListener (this); -this.outputmenu.setLabel (jalview.util.MessageManager.getString ("label.out_to_textbox")); -this.seqMenu.setLabel (jalview.util.MessageManager.getString ("label.sequence")); -this.pdb.setLabel (jalview.util.MessageManager.getString ("label.view_pdb_structure")); -this.hideSeqs.setLabel (jalview.util.MessageManager.getString ("action.hide_sequences")); -this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [""]))); -this.revealAll.setLabel (jalview.util.MessageManager.getString ("action.reveal_all")); -this.revealSeq.setLabel (jalview.util.MessageManager.getString ("action.reveal_sequences")); -this.menu1.setLabel (jalview.util.MessageManager.getString ("label.group") + ":"); -this.add (this.groupMenu); -this.add (this.seqMenu); -this.add (this.hideSeqs); -this.add (this.revealSeq); -this.add (this.revealAll); -this.groupMenu.add (this.groupShowAnnotationsMenu); -this.groupMenu.add (this.groupHideAnnotationsMenu); -this.groupMenu.add (this.groupAddReferenceAnnotations); -this.groupMenu.add (this.editMenu); -this.groupMenu.add (this.outputmenu); -this.groupMenu.add (this.sequenceFeature); -this.groupMenu.add (this.createGroupMenuItem); -this.groupMenu.add (this.unGroupMenuItem); -this.groupMenu.add (this.menu1); -this.colourMenu.add (this.noColourmenuItem); -this.colourMenu.add (this.clustalColour); -this.colourMenu.add (this.BLOSUM62Colour); -this.colourMenu.add (this.PIDColour); -this.colourMenu.add (this.zappoColour); -this.colourMenu.add (this.taylorColour); -this.colourMenu.add (this.hydrophobicityColour); -this.colourMenu.add (this.helixColour); -this.colourMenu.add (this.strandColour); -this.colourMenu.add (this.turnColour); -this.colourMenu.add (this.buriedColour); -this.colourMenu.add (this.nucleotideMenuItem); -this.colourMenu.add (this.userDefinedColour); -this.colourMenu.addSeparator (); -this.colourMenu.add (this.abovePIDColour); -this.colourMenu.add (this.conservationMenuItem); -this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none")); -this.noColourmenuItem.addActionListener (this); -this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx_colours")); -this.clustalColour.addActionListener (this); -this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo")); -this.zappoColour.addActionListener (this); -this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor")); -this.taylorColour.addActionListener (this); -this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity")); -this.hydrophobicityColour.addActionListener (this); -this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity")); -this.helixColour.addActionListener (this); -this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity")); -this.strandColour.addActionListener (this); -this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity")); -this.turnColour.addActionListener (this); -this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index")); -this.buriedColour.addActionListener (this); -this.abovePIDColour.setLabel (jalview.util.MessageManager.getString ("label.above_identity_percentage")); -this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined")); -this.userDefinedColour.addActionListener (this); -this.PIDColour.setLabel (jalview.util.MessageManager.getString ("action.percentage_identity")); -this.PIDColour.addActionListener (this); -this.BLOSUM62Colour.setLabel ("BLOSUM62"); -this.BLOSUM62Colour.addActionListener (this); -this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("label.conservation")); -this.editMenu.add (this.copy); -this.copy.addActionListener (this); -this.editMenu.add (this.cut); -this.cut.addActionListener (this); -this.editMenu.add (this.editSequence); -this.editSequence.addActionListener (this); -this.editMenu.add (this.toUpper); -this.toUpper.addActionListener (this); -this.editMenu.add (this.toLower); -this.toLower.addActionListener (this); -this.editMenu.add (this.toggleCase); -this.seqMenu.add (this.seqShowAnnotationsMenu); -this.seqMenu.add (this.seqHideAnnotationsMenu); -this.seqMenu.add (this.seqAddReferenceAnnotations); -this.seqMenu.add (this.sequenceName); -this.seqMenu.add (this.makeReferenceSeq); -if (!this.ap.av.applet.useXtrnalSviewer) { -this.seqMenu.add (this.pdb); -}this.seqMenu.add (this.repGroup); -this.menu1.add (this.editGroupName); -this.menu1.add (this.colourMenu); -this.menu1.add (this.showBoxes); -this.menu1.add (this.showText); -this.menu1.add (this.showColourText); -this.menu1.add (this.displayNonconserved); -this.toggleCase.addActionListener (this); -this.pdb.addActionListener (this); -this.hideSeqs.addActionListener (this); -this.repGroup.addActionListener (this); -this.revealAll.addActionListener (this); -this.revealSeq.addActionListener (this); -this.makeReferenceSeq.addActionListener (this); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "refresh", -function () { -this.ap.paintAlignment (true); -}); -Clazz.defineMethod (c$, "clustalColour_actionPerformed", -function () { -var sg = this.getGroup (); -sg.cs = new jalview.schemes.ClustalxColourScheme (sg, this.ap.av.getHiddenRepSequences ()); -this.refresh (); -}); -Clazz.defineMethod (c$, "zappoColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.ZappoColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "taylorColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.TaylorColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "hydrophobicityColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.HydrophobicColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "helixColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.HelixColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "strandColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.StrandColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "turnColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.TurnColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "buriedColour_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.BuriedColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "nucleotideMenuItem_actionPerformed", -function () { -this.getGroup ().cs = new jalview.schemes.NucleotideColourScheme (); -this.refresh (); -}); -Clazz.defineMethod (c$, "abovePIDColour_itemStateChanged", -function () { -var sg = this.getGroup (); -if (sg.cs == null) { -return; -}if (this.abovePIDColour.getState ()) { -sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ())); -var threshold = jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, sg.cs, this.getGroup ().getName ()); -sg.cs.setThreshold (threshold, this.ap.av.isIgnoreGapsConsensus ()); -jalview.appletgui.SliderPanel.showPIDSlider (); -} else { -sg.cs.setThreshold (0, this.ap.av.isIgnoreGapsConsensus ()); -}this.refresh (); -}); -Clazz.defineMethod (c$, "userDefinedColour_actionPerformed", -function () { - new jalview.appletgui.UserDefinedColours (this.ap, this.getGroup ()); -}); -Clazz.defineMethod (c$, "PIDColour_actionPerformed", -function () { -var sg = this.getGroup (); -sg.cs = new jalview.schemes.PIDColourScheme (); -sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ())); -this.refresh (); -}); -Clazz.defineMethod (c$, "BLOSUM62Colour_actionPerformed", -function () { -var sg = this.getGroup (); -sg.cs = new jalview.schemes.Blosum62ColourScheme (); -sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ())); -this.refresh (); -}); -Clazz.defineMethod (c$, "noColourmenuItem_actionPerformed", -function () { -this.getGroup ().cs = null; -this.refresh (); -}); -Clazz.defineMethod (c$, "conservationMenuItem_itemStateChanged", -function () { -var sg = this.getGroup (); -if (sg.cs == null) { -return; -}if (this.conservationMenuItem.getState ()) { -sg.cs.setConservation (jalview.analysis.Conservation.calculateConservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth (), false, this.ap.av.getConsPercGaps (), false)); -jalview.appletgui.SliderPanel.setConservationSlider (this.ap, sg.cs, sg.getName ()); -jalview.appletgui.SliderPanel.showConservationSlider (); -} else { -sg.cs.setConservation (null); -}this.refresh (); -}); -Clazz.defineMethod (c$, "getGroup", -function () { -var sg = this.ap.av.getSelectionGroup (); -if (sg != null) { -this.ap.av.getAlignment ().addGroup (sg); -}return sg; -}); -Clazz.defineMethod (c$, "unGroupMenuItem_actionPerformed", -function () { -var sg = this.ap.av.getSelectionGroup (); -this.ap.av.getAlignment ().deleteGroup (sg); -this.ap.av.setSelectionGroup (null); -this.ap.paintAlignment (true); -}); -Clazz.defineMethod (c$, "createGroupMenuItem_actionPerformed", -function () { -this.getGroup (); -this.refresh (); -}); -Clazz.defineMethod (c$, "showColourText_itemStateChanged", -function () { -this.getGroup ().setColourText (this.showColourText.getState ()); -this.refresh (); -}); -Clazz.defineMethod (c$, "showText_itemStateChanged", -function () { -this.getGroup ().setDisplayText (this.showText.getState ()); -this.refresh (); -}); -Clazz.defineMethod (c$, "makeReferenceSeq_actionPerformed", -function () { -if (!this.ap.av.getAlignment ().hasSeqrep ()) { -this.ap.av.setDisplayReferenceSeq (true); -this.ap.av.setColourByReferenceSeq (true); -this.ap.av.getAlignment ().setSeqrep (this.seq); -} else { -if (this.ap.av.getAlignment ().getSeqrep () === this.seq) { -this.ap.av.getAlignment ().setSeqrep (null); -} else { -this.ap.av.getAlignment ().setSeqrep (this.seq); -}}this.refresh (); -}); -Clazz.defineMethod (c$, "showNonconserved_itemStateChanged", -function () { -this.getGroup ().setShowNonconserved (this.displayNonconserved.getState ()); -this.refresh (); -}); -Clazz.defineMethod (c$, "showBoxes_itemStateChanged", -function () { -this.getGroup ().setDisplayBoxes (this.showBoxes.getState ()); -this.refresh (); -}); -Clazz.defineMethod (c$, "hideSequences", -function (representGroup) { -var sg = this.ap.av.getSelectionGroup (); -if (sg == null || sg.getSize () < 1) { -this.ap.av.hideSequence ( Clazz.newArray (-1, [this.seq])); -return; -}this.ap.av.setSelectionGroup (null); -if (representGroup) { -this.ap.av.hideRepSequences (this.seq, sg); -return; -}var gsize = sg.getSize (); -var hseqs; -hseqs = new Array (gsize); -var index = 0; -for (var i = 0; i < gsize; i++) { -hseqs[index++] = sg.getSequenceAt (i); -} -this.ap.av.hideSequence (hseqs); -this.ap.av.sendSelection (); -}, "~B"); -Clazz.defineMethod (c$, "buildAnnotationTypesMenus", -function (showMenu, hideMenu, forSequences) { -showMenu.removeAll (); -hideMenu.removeAll (); -var all = java.util.Arrays.asList (["All"]); -this.addAnnotationTypeToShowHide (showMenu, forSequences, "", all, true, true); -this.addAnnotationTypeToShowHide (hideMenu, forSequences, "", all, true, false); -showMenu.addSeparator (); -hideMenu.addSeparator (); -var annotations = this.ap.getAlignment ().getAlignmentAnnotation (); -var shownTypes = new java.util.LinkedHashMap (); -var hiddenTypes = new java.util.LinkedHashMap (); -jalview.analysis.AlignmentAnnotationUtils.getShownHiddenTypes (shownTypes, hiddenTypes, jalview.analysis.AlignmentAnnotationUtils.asList (annotations), forSequences); -for (var calcId, $calcId = hiddenTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) { -for (var type, $type = hiddenTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) { -this.addAnnotationTypeToShowHide (showMenu, forSequences, calcId, type, false, true); -} -} -showMenu.setEnabled (!hiddenTypes.isEmpty ()); -for (var calcId, $calcId = shownTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) { -for (var type, $type = shownTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) { -this.addAnnotationTypeToShowHide (hideMenu, forSequences, calcId, type, false, false); -} -} -hideMenu.setEnabled (!shownTypes.isEmpty ()); -}, "awt2swing.Menu,awt2swing.Menu,java.util.List"); -Clazz.defineMethod (c$, "addAnnotationTypeToShowHide", -function (showOrHideMenu, forSequences, calcId, types, allTypes, actionIsShow) { -var label = types.toString (); -label = label.substring (1, label.length - 1); -var item = new awt2swing.MenuItem (label); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$3") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$3, this, Clazz.cloneFinals ("types", types, "forSequences", forSequences, "allTypes", allTypes, "actionIsShow", actionIsShow)))); -showOrHideMenu.add (item); -}, "awt2swing.Menu,java.util.List,~S,java.util.List,~B,~B"); -c$.$APopupMenu$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$1", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.APopupMenu"].addReferenceAnnotations_actionPerformed (this.f$.candidates); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$APopupMenu$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$2", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.APopupMenu"].ap.alignFrame.showURL (this.f$.url, this.f$.target); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$APopupMenu$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$3", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations (this.b$["jalview.appletgui.APopupMenu"].ap.getAlignment (), this.f$.types, this.f$.forSequences, this.f$.allTypes, this.f$.actionIsShow); -this.b$["jalview.appletgui.APopupMenu"].refresh (); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"ALL_ANNOTATIONS", "All"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.PopupMenu", "java.awt.event.ActionListener", "$.ItemListener", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuItem", "jalview.util.MessageManager"], "jalview.appletgui.APopupMenu", ["awt2swing.Frame", "jalview.analysis.AAFrequency", "$.AlignmentAnnotationUtils", "$.AlignmentUtils", "$.Conservation", "jalview.appletgui.AppletJmol", "$.CutAndPasteTransfer", "$.EditNameDialog", "$.SliderPanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.ChangeCaseCommand", "$.EditCommand", "jalview.datamodel.SequenceFeature", "jalview.io.AppletFormatAdapter", "$.SequenceAnnotationReport", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "$.StrandColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.util.DBRefUtils", "$.UrlLink", "java.lang.StringBuffer", "$.StringBuilder", "java.util.Arrays", "$.Collections", "$.LinkedHashMap", "$.TreeMap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.groupMenu = null; +this.editGroupName = null; +this.clustalColour = null; +this.zappoColour = null; +this.taylorColour = null; +this.hydrophobicityColour = null; +this.helixColour = null; +this.strandColour = null; +this.turnColour = null; +this.buriedColour = null; +this.abovePIDColour = null; +this.userDefinedColour = null; +this.PIDColour = null; +this.BLOSUM62Colour = null; +this.noColourmenuItem = null; +this.conservationMenuItem = null; +this.ap = null; +this.unGroupMenuItem = null; +this.createGroupMenuItem = null; +this.nucleotideMenuItem = null; +this.colourMenu = null; +this.showBoxes = null; +this.showText = null; +this.showColourText = null; +this.displayNonconserved = null; +this.seqShowAnnotationsMenu = null; +this.seqHideAnnotationsMenu = null; +this.seqAddReferenceAnnotations = null; +this.groupShowAnnotationsMenu = null; +this.groupHideAnnotationsMenu = null; +this.groupAddReferenceAnnotations = null; +this.editMenu = null; +this.copy = null; +this.cut = null; +this.toUpper = null; +this.toLower = null; +this.toggleCase = null; +this.outputmenu = null; +this.seqMenu = null; +this.pdb = null; +this.hideSeqs = null; +this.repGroup = null; +this.sequenceName = null; +this.sequenceFeature = null; +this.editSequence = null; +this.sequenceDetails = null; +this.selSeqDetails = null; +this.makeReferenceSeq = null; +this.seq = null; +this.revealAll = null; +this.revealSeq = null; +this.revealSeq_index = -1; +this.menu1 = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "APopupMenu", awt2swing.PopupMenu, [java.awt.event.ActionListener, java.awt.event.ItemListener]); +Clazz.prepareFields (c$, function () { +this.groupMenu = new awt2swing.Menu (); +this.editGroupName = new awt2swing.MenuItem (); +this.clustalColour = new awt2swing.MenuItem (); +this.zappoColour = new awt2swing.MenuItem (); +this.taylorColour = new awt2swing.MenuItem (); +this.hydrophobicityColour = new awt2swing.MenuItem (); +this.helixColour = new awt2swing.MenuItem (); +this.strandColour = new awt2swing.MenuItem (); +this.turnColour = new awt2swing.MenuItem (); +this.buriedColour = new awt2swing.MenuItem (); +this.abovePIDColour = new awt2swing.CheckboxMenuItem (); +this.userDefinedColour = new awt2swing.MenuItem (); +this.PIDColour = new awt2swing.MenuItem (); +this.BLOSUM62Colour = new awt2swing.MenuItem (); +this.noColourmenuItem = new awt2swing.MenuItem (); +this.conservationMenuItem = new awt2swing.CheckboxMenuItem (); +this.unGroupMenuItem = new awt2swing.MenuItem (); +this.createGroupMenuItem = new awt2swing.MenuItem (); +this.nucleotideMenuItem = new awt2swing.MenuItem (); +this.colourMenu = new awt2swing.Menu (); +this.showBoxes = new awt2swing.CheckboxMenuItem (); +this.showText = new awt2swing.CheckboxMenuItem (); +this.showColourText = new awt2swing.CheckboxMenuItem (); +this.displayNonconserved = new awt2swing.CheckboxMenuItem (); +this.seqShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations")); +this.seqHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations")); +this.seqAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations")); +this.groupShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations")); +this.groupHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations")); +this.groupAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations")); +this.editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit")); +this.copy = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.copy")); +this.cut = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.cut")); +this.toUpper = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_upper_case")); +this.toLower = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_lower_case")); +this.toggleCase = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.toggle_case")); +this.outputmenu = new awt2swing.Menu (); +this.seqMenu = new awt2swing.Menu (); +this.pdb = new awt2swing.MenuItem (); +this.hideSeqs = new awt2swing.MenuItem (); +this.repGroup = new awt2swing.MenuItem (); +this.sequenceName = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_name_description")); +this.sequenceFeature = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.create_sequence_feature")); +this.editSequence = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_sequence")); +this.sequenceDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "..."); +this.selSeqDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "..."); +this.makeReferenceSeq = new awt2swing.MenuItem (); +this.revealAll = new awt2swing.MenuItem (); +this.revealSeq = new awt2swing.MenuItem (); +this.menu1 = new awt2swing.Menu (); +}); +Clazz.makeConstructor (c$, +function (apanel, seq, links) { +Clazz.superConstructor (this, jalview.appletgui.APopupMenu, []); +this.ap = apanel; +this.seq = seq; +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { +var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); +item.addActionListener (this); +this.outputmenu.add (item); +} +this.buildAnnotationSubmenus (); +var sg = this.ap.av.getSelectionGroup (); +if (sg != null && sg.getSize () > 0) { +this.editGroupName.setLabel (jalview.util.MessageManager.formatMessage ("label.name_param", Clazz.newArray (-1, [sg.getName ()]))); +this.showText.setState (sg.getDisplayText ()); +this.showColourText.setState (sg.getColourText ()); +this.showBoxes.setState (sg.getDisplayBoxes ()); +this.displayNonconserved.setState (sg.getShowNonconserved ()); +if (!this.ap.av.getAlignment ().getGroups ().contains (sg)) { +this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_new_group")); +this.groupMenu.remove (this.unGroupMenuItem); +} else { +this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_group")); +this.groupMenu.remove (this.createGroupMenuItem); +}} else { +this.remove (this.hideSeqs); +this.remove (this.groupMenu); +}if (links != null && links.size () > 0) { +var linkMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.link")); +for (var i = 0; i < links.size (); i++) { +var link = links.elementAt (i); +var urlLink = new jalview.util.UrlLink (link); +if (!urlLink.isValid ()) { +System.err.println (urlLink.getInvalidMessage ()); +continue; +}var target = urlLink.getTarget (); +var label = urlLink.getLabel (); +if (seq != null && urlLink.isDynamic ()) { +var dbr = jalview.util.DBRefUtils.selectRefs (seq.getDBRef (), Clazz.newArray (-1, [target])); +var id = seq.getName (); +var descr = seq.getDescription (); +if (descr != null && descr.length < 1) { +descr = null; +}if (dbr != null) { +for (var r = 0; r < dbr.length; r++) { +if (id != null && dbr[r].getAccessionId ().equals (id)) { +id = null; +}var urls = urlLink.makeUrls (dbr[r].getAccessionId (), true); +if (urls != null) { +for (var u = 0; u < urls.length; u += 2) { +this.addshowLink (linkMenu, label + "|" + urls[u], urls[u + 1]); +} +}} +}if (id != null) { +var urls = urlLink.makeUrls (id, true); +if (urls != null) { +for (var u = 0; u < urls.length; u += 2) { +this.addshowLink (linkMenu, label, urls[u + 1]); +} +}}if (descr != null && urlLink.getRegexReplace () != null) { +var urls = urlLink.makeUrls (descr, true); +if (urls != null) { +for (var u = 0; u < urls.length; u += 2) { +this.addshowLink (linkMenu, label, urls[u + 1]); +} +}}} else { +this.addshowLink (linkMenu, target, urlLink.getUrl_prefix ()); +}} +if (linkMenu.getItemCount () > 0) { +if (seq != null) { +this.seqMenu.add (linkMenu); +} else { +this.add (linkMenu); +}}}if (seq != null) { +this.seqMenu.setLabel (seq.getName ()); +if (seq === this.ap.av.getAlignment ().getSeqrep ()) { +this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.unmark_as_reference")); +} else { +this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.set_as_reference")); +}this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [seq.getName ()]))); +} else { +this.remove (this.seqMenu); +}if (!this.ap.av.hasHiddenRows ()) { +this.remove (this.revealAll); +this.remove (this.revealSeq); +} else { +var index = this.ap.av.getAlignment ().findIndex (seq); +if (this.ap.av.adjustForHiddenSeqs (index) - this.ap.av.adjustForHiddenSeqs (index - 1) > 1) { +this.revealSeq_index = index; +} else { +this.remove (this.revealSeq); +}}}, "jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceI,java.util.Vector"); +Clazz.defineMethod (c$, "buildAnnotationSubmenus", +($fz = function () { +var selectedSequence = (this.seq == null ? java.util.Collections.emptyList () : java.util.Arrays.asList ([this.seq])); +this.buildAnnotationTypesMenus (this.seqShowAnnotationsMenu, this.seqHideAnnotationsMenu, selectedSequence); +this.configureReferenceAnnotationsMenu (this.seqAddReferenceAnnotations, selectedSequence); +var selectedGroup = (this.ap.av.getSelectionGroup () == null ? java.util.Collections.emptyList () : this.ap.av.getSelectionGroup ().getSequences ()); +this.buildAnnotationTypesMenus (this.groupShowAnnotationsMenu, this.groupHideAnnotationsMenu, selectedGroup); +this.configureReferenceAnnotationsMenu (this.groupAddReferenceAnnotations, selectedGroup); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "configureReferenceAnnotationsMenu", +($fz = function (menuItem, forSequences) { +menuItem.setEnabled (false); +var tipEntries = new java.util.TreeMap (); +var candidates = new java.util.LinkedHashMap (); +var al = this.ap.av.getAlignment (); +jalview.analysis.AlignmentUtils.findAddableReferenceAnnotations (forSequences, tipEntries, candidates, al); +if (!candidates.isEmpty ()) { +var tooltip = new StringBuilder (64); +tooltip.append (jalview.util.MessageManager.getString ("label.add_annotations_for")); +menuItem.setEnabled (true); +menuItem.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$1") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$1, this, Clazz.cloneFinals ("candidates", candidates)))); +}}, $fz.isPrivate = true, $fz), "awt2swing.MenuItem,java.util.List"); +Clazz.defineMethod (c$, "addReferenceAnnotations_actionPerformed", +function (candidates) { +var selectionGroup = this.ap.av.getSelectionGroup (); +var alignment = this.ap.getAlignment (); +jalview.analysis.AlignmentUtils.addReferenceAnnotations (candidates, alignment, selectionGroup); +this.refresh (); +}, "java.util.Map"); +Clazz.defineMethod (c$, "addshowLink", +($fz = function (linkMenu, target, url) { +this.addshowLink (linkMenu, target, target, url); +}, $fz.isPrivate = true, $fz), "awt2swing.Menu,~S,~S"); +Clazz.defineMethod (c$, "addshowLink", +($fz = function (linkMenu, target, label, url) { +var item = new awt2swing.MenuItem (label); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$2") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$2, this, Clazz.cloneFinals ("url", url, "target", target)))); +linkMenu.add (item); +}, $fz.isPrivate = true, $fz), "awt2swing.Menu,~S,~S,~S"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +if (evt.getSource () === this.abovePIDColour) { +this.abovePIDColour_itemStateChanged (); +} else if (evt.getSource () === this.showColourText) { +this.showColourText_itemStateChanged (); +} else if (evt.getSource () === this.showText) { +this.showText_itemStateChanged (); +} else if (evt.getSource () === this.showBoxes) { +this.showBoxes_itemStateChanged (); +} else if (evt.getSource () === this.displayNonconserved) { +this.showNonconserved_itemStateChanged (); +}}, "java.awt.event.ItemEvent"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +var source = evt.getSource (); +if (source === this.clustalColour) { +this.clustalColour_actionPerformed (); +} else if (source === this.zappoColour) { +this.zappoColour_actionPerformed (); +} else if (source === this.taylorColour) { +this.taylorColour_actionPerformed (); +} else if (source === this.hydrophobicityColour) { +this.hydrophobicityColour_actionPerformed (); +} else if (source === this.helixColour) { +this.helixColour_actionPerformed (); +} else if (source === this.strandColour) { +this.strandColour_actionPerformed (); +} else if (source === this.turnColour) { +this.turnColour_actionPerformed (); +} else if (source === this.buriedColour) { +this.buriedColour_actionPerformed (); +} else if (source === this.nucleotideMenuItem) { +this.nucleotideMenuItem_actionPerformed (); +} else if (source === this.userDefinedColour) { +this.userDefinedColour_actionPerformed (); +} else if (source === this.PIDColour) { +this.PIDColour_actionPerformed (); +} else if (source === this.BLOSUM62Colour) { +this.BLOSUM62Colour_actionPerformed (); +} else if (source === this.noColourmenuItem) { +this.noColourmenuItem_actionPerformed (); +} else if (source === this.conservationMenuItem) { +this.conservationMenuItem_itemStateChanged (); +} else if (source === this.unGroupMenuItem) { +this.unGroupMenuItem_actionPerformed (); +} else if (source === this.createGroupMenuItem) { +this.createGroupMenuItem_actionPerformed (); +} else if (source === this.sequenceName) { +this.editName (); +} else if (source === this.makeReferenceSeq) { +this.makeReferenceSeq_actionPerformed (); +} else if (source === this.sequenceDetails) { +this.showSequenceDetails (); +} else if (source === this.selSeqDetails) { +this.showSequenceSelectionDetails (); +} else if (source === this.pdb) { +this.addPDB (); +} else if (source === this.hideSeqs) { +this.hideSequences (false); +} else if (source === this.repGroup) { +this.hideSequences (true); +} else if (source === this.revealSeq) { +this.ap.av.showSequence (this.revealSeq_index); +} else if (source === this.revealAll) { +this.ap.av.showAllHiddenSeqs (); +} else if (source === this.editGroupName) { +var dialog = new jalview.appletgui.EditNameDialog (this.getGroup ().getName (), this.getGroup ().getDescription (), " Group Name", "Group Description", this.ap.alignFrame, "Edit Group Name / Description", 500, 100, true); +if (dialog.accept) { +this.getGroup ().setName (dialog.getName ().$replace (' ', '_')); +this.getGroup ().setDescription (dialog.getDescription ()); +}} else if (source === this.copy) { +this.ap.alignFrame.copy_actionPerformed (); +} else if (source === this.cut) { +this.ap.alignFrame.cut_actionPerformed (); +} else if (source === this.editSequence) { +var sg = this.ap.av.getSelectionGroup (); +if (sg != null) { +if (this.seq == null) { +this.seq = sg.getSequenceAt (0); +}var dialog = new jalview.appletgui.EditNameDialog (this.seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1), null, "Edit Sequence ", null, this.ap.alignFrame, "Edit Sequence", 500, 100, true); +if (dialog.accept) { +var editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.edit_sequences"), jalview.commands.EditCommand.Action.REPLACE, dialog.getName ().$replace (' ', this.ap.av.getGapCharacter ()), sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), sg.getStartRes (), sg.getEndRes () + 1, this.ap.av.getAlignment ()); +this.ap.alignFrame.addHistoryItem (editCommand); +this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); +}}} else if (source === this.toUpper || source === this.toLower || source === this.toggleCase) { +var sg = this.ap.av.getSelectionGroup (); +if (sg != null) { +var startEnd = this.ap.av.getVisibleRegionBoundaries (sg.getStartRes (), sg.getEndRes () + 1); +var description; +var caseChange; +if (source === this.toggleCase) { +description = "Toggle Case"; +caseChange = jalview.commands.ChangeCaseCommand.TOGGLE_CASE; +} else if (source === this.toUpper) { +description = "To Upper Case"; +caseChange = jalview.commands.ChangeCaseCommand.TO_UPPER; +} else { +description = "To Lower Case"; +caseChange = jalview.commands.ChangeCaseCommand.TO_LOWER; +}var caseCommand = new jalview.commands.ChangeCaseCommand (description, sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), startEnd, caseChange); +this.ap.alignFrame.addHistoryItem (caseCommand); +this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); +}} else if (source === this.sequenceFeature) { +var sg = this.ap.av.getSelectionGroup (); +if (sg == null) { +return; +}var rsize = 0; +var gSize = sg.getSize (); +var rseqs; +var seqs = new Array (gSize); +var tfeatures; +var features = new Array (gSize); +for (var i = 0; i < gSize; i++) { +var start = sg.getSequenceAt (i).findPosition (sg.getStartRes ()); +var end = sg.findEndRes (sg.getSequenceAt (i)); +if (start <= end) { +seqs[rsize] = sg.getSequenceAt (i); +features[rsize] = new jalview.datamodel.SequenceFeature (null, null, null, start, end, "Jalview"); +rsize++; +}} +rseqs = new Array (rsize); +tfeatures = new Array (rsize); +System.arraycopy (seqs, 0, rseqs, 0, rsize); +System.arraycopy (features, 0, tfeatures, 0, rsize); +features = tfeatures; +seqs = rseqs; +if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) { +this.ap.alignFrame.sequenceFeatures.setState (true); +this.ap.av.setShowSequenceFeatures (true); +;this.ap.highlightSearchResults (null); +}} else { +this.outputText (evt); +}}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "outputText", +function (e) { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.selection_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500); +cap.setText ( new jalview.io.AppletFormatAdapter ().formatSequences (e.getActionCommand (), this.ap.av.getShowJVSuffix (), this.ap, true)); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "showSequenceSelectionDetails", +function () { +this.createSequenceDetailsReport (this.ap.av.getSequenceSelection ()); +}); +Clazz.defineMethod (c$, "showSequenceDetails", +function () { +this.createSequenceDetailsReport ( Clazz.newArray (-1, [this.seq])); +}); +Clazz.defineMethod (c$, "createSequenceDetailsReport", +function (sequences) { +var cap = new jalview.appletgui.CutAndPasteTransfer (false, this.ap.alignFrame); +var contents = new StringBuffer (); +for (var seq, $seq = 0, $$seq = sequences; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { +contents.append (jalview.util.MessageManager.formatMessage ("label.annotation_for_displayid", Clazz.newArray (-1, [seq.getDisplayId (true)]))); + new jalview.io.SequenceAnnotationReport (null).createSequenceAnnotationReport (contents, seq, true, true, false, (this.ap.seqPanel.seqCanvas.fr != null) ? this.ap.seqPanel.seqCanvas.fr.getMinMax () : null); +contents.append ("

"); +} +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, "Sequence Details for " + (sequences.length == 1 ? sequences[0].getDisplayId (true) : "Selection"), 600, 500); +cap.setText (jalview.util.MessageManager.formatMessage ("label.html_content", Clazz.newArray (-1, [contents.toString ()]))); +}, "~A"); +Clazz.defineMethod (c$, "editName", +function () { +var dialog = new jalview.appletgui.EditNameDialog (this.seq.getName (), this.seq.getDescription (), " Sequence Name", "Sequence Description", this.ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true); +if (dialog.accept) { +this.seq.setName (dialog.getName ()); +this.seq.setDescription (dialog.getDescription ()); +this.ap.paintAlignment (false); +}}); +Clazz.defineMethod (c$, "addPDB", +function () { +if (this.seq.getPDBId () != null) { +var entry = this.seq.getPDBId ().firstElement (); +if (this.ap.av.applet.jmolAvailable) { + new jalview.appletgui.AppletJmol (entry, Clazz.newArray (-1, [this.seq]), null, this.ap, jalview.io.AppletFormatAdapter.URL); +}} else { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame); +cap.setText (jalview.util.MessageManager.getString ("label.paste_pdb_file")); +cap.setPDBImport (this.seq); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.paste_pdb_file_for_sequence", Clazz.newArray (-1, [this.seq.getName ()])), 400, 300); +}}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.groupMenu.setLabel (jalview.util.MessageManager.getString ("label.selection")); +this.sequenceFeature.addActionListener (this); +this.editGroupName.addActionListener (this); +this.unGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_group")); +this.unGroupMenuItem.addActionListener (this); +this.createGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.create_group")); +this.createGroupMenuItem.addActionListener (this); +this.nucleotideMenuItem.setLabel (jalview.util.MessageManager.getString ("label.nucleotide")); +this.nucleotideMenuItem.addActionListener (this); +this.conservationMenuItem.addItemListener (this); +this.abovePIDColour.addItemListener (this); +this.colourMenu.setLabel (jalview.util.MessageManager.getString ("label.group_colour")); +this.showBoxes.setLabel (jalview.util.MessageManager.getString ("action.boxes")); +this.showBoxes.setState (true); +this.showBoxes.addItemListener (this); +this.sequenceName.addActionListener (this); +this.sequenceDetails.addActionListener (this); +this.selSeqDetails.addActionListener (this); +this.displayNonconserved.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed")); +this.displayNonconserved.setState (false); +this.displayNonconserved.addItemListener (this); +this.showText.setLabel (jalview.util.MessageManager.getString ("action.text")); +this.showText.addItemListener (this); +this.showColourText.setLabel (jalview.util.MessageManager.getString ("label.colour_text")); +this.showColourText.addItemListener (this); +this.outputmenu.setLabel (jalview.util.MessageManager.getString ("label.out_to_textbox")); +this.seqMenu.setLabel (jalview.util.MessageManager.getString ("label.sequence")); +this.pdb.setLabel (jalview.util.MessageManager.getString ("label.view_pdb_structure")); +this.hideSeqs.setLabel (jalview.util.MessageManager.getString ("action.hide_sequences")); +this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [""]))); +this.revealAll.setLabel (jalview.util.MessageManager.getString ("action.reveal_all")); +this.revealSeq.setLabel (jalview.util.MessageManager.getString ("action.reveal_sequences")); +this.menu1.setLabel (jalview.util.MessageManager.getString ("label.group") + ":"); +this.add (this.groupMenu); +this.add (this.seqMenu); +this.add (this.hideSeqs); +this.add (this.revealSeq); +this.add (this.revealAll); +this.groupMenu.add (this.groupShowAnnotationsMenu); +this.groupMenu.add (this.groupHideAnnotationsMenu); +this.groupMenu.add (this.groupAddReferenceAnnotations); +this.groupMenu.add (this.editMenu); +this.groupMenu.add (this.outputmenu); +this.groupMenu.add (this.sequenceFeature); +this.groupMenu.add (this.createGroupMenuItem); +this.groupMenu.add (this.unGroupMenuItem); +this.groupMenu.add (this.menu1); +this.colourMenu.add (this.noColourmenuItem); +this.colourMenu.add (this.clustalColour); +this.colourMenu.add (this.BLOSUM62Colour); +this.colourMenu.add (this.PIDColour); +this.colourMenu.add (this.zappoColour); +this.colourMenu.add (this.taylorColour); +this.colourMenu.add (this.hydrophobicityColour); +this.colourMenu.add (this.helixColour); +this.colourMenu.add (this.strandColour); +this.colourMenu.add (this.turnColour); +this.colourMenu.add (this.buriedColour); +this.colourMenu.add (this.nucleotideMenuItem); +this.colourMenu.add (this.userDefinedColour); +this.colourMenu.addSeparator (); +this.colourMenu.add (this.abovePIDColour); +this.colourMenu.add (this.conservationMenuItem); +this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none")); +this.noColourmenuItem.addActionListener (this); +this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx_colours")); +this.clustalColour.addActionListener (this); +this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo")); +this.zappoColour.addActionListener (this); +this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor")); +this.taylorColour.addActionListener (this); +this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity")); +this.hydrophobicityColour.addActionListener (this); +this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity")); +this.helixColour.addActionListener (this); +this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity")); +this.strandColour.addActionListener (this); +this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity")); +this.turnColour.addActionListener (this); +this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index")); +this.buriedColour.addActionListener (this); +this.abovePIDColour.setLabel (jalview.util.MessageManager.getString ("label.above_identity_percentage")); +this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined")); +this.userDefinedColour.addActionListener (this); +this.PIDColour.setLabel (jalview.util.MessageManager.getString ("action.percentage_identity")); +this.PIDColour.addActionListener (this); +this.BLOSUM62Colour.setLabel ("BLOSUM62"); +this.BLOSUM62Colour.addActionListener (this); +this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("label.conservation")); +this.editMenu.add (this.copy); +this.copy.addActionListener (this); +this.editMenu.add (this.cut); +this.cut.addActionListener (this); +this.editMenu.add (this.editSequence); +this.editSequence.addActionListener (this); +this.editMenu.add (this.toUpper); +this.toUpper.addActionListener (this); +this.editMenu.add (this.toLower); +this.toLower.addActionListener (this); +this.editMenu.add (this.toggleCase); +this.seqMenu.add (this.seqShowAnnotationsMenu); +this.seqMenu.add (this.seqHideAnnotationsMenu); +this.seqMenu.add (this.seqAddReferenceAnnotations); +this.seqMenu.add (this.sequenceName); +this.seqMenu.add (this.makeReferenceSeq); +if (!this.ap.av.applet.useXtrnalSviewer) { +this.seqMenu.add (this.pdb); +}this.seqMenu.add (this.repGroup); +this.menu1.add (this.editGroupName); +this.menu1.add (this.colourMenu); +this.menu1.add (this.showBoxes); +this.menu1.add (this.showText); +this.menu1.add (this.showColourText); +this.menu1.add (this.displayNonconserved); +this.toggleCase.addActionListener (this); +this.pdb.addActionListener (this); +this.hideSeqs.addActionListener (this); +this.repGroup.addActionListener (this); +this.revealAll.addActionListener (this); +this.revealSeq.addActionListener (this); +this.makeReferenceSeq.addActionListener (this); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "refresh", +function () { +this.ap.paintAlignment (true); +}); +Clazz.defineMethod (c$, "clustalColour_actionPerformed", +function () { +var sg = this.getGroup (); +sg.cs = new jalview.schemes.ClustalxColourScheme (sg, this.ap.av.getHiddenRepSequences ()); +this.refresh (); +}); +Clazz.defineMethod (c$, "zappoColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.ZappoColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "taylorColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.TaylorColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "hydrophobicityColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.HydrophobicColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "helixColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.HelixColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "strandColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.StrandColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "turnColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.TurnColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "buriedColour_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.BuriedColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "nucleotideMenuItem_actionPerformed", +function () { +this.getGroup ().cs = new jalview.schemes.NucleotideColourScheme (); +this.refresh (); +}); +Clazz.defineMethod (c$, "abovePIDColour_itemStateChanged", +function () { +var sg = this.getGroup (); +if (sg.cs == null) { +return; +}if (this.abovePIDColour.getState ()) { +sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ())); +var threshold = jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, sg.cs, this.getGroup ().getName ()); +sg.cs.setThreshold (threshold, this.ap.av.isIgnoreGapsConsensus ()); +jalview.appletgui.SliderPanel.showPIDSlider (); +} else { +sg.cs.setThreshold (0, this.ap.av.isIgnoreGapsConsensus ()); +}this.refresh (); +}); +Clazz.defineMethod (c$, "userDefinedColour_actionPerformed", +function () { + new jalview.appletgui.UserDefinedColours (this.ap, this.getGroup ()); +}); +Clazz.defineMethod (c$, "PIDColour_actionPerformed", +function () { +var sg = this.getGroup (); +sg.cs = new jalview.schemes.PIDColourScheme (); +sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ())); +this.refresh (); +}); +Clazz.defineMethod (c$, "BLOSUM62Colour_actionPerformed", +function () { +var sg = this.getGroup (); +sg.cs = new jalview.schemes.Blosum62ColourScheme (); +sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ())); +this.refresh (); +}); +Clazz.defineMethod (c$, "noColourmenuItem_actionPerformed", +function () { +this.getGroup ().cs = null; +this.refresh (); +}); +Clazz.defineMethod (c$, "conservationMenuItem_itemStateChanged", +function () { +var sg = this.getGroup (); +if (sg.cs == null) { +return; +}if (this.conservationMenuItem.getState ()) { +sg.cs.setConservation (jalview.analysis.Conservation.calculateConservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth (), false, this.ap.av.getConsPercGaps (), false)); +jalview.appletgui.SliderPanel.setConservationSlider (this.ap, sg.cs, sg.getName ()); +jalview.appletgui.SliderPanel.showConservationSlider (); +} else { +sg.cs.setConservation (null); +}this.refresh (); +}); +Clazz.defineMethod (c$, "getGroup", +function () { +var sg = this.ap.av.getSelectionGroup (); +if (sg != null) { +this.ap.av.getAlignment ().addGroup (sg); +}return sg; +}); +Clazz.defineMethod (c$, "unGroupMenuItem_actionPerformed", +function () { +var sg = this.ap.av.getSelectionGroup (); +this.ap.av.getAlignment ().deleteGroup (sg); +this.ap.av.setSelectionGroup (null); +this.ap.paintAlignment (true); +}); +Clazz.defineMethod (c$, "createGroupMenuItem_actionPerformed", +function () { +this.getGroup (); +this.refresh (); +}); +Clazz.defineMethod (c$, "showColourText_itemStateChanged", +function () { +this.getGroup ().setColourText (this.showColourText.getState ()); +this.refresh (); +}); +Clazz.defineMethod (c$, "showText_itemStateChanged", +function () { +this.getGroup ().setDisplayText (this.showText.getState ()); +this.refresh (); +}); +Clazz.defineMethod (c$, "makeReferenceSeq_actionPerformed", +function () { +if (!this.ap.av.getAlignment ().hasSeqrep ()) { +this.ap.av.setDisplayReferenceSeq (true); +this.ap.av.setColourByReferenceSeq (true); +this.ap.av.getAlignment ().setSeqrep (this.seq); +} else { +if (this.ap.av.getAlignment ().getSeqrep () === this.seq) { +this.ap.av.getAlignment ().setSeqrep (null); +} else { +this.ap.av.getAlignment ().setSeqrep (this.seq); +}}this.refresh (); +}); +Clazz.defineMethod (c$, "showNonconserved_itemStateChanged", +function () { +this.getGroup ().setShowNonconserved (this.displayNonconserved.getState ()); +this.refresh (); +}); +Clazz.defineMethod (c$, "showBoxes_itemStateChanged", +function () { +this.getGroup ().setDisplayBoxes (this.showBoxes.getState ()); +this.refresh (); +}); +Clazz.defineMethod (c$, "hideSequences", +function (representGroup) { +var sg = this.ap.av.getSelectionGroup (); +if (sg == null || sg.getSize () < 1) { +this.ap.av.hideSequence ( Clazz.newArray (-1, [this.seq])); +return; +}this.ap.av.setSelectionGroup (null); +if (representGroup) { +this.ap.av.hideRepSequences (this.seq, sg); +return; +}var gsize = sg.getSize (); +var hseqs; +hseqs = new Array (gsize); +var index = 0; +for (var i = 0; i < gsize; i++) { +hseqs[index++] = sg.getSequenceAt (i); +} +this.ap.av.hideSequence (hseqs); +this.ap.av.sendSelection (); +}, "~B"); +Clazz.defineMethod (c$, "buildAnnotationTypesMenus", +function (showMenu, hideMenu, forSequences) { +showMenu.removeAll (); +hideMenu.removeAll (); +var all = java.util.Arrays.asList (["All"]); +this.addAnnotationTypeToShowHide (showMenu, forSequences, "", all, true, true); +this.addAnnotationTypeToShowHide (hideMenu, forSequences, "", all, true, false); +showMenu.addSeparator (); +hideMenu.addSeparator (); +var annotations = this.ap.getAlignment ().getAlignmentAnnotation (); +var shownTypes = new java.util.LinkedHashMap (); +var hiddenTypes = new java.util.LinkedHashMap (); +jalview.analysis.AlignmentAnnotationUtils.getShownHiddenTypes (shownTypes, hiddenTypes, jalview.analysis.AlignmentAnnotationUtils.asList (annotations), forSequences); +for (var calcId, $calcId = hiddenTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) { +for (var type, $type = hiddenTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) { +this.addAnnotationTypeToShowHide (showMenu, forSequences, calcId, type, false, true); +} +} +showMenu.setEnabled (!hiddenTypes.isEmpty ()); +for (var calcId, $calcId = shownTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) { +for (var type, $type = shownTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) { +this.addAnnotationTypeToShowHide (hideMenu, forSequences, calcId, type, false, false); +} +} +hideMenu.setEnabled (!shownTypes.isEmpty ()); +}, "awt2swing.Menu,awt2swing.Menu,java.util.List"); +Clazz.defineMethod (c$, "addAnnotationTypeToShowHide", +function (showOrHideMenu, forSequences, calcId, types, allTypes, actionIsShow) { +var label = types.toString (); +label = label.substring (1, label.length - 1); +var item = new awt2swing.MenuItem (label); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$3") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$3, this, Clazz.cloneFinals ("types", types, "forSequences", forSequences, "allTypes", allTypes, "actionIsShow", actionIsShow)))); +showOrHideMenu.add (item); +}, "awt2swing.Menu,java.util.List,~S,java.util.List,~B,~B"); +c$.$APopupMenu$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$1", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.APopupMenu"].addReferenceAnnotations_actionPerformed (this.f$.candidates); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$APopupMenu$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$2", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.APopupMenu"].ap.alignFrame.showURL (this.f$.url, this.f$.target); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$APopupMenu$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$3", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations (this.b$["jalview.appletgui.APopupMenu"].ap.getAlignment (), this.f$.types, this.f$.forSequences, this.f$.allTypes, this.f$.actionIsShow); +this.b$["jalview.appletgui.APopupMenu"].refresh (); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"ALL_ANNOTATIONS", "All"); +}); diff --git a/bin/jalview/appletgui/AlignFrame.class b/bin/jalview/appletgui/AlignFrame.class index c5a8472..f1ac80b 100644 Binary files a/bin/jalview/appletgui/AlignFrame.class and b/bin/jalview/appletgui/AlignFrame.class differ diff --git a/bin/jalview/appletgui/AlignFrame.js b/bin/jalview/appletgui/AlignFrame.js index 7221f66..f3c3d8e 100644 --- a/bin/jalview/appletgui/AlignFrame.js +++ b/bin/jalview/appletgui/AlignFrame.js @@ -1,2390 +1,2390 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Canvas", "jalview.api.AlignViewControllerGuiI", "jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "$.KeyListener", "awt2swing.CheckboxMenuItem", "$.Label", "$.Menu", "$.MenuBar", "$.MenuItem", "jalview.util.MessageManager", "java.awt.BorderLayout"], "jalview.appletgui.AlignFrame", ["awt2swing.Frame", "jalview.analysis.AlignmentSorter", "$.AnnotationSorter", "jalview.appletgui.AlignViewport", "$.AlignmentPanel", "$.AnnotationColourChooser", "$.AnnotationColumnChooser", "$.AppletJmol", "$.CutAndPasteTransfer", "$.FeatureSettings", "$.Finder", "$.FontChooser", "$.OverviewPanel", "$.PCAPanel", "$.PaintRefresher", "$.PairwiseAlignPanel", "$.RedundancyPanel", "$.SliderPanel", "$.TreePanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "$.OrderCommand", "$.RemoveGapColCommand", "$.RemoveGapsCommand", "$.SlideSequencesCommand", "$.TrimRegionCommand", "jalview.controller.AlignViewController", "jalview.datamodel.Alignment", "$.PDBEntry", "$.Sequence", "$.SequenceGroup", "jalview.io.AlignmentProperties", "$.AnnotationFile", "$.AppletFormatAdapter", "$.FeaturesFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColourChooser", "$.RNAInteractionColourScheme", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.structure.StructureSelectionManager", "jalview.util.Comparison", "$.MappingUtils", "java.awt.Color", "$.Font", "java.awt.event.FocusListener", "$.WindowAdapter", "java.lang.Character", "$.StringBuffer", "java.net.URL", "$.URLEncoder", "java.util.Arrays", "$.HashMap", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.avc = null; -this.alignPanel = null; -this.viewport = null; -this.frameWidth = 700; -this.frameHeight = 500; -this.jalviewServletURL = null; -this.showAutoCalculatedAbove = false; -this.annotationSortOrder = null; -this.alignFrameMenuBar = null; -this.fileMenu = null; -this.loadApplication = null; -this.$loadTree = null; -this.$loadAnnotations = null; -this.$outputFeatures = null; -this.$outputAnnotations = null; -this.closeMenuItem = null; -this.selectAllSequenceMenuItem = null; -this.deselectAllSequenceMenuItem = null; -this.invertSequenceMenuItem = null; -this.remove2LeftMenuItem = null; -this.remove2RightMenuItem = null; -this.removeGappedColumnMenuItem = null; -this.removeAllGapsMenuItem = null; -this.viewBoxesMenuItem = null; -this.viewTextMenuItem = null; -this.sortPairwiseMenuItem = null; -this.sortIDMenuItem = null; -this.sortLengthMenuItem = null; -this.sortGroupMenuItem = null; -this.removeRedundancyMenuItem = null; -this.pairwiseAlignmentMenuItem = null; -this.PCAMenuItem = null; -this.averageDistanceTreeMenuItem = null; -this.neighbourTreeMenuItem = null; -this.borderLayout1 = null; -this.statusBar = null; -this.clustalColour = null; -this.zappoColour = null; -this.taylorColour = null; -this.hydrophobicityColour = null; -this.helixColour = null; -this.strandColour = null; -this.turnColour = null; -this.buriedColour = null; -this.purinePyrimidineColour = null; -this.RNAInteractionColour = null; -this.RNAHelixColour = null; -this.userDefinedColour = null; -this.PIDColour = null; -this.BLOSUM62Colour = null; -this.tcoffeeColour = null; -this.njTreeBlosumMenuItem = null; -this.avDistanceTreeBlosumMenuItem = null; -this.annotationPanelMenuItem = null; -this.colourTextMenuItem = null; -this.displayNonconservedMenuItem = null; -this.alProperties = null; -this.overviewMenuItem = null; -this.undoMenuItem = null; -this.redoMenuItem = null; -this.conservationMenuItem = null; -this.noColourmenuItem = null; -this.wrapMenuItem = null; -this.renderGapsMenuItem = null; -this.findMenuItem = null; -this.abovePIDThreshold = null; -this.nucleotideColour = null; -this.deleteGroups = null; -this.grpsFromSelection = null; -this.createGroup = null; -this.unGroup = null; -this.$delete = null; -this.copy = null; -this.cut = null; -this.pasteMenu = null; -this.pasteNew = null; -this.pasteThis = null; -this.applyToAllGroups = null; -this.$font = null; -this.scaleAbove = null; -this.scaleLeft = null; -this.scaleRight = null; -this.modifyPID = null; -this.modifyConservation = null; -this.autoCalculate = null; -this.$sortByTree = null; -this.sortByTreeMenu = null; -this.inputText = null; -this.documentation = null; -this.about = null; -this.seqLimits = null; -this.centreColumnLabelFlag = null; -this.followMouseOverFlag = null; -this.showSequenceLogo = null; -this.applyAutoAnnotationSettings = null; -this.showConsensusHistogram = null; -this.showGroupConsensus = null; -this.showGroupConservation = null; -this.normSequenceLogo = null; -this.featureSettings = null; -this.sequenceFeatures = null; -this.annotationColour = null; -this.annotationColumnSelection = null; -this.invertColSel = null; -this.showColumns = null; -this.showSeqs = null; -this.hideColumns = null; -this.hideSequences = null; -this.hideAllButSelection = null; -this.hideAllSelection = null; -this.showAllHidden = null; -this.$newView = null; -this.showAlignmentAnnotations = null; -this.showSequenceAnnotations = null; -this.sortAnnBySequence = null; -this.sortAnnByLabel = null; -this.showAutoFirst = null; -this.showAutoLast = null; -this.splitFrame = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AlignFrame", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.KeyListener, jalview.api.AlignViewControllerGuiI]); -Clazz.prepareFields (c$, function () { -this.alignFrameMenuBar = new awt2swing.MenuBar (); -this.fileMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.file")); -this.loadApplication = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.view_full_application")); -this.$loadTree = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.load_associated_tree")); -this.$loadAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.load_features_annotations")); -this.$outputFeatures = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.export_features").concat ("...")); -this.$outputAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.export_annotations").concat ("...")); -this.closeMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.close")); -this.selectAllSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.select_all")); -this.deselectAllSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.deselect_all")); -this.invertSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.invert_selection")); -this.remove2LeftMenuItem = new awt2swing.MenuItem (); -this.remove2RightMenuItem = new awt2swing.MenuItem (); -this.removeGappedColumnMenuItem = new awt2swing.MenuItem (); -this.removeAllGapsMenuItem = new awt2swing.MenuItem (); -this.viewBoxesMenuItem = new awt2swing.CheckboxMenuItem (); -this.viewTextMenuItem = new awt2swing.CheckboxMenuItem (); -this.sortPairwiseMenuItem = new awt2swing.MenuItem (); -this.sortIDMenuItem = new awt2swing.MenuItem (); -this.sortLengthMenuItem = new awt2swing.MenuItem (); -this.sortGroupMenuItem = new awt2swing.MenuItem (); -this.removeRedundancyMenuItem = new awt2swing.MenuItem (); -this.pairwiseAlignmentMenuItem = new awt2swing.MenuItem (); -this.PCAMenuItem = new awt2swing.MenuItem (); -this.averageDistanceTreeMenuItem = new awt2swing.MenuItem (); -this.neighbourTreeMenuItem = new awt2swing.MenuItem (); -this.borderLayout1 = new java.awt.BorderLayout (); -this.statusBar = new awt2swing.Label (); -this.clustalColour = new awt2swing.MenuItem (); -this.zappoColour = new awt2swing.MenuItem (); -this.taylorColour = new awt2swing.MenuItem (); -this.hydrophobicityColour = new awt2swing.MenuItem (); -this.helixColour = new awt2swing.MenuItem (); -this.strandColour = new awt2swing.MenuItem (); -this.turnColour = new awt2swing.MenuItem (); -this.buriedColour = new awt2swing.MenuItem (); -this.purinePyrimidineColour = new awt2swing.MenuItem (); -this.RNAInteractionColour = new awt2swing.MenuItem (); -this.RNAHelixColour = new awt2swing.MenuItem (); -this.userDefinedColour = new awt2swing.MenuItem (); -this.PIDColour = new awt2swing.MenuItem (); -this.BLOSUM62Colour = new awt2swing.MenuItem (); -this.tcoffeeColour = new awt2swing.MenuItem (); -this.njTreeBlosumMenuItem = new awt2swing.MenuItem (); -this.avDistanceTreeBlosumMenuItem = new awt2swing.MenuItem (); -this.annotationPanelMenuItem = new awt2swing.CheckboxMenuItem (); -this.colourTextMenuItem = new awt2swing.CheckboxMenuItem (); -this.displayNonconservedMenuItem = new awt2swing.CheckboxMenuItem (); -this.alProperties = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.alignment_props")); -this.overviewMenuItem = new awt2swing.MenuItem (); -this.undoMenuItem = new awt2swing.MenuItem (); -this.redoMenuItem = new awt2swing.MenuItem (); -this.conservationMenuItem = new awt2swing.CheckboxMenuItem (); -this.noColourmenuItem = new awt2swing.MenuItem (); -this.wrapMenuItem = new awt2swing.CheckboxMenuItem (); -this.renderGapsMenuItem = new awt2swing.CheckboxMenuItem (); -this.findMenuItem = new awt2swing.MenuItem (); -this.abovePIDThreshold = new awt2swing.CheckboxMenuItem (); -this.nucleotideColour = new awt2swing.MenuItem (); -this.deleteGroups = new awt2swing.MenuItem (); -this.grpsFromSelection = new awt2swing.MenuItem (); -this.createGroup = new awt2swing.MenuItem (); -this.unGroup = new awt2swing.MenuItem (); -this.$delete = new awt2swing.MenuItem (); -this.copy = new awt2swing.MenuItem (); -this.cut = new awt2swing.MenuItem (); -this.pasteMenu = new awt2swing.Menu (); -this.pasteNew = new awt2swing.MenuItem (); -this.pasteThis = new awt2swing.MenuItem (); -this.applyToAllGroups = new awt2swing.CheckboxMenuItem (); -this.$font = new awt2swing.MenuItem (); -this.scaleAbove = new awt2swing.CheckboxMenuItem (); -this.scaleLeft = new awt2swing.CheckboxMenuItem (); -this.scaleRight = new awt2swing.CheckboxMenuItem (); -this.modifyPID = new awt2swing.MenuItem (); -this.modifyConservation = new awt2swing.MenuItem (); -this.$sortByTree = new awt2swing.CheckboxMenuItem ("Sort Alignment With New Tree", true); -this.sortByTreeMenu = new awt2swing.Menu (); -this.inputText = new awt2swing.MenuItem (); -this.documentation = new awt2swing.MenuItem (); -this.about = new awt2swing.MenuItem (); -this.seqLimits = new awt2swing.CheckboxMenuItem (); -this.centreColumnLabelFlag = new awt2swing.CheckboxMenuItem (); -this.followMouseOverFlag = new awt2swing.CheckboxMenuItem (); -this.showSequenceLogo = new awt2swing.CheckboxMenuItem (); -this.applyAutoAnnotationSettings = new awt2swing.CheckboxMenuItem (); -this.showConsensusHistogram = new awt2swing.CheckboxMenuItem (); -this.showGroupConsensus = new awt2swing.CheckboxMenuItem (); -this.showGroupConservation = new awt2swing.CheckboxMenuItem (); -this.normSequenceLogo = new awt2swing.CheckboxMenuItem (); -this.featureSettings = new awt2swing.MenuItem (); -this.sequenceFeatures = new awt2swing.CheckboxMenuItem (); -this.annotationColour = new awt2swing.MenuItem (); -this.annotationColumnSelection = new awt2swing.MenuItem (); -this.invertColSel = new awt2swing.MenuItem (); -this.showColumns = new awt2swing.MenuItem (); -this.showSeqs = new awt2swing.MenuItem (); -this.hideColumns = new awt2swing.MenuItem (); -this.hideSequences = new awt2swing.MenuItem (); -this.hideAllButSelection = new awt2swing.MenuItem (); -this.hideAllSelection = new awt2swing.MenuItem (); -this.showAllHidden = new awt2swing.MenuItem (); -this.$newView = new awt2swing.MenuItem (); -}); -Clazz.makeConstructor (c$, -function (al, applet, title, embedded) { -this.construct (al, applet, title, embedded, true); -}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B"); -Clazz.makeConstructor (c$, -function (al, applet, title, embedded, addToDisplay) { -this.construct (al, null, null, applet, title, embedded, addToDisplay); -}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B"); -Clazz.makeConstructor (c$, -function (al, hiddenSeqs, columnSelection, applet, title, embedded) { -this.construct (al, hiddenSeqs, columnSelection, applet, title, embedded, true); -}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B"); -Clazz.makeConstructor (c$, -function (al, hiddenSeqs, columnSelection, applet, title, embedded, addToDisplay) { -Clazz.superConstructor (this, jalview.appletgui.AlignFrame, []); -if (applet != null) { -this.jalviewServletURL = applet.jalviewServletURL; -}try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -if (applet != null) { -var param; -try { -param = applet.windowWidth; -if (param != null) { -var width = Integer.parseInt (param); -this.frameWidth = width; -}param = applet.windowHeight; -if (param != null) { -var height = Integer.parseInt (param); -this.frameHeight = height; -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}this.viewport = new jalview.appletgui.AlignViewport (al, applet); -if (hiddenSeqs != null && hiddenSeqs.length > 0) { -this.viewport.hideSequence (hiddenSeqs); -}if (columnSelection != null) { -this.viewport.setColumnSelection (columnSelection); -}this.alignPanel = new jalview.appletgui.AlignmentPanel (this, this.viewport); -this.avc = new jalview.controller.AlignViewController (this, this.viewport, this.alignPanel); -this.viewport.updateConservation (this.alignPanel); -this.viewport.updateConsensus (this.alignPanel); -this.displayNonconservedMenuItem.setState (this.viewport.getShowUnconserved ()); -this.followMouseOverFlag.setState (this.viewport.isFollowHighlight ()); -this.showGroupConsensus.setState (this.viewport.isShowGroupConsensus ()); -this.showGroupConservation.setState (this.viewport.isShowGroupConservation ()); -this.showConsensusHistogram.setState (this.viewport.isShowConsensusHistogram ()); -this.showSequenceLogo.setState (this.viewport.isShowSequenceLogo ()); -this.normSequenceLogo.setState (this.viewport.isNormaliseSequenceLogo ()); -this.applyToAllGroups.setState (this.viewport.getColourAppliesToAllGroups ()); -this.annotationPanelMenuItem.setState (this.viewport.isShowAnnotation ()); -this.showAlignmentAnnotations.setState (this.viewport.isShowAnnotation ()); -this.showSequenceAnnotations.setState (this.viewport.isShowAnnotation ()); -this.seqLimits.setState (this.viewport.getShowJVSuffix ()); -if (applet != null) { -var param = applet.sortBy; -if (param != null) { -if (param.equalsIgnoreCase ("Id")) { -this.sortIDMenuItem_actionPerformed (); -} else if (param.equalsIgnoreCase ("Pairwise Identity")) { -this.sortPairwiseMenuItem_actionPerformed (); -} else if (param.equalsIgnoreCase ("Length")) { -this.sortLengthMenuItem_actionPerformed (); -}}param = applet.wrap; -if (param != null) { -if (param.equalsIgnoreCase ("true")) { -this.wrapMenuItem.setState (true); -this.wrapMenuItem_actionPerformed (); -}}param = applet.centrecolumnlabels; -if (param != null) { -this.centreColumnLabelFlag.setState (true); -this.centreColumnLabelFlag_stateChanged (); -}}if (this.viewport.getAlignment ().isNucleotide ()) { -this.viewport.updateStrucConsensus (this.alignPanel); -if (this.viewport.getAlignment ().hasRNAStructure ()) { -this.RNAHelixColour.setEnabled (true); -} else { -this.RNAHelixColour.setEnabled (false); -}} else { -this.RNAHelixColour.setEnabled (false); -this.purinePyrimidineColour.setEnabled (false); -}this.addKeyListener (this); -this.alignPanel.seqPanel.seqCanvas.addKeyListener (this); -this.alignPanel.idPanel.idCanvas.addKeyListener (this); -this.alignPanel.scalePanel.addKeyListener (this); -this.alignPanel.annotationPanel.addKeyListener (this); -this.alignPanel.annotationPanelHolder.addKeyListener (this); -this.alignPanel.annotationSpaceFillerHolder.addKeyListener (this); -this.alignPanel.alabels.addKeyListener (this); -if (addToDisplay) { -this.addToDisplay (embedded); -}}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B"); -Clazz.defineMethod (c$, "addToDisplay", -function (embedded) { -this.createAlignFrameWindow (embedded); -this.validate (); -this.alignPanel.adjustAnnotationHeight (); -this.alignPanel.paintAlignment (true); -}, "~B"); -Clazz.defineMethod (c$, "getAlignViewport", -function () { -return this.viewport; -}); -Clazz.defineMethod (c$, "getSeqcanvas", -function () { -return this.alignPanel.seqPanel.seqCanvas; -}); -Clazz.defineMethod (c$, "parseFeaturesFile", -function (file, type) { -return this.parseFeaturesFile (file, type, true); -}, "~S,~S"); -Clazz.defineMethod (c$, "parseFeaturesFile", -function (file, type, autoenabledisplay) { -var featureLinks = new java.util.Hashtable (); -var featuresFile = false; -try { -featuresFile = new jalview.io.FeaturesFile (file, type).parse (this.viewport.getAlignment (), this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().getFeatureColours (), featureLinks, true, this.viewport.applet.getDefaultParameter ("relaxedidmatch", false)); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -if (featuresFile) { -if (featureLinks.size () > 0) { -this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().featureLinks = featureLinks; -}if (autoenabledisplay) { -this.viewport.setShowSequenceFeatures (true); -this.sequenceFeatures.setState (true); -}if (this.alignPanel.seqPanel.seqCanvas.fr != null) { -this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures (true); -}if (this.viewport.featureSettings != null) { -this.viewport.featureSettings.refreshTable (); -}this.alignPanel.paintAlignment (true); -this.setStatus (jalview.util.MessageManager.getString ("label.successfully_added_features_alignment")); -}return featuresFile; -}, "~S,~S,~B"); -Clazz.overrideMethod (c$, "keyPressed", -function (evt) { -if (this.viewport.cursorMode && ((evt.getKeyCode () >= 48 && evt.getKeyCode () <= 57) || (evt.getKeyCode () >= 96 && evt.getKeyCode () <= 105)) && Character.isDigit (evt.getKeyChar ())) { -this.alignPanel.seqPanel.numberPressed (evt.getKeyChar ()); -}switch (evt.getKeyCode ()) { -case 27: -this.deselectAllSequenceMenuItem_actionPerformed (); -this.alignPanel.alabels.cancelDrag (); -break; -case 88: -if (evt.isControlDown () || evt.isMetaDown ()) { -this.cut_actionPerformed (); -}break; -case 67: -if (this.viewport.cursorMode && !evt.isControlDown ()) { -this.alignPanel.seqPanel.setCursorColumn (); -}if (evt.isControlDown () || evt.isMetaDown ()) { -this.copy_actionPerformed (); -}break; -case 86: -if (evt.isControlDown ()) { -this.paste (evt.isShiftDown ()); -}break; -case 65: -if (evt.isControlDown () || evt.isMetaDown ()) { -this.selectAllSequenceMenuItem_actionPerformed (); -}break; -case 40: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (0, 1); -} else { -this.moveSelectedSequences (false); -}break; -case 38: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (0, -1); -} else { -this.moveSelectedSequences (true); -}break; -case 37: -if (evt.isAltDown () || !this.viewport.cursorMode) { -this.slideSequences (false, this.alignPanel.seqPanel.getKeyboardNo1 ()); -} else { -this.alignPanel.seqPanel.moveCursor (-1, 0); -}break; -case 39: -if (evt.isAltDown () || !this.viewport.cursorMode) { -this.slideSequences (true, this.alignPanel.seqPanel.getKeyboardNo1 ()); -} else { -this.alignPanel.seqPanel.moveCursor (1, 0); -}break; -case 32: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.insertGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); -}break; -case 127: -case 8: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.deleteGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); -} else { -this.cut_actionPerformed (); -this.alignPanel.seqPanel.seqCanvas.repaint (); -}break; -case 83: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setCursorRow (); -}break; -case 80: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setCursorPosition (); -}break; -case 10: -case 44: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setCursorRowAndColumn (); -}break; -case 81: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setSelectionAreaAtCursor (true); -}break; -case 77: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setSelectionAreaAtCursor (false); -}break; -case 113: -this.viewport.cursorMode = !this.viewport.cursorMode; -this.setStatus (jalview.util.MessageManager.formatMessage ("label.keyboard_editing_mode", Clazz.newArray (-1, [(this.viewport.cursorMode ? "on" : "off")]))); -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.seqCanvas.cursorX = this.viewport.startRes; -this.alignPanel.seqPanel.seqCanvas.cursorY = this.viewport.startSeq; -}break; -case 70: -if (evt.isControlDown ()) { -this.findMenuItem_actionPerformed (); -}break; -case 72: -{ -var toggleSeqs = !evt.isControlDown (); -var toggleCols = !evt.isShiftDown (); -this.toggleHiddenRegions (toggleSeqs, toggleCols); -break; -}case 33: -if (this.viewport.getWrapAlignment ()) { -this.alignPanel.scrollUp (true); -} else { -this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq - this.viewport.endSeq + this.viewport.startSeq); -}break; -case 34: -if (this.viewport.getWrapAlignment ()) { -this.alignPanel.scrollUp (false); -} else { -this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq + this.viewport.endSeq - this.viewport.startSeq); -}break; -case 90: -if (evt.isControlDown ()) { -this.undoMenuItem_actionPerformed (); -}break; -case 89: -if (evt.isControlDown ()) { -this.redoMenuItem_actionPerformed (); -}break; -case 76: -if (evt.isControlDown ()) { -this.trimAlignment (true); -}break; -case 82: -if (evt.isControlDown ()) { -this.trimAlignment (false); -}break; -case 69: -if (evt.isControlDown ()) { -if (evt.isShiftDown ()) { -this.removeAllGapsMenuItem_actionPerformed (); -} else { -this.removeGappedColumnMenuItem_actionPerformed (); -}}break; -case 73: -if (evt.isControlDown ()) { -if (evt.isAltDown ()) { -this.invertColSel_actionPerformed (); -} else { -this.invertSequenceMenuItem_actionPerformed (); -}}break; -case 71: -if (evt.isControlDown ()) { -if (evt.isShiftDown ()) { -this.unGroup_actionPerformed (); -} else { -this.createGroup_actionPerformed (); -}}break; -case 85: -if (evt.isControlDown ()) { -this.deleteGroups_actionPerformed (); -}break; -case 84: -if (evt.isControlDown ()) { -this.newView (null); -}break; -} -this.alignPanel.paintAlignment (true); -}, "java.awt.event.KeyEvent"); -Clazz.defineMethod (c$, "toggleHiddenRegions", -($fz = function (toggleSeqs, toggleCols) { -var hide = false; -var sg = this.viewport.getSelectionGroup (); -if (!toggleSeqs && !toggleCols) { -if ((this.viewport.getColumnSelection () != null && this.viewport.getColumnSelection ().getSelected () != null && this.viewport.getColumnSelection ().getSelected ().size () > 0) || (sg != null && sg.getSize () > 0 && sg.getStartRes () <= sg.getEndRes ())) { -if (sg != null) { -this.invertSequenceMenuItem_actionPerformed (); -sg = this.viewport.getSelectionGroup (); -toggleSeqs = true; -}this.viewport.expandColSelection (sg, true); -this.invertColSel_actionPerformed (); -toggleCols = true; -}}if (toggleSeqs) { -if (sg != null && sg.getSize () != this.viewport.getAlignment ().getHeight ()) { -hide = true; -this.viewport.hideAllSelectedSeqs (); -} else if (!(toggleCols && this.viewport.getColumnSelection ().getSelected ().size () > 0)) { -this.viewport.showAllHiddenSeqs (); -}}if (toggleCols) { -if (this.viewport.getColumnSelection ().getSelected ().size () > 0) { -this.viewport.hideSelectedColumns (); -if (!toggleSeqs) { -this.viewport.setSelectionGroup (sg); -}} else if (!hide) { -this.viewport.showAllHiddenColumns (); -}}}, $fz.isPrivate = true, $fz), "~B,~B"); -Clazz.overrideMethod (c$, "keyReleased", -function (evt) { -}, "java.awt.event.KeyEvent"); -Clazz.overrideMethod (c$, "keyTyped", -function (evt) { -}, "java.awt.event.KeyEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -var source = evt.getSource (); -if (source === this.displayNonconservedMenuItem) { -this.displayNonconservedMenuItem_actionPerformed (); -} else if (source === this.colourTextMenuItem) { -this.colourTextMenuItem_actionPerformed (); -} else if (source === this.wrapMenuItem) { -this.wrapMenuItem_actionPerformed (); -} else if (source === this.scaleAbove) { -this.viewport.setScaleAboveWrapped (this.scaleAbove.getState ()); -} else if (source === this.scaleLeft) { -this.viewport.setScaleLeftWrapped (this.scaleLeft.getState ()); -} else if (source === this.scaleRight) { -this.viewport.setScaleRightWrapped (this.scaleRight.getState ()); -} else if (source === this.seqLimits) { -this.seqLimits_itemStateChanged (); -} else if (source === this.viewBoxesMenuItem) { -this.viewport.setShowBoxes (this.viewBoxesMenuItem.getState ()); -} else if (source === this.viewTextMenuItem) { -this.viewport.setShowText (this.viewTextMenuItem.getState ()); -} else if (source === this.renderGapsMenuItem) { -this.viewport.setRenderGaps (this.renderGapsMenuItem.getState ()); -} else if (source === this.annotationPanelMenuItem) { -this.viewport.setShowAnnotation (this.annotationPanelMenuItem.getState ()); -this.alignPanel.setAnnotationVisible (this.annotationPanelMenuItem.getState ()); -} else if (source === this.sequenceFeatures) { -this.viewport.setShowSequenceFeatures (this.sequenceFeatures.getState ()); -this.alignPanel.seqPanel.seqCanvas.repaint (); -} else if (source === this.showAlignmentAnnotations) { -this.setAnnotationsVisibility (); -} else if (source === this.showSequenceAnnotations) { -this.setAnnotationsVisibility (); -} else if (source === this.sortAnnBySequence) { -var newState = this.sortAnnBySequence.getState (); -this.sortAnnByLabel.setState (false); -this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); -this.setViewportAnnotationOrder (); -} else if (source === this.sortAnnByLabel) { -var newState = this.sortAnnByLabel.getState (); -this.sortAnnBySequence.setState (false); -this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); -this.setViewportAnnotationOrder (); -} else if (source === this.showAutoFirst) { -this.showAutoLast.setState (!this.showAutoFirst.getState ()); -this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); -this.setViewportAnnotationOrder (); -} else if (source === this.showAutoLast) { -this.showAutoFirst.setState (!this.showAutoLast.getState ()); -this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); -this.setViewportAnnotationOrder (); -} else if (source === this.conservationMenuItem) { -this.conservationMenuItem_actionPerformed (); -} else if (source === this.abovePIDThreshold) { -this.abovePIDThreshold_actionPerformed (); -} else if (source === this.applyToAllGroups) { -this.viewport.setColourAppliesToAllGroups (this.applyToAllGroups.getState ()); -} else if (source === this.autoCalculate) { -this.viewport.autoCalculateConsensus = this.autoCalculate.getState (); -} else if (source === this.$sortByTree) { -this.viewport.sortByTree = this.$sortByTree.getState (); -} else if (source === this.centreColumnLabelFlag) { -this.centreColumnLabelFlag_stateChanged (); -} else if (source === this.followMouseOverFlag) { -this.mouseOverFlag_stateChanged (); -} else if (source === this.showGroupConsensus) { -this.showGroupConsensus_actionPerformed (); -} else if (source === this.showGroupConservation) { -this.showGroupConservation_actionPerformed (); -} else if (source === this.showSequenceLogo) { -this.showSequenceLogo_actionPerformed (); -} else if (source === this.normSequenceLogo) { -this.normSequenceLogo_actionPerformed (); -} else if (source === this.showConsensusHistogram) { -this.showConsensusHistogram_actionPerformed (); -} else if (source === this.applyAutoAnnotationSettings) { -this.applyAutoAnnotationSettings_actionPerformed (); -}this.alignPanel.paintAlignment (true); -}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "setAnnotationsVisibility", -($fz = function () { -var showForAlignment = this.showAlignmentAnnotations.getState (); -var showForSequences = this.showSequenceAnnotations.getState (); -for (var aa, $aa = 0, $$aa = this.alignPanel.getAlignment ().getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { -var visible = (aa.sequenceRef == null ? showForAlignment : showForSequences); -aa.visible = visible; -} -this.alignPanel.validateAnnotationDimensions (true); -this.validate (); -this.repaint (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "setAnnotationSortOrder", -($fz = function (order) { -this.annotationSortOrder = order; -}, $fz.isPrivate = true, $fz), "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); -Clazz.defineMethod (c$, "setViewportAnnotationOrder", -($fz = function () { -this.alignPanel.av.setSortAnnotationsBy (this.annotationSortOrder); -this.alignPanel.av.setShowAutocalculatedAbove (this.showAutoCalculatedAbove); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "setShowAutoCalculatedAbove", -($fz = function (showAbove) { -this.showAutoCalculatedAbove = showAbove; -}, $fz.isPrivate = true, $fz), "~B"); -Clazz.defineMethod (c$, "mouseOverFlag_stateChanged", -($fz = function () { -this.viewport.setFollowHighlight (this.followMouseOverFlag.getState ()); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "centreColumnLabelFlag_stateChanged", -($fz = function () { -this.viewport.centreColumnLabels = this.centreColumnLabelFlag.getState (); -this.alignPanel.annotationPanel.repaint (); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -var source = evt.getSource (); -if (source === this.inputText) { -this.inputText_actionPerformed (); -} else if (source === this.$loadTree) { -this.loadTree_actionPerformed (); -} else if (source === this.loadApplication) { -this.launchFullApplication (); -} else if (source === this.$loadAnnotations) { -this.loadAnnotations (); -} else if (source === this.$outputAnnotations) { -this.outputAnnotations (true); -} else if (source === this.$outputFeatures) { -this.outputFeatures (true, "Jalview"); -} else if (source === this.closeMenuItem) { -this.closeMenuItem_actionPerformed (); -} else if (source === this.copy) { -this.copy_actionPerformed (); -} else if (source === this.undoMenuItem) { -this.undoMenuItem_actionPerformed (); -} else if (source === this.redoMenuItem) { -this.redoMenuItem_actionPerformed (); -} else if (source === this.inputText) { -this.inputText_actionPerformed (); -} else if (source === this.closeMenuItem) { -this.closeMenuItem_actionPerformed (); -} else if (source === this.undoMenuItem) { -this.undoMenuItem_actionPerformed (); -} else if (source === this.redoMenuItem) { -this.redoMenuItem_actionPerformed (); -} else if (source === this.copy) { -this.copy_actionPerformed (); -} else if (source === this.pasteNew) { -this.pasteNew_actionPerformed (); -} else if (source === this.pasteThis) { -this.pasteThis_actionPerformed (); -} else if (source === this.cut) { -this.cut_actionPerformed (); -} else if (source === this.$delete) { -this.delete_actionPerformed (); -} else if (source === this.grpsFromSelection) { -this.makeGrpsFromSelection_actionPerformed (); -} else if (source === this.deleteGroups) { -this.deleteGroups_actionPerformed (); -} else if (source === this.selectAllSequenceMenuItem) { -this.selectAllSequenceMenuItem_actionPerformed (); -} else if (source === this.deselectAllSequenceMenuItem) { -this.deselectAllSequenceMenuItem_actionPerformed (); -} else if (source === this.invertSequenceMenuItem) { -this.invertSequenceMenuItem_actionPerformed (); -} else if (source === this.invertColSel) { -this.viewport.invertColumnSelection (); -this.alignPanel.paintAlignment (true); -} else if (source === this.remove2LeftMenuItem) { -this.trimAlignment (true); -} else if (source === this.remove2RightMenuItem) { -this.trimAlignment (false); -} else if (source === this.removeGappedColumnMenuItem) { -this.removeGappedColumnMenuItem_actionPerformed (); -} else if (source === this.removeAllGapsMenuItem) { -this.removeAllGapsMenuItem_actionPerformed (); -} else if (source === this.findMenuItem) { -this.findMenuItem_actionPerformed (); -} else if (source === this.$font) { - new jalview.appletgui.FontChooser (this.alignPanel); -} else if (source === this.$newView) { -this.newView (null); -} else if (source === this.showColumns) { -this.viewport.showAllHiddenColumns (); -this.alignPanel.paintAlignment (true); -} else if (source === this.showSeqs) { -this.viewport.showAllHiddenSeqs (); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideColumns) { -this.viewport.hideSelectedColumns (); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideSequences && this.viewport.getSelectionGroup () != null) { -this.viewport.hideAllSelectedSeqs (); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideAllButSelection) { -this.toggleHiddenRegions (false, false); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideAllSelection) { -var sg = this.viewport.getSelectionGroup (); -this.viewport.expandColSelection (sg, false); -this.viewport.hideAllSelectedSeqs (); -this.viewport.hideSelectedColumns (); -this.alignPanel.paintAlignment (true); -} else if (source === this.showAllHidden) { -this.viewport.showAllHiddenColumns (); -this.viewport.showAllHiddenSeqs (); -this.alignPanel.paintAlignment (true); -} else if (source === this.showGroupConsensus) { -this.showGroupConsensus_actionPerformed (); -} else if (source === this.showGroupConservation) { -this.showGroupConservation_actionPerformed (); -} else if (source === this.showSequenceLogo) { -this.showSequenceLogo_actionPerformed (); -} else if (source === this.normSequenceLogo) { -this.normSequenceLogo_actionPerformed (); -} else if (source === this.showConsensusHistogram) { -this.showConsensusHistogram_actionPerformed (); -} else if (source === this.applyAutoAnnotationSettings) { -this.applyAutoAnnotationSettings_actionPerformed (); -} else if (source === this.featureSettings) { - new jalview.appletgui.FeatureSettings (this.alignPanel); -} else if (source === this.alProperties) { -var contents = new jalview.io.AlignmentProperties (this.viewport.getAlignment ()).formatAsString (); -var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); -cap.setText (contents.toString ()); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_properties", Clazz.newArray (-1, [this.getTitle ()])), 400, 250); -} else if (source === this.overviewMenuItem) { -this.overviewMenuItem_actionPerformed (); -} else if (source === this.noColourmenuItem) { -this.changeColour (null); -} else if (source === this.clustalColour) { -this.abovePIDThreshold.setState (false); -this.changeColour ( new jalview.schemes.ClustalxColourScheme (this.viewport.getAlignment (), null)); -} else if (source === this.zappoColour) { -this.changeColour ( new jalview.schemes.ZappoColourScheme ()); -} else if (source === this.taylorColour) { -this.changeColour ( new jalview.schemes.TaylorColourScheme ()); -} else if (source === this.hydrophobicityColour) { -this.changeColour ( new jalview.schemes.HydrophobicColourScheme ()); -} else if (source === this.helixColour) { -this.changeColour ( new jalview.schemes.HelixColourScheme ()); -} else if (source === this.strandColour) { -this.changeColour ( new jalview.schemes.StrandColourScheme ()); -} else if (source === this.turnColour) { -this.changeColour ( new jalview.schemes.TurnColourScheme ()); -} else if (source === this.buriedColour) { -this.changeColour ( new jalview.schemes.BuriedColourScheme ()); -} else if (source === this.nucleotideColour) { -this.changeColour ( new jalview.schemes.NucleotideColourScheme ()); -} else if (source === this.purinePyrimidineColour) { -this.changeColour ( new jalview.schemes.PurinePyrimidineColourScheme ()); -} else if (source === this.RNAInteractionColour) { -this.changeColour ( new jalview.schemes.RNAInteractionColourScheme ()); -} else if (source === this.RNAHelixColour) { - new jalview.schemes.RNAHelicesColourChooser (this.viewport, this.alignPanel); -} else if (source === this.modifyPID) { -this.modifyPID_actionPerformed (); -} else if (source === this.modifyConservation) { -this.modifyConservation_actionPerformed (); -} else if (source === this.userDefinedColour) { - new jalview.appletgui.UserDefinedColours (this.alignPanel, null); -} else if (source === this.PIDColour) { -this.changeColour ( new jalview.schemes.PIDColourScheme ()); -} else if (source === this.BLOSUM62Colour) { -this.changeColour ( new jalview.schemes.Blosum62ColourScheme ()); -} else if (source === this.tcoffeeColour) { -this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); -} else if (source === this.annotationColour) { - new jalview.appletgui.AnnotationColourChooser (this.viewport, this.alignPanel); -} else if (source === this.annotationColumnSelection) { - new jalview.appletgui.AnnotationColumnChooser (this.viewport, this.alignPanel); -} else if (source === this.sortPairwiseMenuItem) { -this.sortPairwiseMenuItem_actionPerformed (); -} else if (source === this.sortIDMenuItem) { -this.sortIDMenuItem_actionPerformed (); -} else if (source === this.sortLengthMenuItem) { -this.sortLengthMenuItem_actionPerformed (); -} else if (source === this.sortGroupMenuItem) { -this.sortGroupMenuItem_actionPerformed (); -} else if (source === this.removeRedundancyMenuItem) { -this.removeRedundancyMenuItem_actionPerformed (); -} else if (source === this.pairwiseAlignmentMenuItem) { -this.pairwiseAlignmentMenuItem_actionPerformed (); -} else if (source === this.PCAMenuItem) { -this.PCAMenuItem_actionPerformed (); -} else if (source === this.averageDistanceTreeMenuItem) { -this.averageDistanceTreeMenuItem_actionPerformed (); -} else if (source === this.neighbourTreeMenuItem) { -this.neighbourTreeMenuItem_actionPerformed (); -} else if (source === this.njTreeBlosumMenuItem) { -this.njTreeBlosumMenuItem_actionPerformed (); -} else if (source === this.avDistanceTreeBlosumMenuItem) { -this.avTreeBlosumMenuItem_actionPerformed (); -} else if (source === this.documentation) { -this.documentation_actionPerformed (); -} else if (source === this.about) { -this.about_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "inputText_actionPerformed", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.input_cut_paste"), 500, 500); -}); -Clazz.defineMethod (c$, "outputText_actionPerformed", -function (e) { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500); -var fr = this.alignPanel.cloneFeatureRenderer (); -cap.setText ( new jalview.io.AppletFormatAdapter (this.alignPanel).formatSequences (e.getActionCommand (), this.viewport.getAlignment (), this.viewport.getShowJVSuffix ())); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "loadAnnotations", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -cap.setText (jalview.util.MessageManager.getString ("label.paste_features_annotations_Tcoffee_here")); -cap.setAnnotationImport (); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.paste_annotations"), 400, 300); -}); -Clazz.defineMethod (c$, "outputAnnotations", -function (displayTextbox) { -var annotation = new jalview.io.AnnotationFile ().printAnnotationsForView (this.viewport); -if (displayTextbox) { -var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.annotations"), 600, 500); -cap.setText (annotation); -}return annotation; -}, "~B"); -Clazz.defineMethod (c$, "getDisplayedFeatureCols", -($fz = function () { -if (this.alignPanel.getFeatureRenderer () != null && this.viewport.getFeaturesDisplayed () != null) { -return this.alignPanel.getFeatureRenderer ().getDisplayedFeatureCols (); -}return null; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "outputFeatures", -function (displayTextbox, format) { -var features; -if (format.equalsIgnoreCase ("Jalview")) { -features = new jalview.io.FeaturesFile ().printJalviewFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); -} else { -features = new jalview.io.FeaturesFile ().printGFFFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); -}if (displayTextbox) { -var frimport = false; -if (features == null || features.equals ("No Features Visible")) { -features = "# No features visible - paste some and import them here."; -frimport = true; -}var cap = new jalview.appletgui.CutAndPasteTransfer (frimport, this); -if (frimport) { -cap.setAnnotationImport (); -}var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.features"), 600, 500); -cap.setText (features); -} else { -if (features == null) { -features = ""; -}}return features; -}, "~B,~S"); -Clazz.defineMethod (c$, "launchFullApplication", -function () { -var url = new StringBuffer (this.jalviewServletURL); -var firstSep = url.lastIndexOf ("?") > url.lastIndexOf ("/") ? "&" : "?"; -url.append (firstSep); -var applet = this.viewport.applet; -var s = applet.startupFile; -url.append ("open=" + this.appendProtocol (s)); -if (this.viewport.applet.features != null) { -url.append ("&features="); -url.append (this.appendProtocol (applet.features)); -}if (applet.annotations != null) { -url.append ("&annotations="); -url.append (this.appendProtocol (applet.annotations)); -}if (applet.jnetFile != null) { -url.append ("&annotations="); -url.append (this.appendProtocol (applet.jnetFile)); -}if (applet.defaultColour != null) { -url.append ("&colour=" + this.removeWhiteSpace (applet.defaultColour)); -}if (applet.userDefinedColour != null) { -url.append ("&colour=" + this.removeWhiteSpace (applet.userDefinedColour)); -}if (applet.treeFile != null) { -url.append ("&tree=" + this.appendProtocol (applet.treeFile)); -}this.showURL (url.toString (), "FULL_APP"); -}); -Clazz.defineMethod (c$, "removeWhiteSpace", -function (colour) { -var sb = new StringBuffer (); -for (var i = 0; i < colour.length; i++) { -if (Character.isWhitespace (colour.charAt (i))) { -sb.append ("%20"); -} else { -sb.append (colour.charAt (i)); -}} -return sb.toString (); -}, "~S"); -Clazz.defineMethod (c$, "appendProtocol", -function (url) { -try { - new java.net.URL (url); -url = java.net.URLEncoder.encode (url); -} catch (ex) { -if (Clazz.exceptionOf (ex, java.net.MalformedURLException)) { -url = this.viewport.applet.getCodeBase () + url; -} else { -throw ex; -} -} -return url; -}, "~S"); -Clazz.defineMethod (c$, "closeMenuItem_actionPerformed", -function () { -jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel); -if (this.alignPanel.seqPanel != null && this.alignPanel.seqPanel.seqCanvas != null) { -jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.seqPanel.seqCanvas); -}if (this.alignPanel.idPanel != null && this.alignPanel.idPanel.idCanvas != null) { -jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.idPanel.idCanvas); -}if (jalview.appletgui.PaintRefresher.components.size () == 0 && this.viewport.applet == null) { -System.exit (0); -} else { -}this.viewport = null; -this.alignPanel = null; -this.dispose (); -}); -Clazz.defineMethod (c$, "updateEditMenuBar", -function () { -if (this.viewport.getHistoryList ().size () > 0) { -this.undoMenuItem.setEnabled (true); -var command = this.viewport.getHistoryList ().peek (); -this.undoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.undo_command", Clazz.newArray (-1, [command.getDescription ()]))); -} else { -this.undoMenuItem.setEnabled (false); -this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); -}if (this.viewport.getRedoList ().size () > 0) { -this.redoMenuItem.setEnabled (true); -var command = this.viewport.getRedoList ().peek (); -this.redoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.redo_command", Clazz.newArray (-1, [command.getDescription ()]))); -} else { -this.redoMenuItem.setEnabled (false); -this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); -}}); -Clazz.overrideMethod (c$, "addHistoryItem", -function (command) { -if (command.getSize () > 0) { -this.viewport.addToHistoryList (command); -this.viewport.clearRedoList (); -this.updateEditMenuBar (); -this.viewport.updateHiddenColumns (); -}}, "jalview.commands.CommandI"); -Clazz.defineMethod (c$, "undoMenuItem_actionPerformed", -function () { -if (this.viewport.getHistoryList ().isEmpty ()) { -return; -}var command = this.viewport.getHistoryList ().pop (); -this.viewport.addToRedoList (command); -command.undoCommand (null); -var originalSource = this.getOriginatingSource (command); -if (originalSource !== this.viewport) { -System.err.println ("Warning: Viewport object mismatch whilst undoing"); -}originalSource.updateHiddenColumns (); -this.updateEditMenuBar (); -originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "redoMenuItem_actionPerformed", -function () { -if (this.viewport.getRedoList ().isEmpty ()) { -return; -}var command = this.viewport.getRedoList ().pop (); -this.viewport.addToHistoryList (command); -command.doCommand (null); -var originalSource = this.getOriginatingSource (command); -if (originalSource !== this.viewport) { -System.err.println ("Warning: Viewport object mismatch whilst re-doing"); -}originalSource.updateHiddenColumns (); -this.updateEditMenuBar (); -originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "getOriginatingSource", -function (command) { -var originalSource = null; -var al = null; -if (Clazz.instanceOf (command, jalview.commands.EditCommand)) { -var editCommand = command; -al = editCommand.getAlignment (); -var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); -for (var i = 0; i < comps.size (); i++) { -if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { -if (al === (comps.elementAt (i)).av.getAlignment ()) { -originalSource = (comps.elementAt (i)).av; -break; -}}} -}if (originalSource == null) { -if (al != null) { -jalview.appletgui.PaintRefresher.validateSequences (al, this.viewport.getAlignment ()); -}originalSource = this.viewport; -}return originalSource; -}, "jalview.commands.CommandI"); -Clazz.defineMethod (c$, "moveSelectedSequences", -function (up) { -var sg = this.viewport.getSelectionGroup (); -if (sg == null) { -return; -}this.viewport.getAlignment ().moveSelectedSequencesByOne (sg, up ? null : this.viewport.getHiddenRepSequences (), up); -this.alignPanel.paintAlignment (true); -var complement = this.viewport.getCodingComplement (); -if (complement != null) { -var mappedSelection = jalview.util.MappingUtils.mapSequenceGroup (sg, this.viewport, complement); -complement.getAlignment ().moveSelectedSequencesByOne (mappedSelection, up ? null : complement.getHiddenRepSequences (), up); -}}, "~B"); -Clazz.defineMethod (c$, "slideSequences", -function (right, size) { -var sg = new java.util.Vector (); -if (this.viewport.cursorMode) { -sg.add (this.viewport.getAlignment ().getSequenceAt (this.alignPanel.seqPanel.seqCanvas.cursorY)); -} else if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () != this.viewport.getAlignment ().getHeight ()) { -sg = this.viewport.getSelectionGroup ().getSequences (this.viewport.getHiddenRepSequences ()); -}if (sg.size () < 1) { -return; -}var invertGroup = new java.util.Vector (); -for (var i = 0; i < this.viewport.getAlignment ().getHeight (); i++) { -if (!sg.contains (this.viewport.getAlignment ().getSequenceAt (i))) { -invertGroup.addElement (this.viewport.getAlignment ().getSequenceAt (i)); -}} -var seqs1 = sg.toArray ( new Array (sg.size ())); -var seqs2 = invertGroup.toArray ( new Array (invertGroup.size ())); -for (var i = 0; i < invertGroup.size (); i++) { -seqs2[i] = invertGroup.elementAt (i); -} -var ssc; -if (right) { -ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs2, seqs1, size, this.viewport.getGapCharacter ()); -} else { -ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs1, seqs2, size, this.viewport.getGapCharacter ()); -}var groupAdjustment = 0; -if (ssc.getGapsInsertedBegin () && right) { -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (size, 0); -} else { -groupAdjustment = size; -}} else if (!ssc.getGapsInsertedBegin () && !right) { -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (-size, 0); -} else { -groupAdjustment = -size; -}}if (groupAdjustment != 0) { -this.viewport.getSelectionGroup ().setStartRes (this.viewport.getSelectionGroup ().getStartRes () + groupAdjustment); -this.viewport.getSelectionGroup ().setEndRes (this.viewport.getSelectionGroup ().getEndRes () + groupAdjustment); -}var appendHistoryItem = false; -var historyList = this.viewport.getHistoryList (); -if (historyList != null && historyList.size () > 0 && Clazz.instanceOf (historyList.peek (), jalview.commands.SlideSequencesCommand)) { -appendHistoryItem = ssc.appendSlideCommand (historyList.peek ()); -}if (!appendHistoryItem) { -this.addHistoryItem (ssc); -}this.repaint (); -}, "~B,~N"); -Clazz.defineMethod (c$, "copy_actionPerformed", -function () { -if (this.viewport.getSelectionGroup () == null) { -return; -}var sg = this.viewport.getSelectionGroup (); -jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer (); -var orderedSeqs = new java.util.HashMap (); -for (var i = 0; i < sg.getSize (); i++) { -var seq = sg.getSequenceAt (i); -var index = this.viewport.getAlignment ().findIndex (seq); -orderedSeqs.put (new Integer (index), seq); -} -var index = 0; -var startRes; -var endRes; -var ch; -if (this.viewport.hasHiddenColumns () && this.viewport.getSelectionGroup () != null) { -jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector (); -var hiddenOffset = this.viewport.getSelectionGroup ().getStartRes (); -for (var region, $region = this.viewport.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { -jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0] - hiddenOffset, region[1] - hiddenOffset])); -} -} else { -jalview.appletgui.AlignFrame.copiedHiddenColumns = null; -}for (var i = 0; i < sg.getSize (); i++) { -var seq = null; -while (seq == null) { -if (orderedSeqs.containsKey (new Integer (index))) { -seq = orderedSeqs.get (new Integer (index)); -index++; -break; -} else { -index++; -}} -startRes = seq.findPosition (sg.getStartRes ()); -endRes = 0; -for (var j = 0; j < sg.getEndRes () + 1 && j < seq.getLength (); j++) { -ch = seq.getCharAt (j); -if (!jalview.util.Comparison.isGap ((ch))) { -endRes++; -}} -if (endRes > 0) { -endRes += seq.getStart () - 1; -}jalview.appletgui.AlignFrame.copiedSequences.append (seq.getName () + "\t" + startRes + "\t" + endRes + "\t" + seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1) + "\n"); -} -}); -Clazz.defineMethod (c$, "pasteNew_actionPerformed", -function () { -this.paste (true); -}); -Clazz.defineMethod (c$, "pasteThis_actionPerformed", -function () { -this.paste (false); -}); -Clazz.defineMethod (c$, "paste", -function (newAlignment) { -try { -if (jalview.appletgui.AlignFrame.copiedSequences == null) { -return; -}var st = new java.util.StringTokenizer (jalview.appletgui.AlignFrame.copiedSequences.toString ()); -var seqs = new java.util.Vector (); -while (st.hasMoreElements ()) { -var name = st.nextToken (); -var start = Integer.parseInt (st.nextToken ()); -var end = Integer.parseInt (st.nextToken ()); -seqs.addElement ( new jalview.datamodel.Sequence (name, st.nextToken (), start, end)); -} -var newSeqs = new Array (seqs.size ()); -for (var i = 0; i < seqs.size (); i++) { -newSeqs[i] = seqs.elementAt (i); -} -if (newAlignment) { -var newtitle = jalview.util.MessageManager.getString ("label.copied_sequences"); -if (this.getTitle ().startsWith (jalview.util.MessageManager.getString ("label.copied_sequences"))) { -newtitle = this.getTitle (); -} else { -newtitle = newtitle.concat (jalview.util.MessageManager.formatMessage ("label.from_msname", Clazz.newArray (-1, [this.getTitle ()]))); -}var af = new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (newSeqs), this.viewport.applet, newtitle, false); -if (jalview.appletgui.AlignFrame.copiedHiddenColumns != null) { -for (var i = 0; i < jalview.appletgui.AlignFrame.copiedHiddenColumns.size (); i++) { -var region = jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt (i); -af.viewport.hideColumns (region[0], region[1]); -} -}jalview.bin.JalviewLite.addFrame (af, newtitle, this.frameWidth, this.frameHeight); -} else { -this.addSequences (newSeqs); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}, "~B"); -Clazz.defineMethod (c$, "addSequences", -function (seqs) { -for (var i = 0; i < seqs.length; i++) { -this.viewport.getAlignment ().addSequence (seqs[i]); -} -this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.add_sequences"), jalview.commands.EditCommand.Action.PASTE, seqs, 0, this.viewport.getAlignment ().getWidth (), this.viewport.getAlignment ())); -this.viewport.setEndSeq (this.viewport.getAlignment ().getHeight ()); -this.viewport.getAlignment ().getWidth (); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}, "~A"); -Clazz.defineMethod (c$, "cut_actionPerformed", -function () { -this.copy_actionPerformed (); -this.delete_actionPerformed (); -}); -Clazz.defineMethod (c$, "delete_actionPerformed", -function () { -var sg = this.viewport.getSelectionGroup (); -if (sg == null) { -return; -}var seqs = new java.util.Vector (); -var seq; -for (var i = 0; i < sg.getSize (); i++) { -seq = sg.getSequenceAt (i); -seqs.addElement (seq); -} -if (sg.getSize () == this.viewport.getAlignment ().getHeight ()) { -this.viewport.getColumnSelection ().removeElements (sg.getStartRes (), sg.getEndRes () + 1); -}var cut = new Array (seqs.size ()); -for (var i = 0; i < seqs.size (); i++) { -cut[i] = seqs.elementAt (i); -} -this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.cut_sequences"), jalview.commands.EditCommand.Action.CUT, cut, sg.getStartRes (), sg.getEndRes () - sg.getStartRes () + 1, this.viewport.getAlignment ())); -this.viewport.setSelectionGroup (null); -this.viewport.getAlignment ().deleteGroup (sg); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -if (this.viewport.getAlignment ().getHeight () < 1) { -this.setVisible (false); -}this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "showGroupConsensus_actionPerformed", -function () { -this.viewport.setShowGroupConsensus (this.showGroupConsensus.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "showGroupConservation_actionPerformed", -function () { -this.viewport.setShowGroupConservation (this.showGroupConservation.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "showConsensusHistogram_actionPerformed", -function () { -this.viewport.setShowConsensusHistogram (this.showConsensusHistogram.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "showSequenceLogo_actionPerformed", -function () { -this.viewport.setShowSequenceLogo (this.showSequenceLogo.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "normSequenceLogo_actionPerformed", -function () { -this.showSequenceLogo.setState (true); -this.viewport.setShowSequenceLogo (true); -this.viewport.setNormaliseSequenceLogo (this.normSequenceLogo.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "applyAutoAnnotationSettings_actionPerformed", -function () { -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "makeGrpsFromSelection_actionPerformed", -function () { -if (this.avc.makeGroupsFromSelection ()) { -jalview.appletgui.PaintRefresher.Refresh (this, this.viewport.getSequenceSetId ()); -this.alignPanel.updateAnnotation (); -this.alignPanel.paintAlignment (true); -}}); -Clazz.defineMethod (c$, "createGroup_actionPerformed", -function () { -this.avc.createGroup (); -}); -Clazz.defineMethod (c$, "unGroup_actionPerformed", -function () { -if (this.avc.unGroup ()) { -this.alignPanel.alignmentChanged (); -}}); -Clazz.defineMethod (c$, "deleteGroups_actionPerformed", -function () { -if (this.avc.deleteGroups ()) { -this.alignPanel.alignmentChanged (); -}}); -Clazz.defineMethod (c$, "selectAllSequenceMenuItem_actionPerformed", -function () { -var sg = new jalview.datamodel.SequenceGroup (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -sg.addSequence (this.viewport.getAlignment ().getSequenceAt (i), false); -} -sg.setEndRes (this.viewport.getAlignment ().getWidth () - 1); -this.viewport.setSelectionGroup (sg); -this.alignPanel.paintAlignment (true); -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "deselectAllSequenceMenuItem_actionPerformed", -function () { -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.keyboardNo1 = null; -this.alignPanel.seqPanel.keyboardNo2 = null; -}this.viewport.setSelectionGroup (null); -this.viewport.getColumnSelection ().clear (); -this.viewport.setSelectionGroup (null); -this.alignPanel.idPanel.idCanvas.searchResults = null; -this.alignPanel.seqPanel.seqCanvas.highlightSearchResults (null); -this.alignPanel.paintAlignment (true); -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "invertSequenceMenuItem_actionPerformed", -function () { -var sg = this.viewport.getSelectionGroup (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -sg.addOrRemove (this.viewport.getAlignment ().getSequenceAt (i), false); -} -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "invertColSel_actionPerformed", -function () { -this.viewport.invertColumnSelection (); -this.alignPanel.paintAlignment (true); -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "trimAlignment", -function (trimLeft) { -var colSel = this.viewport.getColumnSelection (); -var column; -if (colSel.size () > 0) { -if (trimLeft) { -column = colSel.getMin (); -} else { -column = colSel.getMax (); -}var seqs; -if (this.viewport.getSelectionGroup () != null) { -seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); -} else { -seqs = this.viewport.getAlignment ().getSequencesArray (); -}var trimRegion; -if (trimLeft) { -trimRegion = new jalview.commands.TrimRegionCommand ("Remove Left", jalview.commands.TrimRegionCommand.TRIM_LEFT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); -this.viewport.setStartRes (0); -} else { -trimRegion = new jalview.commands.TrimRegionCommand ("Remove Right", jalview.commands.TrimRegionCommand.TRIM_RIGHT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); -}this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_columns", Clazz.newArray (-1, [Integer.$valueOf (trimRegion.getSize ()).toString ()]))); -this.addHistoryItem (trimRegion); -for (var sg, $sg = this.viewport.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if ((trimLeft && !sg.adjustForRemoveLeft (column)) || (!trimLeft && !sg.adjustForRemoveRight (column))) { -this.viewport.getAlignment ().deleteGroup (sg); -}} -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}}, "~B"); -Clazz.defineMethod (c$, "removeGappedColumnMenuItem_actionPerformed", -function () { -var start = 0; -var end = this.viewport.getAlignment ().getWidth () - 1; -var seqs; -if (this.viewport.getSelectionGroup () != null) { -seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); -start = this.viewport.getSelectionGroup ().getStartRes (); -end = this.viewport.getSelectionGroup ().getEndRes (); -} else { -seqs = this.viewport.getAlignment ().getSequencesArray (); -}var removeGapCols = new jalview.commands.RemoveGapColCommand ("Remove Gapped Columns", seqs, start, end, this.viewport.getAlignment ()); -this.addHistoryItem (removeGapCols); -this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_empty_columns", Clazz.newArray (-1, [Integer.$valueOf (removeGapCols.getSize ()).toString ()]))); -var seq = this.viewport.getAlignment ().getSequenceAt (0); -var startRes = seq.findPosition (this.viewport.startRes); -this.viewport.setStartRes (seq.findIndex (startRes) - 1); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "removeAllGapsMenuItem_actionPerformed", -function () { -var start = 0; -var end = this.viewport.getAlignment ().getWidth () - 1; -var seqs; -if (this.viewport.getSelectionGroup () != null) { -seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); -start = this.viewport.getSelectionGroup ().getStartRes (); -end = this.viewport.getSelectionGroup ().getEndRes (); -} else { -seqs = this.viewport.getAlignment ().getSequencesArray (); -}var seq = this.viewport.getAlignment ().getSequenceAt (0); -var startRes = seq.findPosition (this.viewport.startRes); -this.addHistoryItem ( new jalview.commands.RemoveGapsCommand ("Remove Gaps", seqs, start, end, this.viewport.getAlignment ())); -this.viewport.setStartRes (seq.findIndex (startRes) - 1); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "findMenuItem_actionPerformed", -function () { - new jalview.appletgui.Finder (this.alignPanel); -}); -Clazz.defineMethod (c$, "newView", -function (viewtitle) { -var newal; -if (this.viewport.hasHiddenRows ()) { -newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getHiddenSequences ().getFullAlignment ().getSequencesArray ()); -} else { -newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getSequencesArray ()); -}if (this.viewport.getAlignment ().getAlignmentAnnotation () != null) { -for (var i = 0; i < this.viewport.getAlignment ().getAlignmentAnnotation ().length; i++) { -if (!this.viewport.getAlignment ().getAlignmentAnnotation ()[i].autoCalculated) { -newal.addAnnotation (this.viewport.getAlignment ().getAlignmentAnnotation ()[i]); -}} -}var newaf = new jalview.appletgui.AlignFrame (newal, this.viewport.applet, "", false); -newaf.viewport.setSequenceSetId (this.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (this.alignPanel, this.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (newaf.alignPanel, newaf.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.idPanel.idCanvas, newaf.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId ()); -var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); -var viewSize = -1; -for (var i = 0; i < comps.size (); i++) { -if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { -viewSize++; -}} -var title = String.instantialize (this.getTitle ()); -if (viewtitle != null) { -title = viewtitle + " ( " + title + ")"; -} else { -if (title.indexOf ("(View") > -1) { -title = title.substring (0, title.indexOf ("(View")); -}title += "(View " + viewSize + ")"; -}newaf.setTitle (title.toString ()); -newaf.viewport.setHistoryList (this.viewport.getHistoryList ()); -newaf.viewport.setRedoList (this.viewport.getRedoList ()); -return newaf; -}, "~S"); -Clazz.defineMethod (c$, "getFeatureGroups", -function () { -var fr = null; -if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { -var gps = fr.getFeatureGroups (); -var _gps = gps.toArray ( new Array (gps.size ())); -return _gps; -}return null; -}); -Clazz.defineMethod (c$, "getFeatureGroupsOfState", -function (visible) { -var fr = null; -if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { -var gps = fr.getGroups (visible); -var _gps = gps.toArray ( new Array (gps.size ())); -return _gps; -}return null; -}, "~B"); -Clazz.defineMethod (c$, "setFeatureGroupState", -function (groups, state) { -var fr = null; -this.sequenceFeatures.setState (true); -this.viewport.setShowSequenceFeatures (true); -if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { -fr.setGroupVisibility (java.util.Arrays.asList (groups), state); -this.alignPanel.seqPanel.seqCanvas.repaint (); -if (this.alignPanel.overviewPanel != null) { -this.alignPanel.overviewPanel.updateOverviewImage (); -}}}, "~A,~B"); -Clazz.defineMethod (c$, "seqLimits_itemStateChanged", -function () { -this.viewport.setShowJVSuffix (this.seqLimits.getState ()); -this.alignPanel.fontChanged (); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "colourTextMenuItem_actionPerformed", -function () { -this.viewport.setColourText (this.colourTextMenuItem.getState ()); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "displayNonconservedMenuItem_actionPerformed", -function () { -this.viewport.setShowUnconserved (this.displayNonconservedMenuItem.getState ()); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "wrapMenuItem_actionPerformed", -function () { -this.viewport.setWrapAlignment (this.wrapMenuItem.getState ()); -this.alignPanel.setWrapAlignment (this.wrapMenuItem.getState ()); -this.scaleAbove.setEnabled (this.wrapMenuItem.getState ()); -this.scaleLeft.setEnabled (this.wrapMenuItem.getState ()); -this.scaleRight.setEnabled (this.wrapMenuItem.getState ()); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "overviewMenuItem_actionPerformed", -function () { -if (this.alignPanel.overviewPanel != null) { -return; -}var frame = new awt2swing.Frame (); -var overview = new jalview.appletgui.OverviewPanel (this.alignPanel); -frame.add (overview); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.overview_params", Clazz.newArray (-1, [this.getTitle ()])), overview.getPreferredSize ().width, overview.getPreferredSize ().height + 50); -frame.pack (); -var ap = this.alignPanel; -frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1, this, Clazz.cloneFinals ("ap", ap)))); -this.alignPanel.setOverviewPanel (overview); -}); -Clazz.overrideMethod (c$, "changeColour", -function (cs) { -var threshold = 0; -if (cs != null) { -if (this.viewport.getAbovePIDThreshold ()) { -this.viewport.setThreshold (jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, cs, "Background")); -}if (this.viewport.getConservationSelected ()) { -cs.setConservationApplied (true); -this.viewport.setIncrement (jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, cs, "Background")); -} else { -cs.setConservationApplied (false); -}}this.viewport.setGlobalColourScheme (cs); -if (this.alignPanel.getOverviewPanel () != null) { -this.alignPanel.getOverviewPanel ().updateOverviewImage (); -}jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.viewport.applet).sequenceColoursChanged (this.alignPanel); -this.alignPanel.paintAlignment (true); -}, "jalview.schemes.ColourSchemeI"); -Clazz.defineMethod (c$, "modifyPID_actionPerformed", -function () { -if (this.viewport.getAbovePIDThreshold () && this.viewport.getGlobalColourScheme () != null) { -jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); -jalview.appletgui.SliderPanel.showPIDSlider (); -}}); -Clazz.defineMethod (c$, "modifyConservation_actionPerformed", -function () { -if (this.viewport.getConservationSelected () && this.viewport.getGlobalColourScheme () != null) { -jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); -jalview.appletgui.SliderPanel.showConservationSlider (); -}}); -Clazz.defineMethod (c$, "conservationMenuItem_actionPerformed", -function () { -this.viewport.setConservationSelected (this.conservationMenuItem.getState ()); -this.viewport.setAbovePIDThreshold (false); -this.abovePIDThreshold.setState (false); -this.changeColour (this.viewport.getGlobalColourScheme ()); -this.modifyConservation_actionPerformed (); -}); -Clazz.defineMethod (c$, "abovePIDThreshold_actionPerformed", -function () { -this.viewport.setAbovePIDThreshold (this.abovePIDThreshold.getState ()); -this.conservationMenuItem.setState (false); -this.viewport.setConservationSelected (false); -this.changeColour (this.viewport.getGlobalColourScheme ()); -this.modifyPID_actionPerformed (); -}); -Clazz.defineMethod (c$, "sortPairwiseMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByPID (this.viewport.getAlignment (), this.viewport.getAlignment ().getSequenceAt (0), null); -this.addHistoryItem ( new jalview.commands.OrderCommand ("Pairwise Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "sortIDMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByID (this.viewport.getAlignment ()); -this.addHistoryItem ( new jalview.commands.OrderCommand ("ID Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "sortLengthMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByLength (this.viewport.getAlignment ()); -this.addHistoryItem ( new jalview.commands.OrderCommand ("Length Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "sortGroupMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByGroup (this.viewport.getAlignment ()); -this.addHistoryItem ( new jalview.commands.OrderCommand ("Group Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "removeRedundancyMenuItem_actionPerformed", -function () { - new jalview.appletgui.RedundancyPanel (this.alignPanel); -}); -Clazz.defineMethod (c$, "pairwiseAlignmentMenuItem_actionPerformed", -function () { -if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) { -var frame = new awt2swing.Frame (); -frame.add ( new jalview.appletgui.PairwiseAlignPanel (this.alignPanel)); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.pairwise_alignment"), 600, 500); -}}); -Clazz.defineMethod (c$, "PCAMenuItem_actionPerformed", -function () { -if (!this.viewport.getAlignment ().isAligned (false)) { -var current; -var Width = this.viewport.getAlignment ().getWidth (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -current = this.viewport.getAlignment ().getSequenceAt (i); -if (current.getLength () < Width) { -current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); -}} -this.alignPanel.paintAlignment (true); -}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () < 4 && this.viewport.getSelectionGroup ().getSize () > 0) || this.viewport.getAlignment ().getHeight () < 4) { -return; -}try { - new jalview.appletgui.PCAPanel (this.viewport); -} catch (ex) { -if (Clazz.exceptionOf (ex, OutOfMemoryError)) { -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "averageDistanceTreeMenuItem_actionPerformed", -function () { -this.NewTreePanel ("AV", "PID", "Average distance tree using PID"); -}); -Clazz.defineMethod (c$, "neighbourTreeMenuItem_actionPerformed", -function () { -this.NewTreePanel ("NJ", "PID", "Neighbour joining tree using PID"); -}); -Clazz.defineMethod (c$, "njTreeBlosumMenuItem_actionPerformed", -function () { -this.NewTreePanel ("NJ", "BL", "Neighbour joining tree using BLOSUM62"); -}); -Clazz.defineMethod (c$, "avTreeBlosumMenuItem_actionPerformed", -function () { -this.NewTreePanel ("AV", "BL", "Average distance tree using BLOSUM62"); -}); -Clazz.defineMethod (c$, "NewTreePanel", -function (type, pwType, title) { -if (!this.viewport.getAlignment ().isAligned (false)) { -var current; -var Width = this.viewport.getAlignment ().getWidth (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -current = this.viewport.getAlignment ().getSequenceAt (i); -if (current.getLength () < Width) { -current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); -}} -this.alignPanel.paintAlignment (true); -}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) || (this.viewport.getAlignment ().getHeight () > 1)) { -var tp = new jalview.appletgui.TreePanel (this.alignPanel, type, pwType); -this.addTreeMenuItem (tp, title); -jalview.bin.JalviewLite.addFrame (tp, title, 600, 500); -}}, "~S,~S,~S"); -Clazz.defineMethod (c$, "loadTree_actionPerformed", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -cap.setText (jalview.util.MessageManager.getString ("label.paste_newick_tree_file")); -cap.setTreeImport (); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.paste_newick_file"), 400, 300); -}); -Clazz.defineMethod (c$, "loadTree", -function (tree, treeFile) { -var tp = new jalview.appletgui.TreePanel (this.alignPanel, treeFile, jalview.util.MessageManager.getString ("label.load_tree_from_file"), tree); -jalview.bin.JalviewLite.addFrame (tp, treeFile, 600, 500); -this.addTreeMenuItem (tp, treeFile); -}, "jalview.io.NewickFile,~S"); -Clazz.defineMethod (c$, "sortByTree", -function (treePanel, title) { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByTree (this.viewport.getAlignment (), treePanel.getTree ()); -this.addHistoryItem ( new jalview.commands.OrderCommand (jalview.util.MessageManager.formatMessage ("label.order_by_params", Clazz.newArray (-1, [title])), oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}, "jalview.appletgui.TreePanel,~S"); -Clazz.defineMethod (c$, "addTreeMenuItem", -function (treePanel, title) { -var item = new awt2swing.MenuItem (title); -this.sortByTreeMenu.add (item); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$2") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$2, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title)))); -treePanel.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$3") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$3, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title, "item", item)))); -}, "jalview.appletgui.TreePanel,~S"); -Clazz.defineMethod (c$, "sortBy", -function (alorder, undoname) { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -if ((this.viewport.applet, jalview.bin.JalviewLite).debug) { -System.err.println ("Sorting " + alorder.getOrder ().size () + " in alignment '" + this.getTitle () + "'"); -}jalview.analysis.AlignmentSorter.sortBy (this.viewport.getAlignment (), alorder); -if (undoname != null) { -this.addHistoryItem ( new jalview.commands.OrderCommand (undoname, oldOrder, this.viewport.getAlignment ())); -}this.alignPanel.paintAlignment (true); -return true; -}, "jalview.datamodel.AlignmentOrder,~S"); -Clazz.defineMethod (c$, "documentation_actionPerformed", -function () { -this.alignPanel.av.applet.openJalviewHelpUrl (); -}); -Clazz.defineMethod (c$, "about_actionPerformed", -function () { -if (!Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1AboutPanel")) { -jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$ (); -} -var frame = new awt2swing.Frame (); -frame.add (Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1AboutPanel, this, null, jalview.bin.JalviewLite.getVersion (), jalview.bin.JalviewLite.getBuildDate ())); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.jalview"), 580, 220); -}); -Clazz.defineMethod (c$, "showURL", -function (url, target) { -if (this.viewport.applet == null) { -System.out.println ("Not running as applet - no browser available."); -} else { -this.viewport.applet.showURL (url, target); -}}, "~S,~S"); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setMenuBar (this.alignFrameMenuBar); -this.inputText.setLabel (jalview.util.MessageManager.getString ("label.input_from_textbox")); -this.inputText.addActionListener (this); -var outputTextboxMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.out_to_textbox")); -for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { -var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$4") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$4, this, null))); -outputTextboxMenu.add (item); -} -this.closeMenuItem.addActionListener (this); -this.loadApplication.addActionListener (this); -this.$loadTree.addActionListener (this); -this.$loadAnnotations.addActionListener (this); -this.$outputFeatures.addActionListener (this); -this.$outputAnnotations.addActionListener (this); -this.undoMenuItem.setEnabled (false); -this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); -this.undoMenuItem.addActionListener (this); -this.redoMenuItem.setEnabled (false); -this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); -this.redoMenuItem.addActionListener (this); -this.copy.setLabel (jalview.util.MessageManager.getString ("action.copy")); -this.copy.addActionListener (this); -this.cut.setLabel (jalview.util.MessageManager.getString ("action.cut")); -this.cut.addActionListener (this); -this.$delete.setLabel (jalview.util.MessageManager.getString ("action.delete")); -this.$delete.addActionListener (this); -this.pasteMenu.setLabel (jalview.util.MessageManager.getString ("action.paste")); -this.pasteNew.setLabel (jalview.util.MessageManager.getString ("label.to_new_alignment")); -this.pasteNew.addActionListener (this); -this.pasteThis.setLabel (jalview.util.MessageManager.getString ("label.to_this_alignment")); -this.pasteThis.addActionListener (this); -this.remove2LeftMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_left")); -this.remove2LeftMenuItem.addActionListener (this); -this.remove2RightMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_right")); -this.remove2RightMenuItem.addActionListener (this); -this.removeGappedColumnMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_empty_columns")); -this.removeGappedColumnMenuItem.addActionListener (this); -this.removeAllGapsMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_all_gaps")); -this.removeAllGapsMenuItem.addActionListener (this); -this.removeRedundancyMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_redundancy").concat ("...")); -this.removeRedundancyMenuItem.addActionListener (this); -this.findMenuItem.setLabel (jalview.util.MessageManager.getString ("action.find")); -this.findMenuItem.addActionListener (this); -this.selectAllSequenceMenuItem.addActionListener (this); -this.deselectAllSequenceMenuItem.addActionListener (this); -this.invertSequenceMenuItem.setLabel (jalview.util.MessageManager.getString ("action.invert_sequence_selection")); -this.invertSequenceMenuItem.addActionListener (this); -this.invertColSel.setLabel (jalview.util.MessageManager.getString ("action.invert_column_selection")); -this.invertColSel.addActionListener (this); -this.deleteGroups.setLabel (jalview.util.MessageManager.getString ("action.undefine_groups")); -this.deleteGroups.addActionListener (this); -this.grpsFromSelection.setLabel (jalview.util.MessageManager.getString ("action.make_groups_selection")); -this.grpsFromSelection.addActionListener (this); -this.createGroup.setLabel (jalview.util.MessageManager.getString ("action.create_group")); -this.unGroup.setLabel (jalview.util.MessageManager.getString ("action.remove_group")); -this.annotationColumnSelection.setLabel ("Select by Annotation"); -this.annotationColumnSelection.addActionListener (this); -this.$newView.setLabel (jalview.util.MessageManager.getString ("action.new_view")); -this.$newView.addActionListener (this); -var showMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.show")); -this.showColumns.setLabel (jalview.util.MessageManager.getString ("label.all_columns")); -this.showSeqs.setLabel (jalview.util.MessageManager.getString ("label.all_sequences")); -var hideMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.hide")); -this.hideColumns.setLabel (jalview.util.MessageManager.getString ("label.selected_columns")); -this.hideSequences.setLabel (jalview.util.MessageManager.getString ("label.selected_sequences")); -this.hideAllButSelection.setLabel (jalview.util.MessageManager.getString ("label.all_but_selected_region")); -this.hideAllSelection.setLabel (jalview.util.MessageManager.getString ("label.selected_region")); -this.showAllHidden.setLabel (jalview.util.MessageManager.getString ("label.all_sequences_columns")); -this.showColumns.addActionListener (this); -this.showSeqs.addActionListener (this); -this.hideColumns.addActionListener (this); -this.hideSequences.addActionListener (this); -this.hideAllButSelection.addActionListener (this); -this.hideAllSelection.addActionListener (this); -this.showAllHidden.addActionListener (this); -this.featureSettings.setLabel (jalview.util.MessageManager.getString ("label.feature_settings")); -this.featureSettings.addActionListener (this); -this.sequenceFeatures.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_features")); -this.sequenceFeatures.addItemListener (this); -this.sequenceFeatures.setState (false); -this.followMouseOverFlag.setLabel (jalview.util.MessageManager.getString ("label.automatic_scrolling")); -this.followMouseOverFlag.addItemListener (this); -this.alProperties.addActionListener (this); -this.overviewMenuItem.setLabel (jalview.util.MessageManager.getString ("label.overview_window")); -this.overviewMenuItem.addActionListener (this); -this.annotationPanelMenuItem.setLabel (jalview.util.MessageManager.getString ("label.show_annotations")); -this.annotationPanelMenuItem.addItemListener (this); -this.showGroupConsensus.setLabel (jalview.util.MessageManager.getString ("label.group_consensus")); -this.showGroupConservation.setLabel (jalview.util.MessageManager.getString ("label.group_conservation")); -this.showConsensusHistogram.setLabel (jalview.util.MessageManager.getString ("label.show_consensus_histogram")); -this.showSequenceLogo.setLabel (jalview.util.MessageManager.getString ("label.show_consensus_logo")); -this.normSequenceLogo.setLabel (jalview.util.MessageManager.getString ("label.norm_consensus_logo")); -this.applyAutoAnnotationSettings.setLabel (jalview.util.MessageManager.getString ("label.apply_all_groups")); -this.applyAutoAnnotationSettings.setState (true); -var autoAnnMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.autocalculated_annotation")); -this.showGroupConsensus.addItemListener (this); -this.showGroupConservation.addItemListener (this); -this.showConsensusHistogram.addItemListener (this); -this.showSequenceLogo.addItemListener (this); -this.normSequenceLogo.addItemListener (this); -this.applyAutoAnnotationSettings.addItemListener (this); -this.showAlignmentAnnotations = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_all_al_annotations")); -this.showSequenceAnnotations = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_all_seq_annotations")); -this.sortAnnBySequence = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.sort_annotations_by_sequence")); -this.sortAnnByLabel = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.sort_annotations_by_label")); -this.showAutoFirst = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_first")); -this.showAutoLast = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_last")); -this.showAlignmentAnnotations.addItemListener (this); -this.showSequenceAnnotations.addItemListener (this); -this.sortAnnBySequence.addItemListener (this); -this.sortAnnByLabel.addItemListener (this); -this.showAutoFirst.addItemListener (this); -this.showAutoLast.addItemListener (this); -this.$font.setLabel (jalview.util.MessageManager.getString ("action.font")); -this.$font.addActionListener (this); -this.scaleAbove.setLabel (jalview.util.MessageManager.getString ("action.scale_above")); -this.scaleAbove.setState (true); -this.scaleAbove.setEnabled (false); -this.scaleAbove.addItemListener (this); -this.scaleLeft.setEnabled (false); -this.scaleLeft.setState (true); -this.scaleLeft.setLabel (jalview.util.MessageManager.getString ("action.scale_left")); -this.scaleLeft.addItemListener (this); -this.scaleRight.setEnabled (false); -this.scaleRight.setState (true); -this.scaleRight.setLabel (jalview.util.MessageManager.getString ("action.scale_right")); -this.scaleRight.addItemListener (this); -this.viewBoxesMenuItem.setLabel (jalview.util.MessageManager.getString ("action.boxes")); -this.viewBoxesMenuItem.setState (true); -this.viewBoxesMenuItem.addItemListener (this); -this.viewTextMenuItem.setLabel (jalview.util.MessageManager.getString ("action.text")); -this.viewTextMenuItem.setState (true); -this.viewTextMenuItem.addItemListener (this); -this.colourTextMenuItem.setLabel (jalview.util.MessageManager.getString ("label.colour_text")); -this.colourTextMenuItem.addItemListener (this); -this.displayNonconservedMenuItem.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed")); -this.displayNonconservedMenuItem.addItemListener (this); -this.wrapMenuItem.setLabel (jalview.util.MessageManager.getString ("action.wrap")); -this.wrapMenuItem.addItemListener (this); -this.renderGapsMenuItem.setLabel (jalview.util.MessageManager.getString ("action.show_gaps")); -this.renderGapsMenuItem.setState (true); -this.renderGapsMenuItem.addItemListener (this); -this.centreColumnLabelFlag.setLabel (jalview.util.MessageManager.getString ("label.centre_column_labels")); -this.centreColumnLabelFlag.addItemListener (this); -this.seqLimits.setState (true); -this.seqLimits.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_limits")); -this.seqLimits.addItemListener (this); -this.applyToAllGroups.setLabel (jalview.util.MessageManager.getString ("label.apply_colour_to_all_groups")); -this.applyToAllGroups.setState (true); -this.applyToAllGroups.addItemListener (this); -this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx")); -this.clustalColour.addActionListener (this); -this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo")); -this.zappoColour.addActionListener (this); -this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor")); -this.taylorColour.addActionListener (this); -this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity")); -this.hydrophobicityColour.addActionListener (this); -this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity")); -this.helixColour.addActionListener (this); -this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity")); -this.strandColour.addActionListener (this); -this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity")); -this.turnColour.addActionListener (this); -this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index")); -this.buriedColour.addActionListener (this); -this.purinePyrimidineColour.setLabel (jalview.util.MessageManager.getString ("label.purine_pyrimidine")); -this.purinePyrimidineColour.addActionListener (this); -this.RNAInteractionColour.setLabel (jalview.util.MessageManager.getString ("label.rna_interaction")); -this.RNAInteractionColour.addActionListener (this); -this.RNAHelixColour.setLabel (jalview.util.MessageManager.getString ("action.by_rna_helixes")); -this.RNAHelixColour.addActionListener (this); -this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined")); -this.userDefinedColour.addActionListener (this); -this.PIDColour.setLabel (jalview.util.MessageManager.getString ("label.percentage_identity")); -this.PIDColour.addActionListener (this); -this.BLOSUM62Colour.setLabel (jalview.util.MessageManager.getString ("label.blosum62_score")); -this.BLOSUM62Colour.addActionListener (this); -this.tcoffeeColour.setLabel (jalview.util.MessageManager.getString ("label.tcoffee_scores")); -this.tcoffeeColour.setEnabled (false); -this.tcoffeeColour.addActionListener (this); -this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_conservation")); -this.conservationMenuItem.addItemListener (this); -this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none")); -this.noColourmenuItem.addActionListener (this); -this.abovePIDThreshold.setLabel (jalview.util.MessageManager.getString ("label.above_identity_threshold")); -this.abovePIDThreshold.addItemListener (this); -this.nucleotideColour.setLabel (jalview.util.MessageManager.getString ("label.nucleotide")); -this.nucleotideColour.addActionListener (this); -this.modifyPID.setLabel (jalview.util.MessageManager.getString ("label.modify_identity_thereshold")); -this.modifyPID.addActionListener (this); -this.modifyConservation.setLabel (jalview.util.MessageManager.getString ("label.modify_conservation_thereshold")); -this.modifyConservation.addActionListener (this); -this.annotationColour.setLabel (jalview.util.MessageManager.getString ("action.by_annotation")); -this.annotationColour.addActionListener (this); -this.sortPairwiseMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_pairwise_id")); -this.sortPairwiseMenuItem.addActionListener (this); -this.sortIDMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_id")); -this.sortIDMenuItem.addActionListener (this); -this.sortLengthMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_length")); -this.sortLengthMenuItem.addActionListener (this); -this.sortGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_group")); -this.sortGroupMenuItem.addActionListener (this); -this.pairwiseAlignmentMenuItem.setLabel (jalview.util.MessageManager.getString ("action.pairwise_alignment")); -this.pairwiseAlignmentMenuItem.addActionListener (this); -this.PCAMenuItem.setLabel (jalview.util.MessageManager.getString ("label.principal_component_analysis")); -this.PCAMenuItem.addActionListener (this); -this.autoCalculate = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.autocalculate_consensus"), true); -this.averageDistanceTreeMenuItem.setLabel (jalview.util.MessageManager.getString ("label.average_distance_identity")); -this.averageDistanceTreeMenuItem.addActionListener (this); -this.neighbourTreeMenuItem.setLabel (jalview.util.MessageManager.getString ("label.neighbour_joining_identity")); -this.neighbourTreeMenuItem.addActionListener (this); -this.avDistanceTreeBlosumMenuItem.setLabel (jalview.util.MessageManager.getString ("label.average_distance_bloslum62")); -this.avDistanceTreeBlosumMenuItem.addActionListener (this); -this.njTreeBlosumMenuItem.setLabel (jalview.util.MessageManager.getString ("label.neighbour_blosum62")); -this.njTreeBlosumMenuItem.addActionListener (this); -this.sortByTreeMenu.setLabel (jalview.util.MessageManager.getString ("action.by_tree_order")); -var sortMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.sort")); -var calculateTreeMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate_tree")); -this.autoCalculate.addItemListener (this); -this.$sortByTree.addItemListener (this); -var helpMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.help")); -this.documentation.setLabel (jalview.util.MessageManager.getString ("label.documentation")); -this.documentation.addActionListener (this); -this.about.setLabel (jalview.util.MessageManager.getString ("label.about")); -this.about.addActionListener (this); -this.alignFrameMenuBar.add (this.fileMenu); -var editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit")); -this.alignFrameMenuBar.add (editMenu); -var selectMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.select")); -this.alignFrameMenuBar.add (selectMenu); -var viewMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.view")); -this.alignFrameMenuBar.add (viewMenu); -var annotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.annotations")); -this.alignFrameMenuBar.add (annotationsMenu); -var formatMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.format")); -this.alignFrameMenuBar.add (formatMenu); -var colourMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.colour")); -this.alignFrameMenuBar.add (colourMenu); -var calculateMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate")); -this.alignFrameMenuBar.add (calculateMenu); -this.alignFrameMenuBar.add (helpMenu); -this.fileMenu.add (this.inputText); -this.fileMenu.add (this.$loadTree); -this.fileMenu.add (this.$loadAnnotations); -this.fileMenu.addSeparator (); -this.fileMenu.add (outputTextboxMenu); -this.fileMenu.add (this.$outputFeatures); -this.fileMenu.add (this.$outputAnnotations); -if (this.jalviewServletURL != null) { -this.fileMenu.add (this.loadApplication); -}this.fileMenu.addSeparator (); -this.fileMenu.add (this.closeMenuItem); -editMenu.add (this.undoMenuItem); -editMenu.add (this.redoMenuItem); -editMenu.add (this.cut); -editMenu.add (this.copy); -this.pasteMenu.add (this.pasteNew); -this.pasteMenu.add (this.pasteThis); -editMenu.add (this.pasteMenu); -editMenu.add (this.$delete); -editMenu.addSeparator (); -editMenu.add (this.remove2LeftMenuItem); -editMenu.add (this.remove2RightMenuItem); -editMenu.add (this.removeGappedColumnMenuItem); -editMenu.add (this.removeAllGapsMenuItem); -editMenu.add (this.removeRedundancyMenuItem); -selectMenu.add (this.findMenuItem); -selectMenu.addSeparator (); -selectMenu.add (this.selectAllSequenceMenuItem); -selectMenu.add (this.deselectAllSequenceMenuItem); -selectMenu.add (this.invertSequenceMenuItem); -selectMenu.add (this.invertColSel); -selectMenu.add (this.createGroup); -selectMenu.add (this.unGroup); -selectMenu.add (this.grpsFromSelection); -selectMenu.add (this.deleteGroups); -selectMenu.add (this.annotationColumnSelection); -viewMenu.add (this.$newView); -viewMenu.addSeparator (); -showMenu.add (this.showColumns); -showMenu.add (this.showSeqs); -showMenu.add (this.showAllHidden); -viewMenu.add (showMenu); -hideMenu.add (this.hideColumns); -hideMenu.add (this.hideSequences); -hideMenu.add (this.hideAllSelection); -hideMenu.add (this.hideAllButSelection); -viewMenu.add (hideMenu); -viewMenu.addSeparator (); -viewMenu.add (this.followMouseOverFlag); -viewMenu.addSeparator (); -viewMenu.add (this.sequenceFeatures); -viewMenu.add (this.featureSettings); -viewMenu.addSeparator (); -viewMenu.add (this.alProperties); -viewMenu.addSeparator (); -viewMenu.add (this.overviewMenuItem); -annotationsMenu.add (this.annotationPanelMenuItem); -annotationsMenu.addSeparator (); -annotationsMenu.add (this.showAlignmentAnnotations); -annotationsMenu.add (this.showSequenceAnnotations); -annotationsMenu.add (this.sortAnnBySequence); -annotationsMenu.add (this.sortAnnByLabel); -annotationsMenu.addSeparator (); -autoAnnMenu.add (this.showAutoFirst); -autoAnnMenu.add (this.showAutoLast); -autoAnnMenu.addSeparator (); -autoAnnMenu.add (this.applyAutoAnnotationSettings); -autoAnnMenu.add (this.showConsensusHistogram); -autoAnnMenu.add (this.showSequenceLogo); -autoAnnMenu.add (this.normSequenceLogo); -autoAnnMenu.addSeparator (); -autoAnnMenu.add (this.showGroupConservation); -autoAnnMenu.add (this.showGroupConsensus); -annotationsMenu.add (autoAnnMenu); -formatMenu.add (this.$font); -formatMenu.add (this.seqLimits); -formatMenu.add (this.wrapMenuItem); -formatMenu.add (this.scaleAbove); -formatMenu.add (this.scaleLeft); -formatMenu.add (this.scaleRight); -formatMenu.add (this.viewBoxesMenuItem); -formatMenu.add (this.viewTextMenuItem); -formatMenu.add (this.colourTextMenuItem); -formatMenu.add (this.displayNonconservedMenuItem); -formatMenu.add (this.renderGapsMenuItem); -formatMenu.add (this.centreColumnLabelFlag); -colourMenu.add (this.applyToAllGroups); -colourMenu.addSeparator (); -colourMenu.add (this.noColourmenuItem); -colourMenu.add (this.clustalColour); -colourMenu.add (this.BLOSUM62Colour); -colourMenu.add (this.PIDColour); -colourMenu.add (this.zappoColour); -colourMenu.add (this.taylorColour); -colourMenu.add (this.hydrophobicityColour); -colourMenu.add (this.helixColour); -colourMenu.add (this.strandColour); -colourMenu.add (this.turnColour); -colourMenu.add (this.buriedColour); -colourMenu.add (this.nucleotideColour); -colourMenu.add (this.purinePyrimidineColour); -colourMenu.add (this.tcoffeeColour); -colourMenu.add (this.userDefinedColour); -colourMenu.addSeparator (); -colourMenu.add (this.conservationMenuItem); -colourMenu.add (this.modifyConservation); -colourMenu.add (this.abovePIDThreshold); -colourMenu.add (this.modifyPID); -colourMenu.add (this.annotationColour); -colourMenu.add (this.RNAHelixColour); -sortMenu.add (this.sortIDMenuItem); -sortMenu.add (this.sortLengthMenuItem); -sortMenu.add (this.sortByTreeMenu); -sortMenu.add (this.sortGroupMenuItem); -sortMenu.add (this.sortPairwiseMenuItem); -calculateMenu.add (sortMenu); -calculateTreeMenu.add (this.averageDistanceTreeMenuItem); -calculateTreeMenu.add (this.neighbourTreeMenuItem); -calculateTreeMenu.add (this.avDistanceTreeBlosumMenuItem); -calculateTreeMenu.add (this.njTreeBlosumMenuItem); -calculateMenu.add (calculateTreeMenu); -calculateMenu.addSeparator (); -calculateMenu.add (this.pairwiseAlignmentMenuItem); -calculateMenu.add (this.PCAMenuItem); -calculateMenu.add (this.autoCalculate); -calculateMenu.add (this.$sortByTree); -helpMenu.add (this.documentation); -helpMenu.add (this.about); -this.statusBar.setBackground (java.awt.Color.white); -this.statusBar.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.setStatus (jalview.util.MessageManager.getString ("label.status_bar")); -this.add (this.statusBar, "South"); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "setStatus", -function (string) { -this.statusBar.setText (string); -}, "~S"); -Clazz.defineMethod (c$, "createAlignFrameWindow", -function (reallyEmbedded) { -if (reallyEmbedded) { -this.embedAlignFrameInApplet (this.viewport.applet); -} else { -if (this.embedMenuIfNeeded (this.alignPanel)) { -this.alignPanel.setSize (this.getSize ().width, this.getSize ().height - this.statusBar.getHeight ()); -}this.add (this.statusBar, "South"); -this.add (this.alignPanel, "Center"); -jalview.bin.JalviewLite.addFrame (this, this.getTitle (), this.frameWidth, this.frameHeight); -}}, "~B"); -Clazz.defineMethod (c$, "embedAlignFrameInApplet", -function (theApplet) { -this.fileMenu.remove (this.closeMenuItem); -this.fileMenu.remove (3); -this.embeddedMenu = this.makeEmbeddedPopupMenu (this.alignFrameMenuBar, false, false); -theApplet.setLayout ( new java.awt.BorderLayout ()); -theApplet.add (this.embeddedMenu, "North"); -theApplet.add (this.statusBar, "South"); -this.alignPanel.setSize (theApplet.getSize ().width, theApplet.getSize ().height - this.embeddedMenu.getHeight () - this.statusBar.getHeight ()); -theApplet.add (this.alignPanel, "Center"); -var me = this; -theApplet.addFocusListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$5") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$5, this, Clazz.cloneFinals ("theApplet", theApplet, "me", me)))); -theApplet.validate (); -}, "jalview.bin.JalviewLite"); -Clazz.defineMethod (c$, "addStructureViewInstance", -function (jmolviewer, sequenceIds) { -return null; -}, "~O,~A"); -Clazz.defineMethod (c$, "addPdbFile", -function (sequenceId, pdbEntryString, pdbFile) { -var toaddpdb = this.viewport.getAlignment ().findName (sequenceId); -var needtoadd = false; -if (toaddpdb != null) { -var pdbe = toaddpdb.getPDBId (); -var pdbentry = null; -if (pdbe != null && pdbe.size () > 0) { -for (var pe = 0, peSize = pdbe.size (); pe < peSize; pe++) { -pdbentry = pdbe.elementAt (pe); -if (!pdbentry.getId ().equals (pdbEntryString) && !pdbentry.getFile ().equals (pdbFile)) { -pdbentry = null; -} else { -continue; -}} -}if (pdbentry == null) { -pdbentry = new jalview.datamodel.PDBEntry (); -pdbentry.setId (pdbEntryString); -pdbentry.setFile (pdbFile); -needtoadd = true; -}var protocol = jalview.io.AppletFormatAdapter.resolveProtocol (pdbFile, "PDB"); -if (protocol == null) { -return false; -}if (needtoadd) { -if (pdbentry.getProperty () == null) { -pdbentry.setProperty ( new java.util.Hashtable ()); -}pdbentry.getProperty ().put ("protocol", protocol); -toaddpdb.addPDBId (pdbentry); -this.alignPanel.getStructureSelectionManager ().registerPDBEntry (pdbentry); -}}return true; -}, "~S,~S,~S"); -Clazz.defineMethod (c$, "cleanSeqChainArrays", -($fz = function (seqs, chains) { -if (seqs != null) { -var sequences = new java.util.Vector (); -for (var i = 0; i < seqs.length; i++) { -if (seqs[i] != null) { -sequences.addElement ( Clazz.newArray (-1, [seqs[i], (chains != null) ? chains[i] : null])); -}} -seqs = new Array (sequences.size ()); -chains = new Array (sequences.size ()); -for (var i = 0, isize = sequences.size (); i < isize; i++) { -var oj = sequences.elementAt (i); -seqs[i] = oj[0]; -chains[i] = oj[1]; -} -}return Clazz.newArray (-1, [seqs, chains]); -}, $fz.isPrivate = true, $fz), "~A,~A"); -Clazz.defineMethod (c$, "newStructureView", -function (applet, pdb, seqs, chains, protocol) { -var sqch = this.cleanSeqChainArrays (seqs, chains); -seqs = sqch[0]; -chains = sqch[1]; -if (seqs == null || seqs.length == 0) { -System.err.println ("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); -}if (protocol == null || protocol.trim ().length == 0 || protocol.equals ("null")) { -protocol = pdb.getProperty ().get ("protocol"); -if (protocol == null) { -System.err.println ("Couldn't work out protocol to open structure: " + pdb.getId ()); -return; -}}if (applet.useXtrnalSviewer) { -if (jalview.structure.StructureSelectionManager.getStructureSelectionManager (applet).setMapping (seqs, chains, pdb.getFile (), protocol) == null) { -System.err.println ("Failed to map " + pdb.getFile () + " (" + protocol + ") to any sequences"); -}return; -}if (applet.isAlignPdbStructures () && applet.jmolAvailable) { -var ajm = null; -var tajm; -var jmols = applet.getAppletWindow (jalview.appletgui.AppletJmol); -for (var i = 0, iSize = jmols.size (); i < iSize; i++) { -tajm = jmols.elementAt (i); -if (tajm.ap.alignFrame === this) { -ajm = tajm; -break; -}} -if (ajm != null) { -System.err.println ("Incremental adding and aligning structure to existing Jmol view not yet implemented."); -ajm = null; -}} new jalview.appletgui.AppletJmol (pdb, seqs, chains, this.alignPanel, protocol); -jalview.bin.JalviewLite.lastFrameX += 40; -jalview.bin.JalviewLite.lastFrameY += 40; -}, "jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S"); -Clazz.defineMethod (c$, "alignedStructureView", -function (applet, pdb, seqs, chains, protocols) { -System.err.println ("Aligned Structure View: Not yet implemented."); -}, "jalview.bin.JalviewLite,~A,~A,~A,~A"); -Clazz.defineMethod (c$, "select", -function (sel, csel) { -this.alignPanel.seqPanel.selection (sel, csel, null); -}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection"); -Clazz.defineMethod (c$, "scrollTo", -function (row, column) { -this.alignPanel.seqPanel.scrollTo (row, column); -}, "~N,~N"); -Clazz.defineMethod (c$, "scrollToRow", -function (row) { -this.alignPanel.seqPanel.scrollToRow (row); -}, "~N"); -Clazz.defineMethod (c$, "scrollToColumn", -function (column) { -this.alignPanel.seqPanel.scrollToColumn (column); -}, "~N"); -Clazz.defineMethod (c$, "getSequenceSetId", -function () { -return this.viewport.getSequenceSetId (); -}); -Clazz.defineMethod (c$, "loadScoreFile", -function (inFile) { -var file = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [inFile, jalview.io.AppletFormatAdapter.checkProtocol (inFile)]); -if (!file.isValid ()) { -System.err.println ("Problems parsing T-Coffee scores: " + file.getWarningMessage ()); -System.err.println ("Origin was:\n" + inFile); -return false; -}var aln; -if ((aln = this.viewport.getAlignment ()) != null && (aln.getHeight () != file.getHeight () || aln.getWidth () != file.getWidth ())) { -System.err.println ("The scores matrix does not match the alignment dimensions"); -}if (file.annotateAlignment (this.alignPanel.getAlignment (), false)) { -this.alignPanel.fontChanged (); -this.tcoffeeColour.setEnabled (true); -this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); -return true; -} else { -System.err.println ("Problems resolving T-Coffee scores:"); -if (file.getWarningMessage () != null) { -System.err.println (file.getWarningMessage ()); -}}return false; -}, "~S"); -Clazz.defineMethod (c$, "getSplitFrame", -function () { -return this.splitFrame; -}); -Clazz.defineMethod (c$, "setSplitFrame", -function (sf) { -this.splitFrame = sf; -}, "jalview.appletgui.SplitFrame"); -Clazz.overrideMethod (c$, "setShowSeqFeatures", -function (b) { -this.viewport.setShowSequenceFeatures (b); -}, "~B"); -Clazz.overrideMethod (c$, "setMenusForViewport", -function () { -}); -Clazz.overrideMethod (c$, "refreshFeatureUI", -function (enableIfNecessary) { -if (enableIfNecessary) { -this.sequenceFeatures.setState (true); -this.alignPanel.av.setShowSequenceFeatures (true); -}}, "~B"); -Clazz.overrideMethod (c$, "getFeatureSettingsUI", -function () { -return this.alignPanel.av.featureSettings; -}); -c$.$AlignFrame$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$1", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -if (this.f$.ap != null) { -this.f$.ap.setOverviewPanel (null); -}}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$2", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$3", java.awt.event.WindowAdapter); -Clazz.defineMethod (c$, "windowOpened", -function (e) { -if (this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree) { -this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); -}Clazz.superCall (this, jalview.appletgui.AlignFrame$3, "windowOpened", [e]); -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove (this.f$.item); -}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$1AboutPanel$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.version = null; -this.builddate = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AlignFrame$1AboutPanel", awt2swing.Canvas); -Clazz.makeConstructor (c$, -function (a, b) { -Clazz.superConstructor (this, jalview.appletgui.AlignFrame$1AboutPanel, []); -this.version = a; -this.builddate = b; -}, "~S,~S"); -Clazz.overrideMethod (c$, "paintComponent", -function (a) { -a.setColor (java.awt.Color.white); -a.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -a.setFont ( new java.awt.Font ("Helvetica", 0, 12)); -var b = a.getFontMetrics (); -var c = b.getHeight (); -var d = 5; -var e = 7; -a.setColor (java.awt.Color.black); -a.setFont ( new java.awt.Font ("Helvetica", 1, 14)); -a.drawString (jalview.util.MessageManager.formatMessage ("label.jalviewLite_release", Clazz.newArray (-1, [this.version])), e, d += c); -a.setFont ( new java.awt.Font ("Helvetica", 1, 12)); -a.drawString (jalview.util.MessageManager.formatMessage ("label.jaview_build_date", Clazz.newArray (-1, [this.builddate])), e, d += c); -a.setFont ( new java.awt.Font ("Helvetica", 0, 12)); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_1"), e, d += c * 1.5); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_2"), e + 50, d += c + 8); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_dev_managers"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_distribution_lists"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_please_cite"), e, d += c + 8); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_authors"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_title"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_ref"), e, d += c); -}, "java.awt.Graphics"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$4$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$4", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.AlignFrame"].outputText_actionPerformed (e); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$5$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$5", null, java.awt.event.FocusListener); -Clazz.overrideMethod (c$, "focusLost", -function (e) { -if (this.f$.theApplet.currentAlignFrame === this.f$.me) { -this.f$.theApplet.currentAlignFrame = null; -}}, "java.awt.event.FocusEvent"); -Clazz.overrideMethod (c$, "focusGained", -function (e) { -this.f$.theApplet.currentAlignFrame = this.f$.me; -}, "java.awt.event.FocusEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"copiedSequences", null, -"copiedHiddenColumns", null); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Canvas", "jalview.api.AlignViewControllerGuiI", "jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "$.KeyListener", "awt2swing.CheckboxMenuItem", "$.Label", "$.Menu", "$.MenuBar", "$.MenuItem", "jalview.util.MessageManager", "java.awt.BorderLayout"], "jalview.appletgui.AlignFrame", ["awt2swing.Frame", "jalview.analysis.AlignmentSorter", "$.AnnotationSorter", "jalview.appletgui.AlignViewport", "$.AlignmentPanel", "$.AnnotationColourChooser", "$.AnnotationColumnChooser", "$.AppletJmol", "$.CutAndPasteTransfer", "$.FeatureSettings", "$.Finder", "$.FontChooser", "$.OverviewPanel", "$.PCAPanel", "$.PaintRefresher", "$.PairwiseAlignPanel", "$.RedundancyPanel", "$.SliderPanel", "$.TreePanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "$.OrderCommand", "$.RemoveGapColCommand", "$.RemoveGapsCommand", "$.SlideSequencesCommand", "$.TrimRegionCommand", "jalview.controller.AlignViewController", "jalview.datamodel.Alignment", "$.PDBEntry", "$.Sequence", "$.SequenceGroup", "jalview.io.AlignmentProperties", "$.AnnotationFile", "$.AppletFormatAdapter", "$.FeaturesFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColourChooser", "$.RNAInteractionColourScheme", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.structure.StructureSelectionManager", "jalview.util.Comparison", "$.MappingUtils", "java.awt.Color", "$.Font", "java.awt.event.FocusListener", "$.WindowAdapter", "java.lang.Character", "$.StringBuffer", "java.net.URL", "$.URLEncoder", "java.util.Arrays", "$.HashMap", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.avc = null; +this.alignPanel = null; +this.viewport = null; +this.frameWidth = 700; +this.frameHeight = 500; +this.jalviewServletURL = null; +this.showAutoCalculatedAbove = false; +this.annotationSortOrder = null; +this.alignFrameMenuBar = null; +this.fileMenu = null; +this.loadApplication = null; +this.$loadTree = null; +this.$loadAnnotations = null; +this.$outputFeatures = null; +this.$outputAnnotations = null; +this.closeMenuItem = null; +this.selectAllSequenceMenuItem = null; +this.deselectAllSequenceMenuItem = null; +this.invertSequenceMenuItem = null; +this.remove2LeftMenuItem = null; +this.remove2RightMenuItem = null; +this.removeGappedColumnMenuItem = null; +this.removeAllGapsMenuItem = null; +this.viewBoxesMenuItem = null; +this.viewTextMenuItem = null; +this.sortPairwiseMenuItem = null; +this.sortIDMenuItem = null; +this.sortLengthMenuItem = null; +this.sortGroupMenuItem = null; +this.removeRedundancyMenuItem = null; +this.pairwiseAlignmentMenuItem = null; +this.PCAMenuItem = null; +this.averageDistanceTreeMenuItem = null; +this.neighbourTreeMenuItem = null; +this.borderLayout1 = null; +this.statusBar = null; +this.clustalColour = null; +this.zappoColour = null; +this.taylorColour = null; +this.hydrophobicityColour = null; +this.helixColour = null; +this.strandColour = null; +this.turnColour = null; +this.buriedColour = null; +this.purinePyrimidineColour = null; +this.RNAInteractionColour = null; +this.RNAHelixColour = null; +this.userDefinedColour = null; +this.PIDColour = null; +this.BLOSUM62Colour = null; +this.tcoffeeColour = null; +this.njTreeBlosumMenuItem = null; +this.avDistanceTreeBlosumMenuItem = null; +this.annotationPanelMenuItem = null; +this.colourTextMenuItem = null; +this.displayNonconservedMenuItem = null; +this.alProperties = null; +this.overviewMenuItem = null; +this.undoMenuItem = null; +this.redoMenuItem = null; +this.conservationMenuItem = null; +this.noColourmenuItem = null; +this.wrapMenuItem = null; +this.renderGapsMenuItem = null; +this.findMenuItem = null; +this.abovePIDThreshold = null; +this.nucleotideColour = null; +this.deleteGroups = null; +this.grpsFromSelection = null; +this.createGroup = null; +this.unGroup = null; +this.$delete = null; +this.copy = null; +this.cut = null; +this.pasteMenu = null; +this.pasteNew = null; +this.pasteThis = null; +this.applyToAllGroups = null; +this.$font = null; +this.scaleAbove = null; +this.scaleLeft = null; +this.scaleRight = null; +this.modifyPID = null; +this.modifyConservation = null; +this.autoCalculate = null; +this.$sortByTree = null; +this.sortByTreeMenu = null; +this.inputText = null; +this.documentation = null; +this.about = null; +this.seqLimits = null; +this.centreColumnLabelFlag = null; +this.followMouseOverFlag = null; +this.showSequenceLogo = null; +this.applyAutoAnnotationSettings = null; +this.showConsensusHistogram = null; +this.showGroupConsensus = null; +this.showGroupConservation = null; +this.normSequenceLogo = null; +this.featureSettings = null; +this.sequenceFeatures = null; +this.annotationColour = null; +this.annotationColumnSelection = null; +this.invertColSel = null; +this.showColumns = null; +this.showSeqs = null; +this.hideColumns = null; +this.hideSequences = null; +this.hideAllButSelection = null; +this.hideAllSelection = null; +this.showAllHidden = null; +this.$newView = null; +this.showAlignmentAnnotations = null; +this.showSequenceAnnotations = null; +this.sortAnnBySequence = null; +this.sortAnnByLabel = null; +this.showAutoFirst = null; +this.showAutoLast = null; +this.splitFrame = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AlignFrame", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.KeyListener, jalview.api.AlignViewControllerGuiI]); +Clazz.prepareFields (c$, function () { +this.alignFrameMenuBar = new awt2swing.MenuBar (); +this.fileMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.file")); +this.loadApplication = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.view_full_application")); +this.$loadTree = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.load_associated_tree")); +this.$loadAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.load_features_annotations")); +this.$outputFeatures = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.export_features").concat ("...")); +this.$outputAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.export_annotations").concat ("...")); +this.closeMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.close")); +this.selectAllSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.select_all")); +this.deselectAllSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.deselect_all")); +this.invertSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.invert_selection")); +this.remove2LeftMenuItem = new awt2swing.MenuItem (); +this.remove2RightMenuItem = new awt2swing.MenuItem (); +this.removeGappedColumnMenuItem = new awt2swing.MenuItem (); +this.removeAllGapsMenuItem = new awt2swing.MenuItem (); +this.viewBoxesMenuItem = new awt2swing.CheckboxMenuItem (); +this.viewTextMenuItem = new awt2swing.CheckboxMenuItem (); +this.sortPairwiseMenuItem = new awt2swing.MenuItem (); +this.sortIDMenuItem = new awt2swing.MenuItem (); +this.sortLengthMenuItem = new awt2swing.MenuItem (); +this.sortGroupMenuItem = new awt2swing.MenuItem (); +this.removeRedundancyMenuItem = new awt2swing.MenuItem (); +this.pairwiseAlignmentMenuItem = new awt2swing.MenuItem (); +this.PCAMenuItem = new awt2swing.MenuItem (); +this.averageDistanceTreeMenuItem = new awt2swing.MenuItem (); +this.neighbourTreeMenuItem = new awt2swing.MenuItem (); +this.borderLayout1 = new java.awt.BorderLayout (); +this.statusBar = new awt2swing.Label (); +this.clustalColour = new awt2swing.MenuItem (); +this.zappoColour = new awt2swing.MenuItem (); +this.taylorColour = new awt2swing.MenuItem (); +this.hydrophobicityColour = new awt2swing.MenuItem (); +this.helixColour = new awt2swing.MenuItem (); +this.strandColour = new awt2swing.MenuItem (); +this.turnColour = new awt2swing.MenuItem (); +this.buriedColour = new awt2swing.MenuItem (); +this.purinePyrimidineColour = new awt2swing.MenuItem (); +this.RNAInteractionColour = new awt2swing.MenuItem (); +this.RNAHelixColour = new awt2swing.MenuItem (); +this.userDefinedColour = new awt2swing.MenuItem (); +this.PIDColour = new awt2swing.MenuItem (); +this.BLOSUM62Colour = new awt2swing.MenuItem (); +this.tcoffeeColour = new awt2swing.MenuItem (); +this.njTreeBlosumMenuItem = new awt2swing.MenuItem (); +this.avDistanceTreeBlosumMenuItem = new awt2swing.MenuItem (); +this.annotationPanelMenuItem = new awt2swing.CheckboxMenuItem (); +this.colourTextMenuItem = new awt2swing.CheckboxMenuItem (); +this.displayNonconservedMenuItem = new awt2swing.CheckboxMenuItem (); +this.alProperties = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.alignment_props")); +this.overviewMenuItem = new awt2swing.MenuItem (); +this.undoMenuItem = new awt2swing.MenuItem (); +this.redoMenuItem = new awt2swing.MenuItem (); +this.conservationMenuItem = new awt2swing.CheckboxMenuItem (); +this.noColourmenuItem = new awt2swing.MenuItem (); +this.wrapMenuItem = new awt2swing.CheckboxMenuItem (); +this.renderGapsMenuItem = new awt2swing.CheckboxMenuItem (); +this.findMenuItem = new awt2swing.MenuItem (); +this.abovePIDThreshold = new awt2swing.CheckboxMenuItem (); +this.nucleotideColour = new awt2swing.MenuItem (); +this.deleteGroups = new awt2swing.MenuItem (); +this.grpsFromSelection = new awt2swing.MenuItem (); +this.createGroup = new awt2swing.MenuItem (); +this.unGroup = new awt2swing.MenuItem (); +this.$delete = new awt2swing.MenuItem (); +this.copy = new awt2swing.MenuItem (); +this.cut = new awt2swing.MenuItem (); +this.pasteMenu = new awt2swing.Menu (); +this.pasteNew = new awt2swing.MenuItem (); +this.pasteThis = new awt2swing.MenuItem (); +this.applyToAllGroups = new awt2swing.CheckboxMenuItem (); +this.$font = new awt2swing.MenuItem (); +this.scaleAbove = new awt2swing.CheckboxMenuItem (); +this.scaleLeft = new awt2swing.CheckboxMenuItem (); +this.scaleRight = new awt2swing.CheckboxMenuItem (); +this.modifyPID = new awt2swing.MenuItem (); +this.modifyConservation = new awt2swing.MenuItem (); +this.$sortByTree = new awt2swing.CheckboxMenuItem ("Sort Alignment With New Tree", true); +this.sortByTreeMenu = new awt2swing.Menu (); +this.inputText = new awt2swing.MenuItem (); +this.documentation = new awt2swing.MenuItem (); +this.about = new awt2swing.MenuItem (); +this.seqLimits = new awt2swing.CheckboxMenuItem (); +this.centreColumnLabelFlag = new awt2swing.CheckboxMenuItem (); +this.followMouseOverFlag = new awt2swing.CheckboxMenuItem (); +this.showSequenceLogo = new awt2swing.CheckboxMenuItem (); +this.applyAutoAnnotationSettings = new awt2swing.CheckboxMenuItem (); +this.showConsensusHistogram = new awt2swing.CheckboxMenuItem (); +this.showGroupConsensus = new awt2swing.CheckboxMenuItem (); +this.showGroupConservation = new awt2swing.CheckboxMenuItem (); +this.normSequenceLogo = new awt2swing.CheckboxMenuItem (); +this.featureSettings = new awt2swing.MenuItem (); +this.sequenceFeatures = new awt2swing.CheckboxMenuItem (); +this.annotationColour = new awt2swing.MenuItem (); +this.annotationColumnSelection = new awt2swing.MenuItem (); +this.invertColSel = new awt2swing.MenuItem (); +this.showColumns = new awt2swing.MenuItem (); +this.showSeqs = new awt2swing.MenuItem (); +this.hideColumns = new awt2swing.MenuItem (); +this.hideSequences = new awt2swing.MenuItem (); +this.hideAllButSelection = new awt2swing.MenuItem (); +this.hideAllSelection = new awt2swing.MenuItem (); +this.showAllHidden = new awt2swing.MenuItem (); +this.$newView = new awt2swing.MenuItem (); +}); +Clazz.makeConstructor (c$, +function (al, applet, title, embedded) { +this.construct (al, applet, title, embedded, true); +}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B"); +Clazz.makeConstructor (c$, +function (al, applet, title, embedded, addToDisplay) { +this.construct (al, null, null, applet, title, embedded, addToDisplay); +}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B"); +Clazz.makeConstructor (c$, +function (al, hiddenSeqs, columnSelection, applet, title, embedded) { +this.construct (al, hiddenSeqs, columnSelection, applet, title, embedded, true); +}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B"); +Clazz.makeConstructor (c$, +function (al, hiddenSeqs, columnSelection, applet, title, embedded, addToDisplay) { +Clazz.superConstructor (this, jalview.appletgui.AlignFrame, []); +if (applet != null) { +this.jalviewServletURL = applet.jalviewServletURL; +}try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +if (applet != null) { +var param; +try { +param = applet.windowWidth; +if (param != null) { +var width = Integer.parseInt (param); +this.frameWidth = width; +}param = applet.windowHeight; +if (param != null) { +var height = Integer.parseInt (param); +this.frameHeight = height; +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}this.viewport = new jalview.appletgui.AlignViewport (al, applet); +if (hiddenSeqs != null && hiddenSeqs.length > 0) { +this.viewport.hideSequence (hiddenSeqs); +}if (columnSelection != null) { +this.viewport.setColumnSelection (columnSelection); +}this.alignPanel = new jalview.appletgui.AlignmentPanel (this, this.viewport); +this.avc = new jalview.controller.AlignViewController (this, this.viewport, this.alignPanel); +this.viewport.updateConservation (this.alignPanel); +this.viewport.updateConsensus (this.alignPanel); +this.displayNonconservedMenuItem.setState (this.viewport.getShowUnconserved ()); +this.followMouseOverFlag.setState (this.viewport.isFollowHighlight ()); +this.showGroupConsensus.setState (this.viewport.isShowGroupConsensus ()); +this.showGroupConservation.setState (this.viewport.isShowGroupConservation ()); +this.showConsensusHistogram.setState (this.viewport.isShowConsensusHistogram ()); +this.showSequenceLogo.setState (this.viewport.isShowSequenceLogo ()); +this.normSequenceLogo.setState (this.viewport.isNormaliseSequenceLogo ()); +this.applyToAllGroups.setState (this.viewport.getColourAppliesToAllGroups ()); +this.annotationPanelMenuItem.setState (this.viewport.isShowAnnotation ()); +this.showAlignmentAnnotations.setState (this.viewport.isShowAnnotation ()); +this.showSequenceAnnotations.setState (this.viewport.isShowAnnotation ()); +this.seqLimits.setState (this.viewport.getShowJVSuffix ()); +if (applet != null) { +var param = applet.sortBy; +if (param != null) { +if (param.equalsIgnoreCase ("Id")) { +this.sortIDMenuItem_actionPerformed (); +} else if (param.equalsIgnoreCase ("Pairwise Identity")) { +this.sortPairwiseMenuItem_actionPerformed (); +} else if (param.equalsIgnoreCase ("Length")) { +this.sortLengthMenuItem_actionPerformed (); +}}param = applet.wrap; +if (param != null) { +if (param.equalsIgnoreCase ("true")) { +this.wrapMenuItem.setState (true); +this.wrapMenuItem_actionPerformed (); +}}param = applet.centrecolumnlabels; +if (param != null) { +this.centreColumnLabelFlag.setState (true); +this.centreColumnLabelFlag_stateChanged (); +}}if (this.viewport.getAlignment ().isNucleotide ()) { +this.viewport.updateStrucConsensus (this.alignPanel); +if (this.viewport.getAlignment ().hasRNAStructure ()) { +this.RNAHelixColour.setEnabled (true); +} else { +this.RNAHelixColour.setEnabled (false); +}} else { +this.RNAHelixColour.setEnabled (false); +this.purinePyrimidineColour.setEnabled (false); +}this.addKeyListener (this); +this.alignPanel.seqPanel.seqCanvas.addKeyListener (this); +this.alignPanel.idPanel.idCanvas.addKeyListener (this); +this.alignPanel.scalePanel.addKeyListener (this); +this.alignPanel.annotationPanel.addKeyListener (this); +this.alignPanel.annotationPanelHolder.addKeyListener (this); +this.alignPanel.annotationSpaceFillerHolder.addKeyListener (this); +this.alignPanel.alabels.addKeyListener (this); +if (addToDisplay) { +this.addToDisplay (embedded); +}}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B"); +Clazz.defineMethod (c$, "addToDisplay", +function (embedded) { +this.createAlignFrameWindow (embedded); +this.validate (); +this.alignPanel.adjustAnnotationHeight (); +this.alignPanel.paintAlignment (true); +}, "~B"); +Clazz.defineMethod (c$, "getAlignViewport", +function () { +return this.viewport; +}); +Clazz.defineMethod (c$, "getSeqcanvas", +function () { +return this.alignPanel.seqPanel.seqCanvas; +}); +Clazz.defineMethod (c$, "parseFeaturesFile", +function (file, type) { +return this.parseFeaturesFile (file, type, true); +}, "~S,~S"); +Clazz.defineMethod (c$, "parseFeaturesFile", +function (file, type, autoenabledisplay) { +var featureLinks = new java.util.Hashtable (); +var featuresFile = false; +try { +featuresFile = new jalview.io.FeaturesFile (file, type).parse (this.viewport.getAlignment (), this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().getFeatureColours (), featureLinks, true, this.viewport.applet.getDefaultParameter ("relaxedidmatch", false)); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +if (featuresFile) { +if (featureLinks.size () > 0) { +this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().featureLinks = featureLinks; +}if (autoenabledisplay) { +this.viewport.setShowSequenceFeatures (true); +this.sequenceFeatures.setState (true); +}if (this.alignPanel.seqPanel.seqCanvas.fr != null) { +this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures (true); +}if (this.viewport.featureSettings != null) { +this.viewport.featureSettings.refreshTable (); +}this.alignPanel.paintAlignment (true); +this.setStatus (jalview.util.MessageManager.getString ("label.successfully_added_features_alignment")); +}return featuresFile; +}, "~S,~S,~B"); +Clazz.overrideMethod (c$, "keyPressed", +function (evt) { +if (this.viewport.cursorMode && ((evt.getKeyCode () >= 48 && evt.getKeyCode () <= 57) || (evt.getKeyCode () >= 96 && evt.getKeyCode () <= 105)) && Character.isDigit (evt.getKeyChar ())) { +this.alignPanel.seqPanel.numberPressed (evt.getKeyChar ()); +}switch (evt.getKeyCode ()) { +case 27: +this.deselectAllSequenceMenuItem_actionPerformed (); +this.alignPanel.alabels.cancelDrag (); +break; +case 88: +if (evt.isControlDown () || evt.isMetaDown ()) { +this.cut_actionPerformed (); +}break; +case 67: +if (this.viewport.cursorMode && !evt.isControlDown ()) { +this.alignPanel.seqPanel.setCursorColumn (); +}if (evt.isControlDown () || evt.isMetaDown ()) { +this.copy_actionPerformed (); +}break; +case 86: +if (evt.isControlDown ()) { +this.paste (evt.isShiftDown ()); +}break; +case 65: +if (evt.isControlDown () || evt.isMetaDown ()) { +this.selectAllSequenceMenuItem_actionPerformed (); +}break; +case 40: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (0, 1); +} else { +this.moveSelectedSequences (false); +}break; +case 38: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (0, -1); +} else { +this.moveSelectedSequences (true); +}break; +case 37: +if (evt.isAltDown () || !this.viewport.cursorMode) { +this.slideSequences (false, this.alignPanel.seqPanel.getKeyboardNo1 ()); +} else { +this.alignPanel.seqPanel.moveCursor (-1, 0); +}break; +case 39: +if (evt.isAltDown () || !this.viewport.cursorMode) { +this.slideSequences (true, this.alignPanel.seqPanel.getKeyboardNo1 ()); +} else { +this.alignPanel.seqPanel.moveCursor (1, 0); +}break; +case 32: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.insertGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); +}break; +case 127: +case 8: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.deleteGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); +} else { +this.cut_actionPerformed (); +this.alignPanel.seqPanel.seqCanvas.repaint (); +}break; +case 83: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setCursorRow (); +}break; +case 80: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setCursorPosition (); +}break; +case 10: +case 44: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setCursorRowAndColumn (); +}break; +case 81: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setSelectionAreaAtCursor (true); +}break; +case 77: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setSelectionAreaAtCursor (false); +}break; +case 113: +this.viewport.cursorMode = !this.viewport.cursorMode; +this.setStatus (jalview.util.MessageManager.formatMessage ("label.keyboard_editing_mode", Clazz.newArray (-1, [(this.viewport.cursorMode ? "on" : "off")]))); +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.seqCanvas.cursorX = this.viewport.startRes; +this.alignPanel.seqPanel.seqCanvas.cursorY = this.viewport.startSeq; +}break; +case 70: +if (evt.isControlDown ()) { +this.findMenuItem_actionPerformed (); +}break; +case 72: +{ +var toggleSeqs = !evt.isControlDown (); +var toggleCols = !evt.isShiftDown (); +this.toggleHiddenRegions (toggleSeqs, toggleCols); +break; +}case 33: +if (this.viewport.getWrapAlignment ()) { +this.alignPanel.scrollUp (true); +} else { +this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq - this.viewport.endSeq + this.viewport.startSeq); +}break; +case 34: +if (this.viewport.getWrapAlignment ()) { +this.alignPanel.scrollUp (false); +} else { +this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq + this.viewport.endSeq - this.viewport.startSeq); +}break; +case 90: +if (evt.isControlDown ()) { +this.undoMenuItem_actionPerformed (); +}break; +case 89: +if (evt.isControlDown ()) { +this.redoMenuItem_actionPerformed (); +}break; +case 76: +if (evt.isControlDown ()) { +this.trimAlignment (true); +}break; +case 82: +if (evt.isControlDown ()) { +this.trimAlignment (false); +}break; +case 69: +if (evt.isControlDown ()) { +if (evt.isShiftDown ()) { +this.removeAllGapsMenuItem_actionPerformed (); +} else { +this.removeGappedColumnMenuItem_actionPerformed (); +}}break; +case 73: +if (evt.isControlDown ()) { +if (evt.isAltDown ()) { +this.invertColSel_actionPerformed (); +} else { +this.invertSequenceMenuItem_actionPerformed (); +}}break; +case 71: +if (evt.isControlDown ()) { +if (evt.isShiftDown ()) { +this.unGroup_actionPerformed (); +} else { +this.createGroup_actionPerformed (); +}}break; +case 85: +if (evt.isControlDown ()) { +this.deleteGroups_actionPerformed (); +}break; +case 84: +if (evt.isControlDown ()) { +this.newView (null); +}break; +} +this.alignPanel.paintAlignment (true); +}, "java.awt.event.KeyEvent"); +Clazz.defineMethod (c$, "toggleHiddenRegions", +($fz = function (toggleSeqs, toggleCols) { +var hide = false; +var sg = this.viewport.getSelectionGroup (); +if (!toggleSeqs && !toggleCols) { +if ((this.viewport.getColumnSelection () != null && this.viewport.getColumnSelection ().getSelected () != null && this.viewport.getColumnSelection ().getSelected ().size () > 0) || (sg != null && sg.getSize () > 0 && sg.getStartRes () <= sg.getEndRes ())) { +if (sg != null) { +this.invertSequenceMenuItem_actionPerformed (); +sg = this.viewport.getSelectionGroup (); +toggleSeqs = true; +}this.viewport.expandColSelection (sg, true); +this.invertColSel_actionPerformed (); +toggleCols = true; +}}if (toggleSeqs) { +if (sg != null && sg.getSize () != this.viewport.getAlignment ().getHeight ()) { +hide = true; +this.viewport.hideAllSelectedSeqs (); +} else if (!(toggleCols && this.viewport.getColumnSelection ().getSelected ().size () > 0)) { +this.viewport.showAllHiddenSeqs (); +}}if (toggleCols) { +if (this.viewport.getColumnSelection ().getSelected ().size () > 0) { +this.viewport.hideSelectedColumns (); +if (!toggleSeqs) { +this.viewport.setSelectionGroup (sg); +}} else if (!hide) { +this.viewport.showAllHiddenColumns (); +}}}, $fz.isPrivate = true, $fz), "~B,~B"); +Clazz.overrideMethod (c$, "keyReleased", +function (evt) { +}, "java.awt.event.KeyEvent"); +Clazz.overrideMethod (c$, "keyTyped", +function (evt) { +}, "java.awt.event.KeyEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +var source = evt.getSource (); +if (source === this.displayNonconservedMenuItem) { +this.displayNonconservedMenuItem_actionPerformed (); +} else if (source === this.colourTextMenuItem) { +this.colourTextMenuItem_actionPerformed (); +} else if (source === this.wrapMenuItem) { +this.wrapMenuItem_actionPerformed (); +} else if (source === this.scaleAbove) { +this.viewport.setScaleAboveWrapped (this.scaleAbove.getState ()); +} else if (source === this.scaleLeft) { +this.viewport.setScaleLeftWrapped (this.scaleLeft.getState ()); +} else if (source === this.scaleRight) { +this.viewport.setScaleRightWrapped (this.scaleRight.getState ()); +} else if (source === this.seqLimits) { +this.seqLimits_itemStateChanged (); +} else if (source === this.viewBoxesMenuItem) { +this.viewport.setShowBoxes (this.viewBoxesMenuItem.getState ()); +} else if (source === this.viewTextMenuItem) { +this.viewport.setShowText (this.viewTextMenuItem.getState ()); +} else if (source === this.renderGapsMenuItem) { +this.viewport.setRenderGaps (this.renderGapsMenuItem.getState ()); +} else if (source === this.annotationPanelMenuItem) { +this.viewport.setShowAnnotation (this.annotationPanelMenuItem.getState ()); +this.alignPanel.setAnnotationVisible (this.annotationPanelMenuItem.getState ()); +} else if (source === this.sequenceFeatures) { +this.viewport.setShowSequenceFeatures (this.sequenceFeatures.getState ()); +this.alignPanel.seqPanel.seqCanvas.repaint (); +} else if (source === this.showAlignmentAnnotations) { +this.setAnnotationsVisibility (); +} else if (source === this.showSequenceAnnotations) { +this.setAnnotationsVisibility (); +} else if (source === this.sortAnnBySequence) { +var newState = this.sortAnnBySequence.getState (); +this.sortAnnByLabel.setState (false); +this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); +this.setViewportAnnotationOrder (); +} else if (source === this.sortAnnByLabel) { +var newState = this.sortAnnByLabel.getState (); +this.sortAnnBySequence.setState (false); +this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); +this.setViewportAnnotationOrder (); +} else if (source === this.showAutoFirst) { +this.showAutoLast.setState (!this.showAutoFirst.getState ()); +this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); +this.setViewportAnnotationOrder (); +} else if (source === this.showAutoLast) { +this.showAutoFirst.setState (!this.showAutoLast.getState ()); +this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); +this.setViewportAnnotationOrder (); +} else if (source === this.conservationMenuItem) { +this.conservationMenuItem_actionPerformed (); +} else if (source === this.abovePIDThreshold) { +this.abovePIDThreshold_actionPerformed (); +} else if (source === this.applyToAllGroups) { +this.viewport.setColourAppliesToAllGroups (this.applyToAllGroups.getState ()); +} else if (source === this.autoCalculate) { +this.viewport.autoCalculateConsensus = this.autoCalculate.getState (); +} else if (source === this.$sortByTree) { +this.viewport.sortByTree = this.$sortByTree.getState (); +} else if (source === this.centreColumnLabelFlag) { +this.centreColumnLabelFlag_stateChanged (); +} else if (source === this.followMouseOverFlag) { +this.mouseOverFlag_stateChanged (); +} else if (source === this.showGroupConsensus) { +this.showGroupConsensus_actionPerformed (); +} else if (source === this.showGroupConservation) { +this.showGroupConservation_actionPerformed (); +} else if (source === this.showSequenceLogo) { +this.showSequenceLogo_actionPerformed (); +} else if (source === this.normSequenceLogo) { +this.normSequenceLogo_actionPerformed (); +} else if (source === this.showConsensusHistogram) { +this.showConsensusHistogram_actionPerformed (); +} else if (source === this.applyAutoAnnotationSettings) { +this.applyAutoAnnotationSettings_actionPerformed (); +}this.alignPanel.paintAlignment (true); +}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "setAnnotationsVisibility", +($fz = function () { +var showForAlignment = this.showAlignmentAnnotations.getState (); +var showForSequences = this.showSequenceAnnotations.getState (); +for (var aa, $aa = 0, $$aa = this.alignPanel.getAlignment ().getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { +var visible = (aa.sequenceRef == null ? showForAlignment : showForSequences); +aa.visible = visible; +} +this.alignPanel.validateAnnotationDimensions (true); +this.validate (); +this.repaint (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "setAnnotationSortOrder", +($fz = function (order) { +this.annotationSortOrder = order; +}, $fz.isPrivate = true, $fz), "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); +Clazz.defineMethod (c$, "setViewportAnnotationOrder", +($fz = function () { +this.alignPanel.av.setSortAnnotationsBy (this.annotationSortOrder); +this.alignPanel.av.setShowAutocalculatedAbove (this.showAutoCalculatedAbove); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "setShowAutoCalculatedAbove", +($fz = function (showAbove) { +this.showAutoCalculatedAbove = showAbove; +}, $fz.isPrivate = true, $fz), "~B"); +Clazz.defineMethod (c$, "mouseOverFlag_stateChanged", +($fz = function () { +this.viewport.setFollowHighlight (this.followMouseOverFlag.getState ()); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "centreColumnLabelFlag_stateChanged", +($fz = function () { +this.viewport.centreColumnLabels = this.centreColumnLabelFlag.getState (); +this.alignPanel.annotationPanel.repaint (); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +var source = evt.getSource (); +if (source === this.inputText) { +this.inputText_actionPerformed (); +} else if (source === this.$loadTree) { +this.loadTree_actionPerformed (); +} else if (source === this.loadApplication) { +this.launchFullApplication (); +} else if (source === this.$loadAnnotations) { +this.loadAnnotations (); +} else if (source === this.$outputAnnotations) { +this.outputAnnotations (true); +} else if (source === this.$outputFeatures) { +this.outputFeatures (true, "Jalview"); +} else if (source === this.closeMenuItem) { +this.closeMenuItem_actionPerformed (); +} else if (source === this.copy) { +this.copy_actionPerformed (); +} else if (source === this.undoMenuItem) { +this.undoMenuItem_actionPerformed (); +} else if (source === this.redoMenuItem) { +this.redoMenuItem_actionPerformed (); +} else if (source === this.inputText) { +this.inputText_actionPerformed (); +} else if (source === this.closeMenuItem) { +this.closeMenuItem_actionPerformed (); +} else if (source === this.undoMenuItem) { +this.undoMenuItem_actionPerformed (); +} else if (source === this.redoMenuItem) { +this.redoMenuItem_actionPerformed (); +} else if (source === this.copy) { +this.copy_actionPerformed (); +} else if (source === this.pasteNew) { +this.pasteNew_actionPerformed (); +} else if (source === this.pasteThis) { +this.pasteThis_actionPerformed (); +} else if (source === this.cut) { +this.cut_actionPerformed (); +} else if (source === this.$delete) { +this.delete_actionPerformed (); +} else if (source === this.grpsFromSelection) { +this.makeGrpsFromSelection_actionPerformed (); +} else if (source === this.deleteGroups) { +this.deleteGroups_actionPerformed (); +} else if (source === this.selectAllSequenceMenuItem) { +this.selectAllSequenceMenuItem_actionPerformed (); +} else if (source === this.deselectAllSequenceMenuItem) { +this.deselectAllSequenceMenuItem_actionPerformed (); +} else if (source === this.invertSequenceMenuItem) { +this.invertSequenceMenuItem_actionPerformed (); +} else if (source === this.invertColSel) { +this.viewport.invertColumnSelection (); +this.alignPanel.paintAlignment (true); +} else if (source === this.remove2LeftMenuItem) { +this.trimAlignment (true); +} else if (source === this.remove2RightMenuItem) { +this.trimAlignment (false); +} else if (source === this.removeGappedColumnMenuItem) { +this.removeGappedColumnMenuItem_actionPerformed (); +} else if (source === this.removeAllGapsMenuItem) { +this.removeAllGapsMenuItem_actionPerformed (); +} else if (source === this.findMenuItem) { +this.findMenuItem_actionPerformed (); +} else if (source === this.$font) { + new jalview.appletgui.FontChooser (this.alignPanel); +} else if (source === this.$newView) { +this.newView (null); +} else if (source === this.showColumns) { +this.viewport.showAllHiddenColumns (); +this.alignPanel.paintAlignment (true); +} else if (source === this.showSeqs) { +this.viewport.showAllHiddenSeqs (); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideColumns) { +this.viewport.hideSelectedColumns (); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideSequences && this.viewport.getSelectionGroup () != null) { +this.viewport.hideAllSelectedSeqs (); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideAllButSelection) { +this.toggleHiddenRegions (false, false); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideAllSelection) { +var sg = this.viewport.getSelectionGroup (); +this.viewport.expandColSelection (sg, false); +this.viewport.hideAllSelectedSeqs (); +this.viewport.hideSelectedColumns (); +this.alignPanel.paintAlignment (true); +} else if (source === this.showAllHidden) { +this.viewport.showAllHiddenColumns (); +this.viewport.showAllHiddenSeqs (); +this.alignPanel.paintAlignment (true); +} else if (source === this.showGroupConsensus) { +this.showGroupConsensus_actionPerformed (); +} else if (source === this.showGroupConservation) { +this.showGroupConservation_actionPerformed (); +} else if (source === this.showSequenceLogo) { +this.showSequenceLogo_actionPerformed (); +} else if (source === this.normSequenceLogo) { +this.normSequenceLogo_actionPerformed (); +} else if (source === this.showConsensusHistogram) { +this.showConsensusHistogram_actionPerformed (); +} else if (source === this.applyAutoAnnotationSettings) { +this.applyAutoAnnotationSettings_actionPerformed (); +} else if (source === this.featureSettings) { + new jalview.appletgui.FeatureSettings (this.alignPanel); +} else if (source === this.alProperties) { +var contents = new jalview.io.AlignmentProperties (this.viewport.getAlignment ()).formatAsString (); +var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); +cap.setText (contents.toString ()); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_properties", Clazz.newArray (-1, [this.getTitle ()])), 400, 250); +} else if (source === this.overviewMenuItem) { +this.overviewMenuItem_actionPerformed (); +} else if (source === this.noColourmenuItem) { +this.changeColour (null); +} else if (source === this.clustalColour) { +this.abovePIDThreshold.setState (false); +this.changeColour ( new jalview.schemes.ClustalxColourScheme (this.viewport.getAlignment (), null)); +} else if (source === this.zappoColour) { +this.changeColour ( new jalview.schemes.ZappoColourScheme ()); +} else if (source === this.taylorColour) { +this.changeColour ( new jalview.schemes.TaylorColourScheme ()); +} else if (source === this.hydrophobicityColour) { +this.changeColour ( new jalview.schemes.HydrophobicColourScheme ()); +} else if (source === this.helixColour) { +this.changeColour ( new jalview.schemes.HelixColourScheme ()); +} else if (source === this.strandColour) { +this.changeColour ( new jalview.schemes.StrandColourScheme ()); +} else if (source === this.turnColour) { +this.changeColour ( new jalview.schemes.TurnColourScheme ()); +} else if (source === this.buriedColour) { +this.changeColour ( new jalview.schemes.BuriedColourScheme ()); +} else if (source === this.nucleotideColour) { +this.changeColour ( new jalview.schemes.NucleotideColourScheme ()); +} else if (source === this.purinePyrimidineColour) { +this.changeColour ( new jalview.schemes.PurinePyrimidineColourScheme ()); +} else if (source === this.RNAInteractionColour) { +this.changeColour ( new jalview.schemes.RNAInteractionColourScheme ()); +} else if (source === this.RNAHelixColour) { + new jalview.schemes.RNAHelicesColourChooser (this.viewport, this.alignPanel); +} else if (source === this.modifyPID) { +this.modifyPID_actionPerformed (); +} else if (source === this.modifyConservation) { +this.modifyConservation_actionPerformed (); +} else if (source === this.userDefinedColour) { + new jalview.appletgui.UserDefinedColours (this.alignPanel, null); +} else if (source === this.PIDColour) { +this.changeColour ( new jalview.schemes.PIDColourScheme ()); +} else if (source === this.BLOSUM62Colour) { +this.changeColour ( new jalview.schemes.Blosum62ColourScheme ()); +} else if (source === this.tcoffeeColour) { +this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); +} else if (source === this.annotationColour) { + new jalview.appletgui.AnnotationColourChooser (this.viewport, this.alignPanel); +} else if (source === this.annotationColumnSelection) { + new jalview.appletgui.AnnotationColumnChooser (this.viewport, this.alignPanel); +} else if (source === this.sortPairwiseMenuItem) { +this.sortPairwiseMenuItem_actionPerformed (); +} else if (source === this.sortIDMenuItem) { +this.sortIDMenuItem_actionPerformed (); +} else if (source === this.sortLengthMenuItem) { +this.sortLengthMenuItem_actionPerformed (); +} else if (source === this.sortGroupMenuItem) { +this.sortGroupMenuItem_actionPerformed (); +} else if (source === this.removeRedundancyMenuItem) { +this.removeRedundancyMenuItem_actionPerformed (); +} else if (source === this.pairwiseAlignmentMenuItem) { +this.pairwiseAlignmentMenuItem_actionPerformed (); +} else if (source === this.PCAMenuItem) { +this.PCAMenuItem_actionPerformed (); +} else if (source === this.averageDistanceTreeMenuItem) { +this.averageDistanceTreeMenuItem_actionPerformed (); +} else if (source === this.neighbourTreeMenuItem) { +this.neighbourTreeMenuItem_actionPerformed (); +} else if (source === this.njTreeBlosumMenuItem) { +this.njTreeBlosumMenuItem_actionPerformed (); +} else if (source === this.avDistanceTreeBlosumMenuItem) { +this.avTreeBlosumMenuItem_actionPerformed (); +} else if (source === this.documentation) { +this.documentation_actionPerformed (); +} else if (source === this.about) { +this.about_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "inputText_actionPerformed", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.input_cut_paste"), 500, 500); +}); +Clazz.defineMethod (c$, "outputText_actionPerformed", +function (e) { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500); +var fr = this.alignPanel.cloneFeatureRenderer (); +cap.setText ( new jalview.io.AppletFormatAdapter (this.alignPanel).formatSequences (e.getActionCommand (), this.viewport.getAlignment (), this.viewport.getShowJVSuffix ())); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "loadAnnotations", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +cap.setText (jalview.util.MessageManager.getString ("label.paste_features_annotations_Tcoffee_here")); +cap.setAnnotationImport (); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.paste_annotations"), 400, 300); +}); +Clazz.defineMethod (c$, "outputAnnotations", +function (displayTextbox) { +var annotation = new jalview.io.AnnotationFile ().printAnnotationsForView (this.viewport); +if (displayTextbox) { +var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.annotations"), 600, 500); +cap.setText (annotation); +}return annotation; +}, "~B"); +Clazz.defineMethod (c$, "getDisplayedFeatureCols", +($fz = function () { +if (this.alignPanel.getFeatureRenderer () != null && this.viewport.getFeaturesDisplayed () != null) { +return this.alignPanel.getFeatureRenderer ().getDisplayedFeatureCols (); +}return null; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "outputFeatures", +function (displayTextbox, format) { +var features; +if (format.equalsIgnoreCase ("Jalview")) { +features = new jalview.io.FeaturesFile ().printJalviewFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); +} else { +features = new jalview.io.FeaturesFile ().printGFFFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); +}if (displayTextbox) { +var frimport = false; +if (features == null || features.equals ("No Features Visible")) { +features = "# No features visible - paste some and import them here."; +frimport = true; +}var cap = new jalview.appletgui.CutAndPasteTransfer (frimport, this); +if (frimport) { +cap.setAnnotationImport (); +}var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.features"), 600, 500); +cap.setText (features); +} else { +if (features == null) { +features = ""; +}}return features; +}, "~B,~S"); +Clazz.defineMethod (c$, "launchFullApplication", +function () { +var url = new StringBuffer (this.jalviewServletURL); +var firstSep = url.lastIndexOf ("?") > url.lastIndexOf ("/") ? "&" : "?"; +url.append (firstSep); +var applet = this.viewport.applet; +var s = applet.startupFile; +url.append ("open=" + this.appendProtocol (s)); +if (this.viewport.applet.features != null) { +url.append ("&features="); +url.append (this.appendProtocol (applet.features)); +}if (applet.annotations != null) { +url.append ("&annotations="); +url.append (this.appendProtocol (applet.annotations)); +}if (applet.jnetFile != null) { +url.append ("&annotations="); +url.append (this.appendProtocol (applet.jnetFile)); +}if (applet.defaultColour != null) { +url.append ("&colour=" + this.removeWhiteSpace (applet.defaultColour)); +}if (applet.userDefinedColour != null) { +url.append ("&colour=" + this.removeWhiteSpace (applet.userDefinedColour)); +}if (applet.treeFile != null) { +url.append ("&tree=" + this.appendProtocol (applet.treeFile)); +}this.showURL (url.toString (), "FULL_APP"); +}); +Clazz.defineMethod (c$, "removeWhiteSpace", +function (colour) { +var sb = new StringBuffer (); +for (var i = 0; i < colour.length; i++) { +if (Character.isWhitespace (colour.charAt (i))) { +sb.append ("%20"); +} else { +sb.append (colour.charAt (i)); +}} +return sb.toString (); +}, "~S"); +Clazz.defineMethod (c$, "appendProtocol", +function (url) { +try { + new java.net.URL (url); +url = java.net.URLEncoder.encode (url); +} catch (ex) { +if (Clazz.exceptionOf (ex, java.net.MalformedURLException)) { +url = this.viewport.applet.getCodeBase () + url; +} else { +throw ex; +} +} +return url; +}, "~S"); +Clazz.defineMethod (c$, "closeMenuItem_actionPerformed", +function () { +jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel); +if (this.alignPanel.seqPanel != null && this.alignPanel.seqPanel.seqCanvas != null) { +jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.seqPanel.seqCanvas); +}if (this.alignPanel.idPanel != null && this.alignPanel.idPanel.idCanvas != null) { +jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.idPanel.idCanvas); +}if (jalview.appletgui.PaintRefresher.components.size () == 0 && this.viewport.applet == null) { +System.exit (0); +} else { +}this.viewport = null; +this.alignPanel = null; +this.dispose (); +}); +Clazz.defineMethod (c$, "updateEditMenuBar", +function () { +if (this.viewport.getHistoryList ().size () > 0) { +this.undoMenuItem.setEnabled (true); +var command = this.viewport.getHistoryList ().peek (); +this.undoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.undo_command", Clazz.newArray (-1, [command.getDescription ()]))); +} else { +this.undoMenuItem.setEnabled (false); +this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); +}if (this.viewport.getRedoList ().size () > 0) { +this.redoMenuItem.setEnabled (true); +var command = this.viewport.getRedoList ().peek (); +this.redoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.redo_command", Clazz.newArray (-1, [command.getDescription ()]))); +} else { +this.redoMenuItem.setEnabled (false); +this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); +}}); +Clazz.overrideMethod (c$, "addHistoryItem", +function (command) { +if (command.getSize () > 0) { +this.viewport.addToHistoryList (command); +this.viewport.clearRedoList (); +this.updateEditMenuBar (); +this.viewport.updateHiddenColumns (); +}}, "jalview.commands.CommandI"); +Clazz.defineMethod (c$, "undoMenuItem_actionPerformed", +function () { +if (this.viewport.getHistoryList ().isEmpty ()) { +return; +}var command = this.viewport.getHistoryList ().pop (); +this.viewport.addToRedoList (command); +command.undoCommand (null); +var originalSource = this.getOriginatingSource (command); +if (originalSource !== this.viewport) { +System.err.println ("Warning: Viewport object mismatch whilst undoing"); +}originalSource.updateHiddenColumns (); +this.updateEditMenuBar (); +originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "redoMenuItem_actionPerformed", +function () { +if (this.viewport.getRedoList ().isEmpty ()) { +return; +}var command = this.viewport.getRedoList ().pop (); +this.viewport.addToHistoryList (command); +command.doCommand (null); +var originalSource = this.getOriginatingSource (command); +if (originalSource !== this.viewport) { +System.err.println ("Warning: Viewport object mismatch whilst re-doing"); +}originalSource.updateHiddenColumns (); +this.updateEditMenuBar (); +originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "getOriginatingSource", +function (command) { +var originalSource = null; +var al = null; +if (Clazz.instanceOf (command, jalview.commands.EditCommand)) { +var editCommand = command; +al = editCommand.getAlignment (); +var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); +for (var i = 0; i < comps.size (); i++) { +if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { +if (al === (comps.elementAt (i)).av.getAlignment ()) { +originalSource = (comps.elementAt (i)).av; +break; +}}} +}if (originalSource == null) { +if (al != null) { +jalview.appletgui.PaintRefresher.validateSequences (al, this.viewport.getAlignment ()); +}originalSource = this.viewport; +}return originalSource; +}, "jalview.commands.CommandI"); +Clazz.defineMethod (c$, "moveSelectedSequences", +function (up) { +var sg = this.viewport.getSelectionGroup (); +if (sg == null) { +return; +}this.viewport.getAlignment ().moveSelectedSequencesByOne (sg, up ? null : this.viewport.getHiddenRepSequences (), up); +this.alignPanel.paintAlignment (true); +var complement = this.viewport.getCodingComplement (); +if (complement != null) { +var mappedSelection = jalview.util.MappingUtils.mapSequenceGroup (sg, this.viewport, complement); +complement.getAlignment ().moveSelectedSequencesByOne (mappedSelection, up ? null : complement.getHiddenRepSequences (), up); +}}, "~B"); +Clazz.defineMethod (c$, "slideSequences", +function (right, size) { +var sg = new java.util.Vector (); +if (this.viewport.cursorMode) { +sg.add (this.viewport.getAlignment ().getSequenceAt (this.alignPanel.seqPanel.seqCanvas.cursorY)); +} else if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () != this.viewport.getAlignment ().getHeight ()) { +sg = this.viewport.getSelectionGroup ().getSequences (this.viewport.getHiddenRepSequences ()); +}if (sg.size () < 1) { +return; +}var invertGroup = new java.util.Vector (); +for (var i = 0; i < this.viewport.getAlignment ().getHeight (); i++) { +if (!sg.contains (this.viewport.getAlignment ().getSequenceAt (i))) { +invertGroup.addElement (this.viewport.getAlignment ().getSequenceAt (i)); +}} +var seqs1 = sg.toArray ( new Array (sg.size ())); +var seqs2 = invertGroup.toArray ( new Array (invertGroup.size ())); +for (var i = 0; i < invertGroup.size (); i++) { +seqs2[i] = invertGroup.elementAt (i); +} +var ssc; +if (right) { +ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs2, seqs1, size, this.viewport.getGapCharacter ()); +} else { +ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs1, seqs2, size, this.viewport.getGapCharacter ()); +}var groupAdjustment = 0; +if (ssc.getGapsInsertedBegin () && right) { +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (size, 0); +} else { +groupAdjustment = size; +}} else if (!ssc.getGapsInsertedBegin () && !right) { +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (-size, 0); +} else { +groupAdjustment = -size; +}}if (groupAdjustment != 0) { +this.viewport.getSelectionGroup ().setStartRes (this.viewport.getSelectionGroup ().getStartRes () + groupAdjustment); +this.viewport.getSelectionGroup ().setEndRes (this.viewport.getSelectionGroup ().getEndRes () + groupAdjustment); +}var appendHistoryItem = false; +var historyList = this.viewport.getHistoryList (); +if (historyList != null && historyList.size () > 0 && Clazz.instanceOf (historyList.peek (), jalview.commands.SlideSequencesCommand)) { +appendHistoryItem = ssc.appendSlideCommand (historyList.peek ()); +}if (!appendHistoryItem) { +this.addHistoryItem (ssc); +}this.repaint (); +}, "~B,~N"); +Clazz.defineMethod (c$, "copy_actionPerformed", +function () { +if (this.viewport.getSelectionGroup () == null) { +return; +}var sg = this.viewport.getSelectionGroup (); +jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer (); +var orderedSeqs = new java.util.HashMap (); +for (var i = 0; i < sg.getSize (); i++) { +var seq = sg.getSequenceAt (i); +var index = this.viewport.getAlignment ().findIndex (seq); +orderedSeqs.put (new Integer (index), seq); +} +var index = 0; +var startRes; +var endRes; +var ch; +if (this.viewport.hasHiddenColumns () && this.viewport.getSelectionGroup () != null) { +jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector (); +var hiddenOffset = this.viewport.getSelectionGroup ().getStartRes (); +for (var region, $region = this.viewport.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { +jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0] - hiddenOffset, region[1] - hiddenOffset])); +} +} else { +jalview.appletgui.AlignFrame.copiedHiddenColumns = null; +}for (var i = 0; i < sg.getSize (); i++) { +var seq = null; +while (seq == null) { +if (orderedSeqs.containsKey (new Integer (index))) { +seq = orderedSeqs.get (new Integer (index)); +index++; +break; +} else { +index++; +}} +startRes = seq.findPosition (sg.getStartRes ()); +endRes = 0; +for (var j = 0; j < sg.getEndRes () + 1 && j < seq.getLength (); j++) { +ch = seq.getCharAt (j); +if (!jalview.util.Comparison.isGap ((ch))) { +endRes++; +}} +if (endRes > 0) { +endRes += seq.getStart () - 1; +}jalview.appletgui.AlignFrame.copiedSequences.append (seq.getName () + "\t" + startRes + "\t" + endRes + "\t" + seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1) + "\n"); +} +}); +Clazz.defineMethod (c$, "pasteNew_actionPerformed", +function () { +this.paste (true); +}); +Clazz.defineMethod (c$, "pasteThis_actionPerformed", +function () { +this.paste (false); +}); +Clazz.defineMethod (c$, "paste", +function (newAlignment) { +try { +if (jalview.appletgui.AlignFrame.copiedSequences == null) { +return; +}var st = new java.util.StringTokenizer (jalview.appletgui.AlignFrame.copiedSequences.toString ()); +var seqs = new java.util.Vector (); +while (st.hasMoreElements ()) { +var name = st.nextToken (); +var start = Integer.parseInt (st.nextToken ()); +var end = Integer.parseInt (st.nextToken ()); +seqs.addElement ( new jalview.datamodel.Sequence (name, st.nextToken (), start, end)); +} +var newSeqs = new Array (seqs.size ()); +for (var i = 0; i < seqs.size (); i++) { +newSeqs[i] = seqs.elementAt (i); +} +if (newAlignment) { +var newtitle = jalview.util.MessageManager.getString ("label.copied_sequences"); +if (this.getTitle ().startsWith (jalview.util.MessageManager.getString ("label.copied_sequences"))) { +newtitle = this.getTitle (); +} else { +newtitle = newtitle.concat (jalview.util.MessageManager.formatMessage ("label.from_msname", Clazz.newArray (-1, [this.getTitle ()]))); +}var af = new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (newSeqs), this.viewport.applet, newtitle, false); +if (jalview.appletgui.AlignFrame.copiedHiddenColumns != null) { +for (var i = 0; i < jalview.appletgui.AlignFrame.copiedHiddenColumns.size (); i++) { +var region = jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt (i); +af.viewport.hideColumns (region[0], region[1]); +} +}jalview.bin.JalviewLite.addFrame (af, newtitle, this.frameWidth, this.frameHeight); +} else { +this.addSequences (newSeqs); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}, "~B"); +Clazz.defineMethod (c$, "addSequences", +function (seqs) { +for (var i = 0; i < seqs.length; i++) { +this.viewport.getAlignment ().addSequence (seqs[i]); +} +this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.add_sequences"), jalview.commands.EditCommand.Action.PASTE, seqs, 0, this.viewport.getAlignment ().getWidth (), this.viewport.getAlignment ())); +this.viewport.setEndSeq (this.viewport.getAlignment ().getHeight ()); +this.viewport.getAlignment ().getWidth (); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}, "~A"); +Clazz.defineMethod (c$, "cut_actionPerformed", +function () { +this.copy_actionPerformed (); +this.delete_actionPerformed (); +}); +Clazz.defineMethod (c$, "delete_actionPerformed", +function () { +var sg = this.viewport.getSelectionGroup (); +if (sg == null) { +return; +}var seqs = new java.util.Vector (); +var seq; +for (var i = 0; i < sg.getSize (); i++) { +seq = sg.getSequenceAt (i); +seqs.addElement (seq); +} +if (sg.getSize () == this.viewport.getAlignment ().getHeight ()) { +this.viewport.getColumnSelection ().removeElements (sg.getStartRes (), sg.getEndRes () + 1); +}var cut = new Array (seqs.size ()); +for (var i = 0; i < seqs.size (); i++) { +cut[i] = seqs.elementAt (i); +} +this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.cut_sequences"), jalview.commands.EditCommand.Action.CUT, cut, sg.getStartRes (), sg.getEndRes () - sg.getStartRes () + 1, this.viewport.getAlignment ())); +this.viewport.setSelectionGroup (null); +this.viewport.getAlignment ().deleteGroup (sg); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +if (this.viewport.getAlignment ().getHeight () < 1) { +this.setVisible (false); +}this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "showGroupConsensus_actionPerformed", +function () { +this.viewport.setShowGroupConsensus (this.showGroupConsensus.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "showGroupConservation_actionPerformed", +function () { +this.viewport.setShowGroupConservation (this.showGroupConservation.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "showConsensusHistogram_actionPerformed", +function () { +this.viewport.setShowConsensusHistogram (this.showConsensusHistogram.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "showSequenceLogo_actionPerformed", +function () { +this.viewport.setShowSequenceLogo (this.showSequenceLogo.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "normSequenceLogo_actionPerformed", +function () { +this.showSequenceLogo.setState (true); +this.viewport.setShowSequenceLogo (true); +this.viewport.setNormaliseSequenceLogo (this.normSequenceLogo.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "applyAutoAnnotationSettings_actionPerformed", +function () { +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "makeGrpsFromSelection_actionPerformed", +function () { +if (this.avc.makeGroupsFromSelection ()) { +jalview.appletgui.PaintRefresher.Refresh (this, this.viewport.getSequenceSetId ()); +this.alignPanel.updateAnnotation (); +this.alignPanel.paintAlignment (true); +}}); +Clazz.defineMethod (c$, "createGroup_actionPerformed", +function () { +this.avc.createGroup (); +}); +Clazz.defineMethod (c$, "unGroup_actionPerformed", +function () { +if (this.avc.unGroup ()) { +this.alignPanel.alignmentChanged (); +}}); +Clazz.defineMethod (c$, "deleteGroups_actionPerformed", +function () { +if (this.avc.deleteGroups ()) { +this.alignPanel.alignmentChanged (); +}}); +Clazz.defineMethod (c$, "selectAllSequenceMenuItem_actionPerformed", +function () { +var sg = new jalview.datamodel.SequenceGroup (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +sg.addSequence (this.viewport.getAlignment ().getSequenceAt (i), false); +} +sg.setEndRes (this.viewport.getAlignment ().getWidth () - 1); +this.viewport.setSelectionGroup (sg); +this.alignPanel.paintAlignment (true); +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "deselectAllSequenceMenuItem_actionPerformed", +function () { +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.keyboardNo1 = null; +this.alignPanel.seqPanel.keyboardNo2 = null; +}this.viewport.setSelectionGroup (null); +this.viewport.getColumnSelection ().clear (); +this.viewport.setSelectionGroup (null); +this.alignPanel.idPanel.idCanvas.searchResults = null; +this.alignPanel.seqPanel.seqCanvas.highlightSearchResults (null); +this.alignPanel.paintAlignment (true); +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "invertSequenceMenuItem_actionPerformed", +function () { +var sg = this.viewport.getSelectionGroup (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +sg.addOrRemove (this.viewport.getAlignment ().getSequenceAt (i), false); +} +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "invertColSel_actionPerformed", +function () { +this.viewport.invertColumnSelection (); +this.alignPanel.paintAlignment (true); +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "trimAlignment", +function (trimLeft) { +var colSel = this.viewport.getColumnSelection (); +var column; +if (colSel.size () > 0) { +if (trimLeft) { +column = colSel.getMin (); +} else { +column = colSel.getMax (); +}var seqs; +if (this.viewport.getSelectionGroup () != null) { +seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); +} else { +seqs = this.viewport.getAlignment ().getSequencesArray (); +}var trimRegion; +if (trimLeft) { +trimRegion = new jalview.commands.TrimRegionCommand ("Remove Left", jalview.commands.TrimRegionCommand.TRIM_LEFT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); +this.viewport.setStartRes (0); +} else { +trimRegion = new jalview.commands.TrimRegionCommand ("Remove Right", jalview.commands.TrimRegionCommand.TRIM_RIGHT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); +}this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_columns", Clazz.newArray (-1, [Integer.$valueOf (trimRegion.getSize ()).toString ()]))); +this.addHistoryItem (trimRegion); +for (var sg, $sg = this.viewport.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if ((trimLeft && !sg.adjustForRemoveLeft (column)) || (!trimLeft && !sg.adjustForRemoveRight (column))) { +this.viewport.getAlignment ().deleteGroup (sg); +}} +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}}, "~B"); +Clazz.defineMethod (c$, "removeGappedColumnMenuItem_actionPerformed", +function () { +var start = 0; +var end = this.viewport.getAlignment ().getWidth () - 1; +var seqs; +if (this.viewport.getSelectionGroup () != null) { +seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); +start = this.viewport.getSelectionGroup ().getStartRes (); +end = this.viewport.getSelectionGroup ().getEndRes (); +} else { +seqs = this.viewport.getAlignment ().getSequencesArray (); +}var removeGapCols = new jalview.commands.RemoveGapColCommand ("Remove Gapped Columns", seqs, start, end, this.viewport.getAlignment ()); +this.addHistoryItem (removeGapCols); +this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_empty_columns", Clazz.newArray (-1, [Integer.$valueOf (removeGapCols.getSize ()).toString ()]))); +var seq = this.viewport.getAlignment ().getSequenceAt (0); +var startRes = seq.findPosition (this.viewport.startRes); +this.viewport.setStartRes (seq.findIndex (startRes) - 1); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "removeAllGapsMenuItem_actionPerformed", +function () { +var start = 0; +var end = this.viewport.getAlignment ().getWidth () - 1; +var seqs; +if (this.viewport.getSelectionGroup () != null) { +seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); +start = this.viewport.getSelectionGroup ().getStartRes (); +end = this.viewport.getSelectionGroup ().getEndRes (); +} else { +seqs = this.viewport.getAlignment ().getSequencesArray (); +}var seq = this.viewport.getAlignment ().getSequenceAt (0); +var startRes = seq.findPosition (this.viewport.startRes); +this.addHistoryItem ( new jalview.commands.RemoveGapsCommand ("Remove Gaps", seqs, start, end, this.viewport.getAlignment ())); +this.viewport.setStartRes (seq.findIndex (startRes) - 1); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "findMenuItem_actionPerformed", +function () { + new jalview.appletgui.Finder (this.alignPanel); +}); +Clazz.defineMethod (c$, "newView", +function (viewtitle) { +var newal; +if (this.viewport.hasHiddenRows ()) { +newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getHiddenSequences ().getFullAlignment ().getSequencesArray ()); +} else { +newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getSequencesArray ()); +}if (this.viewport.getAlignment ().getAlignmentAnnotation () != null) { +for (var i = 0; i < this.viewport.getAlignment ().getAlignmentAnnotation ().length; i++) { +if (!this.viewport.getAlignment ().getAlignmentAnnotation ()[i].autoCalculated) { +newal.addAnnotation (this.viewport.getAlignment ().getAlignmentAnnotation ()[i]); +}} +}var newaf = new jalview.appletgui.AlignFrame (newal, this.viewport.applet, "", false); +newaf.viewport.setSequenceSetId (this.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (this.alignPanel, this.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (newaf.alignPanel, newaf.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.idPanel.idCanvas, newaf.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId ()); +var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); +var viewSize = -1; +for (var i = 0; i < comps.size (); i++) { +if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { +viewSize++; +}} +var title = String.instantialize (this.getTitle ()); +if (viewtitle != null) { +title = viewtitle + " ( " + title + ")"; +} else { +if (title.indexOf ("(View") > -1) { +title = title.substring (0, title.indexOf ("(View")); +}title += "(View " + viewSize + ")"; +}newaf.setTitle (title.toString ()); +newaf.viewport.setHistoryList (this.viewport.getHistoryList ()); +newaf.viewport.setRedoList (this.viewport.getRedoList ()); +return newaf; +}, "~S"); +Clazz.defineMethod (c$, "getFeatureGroups", +function () { +var fr = null; +if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { +var gps = fr.getFeatureGroups (); +var _gps = gps.toArray ( new Array (gps.size ())); +return _gps; +}return null; +}); +Clazz.defineMethod (c$, "getFeatureGroupsOfState", +function (visible) { +var fr = null; +if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { +var gps = fr.getGroups (visible); +var _gps = gps.toArray ( new Array (gps.size ())); +return _gps; +}return null; +}, "~B"); +Clazz.defineMethod (c$, "setFeatureGroupState", +function (groups, state) { +var fr = null; +this.sequenceFeatures.setState (true); +this.viewport.setShowSequenceFeatures (true); +if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { +fr.setGroupVisibility (java.util.Arrays.asList (groups), state); +this.alignPanel.seqPanel.seqCanvas.repaint (); +if (this.alignPanel.overviewPanel != null) { +this.alignPanel.overviewPanel.updateOverviewImage (); +}}}, "~A,~B"); +Clazz.defineMethod (c$, "seqLimits_itemStateChanged", +function () { +this.viewport.setShowJVSuffix (this.seqLimits.getState ()); +this.alignPanel.fontChanged (); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "colourTextMenuItem_actionPerformed", +function () { +this.viewport.setColourText (this.colourTextMenuItem.getState ()); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "displayNonconservedMenuItem_actionPerformed", +function () { +this.viewport.setShowUnconserved (this.displayNonconservedMenuItem.getState ()); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "wrapMenuItem_actionPerformed", +function () { +this.viewport.setWrapAlignment (this.wrapMenuItem.getState ()); +this.alignPanel.setWrapAlignment (this.wrapMenuItem.getState ()); +this.scaleAbove.setEnabled (this.wrapMenuItem.getState ()); +this.scaleLeft.setEnabled (this.wrapMenuItem.getState ()); +this.scaleRight.setEnabled (this.wrapMenuItem.getState ()); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "overviewMenuItem_actionPerformed", +function () { +if (this.alignPanel.overviewPanel != null) { +return; +}var frame = new awt2swing.Frame (); +var overview = new jalview.appletgui.OverviewPanel (this.alignPanel); +frame.add (overview); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.overview_params", Clazz.newArray (-1, [this.getTitle ()])), overview.getPreferredSize ().width, overview.getPreferredSize ().height + 50); +frame.pack (); +var ap = this.alignPanel; +frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1, this, Clazz.cloneFinals ("ap", ap)))); +this.alignPanel.setOverviewPanel (overview); +}); +Clazz.overrideMethod (c$, "changeColour", +function (cs) { +var threshold = 0; +if (cs != null) { +if (this.viewport.getAbovePIDThreshold ()) { +this.viewport.setThreshold (jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, cs, "Background")); +}if (this.viewport.getConservationSelected ()) { +cs.setConservationApplied (true); +this.viewport.setIncrement (jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, cs, "Background")); +} else { +cs.setConservationApplied (false); +}}this.viewport.setGlobalColourScheme (cs); +if (this.alignPanel.getOverviewPanel () != null) { +this.alignPanel.getOverviewPanel ().updateOverviewImage (); +}jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.viewport.applet).sequenceColoursChanged (this.alignPanel); +this.alignPanel.paintAlignment (true); +}, "jalview.schemes.ColourSchemeI"); +Clazz.defineMethod (c$, "modifyPID_actionPerformed", +function () { +if (this.viewport.getAbovePIDThreshold () && this.viewport.getGlobalColourScheme () != null) { +jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); +jalview.appletgui.SliderPanel.showPIDSlider (); +}}); +Clazz.defineMethod (c$, "modifyConservation_actionPerformed", +function () { +if (this.viewport.getConservationSelected () && this.viewport.getGlobalColourScheme () != null) { +jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); +jalview.appletgui.SliderPanel.showConservationSlider (); +}}); +Clazz.defineMethod (c$, "conservationMenuItem_actionPerformed", +function () { +this.viewport.setConservationSelected (this.conservationMenuItem.getState ()); +this.viewport.setAbovePIDThreshold (false); +this.abovePIDThreshold.setState (false); +this.changeColour (this.viewport.getGlobalColourScheme ()); +this.modifyConservation_actionPerformed (); +}); +Clazz.defineMethod (c$, "abovePIDThreshold_actionPerformed", +function () { +this.viewport.setAbovePIDThreshold (this.abovePIDThreshold.getState ()); +this.conservationMenuItem.setState (false); +this.viewport.setConservationSelected (false); +this.changeColour (this.viewport.getGlobalColourScheme ()); +this.modifyPID_actionPerformed (); +}); +Clazz.defineMethod (c$, "sortPairwiseMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByPID (this.viewport.getAlignment (), this.viewport.getAlignment ().getSequenceAt (0), null); +this.addHistoryItem ( new jalview.commands.OrderCommand ("Pairwise Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "sortIDMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByID (this.viewport.getAlignment ()); +this.addHistoryItem ( new jalview.commands.OrderCommand ("ID Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "sortLengthMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByLength (this.viewport.getAlignment ()); +this.addHistoryItem ( new jalview.commands.OrderCommand ("Length Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "sortGroupMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByGroup (this.viewport.getAlignment ()); +this.addHistoryItem ( new jalview.commands.OrderCommand ("Group Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "removeRedundancyMenuItem_actionPerformed", +function () { + new jalview.appletgui.RedundancyPanel (this.alignPanel); +}); +Clazz.defineMethod (c$, "pairwiseAlignmentMenuItem_actionPerformed", +function () { +if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) { +var frame = new awt2swing.Frame (); +frame.add ( new jalview.appletgui.PairwiseAlignPanel (this.alignPanel)); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.pairwise_alignment"), 600, 500); +}}); +Clazz.defineMethod (c$, "PCAMenuItem_actionPerformed", +function () { +if (!this.viewport.getAlignment ().isAligned (false)) { +var current; +var Width = this.viewport.getAlignment ().getWidth (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +current = this.viewport.getAlignment ().getSequenceAt (i); +if (current.getLength () < Width) { +current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); +}} +this.alignPanel.paintAlignment (true); +}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () < 4 && this.viewport.getSelectionGroup ().getSize () > 0) || this.viewport.getAlignment ().getHeight () < 4) { +return; +}try { + new jalview.appletgui.PCAPanel (this.viewport); +} catch (ex) { +if (Clazz.exceptionOf (ex, OutOfMemoryError)) { +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "averageDistanceTreeMenuItem_actionPerformed", +function () { +this.NewTreePanel ("AV", "PID", "Average distance tree using PID"); +}); +Clazz.defineMethod (c$, "neighbourTreeMenuItem_actionPerformed", +function () { +this.NewTreePanel ("NJ", "PID", "Neighbour joining tree using PID"); +}); +Clazz.defineMethod (c$, "njTreeBlosumMenuItem_actionPerformed", +function () { +this.NewTreePanel ("NJ", "BL", "Neighbour joining tree using BLOSUM62"); +}); +Clazz.defineMethod (c$, "avTreeBlosumMenuItem_actionPerformed", +function () { +this.NewTreePanel ("AV", "BL", "Average distance tree using BLOSUM62"); +}); +Clazz.defineMethod (c$, "NewTreePanel", +function (type, pwType, title) { +if (!this.viewport.getAlignment ().isAligned (false)) { +var current; +var Width = this.viewport.getAlignment ().getWidth (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +current = this.viewport.getAlignment ().getSequenceAt (i); +if (current.getLength () < Width) { +current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); +}} +this.alignPanel.paintAlignment (true); +}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) || (this.viewport.getAlignment ().getHeight () > 1)) { +var tp = new jalview.appletgui.TreePanel (this.alignPanel, type, pwType); +this.addTreeMenuItem (tp, title); +jalview.bin.JalviewLite.addFrame (tp, title, 600, 500); +}}, "~S,~S,~S"); +Clazz.defineMethod (c$, "loadTree_actionPerformed", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +cap.setText (jalview.util.MessageManager.getString ("label.paste_newick_tree_file")); +cap.setTreeImport (); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.paste_newick_file"), 400, 300); +}); +Clazz.defineMethod (c$, "loadTree", +function (tree, treeFile) { +var tp = new jalview.appletgui.TreePanel (this.alignPanel, treeFile, jalview.util.MessageManager.getString ("label.load_tree_from_file"), tree); +jalview.bin.JalviewLite.addFrame (tp, treeFile, 600, 500); +this.addTreeMenuItem (tp, treeFile); +}, "jalview.io.NewickFile,~S"); +Clazz.defineMethod (c$, "sortByTree", +function (treePanel, title) { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByTree (this.viewport.getAlignment (), treePanel.getTree ()); +this.addHistoryItem ( new jalview.commands.OrderCommand (jalview.util.MessageManager.formatMessage ("label.order_by_params", Clazz.newArray (-1, [title])), oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}, "jalview.appletgui.TreePanel,~S"); +Clazz.defineMethod (c$, "addTreeMenuItem", +function (treePanel, title) { +var item = new awt2swing.MenuItem (title); +this.sortByTreeMenu.add (item); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$2") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$2, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title)))); +treePanel.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$3") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$3, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title, "item", item)))); +}, "jalview.appletgui.TreePanel,~S"); +Clazz.defineMethod (c$, "sortBy", +function (alorder, undoname) { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +if ((this.viewport.applet, jalview.bin.JalviewLite).debug) { +System.err.println ("Sorting " + alorder.getOrder ().size () + " in alignment '" + this.getTitle () + "'"); +}jalview.analysis.AlignmentSorter.sortBy (this.viewport.getAlignment (), alorder); +if (undoname != null) { +this.addHistoryItem ( new jalview.commands.OrderCommand (undoname, oldOrder, this.viewport.getAlignment ())); +}this.alignPanel.paintAlignment (true); +return true; +}, "jalview.datamodel.AlignmentOrder,~S"); +Clazz.defineMethod (c$, "documentation_actionPerformed", +function () { +this.alignPanel.av.applet.openJalviewHelpUrl (); +}); +Clazz.defineMethod (c$, "about_actionPerformed", +function () { +if (!Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1AboutPanel")) { +jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$ (); +} +var frame = new awt2swing.Frame (); +frame.add (Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1AboutPanel, this, null, jalview.bin.JalviewLite.getVersion (), jalview.bin.JalviewLite.getBuildDate ())); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.jalview"), 580, 220); +}); +Clazz.defineMethod (c$, "showURL", +function (url, target) { +if (this.viewport.applet == null) { +System.out.println ("Not running as applet - no browser available."); +} else { +this.viewport.applet.showURL (url, target); +}}, "~S,~S"); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setMenuBar (this.alignFrameMenuBar); +this.inputText.setLabel (jalview.util.MessageManager.getString ("label.input_from_textbox")); +this.inputText.addActionListener (this); +var outputTextboxMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.out_to_textbox")); +for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { +var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$4") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$4, this, null))); +outputTextboxMenu.add (item); +} +this.closeMenuItem.addActionListener (this); +this.loadApplication.addActionListener (this); +this.$loadTree.addActionListener (this); +this.$loadAnnotations.addActionListener (this); +this.$outputFeatures.addActionListener (this); +this.$outputAnnotations.addActionListener (this); +this.undoMenuItem.setEnabled (false); +this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); +this.undoMenuItem.addActionListener (this); +this.redoMenuItem.setEnabled (false); +this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); +this.redoMenuItem.addActionListener (this); +this.copy.setLabel (jalview.util.MessageManager.getString ("action.copy")); +this.copy.addActionListener (this); +this.cut.setLabel (jalview.util.MessageManager.getString ("action.cut")); +this.cut.addActionListener (this); +this.$delete.setLabel (jalview.util.MessageManager.getString ("action.delete")); +this.$delete.addActionListener (this); +this.pasteMenu.setLabel (jalview.util.MessageManager.getString ("action.paste")); +this.pasteNew.setLabel (jalview.util.MessageManager.getString ("label.to_new_alignment")); +this.pasteNew.addActionListener (this); +this.pasteThis.setLabel (jalview.util.MessageManager.getString ("label.to_this_alignment")); +this.pasteThis.addActionListener (this); +this.remove2LeftMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_left")); +this.remove2LeftMenuItem.addActionListener (this); +this.remove2RightMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_right")); +this.remove2RightMenuItem.addActionListener (this); +this.removeGappedColumnMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_empty_columns")); +this.removeGappedColumnMenuItem.addActionListener (this); +this.removeAllGapsMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_all_gaps")); +this.removeAllGapsMenuItem.addActionListener (this); +this.removeRedundancyMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_redundancy").concat ("...")); +this.removeRedundancyMenuItem.addActionListener (this); +this.findMenuItem.setLabel (jalview.util.MessageManager.getString ("action.find")); +this.findMenuItem.addActionListener (this); +this.selectAllSequenceMenuItem.addActionListener (this); +this.deselectAllSequenceMenuItem.addActionListener (this); +this.invertSequenceMenuItem.setLabel (jalview.util.MessageManager.getString ("action.invert_sequence_selection")); +this.invertSequenceMenuItem.addActionListener (this); +this.invertColSel.setLabel (jalview.util.MessageManager.getString ("action.invert_column_selection")); +this.invertColSel.addActionListener (this); +this.deleteGroups.setLabel (jalview.util.MessageManager.getString ("action.undefine_groups")); +this.deleteGroups.addActionListener (this); +this.grpsFromSelection.setLabel (jalview.util.MessageManager.getString ("action.make_groups_selection")); +this.grpsFromSelection.addActionListener (this); +this.createGroup.setLabel (jalview.util.MessageManager.getString ("action.create_group")); +this.unGroup.setLabel (jalview.util.MessageManager.getString ("action.remove_group")); +this.annotationColumnSelection.setLabel ("Select by Annotation"); +this.annotationColumnSelection.addActionListener (this); +this.$newView.setLabel (jalview.util.MessageManager.getString ("action.new_view")); +this.$newView.addActionListener (this); +var showMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.show")); +this.showColumns.setLabel (jalview.util.MessageManager.getString ("label.all_columns")); +this.showSeqs.setLabel (jalview.util.MessageManager.getString ("label.all_sequences")); +var hideMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.hide")); +this.hideColumns.setLabel (jalview.util.MessageManager.getString ("label.selected_columns")); +this.hideSequences.setLabel (jalview.util.MessageManager.getString ("label.selected_sequences")); +this.hideAllButSelection.setLabel (jalview.util.MessageManager.getString ("label.all_but_selected_region")); +this.hideAllSelection.setLabel (jalview.util.MessageManager.getString ("label.selected_region")); +this.showAllHidden.setLabel (jalview.util.MessageManager.getString ("label.all_sequences_columns")); +this.showColumns.addActionListener (this); +this.showSeqs.addActionListener (this); +this.hideColumns.addActionListener (this); +this.hideSequences.addActionListener (this); +this.hideAllButSelection.addActionListener (this); +this.hideAllSelection.addActionListener (this); +this.showAllHidden.addActionListener (this); +this.featureSettings.setLabel (jalview.util.MessageManager.getString ("label.feature_settings")); +this.featureSettings.addActionListener (this); +this.sequenceFeatures.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_features")); +this.sequenceFeatures.addItemListener (this); +this.sequenceFeatures.setState (false); +this.followMouseOverFlag.setLabel (jalview.util.MessageManager.getString ("label.automatic_scrolling")); +this.followMouseOverFlag.addItemListener (this); +this.alProperties.addActionListener (this); +this.overviewMenuItem.setLabel (jalview.util.MessageManager.getString ("label.overview_window")); +this.overviewMenuItem.addActionListener (this); +this.annotationPanelMenuItem.setLabel (jalview.util.MessageManager.getString ("label.show_annotations")); +this.annotationPanelMenuItem.addItemListener (this); +this.showGroupConsensus.setLabel (jalview.util.MessageManager.getString ("label.group_consensus")); +this.showGroupConservation.setLabel (jalview.util.MessageManager.getString ("label.group_conservation")); +this.showConsensusHistogram.setLabel (jalview.util.MessageManager.getString ("label.show_consensus_histogram")); +this.showSequenceLogo.setLabel (jalview.util.MessageManager.getString ("label.show_consensus_logo")); +this.normSequenceLogo.setLabel (jalview.util.MessageManager.getString ("label.norm_consensus_logo")); +this.applyAutoAnnotationSettings.setLabel (jalview.util.MessageManager.getString ("label.apply_all_groups")); +this.applyAutoAnnotationSettings.setState (true); +var autoAnnMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.autocalculated_annotation")); +this.showGroupConsensus.addItemListener (this); +this.showGroupConservation.addItemListener (this); +this.showConsensusHistogram.addItemListener (this); +this.showSequenceLogo.addItemListener (this); +this.normSequenceLogo.addItemListener (this); +this.applyAutoAnnotationSettings.addItemListener (this); +this.showAlignmentAnnotations = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_all_al_annotations")); +this.showSequenceAnnotations = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_all_seq_annotations")); +this.sortAnnBySequence = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.sort_annotations_by_sequence")); +this.sortAnnByLabel = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.sort_annotations_by_label")); +this.showAutoFirst = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_first")); +this.showAutoLast = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_last")); +this.showAlignmentAnnotations.addItemListener (this); +this.showSequenceAnnotations.addItemListener (this); +this.sortAnnBySequence.addItemListener (this); +this.sortAnnByLabel.addItemListener (this); +this.showAutoFirst.addItemListener (this); +this.showAutoLast.addItemListener (this); +this.$font.setLabel (jalview.util.MessageManager.getString ("action.font")); +this.$font.addActionListener (this); +this.scaleAbove.setLabel (jalview.util.MessageManager.getString ("action.scale_above")); +this.scaleAbove.setState (true); +this.scaleAbove.setEnabled (false); +this.scaleAbove.addItemListener (this); +this.scaleLeft.setEnabled (false); +this.scaleLeft.setState (true); +this.scaleLeft.setLabel (jalview.util.MessageManager.getString ("action.scale_left")); +this.scaleLeft.addItemListener (this); +this.scaleRight.setEnabled (false); +this.scaleRight.setState (true); +this.scaleRight.setLabel (jalview.util.MessageManager.getString ("action.scale_right")); +this.scaleRight.addItemListener (this); +this.viewBoxesMenuItem.setLabel (jalview.util.MessageManager.getString ("action.boxes")); +this.viewBoxesMenuItem.setState (true); +this.viewBoxesMenuItem.addItemListener (this); +this.viewTextMenuItem.setLabel (jalview.util.MessageManager.getString ("action.text")); +this.viewTextMenuItem.setState (true); +this.viewTextMenuItem.addItemListener (this); +this.colourTextMenuItem.setLabel (jalview.util.MessageManager.getString ("label.colour_text")); +this.colourTextMenuItem.addItemListener (this); +this.displayNonconservedMenuItem.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed")); +this.displayNonconservedMenuItem.addItemListener (this); +this.wrapMenuItem.setLabel (jalview.util.MessageManager.getString ("action.wrap")); +this.wrapMenuItem.addItemListener (this); +this.renderGapsMenuItem.setLabel (jalview.util.MessageManager.getString ("action.show_gaps")); +this.renderGapsMenuItem.setState (true); +this.renderGapsMenuItem.addItemListener (this); +this.centreColumnLabelFlag.setLabel (jalview.util.MessageManager.getString ("label.centre_column_labels")); +this.centreColumnLabelFlag.addItemListener (this); +this.seqLimits.setState (true); +this.seqLimits.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_limits")); +this.seqLimits.addItemListener (this); +this.applyToAllGroups.setLabel (jalview.util.MessageManager.getString ("label.apply_colour_to_all_groups")); +this.applyToAllGroups.setState (true); +this.applyToAllGroups.addItemListener (this); +this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx")); +this.clustalColour.addActionListener (this); +this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo")); +this.zappoColour.addActionListener (this); +this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor")); +this.taylorColour.addActionListener (this); +this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity")); +this.hydrophobicityColour.addActionListener (this); +this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity")); +this.helixColour.addActionListener (this); +this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity")); +this.strandColour.addActionListener (this); +this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity")); +this.turnColour.addActionListener (this); +this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index")); +this.buriedColour.addActionListener (this); +this.purinePyrimidineColour.setLabel (jalview.util.MessageManager.getString ("label.purine_pyrimidine")); +this.purinePyrimidineColour.addActionListener (this); +this.RNAInteractionColour.setLabel (jalview.util.MessageManager.getString ("label.rna_interaction")); +this.RNAInteractionColour.addActionListener (this); +this.RNAHelixColour.setLabel (jalview.util.MessageManager.getString ("action.by_rna_helixes")); +this.RNAHelixColour.addActionListener (this); +this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined")); +this.userDefinedColour.addActionListener (this); +this.PIDColour.setLabel (jalview.util.MessageManager.getString ("label.percentage_identity")); +this.PIDColour.addActionListener (this); +this.BLOSUM62Colour.setLabel (jalview.util.MessageManager.getString ("label.blosum62_score")); +this.BLOSUM62Colour.addActionListener (this); +this.tcoffeeColour.setLabel (jalview.util.MessageManager.getString ("label.tcoffee_scores")); +this.tcoffeeColour.setEnabled (false); +this.tcoffeeColour.addActionListener (this); +this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_conservation")); +this.conservationMenuItem.addItemListener (this); +this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none")); +this.noColourmenuItem.addActionListener (this); +this.abovePIDThreshold.setLabel (jalview.util.MessageManager.getString ("label.above_identity_threshold")); +this.abovePIDThreshold.addItemListener (this); +this.nucleotideColour.setLabel (jalview.util.MessageManager.getString ("label.nucleotide")); +this.nucleotideColour.addActionListener (this); +this.modifyPID.setLabel (jalview.util.MessageManager.getString ("label.modify_identity_thereshold")); +this.modifyPID.addActionListener (this); +this.modifyConservation.setLabel (jalview.util.MessageManager.getString ("label.modify_conservation_thereshold")); +this.modifyConservation.addActionListener (this); +this.annotationColour.setLabel (jalview.util.MessageManager.getString ("action.by_annotation")); +this.annotationColour.addActionListener (this); +this.sortPairwiseMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_pairwise_id")); +this.sortPairwiseMenuItem.addActionListener (this); +this.sortIDMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_id")); +this.sortIDMenuItem.addActionListener (this); +this.sortLengthMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_length")); +this.sortLengthMenuItem.addActionListener (this); +this.sortGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_group")); +this.sortGroupMenuItem.addActionListener (this); +this.pairwiseAlignmentMenuItem.setLabel (jalview.util.MessageManager.getString ("action.pairwise_alignment")); +this.pairwiseAlignmentMenuItem.addActionListener (this); +this.PCAMenuItem.setLabel (jalview.util.MessageManager.getString ("label.principal_component_analysis")); +this.PCAMenuItem.addActionListener (this); +this.autoCalculate = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.autocalculate_consensus"), true); +this.averageDistanceTreeMenuItem.setLabel (jalview.util.MessageManager.getString ("label.average_distance_identity")); +this.averageDistanceTreeMenuItem.addActionListener (this); +this.neighbourTreeMenuItem.setLabel (jalview.util.MessageManager.getString ("label.neighbour_joining_identity")); +this.neighbourTreeMenuItem.addActionListener (this); +this.avDistanceTreeBlosumMenuItem.setLabel (jalview.util.MessageManager.getString ("label.average_distance_bloslum62")); +this.avDistanceTreeBlosumMenuItem.addActionListener (this); +this.njTreeBlosumMenuItem.setLabel (jalview.util.MessageManager.getString ("label.neighbour_blosum62")); +this.njTreeBlosumMenuItem.addActionListener (this); +this.sortByTreeMenu.setLabel (jalview.util.MessageManager.getString ("action.by_tree_order")); +var sortMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.sort")); +var calculateTreeMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate_tree")); +this.autoCalculate.addItemListener (this); +this.$sortByTree.addItemListener (this); +var helpMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.help")); +this.documentation.setLabel (jalview.util.MessageManager.getString ("label.documentation")); +this.documentation.addActionListener (this); +this.about.setLabel (jalview.util.MessageManager.getString ("label.about")); +this.about.addActionListener (this); +this.alignFrameMenuBar.add (this.fileMenu); +var editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit")); +this.alignFrameMenuBar.add (editMenu); +var selectMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.select")); +this.alignFrameMenuBar.add (selectMenu); +var viewMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.view")); +this.alignFrameMenuBar.add (viewMenu); +var annotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.annotations")); +this.alignFrameMenuBar.add (annotationsMenu); +var formatMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.format")); +this.alignFrameMenuBar.add (formatMenu); +var colourMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.colour")); +this.alignFrameMenuBar.add (colourMenu); +var calculateMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate")); +this.alignFrameMenuBar.add (calculateMenu); +this.alignFrameMenuBar.add (helpMenu); +this.fileMenu.add (this.inputText); +this.fileMenu.add (this.$loadTree); +this.fileMenu.add (this.$loadAnnotations); +this.fileMenu.addSeparator (); +this.fileMenu.add (outputTextboxMenu); +this.fileMenu.add (this.$outputFeatures); +this.fileMenu.add (this.$outputAnnotations); +if (this.jalviewServletURL != null) { +this.fileMenu.add (this.loadApplication); +}this.fileMenu.addSeparator (); +this.fileMenu.add (this.closeMenuItem); +editMenu.add (this.undoMenuItem); +editMenu.add (this.redoMenuItem); +editMenu.add (this.cut); +editMenu.add (this.copy); +this.pasteMenu.add (this.pasteNew); +this.pasteMenu.add (this.pasteThis); +editMenu.add (this.pasteMenu); +editMenu.add (this.$delete); +editMenu.addSeparator (); +editMenu.add (this.remove2LeftMenuItem); +editMenu.add (this.remove2RightMenuItem); +editMenu.add (this.removeGappedColumnMenuItem); +editMenu.add (this.removeAllGapsMenuItem); +editMenu.add (this.removeRedundancyMenuItem); +selectMenu.add (this.findMenuItem); +selectMenu.addSeparator (); +selectMenu.add (this.selectAllSequenceMenuItem); +selectMenu.add (this.deselectAllSequenceMenuItem); +selectMenu.add (this.invertSequenceMenuItem); +selectMenu.add (this.invertColSel); +selectMenu.add (this.createGroup); +selectMenu.add (this.unGroup); +selectMenu.add (this.grpsFromSelection); +selectMenu.add (this.deleteGroups); +selectMenu.add (this.annotationColumnSelection); +viewMenu.add (this.$newView); +viewMenu.addSeparator (); +showMenu.add (this.showColumns); +showMenu.add (this.showSeqs); +showMenu.add (this.showAllHidden); +viewMenu.add (showMenu); +hideMenu.add (this.hideColumns); +hideMenu.add (this.hideSequences); +hideMenu.add (this.hideAllSelection); +hideMenu.add (this.hideAllButSelection); +viewMenu.add (hideMenu); +viewMenu.addSeparator (); +viewMenu.add (this.followMouseOverFlag); +viewMenu.addSeparator (); +viewMenu.add (this.sequenceFeatures); +viewMenu.add (this.featureSettings); +viewMenu.addSeparator (); +viewMenu.add (this.alProperties); +viewMenu.addSeparator (); +viewMenu.add (this.overviewMenuItem); +annotationsMenu.add (this.annotationPanelMenuItem); +annotationsMenu.addSeparator (); +annotationsMenu.add (this.showAlignmentAnnotations); +annotationsMenu.add (this.showSequenceAnnotations); +annotationsMenu.add (this.sortAnnBySequence); +annotationsMenu.add (this.sortAnnByLabel); +annotationsMenu.addSeparator (); +autoAnnMenu.add (this.showAutoFirst); +autoAnnMenu.add (this.showAutoLast); +autoAnnMenu.addSeparator (); +autoAnnMenu.add (this.applyAutoAnnotationSettings); +autoAnnMenu.add (this.showConsensusHistogram); +autoAnnMenu.add (this.showSequenceLogo); +autoAnnMenu.add (this.normSequenceLogo); +autoAnnMenu.addSeparator (); +autoAnnMenu.add (this.showGroupConservation); +autoAnnMenu.add (this.showGroupConsensus); +annotationsMenu.add (autoAnnMenu); +formatMenu.add (this.$font); +formatMenu.add (this.seqLimits); +formatMenu.add (this.wrapMenuItem); +formatMenu.add (this.scaleAbove); +formatMenu.add (this.scaleLeft); +formatMenu.add (this.scaleRight); +formatMenu.add (this.viewBoxesMenuItem); +formatMenu.add (this.viewTextMenuItem); +formatMenu.add (this.colourTextMenuItem); +formatMenu.add (this.displayNonconservedMenuItem); +formatMenu.add (this.renderGapsMenuItem); +formatMenu.add (this.centreColumnLabelFlag); +colourMenu.add (this.applyToAllGroups); +colourMenu.addSeparator (); +colourMenu.add (this.noColourmenuItem); +colourMenu.add (this.clustalColour); +colourMenu.add (this.BLOSUM62Colour); +colourMenu.add (this.PIDColour); +colourMenu.add (this.zappoColour); +colourMenu.add (this.taylorColour); +colourMenu.add (this.hydrophobicityColour); +colourMenu.add (this.helixColour); +colourMenu.add (this.strandColour); +colourMenu.add (this.turnColour); +colourMenu.add (this.buriedColour); +colourMenu.add (this.nucleotideColour); +colourMenu.add (this.purinePyrimidineColour); +colourMenu.add (this.tcoffeeColour); +colourMenu.add (this.userDefinedColour); +colourMenu.addSeparator (); +colourMenu.add (this.conservationMenuItem); +colourMenu.add (this.modifyConservation); +colourMenu.add (this.abovePIDThreshold); +colourMenu.add (this.modifyPID); +colourMenu.add (this.annotationColour); +colourMenu.add (this.RNAHelixColour); +sortMenu.add (this.sortIDMenuItem); +sortMenu.add (this.sortLengthMenuItem); +sortMenu.add (this.sortByTreeMenu); +sortMenu.add (this.sortGroupMenuItem); +sortMenu.add (this.sortPairwiseMenuItem); +calculateMenu.add (sortMenu); +calculateTreeMenu.add (this.averageDistanceTreeMenuItem); +calculateTreeMenu.add (this.neighbourTreeMenuItem); +calculateTreeMenu.add (this.avDistanceTreeBlosumMenuItem); +calculateTreeMenu.add (this.njTreeBlosumMenuItem); +calculateMenu.add (calculateTreeMenu); +calculateMenu.addSeparator (); +calculateMenu.add (this.pairwiseAlignmentMenuItem); +calculateMenu.add (this.PCAMenuItem); +calculateMenu.add (this.autoCalculate); +calculateMenu.add (this.$sortByTree); +helpMenu.add (this.documentation); +helpMenu.add (this.about); +this.statusBar.setBackground (java.awt.Color.white); +this.statusBar.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.setStatus (jalview.util.MessageManager.getString ("label.status_bar")); +this.add (this.statusBar, "South"); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "setStatus", +function (string) { +this.statusBar.setText (string); +}, "~S"); +Clazz.defineMethod (c$, "createAlignFrameWindow", +function (reallyEmbedded) { +if (reallyEmbedded) { +this.embedAlignFrameInApplet (this.viewport.applet); +} else { +if (this.embedMenuIfNeeded (this.alignPanel)) { +this.alignPanel.setSize (this.getSize ().width, this.getSize ().height - this.statusBar.getHeight ()); +}this.add (this.statusBar, "South"); +this.add (this.alignPanel, "Center"); +jalview.bin.JalviewLite.addFrame (this, this.getTitle (), this.frameWidth, this.frameHeight); +}}, "~B"); +Clazz.defineMethod (c$, "embedAlignFrameInApplet", +function (theApplet) { +this.fileMenu.remove (this.closeMenuItem); +this.fileMenu.remove (3); +this.embeddedMenu = this.makeEmbeddedPopupMenu (this.alignFrameMenuBar, false, false); +theApplet.setLayout ( new java.awt.BorderLayout ()); +theApplet.add (this.embeddedMenu, "North"); +theApplet.add (this.statusBar, "South"); +this.alignPanel.setSize (theApplet.getSize ().width, theApplet.getSize ().height - this.embeddedMenu.getHeight () - this.statusBar.getHeight ()); +theApplet.add (this.alignPanel, "Center"); +var me = this; +theApplet.addFocusListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$5") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$5, this, Clazz.cloneFinals ("theApplet", theApplet, "me", me)))); +theApplet.validate (); +}, "jalview.bin.JalviewLite"); +Clazz.defineMethod (c$, "addStructureViewInstance", +function (jmolviewer, sequenceIds) { +return null; +}, "~O,~A"); +Clazz.defineMethod (c$, "addPdbFile", +function (sequenceId, pdbEntryString, pdbFile) { +var toaddpdb = this.viewport.getAlignment ().findName (sequenceId); +var needtoadd = false; +if (toaddpdb != null) { +var pdbe = toaddpdb.getPDBId (); +var pdbentry = null; +if (pdbe != null && pdbe.size () > 0) { +for (var pe = 0, peSize = pdbe.size (); pe < peSize; pe++) { +pdbentry = pdbe.elementAt (pe); +if (!pdbentry.getId ().equals (pdbEntryString) && !pdbentry.getFile ().equals (pdbFile)) { +pdbentry = null; +} else { +continue; +}} +}if (pdbentry == null) { +pdbentry = new jalview.datamodel.PDBEntry (); +pdbentry.setId (pdbEntryString); +pdbentry.setFile (pdbFile); +needtoadd = true; +}var protocol = jalview.io.AppletFormatAdapter.resolveProtocol (pdbFile, "PDB"); +if (protocol == null) { +return false; +}if (needtoadd) { +if (pdbentry.getProperty () == null) { +pdbentry.setProperty ( new java.util.Hashtable ()); +}pdbentry.getProperty ().put ("protocol", protocol); +toaddpdb.addPDBId (pdbentry); +this.alignPanel.getStructureSelectionManager ().registerPDBEntry (pdbentry); +}}return true; +}, "~S,~S,~S"); +Clazz.defineMethod (c$, "cleanSeqChainArrays", +($fz = function (seqs, chains) { +if (seqs != null) { +var sequences = new java.util.Vector (); +for (var i = 0; i < seqs.length; i++) { +if (seqs[i] != null) { +sequences.addElement ( Clazz.newArray (-1, [seqs[i], (chains != null) ? chains[i] : null])); +}} +seqs = new Array (sequences.size ()); +chains = new Array (sequences.size ()); +for (var i = 0, isize = sequences.size (); i < isize; i++) { +var oj = sequences.elementAt (i); +seqs[i] = oj[0]; +chains[i] = oj[1]; +} +}return Clazz.newArray (-1, [seqs, chains]); +}, $fz.isPrivate = true, $fz), "~A,~A"); +Clazz.defineMethod (c$, "newStructureView", +function (applet, pdb, seqs, chains, protocol) { +var sqch = this.cleanSeqChainArrays (seqs, chains); +seqs = sqch[0]; +chains = sqch[1]; +if (seqs == null || seqs.length == 0) { +System.err.println ("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); +}if (protocol == null || protocol.trim ().length == 0 || protocol.equals ("null")) { +protocol = pdb.getProperty ().get ("protocol"); +if (protocol == null) { +System.err.println ("Couldn't work out protocol to open structure: " + pdb.getId ()); +return; +}}if (applet.useXtrnalSviewer) { +if (jalview.structure.StructureSelectionManager.getStructureSelectionManager (applet).setMapping (seqs, chains, pdb.getFile (), protocol) == null) { +System.err.println ("Failed to map " + pdb.getFile () + " (" + protocol + ") to any sequences"); +}return; +}if (applet.isAlignPdbStructures () && applet.jmolAvailable) { +var ajm = null; +var tajm; +var jmols = applet.getAppletWindow (jalview.appletgui.AppletJmol); +for (var i = 0, iSize = jmols.size (); i < iSize; i++) { +tajm = jmols.elementAt (i); +if (tajm.ap.alignFrame === this) { +ajm = tajm; +break; +}} +if (ajm != null) { +System.err.println ("Incremental adding and aligning structure to existing Jmol view not yet implemented."); +ajm = null; +}} new jalview.appletgui.AppletJmol (pdb, seqs, chains, this.alignPanel, protocol); +jalview.bin.JalviewLite.lastFrameX += 40; +jalview.bin.JalviewLite.lastFrameY += 40; +}, "jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S"); +Clazz.defineMethod (c$, "alignedStructureView", +function (applet, pdb, seqs, chains, protocols) { +System.err.println ("Aligned Structure View: Not yet implemented."); +}, "jalview.bin.JalviewLite,~A,~A,~A,~A"); +Clazz.defineMethod (c$, "select", +function (sel, csel) { +this.alignPanel.seqPanel.selection (sel, csel, null); +}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection"); +Clazz.defineMethod (c$, "scrollTo", +function (row, column) { +this.alignPanel.seqPanel.scrollTo (row, column); +}, "~N,~N"); +Clazz.defineMethod (c$, "scrollToRow", +function (row) { +this.alignPanel.seqPanel.scrollToRow (row); +}, "~N"); +Clazz.defineMethod (c$, "scrollToColumn", +function (column) { +this.alignPanel.seqPanel.scrollToColumn (column); +}, "~N"); +Clazz.defineMethod (c$, "getSequenceSetId", +function () { +return this.viewport.getSequenceSetId (); +}); +Clazz.defineMethod (c$, "loadScoreFile", +function (inFile) { +var file = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [inFile, jalview.io.AppletFormatAdapter.checkProtocol (inFile)]); +if (!file.isValid ()) { +System.err.println ("Problems parsing T-Coffee scores: " + file.getWarningMessage ()); +System.err.println ("Origin was:\n" + inFile); +return false; +}var aln; +if ((aln = this.viewport.getAlignment ()) != null && (aln.getHeight () != file.getHeight () || aln.getWidth () != file.getWidth ())) { +System.err.println ("The scores matrix does not match the alignment dimensions"); +}if (file.annotateAlignment (this.alignPanel.getAlignment (), false)) { +this.alignPanel.fontChanged (); +this.tcoffeeColour.setEnabled (true); +this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); +return true; +} else { +System.err.println ("Problems resolving T-Coffee scores:"); +if (file.getWarningMessage () != null) { +System.err.println (file.getWarningMessage ()); +}}return false; +}, "~S"); +Clazz.defineMethod (c$, "getSplitFrame", +function () { +return this.splitFrame; +}); +Clazz.defineMethod (c$, "setSplitFrame", +function (sf) { +this.splitFrame = sf; +}, "jalview.appletgui.SplitFrame"); +Clazz.overrideMethod (c$, "setShowSeqFeatures", +function (b) { +this.viewport.setShowSequenceFeatures (b); +}, "~B"); +Clazz.overrideMethod (c$, "setMenusForViewport", +function () { +}); +Clazz.overrideMethod (c$, "refreshFeatureUI", +function (enableIfNecessary) { +if (enableIfNecessary) { +this.sequenceFeatures.setState (true); +this.alignPanel.av.setShowSequenceFeatures (true); +}}, "~B"); +Clazz.overrideMethod (c$, "getFeatureSettingsUI", +function () { +return this.alignPanel.av.featureSettings; +}); +c$.$AlignFrame$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$1", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +if (this.f$.ap != null) { +this.f$.ap.setOverviewPanel (null); +}}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$2", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$3", java.awt.event.WindowAdapter); +Clazz.defineMethod (c$, "windowOpened", +function (e) { +if (this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree) { +this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); +}Clazz.superCall (this, jalview.appletgui.AlignFrame$3, "windowOpened", [e]); +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove (this.f$.item); +}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$1AboutPanel$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.version = null; +this.builddate = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AlignFrame$1AboutPanel", awt2swing.Canvas); +Clazz.makeConstructor (c$, +function (a, b) { +Clazz.superConstructor (this, jalview.appletgui.AlignFrame$1AboutPanel, []); +this.version = a; +this.builddate = b; +}, "~S,~S"); +Clazz.overrideMethod (c$, "paintComponent", +function (a) { +a.setColor (java.awt.Color.white); +a.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +a.setFont ( new java.awt.Font ("Helvetica", 0, 12)); +var b = a.getFontMetrics (); +var c = b.getHeight (); +var d = 5; +var e = 7; +a.setColor (java.awt.Color.black); +a.setFont ( new java.awt.Font ("Helvetica", 1, 14)); +a.drawString (jalview.util.MessageManager.formatMessage ("label.jalviewLite_release", Clazz.newArray (-1, [this.version])), e, d += c); +a.setFont ( new java.awt.Font ("Helvetica", 1, 12)); +a.drawString (jalview.util.MessageManager.formatMessage ("label.jaview_build_date", Clazz.newArray (-1, [this.builddate])), e, d += c); +a.setFont ( new java.awt.Font ("Helvetica", 0, 12)); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_1"), e, d += c * 1.5); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_2"), e + 50, d += c + 8); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_dev_managers"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_distribution_lists"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_please_cite"), e, d += c + 8); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_authors"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_title"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_ref"), e, d += c); +}, "java.awt.Graphics"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$4$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$4", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.AlignFrame"].outputText_actionPerformed (e); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$5$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$5", null, java.awt.event.FocusListener); +Clazz.overrideMethod (c$, "focusLost", +function (e) { +if (this.f$.theApplet.currentAlignFrame === this.f$.me) { +this.f$.theApplet.currentAlignFrame = null; +}}, "java.awt.event.FocusEvent"); +Clazz.overrideMethod (c$, "focusGained", +function (e) { +this.f$.theApplet.currentAlignFrame = this.f$.me; +}, "java.awt.event.FocusEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"copiedSequences", null, +"copiedHiddenColumns", null); +}); diff --git a/bin/jalview/appletgui/AlignViewport.js b/bin/jalview/appletgui/AlignViewport.js index 8ea8971..1d890fc 100644 --- a/bin/jalview/appletgui/AlignViewport.js +++ b/bin/jalview/appletgui/AlignViewport.js @@ -1,229 +1,229 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.structure.CommandListener", "$.SelectionSource", "$.VamsasSource", "jalview.viewmodel.AlignmentViewport", "java.awt.Font"], "jalview.appletgui.AlignViewport", ["awt2swing.Frame", "jalview.api.AlignViewportI", "jalview.bin.JalviewLite", "jalview.datamodel.ColumnSelection", "$.SearchResults", "$.Sequence", "$.SequenceGroup", "jalview.schemes.ColourSchemeProperty", "jalview.structure.StructureSelectionManager", "jalview.util.Platform", "jalview.workers.AlignCalcManager", "java.lang.Float", "$.StringBuilder"], function () { -c$ = Clazz.decorateAsClass (function () { -this.cursorMode = false; -this.font = null; -this.validCharWidth = true; -this.currentTree = null; -this.applet = null; -this.MAC = false; -this.annotationColumnSelectionState = null; -this.nullFrame = null; -this.featureSettings = null; -this.heightScale = 1; -this.widthScale = 1; -this.centreColumnLabels = false; -this.followSelection = true; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AlignViewport", jalview.viewmodel.AlignmentViewport, [jalview.structure.SelectionSource, jalview.structure.VamsasSource, jalview.structure.CommandListener]); -Clazz.prepareFields (c$, function () { -this.font = new java.awt.Font ("SansSerif", 0, 10); -}); -Clazz.overrideMethod (c$, "finalize", -function () { -this.applet = null; -this.quality = null; -this.alignment = null; -this.colSel = null; -}); -Clazz.makeConstructor (c$, -function (al, applet) { -Clazz.superConstructor (this, jalview.appletgui.AlignViewport); -this.calculator = new jalview.workers.AlignCalcManager (); -this.applet = applet; -this.alignment = al; -this.setPadGaps (true); -this.startRes = 0; -this.endRes = al.getWidth () - 1; -this.startSeq = 0; -this.endSeq = al.getHeight () - 1; -if (applet != null) { -var param = applet.widthScale; -if (param != null) { -try { -this.widthScale = new Float (param).floatValue (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -if (this.widthScale <= 1.0) { -System.err.println ("Invalid alignment character width scaling factor (" + this.widthScale + "). Ignoring."); -this.widthScale = 1; -}if (jalview.bin.JalviewLite.debug) { -System.err.println ("Alignment character width scaling factor is now " + this.widthScale); -}}param = applet.heightScale; -if (param != null) { -try { -this.heightScale = new Float (param).floatValue (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -if (this.heightScale <= 1.0) { -System.err.println ("Invalid alignment character height scaling factor (" + this.heightScale + "). Ignoring."); -this.heightScale = 1; -}if (jalview.bin.JalviewLite.debug) { -System.err.println ("Alignment character height scaling factor is now " + this.heightScale); -}}}this.setFont (this.font); -this.MAC = jalview.util.Platform.isAMac (); -if (applet != null) { -this.setShowJVSuffix (applet.getDefaultParameter ("showFullId", this.getShowJVSuffix ())); -this.setShowAnnotation (applet.getDefaultParameter ("showAnnotation", this.isShowAnnotation ())); -this.showConservation = applet.getDefaultParameter ("showConservation", this.showConservation); -this.showQuality = applet.getDefaultParameter ("showQuality", this.showQuality); -this.showConsensus = applet.getDefaultParameter ("showConsensus", this.showConsensus); -this.setShowUnconserved (applet.getDefaultParameter ("showUnconserved", this.getShowUnconserved ())); -this.setScaleProteinAsCdna (applet.getDefaultParameter ("scaleProteinAsCdna", this.isScaleProteinAsCdna ())); -var param = applet.upperCase; -if (param != null) { -if (param.equalsIgnoreCase ("bold")) { -this.setUpperCasebold (true); -}}this.sortByTree = applet.getDefaultParameter ("sortByTree", this.sortByTree); -this.setFollowHighlight (applet.getDefaultParameter ("automaticScrolling", this.isFollowHighlight ())); -this.followSelection = this.isFollowHighlight (); -this.showSequenceLogo = applet.getDefaultParameter ("showSequenceLogo", this.showSequenceLogo); -this.normaliseSequenceLogo = applet.getDefaultParameter ("normaliseSequenceLogo", applet.getDefaultParameter ("normaliseLogo", this.normaliseSequenceLogo)); -this.showGroupConsensus = applet.getDefaultParameter ("showGroupConsensus", this.showGroupConsensus); -this.showGroupConservation = applet.getDefaultParameter ("showGroupConservation", this.showGroupConservation); -this.showConsensusHistogram = applet.getDefaultParameter ("showConsensusHistogram", this.showConsensusHistogram); -}if (applet != null) { -var colour = applet.defaultColour; -if (colour == null) { -colour = applet.userDefinedColour; -if (colour != null) { -colour = "User Defined"; -}}if (colour != null) { -this.globalColourScheme = jalview.schemes.ColourSchemeProperty.getColour (this.alignment, colour); -if (this.globalColourScheme != null) { -this.globalColourScheme.setConsensus (this.hconsensus); -}}if (applet.userDefinedColour != null) { -(this.globalColourScheme).parseAppletParameter (applet.userDefinedColour); -}}this.initAutoAnnotation (); -}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite"); -Clazz.defineMethod (c$, "getConsensusSeq", -function () { -if (this.consensus == null) { -this.updateConsensus (null); -}if (this.consensus == null) { -return null; -}var seqs = new StringBuilder (this.consensus.annotations.length); -for (var i = 0; i < this.consensus.annotations.length; i++) { -if (this.consensus.annotations[i] != null) { -if (this.consensus.annotations[i].description.charAt (0) == '[') { -seqs.append (this.consensus.annotations[i].description.charAt (1)); -} else { -seqs.append (this.consensus.annotations[i].displayCharacter); -}}} -var sq = new jalview.datamodel.Sequence ("Consensus", seqs.toString ()); -sq.setDescription ("Percentage Identity Consensus " + ((this.ignoreGapsInConsensusCalculation) ? " without gaps" : "")); -return sq; -}); -Clazz.defineMethod (c$, "setFont", -function (f) { -this.font = f; -if (this.nullFrame == null) { -this.nullFrame = new awt2swing.Frame (); -this.nullFrame.addNotify (); -this.nullFrame.setFont (this.font); -}var fm = this.nullFrame.getGraphics ().getFontMetrics (this.font); -this.setCharHeight (Clazz.floatToInt (this.heightScale * fm.getHeight ())); -this.setCharWidth (Clazz.floatToInt (this.widthScale * fm.charWidth ('M'))); -if (this.isUpperCasebold ()) { -var f2 = new java.awt.Font (f.getName (), 1, f.getSize ()); -fm = this.nullFrame.getGraphics ().getFontMetrics (f2); -this.setCharWidth (Clazz.floatToInt (this.widthScale * (Clazz.doubleToInt (fm.stringWidth ("MMMMMMMMMMM") / 10)))); -}}, "java.awt.Font"); -Clazz.defineMethod (c$, "getFont", -function () { -return this.font; -}); -Clazz.defineMethod (c$, "resetSeqLimits", -function (height) { -this.setEndSeq (Clazz.doubleToInt (height / this.getCharHeight ())); -}, "~N"); -Clazz.defineMethod (c$, "setCurrentTree", -function (tree) { -this.currentTree = tree; -}, "jalview.analysis.NJTree"); -Clazz.defineMethod (c$, "getCurrentTree", -function () { -return this.currentTree; -}); -Clazz.defineMethod (c$, "getCentreColumnLabels", -function () { -return this.centreColumnLabels; -}); -Clazz.defineMethod (c$, "getFollowSelection", -function () { -return this.followSelection; -}); -Clazz.overrideMethod (c$, "sendSelection", -function () { -this.getStructureSelectionManager ().sendSelection ( new jalview.datamodel.SequenceGroup (this.getSelectionGroup ()), new jalview.datamodel.ColumnSelection (this.getColumnSelection ()), this); -}); -Clazz.overrideMethod (c$, "getStructureSelectionManager", -function () { -return jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.applet); -}); -Clazz.defineMethod (c$, "expandColSelection", -function (sg, wholewidth) { -var sgs; -var sge; -if (sg != null && (sgs = sg.getStartRes ()) >= 0 && sg.getStartRes () <= (sge = sg.getEndRes ()) && (this.colSel == null || this.colSel.getSelected () == null || this.colSel.getSelected ().size () == 0)) { -if (!wholewidth && this.alignment.getWidth () == (1 + sge - sgs)) { -return; -}if (this.colSel == null) { -this.colSel = new jalview.datamodel.ColumnSelection (); -}for (var cspos = sg.getStartRes (); cspos <= sg.getEndRes (); cspos++) { -this.colSel.addElement (cspos); -} -}}, "jalview.datamodel.SequenceGroup,~B"); -Clazz.overrideMethod (c$, "isNormaliseSequenceLogo", -function () { -return this.normaliseSequenceLogo; -}); -Clazz.defineMethod (c$, "setNormaliseSequenceLogo", -function (state) { -this.normaliseSequenceLogo = state; -}, "~B"); -Clazz.overrideMethod (c$, "isValidCharWidth", -function () { -return this.validCharWidth; -}); -Clazz.defineMethod (c$, "getAnnotationColumnSelectionState", -function () { -return this.annotationColumnSelectionState; -}); -Clazz.defineMethod (c$, "setAnnotationColumnSelectionState", -function (annotationColumnSelectionState) { -this.annotationColumnSelectionState = annotationColumnSelectionState; -}, "jalview.appletgui.AnnotationColumnChooser"); -Clazz.overrideMethod (c$, "mirrorCommand", -function (command, undo, ssm, source) { -if (Clazz.instanceOf (source, jalview.api.AlignViewportI) && (source).getCodingComplement () === this) { -} else { -return; -}var mappedCommand = ssm.mapCommand (command, undo, this.getAlignment (), this.getGapCharacter ()); -if (mappedCommand != null) { -mappedCommand.doCommand (null); -this.firePropertyChange ("alignment", null, this.getAlignment ().getSequences ()); -}}, "jalview.commands.CommandI,~B,jalview.structure.StructureSelectionManager,jalview.structure.VamsasSource"); -Clazz.overrideMethod (c$, "getVamsasSource", -function () { -return this; -}); -Clazz.defineMethod (c$, "scrollComplementaryAlignment", -function (complementPanel) { -if (complementPanel == null) { -return; -}var sr = new jalview.datamodel.SearchResults (); -var seqOffset = this.findComplementScrollTarget (sr); -if (!sr.isEmpty ()) { -complementPanel.setFollowingComplementScroll (true); -complementPanel.scrollToCentre (sr, seqOffset); -}}, "jalview.appletgui.AlignmentPanel"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.structure.CommandListener", "$.SelectionSource", "$.VamsasSource", "jalview.viewmodel.AlignmentViewport", "java.awt.Font"], "jalview.appletgui.AlignViewport", ["awt2swing.Frame", "jalview.api.AlignViewportI", "jalview.bin.JalviewLite", "jalview.datamodel.ColumnSelection", "$.SearchResults", "$.Sequence", "$.SequenceGroup", "jalview.schemes.ColourSchemeProperty", "jalview.structure.StructureSelectionManager", "jalview.util.Platform", "jalview.workers.AlignCalcManager", "java.lang.Float", "$.StringBuilder"], function () { +c$ = Clazz.decorateAsClass (function () { +this.cursorMode = false; +this.font = null; +this.validCharWidth = true; +this.currentTree = null; +this.applet = null; +this.MAC = false; +this.annotationColumnSelectionState = null; +this.nullFrame = null; +this.featureSettings = null; +this.heightScale = 1; +this.widthScale = 1; +this.centreColumnLabels = false; +this.followSelection = true; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AlignViewport", jalview.viewmodel.AlignmentViewport, [jalview.structure.SelectionSource, jalview.structure.VamsasSource, jalview.structure.CommandListener]); +Clazz.prepareFields (c$, function () { +this.font = new java.awt.Font ("SansSerif", 0, 10); +}); +Clazz.overrideMethod (c$, "finalize", +function () { +this.applet = null; +this.quality = null; +this.alignment = null; +this.colSel = null; +}); +Clazz.makeConstructor (c$, +function (al, applet) { +Clazz.superConstructor (this, jalview.appletgui.AlignViewport); +this.calculator = new jalview.workers.AlignCalcManager (); +this.applet = applet; +this.alignment = al; +this.setPadGaps (true); +this.startRes = 0; +this.endRes = al.getWidth () - 1; +this.startSeq = 0; +this.endSeq = al.getHeight () - 1; +if (applet != null) { +var param = applet.widthScale; +if (param != null) { +try { +this.widthScale = new Float (param).floatValue (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +if (this.widthScale <= 1.0) { +System.err.println ("Invalid alignment character width scaling factor (" + this.widthScale + "). Ignoring."); +this.widthScale = 1; +}if (jalview.bin.JalviewLite.debug) { +System.err.println ("Alignment character width scaling factor is now " + this.widthScale); +}}param = applet.heightScale; +if (param != null) { +try { +this.heightScale = new Float (param).floatValue (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +if (this.heightScale <= 1.0) { +System.err.println ("Invalid alignment character height scaling factor (" + this.heightScale + "). Ignoring."); +this.heightScale = 1; +}if (jalview.bin.JalviewLite.debug) { +System.err.println ("Alignment character height scaling factor is now " + this.heightScale); +}}}this.setFont (this.font); +this.MAC = jalview.util.Platform.isAMac (); +if (applet != null) { +this.setShowJVSuffix (applet.getDefaultParameter ("showFullId", this.getShowJVSuffix ())); +this.setShowAnnotation (applet.getDefaultParameter ("showAnnotation", this.isShowAnnotation ())); +this.showConservation = applet.getDefaultParameter ("showConservation", this.showConservation); +this.showQuality = applet.getDefaultParameter ("showQuality", this.showQuality); +this.showConsensus = applet.getDefaultParameter ("showConsensus", this.showConsensus); +this.setShowUnconserved (applet.getDefaultParameter ("showUnconserved", this.getShowUnconserved ())); +this.setScaleProteinAsCdna (applet.getDefaultParameter ("scaleProteinAsCdna", this.isScaleProteinAsCdna ())); +var param = applet.upperCase; +if (param != null) { +if (param.equalsIgnoreCase ("bold")) { +this.setUpperCasebold (true); +}}this.sortByTree = applet.getDefaultParameter ("sortByTree", this.sortByTree); +this.setFollowHighlight (applet.getDefaultParameter ("automaticScrolling", this.isFollowHighlight ())); +this.followSelection = this.isFollowHighlight (); +this.showSequenceLogo = applet.getDefaultParameter ("showSequenceLogo", this.showSequenceLogo); +this.normaliseSequenceLogo = applet.getDefaultParameter ("normaliseSequenceLogo", applet.getDefaultParameter ("normaliseLogo", this.normaliseSequenceLogo)); +this.showGroupConsensus = applet.getDefaultParameter ("showGroupConsensus", this.showGroupConsensus); +this.showGroupConservation = applet.getDefaultParameter ("showGroupConservation", this.showGroupConservation); +this.showConsensusHistogram = applet.getDefaultParameter ("showConsensusHistogram", this.showConsensusHistogram); +}if (applet != null) { +var colour = applet.defaultColour; +if (colour == null) { +colour = applet.userDefinedColour; +if (colour != null) { +colour = "User Defined"; +}}if (colour != null) { +this.globalColourScheme = jalview.schemes.ColourSchemeProperty.getColour (this.alignment, colour); +if (this.globalColourScheme != null) { +this.globalColourScheme.setConsensus (this.hconsensus); +}}if (applet.userDefinedColour != null) { +(this.globalColourScheme).parseAppletParameter (applet.userDefinedColour); +}}this.initAutoAnnotation (); +}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite"); +Clazz.defineMethod (c$, "getConsensusSeq", +function () { +if (this.consensus == null) { +this.updateConsensus (null); +}if (this.consensus == null) { +return null; +}var seqs = new StringBuilder (this.consensus.annotations.length); +for (var i = 0; i < this.consensus.annotations.length; i++) { +if (this.consensus.annotations[i] != null) { +if (this.consensus.annotations[i].description.charAt (0) == '[') { +seqs.append (this.consensus.annotations[i].description.charAt (1)); +} else { +seqs.append (this.consensus.annotations[i].displayCharacter); +}}} +var sq = new jalview.datamodel.Sequence ("Consensus", seqs.toString ()); +sq.setDescription ("Percentage Identity Consensus " + ((this.ignoreGapsInConsensusCalculation) ? " without gaps" : "")); +return sq; +}); +Clazz.defineMethod (c$, "setFont", +function (f) { +this.font = f; +if (this.nullFrame == null) { +this.nullFrame = new awt2swing.Frame (); +this.nullFrame.addNotify (); +this.nullFrame.setFont (this.font); +}var fm = this.nullFrame.getGraphics ().getFontMetrics (this.font); +this.setCharHeight (Clazz.floatToInt (this.heightScale * fm.getHeight ())); +this.setCharWidth (Clazz.floatToInt (this.widthScale * fm.charWidth ('M'))); +if (this.isUpperCasebold ()) { +var f2 = new java.awt.Font (f.getName (), 1, f.getSize ()); +fm = this.nullFrame.getGraphics ().getFontMetrics (f2); +this.setCharWidth (Clazz.floatToInt (this.widthScale * (Clazz.doubleToInt (fm.stringWidth ("MMMMMMMMMMM") / 10)))); +}}, "java.awt.Font"); +Clazz.defineMethod (c$, "getFont", +function () { +return this.font; +}); +Clazz.defineMethod (c$, "resetSeqLimits", +function (height) { +this.setEndSeq (Clazz.doubleToInt (height / this.getCharHeight ())); +}, "~N"); +Clazz.defineMethod (c$, "setCurrentTree", +function (tree) { +this.currentTree = tree; +}, "jalview.analysis.NJTree"); +Clazz.defineMethod (c$, "getCurrentTree", +function () { +return this.currentTree; +}); +Clazz.defineMethod (c$, "getCentreColumnLabels", +function () { +return this.centreColumnLabels; +}); +Clazz.defineMethod (c$, "getFollowSelection", +function () { +return this.followSelection; +}); +Clazz.overrideMethod (c$, "sendSelection", +function () { +this.getStructureSelectionManager ().sendSelection ( new jalview.datamodel.SequenceGroup (this.getSelectionGroup ()), new jalview.datamodel.ColumnSelection (this.getColumnSelection ()), this); +}); +Clazz.overrideMethod (c$, "getStructureSelectionManager", +function () { +return jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.applet); +}); +Clazz.defineMethod (c$, "expandColSelection", +function (sg, wholewidth) { +var sgs; +var sge; +if (sg != null && (sgs = sg.getStartRes ()) >= 0 && sg.getStartRes () <= (sge = sg.getEndRes ()) && (this.colSel == null || this.colSel.getSelected () == null || this.colSel.getSelected ().size () == 0)) { +if (!wholewidth && this.alignment.getWidth () == (1 + sge - sgs)) { +return; +}if (this.colSel == null) { +this.colSel = new jalview.datamodel.ColumnSelection (); +}for (var cspos = sg.getStartRes (); cspos <= sg.getEndRes (); cspos++) { +this.colSel.addElement (cspos); +} +}}, "jalview.datamodel.SequenceGroup,~B"); +Clazz.overrideMethod (c$, "isNormaliseSequenceLogo", +function () { +return this.normaliseSequenceLogo; +}); +Clazz.defineMethod (c$, "setNormaliseSequenceLogo", +function (state) { +this.normaliseSequenceLogo = state; +}, "~B"); +Clazz.overrideMethod (c$, "isValidCharWidth", +function () { +return this.validCharWidth; +}); +Clazz.defineMethod (c$, "getAnnotationColumnSelectionState", +function () { +return this.annotationColumnSelectionState; +}); +Clazz.defineMethod (c$, "setAnnotationColumnSelectionState", +function (annotationColumnSelectionState) { +this.annotationColumnSelectionState = annotationColumnSelectionState; +}, "jalview.appletgui.AnnotationColumnChooser"); +Clazz.overrideMethod (c$, "mirrorCommand", +function (command, undo, ssm, source) { +if (Clazz.instanceOf (source, jalview.api.AlignViewportI) && (source).getCodingComplement () === this) { +} else { +return; +}var mappedCommand = ssm.mapCommand (command, undo, this.getAlignment (), this.getGapCharacter ()); +if (mappedCommand != null) { +mappedCommand.doCommand (null); +this.firePropertyChange ("alignment", null, this.getAlignment ().getSequences ()); +}}, "jalview.commands.CommandI,~B,jalview.structure.StructureSelectionManager,jalview.structure.VamsasSource"); +Clazz.overrideMethod (c$, "getVamsasSource", +function () { +return this; +}); +Clazz.defineMethod (c$, "scrollComplementaryAlignment", +function (complementPanel) { +if (complementPanel == null) { +return; +}var sr = new jalview.datamodel.SearchResults (); +var seqOffset = this.findComplementScrollTarget (sr); +if (!sr.isEmpty ()) { +complementPanel.setFollowingComplementScroll (true); +complementPanel.scrollToCentre (sr, seqOffset); +}}, "jalview.appletgui.AlignmentPanel"); +}); diff --git a/bin/jalview/appletgui/AlignmentPanel.class b/bin/jalview/appletgui/AlignmentPanel.class index 49b001d..873616b 100644 Binary files a/bin/jalview/appletgui/AlignmentPanel.class and b/bin/jalview/appletgui/AlignmentPanel.class differ diff --git a/bin/jalview/appletgui/AlignmentPanel.js b/bin/jalview/appletgui/AlignmentPanel.js index 8989731..1d6069d 100644 --- a/bin/jalview/appletgui/AlignmentPanel.js +++ b/bin/jalview/appletgui/AlignmentPanel.js @@ -1,610 +1,610 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "jalview.api.AlignmentViewPanel", "java.awt.event.AdjustmentListener", "awt2swing.Scrollbar"], "jalview.appletgui.AlignmentPanel", ["awt2swing.Frame", "jalview.analysis.AnnotationSorter", "jalview.appletgui.AnnotationLabels", "$.AnnotationPanel", "$.FeatureRenderer", "$.IdPanel", "$.IdwidthAdjuster", "$.PaintRefresher", "$.ScalePanel", "$.SeqPanel", "jalview.bin.JalviewLite", "jalview.structure.StructureSelectionManager", "java.awt.BorderLayout", "$.Color", "$.Dimension", "java.awt.event.ComponentAdapter", "java.beans.PropertyChangeListener"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.overviewPanel = null; -this.seqPanel = null; -this.idPanel = null; -this.idwidthAdjuster = null; -this.alignFrame = null; -this.scalePanel = null; -this.annotationPanel = null; -this.alabels = null; -this.fastPaint = true; -this.hextent = 0; -this.vextent = 0; -this.sequenceHolderPanel = null; -this.vscroll = null; -this.hscroll = null; -this.seqPanelHolder = null; -this.scalePanelHolder = null; -this.idPanelHolder = null; -this.idSpaceFillerPanel1 = null; -this.annotationSpaceFillerHolder = null; -this.hscrollFillerPanel = null; -this.annotationPanelHolder = null; -this.apvscroll = null; -this.followingComplementScroll = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AlignmentPanel", awt2swing.Panel, [java.awt.event.AdjustmentListener, jalview.api.AlignmentViewPanel]); -Clazz.prepareFields (c$, function () { -this.sequenceHolderPanel = new awt2swing.Panel (); -this.vscroll = new awt2swing.Scrollbar (); -this.hscroll = new awt2swing.Scrollbar (); -this.seqPanelHolder = new awt2swing.Panel (); -this.scalePanelHolder = new awt2swing.Panel (); -this.idPanelHolder = new awt2swing.Panel (); -this.idSpaceFillerPanel1 = new awt2swing.Panel (); -this.annotationSpaceFillerHolder = new awt2swing.Panel (); -this.hscrollFillerPanel = new awt2swing.Panel (); -this.annotationPanelHolder = new awt2swing.Panel (); -this.apvscroll = new awt2swing.Scrollbar (); -}); -Clazz.overrideMethod (c$, "finalize", -function () { -this.alignFrame = null; -this.av = null; -this.seqPanel = null; -this.seqPanelHolder = null; -this.sequenceHolderPanel = null; -this.scalePanel = null; -this.scalePanelHolder = null; -this.annotationPanel = null; -this.annotationPanelHolder = null; -this.annotationSpaceFillerHolder = null; -}); -Clazz.makeConstructor (c$, -function (af, av) { -Clazz.superConstructor (this, jalview.appletgui.AlignmentPanel, []); -this.setName ("alignmentPanel"); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.alignFrame = af; -this.av = av; -this.seqPanel = new jalview.appletgui.SeqPanel (av, this); -this.idPanel = new jalview.appletgui.IdPanel (av, this); -this.scalePanel = new jalview.appletgui.ScalePanel (av, this); -this.idwidthAdjuster = new jalview.appletgui.IdwidthAdjuster (this); -this.annotationPanel = new jalview.appletgui.AnnotationPanel (this); -this.annotationPanelHolder.add (this.annotationPanel, "Center"); -this.sequenceHolderPanel.add (this.annotationPanelHolder, "South"); -this.alabels = new jalview.appletgui.AnnotationLabels (this); -this.setAnnotationVisible (av.isShowAnnotation ()); -this.idPanelHolder.add (this.idPanel, "Center"); -this.idSpaceFillerPanel1.add (this.idwidthAdjuster, "Center"); -this.annotationSpaceFillerHolder.add (this.alabels, "Center"); -this.scalePanelHolder.add (this.scalePanel, "Center"); -this.seqPanelHolder.add (this.seqPanel, "Center"); -this.fontChanged (); -this.setScrollValues (0, 0); -this.apvscroll.addAdjustmentListener (this); -this.hscroll.addAdjustmentListener (this); -this.vscroll.addAdjustmentListener (this); -this.addComponentListener (((Clazz.isClassDefined ("jalview.appletgui.AlignmentPanel$1") ? 0 : jalview.appletgui.AlignmentPanel.$AlignmentPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignmentPanel$1, this, Clazz.cloneFinals ("av", av)))); -var d = this.calculateIdWidth (); -this.idPanel.idCanvas.setSize (d); -this.hscrollFillerPanel.setSize (d.width, this.annotationPanel.getSize ().height); -this.idPanel.idCanvas.setSize (d.width, this.seqPanel.seqCanvas.getSize ().height); -this.annotationSpaceFillerHolder.setSize (d.width, this.annotationPanel.getSize ().height); -this.alabels.setSize (d.width, this.annotationPanel.getSize ().height); -var ap = this; -av.addPropertyChangeListener (((Clazz.isClassDefined ("jalview.appletgui.AlignmentPanel$2") ? 0 : jalview.appletgui.AlignmentPanel.$AlignmentPanel$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignmentPanel$2, this, Clazz.cloneFinals ("ap", ap, "av", av)))); -}, "jalview.appletgui.AlignFrame,jalview.appletgui.AlignViewport"); -Clazz.overrideMethod (c$, "getAlignViewport", -function () { -return this.av; -}); -Clazz.defineMethod (c$, "getSequenceRenderer", -function () { -return this.seqPanel.seqCanvas.sr; -}); -Clazz.overrideMethod (c$, "getFeatureRenderer", -function () { -return this.seqPanel.seqCanvas.fr; -}); -Clazz.overrideMethod (c$, "cloneFeatureRenderer", -function () { -var nfr = new jalview.appletgui.FeatureRenderer (this.av); -nfr.transferSettings (this.seqPanel.seqCanvas.fr); -return nfr; -}); -Clazz.defineMethod (c$, "alignmentChanged", -function () { -this.av.alignmentChanged (this); -if (this.overviewPanel != null) { -this.overviewPanel.updateOverviewImage (); -}this.alignFrame.updateEditMenuBar (); -this.repaint (); -}); -Clazz.defineMethod (c$, "fontChanged", -function () { -this.idPanel.idCanvas.image = null; -var fm = this.getFontMetrics (this.av.getFont ()); -this.scalePanel.setSize ( new java.awt.Dimension (10, this.av.getCharHeight () + fm.getDescent ())); -this.idwidthAdjuster.setSize ( new java.awt.Dimension (10, this.av.getCharHeight () + fm.getDescent ())); -this.av.updateSequenceIdColours (); -this.annotationPanel.image = null; -var ap = this.annotationPanel.adjustPanelHeight (false); -var d = this.calculateIdWidth (); -d.setSize (d.width + 4, this.seqPanel.seqCanvas.getSize ().height); -this.alabels.setSize (d.width + 4, ap); -this.idPanel.idCanvas.setSize (d); -this.hscrollFillerPanel.setSize (d); -this.validateAnnotationDimensions (false); -this.annotationPanel.repaint (); -this.validate (); -this.repaint (); -if (this.overviewPanel != null) { -this.overviewPanel.updateOverviewImage (); -}}); -Clazz.defineMethod (c$, "setIdWidth", -function (w, h) { -this.idPanel.idCanvas.setSize (w, h); -this.idPanelHolder.setSize (w, this.idPanelHolder.getSize ().height); -this.annotationSpaceFillerHolder.setSize (w, this.annotationSpaceFillerHolder.getSize ().height); -this.alabels.setSize (w, this.alabels.getSize ().height); -this.validate (); -}, "~N,~N"); -Clazz.defineMethod (c$, "calculateIdWidth", -function () { -if (this.av.nullFrame == null) { -this.av.nullFrame = new awt2swing.Frame (); -this.av.nullFrame.addNotify (); -this.av.nullFrame.setFont (this.av.font); -}var g = this.av.nullFrame.getGraphics (); -var fm = g.getFontMetrics (this.av.font); -var al = this.av.getAlignment (); -var i = 0; -var idWidth = 0; -var id; -while (i < al.getHeight () && al.getSequenceAt (i) != null) { -var s = al.getSequenceAt (i); -id = s.getDisplayId (this.av.getShowJVSuffix ()); -if (fm.stringWidth (id) > idWidth) { -idWidth = fm.stringWidth (id); -}i++; -} -i = 0; -if (al.getAlignmentAnnotation () != null) { -fm = g.getFontMetrics (this.av.nullFrame.getFont ()); -while (i < al.getAlignmentAnnotation ().length) { -var label = al.getAlignmentAnnotation ()[i].label; -if (fm.stringWidth (label) > idWidth) { -idWidth = fm.stringWidth (label); -}i++; -} -}return new java.awt.Dimension (idWidth, this.idPanel.idCanvas.getSize ().height); -}); -Clazz.defineMethod (c$, "highlightSearchResults", -function (results) { -this.scrollToPosition (results); -this.seqPanel.seqCanvas.highlightSearchResults (results); -}, "jalview.datamodel.SearchResults"); -Clazz.defineMethod (c$, "scrollToPosition", -function (results) { -return this.scrollToPosition (results, true); -}, "jalview.datamodel.SearchResults"); -Clazz.defineMethod (c$, "scrollToPosition", -function (results, redrawOverview) { -return this.scrollToPosition (results, redrawOverview, false); -}, "jalview.datamodel.SearchResults,~B"); -Clazz.defineMethod (c$, "scrollToPosition", -function (results, redrawOverview, centre) { -if (results != null && results.getSize () > 0) { -var alignment = this.av.getAlignment (); -var seqIndex = alignment.findIndex (results); -if (seqIndex == -1) { -return false; -}var seq = alignment.getSequenceAt (seqIndex); -var r = results.getResults (seq, 0, alignment.getWidth ()); -if (r == null) { -if (jalview.bin.JalviewLite.debug) { -System.out.println ("DEBUG: scroll didn't happen - results not within alignment : " + seq.getStart () + "," + seq.getEnd ()); -}return false; -}if (jalview.bin.JalviewLite.debug) { -}var start = r[0]; -var end = r[1]; -if (centre) { -var offset = Clazz.doubleToInt ((this.av.getEndRes () - this.av.getStartRes () + 1) / 2) - 1; -start = Math.max (start - offset, 0); -end = Math.min (end + offset, seq.getEnd () - 1); -}if (start < 0) { -return false; -}if (end == seq.getEnd ()) { -return false; -}return this.scrollTo (start, end, seqIndex, false, redrawOverview); -}return true; -}, "jalview.datamodel.SearchResults,~B,~B"); -Clazz.defineMethod (c$, "scrollTo", -function (ostart, end, seqIndex, scrollToNearest, redrawOverview) { -var startv; -var endv; -var starts; -var ends; -var width; -var start = -1; -if (this.av.hasHiddenColumns ()) { -start = this.av.getColumnSelection ().findColumnPosition (ostart); -end = this.av.getColumnSelection ().findColumnPosition (end); -if (start == end) { -if (!scrollToNearest && !this.av.getColumnSelection ().isVisible (ostart)) { -return false; -}}} else { -start = ostart; -}if (!this.av.getWrapAlignment ()) { -if ((startv = this.av.getStartRes ()) >= start) { -this.setScrollValues (start - 1, seqIndex); -} else if ((endv = this.av.getEndRes ()) <= end) { -this.setScrollValues (startv + 1 + end - endv, seqIndex); -} else if ((starts = this.av.getStartSeq ()) > seqIndex) { -this.setScrollValues (this.av.getStartRes (), seqIndex); -} else if ((ends = this.av.getEndSeq ()) <= seqIndex) { -this.setScrollValues (this.av.getStartRes (), starts + seqIndex - ends + 1); -}} else { -this.scrollToWrappedVisible (start); -}if (redrawOverview && this.overviewPanel != null) { -this.overviewPanel.setBoxPosition (); -}this.paintAlignment (redrawOverview); -return true; -}, "~N,~N,~N,~B,~B"); -Clazz.defineMethod (c$, "scrollToWrappedVisible", -function (res) { -var cwidth = this.seqPanel.seqCanvas.getWrappedCanvasWidth (this.seqPanel.seqCanvas.getSize ().width); -if (res <= this.av.getStartRes () || res >= (this.av.getStartRes () + cwidth)) { -this.vscroll.setValue (Clazz.doubleToInt (res / cwidth)); -this.av.startRes = this.vscroll.getValue () * cwidth; -}}, "~N"); -Clazz.defineMethod (c$, "getOverviewPanel", -function () { -return this.overviewPanel; -}); -Clazz.defineMethod (c$, "setOverviewPanel", -function (op) { -this.overviewPanel = op; -}, "jalview.appletgui.OverviewPanel"); -Clazz.defineMethod (c$, "setAnnotationVisible", -function (b) { -if (!this.av.getWrapAlignment ()) { -this.annotationSpaceFillerHolder.setVisible (b); -this.annotationPanelHolder.setVisible (b); -} else { -this.annotationSpaceFillerHolder.setVisible (false); -this.annotationPanelHolder.setVisible (false); -}this.validate (); -this.repaint (); -}, "~B"); -Clazz.overrideMethod (c$, "adjustAnnotationHeight", -function () { -if (this.alignFrame.getSize ().height == 0) { -System.out.println ("adjustAnnotationHeight frame size zero NEEDS FIXING"); -}this.fontChanged (); -this.validateAnnotationDimensions (true); -this.apvscroll.addNotify (); -this.hscroll.addNotify (); -this.validate (); -this.paintAlignment (true); -}); -Clazz.defineMethod (c$, "validateAnnotationDimensions", -function (adjustPanelHeight) { -var rowHeight = this.av.getCharHeight (); -var alignmentHeight = rowHeight * this.av.getAlignment ().getHeight (); -var annotationHeight = this.av.calcPanelHeight (); -var mheight = annotationHeight; -var d = this.sequenceHolderPanel.getSize (); -var availableHeight = d.height - this.scalePanelHolder.getHeight (); -if (adjustPanelHeight) { -if (annotationHeight + alignmentHeight > availableHeight) { -annotationHeight = Math.min (annotationHeight, availableHeight - 2 * rowHeight); -}} else { -annotationHeight = this.annotationPanelHolder.getSize ().height; -}if (availableHeight - annotationHeight < 5) { -annotationHeight = availableHeight; -}this.annotationPanel.setSize ( new java.awt.Dimension (d.width, annotationHeight)); -this.annotationPanelHolder.setSize ( new java.awt.Dimension (d.width, annotationHeight)); -this.seqPanel.seqCanvas.setSize (d.width, this.seqPanel.seqCanvas.getSize ().height); -var e = this.idPanel.getSize (); -this.alabels.setSize ( new java.awt.Dimension (e.width, annotationHeight)); -this.annotationSpaceFillerHolder.setSize ( new java.awt.Dimension (e.width, annotationHeight)); -var s = this.apvscroll.getValue (); -if (s > mheight - annotationHeight) { -s = 0; -}this.apvscroll.setValues (s, annotationHeight, 0, mheight); -this.annotationPanel.setScrollOffset (this.apvscroll.getValue (), false); -this.alabels.setScrollOffset (this.apvscroll.getValue (), false); -}, "~B"); -Clazz.defineMethod (c$, "setWrapAlignment", -function (wrap) { -this.av.startSeq = 0; -this.av.startRes = 0; -this.scalePanelHolder.setVisible (!wrap); -this.hscroll.setVisible (!wrap); -this.idwidthAdjuster.setVisible (!wrap); -if (wrap) { -this.annotationPanelHolder.setVisible (false); -this.annotationSpaceFillerHolder.setVisible (false); -} else if (this.av.isShowAnnotation ()) { -this.annotationPanelHolder.setVisible (true); -this.annotationSpaceFillerHolder.setVisible (true); -}this.idSpaceFillerPanel1.setVisible (!wrap); -this.fontChanged (); -this.validate (); -this.sequenceHolderPanel.validate (); -this.repaint (); -}, "~B"); -Clazz.defineMethod (c$, "scrollUp", -function (up) { -if (up) { -if (this.vscroll.getValue () < 1) { -return false; -}this.setScrollValues (this.hscroll.getValue (), this.vscroll.getValue () - 1); -} else { -if (this.vextent + this.vscroll.getValue () >= this.av.getAlignment ().getHeight ()) { -return false; -}this.setScrollValues (this.hscroll.getValue (), this.vscroll.getValue () + 1); -}this.repaint (); -return true; -}, "~B"); -Clazz.defineMethod (c$, "scrollRight", -function (right) { -if (!right) { -if (this.hscroll.getValue () < 1) { -return false; -}this.setScrollValues (this.hscroll.getValue () - 1, this.vscroll.getValue ()); -} else { -if (this.hextent + this.hscroll.getValue () >= this.av.getAlignment ().getWidth ()) { -return false; -}this.setScrollValues (this.hscroll.getValue () + 1, this.vscroll.getValue ()); -}this.repaint (); -return true; -}, "~B"); -Clazz.defineMethod (c$, "setScrollValues", -function (x, y) { -var width = this.av.getAlignment ().getWidth (); -var height = this.av.getAlignment ().getHeight (); -if (this.av.hasHiddenColumns ()) { -width = this.av.getColumnSelection ().findColumnPosition (width); -}if (x < 0) { -x = 0; -};this.hextent = Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().width / this.av.getCharWidth ()); -this.vextent = Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().height / this.av.getCharHeight ()); -if (this.hextent > width) { -this.hextent = width; -}if (this.vextent > height) { -this.vextent = height; -}if ((this.hextent + x) > width) { -System.err.println ("hextent was " + this.hextent + " and x was " + x); -x = width - this.hextent; -}if ((this.vextent + y) > height) { -y = height - this.vextent; -}if (y < 0) { -y = 0; -}if (x < 0) { -System.err.println ("x was " + x); -x = 0; -}this.av.setStartSeq (y); -var endSeq = y + this.vextent; -if (endSeq > this.av.getAlignment ().getHeight ()) { -endSeq = this.av.getAlignment ().getHeight (); -}this.av.setEndSeq (endSeq); -this.av.setStartRes (x); -this.av.setEndRes ((x + (Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().width / this.av.getCharWidth ()))) - 1); -this.hscroll.setValues (x, this.hextent, 0, width); -this.vscroll.setValues (y, this.vextent, 0, height); -if (this.overviewPanel != null) { -this.overviewPanel.setBoxPosition (); -}this.sendViewPosition (); -}, "~N,~N"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -if (this.annotationPanel == null) return; -var oldX = this.av.getStartRes (); -var oldY = this.av.getStartSeq (); -if (evt == null || evt.getSource () === this.apvscroll) { -this.annotationPanel.setScrollOffset (this.apvscroll.getValue (), false); -this.alabels.setScrollOffset (this.apvscroll.getValue (), false); -}if (evt == null || evt.getSource () === this.hscroll) { -var x = this.hscroll.getValue (); -this.av.setStartRes (x); -this.av.setEndRes (x + Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().width / this.av.getCharWidth ()) - 1); -}if (evt == null || evt.getSource () === this.vscroll) { -var offy = this.vscroll.getValue (); -if (this.av.getWrapAlignment ()) { -var rowSize = this.seqPanel.seqCanvas.getWrappedCanvasWidth (this.seqPanel.seqCanvas.getSize ().width); -this.av.setStartRes (this.vscroll.getValue () * rowSize); -this.av.setEndRes ((this.vscroll.getValue () + 1) * rowSize); -} else { -this.av.setStartSeq (offy); -this.av.setEndSeq (offy + Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().height / this.av.getCharHeight ())); -}}if (this.overviewPanel != null) { -this.overviewPanel.setBoxPosition (); -}var scrollX = this.av.startRes - oldX; -var scrollY = this.av.startSeq - oldY; -if (this.av.getWrapAlignment () || !this.fastPaint || this.av.MAC) { -this.repaint (); -} else { -if (scrollX > this.av.endRes - this.av.startRes) { -scrollX = this.av.endRes - this.av.startRes; -} else if (scrollX < this.av.startRes - this.av.endRes) { -scrollX = this.av.startRes - this.av.endRes; -}this.idPanel.idCanvas.fastPaint (scrollY); -this.seqPanel.seqCanvas.fastPaint (scrollX, scrollY); -this.scalePanel.repaint (); -if (this.av.isShowAnnotation ()) { -this.annotationPanel.fastPaint (this.av.getStartRes () - oldX); -}}this.sendViewPosition (); -if (this.isFollowingComplementScroll ()) { -this.setFollowingComplementScroll (false); -} else { -var ap = this.getComplementPanel (); -this.av.scrollComplementaryAlignment (ap); -}}, "java.awt.event.AdjustmentEvent"); -Clazz.defineMethod (c$, "getComplementPanel", -($fz = function () { -var ap = null; -if (this.alignFrame != null) { -var sf = this.alignFrame.getSplitFrame (); -if (sf != null) { -var other = sf.getComplement (this.alignFrame); -if (other != null) { -ap = other.alignPanel; -}}}return ap; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "scrollToCentre", -function (sr, seqOffset) { -var mappedTo = sr.getResultSequence (0); -var seqs = this.av.getAlignment ().getSequences (); -var sequenceIndex = 0; -var matched = false; -for (var seq, $seq = seqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -if (mappedTo === seq.getDatasetSequence ()) { -matched = true; -break; -}sequenceIndex++; -} -if (!matched) { -return; -}sequenceIndex = Math.max (0, sequenceIndex - seqOffset); -sr.getResults ().get (0).setSequence (this.av.getAlignment ().getSequenceAt (sequenceIndex)); -this.setFollowingComplementScroll (true); -this.scrollToPosition (sr, true, true); -}, "jalview.datamodel.SearchResults,~N"); -Clazz.defineMethod (c$, "sendViewPosition", -($fz = function () { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet).sendViewPosition (this, this.av.startRes, this.av.endRes, this.av.startSeq, this.av.endSeq); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "paintAlignment", -function (updateOverview) { -var sorter = new jalview.analysis.AnnotationSorter (this.getAlignment (), this.av.isShowAutocalculatedAbove ()); -sorter.sort (this.getAlignment ().getAlignmentAnnotation (), this.av.getSortAnnotationsBy ()); -this.repaint (); -if (updateOverview) { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet).sequenceColoursChanged (this); -if (this.overviewPanel != null) { -this.overviewPanel.updateOverviewImage (); -}}}, "~B"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -System.out.println ("alignframe paintcomp"); -this.invalidate (); -var d = this.idPanel.idCanvas.getSize (); -var canvasHeight = this.seqPanel.seqCanvas.getSize ().height; -if (canvasHeight != d.height) { -this.idPanel.idCanvas.setSize (d.width, canvasHeight); -}if (this.av.getWrapAlignment ()) { -var maxwidth = this.av.getAlignment ().getWidth (); -if (this.av.hasHiddenColumns ()) { -maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; -}var canvasWidth = this.seqPanel.seqCanvas.getWrappedCanvasWidth (this.seqPanel.seqCanvas.getSize ().width); -if (canvasWidth > 0) { -var max = Clazz.doubleToInt (maxwidth / canvasWidth); -this.vscroll.setMaximum (1 + max); -this.vscroll.setUnitIncrement (1); -this.vscroll.setVisibleAmount (1); -}} else { -this.setScrollValues (this.av.getStartRes (), this.av.getStartSeq ()); -}}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout ( new java.awt.BorderLayout ()); -this.sequenceHolderPanel.setLayout ( new java.awt.BorderLayout ()); -this.seqPanelHolder.setLayout ( new java.awt.BorderLayout ()); -this.scalePanelHolder.setBackground (java.awt.Color.white); -this.scalePanelHolder.setLayout ( new java.awt.BorderLayout ()); -this.idPanelHolder.setLayout ( new java.awt.BorderLayout ()); -this.idSpaceFillerPanel1.setBackground (java.awt.Color.white); -this.idSpaceFillerPanel1.setLayout ( new java.awt.BorderLayout ()); -this.annotationSpaceFillerHolder.setBackground (java.awt.Color.white); -this.annotationSpaceFillerHolder.setLayout ( new java.awt.BorderLayout ()); -this.hscroll.setOrientation (0); -var hscrollHolder = new awt2swing.Panel (); -hscrollHolder.setLayout ( new java.awt.BorderLayout ()); -this.hscrollFillerPanel.setBackground (java.awt.Color.white); -this.apvscroll.setOrientation (1); -this.apvscroll.setVisible (true); -this.apvscroll.addAdjustmentListener (this); -this.annotationPanelHolder.setBackground (java.awt.Color.white); -this.annotationPanelHolder.setLayout ( new java.awt.BorderLayout ()); -this.annotationPanelHolder.add (this.apvscroll, "East"); -hscrollHolder.setBackground (java.awt.Color.white); -this.seqPanelHolder.setBackground (java.awt.Color.white); -this.idPanelHolder.setBackground (java.awt.Color.white); -this.sequenceHolderPanel.add (this.scalePanelHolder, "North"); -this.sequenceHolderPanel.add (this.seqPanelHolder, "Center"); -this.seqPanelHolder.add (this.vscroll, "East"); -this.add (this.idPanelHolder, "West"); -this.idPanelHolder.add (this.idSpaceFillerPanel1, "North"); -this.idPanelHolder.add (this.annotationSpaceFillerHolder, "South"); -this.add (hscrollHolder, "South"); -hscrollHolder.add (this.hscroll, "Center"); -hscrollHolder.add (this.hscrollFillerPanel, "West"); -this.add (this.sequenceHolderPanel, "Center"); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "updateAnnotation", -function () { -this.updateAnnotation (false); -}); -Clazz.defineMethod (c$, "updateAnnotation", -function (applyGlobalSettings) { -this.updateAnnotation (applyGlobalSettings, false); -}, "~B"); -Clazz.defineMethod (c$, "updateAnnotation", -function (applyGlobalSettings, preserveNewGroupSettings) { -this.av.updateGroupAnnotationSettings (applyGlobalSettings, preserveNewGroupSettings); -this.adjustAnnotationHeight (); -}, "~B,~B"); -Clazz.overrideMethod (c$, "getAlignment", -function () { -return this.av.getAlignment (); -}); -Clazz.overrideMethod (c$, "getViewName", -function () { -return this.getName (); -}); -Clazz.overrideMethod (c$, "getStructureSelectionManager", -function () { -return jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet); -}); -Clazz.overrideMethod (c$, "raiseOOMWarning", -function (string, error) { -System.err.println ("Out of memory whilst '" + string + "'"); -error.printStackTrace (); -}, "~S,OutOfMemoryError"); -Clazz.defineMethod (c$, "setFollowingComplementScroll", -function (b) { -this.followingComplementScroll = b; -}, "~B"); -Clazz.defineMethod (c$, "isFollowingComplementScroll", -function () { -return this.followingComplementScroll; -}); -c$.$AlignmentPanel$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignmentPanel$1", java.awt.event.ComponentAdapter); -Clazz.overrideMethod (c$, "componentResized", -function (evt) { -this.b$["jalview.appletgui.AlignmentPanel"].setScrollValues (this.f$.av.getStartRes (), this.f$.av.getStartSeq ()); -if (this.b$["jalview.appletgui.AlignmentPanel"].getSize ().height > 0 && this.b$["jalview.appletgui.AlignmentPanel"].annotationPanelHolder.getSize ().height > 0) { -this.b$["jalview.appletgui.AlignmentPanel"].validateAnnotationDimensions (false); -}this.b$["jalview.appletgui.AlignmentPanel"].repaint (); -}, "java.awt.event.ComponentEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignmentPanel$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignmentPanel$2", null, java.beans.PropertyChangeListener); -Clazz.overrideMethod (c$, "propertyChange", -function (evt) { -if (evt.getPropertyName ().equals ("alignment")) { -jalview.appletgui.PaintRefresher.Refresh (this.f$.ap, this.f$.av.getSequenceSetId (), true, true); -this.b$["jalview.appletgui.AlignmentPanel"].alignmentChanged (); -}}, "java.beans.PropertyChangeEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "jalview.api.AlignmentViewPanel", "java.awt.event.AdjustmentListener", "awt2swing.Scrollbar"], "jalview.appletgui.AlignmentPanel", ["awt2swing.Frame", "jalview.analysis.AnnotationSorter", "jalview.appletgui.AnnotationLabels", "$.AnnotationPanel", "$.FeatureRenderer", "$.IdPanel", "$.IdwidthAdjuster", "$.PaintRefresher", "$.ScalePanel", "$.SeqPanel", "jalview.bin.JalviewLite", "jalview.structure.StructureSelectionManager", "java.awt.BorderLayout", "$.Color", "$.Dimension", "java.awt.event.ComponentAdapter", "java.beans.PropertyChangeListener"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.overviewPanel = null; +this.seqPanel = null; +this.idPanel = null; +this.idwidthAdjuster = null; +this.alignFrame = null; +this.scalePanel = null; +this.annotationPanel = null; +this.alabels = null; +this.fastPaint = true; +this.hextent = 0; +this.vextent = 0; +this.sequenceHolderPanel = null; +this.vscroll = null; +this.hscroll = null; +this.seqPanelHolder = null; +this.scalePanelHolder = null; +this.idPanelHolder = null; +this.idSpaceFillerPanel1 = null; +this.annotationSpaceFillerHolder = null; +this.hscrollFillerPanel = null; +this.annotationPanelHolder = null; +this.apvscroll = null; +this.followingComplementScroll = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AlignmentPanel", awt2swing.Panel, [java.awt.event.AdjustmentListener, jalview.api.AlignmentViewPanel]); +Clazz.prepareFields (c$, function () { +this.sequenceHolderPanel = new awt2swing.Panel (); +this.vscroll = new awt2swing.Scrollbar (); +this.hscroll = new awt2swing.Scrollbar (); +this.seqPanelHolder = new awt2swing.Panel (); +this.scalePanelHolder = new awt2swing.Panel (); +this.idPanelHolder = new awt2swing.Panel (); +this.idSpaceFillerPanel1 = new awt2swing.Panel (); +this.annotationSpaceFillerHolder = new awt2swing.Panel (); +this.hscrollFillerPanel = new awt2swing.Panel (); +this.annotationPanelHolder = new awt2swing.Panel (); +this.apvscroll = new awt2swing.Scrollbar (); +}); +Clazz.overrideMethod (c$, "finalize", +function () { +this.alignFrame = null; +this.av = null; +this.seqPanel = null; +this.seqPanelHolder = null; +this.sequenceHolderPanel = null; +this.scalePanel = null; +this.scalePanelHolder = null; +this.annotationPanel = null; +this.annotationPanelHolder = null; +this.annotationSpaceFillerHolder = null; +}); +Clazz.makeConstructor (c$, +function (af, av) { +Clazz.superConstructor (this, jalview.appletgui.AlignmentPanel, []); +this.setName ("alignmentPanel"); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.alignFrame = af; +this.av = av; +this.seqPanel = new jalview.appletgui.SeqPanel (av, this); +this.idPanel = new jalview.appletgui.IdPanel (av, this); +this.scalePanel = new jalview.appletgui.ScalePanel (av, this); +this.idwidthAdjuster = new jalview.appletgui.IdwidthAdjuster (this); +this.annotationPanel = new jalview.appletgui.AnnotationPanel (this); +this.annotationPanelHolder.add (this.annotationPanel, "Center"); +this.sequenceHolderPanel.add (this.annotationPanelHolder, "South"); +this.alabels = new jalview.appletgui.AnnotationLabels (this); +this.setAnnotationVisible (av.isShowAnnotation ()); +this.idPanelHolder.add (this.idPanel, "Center"); +this.idSpaceFillerPanel1.add (this.idwidthAdjuster, "Center"); +this.annotationSpaceFillerHolder.add (this.alabels, "Center"); +this.scalePanelHolder.add (this.scalePanel, "Center"); +this.seqPanelHolder.add (this.seqPanel, "Center"); +this.fontChanged (); +this.setScrollValues (0, 0); +this.apvscroll.addAdjustmentListener (this); +this.hscroll.addAdjustmentListener (this); +this.vscroll.addAdjustmentListener (this); +this.addComponentListener (((Clazz.isClassDefined ("jalview.appletgui.AlignmentPanel$1") ? 0 : jalview.appletgui.AlignmentPanel.$AlignmentPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignmentPanel$1, this, Clazz.cloneFinals ("av", av)))); +var d = this.calculateIdWidth (); +this.idPanel.idCanvas.setSize (d); +this.hscrollFillerPanel.setSize (d.width, this.annotationPanel.getSize ().height); +this.idPanel.idCanvas.setSize (d.width, this.seqPanel.seqCanvas.getSize ().height); +this.annotationSpaceFillerHolder.setSize (d.width, this.annotationPanel.getSize ().height); +this.alabels.setSize (d.width, this.annotationPanel.getSize ().height); +var ap = this; +av.addPropertyChangeListener (((Clazz.isClassDefined ("jalview.appletgui.AlignmentPanel$2") ? 0 : jalview.appletgui.AlignmentPanel.$AlignmentPanel$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignmentPanel$2, this, Clazz.cloneFinals ("ap", ap, "av", av)))); +}, "jalview.appletgui.AlignFrame,jalview.appletgui.AlignViewport"); +Clazz.overrideMethod (c$, "getAlignViewport", +function () { +return this.av; +}); +Clazz.defineMethod (c$, "getSequenceRenderer", +function () { +return this.seqPanel.seqCanvas.sr; +}); +Clazz.overrideMethod (c$, "getFeatureRenderer", +function () { +return this.seqPanel.seqCanvas.fr; +}); +Clazz.overrideMethod (c$, "cloneFeatureRenderer", +function () { +var nfr = new jalview.appletgui.FeatureRenderer (this.av); +nfr.transferSettings (this.seqPanel.seqCanvas.fr); +return nfr; +}); +Clazz.defineMethod (c$, "alignmentChanged", +function () { +this.av.alignmentChanged (this); +if (this.overviewPanel != null) { +this.overviewPanel.updateOverviewImage (); +}this.alignFrame.updateEditMenuBar (); +this.repaint (); +}); +Clazz.defineMethod (c$, "fontChanged", +function () { +this.idPanel.idCanvas.image = null; +var fm = this.getFontMetrics (this.av.getFont ()); +this.scalePanel.setSize ( new java.awt.Dimension (10, this.av.getCharHeight () + fm.getDescent ())); +this.idwidthAdjuster.setSize ( new java.awt.Dimension (10, this.av.getCharHeight () + fm.getDescent ())); +this.av.updateSequenceIdColours (); +this.annotationPanel.image = null; +var ap = this.annotationPanel.adjustPanelHeight (false); +var d = this.calculateIdWidth (); +d.setSize (d.width + 4, this.seqPanel.seqCanvas.getSize ().height); +this.alabels.setSize (d.width + 4, ap); +this.idPanel.idCanvas.setSize (d); +this.hscrollFillerPanel.setSize (d); +this.validateAnnotationDimensions (false); +this.annotationPanel.repaint (); +this.validate (); +this.repaint (); +if (this.overviewPanel != null) { +this.overviewPanel.updateOverviewImage (); +}}); +Clazz.defineMethod (c$, "setIdWidth", +function (w, h) { +this.idPanel.idCanvas.setSize (w, h); +this.idPanelHolder.setSize (w, this.idPanelHolder.getSize ().height); +this.annotationSpaceFillerHolder.setSize (w, this.annotationSpaceFillerHolder.getSize ().height); +this.alabels.setSize (w, this.alabels.getSize ().height); +this.validate (); +}, "~N,~N"); +Clazz.defineMethod (c$, "calculateIdWidth", +function () { +if (this.av.nullFrame == null) { +this.av.nullFrame = new awt2swing.Frame (); +this.av.nullFrame.addNotify (); +this.av.nullFrame.setFont (this.av.font); +}var g = this.av.nullFrame.getGraphics (); +var fm = g.getFontMetrics (this.av.font); +var al = this.av.getAlignment (); +var i = 0; +var idWidth = 0; +var id; +while (i < al.getHeight () && al.getSequenceAt (i) != null) { +var s = al.getSequenceAt (i); +id = s.getDisplayId (this.av.getShowJVSuffix ()); +if (fm.stringWidth (id) > idWidth) { +idWidth = fm.stringWidth (id); +}i++; +} +i = 0; +if (al.getAlignmentAnnotation () != null) { +fm = g.getFontMetrics (this.av.nullFrame.getFont ()); +while (i < al.getAlignmentAnnotation ().length) { +var label = al.getAlignmentAnnotation ()[i].label; +if (fm.stringWidth (label) > idWidth) { +idWidth = fm.stringWidth (label); +}i++; +} +}return new java.awt.Dimension (idWidth, this.idPanel.idCanvas.getSize ().height); +}); +Clazz.defineMethod (c$, "highlightSearchResults", +function (results) { +this.scrollToPosition (results); +this.seqPanel.seqCanvas.highlightSearchResults (results); +}, "jalview.datamodel.SearchResults"); +Clazz.defineMethod (c$, "scrollToPosition", +function (results) { +return this.scrollToPosition (results, true); +}, "jalview.datamodel.SearchResults"); +Clazz.defineMethod (c$, "scrollToPosition", +function (results, redrawOverview) { +return this.scrollToPosition (results, redrawOverview, false); +}, "jalview.datamodel.SearchResults,~B"); +Clazz.defineMethod (c$, "scrollToPosition", +function (results, redrawOverview, centre) { +if (results != null && results.getSize () > 0) { +var alignment = this.av.getAlignment (); +var seqIndex = alignment.findIndex (results); +if (seqIndex == -1) { +return false; +}var seq = alignment.getSequenceAt (seqIndex); +var r = results.getResults (seq, 0, alignment.getWidth ()); +if (r == null) { +if (jalview.bin.JalviewLite.debug) { +System.out.println ("DEBUG: scroll didn't happen - results not within alignment : " + seq.getStart () + "," + seq.getEnd ()); +}return false; +}if (jalview.bin.JalviewLite.debug) { +}var start = r[0]; +var end = r[1]; +if (centre) { +var offset = Clazz.doubleToInt ((this.av.getEndRes () - this.av.getStartRes () + 1) / 2) - 1; +start = Math.max (start - offset, 0); +end = Math.min (end + offset, seq.getEnd () - 1); +}if (start < 0) { +return false; +}if (end == seq.getEnd ()) { +return false; +}return this.scrollTo (start, end, seqIndex, false, redrawOverview); +}return true; +}, "jalview.datamodel.SearchResults,~B,~B"); +Clazz.defineMethod (c$, "scrollTo", +function (ostart, end, seqIndex, scrollToNearest, redrawOverview) { +var startv; +var endv; +var starts; +var ends; +var width; +var start = -1; +if (this.av.hasHiddenColumns ()) { +start = this.av.getColumnSelection ().findColumnPosition (ostart); +end = this.av.getColumnSelection ().findColumnPosition (end); +if (start == end) { +if (!scrollToNearest && !this.av.getColumnSelection ().isVisible (ostart)) { +return false; +}}} else { +start = ostart; +}if (!this.av.getWrapAlignment ()) { +if ((startv = this.av.getStartRes ()) >= start) { +this.setScrollValues (start - 1, seqIndex); +} else if ((endv = this.av.getEndRes ()) <= end) { +this.setScrollValues (startv + 1 + end - endv, seqIndex); +} else if ((starts = this.av.getStartSeq ()) > seqIndex) { +this.setScrollValues (this.av.getStartRes (), seqIndex); +} else if ((ends = this.av.getEndSeq ()) <= seqIndex) { +this.setScrollValues (this.av.getStartRes (), starts + seqIndex - ends + 1); +}} else { +this.scrollToWrappedVisible (start); +}if (redrawOverview && this.overviewPanel != null) { +this.overviewPanel.setBoxPosition (); +}this.paintAlignment (redrawOverview); +return true; +}, "~N,~N,~N,~B,~B"); +Clazz.defineMethod (c$, "scrollToWrappedVisible", +function (res) { +var cwidth = this.seqPanel.seqCanvas.getWrappedCanvasWidth (this.seqPanel.seqCanvas.getSize ().width); +if (res <= this.av.getStartRes () || res >= (this.av.getStartRes () + cwidth)) { +this.vscroll.setValue (Clazz.doubleToInt (res / cwidth)); +this.av.startRes = this.vscroll.getValue () * cwidth; +}}, "~N"); +Clazz.defineMethod (c$, "getOverviewPanel", +function () { +return this.overviewPanel; +}); +Clazz.defineMethod (c$, "setOverviewPanel", +function (op) { +this.overviewPanel = op; +}, "jalview.appletgui.OverviewPanel"); +Clazz.defineMethod (c$, "setAnnotationVisible", +function (b) { +if (!this.av.getWrapAlignment ()) { +this.annotationSpaceFillerHolder.setVisible (b); +this.annotationPanelHolder.setVisible (b); +} else { +this.annotationSpaceFillerHolder.setVisible (false); +this.annotationPanelHolder.setVisible (false); +}this.validate (); +this.repaint (); +}, "~B"); +Clazz.overrideMethod (c$, "adjustAnnotationHeight", +function () { +if (this.alignFrame.getSize ().height == 0) { +System.out.println ("adjustAnnotationHeight frame size zero NEEDS FIXING"); +}this.fontChanged (); +this.validateAnnotationDimensions (true); +this.apvscroll.addNotify (); +this.hscroll.addNotify (); +this.validate (); +this.paintAlignment (true); +}); +Clazz.defineMethod (c$, "validateAnnotationDimensions", +function (adjustPanelHeight) { +var rowHeight = this.av.getCharHeight (); +var alignmentHeight = rowHeight * this.av.getAlignment ().getHeight (); +var annotationHeight = this.av.calcPanelHeight (); +var mheight = annotationHeight; +var d = this.sequenceHolderPanel.getSize (); +var availableHeight = d.height - this.scalePanelHolder.getHeight (); +if (adjustPanelHeight) { +if (annotationHeight + alignmentHeight > availableHeight) { +annotationHeight = Math.min (annotationHeight, availableHeight - 2 * rowHeight); +}} else { +annotationHeight = this.annotationPanelHolder.getSize ().height; +}if (availableHeight - annotationHeight < 5) { +annotationHeight = availableHeight; +}this.annotationPanel.setSize ( new java.awt.Dimension (d.width, annotationHeight)); +this.annotationPanelHolder.setSize ( new java.awt.Dimension (d.width, annotationHeight)); +this.seqPanel.seqCanvas.setSize (d.width, this.seqPanel.seqCanvas.getSize ().height); +var e = this.idPanel.getSize (); +this.alabels.setSize ( new java.awt.Dimension (e.width, annotationHeight)); +this.annotationSpaceFillerHolder.setSize ( new java.awt.Dimension (e.width, annotationHeight)); +var s = this.apvscroll.getValue (); +if (s > mheight - annotationHeight) { +s = 0; +}this.apvscroll.setValues (s, annotationHeight, 0, mheight); +this.annotationPanel.setScrollOffset (this.apvscroll.getValue (), false); +this.alabels.setScrollOffset (this.apvscroll.getValue (), false); +}, "~B"); +Clazz.defineMethod (c$, "setWrapAlignment", +function (wrap) { +this.av.startSeq = 0; +this.av.startRes = 0; +this.scalePanelHolder.setVisible (!wrap); +this.hscroll.setVisible (!wrap); +this.idwidthAdjuster.setVisible (!wrap); +if (wrap) { +this.annotationPanelHolder.setVisible (false); +this.annotationSpaceFillerHolder.setVisible (false); +} else if (this.av.isShowAnnotation ()) { +this.annotationPanelHolder.setVisible (true); +this.annotationSpaceFillerHolder.setVisible (true); +}this.idSpaceFillerPanel1.setVisible (!wrap); +this.fontChanged (); +this.validate (); +this.sequenceHolderPanel.validate (); +this.repaint (); +}, "~B"); +Clazz.defineMethod (c$, "scrollUp", +function (up) { +if (up) { +if (this.vscroll.getValue () < 1) { +return false; +}this.setScrollValues (this.hscroll.getValue (), this.vscroll.getValue () - 1); +} else { +if (this.vextent + this.vscroll.getValue () >= this.av.getAlignment ().getHeight ()) { +return false; +}this.setScrollValues (this.hscroll.getValue (), this.vscroll.getValue () + 1); +}this.repaint (); +return true; +}, "~B"); +Clazz.defineMethod (c$, "scrollRight", +function (right) { +if (!right) { +if (this.hscroll.getValue () < 1) { +return false; +}this.setScrollValues (this.hscroll.getValue () - 1, this.vscroll.getValue ()); +} else { +if (this.hextent + this.hscroll.getValue () >= this.av.getAlignment ().getWidth ()) { +return false; +}this.setScrollValues (this.hscroll.getValue () + 1, this.vscroll.getValue ()); +}this.repaint (); +return true; +}, "~B"); +Clazz.defineMethod (c$, "setScrollValues", +function (x, y) { +var width = this.av.getAlignment ().getWidth (); +var height = this.av.getAlignment ().getHeight (); +if (this.av.hasHiddenColumns ()) { +width = this.av.getColumnSelection ().findColumnPosition (width); +}if (x < 0) { +x = 0; +};this.hextent = Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().width / this.av.getCharWidth ()); +this.vextent = Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().height / this.av.getCharHeight ()); +if (this.hextent > width) { +this.hextent = width; +}if (this.vextent > height) { +this.vextent = height; +}if ((this.hextent + x) > width) { +System.err.println ("hextent was " + this.hextent + " and x was " + x); +x = width - this.hextent; +}if ((this.vextent + y) > height) { +y = height - this.vextent; +}if (y < 0) { +y = 0; +}if (x < 0) { +System.err.println ("x was " + x); +x = 0; +}this.av.setStartSeq (y); +var endSeq = y + this.vextent; +if (endSeq > this.av.getAlignment ().getHeight ()) { +endSeq = this.av.getAlignment ().getHeight (); +}this.av.setEndSeq (endSeq); +this.av.setStartRes (x); +this.av.setEndRes ((x + (Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().width / this.av.getCharWidth ()))) - 1); +this.hscroll.setValues (x, this.hextent, 0, width); +this.vscroll.setValues (y, this.vextent, 0, height); +if (this.overviewPanel != null) { +this.overviewPanel.setBoxPosition (); +}this.sendViewPosition (); +}, "~N,~N"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +if (this.annotationPanel == null) return; +var oldX = this.av.getStartRes (); +var oldY = this.av.getStartSeq (); +if (evt == null || evt.getSource () === this.apvscroll) { +this.annotationPanel.setScrollOffset (this.apvscroll.getValue (), false); +this.alabels.setScrollOffset (this.apvscroll.getValue (), false); +}if (evt == null || evt.getSource () === this.hscroll) { +var x = this.hscroll.getValue (); +this.av.setStartRes (x); +this.av.setEndRes (x + Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().width / this.av.getCharWidth ()) - 1); +}if (evt == null || evt.getSource () === this.vscroll) { +var offy = this.vscroll.getValue (); +if (this.av.getWrapAlignment ()) { +var rowSize = this.seqPanel.seqCanvas.getWrappedCanvasWidth (this.seqPanel.seqCanvas.getSize ().width); +this.av.setStartRes (this.vscroll.getValue () * rowSize); +this.av.setEndRes ((this.vscroll.getValue () + 1) * rowSize); +} else { +this.av.setStartSeq (offy); +this.av.setEndSeq (offy + Clazz.doubleToInt (this.seqPanel.seqCanvas.getSize ().height / this.av.getCharHeight ())); +}}if (this.overviewPanel != null) { +this.overviewPanel.setBoxPosition (); +}var scrollX = this.av.startRes - oldX; +var scrollY = this.av.startSeq - oldY; +if (this.av.getWrapAlignment () || !this.fastPaint || this.av.MAC) { +this.repaint (); +} else { +if (scrollX > this.av.endRes - this.av.startRes) { +scrollX = this.av.endRes - this.av.startRes; +} else if (scrollX < this.av.startRes - this.av.endRes) { +scrollX = this.av.startRes - this.av.endRes; +}this.idPanel.idCanvas.fastPaint (scrollY); +this.seqPanel.seqCanvas.fastPaint (scrollX, scrollY); +this.scalePanel.repaint (); +if (this.av.isShowAnnotation ()) { +this.annotationPanel.fastPaint (this.av.getStartRes () - oldX); +}}this.sendViewPosition (); +if (this.isFollowingComplementScroll ()) { +this.setFollowingComplementScroll (false); +} else { +var ap = this.getComplementPanel (); +this.av.scrollComplementaryAlignment (ap); +}}, "java.awt.event.AdjustmentEvent"); +Clazz.defineMethod (c$, "getComplementPanel", +($fz = function () { +var ap = null; +if (this.alignFrame != null) { +var sf = this.alignFrame.getSplitFrame (); +if (sf != null) { +var other = sf.getComplement (this.alignFrame); +if (other != null) { +ap = other.alignPanel; +}}}return ap; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "scrollToCentre", +function (sr, seqOffset) { +var mappedTo = sr.getResultSequence (0); +var seqs = this.av.getAlignment ().getSequences (); +var sequenceIndex = 0; +var matched = false; +for (var seq, $seq = seqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +if (mappedTo === seq.getDatasetSequence ()) { +matched = true; +break; +}sequenceIndex++; +} +if (!matched) { +return; +}sequenceIndex = Math.max (0, sequenceIndex - seqOffset); +sr.getResults ().get (0).setSequence (this.av.getAlignment ().getSequenceAt (sequenceIndex)); +this.setFollowingComplementScroll (true); +this.scrollToPosition (sr, true, true); +}, "jalview.datamodel.SearchResults,~N"); +Clazz.defineMethod (c$, "sendViewPosition", +($fz = function () { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet).sendViewPosition (this, this.av.startRes, this.av.endRes, this.av.startSeq, this.av.endSeq); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "paintAlignment", +function (updateOverview) { +var sorter = new jalview.analysis.AnnotationSorter (this.getAlignment (), this.av.isShowAutocalculatedAbove ()); +sorter.sort (this.getAlignment ().getAlignmentAnnotation (), this.av.getSortAnnotationsBy ()); +this.repaint (); +if (updateOverview) { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet).sequenceColoursChanged (this); +if (this.overviewPanel != null) { +this.overviewPanel.updateOverviewImage (); +}}}, "~B"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +System.out.println ("alignframe paintcomp"); +this.invalidate (); +var d = this.idPanel.idCanvas.getSize (); +var canvasHeight = this.seqPanel.seqCanvas.getSize ().height; +if (canvasHeight != d.height) { +this.idPanel.idCanvas.setSize (d.width, canvasHeight); +}if (this.av.getWrapAlignment ()) { +var maxwidth = this.av.getAlignment ().getWidth (); +if (this.av.hasHiddenColumns ()) { +maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; +}var canvasWidth = this.seqPanel.seqCanvas.getWrappedCanvasWidth (this.seqPanel.seqCanvas.getSize ().width); +if (canvasWidth > 0) { +var max = Clazz.doubleToInt (maxwidth / canvasWidth); +this.vscroll.setMaximum (1 + max); +this.vscroll.setUnitIncrement (1); +this.vscroll.setVisibleAmount (1); +}} else { +this.setScrollValues (this.av.getStartRes (), this.av.getStartSeq ()); +}}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout ( new java.awt.BorderLayout ()); +this.sequenceHolderPanel.setLayout ( new java.awt.BorderLayout ()); +this.seqPanelHolder.setLayout ( new java.awt.BorderLayout ()); +this.scalePanelHolder.setBackground (java.awt.Color.white); +this.scalePanelHolder.setLayout ( new java.awt.BorderLayout ()); +this.idPanelHolder.setLayout ( new java.awt.BorderLayout ()); +this.idSpaceFillerPanel1.setBackground (java.awt.Color.white); +this.idSpaceFillerPanel1.setLayout ( new java.awt.BorderLayout ()); +this.annotationSpaceFillerHolder.setBackground (java.awt.Color.white); +this.annotationSpaceFillerHolder.setLayout ( new java.awt.BorderLayout ()); +this.hscroll.setOrientation (0); +var hscrollHolder = new awt2swing.Panel (); +hscrollHolder.setLayout ( new java.awt.BorderLayout ()); +this.hscrollFillerPanel.setBackground (java.awt.Color.white); +this.apvscroll.setOrientation (1); +this.apvscroll.setVisible (true); +this.apvscroll.addAdjustmentListener (this); +this.annotationPanelHolder.setBackground (java.awt.Color.white); +this.annotationPanelHolder.setLayout ( new java.awt.BorderLayout ()); +this.annotationPanelHolder.add (this.apvscroll, "East"); +hscrollHolder.setBackground (java.awt.Color.white); +this.seqPanelHolder.setBackground (java.awt.Color.white); +this.idPanelHolder.setBackground (java.awt.Color.white); +this.sequenceHolderPanel.add (this.scalePanelHolder, "North"); +this.sequenceHolderPanel.add (this.seqPanelHolder, "Center"); +this.seqPanelHolder.add (this.vscroll, "East"); +this.add (this.idPanelHolder, "West"); +this.idPanelHolder.add (this.idSpaceFillerPanel1, "North"); +this.idPanelHolder.add (this.annotationSpaceFillerHolder, "South"); +this.add (hscrollHolder, "South"); +hscrollHolder.add (this.hscroll, "Center"); +hscrollHolder.add (this.hscrollFillerPanel, "West"); +this.add (this.sequenceHolderPanel, "Center"); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "updateAnnotation", +function () { +this.updateAnnotation (false); +}); +Clazz.defineMethod (c$, "updateAnnotation", +function (applyGlobalSettings) { +this.updateAnnotation (applyGlobalSettings, false); +}, "~B"); +Clazz.defineMethod (c$, "updateAnnotation", +function (applyGlobalSettings, preserveNewGroupSettings) { +this.av.updateGroupAnnotationSettings (applyGlobalSettings, preserveNewGroupSettings); +this.adjustAnnotationHeight (); +}, "~B,~B"); +Clazz.overrideMethod (c$, "getAlignment", +function () { +return this.av.getAlignment (); +}); +Clazz.overrideMethod (c$, "getViewName", +function () { +return this.getName (); +}); +Clazz.overrideMethod (c$, "getStructureSelectionManager", +function () { +return jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet); +}); +Clazz.overrideMethod (c$, "raiseOOMWarning", +function (string, error) { +System.err.println ("Out of memory whilst '" + string + "'"); +error.printStackTrace (); +}, "~S,OutOfMemoryError"); +Clazz.defineMethod (c$, "setFollowingComplementScroll", +function (b) { +this.followingComplementScroll = b; +}, "~B"); +Clazz.defineMethod (c$, "isFollowingComplementScroll", +function () { +return this.followingComplementScroll; +}); +c$.$AlignmentPanel$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignmentPanel$1", java.awt.event.ComponentAdapter); +Clazz.overrideMethod (c$, "componentResized", +function (evt) { +this.b$["jalview.appletgui.AlignmentPanel"].setScrollValues (this.f$.av.getStartRes (), this.f$.av.getStartSeq ()); +if (this.b$["jalview.appletgui.AlignmentPanel"].getSize ().height > 0 && this.b$["jalview.appletgui.AlignmentPanel"].annotationPanelHolder.getSize ().height > 0) { +this.b$["jalview.appletgui.AlignmentPanel"].validateAnnotationDimensions (false); +}this.b$["jalview.appletgui.AlignmentPanel"].repaint (); +}, "java.awt.event.ComponentEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignmentPanel$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignmentPanel$2", null, java.beans.PropertyChangeListener); +Clazz.overrideMethod (c$, "propertyChange", +function (evt) { +if (evt.getPropertyName ().equals ("alignment")) { +jalview.appletgui.PaintRefresher.Refresh (this.f$.ap, this.f$.av.getSequenceSetId (), true, true); +this.b$["jalview.appletgui.AlignmentPanel"].alignmentChanged (); +}}, "java.beans.PropertyChangeEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/AnnotationColourChooser.class b/bin/jalview/appletgui/AnnotationColourChooser.class index 15ef662..e2ee296 100644 Binary files a/bin/jalview/appletgui/AnnotationColourChooser.class and b/bin/jalview/appletgui/AnnotationColourChooser.class differ diff --git a/bin/jalview/appletgui/AnnotationColourChooser.js b/bin/jalview/appletgui/AnnotationColourChooser.js index fce2267..668d9cd 100644 --- a/bin/jalview/appletgui/AnnotationColourChooser.js +++ b/bin/jalview/appletgui/AnnotationColourChooser.js @@ -1,348 +1,348 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Button", "$.Checkbox", "$.Choice", "$.Scrollbar", "$.TextField", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.AnnotationColourChooser", ["awt2swing.Frame", "jalview.appletgui.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.datamodel.GraphLine", "jalview.schemes.AnnotationColourGradient", "$.ColourSchemeI", "jalview.util.MessageManager", "java.awt.Color", "$.Dimension", "$.Font", "java.lang.Error", "$.Float", "java.util.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.frame = null; -this.av = null; -this.ap = null; -this.oldcs = null; -this.oldgroupColours = null; -this.currentAnnotation = null; -this.adjusting = false; -this.annotations = null; -this.minColour = null; -this.maxColour = null; -this.ok = null; -this.cancel = null; -this.defColours = null; -this.jPanel1 = null; -this.jPanel2 = null; -this.threshold = null; -this.flowLayout1 = null; -this.jPanel3 = null; -this.slider = null; -this.thresholdValue = null; -this.currentColours = null; -this.borderLayout1 = null; -this.thresholdIsMin = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AnnotationColourChooser", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]); -Clazz.prepareFields (c$, function () { -this.annotations = new awt2swing.Choice (); -this.minColour = new awt2swing.Button (); -this.maxColour = new awt2swing.Button (); -this.ok = new awt2swing.Button (); -this.cancel = new awt2swing.Button (); -this.defColours = new awt2swing.Button (); -this.jPanel1 = new awt2swing.Panel (); -this.jPanel2 = new awt2swing.Panel (); -this.threshold = new awt2swing.Choice (); -this.flowLayout1 = new java.awt.FlowLayout (); -this.jPanel3 = new awt2swing.Panel (); -this.slider = new awt2swing.Scrollbar (0); -this.thresholdValue = new awt2swing.TextField (20); -this.currentColours = new awt2swing.Checkbox (); -this.borderLayout1 = new java.awt.BorderLayout (); -this.thresholdIsMin = new awt2swing.Checkbox (); -}); -Clazz.makeConstructor (c$, -function (av, ap) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []); -try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -this.oldcs = av.getGlobalColourScheme (); -if (av.getAlignment ().getGroups () != null) { -this.oldgroupColours = new java.util.Hashtable (); -for (var sg, $sg = ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.cs != null) { -this.oldgroupColours.put (sg, sg.cs); -} else { -this.oldgroupColours.put (sg, "null"); -}} -}this.av = av; -this.ap = ap; -this.slider.addAdjustmentListener (this); -this.slider.addMouseListener (this); -if (av.getAlignment ().getAlignmentAnnotation () == null) { -return; -}this.setDefaultMinMax (); -this.adjusting = true; -if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) { -var acg = this.oldcs; -this.currentColours.setState (acg.isPredefinedColours () || acg.getBaseColour () != null); -if (!acg.isPredefinedColours () && acg.getBaseColour () == null) { -this.minColour.setBackground (acg.getMinColour ()); -this.maxColour.setBackground (acg.getMaxColour ()); -}}var list = new java.util.Vector (); -var index = 1; -for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) { -var label = av.getAlignment ().getAlignmentAnnotation ()[i].label; -if (!list.contains (label)) { -list.addElement (label); -} else { -list.addElement (label + "_" + (index++)); -}} -for (var i = 0; i < list.size (); i++) { -this.annotations.addItem (list.elementAt (i).toString ()); -} -this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold")); -this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold")); -this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold")); -if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) { -var acg = this.oldcs; -this.annotations.select (acg.getAnnotation ()); -switch (acg.getAboveThreshold ()) { -case -1: -this.threshold.select (new Integer (0)); -break; -case 1: -this.threshold.select (new Integer (1)); -break; -case 0: -this.threshold.select (new Integer (1)); -break; -default: -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_dont_know_thereshold_annotationcolourgradient")); -} -this.thresholdIsMin.setState (acg.thresholdIsMinMax); -this.thresholdValue.setText ("" + acg.getAnnotationThreshold ()); -}this.adjusting = false; -this.changeColour (); -this.frame = new awt2swing.Frame (); -this.frame.add (this); -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.colour_by_annotation"), 560, 175); -this.validate (); -}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); -Clazz.defineMethod (c$, "setDefaultMinMax", -($fz = function () { -this.minColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MIN", java.awt.Color.orange)); -this.maxColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MAX", java.awt.Color.red)); -}, $fz.isPrivate = true, $fz)); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []); -try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.minColour.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.minColour.setLabel (jalview.util.MessageManager.getString ("label.min_colour")); -this.minColour.addActionListener (this); -this.maxColour.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.maxColour.setLabel (jalview.util.MessageManager.getString ("label.max_colour")); -this.maxColour.addActionListener (this); -this.thresholdIsMin.addItemListener (this); -this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok")); -this.ok.addActionListener (this); -this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel")); -this.cancel.addActionListener (this); -this.defColours.setLabel (jalview.util.MessageManager.getString ("action.set_defaults")); -this.defColours.addActionListener (this); -this.annotations.addItemListener (this); -this.thresholdValue.addActionListener (this); -this.slider.setBackground (java.awt.Color.white); -this.slider.setPreferredSize ( new java.awt.Dimension (193, 21)); -this.slider.setEnabled (false); -this.thresholdValue.setPreferredSize ( new java.awt.Dimension (79, 22)); -this.thresholdValue.setEnabled (false); -this.thresholdValue.setColumns (5); -this.currentColours.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.currentColours.setLabel (jalview.util.MessageManager.getString ("label.use_original_colours")); -this.currentColours.addItemListener (this); -this.thresholdIsMin.setBackground (java.awt.Color.white); -this.thresholdIsMin.setLabel (jalview.util.MessageManager.getString ("label.threshold_minmax")); -this.setLayout (this.borderLayout1); -this.jPanel1.setBackground (java.awt.Color.white); -this.jPanel2.setLayout ( new java.awt.FlowLayout ()); -this.jPanel2.setBackground (java.awt.Color.white); -this.threshold.addItemListener (this); -this.jPanel3.setLayout ( new java.awt.FlowLayout ()); -this.jPanel3.setBackground (java.awt.Color.white); -var jPanel4 = new awt2swing.Panel (); -jPanel4.setLayout ( new java.awt.BorderLayout ()); -jPanel4.setBackground (java.awt.Color.white); -this.jPanel1.add (this.ok); -this.jPanel1.add (this.cancel); -this.jPanel2.add (this.annotations); -this.jPanel2.add (this.currentColours); -this.jPanel2.add (this.minColour); -this.jPanel2.add (this.maxColour); -jPanel4.add (this.thresholdIsMin, "West"); -jPanel4.add (this.slider, "Center"); -jPanel4.add (this.thresholdValue, "East"); -var jPanel34 = new awt2swing.Panel (); -jPanel34.setLayout ( new java.awt.BorderLayout ()); -jPanel34.setBackground (java.awt.Color.white); -jPanel34.add (this.jPanel2, "North"); -jPanel34.add (this.threshold, "West"); -this.jPanel3.add (this.defColours); -jPanel34.add (this.jPanel3, "East"); -jPanel34.add (jPanel4, "South"); -this.add (jPanel34, "Center"); -this.add (this.jPanel1, "South"); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.thresholdValue) { -try { -var f = new Float (this.thresholdValue.getText ()).floatValue (); -this.slider.setValue (Clazz.floatToInt (f * 1000)); -this.adjustmentValueChanged (null); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -} else if (evt.getSource () === this.minColour) { -this.minColour_actionPerformed (null); -} else if (evt.getSource () === this.maxColour) { -this.maxColour_actionPerformed (null); -} else if (evt.getSource () === this.defColours) { -this.defColour_actionPerformed (); -} else if (evt.getSource () === this.ok) { -this.changeColour (); -this.frame.setVisible (false); -} else if (evt.getSource () === this.cancel) { -this.reset (); -this.ap.paintAlignment (true); -this.frame.setVisible (false); -} else { -this.changeColour (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -if (evt.getSource () === this.currentColours) { -if (this.currentColours.getState ()) { -this.reset (); -}this.maxColour.setEnabled (!this.currentColours.getState ()); -this.minColour.setEnabled (!this.currentColours.getState ()); -}this.changeColour (); -}, "java.awt.event.ItemEvent"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -if (!this.adjusting) { -this.thresholdValue.setText ((this.slider.getValue () / 1000) + ""); -if (this.currentColours.getState () && !(Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.AnnotationColourGradient))) { -this.changeColour (); -}this.currentAnnotation.threshold.value = this.slider.getValue () / 1000; -this.ap.paintAlignment (false); -}}, "java.awt.event.AdjustmentEvent"); -Clazz.defineMethod (c$, "minColour_actionPerformed", -function (newCol) { -if (newCol != null) { -this.minColour.setBackground (newCol); -this.minColour.repaint (); -this.changeColour (); -} else { - new jalview.appletgui.UserDefinedColours (this, "Min Colour", this.minColour.getBackground ()); -}}, "java.awt.Color"); -Clazz.defineMethod (c$, "maxColour_actionPerformed", -function (newCol) { -if (newCol != null) { -this.maxColour.setBackground (newCol); -this.maxColour.repaint (); -this.changeColour (); -} else { - new jalview.appletgui.UserDefinedColours (this, "Max Colour", this.maxColour.getBackground ()); -}}, "java.awt.Color"); -Clazz.defineMethod (c$, "defColour_actionPerformed", -function () { -this.setDefaultMinMax (); -this.minColour.repaint (); -this.maxColour.repaint (); -this.changeColour (); -}); -Clazz.defineMethod (c$, "changeColour", -function () { -if (this.adjusting) { -return; -}this.currentAnnotation = this.av.getAlignment ().getAlignmentAnnotation ()[this.annotations.getSelectedIndex ()]; -var aboveThreshold = -1; -if (this.threshold.getSelectedIndex () == 1) { -aboveThreshold = 1; -} else if (this.threshold.getSelectedIndex () == 2) { -aboveThreshold = 0; -}this.slider.setEnabled (true); -this.thresholdValue.setEnabled (true); -this.thresholdIsMin.setEnabled (true); -if (aboveThreshold == -1) { -this.slider.setEnabled (false); -this.thresholdValue.setEnabled (false); -this.thresholdIsMin.setEnabled (false); -this.thresholdValue.setText (""); -} else if (aboveThreshold != -1 && this.currentAnnotation.threshold == null) { -this.currentAnnotation.setThreshold ( new jalview.datamodel.GraphLine ((this.currentAnnotation.graphMax - this.currentAnnotation.graphMin) / 2, "Threshold", java.awt.Color.black)); -}if (aboveThreshold != -1) { -this.adjusting = true; -this.slider.setMinimum (Clazz.floatToInt (this.currentAnnotation.graphMin * 1000)); -this.slider.setMaximum (Clazz.floatToInt (this.currentAnnotation.graphMax * 1000)); -this.slider.setValue (Clazz.floatToInt (this.currentAnnotation.threshold.value * 1000)); -this.thresholdValue.setText (this.currentAnnotation.threshold.value + ""); -this.slider.setEnabled (true); -this.thresholdValue.setEnabled (true); -this.adjusting = false; -}var acg = null; -if (this.currentColours.getState ()) { -acg = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.av.getGlobalColourScheme (), aboveThreshold); -} else { -acg = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold); -}if (this.currentAnnotation.graphMin == 0 && this.currentAnnotation.graphMax == 0) { -acg.setPredefinedColours (true); -}acg.thresholdIsMinMax = this.thresholdIsMin.getState (); -this.av.setGlobalColourScheme (acg); -if (this.av.getAlignment ().getGroups () != null) { -for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.cs == null) { -continue; -}if (this.currentColours.getState ()) { -sg.cs = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, sg.cs, aboveThreshold); -} else { -sg.cs = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold); -}} -}this.ap.alignmentChanged (); -this.ap.paintAlignment (true); -}); -Clazz.defineMethod (c$, "reset", -function () { -this.av.setGlobalColourScheme (this.oldcs); -if (this.av.getAlignment ().getGroups () != null) { -for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -var cs = this.oldgroupColours.get (sg); -if (Clazz.instanceOf (cs, jalview.schemes.ColourSchemeI)) { -sg.cs = cs; -} else { -sg.cs = null; -}} -}this.ap.paintAlignment (true); -}); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.ap.paintAlignment (true); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Button", "$.Checkbox", "$.Choice", "$.Scrollbar", "$.TextField", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.AnnotationColourChooser", ["awt2swing.Frame", "jalview.appletgui.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.datamodel.GraphLine", "jalview.schemes.AnnotationColourGradient", "$.ColourSchemeI", "jalview.util.MessageManager", "java.awt.Color", "$.Dimension", "$.Font", "java.lang.Error", "$.Float", "java.util.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.frame = null; +this.av = null; +this.ap = null; +this.oldcs = null; +this.oldgroupColours = null; +this.currentAnnotation = null; +this.adjusting = false; +this.annotations = null; +this.minColour = null; +this.maxColour = null; +this.ok = null; +this.cancel = null; +this.defColours = null; +this.jPanel1 = null; +this.jPanel2 = null; +this.threshold = null; +this.flowLayout1 = null; +this.jPanel3 = null; +this.slider = null; +this.thresholdValue = null; +this.currentColours = null; +this.borderLayout1 = null; +this.thresholdIsMin = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AnnotationColourChooser", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]); +Clazz.prepareFields (c$, function () { +this.annotations = new awt2swing.Choice (); +this.minColour = new awt2swing.Button (); +this.maxColour = new awt2swing.Button (); +this.ok = new awt2swing.Button (); +this.cancel = new awt2swing.Button (); +this.defColours = new awt2swing.Button (); +this.jPanel1 = new awt2swing.Panel (); +this.jPanel2 = new awt2swing.Panel (); +this.threshold = new awt2swing.Choice (); +this.flowLayout1 = new java.awt.FlowLayout (); +this.jPanel3 = new awt2swing.Panel (); +this.slider = new awt2swing.Scrollbar (0); +this.thresholdValue = new awt2swing.TextField (20); +this.currentColours = new awt2swing.Checkbox (); +this.borderLayout1 = new java.awt.BorderLayout (); +this.thresholdIsMin = new awt2swing.Checkbox (); +}); +Clazz.makeConstructor (c$, +function (av, ap) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []); +try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +this.oldcs = av.getGlobalColourScheme (); +if (av.getAlignment ().getGroups () != null) { +this.oldgroupColours = new java.util.Hashtable (); +for (var sg, $sg = ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.cs != null) { +this.oldgroupColours.put (sg, sg.cs); +} else { +this.oldgroupColours.put (sg, "null"); +}} +}this.av = av; +this.ap = ap; +this.slider.addAdjustmentListener (this); +this.slider.addMouseListener (this); +if (av.getAlignment ().getAlignmentAnnotation () == null) { +return; +}this.setDefaultMinMax (); +this.adjusting = true; +if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) { +var acg = this.oldcs; +this.currentColours.setState (acg.isPredefinedColours () || acg.getBaseColour () != null); +if (!acg.isPredefinedColours () && acg.getBaseColour () == null) { +this.minColour.setBackground (acg.getMinColour ()); +this.maxColour.setBackground (acg.getMaxColour ()); +}}var list = new java.util.Vector (); +var index = 1; +for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) { +var label = av.getAlignment ().getAlignmentAnnotation ()[i].label; +if (!list.contains (label)) { +list.addElement (label); +} else { +list.addElement (label + "_" + (index++)); +}} +for (var i = 0; i < list.size (); i++) { +this.annotations.addItem (list.elementAt (i).toString ()); +} +this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold")); +this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold")); +this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold")); +if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) { +var acg = this.oldcs; +this.annotations.select (acg.getAnnotation ()); +switch (acg.getAboveThreshold ()) { +case -1: +this.threshold.select (new Integer (0)); +break; +case 1: +this.threshold.select (new Integer (1)); +break; +case 0: +this.threshold.select (new Integer (1)); +break; +default: +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_dont_know_thereshold_annotationcolourgradient")); +} +this.thresholdIsMin.setState (acg.thresholdIsMinMax); +this.thresholdValue.setText ("" + acg.getAnnotationThreshold ()); +}this.adjusting = false; +this.changeColour (); +this.frame = new awt2swing.Frame (); +this.frame.add (this); +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.colour_by_annotation"), 560, 175); +this.validate (); +}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); +Clazz.defineMethod (c$, "setDefaultMinMax", +($fz = function () { +this.minColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MIN", java.awt.Color.orange)); +this.maxColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MAX", java.awt.Color.red)); +}, $fz.isPrivate = true, $fz)); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []); +try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.minColour.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.minColour.setLabel (jalview.util.MessageManager.getString ("label.min_colour")); +this.minColour.addActionListener (this); +this.maxColour.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.maxColour.setLabel (jalview.util.MessageManager.getString ("label.max_colour")); +this.maxColour.addActionListener (this); +this.thresholdIsMin.addItemListener (this); +this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok")); +this.ok.addActionListener (this); +this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel")); +this.cancel.addActionListener (this); +this.defColours.setLabel (jalview.util.MessageManager.getString ("action.set_defaults")); +this.defColours.addActionListener (this); +this.annotations.addItemListener (this); +this.thresholdValue.addActionListener (this); +this.slider.setBackground (java.awt.Color.white); +this.slider.setPreferredSize ( new java.awt.Dimension (193, 21)); +this.slider.setEnabled (false); +this.thresholdValue.setPreferredSize ( new java.awt.Dimension (79, 22)); +this.thresholdValue.setEnabled (false); +this.thresholdValue.setColumns (5); +this.currentColours.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.currentColours.setLabel (jalview.util.MessageManager.getString ("label.use_original_colours")); +this.currentColours.addItemListener (this); +this.thresholdIsMin.setBackground (java.awt.Color.white); +this.thresholdIsMin.setLabel (jalview.util.MessageManager.getString ("label.threshold_minmax")); +this.setLayout (this.borderLayout1); +this.jPanel1.setBackground (java.awt.Color.white); +this.jPanel2.setLayout ( new java.awt.FlowLayout ()); +this.jPanel2.setBackground (java.awt.Color.white); +this.threshold.addItemListener (this); +this.jPanel3.setLayout ( new java.awt.FlowLayout ()); +this.jPanel3.setBackground (java.awt.Color.white); +var jPanel4 = new awt2swing.Panel (); +jPanel4.setLayout ( new java.awt.BorderLayout ()); +jPanel4.setBackground (java.awt.Color.white); +this.jPanel1.add (this.ok); +this.jPanel1.add (this.cancel); +this.jPanel2.add (this.annotations); +this.jPanel2.add (this.currentColours); +this.jPanel2.add (this.minColour); +this.jPanel2.add (this.maxColour); +jPanel4.add (this.thresholdIsMin, "West"); +jPanel4.add (this.slider, "Center"); +jPanel4.add (this.thresholdValue, "East"); +var jPanel34 = new awt2swing.Panel (); +jPanel34.setLayout ( new java.awt.BorderLayout ()); +jPanel34.setBackground (java.awt.Color.white); +jPanel34.add (this.jPanel2, "North"); +jPanel34.add (this.threshold, "West"); +this.jPanel3.add (this.defColours); +jPanel34.add (this.jPanel3, "East"); +jPanel34.add (jPanel4, "South"); +this.add (jPanel34, "Center"); +this.add (this.jPanel1, "South"); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.thresholdValue) { +try { +var f = new Float (this.thresholdValue.getText ()).floatValue (); +this.slider.setValue (Clazz.floatToInt (f * 1000)); +this.adjustmentValueChanged (null); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +} else if (evt.getSource () === this.minColour) { +this.minColour_actionPerformed (null); +} else if (evt.getSource () === this.maxColour) { +this.maxColour_actionPerformed (null); +} else if (evt.getSource () === this.defColours) { +this.defColour_actionPerformed (); +} else if (evt.getSource () === this.ok) { +this.changeColour (); +this.frame.setVisible (false); +} else if (evt.getSource () === this.cancel) { +this.reset (); +this.ap.paintAlignment (true); +this.frame.setVisible (false); +} else { +this.changeColour (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +if (evt.getSource () === this.currentColours) { +if (this.currentColours.getState ()) { +this.reset (); +}this.maxColour.setEnabled (!this.currentColours.getState ()); +this.minColour.setEnabled (!this.currentColours.getState ()); +}this.changeColour (); +}, "java.awt.event.ItemEvent"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +if (!this.adjusting) { +this.thresholdValue.setText ((this.slider.getValue () / 1000) + ""); +if (this.currentColours.getState () && !(Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.AnnotationColourGradient))) { +this.changeColour (); +}this.currentAnnotation.threshold.value = this.slider.getValue () / 1000; +this.ap.paintAlignment (false); +}}, "java.awt.event.AdjustmentEvent"); +Clazz.defineMethod (c$, "minColour_actionPerformed", +function (newCol) { +if (newCol != null) { +this.minColour.setBackground (newCol); +this.minColour.repaint (); +this.changeColour (); +} else { + new jalview.appletgui.UserDefinedColours (this, "Min Colour", this.minColour.getBackground ()); +}}, "java.awt.Color"); +Clazz.defineMethod (c$, "maxColour_actionPerformed", +function (newCol) { +if (newCol != null) { +this.maxColour.setBackground (newCol); +this.maxColour.repaint (); +this.changeColour (); +} else { + new jalview.appletgui.UserDefinedColours (this, "Max Colour", this.maxColour.getBackground ()); +}}, "java.awt.Color"); +Clazz.defineMethod (c$, "defColour_actionPerformed", +function () { +this.setDefaultMinMax (); +this.minColour.repaint (); +this.maxColour.repaint (); +this.changeColour (); +}); +Clazz.defineMethod (c$, "changeColour", +function () { +if (this.adjusting) { +return; +}this.currentAnnotation = this.av.getAlignment ().getAlignmentAnnotation ()[this.annotations.getSelectedIndex ()]; +var aboveThreshold = -1; +if (this.threshold.getSelectedIndex () == 1) { +aboveThreshold = 1; +} else if (this.threshold.getSelectedIndex () == 2) { +aboveThreshold = 0; +}this.slider.setEnabled (true); +this.thresholdValue.setEnabled (true); +this.thresholdIsMin.setEnabled (true); +if (aboveThreshold == -1) { +this.slider.setEnabled (false); +this.thresholdValue.setEnabled (false); +this.thresholdIsMin.setEnabled (false); +this.thresholdValue.setText (""); +} else if (aboveThreshold != -1 && this.currentAnnotation.threshold == null) { +this.currentAnnotation.setThreshold ( new jalview.datamodel.GraphLine ((this.currentAnnotation.graphMax - this.currentAnnotation.graphMin) / 2, "Threshold", java.awt.Color.black)); +}if (aboveThreshold != -1) { +this.adjusting = true; +this.slider.setMinimum (Clazz.floatToInt (this.currentAnnotation.graphMin * 1000)); +this.slider.setMaximum (Clazz.floatToInt (this.currentAnnotation.graphMax * 1000)); +this.slider.setValue (Clazz.floatToInt (this.currentAnnotation.threshold.value * 1000)); +this.thresholdValue.setText (this.currentAnnotation.threshold.value + ""); +this.slider.setEnabled (true); +this.thresholdValue.setEnabled (true); +this.adjusting = false; +}var acg = null; +if (this.currentColours.getState ()) { +acg = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.av.getGlobalColourScheme (), aboveThreshold); +} else { +acg = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold); +}if (this.currentAnnotation.graphMin == 0 && this.currentAnnotation.graphMax == 0) { +acg.setPredefinedColours (true); +}acg.thresholdIsMinMax = this.thresholdIsMin.getState (); +this.av.setGlobalColourScheme (acg); +if (this.av.getAlignment ().getGroups () != null) { +for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.cs == null) { +continue; +}if (this.currentColours.getState ()) { +sg.cs = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, sg.cs, aboveThreshold); +} else { +sg.cs = new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold); +}} +}this.ap.alignmentChanged (); +this.ap.paintAlignment (true); +}); +Clazz.defineMethod (c$, "reset", +function () { +this.av.setGlobalColourScheme (this.oldcs); +if (this.av.getAlignment ().getGroups () != null) { +for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +var cs = this.oldgroupColours.get (sg); +if (Clazz.instanceOf (cs, jalview.schemes.ColourSchemeI)) { +sg.cs = cs; +} else { +sg.cs = null; +}} +}this.ap.paintAlignment (true); +}); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.ap.paintAlignment (true); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +}); diff --git a/bin/jalview/appletgui/AnnotationColumnChooser.class b/bin/jalview/appletgui/AnnotationColumnChooser.class index 4cce256..27e6c60 100644 Binary files a/bin/jalview/appletgui/AnnotationColumnChooser.class and b/bin/jalview/appletgui/AnnotationColumnChooser.class differ diff --git a/bin/jalview/appletgui/AnnotationColumnChooser.js b/bin/jalview/appletgui/AnnotationColumnChooser.js index f50bb0c..340a161 100644 --- a/bin/jalview/appletgui/AnnotationColumnChooser.js +++ b/bin/jalview/appletgui/AnnotationColumnChooser.js @@ -1,622 +1,622 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "jalview.appletgui.AnnotationRowFilter", "$.TitledPanel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Checkbox", "$.Choice", "$.TextField", "java.awt.BorderLayout", "$.CardLayout"], "jalview.appletgui.AnnotationColumnChooser", ["awt2swing.Frame", "jalview.bin.JalviewLite", "jalview.datamodel.ColumnSelection", "$.GraphLine", "jalview.util.MessageManager", "jalview.viewmodel.annotationfilter.AnnotationFilterParameter", "java.awt.Color", "$.Dimension", "java.awt.event.MouseAdapter", "$.TextListener", "java.lang.Float", "java.util.Vector", "javax.swing.JPanel"], function () { -c$ = Clazz.decorateAsClass (function () { -this.annotations = null; -this.actionPanel = null; -this.thresholdPanel = null; -this.switchableViewsPanel = null; -this.switchableViewsLayout = null; -this.noGraphFilterView = null; -this.graphFilterView = null; -this.annotationComboBoxPanel = null; -this.borderLayout1 = null; -this.gBorderLayout = null; -this.ngBorderLayout = null; -this.threshold = null; -this.gStructureFilterPanel = null; -this.ngStructureFilterPanel = null; -this.currentStructureFilterPanel = null; -this.currentSearchPanel = null; -this.gSearchPanel = null; -this.ngSearchPanel = null; -this.currentFurtherActionPanel = null; -this.gFurtherActionPanel = null; -this.ngFurtherActionPanel = null; -this.actionOption = 1; -this.oldColumnSelection = null; -if (!Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel")) { -jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$FurtherActionPanel$ (); -} -if (!Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel")) { -jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$StructureFilterPanel$ (); -} -if (!Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser.SearchPanel")) { -jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$SearchPanel$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AnnotationColumnChooser", jalview.appletgui.AnnotationRowFilter, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]); -Clazz.prepareFields (c$, function () { -this.annotations = new awt2swing.Choice (); -this.actionPanel = new awt2swing.Panel (); -this.thresholdPanel = new jalview.appletgui.TitledPanel (); -this.switchableViewsPanel = new awt2swing.Panel ( new java.awt.CardLayout ()); -this.switchableViewsLayout = (this.switchableViewsPanel.getLayout ()); -this.noGraphFilterView = new awt2swing.Panel (); -this.graphFilterView = new awt2swing.Panel (); -this.annotationComboBoxPanel = new awt2swing.Panel (); -this.borderLayout1 = new java.awt.BorderLayout (); -this.gBorderLayout = new java.awt.BorderLayout (); -this.ngBorderLayout = new java.awt.BorderLayout (); -this.threshold = new awt2swing.Choice (); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser, []); -try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}); -Clazz.makeConstructor (c$, -function (av, ap) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser, [av, ap]); -this.frame = new awt2swing.Frame (); -this.frame.add (this); -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.select_by_annotation"), 520, 215); -this.slider.addAdjustmentListener (this); -this.slider.addMouseListener (this); -if (av.getAlignment ().getAlignmentAnnotation () == null) { -return; -}this.setOldColumnSelection (av.getColumnSelection ()); -this.adjusting = true; -var list = new java.util.Vector (); -var index = 1; -for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) { -var label = av.getAlignment ().getAlignmentAnnotation ()[i].label; -if (!list.contains (label)) { -list.addElement (label); -} else { -list.addElement (label + "_" + (index++)); -}} -for (var i = 0; i < list.size (); i++) { -this.annotations.addItem (list.elementAt (i).toString ()); -} -this.populateThresholdComboBox (this.threshold); -if (av.getAnnotationColumnSelectionState () != null) { -this.currentSearchPanel = av.getAnnotationColumnSelectionState ().getCurrentSearchPanel (); -this.currentStructureFilterPanel = av.getAnnotationColumnSelectionState ().getCurrentStructureFilterPanel (); -this.annotations.select (new Integer (av.getAnnotationColumnSelectionState ().getAnnotations ().getSelectedIndex ())); -this.threshold.select (new Integer (av.getAnnotationColumnSelectionState ().getThreshold ().getSelectedIndex ())); -this.actionOption = av.getAnnotationColumnSelectionState ().getActionOption (); -}try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -this.adjusting = false; -this.updateView (); -this.frame.invalidate (); -this.frame.pack (); -}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok")); -this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel")); -this.thresholdValue.setEnabled (false); -this.thresholdValue.setColumns (7); -this.ok.addActionListener (this); -this.cancel.addActionListener (this); -this.annotations.addItemListener (this); -this.thresholdValue.addActionListener (this); -this.threshold.addItemListener (this); -this.slider.setBackground (java.awt.Color.white); -this.slider.setEnabled (false); -this.slider.setPreferredSize ( new java.awt.Dimension (100, 32)); -this.thresholdPanel.setBackground (java.awt.Color.white); -this.actionPanel.setBackground (java.awt.Color.white); -this.graphFilterView.setLayout (this.gBorderLayout); -this.graphFilterView.setBackground (java.awt.Color.white); -this.noGraphFilterView.setLayout (this.ngBorderLayout); -this.noGraphFilterView.setBackground (java.awt.Color.white); -this.annotationComboBoxPanel.setBackground (java.awt.Color.white); -this.gSearchPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.SearchPanel, this, null, this); -this.ngSearchPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.SearchPanel, this, null, this); -this.gFurtherActionPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel, this, null, this); -this.ngFurtherActionPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel, this, null, this); -this.gStructureFilterPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel, this, null, this); -this.ngStructureFilterPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel, this, null, this); -this.thresholdPanel.setTitle ("Threshold Filter"); -this.thresholdPanel.add (this.getThreshold ()); -this.thresholdPanel.add (this.slider); -this.thresholdPanel.add (this.thresholdValue); -this.actionPanel.add (this.ok); -this.actionPanel.add (this.cancel); -var staticPanel = new javax.swing.JPanel (); -staticPanel.setLayout ( new java.awt.BorderLayout ()); -staticPanel.setBackground (java.awt.Color.white); -staticPanel.add (this.gSearchPanel, "North"); -staticPanel.add (this.gStructureFilterPanel, "South"); -this.graphFilterView.add (staticPanel, "North"); -this.graphFilterView.add (this.thresholdPanel, "Center"); -this.graphFilterView.add (this.gFurtherActionPanel, "South"); -this.noGraphFilterView.add (this.ngSearchPanel, "First"); -this.noGraphFilterView.add (this.ngStructureFilterPanel, "Center"); -this.noGraphFilterView.add (this.ngFurtherActionPanel, "Center"); -this.annotationComboBoxPanel.add (this.getAnnotations ()); -this.switchableViewsPanel.add (this.noGraphFilterView, jalview.appletgui.AnnotationColumnChooser.NO_GRAPH_VIEW); -this.switchableViewsPanel.add (this.graphFilterView, jalview.appletgui.AnnotationColumnChooser.GRAPH_VIEW); -this.setLayout (this.borderLayout1); -this.add (this.annotationComboBoxPanel, "First"); -this.add (this.switchableViewsPanel, "Center"); -this.add (this.actionPanel, "South"); -this.selectedAnnotationChanged (); -this.validate (); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "reset", -function () { -if (this.getOldColumnSelection () != null) { -this.av.getColumnSelection ().clear (); -if (this.av.getAnnotationColumnSelectionState () != null) { -var oldSelection = this.av.getAnnotationColumnSelectionState ().getOldColumnSelection (); -if (oldSelection != null && oldSelection.getHiddenColumns () != null && !oldSelection.getHiddenColumns ().isEmpty ()) { -for (var itr = oldSelection.getHiddenColumns ().iterator (); itr.hasNext (); ) { -var positions = itr.next (); -this.av.hideColumns (positions[0], positions[1]); -} -}this.av.setColumnSelection (oldSelection); -}this.ap.paintAlignment (true); -}}); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -if (!this.adjusting) { -this.thresholdValue.setText ((this.slider.getValue () / 1000) + ""); -this.valueChanged (!this.sliderDragging); -}}, "java.awt.event.AdjustmentEvent"); -Clazz.defineMethod (c$, "addSliderMouseListeners", -function () { -this.slider.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser$1") ? 0 : jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser$1, this, null))); -}); -Clazz.overrideMethod (c$, "valueChanged", -function (updateAllAnnotation) { -if (this.slider.isEnabled ()) { -this.getCurrentAnnotation ().threshold.value = this.slider.getValue () / 1000; -this.updateView (); -this.ap.paintAlignment (false); -}}, "~B"); -Clazz.defineMethod (c$, "getThreshold", -function () { -return this.threshold; -}); -Clazz.defineMethod (c$, "setThreshold", -function (threshold) { -this.threshold = threshold; -}, "awt2swing.Choice"); -Clazz.defineMethod (c$, "getAnnotations", -function () { -return this.annotations; -}); -Clazz.defineMethod (c$, "setAnnotations", -function (annotations) { -this.annotations = annotations; -}, "awt2swing.Choice"); -Clazz.overrideMethod (c$, "updateView", -function () { -if (this.adjusting) { -return; -}var filterParams = new jalview.viewmodel.annotationfilter.AnnotationFilterParameter (); -this.setCurrentAnnotation (this.av.getAlignment ().getAlignmentAnnotation ()[this.getAnnotations ().getSelectedIndex ()]); -var selectedThresholdItem = this.getSelectedThresholdItem (this.getThreshold ().getSelectedIndex ()); -this.slider.setEnabled (true); -this.thresholdValue.setEnabled (true); -if (selectedThresholdItem == -1) { -this.slider.setEnabled (false); -this.thresholdValue.setEnabled (false); -this.thresholdValue.setText (""); -} else if (selectedThresholdItem != -1) { -if (this.getCurrentAnnotation ().threshold == null) { -this.getCurrentAnnotation ().setThreshold ( new jalview.datamodel.GraphLine ((this.getCurrentAnnotation ().graphMax - this.getCurrentAnnotation ().graphMin) / 2, "Threshold", java.awt.Color.black)); -}this.adjusting = true; -var range = this.getCurrentAnnotation ().graphMax * 1000 - this.getCurrentAnnotation ().graphMin * 1000; -this.slider.setMinimum (Clazz.floatToInt (this.getCurrentAnnotation ().graphMin * 1000)); -this.slider.setMaximum (Clazz.floatToInt (this.getCurrentAnnotation ().graphMax * 1000)); -this.slider.setValue (Clazz.floatToInt (this.getCurrentAnnotation ().threshold.value * 1000)); -this.thresholdValue.setText (this.getCurrentAnnotation ().threshold.value + ""); -this.slider.setEnabled (true); -this.thresholdValue.setEnabled (true); -this.adjusting = false; -filterParams.setThresholdType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); -if (this.getCurrentAnnotation ().graph != 0) { -filterParams.setThresholdValue (this.getCurrentAnnotation ().threshold.value); -if (selectedThresholdItem == 1) { -filterParams.setThresholdType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD); -} else if (selectedThresholdItem == 0) { -filterParams.setThresholdType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD); -}}}if (this.currentStructureFilterPanel != null) { -if (this.currentStructureFilterPanel.alphaHelix.getState ()) { -filterParams.setFilterAlphaHelix (true); -}if (this.currentStructureFilterPanel.betaStrand.getState ()) { -filterParams.setFilterBetaSheet (true); -}if (this.currentStructureFilterPanel.turn.getState ()) { -filterParams.setFilterTurn (true); -}}if (this.currentSearchPanel != null) { -if (!this.currentSearchPanel.searchBox.getText ().isEmpty ()) { -this.currentSearchPanel.description.setEnabled (true); -this.currentSearchPanel.displayName.setEnabled (true); -filterParams.setRegexString (this.currentSearchPanel.searchBox.getText ()); -if (this.currentSearchPanel.displayName.getState ()) { -filterParams.addRegexSearchField (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING); -}if (this.currentSearchPanel.description.getState ()) { -filterParams.addRegexSearchField (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION); -}} else { -this.currentSearchPanel.description.setEnabled (false); -this.currentSearchPanel.displayName.setEnabled (false); -}}this.av.getColumnSelection ().filterAnnotations (this.getCurrentAnnotation ().annotations, filterParams); -this.av.showAllHiddenColumns (); -if (this.getActionOption () == jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE) { -this.av.hideSelectedColumns (); -}filterParams = null; -this.av.setAnnotationColumnSelectionState (this); -this.ap.paintAlignment (true); -}); -Clazz.defineMethod (c$, "getOldColumnSelection", -function () { -return this.oldColumnSelection; -}); -Clazz.defineMethod (c$, "setOldColumnSelection", -function (currentColumnSelection) { -if (currentColumnSelection != null) { -this.oldColumnSelection = new jalview.datamodel.ColumnSelection (currentColumnSelection); -}}, "jalview.datamodel.ColumnSelection"); -Clazz.defineMethod (c$, "getCurrentFutherActionPanel", -function () { -return this.currentFurtherActionPanel; -}); -Clazz.defineMethod (c$, "setCurrentFutherActionPanel", -function (currentFutherActionPanel) { -this.currentFurtherActionPanel = currentFutherActionPanel; -}, "jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel"); -Clazz.defineMethod (c$, "getCurrentSearchPanel", -function () { -return this.currentSearchPanel; -}); -Clazz.defineMethod (c$, "setCurrentSearchPanel", -function (currentSearchPanel) { -this.currentSearchPanel = currentSearchPanel; -}, "jalview.appletgui.AnnotationColumnChooser.SearchPanel"); -Clazz.defineMethod (c$, "getActionOption", -function () { -return this.actionOption; -}); -Clazz.defineMethod (c$, "setActionOption", -function (actionOption) { -this.actionOption = actionOption; -}, "~N"); -Clazz.defineMethod (c$, "getCurrentStructureFilterPanel", -function () { -return this.currentStructureFilterPanel; -}); -Clazz.defineMethod (c$, "setCurrentStructureFilterPanel", -function (currentStructureFilterPanel) { -this.currentStructureFilterPanel = currentStructureFilterPanel; -}, "jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -if (e.getSource () === this.annotations) { -this.selectedAnnotationChanged (); -} else if (e.getSource () === this.threshold) { -this.threshold_actionPerformed (null); -}}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "selectedAnnotationChanged", -function () { -var currentView = jalview.appletgui.AnnotationColumnChooser.NO_GRAPH_VIEW; -if (this.av.getAlignment ().getAlignmentAnnotation ()[this.getAnnotations ().getSelectedIndex ()].graph != 0) { -currentView = jalview.appletgui.AnnotationColumnChooser.GRAPH_VIEW; -}this.gSearchPanel.syncState (); -this.gFurtherActionPanel.syncState (); -this.gStructureFilterPanel.syncState (); -this.ngSearchPanel.syncState (); -this.ngFurtherActionPanel.syncState (); -this.ngStructureFilterPanel.syncState (); -this.switchableViewsLayout.show (this.switchableViewsPanel, currentView); -this.updateView (); -}); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.thresholdValue) { -try { -var f = new Float (this.thresholdValue.getText ()).floatValue (); -this.slider.setValue (Clazz.floatToInt (f * 1000)); -this.adjustmentValueChanged (null); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -} else if (evt.getSource () === this.ok) { -this.ok_actionPerformed (null); -} else if (evt.getSource () === this.cancel) { -this.cancel_actionPerformed (null); -} else if (evt.getSource () === this.thresholdValue) { -this.thresholdValue_actionPerformed (null); -} else { -this.updateView (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (e) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (e) { -if (e.getSource () === this.slider) { -this.updateView (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (e) { -if (e.getSource () === this.slider) { -this.updateView (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (e) { -if (e.getSource () === this.slider) { -this.updateView (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (e) { -if (e.getSource () === this.slider) { -this.updateView (); -}}, "java.awt.event.MouseEvent"); -c$.$AnnotationColumnChooser$FurtherActionPanel$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.aColChooser = null; -this.furtherAction = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.AnnotationColumnChooser, "FurtherActionPanel", awt2swing.Panel, java.awt.event.ItemListener); -Clazz.prepareFields (c$, function () { -this.furtherAction = new awt2swing.Choice (); -}); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel, []); -this.aColChooser = a; -this.furtherAction.addItem ("Select"); -this.furtherAction.addItem ("Hide"); -this.furtherAction.addItemListener (this); -this.syncState (); -this.add (this.furtherAction); -}, "jalview.appletgui.AnnotationColumnChooser"); -Clazz.defineMethod (c$, "syncState", -function () { -if (this.aColChooser.getActionOption () == jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE) { -this.furtherAction.select ("Hide"); -} else { -this.furtherAction.select ("Select"); -}}); -Clazz.overrideMethod (c$, "itemStateChanged", -function (a) { -this.aColChooser.setCurrentFutherActionPanel (this); -if (this.furtherAction.getSelectedItem ().toString ().equalsIgnoreCase ("Select")) { -this.b$["jalview.appletgui.AnnotationColumnChooser"].setActionOption (1); -this.b$["jalview.appletgui.AnnotationColumnChooser"].updateView (); -} else { -this.b$["jalview.appletgui.AnnotationColumnChooser"].setActionOption (jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE); -this.b$["jalview.appletgui.AnnotationColumnChooser"].updateView (); -}}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationColumnChooser$StructureFilterPanel$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.aColChooser = null; -this.alphaHelix = null; -this.betaStrand = null; -this.turn = null; -this.all = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.AnnotationColumnChooser, "StructureFilterPanel", jalview.appletgui.TitledPanel, java.awt.event.ItemListener); -Clazz.prepareFields (c$, function () { -this.alphaHelix = new awt2swing.Checkbox (); -this.betaStrand = new awt2swing.Checkbox (); -this.turn = new awt2swing.Checkbox (); -this.all = new awt2swing.Checkbox (); -}); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel, []); -this.aColChooser = a; -this.alphaHelix.setLabel (jalview.util.MessageManager.getString ("label.alpha_helix")); -this.alphaHelix.setBackground (java.awt.Color.white); -this.alphaHelix.addItemListener (this); -this.betaStrand.setLabel (jalview.util.MessageManager.getString ("label.beta_strand")); -this.betaStrand.setBackground (java.awt.Color.white); -this.betaStrand.addItemListener (this); -this.turn.setLabel (jalview.util.MessageManager.getString ("label.turn")); -this.turn.setBackground (java.awt.Color.white); -this.turn.addItemListener (this); -this.all.setLabel (jalview.util.MessageManager.getString ("label.select_all")); -this.all.setBackground (java.awt.Color.white); -this.all.addItemListener (this); -this.setBackground (java.awt.Color.white); -this.setTitle ("Structure Filter"); -this.add (this.all); -this.add (this.alphaHelix); -this.add (this.betaStrand); -this.add (this.turn); -}, "jalview.appletgui.AnnotationColumnChooser"); -Clazz.defineMethod (c$, "alphaHelix_actionPerformed", -function () { -this.updateSelectAllState (); -this.aColChooser.setCurrentStructureFilterPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "betaStrand_actionPerformed", -function () { -this.updateSelectAllState (); -this.aColChooser.setCurrentStructureFilterPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "turn_actionPerformed", -function () { -this.updateSelectAllState (); -this.aColChooser.setCurrentStructureFilterPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "all_actionPerformed", -function () { -if (this.all.getState ()) { -this.alphaHelix.setState (true); -this.betaStrand.setState (true); -this.turn.setState (true); -} else { -this.alphaHelix.setState (false); -this.betaStrand.setState (false); -this.turn.setState (false); -}this.aColChooser.setCurrentStructureFilterPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "updateSelectAllState", -function () { -if (this.alphaHelix.getState () && this.betaStrand.getState () && this.turn.getState ()) { -this.all.setState (true); -} else { -this.all.setState (false); -}}); -Clazz.defineMethod (c$, "syncState", -function () { -var a = this.aColChooser.getCurrentStructureFilterPanel (); -if (a != null) { -this.alphaHelix.setState (a.alphaHelix.getState ()); -this.betaStrand.setState (a.betaStrand.getState ()); -this.turn.setState (a.turn.getState ()); -if (a.all.getState ()) { -this.all.setState (true); -this.alphaHelix.setState (true); -this.betaStrand.setState (true); -this.turn.setState (true); -}}}); -Clazz.overrideMethod (c$, "itemStateChanged", -function (a) { -if (a.getSource () === this.alphaHelix) { -this.alphaHelix_actionPerformed (); -} else if (a.getSource () === this.betaStrand) { -this.betaStrand_actionPerformed (); -} else if (a.getSource () === this.turn) { -this.turn_actionPerformed (); -} else if (a.getSource () === this.all) { -this.all_actionPerformed (); -}}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationColumnChooser$SearchPanel$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.aColChooser = null; -this.displayName = null; -this.description = null; -this.searchBox = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.AnnotationColumnChooser, "SearchPanel", jalview.appletgui.TitledPanel, java.awt.event.ItemListener); -Clazz.prepareFields (c$, function () { -this.displayName = new awt2swing.Checkbox (); -this.description = new awt2swing.Checkbox (); -this.searchBox = new awt2swing.TextField (10); -}); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser.SearchPanel, []); -this.aColChooser = a; -this.searchBox.addTextListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser$SearchPanel$1") ? 0 : jalview.appletgui.AnnotationColumnChooser.SearchPanel.$AnnotationColumnChooser$SearchPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser$SearchPanel$1, this, null))); -this.displayName.setLabel (jalview.util.MessageManager.getString ("label.display_name")); -this.displayName.setEnabled (false); -this.displayName.addItemListener (this); -this.description.setLabel (jalview.util.MessageManager.getString ("label.description")); -this.description.setEnabled (false); -this.description.addItemListener (this); -this.setTitle ("Search Filter"); -this.syncState (); -this.add (this.searchBox); -this.add (this.displayName); -this.add (this.description); -}, "jalview.appletgui.AnnotationColumnChooser"); -Clazz.defineMethod (c$, "displayNameCheckboxAction", -function () { -this.aColChooser.setCurrentSearchPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "discriptionCheckboxAction", -function () { -this.aColChooser.setCurrentSearchPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "searchStringAction", -function () { -this.aColChooser.setCurrentSearchPanel (this); -this.aColChooser.updateView (); -}); -Clazz.defineMethod (c$, "syncState", -function () { -var a = this.aColChooser.getCurrentSearchPanel (); -if (a != null) { -this.description.setEnabled (a.description.isEnabled ()); -this.description.setState (a.description.getState ()); -this.displayName.setEnabled (a.displayName.isEnabled ()); -this.displayName.setState (a.displayName.getState ()); -this.searchBox.setText (a.searchBox.getText ()); -}}); -Clazz.overrideMethod (c$, "itemStateChanged", -function (a) { -if (a.getSource () === this.displayName) { -this.displayNameCheckboxAction (); -} else if (a.getSource () === this.description) { -this.discriptionCheckboxAction (); -}}, "java.awt.event.ItemEvent"); -c$.$AnnotationColumnChooser$SearchPanel$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationColumnChooser$SearchPanel$1", null, java.awt.event.TextListener); -Clazz.overrideMethod (c$, "textValueChanged", -function (a) { -this.b$["jalview.appletgui.AnnotationColumnChooser.SearchPanel"].searchStringAction (); -}, "java.awt.event.TextEvent"); -c$ = Clazz.p0p (); -}; -c$ = Clazz.p0p (); -}; -c$.$AnnotationColumnChooser$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationColumnChooser$1", java.awt.event.MouseAdapter); -Clazz.defineMethod (c$, "mousePressed", -function (e) { -this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging = true; -Clazz.superCall (this, jalview.appletgui.AnnotationColumnChooser$1, "mousePressed", [e]); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mouseDragged", -function (e) { -this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging = true; -Clazz.superCall (this, jalview.appletgui.AnnotationColumnChooser$1, "mouseDragged", [e]); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -if (this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging) { -this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging = false; -this.b$["jalview.appletgui.AnnotationColumnChooser"].valueChanged (true); -}this.b$["jalview.appletgui.AnnotationColumnChooser"].ap.paintAlignment (true); -}, "java.awt.event.MouseEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"ACTION_OPTION_SELECT", 1, -"ACTION_OPTION_HIDE", 2, -"NO_GRAPH_VIEW", "0", -"GRAPH_VIEW", "1"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "jalview.appletgui.AnnotationRowFilter", "$.TitledPanel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Checkbox", "$.Choice", "$.TextField", "java.awt.BorderLayout", "$.CardLayout"], "jalview.appletgui.AnnotationColumnChooser", ["awt2swing.Frame", "jalview.bin.JalviewLite", "jalview.datamodel.ColumnSelection", "$.GraphLine", "jalview.util.MessageManager", "jalview.viewmodel.annotationfilter.AnnotationFilterParameter", "java.awt.Color", "$.Dimension", "java.awt.event.MouseAdapter", "$.TextListener", "java.lang.Float", "java.util.Vector", "javax.swing.JPanel"], function () { +c$ = Clazz.decorateAsClass (function () { +this.annotations = null; +this.actionPanel = null; +this.thresholdPanel = null; +this.switchableViewsPanel = null; +this.switchableViewsLayout = null; +this.noGraphFilterView = null; +this.graphFilterView = null; +this.annotationComboBoxPanel = null; +this.borderLayout1 = null; +this.gBorderLayout = null; +this.ngBorderLayout = null; +this.threshold = null; +this.gStructureFilterPanel = null; +this.ngStructureFilterPanel = null; +this.currentStructureFilterPanel = null; +this.currentSearchPanel = null; +this.gSearchPanel = null; +this.ngSearchPanel = null; +this.currentFurtherActionPanel = null; +this.gFurtherActionPanel = null; +this.ngFurtherActionPanel = null; +this.actionOption = 1; +this.oldColumnSelection = null; +if (!Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel")) { +jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$FurtherActionPanel$ (); +} +if (!Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel")) { +jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$StructureFilterPanel$ (); +} +if (!Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser.SearchPanel")) { +jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$SearchPanel$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AnnotationColumnChooser", jalview.appletgui.AnnotationRowFilter, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]); +Clazz.prepareFields (c$, function () { +this.annotations = new awt2swing.Choice (); +this.actionPanel = new awt2swing.Panel (); +this.thresholdPanel = new jalview.appletgui.TitledPanel (); +this.switchableViewsPanel = new awt2swing.Panel ( new java.awt.CardLayout ()); +this.switchableViewsLayout = (this.switchableViewsPanel.getLayout ()); +this.noGraphFilterView = new awt2swing.Panel (); +this.graphFilterView = new awt2swing.Panel (); +this.annotationComboBoxPanel = new awt2swing.Panel (); +this.borderLayout1 = new java.awt.BorderLayout (); +this.gBorderLayout = new java.awt.BorderLayout (); +this.ngBorderLayout = new java.awt.BorderLayout (); +this.threshold = new awt2swing.Choice (); +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser, []); +try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}); +Clazz.makeConstructor (c$, +function (av, ap) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser, [av, ap]); +this.frame = new awt2swing.Frame (); +this.frame.add (this); +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.select_by_annotation"), 520, 215); +this.slider.addAdjustmentListener (this); +this.slider.addMouseListener (this); +if (av.getAlignment ().getAlignmentAnnotation () == null) { +return; +}this.setOldColumnSelection (av.getColumnSelection ()); +this.adjusting = true; +var list = new java.util.Vector (); +var index = 1; +for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) { +var label = av.getAlignment ().getAlignmentAnnotation ()[i].label; +if (!list.contains (label)) { +list.addElement (label); +} else { +list.addElement (label + "_" + (index++)); +}} +for (var i = 0; i < list.size (); i++) { +this.annotations.addItem (list.elementAt (i).toString ()); +} +this.populateThresholdComboBox (this.threshold); +if (av.getAnnotationColumnSelectionState () != null) { +this.currentSearchPanel = av.getAnnotationColumnSelectionState ().getCurrentSearchPanel (); +this.currentStructureFilterPanel = av.getAnnotationColumnSelectionState ().getCurrentStructureFilterPanel (); +this.annotations.select (new Integer (av.getAnnotationColumnSelectionState ().getAnnotations ().getSelectedIndex ())); +this.threshold.select (new Integer (av.getAnnotationColumnSelectionState ().getThreshold ().getSelectedIndex ())); +this.actionOption = av.getAnnotationColumnSelectionState ().getActionOption (); +}try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +this.adjusting = false; +this.updateView (); +this.frame.invalidate (); +this.frame.pack (); +}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok")); +this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel")); +this.thresholdValue.setEnabled (false); +this.thresholdValue.setColumns (7); +this.ok.addActionListener (this); +this.cancel.addActionListener (this); +this.annotations.addItemListener (this); +this.thresholdValue.addActionListener (this); +this.threshold.addItemListener (this); +this.slider.setBackground (java.awt.Color.white); +this.slider.setEnabled (false); +this.slider.setPreferredSize ( new java.awt.Dimension (100, 32)); +this.thresholdPanel.setBackground (java.awt.Color.white); +this.actionPanel.setBackground (java.awt.Color.white); +this.graphFilterView.setLayout (this.gBorderLayout); +this.graphFilterView.setBackground (java.awt.Color.white); +this.noGraphFilterView.setLayout (this.ngBorderLayout); +this.noGraphFilterView.setBackground (java.awt.Color.white); +this.annotationComboBoxPanel.setBackground (java.awt.Color.white); +this.gSearchPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.SearchPanel, this, null, this); +this.ngSearchPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.SearchPanel, this, null, this); +this.gFurtherActionPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel, this, null, this); +this.ngFurtherActionPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel, this, null, this); +this.gStructureFilterPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel, this, null, this); +this.ngStructureFilterPanel = Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel, this, null, this); +this.thresholdPanel.setTitle ("Threshold Filter"); +this.thresholdPanel.add (this.getThreshold ()); +this.thresholdPanel.add (this.slider); +this.thresholdPanel.add (this.thresholdValue); +this.actionPanel.add (this.ok); +this.actionPanel.add (this.cancel); +var staticPanel = new javax.swing.JPanel (); +staticPanel.setLayout ( new java.awt.BorderLayout ()); +staticPanel.setBackground (java.awt.Color.white); +staticPanel.add (this.gSearchPanel, "North"); +staticPanel.add (this.gStructureFilterPanel, "South"); +this.graphFilterView.add (staticPanel, "North"); +this.graphFilterView.add (this.thresholdPanel, "Center"); +this.graphFilterView.add (this.gFurtherActionPanel, "South"); +this.noGraphFilterView.add (this.ngSearchPanel, "First"); +this.noGraphFilterView.add (this.ngStructureFilterPanel, "Center"); +this.noGraphFilterView.add (this.ngFurtherActionPanel, "Center"); +this.annotationComboBoxPanel.add (this.getAnnotations ()); +this.switchableViewsPanel.add (this.noGraphFilterView, jalview.appletgui.AnnotationColumnChooser.NO_GRAPH_VIEW); +this.switchableViewsPanel.add (this.graphFilterView, jalview.appletgui.AnnotationColumnChooser.GRAPH_VIEW); +this.setLayout (this.borderLayout1); +this.add (this.annotationComboBoxPanel, "First"); +this.add (this.switchableViewsPanel, "Center"); +this.add (this.actionPanel, "South"); +this.selectedAnnotationChanged (); +this.validate (); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "reset", +function () { +if (this.getOldColumnSelection () != null) { +this.av.getColumnSelection ().clear (); +if (this.av.getAnnotationColumnSelectionState () != null) { +var oldSelection = this.av.getAnnotationColumnSelectionState ().getOldColumnSelection (); +if (oldSelection != null && oldSelection.getHiddenColumns () != null && !oldSelection.getHiddenColumns ().isEmpty ()) { +for (var itr = oldSelection.getHiddenColumns ().iterator (); itr.hasNext (); ) { +var positions = itr.next (); +this.av.hideColumns (positions[0], positions[1]); +} +}this.av.setColumnSelection (oldSelection); +}this.ap.paintAlignment (true); +}}); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +if (!this.adjusting) { +this.thresholdValue.setText ((this.slider.getValue () / 1000) + ""); +this.valueChanged (!this.sliderDragging); +}}, "java.awt.event.AdjustmentEvent"); +Clazz.defineMethod (c$, "addSliderMouseListeners", +function () { +this.slider.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser$1") ? 0 : jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser$1, this, null))); +}); +Clazz.overrideMethod (c$, "valueChanged", +function (updateAllAnnotation) { +if (this.slider.isEnabled ()) { +this.getCurrentAnnotation ().threshold.value = this.slider.getValue () / 1000; +this.updateView (); +this.ap.paintAlignment (false); +}}, "~B"); +Clazz.defineMethod (c$, "getThreshold", +function () { +return this.threshold; +}); +Clazz.defineMethod (c$, "setThreshold", +function (threshold) { +this.threshold = threshold; +}, "awt2swing.Choice"); +Clazz.defineMethod (c$, "getAnnotations", +function () { +return this.annotations; +}); +Clazz.defineMethod (c$, "setAnnotations", +function (annotations) { +this.annotations = annotations; +}, "awt2swing.Choice"); +Clazz.overrideMethod (c$, "updateView", +function () { +if (this.adjusting) { +return; +}var filterParams = new jalview.viewmodel.annotationfilter.AnnotationFilterParameter (); +this.setCurrentAnnotation (this.av.getAlignment ().getAlignmentAnnotation ()[this.getAnnotations ().getSelectedIndex ()]); +var selectedThresholdItem = this.getSelectedThresholdItem (this.getThreshold ().getSelectedIndex ()); +this.slider.setEnabled (true); +this.thresholdValue.setEnabled (true); +if (selectedThresholdItem == -1) { +this.slider.setEnabled (false); +this.thresholdValue.setEnabled (false); +this.thresholdValue.setText (""); +} else if (selectedThresholdItem != -1) { +if (this.getCurrentAnnotation ().threshold == null) { +this.getCurrentAnnotation ().setThreshold ( new jalview.datamodel.GraphLine ((this.getCurrentAnnotation ().graphMax - this.getCurrentAnnotation ().graphMin) / 2, "Threshold", java.awt.Color.black)); +}this.adjusting = true; +var range = this.getCurrentAnnotation ().graphMax * 1000 - this.getCurrentAnnotation ().graphMin * 1000; +this.slider.setMinimum (Clazz.floatToInt (this.getCurrentAnnotation ().graphMin * 1000)); +this.slider.setMaximum (Clazz.floatToInt (this.getCurrentAnnotation ().graphMax * 1000)); +this.slider.setValue (Clazz.floatToInt (this.getCurrentAnnotation ().threshold.value * 1000)); +this.thresholdValue.setText (this.getCurrentAnnotation ().threshold.value + ""); +this.slider.setEnabled (true); +this.thresholdValue.setEnabled (true); +this.adjusting = false; +filterParams.setThresholdType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); +if (this.getCurrentAnnotation ().graph != 0) { +filterParams.setThresholdValue (this.getCurrentAnnotation ().threshold.value); +if (selectedThresholdItem == 1) { +filterParams.setThresholdType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD); +} else if (selectedThresholdItem == 0) { +filterParams.setThresholdType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD); +}}}if (this.currentStructureFilterPanel != null) { +if (this.currentStructureFilterPanel.alphaHelix.getState ()) { +filterParams.setFilterAlphaHelix (true); +}if (this.currentStructureFilterPanel.betaStrand.getState ()) { +filterParams.setFilterBetaSheet (true); +}if (this.currentStructureFilterPanel.turn.getState ()) { +filterParams.setFilterTurn (true); +}}if (this.currentSearchPanel != null) { +if (!this.currentSearchPanel.searchBox.getText ().isEmpty ()) { +this.currentSearchPanel.description.setEnabled (true); +this.currentSearchPanel.displayName.setEnabled (true); +filterParams.setRegexString (this.currentSearchPanel.searchBox.getText ()); +if (this.currentSearchPanel.displayName.getState ()) { +filterParams.addRegexSearchField (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING); +}if (this.currentSearchPanel.description.getState ()) { +filterParams.addRegexSearchField (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION); +}} else { +this.currentSearchPanel.description.setEnabled (false); +this.currentSearchPanel.displayName.setEnabled (false); +}}this.av.getColumnSelection ().filterAnnotations (this.getCurrentAnnotation ().annotations, filterParams); +this.av.showAllHiddenColumns (); +if (this.getActionOption () == jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE) { +this.av.hideSelectedColumns (); +}filterParams = null; +this.av.setAnnotationColumnSelectionState (this); +this.ap.paintAlignment (true); +}); +Clazz.defineMethod (c$, "getOldColumnSelection", +function () { +return this.oldColumnSelection; +}); +Clazz.defineMethod (c$, "setOldColumnSelection", +function (currentColumnSelection) { +if (currentColumnSelection != null) { +this.oldColumnSelection = new jalview.datamodel.ColumnSelection (currentColumnSelection); +}}, "jalview.datamodel.ColumnSelection"); +Clazz.defineMethod (c$, "getCurrentFutherActionPanel", +function () { +return this.currentFurtherActionPanel; +}); +Clazz.defineMethod (c$, "setCurrentFutherActionPanel", +function (currentFutherActionPanel) { +this.currentFurtherActionPanel = currentFutherActionPanel; +}, "jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel"); +Clazz.defineMethod (c$, "getCurrentSearchPanel", +function () { +return this.currentSearchPanel; +}); +Clazz.defineMethod (c$, "setCurrentSearchPanel", +function (currentSearchPanel) { +this.currentSearchPanel = currentSearchPanel; +}, "jalview.appletgui.AnnotationColumnChooser.SearchPanel"); +Clazz.defineMethod (c$, "getActionOption", +function () { +return this.actionOption; +}); +Clazz.defineMethod (c$, "setActionOption", +function (actionOption) { +this.actionOption = actionOption; +}, "~N"); +Clazz.defineMethod (c$, "getCurrentStructureFilterPanel", +function () { +return this.currentStructureFilterPanel; +}); +Clazz.defineMethod (c$, "setCurrentStructureFilterPanel", +function (currentStructureFilterPanel) { +this.currentStructureFilterPanel = currentStructureFilterPanel; +}, "jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +if (e.getSource () === this.annotations) { +this.selectedAnnotationChanged (); +} else if (e.getSource () === this.threshold) { +this.threshold_actionPerformed (null); +}}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "selectedAnnotationChanged", +function () { +var currentView = jalview.appletgui.AnnotationColumnChooser.NO_GRAPH_VIEW; +if (this.av.getAlignment ().getAlignmentAnnotation ()[this.getAnnotations ().getSelectedIndex ()].graph != 0) { +currentView = jalview.appletgui.AnnotationColumnChooser.GRAPH_VIEW; +}this.gSearchPanel.syncState (); +this.gFurtherActionPanel.syncState (); +this.gStructureFilterPanel.syncState (); +this.ngSearchPanel.syncState (); +this.ngFurtherActionPanel.syncState (); +this.ngStructureFilterPanel.syncState (); +this.switchableViewsLayout.show (this.switchableViewsPanel, currentView); +this.updateView (); +}); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.thresholdValue) { +try { +var f = new Float (this.thresholdValue.getText ()).floatValue (); +this.slider.setValue (Clazz.floatToInt (f * 1000)); +this.adjustmentValueChanged (null); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +} else if (evt.getSource () === this.ok) { +this.ok_actionPerformed (null); +} else if (evt.getSource () === this.cancel) { +this.cancel_actionPerformed (null); +} else if (evt.getSource () === this.thresholdValue) { +this.thresholdValue_actionPerformed (null); +} else { +this.updateView (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (e) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (e) { +if (e.getSource () === this.slider) { +this.updateView (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (e) { +if (e.getSource () === this.slider) { +this.updateView (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (e) { +if (e.getSource () === this.slider) { +this.updateView (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (e) { +if (e.getSource () === this.slider) { +this.updateView (); +}}, "java.awt.event.MouseEvent"); +c$.$AnnotationColumnChooser$FurtherActionPanel$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.aColChooser = null; +this.furtherAction = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.AnnotationColumnChooser, "FurtherActionPanel", awt2swing.Panel, java.awt.event.ItemListener); +Clazz.prepareFields (c$, function () { +this.furtherAction = new awt2swing.Choice (); +}); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel, []); +this.aColChooser = a; +this.furtherAction.addItem ("Select"); +this.furtherAction.addItem ("Hide"); +this.furtherAction.addItemListener (this); +this.syncState (); +this.add (this.furtherAction); +}, "jalview.appletgui.AnnotationColumnChooser"); +Clazz.defineMethod (c$, "syncState", +function () { +if (this.aColChooser.getActionOption () == jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE) { +this.furtherAction.select ("Hide"); +} else { +this.furtherAction.select ("Select"); +}}); +Clazz.overrideMethod (c$, "itemStateChanged", +function (a) { +this.aColChooser.setCurrentFutherActionPanel (this); +if (this.furtherAction.getSelectedItem ().toString ().equalsIgnoreCase ("Select")) { +this.b$["jalview.appletgui.AnnotationColumnChooser"].setActionOption (1); +this.b$["jalview.appletgui.AnnotationColumnChooser"].updateView (); +} else { +this.b$["jalview.appletgui.AnnotationColumnChooser"].setActionOption (jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE); +this.b$["jalview.appletgui.AnnotationColumnChooser"].updateView (); +}}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationColumnChooser$StructureFilterPanel$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.aColChooser = null; +this.alphaHelix = null; +this.betaStrand = null; +this.turn = null; +this.all = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.AnnotationColumnChooser, "StructureFilterPanel", jalview.appletgui.TitledPanel, java.awt.event.ItemListener); +Clazz.prepareFields (c$, function () { +this.alphaHelix = new awt2swing.Checkbox (); +this.betaStrand = new awt2swing.Checkbox (); +this.turn = new awt2swing.Checkbox (); +this.all = new awt2swing.Checkbox (); +}); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel, []); +this.aColChooser = a; +this.alphaHelix.setLabel (jalview.util.MessageManager.getString ("label.alpha_helix")); +this.alphaHelix.setBackground (java.awt.Color.white); +this.alphaHelix.addItemListener (this); +this.betaStrand.setLabel (jalview.util.MessageManager.getString ("label.beta_strand")); +this.betaStrand.setBackground (java.awt.Color.white); +this.betaStrand.addItemListener (this); +this.turn.setLabel (jalview.util.MessageManager.getString ("label.turn")); +this.turn.setBackground (java.awt.Color.white); +this.turn.addItemListener (this); +this.all.setLabel (jalview.util.MessageManager.getString ("label.select_all")); +this.all.setBackground (java.awt.Color.white); +this.all.addItemListener (this); +this.setBackground (java.awt.Color.white); +this.setTitle ("Structure Filter"); +this.add (this.all); +this.add (this.alphaHelix); +this.add (this.betaStrand); +this.add (this.turn); +}, "jalview.appletgui.AnnotationColumnChooser"); +Clazz.defineMethod (c$, "alphaHelix_actionPerformed", +function () { +this.updateSelectAllState (); +this.aColChooser.setCurrentStructureFilterPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "betaStrand_actionPerformed", +function () { +this.updateSelectAllState (); +this.aColChooser.setCurrentStructureFilterPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "turn_actionPerformed", +function () { +this.updateSelectAllState (); +this.aColChooser.setCurrentStructureFilterPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "all_actionPerformed", +function () { +if (this.all.getState ()) { +this.alphaHelix.setState (true); +this.betaStrand.setState (true); +this.turn.setState (true); +} else { +this.alphaHelix.setState (false); +this.betaStrand.setState (false); +this.turn.setState (false); +}this.aColChooser.setCurrentStructureFilterPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "updateSelectAllState", +function () { +if (this.alphaHelix.getState () && this.betaStrand.getState () && this.turn.getState ()) { +this.all.setState (true); +} else { +this.all.setState (false); +}}); +Clazz.defineMethod (c$, "syncState", +function () { +var a = this.aColChooser.getCurrentStructureFilterPanel (); +if (a != null) { +this.alphaHelix.setState (a.alphaHelix.getState ()); +this.betaStrand.setState (a.betaStrand.getState ()); +this.turn.setState (a.turn.getState ()); +if (a.all.getState ()) { +this.all.setState (true); +this.alphaHelix.setState (true); +this.betaStrand.setState (true); +this.turn.setState (true); +}}}); +Clazz.overrideMethod (c$, "itemStateChanged", +function (a) { +if (a.getSource () === this.alphaHelix) { +this.alphaHelix_actionPerformed (); +} else if (a.getSource () === this.betaStrand) { +this.betaStrand_actionPerformed (); +} else if (a.getSource () === this.turn) { +this.turn_actionPerformed (); +} else if (a.getSource () === this.all) { +this.all_actionPerformed (); +}}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationColumnChooser$SearchPanel$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.aColChooser = null; +this.displayName = null; +this.description = null; +this.searchBox = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.AnnotationColumnChooser, "SearchPanel", jalview.appletgui.TitledPanel, java.awt.event.ItemListener); +Clazz.prepareFields (c$, function () { +this.displayName = new awt2swing.Checkbox (); +this.description = new awt2swing.Checkbox (); +this.searchBox = new awt2swing.TextField (10); +}); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationColumnChooser.SearchPanel, []); +this.aColChooser = a; +this.searchBox.addTextListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationColumnChooser$SearchPanel$1") ? 0 : jalview.appletgui.AnnotationColumnChooser.SearchPanel.$AnnotationColumnChooser$SearchPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationColumnChooser$SearchPanel$1, this, null))); +this.displayName.setLabel (jalview.util.MessageManager.getString ("label.display_name")); +this.displayName.setEnabled (false); +this.displayName.addItemListener (this); +this.description.setLabel (jalview.util.MessageManager.getString ("label.description")); +this.description.setEnabled (false); +this.description.addItemListener (this); +this.setTitle ("Search Filter"); +this.syncState (); +this.add (this.searchBox); +this.add (this.displayName); +this.add (this.description); +}, "jalview.appletgui.AnnotationColumnChooser"); +Clazz.defineMethod (c$, "displayNameCheckboxAction", +function () { +this.aColChooser.setCurrentSearchPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "discriptionCheckboxAction", +function () { +this.aColChooser.setCurrentSearchPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "searchStringAction", +function () { +this.aColChooser.setCurrentSearchPanel (this); +this.aColChooser.updateView (); +}); +Clazz.defineMethod (c$, "syncState", +function () { +var a = this.aColChooser.getCurrentSearchPanel (); +if (a != null) { +this.description.setEnabled (a.description.isEnabled ()); +this.description.setState (a.description.getState ()); +this.displayName.setEnabled (a.displayName.isEnabled ()); +this.displayName.setState (a.displayName.getState ()); +this.searchBox.setText (a.searchBox.getText ()); +}}); +Clazz.overrideMethod (c$, "itemStateChanged", +function (a) { +if (a.getSource () === this.displayName) { +this.displayNameCheckboxAction (); +} else if (a.getSource () === this.description) { +this.discriptionCheckboxAction (); +}}, "java.awt.event.ItemEvent"); +c$.$AnnotationColumnChooser$SearchPanel$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationColumnChooser$SearchPanel$1", null, java.awt.event.TextListener); +Clazz.overrideMethod (c$, "textValueChanged", +function (a) { +this.b$["jalview.appletgui.AnnotationColumnChooser.SearchPanel"].searchStringAction (); +}, "java.awt.event.TextEvent"); +c$ = Clazz.p0p (); +}; +c$ = Clazz.p0p (); +}; +c$.$AnnotationColumnChooser$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationColumnChooser$1", java.awt.event.MouseAdapter); +Clazz.defineMethod (c$, "mousePressed", +function (e) { +this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging = true; +Clazz.superCall (this, jalview.appletgui.AnnotationColumnChooser$1, "mousePressed", [e]); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mouseDragged", +function (e) { +this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging = true; +Clazz.superCall (this, jalview.appletgui.AnnotationColumnChooser$1, "mouseDragged", [e]); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +if (this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging) { +this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging = false; +this.b$["jalview.appletgui.AnnotationColumnChooser"].valueChanged (true); +}this.b$["jalview.appletgui.AnnotationColumnChooser"].ap.paintAlignment (true); +}, "java.awt.event.MouseEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"ACTION_OPTION_SELECT", 1, +"ACTION_OPTION_HIDE", 2, +"NO_GRAPH_VIEW", "0", +"GRAPH_VIEW", "1"); +}); diff --git a/bin/jalview/appletgui/AnnotationLabels.class b/bin/jalview/appletgui/AnnotationLabels.class index 89f6aaa..e82534c 100644 Binary files a/bin/jalview/appletgui/AnnotationLabels.class and b/bin/jalview/appletgui/AnnotationLabels.class differ diff --git a/bin/jalview/appletgui/AnnotationLabels.js b/bin/jalview/appletgui/AnnotationLabels.js index 195bfa5..27cabd2 100644 --- a/bin/jalview/appletgui/AnnotationLabels.js +++ b/bin/jalview/appletgui/AnnotationLabels.js @@ -1,466 +1,466 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.AnnotationLabels", ["awt2swing.Checkbox", "$.CheckboxMenuItem", "$.Frame", "$.MenuItem", "$.PopupMenu", "jalview.analysis.AlignmentUtils", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.EditNameDialog", "$.PaintRefresher", "$.Tooltip", "jalview.bin.JalviewLite", "jalview.datamodel.AlignmentAnnotation", "$.SequenceGroup", "jalview.util.MessageManager", "$.ParseHtmlBodyAndLinks", "java.awt.Color", "$.Dimension", "$.FlowLayout", "java.awt.event.ItemListener", "java.lang.StringBuffer", "java.util.Arrays", "$.Collections", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.image = null; -this.active = false; -this.ap = null; -this.av = null; -this.resizing = false; -this.oldY = 0; -this.mouseX = 0; -this.scrollOffset = 0; -this.selectedRow = -1; -this.tooltip = null; -this.hasHiddenRows = false; -this.resizePanel = false; -this.dragEvent = null; -this.dragCancelled = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AnnotationLabels", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationLabels, []); -this.ap = ap; -this.av = ap.av; -this.setLayout (null); -this.addMouseListener (this); -this.addMouseMotionListener (this); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationLabels, []); -this.av = av; -}, "jalview.appletgui.AlignViewport"); -Clazz.defineMethod (c$, "setScrollOffset", -function (y, repaint) { -this.scrollOffset = y; -if (repaint) { -this.repaint (); -}}, "~N,~B"); -Clazz.defineMethod (c$, "getSelectedRow", -function (y) { -var row = -2; -var aa = this.ap.av.getAlignment ().getAlignmentAnnotation (); -if (aa == null) { -return row; -}var height = 0; -for (var i = 0; i < aa.length; i++) { -row = -1; -if (!aa[i].visible) { -continue; -}height += aa[i].height; -if (y < height) { -row = i; -break; -}} -return row; -}, "~N"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -var aa = this.av.getAlignment ().getAlignmentAnnotation (); -if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.ADDNEW)) { -var newAnnotation = new jalview.datamodel.AlignmentAnnotation ("", null, new Array (this.ap.av.getAlignment ().getWidth ())); -if (!this.editLabelDescription (newAnnotation)) { -return; -}this.ap.av.getAlignment ().addAnnotation (newAnnotation); -this.ap.av.getAlignment ().setAnnotationIndex (newAnnotation, 0); -} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.EDITNAME)) { -this.editLabelDescription (aa[this.selectedRow]); -} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.HIDE)) { -aa[this.selectedRow].visible = false; -} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.SHOWALL)) { -for (var i = 0; i < aa.length; i++) { -aa[i].visible = (aa[i].annotations == null) ? false : true; -} -} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.OUTPUT_TEXT)) { -var cap = new jalview.appletgui.CutAndPasteTransfer (false, this.ap.alignFrame); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, this.ap.alignFrame.getTitle () + " - " + aa[this.selectedRow].label, 500, 100); -cap.setText (aa[this.selectedRow].toString ()); -} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.COPYCONS_SEQ)) { -var cons = this.av.getConsensusSeq (); -if (cons != null) { -this.copy_annotseqtoclipboard (cons); -}}this.refresh (); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "refresh", -function () { -this.ap.annotationPanel.adjustPanelHeight (); -this.setSize (this.getSize ().width, this.ap.annotationPanel.getSize ().height); -this.ap.validate (); -this.ap.paintAlignment (true); -}); -Clazz.defineMethod (c$, "editLabelDescription", -function (annotation) { -var padGaps = new awt2swing.Checkbox ("Fill Empty Gaps With \"" + this.ap.av.getGapCharacter () + "\"", annotation.padGaps); -var dialog = new jalview.appletgui.EditNameDialog (annotation.label, annotation.description, " Annotation Label", "Annotation Description", this.ap.alignFrame, "Edit Annotation Name / Description", 500, 180, false); -var empty = new awt2swing.Panel ( new java.awt.FlowLayout ()); -empty.add (padGaps); -dialog.add (empty); -dialog.pack (); -dialog.setVisible (true); -if (dialog.accept) { -annotation.label = dialog.getName (); -annotation.description = dialog.getDescription (); -annotation.setPadGaps (padGaps.getState (), this.av.getGapCharacter ()); -this.repaint (); -return true; -} else { -return false; -}}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -this.resizePanel = evt.getY () < 10 && evt.getX () < 14; -var row = this.getSelectedRow (evt.getY () + this.scrollOffset); -if (row > -1) { -var phb = new jalview.util.ParseHtmlBodyAndLinks (this.av.getAlignment ().getAlignmentAnnotation ()[row].getDescription (true), true, "\n"); -if (this.tooltip == null) { -this.tooltip = new jalview.appletgui.Tooltip (phb.getNonHtmlContent (), this); -} else { -this.tooltip.setTip (phb.getNonHtmlContent ()); -}} else if (this.tooltip != null) { -this.tooltip.setTip (""); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "cancelDrag", -function () { -this.dragEvent = null; -this.dragCancelled = true; -}); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -if (this.dragCancelled) { -return; -};this.dragEvent = evt; -if (this.resizePanel) { -var d = this.ap.annotationPanelHolder.getSize (); -var e = this.ap.annotationSpaceFillerHolder.getSize (); -var f = this.ap.seqPanelHolder.getSize (); -var dif = evt.getY () - this.oldY; -dif /= this.ap.av.getCharHeight (); -dif *= this.ap.av.getCharHeight (); -if ((d.height - dif) > 20 && (f.height + dif) > 20) { -this.ap.annotationPanel.setSize (d.width, d.height - dif); -this.setSize ( new java.awt.Dimension (e.width, d.height - dif)); -this.ap.annotationSpaceFillerHolder.setSize ( new java.awt.Dimension (e.width, d.height - dif)); -this.ap.annotationPanelHolder.setSize ( new java.awt.Dimension (d.width, d.height - dif)); -this.ap.apvscroll.setValues (this.ap.apvscroll.getValue (), d.height - dif, 0, this.av.calcPanelHeight ()); -f.height += dif; -this.ap.seqPanelHolder.setPreferredSize (f); -this.ap.setScrollValues (this.av.getStartRes (), this.av.getStartSeq ()); -this.ap.validate (); -this.ap.addNotify (); -}} else { -var diff; -if ((diff = 6 - evt.getY ()) > 0) { -this.ap.apvscroll.setValue (this.ap.apvscroll.getValue () - diff); -this.ap.adjustmentValueChanged (null); -} else if ((0 < (diff = 6 - this.ap.annotationSpaceFillerHolder.getSize ().height + evt.getY ()))) { -this.ap.apvscroll.setValue (this.ap.apvscroll.getValue () + diff); -this.ap.adjustmentValueChanged (null); -}this.repaint (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -if (!this.resizePanel && !this.dragCancelled) { -var start = this.selectedRow; -var end = this.getSelectedRow (evt.getY () + this.scrollOffset); -if (start > -1 && start != end) { -var startAA = this.ap.av.getAlignment ().getAlignmentAnnotation ()[start]; -if (end == -1) { -end = this.ap.av.getAlignment ().getAlignmentAnnotation ().length - 1; -}var endAA = this.ap.av.getAlignment ().getAlignmentAnnotation ()[end]; -this.ap.av.getAlignment ().getAlignmentAnnotation ()[end] = startAA; -this.ap.av.getAlignment ().getAlignmentAnnotation ()[start] = endAA; -}}this.resizePanel = false; -this.dragEvent = null; -this.dragCancelled = false; -this.repaint (); -this.ap.annotationPanel.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -if (evt.getY () < 10 && evt.getX () < 14) { -this.resizePanel = true; -this.repaint (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -this.dragCancelled = false; -if (this.dragEvent == null) { -this.resizePanel = false; -} else { -if (!this.resizePanel) { -this.dragEvent = null; -}}this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -this.oldY = evt.getY (); -if (this.resizePanel) { -return; -}this.dragCancelled = false; -this.selectedRow = this.getSelectedRow (evt.getY () + this.scrollOffset); -var aa = this.ap.av.getAlignment ().getAlignmentAnnotation (); -if ((evt.getModifiers () & 4) == 4) { -var popup = new awt2swing.PopupMenu (jalview.util.MessageManager.getString ("label.annotations")); -var item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.ADDNEW); -item.addActionListener (this); -popup.add (item); -if (this.selectedRow < 0) { -if (this.hasHiddenRows) { -item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.SHOWALL); -item.addActionListener (this); -popup.add (item); -}this.add (popup); -popup.show (this, evt.getX (), evt.getY ()); -return; -}item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.EDITNAME); -item.addActionListener (this); -popup.add (item); -item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.HIDE); -item.addActionListener (this); -popup.add (item); -if (this.selectedRow < aa.length) { -if (aa[this.selectedRow].sequenceRef != null) { -var label = aa[this.selectedRow].label; -var hideType = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.hide_all") + " " + label); -hideType.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$1") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$1, this, Clazz.cloneFinals ("label", label)))); -popup.add (hideType); -}}if (this.hasHiddenRows) { -item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.SHOWALL); -item.addActionListener (this); -popup.add (item); -}this.add (popup); -item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.OUTPUT_TEXT); -item.addActionListener (this); -popup.add (item); -if (this.selectedRow < aa.length) { -if (aa[this.selectedRow].autoCalculated) { -if (aa[this.selectedRow].label.indexOf ("Consensus") > -1) { -popup.addSeparator (); -var cbmi = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.ignore_gaps_consensus"), (aa[this.selectedRow].groupRef != null) ? aa[this.selectedRow].groupRef.getIgnoreGapsConsensus () : this.ap.av.isIgnoreGapsConsensus ()); -var aaa = aa[this.selectedRow]; -cbmi.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$2") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$2, this, Clazz.cloneFinals ("aaa", aaa, "cbmi", cbmi)))); -popup.add (cbmi); -if (aaa.groupRef != null) { -var chist = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_group_histogram"), aa[this.selectedRow].groupRef.isShowConsensusHistogram ()); -chist.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$3") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$3, this, Clazz.cloneFinals ("aaa", aaa, "chist", chist)))); -popup.add (chist); -var cprofl = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_group_logo"), aa[this.selectedRow].groupRef.isShowSequenceLogo ()); -cprofl.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$4") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$4, this, Clazz.cloneFinals ("aaa", aaa, "cprofl", cprofl)))); -popup.add (cprofl); -var cprofn = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.normalise_group_logo"), aa[this.selectedRow].groupRef.isNormaliseSequenceLogo ()); -cprofn.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$5") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$5, this, Clazz.cloneFinals ("aaa", aaa, "cprofn", cprofn)))); -popup.add (cprofn); -} else { -var chist = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_histogram"), this.av.isShowConsensusHistogram ()); -chist.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$6") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$6$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$6, this, Clazz.cloneFinals ("chist", chist)))); -popup.add (chist); -var cprof = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_logo"), this.av.isShowSequenceLogo ()); -cprof.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$7") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$7$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$7, this, Clazz.cloneFinals ("cprof", cprof)))); -popup.add (cprof); -var cprofn = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.normalise_logo"), this.av.isNormaliseSequenceLogo ()); -cprofn.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$8") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$8$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$8, this, Clazz.cloneFinals ("cprofn", cprofn)))); -popup.add (cprofn); -}item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.COPYCONS_SEQ); -item.addActionListener (this); -popup.add (item); -}}}popup.show (this, evt.getX (), evt.getY ()); -} else { -if (this.selectedRow > -1 && this.selectedRow < aa.length) { -if (aa[this.selectedRow].groupRef != null) { -if (evt.getClickCount () >= 2) { -this.ap.seqPanel.ap.idPanel.highlightSearchResults (null); -this.ap.av.setSelectionGroup (aa[this.selectedRow].groupRef); -this.ap.av.sendSelection (); -this.ap.paintAlignment (false); -jalview.appletgui.PaintRefresher.Refresh (this.ap, this.ap.av.getSequenceSetId ()); -} else { -this.ap.seqPanel.ap.idPanel.highlightSearchResults (aa[this.selectedRow].groupRef.getSequences (null)); -}return; -} else if (aa[this.selectedRow].sequenceRef != null) { -if (evt.getClickCount () == 1) { -this.ap.seqPanel.ap.idPanel.highlightSearchResults (java.util.Arrays.asList ( Clazz.newArray (-1, [aa[this.selectedRow].sequenceRef]))); -} else if (evt.getClickCount () >= 2) { -this.ap.seqPanel.ap.idPanel.highlightSearchResults (null); -var sg = this.ap.av.getSelectionGroup (); -if (sg != null) { -if (!(evt.isControlDown () || evt.isShiftDown ())) { -sg = new jalview.datamodel.SequenceGroup (sg); -sg.clear (); -sg.addSequence (aa[this.selectedRow].sequenceRef, false); -} else { -if (evt.isControlDown ()) { -sg.addOrRemove (aa[this.selectedRow].sequenceRef, true); -} else { -sg.addSequence (aa[this.selectedRow].sequenceRef, true); -}}} else { -sg = new jalview.datamodel.SequenceGroup (); -sg.setStartRes (0); -sg.setEndRes (this.ap.av.getAlignment ().getWidth () - 1); -sg.addSequence (aa[this.selectedRow].sequenceRef, false); -}this.ap.av.setSelectionGroup (sg); -this.ap.paintAlignment (false); -jalview.appletgui.PaintRefresher.Refresh (this.ap, this.ap.av.getSequenceSetId ()); -this.ap.av.sendSelection (); -}}}}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "copy_annotseqtoclipboard", -function (sq) { -if (sq == null || sq.getLength () < 1) { -return; -}jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer (); -jalview.appletgui.AlignFrame.copiedSequences.append (sq.getName () + "\t" + sq.getStart () + "\t" + sq.getEnd () + "\t" + sq.getSequenceAsString () + "\n"); -if (this.av.hasHiddenColumns ()) { -jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector (); -for (var region, $region = this.av.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { -jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0], region[1]])); -} -}}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -if (this.av.getWrapAlignment () || !this.av.isShowAnnotation ()) return; -var w = this.getSize ().width; -var h = this.getSize ().height; -if (this.image == null || w != this.image.getWidth (this) || h != this.image.getHeight (this)) { -this.image = this.createImage (w, this.ap.annotationPanel.getSize ().height); -}this.drawComponent (this.image.getGraphics (), w); -g.drawImage (this.image, 0, 0, this); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "drawComponent", -function (g, width) { -g.setFont (this.av.getFont ()); -var fm = g.getFontMetrics (this.av.getFont ()); -g.setColor (java.awt.Color.white); -g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -g.translate (0, -this.scrollOffset); -g.setColor (java.awt.Color.black); -var aa = this.av.getAlignment ().getAlignmentAnnotation (); -var y = 0; -var fy = g.getFont ().getSize (); -var x = 0; -var offset; -if (aa != null) { -this.hasHiddenRows = false; -for (var i = 0; i < aa.length; i++) { -if (!aa[i].visible) { -this.hasHiddenRows = true; -continue; -}x = width - fm.stringWidth (aa[i].label) - 3; -y += aa[i].height; -offset = Clazz.doubleToInt (-(aa[i].height - fy) / 2); -g.drawString (aa[i].label, x, y + offset); -} -}g.translate (0, +this.scrollOffset); -if (this.resizePanel) { -g.setColor (java.awt.Color.red); -g.setPaintMode (); -g.drawLine (2, 8, 5, 2); -g.drawLine (5, 2, 8, 8); -} else if (!this.dragCancelled && this.dragEvent != null && aa != null) { -g.setColor (java.awt.Color.lightGray); -g.drawString (aa[this.selectedRow].label, this.dragEvent.getX (), this.dragEvent.getY ()); -}if (!this.av.getWrapAlignment () && ((aa == null) || (aa.length < 1))) { -g.setColor (java.awt.Color.black); -g.drawString (jalview.util.MessageManager.getString ("label.right_click"), 2, 8); -g.drawString (jalview.util.MessageManager.getString ("label.to_add_annotation"), 2, 18); -}}, "java.awt.Graphics,~N"); -c$.$AnnotationLabels$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$1", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations (this.b$["jalview.appletgui.AnnotationLabels"].ap.av.getAlignment (), java.util.Collections.singleton (this.f$.label), null, false, false); -this.b$["jalview.appletgui.AnnotationLabels"].refresh (); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$2", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -if (this.f$.aaa.groupRef != null) { -this.f$.aaa.groupRef.setIgnoreGapsConsensus (this.f$.cbmi.getState ()); -} else { -this.b$["jalview.appletgui.AnnotationLabels"].ap.av.setIgnoreGapsConsensus (this.f$.cbmi.getState (), this.b$["jalview.appletgui.AnnotationLabels"].ap); -}this.b$["jalview.appletgui.AnnotationLabels"].ap.paintAlignment (true); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$3", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -this.f$.aaa.groupRef.setShowConsensusHistogram (this.f$.chist.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$4$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$4", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -this.f$.aaa.groupRef.setshowSequenceLogo (this.f$.cprofl.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$5$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$5", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -this.f$.aaa.groupRef.setshowSequenceLogo (true); -this.f$.aaa.groupRef.setNormaliseSequenceLogo (this.f$.cprofn.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$6$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$6", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -this.b$["jalview.appletgui.AnnotationLabels"].av.setShowConsensusHistogram (this.f$.chist.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.alignFrame.showConsensusHistogram.setState (this.f$.chist.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$7$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$7", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -this.b$["jalview.appletgui.AnnotationLabels"].av.setShowSequenceLogo (this.f$.cprof.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.alignFrame.showSequenceLogo.setState (this.f$.cprof.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$AnnotationLabels$8$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$8", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -this.b$["jalview.appletgui.AnnotationLabels"].av.setShowSequenceLogo (true); -this.b$["jalview.appletgui.AnnotationLabels"].ap.alignFrame.normSequenceLogo.setState (this.f$.cprofn.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].av.setNormaliseSequenceLogo (this.f$.cprofn.getState ()); -this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"ADDNEW", "Add New Row", -"EDITNAME", "Edit Label/Description", -"HIDE", "Hide This Row", -"SHOWALL", "Show All Hidden Rows", -"OUTPUT_TEXT", "Show Values In Textbox", -"COPYCONS_SEQ", "Copy Consensus Sequence"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.AnnotationLabels", ["awt2swing.Checkbox", "$.CheckboxMenuItem", "$.Frame", "$.MenuItem", "$.PopupMenu", "jalview.analysis.AlignmentUtils", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.EditNameDialog", "$.PaintRefresher", "$.Tooltip", "jalview.bin.JalviewLite", "jalview.datamodel.AlignmentAnnotation", "$.SequenceGroup", "jalview.util.MessageManager", "$.ParseHtmlBodyAndLinks", "java.awt.Color", "$.Dimension", "$.FlowLayout", "java.awt.event.ItemListener", "java.lang.StringBuffer", "java.util.Arrays", "$.Collections", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.image = null; +this.active = false; +this.ap = null; +this.av = null; +this.resizing = false; +this.oldY = 0; +this.mouseX = 0; +this.scrollOffset = 0; +this.selectedRow = -1; +this.tooltip = null; +this.hasHiddenRows = false; +this.resizePanel = false; +this.dragEvent = null; +this.dragCancelled = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AnnotationLabels", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationLabels, []); +this.ap = ap; +this.av = ap.av; +this.setLayout (null); +this.addMouseListener (this); +this.addMouseMotionListener (this); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationLabels, []); +this.av = av; +}, "jalview.appletgui.AlignViewport"); +Clazz.defineMethod (c$, "setScrollOffset", +function (y, repaint) { +this.scrollOffset = y; +if (repaint) { +this.repaint (); +}}, "~N,~B"); +Clazz.defineMethod (c$, "getSelectedRow", +function (y) { +var row = -2; +var aa = this.ap.av.getAlignment ().getAlignmentAnnotation (); +if (aa == null) { +return row; +}var height = 0; +for (var i = 0; i < aa.length; i++) { +row = -1; +if (!aa[i].visible) { +continue; +}height += aa[i].height; +if (y < height) { +row = i; +break; +}} +return row; +}, "~N"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +var aa = this.av.getAlignment ().getAlignmentAnnotation (); +if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.ADDNEW)) { +var newAnnotation = new jalview.datamodel.AlignmentAnnotation ("", null, new Array (this.ap.av.getAlignment ().getWidth ())); +if (!this.editLabelDescription (newAnnotation)) { +return; +}this.ap.av.getAlignment ().addAnnotation (newAnnotation); +this.ap.av.getAlignment ().setAnnotationIndex (newAnnotation, 0); +} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.EDITNAME)) { +this.editLabelDescription (aa[this.selectedRow]); +} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.HIDE)) { +aa[this.selectedRow].visible = false; +} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.SHOWALL)) { +for (var i = 0; i < aa.length; i++) { +aa[i].visible = (aa[i].annotations == null) ? false : true; +} +} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.OUTPUT_TEXT)) { +var cap = new jalview.appletgui.CutAndPasteTransfer (false, this.ap.alignFrame); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, this.ap.alignFrame.getTitle () + " - " + aa[this.selectedRow].label, 500, 100); +cap.setText (aa[this.selectedRow].toString ()); +} else if (evt.getActionCommand ().equals (jalview.appletgui.AnnotationLabels.COPYCONS_SEQ)) { +var cons = this.av.getConsensusSeq (); +if (cons != null) { +this.copy_annotseqtoclipboard (cons); +}}this.refresh (); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "refresh", +function () { +this.ap.annotationPanel.adjustPanelHeight (); +this.setSize (this.getSize ().width, this.ap.annotationPanel.getSize ().height); +this.ap.validate (); +this.ap.paintAlignment (true); +}); +Clazz.defineMethod (c$, "editLabelDescription", +function (annotation) { +var padGaps = new awt2swing.Checkbox ("Fill Empty Gaps With \"" + this.ap.av.getGapCharacter () + "\"", annotation.padGaps); +var dialog = new jalview.appletgui.EditNameDialog (annotation.label, annotation.description, " Annotation Label", "Annotation Description", this.ap.alignFrame, "Edit Annotation Name / Description", 500, 180, false); +var empty = new awt2swing.Panel ( new java.awt.FlowLayout ()); +empty.add (padGaps); +dialog.add (empty); +dialog.pack (); +dialog.setVisible (true); +if (dialog.accept) { +annotation.label = dialog.getName (); +annotation.description = dialog.getDescription (); +annotation.setPadGaps (padGaps.getState (), this.av.getGapCharacter ()); +this.repaint (); +return true; +} else { +return false; +}}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +this.resizePanel = evt.getY () < 10 && evt.getX () < 14; +var row = this.getSelectedRow (evt.getY () + this.scrollOffset); +if (row > -1) { +var phb = new jalview.util.ParseHtmlBodyAndLinks (this.av.getAlignment ().getAlignmentAnnotation ()[row].getDescription (true), true, "\n"); +if (this.tooltip == null) { +this.tooltip = new jalview.appletgui.Tooltip (phb.getNonHtmlContent (), this); +} else { +this.tooltip.setTip (phb.getNonHtmlContent ()); +}} else if (this.tooltip != null) { +this.tooltip.setTip (""); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "cancelDrag", +function () { +this.dragEvent = null; +this.dragCancelled = true; +}); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +if (this.dragCancelled) { +return; +};this.dragEvent = evt; +if (this.resizePanel) { +var d = this.ap.annotationPanelHolder.getSize (); +var e = this.ap.annotationSpaceFillerHolder.getSize (); +var f = this.ap.seqPanelHolder.getSize (); +var dif = evt.getY () - this.oldY; +dif /= this.ap.av.getCharHeight (); +dif *= this.ap.av.getCharHeight (); +if ((d.height - dif) > 20 && (f.height + dif) > 20) { +this.ap.annotationPanel.setSize (d.width, d.height - dif); +this.setSize ( new java.awt.Dimension (e.width, d.height - dif)); +this.ap.annotationSpaceFillerHolder.setSize ( new java.awt.Dimension (e.width, d.height - dif)); +this.ap.annotationPanelHolder.setSize ( new java.awt.Dimension (d.width, d.height - dif)); +this.ap.apvscroll.setValues (this.ap.apvscroll.getValue (), d.height - dif, 0, this.av.calcPanelHeight ()); +f.height += dif; +this.ap.seqPanelHolder.setPreferredSize (f); +this.ap.setScrollValues (this.av.getStartRes (), this.av.getStartSeq ()); +this.ap.validate (); +this.ap.addNotify (); +}} else { +var diff; +if ((diff = 6 - evt.getY ()) > 0) { +this.ap.apvscroll.setValue (this.ap.apvscroll.getValue () - diff); +this.ap.adjustmentValueChanged (null); +} else if ((0 < (diff = 6 - this.ap.annotationSpaceFillerHolder.getSize ().height + evt.getY ()))) { +this.ap.apvscroll.setValue (this.ap.apvscroll.getValue () + diff); +this.ap.adjustmentValueChanged (null); +}this.repaint (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +if (!this.resizePanel && !this.dragCancelled) { +var start = this.selectedRow; +var end = this.getSelectedRow (evt.getY () + this.scrollOffset); +if (start > -1 && start != end) { +var startAA = this.ap.av.getAlignment ().getAlignmentAnnotation ()[start]; +if (end == -1) { +end = this.ap.av.getAlignment ().getAlignmentAnnotation ().length - 1; +}var endAA = this.ap.av.getAlignment ().getAlignmentAnnotation ()[end]; +this.ap.av.getAlignment ().getAlignmentAnnotation ()[end] = startAA; +this.ap.av.getAlignment ().getAlignmentAnnotation ()[start] = endAA; +}}this.resizePanel = false; +this.dragEvent = null; +this.dragCancelled = false; +this.repaint (); +this.ap.annotationPanel.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +if (evt.getY () < 10 && evt.getX () < 14) { +this.resizePanel = true; +this.repaint (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +this.dragCancelled = false; +if (this.dragEvent == null) { +this.resizePanel = false; +} else { +if (!this.resizePanel) { +this.dragEvent = null; +}}this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +this.oldY = evt.getY (); +if (this.resizePanel) { +return; +}this.dragCancelled = false; +this.selectedRow = this.getSelectedRow (evt.getY () + this.scrollOffset); +var aa = this.ap.av.getAlignment ().getAlignmentAnnotation (); +if ((evt.getModifiers () & 4) == 4) { +var popup = new awt2swing.PopupMenu (jalview.util.MessageManager.getString ("label.annotations")); +var item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.ADDNEW); +item.addActionListener (this); +popup.add (item); +if (this.selectedRow < 0) { +if (this.hasHiddenRows) { +item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.SHOWALL); +item.addActionListener (this); +popup.add (item); +}this.add (popup); +popup.show (this, evt.getX (), evt.getY ()); +return; +}item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.EDITNAME); +item.addActionListener (this); +popup.add (item); +item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.HIDE); +item.addActionListener (this); +popup.add (item); +if (this.selectedRow < aa.length) { +if (aa[this.selectedRow].sequenceRef != null) { +var label = aa[this.selectedRow].label; +var hideType = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.hide_all") + " " + label); +hideType.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$1") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$1, this, Clazz.cloneFinals ("label", label)))); +popup.add (hideType); +}}if (this.hasHiddenRows) { +item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.SHOWALL); +item.addActionListener (this); +popup.add (item); +}this.add (popup); +item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.OUTPUT_TEXT); +item.addActionListener (this); +popup.add (item); +if (this.selectedRow < aa.length) { +if (aa[this.selectedRow].autoCalculated) { +if (aa[this.selectedRow].label.indexOf ("Consensus") > -1) { +popup.addSeparator (); +var cbmi = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.ignore_gaps_consensus"), (aa[this.selectedRow].groupRef != null) ? aa[this.selectedRow].groupRef.getIgnoreGapsConsensus () : this.ap.av.isIgnoreGapsConsensus ()); +var aaa = aa[this.selectedRow]; +cbmi.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$2") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$2, this, Clazz.cloneFinals ("aaa", aaa, "cbmi", cbmi)))); +popup.add (cbmi); +if (aaa.groupRef != null) { +var chist = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_group_histogram"), aa[this.selectedRow].groupRef.isShowConsensusHistogram ()); +chist.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$3") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$3, this, Clazz.cloneFinals ("aaa", aaa, "chist", chist)))); +popup.add (chist); +var cprofl = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_group_logo"), aa[this.selectedRow].groupRef.isShowSequenceLogo ()); +cprofl.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$4") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$4, this, Clazz.cloneFinals ("aaa", aaa, "cprofl", cprofl)))); +popup.add (cprofl); +var cprofn = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.normalise_group_logo"), aa[this.selectedRow].groupRef.isNormaliseSequenceLogo ()); +cprofn.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$5") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$5, this, Clazz.cloneFinals ("aaa", aaa, "cprofn", cprofn)))); +popup.add (cprofn); +} else { +var chist = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_histogram"), this.av.isShowConsensusHistogram ()); +chist.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$6") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$6$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$6, this, Clazz.cloneFinals ("chist", chist)))); +popup.add (chist); +var cprof = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_logo"), this.av.isShowSequenceLogo ()); +cprof.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$7") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$7$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$7, this, Clazz.cloneFinals ("cprof", cprof)))); +popup.add (cprof); +var cprofn = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.normalise_logo"), this.av.isNormaliseSequenceLogo ()); +cprofn.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.AnnotationLabels$8") ? 0 : jalview.appletgui.AnnotationLabels.$AnnotationLabels$8$ ()), Clazz.innerTypeInstance (jalview.appletgui.AnnotationLabels$8, this, Clazz.cloneFinals ("cprofn", cprofn)))); +popup.add (cprofn); +}item = new awt2swing.MenuItem (jalview.appletgui.AnnotationLabels.COPYCONS_SEQ); +item.addActionListener (this); +popup.add (item); +}}}popup.show (this, evt.getX (), evt.getY ()); +} else { +if (this.selectedRow > -1 && this.selectedRow < aa.length) { +if (aa[this.selectedRow].groupRef != null) { +if (evt.getClickCount () >= 2) { +this.ap.seqPanel.ap.idPanel.highlightSearchResults (null); +this.ap.av.setSelectionGroup (aa[this.selectedRow].groupRef); +this.ap.av.sendSelection (); +this.ap.paintAlignment (false); +jalview.appletgui.PaintRefresher.Refresh (this.ap, this.ap.av.getSequenceSetId ()); +} else { +this.ap.seqPanel.ap.idPanel.highlightSearchResults (aa[this.selectedRow].groupRef.getSequences (null)); +}return; +} else if (aa[this.selectedRow].sequenceRef != null) { +if (evt.getClickCount () == 1) { +this.ap.seqPanel.ap.idPanel.highlightSearchResults (java.util.Arrays.asList ( Clazz.newArray (-1, [aa[this.selectedRow].sequenceRef]))); +} else if (evt.getClickCount () >= 2) { +this.ap.seqPanel.ap.idPanel.highlightSearchResults (null); +var sg = this.ap.av.getSelectionGroup (); +if (sg != null) { +if (!(evt.isControlDown () || evt.isShiftDown ())) { +sg = new jalview.datamodel.SequenceGroup (sg); +sg.clear (); +sg.addSequence (aa[this.selectedRow].sequenceRef, false); +} else { +if (evt.isControlDown ()) { +sg.addOrRemove (aa[this.selectedRow].sequenceRef, true); +} else { +sg.addSequence (aa[this.selectedRow].sequenceRef, true); +}}} else { +sg = new jalview.datamodel.SequenceGroup (); +sg.setStartRes (0); +sg.setEndRes (this.ap.av.getAlignment ().getWidth () - 1); +sg.addSequence (aa[this.selectedRow].sequenceRef, false); +}this.ap.av.setSelectionGroup (sg); +this.ap.paintAlignment (false); +jalview.appletgui.PaintRefresher.Refresh (this.ap, this.ap.av.getSequenceSetId ()); +this.ap.av.sendSelection (); +}}}}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "copy_annotseqtoclipboard", +function (sq) { +if (sq == null || sq.getLength () < 1) { +return; +}jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer (); +jalview.appletgui.AlignFrame.copiedSequences.append (sq.getName () + "\t" + sq.getStart () + "\t" + sq.getEnd () + "\t" + sq.getSequenceAsString () + "\n"); +if (this.av.hasHiddenColumns ()) { +jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector (); +for (var region, $region = this.av.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { +jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0], region[1]])); +} +}}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +if (this.av.getWrapAlignment () || !this.av.isShowAnnotation ()) return; +var w = this.getSize ().width; +var h = this.getSize ().height; +if (this.image == null || w != this.image.getWidth (this) || h != this.image.getHeight (this)) { +this.image = this.createImage (w, this.ap.annotationPanel.getSize ().height); +}this.drawComponent (this.image.getGraphics (), w); +g.drawImage (this.image, 0, 0, this); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "drawComponent", +function (g, width) { +g.setFont (this.av.getFont ()); +var fm = g.getFontMetrics (this.av.getFont ()); +g.setColor (java.awt.Color.white); +g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +g.translate (0, -this.scrollOffset); +g.setColor (java.awt.Color.black); +var aa = this.av.getAlignment ().getAlignmentAnnotation (); +var y = 0; +var fy = g.getFont ().getSize (); +var x = 0; +var offset; +if (aa != null) { +this.hasHiddenRows = false; +for (var i = 0; i < aa.length; i++) { +if (!aa[i].visible) { +this.hasHiddenRows = true; +continue; +}x = width - fm.stringWidth (aa[i].label) - 3; +y += aa[i].height; +offset = Clazz.doubleToInt (-(aa[i].height - fy) / 2); +g.drawString (aa[i].label, x, y + offset); +} +}g.translate (0, +this.scrollOffset); +if (this.resizePanel) { +g.setColor (java.awt.Color.red); +g.setPaintMode (); +g.drawLine (2, 8, 5, 2); +g.drawLine (5, 2, 8, 8); +} else if (!this.dragCancelled && this.dragEvent != null && aa != null) { +g.setColor (java.awt.Color.lightGray); +g.drawString (aa[this.selectedRow].label, this.dragEvent.getX (), this.dragEvent.getY ()); +}if (!this.av.getWrapAlignment () && ((aa == null) || (aa.length < 1))) { +g.setColor (java.awt.Color.black); +g.drawString (jalview.util.MessageManager.getString ("label.right_click"), 2, 8); +g.drawString (jalview.util.MessageManager.getString ("label.to_add_annotation"), 2, 18); +}}, "java.awt.Graphics,~N"); +c$.$AnnotationLabels$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$1", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations (this.b$["jalview.appletgui.AnnotationLabels"].ap.av.getAlignment (), java.util.Collections.singleton (this.f$.label), null, false, false); +this.b$["jalview.appletgui.AnnotationLabels"].refresh (); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$2", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +if (this.f$.aaa.groupRef != null) { +this.f$.aaa.groupRef.setIgnoreGapsConsensus (this.f$.cbmi.getState ()); +} else { +this.b$["jalview.appletgui.AnnotationLabels"].ap.av.setIgnoreGapsConsensus (this.f$.cbmi.getState (), this.b$["jalview.appletgui.AnnotationLabels"].ap); +}this.b$["jalview.appletgui.AnnotationLabels"].ap.paintAlignment (true); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$3", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +this.f$.aaa.groupRef.setShowConsensusHistogram (this.f$.chist.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$4$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$4", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +this.f$.aaa.groupRef.setshowSequenceLogo (this.f$.cprofl.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$5$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$5", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +this.f$.aaa.groupRef.setshowSequenceLogo (true); +this.f$.aaa.groupRef.setNormaliseSequenceLogo (this.f$.cprofn.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$6$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$6", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +this.b$["jalview.appletgui.AnnotationLabels"].av.setShowConsensusHistogram (this.f$.chist.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.alignFrame.showConsensusHistogram.setState (this.f$.chist.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$7$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$7", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +this.b$["jalview.appletgui.AnnotationLabels"].av.setShowSequenceLogo (this.f$.cprof.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.alignFrame.showSequenceLogo.setState (this.f$.cprof.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$AnnotationLabels$8$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AnnotationLabels$8", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +this.b$["jalview.appletgui.AnnotationLabels"].av.setShowSequenceLogo (true); +this.b$["jalview.appletgui.AnnotationLabels"].ap.alignFrame.normSequenceLogo.setState (this.f$.cprofn.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].av.setNormaliseSequenceLogo (this.f$.cprofn.getState ()); +this.b$["jalview.appletgui.AnnotationLabels"].ap.repaint (); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"ADDNEW", "Add New Row", +"EDITNAME", "Edit Label/Description", +"HIDE", "Hide This Row", +"SHOWALL", "Show All Hidden Rows", +"OUTPUT_TEXT", "Show Values In Textbox", +"COPYCONS_SEQ", "Copy Consensus Sequence"); +}); diff --git a/bin/jalview/appletgui/AnnotationPanel.class b/bin/jalview/appletgui/AnnotationPanel.class index ec1d4ce..8d48e90 100644 Binary files a/bin/jalview/appletgui/AnnotationPanel.class and b/bin/jalview/appletgui/AnnotationPanel.class differ diff --git a/bin/jalview/appletgui/AnnotationPanel.js b/bin/jalview/appletgui/AnnotationPanel.js index 33f7259..6234bd3 100644 --- a/bin/jalview/appletgui/AnnotationPanel.js +++ b/bin/jalview/appletgui/AnnotationPanel.js @@ -1,364 +1,364 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "jalview.renderer.AwtRenderPanelI", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.MouseListener", "$.MouseMotionListener", "java.awt.Color"], "jalview.appletgui.AnnotationPanel", ["awt2swing.MenuItem", "$.PopupMenu", "jalview.appletgui.EditNameDialog", "$.UserDefinedColours", "jalview.datamodel.Annotation", "jalview.renderer.AnnotationRenderer", "jalview.util.MessageManager", "$.Platform", "java.awt.Dimension", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.ap = null; -this.activeRow = -1; -this.HELIX = "Helix"; -this.SHEET = "Sheet"; -this.STEM = "RNA Helix"; -this.LABEL = "Label"; -this.REMOVE = "Remove Annotation"; -this.COLOUR = "Colour"; -this.HELIX_COLOUR = null; -this.SHEET_COLOUR = null; -this.image = null; -this.gg = null; -this.fm = null; -this.imgWidth = 0; -this.$fastPaint = false; -this.graphStretch = -1; -this.graphStretchY = -1; -this.mouseDragging = false; -this.MAC = false; -this.renderer = null; -this.needValidating = false; -this.scrollOffset = 0; -this.$bounds = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AnnotationPanel", awt2swing.Panel, [jalview.renderer.AwtRenderPanelI, java.awt.event.AdjustmentListener, java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); -Clazz.prepareFields (c$, function () { -this.HELIX_COLOUR = java.awt.Color.red.darker (); -this.SHEET_COLOUR = java.awt.Color.green.darker ().darker (); -this.$bounds = Clazz.newIntArray (2, 0); -}); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationPanel, []); -this.MAC = jalview.util.Platform.isAMac (); -this.ap = ap; -this.av = ap.av; -this.setLayout (null); -var height = this.adjustPanelHeight (); -ap.apvscroll.setValues (0, this.getSize ().height, 0, height); -this.addMouseMotionListener (this); -this.addMouseListener (this); -this.renderer = new jalview.renderer.AnnotationRenderer (); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationPanel, []); -this.av = av; -this.renderer = new jalview.renderer.AnnotationRenderer (); -}, "jalview.appletgui.AlignViewport"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -}, "java.awt.event.AdjustmentEvent"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -var aa = this.av.getAlignment ().getAlignmentAnnotation (); -if (aa == null) { -return; -}var anot = aa[this.activeRow].annotations; -if (anot.length < this.av.getColumnSelection ().getMax ()) { -var temp = new Array (this.av.getColumnSelection ().getMax () + 2); -System.arraycopy (anot, 0, temp, 0, anot.length); -anot = temp; -aa[this.activeRow].annotations = anot; -}var label = ""; -if (this.av.getColumnSelection () != null && this.av.getColumnSelection ().size () > 0 && anot[this.av.getColumnSelection ().getMin ()] != null) { -label = anot[this.av.getColumnSelection ().getMin ()].displayCharacter; -}if (evt.getActionCommand ().equals ("Remove Annotation")) { -for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { -anot[this.av.getColumnSelection ().columnAt (i)] = null; -} -} else if (evt.getActionCommand ().equals ("Label")) { -label = this.enterLabel (label, "Enter Label"); -if (label == null) { -return; -}if ((label.length > 0) && !aa[this.activeRow].hasText) { -aa[this.activeRow].hasText = true; -}for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { -var index = this.av.getColumnSelection ().columnAt (i); -if (!this.av.getColumnSelection ().isVisible (index)) { -continue; -}if (anot[index] == null) { -anot[index] = new jalview.datamodel.Annotation (label, "", ' ', 0); -}anot[index].displayCharacter = label; -} -} else if (evt.getActionCommand ().equals ("Colour")) { -var udc = new jalview.appletgui.UserDefinedColours (this, java.awt.Color.black, this.ap.alignFrame); -var col = udc.getColor (); -for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { -var index = this.av.getColumnSelection ().columnAt (i); -if (!this.av.getColumnSelection ().isVisible (index)) { -continue; -}if (anot[index] == null) { -anot[index] = new jalview.datamodel.Annotation ("", "", ' ', 0); -}anot[index].colour = col; -} -} else { -var type = String.fromCharCode (0); -var symbol = "\u03B1"; -if (evt.getActionCommand ().equals ("Helix")) { -type = 'H'; -} else if (evt.getActionCommand ().equals ("Sheet")) { -type = 'E'; -symbol = "\u03B2"; -} else if (evt.getActionCommand ().equals ("RNA Helix")) { -type = 'S'; -symbol = "\u03C3"; -}if (!aa[this.activeRow].hasIcons) { -aa[this.activeRow].hasIcons = true; -}label = this.enterLabel (symbol, "Enter Label"); -if (label == null) { -return; -}if ((label.length > 0) && !aa[this.activeRow].hasText) { -aa[this.activeRow].hasText = true; -if (evt.getActionCommand ().equals ("RNA Helix")) { -aa[this.activeRow].showAllColLabels = true; -}}for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { -var index = this.av.getColumnSelection ().columnAt (i); -if (!this.av.getColumnSelection ().isVisible (index)) { -continue; -}if (anot[index] == null) { -anot[index] = new jalview.datamodel.Annotation (label, "", type, 0); -}anot[index].secondaryStructure = type != 'S' ? type : label.length == 0 ? ' ' : label.charAt (0); -anot[index].displayCharacter = label; -} -}this.av.getAlignment ().validateAnnotation (aa[this.activeRow]); -this.ap.alignmentChanged (); -this.adjustPanelHeight (); -this.repaint (); -return; -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "enterLabel", -function (text, label) { -var dialog = new jalview.appletgui.EditNameDialog (text, null, label, null, this.ap.alignFrame, "Enter Label", 400, 200, true); -if (dialog.accept) { -return dialog.getName (); -} else { -return null; -}}, "~S,~S"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -var aa = this.av.getAlignment ().getAlignmentAnnotation (); -if (aa == null) { -return; -}var height = -this.scrollOffset; -this.activeRow = -1; -for (var i = 0; i < aa.length; i++) { -if (aa[i].visible) { -height += aa[i].height; -}if (evt.getY () < height) { -if (aa[i].editable) { -this.activeRow = i; -} else if (aa[i].graph > 0) { -this.graphStretch = i; -this.graphStretchY = evt.getY (); -}break; -}} -if ((evt.getModifiers () & 4) == 4 && this.activeRow != -1) { -if (this.av.getColumnSelection () == null) { -return; -}var pop = new awt2swing.PopupMenu (jalview.util.MessageManager.getString ("label.structure_type")); -var item; -if (this.av.getAlignment ().isNucleotide () == true) { -item = new awt2swing.MenuItem ("RNA Helix"); -item.addActionListener (this); -pop.add (item); -} else { -item = new awt2swing.MenuItem ("Helix"); -item.addActionListener (this); -pop.add (item); -item = new awt2swing.MenuItem ("Sheet"); -item.addActionListener (this); -pop.add (item); -}item = new awt2swing.MenuItem ("Label"); -item.addActionListener (this); -pop.add (item); -item = new awt2swing.MenuItem ("Colour"); -item.addActionListener (this); -pop.add (item); -item = new awt2swing.MenuItem ("Remove Annotation"); -item.addActionListener (this); -pop.add (item); -this.ap.alignFrame.add (pop); -pop.show (this, evt.getX (), evt.getY ()); -return; -}this.ap.scalePanel.mousePressed (evt); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.graphStretch = -1; -this.graphStretchY = -1; -this.mouseDragging = false; -if (this.needValidating) { -this.ap.validate (); -this.needValidating = false; -}this.ap.scalePanel.mouseReleased (evt); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -if (this.graphStretch > -1) { -this.av.getAlignment ().getAlignmentAnnotation ()[this.graphStretch].graphHeight += this.graphStretchY - evt.getY (); -if (this.av.getAlignment ().getAlignmentAnnotation ()[this.graphStretch].graphHeight < 0) { -this.av.getAlignment ().getAlignmentAnnotation ()[this.graphStretch].graphHeight = 0; -}this.graphStretchY = evt.getY (); -this.av.calcPanelHeight (); -this.needValidating = true; -this.ap.paintAlignment (true); -} else { -this.ap.scalePanel.mouseDragged (evt); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -var aa = this.av.getAlignment ().getAlignmentAnnotation (); -if (aa == null) { -return; -}var row = -1; -var height = -this.scrollOffset; -for (var i = 0; i < aa.length; i++) { -if (aa[i].visible) { -height += aa[i].height; -}if (evt.getY () < height) { -row = i; -break; -}} -var res = Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ()) + this.av.getStartRes (); -if (this.av.hasHiddenColumns ()) { -res = this.av.getColumnSelection ().adjustForHiddenColumns (res); -}if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null) { -var text = new StringBuffer ("Sequence position " + (res + 1)); -if (aa[row].annotations[res].description != null) { -text.append (" " + aa[row].annotations[res].description); -}this.ap.alignFrame.setStatus (text.toString ()); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -this.ap.scalePanel.mouseEntered (evt); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -this.ap.scalePanel.mouseExited (evt); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "adjustPanelHeight", -function () { -return this.adjustPanelHeight (true); -}); -Clazz.defineMethod (c$, "adjustPanelHeight", -function (repaint) { -var height = this.av.calcPanelHeight (); -this.setSize ( new java.awt.Dimension (this.getSize ().width, height)); -if (repaint) { -this.repaint (); -}return height; -}, "~B"); -Clazz.defineMethod (c$, "addEditableColumn", -function (i) { -if (this.activeRow == -1) { -var aa = this.av.getAlignment ().getAlignmentAnnotation (); -if (aa == null) { -return; -}for (var j = 0; j < aa.length; j++) { -if (aa[j].editable) { -this.activeRow = j; -break; -}} -}}, "~N"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -if (this.av.getWrapAlignment () || !this.av.isShowAnnotation ()) return; -var d = this.getSize (); -this.imgWidth = d.width; -if (this.imgWidth < 1 || d.height < 1) { -return; -}if (this.image == null || this.imgWidth != this.image.getWidth (this) || d.height != this.image.getHeight (this)) { -this.image = this.createImage (this.imgWidth, d.height); -this.gg = this.image.getGraphics (); -this.gg.setFont (this.av.getFont ()); -this.fm = this.gg.getFontMetrics (); -this.$fastPaint = false; -}if (this.$fastPaint) { -g.drawImage (this.image, 0, 0, this); -this.$fastPaint = false; -return; -}this.gg.setColor (java.awt.Color.white); -this.gg.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -this.drawComponent (this.gg, this.av.startRes, this.av.endRes + 1); -g.drawImage (this.image, 0, 0, this); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "fastPaint", -function (horizontal) { -if (horizontal == 0 || this.av.getAlignment ().getAlignmentAnnotation () == null || this.av.getAlignment ().getAlignmentAnnotation ().length < 1) { -this.repaint (); -return; -}this.gg.copyArea (0, 0, this.imgWidth, this.getSize ().height, -horizontal * this.av.getCharWidth (), 0); -var sr = this.av.startRes; -var er = this.av.endRes + 1; -var transX = 0; -if (horizontal > 0) { -transX = (er - sr - horizontal) * this.av.getCharWidth (); -sr = er - horizontal; -} else if (horizontal < 0) { -er = sr - horizontal; -}this.gg.translate (transX, 0); -this.drawComponent (this.gg, sr, er); -this.gg.translate (-transX, 0); -this.$fastPaint = true; -this.repaint (); -}, "~N"); -Clazz.defineMethod (c$, "drawComponent", -function (g, startRes, endRes) { -var ofont = this.av.getFont (); -g.setFont (ofont); -g.setColor (java.awt.Color.white); -g.fillRect (0, 0, (endRes - startRes) * this.av.getCharWidth (), this.getSize ().height); -if (this.fm == null) { -this.fm = g.getFontMetrics (); -}if ((this.av.getAlignment ().getAlignmentAnnotation () == null) || (this.av.getAlignment ().getAlignmentAnnotation ().length < 1)) { -g.setColor (java.awt.Color.white); -g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -g.setColor (java.awt.Color.black); -if (this.av.validCharWidth) { -g.drawString (jalview.util.MessageManager.getString ("label.alignment_has_no_annotations"), 20, 15); -}return; -}g.translate (0, -this.scrollOffset); -this.renderer.drawComponent (this, this.av, g, this.activeRow, startRes, endRes); -g.translate (0, +this.scrollOffset); -}, "java.awt.Graphics,~N,~N"); -Clazz.defineMethod (c$, "setScrollOffset", -function (value, repaint) { -this.scrollOffset = value; -if (repaint) { -this.repaint (); -}}, "~N,~B"); -Clazz.defineMethod (c$, "getFontMetrics", -function () { -return this.fm; -}); -Clazz.overrideMethod (c$, "getFadedImage", -function () { -return this.image; -}); -Clazz.overrideMethod (c$, "getFadedImageWidth", -function () { -return this.imgWidth; -}); -Clazz.overrideMethod (c$, "getVisibleVRange", -function () { -if (this.ap != null && this.ap.alabels != null) { -var sOffset = -this.ap.alabels.scrollOffset; -var visHeight = sOffset + this.ap.annotationPanelHolder.getHeight (); -this.$bounds[0] = sOffset; -this.$bounds[1] = visHeight; -return this.$bounds; -} else { -return null; -}}); -Clazz.defineStatics (c$, -"GRAPH_HEIGHT", 40); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "jalview.renderer.AwtRenderPanelI", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.MouseListener", "$.MouseMotionListener", "java.awt.Color"], "jalview.appletgui.AnnotationPanel", ["awt2swing.MenuItem", "$.PopupMenu", "jalview.appletgui.EditNameDialog", "$.UserDefinedColours", "jalview.datamodel.Annotation", "jalview.renderer.AnnotationRenderer", "jalview.util.MessageManager", "$.Platform", "java.awt.Dimension", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.ap = null; +this.activeRow = -1; +this.HELIX = "Helix"; +this.SHEET = "Sheet"; +this.STEM = "RNA Helix"; +this.LABEL = "Label"; +this.REMOVE = "Remove Annotation"; +this.COLOUR = "Colour"; +this.HELIX_COLOUR = null; +this.SHEET_COLOUR = null; +this.image = null; +this.gg = null; +this.fm = null; +this.imgWidth = 0; +this.$fastPaint = false; +this.graphStretch = -1; +this.graphStretchY = -1; +this.mouseDragging = false; +this.MAC = false; +this.renderer = null; +this.needValidating = false; +this.scrollOffset = 0; +this.$bounds = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AnnotationPanel", awt2swing.Panel, [jalview.renderer.AwtRenderPanelI, java.awt.event.AdjustmentListener, java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); +Clazz.prepareFields (c$, function () { +this.HELIX_COLOUR = java.awt.Color.red.darker (); +this.SHEET_COLOUR = java.awt.Color.green.darker ().darker (); +this.$bounds = Clazz.newIntArray (2, 0); +}); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationPanel, []); +this.MAC = jalview.util.Platform.isAMac (); +this.ap = ap; +this.av = ap.av; +this.setLayout (null); +var height = this.adjustPanelHeight (); +ap.apvscroll.setValues (0, this.getSize ().height, 0, height); +this.addMouseMotionListener (this); +this.addMouseListener (this); +this.renderer = new jalview.renderer.AnnotationRenderer (); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationPanel, []); +this.av = av; +this.renderer = new jalview.renderer.AnnotationRenderer (); +}, "jalview.appletgui.AlignViewport"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +}, "java.awt.event.AdjustmentEvent"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +var aa = this.av.getAlignment ().getAlignmentAnnotation (); +if (aa == null) { +return; +}var anot = aa[this.activeRow].annotations; +if (anot.length < this.av.getColumnSelection ().getMax ()) { +var temp = new Array (this.av.getColumnSelection ().getMax () + 2); +System.arraycopy (anot, 0, temp, 0, anot.length); +anot = temp; +aa[this.activeRow].annotations = anot; +}var label = ""; +if (this.av.getColumnSelection () != null && this.av.getColumnSelection ().size () > 0 && anot[this.av.getColumnSelection ().getMin ()] != null) { +label = anot[this.av.getColumnSelection ().getMin ()].displayCharacter; +}if (evt.getActionCommand ().equals ("Remove Annotation")) { +for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { +anot[this.av.getColumnSelection ().columnAt (i)] = null; +} +} else if (evt.getActionCommand ().equals ("Label")) { +label = this.enterLabel (label, "Enter Label"); +if (label == null) { +return; +}if ((label.length > 0) && !aa[this.activeRow].hasText) { +aa[this.activeRow].hasText = true; +}for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { +var index = this.av.getColumnSelection ().columnAt (i); +if (!this.av.getColumnSelection ().isVisible (index)) { +continue; +}if (anot[index] == null) { +anot[index] = new jalview.datamodel.Annotation (label, "", ' ', 0); +}anot[index].displayCharacter = label; +} +} else if (evt.getActionCommand ().equals ("Colour")) { +var udc = new jalview.appletgui.UserDefinedColours (this, java.awt.Color.black, this.ap.alignFrame); +var col = udc.getColor (); +for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { +var index = this.av.getColumnSelection ().columnAt (i); +if (!this.av.getColumnSelection ().isVisible (index)) { +continue; +}if (anot[index] == null) { +anot[index] = new jalview.datamodel.Annotation ("", "", ' ', 0); +}anot[index].colour = col; +} +} else { +var type = String.fromCharCode (0); +var symbol = "\u03B1"; +if (evt.getActionCommand ().equals ("Helix")) { +type = 'H'; +} else if (evt.getActionCommand ().equals ("Sheet")) { +type = 'E'; +symbol = "\u03B2"; +} else if (evt.getActionCommand ().equals ("RNA Helix")) { +type = 'S'; +symbol = "\u03C3"; +}if (!aa[this.activeRow].hasIcons) { +aa[this.activeRow].hasIcons = true; +}label = this.enterLabel (symbol, "Enter Label"); +if (label == null) { +return; +}if ((label.length > 0) && !aa[this.activeRow].hasText) { +aa[this.activeRow].hasText = true; +if (evt.getActionCommand ().equals ("RNA Helix")) { +aa[this.activeRow].showAllColLabels = true; +}}for (var i = 0; i < this.av.getColumnSelection ().size (); i++) { +var index = this.av.getColumnSelection ().columnAt (i); +if (!this.av.getColumnSelection ().isVisible (index)) { +continue; +}if (anot[index] == null) { +anot[index] = new jalview.datamodel.Annotation (label, "", type, 0); +}anot[index].secondaryStructure = type != 'S' ? type : label.length == 0 ? ' ' : label.charAt (0); +anot[index].displayCharacter = label; +} +}this.av.getAlignment ().validateAnnotation (aa[this.activeRow]); +this.ap.alignmentChanged (); +this.adjustPanelHeight (); +this.repaint (); +return; +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "enterLabel", +function (text, label) { +var dialog = new jalview.appletgui.EditNameDialog (text, null, label, null, this.ap.alignFrame, "Enter Label", 400, 200, true); +if (dialog.accept) { +return dialog.getName (); +} else { +return null; +}}, "~S,~S"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +var aa = this.av.getAlignment ().getAlignmentAnnotation (); +if (aa == null) { +return; +}var height = -this.scrollOffset; +this.activeRow = -1; +for (var i = 0; i < aa.length; i++) { +if (aa[i].visible) { +height += aa[i].height; +}if (evt.getY () < height) { +if (aa[i].editable) { +this.activeRow = i; +} else if (aa[i].graph > 0) { +this.graphStretch = i; +this.graphStretchY = evt.getY (); +}break; +}} +if ((evt.getModifiers () & 4) == 4 && this.activeRow != -1) { +if (this.av.getColumnSelection () == null) { +return; +}var pop = new awt2swing.PopupMenu (jalview.util.MessageManager.getString ("label.structure_type")); +var item; +if (this.av.getAlignment ().isNucleotide () == true) { +item = new awt2swing.MenuItem ("RNA Helix"); +item.addActionListener (this); +pop.add (item); +} else { +item = new awt2swing.MenuItem ("Helix"); +item.addActionListener (this); +pop.add (item); +item = new awt2swing.MenuItem ("Sheet"); +item.addActionListener (this); +pop.add (item); +}item = new awt2swing.MenuItem ("Label"); +item.addActionListener (this); +pop.add (item); +item = new awt2swing.MenuItem ("Colour"); +item.addActionListener (this); +pop.add (item); +item = new awt2swing.MenuItem ("Remove Annotation"); +item.addActionListener (this); +pop.add (item); +this.ap.alignFrame.add (pop); +pop.show (this, evt.getX (), evt.getY ()); +return; +}this.ap.scalePanel.mousePressed (evt); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.graphStretch = -1; +this.graphStretchY = -1; +this.mouseDragging = false; +if (this.needValidating) { +this.ap.validate (); +this.needValidating = false; +}this.ap.scalePanel.mouseReleased (evt); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +if (this.graphStretch > -1) { +this.av.getAlignment ().getAlignmentAnnotation ()[this.graphStretch].graphHeight += this.graphStretchY - evt.getY (); +if (this.av.getAlignment ().getAlignmentAnnotation ()[this.graphStretch].graphHeight < 0) { +this.av.getAlignment ().getAlignmentAnnotation ()[this.graphStretch].graphHeight = 0; +}this.graphStretchY = evt.getY (); +this.av.calcPanelHeight (); +this.needValidating = true; +this.ap.paintAlignment (true); +} else { +this.ap.scalePanel.mouseDragged (evt); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +var aa = this.av.getAlignment ().getAlignmentAnnotation (); +if (aa == null) { +return; +}var row = -1; +var height = -this.scrollOffset; +for (var i = 0; i < aa.length; i++) { +if (aa[i].visible) { +height += aa[i].height; +}if (evt.getY () < height) { +row = i; +break; +}} +var res = Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ()) + this.av.getStartRes (); +if (this.av.hasHiddenColumns ()) { +res = this.av.getColumnSelection ().adjustForHiddenColumns (res); +}if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null) { +var text = new StringBuffer ("Sequence position " + (res + 1)); +if (aa[row].annotations[res].description != null) { +text.append (" " + aa[row].annotations[res].description); +}this.ap.alignFrame.setStatus (text.toString ()); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +this.ap.scalePanel.mouseEntered (evt); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +this.ap.scalePanel.mouseExited (evt); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "adjustPanelHeight", +function () { +return this.adjustPanelHeight (true); +}); +Clazz.defineMethod (c$, "adjustPanelHeight", +function (repaint) { +var height = this.av.calcPanelHeight (); +this.setSize ( new java.awt.Dimension (this.getSize ().width, height)); +if (repaint) { +this.repaint (); +}return height; +}, "~B"); +Clazz.defineMethod (c$, "addEditableColumn", +function (i) { +if (this.activeRow == -1) { +var aa = this.av.getAlignment ().getAlignmentAnnotation (); +if (aa == null) { +return; +}for (var j = 0; j < aa.length; j++) { +if (aa[j].editable) { +this.activeRow = j; +break; +}} +}}, "~N"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +if (this.av.getWrapAlignment () || !this.av.isShowAnnotation ()) return; +var d = this.getSize (); +this.imgWidth = d.width; +if (this.imgWidth < 1 || d.height < 1) { +return; +}if (this.image == null || this.imgWidth != this.image.getWidth (this) || d.height != this.image.getHeight (this)) { +this.image = this.createImage (this.imgWidth, d.height); +this.gg = this.image.getGraphics (); +this.gg.setFont (this.av.getFont ()); +this.fm = this.gg.getFontMetrics (); +this.$fastPaint = false; +}if (this.$fastPaint) { +g.drawImage (this.image, 0, 0, this); +this.$fastPaint = false; +return; +}this.gg.setColor (java.awt.Color.white); +this.gg.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +this.drawComponent (this.gg, this.av.startRes, this.av.endRes + 1); +g.drawImage (this.image, 0, 0, this); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "fastPaint", +function (horizontal) { +if (horizontal == 0 || this.av.getAlignment ().getAlignmentAnnotation () == null || this.av.getAlignment ().getAlignmentAnnotation ().length < 1) { +this.repaint (); +return; +}this.gg.copyArea (0, 0, this.imgWidth, this.getSize ().height, -horizontal * this.av.getCharWidth (), 0); +var sr = this.av.startRes; +var er = this.av.endRes + 1; +var transX = 0; +if (horizontal > 0) { +transX = (er - sr - horizontal) * this.av.getCharWidth (); +sr = er - horizontal; +} else if (horizontal < 0) { +er = sr - horizontal; +}this.gg.translate (transX, 0); +this.drawComponent (this.gg, sr, er); +this.gg.translate (-transX, 0); +this.$fastPaint = true; +this.repaint (); +}, "~N"); +Clazz.defineMethod (c$, "drawComponent", +function (g, startRes, endRes) { +var ofont = this.av.getFont (); +g.setFont (ofont); +g.setColor (java.awt.Color.white); +g.fillRect (0, 0, (endRes - startRes) * this.av.getCharWidth (), this.getSize ().height); +if (this.fm == null) { +this.fm = g.getFontMetrics (); +}if ((this.av.getAlignment ().getAlignmentAnnotation () == null) || (this.av.getAlignment ().getAlignmentAnnotation ().length < 1)) { +g.setColor (java.awt.Color.white); +g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +g.setColor (java.awt.Color.black); +if (this.av.validCharWidth) { +g.drawString (jalview.util.MessageManager.getString ("label.alignment_has_no_annotations"), 20, 15); +}return; +}g.translate (0, -this.scrollOffset); +this.renderer.drawComponent (this, this.av, g, this.activeRow, startRes, endRes); +g.translate (0, +this.scrollOffset); +}, "java.awt.Graphics,~N,~N"); +Clazz.defineMethod (c$, "setScrollOffset", +function (value, repaint) { +this.scrollOffset = value; +if (repaint) { +this.repaint (); +}}, "~N,~B"); +Clazz.defineMethod (c$, "getFontMetrics", +function () { +return this.fm; +}); +Clazz.overrideMethod (c$, "getFadedImage", +function () { +return this.image; +}); +Clazz.overrideMethod (c$, "getFadedImageWidth", +function () { +return this.imgWidth; +}); +Clazz.overrideMethod (c$, "getVisibleVRange", +function () { +if (this.ap != null && this.ap.alabels != null) { +var sOffset = -this.ap.alabels.scrollOffset; +var visHeight = sOffset + this.ap.annotationPanelHolder.getHeight (); +this.$bounds[0] = sOffset; +this.$bounds[1] = visHeight; +return this.$bounds; +} else { +return null; +}}); +Clazz.defineStatics (c$, +"GRAPH_HEIGHT", 40); +}); diff --git a/bin/jalview/appletgui/AnnotationRowFilter.js b/bin/jalview/appletgui/AnnotationRowFilter.js index 8b9fe70..aafbcad 100644 --- a/bin/jalview/appletgui/AnnotationRowFilter.js +++ b/bin/jalview/appletgui/AnnotationRowFilter.js @@ -1,131 +1,131 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "$.Button", "$.Checkbox", "$.Scrollbar", "$.TextField"], "jalview.appletgui.AnnotationRowFilter", ["jalview.util.MessageManager", "java.lang.Float", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.ap = null; -this.annmap = null; -this.enableSeqAss = false; -this.currentAnnotation = null; -this.adjusting = false; -this.currentColours = null; -this.minColour = null; -this.maxColour = null; -this.seqAssociated = null; -this.thresholdIsMin = null; -this.slider = null; -this.thresholdValue = null; -this.frame = null; -this.ok = null; -this.cancel = null; -this.sliderDragging = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AnnotationRowFilter", awt2swing.Panel); -Clazz.prepareFields (c$, function () { -this.currentColours = new awt2swing.Checkbox (); -this.minColour = new awt2swing.Panel (); -this.maxColour = new awt2swing.Panel (); -this.seqAssociated = new awt2swing.Checkbox (); -this.thresholdIsMin = new awt2swing.Checkbox (); -this.slider = new awt2swing.Scrollbar (0); -this.thresholdValue = new awt2swing.TextField (20); -this.ok = new awt2swing.Button (); -this.cancel = new awt2swing.Button (); -}); -Clazz.makeConstructor (c$, -function (av, ap) { -Clazz.superConstructor (this, jalview.appletgui.AnnotationRowFilter, []); -this.av = av; -this.ap = ap; -}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.appletgui.AnnotationRowFilter, []); -}); -Clazz.defineMethod (c$, "getAnnotationItems", -function (isSeqAssociated) { -var list = new java.util.Vector (); -var index = 1; -var anmap = Clazz.newIntArray (this.av.getAlignment ().getAlignmentAnnotation ().length, 0); -for (var i = 0; i < this.av.getAlignment ().getAlignmentAnnotation ().length; i++) { -if (this.av.getAlignment ().getAlignmentAnnotation ()[i].sequenceRef == null) { -if (isSeqAssociated) { -continue; -}} else { -this.enableSeqAss = true; -}var label = this.av.getAlignment ().getAlignmentAnnotation ()[i].label; -if (!list.contains (label)) { -anmap[list.size ()] = i; -list.add (label); -} else { -if (!isSeqAssociated) { -anmap[list.size ()] = i; -list.add (label + "_" + (index++)); -}}} -this.annmap = Clazz.newIntArray (list.size (), 0); -System.arraycopy (anmap, 0, this.annmap, 0, this.annmap.length); -return list; -}, "~B"); -Clazz.defineMethod (c$, "getSelectedThresholdItem", -function (indexValue) { -var selectedThresholdItem = -1; -if (indexValue == 1) { -selectedThresholdItem = 1; -} else if (indexValue == 2) { -selectedThresholdItem = 0; -}return selectedThresholdItem; -}, "~N"); -Clazz.defineMethod (c$, "modelChanged", -function () { -this.seqAssociated.setEnabled (this.enableSeqAss); -}); -Clazz.defineMethod (c$, "ok_actionPerformed", -function (e) { -this.updateView (); -this.frame.setVisible (false); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "cancel_actionPerformed", -function (e) { -this.reset (); -this.ap.paintAlignment (true); -this.frame.setVisible (false); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "thresholdCheck_actionPerformed", -function (e) { -this.updateView (); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "annotations_actionPerformed", -function (e) { -this.updateView (); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "threshold_actionPerformed", -function (e) { -this.updateView (); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "thresholdValue_actionPerformed", -function (e) { -try { -var f = Float.parseFloat (this.thresholdValue.getText ()); -this.slider.setValue (Clazz.floatToInt (f * 1000)); -this.updateView (); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "populateThresholdComboBox", -function (threshold) { -threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold")); -threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold")); -threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold")); -}, "awt2swing.Choice"); -Clazz.defineMethod (c$, "getCurrentAnnotation", -function () { -return this.currentAnnotation; -}); -Clazz.defineMethod (c$, "setCurrentAnnotation", -function (currentAnnotation) { -this.currentAnnotation = currentAnnotation; -}, "jalview.datamodel.AlignmentAnnotation"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "$.Button", "$.Checkbox", "$.Scrollbar", "$.TextField"], "jalview.appletgui.AnnotationRowFilter", ["jalview.util.MessageManager", "java.lang.Float", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.ap = null; +this.annmap = null; +this.enableSeqAss = false; +this.currentAnnotation = null; +this.adjusting = false; +this.currentColours = null; +this.minColour = null; +this.maxColour = null; +this.seqAssociated = null; +this.thresholdIsMin = null; +this.slider = null; +this.thresholdValue = null; +this.frame = null; +this.ok = null; +this.cancel = null; +this.sliderDragging = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AnnotationRowFilter", awt2swing.Panel); +Clazz.prepareFields (c$, function () { +this.currentColours = new awt2swing.Checkbox (); +this.minColour = new awt2swing.Panel (); +this.maxColour = new awt2swing.Panel (); +this.seqAssociated = new awt2swing.Checkbox (); +this.thresholdIsMin = new awt2swing.Checkbox (); +this.slider = new awt2swing.Scrollbar (0); +this.thresholdValue = new awt2swing.TextField (20); +this.ok = new awt2swing.Button (); +this.cancel = new awt2swing.Button (); +}); +Clazz.makeConstructor (c$, +function (av, ap) { +Clazz.superConstructor (this, jalview.appletgui.AnnotationRowFilter, []); +this.av = av; +this.ap = ap; +}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.appletgui.AnnotationRowFilter, []); +}); +Clazz.defineMethod (c$, "getAnnotationItems", +function (isSeqAssociated) { +var list = new java.util.Vector (); +var index = 1; +var anmap = Clazz.newIntArray (this.av.getAlignment ().getAlignmentAnnotation ().length, 0); +for (var i = 0; i < this.av.getAlignment ().getAlignmentAnnotation ().length; i++) { +if (this.av.getAlignment ().getAlignmentAnnotation ()[i].sequenceRef == null) { +if (isSeqAssociated) { +continue; +}} else { +this.enableSeqAss = true; +}var label = this.av.getAlignment ().getAlignmentAnnotation ()[i].label; +if (!list.contains (label)) { +anmap[list.size ()] = i; +list.add (label); +} else { +if (!isSeqAssociated) { +anmap[list.size ()] = i; +list.add (label + "_" + (index++)); +}}} +this.annmap = Clazz.newIntArray (list.size (), 0); +System.arraycopy (anmap, 0, this.annmap, 0, this.annmap.length); +return list; +}, "~B"); +Clazz.defineMethod (c$, "getSelectedThresholdItem", +function (indexValue) { +var selectedThresholdItem = -1; +if (indexValue == 1) { +selectedThresholdItem = 1; +} else if (indexValue == 2) { +selectedThresholdItem = 0; +}return selectedThresholdItem; +}, "~N"); +Clazz.defineMethod (c$, "modelChanged", +function () { +this.seqAssociated.setEnabled (this.enableSeqAss); +}); +Clazz.defineMethod (c$, "ok_actionPerformed", +function (e) { +this.updateView (); +this.frame.setVisible (false); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "cancel_actionPerformed", +function (e) { +this.reset (); +this.ap.paintAlignment (true); +this.frame.setVisible (false); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "thresholdCheck_actionPerformed", +function (e) { +this.updateView (); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "annotations_actionPerformed", +function (e) { +this.updateView (); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "threshold_actionPerformed", +function (e) { +this.updateView (); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "thresholdValue_actionPerformed", +function (e) { +try { +var f = Float.parseFloat (this.thresholdValue.getText ()); +this.slider.setValue (Clazz.floatToInt (f * 1000)); +this.updateView (); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "populateThresholdComboBox", +function (threshold) { +threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold")); +threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold")); +threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold")); +}, "awt2swing.Choice"); +Clazz.defineMethod (c$, "getCurrentAnnotation", +function () { +return this.currentAnnotation; +}); +Clazz.defineMethod (c$, "setCurrentAnnotation", +function (currentAnnotation) { +this.currentAnnotation = currentAnnotation; +}, "jalview.datamodel.AlignmentAnnotation"); +}); diff --git a/bin/jalview/appletgui/AppletJmol.js b/bin/jalview/appletgui/AppletJmol.js index d2a97b8..b8f808a 100644 --- a/bin/jalview/appletgui/AppletJmol.js +++ b/bin/jalview/appletgui/AppletJmol.js @@ -1,48 +1,48 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.Dimension", "java.util.ArrayList"], "jalview.appletgui.AppletJmol", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.scriptWindow = null; -this.inputLine = null; -this.history = null; -this.renderPanel = null; -this.ap = null; -this._aps = null; -this.fileLoadingError = null; -this.loadedInline = false; -this.fr = null; -this.jmb = null; -if (!Clazz.isClassDefined ("jalview.appletgui.AppletJmol.RenderPanel")) { -jalview.appletgui.AppletJmol.$AppletJmol$RenderPanel$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AppletJmol"); -Clazz.prepareFields (c$, function () { -this._aps = new java.util.ArrayList (); -}); -Clazz.makeConstructor (c$, -function (entry, sequenceIs, object, ap2, uRL) { -}, "jalview.datamodel.PDBEntry,~A,~O,jalview.appletgui.AlignmentPanel,~S"); -Clazz.defineMethod (c$, "setJalviewColourScheme", -function (ucs) { -}, "jalview.schemes.UserColourScheme"); -c$.$AppletJmol$RenderPanel$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.currentSize = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.AppletJmol, "RenderPanel", awt2swing.Panel); -Clazz.prepareFields (c$, function () { -this.currentSize = new java.awt.Dimension (); -}); -Clazz.overrideMethod (c$, "update", -function (a) { -this.paint (a); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "PaintComponent", -function (a) { -this.currentSize = this.getSize (); -}, "java.awt.Graphics"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.Dimension", "java.util.ArrayList"], "jalview.appletgui.AppletJmol", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.scriptWindow = null; +this.inputLine = null; +this.history = null; +this.renderPanel = null; +this.ap = null; +this._aps = null; +this.fileLoadingError = null; +this.loadedInline = false; +this.fr = null; +this.jmb = null; +if (!Clazz.isClassDefined ("jalview.appletgui.AppletJmol.RenderPanel")) { +jalview.appletgui.AppletJmol.$AppletJmol$RenderPanel$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AppletJmol"); +Clazz.prepareFields (c$, function () { +this._aps = new java.util.ArrayList (); +}); +Clazz.makeConstructor (c$, +function (entry, sequenceIs, object, ap2, uRL) { +}, "jalview.datamodel.PDBEntry,~A,~O,jalview.appletgui.AlignmentPanel,~S"); +Clazz.defineMethod (c$, "setJalviewColourScheme", +function (ucs) { +}, "jalview.schemes.UserColourScheme"); +c$.$AppletJmol$RenderPanel$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.currentSize = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.AppletJmol, "RenderPanel", awt2swing.Panel); +Clazz.prepareFields (c$, function () { +this.currentSize = new java.awt.Dimension (); +}); +Clazz.overrideMethod (c$, "update", +function (a) { +this.paint (a); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "PaintComponent", +function (a) { +this.currentSize = this.getSize (); +}, "java.awt.Graphics"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/AppletJmolBinding.js b/bin/jalview/appletgui/AppletJmolBinding.js index cdb8890..7f93e13 100644 --- a/bin/jalview/appletgui/AppletJmolBinding.js +++ b/bin/jalview/appletgui/AppletJmolBinding.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.appletgui"); -c$ = Clazz.declareType (jalview.appletgui, "AppletJmolBinding"); +Clazz.declarePackage ("jalview.appletgui"); +c$ = Clazz.declareType (jalview.appletgui, "AppletJmolBinding"); diff --git a/bin/jalview/appletgui/CutAndPasteTransfer.class b/bin/jalview/appletgui/CutAndPasteTransfer.class index 31c248d..9292d36 100644 Binary files a/bin/jalview/appletgui/CutAndPasteTransfer.class and b/bin/jalview/appletgui/CutAndPasteTransfer.class differ diff --git a/bin/jalview/appletgui/CutAndPasteTransfer.js b/bin/jalview/appletgui/CutAndPasteTransfer.js index c1e339a..4030094 100644 --- a/bin/jalview/appletgui/CutAndPasteTransfer.js +++ b/bin/jalview/appletgui/CutAndPasteTransfer.js @@ -1,264 +1,264 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.MouseListener", "awt2swing.Button", "$.TextArea", "java.awt.BorderLayout"], "jalview.appletgui.CutAndPasteTransfer", ["awt2swing.Frame", "$.Label", "jalview.analysis.AlignmentUtils", "jalview.api.ComplexAlignFile", "jalview.appletgui.AlignFrame", "$.AppletJmol", "$.JVDialog", "$.SplitFrame", "jalview.datamodel.PDBEntry", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.IdentifyFile", "$.NewickFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.TCoffeeColourScheme", "jalview.util.MessageManager", "java.awt.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.pdbImport = false; -this.treeImport = false; -this.annotationImport = false; -this.seq = null; -this.alignFrame = null; -this.source = null; -this.textarea = null; -this.accept = null; -this.addSequences = null; -this.$cancel = null; -this.buttonPanel = null; -this.borderLayout1 = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "CutAndPasteTransfer", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.MouseListener]); -Clazz.prepareFields (c$, function () { -this.textarea = new awt2swing.TextArea (); -this.accept = new awt2swing.Button ("New Window"); -this.addSequences = new awt2swing.Button ("Add to Current Alignment"); -this.$cancel = new awt2swing.Button ("Close"); -this.buttonPanel = new awt2swing.Panel (); -this.borderLayout1 = new java.awt.BorderLayout (); -}); -Clazz.makeConstructor (c$, -function (forImport, alignFrame) { -Clazz.superConstructor (this, jalview.appletgui.CutAndPasteTransfer, []); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.alignFrame = alignFrame; -if (!forImport) { -this.buttonPanel.setVisible (false); -}}, "~B,jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "getText", -function () { -return this.textarea.getText (); -}); -Clazz.defineMethod (c$, "setText", -function (text) { -this.textarea.setText (text); -}, "~S"); -Clazz.defineMethod (c$, "setPDBImport", -function (seq) { -this.seq = seq; -this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept")); -this.addSequences.setVisible (false); -this.pdbImport = true; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "setTreeImport", -function () { -this.treeImport = true; -this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept")); -this.addSequences.setVisible (false); -}); -Clazz.defineMethod (c$, "setAnnotationImport", -function () { -this.annotationImport = true; -this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept")); -this.addSequences.setVisible (false); -}); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.accept) { -this.ok (true); -} else if (evt.getSource () === this.addSequences) { -this.ok (false); -} else if (evt.getSource () === this.$cancel) { -this.cancel (); -}}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "ok", -function (newWindow) { -var text = this.getText (); -var length = text.length; -this.textarea.append ("\n"); -if (this.textarea.getText ().length == length) { -var warning = "\n\n#################################################\nWARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n\nCAN\'T INPUT FULL ALIGNMENT\n\nYOU MUST DELETE THIS WARNING TO CONTINUE\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE\n#################################################\n"; -this.textarea.setText (text.substring (0, text.length - warning.length) + warning); -this.textarea.setCaretPosition (text.length); -}if (this.pdbImport) { -this.openPdbViewer (text); -} else if (this.treeImport) { -if (!this.loadTree ()) { -return; -}} else if (this.annotationImport) { -this.loadAnnotations (); -} else if (this.alignFrame != null) { -this.loadAlignment (text, newWindow, this.alignFrame.getAlignViewport ()); -}if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) { -(this.getParent ()).setVisible (false); -} else { -(this.getParent ()).setVisible (false); -}}, "~B"); -Clazz.defineMethod (c$, "loadTree", -function () { -try { -var fin = new jalview.io.NewickFile (this.textarea.getText (), "Paste"); -fin.parse (); -if (fin.getTree () != null) { -this.alignFrame.loadTree (fin, "Pasted tree file"); -return true; -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -this.textarea.setText (jalview.util.MessageManager.formatMessage ("label.could_not_parse_newick_file", Clazz.newArray (-1, [ex.getMessage ()]))); -return false; -} else { -throw ex; -} -} -return false; -}); -Clazz.defineMethod (c$, "loadAlignment", -function (text, newWindow, viewport) { -var al = null; -var format = new jalview.io.IdentifyFile ().Identify (text, jalview.io.AppletFormatAdapter.PASTE); -var afa = new jalview.io.AppletFormatAdapter (this.alignFrame.alignPanel); -try { -al = afa.readFile (text, jalview.io.AppletFormatAdapter.PASTE, format); -this.source = afa.getAlignFile (); -} catch (ex) { -if (Clazz.exceptionOf (ex, java.io.IOException)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -if (al != null) { -al.setDataset (null); -var allowSplitFrame = this.alignFrame.viewport.applet.getDefaultParameter ("enableSplitFrame", false); -if (allowSplitFrame && this.openSplitFrame (al, format)) { -return; -}if (newWindow) { -var af; -if (Clazz.instanceOf (this.source, jalview.api.ComplexAlignFile)) { -var colSel = (this.source).getColumnSelection (); -var hiddenSeqs = (this.source).getHiddenSequences (); -var showSeqFeatures = (this.source).isShowSeqFeatures (); -var cs = (this.source).getColourScheme (); -af = new jalview.appletgui.AlignFrame (al, hiddenSeqs, colSel, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false); -af.getAlignViewport ().setShowSequenceFeatures (showSeqFeatures); -af.changeColour (cs); -} else { -af = new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false); -}af.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment")); -} else { -this.alignFrame.addSequences (al.getSequencesArray ()); -this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_alignment_file")); -}}}, "~S,~B,jalview.appletgui.AlignViewport"); -Clazz.defineMethod (c$, "openSplitFrame", -function (al, format) { -var thisAlignment = this.alignFrame.getAlignViewport ().getAlignment (); -if (thisAlignment.isNucleotide () == al.isNucleotide ()) { -return false; -}var protein = thisAlignment.isNucleotide () ? al : thisAlignment; -var dna = thisAlignment.isNucleotide () ? thisAlignment : al; -var mapped = jalview.analysis.AlignmentUtils.mapProteinToCdna (protein, dna); -if (!mapped) { -return false; -}var title = jalview.util.MessageManager.getString ("label.open_split_window"); -var dialog = new jalview.appletgui.JVDialog (this.getParent (), title, true, 100, 400); -dialog.ok.setLabel (jalview.util.MessageManager.getString ("action.yes")); -dialog.cancel.setLabel (jalview.util.MessageManager.getString ("action.no")); -var question = new awt2swing.Panel ( new java.awt.BorderLayout ()); -var text = jalview.util.MessageManager.getString ("label.open_split_window?"); -question.add ( new awt2swing.Label (text, 0), "Center"); -dialog.setMainPanel (question); -dialog.setVisible (true); -dialog.toFront (); -if (!dialog.accept) { -return false; -}var applet = this.alignFrame.viewport.applet; -var copyFrame = new jalview.appletgui.AlignFrame (this.alignFrame.viewport.getAlignment (), applet, this.alignFrame.getTitle (), false, false); -var newFrame = new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false, false); -var dnaFrame = al.isNucleotide () ? newFrame : copyFrame; -var proteinFrame = al.isNucleotide () ? copyFrame : newFrame; -var sf = new jalview.appletgui.SplitFrame (dnaFrame, proteinFrame); -sf.addToDisplay (false, applet); -return true; -}, "jalview.datamodel.AlignmentI,~S"); -Clazz.defineMethod (c$, "loadAnnotations", -function () { -var tcf = null; -try { -tcf = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE]); -if (tcf.isValid ()) { -if (tcf.annotateAlignment (this.alignFrame.viewport.getAlignment (), true)) { -this.alignFrame.tcoffeeColour.setEnabled (true); -this.alignFrame.alignPanel.fontChanged (); -this.alignFrame.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignFrame.viewport.getAlignment ())); -this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_tcoffee_scores_to_alignment")); -} else { -this.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.failed_add_tcoffee_scores", Clazz.newArray (-1, [(tcf.getWarningMessage () != null ? tcf.getWarningMessage () : "")]))); -}} else { -tcf = null; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -tcf = null; -} else { -throw x; -} -} -if (tcf == null) { -if ( new jalview.io.AnnotationFile ().annotateAlignmentView (this.alignFrame.viewport, this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) { -this.alignFrame.alignPanel.fontChanged (); -this.alignFrame.alignPanel.setScrollValues (0, 0); -this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment")); -} else { -if (!this.alignFrame.parseFeaturesFile (this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) { -this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); -}}}}); -Clazz.defineMethod (c$, "openPdbViewer", -function (text) { -var pdb = new jalview.datamodel.PDBEntry (); -pdb.setFile (text); - new jalview.appletgui.AppletJmol (pdb, Clazz.newArray (-1, [this.seq]), null, this.alignFrame.alignPanel, jalview.io.AppletFormatAdapter.PASTE); -}, "~S"); -Clazz.defineMethod (c$, "cancel", -function () { -this.textarea.setText (""); -if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) { -(this.getParent ()).setVisible (false); -} else { -(this.getParent ()).setVisible (false); -}}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 10)); -this.textarea.setText (jalview.util.MessageManager.getString ("label.paste_your_alignment_file")); -this.textarea.addMouseListener (this); -this.setLayout (this.borderLayout1); -this.accept.addActionListener (this); -this.addSequences.addActionListener (this); -this.$cancel.addActionListener (this); -this.add (this.buttonPanel, "South"); -this.buttonPanel.add (this.accept, null); -this.buttonPanel.add (this.addSequences); -this.buttonPanel.add (this.$cancel, null); -this.add (this.textarea, "Center"); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -if (this.textarea.getText ().startsWith (jalview.util.MessageManager.getString ("label.paste_your"))) { -this.textarea.setText (""); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.MouseListener", "awt2swing.Button", "$.TextArea", "java.awt.BorderLayout"], "jalview.appletgui.CutAndPasteTransfer", ["awt2swing.Frame", "$.Label", "jalview.analysis.AlignmentUtils", "jalview.api.ComplexAlignFile", "jalview.appletgui.AlignFrame", "$.AppletJmol", "$.JVDialog", "$.SplitFrame", "jalview.datamodel.PDBEntry", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.IdentifyFile", "$.NewickFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.TCoffeeColourScheme", "jalview.util.MessageManager", "java.awt.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.pdbImport = false; +this.treeImport = false; +this.annotationImport = false; +this.seq = null; +this.alignFrame = null; +this.source = null; +this.textarea = null; +this.accept = null; +this.addSequences = null; +this.$cancel = null; +this.buttonPanel = null; +this.borderLayout1 = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "CutAndPasteTransfer", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.MouseListener]); +Clazz.prepareFields (c$, function () { +this.textarea = new awt2swing.TextArea (); +this.accept = new awt2swing.Button ("New Window"); +this.addSequences = new awt2swing.Button ("Add to Current Alignment"); +this.$cancel = new awt2swing.Button ("Close"); +this.buttonPanel = new awt2swing.Panel (); +this.borderLayout1 = new java.awt.BorderLayout (); +}); +Clazz.makeConstructor (c$, +function (forImport, alignFrame) { +Clazz.superConstructor (this, jalview.appletgui.CutAndPasteTransfer, []); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.alignFrame = alignFrame; +if (!forImport) { +this.buttonPanel.setVisible (false); +}}, "~B,jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "getText", +function () { +return this.textarea.getText (); +}); +Clazz.defineMethod (c$, "setText", +function (text) { +this.textarea.setText (text); +}, "~S"); +Clazz.defineMethod (c$, "setPDBImport", +function (seq) { +this.seq = seq; +this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept")); +this.addSequences.setVisible (false); +this.pdbImport = true; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "setTreeImport", +function () { +this.treeImport = true; +this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept")); +this.addSequences.setVisible (false); +}); +Clazz.defineMethod (c$, "setAnnotationImport", +function () { +this.annotationImport = true; +this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept")); +this.addSequences.setVisible (false); +}); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.accept) { +this.ok (true); +} else if (evt.getSource () === this.addSequences) { +this.ok (false); +} else if (evt.getSource () === this.$cancel) { +this.cancel (); +}}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "ok", +function (newWindow) { +var text = this.getText (); +var length = text.length; +this.textarea.append ("\n"); +if (this.textarea.getText ().length == length) { +var warning = "\n\n#################################################\nWARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n\nCAN\'T INPUT FULL ALIGNMENT\n\nYOU MUST DELETE THIS WARNING TO CONTINUE\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE\n#################################################\n"; +this.textarea.setText (text.substring (0, text.length - warning.length) + warning); +this.textarea.setCaretPosition (text.length); +}if (this.pdbImport) { +this.openPdbViewer (text); +} else if (this.treeImport) { +if (!this.loadTree ()) { +return; +}} else if (this.annotationImport) { +this.loadAnnotations (); +} else if (this.alignFrame != null) { +this.loadAlignment (text, newWindow, this.alignFrame.getAlignViewport ()); +}if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) { +(this.getParent ()).setVisible (false); +} else { +(this.getParent ()).setVisible (false); +}}, "~B"); +Clazz.defineMethod (c$, "loadTree", +function () { +try { +var fin = new jalview.io.NewickFile (this.textarea.getText (), "Paste"); +fin.parse (); +if (fin.getTree () != null) { +this.alignFrame.loadTree (fin, "Pasted tree file"); +return true; +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +this.textarea.setText (jalview.util.MessageManager.formatMessage ("label.could_not_parse_newick_file", Clazz.newArray (-1, [ex.getMessage ()]))); +return false; +} else { +throw ex; +} +} +return false; +}); +Clazz.defineMethod (c$, "loadAlignment", +function (text, newWindow, viewport) { +var al = null; +var format = new jalview.io.IdentifyFile ().Identify (text, jalview.io.AppletFormatAdapter.PASTE); +var afa = new jalview.io.AppletFormatAdapter (this.alignFrame.alignPanel); +try { +al = afa.readFile (text, jalview.io.AppletFormatAdapter.PASTE, format); +this.source = afa.getAlignFile (); +} catch (ex) { +if (Clazz.exceptionOf (ex, java.io.IOException)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +if (al != null) { +al.setDataset (null); +var allowSplitFrame = this.alignFrame.viewport.applet.getDefaultParameter ("enableSplitFrame", false); +if (allowSplitFrame && this.openSplitFrame (al, format)) { +return; +}if (newWindow) { +var af; +if (Clazz.instanceOf (this.source, jalview.api.ComplexAlignFile)) { +var colSel = (this.source).getColumnSelection (); +var hiddenSeqs = (this.source).getHiddenSequences (); +var showSeqFeatures = (this.source).isShowSeqFeatures (); +var cs = (this.source).getColourScheme (); +af = new jalview.appletgui.AlignFrame (al, hiddenSeqs, colSel, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false); +af.getAlignViewport ().setShowSequenceFeatures (showSeqFeatures); +af.changeColour (cs); +} else { +af = new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false); +}af.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment")); +} else { +this.alignFrame.addSequences (al.getSequencesArray ()); +this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_alignment_file")); +}}}, "~S,~B,jalview.appletgui.AlignViewport"); +Clazz.defineMethod (c$, "openSplitFrame", +function (al, format) { +var thisAlignment = this.alignFrame.getAlignViewport ().getAlignment (); +if (thisAlignment.isNucleotide () == al.isNucleotide ()) { +return false; +}var protein = thisAlignment.isNucleotide () ? al : thisAlignment; +var dna = thisAlignment.isNucleotide () ? thisAlignment : al; +var mapped = jalview.analysis.AlignmentUtils.mapProteinToCdna (protein, dna); +if (!mapped) { +return false; +}var title = jalview.util.MessageManager.getString ("label.open_split_window"); +var dialog = new jalview.appletgui.JVDialog (this.getParent (), title, true, 100, 400); +dialog.ok.setLabel (jalview.util.MessageManager.getString ("action.yes")); +dialog.cancel.setLabel (jalview.util.MessageManager.getString ("action.no")); +var question = new awt2swing.Panel ( new java.awt.BorderLayout ()); +var text = jalview.util.MessageManager.getString ("label.open_split_window?"); +question.add ( new awt2swing.Label (text, 0), "Center"); +dialog.setMainPanel (question); +dialog.setVisible (true); +dialog.toFront (); +if (!dialog.accept) { +return false; +}var applet = this.alignFrame.viewport.applet; +var copyFrame = new jalview.appletgui.AlignFrame (this.alignFrame.viewport.getAlignment (), applet, this.alignFrame.getTitle (), false, false); +var newFrame = new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false, false); +var dnaFrame = al.isNucleotide () ? newFrame : copyFrame; +var proteinFrame = al.isNucleotide () ? copyFrame : newFrame; +var sf = new jalview.appletgui.SplitFrame (dnaFrame, proteinFrame); +sf.addToDisplay (false, applet); +return true; +}, "jalview.datamodel.AlignmentI,~S"); +Clazz.defineMethod (c$, "loadAnnotations", +function () { +var tcf = null; +try { +tcf = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE]); +if (tcf.isValid ()) { +if (tcf.annotateAlignment (this.alignFrame.viewport.getAlignment (), true)) { +this.alignFrame.tcoffeeColour.setEnabled (true); +this.alignFrame.alignPanel.fontChanged (); +this.alignFrame.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignFrame.viewport.getAlignment ())); +this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_tcoffee_scores_to_alignment")); +} else { +this.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.failed_add_tcoffee_scores", Clazz.newArray (-1, [(tcf.getWarningMessage () != null ? tcf.getWarningMessage () : "")]))); +}} else { +tcf = null; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +tcf = null; +} else { +throw x; +} +} +if (tcf == null) { +if ( new jalview.io.AnnotationFile ().annotateAlignmentView (this.alignFrame.viewport, this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) { +this.alignFrame.alignPanel.fontChanged (); +this.alignFrame.alignPanel.setScrollValues (0, 0); +this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment")); +} else { +if (!this.alignFrame.parseFeaturesFile (this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) { +this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); +}}}}); +Clazz.defineMethod (c$, "openPdbViewer", +function (text) { +var pdb = new jalview.datamodel.PDBEntry (); +pdb.setFile (text); + new jalview.appletgui.AppletJmol (pdb, Clazz.newArray (-1, [this.seq]), null, this.alignFrame.alignPanel, jalview.io.AppletFormatAdapter.PASTE); +}, "~S"); +Clazz.defineMethod (c$, "cancel", +function () { +this.textarea.setText (""); +if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) { +(this.getParent ()).setVisible (false); +} else { +(this.getParent ()).setVisible (false); +}}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 10)); +this.textarea.setText (jalview.util.MessageManager.getString ("label.paste_your_alignment_file")); +this.textarea.addMouseListener (this); +this.setLayout (this.borderLayout1); +this.accept.addActionListener (this); +this.addSequences.addActionListener (this); +this.$cancel.addActionListener (this); +this.add (this.buttonPanel, "South"); +this.buttonPanel.add (this.accept, null); +this.buttonPanel.add (this.addSequences); +this.buttonPanel.add (this.$cancel, null); +this.add (this.textarea, "Center"); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +if (this.textarea.getText ().startsWith (jalview.util.MessageManager.getString ("label.paste_your"))) { +this.textarea.setText (""); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +}); diff --git a/bin/jalview/appletgui/EditNameDialog.js b/bin/jalview/appletgui/EditNameDialog.js index efedf02..68044ad 100644 --- a/bin/jalview/appletgui/EditNameDialog.js +++ b/bin/jalview/appletgui/EditNameDialog.js @@ -1,44 +1,44 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.appletgui.JVDialog"], "jalview.appletgui.EditNameDialog", ["awt2swing.Label", "$.Panel", "$.TextField", "java.awt.BorderLayout", "$.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.id = null; -this.description = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "EditNameDialog", jalview.appletgui.JVDialog); -Clazz.overrideMethod (c$, "getName", -function () { -return this.id.getText (); -}); -Clazz.defineMethod (c$, "getDescription", -function () { -if (this.description.getText ().length < 1) { -return null; -} else { -return this.description.getText (); -}}); -Clazz.makeConstructor (c$, -function (name, desc, label1, label2, owner, title, width, height, display) { -Clazz.superConstructor (this, jalview.appletgui.EditNameDialog, [owner, title, true, width, height]); -var mono = new java.awt.Font ("Monospaced", 0, 12); -var panel = new awt2swing.Panel ( new java.awt.BorderLayout ()); -var panel2 = new awt2swing.Panel ( new java.awt.BorderLayout ()); -this.id = new awt2swing.TextField (name, 40); -this.id.setFont (mono); -var label = new awt2swing.Label (label1); -label.setFont (mono); -panel2.add (label, "West"); -panel2.add (this.id, "Center"); -panel.add (panel2, "North"); -if (label2 != null) { -panel2 = new awt2swing.Panel ( new java.awt.BorderLayout ()); -this.description = new awt2swing.TextField (desc, 40); -this.description.setFont (mono); -label = new awt2swing.Label (label2); -label.setFont (mono); -panel2.add (label, "West"); -panel2.add (this.description, "Center"); -panel.add (panel2, "Center"); -}this.setMainPanel (panel); -this.setVisible (display); -}, "~S,~S,~S,~S,awt2swing.Frame,~S,~N,~N,~B"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.appletgui.JVDialog"], "jalview.appletgui.EditNameDialog", ["awt2swing.Label", "$.Panel", "$.TextField", "java.awt.BorderLayout", "$.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.id = null; +this.description = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "EditNameDialog", jalview.appletgui.JVDialog); +Clazz.overrideMethod (c$, "getName", +function () { +return this.id.getText (); +}); +Clazz.defineMethod (c$, "getDescription", +function () { +if (this.description.getText ().length < 1) { +return null; +} else { +return this.description.getText (); +}}); +Clazz.makeConstructor (c$, +function (name, desc, label1, label2, owner, title, width, height, display) { +Clazz.superConstructor (this, jalview.appletgui.EditNameDialog, [owner, title, true, width, height]); +var mono = new java.awt.Font ("Monospaced", 0, 12); +var panel = new awt2swing.Panel ( new java.awt.BorderLayout ()); +var panel2 = new awt2swing.Panel ( new java.awt.BorderLayout ()); +this.id = new awt2swing.TextField (name, 40); +this.id.setFont (mono); +var label = new awt2swing.Label (label1); +label.setFont (mono); +panel2.add (label, "West"); +panel2.add (this.id, "Center"); +panel.add (panel2, "North"); +if (label2 != null) { +panel2 = new awt2swing.Panel ( new java.awt.BorderLayout ()); +this.description = new awt2swing.TextField (desc, 40); +this.description.setFont (mono); +label = new awt2swing.Label (label2); +label.setFont (mono); +panel2.add (label, "West"); +panel2.add (this.description, "Center"); +panel.add (panel2, "Center"); +}this.setMainPanel (panel); +this.setVisible (display); +}, "~S,~S,~S,~S,awt2swing.Frame,~S,~N,~N,~B"); +}); diff --git a/bin/jalview/appletgui/EmbmenuFrame.js b/bin/jalview/appletgui/EmbmenuFrame.js index 13a7183..7a5362c 100644 --- a/bin/jalview/appletgui/EmbmenuFrame.js +++ b/bin/jalview/appletgui/EmbmenuFrame.js @@ -1,110 +1,110 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Frame", "java.awt.event.MouseListener", "java.awt.Font", "java.util.HashMap"], "jalview.appletgui.EmbmenuFrame", ["awt2swing.Label", "$.Panel", "$.PopupMenu", "jalview.util.Platform", "java.awt.Color", "$.FlowLayout"], function () { -c$ = Clazz.decorateAsClass (function () { -this.embeddedPopup = null; -this.embeddedMenu = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "EmbmenuFrame", awt2swing.Frame, java.awt.event.MouseListener); -Clazz.prepareFields (c$, function () { -this.embeddedPopup = new java.util.HashMap (); -}); -Clazz.defineMethod (c$, "embedMenuIfNeeded", -function (tobeAdjusted) { -var topMenuBar = this.getJMenuBar (); -if (topMenuBar == null) { -return false; -}if (jalview.util.Platform.isAMac ()) { -this.embeddedMenu = this.makeEmbeddedPopupMenu (topMenuBar, true, false); -this.unsetMenuBar (); -this.add (this.embeddedMenu, "North"); -tobeAdjusted.setSize (this.getSize ().width, this.getSize ().height - this.embeddedMenu.getHeight ()); -return true; -}return false; -}, "awt2swing.Panel"); -Clazz.defineMethod (c$, "makeEmbeddedPopupMenu", -function (menuBar, overrideFonts, append) { -if (!append) { -this.embeddedPopup.clear (); -if (this.embeddedMenu != null) { -this.embeddedMenu.removeAll (); -}}this.embeddedMenu = this.makeEmbeddedPopupMenu (menuBar, jalview.appletgui.EmbmenuFrame.DEFAULT_MENU_FONT, overrideFonts, new awt2swing.Panel (), this); -return this.embeddedMenu; -}, "awt2swing.MenuBar,~B,~B"); -Clazz.defineMethod (c$, "makeEmbeddedPopupMenu", -function (menuBar, font, overrideFonts, embeddedMenu, clickHandler) { -if (overrideFonts) { -var mbf = menuBar.getFont (); -if (mbf != null) { -font = mbf; -}}if (embeddedMenu == null) { -embeddedMenu = new awt2swing.Panel (); -}var flowLayout1 = new java.awt.FlowLayout (); -embeddedMenu.setBackground (java.awt.Color.lightGray); -embeddedMenu.setLayout (flowLayout1); -for (var mbi = 0, nMbi = menuBar.getMenuCount (); mbi < nMbi; mbi++) { -var mi = menuBar.getMenu (mbi); -var elab = new awt2swing.Label (mi.getLabel ()); -elab.setFont (font); -var popup = new awt2swing.PopupMenu (); -var m; -var mSize = mi.getItemCount (); -for (m = 0; m < mSize; m++) { -if (mi.getItem (m) == null) popup.addSeparator (); - else popup.add (mi.getItem (m)); -mSize--; -m--; -} -this.embeddedPopup.put (elab, popup); -embeddedMenu.add (elab); -elab.addMouseListener (clickHandler); -} -flowLayout1.setAlignment (0); -flowLayout1.setHgap (2); -flowLayout1.setVgap (0); -return embeddedMenu; -}, "awt2swing.MenuBar,java.awt.Font,~B,awt2swing.Panel,java.awt.event.MouseListener"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -var popup = null; -var source = evt.getSource (); -popup = this.getPopupMenu (source); -if (popup != null) { -this.embeddedMenu.add (popup); -popup.show (this.embeddedMenu, source.getBounds ().x, source.getBounds ().y + source.getBounds ().getSize ().height); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "getPopupMenu", -function (source) { -return this.embeddedPopup.get (source); -}, "awt2swing.Label"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "destroyMenus", -function () { -if (this.embeddedPopup != null) { -for (var lb, $lb = this.embeddedPopup.keySet ().iterator (); $lb.hasNext () && ((lb = $lb.next ()) || true);) { -lb.removeMouseListener (this); -} -this.embeddedPopup.clear (); -}if (this.embeddedMenu != null) { -this.embeddedMenu.removeAll (); -}}); -Clazz.defineMethod (c$, "finalize", -function () { -this.destroyMenus (); -this.embeddedPopup = null; -this.embeddedMenu = null; -Clazz.superCall (this, jalview.appletgui.EmbmenuFrame, "finalize", []); -}); -c$.FONT_ARIAL_PLAIN_11 = c$.prototype.FONT_ARIAL_PLAIN_11 = new java.awt.Font ("Arial", 0, 11); -c$.DEFAULT_MENU_FONT = c$.prototype.DEFAULT_MENU_FONT = jalview.appletgui.EmbmenuFrame.FONT_ARIAL_PLAIN_11; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Frame", "java.awt.event.MouseListener", "java.awt.Font", "java.util.HashMap"], "jalview.appletgui.EmbmenuFrame", ["awt2swing.Label", "$.Panel", "$.PopupMenu", "jalview.util.Platform", "java.awt.Color", "$.FlowLayout"], function () { +c$ = Clazz.decorateAsClass (function () { +this.embeddedPopup = null; +this.embeddedMenu = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "EmbmenuFrame", awt2swing.Frame, java.awt.event.MouseListener); +Clazz.prepareFields (c$, function () { +this.embeddedPopup = new java.util.HashMap (); +}); +Clazz.defineMethod (c$, "embedMenuIfNeeded", +function (tobeAdjusted) { +var topMenuBar = this.getJMenuBar (); +if (topMenuBar == null) { +return false; +}if (jalview.util.Platform.isAMac ()) { +this.embeddedMenu = this.makeEmbeddedPopupMenu (topMenuBar, true, false); +this.unsetMenuBar (); +this.add (this.embeddedMenu, "North"); +tobeAdjusted.setSize (this.getSize ().width, this.getSize ().height - this.embeddedMenu.getHeight ()); +return true; +}return false; +}, "awt2swing.Panel"); +Clazz.defineMethod (c$, "makeEmbeddedPopupMenu", +function (menuBar, overrideFonts, append) { +if (!append) { +this.embeddedPopup.clear (); +if (this.embeddedMenu != null) { +this.embeddedMenu.removeAll (); +}}this.embeddedMenu = this.makeEmbeddedPopupMenu (menuBar, jalview.appletgui.EmbmenuFrame.DEFAULT_MENU_FONT, overrideFonts, new awt2swing.Panel (), this); +return this.embeddedMenu; +}, "awt2swing.MenuBar,~B,~B"); +Clazz.defineMethod (c$, "makeEmbeddedPopupMenu", +function (menuBar, font, overrideFonts, embeddedMenu, clickHandler) { +if (overrideFonts) { +var mbf = menuBar.getFont (); +if (mbf != null) { +font = mbf; +}}if (embeddedMenu == null) { +embeddedMenu = new awt2swing.Panel (); +}var flowLayout1 = new java.awt.FlowLayout (); +embeddedMenu.setBackground (java.awt.Color.lightGray); +embeddedMenu.setLayout (flowLayout1); +for (var mbi = 0, nMbi = menuBar.getMenuCount (); mbi < nMbi; mbi++) { +var mi = menuBar.getMenu (mbi); +var elab = new awt2swing.Label (mi.getLabel ()); +elab.setFont (font); +var popup = new awt2swing.PopupMenu (); +var m; +var mSize = mi.getItemCount (); +for (m = 0; m < mSize; m++) { +if (mi.getItem (m) == null) popup.addSeparator (); + else popup.add (mi.getItem (m)); +mSize--; +m--; +} +this.embeddedPopup.put (elab, popup); +embeddedMenu.add (elab); +elab.addMouseListener (clickHandler); +} +flowLayout1.setAlignment (0); +flowLayout1.setHgap (2); +flowLayout1.setVgap (0); +return embeddedMenu; +}, "awt2swing.MenuBar,java.awt.Font,~B,awt2swing.Panel,java.awt.event.MouseListener"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +var popup = null; +var source = evt.getSource (); +popup = this.getPopupMenu (source); +if (popup != null) { +this.embeddedMenu.add (popup); +popup.show (this.embeddedMenu, source.getBounds ().x, source.getBounds ().y + source.getBounds ().getSize ().height); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "getPopupMenu", +function (source) { +return this.embeddedPopup.get (source); +}, "awt2swing.Label"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "destroyMenus", +function () { +if (this.embeddedPopup != null) { +for (var lb, $lb = this.embeddedPopup.keySet ().iterator (); $lb.hasNext () && ((lb = $lb.next ()) || true);) { +lb.removeMouseListener (this); +} +this.embeddedPopup.clear (); +}if (this.embeddedMenu != null) { +this.embeddedMenu.removeAll (); +}}); +Clazz.defineMethod (c$, "finalize", +function () { +this.destroyMenus (); +this.embeddedPopup = null; +this.embeddedMenu = null; +Clazz.superCall (this, jalview.appletgui.EmbmenuFrame, "finalize", []); +}); +c$.FONT_ARIAL_PLAIN_11 = c$.prototype.FONT_ARIAL_PLAIN_11 = new java.awt.Font ("Arial", 0, 11); +c$.DEFAULT_MENU_FONT = c$.prototype.DEFAULT_MENU_FONT = jalview.appletgui.EmbmenuFrame.FONT_ARIAL_PLAIN_11; +}); diff --git a/bin/jalview/appletgui/ExtJmol.js b/bin/jalview/appletgui/ExtJmol.js index 170d005..150efd5 100644 --- a/bin/jalview/appletgui/ExtJmol.js +++ b/bin/jalview/appletgui/ExtJmol.js @@ -1,17 +1,17 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.structures.models.AAStructureBindingModel"], "jalview.appletgui.ExtJmol", null, function () { -c$ = Clazz.declareType (jalview.appletgui, "ExtJmol", jalview.structures.models.AAStructureBindingModel); -Clazz.overrideMethod (c$, "getPdbFile", -function () { -return null; -}); -Clazz.overrideMethod (c$, "updateColours", -function (source) { -}, "~O"); -Clazz.overrideMethod (c$, "releaseReferences", -function (svl) { -}, "~O"); -Clazz.overrideMethod (c$, "highlightAtoms", -function (atoms) { -}, "java.util.List"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.structures.models.AAStructureBindingModel"], "jalview.appletgui.ExtJmol", null, function () { +c$ = Clazz.declareType (jalview.appletgui, "ExtJmol", jalview.structures.models.AAStructureBindingModel); +Clazz.overrideMethod (c$, "getPdbFile", +function () { +return null; +}); +Clazz.overrideMethod (c$, "updateColours", +function (source) { +}, "~O"); +Clazz.overrideMethod (c$, "releaseReferences", +function (svl) { +}, "~O"); +Clazz.overrideMethod (c$, "highlightAtoms", +function (atoms) { +}, "java.util.List"); +}); diff --git a/bin/jalview/appletgui/FeatureColourChooser.class b/bin/jalview/appletgui/FeatureColourChooser.class index 0c8e554..8aee64e 100644 Binary files a/bin/jalview/appletgui/FeatureColourChooser.class and b/bin/jalview/appletgui/FeatureColourChooser.class differ diff --git a/bin/jalview/appletgui/FeatureColourChooser.js b/bin/jalview/appletgui/FeatureColourChooser.js index cfa5380..929c04b 100644 --- a/bin/jalview/appletgui/FeatureColourChooser.js +++ b/bin/jalview/appletgui/FeatureColourChooser.js @@ -1,292 +1,292 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Checkbox", "$.Choice", "$.Scrollbar", "$.TextField"], "jalview.appletgui.FeatureColourChooser", ["awt2swing.Label", "jalview.appletgui.JVDialog", "$.PaintRefresher", "$.UserDefinedColours", "jalview.datamodel.GraphLine", "jalview.schemes.GraduatedColor", "jalview.util.MessageManager", "java.awt.Color", "$.Dimension", "$.FlowLayout", "$.Font", "$.GridLayout", "java.awt.event.ActionEvent", "java.lang.Float"], function () { -c$ = Clazz.decorateAsClass (function () { -this.frame = null; -this.owner = null; -this.fr = null; -this.fs = null; -this.cs = null; -this.oldcs = null; -this.oldgroupColours = null; -this.adjusting = false; -this.min = 0; -this.max = 0; -this.type = null; -this.af = null; -this.minColour = null; -this.maxColour = null; -this.jPanel1 = null; -this.jPanel2 = null; -this.threshold = null; -this.jPanel3 = null; -this.jPanel4 = null; -this.slider = null; -this.thresholdValue = null; -this.thresholdIsMin = null; -this.colourFromLabel = null; -this.threshline = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "FeatureColourChooser", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]); -Clazz.prepareFields (c$, function () { -this.minColour = new awt2swing.Panel (); -this.maxColour = new awt2swing.Panel (); -this.jPanel1 = new awt2swing.Panel (); -this.jPanel2 = new awt2swing.Panel (); -this.threshold = new awt2swing.Choice (); -this.jPanel3 = new awt2swing.Panel (); -this.jPanel4 = new awt2swing.Panel (); -this.slider = new awt2swing.Scrollbar (0); -this.thresholdValue = new awt2swing.TextField (20); -this.thresholdIsMin = new awt2swing.Checkbox (); -this.colourFromLabel = new awt2swing.Checkbox (); -}); -Clazz.makeConstructor (c$, -function (af, type) { -Clazz.superConstructor (this, jalview.appletgui.FeatureColourChooser, []); -this.af = af; -this.init (af.getSeqcanvas ().getFeatureRenderer (), type); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.makeConstructor (c$, -function (fsettings, type) { -Clazz.superConstructor (this, jalview.appletgui.FeatureColourChooser, []); -this.fs = fsettings; -this.init (fsettings.fr, type); -}, "jalview.appletgui.FeatureSettings,~S"); -Clazz.defineMethod (c$, "init", -($fz = function (frenderer, type) { -this.type = type; -this.fr = frenderer; -var mm = (this.fr.getMinMax ().get (type))[0]; -this.min = mm[0]; -this.max = mm[1]; -this.oldcs = this.fr.getFeatureColours ().get (type); -if (Clazz.instanceOf (this.oldcs, jalview.schemes.GraduatedColor)) { -this.cs = new jalview.schemes.GraduatedColor (this.oldcs, this.min, this.max); -} else { -var bl = java.awt.Color.black; -if (Clazz.instanceOf (this.oldcs, java.awt.Color)) { -bl = this.oldcs; -}this.cs = new jalview.schemes.GraduatedColor (java.awt.Color.white, bl, mm[0], mm[1]); -}this.minColour.setBackground (this.cs.getMinColor ()); -this.maxColour.setBackground (this.cs.getMaxColor ()); -this.minColour.setForeground (this.cs.getMinColor ()); -this.maxColour.setForeground (this.cs.getMaxColor ()); -this.colourFromLabel.setState (this.cs.isColourByLabel ()); -this.adjusting = true; -try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -this.threshold.select (new Integer (this.cs.getThreshType () == -1 ? 0 : this.cs.getThreshType () == 1 ? 1 : 2)); -this.adjusting = false; -this.changeColour (); -this.colourFromLabel.addItemListener (this); -this.slider.addAdjustmentListener (this); -this.slider.addMouseListener (this); -this.owner = (this.af != null) ? this.af : this.fs.frame; -this.frame = new jalview.appletgui.JVDialog (this.owner, jalview.util.MessageManager.formatMessage ("label.graduated_color_for_params", Clazz.newArray (-1, [type])), true, 480, 248); -this.frame.setMainPanel (this); -this.validate (); -this.frame.setVisible (true); -if (this.frame.accept) { -this.changeColour (); -} else { -this.reset (); -jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); -this.frame.setVisible (false); -}}, $fz.isPrivate = true, $fz), "jalview.appletgui.FeatureRenderer,~S"); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.appletgui.FeatureColourChooser, []); -try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -var minLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.min")); -var maxLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.max")); -minLabel.setFont ( new java.awt.Font ("Verdana", 0, 11)); -maxLabel.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.minColour.setBounds (0, 0, 40, 27); -this.maxColour.setBounds (0, 0, 40, 27); -this.minColour.addMouseListener (this); -this.maxColour.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.maxColour.addMouseListener (this); -this.thresholdIsMin.addItemListener (this); -this.setLayout ( new java.awt.GridLayout (4, 1)); -this.jPanel1.setLayout ( new java.awt.FlowLayout ()); -this.jPanel2.setLayout ( new java.awt.FlowLayout ()); -this.jPanel3.setLayout ( new java.awt.GridLayout (1, 1)); -this.jPanel4.setLayout ( new java.awt.FlowLayout ()); -this.jPanel1.setBackground (java.awt.Color.white); -this.jPanel2.setBackground (java.awt.Color.white); -this.jPanel4.setBackground (java.awt.Color.white); -this.threshold.addItemListener (this); -this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold")); -this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold")); -this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold")); -this.thresholdValue.addActionListener (this); -this.slider.setBackground (java.awt.Color.white); -this.slider.setEnabled (false); -this.slider.setSize ( new java.awt.Dimension (93, 21)); -this.thresholdValue.setEnabled (false); -this.thresholdValue.setSize ( new java.awt.Dimension (79, 22)); -this.thresholdValue.setColumns (5); -this.jPanel3.setBackground (java.awt.Color.white); -this.colourFromLabel.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.colourFromLabel.setLabel (jalview.util.MessageManager.getString ("label.colour_by_label")); -this.colourFromLabel.setSize ( new java.awt.Dimension (139, 22)); -this.thresholdIsMin.setBackground (java.awt.Color.white); -this.thresholdIsMin.setLabel (jalview.util.MessageManager.getString ("label.threshold_minmax")); -this.thresholdIsMin.setSize ( new java.awt.Dimension (135, 23)); -this.jPanel1.add (minLabel); -this.jPanel1.add (this.minColour); -this.jPanel1.add (maxLabel); -this.jPanel1.add (this.maxColour); -this.jPanel1.add (this.colourFromLabel); -this.jPanel2.add (this.threshold); -this.jPanel3.add (this.slider); -this.jPanel4.add (this.thresholdValue); -this.jPanel4.add (this.thresholdIsMin); -this.add (this.jPanel1); -this.add (this.jPanel2); -this.add (this.jPanel3); -this.add (this.jPanel4); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.thresholdValue) { -try { -var f = new Float (this.thresholdValue.getText ()).floatValue (); -this.slider.setValue (Clazz.floatToInt (f * 1000)); -this.adjustmentValueChanged (null); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -} else if (evt.getSource () === this.minColour) { -this.minColour_actionPerformed (null); -} else if (evt.getSource () === this.maxColour) { -this.maxColour_actionPerformed (null); -} else { -this.changeColour (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -this.maxColour.setEnabled (!this.colourFromLabel.getState ()); -this.minColour.setEnabled (!this.colourFromLabel.getState ()); -this.changeColour (); -}, "java.awt.event.ItemEvent"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -if (!this.adjusting) { -this.thresholdValue.setText ((this.slider.getValue () / 1000) + ""); -this.valueChanged (); -}}, "java.awt.event.AdjustmentEvent"); -Clazz.defineMethod (c$, "valueChanged", -function () { -this.threshline.value = this.slider.getValue () / 1000; -this.cs.setThresh (this.threshline.value); -this.changeColour (); -jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); -}); -Clazz.defineMethod (c$, "minColour_actionPerformed", -function (newCol) { -if (newCol == null) { -var udc = new jalview.appletgui.UserDefinedColours (this, this.minColour.getBackground (), this.owner, jalview.util.MessageManager.getString ("label.select_colour_minimum_value")); -} else { -this.minColour.setBackground (newCol); -this.minColour.setForeground (newCol); -this.minColour.repaint (); -this.changeColour (); -}}, "java.awt.Color"); -Clazz.defineMethod (c$, "maxColour_actionPerformed", -function (newCol) { -if (newCol == null) { -var udc = new jalview.appletgui.UserDefinedColours (this, this.maxColour.getBackground (), this.owner, jalview.util.MessageManager.getString ("label.select_colour_maximum_value")); -} else { -this.maxColour.setBackground (newCol); -this.maxColour.setForeground (newCol); -this.maxColour.repaint (); -this.changeColour (); -}}, "java.awt.Color"); -Clazz.defineMethod (c$, "changeColour", -function () { -if (this.adjusting) { -return; -}var aboveThreshold = -1; -if (this.threshold.getSelectedIndex () == 1) { -aboveThreshold = 1; -} else if (this.threshold.getSelectedIndex () == 2) { -aboveThreshold = 0; -}this.slider.setEnabled (true); -this.thresholdValue.setEnabled (true); -var acg = new jalview.schemes.GraduatedColor (this.minColour.getBackground (), this.maxColour.getBackground (), this.min, this.max); -acg.setColourByLabel (this.colourFromLabel.getState ()); -this.maxColour.setEnabled (!this.colourFromLabel.getState ()); -this.minColour.setEnabled (!this.colourFromLabel.getState ()); -if (aboveThreshold == -1) { -this.slider.setEnabled (false); -this.thresholdValue.setEnabled (false); -this.thresholdValue.setText (""); -} else if (aboveThreshold != -1 && this.threshline == null) { -this.threshline = new jalview.datamodel.GraphLine ((this.max - this.min) / 2, "Threshold", java.awt.Color.black); -}if (aboveThreshold != -1) { -this.adjusting = true; -acg.setThresh (this.threshline.value); -var range = this.max * 1000 - this.min * 1000; -this.slider.setMinimum (Clazz.floatToInt (this.min * 1000)); -this.slider.setMaximum (Clazz.floatToInt (this.max * 1000)); -this.slider.setValue (Clazz.floatToInt (this.threshline.value * 1000)); -this.thresholdValue.setText (this.threshline.value + ""); -this.slider.setEnabled (true); -this.thresholdValue.setEnabled (true); -this.adjusting = false; -}acg.setThreshType (aboveThreshold); -if (this.thresholdIsMin.getState () && aboveThreshold != -1) { -if (aboveThreshold == 1) { -acg = new jalview.schemes.GraduatedColor (acg, this.threshline.value, this.max); -} else { -acg = new jalview.schemes.GraduatedColor (acg, this.min, this.threshline.value); -}}this.fr.setColour (this.type, acg); -this.cs = acg; -jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); -}); -Clazz.defineMethod (c$, "reset", -function () { -this.fr.setColour (this.type, this.oldcs); -jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); -}); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -if (evt.getSource () === this.minColour || evt.getSource () === this.maxColour) { -this.actionPerformed ( new java.awt.event.ActionEvent (evt.getSource (), 1, "Clicked")); -} else { -jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Checkbox", "$.Choice", "$.Scrollbar", "$.TextField"], "jalview.appletgui.FeatureColourChooser", ["awt2swing.Label", "jalview.appletgui.JVDialog", "$.PaintRefresher", "$.UserDefinedColours", "jalview.datamodel.GraphLine", "jalview.schemes.GraduatedColor", "jalview.util.MessageManager", "java.awt.Color", "$.Dimension", "$.FlowLayout", "$.Font", "$.GridLayout", "java.awt.event.ActionEvent", "java.lang.Float"], function () { +c$ = Clazz.decorateAsClass (function () { +this.frame = null; +this.owner = null; +this.fr = null; +this.fs = null; +this.cs = null; +this.oldcs = null; +this.oldgroupColours = null; +this.adjusting = false; +this.min = 0; +this.max = 0; +this.type = null; +this.af = null; +this.minColour = null; +this.maxColour = null; +this.jPanel1 = null; +this.jPanel2 = null; +this.threshold = null; +this.jPanel3 = null; +this.jPanel4 = null; +this.slider = null; +this.thresholdValue = null; +this.thresholdIsMin = null; +this.colourFromLabel = null; +this.threshline = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "FeatureColourChooser", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]); +Clazz.prepareFields (c$, function () { +this.minColour = new awt2swing.Panel (); +this.maxColour = new awt2swing.Panel (); +this.jPanel1 = new awt2swing.Panel (); +this.jPanel2 = new awt2swing.Panel (); +this.threshold = new awt2swing.Choice (); +this.jPanel3 = new awt2swing.Panel (); +this.jPanel4 = new awt2swing.Panel (); +this.slider = new awt2swing.Scrollbar (0); +this.thresholdValue = new awt2swing.TextField (20); +this.thresholdIsMin = new awt2swing.Checkbox (); +this.colourFromLabel = new awt2swing.Checkbox (); +}); +Clazz.makeConstructor (c$, +function (af, type) { +Clazz.superConstructor (this, jalview.appletgui.FeatureColourChooser, []); +this.af = af; +this.init (af.getSeqcanvas ().getFeatureRenderer (), type); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.makeConstructor (c$, +function (fsettings, type) { +Clazz.superConstructor (this, jalview.appletgui.FeatureColourChooser, []); +this.fs = fsettings; +this.init (fsettings.fr, type); +}, "jalview.appletgui.FeatureSettings,~S"); +Clazz.defineMethod (c$, "init", +($fz = function (frenderer, type) { +this.type = type; +this.fr = frenderer; +var mm = (this.fr.getMinMax ().get (type))[0]; +this.min = mm[0]; +this.max = mm[1]; +this.oldcs = this.fr.getFeatureColours ().get (type); +if (Clazz.instanceOf (this.oldcs, jalview.schemes.GraduatedColor)) { +this.cs = new jalview.schemes.GraduatedColor (this.oldcs, this.min, this.max); +} else { +var bl = java.awt.Color.black; +if (Clazz.instanceOf (this.oldcs, java.awt.Color)) { +bl = this.oldcs; +}this.cs = new jalview.schemes.GraduatedColor (java.awt.Color.white, bl, mm[0], mm[1]); +}this.minColour.setBackground (this.cs.getMinColor ()); +this.maxColour.setBackground (this.cs.getMaxColor ()); +this.minColour.setForeground (this.cs.getMinColor ()); +this.maxColour.setForeground (this.cs.getMaxColor ()); +this.colourFromLabel.setState (this.cs.isColourByLabel ()); +this.adjusting = true; +try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +this.threshold.select (new Integer (this.cs.getThreshType () == -1 ? 0 : this.cs.getThreshType () == 1 ? 1 : 2)); +this.adjusting = false; +this.changeColour (); +this.colourFromLabel.addItemListener (this); +this.slider.addAdjustmentListener (this); +this.slider.addMouseListener (this); +this.owner = (this.af != null) ? this.af : this.fs.frame; +this.frame = new jalview.appletgui.JVDialog (this.owner, jalview.util.MessageManager.formatMessage ("label.graduated_color_for_params", Clazz.newArray (-1, [type])), true, 480, 248); +this.frame.setMainPanel (this); +this.validate (); +this.frame.setVisible (true); +if (this.frame.accept) { +this.changeColour (); +} else { +this.reset (); +jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); +this.frame.setVisible (false); +}}, $fz.isPrivate = true, $fz), "jalview.appletgui.FeatureRenderer,~S"); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.appletgui.FeatureColourChooser, []); +try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +var minLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.min")); +var maxLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.max")); +minLabel.setFont ( new java.awt.Font ("Verdana", 0, 11)); +maxLabel.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.minColour.setBounds (0, 0, 40, 27); +this.maxColour.setBounds (0, 0, 40, 27); +this.minColour.addMouseListener (this); +this.maxColour.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.maxColour.addMouseListener (this); +this.thresholdIsMin.addItemListener (this); +this.setLayout ( new java.awt.GridLayout (4, 1)); +this.jPanel1.setLayout ( new java.awt.FlowLayout ()); +this.jPanel2.setLayout ( new java.awt.FlowLayout ()); +this.jPanel3.setLayout ( new java.awt.GridLayout (1, 1)); +this.jPanel4.setLayout ( new java.awt.FlowLayout ()); +this.jPanel1.setBackground (java.awt.Color.white); +this.jPanel2.setBackground (java.awt.Color.white); +this.jPanel4.setBackground (java.awt.Color.white); +this.threshold.addItemListener (this); +this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold")); +this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold")); +this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold")); +this.thresholdValue.addActionListener (this); +this.slider.setBackground (java.awt.Color.white); +this.slider.setEnabled (false); +this.slider.setSize ( new java.awt.Dimension (93, 21)); +this.thresholdValue.setEnabled (false); +this.thresholdValue.setSize ( new java.awt.Dimension (79, 22)); +this.thresholdValue.setColumns (5); +this.jPanel3.setBackground (java.awt.Color.white); +this.colourFromLabel.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.colourFromLabel.setLabel (jalview.util.MessageManager.getString ("label.colour_by_label")); +this.colourFromLabel.setSize ( new java.awt.Dimension (139, 22)); +this.thresholdIsMin.setBackground (java.awt.Color.white); +this.thresholdIsMin.setLabel (jalview.util.MessageManager.getString ("label.threshold_minmax")); +this.thresholdIsMin.setSize ( new java.awt.Dimension (135, 23)); +this.jPanel1.add (minLabel); +this.jPanel1.add (this.minColour); +this.jPanel1.add (maxLabel); +this.jPanel1.add (this.maxColour); +this.jPanel1.add (this.colourFromLabel); +this.jPanel2.add (this.threshold); +this.jPanel3.add (this.slider); +this.jPanel4.add (this.thresholdValue); +this.jPanel4.add (this.thresholdIsMin); +this.add (this.jPanel1); +this.add (this.jPanel2); +this.add (this.jPanel3); +this.add (this.jPanel4); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.thresholdValue) { +try { +var f = new Float (this.thresholdValue.getText ()).floatValue (); +this.slider.setValue (Clazz.floatToInt (f * 1000)); +this.adjustmentValueChanged (null); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +} else if (evt.getSource () === this.minColour) { +this.minColour_actionPerformed (null); +} else if (evt.getSource () === this.maxColour) { +this.maxColour_actionPerformed (null); +} else { +this.changeColour (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +this.maxColour.setEnabled (!this.colourFromLabel.getState ()); +this.minColour.setEnabled (!this.colourFromLabel.getState ()); +this.changeColour (); +}, "java.awt.event.ItemEvent"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +if (!this.adjusting) { +this.thresholdValue.setText ((this.slider.getValue () / 1000) + ""); +this.valueChanged (); +}}, "java.awt.event.AdjustmentEvent"); +Clazz.defineMethod (c$, "valueChanged", +function () { +this.threshline.value = this.slider.getValue () / 1000; +this.cs.setThresh (this.threshline.value); +this.changeColour (); +jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); +}); +Clazz.defineMethod (c$, "minColour_actionPerformed", +function (newCol) { +if (newCol == null) { +var udc = new jalview.appletgui.UserDefinedColours (this, this.minColour.getBackground (), this.owner, jalview.util.MessageManager.getString ("label.select_colour_minimum_value")); +} else { +this.minColour.setBackground (newCol); +this.minColour.setForeground (newCol); +this.minColour.repaint (); +this.changeColour (); +}}, "java.awt.Color"); +Clazz.defineMethod (c$, "maxColour_actionPerformed", +function (newCol) { +if (newCol == null) { +var udc = new jalview.appletgui.UserDefinedColours (this, this.maxColour.getBackground (), this.owner, jalview.util.MessageManager.getString ("label.select_colour_maximum_value")); +} else { +this.maxColour.setBackground (newCol); +this.maxColour.setForeground (newCol); +this.maxColour.repaint (); +this.changeColour (); +}}, "java.awt.Color"); +Clazz.defineMethod (c$, "changeColour", +function () { +if (this.adjusting) { +return; +}var aboveThreshold = -1; +if (this.threshold.getSelectedIndex () == 1) { +aboveThreshold = 1; +} else if (this.threshold.getSelectedIndex () == 2) { +aboveThreshold = 0; +}this.slider.setEnabled (true); +this.thresholdValue.setEnabled (true); +var acg = new jalview.schemes.GraduatedColor (this.minColour.getBackground (), this.maxColour.getBackground (), this.min, this.max); +acg.setColourByLabel (this.colourFromLabel.getState ()); +this.maxColour.setEnabled (!this.colourFromLabel.getState ()); +this.minColour.setEnabled (!this.colourFromLabel.getState ()); +if (aboveThreshold == -1) { +this.slider.setEnabled (false); +this.thresholdValue.setEnabled (false); +this.thresholdValue.setText (""); +} else if (aboveThreshold != -1 && this.threshline == null) { +this.threshline = new jalview.datamodel.GraphLine ((this.max - this.min) / 2, "Threshold", java.awt.Color.black); +}if (aboveThreshold != -1) { +this.adjusting = true; +acg.setThresh (this.threshline.value); +var range = this.max * 1000 - this.min * 1000; +this.slider.setMinimum (Clazz.floatToInt (this.min * 1000)); +this.slider.setMaximum (Clazz.floatToInt (this.max * 1000)); +this.slider.setValue (Clazz.floatToInt (this.threshline.value * 1000)); +this.thresholdValue.setText (this.threshline.value + ""); +this.slider.setEnabled (true); +this.thresholdValue.setEnabled (true); +this.adjusting = false; +}acg.setThreshType (aboveThreshold); +if (this.thresholdIsMin.getState () && aboveThreshold != -1) { +if (aboveThreshold == 1) { +acg = new jalview.schemes.GraduatedColor (acg, this.threshline.value, this.max); +} else { +acg = new jalview.schemes.GraduatedColor (acg, this.min, this.threshline.value); +}}this.fr.setColour (this.type, acg); +this.cs = acg; +jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); +}); +Clazz.defineMethod (c$, "reset", +function () { +this.fr.setColour (this.type, this.oldcs); +jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); +}); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +if (evt.getSource () === this.minColour || evt.getSource () === this.maxColour) { +this.actionPerformed ( new java.awt.event.ActionEvent (evt.getSource (), 1, "Clicked")); +} else { +jalview.appletgui.PaintRefresher.Refresh (this, this.fr.getViewport ().getSequenceSetId ()); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +}); diff --git a/bin/jalview/appletgui/FeatureRenderer.class b/bin/jalview/appletgui/FeatureRenderer.class index 94cc9b3..6582fe7 100644 Binary files a/bin/jalview/appletgui/FeatureRenderer.class and b/bin/jalview/appletgui/FeatureRenderer.class differ diff --git a/bin/jalview/appletgui/FeatureRenderer.js b/bin/jalview/appletgui/FeatureRenderer.js index 05b643c..3d688fd 100644 --- a/bin/jalview/appletgui/FeatureRenderer.js +++ b/bin/jalview/appletgui/FeatureRenderer.js @@ -1,272 +1,272 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "jalview.renderer.seqfeatures.FeatureRenderer"], "jalview.appletgui.FeatureRenderer", ["awt2swing.Button", "$.Choice", "$.Label", "$.ScrollPane", "$.TextArea", "$.TextField", "jalview.appletgui.FeatureColourChooser", "$.JVDialog", "$.UserDefinedColours", "jalview.datamodel.SearchResults", "jalview.io.FeaturesFile", "jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.Font", "$.GridLayout", "java.awt.event.ActionListener", "$.ItemListener", "$.MouseAdapter", "java.lang.Error"], function () { -c$ = Clazz.decorateAsClass (function () { -this.featureLinks = null; -this.featureIndex = 0; -this.deleteFeature = false; -this.colourPanel = null; -if (!Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer.FeatureColourPanel")) { -jalview.appletgui.FeatureRenderer.$FeatureRenderer$FeatureColourPanel$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "FeatureRenderer", jalview.renderer.seqfeatures.FeatureRenderer); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer); -this.av = av; -this.setTransparencyAvailable (!System.getProperty ("java.version").startsWith ("1.1")); -}, "jalview.viewmodel.AlignmentViewport"); -Clazz.defineMethod (c$, "amendFeatures", -function (sequences, features, newFeatures, ap) { -var bigPanel = new awt2swing.Panel ( new java.awt.BorderLayout ()); -var name = new awt2swing.TextField (16); -var source = new awt2swing.TextField (16); -var description = new awt2swing.TextArea (3, 35); -var start = new awt2swing.TextField (8); -var end = new awt2swing.TextField (8); -var overlaps; -var deleteButton = new awt2swing.Button ("Delete"); -this.deleteFeature = false; -this.colourPanel = Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer.FeatureColourPanel, this, null); -this.colourPanel.setSize (110, 15); -var fr = this; -var panel = new awt2swing.Panel ( new java.awt.GridLayout (3, 1)); -this.featureIndex = 0; -var tmp; -if (!newFeatures && features.length > 1) { -panel = new awt2swing.Panel ( new java.awt.GridLayout (4, 1)); -tmp = new awt2swing.Panel (); -tmp.add ( new awt2swing.Label ("Select Feature: ")); -overlaps = new awt2swing.Choice (); -for (var i = 0; i < features.length; i++) { -var item = features[i].getType () + "/" + features[i].getBegin () + "-" + features[i].getEnd (); -if (features[i].getFeatureGroup () != null) { -item += " (" + features[i].getFeatureGroup () + ")"; -}overlaps.addItem (item); -} -tmp.add (overlaps); -overlaps.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$1") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$1, this, Clazz.cloneFinals ("overlaps", overlaps, "name", name, "features", features, "description", description, "source", source, "start", start, "end", end, "sequences", sequences, "ap", ap)))); -panel.add (tmp); -}tmp = new awt2swing.Panel (); -panel.add (tmp); -tmp.add ( new awt2swing.Label ("Name: ", 4)); -tmp.add (name); -tmp = new awt2swing.Panel (); -panel.add (tmp); -tmp.add ( new awt2swing.Label ("Group: ", 4)); -tmp.add (source); -tmp = new awt2swing.Panel (); -panel.add (tmp); -tmp.add ( new awt2swing.Label ("Colour: ", 4)); -tmp.add (this.colourPanel); -bigPanel.add (panel, "North"); -panel = new awt2swing.Panel (); -panel.add ( new awt2swing.Label ("Description: ", 4)); -panel.add ( new awt2swing.ScrollPane ().add (description)); -if (!newFeatures) { -bigPanel.add (panel, "South"); -panel = new awt2swing.Panel (); -panel.add ( new awt2swing.Label (" Start:", 4)); -panel.add (start); -panel.add ( new awt2swing.Label (" End:", 4)); -panel.add (end); -bigPanel.add (panel, "Center"); -} else { -bigPanel.add (panel, "Center"); -}if (jalview.appletgui.FeatureRenderer.lastFeatureAdded == null) { -if (features[0].type != null) { -jalview.appletgui.FeatureRenderer.lastFeatureAdded = features[0].type; -} else { -jalview.appletgui.FeatureRenderer.lastFeatureAdded = "feature_1"; -}}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded == null) { -if (features[0].featureGroup != null) { -jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = features[0].featureGroup; -} else { -jalview.appletgui.FeatureRenderer.lastFeatureAdded = "Jalview"; -}}var title = newFeatures ? jalview.util.MessageManager.getString ("label.create_new_sequence_features") : jalview.util.MessageManager.formatMessage ("label.amend_delete_features", Clazz.newArray (-1, [sequences[0].getName ()])); -var dialog = new jalview.appletgui.JVDialog (ap.alignFrame, title, true, 385, 240); -dialog.setMainPanel (bigPanel); -if (newFeatures) { -name.setText (jalview.appletgui.FeatureRenderer.lastFeatureAdded); -source.setText (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded); -} else { -dialog.ok.setLabel (jalview.util.MessageManager.getString ("label.amend")); -dialog.buttonPanel.add (deleteButton, 1); -deleteButton.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$2") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$2, this, Clazz.cloneFinals ("dialog", dialog)))); -name.setText (features[0].getType ()); -source.setText (features[0].getFeatureGroup ()); -}start.setText (features[0].getBegin () + ""); -end.setText (features[0].getEnd () + ""); -description.setText (features[0].getDescription ()); -var col = this.getColour (name.getText ()); -if (col == null) { -col = new jalview.schemes.UserColourScheme ().createColourFromName (name.getText ()); -}var fcol = this.getFeatureStyle (name.getText ()); -this.colourPanel.updateColor (fcol); -dialog.setResizable (true); -this.colourPanel.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$3") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$3, this, Clazz.cloneFinals ("fr", fr, "ap", ap, "name", name, "dialog", dialog)))); -dialog.setVisible (true); -var ffile = new jalview.io.FeaturesFile (); -if (dialog.accept) { -this.lastSeq = null; -jalview.appletgui.FeatureRenderer.lastFeatureAdded = name.getText ().trim (); -jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = source.getText ().trim (); -jalview.appletgui.FeatureRenderer.lastDescriptionAdded = description.getText ().$replace ('\n', ' '); -}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null && jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded.length < 1) { -jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = null; -}if (!newFeatures) { -var sf = features[this.featureIndex]; -if (dialog.accept) { -sf.type = jalview.appletgui.FeatureRenderer.lastFeatureAdded; -sf.featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded; -sf.description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded; -if (!this.colourPanel.isGcol) { -this.setColour (sf.type, this.colourPanel.getBackground ()); -}try { -sf.begin = Integer.parseInt (start.getText ()); -sf.end = Integer.parseInt (end.getText ()); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -ffile.parseDescriptionHTML (sf, false); -this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded); -}if (this.deleteFeature) { -sequences[0].deleteFeature (sf); -}} else { -if (dialog.accept && name.getText ().length > 0) { -for (var i = 0; i < sequences.length; i++) { -features[i].type = jalview.appletgui.FeatureRenderer.lastFeatureAdded; -features[i].featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded; -features[i].description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded; -sequences[i].addSequenceFeature (features[i]); -ffile.parseDescriptionHTML (features[i], false); -} -var newColour = this.colourPanel.getBackground (); -if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null) { -this.setGroupVisibility (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded, true); -}this.setColour (jalview.appletgui.FeatureRenderer.lastFeatureAdded, newColour); -this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded); -this.findAllFeatures (false); -} else { -return false; -}}if ((this.av).featureSettings != null) { -(this.av).featureSettings.refreshTable (); -}ap.paintAlignment (true); -return true; -}, "~A,~A,~B,jalview.appletgui.AlignmentPanel"); -c$.$FeatureRenderer$FeatureColourPanel$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.label = ""; -this.maxCol = null; -this.isColourByLabel = false; -this.isGcol = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.FeatureRenderer, "FeatureColourPanel", awt2swing.Panel); -Clazz.defineMethod (c$, "updateColor", -function (a) { -var b; -var c = null; -var d = null; -var e = ""; -if (Clazz.instanceOf (a, java.awt.Color)) { -this.isGcol = false; -c = a; -d = null; -} else if (Clazz.instanceOf (a, jalview.schemes.GraduatedColor)) { -this.isGcol = true; -d = a; -c = null; -} else { -throw new Error (jalview.util.MessageManager.getString ("error.invalid_colour_for_mycheckbox")); -}if (c != null) { -this.setBackground (b = c); -} else { -if (d.getThreshType () != -1) { -e += " " + ((d.getThreshType () == 1) ? "(>)" : "(<)"); -}if (this.isColourByLabel = d.isColourByLabel ()) { -this.setBackground (b = java.awt.Color.white); -e += " (by Label)"; -} else { -this.setBackground (b = d.getMinColor ()); -this.maxCol = d.getMaxColor (); -}}this.label = e; -this.setBackground (b); -this.repaint (); -}, "~O"); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer.FeatureColourPanel, [null]); -}); -Clazz.defineMethod (c$, "PaintComponent", -function (a) { -var b = this.getSize (); -if (this.isGcol) { -if (this.isColourByLabel) { -a.setColor (java.awt.Color.white); -a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); -a.setColor (java.awt.Color.black); -var c = new java.awt.Font ("Verdana", 0, 10); -a.setFont (c); -a.drawString (jalview.util.MessageManager.getString ("label.label"), 0, 0); -} else { -a.setColor (this.maxCol); -a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); -}}}, "java.awt.Graphics"); -c$ = Clazz.p0p (); -}; -c$.$FeatureRenderer$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$1", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (e) { -var index = this.f$.overlaps.getSelectedIndex (); -if (index != -1) { -this.b$["jalview.appletgui.FeatureRenderer"].featureIndex = index; -this.f$.name.setText (this.f$.features[index].getType ()); -this.f$.description.setText (this.f$.features[index].getDescription ()); -this.f$.source.setText (this.f$.features[index].getFeatureGroup ()); -this.f$.start.setText (this.f$.features[index].getBegin () + ""); -this.f$.end.setText (this.f$.features[index].getEnd () + ""); -var highlight = new jalview.datamodel.SearchResults (); -highlight.addResult (this.f$.sequences[0], this.f$.features[index].getBegin (), this.f$.features[index].getEnd ()); -this.f$.ap.seqPanel.seqCanvas.highlightSearchResults (highlight); -}var col = this.b$["jalview.appletgui.FeatureRenderer"].getFeatureStyle (this.f$.name.getText ()); -if (col == null) { -col = new jalview.schemes.UserColourScheme ().createColourFromName (this.f$.name.getText ()); -}this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.updateColor (col); -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$FeatureRenderer$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$2", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -this.b$["jalview.appletgui.FeatureRenderer"].deleteFeature = true; -this.f$.dialog.setVisible (false); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$FeatureRenderer$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$3", java.awt.event.MouseAdapter); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -if (!this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.isGcol) { - new jalview.appletgui.UserDefinedColours (this.f$.fr, this.f$.ap.alignFrame); -} else { -var fcc = new jalview.appletgui.FeatureColourChooser (this.f$.ap.alignFrame, this.f$.name.getText ()); -this.f$.dialog.transferFocus (); -}}, "java.awt.event.MouseEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"lastFeatureAdded", null, -"lastFeatureGroupAdded", null, -"lastDescriptionAdded", null); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "jalview.renderer.seqfeatures.FeatureRenderer"], "jalview.appletgui.FeatureRenderer", ["awt2swing.Button", "$.Choice", "$.Label", "$.ScrollPane", "$.TextArea", "$.TextField", "jalview.appletgui.FeatureColourChooser", "$.JVDialog", "$.UserDefinedColours", "jalview.datamodel.SearchResults", "jalview.io.FeaturesFile", "jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.Font", "$.GridLayout", "java.awt.event.ActionListener", "$.ItemListener", "$.MouseAdapter", "java.lang.Error"], function () { +c$ = Clazz.decorateAsClass (function () { +this.featureLinks = null; +this.featureIndex = 0; +this.deleteFeature = false; +this.colourPanel = null; +if (!Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer.FeatureColourPanel")) { +jalview.appletgui.FeatureRenderer.$FeatureRenderer$FeatureColourPanel$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "FeatureRenderer", jalview.renderer.seqfeatures.FeatureRenderer); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer); +this.av = av; +this.setTransparencyAvailable (!System.getProperty ("java.version").startsWith ("1.1")); +}, "jalview.viewmodel.AlignmentViewport"); +Clazz.defineMethod (c$, "amendFeatures", +function (sequences, features, newFeatures, ap) { +var bigPanel = new awt2swing.Panel ( new java.awt.BorderLayout ()); +var name = new awt2swing.TextField (16); +var source = new awt2swing.TextField (16); +var description = new awt2swing.TextArea (3, 35); +var start = new awt2swing.TextField (8); +var end = new awt2swing.TextField (8); +var overlaps; +var deleteButton = new awt2swing.Button ("Delete"); +this.deleteFeature = false; +this.colourPanel = Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer.FeatureColourPanel, this, null); +this.colourPanel.setSize (110, 15); +var fr = this; +var panel = new awt2swing.Panel ( new java.awt.GridLayout (3, 1)); +this.featureIndex = 0; +var tmp; +if (!newFeatures && features.length > 1) { +panel = new awt2swing.Panel ( new java.awt.GridLayout (4, 1)); +tmp = new awt2swing.Panel (); +tmp.add ( new awt2swing.Label ("Select Feature: ")); +overlaps = new awt2swing.Choice (); +for (var i = 0; i < features.length; i++) { +var item = features[i].getType () + "/" + features[i].getBegin () + "-" + features[i].getEnd (); +if (features[i].getFeatureGroup () != null) { +item += " (" + features[i].getFeatureGroup () + ")"; +}overlaps.addItem (item); +} +tmp.add (overlaps); +overlaps.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$1") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$1, this, Clazz.cloneFinals ("overlaps", overlaps, "name", name, "features", features, "description", description, "source", source, "start", start, "end", end, "sequences", sequences, "ap", ap)))); +panel.add (tmp); +}tmp = new awt2swing.Panel (); +panel.add (tmp); +tmp.add ( new awt2swing.Label ("Name: ", 4)); +tmp.add (name); +tmp = new awt2swing.Panel (); +panel.add (tmp); +tmp.add ( new awt2swing.Label ("Group: ", 4)); +tmp.add (source); +tmp = new awt2swing.Panel (); +panel.add (tmp); +tmp.add ( new awt2swing.Label ("Colour: ", 4)); +tmp.add (this.colourPanel); +bigPanel.add (panel, "North"); +panel = new awt2swing.Panel (); +panel.add ( new awt2swing.Label ("Description: ", 4)); +panel.add ( new awt2swing.ScrollPane ().add (description)); +if (!newFeatures) { +bigPanel.add (panel, "South"); +panel = new awt2swing.Panel (); +panel.add ( new awt2swing.Label (" Start:", 4)); +panel.add (start); +panel.add ( new awt2swing.Label (" End:", 4)); +panel.add (end); +bigPanel.add (panel, "Center"); +} else { +bigPanel.add (panel, "Center"); +}if (jalview.appletgui.FeatureRenderer.lastFeatureAdded == null) { +if (features[0].type != null) { +jalview.appletgui.FeatureRenderer.lastFeatureAdded = features[0].type; +} else { +jalview.appletgui.FeatureRenderer.lastFeatureAdded = "feature_1"; +}}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded == null) { +if (features[0].featureGroup != null) { +jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = features[0].featureGroup; +} else { +jalview.appletgui.FeatureRenderer.lastFeatureAdded = "Jalview"; +}}var title = newFeatures ? jalview.util.MessageManager.getString ("label.create_new_sequence_features") : jalview.util.MessageManager.formatMessage ("label.amend_delete_features", Clazz.newArray (-1, [sequences[0].getName ()])); +var dialog = new jalview.appletgui.JVDialog (ap.alignFrame, title, true, 385, 240); +dialog.setMainPanel (bigPanel); +if (newFeatures) { +name.setText (jalview.appletgui.FeatureRenderer.lastFeatureAdded); +source.setText (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded); +} else { +dialog.ok.setLabel (jalview.util.MessageManager.getString ("label.amend")); +dialog.buttonPanel.add (deleteButton, 1); +deleteButton.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$2") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$2, this, Clazz.cloneFinals ("dialog", dialog)))); +name.setText (features[0].getType ()); +source.setText (features[0].getFeatureGroup ()); +}start.setText (features[0].getBegin () + ""); +end.setText (features[0].getEnd () + ""); +description.setText (features[0].getDescription ()); +var col = this.getColour (name.getText ()); +if (col == null) { +col = new jalview.schemes.UserColourScheme ().createColourFromName (name.getText ()); +}var fcol = this.getFeatureStyle (name.getText ()); +this.colourPanel.updateColor (fcol); +dialog.setResizable (true); +this.colourPanel.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$3") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$3, this, Clazz.cloneFinals ("fr", fr, "ap", ap, "name", name, "dialog", dialog)))); +dialog.setVisible (true); +var ffile = new jalview.io.FeaturesFile (); +if (dialog.accept) { +this.lastSeq = null; +jalview.appletgui.FeatureRenderer.lastFeatureAdded = name.getText ().trim (); +jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = source.getText ().trim (); +jalview.appletgui.FeatureRenderer.lastDescriptionAdded = description.getText ().$replace ('\n', ' '); +}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null && jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded.length < 1) { +jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = null; +}if (!newFeatures) { +var sf = features[this.featureIndex]; +if (dialog.accept) { +sf.type = jalview.appletgui.FeatureRenderer.lastFeatureAdded; +sf.featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded; +sf.description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded; +if (!this.colourPanel.isGcol) { +this.setColour (sf.type, this.colourPanel.getBackground ()); +}try { +sf.begin = Integer.parseInt (start.getText ()); +sf.end = Integer.parseInt (end.getText ()); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +ffile.parseDescriptionHTML (sf, false); +this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded); +}if (this.deleteFeature) { +sequences[0].deleteFeature (sf); +}} else { +if (dialog.accept && name.getText ().length > 0) { +for (var i = 0; i < sequences.length; i++) { +features[i].type = jalview.appletgui.FeatureRenderer.lastFeatureAdded; +features[i].featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded; +features[i].description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded; +sequences[i].addSequenceFeature (features[i]); +ffile.parseDescriptionHTML (features[i], false); +} +var newColour = this.colourPanel.getBackground (); +if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null) { +this.setGroupVisibility (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded, true); +}this.setColour (jalview.appletgui.FeatureRenderer.lastFeatureAdded, newColour); +this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded); +this.findAllFeatures (false); +} else { +return false; +}}if ((this.av).featureSettings != null) { +(this.av).featureSettings.refreshTable (); +}ap.paintAlignment (true); +return true; +}, "~A,~A,~B,jalview.appletgui.AlignmentPanel"); +c$.$FeatureRenderer$FeatureColourPanel$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.label = ""; +this.maxCol = null; +this.isColourByLabel = false; +this.isGcol = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.FeatureRenderer, "FeatureColourPanel", awt2swing.Panel); +Clazz.defineMethod (c$, "updateColor", +function (a) { +var b; +var c = null; +var d = null; +var e = ""; +if (Clazz.instanceOf (a, java.awt.Color)) { +this.isGcol = false; +c = a; +d = null; +} else if (Clazz.instanceOf (a, jalview.schemes.GraduatedColor)) { +this.isGcol = true; +d = a; +c = null; +} else { +throw new Error (jalview.util.MessageManager.getString ("error.invalid_colour_for_mycheckbox")); +}if (c != null) { +this.setBackground (b = c); +} else { +if (d.getThreshType () != -1) { +e += " " + ((d.getThreshType () == 1) ? "(>)" : "(<)"); +}if (this.isColourByLabel = d.isColourByLabel ()) { +this.setBackground (b = java.awt.Color.white); +e += " (by Label)"; +} else { +this.setBackground (b = d.getMinColor ()); +this.maxCol = d.getMaxColor (); +}}this.label = e; +this.setBackground (b); +this.repaint (); +}, "~O"); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer.FeatureColourPanel, [null]); +}); +Clazz.defineMethod (c$, "PaintComponent", +function (a) { +var b = this.getSize (); +if (this.isGcol) { +if (this.isColourByLabel) { +a.setColor (java.awt.Color.white); +a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); +a.setColor (java.awt.Color.black); +var c = new java.awt.Font ("Verdana", 0, 10); +a.setFont (c); +a.drawString (jalview.util.MessageManager.getString ("label.label"), 0, 0); +} else { +a.setColor (this.maxCol); +a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); +}}}, "java.awt.Graphics"); +c$ = Clazz.p0p (); +}; +c$.$FeatureRenderer$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$1", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (e) { +var index = this.f$.overlaps.getSelectedIndex (); +if (index != -1) { +this.b$["jalview.appletgui.FeatureRenderer"].featureIndex = index; +this.f$.name.setText (this.f$.features[index].getType ()); +this.f$.description.setText (this.f$.features[index].getDescription ()); +this.f$.source.setText (this.f$.features[index].getFeatureGroup ()); +this.f$.start.setText (this.f$.features[index].getBegin () + ""); +this.f$.end.setText (this.f$.features[index].getEnd () + ""); +var highlight = new jalview.datamodel.SearchResults (); +highlight.addResult (this.f$.sequences[0], this.f$.features[index].getBegin (), this.f$.features[index].getEnd ()); +this.f$.ap.seqPanel.seqCanvas.highlightSearchResults (highlight); +}var col = this.b$["jalview.appletgui.FeatureRenderer"].getFeatureStyle (this.f$.name.getText ()); +if (col == null) { +col = new jalview.schemes.UserColourScheme ().createColourFromName (this.f$.name.getText ()); +}this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.updateColor (col); +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$FeatureRenderer$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$2", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +this.b$["jalview.appletgui.FeatureRenderer"].deleteFeature = true; +this.f$.dialog.setVisible (false); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$FeatureRenderer$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$3", java.awt.event.MouseAdapter); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +if (!this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.isGcol) { + new jalview.appletgui.UserDefinedColours (this.f$.fr, this.f$.ap.alignFrame); +} else { +var fcc = new jalview.appletgui.FeatureColourChooser (this.f$.ap.alignFrame, this.f$.name.getText ()); +this.f$.dialog.transferFocus (); +}}, "java.awt.event.MouseEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"lastFeatureAdded", null, +"lastFeatureGroupAdded", null, +"lastDescriptionAdded", null); +}); diff --git a/bin/jalview/appletgui/FeatureSettings.js b/bin/jalview/appletgui/FeatureSettings.js index c10ac3f..cc92844 100644 --- a/bin/jalview/appletgui/FeatureSettings.js +++ b/bin/jalview/appletgui/FeatureSettings.js @@ -1,444 +1,444 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Checkbox", "$.Panel", "jalview.api.FeatureSettingsControllerI", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.FeatureSettings", ["awt2swing.Button", "$.Frame", "$.Label", "$.MenuItem", "$.PopupMenu", "$.ScrollPane", "$.Scrollbar", "jalview.appletgui.FeatureColourChooser", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.schemes.GraduatedColor", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.Font", "$.GridLayout", "$.Toolkit", "java.awt.event.WindowAdapter", "java.lang.Boolean", "$.Error", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fr = null; -this.ap = null; -this.av = null; -this.frame = null; -this.groupPanel = null; -this.featurePanel = null; -this.scrollPane = null; -this.linkImage = null; -this.transparency = null; -this.groupItemListener = null; -this.selectedCheck = null; -this.dragging = false; -if (!Clazz.isClassDefined ("jalview.appletgui.FeatureSettings.MyCheckbox")) { -jalview.appletgui.FeatureSettings.$FeatureSettings$MyCheckbox$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "FeatureSettings", awt2swing.Panel, [java.awt.event.ItemListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.ActionListener, java.awt.event.AdjustmentListener, jalview.api.FeatureSettingsControllerI]); -Clazz.prepareFields (c$, function () { -this.featurePanel = new awt2swing.Panel (); -this.groupItemListener = ((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$1") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$1, this, null)); -}); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.FeatureSettings, []); -this.ap = ap; -this.av = ap.av; -ap.av.featureSettings = this; -this.fr = ap.seqPanel.seqCanvas.getFeatureRenderer (); -this.transparency = new awt2swing.Scrollbar (0, 100 - Clazz.floatToInt (this.fr.getTransparency () * 100), 1, 1, 100); -if (this.fr.isTransparencyAvailable ()) { -this.transparency.addAdjustmentListener (this); -} else { -this.transparency.setEnabled (false); -}var url = this.getClass ().getResource ("/images/link.gif"); -if (url != null) { -this.linkImage = java.awt.Toolkit.getDefaultToolkit ().getImage (url); -}if (this.av.isShowSequenceFeatures () || !this.fr.hasRenderOrder ()) { -this.fr.findAllFeatures (true); -}this.discoverAllFeatureData (); -this.setLayout ( new java.awt.BorderLayout ()); -this.scrollPane = new awt2swing.ScrollPane (); -this.scrollPane.add (this.featurePanel); -if (this.fr.getAllFeatureColours () != null && this.fr.getAllFeatureColours ().size () > 0) { -this.add (this.scrollPane, "Center"); -}var invert = new awt2swing.Button ("Invert Selection"); -invert.addActionListener (this); -var lowerPanel = new awt2swing.Panel ( new java.awt.GridLayout (2, 1, 5, 10)); -lowerPanel.add (invert); -var tPanel = new awt2swing.Panel ( new java.awt.BorderLayout ()); -if (this.fr.isTransparencyAvailable ()) { -tPanel.add (this.transparency, "Center"); -tPanel.add ( new awt2swing.Label ("Transparency"), "East"); -} else { -tPanel.add ( new awt2swing.Label ("Transparency not available in this web browser"), "Center"); -}lowerPanel.add (tPanel, "South"); -this.add (lowerPanel, "South"); -if (this.groupPanel != null) { -this.groupPanel.setLayout ( new java.awt.GridLayout (Clazz.doubleToInt ((this.fr.getFeatureGroupsSize ()) / 4) + 1, 4)); -this.groupPanel.validate (); -this.add (this.groupPanel, "North"); -}this.frame = new awt2swing.Frame (); -this.frame.add (this); -var me = this; -this.frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$2") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$2, this, Clazz.cloneFinals ("me", me)))); -var height = this.featurePanel.getComponentCount () * 50 + 60; -height = Math.max (200, height); -height = Math.min (400, height); -var width = 300; -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.feature_settings"), width, height); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.defineMethod (c$, "PaintComponent", -function (g) { -g.setColor (java.awt.Color.black); -g.drawString (jalview.util.MessageManager.getString ("label.no_features_added_to_this_alignment"), 10, 20); -g.drawString (jalview.util.MessageManager.getString ("label.features_can_be_added_from_searches_1"), 10, 40); -g.drawString (jalview.util.MessageManager.getString ("label.features_can_be_added_from_searches_2"), 10, 60); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "popupSort", -function (check, minmax, x, y) { -var type = check.type; -var typeCol = this.fr.getFeatureStyle (type); -var men = new awt2swing.PopupMenu (jalview.util.MessageManager.formatMessage ("label.settings_for_type", Clazz.newArray (-1, [type]))); -var scr = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sort_by_score")); -men.add (scr); -var me = this; -scr.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$3") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$3, this, Clazz.cloneFinals ("me", me, "type", type)))); -var dens = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sort_by_density")); -dens.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$4") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$4, this, Clazz.cloneFinals ("me", me, "type", type)))); -men.add (dens); -if (minmax != null) { -var typeMinMax = minmax.get (type); -if (typeMinMax != null && (typeMinMax)[0] != null) { -var mxcol = new awt2swing.MenuItem ((Clazz.instanceOf (typeCol, java.awt.Color)) ? "Graduated Colour" : "Single Colour"); -men.add (mxcol); -mxcol.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$5") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$5, this, Clazz.cloneFinals ("typeCol", typeCol, "me", me, "type", type, "check", check)))); -}}this.featurePanel.add (men); -men.show (this.featurePanel, x, y); -}, "jalview.appletgui.FeatureSettings.MyCheckbox,java.util.Hashtable,~N,~N"); -Clazz.overrideMethod (c$, "discoverAllFeatureData", -function () { -if (this.fr.getAllFeatureColours () != null && this.fr.getAllFeatureColours ().size () > 0) { -this.rebuildGroups (); -}this.resetTable (false); -}); -Clazz.defineMethod (c$, "rebuildGroups", -function () { -var rdrw = false; -if (this.groupPanel == null) { -this.groupPanel = new awt2swing.Panel (); -} else { -rdrw = true; -this.groupPanel.removeAll (); -}for (var group, $group = this.fr.getFeatureGroups ().iterator (); $group.hasNext () && ((group = $group.next ()) || true);) { -var vis = this.fr.checkGroupVisibility (group, false); -var check = Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings.MyCheckbox, this, null, group, vis, (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (group))); -check.addMouseListener (this); -check.setFont ( new java.awt.Font ("Serif", 1, 12)); -check.addItemListener (this.groupItemListener); -check.setVisible (vis); -this.groupPanel.add (check); -} -if (rdrw) { -this.groupPanel.validate (); -}}); -Clazz.defineMethod (c$, "resetTable", -function (groupsChanged) { -var tmpfeatures; -var group = null; -var type; -var visibleChecks = new java.util.Vector (); -var alignment = this.av.getAlignment (); -for (var i = 0; i < alignment.getHeight (); i++) { -if (alignment.getSequenceAt (i).getSequenceFeatures () == null) { -continue; -}tmpfeatures = alignment.getSequenceAt (i).getSequenceFeatures (); -var index = 0; -while (index < tmpfeatures.length) { -group = tmpfeatures[index].featureGroup; -if (group == null || this.fr.checkGroupVisibility (group, true)) { -type = tmpfeatures[index].getType (); -if (!visibleChecks.contains (type)) { -visibleChecks.addElement (type); -}}index++; -} -} -var comps; -var cSize = this.featurePanel.getComponentCount (); -var check; -for (var i = 0; i < cSize; i++) { -comps = this.featurePanel.getComponents (); -check = comps[i]; -if (!visibleChecks.contains (check.type)) { -this.featurePanel.remove (i); -cSize--; -i--; -}} -if (this.fr.getRenderOrder () != null) { -var rol = this.fr.getRenderOrder (); -for (var ro = rol.size () - 1; ro > -1; ro--) { -var item = rol.get (ro); -if (!visibleChecks.contains (item)) { -continue; -}visibleChecks.removeElement (item); -this.addCheck (false, item); -} -}var en = visibleChecks.elements (); -while (en.hasMoreElements ()) { -this.addCheck (groupsChanged, en.nextElement ().toString ()); -} -this.featurePanel.setLayout ( new java.awt.GridLayout (this.featurePanel.getComponentCount (), 1, 10, 5)); -this.featurePanel.validate (); -if (this.scrollPane != null) { -this.scrollPane.validate (); -}this.itemStateChanged (null); -}, "~B"); -Clazz.defineMethod (c$, "addCheck", -function (groupsChanged, type) { -var addCheck; -var comps = this.featurePanel.getComponents (); -var check; -addCheck = true; -for (var i = 0; i < this.featurePanel.getComponentCount (); i++) { -check = comps[i]; -if (check.type.equals (type)) { -addCheck = false; -break; -}} -if (addCheck) { -var selected = false; -if (groupsChanged || this.av.getFeaturesDisplayed ().isVisible (type)) { -selected = true; -}check = Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings.MyCheckbox, this, null, type, selected, (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (type)), this.fr.getFeatureStyle (type)); -check.addMouseListener (this); -check.addMouseMotionListener (this); -check.addItemListener (this); -if (groupsChanged) { -this.featurePanel.add (check, 0); -} else { -this.featurePanel.add (check); -}}}, "~B,~S"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -for (var i = 0; i < this.featurePanel.getComponentCount (); i++) { -var check = this.featurePanel.getComponent (i); -check.setState (!check.getState ()); -} -this.selectionChanged (); -}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -this.selectionChanged (); -}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "selectionChanged", -function () { -var comps = this.featurePanel.getComponents (); -var cSize = comps.length; -var tmp = Clazz.newArray (cSize, 3, null); -var tmpSize = 0; -for (var i = 0; i < cSize; i++) { -var check = comps[i]; -tmp[tmpSize][0] = check.type; -tmp[tmpSize][1] = this.fr.getFeatureStyle (check.type); -tmp[tmpSize][2] = new Boolean (check.getState ()); -tmpSize++; -} -var data = Clazz.newArray (tmpSize, 3, null); -System.arraycopy (tmp, 0, data, 0, tmpSize); -this.fr.setFeaturePriority (data); -this.ap.paintAlignment (true); -}); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -this.selectedCheck = evt.getSource (); -if (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (this.selectedCheck.type)) { -if (evt.getX () > this.selectedCheck.stringWidth + 20) { -evt.consume (); -}}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -if ((evt.getSource ()).getParent () !== this.featurePanel) { -return; -}this.dragging = true; -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -if ((evt.getSource ()).getParent () !== this.featurePanel) { -return; -}var comp = null; -var target = null; -var height = evt.getY () + evt.getComponent ().getLocation ().y; -if (height > this.featurePanel.getSize ().height) { -comp = this.featurePanel.getComponent (this.featurePanel.getComponentCount () - 1); -} else if (height < 0) { -comp = this.featurePanel.getComponent (0); -} else { -comp = this.featurePanel.getComponentAt (evt.getX (), evt.getY () + evt.getComponent ().getLocation ().y); -}if (comp != null && Clazz.instanceOf (comp, awt2swing.Checkbox)) { -target = comp; -}if (this.selectedCheck != null && target != null && this.selectedCheck !== target) { -var targetIndex = -1; -for (var i = 0; i < this.featurePanel.getComponentCount (); i++) { -if (target === this.featurePanel.getComponent (i)) { -targetIndex = i; -break; -}} -this.featurePanel.remove (this.selectedCheck); -this.featurePanel.add (this.selectedCheck, targetIndex); -this.featurePanel.validate (); -this.itemStateChanged (null); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "setUserColour", -function (feature, originalColour) { -if (Clazz.instanceOf (originalColour, java.awt.Color) || Clazz.instanceOf (originalColour, jalview.schemes.GraduatedColor)) { -this.fr.setColour (feature, originalColour); -} else { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_unsupported_feature_colour_object")); -}this.refreshTable (); -}, "~S,~O"); -Clazz.defineMethod (c$, "refreshTable", -function () { -this.featurePanel.removeAll (); -this.resetTable (false); -this.ap.paintAlignment (true); -}); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -var check = evt.getSource (); -if ((evt.getModifiers () & 4) != 0) { -this.popupSort (check, this.fr.getMinMax (), evt.getX (), evt.getY ()); -}if (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (check.type)) { -if (evt.getX () > check.stringWidth + 20) { -evt.consume (); -var link = this.fr.featureLinks.get (check.type).toString (); -this.ap.alignFrame.showURL (link.substring (link.indexOf ("|") + 1), link.substring (0, link.indexOf ("|"))); -}}if (check.getParent () !== this.featurePanel) { -return; -}if (evt.getClickCount () > 1) { -var fcol = this.fr.getFeatureStyle (check.type); -if (Clazz.instanceOf (fcol, java.awt.Color)) { - new jalview.appletgui.UserDefinedColours (this, check.type, fcol); -} else { - new jalview.appletgui.FeatureColourChooser (this, check.type); -check.updateColor (this.fr.getFeatureStyle (check.type)); -}}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -this.fr.setTransparency ((100 - this.transparency.getValue ()) / 100); -this.ap.seqPanel.seqCanvas.repaint (); -}, "java.awt.event.AdjustmentEvent"); -c$.$FeatureSettings$MyCheckbox$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.type = null; -this.stringWidth = 0; -this.hasLink = false; -this.gcol = null; -this.col = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.FeatureSettings, "MyCheckbox", awt2swing.Checkbox); -Clazz.defineMethod (c$, "updateColor", -function (a) { -if (Clazz.instanceOf (a, java.awt.Color)) { -this.col = a; -this.gcol = null; -} else if (Clazz.instanceOf (a, jalview.schemes.GraduatedColor)) { -this.gcol = a; -this.col = null; -} else { -throw new Error (jalview.util.MessageManager.getString ("error.invalid_colour_for_mycheckbox")); -}if (this.col != null) { -this.setBackground (this.col); -} else { -var b = this.type; -if (this.gcol.getThreshType () != -1) { -b += " " + ((this.gcol.getThreshType () == 1) ? "(>)" : "(<)"); -}if (this.gcol.isColourByLabel ()) { -this.setBackground (java.awt.Color.white); -b += " (by Label)"; -} else { -this.setBackground (this.gcol.getMinColor ()); -}this.setLabel (b); -}this.repaint (); -}, "~O"); -Clazz.makeConstructor (c$, -function (a, b, c) { -Clazz.superConstructor (this, jalview.appletgui.FeatureSettings.MyCheckbox, [a, b]); -this.type = a; -var d = this.b$["jalview.appletgui.FeatureSettings"].av.nullFrame.getFontMetrics (this.b$["jalview.appletgui.FeatureSettings"].av.nullFrame.getFont ()); -this.stringWidth = d.stringWidth (a); -this.hasLink = c; -}, "~S,~B,~B"); -Clazz.makeConstructor (c$, -function (a, b, c, d) { -this.construct (a, b, c); -this.updateColor (d); -}, "~S,~B,~B,~O"); -Clazz.defineMethod (c$, "PaintComponent", -function (a) { -var b = this.getSize (); -if (this.gcol != null) { -if (this.gcol.isColourByLabel ()) { -a.setColor (java.awt.Color.white); -a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); -} else { -var c = this.gcol.getMaxColor (); -a.setColor (c); -a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); -}}if (this.hasLink) { -a.drawImage (this.b$["jalview.appletgui.FeatureSettings"].linkImage, this.stringWidth + 25, Clazz.doubleToInt ((this.getSize ().height - this.b$["jalview.appletgui.FeatureSettings"].linkImage.getHeight (this)) / 2), this); -}}, "java.awt.Graphics"); -c$ = Clazz.p0p (); -}; -c$.$FeatureSettings$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$1", null, java.awt.event.ItemListener); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -var source = evt.getSource (); -this.b$["jalview.appletgui.FeatureSettings"].fr.setGroupVisibility (source.getLabel (), source.getState ()); -this.b$["jalview.appletgui.FeatureSettings"].ap.seqPanel.seqCanvas.repaint (); -if (this.b$["jalview.appletgui.FeatureSettings"].ap.overviewPanel != null) { -this.b$["jalview.appletgui.FeatureSettings"].ap.overviewPanel.updateOverviewImage (); -}this.b$["jalview.appletgui.FeatureSettings"].resetTable (true); -return; -}, "java.awt.event.ItemEvent"); -c$ = Clazz.p0p (); -}; -c$.$FeatureSettings$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$2", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -if (this.f$.me.av.featureSettings === this.f$.me) { -this.f$.me.av.featureSettings = null; -this.f$.me.ap = null; -this.f$.me.av = null; -}}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$FeatureSettings$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$3", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.f$.me.ap.alignFrame.avc.sortAlignmentByFeatureScore ( Clazz.newArray (-1, [this.f$.type])); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$FeatureSettings$4$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$4", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.f$.me.ap.alignFrame.avc.sortAlignmentByFeatureDensity ( Clazz.newArray (-1, [this.f$.type])); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$FeatureSettings$5$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$5", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -if (Clazz.instanceOf (this.f$.typeCol, java.awt.Color)) { - new jalview.appletgui.FeatureColourChooser (this.f$.me, this.f$.type); -this.f$.check.updateColor (this.b$["jalview.appletgui.FeatureSettings"].fr.getFeatureStyle (this.f$.type)); -} else { - new jalview.appletgui.UserDefinedColours (this.f$.me, this.f$.check.type, (this.f$.typeCol)); -}}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Checkbox", "$.Panel", "jalview.api.FeatureSettingsControllerI", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.FeatureSettings", ["awt2swing.Button", "$.Frame", "$.Label", "$.MenuItem", "$.PopupMenu", "$.ScrollPane", "$.Scrollbar", "jalview.appletgui.FeatureColourChooser", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.schemes.GraduatedColor", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.Font", "$.GridLayout", "$.Toolkit", "java.awt.event.WindowAdapter", "java.lang.Boolean", "$.Error", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fr = null; +this.ap = null; +this.av = null; +this.frame = null; +this.groupPanel = null; +this.featurePanel = null; +this.scrollPane = null; +this.linkImage = null; +this.transparency = null; +this.groupItemListener = null; +this.selectedCheck = null; +this.dragging = false; +if (!Clazz.isClassDefined ("jalview.appletgui.FeatureSettings.MyCheckbox")) { +jalview.appletgui.FeatureSettings.$FeatureSettings$MyCheckbox$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "FeatureSettings", awt2swing.Panel, [java.awt.event.ItemListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.ActionListener, java.awt.event.AdjustmentListener, jalview.api.FeatureSettingsControllerI]); +Clazz.prepareFields (c$, function () { +this.featurePanel = new awt2swing.Panel (); +this.groupItemListener = ((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$1") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$1, this, null)); +}); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.FeatureSettings, []); +this.ap = ap; +this.av = ap.av; +ap.av.featureSettings = this; +this.fr = ap.seqPanel.seqCanvas.getFeatureRenderer (); +this.transparency = new awt2swing.Scrollbar (0, 100 - Clazz.floatToInt (this.fr.getTransparency () * 100), 1, 1, 100); +if (this.fr.isTransparencyAvailable ()) { +this.transparency.addAdjustmentListener (this); +} else { +this.transparency.setEnabled (false); +}var url = this.getClass ().getResource ("/images/link.gif"); +if (url != null) { +this.linkImage = java.awt.Toolkit.getDefaultToolkit ().getImage (url); +}if (this.av.isShowSequenceFeatures () || !this.fr.hasRenderOrder ()) { +this.fr.findAllFeatures (true); +}this.discoverAllFeatureData (); +this.setLayout ( new java.awt.BorderLayout ()); +this.scrollPane = new awt2swing.ScrollPane (); +this.scrollPane.add (this.featurePanel); +if (this.fr.getAllFeatureColours () != null && this.fr.getAllFeatureColours ().size () > 0) { +this.add (this.scrollPane, "Center"); +}var invert = new awt2swing.Button ("Invert Selection"); +invert.addActionListener (this); +var lowerPanel = new awt2swing.Panel ( new java.awt.GridLayout (2, 1, 5, 10)); +lowerPanel.add (invert); +var tPanel = new awt2swing.Panel ( new java.awt.BorderLayout ()); +if (this.fr.isTransparencyAvailable ()) { +tPanel.add (this.transparency, "Center"); +tPanel.add ( new awt2swing.Label ("Transparency"), "East"); +} else { +tPanel.add ( new awt2swing.Label ("Transparency not available in this web browser"), "Center"); +}lowerPanel.add (tPanel, "South"); +this.add (lowerPanel, "South"); +if (this.groupPanel != null) { +this.groupPanel.setLayout ( new java.awt.GridLayout (Clazz.doubleToInt ((this.fr.getFeatureGroupsSize ()) / 4) + 1, 4)); +this.groupPanel.validate (); +this.add (this.groupPanel, "North"); +}this.frame = new awt2swing.Frame (); +this.frame.add (this); +var me = this; +this.frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$2") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$2, this, Clazz.cloneFinals ("me", me)))); +var height = this.featurePanel.getComponentCount () * 50 + 60; +height = Math.max (200, height); +height = Math.min (400, height); +var width = 300; +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.feature_settings"), width, height); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.defineMethod (c$, "PaintComponent", +function (g) { +g.setColor (java.awt.Color.black); +g.drawString (jalview.util.MessageManager.getString ("label.no_features_added_to_this_alignment"), 10, 20); +g.drawString (jalview.util.MessageManager.getString ("label.features_can_be_added_from_searches_1"), 10, 40); +g.drawString (jalview.util.MessageManager.getString ("label.features_can_be_added_from_searches_2"), 10, 60); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "popupSort", +function (check, minmax, x, y) { +var type = check.type; +var typeCol = this.fr.getFeatureStyle (type); +var men = new awt2swing.PopupMenu (jalview.util.MessageManager.formatMessage ("label.settings_for_type", Clazz.newArray (-1, [type]))); +var scr = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sort_by_score")); +men.add (scr); +var me = this; +scr.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$3") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$3, this, Clazz.cloneFinals ("me", me, "type", type)))); +var dens = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sort_by_density")); +dens.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$4") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$4, this, Clazz.cloneFinals ("me", me, "type", type)))); +men.add (dens); +if (minmax != null) { +var typeMinMax = minmax.get (type); +if (typeMinMax != null && (typeMinMax)[0] != null) { +var mxcol = new awt2swing.MenuItem ((Clazz.instanceOf (typeCol, java.awt.Color)) ? "Graduated Colour" : "Single Colour"); +men.add (mxcol); +mxcol.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureSettings$5") ? 0 : jalview.appletgui.FeatureSettings.$FeatureSettings$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings$5, this, Clazz.cloneFinals ("typeCol", typeCol, "me", me, "type", type, "check", check)))); +}}this.featurePanel.add (men); +men.show (this.featurePanel, x, y); +}, "jalview.appletgui.FeatureSettings.MyCheckbox,java.util.Hashtable,~N,~N"); +Clazz.overrideMethod (c$, "discoverAllFeatureData", +function () { +if (this.fr.getAllFeatureColours () != null && this.fr.getAllFeatureColours ().size () > 0) { +this.rebuildGroups (); +}this.resetTable (false); +}); +Clazz.defineMethod (c$, "rebuildGroups", +function () { +var rdrw = false; +if (this.groupPanel == null) { +this.groupPanel = new awt2swing.Panel (); +} else { +rdrw = true; +this.groupPanel.removeAll (); +}for (var group, $group = this.fr.getFeatureGroups ().iterator (); $group.hasNext () && ((group = $group.next ()) || true);) { +var vis = this.fr.checkGroupVisibility (group, false); +var check = Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings.MyCheckbox, this, null, group, vis, (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (group))); +check.addMouseListener (this); +check.setFont ( new java.awt.Font ("Serif", 1, 12)); +check.addItemListener (this.groupItemListener); +check.setVisible (vis); +this.groupPanel.add (check); +} +if (rdrw) { +this.groupPanel.validate (); +}}); +Clazz.defineMethod (c$, "resetTable", +function (groupsChanged) { +var tmpfeatures; +var group = null; +var type; +var visibleChecks = new java.util.Vector (); +var alignment = this.av.getAlignment (); +for (var i = 0; i < alignment.getHeight (); i++) { +if (alignment.getSequenceAt (i).getSequenceFeatures () == null) { +continue; +}tmpfeatures = alignment.getSequenceAt (i).getSequenceFeatures (); +var index = 0; +while (index < tmpfeatures.length) { +group = tmpfeatures[index].featureGroup; +if (group == null || this.fr.checkGroupVisibility (group, true)) { +type = tmpfeatures[index].getType (); +if (!visibleChecks.contains (type)) { +visibleChecks.addElement (type); +}}index++; +} +} +var comps; +var cSize = this.featurePanel.getComponentCount (); +var check; +for (var i = 0; i < cSize; i++) { +comps = this.featurePanel.getComponents (); +check = comps[i]; +if (!visibleChecks.contains (check.type)) { +this.featurePanel.remove (i); +cSize--; +i--; +}} +if (this.fr.getRenderOrder () != null) { +var rol = this.fr.getRenderOrder (); +for (var ro = rol.size () - 1; ro > -1; ro--) { +var item = rol.get (ro); +if (!visibleChecks.contains (item)) { +continue; +}visibleChecks.removeElement (item); +this.addCheck (false, item); +} +}var en = visibleChecks.elements (); +while (en.hasMoreElements ()) { +this.addCheck (groupsChanged, en.nextElement ().toString ()); +} +this.featurePanel.setLayout ( new java.awt.GridLayout (this.featurePanel.getComponentCount (), 1, 10, 5)); +this.featurePanel.validate (); +if (this.scrollPane != null) { +this.scrollPane.validate (); +}this.itemStateChanged (null); +}, "~B"); +Clazz.defineMethod (c$, "addCheck", +function (groupsChanged, type) { +var addCheck; +var comps = this.featurePanel.getComponents (); +var check; +addCheck = true; +for (var i = 0; i < this.featurePanel.getComponentCount (); i++) { +check = comps[i]; +if (check.type.equals (type)) { +addCheck = false; +break; +}} +if (addCheck) { +var selected = false; +if (groupsChanged || this.av.getFeaturesDisplayed ().isVisible (type)) { +selected = true; +}check = Clazz.innerTypeInstance (jalview.appletgui.FeatureSettings.MyCheckbox, this, null, type, selected, (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (type)), this.fr.getFeatureStyle (type)); +check.addMouseListener (this); +check.addMouseMotionListener (this); +check.addItemListener (this); +if (groupsChanged) { +this.featurePanel.add (check, 0); +} else { +this.featurePanel.add (check); +}}}, "~B,~S"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +for (var i = 0; i < this.featurePanel.getComponentCount (); i++) { +var check = this.featurePanel.getComponent (i); +check.setState (!check.getState ()); +} +this.selectionChanged (); +}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +this.selectionChanged (); +}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "selectionChanged", +function () { +var comps = this.featurePanel.getComponents (); +var cSize = comps.length; +var tmp = Clazz.newArray (cSize, 3, null); +var tmpSize = 0; +for (var i = 0; i < cSize; i++) { +var check = comps[i]; +tmp[tmpSize][0] = check.type; +tmp[tmpSize][1] = this.fr.getFeatureStyle (check.type); +tmp[tmpSize][2] = new Boolean (check.getState ()); +tmpSize++; +} +var data = Clazz.newArray (tmpSize, 3, null); +System.arraycopy (tmp, 0, data, 0, tmpSize); +this.fr.setFeaturePriority (data); +this.ap.paintAlignment (true); +}); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +this.selectedCheck = evt.getSource (); +if (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (this.selectedCheck.type)) { +if (evt.getX () > this.selectedCheck.stringWidth + 20) { +evt.consume (); +}}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +if ((evt.getSource ()).getParent () !== this.featurePanel) { +return; +}this.dragging = true; +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +if ((evt.getSource ()).getParent () !== this.featurePanel) { +return; +}var comp = null; +var target = null; +var height = evt.getY () + evt.getComponent ().getLocation ().y; +if (height > this.featurePanel.getSize ().height) { +comp = this.featurePanel.getComponent (this.featurePanel.getComponentCount () - 1); +} else if (height < 0) { +comp = this.featurePanel.getComponent (0); +} else { +comp = this.featurePanel.getComponentAt (evt.getX (), evt.getY () + evt.getComponent ().getLocation ().y); +}if (comp != null && Clazz.instanceOf (comp, awt2swing.Checkbox)) { +target = comp; +}if (this.selectedCheck != null && target != null && this.selectedCheck !== target) { +var targetIndex = -1; +for (var i = 0; i < this.featurePanel.getComponentCount (); i++) { +if (target === this.featurePanel.getComponent (i)) { +targetIndex = i; +break; +}} +this.featurePanel.remove (this.selectedCheck); +this.featurePanel.add (this.selectedCheck, targetIndex); +this.featurePanel.validate (); +this.itemStateChanged (null); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "setUserColour", +function (feature, originalColour) { +if (Clazz.instanceOf (originalColour, java.awt.Color) || Clazz.instanceOf (originalColour, jalview.schemes.GraduatedColor)) { +this.fr.setColour (feature, originalColour); +} else { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_unsupported_feature_colour_object")); +}this.refreshTable (); +}, "~S,~O"); +Clazz.defineMethod (c$, "refreshTable", +function () { +this.featurePanel.removeAll (); +this.resetTable (false); +this.ap.paintAlignment (true); +}); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +var check = evt.getSource (); +if ((evt.getModifiers () & 4) != 0) { +this.popupSort (check, this.fr.getMinMax (), evt.getX (), evt.getY ()); +}if (this.fr.featureLinks != null && this.fr.featureLinks.containsKey (check.type)) { +if (evt.getX () > check.stringWidth + 20) { +evt.consume (); +var link = this.fr.featureLinks.get (check.type).toString (); +this.ap.alignFrame.showURL (link.substring (link.indexOf ("|") + 1), link.substring (0, link.indexOf ("|"))); +}}if (check.getParent () !== this.featurePanel) { +return; +}if (evt.getClickCount () > 1) { +var fcol = this.fr.getFeatureStyle (check.type); +if (Clazz.instanceOf (fcol, java.awt.Color)) { + new jalview.appletgui.UserDefinedColours (this, check.type, fcol); +} else { + new jalview.appletgui.FeatureColourChooser (this, check.type); +check.updateColor (this.fr.getFeatureStyle (check.type)); +}}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +this.fr.setTransparency ((100 - this.transparency.getValue ()) / 100); +this.ap.seqPanel.seqCanvas.repaint (); +}, "java.awt.event.AdjustmentEvent"); +c$.$FeatureSettings$MyCheckbox$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.type = null; +this.stringWidth = 0; +this.hasLink = false; +this.gcol = null; +this.col = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.FeatureSettings, "MyCheckbox", awt2swing.Checkbox); +Clazz.defineMethod (c$, "updateColor", +function (a) { +if (Clazz.instanceOf (a, java.awt.Color)) { +this.col = a; +this.gcol = null; +} else if (Clazz.instanceOf (a, jalview.schemes.GraduatedColor)) { +this.gcol = a; +this.col = null; +} else { +throw new Error (jalview.util.MessageManager.getString ("error.invalid_colour_for_mycheckbox")); +}if (this.col != null) { +this.setBackground (this.col); +} else { +var b = this.type; +if (this.gcol.getThreshType () != -1) { +b += " " + ((this.gcol.getThreshType () == 1) ? "(>)" : "(<)"); +}if (this.gcol.isColourByLabel ()) { +this.setBackground (java.awt.Color.white); +b += " (by Label)"; +} else { +this.setBackground (this.gcol.getMinColor ()); +}this.setLabel (b); +}this.repaint (); +}, "~O"); +Clazz.makeConstructor (c$, +function (a, b, c) { +Clazz.superConstructor (this, jalview.appletgui.FeatureSettings.MyCheckbox, [a, b]); +this.type = a; +var d = this.b$["jalview.appletgui.FeatureSettings"].av.nullFrame.getFontMetrics (this.b$["jalview.appletgui.FeatureSettings"].av.nullFrame.getFont ()); +this.stringWidth = d.stringWidth (a); +this.hasLink = c; +}, "~S,~B,~B"); +Clazz.makeConstructor (c$, +function (a, b, c, d) { +this.construct (a, b, c); +this.updateColor (d); +}, "~S,~B,~B,~O"); +Clazz.defineMethod (c$, "PaintComponent", +function (a) { +var b = this.getSize (); +if (this.gcol != null) { +if (this.gcol.isColourByLabel ()) { +a.setColor (java.awt.Color.white); +a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); +} else { +var c = this.gcol.getMaxColor (); +a.setColor (c); +a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height); +}}if (this.hasLink) { +a.drawImage (this.b$["jalview.appletgui.FeatureSettings"].linkImage, this.stringWidth + 25, Clazz.doubleToInt ((this.getSize ().height - this.b$["jalview.appletgui.FeatureSettings"].linkImage.getHeight (this)) / 2), this); +}}, "java.awt.Graphics"); +c$ = Clazz.p0p (); +}; +c$.$FeatureSettings$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$1", null, java.awt.event.ItemListener); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +var source = evt.getSource (); +this.b$["jalview.appletgui.FeatureSettings"].fr.setGroupVisibility (source.getLabel (), source.getState ()); +this.b$["jalview.appletgui.FeatureSettings"].ap.seqPanel.seqCanvas.repaint (); +if (this.b$["jalview.appletgui.FeatureSettings"].ap.overviewPanel != null) { +this.b$["jalview.appletgui.FeatureSettings"].ap.overviewPanel.updateOverviewImage (); +}this.b$["jalview.appletgui.FeatureSettings"].resetTable (true); +return; +}, "java.awt.event.ItemEvent"); +c$ = Clazz.p0p (); +}; +c$.$FeatureSettings$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$2", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +if (this.f$.me.av.featureSettings === this.f$.me) { +this.f$.me.av.featureSettings = null; +this.f$.me.ap = null; +this.f$.me.av = null; +}}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$FeatureSettings$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$3", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.f$.me.ap.alignFrame.avc.sortAlignmentByFeatureScore ( Clazz.newArray (-1, [this.f$.type])); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$FeatureSettings$4$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$4", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.f$.me.ap.alignFrame.avc.sortAlignmentByFeatureDensity ( Clazz.newArray (-1, [this.f$.type])); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$FeatureSettings$5$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureSettings$5", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +if (Clazz.instanceOf (this.f$.typeCol, java.awt.Color)) { + new jalview.appletgui.FeatureColourChooser (this.f$.me, this.f$.type); +this.f$.check.updateColor (this.b$["jalview.appletgui.FeatureSettings"].fr.getFeatureStyle (this.f$.type)); +} else { + new jalview.appletgui.UserDefinedColours (this.f$.me, this.f$.check.type, (this.f$.typeCol)); +}}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/Finder.js b/bin/jalview/appletgui/Finder.js index d64e048..22e3c84 100644 --- a/bin/jalview/appletgui/Finder.js +++ b/bin/jalview/appletgui/Finder.js @@ -1,184 +1,184 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.Checkbox", "$.Label", "$.TextField", "java.awt.GridLayout"], "jalview.appletgui.Finder", ["awt2swing.Frame", "jalview.analysis.Finder", "jalview.bin.JalviewLite", "jalview.datamodel.SequenceFeature", "jalview.util.MessageManager", "java.awt.Font", "$.Rectangle", "java.awt.event.KeyAdapter", "$.WindowAdapter"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.ap = null; -this.frame = null; -this.searchResults = null; -this.seqIndex = 0; -this.resIndex = -1; -this.jLabel1 = null; -this.textfield = null; -this.findAll = null; -this.findNext = null; -this.actionsPanel = null; -this.gridLayout1 = null; -this.createNewGroup = null; -this.caseSensitive = null; -this.searchDescription = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "Finder", awt2swing.Panel, java.awt.event.ActionListener); -Clazz.prepareFields (c$, function () { -this.jLabel1 = new awt2swing.Label (); -this.textfield = new awt2swing.TextField (); -this.findAll = new awt2swing.Button (); -this.findNext = new awt2swing.Button (); -this.actionsPanel = new awt2swing.Panel (); -this.gridLayout1 = new java.awt.GridLayout (); -this.createNewGroup = new awt2swing.Button (); -this.caseSensitive = new awt2swing.Checkbox (); -this.searchDescription = new awt2swing.Checkbox (); -}); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.Finder, []); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.av = ap.av; -this.ap = ap; -this.frame = new awt2swing.Frame (); -this.frame.add (this); -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("action.find"), 340, 120); -this.frame.repaint (); -this.frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$1") ? 0 : jalview.appletgui.Finder.$Finder$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$1, this, Clazz.cloneFinals ("ap", ap)))); -this.textfield.requestFocus (); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.textfield) { -this.doSearch (false); -} else if (evt.getSource () === this.findNext) { -this.doSearch (false); -} else if (evt.getSource () === this.findAll) { -this.resIndex = -1; -this.seqIndex = 0; -this.doSearch (true); -} else if (evt.getSource () === this.createNewGroup) { -this.createNewGroup_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "createNewGroup_actionPerformed", -function () { -var seqs = new Array (this.searchResults.getSize ()); -var features = new Array (this.searchResults.getSize ()); -for (var i = 0; i < this.searchResults.getSize (); i++) { -seqs[i] = this.searchResults.getResultSequence (i); -features[i] = new jalview.datamodel.SequenceFeature (this.textfield.getText ().trim (), "Search Results", null, this.searchResults.getResultStart (i), this.searchResults.getResultEnd (i), "Search Results"); -} -if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) { -this.ap.alignFrame.sequenceFeatures.setState (true); -this.av.setShowSequenceFeatures (true); -this.ap.highlightSearchResults (null); -}}); -Clazz.defineMethod (c$, "doSearch", -function (findAll) { -if (this.ap.av.applet.currentAlignFrame != null) { -this.ap = this.ap.av.applet.currentAlignFrame.alignPanel; -this.av = this.ap.av; -}this.createNewGroup.setEnabled (false); -var finder = new jalview.analysis.Finder (this.av.getAlignment (), this.av.getSelectionGroup (), this.seqIndex, this.resIndex); -finder.setCaseSensitive (this.caseSensitive.getState ()); -finder.setIncludeDescription (this.searchDescription.getState ()); -finder.setFindAll (findAll); -var searchString = this.textfield.getText (); -finder.find (searchString); -this.seqIndex = finder.getSeqIndex (); -this.resIndex = finder.getResIndex (); -this.searchResults = finder.getSearchResults (); -var idMatch = finder.getIdMatch (); -var haveResults = false; -if ((idMatch.size () > 0)) { -haveResults = true; -this.ap.idPanel.highlightSearchResults (idMatch); -} else { -this.ap.idPanel.highlightSearchResults (null); -}if (this.searchResults.getSize () > 0) { -haveResults = true; -this.createNewGroup.setEnabled (true); -} else { -this.searchResults = null; -}this.ap.highlightSearchResults (this.searchResults); -if (!haveResults) { -this.ap.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.finished_searching")); -this.resIndex = -1; -this.seqIndex = 0; -} else { -if (findAll) { -var message = (idMatch.size () > 0) ? "" + idMatch.size () + " IDs" : ""; -if (idMatch.size () > 0 && this.searchResults != null && this.searchResults.getSize () > 0) { -message += " and "; -}if (this.searchResults != null) { -message += this.searchResults.getSize () + " subsequence matches."; -}this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.search_results", Clazz.newArray (-1, [searchString, message]))); -} else { -this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.found_match_for", Clazz.newArray (-1, [searchString]))); -}}}, "~B"); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.jLabel1.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.jLabel1.setText (jalview.util.MessageManager.getString ("action.find")); -this.jLabel1.setBounds ( new java.awt.Rectangle (3, 30, 34, 15)); -this.setLayout (null); -this.textfield.setFont ( new java.awt.Font ("Verdana", 0, 10)); -this.textfield.setText (""); -this.textfield.setBounds ( new java.awt.Rectangle (40, 17, 133, 21)); -this.textfield.addKeyListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$2") ? 0 : jalview.appletgui.Finder.$Finder$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$2, this, null))); -this.textfield.addActionListener (this); -this.findAll.setFont ( new java.awt.Font ("Verdana", 0, 10)); -this.findAll.setLabel (jalview.util.MessageManager.getString ("action.find_all")); -this.findAll.addActionListener (this); -this.findNext.setEnabled (false); -this.findNext.setFont ( new java.awt.Font ("Verdana", 0, 10)); -this.findNext.setLabel (jalview.util.MessageManager.getString ("action.find_next")); -this.findNext.addActionListener (this); -this.actionsPanel.setBounds ( new java.awt.Rectangle (195, 5, 141, 64)); -this.actionsPanel.setLayout (this.gridLayout1); -this.gridLayout1.setHgap (0); -this.gridLayout1.setRows (3); -this.gridLayout1.setVgap (2); -this.createNewGroup.setEnabled (false); -this.createNewGroup.setFont ( new java.awt.Font ("Verdana", 0, 10)); -this.createNewGroup.setLabel (jalview.util.MessageManager.getString ("label.new_feature")); -this.createNewGroup.addActionListener (this); -this.caseSensitive.setLabel (jalview.util.MessageManager.getString ("label.match_case")); -this.caseSensitive.setBounds ( new java.awt.Rectangle (30, 39, 126, 23)); -this.searchDescription.setLabel (jalview.util.MessageManager.getString ("label.include_description")); -this.searchDescription.setBounds ( new java.awt.Rectangle (30, 59, 170, 23)); -this.actionsPanel.add (this.findNext, null); -this.actionsPanel.add (this.findAll, null); -this.actionsPanel.add (this.createNewGroup, null); -this.add (this.caseSensitive); -this.add (this.textfield, null); -this.add (this.jLabel1, null); -this.add (this.actionsPanel, null); -this.add (this.searchDescription); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "textfield_keyTyped", -function (e) { -this.findNext.setEnabled (true); -}, "java.awt.event.KeyEvent"); -c$.$Finder$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$1", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (evt) { -this.f$.ap.highlightSearchResults (null); -}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$Finder$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$2", java.awt.event.KeyAdapter); -Clazz.overrideMethod (c$, "keyTyped", -function (e) { -this.b$["jalview.appletgui.Finder"].textfield_keyTyped (e); -}, "java.awt.event.KeyEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.Checkbox", "$.Label", "$.TextField", "java.awt.GridLayout"], "jalview.appletgui.Finder", ["awt2swing.Frame", "jalview.analysis.Finder", "jalview.bin.JalviewLite", "jalview.datamodel.SequenceFeature", "jalview.util.MessageManager", "java.awt.Font", "$.Rectangle", "java.awt.event.KeyAdapter", "$.WindowAdapter"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.ap = null; +this.frame = null; +this.searchResults = null; +this.seqIndex = 0; +this.resIndex = -1; +this.jLabel1 = null; +this.textfield = null; +this.findAll = null; +this.findNext = null; +this.actionsPanel = null; +this.gridLayout1 = null; +this.createNewGroup = null; +this.caseSensitive = null; +this.searchDescription = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "Finder", awt2swing.Panel, java.awt.event.ActionListener); +Clazz.prepareFields (c$, function () { +this.jLabel1 = new awt2swing.Label (); +this.textfield = new awt2swing.TextField (); +this.findAll = new awt2swing.Button (); +this.findNext = new awt2swing.Button (); +this.actionsPanel = new awt2swing.Panel (); +this.gridLayout1 = new java.awt.GridLayout (); +this.createNewGroup = new awt2swing.Button (); +this.caseSensitive = new awt2swing.Checkbox (); +this.searchDescription = new awt2swing.Checkbox (); +}); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.Finder, []); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.av = ap.av; +this.ap = ap; +this.frame = new awt2swing.Frame (); +this.frame.add (this); +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("action.find"), 340, 120); +this.frame.repaint (); +this.frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$1") ? 0 : jalview.appletgui.Finder.$Finder$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$1, this, Clazz.cloneFinals ("ap", ap)))); +this.textfield.requestFocus (); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.textfield) { +this.doSearch (false); +} else if (evt.getSource () === this.findNext) { +this.doSearch (false); +} else if (evt.getSource () === this.findAll) { +this.resIndex = -1; +this.seqIndex = 0; +this.doSearch (true); +} else if (evt.getSource () === this.createNewGroup) { +this.createNewGroup_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "createNewGroup_actionPerformed", +function () { +var seqs = new Array (this.searchResults.getSize ()); +var features = new Array (this.searchResults.getSize ()); +for (var i = 0; i < this.searchResults.getSize (); i++) { +seqs[i] = this.searchResults.getResultSequence (i); +features[i] = new jalview.datamodel.SequenceFeature (this.textfield.getText ().trim (), "Search Results", null, this.searchResults.getResultStart (i), this.searchResults.getResultEnd (i), "Search Results"); +} +if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) { +this.ap.alignFrame.sequenceFeatures.setState (true); +this.av.setShowSequenceFeatures (true); +this.ap.highlightSearchResults (null); +}}); +Clazz.defineMethod (c$, "doSearch", +function (findAll) { +if (this.ap.av.applet.currentAlignFrame != null) { +this.ap = this.ap.av.applet.currentAlignFrame.alignPanel; +this.av = this.ap.av; +}this.createNewGroup.setEnabled (false); +var finder = new jalview.analysis.Finder (this.av.getAlignment (), this.av.getSelectionGroup (), this.seqIndex, this.resIndex); +finder.setCaseSensitive (this.caseSensitive.getState ()); +finder.setIncludeDescription (this.searchDescription.getState ()); +finder.setFindAll (findAll); +var searchString = this.textfield.getText (); +finder.find (searchString); +this.seqIndex = finder.getSeqIndex (); +this.resIndex = finder.getResIndex (); +this.searchResults = finder.getSearchResults (); +var idMatch = finder.getIdMatch (); +var haveResults = false; +if ((idMatch.size () > 0)) { +haveResults = true; +this.ap.idPanel.highlightSearchResults (idMatch); +} else { +this.ap.idPanel.highlightSearchResults (null); +}if (this.searchResults.getSize () > 0) { +haveResults = true; +this.createNewGroup.setEnabled (true); +} else { +this.searchResults = null; +}this.ap.highlightSearchResults (this.searchResults); +if (!haveResults) { +this.ap.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.finished_searching")); +this.resIndex = -1; +this.seqIndex = 0; +} else { +if (findAll) { +var message = (idMatch.size () > 0) ? "" + idMatch.size () + " IDs" : ""; +if (idMatch.size () > 0 && this.searchResults != null && this.searchResults.getSize () > 0) { +message += " and "; +}if (this.searchResults != null) { +message += this.searchResults.getSize () + " subsequence matches."; +}this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.search_results", Clazz.newArray (-1, [searchString, message]))); +} else { +this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.found_match_for", Clazz.newArray (-1, [searchString]))); +}}}, "~B"); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.jLabel1.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.jLabel1.setText (jalview.util.MessageManager.getString ("action.find")); +this.jLabel1.setBounds ( new java.awt.Rectangle (3, 30, 34, 15)); +this.setLayout (null); +this.textfield.setFont ( new java.awt.Font ("Verdana", 0, 10)); +this.textfield.setText (""); +this.textfield.setBounds ( new java.awt.Rectangle (40, 17, 133, 21)); +this.textfield.addKeyListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$2") ? 0 : jalview.appletgui.Finder.$Finder$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$2, this, null))); +this.textfield.addActionListener (this); +this.findAll.setFont ( new java.awt.Font ("Verdana", 0, 10)); +this.findAll.setLabel (jalview.util.MessageManager.getString ("action.find_all")); +this.findAll.addActionListener (this); +this.findNext.setEnabled (false); +this.findNext.setFont ( new java.awt.Font ("Verdana", 0, 10)); +this.findNext.setLabel (jalview.util.MessageManager.getString ("action.find_next")); +this.findNext.addActionListener (this); +this.actionsPanel.setBounds ( new java.awt.Rectangle (195, 5, 141, 64)); +this.actionsPanel.setLayout (this.gridLayout1); +this.gridLayout1.setHgap (0); +this.gridLayout1.setRows (3); +this.gridLayout1.setVgap (2); +this.createNewGroup.setEnabled (false); +this.createNewGroup.setFont ( new java.awt.Font ("Verdana", 0, 10)); +this.createNewGroup.setLabel (jalview.util.MessageManager.getString ("label.new_feature")); +this.createNewGroup.addActionListener (this); +this.caseSensitive.setLabel (jalview.util.MessageManager.getString ("label.match_case")); +this.caseSensitive.setBounds ( new java.awt.Rectangle (30, 39, 126, 23)); +this.searchDescription.setLabel (jalview.util.MessageManager.getString ("label.include_description")); +this.searchDescription.setBounds ( new java.awt.Rectangle (30, 59, 170, 23)); +this.actionsPanel.add (this.findNext, null); +this.actionsPanel.add (this.findAll, null); +this.actionsPanel.add (this.createNewGroup, null); +this.add (this.caseSensitive); +this.add (this.textfield, null); +this.add (this.jLabel1, null); +this.add (this.actionsPanel, null); +this.add (this.searchDescription); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "textfield_keyTyped", +function (e) { +this.findNext.setEnabled (true); +}, "java.awt.event.KeyEvent"); +c$.$Finder$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$1", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (evt) { +this.f$.ap.highlightSearchResults (null); +}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$Finder$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$2", java.awt.event.KeyAdapter); +Clazz.overrideMethod (c$, "keyTyped", +function (e) { +this.b$["jalview.appletgui.Finder"].textfield_keyTyped (e); +}, "java.awt.event.KeyEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/FontChooser.js b/bin/jalview/appletgui/FontChooser.js index c8a21c0..a0154ca 100644 --- a/bin/jalview/appletgui/FontChooser.js +++ b/bin/jalview/appletgui/FontChooser.js @@ -1,259 +1,259 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ItemListener", "awt2swing.Button", "$.Checkbox", "$.Choice", "java.awt.Font"], "jalview.appletgui.FontChooser", ["awt2swing.Frame", "$.Label", "jalview.appletgui.JVDialog", "jalview.bin.JalviewLite", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.FlowLayout", "$.Toolkit", "java.awt.event.ActionListener"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fontSize = null; -this.fontStyle = null; -this.fontName = null; -this.scaleAsCdna = null; -this.ok = null; -this.cancel = null; -this.ap = null; -this.tp = null; -this.oldFont = null; -this.oldCharWidth = 0; -this.oldScaleProtein = false; -this.lastSelected = null; -this.lastSelStyle = 0; -this.lastSelSize = 0; -this.$init = true; -this.frame = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "FontChooser", awt2swing.Panel, java.awt.event.ItemListener); -Clazz.prepareFields (c$, function () { -this.fontSize = new awt2swing.Choice (); -this.fontStyle = new awt2swing.Choice (); -this.fontName = new awt2swing.Choice (); -this.scaleAsCdna = new awt2swing.Checkbox (); -this.ok = new awt2swing.Button (); -this.cancel = new awt2swing.Button (); -}); -Clazz.makeConstructor (c$, -function (tp) { -Clazz.superConstructor (this, jalview.appletgui.FontChooser, []); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.tp = tp; -this.oldFont = tp.getTreeFont (); -this.init (); -}, "jalview.appletgui.TreePanel"); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.FontChooser, []); -this.ap = ap; -this.oldFont = ap.av.getFont (); -this.oldCharWidth = ap.av.getViewStyle ().getCharWidth (); -this.oldScaleProtein = ap.av.getViewStyle ().isScaleProteinAsCdna (); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.init (); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.defineMethod (c$, "init", -function () { -var fonts = java.awt.Toolkit.getDefaultToolkit ().getFontList (); -for (var i = 0; i < fonts.length; i++) { -this.fontName.addItem (fonts[i]); -} -for (var i = 1; i < 31; i++) { -this.fontSize.addItem (i + ""); -} -this.fontStyle.addItem ("plain"); -this.fontStyle.addItem ("bold"); -this.fontStyle.addItem ("italic"); -this.fontName.select (this.oldFont.getName ()); -this.fontSize.select (this.oldFont.getSize () + ""); -this.fontStyle.select (new Integer (this.oldFont.getStyle ())); -this.frame = new awt2swing.Frame (); -this.frame.add (this); -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("action.change_font"), 440, 115); -this.$init = false; -}); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -var source = evt.getSource (); -if (source === this.fontName) { -this.fontName_actionPerformed (); -} else if (source === this.fontSize) { -this.fontSize_actionPerformed (); -} else if (source === this.fontStyle) { -this.fontStyle_actionPerformed (); -} else if (source === this.scaleAsCdna) { -this.scaleAsCdna_actionPerformed (); -}}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "ok_actionPerformed", -function () { -this.frame.setVisible (false); -if (this.ap != null) { -if (this.ap.getOverviewPanel () != null) { -this.ap.getOverviewPanel ().updateOverviewImage (); -}}}); -Clazz.defineMethod (c$, "cancel_actionPerformed", -function () { -if (this.ap != null) { -this.ap.av.setScaleProteinAsCdna (this.oldScaleProtein); -if (this.ap.av.getCodingComplement () != null) { -this.ap.av.getCodingComplement ().setScaleProteinAsCdna (this.oldScaleProtein); -this.ap.alignFrame.getSplitFrame ().repaint (); -}this.ap.av.setFont (this.oldFont); -var style = this.ap.av.getViewStyle (); -if (style.getCharWidth () != this.oldCharWidth) { -style.setCharWidth (this.oldCharWidth); -this.ap.av.setViewStyle (style); -}this.ap.paintAlignment (true); -} else if (this.tp != null) { -this.tp.setTreeFont (this.oldFont); -this.tp.treeCanvas.repaint (); -}this.fontName.select (this.oldFont.getName ()); -this.fontSize.select (this.oldFont.getSize () + ""); -this.fontStyle.select (new Integer (this.oldFont.getStyle ())); -this.frame.setVisible (false); -}); -Clazz.defineMethod (c$, "changeFont", -function () { -if (this.lastSelected == null) { -this.lastSelected = this.oldFont; -this.lastSelSize = this.oldFont.getSize (); -this.lastSelStyle = this.oldFont.getStyle (); -}var newFont = new java.awt.Font (this.fontName.getSelectedItem ().toString (), this.fontStyle.getSelectedIndex (), Integer.parseInt (this.fontSize.getSelectedItem ().toString ())); -var fm = this.getGraphics ().getFontMetrics (newFont); -var mw = fm.getStringBounds ("M", this.getGraphics ()).getWidth (); -var iw = fm.getStringBounds ("I", this.getGraphics ()).getWidth (); -if (mw < 1 || iw < 1) { -this.fontName.select (this.lastSelected.getName ()); -this.fontStyle.select (new Integer (this.lastSelStyle)); -this.fontSize.select ("" + this.lastSelSize); -var d = new jalview.appletgui.JVDialog (this.frame, jalview.util.MessageManager.getString ("label.invalid_font"), true, 350, 200); -var mp = new awt2swing.Panel (); -d.cancel.setVisible (false); -mp.setLayout ( new java.awt.FlowLayout ()); -mp.add ( new awt2swing.Label ("Font doesn't have letters defined\nso cannot be used\nwith alignment data.")); -d.setMainPanel (mp); -d.setVisible (true); -return; -}if (this.tp != null) { -this.tp.setTreeFont (newFont); -} else if (this.ap != null) { -this.ap.av.setFont (newFont); -this.ap.fontChanged (); -}this.lastSelected = newFont; -}); -Clazz.defineMethod (c$, "fontName_actionPerformed", -function () { -if (this.$init) { -return; -}this.changeFont (); -}); -Clazz.defineMethod (c$, "fontSize_actionPerformed", -function () { -if (this.$init) { -return; -}this.changeFont (); -}); -Clazz.defineMethod (c$, "fontStyle_actionPerformed", -function () { -if (this.$init) { -return; -}this.changeFont (); -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout ( new java.awt.BorderLayout ()); -this.setBackground (java.awt.Color.white); -var fontLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.font")); -fontLabel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -fontLabel.setAlignment (4); -this.fontSize.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.fontSize.addItemListener (this); -this.fontStyle.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.fontStyle.addItemListener (this); -var sizeLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.size")); -sizeLabel.setAlignment (4); -sizeLabel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -var styleLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.style")); -styleLabel.setAlignment (4); -styleLabel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.fontName.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.fontName.addItemListener (this); -this.scaleAsCdna.setLabel (jalview.util.MessageManager.getString ("label.scale_as_cdna")); -this.scaleAsCdna.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.scaleAsCdna.addItemListener (this); -this.scaleAsCdna.setState (this.ap.av.isScaleProteinAsCdna ()); -this.ok.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok")); -this.ok.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FontChooser$1") ? 0 : jalview.appletgui.FontChooser.$FontChooser$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FontChooser$1, this, null))); -this.cancel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); -this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel")); -this.cancel.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FontChooser$2") ? 0 : jalview.appletgui.FontChooser.$FontChooser$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FontChooser$2, this, null))); -var fontPanel = new awt2swing.Panel (); -fontPanel.setLayout ( new java.awt.BorderLayout ()); -var stylePanel = new awt2swing.Panel (); -stylePanel.setLayout ( new java.awt.BorderLayout ()); -var sizePanel = new awt2swing.Panel (); -sizePanel.setLayout ( new java.awt.BorderLayout ()); -var scalePanel = new awt2swing.Panel (); -scalePanel.setLayout ( new java.awt.BorderLayout ()); -var okCancelPanel = new awt2swing.Panel (); -var optionsPanel = new awt2swing.Panel (); -fontPanel.setBackground (java.awt.Color.white); -stylePanel.setBackground (java.awt.Color.white); -sizePanel.setBackground (java.awt.Color.white); -okCancelPanel.setBackground (java.awt.Color.white); -optionsPanel.setBackground (java.awt.Color.white); -fontPanel.add (fontLabel, "West"); -fontPanel.add (this.fontName, "Center"); -stylePanel.add (styleLabel, "West"); -stylePanel.add (this.fontStyle, "Center"); -sizePanel.add (sizeLabel, "West"); -sizePanel.add (this.fontSize, "Center"); -scalePanel.add (this.scaleAsCdna, "Center"); -okCancelPanel.add (this.ok, null); -okCancelPanel.add (this.cancel, null); -optionsPanel.add (fontPanel, null); -optionsPanel.add (sizePanel, null); -optionsPanel.add (stylePanel, null); -this.add (optionsPanel, "North"); -if (this.ap.alignFrame.getSplitFrame () != null) { -this.add (scalePanel, "Center"); -}this.add (okCancelPanel, "South"); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "scaleAsCdna_actionPerformed", -function () { -this.ap.av.setScaleProteinAsCdna (this.scaleAsCdna.getState ()); -this.ap.av.getCodingComplement ().setScaleProteinAsCdna (this.scaleAsCdna.getState ()); -this.ap.alignFrame.getSplitFrame ().adjustLayout (); -this.ap.paintAlignment (true); -this.ap.alignFrame.getSplitFrame ().repaint (); -}); -c$.$FontChooser$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FontChooser$1", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.FontChooser"].ok_actionPerformed (); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$FontChooser$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "FontChooser$2", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.FontChooser"].cancel_actionPerformed (); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.VERDANA_11PT = c$.prototype.VERDANA_11PT = new java.awt.Font ("Verdana", 0, 11); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ItemListener", "awt2swing.Button", "$.Checkbox", "$.Choice", "java.awt.Font"], "jalview.appletgui.FontChooser", ["awt2swing.Frame", "$.Label", "jalview.appletgui.JVDialog", "jalview.bin.JalviewLite", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.FlowLayout", "$.Toolkit", "java.awt.event.ActionListener"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fontSize = null; +this.fontStyle = null; +this.fontName = null; +this.scaleAsCdna = null; +this.ok = null; +this.cancel = null; +this.ap = null; +this.tp = null; +this.oldFont = null; +this.oldCharWidth = 0; +this.oldScaleProtein = false; +this.lastSelected = null; +this.lastSelStyle = 0; +this.lastSelSize = 0; +this.$init = true; +this.frame = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "FontChooser", awt2swing.Panel, java.awt.event.ItemListener); +Clazz.prepareFields (c$, function () { +this.fontSize = new awt2swing.Choice (); +this.fontStyle = new awt2swing.Choice (); +this.fontName = new awt2swing.Choice (); +this.scaleAsCdna = new awt2swing.Checkbox (); +this.ok = new awt2swing.Button (); +this.cancel = new awt2swing.Button (); +}); +Clazz.makeConstructor (c$, +function (tp) { +Clazz.superConstructor (this, jalview.appletgui.FontChooser, []); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.tp = tp; +this.oldFont = tp.getTreeFont (); +this.init (); +}, "jalview.appletgui.TreePanel"); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.FontChooser, []); +this.ap = ap; +this.oldFont = ap.av.getFont (); +this.oldCharWidth = ap.av.getViewStyle ().getCharWidth (); +this.oldScaleProtein = ap.av.getViewStyle ().isScaleProteinAsCdna (); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.init (); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.defineMethod (c$, "init", +function () { +var fonts = java.awt.Toolkit.getDefaultToolkit ().getFontList (); +for (var i = 0; i < fonts.length; i++) { +this.fontName.addItem (fonts[i]); +} +for (var i = 1; i < 31; i++) { +this.fontSize.addItem (i + ""); +} +this.fontStyle.addItem ("plain"); +this.fontStyle.addItem ("bold"); +this.fontStyle.addItem ("italic"); +this.fontName.select (this.oldFont.getName ()); +this.fontSize.select (this.oldFont.getSize () + ""); +this.fontStyle.select (new Integer (this.oldFont.getStyle ())); +this.frame = new awt2swing.Frame (); +this.frame.add (this); +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("action.change_font"), 440, 115); +this.$init = false; +}); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +var source = evt.getSource (); +if (source === this.fontName) { +this.fontName_actionPerformed (); +} else if (source === this.fontSize) { +this.fontSize_actionPerformed (); +} else if (source === this.fontStyle) { +this.fontStyle_actionPerformed (); +} else if (source === this.scaleAsCdna) { +this.scaleAsCdna_actionPerformed (); +}}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "ok_actionPerformed", +function () { +this.frame.setVisible (false); +if (this.ap != null) { +if (this.ap.getOverviewPanel () != null) { +this.ap.getOverviewPanel ().updateOverviewImage (); +}}}); +Clazz.defineMethod (c$, "cancel_actionPerformed", +function () { +if (this.ap != null) { +this.ap.av.setScaleProteinAsCdna (this.oldScaleProtein); +if (this.ap.av.getCodingComplement () != null) { +this.ap.av.getCodingComplement ().setScaleProteinAsCdna (this.oldScaleProtein); +this.ap.alignFrame.getSplitFrame ().repaint (); +}this.ap.av.setFont (this.oldFont); +var style = this.ap.av.getViewStyle (); +if (style.getCharWidth () != this.oldCharWidth) { +style.setCharWidth (this.oldCharWidth); +this.ap.av.setViewStyle (style); +}this.ap.paintAlignment (true); +} else if (this.tp != null) { +this.tp.setTreeFont (this.oldFont); +this.tp.treeCanvas.repaint (); +}this.fontName.select (this.oldFont.getName ()); +this.fontSize.select (this.oldFont.getSize () + ""); +this.fontStyle.select (new Integer (this.oldFont.getStyle ())); +this.frame.setVisible (false); +}); +Clazz.defineMethod (c$, "changeFont", +function () { +if (this.lastSelected == null) { +this.lastSelected = this.oldFont; +this.lastSelSize = this.oldFont.getSize (); +this.lastSelStyle = this.oldFont.getStyle (); +}var newFont = new java.awt.Font (this.fontName.getSelectedItem ().toString (), this.fontStyle.getSelectedIndex (), Integer.parseInt (this.fontSize.getSelectedItem ().toString ())); +var fm = this.getGraphics ().getFontMetrics (newFont); +var mw = fm.getStringBounds ("M", this.getGraphics ()).getWidth (); +var iw = fm.getStringBounds ("I", this.getGraphics ()).getWidth (); +if (mw < 1 || iw < 1) { +this.fontName.select (this.lastSelected.getName ()); +this.fontStyle.select (new Integer (this.lastSelStyle)); +this.fontSize.select ("" + this.lastSelSize); +var d = new jalview.appletgui.JVDialog (this.frame, jalview.util.MessageManager.getString ("label.invalid_font"), true, 350, 200); +var mp = new awt2swing.Panel (); +d.cancel.setVisible (false); +mp.setLayout ( new java.awt.FlowLayout ()); +mp.add ( new awt2swing.Label ("Font doesn't have letters defined\nso cannot be used\nwith alignment data.")); +d.setMainPanel (mp); +d.setVisible (true); +return; +}if (this.tp != null) { +this.tp.setTreeFont (newFont); +} else if (this.ap != null) { +this.ap.av.setFont (newFont); +this.ap.fontChanged (); +}this.lastSelected = newFont; +}); +Clazz.defineMethod (c$, "fontName_actionPerformed", +function () { +if (this.$init) { +return; +}this.changeFont (); +}); +Clazz.defineMethod (c$, "fontSize_actionPerformed", +function () { +if (this.$init) { +return; +}this.changeFont (); +}); +Clazz.defineMethod (c$, "fontStyle_actionPerformed", +function () { +if (this.$init) { +return; +}this.changeFont (); +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout ( new java.awt.BorderLayout ()); +this.setBackground (java.awt.Color.white); +var fontLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.font")); +fontLabel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +fontLabel.setAlignment (4); +this.fontSize.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.fontSize.addItemListener (this); +this.fontStyle.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.fontStyle.addItemListener (this); +var sizeLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.size")); +sizeLabel.setAlignment (4); +sizeLabel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +var styleLabel = new awt2swing.Label (jalview.util.MessageManager.getString ("label.style")); +styleLabel.setAlignment (4); +styleLabel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.fontName.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.fontName.addItemListener (this); +this.scaleAsCdna.setLabel (jalview.util.MessageManager.getString ("label.scale_as_cdna")); +this.scaleAsCdna.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.scaleAsCdna.addItemListener (this); +this.scaleAsCdna.setState (this.ap.av.isScaleProteinAsCdna ()); +this.ok.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok")); +this.ok.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FontChooser$1") ? 0 : jalview.appletgui.FontChooser.$FontChooser$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FontChooser$1, this, null))); +this.cancel.setFont (jalview.appletgui.FontChooser.VERDANA_11PT); +this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel")); +this.cancel.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FontChooser$2") ? 0 : jalview.appletgui.FontChooser.$FontChooser$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FontChooser$2, this, null))); +var fontPanel = new awt2swing.Panel (); +fontPanel.setLayout ( new java.awt.BorderLayout ()); +var stylePanel = new awt2swing.Panel (); +stylePanel.setLayout ( new java.awt.BorderLayout ()); +var sizePanel = new awt2swing.Panel (); +sizePanel.setLayout ( new java.awt.BorderLayout ()); +var scalePanel = new awt2swing.Panel (); +scalePanel.setLayout ( new java.awt.BorderLayout ()); +var okCancelPanel = new awt2swing.Panel (); +var optionsPanel = new awt2swing.Panel (); +fontPanel.setBackground (java.awt.Color.white); +stylePanel.setBackground (java.awt.Color.white); +sizePanel.setBackground (java.awt.Color.white); +okCancelPanel.setBackground (java.awt.Color.white); +optionsPanel.setBackground (java.awt.Color.white); +fontPanel.add (fontLabel, "West"); +fontPanel.add (this.fontName, "Center"); +stylePanel.add (styleLabel, "West"); +stylePanel.add (this.fontStyle, "Center"); +sizePanel.add (sizeLabel, "West"); +sizePanel.add (this.fontSize, "Center"); +scalePanel.add (this.scaleAsCdna, "Center"); +okCancelPanel.add (this.ok, null); +okCancelPanel.add (this.cancel, null); +optionsPanel.add (fontPanel, null); +optionsPanel.add (sizePanel, null); +optionsPanel.add (stylePanel, null); +this.add (optionsPanel, "North"); +if (this.ap.alignFrame.getSplitFrame () != null) { +this.add (scalePanel, "Center"); +}this.add (okCancelPanel, "South"); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "scaleAsCdna_actionPerformed", +function () { +this.ap.av.setScaleProteinAsCdna (this.scaleAsCdna.getState ()); +this.ap.av.getCodingComplement ().setScaleProteinAsCdna (this.scaleAsCdna.getState ()); +this.ap.alignFrame.getSplitFrame ().adjustLayout (); +this.ap.paintAlignment (true); +this.ap.alignFrame.getSplitFrame ().repaint (); +}); +c$.$FontChooser$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FontChooser$1", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.FontChooser"].ok_actionPerformed (); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$FontChooser$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "FontChooser$2", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.FontChooser"].cancel_actionPerformed (); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.VERDANA_11PT = c$.prototype.VERDANA_11PT = new java.awt.Font ("Verdana", 0, 11); +}); diff --git a/bin/jalview/appletgui/IdCanvas.class b/bin/jalview/appletgui/IdCanvas.class index c079bc6..2c2cb6f 100644 Binary files a/bin/jalview/appletgui/IdCanvas.class and b/bin/jalview/appletgui/IdCanvas.class differ diff --git a/bin/jalview/appletgui/IdCanvas.js b/bin/jalview/appletgui/IdCanvas.js index 7c5a1c2..673b00e 100644 --- a/bin/jalview/appletgui/IdCanvas.js +++ b/bin/jalview/appletgui/IdCanvas.js @@ -1,191 +1,191 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel"], "jalview.appletgui.IdCanvas", ["jalview.appletgui.AnnotationLabels", "$.AnnotationPanel", "$.PaintRefresher", "java.awt.Color", "$.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.showScores = true; -this.maxIdLength = -1; -this.maxIdStr = null; -this.image = null; -this.gg = null; -this.imgHeight = 0; -this.$fastPaint = false; -this.searchResults = null; -this.avcharHeight = 0; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "IdCanvas", awt2swing.Panel); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.IdCanvas, []); -this.setLayout (null); -this.av = av; -jalview.appletgui.PaintRefresher.Register (this, av.getSequenceSetId ()); -}, "jalview.appletgui.AlignViewport"); -Clazz.defineMethod (c$, "drawIdString", -function (gg, hiddenRows, s, i, starty, ypos) { -var charHeight = this.av.getCharHeight (); -if (this.searchResults != null && this.searchResults.contains (s)) { -gg.setColor (java.awt.Color.black); -gg.fillRect (0, ((i - starty) * charHeight) + ypos, this.getSize ().width, charHeight); -gg.setColor (java.awt.Color.white); -} else if (this.av.getSelectionGroup () != null && this.av.getSelectionGroup ().getSequences (null).contains (s)) { -gg.setColor (java.awt.Color.lightGray); -gg.fillRect (0, ((i - starty) * charHeight) + ypos, this.getSize ().width, charHeight); -gg.setColor (java.awt.Color.white); -} else { -gg.setColor (this.av.getSequenceColour (s)); -gg.fillRect (0, ((i - starty) * charHeight) + ypos, this.getSize ().width, charHeight); -gg.setColor (java.awt.Color.black); -}gg.drawString (s.getDisplayId (this.av.getShowJVSuffix ()), 0, ((i - starty) * charHeight) + ypos + charHeight - (Clazz.doubleToInt (charHeight / 5))); -if (hiddenRows) { -this.drawMarker (i, starty, ypos); -}}, "java.awt.Graphics,~B,jalview.datamodel.SequenceI,~N,~N,~N"); -Clazz.defineMethod (c$, "fastPaint", -function (vertical) { -if (this.gg == null) { -this.repaint (); -return; -}this.gg.copyArea (0, 0, this.getSize ().width, this.imgHeight, 0, -vertical * this.av.getCharHeight ()); -var ss = this.av.startSeq; -var es = this.av.endSeq; -var transY = 0; -if (vertical > 0) { -ss = es - vertical; -if (ss < this.av.startSeq) { -ss = this.av.startSeq; -} else { -transY = this.imgHeight - vertical * this.av.getCharHeight (); -}} else if (vertical < 0) { -es = ss - vertical; -if (es > this.av.endSeq) { -es = this.av.endSeq; -}}this.gg.translate (0, transY); -this.drawIds (ss, es); -this.gg.translate (0, -transY); -this.$fastPaint = true; -this.repaint (); -}, "~N"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -if (this.getSize ().height < 0 || this.getSize ().width < 0) { -return; -}if (this.$fastPaint) { -this.$fastPaint = false; -g.drawImage (this.image, 0, 0, this); -return; -}this.imgHeight = this.getSize ().height; -this.imgHeight -= this.imgHeight % this.av.getCharHeight (); -if (this.imgHeight < 1) { -return; -}if (this.image == null || this.imgHeight != this.image.getHeight (this)) { -this.image = this.createImage (this.getSize ().width, this.imgHeight); -this.gg = this.image.getGraphics (); -this.gg.setFont (this.av.getFont ()); -}this.gg.setColor (java.awt.Color.white); -var italic = new java.awt.Font (this.av.getFont ().getName (), 2, this.av.getFont ().getSize ()); -this.gg.setFont (italic); -this.gg.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -this.drawIds (this.av.startSeq, this.av.endSeq); -g.drawImage (this.image, 0, 0, this); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "drawIds", -function (starty, endy) { -var italic = new java.awt.Font (this.av.getFont ().getName (), 2, this.av.getFont ().getSize ()); -this.avcharHeight = this.av.getCharHeight (); -this.gg.setFont (italic); -var currentColor = java.awt.Color.white; -var currentTextColor = java.awt.Color.black; -var doHiddenCheck = this.av.isDisplayReferenceSeq () || this.av.hasHiddenRows (); -var hiddenRows = this.av.hasHiddenRows () && this.av.getShowHiddenMarkers (); -if (this.av.getWrapAlignment ()) { -var maxwidth = this.av.getAlignment ().getWidth (); -var alheight = this.av.getAlignment ().getHeight (); -if (this.av.hasHiddenColumns ()) { -maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; -}var annotationHeight = 0; -var labels = null; -if (this.av.isShowAnnotation ()) { -var ap = new jalview.appletgui.AnnotationPanel (this.av); -annotationHeight = ap.adjustPanelHeight (); -labels = new jalview.appletgui.AnnotationLabels (this.av); -}var hgap = this.avcharHeight; -if (this.av.getScaleAboveWrapped ()) { -hgap += this.avcharHeight; -}var cHeight = alheight * this.avcharHeight + hgap + annotationHeight; -var rowSize = this.av.getEndRes () - this.av.getStartRes (); -for (var ypos = hgap, row = this.av.startRes; (ypos <= this.getSize ().height) && (row < maxwidth); ypos += cHeight, row += rowSize) { -for (var i = starty; i < alheight; i++) { -var s = this.av.getAlignment ().getSequenceAt (i); -this.gg.setFont (italic); -if (doHiddenCheck) { -this.setHiddenFont (s); -}this.drawIdString (this.gg, hiddenRows, s, i, 0, ypos); -} -if (labels != null) { -this.gg.translate (0, ypos + (alheight * this.avcharHeight)); -labels.drawComponent (this.gg, this.getSize ().width); -this.gg.translate (0, -ypos - (alheight * this.avcharHeight)); -}} -} else { -var seq; -for (var i = starty; i < endy; i++) { -seq = this.av.getAlignment ().getSequenceAt (i); -if (seq == null) { -continue; -}this.gg.setFont (italic); -if (doHiddenCheck) { -this.setHiddenFont (seq); -}if ((this.searchResults != null) && this.searchResults.contains (seq)) { -currentColor = java.awt.Color.black; -currentTextColor = java.awt.Color.white; -} else if ((this.av.getSelectionGroup () != null) && this.av.getSelectionGroup ().getSequences (null).contains (seq)) { -currentColor = java.awt.Color.lightGray; -currentTextColor = java.awt.Color.black; -} else { -currentColor = this.av.getSequenceColour (seq); -currentTextColor = java.awt.Color.black; -}this.gg.setColor (currentColor); -this.gg.fillRect (0, (i - starty) * this.avcharHeight, this.getSize ().width, this.avcharHeight); -this.gg.setColor (currentTextColor); -this.gg.drawString (seq.getDisplayId (this.av.getShowJVSuffix ()), 0, (((i - starty) * this.avcharHeight) + this.avcharHeight) - (Clazz.doubleToInt (this.avcharHeight / 5))); -if (hiddenRows) { -this.drawMarker (i, starty, 0); -}} -}}, "~N,~N"); -Clazz.defineMethod (c$, "setHighlighted", -function (list) { -this.searchResults = list; -this.repaint (); -}, "java.util.List"); -Clazz.defineMethod (c$, "drawMarker", -function (i, starty, yoffset) { -var hseqs = this.av.getAlignment ().getHiddenSequences ().hiddenSequences; -var hSize = hseqs.length; -var hiddenIndex = i; -var lastIndex = i - 1; -var nextIndex = i + 1; -for (var j = 0; j < hSize; j++) { -if (hseqs[j] != null) { -if (j - 1 < hiddenIndex) { -hiddenIndex++; -}if (j - 1 < lastIndex) { -lastIndex++; -}if (j - 1 < nextIndex) { -nextIndex++; -}}} -var below = (hiddenIndex > lastIndex + 1); -var above = (nextIndex > hiddenIndex + 1); -this.gg.setColor (java.awt.Color.blue); -if (below) { -this.gg.fillPolygon ( Clazz.newIntArray (-1, [this.getSize ().width - this.avcharHeight, this.getSize ().width - this.avcharHeight, this.getSize ().width]), Clazz.newIntArray (-1, [(i - starty) * this.avcharHeight + yoffset, (i - starty) * this.avcharHeight + yoffset + Clazz.doubleToInt (this.avcharHeight / 4), (i - starty) * this.avcharHeight + yoffset]), 3); -}if (above) { -this.gg.fillPolygon ( Clazz.newIntArray (-1, [this.getSize ().width - this.avcharHeight, this.getSize ().width - this.avcharHeight, this.getSize ().width]), Clazz.newIntArray (-1, [(i - starty + 1) * this.avcharHeight + yoffset, (i - starty + 1) * this.avcharHeight + yoffset - Clazz.doubleToInt (this.avcharHeight / 4), (i - starty + 1) * this.avcharHeight + yoffset]), 3); -}}, "~N,~N,~N"); -Clazz.defineMethod (c$, "setHiddenFont", -function (seq) { -var bold = new java.awt.Font (this.av.getFont ().getName (), 1, this.av.getFont ().getSize ()); -if (this.av.isHiddenRepSequence (seq)) { -this.gg.setFont (bold); -return true; -}return false; -}, "jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel"], "jalview.appletgui.IdCanvas", ["jalview.appletgui.AnnotationLabels", "$.AnnotationPanel", "$.PaintRefresher", "java.awt.Color", "$.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.showScores = true; +this.maxIdLength = -1; +this.maxIdStr = null; +this.image = null; +this.gg = null; +this.imgHeight = 0; +this.$fastPaint = false; +this.searchResults = null; +this.avcharHeight = 0; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "IdCanvas", awt2swing.Panel); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.IdCanvas, []); +this.setLayout (null); +this.av = av; +jalview.appletgui.PaintRefresher.Register (this, av.getSequenceSetId ()); +}, "jalview.appletgui.AlignViewport"); +Clazz.defineMethod (c$, "drawIdString", +function (gg, hiddenRows, s, i, starty, ypos) { +var charHeight = this.av.getCharHeight (); +if (this.searchResults != null && this.searchResults.contains (s)) { +gg.setColor (java.awt.Color.black); +gg.fillRect (0, ((i - starty) * charHeight) + ypos, this.getSize ().width, charHeight); +gg.setColor (java.awt.Color.white); +} else if (this.av.getSelectionGroup () != null && this.av.getSelectionGroup ().getSequences (null).contains (s)) { +gg.setColor (java.awt.Color.lightGray); +gg.fillRect (0, ((i - starty) * charHeight) + ypos, this.getSize ().width, charHeight); +gg.setColor (java.awt.Color.white); +} else { +gg.setColor (this.av.getSequenceColour (s)); +gg.fillRect (0, ((i - starty) * charHeight) + ypos, this.getSize ().width, charHeight); +gg.setColor (java.awt.Color.black); +}gg.drawString (s.getDisplayId (this.av.getShowJVSuffix ()), 0, ((i - starty) * charHeight) + ypos + charHeight - (Clazz.doubleToInt (charHeight / 5))); +if (hiddenRows) { +this.drawMarker (i, starty, ypos); +}}, "java.awt.Graphics,~B,jalview.datamodel.SequenceI,~N,~N,~N"); +Clazz.defineMethod (c$, "fastPaint", +function (vertical) { +if (this.gg == null) { +this.repaint (); +return; +}this.gg.copyArea (0, 0, this.getSize ().width, this.imgHeight, 0, -vertical * this.av.getCharHeight ()); +var ss = this.av.startSeq; +var es = this.av.endSeq; +var transY = 0; +if (vertical > 0) { +ss = es - vertical; +if (ss < this.av.startSeq) { +ss = this.av.startSeq; +} else { +transY = this.imgHeight - vertical * this.av.getCharHeight (); +}} else if (vertical < 0) { +es = ss - vertical; +if (es > this.av.endSeq) { +es = this.av.endSeq; +}}this.gg.translate (0, transY); +this.drawIds (ss, es); +this.gg.translate (0, -transY); +this.$fastPaint = true; +this.repaint (); +}, "~N"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +if (this.getSize ().height < 0 || this.getSize ().width < 0) { +return; +}if (this.$fastPaint) { +this.$fastPaint = false; +g.drawImage (this.image, 0, 0, this); +return; +}this.imgHeight = this.getSize ().height; +this.imgHeight -= this.imgHeight % this.av.getCharHeight (); +if (this.imgHeight < 1) { +return; +}if (this.image == null || this.imgHeight != this.image.getHeight (this)) { +this.image = this.createImage (this.getSize ().width, this.imgHeight); +this.gg = this.image.getGraphics (); +this.gg.setFont (this.av.getFont ()); +}this.gg.setColor (java.awt.Color.white); +var italic = new java.awt.Font (this.av.getFont ().getName (), 2, this.av.getFont ().getSize ()); +this.gg.setFont (italic); +this.gg.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +this.drawIds (this.av.startSeq, this.av.endSeq); +g.drawImage (this.image, 0, 0, this); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "drawIds", +function (starty, endy) { +var italic = new java.awt.Font (this.av.getFont ().getName (), 2, this.av.getFont ().getSize ()); +this.avcharHeight = this.av.getCharHeight (); +this.gg.setFont (italic); +var currentColor = java.awt.Color.white; +var currentTextColor = java.awt.Color.black; +var doHiddenCheck = this.av.isDisplayReferenceSeq () || this.av.hasHiddenRows (); +var hiddenRows = this.av.hasHiddenRows () && this.av.getShowHiddenMarkers (); +if (this.av.getWrapAlignment ()) { +var maxwidth = this.av.getAlignment ().getWidth (); +var alheight = this.av.getAlignment ().getHeight (); +if (this.av.hasHiddenColumns ()) { +maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; +}var annotationHeight = 0; +var labels = null; +if (this.av.isShowAnnotation ()) { +var ap = new jalview.appletgui.AnnotationPanel (this.av); +annotationHeight = ap.adjustPanelHeight (); +labels = new jalview.appletgui.AnnotationLabels (this.av); +}var hgap = this.avcharHeight; +if (this.av.getScaleAboveWrapped ()) { +hgap += this.avcharHeight; +}var cHeight = alheight * this.avcharHeight + hgap + annotationHeight; +var rowSize = this.av.getEndRes () - this.av.getStartRes (); +for (var ypos = hgap, row = this.av.startRes; (ypos <= this.getSize ().height) && (row < maxwidth); ypos += cHeight, row += rowSize) { +for (var i = starty; i < alheight; i++) { +var s = this.av.getAlignment ().getSequenceAt (i); +this.gg.setFont (italic); +if (doHiddenCheck) { +this.setHiddenFont (s); +}this.drawIdString (this.gg, hiddenRows, s, i, 0, ypos); +} +if (labels != null) { +this.gg.translate (0, ypos + (alheight * this.avcharHeight)); +labels.drawComponent (this.gg, this.getSize ().width); +this.gg.translate (0, -ypos - (alheight * this.avcharHeight)); +}} +} else { +var seq; +for (var i = starty; i < endy; i++) { +seq = this.av.getAlignment ().getSequenceAt (i); +if (seq == null) { +continue; +}this.gg.setFont (italic); +if (doHiddenCheck) { +this.setHiddenFont (seq); +}if ((this.searchResults != null) && this.searchResults.contains (seq)) { +currentColor = java.awt.Color.black; +currentTextColor = java.awt.Color.white; +} else if ((this.av.getSelectionGroup () != null) && this.av.getSelectionGroup ().getSequences (null).contains (seq)) { +currentColor = java.awt.Color.lightGray; +currentTextColor = java.awt.Color.black; +} else { +currentColor = this.av.getSequenceColour (seq); +currentTextColor = java.awt.Color.black; +}this.gg.setColor (currentColor); +this.gg.fillRect (0, (i - starty) * this.avcharHeight, this.getSize ().width, this.avcharHeight); +this.gg.setColor (currentTextColor); +this.gg.drawString (seq.getDisplayId (this.av.getShowJVSuffix ()), 0, (((i - starty) * this.avcharHeight) + this.avcharHeight) - (Clazz.doubleToInt (this.avcharHeight / 5))); +if (hiddenRows) { +this.drawMarker (i, starty, 0); +}} +}}, "~N,~N"); +Clazz.defineMethod (c$, "setHighlighted", +function (list) { +this.searchResults = list; +this.repaint (); +}, "java.util.List"); +Clazz.defineMethod (c$, "drawMarker", +function (i, starty, yoffset) { +var hseqs = this.av.getAlignment ().getHiddenSequences ().hiddenSequences; +var hSize = hseqs.length; +var hiddenIndex = i; +var lastIndex = i - 1; +var nextIndex = i + 1; +for (var j = 0; j < hSize; j++) { +if (hseqs[j] != null) { +if (j - 1 < hiddenIndex) { +hiddenIndex++; +}if (j - 1 < lastIndex) { +lastIndex++; +}if (j - 1 < nextIndex) { +nextIndex++; +}}} +var below = (hiddenIndex > lastIndex + 1); +var above = (nextIndex > hiddenIndex + 1); +this.gg.setColor (java.awt.Color.blue); +if (below) { +this.gg.fillPolygon ( Clazz.newIntArray (-1, [this.getSize ().width - this.avcharHeight, this.getSize ().width - this.avcharHeight, this.getSize ().width]), Clazz.newIntArray (-1, [(i - starty) * this.avcharHeight + yoffset, (i - starty) * this.avcharHeight + yoffset + Clazz.doubleToInt (this.avcharHeight / 4), (i - starty) * this.avcharHeight + yoffset]), 3); +}if (above) { +this.gg.fillPolygon ( Clazz.newIntArray (-1, [this.getSize ().width - this.avcharHeight, this.getSize ().width - this.avcharHeight, this.getSize ().width]), Clazz.newIntArray (-1, [(i - starty + 1) * this.avcharHeight + yoffset, (i - starty + 1) * this.avcharHeight + yoffset - Clazz.doubleToInt (this.avcharHeight / 4), (i - starty + 1) * this.avcharHeight + yoffset]), 3); +}}, "~N,~N,~N"); +Clazz.defineMethod (c$, "setHiddenFont", +function (seq) { +var bold = new java.awt.Font (this.av.getFont ().getName (), 1, this.av.getFont ().getSize ()); +if (this.av.isHiddenRepSequence (seq)) { +this.gg.setFont (bold); +return true; +}return false; +}, "jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/appletgui/IdPanel.js b/bin/jalview/appletgui/IdPanel.js index 1419a24..4f70687 100644 --- a/bin/jalview/appletgui/IdPanel.js +++ b/bin/jalview/appletgui/IdPanel.js @@ -1,285 +1,285 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.lang.Thread", "java.util.Vector"], "jalview.appletgui.IdPanel", ["jalview.appletgui.APopupMenu", "$.IdCanvas", "$.PaintRefresher", "$.Tooltip", "jalview.datamodel.SequenceGroup", "jalview.util.UrlLink", "java.awt.BorderLayout", "java.lang.Float", "$.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.idCanvas = null; -this.av = null; -this.alignPanel = null; -this.scrollThread = null; -this.lastid = -1; -this.mouseDragging = false; -this.links = null; -this.tooltip = null; -if (!Clazz.isClassDefined ("jalview.appletgui.IdPanel.ScrollThread")) { -jalview.appletgui.IdPanel.$IdPanel$ScrollThread$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "IdPanel", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); -Clazz.prepareFields (c$, function () { -this.links = new java.util.Vector (); -}); -Clazz.makeConstructor (c$, -function (av, parent) { -Clazz.superConstructor (this, jalview.appletgui.IdPanel, []); -this.setName ("idPanel"); -this.av = av; -this.alignPanel = parent; -this.idCanvas = new jalview.appletgui.IdCanvas (av); -this.setLayout ( new java.awt.BorderLayout ()); -this.add (this.idCanvas, "Center"); -this.idCanvas.addMouseListener (this); -this.idCanvas.addMouseMotionListener (this); -if (av.applet != null) { -av.applet.getLinkParams (this.links); -}{ -var srsPos = this.links.indexOf ("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); -if (srsPos > -1) { -this.links.setElementAt ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", srsPos); -}}if (this.links.size () < 1) { -this.links = new java.util.Vector (); -this.links.addElement ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); -}}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "mouseMoved", -function (e) { -var seq = this.alignPanel.seqPanel.findSeq (e); -var sequence = this.av.getAlignment ().getSequenceAt (seq); -var tooltiptext = new StringBuffer (); -if (sequence != null) { -if (sequence.getDescription () != null) { -tooltiptext.append (sequence.getDescription ()); -tooltiptext.append ("\n"); -}var sf = sequence.getSequenceFeatures (); -for (var sl = 0; sf != null && sl < sf.length; sl++) { -if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) { -var nl = false; -if (sf[sl].getFeatureGroup () != null) { -tooltiptext.append (sf[sl].getFeatureGroup ()); -nl = true; -};if (sf[sl].getType () != null) { -tooltiptext.append (" "); -tooltiptext.append (sf[sl].getType ()); -nl = true; -};if (sf[sl].getDescription () != null) { -tooltiptext.append (" "); -tooltiptext.append (sf[sl].getDescription ()); -nl = true; -};if (!Float.isNaN (sf[sl].getScore ()) && sf[sl].getScore () != 0) { -tooltiptext.append (" Score = "); -tooltiptext.append (sf[sl].getScore ()); -nl = true; -};if (sf[sl].getStatus () != null && sf[sl].getStatus ().length > 0) { -tooltiptext.append (" ("); -tooltiptext.append (sf[sl].getStatus ()); -tooltiptext.append (")"); -nl = true; -};if (nl) { -tooltiptext.append ("\n"); -}}} -}if (tooltiptext.length () == 0) { -if (this.tooltip != null) { -this.tooltip.setVisible (false); -}this.tooltip = null; -tooltiptext = null; -return; -}if (this.tooltip == null) { -this.tooltip = new jalview.appletgui.Tooltip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString (), this.idCanvas); -} else { -this.tooltip.setTip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString ()); -}tooltiptext = null; -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (e) { -this.mouseDragging = true; -var seq = Math.max (0, this.alignPanel.seqPanel.findSeq (e)); -if (seq < this.lastid) { -this.selectSeqs (this.lastid - 1, seq); -} else if (seq > this.lastid) { -this.selectSeqs (this.lastid + 1, seq); -}this.lastid = seq; -this.alignPanel.paintAlignment (false); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (e) { -if (e.getClickCount () < 2) { -return; -}var seq = this.alignPanel.seqPanel.findSeq (e); -var sq = this.av.getAlignment ().getSequenceAt (seq); -if (sq == null) { -return; -}var id = sq.getName (); -var target = null; -var url = null; -var i = 0; -while (url == null && i < this.links.size ()) { -url = this.links.elementAt (i++).toString (); -var urlLink = null; -try { -urlLink = new jalview.util.UrlLink (url); -target = urlLink.getTarget (); -} catch (foo) { -if (Clazz.exceptionOf (foo, Exception)) { -System.err.println ("Exception for URLLink '" + url + "'"); -foo.printStackTrace (); -url = null; -continue; -} else { -throw foo; -} -} -;if (!urlLink.isValid ()) { -System.err.println (urlLink.getInvalidMessage ()); -url = null; -continue; -}var urls = urlLink.makeUrls (id, true); -if (urls == null || urls[0] == null || urls[0].length < 1) { -url = null; -continue; -}url = urls[1]; -} -try { -this.alignPanel.alignFrame.showURL (url, target); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (e) { -if (this.scrollThread != null) { -this.scrollThread.running = false; -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (e) { -if (this.av.getWrapAlignment ()) { -return; -}if (this.mouseDragging && e.getY () < 0 && this.av.getStartSeq () > 0) { -this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, true); -}if (this.mouseDragging && e.getY () >= this.getSize ().height && this.av.getAlignment ().getHeight () > this.av.getEndSeq ()) { -this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, false); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (e) { -if (e.getClickCount () > 1) { -return; -}var y = e.getY (); -if (this.av.getWrapAlignment ()) { -y -= 2 * this.av.getCharHeight (); -}var seq = this.alignPanel.seqPanel.findSeq (e); -if ((e.getModifiers () & 4) == 4) { -var sq = this.av.getAlignment ().getSequenceAt (seq); -var nlinks = new java.util.Vector (); -for (var l = 0, lSize = this.links.size (); l < lSize; l++) { -nlinks.addElement (this.links.elementAt (l)); -} -var sf = sq == null ? null : sq.getSequenceFeatures (); -for (var sl = 0; sf != null && sl < sf.length; sl++) { -if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) { -if (sf[sl].links != null && sf[sl].links.size () > 0) { -for (var l = 0, lSize = sf[sl].links.size (); l < lSize; l++) { -nlinks.addElement (sf[sl].links.elementAt (l)); -} -}}} -var popup = new jalview.appletgui.APopupMenu (this.alignPanel, sq, nlinks); -this.add (popup); -popup.show (this, e.getX (), e.getY ()); -return; -}if ((this.av.getSelectionGroup () == null) || ((!e.isControlDown () && !e.isShiftDown ()) && this.av.getSelectionGroup () != null)) { -this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ()); -this.av.getSelectionGroup ().setStartRes (0); -this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1); -}if (e.isShiftDown () && this.lastid != -1) { -this.selectSeqs (this.lastid, seq); -} else { -this.selectSeq (seq); -}this.alignPanel.paintAlignment (false); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "selectSeq", -function (seq) { -this.lastid = seq; -var pickedSeq = this.av.getAlignment ().getSequenceAt (seq); -this.av.getSelectionGroup ().addOrRemove (pickedSeq, true); -}, "~N"); -Clazz.defineMethod (c$, "selectSeqs", -function (start, end) { -this.lastid = start; -if (end >= this.av.getAlignment ().getHeight ()) { -end = this.av.getAlignment ().getHeight () - 1; -}if (end < start) { -var tmp = start; -start = end; -end = tmp; -this.lastid = end; -}if (this.av.getSelectionGroup () == null) { -this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ()); -}for (var i = start; i <= end; i++) { -this.av.getSelectionGroup ().addSequence (this.av.getAlignment ().getSequenceAt (i), i == end); -} -}, "~N,~N"); -Clazz.overrideMethod (c$, "mouseReleased", -function (e) { -if (this.scrollThread != null) { -this.scrollThread.running = false; -}if (this.av.getSelectionGroup () != null) { -this.av.getSelectionGroup ().recalcConservation (); -}this.mouseDragging = false; -jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); -this.av.sendSelection (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "highlightSearchResults", -function (list) { -this.idCanvas.setHighlighted (list); -if (list == null) { -return; -}var index = this.av.getAlignment ().findIndex (list.get (0)); -if (this.av.getStartSeq () > index || this.av.getEndSeq () < index) { -this.alignPanel.setScrollValues (this.av.getStartRes (), index); -}}, "java.util.List"); -c$.$IdPanel$ScrollThread$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.running = false; -this.up = true; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.IdPanel, "ScrollThread", Thread); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, jalview.appletgui.IdPanel.ScrollThread, []); -this.up = a; -this.start (); -}, "~B"); -Clazz.defineMethod (c$, "stopScrolling", -function () { -this.running = false; -}); -Clazz.overrideMethod (c$, "run", -function () { -this.running = true; -while (this.running) { -if (this.b$["jalview.appletgui.IdPanel"].alignPanel.scrollUp (this.up)) { -var a = this.b$["jalview.appletgui.IdPanel"].av.getStartSeq (); -if (!this.up) { -a = this.b$["jalview.appletgui.IdPanel"].av.getEndSeq (); -}if (a < this.b$["jalview.appletgui.IdPanel"].lastid) { -this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid - 1, a); -} else if (a > this.b$["jalview.appletgui.IdPanel"].lastid && a < this.b$["jalview.appletgui.IdPanel"].av.getAlignment ().getHeight ()) { -this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid + 1, a); -}this.b$["jalview.appletgui.IdPanel"].lastid = a; -} else { -this.running = false; -}this.b$["jalview.appletgui.IdPanel"].alignPanel.paintAlignment (true); -try { -Thread.sleep (100); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -} -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.lang.Thread", "java.util.Vector"], "jalview.appletgui.IdPanel", ["jalview.appletgui.APopupMenu", "$.IdCanvas", "$.PaintRefresher", "$.Tooltip", "jalview.datamodel.SequenceGroup", "jalview.util.UrlLink", "java.awt.BorderLayout", "java.lang.Float", "$.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.idCanvas = null; +this.av = null; +this.alignPanel = null; +this.scrollThread = null; +this.lastid = -1; +this.mouseDragging = false; +this.links = null; +this.tooltip = null; +if (!Clazz.isClassDefined ("jalview.appletgui.IdPanel.ScrollThread")) { +jalview.appletgui.IdPanel.$IdPanel$ScrollThread$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "IdPanel", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); +Clazz.prepareFields (c$, function () { +this.links = new java.util.Vector (); +}); +Clazz.makeConstructor (c$, +function (av, parent) { +Clazz.superConstructor (this, jalview.appletgui.IdPanel, []); +this.setName ("idPanel"); +this.av = av; +this.alignPanel = parent; +this.idCanvas = new jalview.appletgui.IdCanvas (av); +this.setLayout ( new java.awt.BorderLayout ()); +this.add (this.idCanvas, "Center"); +this.idCanvas.addMouseListener (this); +this.idCanvas.addMouseMotionListener (this); +if (av.applet != null) { +av.applet.getLinkParams (this.links); +}{ +var srsPos = this.links.indexOf ("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); +if (srsPos > -1) { +this.links.setElementAt ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", srsPos); +}}if (this.links.size () < 1) { +this.links = new java.util.Vector (); +this.links.addElement ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); +}}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "mouseMoved", +function (e) { +var seq = this.alignPanel.seqPanel.findSeq (e); +var sequence = this.av.getAlignment ().getSequenceAt (seq); +var tooltiptext = new StringBuffer (); +if (sequence != null) { +if (sequence.getDescription () != null) { +tooltiptext.append (sequence.getDescription ()); +tooltiptext.append ("\n"); +}var sf = sequence.getSequenceFeatures (); +for (var sl = 0; sf != null && sl < sf.length; sl++) { +if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) { +var nl = false; +if (sf[sl].getFeatureGroup () != null) { +tooltiptext.append (sf[sl].getFeatureGroup ()); +nl = true; +};if (sf[sl].getType () != null) { +tooltiptext.append (" "); +tooltiptext.append (sf[sl].getType ()); +nl = true; +};if (sf[sl].getDescription () != null) { +tooltiptext.append (" "); +tooltiptext.append (sf[sl].getDescription ()); +nl = true; +};if (!Float.isNaN (sf[sl].getScore ()) && sf[sl].getScore () != 0) { +tooltiptext.append (" Score = "); +tooltiptext.append (sf[sl].getScore ()); +nl = true; +};if (sf[sl].getStatus () != null && sf[sl].getStatus ().length > 0) { +tooltiptext.append (" ("); +tooltiptext.append (sf[sl].getStatus ()); +tooltiptext.append (")"); +nl = true; +};if (nl) { +tooltiptext.append ("\n"); +}}} +}if (tooltiptext.length () == 0) { +if (this.tooltip != null) { +this.tooltip.setVisible (false); +}this.tooltip = null; +tooltiptext = null; +return; +}if (this.tooltip == null) { +this.tooltip = new jalview.appletgui.Tooltip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString (), this.idCanvas); +} else { +this.tooltip.setTip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString ()); +}tooltiptext = null; +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (e) { +this.mouseDragging = true; +var seq = Math.max (0, this.alignPanel.seqPanel.findSeq (e)); +if (seq < this.lastid) { +this.selectSeqs (this.lastid - 1, seq); +} else if (seq > this.lastid) { +this.selectSeqs (this.lastid + 1, seq); +}this.lastid = seq; +this.alignPanel.paintAlignment (false); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (e) { +if (e.getClickCount () < 2) { +return; +}var seq = this.alignPanel.seqPanel.findSeq (e); +var sq = this.av.getAlignment ().getSequenceAt (seq); +if (sq == null) { +return; +}var id = sq.getName (); +var target = null; +var url = null; +var i = 0; +while (url == null && i < this.links.size ()) { +url = this.links.elementAt (i++).toString (); +var urlLink = null; +try { +urlLink = new jalview.util.UrlLink (url); +target = urlLink.getTarget (); +} catch (foo) { +if (Clazz.exceptionOf (foo, Exception)) { +System.err.println ("Exception for URLLink '" + url + "'"); +foo.printStackTrace (); +url = null; +continue; +} else { +throw foo; +} +} +;if (!urlLink.isValid ()) { +System.err.println (urlLink.getInvalidMessage ()); +url = null; +continue; +}var urls = urlLink.makeUrls (id, true); +if (urls == null || urls[0] == null || urls[0].length < 1) { +url = null; +continue; +}url = urls[1]; +} +try { +this.alignPanel.alignFrame.showURL (url, target); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (e) { +if (this.scrollThread != null) { +this.scrollThread.running = false; +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (e) { +if (this.av.getWrapAlignment ()) { +return; +}if (this.mouseDragging && e.getY () < 0 && this.av.getStartSeq () > 0) { +this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, true); +}if (this.mouseDragging && e.getY () >= this.getSize ().height && this.av.getAlignment ().getHeight () > this.av.getEndSeq ()) { +this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, false); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (e) { +if (e.getClickCount () > 1) { +return; +}var y = e.getY (); +if (this.av.getWrapAlignment ()) { +y -= 2 * this.av.getCharHeight (); +}var seq = this.alignPanel.seqPanel.findSeq (e); +if ((e.getModifiers () & 4) == 4) { +var sq = this.av.getAlignment ().getSequenceAt (seq); +var nlinks = new java.util.Vector (); +for (var l = 0, lSize = this.links.size (); l < lSize; l++) { +nlinks.addElement (this.links.elementAt (l)); +} +var sf = sq == null ? null : sq.getSequenceFeatures (); +for (var sl = 0; sf != null && sl < sf.length; sl++) { +if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) { +if (sf[sl].links != null && sf[sl].links.size () > 0) { +for (var l = 0, lSize = sf[sl].links.size (); l < lSize; l++) { +nlinks.addElement (sf[sl].links.elementAt (l)); +} +}}} +var popup = new jalview.appletgui.APopupMenu (this.alignPanel, sq, nlinks); +this.add (popup); +popup.show (this, e.getX (), e.getY ()); +return; +}if ((this.av.getSelectionGroup () == null) || ((!e.isControlDown () && !e.isShiftDown ()) && this.av.getSelectionGroup () != null)) { +this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ()); +this.av.getSelectionGroup ().setStartRes (0); +this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1); +}if (e.isShiftDown () && this.lastid != -1) { +this.selectSeqs (this.lastid, seq); +} else { +this.selectSeq (seq); +}this.alignPanel.paintAlignment (false); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "selectSeq", +function (seq) { +this.lastid = seq; +var pickedSeq = this.av.getAlignment ().getSequenceAt (seq); +this.av.getSelectionGroup ().addOrRemove (pickedSeq, true); +}, "~N"); +Clazz.defineMethod (c$, "selectSeqs", +function (start, end) { +this.lastid = start; +if (end >= this.av.getAlignment ().getHeight ()) { +end = this.av.getAlignment ().getHeight () - 1; +}if (end < start) { +var tmp = start; +start = end; +end = tmp; +this.lastid = end; +}if (this.av.getSelectionGroup () == null) { +this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ()); +}for (var i = start; i <= end; i++) { +this.av.getSelectionGroup ().addSequence (this.av.getAlignment ().getSequenceAt (i), i == end); +} +}, "~N,~N"); +Clazz.overrideMethod (c$, "mouseReleased", +function (e) { +if (this.scrollThread != null) { +this.scrollThread.running = false; +}if (this.av.getSelectionGroup () != null) { +this.av.getSelectionGroup ().recalcConservation (); +}this.mouseDragging = false; +jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); +this.av.sendSelection (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "highlightSearchResults", +function (list) { +this.idCanvas.setHighlighted (list); +if (list == null) { +return; +}var index = this.av.getAlignment ().findIndex (list.get (0)); +if (this.av.getStartSeq () > index || this.av.getEndSeq () < index) { +this.alignPanel.setScrollValues (this.av.getStartRes (), index); +}}, "java.util.List"); +c$.$IdPanel$ScrollThread$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.running = false; +this.up = true; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.IdPanel, "ScrollThread", Thread); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, jalview.appletgui.IdPanel.ScrollThread, []); +this.up = a; +this.start (); +}, "~B"); +Clazz.defineMethod (c$, "stopScrolling", +function () { +this.running = false; +}); +Clazz.overrideMethod (c$, "run", +function () { +this.running = true; +while (this.running) { +if (this.b$["jalview.appletgui.IdPanel"].alignPanel.scrollUp (this.up)) { +var a = this.b$["jalview.appletgui.IdPanel"].av.getStartSeq (); +if (!this.up) { +a = this.b$["jalview.appletgui.IdPanel"].av.getEndSeq (); +}if (a < this.b$["jalview.appletgui.IdPanel"].lastid) { +this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid - 1, a); +} else if (a > this.b$["jalview.appletgui.IdPanel"].lastid && a < this.b$["jalview.appletgui.IdPanel"].av.getAlignment ().getHeight ()) { +this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid + 1, a); +}this.b$["jalview.appletgui.IdPanel"].lastid = a; +} else { +this.running = false; +}this.b$["jalview.appletgui.IdPanel"].alignPanel.paintAlignment (true); +try { +Thread.sleep (100); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +} +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/IdwidthAdjuster.js b/bin/jalview/appletgui/IdwidthAdjuster.js index 80a0c59..e7b92f7 100644 --- a/bin/jalview/appletgui/IdwidthAdjuster.js +++ b/bin/jalview/appletgui/IdwidthAdjuster.js @@ -1,66 +1,66 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.IdwidthAdjuster", ["java.awt.Color", "$.Toolkit"], function () { -c$ = Clazz.decorateAsClass (function () { -this.active = false; -this.oldX = 0; -this.image = null; -this.ap = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "IdwidthAdjuster", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.IdwidthAdjuster, []); -this.setName ("IdwidthAdjuster"); -this.setLayout (null); -this.ap = ap; -var url = this.getClass ().getResource ("/images/idwidth.gif"); -if (url != null) { -this.image = java.awt.Toolkit.getDefaultToolkit ().getImage (url); -}this.addMouseListener (this); -this.addMouseMotionListener (this); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -this.oldX = evt.getX (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.active = false; -this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -this.active = true; -this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -this.active = false; -this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -this.active = true; -var d = this.ap.idPanel.idCanvas.getSize (); -var dif = evt.getX () - this.oldX; -var newWidth = d.width + dif; -if (newWidth > 20 || dif > 0) { -this.ap.setIdWidth (newWidth, d.height); -this.setSize (newWidth, this.getSize ().height); -this.oldX = evt.getX (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "PaintComponent", -function (g) { -g.setColor (java.awt.Color.white); -g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -if (this.active) { -if (this.image != null) { -g.drawImage (this.image, this.getSize ().width - 20, 2, this); -}}}, "java.awt.Graphics"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.IdwidthAdjuster", ["java.awt.Color", "$.Toolkit"], function () { +c$ = Clazz.decorateAsClass (function () { +this.active = false; +this.oldX = 0; +this.image = null; +this.ap = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "IdwidthAdjuster", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.IdwidthAdjuster, []); +this.setName ("IdwidthAdjuster"); +this.setLayout (null); +this.ap = ap; +var url = this.getClass ().getResource ("/images/idwidth.gif"); +if (url != null) { +this.image = java.awt.Toolkit.getDefaultToolkit ().getImage (url); +}this.addMouseListener (this); +this.addMouseMotionListener (this); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +this.oldX = evt.getX (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.active = false; +this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +this.active = true; +this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +this.active = false; +this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +this.active = true; +var d = this.ap.idPanel.idCanvas.getSize (); +var dif = evt.getX () - this.oldX; +var newWidth = d.width + dif; +if (newWidth > 20 || dif > 0) { +this.ap.setIdWidth (newWidth, d.height); +this.setSize (newWidth, this.getSize ().height); +this.oldX = evt.getX (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "PaintComponent", +function (g) { +g.setColor (java.awt.Color.white); +g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +if (this.active) { +if (this.image != null) { +g.drawImage (this.image, this.getSize ().width - 20, 2, this); +}}}, "java.awt.Graphics"); +}); diff --git a/bin/jalview/appletgui/JVDialog.js b/bin/jalview/appletgui/JVDialog.js index 6f85ed1..ed9ee14 100644 --- a/bin/jalview/appletgui/JVDialog.js +++ b/bin/jalview/appletgui/JVDialog.js @@ -1,40 +1,40 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["java.awt.Dialog", "java.awt.event.ActionListener", "awt2swing.Button"], "jalview.appletgui.JVDialog", ["awt2swing.Panel", "java.awt.FlowLayout"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ap = null; -this.buttonPanel = null; -this.ok = null; -this.cancel = null; -this.accept = false; -this.owner = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "JVDialog", java.awt.Dialog, java.awt.event.ActionListener); -Clazz.prepareFields (c$, function () { -this.ok = new awt2swing.Button ("Accept"); -this.cancel = new awt2swing.Button ("Cancel"); -}); -Clazz.makeConstructor (c$, -function (owner, title, modal, width, height) { -Clazz.superConstructor (this, jalview.appletgui.JVDialog, [owner, title, modal]); -this.owner = owner; -height += owner.getInsets ().top + this.getInsets ().bottom; -this.setBounds (owner.getBounds ().x + Clazz.doubleToInt ((owner.getSize ().width - width) / 2), owner.getBounds ().y + Clazz.doubleToInt ((owner.getSize ().height - height) / 2), width, height); -}, "awt2swing.Frame,~S,~B,~N,~N"); -Clazz.defineMethod (c$, "setMainPanel", -function (panel) { -this.add (panel, "North"); -this.buttonPanel = new awt2swing.Panel ( new java.awt.FlowLayout ()); -this.buttonPanel.add (this.ok); -this.buttonPanel.add (this.cancel); -this.ok.addActionListener (this); -this.cancel.addActionListener (this); -this.add (this.buttonPanel, "South"); -this.pack (); -}, "awt2swing.Panel"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.ok) { -this.accept = true; -}this.setVisible (false); -}, "java.awt.event.ActionEvent"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["java.awt.Dialog", "java.awt.event.ActionListener", "awt2swing.Button"], "jalview.appletgui.JVDialog", ["awt2swing.Panel", "java.awt.FlowLayout"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ap = null; +this.buttonPanel = null; +this.ok = null; +this.cancel = null; +this.accept = false; +this.owner = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "JVDialog", java.awt.Dialog, java.awt.event.ActionListener); +Clazz.prepareFields (c$, function () { +this.ok = new awt2swing.Button ("Accept"); +this.cancel = new awt2swing.Button ("Cancel"); +}); +Clazz.makeConstructor (c$, +function (owner, title, modal, width, height) { +Clazz.superConstructor (this, jalview.appletgui.JVDialog, [owner, title, modal]); +this.owner = owner; +height += owner.getInsets ().top + this.getInsets ().bottom; +this.setBounds (owner.getBounds ().x + Clazz.doubleToInt ((owner.getSize ().width - width) / 2), owner.getBounds ().y + Clazz.doubleToInt ((owner.getSize ().height - height) / 2), width, height); +}, "awt2swing.Frame,~S,~B,~N,~N"); +Clazz.defineMethod (c$, "setMainPanel", +function (panel) { +this.add (panel, "North"); +this.buttonPanel = new awt2swing.Panel ( new java.awt.FlowLayout ()); +this.buttonPanel.add (this.ok); +this.buttonPanel.add (this.cancel); +this.ok.addActionListener (this); +this.cancel.addActionListener (this); +this.add (this.buttonPanel, "South"); +this.pack (); +}, "awt2swing.Panel"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.ok) { +this.accept = true; +}this.setVisible (false); +}, "java.awt.event.ActionEvent"); +}); diff --git a/bin/jalview/appletgui/OverviewPanel.class b/bin/jalview/appletgui/OverviewPanel.class index 58462cb..e63efea 100644 Binary files a/bin/jalview/appletgui/OverviewPanel.class and b/bin/jalview/appletgui/OverviewPanel.class differ diff --git a/bin/jalview/appletgui/OverviewPanel.js b/bin/jalview/appletgui/OverviewPanel.js index cadd6b7..41baadd 100644 --- a/bin/jalview/appletgui/OverviewPanel.js +++ b/bin/jalview/appletgui/OverviewPanel.js @@ -1,262 +1,262 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.OverviewPanel", ["awt2swing.Frame", "jalview.appletgui.FeatureRenderer", "$.SequenceRenderer", "java.awt.Color", "$.Dimension", "java.awt.event.ComponentAdapter", "java.lang.Thread"], function () { -c$ = Clazz.decorateAsClass (function () { -this.miniMe = null; -this.offscreen = null; -this.av = null; -this.ap = null; -this.scalew = 1; -this.scaleh = 1; -this.$width = 0; -this.sequencesHeight = 0; -this.graphHeight = 20; -this.boxX = -1; -this.boxY = -1; -this.boxWidth = -1; -this.boxHeight = -1; -this.resizing = false; -this.sr = null; -this.fr = null; -this.nullFrame = null; -this.resizeAgain = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "OverviewPanel", awt2swing.Panel, [Runnable, java.awt.event.MouseMotionListener, java.awt.event.MouseListener]); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.OverviewPanel, []); -this.av = ap.av; -this.ap = ap; -this.setLayout (null); -this.nullFrame = new awt2swing.Frame (); -this.nullFrame.addNotify (); -this.sr = new jalview.appletgui.SequenceRenderer (this.av); -this.sr.graphics = this.nullFrame.getGraphics (); -this.sr.renderGaps = false; -this.sr.forOverview = true; -this.fr = new jalview.appletgui.FeatureRenderer (this.av); -var initialScale = this.av.getAlignment ().getWidth () / this.av.getAlignment ().getHeight (); -if (this.av.getSequenceConsensusHash () == null) { -this.graphHeight = 0; -}if (this.av.getAlignment ().getWidth () > this.av.getAlignment ().getHeight ()) { -this.$width = 400; -this.sequencesHeight = Clazz.floatToInt (400 / initialScale); -if (this.sequencesHeight < 40) { -this.sequencesHeight = 40; -}} else { -this.$width = Clazz.floatToInt (400 * initialScale); -this.sequencesHeight = 300; -if (this.$width < 120) { -this.$width = 120; -}}this.setSize ( new java.awt.Dimension (this.$width, this.sequencesHeight + this.graphHeight)); -this.addComponentListener (((Clazz.isClassDefined ("jalview.appletgui.OverviewPanel$1") ? 0 : jalview.appletgui.OverviewPanel.$OverviewPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.OverviewPanel$1, this, null))); -this.addMouseMotionListener (this); -this.addMouseListener (this); -this.updateOverviewImage (); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -this.boxX = evt.getX (); -this.boxY = evt.getY (); -this.checkValid (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.boxX = evt.getX (); -this.boxY = evt.getY (); -this.checkValid (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -this.boxX = evt.getX (); -this.boxY = evt.getY (); -this.checkValid (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "checkValid", -function () { -if (this.boxY < 0) { -this.boxY = 0; -}if (this.boxY > (this.sequencesHeight - this.boxHeight)) { -this.boxY = this.sequencesHeight - this.boxHeight + 1; -}if (this.boxX < 0) { -this.boxX = 0; -}if (this.boxX > (this.$width - this.boxWidth)) { -if (this.av.hasHiddenColumns ()) { -this.boxWidth = Clazz.floatToInt ((this.av.endRes - this.av.startRes + 1) * this.av.getCharWidth () * this.scalew); -}this.boxX = this.$width - this.boxWidth; -}var col = Clazz.floatToInt (this.boxX / this.scalew / this.av.getCharWidth ()); -var row = Clazz.floatToInt (this.boxY / this.scaleh / this.av.getCharHeight ()); -if (this.av.hasHiddenColumns ()) { -if (!this.av.getColumnSelection ().isVisible (col)) { -return; -}col = this.av.getColumnSelection ().findColumnPosition (col); -}if (this.av.hasHiddenRows ()) { -row = this.av.getAlignment ().getHiddenSequences ().findIndexWithoutHiddenSeqs (row); -}this.ap.setScrollValues (col, row); -this.ap.paintAlignment (false); -}); -Clazz.defineMethod (c$, "updateOverviewImage", -function () { -if (this.resizing) { -this.resizeAgain = true; -return; -}if (this.av.isShowSequenceFeatures ()) { -this.fr.transferSettings (this.ap.seqPanel.seqCanvas.fr); -}this.resizing = true; -if ((this.getSize ().width > 0) && (this.getSize ().height > 0)) { -this.$width = this.getSize ().width; -this.sequencesHeight = this.getSize ().height - this.graphHeight; -}this.setSize ( new java.awt.Dimension (this.$width, this.sequencesHeight + this.graphHeight)); -var thread = new Thread (this); -thread.start (); -this.repaint (); -}); -Clazz.overrideMethod (c$, "run", -function () { -this.miniMe = null; -var alwidth = this.av.getAlignment ().getWidth (); -var alheight = this.av.getAlignment ().getHeight (); -if (this.av.isShowSequenceFeatures ()) { -this.fr.transferSettings (this.ap.seqPanel.seqCanvas.getFeatureRenderer ()); -}if (this.getSize ().width > 0 && this.getSize ().height > 0) { -this.$width = this.getSize ().width; -this.sequencesHeight = this.getSize ().height - this.graphHeight; -}this.setSize ( new java.awt.Dimension (this.$width, this.sequencesHeight + this.graphHeight)); -var fullsizeWidth = alwidth * this.av.getCharWidth (); -var fullsizeHeight = alheight * this.av.getCharHeight (); -this.scalew = this.$width / fullsizeWidth; -this.scaleh = this.sequencesHeight / fullsizeHeight; -this.miniMe = this.nullFrame.createImage (this.$width, this.sequencesHeight + this.graphHeight); -this.offscreen = this.nullFrame.createImage (this.$width, this.sequencesHeight + this.graphHeight); -var mg = this.miniMe.getGraphics (); -var sampleCol = alwidth / this.$width; -var sampleRow = alheight / this.sequencesHeight; -var lastcol = 0; -var lastrow = 0; -var xstart = 0; -var ystart = 0; -var color = java.awt.Color.yellow; -var row; -var col; -var sameRow = 0; -var sameCol = 0; -var seq; -var hasHiddenRows = this.av.hasHiddenRows (); -var hasHiddenCols = this.av.hasHiddenColumns (); -var hiddenRow = false; -var alignment = this.av.getAlignment (); -for (row = 0; row <= this.sequencesHeight; row++) { -if (Clazz.floatToInt (row * sampleRow) == lastrow) { -sameRow++; -continue; -}hiddenRow = false; -if (hasHiddenRows) { -seq = alignment.getHiddenSequences ().getHiddenSequence (lastrow); -if (seq == null) { -var index = alignment.getHiddenSequences ().findIndexWithoutHiddenSeqs (lastrow); -seq = alignment.getSequenceAt (index); -} else { -hiddenRow = true; -}} else { -seq = alignment.getSequenceAt (lastrow); -}for (col = 0; col < this.$width; col++) { -if (Clazz.floatToInt (col * sampleCol) == lastcol && Clazz.floatToInt (row * sampleRow) == lastrow) { -sameCol++; -continue; -}lastcol = Clazz.floatToInt (col * sampleCol); -if (seq.getLength () > lastcol) { -color = this.sr.getResidueBoxColour (seq, lastcol); -if (this.av.isShowSequenceFeatures ()) { -color = this.fr.findFeatureColour (color, seq, lastcol); -}} else { -color = java.awt.Color.white; -}if (hiddenRow || (hasHiddenCols && !this.av.getColumnSelection ().isVisible (lastcol))) { -color = color.darker ().darker (); -}mg.setColor (color); -if (sameCol == 1 && sameRow == 1) { -mg.drawLine (xstart, ystart, xstart, ystart); -} else { -mg.fillRect (xstart, ystart, sameCol, sameRow); -}xstart = col; -sameCol = 1; -} -lastrow = Clazz.floatToInt (row * sampleRow); -ystart = row; -sameRow = 1; -} -if (this.av.getAlignmentConservationAnnotation () != null) { -for (col = 0; col < this.$width; col++) { -lastcol = Clazz.floatToInt (col * sampleCol); -{ -mg.translate (col, this.sequencesHeight); -this.ap.annotationPanel.renderer.drawGraph (mg, this.av.getAlignmentConservationAnnotation (), this.av.getAlignmentConservationAnnotation ().annotations, Clazz.floatToInt (sampleCol) + 1, this.graphHeight, Clazz.floatToInt (col * sampleCol), Clazz.floatToInt (col * sampleCol) + 1); -mg.translate (-col, -this.sequencesHeight); -}} -}System.gc (); -this.resizing = false; -this.setBoxPosition (); -if (this.resizeAgain) { -this.resizeAgain = false; -this.updateOverviewImage (); -}}); -Clazz.defineMethod (c$, "setBoxPosition", -function () { -var fullsizeWidth = this.av.getAlignment ().getWidth () * this.av.getCharWidth (); -var fullsizeHeight = (this.av.getAlignment ().getHeight () + this.av.getAlignment ().getHiddenSequences ().getSize ()) * this.av.getCharHeight (); -var startRes = this.av.getStartRes (); -var endRes = this.av.getEndRes (); -if (this.av.hasHiddenColumns ()) { -startRes = this.av.getColumnSelection ().adjustForHiddenColumns (startRes); -endRes = this.av.getColumnSelection ().adjustForHiddenColumns (endRes); -}var startSeq = this.av.startSeq; -var endSeq = this.av.endSeq; -if (this.av.hasHiddenRows ()) { -startSeq = this.av.getAlignment ().getHiddenSequences ().adjustForHiddenSeqs (startSeq); -endSeq = this.av.getAlignment ().getHiddenSequences ().adjustForHiddenSeqs (endSeq); -}this.scalew = this.$width / fullsizeWidth; -this.scaleh = this.sequencesHeight / fullsizeHeight; -this.boxX = Clazz.floatToInt (startRes * this.av.getCharWidth () * this.scalew); -this.boxY = Clazz.floatToInt (startSeq * this.av.getCharHeight () * this.scaleh); -if (this.av.hasHiddenColumns ()) { -this.boxWidth = Clazz.floatToInt ((endRes - startRes + 1) * this.av.getCharWidth () * this.scalew); -} else { -this.boxWidth = Clazz.floatToInt ((endRes - startRes + 1) * this.av.getCharWidth () * this.scalew); -}this.boxHeight = Clazz.floatToInt ((endSeq - startSeq) * this.av.getCharHeight () * this.scaleh); -this.repaint (); -}); -Clazz.overrideMethod (c$, "update", -function (g) { -this.paint (g); -}, "java.awt.Graphics"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -var og = this.offscreen.getGraphics (); -if (this.miniMe != null) { -og.drawImage (this.miniMe, 0, 0, this); -og.setColor (java.awt.Color.red); -og.drawRect (this.boxX, this.boxY, this.boxWidth, this.boxHeight); -og.drawRect (this.boxX + 1, this.boxY + 1, this.boxWidth - 2, this.boxHeight - 2); -g.drawImage (this.offscreen, 0, 0, this); -}}, "java.awt.Graphics"); -c$.$OverviewPanel$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "OverviewPanel$1", java.awt.event.ComponentAdapter); -Clazz.overrideMethod (c$, "componentResized", -function (evt) { -if (this.b$["jalview.appletgui.OverviewPanel"].getSize ().width != this.b$["jalview.appletgui.OverviewPanel"].$width || this.b$["jalview.appletgui.OverviewPanel"].getSize ().height != this.b$["jalview.appletgui.OverviewPanel"].sequencesHeight + this.b$["jalview.appletgui.OverviewPanel"].graphHeight) { -this.b$["jalview.appletgui.OverviewPanel"].updateOverviewImage (); -}}, "java.awt.event.ComponentEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.OverviewPanel", ["awt2swing.Frame", "jalview.appletgui.FeatureRenderer", "$.SequenceRenderer", "java.awt.Color", "$.Dimension", "java.awt.event.ComponentAdapter", "java.lang.Thread"], function () { +c$ = Clazz.decorateAsClass (function () { +this.miniMe = null; +this.offscreen = null; +this.av = null; +this.ap = null; +this.scalew = 1; +this.scaleh = 1; +this.$width = 0; +this.sequencesHeight = 0; +this.graphHeight = 20; +this.boxX = -1; +this.boxY = -1; +this.boxWidth = -1; +this.boxHeight = -1; +this.resizing = false; +this.sr = null; +this.fr = null; +this.nullFrame = null; +this.resizeAgain = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "OverviewPanel", awt2swing.Panel, [Runnable, java.awt.event.MouseMotionListener, java.awt.event.MouseListener]); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.OverviewPanel, []); +this.av = ap.av; +this.ap = ap; +this.setLayout (null); +this.nullFrame = new awt2swing.Frame (); +this.nullFrame.addNotify (); +this.sr = new jalview.appletgui.SequenceRenderer (this.av); +this.sr.graphics = this.nullFrame.getGraphics (); +this.sr.renderGaps = false; +this.sr.forOverview = true; +this.fr = new jalview.appletgui.FeatureRenderer (this.av); +var initialScale = this.av.getAlignment ().getWidth () / this.av.getAlignment ().getHeight (); +if (this.av.getSequenceConsensusHash () == null) { +this.graphHeight = 0; +}if (this.av.getAlignment ().getWidth () > this.av.getAlignment ().getHeight ()) { +this.$width = 400; +this.sequencesHeight = Clazz.floatToInt (400 / initialScale); +if (this.sequencesHeight < 40) { +this.sequencesHeight = 40; +}} else { +this.$width = Clazz.floatToInt (400 * initialScale); +this.sequencesHeight = 300; +if (this.$width < 120) { +this.$width = 120; +}}this.setSize ( new java.awt.Dimension (this.$width, this.sequencesHeight + this.graphHeight)); +this.addComponentListener (((Clazz.isClassDefined ("jalview.appletgui.OverviewPanel$1") ? 0 : jalview.appletgui.OverviewPanel.$OverviewPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.OverviewPanel$1, this, null))); +this.addMouseMotionListener (this); +this.addMouseListener (this); +this.updateOverviewImage (); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +this.boxX = evt.getX (); +this.boxY = evt.getY (); +this.checkValid (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.boxX = evt.getX (); +this.boxY = evt.getY (); +this.checkValid (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +this.boxX = evt.getX (); +this.boxY = evt.getY (); +this.checkValid (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "checkValid", +function () { +if (this.boxY < 0) { +this.boxY = 0; +}if (this.boxY > (this.sequencesHeight - this.boxHeight)) { +this.boxY = this.sequencesHeight - this.boxHeight + 1; +}if (this.boxX < 0) { +this.boxX = 0; +}if (this.boxX > (this.$width - this.boxWidth)) { +if (this.av.hasHiddenColumns ()) { +this.boxWidth = Clazz.floatToInt ((this.av.endRes - this.av.startRes + 1) * this.av.getCharWidth () * this.scalew); +}this.boxX = this.$width - this.boxWidth; +}var col = Clazz.floatToInt (this.boxX / this.scalew / this.av.getCharWidth ()); +var row = Clazz.floatToInt (this.boxY / this.scaleh / this.av.getCharHeight ()); +if (this.av.hasHiddenColumns ()) { +if (!this.av.getColumnSelection ().isVisible (col)) { +return; +}col = this.av.getColumnSelection ().findColumnPosition (col); +}if (this.av.hasHiddenRows ()) { +row = this.av.getAlignment ().getHiddenSequences ().findIndexWithoutHiddenSeqs (row); +}this.ap.setScrollValues (col, row); +this.ap.paintAlignment (false); +}); +Clazz.defineMethod (c$, "updateOverviewImage", +function () { +if (this.resizing) { +this.resizeAgain = true; +return; +}if (this.av.isShowSequenceFeatures ()) { +this.fr.transferSettings (this.ap.seqPanel.seqCanvas.fr); +}this.resizing = true; +if ((this.getSize ().width > 0) && (this.getSize ().height > 0)) { +this.$width = this.getSize ().width; +this.sequencesHeight = this.getSize ().height - this.graphHeight; +}this.setSize ( new java.awt.Dimension (this.$width, this.sequencesHeight + this.graphHeight)); +var thread = new Thread (this); +thread.start (); +this.repaint (); +}); +Clazz.overrideMethod (c$, "run", +function () { +this.miniMe = null; +var alwidth = this.av.getAlignment ().getWidth (); +var alheight = this.av.getAlignment ().getHeight (); +if (this.av.isShowSequenceFeatures ()) { +this.fr.transferSettings (this.ap.seqPanel.seqCanvas.getFeatureRenderer ()); +}if (this.getSize ().width > 0 && this.getSize ().height > 0) { +this.$width = this.getSize ().width; +this.sequencesHeight = this.getSize ().height - this.graphHeight; +}this.setSize ( new java.awt.Dimension (this.$width, this.sequencesHeight + this.graphHeight)); +var fullsizeWidth = alwidth * this.av.getCharWidth (); +var fullsizeHeight = alheight * this.av.getCharHeight (); +this.scalew = this.$width / fullsizeWidth; +this.scaleh = this.sequencesHeight / fullsizeHeight; +this.miniMe = this.nullFrame.createImage (this.$width, this.sequencesHeight + this.graphHeight); +this.offscreen = this.nullFrame.createImage (this.$width, this.sequencesHeight + this.graphHeight); +var mg = this.miniMe.getGraphics (); +var sampleCol = alwidth / this.$width; +var sampleRow = alheight / this.sequencesHeight; +var lastcol = 0; +var lastrow = 0; +var xstart = 0; +var ystart = 0; +var color = java.awt.Color.yellow; +var row; +var col; +var sameRow = 0; +var sameCol = 0; +var seq; +var hasHiddenRows = this.av.hasHiddenRows (); +var hasHiddenCols = this.av.hasHiddenColumns (); +var hiddenRow = false; +var alignment = this.av.getAlignment (); +for (row = 0; row <= this.sequencesHeight; row++) { +if (Clazz.floatToInt (row * sampleRow) == lastrow) { +sameRow++; +continue; +}hiddenRow = false; +if (hasHiddenRows) { +seq = alignment.getHiddenSequences ().getHiddenSequence (lastrow); +if (seq == null) { +var index = alignment.getHiddenSequences ().findIndexWithoutHiddenSeqs (lastrow); +seq = alignment.getSequenceAt (index); +} else { +hiddenRow = true; +}} else { +seq = alignment.getSequenceAt (lastrow); +}for (col = 0; col < this.$width; col++) { +if (Clazz.floatToInt (col * sampleCol) == lastcol && Clazz.floatToInt (row * sampleRow) == lastrow) { +sameCol++; +continue; +}lastcol = Clazz.floatToInt (col * sampleCol); +if (seq.getLength () > lastcol) { +color = this.sr.getResidueBoxColour (seq, lastcol); +if (this.av.isShowSequenceFeatures ()) { +color = this.fr.findFeatureColour (color, seq, lastcol); +}} else { +color = java.awt.Color.white; +}if (hiddenRow || (hasHiddenCols && !this.av.getColumnSelection ().isVisible (lastcol))) { +color = color.darker ().darker (); +}mg.setColor (color); +if (sameCol == 1 && sameRow == 1) { +mg.drawLine (xstart, ystart, xstart, ystart); +} else { +mg.fillRect (xstart, ystart, sameCol, sameRow); +}xstart = col; +sameCol = 1; +} +lastrow = Clazz.floatToInt (row * sampleRow); +ystart = row; +sameRow = 1; +} +if (this.av.getAlignmentConservationAnnotation () != null) { +for (col = 0; col < this.$width; col++) { +lastcol = Clazz.floatToInt (col * sampleCol); +{ +mg.translate (col, this.sequencesHeight); +this.ap.annotationPanel.renderer.drawGraph (mg, this.av.getAlignmentConservationAnnotation (), this.av.getAlignmentConservationAnnotation ().annotations, Clazz.floatToInt (sampleCol) + 1, this.graphHeight, Clazz.floatToInt (col * sampleCol), Clazz.floatToInt (col * sampleCol) + 1); +mg.translate (-col, -this.sequencesHeight); +}} +}System.gc (); +this.resizing = false; +this.setBoxPosition (); +if (this.resizeAgain) { +this.resizeAgain = false; +this.updateOverviewImage (); +}}); +Clazz.defineMethod (c$, "setBoxPosition", +function () { +var fullsizeWidth = this.av.getAlignment ().getWidth () * this.av.getCharWidth (); +var fullsizeHeight = (this.av.getAlignment ().getHeight () + this.av.getAlignment ().getHiddenSequences ().getSize ()) * this.av.getCharHeight (); +var startRes = this.av.getStartRes (); +var endRes = this.av.getEndRes (); +if (this.av.hasHiddenColumns ()) { +startRes = this.av.getColumnSelection ().adjustForHiddenColumns (startRes); +endRes = this.av.getColumnSelection ().adjustForHiddenColumns (endRes); +}var startSeq = this.av.startSeq; +var endSeq = this.av.endSeq; +if (this.av.hasHiddenRows ()) { +startSeq = this.av.getAlignment ().getHiddenSequences ().adjustForHiddenSeqs (startSeq); +endSeq = this.av.getAlignment ().getHiddenSequences ().adjustForHiddenSeqs (endSeq); +}this.scalew = this.$width / fullsizeWidth; +this.scaleh = this.sequencesHeight / fullsizeHeight; +this.boxX = Clazz.floatToInt (startRes * this.av.getCharWidth () * this.scalew); +this.boxY = Clazz.floatToInt (startSeq * this.av.getCharHeight () * this.scaleh); +if (this.av.hasHiddenColumns ()) { +this.boxWidth = Clazz.floatToInt ((endRes - startRes + 1) * this.av.getCharWidth () * this.scalew); +} else { +this.boxWidth = Clazz.floatToInt ((endRes - startRes + 1) * this.av.getCharWidth () * this.scalew); +}this.boxHeight = Clazz.floatToInt ((endSeq - startSeq) * this.av.getCharHeight () * this.scaleh); +this.repaint (); +}); +Clazz.overrideMethod (c$, "update", +function (g) { +this.paint (g); +}, "java.awt.Graphics"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +var og = this.offscreen.getGraphics (); +if (this.miniMe != null) { +og.drawImage (this.miniMe, 0, 0, this); +og.setColor (java.awt.Color.red); +og.drawRect (this.boxX, this.boxY, this.boxWidth, this.boxHeight); +og.drawRect (this.boxX + 1, this.boxY + 1, this.boxWidth - 2, this.boxHeight - 2); +g.drawImage (this.offscreen, 0, 0, this); +}}, "java.awt.Graphics"); +c$.$OverviewPanel$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "OverviewPanel$1", java.awt.event.ComponentAdapter); +Clazz.overrideMethod (c$, "componentResized", +function (evt) { +if (this.b$["jalview.appletgui.OverviewPanel"].getSize ().width != this.b$["jalview.appletgui.OverviewPanel"].$width || this.b$["jalview.appletgui.OverviewPanel"].getSize ().height != this.b$["jalview.appletgui.OverviewPanel"].sequencesHeight + this.b$["jalview.appletgui.OverviewPanel"].graphHeight) { +this.b$["jalview.appletgui.OverviewPanel"].updateOverviewImage (); +}}, "java.awt.event.ComponentEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/PCAPanel.class b/bin/jalview/appletgui/PCAPanel.class index 92d23e5..fbccea5 100644 Binary files a/bin/jalview/appletgui/PCAPanel.class and b/bin/jalview/appletgui/PCAPanel.class differ diff --git a/bin/jalview/appletgui/PCAPanel.js b/bin/jalview/appletgui/PCAPanel.js index 7813b4d..77168bf 100644 --- a/bin/jalview/appletgui/PCAPanel.js +++ b/bin/jalview/appletgui/PCAPanel.js @@ -1,253 +1,253 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "awt2swing.Button", "$.CheckboxMenuItem", "$.Choice", "$.Label", "$.Menu", "$.MenuBar", "$.MenuItem", "$.Panel", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.PCAPanel", ["awt2swing.Frame", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.RotatableCanvas", "jalview.bin.JalviewLite", "jalview.datamodel.Alignment", "jalview.util.MessageManager", "jalview.viewmodel.PCAModel", "java.awt.Color", "$.Font", "java.lang.Thread"], function () { -c$ = Clazz.decorateAsClass (function () { -this.rc = null; -this.av = null; -this.pcaModel = null; -this.top = 0; -this.jPanel2 = null; -this.jLabel1 = null; -this.jLabel2 = null; -this.jLabel3 = null; -this.xCombobox = null; -this.yCombobox = null; -this.zCombobox = null; -this.resetButton = null; -this.flowLayout1 = null; -this.borderLayout1 = null; -this.menuBar1 = null; -this.menu1 = null; -this.menu2 = null; -this.calcSettings = null; -this.labels = null; -this.protSetting = null; -this.nuclSetting = null; -this.values = null; -this.inputData = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "PCAPanel", jalview.appletgui.EmbmenuFrame, [Runnable, java.awt.event.ActionListener, java.awt.event.ItemListener]); -Clazz.prepareFields (c$, function () { -this.jPanel2 = new awt2swing.Panel (); -this.jLabel1 = new awt2swing.Label (); -this.jLabel2 = new awt2swing.Label (); -this.jLabel3 = new awt2swing.Label (); -this.xCombobox = new awt2swing.Choice (); -this.yCombobox = new awt2swing.Choice (); -this.zCombobox = new awt2swing.Choice (); -this.resetButton = new awt2swing.Button (); -this.flowLayout1 = new java.awt.FlowLayout (); -this.borderLayout1 = new java.awt.BorderLayout (); -this.menuBar1 = new awt2swing.MenuBar (); -this.menu1 = new awt2swing.Menu (); -this.menu2 = new awt2swing.Menu (); -this.calcSettings = new awt2swing.Menu (); -this.labels = new awt2swing.CheckboxMenuItem (); -this.protSetting = new awt2swing.CheckboxMenuItem (); -this.nuclSetting = new awt2swing.CheckboxMenuItem (); -this.values = new awt2swing.MenuItem (); -this.inputData = new awt2swing.MenuItem (); -}); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.PCAPanel, []); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -for (var i = 1; i < 8; i++) { -this.xCombobox.addItem ("dim " + i); -this.yCombobox.addItem ("dim " + i); -this.zCombobox.addItem ("dim " + i); -} -this.av = av; -var selected = av.getSelectionGroup () != null && av.getSelectionGroup ().getSize () > 0; -var seqstrings = av.getAlignmentView (selected); -var nucleotide = av.getAlignment ().isNucleotide (); -var seqs; -if (!selected) { -seqs = av.getAlignment ().getSequencesArray (); -} else { -seqs = av.getSelectionGroup ().getSequencesInOrder (av.getAlignment ()); -}var sq = seqstrings.getSequences (); -var length = sq[0].getWidth (); -for (var i = 0; i < seqs.length; i++) { -if (sq[i].getWidth () != length) { -System.out.println ("Sequences must be equal length for PCA analysis"); -return; -}} -this.pcaModel = new jalview.viewmodel.PCAModel (seqstrings, seqs, nucleotide); -this.rc = new jalview.appletgui.RotatableCanvas (av); -this.embedMenuIfNeeded (this.rc); -this.add (this.rc, "Center"); -jalview.bin.JalviewLite.addFrame (this, jalview.util.MessageManager.getString ("label.principal_component_analysis"), 475, 400); -var worker = new Thread (this); -worker.start (); -}, "jalview.appletgui.AlignViewport"); -Clazz.overrideMethod (c$, "run", -function () { -this.calcSettings.setEnabled (false); -this.rc.setEnabled (false); -try { -this.nuclSetting.setState (this.pcaModel.isNucleotide ()); -this.protSetting.setState (!this.pcaModel.isNucleotide ()); -this.pcaModel.run (); -this.xCombobox.select (new Integer (0)); -this.yCombobox.select (new Integer (1)); -this.zCombobox.select (new Integer (2)); -this.pcaModel.updateRc (this.rc); -this.top = this.pcaModel.getTop (); -} catch (x) { -if (Clazz.exceptionOf (x, OutOfMemoryError)) { -System.err.println ("Out of memory when calculating PCA."); -return; -} else { -throw x; -} -} -this.calcSettings.setEnabled (true); -this.rc.setEnabled (true); -this.rc.repaint (); -this.repaint (); -}); -Clazz.defineMethod (c$, "doDimensionChange", -function () { -if (this.top == 0) { -return; -}var dim1 = this.top - this.xCombobox.getSelectedIndex (); -var dim2 = this.top - this.yCombobox.getSelectedIndex (); -var dim3 = this.top - this.zCombobox.getSelectedIndex (); -this.pcaModel.updateRcView (dim1, dim2, dim3); -this.rc.img = null; -this.rc.rotmat.setIdentity (); -this.rc.initAxes (); -this.rc.paint (this.rc.getGraphics ()); -}); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.inputData) { -this.showOriginalData (); -}if (evt.getSource () === this.resetButton) { -this.xCombobox.select (new Integer (0)); -this.yCombobox.select (new Integer (1)); -this.zCombobox.select (new Integer (2)); -this.doDimensionChange (); -}if (evt.getSource () === this.values) { -this.values_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -if (evt.getSource () === this.xCombobox) { -this.xCombobox_actionPerformed (); -} else if (evt.getSource () === this.yCombobox) { -this.yCombobox_actionPerformed (); -} else if (evt.getSource () === this.zCombobox) { -this.zCombobox_actionPerformed (); -} else if (evt.getSource () === this.labels) { -this.labels_itemStateChanged (evt); -} else if (evt.getSource () === this.nuclSetting) { -if (!this.pcaModel.isNucleotide ()) { -this.pcaModel.setNucleotide (true); - new Thread (this).start (); -}} else if (evt.getSource () === this.protSetting) { -if (this.pcaModel.isNucleotide ()) { -this.pcaModel.setNucleotide (false); - new Thread (this).start (); -}}}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "xCombobox_actionPerformed", -function () { -this.doDimensionChange (); -}); -Clazz.defineMethod (c$, "yCombobox_actionPerformed", -function () { -this.doDimensionChange (); -}); -Clazz.defineMethod (c$, "zCombobox_actionPerformed", -function () { -this.doDimensionChange (); -}); -Clazz.defineMethod (c$, "values_actionPerformed", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (false, null); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.pca_details"), 500, 500); -cap.setText (this.pcaModel.getDetails ()); -}); -Clazz.defineMethod (c$, "showOriginalData", -function () { -var gc = '-'; -try { -gc = this.av.getGapCharacter (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -;var alAndColsel = this.pcaModel.getSeqtrings ().getAlignmentAndColumnSelection (gc); -if (alAndColsel != null && alAndColsel[0] != null) { -var al = new jalview.datamodel.Alignment (alAndColsel[0]); -var af = new jalview.appletgui.AlignFrame (al, this.av.applet, "Original Data for PCA", false); -af.viewport.setHiddenColumns (alAndColsel[1]); -}}); -Clazz.defineMethod (c$, "labels_itemStateChanged", -function (itemEvent) { -this.rc.showLabels (this.labels.getState ()); -}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout (this.borderLayout1); -this.jPanel2.setLayout (this.flowLayout1); -this.jLabel1.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.jLabel1.setText ("x="); -this.jLabel2.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.jLabel2.setText ("y="); -this.jLabel3.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.jLabel3.setText ("z="); -this.jPanel2.setBackground (java.awt.Color.white); -this.zCombobox.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.zCombobox.addItemListener (this); -this.yCombobox.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.yCombobox.addItemListener (this); -this.xCombobox.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.xCombobox.addItemListener (this); -this.resetButton.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.resetButton.setLabel (jalview.util.MessageManager.getString ("action.reset")); -this.resetButton.addActionListener (this); -this.setMenuBar (this.menuBar1); -this.menu1.setLabel (jalview.util.MessageManager.getString ("action.file")); -this.menu2.setLabel (jalview.util.MessageManager.getString ("action.view")); -this.calcSettings.setLabel (jalview.util.MessageManager.getString ("action.change_params")); -this.labels.setLabel (jalview.util.MessageManager.getString ("label.labels")); -this.labels.addItemListener (this); -this.values.setLabel (jalview.util.MessageManager.getString ("label.output_values")); -this.values.addActionListener (this); -this.inputData.setLabel (jalview.util.MessageManager.getString ("label.input_data")); -this.nuclSetting.setLabel (jalview.util.MessageManager.getString ("label.nucleotide_matrix")); -this.nuclSetting.addItemListener (this); -this.protSetting.setLabel (jalview.util.MessageManager.getString ("label.protein_matrix")); -this.protSetting.addItemListener (this); -this.add (this.jPanel2, "South"); -this.jPanel2.add (this.jLabel1, null); -this.jPanel2.add (this.xCombobox, null); -this.jPanel2.add (this.jLabel2, null); -this.jPanel2.add (this.yCombobox, null); -this.jPanel2.add (this.jLabel3, null); -this.jPanel2.add (this.zCombobox, null); -this.jPanel2.add (this.resetButton, null); -this.menuBar1.add (this.menu1); -this.menuBar1.add (this.menu2); -this.menuBar1.add (this.calcSettings); -this.menu2.add (this.labels); -this.menu1.add (this.values); -this.menu1.add (this.inputData); -this.calcSettings.add (this.nuclSetting); -this.calcSettings.add (this.protSetting); -this.inputData.addActionListener (this); -}, $fz.isPrivate = true, $fz)); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "awt2swing.Button", "$.CheckboxMenuItem", "$.Choice", "$.Label", "$.Menu", "$.MenuBar", "$.MenuItem", "$.Panel", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.PCAPanel", ["awt2swing.Frame", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.RotatableCanvas", "jalview.bin.JalviewLite", "jalview.datamodel.Alignment", "jalview.util.MessageManager", "jalview.viewmodel.PCAModel", "java.awt.Color", "$.Font", "java.lang.Thread"], function () { +c$ = Clazz.decorateAsClass (function () { +this.rc = null; +this.av = null; +this.pcaModel = null; +this.top = 0; +this.jPanel2 = null; +this.jLabel1 = null; +this.jLabel2 = null; +this.jLabel3 = null; +this.xCombobox = null; +this.yCombobox = null; +this.zCombobox = null; +this.resetButton = null; +this.flowLayout1 = null; +this.borderLayout1 = null; +this.menuBar1 = null; +this.menu1 = null; +this.menu2 = null; +this.calcSettings = null; +this.labels = null; +this.protSetting = null; +this.nuclSetting = null; +this.values = null; +this.inputData = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "PCAPanel", jalview.appletgui.EmbmenuFrame, [Runnable, java.awt.event.ActionListener, java.awt.event.ItemListener]); +Clazz.prepareFields (c$, function () { +this.jPanel2 = new awt2swing.Panel (); +this.jLabel1 = new awt2swing.Label (); +this.jLabel2 = new awt2swing.Label (); +this.jLabel3 = new awt2swing.Label (); +this.xCombobox = new awt2swing.Choice (); +this.yCombobox = new awt2swing.Choice (); +this.zCombobox = new awt2swing.Choice (); +this.resetButton = new awt2swing.Button (); +this.flowLayout1 = new java.awt.FlowLayout (); +this.borderLayout1 = new java.awt.BorderLayout (); +this.menuBar1 = new awt2swing.MenuBar (); +this.menu1 = new awt2swing.Menu (); +this.menu2 = new awt2swing.Menu (); +this.calcSettings = new awt2swing.Menu (); +this.labels = new awt2swing.CheckboxMenuItem (); +this.protSetting = new awt2swing.CheckboxMenuItem (); +this.nuclSetting = new awt2swing.CheckboxMenuItem (); +this.values = new awt2swing.MenuItem (); +this.inputData = new awt2swing.MenuItem (); +}); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.PCAPanel, []); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +for (var i = 1; i < 8; i++) { +this.xCombobox.addItem ("dim " + i); +this.yCombobox.addItem ("dim " + i); +this.zCombobox.addItem ("dim " + i); +} +this.av = av; +var selected = av.getSelectionGroup () != null && av.getSelectionGroup ().getSize () > 0; +var seqstrings = av.getAlignmentView (selected); +var nucleotide = av.getAlignment ().isNucleotide (); +var seqs; +if (!selected) { +seqs = av.getAlignment ().getSequencesArray (); +} else { +seqs = av.getSelectionGroup ().getSequencesInOrder (av.getAlignment ()); +}var sq = seqstrings.getSequences (); +var length = sq[0].getWidth (); +for (var i = 0; i < seqs.length; i++) { +if (sq[i].getWidth () != length) { +System.out.println ("Sequences must be equal length for PCA analysis"); +return; +}} +this.pcaModel = new jalview.viewmodel.PCAModel (seqstrings, seqs, nucleotide); +this.rc = new jalview.appletgui.RotatableCanvas (av); +this.embedMenuIfNeeded (this.rc); +this.add (this.rc, "Center"); +jalview.bin.JalviewLite.addFrame (this, jalview.util.MessageManager.getString ("label.principal_component_analysis"), 475, 400); +var worker = new Thread (this); +worker.start (); +}, "jalview.appletgui.AlignViewport"); +Clazz.overrideMethod (c$, "run", +function () { +this.calcSettings.setEnabled (false); +this.rc.setEnabled (false); +try { +this.nuclSetting.setState (this.pcaModel.isNucleotide ()); +this.protSetting.setState (!this.pcaModel.isNucleotide ()); +this.pcaModel.run (); +this.xCombobox.select (new Integer (0)); +this.yCombobox.select (new Integer (1)); +this.zCombobox.select (new Integer (2)); +this.pcaModel.updateRc (this.rc); +this.top = this.pcaModel.getTop (); +} catch (x) { +if (Clazz.exceptionOf (x, OutOfMemoryError)) { +System.err.println ("Out of memory when calculating PCA."); +return; +} else { +throw x; +} +} +this.calcSettings.setEnabled (true); +this.rc.setEnabled (true); +this.rc.repaint (); +this.repaint (); +}); +Clazz.defineMethod (c$, "doDimensionChange", +function () { +if (this.top == 0) { +return; +}var dim1 = this.top - this.xCombobox.getSelectedIndex (); +var dim2 = this.top - this.yCombobox.getSelectedIndex (); +var dim3 = this.top - this.zCombobox.getSelectedIndex (); +this.pcaModel.updateRcView (dim1, dim2, dim3); +this.rc.img = null; +this.rc.rotmat.setIdentity (); +this.rc.initAxes (); +this.rc.paint (this.rc.getGraphics ()); +}); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.inputData) { +this.showOriginalData (); +}if (evt.getSource () === this.resetButton) { +this.xCombobox.select (new Integer (0)); +this.yCombobox.select (new Integer (1)); +this.zCombobox.select (new Integer (2)); +this.doDimensionChange (); +}if (evt.getSource () === this.values) { +this.values_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +if (evt.getSource () === this.xCombobox) { +this.xCombobox_actionPerformed (); +} else if (evt.getSource () === this.yCombobox) { +this.yCombobox_actionPerformed (); +} else if (evt.getSource () === this.zCombobox) { +this.zCombobox_actionPerformed (); +} else if (evt.getSource () === this.labels) { +this.labels_itemStateChanged (evt); +} else if (evt.getSource () === this.nuclSetting) { +if (!this.pcaModel.isNucleotide ()) { +this.pcaModel.setNucleotide (true); + new Thread (this).start (); +}} else if (evt.getSource () === this.protSetting) { +if (this.pcaModel.isNucleotide ()) { +this.pcaModel.setNucleotide (false); + new Thread (this).start (); +}}}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "xCombobox_actionPerformed", +function () { +this.doDimensionChange (); +}); +Clazz.defineMethod (c$, "yCombobox_actionPerformed", +function () { +this.doDimensionChange (); +}); +Clazz.defineMethod (c$, "zCombobox_actionPerformed", +function () { +this.doDimensionChange (); +}); +Clazz.defineMethod (c$, "values_actionPerformed", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (false, null); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.pca_details"), 500, 500); +cap.setText (this.pcaModel.getDetails ()); +}); +Clazz.defineMethod (c$, "showOriginalData", +function () { +var gc = '-'; +try { +gc = this.av.getGapCharacter (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +;var alAndColsel = this.pcaModel.getSeqtrings ().getAlignmentAndColumnSelection (gc); +if (alAndColsel != null && alAndColsel[0] != null) { +var al = new jalview.datamodel.Alignment (alAndColsel[0]); +var af = new jalview.appletgui.AlignFrame (al, this.av.applet, "Original Data for PCA", false); +af.viewport.setHiddenColumns (alAndColsel[1]); +}}); +Clazz.defineMethod (c$, "labels_itemStateChanged", +function (itemEvent) { +this.rc.showLabels (this.labels.getState ()); +}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout (this.borderLayout1); +this.jPanel2.setLayout (this.flowLayout1); +this.jLabel1.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.jLabel1.setText ("x="); +this.jLabel2.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.jLabel2.setText ("y="); +this.jLabel3.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.jLabel3.setText ("z="); +this.jPanel2.setBackground (java.awt.Color.white); +this.zCombobox.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.zCombobox.addItemListener (this); +this.yCombobox.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.yCombobox.addItemListener (this); +this.xCombobox.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.xCombobox.addItemListener (this); +this.resetButton.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.resetButton.setLabel (jalview.util.MessageManager.getString ("action.reset")); +this.resetButton.addActionListener (this); +this.setMenuBar (this.menuBar1); +this.menu1.setLabel (jalview.util.MessageManager.getString ("action.file")); +this.menu2.setLabel (jalview.util.MessageManager.getString ("action.view")); +this.calcSettings.setLabel (jalview.util.MessageManager.getString ("action.change_params")); +this.labels.setLabel (jalview.util.MessageManager.getString ("label.labels")); +this.labels.addItemListener (this); +this.values.setLabel (jalview.util.MessageManager.getString ("label.output_values")); +this.values.addActionListener (this); +this.inputData.setLabel (jalview.util.MessageManager.getString ("label.input_data")); +this.nuclSetting.setLabel (jalview.util.MessageManager.getString ("label.nucleotide_matrix")); +this.nuclSetting.addItemListener (this); +this.protSetting.setLabel (jalview.util.MessageManager.getString ("label.protein_matrix")); +this.protSetting.addItemListener (this); +this.add (this.jPanel2, "South"); +this.jPanel2.add (this.jLabel1, null); +this.jPanel2.add (this.xCombobox, null); +this.jPanel2.add (this.jLabel2, null); +this.jPanel2.add (this.yCombobox, null); +this.jPanel2.add (this.jLabel3, null); +this.jPanel2.add (this.zCombobox, null); +this.jPanel2.add (this.resetButton, null); +this.menuBar1.add (this.menu1); +this.menuBar1.add (this.menu2); +this.menuBar1.add (this.calcSettings); +this.menu2.add (this.labels); +this.menu1.add (this.values); +this.menu1.add (this.inputData); +this.calcSettings.add (this.nuclSetting); +this.calcSettings.add (this.protSetting); +this.inputData.addActionListener (this); +}, $fz.isPrivate = true, $fz)); +}); diff --git a/bin/jalview/appletgui/PaintRefresher.class b/bin/jalview/appletgui/PaintRefresher.class index 0086f7e..8d0e0cc 100644 Binary files a/bin/jalview/appletgui/PaintRefresher.class and b/bin/jalview/appletgui/PaintRefresher.class differ diff --git a/bin/jalview/appletgui/PaintRefresher.js b/bin/jalview/appletgui/PaintRefresher.js index 09c8d0a..7bd9686 100644 --- a/bin/jalview/appletgui/PaintRefresher.js +++ b/bin/jalview/appletgui/PaintRefresher.js @@ -1,126 +1,126 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (null, "jalview.appletgui.PaintRefresher", ["jalview.appletgui.AlignmentPanel", "java.util.Hashtable", "$.Vector"], function () { -c$ = Clazz.declareType (jalview.appletgui, "PaintRefresher"); -c$.Register = Clazz.defineMethod (c$, "Register", -function (comp, seqSetId) { -if (jalview.appletgui.PaintRefresher.components == null) { -jalview.appletgui.PaintRefresher.components = new java.util.Hashtable (); -}if (jalview.appletgui.PaintRefresher.components.containsKey (seqSetId)) { -var comps = jalview.appletgui.PaintRefresher.components.get (seqSetId); -if (!comps.contains (comp)) { -comps.addElement (comp); -}} else { -var vcoms = new java.util.Vector (); -vcoms.addElement (comp); -jalview.appletgui.PaintRefresher.components.put (seqSetId, vcoms); -}}, "java.awt.Component,~S"); -c$.RemoveComponent = Clazz.defineMethod (c$, "RemoveComponent", -function (comp) { -if (jalview.appletgui.PaintRefresher.components == null) { -return; -}var en = jalview.appletgui.PaintRefresher.components.keys (); -while (en.hasMoreElements ()) { -var id = en.nextElement ().toString (); -var comps = jalview.appletgui.PaintRefresher.components.get (id); -comps.removeElement (comp); -if (comps.size () == 0) { -jalview.appletgui.PaintRefresher.components.remove (id); -}} -}, "java.awt.Component"); -c$.Refresh = Clazz.defineMethod (c$, "Refresh", -function (source, id) { -jalview.appletgui.PaintRefresher.Refresh (source, id, false, false); -}, "java.awt.Component,~S"); -c$.Refresh = Clazz.defineMethod (c$, "Refresh", -function (source, id, alignmentChanged, validateSequences) { -if (jalview.appletgui.PaintRefresher.components == null) { -return; -}var comp; -var comps = jalview.appletgui.PaintRefresher.components.get (id); -if (comps == null) { -return; -}var e = comps.elements (); -while (e.hasMoreElements ()) { -comp = e.nextElement (); -if (comp === source) { -continue; -}if (!comp.isValid ()) { -comps.removeElement (comp); -} else if (validateSequences && Clazz.instanceOf (comp, jalview.appletgui.AlignmentPanel) && Clazz.instanceOf (source, jalview.appletgui.AlignmentPanel)) { -jalview.appletgui.PaintRefresher.validateSequences ((source).av.getAlignment (), (comp).av.getAlignment ()); -}if (Clazz.instanceOf (comp, jalview.appletgui.AlignmentPanel) && alignmentChanged) { -(comp).alignmentChanged (); -}comp.repaint (); -} -}, "java.awt.Component,~S,~B,~B"); -c$.validateSequences = Clazz.defineMethod (c$, "validateSequences", -function (source, comp) { -var a1; -if (source.getHiddenSequences ().getSize () > 0) { -a1 = source.getHiddenSequences ().getFullAlignment ().getSequencesArray (); -} else { -a1 = source.getSequencesArray (); -}var a2; -if (comp.getHiddenSequences ().getSize () > 0) { -a2 = comp.getHiddenSequences ().getFullAlignment ().getSequencesArray (); -} else { -a2 = comp.getSequencesArray (); -}var i; -var iSize = a1.length; -var j; -var jSize = a2.length; -if (iSize == jSize) { -return; -}var exists = false; -for (i = 0; i < iSize; i++) { -exists = false; -for (j = 0; j < jSize; j++) { -if (a2[j] === a1[i]) { -exists = true; -break; -}} -if (!exists) { -if (i < comp.getHeight ()) { -var alsq; -{ -alsq.add (i, a1[i]); -}} else { -comp.addSequence (a1[i]); -}if (comp.getHiddenSequences ().getSize () > 0) { -a2 = comp.getHiddenSequences ().getFullAlignment ().getSequencesArray (); -} else { -a2 = comp.getSequencesArray (); -}jSize = a2.length; -}} -iSize = a1.length; -jSize = a2.length; -for (j = 0; j < jSize; j++) { -exists = false; -for (i = 0; i < iSize; i++) { -if (a2[j] === a1[i]) { -exists = true; -break; -}} -if (!exists) { -comp.deleteSequence (a2[j]); -}} -}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); -c$.getAssociatedPanels = Clazz.defineMethod (c$, "getAssociatedPanels", -function (id) { -var comps = jalview.appletgui.PaintRefresher.components.get (id); -var tmp = new java.util.Vector (); -var i; -var iSize = comps.size (); -for (i = 0; i < iSize; i++) { -if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { -tmp.addElement (comps.elementAt (i)); -}} -var result = new Array (tmp.size ()); -for (var ix = 0; ix < result.length; ix++) { -result[ix] = tmp.elementAt (ix); -} -return result; -}, "~S"); -Clazz.defineStatics (c$, -"components", null); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (null, "jalview.appletgui.PaintRefresher", ["jalview.appletgui.AlignmentPanel", "java.util.Hashtable", "$.Vector"], function () { +c$ = Clazz.declareType (jalview.appletgui, "PaintRefresher"); +c$.Register = Clazz.defineMethod (c$, "Register", +function (comp, seqSetId) { +if (jalview.appletgui.PaintRefresher.components == null) { +jalview.appletgui.PaintRefresher.components = new java.util.Hashtable (); +}if (jalview.appletgui.PaintRefresher.components.containsKey (seqSetId)) { +var comps = jalview.appletgui.PaintRefresher.components.get (seqSetId); +if (!comps.contains (comp)) { +comps.addElement (comp); +}} else { +var vcoms = new java.util.Vector (); +vcoms.addElement (comp); +jalview.appletgui.PaintRefresher.components.put (seqSetId, vcoms); +}}, "java.awt.Component,~S"); +c$.RemoveComponent = Clazz.defineMethod (c$, "RemoveComponent", +function (comp) { +if (jalview.appletgui.PaintRefresher.components == null) { +return; +}var en = jalview.appletgui.PaintRefresher.components.keys (); +while (en.hasMoreElements ()) { +var id = en.nextElement ().toString (); +var comps = jalview.appletgui.PaintRefresher.components.get (id); +comps.removeElement (comp); +if (comps.size () == 0) { +jalview.appletgui.PaintRefresher.components.remove (id); +}} +}, "java.awt.Component"); +c$.Refresh = Clazz.defineMethod (c$, "Refresh", +function (source, id) { +jalview.appletgui.PaintRefresher.Refresh (source, id, false, false); +}, "java.awt.Component,~S"); +c$.Refresh = Clazz.defineMethod (c$, "Refresh", +function (source, id, alignmentChanged, validateSequences) { +if (jalview.appletgui.PaintRefresher.components == null) { +return; +}var comp; +var comps = jalview.appletgui.PaintRefresher.components.get (id); +if (comps == null) { +return; +}var e = comps.elements (); +while (e.hasMoreElements ()) { +comp = e.nextElement (); +if (comp === source) { +continue; +}if (!comp.isValid ()) { +comps.removeElement (comp); +} else if (validateSequences && Clazz.instanceOf (comp, jalview.appletgui.AlignmentPanel) && Clazz.instanceOf (source, jalview.appletgui.AlignmentPanel)) { +jalview.appletgui.PaintRefresher.validateSequences ((source).av.getAlignment (), (comp).av.getAlignment ()); +}if (Clazz.instanceOf (comp, jalview.appletgui.AlignmentPanel) && alignmentChanged) { +(comp).alignmentChanged (); +}comp.repaint (); +} +}, "java.awt.Component,~S,~B,~B"); +c$.validateSequences = Clazz.defineMethod (c$, "validateSequences", +function (source, comp) { +var a1; +if (source.getHiddenSequences ().getSize () > 0) { +a1 = source.getHiddenSequences ().getFullAlignment ().getSequencesArray (); +} else { +a1 = source.getSequencesArray (); +}var a2; +if (comp.getHiddenSequences ().getSize () > 0) { +a2 = comp.getHiddenSequences ().getFullAlignment ().getSequencesArray (); +} else { +a2 = comp.getSequencesArray (); +}var i; +var iSize = a1.length; +var j; +var jSize = a2.length; +if (iSize == jSize) { +return; +}var exists = false; +for (i = 0; i < iSize; i++) { +exists = false; +for (j = 0; j < jSize; j++) { +if (a2[j] === a1[i]) { +exists = true; +break; +}} +if (!exists) { +if (i < comp.getHeight ()) { +var alsq; +{ +alsq.add (i, a1[i]); +}} else { +comp.addSequence (a1[i]); +}if (comp.getHiddenSequences ().getSize () > 0) { +a2 = comp.getHiddenSequences ().getFullAlignment ().getSequencesArray (); +} else { +a2 = comp.getSequencesArray (); +}jSize = a2.length; +}} +iSize = a1.length; +jSize = a2.length; +for (j = 0; j < jSize; j++) { +exists = false; +for (i = 0; i < iSize; i++) { +if (a2[j] === a1[i]) { +exists = true; +break; +}} +if (!exists) { +comp.deleteSequence (a2[j]); +}} +}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI"); +c$.getAssociatedPanels = Clazz.defineMethod (c$, "getAssociatedPanels", +function (id) { +var comps = jalview.appletgui.PaintRefresher.components.get (id); +var tmp = new java.util.Vector (); +var i; +var iSize = comps.size (); +for (i = 0; i < iSize; i++) { +if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { +tmp.addElement (comps.elementAt (i)); +}} +var result = new Array (tmp.size ()); +for (var ix = 0; ix < result.length; ix++) { +result[ix] = tmp.elementAt (ix); +} +return result; +}, "~S"); +Clazz.defineStatics (c$, +"components", null); +}); diff --git a/bin/jalview/appletgui/PairwiseAlignPanel.class b/bin/jalview/appletgui/PairwiseAlignPanel.class index 22c33f9..202bf5c 100644 Binary files a/bin/jalview/appletgui/PairwiseAlignPanel.class and b/bin/jalview/appletgui/PairwiseAlignPanel.class differ diff --git a/bin/jalview/appletgui/PairwiseAlignPanel.js b/bin/jalview/appletgui/PairwiseAlignPanel.js index ddb1948..e91c56d 100644 --- a/bin/jalview/appletgui/PairwiseAlignPanel.js +++ b/bin/jalview/appletgui/PairwiseAlignPanel.js @@ -1,100 +1,100 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.ScrollPane", "$.TextArea", "java.awt.BorderLayout", "java.util.Vector"], "jalview.appletgui.PairwiseAlignPanel", ["jalview.analysis.AlignSeq", "jalview.appletgui.AlignFrame", "jalview.datamodel.Alignment", "jalview.util.Format", "$.MessageManager", "java.awt.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.sequences = null; -this.ap = null; -this.scrollPane = null; -this.textarea = null; -this.viewInEditorButton = null; -this.jPanel1 = null; -this.borderLayout1 = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "PairwiseAlignPanel", awt2swing.Panel, java.awt.event.ActionListener); -Clazz.prepareFields (c$, function () { -this.sequences = new java.util.Vector (); -this.scrollPane = new awt2swing.ScrollPane (); -this.textarea = new awt2swing.TextArea (); -this.viewInEditorButton = new awt2swing.Button (); -this.jPanel1 = new awt2swing.Panel (); -this.borderLayout1 = new java.awt.BorderLayout (); -}); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.PairwiseAlignPanel, []); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.ap = ap; -this.sequences = new java.util.Vector (); -var seqs; -var seqStrings = ap.av.getViewAsString (true); -if (ap.av.getSelectionGroup () == null) { -seqs = ap.av.getAlignment ().getSequencesArray (); -} else { -seqs = ap.av.getSelectionGroup ().getSequencesInOrder (ap.av.getAlignment ()); -}var scores = Clazz.newFloatArray (seqs.length, seqs.length, 0); -var totscore = 0; -var count = ap.av.getSelectionGroup ().getSize (); -var type = (ap.av.getAlignment ().isNucleotide ()) ? "dna" : "pep"; -var seq; -for (var i = 1; i < count; i++) { -for (var j = 0; j < i; j++) { -var as = new jalview.analysis.AlignSeq (seqs[i], seqStrings[i], seqs[j], seqStrings[j], type); -if (as.s1str.length == 0 || as.s2str.length == 0) { -continue; -}as.calcScoreMatrix (); -as.traceAlignment (); -as.printAlignment (System.out); -scores[i][j] = as.getMaxScore () / as.getASeq1 ().length; -totscore = totscore + scores[i][j]; -this.textarea.append (as.getOutput ()); -this.sequences.add (as.getAlignedSeq1 ()); -this.sequences.add (as.getAlignedSeq1 ()); -} -} -if (count > 2) { -System.out.println ("Pairwise alignment scaled similarity score matrix\n"); -for (var i = 0; i < count; i++) { -jalview.util.Format.print (System.out, "%s \n", ("" + i) + " " + seqs[i].getName ()); -} -System.out.println ("\n"); -for (var i = 0; i < count; i++) { -for (var j = 0; j < i; j++) { -jalview.util.Format.printDouble (System.out, "%7.3f", scores[i][j] / totscore); -} -} -System.out.println ("\n"); -}}, "jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.viewInEditorButton) { -this.viewInEditorButton_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "viewInEditorButton_actionPerformed", -function () { -var seq = new Array (this.sequences.size ()); -for (var i = 0; i < this.sequences.size (); i++) { -seq[i] = this.sequences.elementAt (i); -} - new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (seq), this.ap.av.applet, "Pairwise Aligned Sequences", false); -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout (this.borderLayout1); -this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 12)); -this.textarea.setText (""); -this.viewInEditorButton.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.viewInEditorButton.setLabel (jalview.util.MessageManager.getString ("label.view_alignment_editor")); -this.viewInEditorButton.addActionListener (this); -this.add (this.scrollPane, "Center"); -this.scrollPane.add (this.textarea); -this.add (this.jPanel1, "South"); -this.jPanel1.add (this.viewInEditorButton, null); -}, $fz.isPrivate = true, $fz)); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.ScrollPane", "$.TextArea", "java.awt.BorderLayout", "java.util.Vector"], "jalview.appletgui.PairwiseAlignPanel", ["jalview.analysis.AlignSeq", "jalview.appletgui.AlignFrame", "jalview.datamodel.Alignment", "jalview.util.Format", "$.MessageManager", "java.awt.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.sequences = null; +this.ap = null; +this.scrollPane = null; +this.textarea = null; +this.viewInEditorButton = null; +this.jPanel1 = null; +this.borderLayout1 = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "PairwiseAlignPanel", awt2swing.Panel, java.awt.event.ActionListener); +Clazz.prepareFields (c$, function () { +this.sequences = new java.util.Vector (); +this.scrollPane = new awt2swing.ScrollPane (); +this.textarea = new awt2swing.TextArea (); +this.viewInEditorButton = new awt2swing.Button (); +this.jPanel1 = new awt2swing.Panel (); +this.borderLayout1 = new java.awt.BorderLayout (); +}); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.PairwiseAlignPanel, []); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.ap = ap; +this.sequences = new java.util.Vector (); +var seqs; +var seqStrings = ap.av.getViewAsString (true); +if (ap.av.getSelectionGroup () == null) { +seqs = ap.av.getAlignment ().getSequencesArray (); +} else { +seqs = ap.av.getSelectionGroup ().getSequencesInOrder (ap.av.getAlignment ()); +}var scores = Clazz.newFloatArray (seqs.length, seqs.length, 0); +var totscore = 0; +var count = ap.av.getSelectionGroup ().getSize (); +var type = (ap.av.getAlignment ().isNucleotide ()) ? "dna" : "pep"; +var seq; +for (var i = 1; i < count; i++) { +for (var j = 0; j < i; j++) { +var as = new jalview.analysis.AlignSeq (seqs[i], seqStrings[i], seqs[j], seqStrings[j], type); +if (as.s1str.length == 0 || as.s2str.length == 0) { +continue; +}as.calcScoreMatrix (); +as.traceAlignment (); +as.printAlignment (System.out); +scores[i][j] = as.getMaxScore () / as.getASeq1 ().length; +totscore = totscore + scores[i][j]; +this.textarea.append (as.getOutput ()); +this.sequences.add (as.getAlignedSeq1 ()); +this.sequences.add (as.getAlignedSeq1 ()); +} +} +if (count > 2) { +System.out.println ("Pairwise alignment scaled similarity score matrix\n"); +for (var i = 0; i < count; i++) { +jalview.util.Format.print (System.out, "%s \n", ("" + i) + " " + seqs[i].getName ()); +} +System.out.println ("\n"); +for (var i = 0; i < count; i++) { +for (var j = 0; j < i; j++) { +jalview.util.Format.printDouble (System.out, "%7.3f", scores[i][j] / totscore); +} +} +System.out.println ("\n"); +}}, "jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.viewInEditorButton) { +this.viewInEditorButton_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "viewInEditorButton_actionPerformed", +function () { +var seq = new Array (this.sequences.size ()); +for (var i = 0; i < this.sequences.size (); i++) { +seq[i] = this.sequences.elementAt (i); +} + new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (seq), this.ap.av.applet, "Pairwise Aligned Sequences", false); +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout (this.borderLayout1); +this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 12)); +this.textarea.setText (""); +this.viewInEditorButton.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.viewInEditorButton.setLabel (jalview.util.MessageManager.getString ("label.view_alignment_editor")); +this.viewInEditorButton.addActionListener (this); +this.add (this.scrollPane, "Center"); +this.scrollPane.add (this.textarea); +this.add (this.jPanel1, "South"); +this.jPanel1.add (this.viewInEditorButton, null); +}, $fz.isPrivate = true, $fz)); +}); diff --git a/bin/jalview/appletgui/RedundancyPanel.js b/bin/jalview/appletgui/RedundancyPanel.js index f6b850d..647ac1b 100644 --- a/bin/jalview/appletgui/RedundancyPanel.js +++ b/bin/jalview/appletgui/RedundancyPanel.js @@ -1,165 +1,165 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.appletgui.SliderPanel", "java.awt.event.WindowListener", "java.util.Stack"], "jalview.appletgui.RedundancyPanel", ["awt2swing.Frame", "jalview.analysis.AlignSeq", "jalview.appletgui.PaintRefresher", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "jalview.util.MessageManager", "java.awt.event.AdjustmentListener", "java.lang.Thread", "java.util.ArrayList", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.historyList = null; -this.redundancy = null; -this.originalSequences = null; -this.frame = null; -this.redundantSeqs = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "RedundancyPanel", jalview.appletgui.SliderPanel, [Runnable, java.awt.event.WindowListener]); -Clazz.prepareFields (c$, function () { -this.historyList = new java.util.Stack (); -}); -Clazz.makeConstructor (c$, -function (ap) { -Clazz.superConstructor (this, jalview.appletgui.RedundancyPanel, [ap, 0, false, null]); -this.redundantSeqs = new java.util.Vector (); -this.ap = ap; -this.undoButton.setVisible (true); -this.applyButton.setVisible (true); -this.allGroupsCheck.setVisible (false); -this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold")); -this.valueField.setText ("100"); -this.slider.setVisibleAmount (1); -this.slider.setMinimum (0); -this.slider.setMaximum (100 + this.slider.getVisibleAmount ()); -this.slider.setValue (100); -this.slider.addAdjustmentListener (((Clazz.isClassDefined ("jalview.appletgui.RedundancyPanel$1") ? 0 : jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.RedundancyPanel$1, this, null))); -this.frame = new awt2swing.Frame (); -this.frame.add (this); -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.redundancy_threshold_selection"), 400, 100); -this.frame.addWindowListener (this); -var worker = new Thread (this); -worker.start (); -}, "jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "run", -function () { -this.label.setText (jalview.util.MessageManager.getString ("label.calculating")); -this.slider.setVisible (false); -this.applyButton.setEnabled (false); -this.valueField.setVisible (false); -this.validate (); -var omitHidden = null; -var sg = this.ap.av.getSelectionGroup (); -var height; -var start; -var end; -if ((sg != null) && (sg.getSize () >= 1)) { -this.originalSequences = sg.getSequencesInOrder (this.ap.av.getAlignment ()); -start = sg.getStartRes (); -end = sg.getEndRes (); -} else { -this.originalSequences = this.ap.av.getAlignment ().getSequencesArray (); -start = 0; -end = this.ap.av.getAlignment ().getWidth (); -}height = this.originalSequences.length; -this.redundancy = jalview.analysis.AlignSeq.computeRedundancyMatrix (this.originalSequences, omitHidden, start, end, false); -this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold")); -this.slider.setVisible (true); -this.applyButton.setEnabled (true); -this.valueField.setVisible (true); -this.validate (); -this.sliderValueChanged (); -}); -Clazz.defineMethod (c$, "sliderValueChanged", -function () { -if (this.redundancy == null) { -return; -}var value = this.slider.getValue (); -var redundantSequences = new java.util.ArrayList (); -for (var i = 0; i < this.redundancy.length; i++) { -if (value <= this.redundancy[i]) { -redundantSequences.add (this.originalSequences[i]); -}} -this.ap.idPanel.idCanvas.setHighlighted (redundantSequences); -jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true); -}); -Clazz.overrideMethod (c$, "applyButton_actionPerformed", -function () { -var del = new java.util.Vector (); -this.undoButton.setEnabled (true); -var value = this.slider.getValue (); -var sg = this.ap.av.getSelectionGroup (); -for (var i = 0; i < this.redundancy.length; i++) { -if (value <= this.redundancy[i]) { -del.addElement (this.originalSequences[i]); -}} -if (del.size () > 0) { -var deleted = new Array (del.size ()); -var width = 0; -for (var i = 0; i < del.size (); i++) { -deleted[i] = del.elementAt (i); -if (deleted[i].getLength () > width) { -width = deleted[i].getLength (); -}} -var cut = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.remove_redundancy"), jalview.commands.EditCommand.Action.CUT, deleted, 0, width, this.ap.av.getAlignment ()); -var alignment = this.ap.av.getAlignment (); -for (var i = 0; i < del.size (); i++) { -alignment.deleteSequence (deleted[i]); -if (sg != null) { -sg.deleteSequence (deleted[i], false); -}} -this.historyList.push (cut); -this.ap.alignFrame.addHistoryItem (cut); -jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true); -this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); -}}); -Clazz.overrideMethod (c$, "undoButton_actionPerformed", -function () { -var command = this.historyList.pop (); -command.undoCommand (null); -if (this.ap.av.getHistoryList ().contains (command)) { -this.ap.av.getHistoryList ().remove (command); -this.ap.alignFrame.updateEditMenuBar (); -this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); -}this.ap.paintAlignment (true); -if (this.historyList.size () == 0) { -this.undoButton.setEnabled (false); -}}); -Clazz.defineMethod (c$, "valueField_actionPerformed", -function (e) { -try { -var i = Integer.parseInt (this.valueField.getText ()); -this.slider.setValue (i); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -this.valueField.setText (this.slider.getValue () + ""); -} else { -throw ex; -} -} -}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "windowOpened", -function (evt) { -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowClosing", -function (evt) { -this.ap.idPanel.idCanvas.setHighlighted (null); -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowClosed", -function (evt) { -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowActivated", -function (evt) { -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowDeactivated", -function (evt) { -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowIconified", -function (evt) { -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowDeiconified", -function (evt) { -}, "java.awt.event.WindowEvent"); -c$.$RedundancyPanel$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "RedundancyPanel$1", null, java.awt.event.AdjustmentListener); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText (this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue () + ""); -this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged (); -}, "java.awt.event.AdjustmentEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.appletgui.SliderPanel", "java.awt.event.WindowListener", "java.util.Stack"], "jalview.appletgui.RedundancyPanel", ["awt2swing.Frame", "jalview.analysis.AlignSeq", "jalview.appletgui.PaintRefresher", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "jalview.util.MessageManager", "java.awt.event.AdjustmentListener", "java.lang.Thread", "java.util.ArrayList", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.historyList = null; +this.redundancy = null; +this.originalSequences = null; +this.frame = null; +this.redundantSeqs = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "RedundancyPanel", jalview.appletgui.SliderPanel, [Runnable, java.awt.event.WindowListener]); +Clazz.prepareFields (c$, function () { +this.historyList = new java.util.Stack (); +}); +Clazz.makeConstructor (c$, +function (ap) { +Clazz.superConstructor (this, jalview.appletgui.RedundancyPanel, [ap, 0, false, null]); +this.redundantSeqs = new java.util.Vector (); +this.ap = ap; +this.undoButton.setVisible (true); +this.applyButton.setVisible (true); +this.allGroupsCheck.setVisible (false); +this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold")); +this.valueField.setText ("100"); +this.slider.setVisibleAmount (1); +this.slider.setMinimum (0); +this.slider.setMaximum (100 + this.slider.getVisibleAmount ()); +this.slider.setValue (100); +this.slider.addAdjustmentListener (((Clazz.isClassDefined ("jalview.appletgui.RedundancyPanel$1") ? 0 : jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.RedundancyPanel$1, this, null))); +this.frame = new awt2swing.Frame (); +this.frame.add (this); +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.redundancy_threshold_selection"), 400, 100); +this.frame.addWindowListener (this); +var worker = new Thread (this); +worker.start (); +}, "jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "run", +function () { +this.label.setText (jalview.util.MessageManager.getString ("label.calculating")); +this.slider.setVisible (false); +this.applyButton.setEnabled (false); +this.valueField.setVisible (false); +this.validate (); +var omitHidden = null; +var sg = this.ap.av.getSelectionGroup (); +var height; +var start; +var end; +if ((sg != null) && (sg.getSize () >= 1)) { +this.originalSequences = sg.getSequencesInOrder (this.ap.av.getAlignment ()); +start = sg.getStartRes (); +end = sg.getEndRes (); +} else { +this.originalSequences = this.ap.av.getAlignment ().getSequencesArray (); +start = 0; +end = this.ap.av.getAlignment ().getWidth (); +}height = this.originalSequences.length; +this.redundancy = jalview.analysis.AlignSeq.computeRedundancyMatrix (this.originalSequences, omitHidden, start, end, false); +this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold")); +this.slider.setVisible (true); +this.applyButton.setEnabled (true); +this.valueField.setVisible (true); +this.validate (); +this.sliderValueChanged (); +}); +Clazz.defineMethod (c$, "sliderValueChanged", +function () { +if (this.redundancy == null) { +return; +}var value = this.slider.getValue (); +var redundantSequences = new java.util.ArrayList (); +for (var i = 0; i < this.redundancy.length; i++) { +if (value <= this.redundancy[i]) { +redundantSequences.add (this.originalSequences[i]); +}} +this.ap.idPanel.idCanvas.setHighlighted (redundantSequences); +jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true); +}); +Clazz.overrideMethod (c$, "applyButton_actionPerformed", +function () { +var del = new java.util.Vector (); +this.undoButton.setEnabled (true); +var value = this.slider.getValue (); +var sg = this.ap.av.getSelectionGroup (); +for (var i = 0; i < this.redundancy.length; i++) { +if (value <= this.redundancy[i]) { +del.addElement (this.originalSequences[i]); +}} +if (del.size () > 0) { +var deleted = new Array (del.size ()); +var width = 0; +for (var i = 0; i < del.size (); i++) { +deleted[i] = del.elementAt (i); +if (deleted[i].getLength () > width) { +width = deleted[i].getLength (); +}} +var cut = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.remove_redundancy"), jalview.commands.EditCommand.Action.CUT, deleted, 0, width, this.ap.av.getAlignment ()); +var alignment = this.ap.av.getAlignment (); +for (var i = 0; i < del.size (); i++) { +alignment.deleteSequence (deleted[i]); +if (sg != null) { +sg.deleteSequence (deleted[i], false); +}} +this.historyList.push (cut); +this.ap.alignFrame.addHistoryItem (cut); +jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true); +this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); +}}); +Clazz.overrideMethod (c$, "undoButton_actionPerformed", +function () { +var command = this.historyList.pop (); +command.undoCommand (null); +if (this.ap.av.getHistoryList ().contains (command)) { +this.ap.av.getHistoryList ().remove (command); +this.ap.alignFrame.updateEditMenuBar (); +this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); +}this.ap.paintAlignment (true); +if (this.historyList.size () == 0) { +this.undoButton.setEnabled (false); +}}); +Clazz.defineMethod (c$, "valueField_actionPerformed", +function (e) { +try { +var i = Integer.parseInt (this.valueField.getText ()); +this.slider.setValue (i); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +this.valueField.setText (this.slider.getValue () + ""); +} else { +throw ex; +} +} +}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "windowOpened", +function (evt) { +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowClosing", +function (evt) { +this.ap.idPanel.idCanvas.setHighlighted (null); +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowClosed", +function (evt) { +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowActivated", +function (evt) { +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowDeactivated", +function (evt) { +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowIconified", +function (evt) { +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowDeiconified", +function (evt) { +}, "java.awt.event.WindowEvent"); +c$.$RedundancyPanel$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "RedundancyPanel$1", null, java.awt.event.AdjustmentListener); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText (this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue () + ""); +this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged (); +}, "java.awt.event.AdjustmentEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/RotatableCanvas.js b/bin/jalview/appletgui/RotatableCanvas.js index 0bb0b4a..5e61dea 100644 --- a/bin/jalview/appletgui/RotatableCanvas.js +++ b/bin/jalview/appletgui/RotatableCanvas.js @@ -1,371 +1,371 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "jalview.api.RotatableCanvasI", "java.awt.event.KeyListener", "$.MouseListener", "$.MouseMotionListener", "jalview.math.RotatableMatrix"], "jalview.appletgui.RotatableCanvas", ["jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "jalview.util.Format", "$.MessageManager", "java.awt.Color", "$.Dimension", "$.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.idmat = null; -this.objmat = null; -this.rotmat = null; -this.tooltip = null; -this.toolx = 0; -this.tooly = 0; -this.$drawAxes = true; -this.omx = 0; -this.mx = 0; -this.omy = 0; -this.my = 0; -this.img = null; -this.ig = null; -this.prefsize = null; -this.centre = null; -this.$width = null; -this.max = null; -this.min = null; -this.maxwidth = 0; -this.scale = 0; -this.npoint = 0; -this.points = null; -this.orig = null; -this.axes = null; -this.startx = 0; -this.starty = 0; -this.lastx = 0; -this.lasty = 0; -this.rectx1 = 0; -this.recty1 = 0; -this.rectx2 = 0; -this.recty2 = 0; -this.scalefactor = 1; -this.av = null; -this.$showLabels = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "RotatableCanvas", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.KeyListener, jalview.api.RotatableCanvasI]); -Clazz.prepareFields (c$, function () { -this.idmat = new jalview.math.RotatableMatrix (3, 3); -this.objmat = new jalview.math.RotatableMatrix (3, 3); -this.rotmat = new jalview.math.RotatableMatrix (3, 3); -this.centre = Clazz.newFloatArray (3, 0); -this.$width = Clazz.newFloatArray (3, 0); -this.max = Clazz.newFloatArray (3, 0); -this.min = Clazz.newFloatArray (3, 0); -}); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.RotatableCanvas, []); -this.av = av; -}, "jalview.viewmodel.AlignmentViewport"); -Clazz.defineMethod (c$, "showLabels", -function (b) { -this.$showLabels = b; -this.repaint (); -}, "~B"); -Clazz.overrideMethod (c$, "setPoints", -function (points, npoint) { -this.points = points; -this.npoint = npoint; -jalview.appletgui.PaintRefresher.Register (this, this.av.getSequenceSetId ()); -this.prefsize = this.getPreferredSize (); -this.orig = Clazz.newFloatArray (npoint, 3, 0); -for (var i = 0; i < npoint; i++) { -var sp = points.elementAt (i); -for (var j = 0; j < 3; j++) { -this.orig[i][j] = sp.coord[j]; -} -} -for (var i = 0; i < 3; i++) { -for (var j = 0; j < 3; j++) { -if (i != j) { -this.idmat.addElement (i, j, 0); -this.objmat.addElement (i, j, 0); -this.rotmat.addElement (i, j, 0); -} else { -this.idmat.addElement (i, j, 0); -this.objmat.addElement (i, j, 0); -this.rotmat.addElement (i, j, 0); -}} -} -this.axes = Clazz.newFloatArray (3, 3, 0); -this.initAxes (); -this.findCentre (); -this.findWidth (); -this.scale = this.findScale (); -this.addMouseListener (this); -this.addKeyListener (this); -this.addMouseMotionListener (this); -}, "java.util.Vector,~N"); -Clazz.defineMethod (c$, "initAxes", -function () { -for (var i = 0; i < 3; i++) { -for (var j = 0; j < 3; j++) { -if (i != j) { -this.axes[i][j] = 0; -} else { -this.axes[i][j] = 1; -}} -} -}); -Clazz.defineMethod (c$, "findWidth", -function () { -this.max = Clazz.newFloatArray (3, 0); -this.min = Clazz.newFloatArray (3, 0); -this.max[0] = -1.0E30; -this.max[1] = -1.0E30; -this.max[2] = -1.0E30; -this.min[0] = 1e30; -this.min[1] = 1e30; -this.min[2] = 1e30; -for (var i = 0; i < 3; i++) { -for (var j = 0; j < this.npoint; j++) { -var sp = this.points.elementAt (j); -if (sp.coord[i] >= this.max[i]) { -this.max[i] = sp.coord[i]; -}if (sp.coord[i] <= this.min[i]) { -this.min[i] = sp.coord[i]; -}} -} -this.$width[0] = Math.abs (this.max[0] - this.min[0]); -this.$width[1] = Math.abs (this.max[1] - this.min[1]); -this.$width[2] = Math.abs (this.max[2] - this.min[2]); -this.maxwidth = this.$width[0]; -if (this.$width[1] > this.$width[0]) { -this.maxwidth = this.$width[1]; -}if (this.$width[2] > this.$width[1]) { -this.maxwidth = this.$width[2]; -}}); -Clazz.defineMethod (c$, "findScale", -function () { -var dim; -var width; -var height; -if (this.getSize ().width != 0) { -width = this.getSize ().width; -height = this.getSize ().height; -} else { -width = this.prefsize.width; -height = this.prefsize.height; -}if (width < height) { -dim = width; -} else { -dim = height; -}return dim * this.scalefactor / (2 * this.maxwidth); -}); -Clazz.defineMethod (c$, "findCentre", -function () { -this.findWidth (); -this.centre[0] = (this.max[0] + this.min[0]) / 2; -this.centre[1] = (this.max[1] + this.min[1]) / 2; -this.centre[2] = (this.max[2] + this.min[2]) / 2; -}); -Clazz.overrideMethod (c$, "getPreferredSize", -function () { -if (this.prefsize != null) { -return this.prefsize; -} else { -return new java.awt.Dimension (400, 400); -}}); -Clazz.overrideMethod (c$, "getMinimumSize", -function () { -return this.getPreferredSize (); -}); -Clazz.overrideMethod (c$, "update", -function (g) { -this.paint (g); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "PaintComponent", -function (g) { -if (this.points == null) { -g.setFont ( new java.awt.Font ("Verdana", 0, 18)); -g.drawString (jalview.util.MessageManager.getString ("label.calculating_pca") + "....", 20, Clazz.doubleToInt (this.getSize ().height / 2)); -} else { -if ((this.img == null) || (this.prefsize.width != this.getSize ().width) || (this.prefsize.height != this.getSize ().height)) { -this.prefsize.width = this.getSize ().width; -this.prefsize.height = this.getSize ().height; -this.scale = this.findScale (); -this.img = this.createImage (this.getSize ().width, this.getSize ().height); -this.ig = this.img.getGraphics (); -}this.drawBackground (this.ig, java.awt.Color.black); -this.drawScene (this.ig); -if (this.$drawAxes == true) { -this.drawAxes (this.ig); -}if (this.tooltip != null) { -this.ig.setColor (java.awt.Color.red); -this.ig.drawString (this.tooltip, this.toolx, this.tooly); -}g.drawImage (this.img, 0, 0, this); -}}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "drawAxes", -function (g) { -g.setColor (java.awt.Color.yellow); -for (var i = 0; i < 3; i++) { -g.drawLine (Clazz.doubleToInt (this.getSize ().width / 2), Clazz.doubleToInt (this.getSize ().height / 2), Clazz.floatToInt (this.axes[i][0] * this.scale * this.max[0] + Clazz.doubleToInt (this.getSize ().width / 2)), Clazz.floatToInt (this.axes[i][1] * this.scale * this.max[1] + Clazz.doubleToInt (this.getSize ().height / 2))); -} -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "drawBackground", -function (g, col) { -g.setColor (col); -g.fillRect (0, 0, this.prefsize.width, this.prefsize.height); -}, "java.awt.Graphics,java.awt.Color"); -Clazz.defineMethod (c$, "drawScene", -function (g) { -var halfwidth = Clazz.doubleToInt (this.getSize ().width / 2); -var halfheight = Clazz.doubleToInt (this.getSize ().height / 2); -for (var i = 0; i < this.npoint; i++) { -var sp = this.points.elementAt (i); -var x = Clazz.floatToInt ((sp.coord[0] - this.centre[0]) * this.scale) + halfwidth; -var y = Clazz.floatToInt ((sp.coord[1] - this.centre[1]) * this.scale) + halfheight; -var z = sp.coord[1] - this.centre[2]; -if (this.av.getSequenceColour (sp.sequence) === java.awt.Color.black) { -g.setColor (java.awt.Color.white); -} else { -g.setColor (this.av.getSequenceColour (sp.sequence)); -}if (this.av.getSelectionGroup () != null) { -if (this.av.getSelectionGroup ().getSequences (null).contains ((this.points.elementAt (i)).sequence)) { -g.setColor (java.awt.Color.gray); -}}if (z < 0) { -g.setColor (g.getColor ().darker ()); -}g.fillRect (x - 3, y - 3, 6, 6); -if (this.$showLabels) { -g.setColor (java.awt.Color.red); -g.drawString ((this.points.elementAt (i)).sequence.getName (), x - 3, y - 4); -}} -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "minimumsize", -function () { -return this.prefsize; -}); -Clazz.defineMethod (c$, "preferredsize", -function () { -return this.prefsize; -}); -Clazz.overrideMethod (c$, "keyTyped", -function (evt) { -}, "java.awt.event.KeyEvent"); -Clazz.overrideMethod (c$, "keyReleased", -function (evt) { -}, "java.awt.event.KeyEvent"); -Clazz.overrideMethod (c$, "keyPressed", -function (evt) { -if (evt.getKeyCode () == 38) { -this.scalefactor = (this.scalefactor * 1.1); -this.scale = this.findScale (); -} else if (evt.getKeyCode () == 40) { -this.scalefactor = (this.scalefactor * 0.9); -this.scale = this.findScale (); -} else if (evt.getKeyChar () == 's') { -System.err.println ("DEBUG: Rectangle selection"); -if (this.rectx2 != -1 && this.recty2 != -1) { -this.rectSelect (this.rectx1, this.recty1, this.rectx2, this.recty2); -}}this.repaint (); -}, "java.awt.event.KeyEvent"); -Clazz.defineMethod (c$, "printPoints", -function () { -for (var i = 0; i < this.npoint; i++) { -var sp = this.points.elementAt (i); -jalview.util.Format.printLong (System.out, "%5d ", i); -for (var j = 0; j < 3; j++) { -jalview.util.Format.printDouble (System.out, "%13.3f ", sp.coord[j]); -} -System.out.println (); -} -}); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -var x = evt.getX (); -var y = evt.getY (); -this.mx = x; -this.my = y; -this.omx = this.mx; -this.omy = this.my; -this.startx = x; -this.starty = y; -this.rectx1 = x; -this.recty1 = y; -this.rectx2 = -1; -this.recty2 = -1; -var found = this.findPoint (x, y); -if (found != null) { -if (this.av.getSelectionGroup () != null) { -this.av.getSelectionGroup ().addOrRemove (found, true); -this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1); -} else { -this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ()); -this.av.getSelectionGroup ().addOrRemove (found, true); -this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1); -}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); -this.av.sendSelection (); -}this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -var found = this.findPoint (evt.getX (), evt.getY ()); -if (found == null) { -this.tooltip = null; -} else { -this.tooltip = found.getName (); -this.toolx = evt.getX (); -this.tooly = evt.getY (); -}this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -this.mx = evt.getX (); -this.my = evt.getY (); -this.rotmat.setIdentity (); -this.rotmat.rotate (this.my - this.omy, 'x'); -this.rotmat.rotate (this.mx - this.omx, 'y'); -for (var i = 0; i < this.npoint; i++) { -var sp = this.points.elementAt (i); -sp.coord[0] -= this.centre[0]; -sp.coord[1] -= this.centre[1]; -sp.coord[2] -= this.centre[2]; -sp.coord = this.rotmat.vectorMultiply (sp.coord); -sp.coord[0] += this.centre[0]; -sp.coord[1] += this.centre[1]; -sp.coord[2] += this.centre[2]; -} -for (var i = 0; i < 3; i++) { -this.axes[i] = this.rotmat.vectorMultiply (this.axes[i]); -} -this.omx = this.mx; -this.omy = this.my; -this.paint (this.getGraphics ()); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "rectSelect", -function (x1, y1, x2, y2) { -for (var i = 0; i < this.npoint; i++) { -var sp = this.points.elementAt (i); -var tmp1 = Clazz.doubleToInt ((sp.coord[0] - this.centre[0]) * this.scale + this.getSize ().width / 2.0); -var tmp2 = Clazz.doubleToInt ((sp.coord[1] - this.centre[1]) * this.scale + this.getSize ().height / 2.0); -if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) { -if (this.av != null) { -if (!this.av.getSelectionGroup ().getSequences (null).contains (sp.sequence)) { -this.av.getSelectionGroup ().addSequence (sp.sequence, true); -}}}} -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "findPoint", -function (x, y) { -var halfwidth = Clazz.doubleToInt (this.getSize ().width / 2); -var halfheight = Clazz.doubleToInt (this.getSize ().height / 2); -var found = -1; -for (var i = 0; i < this.npoint; i++) { -var sp = this.points.elementAt (i); -var px = Clazz.floatToInt ((sp.coord[0] - this.centre[0]) * this.scale) + halfwidth; -var py = Clazz.floatToInt ((sp.coord[1] - this.centre[1]) * this.scale) + halfheight; -if (Math.abs (px - x) < 3 && Math.abs (py - y) < 3) { -found = i; -}} -if (found != -1) { -return (this.points.elementAt (found)).sequence; -} else { -return null; -}}, "~N,~N"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "jalview.api.RotatableCanvasI", "java.awt.event.KeyListener", "$.MouseListener", "$.MouseMotionListener", "jalview.math.RotatableMatrix"], "jalview.appletgui.RotatableCanvas", ["jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "jalview.util.Format", "$.MessageManager", "java.awt.Color", "$.Dimension", "$.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.idmat = null; +this.objmat = null; +this.rotmat = null; +this.tooltip = null; +this.toolx = 0; +this.tooly = 0; +this.$drawAxes = true; +this.omx = 0; +this.mx = 0; +this.omy = 0; +this.my = 0; +this.img = null; +this.ig = null; +this.prefsize = null; +this.centre = null; +this.$width = null; +this.max = null; +this.min = null; +this.maxwidth = 0; +this.scale = 0; +this.npoint = 0; +this.points = null; +this.orig = null; +this.axes = null; +this.startx = 0; +this.starty = 0; +this.lastx = 0; +this.lasty = 0; +this.rectx1 = 0; +this.recty1 = 0; +this.rectx2 = 0; +this.recty2 = 0; +this.scalefactor = 1; +this.av = null; +this.$showLabels = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "RotatableCanvas", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.KeyListener, jalview.api.RotatableCanvasI]); +Clazz.prepareFields (c$, function () { +this.idmat = new jalview.math.RotatableMatrix (3, 3); +this.objmat = new jalview.math.RotatableMatrix (3, 3); +this.rotmat = new jalview.math.RotatableMatrix (3, 3); +this.centre = Clazz.newFloatArray (3, 0); +this.$width = Clazz.newFloatArray (3, 0); +this.max = Clazz.newFloatArray (3, 0); +this.min = Clazz.newFloatArray (3, 0); +}); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.RotatableCanvas, []); +this.av = av; +}, "jalview.viewmodel.AlignmentViewport"); +Clazz.defineMethod (c$, "showLabels", +function (b) { +this.$showLabels = b; +this.repaint (); +}, "~B"); +Clazz.overrideMethod (c$, "setPoints", +function (points, npoint) { +this.points = points; +this.npoint = npoint; +jalview.appletgui.PaintRefresher.Register (this, this.av.getSequenceSetId ()); +this.prefsize = this.getPreferredSize (); +this.orig = Clazz.newFloatArray (npoint, 3, 0); +for (var i = 0; i < npoint; i++) { +var sp = points.elementAt (i); +for (var j = 0; j < 3; j++) { +this.orig[i][j] = sp.coord[j]; +} +} +for (var i = 0; i < 3; i++) { +for (var j = 0; j < 3; j++) { +if (i != j) { +this.idmat.addElement (i, j, 0); +this.objmat.addElement (i, j, 0); +this.rotmat.addElement (i, j, 0); +} else { +this.idmat.addElement (i, j, 0); +this.objmat.addElement (i, j, 0); +this.rotmat.addElement (i, j, 0); +}} +} +this.axes = Clazz.newFloatArray (3, 3, 0); +this.initAxes (); +this.findCentre (); +this.findWidth (); +this.scale = this.findScale (); +this.addMouseListener (this); +this.addKeyListener (this); +this.addMouseMotionListener (this); +}, "java.util.Vector,~N"); +Clazz.defineMethod (c$, "initAxes", +function () { +for (var i = 0; i < 3; i++) { +for (var j = 0; j < 3; j++) { +if (i != j) { +this.axes[i][j] = 0; +} else { +this.axes[i][j] = 1; +}} +} +}); +Clazz.defineMethod (c$, "findWidth", +function () { +this.max = Clazz.newFloatArray (3, 0); +this.min = Clazz.newFloatArray (3, 0); +this.max[0] = -1.0E30; +this.max[1] = -1.0E30; +this.max[2] = -1.0E30; +this.min[0] = 1e30; +this.min[1] = 1e30; +this.min[2] = 1e30; +for (var i = 0; i < 3; i++) { +for (var j = 0; j < this.npoint; j++) { +var sp = this.points.elementAt (j); +if (sp.coord[i] >= this.max[i]) { +this.max[i] = sp.coord[i]; +}if (sp.coord[i] <= this.min[i]) { +this.min[i] = sp.coord[i]; +}} +} +this.$width[0] = Math.abs (this.max[0] - this.min[0]); +this.$width[1] = Math.abs (this.max[1] - this.min[1]); +this.$width[2] = Math.abs (this.max[2] - this.min[2]); +this.maxwidth = this.$width[0]; +if (this.$width[1] > this.$width[0]) { +this.maxwidth = this.$width[1]; +}if (this.$width[2] > this.$width[1]) { +this.maxwidth = this.$width[2]; +}}); +Clazz.defineMethod (c$, "findScale", +function () { +var dim; +var width; +var height; +if (this.getSize ().width != 0) { +width = this.getSize ().width; +height = this.getSize ().height; +} else { +width = this.prefsize.width; +height = this.prefsize.height; +}if (width < height) { +dim = width; +} else { +dim = height; +}return dim * this.scalefactor / (2 * this.maxwidth); +}); +Clazz.defineMethod (c$, "findCentre", +function () { +this.findWidth (); +this.centre[0] = (this.max[0] + this.min[0]) / 2; +this.centre[1] = (this.max[1] + this.min[1]) / 2; +this.centre[2] = (this.max[2] + this.min[2]) / 2; +}); +Clazz.overrideMethod (c$, "getPreferredSize", +function () { +if (this.prefsize != null) { +return this.prefsize; +} else { +return new java.awt.Dimension (400, 400); +}}); +Clazz.overrideMethod (c$, "getMinimumSize", +function () { +return this.getPreferredSize (); +}); +Clazz.overrideMethod (c$, "update", +function (g) { +this.paint (g); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "PaintComponent", +function (g) { +if (this.points == null) { +g.setFont ( new java.awt.Font ("Verdana", 0, 18)); +g.drawString (jalview.util.MessageManager.getString ("label.calculating_pca") + "....", 20, Clazz.doubleToInt (this.getSize ().height / 2)); +} else { +if ((this.img == null) || (this.prefsize.width != this.getSize ().width) || (this.prefsize.height != this.getSize ().height)) { +this.prefsize.width = this.getSize ().width; +this.prefsize.height = this.getSize ().height; +this.scale = this.findScale (); +this.img = this.createImage (this.getSize ().width, this.getSize ().height); +this.ig = this.img.getGraphics (); +}this.drawBackground (this.ig, java.awt.Color.black); +this.drawScene (this.ig); +if (this.$drawAxes == true) { +this.drawAxes (this.ig); +}if (this.tooltip != null) { +this.ig.setColor (java.awt.Color.red); +this.ig.drawString (this.tooltip, this.toolx, this.tooly); +}g.drawImage (this.img, 0, 0, this); +}}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "drawAxes", +function (g) { +g.setColor (java.awt.Color.yellow); +for (var i = 0; i < 3; i++) { +g.drawLine (Clazz.doubleToInt (this.getSize ().width / 2), Clazz.doubleToInt (this.getSize ().height / 2), Clazz.floatToInt (this.axes[i][0] * this.scale * this.max[0] + Clazz.doubleToInt (this.getSize ().width / 2)), Clazz.floatToInt (this.axes[i][1] * this.scale * this.max[1] + Clazz.doubleToInt (this.getSize ().height / 2))); +} +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "drawBackground", +function (g, col) { +g.setColor (col); +g.fillRect (0, 0, this.prefsize.width, this.prefsize.height); +}, "java.awt.Graphics,java.awt.Color"); +Clazz.defineMethod (c$, "drawScene", +function (g) { +var halfwidth = Clazz.doubleToInt (this.getSize ().width / 2); +var halfheight = Clazz.doubleToInt (this.getSize ().height / 2); +for (var i = 0; i < this.npoint; i++) { +var sp = this.points.elementAt (i); +var x = Clazz.floatToInt ((sp.coord[0] - this.centre[0]) * this.scale) + halfwidth; +var y = Clazz.floatToInt ((sp.coord[1] - this.centre[1]) * this.scale) + halfheight; +var z = sp.coord[1] - this.centre[2]; +if (this.av.getSequenceColour (sp.sequence) === java.awt.Color.black) { +g.setColor (java.awt.Color.white); +} else { +g.setColor (this.av.getSequenceColour (sp.sequence)); +}if (this.av.getSelectionGroup () != null) { +if (this.av.getSelectionGroup ().getSequences (null).contains ((this.points.elementAt (i)).sequence)) { +g.setColor (java.awt.Color.gray); +}}if (z < 0) { +g.setColor (g.getColor ().darker ()); +}g.fillRect (x - 3, y - 3, 6, 6); +if (this.$showLabels) { +g.setColor (java.awt.Color.red); +g.drawString ((this.points.elementAt (i)).sequence.getName (), x - 3, y - 4); +}} +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "minimumsize", +function () { +return this.prefsize; +}); +Clazz.defineMethod (c$, "preferredsize", +function () { +return this.prefsize; +}); +Clazz.overrideMethod (c$, "keyTyped", +function (evt) { +}, "java.awt.event.KeyEvent"); +Clazz.overrideMethod (c$, "keyReleased", +function (evt) { +}, "java.awt.event.KeyEvent"); +Clazz.overrideMethod (c$, "keyPressed", +function (evt) { +if (evt.getKeyCode () == 38) { +this.scalefactor = (this.scalefactor * 1.1); +this.scale = this.findScale (); +} else if (evt.getKeyCode () == 40) { +this.scalefactor = (this.scalefactor * 0.9); +this.scale = this.findScale (); +} else if (evt.getKeyChar () == 's') { +System.err.println ("DEBUG: Rectangle selection"); +if (this.rectx2 != -1 && this.recty2 != -1) { +this.rectSelect (this.rectx1, this.recty1, this.rectx2, this.recty2); +}}this.repaint (); +}, "java.awt.event.KeyEvent"); +Clazz.defineMethod (c$, "printPoints", +function () { +for (var i = 0; i < this.npoint; i++) { +var sp = this.points.elementAt (i); +jalview.util.Format.printLong (System.out, "%5d ", i); +for (var j = 0; j < 3; j++) { +jalview.util.Format.printDouble (System.out, "%13.3f ", sp.coord[j]); +} +System.out.println (); +} +}); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +var x = evt.getX (); +var y = evt.getY (); +this.mx = x; +this.my = y; +this.omx = this.mx; +this.omy = this.my; +this.startx = x; +this.starty = y; +this.rectx1 = x; +this.recty1 = y; +this.rectx2 = -1; +this.recty2 = -1; +var found = this.findPoint (x, y); +if (found != null) { +if (this.av.getSelectionGroup () != null) { +this.av.getSelectionGroup ().addOrRemove (found, true); +this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1); +} else { +this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ()); +this.av.getSelectionGroup ().addOrRemove (found, true); +this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1); +}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); +this.av.sendSelection (); +}this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +var found = this.findPoint (evt.getX (), evt.getY ()); +if (found == null) { +this.tooltip = null; +} else { +this.tooltip = found.getName (); +this.toolx = evt.getX (); +this.tooly = evt.getY (); +}this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +this.mx = evt.getX (); +this.my = evt.getY (); +this.rotmat.setIdentity (); +this.rotmat.rotate (this.my - this.omy, 'x'); +this.rotmat.rotate (this.mx - this.omx, 'y'); +for (var i = 0; i < this.npoint; i++) { +var sp = this.points.elementAt (i); +sp.coord[0] -= this.centre[0]; +sp.coord[1] -= this.centre[1]; +sp.coord[2] -= this.centre[2]; +sp.coord = this.rotmat.vectorMultiply (sp.coord); +sp.coord[0] += this.centre[0]; +sp.coord[1] += this.centre[1]; +sp.coord[2] += this.centre[2]; +} +for (var i = 0; i < 3; i++) { +this.axes[i] = this.rotmat.vectorMultiply (this.axes[i]); +} +this.omx = this.mx; +this.omy = this.my; +this.paint (this.getGraphics ()); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "rectSelect", +function (x1, y1, x2, y2) { +for (var i = 0; i < this.npoint; i++) { +var sp = this.points.elementAt (i); +var tmp1 = Clazz.doubleToInt ((sp.coord[0] - this.centre[0]) * this.scale + this.getSize ().width / 2.0); +var tmp2 = Clazz.doubleToInt ((sp.coord[1] - this.centre[1]) * this.scale + this.getSize ().height / 2.0); +if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) { +if (this.av != null) { +if (!this.av.getSelectionGroup ().getSequences (null).contains (sp.sequence)) { +this.av.getSelectionGroup ().addSequence (sp.sequence, true); +}}}} +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "findPoint", +function (x, y) { +var halfwidth = Clazz.doubleToInt (this.getSize ().width / 2); +var halfheight = Clazz.doubleToInt (this.getSize ().height / 2); +var found = -1; +for (var i = 0; i < this.npoint; i++) { +var sp = this.points.elementAt (i); +var px = Clazz.floatToInt ((sp.coord[0] - this.centre[0]) * this.scale) + halfwidth; +var py = Clazz.floatToInt ((sp.coord[1] - this.centre[1]) * this.scale) + halfheight; +if (Math.abs (px - x) < 3 && Math.abs (py - y) < 3) { +found = i; +}} +if (found != -1) { +return (this.points.elementAt (found)).sequence; +} else { +return null; +}}, "~N,~N"); +}); diff --git a/bin/jalview/appletgui/ScalePanel.class b/bin/jalview/appletgui/ScalePanel.class index 66ccdcb..332e353 100644 Binary files a/bin/jalview/appletgui/ScalePanel.class and b/bin/jalview/appletgui/ScalePanel.class differ diff --git a/bin/jalview/appletgui/ScalePanel.js b/bin/jalview/appletgui/ScalePanel.js index 755df0a..eddee91 100644 --- a/bin/jalview/appletgui/ScalePanel.js +++ b/bin/jalview/appletgui/ScalePanel.js @@ -1,248 +1,248 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.ScalePanel", ["awt2swing.MenuItem", "$.PopupMenu", "jalview.datamodel.SequenceGroup", "jalview.util.MessageManager", "java.awt.Color", "java.awt.event.ActionListener"], function () { -c$ = Clazz.decorateAsClass (function () { -this.offy = 4; -this.$width = 0; -this.av = null; -this.ap = null; -this.stretchingGroup = false; -this.min = 0; -this.max = 0; -this.mouseDragging = false; -this.reveal = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "ScalePanel", awt2swing.Panel, [java.awt.event.MouseMotionListener, java.awt.event.MouseListener]); -Clazz.makeConstructor (c$, -function (av, ap) { -Clazz.superConstructor (this, jalview.appletgui.ScalePanel, []); -this.setName ("scalePanel"); -this.setLayout (null); -this.av = av; -this.ap = ap; -this.addMouseListener (this); -this.addMouseMotionListener (this); -}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -var x = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); -var res; -if (this.av.hasHiddenColumns ()) { -res = this.av.getColumnSelection ().adjustForHiddenColumns (x); -} else { -res = x; -}this.min = res; -this.max = res; -if ((evt.getModifiers () & 4) == 4) { -var pop = new awt2swing.PopupMenu (); -if (this.reveal != null) { -var item = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.reveal")); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.ScalePanel$1") ? 0 : jalview.appletgui.ScalePanel.$ScalePanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.ScalePanel$1, this, null))); -pop.add (item); -if (this.av.getColumnSelection ().hasManyHiddenColumns ()) { -item = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.reveal_all")); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.ScalePanel$2") ? 0 : jalview.appletgui.ScalePanel.$ScalePanel$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.ScalePanel$2, this, null))); -pop.add (item); -}this.add (pop); -pop.show (this, evt.getX (), evt.getY ()); -} else if (this.av.getColumnSelection ().contains (res)) { -var item = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.hide_columns")); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.ScalePanel$3") ? 0 : jalview.appletgui.ScalePanel.$ScalePanel$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.ScalePanel$3, this, Clazz.cloneFinals ("res", res)))); -pop.add (item); -this.add (pop); -pop.show (this, evt.getX (), evt.getY ()); -}} else { -if (!evt.isControlDown () && !evt.isShiftDown ()) { -this.av.getColumnSelection ().clear (); -}this.av.getColumnSelection ().addElement (res); -var sg = new jalview.datamodel.SequenceGroup (); -for (var i = 0; i < this.av.getAlignment ().getSequences ().size (); i++) { -sg.addSequence (this.av.getAlignment ().getSequenceAt (i), false); -} -sg.setStartRes (res); -sg.setEndRes (res); -this.av.setSelectionGroup (sg); -if (evt.isShiftDown ()) { -var min = Math.min (this.av.getColumnSelection ().getMin (), res); -var max = Math.max (this.av.getColumnSelection ().getMax (), res); -for (var i = min; i < max; i++) { -this.av.getColumnSelection ().addElement (i); -} -sg.setStartRes (min); -sg.setEndRes (max); -}}this.ap.paintAlignment (true); -this.av.sendSelection (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.mouseDragging = false; -var res = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); -if (res > this.av.getAlignment ().getWidth ()) { -res = this.av.getAlignment ().getWidth () - 1; -}if (this.av.hasHiddenColumns ()) { -res = this.av.getColumnSelection ().adjustForHiddenColumns (res); -}if (!this.stretchingGroup) { -this.ap.paintAlignment (false); -return; -}var sg = this.av.getSelectionGroup (); -if (res > sg.getStartRes ()) { -sg.setEndRes (res); -} else if (res < sg.getStartRes ()) { -sg.setStartRes (res); -}this.stretchingGroup = false; -this.ap.paintAlignment (false); -this.av.sendSelection (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -this.mouseDragging = true; -var res = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); -if (res < 0) { -res = 0; -}if (this.av.hasHiddenColumns ()) { -res = this.av.getColumnSelection ().adjustForHiddenColumns (res); -}if (res > this.av.getAlignment ().getWidth ()) { -res = this.av.getAlignment ().getWidth () - 1; -}if (res < this.min) { -this.min = res; -}if (res > this.max) { -this.max = res; -}var sg = this.av.getSelectionGroup (); -if (sg != null) { -this.stretchingGroup = true; -if (!this.av.getColumnSelection ().contains (res)) { -this.av.getColumnSelection ().addElement (res); -}if (res > sg.getStartRes ()) { -sg.setEndRes (res); -}if (res < sg.getStartRes ()) { -sg.setStartRes (res); -}var col; -for (var i = this.min; i <= this.max; i++) { -col = this.av.getColumnSelection ().adjustForHiddenColumns (i); -if ((col < sg.getStartRes ()) || (col > sg.getEndRes ())) { -this.av.getColumnSelection ().removeElement (col); -} else { -this.av.getColumnSelection ().addElement (col); -}} -this.ap.paintAlignment (false); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -if (this.mouseDragging) { -this.ap.seqPanel.scrollCanvas (null); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -if (this.mouseDragging) { -this.ap.seqPanel.scrollCanvas (evt); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -if (!this.av.hasHiddenColumns ()) { -return; -}var res = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); -res = this.av.getColumnSelection ().adjustForHiddenColumns (res); -this.reveal = null; -for (var region, $region = this.av.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { -if (res + 1 == region[0] || res - 1 == region[1]) { -this.reveal = region; -break; -}} -this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -if (this.av.getWrapAlignment ()) return; -this.drawScale (g, this.av.getStartRes (), this.av.getEndRes (), this.getSize ().width, this.getSize ().height); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "drawScale", -function (gg, startx, endx, width, height) { -gg.setFont (this.av.getFont ()); -gg.setColor (java.awt.Color.white); -gg.fillRect (0, 0, width, height); -gg.setColor (java.awt.Color.black); -var cs = this.av.getColumnSelection (); -gg.setColor ( new java.awt.Color (220, 0, 0)); -var avcharWidth = this.av.getCharWidth (); -var avcharHeight = this.av.getCharHeight (); -for (var i = 0; i < cs.size (); i++) { -var sel = cs.columnAt (i); -if (this.av.hasHiddenColumns ()) { -sel = this.av.getColumnSelection ().findColumnPosition (sel); -}if ((sel >= startx) && (sel <= endx)) { -gg.fillRect ((sel - startx) * avcharWidth, 0, avcharWidth, this.getSize ().height); -}} -gg.setColor (java.awt.Color.black); -var scalestartx = (Clazz.doubleToInt (startx / 10)) * 10; -var fm = gg.getFontMetrics (this.av.getFont ()); -var y = avcharHeight - fm.getDescent (); -if ((scalestartx % 10) == 0) { -scalestartx += 5; -}var string; -var maxX = 0; -for (var i = scalestartx; i < endx; i += 5) { -if ((i % 10) == 0) { -string = String.valueOf (this.av.getColumnSelection ().adjustForHiddenColumns (i)); -if ((i - startx - 1) * avcharWidth > maxX) { -gg.drawString (string, (i - startx - 1) * avcharWidth, y); -maxX = (i - startx + 1) * avcharWidth + fm.stringWidth (string); -}gg.drawLine (((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + 2, ((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + (fm.getDescent () * 2)); -} else { -gg.drawLine (((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + fm.getDescent (), ((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + (fm.getDescent () * 2)); -}} -if (this.av.hasHiddenColumns ()) { -gg.setColor (java.awt.Color.blue); -var res; -if (this.av.getShowHiddenMarkers ()) { -for (var i = 0; i < this.av.getColumnSelection ().getHiddenColumns ().size (); i++) { -res = this.av.getColumnSelection ().findHiddenRegionPosition (i) - startx; -if (res < 0 || res > endx - scalestartx) { -continue; -}gg.fillPolygon ( Clazz.newIntArray (-1, [res * avcharWidth - Clazz.doubleToInt (avcharHeight / 4), res * avcharWidth + Clazz.doubleToInt (avcharHeight / 4), res * avcharWidth]), Clazz.newIntArray (-1, [y - Clazz.doubleToInt (avcharHeight / 2), y - Clazz.doubleToInt (avcharHeight / 2), y + 8]), 3); -} -}if (this.reveal != null && this.reveal[0] > startx && this.reveal[0] < endx) { -gg.drawString (jalview.util.MessageManager.getString ("label.reveal_columns"), this.reveal[0] * avcharWidth, 0); -}}}, "java.awt.Graphics,~N,~N,~N,~N"); -c$.$ScalePanel$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "ScalePanel$1", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.ScalePanel"].av.showColumn (this.b$["jalview.appletgui.ScalePanel"].reveal[0]); -this.b$["jalview.appletgui.ScalePanel"].reveal = null; -this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment (true); -if (this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel != null) { -this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage (); -}}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$ScalePanel$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "ScalePanel$2", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.ScalePanel"].av.showAllHiddenColumns (); -this.b$["jalview.appletgui.ScalePanel"].reveal = null; -this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment (true); -if (this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel != null) { -this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage (); -}}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$ScalePanel$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "ScalePanel$3", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.ScalePanel"].av.hideColumns (this.f$.res, this.f$.res); -if (this.b$["jalview.appletgui.ScalePanel"].av.getSelectionGroup () != null && this.b$["jalview.appletgui.ScalePanel"].av.getSelectionGroup ().getSize () == this.b$["jalview.appletgui.ScalePanel"].av.getAlignment ().getHeight ()) { -this.b$["jalview.appletgui.ScalePanel"].av.setSelectionGroup (null); -}this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment (true); -if (this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel != null) { -this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage (); -}}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener"], "jalview.appletgui.ScalePanel", ["awt2swing.MenuItem", "$.PopupMenu", "jalview.datamodel.SequenceGroup", "jalview.util.MessageManager", "java.awt.Color", "java.awt.event.ActionListener"], function () { +c$ = Clazz.decorateAsClass (function () { +this.offy = 4; +this.$width = 0; +this.av = null; +this.ap = null; +this.stretchingGroup = false; +this.min = 0; +this.max = 0; +this.mouseDragging = false; +this.reveal = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "ScalePanel", awt2swing.Panel, [java.awt.event.MouseMotionListener, java.awt.event.MouseListener]); +Clazz.makeConstructor (c$, +function (av, ap) { +Clazz.superConstructor (this, jalview.appletgui.ScalePanel, []); +this.setName ("scalePanel"); +this.setLayout (null); +this.av = av; +this.ap = ap; +this.addMouseListener (this); +this.addMouseMotionListener (this); +}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +var x = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); +var res; +if (this.av.hasHiddenColumns ()) { +res = this.av.getColumnSelection ().adjustForHiddenColumns (x); +} else { +res = x; +}this.min = res; +this.max = res; +if ((evt.getModifiers () & 4) == 4) { +var pop = new awt2swing.PopupMenu (); +if (this.reveal != null) { +var item = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.reveal")); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.ScalePanel$1") ? 0 : jalview.appletgui.ScalePanel.$ScalePanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.ScalePanel$1, this, null))); +pop.add (item); +if (this.av.getColumnSelection ().hasManyHiddenColumns ()) { +item = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.reveal_all")); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.ScalePanel$2") ? 0 : jalview.appletgui.ScalePanel.$ScalePanel$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.ScalePanel$2, this, null))); +pop.add (item); +}this.add (pop); +pop.show (this, evt.getX (), evt.getY ()); +} else if (this.av.getColumnSelection ().contains (res)) { +var item = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.hide_columns")); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.ScalePanel$3") ? 0 : jalview.appletgui.ScalePanel.$ScalePanel$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.ScalePanel$3, this, Clazz.cloneFinals ("res", res)))); +pop.add (item); +this.add (pop); +pop.show (this, evt.getX (), evt.getY ()); +}} else { +if (!evt.isControlDown () && !evt.isShiftDown ()) { +this.av.getColumnSelection ().clear (); +}this.av.getColumnSelection ().addElement (res); +var sg = new jalview.datamodel.SequenceGroup (); +for (var i = 0; i < this.av.getAlignment ().getSequences ().size (); i++) { +sg.addSequence (this.av.getAlignment ().getSequenceAt (i), false); +} +sg.setStartRes (res); +sg.setEndRes (res); +this.av.setSelectionGroup (sg); +if (evt.isShiftDown ()) { +var min = Math.min (this.av.getColumnSelection ().getMin (), res); +var max = Math.max (this.av.getColumnSelection ().getMax (), res); +for (var i = min; i < max; i++) { +this.av.getColumnSelection ().addElement (i); +} +sg.setStartRes (min); +sg.setEndRes (max); +}}this.ap.paintAlignment (true); +this.av.sendSelection (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.mouseDragging = false; +var res = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); +if (res > this.av.getAlignment ().getWidth ()) { +res = this.av.getAlignment ().getWidth () - 1; +}if (this.av.hasHiddenColumns ()) { +res = this.av.getColumnSelection ().adjustForHiddenColumns (res); +}if (!this.stretchingGroup) { +this.ap.paintAlignment (false); +return; +}var sg = this.av.getSelectionGroup (); +if (res > sg.getStartRes ()) { +sg.setEndRes (res); +} else if (res < sg.getStartRes ()) { +sg.setStartRes (res); +}this.stretchingGroup = false; +this.ap.paintAlignment (false); +this.av.sendSelection (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +this.mouseDragging = true; +var res = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); +if (res < 0) { +res = 0; +}if (this.av.hasHiddenColumns ()) { +res = this.av.getColumnSelection ().adjustForHiddenColumns (res); +}if (res > this.av.getAlignment ().getWidth ()) { +res = this.av.getAlignment ().getWidth () - 1; +}if (res < this.min) { +this.min = res; +}if (res > this.max) { +this.max = res; +}var sg = this.av.getSelectionGroup (); +if (sg != null) { +this.stretchingGroup = true; +if (!this.av.getColumnSelection ().contains (res)) { +this.av.getColumnSelection ().addElement (res); +}if (res > sg.getStartRes ()) { +sg.setEndRes (res); +}if (res < sg.getStartRes ()) { +sg.setStartRes (res); +}var col; +for (var i = this.min; i <= this.max; i++) { +col = this.av.getColumnSelection ().adjustForHiddenColumns (i); +if ((col < sg.getStartRes ()) || (col > sg.getEndRes ())) { +this.av.getColumnSelection ().removeElement (col); +} else { +this.av.getColumnSelection ().addElement (col); +}} +this.ap.paintAlignment (false); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +if (this.mouseDragging) { +this.ap.seqPanel.scrollCanvas (null); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +if (this.mouseDragging) { +this.ap.seqPanel.scrollCanvas (evt); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +if (!this.av.hasHiddenColumns ()) { +return; +}var res = (Clazz.doubleToInt (evt.getX () / this.av.getCharWidth ())) + this.av.getStartRes (); +res = this.av.getColumnSelection ().adjustForHiddenColumns (res); +this.reveal = null; +for (var region, $region = this.av.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { +if (res + 1 == region[0] || res - 1 == region[1]) { +this.reveal = region; +break; +}} +this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +if (this.av.getWrapAlignment ()) return; +this.drawScale (g, this.av.getStartRes (), this.av.getEndRes (), this.getSize ().width, this.getSize ().height); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "drawScale", +function (gg, startx, endx, width, height) { +gg.setFont (this.av.getFont ()); +gg.setColor (java.awt.Color.white); +gg.fillRect (0, 0, width, height); +gg.setColor (java.awt.Color.black); +var cs = this.av.getColumnSelection (); +gg.setColor ( new java.awt.Color (220, 0, 0)); +var avcharWidth = this.av.getCharWidth (); +var avcharHeight = this.av.getCharHeight (); +for (var i = 0; i < cs.size (); i++) { +var sel = cs.columnAt (i); +if (this.av.hasHiddenColumns ()) { +sel = this.av.getColumnSelection ().findColumnPosition (sel); +}if ((sel >= startx) && (sel <= endx)) { +gg.fillRect ((sel - startx) * avcharWidth, 0, avcharWidth, this.getSize ().height); +}} +gg.setColor (java.awt.Color.black); +var scalestartx = (Clazz.doubleToInt (startx / 10)) * 10; +var fm = gg.getFontMetrics (this.av.getFont ()); +var y = avcharHeight - fm.getDescent (); +if ((scalestartx % 10) == 0) { +scalestartx += 5; +}var string; +var maxX = 0; +for (var i = scalestartx; i < endx; i += 5) { +if ((i % 10) == 0) { +string = String.valueOf (this.av.getColumnSelection ().adjustForHiddenColumns (i)); +if ((i - startx - 1) * avcharWidth > maxX) { +gg.drawString (string, (i - startx - 1) * avcharWidth, y); +maxX = (i - startx + 1) * avcharWidth + fm.stringWidth (string); +}gg.drawLine (((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + 2, ((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + (fm.getDescent () * 2)); +} else { +gg.drawLine (((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + fm.getDescent (), ((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + (fm.getDescent () * 2)); +}} +if (this.av.hasHiddenColumns ()) { +gg.setColor (java.awt.Color.blue); +var res; +if (this.av.getShowHiddenMarkers ()) { +for (var i = 0; i < this.av.getColumnSelection ().getHiddenColumns ().size (); i++) { +res = this.av.getColumnSelection ().findHiddenRegionPosition (i) - startx; +if (res < 0 || res > endx - scalestartx) { +continue; +}gg.fillPolygon ( Clazz.newIntArray (-1, [res * avcharWidth - Clazz.doubleToInt (avcharHeight / 4), res * avcharWidth + Clazz.doubleToInt (avcharHeight / 4), res * avcharWidth]), Clazz.newIntArray (-1, [y - Clazz.doubleToInt (avcharHeight / 2), y - Clazz.doubleToInt (avcharHeight / 2), y + 8]), 3); +} +}if (this.reveal != null && this.reveal[0] > startx && this.reveal[0] < endx) { +gg.drawString (jalview.util.MessageManager.getString ("label.reveal_columns"), this.reveal[0] * avcharWidth, 0); +}}}, "java.awt.Graphics,~N,~N,~N,~N"); +c$.$ScalePanel$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "ScalePanel$1", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.ScalePanel"].av.showColumn (this.b$["jalview.appletgui.ScalePanel"].reveal[0]); +this.b$["jalview.appletgui.ScalePanel"].reveal = null; +this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment (true); +if (this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel != null) { +this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage (); +}}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$ScalePanel$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "ScalePanel$2", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.ScalePanel"].av.showAllHiddenColumns (); +this.b$["jalview.appletgui.ScalePanel"].reveal = null; +this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment (true); +if (this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel != null) { +this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage (); +}}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$ScalePanel$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "ScalePanel$3", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.ScalePanel"].av.hideColumns (this.f$.res, this.f$.res); +if (this.b$["jalview.appletgui.ScalePanel"].av.getSelectionGroup () != null && this.b$["jalview.appletgui.ScalePanel"].av.getSelectionGroup ().getSize () == this.b$["jalview.appletgui.ScalePanel"].av.getAlignment ().getHeight ()) { +this.b$["jalview.appletgui.ScalePanel"].av.setSelectionGroup (null); +}this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment (true); +if (this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel != null) { +this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage (); +}}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/SeqCanvas.class b/bin/jalview/appletgui/SeqCanvas.class index a5ce5f0..c3feb04 100644 Binary files a/bin/jalview/appletgui/SeqCanvas.class and b/bin/jalview/appletgui/SeqCanvas.class differ diff --git a/bin/jalview/appletgui/SeqCanvas.js b/bin/jalview/appletgui/SeqCanvas.js index ac84c24..af5372b 100644 --- a/bin/jalview/appletgui/SeqCanvas.js +++ b/bin/jalview/appletgui/SeqCanvas.js @@ -1,411 +1,411 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel"], "jalview.appletgui.SeqCanvas", ["jalview.appletgui.AnnotationPanel", "$.FeatureRenderer", "$.PaintRefresher", "$.SequenceRenderer", "jalview.util.Comparison", "java.awt.Color"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fr = null; -this.sr = null; -this.img = null; -this.gg = null; -this.imgWidth = 0; -this.imgHeight = 0; -this.av = null; -this.searchResults = null; -this.$fastPaint = false; -this.cursorX = 0; -this.cursorY = 0; -this.avcharHeight = 0; -this.avcharWidth = 0; -this.lastsr = 0; -this.LABEL_WEST = 0; -this.LABEL_EAST = 0; -this.annotations = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "SeqCanvas", awt2swing.Panel); -Clazz.makeConstructor (c$, -function (av) { -Clazz.superConstructor (this, jalview.appletgui.SeqCanvas, []); -this.av = av; -this.fr = new jalview.appletgui.FeatureRenderer (av); -this.sr = new jalview.appletgui.SequenceRenderer (av); -jalview.appletgui.PaintRefresher.Register (this, av.getSequenceSetId ()); -this.updateViewport (); -}, "jalview.appletgui.AlignViewport"); -Clazz.defineMethod (c$, "updateViewport", -($fz = function () { -this.avcharHeight = this.av.getCharHeight (); -this.avcharWidth = this.av.getCharWidth (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getViewport", -function () { -return this.av; -}); -Clazz.defineMethod (c$, "getFeatureRenderer", -function () { -return this.fr; -}); -Clazz.defineMethod (c$, "getSequenceRenderer", -function () { -return this.sr; -}); -Clazz.defineMethod (c$, "drawNorthScale", -($fz = function (g, startx, endx, ypos) { -var scalestartx = startx - startx % 10 + 10; -g.setColor (java.awt.Color.black); -for (var i = scalestartx; i < endx; i += 10) { -var value = i; -if (this.av.hasHiddenColumns ()) { -value = this.av.getColumnSelection ().adjustForHiddenColumns (value); -}g.drawString (String.valueOf (value), (i - startx - 1) * this.avcharWidth, ypos - (Clazz.doubleToInt (this.avcharHeight / 2))); -g.drawLine (((i - startx - 1) * this.avcharWidth) + (Clazz.doubleToInt (this.avcharWidth / 2)), (ypos + 2) - (Clazz.doubleToInt (this.avcharHeight / 2)), ((i - startx - 1) * this.avcharWidth) + (Clazz.doubleToInt (this.avcharWidth / 2)), ypos - 2); -} -}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); -Clazz.defineMethod (c$, "drawWestScale", -($fz = function (g, startx, endx, ypos) { -var fm = this.getFontMetrics (this.av.getFont ()); -ypos += this.avcharHeight; -if (this.av.hasHiddenColumns ()) { -startx = this.av.getColumnSelection ().adjustForHiddenColumns (startx); -endx = this.av.getColumnSelection ().adjustForHiddenColumns (endx); -}var maxwidth = this.av.getAlignment ().getWidth (); -if (this.av.hasHiddenColumns ()) { -maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; -}for (var i = 0; i < this.av.getAlignment ().getHeight (); i++) { -var seq = this.av.getAlignment ().getSequenceAt (i); -var index = startx; -var value = -1; -while (index < endx) { -if (jalview.util.Comparison.isGap (seq.getCharAt (index))) { -index++; -continue; -}value = this.av.getAlignment ().getSequenceAt (i).findPosition (index); -break; -} -if (value != -1) { -var x = this.LABEL_WEST - fm.stringWidth (String.valueOf (value)) - Clazz.doubleToInt (this.avcharWidth / 2); -g.drawString (value + "", x, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); -}} -}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); -Clazz.defineMethod (c$, "drawEastScale", -($fz = function (g, startx, endx, ypos) { -ypos += this.avcharHeight; -if (this.av.hasHiddenColumns ()) { -endx = this.av.getColumnSelection ().adjustForHiddenColumns (endx); -}var seq; -for (var i = 0; i < this.av.getAlignment ().getHeight (); i++) { -seq = this.av.getAlignment ().getSequenceAt (i); -var index = endx; -var value = -1; -while (index > startx) { -if (jalview.util.Comparison.isGap (seq.getCharAt (index))) { -index--; -continue; -}value = seq.findPosition (index); -break; -} -if (value != -1) { -g.drawString (String.valueOf (value), 0, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); -}} -}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); -Clazz.defineMethod (c$, "fastPaint", -function (horizontal, vertical) { -if (this.$fastPaint || this.gg == null) { -return; -}this.updateViewport (); -if (this.lastsr + horizontal != this.av.startRes) { -horizontal = this.av.startRes - this.lastsr; -}this.lastsr = this.av.startRes; -this.$fastPaint = true; -this.gg.copyArea (horizontal * this.avcharWidth, vertical * this.avcharHeight, this.imgWidth - horizontal * this.avcharWidth, this.imgHeight - vertical * this.avcharHeight, -horizontal * this.avcharWidth, -vertical * this.avcharHeight); -var sr = this.av.startRes; -var er = this.av.endRes; -var ss = this.av.startSeq; -var es = this.av.endSeq; -var transX = 0; -var transY = 0; -if (horizontal > 0) { -transX = (er - sr - horizontal) * this.avcharWidth; -sr = er - horizontal; -} else if (horizontal < 0) { -er = sr - horizontal; -} else if (vertical > 0) { -ss = es - vertical; -if (ss < this.av.startSeq) { -ss = this.av.startSeq; -} else { -transY = this.imgHeight - vertical * this.avcharHeight; -}} else if (vertical < 0) { -es = ss - vertical; -if (es > this.av.endSeq) { -es = this.av.endSeq; -}}this.gg.translate (transX, transY); -this.drawPanel (this.gg, sr, er, ss, es, 0); -this.gg.translate (-transX, -transY); -this.repaint (); -}, "~N,~N"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -if (this.img != null && (this.$fastPaint || (this.getSize ().width != g.getClipBounds ().width) || (this.getSize ().height != g.getClipBounds ().height))) { -g.drawImage (this.img, 0, 0, this); -this.$fastPaint = false; -return; -}if (this.$fastPaint) { -g.drawImage (this.img, 0, 0, this); -this.$fastPaint = false; -return; -}this.updateViewport (); -this.imgWidth = this.getSize ().width; -this.imgHeight = this.getSize ().height; -this.imgWidth -= this.imgWidth % this.avcharWidth; -this.imgHeight -= this.imgHeight % this.avcharHeight; -if (this.imgWidth < 1 || this.imgHeight < 1) { -return; -}if (this.img == null || this.imgWidth != this.img.getWidth (this) || this.imgHeight != this.img.getHeight (this)) { -this.img = this.createImage (this.imgWidth, this.imgHeight); -this.gg = this.img.getGraphics (); -this.gg.setFont (this.av.getFont ()); -}this.gg.setColor (java.awt.Color.white); -this.gg.fillRect (0, 0, this.imgWidth, this.imgHeight); -if (this.av.getWrapAlignment ()) { -this.drawWrappedPanel (this.gg, this.imgWidth, this.imgHeight, this.av.startRes); -} else { -this.drawPanel (this.gg, this.av.startRes, this.av.endRes, this.av.startSeq, this.av.endSeq, 0); -}g.drawImage (this.img, 0, 0, this); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "getWrappedCanvasWidth", -function (cwidth) { -cwidth -= cwidth % this.av.getCharWidth (); -var fm = this.getFontMetrics (this.av.getFont ()); -this.LABEL_EAST = 0; -this.LABEL_WEST = 0; -if (this.av.getScaleRightWrapped ()) { -this.LABEL_EAST = fm.stringWidth (this.getMask ()); -}if (this.av.getScaleLeftWrapped ()) { -this.LABEL_WEST = fm.stringWidth (this.getMask ()); -}return Clazz.doubleToInt ((cwidth - this.LABEL_EAST - this.LABEL_WEST) / this.av.getCharWidth ()); -}, "~N"); -Clazz.defineMethod (c$, "getMask", -function () { -var mask = "0"; -var maxWidth = 0; -var tmp; -var alignment = this.av.getAlignment (); -for (var i = 0; i < alignment.getHeight (); i++) { -tmp = alignment.getSequenceAt (i).getEnd (); -if (tmp > maxWidth) { -maxWidth = tmp; -}} -for (var i = maxWidth; i > 0; i /= 10) { -mask += "0"; -} -return mask; -}); -Clazz.defineMethod (c$, "drawWrappedPanel", -($fz = function (g, canvasWidth, canvasHeight, startRes) { -var al = this.av.getAlignment (); -var fm = this.getFontMetrics (this.av.getFont ()); -if (this.av.getScaleRightWrapped ()) { -this.LABEL_EAST = fm.stringWidth (this.getMask ()); -}if (this.av.getScaleLeftWrapped ()) { -this.LABEL_WEST = fm.stringWidth (this.getMask ()); -}var hgap = this.avcharHeight; -if (this.av.getScaleAboveWrapped ()) { -hgap += this.avcharHeight; -}var cWidth = Clazz.doubleToInt ((canvasWidth - this.LABEL_EAST - this.LABEL_WEST) / this.avcharWidth); -var cHeight = this.av.getAlignment ().getHeight () * this.avcharHeight; -this.av.setWrappedWidth (cWidth); -this.av.endRes = this.av.startRes + cWidth; -var endx; -var ypos = hgap; -var maxwidth = this.av.getAlignment ().getWidth () - 1; -if (this.av.hasHiddenColumns ()) { -maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; -}while ((ypos <= canvasHeight) && (startRes < maxwidth)) { -endx = startRes + cWidth - 1; -if (endx > maxwidth) { -endx = maxwidth; -}g.setColor (java.awt.Color.black); -if (this.av.getScaleLeftWrapped ()) { -this.drawWestScale (g, startRes, endx, ypos); -}if (this.av.getScaleRightWrapped ()) { -g.translate (canvasWidth - this.LABEL_EAST, 0); -this.drawEastScale (g, startRes, endx, ypos); -g.translate (-(canvasWidth - this.LABEL_EAST), 0); -}g.translate (this.LABEL_WEST, 0); -if (this.av.getScaleAboveWrapped ()) { -this.drawNorthScale (g, startRes, endx, ypos); -}if (this.av.hasHiddenColumns () && this.av.getShowHiddenMarkers ()) { -g.setColor (java.awt.Color.blue); -var res; -for (var i = 0; i < this.av.getColumnSelection ().getHiddenColumns ().size (); i++) { -res = this.av.getColumnSelection ().findHiddenRegionPosition (i) - startRes; -if (res < 0 || res > endx - startRes) { -continue; -}this.gg.fillPolygon ( Clazz.newIntArray (-1, [res * this.avcharWidth - Clazz.doubleToInt (this.avcharHeight / 4), res * this.avcharWidth + Clazz.doubleToInt (this.avcharHeight / 4), res * this.avcharWidth]), Clazz.newIntArray (-1, [ypos - (Clazz.doubleToInt (this.avcharHeight / 2)), ypos - (Clazz.doubleToInt (this.avcharHeight / 2)), ypos - (Clazz.doubleToInt (this.avcharHeight / 2)) + 8]), 3); -} -}if (g.getClip () == null) { -g.setClip (0, 0, cWidth * this.avcharWidth, canvasHeight); -}this.drawPanel (g, startRes, endx, 0, al.getHeight (), ypos); -g.setClip (null); -if (this.av.isShowAnnotation ()) { -g.translate (0, cHeight + ypos + 4); -if (this.annotations == null) { -this.annotations = new jalview.appletgui.AnnotationPanel (this.av); -}this.annotations.drawComponent (g, startRes, endx + 1); -g.translate (0, -cHeight - ypos - 4); -}g.translate (-this.LABEL_WEST, 0); -ypos += cHeight + this.getAnnotationHeight () + hgap; -startRes += cWidth; -} -}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); -Clazz.defineMethod (c$, "getAnnotationHeight", -function () { -if (!this.av.isShowAnnotation ()) { -return 0; -}if (this.annotations == null) { -this.annotations = new jalview.appletgui.AnnotationPanel (this.av); -}return this.annotations.adjustPanelHeight (); -}); -Clazz.defineMethod (c$, "drawPanel", -($fz = function (g1, startRes, endRes, startSeq, endSeq, offset) { -if (!this.av.hasHiddenColumns ()) { -this.draw (g1, startRes, endRes, startSeq, endSeq, offset); -} else { -var screenY = 0; -var blockStart = startRes; -var blockEnd = endRes; -if (this.av.hasHiddenColumns ()) { -for (var region, $region = this.av.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { -var hideStart = region[0]; -var hideEnd = region[1]; -if (hideStart <= blockStart) { -blockStart += (hideEnd - hideStart) + 1; -continue; -}blockEnd = hideStart - 1; -g1.translate (screenY * this.avcharWidth, 0); -this.draw (g1, blockStart, blockEnd, startSeq, endSeq, offset); -if (this.av.getShowHiddenMarkers ()) { -g1.setColor (java.awt.Color.blue); -g1.drawLine ((blockEnd - blockStart + 1) * this.avcharWidth - 1, 0 + offset, (blockEnd - blockStart + 1) * this.avcharWidth - 1, (endSeq - startSeq) * this.avcharHeight + offset); -}g1.translate (-screenY * this.avcharWidth, 0); -screenY += blockEnd - blockStart + 1; -blockStart = hideEnd + 1; -} -}if (screenY <= (endRes - startRes)) { -blockEnd = blockStart + (endRes - startRes) - screenY; -g1.translate (screenY * this.avcharWidth, 0); -this.draw (g1, blockStart, blockEnd, startSeq, endSeq, offset); -g1.translate (-screenY * this.avcharWidth, 0); -}}}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "draw", -function (g, startRes, endRes, startSeq, endSeq, offset) { -g.setFont (this.av.getFont ()); -this.sr.prepare (g, this.av.isRenderGaps ()); -this.updateViewport (); -var nextSeq; -for (var i = startSeq; i < endSeq; i++) { -nextSeq = this.av.getAlignment ().getSequenceAt (i); -if (nextSeq == null) { -continue; -}this.sr.drawSequence (nextSeq, this.av.getAlignment ().findAllGroups (nextSeq), startRes, endRes, offset + ((i - startSeq) * this.avcharHeight)); -if (this.av.isShowSequenceFeatures ()) { -this.fr.drawSequence (g, nextSeq, startRes, endRes, offset + ((i - startSeq) * this.avcharHeight)); -}if (this.searchResults != null) { -var visibleResults = this.searchResults.getResults (nextSeq, startRes, endRes); -if (visibleResults != null) { -for (var r = 0; r < visibleResults.length; r += 2) { -this.sr.drawHighlightedText (nextSeq, visibleResults[r], visibleResults[r + 1], (visibleResults[r] - startRes) * this.avcharWidth, offset + ((i - startSeq) * this.avcharHeight)); -} -}}if (this.av.cursorMode && this.cursorY == i && this.cursorX >= startRes && this.cursorX <= endRes) { -this.sr.drawCursor (nextSeq, this.cursorX, (this.cursorX - startRes) * this.avcharWidth, offset + ((i - startSeq) * this.avcharHeight)); -}} -if (this.av.getSelectionGroup () != null || this.av.getAlignment ().getGroups ().size () > 0) { -this.drawGroupsBoundaries (g, startRes, endRes, startSeq, endSeq, offset); -}}, "java.awt.Graphics,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "drawGroupsBoundaries", -($fz = function (g, startRes, endRes, startSeq, endSeq, offset) { -var group = this.av.getSelectionGroup (); -var sx = -1; -var sy = -1; -var ex = -1; -var groupIndex = -1; -if ((group == null) && (this.av.getAlignment ().getGroups ().size () > 0)) { -group = this.av.getAlignment ().getGroups ().get (0); -groupIndex = 0; -}if (group != null) { -do { -var oldY = -1; -var i = 0; -var inGroup = false; -var top = -1; -var bottom = -1; -var alHeight = this.av.getAlignment ().getHeight () - 1; -for (i = startSeq; i < endSeq; i++) { -sx = (group.getStartRes () - startRes) * this.avcharWidth; -sy = offset + ((i - startSeq) * this.avcharHeight); -ex = (((group.getEndRes () + 1) - group.getStartRes ()) * this.avcharWidth) - 1; -if (sx + ex < 0 || sx > this.imgWidth) { -continue; -}if ((sx <= (endRes - startRes) * this.avcharWidth) && group.getSequences (null).contains (this.av.getAlignment ().getSequenceAt (i))) { -if ((bottom == -1) && (i >= alHeight || !group.getSequences (null).contains (this.av.getAlignment ().getSequenceAt (i + 1)))) { -bottom = sy + this.avcharHeight; -}if (!inGroup) { -if (((top == -1) && (i == 0)) || !group.getSequences (null).contains (this.av.getAlignment ().getSequenceAt (i - 1))) { -top = sy; -}oldY = sy; -inGroup = true; -if (group === this.av.getSelectionGroup ()) { -g.setColor (java.awt.Color.red); -} else { -g.setColor (group.getOutlineColour ()); -}}} else { -if (inGroup) { -if (sx >= 0 && sx < this.imgWidth) { -g.drawLine (sx, oldY, sx, sy); -}if (sx + ex < this.imgWidth) { -g.drawLine (sx + ex, oldY, sx + ex, sy); -}if (sx < 0) { -ex += sx; -sx = 0; -}if (sx + ex > this.imgWidth) { -ex = this.imgWidth; -} else if (sx + ex >= (endRes - startRes + 1) * this.avcharWidth) { -ex = (endRes - startRes + 1) * this.avcharWidth; -}if (top != -1) { -g.drawLine (sx, top, sx + ex, top); -top = -1; -}if (bottom != -1) { -g.drawLine (sx, bottom, sx + ex, bottom); -bottom = -1; -}inGroup = false; -}}} -if (inGroup) { -sy = offset + ((i - startSeq) * this.avcharHeight); -if (sx >= 0 && sx < this.imgWidth) { -g.drawLine (sx, oldY, sx, sy); -}if (sx + ex < this.imgWidth) { -g.drawLine (sx + ex, oldY, sx + ex, sy); -}if (sx < 0) { -ex += sx; -sx = 0; -}if (sx + ex > this.imgWidth) { -ex = this.imgWidth; -} else if (sx + ex >= (endRes - startRes + 1) * this.avcharWidth) { -ex = (endRes - startRes + 1) * this.avcharWidth; -}if (top != -1) { -g.drawLine (sx, top, sx + ex, top); -top = -1; -}if (bottom != -1) { -g.drawLine (sx, bottom - 1, sx + ex, bottom - 1); -bottom = -1; -}inGroup = false; -}groupIndex++; -if (groupIndex >= this.av.getAlignment ().getGroups ().size ()) { -break; -}group = this.av.getAlignment ().getGroups ().get (groupIndex); -} while (groupIndex < this.av.getAlignment ().getGroups ().size ()); -}}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "highlightSearchResults", -function (results) { -this.searchResults = results; -this.repaint (); -}, "jalview.datamodel.SearchResults"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel"], "jalview.appletgui.SeqCanvas", ["jalview.appletgui.AnnotationPanel", "$.FeatureRenderer", "$.PaintRefresher", "$.SequenceRenderer", "jalview.util.Comparison", "java.awt.Color"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fr = null; +this.sr = null; +this.img = null; +this.gg = null; +this.imgWidth = 0; +this.imgHeight = 0; +this.av = null; +this.searchResults = null; +this.$fastPaint = false; +this.cursorX = 0; +this.cursorY = 0; +this.avcharHeight = 0; +this.avcharWidth = 0; +this.lastsr = 0; +this.LABEL_WEST = 0; +this.LABEL_EAST = 0; +this.annotations = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "SeqCanvas", awt2swing.Panel); +Clazz.makeConstructor (c$, +function (av) { +Clazz.superConstructor (this, jalview.appletgui.SeqCanvas, []); +this.av = av; +this.fr = new jalview.appletgui.FeatureRenderer (av); +this.sr = new jalview.appletgui.SequenceRenderer (av); +jalview.appletgui.PaintRefresher.Register (this, av.getSequenceSetId ()); +this.updateViewport (); +}, "jalview.appletgui.AlignViewport"); +Clazz.defineMethod (c$, "updateViewport", +($fz = function () { +this.avcharHeight = this.av.getCharHeight (); +this.avcharWidth = this.av.getCharWidth (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getViewport", +function () { +return this.av; +}); +Clazz.defineMethod (c$, "getFeatureRenderer", +function () { +return this.fr; +}); +Clazz.defineMethod (c$, "getSequenceRenderer", +function () { +return this.sr; +}); +Clazz.defineMethod (c$, "drawNorthScale", +($fz = function (g, startx, endx, ypos) { +var scalestartx = startx - startx % 10 + 10; +g.setColor (java.awt.Color.black); +for (var i = scalestartx; i < endx; i += 10) { +var value = i; +if (this.av.hasHiddenColumns ()) { +value = this.av.getColumnSelection ().adjustForHiddenColumns (value); +}g.drawString (String.valueOf (value), (i - startx - 1) * this.avcharWidth, ypos - (Clazz.doubleToInt (this.avcharHeight / 2))); +g.drawLine (((i - startx - 1) * this.avcharWidth) + (Clazz.doubleToInt (this.avcharWidth / 2)), (ypos + 2) - (Clazz.doubleToInt (this.avcharHeight / 2)), ((i - startx - 1) * this.avcharWidth) + (Clazz.doubleToInt (this.avcharWidth / 2)), ypos - 2); +} +}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); +Clazz.defineMethod (c$, "drawWestScale", +($fz = function (g, startx, endx, ypos) { +var fm = this.getFontMetrics (this.av.getFont ()); +ypos += this.avcharHeight; +if (this.av.hasHiddenColumns ()) { +startx = this.av.getColumnSelection ().adjustForHiddenColumns (startx); +endx = this.av.getColumnSelection ().adjustForHiddenColumns (endx); +}var maxwidth = this.av.getAlignment ().getWidth (); +if (this.av.hasHiddenColumns ()) { +maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; +}for (var i = 0; i < this.av.getAlignment ().getHeight (); i++) { +var seq = this.av.getAlignment ().getSequenceAt (i); +var index = startx; +var value = -1; +while (index < endx) { +if (jalview.util.Comparison.isGap (seq.getCharAt (index))) { +index++; +continue; +}value = this.av.getAlignment ().getSequenceAt (i).findPosition (index); +break; +} +if (value != -1) { +var x = this.LABEL_WEST - fm.stringWidth (String.valueOf (value)) - Clazz.doubleToInt (this.avcharWidth / 2); +g.drawString (value + "", x, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); +}} +}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); +Clazz.defineMethod (c$, "drawEastScale", +($fz = function (g, startx, endx, ypos) { +ypos += this.avcharHeight; +if (this.av.hasHiddenColumns ()) { +endx = this.av.getColumnSelection ().adjustForHiddenColumns (endx); +}var seq; +for (var i = 0; i < this.av.getAlignment ().getHeight (); i++) { +seq = this.av.getAlignment ().getSequenceAt (i); +var index = endx; +var value = -1; +while (index > startx) { +if (jalview.util.Comparison.isGap (seq.getCharAt (index))) { +index--; +continue; +}value = seq.findPosition (index); +break; +} +if (value != -1) { +g.drawString (String.valueOf (value), 0, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); +}} +}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); +Clazz.defineMethod (c$, "fastPaint", +function (horizontal, vertical) { +if (this.$fastPaint || this.gg == null) { +return; +}this.updateViewport (); +if (this.lastsr + horizontal != this.av.startRes) { +horizontal = this.av.startRes - this.lastsr; +}this.lastsr = this.av.startRes; +this.$fastPaint = true; +this.gg.copyArea (horizontal * this.avcharWidth, vertical * this.avcharHeight, this.imgWidth - horizontal * this.avcharWidth, this.imgHeight - vertical * this.avcharHeight, -horizontal * this.avcharWidth, -vertical * this.avcharHeight); +var sr = this.av.startRes; +var er = this.av.endRes; +var ss = this.av.startSeq; +var es = this.av.endSeq; +var transX = 0; +var transY = 0; +if (horizontal > 0) { +transX = (er - sr - horizontal) * this.avcharWidth; +sr = er - horizontal; +} else if (horizontal < 0) { +er = sr - horizontal; +} else if (vertical > 0) { +ss = es - vertical; +if (ss < this.av.startSeq) { +ss = this.av.startSeq; +} else { +transY = this.imgHeight - vertical * this.avcharHeight; +}} else if (vertical < 0) { +es = ss - vertical; +if (es > this.av.endSeq) { +es = this.av.endSeq; +}}this.gg.translate (transX, transY); +this.drawPanel (this.gg, sr, er, ss, es, 0); +this.gg.translate (-transX, -transY); +this.repaint (); +}, "~N,~N"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +if (this.img != null && (this.$fastPaint || (this.getSize ().width != g.getClipBounds ().width) || (this.getSize ().height != g.getClipBounds ().height))) { +g.drawImage (this.img, 0, 0, this); +this.$fastPaint = false; +return; +}if (this.$fastPaint) { +g.drawImage (this.img, 0, 0, this); +this.$fastPaint = false; +return; +}this.updateViewport (); +this.imgWidth = this.getSize ().width; +this.imgHeight = this.getSize ().height; +this.imgWidth -= this.imgWidth % this.avcharWidth; +this.imgHeight -= this.imgHeight % this.avcharHeight; +if (this.imgWidth < 1 || this.imgHeight < 1) { +return; +}if (this.img == null || this.imgWidth != this.img.getWidth (this) || this.imgHeight != this.img.getHeight (this)) { +this.img = this.createImage (this.imgWidth, this.imgHeight); +this.gg = this.img.getGraphics (); +this.gg.setFont (this.av.getFont ()); +}this.gg.setColor (java.awt.Color.white); +this.gg.fillRect (0, 0, this.imgWidth, this.imgHeight); +if (this.av.getWrapAlignment ()) { +this.drawWrappedPanel (this.gg, this.imgWidth, this.imgHeight, this.av.startRes); +} else { +this.drawPanel (this.gg, this.av.startRes, this.av.endRes, this.av.startSeq, this.av.endSeq, 0); +}g.drawImage (this.img, 0, 0, this); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "getWrappedCanvasWidth", +function (cwidth) { +cwidth -= cwidth % this.av.getCharWidth (); +var fm = this.getFontMetrics (this.av.getFont ()); +this.LABEL_EAST = 0; +this.LABEL_WEST = 0; +if (this.av.getScaleRightWrapped ()) { +this.LABEL_EAST = fm.stringWidth (this.getMask ()); +}if (this.av.getScaleLeftWrapped ()) { +this.LABEL_WEST = fm.stringWidth (this.getMask ()); +}return Clazz.doubleToInt ((cwidth - this.LABEL_EAST - this.LABEL_WEST) / this.av.getCharWidth ()); +}, "~N"); +Clazz.defineMethod (c$, "getMask", +function () { +var mask = "0"; +var maxWidth = 0; +var tmp; +var alignment = this.av.getAlignment (); +for (var i = 0; i < alignment.getHeight (); i++) { +tmp = alignment.getSequenceAt (i).getEnd (); +if (tmp > maxWidth) { +maxWidth = tmp; +}} +for (var i = maxWidth; i > 0; i /= 10) { +mask += "0"; +} +return mask; +}); +Clazz.defineMethod (c$, "drawWrappedPanel", +($fz = function (g, canvasWidth, canvasHeight, startRes) { +var al = this.av.getAlignment (); +var fm = this.getFontMetrics (this.av.getFont ()); +if (this.av.getScaleRightWrapped ()) { +this.LABEL_EAST = fm.stringWidth (this.getMask ()); +}if (this.av.getScaleLeftWrapped ()) { +this.LABEL_WEST = fm.stringWidth (this.getMask ()); +}var hgap = this.avcharHeight; +if (this.av.getScaleAboveWrapped ()) { +hgap += this.avcharHeight; +}var cWidth = Clazz.doubleToInt ((canvasWidth - this.LABEL_EAST - this.LABEL_WEST) / this.avcharWidth); +var cHeight = this.av.getAlignment ().getHeight () * this.avcharHeight; +this.av.setWrappedWidth (cWidth); +this.av.endRes = this.av.startRes + cWidth; +var endx; +var ypos = hgap; +var maxwidth = this.av.getAlignment ().getWidth () - 1; +if (this.av.hasHiddenColumns ()) { +maxwidth = this.av.getColumnSelection ().findColumnPosition (maxwidth) - 1; +}while ((ypos <= canvasHeight) && (startRes < maxwidth)) { +endx = startRes + cWidth - 1; +if (endx > maxwidth) { +endx = maxwidth; +}g.setColor (java.awt.Color.black); +if (this.av.getScaleLeftWrapped ()) { +this.drawWestScale (g, startRes, endx, ypos); +}if (this.av.getScaleRightWrapped ()) { +g.translate (canvasWidth - this.LABEL_EAST, 0); +this.drawEastScale (g, startRes, endx, ypos); +g.translate (-(canvasWidth - this.LABEL_EAST), 0); +}g.translate (this.LABEL_WEST, 0); +if (this.av.getScaleAboveWrapped ()) { +this.drawNorthScale (g, startRes, endx, ypos); +}if (this.av.hasHiddenColumns () && this.av.getShowHiddenMarkers ()) { +g.setColor (java.awt.Color.blue); +var res; +for (var i = 0; i < this.av.getColumnSelection ().getHiddenColumns ().size (); i++) { +res = this.av.getColumnSelection ().findHiddenRegionPosition (i) - startRes; +if (res < 0 || res > endx - startRes) { +continue; +}this.gg.fillPolygon ( Clazz.newIntArray (-1, [res * this.avcharWidth - Clazz.doubleToInt (this.avcharHeight / 4), res * this.avcharWidth + Clazz.doubleToInt (this.avcharHeight / 4), res * this.avcharWidth]), Clazz.newIntArray (-1, [ypos - (Clazz.doubleToInt (this.avcharHeight / 2)), ypos - (Clazz.doubleToInt (this.avcharHeight / 2)), ypos - (Clazz.doubleToInt (this.avcharHeight / 2)) + 8]), 3); +} +}if (g.getClip () == null) { +g.setClip (0, 0, cWidth * this.avcharWidth, canvasHeight); +}this.drawPanel (g, startRes, endx, 0, al.getHeight (), ypos); +g.setClip (null); +if (this.av.isShowAnnotation ()) { +g.translate (0, cHeight + ypos + 4); +if (this.annotations == null) { +this.annotations = new jalview.appletgui.AnnotationPanel (this.av); +}this.annotations.drawComponent (g, startRes, endx + 1); +g.translate (0, -cHeight - ypos - 4); +}g.translate (-this.LABEL_WEST, 0); +ypos += cHeight + this.getAnnotationHeight () + hgap; +startRes += cWidth; +} +}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N"); +Clazz.defineMethod (c$, "getAnnotationHeight", +function () { +if (!this.av.isShowAnnotation ()) { +return 0; +}if (this.annotations == null) { +this.annotations = new jalview.appletgui.AnnotationPanel (this.av); +}return this.annotations.adjustPanelHeight (); +}); +Clazz.defineMethod (c$, "drawPanel", +($fz = function (g1, startRes, endRes, startSeq, endSeq, offset) { +if (!this.av.hasHiddenColumns ()) { +this.draw (g1, startRes, endRes, startSeq, endSeq, offset); +} else { +var screenY = 0; +var blockStart = startRes; +var blockEnd = endRes; +if (this.av.hasHiddenColumns ()) { +for (var region, $region = this.av.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { +var hideStart = region[0]; +var hideEnd = region[1]; +if (hideStart <= blockStart) { +blockStart += (hideEnd - hideStart) + 1; +continue; +}blockEnd = hideStart - 1; +g1.translate (screenY * this.avcharWidth, 0); +this.draw (g1, blockStart, blockEnd, startSeq, endSeq, offset); +if (this.av.getShowHiddenMarkers ()) { +g1.setColor (java.awt.Color.blue); +g1.drawLine ((blockEnd - blockStart + 1) * this.avcharWidth - 1, 0 + offset, (blockEnd - blockStart + 1) * this.avcharWidth - 1, (endSeq - startSeq) * this.avcharHeight + offset); +}g1.translate (-screenY * this.avcharWidth, 0); +screenY += blockEnd - blockStart + 1; +blockStart = hideEnd + 1; +} +}if (screenY <= (endRes - startRes)) { +blockEnd = blockStart + (endRes - startRes) - screenY; +g1.translate (screenY * this.avcharWidth, 0); +this.draw (g1, blockStart, blockEnd, startSeq, endSeq, offset); +g1.translate (-screenY * this.avcharWidth, 0); +}}}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "draw", +function (g, startRes, endRes, startSeq, endSeq, offset) { +g.setFont (this.av.getFont ()); +this.sr.prepare (g, this.av.isRenderGaps ()); +this.updateViewport (); +var nextSeq; +for (var i = startSeq; i < endSeq; i++) { +nextSeq = this.av.getAlignment ().getSequenceAt (i); +if (nextSeq == null) { +continue; +}this.sr.drawSequence (nextSeq, this.av.getAlignment ().findAllGroups (nextSeq), startRes, endRes, offset + ((i - startSeq) * this.avcharHeight)); +if (this.av.isShowSequenceFeatures ()) { +this.fr.drawSequence (g, nextSeq, startRes, endRes, offset + ((i - startSeq) * this.avcharHeight)); +}if (this.searchResults != null) { +var visibleResults = this.searchResults.getResults (nextSeq, startRes, endRes); +if (visibleResults != null) { +for (var r = 0; r < visibleResults.length; r += 2) { +this.sr.drawHighlightedText (nextSeq, visibleResults[r], visibleResults[r + 1], (visibleResults[r] - startRes) * this.avcharWidth, offset + ((i - startSeq) * this.avcharHeight)); +} +}}if (this.av.cursorMode && this.cursorY == i && this.cursorX >= startRes && this.cursorX <= endRes) { +this.sr.drawCursor (nextSeq, this.cursorX, (this.cursorX - startRes) * this.avcharWidth, offset + ((i - startSeq) * this.avcharHeight)); +}} +if (this.av.getSelectionGroup () != null || this.av.getAlignment ().getGroups ().size () > 0) { +this.drawGroupsBoundaries (g, startRes, endRes, startSeq, endSeq, offset); +}}, "java.awt.Graphics,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "drawGroupsBoundaries", +($fz = function (g, startRes, endRes, startSeq, endSeq, offset) { +var group = this.av.getSelectionGroup (); +var sx = -1; +var sy = -1; +var ex = -1; +var groupIndex = -1; +if ((group == null) && (this.av.getAlignment ().getGroups ().size () > 0)) { +group = this.av.getAlignment ().getGroups ().get (0); +groupIndex = 0; +}if (group != null) { +do { +var oldY = -1; +var i = 0; +var inGroup = false; +var top = -1; +var bottom = -1; +var alHeight = this.av.getAlignment ().getHeight () - 1; +for (i = startSeq; i < endSeq; i++) { +sx = (group.getStartRes () - startRes) * this.avcharWidth; +sy = offset + ((i - startSeq) * this.avcharHeight); +ex = (((group.getEndRes () + 1) - group.getStartRes ()) * this.avcharWidth) - 1; +if (sx + ex < 0 || sx > this.imgWidth) { +continue; +}if ((sx <= (endRes - startRes) * this.avcharWidth) && group.getSequences (null).contains (this.av.getAlignment ().getSequenceAt (i))) { +if ((bottom == -1) && (i >= alHeight || !group.getSequences (null).contains (this.av.getAlignment ().getSequenceAt (i + 1)))) { +bottom = sy + this.avcharHeight; +}if (!inGroup) { +if (((top == -1) && (i == 0)) || !group.getSequences (null).contains (this.av.getAlignment ().getSequenceAt (i - 1))) { +top = sy; +}oldY = sy; +inGroup = true; +if (group === this.av.getSelectionGroup ()) { +g.setColor (java.awt.Color.red); +} else { +g.setColor (group.getOutlineColour ()); +}}} else { +if (inGroup) { +if (sx >= 0 && sx < this.imgWidth) { +g.drawLine (sx, oldY, sx, sy); +}if (sx + ex < this.imgWidth) { +g.drawLine (sx + ex, oldY, sx + ex, sy); +}if (sx < 0) { +ex += sx; +sx = 0; +}if (sx + ex > this.imgWidth) { +ex = this.imgWidth; +} else if (sx + ex >= (endRes - startRes + 1) * this.avcharWidth) { +ex = (endRes - startRes + 1) * this.avcharWidth; +}if (top != -1) { +g.drawLine (sx, top, sx + ex, top); +top = -1; +}if (bottom != -1) { +g.drawLine (sx, bottom, sx + ex, bottom); +bottom = -1; +}inGroup = false; +}}} +if (inGroup) { +sy = offset + ((i - startSeq) * this.avcharHeight); +if (sx >= 0 && sx < this.imgWidth) { +g.drawLine (sx, oldY, sx, sy); +}if (sx + ex < this.imgWidth) { +g.drawLine (sx + ex, oldY, sx + ex, sy); +}if (sx < 0) { +ex += sx; +sx = 0; +}if (sx + ex > this.imgWidth) { +ex = this.imgWidth; +} else if (sx + ex >= (endRes - startRes + 1) * this.avcharWidth) { +ex = (endRes - startRes + 1) * this.avcharWidth; +}if (top != -1) { +g.drawLine (sx, top, sx + ex, top); +top = -1; +}if (bottom != -1) { +g.drawLine (sx, bottom - 1, sx + ex, bottom - 1); +bottom = -1; +}inGroup = false; +}groupIndex++; +if (groupIndex >= this.av.getAlignment ().getGroups ().size ()) { +break; +}group = this.av.getAlignment ().getGroups ().get (groupIndex); +} while (groupIndex < this.av.getAlignment ().getGroups ().size ()); +}}, $fz.isPrivate = true, $fz), "java.awt.Graphics,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "highlightSearchResults", +function (results) { +this.searchResults = results; +this.repaint (); +}, "jalview.datamodel.SearchResults"); +}); diff --git a/bin/jalview/appletgui/SeqPanel.class b/bin/jalview/appletgui/SeqPanel.class index 90a2222..f3e19d0 100644 Binary files a/bin/jalview/appletgui/SeqPanel.class and b/bin/jalview/appletgui/SeqPanel.class differ diff --git a/bin/jalview/appletgui/SeqPanel.js b/bin/jalview/appletgui/SeqPanel.js index 7f97353..d500d0e 100644 --- a/bin/jalview/appletgui/SeqPanel.js +++ b/bin/jalview/appletgui/SeqPanel.js @@ -1,962 +1,962 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "jalview.structure.SelectionListener", "$.SequenceListener", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.lang.Thread"], "jalview.appletgui.SeqPanel", ["jalview.api.AlignViewportI", "jalview.appletgui.APopupMenu", "$.AlignViewport", "$.PaintRefresher", "$.SeqCanvas", "$.SliderPanel", "$.Tooltip", "jalview.commands.EditCommand", "jalview.datamodel.ColumnSelection", "$.SearchResults", "$.SequenceGroup", "jalview.schemes.ResidueProperties", "jalview.structure.StructureSelectionManager", "jalview.util.Comparison", "$.MappingUtils", "$.MessageManager", "java.awt.BorderLayout", "$.Font", "java.lang.StringBuffer", "$.StringBuilder", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.seqCanvas = null; -this.ap = null; -this.lastres = 0; -this.startseq = 0; -this.av = null; -this.seqEditOccurred = false; -this.scrollThread = null; -this.mouseDragging = false; -this.editingSeqs = false; -this.groupEditing = false; -this.oldSeq = -1; -this.changeEndSeq = false; -this.changeStartSeq = false; -this.changeEndRes = false; -this.changeStartRes = false; -this.stretchGroup = null; -this.keyboardNo1 = null; -this.keyboardNo2 = null; -this.mouseWheelPressed = false; -this.lastMousePress = null; -this.editCommand = null; -this.ssm = null; -this.startWrapBlock = -1; -this.wrappedBlock = -1; -this.lastMessage = null; -this.tooltip = null; -if (!Clazz.isClassDefined ("jalview.appletgui.SeqPanel.ScrollThread")) { -jalview.appletgui.SeqPanel.$SeqPanel$ScrollThread$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "SeqPanel", awt2swing.Panel, [java.awt.event.MouseMotionListener, java.awt.event.MouseListener, jalview.structure.SequenceListener, jalview.structure.SelectionListener]); -Clazz.makeConstructor (c$, -function (avp, p) { -Clazz.superConstructor (this, jalview.appletgui.SeqPanel, []); -this.av = avp; -this.setName ("seqPanel"); -this.seqCanvas = new jalview.appletgui.SeqCanvas (avp); -this.setLayout ( new java.awt.BorderLayout ()); -this.add (this.seqCanvas); -this.ap = p; -this.seqCanvas.addMouseMotionListener (this); -this.seqCanvas.addMouseListener (this); -this.ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet); -this.ssm.addStructureViewerListener (this); -this.ssm.addSelectionListener (this); -this.seqCanvas.repaint (); -}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); -Clazz.defineMethod (c$, "endEditing", -function () { -if (this.editCommand != null && this.editCommand.getSize () > 0) { -this.ap.alignFrame.addHistoryItem (this.editCommand); -this.av.firePropertyChange ("alignment", null, this.av.getAlignment ().getSequences ()); -}this.startseq = -1; -this.lastres = -1; -this.editingSeqs = false; -this.groupEditing = false; -this.keyboardNo1 = null; -this.keyboardNo2 = null; -this.editCommand = null; -}); -Clazz.defineMethod (c$, "setCursorRow", -function () { -this.seqCanvas.cursorY = this.getKeyboardNo1 () - 1; -this.scrollToVisible (); -}); -Clazz.defineMethod (c$, "setCursorColumn", -function () { -this.seqCanvas.cursorX = this.getKeyboardNo1 () - 1; -this.scrollToVisible (); -}); -Clazz.defineMethod (c$, "setCursorRowAndColumn", -function () { -if (this.keyboardNo2 == null) { -this.keyboardNo2 = new StringBuffer (); -} else { -this.seqCanvas.cursorX = this.getKeyboardNo1 () - 1; -this.seqCanvas.cursorY = this.getKeyboardNo2 () - 1; -this.scrollToVisible (); -}}); -Clazz.defineMethod (c$, "setCursorPosition", -function () { -var sequence = this.av.getAlignment ().getSequenceAt (this.seqCanvas.cursorY); -this.seqCanvas.cursorX = sequence.findIndex (this.getKeyboardNo1 ()) - 1; -this.scrollToVisible (); -}); -Clazz.defineMethod (c$, "moveCursor", -function (dx, dy) { -this.seqCanvas.cursorX += dx; -this.seqCanvas.cursorY += dy; -if (this.av.hasHiddenColumns () && !this.av.getColumnSelection ().isVisible (this.seqCanvas.cursorX)) { -var original = this.seqCanvas.cursorX - dx; -var maxWidth = this.av.getAlignment ().getWidth (); -while (!this.av.getColumnSelection ().isVisible (this.seqCanvas.cursorX) && this.seqCanvas.cursorX < maxWidth && this.seqCanvas.cursorX > 0) { -this.seqCanvas.cursorX += dx; -} -if (this.seqCanvas.cursorX >= maxWidth || !this.av.getColumnSelection ().isVisible (this.seqCanvas.cursorX)) { -this.seqCanvas.cursorX = original; -}}this.scrollToVisible (); -}, "~N,~N"); -Clazz.defineMethod (c$, "scrollToVisible", -function () { -if (this.seqCanvas.cursorX < 0) { -this.seqCanvas.cursorX = 0; -} else if (this.seqCanvas.cursorX > this.av.getAlignment ().getWidth () - 1) { -this.seqCanvas.cursorX = this.av.getAlignment ().getWidth () - 1; -}if (this.seqCanvas.cursorY < 0) { -this.seqCanvas.cursorY = 0; -} else if (this.seqCanvas.cursorY > this.av.getAlignment ().getHeight () - 1) { -this.seqCanvas.cursorY = this.av.getAlignment ().getHeight () - 1; -}this.endEditing (); -if (this.av.getWrapAlignment ()) { -this.ap.scrollToWrappedVisible (this.seqCanvas.cursorX); -} else { -while (this.seqCanvas.cursorY < this.av.startSeq) { -this.ap.scrollUp (true); -} -while (this.seqCanvas.cursorY + 1 > this.av.endSeq) { -this.ap.scrollUp (false); -} -while (this.seqCanvas.cursorX < this.av.getColumnSelection ().adjustForHiddenColumns (this.av.startRes)) { -if (!this.ap.scrollRight (false)) { -break; -}} -while (this.seqCanvas.cursorX > this.av.getColumnSelection ().adjustForHiddenColumns (this.av.endRes)) { -if (!this.ap.scrollRight (true)) { -break; -}} -}this.setStatusMessage (this.av.getAlignment ().getSequenceAt (this.seqCanvas.cursorY), this.seqCanvas.cursorX, this.seqCanvas.cursorY); -this.seqCanvas.repaint (); -}); -Clazz.defineMethod (c$, "setSelectionAreaAtCursor", -function (topLeft) { -var sequence = this.av.getAlignment ().getSequenceAt (this.seqCanvas.cursorY); -if (this.av.getSelectionGroup () != null) { -var sg = this.av.getSelectionGroup (); -var min = this.av.getAlignment ().getHeight (); -var max = 0; -for (var i = 0; i < sg.getSize (); i++) { -var index = this.av.getAlignment ().findIndex (sg.getSequenceAt (i)); -if (index > max) { -max = index; -}if (index < min) { -min = index; -}} -max++; -if (topLeft) { -sg.setStartRes (this.seqCanvas.cursorX); -if (sg.getEndRes () < this.seqCanvas.cursorX) { -sg.setEndRes (this.seqCanvas.cursorX); -}min = this.seqCanvas.cursorY; -} else { -sg.setEndRes (this.seqCanvas.cursorX); -if (sg.getStartRes () > this.seqCanvas.cursorX) { -sg.setStartRes (this.seqCanvas.cursorX); -}max = this.seqCanvas.cursorY + 1; -}if (min > max) { -this.av.setSelectionGroup (null); -} else { -sg.clear (); -for (var i = min; i < max; i++) { -sg.addSequence (this.av.getAlignment ().getSequenceAt (i), false); -} -}}if (this.av.getSelectionGroup () == null) { -var sg = new jalview.datamodel.SequenceGroup (); -sg.setStartRes (this.seqCanvas.cursorX); -sg.setEndRes (this.seqCanvas.cursorX); -sg.addSequence (sequence, false); -this.av.setSelectionGroup (sg); -}this.ap.paintAlignment (false); -this.av.sendSelection (); -}, "~B"); -Clazz.defineMethod (c$, "insertGapAtCursor", -function (group) { -this.groupEditing = group; -this.startseq = this.seqCanvas.cursorY; -this.lastres = this.seqCanvas.cursorX; -this.editSequence (true, this.seqCanvas.cursorX + this.getKeyboardNo1 ()); -this.endEditing (); -}, "~B"); -Clazz.defineMethod (c$, "deleteGapAtCursor", -function (group) { -this.groupEditing = group; -this.startseq = this.seqCanvas.cursorY; -this.lastres = this.seqCanvas.cursorX + this.getKeyboardNo1 (); -this.editSequence (false, this.seqCanvas.cursorX); -this.endEditing (); -}, "~B"); -Clazz.defineMethod (c$, "numberPressed", -function (value) { -if (this.keyboardNo1 == null) { -this.keyboardNo1 = new StringBuffer (); -}if (this.keyboardNo2 != null) { -this.keyboardNo2.append (value); -} else { -this.keyboardNo1.append (value); -}}, "~S"); -Clazz.defineMethod (c$, "getKeyboardNo1", -function () { -try { -if (this.keyboardNo1 != null) { -var value = Integer.parseInt (this.keyboardNo1.toString ()); -this.keyboardNo1 = null; -return value; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -} else { -throw x; -} -} -this.keyboardNo1 = null; -return 1; -}); -Clazz.defineMethod (c$, "getKeyboardNo2", -function () { -try { -if (this.keyboardNo2 != null) { -var value = Integer.parseInt (this.keyboardNo2.toString ()); -this.keyboardNo2 = null; -return value; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -} else { -throw x; -} -} -this.keyboardNo2 = null; -return 1; -}); -Clazz.defineMethod (c$, "setStatusMessage", -function (sequence, res, seq) { -var text = new StringBuilder (32); -var seqno = seq == -1 ? "" : " " + (seq + 1); -text.append ("Sequence" + seqno + " ID: " + sequence.getName ()); -var residue = null; -var displayChar = String.valueOf (sequence.getCharAt (res)); -if (this.av.getAlignment ().isNucleotide ()) { -residue = jalview.schemes.ResidueProperties.nucleotideName.get (displayChar); -if (residue != null) { -text.append (" Nucleotide: ").append (residue); -}} else { -residue = "X".equalsIgnoreCase (displayChar) ? "X" : jalview.schemes.ResidueProperties.aa2Triplet.get (displayChar); -if (residue != null) { -text.append (" Residue: ").append (residue); -}}var pos = -1; -if (residue != null) { -pos = sequence.findPosition (res); -text.append (" (").append (Integer.toString (pos)).append (")"); -}this.ap.alignFrame.setStatus (text.toString ()); -}, "jalview.datamodel.SequenceI,~N,~N"); -Clazz.defineMethod (c$, "setStatusMessage", -($fz = function (results) { -var matches = results.getResults (); -if (!matches.isEmpty ()) { -var m = matches.get (0); -var seq = m.getSequence (); -var sequenceIndex = this.av.getAlignment ().findIndex (seq); -var start = m.getStart () - 1; -this.setStatusMessage (seq, start, sequenceIndex); -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SearchResults"); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -this.lastMousePress = evt.getPoint (); -if ((evt.getModifiers () & 8) == 8 && !this.av.MAC) { -this.mouseWheelPressed = true; -return; -}if (evt.isShiftDown () || evt.isControlDown () || evt.isAltDown ()) { -if (evt.isControlDown () || evt.isAltDown ()) { -this.groupEditing = true; -}this.editingSeqs = true; -} else { -this.doMousePressedDefineMode (evt); -return; -}var seq = this.findSeq (evt); -var res = this.findRes (evt); -if (seq < 0 || res < 0) { -return; -}if ((seq < this.av.getAlignment ().getHeight ()) && (res < this.av.getAlignment ().getSequenceAt (seq).getLength ())) { -this.startseq = seq; -this.lastres = res; -} else { -this.startseq = -1; -this.lastres = -1; -}return; -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -var sequence = this.av.getAlignment ().getSequenceAt (this.findSeq (evt)); -if (evt.getClickCount () > 1) { -if (this.av.getSelectionGroup () != null && this.av.getSelectionGroup ().getSize () == 1 && this.av.getSelectionGroup ().getEndRes () - this.av.getSelectionGroup ().getStartRes () < 2) { -this.av.setSelectionGroup (null); -}var features = this.findFeaturesAtRes (sequence, sequence.findPosition (this.findRes (evt))); -if (features != null && features.length > 0) { -var highlight = new jalview.datamodel.SearchResults (); -highlight.addResult (sequence, features[0].getBegin (), features[0].getEnd ()); -this.seqCanvas.highlightSearchResults (highlight); -}if (features != null && features.length > 0) { -this.seqCanvas.getFeatureRenderer ().amendFeatures ( Clazz.newArray (-1, [sequence]), features, false, this.ap); -this.seqCanvas.highlightSearchResults (null); -}}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.mouseDragging = false; -this.mouseWheelPressed = false; -this.ap.paintAlignment (true); -if (!this.editingSeqs) { -this.doMouseReleasedDefineMode (evt); -return; -}this.endEditing (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "findRes", -function (evt) { -var res = 0; -var x = evt.getX (); -if (this.av.getWrapAlignment ()) { -var hgap = this.av.getCharHeight (); -if (this.av.getScaleAboveWrapped ()) { -hgap += this.av.getCharHeight (); -}var cHeight = this.av.getAlignment ().getHeight () * this.av.getCharHeight () + hgap + this.seqCanvas.getAnnotationHeight (); -var y = evt.getY (); -y -= hgap; -x -= this.seqCanvas.LABEL_WEST; -var cwidth = this.seqCanvas.getWrappedCanvasWidth (this.getSize ().width); -if (cwidth < 1) { -return 0; -}this.wrappedBlock = Clazz.doubleToInt (y / cHeight); -this.wrappedBlock += Clazz.doubleToInt (this.av.getStartRes () / cwidth); -res = this.wrappedBlock * cwidth + Clazz.doubleToInt (x / this.av.getCharWidth ()); -} else { -res = (Clazz.doubleToInt (x / this.av.getCharWidth ())) + this.av.getStartRes (); -}if (this.av.hasHiddenColumns ()) { -res = this.av.getColumnSelection ().adjustForHiddenColumns (res); -}return res; -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "findSeq", -function (evt) { -var sqnum = this.findAlRow (evt); -return (sqnum < 0) ? 0 : sqnum; -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "findAlRow", -($fz = function (evt) { -var seq = 0; -var y = evt.getY (); -if (this.av.getWrapAlignment ()) { -var hgap = this.av.getCharHeight (); -if (this.av.getScaleAboveWrapped ()) { -hgap += this.av.getCharHeight (); -}var cHeight = this.av.getAlignment ().getHeight () * this.av.getCharHeight () + hgap + this.seqCanvas.getAnnotationHeight (); -y -= hgap; -seq = Math.min (Clazz.doubleToInt ((y % cHeight) / this.av.getCharHeight ()), this.av.getAlignment ().getHeight () - 1); -if (seq < 0) { -seq = -1; -}} else { -seq = Math.min ((Clazz.doubleToInt (y / this.av.getCharHeight ())) + this.av.getStartSeq (), this.av.getAlignment ().getHeight () - 1); -if (seq < 0) { -seq = -1; -}}return seq; -}, $fz.isPrivate = true, $fz), "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "doMousePressed", -function (evt) { -var seq = this.findSeq (evt); -var res = this.findRes (evt); -if (seq < this.av.getAlignment ().getHeight () && res < this.av.getAlignment ().getSequenceAt (seq).getLength ()) { -this.startseq = seq; -this.lastres = res; -} else { -this.startseq = -1; -this.lastres = -1; -}return; -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseOverSequence", -function (sequence, index, pos) { -var tmp = sequence.hashCode () + index + ""; -if (this.lastMessage == null || !this.lastMessage.equals (tmp)) { -this.ssm.mouseOverSequence (sequence, index, pos, this.av); -}this.lastMessage = tmp; -}, "jalview.datamodel.SequenceI,~N,~N"); -Clazz.overrideMethod (c$, "highlightSequence", -function (results) { -if (this.av.isFollowHighlight ()) { -if (this.ap.scrollToPosition (results, true)) { -this.ap.alignFrame.repaint (); -}}this.setStatusMessage (results); -this.seqCanvas.highlightSearchResults (results); -}, "jalview.datamodel.SearchResults"); -Clazz.overrideMethod (c$, "getVamsasSource", -function () { -return this.ap == null ? null : this.ap.av; -}); -Clazz.overrideMethod (c$, "updateColours", -function (seq, index) { -System.out.println ("update the seqPanel colours"); -}, "jalview.datamodel.SequenceI,~N"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -var res = this.findRes (evt); -var seq = this.findSeq (evt); -if (seq >= this.av.getAlignment ().getHeight () || seq < 0 || res < 0) { -if (this.tooltip != null) { -this.tooltip.setTip (""); -}return; -}var sequence = this.av.getAlignment ().getSequenceAt (seq); -if (res > sequence.getLength ()) { -if (this.tooltip != null) { -this.tooltip.setTip (""); -}return; -}var respos = sequence.findPosition (res); -if (this.ssm != null) { -this.mouseOverSequence (sequence, res, respos); -}var text = new StringBuilder (); -text.append ("Sequence ").append (Integer.toString (seq + 1)).append (" ID: ").append (sequence.getName ()); -var obj = null; -var ch = String.valueOf (sequence.getCharAt (res)); -if (this.av.getAlignment ().isNucleotide ()) { -obj = jalview.schemes.ResidueProperties.nucleotideName.get (ch); -if (obj != null) { -text.append (" Nucleotide: ").append (obj); -}} else { -obj = "X".equalsIgnoreCase (ch) ? "X" : jalview.schemes.ResidueProperties.aa2Triplet.get (ch); -if (obj != null) { -text.append (" Residue: ").append (obj); -}}if (obj != null) { -text.append (" (").append (Integer.toString (respos)).append (")"); -}this.ap.alignFrame.setStatus (text.toString ()); -var tooltipText = new StringBuilder (); -var groups = this.av.getAlignment ().findAllGroups (sequence); -if (groups != null) { -for (var g = 0; g < groups.length; g++) { -if (groups[g].getStartRes () <= res && groups[g].getEndRes () >= res) { -if (!groups[g].getName ().startsWith ("JTreeGroup") && !groups[g].getName ().startsWith ("JGroup")) { -tooltipText.append (groups[g].getName ()).append (" "); -}if (groups[g].getDescription () != null) { -tooltipText.append (groups[g].getDescription ()); -}tooltipText.append ("\n"); -}} -}var allFeatures = this.findFeaturesAtRes (sequence, sequence.findPosition (res)); -var index = 0; -while (index < allFeatures.length) { -var sf = allFeatures[index]; -tooltipText.append (sf.getType () + " " + sf.begin + ":" + sf.end); -if (sf.getDescription () != null) { -tooltipText.append (" " + sf.getDescription ()); -}if (sf.getValue ("status") != null) { -var status = sf.getValue ("status").toString (); -if (status.length > 0) { -tooltipText.append (" (" + sf.getValue ("status") + ")"); -}}tooltipText.append ("\n"); -index++; -} -if (this.tooltip == null) { -this.tooltip = new jalview.appletgui.Tooltip (tooltipText.toString (), this.seqCanvas); -} else { -this.tooltip.setTip (tooltipText.toString ()); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "findFeaturesAtRes", -function (sequence, res) { -var tmp = new java.util.Vector (); -var features = sequence.getSequenceFeatures (); -if (features != null) { -for (var i = 0; i < features.length; i++) { -if (this.av.getFeaturesDisplayed () == null || !this.av.getFeaturesDisplayed ().isVisible (features[i].getType ())) { -continue; -}if (features[i].featureGroup != null && !this.seqCanvas.fr.checkGroupVisibility (features[i].featureGroup, false)) { -continue; -}if ((features[i].getBegin () <= res) && (features[i].getEnd () >= res)) { -tmp.addElement (features[i]); -}} -}features = new Array (tmp.size ()); -tmp.copyInto (features); -return features; -}, "jalview.datamodel.SequenceI,~N"); -Clazz.overrideMethod (c$, "mouseDragged", -function (evt) { -if (this.mouseWheelPressed) { -var oldWidth = this.av.getCharWidth (); -if (Math.abs (evt.getY () - this.lastMousePress.y) > Math.abs (evt.getX () - this.lastMousePress.x)) { -var fontSize = this.av.font.getSize (); -if (evt.getY () < this.lastMousePress.y && this.av.getCharHeight () > 1) { -fontSize--; -} else if (evt.getY () > this.lastMousePress.y) { -fontSize++; -}if (fontSize < 1) { -fontSize = 1; -}this.av.setFont ( new java.awt.Font (this.av.font.getName (), this.av.font.getStyle (), fontSize)); -this.av.setCharWidth (oldWidth); -} else { -if (evt.getX () < this.lastMousePress.x && this.av.getCharWidth () > 1) { -this.av.setCharWidth (this.av.getCharWidth () - 1); -} else if (evt.getX () > this.lastMousePress.x) { -this.av.setCharWidth (this.av.getCharWidth () + 1); -}if (this.av.getCharWidth () < 1) { -this.av.setCharWidth (1); -}}this.ap.fontChanged (); -var fm = this.getFontMetrics (this.av.getFont ()); -this.av.validCharWidth = fm.charWidth ('M') <= this.av.getCharWidth (); -this.lastMousePress = evt.getPoint (); -this.ap.paintAlignment (false); -this.ap.annotationPanel.image = null; -return; -}if (!this.editingSeqs) { -this.doMouseDraggedDefineMode (evt); -return; -}var res = this.findRes (evt); -if (res < 0) { -res = 0; -}if ((this.lastres == -1) || (this.lastres == res)) { -return; -}if ((res < this.av.getAlignment ().getWidth ()) && (res < this.lastres)) { -this.editSequence (false, res); -} else { -this.editSequence (true, res); -}this.mouseDragging = true; -if (this.scrollThread != null) { -this.scrollThread.setEvent (evt); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "editSequence", -function (insertGap, startres) { -var fixedLeft = -1; -var fixedRight = -1; -var fixedColumns = false; -var sg = this.av.getSelectionGroup (); -var seq = this.av.getAlignment ().getSequenceAt (this.startseq); -if (!this.groupEditing && this.av.hasHiddenRows ()) { -if (this.av.isHiddenRepSequence (seq)) { -sg = this.av.getRepresentedSequences (seq); -this.groupEditing = true; -}}var message = new StringBuffer (); -if (this.groupEditing) { -message.append (jalview.util.MessageManager.getString ("action.edit_group")).append (":"); -if (this.editCommand == null) { -this.editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.edit_group")); -}} else { -message.append (jalview.util.MessageManager.getString ("label.edit_sequence")).append (" " + seq.getName ()); -var label = seq.getName (); -if (label.length > 10) { -label = label.substring (0, 10); -}if (this.editCommand == null) { -this.editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.formatMessage ("label.edit_params", Clazz.newArray (-1, [label]))); -}}if (insertGap) { -message.append (" insert "); -} else { -message.append (" delete "); -}message.append (Math.abs (startres - this.lastres) + " gaps."); -this.ap.alignFrame.setStatus (message.toString ()); -if (this.groupEditing || (sg != null && sg.getSequences (this.av.getHiddenRepSequences ()).contains (seq))) { -fixedColumns = true; -if (sg == null) { -if (!this.av.isHiddenRepSequence (seq)) { -this.endEditing (); -return; -}sg = this.av.getRepresentedSequences (seq); -}fixedLeft = sg.getStartRes (); -fixedRight = sg.getEndRes (); -if ((startres < fixedLeft && this.lastres >= fixedLeft) || (startres >= fixedLeft && this.lastres < fixedLeft) || (startres > fixedRight && this.lastres <= fixedRight) || (startres <= fixedRight && this.lastres > fixedRight)) { -this.endEditing (); -return; -}if (fixedLeft > startres) { -fixedRight = fixedLeft - 1; -fixedLeft = 0; -} else if (fixedRight < startres) { -fixedLeft = fixedRight; -fixedRight = -1; -}}if (this.av.hasHiddenColumns ()) { -fixedColumns = true; -var y1 = this.av.getColumnSelection ().getHiddenBoundaryLeft (startres); -var y2 = this.av.getColumnSelection ().getHiddenBoundaryRight (startres); -if ((insertGap && startres > y1 && this.lastres < y1) || (!insertGap && startres < y2 && this.lastres > y2)) { -this.endEditing (); -return; -}if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) { -if (startres >= y2) { -fixedLeft = y2; -} else { -fixedRight = y2 - 1; -}}}if (this.groupEditing) { -var groupSeqs = sg.getSequences (this.av.getHiddenRepSequences ()).toArray ( new Array (0)); -if (insertGap) { -if (sg.getStartRes () == 0 && sg.getEndRes () == fixedRight && sg.getEndRes () == this.av.getAlignment ().getWidth () - 1) { -sg.setEndRes (this.av.getAlignment ().getWidth () + startres - this.lastres); -fixedRight = sg.getEndRes (); -}var blank = false; -for (fixedRight = fixedRight; fixedRight > this.lastres; fixedRight--) { -blank = true; -for (var gs, $gs = 0, $$gs = groupSeqs; $gs < $$gs.length && ((gs = $$gs[$gs]) || true); $gs++) { -for (var j = 0; j < startres - this.lastres; j++) { -if (!jalview.util.Comparison.isGap (gs.getCharAt (fixedRight - j))) { -blank = false; -break; -}} -} -if (blank) { -break; -}} -if (!blank) { -if (sg.getSize () == this.av.getAlignment ().getHeight ()) { -if ((this.av.hasHiddenColumns () && startres < this.av.getColumnSelection ().getHiddenBoundaryRight (startres))) { -this.endEditing (); -return; -}var alWidth = this.av.getAlignment ().getWidth (); -if (this.av.hasHiddenRows ()) { -var hwidth = this.av.getAlignment ().getHiddenSequences ().getWidth (); -if (hwidth > alWidth) { -alWidth = hwidth; -}}sg.setEndRes (sg.getEndRes () + startres - this.lastres); -fixedRight = alWidth + startres - this.lastres; -} else { -this.endEditing (); -return; -}}} else if (!insertGap) { -for (var gs, $gs = 0, $$gs = groupSeqs; $gs < $$gs.length && ((gs = $$gs[$gs]) || true); $gs++) { -for (var j = startres; j < this.lastres; j++) { -if (gs.getLength () <= j) { -continue; -}if (!jalview.util.Comparison.isGap (gs.getCharAt (j))) { -this.endEditing (); -return; -}} -} -}if (insertGap) { -if (fixedColumns && fixedRight != -1) { -for (var j = this.lastres; j < startres; j++) { -this.insertChar (j, groupSeqs, fixedRight); -} -} else { -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, groupSeqs, startres, startres - this.lastres, this.av.getAlignment (), true); -}} else { -if (fixedColumns && fixedRight != -1) { -for (var j = this.lastres; j > startres; j--) { -this.deleteChar (startres, groupSeqs, fixedRight); -} -} else { -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, groupSeqs, startres, this.lastres - startres, this.av.getAlignment (), true); -}}} else { -if (insertGap) { -if (fixedColumns && fixedRight != -1) { -for (var j = this.lastres; j < startres; j++) { -this.insertChar (j, Clazz.newArray (-1, [seq]), fixedRight); -} -} else { -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, Clazz.newArray (-1, [seq]), this.lastres, startres - this.lastres, this.av.getAlignment (), true); -}} else { -if (fixedColumns && fixedRight != -1) { -for (var j = this.lastres; j > startres; j--) { -if (!jalview.util.Comparison.isGap (seq.getCharAt (startres))) { -this.endEditing (); -break; -}this.deleteChar (startres, Clazz.newArray (-1, [seq]), fixedRight); -} -} else { -var max = 0; -for (var m = startres; m < this.lastres; m++) { -if (!jalview.util.Comparison.isGap (seq.getCharAt (m))) { -break; -}max++; -} -if (max > 0) { -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, Clazz.newArray (-1, [seq]), startres, max, this.av.getAlignment (), true); -}}}}this.lastres = startres; -this.seqCanvas.repaint (); -}, "~B,~N"); -Clazz.defineMethod (c$, "insertChar", -function (j, seq, fixedColumn) { -var blankColumn = fixedColumn; -for (var s = 0; s < seq.length; s++) { -for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { -if (jalview.util.Comparison.isGap (seq[s].getCharAt (blankColumn))) { -break; -}} -if (blankColumn <= j) { -blankColumn = fixedColumn; -this.endEditing (); -return; -}} -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seq, blankColumn, 1, this.av.getAlignment (), true); -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, seq, j, 1, this.av.getAlignment (), true); -}, "~N,~A,~N"); -Clazz.defineMethod (c$, "deleteChar", -function (j, seq, fixedColumn) { -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seq, j, 1, this.av.getAlignment (), true); -this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, seq, fixedColumn, 1, this.av.getAlignment (), true); -}, "~N,~A,~N"); -Clazz.defineMethod (c$, "doMousePressedDefineMode", -function (evt) { -if (this.scrollThread != null) { -this.scrollThread.running = false; -this.scrollThread = null; -}var res = this.findRes (evt); -var seq = this.findSeq (evt); -this.oldSeq = seq; -this.startWrapBlock = this.wrappedBlock; -if (seq == -1) { -return; -}var sequence = this.av.getAlignment ().getSequenceAt (seq); -if (sequence == null || res > sequence.getLength ()) { -return; -}this.stretchGroup = this.av.getSelectionGroup (); -if (this.stretchGroup == null) { -this.stretchGroup = this.av.getAlignment ().findGroup (sequence); -if (this.stretchGroup != null && res > this.stretchGroup.getStartRes () && res < this.stretchGroup.getEndRes ()) { -this.av.setSelectionGroup (this.stretchGroup); -} else { -this.stretchGroup = null; -}} else if (!this.stretchGroup.getSequences (null).contains (sequence) || this.stretchGroup.getStartRes () > res || this.stretchGroup.getEndRes () < res) { -this.stretchGroup = null; -var allGroups = this.av.getAlignment ().findAllGroups (sequence); -if (allGroups != null) { -for (var i = 0; i < allGroups.length; i++) { -if (allGroups[i].getStartRes () <= res && allGroups[i].getEndRes () >= res) { -this.stretchGroup = allGroups[i]; -break; -}} -}this.av.setSelectionGroup (this.stretchGroup); -}if ((evt.getModifiers () & 4) == 4) { -var allFeatures = this.findFeaturesAtRes (sequence, sequence.findPosition (res)); -var links = null; -if (allFeatures != null) { -for (var i = 0; i < allFeatures.length; i++) { -if (allFeatures[i].links != null) { -if (links == null) { -links = new java.util.Vector (); -}for (var j = 0; j < allFeatures[i].links.size (); j++) { -links.addElement (allFeatures[i].links.elementAt (j)); -} -}} -}var popup = new jalview.appletgui.APopupMenu (this.ap, null, links); -this.add (popup); -popup.show (this, evt.getX (), evt.getY ()); -return; -}if (this.av.cursorMode) { -this.seqCanvas.cursorX = this.findRes (evt); -this.seqCanvas.cursorY = this.findSeq (evt); -this.seqCanvas.repaint (); -return; -}if (this.stretchGroup == null) { -var sg = new jalview.datamodel.SequenceGroup (); -sg.setStartRes (res); -sg.setEndRes (res); -sg.addSequence (sequence, false); -this.av.setSelectionGroup (sg); -this.stretchGroup = sg; -if (this.av.getConservationSelected ()) { -jalview.appletgui.SliderPanel.setConservationSlider (this.ap, this.av.getGlobalColourScheme (), "Background"); -}if (this.av.getAbovePIDThreshold ()) { -jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, this.av.getGlobalColourScheme (), "Background"); -}}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "doMouseReleasedDefineMode", -function (evt) { -if (this.stretchGroup == null) { -return; -}this.stretchGroup.recalcConservation (); -if (this.stretchGroup.cs != null) { -this.stretchGroup.cs.alignmentChanged (this.stretchGroup, this.av.getHiddenRepSequences ()); -if (this.stretchGroup.cs.conservationApplied ()) { -jalview.appletgui.SliderPanel.setConservationSlider (this.ap, this.stretchGroup.cs, this.stretchGroup.getName ()); -} else { -jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, this.stretchGroup.cs, this.stretchGroup.getName ()); -}}this.changeEndRes = false; -this.changeStartRes = false; -this.stretchGroup = null; -jalview.appletgui.PaintRefresher.Refresh (this.ap, this.av.getSequenceSetId ()); -this.ap.paintAlignment (true); -this.av.sendSelection (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "doMouseDraggedDefineMode", -function (evt) { -var res = this.findRes (evt); -var y = this.findSeq (evt); -if (this.wrappedBlock != this.startWrapBlock) { -return; -}if (this.stretchGroup == null) { -return; -}this.mouseDragging = true; -if (y > this.av.getAlignment ().getHeight ()) { -y = this.av.getAlignment ().getHeight () - 1; -}if (res >= this.av.getAlignment ().getWidth ()) { -res = this.av.getAlignment ().getWidth () - 1; -}if (this.stretchGroup.getEndRes () == res) { -this.changeEndRes = true; -} else if (this.stretchGroup.getStartRes () == res) { -this.changeStartRes = true; -}if (res < 0) { -res = 0; -}if (this.changeEndRes) { -if (res > (this.stretchGroup.getStartRes () - 1)) { -this.stretchGroup.setEndRes (res); -}} else if (this.changeStartRes) { -if (res < (this.stretchGroup.getEndRes () + 1)) { -this.stretchGroup.setStartRes (res); -}}var dragDirection = 0; -if (y > this.oldSeq) { -dragDirection = 1; -} else if (y < this.oldSeq) { -dragDirection = -1; -}while ((y != this.oldSeq) && (this.oldSeq > -1) && (y < this.av.getAlignment ().getHeight ())) { -var seq = this.av.getAlignment ().getSequenceAt (this.oldSeq); -this.oldSeq += dragDirection; -if (this.oldSeq < 0) { -break; -}var nextSeq = this.av.getAlignment ().getSequenceAt (this.oldSeq); -if (this.stretchGroup.getSequences (null).contains (nextSeq)) { -this.stretchGroup.deleteSequence (seq, false); -} else { -if (seq != null) { -this.stretchGroup.addSequence (seq, false); -}this.stretchGroup.addSequence (nextSeq, false); -}} -if (this.oldSeq < 0) { -this.oldSeq = -1; -}if (res > this.av.endRes || res < this.av.startRes || y < this.av.startSeq || y > this.av.endSeq) { -this.mouseExited (evt); -}if (this.scrollThread != null) { -this.scrollThread.setEvent (evt); -}this.seqCanvas.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (e) { -if (this.oldSeq < 0) { -this.oldSeq = 0; -}if (this.scrollThread != null) { -this.scrollThread.running = false; -this.scrollThread = null; -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (e) { -if (this.av.getWrapAlignment ()) { -return; -}if (this.mouseDragging && this.scrollThread == null) { -this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.SeqPanel.ScrollThread, this, null); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "scrollCanvas", -function (evt) { -if (evt == null) { -if (this.scrollThread != null) { -this.scrollThread.running = false; -this.scrollThread = null; -}this.mouseDragging = false; -} else { -if (this.scrollThread == null) { -this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.SeqPanel.ScrollThread, this, null); -}this.mouseDragging = true; -this.scrollThread.setEvent (evt); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "selection", -function (seqsel, colsel, source) { -if (this.av != null && (this.av === source || !this.av.followSelection || (Clazz.instanceOf (source, jalview.appletgui.AlignViewport) && (source).getSequenceSetId ().equals (this.av.getSequenceSetId ())))) { -return; -}if (this.selectionFromTranslation (seqsel, colsel, source)) { -return; -}var repaint = false; -var copycolsel = true; -if (this.av.getSelectionGroup () == null || !this.av.isSelectionGroupChanged (true)) { -var sgroup = null; -if (seqsel != null && seqsel.getSize () > 0) { -if (this.av.getAlignment () == null) { -System.out.println ("Selection message: alignviewport av SeqSetId=" + this.av.getSequenceSetId () + " ViewId=" + this.av.getViewId () + " 's alignment is NULL! returning immediatly."); -return; -}sgroup = seqsel.intersect (this.av.getAlignment (), (this.av.hasHiddenRows ()) ? this.av.getHiddenRepSequences () : null); -if ((sgroup == null || sgroup.getSize () == 0) && (colsel == null || colsel.size () == 0)) { -copycolsel = false; -}}if (sgroup != null && sgroup.getSize () > 0) { -this.av.setSelectionGroup (sgroup); -} else { -this.av.setSelectionGroup (null); -}repaint = this.av.isSelectionGroupChanged (true); -}if (copycolsel && (this.av.getColumnSelection () == null || !this.av.isColSelChanged (true))) { -if (colsel == null || colsel.size () == 0) { -if (this.av.getColumnSelection () != null) { -this.av.getColumnSelection ().clear (); -}} else { -if (this.av.getColumnSelection () == null) { -this.av.setColumnSelection ( new jalview.datamodel.ColumnSelection (colsel)); -} else { -this.av.getColumnSelection ().setElementsFrom (colsel); -}}repaint = new Boolean (repaint | this.av.isColSelChanged (true)).valueOf (); -}if (copycolsel && this.av.hasHiddenColumns () && (this.av.getColumnSelection () == null || this.av.getColumnSelection ().getHiddenColumns () == null)) { -System.err.println ("Bad things"); -}if (repaint) { -this.ap.scalePanelHolder.repaint (); -this.ap.repaint (); -}}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); -Clazz.defineMethod (c$, "scrollTo", -function (row, column) { -row = row < 0 ? this.ap.av.startSeq : row; -column = column < 0 ? this.ap.av.startRes : column; -this.ap.scrollTo (column, column, row, true, true); -}, "~N,~N"); -Clazz.defineMethod (c$, "scrollToRow", -function (row) { -row = row < 0 ? this.ap.av.startSeq : row; -this.ap.scrollTo (this.ap.av.startRes, this.ap.av.startRes, row, true, true); -}, "~N"); -Clazz.defineMethod (c$, "scrollToColumn", -function (column) { -column = column < 0 ? this.ap.av.startRes : column; -this.ap.scrollTo (column, column, this.ap.av.startSeq, true, true); -}, "~N"); -Clazz.defineMethod (c$, "selectionFromTranslation", -function (seqsel, colsel, source) { -if (!(Clazz.instanceOf (source, jalview.api.AlignViewportI))) { -return false; -}var sourceAv = source; -if (sourceAv.getCodingComplement () !== this.av && this.av.getCodingComplement () !== sourceAv) { -return false; -}var sg = jalview.util.MappingUtils.mapSequenceGroup (seqsel, sourceAv, this.av); -this.av.setSelectionGroup (sg); -this.av.isSelectionGroupChanged (true); -var cs = jalview.util.MappingUtils.mapColumnSelection (colsel, sourceAv, this.av); -this.av.setColumnSelection (cs); -this.av.isColSelChanged (true); -this.ap.scalePanelHolder.repaint (); -this.ap.repaint (); -return true; -}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); -c$.$SeqPanel$ScrollThread$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.evt = null; -this.running = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.SeqPanel, "ScrollThread", Thread); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.appletgui.SeqPanel.ScrollThread, []); -this.start (); -}); -Clazz.defineMethod (c$, "setEvent", -function (a) { -this.evt = a; -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "stopScrolling", -function () { -this.running = false; -}); -Clazz.overrideMethod (c$, "run", -function () { -this.running = true; -while (this.running) { -if (this.evt != null) { -if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getY () < 0 && this.b$["jalview.appletgui.SeqPanel"].av.getStartSeq () > 0) { -this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollUp (true); -}if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getY () >= this.b$["jalview.appletgui.SeqPanel"].getSize ().height && this.b$["jalview.appletgui.SeqPanel"].av.getAlignment ().getHeight () > this.b$["jalview.appletgui.SeqPanel"].av.getEndSeq ()) { -this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollUp (false); -}if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getX () < 0) { -this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollRight (false); -} else if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getX () >= this.b$["jalview.appletgui.SeqPanel"].getSize ().width) { -this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollRight (true); -}}try { -Thread.sleep (75); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -} -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "jalview.structure.SelectionListener", "$.SequenceListener", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.lang.Thread"], "jalview.appletgui.SeqPanel", ["jalview.api.AlignViewportI", "jalview.appletgui.APopupMenu", "$.AlignViewport", "$.PaintRefresher", "$.SeqCanvas", "$.SliderPanel", "$.Tooltip", "jalview.commands.EditCommand", "jalview.datamodel.ColumnSelection", "$.SearchResults", "$.SequenceGroup", "jalview.schemes.ResidueProperties", "jalview.structure.StructureSelectionManager", "jalview.util.Comparison", "$.MappingUtils", "$.MessageManager", "java.awt.BorderLayout", "$.Font", "java.lang.StringBuffer", "$.StringBuilder", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.seqCanvas = null; +this.ap = null; +this.lastres = 0; +this.startseq = 0; +this.av = null; +this.seqEditOccurred = false; +this.scrollThread = null; +this.mouseDragging = false; +this.editingSeqs = false; +this.groupEditing = false; +this.oldSeq = -1; +this.changeEndSeq = false; +this.changeStartSeq = false; +this.changeEndRes = false; +this.changeStartRes = false; +this.stretchGroup = null; +this.keyboardNo1 = null; +this.keyboardNo2 = null; +this.mouseWheelPressed = false; +this.lastMousePress = null; +this.editCommand = null; +this.ssm = null; +this.startWrapBlock = -1; +this.wrappedBlock = -1; +this.lastMessage = null; +this.tooltip = null; +if (!Clazz.isClassDefined ("jalview.appletgui.SeqPanel.ScrollThread")) { +jalview.appletgui.SeqPanel.$SeqPanel$ScrollThread$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "SeqPanel", awt2swing.Panel, [java.awt.event.MouseMotionListener, java.awt.event.MouseListener, jalview.structure.SequenceListener, jalview.structure.SelectionListener]); +Clazz.makeConstructor (c$, +function (avp, p) { +Clazz.superConstructor (this, jalview.appletgui.SeqPanel, []); +this.av = avp; +this.setName ("seqPanel"); +this.seqCanvas = new jalview.appletgui.SeqCanvas (avp); +this.setLayout ( new java.awt.BorderLayout ()); +this.add (this.seqCanvas); +this.ap = p; +this.seqCanvas.addMouseMotionListener (this); +this.seqCanvas.addMouseListener (this); +this.ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.av.applet); +this.ssm.addStructureViewerListener (this); +this.ssm.addSelectionListener (this); +this.seqCanvas.repaint (); +}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel"); +Clazz.defineMethod (c$, "endEditing", +function () { +if (this.editCommand != null && this.editCommand.getSize () > 0) { +this.ap.alignFrame.addHistoryItem (this.editCommand); +this.av.firePropertyChange ("alignment", null, this.av.getAlignment ().getSequences ()); +}this.startseq = -1; +this.lastres = -1; +this.editingSeqs = false; +this.groupEditing = false; +this.keyboardNo1 = null; +this.keyboardNo2 = null; +this.editCommand = null; +}); +Clazz.defineMethod (c$, "setCursorRow", +function () { +this.seqCanvas.cursorY = this.getKeyboardNo1 () - 1; +this.scrollToVisible (); +}); +Clazz.defineMethod (c$, "setCursorColumn", +function () { +this.seqCanvas.cursorX = this.getKeyboardNo1 () - 1; +this.scrollToVisible (); +}); +Clazz.defineMethod (c$, "setCursorRowAndColumn", +function () { +if (this.keyboardNo2 == null) { +this.keyboardNo2 = new StringBuffer (); +} else { +this.seqCanvas.cursorX = this.getKeyboardNo1 () - 1; +this.seqCanvas.cursorY = this.getKeyboardNo2 () - 1; +this.scrollToVisible (); +}}); +Clazz.defineMethod (c$, "setCursorPosition", +function () { +var sequence = this.av.getAlignment ().getSequenceAt (this.seqCanvas.cursorY); +this.seqCanvas.cursorX = sequence.findIndex (this.getKeyboardNo1 ()) - 1; +this.scrollToVisible (); +}); +Clazz.defineMethod (c$, "moveCursor", +function (dx, dy) { +this.seqCanvas.cursorX += dx; +this.seqCanvas.cursorY += dy; +if (this.av.hasHiddenColumns () && !this.av.getColumnSelection ().isVisible (this.seqCanvas.cursorX)) { +var original = this.seqCanvas.cursorX - dx; +var maxWidth = this.av.getAlignment ().getWidth (); +while (!this.av.getColumnSelection ().isVisible (this.seqCanvas.cursorX) && this.seqCanvas.cursorX < maxWidth && this.seqCanvas.cursorX > 0) { +this.seqCanvas.cursorX += dx; +} +if (this.seqCanvas.cursorX >= maxWidth || !this.av.getColumnSelection ().isVisible (this.seqCanvas.cursorX)) { +this.seqCanvas.cursorX = original; +}}this.scrollToVisible (); +}, "~N,~N"); +Clazz.defineMethod (c$, "scrollToVisible", +function () { +if (this.seqCanvas.cursorX < 0) { +this.seqCanvas.cursorX = 0; +} else if (this.seqCanvas.cursorX > this.av.getAlignment ().getWidth () - 1) { +this.seqCanvas.cursorX = this.av.getAlignment ().getWidth () - 1; +}if (this.seqCanvas.cursorY < 0) { +this.seqCanvas.cursorY = 0; +} else if (this.seqCanvas.cursorY > this.av.getAlignment ().getHeight () - 1) { +this.seqCanvas.cursorY = this.av.getAlignment ().getHeight () - 1; +}this.endEditing (); +if (this.av.getWrapAlignment ()) { +this.ap.scrollToWrappedVisible (this.seqCanvas.cursorX); +} else { +while (this.seqCanvas.cursorY < this.av.startSeq) { +this.ap.scrollUp (true); +} +while (this.seqCanvas.cursorY + 1 > this.av.endSeq) { +this.ap.scrollUp (false); +} +while (this.seqCanvas.cursorX < this.av.getColumnSelection ().adjustForHiddenColumns (this.av.startRes)) { +if (!this.ap.scrollRight (false)) { +break; +}} +while (this.seqCanvas.cursorX > this.av.getColumnSelection ().adjustForHiddenColumns (this.av.endRes)) { +if (!this.ap.scrollRight (true)) { +break; +}} +}this.setStatusMessage (this.av.getAlignment ().getSequenceAt (this.seqCanvas.cursorY), this.seqCanvas.cursorX, this.seqCanvas.cursorY); +this.seqCanvas.repaint (); +}); +Clazz.defineMethod (c$, "setSelectionAreaAtCursor", +function (topLeft) { +var sequence = this.av.getAlignment ().getSequenceAt (this.seqCanvas.cursorY); +if (this.av.getSelectionGroup () != null) { +var sg = this.av.getSelectionGroup (); +var min = this.av.getAlignment ().getHeight (); +var max = 0; +for (var i = 0; i < sg.getSize (); i++) { +var index = this.av.getAlignment ().findIndex (sg.getSequenceAt (i)); +if (index > max) { +max = index; +}if (index < min) { +min = index; +}} +max++; +if (topLeft) { +sg.setStartRes (this.seqCanvas.cursorX); +if (sg.getEndRes () < this.seqCanvas.cursorX) { +sg.setEndRes (this.seqCanvas.cursorX); +}min = this.seqCanvas.cursorY; +} else { +sg.setEndRes (this.seqCanvas.cursorX); +if (sg.getStartRes () > this.seqCanvas.cursorX) { +sg.setStartRes (this.seqCanvas.cursorX); +}max = this.seqCanvas.cursorY + 1; +}if (min > max) { +this.av.setSelectionGroup (null); +} else { +sg.clear (); +for (var i = min; i < max; i++) { +sg.addSequence (this.av.getAlignment ().getSequenceAt (i), false); +} +}}if (this.av.getSelectionGroup () == null) { +var sg = new jalview.datamodel.SequenceGroup (); +sg.setStartRes (this.seqCanvas.cursorX); +sg.setEndRes (this.seqCanvas.cursorX); +sg.addSequence (sequence, false); +this.av.setSelectionGroup (sg); +}this.ap.paintAlignment (false); +this.av.sendSelection (); +}, "~B"); +Clazz.defineMethod (c$, "insertGapAtCursor", +function (group) { +this.groupEditing = group; +this.startseq = this.seqCanvas.cursorY; +this.lastres = this.seqCanvas.cursorX; +this.editSequence (true, this.seqCanvas.cursorX + this.getKeyboardNo1 ()); +this.endEditing (); +}, "~B"); +Clazz.defineMethod (c$, "deleteGapAtCursor", +function (group) { +this.groupEditing = group; +this.startseq = this.seqCanvas.cursorY; +this.lastres = this.seqCanvas.cursorX + this.getKeyboardNo1 (); +this.editSequence (false, this.seqCanvas.cursorX); +this.endEditing (); +}, "~B"); +Clazz.defineMethod (c$, "numberPressed", +function (value) { +if (this.keyboardNo1 == null) { +this.keyboardNo1 = new StringBuffer (); +}if (this.keyboardNo2 != null) { +this.keyboardNo2.append (value); +} else { +this.keyboardNo1.append (value); +}}, "~S"); +Clazz.defineMethod (c$, "getKeyboardNo1", +function () { +try { +if (this.keyboardNo1 != null) { +var value = Integer.parseInt (this.keyboardNo1.toString ()); +this.keyboardNo1 = null; +return value; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +} else { +throw x; +} +} +this.keyboardNo1 = null; +return 1; +}); +Clazz.defineMethod (c$, "getKeyboardNo2", +function () { +try { +if (this.keyboardNo2 != null) { +var value = Integer.parseInt (this.keyboardNo2.toString ()); +this.keyboardNo2 = null; +return value; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +} else { +throw x; +} +} +this.keyboardNo2 = null; +return 1; +}); +Clazz.defineMethod (c$, "setStatusMessage", +function (sequence, res, seq) { +var text = new StringBuilder (32); +var seqno = seq == -1 ? "" : " " + (seq + 1); +text.append ("Sequence" + seqno + " ID: " + sequence.getName ()); +var residue = null; +var displayChar = String.valueOf (sequence.getCharAt (res)); +if (this.av.getAlignment ().isNucleotide ()) { +residue = jalview.schemes.ResidueProperties.nucleotideName.get (displayChar); +if (residue != null) { +text.append (" Nucleotide: ").append (residue); +}} else { +residue = "X".equalsIgnoreCase (displayChar) ? "X" : jalview.schemes.ResidueProperties.aa2Triplet.get (displayChar); +if (residue != null) { +text.append (" Residue: ").append (residue); +}}var pos = -1; +if (residue != null) { +pos = sequence.findPosition (res); +text.append (" (").append (Integer.toString (pos)).append (")"); +}this.ap.alignFrame.setStatus (text.toString ()); +}, "jalview.datamodel.SequenceI,~N,~N"); +Clazz.defineMethod (c$, "setStatusMessage", +($fz = function (results) { +var matches = results.getResults (); +if (!matches.isEmpty ()) { +var m = matches.get (0); +var seq = m.getSequence (); +var sequenceIndex = this.av.getAlignment ().findIndex (seq); +var start = m.getStart () - 1; +this.setStatusMessage (seq, start, sequenceIndex); +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SearchResults"); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +this.lastMousePress = evt.getPoint (); +if ((evt.getModifiers () & 8) == 8 && !this.av.MAC) { +this.mouseWheelPressed = true; +return; +}if (evt.isShiftDown () || evt.isControlDown () || evt.isAltDown ()) { +if (evt.isControlDown () || evt.isAltDown ()) { +this.groupEditing = true; +}this.editingSeqs = true; +} else { +this.doMousePressedDefineMode (evt); +return; +}var seq = this.findSeq (evt); +var res = this.findRes (evt); +if (seq < 0 || res < 0) { +return; +}if ((seq < this.av.getAlignment ().getHeight ()) && (res < this.av.getAlignment ().getSequenceAt (seq).getLength ())) { +this.startseq = seq; +this.lastres = res; +} else { +this.startseq = -1; +this.lastres = -1; +}return; +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +var sequence = this.av.getAlignment ().getSequenceAt (this.findSeq (evt)); +if (evt.getClickCount () > 1) { +if (this.av.getSelectionGroup () != null && this.av.getSelectionGroup ().getSize () == 1 && this.av.getSelectionGroup ().getEndRes () - this.av.getSelectionGroup ().getStartRes () < 2) { +this.av.setSelectionGroup (null); +}var features = this.findFeaturesAtRes (sequence, sequence.findPosition (this.findRes (evt))); +if (features != null && features.length > 0) { +var highlight = new jalview.datamodel.SearchResults (); +highlight.addResult (sequence, features[0].getBegin (), features[0].getEnd ()); +this.seqCanvas.highlightSearchResults (highlight); +}if (features != null && features.length > 0) { +this.seqCanvas.getFeatureRenderer ().amendFeatures ( Clazz.newArray (-1, [sequence]), features, false, this.ap); +this.seqCanvas.highlightSearchResults (null); +}}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.mouseDragging = false; +this.mouseWheelPressed = false; +this.ap.paintAlignment (true); +if (!this.editingSeqs) { +this.doMouseReleasedDefineMode (evt); +return; +}this.endEditing (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "findRes", +function (evt) { +var res = 0; +var x = evt.getX (); +if (this.av.getWrapAlignment ()) { +var hgap = this.av.getCharHeight (); +if (this.av.getScaleAboveWrapped ()) { +hgap += this.av.getCharHeight (); +}var cHeight = this.av.getAlignment ().getHeight () * this.av.getCharHeight () + hgap + this.seqCanvas.getAnnotationHeight (); +var y = evt.getY (); +y -= hgap; +x -= this.seqCanvas.LABEL_WEST; +var cwidth = this.seqCanvas.getWrappedCanvasWidth (this.getSize ().width); +if (cwidth < 1) { +return 0; +}this.wrappedBlock = Clazz.doubleToInt (y / cHeight); +this.wrappedBlock += Clazz.doubleToInt (this.av.getStartRes () / cwidth); +res = this.wrappedBlock * cwidth + Clazz.doubleToInt (x / this.av.getCharWidth ()); +} else { +res = (Clazz.doubleToInt (x / this.av.getCharWidth ())) + this.av.getStartRes (); +}if (this.av.hasHiddenColumns ()) { +res = this.av.getColumnSelection ().adjustForHiddenColumns (res); +}return res; +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "findSeq", +function (evt) { +var sqnum = this.findAlRow (evt); +return (sqnum < 0) ? 0 : sqnum; +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "findAlRow", +($fz = function (evt) { +var seq = 0; +var y = evt.getY (); +if (this.av.getWrapAlignment ()) { +var hgap = this.av.getCharHeight (); +if (this.av.getScaleAboveWrapped ()) { +hgap += this.av.getCharHeight (); +}var cHeight = this.av.getAlignment ().getHeight () * this.av.getCharHeight () + hgap + this.seqCanvas.getAnnotationHeight (); +y -= hgap; +seq = Math.min (Clazz.doubleToInt ((y % cHeight) / this.av.getCharHeight ()), this.av.getAlignment ().getHeight () - 1); +if (seq < 0) { +seq = -1; +}} else { +seq = Math.min ((Clazz.doubleToInt (y / this.av.getCharHeight ())) + this.av.getStartSeq (), this.av.getAlignment ().getHeight () - 1); +if (seq < 0) { +seq = -1; +}}return seq; +}, $fz.isPrivate = true, $fz), "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "doMousePressed", +function (evt) { +var seq = this.findSeq (evt); +var res = this.findRes (evt); +if (seq < this.av.getAlignment ().getHeight () && res < this.av.getAlignment ().getSequenceAt (seq).getLength ()) { +this.startseq = seq; +this.lastres = res; +} else { +this.startseq = -1; +this.lastres = -1; +}return; +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseOverSequence", +function (sequence, index, pos) { +var tmp = sequence.hashCode () + index + ""; +if (this.lastMessage == null || !this.lastMessage.equals (tmp)) { +this.ssm.mouseOverSequence (sequence, index, pos, this.av); +}this.lastMessage = tmp; +}, "jalview.datamodel.SequenceI,~N,~N"); +Clazz.overrideMethod (c$, "highlightSequence", +function (results) { +if (this.av.isFollowHighlight ()) { +if (this.ap.scrollToPosition (results, true)) { +this.ap.alignFrame.repaint (); +}}this.setStatusMessage (results); +this.seqCanvas.highlightSearchResults (results); +}, "jalview.datamodel.SearchResults"); +Clazz.overrideMethod (c$, "getVamsasSource", +function () { +return this.ap == null ? null : this.ap.av; +}); +Clazz.overrideMethod (c$, "updateColours", +function (seq, index) { +System.out.println ("update the seqPanel colours"); +}, "jalview.datamodel.SequenceI,~N"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +var res = this.findRes (evt); +var seq = this.findSeq (evt); +if (seq >= this.av.getAlignment ().getHeight () || seq < 0 || res < 0) { +if (this.tooltip != null) { +this.tooltip.setTip (""); +}return; +}var sequence = this.av.getAlignment ().getSequenceAt (seq); +if (res > sequence.getLength ()) { +if (this.tooltip != null) { +this.tooltip.setTip (""); +}return; +}var respos = sequence.findPosition (res); +if (this.ssm != null) { +this.mouseOverSequence (sequence, res, respos); +}var text = new StringBuilder (); +text.append ("Sequence ").append (Integer.toString (seq + 1)).append (" ID: ").append (sequence.getName ()); +var obj = null; +var ch = String.valueOf (sequence.getCharAt (res)); +if (this.av.getAlignment ().isNucleotide ()) { +obj = jalview.schemes.ResidueProperties.nucleotideName.get (ch); +if (obj != null) { +text.append (" Nucleotide: ").append (obj); +}} else { +obj = "X".equalsIgnoreCase (ch) ? "X" : jalview.schemes.ResidueProperties.aa2Triplet.get (ch); +if (obj != null) { +text.append (" Residue: ").append (obj); +}}if (obj != null) { +text.append (" (").append (Integer.toString (respos)).append (")"); +}this.ap.alignFrame.setStatus (text.toString ()); +var tooltipText = new StringBuilder (); +var groups = this.av.getAlignment ().findAllGroups (sequence); +if (groups != null) { +for (var g = 0; g < groups.length; g++) { +if (groups[g].getStartRes () <= res && groups[g].getEndRes () >= res) { +if (!groups[g].getName ().startsWith ("JTreeGroup") && !groups[g].getName ().startsWith ("JGroup")) { +tooltipText.append (groups[g].getName ()).append (" "); +}if (groups[g].getDescription () != null) { +tooltipText.append (groups[g].getDescription ()); +}tooltipText.append ("\n"); +}} +}var allFeatures = this.findFeaturesAtRes (sequence, sequence.findPosition (res)); +var index = 0; +while (index < allFeatures.length) { +var sf = allFeatures[index]; +tooltipText.append (sf.getType () + " " + sf.begin + ":" + sf.end); +if (sf.getDescription () != null) { +tooltipText.append (" " + sf.getDescription ()); +}if (sf.getValue ("status") != null) { +var status = sf.getValue ("status").toString (); +if (status.length > 0) { +tooltipText.append (" (" + sf.getValue ("status") + ")"); +}}tooltipText.append ("\n"); +index++; +} +if (this.tooltip == null) { +this.tooltip = new jalview.appletgui.Tooltip (tooltipText.toString (), this.seqCanvas); +} else { +this.tooltip.setTip (tooltipText.toString ()); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "findFeaturesAtRes", +function (sequence, res) { +var tmp = new java.util.Vector (); +var features = sequence.getSequenceFeatures (); +if (features != null) { +for (var i = 0; i < features.length; i++) { +if (this.av.getFeaturesDisplayed () == null || !this.av.getFeaturesDisplayed ().isVisible (features[i].getType ())) { +continue; +}if (features[i].featureGroup != null && !this.seqCanvas.fr.checkGroupVisibility (features[i].featureGroup, false)) { +continue; +}if ((features[i].getBegin () <= res) && (features[i].getEnd () >= res)) { +tmp.addElement (features[i]); +}} +}features = new Array (tmp.size ()); +tmp.copyInto (features); +return features; +}, "jalview.datamodel.SequenceI,~N"); +Clazz.overrideMethod (c$, "mouseDragged", +function (evt) { +if (this.mouseWheelPressed) { +var oldWidth = this.av.getCharWidth (); +if (Math.abs (evt.getY () - this.lastMousePress.y) > Math.abs (evt.getX () - this.lastMousePress.x)) { +var fontSize = this.av.font.getSize (); +if (evt.getY () < this.lastMousePress.y && this.av.getCharHeight () > 1) { +fontSize--; +} else if (evt.getY () > this.lastMousePress.y) { +fontSize++; +}if (fontSize < 1) { +fontSize = 1; +}this.av.setFont ( new java.awt.Font (this.av.font.getName (), this.av.font.getStyle (), fontSize)); +this.av.setCharWidth (oldWidth); +} else { +if (evt.getX () < this.lastMousePress.x && this.av.getCharWidth () > 1) { +this.av.setCharWidth (this.av.getCharWidth () - 1); +} else if (evt.getX () > this.lastMousePress.x) { +this.av.setCharWidth (this.av.getCharWidth () + 1); +}if (this.av.getCharWidth () < 1) { +this.av.setCharWidth (1); +}}this.ap.fontChanged (); +var fm = this.getFontMetrics (this.av.getFont ()); +this.av.validCharWidth = fm.charWidth ('M') <= this.av.getCharWidth (); +this.lastMousePress = evt.getPoint (); +this.ap.paintAlignment (false); +this.ap.annotationPanel.image = null; +return; +}if (!this.editingSeqs) { +this.doMouseDraggedDefineMode (evt); +return; +}var res = this.findRes (evt); +if (res < 0) { +res = 0; +}if ((this.lastres == -1) || (this.lastres == res)) { +return; +}if ((res < this.av.getAlignment ().getWidth ()) && (res < this.lastres)) { +this.editSequence (false, res); +} else { +this.editSequence (true, res); +}this.mouseDragging = true; +if (this.scrollThread != null) { +this.scrollThread.setEvent (evt); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "editSequence", +function (insertGap, startres) { +var fixedLeft = -1; +var fixedRight = -1; +var fixedColumns = false; +var sg = this.av.getSelectionGroup (); +var seq = this.av.getAlignment ().getSequenceAt (this.startseq); +if (!this.groupEditing && this.av.hasHiddenRows ()) { +if (this.av.isHiddenRepSequence (seq)) { +sg = this.av.getRepresentedSequences (seq); +this.groupEditing = true; +}}var message = new StringBuffer (); +if (this.groupEditing) { +message.append (jalview.util.MessageManager.getString ("action.edit_group")).append (":"); +if (this.editCommand == null) { +this.editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.edit_group")); +}} else { +message.append (jalview.util.MessageManager.getString ("label.edit_sequence")).append (" " + seq.getName ()); +var label = seq.getName (); +if (label.length > 10) { +label = label.substring (0, 10); +}if (this.editCommand == null) { +this.editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.formatMessage ("label.edit_params", Clazz.newArray (-1, [label]))); +}}if (insertGap) { +message.append (" insert "); +} else { +message.append (" delete "); +}message.append (Math.abs (startres - this.lastres) + " gaps."); +this.ap.alignFrame.setStatus (message.toString ()); +if (this.groupEditing || (sg != null && sg.getSequences (this.av.getHiddenRepSequences ()).contains (seq))) { +fixedColumns = true; +if (sg == null) { +if (!this.av.isHiddenRepSequence (seq)) { +this.endEditing (); +return; +}sg = this.av.getRepresentedSequences (seq); +}fixedLeft = sg.getStartRes (); +fixedRight = sg.getEndRes (); +if ((startres < fixedLeft && this.lastres >= fixedLeft) || (startres >= fixedLeft && this.lastres < fixedLeft) || (startres > fixedRight && this.lastres <= fixedRight) || (startres <= fixedRight && this.lastres > fixedRight)) { +this.endEditing (); +return; +}if (fixedLeft > startres) { +fixedRight = fixedLeft - 1; +fixedLeft = 0; +} else if (fixedRight < startres) { +fixedLeft = fixedRight; +fixedRight = -1; +}}if (this.av.hasHiddenColumns ()) { +fixedColumns = true; +var y1 = this.av.getColumnSelection ().getHiddenBoundaryLeft (startres); +var y2 = this.av.getColumnSelection ().getHiddenBoundaryRight (startres); +if ((insertGap && startres > y1 && this.lastres < y1) || (!insertGap && startres < y2 && this.lastres > y2)) { +this.endEditing (); +return; +}if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) { +if (startres >= y2) { +fixedLeft = y2; +} else { +fixedRight = y2 - 1; +}}}if (this.groupEditing) { +var groupSeqs = sg.getSequences (this.av.getHiddenRepSequences ()).toArray ( new Array (0)); +if (insertGap) { +if (sg.getStartRes () == 0 && sg.getEndRes () == fixedRight && sg.getEndRes () == this.av.getAlignment ().getWidth () - 1) { +sg.setEndRes (this.av.getAlignment ().getWidth () + startres - this.lastres); +fixedRight = sg.getEndRes (); +}var blank = false; +for (fixedRight = fixedRight; fixedRight > this.lastres; fixedRight--) { +blank = true; +for (var gs, $gs = 0, $$gs = groupSeqs; $gs < $$gs.length && ((gs = $$gs[$gs]) || true); $gs++) { +for (var j = 0; j < startres - this.lastres; j++) { +if (!jalview.util.Comparison.isGap (gs.getCharAt (fixedRight - j))) { +blank = false; +break; +}} +} +if (blank) { +break; +}} +if (!blank) { +if (sg.getSize () == this.av.getAlignment ().getHeight ()) { +if ((this.av.hasHiddenColumns () && startres < this.av.getColumnSelection ().getHiddenBoundaryRight (startres))) { +this.endEditing (); +return; +}var alWidth = this.av.getAlignment ().getWidth (); +if (this.av.hasHiddenRows ()) { +var hwidth = this.av.getAlignment ().getHiddenSequences ().getWidth (); +if (hwidth > alWidth) { +alWidth = hwidth; +}}sg.setEndRes (sg.getEndRes () + startres - this.lastres); +fixedRight = alWidth + startres - this.lastres; +} else { +this.endEditing (); +return; +}}} else if (!insertGap) { +for (var gs, $gs = 0, $$gs = groupSeqs; $gs < $$gs.length && ((gs = $$gs[$gs]) || true); $gs++) { +for (var j = startres; j < this.lastres; j++) { +if (gs.getLength () <= j) { +continue; +}if (!jalview.util.Comparison.isGap (gs.getCharAt (j))) { +this.endEditing (); +return; +}} +} +}if (insertGap) { +if (fixedColumns && fixedRight != -1) { +for (var j = this.lastres; j < startres; j++) { +this.insertChar (j, groupSeqs, fixedRight); +} +} else { +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, groupSeqs, startres, startres - this.lastres, this.av.getAlignment (), true); +}} else { +if (fixedColumns && fixedRight != -1) { +for (var j = this.lastres; j > startres; j--) { +this.deleteChar (startres, groupSeqs, fixedRight); +} +} else { +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, groupSeqs, startres, this.lastres - startres, this.av.getAlignment (), true); +}}} else { +if (insertGap) { +if (fixedColumns && fixedRight != -1) { +for (var j = this.lastres; j < startres; j++) { +this.insertChar (j, Clazz.newArray (-1, [seq]), fixedRight); +} +} else { +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, Clazz.newArray (-1, [seq]), this.lastres, startres - this.lastres, this.av.getAlignment (), true); +}} else { +if (fixedColumns && fixedRight != -1) { +for (var j = this.lastres; j > startres; j--) { +if (!jalview.util.Comparison.isGap (seq.getCharAt (startres))) { +this.endEditing (); +break; +}this.deleteChar (startres, Clazz.newArray (-1, [seq]), fixedRight); +} +} else { +var max = 0; +for (var m = startres; m < this.lastres; m++) { +if (!jalview.util.Comparison.isGap (seq.getCharAt (m))) { +break; +}max++; +} +if (max > 0) { +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, Clazz.newArray (-1, [seq]), startres, max, this.av.getAlignment (), true); +}}}}this.lastres = startres; +this.seqCanvas.repaint (); +}, "~B,~N"); +Clazz.defineMethod (c$, "insertChar", +function (j, seq, fixedColumn) { +var blankColumn = fixedColumn; +for (var s = 0; s < seq.length; s++) { +for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { +if (jalview.util.Comparison.isGap (seq[s].getCharAt (blankColumn))) { +break; +}} +if (blankColumn <= j) { +blankColumn = fixedColumn; +this.endEditing (); +return; +}} +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seq, blankColumn, 1, this.av.getAlignment (), true); +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, seq, j, 1, this.av.getAlignment (), true); +}, "~N,~A,~N"); +Clazz.defineMethod (c$, "deleteChar", +function (j, seq, fixedColumn) { +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seq, j, 1, this.av.getAlignment (), true); +this.editCommand.appendEdit (jalview.commands.EditCommand.Action.INSERT_GAP, seq, fixedColumn, 1, this.av.getAlignment (), true); +}, "~N,~A,~N"); +Clazz.defineMethod (c$, "doMousePressedDefineMode", +function (evt) { +if (this.scrollThread != null) { +this.scrollThread.running = false; +this.scrollThread = null; +}var res = this.findRes (evt); +var seq = this.findSeq (evt); +this.oldSeq = seq; +this.startWrapBlock = this.wrappedBlock; +if (seq == -1) { +return; +}var sequence = this.av.getAlignment ().getSequenceAt (seq); +if (sequence == null || res > sequence.getLength ()) { +return; +}this.stretchGroup = this.av.getSelectionGroup (); +if (this.stretchGroup == null) { +this.stretchGroup = this.av.getAlignment ().findGroup (sequence); +if (this.stretchGroup != null && res > this.stretchGroup.getStartRes () && res < this.stretchGroup.getEndRes ()) { +this.av.setSelectionGroup (this.stretchGroup); +} else { +this.stretchGroup = null; +}} else if (!this.stretchGroup.getSequences (null).contains (sequence) || this.stretchGroup.getStartRes () > res || this.stretchGroup.getEndRes () < res) { +this.stretchGroup = null; +var allGroups = this.av.getAlignment ().findAllGroups (sequence); +if (allGroups != null) { +for (var i = 0; i < allGroups.length; i++) { +if (allGroups[i].getStartRes () <= res && allGroups[i].getEndRes () >= res) { +this.stretchGroup = allGroups[i]; +break; +}} +}this.av.setSelectionGroup (this.stretchGroup); +}if ((evt.getModifiers () & 4) == 4) { +var allFeatures = this.findFeaturesAtRes (sequence, sequence.findPosition (res)); +var links = null; +if (allFeatures != null) { +for (var i = 0; i < allFeatures.length; i++) { +if (allFeatures[i].links != null) { +if (links == null) { +links = new java.util.Vector (); +}for (var j = 0; j < allFeatures[i].links.size (); j++) { +links.addElement (allFeatures[i].links.elementAt (j)); +} +}} +}var popup = new jalview.appletgui.APopupMenu (this.ap, null, links); +this.add (popup); +popup.show (this, evt.getX (), evt.getY ()); +return; +}if (this.av.cursorMode) { +this.seqCanvas.cursorX = this.findRes (evt); +this.seqCanvas.cursorY = this.findSeq (evt); +this.seqCanvas.repaint (); +return; +}if (this.stretchGroup == null) { +var sg = new jalview.datamodel.SequenceGroup (); +sg.setStartRes (res); +sg.setEndRes (res); +sg.addSequence (sequence, false); +this.av.setSelectionGroup (sg); +this.stretchGroup = sg; +if (this.av.getConservationSelected ()) { +jalview.appletgui.SliderPanel.setConservationSlider (this.ap, this.av.getGlobalColourScheme (), "Background"); +}if (this.av.getAbovePIDThreshold ()) { +jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, this.av.getGlobalColourScheme (), "Background"); +}}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "doMouseReleasedDefineMode", +function (evt) { +if (this.stretchGroup == null) { +return; +}this.stretchGroup.recalcConservation (); +if (this.stretchGroup.cs != null) { +this.stretchGroup.cs.alignmentChanged (this.stretchGroup, this.av.getHiddenRepSequences ()); +if (this.stretchGroup.cs.conservationApplied ()) { +jalview.appletgui.SliderPanel.setConservationSlider (this.ap, this.stretchGroup.cs, this.stretchGroup.getName ()); +} else { +jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, this.stretchGroup.cs, this.stretchGroup.getName ()); +}}this.changeEndRes = false; +this.changeStartRes = false; +this.stretchGroup = null; +jalview.appletgui.PaintRefresher.Refresh (this.ap, this.av.getSequenceSetId ()); +this.ap.paintAlignment (true); +this.av.sendSelection (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "doMouseDraggedDefineMode", +function (evt) { +var res = this.findRes (evt); +var y = this.findSeq (evt); +if (this.wrappedBlock != this.startWrapBlock) { +return; +}if (this.stretchGroup == null) { +return; +}this.mouseDragging = true; +if (y > this.av.getAlignment ().getHeight ()) { +y = this.av.getAlignment ().getHeight () - 1; +}if (res >= this.av.getAlignment ().getWidth ()) { +res = this.av.getAlignment ().getWidth () - 1; +}if (this.stretchGroup.getEndRes () == res) { +this.changeEndRes = true; +} else if (this.stretchGroup.getStartRes () == res) { +this.changeStartRes = true; +}if (res < 0) { +res = 0; +}if (this.changeEndRes) { +if (res > (this.stretchGroup.getStartRes () - 1)) { +this.stretchGroup.setEndRes (res); +}} else if (this.changeStartRes) { +if (res < (this.stretchGroup.getEndRes () + 1)) { +this.stretchGroup.setStartRes (res); +}}var dragDirection = 0; +if (y > this.oldSeq) { +dragDirection = 1; +} else if (y < this.oldSeq) { +dragDirection = -1; +}while ((y != this.oldSeq) && (this.oldSeq > -1) && (y < this.av.getAlignment ().getHeight ())) { +var seq = this.av.getAlignment ().getSequenceAt (this.oldSeq); +this.oldSeq += dragDirection; +if (this.oldSeq < 0) { +break; +}var nextSeq = this.av.getAlignment ().getSequenceAt (this.oldSeq); +if (this.stretchGroup.getSequences (null).contains (nextSeq)) { +this.stretchGroup.deleteSequence (seq, false); +} else { +if (seq != null) { +this.stretchGroup.addSequence (seq, false); +}this.stretchGroup.addSequence (nextSeq, false); +}} +if (this.oldSeq < 0) { +this.oldSeq = -1; +}if (res > this.av.endRes || res < this.av.startRes || y < this.av.startSeq || y > this.av.endSeq) { +this.mouseExited (evt); +}if (this.scrollThread != null) { +this.scrollThread.setEvent (evt); +}this.seqCanvas.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (e) { +if (this.oldSeq < 0) { +this.oldSeq = 0; +}if (this.scrollThread != null) { +this.scrollThread.running = false; +this.scrollThread = null; +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (e) { +if (this.av.getWrapAlignment ()) { +return; +}if (this.mouseDragging && this.scrollThread == null) { +this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.SeqPanel.ScrollThread, this, null); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "scrollCanvas", +function (evt) { +if (evt == null) { +if (this.scrollThread != null) { +this.scrollThread.running = false; +this.scrollThread = null; +}this.mouseDragging = false; +} else { +if (this.scrollThread == null) { +this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.SeqPanel.ScrollThread, this, null); +}this.mouseDragging = true; +this.scrollThread.setEvent (evt); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "selection", +function (seqsel, colsel, source) { +if (this.av != null && (this.av === source || !this.av.followSelection || (Clazz.instanceOf (source, jalview.appletgui.AlignViewport) && (source).getSequenceSetId ().equals (this.av.getSequenceSetId ())))) { +return; +}if (this.selectionFromTranslation (seqsel, colsel, source)) { +return; +}var repaint = false; +var copycolsel = true; +if (this.av.getSelectionGroup () == null || !this.av.isSelectionGroupChanged (true)) { +var sgroup = null; +if (seqsel != null && seqsel.getSize () > 0) { +if (this.av.getAlignment () == null) { +System.out.println ("Selection message: alignviewport av SeqSetId=" + this.av.getSequenceSetId () + " ViewId=" + this.av.getViewId () + " 's alignment is NULL! returning immediatly."); +return; +}sgroup = seqsel.intersect (this.av.getAlignment (), (this.av.hasHiddenRows ()) ? this.av.getHiddenRepSequences () : null); +if ((sgroup == null || sgroup.getSize () == 0) && (colsel == null || colsel.size () == 0)) { +copycolsel = false; +}}if (sgroup != null && sgroup.getSize () > 0) { +this.av.setSelectionGroup (sgroup); +} else { +this.av.setSelectionGroup (null); +}repaint = this.av.isSelectionGroupChanged (true); +}if (copycolsel && (this.av.getColumnSelection () == null || !this.av.isColSelChanged (true))) { +if (colsel == null || colsel.size () == 0) { +if (this.av.getColumnSelection () != null) { +this.av.getColumnSelection ().clear (); +}} else { +if (this.av.getColumnSelection () == null) { +this.av.setColumnSelection ( new jalview.datamodel.ColumnSelection (colsel)); +} else { +this.av.getColumnSelection ().setElementsFrom (colsel); +}}repaint = new Boolean (repaint | this.av.isColSelChanged (true)).valueOf (); +}if (copycolsel && this.av.hasHiddenColumns () && (this.av.getColumnSelection () == null || this.av.getColumnSelection ().getHiddenColumns () == null)) { +System.err.println ("Bad things"); +}if (repaint) { +this.ap.scalePanelHolder.repaint (); +this.ap.repaint (); +}}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); +Clazz.defineMethod (c$, "scrollTo", +function (row, column) { +row = row < 0 ? this.ap.av.startSeq : row; +column = column < 0 ? this.ap.av.startRes : column; +this.ap.scrollTo (column, column, row, true, true); +}, "~N,~N"); +Clazz.defineMethod (c$, "scrollToRow", +function (row) { +row = row < 0 ? this.ap.av.startSeq : row; +this.ap.scrollTo (this.ap.av.startRes, this.ap.av.startRes, row, true, true); +}, "~N"); +Clazz.defineMethod (c$, "scrollToColumn", +function (column) { +column = column < 0 ? this.ap.av.startRes : column; +this.ap.scrollTo (column, column, this.ap.av.startSeq, true, true); +}, "~N"); +Clazz.defineMethod (c$, "selectionFromTranslation", +function (seqsel, colsel, source) { +if (!(Clazz.instanceOf (source, jalview.api.AlignViewportI))) { +return false; +}var sourceAv = source; +if (sourceAv.getCodingComplement () !== this.av && this.av.getCodingComplement () !== sourceAv) { +return false; +}var sg = jalview.util.MappingUtils.mapSequenceGroup (seqsel, sourceAv, this.av); +this.av.setSelectionGroup (sg); +this.av.isSelectionGroupChanged (true); +var cs = jalview.util.MappingUtils.mapColumnSelection (colsel, sourceAv, this.av); +this.av.setColumnSelection (cs); +this.av.isColSelChanged (true); +this.ap.scalePanelHolder.repaint (); +this.ap.repaint (); +return true; +}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); +c$.$SeqPanel$ScrollThread$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.evt = null; +this.running = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.SeqPanel, "ScrollThread", Thread); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.appletgui.SeqPanel.ScrollThread, []); +this.start (); +}); +Clazz.defineMethod (c$, "setEvent", +function (a) { +this.evt = a; +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "stopScrolling", +function () { +this.running = false; +}); +Clazz.overrideMethod (c$, "run", +function () { +this.running = true; +while (this.running) { +if (this.evt != null) { +if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getY () < 0 && this.b$["jalview.appletgui.SeqPanel"].av.getStartSeq () > 0) { +this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollUp (true); +}if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getY () >= this.b$["jalview.appletgui.SeqPanel"].getSize ().height && this.b$["jalview.appletgui.SeqPanel"].av.getAlignment ().getHeight () > this.b$["jalview.appletgui.SeqPanel"].av.getEndSeq ()) { +this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollUp (false); +}if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getX () < 0) { +this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollRight (false); +} else if (this.b$["jalview.appletgui.SeqPanel"].mouseDragging && this.evt.getX () >= this.b$["jalview.appletgui.SeqPanel"].getSize ().width) { +this.running = this.b$["jalview.appletgui.SeqPanel"].ap.scrollRight (true); +}}try { +Thread.sleep (75); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +} +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/SequenceRenderer.class b/bin/jalview/appletgui/SequenceRenderer.class index a758da7..d15b02f 100644 Binary files a/bin/jalview/appletgui/SequenceRenderer.class and b/bin/jalview/appletgui/SequenceRenderer.class differ diff --git a/bin/jalview/appletgui/SequenceRenderer.js b/bin/jalview/appletgui/SequenceRenderer.js index 449c271..43ee455 100644 --- a/bin/jalview/appletgui/SequenceRenderer.js +++ b/bin/jalview/appletgui/SequenceRenderer.js @@ -1,196 +1,196 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.api.SequenceRenderer"], "jalview.appletgui.SequenceRenderer", ["jalview.util.Comparison", "java.awt.Color", "$.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.fm = null; -this.renderGaps = true; -this.currentSequenceGroup = null; -this.allGroups = null; -this.resBoxColour = null; -this.graphics = null; -this.forOverview = false; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "SequenceRenderer", null, jalview.api.SequenceRenderer); -Clazz.makeConstructor (c$, -function (av) { -this.av = av; -}, "jalview.appletgui.AlignViewport"); -Clazz.defineMethod (c$, "prepare", -function (g, renderGaps) { -this.graphics = g; -this.fm = g.getFontMetrics (); -this.renderGaps = renderGaps; -}, "java.awt.Graphics,~B"); -Clazz.overrideMethod (c$, "getResidueBoxColour", -function (seq, i) { -this.allGroups = this.av.getAlignment ().findAllGroups (seq); -if (this.inCurrentSequenceGroup (i)) { -if (this.currentSequenceGroup.getDisplayBoxes ()) { -this.getBoxColour (this.currentSequenceGroup.cs, seq, i); -}} else if (this.av.getShowBoxes ()) { -this.getBoxColour (this.av.getGlobalColourScheme (), seq, i); -}return this.resBoxColour; -}, "jalview.datamodel.SequenceI,~N"); -Clazz.overrideMethod (c$, "getResidueColour", -function (seq, position, fr) { -var col = this.getResidueBoxColour (seq, position); -if (fr != null) { -col = fr.findFeatureColour (col, seq, position); -}return col; -}, "jalview.datamodel.SequenceI,~N,jalview.api.FeatureRenderer"); -Clazz.defineMethod (c$, "getBoxColour", -function (cs, seq, i) { -if (cs != null) { -this.resBoxColour = cs.findColour (seq.getCharAt (i), i, seq); -} else if (this.forOverview && !jalview.util.Comparison.isGap (seq.getCharAt (i))) { -this.resBoxColour = java.awt.Color.lightGray; -} else { -this.resBoxColour = java.awt.Color.white; -}}, "jalview.schemes.ColourSchemeI,jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "findSequenceColour", -function (seq, i) { -this.allGroups = this.av.getAlignment ().findAllGroups (seq); -this.drawBoxes (seq, i, i, 0); -return this.resBoxColour; -}, "jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "drawSequence", -function (seq, sg, start, end, y1) { -if (seq == null) { -return; -}this.allGroups = sg; -this.drawBoxes (seq, start, end, y1); -if (this.av.validCharWidth) { -this.drawText (seq, start, end, y1); -}}, "jalview.datamodel.SequenceI,~A,~N,~N,~N"); -Clazz.defineMethod (c$, "drawBoxes", -function (seq, start, end, y1) { -var i = start; -var length = seq.getLength (); -var curStart = -1; -var curWidth = this.av.getCharWidth (); -var avCharWidth = this.av.getCharWidth (); -var avCharHeight = this.av.getCharHeight (); -var tempColour = null; -while (i <= end) { -this.resBoxColour = java.awt.Color.white; -if (i < length) { -if (this.inCurrentSequenceGroup (i)) { -if (this.currentSequenceGroup.getDisplayBoxes ()) { -this.getBoxColour (this.currentSequenceGroup.cs, seq, i); -}} else if (this.av.getShowBoxes ()) { -this.getBoxColour (this.av.getGlobalColourScheme (), seq, i); -}}if (this.resBoxColour !== tempColour) { -if (tempColour != null) { -this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight); -}this.graphics.setColor (this.resBoxColour); -curStart = i; -curWidth = avCharWidth; -tempColour = this.resBoxColour; -} else { -curWidth += avCharWidth; -}i++; -} -this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight); -}, "jalview.datamodel.SequenceI,~N,~N,~N"); -Clazz.defineMethod (c$, "drawText", -function (seq, start, end, y1) { -var avCharWidth = this.av.getCharWidth (); -var avCharHeight = this.av.getCharHeight (); -var boldFont = null; -var bold = false; -if (this.av.isUpperCasebold ()) { -boldFont = new java.awt.Font (this.av.getFont ().getName (), 1, avCharHeight); -this.graphics.setFont (this.av.getFont ()); -}y1 += avCharHeight - Clazz.doubleToInt (avCharHeight / 5); -var charOffset = 0; -if (end + 1 >= seq.getLength ()) { -end = seq.getLength () - 1; -}var s = ' '; -var srep = this.av.isDisplayReferenceSeq (); -for (var i = start; i <= end; i++) { -this.graphics.setColor (java.awt.Color.black); -s = seq.getCharAt (i); -if (!this.renderGaps && jalview.util.Comparison.isGap (s)) { -continue; -}if (this.inCurrentSequenceGroup (i)) { -if (!this.currentSequenceGroup.getDisplayText ()) { -continue; -}if (this.currentSequenceGroup.getColourText ()) { -this.getBoxColour (this.currentSequenceGroup.cs, seq, i); -this.graphics.setColor (this.resBoxColour.darker ()); -}if (this.currentSequenceGroup.getShowNonconserved ()) { -s = this.getDisplayChar (srep, i, s, '.'); -}} else { -if (!this.av.getShowText ()) { -continue; -}if (this.av.getColourText ()) { -this.getBoxColour (this.av.getGlobalColourScheme (), seq, i); -if (this.av.getShowBoxes ()) { -this.graphics.setColor (this.resBoxColour.darker ()); -} else { -this.graphics.setColor (this.resBoxColour); -}}if (this.av.getShowUnconserved ()) { -s = this.getDisplayChar (srep, i, s, '.'); -}}if (this.av.isUpperCasebold ()) { -this.fm = this.graphics.getFontMetrics (); -if ('A' <= s && s <= 'Z') { -if (!bold) { -this.graphics.setFont (boldFont); -}bold = true; -} else if (bold) { -this.graphics.setFont (this.av.font); -bold = false; -}}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2); -this.graphics.drawString (String.valueOf (s), charOffset + avCharWidth * (i - start), y1); -} -}, "jalview.datamodel.SequenceI,~N,~N,~N"); -Clazz.defineMethod (c$, "getDisplayChar", -($fz = function (usesrep, position, s, c) { -var conschar = (usesrep) ? this.av.getAlignment ().getSeqrep ().getCharAt (position) : this.av.getAlignmentConsensusAnnotation ().annotations[position].displayCharacter.charAt (0); -if (conschar != '-' && s == conschar) { -s = c; -}return s; -}, $fz.isPrivate = true, $fz), "~B,~N,~S,~S"); -Clazz.defineMethod (c$, "inCurrentSequenceGroup", -function (res) { -if (this.allGroups == null) { -return false; -}for (var i = 0; i < this.allGroups.length; i++) { -if (this.allGroups[i].getStartRes () <= res && this.allGroups[i].getEndRes () >= res) { -this.currentSequenceGroup = this.allGroups[i]; -return true; -}} -return false; -}, "~N"); -Clazz.defineMethod (c$, "drawHighlightedText", -function (seq, start, end, x1, y1) { -var avCharWidth = this.av.getCharWidth (); -var avCharHeight = this.av.getCharHeight (); -var pady = Clazz.doubleToInt (avCharHeight / 5); -var charOffset = 0; -this.graphics.setColor (java.awt.Color.black); -this.graphics.fillRect (x1, y1, avCharWidth * (end - start + 1), avCharHeight); -this.graphics.setColor (java.awt.Color.white); -var s = '~'; -if (this.av.validCharWidth) { -for (var i = start; i <= end; i++) { -if (i < seq.getLength ()) { -s = seq.getCharAt (i); -}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2); -this.graphics.drawString (String.valueOf (s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady); -} -}}, "jalview.datamodel.SequenceI,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "drawCursor", -function (seq, res, x1, y1) { -var pady = Clazz.doubleToInt (this.av.getCharHeight () / 5); -var charOffset = 0; -this.graphics.setColor (java.awt.Color.black); -this.graphics.fillRect (x1, y1, this.av.getCharWidth (), this.av.getCharHeight ()); -this.graphics.setColor (java.awt.Color.white); -this.graphics.setColor (java.awt.Color.white); -var s = seq.getCharAt (res); -if (this.av.validCharWidth) { -charOffset = Clazz.doubleToInt ((this.av.getCharWidth () - this.fm.charWidth (s)) / 2); -this.graphics.drawString (String.valueOf (s), charOffset + x1, (y1 + this.av.getCharHeight ()) - pady); -}}, "jalview.datamodel.SequenceI,~N,~N,~N"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.api.SequenceRenderer"], "jalview.appletgui.SequenceRenderer", ["jalview.util.Comparison", "java.awt.Color", "$.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.fm = null; +this.renderGaps = true; +this.currentSequenceGroup = null; +this.allGroups = null; +this.resBoxColour = null; +this.graphics = null; +this.forOverview = false; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "SequenceRenderer", null, jalview.api.SequenceRenderer); +Clazz.makeConstructor (c$, +function (av) { +this.av = av; +}, "jalview.appletgui.AlignViewport"); +Clazz.defineMethod (c$, "prepare", +function (g, renderGaps) { +this.graphics = g; +this.fm = g.getFontMetrics (); +this.renderGaps = renderGaps; +}, "java.awt.Graphics,~B"); +Clazz.overrideMethod (c$, "getResidueBoxColour", +function (seq, i) { +this.allGroups = this.av.getAlignment ().findAllGroups (seq); +if (this.inCurrentSequenceGroup (i)) { +if (this.currentSequenceGroup.getDisplayBoxes ()) { +this.getBoxColour (this.currentSequenceGroup.cs, seq, i); +}} else if (this.av.getShowBoxes ()) { +this.getBoxColour (this.av.getGlobalColourScheme (), seq, i); +}return this.resBoxColour; +}, "jalview.datamodel.SequenceI,~N"); +Clazz.overrideMethod (c$, "getResidueColour", +function (seq, position, fr) { +var col = this.getResidueBoxColour (seq, position); +if (fr != null) { +col = fr.findFeatureColour (col, seq, position); +}return col; +}, "jalview.datamodel.SequenceI,~N,jalview.api.FeatureRenderer"); +Clazz.defineMethod (c$, "getBoxColour", +function (cs, seq, i) { +if (cs != null) { +this.resBoxColour = cs.findColour (seq.getCharAt (i), i, seq); +} else if (this.forOverview && !jalview.util.Comparison.isGap (seq.getCharAt (i))) { +this.resBoxColour = java.awt.Color.lightGray; +} else { +this.resBoxColour = java.awt.Color.white; +}}, "jalview.schemes.ColourSchemeI,jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "findSequenceColour", +function (seq, i) { +this.allGroups = this.av.getAlignment ().findAllGroups (seq); +this.drawBoxes (seq, i, i, 0); +return this.resBoxColour; +}, "jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "drawSequence", +function (seq, sg, start, end, y1) { +if (seq == null) { +return; +}this.allGroups = sg; +this.drawBoxes (seq, start, end, y1); +if (this.av.validCharWidth) { +this.drawText (seq, start, end, y1); +}}, "jalview.datamodel.SequenceI,~A,~N,~N,~N"); +Clazz.defineMethod (c$, "drawBoxes", +function (seq, start, end, y1) { +var i = start; +var length = seq.getLength (); +var curStart = -1; +var curWidth = this.av.getCharWidth (); +var avCharWidth = this.av.getCharWidth (); +var avCharHeight = this.av.getCharHeight (); +var tempColour = null; +while (i <= end) { +this.resBoxColour = java.awt.Color.white; +if (i < length) { +if (this.inCurrentSequenceGroup (i)) { +if (this.currentSequenceGroup.getDisplayBoxes ()) { +this.getBoxColour (this.currentSequenceGroup.cs, seq, i); +}} else if (this.av.getShowBoxes ()) { +this.getBoxColour (this.av.getGlobalColourScheme (), seq, i); +}}if (this.resBoxColour !== tempColour) { +if (tempColour != null) { +this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight); +}this.graphics.setColor (this.resBoxColour); +curStart = i; +curWidth = avCharWidth; +tempColour = this.resBoxColour; +} else { +curWidth += avCharWidth; +}i++; +} +this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight); +}, "jalview.datamodel.SequenceI,~N,~N,~N"); +Clazz.defineMethod (c$, "drawText", +function (seq, start, end, y1) { +var avCharWidth = this.av.getCharWidth (); +var avCharHeight = this.av.getCharHeight (); +var boldFont = null; +var bold = false; +if (this.av.isUpperCasebold ()) { +boldFont = new java.awt.Font (this.av.getFont ().getName (), 1, avCharHeight); +this.graphics.setFont (this.av.getFont ()); +}y1 += avCharHeight - Clazz.doubleToInt (avCharHeight / 5); +var charOffset = 0; +if (end + 1 >= seq.getLength ()) { +end = seq.getLength () - 1; +}var s = ' '; +var srep = this.av.isDisplayReferenceSeq (); +for (var i = start; i <= end; i++) { +this.graphics.setColor (java.awt.Color.black); +s = seq.getCharAt (i); +if (!this.renderGaps && jalview.util.Comparison.isGap (s)) { +continue; +}if (this.inCurrentSequenceGroup (i)) { +if (!this.currentSequenceGroup.getDisplayText ()) { +continue; +}if (this.currentSequenceGroup.getColourText ()) { +this.getBoxColour (this.currentSequenceGroup.cs, seq, i); +this.graphics.setColor (this.resBoxColour.darker ()); +}if (this.currentSequenceGroup.getShowNonconserved ()) { +s = this.getDisplayChar (srep, i, s, '.'); +}} else { +if (!this.av.getShowText ()) { +continue; +}if (this.av.getColourText ()) { +this.getBoxColour (this.av.getGlobalColourScheme (), seq, i); +if (this.av.getShowBoxes ()) { +this.graphics.setColor (this.resBoxColour.darker ()); +} else { +this.graphics.setColor (this.resBoxColour); +}}if (this.av.getShowUnconserved ()) { +s = this.getDisplayChar (srep, i, s, '.'); +}}if (this.av.isUpperCasebold ()) { +this.fm = this.graphics.getFontMetrics (); +if ('A' <= s && s <= 'Z') { +if (!bold) { +this.graphics.setFont (boldFont); +}bold = true; +} else if (bold) { +this.graphics.setFont (this.av.font); +bold = false; +}}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2); +this.graphics.drawString (String.valueOf (s), charOffset + avCharWidth * (i - start), y1); +} +}, "jalview.datamodel.SequenceI,~N,~N,~N"); +Clazz.defineMethod (c$, "getDisplayChar", +($fz = function (usesrep, position, s, c) { +var conschar = (usesrep) ? this.av.getAlignment ().getSeqrep ().getCharAt (position) : this.av.getAlignmentConsensusAnnotation ().annotations[position].displayCharacter.charAt (0); +if (conschar != '-' && s == conschar) { +s = c; +}return s; +}, $fz.isPrivate = true, $fz), "~B,~N,~S,~S"); +Clazz.defineMethod (c$, "inCurrentSequenceGroup", +function (res) { +if (this.allGroups == null) { +return false; +}for (var i = 0; i < this.allGroups.length; i++) { +if (this.allGroups[i].getStartRes () <= res && this.allGroups[i].getEndRes () >= res) { +this.currentSequenceGroup = this.allGroups[i]; +return true; +}} +return false; +}, "~N"); +Clazz.defineMethod (c$, "drawHighlightedText", +function (seq, start, end, x1, y1) { +var avCharWidth = this.av.getCharWidth (); +var avCharHeight = this.av.getCharHeight (); +var pady = Clazz.doubleToInt (avCharHeight / 5); +var charOffset = 0; +this.graphics.setColor (java.awt.Color.black); +this.graphics.fillRect (x1, y1, avCharWidth * (end - start + 1), avCharHeight); +this.graphics.setColor (java.awt.Color.white); +var s = '~'; +if (this.av.validCharWidth) { +for (var i = start; i <= end; i++) { +if (i < seq.getLength ()) { +s = seq.getCharAt (i); +}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2); +this.graphics.drawString (String.valueOf (s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady); +} +}}, "jalview.datamodel.SequenceI,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "drawCursor", +function (seq, res, x1, y1) { +var pady = Clazz.doubleToInt (this.av.getCharHeight () / 5); +var charOffset = 0; +this.graphics.setColor (java.awt.Color.black); +this.graphics.fillRect (x1, y1, this.av.getCharWidth (), this.av.getCharHeight ()); +this.graphics.setColor (java.awt.Color.white); +this.graphics.setColor (java.awt.Color.white); +var s = seq.getCharAt (res); +if (this.av.validCharWidth) { +charOffset = Clazz.doubleToInt ((this.av.getCharWidth () - this.fm.charWidth (s)) / 2); +this.graphics.drawString (String.valueOf (s), charOffset + x1, (y1 + this.av.getCharHeight ()) - pady); +}}, "jalview.datamodel.SequenceI,~N,~N,~N"); +}); diff --git a/bin/jalview/appletgui/SliderPanel.class b/bin/jalview/appletgui/SliderPanel.class index ae2daac..58ba84c 100644 Binary files a/bin/jalview/appletgui/SliderPanel.class and b/bin/jalview/appletgui/SliderPanel.class differ diff --git a/bin/jalview/appletgui/SliderPanel.js b/bin/jalview/appletgui/SliderPanel.js index dc38cc2..8ba7a20 100644 --- a/bin/jalview/appletgui/SliderPanel.js +++ b/bin/jalview/appletgui/SliderPanel.js @@ -1,270 +1,270 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.MouseListener", "awt2swing.Button", "$.Checkbox", "$.Label", "$.Scrollbar", "$.TextField", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.SliderPanel", ["awt2swing.Frame", "jalview.bin.JalviewLite", "jalview.util.MessageManager", "java.awt.Color", "$.Font", "java.awt.event.WindowAdapter"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ap = null; -this.forConservation = true; -this.cs = null; -this.slider = null; -this.valueField = null; -this.label = null; -this.jPanel1 = null; -this.jPanel2 = null; -this.applyButton = null; -this.undoButton = null; -this.flowLayout1 = null; -this.allGroupsCheck = null; -this.borderLayout1 = null; -this.borderLayout2 = null; -this.flowLayout2 = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "SliderPanel", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.MouseListener]); -Clazz.prepareFields (c$, function () { -this.slider = new awt2swing.Scrollbar (); -this.valueField = new awt2swing.TextField (); -this.label = new awt2swing.Label (); -this.jPanel1 = new awt2swing.Panel (); -this.jPanel2 = new awt2swing.Panel (); -this.applyButton = new awt2swing.Button (); -this.undoButton = new awt2swing.Button (); -this.flowLayout1 = new java.awt.FlowLayout (); -this.allGroupsCheck = new awt2swing.Checkbox (); -this.borderLayout1 = new java.awt.BorderLayout (); -this.borderLayout2 = new java.awt.BorderLayout (); -this.flowLayout2 = new java.awt.FlowLayout (); -}); -c$.setConservationSlider = Clazz.defineMethod (c$, "setConservationSlider", -function (ap, cs, source) { -var sp = null; -if (jalview.appletgui.SliderPanel.conservationSlider == null) { -sp = new jalview.appletgui.SliderPanel (ap, cs.getConservationInc (), true, cs); -jalview.appletgui.SliderPanel.conservationSlider = new awt2swing.Frame (); -jalview.appletgui.SliderPanel.conservationSlider.add (sp); -} else { -sp = jalview.appletgui.SliderPanel.conservationSlider.getComponent (0); -sp.cs = cs; -}jalview.appletgui.SliderPanel.conservationSlider.setTitle (jalview.util.MessageManager.formatMessage ("label.conservation_colour_increment", Clazz.newArray (-1, [source]))); -if (ap.av.getAlignment ().getGroups () != null) { -sp.setAllGroupsCheckEnabled (true); -} else { -sp.setAllGroupsCheckEnabled (false); -}return sp.getValue (); -}, "jalview.appletgui.AlignmentPanel,jalview.schemes.ColourSchemeI,~S"); -c$.showConservationSlider = Clazz.defineMethod (c$, "showConservationSlider", -function () { -try { -jalview.appletgui.SliderPanel.PIDSlider.setVisible (false); -jalview.appletgui.SliderPanel.PIDSlider = null; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -if (!jalview.appletgui.SliderPanel.conservationSlider.isVisible ()) { -jalview.bin.JalviewLite.addFrame (jalview.appletgui.SliderPanel.conservationSlider, jalview.appletgui.SliderPanel.conservationSlider.getTitle (), 420, 100); -jalview.appletgui.SliderPanel.conservationSlider.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.SliderPanel$1") ? 0 : jalview.appletgui.SliderPanel.$SliderPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.SliderPanel$1, this, null))); -}}); -c$.setPIDSliderSource = Clazz.defineMethod (c$, "setPIDSliderSource", -function (ap, cs, source) { -var pid = null; -if (jalview.appletgui.SliderPanel.PIDSlider == null) { -pid = new jalview.appletgui.SliderPanel (ap, 50, false, cs); -jalview.appletgui.SliderPanel.PIDSlider = new awt2swing.Frame (); -jalview.appletgui.SliderPanel.PIDSlider.add (pid); -} else { -pid = jalview.appletgui.SliderPanel.PIDSlider.getComponent (0); -pid.cs = cs; -}jalview.appletgui.SliderPanel.PIDSlider.setTitle (jalview.util.MessageManager.formatMessage ("label.percentage_identity_thereshold", Clazz.newArray (-1, [source]))); -if (ap.av.getAlignment ().getGroups () != null) { -pid.setAllGroupsCheckEnabled (true); -} else { -pid.setAllGroupsCheckEnabled (false); -}return pid.getValue (); -}, "jalview.appletgui.AlignmentPanel,jalview.schemes.ColourSchemeI,~S"); -c$.showPIDSlider = Clazz.defineMethod (c$, "showPIDSlider", -function () { -try { -jalview.appletgui.SliderPanel.conservationSlider.setVisible (false); -jalview.appletgui.SliderPanel.conservationSlider = null; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -if (!jalview.appletgui.SliderPanel.PIDSlider.isVisible ()) { -jalview.bin.JalviewLite.addFrame (jalview.appletgui.SliderPanel.PIDSlider, jalview.appletgui.SliderPanel.PIDSlider.getTitle (), 420, 100); -jalview.appletgui.SliderPanel.PIDSlider.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.SliderPanel$2") ? 0 : jalview.appletgui.SliderPanel.$SliderPanel$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.SliderPanel$2, this, null))); -}}); -Clazz.makeConstructor (c$, -function (ap, value, forConserve, cs) { -Clazz.superConstructor (this, jalview.appletgui.SliderPanel, []); -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.ap = ap; -this.cs = cs; -this.forConservation = forConserve; -this.undoButton.setVisible (false); -this.applyButton.setVisible (false); -if (this.forConservation) { -this.label.setText (jalview.util.MessageManager.getString ("label.modify_conservation_visibility")); -this.slider.setMinimum (0); -this.slider.setMaximum (50 + this.slider.getVisibleAmount ()); -this.slider.setUnitIncrement (1); -} else { -this.label.setText (jalview.util.MessageManager.getString ("label.colour_residues_above_occurence")); -this.slider.setMinimum (0); -this.slider.setMaximum (100 + this.slider.getVisibleAmount ()); -this.slider.setBlockIncrement (1); -}this.slider.addAdjustmentListener (this); -this.slider.addMouseListener (this); -this.slider.setValue (value); -this.valueField.setText (value + ""); -}, "jalview.appletgui.AlignmentPanel,~N,~B,jalview.schemes.ColourSchemeI"); -Clazz.defineMethod (c$, "valueChanged", -function (i) { -if (this.cs == null) { -return; -}var toChange = this.cs; -var allGroups = null; -if (this.allGroupsCheck.getState ()) { -allGroups = this.ap.av.getAlignment ().getGroups ().listIterator (); -}while (toChange != null) { -if (this.forConservation) { -toChange.setConservationInc (i); -} else { -toChange.setThreshold (i, this.ap.av.isIgnoreGapsConsensus ()); -}if (allGroups != null && allGroups.hasNext ()) { -while ((toChange = allGroups.next ().cs) == null && allGroups.hasNext ()) { -;} -} else { -toChange = null; -}} -this.ap.seqPanel.seqCanvas.repaint (); -}, "~N"); -Clazz.defineMethod (c$, "setAllGroupsCheckEnabled", -function (b) { -this.allGroupsCheck.setEnabled (b); -}, "~B"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.applyButton) { -this.applyButton_actionPerformed (); -} else if (evt.getSource () === this.undoButton) { -this.undoButton_actionPerformed (); -} else if (evt.getSource () === this.valueField) { -this.valueField_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -this.valueField.setText (this.slider.getValue () + ""); -this.valueChanged (this.slider.getValue ()); -}, "java.awt.event.AdjustmentEvent"); -Clazz.defineMethod (c$, "valueField_actionPerformed", -function () { -try { -var i = Integer.parseInt (this.valueField.getText ()); -this.slider.setValue (i); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -this.valueField.setText (this.slider.getValue () + ""); -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "setValue", -function (value) { -this.slider.setValue (value); -}, "~N"); -Clazz.defineMethod (c$, "getValue", -function () { -return Integer.parseInt (this.valueField.getText ()); -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout (this.borderLayout2); -this.slider.setBackground (java.awt.Color.white); -this.slider.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.slider.setOrientation (0); -this.valueField.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.valueField.setText (" "); -this.valueField.addActionListener (this); -this.valueField.setColumns (3); -this.label.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.label.setText (jalview.util.MessageManager.getString ("label.set_this_label_text")); -this.jPanel1.setLayout (this.borderLayout1); -this.jPanel2.setLayout (this.flowLayout1); -this.applyButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.applyButton.setLabel (jalview.util.MessageManager.getString ("action.apply")); -this.applyButton.addActionListener (this); -this.undoButton.setEnabled (false); -this.undoButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.undoButton.setLabel (jalview.util.MessageManager.getString ("action.undo")); -this.undoButton.addActionListener (this); -this.allGroupsCheck.setEnabled (false); -this.allGroupsCheck.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.allGroupsCheck.setLabel (jalview.util.MessageManager.getString ("action.apply_threshold_all_groups")); -this.allGroupsCheck.setName (jalview.util.MessageManager.getString ("action.apply_all_groups")); -this.setBackground (java.awt.Color.white); -this.setForeground (java.awt.Color.black); -this.jPanel2.add (this.label, null); -this.jPanel2.add (this.applyButton, null); -this.jPanel2.add (this.undoButton, null); -this.jPanel2.add (this.allGroupsCheck); -this.jPanel1.add (this.valueField, "East"); -this.jPanel1.add (this.slider, "Center"); -this.add (this.jPanel1, "South"); -this.add (this.jPanel2, "Center"); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "applyButton_actionPerformed", -function () { -}); -Clazz.defineMethod (c$, "undoButton_actionPerformed", -function () { -}); -Clazz.overrideMethod (c$, "mousePressed", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseReleased", -function (evt) { -this.ap.paintAlignment (true); -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (evt) { -}, "java.awt.event.MouseEvent"); -c$.$SliderPanel$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "SliderPanel$1", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -jalview.appletgui.SliderPanel.conservationSlider = null; -}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$SliderPanel$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "SliderPanel$2", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -jalview.appletgui.SliderPanel.PIDSlider = null; -}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"conservationSlider", null, -"PIDSlider", null); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.MouseListener", "awt2swing.Button", "$.Checkbox", "$.Label", "$.Scrollbar", "$.TextField", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.SliderPanel", ["awt2swing.Frame", "jalview.bin.JalviewLite", "jalview.util.MessageManager", "java.awt.Color", "$.Font", "java.awt.event.WindowAdapter"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ap = null; +this.forConservation = true; +this.cs = null; +this.slider = null; +this.valueField = null; +this.label = null; +this.jPanel1 = null; +this.jPanel2 = null; +this.applyButton = null; +this.undoButton = null; +this.flowLayout1 = null; +this.allGroupsCheck = null; +this.borderLayout1 = null; +this.borderLayout2 = null; +this.flowLayout2 = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "SliderPanel", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.MouseListener]); +Clazz.prepareFields (c$, function () { +this.slider = new awt2swing.Scrollbar (); +this.valueField = new awt2swing.TextField (); +this.label = new awt2swing.Label (); +this.jPanel1 = new awt2swing.Panel (); +this.jPanel2 = new awt2swing.Panel (); +this.applyButton = new awt2swing.Button (); +this.undoButton = new awt2swing.Button (); +this.flowLayout1 = new java.awt.FlowLayout (); +this.allGroupsCheck = new awt2swing.Checkbox (); +this.borderLayout1 = new java.awt.BorderLayout (); +this.borderLayout2 = new java.awt.BorderLayout (); +this.flowLayout2 = new java.awt.FlowLayout (); +}); +c$.setConservationSlider = Clazz.defineMethod (c$, "setConservationSlider", +function (ap, cs, source) { +var sp = null; +if (jalview.appletgui.SliderPanel.conservationSlider == null) { +sp = new jalview.appletgui.SliderPanel (ap, cs.getConservationInc (), true, cs); +jalview.appletgui.SliderPanel.conservationSlider = new awt2swing.Frame (); +jalview.appletgui.SliderPanel.conservationSlider.add (sp); +} else { +sp = jalview.appletgui.SliderPanel.conservationSlider.getComponent (0); +sp.cs = cs; +}jalview.appletgui.SliderPanel.conservationSlider.setTitle (jalview.util.MessageManager.formatMessage ("label.conservation_colour_increment", Clazz.newArray (-1, [source]))); +if (ap.av.getAlignment ().getGroups () != null) { +sp.setAllGroupsCheckEnabled (true); +} else { +sp.setAllGroupsCheckEnabled (false); +}return sp.getValue (); +}, "jalview.appletgui.AlignmentPanel,jalview.schemes.ColourSchemeI,~S"); +c$.showConservationSlider = Clazz.defineMethod (c$, "showConservationSlider", +function () { +try { +jalview.appletgui.SliderPanel.PIDSlider.setVisible (false); +jalview.appletgui.SliderPanel.PIDSlider = null; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +if (!jalview.appletgui.SliderPanel.conservationSlider.isVisible ()) { +jalview.bin.JalviewLite.addFrame (jalview.appletgui.SliderPanel.conservationSlider, jalview.appletgui.SliderPanel.conservationSlider.getTitle (), 420, 100); +jalview.appletgui.SliderPanel.conservationSlider.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.SliderPanel$1") ? 0 : jalview.appletgui.SliderPanel.$SliderPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.SliderPanel$1, this, null))); +}}); +c$.setPIDSliderSource = Clazz.defineMethod (c$, "setPIDSliderSource", +function (ap, cs, source) { +var pid = null; +if (jalview.appletgui.SliderPanel.PIDSlider == null) { +pid = new jalview.appletgui.SliderPanel (ap, 50, false, cs); +jalview.appletgui.SliderPanel.PIDSlider = new awt2swing.Frame (); +jalview.appletgui.SliderPanel.PIDSlider.add (pid); +} else { +pid = jalview.appletgui.SliderPanel.PIDSlider.getComponent (0); +pid.cs = cs; +}jalview.appletgui.SliderPanel.PIDSlider.setTitle (jalview.util.MessageManager.formatMessage ("label.percentage_identity_thereshold", Clazz.newArray (-1, [source]))); +if (ap.av.getAlignment ().getGroups () != null) { +pid.setAllGroupsCheckEnabled (true); +} else { +pid.setAllGroupsCheckEnabled (false); +}return pid.getValue (); +}, "jalview.appletgui.AlignmentPanel,jalview.schemes.ColourSchemeI,~S"); +c$.showPIDSlider = Clazz.defineMethod (c$, "showPIDSlider", +function () { +try { +jalview.appletgui.SliderPanel.conservationSlider.setVisible (false); +jalview.appletgui.SliderPanel.conservationSlider = null; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +if (!jalview.appletgui.SliderPanel.PIDSlider.isVisible ()) { +jalview.bin.JalviewLite.addFrame (jalview.appletgui.SliderPanel.PIDSlider, jalview.appletgui.SliderPanel.PIDSlider.getTitle (), 420, 100); +jalview.appletgui.SliderPanel.PIDSlider.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.SliderPanel$2") ? 0 : jalview.appletgui.SliderPanel.$SliderPanel$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.SliderPanel$2, this, null))); +}}); +Clazz.makeConstructor (c$, +function (ap, value, forConserve, cs) { +Clazz.superConstructor (this, jalview.appletgui.SliderPanel, []); +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.ap = ap; +this.cs = cs; +this.forConservation = forConserve; +this.undoButton.setVisible (false); +this.applyButton.setVisible (false); +if (this.forConservation) { +this.label.setText (jalview.util.MessageManager.getString ("label.modify_conservation_visibility")); +this.slider.setMinimum (0); +this.slider.setMaximum (50 + this.slider.getVisibleAmount ()); +this.slider.setUnitIncrement (1); +} else { +this.label.setText (jalview.util.MessageManager.getString ("label.colour_residues_above_occurence")); +this.slider.setMinimum (0); +this.slider.setMaximum (100 + this.slider.getVisibleAmount ()); +this.slider.setBlockIncrement (1); +}this.slider.addAdjustmentListener (this); +this.slider.addMouseListener (this); +this.slider.setValue (value); +this.valueField.setText (value + ""); +}, "jalview.appletgui.AlignmentPanel,~N,~B,jalview.schemes.ColourSchemeI"); +Clazz.defineMethod (c$, "valueChanged", +function (i) { +if (this.cs == null) { +return; +}var toChange = this.cs; +var allGroups = null; +if (this.allGroupsCheck.getState ()) { +allGroups = this.ap.av.getAlignment ().getGroups ().listIterator (); +}while (toChange != null) { +if (this.forConservation) { +toChange.setConservationInc (i); +} else { +toChange.setThreshold (i, this.ap.av.isIgnoreGapsConsensus ()); +}if (allGroups != null && allGroups.hasNext ()) { +while ((toChange = allGroups.next ().cs) == null && allGroups.hasNext ()) { +;} +} else { +toChange = null; +}} +this.ap.seqPanel.seqCanvas.repaint (); +}, "~N"); +Clazz.defineMethod (c$, "setAllGroupsCheckEnabled", +function (b) { +this.allGroupsCheck.setEnabled (b); +}, "~B"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.applyButton) { +this.applyButton_actionPerformed (); +} else if (evt.getSource () === this.undoButton) { +this.undoButton_actionPerformed (); +} else if (evt.getSource () === this.valueField) { +this.valueField_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +this.valueField.setText (this.slider.getValue () + ""); +this.valueChanged (this.slider.getValue ()); +}, "java.awt.event.AdjustmentEvent"); +Clazz.defineMethod (c$, "valueField_actionPerformed", +function () { +try { +var i = Integer.parseInt (this.valueField.getText ()); +this.slider.setValue (i); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +this.valueField.setText (this.slider.getValue () + ""); +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "setValue", +function (value) { +this.slider.setValue (value); +}, "~N"); +Clazz.defineMethod (c$, "getValue", +function () { +return Integer.parseInt (this.valueField.getText ()); +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout (this.borderLayout2); +this.slider.setBackground (java.awt.Color.white); +this.slider.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.slider.setOrientation (0); +this.valueField.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.valueField.setText (" "); +this.valueField.addActionListener (this); +this.valueField.setColumns (3); +this.label.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.label.setText (jalview.util.MessageManager.getString ("label.set_this_label_text")); +this.jPanel1.setLayout (this.borderLayout1); +this.jPanel2.setLayout (this.flowLayout1); +this.applyButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.applyButton.setLabel (jalview.util.MessageManager.getString ("action.apply")); +this.applyButton.addActionListener (this); +this.undoButton.setEnabled (false); +this.undoButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.undoButton.setLabel (jalview.util.MessageManager.getString ("action.undo")); +this.undoButton.addActionListener (this); +this.allGroupsCheck.setEnabled (false); +this.allGroupsCheck.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.allGroupsCheck.setLabel (jalview.util.MessageManager.getString ("action.apply_threshold_all_groups")); +this.allGroupsCheck.setName (jalview.util.MessageManager.getString ("action.apply_all_groups")); +this.setBackground (java.awt.Color.white); +this.setForeground (java.awt.Color.black); +this.jPanel2.add (this.label, null); +this.jPanel2.add (this.applyButton, null); +this.jPanel2.add (this.undoButton, null); +this.jPanel2.add (this.allGroupsCheck); +this.jPanel1.add (this.valueField, "East"); +this.jPanel1.add (this.slider, "Center"); +this.add (this.jPanel1, "South"); +this.add (this.jPanel2, "Center"); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "applyButton_actionPerformed", +function () { +}); +Clazz.defineMethod (c$, "undoButton_actionPerformed", +function () { +}); +Clazz.overrideMethod (c$, "mousePressed", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseReleased", +function (evt) { +this.ap.paintAlignment (true); +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (evt) { +}, "java.awt.event.MouseEvent"); +c$.$SliderPanel$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "SliderPanel$1", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +jalview.appletgui.SliderPanel.conservationSlider = null; +}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$SliderPanel$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "SliderPanel$2", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +jalview.appletgui.SliderPanel.PIDSlider = null; +}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"conservationSlider", null, +"PIDSlider", null); +}); diff --git a/bin/jalview/appletgui/SplitFrame.js b/bin/jalview/appletgui/SplitFrame.js index 7818eaf..eb3570a 100644 --- a/bin/jalview/appletgui/SplitFrame.js +++ b/bin/jalview/appletgui/SplitFrame.js @@ -1,108 +1,108 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.appletgui.EmbmenuFrame"], "jalview.appletgui.SplitFrame", ["awt2swing.Panel", "jalview.analysis.AlignmentUtils", "jalview.bin.JalviewLite", "jalview.structure.StructureSelectionManager", "java.awt.BorderLayout", "$.Dimension", "$.GridLayout"], function () { -c$ = Clazz.decorateAsClass (function () { -this.topFrame = null; -this.bottomFrame = null; -this.outermost = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "SplitFrame", jalview.appletgui.EmbmenuFrame); -Clazz.makeConstructor (c$, -function (af1, af2) { -Clazz.superConstructor (this, jalview.appletgui.SplitFrame, []); -this.topFrame = af1; -this.bottomFrame = af2; -this.init (); -}, "jalview.appletgui.AlignFrame,jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "init", -function () { -var $private = Clazz.checkPrivateMethod (arguments); -if ($private != null) { -return $private.apply (this, arguments); -} -this.constructSplit (); -var topViewport = this.topFrame.viewport; -var bottomViewport = this.bottomFrame.viewport; -var topAlignment = topViewport.getAlignment (); -var bottomAlignment = bottomViewport.getAlignment (); -var cdna = topAlignment.isNucleotide () ? topViewport : (bottomAlignment.isNucleotide () ? bottomViewport : null); -var protein = !topAlignment.isNucleotide () ? topViewport : (!bottomAlignment.isNucleotide () ? bottomViewport : null); -var mapped = jalview.analysis.AlignmentUtils.mapProteinToCdna (protein.getAlignment (), cdna.getAlignment ()); -if (mapped) { -var ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (topViewport.applet); -ssm.addMappings (protein.getAlignment ().getCodonFrames ()); -topViewport.setCodingComplement (bottomViewport); -ssm.addCommandListener (cdna); -ssm.addCommandListener (protein); -}protein.initComplementConsensus (); -var ap = topAlignment.isNucleotide () ? this.bottomFrame.alignPanel : this.topFrame.alignPanel; -protein.updateConsensus (ap); -this.adjustLayout (); -}); -Clazz.defineMethod (c$, "constructSplit", -function () { -this.unsetMenuBar (); -this.outermost = new awt2swing.Panel ( new java.awt.GridLayout (2, 1)); -var topPanel = new awt2swing.Panel (); -var bottomPanel = new awt2swing.Panel (); -this.outermost.add (topPanel); -this.outermost.add (bottomPanel); -this.addAlignFrameComponents (this.topFrame, topPanel); -this.addAlignFrameComponents (this.bottomFrame, bottomPanel); -}); -Clazz.defineMethod (c$, "adjustLayout", -function () { -var cdna = this.topFrame.getAlignViewport ().getAlignment ().isNucleotide () ? this.topFrame.viewport : this.bottomFrame.viewport; -var protein = cdna === this.topFrame.viewport ? this.bottomFrame.viewport : this.topFrame.viewport; -var w1 = this.topFrame.alignPanel.idPanel.idCanvas.getWidth (); -var w2 = this.bottomFrame.alignPanel.idPanel.idCanvas.getWidth (); -var w3 = Math.max (w1, w2); -if (w1 != w3) { -var d = this.topFrame.alignPanel.idPanel.idCanvas.getSize (); -this.topFrame.alignPanel.idPanel.idCanvas.setSize ( new java.awt.Dimension (w3, d.height)); -}if (w2 != w3) { -var d = this.bottomFrame.alignPanel.idPanel.idCanvas.getSize (); -this.bottomFrame.alignPanel.idPanel.idCanvas.setSize ( new java.awt.Dimension (w3, d.height)); -}if (protein != null && cdna != null) { -var vs = protein.getViewStyle (); -var scale = vs.isScaleProteinAsCdna () ? 3 : 1; -vs.setCharWidth (scale * cdna.getViewStyle ().getCharWidth ()); -protein.setViewStyle (vs); -}}); -Clazz.defineMethod (c$, "addAlignFrameComponents", -($fz = function (af, panel) { -panel.setLayout ( new java.awt.BorderLayout ()); -var menuPanel = af.makeEmbeddedPopupMenu (af.getJMenuBar (), true, false); -panel.add (menuPanel, "North"); -panel.add (af.statusBar, "South"); -panel.add (af.alignPanel, "Center"); -af.setSplitFrame (this); -}, $fz.isPrivate = true, $fz), "jalview.appletgui.AlignFrame,awt2swing.Panel"); -Clazz.defineMethod (c$, "addToDisplay", -function (embedded, applet) { -this.createSplitFrameWindow (embedded, applet); -this.validate (); -this.topFrame.alignPanel.adjustAnnotationHeight (); -this.topFrame.alignPanel.paintAlignment (true); -this.bottomFrame.alignPanel.adjustAnnotationHeight (); -this.bottomFrame.alignPanel.paintAlignment (true); -}, "~B,jalview.bin.JalviewLite"); -Clazz.defineMethod (c$, "createSplitFrameWindow", -function (embed, applet) { -if (embed) { -applet.add (this.outermost); -applet.validate (); -} else { -this.add (this.outermost); -var width = Math.max (this.topFrame.frameWidth, this.bottomFrame.frameWidth); -var height = this.topFrame.frameHeight + this.bottomFrame.frameHeight; -jalview.bin.JalviewLite.addFrame (this, this.getTitle (), width, height); -}}, "~B,jalview.bin.JalviewLite"); -Clazz.defineMethod (c$, "getComplement", -function (af) { -if (this.topFrame === af) { -return this.bottomFrame; -} else if (this.bottomFrame === af) { -return this.topFrame; -}return null; -}, "jalview.appletgui.AlignFrame"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.appletgui.EmbmenuFrame"], "jalview.appletgui.SplitFrame", ["awt2swing.Panel", "jalview.analysis.AlignmentUtils", "jalview.bin.JalviewLite", "jalview.structure.StructureSelectionManager", "java.awt.BorderLayout", "$.Dimension", "$.GridLayout"], function () { +c$ = Clazz.decorateAsClass (function () { +this.topFrame = null; +this.bottomFrame = null; +this.outermost = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "SplitFrame", jalview.appletgui.EmbmenuFrame); +Clazz.makeConstructor (c$, +function (af1, af2) { +Clazz.superConstructor (this, jalview.appletgui.SplitFrame, []); +this.topFrame = af1; +this.bottomFrame = af2; +this.init (); +}, "jalview.appletgui.AlignFrame,jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "init", +function () { +var $private = Clazz.checkPrivateMethod (arguments); +if ($private != null) { +return $private.apply (this, arguments); +} +this.constructSplit (); +var topViewport = this.topFrame.viewport; +var bottomViewport = this.bottomFrame.viewport; +var topAlignment = topViewport.getAlignment (); +var bottomAlignment = bottomViewport.getAlignment (); +var cdna = topAlignment.isNucleotide () ? topViewport : (bottomAlignment.isNucleotide () ? bottomViewport : null); +var protein = !topAlignment.isNucleotide () ? topViewport : (!bottomAlignment.isNucleotide () ? bottomViewport : null); +var mapped = jalview.analysis.AlignmentUtils.mapProteinToCdna (protein.getAlignment (), cdna.getAlignment ()); +if (mapped) { +var ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (topViewport.applet); +ssm.addMappings (protein.getAlignment ().getCodonFrames ()); +topViewport.setCodingComplement (bottomViewport); +ssm.addCommandListener (cdna); +ssm.addCommandListener (protein); +}protein.initComplementConsensus (); +var ap = topAlignment.isNucleotide () ? this.bottomFrame.alignPanel : this.topFrame.alignPanel; +protein.updateConsensus (ap); +this.adjustLayout (); +}); +Clazz.defineMethod (c$, "constructSplit", +function () { +this.unsetMenuBar (); +this.outermost = new awt2swing.Panel ( new java.awt.GridLayout (2, 1)); +var topPanel = new awt2swing.Panel (); +var bottomPanel = new awt2swing.Panel (); +this.outermost.add (topPanel); +this.outermost.add (bottomPanel); +this.addAlignFrameComponents (this.topFrame, topPanel); +this.addAlignFrameComponents (this.bottomFrame, bottomPanel); +}); +Clazz.defineMethod (c$, "adjustLayout", +function () { +var cdna = this.topFrame.getAlignViewport ().getAlignment ().isNucleotide () ? this.topFrame.viewport : this.bottomFrame.viewport; +var protein = cdna === this.topFrame.viewport ? this.bottomFrame.viewport : this.topFrame.viewport; +var w1 = this.topFrame.alignPanel.idPanel.idCanvas.getWidth (); +var w2 = this.bottomFrame.alignPanel.idPanel.idCanvas.getWidth (); +var w3 = Math.max (w1, w2); +if (w1 != w3) { +var d = this.topFrame.alignPanel.idPanel.idCanvas.getSize (); +this.topFrame.alignPanel.idPanel.idCanvas.setSize ( new java.awt.Dimension (w3, d.height)); +}if (w2 != w3) { +var d = this.bottomFrame.alignPanel.idPanel.idCanvas.getSize (); +this.bottomFrame.alignPanel.idPanel.idCanvas.setSize ( new java.awt.Dimension (w3, d.height)); +}if (protein != null && cdna != null) { +var vs = protein.getViewStyle (); +var scale = vs.isScaleProteinAsCdna () ? 3 : 1; +vs.setCharWidth (scale * cdna.getViewStyle ().getCharWidth ()); +protein.setViewStyle (vs); +}}); +Clazz.defineMethod (c$, "addAlignFrameComponents", +($fz = function (af, panel) { +panel.setLayout ( new java.awt.BorderLayout ()); +var menuPanel = af.makeEmbeddedPopupMenu (af.getJMenuBar (), true, false); +panel.add (menuPanel, "North"); +panel.add (af.statusBar, "South"); +panel.add (af.alignPanel, "Center"); +af.setSplitFrame (this); +}, $fz.isPrivate = true, $fz), "jalview.appletgui.AlignFrame,awt2swing.Panel"); +Clazz.defineMethod (c$, "addToDisplay", +function (embedded, applet) { +this.createSplitFrameWindow (embedded, applet); +this.validate (); +this.topFrame.alignPanel.adjustAnnotationHeight (); +this.topFrame.alignPanel.paintAlignment (true); +this.bottomFrame.alignPanel.adjustAnnotationHeight (); +this.bottomFrame.alignPanel.paintAlignment (true); +}, "~B,jalview.bin.JalviewLite"); +Clazz.defineMethod (c$, "createSplitFrameWindow", +function (embed, applet) { +if (embed) { +applet.add (this.outermost); +applet.validate (); +} else { +this.add (this.outermost); +var width = Math.max (this.topFrame.frameWidth, this.bottomFrame.frameWidth); +var height = this.topFrame.frameHeight + this.bottomFrame.frameHeight; +jalview.bin.JalviewLite.addFrame (this, this.getTitle (), width, height); +}}, "~B,jalview.bin.JalviewLite"); +Clazz.defineMethod (c$, "getComplement", +function (af) { +if (this.topFrame === af) { +return this.bottomFrame; +} else if (this.bottomFrame === af) { +return this.topFrame; +}return null; +}, "jalview.appletgui.AlignFrame"); +}); diff --git a/bin/jalview/appletgui/TitledPanel.js b/bin/jalview/appletgui/TitledPanel.js index 351c3ff..026a455 100644 --- a/bin/jalview/appletgui/TitledPanel.js +++ b/bin/jalview/appletgui/TitledPanel.js @@ -1,43 +1,43 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.Insets"], "jalview.appletgui.TitledPanel", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.title = null; -this.$insets = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "TitledPanel", awt2swing.Panel); -Clazz.prepareFields (c$, function () { -this.$insets = new java.awt.Insets (10, 10, 10, 10); -}); -Clazz.makeConstructor (c$, -function () { -this.construct (""); -}); -Clazz.makeConstructor (c$, -function (title) { -Clazz.superConstructor (this, jalview.appletgui.TitledPanel, []); -this.setTitle (title); -}, "~S"); -Clazz.defineMethod (c$, "getInsets", -function () { -return this.$insets; -}); -Clazz.defineMethod (c$, "paintComponent", -function (g) { -Clazz.superCall (this, jalview.appletgui.TitledPanel, "paintComponent", [g]); -g.setColor (this.getForeground ()); -g.drawRect (5, 5, this.getWidth () - 10, this.getHeight () - 10); -var width = g.getFontMetrics ().stringWidth (this.getTitle ()); -g.setColor (this.getBackground ()); -g.fillRect (10, 0, width, 10); -g.setColor (this.getForeground ()); -g.drawString (this.getTitle (), 10, 10); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "getTitle", -function () { -return this.title; -}); -Clazz.defineMethod (c$, "setTitle", -function (title) { -this.title = title; -}, "~S"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.Insets"], "jalview.appletgui.TitledPanel", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.title = null; +this.$insets = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "TitledPanel", awt2swing.Panel); +Clazz.prepareFields (c$, function () { +this.$insets = new java.awt.Insets (10, 10, 10, 10); +}); +Clazz.makeConstructor (c$, +function () { +this.construct (""); +}); +Clazz.makeConstructor (c$, +function (title) { +Clazz.superConstructor (this, jalview.appletgui.TitledPanel, []); +this.setTitle (title); +}, "~S"); +Clazz.defineMethod (c$, "getInsets", +function () { +return this.$insets; +}); +Clazz.defineMethod (c$, "paintComponent", +function (g) { +Clazz.superCall (this, jalview.appletgui.TitledPanel, "paintComponent", [g]); +g.setColor (this.getForeground ()); +g.drawRect (5, 5, this.getWidth () - 10, this.getHeight () - 10); +var width = g.getFontMetrics ().stringWidth (this.getTitle ()); +g.setColor (this.getBackground ()); +g.fillRect (10, 0, width, 10); +g.setColor (this.getForeground ()); +g.drawString (this.getTitle (), 10, 10); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "getTitle", +function () { +return this.title; +}); +Clazz.defineMethod (c$, "setTitle", +function (title) { +this.title = title; +}, "~S"); +}); diff --git a/bin/jalview/appletgui/Tooltip.js b/bin/jalview/appletgui/Tooltip.js index cb48e62..425b8d7 100644 --- a/bin/jalview/appletgui/Tooltip.js +++ b/bin/jalview/appletgui/Tooltip.js @@ -1,67 +1,67 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (null, "jalview.appletgui.Tooltip", ["awt2swing.Frame", "java.applet.Applet", "java.awt.Toolkit"], function () { -c$ = Clazz.decorateAsClass (function () { -this.tip = null; -this.lastTip = ""; -this.setPosition = false; -this.owner = null; -this.mainContainer = null; -this.mainLayout = null; -this.shown = false; -this.VERTICAL_OFFSET = 20; -this.HORIZONTAL_ENLARGE = 10; -this.fontHeight = 0; -this.linkImage = null; -this.fm = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "Tooltip"); -Clazz.defineMethod (c$, "setVisible", -function (b) { -}, "~B"); -Clazz.makeConstructor (c$, -function (tip, owner) { -this.owner = owner; -this.setTip (tip); -var url = this.getClass ().getResource ("/images/link.gif"); -if (url != null) { -this.linkImage = java.awt.Toolkit.getDefaultToolkit ().getImage (url); -}}, "~S,java.awt.Component"); -Clazz.defineMethod (c$, "setTip", -function (tip) { -System.err.println ("Tooltip: " + tip); -}, "~S"); -Clazz.defineMethod (c$, "setTipLocation", -function (evt) { -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "removeToolTip", -($fz = function () { -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "mouseEntered", -function (me) { -this.setTipLocation (me); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mouseExited", -function (me) { -this.removeToolTip (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mousePressed", -function (me) { -this.removeToolTip (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mouseReleased", -function (me) { -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mouseClicked", -function (me) { -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mouseMoved", -function (me) { -if (!this.shown) { -this.setTipLocation (me); -} else if (this.setPosition) { -this.setTipLocation (me); -}}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "mouseDragged", -function (me) { -}, "java.awt.event.MouseEvent"); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (null, "jalview.appletgui.Tooltip", ["awt2swing.Frame", "java.applet.Applet", "java.awt.Toolkit"], function () { +c$ = Clazz.decorateAsClass (function () { +this.tip = null; +this.lastTip = ""; +this.setPosition = false; +this.owner = null; +this.mainContainer = null; +this.mainLayout = null; +this.shown = false; +this.VERTICAL_OFFSET = 20; +this.HORIZONTAL_ENLARGE = 10; +this.fontHeight = 0; +this.linkImage = null; +this.fm = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "Tooltip"); +Clazz.defineMethod (c$, "setVisible", +function (b) { +}, "~B"); +Clazz.makeConstructor (c$, +function (tip, owner) { +this.owner = owner; +this.setTip (tip); +var url = this.getClass ().getResource ("/images/link.gif"); +if (url != null) { +this.linkImage = java.awt.Toolkit.getDefaultToolkit ().getImage (url); +}}, "~S,java.awt.Component"); +Clazz.defineMethod (c$, "setTip", +function (tip) { +System.err.println ("Tooltip: " + tip); +}, "~S"); +Clazz.defineMethod (c$, "setTipLocation", +function (evt) { +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "removeToolTip", +($fz = function () { +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "mouseEntered", +function (me) { +this.setTipLocation (me); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mouseExited", +function (me) { +this.removeToolTip (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mousePressed", +function (me) { +this.removeToolTip (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mouseReleased", +function (me) { +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mouseClicked", +function (me) { +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mouseMoved", +function (me) { +if (!this.shown) { +this.setTipLocation (me); +} else if (this.setPosition) { +this.setTipLocation (me); +}}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "mouseDragged", +function (me) { +}, "java.awt.event.MouseEvent"); +}); diff --git a/bin/jalview/appletgui/TreeCanvas.class b/bin/jalview/appletgui/TreeCanvas.class index ee9c1c1..b5cddc1 100644 Binary files a/bin/jalview/appletgui/TreeCanvas.class and b/bin/jalview/appletgui/TreeCanvas.class differ diff --git a/bin/jalview/appletgui/TreeCanvas.js b/bin/jalview/appletgui/TreeCanvas.js index da76a3e..69da9f2 100644 --- a/bin/jalview/appletgui/TreeCanvas.js +++ b/bin/jalview/appletgui/TreeCanvas.js @@ -1,375 +1,375 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.util.Hashtable"], "jalview.appletgui.TreeCanvas", ["jalview.analysis.Conservation", "jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "$.SequenceI", "$.SequenceNode", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Format", "$.MappingUtils", "java.awt.Color", "$.Dimension", "$.Point", "$.Rectangle", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.tree = null; -this.scrollPane = null; -this.av = null; -this.$font = null; -this.fitToWindow = true; -this.showDistances = false; -this.showBootstrap = false; -this.markPlaceholders = false; -this.offx = 20; -this.offy = 0; -this.threshold = 0; -this.longestName = null; -this.labelLength = -1; -this.nameHash = null; -this.nodeHash = null; -this.highlightNode = null; -this.ap = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "TreeCanvas", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); -Clazz.prepareFields (c$, function () { -this.nameHash = new java.util.Hashtable (); -this.nodeHash = new java.util.Hashtable (); -}); -Clazz.makeConstructor (c$, -function (ap, scroller) { -Clazz.superConstructor (this, jalview.appletgui.TreeCanvas, []); -this.ap = ap; -this.av = ap.av; -this.$font = this.av.getFont (); -this.scrollPane = scroller; -this.addMouseListener (this); -this.addMouseMotionListener (this); -this.setLayout (null); -jalview.appletgui.PaintRefresher.Register (this, this.av.getSequenceSetId ()); -}, "jalview.appletgui.AlignmentPanel,awt2swing.ScrollPane"); -Clazz.defineMethod (c$, "treeSelectionChanged", -function (sequence) { -var selected = this.av.getSelectionGroup (); -if (selected == null) { -selected = new jalview.datamodel.SequenceGroup (); -this.av.setSelectionGroup (selected); -}selected.setEndRes (this.av.getAlignment ().getWidth () - 1); -selected.addOrRemove (sequence, true); -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "setTree", -function (tree) { -this.tree = tree; -tree.findHeight (tree.getTopNode ()); -var leaves = tree.findLeaves (tree.getTopNode (), new java.util.Vector ()); -var has_placeholders = false; -this.longestName = ""; -for (var i = 0; i < leaves.size (); i++) { -var lf = leaves.elementAt (i); -if (lf.isPlaceholder ()) { -has_placeholders = true; -}if (this.longestName.length < (lf.element ()).getName ().length) { -this.longestName = " * " + (lf.element ()).getName (); -}} -this.setMarkPlaceholders (has_placeholders); -}, "jalview.analysis.NJTree"); -Clazz.defineMethod (c$, "drawNode", -function (g, node, chunk, scale, width, offx, offy) { -if (node == null) { -return; -}if (node.left () == null && node.right () == null) { -var height = node.height; -var dist = node.dist; -var xstart = Clazz.floatToInt ((height - dist) * scale) + offx; -var xend = Clazz.floatToInt (height * scale) + offx; -var ypos = Clazz.floatToInt (node.ycount * chunk) + offy; -if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { -var seq = node.element (); -if (this.av.getSequenceColour (seq) === java.awt.Color.white) { -g.setColor (java.awt.Color.black); -} else { -g.setColor (this.av.getSequenceColour (seq).darker ()); -}} else { -g.setColor (java.awt.Color.black); -}g.drawLine (xstart, ypos, xend, ypos); -var nodeLabel = ""; -if (this.showDistances && node.dist > 0) { -nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist); -}if (this.showBootstrap) { -var btstrap = node.getBootstrap (); -if (btstrap > -1) { -if (this.showDistances) { -nodeLabel = nodeLabel + " : "; -}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ()); -}}if (!nodeLabel.equals ("")) { -g.drawString (nodeLabel, xstart + 2, ypos - 2); -}var name = (this.markPlaceholders && node.isPlaceholder ()) ? (" * " + node.getName ()) : node.getName (); -var fm = g.getFontMetrics (this.$font); -var charWidth = fm.stringWidth (name) + 3; -var charHeight = fm.getHeight (); -var rect = new java.awt.Rectangle (xend + 10, ypos - charHeight, charWidth, charHeight); -this.nameHash.put (node.element (), rect); -var selected = this.av.getSelectionGroup (); -if (selected != null && selected.getSequences (null).contains (node.element ())) { -g.setColor (java.awt.Color.gray); -g.fillRect (xend + 10, ypos - charHeight + 3, charWidth, charHeight); -g.setColor (java.awt.Color.white); -}g.drawString (name, xend + 10, ypos); -g.setColor (java.awt.Color.black); -} else { -this.drawNode (g, node.left (), chunk, scale, width, offx, offy); -this.drawNode (g, node.right (), chunk, scale, width, offx, offy); -var height = node.height; -var dist = node.dist; -var xstart = Clazz.floatToInt ((height - dist) * scale) + offx; -var xend = Clazz.floatToInt (height * scale) + offx; -var ypos = Clazz.floatToInt (node.ycount * chunk) + offy; -g.setColor (node.color.darker ()); -g.drawLine (xstart, ypos, xend, ypos); -if (node === this.highlightNode) { -g.fillRect (xend - 3, ypos - 3, 6, 6); -} else { -g.fillRect (xend - 2, ypos - 2, 4, 4); -}var ystart = Clazz.floatToInt ((node.left ()).ycount * chunk) + offy; -var yend = Clazz.floatToInt ((node.right ()).ycount * chunk) + offy; -var pos = new java.awt.Rectangle (xend - 2, ypos - 2, 5, 5); -this.nodeHash.put (node, pos); -g.drawLine (Clazz.floatToInt (height * scale) + offx, ystart, Clazz.floatToInt (height * scale) + offx, yend); -var nodeLabel = ""; -if (this.showDistances && (node.dist > 0)) { -nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist); -}if (this.showBootstrap) { -var btstrap = node.getBootstrap (); -if (btstrap > -1) { -if (this.showDistances) { -nodeLabel = nodeLabel + " : "; -}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ()); -}}if (!nodeLabel.equals ("")) { -g.drawString (nodeLabel, xstart + 2, ypos - 2); -}}}, "java.awt.Graphics,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "findElement", -function (x, y) { -var keys = this.nameHash.keys (); -while (keys.hasMoreElements ()) { -var ob = keys.nextElement (); -var rect = this.nameHash.get (ob); -if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) { -return ob; -}} -keys = this.nodeHash.keys (); -while (keys.hasMoreElements ()) { -var ob = keys.nextElement (); -var rect = this.nodeHash.get (ob); -if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) { -return ob; -}} -return null; -}, "~N,~N"); -Clazz.defineMethod (c$, "pickNodes", -function (pickBox) { -var width = this.getSize ().width; -var height = this.getSize ().height; -var top = this.tree.getTopNode (); -var wscale = (width * .8 - this.offx * 2) / this.tree.getMaxHeight (); -if (top.count == 0) { -top.count = (top.left ()).count + (top.right ()).count; -}var chunk = (height - this.offy) / top.count; -this.pickNode (pickBox, top, chunk, wscale, width, this.offx, this.offy); -}, "java.awt.Rectangle"); -Clazz.defineMethod (c$, "pickNode", -function (pickBox, node, chunk, scale, width, offx, offy) { -if (node == null) { -return; -}if (node.left () == null && node.right () == null) { -var height = node.height; -var xend = Clazz.floatToInt (height * scale) + offx; -var ypos = Clazz.floatToInt (node.ycount * chunk) + offy; -if (pickBox.contains ( new java.awt.Point (xend, ypos))) { -if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { -var seq = node.element (); -var sg = this.av.getSelectionGroup (); -if (sg != null) { -sg.addOrRemove (seq, true); -}}}} else { -this.pickNode (pickBox, node.left (), chunk, scale, width, offx, offy); -this.pickNode (pickBox, node.right (), chunk, scale, width, offx, offy); -}}, "java.awt.Rectangle,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "setColor", -function (node, c) { -if (node == null) { -return; -}if (node.left () == null && node.right () == null) { -node.color = c; -if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { -this.av.setSequenceColour (node.element (), c); -}} else { -node.color = c; -this.setColor (node.left (), c); -this.setColor (node.right (), c); -}}, "jalview.datamodel.SequenceNode,java.awt.Color"); -Clazz.overrideMethod (c$, "update", -function (g) { -this.paint (g); -}, "java.awt.Graphics"); -Clazz.overrideMethod (c$, "paintComponent", -function (g) { -if (this.tree == null) { -return; -}if (this.nameHash.size () == 0) { -this.repaint (); -}var width = this.scrollPane.getSize ().width; -var height = this.scrollPane.getSize ().height; -if (!this.fitToWindow) { -height = g.getFontMetrics (this.$font).getHeight () * this.nameHash.size (); -}if (this.getSize ().width > width) { -this.setSize ( new java.awt.Dimension (width, height)); -this.scrollPane.validate (); -return; -}this.setSize ( new java.awt.Dimension (width, height)); -g.setFont (this.$font); -this.draw (g, width, height); -this.validate (); -}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "draw", -function (g, width, height) { -this.offy = this.$font.getSize () + 10; -g.setColor (java.awt.Color.white); -g.fillRect (0, 0, width, height); -this.labelLength = g.getFontMetrics (this.$font).stringWidth (this.longestName) + 20; -var wscale = (width - this.labelLength - this.offx * 2) / this.tree.getMaxHeight (); -var top = this.tree.getTopNode (); -if (top.count == 0) { -top.count = (top.left ()).count + (top.right ()).count; -}var chunk = (height - this.offy) / top.count; -this.drawNode (g, this.tree.getTopNode (), chunk, wscale, width, this.offx, this.offy); -if (this.threshold != 0) { -if (this.av.getCurrentTree () === this.tree) { -g.setColor (java.awt.Color.red); -} else { -g.setColor (java.awt.Color.gray); -}var x = Clazz.floatToInt (this.threshold * (this.getSize ().width - this.labelLength - 2 * this.offx) + this.offx); -g.drawLine (x, 0, x, this.getSize ().height); -}}, "java.awt.Graphics,~N,~N"); -Clazz.overrideMethod (c$, "mouseReleased", -function (e) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseEntered", -function (e) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseExited", -function (e) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseClicked", -function (evt) { -if (this.highlightNode != null) { -if (evt.getClickCount () > 1) { -this.tree.swapNodes (this.highlightNode); -this.tree.reCount (this.tree.getTopNode ()); -this.tree.findHeight (this.tree.getTopNode ()); -} else { -var leaves = new java.util.Vector (); -this.tree.findLeaves (this.highlightNode, leaves); -for (var i = 0; i < leaves.size (); i++) { -var seq = (leaves.elementAt (i)).element (); -this.treeSelectionChanged (seq); -} -}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); -this.repaint (); -this.av.sendSelection (); -}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseDragged", -function (ect) { -}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mouseMoved", -function (evt) { -this.av.setCurrentTree (this.tree); -var ob = this.findElement (evt.getX (), evt.getY ()); -if (Clazz.instanceOf (ob, jalview.datamodel.SequenceNode)) { -this.highlightNode = ob; -this.repaint (); -} else { -if (this.highlightNode != null) { -this.highlightNode = null; -this.repaint (); -}}}, "java.awt.event.MouseEvent"); -Clazz.overrideMethod (c$, "mousePressed", -function (e) { -this.av.setCurrentTree (this.tree); -var x = e.getX (); -var y = e.getY (); -var ob = this.findElement (x, y); -if (Clazz.instanceOf (ob, jalview.datamodel.SequenceI)) { -this.treeSelectionChanged (ob); -jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); -this.repaint (); -this.av.sendSelection (); -return; -} else if (!(Clazz.instanceOf (ob, jalview.datamodel.SequenceNode))) { -if (this.tree.getMaxHeight () != 0) { -this.threshold = (x - this.offx) / (this.getSize ().width - this.labelLength - 2 * this.offx); -this.tree.getGroups ().removeAllElements (); -this.tree.groupNodes (this.tree.getTopNode (), this.threshold); -this.setColor (this.tree.getTopNode (), java.awt.Color.black); -this.av.setSelectionGroup (null); -this.av.getAlignment ().deleteAllGroups (); -this.av.clearSequenceColours (); -var codingComplement = this.av.getCodingComplement (); -if (codingComplement != null) { -codingComplement.setSelectionGroup (null); -codingComplement.getAlignment ().deleteAllGroups (); -codingComplement.clearSequenceColours (); -}this.colourGroups (); -}}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); -this.repaint (); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "colourGroups", -function () { -for (var i = 0; i < this.tree.getGroups ().size (); i++) { -var col = new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255)); -this.setColor (this.tree.getGroups ().elementAt (i), col.brighter ()); -var l = this.tree.findLeaves (this.tree.getGroups ().elementAt (i), new java.util.Vector ()); -var sequences = new java.util.Vector (); -for (var j = 0; j < l.size (); j++) { -var s1 = (l.elementAt (j)).element (); -if (!sequences.contains (s1)) { -sequences.addElement (s1); -}} -var cs = null; -var sg = new jalview.datamodel.SequenceGroup (sequences, "", cs, true, true, false, 0, this.av.getAlignment ().getWidth () - 1); -if (this.av.getGlobalColourScheme () != null) { -if (Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.UserColourScheme)) { -cs = new jalview.schemes.UserColourScheme ((this.av.getGlobalColourScheme ()).getColours ()); -} else { -cs = jalview.schemes.ColourSchemeProperty.getColour (sg, jalview.schemes.ColourSchemeProperty.getColourName (this.av.getGlobalColourScheme ())); -}if (cs != null) { -cs.setThreshold (this.av.getGlobalColourScheme ().getThreshold (), this.av.isIgnoreGapsConsensus ()); -}}sg.cs = cs; -sg.setName ("JTreeGroup:" + sg.hashCode ()); -sg.setIdColour (col); -if (this.av.getGlobalColourScheme () != null && this.av.getGlobalColourScheme ().conservationApplied ()) { -var c = new jalview.analysis.Conservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (null), sg.getStartRes (), sg.getEndRes ()); -c.calculate (); -c.verdict (false, this.av.getConsPercGaps ()); -cs.setConservation (c); -sg.cs = cs; -}this.av.getAlignment ().addGroup (sg); -this.av.getAlignment ().addGroup (sg); -var codingComplement = this.av.getCodingComplement (); -if (codingComplement != null) { -var mappedGroup = jalview.util.MappingUtils.mapSequenceGroup (sg, this.av, codingComplement); -if (mappedGroup.getSequences ().size () > 0) { -codingComplement.getAlignment ().addGroup (mappedGroup); -for (var seq, $seq = mappedGroup.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -codingComplement.setSequenceColour (seq, col); -} -}}} -this.ap.updateAnnotation (); -if (this.av.getCodingComplement () != null) { -(this.av.getCodingComplement ()).firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); -}}); -Clazz.defineMethod (c$, "setShowDistances", -function (state) { -this.showDistances = state; -this.repaint (); -}, "~B"); -Clazz.defineMethod (c$, "setShowBootstrap", -function (state) { -this.showBootstrap = state; -this.repaint (); -}, "~B"); -Clazz.defineMethod (c$, "setMarkPlaceholders", -function (state) { -this.markPlaceholders = state; -this.repaint (); -}, "~B"); -Clazz.defineStatics (c$, -"PLACEHOLDER", " * "); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.util.Hashtable"], "jalview.appletgui.TreeCanvas", ["jalview.analysis.Conservation", "jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "$.SequenceI", "$.SequenceNode", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Format", "$.MappingUtils", "java.awt.Color", "$.Dimension", "$.Point", "$.Rectangle", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.tree = null; +this.scrollPane = null; +this.av = null; +this.$font = null; +this.fitToWindow = true; +this.showDistances = false; +this.showBootstrap = false; +this.markPlaceholders = false; +this.offx = 20; +this.offy = 0; +this.threshold = 0; +this.longestName = null; +this.labelLength = -1; +this.nameHash = null; +this.nodeHash = null; +this.highlightNode = null; +this.ap = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "TreeCanvas", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]); +Clazz.prepareFields (c$, function () { +this.nameHash = new java.util.Hashtable (); +this.nodeHash = new java.util.Hashtable (); +}); +Clazz.makeConstructor (c$, +function (ap, scroller) { +Clazz.superConstructor (this, jalview.appletgui.TreeCanvas, []); +this.ap = ap; +this.av = ap.av; +this.$font = this.av.getFont (); +this.scrollPane = scroller; +this.addMouseListener (this); +this.addMouseMotionListener (this); +this.setLayout (null); +jalview.appletgui.PaintRefresher.Register (this, this.av.getSequenceSetId ()); +}, "jalview.appletgui.AlignmentPanel,awt2swing.ScrollPane"); +Clazz.defineMethod (c$, "treeSelectionChanged", +function (sequence) { +var selected = this.av.getSelectionGroup (); +if (selected == null) { +selected = new jalview.datamodel.SequenceGroup (); +this.av.setSelectionGroup (selected); +}selected.setEndRes (this.av.getAlignment ().getWidth () - 1); +selected.addOrRemove (sequence, true); +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "setTree", +function (tree) { +this.tree = tree; +tree.findHeight (tree.getTopNode ()); +var leaves = tree.findLeaves (tree.getTopNode (), new java.util.Vector ()); +var has_placeholders = false; +this.longestName = ""; +for (var i = 0; i < leaves.size (); i++) { +var lf = leaves.elementAt (i); +if (lf.isPlaceholder ()) { +has_placeholders = true; +}if (this.longestName.length < (lf.element ()).getName ().length) { +this.longestName = " * " + (lf.element ()).getName (); +}} +this.setMarkPlaceholders (has_placeholders); +}, "jalview.analysis.NJTree"); +Clazz.defineMethod (c$, "drawNode", +function (g, node, chunk, scale, width, offx, offy) { +if (node == null) { +return; +}if (node.left () == null && node.right () == null) { +var height = node.height; +var dist = node.dist; +var xstart = Clazz.floatToInt ((height - dist) * scale) + offx; +var xend = Clazz.floatToInt (height * scale) + offx; +var ypos = Clazz.floatToInt (node.ycount * chunk) + offy; +if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { +var seq = node.element (); +if (this.av.getSequenceColour (seq) === java.awt.Color.white) { +g.setColor (java.awt.Color.black); +} else { +g.setColor (this.av.getSequenceColour (seq).darker ()); +}} else { +g.setColor (java.awt.Color.black); +}g.drawLine (xstart, ypos, xend, ypos); +var nodeLabel = ""; +if (this.showDistances && node.dist > 0) { +nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist); +}if (this.showBootstrap) { +var btstrap = node.getBootstrap (); +if (btstrap > -1) { +if (this.showDistances) { +nodeLabel = nodeLabel + " : "; +}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ()); +}}if (!nodeLabel.equals ("")) { +g.drawString (nodeLabel, xstart + 2, ypos - 2); +}var name = (this.markPlaceholders && node.isPlaceholder ()) ? (" * " + node.getName ()) : node.getName (); +var fm = g.getFontMetrics (this.$font); +var charWidth = fm.stringWidth (name) + 3; +var charHeight = fm.getHeight (); +var rect = new java.awt.Rectangle (xend + 10, ypos - charHeight, charWidth, charHeight); +this.nameHash.put (node.element (), rect); +var selected = this.av.getSelectionGroup (); +if (selected != null && selected.getSequences (null).contains (node.element ())) { +g.setColor (java.awt.Color.gray); +g.fillRect (xend + 10, ypos - charHeight + 3, charWidth, charHeight); +g.setColor (java.awt.Color.white); +}g.drawString (name, xend + 10, ypos); +g.setColor (java.awt.Color.black); +} else { +this.drawNode (g, node.left (), chunk, scale, width, offx, offy); +this.drawNode (g, node.right (), chunk, scale, width, offx, offy); +var height = node.height; +var dist = node.dist; +var xstart = Clazz.floatToInt ((height - dist) * scale) + offx; +var xend = Clazz.floatToInt (height * scale) + offx; +var ypos = Clazz.floatToInt (node.ycount * chunk) + offy; +g.setColor (node.color.darker ()); +g.drawLine (xstart, ypos, xend, ypos); +if (node === this.highlightNode) { +g.fillRect (xend - 3, ypos - 3, 6, 6); +} else { +g.fillRect (xend - 2, ypos - 2, 4, 4); +}var ystart = Clazz.floatToInt ((node.left ()).ycount * chunk) + offy; +var yend = Clazz.floatToInt ((node.right ()).ycount * chunk) + offy; +var pos = new java.awt.Rectangle (xend - 2, ypos - 2, 5, 5); +this.nodeHash.put (node, pos); +g.drawLine (Clazz.floatToInt (height * scale) + offx, ystart, Clazz.floatToInt (height * scale) + offx, yend); +var nodeLabel = ""; +if (this.showDistances && (node.dist > 0)) { +nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist); +}if (this.showBootstrap) { +var btstrap = node.getBootstrap (); +if (btstrap > -1) { +if (this.showDistances) { +nodeLabel = nodeLabel + " : "; +}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ()); +}}if (!nodeLabel.equals ("")) { +g.drawString (nodeLabel, xstart + 2, ypos - 2); +}}}, "java.awt.Graphics,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "findElement", +function (x, y) { +var keys = this.nameHash.keys (); +while (keys.hasMoreElements ()) { +var ob = keys.nextElement (); +var rect = this.nameHash.get (ob); +if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) { +return ob; +}} +keys = this.nodeHash.keys (); +while (keys.hasMoreElements ()) { +var ob = keys.nextElement (); +var rect = this.nodeHash.get (ob); +if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) { +return ob; +}} +return null; +}, "~N,~N"); +Clazz.defineMethod (c$, "pickNodes", +function (pickBox) { +var width = this.getSize ().width; +var height = this.getSize ().height; +var top = this.tree.getTopNode (); +var wscale = (width * .8 - this.offx * 2) / this.tree.getMaxHeight (); +if (top.count == 0) { +top.count = (top.left ()).count + (top.right ()).count; +}var chunk = (height - this.offy) / top.count; +this.pickNode (pickBox, top, chunk, wscale, width, this.offx, this.offy); +}, "java.awt.Rectangle"); +Clazz.defineMethod (c$, "pickNode", +function (pickBox, node, chunk, scale, width, offx, offy) { +if (node == null) { +return; +}if (node.left () == null && node.right () == null) { +var height = node.height; +var xend = Clazz.floatToInt (height * scale) + offx; +var ypos = Clazz.floatToInt (node.ycount * chunk) + offy; +if (pickBox.contains ( new java.awt.Point (xend, ypos))) { +if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { +var seq = node.element (); +var sg = this.av.getSelectionGroup (); +if (sg != null) { +sg.addOrRemove (seq, true); +}}}} else { +this.pickNode (pickBox, node.left (), chunk, scale, width, offx, offy); +this.pickNode (pickBox, node.right (), chunk, scale, width, offx, offy); +}}, "java.awt.Rectangle,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "setColor", +function (node, c) { +if (node == null) { +return; +}if (node.left () == null && node.right () == null) { +node.color = c; +if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) { +this.av.setSequenceColour (node.element (), c); +}} else { +node.color = c; +this.setColor (node.left (), c); +this.setColor (node.right (), c); +}}, "jalview.datamodel.SequenceNode,java.awt.Color"); +Clazz.overrideMethod (c$, "update", +function (g) { +this.paint (g); +}, "java.awt.Graphics"); +Clazz.overrideMethod (c$, "paintComponent", +function (g) { +if (this.tree == null) { +return; +}if (this.nameHash.size () == 0) { +this.repaint (); +}var width = this.scrollPane.getSize ().width; +var height = this.scrollPane.getSize ().height; +if (!this.fitToWindow) { +height = g.getFontMetrics (this.$font).getHeight () * this.nameHash.size (); +}if (this.getSize ().width > width) { +this.setSize ( new java.awt.Dimension (width, height)); +this.scrollPane.validate (); +return; +}this.setSize ( new java.awt.Dimension (width, height)); +g.setFont (this.$font); +this.draw (g, width, height); +this.validate (); +}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "draw", +function (g, width, height) { +this.offy = this.$font.getSize () + 10; +g.setColor (java.awt.Color.white); +g.fillRect (0, 0, width, height); +this.labelLength = g.getFontMetrics (this.$font).stringWidth (this.longestName) + 20; +var wscale = (width - this.labelLength - this.offx * 2) / this.tree.getMaxHeight (); +var top = this.tree.getTopNode (); +if (top.count == 0) { +top.count = (top.left ()).count + (top.right ()).count; +}var chunk = (height - this.offy) / top.count; +this.drawNode (g, this.tree.getTopNode (), chunk, wscale, width, this.offx, this.offy); +if (this.threshold != 0) { +if (this.av.getCurrentTree () === this.tree) { +g.setColor (java.awt.Color.red); +} else { +g.setColor (java.awt.Color.gray); +}var x = Clazz.floatToInt (this.threshold * (this.getSize ().width - this.labelLength - 2 * this.offx) + this.offx); +g.drawLine (x, 0, x, this.getSize ().height); +}}, "java.awt.Graphics,~N,~N"); +Clazz.overrideMethod (c$, "mouseReleased", +function (e) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseEntered", +function (e) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseExited", +function (e) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseClicked", +function (evt) { +if (this.highlightNode != null) { +if (evt.getClickCount () > 1) { +this.tree.swapNodes (this.highlightNode); +this.tree.reCount (this.tree.getTopNode ()); +this.tree.findHeight (this.tree.getTopNode ()); +} else { +var leaves = new java.util.Vector (); +this.tree.findLeaves (this.highlightNode, leaves); +for (var i = 0; i < leaves.size (); i++) { +var seq = (leaves.elementAt (i)).element (); +this.treeSelectionChanged (seq); +} +}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); +this.repaint (); +this.av.sendSelection (); +}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseDragged", +function (ect) { +}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mouseMoved", +function (evt) { +this.av.setCurrentTree (this.tree); +var ob = this.findElement (evt.getX (), evt.getY ()); +if (Clazz.instanceOf (ob, jalview.datamodel.SequenceNode)) { +this.highlightNode = ob; +this.repaint (); +} else { +if (this.highlightNode != null) { +this.highlightNode = null; +this.repaint (); +}}}, "java.awt.event.MouseEvent"); +Clazz.overrideMethod (c$, "mousePressed", +function (e) { +this.av.setCurrentTree (this.tree); +var x = e.getX (); +var y = e.getY (); +var ob = this.findElement (x, y); +if (Clazz.instanceOf (ob, jalview.datamodel.SequenceI)) { +this.treeSelectionChanged (ob); +jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); +this.repaint (); +this.av.sendSelection (); +return; +} else if (!(Clazz.instanceOf (ob, jalview.datamodel.SequenceNode))) { +if (this.tree.getMaxHeight () != 0) { +this.threshold = (x - this.offx) / (this.getSize ().width - this.labelLength - 2 * this.offx); +this.tree.getGroups ().removeAllElements (); +this.tree.groupNodes (this.tree.getTopNode (), this.threshold); +this.setColor (this.tree.getTopNode (), java.awt.Color.black); +this.av.setSelectionGroup (null); +this.av.getAlignment ().deleteAllGroups (); +this.av.clearSequenceColours (); +var codingComplement = this.av.getCodingComplement (); +if (codingComplement != null) { +codingComplement.setSelectionGroup (null); +codingComplement.getAlignment ().deleteAllGroups (); +codingComplement.clearSequenceColours (); +}this.colourGroups (); +}}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ()); +this.repaint (); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "colourGroups", +function () { +for (var i = 0; i < this.tree.getGroups ().size (); i++) { +var col = new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255)); +this.setColor (this.tree.getGroups ().elementAt (i), col.brighter ()); +var l = this.tree.findLeaves (this.tree.getGroups ().elementAt (i), new java.util.Vector ()); +var sequences = new java.util.Vector (); +for (var j = 0; j < l.size (); j++) { +var s1 = (l.elementAt (j)).element (); +if (!sequences.contains (s1)) { +sequences.addElement (s1); +}} +var cs = null; +var sg = new jalview.datamodel.SequenceGroup (sequences, "", cs, true, true, false, 0, this.av.getAlignment ().getWidth () - 1); +if (this.av.getGlobalColourScheme () != null) { +if (Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.UserColourScheme)) { +cs = new jalview.schemes.UserColourScheme ((this.av.getGlobalColourScheme ()).getColours ()); +} else { +cs = jalview.schemes.ColourSchemeProperty.getColour (sg, jalview.schemes.ColourSchemeProperty.getColourName (this.av.getGlobalColourScheme ())); +}if (cs != null) { +cs.setThreshold (this.av.getGlobalColourScheme ().getThreshold (), this.av.isIgnoreGapsConsensus ()); +}}sg.cs = cs; +sg.setName ("JTreeGroup:" + sg.hashCode ()); +sg.setIdColour (col); +if (this.av.getGlobalColourScheme () != null && this.av.getGlobalColourScheme ().conservationApplied ()) { +var c = new jalview.analysis.Conservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (null), sg.getStartRes (), sg.getEndRes ()); +c.calculate (); +c.verdict (false, this.av.getConsPercGaps ()); +cs.setConservation (c); +sg.cs = cs; +}this.av.getAlignment ().addGroup (sg); +this.av.getAlignment ().addGroup (sg); +var codingComplement = this.av.getCodingComplement (); +if (codingComplement != null) { +var mappedGroup = jalview.util.MappingUtils.mapSequenceGroup (sg, this.av, codingComplement); +if (mappedGroup.getSequences ().size () > 0) { +codingComplement.getAlignment ().addGroup (mappedGroup); +for (var seq, $seq = mappedGroup.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +codingComplement.setSequenceColour (seq, col); +} +}}} +this.ap.updateAnnotation (); +if (this.av.getCodingComplement () != null) { +(this.av.getCodingComplement ()).firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ()); +}}); +Clazz.defineMethod (c$, "setShowDistances", +function (state) { +this.showDistances = state; +this.repaint (); +}, "~B"); +Clazz.defineMethod (c$, "setShowBootstrap", +function (state) { +this.showBootstrap = state; +this.repaint (); +}, "~B"); +Clazz.defineMethod (c$, "setMarkPlaceholders", +function (state) { +this.markPlaceholders = state; +this.repaint (); +}, "~B"); +Clazz.defineStatics (c$, +"PLACEHOLDER", " * "); +}); diff --git a/bin/jalview/appletgui/TreePanel$TreeLoader.class b/bin/jalview/appletgui/TreePanel$TreeLoader.class index 9a214e5..cd993a2 100644 Binary files a/bin/jalview/appletgui/TreePanel$TreeLoader.class and b/bin/jalview/appletgui/TreePanel$TreeLoader.class differ diff --git a/bin/jalview/appletgui/TreePanel.class b/bin/jalview/appletgui/TreePanel.class index a2409c8..b8a678d 100644 Binary files a/bin/jalview/appletgui/TreePanel.class and b/bin/jalview/appletgui/TreePanel.class differ diff --git a/bin/jalview/appletgui/TreePanel.js b/bin/jalview/appletgui/TreePanel.js index 4d0d747..77a1db5 100644 --- a/bin/jalview/appletgui/TreePanel.js +++ b/bin/jalview/appletgui/TreePanel.js @@ -1,261 +1,261 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "java.lang.Thread", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuBar", "$.MenuItem", "$.ScrollPane", "java.awt.BorderLayout"], "jalview.appletgui.TreePanel", ["awt2swing.Frame", "jalview.analysis.NJTree", "jalview.api.analysis.ViewBasedAnalysisI", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.FontChooser", "$.TreeCanvas", "jalview.bin.JalviewLite", "jalview.datamodel.Alignment", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.MessageManager", "java.awt.Color", "$.Font"], function () { -c$ = Clazz.decorateAsClass (function () { -this.seq = null; -this.$type = null; -this.pwtype = null; -this.start = 0; -this.end = 0; -this.treeCanvas = null; -this.tree = null; -this.ap = null; -this.av = null; -if (!Clazz.isClassDefined ("jalview.appletgui.TreePanel.TreeLoader")) { -jalview.appletgui.TreePanel.$TreePanel$TreeLoader$ (); -} -this.borderLayout1 = null; -this.scrollPane = null; -this.jMenuBar1 = null; -this.jMenu2 = null; -this.fontSize = null; -this.bootstrapMenu = null; -this.distanceMenu = null; -this.placeholdersMenu = null; -this.fitToWindow = null; -this.fileMenu = null; -this.newickOutput = null; -this.inputData = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "TreePanel", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener]); -Clazz.prepareFields (c$, function () { -this.borderLayout1 = new java.awt.BorderLayout (); -this.scrollPane = new awt2swing.ScrollPane (); -this.jMenuBar1 = new awt2swing.MenuBar (); -this.jMenu2 = new awt2swing.Menu (); -this.fontSize = new awt2swing.MenuItem (); -this.bootstrapMenu = new awt2swing.CheckboxMenuItem (); -this.distanceMenu = new awt2swing.CheckboxMenuItem (); -this.placeholdersMenu = new awt2swing.CheckboxMenuItem (); -this.fitToWindow = new awt2swing.CheckboxMenuItem (); -this.fileMenu = new awt2swing.Menu (); -this.newickOutput = new awt2swing.MenuItem (); -this.inputData = new awt2swing.MenuItem (); -}); -Clazz.defineMethod (c$, "getTree", -function () { -return this.tree; -}); -Clazz.defineMethod (c$, "finalize", -function () { -this.ap = null; -this.av = null; -Clazz.superCall (this, jalview.appletgui.TreePanel, "finalize", []); -}); -Clazz.makeConstructor (c$, -function (ap, type, pwtype) { -Clazz.superConstructor (this, jalview.appletgui.TreePanel, []); -try { -this.jbInit (); -this.setMenuBar (this.jMenuBar1); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -this.initTreePanel (ap, type, pwtype, null); -}, "jalview.appletgui.AlignmentPanel,~S,~S"); -Clazz.makeConstructor (c$, -function (ap, type, pwtype, newtree) { -Clazz.superConstructor (this, jalview.appletgui.TreePanel, []); -try { -this.jbInit (); -this.setMenuBar (this.jMenuBar1); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.initTreePanel (ap, type, pwtype, newtree); -}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile"); -Clazz.defineMethod (c$, "initTreePanel", -function (ap, type, pwtype, newTree) { -this.ap = ap; -this.av = ap.av; -this.$type = type; -this.pwtype = pwtype; -this.treeCanvas = new jalview.appletgui.TreeCanvas (ap, this.scrollPane); -var tl = Clazz.innerTypeInstance (jalview.appletgui.TreePanel.TreeLoader, this, null, newTree); -tl.start (); -this.embedMenuIfNeeded (this.treeCanvas); -this.scrollPane.add (this.treeCanvas, "Center"); -}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile"); -Clazz.defineMethod (c$, "showOriginalData", -function () { -if (this.tree.seqData != null) { -var gc = '-'; -try { -gc = this.av.getGapCharacter (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -;var alAndColsel = this.tree.seqData.getAlignmentAndColumnSelection (gc); -if (alAndColsel != null && alAndColsel[0] != null) { -var al = new jalview.datamodel.Alignment (alAndColsel[0]); -var af = new jalview.appletgui.AlignFrame (al, this.av.applet, "Original Data for Tree", false); -af.viewport.setHiddenColumns (alAndColsel[1]); -}} else { -System.out.println ("Original Tree Data not available"); -}}); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -if (evt.getSource () === this.newickOutput) { -this.newickOutput_actionPerformed (); -} else if (evt.getSource () === this.fontSize) { -this.fontSize_actionPerformed (); -} else if (evt.getSource () === this.inputData) { -this.showOriginalData (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -if (evt.getSource () === this.fitToWindow) { -this.treeCanvas.fitToWindow = this.fitToWindow.getState (); -} else if (evt.getSource () === this.distanceMenu) { -this.treeCanvas.setShowDistances (this.distanceMenu.getState ()); -} else if (evt.getSource () === this.bootstrapMenu) { -this.treeCanvas.setShowBootstrap (this.bootstrapMenu.getState ()); -} else if (evt.getSource () === this.placeholdersMenu) { -this.treeCanvas.setMarkPlaceholders (this.placeholdersMenu.getState ()); -}this.treeCanvas.repaint (); -}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "newickOutput_actionPerformed", -function () { -var fout = new jalview.io.NewickFile (this.tree.getTopNode ()); -var output = fout.print (false, true); -var cap = new jalview.appletgui.CutAndPasteTransfer (false, null); -cap.setText (output); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, this.$type + " " + this.pwtype, 500, 100); -}); -Clazz.defineMethod (c$, "getTreeFont", -function () { -return this.treeCanvas.$font; -}); -Clazz.defineMethod (c$, "setTreeFont", -function (font) { -this.treeCanvas.$font = font; -this.treeCanvas.repaint (); -}, "java.awt.Font"); -Clazz.defineMethod (c$, "fontSize_actionPerformed", -function () { -if (this.treeCanvas == null) { -return; -} new jalview.appletgui.FontChooser (this); -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout (this.borderLayout1); -this.setBackground (java.awt.Color.white); -this.setFont ( new java.awt.Font ("Verdana", 0, 12)); -this.jMenu2.setLabel (jalview.util.MessageManager.getString ("action.view")); -this.fontSize.setLabel (jalview.util.MessageManager.getString ("action.font")); -this.fontSize.addActionListener (this); -this.bootstrapMenu.setLabel (jalview.util.MessageManager.getString ("label.show_bootstrap_values")); -this.bootstrapMenu.addItemListener (this); -this.distanceMenu.setLabel (jalview.util.MessageManager.getString ("label.show_distances")); -this.distanceMenu.addItemListener (this); -this.placeholdersMenu.setLabel (jalview.util.MessageManager.getString ("label.mark_unassociated_leaves")); -this.placeholdersMenu.addItemListener (this); -this.fitToWindow.setState (true); -this.fitToWindow.setLabel (jalview.util.MessageManager.getString ("label.fit_to_window")); -this.fitToWindow.addItemListener (this); -this.fileMenu.setLabel (jalview.util.MessageManager.getString ("action.file")); -this.newickOutput.setLabel (jalview.util.MessageManager.getString ("label.newick_format")); -this.newickOutput.addActionListener (this); -this.inputData.setLabel (jalview.util.MessageManager.getString ("label.input_data")); -this.add (this.scrollPane, "Center"); -this.jMenuBar1.add (this.fileMenu); -this.jMenuBar1.add (this.jMenu2); -this.jMenu2.add (this.fitToWindow); -this.jMenu2.add (this.fontSize); -this.jMenu2.add (this.distanceMenu); -this.jMenu2.add (this.bootstrapMenu); -this.jMenu2.add (this.placeholdersMenu); -this.fileMenu.add (this.newickOutput); -this.fileMenu.add (this.inputData); -this.inputData.addActionListener (this); -}, $fz.isPrivate = true, $fz)); -c$.$TreePanel$TreeLoader$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.newtree = null; -this.odata = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui.TreePanel, "TreeLoader", Thread); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, jalview.appletgui.TreePanel.TreeLoader, []); -this.newtree = a; -}, "jalview.io.NewickFile"); -Clazz.overrideMethod (c$, "run", -function () { -if (this.newtree != null) { -if (this.odata == null) { -this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.newtree); -} else { -this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.odata, this.newtree); -}} else { -var a; -var b; -var c; -var d = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup () != null && this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSize () > 1; -var e = this.b$["jalview.appletgui.TreePanel"].av.getAlignmentView (d); -if (!d) { -a = 0; -b = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getWidth (); -c = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (); -} else { -a = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getStartRes (); -b = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getEndRes () + 1; -c = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSequencesInOrder (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ()); -}var f = jalview.schemes.ResidueProperties.getScoreModel (this.b$["jalview.appletgui.TreePanel"].pwtype); -if (Clazz.instanceOf (f, jalview.api.analysis.ViewBasedAnalysisI)) { -try { -f = f.getClass ().newInstance (); -(f).configureFromAlignmentView (this.b$["jalview.appletgui.TreePanel"].treeCanvas.ap); -} catch (q) { -if (Clazz.exceptionOf (q, Exception)) { -System.err.println ("Couldn't create a scoremodel instance for " + f.getName ()); -q.printStackTrace (); -} else { -throw q; -} -} -this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, f, a, b); -} else { -this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, null, a, b); -}}this.b$["jalview.appletgui.TreePanel"].tree.reCount (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ()); -this.b$["jalview.appletgui.TreePanel"].tree.findHeight (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ()); -this.b$["jalview.appletgui.TreePanel"].treeCanvas.setTree (this.b$["jalview.appletgui.TreePanel"].tree); -if (this.newtree != null) { -var a = this.newtree.HasDistances () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeDistances", this.newtree.HasDistances ()); -var b = this.newtree.HasBootstrap () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeBootstraps", this.newtree.HasBootstrap ()); -this.b$["jalview.appletgui.TreePanel"].distanceMenu.setState (a); -this.b$["jalview.appletgui.TreePanel"].bootstrapMenu.setState (b); -this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowBootstrap (b); -this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowDistances (a); -this.b$["jalview.appletgui.TreePanel"].treeCanvas.setMarkPlaceholders (this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showUnlinkedTreeNodes", false)); -}this.b$["jalview.appletgui.TreePanel"].treeCanvas.repaint (); -this.b$["jalview.appletgui.TreePanel"].av.setCurrentTree (this.b$["jalview.appletgui.TreePanel"].tree); -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "java.lang.Thread", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuBar", "$.MenuItem", "$.ScrollPane", "java.awt.BorderLayout"], "jalview.appletgui.TreePanel", ["awt2swing.Frame", "jalview.analysis.NJTree", "jalview.api.analysis.ViewBasedAnalysisI", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.FontChooser", "$.TreeCanvas", "jalview.bin.JalviewLite", "jalview.datamodel.Alignment", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.MessageManager", "java.awt.Color", "$.Font"], function () { +c$ = Clazz.decorateAsClass (function () { +this.seq = null; +this.$type = null; +this.pwtype = null; +this.start = 0; +this.end = 0; +this.treeCanvas = null; +this.tree = null; +this.ap = null; +this.av = null; +if (!Clazz.isClassDefined ("jalview.appletgui.TreePanel.TreeLoader")) { +jalview.appletgui.TreePanel.$TreePanel$TreeLoader$ (); +} +this.borderLayout1 = null; +this.scrollPane = null; +this.jMenuBar1 = null; +this.jMenu2 = null; +this.fontSize = null; +this.bootstrapMenu = null; +this.distanceMenu = null; +this.placeholdersMenu = null; +this.fitToWindow = null; +this.fileMenu = null; +this.newickOutput = null; +this.inputData = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "TreePanel", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener]); +Clazz.prepareFields (c$, function () { +this.borderLayout1 = new java.awt.BorderLayout (); +this.scrollPane = new awt2swing.ScrollPane (); +this.jMenuBar1 = new awt2swing.MenuBar (); +this.jMenu2 = new awt2swing.Menu (); +this.fontSize = new awt2swing.MenuItem (); +this.bootstrapMenu = new awt2swing.CheckboxMenuItem (); +this.distanceMenu = new awt2swing.CheckboxMenuItem (); +this.placeholdersMenu = new awt2swing.CheckboxMenuItem (); +this.fitToWindow = new awt2swing.CheckboxMenuItem (); +this.fileMenu = new awt2swing.Menu (); +this.newickOutput = new awt2swing.MenuItem (); +this.inputData = new awt2swing.MenuItem (); +}); +Clazz.defineMethod (c$, "getTree", +function () { +return this.tree; +}); +Clazz.defineMethod (c$, "finalize", +function () { +this.ap = null; +this.av = null; +Clazz.superCall (this, jalview.appletgui.TreePanel, "finalize", []); +}); +Clazz.makeConstructor (c$, +function (ap, type, pwtype) { +Clazz.superConstructor (this, jalview.appletgui.TreePanel, []); +try { +this.jbInit (); +this.setMenuBar (this.jMenuBar1); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +this.initTreePanel (ap, type, pwtype, null); +}, "jalview.appletgui.AlignmentPanel,~S,~S"); +Clazz.makeConstructor (c$, +function (ap, type, pwtype, newtree) { +Clazz.superConstructor (this, jalview.appletgui.TreePanel, []); +try { +this.jbInit (); +this.setMenuBar (this.jMenuBar1); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.initTreePanel (ap, type, pwtype, newtree); +}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile"); +Clazz.defineMethod (c$, "initTreePanel", +function (ap, type, pwtype, newTree) { +this.ap = ap; +this.av = ap.av; +this.$type = type; +this.pwtype = pwtype; +this.treeCanvas = new jalview.appletgui.TreeCanvas (ap, this.scrollPane); +var tl = Clazz.innerTypeInstance (jalview.appletgui.TreePanel.TreeLoader, this, null, newTree); +tl.start (); +this.embedMenuIfNeeded (this.treeCanvas); +this.scrollPane.add (this.treeCanvas, "Center"); +}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile"); +Clazz.defineMethod (c$, "showOriginalData", +function () { +if (this.tree.seqData != null) { +var gc = '-'; +try { +gc = this.av.getGapCharacter (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +;var alAndColsel = this.tree.seqData.getAlignmentAndColumnSelection (gc); +if (alAndColsel != null && alAndColsel[0] != null) { +var al = new jalview.datamodel.Alignment (alAndColsel[0]); +var af = new jalview.appletgui.AlignFrame (al, this.av.applet, "Original Data for Tree", false); +af.viewport.setHiddenColumns (alAndColsel[1]); +}} else { +System.out.println ("Original Tree Data not available"); +}}); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +if (evt.getSource () === this.newickOutput) { +this.newickOutput_actionPerformed (); +} else if (evt.getSource () === this.fontSize) { +this.fontSize_actionPerformed (); +} else if (evt.getSource () === this.inputData) { +this.showOriginalData (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +if (evt.getSource () === this.fitToWindow) { +this.treeCanvas.fitToWindow = this.fitToWindow.getState (); +} else if (evt.getSource () === this.distanceMenu) { +this.treeCanvas.setShowDistances (this.distanceMenu.getState ()); +} else if (evt.getSource () === this.bootstrapMenu) { +this.treeCanvas.setShowBootstrap (this.bootstrapMenu.getState ()); +} else if (evt.getSource () === this.placeholdersMenu) { +this.treeCanvas.setMarkPlaceholders (this.placeholdersMenu.getState ()); +}this.treeCanvas.repaint (); +}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "newickOutput_actionPerformed", +function () { +var fout = new jalview.io.NewickFile (this.tree.getTopNode ()); +var output = fout.print (false, true); +var cap = new jalview.appletgui.CutAndPasteTransfer (false, null); +cap.setText (output); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, this.$type + " " + this.pwtype, 500, 100); +}); +Clazz.defineMethod (c$, "getTreeFont", +function () { +return this.treeCanvas.$font; +}); +Clazz.defineMethod (c$, "setTreeFont", +function (font) { +this.treeCanvas.$font = font; +this.treeCanvas.repaint (); +}, "java.awt.Font"); +Clazz.defineMethod (c$, "fontSize_actionPerformed", +function () { +if (this.treeCanvas == null) { +return; +} new jalview.appletgui.FontChooser (this); +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout (this.borderLayout1); +this.setBackground (java.awt.Color.white); +this.setFont ( new java.awt.Font ("Verdana", 0, 12)); +this.jMenu2.setLabel (jalview.util.MessageManager.getString ("action.view")); +this.fontSize.setLabel (jalview.util.MessageManager.getString ("action.font")); +this.fontSize.addActionListener (this); +this.bootstrapMenu.setLabel (jalview.util.MessageManager.getString ("label.show_bootstrap_values")); +this.bootstrapMenu.addItemListener (this); +this.distanceMenu.setLabel (jalview.util.MessageManager.getString ("label.show_distances")); +this.distanceMenu.addItemListener (this); +this.placeholdersMenu.setLabel (jalview.util.MessageManager.getString ("label.mark_unassociated_leaves")); +this.placeholdersMenu.addItemListener (this); +this.fitToWindow.setState (true); +this.fitToWindow.setLabel (jalview.util.MessageManager.getString ("label.fit_to_window")); +this.fitToWindow.addItemListener (this); +this.fileMenu.setLabel (jalview.util.MessageManager.getString ("action.file")); +this.newickOutput.setLabel (jalview.util.MessageManager.getString ("label.newick_format")); +this.newickOutput.addActionListener (this); +this.inputData.setLabel (jalview.util.MessageManager.getString ("label.input_data")); +this.add (this.scrollPane, "Center"); +this.jMenuBar1.add (this.fileMenu); +this.jMenuBar1.add (this.jMenu2); +this.jMenu2.add (this.fitToWindow); +this.jMenu2.add (this.fontSize); +this.jMenu2.add (this.distanceMenu); +this.jMenu2.add (this.bootstrapMenu); +this.jMenu2.add (this.placeholdersMenu); +this.fileMenu.add (this.newickOutput); +this.fileMenu.add (this.inputData); +this.inputData.addActionListener (this); +}, $fz.isPrivate = true, $fz)); +c$.$TreePanel$TreeLoader$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.newtree = null; +this.odata = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui.TreePanel, "TreeLoader", Thread); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, jalview.appletgui.TreePanel.TreeLoader, []); +this.newtree = a; +}, "jalview.io.NewickFile"); +Clazz.overrideMethod (c$, "run", +function () { +if (this.newtree != null) { +if (this.odata == null) { +this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.newtree); +} else { +this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.odata, this.newtree); +}} else { +var a; +var b; +var c; +var d = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup () != null && this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSize () > 1; +var e = this.b$["jalview.appletgui.TreePanel"].av.getAlignmentView (d); +if (!d) { +a = 0; +b = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getWidth (); +c = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (); +} else { +a = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getStartRes (); +b = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getEndRes () + 1; +c = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSequencesInOrder (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ()); +}var f = jalview.schemes.ResidueProperties.getScoreModel (this.b$["jalview.appletgui.TreePanel"].pwtype); +if (Clazz.instanceOf (f, jalview.api.analysis.ViewBasedAnalysisI)) { +try { +f = f.getClass ().newInstance (); +(f).configureFromAlignmentView (this.b$["jalview.appletgui.TreePanel"].treeCanvas.ap); +} catch (q) { +if (Clazz.exceptionOf (q, Exception)) { +System.err.println ("Couldn't create a scoremodel instance for " + f.getName ()); +q.printStackTrace (); +} else { +throw q; +} +} +this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, f, a, b); +} else { +this.b$["jalview.appletgui.TreePanel"].tree = new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, null, a, b); +}}this.b$["jalview.appletgui.TreePanel"].tree.reCount (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ()); +this.b$["jalview.appletgui.TreePanel"].tree.findHeight (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ()); +this.b$["jalview.appletgui.TreePanel"].treeCanvas.setTree (this.b$["jalview.appletgui.TreePanel"].tree); +if (this.newtree != null) { +var a = this.newtree.HasDistances () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeDistances", this.newtree.HasDistances ()); +var b = this.newtree.HasBootstrap () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeBootstraps", this.newtree.HasBootstrap ()); +this.b$["jalview.appletgui.TreePanel"].distanceMenu.setState (a); +this.b$["jalview.appletgui.TreePanel"].bootstrapMenu.setState (b); +this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowBootstrap (b); +this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowDistances (a); +this.b$["jalview.appletgui.TreePanel"].treeCanvas.setMarkPlaceholders (this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showUnlinkedTreeNodes", false)); +}this.b$["jalview.appletgui.TreePanel"].treeCanvas.repaint (); +this.b$["jalview.appletgui.TreePanel"].av.setCurrentTree (this.b$["jalview.appletgui.TreePanel"].tree); +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/appletgui/UserDefinedColours.class b/bin/jalview/appletgui/UserDefinedColours.class index c53d7e0..593d23d 100644 Binary files a/bin/jalview/appletgui/UserDefinedColours.class and b/bin/jalview/appletgui/UserDefinedColours.class differ diff --git a/bin/jalview/appletgui/UserDefinedColours.js b/bin/jalview/appletgui/UserDefinedColours.js index 2cc0d9b..a1b23f6 100644 --- a/bin/jalview/appletgui/UserDefinedColours.js +++ b/bin/jalview/appletgui/UserDefinedColours.js @@ -1,481 +1,481 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.FocusListener", "awt2swing.Button", "$.Label", "$.Scrollbar", "$.TextField", "java.awt.GridLayout", "java.util.Vector"], "jalview.appletgui.UserDefinedColours", ["awt2swing.Frame", "jalview.appletgui.AnnotationColourChooser", "$.FeatureColourChooser", "$.FeatureRenderer", "$.FeatureSettings", "jalview.bin.JalviewLite", "jalview.schemes.ResidueProperties", "$.UserColourScheme", "jalview.util.MessageManager", "java.awt.Color", "$.Dialog", "$.Font", "$.Rectangle", "java.awt.event.MouseAdapter", "java.lang.Error"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ap = null; -this.seqGroup = null; -this.selectedButton = null; -this.oldColours = null; -this.oldColourScheme = null; -this.frame = null; -this.jmol = null; -this.dialog = null; -this.caller = null; -this.originalLabel = null; -this.originalColour = null; -this.R = 0; -this.G = 0; -this.B = 0; -this.buttonPanel = null; -this.gridLayout = null; -this.okcancelPanel = null; -this.okButton = null; -this.applyButton = null; -this.cancelButton = null; -this.rScroller = null; -this.label1 = null; -this.rText = null; -this.label4 = null; -this.gScroller = null; -this.gText = null; -this.label5 = null; -this.bScroller = null; -this.bText = null; -this.target = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "UserDefinedColours", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.FocusListener]); -Clazz.prepareFields (c$, function () { -this.oldColours = new java.util.Vector (); -this.buttonPanel = new awt2swing.Panel (); -this.gridLayout = new java.awt.GridLayout (); -this.okcancelPanel = new awt2swing.Panel (); -this.okButton = new awt2swing.Button (); -this.applyButton = new awt2swing.Button (); -this.cancelButton = new awt2swing.Button (); -this.rScroller = new awt2swing.Scrollbar (); -this.label1 = new awt2swing.Label (); -this.rText = new awt2swing.TextField (); -this.label4 = new awt2swing.Label (); -this.gScroller = new awt2swing.Scrollbar (); -this.gText = new awt2swing.TextField (); -this.label5 = new awt2swing.Label (); -this.bScroller = new awt2swing.Scrollbar (); -this.bText = new awt2swing.TextField (); -this.target = new awt2swing.Panel (); -}); -Clazz.defineMethod (c$, "loadDefaultColours", -function () { -return null; -}); -Clazz.makeConstructor (c$, -function (ap, sg) { -Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); -this.ap = ap; -this.seqGroup = sg; -if (this.seqGroup != null) { -this.oldColourScheme = this.seqGroup.cs; -} else { -this.oldColourScheme = ap.av.getGlobalColourScheme (); -}this.init (); -}, "jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceGroup"); -Clazz.makeConstructor (c$, -function (jmol) { -Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); -this.jmol = jmol; -this.init (); -}, "jalview.appletgui.AppletJmol"); -Clazz.makeConstructor (c$, -function (fr, alignframe) { -Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); -this.caller = fr; -this.originalColour = fr.colourPanel.getBackground (); -this.originalLabel = "Feature Colour"; -this.setForDialog ("Select Feature Colour", alignframe); -this.setTargetColour (fr.colourPanel.getBackground ()); -this.dialog.setVisible (true); -}, "jalview.appletgui.FeatureRenderer,awt2swing.Frame"); -Clazz.makeConstructor (c$, -function (caller, col1, alignframe) { -this.construct (caller, col1, alignframe, "Select Colour"); -}, "java.awt.Component,java.awt.Color,awt2swing.Frame"); -Clazz.makeConstructor (c$, -function (caller, col1, alignframe, title) { -Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); -this.caller = caller; -this.originalColour = col1; -this.originalLabel = title; -this.setForDialog (title, alignframe); -this.setTargetColour (col1); -this.dialog.setVisible (true); -}, "java.awt.Component,java.awt.Color,awt2swing.Frame,~S"); -Clazz.makeConstructor (c$, -function (caller, label, colour) { -this.construct (caller, label, colour, colour); -}, "~O,~S,java.awt.Color"); -Clazz.makeConstructor (c$, -function (me, type, graduatedColor) { -this.construct (me, type, graduatedColor, graduatedColor.getMaxColor ()); -}, "jalview.appletgui.FeatureSettings,~S,jalview.schemes.GraduatedColor"); -Clazz.makeConstructor (c$, -($fz = function (caller, label, ocolour, colour) { -Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); -this.caller = caller; -this.originalColour = ocolour; -this.originalLabel = label; -this.init (); -this.remove (this.buttonPanel); -this.setTargetColour (colour); -this.okcancelPanel.setBounds ( new java.awt.Rectangle (0, 113, 400, 35)); -this.frame.setTitle (jalview.util.MessageManager.getString ("label.user_defined_colours") + " - " + label); -this.frame.setSize (420, 200); -}, $fz.isPrivate = true, $fz), "~O,~S,~O,java.awt.Color"); -Clazz.defineMethod (c$, "setForDialog", -function (title, alignframe) { -this.init (); -this.frame.setVisible (false); -this.remove (this.buttonPanel); -if (Clazz.instanceOf (alignframe, awt2swing.Frame)) { -this.dialog = new java.awt.Dialog (alignframe, title, true); -} else { -throw new Error (jalview.util.MessageManager.getString ("label.error_unsupported_owwner_user_colour_scheme")); -}this.dialog.add (this); -this.setSize (400, 123); -this.okcancelPanel.setBounds ( new java.awt.Rectangle (0, 123, 400, 35)); -var height = 160 + alignframe.getInsets ().top + this.getInsets ().bottom; -var width = 400; -this.dialog.setBounds (alignframe.getBounds ().x + Clazz.doubleToInt ((alignframe.getSize ().width - width) / 2), alignframe.getBounds ().y + Clazz.doubleToInt ((alignframe.getSize ().height - height) / 2), width, height); -}, "~S,java.awt.Container"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -var source = evt.getSource (); -if (source === this.okButton) { -this.okButton_actionPerformed (); -} else if (source === this.applyButton) { -this.applyButton_actionPerformed (); -} else if (source === this.cancelButton) { -this.cancelButton_actionPerformed (); -} else if (source === this.rText) { -this.rText_actionPerformed (); -} else if (source === this.gText) { -this.gText_actionPerformed (); -} else if (source === this.bText) { -this.bText_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "adjustmentValueChanged", -function (evt) { -if (evt.getSource () === this.rScroller) { -this.rScroller_adjustmentValueChanged (); -} else if (evt.getSource () === this.gScroller) { -this.gScroller_adjustmentValueChanged (); -} else if (evt.getSource () === this.bScroller) { -this.bScroller_adjustmentValueChanged (); -}}, "java.awt.event.AdjustmentEvent"); -Clazz.defineMethod (c$, "init", -function () { -try { -this.jbInit (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -} else { -throw e; -} -} -this.frame = new awt2swing.Frame (); -this.frame.add (this); -jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.user_defined_colours"), 420, 345); -if (this.seqGroup != null) { -this.frame.setTitle (this.frame.getTitle () + " (" + this.seqGroup.getName () + ")"); -}for (var i = 0; i < 20; i++) { -this.makeButton (jalview.schemes.ResidueProperties.aa2Triplet.get (jalview.schemes.ResidueProperties.aa[i]) + "", jalview.schemes.ResidueProperties.aa[i]); -} -this.makeButton ("B", "B"); -this.makeButton ("Z", "Z"); -this.makeButton ("X", "X"); -this.makeButton ("Gap", "'.','-',' '"); -this.validate (); -}); -Clazz.defineMethod (c$, "rText_actionPerformed", -function () { -try { -var i = Integer.parseInt (this.rText.getText ()); -this.rScroller.setValue (i); -this.rScroller_adjustmentValueChanged (); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "gText_actionPerformed", -function () { -try { -var i = Integer.parseInt (this.gText.getText ()); -this.gScroller.setValue (i); -this.gScroller_adjustmentValueChanged (); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "bText_actionPerformed", -function () { -try { -var i = Integer.parseInt (this.bText.getText ()); -this.bScroller.setValue (i); -this.bScroller_adjustmentValueChanged (); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "rScroller_adjustmentValueChanged", -function () { -this.R = this.rScroller.getValue (); -this.rText.setText (this.R + ""); -this.colourChanged (); -}); -Clazz.defineMethod (c$, "gScroller_adjustmentValueChanged", -function () { -this.G = this.gScroller.getValue (); -this.gText.setText (this.G + ""); -this.colourChanged (); -}); -Clazz.defineMethod (c$, "bScroller_adjustmentValueChanged", -function () { -this.B = this.bScroller.getValue (); -this.bText.setText (this.B + ""); -this.colourChanged (); -}); -Clazz.defineMethod (c$, "colourChanged", -function () { -var col = new java.awt.Color (this.R, this.G, this.B); -this.target.setBackground (col); -this.target.repaint (); -if (this.selectedButton != null) { -this.selectedButton.setBackground (col); -this.selectedButton.repaint (); -}}); -Clazz.defineMethod (c$, "setTargetColour", -function (col) { -this.R = col.getRed (); -this.G = col.getGreen (); -this.B = col.getBlue (); -this.rScroller.setValue (this.R); -this.gScroller.setValue (this.G); -this.bScroller.setValue (this.B); -this.rText.setText (this.R + ""); -this.gText.setText (this.G + ""); -this.bText.setText (this.B + ""); -this.colourChanged (); -}, "java.awt.Color"); -Clazz.defineMethod (c$, "colourButtonPressed", -function (e) { -this.selectedButton = e.getSource (); -this.setTargetColour (this.selectedButton.getBackground ()); -}, "java.awt.event.MouseEvent"); -Clazz.defineMethod (c$, "makeButton", -function (label, aa) { -var button = new awt2swing.Button (); -var col = java.awt.Color.white; -if (this.oldColourScheme != null) { -try { -col = this.oldColourScheme.findColour (aa.charAt (0), -1, null); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}button.setBackground (col); -this.oldColours.addElement (col); -button.setLabel (label); -button.setForeground (col.darker ().darker ().darker ()); -button.setFont ( new java.awt.Font ("Verdana", 1, 10)); -button.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.UserDefinedColours$1") ? 0 : jalview.appletgui.UserDefinedColours.$UserDefinedColours$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.UserDefinedColours$1, this, null))); -this.buttonPanel.add (button, null); -}, "~S,~S"); -Clazz.defineMethod (c$, "okButton_actionPerformed", -function () { -this.applyButton_actionPerformed (); -if (this.dialog != null) { -this.dialog.setVisible (false); -}this.frame.setVisible (false); -}); -Clazz.defineMethod (c$, "getColor", -function () { -return new java.awt.Color (this.R, this.G, this.B); -}); -Clazz.defineMethod (c$, "applyButton_actionPerformed", -function () { -if (this.caller != null) { -if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureSettings)) { -(this.caller).setUserColour (this.originalLabel, this.getColor ()); -} else if (Clazz.instanceOf (this.caller, jalview.appletgui.AnnotationColourChooser)) { -if (this.originalLabel.equals ("Min Colour")) { -(this.caller).minColour_actionPerformed (this.getColor ()); -} else { -(this.caller).maxColour_actionPerformed (this.getColor ()); -}} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureRenderer)) { -(this.caller).colourPanel.updateColor (this.getColor ()); -} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureColourChooser)) { -if (this.originalLabel.indexOf ("inimum") > -1) { -(this.caller).minColour_actionPerformed (this.getColor ()); -} else { -(this.caller).maxColour_actionPerformed (this.getColor ()); -}}return; -}var newColours = new Array (24); -for (var i = 0; i < 24; i++) { -var button = this.buttonPanel.getComponent (i); -newColours[i] = button.getBackground (); -} -var ucs = new jalview.schemes.UserColourScheme (newColours); -if (this.ap != null) { -ucs.setThreshold (0, this.ap.av.isIgnoreGapsConsensus ()); -}if (this.ap != null) { -if (this.seqGroup != null) { -this.seqGroup.cs = ucs; -} else { -this.ap.av.setGlobalColourScheme (ucs); -}this.ap.seqPanel.seqCanvas.img = null; -this.ap.paintAlignment (true); -} else if (this.jmol != null) { -this.jmol.setJalviewColourScheme (ucs); -}}); -Clazz.defineMethod (c$, "cancelButton_actionPerformed", -function () { -if (this.caller != null) { -if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureSettings)) { -(this.caller).setUserColour (this.originalLabel, this.originalColour); -} else if (Clazz.instanceOf (this.caller, jalview.appletgui.AnnotationColourChooser)) { -if (this.originalLabel.equals ("Min Colour")) { -(this.caller).minColour_actionPerformed (this.originalColour); -} else { -(this.caller).maxColour_actionPerformed (this.originalColour); -}} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureRenderer)) { -(this.caller).colourPanel.updateColor (this.originalColour); -} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureColourChooser)) { -if (this.originalLabel.indexOf ("inimum") > -1) { -(this.caller).minColour_actionPerformed (this.originalColour); -} else { -(this.caller).maxColour_actionPerformed (this.originalColour); -}}if (this.dialog != null) { -this.dialog.setVisible (false); -}this.frame.setVisible (false); -return; -}var newColours = new Array (24); -for (var i = 0; i < 24; i++) { -newColours[i] = this.oldColours.elementAt (i); -this.buttonPanel.getComponent (i).setBackground (newColours[i]); -} -var ucs = new jalview.schemes.UserColourScheme (newColours); -if (this.ap != null) { -if (this.seqGroup != null) { -this.seqGroup.cs = ucs; -} else { -this.ap.av.setGlobalColourScheme (ucs); -}this.ap.paintAlignment (true); -} else if (this.jmol != null) { -this.jmol.setJalviewColourScheme (ucs); -}this.frame.setVisible (false); -}); -Clazz.defineMethod (c$, "jbInit", -($fz = function () { -this.setLayout (null); -this.buttonPanel.setLayout (this.gridLayout); -this.gridLayout.setColumns (6); -this.gridLayout.setRows (4); -this.okButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.okButton.setLabel (jalview.util.MessageManager.getString ("action.ok")); -this.okButton.addActionListener (this); -this.applyButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.applyButton.setLabel (jalview.util.MessageManager.getString ("action.apply")); -this.applyButton.addActionListener (this); -this.cancelButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); -this.cancelButton.setLabel (jalview.util.MessageManager.getString ("action.cancel")); -this.cancelButton.addActionListener (this); -this.setBackground ( new java.awt.Color (212, 208, 223)); -this.okcancelPanel.setBounds ( new java.awt.Rectangle (0, 265, 400, 35)); -this.buttonPanel.setBounds ( new java.awt.Rectangle (0, 123, 400, 142)); -this.rScroller.setMaximum (256); -this.rScroller.setMinimum (0); -this.rScroller.setOrientation (0); -this.rScroller.setUnitIncrement (1); -this.rScroller.setVisibleAmount (1); -this.rScroller.setBounds ( new java.awt.Rectangle (36, 27, 119, 19)); -this.rScroller.addAdjustmentListener (this); -this.label1.setAlignment (4); -this.label1.setText ("R"); -this.label1.setBounds ( new java.awt.Rectangle (19, 30, 16, 15)); -this.rText.setFont ( new java.awt.Font ("Dialog", 0, 10)); -this.rText.setText ("0 "); -this.rText.setBounds ( new java.awt.Rectangle (156, 27, 53, 19)); -this.rText.addActionListener (this); -this.rText.addFocusListener (this); -this.label4.setAlignment (4); -this.label4.setText ("G"); -this.label4.setBounds ( new java.awt.Rectangle (15, 56, 20, 15)); -this.gScroller.setMaximum (256); -this.gScroller.setMinimum (0); -this.gScroller.setOrientation (0); -this.gScroller.setUnitIncrement (1); -this.gScroller.setVisibleAmount (1); -this.gScroller.setBounds ( new java.awt.Rectangle (35, 52, 120, 20)); -this.gScroller.addAdjustmentListener (this); -this.gText.setFont ( new java.awt.Font ("Dialog", 0, 10)); -this.gText.setText ("0 "); -this.gText.setBounds ( new java.awt.Rectangle (156, 52, 53, 20)); -this.gText.addActionListener (this); -this.gText.addFocusListener (this); -this.label5.setAlignment (4); -this.label5.setText ("B"); -this.label5.setBounds ( new java.awt.Rectangle (14, 82, 20, 15)); -this.bScroller.setMaximum (256); -this.bScroller.setMinimum (0); -this.bScroller.setOrientation (0); -this.bScroller.setUnitIncrement (1); -this.bScroller.setVisibleAmount (1); -this.bScroller.setBounds ( new java.awt.Rectangle (35, 78, 120, 20)); -this.bScroller.addAdjustmentListener (this); -this.bText.setFont ( new java.awt.Font ("Dialog", 0, 10)); -this.bText.setText ("0 "); -this.bText.setBounds ( new java.awt.Rectangle (157, 78, 52, 20)); -this.bText.addActionListener (this); -this.bText.addFocusListener (this); -this.target.setBackground (java.awt.Color.black); -this.target.setBounds ( new java.awt.Rectangle (229, 26, 134, 79)); -this.add (this.okcancelPanel, null); -this.okcancelPanel.add (this.okButton, null); -this.okcancelPanel.add (this.applyButton, null); -this.okcancelPanel.add (this.cancelButton, null); -this.add (this.rText); -this.add (this.gText); -this.add (this.bText); -this.add (this.buttonPanel, null); -this.add (this.target, null); -this.add (this.gScroller); -this.add (this.rScroller); -this.add (this.bScroller); -this.add (this.label5); -this.add (this.label4); -this.add (this.label1); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "focusGained", -function (e) { -}, "java.awt.event.FocusEvent"); -Clazz.overrideMethod (c$, "focusLost", -function (e) { -var c = e.getComponent (); -if (c === this.rText) { -this.rText_actionPerformed (); -} else { -if (c === this.gText) { -this.gText_actionPerformed (); -} else { -if (c === this.bText) { -this.bText_actionPerformed (); -}}}}, "java.awt.event.FocusEvent"); -c$.$UserDefinedColours$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.appletgui, "UserDefinedColours$1", java.awt.event.MouseAdapter); -Clazz.overrideMethod (c$, "mousePressed", -function (e) { -this.b$["jalview.appletgui.UserDefinedColours"].colourButtonPressed (e); -}, "java.awt.event.MouseEvent"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.FocusListener", "awt2swing.Button", "$.Label", "$.Scrollbar", "$.TextField", "java.awt.GridLayout", "java.util.Vector"], "jalview.appletgui.UserDefinedColours", ["awt2swing.Frame", "jalview.appletgui.AnnotationColourChooser", "$.FeatureColourChooser", "$.FeatureRenderer", "$.FeatureSettings", "jalview.bin.JalviewLite", "jalview.schemes.ResidueProperties", "$.UserColourScheme", "jalview.util.MessageManager", "java.awt.Color", "$.Dialog", "$.Font", "$.Rectangle", "java.awt.event.MouseAdapter", "java.lang.Error"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ap = null; +this.seqGroup = null; +this.selectedButton = null; +this.oldColours = null; +this.oldColourScheme = null; +this.frame = null; +this.jmol = null; +this.dialog = null; +this.caller = null; +this.originalLabel = null; +this.originalColour = null; +this.R = 0; +this.G = 0; +this.B = 0; +this.buttonPanel = null; +this.gridLayout = null; +this.okcancelPanel = null; +this.okButton = null; +this.applyButton = null; +this.cancelButton = null; +this.rScroller = null; +this.label1 = null; +this.rText = null; +this.label4 = null; +this.gScroller = null; +this.gText = null; +this.label5 = null; +this.bScroller = null; +this.bText = null; +this.target = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "UserDefinedColours", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.FocusListener]); +Clazz.prepareFields (c$, function () { +this.oldColours = new java.util.Vector (); +this.buttonPanel = new awt2swing.Panel (); +this.gridLayout = new java.awt.GridLayout (); +this.okcancelPanel = new awt2swing.Panel (); +this.okButton = new awt2swing.Button (); +this.applyButton = new awt2swing.Button (); +this.cancelButton = new awt2swing.Button (); +this.rScroller = new awt2swing.Scrollbar (); +this.label1 = new awt2swing.Label (); +this.rText = new awt2swing.TextField (); +this.label4 = new awt2swing.Label (); +this.gScroller = new awt2swing.Scrollbar (); +this.gText = new awt2swing.TextField (); +this.label5 = new awt2swing.Label (); +this.bScroller = new awt2swing.Scrollbar (); +this.bText = new awt2swing.TextField (); +this.target = new awt2swing.Panel (); +}); +Clazz.defineMethod (c$, "loadDefaultColours", +function () { +return null; +}); +Clazz.makeConstructor (c$, +function (ap, sg) { +Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); +this.ap = ap; +this.seqGroup = sg; +if (this.seqGroup != null) { +this.oldColourScheme = this.seqGroup.cs; +} else { +this.oldColourScheme = ap.av.getGlobalColourScheme (); +}this.init (); +}, "jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceGroup"); +Clazz.makeConstructor (c$, +function (jmol) { +Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); +this.jmol = jmol; +this.init (); +}, "jalview.appletgui.AppletJmol"); +Clazz.makeConstructor (c$, +function (fr, alignframe) { +Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); +this.caller = fr; +this.originalColour = fr.colourPanel.getBackground (); +this.originalLabel = "Feature Colour"; +this.setForDialog ("Select Feature Colour", alignframe); +this.setTargetColour (fr.colourPanel.getBackground ()); +this.dialog.setVisible (true); +}, "jalview.appletgui.FeatureRenderer,awt2swing.Frame"); +Clazz.makeConstructor (c$, +function (caller, col1, alignframe) { +this.construct (caller, col1, alignframe, "Select Colour"); +}, "java.awt.Component,java.awt.Color,awt2swing.Frame"); +Clazz.makeConstructor (c$, +function (caller, col1, alignframe, title) { +Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); +this.caller = caller; +this.originalColour = col1; +this.originalLabel = title; +this.setForDialog (title, alignframe); +this.setTargetColour (col1); +this.dialog.setVisible (true); +}, "java.awt.Component,java.awt.Color,awt2swing.Frame,~S"); +Clazz.makeConstructor (c$, +function (caller, label, colour) { +this.construct (caller, label, colour, colour); +}, "~O,~S,java.awt.Color"); +Clazz.makeConstructor (c$, +function (me, type, graduatedColor) { +this.construct (me, type, graduatedColor, graduatedColor.getMaxColor ()); +}, "jalview.appletgui.FeatureSettings,~S,jalview.schemes.GraduatedColor"); +Clazz.makeConstructor (c$, +($fz = function (caller, label, ocolour, colour) { +Clazz.superConstructor (this, jalview.appletgui.UserDefinedColours, []); +this.caller = caller; +this.originalColour = ocolour; +this.originalLabel = label; +this.init (); +this.remove (this.buttonPanel); +this.setTargetColour (colour); +this.okcancelPanel.setBounds ( new java.awt.Rectangle (0, 113, 400, 35)); +this.frame.setTitle (jalview.util.MessageManager.getString ("label.user_defined_colours") + " - " + label); +this.frame.setSize (420, 200); +}, $fz.isPrivate = true, $fz), "~O,~S,~O,java.awt.Color"); +Clazz.defineMethod (c$, "setForDialog", +function (title, alignframe) { +this.init (); +this.frame.setVisible (false); +this.remove (this.buttonPanel); +if (Clazz.instanceOf (alignframe, awt2swing.Frame)) { +this.dialog = new java.awt.Dialog (alignframe, title, true); +} else { +throw new Error (jalview.util.MessageManager.getString ("label.error_unsupported_owwner_user_colour_scheme")); +}this.dialog.add (this); +this.setSize (400, 123); +this.okcancelPanel.setBounds ( new java.awt.Rectangle (0, 123, 400, 35)); +var height = 160 + alignframe.getInsets ().top + this.getInsets ().bottom; +var width = 400; +this.dialog.setBounds (alignframe.getBounds ().x + Clazz.doubleToInt ((alignframe.getSize ().width - width) / 2), alignframe.getBounds ().y + Clazz.doubleToInt ((alignframe.getSize ().height - height) / 2), width, height); +}, "~S,java.awt.Container"); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +var source = evt.getSource (); +if (source === this.okButton) { +this.okButton_actionPerformed (); +} else if (source === this.applyButton) { +this.applyButton_actionPerformed (); +} else if (source === this.cancelButton) { +this.cancelButton_actionPerformed (); +} else if (source === this.rText) { +this.rText_actionPerformed (); +} else if (source === this.gText) { +this.gText_actionPerformed (); +} else if (source === this.bText) { +this.bText_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.overrideMethod (c$, "adjustmentValueChanged", +function (evt) { +if (evt.getSource () === this.rScroller) { +this.rScroller_adjustmentValueChanged (); +} else if (evt.getSource () === this.gScroller) { +this.gScroller_adjustmentValueChanged (); +} else if (evt.getSource () === this.bScroller) { +this.bScroller_adjustmentValueChanged (); +}}, "java.awt.event.AdjustmentEvent"); +Clazz.defineMethod (c$, "init", +function () { +try { +this.jbInit (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +} else { +throw e; +} +} +this.frame = new awt2swing.Frame (); +this.frame.add (this); +jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.user_defined_colours"), 420, 345); +if (this.seqGroup != null) { +this.frame.setTitle (this.frame.getTitle () + " (" + this.seqGroup.getName () + ")"); +}for (var i = 0; i < 20; i++) { +this.makeButton (jalview.schemes.ResidueProperties.aa2Triplet.get (jalview.schemes.ResidueProperties.aa[i]) + "", jalview.schemes.ResidueProperties.aa[i]); +} +this.makeButton ("B", "B"); +this.makeButton ("Z", "Z"); +this.makeButton ("X", "X"); +this.makeButton ("Gap", "'.','-',' '"); +this.validate (); +}); +Clazz.defineMethod (c$, "rText_actionPerformed", +function () { +try { +var i = Integer.parseInt (this.rText.getText ()); +this.rScroller.setValue (i); +this.rScroller_adjustmentValueChanged (); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "gText_actionPerformed", +function () { +try { +var i = Integer.parseInt (this.gText.getText ()); +this.gScroller.setValue (i); +this.gScroller_adjustmentValueChanged (); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "bText_actionPerformed", +function () { +try { +var i = Integer.parseInt (this.bText.getText ()); +this.bScroller.setValue (i); +this.bScroller_adjustmentValueChanged (); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "rScroller_adjustmentValueChanged", +function () { +this.R = this.rScroller.getValue (); +this.rText.setText (this.R + ""); +this.colourChanged (); +}); +Clazz.defineMethod (c$, "gScroller_adjustmentValueChanged", +function () { +this.G = this.gScroller.getValue (); +this.gText.setText (this.G + ""); +this.colourChanged (); +}); +Clazz.defineMethod (c$, "bScroller_adjustmentValueChanged", +function () { +this.B = this.bScroller.getValue (); +this.bText.setText (this.B + ""); +this.colourChanged (); +}); +Clazz.defineMethod (c$, "colourChanged", +function () { +var col = new java.awt.Color (this.R, this.G, this.B); +this.target.setBackground (col); +this.target.repaint (); +if (this.selectedButton != null) { +this.selectedButton.setBackground (col); +this.selectedButton.repaint (); +}}); +Clazz.defineMethod (c$, "setTargetColour", +function (col) { +this.R = col.getRed (); +this.G = col.getGreen (); +this.B = col.getBlue (); +this.rScroller.setValue (this.R); +this.gScroller.setValue (this.G); +this.bScroller.setValue (this.B); +this.rText.setText (this.R + ""); +this.gText.setText (this.G + ""); +this.bText.setText (this.B + ""); +this.colourChanged (); +}, "java.awt.Color"); +Clazz.defineMethod (c$, "colourButtonPressed", +function (e) { +this.selectedButton = e.getSource (); +this.setTargetColour (this.selectedButton.getBackground ()); +}, "java.awt.event.MouseEvent"); +Clazz.defineMethod (c$, "makeButton", +function (label, aa) { +var button = new awt2swing.Button (); +var col = java.awt.Color.white; +if (this.oldColourScheme != null) { +try { +col = this.oldColourScheme.findColour (aa.charAt (0), -1, null); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}button.setBackground (col); +this.oldColours.addElement (col); +button.setLabel (label); +button.setForeground (col.darker ().darker ().darker ()); +button.setFont ( new java.awt.Font ("Verdana", 1, 10)); +button.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.UserDefinedColours$1") ? 0 : jalview.appletgui.UserDefinedColours.$UserDefinedColours$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.UserDefinedColours$1, this, null))); +this.buttonPanel.add (button, null); +}, "~S,~S"); +Clazz.defineMethod (c$, "okButton_actionPerformed", +function () { +this.applyButton_actionPerformed (); +if (this.dialog != null) { +this.dialog.setVisible (false); +}this.frame.setVisible (false); +}); +Clazz.defineMethod (c$, "getColor", +function () { +return new java.awt.Color (this.R, this.G, this.B); +}); +Clazz.defineMethod (c$, "applyButton_actionPerformed", +function () { +if (this.caller != null) { +if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureSettings)) { +(this.caller).setUserColour (this.originalLabel, this.getColor ()); +} else if (Clazz.instanceOf (this.caller, jalview.appletgui.AnnotationColourChooser)) { +if (this.originalLabel.equals ("Min Colour")) { +(this.caller).minColour_actionPerformed (this.getColor ()); +} else { +(this.caller).maxColour_actionPerformed (this.getColor ()); +}} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureRenderer)) { +(this.caller).colourPanel.updateColor (this.getColor ()); +} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureColourChooser)) { +if (this.originalLabel.indexOf ("inimum") > -1) { +(this.caller).minColour_actionPerformed (this.getColor ()); +} else { +(this.caller).maxColour_actionPerformed (this.getColor ()); +}}return; +}var newColours = new Array (24); +for (var i = 0; i < 24; i++) { +var button = this.buttonPanel.getComponent (i); +newColours[i] = button.getBackground (); +} +var ucs = new jalview.schemes.UserColourScheme (newColours); +if (this.ap != null) { +ucs.setThreshold (0, this.ap.av.isIgnoreGapsConsensus ()); +}if (this.ap != null) { +if (this.seqGroup != null) { +this.seqGroup.cs = ucs; +} else { +this.ap.av.setGlobalColourScheme (ucs); +}this.ap.seqPanel.seqCanvas.img = null; +this.ap.paintAlignment (true); +} else if (this.jmol != null) { +this.jmol.setJalviewColourScheme (ucs); +}}); +Clazz.defineMethod (c$, "cancelButton_actionPerformed", +function () { +if (this.caller != null) { +if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureSettings)) { +(this.caller).setUserColour (this.originalLabel, this.originalColour); +} else if (Clazz.instanceOf (this.caller, jalview.appletgui.AnnotationColourChooser)) { +if (this.originalLabel.equals ("Min Colour")) { +(this.caller).minColour_actionPerformed (this.originalColour); +} else { +(this.caller).maxColour_actionPerformed (this.originalColour); +}} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureRenderer)) { +(this.caller).colourPanel.updateColor (this.originalColour); +} else if (Clazz.instanceOf (this.caller, jalview.appletgui.FeatureColourChooser)) { +if (this.originalLabel.indexOf ("inimum") > -1) { +(this.caller).minColour_actionPerformed (this.originalColour); +} else { +(this.caller).maxColour_actionPerformed (this.originalColour); +}}if (this.dialog != null) { +this.dialog.setVisible (false); +}this.frame.setVisible (false); +return; +}var newColours = new Array (24); +for (var i = 0; i < 24; i++) { +newColours[i] = this.oldColours.elementAt (i); +this.buttonPanel.getComponent (i).setBackground (newColours[i]); +} +var ucs = new jalview.schemes.UserColourScheme (newColours); +if (this.ap != null) { +if (this.seqGroup != null) { +this.seqGroup.cs = ucs; +} else { +this.ap.av.setGlobalColourScheme (ucs); +}this.ap.paintAlignment (true); +} else if (this.jmol != null) { +this.jmol.setJalviewColourScheme (ucs); +}this.frame.setVisible (false); +}); +Clazz.defineMethod (c$, "jbInit", +($fz = function () { +this.setLayout (null); +this.buttonPanel.setLayout (this.gridLayout); +this.gridLayout.setColumns (6); +this.gridLayout.setRows (4); +this.okButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.okButton.setLabel (jalview.util.MessageManager.getString ("action.ok")); +this.okButton.addActionListener (this); +this.applyButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.applyButton.setLabel (jalview.util.MessageManager.getString ("action.apply")); +this.applyButton.addActionListener (this); +this.cancelButton.setFont ( new java.awt.Font ("Verdana", 0, 11)); +this.cancelButton.setLabel (jalview.util.MessageManager.getString ("action.cancel")); +this.cancelButton.addActionListener (this); +this.setBackground ( new java.awt.Color (212, 208, 223)); +this.okcancelPanel.setBounds ( new java.awt.Rectangle (0, 265, 400, 35)); +this.buttonPanel.setBounds ( new java.awt.Rectangle (0, 123, 400, 142)); +this.rScroller.setMaximum (256); +this.rScroller.setMinimum (0); +this.rScroller.setOrientation (0); +this.rScroller.setUnitIncrement (1); +this.rScroller.setVisibleAmount (1); +this.rScroller.setBounds ( new java.awt.Rectangle (36, 27, 119, 19)); +this.rScroller.addAdjustmentListener (this); +this.label1.setAlignment (4); +this.label1.setText ("R"); +this.label1.setBounds ( new java.awt.Rectangle (19, 30, 16, 15)); +this.rText.setFont ( new java.awt.Font ("Dialog", 0, 10)); +this.rText.setText ("0 "); +this.rText.setBounds ( new java.awt.Rectangle (156, 27, 53, 19)); +this.rText.addActionListener (this); +this.rText.addFocusListener (this); +this.label4.setAlignment (4); +this.label4.setText ("G"); +this.label4.setBounds ( new java.awt.Rectangle (15, 56, 20, 15)); +this.gScroller.setMaximum (256); +this.gScroller.setMinimum (0); +this.gScroller.setOrientation (0); +this.gScroller.setUnitIncrement (1); +this.gScroller.setVisibleAmount (1); +this.gScroller.setBounds ( new java.awt.Rectangle (35, 52, 120, 20)); +this.gScroller.addAdjustmentListener (this); +this.gText.setFont ( new java.awt.Font ("Dialog", 0, 10)); +this.gText.setText ("0 "); +this.gText.setBounds ( new java.awt.Rectangle (156, 52, 53, 20)); +this.gText.addActionListener (this); +this.gText.addFocusListener (this); +this.label5.setAlignment (4); +this.label5.setText ("B"); +this.label5.setBounds ( new java.awt.Rectangle (14, 82, 20, 15)); +this.bScroller.setMaximum (256); +this.bScroller.setMinimum (0); +this.bScroller.setOrientation (0); +this.bScroller.setUnitIncrement (1); +this.bScroller.setVisibleAmount (1); +this.bScroller.setBounds ( new java.awt.Rectangle (35, 78, 120, 20)); +this.bScroller.addAdjustmentListener (this); +this.bText.setFont ( new java.awt.Font ("Dialog", 0, 10)); +this.bText.setText ("0 "); +this.bText.setBounds ( new java.awt.Rectangle (157, 78, 52, 20)); +this.bText.addActionListener (this); +this.bText.addFocusListener (this); +this.target.setBackground (java.awt.Color.black); +this.target.setBounds ( new java.awt.Rectangle (229, 26, 134, 79)); +this.add (this.okcancelPanel, null); +this.okcancelPanel.add (this.okButton, null); +this.okcancelPanel.add (this.applyButton, null); +this.okcancelPanel.add (this.cancelButton, null); +this.add (this.rText); +this.add (this.gText); +this.add (this.bText); +this.add (this.buttonPanel, null); +this.add (this.target, null); +this.add (this.gScroller); +this.add (this.rScroller); +this.add (this.bScroller); +this.add (this.label5); +this.add (this.label4); +this.add (this.label1); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "focusGained", +function (e) { +}, "java.awt.event.FocusEvent"); +Clazz.overrideMethod (c$, "focusLost", +function (e) { +var c = e.getComponent (); +if (c === this.rText) { +this.rText_actionPerformed (); +} else { +if (c === this.gText) { +this.gText_actionPerformed (); +} else { +if (c === this.bText) { +this.bText_actionPerformed (); +}}}}, "java.awt.event.FocusEvent"); +c$.$UserDefinedColours$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.appletgui, "UserDefinedColours$1", java.awt.event.MouseAdapter); +Clazz.overrideMethod (c$, "mousePressed", +function (e) { +this.b$["jalview.appletgui.UserDefinedColours"].colourButtonPressed (e); +}, "java.awt.event.MouseEvent"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/bin/Cache.js b/bin/jalview/bin/Cache.js index b2a7cae..3013f58 100644 --- a/bin/jalview/bin/Cache.js +++ b/bin/jalview/bin/Cache.js @@ -1,29 +1,29 @@ -Clazz.declarePackage ("jalview.bin"); -c$ = Clazz.decorateAsClass (function () { -if (!Clazz.isClassDefined ("jalview.bin.Cache.Log")) { -jalview.bin.Cache.$Cache$Log$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.bin, "Cache"); -c$.getDefault = Clazz.defineMethod (c$, "getDefault", -function (string, string2) { -return null; -}, "~S,~S"); -c$.$Cache$Log$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -Clazz.instantialize (this, arguments); -}, jalview.bin.Cache, "Log"); -Clazz.defineMethod (c$, "error", -function (a) { -}, "~S"); -Clazz.defineMethod (c$, "isDebugEnabled", -function () { -return false; -}); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"CASTORLOGLEVEL", null, -"log", null); +Clazz.declarePackage ("jalview.bin"); +c$ = Clazz.decorateAsClass (function () { +if (!Clazz.isClassDefined ("jalview.bin.Cache.Log")) { +jalview.bin.Cache.$Cache$Log$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.bin, "Cache"); +c$.getDefault = Clazz.defineMethod (c$, "getDefault", +function (string, string2) { +return null; +}, "~S,~S"); +c$.$Cache$Log$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +Clazz.instantialize (this, arguments); +}, jalview.bin.Cache, "Log"); +Clazz.defineMethod (c$, "error", +function (a) { +}, "~S"); +Clazz.defineMethod (c$, "isDebugEnabled", +function () { +return false; +}); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"CASTORLOGLEVEL", null, +"log", null); diff --git a/bin/jalview/bin/JalviewLite$4.class b/bin/jalview/bin/JalviewLite$4.class index 09353ff..884af19 100644 Binary files a/bin/jalview/bin/JalviewLite$4.class and b/bin/jalview/bin/JalviewLite$4.class differ diff --git a/bin/jalview/bin/JalviewLite$LoadJmolThread.class b/bin/jalview/bin/JalviewLite$LoadJmolThread.class index 17bcf98..94eb08f 100644 Binary files a/bin/jalview/bin/JalviewLite$LoadJmolThread.class and b/bin/jalview/bin/JalviewLite$LoadJmolThread.class differ diff --git a/bin/jalview/bin/JalviewLite$LoadingThread.class b/bin/jalview/bin/JalviewLite$LoadingThread.class index 6ffac37..4dc6751 100644 Binary files a/bin/jalview/bin/JalviewLite$LoadingThread.class and b/bin/jalview/bin/JalviewLite$LoadingThread.class differ diff --git a/bin/jalview/bin/JalviewLite.class b/bin/jalview/bin/JalviewLite.class index ae19296..7d70007 100644 Binary files a/bin/jalview/bin/JalviewLite.class and b/bin/jalview/bin/JalviewLite.class differ diff --git a/bin/jalview/bin/JalviewLite.js b/bin/jalview/bin/JalviewLite.js index 23d66b7..1049dcb 100644 --- a/bin/jalview/bin/JalviewLite.js +++ b/bin/jalview/bin/JalviewLite.js @@ -1,1617 +1,1617 @@ -Clazz.declarePackage ("jalview.bin"); -Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.javascript.JalviewLiteJsApi", "java.lang.Thread", "javax.swing.JApplet", "jalview.util.MessageManager", "java.util.Hashtable", "$.Vector", "javax.swing.JButton"], "jalview.bin.JalviewLite", ["jalview.analysis.SequenceIdMatcher", "jalview.appletgui.AlignFrame", "$.EmbmenuFrame", "$.FeatureSettings", "$.SplitFrame", "jalview.datamodel.Alignment", "$.AlignmentOrder", "$.ColumnSelection", "$.PDBEntry", "$.SequenceGroup", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.FileParse", "$.IdentifyFile", "$.JnetAnnotationMaker", "$.NewickFile", "jalview.javascript.JSFunctionExec", "$.JsSelectionSender", "$.MouseOverListener", "$.MouseOverStructureListener", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.ColourSchemeProperty", "$.UserColourScheme", "jalview.structure.SelectionListener", "$.StructureSelectionManager", "java.awt.Color", "$.EventQueue", "$.Font", "java.awt.event.ActionListener", "$.WindowAdapter", "java.io.BufferedReader", "$.InputStreamReader", "java.lang.Error", "$.StringBuffer", "java.net.URL", "java.util.StringTokenizer", "netscape.javascript.JSObject"], function () { -c$ = Clazz.decorateAsClass (function () { -this.embedded = false; -this.enableSplitFrame = false; -this.showButton = true; -this.checkForJmol = true; -this.jalviewServletURL = null; -this.startupFile = "No file"; -this.helpUrl = null; -this.externalstructureviewer = null; -this.sep = null; -this.rgb = null; -this.labelColour = null; -this.initjscallback = null; -this.pdbFile = null; -this.sequence = null; -this.jnetFile = null; -this.annotations = null; -this.hideFeatureGroups = null; -this.showFeatureGroups = null; -this.features = null; -this.showFeatureSettings = null; -this.scoreFile = null; -this.treeFile = null; -this.windowWidth = null; -this.windowHeight = null; -this.defaultColour = null; -this.sortBy = null; -this.wrap = null; -this.centrecolumnlabels = null; -this.userDefinedColour = null; -this.widthScale = null; -this.heightScale = null; -this.upperCase = null; -this.file2 = null; -this.javascriptListeners = null; -this.jsFunctionExec = null; -this.fileFound = true; -this.launcher = null; -this.currentAlignFrame = null; -this.initialAlignFrame = null; -this.checkedForJmol = false; -this.jmolAvailable = false; -this.alignPdbStructures = false; -this.useXtrnalSviewer = false; -this.haveShownLoadMessage = false; -if (!Clazz.isClassDefined ("jalview.bin.JalviewLite.LoadJmolThread")) { -jalview.bin.JalviewLite.$JalviewLite$LoadJmolThread$ (); -} -if (!Clazz.isClassDefined ("jalview.bin.JalviewLite.LoadingThread")) { -jalview.bin.JalviewLite.$JalviewLite$LoadingThread$ (); -} -this.separator = "\u00ac"; -this.jsfallbackEnabled = false; -this.jshashes = null; -this.jsmessages = null; -this.jsExecQueue = null; -Clazz.instantialize (this, arguments); -}, jalview.bin, "JalviewLite", javax.swing.JApplet, [jalview.api.StructureSelectionManagerProvider, jalview.javascript.JalviewLiteJsApi]); -Clazz.prepareFields (c$, function () { -this.javascriptListeners = new java.util.Vector (); -this.launcher = new javax.swing.JButton (jalview.util.MessageManager.getString ("label.start_jalview")); -this.jshashes = new java.util.Hashtable (); -this.jsmessages = new java.util.Hashtable (); -this.jsExecQueue = new java.util.Vector (); -}); -Clazz.defineMethod (c$, "setParams", -($fz = function () { -jalview.bin.JalviewLite.debug = "true".equalsIgnoreCase (this.getParameter ("debug")); -this.enableSplitFrame = "true".equalsIgnoreCase (this.getParameter ("enableSplitFrame")); -this.embedded = "true".equalsIgnoreCase (this.getParameter ("embedded")); -this.showButton = !"false".equalsIgnoreCase (this.getParameter ("showbutton")); -this.jalviewServletURL = this.getParameter ("APPLICATION_URL"); -this.startupFile = this.getParameter ("file"); -this.helpUrl = this.getParameter ("jalviewhelpurl"); -this.externalstructureviewer = this.getParameter ("externalstructureviewer"); -this.checkForJmol = !"true".equals (this.getParameter ("nojmol")); -this.sep = this.getParameter ("separator"); -this.rgb = this.getParameter ("RGB"); -this.labelColour = this.getParameter ("label"); -this.initjscallback = this.getParameter ("oninit"); -this.pdbFile = this.getParameter ("PDBFILE"); -this.sequence = this.getParameter ("PDBSEQ"); -this.jnetFile = this.getParameter ("jnetfile"); -this.annotations = this.getParameter ("annotations"); -this.hideFeatureGroups = this.getParameter ("hidefeaturegroups"); -this.showFeatureGroups = this.getParameter ("showfeaturegroups"); -this.features = this.getParameter ("features"); -this.showFeatureSettings = this.getParameter ("showFeatureSettings"); -this.scoreFile = this.getParameter ("scoreFile"); -this.treeFile = this.getParameter ("tree"); -if (this.treeFile == null) this.treeFile = this.getParameter ("treeFile"); -this.windowWidth = this.getParameter ("windowWidth"); -this.windowHeight = this.getParameter ("windowHeight"); -this.defaultColour = this.getParameter ("defaultColour"); -this.sortBy = this.getParameter ("sortBy"); -this.wrap = this.getParameter ("wrap"); -this.centrecolumnlabels = this.getParameter ("centrecolumnlabels"); -this.userDefinedColour = this.getParameter ("userDefinedColour"); -this.widthScale = this.getParameter ("widthScale"); -this.heightScale = this.getParameter ("heightScale"); -this.upperCase = this.getParameter ("upperCase"); -this.file2 = this.getParameter ("file2"); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getDefaultParameter", -function (name, def) { -var stn; -if ((stn = this.getParameter (name)) == null) { -return def; -}if (stn.toLowerCase ().equals ("true")) { -return true; -}return false; -}, "~S,~B"); -Clazz.defineMethod (c$, "getLinkParams", -function (links) { -var label; -var url; -for (var i = 1; i < 10; i++) { -label = this.getParameter ("linkLabel_" + i); -url = this.getParameter ("linkURL_" + i); -if (label != null && url != null) { -links.addElement (label + "|" + url); -}} -}, "java.util.Vector"); -Clazz.defineMethod (c$, "getStructureSelectionManager", -function () { -return jalview.structure.StructureSelectionManager.getStructureSelectionManager (this); -}); -Clazz.defineMethod (c$, "getSelectedSequences", -function () { -return this.getSelectedSequencesFrom (this.getDefaultTargetFrame ()); -}); -Clazz.defineMethod (c$, "getSelectedSequences", -function (sep) { -return this.getSelectedSequencesFrom (this.getDefaultTargetFrame (), sep); -}, "~S"); -Clazz.defineMethod (c$, "getSelectedSequencesFrom", -function (alf) { -return this.getSelectedSequencesFrom (alf, this.separator); -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "getSelectedSequencesFrom", -function (alf, sep) { -var result = new StringBuffer (""); -if (sep == null || sep.length == 0) { -sep = this.separator; -}if (alf.viewport.getSelectionGroup () != null) { -var seqs = alf.viewport.getSelectionGroup ().getSequencesInOrder (alf.viewport.getAlignment ()); -for (var i = 0; i < seqs.length; i++) { -result.append (seqs[i].getName ()); -result.append (sep); -} -}return result.toString (); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "highlight", -function (sequenceId, position, alignedPosition) { -this.highlightIn (this.getDefaultTargetFrame (), sequenceId, position, alignedPosition); -}, "~S,~S,~S"); -Clazz.overrideMethod (c$, "highlightIn", -function (alf, sequenceId, position, alignedPosition) { -var matcher = new jalview.analysis.SequenceIdMatcher (alf.viewport.getAlignment ().getSequencesArray ()); -var sq = matcher.findIdMatch (sequenceId); -if (sq != null) { -var apos = -1; -try { -apos = new Integer (position).intValue (); -apos--; -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -return; -} else { -throw ex; -} -} -var me = this; -var pos = apos; -if (alignedPosition != null && (alignedPosition.trim ().length == 0 || alignedPosition.toLowerCase ().indexOf ("false") > -1)) { -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$1") ? 0 : jalview.bin.JalviewLite.$JalviewLite$1$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$1, this, Clazz.cloneFinals ("me", me, "sq", sq, "pos", pos)))); -} else { -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$2") ? 0 : jalview.bin.JalviewLite.$JalviewLite$2$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$2, this, Clazz.cloneFinals ("me", me, "sq", sq, "pos", pos)))); -}}}, "jalview.appletgui.AlignFrame,~S,~S,~S"); -Clazz.defineMethod (c$, "select", -function (sequenceIds, columns) { -this.selectIn (this.getDefaultTargetFrame (), sequenceIds, columns, this.separator); -}, "~S,~S"); -Clazz.defineMethod (c$, "select", -function (sequenceIds, columns, sep) { -this.selectIn (this.getDefaultTargetFrame (), sequenceIds, columns, sep); -}, "~S,~S,~S"); -Clazz.defineMethod (c$, "selectIn", -function (alf, sequenceIds, columns) { -this.selectIn (alf, sequenceIds, columns, this.separator); -}, "jalview.appletgui.AlignFrame,~S,~S"); -Clazz.defineMethod (c$, "selectIn", -function (alf, sequenceIds, columns, sep) { -if (sep == null || sep.length == 0) { -sep = this.separator; -} else { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Selecting region using separator string '" + this.separator + "'"); -}}var ids = this.separatorListToArray (sequenceIds, sep); -var cols = this.separatorListToArray (columns, sep); -var sel = new jalview.datamodel.SequenceGroup (); -var csel = new jalview.datamodel.ColumnSelection (); -var al = alf.viewport.getAlignment (); -var matcher = new jalview.analysis.SequenceIdMatcher (alf.viewport.getAlignment ().getSequencesArray ()); -var start = 0; -var end = al.getWidth (); -var alw = al.getWidth (); -var seqsfound = true; -if (ids != null && ids.length > 0) { -seqsfound = false; -for (var i = 0; i < ids.length; i++) { -if (ids[i].trim ().length == 0) { -continue; -}var sq = matcher.findIdMatch (ids[i]); -if (sq != null) { -seqsfound = true; -sel.addSequence (sq, false); -}} -}var inseqpos = false; -if (cols != null && cols.length > 0) { -var seset = false; -for (var i = 0; i < cols.length; i++) { -var cl = cols[i].trim (); -if (cl.length == 0) { -continue; -}var p; -if ((p = cl.indexOf ("-")) > -1) { -var from = -1; -var to = -1; -try { -from = new Integer (cl.substring (0, p)).intValue (); -from--; -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -System.err.println ("ERROR: Couldn't parse first integer in range element column selection string '" + cl + "' - format is 'from-to'"); -return; -} else { -throw ex; -} -} -try { -to = new Integer (cl.substring (p + 1)).intValue (); -to--; -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -System.err.println ("ERROR: Couldn't parse second integer in range element column selection string '" + cl + "' - format is 'from-to'"); -return; -} else { -throw ex; -} -} -if (from >= 0 && to >= 0) { -if (from < to) { -var t = to; -to = from; -to = t; -}if (!seset) { -start = from; -end = to; -seset = true; -} else { -if (start > from) { -start = from; -}if (end < to) { -end = to; -}}for (var r = from; r <= to; r++) { -if (r >= 0 && r < alw) { -csel.addElement (r); -}} -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Range '" + cl + "' deparsed as [" + from + "," + to + "]"); -}} else { -System.err.println ("ERROR: Invalid Range '" + cl + "' deparsed as [" + from + "," + to + "]"); -}} else { -var r = -1; -try { -r = new Integer (cl).intValue (); -r--; -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -if (cl.toLowerCase ().equals ("sequence")) { -inseqpos = true; -} else { -System.err.println ("ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); -return; -}} else { -throw ex; -} -} -if (r >= 0 && r <= alw) { -if (!seset) { -start = r; -end = r; -seset = true; -} else { -if (start > r) { -start = r; -}if (end < r) { -end = r; -}}csel.addElement (r); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Point selection '" + cl + "' deparsed as [" + r + "]"); -}} else { -System.err.println ("ERROR: Invalid Point selection '" + cl + "' deparsed as [" + r + "]"); -}}} -}if (seqsfound) { -if (inseqpos && sel.getSize () > 0) { -var rs = sel.getSequenceAt (0); -start = rs.findIndex (start); -end = rs.findIndex (end); -if (csel != null) { -var cs = csel.getSelected (); -csel.clear (); -for (var selectedCol, $selectedCol = cs.iterator (); $selectedCol.hasNext () && ((selectedCol = $selectedCol.next ()) || true);) { -csel.addElement (rs.findIndex ((selectedCol).intValue ())); -} -}}sel.setStartRes (start); -sel.setEndRes (end); -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$3") ? 0 : jalview.bin.JalviewLite.$JalviewLite$3$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$3, this, Clazz.cloneFinals ("alf", alf, "sel", sel, "csel", csel)))); -}}, "jalview.appletgui.AlignFrame,~S,~S,~S"); -Clazz.overrideMethod (c$, "getSelectedSequencesAsAlignment", -function (format, suffix) { -return this.getSelectedSequencesAsAlignmentFrom (this.getDefaultTargetFrame (), format, suffix); -}, "~S,~S"); -Clazz.overrideMethod (c$, "getSelectedSequencesAsAlignmentFrom", -function (alf, format, suffix) { -try { -var seqlimits = suffix.equalsIgnoreCase ("true"); -if (alf.viewport.getSelectionGroup () != null) { -var reply = new jalview.io.AppletFormatAdapter ().formatSequences (format, new jalview.datamodel.Alignment (alf.viewport.getSelectionAsNewSequence ()), seqlimits); -return reply; -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -return "Error retrieving alignment in " + format + " format. "; -} else { -throw ex; -} -} -return ""; -}, "jalview.appletgui.AlignFrame,~S,~S"); -Clazz.overrideMethod (c$, "getAlignmentOrder", -function () { -return this.getAlignmentOrderFrom (this.getDefaultTargetFrame ()); -}); -Clazz.defineMethod (c$, "getAlignmentOrderFrom", -function (alf) { -return this.getAlignmentOrderFrom (alf, this.separator); -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "getAlignmentOrderFrom", -function (alf, sep) { -var alorder = alf.getAlignViewport ().getAlignment (); -var order = new Array (alorder.getHeight ()); -for (var i = 0; i < order.length; i++) { -order[i] = alorder.getSequenceAt (i).getName (); -} -return this.arrayToSeparatorList (order); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.defineMethod (c$, "orderBy", -function (order, undoName) { -return this.orderBy (order, undoName, this.separator); -}, "~S,~S"); -Clazz.defineMethod (c$, "orderBy", -function (order, undoName, sep) { -return this.orderAlignmentBy (this.getDefaultTargetFrame (), order, undoName, sep); -}, "~S,~S,~S"); -Clazz.overrideMethod (c$, "orderAlignmentBy", -function (alf, order, undoName, sep) { -var ids = this.separatorListToArray (order, sep); -var sqs = null; -if (ids != null && ids.length > 0) { -var matcher = new jalview.analysis.SequenceIdMatcher (alf.viewport.getAlignment ().getSequencesArray ()); -var s = 0; -sqs = new Array (ids.length); -for (var i = 0; i < ids.length; i++) { -if (ids[i].trim ().length == 0) { -continue; -}var sq = matcher.findIdMatch (ids[i]); -if (sq != null) { -sqs[s++] = sq; -}} -if (s > 0) { -var sqq = new Array (s); -System.arraycopy (sqs, 0, sqq, 0, s); -sqs = sqq; -} else { -sqs = null; -}}if (sqs == null) { -return ""; -};var aorder = new jalview.datamodel.AlignmentOrder (sqs); -if (undoName != null && undoName.trim ().length == 0) { -undoName = null; -}var _undoName = undoName; -return alf.sortBy (aorder, _undoName) ? "true" : ""; -}, "jalview.appletgui.AlignFrame,~S,~S,~S"); -Clazz.defineMethod (c$, "getAlignment", -function (format) { -return this.getAlignmentFrom (this.getDefaultTargetFrame (), format, "true"); -}, "~S"); -Clazz.defineMethod (c$, "getAlignmentFrom", -function (alf, format) { -return this.getAlignmentFrom (alf, format, "true"); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.defineMethod (c$, "getAlignment", -function (format, suffix) { -return this.getAlignmentFrom (this.getDefaultTargetFrame (), format, suffix); -}, "~S,~S"); -Clazz.defineMethod (c$, "getAlignmentFrom", -function (alf, format, suffix) { -try { -var seqlimits = suffix.equalsIgnoreCase ("true"); -var reply = new jalview.io.AppletFormatAdapter ().formatSequences (format, alf.viewport.getAlignment (), seqlimits); -return reply; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -return "Error retrieving alignment in " + format + " format. "; -} else { -throw ex; -} -} -}, "jalview.appletgui.AlignFrame,~S,~S"); -Clazz.overrideMethod (c$, "loadAnnotation", -function (annotation) { -this.loadAnnotationFrom (this.getDefaultTargetFrame (), annotation); -}, "~S"); -Clazz.overrideMethod (c$, "loadAnnotationFrom", -function (alf, annotation) { -if ( new jalview.io.AnnotationFile ().annotateAlignmentView (alf.getAlignViewport (), annotation, jalview.io.AppletFormatAdapter.PASTE)) { -alf.alignPanel.fontChanged (); -alf.alignPanel.setScrollValues (0, 0); -} else { -alf.parseFeaturesFile (annotation, jalview.io.AppletFormatAdapter.PASTE); -}}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "loadFeatures", -function (features, autoenabledisplay) { -this.loadFeaturesFrom (this.getDefaultTargetFrame (), features, autoenabledisplay); -}, "~S,~B"); -Clazz.overrideMethod (c$, "loadFeaturesFrom", -function (alf, features, autoenabledisplay) { -return alf.parseFeaturesFile (features, jalview.io.AppletFormatAdapter.PASTE, autoenabledisplay); -}, "jalview.appletgui.AlignFrame,~S,~B"); -Clazz.overrideMethod (c$, "getFeatures", -function (format) { -return this.getFeaturesFrom (this.getDefaultTargetFrame (), format); -}, "~S"); -Clazz.overrideMethod (c$, "getFeaturesFrom", -function (alf, format) { -return alf.outputFeatures (false, format); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "getAnnotation", -function () { -return this.getAnnotationFrom (this.getDefaultTargetFrame ()); -}); -Clazz.overrideMethod (c$, "getAnnotationFrom", -function (alf) { -return alf.outputAnnotations (false); -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "newView", -function () { -return this.newViewFrom (this.getDefaultTargetFrame ()); -}); -Clazz.defineMethod (c$, "newView", -function (name) { -return this.newViewFrom (this.getDefaultTargetFrame (), name); -}, "~S"); -Clazz.defineMethod (c$, "newViewFrom", -function (alf) { -return alf.newView (null); -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "newViewFrom", -function (alf, name) { -return alf.newView (name); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "loadAlignment", -function (text, title) { -var al = null; -var format = new jalview.io.IdentifyFile ().Identify (text, jalview.io.AppletFormatAdapter.PASTE); -try { -al = new jalview.io.AppletFormatAdapter ().readFile (text, jalview.io.AppletFormatAdapter.PASTE, format); -if (al.getHeight () > 0) { -return new jalview.appletgui.AlignFrame (al, this, title, false); -}} catch (ex) { -if (Clazz.exceptionOf (ex, java.io.IOException)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -return null; -}, "~S,~S"); -Clazz.defineMethod (c$, "setMouseoverListener", -function (listener) { -this.setMouseoverListener (this.currentAlignFrame, listener); -}, "~S"); -Clazz.defineMethod (c$, "setMouseoverListener", -function (af, listener) { -if (listener != null) { -listener = listener.trim (); -if (listener.length == 0) { -System.err.println ("jalview Javascript error: Ignoring empty function for mouseover listener."); -return; -}}var mol = new jalview.javascript.MouseOverListener (this, af, listener); -this.javascriptListeners.addElement (mol); -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).addStructureViewerListener (mol); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Added a mouseover listener for " + ((af == null) ? "All frames" : "Just views for " + af.getAlignViewport ().getSequenceSetId ())); -System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); -}}, "jalview.appletgui.AlignFrame,~S"); -Clazz.defineMethod (c$, "setSelectionListener", -function (listener) { -this.setSelectionListener (null, listener); -}, "~S"); -Clazz.defineMethod (c$, "setSelectionListener", -function (af, listener) { -if (listener != null) { -listener = listener.trim (); -if (listener.length == 0) { -System.err.println ("jalview Javascript error: Ignoring empty function for selection listener."); -return; -}}var mol = new jalview.javascript.JsSelectionSender (this, af, listener); -this.javascriptListeners.addElement (mol); -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).addSelectionListener (mol); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Added a selection listener for " + ((af == null) ? "All frames" : "Just views for " + af.getAlignViewport ().getSequenceSetId ())); -System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); -}}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "setStructureListener", -function (listener, modelSet) { -if (listener != null) { -listener = listener.trim (); -if (listener.length == 0) { -System.err.println ("jalview Javascript error: Ignoring empty function for selection listener."); -return; -}}var mol = new jalview.javascript.MouseOverStructureListener (this, listener, this.separatorListToArray (modelSet)); -this.javascriptListeners.addElement (mol); -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).addStructureViewerListener (mol); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Added a javascript structure viewer listener '" + listener + "'"); -System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); -}}, "~S,~S"); -Clazz.overrideMethod (c$, "removeJavascriptListener", -function (af, listener) { -if (listener != null) { -listener = listener.trim (); -if (listener.length == 0) { -listener = null; -}}var rprt = false; -for (var ms = 0, msSize = this.javascriptListeners.size (); ms < msSize; ) { -var lstn = this.javascriptListeners.elementAt (ms); -var lstner = lstn; -if ((af == null || lstner.getAlignFrame () === af) && (listener == null || lstner.getListenerFunction ().equals (listener))) { -this.javascriptListeners.removeElement (lstner); -msSize--; -if (Clazz.instanceOf (lstner, jalview.structure.SelectionListener)) { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeSelectionListener (lstner); -} else { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeStructureViewerListener (lstner, null); -}rprt = jalview.bin.JalviewLite.debug; -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Removed listener '" + listener + "'"); -}} else { -ms++; -}} -if (rprt) { -System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); -}}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "stop", -function () { -System.err.println ("Applet " + this.getName () + " stop()."); -this.tidyUp (); -}); -Clazz.overrideMethod (c$, "destroy", -function () { -System.err.println ("Applet " + this.getName () + " destroy()."); -this.tidyUp (); -}); -Clazz.defineMethod (c$, "tidyUp", -($fz = function () { -this.removeAll (); -if (this.currentAlignFrame != null && this.currentAlignFrame.viewport != null && this.currentAlignFrame.viewport.applet != null) { -var av = this.currentAlignFrame.viewport; -this.currentAlignFrame.closeMenuItem_actionPerformed (); -av.applet = null; -this.currentAlignFrame = null; -}if (this.javascriptListeners != null) { -while (this.javascriptListeners.size () > 0) { -var mol = this.javascriptListeners.elementAt (0); -this.javascriptListeners.removeElement (mol); -if (Clazz.instanceOf (mol, jalview.structure.SelectionListener)) { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeSelectionListener (mol); -} else { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeStructureViewerListener (mol, null); -}mol.jvlite = null; -} -}if (this.jsFunctionExec != null) { -this.jsFunctionExec.stopQueue (); -this.jsFunctionExec.jvlite = null; -}this.initialAlignFrame = null; -this.jsFunctionExec = null; -this.javascriptListeners = null; -jalview.structure.StructureSelectionManager.release (this); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "mouseOverStructure", -function (pdbResNum, chain, pdbfile) { -var me = this; -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$4") ? 0 : jalview.bin.JalviewLite.$JalviewLite$4$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$4, this, Clazz.cloneFinals ("me", me, "pdbResNum", pdbResNum, "chain", chain, "pdbfile", pdbfile)))); -}, "~S,~S,~S"); -Clazz.overrideMethod (c$, "scrollViewToIn", -function (alf, topRow, leftHandColumn) { -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$5") ? 0 : jalview.bin.JalviewLite.$JalviewLite$5$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$5, this, Clazz.cloneFinals ("alf", alf, "topRow", topRow, "leftHandColumn", leftHandColumn)))); -}, "jalview.appletgui.AlignFrame,~S,~S"); -Clazz.overrideMethod (c$, "scrollViewToRowIn", -function (alf, topRow) { -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$6") ? 0 : jalview.bin.JalviewLite.$JalviewLite$6$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$6, this, Clazz.cloneFinals ("alf", alf, "topRow", topRow)))); -}, "jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "scrollViewToColumnIn", -function (alf, leftHandColumn) { -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$7") ? 0 : jalview.bin.JalviewLite.$JalviewLite$7$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$7, this, Clazz.cloneFinals ("alf", alf, "leftHandColumn", leftHandColumn)))); -}, "jalview.appletgui.AlignFrame,~S"); -c$.initBuildDetails = Clazz.defineMethod (c$, "initBuildDetails", -($fz = function () { -if (jalview.bin.JalviewLite.builddate == null) { -jalview.bin.JalviewLite.builddate = "unknown"; -jalview.bin.JalviewLite.version = "test"; -jalview.bin.JalviewLite.installation = "Webstart"; -var url = jalview.bin.JalviewLite.getResource ("/.build_properties"); -if (url != null) { -try { -var reader = new java.io.BufferedReader ( new java.io.InputStreamReader (url.openStream ())); -var line; -while ((line = reader.readLine ()) != null) { -if (line.indexOf ("VERSION") > -1) { -jalview.bin.JalviewLite.version = line.substring (line.indexOf ("=") + 1); -}if (line.indexOf ("BUILD_DATE") > -1) { -jalview.bin.JalviewLite.builddate = line.substring (line.indexOf ("=") + 1); -}if (line.indexOf ("INSTALLATION") > -1) { -jalview.bin.JalviewLite.installation = line.substring (line.indexOf ("=") + 1); -}} -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}}}, $fz.isPrivate = true, $fz)); -c$.getBuildDate = Clazz.defineMethod (c$, "getBuildDate", -function () { -jalview.bin.JalviewLite.initBuildDetails (); -return jalview.bin.JalviewLite.builddate; -}); -c$.getInstallation = Clazz.defineMethod (c$, "getInstallation", -function () { -jalview.bin.JalviewLite.initBuildDetails (); -return jalview.bin.JalviewLite.installation; -}); -c$.getVersion = Clazz.defineMethod (c$, "getVersion", -function () { -jalview.bin.JalviewLite.initBuildDetails (); -return jalview.bin.JalviewLite.version; -}); -Clazz.overrideMethod (c$, "init", -function () { -this.setParams (); -try { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Applet context is '" + this.getAppletContext ().getClass ().toString () + "'"); -}var scriptObject = netscape.javascript.JSObject.getWindow (this); -if (jalview.bin.JalviewLite.debug && scriptObject != null) { -System.err.println ("Applet has Javascript callback support."); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Warning: No JalviewLite javascript callbacks available."); -if (jalview.bin.JalviewLite.debug) { -ex.printStackTrace (); -}} else { -throw ex; -} -} -if (jalview.bin.JalviewLite.debug) { -System.err.println ("JalviewLite Version " + jalview.bin.JalviewLite.getVersion ()); -System.err.println ("Build Date : " + jalview.bin.JalviewLite.getBuildDate ()); -System.err.println ("Installation : " + jalview.bin.JalviewLite.getInstallation ()); -}if (this.externalstructureviewer != null) { -this.useXtrnalSviewer = this.externalstructureviewer.trim ().toLowerCase ().equals ("true"); -}if (this.sep != null) { -if (this.sep.length > 0) { -this.separator = this.sep; -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Separator set to '" + this.separator + "'"); -}} else { -throw new Error (jalview.util.MessageManager.getString ("error.invalid_separator_parameter")); -}}var r = 255; -var g = 255; -var b = 255; -if (this.rgb != null) { -try { -r = Integer.parseInt (this.rgb.substring (0, 2), 16); -g = Integer.parseInt (this.rgb.substring (2, 4), 16); -b = Integer.parseInt (this.rgb.substring (4, 6), 16); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -r = 255; -g = 255; -b = 255; -} else { -throw ex; -} -} -}this.rgb = this.labelColour; -if (this.rgb != null) { -this.launcher.setLabel (this.rgb); -}this.setBackground ( new java.awt.Color (r, g, b)); -if (this.startupFile == null) { -var data = new StringBuffer ("PASTE"); -var i = 1; -while ((this.startupFile = this.getParameter ("sequence" + i)) != null) { -data.append (this.startupFile.toString () + "\n"); -i++; -} -if (data.length () > 5) { -this.startupFile = data.toString (); -}}if (!this.enableSplitFrame) { -this.file2 = null; -}if (this.embedded) { -var loader = Clazz.innerTypeInstance (jalview.bin.JalviewLite.LoadingThread, this, null, this.startupFile, this.file2, this); -{ -loader.run(); -}} else if (this.startupFile != null) { -if (!this.showButton) { -var loader = Clazz.innerTypeInstance (jalview.bin.JalviewLite.LoadingThread, this, null, this.startupFile, this.file2, this); -loader.start (); -} else { -this.add (this.launcher); -this.launcher.addActionListener (((Clazz.isClassDefined ("jalview.bin.JalviewLite$8") ? 0 : jalview.bin.JalviewLite.$JalviewLite$8$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$8, this, null))); -}} else { -this.startupFile = "NO FILE"; -this.fileFound = false; -this.callInitCallback (); -}}); -Clazz.defineMethod (c$, "initLiveConnect", -($fz = function () { -var notFailed = false; -var tries = 0; -while (!notFailed && tries < 10) { -if (tries > 0) { -System.err.println ("LiveConnect request thread going to sleep."); -}try { -Thread.sleep (700 * (1 + tries)); -} catch (q) { -if (Clazz.exceptionOf (q, InterruptedException)) { -} else { -throw q; -} -} -;if (tries++ > 0) { -System.err.println ("LiveConnect request thread woken up."); -}try { -var scriptObject = netscape.javascript.JSObject.getWindow (this); -if (scriptObject.eval ("navigator") != null) { -notFailed = true; -}} catch (jsex) { -if (Clazz.exceptionOf (jsex, Exception)) { -System.err.println ("Attempt " + tries + " to access LiveConnect javascript failed."); -} else { -throw jsex; -} -} -} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "callInitCallback", -($fz = function () { -if (this.initjscallback == null) { -return; -}this.initjscallback = this.initjscallback.trim (); -if (this.initjscallback.length > 0) { -var scriptObject = null; -try { -scriptObject = netscape.javascript.JSObject.getWindow (this); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -;this.initLiveConnect (); -if (scriptObject != null) { -try { - new jalview.javascript.JSFunctionExec (this).executeJavascriptFunction (true, this.initjscallback, null, "Calling oninit callback '" + this.initjscallback + "'."); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Exception when executing _oninit callback '" + this.initjscallback + "'."); -e.printStackTrace (); -} else { -throw e; -} -} -} else { -System.err.println ("Not executing _oninit callback '" + this.initjscallback + "' - no scripting allowed."); -}}}, $fz.isPrivate = true, $fz)); -c$.addFrame = Clazz.defineMethod (c$, "addFrame", -function (frame, title, width, height) { -frame.setLocation (jalview.bin.JalviewLite.lastFrameX, jalview.bin.JalviewLite.lastFrameY); -jalview.bin.JalviewLite.lastFrameX += 40; -jalview.bin.JalviewLite.lastFrameY += 40; -frame.setSize (width, height); -frame.setTitle (title); -frame.addWindowListener (((Clazz.isClassDefined ("jalview.bin.JalviewLite$9") ? 0 : jalview.bin.JalviewLite.$JalviewLite$9$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$9, this, Clazz.cloneFinals ("frame", frame)))); -frame.setVisible (true); -}, "javax.swing.JFrame,~S,~N,~N"); -Clazz.defineMethod (c$, "paintComponent", -function (g) { -if (!this.fileFound) { -g.setColor ( new java.awt.Color (200, 200, 200)); -g.setColor (java.awt.Color.cyan); -g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); -g.setColor (java.awt.Color.red); -g.drawString (jalview.util.MessageManager.getString ("label.jalview_cannot_open_file"), 5, 15); -g.drawString ("\"" + this.startupFile + "\"", 5, 30); -} else if (this.embedded && !this.haveShownLoadMessage) { -g.setColor (java.awt.Color.black); -g.setFont ( new java.awt.Font ("Arial", 1, 24)); -g.drawString (jalview.util.MessageManager.getString ("label.jalview_applet"), 50, Clazz.doubleToInt (this.getSize ().height / 2) - 30); -g.drawString (jalview.util.MessageManager.getString ("label.loading_data") + "...", 50, Clazz.doubleToInt (this.getSize ().height / 2)); -this.haveShownLoadMessage = true; -}}, "java.awt.Graphics"); -Clazz.defineMethod (c$, "getAppletWindow", -function (class1) { -var wnds = new java.util.Vector (); -var cmp = this.getComponents (); -if (cmp != null) { -for (var i = 0; i < cmp.length; i++) { -if (class1.isAssignableFrom (cmp[i].getClass ())) { -wnds.addElement (cmp); -}} -}return wnds; -}, "Class"); -Clazz.defineMethod (c$, "getDefaultTargetFrame", -function () { -if (this.currentAlignFrame != null) { -return this.currentAlignFrame; -}if (this.initialAlignFrame != null) { -return this.initialAlignFrame; -}System.err.println ("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); -return null; -}); -Clazz.defineMethod (c$, "separatorListToArray", -function (list) { -return this.separatorListToArray (list, this.separator); -}, "~S"); -Clazz.defineMethod (c$, "separatorListToArray", -function (list, separator) { -var seplen = separator.length; -if (list == null || list.equals ("") || list.equals (separator)) { -return null; -}var jv = new java.util.Vector (); -var cp = 0; -var pos; -while ((pos = list.indexOf (separator, cp)) > cp) { -jv.addElement (list.substring (cp, pos)); -cp = pos + seplen; -} -if (cp < list.length) { -var c = list.substring (cp); -if (!c.equals (separator)) { -jv.addElement (c); -}}if (jv.size () > 0) { -var v = new Array (jv.size ()); -for (var i = 0; i < v.length; i++) { -v[i] = jv.elementAt (i); -} -jv.removeAllElements (); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Array from '" + separator + "' separated List:\n" + v.length); -for (var i = 0; i < v.length; i++) { -System.err.println ("item " + i + " '" + v[i] + "'"); -} -}return v; -}if (jalview.bin.JalviewLite.debug) { -System.err.println ("Empty Array from '" + separator + "' separated List"); -}return null; -}, "~S,~S"); -Clazz.defineMethod (c$, "arrayToSeparatorList", -function (list) { -return this.arrayToSeparatorList (list, this.separator); -}, "~A"); -Clazz.defineMethod (c$, "arrayToSeparatorList", -function (list, separator) { -var v = new StringBuffer (); -if (list != null && list.length > 0) { -for (var i = 0, iSize = list.length; i < iSize; i++) { -if (list[i] != null) { -if (i > 0) { -v.append (separator); -}v.append (list[i]); -}} -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Returning '" + separator + "' separated List:\n"); -System.err.println (v); -}return v.toString (); -}if (jalview.bin.JalviewLite.debug) { -System.err.println ("Returning empty '" + separator + "' separated List\n"); -}return "" + separator; -}, "~A,~S"); -Clazz.overrideMethod (c$, "getFeatureGroups", -function () { -var lst = this.arrayToSeparatorList (this.getDefaultTargetFrame ().getFeatureGroups ()); -return lst; -}); -Clazz.overrideMethod (c$, "getFeatureGroupsOn", -function (alf) { -var lst = this.arrayToSeparatorList (alf.getFeatureGroups ()); -return lst; -}, "jalview.appletgui.AlignFrame"); -Clazz.overrideMethod (c$, "getFeatureGroupsOfState", -function (visible) { -return this.arrayToSeparatorList (this.getDefaultTargetFrame ().getFeatureGroupsOfState (visible)); -}, "~B"); -Clazz.overrideMethod (c$, "getFeatureGroupsOfStateOn", -function (alf, visible) { -return this.arrayToSeparatorList (alf.getFeatureGroupsOfState (visible)); -}, "jalview.appletgui.AlignFrame,~B"); -Clazz.overrideMethod (c$, "setFeatureGroupStateOn", -function (alf, groups, state) { -var st = state; -java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$10") ? 0 : jalview.bin.JalviewLite.$JalviewLite$10$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$10, this, Clazz.cloneFinals ("alf", alf, "groups", groups, "st", st)))); -}, "jalview.appletgui.AlignFrame,~S,~B"); -Clazz.overrideMethod (c$, "setFeatureGroupState", -function (groups, state) { -this.setFeatureGroupStateOn (this.getDefaultTargetFrame (), groups, state); -}, "~S,~B"); -Clazz.overrideMethod (c$, "getSeparator", -function () { -return this.separator; -}); -Clazz.overrideMethod (c$, "setSeparator", -function (separator) { -if (separator == null || separator.length < 1) { -separator = "\u00ac"; -}this.separator = separator; -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Default Separator now: '" + separator + "'"); -}}, "~S"); -Clazz.overrideMethod (c$, "addPdbFile", -function (alFrame, sequenceId, pdbEntryString, pdbFile) { -return alFrame.addPdbFile (sequenceId, pdbEntryString, pdbFile); -}, "jalview.appletgui.AlignFrame,~S,~S,~S"); -Clazz.defineMethod (c$, "setAlignPdbStructures", -function (alignPdbStructures) { -this.alignPdbStructures = alignPdbStructures; -}, "~B"); -Clazz.defineMethod (c$, "isAlignPdbStructures", -function () { -return this.alignPdbStructures; -}); -Clazz.overrideMethod (c$, "start", -function () { -}); -Clazz.defineMethod (c$, "setJsMessageSet", -function (messageclass, viewId, colcommands) { -var msgset = this.jsmessages.get (messageclass); -if (msgset == null) { -msgset = new java.util.Hashtable (); -this.jsmessages.put (messageclass, msgset); -}msgset.put (viewId, colcommands); -var l = Clazz.newLongArray (colcommands.length, 0); -for (var i = 0; i < colcommands.length; i++) { -l[i] = colcommands[i].hashCode (); -} -this.jshashes.put (messageclass + "|" + viewId, l); -}, "~S,~S,~A"); -Clazz.overrideMethod (c$, "getJsMessage", -function (messageclass, viewId) { -var msgset = this.jsmessages.get (messageclass); -if (msgset != null) { -var msgs = msgset.get (viewId); -if (msgs != null) { -for (var i = 0; i < msgs.length; i++) { -if (msgs[i] != null) { -var m = msgs[i]; -msgs[i] = null; -return m; -}} -}}return ""; -}, "~S,~S"); -Clazz.defineMethod (c$, "isJsMessageSetChanged", -function (string, string2, colcommands) { -var l = this.jshashes.get (string + "|" + string2); -if (l == null && colcommands != null) { -return true; -}for (var i = 0; i < colcommands.length; i++) { -if (l[i] != colcommands[i].hashCode ()) { -return true; -}} -return false; -}, "~S,~S,~A"); -Clazz.defineMethod (c$, "getJsExecQueue", -function () { -return this.jsExecQueue; -}); -Clazz.defineMethod (c$, "setExecutor", -function (jsFunctionExec2) { -this.jsFunctionExec = jsFunctionExec2; -}, "jalview.javascript.JSFunctionExec"); -Clazz.defineMethod (c$, "getDefaultColourParameter", -function (colparam, defcolour) { -var colprop = this.getParameter (colparam); -if (colprop == null || colprop.trim ().length == 0) { -return defcolour; -}var col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName (colprop); -if (col == null) { -try { -col = new jalview.schemes.UserColourScheme (colprop).findColour ('A'); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Couldn't parse '" + colprop + "' as a colour for " + colparam); -col = null; -} else { -throw ex; -} -} -}return (col == null) ? defcolour : col; -}, "~S,java.awt.Color"); -Clazz.defineMethod (c$, "openJalviewHelpUrl", -function () { -if (this.helpUrl == null || this.helpUrl.trim ().length < 5) { -this.helpUrl = "http://www.jalview.org/help.html"; -}this.showURL (this.helpUrl, "HELP"); -}); -Clazz.defineMethod (c$, "resolveUrlForLocalOrAbsolute", -($fz = function (url, localref) { -var codebase = localref.toString (); -var pt = codebase.indexOf ("?"); -if (pt < 0) pt = codebase.length; -codebase = codebase.substring (0, pt); -codebase = codebase.substring (0, codebase.lastIndexOf ("/") + 1); -if (url.indexOf ("/") == 0 && !localref.getProtocol ().equals ("file")) { -pt = codebase.indexOf ("/", 8); -return codebase.substring (0, pt) + url; -}return codebase + url; -}, $fz.isPrivate = true, $fz), "~S,java.net.URL"); -Clazz.defineMethod (c$, "showURL", -function (url, target) { -try { -if (url.indexOf (":") == -1) { -var prepend; -url = this.resolveUrlForLocalOrAbsolute (url, prepend = this.getDefaultParameter ("resolvetocodebase", false) ? this.getDocumentBase () : this.getCodeBase ()); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Show url (prepended " + prepend + " - toggle resolvetocodebase if code/docbase resolution is wrong): " + url); -}} else { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Show url: " + url); -}}if (url.indexOf ("javascript:") == 0) { -this.getAppletContext ().showDocument ( new java.net.URL (url)); -} else { -this.getAppletContext ().showDocument ( new java.net.URL (url), target); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}, "~S,~S"); -c$.$JalviewLite$LoadJmolThread$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.running = false; -Clazz.instantialize (this, arguments); -}, jalview.bin.JalviewLite, "LoadJmolThread", Thread); -Clazz.overrideMethod (c$, "run", -function () { -if (this.running || this.b$["jalview.bin.JalviewLite"].checkedForJmol) { -return; -}this.running = true; -if (this.b$["jalview.bin.JalviewLite"].checkForJmol) { -try { -if (!System.getProperty ("java.version").startsWith ("1.1")) { -Class.forName ("org.jmol.adapter.smarter.SmarterJmolAdapter"); -this.b$["jalview.bin.JalviewLite"].jmolAvailable = true; -}if (!this.b$["jalview.bin.JalviewLite"].jmolAvailable) { -System.out.println ("Jmol not available - Using MCview for structures"); -}} catch (ex) { -if (Clazz.exceptionOf (ex, ClassNotFoundException)) { -} else { -throw ex; -} -} -} else { -this.b$["jalview.bin.JalviewLite"].jmolAvailable = false; -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Skipping Jmol check. Will use MCView (probably)"); -}}this.b$["jalview.bin.JalviewLite"].checkedForJmol = true; -this.running = false; -}); -Clazz.defineMethod (c$, "notFinished", -function () { -return this.running || !this.b$["jalview.bin.JalviewLite"].checkedForJmol; -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$LoadingThread$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.protocol = null; -this._file = null; -this._file2 = null; -this.applet = null; -Clazz.instantialize (this, arguments); -}, jalview.bin.JalviewLite, "LoadingThread", Thread); -Clazz.defineMethod (c$, "dbgMsg", -($fz = function (a) { -if (jalview.bin.JalviewLite.debug) { -System.err.println (a); -}}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "setProtocolState", -function (a) { -if (a.startsWith ("PASTE")) { -a = a.substring (5); -this.protocol = jalview.io.AppletFormatAdapter.PASTE; -} else if (this.inArchive (a)) { -this.protocol = jalview.io.AppletFormatAdapter.CLASSLOADER; -} else { -a = this.addProtocol (a); -this.protocol = jalview.io.AppletFormatAdapter.URL; -}this.dbgMsg ("Protocol identified as '" + this.protocol + "'"); -return a; -}, "~S"); -Clazz.makeConstructor (c$, -function (a, b, c) { -Clazz.superConstructor (this, jalview.bin.JalviewLite.LoadingThread, []); -this._file = a; -this._file2 = b; -this.applet = c; -}, "~S,~S,jalview.bin.JalviewLite"); -Clazz.overrideMethod (c$, "run", -function () { -{ -System.out.println("BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY") -}this.startLoading (); -}); -Clazz.defineMethod (c$, "startLoading", -($fz = function () { -this.dbgMsg ("Loading thread started with:\n>>file\n" + this._file + ">>endfile"); -this.dbgMsg ("Loading started."); -var a = this.readAlignment (this._file); -var b = this.readAlignment (this._file2); -if (a != null) { -this.addToDisplay (a, b); -this.loadTree (a); -this.loadScoreFile (a); -this.loadFeatures (a); -this.loadAnnotations (a); -this.loadJnetFile (a); -this.loadPdbFiles (a); -} else { -this.b$["jalview.bin.JalviewLite"].fileFound = false; -this.applet.remove (this.b$["jalview.bin.JalviewLite"].launcher); -this.applet.repaint (); -}this.b$["jalview.bin.JalviewLite"].callInitCallback (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "addToDisplay", -function (a, b) { -if (b == null) { -a.addToDisplay (this.b$["jalview.bin.JalviewLite"].embedded); -} else { -var c = new jalview.appletgui.SplitFrame (a, b); -c.addToDisplay (this.b$["jalview.bin.JalviewLite"].embedded, this.b$["jalview.bin.JalviewLite"]); -}}, "jalview.appletgui.AlignFrame,jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "readAlignment", -function (a) { -if (a == null) { -return null; -}var b = this.setProtocolState (a); -var c = new jalview.io.IdentifyFile ().Identify (b, this.protocol); -this.dbgMsg ("File identified as '" + c + "'"); -var d = null; -try { -d = new jalview.io.AppletFormatAdapter ().readFile (b, this.protocol, c); -if ((d != null) && (d.getHeight () > 0)) { -this.dbgMsg ("Successfully loaded file."); -d.setDataset (null); -var e = new jalview.appletgui.AlignFrame (d, this.applet, b, this.b$["jalview.bin.JalviewLite"].embedded, false); -e.setTitle (b); -if (this.b$["jalview.bin.JalviewLite"].initialAlignFrame == null) { -this.b$["jalview.bin.JalviewLite"].initialAlignFrame = e; -}this.b$["jalview.bin.JalviewLite"].currentAlignFrame = e; -if (this.protocol === jalview.io.AppletFormatAdapter.PASTE) { -e.setTitle (jalview.util.MessageManager.formatMessage ("label.sequences_from", Clazz.newArray (-1, [this.applet.getDocumentBase ().toString ()]))); -}e.setStatus (jalview.util.MessageManager.formatMessage ("label.successfully_loaded_file", Clazz.newArray (-1, [b]))); -return e; -}} catch (ex) { -if (Clazz.exceptionOf (ex, java.io.IOException)) { -this.dbgMsg ("File load exception."); -ex.printStackTrace (); -if (jalview.bin.JalviewLite.debug) { -try { -var e = new jalview.io.FileParse (b, this.protocol); -var f = null; -this.dbgMsg (">>>Dumping contents of '" + b + "' " + "(" + this.protocol + ")"); -while ((f = e.nextLine ()) != null) { -this.dbgMsg (f); -} -this.dbgMsg (">>>Dump finished."); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Exception when trying to dump the content of the file parameter."); -e.printStackTrace (); -} else { -throw e; -} -} -}} else { -throw ex; -} -} -return null; -}, "~S"); -Clazz.defineMethod (c$, "loadPdbFiles", -function (a) { -var b = false; -this.applet.setAlignPdbStructures (this.b$["jalview.bin.JalviewLite"].getDefaultParameter ("alignpdbfiles", false)); -var c = 0; -var d = new java.util.Vector (); -var e = (this.applet.getDefaultParameter ("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher (a.getAlignViewport ().getAlignment ().getSequencesArray ()) : null; -var f; -do { -if (c > 0) { -f = this.applet.getParameter ("PDBFILE" + c); -} else { -f = this.b$["jalview.bin.JalviewLite"].pdbFile; -}if (f != null) { -var g = new jalview.datamodel.PDBEntry (); -var h; -var i = null; -var j = null; -var k = new java.util.StringTokenizer (f, " "); -if (k.countTokens () < 2) { -if (this.b$["jalview.bin.JalviewLite"].sequence != null) { -i = Clazz.newArray (-1, [e == null ? a.getAlignViewport ().getAlignment ().findName (this.b$["jalview.bin.JalviewLite"].sequence) : e.findIdMatch (this.b$["jalview.bin.JalviewLite"].sequence)]); -}} else { -f = k.nextToken (); -var l = new java.util.Vector (); -var m = new java.util.Vector (); -while (k.hasMoreTokens ()) { -h = k.nextToken (); -var n = new java.util.StringTokenizer (h, "="); -if (n.countTokens () > 1) { -m.addElement (n.nextToken ()); -h = n.nextToken (); -}l.addElement (e == null ? a.getAlignViewport ().getAlignment ().findName (h) : e.findIdMatch (h)); -} -i = new Array (l.size ()); -l.copyInto (i); -if (m.size () == l.size ()) { -j = new Array (m.size ()); -m.copyInto (j); -}}f = this.setProtocolState (f); -if (this.protocol === jalview.io.AppletFormatAdapter.CLASSLOADER && !this.b$["jalview.bin.JalviewLite"].useXtrnalSviewer) { -this.protocol = jalview.io.AppletFormatAdapter.URL; -f = this.addProtocol (f); -}g.setFile (f); -if (i != null) { -for (var l = 0; l < i.length; l++) { -if (i[l] != null) { -(i[l]).addPDBId (g); -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.applet).registerPDBEntry (g); -} else { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + l + ")"); -}}} -if (!this.b$["jalview.bin.JalviewLite"].alignPdbStructures) { -a.newStructureView (this.applet, g, i, j, this.protocol); -} else { -d.addElement ( Clazz.newArray (-1, [g, i, j, String.instantialize (this.protocol)])); -}}}c++; -} while (f != null || c < 10); -if (d.size () > 0) { -var g = new Array (d.size ()); -var h = new Array (d.size ()); -var i = new Array (d.size ()); -var j = new Array (d.size ()); -for (var k = 0, l = d.size (); k < l; k++) { -var m = d.elementAt (k); -h[k] = m[0]; -g[k] = m[1]; -i[k] = m[2]; -j[k] = m[3]; -} -a.alignedStructureView (this.applet, h, g, i, j); -b = true; -}return b; -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "loadJnetFile", -function (a) { -var b = false; -var c = this.b$["jalview.bin.JalviewLite"].jnetFile; -if (c != null) { -try { -c = this.setProtocolState (c); -var d = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [c, this.protocol]); -jalview.io.JnetAnnotationMaker.add_annotation (d, a.viewport.getAlignment (), 0, false); -var e = a.viewport.getAlignment ().getSequenceAt (0); -a.viewport.getAlignment ().setSeqrep (e); -var f = new jalview.datamodel.ColumnSelection (); -f.hideInsertionsFor (e); -a.viewport.setColumnSelection (f); -a.alignPanel.fontChanged (); -a.alignPanel.setScrollValues (0, 0); -b = true; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}return b; -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "loadAnnotations", -function (a) { -var b = false; -var c = this.b$["jalview.bin.JalviewLite"].annotations; -if (c != null) { -c = this.setProtocolState (c); -if ( new jalview.io.AnnotationFile ().annotateAlignmentView (a.viewport, c, this.protocol)) { -a.alignPanel.fontChanged (); -a.alignPanel.setScrollValues (0, 0); -b = true; -} else { -System.err.println ("Annotations were not added from annotation file '" + c + "'"); -}}return b; -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "loadFeatures", -function (a) { -var b = false; -var c = this.b$["jalview.bin.JalviewLite"].hideFeatureGroups; -if (c != null) { -a.setFeatureGroupState (this.b$["jalview.bin.JalviewLite"].separatorListToArray (c), false); -}c = this.b$["jalview.bin.JalviewLite"].showFeatureGroups; -if (c != null) { -a.setFeatureGroupState (this.b$["jalview.bin.JalviewLite"].separatorListToArray (c), true); -}c = this.b$["jalview.bin.JalviewLite"].features; -if (c != null) { -c = this.setProtocolState (c); -b = a.parseFeaturesFile (c, this.protocol); -}c = this.b$["jalview.bin.JalviewLite"].showFeatureSettings; -if (c != null && c.equalsIgnoreCase ("true")) { -a.viewport.setShowSequenceFeatures (true); - new jalview.appletgui.FeatureSettings (a.alignPanel); -}return b; -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "loadScoreFile", -function (a) { -var b = false; -if (this.b$["jalview.bin.JalviewLite"].scoreFile != null && !"".equals (this.b$["jalview.bin.JalviewLite"].scoreFile)) { -try { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Attempting to load T-COFFEE score file from the scoreFile parameter"); -}b = a.loadScoreFile (this.b$["jalview.bin.JalviewLite"].scoreFile); -if (!b) { -System.err.println ("Failed to parse T-COFFEE parameter as a valid score file ('" + this.b$["jalview.bin.JalviewLite"].scoreFile + "')"); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.printf ("Cannot read score file: '%s'. Cause: %s \n", [this.b$["jalview.bin.JalviewLite"].scoreFile, e.getMessage ()]); -} else { -throw e; -} -} -}return b; -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "loadTree", -function (a) { -var b = false; -if (this.b$["jalview.bin.JalviewLite"].treeFile == null) { -this.b$["jalview.bin.JalviewLite"].treeFile = this.applet.getParameter ("treeFile"); -}if (this.b$["jalview.bin.JalviewLite"].treeFile != null) { -try { -this.b$["jalview.bin.JalviewLite"].treeFile = this.setProtocolState (this.b$["jalview.bin.JalviewLite"].treeFile); -var c = new jalview.io.NewickFile (this.b$["jalview.bin.JalviewLite"].treeFile, this.protocol); -c.parse (); -if (c.getTree () != null) { -a.loadTree (c, this.b$["jalview.bin.JalviewLite"].treeFile); -b = true; -this.dbgMsg ("Successfully imported tree."); -} else { -this.dbgMsg ("Tree parameter did not resolve to a valid tree."); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -}return b; -}, "jalview.appletgui.AlignFrame"); -Clazz.defineMethod (c$, "inArchive", -function (a) { -try { -var b = (this.getClass ().getResourceAsStream ("/" + a) != null); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Resource '" + a + "' was " + (b ? "" : "not") + " located by classloader."); -}return b; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.out.println ("Exception checking resources: " + a + " " + ex); -return false; -} else { -throw ex; -} -} -}, "~S"); -Clazz.defineMethod (c$, "addProtocol", -function (a) { -if (a.indexOf ("://") == -1) { -var b = this.applet.resolveUrlForLocalOrAbsolute (a, this.b$["jalview.bin.JalviewLite"].getDocumentBase ()); -if (this.urlExists (b)) { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Prepended document base for resource: '" + a + "'"); -}return b; -}b = this.applet.resolveUrlForLocalOrAbsolute (a, this.b$["jalview.bin.JalviewLite"].getCodeBase ()); -if (this.urlExists (b)) { -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Prepended codebase for resource: '" + a + "'"); -}return b; -}}return a; -}, "~S"); -Clazz.defineMethod (c$, "urlExists", -($fz = function (a) { -var b = null; -try { -b = new java.net.URL (a).openStream (); -if (b != null) { -return true; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -} else { -throw x; -} -} finally { -if (b != null) { -try { -b.close (); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -}} -return false; -}, $fz.isPrivate = true, $fz), "~S"); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$1", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.f$.me).mouseOverVamsasSequence (this.f$.sq, this.f$.sq.findIndex (this.f$.pos), null); -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$2", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.f$.me).mouseOverVamsasSequence (this.f$.sq, this.f$.pos, null); -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$3", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -this.f$.alf.select (this.f$.sel, this.f$.csel); -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$4$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$4", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -try { -jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.f$.me).mouseOverStructure ( new Integer (this.f$.pdbResNum).intValue (), this.f$.chain, this.f$.pdbfile); -if (jalview.bin.JalviewLite.debug) { -System.err.println ("mouseOver for '" + this.f$.pdbResNum + "' in chain '" + this.f$.chain + "' in structure '" + this.f$.pdbfile + "'"); -}} catch (e) { -if (Clazz.exceptionOf (e, NumberFormatException)) { -System.err.println ("Ignoring invalid residue number string '" + this.f$.pdbResNum + "'"); -} else { -throw e; -} -} -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$5$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$5", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -try { -this.f$.alf.scrollTo ( new Integer (this.f$.topRow).intValue (), new Integer (this.f$.leftHandColumn).intValue ()); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Couldn't parse integer arguments (topRow='" + this.f$.topRow + "' and leftHandColumn='" + this.f$.leftHandColumn + "')"); -ex.printStackTrace (); -} else { -throw ex; -} -} -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$6$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$6", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -try { -this.f$.alf.scrollToRow ( new Integer (this.f$.topRow).intValue ()); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Couldn't parse integer arguments (topRow='" + this.f$.topRow + "')"); -ex.printStackTrace (); -} else { -throw ex; -} -} -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$7$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$7", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -try { -this.f$.alf.scrollToColumn ( new Integer (this.f$.leftHandColumn).intValue ()); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Couldn't parse integer arguments (leftHandColumn='" + this.f$.leftHandColumn + "')"); -ex.printStackTrace (); -} else { -throw ex; -} -} -}); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$8$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$8", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -var loader = Clazz.innerTypeInstance (jalview.bin.JalviewLite.LoadingThread, this, null, this.b$["jalview.bin.JalviewLite"].startupFile, this.b$["jalview.bin.JalviewLite"].file2, this.b$["jalview.bin.JalviewLite"]); -loader.start (); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$9$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$9", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -if (Clazz.instanceOf (this.f$.frame, jalview.appletgui.AlignFrame)) { -var vp = (this.f$.frame).viewport; -(this.f$.frame).closeMenuItem_actionPerformed (); -if (vp.applet.currentAlignFrame === this.f$.frame) { -vp.applet.currentAlignFrame = null; -}vp.applet = null; -vp = null; -}jalview.bin.JalviewLite.lastFrameX -= 40; -jalview.bin.JalviewLite.lastFrameY -= 40; -if (Clazz.instanceOf (this.f$.frame, jalview.appletgui.EmbmenuFrame)) { -(this.f$.frame).destroyMenus (); -}this.f$.frame.setMenuBar (null); -this.f$.frame.dispose (); -}, "java.awt.event.WindowEvent"); -Clazz.defineMethod (c$, "windowActivated", -function (e) { -if (Clazz.instanceOf (this.f$.frame, jalview.appletgui.AlignFrame)) { -(this.f$.frame).viewport.applet.currentAlignFrame = this.f$.frame; -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Activated window " + this.f$.frame); -}}Clazz.superCall (this, jalview.bin.JalviewLite$9, "windowActivated", [e]); -}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$JalviewLite$10$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$10", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -this.f$.alf.setFeatureGroupState (this.b$["jalview.bin.JalviewLite"].separatorListToArray (this.f$.groups), this.f$.st); -}); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"TRUE", "true", -"FALSE", "false", -"debug", false, -"lastFrameX", 200, -"lastFrameY", 200, -"builddate", null, -"version", null, -"installation", null); -}); +Clazz.declarePackage ("jalview.bin"); +Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.javascript.JalviewLiteJsApi", "java.lang.Thread", "javax.swing.JApplet", "jalview.util.MessageManager", "java.util.Hashtable", "$.Vector", "javax.swing.JButton"], "jalview.bin.JalviewLite", ["jalview.analysis.SequenceIdMatcher", "jalview.appletgui.AlignFrame", "$.EmbmenuFrame", "$.FeatureSettings", "$.SplitFrame", "jalview.datamodel.Alignment", "$.AlignmentOrder", "$.ColumnSelection", "$.PDBEntry", "$.SequenceGroup", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.FileParse", "$.IdentifyFile", "$.JnetAnnotationMaker", "$.NewickFile", "jalview.javascript.JSFunctionExec", "$.JsSelectionSender", "$.MouseOverListener", "$.MouseOverStructureListener", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.ColourSchemeProperty", "$.UserColourScheme", "jalview.structure.SelectionListener", "$.StructureSelectionManager", "java.awt.Color", "$.EventQueue", "$.Font", "java.awt.event.ActionListener", "$.WindowAdapter", "java.io.BufferedReader", "$.InputStreamReader", "java.lang.Error", "$.StringBuffer", "java.net.URL", "java.util.StringTokenizer", "netscape.javascript.JSObject"], function () { +c$ = Clazz.decorateAsClass (function () { +this.embedded = false; +this.enableSplitFrame = false; +this.showButton = true; +this.checkForJmol = true; +this.jalviewServletURL = null; +this.startupFile = "No file"; +this.helpUrl = null; +this.externalstructureviewer = null; +this.sep = null; +this.rgb = null; +this.labelColour = null; +this.initjscallback = null; +this.pdbFile = null; +this.sequence = null; +this.jnetFile = null; +this.annotations = null; +this.hideFeatureGroups = null; +this.showFeatureGroups = null; +this.features = null; +this.showFeatureSettings = null; +this.scoreFile = null; +this.treeFile = null; +this.windowWidth = null; +this.windowHeight = null; +this.defaultColour = null; +this.sortBy = null; +this.wrap = null; +this.centrecolumnlabels = null; +this.userDefinedColour = null; +this.widthScale = null; +this.heightScale = null; +this.upperCase = null; +this.file2 = null; +this.javascriptListeners = null; +this.jsFunctionExec = null; +this.fileFound = true; +this.launcher = null; +this.currentAlignFrame = null; +this.initialAlignFrame = null; +this.checkedForJmol = false; +this.jmolAvailable = false; +this.alignPdbStructures = false; +this.useXtrnalSviewer = false; +this.haveShownLoadMessage = false; +if (!Clazz.isClassDefined ("jalview.bin.JalviewLite.LoadJmolThread")) { +jalview.bin.JalviewLite.$JalviewLite$LoadJmolThread$ (); +} +if (!Clazz.isClassDefined ("jalview.bin.JalviewLite.LoadingThread")) { +jalview.bin.JalviewLite.$JalviewLite$LoadingThread$ (); +} +this.separator = "\u00ac"; +this.jsfallbackEnabled = false; +this.jshashes = null; +this.jsmessages = null; +this.jsExecQueue = null; +Clazz.instantialize (this, arguments); +}, jalview.bin, "JalviewLite", javax.swing.JApplet, [jalview.api.StructureSelectionManagerProvider, jalview.javascript.JalviewLiteJsApi]); +Clazz.prepareFields (c$, function () { +this.javascriptListeners = new java.util.Vector (); +this.launcher = new javax.swing.JButton (jalview.util.MessageManager.getString ("label.start_jalview")); +this.jshashes = new java.util.Hashtable (); +this.jsmessages = new java.util.Hashtable (); +this.jsExecQueue = new java.util.Vector (); +}); +Clazz.defineMethod (c$, "setParams", +($fz = function () { +jalview.bin.JalviewLite.debug = "true".equalsIgnoreCase (this.getParameter ("debug")); +this.enableSplitFrame = "true".equalsIgnoreCase (this.getParameter ("enableSplitFrame")); +this.embedded = "true".equalsIgnoreCase (this.getParameter ("embedded")); +this.showButton = !"false".equalsIgnoreCase (this.getParameter ("showbutton")); +this.jalviewServletURL = this.getParameter ("APPLICATION_URL"); +this.startupFile = this.getParameter ("file"); +this.helpUrl = this.getParameter ("jalviewhelpurl"); +this.externalstructureviewer = this.getParameter ("externalstructureviewer"); +this.checkForJmol = !"true".equals (this.getParameter ("nojmol")); +this.sep = this.getParameter ("separator"); +this.rgb = this.getParameter ("RGB"); +this.labelColour = this.getParameter ("label"); +this.initjscallback = this.getParameter ("oninit"); +this.pdbFile = this.getParameter ("PDBFILE"); +this.sequence = this.getParameter ("PDBSEQ"); +this.jnetFile = this.getParameter ("jnetfile"); +this.annotations = this.getParameter ("annotations"); +this.hideFeatureGroups = this.getParameter ("hidefeaturegroups"); +this.showFeatureGroups = this.getParameter ("showfeaturegroups"); +this.features = this.getParameter ("features"); +this.showFeatureSettings = this.getParameter ("showFeatureSettings"); +this.scoreFile = this.getParameter ("scoreFile"); +this.treeFile = this.getParameter ("tree"); +if (this.treeFile == null) this.treeFile = this.getParameter ("treeFile"); +this.windowWidth = this.getParameter ("windowWidth"); +this.windowHeight = this.getParameter ("windowHeight"); +this.defaultColour = this.getParameter ("defaultColour"); +this.sortBy = this.getParameter ("sortBy"); +this.wrap = this.getParameter ("wrap"); +this.centrecolumnlabels = this.getParameter ("centrecolumnlabels"); +this.userDefinedColour = this.getParameter ("userDefinedColour"); +this.widthScale = this.getParameter ("widthScale"); +this.heightScale = this.getParameter ("heightScale"); +this.upperCase = this.getParameter ("upperCase"); +this.file2 = this.getParameter ("file2"); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getDefaultParameter", +function (name, def) { +var stn; +if ((stn = this.getParameter (name)) == null) { +return def; +}if (stn.toLowerCase ().equals ("true")) { +return true; +}return false; +}, "~S,~B"); +Clazz.defineMethod (c$, "getLinkParams", +function (links) { +var label; +var url; +for (var i = 1; i < 10; i++) { +label = this.getParameter ("linkLabel_" + i); +url = this.getParameter ("linkURL_" + i); +if (label != null && url != null) { +links.addElement (label + "|" + url); +}} +}, "java.util.Vector"); +Clazz.defineMethod (c$, "getStructureSelectionManager", +function () { +return jalview.structure.StructureSelectionManager.getStructureSelectionManager (this); +}); +Clazz.defineMethod (c$, "getSelectedSequences", +function () { +return this.getSelectedSequencesFrom (this.getDefaultTargetFrame ()); +}); +Clazz.defineMethod (c$, "getSelectedSequences", +function (sep) { +return this.getSelectedSequencesFrom (this.getDefaultTargetFrame (), sep); +}, "~S"); +Clazz.defineMethod (c$, "getSelectedSequencesFrom", +function (alf) { +return this.getSelectedSequencesFrom (alf, this.separator); +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "getSelectedSequencesFrom", +function (alf, sep) { +var result = new StringBuffer (""); +if (sep == null || sep.length == 0) { +sep = this.separator; +}if (alf.viewport.getSelectionGroup () != null) { +var seqs = alf.viewport.getSelectionGroup ().getSequencesInOrder (alf.viewport.getAlignment ()); +for (var i = 0; i < seqs.length; i++) { +result.append (seqs[i].getName ()); +result.append (sep); +} +}return result.toString (); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "highlight", +function (sequenceId, position, alignedPosition) { +this.highlightIn (this.getDefaultTargetFrame (), sequenceId, position, alignedPosition); +}, "~S,~S,~S"); +Clazz.overrideMethod (c$, "highlightIn", +function (alf, sequenceId, position, alignedPosition) { +var matcher = new jalview.analysis.SequenceIdMatcher (alf.viewport.getAlignment ().getSequencesArray ()); +var sq = matcher.findIdMatch (sequenceId); +if (sq != null) { +var apos = -1; +try { +apos = new Integer (position).intValue (); +apos--; +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +return; +} else { +throw ex; +} +} +var me = this; +var pos = apos; +if (alignedPosition != null && (alignedPosition.trim ().length == 0 || alignedPosition.toLowerCase ().indexOf ("false") > -1)) { +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$1") ? 0 : jalview.bin.JalviewLite.$JalviewLite$1$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$1, this, Clazz.cloneFinals ("me", me, "sq", sq, "pos", pos)))); +} else { +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$2") ? 0 : jalview.bin.JalviewLite.$JalviewLite$2$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$2, this, Clazz.cloneFinals ("me", me, "sq", sq, "pos", pos)))); +}}}, "jalview.appletgui.AlignFrame,~S,~S,~S"); +Clazz.defineMethod (c$, "select", +function (sequenceIds, columns) { +this.selectIn (this.getDefaultTargetFrame (), sequenceIds, columns, this.separator); +}, "~S,~S"); +Clazz.defineMethod (c$, "select", +function (sequenceIds, columns, sep) { +this.selectIn (this.getDefaultTargetFrame (), sequenceIds, columns, sep); +}, "~S,~S,~S"); +Clazz.defineMethod (c$, "selectIn", +function (alf, sequenceIds, columns) { +this.selectIn (alf, sequenceIds, columns, this.separator); +}, "jalview.appletgui.AlignFrame,~S,~S"); +Clazz.defineMethod (c$, "selectIn", +function (alf, sequenceIds, columns, sep) { +if (sep == null || sep.length == 0) { +sep = this.separator; +} else { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Selecting region using separator string '" + this.separator + "'"); +}}var ids = this.separatorListToArray (sequenceIds, sep); +var cols = this.separatorListToArray (columns, sep); +var sel = new jalview.datamodel.SequenceGroup (); +var csel = new jalview.datamodel.ColumnSelection (); +var al = alf.viewport.getAlignment (); +var matcher = new jalview.analysis.SequenceIdMatcher (alf.viewport.getAlignment ().getSequencesArray ()); +var start = 0; +var end = al.getWidth (); +var alw = al.getWidth (); +var seqsfound = true; +if (ids != null && ids.length > 0) { +seqsfound = false; +for (var i = 0; i < ids.length; i++) { +if (ids[i].trim ().length == 0) { +continue; +}var sq = matcher.findIdMatch (ids[i]); +if (sq != null) { +seqsfound = true; +sel.addSequence (sq, false); +}} +}var inseqpos = false; +if (cols != null && cols.length > 0) { +var seset = false; +for (var i = 0; i < cols.length; i++) { +var cl = cols[i].trim (); +if (cl.length == 0) { +continue; +}var p; +if ((p = cl.indexOf ("-")) > -1) { +var from = -1; +var to = -1; +try { +from = new Integer (cl.substring (0, p)).intValue (); +from--; +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +System.err.println ("ERROR: Couldn't parse first integer in range element column selection string '" + cl + "' - format is 'from-to'"); +return; +} else { +throw ex; +} +} +try { +to = new Integer (cl.substring (p + 1)).intValue (); +to--; +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +System.err.println ("ERROR: Couldn't parse second integer in range element column selection string '" + cl + "' - format is 'from-to'"); +return; +} else { +throw ex; +} +} +if (from >= 0 && to >= 0) { +if (from < to) { +var t = to; +to = from; +to = t; +}if (!seset) { +start = from; +end = to; +seset = true; +} else { +if (start > from) { +start = from; +}if (end < to) { +end = to; +}}for (var r = from; r <= to; r++) { +if (r >= 0 && r < alw) { +csel.addElement (r); +}} +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Range '" + cl + "' deparsed as [" + from + "," + to + "]"); +}} else { +System.err.println ("ERROR: Invalid Range '" + cl + "' deparsed as [" + from + "," + to + "]"); +}} else { +var r = -1; +try { +r = new Integer (cl).intValue (); +r--; +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +if (cl.toLowerCase ().equals ("sequence")) { +inseqpos = true; +} else { +System.err.println ("ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); +return; +}} else { +throw ex; +} +} +if (r >= 0 && r <= alw) { +if (!seset) { +start = r; +end = r; +seset = true; +} else { +if (start > r) { +start = r; +}if (end < r) { +end = r; +}}csel.addElement (r); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Point selection '" + cl + "' deparsed as [" + r + "]"); +}} else { +System.err.println ("ERROR: Invalid Point selection '" + cl + "' deparsed as [" + r + "]"); +}}} +}if (seqsfound) { +if (inseqpos && sel.getSize () > 0) { +var rs = sel.getSequenceAt (0); +start = rs.findIndex (start); +end = rs.findIndex (end); +if (csel != null) { +var cs = csel.getSelected (); +csel.clear (); +for (var selectedCol, $selectedCol = cs.iterator (); $selectedCol.hasNext () && ((selectedCol = $selectedCol.next ()) || true);) { +csel.addElement (rs.findIndex ((selectedCol).intValue ())); +} +}}sel.setStartRes (start); +sel.setEndRes (end); +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$3") ? 0 : jalview.bin.JalviewLite.$JalviewLite$3$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$3, this, Clazz.cloneFinals ("alf", alf, "sel", sel, "csel", csel)))); +}}, "jalview.appletgui.AlignFrame,~S,~S,~S"); +Clazz.overrideMethod (c$, "getSelectedSequencesAsAlignment", +function (format, suffix) { +return this.getSelectedSequencesAsAlignmentFrom (this.getDefaultTargetFrame (), format, suffix); +}, "~S,~S"); +Clazz.overrideMethod (c$, "getSelectedSequencesAsAlignmentFrom", +function (alf, format, suffix) { +try { +var seqlimits = suffix.equalsIgnoreCase ("true"); +if (alf.viewport.getSelectionGroup () != null) { +var reply = new jalview.io.AppletFormatAdapter ().formatSequences (format, new jalview.datamodel.Alignment (alf.viewport.getSelectionAsNewSequence ()), seqlimits); +return reply; +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +return "Error retrieving alignment in " + format + " format. "; +} else { +throw ex; +} +} +return ""; +}, "jalview.appletgui.AlignFrame,~S,~S"); +Clazz.overrideMethod (c$, "getAlignmentOrder", +function () { +return this.getAlignmentOrderFrom (this.getDefaultTargetFrame ()); +}); +Clazz.defineMethod (c$, "getAlignmentOrderFrom", +function (alf) { +return this.getAlignmentOrderFrom (alf, this.separator); +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "getAlignmentOrderFrom", +function (alf, sep) { +var alorder = alf.getAlignViewport ().getAlignment (); +var order = new Array (alorder.getHeight ()); +for (var i = 0; i < order.length; i++) { +order[i] = alorder.getSequenceAt (i).getName (); +} +return this.arrayToSeparatorList (order); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.defineMethod (c$, "orderBy", +function (order, undoName) { +return this.orderBy (order, undoName, this.separator); +}, "~S,~S"); +Clazz.defineMethod (c$, "orderBy", +function (order, undoName, sep) { +return this.orderAlignmentBy (this.getDefaultTargetFrame (), order, undoName, sep); +}, "~S,~S,~S"); +Clazz.overrideMethod (c$, "orderAlignmentBy", +function (alf, order, undoName, sep) { +var ids = this.separatorListToArray (order, sep); +var sqs = null; +if (ids != null && ids.length > 0) { +var matcher = new jalview.analysis.SequenceIdMatcher (alf.viewport.getAlignment ().getSequencesArray ()); +var s = 0; +sqs = new Array (ids.length); +for (var i = 0; i < ids.length; i++) { +if (ids[i].trim ().length == 0) { +continue; +}var sq = matcher.findIdMatch (ids[i]); +if (sq != null) { +sqs[s++] = sq; +}} +if (s > 0) { +var sqq = new Array (s); +System.arraycopy (sqs, 0, sqq, 0, s); +sqs = sqq; +} else { +sqs = null; +}}if (sqs == null) { +return ""; +};var aorder = new jalview.datamodel.AlignmentOrder (sqs); +if (undoName != null && undoName.trim ().length == 0) { +undoName = null; +}var _undoName = undoName; +return alf.sortBy (aorder, _undoName) ? "true" : ""; +}, "jalview.appletgui.AlignFrame,~S,~S,~S"); +Clazz.defineMethod (c$, "getAlignment", +function (format) { +return this.getAlignmentFrom (this.getDefaultTargetFrame (), format, "true"); +}, "~S"); +Clazz.defineMethod (c$, "getAlignmentFrom", +function (alf, format) { +return this.getAlignmentFrom (alf, format, "true"); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.defineMethod (c$, "getAlignment", +function (format, suffix) { +return this.getAlignmentFrom (this.getDefaultTargetFrame (), format, suffix); +}, "~S,~S"); +Clazz.defineMethod (c$, "getAlignmentFrom", +function (alf, format, suffix) { +try { +var seqlimits = suffix.equalsIgnoreCase ("true"); +var reply = new jalview.io.AppletFormatAdapter ().formatSequences (format, alf.viewport.getAlignment (), seqlimits); +return reply; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +return "Error retrieving alignment in " + format + " format. "; +} else { +throw ex; +} +} +}, "jalview.appletgui.AlignFrame,~S,~S"); +Clazz.overrideMethod (c$, "loadAnnotation", +function (annotation) { +this.loadAnnotationFrom (this.getDefaultTargetFrame (), annotation); +}, "~S"); +Clazz.overrideMethod (c$, "loadAnnotationFrom", +function (alf, annotation) { +if ( new jalview.io.AnnotationFile ().annotateAlignmentView (alf.getAlignViewport (), annotation, jalview.io.AppletFormatAdapter.PASTE)) { +alf.alignPanel.fontChanged (); +alf.alignPanel.setScrollValues (0, 0); +} else { +alf.parseFeaturesFile (annotation, jalview.io.AppletFormatAdapter.PASTE); +}}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "loadFeatures", +function (features, autoenabledisplay) { +this.loadFeaturesFrom (this.getDefaultTargetFrame (), features, autoenabledisplay); +}, "~S,~B"); +Clazz.overrideMethod (c$, "loadFeaturesFrom", +function (alf, features, autoenabledisplay) { +return alf.parseFeaturesFile (features, jalview.io.AppletFormatAdapter.PASTE, autoenabledisplay); +}, "jalview.appletgui.AlignFrame,~S,~B"); +Clazz.overrideMethod (c$, "getFeatures", +function (format) { +return this.getFeaturesFrom (this.getDefaultTargetFrame (), format); +}, "~S"); +Clazz.overrideMethod (c$, "getFeaturesFrom", +function (alf, format) { +return alf.outputFeatures (false, format); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "getAnnotation", +function () { +return this.getAnnotationFrom (this.getDefaultTargetFrame ()); +}); +Clazz.overrideMethod (c$, "getAnnotationFrom", +function (alf) { +return alf.outputAnnotations (false); +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "newView", +function () { +return this.newViewFrom (this.getDefaultTargetFrame ()); +}); +Clazz.defineMethod (c$, "newView", +function (name) { +return this.newViewFrom (this.getDefaultTargetFrame (), name); +}, "~S"); +Clazz.defineMethod (c$, "newViewFrom", +function (alf) { +return alf.newView (null); +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "newViewFrom", +function (alf, name) { +return alf.newView (name); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "loadAlignment", +function (text, title) { +var al = null; +var format = new jalview.io.IdentifyFile ().Identify (text, jalview.io.AppletFormatAdapter.PASTE); +try { +al = new jalview.io.AppletFormatAdapter ().readFile (text, jalview.io.AppletFormatAdapter.PASTE, format); +if (al.getHeight () > 0) { +return new jalview.appletgui.AlignFrame (al, this, title, false); +}} catch (ex) { +if (Clazz.exceptionOf (ex, java.io.IOException)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +return null; +}, "~S,~S"); +Clazz.defineMethod (c$, "setMouseoverListener", +function (listener) { +this.setMouseoverListener (this.currentAlignFrame, listener); +}, "~S"); +Clazz.defineMethod (c$, "setMouseoverListener", +function (af, listener) { +if (listener != null) { +listener = listener.trim (); +if (listener.length == 0) { +System.err.println ("jalview Javascript error: Ignoring empty function for mouseover listener."); +return; +}}var mol = new jalview.javascript.MouseOverListener (this, af, listener); +this.javascriptListeners.addElement (mol); +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).addStructureViewerListener (mol); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Added a mouseover listener for " + ((af == null) ? "All frames" : "Just views for " + af.getAlignViewport ().getSequenceSetId ())); +System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); +}}, "jalview.appletgui.AlignFrame,~S"); +Clazz.defineMethod (c$, "setSelectionListener", +function (listener) { +this.setSelectionListener (null, listener); +}, "~S"); +Clazz.defineMethod (c$, "setSelectionListener", +function (af, listener) { +if (listener != null) { +listener = listener.trim (); +if (listener.length == 0) { +System.err.println ("jalview Javascript error: Ignoring empty function for selection listener."); +return; +}}var mol = new jalview.javascript.JsSelectionSender (this, af, listener); +this.javascriptListeners.addElement (mol); +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).addSelectionListener (mol); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Added a selection listener for " + ((af == null) ? "All frames" : "Just views for " + af.getAlignViewport ().getSequenceSetId ())); +System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); +}}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "setStructureListener", +function (listener, modelSet) { +if (listener != null) { +listener = listener.trim (); +if (listener.length == 0) { +System.err.println ("jalview Javascript error: Ignoring empty function for selection listener."); +return; +}}var mol = new jalview.javascript.MouseOverStructureListener (this, listener, this.separatorListToArray (modelSet)); +this.javascriptListeners.addElement (mol); +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).addStructureViewerListener (mol); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Added a javascript structure viewer listener '" + listener + "'"); +System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); +}}, "~S,~S"); +Clazz.overrideMethod (c$, "removeJavascriptListener", +function (af, listener) { +if (listener != null) { +listener = listener.trim (); +if (listener.length == 0) { +listener = null; +}}var rprt = false; +for (var ms = 0, msSize = this.javascriptListeners.size (); ms < msSize; ) { +var lstn = this.javascriptListeners.elementAt (ms); +var lstner = lstn; +if ((af == null || lstner.getAlignFrame () === af) && (listener == null || lstner.getListenerFunction ().equals (listener))) { +this.javascriptListeners.removeElement (lstner); +msSize--; +if (Clazz.instanceOf (lstner, jalview.structure.SelectionListener)) { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeSelectionListener (lstner); +} else { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeStructureViewerListener (lstner, null); +}rprt = jalview.bin.JalviewLite.debug; +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Removed listener '" + listener + "'"); +}} else { +ms++; +}} +if (rprt) { +System.err.println ("There are now " + this.javascriptListeners.size () + " listeners in total."); +}}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "stop", +function () { +System.err.println ("Applet " + this.getName () + " stop()."); +this.tidyUp (); +}); +Clazz.overrideMethod (c$, "destroy", +function () { +System.err.println ("Applet " + this.getName () + " destroy()."); +this.tidyUp (); +}); +Clazz.defineMethod (c$, "tidyUp", +($fz = function () { +this.removeAll (); +if (this.currentAlignFrame != null && this.currentAlignFrame.viewport != null && this.currentAlignFrame.viewport.applet != null) { +var av = this.currentAlignFrame.viewport; +this.currentAlignFrame.closeMenuItem_actionPerformed (); +av.applet = null; +this.currentAlignFrame = null; +}if (this.javascriptListeners != null) { +while (this.javascriptListeners.size () > 0) { +var mol = this.javascriptListeners.elementAt (0); +this.javascriptListeners.removeElement (mol); +if (Clazz.instanceOf (mol, jalview.structure.SelectionListener)) { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeSelectionListener (mol); +} else { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this).removeStructureViewerListener (mol, null); +}mol.jvlite = null; +} +}if (this.jsFunctionExec != null) { +this.jsFunctionExec.stopQueue (); +this.jsFunctionExec.jvlite = null; +}this.initialAlignFrame = null; +this.jsFunctionExec = null; +this.javascriptListeners = null; +jalview.structure.StructureSelectionManager.release (this); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "mouseOverStructure", +function (pdbResNum, chain, pdbfile) { +var me = this; +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$4") ? 0 : jalview.bin.JalviewLite.$JalviewLite$4$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$4, this, Clazz.cloneFinals ("me", me, "pdbResNum", pdbResNum, "chain", chain, "pdbfile", pdbfile)))); +}, "~S,~S,~S"); +Clazz.overrideMethod (c$, "scrollViewToIn", +function (alf, topRow, leftHandColumn) { +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$5") ? 0 : jalview.bin.JalviewLite.$JalviewLite$5$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$5, this, Clazz.cloneFinals ("alf", alf, "topRow", topRow, "leftHandColumn", leftHandColumn)))); +}, "jalview.appletgui.AlignFrame,~S,~S"); +Clazz.overrideMethod (c$, "scrollViewToRowIn", +function (alf, topRow) { +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$6") ? 0 : jalview.bin.JalviewLite.$JalviewLite$6$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$6, this, Clazz.cloneFinals ("alf", alf, "topRow", topRow)))); +}, "jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "scrollViewToColumnIn", +function (alf, leftHandColumn) { +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$7") ? 0 : jalview.bin.JalviewLite.$JalviewLite$7$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$7, this, Clazz.cloneFinals ("alf", alf, "leftHandColumn", leftHandColumn)))); +}, "jalview.appletgui.AlignFrame,~S"); +c$.initBuildDetails = Clazz.defineMethod (c$, "initBuildDetails", +($fz = function () { +if (jalview.bin.JalviewLite.builddate == null) { +jalview.bin.JalviewLite.builddate = "unknown"; +jalview.bin.JalviewLite.version = "test"; +jalview.bin.JalviewLite.installation = "Webstart"; +var url = jalview.bin.JalviewLite.getResource ("/.build_properties"); +if (url != null) { +try { +var reader = new java.io.BufferedReader ( new java.io.InputStreamReader (url.openStream ())); +var line; +while ((line = reader.readLine ()) != null) { +if (line.indexOf ("VERSION") > -1) { +jalview.bin.JalviewLite.version = line.substring (line.indexOf ("=") + 1); +}if (line.indexOf ("BUILD_DATE") > -1) { +jalview.bin.JalviewLite.builddate = line.substring (line.indexOf ("=") + 1); +}if (line.indexOf ("INSTALLATION") > -1) { +jalview.bin.JalviewLite.installation = line.substring (line.indexOf ("=") + 1); +}} +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}}}, $fz.isPrivate = true, $fz)); +c$.getBuildDate = Clazz.defineMethod (c$, "getBuildDate", +function () { +jalview.bin.JalviewLite.initBuildDetails (); +return jalview.bin.JalviewLite.builddate; +}); +c$.getInstallation = Clazz.defineMethod (c$, "getInstallation", +function () { +jalview.bin.JalviewLite.initBuildDetails (); +return jalview.bin.JalviewLite.installation; +}); +c$.getVersion = Clazz.defineMethod (c$, "getVersion", +function () { +jalview.bin.JalviewLite.initBuildDetails (); +return jalview.bin.JalviewLite.version; +}); +Clazz.overrideMethod (c$, "init", +function () { +this.setParams (); +try { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Applet context is '" + this.getAppletContext ().getClass ().toString () + "'"); +}var scriptObject = netscape.javascript.JSObject.getWindow (this); +if (jalview.bin.JalviewLite.debug && scriptObject != null) { +System.err.println ("Applet has Javascript callback support."); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Warning: No JalviewLite javascript callbacks available."); +if (jalview.bin.JalviewLite.debug) { +ex.printStackTrace (); +}} else { +throw ex; +} +} +if (jalview.bin.JalviewLite.debug) { +System.err.println ("JalviewLite Version " + jalview.bin.JalviewLite.getVersion ()); +System.err.println ("Build Date : " + jalview.bin.JalviewLite.getBuildDate ()); +System.err.println ("Installation : " + jalview.bin.JalviewLite.getInstallation ()); +}if (this.externalstructureviewer != null) { +this.useXtrnalSviewer = this.externalstructureviewer.trim ().toLowerCase ().equals ("true"); +}if (this.sep != null) { +if (this.sep.length > 0) { +this.separator = this.sep; +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Separator set to '" + this.separator + "'"); +}} else { +throw new Error (jalview.util.MessageManager.getString ("error.invalid_separator_parameter")); +}}var r = 255; +var g = 255; +var b = 255; +if (this.rgb != null) { +try { +r = Integer.parseInt (this.rgb.substring (0, 2), 16); +g = Integer.parseInt (this.rgb.substring (2, 4), 16); +b = Integer.parseInt (this.rgb.substring (4, 6), 16); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +r = 255; +g = 255; +b = 255; +} else { +throw ex; +} +} +}this.rgb = this.labelColour; +if (this.rgb != null) { +this.launcher.setLabel (this.rgb); +}this.setBackground ( new java.awt.Color (r, g, b)); +if (this.startupFile == null) { +var data = new StringBuffer ("PASTE"); +var i = 1; +while ((this.startupFile = this.getParameter ("sequence" + i)) != null) { +data.append (this.startupFile.toString () + "\n"); +i++; +} +if (data.length () > 5) { +this.startupFile = data.toString (); +}}if (!this.enableSplitFrame) { +this.file2 = null; +}if (this.embedded) { +var loader = Clazz.innerTypeInstance (jalview.bin.JalviewLite.LoadingThread, this, null, this.startupFile, this.file2, this); +{ +loader.run(); +}} else if (this.startupFile != null) { +if (!this.showButton) { +var loader = Clazz.innerTypeInstance (jalview.bin.JalviewLite.LoadingThread, this, null, this.startupFile, this.file2, this); +loader.start (); +} else { +this.add (this.launcher); +this.launcher.addActionListener (((Clazz.isClassDefined ("jalview.bin.JalviewLite$8") ? 0 : jalview.bin.JalviewLite.$JalviewLite$8$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$8, this, null))); +}} else { +this.startupFile = "NO FILE"; +this.fileFound = false; +this.callInitCallback (); +}}); +Clazz.defineMethod (c$, "initLiveConnect", +($fz = function () { +var notFailed = false; +var tries = 0; +while (!notFailed && tries < 10) { +if (tries > 0) { +System.err.println ("LiveConnect request thread going to sleep."); +}try { +Thread.sleep (700 * (1 + tries)); +} catch (q) { +if (Clazz.exceptionOf (q, InterruptedException)) { +} else { +throw q; +} +} +;if (tries++ > 0) { +System.err.println ("LiveConnect request thread woken up."); +}try { +var scriptObject = netscape.javascript.JSObject.getWindow (this); +if (scriptObject.eval ("navigator") != null) { +notFailed = true; +}} catch (jsex) { +if (Clazz.exceptionOf (jsex, Exception)) { +System.err.println ("Attempt " + tries + " to access LiveConnect javascript failed."); +} else { +throw jsex; +} +} +} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "callInitCallback", +($fz = function () { +if (this.initjscallback == null) { +return; +}this.initjscallback = this.initjscallback.trim (); +if (this.initjscallback.length > 0) { +var scriptObject = null; +try { +scriptObject = netscape.javascript.JSObject.getWindow (this); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +;this.initLiveConnect (); +if (scriptObject != null) { +try { + new jalview.javascript.JSFunctionExec (this).executeJavascriptFunction (true, this.initjscallback, null, "Calling oninit callback '" + this.initjscallback + "'."); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Exception when executing _oninit callback '" + this.initjscallback + "'."); +e.printStackTrace (); +} else { +throw e; +} +} +} else { +System.err.println ("Not executing _oninit callback '" + this.initjscallback + "' - no scripting allowed."); +}}}, $fz.isPrivate = true, $fz)); +c$.addFrame = Clazz.defineMethod (c$, "addFrame", +function (frame, title, width, height) { +frame.setLocation (jalview.bin.JalviewLite.lastFrameX, jalview.bin.JalviewLite.lastFrameY); +jalview.bin.JalviewLite.lastFrameX += 40; +jalview.bin.JalviewLite.lastFrameY += 40; +frame.setSize (width, height); +frame.setTitle (title); +frame.addWindowListener (((Clazz.isClassDefined ("jalview.bin.JalviewLite$9") ? 0 : jalview.bin.JalviewLite.$JalviewLite$9$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$9, this, Clazz.cloneFinals ("frame", frame)))); +frame.setVisible (true); +}, "javax.swing.JFrame,~S,~N,~N"); +Clazz.defineMethod (c$, "paintComponent", +function (g) { +if (!this.fileFound) { +g.setColor ( new java.awt.Color (200, 200, 200)); +g.setColor (java.awt.Color.cyan); +g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); +g.setColor (java.awt.Color.red); +g.drawString (jalview.util.MessageManager.getString ("label.jalview_cannot_open_file"), 5, 15); +g.drawString ("\"" + this.startupFile + "\"", 5, 30); +} else if (this.embedded && !this.haveShownLoadMessage) { +g.setColor (java.awt.Color.black); +g.setFont ( new java.awt.Font ("Arial", 1, 24)); +g.drawString (jalview.util.MessageManager.getString ("label.jalview_applet"), 50, Clazz.doubleToInt (this.getSize ().height / 2) - 30); +g.drawString (jalview.util.MessageManager.getString ("label.loading_data") + "...", 50, Clazz.doubleToInt (this.getSize ().height / 2)); +this.haveShownLoadMessage = true; +}}, "java.awt.Graphics"); +Clazz.defineMethod (c$, "getAppletWindow", +function (class1) { +var wnds = new java.util.Vector (); +var cmp = this.getComponents (); +if (cmp != null) { +for (var i = 0; i < cmp.length; i++) { +if (class1.isAssignableFrom (cmp[i].getClass ())) { +wnds.addElement (cmp); +}} +}return wnds; +}, "Class"); +Clazz.defineMethod (c$, "getDefaultTargetFrame", +function () { +if (this.currentAlignFrame != null) { +return this.currentAlignFrame; +}if (this.initialAlignFrame != null) { +return this.initialAlignFrame; +}System.err.println ("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); +return null; +}); +Clazz.defineMethod (c$, "separatorListToArray", +function (list) { +return this.separatorListToArray (list, this.separator); +}, "~S"); +Clazz.defineMethod (c$, "separatorListToArray", +function (list, separator) { +var seplen = separator.length; +if (list == null || list.equals ("") || list.equals (separator)) { +return null; +}var jv = new java.util.Vector (); +var cp = 0; +var pos; +while ((pos = list.indexOf (separator, cp)) > cp) { +jv.addElement (list.substring (cp, pos)); +cp = pos + seplen; +} +if (cp < list.length) { +var c = list.substring (cp); +if (!c.equals (separator)) { +jv.addElement (c); +}}if (jv.size () > 0) { +var v = new Array (jv.size ()); +for (var i = 0; i < v.length; i++) { +v[i] = jv.elementAt (i); +} +jv.removeAllElements (); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Array from '" + separator + "' separated List:\n" + v.length); +for (var i = 0; i < v.length; i++) { +System.err.println ("item " + i + " '" + v[i] + "'"); +} +}return v; +}if (jalview.bin.JalviewLite.debug) { +System.err.println ("Empty Array from '" + separator + "' separated List"); +}return null; +}, "~S,~S"); +Clazz.defineMethod (c$, "arrayToSeparatorList", +function (list) { +return this.arrayToSeparatorList (list, this.separator); +}, "~A"); +Clazz.defineMethod (c$, "arrayToSeparatorList", +function (list, separator) { +var v = new StringBuffer (); +if (list != null && list.length > 0) { +for (var i = 0, iSize = list.length; i < iSize; i++) { +if (list[i] != null) { +if (i > 0) { +v.append (separator); +}v.append (list[i]); +}} +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Returning '" + separator + "' separated List:\n"); +System.err.println (v); +}return v.toString (); +}if (jalview.bin.JalviewLite.debug) { +System.err.println ("Returning empty '" + separator + "' separated List\n"); +}return "" + separator; +}, "~A,~S"); +Clazz.overrideMethod (c$, "getFeatureGroups", +function () { +var lst = this.arrayToSeparatorList (this.getDefaultTargetFrame ().getFeatureGroups ()); +return lst; +}); +Clazz.overrideMethod (c$, "getFeatureGroupsOn", +function (alf) { +var lst = this.arrayToSeparatorList (alf.getFeatureGroups ()); +return lst; +}, "jalview.appletgui.AlignFrame"); +Clazz.overrideMethod (c$, "getFeatureGroupsOfState", +function (visible) { +return this.arrayToSeparatorList (this.getDefaultTargetFrame ().getFeatureGroupsOfState (visible)); +}, "~B"); +Clazz.overrideMethod (c$, "getFeatureGroupsOfStateOn", +function (alf, visible) { +return this.arrayToSeparatorList (alf.getFeatureGroupsOfState (visible)); +}, "jalview.appletgui.AlignFrame,~B"); +Clazz.overrideMethod (c$, "setFeatureGroupStateOn", +function (alf, groups, state) { +var st = state; +java.awt.EventQueue.invokeLater (((Clazz.isClassDefined ("jalview.bin.JalviewLite$10") ? 0 : jalview.bin.JalviewLite.$JalviewLite$10$ ()), Clazz.innerTypeInstance (jalview.bin.JalviewLite$10, this, Clazz.cloneFinals ("alf", alf, "groups", groups, "st", st)))); +}, "jalview.appletgui.AlignFrame,~S,~B"); +Clazz.overrideMethod (c$, "setFeatureGroupState", +function (groups, state) { +this.setFeatureGroupStateOn (this.getDefaultTargetFrame (), groups, state); +}, "~S,~B"); +Clazz.overrideMethod (c$, "getSeparator", +function () { +return this.separator; +}); +Clazz.overrideMethod (c$, "setSeparator", +function (separator) { +if (separator == null || separator.length < 1) { +separator = "\u00ac"; +}this.separator = separator; +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Default Separator now: '" + separator + "'"); +}}, "~S"); +Clazz.overrideMethod (c$, "addPdbFile", +function (alFrame, sequenceId, pdbEntryString, pdbFile) { +return alFrame.addPdbFile (sequenceId, pdbEntryString, pdbFile); +}, "jalview.appletgui.AlignFrame,~S,~S,~S"); +Clazz.defineMethod (c$, "setAlignPdbStructures", +function (alignPdbStructures) { +this.alignPdbStructures = alignPdbStructures; +}, "~B"); +Clazz.defineMethod (c$, "isAlignPdbStructures", +function () { +return this.alignPdbStructures; +}); +Clazz.overrideMethod (c$, "start", +function () { +}); +Clazz.defineMethod (c$, "setJsMessageSet", +function (messageclass, viewId, colcommands) { +var msgset = this.jsmessages.get (messageclass); +if (msgset == null) { +msgset = new java.util.Hashtable (); +this.jsmessages.put (messageclass, msgset); +}msgset.put (viewId, colcommands); +var l = Clazz.newLongArray (colcommands.length, 0); +for (var i = 0; i < colcommands.length; i++) { +l[i] = colcommands[i].hashCode (); +} +this.jshashes.put (messageclass + "|" + viewId, l); +}, "~S,~S,~A"); +Clazz.overrideMethod (c$, "getJsMessage", +function (messageclass, viewId) { +var msgset = this.jsmessages.get (messageclass); +if (msgset != null) { +var msgs = msgset.get (viewId); +if (msgs != null) { +for (var i = 0; i < msgs.length; i++) { +if (msgs[i] != null) { +var m = msgs[i]; +msgs[i] = null; +return m; +}} +}}return ""; +}, "~S,~S"); +Clazz.defineMethod (c$, "isJsMessageSetChanged", +function (string, string2, colcommands) { +var l = this.jshashes.get (string + "|" + string2); +if (l == null && colcommands != null) { +return true; +}for (var i = 0; i < colcommands.length; i++) { +if (l[i] != colcommands[i].hashCode ()) { +return true; +}} +return false; +}, "~S,~S,~A"); +Clazz.defineMethod (c$, "getJsExecQueue", +function () { +return this.jsExecQueue; +}); +Clazz.defineMethod (c$, "setExecutor", +function (jsFunctionExec2) { +this.jsFunctionExec = jsFunctionExec2; +}, "jalview.javascript.JSFunctionExec"); +Clazz.defineMethod (c$, "getDefaultColourParameter", +function (colparam, defcolour) { +var colprop = this.getParameter (colparam); +if (colprop == null || colprop.trim ().length == 0) { +return defcolour; +}var col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName (colprop); +if (col == null) { +try { +col = new jalview.schemes.UserColourScheme (colprop).findColour ('A'); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Couldn't parse '" + colprop + "' as a colour for " + colparam); +col = null; +} else { +throw ex; +} +} +}return (col == null) ? defcolour : col; +}, "~S,java.awt.Color"); +Clazz.defineMethod (c$, "openJalviewHelpUrl", +function () { +if (this.helpUrl == null || this.helpUrl.trim ().length < 5) { +this.helpUrl = "http://www.jalview.org/help.html"; +}this.showURL (this.helpUrl, "HELP"); +}); +Clazz.defineMethod (c$, "resolveUrlForLocalOrAbsolute", +($fz = function (url, localref) { +var codebase = localref.toString (); +var pt = codebase.indexOf ("?"); +if (pt < 0) pt = codebase.length; +codebase = codebase.substring (0, pt); +codebase = codebase.substring (0, codebase.lastIndexOf ("/") + 1); +if (url.indexOf ("/") == 0 && !localref.getProtocol ().equals ("file")) { +pt = codebase.indexOf ("/", 8); +return codebase.substring (0, pt) + url; +}return codebase + url; +}, $fz.isPrivate = true, $fz), "~S,java.net.URL"); +Clazz.defineMethod (c$, "showURL", +function (url, target) { +try { +if (url.indexOf (":") == -1) { +var prepend; +url = this.resolveUrlForLocalOrAbsolute (url, prepend = this.getDefaultParameter ("resolvetocodebase", false) ? this.getDocumentBase () : this.getCodeBase ()); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Show url (prepended " + prepend + " - toggle resolvetocodebase if code/docbase resolution is wrong): " + url); +}} else { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Show url: " + url); +}}if (url.indexOf ("javascript:") == 0) { +this.getAppletContext ().showDocument ( new java.net.URL (url)); +} else { +this.getAppletContext ().showDocument ( new java.net.URL (url), target); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}, "~S,~S"); +c$.$JalviewLite$LoadJmolThread$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.running = false; +Clazz.instantialize (this, arguments); +}, jalview.bin.JalviewLite, "LoadJmolThread", Thread); +Clazz.overrideMethod (c$, "run", +function () { +if (this.running || this.b$["jalview.bin.JalviewLite"].checkedForJmol) { +return; +}this.running = true; +if (this.b$["jalview.bin.JalviewLite"].checkForJmol) { +try { +if (!System.getProperty ("java.version").startsWith ("1.1")) { +Class.forName ("org.jmol.adapter.smarter.SmarterJmolAdapter"); +this.b$["jalview.bin.JalviewLite"].jmolAvailable = true; +}if (!this.b$["jalview.bin.JalviewLite"].jmolAvailable) { +System.out.println ("Jmol not available - Using MCview for structures"); +}} catch (ex) { +if (Clazz.exceptionOf (ex, ClassNotFoundException)) { +} else { +throw ex; +} +} +} else { +this.b$["jalview.bin.JalviewLite"].jmolAvailable = false; +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Skipping Jmol check. Will use MCView (probably)"); +}}this.b$["jalview.bin.JalviewLite"].checkedForJmol = true; +this.running = false; +}); +Clazz.defineMethod (c$, "notFinished", +function () { +return this.running || !this.b$["jalview.bin.JalviewLite"].checkedForJmol; +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$LoadingThread$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.protocol = null; +this._file = null; +this._file2 = null; +this.applet = null; +Clazz.instantialize (this, arguments); +}, jalview.bin.JalviewLite, "LoadingThread", Thread); +Clazz.defineMethod (c$, "dbgMsg", +($fz = function (a) { +if (jalview.bin.JalviewLite.debug) { +System.err.println (a); +}}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "setProtocolState", +function (a) { +if (a.startsWith ("PASTE")) { +a = a.substring (5); +this.protocol = jalview.io.AppletFormatAdapter.PASTE; +} else if (this.inArchive (a)) { +this.protocol = jalview.io.AppletFormatAdapter.CLASSLOADER; +} else { +a = this.addProtocol (a); +this.protocol = jalview.io.AppletFormatAdapter.URL; +}this.dbgMsg ("Protocol identified as '" + this.protocol + "'"); +return a; +}, "~S"); +Clazz.makeConstructor (c$, +function (a, b, c) { +Clazz.superConstructor (this, jalview.bin.JalviewLite.LoadingThread, []); +this._file = a; +this._file2 = b; +this.applet = c; +}, "~S,~S,jalview.bin.JalviewLite"); +Clazz.overrideMethod (c$, "run", +function () { +{ +System.out.println("BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY") +}this.startLoading (); +}); +Clazz.defineMethod (c$, "startLoading", +($fz = function () { +this.dbgMsg ("Loading thread started with:\n>>file\n" + this._file + ">>endfile"); +this.dbgMsg ("Loading started."); +var a = this.readAlignment (this._file); +var b = this.readAlignment (this._file2); +if (a != null) { +this.addToDisplay (a, b); +this.loadTree (a); +this.loadScoreFile (a); +this.loadFeatures (a); +this.loadAnnotations (a); +this.loadJnetFile (a); +this.loadPdbFiles (a); +} else { +this.b$["jalview.bin.JalviewLite"].fileFound = false; +this.applet.remove (this.b$["jalview.bin.JalviewLite"].launcher); +this.applet.repaint (); +}this.b$["jalview.bin.JalviewLite"].callInitCallback (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "addToDisplay", +function (a, b) { +if (b == null) { +a.addToDisplay (this.b$["jalview.bin.JalviewLite"].embedded); +} else { +var c = new jalview.appletgui.SplitFrame (a, b); +c.addToDisplay (this.b$["jalview.bin.JalviewLite"].embedded, this.b$["jalview.bin.JalviewLite"]); +}}, "jalview.appletgui.AlignFrame,jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "readAlignment", +function (a) { +if (a == null) { +return null; +}var b = this.setProtocolState (a); +var c = new jalview.io.IdentifyFile ().Identify (b, this.protocol); +this.dbgMsg ("File identified as '" + c + "'"); +var d = null; +try { +d = new jalview.io.AppletFormatAdapter ().readFile (b, this.protocol, c); +if ((d != null) && (d.getHeight () > 0)) { +this.dbgMsg ("Successfully loaded file."); +d.setDataset (null); +var e = new jalview.appletgui.AlignFrame (d, this.applet, b, this.b$["jalview.bin.JalviewLite"].embedded, false); +e.setTitle (b); +if (this.b$["jalview.bin.JalviewLite"].initialAlignFrame == null) { +this.b$["jalview.bin.JalviewLite"].initialAlignFrame = e; +}this.b$["jalview.bin.JalviewLite"].currentAlignFrame = e; +if (this.protocol === jalview.io.AppletFormatAdapter.PASTE) { +e.setTitle (jalview.util.MessageManager.formatMessage ("label.sequences_from", Clazz.newArray (-1, [this.applet.getDocumentBase ().toString ()]))); +}e.setStatus (jalview.util.MessageManager.formatMessage ("label.successfully_loaded_file", Clazz.newArray (-1, [b]))); +return e; +}} catch (ex) { +if (Clazz.exceptionOf (ex, java.io.IOException)) { +this.dbgMsg ("File load exception."); +ex.printStackTrace (); +if (jalview.bin.JalviewLite.debug) { +try { +var e = new jalview.io.FileParse (b, this.protocol); +var f = null; +this.dbgMsg (">>>Dumping contents of '" + b + "' " + "(" + this.protocol + ")"); +while ((f = e.nextLine ()) != null) { +this.dbgMsg (f); +} +this.dbgMsg (">>>Dump finished."); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Exception when trying to dump the content of the file parameter."); +e.printStackTrace (); +} else { +throw e; +} +} +}} else { +throw ex; +} +} +return null; +}, "~S"); +Clazz.defineMethod (c$, "loadPdbFiles", +function (a) { +var b = false; +this.applet.setAlignPdbStructures (this.b$["jalview.bin.JalviewLite"].getDefaultParameter ("alignpdbfiles", false)); +var c = 0; +var d = new java.util.Vector (); +var e = (this.applet.getDefaultParameter ("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher (a.getAlignViewport ().getAlignment ().getSequencesArray ()) : null; +var f; +do { +if (c > 0) { +f = this.applet.getParameter ("PDBFILE" + c); +} else { +f = this.b$["jalview.bin.JalviewLite"].pdbFile; +}if (f != null) { +var g = new jalview.datamodel.PDBEntry (); +var h; +var i = null; +var j = null; +var k = new java.util.StringTokenizer (f, " "); +if (k.countTokens () < 2) { +if (this.b$["jalview.bin.JalviewLite"].sequence != null) { +i = Clazz.newArray (-1, [e == null ? a.getAlignViewport ().getAlignment ().findName (this.b$["jalview.bin.JalviewLite"].sequence) : e.findIdMatch (this.b$["jalview.bin.JalviewLite"].sequence)]); +}} else { +f = k.nextToken (); +var l = new java.util.Vector (); +var m = new java.util.Vector (); +while (k.hasMoreTokens ()) { +h = k.nextToken (); +var n = new java.util.StringTokenizer (h, "="); +if (n.countTokens () > 1) { +m.addElement (n.nextToken ()); +h = n.nextToken (); +}l.addElement (e == null ? a.getAlignViewport ().getAlignment ().findName (h) : e.findIdMatch (h)); +} +i = new Array (l.size ()); +l.copyInto (i); +if (m.size () == l.size ()) { +j = new Array (m.size ()); +m.copyInto (j); +}}f = this.setProtocolState (f); +if (this.protocol === jalview.io.AppletFormatAdapter.CLASSLOADER && !this.b$["jalview.bin.JalviewLite"].useXtrnalSviewer) { +this.protocol = jalview.io.AppletFormatAdapter.URL; +f = this.addProtocol (f); +}g.setFile (f); +if (i != null) { +for (var l = 0; l < i.length; l++) { +if (i[l] != null) { +(i[l]).addPDBId (g); +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.applet).registerPDBEntry (g); +} else { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + l + ")"); +}}} +if (!this.b$["jalview.bin.JalviewLite"].alignPdbStructures) { +a.newStructureView (this.applet, g, i, j, this.protocol); +} else { +d.addElement ( Clazz.newArray (-1, [g, i, j, String.instantialize (this.protocol)])); +}}}c++; +} while (f != null || c < 10); +if (d.size () > 0) { +var g = new Array (d.size ()); +var h = new Array (d.size ()); +var i = new Array (d.size ()); +var j = new Array (d.size ()); +for (var k = 0, l = d.size (); k < l; k++) { +var m = d.elementAt (k); +h[k] = m[0]; +g[k] = m[1]; +i[k] = m[2]; +j[k] = m[3]; +} +a.alignedStructureView (this.applet, h, g, i, j); +b = true; +}return b; +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "loadJnetFile", +function (a) { +var b = false; +var c = this.b$["jalview.bin.JalviewLite"].jnetFile; +if (c != null) { +try { +c = this.setProtocolState (c); +var d = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [c, this.protocol]); +jalview.io.JnetAnnotationMaker.add_annotation (d, a.viewport.getAlignment (), 0, false); +var e = a.viewport.getAlignment ().getSequenceAt (0); +a.viewport.getAlignment ().setSeqrep (e); +var f = new jalview.datamodel.ColumnSelection (); +f.hideInsertionsFor (e); +a.viewport.setColumnSelection (f); +a.alignPanel.fontChanged (); +a.alignPanel.setScrollValues (0, 0); +b = true; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}return b; +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "loadAnnotations", +function (a) { +var b = false; +var c = this.b$["jalview.bin.JalviewLite"].annotations; +if (c != null) { +c = this.setProtocolState (c); +if ( new jalview.io.AnnotationFile ().annotateAlignmentView (a.viewport, c, this.protocol)) { +a.alignPanel.fontChanged (); +a.alignPanel.setScrollValues (0, 0); +b = true; +} else { +System.err.println ("Annotations were not added from annotation file '" + c + "'"); +}}return b; +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "loadFeatures", +function (a) { +var b = false; +var c = this.b$["jalview.bin.JalviewLite"].hideFeatureGroups; +if (c != null) { +a.setFeatureGroupState (this.b$["jalview.bin.JalviewLite"].separatorListToArray (c), false); +}c = this.b$["jalview.bin.JalviewLite"].showFeatureGroups; +if (c != null) { +a.setFeatureGroupState (this.b$["jalview.bin.JalviewLite"].separatorListToArray (c), true); +}c = this.b$["jalview.bin.JalviewLite"].features; +if (c != null) { +c = this.setProtocolState (c); +b = a.parseFeaturesFile (c, this.protocol); +}c = this.b$["jalview.bin.JalviewLite"].showFeatureSettings; +if (c != null && c.equalsIgnoreCase ("true")) { +a.viewport.setShowSequenceFeatures (true); + new jalview.appletgui.FeatureSettings (a.alignPanel); +}return b; +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "loadScoreFile", +function (a) { +var b = false; +if (this.b$["jalview.bin.JalviewLite"].scoreFile != null && !"".equals (this.b$["jalview.bin.JalviewLite"].scoreFile)) { +try { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Attempting to load T-COFFEE score file from the scoreFile parameter"); +}b = a.loadScoreFile (this.b$["jalview.bin.JalviewLite"].scoreFile); +if (!b) { +System.err.println ("Failed to parse T-COFFEE parameter as a valid score file ('" + this.b$["jalview.bin.JalviewLite"].scoreFile + "')"); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.printf ("Cannot read score file: '%s'. Cause: %s \n", [this.b$["jalview.bin.JalviewLite"].scoreFile, e.getMessage ()]); +} else { +throw e; +} +} +}return b; +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "loadTree", +function (a) { +var b = false; +if (this.b$["jalview.bin.JalviewLite"].treeFile == null) { +this.b$["jalview.bin.JalviewLite"].treeFile = this.applet.getParameter ("treeFile"); +}if (this.b$["jalview.bin.JalviewLite"].treeFile != null) { +try { +this.b$["jalview.bin.JalviewLite"].treeFile = this.setProtocolState (this.b$["jalview.bin.JalviewLite"].treeFile); +var c = new jalview.io.NewickFile (this.b$["jalview.bin.JalviewLite"].treeFile, this.protocol); +c.parse (); +if (c.getTree () != null) { +a.loadTree (c, this.b$["jalview.bin.JalviewLite"].treeFile); +b = true; +this.dbgMsg ("Successfully imported tree."); +} else { +this.dbgMsg ("Tree parameter did not resolve to a valid tree."); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +}return b; +}, "jalview.appletgui.AlignFrame"); +Clazz.defineMethod (c$, "inArchive", +function (a) { +try { +var b = (this.getClass ().getResourceAsStream ("/" + a) != null); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Resource '" + a + "' was " + (b ? "" : "not") + " located by classloader."); +}return b; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.out.println ("Exception checking resources: " + a + " " + ex); +return false; +} else { +throw ex; +} +} +}, "~S"); +Clazz.defineMethod (c$, "addProtocol", +function (a) { +if (a.indexOf ("://") == -1) { +var b = this.applet.resolveUrlForLocalOrAbsolute (a, this.b$["jalview.bin.JalviewLite"].getDocumentBase ()); +if (this.urlExists (b)) { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Prepended document base for resource: '" + a + "'"); +}return b; +}b = this.applet.resolveUrlForLocalOrAbsolute (a, this.b$["jalview.bin.JalviewLite"].getCodeBase ()); +if (this.urlExists (b)) { +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Prepended codebase for resource: '" + a + "'"); +}return b; +}}return a; +}, "~S"); +Clazz.defineMethod (c$, "urlExists", +($fz = function (a) { +var b = null; +try { +b = new java.net.URL (a).openStream (); +if (b != null) { +return true; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +} else { +throw x; +} +} finally { +if (b != null) { +try { +b.close (); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +}} +return false; +}, $fz.isPrivate = true, $fz), "~S"); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$1", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.f$.me).mouseOverVamsasSequence (this.f$.sq, this.f$.sq.findIndex (this.f$.pos), null); +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$2", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.f$.me).mouseOverVamsasSequence (this.f$.sq, this.f$.pos, null); +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$3", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +this.f$.alf.select (this.f$.sel, this.f$.csel); +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$4$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$4", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +try { +jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.f$.me).mouseOverStructure ( new Integer (this.f$.pdbResNum).intValue (), this.f$.chain, this.f$.pdbfile); +if (jalview.bin.JalviewLite.debug) { +System.err.println ("mouseOver for '" + this.f$.pdbResNum + "' in chain '" + this.f$.chain + "' in structure '" + this.f$.pdbfile + "'"); +}} catch (e) { +if (Clazz.exceptionOf (e, NumberFormatException)) { +System.err.println ("Ignoring invalid residue number string '" + this.f$.pdbResNum + "'"); +} else { +throw e; +} +} +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$5$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$5", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +try { +this.f$.alf.scrollTo ( new Integer (this.f$.topRow).intValue (), new Integer (this.f$.leftHandColumn).intValue ()); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Couldn't parse integer arguments (topRow='" + this.f$.topRow + "' and leftHandColumn='" + this.f$.leftHandColumn + "')"); +ex.printStackTrace (); +} else { +throw ex; +} +} +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$6$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$6", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +try { +this.f$.alf.scrollToRow ( new Integer (this.f$.topRow).intValue ()); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Couldn't parse integer arguments (topRow='" + this.f$.topRow + "')"); +ex.printStackTrace (); +} else { +throw ex; +} +} +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$7$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$7", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +try { +this.f$.alf.scrollToColumn ( new Integer (this.f$.leftHandColumn).intValue ()); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Couldn't parse integer arguments (leftHandColumn='" + this.f$.leftHandColumn + "')"); +ex.printStackTrace (); +} else { +throw ex; +} +} +}); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$8$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$8", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +var loader = Clazz.innerTypeInstance (jalview.bin.JalviewLite.LoadingThread, this, null, this.b$["jalview.bin.JalviewLite"].startupFile, this.b$["jalview.bin.JalviewLite"].file2, this.b$["jalview.bin.JalviewLite"]); +loader.start (); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$9$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$9", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +if (Clazz.instanceOf (this.f$.frame, jalview.appletgui.AlignFrame)) { +var vp = (this.f$.frame).viewport; +(this.f$.frame).closeMenuItem_actionPerformed (); +if (vp.applet.currentAlignFrame === this.f$.frame) { +vp.applet.currentAlignFrame = null; +}vp.applet = null; +vp = null; +}jalview.bin.JalviewLite.lastFrameX -= 40; +jalview.bin.JalviewLite.lastFrameY -= 40; +if (Clazz.instanceOf (this.f$.frame, jalview.appletgui.EmbmenuFrame)) { +(this.f$.frame).destroyMenus (); +}this.f$.frame.setMenuBar (null); +this.f$.frame.dispose (); +}, "java.awt.event.WindowEvent"); +Clazz.defineMethod (c$, "windowActivated", +function (e) { +if (Clazz.instanceOf (this.f$.frame, jalview.appletgui.AlignFrame)) { +(this.f$.frame).viewport.applet.currentAlignFrame = this.f$.frame; +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Activated window " + this.f$.frame); +}}Clazz.superCall (this, jalview.bin.JalviewLite$9, "windowActivated", [e]); +}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$JalviewLite$10$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.bin, "JalviewLite$10", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +this.f$.alf.setFeatureGroupState (this.b$["jalview.bin.JalviewLite"].separatorListToArray (this.f$.groups), this.f$.st); +}); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"TRUE", "true", +"FALSE", "false", +"debug", false, +"lastFrameX", 200, +"lastFrameY", 200, +"builddate", null, +"version", null, +"installation", null); +}); diff --git a/bin/jalview/commands/ChangeCaseCommand.js b/bin/jalview/commands/ChangeCaseCommand.js index fb085d6..0ebfc96 100644 --- a/bin/jalview/commands/ChangeCaseCommand.js +++ b/bin/jalview/commands/ChangeCaseCommand.js @@ -1,74 +1,74 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.CommandI"], "jalview.commands.ChangeCaseCommand", ["java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.description = null; -this.caseChange = -1; -this.seqs = null; -this.regions = null; -Clazz.instantialize (this, arguments); -}, jalview.commands, "ChangeCaseCommand", null, jalview.commands.CommandI); -Clazz.makeConstructor (c$, -function (description, seqs, regions, caseChange) { -this.description = description; -this.seqs = seqs; -this.regions = regions; -this.caseChange = caseChange; -this.doCommand (null); -}, "~S,~A,java.util.List,~N"); -Clazz.overrideMethod (c$, "getDescription", -function () { -return this.description; -}); -Clazz.overrideMethod (c$, "getSize", -function () { -return 1; -}); -Clazz.overrideMethod (c$, "doCommand", -function (views) { -this.changeCase (true); -}, "~A"); -Clazz.overrideMethod (c$, "undoCommand", -function (views) { -this.changeCase (false); -}, "~A"); -Clazz.defineMethod (c$, "changeCase", -function (doCommand) { -var sequence; -var start; -var end; -var nextChar; -for (var r, $r = this.regions.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { -start = r[0]; -for (var s = 0; s < this.seqs.length; s++) { -sequence = this.seqs[s].getSequenceAsString (); -var newSeq = new StringBuffer (); -if (r[1] > sequence.length) { -end = sequence.length; -} else { -end = r[1]; -}if (start > 0) { -newSeq.append (sequence.substring (0, start)); -}if ((this.caseChange == jalview.commands.ChangeCaseCommand.TO_UPPER && doCommand) || (this.caseChange == jalview.commands.ChangeCaseCommand.TO_LOWER && !doCommand)) { -newSeq.append (sequence.substring (start, end).toUpperCase ()); -} else if ((this.caseChange == jalview.commands.ChangeCaseCommand.TO_LOWER && doCommand) || (this.caseChange == jalview.commands.ChangeCaseCommand.TO_UPPER && !doCommand)) { -newSeq.append (sequence.substring (start, end).toLowerCase ()); -} else { -for (var c = start; c < end; c++) { -nextChar = sequence.charAt (c); -if ('a' <= nextChar && nextChar <= 'z') { -nextChar = String.fromCharCode (nextChar.charCodeAt (0) - (32)); -} else if ('A' <= nextChar && nextChar <= 'Z') { -nextChar = String.fromCharCode (nextChar.charCodeAt (0) + (32)); -}newSeq.append (nextChar); -} -}if (end < sequence.length) { -newSeq.append (sequence.substring (end)); -}this.seqs[s].setSequence (newSeq.toString ()); -} -} -}, "~B"); -Clazz.defineStatics (c$, -"TO_LOWER", 0, -"TO_UPPER", 1, -"TOGGLE_CASE", 2); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.CommandI"], "jalview.commands.ChangeCaseCommand", ["java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.description = null; +this.caseChange = -1; +this.seqs = null; +this.regions = null; +Clazz.instantialize (this, arguments); +}, jalview.commands, "ChangeCaseCommand", null, jalview.commands.CommandI); +Clazz.makeConstructor (c$, +function (description, seqs, regions, caseChange) { +this.description = description; +this.seqs = seqs; +this.regions = regions; +this.caseChange = caseChange; +this.doCommand (null); +}, "~S,~A,java.util.List,~N"); +Clazz.overrideMethod (c$, "getDescription", +function () { +return this.description; +}); +Clazz.overrideMethod (c$, "getSize", +function () { +return 1; +}); +Clazz.overrideMethod (c$, "doCommand", +function (views) { +this.changeCase (true); +}, "~A"); +Clazz.overrideMethod (c$, "undoCommand", +function (views) { +this.changeCase (false); +}, "~A"); +Clazz.defineMethod (c$, "changeCase", +function (doCommand) { +var sequence; +var start; +var end; +var nextChar; +for (var r, $r = this.regions.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { +start = r[0]; +for (var s = 0; s < this.seqs.length; s++) { +sequence = this.seqs[s].getSequenceAsString (); +var newSeq = new StringBuffer (); +if (r[1] > sequence.length) { +end = sequence.length; +} else { +end = r[1]; +}if (start > 0) { +newSeq.append (sequence.substring (0, start)); +}if ((this.caseChange == jalview.commands.ChangeCaseCommand.TO_UPPER && doCommand) || (this.caseChange == jalview.commands.ChangeCaseCommand.TO_LOWER && !doCommand)) { +newSeq.append (sequence.substring (start, end).toUpperCase ()); +} else if ((this.caseChange == jalview.commands.ChangeCaseCommand.TO_LOWER && doCommand) || (this.caseChange == jalview.commands.ChangeCaseCommand.TO_UPPER && !doCommand)) { +newSeq.append (sequence.substring (start, end).toLowerCase ()); +} else { +for (var c = start; c < end; c++) { +nextChar = sequence.charAt (c); +if ('a' <= nextChar && nextChar <= 'z') { +nextChar = String.fromCharCode (nextChar.charCodeAt (0) - (32)); +} else if ('A' <= nextChar && nextChar <= 'Z') { +nextChar = String.fromCharCode (nextChar.charCodeAt (0) + (32)); +}newSeq.append (nextChar); +} +}if (end < sequence.length) { +newSeq.append (sequence.substring (end)); +}this.seqs[s].setSequence (newSeq.toString ()); +} +} +}, "~B"); +Clazz.defineStatics (c$, +"TO_LOWER", 0, +"TO_UPPER", 1, +"TOGGLE_CASE", 2); +}); diff --git a/bin/jalview/commands/CommandI.js b/bin/jalview/commands/CommandI.js index 792918f..598c931 100644 --- a/bin/jalview/commands/CommandI.js +++ b/bin/jalview/commands/CommandI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.declareInterface (jalview.commands, "CommandI"); +Clazz.declarePackage ("jalview.commands"); +Clazz.declareInterface (jalview.commands, "CommandI"); diff --git a/bin/jalview/commands/EditCommand.class b/bin/jalview/commands/EditCommand.class index 21a6161..8e6645e 100644 Binary files a/bin/jalview/commands/EditCommand.class and b/bin/jalview/commands/EditCommand.class differ diff --git a/bin/jalview/commands/EditCommand.js b/bin/jalview/commands/EditCommand.js index b556231..0839473 100644 --- a/bin/jalview/commands/EditCommand.js +++ b/bin/jalview/commands/EditCommand.js @@ -1,661 +1,661 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.CommandI", "java.lang.Enum", "java.util.ArrayList"], "jalview.commands.EditCommand", ["jalview.analysis.AlignSeq", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.Sequence", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.ReverseListIterator", "$.StringUtils", "java.lang.StringBuffer", "java.util.HashMap", "$.Hashtable"], function () { -c$ = Clazz.decorateAsClass (function () { -this.edits = null; -this.description = null; -if (!Clazz.isClassDefined ("jalview.commands.EditCommand.Edit")) { -jalview.commands.EditCommand.$EditCommand$Edit$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.commands, "EditCommand", null, jalview.commands.CommandI); -Clazz.prepareFields (c$, function () { -this.edits = new java.util.ArrayList (); -}); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (description) { -this.description = description; -}, "~S"); -Clazz.makeConstructor (c$, -function (description, command, seqs, position, number, al) { -this.description = description; -if (command === jalview.commands.EditCommand.Action.CUT || command === jalview.commands.EditCommand.Action.PASTE) { -this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al)); -}this.performEdit (0, null); -}, "~S,jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI"); -Clazz.makeConstructor (c$, -function (description, command, replace, seqs, position, number, al) { -this.description = description; -if (command === jalview.commands.EditCommand.Action.REPLACE) { -this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al, replace)); -}this.performEdit (0, null); -}, "~S,jalview.commands.EditCommand.Action,~S,~A,~N,~N,jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "setEdit", -function (e) { -this.edits.clear (); -this.edits.add (e); -}, "jalview.commands.EditCommand.Edit"); -Clazz.defineMethod (c$, "addEdit", -function (e) { -if (!jalview.commands.EditCommand.expandEdit (this.edits, e)) { -this.edits.add (e); -}}, "jalview.commands.EditCommand.Edit"); -c$.expandEdit = Clazz.defineMethod (c$, "expandEdit", -function (edits, e) { -if (edits == null || edits.isEmpty ()) { -return false; -}var lastEdit = edits.get (edits.size () - 1); -var action = e.command; -if (lastEdit.command !== action) { -return false; -}if (lastEdit.seqs.length != e.seqs.length) { -return false; -}for (var i = 0; i < e.seqs.length; i++) { -if (lastEdit.seqs[i].getDatasetSequence () !== e.seqs[i].getDatasetSequence ()) { -return false; -}} -var contiguous = (action === jalview.commands.EditCommand.Action.INSERT_GAP && e.position == lastEdit.position + lastEdit.number) || (action === jalview.commands.EditCommand.Action.DELETE_GAP && e.position + e.number == lastEdit.position); -if (contiguous) { -lastEdit.number += e.number; -lastEdit.seqs = e.seqs; -if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { -lastEdit.position--; -}return true; -}return false; -}, "java.util.List,jalview.commands.EditCommand.Edit"); -Clazz.defineMethod (c$, "clearEdits", -function () { -this.edits.clear (); -}); -Clazz.defineMethod (c$, "getEdit", -function (i) { -if (i >= 0 && i < this.edits.size ()) { -return this.edits.get (i); -}return null; -}, "~N"); -Clazz.overrideMethod (c$, "getDescription", -function () { -return this.description; -}); -Clazz.overrideMethod (c$, "getSize", -function () { -return this.edits.size (); -}); -Clazz.defineMethod (c$, "getAlignment", -function () { -return (this.edits.isEmpty () ? null : this.edits.get (0).al); -}); -Clazz.defineMethod (c$, "appendEdit", -function (command, seqs, position, number, al, performEdit) { -this.appendEdit (command, seqs, position, number, al, performEdit, null); -}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B"); -Clazz.defineMethod (c$, "appendEdit", -function (command, seqs, position, number, al, performEdit, views) { -var edit = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al.getGapCharacter ()); -if (al.getHeight () == seqs.length) { -edit.al = al; -edit.fullAlignmentHeight = true; -}this.addEdit (edit); -if (performEdit) { -jalview.commands.EditCommand.performEdit (edit, views); -}}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B,~A"); -Clazz.defineMethod (c$, "appendEdit", -function (edit, al, performEdit, views) { -if (al.getHeight () == edit.seqs.length) { -edit.al = al; -edit.fullAlignmentHeight = true; -}this.addEdit (edit); -if (performEdit) { -jalview.commands.EditCommand.performEdit (edit, views); -}}, "jalview.commands.EditCommand.Edit,jalview.datamodel.AlignmentI,~B,~A"); -Clazz.defineMethod (c$, "performEdit", -function (commandIndex, views) { -var iterator = this.edits.listIterator (commandIndex); -while (iterator.hasNext ()) { -var edit = iterator.next (); -jalview.commands.EditCommand.performEdit (edit, views); -} -}, "~N,~A"); -c$.performEdit = Clazz.defineMethod (c$, "performEdit", -function (edit, views) { -switch (edit.command) { -case jalview.commands.EditCommand.Action.INSERT_GAP: -jalview.commands.EditCommand.insertGap (edit); -break; -case jalview.commands.EditCommand.Action.DELETE_GAP: -jalview.commands.EditCommand.deleteGap (edit); -break; -case jalview.commands.EditCommand.Action.CUT: -jalview.commands.EditCommand.cut (edit, views); -break; -case jalview.commands.EditCommand.Action.PASTE: -jalview.commands.EditCommand.paste (edit, views); -break; -case jalview.commands.EditCommand.Action.REPLACE: -jalview.commands.EditCommand.replace (edit); -break; -case jalview.commands.EditCommand.Action.INSERT_NUC: -break; -default: -break; -} -}, "jalview.commands.EditCommand.Edit,~A"); -Clazz.overrideMethod (c$, "doCommand", -function (views) { -this.performEdit (0, views); -}, "~A"); -Clazz.overrideMethod (c$, "undoCommand", -function (views) { -var iterator = this.edits.listIterator (this.edits.size ()); -while (iterator.hasPrevious ()) { -var e = iterator.previous (); -switch (e.command) { -case jalview.commands.EditCommand.Action.INSERT_GAP: -jalview.commands.EditCommand.deleteGap (e); -break; -case jalview.commands.EditCommand.Action.DELETE_GAP: -jalview.commands.EditCommand.insertGap (e); -break; -case jalview.commands.EditCommand.Action.CUT: -jalview.commands.EditCommand.paste (e, views); -break; -case jalview.commands.EditCommand.Action.PASTE: -jalview.commands.EditCommand.cut (e, views); -break; -case jalview.commands.EditCommand.Action.REPLACE: -jalview.commands.EditCommand.replace (e); -break; -case jalview.commands.EditCommand.Action.INSERT_NUC: -break; -default: -break; -} -} -}, "~A"); -c$.insertGap = Clazz.defineMethod (c$, "insertGap", -($fz = function (command) { -for (var s = 0; s < command.seqs.length; s++) { -command.seqs[s].insertCharAt (command.position, command.number, command.gapChar); -} -jalview.commands.EditCommand.adjustAnnotations (command, true, false, null); -}, $fz.isPrivate = true, $fz), "jalview.commands.EditCommand.Edit"); -c$.deleteGap = Clazz.defineMethod (c$, "deleteGap", -($fz = function (command) { -for (var s = 0; s < command.seqs.length; s++) { -command.seqs[s].deleteChars (command.position, command.position + command.number); -} -jalview.commands.EditCommand.adjustAnnotations (command, false, false, null); -}, $fz.isPrivate = true, $fz), "jalview.commands.EditCommand.Edit"); -c$.cut = Clazz.defineMethod (c$, "cut", -function (command, views) { -var seqDeleted = false; -command.string = Clazz.newCharArray (command.seqs.length, '\0'); -for (var i = 0; i < command.seqs.length; i++) { -var sequence = command.seqs[i]; -if (sequence.getLength () > command.position) { -command.string[i] = sequence.getSequence (command.position, command.position + command.number); -var oldds = sequence.getDatasetSequence (); -if (command.oldds != null && command.oldds[i] != null) { -sequence.setDatasetSequence (null); -}sequence.deleteChars (command.position, command.position + command.number); -if (command.oldds != null && command.oldds[i] != null) { -sequence.setDatasetSequence (command.oldds[i]); -command.oldds[i] = oldds; -} else { -if (oldds !== sequence.getDatasetSequence () || sequence.getSequenceFeatures () != null) { -if (command.oldds == null) { -command.oldds = new Array (command.seqs.length); -}command.oldds[i] = oldds; -jalview.commands.EditCommand.adjustFeatures (command, i, sequence.findPosition (command.position), sequence.findPosition (command.position + command.number), false); -}}}if (sequence.getLength () < 1) { -command.al.deleteSequence (sequence); -seqDeleted = true; -}} -jalview.commands.EditCommand.adjustAnnotations (command, false, seqDeleted, views); -}, "jalview.commands.EditCommand.Edit,~A"); -c$.paste = Clazz.defineMethod (c$, "paste", -function (command, views) { -var tmp; -var newDSNeeded; -var newDSWasNeeded; -var newstart; -var newend; -var seqWasDeleted = false; -var start = 0; -var end = 0; -for (var i = 0; i < command.seqs.length; i++) { -newDSNeeded = false; -newDSWasNeeded = command.oldds != null && command.oldds[i] != null; -if (command.seqs[i].getLength () < 1) { -if (command.alIndex[i] < command.al.getHeight ()) { -var sequences; -{ -if (!(command.alIndex[i] < 0)) { -sequences.add (command.alIndex[i], command.seqs[i]); -}}} else { -command.al.addSequence (command.seqs[i]); -}seqWasDeleted = true; -}newstart = command.seqs[i].getStart (); -newend = command.seqs[i].getEnd (); -tmp = new StringBuffer (); -tmp.append (command.seqs[i].getSequence ()); -if (command.string != null && command.string[i] != null) { -if (command.position >= tmp.length ()) { -var length = command.position - tmp.length (); -while (length > 0) { -tmp.append (command.gapChar); -length--; -} -}tmp.insert (command.position, command.string[i]); -for (var s = 0; s < command.string[i].length; s++) { -if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s].charCodeAt (0)] != 23) { -if (!newDSNeeded) { -newDSNeeded = true; -start = command.seqs[i].findPosition (command.position); -end = command.seqs[i].findPosition (command.position + command.number); -}if (command.seqs[i].getStart () == start) { -newstart--; -} else { -newend++; -}}} -command.string[i] = null; -}command.seqs[i].setSequence (tmp.toString ()); -command.seqs[i].setStart (newstart); -command.seqs[i].setEnd (newend); -if (newDSNeeded) { -if (command.seqs[i].getDatasetSequence () != null) { -var ds; -if (newDSWasNeeded) { -ds = command.oldds[i]; -} else { -ds = new jalview.datamodel.Sequence (command.seqs[i].getName (), jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, command.seqs[i].getSequenceAsString ()), command.seqs[i].getStart (), command.seqs[i].getEnd ()); -ds.setDescription (command.seqs[i].getDescription ()); -}if (command.oldds == null) { -command.oldds = new Array (command.seqs.length); -}command.oldds[i] = command.seqs[i].getDatasetSequence (); -command.seqs[i].setDatasetSequence (ds); -}jalview.commands.EditCommand.adjustFeatures (command, i, start, end, true); -}} -jalview.commands.EditCommand.adjustAnnotations (command, true, seqWasDeleted, views); -command.string = null; -}, "jalview.commands.EditCommand.Edit,~A"); -c$.replace = Clazz.defineMethod (c$, "replace", -function (command) { -var tmp; -var oldstring; -var start = command.position; -var end = command.number; -command.number = start + command.string[0].length; -for (var i = 0; i < command.seqs.length; i++) { -var newDSWasNeeded = command.oldds != null && command.oldds[i] != null; -oldstring = command.seqs[i].getSequenceAsString (); -tmp = new StringBuffer (oldstring.substring (0, start)); -tmp.append (command.string[i]); -var nogaprep = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (command.string[i])); -var ipos = command.seqs[i].findPosition (start) - command.seqs[i].getStart (); -tmp.append (oldstring.substring (end)); -command.seqs[i].setSequence (tmp.toString ()); -command.string[i] = oldstring.substring (start, end).toCharArray (); -var nogapold = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (command.string[i])); -if (!nogaprep.toLowerCase ().equals (nogapold.toLowerCase ())) { -if (newDSWasNeeded) { -var oldds = command.seqs[i].getDatasetSequence (); -command.seqs[i].setDatasetSequence (command.oldds[i]); -command.oldds[i] = oldds; -} else { -if (command.oldds == null) { -command.oldds = new Array (command.seqs.length); -}command.oldds[i] = command.seqs[i].getDatasetSequence (); -var newds = new jalview.datamodel.Sequence (command.seqs[i].getDatasetSequence ()); -var fullseq; -var osp = newds.getSequenceAsString (); -fullseq = osp.substring (0, ipos) + nogaprep + osp.substring (ipos + nogaprep.length); -newds.setSequence (fullseq.toUpperCase ()); -command.seqs[i].setDatasetSequence (newds); -}}tmp = null; -oldstring = null; -} -}, "jalview.commands.EditCommand.Edit"); -c$.adjustAnnotations = Clazz.defineMethod (c$, "adjustAnnotations", -function (command, insert, modifyVisibility, views) { -var annotations = null; -if (modifyVisibility && !insert) { -command.deletedAnnotationRows = new java.util.Hashtable (); -}if (command.fullAlignmentHeight) { -annotations = command.al.getAlignmentAnnotation (); -} else { -var aSize = 0; -var tmp; -for (var s = 0; s < command.seqs.length; s++) { -if (modifyVisibility) { -if (!insert) { -tmp = command.seqs[s].getAnnotation (); -if (tmp != null) { -var alen = tmp.length; -for (var aa = 0; aa < tmp.length; aa++) { -if (!command.al.deleteAnnotation (tmp[aa])) { -tmp[aa] = null; -alen--; -}} -command.seqs[s].setAlignmentAnnotation (null); -if (alen != tmp.length) { -var saved = new Array (alen); -for (var aa = 0, aapos = 0; aa < tmp.length; aa++) { -if (tmp[aa] != null) { -saved[aapos++] = tmp[aa]; -tmp[aa] = null; -}} -tmp = saved; -command.deletedAnnotationRows.put (command.seqs[s], saved); -for (var alview = 0; views != null && alview < views.length; alview++) { -if (views[alview] !== command.al) { -var toremove = views[alview].getAlignmentAnnotation (); -if (toremove == null || toremove.length == 0) { -continue; -}for (var aa = 0; aa < toremove.length; aa++) { -if (toremove[aa].sequenceRef === command.seqs[s]) { -views[alview].deleteAnnotation (toremove[aa]); -}} -}} -} else { -command.deletedAnnotationRows.put (command.seqs[s], tmp); -}}} else { -if (command.deletedAnnotationRows != null && command.deletedAnnotationRows.containsKey (command.seqs[s])) { -var revealed = command.deletedAnnotationRows.get (command.seqs[s]); -command.seqs[s].setAlignmentAnnotation (revealed); -if (revealed != null) { -for (var aa = 0; aa < revealed.length; aa++) { -command.al.addAnnotation (revealed[aa]); -} -for (var aa = 0; aa < revealed.length; aa++) { -command.al.setAnnotationIndex (revealed[aa], aa); -} -for (var vnum = 0; views != null && vnum < views.length; vnum++) { -if (views[vnum] !== command.al) { -var avwidth = views[vnum].getWidth () + 1; -for (var a = 0; a < revealed.length; a++) { -var newann = new jalview.datamodel.AlignmentAnnotation (revealed[a]); -command.seqs[s].addAlignmentAnnotation (newann); -newann.padAnnotation (avwidth); -views[vnum].addAnnotation (newann); -views[vnum].setAnnotationIndex (newann, a); -} -}} -}}}continue; -}if (command.seqs[s].getAnnotation () == null) { -continue; -}if (aSize == 0) { -annotations = command.seqs[s].getAnnotation (); -} else { -tmp = new Array (aSize + command.seqs[s].getAnnotation ().length); -System.arraycopy (annotations, 0, tmp, 0, aSize); -System.arraycopy (command.seqs[s].getAnnotation (), 0, tmp, aSize, command.seqs[s].getAnnotation ().length); -annotations = tmp; -}aSize = annotations.length; -} -}if (annotations == null) { -return; -}if (!insert) { -command.deletedAnnotations = new java.util.Hashtable (); -}var aSize; -var temp; -for (var a = 0; a < annotations.length; a++) { -if (annotations[a].autoCalculated || annotations[a].annotations == null) { -continue; -}var tSize = 0; -aSize = annotations[a].annotations.length; -if (insert) { -temp = new Array (aSize + command.number); -if (annotations[a].padGaps) { -for (var aa = 0; aa < temp.length; aa++) { -temp[aa] = new jalview.datamodel.Annotation (command.gapChar + "", null, ' ', 0); -} -}} else { -if (command.position < aSize) { -if (command.position + command.number >= aSize) { -tSize = aSize; -} else { -tSize = aSize - command.number; -}} else { -tSize = aSize; -}if (tSize < 0) { -tSize = aSize; -}temp = new Array (tSize); -}if (insert) { -if (command.position < annotations[a].annotations.length) { -System.arraycopy (annotations[a].annotations, 0, temp, 0, command.position); -if (command.deletedAnnotations != null && command.deletedAnnotations.containsKey (annotations[a].annotationId)) { -var restore = command.deletedAnnotations.get (annotations[a].annotationId); -System.arraycopy (restore, 0, temp, command.position, command.number); -}System.arraycopy (annotations[a].annotations, command.position, temp, command.position + command.number, aSize - command.position); -} else { -if (command.deletedAnnotations != null && command.deletedAnnotations.containsKey (annotations[a].annotationId)) { -var restore = command.deletedAnnotations.get (annotations[a].annotationId); -temp = new Array (annotations[a].annotations.length + restore.length); -System.arraycopy (annotations[a].annotations, 0, temp, 0, annotations[a].annotations.length); -System.arraycopy (restore, 0, temp, annotations[a].annotations.length, restore.length); -} else { -temp = annotations[a].annotations; -}}} else { -if (tSize != aSize || command.position < 2) { -var copylen = Math.min (command.position, annotations[a].annotations.length); -if (copylen > 0) { -System.arraycopy (annotations[a].annotations, 0, temp, 0, copylen); -}var deleted = new Array (command.number); -if (copylen >= command.position) { -copylen = Math.min (command.number, annotations[a].annotations.length - command.position); -if (copylen > 0) { -System.arraycopy (annotations[a].annotations, command.position, deleted, 0, copylen); -}}command.deletedAnnotations.put (annotations[a].annotationId, deleted); -if (annotations[a].annotations.length > command.position + command.number) { -System.arraycopy (annotations[a].annotations, command.position + command.number, temp, command.position, annotations[a].annotations.length - command.position - command.number); -}} else { -var dSize = aSize - command.position; -if (dSize > 0) { -var deleted = new Array (command.number); -System.arraycopy (annotations[a].annotations, command.position, deleted, 0, dSize); -command.deletedAnnotations.put (annotations[a].annotationId, deleted); -tSize = Math.min (annotations[a].annotations.length, command.position); -temp = new Array (tSize); -System.arraycopy (annotations[a].annotations, 0, temp, 0, tSize); -} else { -temp = annotations[a].annotations; -}}}annotations[a].annotations = temp; -} -}, "jalview.commands.EditCommand.Edit,~B,~B,~A"); -c$.adjustFeatures = Clazz.defineMethod (c$, "adjustFeatures", -function (command, index, i, j, insert) { -var seq = command.seqs[index]; -var sequence = seq.getDatasetSequence (); -if (sequence == null) { -sequence = seq; -}if (insert) { -if (command.editedFeatures != null && command.editedFeatures.containsKey (seq)) { -sequence.setSequenceFeatures (command.editedFeatures.get (seq)); -}return; -}var sf = sequence.getSequenceFeatures (); -if (sf == null) { -return; -}var oldsf = new Array (sf.length); -var cSize = j - i; -for (var s = 0; s < sf.length; s++) { -var copy = new jalview.datamodel.SequenceFeature (sf[s]); -oldsf[s] = copy; -if (sf[s].getEnd () < i) { -continue; -}if (sf[s].getBegin () > j) { -sf[s].setBegin (copy.getBegin () - cSize); -sf[s].setEnd (copy.getEnd () - cSize); -continue; -}if (sf[s].getBegin () >= i) { -sf[s].setBegin (i); -}if (sf[s].getEnd () < j) { -sf[s].setEnd (j - 1); -}sf[s].setEnd (sf[s].getEnd () - (cSize)); -if (sf[s].getBegin () > sf[s].getEnd ()) { -sequence.deleteFeature (sf[s]); -}} -if (command.editedFeatures == null) { -command.editedFeatures = new java.util.Hashtable (); -}command.editedFeatures.put (seq, oldsf); -}, "jalview.commands.EditCommand.Edit,~N,~N,~N,~B"); -Clazz.defineMethod (c$, "getEdits", -function () { -return this.edits; -}); -Clazz.defineMethod (c$, "priorState", -function (forUndo) { -var result = new java.util.HashMap (); -if (this.getEdits () == null) { -return result; -}if (forUndo) { -for (var e, $e = this.getEdits ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) { -for (var seq, $seq = 0, $$seq = e.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { -var ds = seq.getDatasetSequence (); -var preEdit = result.get (ds); -if (preEdit == null) { -preEdit = new jalview.datamodel.Sequence ("", seq.getSequenceAsString ()); -preEdit.setDatasetSequence (ds); -result.put (ds, preEdit); -}} -} -return result; -}var edits = new jalview.util.ReverseListIterator (this.getEdits ()); -while (edits.hasNext ()) { -var oldEdit = edits.next (); -var action = oldEdit.getAction (); -var position = oldEdit.getPosition (); -var number = oldEdit.getNumber (); -var gap = oldEdit.getGapCharacter (); -for (var seq, $seq = 0, $$seq = oldEdit.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { -var ds = seq.getDatasetSequence (); -var preEdit = result.get (ds); -if (preEdit == null) { -preEdit = new jalview.datamodel.Sequence ("", seq.getSequenceAsString ()); -preEdit.setDatasetSequence (ds); -result.put (ds, preEdit); -}if (ds != null) { -if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { -preEdit.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (preEdit.getSequence (), position, number, gap))); -} else if (action === jalview.commands.EditCommand.Action.INSERT_GAP) { -preEdit.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (preEdit.getSequence (), position, position + number))); -} else { -System.err.println ("Can't undo edit action " + action); -}}} -} -return result; -}, "~B"); -Clazz.defineMethod (c$, "getEditIterator", -function (forwards) { -if (forwards) { -return this.getEdits ().iterator (); -} else { -return new jalview.util.ReverseListIterator (this.getEdits ()); -}}, "~B"); -c$.$EditCommand$Edit$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.oldds = null; -this.fullAlignmentHeight = false; -this.deletedAnnotationRows = null; -this.deletedAnnotations = null; -this.editedFeatures = null; -this.al = null; -this.command = null; -this.string = null; -this.seqs = null; -this.alIndex = null; -this.position = 0; -this.number = 0; -this.gapChar = '\0'; -Clazz.instantialize (this, arguments); -}, jalview.commands.EditCommand, "Edit"); -Clazz.makeConstructor (c$, -function (a, b, c, d, e) { -this.command = a; -this.seqs = b; -this.position = c; -this.number = d; -this.gapChar = e; -}, "jalview.commands.EditCommand.Action,~A,~N,~N,~S"); -Clazz.makeConstructor (c$, -function (a, b, c, d, e) { -this.gapChar = e.getGapCharacter (); -this.command = a; -this.seqs = b; -this.position = c; -this.number = d; -this.al = e; -this.alIndex = Clazz.newIntArray (b.length, 0); -for (var f = 0; f < b.length; f++) { -this.alIndex[f] = e.findIndex (b[f]); -} -this.fullAlignmentHeight = (e.getHeight () == b.length); -}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI"); -Clazz.makeConstructor (c$, -function (a, b, c, d, e, f) { -this.command = a; -this.seqs = b; -this.position = c; -this.number = d; -this.al = e; -this.gapChar = e.getGapCharacter (); -this.string = Clazz.newCharArray (b.length, '\0'); -for (var g = 0; g < b.length; g++) { -this.string[g] = f.toCharArray (); -} -this.fullAlignmentHeight = (e.getHeight () == b.length); -}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~S"); -Clazz.defineMethod (c$, "getSequences", -function () { -return this.seqs; -}); -Clazz.defineMethod (c$, "getPosition", -function () { -return this.position; -}); -Clazz.defineMethod (c$, "getAction", -function () { -return this.command; -}); -Clazz.defineMethod (c$, "getNumber", -function () { -return this.number; -}); -Clazz.defineMethod (c$, "getGapCharacter", -function () { -return this.gapChar; -}); -c$ = Clazz.p0p (); -}; -Clazz.pu$h (); -c$ = Clazz.declareType (jalview.commands.EditCommand, "Action", Enum); -Clazz.defineMethod (c$, "getUndoAction", -function () { -switch (this) { -case jalview.commands.EditCommand.Action.INSERT_GAP: -return jalview.commands.EditCommand.Action.DELETE_GAP; -case jalview.commands.EditCommand.Action.CUT: -return jalview.commands.EditCommand.Action.PASTE; -case jalview.commands.EditCommand.Action.DELETE_GAP: -return jalview.commands.EditCommand.Action.INSERT_GAP; -case jalview.commands.EditCommand.Action.INSERT_NUC: -return null; -case jalview.commands.EditCommand.Action.PASTE: -return jalview.commands.EditCommand.Action.CUT; -case jalview.commands.EditCommand.Action.REPLACE: -return jalview.commands.EditCommand.Action.REPLACE; -} -return null; -}); -Clazz.defineEnumConstant (c$, "INSERT_GAP", 0, []); -Clazz.defineEnumConstant (c$, "DELETE_GAP", 1, []); -Clazz.defineEnumConstant (c$, "CUT", 2, []); -Clazz.defineEnumConstant (c$, "PASTE", 3, []); -Clazz.defineEnumConstant (c$, "REPLACE", 4, []); -Clazz.defineEnumConstant (c$, "INSERT_NUC", 5, []); -c$ = Clazz.p0p (); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.CommandI", "java.lang.Enum", "java.util.ArrayList"], "jalview.commands.EditCommand", ["jalview.analysis.AlignSeq", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.Sequence", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.ReverseListIterator", "$.StringUtils", "java.lang.StringBuffer", "java.util.HashMap", "$.Hashtable"], function () { +c$ = Clazz.decorateAsClass (function () { +this.edits = null; +this.description = null; +if (!Clazz.isClassDefined ("jalview.commands.EditCommand.Edit")) { +jalview.commands.EditCommand.$EditCommand$Edit$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.commands, "EditCommand", null, jalview.commands.CommandI); +Clazz.prepareFields (c$, function () { +this.edits = new java.util.ArrayList (); +}); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (description) { +this.description = description; +}, "~S"); +Clazz.makeConstructor (c$, +function (description, command, seqs, position, number, al) { +this.description = description; +if (command === jalview.commands.EditCommand.Action.CUT || command === jalview.commands.EditCommand.Action.PASTE) { +this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al)); +}this.performEdit (0, null); +}, "~S,jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI"); +Clazz.makeConstructor (c$, +function (description, command, replace, seqs, position, number, al) { +this.description = description; +if (command === jalview.commands.EditCommand.Action.REPLACE) { +this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al, replace)); +}this.performEdit (0, null); +}, "~S,jalview.commands.EditCommand.Action,~S,~A,~N,~N,jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "setEdit", +function (e) { +this.edits.clear (); +this.edits.add (e); +}, "jalview.commands.EditCommand.Edit"); +Clazz.defineMethod (c$, "addEdit", +function (e) { +if (!jalview.commands.EditCommand.expandEdit (this.edits, e)) { +this.edits.add (e); +}}, "jalview.commands.EditCommand.Edit"); +c$.expandEdit = Clazz.defineMethod (c$, "expandEdit", +function (edits, e) { +if (edits == null || edits.isEmpty ()) { +return false; +}var lastEdit = edits.get (edits.size () - 1); +var action = e.command; +if (lastEdit.command !== action) { +return false; +}if (lastEdit.seqs.length != e.seqs.length) { +return false; +}for (var i = 0; i < e.seqs.length; i++) { +if (lastEdit.seqs[i].getDatasetSequence () !== e.seqs[i].getDatasetSequence ()) { +return false; +}} +var contiguous = (action === jalview.commands.EditCommand.Action.INSERT_GAP && e.position == lastEdit.position + lastEdit.number) || (action === jalview.commands.EditCommand.Action.DELETE_GAP && e.position + e.number == lastEdit.position); +if (contiguous) { +lastEdit.number += e.number; +lastEdit.seqs = e.seqs; +if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { +lastEdit.position--; +}return true; +}return false; +}, "java.util.List,jalview.commands.EditCommand.Edit"); +Clazz.defineMethod (c$, "clearEdits", +function () { +this.edits.clear (); +}); +Clazz.defineMethod (c$, "getEdit", +function (i) { +if (i >= 0 && i < this.edits.size ()) { +return this.edits.get (i); +}return null; +}, "~N"); +Clazz.overrideMethod (c$, "getDescription", +function () { +return this.description; +}); +Clazz.overrideMethod (c$, "getSize", +function () { +return this.edits.size (); +}); +Clazz.defineMethod (c$, "getAlignment", +function () { +return (this.edits.isEmpty () ? null : this.edits.get (0).al); +}); +Clazz.defineMethod (c$, "appendEdit", +function (command, seqs, position, number, al, performEdit) { +this.appendEdit (command, seqs, position, number, al, performEdit, null); +}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B"); +Clazz.defineMethod (c$, "appendEdit", +function (command, seqs, position, number, al, performEdit, views) { +var edit = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al.getGapCharacter ()); +if (al.getHeight () == seqs.length) { +edit.al = al; +edit.fullAlignmentHeight = true; +}this.addEdit (edit); +if (performEdit) { +jalview.commands.EditCommand.performEdit (edit, views); +}}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B,~A"); +Clazz.defineMethod (c$, "appendEdit", +function (edit, al, performEdit, views) { +if (al.getHeight () == edit.seqs.length) { +edit.al = al; +edit.fullAlignmentHeight = true; +}this.addEdit (edit); +if (performEdit) { +jalview.commands.EditCommand.performEdit (edit, views); +}}, "jalview.commands.EditCommand.Edit,jalview.datamodel.AlignmentI,~B,~A"); +Clazz.defineMethod (c$, "performEdit", +function (commandIndex, views) { +var iterator = this.edits.listIterator (commandIndex); +while (iterator.hasNext ()) { +var edit = iterator.next (); +jalview.commands.EditCommand.performEdit (edit, views); +} +}, "~N,~A"); +c$.performEdit = Clazz.defineMethod (c$, "performEdit", +function (edit, views) { +switch (edit.command) { +case jalview.commands.EditCommand.Action.INSERT_GAP: +jalview.commands.EditCommand.insertGap (edit); +break; +case jalview.commands.EditCommand.Action.DELETE_GAP: +jalview.commands.EditCommand.deleteGap (edit); +break; +case jalview.commands.EditCommand.Action.CUT: +jalview.commands.EditCommand.cut (edit, views); +break; +case jalview.commands.EditCommand.Action.PASTE: +jalview.commands.EditCommand.paste (edit, views); +break; +case jalview.commands.EditCommand.Action.REPLACE: +jalview.commands.EditCommand.replace (edit); +break; +case jalview.commands.EditCommand.Action.INSERT_NUC: +break; +default: +break; +} +}, "jalview.commands.EditCommand.Edit,~A"); +Clazz.overrideMethod (c$, "doCommand", +function (views) { +this.performEdit (0, views); +}, "~A"); +Clazz.overrideMethod (c$, "undoCommand", +function (views) { +var iterator = this.edits.listIterator (this.edits.size ()); +while (iterator.hasPrevious ()) { +var e = iterator.previous (); +switch (e.command) { +case jalview.commands.EditCommand.Action.INSERT_GAP: +jalview.commands.EditCommand.deleteGap (e); +break; +case jalview.commands.EditCommand.Action.DELETE_GAP: +jalview.commands.EditCommand.insertGap (e); +break; +case jalview.commands.EditCommand.Action.CUT: +jalview.commands.EditCommand.paste (e, views); +break; +case jalview.commands.EditCommand.Action.PASTE: +jalview.commands.EditCommand.cut (e, views); +break; +case jalview.commands.EditCommand.Action.REPLACE: +jalview.commands.EditCommand.replace (e); +break; +case jalview.commands.EditCommand.Action.INSERT_NUC: +break; +default: +break; +} +} +}, "~A"); +c$.insertGap = Clazz.defineMethod (c$, "insertGap", +($fz = function (command) { +for (var s = 0; s < command.seqs.length; s++) { +command.seqs[s].insertCharAt (command.position, command.number, command.gapChar); +} +jalview.commands.EditCommand.adjustAnnotations (command, true, false, null); +}, $fz.isPrivate = true, $fz), "jalview.commands.EditCommand.Edit"); +c$.deleteGap = Clazz.defineMethod (c$, "deleteGap", +($fz = function (command) { +for (var s = 0; s < command.seqs.length; s++) { +command.seqs[s].deleteChars (command.position, command.position + command.number); +} +jalview.commands.EditCommand.adjustAnnotations (command, false, false, null); +}, $fz.isPrivate = true, $fz), "jalview.commands.EditCommand.Edit"); +c$.cut = Clazz.defineMethod (c$, "cut", +function (command, views) { +var seqDeleted = false; +command.string = Clazz.newCharArray (command.seqs.length, '\0'); +for (var i = 0; i < command.seqs.length; i++) { +var sequence = command.seqs[i]; +if (sequence.getLength () > command.position) { +command.string[i] = sequence.getSequence (command.position, command.position + command.number); +var oldds = sequence.getDatasetSequence (); +if (command.oldds != null && command.oldds[i] != null) { +sequence.setDatasetSequence (null); +}sequence.deleteChars (command.position, command.position + command.number); +if (command.oldds != null && command.oldds[i] != null) { +sequence.setDatasetSequence (command.oldds[i]); +command.oldds[i] = oldds; +} else { +if (oldds !== sequence.getDatasetSequence () || sequence.getSequenceFeatures () != null) { +if (command.oldds == null) { +command.oldds = new Array (command.seqs.length); +}command.oldds[i] = oldds; +jalview.commands.EditCommand.adjustFeatures (command, i, sequence.findPosition (command.position), sequence.findPosition (command.position + command.number), false); +}}}if (sequence.getLength () < 1) { +command.al.deleteSequence (sequence); +seqDeleted = true; +}} +jalview.commands.EditCommand.adjustAnnotations (command, false, seqDeleted, views); +}, "jalview.commands.EditCommand.Edit,~A"); +c$.paste = Clazz.defineMethod (c$, "paste", +function (command, views) { +var tmp; +var newDSNeeded; +var newDSWasNeeded; +var newstart; +var newend; +var seqWasDeleted = false; +var start = 0; +var end = 0; +for (var i = 0; i < command.seqs.length; i++) { +newDSNeeded = false; +newDSWasNeeded = command.oldds != null && command.oldds[i] != null; +if (command.seqs[i].getLength () < 1) { +if (command.alIndex[i] < command.al.getHeight ()) { +var sequences; +{ +if (!(command.alIndex[i] < 0)) { +sequences.add (command.alIndex[i], command.seqs[i]); +}}} else { +command.al.addSequence (command.seqs[i]); +}seqWasDeleted = true; +}newstart = command.seqs[i].getStart (); +newend = command.seqs[i].getEnd (); +tmp = new StringBuffer (); +tmp.append (command.seqs[i].getSequence ()); +if (command.string != null && command.string[i] != null) { +if (command.position >= tmp.length ()) { +var length = command.position - tmp.length (); +while (length > 0) { +tmp.append (command.gapChar); +length--; +} +}tmp.insert (command.position, command.string[i]); +for (var s = 0; s < command.string[i].length; s++) { +if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s].charCodeAt (0)] != 23) { +if (!newDSNeeded) { +newDSNeeded = true; +start = command.seqs[i].findPosition (command.position); +end = command.seqs[i].findPosition (command.position + command.number); +}if (command.seqs[i].getStart () == start) { +newstart--; +} else { +newend++; +}}} +command.string[i] = null; +}command.seqs[i].setSequence (tmp.toString ()); +command.seqs[i].setStart (newstart); +command.seqs[i].setEnd (newend); +if (newDSNeeded) { +if (command.seqs[i].getDatasetSequence () != null) { +var ds; +if (newDSWasNeeded) { +ds = command.oldds[i]; +} else { +ds = new jalview.datamodel.Sequence (command.seqs[i].getName (), jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, command.seqs[i].getSequenceAsString ()), command.seqs[i].getStart (), command.seqs[i].getEnd ()); +ds.setDescription (command.seqs[i].getDescription ()); +}if (command.oldds == null) { +command.oldds = new Array (command.seqs.length); +}command.oldds[i] = command.seqs[i].getDatasetSequence (); +command.seqs[i].setDatasetSequence (ds); +}jalview.commands.EditCommand.adjustFeatures (command, i, start, end, true); +}} +jalview.commands.EditCommand.adjustAnnotations (command, true, seqWasDeleted, views); +command.string = null; +}, "jalview.commands.EditCommand.Edit,~A"); +c$.replace = Clazz.defineMethod (c$, "replace", +function (command) { +var tmp; +var oldstring; +var start = command.position; +var end = command.number; +command.number = start + command.string[0].length; +for (var i = 0; i < command.seqs.length; i++) { +var newDSWasNeeded = command.oldds != null && command.oldds[i] != null; +oldstring = command.seqs[i].getSequenceAsString (); +tmp = new StringBuffer (oldstring.substring (0, start)); +tmp.append (command.string[i]); +var nogaprep = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (command.string[i])); +var ipos = command.seqs[i].findPosition (start) - command.seqs[i].getStart (); +tmp.append (oldstring.substring (end)); +command.seqs[i].setSequence (tmp.toString ()); +command.string[i] = oldstring.substring (start, end).toCharArray (); +var nogapold = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (command.string[i])); +if (!nogaprep.toLowerCase ().equals (nogapold.toLowerCase ())) { +if (newDSWasNeeded) { +var oldds = command.seqs[i].getDatasetSequence (); +command.seqs[i].setDatasetSequence (command.oldds[i]); +command.oldds[i] = oldds; +} else { +if (command.oldds == null) { +command.oldds = new Array (command.seqs.length); +}command.oldds[i] = command.seqs[i].getDatasetSequence (); +var newds = new jalview.datamodel.Sequence (command.seqs[i].getDatasetSequence ()); +var fullseq; +var osp = newds.getSequenceAsString (); +fullseq = osp.substring (0, ipos) + nogaprep + osp.substring (ipos + nogaprep.length); +newds.setSequence (fullseq.toUpperCase ()); +command.seqs[i].setDatasetSequence (newds); +}}tmp = null; +oldstring = null; +} +}, "jalview.commands.EditCommand.Edit"); +c$.adjustAnnotations = Clazz.defineMethod (c$, "adjustAnnotations", +function (command, insert, modifyVisibility, views) { +var annotations = null; +if (modifyVisibility && !insert) { +command.deletedAnnotationRows = new java.util.Hashtable (); +}if (command.fullAlignmentHeight) { +annotations = command.al.getAlignmentAnnotation (); +} else { +var aSize = 0; +var tmp; +for (var s = 0; s < command.seqs.length; s++) { +if (modifyVisibility) { +if (!insert) { +tmp = command.seqs[s].getAnnotation (); +if (tmp != null) { +var alen = tmp.length; +for (var aa = 0; aa < tmp.length; aa++) { +if (!command.al.deleteAnnotation (tmp[aa])) { +tmp[aa] = null; +alen--; +}} +command.seqs[s].setAlignmentAnnotation (null); +if (alen != tmp.length) { +var saved = new Array (alen); +for (var aa = 0, aapos = 0; aa < tmp.length; aa++) { +if (tmp[aa] != null) { +saved[aapos++] = tmp[aa]; +tmp[aa] = null; +}} +tmp = saved; +command.deletedAnnotationRows.put (command.seqs[s], saved); +for (var alview = 0; views != null && alview < views.length; alview++) { +if (views[alview] !== command.al) { +var toremove = views[alview].getAlignmentAnnotation (); +if (toremove == null || toremove.length == 0) { +continue; +}for (var aa = 0; aa < toremove.length; aa++) { +if (toremove[aa].sequenceRef === command.seqs[s]) { +views[alview].deleteAnnotation (toremove[aa]); +}} +}} +} else { +command.deletedAnnotationRows.put (command.seqs[s], tmp); +}}} else { +if (command.deletedAnnotationRows != null && command.deletedAnnotationRows.containsKey (command.seqs[s])) { +var revealed = command.deletedAnnotationRows.get (command.seqs[s]); +command.seqs[s].setAlignmentAnnotation (revealed); +if (revealed != null) { +for (var aa = 0; aa < revealed.length; aa++) { +command.al.addAnnotation (revealed[aa]); +} +for (var aa = 0; aa < revealed.length; aa++) { +command.al.setAnnotationIndex (revealed[aa], aa); +} +for (var vnum = 0; views != null && vnum < views.length; vnum++) { +if (views[vnum] !== command.al) { +var avwidth = views[vnum].getWidth () + 1; +for (var a = 0; a < revealed.length; a++) { +var newann = new jalview.datamodel.AlignmentAnnotation (revealed[a]); +command.seqs[s].addAlignmentAnnotation (newann); +newann.padAnnotation (avwidth); +views[vnum].addAnnotation (newann); +views[vnum].setAnnotationIndex (newann, a); +} +}} +}}}continue; +}if (command.seqs[s].getAnnotation () == null) { +continue; +}if (aSize == 0) { +annotations = command.seqs[s].getAnnotation (); +} else { +tmp = new Array (aSize + command.seqs[s].getAnnotation ().length); +System.arraycopy (annotations, 0, tmp, 0, aSize); +System.arraycopy (command.seqs[s].getAnnotation (), 0, tmp, aSize, command.seqs[s].getAnnotation ().length); +annotations = tmp; +}aSize = annotations.length; +} +}if (annotations == null) { +return; +}if (!insert) { +command.deletedAnnotations = new java.util.Hashtable (); +}var aSize; +var temp; +for (var a = 0; a < annotations.length; a++) { +if (annotations[a].autoCalculated || annotations[a].annotations == null) { +continue; +}var tSize = 0; +aSize = annotations[a].annotations.length; +if (insert) { +temp = new Array (aSize + command.number); +if (annotations[a].padGaps) { +for (var aa = 0; aa < temp.length; aa++) { +temp[aa] = new jalview.datamodel.Annotation (command.gapChar + "", null, ' ', 0); +} +}} else { +if (command.position < aSize) { +if (command.position + command.number >= aSize) { +tSize = aSize; +} else { +tSize = aSize - command.number; +}} else { +tSize = aSize; +}if (tSize < 0) { +tSize = aSize; +}temp = new Array (tSize); +}if (insert) { +if (command.position < annotations[a].annotations.length) { +System.arraycopy (annotations[a].annotations, 0, temp, 0, command.position); +if (command.deletedAnnotations != null && command.deletedAnnotations.containsKey (annotations[a].annotationId)) { +var restore = command.deletedAnnotations.get (annotations[a].annotationId); +System.arraycopy (restore, 0, temp, command.position, command.number); +}System.arraycopy (annotations[a].annotations, command.position, temp, command.position + command.number, aSize - command.position); +} else { +if (command.deletedAnnotations != null && command.deletedAnnotations.containsKey (annotations[a].annotationId)) { +var restore = command.deletedAnnotations.get (annotations[a].annotationId); +temp = new Array (annotations[a].annotations.length + restore.length); +System.arraycopy (annotations[a].annotations, 0, temp, 0, annotations[a].annotations.length); +System.arraycopy (restore, 0, temp, annotations[a].annotations.length, restore.length); +} else { +temp = annotations[a].annotations; +}}} else { +if (tSize != aSize || command.position < 2) { +var copylen = Math.min (command.position, annotations[a].annotations.length); +if (copylen > 0) { +System.arraycopy (annotations[a].annotations, 0, temp, 0, copylen); +}var deleted = new Array (command.number); +if (copylen >= command.position) { +copylen = Math.min (command.number, annotations[a].annotations.length - command.position); +if (copylen > 0) { +System.arraycopy (annotations[a].annotations, command.position, deleted, 0, copylen); +}}command.deletedAnnotations.put (annotations[a].annotationId, deleted); +if (annotations[a].annotations.length > command.position + command.number) { +System.arraycopy (annotations[a].annotations, command.position + command.number, temp, command.position, annotations[a].annotations.length - command.position - command.number); +}} else { +var dSize = aSize - command.position; +if (dSize > 0) { +var deleted = new Array (command.number); +System.arraycopy (annotations[a].annotations, command.position, deleted, 0, dSize); +command.deletedAnnotations.put (annotations[a].annotationId, deleted); +tSize = Math.min (annotations[a].annotations.length, command.position); +temp = new Array (tSize); +System.arraycopy (annotations[a].annotations, 0, temp, 0, tSize); +} else { +temp = annotations[a].annotations; +}}}annotations[a].annotations = temp; +} +}, "jalview.commands.EditCommand.Edit,~B,~B,~A"); +c$.adjustFeatures = Clazz.defineMethod (c$, "adjustFeatures", +function (command, index, i, j, insert) { +var seq = command.seqs[index]; +var sequence = seq.getDatasetSequence (); +if (sequence == null) { +sequence = seq; +}if (insert) { +if (command.editedFeatures != null && command.editedFeatures.containsKey (seq)) { +sequence.setSequenceFeatures (command.editedFeatures.get (seq)); +}return; +}var sf = sequence.getSequenceFeatures (); +if (sf == null) { +return; +}var oldsf = new Array (sf.length); +var cSize = j - i; +for (var s = 0; s < sf.length; s++) { +var copy = new jalview.datamodel.SequenceFeature (sf[s]); +oldsf[s] = copy; +if (sf[s].getEnd () < i) { +continue; +}if (sf[s].getBegin () > j) { +sf[s].setBegin (copy.getBegin () - cSize); +sf[s].setEnd (copy.getEnd () - cSize); +continue; +}if (sf[s].getBegin () >= i) { +sf[s].setBegin (i); +}if (sf[s].getEnd () < j) { +sf[s].setEnd (j - 1); +}sf[s].setEnd (sf[s].getEnd () - (cSize)); +if (sf[s].getBegin () > sf[s].getEnd ()) { +sequence.deleteFeature (sf[s]); +}} +if (command.editedFeatures == null) { +command.editedFeatures = new java.util.Hashtable (); +}command.editedFeatures.put (seq, oldsf); +}, "jalview.commands.EditCommand.Edit,~N,~N,~N,~B"); +Clazz.defineMethod (c$, "getEdits", +function () { +return this.edits; +}); +Clazz.defineMethod (c$, "priorState", +function (forUndo) { +var result = new java.util.HashMap (); +if (this.getEdits () == null) { +return result; +}if (forUndo) { +for (var e, $e = this.getEdits ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) { +for (var seq, $seq = 0, $$seq = e.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { +var ds = seq.getDatasetSequence (); +var preEdit = result.get (ds); +if (preEdit == null) { +preEdit = new jalview.datamodel.Sequence ("", seq.getSequenceAsString ()); +preEdit.setDatasetSequence (ds); +result.put (ds, preEdit); +}} +} +return result; +}var edits = new jalview.util.ReverseListIterator (this.getEdits ()); +while (edits.hasNext ()) { +var oldEdit = edits.next (); +var action = oldEdit.getAction (); +var position = oldEdit.getPosition (); +var number = oldEdit.getNumber (); +var gap = oldEdit.getGapCharacter (); +for (var seq, $seq = 0, $$seq = oldEdit.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { +var ds = seq.getDatasetSequence (); +var preEdit = result.get (ds); +if (preEdit == null) { +preEdit = new jalview.datamodel.Sequence ("", seq.getSequenceAsString ()); +preEdit.setDatasetSequence (ds); +result.put (ds, preEdit); +}if (ds != null) { +if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { +preEdit.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (preEdit.getSequence (), position, number, gap))); +} else if (action === jalview.commands.EditCommand.Action.INSERT_GAP) { +preEdit.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (preEdit.getSequence (), position, position + number))); +} else { +System.err.println ("Can't undo edit action " + action); +}}} +} +return result; +}, "~B"); +Clazz.defineMethod (c$, "getEditIterator", +function (forwards) { +if (forwards) { +return this.getEdits ().iterator (); +} else { +return new jalview.util.ReverseListIterator (this.getEdits ()); +}}, "~B"); +c$.$EditCommand$Edit$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.oldds = null; +this.fullAlignmentHeight = false; +this.deletedAnnotationRows = null; +this.deletedAnnotations = null; +this.editedFeatures = null; +this.al = null; +this.command = null; +this.string = null; +this.seqs = null; +this.alIndex = null; +this.position = 0; +this.number = 0; +this.gapChar = '\0'; +Clazz.instantialize (this, arguments); +}, jalview.commands.EditCommand, "Edit"); +Clazz.makeConstructor (c$, +function (a, b, c, d, e) { +this.command = a; +this.seqs = b; +this.position = c; +this.number = d; +this.gapChar = e; +}, "jalview.commands.EditCommand.Action,~A,~N,~N,~S"); +Clazz.makeConstructor (c$, +function (a, b, c, d, e) { +this.gapChar = e.getGapCharacter (); +this.command = a; +this.seqs = b; +this.position = c; +this.number = d; +this.al = e; +this.alIndex = Clazz.newIntArray (b.length, 0); +for (var f = 0; f < b.length; f++) { +this.alIndex[f] = e.findIndex (b[f]); +} +this.fullAlignmentHeight = (e.getHeight () == b.length); +}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI"); +Clazz.makeConstructor (c$, +function (a, b, c, d, e, f) { +this.command = a; +this.seqs = b; +this.position = c; +this.number = d; +this.al = e; +this.gapChar = e.getGapCharacter (); +this.string = Clazz.newCharArray (b.length, '\0'); +for (var g = 0; g < b.length; g++) { +this.string[g] = f.toCharArray (); +} +this.fullAlignmentHeight = (e.getHeight () == b.length); +}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~S"); +Clazz.defineMethod (c$, "getSequences", +function () { +return this.seqs; +}); +Clazz.defineMethod (c$, "getPosition", +function () { +return this.position; +}); +Clazz.defineMethod (c$, "getAction", +function () { +return this.command; +}); +Clazz.defineMethod (c$, "getNumber", +function () { +return this.number; +}); +Clazz.defineMethod (c$, "getGapCharacter", +function () { +return this.gapChar; +}); +c$ = Clazz.p0p (); +}; +Clazz.pu$h (); +c$ = Clazz.declareType (jalview.commands.EditCommand, "Action", Enum); +Clazz.defineMethod (c$, "getUndoAction", +function () { +switch (this) { +case jalview.commands.EditCommand.Action.INSERT_GAP: +return jalview.commands.EditCommand.Action.DELETE_GAP; +case jalview.commands.EditCommand.Action.CUT: +return jalview.commands.EditCommand.Action.PASTE; +case jalview.commands.EditCommand.Action.DELETE_GAP: +return jalview.commands.EditCommand.Action.INSERT_GAP; +case jalview.commands.EditCommand.Action.INSERT_NUC: +return null; +case jalview.commands.EditCommand.Action.PASTE: +return jalview.commands.EditCommand.Action.CUT; +case jalview.commands.EditCommand.Action.REPLACE: +return jalview.commands.EditCommand.Action.REPLACE; +} +return null; +}); +Clazz.defineEnumConstant (c$, "INSERT_GAP", 0, []); +Clazz.defineEnumConstant (c$, "DELETE_GAP", 1, []); +Clazz.defineEnumConstant (c$, "CUT", 2, []); +Clazz.defineEnumConstant (c$, "PASTE", 3, []); +Clazz.defineEnumConstant (c$, "REPLACE", 4, []); +Clazz.defineEnumConstant (c$, "INSERT_NUC", 5, []); +c$ = Clazz.p0p (); +}); diff --git a/bin/jalview/commands/OrderCommand.js b/bin/jalview/commands/OrderCommand.js index c85c70b..8939653 100644 --- a/bin/jalview/commands/OrderCommand.js +++ b/bin/jalview/commands/OrderCommand.js @@ -1,38 +1,38 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.CommandI"], "jalview.commands.OrderCommand", ["jalview.analysis.AlignmentSorter"], function () { -c$ = Clazz.decorateAsClass (function () { -this.description = null; -this.seqs = null; -this.seqs2 = null; -this.al = null; -Clazz.instantialize (this, arguments); -}, jalview.commands, "OrderCommand", null, jalview.commands.CommandI); -Clazz.makeConstructor (c$, -function (description, seqs, al) { -this.description = description; -this.seqs = seqs; -this.seqs2 = al.getSequencesArray (); -this.al = al; -this.doCommand (null); -}, "~S,~A,jalview.datamodel.AlignmentI"); -Clazz.overrideMethod (c$, "getDescription", -function () { -return this.description; -}); -Clazz.overrideMethod (c$, "getSize", -function () { -return 1; -}); -Clazz.overrideMethod (c$, "doCommand", -function (views) { -jalview.analysis.AlignmentSorter.setOrder (this.al, this.seqs2); -}, "~A"); -Clazz.overrideMethod (c$, "undoCommand", -function (views) { -jalview.analysis.AlignmentSorter.setOrder (this.al, this.seqs); -}, "~A"); -Clazz.defineMethod (c$, "getSequenceOrder", -function (undo) { -return undo ? this.seqs : this.seqs2; -}, "~B"); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.CommandI"], "jalview.commands.OrderCommand", ["jalview.analysis.AlignmentSorter"], function () { +c$ = Clazz.decorateAsClass (function () { +this.description = null; +this.seqs = null; +this.seqs2 = null; +this.al = null; +Clazz.instantialize (this, arguments); +}, jalview.commands, "OrderCommand", null, jalview.commands.CommandI); +Clazz.makeConstructor (c$, +function (description, seqs, al) { +this.description = description; +this.seqs = seqs; +this.seqs2 = al.getSequencesArray (); +this.al = al; +this.doCommand (null); +}, "~S,~A,jalview.datamodel.AlignmentI"); +Clazz.overrideMethod (c$, "getDescription", +function () { +return this.description; +}); +Clazz.overrideMethod (c$, "getSize", +function () { +return 1; +}); +Clazz.overrideMethod (c$, "doCommand", +function (views) { +jalview.analysis.AlignmentSorter.setOrder (this.al, this.seqs2); +}, "~A"); +Clazz.overrideMethod (c$, "undoCommand", +function (views) { +jalview.analysis.AlignmentSorter.setOrder (this.al, this.seqs); +}, "~A"); +Clazz.defineMethod (c$, "getSequenceOrder", +function (undo) { +return undo ? this.seqs : this.seqs2; +}, "~B"); +}); diff --git a/bin/jalview/commands/RemoveGapColCommand.js b/bin/jalview/commands/RemoveGapColCommand.js index a41e76e..511279b 100644 --- a/bin/jalview/commands/RemoveGapColCommand.js +++ b/bin/jalview/commands/RemoveGapColCommand.js @@ -1,45 +1,45 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapColCommand", ["jalview.util.Comparison"], function () { -c$ = Clazz.decorateAsClass (function () { -this.columnsDeleted = 0; -Clazz.instantialize (this, arguments); -}, jalview.commands, "RemoveGapColCommand", jalview.commands.EditCommand); -Clazz.makeConstructor (c$, -function (description, seqs, start, end, al) { -Clazz.superConstructor (this, jalview.commands.RemoveGapColCommand, []); -this.description = description; -var j; -var jSize = seqs.length; -var startCol = -1; -var endCol = -1; -this.columnsDeleted = 0; -this.clearEdits (); -var $delete = true; -for (var i = start; i <= end; i++) { -$delete = true; -for (j = 0; j < jSize; j++) { -if (seqs[j].getLength () > i) { -if (!jalview.util.Comparison.isGap (seqs[j].getCharAt (i))) { -if ($delete) { -endCol = i; -}$delete = false; -break; -}}} -if ($delete && startCol == -1) { -startCol = i; -}if (!$delete && startCol > -1) { -this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seqs, startCol - this.columnsDeleted, endCol - startCol, al, false, null); -this.columnsDeleted += (endCol - startCol); -startCol = -1; -endCol = -1; -}} -if ($delete && startCol > -1) { -this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seqs, startCol - this.columnsDeleted, end - startCol + 1, al, false, null); -this.columnsDeleted += (end - startCol + 1); -}this.performEdit (0, null); -}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI"); -Clazz.overrideMethod (c$, "getSize", -function () { -return this.columnsDeleted; -}); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapColCommand", ["jalview.util.Comparison"], function () { +c$ = Clazz.decorateAsClass (function () { +this.columnsDeleted = 0; +Clazz.instantialize (this, arguments); +}, jalview.commands, "RemoveGapColCommand", jalview.commands.EditCommand); +Clazz.makeConstructor (c$, +function (description, seqs, start, end, al) { +Clazz.superConstructor (this, jalview.commands.RemoveGapColCommand, []); +this.description = description; +var j; +var jSize = seqs.length; +var startCol = -1; +var endCol = -1; +this.columnsDeleted = 0; +this.clearEdits (); +var $delete = true; +for (var i = start; i <= end; i++) { +$delete = true; +for (j = 0; j < jSize; j++) { +if (seqs[j].getLength () > i) { +if (!jalview.util.Comparison.isGap (seqs[j].getCharAt (i))) { +if ($delete) { +endCol = i; +}$delete = false; +break; +}}} +if ($delete && startCol == -1) { +startCol = i; +}if (!$delete && startCol > -1) { +this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seqs, startCol - this.columnsDeleted, endCol - startCol, al, false, null); +this.columnsDeleted += (endCol - startCol); +startCol = -1; +endCol = -1; +}} +if ($delete && startCol > -1) { +this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seqs, startCol - this.columnsDeleted, end - startCol + 1, al, false, null); +this.columnsDeleted += (end - startCol + 1); +}this.performEdit (0, null); +}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI"); +Clazz.overrideMethod (c$, "getSize", +function () { +return this.columnsDeleted; +}); +}); diff --git a/bin/jalview/commands/RemoveGapsCommand.js b/bin/jalview/commands/RemoveGapsCommand.js index 7097db3..3cc233d 100644 --- a/bin/jalview/commands/RemoveGapsCommand.js +++ b/bin/jalview/commands/RemoveGapsCommand.js @@ -1,56 +1,56 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapsCommand", ["jalview.util.Comparison"], function () { -c$ = Clazz.declareType (jalview.commands, "RemoveGapsCommand", jalview.commands.EditCommand); -Clazz.makeConstructor (c$, -function (description, seqs, al) { -Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []); -this.description = description; -var width = 0; -for (var i = 0; i < seqs.length; i++) { -if (seqs[i].getLength () > width) { -width = seqs[i].getLength (); -}} -this.findGaps (seqs, 0, width, al); -}, "~S,~A,jalview.datamodel.AlignmentI"); -Clazz.makeConstructor (c$, -function (description, seqs, start, end, al) { -Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []); -this.description = description; -this.findGaps (seqs, start, end, al); -}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "findGaps", -function (seqs, start, end, al) { -var startCol = -1; -var endCol = -1; -var deletedCols = 0; -var j; -var jSize; -this.clearEdits (); -var $delete = true; -var sequence; -for (var s = 0; s < seqs.length; s++) { -deletedCols = 0; -startCol = -1; -endCol = -1; -sequence = seqs[s].getSequence (start, end + 1); -jSize = sequence.length; -for (j = 0; j < jSize; j++) { -$delete = true; -if (!jalview.util.Comparison.isGap (sequence[j])) { -if ($delete) { -endCol = j; -}$delete = false; -}if ($delete && startCol == -1) { -startCol = j; -}if (!$delete && startCol > -1) { -this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, endCol - startCol, al, false, null); -deletedCols += (endCol - startCol); -startCol = -1; -endCol = -1; -}} -if ($delete && startCol > -1) { -this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, jSize - startCol, al, false, null); -}} -this.performEdit (0, null); -}, "~A,~N,~N,jalview.datamodel.AlignmentI"); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapsCommand", ["jalview.util.Comparison"], function () { +c$ = Clazz.declareType (jalview.commands, "RemoveGapsCommand", jalview.commands.EditCommand); +Clazz.makeConstructor (c$, +function (description, seqs, al) { +Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []); +this.description = description; +var width = 0; +for (var i = 0; i < seqs.length; i++) { +if (seqs[i].getLength () > width) { +width = seqs[i].getLength (); +}} +this.findGaps (seqs, 0, width, al); +}, "~S,~A,jalview.datamodel.AlignmentI"); +Clazz.makeConstructor (c$, +function (description, seqs, start, end, al) { +Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []); +this.description = description; +this.findGaps (seqs, start, end, al); +}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "findGaps", +function (seqs, start, end, al) { +var startCol = -1; +var endCol = -1; +var deletedCols = 0; +var j; +var jSize; +this.clearEdits (); +var $delete = true; +var sequence; +for (var s = 0; s < seqs.length; s++) { +deletedCols = 0; +startCol = -1; +endCol = -1; +sequence = seqs[s].getSequence (start, end + 1); +jSize = sequence.length; +for (j = 0; j < jSize; j++) { +$delete = true; +if (!jalview.util.Comparison.isGap (sequence[j])) { +if ($delete) { +endCol = j; +}$delete = false; +}if ($delete && startCol == -1) { +startCol = j; +}if (!$delete && startCol > -1) { +this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, endCol - startCol, al, false, null); +deletedCols += (endCol - startCol); +startCol = -1; +endCol = -1; +}} +if ($delete && startCol > -1) { +this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, jSize - startCol, al, false, null); +}} +this.performEdit (0, null); +}, "~A,~N,~N,jalview.datamodel.AlignmentI"); +}); diff --git a/bin/jalview/commands/SlideSequencesCommand.js b/bin/jalview/commands/SlideSequencesCommand.js index 125c732..5a79b67 100644 --- a/bin/jalview/commands/SlideSequencesCommand.js +++ b/bin/jalview/commands/SlideSequencesCommand.js @@ -1,48 +1,48 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.SlideSequencesCommand", ["jalview.util.Comparison"], function () { -c$ = Clazz.decorateAsClass (function () { -this.gapsInsertedBegin = false; -Clazz.instantialize (this, arguments); -}, jalview.commands, "SlideSequencesCommand", jalview.commands.EditCommand); -Clazz.makeConstructor (c$, -function (description, seqsLeft, seqsRight, slideSize, gapChar) { -Clazz.superConstructor (this, jalview.commands.SlideSequencesCommand, []); -this.description = description; -var lSize = seqsLeft.length; -this.gapsInsertedBegin = false; -var i; -var j; -for (i = 0; i < lSize; i++) { -for (j = 0; j < slideSize; j++) { -if (!jalview.util.Comparison.isGap (seqsLeft[i].getCharAt (j))) { -this.gapsInsertedBegin = true; -break; -}} -} -var e = null; -if (!this.gapsInsertedBegin) { -e = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.DELETE_GAP, seqsLeft, 0, slideSize, gapChar); -this.setEdit (e); -} else { -e = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.INSERT_GAP, seqsRight, 0, slideSize, gapChar); -this.setEdit (e); -}jalview.commands.EditCommand.performEdit (e, null); -}, "~S,~A,~A,~N,~S"); -Clazz.defineMethod (c$, "getGapsInsertedBegin", -function () { -return this.gapsInsertedBegin; -}); -Clazz.defineMethod (c$, "appendSlideCommand", -function (command) { -var same = false; -if (command.getEdit (0).seqs.length == this.getEdit (0).seqs.length) { -same = true; -for (var i = 0; i < command.getEdit (0).seqs.length; i++) { -if (this.getEdit (0).seqs[i] !== command.getEdit (0).seqs[i]) { -same = false; -}} -}if (same) { -command.addEdit (this.getEdit (0)); -}return same; -}, "jalview.commands.SlideSequencesCommand"); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.SlideSequencesCommand", ["jalview.util.Comparison"], function () { +c$ = Clazz.decorateAsClass (function () { +this.gapsInsertedBegin = false; +Clazz.instantialize (this, arguments); +}, jalview.commands, "SlideSequencesCommand", jalview.commands.EditCommand); +Clazz.makeConstructor (c$, +function (description, seqsLeft, seqsRight, slideSize, gapChar) { +Clazz.superConstructor (this, jalview.commands.SlideSequencesCommand, []); +this.description = description; +var lSize = seqsLeft.length; +this.gapsInsertedBegin = false; +var i; +var j; +for (i = 0; i < lSize; i++) { +for (j = 0; j < slideSize; j++) { +if (!jalview.util.Comparison.isGap (seqsLeft[i].getCharAt (j))) { +this.gapsInsertedBegin = true; +break; +}} +} +var e = null; +if (!this.gapsInsertedBegin) { +e = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.DELETE_GAP, seqsLeft, 0, slideSize, gapChar); +this.setEdit (e); +} else { +e = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.INSERT_GAP, seqsRight, 0, slideSize, gapChar); +this.setEdit (e); +}jalview.commands.EditCommand.performEdit (e, null); +}, "~S,~A,~A,~N,~S"); +Clazz.defineMethod (c$, "getGapsInsertedBegin", +function () { +return this.gapsInsertedBegin; +}); +Clazz.defineMethod (c$, "appendSlideCommand", +function (command) { +var same = false; +if (command.getEdit (0).seqs.length == this.getEdit (0).seqs.length) { +same = true; +for (var i = 0; i < command.getEdit (0).seqs.length; i++) { +if (this.getEdit (0).seqs[i] !== command.getEdit (0).seqs[i]) { +same = false; +}} +}if (same) { +command.addEdit (this.getEdit (0)); +}return same; +}, "jalview.commands.SlideSequencesCommand"); +}); diff --git a/bin/jalview/commands/TrimRegionCommand.class b/bin/jalview/commands/TrimRegionCommand.class index aace60c..5e4d0bb 100644 Binary files a/bin/jalview/commands/TrimRegionCommand.class and b/bin/jalview/commands/TrimRegionCommand.class differ diff --git a/bin/jalview/commands/TrimRegionCommand.js b/bin/jalview/commands/TrimRegionCommand.js index ff06747..2732ca0 100644 --- a/bin/jalview/commands/TrimRegionCommand.js +++ b/bin/jalview/commands/TrimRegionCommand.js @@ -1,91 +1,91 @@ -Clazz.declarePackage ("jalview.commands"); -Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.TrimRegionCommand", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.colSel = null; -this.start = null; -this.shiftList = null; -this.selectionGroup = null; -this.deletedHiddenColumns = null; -this.columnsDeleted = 0; -Clazz.instantialize (this, arguments); -}, jalview.commands, "TrimRegionCommand", jalview.commands.EditCommand); -Clazz.makeConstructor (c$, -function (description, command, seqs, column, al, colSel, selectedRegion) { -Clazz.superConstructor (this, jalview.commands.TrimRegionCommand, []); -this.description = description; -this.selectionGroup = selectedRegion; -this.colSel = colSel; -if (command.equalsIgnoreCase (jalview.commands.TrimRegionCommand.TRIM_LEFT)) { -if (column == 0) { -return; -}this.columnsDeleted = column; -this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.CUT, seqs, 0, column, al)); -} else if (command.equalsIgnoreCase (jalview.commands.TrimRegionCommand.TRIM_RIGHT)) { -var width = al.getWidth () - column - 1; -if (width < 2) { -return; -}this.columnsDeleted = width - 1; -this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.CUT, seqs, column + 1, width, al)); -}var i; -var isize = this.getEdit (0).seqs.length; -this.start = Clazz.newIntArray (isize, 0); -for (i = 0; i < isize; i++) { -this.start[i] = this.getEdit (0).seqs[i].getStart (); -} -this.performEdit (0, null); -}, "~S,~S,~A,~N,jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "cut", -function (command) { -var column; -var j; -var jSize = command.seqs.length; -for (j = 0; j < jSize; j++) { -if (command.position == 0) { -column = command.seqs[j].findPosition (command.number); -command.seqs[j].setStart (column); -} else { -column = command.seqs[j].findPosition (command.position) - 1; -command.seqs[j].setEnd (column); -}} -Clazz.superCall (this, jalview.commands.TrimRegionCommand, "cut", [command, null]); -if (command.position == 0) { -this.deletedHiddenColumns = this.colSel.compensateForEdit (0, command.number); -if (this.selectionGroup != null) { -this.selectionGroup.adjustForRemoveLeft (command.number); -}} else { -this.deletedHiddenColumns = this.colSel.compensateForEdit (command.position, command.number); -if (this.selectionGroup != null) { -this.selectionGroup.adjustForRemoveRight (command.position); -}}}, "jalview.commands.EditCommand.Edit"); -Clazz.defineMethod (c$, "paste", -function (command) { -Clazz.superCall (this, jalview.commands.TrimRegionCommand, "paste", [command, null]); -var column; -var j; -var jSize = command.seqs.length; -for (j = 0; j < jSize; j++) { -if (command.position == 0) { -command.seqs[j].setStart (this.start[j]); -} else { -column = command.seqs[j].findPosition (command.number + command.position) - 1; -command.seqs[j].setEnd (column); -}} -if (command.position == 0) { -this.colSel.compensateForEdit (0, -command.number); -if (this.selectionGroup != null) { -this.selectionGroup.adjustForRemoveLeft (-command.number); -}}if (this.deletedHiddenColumns != null) { -var region; -for (var i = 0; i < this.deletedHiddenColumns.size (); i++) { -region = this.deletedHiddenColumns.get (i); -this.colSel.hideColumns (region[0], region[1]); -} -}}, "jalview.commands.EditCommand.Edit"); -Clazz.overrideMethod (c$, "getSize", -function () { -return this.columnsDeleted; -}); -Clazz.defineStatics (c$, -"TRIM_LEFT", "TrimLeft", -"TRIM_RIGHT", "TrimRight"); -}); +Clazz.declarePackage ("jalview.commands"); +Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.TrimRegionCommand", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.colSel = null; +this.start = null; +this.shiftList = null; +this.selectionGroup = null; +this.deletedHiddenColumns = null; +this.columnsDeleted = 0; +Clazz.instantialize (this, arguments); +}, jalview.commands, "TrimRegionCommand", jalview.commands.EditCommand); +Clazz.makeConstructor (c$, +function (description, command, seqs, column, al, colSel, selectedRegion) { +Clazz.superConstructor (this, jalview.commands.TrimRegionCommand, []); +this.description = description; +this.selectionGroup = selectedRegion; +this.colSel = colSel; +if (command.equalsIgnoreCase (jalview.commands.TrimRegionCommand.TRIM_LEFT)) { +if (column == 0) { +return; +}this.columnsDeleted = column; +this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.CUT, seqs, 0, column, al)); +} else if (command.equalsIgnoreCase (jalview.commands.TrimRegionCommand.TRIM_RIGHT)) { +var width = al.getWidth () - column - 1; +if (width < 2) { +return; +}this.columnsDeleted = width - 1; +this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, jalview.commands.EditCommand.Action.CUT, seqs, column + 1, width, al)); +}var i; +var isize = this.getEdit (0).seqs.length; +this.start = Clazz.newIntArray (isize, 0); +for (i = 0; i < isize; i++) { +this.start[i] = this.getEdit (0).seqs[i].getStart (); +} +this.performEdit (0, null); +}, "~S,~S,~A,~N,jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "cut", +function (command) { +var column; +var j; +var jSize = command.seqs.length; +for (j = 0; j < jSize; j++) { +if (command.position == 0) { +column = command.seqs[j].findPosition (command.number); +command.seqs[j].setStart (column); +} else { +column = command.seqs[j].findPosition (command.position) - 1; +command.seqs[j].setEnd (column); +}} +Clazz.superCall (this, jalview.commands.TrimRegionCommand, "cut", [command, null]); +if (command.position == 0) { +this.deletedHiddenColumns = this.colSel.compensateForEdit (0, command.number); +if (this.selectionGroup != null) { +this.selectionGroup.adjustForRemoveLeft (command.number); +}} else { +this.deletedHiddenColumns = this.colSel.compensateForEdit (command.position, command.number); +if (this.selectionGroup != null) { +this.selectionGroup.adjustForRemoveRight (command.position); +}}}, "jalview.commands.EditCommand.Edit"); +Clazz.defineMethod (c$, "paste", +function (command) { +Clazz.superCall (this, jalview.commands.TrimRegionCommand, "paste", [command, null]); +var column; +var j; +var jSize = command.seqs.length; +for (j = 0; j < jSize; j++) { +if (command.position == 0) { +command.seqs[j].setStart (this.start[j]); +} else { +column = command.seqs[j].findPosition (command.number + command.position) - 1; +command.seqs[j].setEnd (column); +}} +if (command.position == 0) { +this.colSel.compensateForEdit (0, -command.number); +if (this.selectionGroup != null) { +this.selectionGroup.adjustForRemoveLeft (-command.number); +}}if (this.deletedHiddenColumns != null) { +var region; +for (var i = 0; i < this.deletedHiddenColumns.size (); i++) { +region = this.deletedHiddenColumns.get (i); +this.colSel.hideColumns (region[0], region[1]); +} +}}, "jalview.commands.EditCommand.Edit"); +Clazz.overrideMethod (c$, "getSize", +function () { +return this.columnsDeleted; +}); +Clazz.defineStatics (c$, +"TRIM_LEFT", "TrimLeft", +"TRIM_RIGHT", "TrimRight"); +}); diff --git a/bin/jalview/controller/AlignViewController.class b/bin/jalview/controller/AlignViewController.class index c9c4b78..7507fec 100644 Binary files a/bin/jalview/controller/AlignViewController.class and b/bin/jalview/controller/AlignViewController.class differ diff --git a/bin/jalview/controller/AlignViewController.js b/bin/jalview/controller/AlignViewController.js index 966223d..c773729 100644 --- a/bin/jalview/controller/AlignViewController.js +++ b/bin/jalview/controller/AlignViewController.js @@ -1,219 +1,219 @@ -Clazz.declarePackage ("jalview.controller"); -Clazz.load (["jalview.api.AlignViewControllerI"], "jalview.controller.AlignViewController", ["jalview.analysis.AlignmentSorter", "$.Grouping", "jalview.commands.OrderCommand", "jalview.datamodel.ColumnSelection", "jalview.io.FeaturesFile", "jalview.util.MessageManager", "java.awt.Color", "java.util.ArrayList", "$.BitSet"], function () { -c$ = Clazz.decorateAsClass (function () { -this.viewport = null; -this.alignPanel = null; -this.avcg = null; -Clazz.instantialize (this, arguments); -}, jalview.controller, "AlignViewController", null, jalview.api.AlignViewControllerI); -Clazz.overrideMethod (c$, "finalize", -function () { -this.viewport = null; -this.alignPanel = null; -this.avcg = null; -}); -Clazz.makeConstructor (c$, -function (alignFrame, viewport, alignPanel) { -this.avcg = alignFrame; -this.viewport = viewport; -this.alignPanel = alignPanel; -}, "jalview.api.AlignViewControllerGuiI,jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); -Clazz.overrideMethod (c$, "setViewportAndAlignmentPanel", -function (viewport, alignPanel) { -this.alignPanel = alignPanel; -this.viewport = viewport; -}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); -Clazz.overrideMethod (c$, "makeGroupsFromSelection", -function () { -var sg = this.viewport.getSelectionGroup (); -var cs = this.viewport.getColumnSelection (); -var gps = null; -if (sg != null && (cs == null || cs.getSelected () == null || cs.size () == 0)) { -gps = jalview.analysis.Grouping.makeGroupsFrom (this.viewport.getSequenceSelection (), this.viewport.getAlignmentView (true).getSequenceStrings (this.viewport.getGapCharacter ()), this.viewport.getAlignment ().getGroups ()); -} else { -if (cs != null) { -gps = jalview.analysis.Grouping.makeGroupsFromCols ((sg == null) ? this.viewport.getAlignment ().getSequencesArray () : sg.getSequences ().toArray ( new Array (0)), cs, this.viewport.getAlignment ().getGroups ()); -}}if (gps != null) { -this.viewport.getAlignment ().deleteAllGroups (); -this.viewport.clearSequenceColours (); -this.viewport.setSelectionGroup (null); -for (var g = 0; g < gps.length; g++) { -gps[g].setshowSequenceLogo (this.viewport.isShowSequenceLogo ()); -this.viewport.getAlignment ().addGroup (gps[g]); -var col = new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255)); -col = col.brighter (); -for (var sq, $sq = gps[g].getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -this.viewport.setSequenceColour (sq, col); -} -} -return true; -}return false; -}); -Clazz.overrideMethod (c$, "createGroup", -function () { -var sg = this.viewport.getSelectionGroup (); -if (sg != null) { -this.viewport.getAlignment ().addGroup (sg); -return true; -}return false; -}); -Clazz.overrideMethod (c$, "unGroup", -function () { -var sg = this.viewport.getSelectionGroup (); -if (sg != null) { -this.viewport.getAlignment ().deleteGroup (sg); -return true; -}return false; -}); -Clazz.overrideMethod (c$, "deleteGroups", -function () { -if (this.viewport.getAlignment ().getGroups () != null && this.viewport.getAlignment ().getGroups ().size () > 0) { -this.viewport.getAlignment ().deleteAllGroups (); -this.viewport.clearSequenceColours (); -this.viewport.setSelectionGroup (null); -return true; -}return false; -}); -Clazz.overrideMethod (c$, "markColumnsContainingFeatures", -function (invert, extendCurrent, toggle, featureType) { -var bs = new java.util.BitSet (); -var alw; -var alStart; -var sqcol = (this.viewport.getSelectionGroup () == null ? this.viewport.getAlignment () : this.viewport.getSelectionGroup ()); -alStart = sqcol.getStartRes (); -alw = sqcol.getEndRes () + 1; -var seqs = sqcol.getSequences (); -var nseq = 0; -for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -var tfeat = 0; -if (sq != null) { -var sf = sq.getSequenceFeatures (); -if (sf != null) { -var ist = sq.findIndex (sq.getStart ()); -var iend = sq.findIndex (sq.getEnd ()); -if (iend < alStart || ist > alw) { -continue; -}for (var sfpos, $sfpos = 0, $$sfpos = sf; $sfpos < $$sfpos.length && ((sfpos = $$sfpos[$sfpos]) || true); $sfpos++) { -if (sfpos != null && (featureType.equals (sfpos.getType ()))) { -tfeat++; -var i = sq.findIndex (sfpos.getBegin ()); -var j = sq.findIndex (sfpos.getEnd ()); -if (j < alStart || i > alw) { -continue; -}if (i < alStart) { -i = alStart; -}if (i < ist) { -i = ist; -}if (j > alw) { -j = alw; -}for (; i <= j; i++) { -bs.set (i - 1); -} -}} -}if (tfeat > 0) { -nseq++; -}}} -var cs = this.viewport.getColumnSelection (); -if (bs.cardinality () > 0 || invert) { -if (cs == null) { -cs = new jalview.datamodel.ColumnSelection (); -} else { -if (!extendCurrent) { -cs.clear (); -}}if (invert) { -for (var i = bs.nextClearBit (alStart), ibs = bs.nextSetBit (alStart); i >= alStart && i < (alw); ) { -if (ibs < 0 || i < ibs) { -if (toggle && cs.contains (i)) { -cs.removeElement (i++); -} else { -cs.addElement (i++); -}} else { -i = bs.nextClearBit (ibs); -ibs = bs.nextSetBit (i); -}} -} else { -for (var i = bs.nextSetBit (alStart); i >= alStart; i = bs.nextSetBit (i + 1)) { -if (toggle && cs.contains (i)) { -cs.removeElement (i); -} else { -cs.addElement (i); -}} -}this.viewport.setColumnSelection (cs); -this.alignPanel.paintAlignment (true); -this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.view_controller_toggled_marked", Clazz.newArray (-1, [(toggle ? jalview.util.MessageManager.getString ("label.toggled") : jalview.util.MessageManager.getString ("label.marked")), (invert ? (Integer.$valueOf ((alw - alStart) - bs.cardinality ()).toString ()) : (Integer.$valueOf (bs.cardinality ()).toString ())), featureType, Integer.$valueOf (nseq).toString ()]))); -return true; -} else { -this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.no_feature_of_type_found", Clazz.newArray (-1, [featureType]))); -if (!extendCurrent && cs != null) { -cs.clear (); -this.alignPanel.paintAlignment (true); -}return false; -}}, "~B,~B,~B,~S"); -Clazz.overrideMethod (c$, "sortAlignmentByFeatureDensity", -function (typ) { -this.sortBy (typ, "Sort by Density", jalview.analysis.AlignmentSorter.FEATURE_DENSITY); -}, "~A"); -Clazz.defineMethod (c$, "sortBy", -function (typ, methodText, method) { -var fr = this.alignPanel.getFeatureRenderer (); -if (typ == null) { -typ = fr == null ? null : fr.getDisplayedFeatureTypes (); -}var gps = null; -gps = fr == null ? null : fr.getDisplayedFeatureGroups (); -if (typ != null) { -var types = new java.util.ArrayList (); -for (var i = 0; i < typ.length; i++) { -if (typ[i] != null) { -types.add (typ[i]); -}typ = new Array (types.size ()); -types.toArray (typ); -} -}if (gps != null) { -var grps = new java.util.ArrayList (); -for (var i = 0; i < gps.length; i++) { -if (gps[i] != null) { -grps.add (gps[i]); -}} -gps = new Array (grps.size ()); -grps.toArray (gps); -}var al = this.viewport.getAlignment (); -var start; -var stop; -var sg = this.viewport.getSelectionGroup (); -if (sg != null) { -start = sg.getStartRes (); -stop = sg.getEndRes (); -} else { -start = 0; -stop = al.getWidth (); -}var oldOrder = al.getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByFeature (typ, gps, start, stop, al, method); -this.avcg.addHistoryItem ( new jalview.commands.OrderCommand (methodText, oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}, "~A,~S,~S"); -Clazz.overrideMethod (c$, "sortAlignmentByFeatureScore", -function (typ) { -this.sortBy (typ, "Sort by Feature Score", jalview.analysis.AlignmentSorter.FEATURE_SCORE); -}, "~A"); -Clazz.overrideMethod (c$, "parseFeaturesFile", -function (file, protocol, relaxedIdMatching) { -var featuresFile = false; -try { -featuresFile = new jalview.io.FeaturesFile (file, protocol).parse (this.viewport.getAlignment ().getDataset (), this.alignPanel.getFeatureRenderer ().getFeatureColours (), false, relaxedIdMatching); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -if (featuresFile) { -this.avcg.refreshFeatureUI (true); -if (this.alignPanel.getFeatureRenderer () != null) { -this.alignPanel.getFeatureRenderer ().findAllFeatures (true); -}if (this.avcg.getFeatureSettingsUI () != null) { -this.avcg.getFeatureSettingsUI ().discoverAllFeatureData (); -}this.alignPanel.paintAlignment (true); -}return featuresFile; -}, "~S,~S,~B"); -}); +Clazz.declarePackage ("jalview.controller"); +Clazz.load (["jalview.api.AlignViewControllerI"], "jalview.controller.AlignViewController", ["jalview.analysis.AlignmentSorter", "$.Grouping", "jalview.commands.OrderCommand", "jalview.datamodel.ColumnSelection", "jalview.io.FeaturesFile", "jalview.util.MessageManager", "java.awt.Color", "java.util.ArrayList", "$.BitSet"], function () { +c$ = Clazz.decorateAsClass (function () { +this.viewport = null; +this.alignPanel = null; +this.avcg = null; +Clazz.instantialize (this, arguments); +}, jalview.controller, "AlignViewController", null, jalview.api.AlignViewControllerI); +Clazz.overrideMethod (c$, "finalize", +function () { +this.viewport = null; +this.alignPanel = null; +this.avcg = null; +}); +Clazz.makeConstructor (c$, +function (alignFrame, viewport, alignPanel) { +this.avcg = alignFrame; +this.viewport = viewport; +this.alignPanel = alignPanel; +}, "jalview.api.AlignViewControllerGuiI,jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); +Clazz.overrideMethod (c$, "setViewportAndAlignmentPanel", +function (viewport, alignPanel) { +this.alignPanel = alignPanel; +this.viewport = viewport; +}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); +Clazz.overrideMethod (c$, "makeGroupsFromSelection", +function () { +var sg = this.viewport.getSelectionGroup (); +var cs = this.viewport.getColumnSelection (); +var gps = null; +if (sg != null && (cs == null || cs.getSelected () == null || cs.size () == 0)) { +gps = jalview.analysis.Grouping.makeGroupsFrom (this.viewport.getSequenceSelection (), this.viewport.getAlignmentView (true).getSequenceStrings (this.viewport.getGapCharacter ()), this.viewport.getAlignment ().getGroups ()); +} else { +if (cs != null) { +gps = jalview.analysis.Grouping.makeGroupsFromCols ((sg == null) ? this.viewport.getAlignment ().getSequencesArray () : sg.getSequences ().toArray ( new Array (0)), cs, this.viewport.getAlignment ().getGroups ()); +}}if (gps != null) { +this.viewport.getAlignment ().deleteAllGroups (); +this.viewport.clearSequenceColours (); +this.viewport.setSelectionGroup (null); +for (var g = 0; g < gps.length; g++) { +gps[g].setshowSequenceLogo (this.viewport.isShowSequenceLogo ()); +this.viewport.getAlignment ().addGroup (gps[g]); +var col = new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255)); +col = col.brighter (); +for (var sq, $sq = gps[g].getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +this.viewport.setSequenceColour (sq, col); +} +} +return true; +}return false; +}); +Clazz.overrideMethod (c$, "createGroup", +function () { +var sg = this.viewport.getSelectionGroup (); +if (sg != null) { +this.viewport.getAlignment ().addGroup (sg); +return true; +}return false; +}); +Clazz.overrideMethod (c$, "unGroup", +function () { +var sg = this.viewport.getSelectionGroup (); +if (sg != null) { +this.viewport.getAlignment ().deleteGroup (sg); +return true; +}return false; +}); +Clazz.overrideMethod (c$, "deleteGroups", +function () { +if (this.viewport.getAlignment ().getGroups () != null && this.viewport.getAlignment ().getGroups ().size () > 0) { +this.viewport.getAlignment ().deleteAllGroups (); +this.viewport.clearSequenceColours (); +this.viewport.setSelectionGroup (null); +return true; +}return false; +}); +Clazz.overrideMethod (c$, "markColumnsContainingFeatures", +function (invert, extendCurrent, toggle, featureType) { +var bs = new java.util.BitSet (); +var alw; +var alStart; +var sqcol = (this.viewport.getSelectionGroup () == null ? this.viewport.getAlignment () : this.viewport.getSelectionGroup ()); +alStart = sqcol.getStartRes (); +alw = sqcol.getEndRes () + 1; +var seqs = sqcol.getSequences (); +var nseq = 0; +for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +var tfeat = 0; +if (sq != null) { +var sf = sq.getSequenceFeatures (); +if (sf != null) { +var ist = sq.findIndex (sq.getStart ()); +var iend = sq.findIndex (sq.getEnd ()); +if (iend < alStart || ist > alw) { +continue; +}for (var sfpos, $sfpos = 0, $$sfpos = sf; $sfpos < $$sfpos.length && ((sfpos = $$sfpos[$sfpos]) || true); $sfpos++) { +if (sfpos != null && (featureType.equals (sfpos.getType ()))) { +tfeat++; +var i = sq.findIndex (sfpos.getBegin ()); +var j = sq.findIndex (sfpos.getEnd ()); +if (j < alStart || i > alw) { +continue; +}if (i < alStart) { +i = alStart; +}if (i < ist) { +i = ist; +}if (j > alw) { +j = alw; +}for (; i <= j; i++) { +bs.set (i - 1); +} +}} +}if (tfeat > 0) { +nseq++; +}}} +var cs = this.viewport.getColumnSelection (); +if (bs.cardinality () > 0 || invert) { +if (cs == null) { +cs = new jalview.datamodel.ColumnSelection (); +} else { +if (!extendCurrent) { +cs.clear (); +}}if (invert) { +for (var i = bs.nextClearBit (alStart), ibs = bs.nextSetBit (alStart); i >= alStart && i < (alw); ) { +if (ibs < 0 || i < ibs) { +if (toggle && cs.contains (i)) { +cs.removeElement (i++); +} else { +cs.addElement (i++); +}} else { +i = bs.nextClearBit (ibs); +ibs = bs.nextSetBit (i); +}} +} else { +for (var i = bs.nextSetBit (alStart); i >= alStart; i = bs.nextSetBit (i + 1)) { +if (toggle && cs.contains (i)) { +cs.removeElement (i); +} else { +cs.addElement (i); +}} +}this.viewport.setColumnSelection (cs); +this.alignPanel.paintAlignment (true); +this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.view_controller_toggled_marked", Clazz.newArray (-1, [(toggle ? jalview.util.MessageManager.getString ("label.toggled") : jalview.util.MessageManager.getString ("label.marked")), (invert ? (Integer.$valueOf ((alw - alStart) - bs.cardinality ()).toString ()) : (Integer.$valueOf (bs.cardinality ()).toString ())), featureType, Integer.$valueOf (nseq).toString ()]))); +return true; +} else { +this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.no_feature_of_type_found", Clazz.newArray (-1, [featureType]))); +if (!extendCurrent && cs != null) { +cs.clear (); +this.alignPanel.paintAlignment (true); +}return false; +}}, "~B,~B,~B,~S"); +Clazz.overrideMethod (c$, "sortAlignmentByFeatureDensity", +function (typ) { +this.sortBy (typ, "Sort by Density", jalview.analysis.AlignmentSorter.FEATURE_DENSITY); +}, "~A"); +Clazz.defineMethod (c$, "sortBy", +function (typ, methodText, method) { +var fr = this.alignPanel.getFeatureRenderer (); +if (typ == null) { +typ = fr == null ? null : fr.getDisplayedFeatureTypes (); +}var gps = null; +gps = fr == null ? null : fr.getDisplayedFeatureGroups (); +if (typ != null) { +var types = new java.util.ArrayList (); +for (var i = 0; i < typ.length; i++) { +if (typ[i] != null) { +types.add (typ[i]); +}typ = new Array (types.size ()); +types.toArray (typ); +} +}if (gps != null) { +var grps = new java.util.ArrayList (); +for (var i = 0; i < gps.length; i++) { +if (gps[i] != null) { +grps.add (gps[i]); +}} +gps = new Array (grps.size ()); +grps.toArray (gps); +}var al = this.viewport.getAlignment (); +var start; +var stop; +var sg = this.viewport.getSelectionGroup (); +if (sg != null) { +start = sg.getStartRes (); +stop = sg.getEndRes (); +} else { +start = 0; +stop = al.getWidth (); +}var oldOrder = al.getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByFeature (typ, gps, start, stop, al, method); +this.avcg.addHistoryItem ( new jalview.commands.OrderCommand (methodText, oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}, "~A,~S,~S"); +Clazz.overrideMethod (c$, "sortAlignmentByFeatureScore", +function (typ) { +this.sortBy (typ, "Sort by Feature Score", jalview.analysis.AlignmentSorter.FEATURE_SCORE); +}, "~A"); +Clazz.overrideMethod (c$, "parseFeaturesFile", +function (file, protocol, relaxedIdMatching) { +var featuresFile = false; +try { +featuresFile = new jalview.io.FeaturesFile (file, protocol).parse (this.viewport.getAlignment ().getDataset (), this.alignPanel.getFeatureRenderer ().getFeatureColours (), false, relaxedIdMatching); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +if (featuresFile) { +this.avcg.refreshFeatureUI (true); +if (this.alignPanel.getFeatureRenderer () != null) { +this.alignPanel.getFeatureRenderer ().findAllFeatures (true); +}if (this.avcg.getFeatureSettingsUI () != null) { +this.avcg.getFeatureSettingsUI ().discoverAllFeatureData (); +}this.alignPanel.paintAlignment (true); +}return featuresFile; +}, "~S,~S,~B"); +}); diff --git a/bin/jalview/controller/FeatureSettingsController.js b/bin/jalview/controller/FeatureSettingsController.js index 1a3acab..8a9666e 100644 --- a/bin/jalview/controller/FeatureSettingsController.js +++ b/bin/jalview/controller/FeatureSettingsController.js @@ -1,7 +1,7 @@ -Clazz.declarePackage ("jalview.controller"); -c$ = Clazz.decorateAsClass (function () { -this.settingUI = null; -this.fr = null; -this.fsettings = null; -Clazz.instantialize (this, arguments); -}, jalview.controller, "FeatureSettingsController"); +Clazz.declarePackage ("jalview.controller"); +c$ = Clazz.decorateAsClass (function () { +this.settingUI = null; +this.fr = null; +this.fsettings = null; +Clazz.instantialize (this, arguments); +}, jalview.controller, "FeatureSettingsController"); diff --git a/bin/jalview/controller/FeatureSettingsControllerGuiI.js b/bin/jalview/controller/FeatureSettingsControllerGuiI.js index ec98397..c092514 100644 --- a/bin/jalview/controller/FeatureSettingsControllerGuiI.js +++ b/bin/jalview/controller/FeatureSettingsControllerGuiI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.controller"); -Clazz.declareInterface (jalview.controller, "FeatureSettingsControllerGuiI"); +Clazz.declarePackage ("jalview.controller"); +Clazz.declareInterface (jalview.controller, "FeatureSettingsControllerGuiI"); diff --git a/bin/jalview/datamodel/ASequence.js b/bin/jalview/datamodel/ASequence.js index 1c80545..76a4493 100644 --- a/bin/jalview/datamodel/ASequence.js +++ b/bin/jalview/datamodel/ASequence.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.ASequenceI"], "jalview.datamodel.ASequence", null, function () { -c$ = Clazz.declareType (jalview.datamodel, "ASequence", null, jalview.datamodel.ASequenceI); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.ASequenceI"], "jalview.datamodel.ASequence", null, function () { +c$ = Clazz.declareType (jalview.datamodel, "ASequence", null, jalview.datamodel.ASequenceI); +}); diff --git a/bin/jalview/datamodel/ASequenceI.js b/bin/jalview/datamodel/ASequenceI.js index 91b3544..3d17914 100644 --- a/bin/jalview/datamodel/ASequenceI.js +++ b/bin/jalview/datamodel/ASequenceI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.declareInterface (jalview.datamodel, "ASequenceI"); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.declareInterface (jalview.datamodel, "ASequenceI"); diff --git a/bin/jalview/datamodel/AlignedCodon.js b/bin/jalview/datamodel/AlignedCodon.js index d02ac8a..3b95647 100644 --- a/bin/jalview/datamodel/AlignedCodon.js +++ b/bin/jalview/datamodel/AlignedCodon.js @@ -1,42 +1,42 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.AlignedCodon", ["java.lang.IllegalArgumentException", "$.StringBuilder"], function () { -c$ = Clazz.decorateAsClass (function () { -this.pos1 = 0; -this.pos2 = 0; -this.pos3 = 0; -this.product = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "AlignedCodon"); -Clazz.makeConstructor (c$, -function (i, j, k) { -this.construct (i, j, k, null); -}, "~N,~N,~N"); -Clazz.makeConstructor (c$, -function (i, j, k, prod) { -this.pos1 = i; -this.pos2 = j; -this.pos3 = k; -this.product = prod; -}, "~N,~N,~N,~S"); -Clazz.defineMethod (c$, "getBaseColumn", -function (base) { -if (base < 1 || base > 3) { -throw new IllegalArgumentException (Integer.toString (base)); -}return base == 1 ? this.pos1 : (base == 2 ? this.pos2 : this.pos3); -}, "~N"); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (o == null) { -return true; -}if (!(Clazz.instanceOf (o, jalview.datamodel.AlignedCodon))) { -return false; -}var ac = o; -return (this.pos1 == ac.pos1 && this.pos2 == ac.pos2 && this.pos3 == ac.pos3); -}, "~O"); -Clazz.overrideMethod (c$, "toString", -function () { -var sb = new StringBuilder (); -sb.append ("[").append (this.pos1).append (", ").append (this.pos2).append (", ").append (this.pos3).append ("]"); -return sb.toString (); -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.AlignedCodon", ["java.lang.IllegalArgumentException", "$.StringBuilder"], function () { +c$ = Clazz.decorateAsClass (function () { +this.pos1 = 0; +this.pos2 = 0; +this.pos3 = 0; +this.product = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "AlignedCodon"); +Clazz.makeConstructor (c$, +function (i, j, k) { +this.construct (i, j, k, null); +}, "~N,~N,~N"); +Clazz.makeConstructor (c$, +function (i, j, k, prod) { +this.pos1 = i; +this.pos2 = j; +this.pos3 = k; +this.product = prod; +}, "~N,~N,~N,~S"); +Clazz.defineMethod (c$, "getBaseColumn", +function (base) { +if (base < 1 || base > 3) { +throw new IllegalArgumentException (Integer.toString (base)); +}return base == 1 ? this.pos1 : (base == 2 ? this.pos2 : this.pos3); +}, "~N"); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (o == null) { +return true; +}if (!(Clazz.instanceOf (o, jalview.datamodel.AlignedCodon))) { +return false; +}var ac = o; +return (this.pos1 == ac.pos1 && this.pos2 == ac.pos2 && this.pos3 == ac.pos3); +}, "~O"); +Clazz.overrideMethod (c$, "toString", +function () { +var sb = new StringBuilder (); +sb.append ("[").append (this.pos1).append (", ").append (this.pos2).append (", ").append (this.pos3).append ("]"); +return sb.toString (); +}); +}); diff --git a/bin/jalview/datamodel/AlignedCodonFrame.class b/bin/jalview/datamodel/AlignedCodonFrame.class index dcb271c..071822f 100644 Binary files a/bin/jalview/datamodel/AlignedCodonFrame.class and b/bin/jalview/datamodel/AlignedCodonFrame.class differ diff --git a/bin/jalview/datamodel/AlignedCodonFrame.js b/bin/jalview/datamodel/AlignedCodonFrame.js index 8d854b4..043b032 100644 --- a/bin/jalview/datamodel/AlignedCodonFrame.js +++ b/bin/jalview/datamodel/AlignedCodonFrame.js @@ -1,198 +1,198 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.AlignedCodonFrame", ["jalview.datamodel.Mapping", "jalview.util.MappingUtils", "java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this.dnaSeqs = null; -this.dnaToProt = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "AlignedCodonFrame"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "addMap", -function (dnaseq, aaseq, map) { -var nlen = 1; -if (this.dnaSeqs != null) { -nlen = this.dnaSeqs.length + 1; -}var ndna = new Array (nlen); -var ndtp = new Array (nlen); -if (this.dnaSeqs != null) { -System.arraycopy (this.dnaSeqs, 0, ndna, 0, this.dnaSeqs.length); -System.arraycopy (this.dnaToProt, 0, ndtp, 0, this.dnaSeqs.length); -}this.dnaSeqs = ndna; -this.dnaToProt = ndtp; -nlen--; -this.dnaSeqs[nlen] = (dnaseq.getDatasetSequence () == null) ? dnaseq : dnaseq.getDatasetSequence (); -var mp = new jalview.datamodel.Mapping (map); -mp.to = (aaseq.getDatasetSequence () == null) ? aaseq : aaseq.getDatasetSequence (); -this.dnaToProt[nlen] = mp; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList"); -Clazz.defineMethod (c$, "getdnaSeqs", -function () { -return this.dnaSeqs; -}); -Clazz.defineMethod (c$, "getAaSeqs", -function () { -if (this.dnaToProt == null) { -return null; -}var sqs = new Array (this.dnaToProt.length); -for (var sz = 0; sz < this.dnaToProt.length; sz++) { -sqs[sz] = this.dnaToProt[sz].to; -} -return sqs; -}); -Clazz.defineMethod (c$, "getdnaToProt", -function () { -if (this.dnaToProt == null) { -return null; -}var sqs = new Array (this.dnaToProt.length); -for (var sz = 0; sz < this.dnaToProt.length; sz++) { -sqs[sz] = this.dnaToProt[sz].map; -} -return sqs; -}); -Clazz.defineMethod (c$, "getProtMappings", -function () { -return this.dnaToProt; -}); -Clazz.defineMethod (c$, "getMappingForSequence", -function (seq) { -if (this.dnaSeqs == null) { -return null; -}var seqDs = seq.getDatasetSequence (); -seqDs = seqDs != null ? seqDs : seq; -for (var ds = 0; ds < this.dnaSeqs.length; ds++) { -if (this.dnaSeqs[ds] === seqDs || this.dnaToProt[ds].to === seqDs) { -return this.dnaToProt[ds]; -}} -return null; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getAaForDnaSeq", -function (dnaSeqRef) { -if (this.dnaSeqs == null) { -return null; -}var dnads = dnaSeqRef.getDatasetSequence (); -for (var ds = 0; ds < this.dnaSeqs.length; ds++) { -if (this.dnaSeqs[ds] === dnaSeqRef || this.dnaSeqs[ds] === dnads) { -return this.dnaToProt[ds].to; -}} -return null; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getDnaForAaSeq", -function (aaSeqRef) { -if (this.dnaToProt == null) { -return null; -}var aads = aaSeqRef.getDatasetSequence (); -for (var as = 0; as < this.dnaToProt.length; as++) { -if (this.dnaToProt[as].to === aaSeqRef || this.dnaToProt[as].to === aads) { -return this.dnaSeqs[as]; -}} -return null; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "involvesSequence", -function (seq) { -return this.getAaForDnaSeq (seq) != null || this.getDnaForAaSeq (seq) != null; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "markMappedRegion", -function (seq, index, results) { -if (this.dnaToProt == null) { -return; -}var codon; -var ds = seq.getDatasetSequence (); -for (var mi = 0; mi < this.dnaToProt.length; mi++) { -if (this.dnaSeqs[mi] === seq || this.dnaSeqs[mi] === ds) { -codon = this.dnaToProt[mi].map.locateInTo (index, index); -if (codon != null) { -for (var i = 0; i < codon.length; i += 2) { -results.addResult (this.dnaToProt[mi].to, codon[i], codon[i + 1]); -} -}} else if (this.dnaToProt[mi].to === seq || this.dnaToProt[mi].to === ds) { -{ -codon = this.dnaToProt[mi].map.locateInFrom (index, index); -if (codon != null) { -for (var i = 0; i < codon.length; i += 2) { -results.addResult (this.dnaSeqs[mi], codon[i], codon[i + 1]); -} -}}}} -}, "jalview.datamodel.SequenceI,~N,jalview.datamodel.SearchResults"); -Clazz.defineMethod (c$, "getDnaPosition", -function (seq, aaPos) { -var ml = null; -for (var i = 0; i < this.dnaToProt.length; i++) { -if (this.dnaSeqs[i] === seq) { -ml = this.getdnaToProt ()[i]; -break; -}} -return ml == null ? null : ml.locateInFrom (aaPos, aaPos); -}, "jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "findAlignedSequence", -function (seq, al) { -if (this.dnaToProt != null) { -for (var i = 0; i < this.dnaToProt.length; i++) { -if (this.dnaSeqs[i] === seq) { -for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) { -if (this.dnaToProt[i].to === sourceAligned.getDatasetSequence ()) { -return sourceAligned; -}} -}} -}if (this.dnaToProt != null) { -for (var i = 0; i < this.dnaToProt.length; i++) { -if (this.dnaToProt[i].to === seq) { -for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) { -if (this.dnaSeqs[i] === sourceAligned.getDatasetSequence ()) { -return sourceAligned; -}} -}} -}return null; -}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "getMappedRegion", -function (mappedFrom, mappedTo, pos) { -var targetDs = mappedFrom.getDatasetSequence () == null ? mappedFrom : mappedFrom.getDatasetSequence (); -var sourceDs = mappedTo.getDatasetSequence () == null ? mappedTo : mappedTo.getDatasetSequence (); -if (targetDs == null || sourceDs == null || this.dnaToProt == null) { -return null; -}for (var mi = 0; mi < this.dnaToProt.length; mi++) { -if (this.dnaSeqs[mi] === targetDs && this.dnaToProt[mi].to === sourceDs) { -var codon = this.dnaToProt[mi].map.locateInFrom (pos, pos); -if (codon != null) { -return codon; -}}} -return null; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "getMappedCodon", -function (protein, aaPos) { -if (this.dnaToProt == null) { -return null; -}var ml = null; -var dnaSeq = null; -for (var i = 0; i < this.dnaToProt.length; i++) { -if (this.dnaToProt[i].to === protein) { -ml = this.getdnaToProt ()[i]; -dnaSeq = this.dnaSeqs[i].getSequence (); -break; -}} -if (ml == null) { -return null; -}var codonPos = ml.locateInFrom (aaPos, aaPos); -if (codonPos == null) { -return null; -}codonPos = jalview.util.MappingUtils.flattenRanges (codonPos); -return Clazz.newCharArray (-1, [dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1], dnaSeq[codonPos[2] - 1]]); -}, "jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "getMappingsForSequence", -function (seq) { -var result = new java.util.ArrayList (); -if (this.dnaSeqs == null) { -return result; -}var related = new java.util.ArrayList (); -var seqDs = seq.getDatasetSequence (); -seqDs = seqDs != null ? seqDs : seq; -for (var ds = 0; ds < this.dnaSeqs.length; ds++) { -var mapping = this.dnaToProt[ds]; -if (this.dnaSeqs[ds] === seqDs || mapping.to === seqDs) { -if (!related.contains (mapping.to)) { -result.add (mapping); -related.add (mapping.to); -}}} -return result; -}, "jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.AlignedCodonFrame", ["jalview.datamodel.Mapping", "jalview.util.MappingUtils", "java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this.dnaSeqs = null; +this.dnaToProt = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "AlignedCodonFrame"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "addMap", +function (dnaseq, aaseq, map) { +var nlen = 1; +if (this.dnaSeqs != null) { +nlen = this.dnaSeqs.length + 1; +}var ndna = new Array (nlen); +var ndtp = new Array (nlen); +if (this.dnaSeqs != null) { +System.arraycopy (this.dnaSeqs, 0, ndna, 0, this.dnaSeqs.length); +System.arraycopy (this.dnaToProt, 0, ndtp, 0, this.dnaSeqs.length); +}this.dnaSeqs = ndna; +this.dnaToProt = ndtp; +nlen--; +this.dnaSeqs[nlen] = (dnaseq.getDatasetSequence () == null) ? dnaseq : dnaseq.getDatasetSequence (); +var mp = new jalview.datamodel.Mapping (map); +mp.to = (aaseq.getDatasetSequence () == null) ? aaseq : aaseq.getDatasetSequence (); +this.dnaToProt[nlen] = mp; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList"); +Clazz.defineMethod (c$, "getdnaSeqs", +function () { +return this.dnaSeqs; +}); +Clazz.defineMethod (c$, "getAaSeqs", +function () { +if (this.dnaToProt == null) { +return null; +}var sqs = new Array (this.dnaToProt.length); +for (var sz = 0; sz < this.dnaToProt.length; sz++) { +sqs[sz] = this.dnaToProt[sz].to; +} +return sqs; +}); +Clazz.defineMethod (c$, "getdnaToProt", +function () { +if (this.dnaToProt == null) { +return null; +}var sqs = new Array (this.dnaToProt.length); +for (var sz = 0; sz < this.dnaToProt.length; sz++) { +sqs[sz] = this.dnaToProt[sz].map; +} +return sqs; +}); +Clazz.defineMethod (c$, "getProtMappings", +function () { +return this.dnaToProt; +}); +Clazz.defineMethod (c$, "getMappingForSequence", +function (seq) { +if (this.dnaSeqs == null) { +return null; +}var seqDs = seq.getDatasetSequence (); +seqDs = seqDs != null ? seqDs : seq; +for (var ds = 0; ds < this.dnaSeqs.length; ds++) { +if (this.dnaSeqs[ds] === seqDs || this.dnaToProt[ds].to === seqDs) { +return this.dnaToProt[ds]; +}} +return null; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getAaForDnaSeq", +function (dnaSeqRef) { +if (this.dnaSeqs == null) { +return null; +}var dnads = dnaSeqRef.getDatasetSequence (); +for (var ds = 0; ds < this.dnaSeqs.length; ds++) { +if (this.dnaSeqs[ds] === dnaSeqRef || this.dnaSeqs[ds] === dnads) { +return this.dnaToProt[ds].to; +}} +return null; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getDnaForAaSeq", +function (aaSeqRef) { +if (this.dnaToProt == null) { +return null; +}var aads = aaSeqRef.getDatasetSequence (); +for (var as = 0; as < this.dnaToProt.length; as++) { +if (this.dnaToProt[as].to === aaSeqRef || this.dnaToProt[as].to === aads) { +return this.dnaSeqs[as]; +}} +return null; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "involvesSequence", +function (seq) { +return this.getAaForDnaSeq (seq) != null || this.getDnaForAaSeq (seq) != null; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "markMappedRegion", +function (seq, index, results) { +if (this.dnaToProt == null) { +return; +}var codon; +var ds = seq.getDatasetSequence (); +for (var mi = 0; mi < this.dnaToProt.length; mi++) { +if (this.dnaSeqs[mi] === seq || this.dnaSeqs[mi] === ds) { +codon = this.dnaToProt[mi].map.locateInTo (index, index); +if (codon != null) { +for (var i = 0; i < codon.length; i += 2) { +results.addResult (this.dnaToProt[mi].to, codon[i], codon[i + 1]); +} +}} else if (this.dnaToProt[mi].to === seq || this.dnaToProt[mi].to === ds) { +{ +codon = this.dnaToProt[mi].map.locateInFrom (index, index); +if (codon != null) { +for (var i = 0; i < codon.length; i += 2) { +results.addResult (this.dnaSeqs[mi], codon[i], codon[i + 1]); +} +}}}} +}, "jalview.datamodel.SequenceI,~N,jalview.datamodel.SearchResults"); +Clazz.defineMethod (c$, "getDnaPosition", +function (seq, aaPos) { +var ml = null; +for (var i = 0; i < this.dnaToProt.length; i++) { +if (this.dnaSeqs[i] === seq) { +ml = this.getdnaToProt ()[i]; +break; +}} +return ml == null ? null : ml.locateInFrom (aaPos, aaPos); +}, "jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "findAlignedSequence", +function (seq, al) { +if (this.dnaToProt != null) { +for (var i = 0; i < this.dnaToProt.length; i++) { +if (this.dnaSeqs[i] === seq) { +for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) { +if (this.dnaToProt[i].to === sourceAligned.getDatasetSequence ()) { +return sourceAligned; +}} +}} +}if (this.dnaToProt != null) { +for (var i = 0; i < this.dnaToProt.length; i++) { +if (this.dnaToProt[i].to === seq) { +for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) { +if (this.dnaSeqs[i] === sourceAligned.getDatasetSequence ()) { +return sourceAligned; +}} +}} +}return null; +}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "getMappedRegion", +function (mappedFrom, mappedTo, pos) { +var targetDs = mappedFrom.getDatasetSequence () == null ? mappedFrom : mappedFrom.getDatasetSequence (); +var sourceDs = mappedTo.getDatasetSequence () == null ? mappedTo : mappedTo.getDatasetSequence (); +if (targetDs == null || sourceDs == null || this.dnaToProt == null) { +return null; +}for (var mi = 0; mi < this.dnaToProt.length; mi++) { +if (this.dnaSeqs[mi] === targetDs && this.dnaToProt[mi].to === sourceDs) { +var codon = this.dnaToProt[mi].map.locateInFrom (pos, pos); +if (codon != null) { +return codon; +}}} +return null; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "getMappedCodon", +function (protein, aaPos) { +if (this.dnaToProt == null) { +return null; +}var ml = null; +var dnaSeq = null; +for (var i = 0; i < this.dnaToProt.length; i++) { +if (this.dnaToProt[i].to === protein) { +ml = this.getdnaToProt ()[i]; +dnaSeq = this.dnaSeqs[i].getSequence (); +break; +}} +if (ml == null) { +return null; +}var codonPos = ml.locateInFrom (aaPos, aaPos); +if (codonPos == null) { +return null; +}codonPos = jalview.util.MappingUtils.flattenRanges (codonPos); +return Clazz.newCharArray (-1, [dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1], dnaSeq[codonPos[2] - 1]]); +}, "jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "getMappingsForSequence", +function (seq) { +var result = new java.util.ArrayList (); +if (this.dnaSeqs == null) { +return result; +}var related = new java.util.ArrayList (); +var seqDs = seq.getDatasetSequence (); +seqDs = seqDs != null ? seqDs : seq; +for (var ds = 0; ds < this.dnaSeqs.length; ds++) { +var mapping = this.dnaToProt[ds]; +if (this.dnaSeqs[ds] === seqDs || mapping.to === seqDs) { +if (!related.contains (mapping.to)) { +result.add (mapping); +related.add (mapping.to); +}}} +return result; +}, "jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/datamodel/Alignment.class b/bin/jalview/datamodel/Alignment.class index 5ed53fa..c65b99e 100644 Binary files a/bin/jalview/datamodel/Alignment.class and b/bin/jalview/datamodel/Alignment.class differ diff --git a/bin/jalview/datamodel/Alignment.js b/bin/jalview/datamodel/Alignment.js index f70f6ce..a4d45ee 100644 --- a/bin/jalview/datamodel/Alignment.js +++ b/bin/jalview/datamodel/Alignment.js @@ -1,815 +1,815 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.AlignmentI", "$.HiddenSequences", "java.util.ArrayList", "$.Collections", "$.LinkedHashSet"], "jalview.datamodel.Alignment", ["jalview.analysis.AlignmentUtils", "jalview.datamodel.AlignmentAnnotation", "$.CigarArray", "$.SeqCigar", "$.Sequence", "jalview.util.Comparison", "$.MessageManager", "java.lang.Error", "java.util.HashSet", "$.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.dataset = null; -this.sequences = null; -this.groups = null; -this.gapCharacter = '-'; -this.type = 1; -this.$hasRNAStructure = false; -this.annotations = null; -this.hiddenSequences = null; -this.alignmentProperties = null; -this.codonFrameList = null; -this.alignmentRefs = 0; -this.seqrep = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "Alignment", null, jalview.datamodel.AlignmentI); -Clazz.prepareFields (c$, function () { -this.groups = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); -this.hiddenSequences = new jalview.datamodel.HiddenSequences (this); -this.codonFrameList = new java.util.LinkedHashSet (); -}); -Clazz.defineMethod (c$, "initAlignment", -($fz = function (seqs) { -var i = 0; -if (jalview.util.Comparison.isNucleotide (seqs)) { -this.type = 1; -} else { -this.type = 0; -}this.sequences = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); -for (i = 0; i < seqs.length; i++) { -this.sequences.add (seqs[i]); -} -}, $fz.isPrivate = true, $fz), "~A"); -Clazz.makeConstructor (c$, -function (al) { -var seqs = al.getSequencesArray (); -for (var i = 0; i < seqs.length; i++) { -seqs[i] = new jalview.datamodel.Sequence (seqs[i]); -} -this.codonFrameList = (al).codonFrameList; -this.initAlignment (seqs); -}, "jalview.datamodel.AlignmentI"); -Clazz.makeConstructor (c$, -function (seqs) { -this.initAlignment (seqs); -}, "~A"); -c$.createAlignment = Clazz.defineMethod (c$, "createAlignment", -function (compactAlignment) { -throw new Error (jalview.util.MessageManager.getString ("error.alignment_cigararray_not_implemented")); -}, "jalview.datamodel.CigarArray"); -Clazz.defineMethod (c$, "getSequences", -function () { -return this.sequences; -}); -Clazz.defineMethod (c$, "getSequences", -function (hiddenReps) { -return this.sequences; -}, "java.util.Map"); -Clazz.defineMethod (c$, "getSequencesArray", -function () { -if (this.sequences == null) { -return null; -}{ -return this.sequences.toArray ( new Array (this.sequences.size ())); -}}); -Clazz.overrideMethod (c$, "getSequencesByName", -function () { -return jalview.analysis.AlignmentUtils.getSequencesByName (this); -}); -Clazz.overrideMethod (c$, "getSequenceAt", -function (i) { -{ -if (i > -1 && i < this.sequences.size ()) { -return this.sequences.get (i); -}}return null; -}, "~N"); -Clazz.overrideMethod (c$, "addSequence", -function (snew) { -if (this.dataset != null) { -if (snew.getDatasetSequence () != null) { -this.getDataset ().addSequence (snew.getDatasetSequence ()); -} else { -var adding = snew.deriveSequence (); -this.getDataset ().addSequence (adding.getDatasetSequence ()); -snew = adding; -}}if (this.sequences == null) { -this.initAlignment ( Clazz.newArray (-1, [snew])); -} else { -{ -this.sequences.add (snew); -}}if (this.hiddenSequences != null) { -this.hiddenSequences.adjustHeightSequenceAdded (); -}}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "setSequenceAt", -function (i, snew) { -{ -this.deleteSequence (i); -this.sequences.set (i, snew); -}}, "~N,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getGroups", -function () { -return this.groups; -}); -Clazz.overrideMethod (c$, "finalize", -function () { -if (this.getDataset () != null) { -this.getDataset ().removeAlignmentRef (); -}this.dataset = null; -this.sequences = null; -this.groups = null; -this.annotations = null; -this.hiddenSequences = null; -}); -Clazz.defineMethod (c$, "removeAlignmentRef", -($fz = function () { -if (--this.alignmentRefs == 0) { -this.finalize (); -}}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "deleteSequence", -function (s) { -this.deleteSequence (this.findIndex (s)); -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "deleteSequence", -function (i) { -if (i > -1 && i < this.getHeight ()) { -{ -this.sequences.remove (i); -this.hiddenSequences.adjustHeightSequenceDeleted (i); -}}}, "~N"); -Clazz.overrideMethod (c$, "findGroup", -function (s) { -{ -for (var i = 0; i < this.groups.size (); i++) { -var sg = this.groups.get (i); -if (sg.getSequences (null).contains (s)) { -return sg; -}} -}return null; -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "findAllGroups", -function (s) { -var temp = new java.util.ArrayList (); -{ -var gSize = this.groups.size (); -for (var i = 0; i < gSize; i++) { -var sg = this.groups.get (i); -if (sg == null || sg.getSequences () == null) { -this.deleteGroup (sg); -gSize--; -continue; -}if (sg.getSequences ().contains (s)) { -temp.add (sg); -}} -}var ret = new Array (temp.size ()); -return temp.toArray (ret); -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "addGroup", -function (sg) { -{ -if (!this.groups.contains (sg)) { -if (this.hiddenSequences.getSize () > 0) { -var i; -var iSize = sg.getSize (); -for (i = 0; i < iSize; i++) { -if (!this.sequences.contains (sg.getSequenceAt (i))) { -sg.deleteSequence (sg.getSequenceAt (i), false); -iSize--; -i--; -}} -if (sg.getSize () < 1) { -return; -}}sg.setContext (this); -this.groups.add (sg); -}}}, "jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "removeAnnotationForGroup", -($fz = function (gp) { -if (this.annotations == null || this.annotations.length == 0) { -return; -}var t; -var todelete = new Array (this.annotations.length); -var tokeep = new Array (this.annotations.length); -var i; -var p; -var k; -if (gp == null) { -for (i = 0, p = 0, k = 0; i < this.annotations.length; i++) { -if (this.annotations[i].groupRef != null) { -todelete[p++] = this.annotations[i]; -} else { -tokeep[k++] = this.annotations[i]; -}} -} else { -for (i = 0, p = 0, k = 0; i < this.annotations.length; i++) { -if (this.annotations[i].groupRef === gp) { -todelete[p++] = this.annotations[i]; -} else { -tokeep[k++] = this.annotations[i]; -}} -}if (p > 0) { -for (i = 0; i < p; i++) { -this.unhookAnnotation (todelete[i]); -todelete[i] = null; -} -t = new Array (k); -for (i = 0; i < k; i++) { -t[i] = tokeep[i]; -} -this.annotations = t; -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceGroup"); -Clazz.overrideMethod (c$, "deleteAllGroups", -function () { -{ -if (this.annotations != null) { -this.removeAnnotationForGroup (null); -}for (var sg, $sg = this.groups.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -sg.setContext (null); -} -this.groups.clear (); -}}); -Clazz.overrideMethod (c$, "deleteGroup", -function (g) { -{ -if (this.groups.contains (g)) { -this.removeAnnotationForGroup (g); -this.groups.remove (g); -g.setContext (null); -}}}, "jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "findName", -function (name) { -return this.findName (name, false); -}, "~S"); -Clazz.defineMethod (c$, "findName", -function (token, b) { -return this.findName (null, token, b); -}, "~S,~B"); -Clazz.defineMethod (c$, "findName", -function (startAfter, token, b) { -var i = 0; -var sq = null; -var sqname = null; -if (startAfter != null) { -var matched = false; -while (i < this.sequences.size ()) { -if (this.getSequenceAt (i++) === startAfter) { -matched = true; -break; -}} -if (!matched) { -i = 0; -}}while (i < this.sequences.size ()) { -sq = this.getSequenceAt (i); -sqname = sq.getName (); -if (sqname.equals (token) || (b && (sqname.equalsIgnoreCase (token)))) { -return this.getSequenceAt (i); -}i++; -} -return null; -}, "jalview.datamodel.SequenceI,~S,~B"); -Clazz.overrideMethod (c$, "findSequenceMatch", -function (name) { -var matches = new java.util.Vector (); -var i = 0; -while (i < this.sequences.size ()) { -if (this.getSequenceAt (i).getName ().equals (name)) { -matches.addElement (this.getSequenceAt (i)); -}i++; -} -var result = new Array (matches.size ()); -for (i = 0; i < result.length; i++) { -result[i] = matches.elementAt (i); -} -return result; -}, "~S"); -Clazz.defineMethod (c$, "findIndex", -function (s) { -var i = 0; -while (i < this.sequences.size ()) { -if (s === this.getSequenceAt (i)) { -return i; -}i++; -} -return -1; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "findIndex", -function (results) { -var i = 0; -while (i < this.sequences.size ()) { -if (results.involvesSequence (this.getSequenceAt (i))) { -return i; -}i++; -} -return -1; -}, "jalview.datamodel.SearchResults"); -Clazz.overrideMethod (c$, "getHeight", -function () { -return this.sequences.size (); -}); -Clazz.overrideMethod (c$, "getWidth", -function () { -var maxLength = -1; -for (var i = 0; i < this.sequences.size (); i++) { -if (this.getSequenceAt (i).getLength () > maxLength) { -maxLength = this.getSequenceAt (i).getLength (); -}} -return maxLength; -}); -Clazz.overrideMethod (c$, "setGapCharacter", -function (gc) { -this.gapCharacter = gc; -{ -for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -seq.setSequence (seq.getSequenceAsString ().$replace ('.', gc).$replace ('-', gc).$replace (' ', gc)); -} -}}, "~S"); -Clazz.defineMethod (c$, "getGapCharacter", -function () { -return this.gapCharacter; -}); -Clazz.defineMethod (c$, "isAligned", -function () { -return this.isAligned (false); -}); -Clazz.defineMethod (c$, "isAligned", -function (includeHidden) { -var width = this.getWidth (); -if (this.hiddenSequences == null || this.hiddenSequences.getSize () == 0) { -includeHidden = true; -}for (var i = 0; i < this.sequences.size (); i++) { -if (includeHidden || !this.hiddenSequences.isHidden (this.getSequenceAt (i))) { -if (this.getSequenceAt (i).getLength () != width) { -return false; -}}} -return true; -}, "~B"); -Clazz.overrideMethod (c$, "deleteAllAnnotations", -function (includingAutoCalculated) { -var result = false; -for (var alan, $alan = 0, $$alan = this.getAlignmentAnnotation (); $alan < $$alan.length && ((alan = $$alan[$alan]) || true); $alan++) { -if (!alan.autoCalculated || includingAutoCalculated) { -this.deleteAnnotation (alan); -result = true; -}} -return result; -}, "~B"); -Clazz.defineMethod (c$, "deleteAnnotation", -function (aa) { -return this.deleteAnnotation (aa, true); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "deleteAnnotation", -function (aa, unhook) { -var aSize = 1; -if (this.annotations != null) { -aSize = this.annotations.length; -}if (aSize < 1) { -return false; -}var temp = new Array (aSize - 1); -var swap = false; -var tIndex = 0; -for (var i = 0; i < aSize; i++) { -if (this.annotations[i] === aa) { -swap = true; -continue; -}if (tIndex < temp.length) { -temp[tIndex++] = this.annotations[i]; -}} -if (swap) { -this.annotations = temp; -if (unhook) { -this.unhookAnnotation (aa); -}}return swap; -}, "jalview.datamodel.AlignmentAnnotation,~B"); -Clazz.defineMethod (c$, "unhookAnnotation", -($fz = function (aa) { -if (aa.sequenceRef != null) { -aa.sequenceRef.removeAlignmentAnnotation (aa); -}if (aa.groupRef != null) { -aa.groupRef = null; -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "addAnnotation", -function (aa) { -this.addAnnotation (aa, -1); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "addAnnotation", -function (aa, pos) { -if (aa.getRNAStruc () != null) { -this.$hasRNAStructure = true; -}var aSize = 1; -if (this.annotations != null) { -aSize = this.annotations.length + 1; -}var temp = new Array (aSize); -var i = 0; -if (pos == -1 || pos >= aSize) { -temp[aSize - 1] = aa; -} else { -temp[pos] = aa; -}if (aSize > 1) { -var p = 0; -for (i = 0; i < (aSize - 1); i++, p++) { -if (p == pos) { -p++; -}if (p < temp.length) { -temp[p] = this.annotations[i]; -}} -}this.annotations = temp; -}, "jalview.datamodel.AlignmentAnnotation,~N"); -Clazz.overrideMethod (c$, "setAnnotationIndex", -function (aa, index) { -if (aa == null || this.annotations == null || this.annotations.length - 1 < index) { -return; -}var aSize = this.annotations.length; -var temp = new Array (aSize); -temp[index] = aa; -for (var i = 0; i < aSize; i++) { -if (i == index) { -continue; -}if (i < index) { -temp[i] = this.annotations[i]; -} else { -temp[i] = this.annotations[i - 1]; -}} -this.annotations = temp; -}, "jalview.datamodel.AlignmentAnnotation,~N"); -Clazz.defineMethod (c$, "getAlignmentAnnotation", -function () { -return this.annotations; -}); -Clazz.overrideMethod (c$, "setNucleotide", -function (b) { -if (b) { -this.type = 1; -} else { -this.type = 0; -}}, "~B"); -Clazz.defineMethod (c$, "isNucleotide", -function () { -if (this.type == 1) { -return true; -} else { -return false; -}}); -Clazz.overrideMethod (c$, "hasRNAStructure", -function () { -return this.$hasRNAStructure; -}); -Clazz.overrideMethod (c$, "setDataset", -function (data) { -if (this.dataset == null && data == null) { -var seqs = new Array (this.getHeight ()); -var currentSeq; -for (var i = 0; i < this.getHeight (); i++) { -currentSeq = this.getSequenceAt (i); -if (currentSeq.getDatasetSequence () != null) { -seqs[i] = currentSeq.getDatasetSequence (); -} else { -seqs[i] = currentSeq.createDatasetSequence (); -}} -this.dataset = new jalview.datamodel.Alignment (seqs); -} else if (this.dataset == null && data != null) { -this.dataset = data; -for (var i = 0; i < this.getHeight (); i++) { -var currentSeq = this.getSequenceAt (i); -var dsq = currentSeq.getDatasetSequence (); -if (dsq == null) { -dsq = currentSeq.createDatasetSequence (); -this.dataset.addSequence (dsq); -} else { -while (dsq.getDatasetSequence () != null) { -dsq = dsq.getDatasetSequence (); -} -if (this.dataset.findIndex (dsq) == -1) { -this.dataset.addSequence (dsq); -}}} -}this.dataset.addAlignmentRef (); -}, "jalview.datamodel.Alignment"); -Clazz.defineMethod (c$, "addAlignmentRef", -($fz = function () { -this.alignmentRefs++; -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "getDataset", -function () { -return this.dataset; -}); -Clazz.overrideMethod (c$, "padGaps", -function () { -var modified = false; -var maxLength = -1; -var current; -for (var i = 0; i < this.sequences.size (); i++) { -current = this.getSequenceAt (i); -for (var j = current.getLength (); j > maxLength; j--) { -if (j > maxLength && !jalview.util.Comparison.isGap (current.getCharAt (j))) { -maxLength = j; -break; -}} -} -maxLength++; -var cLength; -for (var i = 0; i < this.sequences.size (); i++) { -current = this.getSequenceAt (i); -cLength = current.getLength (); -if (cLength < maxLength) { -current.insertCharAt (cLength, maxLength - cLength, this.gapCharacter); -modified = true; -} else if (current.getLength () > maxLength) { -current.deleteChars (maxLength, current.getLength ()); -}} -return modified; -}); -Clazz.overrideMethod (c$, "justify", -function (right) { -var modified = false; -var maxLength = -1; -var ends = Clazz.newIntArray (this.sequences.size () * 2, 0); -var current; -for (var i = 0; i < this.sequences.size (); i++) { -current = this.getSequenceAt (i); -ends[i * 2] = current.findIndex (current.getStart ()); -ends[i * 2 + 1] = current.findIndex (current.getStart () + current.getLength ()); -var hitres = false; -for (var j = 0, rs = 0, ssiz = current.getLength (); j < ssiz; j++) { -if (!jalview.util.Comparison.isGap (current.getCharAt (j))) { -if (!hitres) { -ends[i * 2] = j; -hitres = true; -} else { -ends[i * 2 + 1] = j; -if (j - ends[i * 2] > maxLength) { -maxLength = j - ends[i * 2]; -}}}} -} -maxLength++; -var cLength; -var extent; -var diff; -for (var i = 0; i < this.sequences.size (); i++) { -current = this.getSequenceAt (i); -cLength = 1 + ends[i * 2 + 1] - ends[i * 2]; -diff = maxLength - cLength; -extent = current.getLength (); -if (right) { -if (extent > ends[i * 2 + 1]) { -current.deleteChars (ends[i * 2 + 1] + 1, extent); -modified = true; -}if (ends[i * 2] > diff) { -current.deleteChars (0, ends[i * 2] - diff); -modified = true; -} else { -if (ends[i * 2] < diff) { -current.insertCharAt (0, diff - ends[i * 2], this.gapCharacter); -modified = true; -}}} else { -if (ends[i * 2] > 0) { -current.deleteChars (0, ends[i * 2]); -modified = true; -ends[i * 2 + 1] -= ends[i * 2]; -extent -= ends[i * 2]; -}if (extent > maxLength) { -current.deleteChars (maxLength + 1, extent); -modified = true; -} else { -if (extent < maxLength) { -current.insertCharAt (extent, maxLength - extent, this.gapCharacter); -modified = true; -}}}} -return modified; -}, "~B"); -Clazz.defineMethod (c$, "getHiddenSequences", -function () { -return this.hiddenSequences; -}); -Clazz.overrideMethod (c$, "getCompactAlignment", -function () { -{ -var alseqs = new Array (this.sequences.size ()); -var i = 0; -for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -alseqs[i++] = new jalview.datamodel.SeqCigar (seq); -} -var cal = new jalview.datamodel.CigarArray (alseqs); -cal.addOperation ('M', this.getWidth ()); -return cal; -}}); -Clazz.overrideMethod (c$, "setProperty", -function (key, value) { -if (this.alignmentProperties == null) { -this.alignmentProperties = new java.util.Hashtable (); -}this.alignmentProperties.put (key, value); -}, "~O,~O"); -Clazz.defineMethod (c$, "getProperty", -function (key) { -if (this.alignmentProperties != null) { -return this.alignmentProperties.get (key); -} else { -return null; -}}, "~O"); -Clazz.defineMethod (c$, "getProperties", -function () { -return this.alignmentProperties; -}); -Clazz.overrideMethod (c$, "addCodonFrame", -function (codons) { -if (codons != null) { -this.codonFrameList.add (codons); -}}, "jalview.datamodel.AlignedCodonFrame"); -Clazz.overrideMethod (c$, "getCodonFrame", -function (seq) { -if (seq == null) { -return null; -}var cframes = new java.util.ArrayList (); -for (var acf, $acf = this.codonFrameList.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -if (acf.involvesSequence (seq)) { -cframes.add (acf); -}} -return cframes; -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "setCodonFrames", -function (acfs) { -this.codonFrameList = acfs; -}, "java.util.Set"); -Clazz.defineMethod (c$, "getCodonFrames", -function () { -return this.codonFrameList; -}); -Clazz.overrideMethod (c$, "removeCodonFrame", -function (codons) { -if (codons == null || this.codonFrameList == null) { -return false; -}return this.codonFrameList.remove (codons); -}, "jalview.datamodel.AlignedCodonFrame"); -Clazz.overrideMethod (c$, "append", -function (toappend) { -if (toappend === this) { -System.err.println ("Self append may cause a deadlock."); -}var samegap = toappend.getGapCharacter () == this.getGapCharacter (); -var oldc = toappend.getGapCharacter (); -var hashidden = toappend.getHiddenSequences () != null && toappend.getHiddenSequences ().hiddenSequences != null; -var sqs = (hashidden) ? toappend.getHiddenSequences ().getFullAlignment ().getSequences () : toappend.getSequences (); -if (sqs != null) { -{ -for (var addedsq, $addedsq = sqs.iterator (); $addedsq.hasNext () && ((addedsq = $addedsq.next ()) || true);) { -if (!samegap) { -var oldseq = addedsq.getSequence (); -for (var c = 0; c < oldseq.length; c++) { -if (oldseq[c] == oldc) { -oldseq[c] = this.gapCharacter; -}} -}this.addSequence (addedsq); -} -}}var alan = toappend.getAlignmentAnnotation (); -for (var a = 0; alan != null && a < alan.length; a++) { -this.addAnnotation (alan[a]); -} -this.codonFrameList.addAll (toappend.getCodonFrames ()); -var sg = toappend.getGroups (); -if (sg != null) { -for (var _sg, $_sg = sg.iterator (); $_sg.hasNext () && ((_sg = $_sg.next ()) || true);) { -this.addGroup (_sg); -} -}if (toappend.getHiddenSequences () != null) { -var hs = toappend.getHiddenSequences (); -if (this.hiddenSequences == null) { -this.hiddenSequences = new jalview.datamodel.HiddenSequences (this); -}if (hs.hiddenSequences != null) { -for (var s = 0; s < hs.hiddenSequences.length; s++) { -if (hs.hiddenSequences[s] != null) { -this.hiddenSequences.hideSequence (hs.hiddenSequences[s]); -}} -}}if (toappend.getProperties () != null) { -var key = toappend.getProperties ().keys (); -while (key.hasMoreElements ()) { -var k = key.nextElement (); -var ourval = this.getProperty (k); -var toapprop = toappend.getProperty (k); -if (ourval != null) { -if (ourval.getClass ().equals (toapprop.getClass ()) && !ourval.equals (toapprop)) { -if (Clazz.instanceOf (ourval, String)) { -this.setProperty (k, (ourval) + "; " + (toapprop)); -} else { -if (Clazz.instanceOf (ourval, java.util.Vector)) { -var theirv = (toapprop).elements (); -while (theirv.hasMoreElements ()) { -(ourval).addElement (theirv); -} -}}}} else { -this.setProperty (k, toapprop); -}} -}}, "jalview.datamodel.AlignmentI"); -Clazz.overrideMethod (c$, "findOrCreateAnnotation", -function (name, calcId, autoCalc, seqRef, groupRef) { -if (this.annotations != null) { -for (var annot, $annot = 0, $$annot = this.getAlignmentAnnotation (); $annot < $$annot.length && ((annot = $$annot[$annot]) || true); $annot++) { -if (annot.autoCalculated == autoCalc && (name.equals (annot.label)) && (calcId == null || annot.getCalcId ().equals (calcId)) && annot.sequenceRef === seqRef && annot.groupRef === groupRef) { -return annot; -}} -}var annot = new jalview.datamodel.AlignmentAnnotation (name, name, new Array (1), 0, 0, 1); -annot.hasText = false; -annot.setCalcId ( String.instantialize (calcId)); -annot.autoCalculated = autoCalc; -if (seqRef != null) { -annot.setSequenceRef (seqRef); -}annot.groupRef = groupRef; -this.addAnnotation (annot); -return annot; -}, "~S,~S,~B,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); -Clazz.overrideMethod (c$, "findAnnotation", -function (calcId) { -var aa = new java.util.ArrayList (); -for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) { -if (a.getCalcId () === calcId || (a.getCalcId () != null && calcId != null && a.getCalcId ().equals (calcId))) { -aa.add (a); -}} -return aa; -}, "~S"); -Clazz.overrideMethod (c$, "findAnnotations", -function (seq, calcId, label) { -var aa = new java.util.ArrayList (); -for (var ann, $ann = 0, $$ann = this.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { -if (ann.getCalcId () != null && ann.getCalcId ().equals (calcId) && ann.sequenceRef != null && ann.sequenceRef === seq && ann.label != null && ann.label.equals (label)) { -aa.add (ann); -}} -return aa; -}, "jalview.datamodel.SequenceI,~S,~S"); -Clazz.overrideMethod (c$, "moveSelectedSequencesByOne", -function (sg, map, up) { -{ -if (up) { -for (var i = 1, iSize = this.sequences.size (); i < iSize; i++) { -var seq = this.sequences.get (i); -if (!sg.getSequences (map).contains (seq)) { -continue; -}var temp = this.sequences.get (i - 1); -if (sg.getSequences (null).contains (temp)) { -continue; -}this.sequences.set (i, temp); -this.sequences.set (i - 1, seq); -} -} else { -for (var i = this.sequences.size () - 2; i > -1; i--) { -var seq = this.sequences.get (i); -if (!sg.getSequences (map).contains (seq)) { -continue; -}var temp = this.sequences.get (i + 1); -if (sg.getSequences (map).contains (temp)) { -continue; -}this.sequences.set (i, temp); -this.sequences.set (i + 1, seq); -} -}}}, "jalview.datamodel.SequenceGroup,java.util.Map,~B"); -Clazz.overrideMethod (c$, "validateAnnotation", -function (alignmentAnnotation) { -alignmentAnnotation.validateRangeAndDisplay (); -if (this.isNucleotide () && alignmentAnnotation.isValidStruc ()) { -this.$hasRNAStructure = true; -}}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.overrideMethod (c$, "getSeqrep", -function () { -return this.seqrep; -}); -Clazz.overrideMethod (c$, "setSeqrep", -function (seqrep) { -this.seqrep = seqrep; -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "hasSeqrep", -function () { -return this.seqrep != null; -}); -Clazz.overrideMethod (c$, "getEndRes", -function () { -return this.getWidth () - 1; -}); -Clazz.overrideMethod (c$, "getStartRes", -function () { -return 0; -}); -Clazz.overrideMethod (c$, "getContext", -function () { -return this.dataset; -}); -Clazz.defineMethod (c$, "alignAs", -function (al) { -return this.alignAs (al, false, true); -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "alignAs", -function (al, preserveMappedGaps, preserveUnmappedGaps) { -var count = 0; -var thisIsNucleotide = this.isNucleotide (); -var thatIsProtein = !al.isNucleotide (); -if (!thatIsProtein && !thisIsNucleotide) { -return jalview.analysis.AlignmentUtils.alignProteinAsDna (this, al); -}var thisGapChar = this.getGapCharacter (); -var gap = thisIsNucleotide && thatIsProtein ? String.valueOf ( Clazz.newCharArray (-1, [thisGapChar, thisGapChar, thisGapChar])) : String.valueOf (thisGapChar); -for (var alignTo, $alignTo = this.getSequences ().iterator (); $alignTo.hasNext () && ((alignTo = $alignTo.next ()) || true);) { -count += jalview.analysis.AlignmentUtils.alignSequenceAs (alignTo, al, gap, preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0; -} -return count; -}, "jalview.datamodel.AlignmentI,~B,~B"); -Clazz.overrideMethod (c$, "getSequenceNames", -function () { -var names = new java.util.HashSet (); -for (var seq, $seq = this.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -names.add (seq.getName ()); -} -return names; -}); -Clazz.overrideMethod (c$, "toString", -function () { -var seq = this.getSequencesArray (); -{ -return "" + JSON.stringify(seq); -}}); -Clazz.defineStatics (c$, -"PROTEIN", 0, -"NUCLEOTIDE", 1); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.AlignmentI", "$.HiddenSequences", "java.util.ArrayList", "$.Collections", "$.LinkedHashSet"], "jalview.datamodel.Alignment", ["jalview.analysis.AlignmentUtils", "jalview.datamodel.AlignmentAnnotation", "$.CigarArray", "$.SeqCigar", "$.Sequence", "jalview.util.Comparison", "$.MessageManager", "java.lang.Error", "java.util.HashSet", "$.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.dataset = null; +this.sequences = null; +this.groups = null; +this.gapCharacter = '-'; +this.type = 1; +this.$hasRNAStructure = false; +this.annotations = null; +this.hiddenSequences = null; +this.alignmentProperties = null; +this.codonFrameList = null; +this.alignmentRefs = 0; +this.seqrep = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "Alignment", null, jalview.datamodel.AlignmentI); +Clazz.prepareFields (c$, function () { +this.groups = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); +this.hiddenSequences = new jalview.datamodel.HiddenSequences (this); +this.codonFrameList = new java.util.LinkedHashSet (); +}); +Clazz.defineMethod (c$, "initAlignment", +($fz = function (seqs) { +var i = 0; +if (jalview.util.Comparison.isNucleotide (seqs)) { +this.type = 1; +} else { +this.type = 0; +}this.sequences = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); +for (i = 0; i < seqs.length; i++) { +this.sequences.add (seqs[i]); +} +}, $fz.isPrivate = true, $fz), "~A"); +Clazz.makeConstructor (c$, +function (al) { +var seqs = al.getSequencesArray (); +for (var i = 0; i < seqs.length; i++) { +seqs[i] = new jalview.datamodel.Sequence (seqs[i]); +} +this.codonFrameList = (al).codonFrameList; +this.initAlignment (seqs); +}, "jalview.datamodel.AlignmentI"); +Clazz.makeConstructor (c$, +function (seqs) { +this.initAlignment (seqs); +}, "~A"); +c$.createAlignment = Clazz.defineMethod (c$, "createAlignment", +function (compactAlignment) { +throw new Error (jalview.util.MessageManager.getString ("error.alignment_cigararray_not_implemented")); +}, "jalview.datamodel.CigarArray"); +Clazz.defineMethod (c$, "getSequences", +function () { +return this.sequences; +}); +Clazz.defineMethod (c$, "getSequences", +function (hiddenReps) { +return this.sequences; +}, "java.util.Map"); +Clazz.defineMethod (c$, "getSequencesArray", +function () { +if (this.sequences == null) { +return null; +}{ +return this.sequences.toArray ( new Array (this.sequences.size ())); +}}); +Clazz.overrideMethod (c$, "getSequencesByName", +function () { +return jalview.analysis.AlignmentUtils.getSequencesByName (this); +}); +Clazz.overrideMethod (c$, "getSequenceAt", +function (i) { +{ +if (i > -1 && i < this.sequences.size ()) { +return this.sequences.get (i); +}}return null; +}, "~N"); +Clazz.overrideMethod (c$, "addSequence", +function (snew) { +if (this.dataset != null) { +if (snew.getDatasetSequence () != null) { +this.getDataset ().addSequence (snew.getDatasetSequence ()); +} else { +var adding = snew.deriveSequence (); +this.getDataset ().addSequence (adding.getDatasetSequence ()); +snew = adding; +}}if (this.sequences == null) { +this.initAlignment ( Clazz.newArray (-1, [snew])); +} else { +{ +this.sequences.add (snew); +}}if (this.hiddenSequences != null) { +this.hiddenSequences.adjustHeightSequenceAdded (); +}}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "setSequenceAt", +function (i, snew) { +{ +this.deleteSequence (i); +this.sequences.set (i, snew); +}}, "~N,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getGroups", +function () { +return this.groups; +}); +Clazz.overrideMethod (c$, "finalize", +function () { +if (this.getDataset () != null) { +this.getDataset ().removeAlignmentRef (); +}this.dataset = null; +this.sequences = null; +this.groups = null; +this.annotations = null; +this.hiddenSequences = null; +}); +Clazz.defineMethod (c$, "removeAlignmentRef", +($fz = function () { +if (--this.alignmentRefs == 0) { +this.finalize (); +}}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "deleteSequence", +function (s) { +this.deleteSequence (this.findIndex (s)); +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "deleteSequence", +function (i) { +if (i > -1 && i < this.getHeight ()) { +{ +this.sequences.remove (i); +this.hiddenSequences.adjustHeightSequenceDeleted (i); +}}}, "~N"); +Clazz.overrideMethod (c$, "findGroup", +function (s) { +{ +for (var i = 0; i < this.groups.size (); i++) { +var sg = this.groups.get (i); +if (sg.getSequences (null).contains (s)) { +return sg; +}} +}return null; +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "findAllGroups", +function (s) { +var temp = new java.util.ArrayList (); +{ +var gSize = this.groups.size (); +for (var i = 0; i < gSize; i++) { +var sg = this.groups.get (i); +if (sg == null || sg.getSequences () == null) { +this.deleteGroup (sg); +gSize--; +continue; +}if (sg.getSequences ().contains (s)) { +temp.add (sg); +}} +}var ret = new Array (temp.size ()); +return temp.toArray (ret); +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "addGroup", +function (sg) { +{ +if (!this.groups.contains (sg)) { +if (this.hiddenSequences.getSize () > 0) { +var i; +var iSize = sg.getSize (); +for (i = 0; i < iSize; i++) { +if (!this.sequences.contains (sg.getSequenceAt (i))) { +sg.deleteSequence (sg.getSequenceAt (i), false); +iSize--; +i--; +}} +if (sg.getSize () < 1) { +return; +}}sg.setContext (this); +this.groups.add (sg); +}}}, "jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "removeAnnotationForGroup", +($fz = function (gp) { +if (this.annotations == null || this.annotations.length == 0) { +return; +}var t; +var todelete = new Array (this.annotations.length); +var tokeep = new Array (this.annotations.length); +var i; +var p; +var k; +if (gp == null) { +for (i = 0, p = 0, k = 0; i < this.annotations.length; i++) { +if (this.annotations[i].groupRef != null) { +todelete[p++] = this.annotations[i]; +} else { +tokeep[k++] = this.annotations[i]; +}} +} else { +for (i = 0, p = 0, k = 0; i < this.annotations.length; i++) { +if (this.annotations[i].groupRef === gp) { +todelete[p++] = this.annotations[i]; +} else { +tokeep[k++] = this.annotations[i]; +}} +}if (p > 0) { +for (i = 0; i < p; i++) { +this.unhookAnnotation (todelete[i]); +todelete[i] = null; +} +t = new Array (k); +for (i = 0; i < k; i++) { +t[i] = tokeep[i]; +} +this.annotations = t; +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceGroup"); +Clazz.overrideMethod (c$, "deleteAllGroups", +function () { +{ +if (this.annotations != null) { +this.removeAnnotationForGroup (null); +}for (var sg, $sg = this.groups.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +sg.setContext (null); +} +this.groups.clear (); +}}); +Clazz.overrideMethod (c$, "deleteGroup", +function (g) { +{ +if (this.groups.contains (g)) { +this.removeAnnotationForGroup (g); +this.groups.remove (g); +g.setContext (null); +}}}, "jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "findName", +function (name) { +return this.findName (name, false); +}, "~S"); +Clazz.defineMethod (c$, "findName", +function (token, b) { +return this.findName (null, token, b); +}, "~S,~B"); +Clazz.defineMethod (c$, "findName", +function (startAfter, token, b) { +var i = 0; +var sq = null; +var sqname = null; +if (startAfter != null) { +var matched = false; +while (i < this.sequences.size ()) { +if (this.getSequenceAt (i++) === startAfter) { +matched = true; +break; +}} +if (!matched) { +i = 0; +}}while (i < this.sequences.size ()) { +sq = this.getSequenceAt (i); +sqname = sq.getName (); +if (sqname.equals (token) || (b && (sqname.equalsIgnoreCase (token)))) { +return this.getSequenceAt (i); +}i++; +} +return null; +}, "jalview.datamodel.SequenceI,~S,~B"); +Clazz.overrideMethod (c$, "findSequenceMatch", +function (name) { +var matches = new java.util.Vector (); +var i = 0; +while (i < this.sequences.size ()) { +if (this.getSequenceAt (i).getName ().equals (name)) { +matches.addElement (this.getSequenceAt (i)); +}i++; +} +var result = new Array (matches.size ()); +for (i = 0; i < result.length; i++) { +result[i] = matches.elementAt (i); +} +return result; +}, "~S"); +Clazz.defineMethod (c$, "findIndex", +function (s) { +var i = 0; +while (i < this.sequences.size ()) { +if (s === this.getSequenceAt (i)) { +return i; +}i++; +} +return -1; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "findIndex", +function (results) { +var i = 0; +while (i < this.sequences.size ()) { +if (results.involvesSequence (this.getSequenceAt (i))) { +return i; +}i++; +} +return -1; +}, "jalview.datamodel.SearchResults"); +Clazz.overrideMethod (c$, "getHeight", +function () { +return this.sequences.size (); +}); +Clazz.overrideMethod (c$, "getWidth", +function () { +var maxLength = -1; +for (var i = 0; i < this.sequences.size (); i++) { +if (this.getSequenceAt (i).getLength () > maxLength) { +maxLength = this.getSequenceAt (i).getLength (); +}} +return maxLength; +}); +Clazz.overrideMethod (c$, "setGapCharacter", +function (gc) { +this.gapCharacter = gc; +{ +for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +seq.setSequence (seq.getSequenceAsString ().$replace ('.', gc).$replace ('-', gc).$replace (' ', gc)); +} +}}, "~S"); +Clazz.defineMethod (c$, "getGapCharacter", +function () { +return this.gapCharacter; +}); +Clazz.defineMethod (c$, "isAligned", +function () { +return this.isAligned (false); +}); +Clazz.defineMethod (c$, "isAligned", +function (includeHidden) { +var width = this.getWidth (); +if (this.hiddenSequences == null || this.hiddenSequences.getSize () == 0) { +includeHidden = true; +}for (var i = 0; i < this.sequences.size (); i++) { +if (includeHidden || !this.hiddenSequences.isHidden (this.getSequenceAt (i))) { +if (this.getSequenceAt (i).getLength () != width) { +return false; +}}} +return true; +}, "~B"); +Clazz.overrideMethod (c$, "deleteAllAnnotations", +function (includingAutoCalculated) { +var result = false; +for (var alan, $alan = 0, $$alan = this.getAlignmentAnnotation (); $alan < $$alan.length && ((alan = $$alan[$alan]) || true); $alan++) { +if (!alan.autoCalculated || includingAutoCalculated) { +this.deleteAnnotation (alan); +result = true; +}} +return result; +}, "~B"); +Clazz.defineMethod (c$, "deleteAnnotation", +function (aa) { +return this.deleteAnnotation (aa, true); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "deleteAnnotation", +function (aa, unhook) { +var aSize = 1; +if (this.annotations != null) { +aSize = this.annotations.length; +}if (aSize < 1) { +return false; +}var temp = new Array (aSize - 1); +var swap = false; +var tIndex = 0; +for (var i = 0; i < aSize; i++) { +if (this.annotations[i] === aa) { +swap = true; +continue; +}if (tIndex < temp.length) { +temp[tIndex++] = this.annotations[i]; +}} +if (swap) { +this.annotations = temp; +if (unhook) { +this.unhookAnnotation (aa); +}}return swap; +}, "jalview.datamodel.AlignmentAnnotation,~B"); +Clazz.defineMethod (c$, "unhookAnnotation", +($fz = function (aa) { +if (aa.sequenceRef != null) { +aa.sequenceRef.removeAlignmentAnnotation (aa); +}if (aa.groupRef != null) { +aa.groupRef = null; +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "addAnnotation", +function (aa) { +this.addAnnotation (aa, -1); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "addAnnotation", +function (aa, pos) { +if (aa.getRNAStruc () != null) { +this.$hasRNAStructure = true; +}var aSize = 1; +if (this.annotations != null) { +aSize = this.annotations.length + 1; +}var temp = new Array (aSize); +var i = 0; +if (pos == -1 || pos >= aSize) { +temp[aSize - 1] = aa; +} else { +temp[pos] = aa; +}if (aSize > 1) { +var p = 0; +for (i = 0; i < (aSize - 1); i++, p++) { +if (p == pos) { +p++; +}if (p < temp.length) { +temp[p] = this.annotations[i]; +}} +}this.annotations = temp; +}, "jalview.datamodel.AlignmentAnnotation,~N"); +Clazz.overrideMethod (c$, "setAnnotationIndex", +function (aa, index) { +if (aa == null || this.annotations == null || this.annotations.length - 1 < index) { +return; +}var aSize = this.annotations.length; +var temp = new Array (aSize); +temp[index] = aa; +for (var i = 0; i < aSize; i++) { +if (i == index) { +continue; +}if (i < index) { +temp[i] = this.annotations[i]; +} else { +temp[i] = this.annotations[i - 1]; +}} +this.annotations = temp; +}, "jalview.datamodel.AlignmentAnnotation,~N"); +Clazz.defineMethod (c$, "getAlignmentAnnotation", +function () { +return this.annotations; +}); +Clazz.overrideMethod (c$, "setNucleotide", +function (b) { +if (b) { +this.type = 1; +} else { +this.type = 0; +}}, "~B"); +Clazz.defineMethod (c$, "isNucleotide", +function () { +if (this.type == 1) { +return true; +} else { +return false; +}}); +Clazz.overrideMethod (c$, "hasRNAStructure", +function () { +return this.$hasRNAStructure; +}); +Clazz.overrideMethod (c$, "setDataset", +function (data) { +if (this.dataset == null && data == null) { +var seqs = new Array (this.getHeight ()); +var currentSeq; +for (var i = 0; i < this.getHeight (); i++) { +currentSeq = this.getSequenceAt (i); +if (currentSeq.getDatasetSequence () != null) { +seqs[i] = currentSeq.getDatasetSequence (); +} else { +seqs[i] = currentSeq.createDatasetSequence (); +}} +this.dataset = new jalview.datamodel.Alignment (seqs); +} else if (this.dataset == null && data != null) { +this.dataset = data; +for (var i = 0; i < this.getHeight (); i++) { +var currentSeq = this.getSequenceAt (i); +var dsq = currentSeq.getDatasetSequence (); +if (dsq == null) { +dsq = currentSeq.createDatasetSequence (); +this.dataset.addSequence (dsq); +} else { +while (dsq.getDatasetSequence () != null) { +dsq = dsq.getDatasetSequence (); +} +if (this.dataset.findIndex (dsq) == -1) { +this.dataset.addSequence (dsq); +}}} +}this.dataset.addAlignmentRef (); +}, "jalview.datamodel.Alignment"); +Clazz.defineMethod (c$, "addAlignmentRef", +($fz = function () { +this.alignmentRefs++; +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "getDataset", +function () { +return this.dataset; +}); +Clazz.overrideMethod (c$, "padGaps", +function () { +var modified = false; +var maxLength = -1; +var current; +for (var i = 0; i < this.sequences.size (); i++) { +current = this.getSequenceAt (i); +for (var j = current.getLength (); j > maxLength; j--) { +if (j > maxLength && !jalview.util.Comparison.isGap (current.getCharAt (j))) { +maxLength = j; +break; +}} +} +maxLength++; +var cLength; +for (var i = 0; i < this.sequences.size (); i++) { +current = this.getSequenceAt (i); +cLength = current.getLength (); +if (cLength < maxLength) { +current.insertCharAt (cLength, maxLength - cLength, this.gapCharacter); +modified = true; +} else if (current.getLength () > maxLength) { +current.deleteChars (maxLength, current.getLength ()); +}} +return modified; +}); +Clazz.overrideMethod (c$, "justify", +function (right) { +var modified = false; +var maxLength = -1; +var ends = Clazz.newIntArray (this.sequences.size () * 2, 0); +var current; +for (var i = 0; i < this.sequences.size (); i++) { +current = this.getSequenceAt (i); +ends[i * 2] = current.findIndex (current.getStart ()); +ends[i * 2 + 1] = current.findIndex (current.getStart () + current.getLength ()); +var hitres = false; +for (var j = 0, rs = 0, ssiz = current.getLength (); j < ssiz; j++) { +if (!jalview.util.Comparison.isGap (current.getCharAt (j))) { +if (!hitres) { +ends[i * 2] = j; +hitres = true; +} else { +ends[i * 2 + 1] = j; +if (j - ends[i * 2] > maxLength) { +maxLength = j - ends[i * 2]; +}}}} +} +maxLength++; +var cLength; +var extent; +var diff; +for (var i = 0; i < this.sequences.size (); i++) { +current = this.getSequenceAt (i); +cLength = 1 + ends[i * 2 + 1] - ends[i * 2]; +diff = maxLength - cLength; +extent = current.getLength (); +if (right) { +if (extent > ends[i * 2 + 1]) { +current.deleteChars (ends[i * 2 + 1] + 1, extent); +modified = true; +}if (ends[i * 2] > diff) { +current.deleteChars (0, ends[i * 2] - diff); +modified = true; +} else { +if (ends[i * 2] < diff) { +current.insertCharAt (0, diff - ends[i * 2], this.gapCharacter); +modified = true; +}}} else { +if (ends[i * 2] > 0) { +current.deleteChars (0, ends[i * 2]); +modified = true; +ends[i * 2 + 1] -= ends[i * 2]; +extent -= ends[i * 2]; +}if (extent > maxLength) { +current.deleteChars (maxLength + 1, extent); +modified = true; +} else { +if (extent < maxLength) { +current.insertCharAt (extent, maxLength - extent, this.gapCharacter); +modified = true; +}}}} +return modified; +}, "~B"); +Clazz.defineMethod (c$, "getHiddenSequences", +function () { +return this.hiddenSequences; +}); +Clazz.overrideMethod (c$, "getCompactAlignment", +function () { +{ +var alseqs = new Array (this.sequences.size ()); +var i = 0; +for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +alseqs[i++] = new jalview.datamodel.SeqCigar (seq); +} +var cal = new jalview.datamodel.CigarArray (alseqs); +cal.addOperation ('M', this.getWidth ()); +return cal; +}}); +Clazz.overrideMethod (c$, "setProperty", +function (key, value) { +if (this.alignmentProperties == null) { +this.alignmentProperties = new java.util.Hashtable (); +}this.alignmentProperties.put (key, value); +}, "~O,~O"); +Clazz.defineMethod (c$, "getProperty", +function (key) { +if (this.alignmentProperties != null) { +return this.alignmentProperties.get (key); +} else { +return null; +}}, "~O"); +Clazz.defineMethod (c$, "getProperties", +function () { +return this.alignmentProperties; +}); +Clazz.overrideMethod (c$, "addCodonFrame", +function (codons) { +if (codons != null) { +this.codonFrameList.add (codons); +}}, "jalview.datamodel.AlignedCodonFrame"); +Clazz.overrideMethod (c$, "getCodonFrame", +function (seq) { +if (seq == null) { +return null; +}var cframes = new java.util.ArrayList (); +for (var acf, $acf = this.codonFrameList.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +if (acf.involvesSequence (seq)) { +cframes.add (acf); +}} +return cframes; +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "setCodonFrames", +function (acfs) { +this.codonFrameList = acfs; +}, "java.util.Set"); +Clazz.defineMethod (c$, "getCodonFrames", +function () { +return this.codonFrameList; +}); +Clazz.overrideMethod (c$, "removeCodonFrame", +function (codons) { +if (codons == null || this.codonFrameList == null) { +return false; +}return this.codonFrameList.remove (codons); +}, "jalview.datamodel.AlignedCodonFrame"); +Clazz.overrideMethod (c$, "append", +function (toappend) { +if (toappend === this) { +System.err.println ("Self append may cause a deadlock."); +}var samegap = toappend.getGapCharacter () == this.getGapCharacter (); +var oldc = toappend.getGapCharacter (); +var hashidden = toappend.getHiddenSequences () != null && toappend.getHiddenSequences ().hiddenSequences != null; +var sqs = (hashidden) ? toappend.getHiddenSequences ().getFullAlignment ().getSequences () : toappend.getSequences (); +if (sqs != null) { +{ +for (var addedsq, $addedsq = sqs.iterator (); $addedsq.hasNext () && ((addedsq = $addedsq.next ()) || true);) { +if (!samegap) { +var oldseq = addedsq.getSequence (); +for (var c = 0; c < oldseq.length; c++) { +if (oldseq[c] == oldc) { +oldseq[c] = this.gapCharacter; +}} +}this.addSequence (addedsq); +} +}}var alan = toappend.getAlignmentAnnotation (); +for (var a = 0; alan != null && a < alan.length; a++) { +this.addAnnotation (alan[a]); +} +this.codonFrameList.addAll (toappend.getCodonFrames ()); +var sg = toappend.getGroups (); +if (sg != null) { +for (var _sg, $_sg = sg.iterator (); $_sg.hasNext () && ((_sg = $_sg.next ()) || true);) { +this.addGroup (_sg); +} +}if (toappend.getHiddenSequences () != null) { +var hs = toappend.getHiddenSequences (); +if (this.hiddenSequences == null) { +this.hiddenSequences = new jalview.datamodel.HiddenSequences (this); +}if (hs.hiddenSequences != null) { +for (var s = 0; s < hs.hiddenSequences.length; s++) { +if (hs.hiddenSequences[s] != null) { +this.hiddenSequences.hideSequence (hs.hiddenSequences[s]); +}} +}}if (toappend.getProperties () != null) { +var key = toappend.getProperties ().keys (); +while (key.hasMoreElements ()) { +var k = key.nextElement (); +var ourval = this.getProperty (k); +var toapprop = toappend.getProperty (k); +if (ourval != null) { +if (ourval.getClass ().equals (toapprop.getClass ()) && !ourval.equals (toapprop)) { +if (Clazz.instanceOf (ourval, String)) { +this.setProperty (k, (ourval) + "; " + (toapprop)); +} else { +if (Clazz.instanceOf (ourval, java.util.Vector)) { +var theirv = (toapprop).elements (); +while (theirv.hasMoreElements ()) { +(ourval).addElement (theirv); +} +}}}} else { +this.setProperty (k, toapprop); +}} +}}, "jalview.datamodel.AlignmentI"); +Clazz.overrideMethod (c$, "findOrCreateAnnotation", +function (name, calcId, autoCalc, seqRef, groupRef) { +if (this.annotations != null) { +for (var annot, $annot = 0, $$annot = this.getAlignmentAnnotation (); $annot < $$annot.length && ((annot = $$annot[$annot]) || true); $annot++) { +if (annot.autoCalculated == autoCalc && (name.equals (annot.label)) && (calcId == null || annot.getCalcId ().equals (calcId)) && annot.sequenceRef === seqRef && annot.groupRef === groupRef) { +return annot; +}} +}var annot = new jalview.datamodel.AlignmentAnnotation (name, name, new Array (1), 0, 0, 1); +annot.hasText = false; +annot.setCalcId ( String.instantialize (calcId)); +annot.autoCalculated = autoCalc; +if (seqRef != null) { +annot.setSequenceRef (seqRef); +}annot.groupRef = groupRef; +this.addAnnotation (annot); +return annot; +}, "~S,~S,~B,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); +Clazz.overrideMethod (c$, "findAnnotation", +function (calcId) { +var aa = new java.util.ArrayList (); +for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) { +if (a.getCalcId () === calcId || (a.getCalcId () != null && calcId != null && a.getCalcId ().equals (calcId))) { +aa.add (a); +}} +return aa; +}, "~S"); +Clazz.overrideMethod (c$, "findAnnotations", +function (seq, calcId, label) { +var aa = new java.util.ArrayList (); +for (var ann, $ann = 0, $$ann = this.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { +if (ann.getCalcId () != null && ann.getCalcId ().equals (calcId) && ann.sequenceRef != null && ann.sequenceRef === seq && ann.label != null && ann.label.equals (label)) { +aa.add (ann); +}} +return aa; +}, "jalview.datamodel.SequenceI,~S,~S"); +Clazz.overrideMethod (c$, "moveSelectedSequencesByOne", +function (sg, map, up) { +{ +if (up) { +for (var i = 1, iSize = this.sequences.size (); i < iSize; i++) { +var seq = this.sequences.get (i); +if (!sg.getSequences (map).contains (seq)) { +continue; +}var temp = this.sequences.get (i - 1); +if (sg.getSequences (null).contains (temp)) { +continue; +}this.sequences.set (i, temp); +this.sequences.set (i - 1, seq); +} +} else { +for (var i = this.sequences.size () - 2; i > -1; i--) { +var seq = this.sequences.get (i); +if (!sg.getSequences (map).contains (seq)) { +continue; +}var temp = this.sequences.get (i + 1); +if (sg.getSequences (map).contains (temp)) { +continue; +}this.sequences.set (i, temp); +this.sequences.set (i + 1, seq); +} +}}}, "jalview.datamodel.SequenceGroup,java.util.Map,~B"); +Clazz.overrideMethod (c$, "validateAnnotation", +function (alignmentAnnotation) { +alignmentAnnotation.validateRangeAndDisplay (); +if (this.isNucleotide () && alignmentAnnotation.isValidStruc ()) { +this.$hasRNAStructure = true; +}}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.overrideMethod (c$, "getSeqrep", +function () { +return this.seqrep; +}); +Clazz.overrideMethod (c$, "setSeqrep", +function (seqrep) { +this.seqrep = seqrep; +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "hasSeqrep", +function () { +return this.seqrep != null; +}); +Clazz.overrideMethod (c$, "getEndRes", +function () { +return this.getWidth () - 1; +}); +Clazz.overrideMethod (c$, "getStartRes", +function () { +return 0; +}); +Clazz.overrideMethod (c$, "getContext", +function () { +return this.dataset; +}); +Clazz.defineMethod (c$, "alignAs", +function (al) { +return this.alignAs (al, false, true); +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "alignAs", +function (al, preserveMappedGaps, preserveUnmappedGaps) { +var count = 0; +var thisIsNucleotide = this.isNucleotide (); +var thatIsProtein = !al.isNucleotide (); +if (!thatIsProtein && !thisIsNucleotide) { +return jalview.analysis.AlignmentUtils.alignProteinAsDna (this, al); +}var thisGapChar = this.getGapCharacter (); +var gap = thisIsNucleotide && thatIsProtein ? String.valueOf ( Clazz.newCharArray (-1, [thisGapChar, thisGapChar, thisGapChar])) : String.valueOf (thisGapChar); +for (var alignTo, $alignTo = this.getSequences ().iterator (); $alignTo.hasNext () && ((alignTo = $alignTo.next ()) || true);) { +count += jalview.analysis.AlignmentUtils.alignSequenceAs (alignTo, al, gap, preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0; +} +return count; +}, "jalview.datamodel.AlignmentI,~B,~B"); +Clazz.overrideMethod (c$, "getSequenceNames", +function () { +var names = new java.util.HashSet (); +for (var seq, $seq = this.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +names.add (seq.getName ()); +} +return names; +}); +Clazz.overrideMethod (c$, "toString", +function () { +var seq = this.getSequencesArray (); +{ +return "" + JSON.stringify(seq); +}}); +Clazz.defineStatics (c$, +"PROTEIN", 0, +"NUCLEOTIDE", 1); +}); diff --git a/bin/jalview/datamodel/AlignmentAnnotation.class b/bin/jalview/datamodel/AlignmentAnnotation.class index 840fdf1..88e30db 100644 Binary files a/bin/jalview/datamodel/AlignmentAnnotation.class and b/bin/jalview/datamodel/AlignmentAnnotation.class differ diff --git a/bin/jalview/datamodel/AlignmentAnnotation.js b/bin/jalview/datamodel/AlignmentAnnotation.js index 0be7f1c..e321a8d 100644 --- a/bin/jalview/datamodel/AlignmentAnnotation.js +++ b/bin/jalview/datamodel/AlignmentAnnotation.js @@ -1,623 +1,623 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.util.HashMap"], "jalview.datamodel.AlignmentAnnotation", ["jalview.analysis.Rna", "jalview.datamodel.Annotation", "$.GraphLine", "jalview.schemes.ResidueProperties", "java.lang.Double", "$.Error", "$.Long", "$.StringBuffer", "$.StringBuilder", "java.util.Collections"], function () { -c$ = Clazz.decorateAsClass (function () { -this.autoCalculated = false; -this.annotationId = null; -this.sequenceRef = null; -this.label = null; -this.description = null; -this.annotations = null; -this.bps = null; -this._rnasecstr = null; -this.invalidrnastruc = -2; -this.sequenceMapping = null; -this.graphMin = 0; -this.graphMax = 0; -this.score = NaN; -this.$hasScore = false; -this.threshold = null; -this.editable = false; -this.hasIcons = false; -this.hasText = false; -this.visible = true; -this.graphGroup = -1; -this.height = 0; -this.graph = 0; -this.graphHeight = 40; -this.padGaps = false; -this.belowAlignment = true; -this.groupRef = null; -this.showAllColLabels = false; -this.scaleColLabel = false; -this.centreColLabels = false; -this.isrna = false; -if (!Clazz.isClassDefined ("jalview.datamodel.AlignmentAnnotation.AnnotCharSequence")) { -jalview.datamodel.AlignmentAnnotation.$AlignmentAnnotation$AnnotCharSequence$ (); -} -this._lastrnaannot = -1; -this.calcId = ""; -this.properties = null; -this._linecolour = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "AlignmentAnnotation"); -Clazz.prepareFields (c$, function () { -this.properties = new java.util.HashMap (); -}); -Clazz.defineMethod (c$, "_updateRnaSecStr", -($fz = function (RNAannot) { -try { -this._rnasecstr = jalview.analysis.Rna.GetBasePairs (RNAannot); -this.bps = jalview.analysis.Rna.GetModeleBP (RNAannot); -this.invalidrnastruc = -1; -} catch (px) { -if (Clazz.exceptionOf (px, jalview.analysis.WUSSParseException)) { -this.invalidrnastruc = px.getProblemPos (); -} else { -throw px; -} -} -if (this.invalidrnastruc > -1) { -return; -}jalview.analysis.Rna.HelixMap (this._rnasecstr); -if (this._rnasecstr != null && this._rnasecstr.length > 0) { -this.isrna = true; -this.showAllColLabels = true; -this.scaleColLabel = true; -this._markRnaHelices (); -}}, $fz.isPrivate = true, $fz), "CharSequence"); -Clazz.defineMethod (c$, "_markRnaHelices", -($fz = function () { -var mxval = 0; -for (var x = 0; x < this._rnasecstr.length; x++) { -var val = 0; -try { -val = (Integer.$valueOf (this._rnasecstr[x].getFeatureGroup ())).intValue (); -if (mxval < val) { -mxval = val; -}} catch (q) { -if (Clazz.exceptionOf (q, NumberFormatException)) { -} else { -throw q; -} -} -;this.annotations[this._rnasecstr[x].getBegin ()].value = val; -this.annotations[this._rnasecstr[x].getEnd ()].value = val; -} -this.setScore (mxval); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "finalize", -function () { -this.sequenceRef = null; -this.groupRef = null; -Clazz.superCall (this, jalview.datamodel.AlignmentAnnotation, "finalize", []); -}); -c$.getGraphValueFromString = Clazz.defineMethod (c$, "getGraphValueFromString", -function (string) { -if (string.equalsIgnoreCase ("BAR_GRAPH")) { -return 1; -} else if (string.equalsIgnoreCase ("LINE_GRAPH")) { -return 2; -} else { -return 0; -}}, "~S"); -Clazz.defineMethod (c$, "ConcenStru", -function (RNAannot) { -this.bps = jalview.analysis.Rna.GetModeleBP (RNAannot); -}, "CharSequence"); -Clazz.makeConstructor (c$, -function (label, description, annotations) { -this.setAnnotationId (); -this.editable = true; -this.label = label; -this.description = description; -this.annotations = annotations; -this.validateRangeAndDisplay (); -}, "~S,~S,~A"); -Clazz.defineMethod (c$, "areLabelsSecondaryStructure", -function () { -var nonSSLabel = false; -this.isrna = false; -var rnastring = new StringBuffer (); -var firstChar = String.fromCharCode (0); -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] == null) { -continue; -}if (this.annotations[i].secondaryStructure == 'H' || this.annotations[i].secondaryStructure == 'E') { -this.hasIcons = new Boolean (this.hasIcons | true).valueOf (); -} else { -if (this.annotations[i].secondaryStructure == '(' || this.annotations[i].secondaryStructure == '[' || this.annotations[i].secondaryStructure == '<' || this.annotations[i].secondaryStructure == '{' || this.annotations[i].secondaryStructure == 'A' || this.annotations[i].secondaryStructure == 'B' || this.annotations[i].secondaryStructure == 'C' || this.annotations[i].secondaryStructure == 'D' || this.annotations[i].secondaryStructure == 'E' || this.annotations[i].secondaryStructure == 'F' || this.annotations[i].secondaryStructure == 'G' || this.annotations[i].secondaryStructure == 'H' || this.annotations[i].secondaryStructure == 'I' || this.annotations[i].secondaryStructure == 'J' || this.annotations[i].secondaryStructure == 'K' || this.annotations[i].secondaryStructure == 'L' || this.annotations[i].secondaryStructure == 'M' || this.annotations[i].secondaryStructure == 'N' || this.annotations[i].secondaryStructure == 'O' || this.annotations[i].secondaryStructure == 'P' || this.annotations[i].secondaryStructure == 'Q' || this.annotations[i].secondaryStructure == 'R' || this.annotations[i].secondaryStructure == 'S' || this.annotations[i].secondaryStructure == 'T' || this.annotations[i].secondaryStructure == 'U' || this.annotations[i].secondaryStructure == 'V' || this.annotations[i].secondaryStructure == 'W' || this.annotations[i].secondaryStructure == 'X' || this.annotations[i].secondaryStructure == 'Y' || this.annotations[i].secondaryStructure == 'Z') { -this.hasIcons = new Boolean (this.hasIcons | true).valueOf (); -this.isrna = new Boolean (this.isrna | true).valueOf (); -}}if (this.annotations[i].displayCharacter == null || this.annotations[i].displayCharacter.length == 0) { -rnastring.append ('.'); -continue; -}if (this.annotations[i].displayCharacter.length == 1) { -firstChar = this.annotations[i].displayCharacter.charAt (0); -if (this.annotations[i].secondaryStructure != ' ' && !this.hasIcons && firstChar != ' ' && firstChar != '$' && firstChar.charCodeAt (0) != 0xCE && firstChar != '(' && firstChar != '[' && firstChar != '>' && firstChar != '{' && firstChar != 'A' && firstChar != 'B' && firstChar != 'C' && firstChar != 'D' && firstChar != 'E' && firstChar != 'F' && firstChar != 'G' && firstChar != 'H' && firstChar != 'I' && firstChar != 'J' && firstChar != 'K' && firstChar != 'L' && firstChar != 'M' && firstChar != 'N' && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q' && firstChar != 'R' && firstChar != 'S' && firstChar != 'T' && firstChar != 'U' && firstChar != 'V' && firstChar != 'W' && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z' && firstChar != '-' && firstChar.charCodeAt (0) < jalview.schemes.ResidueProperties.aaIndex.length) { -if (jalview.schemes.ResidueProperties.aaIndex[firstChar.charCodeAt (0)] < 23) { -nonSSLabel = true; -}}} else { -rnastring.append (this.annotations[i].displayCharacter.charAt (1)); -}if (this.annotations[i].displayCharacter.length > 0) { -this.hasText = true; -}} -if (nonSSLabel) { -this.hasIcons = false; -for (var j = 0; j < this.annotations.length; j++) { -if (this.annotations[j] != null && this.annotations[j].secondaryStructure != ' ') { -this.annotations[j].displayCharacter = String.valueOf (this.annotations[j].secondaryStructure); -this.annotations[j].secondaryStructure = ' '; -}} -} else { -if (this.isrna) { -this._updateRnaSecStr (Clazz.innerTypeInstance (jalview.datamodel.AlignmentAnnotation.AnnotCharSequence, this, null)); -}}}); -Clazz.defineMethod (c$, "getRNAStruc", -function () { -if (this.isrna) { -var rnastruc = Clazz.innerTypeInstance (jalview.datamodel.AlignmentAnnotation.AnnotCharSequence, this, null).toString (); -if (this._lastrnaannot != rnastruc.hashCode ()) { -this._lastrnaannot = rnastruc.hashCode (); -this._updateRnaSecStr (rnastruc); -}return rnastruc; -}return null; -}); -Clazz.makeConstructor (c$, -function (label, description, annotations, min, max, graphType) { -this.setAnnotationId (); -this.editable = graphType == 0; -this.label = label; -this.description = description; -this.annotations = annotations; -this.graph = graphType; -this.graphMin = min; -this.graphMax = max; -this.validateRangeAndDisplay (); -}, "~S,~S,~A,~N,~N,~N"); -Clazz.defineMethod (c$, "validateRangeAndDisplay", -function () { -if (this.annotations == null) { -this.visible = false; -return; -}var graphType = this.graph; -var min = this.graphMin; -var max = this.graphMax; -var drawValues = true; -this._linecolour = null; -if (min == max) { -min = 999999999; -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] == null) { -continue; -}if (drawValues && this.annotations[i].displayCharacter != null && this.annotations[i].displayCharacter.length > 1) { -drawValues = false; -}if (this.annotations[i].value > max) { -max = this.annotations[i].value; -}if (this.annotations[i].value < min) { -min = this.annotations[i].value; -}if (this._linecolour == null && this.annotations[i].colour != null) { -this._linecolour = this.annotations[i].colour; -}} -if (min > 0) { -min = 0; -} else { -if (max < 0) { -max = 0; -}}}this.graphMin = min; -this.graphMax = max; -this.areLabelsSecondaryStructure (); -if (!drawValues && graphType != 0) { -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] != null) { -this.annotations[i].displayCharacter = ""; -}} -}}); -Clazz.makeConstructor (c$, -function (annotation) { -this.setAnnotationId (); -this.label = String.instantialize (annotation.label); -if (annotation.description != null) { -this.description = String.instantialize (annotation.description); -}this.graphMin = annotation.graphMin; -this.graphMax = annotation.graphMax; -this.graph = annotation.graph; -this.graphHeight = annotation.graphHeight; -this.graphGroup = annotation.graphGroup; -this.groupRef = annotation.groupRef; -this.editable = annotation.editable; -this.autoCalculated = annotation.autoCalculated; -this.hasIcons = annotation.hasIcons; -this.hasText = annotation.hasText; -this.height = annotation.height; -this.label = annotation.label; -this.padGaps = annotation.padGaps; -this.visible = annotation.visible; -this.centreColLabels = annotation.centreColLabels; -this.scaleColLabel = annotation.scaleColLabel; -this.showAllColLabels = annotation.showAllColLabels; -this.calcId = annotation.calcId; -if (annotation.properties != null) { -this.properties = new java.util.HashMap (); -for (var val, $val = annotation.properties.entrySet ().iterator (); $val.hasNext () && ((val = $val.next ()) || true);) { -this.properties.put (val.getKey (), val.getValue ()); -} -}if (this.$hasScore = annotation.$hasScore) { -this.score = annotation.score; -}if (annotation.threshold != null) { -this.threshold = new jalview.datamodel.GraphLine (annotation.threshold); -}var ann = annotation.annotations; -if (annotation.annotations != null) { -this.annotations = new Array (ann.length); -for (var i = 0; i < ann.length; i++) { -if (ann[i] != null) { -this.annotations[i] = new jalview.datamodel.Annotation (ann[i]); -if (this._linecolour != null) { -this._linecolour = this.annotations[i].colour; -}}} -}if (annotation.sequenceRef != null) { -this.sequenceRef = annotation.sequenceRef; -if (annotation.sequenceMapping != null) { -var p = null; -this.sequenceMapping = new java.util.HashMap (); -var pos = annotation.sequenceMapping.keySet ().iterator (); -while (pos.hasNext ()) { -p = pos.next (); -var a = annotation.sequenceMapping.get (p); -if (a == null) { -continue; -}if (ann != null) { -for (var i = 0; i < ann.length; i++) { -if (ann[i] === a) { -this.sequenceMapping.put (p, this.annotations[i]); -}} -}} -} else { -this.sequenceMapping = null; -}}{ -}this.validateRangeAndDisplay (); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "restrict", -function (startRes, endRes) { -if (this.annotations == null) { -return; -}if (startRes < 0) { -startRes = 0; -}if (startRes >= this.annotations.length) { -startRes = this.annotations.length - 1; -}if (endRes >= this.annotations.length) { -endRes = this.annotations.length - 1; -}if (this.annotations == null) { -return; -}var temp = new Array (endRes - startRes + 1); -if (startRes < this.annotations.length) { -System.arraycopy (this.annotations, startRes, temp, 0, endRes - startRes + 1); -}if (this.sequenceRef != null) { -var spos = this.sequenceRef.findPosition (startRes); -var epos = this.sequenceRef.findPosition (endRes); -if (this.sequenceMapping != null) { -var newmapping = new java.util.HashMap (); -var e = this.sequenceMapping.keySet ().iterator (); -while (e.hasNext ()) { -var pos = e.next (); -if (pos.intValue () >= spos && pos.intValue () <= epos) { -newmapping.put (pos, this.sequenceMapping.get (pos)); -}} -this.sequenceMapping.clear (); -this.sequenceMapping = newmapping; -}}this.annotations = temp; -}, "~N,~N"); -Clazz.defineMethod (c$, "padAnnotation", -function (length) { -if (this.annotations == null) { -return true; -}if (this.annotations.length < length) { -var na = new Array (length); -System.arraycopy (this.annotations, 0, na, 0, this.annotations.length); -this.annotations = na; -return true; -}return this.annotations.length > length; -}, "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -var buffer = new StringBuilder (256); -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] != null) { -if (this.graph != 0) { -buffer.append (this.annotations[i].value); -} else if (this.hasIcons) { -buffer.append (this.annotations[i].secondaryStructure); -} else { -buffer.append (this.annotations[i].displayCharacter); -}}buffer.append (", "); -} -if (this.label.indexOf ("Consensus") == 0) { -buffer.append ("\n"); -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] != null) { -buffer.append (this.annotations[i].description); -}buffer.append (", "); -} -}return buffer.toString (); -}); -Clazz.defineMethod (c$, "setThreshold", -function (line) { -this.threshold = line; -}, "jalview.datamodel.GraphLine"); -Clazz.defineMethod (c$, "getThreshold", -function () { -return this.threshold; -}); -Clazz.defineMethod (c$, "createSequenceMapping", -function (seqRef, startRes, alreadyMapped) { -if (seqRef == null) { -return; -}this.sequenceRef = seqRef; -if (this.annotations == null) { -return; -}this.sequenceMapping = new java.util.HashMap (); -var seqPos; -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] != null) { -if (alreadyMapped) { -seqPos = seqRef.findPosition (i); -} else { -seqPos = i + startRes; -}this.sequenceMapping.put ( new Integer (seqPos), this.annotations[i]); -}} -}, "jalview.datamodel.SequenceI,~N,~B"); -Clazz.defineMethod (c$, "adjustForAlignment", -function () { -if (this.sequenceRef == null) { -return; -}if (this.annotations == null) { -return; -}var a = 0; -var aSize = this.sequenceRef.getLength (); -if (aSize == 0) { -return; -}var position; -var temp = new Array (aSize); -var index; -for (a = this.sequenceRef.getStart (); a <= this.sequenceRef.getEnd (); a++) { -index = new Integer (a); -if (this.sequenceMapping.containsKey (index)) { -position = this.sequenceRef.findIndex (a) - 1; -temp[position] = this.sequenceMapping.get (index); -}} -this.annotations = temp; -}); -Clazz.defineMethod (c$, "compactAnnotationArray", -function () { -var i = 0; -var iSize = this.annotations.length; -while (i < iSize) { -if (this.annotations[i] == null) { -if (i + 1 < iSize) { -System.arraycopy (this.annotations, i + 1, this.annotations, i, iSize - i - 1); -}iSize--; -} else { -i++; -}} -var ann = this.annotations; -this.annotations = new Array (i); -System.arraycopy (ann, 0, this.annotations, 0, i); -ann = null; -return iSize; -}); -Clazz.defineMethod (c$, "setSequenceRef", -function (sequenceI) { -if (sequenceI != null) { -if (this.sequenceRef != null) { -var rIsDs = this.sequenceRef.getDatasetSequence () == null; -var tIsDs = sequenceI.getDatasetSequence () == null; -if (this.sequenceRef !== sequenceI && (rIsDs && !tIsDs && this.sequenceRef !== sequenceI.getDatasetSequence ()) && (!rIsDs && tIsDs && this.sequenceRef.getDatasetSequence () !== sequenceI) && (!rIsDs && !tIsDs && this.sequenceRef.getDatasetSequence () !== sequenceI.getDatasetSequence ()) && !this.sequenceRef.equals (sequenceI)) { -this.sequenceRef = null; -if (this.sequenceMapping != null) { -this.sequenceMapping = null; -}this.createSequenceMapping (sequenceI, 1, true); -this.adjustForAlignment (); -} else { -this.sequenceRef = sequenceI; -}} else { -this.createSequenceMapping (sequenceI, 1, true); -this.adjustForAlignment (); -}} else { -this.sequenceMapping = null; -this.sequenceRef = null; -}}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getScore", -function () { -return this.score; -}); -Clazz.defineMethod (c$, "setScore", -function (score) { -this.$hasScore = true; -this.score = score; -}, "~N"); -Clazz.defineMethod (c$, "hasScore", -function () { -return this.$hasScore || !Double.isNaN (this.score); -}); -Clazz.makeConstructor (c$, -function (label, description, score) { -this.construct (label, description, null); -this.setScore (score); -}, "~S,~S,~N"); -Clazz.makeConstructor (c$, -function (alignmentAnnotation, colSel) { -this.construct (alignmentAnnotation); -if (this.annotations == null) { -return; -}colSel.makeVisibleAnnotation (this); -}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.ColumnSelection"); -Clazz.defineMethod (c$, "setPadGaps", -function (padgaps, gapchar) { -this.padGaps = padgaps; -if (padgaps) { -this.hasText = true; -for (var i = 0; i < this.annotations.length; i++) { -if (this.annotations[i] == null) { -this.annotations[i] = new jalview.datamodel.Annotation (String.valueOf (gapchar), null, ' ', 0, null); -} else if (this.annotations[i].displayCharacter == null || this.annotations[i].displayCharacter.equals (" ")) { -this.annotations[i].displayCharacter = String.valueOf (gapchar); -}} -}}, "~B,~S"); -Clazz.defineMethod (c$, "getDescription", -function (seqname) { -if (seqname && this.sequenceRef != null) { -var i = this.description.toLowerCase ().indexOf (""); -if (i > -1) { -return "" + this.sequenceRef.getName () + " : " + this.description.substring (i + 6); -}return this.sequenceRef.getName () + " : " + this.description; -}return this.description; -}, "~B"); -Clazz.defineMethod (c$, "isValidStruc", -function () { -return this.invalidrnastruc == -1; -}); -Clazz.defineMethod (c$, "getInvalidStrucPos", -function () { -return this.invalidrnastruc; -}); -Clazz.defineMethod (c$, "getCalcId", -function () { -return this.calcId; -}); -Clazz.defineMethod (c$, "setCalcId", -function (calcId) { -this.calcId = calcId; -}, "~S"); -Clazz.defineMethod (c$, "isRNA", -function () { -return this.isrna; -}); -Clazz.defineMethod (c$, "liftOver", -function (sq, sp2sq) { -if (sp2sq.getMappedWidth () != sp2sq.getWidth ()) { -throw new Error ("liftOver currently not implemented for transfer of annotation between different types of seqeunce"); -}var mapIsTo = (sp2sq != null) ? (sp2sq.getTo () === sq || sp2sq.getTo () === sq.getDatasetSequence ()) : false; -var mapForsq = new java.util.HashMap (); -if (this.sequenceMapping != null) { -if (sp2sq != null) { -for (var ie, $ie = this.sequenceMapping.entrySet ().iterator (); $ie.hasNext () && ((ie = $ie.next ()) || true);) { -var mpos = Integer.$valueOf (mapIsTo ? sp2sq.getMappedPosition ((ie.getKey ()).intValue ()) : sp2sq.getPosition ((ie.getKey ()).intValue ())); -if ((mpos).intValue () >= sq.getStart () && (mpos).intValue () <= sq.getEnd ()) { -mapForsq.put (mpos, ie.getValue ()); -}} -this.sequenceMapping = mapForsq; -this.sequenceRef = sq; -this.adjustForAlignment (); -} else { -}}}, "jalview.datamodel.SequenceI,jalview.datamodel.Mapping"); -Clazz.defineMethod (c$, "remap", -function (newref, mapping, from, to, idxoffset) { -if (mapping != null) { -var old = this.sequenceMapping; -var remap = new java.util.HashMap (); -var index = -1; -for (var mp, $mp = 0, $$mp = mapping; $mp < $$mp.length && ((mp = $$mp[$mp]) || true); $mp++) { -if (index++ < 0) { -continue; -}var ann = null; -if (from == -1) { -ann = this.sequenceMapping.get (Integer.$valueOf (idxoffset + index)); -} else { -if (mp != null && mp.length > from) { -ann = this.sequenceMapping.get (Integer.$valueOf (mp[from])); -}}if (ann != null) { -if (to == -1) { -remap.put (Integer.$valueOf (idxoffset + index), ann); -} else { -if (to > -1 && to < mp.length) { -remap.put (Integer.$valueOf (mp[to]), ann); -}}}} -this.sequenceMapping = remap; -old.clear (); -if (newref != null) { -this.sequenceRef = newref; -}this.adjustForAlignment (); -}}, "jalview.datamodel.SequenceI,~A,~N,~N,~N"); -Clazz.defineMethod (c$, "getProperty", -function (property) { -if (this.properties == null) { -return null; -}return this.properties.get (property); -}, "~S"); -Clazz.defineMethod (c$, "setProperty", -function (property, value) { -if (this.properties == null) { -this.properties = new java.util.HashMap (); -}this.properties.put (property, value); -}, "~S,~S"); -Clazz.defineMethod (c$, "hasProperties", -function () { -return this.properties != null && this.properties.size () > 0; -}); -Clazz.defineMethod (c$, "getProperties", -function () { -if (this.properties == null) { -return java.util.Collections.emptyList (); -}return this.properties.keySet (); -}); -Clazz.defineMethod (c$, "getAnnotationForPosition", -function (position) { -return this.sequenceMapping == null ? null : this.sequenceMapping.get (new Integer (position)); -}, "~N"); -Clazz.defineMethod (c$, "setAnnotationId", -function () { -this.annotationId = "ann" + Long.toString (jalview.datamodel.AlignmentAnnotation.nextId ()); -}); -c$.nextId = Clazz.defineMethod (c$, "nextId", -function () { -return jalview.datamodel.AlignmentAnnotation.counter++; -}); -c$.$AlignmentAnnotation$AnnotCharSequence$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.offset = 0; -this.max = 0; -Clazz.instantialize (this, arguments); -}, jalview.datamodel.AlignmentAnnotation, "AnnotCharSequence", null, CharSequence); -Clazz.makeConstructor (c$, -function () { -this.construct (0, this.b$["jalview.datamodel.AlignmentAnnotation"].annotations.length); -}); -Clazz.makeConstructor (c$, -function (a, b) { -this.offset = a; -this.max = b; -}, "~N,~N"); -Clazz.overrideMethod (c$, "subSequence", -function (a, b) { -return Clazz.innerTypeInstance (jalview.datamodel.AlignmentAnnotation.AnnotCharSequence, this, null, this.offset + a, this.offset + b); -}, "~N,~N"); -Clazz.overrideMethod (c$, "length", -function () { -return this.max - this.offset; -}); -Clazz.overrideMethod (c$, "charAt", -function (a) { -return ((a + this.offset < 0) || (a + this.offset) >= this.max || this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset] == null || (this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].secondaryStructure <= ' ') ? ' ' : this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].displayCharacter == null || this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].displayCharacter.length == 0 ? this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].secondaryStructure : this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].displayCharacter.charAt (0)); -}, "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -var a = Clazz.newCharArray (this.max - this.offset, '\0'); -var b = this.b$["jalview.datamodel.AlignmentAnnotation"].annotations.length; -for (var c = this.offset; c < b; c++) { -a[c] = (this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c] == null || ((this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].secondaryStructure).charCodeAt (0) <= 32)) ? ' ' : (this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].displayCharacter == null || this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].displayCharacter.length == 0 ? this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].secondaryStructure : this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].displayCharacter.charAt (0)); -} -return String.instantialize (a); -}); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"ANNOTATION_ID_PREFIX", "ann", -"SEQUENCE_PROFILE", 0, -"STRUCTURE_PROFILE", 1, -"CDNA_PROFILE", 2, -"counter", 0, -"NO_GRAPH", 0, -"BAR_GRAPH", 1, -"LINE_GRAPH", 2); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.util.HashMap"], "jalview.datamodel.AlignmentAnnotation", ["jalview.analysis.Rna", "jalview.datamodel.Annotation", "$.GraphLine", "jalview.schemes.ResidueProperties", "java.lang.Double", "$.Error", "$.Long", "$.StringBuffer", "$.StringBuilder", "java.util.Collections"], function () { +c$ = Clazz.decorateAsClass (function () { +this.autoCalculated = false; +this.annotationId = null; +this.sequenceRef = null; +this.label = null; +this.description = null; +this.annotations = null; +this.bps = null; +this._rnasecstr = null; +this.invalidrnastruc = -2; +this.sequenceMapping = null; +this.graphMin = 0; +this.graphMax = 0; +this.score = NaN; +this.$hasScore = false; +this.threshold = null; +this.editable = false; +this.hasIcons = false; +this.hasText = false; +this.visible = true; +this.graphGroup = -1; +this.height = 0; +this.graph = 0; +this.graphHeight = 40; +this.padGaps = false; +this.belowAlignment = true; +this.groupRef = null; +this.showAllColLabels = false; +this.scaleColLabel = false; +this.centreColLabels = false; +this.isrna = false; +if (!Clazz.isClassDefined ("jalview.datamodel.AlignmentAnnotation.AnnotCharSequence")) { +jalview.datamodel.AlignmentAnnotation.$AlignmentAnnotation$AnnotCharSequence$ (); +} +this._lastrnaannot = -1; +this.calcId = ""; +this.properties = null; +this._linecolour = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "AlignmentAnnotation"); +Clazz.prepareFields (c$, function () { +this.properties = new java.util.HashMap (); +}); +Clazz.defineMethod (c$, "_updateRnaSecStr", +($fz = function (RNAannot) { +try { +this._rnasecstr = jalview.analysis.Rna.GetBasePairs (RNAannot); +this.bps = jalview.analysis.Rna.GetModeleBP (RNAannot); +this.invalidrnastruc = -1; +} catch (px) { +if (Clazz.exceptionOf (px, jalview.analysis.WUSSParseException)) { +this.invalidrnastruc = px.getProblemPos (); +} else { +throw px; +} +} +if (this.invalidrnastruc > -1) { +return; +}jalview.analysis.Rna.HelixMap (this._rnasecstr); +if (this._rnasecstr != null && this._rnasecstr.length > 0) { +this.isrna = true; +this.showAllColLabels = true; +this.scaleColLabel = true; +this._markRnaHelices (); +}}, $fz.isPrivate = true, $fz), "CharSequence"); +Clazz.defineMethod (c$, "_markRnaHelices", +($fz = function () { +var mxval = 0; +for (var x = 0; x < this._rnasecstr.length; x++) { +var val = 0; +try { +val = (Integer.$valueOf (this._rnasecstr[x].getFeatureGroup ())).intValue (); +if (mxval < val) { +mxval = val; +}} catch (q) { +if (Clazz.exceptionOf (q, NumberFormatException)) { +} else { +throw q; +} +} +;this.annotations[this._rnasecstr[x].getBegin ()].value = val; +this.annotations[this._rnasecstr[x].getEnd ()].value = val; +} +this.setScore (mxval); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "finalize", +function () { +this.sequenceRef = null; +this.groupRef = null; +Clazz.superCall (this, jalview.datamodel.AlignmentAnnotation, "finalize", []); +}); +c$.getGraphValueFromString = Clazz.defineMethod (c$, "getGraphValueFromString", +function (string) { +if (string.equalsIgnoreCase ("BAR_GRAPH")) { +return 1; +} else if (string.equalsIgnoreCase ("LINE_GRAPH")) { +return 2; +} else { +return 0; +}}, "~S"); +Clazz.defineMethod (c$, "ConcenStru", +function (RNAannot) { +this.bps = jalview.analysis.Rna.GetModeleBP (RNAannot); +}, "CharSequence"); +Clazz.makeConstructor (c$, +function (label, description, annotations) { +this.setAnnotationId (); +this.editable = true; +this.label = label; +this.description = description; +this.annotations = annotations; +this.validateRangeAndDisplay (); +}, "~S,~S,~A"); +Clazz.defineMethod (c$, "areLabelsSecondaryStructure", +function () { +var nonSSLabel = false; +this.isrna = false; +var rnastring = new StringBuffer (); +var firstChar = String.fromCharCode (0); +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] == null) { +continue; +}if (this.annotations[i].secondaryStructure == 'H' || this.annotations[i].secondaryStructure == 'E') { +this.hasIcons = new Boolean (this.hasIcons | true).valueOf (); +} else { +if (this.annotations[i].secondaryStructure == '(' || this.annotations[i].secondaryStructure == '[' || this.annotations[i].secondaryStructure == '<' || this.annotations[i].secondaryStructure == '{' || this.annotations[i].secondaryStructure == 'A' || this.annotations[i].secondaryStructure == 'B' || this.annotations[i].secondaryStructure == 'C' || this.annotations[i].secondaryStructure == 'D' || this.annotations[i].secondaryStructure == 'E' || this.annotations[i].secondaryStructure == 'F' || this.annotations[i].secondaryStructure == 'G' || this.annotations[i].secondaryStructure == 'H' || this.annotations[i].secondaryStructure == 'I' || this.annotations[i].secondaryStructure == 'J' || this.annotations[i].secondaryStructure == 'K' || this.annotations[i].secondaryStructure == 'L' || this.annotations[i].secondaryStructure == 'M' || this.annotations[i].secondaryStructure == 'N' || this.annotations[i].secondaryStructure == 'O' || this.annotations[i].secondaryStructure == 'P' || this.annotations[i].secondaryStructure == 'Q' || this.annotations[i].secondaryStructure == 'R' || this.annotations[i].secondaryStructure == 'S' || this.annotations[i].secondaryStructure == 'T' || this.annotations[i].secondaryStructure == 'U' || this.annotations[i].secondaryStructure == 'V' || this.annotations[i].secondaryStructure == 'W' || this.annotations[i].secondaryStructure == 'X' || this.annotations[i].secondaryStructure == 'Y' || this.annotations[i].secondaryStructure == 'Z') { +this.hasIcons = new Boolean (this.hasIcons | true).valueOf (); +this.isrna = new Boolean (this.isrna | true).valueOf (); +}}if (this.annotations[i].displayCharacter == null || this.annotations[i].displayCharacter.length == 0) { +rnastring.append ('.'); +continue; +}if (this.annotations[i].displayCharacter.length == 1) { +firstChar = this.annotations[i].displayCharacter.charAt (0); +if (this.annotations[i].secondaryStructure != ' ' && !this.hasIcons && firstChar != ' ' && firstChar != '$' && firstChar.charCodeAt (0) != 0xCE && firstChar != '(' && firstChar != '[' && firstChar != '>' && firstChar != '{' && firstChar != 'A' && firstChar != 'B' && firstChar != 'C' && firstChar != 'D' && firstChar != 'E' && firstChar != 'F' && firstChar != 'G' && firstChar != 'H' && firstChar != 'I' && firstChar != 'J' && firstChar != 'K' && firstChar != 'L' && firstChar != 'M' && firstChar != 'N' && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q' && firstChar != 'R' && firstChar != 'S' && firstChar != 'T' && firstChar != 'U' && firstChar != 'V' && firstChar != 'W' && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z' && firstChar != '-' && firstChar.charCodeAt (0) < jalview.schemes.ResidueProperties.aaIndex.length) { +if (jalview.schemes.ResidueProperties.aaIndex[firstChar.charCodeAt (0)] < 23) { +nonSSLabel = true; +}}} else { +rnastring.append (this.annotations[i].displayCharacter.charAt (1)); +}if (this.annotations[i].displayCharacter.length > 0) { +this.hasText = true; +}} +if (nonSSLabel) { +this.hasIcons = false; +for (var j = 0; j < this.annotations.length; j++) { +if (this.annotations[j] != null && this.annotations[j].secondaryStructure != ' ') { +this.annotations[j].displayCharacter = String.valueOf (this.annotations[j].secondaryStructure); +this.annotations[j].secondaryStructure = ' '; +}} +} else { +if (this.isrna) { +this._updateRnaSecStr (Clazz.innerTypeInstance (jalview.datamodel.AlignmentAnnotation.AnnotCharSequence, this, null)); +}}}); +Clazz.defineMethod (c$, "getRNAStruc", +function () { +if (this.isrna) { +var rnastruc = Clazz.innerTypeInstance (jalview.datamodel.AlignmentAnnotation.AnnotCharSequence, this, null).toString (); +if (this._lastrnaannot != rnastruc.hashCode ()) { +this._lastrnaannot = rnastruc.hashCode (); +this._updateRnaSecStr (rnastruc); +}return rnastruc; +}return null; +}); +Clazz.makeConstructor (c$, +function (label, description, annotations, min, max, graphType) { +this.setAnnotationId (); +this.editable = graphType == 0; +this.label = label; +this.description = description; +this.annotations = annotations; +this.graph = graphType; +this.graphMin = min; +this.graphMax = max; +this.validateRangeAndDisplay (); +}, "~S,~S,~A,~N,~N,~N"); +Clazz.defineMethod (c$, "validateRangeAndDisplay", +function () { +if (this.annotations == null) { +this.visible = false; +return; +}var graphType = this.graph; +var min = this.graphMin; +var max = this.graphMax; +var drawValues = true; +this._linecolour = null; +if (min == max) { +min = 999999999; +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] == null) { +continue; +}if (drawValues && this.annotations[i].displayCharacter != null && this.annotations[i].displayCharacter.length > 1) { +drawValues = false; +}if (this.annotations[i].value > max) { +max = this.annotations[i].value; +}if (this.annotations[i].value < min) { +min = this.annotations[i].value; +}if (this._linecolour == null && this.annotations[i].colour != null) { +this._linecolour = this.annotations[i].colour; +}} +if (min > 0) { +min = 0; +} else { +if (max < 0) { +max = 0; +}}}this.graphMin = min; +this.graphMax = max; +this.areLabelsSecondaryStructure (); +if (!drawValues && graphType != 0) { +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] != null) { +this.annotations[i].displayCharacter = ""; +}} +}}); +Clazz.makeConstructor (c$, +function (annotation) { +this.setAnnotationId (); +this.label = String.instantialize (annotation.label); +if (annotation.description != null) { +this.description = String.instantialize (annotation.description); +}this.graphMin = annotation.graphMin; +this.graphMax = annotation.graphMax; +this.graph = annotation.graph; +this.graphHeight = annotation.graphHeight; +this.graphGroup = annotation.graphGroup; +this.groupRef = annotation.groupRef; +this.editable = annotation.editable; +this.autoCalculated = annotation.autoCalculated; +this.hasIcons = annotation.hasIcons; +this.hasText = annotation.hasText; +this.height = annotation.height; +this.label = annotation.label; +this.padGaps = annotation.padGaps; +this.visible = annotation.visible; +this.centreColLabels = annotation.centreColLabels; +this.scaleColLabel = annotation.scaleColLabel; +this.showAllColLabels = annotation.showAllColLabels; +this.calcId = annotation.calcId; +if (annotation.properties != null) { +this.properties = new java.util.HashMap (); +for (var val, $val = annotation.properties.entrySet ().iterator (); $val.hasNext () && ((val = $val.next ()) || true);) { +this.properties.put (val.getKey (), val.getValue ()); +} +}if (this.$hasScore = annotation.$hasScore) { +this.score = annotation.score; +}if (annotation.threshold != null) { +this.threshold = new jalview.datamodel.GraphLine (annotation.threshold); +}var ann = annotation.annotations; +if (annotation.annotations != null) { +this.annotations = new Array (ann.length); +for (var i = 0; i < ann.length; i++) { +if (ann[i] != null) { +this.annotations[i] = new jalview.datamodel.Annotation (ann[i]); +if (this._linecolour != null) { +this._linecolour = this.annotations[i].colour; +}}} +}if (annotation.sequenceRef != null) { +this.sequenceRef = annotation.sequenceRef; +if (annotation.sequenceMapping != null) { +var p = null; +this.sequenceMapping = new java.util.HashMap (); +var pos = annotation.sequenceMapping.keySet ().iterator (); +while (pos.hasNext ()) { +p = pos.next (); +var a = annotation.sequenceMapping.get (p); +if (a == null) { +continue; +}if (ann != null) { +for (var i = 0; i < ann.length; i++) { +if (ann[i] === a) { +this.sequenceMapping.put (p, this.annotations[i]); +}} +}} +} else { +this.sequenceMapping = null; +}}{ +}this.validateRangeAndDisplay (); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "restrict", +function (startRes, endRes) { +if (this.annotations == null) { +return; +}if (startRes < 0) { +startRes = 0; +}if (startRes >= this.annotations.length) { +startRes = this.annotations.length - 1; +}if (endRes >= this.annotations.length) { +endRes = this.annotations.length - 1; +}if (this.annotations == null) { +return; +}var temp = new Array (endRes - startRes + 1); +if (startRes < this.annotations.length) { +System.arraycopy (this.annotations, startRes, temp, 0, endRes - startRes + 1); +}if (this.sequenceRef != null) { +var spos = this.sequenceRef.findPosition (startRes); +var epos = this.sequenceRef.findPosition (endRes); +if (this.sequenceMapping != null) { +var newmapping = new java.util.HashMap (); +var e = this.sequenceMapping.keySet ().iterator (); +while (e.hasNext ()) { +var pos = e.next (); +if (pos.intValue () >= spos && pos.intValue () <= epos) { +newmapping.put (pos, this.sequenceMapping.get (pos)); +}} +this.sequenceMapping.clear (); +this.sequenceMapping = newmapping; +}}this.annotations = temp; +}, "~N,~N"); +Clazz.defineMethod (c$, "padAnnotation", +function (length) { +if (this.annotations == null) { +return true; +}if (this.annotations.length < length) { +var na = new Array (length); +System.arraycopy (this.annotations, 0, na, 0, this.annotations.length); +this.annotations = na; +return true; +}return this.annotations.length > length; +}, "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +var buffer = new StringBuilder (256); +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] != null) { +if (this.graph != 0) { +buffer.append (this.annotations[i].value); +} else if (this.hasIcons) { +buffer.append (this.annotations[i].secondaryStructure); +} else { +buffer.append (this.annotations[i].displayCharacter); +}}buffer.append (", "); +} +if (this.label.indexOf ("Consensus") == 0) { +buffer.append ("\n"); +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] != null) { +buffer.append (this.annotations[i].description); +}buffer.append (", "); +} +}return buffer.toString (); +}); +Clazz.defineMethod (c$, "setThreshold", +function (line) { +this.threshold = line; +}, "jalview.datamodel.GraphLine"); +Clazz.defineMethod (c$, "getThreshold", +function () { +return this.threshold; +}); +Clazz.defineMethod (c$, "createSequenceMapping", +function (seqRef, startRes, alreadyMapped) { +if (seqRef == null) { +return; +}this.sequenceRef = seqRef; +if (this.annotations == null) { +return; +}this.sequenceMapping = new java.util.HashMap (); +var seqPos; +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] != null) { +if (alreadyMapped) { +seqPos = seqRef.findPosition (i); +} else { +seqPos = i + startRes; +}this.sequenceMapping.put ( new Integer (seqPos), this.annotations[i]); +}} +}, "jalview.datamodel.SequenceI,~N,~B"); +Clazz.defineMethod (c$, "adjustForAlignment", +function () { +if (this.sequenceRef == null) { +return; +}if (this.annotations == null) { +return; +}var a = 0; +var aSize = this.sequenceRef.getLength (); +if (aSize == 0) { +return; +}var position; +var temp = new Array (aSize); +var index; +for (a = this.sequenceRef.getStart (); a <= this.sequenceRef.getEnd (); a++) { +index = new Integer (a); +if (this.sequenceMapping.containsKey (index)) { +position = this.sequenceRef.findIndex (a) - 1; +temp[position] = this.sequenceMapping.get (index); +}} +this.annotations = temp; +}); +Clazz.defineMethod (c$, "compactAnnotationArray", +function () { +var i = 0; +var iSize = this.annotations.length; +while (i < iSize) { +if (this.annotations[i] == null) { +if (i + 1 < iSize) { +System.arraycopy (this.annotations, i + 1, this.annotations, i, iSize - i - 1); +}iSize--; +} else { +i++; +}} +var ann = this.annotations; +this.annotations = new Array (i); +System.arraycopy (ann, 0, this.annotations, 0, i); +ann = null; +return iSize; +}); +Clazz.defineMethod (c$, "setSequenceRef", +function (sequenceI) { +if (sequenceI != null) { +if (this.sequenceRef != null) { +var rIsDs = this.sequenceRef.getDatasetSequence () == null; +var tIsDs = sequenceI.getDatasetSequence () == null; +if (this.sequenceRef !== sequenceI && (rIsDs && !tIsDs && this.sequenceRef !== sequenceI.getDatasetSequence ()) && (!rIsDs && tIsDs && this.sequenceRef.getDatasetSequence () !== sequenceI) && (!rIsDs && !tIsDs && this.sequenceRef.getDatasetSequence () !== sequenceI.getDatasetSequence ()) && !this.sequenceRef.equals (sequenceI)) { +this.sequenceRef = null; +if (this.sequenceMapping != null) { +this.sequenceMapping = null; +}this.createSequenceMapping (sequenceI, 1, true); +this.adjustForAlignment (); +} else { +this.sequenceRef = sequenceI; +}} else { +this.createSequenceMapping (sequenceI, 1, true); +this.adjustForAlignment (); +}} else { +this.sequenceMapping = null; +this.sequenceRef = null; +}}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getScore", +function () { +return this.score; +}); +Clazz.defineMethod (c$, "setScore", +function (score) { +this.$hasScore = true; +this.score = score; +}, "~N"); +Clazz.defineMethod (c$, "hasScore", +function () { +return this.$hasScore || !Double.isNaN (this.score); +}); +Clazz.makeConstructor (c$, +function (label, description, score) { +this.construct (label, description, null); +this.setScore (score); +}, "~S,~S,~N"); +Clazz.makeConstructor (c$, +function (alignmentAnnotation, colSel) { +this.construct (alignmentAnnotation); +if (this.annotations == null) { +return; +}colSel.makeVisibleAnnotation (this); +}, "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.ColumnSelection"); +Clazz.defineMethod (c$, "setPadGaps", +function (padgaps, gapchar) { +this.padGaps = padgaps; +if (padgaps) { +this.hasText = true; +for (var i = 0; i < this.annotations.length; i++) { +if (this.annotations[i] == null) { +this.annotations[i] = new jalview.datamodel.Annotation (String.valueOf (gapchar), null, ' ', 0, null); +} else if (this.annotations[i].displayCharacter == null || this.annotations[i].displayCharacter.equals (" ")) { +this.annotations[i].displayCharacter = String.valueOf (gapchar); +}} +}}, "~B,~S"); +Clazz.defineMethod (c$, "getDescription", +function (seqname) { +if (seqname && this.sequenceRef != null) { +var i = this.description.toLowerCase ().indexOf (""); +if (i > -1) { +return "" + this.sequenceRef.getName () + " : " + this.description.substring (i + 6); +}return this.sequenceRef.getName () + " : " + this.description; +}return this.description; +}, "~B"); +Clazz.defineMethod (c$, "isValidStruc", +function () { +return this.invalidrnastruc == -1; +}); +Clazz.defineMethod (c$, "getInvalidStrucPos", +function () { +return this.invalidrnastruc; +}); +Clazz.defineMethod (c$, "getCalcId", +function () { +return this.calcId; +}); +Clazz.defineMethod (c$, "setCalcId", +function (calcId) { +this.calcId = calcId; +}, "~S"); +Clazz.defineMethod (c$, "isRNA", +function () { +return this.isrna; +}); +Clazz.defineMethod (c$, "liftOver", +function (sq, sp2sq) { +if (sp2sq.getMappedWidth () != sp2sq.getWidth ()) { +throw new Error ("liftOver currently not implemented for transfer of annotation between different types of seqeunce"); +}var mapIsTo = (sp2sq != null) ? (sp2sq.getTo () === sq || sp2sq.getTo () === sq.getDatasetSequence ()) : false; +var mapForsq = new java.util.HashMap (); +if (this.sequenceMapping != null) { +if (sp2sq != null) { +for (var ie, $ie = this.sequenceMapping.entrySet ().iterator (); $ie.hasNext () && ((ie = $ie.next ()) || true);) { +var mpos = Integer.$valueOf (mapIsTo ? sp2sq.getMappedPosition ((ie.getKey ()).intValue ()) : sp2sq.getPosition ((ie.getKey ()).intValue ())); +if ((mpos).intValue () >= sq.getStart () && (mpos).intValue () <= sq.getEnd ()) { +mapForsq.put (mpos, ie.getValue ()); +}} +this.sequenceMapping = mapForsq; +this.sequenceRef = sq; +this.adjustForAlignment (); +} else { +}}}, "jalview.datamodel.SequenceI,jalview.datamodel.Mapping"); +Clazz.defineMethod (c$, "remap", +function (newref, mapping, from, to, idxoffset) { +if (mapping != null) { +var old = this.sequenceMapping; +var remap = new java.util.HashMap (); +var index = -1; +for (var mp, $mp = 0, $$mp = mapping; $mp < $$mp.length && ((mp = $$mp[$mp]) || true); $mp++) { +if (index++ < 0) { +continue; +}var ann = null; +if (from == -1) { +ann = this.sequenceMapping.get (Integer.$valueOf (idxoffset + index)); +} else { +if (mp != null && mp.length > from) { +ann = this.sequenceMapping.get (Integer.$valueOf (mp[from])); +}}if (ann != null) { +if (to == -1) { +remap.put (Integer.$valueOf (idxoffset + index), ann); +} else { +if (to > -1 && to < mp.length) { +remap.put (Integer.$valueOf (mp[to]), ann); +}}}} +this.sequenceMapping = remap; +old.clear (); +if (newref != null) { +this.sequenceRef = newref; +}this.adjustForAlignment (); +}}, "jalview.datamodel.SequenceI,~A,~N,~N,~N"); +Clazz.defineMethod (c$, "getProperty", +function (property) { +if (this.properties == null) { +return null; +}return this.properties.get (property); +}, "~S"); +Clazz.defineMethod (c$, "setProperty", +function (property, value) { +if (this.properties == null) { +this.properties = new java.util.HashMap (); +}this.properties.put (property, value); +}, "~S,~S"); +Clazz.defineMethod (c$, "hasProperties", +function () { +return this.properties != null && this.properties.size () > 0; +}); +Clazz.defineMethod (c$, "getProperties", +function () { +if (this.properties == null) { +return java.util.Collections.emptyList (); +}return this.properties.keySet (); +}); +Clazz.defineMethod (c$, "getAnnotationForPosition", +function (position) { +return this.sequenceMapping == null ? null : this.sequenceMapping.get (new Integer (position)); +}, "~N"); +Clazz.defineMethod (c$, "setAnnotationId", +function () { +this.annotationId = "ann" + Long.toString (jalview.datamodel.AlignmentAnnotation.nextId ()); +}); +c$.nextId = Clazz.defineMethod (c$, "nextId", +function () { +return jalview.datamodel.AlignmentAnnotation.counter++; +}); +c$.$AlignmentAnnotation$AnnotCharSequence$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.offset = 0; +this.max = 0; +Clazz.instantialize (this, arguments); +}, jalview.datamodel.AlignmentAnnotation, "AnnotCharSequence", null, CharSequence); +Clazz.makeConstructor (c$, +function () { +this.construct (0, this.b$["jalview.datamodel.AlignmentAnnotation"].annotations.length); +}); +Clazz.makeConstructor (c$, +function (a, b) { +this.offset = a; +this.max = b; +}, "~N,~N"); +Clazz.overrideMethod (c$, "subSequence", +function (a, b) { +return Clazz.innerTypeInstance (jalview.datamodel.AlignmentAnnotation.AnnotCharSequence, this, null, this.offset + a, this.offset + b); +}, "~N,~N"); +Clazz.overrideMethod (c$, "length", +function () { +return this.max - this.offset; +}); +Clazz.overrideMethod (c$, "charAt", +function (a) { +return ((a + this.offset < 0) || (a + this.offset) >= this.max || this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset] == null || (this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].secondaryStructure <= ' ') ? ' ' : this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].displayCharacter == null || this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].displayCharacter.length == 0 ? this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].secondaryStructure : this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[a + this.offset].displayCharacter.charAt (0)); +}, "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +var a = Clazz.newCharArray (this.max - this.offset, '\0'); +var b = this.b$["jalview.datamodel.AlignmentAnnotation"].annotations.length; +for (var c = this.offset; c < b; c++) { +a[c] = (this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c] == null || ((this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].secondaryStructure).charCodeAt (0) <= 32)) ? ' ' : (this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].displayCharacter == null || this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].displayCharacter.length == 0 ? this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].secondaryStructure : this.b$["jalview.datamodel.AlignmentAnnotation"].annotations[c].displayCharacter.charAt (0)); +} +return String.instantialize (a); +}); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"ANNOTATION_ID_PREFIX", "ann", +"SEQUENCE_PROFILE", 0, +"STRUCTURE_PROFILE", 1, +"CDNA_PROFILE", 2, +"counter", 0, +"NO_GRAPH", 0, +"BAR_GRAPH", 1, +"LINE_GRAPH", 2); +}); diff --git a/bin/jalview/datamodel/AlignmentI.js b/bin/jalview/datamodel/AlignmentI.js index d1f3174..80e1794 100644 --- a/bin/jalview/datamodel/AlignmentI.js +++ b/bin/jalview/datamodel/AlignmentI.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.AnnotatedCollectionI"], "jalview.datamodel.AlignmentI", null, function () { -Clazz.declareInterface (jalview.datamodel, "AlignmentI", jalview.datamodel.AnnotatedCollectionI); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.AnnotatedCollectionI"], "jalview.datamodel.AlignmentI", null, function () { +Clazz.declareInterface (jalview.datamodel, "AlignmentI", jalview.datamodel.AnnotatedCollectionI); +}); diff --git a/bin/jalview/datamodel/AlignmentOrder.js b/bin/jalview/datamodel/AlignmentOrder.js index 281aa17..0fb0cbb 100644 --- a/bin/jalview/datamodel/AlignmentOrder.js +++ b/bin/jalview/datamodel/AlignmentOrder.js @@ -1,118 +1,118 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.AlignmentOrder", ["java.lang.Error", "java.util.ArrayList", "$.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.Type = 0; -this.Name = null; -this.Order = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "AlignmentOrder"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (anOrder) { -this.Order = anOrder; -}, "java.util.List"); -Clazz.makeConstructor (c$, -function (orderFrom) { -this.Order = new java.util.ArrayList (); -for (var seq, $seq = orderFrom.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -this.Order.add (seq); -} -}, "jalview.datamodel.AlignmentI"); -Clazz.makeConstructor (c$, -function (orderFrom) { -this.Order = new java.util.ArrayList (java.util.Arrays.asList (orderFrom)); -}, "~A"); -Clazz.defineMethod (c$, "setType", -function (Type) { -this.Type = Type; -}, "~N"); -Clazz.defineMethod (c$, "getType", -function () { -return this.Type; -}); -Clazz.defineMethod (c$, "setName", -function (Name) { -this.Name = Name; -}, "~S"); -Clazz.defineMethod (c$, "getName", -function () { -return this.Name; -}); -Clazz.defineMethod (c$, "setOrder", -function (Order) { -this.Order = Order; -}, "java.util.List"); -Clazz.defineMethod (c$, "getOrder", -function () { -return this.Order; -}); -Clazz.defineMethod (c$, "updateSequence", -function (oldref, newref) { -var found = this.Order.indexOf (oldref); -if (found > -1) { -this.Order.set (found, newref); -}return found > -1; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "equals", -function (o) { -if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.AlignmentOrder))) { -return false; -}return this.equals (o, true); -}, "~O"); -Clazz.defineMethod (c$, "equals", -function (o, identity) { -if (o !== this) { -if (o == null) { -return false; -}if (this.Order != null && o.Order != null && this.Order.size () == o.Order.size ()) { -if (!identity) { -throw new Error ("Weak sequenceI equivalence not yet implemented."); -} else { -for (var i = 0, j = o.Order.size (); i < j; i++) { -if (this.Order.get (i) !== o.Order.get (i)) { -return false; -}} -}} else { -return false; -}}return true; -}, "jalview.datamodel.AlignmentOrder,~B"); -Clazz.defineMethod (c$, "isConsistent", -function (o) { -return this.isConsistent (o, true); -}, "jalview.datamodel.AlignmentOrder"); -Clazz.defineMethod (c$, "isConsistent", -function (o, identity) { -if (o !== this) { -if (o == null) { -return false; -}if (this.Order != null && o.Order != null) { -var c; -var s; -if (o.Order.size () > this.Order.size ()) { -c = o.Order; -s = this.Order; -} else { -c = this.Order; -s = o.Order; -}if (!identity) { -throw new Error ("Weak sequenceI equivalence not yet implemented."); -} else { -var last = -1; -for (var i = 0, j = s.size (); i < j; i++) { -var pos = c.indexOf (s.get (i)); -if (pos > last) { -last = pos; -} else { -return false; -}} -}} else { -return false; -}}return true; -}, "jalview.datamodel.AlignmentOrder,~B"); -Clazz.defineStatics (c$, -"FILE", 0, -"MSA", 1, -"USER", 2); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.AlignmentOrder", ["java.lang.Error", "java.util.ArrayList", "$.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.Type = 0; +this.Name = null; +this.Order = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "AlignmentOrder"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (anOrder) { +this.Order = anOrder; +}, "java.util.List"); +Clazz.makeConstructor (c$, +function (orderFrom) { +this.Order = new java.util.ArrayList (); +for (var seq, $seq = orderFrom.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +this.Order.add (seq); +} +}, "jalview.datamodel.AlignmentI"); +Clazz.makeConstructor (c$, +function (orderFrom) { +this.Order = new java.util.ArrayList (java.util.Arrays.asList (orderFrom)); +}, "~A"); +Clazz.defineMethod (c$, "setType", +function (Type) { +this.Type = Type; +}, "~N"); +Clazz.defineMethod (c$, "getType", +function () { +return this.Type; +}); +Clazz.defineMethod (c$, "setName", +function (Name) { +this.Name = Name; +}, "~S"); +Clazz.defineMethod (c$, "getName", +function () { +return this.Name; +}); +Clazz.defineMethod (c$, "setOrder", +function (Order) { +this.Order = Order; +}, "java.util.List"); +Clazz.defineMethod (c$, "getOrder", +function () { +return this.Order; +}); +Clazz.defineMethod (c$, "updateSequence", +function (oldref, newref) { +var found = this.Order.indexOf (oldref); +if (found > -1) { +this.Order.set (found, newref); +}return found > -1; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "equals", +function (o) { +if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.AlignmentOrder))) { +return false; +}return this.equals (o, true); +}, "~O"); +Clazz.defineMethod (c$, "equals", +function (o, identity) { +if (o !== this) { +if (o == null) { +return false; +}if (this.Order != null && o.Order != null && this.Order.size () == o.Order.size ()) { +if (!identity) { +throw new Error ("Weak sequenceI equivalence not yet implemented."); +} else { +for (var i = 0, j = o.Order.size (); i < j; i++) { +if (this.Order.get (i) !== o.Order.get (i)) { +return false; +}} +}} else { +return false; +}}return true; +}, "jalview.datamodel.AlignmentOrder,~B"); +Clazz.defineMethod (c$, "isConsistent", +function (o) { +return this.isConsistent (o, true); +}, "jalview.datamodel.AlignmentOrder"); +Clazz.defineMethod (c$, "isConsistent", +function (o, identity) { +if (o !== this) { +if (o == null) { +return false; +}if (this.Order != null && o.Order != null) { +var c; +var s; +if (o.Order.size () > this.Order.size ()) { +c = o.Order; +s = this.Order; +} else { +c = this.Order; +s = o.Order; +}if (!identity) { +throw new Error ("Weak sequenceI equivalence not yet implemented."); +} else { +var last = -1; +for (var i = 0, j = s.size (); i < j; i++) { +var pos = c.indexOf (s.get (i)); +if (pos > last) { +last = pos; +} else { +return false; +}} +}} else { +return false; +}}return true; +}, "jalview.datamodel.AlignmentOrder,~B"); +Clazz.defineStatics (c$, +"FILE", 0, +"MSA", 1, +"USER", 2); +}); diff --git a/bin/jalview/datamodel/AlignmentView.class b/bin/jalview/datamodel/AlignmentView.class index 122d311..08408b7 100644 Binary files a/bin/jalview/datamodel/AlignmentView.class and b/bin/jalview/datamodel/AlignmentView.class differ diff --git a/bin/jalview/datamodel/AlignmentView.js b/bin/jalview/datamodel/AlignmentView.js index e88c405..e559e79 100644 --- a/bin/jalview/datamodel/AlignmentView.js +++ b/bin/jalview/datamodel/AlignmentView.js @@ -1,625 +1,625 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.AlignmentView", ["jalview.datamodel.Alignment", "$.CigarArray", "$.ColumnSelection", "$.SeqCigar", "$.SequenceGroup", "jalview.util.MessageManager", "$.ShiftList", "java.lang.Error", "java.util.ArrayList", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.sequences = null; -this.contigs = null; -this.width = 0; -this.firstCol = 0; -this.scGroups = null; -this.$isNa = false; -if (!Clazz.isClassDefined ("jalview.datamodel.AlignmentView.ScGroup")) { -jalview.datamodel.AlignmentView.$AlignmentView$ScGroup$ (); -} -this.selected = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "AlignmentView"); -Clazz.defineMethod (c$, "isNa", -function () { -return this.$isNa; -}); -Clazz.makeConstructor (c$, -function (alignment, columnSelection, selection, hasHiddenColumns, selectedRegionOnly, recordGroups) { -this.construct ( new jalview.datamodel.CigarArray (alignment, (hasHiddenColumns ? columnSelection : null), (selectedRegionOnly ? selection : null)), (selectedRegionOnly && selection != null) ? selection.getStartRes () : 0); -this.$isNa = alignment.isNucleotide (); -var selseqs; -if (selection != null && selection.getSize () > 0) { -var sel = selection.getSequences (null); -this.selected = new java.util.Vector (); -selseqs = selection.getSequencesInOrder (alignment, selectedRegionOnly); -} else { -selseqs = alignment.getSequencesArray (); -}var seqsets = new java.util.ArrayList (); -var grps = new java.util.ArrayList (); -var gg = alignment.getGroups (); -grps.addAll (gg); -var sgrps = null; -var addedgps = null; -if (grps != null) { -if (selection != null && selectedRegionOnly) { -var ssel = selection.getStartRes (); -var esel = selection.getEndRes (); -var isg = new java.util.ArrayList (); -for (var sg, $sg = grps.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (!(sg.getStartRes () > esel || sg.getEndRes () < ssel)) { -if (sg.getStartRes () < ssel) { -sg.setStartRes (ssel); -}if (sg.getEndRes () > esel) { -sg.setEndRes (esel); -}sg.setStartRes (sg.getStartRes () - ssel + 1); -sg.setEndRes (sg.getEndRes () - ssel + 1); -isg.add (sg); -}} -grps = isg; -}sgrps = new Array (grps.size ()); -addedgps = Clazz.newBooleanArray (grps.size (), false); -for (var g = 0; g < sgrps.length; g++) { -var sg = grps.get (g); -sgrps[g] = Clazz.innerTypeInstance (jalview.datamodel.AlignmentView.ScGroup, this, null); -sgrps[g].sg = new jalview.datamodel.SequenceGroup (sg); -addedgps[g] = false; -seqsets.add (sg.getSequences ()); -} -}var csi = 0; -for (var i = 0; i < selseqs.length; i++) { -if (selseqs[i] != null) { -if (selection != null && selection.getSize () > 0 && !selectedRegionOnly) { -this.sequences[csi].setGroupMembership (this.selected); -this.selected.addElement (this.sequences[csi]); -}if (seqsets != null) { -for (var sg = 0; sg < sgrps.length; sg++) { -if ((seqsets.get (sg)).contains (selseqs[i])) { -this.sequences[csi].setGroupMembership (sgrps[sg]); -sgrps[sg].sg.deleteSequence (selseqs[i], false); -sgrps[sg].seqs.addElement (this.sequences[csi]); -if (!addedgps[sg]) { -if (this.scGroups == null) { -this.scGroups = new java.util.ArrayList (); -}addedgps[sg] = true; -this.scGroups.add (sgrps[sg]); -}}} -}csi++; -}} -for (var sg = 0; sg < sgrps.length; sg++) { -var sqs = sgrps[sg].sg.getSequencesAsArray (null); -for (var si = 0; si < sqs.length; si++) { -sgrps[sg].sg.deleteSequence (sqs[si], false); -} -sgrps[sg] = null; -} -}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup,~B,~B,~B"); -Clazz.makeConstructor (c$, -function (seqcigararray) { -if (!seqcigararray.isSeqCigarArray ()) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_can_only_make_alignmnet_from_cigararray")); -}this.contigs = seqcigararray.getDeletedRegions (); -this.sequences = seqcigararray.getSeqCigarArray (); -this.width = seqcigararray.getWidth (); -}, "jalview.datamodel.CigarArray"); -Clazz.makeConstructor (c$, -function (sdata, firstcol) { -this.construct (sdata); -this.firstCol = firstcol; -}, "jalview.datamodel.CigarArray,~N"); -Clazz.defineMethod (c$, "setSequences", -function (sequences) { -this.sequences = sequences; -}, "~A"); -Clazz.defineMethod (c$, "setContigs", -function (contigs) { -this.contigs = contigs; -}, "~A"); -Clazz.defineMethod (c$, "getSequences", -function () { -return this.sequences; -}); -Clazz.defineMethod (c$, "getContigs", -function () { -return this.contigs; -}); -Clazz.defineMethod (c$, "getAlignmentAndColumnSelection", -function (gapCharacter) { -var colsel = new jalview.datamodel.ColumnSelection (); -return Clazz.newArray (-1, [jalview.datamodel.SeqCigar.createAlignmentSequences (this.sequences, gapCharacter, colsel, this.contigs), colsel]); -}, "~S"); -Clazz.defineMethod (c$, "getVisibleAlignment", -function (c) { -var aln = this.getVisibleSeqs (c); -var vcal = new jalview.datamodel.Alignment (aln); -this.addPrunedGroupsInOrder (vcal, -1, -1, true); -return vcal; -}, "~S"); -Clazz.defineMethod (c$, "addPrunedGroupsInOrder", -($fz = function (vcal, gstart, gend, viscontigs) { -var r = false; -if (gstart > -1 && gstart <= gend) { -r = true; -}var aln = vcal.getSequencesArray (); -{ -{ -var nvg = (this.scGroups != null) ? this.scGroups.size () : 0; -if (nvg > 0) { -var nsg = new Array (nvg); -for (var g = 0; g < nvg; g++) { -var sg = this.scGroups.get (g).sg; -if (r) { -if (sg.getStartRes () > gend || sg.getEndRes () < gstart) { -nsg[g] = null; -continue; -}}nsg[g] = new jalview.datamodel.SequenceGroup (sg); -if (r && !viscontigs) { -if (nsg[g].getStartRes () < gstart) { -nsg[g].setStartRes (0); -} else { -nsg[g].setStartRes (nsg[g].getStartRes () - gstart); -nsg[g].setEndRes (nsg[g].getEndRes () - gstart); -}if (nsg[g].getEndRes () > (gend - gstart)) { -nsg[g].setEndRes (gend - gstart); -}}} -if (viscontigs) { -if (this.contigs != null) { -var p = 0; -var prune = new jalview.util.ShiftList (); -if (r) { -prune.addShift (gstart, -gstart); -}for (var h = 0; h < this.contigs.length; h += 3) { -{ -prune.addShift (p + this.contigs[h + 1], this.contigs[h + 2] - this.contigs[h + 1]); -}p = this.contigs[h + 1] + this.contigs[h + 2]; -} -for (var g = 0; g < nsg.length; g++) { -if (nsg[g] != null) { -var s = nsg[g].getStartRes (); -var t = nsg[g].getEndRes (); -var w = 1 + t - s; -if (r) { -if (s < gstart) { -s = gstart; -}if (t > gend) { -t = gend; -}}s = prune.shift (s); -t = prune.shift (t); -nsg[g].setStartRes (s); -nsg[g].setEndRes (t); -}} -}}for (var nsq = 0; nsq < aln.length; nsq++) { -for (var g = 0; g < nvg; g++) { -if (nsg[g] != null && this.sequences[nsq].isMemberOf (this.scGroups.get (g))) { -nsg[g].addSequence (aln[nsq], false); -}} -} -for (var g = 0; g < nvg; g++) { -if (nsg[g] != null && nsg[g].getSize () > 0) { -vcal.addGroup (nsg[g]); -}nsg[g] = null; -} -}}}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~N,~N,~B"); -Clazz.defineMethod (c$, "getVisibleSeqs", -($fz = function (c) { -var aln = new Array (this.sequences.length); -for (var i = 0, j = this.sequences.length; i < j; i++) { -aln[i] = this.sequences[i].getSeq ('-'); -} -var seqs = this.getSequenceStrings ('-'); -for (var i = 0, j = aln.length; i < j; i++) { -aln[i].setSequence (seqs[i]); -} -return aln; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "getVisibleContigAlignments", -function (c) { -var nvc = 0; -var vcontigs = this.getVisibleContigs (); -var contigviews = this.getVisibleContigs (c); -var vcals = new Array (contigviews.length); -for (nvc = 0; nvc < contigviews.length; nvc++) { -vcals[nvc] = new jalview.datamodel.Alignment (contigviews[nvc]); -if (this.scGroups != null && this.scGroups.size () > 0) { -this.addPrunedGroupsInOrder (vcals[nvc], vcontigs[nvc * 2], vcontigs[nvc * 2 + 1], true); -}} -return vcals; -}, "~S"); -Clazz.defineMethod (c$, "getSequenceStrings", -function (c) { -var seqs = new Array (this.sequences.length); -for (var n = 0; n < this.sequences.length; n++) { -var fullseq = this.sequences[n].getSequenceString (c); -if (this.contigs != null) { -seqs[n] = ""; -var p = 0; -for (var h = 0; h < this.contigs.length; h += 3) { -seqs[n] += fullseq.substring (p, this.contigs[h + 1]); -p = this.contigs[h + 1] + this.contigs[h + 2]; -} -seqs[n] += fullseq.substring (p); -} else { -seqs[n] = fullseq; -}} -return seqs; -}, "~S"); -Clazz.defineMethod (c$, "getWidth", -function () { -return this.width; -}); -Clazz.defineMethod (c$, "setWidth", -function (width) { -this.width = width; -}, "~N"); -Clazz.defineMethod (c$, "getVisibleContigs", -function (gapCharacter) { -var smsa; -var njobs = 1; -if (this.sequences == null || this.width <= 0) { -return null; -}if (this.contigs != null && this.contigs.length > 0) { -var start = 0; -njobs = 0; -var fwidth = this.width; -for (var contig = 0; contig < this.contigs.length; contig += 3) { -if ((this.contigs[contig + 1] - start) > 0) { -njobs++; -}fwidth += this.contigs[contig + 2]; -start = this.contigs[contig + 1] + this.contigs[contig + 2]; -} -if (start < fwidth) { -njobs++; -}smsa = new Array (njobs); -start = 0; -var j = 0; -for (var contig = 0; contig < this.contigs.length; contig += 3) { -if (this.contigs[contig + 1] - start > 0) { -var mseq = new Array (this.sequences.length); -for (var s = 0; s < mseq.length; s++) { -mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]); -} -smsa[j] = mseq; -j++; -}start = this.contigs[contig + 1] + this.contigs[contig + 2]; -} -if (start < fwidth) { -var mseq = new Array (this.sequences.length); -for (var s = 0; s < mseq.length; s++) { -mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, fwidth + 1); -} -smsa[j] = mseq; -j++; -}} else { -smsa = new Array (1); -smsa[0] = new Array (this.sequences.length); -for (var s = 0; s < this.sequences.length; s++) { -smsa[0][s] = this.sequences[s].getSeq (gapCharacter); -} -}return smsa; -}, "~S"); -Clazz.defineMethod (c$, "getUpdatedView", -function (nvismsa, orders, gapCharacter) { -if (this.sequences == null || this.width <= 0) { -throw new Error (jalview.util.MessageManager.getString ("error.empty_view_cannot_be_updated")); -}if (nvismsa == null) { -throw new Error ("nvismsa==null. use getAlignmentAndColumnSelection() instead."); -}if (this.contigs != null && this.contigs.length > 0) { -var alignment = new Array (this.sequences.length); -var columnselection = new jalview.datamodel.ColumnSelection (); -if (this.contigs != null && this.contigs.length > 0) { -var start = 0; -var nwidth = 0; -var owidth = this.width; -var j = 0; -for (var contig = 0; contig < this.contigs.length; contig += 3) { -owidth += this.contigs[contig + 2]; -if (this.contigs[contig + 1] - start > 0) { -var swidth = 0; -if (nvismsa[j] != null) { -var mseq = nvismsa[j]; -var order = (orders == null) ? null : orders[j]; -j++; -if (mseq.length != this.sequences.length) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_number_of_sequences_in_block", Clazz.newArray (-1, [Integer.$valueOf (j).toString (), Integer.$valueOf (mseq.length).toString (), Integer.$valueOf (this.sequences.length).toString ()]))); -}swidth = mseq[0].getLength (); -for (var s = 0; s < mseq.length; s++) { -if (alignment[s] == null) { -alignment[s] = mseq[s]; -} else { -alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ()); -if (mseq[s].getStart () <= mseq[s].getEnd ()) { -alignment[s].setEnd (mseq[s].getEnd ()); -}if (order != null) { -order.updateSequence (mseq[s], alignment[s]); -}}} -} else { -if (true) { -for (var s = 0; s < this.sequences.length; s++) { -var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]); -if (swidth < oseq.getLength ()) { -swidth = oseq.getLength (); -}if (alignment[s] == null) { -alignment[s] = oseq; -} else { -alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ()); -if (oseq.getEnd () >= oseq.getStart ()) { -alignment[s].setEnd (oseq.getEnd ()); -}}} -}j++; -}nwidth += swidth; -}start = this.contigs[contig + 1] + this.contigs[contig + 2]; -for (var s = 0; s < this.sequences.length; s++) { -var hseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (this.contigs[contig + 1], start); -if (alignment[s] == null) { -alignment[s] = hseq; -} else { -alignment[s].setSequence (alignment[s].getSequenceAsString () + hseq.getSequenceAsString ()); -if (hseq.getEnd () >= hseq.getStart ()) { -alignment[s].setEnd (hseq.getEnd ()); -}}} -columnselection.hideColumns (nwidth, nwidth + this.contigs[contig + 2] - 1); -nwidth += this.contigs[contig + 2]; -} -if (j < nvismsa.length) { -var swidth = 0; -if (nvismsa[j] != null) { -var mseq = nvismsa[j]; -var order = (orders != null) ? orders[j] : null; -swidth = mseq[0].getLength (); -for (var s = 0; s < mseq.length; s++) { -if (alignment[s] == null) { -alignment[s] = mseq[s]; -} else { -alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ()); -if (mseq[s].getEnd () >= mseq[s].getStart ()) { -alignment[s].setEnd (mseq[s].getEnd ()); -}if (order != null) { -order.updateSequence (mseq[s], alignment[s]); -}}} -} else { -if (start < owidth) { -if (true) { -for (var s = 0; s < this.sequences.length; s++) { -var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, owidth + 1); -if (swidth < oseq.getLength ()) { -swidth = oseq.getLength (); -}if (alignment[s] == null) { -alignment[s] = oseq; -} else { -alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ()); -if (oseq.getEnd () >= oseq.getStart ()) { -alignment[s].setEnd (oseq.getEnd ()); -}}} -nwidth += swidth; -} else { -throw new Error (jalview.util.MessageManager.getString ("error.padding_not_yet_implemented")); -}}}}}return Clazz.newArray (-1, [alignment, columnselection]); -} else { -if (nvismsa.length != 1) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", Clazz.newArray (-1, [Integer.$valueOf (nvismsa.length).toString ()]))); -}if (nvismsa[0] != null) { -return Clazz.newArray (-1, [nvismsa[0], new jalview.datamodel.ColumnSelection ()]); -} else { -return this.getAlignmentAndColumnSelection (gapCharacter); -}}}, "~A,~A,~S"); -Clazz.defineMethod (c$, "getVisibleContigs", -function () { -if (this.contigs != null && this.contigs.length > 0) { -var start = 0; -var nvis = 0; -var fwidth = this.width; -for (var contig = 0; contig < this.contigs.length; contig += 3) { -if ((this.contigs[contig + 1] - start) > 0) { -nvis++; -}fwidth += this.contigs[contig + 2]; -start = this.contigs[contig + 1] + this.contigs[contig + 2]; -} -if (start < fwidth) { -nvis++; -}var viscontigs = Clazz.newIntArray (nvis * 2, 0); -nvis = 0; -start = 0; -for (var contig = 0; contig < this.contigs.length; contig += 3) { -if ((this.contigs[contig + 1] - start) > 0) { -viscontigs[nvis] = start; -viscontigs[nvis + 1] = this.contigs[contig + 1] - 1; -nvis += 2; -}start = this.contigs[contig + 1] + this.contigs[contig + 2]; -} -if (start < fwidth) { -viscontigs[nvis] = start; -viscontigs[nvis + 1] = fwidth; -nvis += 2; -}return viscontigs; -} else { -return Clazz.newIntArray (-1, [0, this.width]); -}}); -Clazz.defineMethod (c$, "getAlignmentOrigin", -function () { -return this.firstCol; -}); -Clazz.defineMethod (c$, "getVisibleContigMapFor", -function (gapMap) { -var delMap = null; -var viscontigs = this.getVisibleContigs (); -var spos = 0; -var i = 0; -if (viscontigs != null) { -delMap = Clazz.newIntArray (gapMap.length, 0); -for (var contig = 0; contig < viscontigs.length; contig += 2) { -while (spos < gapMap.length && gapMap[spos] < viscontigs[contig]) { -spos++; -} -while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1]) { -delMap[i++] = spos++; -} -} -var tmap = Clazz.newIntArray (i, 0); -System.arraycopy (delMap, 0, tmap, 0, i); -delMap = tmap; -}return delMap; -}, "~A"); -Clazz.defineMethod (c$, "getEditedSequences", -function (gc, $delete) { -var msf = this.getSequences (); -var aln = new Array (msf.length); -for (var i = 0, j = msf.length; i < j; i++) { -aln[i] = msf[i].getSeq (gc); -} -if ($delete) { -var sqs = this.getSequenceStrings (gc); -for (var i = 0; i < sqs.length; i++) { -aln[i].setSequence (sqs[i]); -sqs[i] = null; -} -}return aln; -}, "~S,~B"); -c$.summariseAlignmentView = Clazz.defineMethod (c$, "summariseAlignmentView", -function (view, os) { -os.print ("View has " + view.sequences.length + " of which "); -if (view.selected == null) { -os.print ("None"); -} else { -os.print (" " + view.selected.size ()); -}os.println (" are selected."); -os.print ("View is " + view.getWidth () + " columns wide"); -var viswid = 0; -var contigs = view.getContigs (); -if (contigs != null) { -viswid = view.width; -for (var i = 0; i < contigs.length; i += 3) { -viswid += contigs[i + 2]; -} -os.println ("with " + viswid + " visible columns spread over " + Clazz.doubleToInt (contigs.length / 3) + " regions."); -} else { -viswid = view.width; -os.println ("."); -}if (view.scGroups != null) { -os.println ("There are " + view.scGroups.size () + " groups defined on the view."); -for (var g = 0; g < view.scGroups.size (); g++) { -var sgr = view.scGroups.get (g); -os.println ("Group " + g + ": Name = " + sgr.sg.getName () + " Contains " + sgr.seqs.size () + " Seqs."); -os.println ("This group runs from " + sgr.sg.getStartRes () + " to " + sgr.sg.getEndRes ()); -for (var s = 0; s < sgr.seqs.size (); s++) { -if (!(sgr.seqs.elementAt (s)).isMemberOf (sgr)) { -os.println ("** WARNING: sequence " + (sgr.seqs.elementAt (s)).toString () + " is not marked as member of group."); -}} -} -var visal = view.getVisibleAlignment ('-'); -if (visal != null) { -os.println ("Vis. alignment is " + visal.getWidth () + " wide and has " + visal.getHeight () + " seqs."); -if (visal.getGroups () != null && visal.getGroups ().size () > 0) { -var i = 1; -for (var sg, $sg = visal.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -os.println ("Group " + (i++) + " begins at column " + sg.getStartRes () + " and ends at " + sg.getEndRes ()); -} -}}}}, "jalview.datamodel.AlignmentView,java.io.PrintStream"); -c$.testSelectionViews = Clazz.defineMethod (c$, "testSelectionViews", -function (alignment, csel, selection) { -System.out.println ("Testing standard view creation:\n"); -var view = null; -try { -System.out.println ("View with no hidden columns, no limit to selection, no groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, false); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection but no groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View with no hidden columns, no limit to selection, and all groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, true); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection marked but no groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View with no hidden columns, limited to selection and no groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, false); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection restricted but no groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View with no hidden columns, limited to selection, and all groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, true); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection restricted and groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View *with* hidden columns, no limit to selection, no groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, false); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection but no groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View *with* hidden columns, no limit to selection, and all groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, true); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection marked but no groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View *with* hidden columns, limited to selection and no groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, false); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection restricted but no groups marked."); -} else { -throw e; -} -} -try { -System.out.println ("View *with* hidden columns, limited to selection, and all groups to be collected:"); -view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, true); -jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to generate alignment with selection restricted and groups marked."); -} else { -throw e; -} -} -}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup"); -c$.$AlignmentView$ScGroup$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.seqs = null; -this.sg = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel.AlignmentView, "ScGroup"); -Clazz.makeConstructor (c$, -function () { -this.seqs = new java.util.Vector (); -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.AlignmentView", ["jalview.datamodel.Alignment", "$.CigarArray", "$.ColumnSelection", "$.SeqCigar", "$.SequenceGroup", "jalview.util.MessageManager", "$.ShiftList", "java.lang.Error", "java.util.ArrayList", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.sequences = null; +this.contigs = null; +this.width = 0; +this.firstCol = 0; +this.scGroups = null; +this.$isNa = false; +if (!Clazz.isClassDefined ("jalview.datamodel.AlignmentView.ScGroup")) { +jalview.datamodel.AlignmentView.$AlignmentView$ScGroup$ (); +} +this.selected = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "AlignmentView"); +Clazz.defineMethod (c$, "isNa", +function () { +return this.$isNa; +}); +Clazz.makeConstructor (c$, +function (alignment, columnSelection, selection, hasHiddenColumns, selectedRegionOnly, recordGroups) { +this.construct ( new jalview.datamodel.CigarArray (alignment, (hasHiddenColumns ? columnSelection : null), (selectedRegionOnly ? selection : null)), (selectedRegionOnly && selection != null) ? selection.getStartRes () : 0); +this.$isNa = alignment.isNucleotide (); +var selseqs; +if (selection != null && selection.getSize () > 0) { +var sel = selection.getSequences (null); +this.selected = new java.util.Vector (); +selseqs = selection.getSequencesInOrder (alignment, selectedRegionOnly); +} else { +selseqs = alignment.getSequencesArray (); +}var seqsets = new java.util.ArrayList (); +var grps = new java.util.ArrayList (); +var gg = alignment.getGroups (); +grps.addAll (gg); +var sgrps = null; +var addedgps = null; +if (grps != null) { +if (selection != null && selectedRegionOnly) { +var ssel = selection.getStartRes (); +var esel = selection.getEndRes (); +var isg = new java.util.ArrayList (); +for (var sg, $sg = grps.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (!(sg.getStartRes () > esel || sg.getEndRes () < ssel)) { +if (sg.getStartRes () < ssel) { +sg.setStartRes (ssel); +}if (sg.getEndRes () > esel) { +sg.setEndRes (esel); +}sg.setStartRes (sg.getStartRes () - ssel + 1); +sg.setEndRes (sg.getEndRes () - ssel + 1); +isg.add (sg); +}} +grps = isg; +}sgrps = new Array (grps.size ()); +addedgps = Clazz.newBooleanArray (grps.size (), false); +for (var g = 0; g < sgrps.length; g++) { +var sg = grps.get (g); +sgrps[g] = Clazz.innerTypeInstance (jalview.datamodel.AlignmentView.ScGroup, this, null); +sgrps[g].sg = new jalview.datamodel.SequenceGroup (sg); +addedgps[g] = false; +seqsets.add (sg.getSequences ()); +} +}var csi = 0; +for (var i = 0; i < selseqs.length; i++) { +if (selseqs[i] != null) { +if (selection != null && selection.getSize () > 0 && !selectedRegionOnly) { +this.sequences[csi].setGroupMembership (this.selected); +this.selected.addElement (this.sequences[csi]); +}if (seqsets != null) { +for (var sg = 0; sg < sgrps.length; sg++) { +if ((seqsets.get (sg)).contains (selseqs[i])) { +this.sequences[csi].setGroupMembership (sgrps[sg]); +sgrps[sg].sg.deleteSequence (selseqs[i], false); +sgrps[sg].seqs.addElement (this.sequences[csi]); +if (!addedgps[sg]) { +if (this.scGroups == null) { +this.scGroups = new java.util.ArrayList (); +}addedgps[sg] = true; +this.scGroups.add (sgrps[sg]); +}}} +}csi++; +}} +for (var sg = 0; sg < sgrps.length; sg++) { +var sqs = sgrps[sg].sg.getSequencesAsArray (null); +for (var si = 0; si < sqs.length; si++) { +sgrps[sg].sg.deleteSequence (sqs[si], false); +} +sgrps[sg] = null; +} +}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup,~B,~B,~B"); +Clazz.makeConstructor (c$, +function (seqcigararray) { +if (!seqcigararray.isSeqCigarArray ()) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_can_only_make_alignmnet_from_cigararray")); +}this.contigs = seqcigararray.getDeletedRegions (); +this.sequences = seqcigararray.getSeqCigarArray (); +this.width = seqcigararray.getWidth (); +}, "jalview.datamodel.CigarArray"); +Clazz.makeConstructor (c$, +function (sdata, firstcol) { +this.construct (sdata); +this.firstCol = firstcol; +}, "jalview.datamodel.CigarArray,~N"); +Clazz.defineMethod (c$, "setSequences", +function (sequences) { +this.sequences = sequences; +}, "~A"); +Clazz.defineMethod (c$, "setContigs", +function (contigs) { +this.contigs = contigs; +}, "~A"); +Clazz.defineMethod (c$, "getSequences", +function () { +return this.sequences; +}); +Clazz.defineMethod (c$, "getContigs", +function () { +return this.contigs; +}); +Clazz.defineMethod (c$, "getAlignmentAndColumnSelection", +function (gapCharacter) { +var colsel = new jalview.datamodel.ColumnSelection (); +return Clazz.newArray (-1, [jalview.datamodel.SeqCigar.createAlignmentSequences (this.sequences, gapCharacter, colsel, this.contigs), colsel]); +}, "~S"); +Clazz.defineMethod (c$, "getVisibleAlignment", +function (c) { +var aln = this.getVisibleSeqs (c); +var vcal = new jalview.datamodel.Alignment (aln); +this.addPrunedGroupsInOrder (vcal, -1, -1, true); +return vcal; +}, "~S"); +Clazz.defineMethod (c$, "addPrunedGroupsInOrder", +($fz = function (vcal, gstart, gend, viscontigs) { +var r = false; +if (gstart > -1 && gstart <= gend) { +r = true; +}var aln = vcal.getSequencesArray (); +{ +{ +var nvg = (this.scGroups != null) ? this.scGroups.size () : 0; +if (nvg > 0) { +var nsg = new Array (nvg); +for (var g = 0; g < nvg; g++) { +var sg = this.scGroups.get (g).sg; +if (r) { +if (sg.getStartRes () > gend || sg.getEndRes () < gstart) { +nsg[g] = null; +continue; +}}nsg[g] = new jalview.datamodel.SequenceGroup (sg); +if (r && !viscontigs) { +if (nsg[g].getStartRes () < gstart) { +nsg[g].setStartRes (0); +} else { +nsg[g].setStartRes (nsg[g].getStartRes () - gstart); +nsg[g].setEndRes (nsg[g].getEndRes () - gstart); +}if (nsg[g].getEndRes () > (gend - gstart)) { +nsg[g].setEndRes (gend - gstart); +}}} +if (viscontigs) { +if (this.contigs != null) { +var p = 0; +var prune = new jalview.util.ShiftList (); +if (r) { +prune.addShift (gstart, -gstart); +}for (var h = 0; h < this.contigs.length; h += 3) { +{ +prune.addShift (p + this.contigs[h + 1], this.contigs[h + 2] - this.contigs[h + 1]); +}p = this.contigs[h + 1] + this.contigs[h + 2]; +} +for (var g = 0; g < nsg.length; g++) { +if (nsg[g] != null) { +var s = nsg[g].getStartRes (); +var t = nsg[g].getEndRes (); +var w = 1 + t - s; +if (r) { +if (s < gstart) { +s = gstart; +}if (t > gend) { +t = gend; +}}s = prune.shift (s); +t = prune.shift (t); +nsg[g].setStartRes (s); +nsg[g].setEndRes (t); +}} +}}for (var nsq = 0; nsq < aln.length; nsq++) { +for (var g = 0; g < nvg; g++) { +if (nsg[g] != null && this.sequences[nsq].isMemberOf (this.scGroups.get (g))) { +nsg[g].addSequence (aln[nsq], false); +}} +} +for (var g = 0; g < nvg; g++) { +if (nsg[g] != null && nsg[g].getSize () > 0) { +vcal.addGroup (nsg[g]); +}nsg[g] = null; +} +}}}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~N,~N,~B"); +Clazz.defineMethod (c$, "getVisibleSeqs", +($fz = function (c) { +var aln = new Array (this.sequences.length); +for (var i = 0, j = this.sequences.length; i < j; i++) { +aln[i] = this.sequences[i].getSeq ('-'); +} +var seqs = this.getSequenceStrings ('-'); +for (var i = 0, j = aln.length; i < j; i++) { +aln[i].setSequence (seqs[i]); +} +return aln; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "getVisibleContigAlignments", +function (c) { +var nvc = 0; +var vcontigs = this.getVisibleContigs (); +var contigviews = this.getVisibleContigs (c); +var vcals = new Array (contigviews.length); +for (nvc = 0; nvc < contigviews.length; nvc++) { +vcals[nvc] = new jalview.datamodel.Alignment (contigviews[nvc]); +if (this.scGroups != null && this.scGroups.size () > 0) { +this.addPrunedGroupsInOrder (vcals[nvc], vcontigs[nvc * 2], vcontigs[nvc * 2 + 1], true); +}} +return vcals; +}, "~S"); +Clazz.defineMethod (c$, "getSequenceStrings", +function (c) { +var seqs = new Array (this.sequences.length); +for (var n = 0; n < this.sequences.length; n++) { +var fullseq = this.sequences[n].getSequenceString (c); +if (this.contigs != null) { +seqs[n] = ""; +var p = 0; +for (var h = 0; h < this.contigs.length; h += 3) { +seqs[n] += fullseq.substring (p, this.contigs[h + 1]); +p = this.contigs[h + 1] + this.contigs[h + 2]; +} +seqs[n] += fullseq.substring (p); +} else { +seqs[n] = fullseq; +}} +return seqs; +}, "~S"); +Clazz.defineMethod (c$, "getWidth", +function () { +return this.width; +}); +Clazz.defineMethod (c$, "setWidth", +function (width) { +this.width = width; +}, "~N"); +Clazz.defineMethod (c$, "getVisibleContigs", +function (gapCharacter) { +var smsa; +var njobs = 1; +if (this.sequences == null || this.width <= 0) { +return null; +}if (this.contigs != null && this.contigs.length > 0) { +var start = 0; +njobs = 0; +var fwidth = this.width; +for (var contig = 0; contig < this.contigs.length; contig += 3) { +if ((this.contigs[contig + 1] - start) > 0) { +njobs++; +}fwidth += this.contigs[contig + 2]; +start = this.contigs[contig + 1] + this.contigs[contig + 2]; +} +if (start < fwidth) { +njobs++; +}smsa = new Array (njobs); +start = 0; +var j = 0; +for (var contig = 0; contig < this.contigs.length; contig += 3) { +if (this.contigs[contig + 1] - start > 0) { +var mseq = new Array (this.sequences.length); +for (var s = 0; s < mseq.length; s++) { +mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]); +} +smsa[j] = mseq; +j++; +}start = this.contigs[contig + 1] + this.contigs[contig + 2]; +} +if (start < fwidth) { +var mseq = new Array (this.sequences.length); +for (var s = 0; s < mseq.length; s++) { +mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, fwidth + 1); +} +smsa[j] = mseq; +j++; +}} else { +smsa = new Array (1); +smsa[0] = new Array (this.sequences.length); +for (var s = 0; s < this.sequences.length; s++) { +smsa[0][s] = this.sequences[s].getSeq (gapCharacter); +} +}return smsa; +}, "~S"); +Clazz.defineMethod (c$, "getUpdatedView", +function (nvismsa, orders, gapCharacter) { +if (this.sequences == null || this.width <= 0) { +throw new Error (jalview.util.MessageManager.getString ("error.empty_view_cannot_be_updated")); +}if (nvismsa == null) { +throw new Error ("nvismsa==null. use getAlignmentAndColumnSelection() instead."); +}if (this.contigs != null && this.contigs.length > 0) { +var alignment = new Array (this.sequences.length); +var columnselection = new jalview.datamodel.ColumnSelection (); +if (this.contigs != null && this.contigs.length > 0) { +var start = 0; +var nwidth = 0; +var owidth = this.width; +var j = 0; +for (var contig = 0; contig < this.contigs.length; contig += 3) { +owidth += this.contigs[contig + 2]; +if (this.contigs[contig + 1] - start > 0) { +var swidth = 0; +if (nvismsa[j] != null) { +var mseq = nvismsa[j]; +var order = (orders == null) ? null : orders[j]; +j++; +if (mseq.length != this.sequences.length) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_number_of_sequences_in_block", Clazz.newArray (-1, [Integer.$valueOf (j).toString (), Integer.$valueOf (mseq.length).toString (), Integer.$valueOf (this.sequences.length).toString ()]))); +}swidth = mseq[0].getLength (); +for (var s = 0; s < mseq.length; s++) { +if (alignment[s] == null) { +alignment[s] = mseq[s]; +} else { +alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ()); +if (mseq[s].getStart () <= mseq[s].getEnd ()) { +alignment[s].setEnd (mseq[s].getEnd ()); +}if (order != null) { +order.updateSequence (mseq[s], alignment[s]); +}}} +} else { +if (true) { +for (var s = 0; s < this.sequences.length; s++) { +var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]); +if (swidth < oseq.getLength ()) { +swidth = oseq.getLength (); +}if (alignment[s] == null) { +alignment[s] = oseq; +} else { +alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ()); +if (oseq.getEnd () >= oseq.getStart ()) { +alignment[s].setEnd (oseq.getEnd ()); +}}} +}j++; +}nwidth += swidth; +}start = this.contigs[contig + 1] + this.contigs[contig + 2]; +for (var s = 0; s < this.sequences.length; s++) { +var hseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (this.contigs[contig + 1], start); +if (alignment[s] == null) { +alignment[s] = hseq; +} else { +alignment[s].setSequence (alignment[s].getSequenceAsString () + hseq.getSequenceAsString ()); +if (hseq.getEnd () >= hseq.getStart ()) { +alignment[s].setEnd (hseq.getEnd ()); +}}} +columnselection.hideColumns (nwidth, nwidth + this.contigs[contig + 2] - 1); +nwidth += this.contigs[contig + 2]; +} +if (j < nvismsa.length) { +var swidth = 0; +if (nvismsa[j] != null) { +var mseq = nvismsa[j]; +var order = (orders != null) ? orders[j] : null; +swidth = mseq[0].getLength (); +for (var s = 0; s < mseq.length; s++) { +if (alignment[s] == null) { +alignment[s] = mseq[s]; +} else { +alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ()); +if (mseq[s].getEnd () >= mseq[s].getStart ()) { +alignment[s].setEnd (mseq[s].getEnd ()); +}if (order != null) { +order.updateSequence (mseq[s], alignment[s]); +}}} +} else { +if (start < owidth) { +if (true) { +for (var s = 0; s < this.sequences.length; s++) { +var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, owidth + 1); +if (swidth < oseq.getLength ()) { +swidth = oseq.getLength (); +}if (alignment[s] == null) { +alignment[s] = oseq; +} else { +alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ()); +if (oseq.getEnd () >= oseq.getStart ()) { +alignment[s].setEnd (oseq.getEnd ()); +}}} +nwidth += swidth; +} else { +throw new Error (jalview.util.MessageManager.getString ("error.padding_not_yet_implemented")); +}}}}}return Clazz.newArray (-1, [alignment, columnselection]); +} else { +if (nvismsa.length != 1) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", Clazz.newArray (-1, [Integer.$valueOf (nvismsa.length).toString ()]))); +}if (nvismsa[0] != null) { +return Clazz.newArray (-1, [nvismsa[0], new jalview.datamodel.ColumnSelection ()]); +} else { +return this.getAlignmentAndColumnSelection (gapCharacter); +}}}, "~A,~A,~S"); +Clazz.defineMethod (c$, "getVisibleContigs", +function () { +if (this.contigs != null && this.contigs.length > 0) { +var start = 0; +var nvis = 0; +var fwidth = this.width; +for (var contig = 0; contig < this.contigs.length; contig += 3) { +if ((this.contigs[contig + 1] - start) > 0) { +nvis++; +}fwidth += this.contigs[contig + 2]; +start = this.contigs[contig + 1] + this.contigs[contig + 2]; +} +if (start < fwidth) { +nvis++; +}var viscontigs = Clazz.newIntArray (nvis * 2, 0); +nvis = 0; +start = 0; +for (var contig = 0; contig < this.contigs.length; contig += 3) { +if ((this.contigs[contig + 1] - start) > 0) { +viscontigs[nvis] = start; +viscontigs[nvis + 1] = this.contigs[contig + 1] - 1; +nvis += 2; +}start = this.contigs[contig + 1] + this.contigs[contig + 2]; +} +if (start < fwidth) { +viscontigs[nvis] = start; +viscontigs[nvis + 1] = fwidth; +nvis += 2; +}return viscontigs; +} else { +return Clazz.newIntArray (-1, [0, this.width]); +}}); +Clazz.defineMethod (c$, "getAlignmentOrigin", +function () { +return this.firstCol; +}); +Clazz.defineMethod (c$, "getVisibleContigMapFor", +function (gapMap) { +var delMap = null; +var viscontigs = this.getVisibleContigs (); +var spos = 0; +var i = 0; +if (viscontigs != null) { +delMap = Clazz.newIntArray (gapMap.length, 0); +for (var contig = 0; contig < viscontigs.length; contig += 2) { +while (spos < gapMap.length && gapMap[spos] < viscontigs[contig]) { +spos++; +} +while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1]) { +delMap[i++] = spos++; +} +} +var tmap = Clazz.newIntArray (i, 0); +System.arraycopy (delMap, 0, tmap, 0, i); +delMap = tmap; +}return delMap; +}, "~A"); +Clazz.defineMethod (c$, "getEditedSequences", +function (gc, $delete) { +var msf = this.getSequences (); +var aln = new Array (msf.length); +for (var i = 0, j = msf.length; i < j; i++) { +aln[i] = msf[i].getSeq (gc); +} +if ($delete) { +var sqs = this.getSequenceStrings (gc); +for (var i = 0; i < sqs.length; i++) { +aln[i].setSequence (sqs[i]); +sqs[i] = null; +} +}return aln; +}, "~S,~B"); +c$.summariseAlignmentView = Clazz.defineMethod (c$, "summariseAlignmentView", +function (view, os) { +os.print ("View has " + view.sequences.length + " of which "); +if (view.selected == null) { +os.print ("None"); +} else { +os.print (" " + view.selected.size ()); +}os.println (" are selected."); +os.print ("View is " + view.getWidth () + " columns wide"); +var viswid = 0; +var contigs = view.getContigs (); +if (contigs != null) { +viswid = view.width; +for (var i = 0; i < contigs.length; i += 3) { +viswid += contigs[i + 2]; +} +os.println ("with " + viswid + " visible columns spread over " + Clazz.doubleToInt (contigs.length / 3) + " regions."); +} else { +viswid = view.width; +os.println ("."); +}if (view.scGroups != null) { +os.println ("There are " + view.scGroups.size () + " groups defined on the view."); +for (var g = 0; g < view.scGroups.size (); g++) { +var sgr = view.scGroups.get (g); +os.println ("Group " + g + ": Name = " + sgr.sg.getName () + " Contains " + sgr.seqs.size () + " Seqs."); +os.println ("This group runs from " + sgr.sg.getStartRes () + " to " + sgr.sg.getEndRes ()); +for (var s = 0; s < sgr.seqs.size (); s++) { +if (!(sgr.seqs.elementAt (s)).isMemberOf (sgr)) { +os.println ("** WARNING: sequence " + (sgr.seqs.elementAt (s)).toString () + " is not marked as member of group."); +}} +} +var visal = view.getVisibleAlignment ('-'); +if (visal != null) { +os.println ("Vis. alignment is " + visal.getWidth () + " wide and has " + visal.getHeight () + " seqs."); +if (visal.getGroups () != null && visal.getGroups ().size () > 0) { +var i = 1; +for (var sg, $sg = visal.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +os.println ("Group " + (i++) + " begins at column " + sg.getStartRes () + " and ends at " + sg.getEndRes ()); +} +}}}}, "jalview.datamodel.AlignmentView,java.io.PrintStream"); +c$.testSelectionViews = Clazz.defineMethod (c$, "testSelectionViews", +function (alignment, csel, selection) { +System.out.println ("Testing standard view creation:\n"); +var view = null; +try { +System.out.println ("View with no hidden columns, no limit to selection, no groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, false); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection but no groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View with no hidden columns, no limit to selection, and all groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, true); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection marked but no groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View with no hidden columns, limited to selection and no groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, false); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection restricted but no groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View with no hidden columns, limited to selection, and all groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, true); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection restricted and groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View *with* hidden columns, no limit to selection, no groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, false); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection but no groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View *with* hidden columns, no limit to selection, and all groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, true); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection marked but no groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View *with* hidden columns, limited to selection and no groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, false); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection restricted but no groups marked."); +} else { +throw e; +} +} +try { +System.out.println ("View *with* hidden columns, limited to selection, and all groups to be collected:"); +view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, true); +jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to generate alignment with selection restricted and groups marked."); +} else { +throw e; +} +} +}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup"); +c$.$AlignmentView$ScGroup$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.seqs = null; +this.sg = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel.AlignmentView, "ScGroup"); +Clazz.makeConstructor (c$, +function () { +this.seqs = new java.util.Vector (); +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/datamodel/AnnotatedCollectionI.js b/bin/jalview/datamodel/AnnotatedCollectionI.js index 0dda32c..fd7a804 100644 --- a/bin/jalview/datamodel/AnnotatedCollectionI.js +++ b/bin/jalview/datamodel/AnnotatedCollectionI.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.SequenceCollectionI"], "jalview.datamodel.AnnotatedCollectionI", null, function () { -Clazz.declareInterface (jalview.datamodel, "AnnotatedCollectionI", jalview.datamodel.SequenceCollectionI); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.SequenceCollectionI"], "jalview.datamodel.AnnotatedCollectionI", null, function () { +Clazz.declareInterface (jalview.datamodel, "AnnotatedCollectionI", jalview.datamodel.SequenceCollectionI); +}); diff --git a/bin/jalview/datamodel/Annotation.class b/bin/jalview/datamodel/Annotation.class index ad9b0f6..043f330 100644 Binary files a/bin/jalview/datamodel/Annotation.class and b/bin/jalview/datamodel/Annotation.class differ diff --git a/bin/jalview/datamodel/Annotation.js b/bin/jalview/datamodel/Annotation.js index 92e1248..76f42d8 100644 --- a/bin/jalview/datamodel/Annotation.js +++ b/bin/jalview/datamodel/Annotation.js @@ -1,72 +1,72 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.Annotation", ["java.lang.Float", "$.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.displayCharacter = ""; -this.description = ""; -this.secondaryStructure = ' '; -this.value = 0; -this.colour = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "Annotation"); -Clazz.makeConstructor (c$, -function (displayChar, desc, ss, val) { -this.displayCharacter = displayChar; -this.description = desc; -this.secondaryStructure = ss; -this.value = val; -}, "~S,~S,~S,~N"); -Clazz.makeConstructor (c$, -function (displayChar, desc, ss, val, colour) { -this.construct (displayChar, desc, ss, val); -this.colour = colour; -}, "~S,~S,~S,~N,java.awt.Color"); -Clazz.makeConstructor (c$, -function (that) { -if (that == null || this === that) { -return; -}if (that.displayCharacter != null) this.displayCharacter = String.instantialize (that.displayCharacter); -if (that.description != null) this.description = String.instantialize (that.description); -this.secondaryStructure = that.secondaryStructure; -this.value = that.value; -this.colour = that.colour; -}, "jalview.datamodel.Annotation"); -Clazz.makeConstructor (c$, -function (val) { -this.construct (null, null, ' ', val, null); -}, "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -var sb = new StringBuffer (); -if (this.displayCharacter != null) { -sb.append ("\'"); -sb.append (this.displayCharacter); -sb.append ("\'"); -}{ -sb.append (","); -}if (this.secondaryStructure.charCodeAt (0) != 0 && !("" + this.displayCharacter).equals ("" + this.secondaryStructure)) { -sb.append ("\'"); -sb.append (this.secondaryStructure); -sb.append ("\'"); -}{ -sb.append (","); -}if (this.description != null && this.description.length > 0) { -sb.append ("\""); -sb.append (this.description); -sb.append ("\""); -}{ -sb.append (","); -}if (!Float.isNaN (this.value)) { -sb.append (this.value); -}if (this.colour != null) { -if (sb.length () > 0) { -sb.append (","); -}sb.append ("["); -sb.append (this.colour.getRed ()); -sb.append (","); -sb.append (this.colour.getGreen ()); -sb.append (","); -sb.append (this.colour.getBlue ()); -sb.append ("]"); -}return sb.toString (); -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.Annotation", ["java.lang.Float", "$.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.displayCharacter = ""; +this.description = ""; +this.secondaryStructure = ' '; +this.value = 0; +this.colour = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "Annotation"); +Clazz.makeConstructor (c$, +function (displayChar, desc, ss, val) { +this.displayCharacter = displayChar; +this.description = desc; +this.secondaryStructure = ss; +this.value = val; +}, "~S,~S,~S,~N"); +Clazz.makeConstructor (c$, +function (displayChar, desc, ss, val, colour) { +this.construct (displayChar, desc, ss, val); +this.colour = colour; +}, "~S,~S,~S,~N,java.awt.Color"); +Clazz.makeConstructor (c$, +function (that) { +if (that == null || this === that) { +return; +}if (that.displayCharacter != null) this.displayCharacter = String.instantialize (that.displayCharacter); +if (that.description != null) this.description = String.instantialize (that.description); +this.secondaryStructure = that.secondaryStructure; +this.value = that.value; +this.colour = that.colour; +}, "jalview.datamodel.Annotation"); +Clazz.makeConstructor (c$, +function (val) { +this.construct (null, null, ' ', val, null); +}, "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +var sb = new StringBuffer (); +if (this.displayCharacter != null) { +sb.append ("\'"); +sb.append (this.displayCharacter); +sb.append ("\'"); +}{ +sb.append (","); +}if (this.secondaryStructure.charCodeAt (0) != 0 && !("" + this.displayCharacter).equals ("" + this.secondaryStructure)) { +sb.append ("\'"); +sb.append (this.secondaryStructure); +sb.append ("\'"); +}{ +sb.append (","); +}if (this.description != null && this.description.length > 0) { +sb.append ("\""); +sb.append (this.description); +sb.append ("\""); +}{ +sb.append (","); +}if (!Float.isNaN (this.value)) { +sb.append (this.value); +}if (this.colour != null) { +if (sb.length () > 0) { +sb.append (","); +}sb.append ("["); +sb.append ("" + this.colour.getRed ()); +sb.append (","); +sb.append ("" + this.colour.getGreen ()); +sb.append (","); +sb.append ("" + this.colour.getBlue ()); +sb.append ("]"); +}return sb.toString (); +}); +}); diff --git a/bin/jalview/datamodel/BinaryNode.js b/bin/jalview/datamodel/BinaryNode.js index 64fb764..7575508 100644 --- a/bin/jalview/datamodel/BinaryNode.js +++ b/bin/jalview/datamodel/BinaryNode.js @@ -1,112 +1,112 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this.$element = null; -this.name = null; -this.$left = null; -this.$right = null; -this.$parent = null; -this.bootstrap = 0; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "BinaryNode"); -Clazz.makeConstructor (c$, -function () { -this.$left = this.$right = this.$parent = null; -this.bootstrap = 0; -}); -Clazz.makeConstructor (c$, -function (element, parent, name) { -this.$element = element; -this.$parent = parent; -this.name = name; -this.$left = this.$right = null; -}, "~O,jalview.datamodel.BinaryNode,~S"); -Clazz.defineMethod (c$, "element", -function () { -return this.$element; -}); -Clazz.defineMethod (c$, "setElement", -function (v) { -return this.$element = v; -}, "~O"); -Clazz.defineMethod (c$, "left", -function () { -return this.$left; -}); -Clazz.defineMethod (c$, "setLeft", -function (n) { -return this.$left = n; -}, "jalview.datamodel.BinaryNode"); -Clazz.defineMethod (c$, "right", -function () { -return this.$right; -}); -Clazz.defineMethod (c$, "setRight", -function (n) { -return this.$right = n; -}, "jalview.datamodel.BinaryNode"); -Clazz.defineMethod (c$, "parent", -function () { -return this.$parent; -}); -Clazz.defineMethod (c$, "setParent", -function (n) { -return this.$parent = n; -}, "jalview.datamodel.BinaryNode"); -Clazz.defineMethod (c$, "isLeaf", -function () { -return (this.$left == null) && (this.$right == null); -}); -Clazz.defineMethod (c$, "SetChildren", -function (leftchild, rightchild) { -if (leftchild != null) { -this.setLeft (leftchild); -leftchild.detach (); -leftchild.setParent (this); -}if (rightchild != null) { -this.setRight (rightchild); -rightchild.detach (); -rightchild.setParent (this); -}}, "jalview.datamodel.BinaryNode,jalview.datamodel.BinaryNode"); -Clazz.defineMethod (c$, "detach", -function () { -if (this.$parent != null) { -if (this.$parent.$left === this) { -this.$parent.$left = null; -} else { -if (this.$parent.$right === this) { -this.$parent.$right = null; -}}}this.$parent = null; -return this; -}); -Clazz.defineMethod (c$, "ascendLeft", -function () { -var c = this; -do { -c = c.parent (); -} while ((c != null) && (c.left () != null) && !c.left ().isLeaf ()); -return c; -}); -Clazz.defineMethod (c$, "ascendRight", -function () { -var c = this; -do { -c = c.parent (); -} while ((c != null) && (c.right () != null) && !c.right ().isLeaf ()); -return c; -}); -Clazz.defineMethod (c$, "setName", -function (name) { -this.name = name; -}, "~S"); -Clazz.defineMethod (c$, "getName", -function () { -return this.name; -}); -Clazz.defineMethod (c$, "setBootstrap", -function (boot) { -this.bootstrap = boot; -}, "~N"); -Clazz.defineMethod (c$, "getBootstrap", -function () { -return this.bootstrap; -}); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this.$element = null; +this.name = null; +this.$left = null; +this.$right = null; +this.$parent = null; +this.bootstrap = 0; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "BinaryNode"); +Clazz.makeConstructor (c$, +function () { +this.$left = this.$right = this.$parent = null; +this.bootstrap = 0; +}); +Clazz.makeConstructor (c$, +function (element, parent, name) { +this.$element = element; +this.$parent = parent; +this.name = name; +this.$left = this.$right = null; +}, "~O,jalview.datamodel.BinaryNode,~S"); +Clazz.defineMethod (c$, "element", +function () { +return this.$element; +}); +Clazz.defineMethod (c$, "setElement", +function (v) { +return this.$element = v; +}, "~O"); +Clazz.defineMethod (c$, "left", +function () { +return this.$left; +}); +Clazz.defineMethod (c$, "setLeft", +function (n) { +return this.$left = n; +}, "jalview.datamodel.BinaryNode"); +Clazz.defineMethod (c$, "right", +function () { +return this.$right; +}); +Clazz.defineMethod (c$, "setRight", +function (n) { +return this.$right = n; +}, "jalview.datamodel.BinaryNode"); +Clazz.defineMethod (c$, "parent", +function () { +return this.$parent; +}); +Clazz.defineMethod (c$, "setParent", +function (n) { +return this.$parent = n; +}, "jalview.datamodel.BinaryNode"); +Clazz.defineMethod (c$, "isLeaf", +function () { +return (this.$left == null) && (this.$right == null); +}); +Clazz.defineMethod (c$, "SetChildren", +function (leftchild, rightchild) { +if (leftchild != null) { +this.setLeft (leftchild); +leftchild.detach (); +leftchild.setParent (this); +}if (rightchild != null) { +this.setRight (rightchild); +rightchild.detach (); +rightchild.setParent (this); +}}, "jalview.datamodel.BinaryNode,jalview.datamodel.BinaryNode"); +Clazz.defineMethod (c$, "detach", +function () { +if (this.$parent != null) { +if (this.$parent.$left === this) { +this.$parent.$left = null; +} else { +if (this.$parent.$right === this) { +this.$parent.$right = null; +}}}this.$parent = null; +return this; +}); +Clazz.defineMethod (c$, "ascendLeft", +function () { +var c = this; +do { +c = c.parent (); +} while ((c != null) && (c.left () != null) && !c.left ().isLeaf ()); +return c; +}); +Clazz.defineMethod (c$, "ascendRight", +function () { +var c = this; +do { +c = c.parent (); +} while ((c != null) && (c.right () != null) && !c.right ().isLeaf ()); +return c; +}); +Clazz.defineMethod (c$, "setName", +function (name) { +this.name = name; +}, "~S"); +Clazz.defineMethod (c$, "getName", +function () { +return this.name; +}); +Clazz.defineMethod (c$, "setBootstrap", +function (boot) { +this.bootstrap = boot; +}, "~N"); +Clazz.defineMethod (c$, "getBootstrap", +function () { +return this.bootstrap; +}); diff --git a/bin/jalview/datamodel/BinarySequence.js b/bin/jalview/datamodel/BinarySequence.js index 2285387..90b6b95 100644 --- a/bin/jalview/datamodel/BinarySequence.js +++ b/bin/jalview/datamodel/BinarySequence.js @@ -1,99 +1,99 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.Sequence", "java.lang.Exception"], "jalview.datamodel.BinarySequence", ["jalview.schemes.ResidueProperties"], function () { -c$ = Clazz.decorateAsClass (function () { -if (!Clazz.isClassDefined ("jalview.datamodel.BinarySequence.InvalidSequenceTypeException")) { -jalview.datamodel.BinarySequence.$BinarySequence$InvalidSequenceTypeException$ (); -} -this.binary = null; -this.dbinary = null; -this.isNa = false; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "BinarySequence", jalview.datamodel.Sequence); -Clazz.makeConstructor (c$, -function (s, isNa) { -Clazz.superConstructor (this, jalview.datamodel.BinarySequence, ["", s, 0, s.length]); -this.isNa = isNa; -}, "~S,~B"); -Clazz.defineMethod (c$, "initMatrixGetNoRes", -($fz = function () { -var nores = (this.isNa) ? 10 : 23; -this.dbinary = Clazz.newDoubleArray (this.getSequence ().length * nores, 0); -for (var i = 0; i < this.dbinary.length; i++) { -this.dbinary[i] = 0.0; -} -return nores; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getSymbolmatrix", -($fz = function () { -return (this.isNa) ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "encode", -function () { -var nores = this.initMatrixGetNoRes (); -var sindex = this.getSymbolmatrix (); -for (var i = 0; i < this.getSequence ().length; i++) { -var aanum = nores - 1; -try { -aanum = sindex[this.getCharAt (i).charCodeAt (0)]; -} catch (e) { -if (Clazz.exceptionOf (e, NullPointerException)) { -aanum = nores - 1; -} else { -throw e; -} -} -if (aanum >= nores) { -aanum = nores - 1; -}this.dbinary[(i * nores) + aanum] = 1.0; -} -}); -Clazz.defineMethod (c$, "matrixEncode", -function (matrix) { -if (this.isNa != matrix.isDNA ()) { -throw Clazz.innerTypeInstance (jalview.datamodel.BinarySequence.InvalidSequenceTypeException, this, null, "matrix " + matrix.getClass ().getCanonicalName () + " is not a valid matrix for " + (this.isNa ? "nucleotide" : "protein") + "sequences"); -}this.matrixEncode (matrix.isDNA () ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex, matrix.getMatrix ()); -}, "jalview.schemes.ScoreMatrix"); -Clazz.defineMethod (c$, "matrixEncode", -($fz = function (aaIndex, matrix) { -var nores = this.initMatrixGetNoRes (); -for (var i = 0, iSize = this.getSequence ().length; i < iSize; i++) { -var aanum = nores - 1; -try { -aanum = aaIndex[this.getCharAt (i).charCodeAt (0)]; -} catch (e) { -if (Clazz.exceptionOf (e, NullPointerException)) { -aanum = nores - 1; -} else { -throw e; -} -} -if (aanum >= nores) { -aanum = nores - 1; -}for (var j = 0; j < nores; j++) { -this.dbinary[(i * nores) + j] = matrix[aanum][j]; -} -} -}, $fz.isPrivate = true, $fz), "~A,~A"); -Clazz.defineMethod (c$, "toBinaryString", -function () { -var out = ""; -for (var i = 0; i < this.binary.length; i++) { -out += ( new Integer (this.binary[i])).toString (); -if (i < (this.binary.length - 1)) { -out += " "; -}} -return out; -}); -Clazz.defineMethod (c$, "getDBinary", -function () { -return this.dbinary; -}); -c$.$BinarySequence$InvalidSequenceTypeException$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -Clazz.instantialize (this, arguments); -}, jalview.datamodel.BinarySequence, "InvalidSequenceTypeException", Exception); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.Sequence", "java.lang.Exception"], "jalview.datamodel.BinarySequence", ["jalview.schemes.ResidueProperties"], function () { +c$ = Clazz.decorateAsClass (function () { +if (!Clazz.isClassDefined ("jalview.datamodel.BinarySequence.InvalidSequenceTypeException")) { +jalview.datamodel.BinarySequence.$BinarySequence$InvalidSequenceTypeException$ (); +} +this.binary = null; +this.dbinary = null; +this.isNa = false; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "BinarySequence", jalview.datamodel.Sequence); +Clazz.makeConstructor (c$, +function (s, isNa) { +Clazz.superConstructor (this, jalview.datamodel.BinarySequence, ["", s, 0, s.length]); +this.isNa = isNa; +}, "~S,~B"); +Clazz.defineMethod (c$, "initMatrixGetNoRes", +($fz = function () { +var nores = (this.isNa) ? 10 : 23; +this.dbinary = Clazz.newDoubleArray (this.getSequence ().length * nores, 0); +for (var i = 0; i < this.dbinary.length; i++) { +this.dbinary[i] = 0.0; +} +return nores; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getSymbolmatrix", +($fz = function () { +return (this.isNa) ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "encode", +function () { +var nores = this.initMatrixGetNoRes (); +var sindex = this.getSymbolmatrix (); +for (var i = 0; i < this.getSequence ().length; i++) { +var aanum = nores - 1; +try { +aanum = sindex[this.getCharAt (i).charCodeAt (0)]; +} catch (e) { +if (Clazz.exceptionOf (e, NullPointerException)) { +aanum = nores - 1; +} else { +throw e; +} +} +if (aanum >= nores) { +aanum = nores - 1; +}this.dbinary[(i * nores) + aanum] = 1.0; +} +}); +Clazz.defineMethod (c$, "matrixEncode", +function (matrix) { +if (this.isNa != matrix.isDNA ()) { +throw Clazz.innerTypeInstance (jalview.datamodel.BinarySequence.InvalidSequenceTypeException, this, null, "matrix " + matrix.getClass ().getCanonicalName () + " is not a valid matrix for " + (this.isNa ? "nucleotide" : "protein") + "sequences"); +}this.matrixEncode (matrix.isDNA () ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex, matrix.getMatrix ()); +}, "jalview.schemes.ScoreMatrix"); +Clazz.defineMethod (c$, "matrixEncode", +($fz = function (aaIndex, matrix) { +var nores = this.initMatrixGetNoRes (); +for (var i = 0, iSize = this.getSequence ().length; i < iSize; i++) { +var aanum = nores - 1; +try { +aanum = aaIndex[this.getCharAt (i).charCodeAt (0)]; +} catch (e) { +if (Clazz.exceptionOf (e, NullPointerException)) { +aanum = nores - 1; +} else { +throw e; +} +} +if (aanum >= nores) { +aanum = nores - 1; +}for (var j = 0; j < nores; j++) { +this.dbinary[(i * nores) + j] = matrix[aanum][j]; +} +} +}, $fz.isPrivate = true, $fz), "~A,~A"); +Clazz.defineMethod (c$, "toBinaryString", +function () { +var out = ""; +for (var i = 0; i < this.binary.length; i++) { +out += ( new Integer (this.binary[i])).toString (); +if (i < (this.binary.length - 1)) { +out += " "; +}} +return out; +}); +Clazz.defineMethod (c$, "getDBinary", +function () { +return this.dbinary; +}); +c$.$BinarySequence$InvalidSequenceTypeException$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +Clazz.instantialize (this, arguments); +}, jalview.datamodel.BinarySequence, "InvalidSequenceTypeException", Exception); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/datamodel/CigarArray.class b/bin/jalview/datamodel/CigarArray.class index c31f49e..10b48a9 100644 Binary files a/bin/jalview/datamodel/CigarArray.class and b/bin/jalview/datamodel/CigarArray.class differ diff --git a/bin/jalview/datamodel/CigarArray.js b/bin/jalview/datamodel/CigarArray.js index b18df9f..7f45aff 100644 --- a/bin/jalview/datamodel/CigarArray.js +++ b/bin/jalview/datamodel/CigarArray.js @@ -1,188 +1,188 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.CigarBase"], "jalview.datamodel.CigarArray", ["jalview.datamodel.CigarCigar", "$.SeqCigar", "java.lang.StringBuffer", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.refCigars = null; -this.seqcigararray = false; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "CigarArray", jalview.datamodel.CigarBase); -Clazz.defineMethod (c$, "isSeqCigarArray", -function () { -return this.seqcigararray; -}); -Clazz.makeConstructor (c$, -function (cigars) { -Clazz.superConstructor (this, jalview.datamodel.CigarArray); -this.seqcigararray = true; -if (cigars != null && cigars.length > 0) { -this.refCigars = new Array (cigars.length); -for (var c = 0; c < cigars.length; c++) { -this.refCigars[c] = cigars[c]; -if (!((Clazz.instanceOf (cigars[c], jalview.datamodel.SeqCigar)) || Clazz.instanceOf (cigars[c], jalview.datamodel.CigarCigar))) { -this.seqcigararray = false; -}} -}}, "~A"); -Clazz.makeConstructor (c$, -function (alignment, columnSelection, selectionGroup) { -this.construct (jalview.datamodel.CigarArray.constructSeqCigarArray (alignment, selectionGroup)); -this.constructFromAlignment (alignment, columnSelection != null ? columnSelection.getHiddenColumns () : null, selectionGroup); -}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup"); -c$._calcStartEndBounds = Clazz.defineMethod (c$, "_calcStartEndBounds", -($fz = function (alignment, selectionGroup) { -var startend = Clazz.newIntArray (-1, [0, 0, 0]); -if (selectionGroup != null) { -startend[0] = selectionGroup.getSize (); -startend[1] = selectionGroup.getStartRes (); -startend[2] = selectionGroup.getEndRes (); -} else { -startend[0] = alignment.getHeight (); -startend[2] = alignment.getWidth () - 1; -}return startend; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); -c$.constructSeqCigarArray = Clazz.defineMethod (c$, "constructSeqCigarArray", -function (alignment, selectionGroup) { -var seqs = null; -var i; -var iSize; -var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup); -var start = _startend[1]; -var end = _startend[2]; -if (selectionGroup != null) { -iSize = selectionGroup.getSize (); -seqs = selectionGroup.getSequencesInOrder (alignment); -start = selectionGroup.getStartRes (); -end = selectionGroup.getEndRes (); -} else { -iSize = alignment.getHeight (); -seqs = alignment.getSequencesArray (); -end = alignment.getWidth () - 1; -}var selseqs = new Array (iSize); -for (i = 0; i < iSize; i++) { -selseqs[i] = new jalview.datamodel.SeqCigar (seqs[i], start, end); -} -return selseqs; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "constructFromAlignment", -($fz = function (alignment, list, selectionGroup) { -var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup); -var start = _startend[1]; -var end = _startend[2]; -if (list != null) { -var region; -var hideStart; -var hideEnd; -var last = start; -for (var j = 0; new Boolean (last < end & j < list.size ()).valueOf (); j++) { -region = list.get (j); -hideStart = region[0]; -hideEnd = region[1]; -if (hideStart < last) { -if (hideEnd > last) { -hideStart = last; -} else { -continue; -}}if (hideStart > end) { -break; -}if (hideEnd > end) { -hideEnd = end; -}if (hideStart > hideEnd) { -break; -}if (last < hideStart) { -this.addOperation ('M', hideStart - last); -}this.addOperation ('D', 1 + hideEnd - hideStart); -last = hideEnd + 1; -} -if (last < end) { -this.addOperation ('M', end - last + 1); -}} else { -this.addOperation ('M', end - start + 1); -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "getArrayofSequenceAndDeletions", -function (GapChar) { -if (this.refCigars == null || this.refCigars.length == 0 || this.length == 0) { -return null; -}var sqanddels = new Array (this.refCigars.length); -for (var c = 0; c < this.refCigars.length; c++) { -var refString = this.refCigars[c].getSequenceString (GapChar); -if (refString != null) { -sqanddels[c] = this.getSequenceAndDeletions (refString, GapChar); -} else { -sqanddels[c] = null; -}} -return sqanddels; -}, "~S"); -Clazz.defineMethod (c$, "getSequenceString", -function (GapChar) { -if (this.length == 0 || this.refCigars == null) { -return ""; -}var seqStrings = new StringBuffer (); -var sqanddels = this.getArrayofSequenceAndDeletions (GapChar); -for (var c = 0; c < this.refCigars.length; c++) { -if (sqanddels[c] != null) { -seqStrings.append (sqanddels[c][0]); -sqanddels[c][0] = null; -}seqStrings.append ('\n'); -} -return seqStrings.toString (); -}, "~S"); -Clazz.defineMethod (c$, "getSequenceStrings", -function (GapChar) { -if (this.length == 0 || this.refCigars == null || this.refCigars.length == 0) { -return null; -}var sqanddels = this.getArrayofSequenceAndDeletions (GapChar); -var seqs = new Array (sqanddels.length); -for (var c = 0; c < this.refCigars.length; c++) { -seqs[c] = sqanddels[c][0]; -} -return seqs; -}, "~S"); -Clazz.defineMethod (c$, "applyDeletions", -function () { -var delpos = null; -if (this.length == 0) { -return null; -}var cursor = 0; -var vcursor = 0; -var offset = 0; -var i = 0; -while (i < this.length) { -if (this.operation[i] != 'D') { -if (this.operation[i] == 'M') { -cursor += this.range[i]; -}vcursor += this.range[i++]; -} else { -if (delpos == null) { -delpos = new java.util.Vector (); -}var delstart = cursor; -var delend = cursor + this.range[i] - 1; -delpos.addElement ( Clazz.newIntArray (-1, [vcursor + offset, this.range[i]])); -offset += this.range[i] - 1; -System.arraycopy (this.operation, i + 1, this.operation, i, this.length - i); -System.arraycopy (this.range, i + 1, this.range, i, this.length - i); -this.length--; -for (var s = 0; s < this.refCigars.length; s++) { -var d = this.refCigars[s].deleteRange (delstart, delend); -} -}} -if (delpos != null) { -var pos = Clazz.newIntArray (delpos.size () * 2, 0); -for (var k = 0, l = delpos.size (); k < l; k++) { -var dr = (delpos.elementAt (k)); -pos[k * 2] = dr[0]; -pos[k * 2 + 1] = dr[1]; -delpos.setElementAt (null, k); -} -delpos = null; -return pos; -}return null; -}); -Clazz.defineMethod (c$, "getSeqCigarArray", -function () { -if (!this.isSeqCigarArray ()) { -return null; -}var sa = new Array (this.refCigars.length); -for (var i = 0; i < this.refCigars.length; i++) { -sa[i] = this.refCigars[i]; -} -return sa; -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.CigarBase"], "jalview.datamodel.CigarArray", ["jalview.datamodel.CigarCigar", "$.SeqCigar", "java.lang.StringBuffer", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.refCigars = null; +this.seqcigararray = false; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "CigarArray", jalview.datamodel.CigarBase); +Clazz.defineMethod (c$, "isSeqCigarArray", +function () { +return this.seqcigararray; +}); +Clazz.makeConstructor (c$, +function (cigars) { +Clazz.superConstructor (this, jalview.datamodel.CigarArray); +this.seqcigararray = true; +if (cigars != null && cigars.length > 0) { +this.refCigars = new Array (cigars.length); +for (var c = 0; c < cigars.length; c++) { +this.refCigars[c] = cigars[c]; +if (!((Clazz.instanceOf (cigars[c], jalview.datamodel.SeqCigar)) || Clazz.instanceOf (cigars[c], jalview.datamodel.CigarCigar))) { +this.seqcigararray = false; +}} +}}, "~A"); +Clazz.makeConstructor (c$, +function (alignment, columnSelection, selectionGroup) { +this.construct (jalview.datamodel.CigarArray.constructSeqCigarArray (alignment, selectionGroup)); +this.constructFromAlignment (alignment, columnSelection != null ? columnSelection.getHiddenColumns () : null, selectionGroup); +}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup"); +c$._calcStartEndBounds = Clazz.defineMethod (c$, "_calcStartEndBounds", +($fz = function (alignment, selectionGroup) { +var startend = Clazz.newIntArray (-1, [0, 0, 0]); +if (selectionGroup != null) { +startend[0] = selectionGroup.getSize (); +startend[1] = selectionGroup.getStartRes (); +startend[2] = selectionGroup.getEndRes (); +} else { +startend[0] = alignment.getHeight (); +startend[2] = alignment.getWidth () - 1; +}return startend; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); +c$.constructSeqCigarArray = Clazz.defineMethod (c$, "constructSeqCigarArray", +function (alignment, selectionGroup) { +var seqs = null; +var i; +var iSize; +var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup); +var start = _startend[1]; +var end = _startend[2]; +if (selectionGroup != null) { +iSize = selectionGroup.getSize (); +seqs = selectionGroup.getSequencesInOrder (alignment); +start = selectionGroup.getStartRes (); +end = selectionGroup.getEndRes (); +} else { +iSize = alignment.getHeight (); +seqs = alignment.getSequencesArray (); +end = alignment.getWidth () - 1; +}var selseqs = new Array (iSize); +for (i = 0; i < iSize; i++) { +selseqs[i] = new jalview.datamodel.SeqCigar (seqs[i], start, end); +} +return selseqs; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "constructFromAlignment", +($fz = function (alignment, list, selectionGroup) { +var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup); +var start = _startend[1]; +var end = _startend[2]; +if (list != null) { +var region; +var hideStart; +var hideEnd; +var last = start; +for (var j = 0; new Boolean (last < end & j < list.size ()).valueOf (); j++) { +region = list.get (j); +hideStart = region[0]; +hideEnd = region[1]; +if (hideStart < last) { +if (hideEnd > last) { +hideStart = last; +} else { +continue; +}}if (hideStart > end) { +break; +}if (hideEnd > end) { +hideEnd = end; +}if (hideStart > hideEnd) { +break; +}if (last < hideStart) { +this.addOperation ('M', hideStart - last); +}this.addOperation ('D', 1 + hideEnd - hideStart); +last = hideEnd + 1; +} +if (last < end) { +this.addOperation ('M', end - last + 1); +}} else { +this.addOperation ('M', end - start + 1); +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "getArrayofSequenceAndDeletions", +function (GapChar) { +if (this.refCigars == null || this.refCigars.length == 0 || this.length == 0) { +return null; +}var sqanddels = new Array (this.refCigars.length); +for (var c = 0; c < this.refCigars.length; c++) { +var refString = this.refCigars[c].getSequenceString (GapChar); +if (refString != null) { +sqanddels[c] = this.getSequenceAndDeletions (refString, GapChar); +} else { +sqanddels[c] = null; +}} +return sqanddels; +}, "~S"); +Clazz.defineMethod (c$, "getSequenceString", +function (GapChar) { +if (this.length == 0 || this.refCigars == null) { +return ""; +}var seqStrings = new StringBuffer (); +var sqanddels = this.getArrayofSequenceAndDeletions (GapChar); +for (var c = 0; c < this.refCigars.length; c++) { +if (sqanddels[c] != null) { +seqStrings.append (sqanddels[c][0]); +sqanddels[c][0] = null; +}seqStrings.append ('\n'); +} +return seqStrings.toString (); +}, "~S"); +Clazz.defineMethod (c$, "getSequenceStrings", +function (GapChar) { +if (this.length == 0 || this.refCigars == null || this.refCigars.length == 0) { +return null; +}var sqanddels = this.getArrayofSequenceAndDeletions (GapChar); +var seqs = new Array (sqanddels.length); +for (var c = 0; c < this.refCigars.length; c++) { +seqs[c] = sqanddels[c][0]; +} +return seqs; +}, "~S"); +Clazz.defineMethod (c$, "applyDeletions", +function () { +var delpos = null; +if (this.length == 0) { +return null; +}var cursor = 0; +var vcursor = 0; +var offset = 0; +var i = 0; +while (i < this.length) { +if (this.operation[i] != 'D') { +if (this.operation[i] == 'M') { +cursor += this.range[i]; +}vcursor += this.range[i++]; +} else { +if (delpos == null) { +delpos = new java.util.Vector (); +}var delstart = cursor; +var delend = cursor + this.range[i] - 1; +delpos.addElement ( Clazz.newIntArray (-1, [vcursor + offset, this.range[i]])); +offset += this.range[i] - 1; +System.arraycopy (this.operation, i + 1, this.operation, i, this.length - i); +System.arraycopy (this.range, i + 1, this.range, i, this.length - i); +this.length--; +for (var s = 0; s < this.refCigars.length; s++) { +var d = this.refCigars[s].deleteRange (delstart, delend); +} +}} +if (delpos != null) { +var pos = Clazz.newIntArray (delpos.size () * 2, 0); +for (var k = 0, l = delpos.size (); k < l; k++) { +var dr = (delpos.elementAt (k)); +pos[k * 2] = dr[0]; +pos[k * 2 + 1] = dr[1]; +delpos.setElementAt (null, k); +} +delpos = null; +return pos; +}return null; +}); +Clazz.defineMethod (c$, "getSeqCigarArray", +function () { +if (!this.isSeqCigarArray ()) { +return null; +}var sa = new Array (this.refCigars.length); +for (var i = 0; i < this.refCigars.length; i++) { +sa[i] = this.refCigars[i]; +} +return sa; +}); +}); diff --git a/bin/jalview/datamodel/CigarBase.class b/bin/jalview/datamodel/CigarBase.class index d658368..7417a4d 100644 Binary files a/bin/jalview/datamodel/CigarBase.class and b/bin/jalview/datamodel/CigarBase.class differ diff --git a/bin/jalview/datamodel/CigarBase.js b/bin/jalview/datamodel/CigarBase.js index bd75085..5b88b3f 100644 --- a/bin/jalview/datamodel/CigarBase.js +++ b/bin/jalview/datamodel/CigarBase.js @@ -1,310 +1,310 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.CigarBase", ["jalview.util.MessageManager", "java.lang.Error", "$.Exception", "$.StringBuffer", "java.util.Vector", "javajs.util.AU"], function () { -c$ = Clazz.decorateAsClass (function () { -this.length = 0; -this._inc_length = 10; -this.operation = null; -this.range = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "CigarBase"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "getSequenceAndDeletions", -function (reference, GapChar) { -var rlength = 0; -var deletions = javajs.util.AU.newInt2 (this.length); -var trunc_deletions = null; -var sq = new StringBuffer (); -var cursor = 0; -var alcursor = 0; -var start = 0; -var startpos = 0; -var end = 0; -var endpos = 0; -var delcount = -1; -var consecutive_del = false; -if (this.length == 0) { -return null; -}if (reference != null) { -rlength = reference.length; -}var modstart = true; -for (var i = 0; i < this.length; i++) { -switch (this.operation[i]) { -case 'D': -if (!consecutive_del) { -deletions[++delcount] = Clazz.newIntArray (-1, [cursor, 0, alcursor]); -}cursor += this.range[i]; -deletions[delcount][1] = cursor - 1; -consecutive_del = true; -break; -case 'I': -consecutive_del = false; -for (var r = 0; r < this.range[i]; r++) { -sq.append (GapChar); -alcursor++; -} -break; -case 'M': -consecutive_del = false; -if (modstart) { -start = cursor; -startpos = alcursor; -modstart = false; -}if (reference != null) { -var sbend = cursor + this.range[i]; -if (sbend > rlength) { -sq.append (reference.substring (cursor, rlength)); -while (sbend-- >= rlength) { -sq.append (GapChar); -} -} else { -sq.append (reference.substring (cursor, sbend)); -}}alcursor += this.range[i]; -cursor += this.range[i]; -end = cursor - 1; -endpos = alcursor; -break; -default: -throw new Error (jalview.util.MessageManager.formatMessage ("error.unknown_seq_cigar_operation", Clazz.newArray (-1, [ new StringBuffer (this.operation[i].charCodeAt (0)).toString ()]))); -} -} -if (++delcount > 0) { -trunc_deletions = Clazz.newIntArray (delcount, 0); -System.arraycopy (deletions, 0, trunc_deletions, 0, delcount); -}deletions = null; -return Clazz.newArray (-1, [((reference != null) ? sq.toString () : null), Clazz.newIntArray (-1, [start, startpos, end, endpos]), trunc_deletions]); -}, "~S,~S"); -Clazz.defineMethod (c$, "compact_operations", -function () { -var i = 1; -if (this.operation == null) { -return; -}var last = this.operation[0]; -while (i < this.length) { -if (last == this.operation[i]) { -this.range[i - 1] += this.range[i]; -var r = this.length - i; -if (r > 0) { -System.arraycopy (this.range, i + 1, this.range, i, r); -System.arraycopy (this.operation, i + 1, this.operation, i, r); -}this.length--; -} else { -last = this.operation[i++]; -}} -}); -c$.parseCigarString = Clazz.defineMethod (c$, "parseCigarString", -function (cigarString) { -var ops = 0; -for (var i = 0, l = cigarString.length; i < l; i++) { -var c = cigarString.charAt (i); -if (c == 'M' || c.charCodeAt (0) == (45) || c == 'I' || c.charCodeAt (0) == (41) || c == 'D' || c.charCodeAt (0) == (36)) { -ops++; -}} -var operation = Clazz.newCharArray (ops, '\0'); -var range = Clazz.newIntArray (ops, 0); -var op = 0; -var i = 0; -var l = cigarString.length; -while (i < l) { -var c; -var j = i; -do { -c = cigarString.charAt (j++); -} while (c >= '0' && c <= '9' && j < l); -if (j >= l && c >= '0' && c <= '9') { -throw new Exception (jalview.util.MessageManager.getString ("exception.unterminated_cigar_string")); -}try { -var rangeint = cigarString.substring (i, j - 1); -range[op] = Integer.parseInt (rangeint); -i = j; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_bug_parse_cigar_string")); -} else { -throw e; -} -} -if (c >= 'a' && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) - 32); -}if ((c == 'M' || c == 'I' || c == 'D')) { -operation[op++] = c; -} else { -throw new Exception (jalview.util.MessageManager.formatMessage ("exception.unexpected_operation_cigar_string_pos", Clazz.newArray (-1, [ new StringBuffer (c.charCodeAt (0)).toString (), Integer.$valueOf (i).toString (), cigarString]))); -}} -return Clazz.newArray (-1, [operation, range]); -}, "~S"); -Clazz.defineMethod (c$, "addOperation", -function (op, range) { -if (op >= 'a' && op <= 'z') { -op = String.fromCharCode (op.charCodeAt (0) - 32); -}if (op != 'M' && op != 'D' && op != 'I') { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_invalid_operation_string")); -}if (range == 0) { -return; -}if (range < 0) { -throw new Error (jalview.util.MessageManager.getString ("error.invalid_range_string")); -}var lngth = 0; -if (this.operation == null) { -this.operation = Clazz.newCharArray (this._inc_length, '\0'); -this.range = Clazz.newIntArray (this._inc_length, 0); -}if (this.length + 1 == this.operation.length) { -var ops = this.operation; -this.operation = Clazz.newCharArray (this.length + 1 + this._inc_length, '\0'); -System.arraycopy (ops, 0, this.operation, 0, this.length); -ops = null; -var rng = this.range; -this.range = Clazz.newIntArray (this.length + 1 + this._inc_length, 0); -System.arraycopy (rng, 0, this.range, 0, this.length); -rng = null; -}if ((this.length > 0) && (this.operation[this.length - 1] == op)) { -this.length--; -} else { -this.range[this.length] = 0; -}this.operation[this.length] = op; -this.range[this.length++] += range; -}, "~S,~N"); -Clazz.defineMethod (c$, "deleteRange", -function (start, end) { -var deleted = 0; -if (this.length == 0) { -return deleted; -}if (start < 0 || start > end) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_delete_range_out_of_bounds")); -}var cursor = 0; -var rlength = 1 + end - start; -var oldlen = this.length; -var o = 0; -var editing = false; -var oldops = this.operation; -var oldrange = this.range; -this.length = 0; -this.operation = null; -this.range = null; -this.compact_operations (); -while (o < oldlen && cursor <= end && rlength > 0) { -if (oldops[o] == 'D') { -this.addDeleted (oldrange[o++]); -continue; -}var remain = oldrange[o]; -if (!editing) { -if ((cursor + remain) <= start) { -this.addOperation (oldops[o], oldrange[o]); -cursor += oldrange[o++]; -continue; -}editing = true; -if (start - cursor > 0) { -this.addOperation (oldops[o], start - cursor); -remain -= start - cursor; -}}if (o < oldlen && editing && rlength > 0 && remain > 0) { -switch (oldops[o]) { -case 'M': -if (rlength > remain) { -this.addDeleted (remain); -deleted += remain; -} else { -deleted += rlength; -this.addDeleted (rlength); -if (remain - rlength > 0) { -this.addOperation ('M', remain - rlength); -}rlength = 0; -remain = 0; -}break; -case 'I': -if (remain - rlength > 0) { -this.addInsertion (remain - rlength); -rlength = 0; -}break; -case 'D': -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error")); -default: -throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_unknown_operation", Clazz.newArray (-1, [ new StringBuffer (oldops[o].charCodeAt (0)).toString ()]))); -} -rlength -= remain; -remain = oldrange[++o]; -}} -while (o < oldlen) { -this.addOperation (oldops[o], oldrange[o++]); -} -return deleted; -}, "~N,~N"); -Clazz.defineMethod (c$, "hasDeletedRegions", -function () { -for (var i = 0; i < this.length; i++) { -if (this.operation[i] == 'D') { -return true; -}} -return false; -}); -Clazz.defineMethod (c$, "getDeletedRegions", -function () { -if (this.length == 0) { -return null; -}var dr = new java.util.Vector (); -var cursor = 0; -var vcursor = 0; -for (var i = 0; i < this.length; i++) { -switch (this.operation[i]) { -case 'M': -cursor += this.range[i]; -case 'I': -vcursor += this.range[i]; -break; -case 'D': -dr.addElement ( Clazz.newIntArray (-1, [vcursor, cursor, this.range[i]])); -cursor += this.range[i]; -} -} -if (dr.size () == 0) { -return null; -}var delregions = Clazz.newIntArray (dr.size () * 3, 0); -for (var i = 0, l = dr.size (); i < l; i++) { -var reg = dr.elementAt (i); -delregions[i * 3] = reg[0]; -delregions[i * 3 + 1] = reg[1]; -delregions[i * 3 + 2] = reg[2]; -} -return delregions; -}); -Clazz.defineMethod (c$, "getFullWidth", -function () { -var w = 0; -if (this.range != null) { -for (var i = 0; i < this.length; i++) { -w += this.range[i]; -} -}return w; -}); -Clazz.defineMethod (c$, "getWidth", -function () { -var w = 0; -if (this.range != null) { -for (var i = 0; i < this.length; i++) { -if (this.operation[i] == 'M' || this.operation[i] == 'I') { -w += this.range[i]; -}} -}return w; -}); -Clazz.defineMethod (c$, "addInsertion", -function (range) { -this.addOperation ('I', range); -}, "~N"); -Clazz.defineMethod (c$, "addDeleted", -function (range) { -this.addOperation ('D', range); -}, "~N"); -Clazz.defineMethod (c$, "getCigarstring", -function () { -var cigarString = new StringBuffer (); -for (var i = 0; i < this.length; i++) { -cigarString.append ("" + this.range[i]); -cigarString.append (this.operation[i]); -} -return cigarString.toString (); -}); -Clazz.defineStatics (c$, -"D", 'D', -"I", 'I', -"M", 'M', -"_case_shift", String.fromCharCode (32)); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.CigarBase", ["jalview.util.MessageManager", "java.lang.Error", "$.Exception", "$.StringBuffer", "java.util.Vector", "javajs.util.AU"], function () { +c$ = Clazz.decorateAsClass (function () { +this.length = 0; +this._inc_length = 10; +this.operation = null; +this.range = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "CigarBase"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "getSequenceAndDeletions", +function (reference, GapChar) { +var rlength = 0; +var deletions = javajs.util.AU.newInt2 (this.length); +var trunc_deletions = null; +var sq = new StringBuffer (); +var cursor = 0; +var alcursor = 0; +var start = 0; +var startpos = 0; +var end = 0; +var endpos = 0; +var delcount = -1; +var consecutive_del = false; +if (this.length == 0) { +return null; +}if (reference != null) { +rlength = reference.length; +}var modstart = true; +for (var i = 0; i < this.length; i++) { +switch (this.operation[i]) { +case 'D': +if (!consecutive_del) { +deletions[++delcount] = Clazz.newIntArray (-1, [cursor, 0, alcursor]); +}cursor += this.range[i]; +deletions[delcount][1] = cursor - 1; +consecutive_del = true; +break; +case 'I': +consecutive_del = false; +for (var r = 0; r < this.range[i]; r++) { +sq.append (GapChar); +alcursor++; +} +break; +case 'M': +consecutive_del = false; +if (modstart) { +start = cursor; +startpos = alcursor; +modstart = false; +}if (reference != null) { +var sbend = cursor + this.range[i]; +if (sbend > rlength) { +sq.append (reference.substring (cursor, rlength)); +while (sbend-- >= rlength) { +sq.append (GapChar); +} +} else { +sq.append (reference.substring (cursor, sbend)); +}}alcursor += this.range[i]; +cursor += this.range[i]; +end = cursor - 1; +endpos = alcursor; +break; +default: +throw new Error (jalview.util.MessageManager.formatMessage ("error.unknown_seq_cigar_operation", Clazz.newArray (-1, [ new StringBuffer (this.operation[i].charCodeAt (0)).toString ()]))); +} +} +if (++delcount > 0) { +trunc_deletions = Clazz.newIntArray (delcount, 0); +System.arraycopy (deletions, 0, trunc_deletions, 0, delcount); +}deletions = null; +return Clazz.newArray (-1, [((reference != null) ? sq.toString () : null), Clazz.newIntArray (-1, [start, startpos, end, endpos]), trunc_deletions]); +}, "~S,~S"); +Clazz.defineMethod (c$, "compact_operations", +function () { +var i = 1; +if (this.operation == null) { +return; +}var last = this.operation[0]; +while (i < this.length) { +if (last == this.operation[i]) { +this.range[i - 1] += this.range[i]; +var r = this.length - i; +if (r > 0) { +System.arraycopy (this.range, i + 1, this.range, i, r); +System.arraycopy (this.operation, i + 1, this.operation, i, r); +}this.length--; +} else { +last = this.operation[i++]; +}} +}); +c$.parseCigarString = Clazz.defineMethod (c$, "parseCigarString", +function (cigarString) { +var ops = 0; +for (var i = 0, l = cigarString.length; i < l; i++) { +var c = cigarString.charAt (i); +if (c == 'M' || c.charCodeAt (0) == (45) || c == 'I' || c.charCodeAt (0) == (41) || c == 'D' || c.charCodeAt (0) == (36)) { +ops++; +}} +var operation = Clazz.newCharArray (ops, '\0'); +var range = Clazz.newIntArray (ops, 0); +var op = 0; +var i = 0; +var l = cigarString.length; +while (i < l) { +var c; +var j = i; +do { +c = cigarString.charAt (j++); +} while (c >= '0' && c <= '9' && j < l); +if (j >= l && c >= '0' && c <= '9') { +throw new Exception (jalview.util.MessageManager.getString ("exception.unterminated_cigar_string")); +}try { +var rangeint = cigarString.substring (i, j - 1); +range[op] = Integer.parseInt (rangeint); +i = j; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_bug_parse_cigar_string")); +} else { +throw e; +} +} +if (c >= 'a' && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) - 32); +}if ((c == 'M' || c == 'I' || c == 'D')) { +operation[op++] = c; +} else { +throw new Exception (jalview.util.MessageManager.formatMessage ("exception.unexpected_operation_cigar_string_pos", Clazz.newArray (-1, [ new StringBuffer (c.charCodeAt (0)).toString (), Integer.$valueOf (i).toString (), cigarString]))); +}} +return Clazz.newArray (-1, [operation, range]); +}, "~S"); +Clazz.defineMethod (c$, "addOperation", +function (op, range) { +if (op >= 'a' && op <= 'z') { +op = String.fromCharCode (op.charCodeAt (0) - 32); +}if (op != 'M' && op != 'D' && op != 'I') { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_invalid_operation_string")); +}if (range == 0) { +return; +}if (range < 0) { +throw new Error (jalview.util.MessageManager.getString ("error.invalid_range_string")); +}var lngth = 0; +if (this.operation == null) { +this.operation = Clazz.newCharArray (this._inc_length, '\0'); +this.range = Clazz.newIntArray (this._inc_length, 0); +}if (this.length + 1 == this.operation.length) { +var ops = this.operation; +this.operation = Clazz.newCharArray (this.length + 1 + this._inc_length, '\0'); +System.arraycopy (ops, 0, this.operation, 0, this.length); +ops = null; +var rng = this.range; +this.range = Clazz.newIntArray (this.length + 1 + this._inc_length, 0); +System.arraycopy (rng, 0, this.range, 0, this.length); +rng = null; +}if ((this.length > 0) && (this.operation[this.length - 1] == op)) { +this.length--; +} else { +this.range[this.length] = 0; +}this.operation[this.length] = op; +this.range[this.length++] += range; +}, "~S,~N"); +Clazz.defineMethod (c$, "deleteRange", +function (start, end) { +var deleted = 0; +if (this.length == 0) { +return deleted; +}if (start < 0 || start > end) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_delete_range_out_of_bounds")); +}var cursor = 0; +var rlength = 1 + end - start; +var oldlen = this.length; +var o = 0; +var editing = false; +var oldops = this.operation; +var oldrange = this.range; +this.length = 0; +this.operation = null; +this.range = null; +this.compact_operations (); +while (o < oldlen && cursor <= end && rlength > 0) { +if (oldops[o] == 'D') { +this.addDeleted (oldrange[o++]); +continue; +}var remain = oldrange[o]; +if (!editing) { +if ((cursor + remain) <= start) { +this.addOperation (oldops[o], oldrange[o]); +cursor += oldrange[o++]; +continue; +}editing = true; +if (start - cursor > 0) { +this.addOperation (oldops[o], start - cursor); +remain -= start - cursor; +}}if (o < oldlen && editing && rlength > 0 && remain > 0) { +switch (oldops[o]) { +case 'M': +if (rlength > remain) { +this.addDeleted (remain); +deleted += remain; +} else { +deleted += rlength; +this.addDeleted (rlength); +if (remain - rlength > 0) { +this.addOperation ('M', remain - rlength); +}rlength = 0; +remain = 0; +}break; +case 'I': +if (remain - rlength > 0) { +this.addInsertion (remain - rlength); +rlength = 0; +}break; +case 'D': +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error")); +default: +throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_unknown_operation", Clazz.newArray (-1, [ new StringBuffer (oldops[o].charCodeAt (0)).toString ()]))); +} +rlength -= remain; +remain = oldrange[++o]; +}} +while (o < oldlen) { +this.addOperation (oldops[o], oldrange[o++]); +} +return deleted; +}, "~N,~N"); +Clazz.defineMethod (c$, "hasDeletedRegions", +function () { +for (var i = 0; i < this.length; i++) { +if (this.operation[i] == 'D') { +return true; +}} +return false; +}); +Clazz.defineMethod (c$, "getDeletedRegions", +function () { +if (this.length == 0) { +return null; +}var dr = new java.util.Vector (); +var cursor = 0; +var vcursor = 0; +for (var i = 0; i < this.length; i++) { +switch (this.operation[i]) { +case 'M': +cursor += this.range[i]; +case 'I': +vcursor += this.range[i]; +break; +case 'D': +dr.addElement ( Clazz.newIntArray (-1, [vcursor, cursor, this.range[i]])); +cursor += this.range[i]; +} +} +if (dr.size () == 0) { +return null; +}var delregions = Clazz.newIntArray (dr.size () * 3, 0); +for (var i = 0, l = dr.size (); i < l; i++) { +var reg = dr.elementAt (i); +delregions[i * 3] = reg[0]; +delregions[i * 3 + 1] = reg[1]; +delregions[i * 3 + 2] = reg[2]; +} +return delregions; +}); +Clazz.defineMethod (c$, "getFullWidth", +function () { +var w = 0; +if (this.range != null) { +for (var i = 0; i < this.length; i++) { +w += this.range[i]; +} +}return w; +}); +Clazz.defineMethod (c$, "getWidth", +function () { +var w = 0; +if (this.range != null) { +for (var i = 0; i < this.length; i++) { +if (this.operation[i] == 'M' || this.operation[i] == 'I') { +w += this.range[i]; +}} +}return w; +}); +Clazz.defineMethod (c$, "addInsertion", +function (range) { +this.addOperation ('I', range); +}, "~N"); +Clazz.defineMethod (c$, "addDeleted", +function (range) { +this.addOperation ('D', range); +}, "~N"); +Clazz.defineMethod (c$, "getCigarstring", +function () { +var cigarString = new StringBuffer (); +for (var i = 0; i < this.length; i++) { +cigarString.append ("" + this.range[i]); +cigarString.append (this.operation[i]); +} +return cigarString.toString (); +}); +Clazz.defineStatics (c$, +"D", 'D', +"I", 'I', +"M", 'M', +"_case_shift", String.fromCharCode (32)); +}); diff --git a/bin/jalview/datamodel/CigarCigar.js b/bin/jalview/datamodel/CigarCigar.js index 12f3e39..9448de4 100644 --- a/bin/jalview/datamodel/CigarCigar.js +++ b/bin/jalview/datamodel/CigarCigar.js @@ -1,22 +1,22 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.CigarSimple"], "jalview.datamodel.CigarCigar", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.refCigar = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "CigarCigar", jalview.datamodel.CigarSimple); -Clazz.makeConstructor (c$, -function (cigar) { -Clazz.superConstructor (this, jalview.datamodel.CigarCigar); -this.refCigar = cigar; -}, "jalview.datamodel.SeqCigar"); -Clazz.overrideMethod (c$, "getSequenceString", -function (GapChar) { -if (this.length == 0) { -return ""; -}var refString = this.refCigar.getSequenceString (GapChar); -if (refString != null) { -return (this.length == 0) ? "" : this.getSequenceAndDeletions (refString, GapChar)[0]; -} else { -return null; -}}, "~S"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.CigarSimple"], "jalview.datamodel.CigarCigar", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.refCigar = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "CigarCigar", jalview.datamodel.CigarSimple); +Clazz.makeConstructor (c$, +function (cigar) { +Clazz.superConstructor (this, jalview.datamodel.CigarCigar); +this.refCigar = cigar; +}, "jalview.datamodel.SeqCigar"); +Clazz.overrideMethod (c$, "getSequenceString", +function (GapChar) { +if (this.length == 0) { +return ""; +}var refString = this.refCigar.getSequenceString (GapChar); +if (refString != null) { +return (this.length == 0) ? "" : this.getSequenceAndDeletions (refString, GapChar)[0]; +} else { +return null; +}}, "~S"); +}); diff --git a/bin/jalview/datamodel/CigarSimple.js b/bin/jalview/datamodel/CigarSimple.js index 776f62a..1f9da1c 100644 --- a/bin/jalview/datamodel/CigarSimple.js +++ b/bin/jalview/datamodel/CigarSimple.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.CigarBase"], "jalview.datamodel.CigarSimple", null, function () { -c$ = Clazz.declareType (jalview.datamodel, "CigarSimple", jalview.datamodel.CigarBase); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.CigarBase"], "jalview.datamodel.CigarSimple", null, function () { +c$ = Clazz.declareType (jalview.datamodel, "CigarSimple", jalview.datamodel.CigarBase); +}); diff --git a/bin/jalview/datamodel/ColumnSelection.class b/bin/jalview/datamodel/ColumnSelection.class index c770c96..e80a262 100644 Binary files a/bin/jalview/datamodel/ColumnSelection.class and b/bin/jalview/datamodel/ColumnSelection.class differ diff --git a/bin/jalview/datamodel/ColumnSelection.js b/bin/jalview/datamodel/ColumnSelection.js index 6cab54c..b9e3e99 100644 --- a/bin/jalview/datamodel/ColumnSelection.js +++ b/bin/jalview/datamodel/ColumnSelection.js @@ -1,682 +1,682 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.util.Vector"], "jalview.datamodel.ColumnSelection", ["jalview.util.ShiftList", "jalview.viewmodel.annotationfilter.AnnotationFilterParameter", "java.lang.StringBuffer", "java.util.ArrayList", "$.Collections"], function () { -c$ = Clazz.decorateAsClass (function () { -this.selected = null; -this.hiddenColumns = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "ColumnSelection"); -Clazz.prepareFields (c$, function () { -this.selected = new java.util.Vector (); -}); -Clazz.defineMethod (c$, "addElement", -function (col) { -var column = new Integer (col); -if (!this.selected.contains (column)) { -this.selected.addElement (column); -}}, "~N"); -Clazz.defineMethod (c$, "clear", -function () { -this.selected.removeAllElements (); -}); -Clazz.defineMethod (c$, "removeElement", -function (col) { -var colInt = new Integer (col); -if (this.selected.contains (colInt)) { -this.selected.removeElement (colInt); -}}, "~N"); -Clazz.defineMethod (c$, "removeElements", -function (start, end) { -var colInt; -for (var i = start; i < end; i++) { -colInt = new Integer (i); -if (this.selected.contains (colInt)) { -this.selected.removeElement (colInt); -}} -}, "~N,~N"); -Clazz.defineMethod (c$, "getSelected", -function () { -return this.selected; -}); -Clazz.defineMethod (c$, "contains", -function (col) { -return this.selected.contains ( new Integer (col)); -}, "~N"); -Clazz.defineMethod (c$, "columnAt", -function (i) { -return this.selected.elementAt (i).intValue (); -}, "~N"); -Clazz.defineMethod (c$, "size", -function () { -return this.selected.size (); -}); -Clazz.defineMethod (c$, "getMax", -function () { -var max = -1; -for (var i = 0; i < this.selected.size (); i++) { -if (this.columnAt (i) > max) { -max = this.columnAt (i); -}} -return max; -}); -Clazz.defineMethod (c$, "getMin", -function () { -var min = 1000000000; -for (var i = 0; i < this.selected.size (); i++) { -if (this.columnAt (i) < min) { -min = this.columnAt (i); -}} -return min; -}); -Clazz.defineMethod (c$, "compensateForEdit", -function (start, change) { -var deletedHiddenColumns = null; -for (var i = 0; i < this.size (); i++) { -var temp = this.columnAt (i); -if (temp >= start) { -this.selected.setElementAt ( new Integer (temp - change), i); -}} -if (this.hiddenColumns != null) { -deletedHiddenColumns = new java.util.ArrayList (); -var hSize = this.hiddenColumns.size (); -for (var i = 0; i < hSize; i++) { -var region = this.hiddenColumns.elementAt (i); -if (region[0] > start && start + change > region[1]) { -deletedHiddenColumns.add (region); -this.hiddenColumns.removeElementAt (i); -i--; -hSize--; -continue; -}if (region[0] > start) { -region[0] -= change; -region[1] -= change; -}if (region[0] < 0) { -region[0] = 0; -}} -this.revealHiddenColumns (0); -}return deletedHiddenColumns; -}, "~N,~N"); -Clazz.defineMethod (c$, "compensateForDelEdits", -($fz = function (start, change) { -for (var i = 0; i < this.size (); i++) { -var temp = this.columnAt (i); -if (temp >= start) { -this.selected.setElementAt ( new Integer (temp - change), i); -}} -if (this.hiddenColumns != null) { -for (var i = 0; i < this.hiddenColumns.size (); i++) { -var region = this.hiddenColumns.elementAt (i); -if (region[0] >= start) { -region[0] -= change; -}if (region[1] >= start) { -region[1] -= change; -}if (region[1] < region[0]) { -this.hiddenColumns.removeElementAt (i--); -}if (region[0] < 0) { -region[0] = 0; -}if (region[1] < 0) { -region[1] = 0; -}} -}}, $fz.isPrivate = true, $fz), "~N,~N"); -Clazz.defineMethod (c$, "compensateForEdits", -function (shiftrecord) { -if (shiftrecord != null) { -var shifts = shiftrecord.getShifts (); -if (shifts != null && shifts.size () > 0) { -var shifted = 0; -for (var i = 0, j = shifts.size (); i < j; i++) { -var sh = shifts.get (i); -this.compensateForDelEdits (shifted + sh[0], sh[1]); -shifted -= sh[1]; -} -}return shiftrecord.getInverse (); -}return null; -}, "jalview.util.ShiftList"); -Clazz.defineMethod (c$, "pruneIntervalVector", -($fz = function (shifts, intervals) { -var pruned = false; -var i = 0; -var j = intervals.size () - 1; -var s = 0; -var t = shifts.size () - 1; -var hr = intervals.elementAt (i); -var sr = shifts.get (s); -while (i <= j && s <= t) { -var trailinghn = hr[1] >= sr[0]; -if (!trailinghn) { -if (i < j) { -hr = intervals.elementAt (++i); -} else { -i++; -}continue; -}var endshift = sr[0] + sr[1]; -if (endshift < hr[0] || endshift < sr[0]) { -if (s < t) { -sr = shifts.get (++s); -} else { -s++; -}continue; -}var leadinghn = hr[0] >= sr[0]; -var leadinghc = hr[0] < endshift; -var trailinghc = hr[1] < endshift; -if (leadinghn) { -if (trailinghc) { -intervals.removeElementAt (i); -pruned = true; -j--; -if (i <= j) { -hr = intervals.elementAt (i); -}continue; -}if (leadinghc) { -hr[0] = endshift; -leadinghn = !leadinghn; -pruned = true; -}}if (!leadinghn) { -if (trailinghc) { -if (trailinghn) { -hr[1] = sr[0] - 1; -pruned = true; -}} else { -if (s < t) { -sr = shifts.get (++s); -} else { -s++; -}continue; -}}} -return pruned; -}, $fz.isPrivate = true, $fz), "java.util.List,java.util.Vector"); -Clazz.defineMethod (c$, "pruneColumnList", -($fz = function (shifts, list) { -var s = 0; -var t = shifts.size (); -var sr = shifts.get (s++); -var pruned = false; -var i = 0; -var j = list.size (); -while (i < j && s <= t) { -var c = list.elementAt (i++).intValue (); -if (sr[0] <= c) { -if (sr[1] + sr[0] >= c) { -list.removeElementAt (--i); -j--; -} else { -if (s < t) { -sr = shifts.get (s); -}s++; -}}} -return pruned; -}, $fz.isPrivate = true, $fz), "java.util.List,java.util.Vector"); -Clazz.defineMethod (c$, "pruneDeletions", -function (deletions) { -if (deletions != null) { -var shifts = deletions.getShifts (); -if (shifts != null && shifts.size () > 0) { -if (this.hiddenColumns != null) { -this.pruneIntervalVector (shifts, this.hiddenColumns); -if (this.hiddenColumns != null && this.hiddenColumns.size () == 0) { -this.hiddenColumns = null; -}}if (this.selected != null && this.selected.size () > 0) { -this.pruneColumnList (shifts, this.selected); -if (this.selected != null && this.selected.size () == 0) { -this.selected = null; -}}this.compensateForEdits (deletions); -}}}, "jalview.util.ShiftList"); -Clazz.defineMethod (c$, "getHiddenColumns", -function () { -return this.hiddenColumns == null ? java.util.Collections.emptyList () : this.hiddenColumns; -}); -Clazz.defineMethod (c$, "adjustForHiddenColumns", -function (column) { -var result = column; -if (this.hiddenColumns != null) { -for (var i = 0; i < this.hiddenColumns.size (); i++) { -var region = this.hiddenColumns.elementAt (i); -if (result >= region[0]) { -result += region[1] - region[0] + 1; -}} -}return result; -}, "~N"); -Clazz.defineMethod (c$, "findColumnPosition", -function (hiddenColumn) { -var result = hiddenColumn; -if (this.hiddenColumns != null) { -var index = 0; -var region; -do { -region = this.hiddenColumns.elementAt (index++); -if (hiddenColumn > region[1]) { -result -= region[1] + 1 - region[0]; -}} while ((hiddenColumn > region[1]) && (index < this.hiddenColumns.size ())); -if (hiddenColumn > region[0] && hiddenColumn < region[1]) { -return region[0] + hiddenColumn - result; -}}return result; -}, "~N"); -Clazz.defineMethod (c$, "findHiddenRegionPosition", -function (hiddenRegion) { -var result = 0; -if (this.hiddenColumns != null) { -var index = 0; -var gaps = 0; -do { -var region = this.hiddenColumns.elementAt (index); -if (hiddenRegion == 0) { -return region[0]; -}gaps += region[1] + 1 - region[0]; -result = region[1] + 1; -index++; -} while (index < hiddenRegion + 1); -result -= gaps; -}return result; -}, "~N"); -Clazz.defineMethod (c$, "getHiddenBoundaryRight", -function (alPos) { -if (this.hiddenColumns != null) { -var index = 0; -do { -var region = this.hiddenColumns.elementAt (index); -if (alPos < region[0]) { -return region[0]; -}index++; -} while (index < this.hiddenColumns.size ()); -}return alPos; -}, "~N"); -Clazz.defineMethod (c$, "getHiddenBoundaryLeft", -function (alPos) { -if (this.hiddenColumns != null) { -var index = this.hiddenColumns.size () - 1; -do { -var region = this.hiddenColumns.elementAt (index); -if (alPos > region[1]) { -return region[1]; -}index--; -} while (index > -1); -}return alPos; -}, "~N"); -Clazz.defineMethod (c$, "hideSelectedColumns", -function () { -while (this.size () > 0) { -var column = this.getSelected ().firstElement ().intValue (); -this.hideColumns (column); -} -}); -Clazz.defineMethod (c$, "hideColumns", -function (start, end) { -if (this.hiddenColumns == null) { -this.hiddenColumns = new java.util.Vector (); -}var added = false; -var overlap = false; -for (var i = 0; i < this.hiddenColumns.size (); i++) { -var region = this.hiddenColumns.elementAt (i); -if (start <= region[1] && end >= region[0]) { -this.hiddenColumns.removeElementAt (i); -overlap = true; -break; -} else if (end < region[0] && start < region[0]) { -this.hiddenColumns.insertElementAt ( Clazz.newIntArray (-1, [start, end]), i); -added = true; -break; -}} -if (overlap) { -this.hideColumns (start, end); -} else if (!added) { -this.hiddenColumns.addElement ( Clazz.newIntArray (-1, [start, end])); -}}, "~N,~N"); -Clazz.defineMethod (c$, "hideColumns", -function (col) { -var min = col; -var max = col + 1; -while (this.contains (min)) { -this.removeElement (min); -min--; -} -while (this.contains (max)) { -this.removeElement (max); -max++; -} -min++; -max--; -if (min > max) { -min = max; -}this.hideColumns (min, max); -}, "~N"); -Clazz.defineMethod (c$, "revealAllHiddenColumns", -function () { -if (this.hiddenColumns != null) { -for (var i = 0; i < this.hiddenColumns.size (); i++) { -var region = this.hiddenColumns.elementAt (i); -for (var j = region[0]; j < region[1] + 1; j++) { -this.addElement (j); -} -} -}this.hiddenColumns = null; -}); -Clazz.defineMethod (c$, "revealHiddenColumns", -function (res) { -for (var i = 0; i < this.hiddenColumns.size (); i++) { -var region = this.hiddenColumns.elementAt (i); -if (res == region[0]) { -for (var j = region[0]; j < region[1] + 1; j++) { -this.addElement (j); -} -this.hiddenColumns.removeElement (region); -break; -}} -if (this.hiddenColumns.size () == 0) { -this.hiddenColumns = null; -}}, "~N"); -Clazz.defineMethod (c$, "isVisible", -function (column) { -if (this.hiddenColumns != null) { -for (var i = 0; i < this.hiddenColumns.size (); i++) { -var region = this.hiddenColumns.elementAt (i); -if (column >= region[0] && column <= region[1]) { -return false; -}} -}return true; -}, "~N"); -Clazz.makeConstructor (c$, -function (copy) { -if (copy != null) { -if (copy.selected != null) { -this.selected = new java.util.Vector (); -for (var i = 0, j = copy.selected.size (); i < j; i++) { -this.selected.addElement (copy.selected.elementAt (i)); -} -}if (copy.hiddenColumns != null) { -this.hiddenColumns = new java.util.Vector (copy.hiddenColumns.size ()); -for (var i = 0, j = copy.hiddenColumns.size (); i < j; i++) { -var rh; -var cp; -rh = copy.hiddenColumns.elementAt (i); -if (rh != null) { -cp = Clazz.newIntArray (rh.length, 0); -System.arraycopy (rh, 0, cp, 0, rh.length); -this.hiddenColumns.addElement (cp); -}} -}}}, "jalview.datamodel.ColumnSelection"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "getVisibleSequenceStrings", -function (start, end, seqs) { -var i; -var iSize = seqs.length; -var selection = new Array (iSize); -if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { -for (i = 0; i < iSize; i++) { -var visibleSeq = new StringBuffer (); -var regions = this.getHiddenColumns (); -var blockStart = start; -var blockEnd = end; -var region; -var hideStart; -var hideEnd; -for (var j = 0; j < regions.size (); j++) { -region = regions.get (j); -hideStart = region[0]; -hideEnd = region[1]; -if (hideStart < start) { -continue; -}blockStart = Math.min (blockStart, hideEnd + 1); -blockEnd = Math.min (blockEnd, hideStart); -if (blockStart > blockEnd) { -break; -}visibleSeq.append (seqs[i].getSequence (blockStart, blockEnd)); -blockStart = hideEnd + 1; -blockEnd = end; -} -if (end > blockStart) { -visibleSeq.append (seqs[i].getSequence (blockStart, end)); -}selection[i] = visibleSeq.toString (); -} -} else { -for (i = 0; i < iSize; i++) { -selection[i] = seqs[i].getSequenceAsString (start, end); -} -}return selection; -}, "~N,~N,~A"); -Clazz.defineMethod (c$, "getVisibleContigs", -function (start, end) { -if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { -var visiblecontigs = new java.util.ArrayList (); -var regions = this.getHiddenColumns (); -var vstart = start; -var region; -var hideStart; -var hideEnd; -for (var j = 0; vstart < end && j < regions.size (); j++) { -region = regions.get (j); -hideStart = region[0]; -hideEnd = region[1]; -if (hideEnd < vstart) { -continue; -}if (hideStart > vstart) { -visiblecontigs.add ( Clazz.newIntArray (-1, [vstart, hideStart - 1])); -}vstart = hideEnd + 1; -} -if (vstart < end) { -visiblecontigs.add ( Clazz.newIntArray (-1, [vstart, end - 1])); -}var vcontigs = Clazz.newIntArray (visiblecontigs.size () * 2, 0); -for (var i = 0, j = visiblecontigs.size (); i < j; i++) { -var vc = visiblecontigs.get (i); -visiblecontigs.set (i, null); -vcontigs[i * 2] = vc[0]; -vcontigs[i * 2 + 1] = vc[1]; -} -visiblecontigs.clear (); -return vcontigs; -} else { -return Clazz.newIntArray (-1, [start, end - 1]); -}}, "~N,~N"); -Clazz.defineMethod (c$, "makeVisibleAnnotation", -function (alignmentAnnotation) { -this.makeVisibleAnnotation (-1, -1, alignmentAnnotation); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "makeVisibleAnnotation", -function (start, end, alignmentAnnotation) { -if (alignmentAnnotation.annotations == null) { -return; -}if (start == end && end == -1) { -start = 0; -end = alignmentAnnotation.annotations.length; -}if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { -var annels = new java.util.Vector (); -var els = null; -var regions = this.getHiddenColumns (); -var blockStart = start; -var blockEnd = end; -var region; -var hideStart; -var hideEnd; -var w = 0; -for (var j = 0; j < regions.size (); j++) { -region = regions.get (j); -hideStart = region[0]; -hideEnd = region[1]; -if (hideStart < start) { -continue; -}blockStart = Math.min (blockStart, hideEnd + 1); -blockEnd = Math.min (blockEnd, hideStart); -if (blockStart > blockEnd) { -break; -}annels.addElement (els = new Array (blockEnd - blockStart)); -System.arraycopy (alignmentAnnotation.annotations, blockStart, els, 0, els.length); -w += els.length; -blockStart = hideEnd + 1; -blockEnd = end; -} -if (end > blockStart) { -annels.addElement (els = new Array (end - blockStart + 1)); -if ((els.length + blockStart) <= alignmentAnnotation.annotations.length) { -System.arraycopy (alignmentAnnotation.annotations, blockStart, els, 0, els.length); -} else { -System.arraycopy (alignmentAnnotation.annotations, blockStart, els, 0, (alignmentAnnotation.annotations.length - blockStart)); -}w += els.length; -}if (w == 0) { -return; -}alignmentAnnotation.annotations = new Array (w); -w = 0; -for (var chnk, $chnk = annels.iterator (); $chnk.hasNext () && ((chnk = $chnk.next ()) || true);) { -System.arraycopy (chnk, 0, alignmentAnnotation.annotations, w, chnk.length); -w += chnk.length; -} -} else { -alignmentAnnotation.restrict (start, end); -}}, "~N,~N,jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "invertColumnSelection", -function (first, width) { -var hasHidden = this.hiddenColumns != null && this.hiddenColumns.size () > 0; -for (var i = first; i < width; i++) { -if (this.contains (i)) { -this.removeElement (i); -} else { -if (!hasHidden || this.isVisible (i)) { -this.addElement (i); -}}} -}, "~N,~N"); -Clazz.defineMethod (c$, "addElementsFrom", -function (colsel) { -if (colsel != null && colsel.size () > 0) { -for (var col, $col = colsel.getSelected ().iterator (); $col.hasNext () && ((col = $col.next ()) || true);) { -if (this.hiddenColumns != null && this.isVisible (col.intValue ())) { -if (!this.selected.contains (col)) { -this.selected.addElement (col); -}}} -}}, "jalview.datamodel.ColumnSelection"); -Clazz.defineMethod (c$, "setElementsFrom", -function (colsel) { -this.selected = new java.util.Vector (); -if (colsel.selected != null && colsel.selected.size () > 0) { -if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { -this.addElementsFrom (colsel); -} else { -for (var col, $col = colsel.getSelected ().iterator (); $col.hasNext () && ((col = $col.next ()) || true);) { -this.addElement ((col).intValue ()); -} -}}}, "jalview.datamodel.ColumnSelection"); -c$.propagateInsertions = Clazz.defineMethod (c$, "propagateInsertions", -function (profileseq, al, input) { -var profsqpos = 0; -var gc = al.getGapCharacter (); -var alandcolsel = input.getAlignmentAndColumnSelection (gc); -var nview = alandcolsel[1]; -var origseq = (alandcolsel[0])[profsqpos]; -nview.propagateInsertions (profileseq, al, origseq); -return nview; -}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentView"); -Clazz.defineMethod (c$, "propagateInsertions", -function (profileseq, al, origseq) { -var gc = al.getGapCharacter (); -this.pruneDeletions (jalview.util.ShiftList.parseMap (origseq.gapMap ())); -var viscontigs = this.getVisibleContigs (0, profileseq.getLength ()); -var spos = 0; -var offset = 0; -for (var v = 0; v < viscontigs.length; v += 2) { -if (viscontigs[v] > spos) { -var sb = new StringBuffer (); -for (var s = 0, ns = viscontigs[v] - spos; s < ns; s++) { -sb.append (gc); -} -for (var s = 0, ns = al.getHeight (); s < ns; s++) { -var sqobj = al.getSequenceAt (s); -if (sqobj !== profileseq) { -var sq = al.getSequenceAt (s).getSequenceAsString (); -if (sq.length <= spos + offset) { -var diff = spos + offset - sq.length - 1; -if (diff > 0) { -sq = sq + sb; -while ((diff = spos + offset - sq.length - 1) > 0) { -if (diff >= sb.length ()) { -sq += sb.toString (); -} else { -var buf = Clazz.newCharArray (diff, '\0'); -sb.getChars (0, diff, buf, 0); -sq += buf.toString (); -}} -}sq += sb.toString (); -} else { -al.getSequenceAt (s).setSequence (sq.substring (0, spos + offset) + sb.toString () + sq.substring (spos + offset)); -}}} -}spos = viscontigs[v + 1] + 1; -} -if ((offset + spos) < profileseq.getLength ()) { -var sb = new StringBuffer (); -for (var s = 0, ns = profileseq.getLength () - spos - offset; s < ns; s++) { -sb.append (gc); -} -for (var s = 0, ns = al.getHeight (); s < ns; s++) { -var sqobj = al.getSequenceAt (s); -if (sqobj === profileseq) { -continue; -}var sq = sqobj.getSequenceAsString (); -var diff = origseq.getLength () - sq.length; -while (diff > 0) { -if (diff >= sb.length ()) { -sq += sb.toString (); -} else { -var buf = Clazz.newCharArray (diff, '\0'); -sb.getChars (0, diff, buf, 0); -sq += buf.toString (); -}diff = origseq.getLength () - sq.length; -} -} -}}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "hasSelectedColumns", -function () { -return (this.selected != null && this.selected.size () > 0); -}); -Clazz.defineMethod (c$, "hasHiddenColumns", -function () { -return this.hiddenColumns != null && this.hiddenColumns.size () > 0; -}); -Clazz.defineMethod (c$, "hasManyHiddenColumns", -function () { -return this.hiddenColumns != null && this.hiddenColumns.size () > 1; -}); -Clazz.defineMethod (c$, "hideInsertionsFor", -function (sr) { -var inserts = sr.getInsertions (); -for (var r, $r = inserts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { -this.hideColumns (r[0], r[1]); -} -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "filterAnnotations", -function (annotations, filterParams) { -this.revealAllHiddenColumns (); -this.clear (); -var count = 0; -do { -if (annotations[count] != null) { -var itemMatched = false; -if (filterParams.getThresholdType () === jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD && annotations[count].value >= filterParams.getThresholdValue ()) { -itemMatched = true; -}if (filterParams.getThresholdType () === jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD && annotations[count].value <= filterParams.getThresholdValue ()) { -itemMatched = true; -}if (filterParams.isFilterAlphaHelix () && annotations[count].secondaryStructure == 'H') { -itemMatched = true; -}if (filterParams.isFilterBetaSheet () && annotations[count].secondaryStructure == 'E') { -itemMatched = true; -}if (filterParams.isFilterTurn () && annotations[count].secondaryStructure == 'S') { -itemMatched = true; -}var regexSearchString = filterParams.getRegexString (); -if (regexSearchString != null && !filterParams.getRegexSearchFields ().isEmpty ()) { -var fields = filterParams.getRegexSearchFields (); -try { -if (fields.contains (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING) && annotations[count].displayCharacter.matches (regexSearchString)) { -itemMatched = true; -}} catch (pse) { -if (Clazz.exceptionOf (pse, java.util.regex.PatternSyntaxException)) { -if (annotations[count].displayCharacter.equals (regexSearchString)) { -itemMatched = true; -}} else { -throw pse; -} -} -if (fields.contains (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION) && annotations[count].description != null && annotations[count].description.matches (regexSearchString)) { -itemMatched = true; -}}if (itemMatched) { -this.addElement (count); -}}count++; -} while (count < annotations.length); -return false; -}, "~A,jalview.viewmodel.annotationfilter.AnnotationFilterParameter"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.util.Vector"], "jalview.datamodel.ColumnSelection", ["jalview.util.ShiftList", "jalview.viewmodel.annotationfilter.AnnotationFilterParameter", "java.lang.StringBuffer", "java.util.ArrayList", "$.Collections"], function () { +c$ = Clazz.decorateAsClass (function () { +this.selected = null; +this.hiddenColumns = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "ColumnSelection"); +Clazz.prepareFields (c$, function () { +this.selected = new java.util.Vector (); +}); +Clazz.defineMethod (c$, "addElement", +function (col) { +var column = new Integer (col); +if (!this.selected.contains (column)) { +this.selected.addElement (column); +}}, "~N"); +Clazz.defineMethod (c$, "clear", +function () { +this.selected.removeAllElements (); +}); +Clazz.defineMethod (c$, "removeElement", +function (col) { +var colInt = new Integer (col); +if (this.selected.contains (colInt)) { +this.selected.removeElement (colInt); +}}, "~N"); +Clazz.defineMethod (c$, "removeElements", +function (start, end) { +var colInt; +for (var i = start; i < end; i++) { +colInt = new Integer (i); +if (this.selected.contains (colInt)) { +this.selected.removeElement (colInt); +}} +}, "~N,~N"); +Clazz.defineMethod (c$, "getSelected", +function () { +return this.selected; +}); +Clazz.defineMethod (c$, "contains", +function (col) { +return this.selected.contains ( new Integer (col)); +}, "~N"); +Clazz.defineMethod (c$, "columnAt", +function (i) { +return this.selected.elementAt (i).intValue (); +}, "~N"); +Clazz.defineMethod (c$, "size", +function () { +return this.selected.size (); +}); +Clazz.defineMethod (c$, "getMax", +function () { +var max = -1; +for (var i = 0; i < this.selected.size (); i++) { +if (this.columnAt (i) > max) { +max = this.columnAt (i); +}} +return max; +}); +Clazz.defineMethod (c$, "getMin", +function () { +var min = 1000000000; +for (var i = 0; i < this.selected.size (); i++) { +if (this.columnAt (i) < min) { +min = this.columnAt (i); +}} +return min; +}); +Clazz.defineMethod (c$, "compensateForEdit", +function (start, change) { +var deletedHiddenColumns = null; +for (var i = 0; i < this.size (); i++) { +var temp = this.columnAt (i); +if (temp >= start) { +this.selected.setElementAt ( new Integer (temp - change), i); +}} +if (this.hiddenColumns != null) { +deletedHiddenColumns = new java.util.ArrayList (); +var hSize = this.hiddenColumns.size (); +for (var i = 0; i < hSize; i++) { +var region = this.hiddenColumns.elementAt (i); +if (region[0] > start && start + change > region[1]) { +deletedHiddenColumns.add (region); +this.hiddenColumns.removeElementAt (i); +i--; +hSize--; +continue; +}if (region[0] > start) { +region[0] -= change; +region[1] -= change; +}if (region[0] < 0) { +region[0] = 0; +}} +this.revealHiddenColumns (0); +}return deletedHiddenColumns; +}, "~N,~N"); +Clazz.defineMethod (c$, "compensateForDelEdits", +($fz = function (start, change) { +for (var i = 0; i < this.size (); i++) { +var temp = this.columnAt (i); +if (temp >= start) { +this.selected.setElementAt ( new Integer (temp - change), i); +}} +if (this.hiddenColumns != null) { +for (var i = 0; i < this.hiddenColumns.size (); i++) { +var region = this.hiddenColumns.elementAt (i); +if (region[0] >= start) { +region[0] -= change; +}if (region[1] >= start) { +region[1] -= change; +}if (region[1] < region[0]) { +this.hiddenColumns.removeElementAt (i--); +}if (region[0] < 0) { +region[0] = 0; +}if (region[1] < 0) { +region[1] = 0; +}} +}}, $fz.isPrivate = true, $fz), "~N,~N"); +Clazz.defineMethod (c$, "compensateForEdits", +function (shiftrecord) { +if (shiftrecord != null) { +var shifts = shiftrecord.getShifts (); +if (shifts != null && shifts.size () > 0) { +var shifted = 0; +for (var i = 0, j = shifts.size (); i < j; i++) { +var sh = shifts.get (i); +this.compensateForDelEdits (shifted + sh[0], sh[1]); +shifted -= sh[1]; +} +}return shiftrecord.getInverse (); +}return null; +}, "jalview.util.ShiftList"); +Clazz.defineMethod (c$, "pruneIntervalVector", +($fz = function (shifts, intervals) { +var pruned = false; +var i = 0; +var j = intervals.size () - 1; +var s = 0; +var t = shifts.size () - 1; +var hr = intervals.elementAt (i); +var sr = shifts.get (s); +while (i <= j && s <= t) { +var trailinghn = hr[1] >= sr[0]; +if (!trailinghn) { +if (i < j) { +hr = intervals.elementAt (++i); +} else { +i++; +}continue; +}var endshift = sr[0] + sr[1]; +if (endshift < hr[0] || endshift < sr[0]) { +if (s < t) { +sr = shifts.get (++s); +} else { +s++; +}continue; +}var leadinghn = hr[0] >= sr[0]; +var leadinghc = hr[0] < endshift; +var trailinghc = hr[1] < endshift; +if (leadinghn) { +if (trailinghc) { +intervals.removeElementAt (i); +pruned = true; +j--; +if (i <= j) { +hr = intervals.elementAt (i); +}continue; +}if (leadinghc) { +hr[0] = endshift; +leadinghn = !leadinghn; +pruned = true; +}}if (!leadinghn) { +if (trailinghc) { +if (trailinghn) { +hr[1] = sr[0] - 1; +pruned = true; +}} else { +if (s < t) { +sr = shifts.get (++s); +} else { +s++; +}continue; +}}} +return pruned; +}, $fz.isPrivate = true, $fz), "java.util.List,java.util.Vector"); +Clazz.defineMethod (c$, "pruneColumnList", +($fz = function (shifts, list) { +var s = 0; +var t = shifts.size (); +var sr = shifts.get (s++); +var pruned = false; +var i = 0; +var j = list.size (); +while (i < j && s <= t) { +var c = list.elementAt (i++).intValue (); +if (sr[0] <= c) { +if (sr[1] + sr[0] >= c) { +list.removeElementAt (--i); +j--; +} else { +if (s < t) { +sr = shifts.get (s); +}s++; +}}} +return pruned; +}, $fz.isPrivate = true, $fz), "java.util.List,java.util.Vector"); +Clazz.defineMethod (c$, "pruneDeletions", +function (deletions) { +if (deletions != null) { +var shifts = deletions.getShifts (); +if (shifts != null && shifts.size () > 0) { +if (this.hiddenColumns != null) { +this.pruneIntervalVector (shifts, this.hiddenColumns); +if (this.hiddenColumns != null && this.hiddenColumns.size () == 0) { +this.hiddenColumns = null; +}}if (this.selected != null && this.selected.size () > 0) { +this.pruneColumnList (shifts, this.selected); +if (this.selected != null && this.selected.size () == 0) { +this.selected = null; +}}this.compensateForEdits (deletions); +}}}, "jalview.util.ShiftList"); +Clazz.defineMethod (c$, "getHiddenColumns", +function () { +return this.hiddenColumns == null ? java.util.Collections.emptyList () : this.hiddenColumns; +}); +Clazz.defineMethod (c$, "adjustForHiddenColumns", +function (column) { +var result = column; +if (this.hiddenColumns != null) { +for (var i = 0; i < this.hiddenColumns.size (); i++) { +var region = this.hiddenColumns.elementAt (i); +if (result >= region[0]) { +result += region[1] - region[0] + 1; +}} +}return result; +}, "~N"); +Clazz.defineMethod (c$, "findColumnPosition", +function (hiddenColumn) { +var result = hiddenColumn; +if (this.hiddenColumns != null) { +var index = 0; +var region; +do { +region = this.hiddenColumns.elementAt (index++); +if (hiddenColumn > region[1]) { +result -= region[1] + 1 - region[0]; +}} while ((hiddenColumn > region[1]) && (index < this.hiddenColumns.size ())); +if (hiddenColumn > region[0] && hiddenColumn < region[1]) { +return region[0] + hiddenColumn - result; +}}return result; +}, "~N"); +Clazz.defineMethod (c$, "findHiddenRegionPosition", +function (hiddenRegion) { +var result = 0; +if (this.hiddenColumns != null) { +var index = 0; +var gaps = 0; +do { +var region = this.hiddenColumns.elementAt (index); +if (hiddenRegion == 0) { +return region[0]; +}gaps += region[1] + 1 - region[0]; +result = region[1] + 1; +index++; +} while (index < hiddenRegion + 1); +result -= gaps; +}return result; +}, "~N"); +Clazz.defineMethod (c$, "getHiddenBoundaryRight", +function (alPos) { +if (this.hiddenColumns != null) { +var index = 0; +do { +var region = this.hiddenColumns.elementAt (index); +if (alPos < region[0]) { +return region[0]; +}index++; +} while (index < this.hiddenColumns.size ()); +}return alPos; +}, "~N"); +Clazz.defineMethod (c$, "getHiddenBoundaryLeft", +function (alPos) { +if (this.hiddenColumns != null) { +var index = this.hiddenColumns.size () - 1; +do { +var region = this.hiddenColumns.elementAt (index); +if (alPos > region[1]) { +return region[1]; +}index--; +} while (index > -1); +}return alPos; +}, "~N"); +Clazz.defineMethod (c$, "hideSelectedColumns", +function () { +while (this.size () > 0) { +var column = this.getSelected ().firstElement ().intValue (); +this.hideColumns (column); +} +}); +Clazz.defineMethod (c$, "hideColumns", +function (start, end) { +if (this.hiddenColumns == null) { +this.hiddenColumns = new java.util.Vector (); +}var added = false; +var overlap = false; +for (var i = 0; i < this.hiddenColumns.size (); i++) { +var region = this.hiddenColumns.elementAt (i); +if (start <= region[1] && end >= region[0]) { +this.hiddenColumns.removeElementAt (i); +overlap = true; +break; +} else if (end < region[0] && start < region[0]) { +this.hiddenColumns.insertElementAt ( Clazz.newIntArray (-1, [start, end]), i); +added = true; +break; +}} +if (overlap) { +this.hideColumns (start, end); +} else if (!added) { +this.hiddenColumns.addElement ( Clazz.newIntArray (-1, [start, end])); +}}, "~N,~N"); +Clazz.defineMethod (c$, "hideColumns", +function (col) { +var min = col; +var max = col + 1; +while (this.contains (min)) { +this.removeElement (min); +min--; +} +while (this.contains (max)) { +this.removeElement (max); +max++; +} +min++; +max--; +if (min > max) { +min = max; +}this.hideColumns (min, max); +}, "~N"); +Clazz.defineMethod (c$, "revealAllHiddenColumns", +function () { +if (this.hiddenColumns != null) { +for (var i = 0; i < this.hiddenColumns.size (); i++) { +var region = this.hiddenColumns.elementAt (i); +for (var j = region[0]; j < region[1] + 1; j++) { +this.addElement (j); +} +} +}this.hiddenColumns = null; +}); +Clazz.defineMethod (c$, "revealHiddenColumns", +function (res) { +for (var i = 0; i < this.hiddenColumns.size (); i++) { +var region = this.hiddenColumns.elementAt (i); +if (res == region[0]) { +for (var j = region[0]; j < region[1] + 1; j++) { +this.addElement (j); +} +this.hiddenColumns.removeElement (region); +break; +}} +if (this.hiddenColumns.size () == 0) { +this.hiddenColumns = null; +}}, "~N"); +Clazz.defineMethod (c$, "isVisible", +function (column) { +if (this.hiddenColumns != null) { +for (var i = 0; i < this.hiddenColumns.size (); i++) { +var region = this.hiddenColumns.elementAt (i); +if (column >= region[0] && column <= region[1]) { +return false; +}} +}return true; +}, "~N"); +Clazz.makeConstructor (c$, +function (copy) { +if (copy != null) { +if (copy.selected != null) { +this.selected = new java.util.Vector (); +for (var i = 0, j = copy.selected.size (); i < j; i++) { +this.selected.addElement (copy.selected.elementAt (i)); +} +}if (copy.hiddenColumns != null) { +this.hiddenColumns = new java.util.Vector (copy.hiddenColumns.size ()); +for (var i = 0, j = copy.hiddenColumns.size (); i < j; i++) { +var rh; +var cp; +rh = copy.hiddenColumns.elementAt (i); +if (rh != null) { +cp = Clazz.newIntArray (rh.length, 0); +System.arraycopy (rh, 0, cp, 0, rh.length); +this.hiddenColumns.addElement (cp); +}} +}}}, "jalview.datamodel.ColumnSelection"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "getVisibleSequenceStrings", +function (start, end, seqs) { +var i; +var iSize = seqs.length; +var selection = new Array (iSize); +if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { +for (i = 0; i < iSize; i++) { +var visibleSeq = new StringBuffer (); +var regions = this.getHiddenColumns (); +var blockStart = start; +var blockEnd = end; +var region; +var hideStart; +var hideEnd; +for (var j = 0; j < regions.size (); j++) { +region = regions.get (j); +hideStart = region[0]; +hideEnd = region[1]; +if (hideStart < start) { +continue; +}blockStart = Math.min (blockStart, hideEnd + 1); +blockEnd = Math.min (blockEnd, hideStart); +if (blockStart > blockEnd) { +break; +}visibleSeq.append (seqs[i].getSequence (blockStart, blockEnd)); +blockStart = hideEnd + 1; +blockEnd = end; +} +if (end > blockStart) { +visibleSeq.append (seqs[i].getSequence (blockStart, end)); +}selection[i] = visibleSeq.toString (); +} +} else { +for (i = 0; i < iSize; i++) { +selection[i] = seqs[i].getSequenceAsString (start, end); +} +}return selection; +}, "~N,~N,~A"); +Clazz.defineMethod (c$, "getVisibleContigs", +function (start, end) { +if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { +var visiblecontigs = new java.util.ArrayList (); +var regions = this.getHiddenColumns (); +var vstart = start; +var region; +var hideStart; +var hideEnd; +for (var j = 0; vstart < end && j < regions.size (); j++) { +region = regions.get (j); +hideStart = region[0]; +hideEnd = region[1]; +if (hideEnd < vstart) { +continue; +}if (hideStart > vstart) { +visiblecontigs.add ( Clazz.newIntArray (-1, [vstart, hideStart - 1])); +}vstart = hideEnd + 1; +} +if (vstart < end) { +visiblecontigs.add ( Clazz.newIntArray (-1, [vstart, end - 1])); +}var vcontigs = Clazz.newIntArray (visiblecontigs.size () * 2, 0); +for (var i = 0, j = visiblecontigs.size (); i < j; i++) { +var vc = visiblecontigs.get (i); +visiblecontigs.set (i, null); +vcontigs[i * 2] = vc[0]; +vcontigs[i * 2 + 1] = vc[1]; +} +visiblecontigs.clear (); +return vcontigs; +} else { +return Clazz.newIntArray (-1, [start, end - 1]); +}}, "~N,~N"); +Clazz.defineMethod (c$, "makeVisibleAnnotation", +function (alignmentAnnotation) { +this.makeVisibleAnnotation (-1, -1, alignmentAnnotation); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "makeVisibleAnnotation", +function (start, end, alignmentAnnotation) { +if (alignmentAnnotation.annotations == null) { +return; +}if (start == end && end == -1) { +start = 0; +end = alignmentAnnotation.annotations.length; +}if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { +var annels = new java.util.Vector (); +var els = null; +var regions = this.getHiddenColumns (); +var blockStart = start; +var blockEnd = end; +var region; +var hideStart; +var hideEnd; +var w = 0; +for (var j = 0; j < regions.size (); j++) { +region = regions.get (j); +hideStart = region[0]; +hideEnd = region[1]; +if (hideStart < start) { +continue; +}blockStart = Math.min (blockStart, hideEnd + 1); +blockEnd = Math.min (blockEnd, hideStart); +if (blockStart > blockEnd) { +break; +}annels.addElement (els = new Array (blockEnd - blockStart)); +System.arraycopy (alignmentAnnotation.annotations, blockStart, els, 0, els.length); +w += els.length; +blockStart = hideEnd + 1; +blockEnd = end; +} +if (end > blockStart) { +annels.addElement (els = new Array (end - blockStart + 1)); +if ((els.length + blockStart) <= alignmentAnnotation.annotations.length) { +System.arraycopy (alignmentAnnotation.annotations, blockStart, els, 0, els.length); +} else { +System.arraycopy (alignmentAnnotation.annotations, blockStart, els, 0, (alignmentAnnotation.annotations.length - blockStart)); +}w += els.length; +}if (w == 0) { +return; +}alignmentAnnotation.annotations = new Array (w); +w = 0; +for (var chnk, $chnk = annels.iterator (); $chnk.hasNext () && ((chnk = $chnk.next ()) || true);) { +System.arraycopy (chnk, 0, alignmentAnnotation.annotations, w, chnk.length); +w += chnk.length; +} +} else { +alignmentAnnotation.restrict (start, end); +}}, "~N,~N,jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "invertColumnSelection", +function (first, width) { +var hasHidden = this.hiddenColumns != null && this.hiddenColumns.size () > 0; +for (var i = first; i < width; i++) { +if (this.contains (i)) { +this.removeElement (i); +} else { +if (!hasHidden || this.isVisible (i)) { +this.addElement (i); +}}} +}, "~N,~N"); +Clazz.defineMethod (c$, "addElementsFrom", +function (colsel) { +if (colsel != null && colsel.size () > 0) { +for (var col, $col = colsel.getSelected ().iterator (); $col.hasNext () && ((col = $col.next ()) || true);) { +if (this.hiddenColumns != null && this.isVisible (col.intValue ())) { +if (!this.selected.contains (col)) { +this.selected.addElement (col); +}}} +}}, "jalview.datamodel.ColumnSelection"); +Clazz.defineMethod (c$, "setElementsFrom", +function (colsel) { +this.selected = new java.util.Vector (); +if (colsel.selected != null && colsel.selected.size () > 0) { +if (this.hiddenColumns != null && this.hiddenColumns.size () > 0) { +this.addElementsFrom (colsel); +} else { +for (var col, $col = colsel.getSelected ().iterator (); $col.hasNext () && ((col = $col.next ()) || true);) { +this.addElement ((col).intValue ()); +} +}}}, "jalview.datamodel.ColumnSelection"); +c$.propagateInsertions = Clazz.defineMethod (c$, "propagateInsertions", +function (profileseq, al, input) { +var profsqpos = 0; +var gc = al.getGapCharacter (); +var alandcolsel = input.getAlignmentAndColumnSelection (gc); +var nview = alandcolsel[1]; +var origseq = (alandcolsel[0])[profsqpos]; +nview.propagateInsertions (profileseq, al, origseq); +return nview; +}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentView"); +Clazz.defineMethod (c$, "propagateInsertions", +function (profileseq, al, origseq) { +var gc = al.getGapCharacter (); +this.pruneDeletions (jalview.util.ShiftList.parseMap (origseq.gapMap ())); +var viscontigs = this.getVisibleContigs (0, profileseq.getLength ()); +var spos = 0; +var offset = 0; +for (var v = 0; v < viscontigs.length; v += 2) { +if (viscontigs[v] > spos) { +var sb = new StringBuffer (); +for (var s = 0, ns = viscontigs[v] - spos; s < ns; s++) { +sb.append (gc); +} +for (var s = 0, ns = al.getHeight (); s < ns; s++) { +var sqobj = al.getSequenceAt (s); +if (sqobj !== profileseq) { +var sq = al.getSequenceAt (s).getSequenceAsString (); +if (sq.length <= spos + offset) { +var diff = spos + offset - sq.length - 1; +if (diff > 0) { +sq = sq + sb; +while ((diff = spos + offset - sq.length - 1) > 0) { +if (diff >= sb.length ()) { +sq += sb.toString (); +} else { +var buf = Clazz.newCharArray (diff, '\0'); +sb.getChars (0, diff, buf, 0); +sq += buf.toString (); +}} +}sq += sb.toString (); +} else { +al.getSequenceAt (s).setSequence (sq.substring (0, spos + offset) + sb.toString () + sq.substring (spos + offset)); +}}} +}spos = viscontigs[v + 1] + 1; +} +if ((offset + spos) < profileseq.getLength ()) { +var sb = new StringBuffer (); +for (var s = 0, ns = profileseq.getLength () - spos - offset; s < ns; s++) { +sb.append (gc); +} +for (var s = 0, ns = al.getHeight (); s < ns; s++) { +var sqobj = al.getSequenceAt (s); +if (sqobj === profileseq) { +continue; +}var sq = sqobj.getSequenceAsString (); +var diff = origseq.getLength () - sq.length; +while (diff > 0) { +if (diff >= sb.length ()) { +sq += sb.toString (); +} else { +var buf = Clazz.newCharArray (diff, '\0'); +sb.getChars (0, diff, buf, 0); +sq += buf.toString (); +}diff = origseq.getLength () - sq.length; +} +} +}}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "hasSelectedColumns", +function () { +return (this.selected != null && this.selected.size () > 0); +}); +Clazz.defineMethod (c$, "hasHiddenColumns", +function () { +return this.hiddenColumns != null && this.hiddenColumns.size () > 0; +}); +Clazz.defineMethod (c$, "hasManyHiddenColumns", +function () { +return this.hiddenColumns != null && this.hiddenColumns.size () > 1; +}); +Clazz.defineMethod (c$, "hideInsertionsFor", +function (sr) { +var inserts = sr.getInsertions (); +for (var r, $r = inserts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { +this.hideColumns (r[0], r[1]); +} +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "filterAnnotations", +function (annotations, filterParams) { +this.revealAllHiddenColumns (); +this.clear (); +var count = 0; +do { +if (annotations[count] != null) { +var itemMatched = false; +if (filterParams.getThresholdType () === jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD && annotations[count].value >= filterParams.getThresholdValue ()) { +itemMatched = true; +}if (filterParams.getThresholdType () === jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD && annotations[count].value <= filterParams.getThresholdValue ()) { +itemMatched = true; +}if (filterParams.isFilterAlphaHelix () && annotations[count].secondaryStructure == 'H') { +itemMatched = true; +}if (filterParams.isFilterBetaSheet () && annotations[count].secondaryStructure == 'E') { +itemMatched = true; +}if (filterParams.isFilterTurn () && annotations[count].secondaryStructure == 'S') { +itemMatched = true; +}var regexSearchString = filterParams.getRegexString (); +if (regexSearchString != null && !filterParams.getRegexSearchFields ().isEmpty ()) { +var fields = filterParams.getRegexSearchFields (); +try { +if (fields.contains (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING) && annotations[count].displayCharacter.matches (regexSearchString)) { +itemMatched = true; +}} catch (pse) { +if (Clazz.exceptionOf (pse, java.util.regex.PatternSyntaxException)) { +if (annotations[count].displayCharacter.equals (regexSearchString)) { +itemMatched = true; +}} else { +throw pse; +} +} +if (fields.contains (jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION) && annotations[count].description != null && annotations[count].description.matches (regexSearchString)) { +itemMatched = true; +}}if (itemMatched) { +this.addElement (count); +}}count++; +} while (count < annotations.length); +return false; +}, "~A,jalview.viewmodel.annotationfilter.AnnotationFilterParameter"); +}); diff --git a/bin/jalview/datamodel/DBRefEntry.js b/bin/jalview/datamodel/DBRefEntry.js index da2e0cb..148cf99 100644 --- a/bin/jalview/datamodel/DBRefEntry.js +++ b/bin/jalview/datamodel/DBRefEntry.js @@ -1,93 +1,93 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.DBRefEntry", ["jalview.datamodel.Mapping"], function () { -c$ = Clazz.decorateAsClass (function () { -this.source = ""; -this.version = ""; -this.accessionId = ""; -this.map = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "DBRefEntry"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (source, version, accessionId) { -this.construct (source, version, accessionId, null); -}, "~S,~S,~S"); -Clazz.makeConstructor (c$, -function (source, version, accessionId, map) { -this.source = source.toUpperCase (); -this.version = version; -this.accessionId = accessionId; -this.map = map; -}, "~S,~S,~S,jalview.datamodel.Mapping"); -Clazz.makeConstructor (c$, -function (entry) { -this.construct ((entry.source == null ? "" : String.instantialize (entry.source)), (entry.version == null ? "" : String.instantialize (entry.version)), (entry.accessionId == null ? "" : String.instantialize (entry.accessionId)), (entry.map == null ? null : new jalview.datamodel.Mapping (entry.map))); -}, "jalview.datamodel.DBRefEntry"); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.DBRefEntry))) { -return false; -}var entry = o; -if (entry === this) { -return true; -}if (this.equalRef (entry) && ((this.map == null && entry.map == null) || (this.map != null && entry.map != null && this.map.equals (entry.map)))) { -return true; -}return false; -}, "~O"); -Clazz.defineMethod (c$, "equalRef", -function (entry) { -if (entry == null) { -return false; -}if (entry === this) { -return true; -}if ((this.source != null && entry.source != null && this.source.equalsIgnoreCase (entry.source)) && (this.accessionId != null && entry.accessionId != null && this.accessionId.equalsIgnoreCase (entry.accessionId)) && (this.version != null && entry.version != null && this.version.equalsIgnoreCase (entry.version))) { -return true; -}return false; -}, "jalview.datamodel.DBRefEntry"); -Clazz.defineMethod (c$, "getSource", -function () { -return this.source; -}); -Clazz.defineMethod (c$, "getVersion", -function () { -return this.version; -}); -Clazz.defineMethod (c$, "getAccessionId", -function () { -return this.accessionId; -}); -Clazz.defineMethod (c$, "setAccessionId", -function (accessionId) { -this.accessionId = accessionId; -}, "~S"); -Clazz.defineMethod (c$, "setSource", -function (source) { -this.source = source; -}, "~S"); -Clazz.defineMethod (c$, "setVersion", -function (version) { -this.version = version; -}, "~S"); -Clazz.defineMethod (c$, "getMap", -function () { -return this.map; -}); -Clazz.defineMethod (c$, "setMap", -function (map) { -this.map = map; -}, "jalview.datamodel.Mapping"); -Clazz.defineMethod (c$, "hasMap", -function () { -return this.map != null; -}); -Clazz.defineMethod (c$, "getSrcAccString", -function () { -return ((this.source != null) ? this.source : "") + ":" + ((this.accessionId != null) ? this.accessionId : ""); -}); -Clazz.overrideMethod (c$, "toString", -function () { -return this.getSrcAccString (); -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.DBRefEntry", ["jalview.datamodel.Mapping"], function () { +c$ = Clazz.decorateAsClass (function () { +this.source = ""; +this.version = ""; +this.accessionId = ""; +this.map = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "DBRefEntry"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (source, version, accessionId) { +this.construct (source, version, accessionId, null); +}, "~S,~S,~S"); +Clazz.makeConstructor (c$, +function (source, version, accessionId, map) { +this.source = source.toUpperCase (); +this.version = version; +this.accessionId = accessionId; +this.map = map; +}, "~S,~S,~S,jalview.datamodel.Mapping"); +Clazz.makeConstructor (c$, +function (entry) { +this.construct ((entry.source == null ? "" : String.instantialize (entry.source)), (entry.version == null ? "" : String.instantialize (entry.version)), (entry.accessionId == null ? "" : String.instantialize (entry.accessionId)), (entry.map == null ? null : new jalview.datamodel.Mapping (entry.map))); +}, "jalview.datamodel.DBRefEntry"); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.DBRefEntry))) { +return false; +}var entry = o; +if (entry === this) { +return true; +}if (this.equalRef (entry) && ((this.map == null && entry.map == null) || (this.map != null && entry.map != null && this.map.equals (entry.map)))) { +return true; +}return false; +}, "~O"); +Clazz.defineMethod (c$, "equalRef", +function (entry) { +if (entry == null) { +return false; +}if (entry === this) { +return true; +}if ((this.source != null && entry.source != null && this.source.equalsIgnoreCase (entry.source)) && (this.accessionId != null && entry.accessionId != null && this.accessionId.equalsIgnoreCase (entry.accessionId)) && (this.version != null && entry.version != null && this.version.equalsIgnoreCase (entry.version))) { +return true; +}return false; +}, "jalview.datamodel.DBRefEntry"); +Clazz.defineMethod (c$, "getSource", +function () { +return this.source; +}); +Clazz.defineMethod (c$, "getVersion", +function () { +return this.version; +}); +Clazz.defineMethod (c$, "getAccessionId", +function () { +return this.accessionId; +}); +Clazz.defineMethod (c$, "setAccessionId", +function (accessionId) { +this.accessionId = accessionId; +}, "~S"); +Clazz.defineMethod (c$, "setSource", +function (source) { +this.source = source; +}, "~S"); +Clazz.defineMethod (c$, "setVersion", +function (version) { +this.version = version; +}, "~S"); +Clazz.defineMethod (c$, "getMap", +function () { +return this.map; +}); +Clazz.defineMethod (c$, "setMap", +function (map) { +this.map = map; +}, "jalview.datamodel.Mapping"); +Clazz.defineMethod (c$, "hasMap", +function () { +return this.map != null; +}); +Clazz.defineMethod (c$, "getSrcAccString", +function () { +return ((this.source != null) ? this.source : "") + ":" + ((this.accessionId != null) ? this.accessionId : ""); +}); +Clazz.overrideMethod (c$, "toString", +function () { +return this.getSrcAccString (); +}); +}); diff --git a/bin/jalview/datamodel/DBRefSource.js b/bin/jalview/datamodel/DBRefSource.js index 587f6f3..00d7337 100644 --- a/bin/jalview/datamodel/DBRefSource.js +++ b/bin/jalview/datamodel/DBRefSource.js @@ -1,29 +1,29 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.declareType (jalview.datamodel, "DBRefSource"); -Clazz.defineStatics (c$, -"UNIPROT", "UNIPROT"); -c$.UP_NAME = c$.prototype.UP_NAME = "UNIPROT_NAME".toUpperCase (); -c$.UNIPROTKB = c$.prototype.UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase (); -c$.EMBLCDSProduct = c$.prototype.EMBLCDSProduct = "EMBLCDSProtein".toUpperCase (); -Clazz.defineStatics (c$, -"PDB", "PDB", -"EMBL", "EMBL", -"EMBLCDS", "EMBLCDS", -"PFAM", "PFAM", -"RFAM", "RFAM"); -c$.GENEDB = c$.prototype.GENEDB = "GeneDB".toUpperCase (); -c$.DNACODINGDBS = c$.prototype.DNACODINGDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.EMBL, jalview.datamodel.DBRefSource.EMBLCDS, jalview.datamodel.DBRefSource.GENEDB]); -c$.CODINGDBS = c$.prototype.CODINGDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.EMBLCDS, jalview.datamodel.DBRefSource.GENEDB]); -c$.PROTEINDBS = c$.prototype.PROTEINDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.UNIPROT, jalview.datamodel.DBRefSource.PDB, jalview.datamodel.DBRefSource.UNIPROTKB, jalview.datamodel.DBRefSource.EMBLCDSProduct]); -c$.PROTEINSEQ = c$.prototype.PROTEINSEQ = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.UNIPROT, jalview.datamodel.DBRefSource.UNIPROTKB, jalview.datamodel.DBRefSource.EMBLCDSProduct]); -c$.PROTEINSTR = c$.prototype.PROTEINSTR = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.PDB]); -c$.DOMAINDBS = c$.prototype.DOMAINDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.PFAM, jalview.datamodel.DBRefSource.RFAM]); -Clazz.defineStatics (c$, -"SEQDB", "SQ", -"DNASEQDB", "NASQ", -"PROTSEQDB", "PROTSQ", -"CODINGSEQDB", "CODING", -"DNACODINGSEQDB", "XONCODING", -"DOMAINDB", "DOMAIN", -"MULTIACC", "MULTIACC", -"ALIGNMENTDB", "ALIGNMENTS"); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.declareType (jalview.datamodel, "DBRefSource"); +Clazz.defineStatics (c$, +"UNIPROT", "UNIPROT"); +c$.UP_NAME = c$.prototype.UP_NAME = "UNIPROT_NAME".toUpperCase (); +c$.UNIPROTKB = c$.prototype.UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase (); +c$.EMBLCDSProduct = c$.prototype.EMBLCDSProduct = "EMBLCDSProtein".toUpperCase (); +Clazz.defineStatics (c$, +"PDB", "PDB", +"EMBL", "EMBL", +"EMBLCDS", "EMBLCDS", +"PFAM", "PFAM", +"RFAM", "RFAM"); +c$.GENEDB = c$.prototype.GENEDB = "GeneDB".toUpperCase (); +c$.DNACODINGDBS = c$.prototype.DNACODINGDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.EMBL, jalview.datamodel.DBRefSource.EMBLCDS, jalview.datamodel.DBRefSource.GENEDB]); +c$.CODINGDBS = c$.prototype.CODINGDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.EMBLCDS, jalview.datamodel.DBRefSource.GENEDB]); +c$.PROTEINDBS = c$.prototype.PROTEINDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.UNIPROT, jalview.datamodel.DBRefSource.PDB, jalview.datamodel.DBRefSource.UNIPROTKB, jalview.datamodel.DBRefSource.EMBLCDSProduct]); +c$.PROTEINSEQ = c$.prototype.PROTEINSEQ = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.UNIPROT, jalview.datamodel.DBRefSource.UNIPROTKB, jalview.datamodel.DBRefSource.EMBLCDSProduct]); +c$.PROTEINSTR = c$.prototype.PROTEINSTR = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.PDB]); +c$.DOMAINDBS = c$.prototype.DOMAINDBS = Clazz.newArray (-1, [jalview.datamodel.DBRefSource.PFAM, jalview.datamodel.DBRefSource.RFAM]); +Clazz.defineStatics (c$, +"SEQDB", "SQ", +"DNASEQDB", "NASQ", +"PROTSEQDB", "PROTSQ", +"CODINGSEQDB", "CODING", +"DNACODINGSEQDB", "XONCODING", +"DOMAINDB", "DOMAIN", +"MULTIACC", "MULTIACC", +"ALIGNMENTDB", "ALIGNMENTS"); diff --git a/bin/jalview/datamodel/FeatureProperties.js b/bin/jalview/datamodel/FeatureProperties.js index 6df3e2b..350148d 100644 --- a/bin/jalview/datamodel/FeatureProperties.js +++ b/bin/jalview/datamodel/FeatureProperties.js @@ -1,20 +1,20 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.FeatureProperties", ["jalview.datamodel.DBRefSource"], function () { -c$ = Clazz.declareType (jalview.datamodel, "FeatureProperties"); -c$.isCodingFeature = Clazz.defineMethod (c$, "isCodingFeature", -function (dbrefsource, type) { -if (type.equalsIgnoreCase ("CDS")) { -return (dbrefsource == null || dbrefsource.equalsIgnoreCase (jalview.datamodel.DBRefSource.EMBL) || dbrefsource.equalsIgnoreCase (jalview.datamodel.DBRefSource.EMBLCDS)); -}return false; -}, "~S,~S"); -c$.getCodingFeature = Clazz.defineMethod (c$, "getCodingFeature", -function (dbrefsource) { -if (jalview.datamodel.DBRefSource.EMBL.equalsIgnoreCase (dbrefsource) || jalview.datamodel.DBRefSource.EMBLCDS.equalsIgnoreCase (dbrefsource)) { -return "CDS"; -}return null; -}, "~S"); -Clazz.defineStatics (c$, -"EMBL_CODING_FEATURE", "CDS", -"EXONPOS", "exon number", -"EXONPRODUCT", "product"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.FeatureProperties", ["jalview.datamodel.DBRefSource"], function () { +c$ = Clazz.declareType (jalview.datamodel, "FeatureProperties"); +c$.isCodingFeature = Clazz.defineMethod (c$, "isCodingFeature", +function (dbrefsource, type) { +if (type.equalsIgnoreCase ("CDS")) { +return (dbrefsource == null || dbrefsource.equalsIgnoreCase (jalview.datamodel.DBRefSource.EMBL) || dbrefsource.equalsIgnoreCase (jalview.datamodel.DBRefSource.EMBLCDS)); +}return false; +}, "~S,~S"); +c$.getCodingFeature = Clazz.defineMethod (c$, "getCodingFeature", +function (dbrefsource) { +if (jalview.datamodel.DBRefSource.EMBL.equalsIgnoreCase (dbrefsource) || jalview.datamodel.DBRefSource.EMBLCDS.equalsIgnoreCase (dbrefsource)) { +return "CDS"; +}return null; +}, "~S"); +Clazz.defineStatics (c$, +"EMBL_CODING_FEATURE", "CDS", +"EXONPOS", "exon number", +"EXONPRODUCT", "product"); +}); diff --git a/bin/jalview/datamodel/GraphLine.js b/bin/jalview/datamodel/GraphLine.js index 564e7f4..83ffc69 100644 --- a/bin/jalview/datamodel/GraphLine.js +++ b/bin/jalview/datamodel/GraphLine.js @@ -1,36 +1,36 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.awt.Color"], "jalview.datamodel.GraphLine", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.value = 0; -this.label = ""; -this.colour = null; -this.displayed = true; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "GraphLine"); -Clazz.prepareFields (c$, function () { -this.colour = java.awt.Color.black; -}); -Clazz.makeConstructor (c$, -function (value, label, col) { -this.value = value; -if (label != null) { -this.label = label; -}if (col != null) { -this.colour = col; -}}, "~N,~S,java.awt.Color"); -Clazz.makeConstructor (c$, -function (from) { -if (from != null) { -this.value = from.value; -this.label = String.instantialize (from.label); -this.colour = from.colour; -this.displayed = from.displayed; -}}, "jalview.datamodel.GraphLine"); -Clazz.overrideMethod (c$, "equals", -function (obj) { -if (obj != null && Clazz.instanceOf (obj, jalview.datamodel.GraphLine)) { -var other = obj; -return this.displayed == other.displayed && this.value == other.value && (this.colour != null ? (other.colour != null && other.colour.equals (this.colour)) : other.colour == null) && (this.label != null ? (other.label != null && other.label.equals (this.label)) : other.label == null); -}return false; -}, "~O"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.awt.Color"], "jalview.datamodel.GraphLine", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.value = 0; +this.label = ""; +this.colour = null; +this.displayed = true; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "GraphLine"); +Clazz.prepareFields (c$, function () { +this.colour = java.awt.Color.black; +}); +Clazz.makeConstructor (c$, +function (value, label, col) { +this.value = value; +if (label != null) { +this.label = label; +}if (col != null) { +this.colour = col; +}}, "~N,~S,java.awt.Color"); +Clazz.makeConstructor (c$, +function (from) { +if (from != null) { +this.value = from.value; +this.label = String.instantialize (from.label); +this.colour = from.colour; +this.displayed = from.displayed; +}}, "jalview.datamodel.GraphLine"); +Clazz.overrideMethod (c$, "equals", +function (obj) { +if (obj != null && Clazz.instanceOf (obj, jalview.datamodel.GraphLine)) { +var other = obj; +return this.displayed == other.displayed && this.value == other.value && (this.colour != null ? (other.colour != null && other.colour.equals (this.colour)) : other.colour == null) && (this.label != null ? (other.label != null && other.label.equals (this.label)) : other.label == null); +}return false; +}, "~O"); +}); diff --git a/bin/jalview/datamodel/HiddenSequences.class b/bin/jalview/datamodel/HiddenSequences.class index a6524e4..5553ae2 100644 Binary files a/bin/jalview/datamodel/HiddenSequences.class and b/bin/jalview/datamodel/HiddenSequences.class differ diff --git a/bin/jalview/datamodel/HiddenSequences.js b/bin/jalview/datamodel/HiddenSequences.js index 9111dd8..65b1c2b 100644 --- a/bin/jalview/datamodel/HiddenSequences.js +++ b/bin/jalview/datamodel/HiddenSequences.js @@ -1,162 +1,162 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.HiddenSequences", ["jalview.datamodel.Alignment", "java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this.hiddenSequences = null; -this.alignment = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "HiddenSequences"); -Clazz.makeConstructor (c$, -function (al) { -this.alignment = al; -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "getSize", -function () { -if (this.hiddenSequences == null) { -return 0; -}var count = 0; -for (var i = 0; i < this.hiddenSequences.length; i++) { -if (this.hiddenSequences[i] != null) { -count++; -}} -return count; -}); -Clazz.defineMethod (c$, "getWidth", -function () { -var width = 0; -for (var i = 0; i < this.hiddenSequences.length; i++) { -if (this.hiddenSequences[i] != null && this.hiddenSequences[i].getLength () > width) { -width = this.hiddenSequences[i].getLength (); -}} -return width; -}); -Clazz.defineMethod (c$, "adjustHeightSequenceDeleted", -function (seqIndex) { -if (this.hiddenSequences == null) { -return; -}var alHeight = this.alignment.getHeight (); -var tmp = new Array (alHeight + this.getSize ()); -var deletionIndex = this.adjustForHiddenSeqs (seqIndex); -for (var i = 0; i < this.hiddenSequences.length; i++) { -if (this.hiddenSequences[i] == null) { -continue; -}if (i > deletionIndex) { -tmp[i - 1] = this.hiddenSequences[i]; -} else { -tmp[i] = this.hiddenSequences[i]; -}} -this.hiddenSequences = tmp; -}, "~N"); -Clazz.defineMethod (c$, "adjustHeightSequenceAdded", -function () { -if (this.hiddenSequences == null) { -return; -}var alHeight = this.alignment.getHeight (); -var tmp = new Array (alHeight + this.getSize ()); -System.arraycopy (this.hiddenSequences, 0, tmp, 0, this.hiddenSequences.length); -this.hiddenSequences = tmp; -}); -Clazz.defineMethod (c$, "hideSequence", -function (sequence) { -if (this.hiddenSequences == null) { -this.hiddenSequences = new Array (this.alignment.getHeight ()); -}var alignmentIndex = this.alignment.findIndex (sequence); -alignmentIndex = this.adjustForHiddenSeqs (alignmentIndex); -if (this.hiddenSequences[alignmentIndex] != null) { -System.out.println ("ERROR!!!!!!!!!!!"); -}this.hiddenSequences[alignmentIndex] = sequence; -this.alignment.deleteSequence (sequence); -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "showAll", -function (hiddenRepSequences) { -var revealedSeqs = new java.util.ArrayList (); -for (var i = 0; i < this.hiddenSequences.length; i++) { -if (this.hiddenSequences[i] != null) { -var tmp = this.showSequence (i, hiddenRepSequences); -for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -revealedSeqs.add (seq); -} -}} -return revealedSeqs; -}, "java.util.Map"); -Clazz.defineMethod (c$, "showSequence", -function (alignmentIndex, hiddenRepSequences) { -var revealedSeqs = new java.util.ArrayList (); -var repSequence = this.alignment.getSequenceAt (alignmentIndex); -if (repSequence != null && hiddenRepSequences != null && hiddenRepSequences.containsKey (repSequence)) { -hiddenRepSequences.remove (repSequence); -revealedSeqs.add (repSequence); -}var start = this.adjustForHiddenSeqs (alignmentIndex - 1); -var end = this.adjustForHiddenSeqs (alignmentIndex); -if (end >= this.hiddenSequences.length) { -end = this.hiddenSequences.length - 1; -}var asequences; -{ -for (var index = end; index > start; index--) { -var seq = this.hiddenSequences[index]; -this.hiddenSequences[index] = null; -if (seq != null) { -if (seq.getLength () > 0) { -revealedSeqs.add (seq); -asequences.add (alignmentIndex, seq); -} else { -System.out.println (seq.getName () + " has been deleted whilst hidden"); -}}} -}return revealedSeqs; -}, "~N,java.util.Map"); -Clazz.defineMethod (c$, "getHiddenSequence", -function (alignmentIndex) { -return this.hiddenSequences[alignmentIndex]; -}, "~N"); -Clazz.defineMethod (c$, "findIndexWithoutHiddenSeqs", -function (alignmentIndex) { -var index = 0; -var hiddenSeqs = 0; -if (this.hiddenSequences.length <= alignmentIndex) { -alignmentIndex = this.hiddenSequences.length - 1; -}while (index <= alignmentIndex) { -if (this.hiddenSequences[index] != null) { -hiddenSeqs++; -}index++; -} -;return (alignmentIndex - hiddenSeqs); -}, "~N"); -Clazz.defineMethod (c$, "adjustForHiddenSeqs", -function (alignmentIndex) { -var index = 0; -var hSize = this.hiddenSequences.length; -while (index <= alignmentIndex && index < hSize) { -if (this.hiddenSequences[index] != null) { -alignmentIndex++; -}index++; -} -;return alignmentIndex; -}, "~N"); -Clazz.defineMethod (c$, "getFullAlignment", -function () { -var isize = this.hiddenSequences.length; -var seq = new Array (isize); -var index = 0; -for (var i = 0; i < this.hiddenSequences.length; i++) { -if (this.hiddenSequences[i] != null) { -seq[i] = this.hiddenSequences[i]; -} else { -seq[i] = this.alignment.getSequenceAt (index); -index++; -}} -var fAlignmt = new jalview.datamodel.Alignment (seq); -fAlignmt.annotations = this.alignment.getAlignmentAnnotation (); -fAlignmt.alignmentProperties = this.alignment.getProperties (); -fAlignmt.groups = this.alignment.getGroups (); -fAlignmt.$hasRNAStructure = this.alignment.hasRNAStructure (); -return fAlignmt; -}); -Clazz.defineMethod (c$, "isHidden", -function (seq) { -if (this.hiddenSequences != null) { -for (var i = 0; i < this.hiddenSequences.length; i++) { -if (this.hiddenSequences[i] != null && this.hiddenSequences[i] === seq) { -return true; -}} -}return false; -}, "jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.HiddenSequences", ["jalview.datamodel.Alignment", "java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this.hiddenSequences = null; +this.alignment = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "HiddenSequences"); +Clazz.makeConstructor (c$, +function (al) { +this.alignment = al; +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "getSize", +function () { +if (this.hiddenSequences == null) { +return 0; +}var count = 0; +for (var i = 0; i < this.hiddenSequences.length; i++) { +if (this.hiddenSequences[i] != null) { +count++; +}} +return count; +}); +Clazz.defineMethod (c$, "getWidth", +function () { +var width = 0; +for (var i = 0; i < this.hiddenSequences.length; i++) { +if (this.hiddenSequences[i] != null && this.hiddenSequences[i].getLength () > width) { +width = this.hiddenSequences[i].getLength (); +}} +return width; +}); +Clazz.defineMethod (c$, "adjustHeightSequenceDeleted", +function (seqIndex) { +if (this.hiddenSequences == null) { +return; +}var alHeight = this.alignment.getHeight (); +var tmp = new Array (alHeight + this.getSize ()); +var deletionIndex = this.adjustForHiddenSeqs (seqIndex); +for (var i = 0; i < this.hiddenSequences.length; i++) { +if (this.hiddenSequences[i] == null) { +continue; +}if (i > deletionIndex) { +tmp[i - 1] = this.hiddenSequences[i]; +} else { +tmp[i] = this.hiddenSequences[i]; +}} +this.hiddenSequences = tmp; +}, "~N"); +Clazz.defineMethod (c$, "adjustHeightSequenceAdded", +function () { +if (this.hiddenSequences == null) { +return; +}var alHeight = this.alignment.getHeight (); +var tmp = new Array (alHeight + this.getSize ()); +System.arraycopy (this.hiddenSequences, 0, tmp, 0, this.hiddenSequences.length); +this.hiddenSequences = tmp; +}); +Clazz.defineMethod (c$, "hideSequence", +function (sequence) { +if (this.hiddenSequences == null) { +this.hiddenSequences = new Array (this.alignment.getHeight ()); +}var alignmentIndex = this.alignment.findIndex (sequence); +alignmentIndex = this.adjustForHiddenSeqs (alignmentIndex); +if (this.hiddenSequences[alignmentIndex] != null) { +System.out.println ("ERROR!!!!!!!!!!!"); +}this.hiddenSequences[alignmentIndex] = sequence; +this.alignment.deleteSequence (sequence); +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "showAll", +function (hiddenRepSequences) { +var revealedSeqs = new java.util.ArrayList (); +for (var i = 0; i < this.hiddenSequences.length; i++) { +if (this.hiddenSequences[i] != null) { +var tmp = this.showSequence (i, hiddenRepSequences); +for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +revealedSeqs.add (seq); +} +}} +return revealedSeqs; +}, "java.util.Map"); +Clazz.defineMethod (c$, "showSequence", +function (alignmentIndex, hiddenRepSequences) { +var revealedSeqs = new java.util.ArrayList (); +var repSequence = this.alignment.getSequenceAt (alignmentIndex); +if (repSequence != null && hiddenRepSequences != null && hiddenRepSequences.containsKey (repSequence)) { +hiddenRepSequences.remove (repSequence); +revealedSeqs.add (repSequence); +}var start = this.adjustForHiddenSeqs (alignmentIndex - 1); +var end = this.adjustForHiddenSeqs (alignmentIndex); +if (end >= this.hiddenSequences.length) { +end = this.hiddenSequences.length - 1; +}var asequences; +{ +for (var index = end; index > start; index--) { +var seq = this.hiddenSequences[index]; +this.hiddenSequences[index] = null; +if (seq != null) { +if (seq.getLength () > 0) { +revealedSeqs.add (seq); +asequences.add (alignmentIndex, seq); +} else { +System.out.println (seq.getName () + " has been deleted whilst hidden"); +}}} +}return revealedSeqs; +}, "~N,java.util.Map"); +Clazz.defineMethod (c$, "getHiddenSequence", +function (alignmentIndex) { +return this.hiddenSequences[alignmentIndex]; +}, "~N"); +Clazz.defineMethod (c$, "findIndexWithoutHiddenSeqs", +function (alignmentIndex) { +var index = 0; +var hiddenSeqs = 0; +if (this.hiddenSequences.length <= alignmentIndex) { +alignmentIndex = this.hiddenSequences.length - 1; +}while (index <= alignmentIndex) { +if (this.hiddenSequences[index] != null) { +hiddenSeqs++; +}index++; +} +;return (alignmentIndex - hiddenSeqs); +}, "~N"); +Clazz.defineMethod (c$, "adjustForHiddenSeqs", +function (alignmentIndex) { +var index = 0; +var hSize = this.hiddenSequences.length; +while (index <= alignmentIndex && index < hSize) { +if (this.hiddenSequences[index] != null) { +alignmentIndex++; +}index++; +} +;return alignmentIndex; +}, "~N"); +Clazz.defineMethod (c$, "getFullAlignment", +function () { +var isize = this.hiddenSequences.length; +var seq = new Array (isize); +var index = 0; +for (var i = 0; i < this.hiddenSequences.length; i++) { +if (this.hiddenSequences[i] != null) { +seq[i] = this.hiddenSequences[i]; +} else { +seq[i] = this.alignment.getSequenceAt (index); +index++; +}} +var fAlignmt = new jalview.datamodel.Alignment (seq); +fAlignmt.annotations = this.alignment.getAlignmentAnnotation (); +fAlignmt.alignmentProperties = this.alignment.getProperties (); +fAlignmt.groups = this.alignment.getGroups (); +fAlignmt.$hasRNAStructure = this.alignment.hasRNAStructure (); +return fAlignmt; +}); +Clazz.defineMethod (c$, "isHidden", +function (seq) { +if (this.hiddenSequences != null) { +for (var i = 0; i < this.hiddenSequences.length; i++) { +if (this.hiddenSequences[i] != null && this.hiddenSequences[i] === seq) { +return true; +}} +}return false; +}, "jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/datamodel/IncompleteCodonException.js b/bin/jalview/datamodel/IncompleteCodonException.js index 372d9dd..924024c 100644 --- a/bin/jalview/datamodel/IncompleteCodonException.js +++ b/bin/jalview/datamodel/IncompleteCodonException.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.lang.RuntimeException"], "jalview.datamodel.IncompleteCodonException", null, function () { -c$ = Clazz.declareType (jalview.datamodel, "IncompleteCodonException", RuntimeException); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.lang.RuntimeException"], "jalview.datamodel.IncompleteCodonException", null, function () { +c$ = Clazz.declareType (jalview.datamodel, "IncompleteCodonException", RuntimeException); +}); diff --git a/bin/jalview/datamodel/Mapping.js b/bin/jalview/datamodel/Mapping.js index fe06fda..a25222e 100644 --- a/bin/jalview/datamodel/Mapping.js +++ b/bin/jalview/datamodel/Mapping.js @@ -1,304 +1,304 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.util.Iterator"], "jalview.datamodel.Mapping", ["jalview.datamodel.AlignedCodon", "$.IncompleteCodonException", "$.SequenceFeature", "jalview.util.MapList", "java.util.NoSuchElementException", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -if (!Clazz.isClassDefined ("jalview.datamodel.Mapping.AlignedCodonIterator")) { -jalview.datamodel.Mapping.$Mapping$AlignedCodonIterator$ (); -} -this.map = null; -this.to = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "Mapping"); -Clazz.makeConstructor (c$, -function (map) { -this.map = map; -}, "jalview.util.MapList"); -Clazz.makeConstructor (c$, -function (to, map) { -this.construct (map); -this.to = to; -}, "jalview.datamodel.SequenceI,jalview.util.MapList"); -Clazz.makeConstructor (c$, -function (to, exon, is, i, j) { -this.construct (to, new jalview.util.MapList (exon, is, i, j)); -}, "jalview.datamodel.SequenceI,~A,~A,~N,~N"); -Clazz.makeConstructor (c$, -function (map2) { -if (map2 !== this && map2 != null) { -if (map2.map != null) { -this.map = new jalview.util.MapList (map2.map); -}this.to = map2.to; -}}, "jalview.datamodel.Mapping"); -Clazz.defineMethod (c$, "getMap", -function () { -return this.map; -}); -Clazz.defineMethod (c$, "setMap", -function (map) { -this.map = map; -}, "jalview.util.MapList"); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.Mapping))) { -return false; -}var other = o; -if (other === this) { -return true; -}if (other.to !== this.to) { -return false; -}if ((this.map != null && other.map == null) || (this.map == null && other.map != null)) { -return false; -}if ((this.map == null && other.map == null) || this.map.equals (other.map)) { -return true; -}return false; -}, "~O"); -Clazz.defineMethod (c$, "getPosition", -function (mpos) { -if (this.map != null) { -var mp = this.map.shiftTo (mpos); -if (mp != null) { -return mp[0]; -}}return mpos; -}, "~N"); -Clazz.defineMethod (c$, "getWord", -function (mpos) { -if (this.map != null) { -return this.map.getToWord (mpos); -}return null; -}, "~N"); -Clazz.defineMethod (c$, "getWidth", -function () { -if (this.map != null) { -return this.map.getFromRatio (); -}return 1; -}); -Clazz.defineMethod (c$, "getMappedWidth", -function () { -if (this.map != null) { -return this.map.getToRatio (); -}return 1; -}); -Clazz.defineMethod (c$, "getMappedPosition", -function (pos) { -if (this.map != null) { -var mp = this.map.shiftFrom (pos); -if (mp != null) { -return mp[0]; -}}return pos; -}, "~N"); -Clazz.defineMethod (c$, "getMappedWord", -function (pos) { -if (this.map != null) { -var mp = this.map.shiftFrom (pos); -if (mp != null) { -return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.map.getToRatio () - 1)]); -}}return null; -}, "~N"); -Clazz.defineMethod (c$, "locateFeature", -function (f) { -if (true) { -if (this.map != null) { -var frange = this.map.locateInFrom (f.getBegin (), f.getEnd ()); -if (frange == null) { -return null; -}var vf = new Array (Clazz.doubleToInt (frange.length / 2)); -for (var i = 0, v = 0; i < frange.length; i += 2, v++) { -vf[v] = new jalview.datamodel.SequenceFeature (f); -vf[v].setBegin (frange[i]); -vf[v].setEnd (frange[i + 1]); -if (frange.length > 2) { -vf[v].setDescription (f.getDescription () + "\nPart " + (v + 1)); -}} -return vf; -}}if (false) { -var word = this.getWord (f.getBegin ()); -if (word[0] < word[1]) { -f.setBegin (word[0]); -} else { -f.setBegin (word[1]); -}word = this.getWord (f.getEnd ()); -if (word[0] > word[1]) { -f.setEnd (word[0]); -} else { -f.setEnd (word[1]); -}}return Clazz.newArray (-1, [f]); -}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "locateRange", -function (from, to) { -if (this.map != null) { -if (from <= to) { -from = (this.map.getToLowest () < from) ? from : this.map.getToLowest (); -to = (this.map.getToHighest () > to) ? to : this.map.getToHighest (); -if (from > to) { -return null; -}} else { -from = (this.map.getToHighest () > from) ? from : this.map.getToHighest (); -to = (this.map.getToLowest () < to) ? to : this.map.getToLowest (); -if (from < to) { -return null; -}}return this.map.locateInFrom (from, to); -}return Clazz.newIntArray (-1, [from, to]); -}, "~N,~N"); -Clazz.defineMethod (c$, "locateMappedRange", -function (from, to) { -if (this.map != null) { -if (from <= to) { -from = (this.map.getFromLowest () < from) ? from : this.map.getFromLowest (); -to = (this.map.getFromHighest () > to) ? to : this.map.getFromHighest (); -if (from > to) { -return null; -}} else { -from = (this.map.getFromHighest () > from) ? from : this.map.getFromHighest (); -to = (this.map.getFromLowest () < to) ? to : this.map.getFromLowest (); -if (from < to) { -return null; -}}return this.map.locateInTo (from, to); -}return Clazz.newIntArray (-1, [from, to]); -}, "~N,~N"); -Clazz.defineMethod (c$, "intersectVisContigs", -function (viscontigs) { -var copy = new jalview.datamodel.Mapping (this); -if (this.map != null) { -var vpos = 0; -var apos = 0; -var toRange = new java.util.Vector (); -var fromRange = new java.util.Vector (); -for (var vc = 0; vc < viscontigs.length; vc += 2) { -var mpr = this.locateMappedRange (1 + viscontigs[vc], viscontigs[vc + 1] - 1); -if (mpr != null) { -for (var m = 0; m < mpr.length; m += 2) { -toRange.addElement ( Clazz.newIntArray (-1, [mpr[m], mpr[m + 1]])); -var xpos = this.locateRange (mpr[m], mpr[m + 1]); -for (var x = 0; x < xpos.length; x += 2) { -fromRange.addElement ( Clazz.newIntArray (-1, [xpos[x], xpos[x + 1]])); -} -} -}} -var from = Clazz.newIntArray (fromRange.size () * 2, 0); -var to = Clazz.newIntArray (toRange.size () * 2, 0); -var r; -for (var f = 0, fSize = fromRange.size (); f < fSize; f++) { -r = fromRange.elementAt (f); -from[f * 2] = r[0]; -from[f * 2 + 1] = r[1]; -} -for (var f = 0, fSize = toRange.size (); f < fSize; f++) { -r = toRange.elementAt (f); -to[f * 2] = r[0]; -to[f * 2 + 1] = r[1]; -} -copy.setMap ( new jalview.util.MapList (from, to, this.map.getFromRatio (), this.map.getToRatio ())); -}return copy; -}, "~A"); -Clazz.defineMethod (c$, "getTo", -function () { -return this.to; -}); -Clazz.defineMethod (c$, "setTo", -function (tto) { -this.to = tto; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "finalize", -function () { -this.map = null; -this.to = null; -Clazz.superCall (this, jalview.datamodel.Mapping, "finalize", []); -}); -Clazz.defineMethod (c$, "getCodonIterator", -function (seq, gapChar) { -return Clazz.innerTypeInstance (jalview.datamodel.Mapping.AlignedCodonIterator, this, null, seq.getSequence (), gapChar); -}, "jalview.datamodel.SequenceI,~S"); -c$.$Mapping$AlignedCodonIterator$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.gap = '\0'; -this.alignedSeq = null; -this.alignedColumn = 0; -this.alignedBases = 0; -this.fromRanges = null; -this.toRanges = null; -this.currentFromRange = null; -this.currentToRange = null; -this.fromPosition = 0; -this.toPosition = 0; -Clazz.instantialize (this, arguments); -}, jalview.datamodel.Mapping, "AlignedCodonIterator", null, java.util.Iterator); -Clazz.makeConstructor (c$, -function (a, b) { -this.alignedSeq = a; -this.gap = b; -this.fromRanges = this.b$["jalview.datamodel.Mapping"].map.getFromRanges ().iterator (); -this.toRanges = this.b$["jalview.datamodel.Mapping"].map.getToRanges ().iterator (); -if (this.fromRanges.hasNext ()) { -this.currentFromRange = this.fromRanges.next (); -this.fromPosition = this.currentFromRange[0]; -}if (this.toRanges.hasNext ()) { -this.currentToRange = this.toRanges.next (); -this.toPosition = this.currentToRange[0]; -}}, "~A,~S"); -Clazz.defineMethod (c$, "hasNext", -function () { -if (this.fromRanges.hasNext ()) { -return true; -}if (this.currentFromRange == null || this.fromPosition >= this.currentFromRange[1]) { -return false; -}return true; -}); -Clazz.overrideMethod (c$, "next", -function () { -if (!this.hasNext ()) { -throw new java.util.NoSuchElementException (); -}var a = this.getNextCodon (); -var b = this.getAlignedCodon (a); -var c = this.getPeptide (); -return new jalview.datamodel.AlignedCodon (b[0], b[1], b[2], c); -}); -Clazz.defineMethod (c$, "getPeptide", -($fz = function () { -if (this.toPosition <= this.currentToRange[1]) { -var a = this.b$["jalview.datamodel.Mapping"].to.getSequence ()[this.toPosition - 1]; -this.toPosition++; -return String.valueOf (a); -}if (!this.toRanges.hasNext ()) { -throw new java.util.NoSuchElementException ("Ran out of peptide at position " + this.toPosition); -}this.currentToRange = this.toRanges.next (); -this.toPosition = this.currentToRange[0]; -return this.getPeptide (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getNextCodon", -($fz = function () { -var a = Clazz.newIntArray (3, 0); -var b = 0; -while (b < 3) { -if (this.fromPosition <= this.currentFromRange[1]) { -a[b++] = this.fromPosition++; -} else { -if (!this.fromRanges.hasNext ()) { -throw new jalview.datamodel.IncompleteCodonException (); -}this.currentFromRange = this.fromRanges.next (); -this.fromPosition = this.currentFromRange[0]; -}} -return a; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getAlignedCodon", -($fz = function (a) { -var b = Clazz.newIntArray (a.length, 0); -for (var c = 0; c < a.length; c++) { -b[c] = this.getAlignedColumn (a[c]); -} -return b; -}, $fz.isPrivate = true, $fz), "~A"); -Clazz.defineMethod (c$, "getAlignedColumn", -($fz = function (a) { -while (this.alignedBases < a && this.alignedColumn < this.alignedSeq.length) { -if (this.alignedSeq[this.alignedColumn++] != this.gap) { -this.alignedBases++; -}} -return this.alignedColumn - 1; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.overrideMethod (c$, "remove", -function () { -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.util.Iterator"], "jalview.datamodel.Mapping", ["jalview.datamodel.AlignedCodon", "$.IncompleteCodonException", "$.SequenceFeature", "jalview.util.MapList", "java.util.NoSuchElementException", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +if (!Clazz.isClassDefined ("jalview.datamodel.Mapping.AlignedCodonIterator")) { +jalview.datamodel.Mapping.$Mapping$AlignedCodonIterator$ (); +} +this.map = null; +this.to = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "Mapping"); +Clazz.makeConstructor (c$, +function (map) { +this.map = map; +}, "jalview.util.MapList"); +Clazz.makeConstructor (c$, +function (to, map) { +this.construct (map); +this.to = to; +}, "jalview.datamodel.SequenceI,jalview.util.MapList"); +Clazz.makeConstructor (c$, +function (to, exon, is, i, j) { +this.construct (to, new jalview.util.MapList (exon, is, i, j)); +}, "jalview.datamodel.SequenceI,~A,~A,~N,~N"); +Clazz.makeConstructor (c$, +function (map2) { +if (map2 !== this && map2 != null) { +if (map2.map != null) { +this.map = new jalview.util.MapList (map2.map); +}this.to = map2.to; +}}, "jalview.datamodel.Mapping"); +Clazz.defineMethod (c$, "getMap", +function () { +return this.map; +}); +Clazz.defineMethod (c$, "setMap", +function (map) { +this.map = map; +}, "jalview.util.MapList"); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.Mapping))) { +return false; +}var other = o; +if (other === this) { +return true; +}if (other.to !== this.to) { +return false; +}if ((this.map != null && other.map == null) || (this.map == null && other.map != null)) { +return false; +}if ((this.map == null && other.map == null) || this.map.equals (other.map)) { +return true; +}return false; +}, "~O"); +Clazz.defineMethod (c$, "getPosition", +function (mpos) { +if (this.map != null) { +var mp = this.map.shiftTo (mpos); +if (mp != null) { +return mp[0]; +}}return mpos; +}, "~N"); +Clazz.defineMethod (c$, "getWord", +function (mpos) { +if (this.map != null) { +return this.map.getToWord (mpos); +}return null; +}, "~N"); +Clazz.defineMethod (c$, "getWidth", +function () { +if (this.map != null) { +return this.map.getFromRatio (); +}return 1; +}); +Clazz.defineMethod (c$, "getMappedWidth", +function () { +if (this.map != null) { +return this.map.getToRatio (); +}return 1; +}); +Clazz.defineMethod (c$, "getMappedPosition", +function (pos) { +if (this.map != null) { +var mp = this.map.shiftFrom (pos); +if (mp != null) { +return mp[0]; +}}return pos; +}, "~N"); +Clazz.defineMethod (c$, "getMappedWord", +function (pos) { +if (this.map != null) { +var mp = this.map.shiftFrom (pos); +if (mp != null) { +return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.map.getToRatio () - 1)]); +}}return null; +}, "~N"); +Clazz.defineMethod (c$, "locateFeature", +function (f) { +if (true) { +if (this.map != null) { +var frange = this.map.locateInFrom (f.getBegin (), f.getEnd ()); +if (frange == null) { +return null; +}var vf = new Array (Clazz.doubleToInt (frange.length / 2)); +for (var i = 0, v = 0; i < frange.length; i += 2, v++) { +vf[v] = new jalview.datamodel.SequenceFeature (f); +vf[v].setBegin (frange[i]); +vf[v].setEnd (frange[i + 1]); +if (frange.length > 2) { +vf[v].setDescription (f.getDescription () + "\nPart " + (v + 1)); +}} +return vf; +}}if (false) { +var word = this.getWord (f.getBegin ()); +if (word[0] < word[1]) { +f.setBegin (word[0]); +} else { +f.setBegin (word[1]); +}word = this.getWord (f.getEnd ()); +if (word[0] > word[1]) { +f.setEnd (word[0]); +} else { +f.setEnd (word[1]); +}}return Clazz.newArray (-1, [f]); +}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "locateRange", +function (from, to) { +if (this.map != null) { +if (from <= to) { +from = (this.map.getToLowest () < from) ? from : this.map.getToLowest (); +to = (this.map.getToHighest () > to) ? to : this.map.getToHighest (); +if (from > to) { +return null; +}} else { +from = (this.map.getToHighest () > from) ? from : this.map.getToHighest (); +to = (this.map.getToLowest () < to) ? to : this.map.getToLowest (); +if (from < to) { +return null; +}}return this.map.locateInFrom (from, to); +}return Clazz.newIntArray (-1, [from, to]); +}, "~N,~N"); +Clazz.defineMethod (c$, "locateMappedRange", +function (from, to) { +if (this.map != null) { +if (from <= to) { +from = (this.map.getFromLowest () < from) ? from : this.map.getFromLowest (); +to = (this.map.getFromHighest () > to) ? to : this.map.getFromHighest (); +if (from > to) { +return null; +}} else { +from = (this.map.getFromHighest () > from) ? from : this.map.getFromHighest (); +to = (this.map.getFromLowest () < to) ? to : this.map.getFromLowest (); +if (from < to) { +return null; +}}return this.map.locateInTo (from, to); +}return Clazz.newIntArray (-1, [from, to]); +}, "~N,~N"); +Clazz.defineMethod (c$, "intersectVisContigs", +function (viscontigs) { +var copy = new jalview.datamodel.Mapping (this); +if (this.map != null) { +var vpos = 0; +var apos = 0; +var toRange = new java.util.Vector (); +var fromRange = new java.util.Vector (); +for (var vc = 0; vc < viscontigs.length; vc += 2) { +var mpr = this.locateMappedRange (1 + viscontigs[vc], viscontigs[vc + 1] - 1); +if (mpr != null) { +for (var m = 0; m < mpr.length; m += 2) { +toRange.addElement ( Clazz.newIntArray (-1, [mpr[m], mpr[m + 1]])); +var xpos = this.locateRange (mpr[m], mpr[m + 1]); +for (var x = 0; x < xpos.length; x += 2) { +fromRange.addElement ( Clazz.newIntArray (-1, [xpos[x], xpos[x + 1]])); +} +} +}} +var from = Clazz.newIntArray (fromRange.size () * 2, 0); +var to = Clazz.newIntArray (toRange.size () * 2, 0); +var r; +for (var f = 0, fSize = fromRange.size (); f < fSize; f++) { +r = fromRange.elementAt (f); +from[f * 2] = r[0]; +from[f * 2 + 1] = r[1]; +} +for (var f = 0, fSize = toRange.size (); f < fSize; f++) { +r = toRange.elementAt (f); +to[f * 2] = r[0]; +to[f * 2 + 1] = r[1]; +} +copy.setMap ( new jalview.util.MapList (from, to, this.map.getFromRatio (), this.map.getToRatio ())); +}return copy; +}, "~A"); +Clazz.defineMethod (c$, "getTo", +function () { +return this.to; +}); +Clazz.defineMethod (c$, "setTo", +function (tto) { +this.to = tto; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "finalize", +function () { +this.map = null; +this.to = null; +Clazz.superCall (this, jalview.datamodel.Mapping, "finalize", []); +}); +Clazz.defineMethod (c$, "getCodonIterator", +function (seq, gapChar) { +return Clazz.innerTypeInstance (jalview.datamodel.Mapping.AlignedCodonIterator, this, null, seq.getSequence (), gapChar); +}, "jalview.datamodel.SequenceI,~S"); +c$.$Mapping$AlignedCodonIterator$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.gap = '\0'; +this.alignedSeq = null; +this.alignedColumn = 0; +this.alignedBases = 0; +this.fromRanges = null; +this.toRanges = null; +this.currentFromRange = null; +this.currentToRange = null; +this.fromPosition = 0; +this.toPosition = 0; +Clazz.instantialize (this, arguments); +}, jalview.datamodel.Mapping, "AlignedCodonIterator", null, java.util.Iterator); +Clazz.makeConstructor (c$, +function (a, b) { +this.alignedSeq = a; +this.gap = b; +this.fromRanges = this.b$["jalview.datamodel.Mapping"].map.getFromRanges ().iterator (); +this.toRanges = this.b$["jalview.datamodel.Mapping"].map.getToRanges ().iterator (); +if (this.fromRanges.hasNext ()) { +this.currentFromRange = this.fromRanges.next (); +this.fromPosition = this.currentFromRange[0]; +}if (this.toRanges.hasNext ()) { +this.currentToRange = this.toRanges.next (); +this.toPosition = this.currentToRange[0]; +}}, "~A,~S"); +Clazz.defineMethod (c$, "hasNext", +function () { +if (this.fromRanges.hasNext ()) { +return true; +}if (this.currentFromRange == null || this.fromPosition >= this.currentFromRange[1]) { +return false; +}return true; +}); +Clazz.overrideMethod (c$, "next", +function () { +if (!this.hasNext ()) { +throw new java.util.NoSuchElementException (); +}var a = this.getNextCodon (); +var b = this.getAlignedCodon (a); +var c = this.getPeptide (); +return new jalview.datamodel.AlignedCodon (b[0], b[1], b[2], c); +}); +Clazz.defineMethod (c$, "getPeptide", +($fz = function () { +if (this.toPosition <= this.currentToRange[1]) { +var a = this.b$["jalview.datamodel.Mapping"].to.getSequence ()[this.toPosition - 1]; +this.toPosition++; +return String.valueOf (a); +}if (!this.toRanges.hasNext ()) { +throw new java.util.NoSuchElementException ("Ran out of peptide at position " + this.toPosition); +}this.currentToRange = this.toRanges.next (); +this.toPosition = this.currentToRange[0]; +return this.getPeptide (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getNextCodon", +($fz = function () { +var a = Clazz.newIntArray (3, 0); +var b = 0; +while (b < 3) { +if (this.fromPosition <= this.currentFromRange[1]) { +a[b++] = this.fromPosition++; +} else { +if (!this.fromRanges.hasNext ()) { +throw new jalview.datamodel.IncompleteCodonException (); +}this.currentFromRange = this.fromRanges.next (); +this.fromPosition = this.currentFromRange[0]; +}} +return a; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getAlignedCodon", +($fz = function (a) { +var b = Clazz.newIntArray (a.length, 0); +for (var c = 0; c < a.length; c++) { +b[c] = this.getAlignedColumn (a[c]); +} +return b; +}, $fz.isPrivate = true, $fz), "~A"); +Clazz.defineMethod (c$, "getAlignedColumn", +($fz = function (a) { +while (this.alignedBases < a && this.alignedColumn < this.alignedSeq.length) { +if (this.alignedSeq[this.alignedColumn++] != this.gap) { +this.alignedBases++; +}} +return this.alignedColumn - 1; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.overrideMethod (c$, "remove", +function () { +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/datamodel/NodeTransformI.js b/bin/jalview/datamodel/NodeTransformI.js index 83ace63..0f7a757 100644 --- a/bin/jalview/datamodel/NodeTransformI.js +++ b/bin/jalview/datamodel/NodeTransformI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.declareInterface (jalview.datamodel, "NodeTransformI"); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.declareInterface (jalview.datamodel, "NodeTransformI"); diff --git a/bin/jalview/datamodel/PDBEntry.js b/bin/jalview/datamodel/PDBEntry.js index e52f785..e153399 100644 --- a/bin/jalview/datamodel/PDBEntry.js +++ b/bin/jalview/datamodel/PDBEntry.js @@ -1,88 +1,88 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.lang.Enum"], "jalview.datamodel.PDBEntry", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.file = null; -this.type = null; -this.id = null; -this.chainCode = null; -this.properties = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "PDBEntry"); -Clazz.overrideMethod (c$, "equals", -function (obj) { -if (obj == null || !(Clazz.instanceOf (obj, jalview.datamodel.PDBEntry))) { -return false; -}if (obj === this) { -return true; -}var o = obj; -return (this.type === o.type || (this.type != null && o.type != null && o.type.equals (this.type))) && (this.id === o.id || (this.id != null && o.id != null && o.id.equalsIgnoreCase (this.id))) && (this.chainCode === o.chainCode || (this.chainCode != null && o.chainCode != null && o.chainCode.equalsIgnoreCase (this.chainCode))) && (this.properties === o.properties || (this.properties != null && o.properties != null && this.properties.equals (o.properties))); -}, "~O"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (pdbId, chain, type, filePath) { -this.id = pdbId; -this.chainCode = chain; -this.type = type == null ? null : type.toString (); -this.file = filePath; -}, "~S,~S,jalview.datamodel.PDBEntry.Type,~S"); -Clazz.makeConstructor (c$, -function (entry) { -this.file = entry.file; -this.type = entry.type; -this.id = entry.id; -this.chainCode = entry.chainCode; -if (entry.properties != null) { -this.properties = entry.properties.clone (); -}}, "jalview.datamodel.PDBEntry"); -Clazz.defineMethod (c$, "setFile", -function (file) { -this.file = file; -}, "~S"); -Clazz.defineMethod (c$, "getFile", -function () { -return this.file; -}); -Clazz.defineMethod (c$, "setType", -function (t) { -this.type = t; -}, "~S"); -Clazz.defineMethod (c$, "setType", -function (type) { -this.type = type == null ? null : type.toString (); -}, "jalview.datamodel.PDBEntry.Type"); -Clazz.defineMethod (c$, "getType", -function () { -return this.type; -}); -Clazz.defineMethod (c$, "setId", -function (id) { -this.id = id; -}, "~S"); -Clazz.defineMethod (c$, "getId", -function () { -return this.id; -}); -Clazz.defineMethod (c$, "setProperty", -function (property) { -this.properties = property; -}, "java.util.Hashtable"); -Clazz.defineMethod (c$, "getProperty", -function () { -return this.properties; -}); -Clazz.defineMethod (c$, "getChainCode", -function () { -return this.chainCode; -}); -Clazz.defineMethod (c$, "setChainCode", -function (chainCode) { -this.chainCode = chainCode; -}, "~S"); -Clazz.pu$h (); -c$ = Clazz.declareType (jalview.datamodel.PDBEntry, "Type", Enum); -Clazz.defineEnumConstant (c$, "PDB", 0, []); -Clazz.defineEnumConstant (c$, "FILE", 1, []); -c$ = Clazz.p0p (); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.lang.Enum"], "jalview.datamodel.PDBEntry", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.file = null; +this.type = null; +this.id = null; +this.chainCode = null; +this.properties = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "PDBEntry"); +Clazz.overrideMethod (c$, "equals", +function (obj) { +if (obj == null || !(Clazz.instanceOf (obj, jalview.datamodel.PDBEntry))) { +return false; +}if (obj === this) { +return true; +}var o = obj; +return (this.type === o.type || (this.type != null && o.type != null && o.type.equals (this.type))) && (this.id === o.id || (this.id != null && o.id != null && o.id.equalsIgnoreCase (this.id))) && (this.chainCode === o.chainCode || (this.chainCode != null && o.chainCode != null && o.chainCode.equalsIgnoreCase (this.chainCode))) && (this.properties === o.properties || (this.properties != null && o.properties != null && this.properties.equals (o.properties))); +}, "~O"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (pdbId, chain, type, filePath) { +this.id = pdbId; +this.chainCode = chain; +this.type = type == null ? null : type.toString (); +this.file = filePath; +}, "~S,~S,jalview.datamodel.PDBEntry.Type,~S"); +Clazz.makeConstructor (c$, +function (entry) { +this.file = entry.file; +this.type = entry.type; +this.id = entry.id; +this.chainCode = entry.chainCode; +if (entry.properties != null) { +this.properties = entry.properties.clone (); +}}, "jalview.datamodel.PDBEntry"); +Clazz.defineMethod (c$, "setFile", +function (file) { +this.file = file; +}, "~S"); +Clazz.defineMethod (c$, "getFile", +function () { +return this.file; +}); +Clazz.defineMethod (c$, "setType", +function (t) { +this.type = t; +}, "~S"); +Clazz.defineMethod (c$, "setType", +function (type) { +this.type = type == null ? null : type.toString (); +}, "jalview.datamodel.PDBEntry.Type"); +Clazz.defineMethod (c$, "getType", +function () { +return this.type; +}); +Clazz.defineMethod (c$, "setId", +function (id) { +this.id = id; +}, "~S"); +Clazz.defineMethod (c$, "getId", +function () { +return this.id; +}); +Clazz.defineMethod (c$, "setProperty", +function (property) { +this.properties = property; +}, "java.util.Hashtable"); +Clazz.defineMethod (c$, "getProperty", +function () { +return this.properties; +}); +Clazz.defineMethod (c$, "getChainCode", +function () { +return this.chainCode; +}); +Clazz.defineMethod (c$, "setChainCode", +function (chainCode) { +this.chainCode = chainCode; +}, "~S"); +Clazz.pu$h (); +c$ = Clazz.declareType (jalview.datamodel.PDBEntry, "Type", Enum); +Clazz.defineEnumConstant (c$, "PDB", 0, []); +Clazz.defineEnumConstant (c$, "FILE", 1, []); +c$ = Clazz.p0p (); +}); diff --git a/bin/jalview/datamodel/Provenance.js b/bin/jalview/datamodel/Provenance.js index 04f873e..c0180ea 100644 --- a/bin/jalview/datamodel/Provenance.js +++ b/bin/jalview/datamodel/Provenance.js @@ -1,25 +1,25 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.util.Vector"], "jalview.datamodel.Provenance", ["jalview.datamodel.ProvenanceEntry"], function () { -c$ = Clazz.decorateAsClass (function () { -this.entries = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "Provenance"); -Clazz.prepareFields (c$, function () { -this.entries = new java.util.Vector (); -}); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "getEntries", -function () { -var ret = new Array (this.entries.size ()); -for (var i = 0; i < this.entries.size (); i++) { -ret[i] = this.entries.elementAt (i); -} -return ret; -}); -Clazz.defineMethod (c$, "addEntry", -function (user, action, date, id) { -this.entries.addElement ( new jalview.datamodel.ProvenanceEntry (user, action, date, id)); -}, "~S,~S,java.util.Date,~S"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.util.Vector"], "jalview.datamodel.Provenance", ["jalview.datamodel.ProvenanceEntry"], function () { +c$ = Clazz.decorateAsClass (function () { +this.entries = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "Provenance"); +Clazz.prepareFields (c$, function () { +this.entries = new java.util.Vector (); +}); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "getEntries", +function () { +var ret = new Array (this.entries.size ()); +for (var i = 0; i < this.entries.size (); i++) { +ret[i] = this.entries.elementAt (i); +} +return ret; +}); +Clazz.defineMethod (c$, "addEntry", +function (user, action, date, id) { +this.entries.addElement ( new jalview.datamodel.ProvenanceEntry (user, action, date, id)); +}, "~S,~S,java.util.Date,~S"); +}); diff --git a/bin/jalview/datamodel/ProvenanceEntry.js b/bin/jalview/datamodel/ProvenanceEntry.js index 5077d90..1283717 100644 --- a/bin/jalview/datamodel/ProvenanceEntry.js +++ b/bin/jalview/datamodel/ProvenanceEntry.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this.user = null; -this.action = null; -this.id = null; -this.date = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "ProvenanceEntry"); -Clazz.makeConstructor (c$, -function (u, a, d, i) { -this.user = u; -this.action = a; -this.date = d; -this.id = i; -}, "~S,~S,java.util.Date,~S"); -Clazz.defineMethod (c$, "getUser", -function () { -return this.user; -}); -Clazz.defineMethod (c$, "getAction", -function () { -return this.action; -}); -Clazz.defineMethod (c$, "getDate", -function () { -return this.date; -}); -Clazz.defineMethod (c$, "getID", -function () { -return this.id; -}); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this.user = null; +this.action = null; +this.id = null; +this.date = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "ProvenanceEntry"); +Clazz.makeConstructor (c$, +function (u, a, d, i) { +this.user = u; +this.action = a; +this.date = d; +this.id = i; +}, "~S,~S,java.util.Date,~S"); +Clazz.defineMethod (c$, "getUser", +function () { +return this.user; +}); +Clazz.defineMethod (c$, "getAction", +function () { +return this.action; +}); +Clazz.defineMethod (c$, "getDate", +function () { +return this.date; +}); +Clazz.defineMethod (c$, "getID", +function () { +return this.id; +}); diff --git a/bin/jalview/datamodel/RnaViewerModel.js b/bin/jalview/datamodel/RnaViewerModel.js index 2e64a80..612cdda 100644 --- a/bin/jalview/datamodel/RnaViewerModel.js +++ b/bin/jalview/datamodel/RnaViewerModel.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this.viewId = null; -this.title = null; -this.x = 0; -this.y = 0; -this.width = 0; -this.height = 0; -this.dividerLocation = 0; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "RnaViewerModel"); -Clazz.makeConstructor (c$, -function (viewId, title, xpos, ypos, width, height, dividerLocation) { -this.viewId = viewId; -this.title = title; -this.x = xpos; -this.y = ypos; -this.width = width; -this.height = height; -this.dividerLocation = dividerLocation; -}, "~S,~S,~N,~N,~N,~N,~N"); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this.viewId = null; +this.title = null; +this.x = 0; +this.y = 0; +this.width = 0; +this.height = 0; +this.dividerLocation = 0; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "RnaViewerModel"); +Clazz.makeConstructor (c$, +function (viewId, title, xpos, ypos, width, height, dividerLocation) { +this.viewId = viewId; +this.title = title; +this.x = xpos; +this.y = ypos; +this.width = width; +this.height = height; +this.dividerLocation = dividerLocation; +}, "~S,~S,~N,~N,~N,~N,~N"); diff --git a/bin/jalview/datamodel/SearchResults.js b/bin/jalview/datamodel/SearchResults.js index 74170de..e82bfa5 100644 --- a/bin/jalview/datamodel/SearchResults.js +++ b/bin/jalview/datamodel/SearchResults.js @@ -1,137 +1,137 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.util.ArrayList"], "jalview.datamodel.SearchResults", ["java.lang.StringBuilder", "java.util.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.matches = null; -if (!Clazz.isClassDefined ("jalview.datamodel.SearchResults.Match")) { -jalview.datamodel.SearchResults.$SearchResults$Match$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SearchResults"); -Clazz.prepareFields (c$, function () { -this.matches = new java.util.ArrayList (); -}); -Clazz.defineMethod (c$, "addResult", -function (seq, start, end) { -this.matches.add (Clazz.innerTypeInstance (jalview.datamodel.SearchResults.Match, this, null, seq, start, end)); -}, "jalview.datamodel.SequenceI,~N,~N"); -Clazz.defineMethod (c$, "involvesSequence", -function (sequence) { -var ds = sequence.getDatasetSequence (); -for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -if (m.sequence != null && (m.sequence === sequence || m.sequence === ds)) { -return true; -}} -return false; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getResults", -function (sequence, start, end) { -if (this.matches.isEmpty ()) { -return null; -}var result = null; -var tmp = null; -var resultLength; -var matchStart = 0; -var matchEnd = 0; -var mfound; -for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -mfound = false; -if (m.sequence === sequence) { -mfound = true; -matchStart = sequence.findIndex (m.start) - 1; -matchEnd = sequence.findIndex (m.end) - 1; -} else if (m.sequence === sequence.getDatasetSequence ()) { -mfound = true; -matchStart = sequence.findIndex (m.start) - 1; -matchEnd = sequence.findIndex (m.end) - 1; -}if (mfound) { -if (matchStart <= end && matchEnd >= start) { -if (matchStart < start) { -matchStart = start; -}if (matchEnd > end) { -matchEnd = end; -}if (result == null) { -result = Clazz.newIntArray (-1, [matchStart, matchEnd]); -} else { -resultLength = result.length; -tmp = Clazz.newIntArray (resultLength + 2, 0); -System.arraycopy (result, 0, tmp, 0, resultLength); -result = tmp; -result[resultLength] = matchStart; -result[resultLength + 1] = matchEnd; -}} else { -}}} -return result; -}, "jalview.datamodel.SequenceI,~N,~N"); -Clazz.defineMethod (c$, "getSize", -function () { -return this.matches.size (); -}); -Clazz.defineMethod (c$, "getResultSequence", -function (index) { -return this.matches.get (index).sequence; -}, "~N"); -Clazz.defineMethod (c$, "getResultStart", -function (i) { -return this.matches.get (i).start; -}, "~N"); -Clazz.defineMethod (c$, "getResultEnd", -function (i) { -return this.matches.get (i).end; -}, "~N"); -Clazz.defineMethod (c$, "isEmpty", -function () { -return this.matches.isEmpty (); -}); -Clazz.defineMethod (c$, "getResults", -function () { -return this.matches; -}); -Clazz.overrideMethod (c$, "toString", -function () { -var result = new StringBuilder (256); -for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -result.append (m.toString ()); -} -return result.toString (); -}); -c$.$SearchResults$Match$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.sequence = null; -this.start = 0; -this.end = 0; -Clazz.instantialize (this, arguments); -}, jalview.datamodel.SearchResults, "Match"); -Clazz.makeConstructor (c$, -function (a, b, c) { -this.sequence = a; -this.start = b; -this.end = c; -}, "jalview.datamodel.SequenceI,~N,~N"); -Clazz.defineMethod (c$, "getSequence", -function () { -return this.sequence; -}); -Clazz.defineMethod (c$, "getStart", -function () { -return this.start; -}); -Clazz.defineMethod (c$, "getEnd", -function () { -return this.end; -}); -Clazz.overrideMethod (c$, "toString", -function () { -var a = this.sequence.getSequence (); -var b = Math.max (this.start - 1, 0); -var c = Math.min (this.end, a.length + 1); -return String.valueOf (java.util.Arrays.copyOfRange (a, b, c)); -}); -Clazz.defineMethod (c$, "setSequence", -function (a) { -this.sequence = a; -}, "jalview.datamodel.SequenceI"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.util.ArrayList"], "jalview.datamodel.SearchResults", ["java.lang.StringBuilder", "java.util.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.matches = null; +if (!Clazz.isClassDefined ("jalview.datamodel.SearchResults.Match")) { +jalview.datamodel.SearchResults.$SearchResults$Match$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SearchResults"); +Clazz.prepareFields (c$, function () { +this.matches = new java.util.ArrayList (); +}); +Clazz.defineMethod (c$, "addResult", +function (seq, start, end) { +this.matches.add (Clazz.innerTypeInstance (jalview.datamodel.SearchResults.Match, this, null, seq, start, end)); +}, "jalview.datamodel.SequenceI,~N,~N"); +Clazz.defineMethod (c$, "involvesSequence", +function (sequence) { +var ds = sequence.getDatasetSequence (); +for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +if (m.sequence != null && (m.sequence === sequence || m.sequence === ds)) { +return true; +}} +return false; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getResults", +function (sequence, start, end) { +if (this.matches.isEmpty ()) { +return null; +}var result = null; +var tmp = null; +var resultLength; +var matchStart = 0; +var matchEnd = 0; +var mfound; +for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +mfound = false; +if (m.sequence === sequence) { +mfound = true; +matchStart = sequence.findIndex (m.start) - 1; +matchEnd = sequence.findIndex (m.end) - 1; +} else if (m.sequence === sequence.getDatasetSequence ()) { +mfound = true; +matchStart = sequence.findIndex (m.start) - 1; +matchEnd = sequence.findIndex (m.end) - 1; +}if (mfound) { +if (matchStart <= end && matchEnd >= start) { +if (matchStart < start) { +matchStart = start; +}if (matchEnd > end) { +matchEnd = end; +}if (result == null) { +result = Clazz.newIntArray (-1, [matchStart, matchEnd]); +} else { +resultLength = result.length; +tmp = Clazz.newIntArray (resultLength + 2, 0); +System.arraycopy (result, 0, tmp, 0, resultLength); +result = tmp; +result[resultLength] = matchStart; +result[resultLength + 1] = matchEnd; +}} else { +}}} +return result; +}, "jalview.datamodel.SequenceI,~N,~N"); +Clazz.defineMethod (c$, "getSize", +function () { +return this.matches.size (); +}); +Clazz.defineMethod (c$, "getResultSequence", +function (index) { +return this.matches.get (index).sequence; +}, "~N"); +Clazz.defineMethod (c$, "getResultStart", +function (i) { +return this.matches.get (i).start; +}, "~N"); +Clazz.defineMethod (c$, "getResultEnd", +function (i) { +return this.matches.get (i).end; +}, "~N"); +Clazz.defineMethod (c$, "isEmpty", +function () { +return this.matches.isEmpty (); +}); +Clazz.defineMethod (c$, "getResults", +function () { +return this.matches; +}); +Clazz.overrideMethod (c$, "toString", +function () { +var result = new StringBuilder (256); +for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +result.append (m.toString ()); +} +return result.toString (); +}); +c$.$SearchResults$Match$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.sequence = null; +this.start = 0; +this.end = 0; +Clazz.instantialize (this, arguments); +}, jalview.datamodel.SearchResults, "Match"); +Clazz.makeConstructor (c$, +function (a, b, c) { +this.sequence = a; +this.start = b; +this.end = c; +}, "jalview.datamodel.SequenceI,~N,~N"); +Clazz.defineMethod (c$, "getSequence", +function () { +return this.sequence; +}); +Clazz.defineMethod (c$, "getStart", +function () { +return this.start; +}); +Clazz.defineMethod (c$, "getEnd", +function () { +return this.end; +}); +Clazz.overrideMethod (c$, "toString", +function () { +var a = this.sequence.getSequence (); +var b = Math.max (this.start - 1, 0); +var c = Math.min (this.end, a.length + 1); +return String.valueOf (java.util.Arrays.copyOfRange (a, b, c)); +}); +Clazz.defineMethod (c$, "setSequence", +function (a) { +this.sequence = a; +}, "jalview.datamodel.SequenceI"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/datamodel/SecondaryStructureAnnotation.js b/bin/jalview/datamodel/SecondaryStructureAnnotation.js index 6a35ad3..2d1eb58 100644 --- a/bin/jalview/datamodel/SecondaryStructureAnnotation.js +++ b/bin/jalview/datamodel/SecondaryStructureAnnotation.js @@ -1,23 +1,23 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.AlignmentAnnotation"], "jalview.datamodel.SecondaryStructureAnnotation", ["jalview.datamodel.Annotation"], function () { -c$ = Clazz.declareType (jalview.datamodel, "SecondaryStructureAnnotation", jalview.datamodel.AlignmentAnnotation); -Clazz.makeConstructor (c$, -function (rna) { -Clazz.superConstructor (this, jalview.datamodel.SecondaryStructureAnnotation, ["Secondary Structure", "Un truc trop cool", jalview.datamodel.SecondaryStructureAnnotation.getAnnotation (rna)]); -jalview.datamodel.SecondaryStructureAnnotation._rna = rna; -}, "fr.orsay.lri.varna.models.rna.RNA"); -Clazz.defineMethod (c$, "getRNA", -function () { -return jalview.datamodel.SecondaryStructureAnnotation._rna; -}); -c$.getAnnotation = Clazz.defineMethod (c$, "getAnnotation", -function (rna) { -var ann = new Array (rna.getSize ()); -for (var i = 0; i < ann.length; i++) { -ann[i] = new jalview.datamodel.Annotation (jalview.datamodel.SecondaryStructureAnnotation._rna.getStructDBN (true), "", ' ', 0); -;} -return ann; -}, "fr.orsay.lri.varna.models.rna.RNA"); -Clazz.defineStatics (c$, -"_rna", null); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.AlignmentAnnotation"], "jalview.datamodel.SecondaryStructureAnnotation", ["jalview.datamodel.Annotation"], function () { +c$ = Clazz.declareType (jalview.datamodel, "SecondaryStructureAnnotation", jalview.datamodel.AlignmentAnnotation); +Clazz.makeConstructor (c$, +function (rna) { +Clazz.superConstructor (this, jalview.datamodel.SecondaryStructureAnnotation, ["Secondary Structure", "Un truc trop cool", jalview.datamodel.SecondaryStructureAnnotation.getAnnotation (rna)]); +jalview.datamodel.SecondaryStructureAnnotation._rna = rna; +}, "fr.orsay.lri.varna.models.rna.RNA"); +Clazz.defineMethod (c$, "getRNA", +function () { +return jalview.datamodel.SecondaryStructureAnnotation._rna; +}); +c$.getAnnotation = Clazz.defineMethod (c$, "getAnnotation", +function (rna) { +var ann = new Array (rna.getSize ()); +for (var i = 0; i < ann.length; i++) { +ann[i] = new jalview.datamodel.Annotation (jalview.datamodel.SecondaryStructureAnnotation._rna.getStructDBN (true), "", ' ', 0); +;} +return ann; +}, "fr.orsay.lri.varna.models.rna.RNA"); +Clazz.defineStatics (c$, +"_rna", null); +}); diff --git a/bin/jalview/datamodel/SeqCigar.class b/bin/jalview/datamodel/SeqCigar.class index 5f54f07..8bb4e15 100644 Binary files a/bin/jalview/datamodel/SeqCigar.class and b/bin/jalview/datamodel/SeqCigar.class differ diff --git a/bin/jalview/datamodel/SeqCigar.js b/bin/jalview/datamodel/SeqCigar.js index c9304ac..d35d16f 100644 --- a/bin/jalview/datamodel/SeqCigar.js +++ b/bin/jalview/datamodel/SeqCigar.js @@ -1,259 +1,259 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.CigarSimple"], "jalview.datamodel.SeqCigar", ["jalview.analysis.AlignSeq", "$.SeqsetUtils", "jalview.datamodel.Sequence", "jalview.util.Comparison", "$.MessageManager", "$.ShiftList", "java.lang.Error", "$.StringBuffer", "java.util.Hashtable"], function () { -c$ = Clazz.decorateAsClass (function () { -this.start = 0; -this.end = 0; -this.refseq = null; -this.seqProps = null; -this.selGroups = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SeqCigar", jalview.datamodel.CigarSimple); -Clazz.defineMethod (c$, "getRefSeq", -function () { -return this.refseq; -}); -Clazz.defineMethod (c$, "getStart", -function () { -return this.start; -}); -Clazz.defineMethod (c$, "getEnd", -function () { -return this.end; -}); -Clazz.overrideMethod (c$, "getSequenceString", -function (GapChar) { -return (this.length == 0) ? "" : this.getSequenceAndDeletions (this.refseq.getSequenceAsString (this.start, this.end), GapChar)[0]; -}, "~S"); -Clazz.defineMethod (c$, "getSeq", -function (GapChar) { -var seq; -if (this.refseq == null || this.length == 0) { -return null; -}var edit_result = this.getSequenceAndDeletions (this.refseq.getSequenceAsString (this.start, this.end), GapChar); -if (edit_result == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_unexpected_null_from_get_sequence_and_deletions")); -}var bounds = edit_result[1]; -seq = new jalview.datamodel.Sequence (this.refseq.getName (), edit_result[0], this.refseq.getStart () + this.start + bounds[0], this.refseq.getStart () + this.start + ((bounds[2] == 0) ? -1 : bounds[2])); -seq.setDescription (this.refseq.getDescription ()); -var sstart = seq.getStart (); -var send = seq.getEnd (); -if (this.seqProps != null) { -jalview.analysis.SeqsetUtils.SeqCharacterUnhash (seq, this.seqProps); -}seq.setDatasetSequence (this.refseq); -seq.setStart (sstart); -seq.setEnd (send); -return seq; -}, "~S"); -Clazz.defineMethod (c$, "_setSeq", -($fz = function (seq, initialDeletion, _s, _e) { -var hasgaps = false; -if (seq == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_set_seq_null")); -}if (_s < 0) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_s", Clazz.newArray (-1, [Integer.$valueOf (_s).toString ()]))); -}var seq_string = seq.getSequenceAsString (); -if (_e == 0 || _e < _s || _e > seq_string.length) { -_e = seq_string.length; -}this.start = seq.findPosition (_s) - seq.getStart (); -this.end = seq.findPosition (_e) - seq.getStart (); -var l_ungapped = this.end - this.start; -var ds = seq.getDatasetSequence (); -if (ds == null) { -var ungapped = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (seq_string)); -l_ungapped = ungapped.length; -if (l_ungapped == seq.getLength ()) { -ds = seq; -} else { -ds = new jalview.datamodel.Sequence (seq.getName (), ungapped, seq.getStart (), seq.getStart () + ungapped.length - 1); -}}if (ds.getStart () < seq.getStart ()) { -var offset = seq.getStart () - ds.getStart (); -if (initialDeletion) { -this.addDeleted (_s + offset); -this.start = 0; -this.end += offset; -} else { -this.start += offset; -this.end += offset; -}}if (l_ungapped != (_e - _s)) { -hasgaps = true; -}this.refseq = ds; -this.seqProps = jalview.analysis.SeqsetUtils.SeqCharacterHash (seq); -if (this.end > ds.getLength ()) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_seqcigar_possible")); -}return hasgaps; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,~B,~N,~N"); -Clazz.makeConstructor (c$, -function (seq, operation, range) { -Clazz.superConstructor (this, jalview.datamodel.SeqCigar); -if (seq == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implmentation_bug_seq_null")); -}if (operation.length != range.length) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_bug_cigar_operation_list_range_list")); -}if (operation != null) { -this.operation = Clazz.newCharArray (operation.length + this._inc_length, '\0'); -this.range = Clazz.newIntArray (operation.length + this._inc_length, 0); -if (this._setSeq (seq, false, 0, 0)) { -throw new Error (jalview.util.MessageManager.getString ("error.not_yet_implemented_cigar_object_from_cigar_string")); -}for (var i = this.length, j = 0; j < operation.length; i++, j++) { -var op = operation[j]; -if (op != 'M' && op != 'I' && op != 'D') { -throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_bug_cigar_operation", Clazz.newArray (-1, [Integer.$valueOf (j).toString (), Integer.$valueOf (op.charCodeAt (0)).toString (), Integer.$valueOf ('M'.charCodeAt (0)).toString (), Integer.$valueOf ('I'.charCodeAt (0)).toString (), Integer.$valueOf ('D'.charCodeAt (0)).toString ()]))); -}this.operation[i] = op; -this.range[i] = range[j]; -} -this.length += operation.length; -} else { -this.operation = null; -this.range = null; -this.length = 0; -if (this._setSeq (seq, false, 0, 0)) { -throw new Error (jalview.util.MessageManager.getString ("error.not_yet_implemented_cigar_object_from_cigar_string")); -}}}, "jalview.datamodel.SequenceI,~A,~A"); -Clazz.defineMethod (c$, "addMatch", -function (range) { -this.addOperation ('M', range); -}, "~N"); -c$.addSequenceOps = Clazz.defineMethod (c$, "addSequenceOps", -function (cigar, seq, startpos, endpos, initialDeletions) { -var op = '\u0000'; -var range = 0; -var p = 0; -var res = seq.getLength (); -if (!initialDeletions) { -p = startpos; -}while (p <= endpos) { -var isGap = (p < res) ? jalview.util.Comparison.isGap (seq.getCharAt (p)) : true; -if ((startpos <= p) && (p <= endpos)) { -if (isGap) { -if (range > 0 && op != 'I') { -cigar.addOperation (op, range); -range = 0; -}op = 'I'; -range++; -} else { -if (range > 0 && op != 'M') { -cigar.addOperation (op, range); -range = 0; -}op = 'M'; -range++; -}} else { -if (!isGap) { -if (range > 0 && op != 'D') { -cigar.addOperation (op, range); -range = 0; -}op = 'D'; -range++; -} else { -}}p++; -} -if (range > 0) { -cigar.addOperation (op, range); -}}, "jalview.datamodel.CigarBase,jalview.datamodel.SequenceI,~N,~N,~B"); -Clazz.makeConstructor (c$, -function (seq) { -Clazz.superConstructor (this, jalview.datamodel.SeqCigar); -if (seq == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_for_new_cigar")); -}this._setSeq (seq, false, 0, 0); -jalview.datamodel.SeqCigar.addSequenceOps (this, seq, 0, seq.getLength () - 1, false); -}, "jalview.datamodel.SequenceI"); -Clazz.makeConstructor (c$, -function (seq, start, end) { -Clazz.superConstructor (this, jalview.datamodel.SeqCigar); -if (seq == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_for_new_cigar")); -}this._setSeq (seq, false, start, end + 1); -jalview.datamodel.SeqCigar.addSequenceOps (this, seq, start, end, false); -}, "jalview.datamodel.SequenceI,~N,~N"); -c$.parseCigar = Clazz.defineMethod (c$, "parseCigar", -function (seq, cigarString) { -var opsandrange = jalview.datamodel.CigarBase.parseCigarString (cigarString); -return new jalview.datamodel.SeqCigar (seq, opsandrange[0], opsandrange[1]); -}, "jalview.datamodel.SequenceI,~S"); -c$.createAlignmentSequences = Clazz.defineMethod (c$, "createAlignmentSequences", -function (alseqs, gapCharacter, colsel, segments) { -var seqs = new Array (alseqs.length); -var g_seqs = new Array (alseqs.length); -var alseqs_string = new Array (alseqs.length); -var gs_regions = new Array (alseqs.length); -for (var i = 0; i < alseqs.length; i++) { -alseqs_string[i] = alseqs[i].getRefSeq ().getSequenceAsString (alseqs[i].start, alseqs[i].end); -gs_regions[i] = alseqs[i].getSequenceAndDeletions (alseqs_string[i], gapCharacter); -if (gs_regions[i] == null) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_cigar_seq_no_operations", Clazz.newArray (-1, [Integer.$valueOf (i).toString ()]))); -}g_seqs[i] = new StringBuffer ((gs_regions[i])[0]); -} -var shifts = new jalview.util.ShiftList (); -for (var i = 0; i < alseqs.length; i++) { -var gs_region = ((gs_regions[i])[2]); -if (gs_region != null) { -for (var hr = 0; hr < gs_region.length; hr++) { -var region = gs_region[hr]; -var insert = Clazz.newCharArray (region[1] - region[0] + 1, '\0'); -for (var s = 0; s < insert.length; s++) { -insert[s] = gapCharacter; -} -var inspos = shifts.shift (region[2]); -for (var s = 0; s < alseqs.length; s++) { -if (s != i) { -if (g_seqs[s].length () <= inspos) { -for (var l = inspos - g_seqs[s].length (); l > 0; l--) { -g_seqs[s].append (gapCharacter); -} -}g_seqs[s].insert (inspos, insert); -} else { -g_seqs[s].insert (inspos, alseqs_string[i].substring (region[0], region[1] + 1)); -}} -shifts.addShift (region[2], insert.length); -if (segments == null) { -colsel.hideColumns (inspos, inspos + insert.length - 1); -}} -}} -for (var i = 0; i < alseqs.length; i++) { -var bounds = ((gs_regions[i])[1]); -var ref = alseqs[i].getRefSeq (); -seqs[i] = new jalview.datamodel.Sequence (ref.getName (), g_seqs[i].toString (), ref.getStart () + alseqs[i].start + bounds[0], ref.getStart () + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2])); -seqs[i].setDatasetSequence (ref); -seqs[i].setDescription (ref.getDescription ()); -} -if (segments != null) { -for (var i = 0; i < segments.length; i += 3) { -colsel.hideColumns (segments[i + 1], segments[i + 1] + segments[i + 2] - 1); -} -}return seqs; -}, "~A,~S,jalview.datamodel.ColumnSelection,~A"); -Clazz.defineMethod (c$, "setGroupMembership", -function (group) { -if (this.selGroups == null) { -this.selGroups = new java.util.Hashtable (); -}this.selGroups.put (group, Clazz.newIntArray (0, 0)); -}, "~O"); -Clazz.defineMethod (c$, "removeGroupMembership", -function (group) { -if (this.selGroups != null && this.selGroups.containsKey (group)) { -this.selGroups.remove (group); -return true; -}return false; -}, "~O"); -Clazz.defineMethod (c$, "clearMemberships", -function () { -if (this.selGroups != null) { -this.selGroups.clear (); -}this.selGroups = null; -}); -Clazz.defineMethod (c$, "getAllMemberships", -function () { -if (this.selGroups == null) { -return null; -}var mmbs = new Array (this.selGroups.size ()); -var en = this.selGroups.keys (); -for (var i = 0; en.hasMoreElements (); i++) { -mmbs[i] = en.nextElement (); -} -return mmbs; -}); -Clazz.defineMethod (c$, "isMemberOf", -function (sgr) { -return (this.selGroups != null) && this.selGroups.get (sgr) != null; -}, "~O"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.CigarSimple"], "jalview.datamodel.SeqCigar", ["jalview.analysis.AlignSeq", "$.SeqsetUtils", "jalview.datamodel.Sequence", "jalview.util.Comparison", "$.MessageManager", "$.ShiftList", "java.lang.Error", "$.StringBuffer", "java.util.Hashtable"], function () { +c$ = Clazz.decorateAsClass (function () { +this.start = 0; +this.end = 0; +this.refseq = null; +this.seqProps = null; +this.selGroups = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SeqCigar", jalview.datamodel.CigarSimple); +Clazz.defineMethod (c$, "getRefSeq", +function () { +return this.refseq; +}); +Clazz.defineMethod (c$, "getStart", +function () { +return this.start; +}); +Clazz.defineMethod (c$, "getEnd", +function () { +return this.end; +}); +Clazz.overrideMethod (c$, "getSequenceString", +function (GapChar) { +return (this.length == 0) ? "" : this.getSequenceAndDeletions (this.refseq.getSequenceAsString (this.start, this.end), GapChar)[0]; +}, "~S"); +Clazz.defineMethod (c$, "getSeq", +function (GapChar) { +var seq; +if (this.refseq == null || this.length == 0) { +return null; +}var edit_result = this.getSequenceAndDeletions (this.refseq.getSequenceAsString (this.start, this.end), GapChar); +if (edit_result == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_unexpected_null_from_get_sequence_and_deletions")); +}var bounds = edit_result[1]; +seq = new jalview.datamodel.Sequence (this.refseq.getName (), edit_result[0], this.refseq.getStart () + this.start + bounds[0], this.refseq.getStart () + this.start + ((bounds[2] == 0) ? -1 : bounds[2])); +seq.setDescription (this.refseq.getDescription ()); +var sstart = seq.getStart (); +var send = seq.getEnd (); +if (this.seqProps != null) { +jalview.analysis.SeqsetUtils.SeqCharacterUnhash (seq, this.seqProps); +}seq.setDatasetSequence (this.refseq); +seq.setStart (sstart); +seq.setEnd (send); +return seq; +}, "~S"); +Clazz.defineMethod (c$, "_setSeq", +($fz = function (seq, initialDeletion, _s, _e) { +var hasgaps = false; +if (seq == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_set_seq_null")); +}if (_s < 0) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_s", Clazz.newArray (-1, [Integer.$valueOf (_s).toString ()]))); +}var seq_string = seq.getSequenceAsString (); +if (_e == 0 || _e < _s || _e > seq_string.length) { +_e = seq_string.length; +}this.start = seq.findPosition (_s) - seq.getStart (); +this.end = seq.findPosition (_e) - seq.getStart (); +var l_ungapped = this.end - this.start; +var ds = seq.getDatasetSequence (); +if (ds == null) { +var ungapped = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (seq_string)); +l_ungapped = ungapped.length; +if (l_ungapped == seq.getLength ()) { +ds = seq; +} else { +ds = new jalview.datamodel.Sequence (seq.getName (), ungapped, seq.getStart (), seq.getStart () + ungapped.length - 1); +}}if (ds.getStart () < seq.getStart ()) { +var offset = seq.getStart () - ds.getStart (); +if (initialDeletion) { +this.addDeleted (_s + offset); +this.start = 0; +this.end += offset; +} else { +this.start += offset; +this.end += offset; +}}if (l_ungapped != (_e - _s)) { +hasgaps = true; +}this.refseq = ds; +this.seqProps = jalview.analysis.SeqsetUtils.SeqCharacterHash (seq); +if (this.end > ds.getLength ()) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_seqcigar_possible")); +}return hasgaps; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,~B,~N,~N"); +Clazz.makeConstructor (c$, +function (seq, operation, range) { +Clazz.superConstructor (this, jalview.datamodel.SeqCigar); +if (seq == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implmentation_bug_seq_null")); +}if (operation.length != range.length) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_bug_cigar_operation_list_range_list")); +}if (operation != null) { +this.operation = Clazz.newCharArray (operation.length + this._inc_length, '\0'); +this.range = Clazz.newIntArray (operation.length + this._inc_length, 0); +if (this._setSeq (seq, false, 0, 0)) { +throw new Error (jalview.util.MessageManager.getString ("error.not_yet_implemented_cigar_object_from_cigar_string")); +}for (var i = this.length, j = 0; j < operation.length; i++, j++) { +var op = operation[j]; +if (op != 'M' && op != 'I' && op != 'D') { +throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_bug_cigar_operation", Clazz.newArray (-1, [Integer.$valueOf (j).toString (), Integer.$valueOf (op.charCodeAt (0)).toString (), Integer.$valueOf ('M'.charCodeAt (0)).toString (), Integer.$valueOf ('I'.charCodeAt (0)).toString (), Integer.$valueOf ('D'.charCodeAt (0)).toString ()]))); +}this.operation[i] = op; +this.range[i] = range[j]; +} +this.length += operation.length; +} else { +this.operation = null; +this.range = null; +this.length = 0; +if (this._setSeq (seq, false, 0, 0)) { +throw new Error (jalview.util.MessageManager.getString ("error.not_yet_implemented_cigar_object_from_cigar_string")); +}}}, "jalview.datamodel.SequenceI,~A,~A"); +Clazz.defineMethod (c$, "addMatch", +function (range) { +this.addOperation ('M', range); +}, "~N"); +c$.addSequenceOps = Clazz.defineMethod (c$, "addSequenceOps", +function (cigar, seq, startpos, endpos, initialDeletions) { +var op = '\u0000'; +var range = 0; +var p = 0; +var res = seq.getLength (); +if (!initialDeletions) { +p = startpos; +}while (p <= endpos) { +var isGap = (p < res) ? jalview.util.Comparison.isGap (seq.getCharAt (p)) : true; +if ((startpos <= p) && (p <= endpos)) { +if (isGap) { +if (range > 0 && op != 'I') { +cigar.addOperation (op, range); +range = 0; +}op = 'I'; +range++; +} else { +if (range > 0 && op != 'M') { +cigar.addOperation (op, range); +range = 0; +}op = 'M'; +range++; +}} else { +if (!isGap) { +if (range > 0 && op != 'D') { +cigar.addOperation (op, range); +range = 0; +}op = 'D'; +range++; +} else { +}}p++; +} +if (range > 0) { +cigar.addOperation (op, range); +}}, "jalview.datamodel.CigarBase,jalview.datamodel.SequenceI,~N,~N,~B"); +Clazz.makeConstructor (c$, +function (seq) { +Clazz.superConstructor (this, jalview.datamodel.SeqCigar); +if (seq == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_for_new_cigar")); +}this._setSeq (seq, false, 0, 0); +jalview.datamodel.SeqCigar.addSequenceOps (this, seq, 0, seq.getLength () - 1, false); +}, "jalview.datamodel.SequenceI"); +Clazz.makeConstructor (c$, +function (seq, start, end) { +Clazz.superConstructor (this, jalview.datamodel.SeqCigar); +if (seq == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_for_new_cigar")); +}this._setSeq (seq, false, start, end + 1); +jalview.datamodel.SeqCigar.addSequenceOps (this, seq, start, end, false); +}, "jalview.datamodel.SequenceI,~N,~N"); +c$.parseCigar = Clazz.defineMethod (c$, "parseCigar", +function (seq, cigarString) { +var opsandrange = jalview.datamodel.CigarBase.parseCigarString (cigarString); +return new jalview.datamodel.SeqCigar (seq, opsandrange[0], opsandrange[1]); +}, "jalview.datamodel.SequenceI,~S"); +c$.createAlignmentSequences = Clazz.defineMethod (c$, "createAlignmentSequences", +function (alseqs, gapCharacter, colsel, segments) { +var seqs = new Array (alseqs.length); +var g_seqs = new Array (alseqs.length); +var alseqs_string = new Array (alseqs.length); +var gs_regions = new Array (alseqs.length); +for (var i = 0; i < alseqs.length; i++) { +alseqs_string[i] = alseqs[i].getRefSeq ().getSequenceAsString (alseqs[i].start, alseqs[i].end); +gs_regions[i] = alseqs[i].getSequenceAndDeletions (alseqs_string[i], gapCharacter); +if (gs_regions[i] == null) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_cigar_seq_no_operations", Clazz.newArray (-1, [Integer.$valueOf (i).toString ()]))); +}g_seqs[i] = new StringBuffer ((gs_regions[i])[0]); +} +var shifts = new jalview.util.ShiftList (); +for (var i = 0; i < alseqs.length; i++) { +var gs_region = ((gs_regions[i])[2]); +if (gs_region != null) { +for (var hr = 0; hr < gs_region.length; hr++) { +var region = gs_region[hr]; +var insert = Clazz.newCharArray (region[1] - region[0] + 1, '\0'); +for (var s = 0; s < insert.length; s++) { +insert[s] = gapCharacter; +} +var inspos = shifts.shift (region[2]); +for (var s = 0; s < alseqs.length; s++) { +if (s != i) { +if (g_seqs[s].length () <= inspos) { +for (var l = inspos - g_seqs[s].length (); l > 0; l--) { +g_seqs[s].append (gapCharacter); +} +}g_seqs[s].insert (inspos, insert); +} else { +g_seqs[s].insert (inspos, alseqs_string[i].substring (region[0], region[1] + 1)); +}} +shifts.addShift (region[2], insert.length); +if (segments == null) { +colsel.hideColumns (inspos, inspos + insert.length - 1); +}} +}} +for (var i = 0; i < alseqs.length; i++) { +var bounds = ((gs_regions[i])[1]); +var ref = alseqs[i].getRefSeq (); +seqs[i] = new jalview.datamodel.Sequence (ref.getName (), g_seqs[i].toString (), ref.getStart () + alseqs[i].start + bounds[0], ref.getStart () + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2])); +seqs[i].setDatasetSequence (ref); +seqs[i].setDescription (ref.getDescription ()); +} +if (segments != null) { +for (var i = 0; i < segments.length; i += 3) { +colsel.hideColumns (segments[i + 1], segments[i + 1] + segments[i + 2] - 1); +} +}return seqs; +}, "~A,~S,jalview.datamodel.ColumnSelection,~A"); +Clazz.defineMethod (c$, "setGroupMembership", +function (group) { +if (this.selGroups == null) { +this.selGroups = new java.util.Hashtable (); +}this.selGroups.put (group, Clazz.newIntArray (0, 0)); +}, "~O"); +Clazz.defineMethod (c$, "removeGroupMembership", +function (group) { +if (this.selGroups != null && this.selGroups.containsKey (group)) { +this.selGroups.remove (group); +return true; +}return false; +}, "~O"); +Clazz.defineMethod (c$, "clearMemberships", +function () { +if (this.selGroups != null) { +this.selGroups.clear (); +}this.selGroups = null; +}); +Clazz.defineMethod (c$, "getAllMemberships", +function () { +if (this.selGroups == null) { +return null; +}var mmbs = new Array (this.selGroups.size ()); +var en = this.selGroups.keys (); +for (var i = 0; en.hasMoreElements (); i++) { +mmbs[i] = en.nextElement (); +} +return mmbs; +}); +Clazz.defineMethod (c$, "isMemberOf", +function (sgr) { +return (this.selGroups != null) && this.selGroups.get (sgr) != null; +}, "~O"); +}); diff --git a/bin/jalview/datamodel/Sequence.class b/bin/jalview/datamodel/Sequence.class index 87bb9e3..f406e42 100644 Binary files a/bin/jalview/datamodel/Sequence.class and b/bin/jalview/datamodel/Sequence.class differ diff --git a/bin/jalview/datamodel/Sequence.js b/bin/jalview/datamodel/Sequence.js index 6a15091..06c8329 100644 --- a/bin/jalview/datamodel/Sequence.js +++ b/bin/jalview/datamodel/Sequence.js @@ -1,658 +1,658 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.ASequence", "$.SequenceI", "jalview.jsdev.RegExp"], "jalview.datamodel.Sequence", ["jalview.analysis.AlignSeq", "jalview.datamodel.AlignmentAnnotation", "$.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.StringUtils", "java.lang.StringBuffer", "java.util.ArrayList", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.datasetSequence = null; -this.name = null; -this.sequence = null; -this.description = null; -this.start = 0; -this.end = 0; -this.pdbIds = null; -this.vamsasId = null; -this.dbrefs = null; -this.rna = null; -this.annotation = null; -this.index = -1; -this.sequenceFeatures = null; -this.limitrx = null; -this.endrx = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "Sequence", jalview.datamodel.ASequence, jalview.datamodel.SequenceI); -Clazz.prepareFields (c$, function () { -this.limitrx = jalview.jsdev.RegExp.newRegex (["[/][0-9]{1,}[-][0-9]{1,}$"]); -this.endrx = jalview.jsdev.RegExp.newRegex (["[0-9]{1,}$"]); -}); -Clazz.makeConstructor (c$, -function (name, sequence, start, end) { -Clazz.superConstructor (this, jalview.datamodel.Sequence, []); -this.initSeqAndName (name, sequence.toCharArray (), start, end); -}, "~S,~S,~N,~N"); -Clazz.makeConstructor (c$, -function (name, sequence, start, end) { -Clazz.superConstructor (this, jalview.datamodel.Sequence, []); -this.initSeqAndName (name, sequence, start, end); -}, "~S,~A,~N,~N"); -Clazz.defineMethod (c$, "initSeqAndName", -function (name2, sequence2, start2, end2) { -this.name = name2; -this.sequence = sequence2; -this.start = start2; -this.end = end2; -this.parseId (); -this.checkValidRange (); -}, "~S,~A,~N,~N"); -Clazz.defineMethod (c$, "parseId", -function () { -if (this.name == null) { -System.err.println ("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); -this.name = ""; -}if (this.limitrx.search (this.name)) { -this.name = this.limitrx.left (); -this.endrx.search (this.limitrx.stringMatched ()); -this.setStart (Integer.parseInt (this.limitrx.stringMatched ().substring (1, this.endrx.matchedFrom () - 1))); -this.setEnd (Integer.parseInt (this.endrx.stringMatched ())); -}}); -Clazz.defineMethod (c$, "checkValidRange", -function () { -{ -var endRes = 0; -for (var j = 0; j < this.sequence.length; j++) { -if (!jalview.util.Comparison.isGap (this.sequence[j])) { -endRes++; -}} -if (endRes > 0) { -endRes += this.start - 1; -}if (this.end < endRes) { -this.end = endRes; -}}}); -Clazz.makeConstructor (c$, -function (name, sequence) { -this.construct (name, sequence, 1, -1); -}, "~S,~S"); -Clazz.makeConstructor (c$, -function (seq) { -this.construct (seq, seq.getAnnotation ()); -}, "jalview.datamodel.SequenceI"); -Clazz.makeConstructor (c$, -function (seq, alAnnotation) { -Clazz.superConstructor (this, jalview.datamodel.Sequence, []); -this.initSeqFrom (seq, alAnnotation); -}, "jalview.datamodel.SequenceI,~A"); -Clazz.defineMethod (c$, "initSeqFrom", -function (seq, alAnnotation) { -this.initSeqAndName (seq.getName (), seq.getSequence (), seq.getStart (), seq.getEnd ()); -this.description = seq.getDescription (); -if (seq.getSequenceFeatures () != null) { -var sf = seq.getSequenceFeatures (); -for (var i = 0; i < sf.length; i++) { -this.addSequenceFeature ( new jalview.datamodel.SequenceFeature (sf[i])); -} -}this.setDatasetSequence (seq.getDatasetSequence ()); -if (this.datasetSequence == null && seq.getDBRef () != null) { -var dbr = seq.getDBRef (); -for (var i = 0; i < dbr.length; i++) { -this.addDBRef ( new jalview.datamodel.DBRefEntry (dbr[i])); -} -}if (seq.getAnnotation () != null) { -var sqann = seq.getAnnotation (); -for (var i = 0; i < sqann.length; i++) { -if (sqann[i] == null) { -continue; -}var found = (alAnnotation == null); -if (!found) { -for (var apos = 0; !found && apos < alAnnotation.length; apos++) { -found = (alAnnotation[apos] === sqann[i]); -} -}if (found) { -var newann = new jalview.datamodel.AlignmentAnnotation (sqann[i]); -this.addAlignmentAnnotation (newann); -}} -}if (seq.getPDBId () != null) { -var ids = seq.getPDBId (); -var e = ids.elements (); -while (e.hasMoreElements ()) { -this.addPDBId ( new jalview.datamodel.PDBEntry (e.nextElement ())); -} -}}, "jalview.datamodel.SequenceI,~A"); -Clazz.defineMethod (c$, "setSequenceFeatures", -function (features) { -this.sequenceFeatures = features; -}, "~A"); -Clazz.overrideMethod (c$, "addSequenceFeature", -function (sf) { -if (this.sequenceFeatures == null) { -this.sequenceFeatures = new Array (0); -}for (var i = 0; i < this.sequenceFeatures.length; i++) { -if (this.sequenceFeatures[i].equals (sf)) { -return; -}} -var temp = new Array (this.sequenceFeatures.length + 1); -System.arraycopy (this.sequenceFeatures, 0, temp, 0, this.sequenceFeatures.length); -temp[this.sequenceFeatures.length] = sf; -this.sequenceFeatures = temp; -}, "jalview.datamodel.SequenceFeature"); -Clazz.overrideMethod (c$, "deleteFeature", -function (sf) { -if (this.sequenceFeatures == null) { -return; -}var index = 0; -for (index = 0; index < this.sequenceFeatures.length; index++) { -if (this.sequenceFeatures[index].equals (sf)) { -break; -}} -if (index == this.sequenceFeatures.length) { -return; -}var sfLength = this.sequenceFeatures.length; -if (sfLength < 2) { -this.sequenceFeatures = null; -} else { -var temp = new Array (sfLength - 1); -System.arraycopy (this.sequenceFeatures, 0, temp, 0, index); -if (index < sfLength) { -System.arraycopy (this.sequenceFeatures, index + 1, temp, index, this.sequenceFeatures.length - index - 1); -}this.sequenceFeatures = temp; -}}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "getSequenceFeatures", -function () { -var features = this.sequenceFeatures; -var seq = this; -var count = 0; -while (features == null && seq.getDatasetSequence () != null && count++ < 10) { -seq = seq.getDatasetSequence (); -features = (seq).sequenceFeatures; -} -return features; -}); -Clazz.overrideMethod (c$, "addPDBId", -function (entry) { -if (this.pdbIds == null) { -this.pdbIds = new java.util.Vector (); -}if (this.pdbIds.contains (entry)) { -jalview.datamodel.Sequence.updatePDBEntry (this.pdbIds.get (this.pdbIds.indexOf (entry)), entry); -} else { -this.pdbIds.addElement (entry); -}}, "jalview.datamodel.PDBEntry"); -c$.updatePDBEntry = Clazz.defineMethod (c$, "updatePDBEntry", -($fz = function (oldEntry, newEntry) { -if (newEntry.getFile () != null) { -oldEntry.setFile (newEntry.getFile ()); -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.PDBEntry,jalview.datamodel.PDBEntry"); -Clazz.defineMethod (c$, "setPDBId", -function (id) { -this.pdbIds = id; -}, "java.util.Vector"); -Clazz.defineMethod (c$, "getPDBId", -function () { -return this.pdbIds; -}); -Clazz.overrideMethod (c$, "getDisplayId", -function (jvsuffix) { -var result = new StringBuffer (this.name); -if (jvsuffix) { -result.append ("/" + this.start + "-" + this.end); -}return result.toString (); -}, "~B"); -Clazz.overrideMethod (c$, "setName", -function (name) { -this.name = name; -this.parseId (); -}, "~S"); -Clazz.defineMethod (c$, "getName", -function () { -return this.name; -}); -Clazz.overrideMethod (c$, "setStart", -function (start) { -this.start = start; -}, "~N"); -Clazz.defineMethod (c$, "getStart", -function () { -return this.start; -}); -Clazz.overrideMethod (c$, "setEnd", -function (end) { -this.end = end; -}, "~N"); -Clazz.defineMethod (c$, "getEnd", -function () { -return this.end; -}); -Clazz.overrideMethod (c$, "getLength", -function () { -return this.sequence.length; -}); -Clazz.defineMethod (c$, "setSequence", -function (seq) { -this.sequence = seq.toCharArray (); -this.checkValidRange (); -}, "~S"); -Clazz.defineMethod (c$, "getSequenceAsString", -function () { -return String.instantialize (this.sequence); -}); -Clazz.defineMethod (c$, "getSequenceAsString", -function (start, end) { -return String.instantialize (this.getSequence (start, end)); -}, "~N,~N"); -Clazz.defineMethod (c$, "getSequence", -function () { -return this.sequence; -}); -Clazz.defineMethod (c$, "getSequence", -function (start, end) { -if (start < 0) { -start = 0; -}if (start >= this.sequence.length) { -return Clazz.newCharArray (0, '\0'); -}if (end >= this.sequence.length) { -end = this.sequence.length; -}var reply = Clazz.newCharArray (end - start, '\0'); -System.arraycopy (this.sequence, start, reply, 0, end - start); -return reply; -}, "~N,~N"); -Clazz.overrideMethod (c$, "getSubSequence", -function (start, end) { -if (start < 0) { -start = 0; -}var seq = this.getSequence (start, end); -if (seq.length == 0) { -return null; -}var nstart = this.findPosition (start); -var nend = this.findPosition (end) - 1; -var nseq = new jalview.datamodel.Sequence (this.getName (), seq, nstart, nend); -nseq.setDescription (this.description); -if (this.datasetSequence != null) { -nseq.setDatasetSequence (this.datasetSequence); -} else { -nseq.setDatasetSequence (this); -}return nseq; -}, "~N,~N"); -Clazz.overrideMethod (c$, "getCharAt", -function (i) { -if (i < this.sequence.length) { -return this.sequence[i]; -} else { -return ' '; -}}, "~N"); -Clazz.defineMethod (c$, "setDescription", -function (desc) { -this.description = desc; -}, "~S"); -Clazz.defineMethod (c$, "getDescription", -function () { -return this.description; -}); -Clazz.overrideMethod (c$, "findIndex", -function (pos) { -var j = this.start; -var i = 0; -while ((i < this.sequence.length) && (j <= this.end) && (j <= pos)) { -if (!jalview.util.Comparison.isGap (this.sequence[i])) { -j++; -}i++; -} -if ((j == this.end) && (j < pos)) { -return this.end + 1; -} else { -return i; -}}, "~N"); -Clazz.overrideMethod (c$, "findPosition", -function (i) { -var j = 0; -var pos = this.start; -var seqlen = this.sequence.length; -while ((j < i) && (j < seqlen)) { -if (!jalview.util.Comparison.isGap (this.sequence[j])) { -pos++; -}j++; -} -return pos; -}, "~N"); -Clazz.overrideMethod (c$, "gapMap", -function () { -var seq = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (this.sequence)); -var map = Clazz.newIntArray (seq.length, 0); -var j = 0; -var p = 0; -while (j < this.sequence.length) { -if (!jalview.util.Comparison.isGap (this.sequence[j])) { -map[p++] = j; -}j++; -} -return map; -}); -Clazz.overrideMethod (c$, "findPositionMap", -function () { -var map = Clazz.newIntArray (this.sequence.length, 0); -var j = 0; -var pos = this.start; -var seqlen = this.sequence.length; -while ((j < seqlen)) { -map[j] = pos; -if (!jalview.util.Comparison.isGap (this.sequence[j])) { -pos++; -}j++; -} -return map; -}); -Clazz.overrideMethod (c$, "getInsertions", -function () { -var map = new java.util.ArrayList (); -var lastj = -1; -var j = 0; -var pos = this.start; -var seqlen = this.sequence.length; -while ((j < seqlen)) { -if (jalview.util.Comparison.isGap (this.sequence[j])) { -if (lastj == -1) { -lastj = j; -}} else { -if (lastj != -1) { -map.add ( Clazz.newIntArray (-1, [lastj, j - 1])); -lastj = -1; -}}j++; -} -if (lastj != -1) { -map.add ( Clazz.newIntArray (-1, [lastj, j - 1])); -lastj = -1; -}return map; -}); -Clazz.overrideMethod (c$, "deleteChars", -function (i, j) { -var newstart = this.start; -var newend = this.end; -if (i >= this.sequence.length || i < 0) { -return; -}var tmp = jalview.util.StringUtils.deleteChars (this.sequence, i, j); -var createNewDs = false; -var eindex = -1; -var sindex = -1; -var ecalc = false; -var scalc = false; -for (var s = i; s < j; s++) { -if (jalview.schemes.ResidueProperties.aaIndex[this.sequence[s].charCodeAt (0)] != 23) { -if (createNewDs) { -newend--; -} else { -if (!scalc) { -sindex = this.findIndex (this.start) - 1; -scalc = true; -}if (sindex == s) { -newstart = this.findPosition (j); -break; -} else { -if (!ecalc) { -eindex = this.findIndex (this.end) - 1; -ecalc = true; -}if (eindex < j) { -newend = this.findPosition (i - 1); -break; -} else { -createNewDs = true; -newend--; -}}}}} -if (createNewDs && this.datasetSequence != null) { -var ds = new jalview.datamodel.Sequence (this.datasetSequence); -ds.deleteChars (i, j); -this.datasetSequence = ds; -}this.start = newstart; -this.end = newend; -this.sequence = tmp; -}, "~N,~N"); -Clazz.defineMethod (c$, "insertCharAt", -function (i, length, c) { -var tmp = Clazz.newCharArray (this.sequence.length + length, '\0'); -if (i >= this.sequence.length) { -System.arraycopy (this.sequence, 0, tmp, 0, this.sequence.length); -i = this.sequence.length; -} else { -System.arraycopy (this.sequence, 0, tmp, 0, i); -}var index = i; -while (length > 0) { -tmp[index++] = c; -length--; -} -if (i < this.sequence.length) { -System.arraycopy (this.sequence, i, tmp, index, this.sequence.length - i); -}this.sequence = tmp; -}, "~N,~N,~S"); -Clazz.defineMethod (c$, "insertCharAt", -function (i, c) { -this.insertCharAt (i, 1, c); -}, "~N,~S"); -Clazz.overrideMethod (c$, "getVamsasId", -function () { -return this.vamsasId; -}); -Clazz.overrideMethod (c$, "setVamsasId", -function (id) { -this.vamsasId = id; -}, "~S"); -Clazz.defineMethod (c$, "setDBRef", -function (dbref) { -this.dbrefs = dbref; -}, "~A"); -Clazz.defineMethod (c$, "getDBRef", -function () { -if (this.dbrefs == null && this.datasetSequence != null && this !== this.datasetSequence) { -return this.datasetSequence.getDBRef (); -}return this.dbrefs; -}); -Clazz.overrideMethod (c$, "addDBRef", -function (entry) { -if (this.dbrefs == null) { -this.dbrefs = new Array (0); -}var i; -var iSize = this.dbrefs.length; -for (i = 0; i < iSize; i++) { -if (this.dbrefs[i].equalRef (entry)) { -if (entry.getMap () != null) { -if (this.dbrefs[i].getMap () == null) { -this.dbrefs[i] = entry; -}}return; -}} -var temp = new Array (iSize + 1); -System.arraycopy (this.dbrefs, 0, temp, 0, iSize); -temp[temp.length - 1] = entry; -this.dbrefs = temp; -}, "jalview.datamodel.DBRefEntry"); -Clazz.defineMethod (c$, "setDatasetSequence", -function (seq) { -this.datasetSequence = seq; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getDatasetSequence", -function () { -return this.datasetSequence; -}); -Clazz.defineMethod (c$, "getAnnotation", -function () { -return this.annotation == null ? null : this.annotation.toArray ( new Array (this.annotation.size ())); -}); -Clazz.overrideMethod (c$, "hasAnnotation", -function (ann) { -return this.annotation == null ? false : this.annotation.contains (ann); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "addAlignmentAnnotation", -function (annotation) { -if (this.annotation == null) { -this.annotation = new java.util.Vector (); -}if (!this.annotation.contains (annotation)) { -this.annotation.addElement (annotation); -}annotation.setSequenceRef (this); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.overrideMethod (c$, "removeAlignmentAnnotation", -function (annotation) { -if (this.annotation != null) { -this.annotation.removeElement (annotation); -if (this.annotation.size () == 0) { -this.annotation = null; -}}}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "isValidDatasetSequence", -($fz = function () { -if (this.datasetSequence != null) { -return false; -}for (var i = 0; i < this.sequence.length; i++) { -if (jalview.util.Comparison.isGap (this.sequence[i])) { -return false; -}} -return true; -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "deriveSequence", -function () { -var seq = new jalview.datamodel.Sequence (this); -if (this.datasetSequence != null) { -seq.setDatasetSequence (this.datasetSequence); -} else { -if (this.isValidDatasetSequence ()) { -seq.setDatasetSequence (this); -} else { -var ds = seq; -ds.setSequence (jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (this.sequence))); -this.setDatasetSequence (ds); -ds.setSequenceFeatures (this.getSequenceFeatures ()); -seq = this; -}}return seq; -}); -Clazz.overrideMethod (c$, "createDatasetSequence", -function () { -if (this.datasetSequence == null) { -this.datasetSequence = new jalview.datamodel.Sequence (this.getName (), jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, this.getSequenceAsString ()), this.getStart (), this.getEnd ()); -this.datasetSequence.setSequenceFeatures (this.getSequenceFeatures ()); -this.datasetSequence.setDescription (this.getDescription ()); -this.setSequenceFeatures (null); -this.datasetSequence.setDBRef (this.getDBRef ()); -this.setDBRef (null); -this.datasetSequence.setPDBId (this.getPDBId ()); -this.setPDBId (null); -this.datasetSequence.updatePDBIds (); -if (this.annotation != null) { -for (var aa, $aa = this.annotation.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { -var _aa = new jalview.datamodel.AlignmentAnnotation (aa); -_aa.sequenceRef = this.datasetSequence; -_aa.adjustForAlignment (); -this.datasetSequence.addAlignmentAnnotation (_aa); -} -}}return this.datasetSequence; -}); -Clazz.overrideMethod (c$, "setAlignmentAnnotation", -function (annotations) { -if (this.annotation != null) { -this.annotation.removeAllElements (); -}if (annotations != null) { -for (var i = 0; i < annotations.length; i++) { -if (annotations[i] != null) { -this.addAlignmentAnnotation (annotations[i]); -}} -}}, "~A"); -Clazz.defineMethod (c$, "getAnnotation", -function (label) { -if (this.annotation == null || this.annotation.size () == 0) { -return null; -}var subset = new java.util.Vector (); -var e = this.annotation.elements (); -while (e.hasMoreElements ()) { -var ann = e.nextElement (); -if (ann.label != null && ann.label.equals (label)) { -subset.addElement (ann); -}} -if (subset.size () == 0) { -return null; -}var anns = new Array (subset.size ()); -var i = 0; -e = subset.elements (); -while (e.hasMoreElements ()) { -anns[i++] = e.nextElement (); -} -subset.removeAllElements (); -return anns; -}, "~S"); -Clazz.defineMethod (c$, "updatePDBIds", -function () { -if (this.datasetSequence != null) { -return this.datasetSequence.updatePDBIds (); -}if (this.dbrefs == null || this.dbrefs.length == 0) { -return false; -}var newpdb = new java.util.Vector (); -for (var i = 0; i < this.dbrefs.length; i++) { -if (jalview.datamodel.DBRefSource.PDB.equals (this.dbrefs[i].getSource ())) { -var pdbe = new jalview.datamodel.PDBEntry (); -pdbe.setId (this.dbrefs[i].getAccessionId ()); -if (this.pdbIds == null || this.pdbIds.size () == 0) { -newpdb.addElement (pdbe); -} else { -var en = this.pdbIds.elements (); -var matched = false; -while (!matched && en.hasMoreElements ()) { -var anentry = en.nextElement (); -if (anentry.getId ().equals (pdbe.getId ())) { -matched = true; -}} -if (!matched) { -newpdb.addElement (pdbe); -}}}} -if (newpdb.size () > 0) { -var en = newpdb.elements (); -while (en.hasMoreElements ()) { -this.addPDBId (en.nextElement ()); -} -return true; -}return false; -}); -Clazz.defineMethod (c$, "transferAnnotation", -function (entry, mp) { -if (this.datasetSequence != null) { -this.datasetSequence.transferAnnotation (entry, mp); -return; -}if (entry.getDatasetSequence () != null) { -this.transferAnnotation (entry.getDatasetSequence (), mp); -return; -}if (entry.getSequenceFeatures () != null) { -var sfs = entry.getSequenceFeatures (); -for (var si = 0; si < sfs.length; si++) { -var sf = (mp != null) ? mp.locateFeature (sfs[si]) : Clazz.newArray (-1, [ new jalview.datamodel.SequenceFeature (sfs[si])]); -if (sf != null && sf.length > 0) { -for (var sfi = 0; sfi < sf.length; sfi++) { -this.addSequenceFeature (sf[sfi]); -} -}} -}if (entry.getPDBId () != null) { -var e = entry.getPDBId ().elements (); -while (e.hasMoreElements ()) { -var pdb = e.nextElement (); -this.addPDBId (pdb); -} -}var entryRefs = entry.getDBRef (); -if (entryRefs != null) { -for (var r = 0; r < entryRefs.length; r++) { -var newref = new jalview.datamodel.DBRefEntry (entryRefs[r]); -if (newref.getMap () != null && mp != null) { -}this.addDBRef (newref); -} -}}, "jalview.datamodel.SequenceI,jalview.datamodel.Mapping"); -Clazz.overrideMethod (c$, "getIndex", -function () { -return this.index; -}); -Clazz.overrideMethod (c$, "setIndex", -function (value) { -this.index = value; -}, "~N"); -Clazz.overrideMethod (c$, "setRNA", -function (r) { -this.rna = r; -}, "jalview.jsdev.api.VarnaRNA"); -Clazz.overrideMethod (c$, "getRNA", -function () { -return this.rna; -}); -Clazz.overrideMethod (c$, "getAlignmentAnnotations", -function (calcId, label) { -var result = new java.util.ArrayList (); -if (this.annotation != null) { -for (var ann, $ann = this.annotation.iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) { -if (ann.calcId != null && ann.calcId.equals (calcId) && ann.label != null && ann.label.equals (label)) { -result.add (ann); -}} -}return result; -}, "~S,~S"); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.ASequence", "$.SequenceI", "jalview.jsdev.RegExp"], "jalview.datamodel.Sequence", ["jalview.analysis.AlignSeq", "jalview.datamodel.AlignmentAnnotation", "$.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.StringUtils", "java.lang.StringBuffer", "java.util.ArrayList", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.datasetSequence = null; +this.name = null; +this.sequence = null; +this.description = null; +this.start = 0; +this.end = 0; +this.pdbIds = null; +this.vamsasId = null; +this.dbrefs = null; +this.rna = null; +this.annotation = null; +this.index = -1; +this.sequenceFeatures = null; +this.limitrx = null; +this.endrx = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "Sequence", jalview.datamodel.ASequence, jalview.datamodel.SequenceI); +Clazz.prepareFields (c$, function () { +this.limitrx = jalview.jsdev.RegExp.newRegex (["[/][0-9]{1,}[-][0-9]{1,}$"]); +this.endrx = jalview.jsdev.RegExp.newRegex (["[0-9]{1,}$"]); +}); +Clazz.makeConstructor (c$, +function (name, sequence, start, end) { +Clazz.superConstructor (this, jalview.datamodel.Sequence, []); +this.initSeqAndName (name, sequence.toCharArray (), start, end); +}, "~S,~S,~N,~N"); +Clazz.makeConstructor (c$, +function (name, sequence, start, end) { +Clazz.superConstructor (this, jalview.datamodel.Sequence, []); +this.initSeqAndName (name, sequence, start, end); +}, "~S,~A,~N,~N"); +Clazz.defineMethod (c$, "initSeqAndName", +function (name2, sequence2, start2, end2) { +this.name = name2; +this.sequence = sequence2; +this.start = start2; +this.end = end2; +this.parseId (); +this.checkValidRange (); +}, "~S,~A,~N,~N"); +Clazz.defineMethod (c$, "parseId", +function () { +if (this.name == null) { +System.err.println ("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); +this.name = ""; +}if (this.limitrx.search (this.name)) { +this.name = this.limitrx.left (); +this.endrx.search (this.limitrx.stringMatched ()); +this.setStart (Integer.parseInt (this.limitrx.stringMatched ().substring (1, this.endrx.matchedFrom () - 1))); +this.setEnd (Integer.parseInt (this.endrx.stringMatched ())); +}}); +Clazz.defineMethod (c$, "checkValidRange", +function () { +{ +var endRes = 0; +for (var j = 0; j < this.sequence.length; j++) { +if (!jalview.util.Comparison.isGap (this.sequence[j])) { +endRes++; +}} +if (endRes > 0) { +endRes += this.start - 1; +}if (this.end < endRes) { +this.end = endRes; +}}}); +Clazz.makeConstructor (c$, +function (name, sequence) { +this.construct (name, sequence, 1, -1); +}, "~S,~S"); +Clazz.makeConstructor (c$, +function (seq) { +this.construct (seq, seq.getAnnotation ()); +}, "jalview.datamodel.SequenceI"); +Clazz.makeConstructor (c$, +function (seq, alAnnotation) { +Clazz.superConstructor (this, jalview.datamodel.Sequence, []); +this.initSeqFrom (seq, alAnnotation); +}, "jalview.datamodel.SequenceI,~A"); +Clazz.defineMethod (c$, "initSeqFrom", +function (seq, alAnnotation) { +this.initSeqAndName (seq.getName (), seq.getSequence (), seq.getStart (), seq.getEnd ()); +this.description = seq.getDescription (); +if (seq.getSequenceFeatures () != null) { +var sf = seq.getSequenceFeatures (); +for (var i = 0; i < sf.length; i++) { +this.addSequenceFeature ( new jalview.datamodel.SequenceFeature (sf[i])); +} +}this.setDatasetSequence (seq.getDatasetSequence ()); +if (this.datasetSequence == null && seq.getDBRef () != null) { +var dbr = seq.getDBRef (); +for (var i = 0; i < dbr.length; i++) { +this.addDBRef ( new jalview.datamodel.DBRefEntry (dbr[i])); +} +}if (seq.getAnnotation () != null) { +var sqann = seq.getAnnotation (); +for (var i = 0; i < sqann.length; i++) { +if (sqann[i] == null) { +continue; +}var found = (alAnnotation == null); +if (!found) { +for (var apos = 0; !found && apos < alAnnotation.length; apos++) { +found = (alAnnotation[apos] === sqann[i]); +} +}if (found) { +var newann = new jalview.datamodel.AlignmentAnnotation (sqann[i]); +this.addAlignmentAnnotation (newann); +}} +}if (seq.getPDBId () != null) { +var ids = seq.getPDBId (); +var e = ids.elements (); +while (e.hasMoreElements ()) { +this.addPDBId ( new jalview.datamodel.PDBEntry (e.nextElement ())); +} +}}, "jalview.datamodel.SequenceI,~A"); +Clazz.defineMethod (c$, "setSequenceFeatures", +function (features) { +this.sequenceFeatures = features; +}, "~A"); +Clazz.overrideMethod (c$, "addSequenceFeature", +function (sf) { +if (this.sequenceFeatures == null) { +this.sequenceFeatures = new Array (0); +}for (var i = 0; i < this.sequenceFeatures.length; i++) { +if (this.sequenceFeatures[i].equals (sf)) { +return; +}} +var temp = new Array (this.sequenceFeatures.length + 1); +System.arraycopy (this.sequenceFeatures, 0, temp, 0, this.sequenceFeatures.length); +temp[this.sequenceFeatures.length] = sf; +this.sequenceFeatures = temp; +}, "jalview.datamodel.SequenceFeature"); +Clazz.overrideMethod (c$, "deleteFeature", +function (sf) { +if (this.sequenceFeatures == null) { +return; +}var index = 0; +for (index = 0; index < this.sequenceFeatures.length; index++) { +if (this.sequenceFeatures[index].equals (sf)) { +break; +}} +if (index == this.sequenceFeatures.length) { +return; +}var sfLength = this.sequenceFeatures.length; +if (sfLength < 2) { +this.sequenceFeatures = null; +} else { +var temp = new Array (sfLength - 1); +System.arraycopy (this.sequenceFeatures, 0, temp, 0, index); +if (index < sfLength) { +System.arraycopy (this.sequenceFeatures, index + 1, temp, index, this.sequenceFeatures.length - index - 1); +}this.sequenceFeatures = temp; +}}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "getSequenceFeatures", +function () { +var features = this.sequenceFeatures; +var seq = this; +var count = 0; +while (features == null && seq.getDatasetSequence () != null && count++ < 10) { +seq = seq.getDatasetSequence (); +features = (seq).sequenceFeatures; +} +return features; +}); +Clazz.overrideMethod (c$, "addPDBId", +function (entry) { +if (this.pdbIds == null) { +this.pdbIds = new java.util.Vector (); +}if (this.pdbIds.contains (entry)) { +jalview.datamodel.Sequence.updatePDBEntry (this.pdbIds.get (this.pdbIds.indexOf (entry)), entry); +} else { +this.pdbIds.addElement (entry); +}}, "jalview.datamodel.PDBEntry"); +c$.updatePDBEntry = Clazz.defineMethod (c$, "updatePDBEntry", +($fz = function (oldEntry, newEntry) { +if (newEntry.getFile () != null) { +oldEntry.setFile (newEntry.getFile ()); +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.PDBEntry,jalview.datamodel.PDBEntry"); +Clazz.defineMethod (c$, "setPDBId", +function (id) { +this.pdbIds = id; +}, "java.util.Vector"); +Clazz.defineMethod (c$, "getPDBId", +function () { +return this.pdbIds; +}); +Clazz.overrideMethod (c$, "getDisplayId", +function (jvsuffix) { +var result = new StringBuffer (this.name); +if (jvsuffix) { +result.append ("/" + this.start + "-" + this.end); +}return result.toString (); +}, "~B"); +Clazz.overrideMethod (c$, "setName", +function (name) { +this.name = name; +this.parseId (); +}, "~S"); +Clazz.defineMethod (c$, "getName", +function () { +return this.name; +}); +Clazz.overrideMethod (c$, "setStart", +function (start) { +this.start = start; +}, "~N"); +Clazz.defineMethod (c$, "getStart", +function () { +return this.start; +}); +Clazz.overrideMethod (c$, "setEnd", +function (end) { +this.end = end; +}, "~N"); +Clazz.defineMethod (c$, "getEnd", +function () { +return this.end; +}); +Clazz.overrideMethod (c$, "getLength", +function () { +return this.sequence.length; +}); +Clazz.defineMethod (c$, "setSequence", +function (seq) { +this.sequence = seq.toCharArray (); +this.checkValidRange (); +}, "~S"); +Clazz.defineMethod (c$, "getSequenceAsString", +function () { +return String.instantialize (this.sequence); +}); +Clazz.defineMethod (c$, "getSequenceAsString", +function (start, end) { +return String.instantialize (this.getSequence (start, end)); +}, "~N,~N"); +Clazz.defineMethod (c$, "getSequence", +function () { +return this.sequence; +}); +Clazz.defineMethod (c$, "getSequence", +function (start, end) { +if (start < 0) { +start = 0; +}if (start >= this.sequence.length) { +return Clazz.newCharArray (0, '\0'); +}if (end >= this.sequence.length) { +end = this.sequence.length; +}var reply = Clazz.newCharArray (end - start, '\0'); +System.arraycopy (this.sequence, start, reply, 0, end - start); +return reply; +}, "~N,~N"); +Clazz.overrideMethod (c$, "getSubSequence", +function (start, end) { +if (start < 0) { +start = 0; +}var seq = this.getSequence (start, end); +if (seq.length == 0) { +return null; +}var nstart = this.findPosition (start); +var nend = this.findPosition (end) - 1; +var nseq = new jalview.datamodel.Sequence (this.getName (), seq, nstart, nend); +nseq.setDescription (this.description); +if (this.datasetSequence != null) { +nseq.setDatasetSequence (this.datasetSequence); +} else { +nseq.setDatasetSequence (this); +}return nseq; +}, "~N,~N"); +Clazz.overrideMethod (c$, "getCharAt", +function (i) { +if (i < this.sequence.length) { +return this.sequence[i]; +} else { +return ' '; +}}, "~N"); +Clazz.defineMethod (c$, "setDescription", +function (desc) { +this.description = desc; +}, "~S"); +Clazz.defineMethod (c$, "getDescription", +function () { +return this.description; +}); +Clazz.overrideMethod (c$, "findIndex", +function (pos) { +var j = this.start; +var i = 0; +while ((i < this.sequence.length) && (j <= this.end) && (j <= pos)) { +if (!jalview.util.Comparison.isGap (this.sequence[i])) { +j++; +}i++; +} +if ((j == this.end) && (j < pos)) { +return this.end + 1; +} else { +return i; +}}, "~N"); +Clazz.overrideMethod (c$, "findPosition", +function (i) { +var j = 0; +var pos = this.start; +var seqlen = this.sequence.length; +while ((j < i) && (j < seqlen)) { +if (!jalview.util.Comparison.isGap (this.sequence[j])) { +pos++; +}j++; +} +return pos; +}, "~N"); +Clazz.overrideMethod (c$, "gapMap", +function () { +var seq = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (this.sequence)); +var map = Clazz.newIntArray (seq.length, 0); +var j = 0; +var p = 0; +while (j < this.sequence.length) { +if (!jalview.util.Comparison.isGap (this.sequence[j])) { +map[p++] = j; +}j++; +} +return map; +}); +Clazz.overrideMethod (c$, "findPositionMap", +function () { +var map = Clazz.newIntArray (this.sequence.length, 0); +var j = 0; +var pos = this.start; +var seqlen = this.sequence.length; +while ((j < seqlen)) { +map[j] = pos; +if (!jalview.util.Comparison.isGap (this.sequence[j])) { +pos++; +}j++; +} +return map; +}); +Clazz.overrideMethod (c$, "getInsertions", +function () { +var map = new java.util.ArrayList (); +var lastj = -1; +var j = 0; +var pos = this.start; +var seqlen = this.sequence.length; +while ((j < seqlen)) { +if (jalview.util.Comparison.isGap (this.sequence[j])) { +if (lastj == -1) { +lastj = j; +}} else { +if (lastj != -1) { +map.add ( Clazz.newIntArray (-1, [lastj, j - 1])); +lastj = -1; +}}j++; +} +if (lastj != -1) { +map.add ( Clazz.newIntArray (-1, [lastj, j - 1])); +lastj = -1; +}return map; +}); +Clazz.overrideMethod (c$, "deleteChars", +function (i, j) { +var newstart = this.start; +var newend = this.end; +if (i >= this.sequence.length || i < 0) { +return; +}var tmp = jalview.util.StringUtils.deleteChars (this.sequence, i, j); +var createNewDs = false; +var eindex = -1; +var sindex = -1; +var ecalc = false; +var scalc = false; +for (var s = i; s < j; s++) { +if (jalview.schemes.ResidueProperties.aaIndex[this.sequence[s].charCodeAt (0)] != 23) { +if (createNewDs) { +newend--; +} else { +if (!scalc) { +sindex = this.findIndex (this.start) - 1; +scalc = true; +}if (sindex == s) { +newstart = this.findPosition (j); +break; +} else { +if (!ecalc) { +eindex = this.findIndex (this.end) - 1; +ecalc = true; +}if (eindex < j) { +newend = this.findPosition (i - 1); +break; +} else { +createNewDs = true; +newend--; +}}}}} +if (createNewDs && this.datasetSequence != null) { +var ds = new jalview.datamodel.Sequence (this.datasetSequence); +ds.deleteChars (i, j); +this.datasetSequence = ds; +}this.start = newstart; +this.end = newend; +this.sequence = tmp; +}, "~N,~N"); +Clazz.defineMethod (c$, "insertCharAt", +function (i, length, c) { +var tmp = Clazz.newCharArray (this.sequence.length + length, '\0'); +if (i >= this.sequence.length) { +System.arraycopy (this.sequence, 0, tmp, 0, this.sequence.length); +i = this.sequence.length; +} else { +System.arraycopy (this.sequence, 0, tmp, 0, i); +}var index = i; +while (length > 0) { +tmp[index++] = c; +length--; +} +if (i < this.sequence.length) { +System.arraycopy (this.sequence, i, tmp, index, this.sequence.length - i); +}this.sequence = tmp; +}, "~N,~N,~S"); +Clazz.defineMethod (c$, "insertCharAt", +function (i, c) { +this.insertCharAt (i, 1, c); +}, "~N,~S"); +Clazz.overrideMethod (c$, "getVamsasId", +function () { +return this.vamsasId; +}); +Clazz.overrideMethod (c$, "setVamsasId", +function (id) { +this.vamsasId = id; +}, "~S"); +Clazz.defineMethod (c$, "setDBRef", +function (dbref) { +this.dbrefs = dbref; +}, "~A"); +Clazz.defineMethod (c$, "getDBRef", +function () { +if (this.dbrefs == null && this.datasetSequence != null && this !== this.datasetSequence) { +return this.datasetSequence.getDBRef (); +}return this.dbrefs; +}); +Clazz.overrideMethod (c$, "addDBRef", +function (entry) { +if (this.dbrefs == null) { +this.dbrefs = new Array (0); +}var i; +var iSize = this.dbrefs.length; +for (i = 0; i < iSize; i++) { +if (this.dbrefs[i].equalRef (entry)) { +if (entry.getMap () != null) { +if (this.dbrefs[i].getMap () == null) { +this.dbrefs[i] = entry; +}}return; +}} +var temp = new Array (iSize + 1); +System.arraycopy (this.dbrefs, 0, temp, 0, iSize); +temp[temp.length - 1] = entry; +this.dbrefs = temp; +}, "jalview.datamodel.DBRefEntry"); +Clazz.defineMethod (c$, "setDatasetSequence", +function (seq) { +this.datasetSequence = seq; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getDatasetSequence", +function () { +return this.datasetSequence; +}); +Clazz.defineMethod (c$, "getAnnotation", +function () { +return this.annotation == null ? null : this.annotation.toArray ( new Array (this.annotation.size ())); +}); +Clazz.overrideMethod (c$, "hasAnnotation", +function (ann) { +return this.annotation == null ? false : this.annotation.contains (ann); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "addAlignmentAnnotation", +function (annotation) { +if (this.annotation == null) { +this.annotation = new java.util.Vector (); +}if (!this.annotation.contains (annotation)) { +this.annotation.addElement (annotation); +}annotation.setSequenceRef (this); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.overrideMethod (c$, "removeAlignmentAnnotation", +function (annotation) { +if (this.annotation != null) { +this.annotation.removeElement (annotation); +if (this.annotation.size () == 0) { +this.annotation = null; +}}}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "isValidDatasetSequence", +($fz = function () { +if (this.datasetSequence != null) { +return false; +}for (var i = 0; i < this.sequence.length; i++) { +if (jalview.util.Comparison.isGap (this.sequence[i])) { +return false; +}} +return true; +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "deriveSequence", +function () { +var seq = new jalview.datamodel.Sequence (this); +if (this.datasetSequence != null) { +seq.setDatasetSequence (this.datasetSequence); +} else { +if (this.isValidDatasetSequence ()) { +seq.setDatasetSequence (this); +} else { +var ds = seq; +ds.setSequence (jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (this.sequence))); +this.setDatasetSequence (ds); +ds.setSequenceFeatures (this.getSequenceFeatures ()); +seq = this; +}}return seq; +}); +Clazz.overrideMethod (c$, "createDatasetSequence", +function () { +if (this.datasetSequence == null) { +this.datasetSequence = new jalview.datamodel.Sequence (this.getName (), jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, this.getSequenceAsString ()), this.getStart (), this.getEnd ()); +this.datasetSequence.setSequenceFeatures (this.getSequenceFeatures ()); +this.datasetSequence.setDescription (this.getDescription ()); +this.setSequenceFeatures (null); +this.datasetSequence.setDBRef (this.getDBRef ()); +this.setDBRef (null); +this.datasetSequence.setPDBId (this.getPDBId ()); +this.setPDBId (null); +this.datasetSequence.updatePDBIds (); +if (this.annotation != null) { +for (var aa, $aa = this.annotation.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { +var _aa = new jalview.datamodel.AlignmentAnnotation (aa); +_aa.sequenceRef = this.datasetSequence; +_aa.adjustForAlignment (); +this.datasetSequence.addAlignmentAnnotation (_aa); +} +}}return this.datasetSequence; +}); +Clazz.overrideMethod (c$, "setAlignmentAnnotation", +function (annotations) { +if (this.annotation != null) { +this.annotation.removeAllElements (); +}if (annotations != null) { +for (var i = 0; i < annotations.length; i++) { +if (annotations[i] != null) { +this.addAlignmentAnnotation (annotations[i]); +}} +}}, "~A"); +Clazz.defineMethod (c$, "getAnnotation", +function (label) { +if (this.annotation == null || this.annotation.size () == 0) { +return null; +}var subset = new java.util.Vector (); +var e = this.annotation.elements (); +while (e.hasMoreElements ()) { +var ann = e.nextElement (); +if (ann.label != null && ann.label.equals (label)) { +subset.addElement (ann); +}} +if (subset.size () == 0) { +return null; +}var anns = new Array (subset.size ()); +var i = 0; +e = subset.elements (); +while (e.hasMoreElements ()) { +anns[i++] = e.nextElement (); +} +subset.removeAllElements (); +return anns; +}, "~S"); +Clazz.defineMethod (c$, "updatePDBIds", +function () { +if (this.datasetSequence != null) { +return this.datasetSequence.updatePDBIds (); +}if (this.dbrefs == null || this.dbrefs.length == 0) { +return false; +}var newpdb = new java.util.Vector (); +for (var i = 0; i < this.dbrefs.length; i++) { +if (jalview.datamodel.DBRefSource.PDB.equals (this.dbrefs[i].getSource ())) { +var pdbe = new jalview.datamodel.PDBEntry (); +pdbe.setId (this.dbrefs[i].getAccessionId ()); +if (this.pdbIds == null || this.pdbIds.size () == 0) { +newpdb.addElement (pdbe); +} else { +var en = this.pdbIds.elements (); +var matched = false; +while (!matched && en.hasMoreElements ()) { +var anentry = en.nextElement (); +if (anentry.getId ().equals (pdbe.getId ())) { +matched = true; +}} +if (!matched) { +newpdb.addElement (pdbe); +}}}} +if (newpdb.size () > 0) { +var en = newpdb.elements (); +while (en.hasMoreElements ()) { +this.addPDBId (en.nextElement ()); +} +return true; +}return false; +}); +Clazz.defineMethod (c$, "transferAnnotation", +function (entry, mp) { +if (this.datasetSequence != null) { +this.datasetSequence.transferAnnotation (entry, mp); +return; +}if (entry.getDatasetSequence () != null) { +this.transferAnnotation (entry.getDatasetSequence (), mp); +return; +}if (entry.getSequenceFeatures () != null) { +var sfs = entry.getSequenceFeatures (); +for (var si = 0; si < sfs.length; si++) { +var sf = (mp != null) ? mp.locateFeature (sfs[si]) : Clazz.newArray (-1, [ new jalview.datamodel.SequenceFeature (sfs[si])]); +if (sf != null && sf.length > 0) { +for (var sfi = 0; sfi < sf.length; sfi++) { +this.addSequenceFeature (sf[sfi]); +} +}} +}if (entry.getPDBId () != null) { +var e = entry.getPDBId ().elements (); +while (e.hasMoreElements ()) { +var pdb = e.nextElement (); +this.addPDBId (pdb); +} +}var entryRefs = entry.getDBRef (); +if (entryRefs != null) { +for (var r = 0; r < entryRefs.length; r++) { +var newref = new jalview.datamodel.DBRefEntry (entryRefs[r]); +if (newref.getMap () != null && mp != null) { +}this.addDBRef (newref); +} +}}, "jalview.datamodel.SequenceI,jalview.datamodel.Mapping"); +Clazz.overrideMethod (c$, "getIndex", +function () { +return this.index; +}); +Clazz.overrideMethod (c$, "setIndex", +function (value) { +this.index = value; +}, "~N"); +Clazz.overrideMethod (c$, "setRNA", +function (r) { +this.rna = r; +}, "jalview.jsdev.api.VarnaRNA"); +Clazz.overrideMethod (c$, "getRNA", +function () { +return this.rna; +}); +Clazz.overrideMethod (c$, "getAlignmentAnnotations", +function (calcId, label) { +var result = new java.util.ArrayList (); +if (this.annotation != null) { +for (var ann, $ann = this.annotation.iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) { +if (ann.calcId != null && ann.calcId.equals (calcId) && ann.label != null && ann.label.equals (label)) { +result.add (ann); +}} +}return result; +}, "~S,~S"); +}); diff --git a/bin/jalview/datamodel/SequenceCollectionI.js b/bin/jalview/datamodel/SequenceCollectionI.js index b0849db..6f0107b 100644 --- a/bin/jalview/datamodel/SequenceCollectionI.js +++ b/bin/jalview/datamodel/SequenceCollectionI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.declareInterface (jalview.datamodel, "SequenceCollectionI"); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.declareInterface (jalview.datamodel, "SequenceCollectionI"); diff --git a/bin/jalview/datamodel/SequenceDummy.js b/bin/jalview/datamodel/SequenceDummy.js index 38b0a3c..d5a179c 100644 --- a/bin/jalview/datamodel/SequenceDummy.js +++ b/bin/jalview/datamodel/SequenceDummy.js @@ -1,20 +1,20 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.Sequence", "$.SequenceI"], "jalview.datamodel.SequenceDummy", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.dummy = true; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SequenceDummy", jalview.datamodel.Sequence, jalview.datamodel.SequenceI); -Clazz.makeConstructor (c$, -function (sequenceId) { -Clazz.superConstructor (this, jalview.datamodel.SequenceDummy, [sequenceId, "THISAPLACEHOLDER"]); -}, "~S"); -Clazz.defineMethod (c$, "become", -function (mseq) { -this.initSeqFrom (mseq, null); -this.dummy = false; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "isDummy", -function () { -return this.dummy; -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.Sequence", "$.SequenceI"], "jalview.datamodel.SequenceDummy", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.dummy = true; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SequenceDummy", jalview.datamodel.Sequence, jalview.datamodel.SequenceI); +Clazz.makeConstructor (c$, +function (sequenceId) { +Clazz.superConstructor (this, jalview.datamodel.SequenceDummy, [sequenceId, "THISAPLACEHOLDER"]); +}, "~S"); +Clazz.defineMethod (c$, "become", +function (mseq) { +this.initSeqFrom (mseq, null); +this.dummy = false; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "isDummy", +function () { +return this.dummy; +}); +}); diff --git a/bin/jalview/datamodel/SequenceFeature.js b/bin/jalview/datamodel/SequenceFeature.js index f8ce548..d2f14a8 100644 --- a/bin/jalview/datamodel/SequenceFeature.js +++ b/bin/jalview/datamodel/SequenceFeature.js @@ -1,170 +1,170 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.SequenceFeature", ["java.util.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.begin = 0; -this.end = 0; -this.score = 0; -this.type = null; -this.description = null; -this.otherDetails = null; -this.links = null; -this.featureGroup = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SequenceFeature"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (cpy) { -if (cpy != null) { -this.begin = cpy.begin; -this.end = cpy.end; -this.score = cpy.score; -if (cpy.type != null) { -this.type = String.instantialize (cpy.type); -}if (cpy.description != null) { -this.description = String.instantialize (cpy.description); -}if (cpy.featureGroup != null) { -this.featureGroup = String.instantialize (cpy.featureGroup); -}if (cpy.otherDetails != null) { -try { -this.otherDetails = cpy.otherDetails.clone (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -}if (cpy.links != null && cpy.links.size () > 0) { -this.links = new java.util.Vector (); -for (var i = 0, iSize = cpy.links.size (); i < iSize; i++) { -this.links.addElement (cpy.links.elementAt (i)); -} -}}}, "jalview.datamodel.SequenceFeature"); -Clazz.makeConstructor (c$, -function (type, desc, status, begin, end, featureGroup) { -this.type = type; -this.description = desc; -this.setValue ("status", status); -this.begin = begin; -this.end = end; -this.featureGroup = featureGroup; -}, "~S,~S,~S,~N,~N,~S"); -Clazz.makeConstructor (c$, -function (type, desc, begin, end, score, featureGroup) { -this.type = type; -this.description = desc; -this.begin = begin; -this.end = end; -this.score = score; -this.featureGroup = featureGroup; -}, "~S,~S,~N,~N,~N,~S"); -Clazz.defineMethod (c$, "equals", -function (sf) { -if (this.begin != sf.begin || this.end != sf.end || this.score != sf.score) { -return false; -}if (!(this.type + this.description + this.featureGroup).equals (sf.type + sf.description + sf.featureGroup)) { -return false; -}return true; -}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "getBegin", -function () { -return this.begin; -}); -Clazz.defineMethod (c$, "setBegin", -function (start) { -this.begin = start; -}, "~N"); -Clazz.defineMethod (c$, "getEnd", -function () { -return this.end; -}); -Clazz.defineMethod (c$, "setEnd", -function (end) { -this.end = end; -}, "~N"); -Clazz.defineMethod (c$, "getType", -function () { -return this.type; -}); -Clazz.defineMethod (c$, "setType", -function (type) { -this.type = type; -}, "~S"); -Clazz.defineMethod (c$, "getDescription", -function () { -return this.description; -}); -Clazz.defineMethod (c$, "setDescription", -function (desc) { -this.description = desc; -}, "~S"); -Clazz.defineMethod (c$, "getFeatureGroup", -function () { -return this.featureGroup; -}); -Clazz.defineMethod (c$, "setFeatureGroup", -function (featureGroup) { -this.featureGroup = featureGroup; -}, "~S"); -Clazz.defineMethod (c$, "addLink", -function (labelLink) { -if (this.links == null) { -this.links = new java.util.Vector (); -}this.links.insertElementAt (labelLink, 0); -}, "~S"); -Clazz.defineMethod (c$, "getScore", -function () { -return this.score; -}); -Clazz.defineMethod (c$, "setScore", -function (value) { -this.score = value; -}, "~N"); -Clazz.defineMethod (c$, "getValue", -function (key) { -if (this.otherDetails == null) { -return null; -} else { -return this.otherDetails.get (key); -}}, "~S"); -Clazz.defineMethod (c$, "setValue", -function (key, value) { -if (value != null) { -if (this.otherDetails == null) { -this.otherDetails = new java.util.Hashtable (); -}this.otherDetails.put (key, value); -}}, "~S,~O"); -Clazz.defineMethod (c$, "setStatus", -function (status) { -this.setValue ("status", status); -}, "~S"); -Clazz.defineMethod (c$, "getStatus", -function () { -if (this.otherDetails != null) { -var stat = this.otherDetails.get ("status"); -if (stat != null) { -return String.instantialize (stat); -}}return null; -}); -Clazz.defineMethod (c$, "setPosition", -function (pos) { -this.begin = pos; -this.end = pos; -}, "~N"); -Clazz.defineMethod (c$, "getPosition", -function () { -return this.begin; -}); -Clazz.defineMethod (c$, "getStrand", -function () { -var str; -if (this.otherDetails == null || (str = this.otherDetails.get ("STRAND").toString ()) == null) { -return 0; -}if (str.equals ("-")) { -return -1; -}if (str.equals ("+")) { -return 1; -}return 0; -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.SequenceFeature", ["java.util.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.begin = 0; +this.end = 0; +this.score = 0; +this.type = null; +this.description = null; +this.otherDetails = null; +this.links = null; +this.featureGroup = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SequenceFeature"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (cpy) { +if (cpy != null) { +this.begin = cpy.begin; +this.end = cpy.end; +this.score = cpy.score; +if (cpy.type != null) { +this.type = String.instantialize (cpy.type); +}if (cpy.description != null) { +this.description = String.instantialize (cpy.description); +}if (cpy.featureGroup != null) { +this.featureGroup = String.instantialize (cpy.featureGroup); +}if (cpy.otherDetails != null) { +try { +this.otherDetails = cpy.otherDetails.clone (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +}if (cpy.links != null && cpy.links.size () > 0) { +this.links = new java.util.Vector (); +for (var i = 0, iSize = cpy.links.size (); i < iSize; i++) { +this.links.addElement (cpy.links.elementAt (i)); +} +}}}, "jalview.datamodel.SequenceFeature"); +Clazz.makeConstructor (c$, +function (type, desc, status, begin, end, featureGroup) { +this.type = type; +this.description = desc; +this.setValue ("status", status); +this.begin = begin; +this.end = end; +this.featureGroup = featureGroup; +}, "~S,~S,~S,~N,~N,~S"); +Clazz.makeConstructor (c$, +function (type, desc, begin, end, score, featureGroup) { +this.type = type; +this.description = desc; +this.begin = begin; +this.end = end; +this.score = score; +this.featureGroup = featureGroup; +}, "~S,~S,~N,~N,~N,~S"); +Clazz.defineMethod (c$, "equals", +function (sf) { +if (this.begin != sf.begin || this.end != sf.end || this.score != sf.score) { +return false; +}if (!(this.type + this.description + this.featureGroup).equals (sf.type + sf.description + sf.featureGroup)) { +return false; +}return true; +}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "getBegin", +function () { +return this.begin; +}); +Clazz.defineMethod (c$, "setBegin", +function (start) { +this.begin = start; +}, "~N"); +Clazz.defineMethod (c$, "getEnd", +function () { +return this.end; +}); +Clazz.defineMethod (c$, "setEnd", +function (end) { +this.end = end; +}, "~N"); +Clazz.defineMethod (c$, "getType", +function () { +return this.type; +}); +Clazz.defineMethod (c$, "setType", +function (type) { +this.type = type; +}, "~S"); +Clazz.defineMethod (c$, "getDescription", +function () { +return this.description; +}); +Clazz.defineMethod (c$, "setDescription", +function (desc) { +this.description = desc; +}, "~S"); +Clazz.defineMethod (c$, "getFeatureGroup", +function () { +return this.featureGroup; +}); +Clazz.defineMethod (c$, "setFeatureGroup", +function (featureGroup) { +this.featureGroup = featureGroup; +}, "~S"); +Clazz.defineMethod (c$, "addLink", +function (labelLink) { +if (this.links == null) { +this.links = new java.util.Vector (); +}this.links.insertElementAt (labelLink, 0); +}, "~S"); +Clazz.defineMethod (c$, "getScore", +function () { +return this.score; +}); +Clazz.defineMethod (c$, "setScore", +function (value) { +this.score = value; +}, "~N"); +Clazz.defineMethod (c$, "getValue", +function (key) { +if (this.otherDetails == null) { +return null; +} else { +return this.otherDetails.get (key); +}}, "~S"); +Clazz.defineMethod (c$, "setValue", +function (key, value) { +if (value != null) { +if (this.otherDetails == null) { +this.otherDetails = new java.util.Hashtable (); +}this.otherDetails.put (key, value); +}}, "~S,~O"); +Clazz.defineMethod (c$, "setStatus", +function (status) { +this.setValue ("status", status); +}, "~S"); +Clazz.defineMethod (c$, "getStatus", +function () { +if (this.otherDetails != null) { +var stat = this.otherDetails.get ("status"); +if (stat != null) { +return String.instantialize (stat); +}}return null; +}); +Clazz.defineMethod (c$, "setPosition", +function (pos) { +this.begin = pos; +this.end = pos; +}, "~N"); +Clazz.defineMethod (c$, "getPosition", +function () { +return this.begin; +}); +Clazz.defineMethod (c$, "getStrand", +function () { +var str; +if (this.otherDetails == null || (str = this.otherDetails.get ("STRAND").toString ()) == null) { +return 0; +}if (str.equals ("-")) { +return -1; +}if (str.equals ("+")) { +return 1; +}return 0; +}); +}); diff --git a/bin/jalview/datamodel/SequenceGroup.class b/bin/jalview/datamodel/SequenceGroup.class index f773fbc..d962521 100644 Binary files a/bin/jalview/datamodel/SequenceGroup.class and b/bin/jalview/datamodel/SequenceGroup.class differ diff --git a/bin/jalview/datamodel/SequenceGroup.js b/bin/jalview/datamodel/SequenceGroup.js index 0e59a62..b8ea520 100644 --- a/bin/jalview/datamodel/SequenceGroup.js +++ b/bin/jalview/datamodel/SequenceGroup.js @@ -1,601 +1,601 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.AnnotatedCollectionI", "java.awt.Color", "java.util.ArrayList"], "jalview.datamodel.SequenceGroup", ["jalview.analysis.AAFrequency", "$.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.groupName = null; -this.description = null; -this.conserve = null; -this.aaFrequency = null; -this.displayBoxes = true; -this.displayText = true; -this.colourText = false; -this.showNonconserved = false; -this.sequences = null; -this.seqrep = null; -this.width = -1; -this.cs = null; -this.startRes = 0; -this.endRes = 0; -this.outlineColour = null; -this.idColour = null; -this.thresholdTextColour = 0; -this.textColour = null; -this.textColour2 = null; -this.ignoreGapsInConsensus = true; -this.showSequenceLogo = false; -this.normaliseSequenceLogo = false; -this.consPercGaps = 25; -this.consensusData = null; -this.hidereps = false; -this.hidecols = false; -this.consensus = null; -this.conservation = null; -this.showConsensusHistogram = false; -this.context = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SequenceGroup", null, jalview.datamodel.AnnotatedCollectionI); -Clazz.prepareFields (c$, function () { -this.sequences = new java.util.ArrayList (); -this.outlineColour = java.awt.Color.black; -this.textColour = java.awt.Color.black; -this.textColour2 = java.awt.Color.white; -}); -Clazz.defineMethod (c$, "isShowSequenceLogo", -function () { -return this.showSequenceLogo; -}); -Clazz.makeConstructor (c$, -function () { -this.groupName = "JGroup:" + this.hashCode (); -}); -Clazz.makeConstructor (c$, -function (sequences, groupName, scheme, displayBoxes, displayText, colourText, start, end) { -this.sequences = sequences; -this.groupName = groupName; -this.displayBoxes = displayBoxes; -this.displayText = displayText; -this.colourText = colourText; -this.cs = scheme; -this.startRes = start; -this.endRes = end; -this.recalcConservation (); -}, "java.util.List,~S,jalview.schemes.ColourSchemeI,~B,~B,~B,~N,~N"); -Clazz.makeConstructor (c$, -function (seqsel) { -if (seqsel != null) { -this.sequences = new java.util.ArrayList (); -this.sequences.addAll (seqsel.sequences); -if (seqsel.groupName != null) { -this.groupName = String.instantialize (seqsel.groupName); -}this.displayBoxes = seqsel.displayBoxes; -this.displayText = seqsel.displayText; -this.colourText = seqsel.colourText; -this.startRes = seqsel.startRes; -this.endRes = seqsel.endRes; -this.cs = seqsel.cs; -if (seqsel.description != null) { -this.description = String.instantialize (seqsel.description); -}this.hidecols = seqsel.hidecols; -this.hidereps = seqsel.hidereps; -this.idColour = seqsel.idColour; -this.outlineColour = seqsel.outlineColour; -this.seqrep = seqsel.seqrep; -this.textColour = seqsel.textColour; -this.textColour2 = seqsel.textColour2; -this.thresholdTextColour = seqsel.thresholdTextColour; -this.width = seqsel.width; -this.ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; -if (seqsel.conserve != null) { -this.recalcConservation (); -}}}, "jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "getSelectionAsNewSequences", -function (align) { -var iSize = this.sequences.size (); -var seqs = new Array (iSize); -var inorder = this.getSequencesInOrder (align); -for (var i = 0, ipos = 0; i < inorder.length; i++) { -var seq = inorder[i]; -seqs[ipos] = seq.getSubSequence (this.startRes, this.endRes + 1); -if (seqs[ipos] != null) { -seqs[ipos].setDescription (seq.getDescription ()); -seqs[ipos].setDBRef (seq.getDBRef ()); -seqs[ipos].setSequenceFeatures (seq.getSequenceFeatures ()); -if (seq.getDatasetSequence () != null) { -seqs[ipos].setDatasetSequence (seq.getDatasetSequence ()); -}if (seq.getAnnotation () != null) { -var alann = align.getAlignmentAnnotation (); -for (var a = 0; a < seq.getAnnotation ().length; a++) { -var tocopy = seq.getAnnotation ()[a]; -if (alann != null) { -var found = false; -for (var pos = 0; pos < alann.length; pos++) { -if (alann[pos] === tocopy) { -found = true; -break; -}} -if (!found) { -continue; -}}var newannot = new jalview.datamodel.AlignmentAnnotation (seq.getAnnotation ()[a]); -newannot.restrict (this.startRes, this.endRes); -newannot.setSequenceRef (seqs[ipos]); -newannot.adjustForAlignment (); -seqs[ipos].addAlignmentAnnotation (newannot); -} -}ipos++; -} else { -iSize--; -}} -if (iSize != inorder.length) { -var nseqs = new Array (iSize); -System.arraycopy (seqs, 0, nseqs, 0, iSize); -seqs = nseqs; -}return seqs; -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "findEndRes", -function (seq) { -var eres = 0; -var ch; -for (var j = 0; j < this.endRes + 1 && j < seq.getLength (); j++) { -ch = seq.getCharAt (j); -if (!jalview.util.Comparison.isGap ((ch))) { -eres++; -}} -if (eres > 0) { -eres += seq.getStart () - 1; -}return eres; -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getSequences", -function () { -return this.sequences; -}); -Clazz.defineMethod (c$, "getSequences", -function (hiddenReps) { -if (hiddenReps == null) { -return this.sequences; -} else { -var allSequences = new java.util.ArrayList (); -for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -allSequences.add (seq); -if (hiddenReps.containsKey (seq)) { -var hsg = hiddenReps.get (seq); -for (var seq2, $seq2 = hsg.getSequences ().iterator (); $seq2.hasNext () && ((seq2 = $seq2.next ()) || true);) { -if (seq2 !== seq && !allSequences.contains (seq2)) { -allSequences.add (seq2); -}} -}} -return allSequences; -}}, "java.util.Map"); -Clazz.defineMethod (c$, "getSequencesAsArray", -function (map) { -var tmp = this.getSequences (map); -if (tmp == null) { -return null; -}return tmp.toArray ( new Array (tmp.size ())); -}, "java.util.Map"); -Clazz.defineMethod (c$, "adjustForRemoveLeft", -function (col) { -if (this.startRes >= col) { -this.startRes = this.startRes - col; -}if (this.endRes >= col) { -this.endRes = this.endRes - col; -if (this.startRes > this.endRes) { -this.startRes = 0; -}} else { -return false; -}return true; -}, "~N"); -Clazz.defineMethod (c$, "adjustForRemoveRight", -function (col) { -if (this.startRes > col) { -return false; -}if (this.endRes >= col) { -this.endRes = col; -}return true; -}, "~N"); -Clazz.defineMethod (c$, "getName", -function () { -return this.groupName; -}); -Clazz.defineMethod (c$, "getDescription", -function () { -return this.description; -}); -Clazz.defineMethod (c$, "setName", -function (name) { -this.groupName = name; -}, "~S"); -Clazz.defineMethod (c$, "setDescription", -function (desc) { -this.description = desc; -}, "~S"); -Clazz.defineMethod (c$, "getConservation", -function () { -return this.conserve; -}); -Clazz.defineMethod (c$, "setConservation", -function (c) { -this.conserve = c; -}, "jalview.analysis.Conservation"); -Clazz.defineMethod (c$, "addSequence", -function (s, recalc) { -{ -if (s != null && !this.sequences.contains (s)) { -this.sequences.add (s); -}if (recalc) { -this.recalcConservation (); -}}}, "jalview.datamodel.SequenceI,~B"); -Clazz.defineMethod (c$, "getConsPercGaps", -function () { -return this.consPercGaps; -}); -Clazz.defineMethod (c$, "setConsPercGaps", -function (consPercGaps) { -this.consPercGaps = consPercGaps; -}, "~N"); -Clazz.defineMethod (c$, "recalcConservation", -function () { -if (this.cs == null && this.consensus == null && this.conservation == null) { -return; -}try { -var cnsns = jalview.analysis.AAFrequency.calculate (this.sequences, this.startRes, this.endRes + 1, this.showSequenceLogo); -if (this.consensus != null) { -this._updateConsensusRow (cnsns, this.sequences.size ()); -}if (this.cs != null) { -this.cs.setConsensus (cnsns); -}if ((this.conservation != null) || (this.cs != null && this.cs.conservationApplied ())) { -var c = new jalview.analysis.Conservation (this.groupName, jalview.schemes.ResidueProperties.propHash, 3, this.sequences, this.startRes, this.endRes + 1); -c.calculate (); -c.verdict (false, this.consPercGaps); -if (this.conservation != null) { -this._updateConservationRow (c); -}if (this.cs != null) { -if (this.cs.conservationApplied ()) { -this.cs.setConservation (c); -}}}if (this.cs != null) { -this.cs.alignmentChanged (this.context != null ? this.context : this, null); -}} catch (err) { -if (Clazz.exceptionOf (err, OutOfMemoryError)) { -System.out.println ("Out of memory loading groups: " + err); -} else { -throw err; -} -} -}); -Clazz.defineMethod (c$, "_updateConservationRow", -($fz = function (c) { -if (this.conservation == null) { -this.getConservation (); -}this.conservation.label = "Conservation for " + this.getName (); -this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps"; -var aWidth = (this.conservation.annotations != null) ? (this.endRes < this.conservation.annotations.length ? this.conservation.annotations.length : this.endRes + 1) : this.endRes + 1; -this.conservation.annotations = null; -this.conservation.annotations = new Array (aWidth); -c.completeAnnotations (this.conservation, null, this.startRes, this.endRes + 1); -}, $fz.isPrivate = true, $fz), "jalview.analysis.Conservation"); -Clazz.defineMethod (c$, "_updateConsensusRow", -($fz = function (cnsns, nseq) { -if (this.consensus == null) { -this.getConsensus (); -}this.consensus.label = "Consensus for " + this.getName (); -this.consensus.description = "Percent Identity"; -this.consensusData = cnsns; -var aWidth = (this.consensus.annotations != null) ? (this.endRes < this.consensus.annotations.length ? this.consensus.annotations.length : this.endRes + 1) : this.endRes + 1; -this.consensus.annotations = null; -this.consensus.annotations = new Array (aWidth); -jalview.analysis.AAFrequency.completeConsensus (this.consensus, cnsns, this.startRes, this.endRes + 1, this.ignoreGapsInConsensus, this.showSequenceLogo, nseq); -}, $fz.isPrivate = true, $fz), "~A,~N"); -Clazz.defineMethod (c$, "addOrRemove", -function (s, recalc) { -{ -if (this.sequences.contains (s)) { -this.deleteSequence (s, recalc); -} else { -this.addSequence (s, recalc); -}}}, "jalview.datamodel.SequenceI,~B"); -Clazz.defineMethod (c$, "deleteSequence", -function (s, recalc) { -{ -this.sequences.remove (s); -if (recalc) { -this.recalcConservation (); -}}}, "jalview.datamodel.SequenceI,~B"); -Clazz.overrideMethod (c$, "getStartRes", -function () { -return this.startRes; -}); -Clazz.overrideMethod (c$, "getEndRes", -function () { -return this.endRes; -}); -Clazz.defineMethod (c$, "setStartRes", -function (i) { -this.startRes = i; -}, "~N"); -Clazz.defineMethod (c$, "setEndRes", -function (i) { -this.endRes = i; -}, "~N"); -Clazz.defineMethod (c$, "getSize", -function () { -return this.sequences.size (); -}); -Clazz.defineMethod (c$, "getSequenceAt", -function (i) { -return this.sequences.get (i); -}, "~N"); -Clazz.defineMethod (c$, "setColourText", -function (state) { -this.colourText = state; -}, "~B"); -Clazz.defineMethod (c$, "getColourText", -function () { -return this.colourText; -}); -Clazz.defineMethod (c$, "setDisplayText", -function (state) { -this.displayText = state; -}, "~B"); -Clazz.defineMethod (c$, "getDisplayText", -function () { -return this.displayText; -}); -Clazz.defineMethod (c$, "setDisplayBoxes", -function (state) { -this.displayBoxes = state; -}, "~B"); -Clazz.defineMethod (c$, "getDisplayBoxes", -function () { -return this.displayBoxes; -}); -Clazz.overrideMethod (c$, "getWidth", -function () { -{ -var first = true; -for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -if (first || seq.getLength () > this.width) { -this.width = seq.getLength (); -first = false; -}} -return this.width; -}}); -Clazz.defineMethod (c$, "setOutlineColour", -function (c) { -this.outlineColour = c; -}, "java.awt.Color"); -Clazz.defineMethod (c$, "getOutlineColour", -function () { -return this.outlineColour; -}); -Clazz.defineMethod (c$, "getSequencesInOrder", -function (al) { -return this.getSequencesInOrder (al, true); -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "getSequencesInOrder", -function (al, trim) { -{ -var sSize = this.sequences.size (); -var alHeight = al.getHeight (); -var seqs = new Array ((trim) ? sSize : alHeight); -var index = 0; -for (var i = 0; i < alHeight && index < sSize; i++) { -if (this.sequences.contains (al.getSequenceAt (i))) { -seqs[(trim) ? index : i] = al.getSequenceAt (i); -index++; -}} -if (index == 0) { -return null; -}if (!trim) { -return seqs; -}if (index < seqs.length) { -var dummy = seqs; -seqs = new Array (index); -while (--index >= 0) { -seqs[index] = dummy[index]; -dummy[index] = null; -} -}return seqs; -}}, "jalview.datamodel.AlignmentI,~B"); -Clazz.defineMethod (c$, "getIdColour", -function () { -return this.idColour; -}); -Clazz.defineMethod (c$, "setIdColour", -function (idColour) { -this.idColour = idColour; -}, "java.awt.Color"); -Clazz.overrideMethod (c$, "getSeqrep", -function () { -return this.seqrep; -}); -Clazz.overrideMethod (c$, "setSeqrep", -function (seqrep) { -this.seqrep = seqrep; -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "hasSeqrep", -function () { -return this.seqrep != null; -}); -Clazz.defineMethod (c$, "setHidereps", -function (visibility) { -this.hidereps = visibility; -}, "~B"); -Clazz.defineMethod (c$, "isHidereps", -function () { -return this.hidereps; -}); -Clazz.defineMethod (c$, "setHideCols", -function (visibility) { -this.hidecols = visibility; -}, "~B"); -Clazz.defineMethod (c$, "isHideCols", -function () { -return this.hidecols; -}); -Clazz.defineMethod (c$, "intersect", -function (alignment, map) { -var sgroup = new jalview.datamodel.SequenceGroup (this); -var insect = this.getSequencesInOrder (alignment); -sgroup.sequences = new java.util.ArrayList (); -for (var s = 0; insect != null && s < insect.length; s++) { -if (map == null || map.containsKey (insect[s])) { -sgroup.sequences.add (insect[s]); -}} -return sgroup; -}, "jalview.datamodel.AlignmentI,java.util.Map"); -Clazz.defineMethod (c$, "getShowNonconserved", -function () { -return this.showNonconserved; -}); -Clazz.defineMethod (c$, "setShowNonconserved", -function (displayNonconserved) { -this.showNonconserved = displayNonconserved; -}, "~B"); -Clazz.defineMethod (c$, "setConsensus", -function (aan) { -if (this.consensus == null) { -this.consensus = aan; -}}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "getConsensus", -function () { -var aWidth = this.getWidth (); -if (aWidth < 0) { -return null; -}if (this.consensus == null) { -this.consensus = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 100, 1); -this.consensus.hasText = true; -this.consensus.autoCalculated = true; -this.consensus.groupRef = this; -this.consensus.label = "Consensus for " + this.getName (); -this.consensus.description = "Percent Identity"; -}return this.consensus; -}); -Clazz.defineMethod (c$, "setConservationRow", -function (aan) { -if (this.conservation == null) { -this.conservation = aan; -}}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "getConservationRow", -function () { -if (this.conservation == null) { -this.conservation = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 11, 1); -}this.conservation.hasText = true; -this.conservation.autoCalculated = true; -this.conservation.groupRef = this; -this.conservation.label = "Conservation for " + this.getName (); -this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps"; -return this.conservation; -}); -Clazz.defineMethod (c$, "hasAnnotationRows", -function () { -return this.consensus != null || this.conservation != null; -}); -Clazz.defineMethod (c$, "getConsensusSeq", -function () { -this.getConsensus (); -var seqs = new StringBuffer (); -for (var i = 0; i < this.consensus.annotations.length; i++) { -if (this.consensus.annotations[i] != null) { -if (this.consensus.annotations[i].description.charAt (0) == '[') { -seqs.append (this.consensus.annotations[i].description.charAt (1)); -} else { -seqs.append (this.consensus.annotations[i].displayCharacter); -}}} -var sq = new jalview.datamodel.Sequence ("Group" + this.getName () + " Consensus", seqs.toString ()); -sq.setDescription ("Percentage Identity Consensus " + ((this.ignoreGapsInConsensus) ? " without gaps" : "")); -return sq; -}); -Clazz.defineMethod (c$, "setIgnoreGapsConsensus", -function (state) { -if (this.ignoreGapsInConsensus != state && this.consensus != null) { -this.ignoreGapsInConsensus = state; -this.recalcConservation (); -}this.ignoreGapsInConsensus = state; -}, "~B"); -Clazz.defineMethod (c$, "getIgnoreGapsConsensus", -function () { -return this.ignoreGapsInConsensus; -}); -Clazz.defineMethod (c$, "setshowSequenceLogo", -function (showSequenceLogo) { -if (this.showSequenceLogo != showSequenceLogo && this.consensus != null) { -this.showSequenceLogo = showSequenceLogo; -this.recalcConservation (); -}this.showSequenceLogo = showSequenceLogo; -}, "~B"); -Clazz.defineMethod (c$, "setShowConsensusHistogram", -function (showConsHist) { -if (this.showConsensusHistogram != showConsHist && this.consensus != null) { -this.showConsensusHistogram = showConsHist; -this.recalcConservation (); -}this.showConsensusHistogram = showConsHist; -}, "~B"); -Clazz.defineMethod (c$, "isShowConsensusHistogram", -function () { -return this.showConsensusHistogram; -}); -Clazz.defineMethod (c$, "setNormaliseSequenceLogo", -function (norm) { -this.normaliseSequenceLogo = norm; -}, "~B"); -Clazz.defineMethod (c$, "isNormaliseSequenceLogo", -function () { -return this.normaliseSequenceLogo; -}); -Clazz.overrideMethod (c$, "getAlignmentAnnotation", -function () { -var annot = new java.util.ArrayList (); -{ -for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -var aa = seq.getAnnotation (); -if (aa != null) { -for (var al, $al = 0, $$al = aa; $al < $$al.length && ((al = $$al[$al]) || true); $al++) { -if (al.groupRef === this) { -annot.add (al); -}} -}} -if (this.consensus != null) { -annot.add (this.consensus); -}if (this.conservation != null) { -annot.add (this.conservation); -}}return annot.toArray ( new Array (0)); -}); -Clazz.overrideMethod (c$, "findAnnotation", -function (calcId) { -var aa = new java.util.ArrayList (); -for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) { -if (a.getCalcId () === calcId) { -aa.add (a); -}} -return aa; -}, "~S"); -Clazz.overrideMethod (c$, "findAnnotations", -function (seq, calcId, label) { -var aa = new java.util.ArrayList (); -for (var ann, $ann = 0, $$ann = this.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { -if (ann.getCalcId () != null && ann.getCalcId ().equals (calcId) && ann.sequenceRef != null && ann.sequenceRef === seq && ann.label != null && ann.label.equals (label)) { -aa.add (ann); -}} -return aa; -}, "jalview.datamodel.SequenceI,~S,~S"); -Clazz.defineMethod (c$, "hasAnnotation", -function (calcId) { -if (calcId != null && !"".equals (calcId)) { -for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) { -if (a.getCalcId () === calcId) { -return true; -}} -}return false; -}, "~S"); -Clazz.defineMethod (c$, "clear", -function () { -{ -this.sequences.clear (); -}}); -Clazz.defineMethod (c$, "setContext", -function (context) { -this.context = context; -}, "jalview.datamodel.AnnotatedCollectionI"); -Clazz.overrideMethod (c$, "getContext", -function () { -return this.context; -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.AnnotatedCollectionI", "java.awt.Color", "java.util.ArrayList"], "jalview.datamodel.SequenceGroup", ["jalview.analysis.AAFrequency", "$.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.groupName = null; +this.description = null; +this.conserve = null; +this.aaFrequency = null; +this.displayBoxes = true; +this.displayText = true; +this.colourText = false; +this.showNonconserved = false; +this.sequences = null; +this.seqrep = null; +this.width = -1; +this.cs = null; +this.startRes = 0; +this.endRes = 0; +this.outlineColour = null; +this.idColour = null; +this.thresholdTextColour = 0; +this.textColour = null; +this.textColour2 = null; +this.ignoreGapsInConsensus = true; +this.showSequenceLogo = false; +this.normaliseSequenceLogo = false; +this.consPercGaps = 25; +this.consensusData = null; +this.hidereps = false; +this.hidecols = false; +this.consensus = null; +this.conservation = null; +this.showConsensusHistogram = false; +this.context = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SequenceGroup", null, jalview.datamodel.AnnotatedCollectionI); +Clazz.prepareFields (c$, function () { +this.sequences = new java.util.ArrayList (); +this.outlineColour = java.awt.Color.black; +this.textColour = java.awt.Color.black; +this.textColour2 = java.awt.Color.white; +}); +Clazz.defineMethod (c$, "isShowSequenceLogo", +function () { +return this.showSequenceLogo; +}); +Clazz.makeConstructor (c$, +function () { +this.groupName = "JGroup:" + this.hashCode (); +}); +Clazz.makeConstructor (c$, +function (sequences, groupName, scheme, displayBoxes, displayText, colourText, start, end) { +this.sequences = sequences; +this.groupName = groupName; +this.displayBoxes = displayBoxes; +this.displayText = displayText; +this.colourText = colourText; +this.cs = scheme; +this.startRes = start; +this.endRes = end; +this.recalcConservation (); +}, "java.util.List,~S,jalview.schemes.ColourSchemeI,~B,~B,~B,~N,~N"); +Clazz.makeConstructor (c$, +function (seqsel) { +if (seqsel != null) { +this.sequences = new java.util.ArrayList (); +this.sequences.addAll (seqsel.sequences); +if (seqsel.groupName != null) { +this.groupName = String.instantialize (seqsel.groupName); +}this.displayBoxes = seqsel.displayBoxes; +this.displayText = seqsel.displayText; +this.colourText = seqsel.colourText; +this.startRes = seqsel.startRes; +this.endRes = seqsel.endRes; +this.cs = seqsel.cs; +if (seqsel.description != null) { +this.description = String.instantialize (seqsel.description); +}this.hidecols = seqsel.hidecols; +this.hidereps = seqsel.hidereps; +this.idColour = seqsel.idColour; +this.outlineColour = seqsel.outlineColour; +this.seqrep = seqsel.seqrep; +this.textColour = seqsel.textColour; +this.textColour2 = seqsel.textColour2; +this.thresholdTextColour = seqsel.thresholdTextColour; +this.width = seqsel.width; +this.ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; +if (seqsel.conserve != null) { +this.recalcConservation (); +}}}, "jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "getSelectionAsNewSequences", +function (align) { +var iSize = this.sequences.size (); +var seqs = new Array (iSize); +var inorder = this.getSequencesInOrder (align); +for (var i = 0, ipos = 0; i < inorder.length; i++) { +var seq = inorder[i]; +seqs[ipos] = seq.getSubSequence (this.startRes, this.endRes + 1); +if (seqs[ipos] != null) { +seqs[ipos].setDescription (seq.getDescription ()); +seqs[ipos].setDBRef (seq.getDBRef ()); +seqs[ipos].setSequenceFeatures (seq.getSequenceFeatures ()); +if (seq.getDatasetSequence () != null) { +seqs[ipos].setDatasetSequence (seq.getDatasetSequence ()); +}if (seq.getAnnotation () != null) { +var alann = align.getAlignmentAnnotation (); +for (var a = 0; a < seq.getAnnotation ().length; a++) { +var tocopy = seq.getAnnotation ()[a]; +if (alann != null) { +var found = false; +for (var pos = 0; pos < alann.length; pos++) { +if (alann[pos] === tocopy) { +found = true; +break; +}} +if (!found) { +continue; +}}var newannot = new jalview.datamodel.AlignmentAnnotation (seq.getAnnotation ()[a]); +newannot.restrict (this.startRes, this.endRes); +newannot.setSequenceRef (seqs[ipos]); +newannot.adjustForAlignment (); +seqs[ipos].addAlignmentAnnotation (newannot); +} +}ipos++; +} else { +iSize--; +}} +if (iSize != inorder.length) { +var nseqs = new Array (iSize); +System.arraycopy (seqs, 0, nseqs, 0, iSize); +seqs = nseqs; +}return seqs; +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "findEndRes", +function (seq) { +var eres = 0; +var ch; +for (var j = 0; j < this.endRes + 1 && j < seq.getLength (); j++) { +ch = seq.getCharAt (j); +if (!jalview.util.Comparison.isGap ((ch))) { +eres++; +}} +if (eres > 0) { +eres += seq.getStart () - 1; +}return eres; +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getSequences", +function () { +return this.sequences; +}); +Clazz.defineMethod (c$, "getSequences", +function (hiddenReps) { +if (hiddenReps == null) { +return this.sequences; +} else { +var allSequences = new java.util.ArrayList (); +for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +allSequences.add (seq); +if (hiddenReps.containsKey (seq)) { +var hsg = hiddenReps.get (seq); +for (var seq2, $seq2 = hsg.getSequences ().iterator (); $seq2.hasNext () && ((seq2 = $seq2.next ()) || true);) { +if (seq2 !== seq && !allSequences.contains (seq2)) { +allSequences.add (seq2); +}} +}} +return allSequences; +}}, "java.util.Map"); +Clazz.defineMethod (c$, "getSequencesAsArray", +function (map) { +var tmp = this.getSequences (map); +if (tmp == null) { +return null; +}return tmp.toArray ( new Array (tmp.size ())); +}, "java.util.Map"); +Clazz.defineMethod (c$, "adjustForRemoveLeft", +function (col) { +if (this.startRes >= col) { +this.startRes = this.startRes - col; +}if (this.endRes >= col) { +this.endRes = this.endRes - col; +if (this.startRes > this.endRes) { +this.startRes = 0; +}} else { +return false; +}return true; +}, "~N"); +Clazz.defineMethod (c$, "adjustForRemoveRight", +function (col) { +if (this.startRes > col) { +return false; +}if (this.endRes >= col) { +this.endRes = col; +}return true; +}, "~N"); +Clazz.defineMethod (c$, "getName", +function () { +return this.groupName; +}); +Clazz.defineMethod (c$, "getDescription", +function () { +return this.description; +}); +Clazz.defineMethod (c$, "setName", +function (name) { +this.groupName = name; +}, "~S"); +Clazz.defineMethod (c$, "setDescription", +function (desc) { +this.description = desc; +}, "~S"); +Clazz.defineMethod (c$, "getConservation", +function () { +return this.conserve; +}); +Clazz.defineMethod (c$, "setConservation", +function (c) { +this.conserve = c; +}, "jalview.analysis.Conservation"); +Clazz.defineMethod (c$, "addSequence", +function (s, recalc) { +{ +if (s != null && !this.sequences.contains (s)) { +this.sequences.add (s); +}if (recalc) { +this.recalcConservation (); +}}}, "jalview.datamodel.SequenceI,~B"); +Clazz.defineMethod (c$, "getConsPercGaps", +function () { +return this.consPercGaps; +}); +Clazz.defineMethod (c$, "setConsPercGaps", +function (consPercGaps) { +this.consPercGaps = consPercGaps; +}, "~N"); +Clazz.defineMethod (c$, "recalcConservation", +function () { +if (this.cs == null && this.consensus == null && this.conservation == null) { +return; +}try { +var cnsns = jalview.analysis.AAFrequency.calculate (this.sequences, this.startRes, this.endRes + 1, this.showSequenceLogo); +if (this.consensus != null) { +this._updateConsensusRow (cnsns, this.sequences.size ()); +}if (this.cs != null) { +this.cs.setConsensus (cnsns); +}if ((this.conservation != null) || (this.cs != null && this.cs.conservationApplied ())) { +var c = new jalview.analysis.Conservation (this.groupName, jalview.schemes.ResidueProperties.propHash, 3, this.sequences, this.startRes, this.endRes + 1); +c.calculate (); +c.verdict (false, this.consPercGaps); +if (this.conservation != null) { +this._updateConservationRow (c); +}if (this.cs != null) { +if (this.cs.conservationApplied ()) { +this.cs.setConservation (c); +}}}if (this.cs != null) { +this.cs.alignmentChanged (this.context != null ? this.context : this, null); +}} catch (err) { +if (Clazz.exceptionOf (err, OutOfMemoryError)) { +System.out.println ("Out of memory loading groups: " + err); +} else { +throw err; +} +} +}); +Clazz.defineMethod (c$, "_updateConservationRow", +($fz = function (c) { +if (this.conservation == null) { +this.getConservation (); +}this.conservation.label = "Conservation for " + this.getName (); +this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps"; +var aWidth = (this.conservation.annotations != null) ? (this.endRes < this.conservation.annotations.length ? this.conservation.annotations.length : this.endRes + 1) : this.endRes + 1; +this.conservation.annotations = null; +this.conservation.annotations = new Array (aWidth); +c.completeAnnotations (this.conservation, null, this.startRes, this.endRes + 1); +}, $fz.isPrivate = true, $fz), "jalview.analysis.Conservation"); +Clazz.defineMethod (c$, "_updateConsensusRow", +($fz = function (cnsns, nseq) { +if (this.consensus == null) { +this.getConsensus (); +}this.consensus.label = "Consensus for " + this.getName (); +this.consensus.description = "Percent Identity"; +this.consensusData = cnsns; +var aWidth = (this.consensus.annotations != null) ? (this.endRes < this.consensus.annotations.length ? this.consensus.annotations.length : this.endRes + 1) : this.endRes + 1; +this.consensus.annotations = null; +this.consensus.annotations = new Array (aWidth); +jalview.analysis.AAFrequency.completeConsensus (this.consensus, cnsns, this.startRes, this.endRes + 1, this.ignoreGapsInConsensus, this.showSequenceLogo, nseq); +}, $fz.isPrivate = true, $fz), "~A,~N"); +Clazz.defineMethod (c$, "addOrRemove", +function (s, recalc) { +{ +if (this.sequences.contains (s)) { +this.deleteSequence (s, recalc); +} else { +this.addSequence (s, recalc); +}}}, "jalview.datamodel.SequenceI,~B"); +Clazz.defineMethod (c$, "deleteSequence", +function (s, recalc) { +{ +this.sequences.remove (s); +if (recalc) { +this.recalcConservation (); +}}}, "jalview.datamodel.SequenceI,~B"); +Clazz.overrideMethod (c$, "getStartRes", +function () { +return this.startRes; +}); +Clazz.overrideMethod (c$, "getEndRes", +function () { +return this.endRes; +}); +Clazz.defineMethod (c$, "setStartRes", +function (i) { +this.startRes = i; +}, "~N"); +Clazz.defineMethod (c$, "setEndRes", +function (i) { +this.endRes = i; +}, "~N"); +Clazz.defineMethod (c$, "getSize", +function () { +return this.sequences.size (); +}); +Clazz.defineMethod (c$, "getSequenceAt", +function (i) { +return this.sequences.get (i); +}, "~N"); +Clazz.defineMethod (c$, "setColourText", +function (state) { +this.colourText = state; +}, "~B"); +Clazz.defineMethod (c$, "getColourText", +function () { +return this.colourText; +}); +Clazz.defineMethod (c$, "setDisplayText", +function (state) { +this.displayText = state; +}, "~B"); +Clazz.defineMethod (c$, "getDisplayText", +function () { +return this.displayText; +}); +Clazz.defineMethod (c$, "setDisplayBoxes", +function (state) { +this.displayBoxes = state; +}, "~B"); +Clazz.defineMethod (c$, "getDisplayBoxes", +function () { +return this.displayBoxes; +}); +Clazz.overrideMethod (c$, "getWidth", +function () { +{ +var first = true; +for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +if (first || seq.getLength () > this.width) { +this.width = seq.getLength (); +first = false; +}} +return this.width; +}}); +Clazz.defineMethod (c$, "setOutlineColour", +function (c) { +this.outlineColour = c; +}, "java.awt.Color"); +Clazz.defineMethod (c$, "getOutlineColour", +function () { +return this.outlineColour; +}); +Clazz.defineMethod (c$, "getSequencesInOrder", +function (al) { +return this.getSequencesInOrder (al, true); +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "getSequencesInOrder", +function (al, trim) { +{ +var sSize = this.sequences.size (); +var alHeight = al.getHeight (); +var seqs = new Array ((trim) ? sSize : alHeight); +var index = 0; +for (var i = 0; i < alHeight && index < sSize; i++) { +if (this.sequences.contains (al.getSequenceAt (i))) { +seqs[(trim) ? index : i] = al.getSequenceAt (i); +index++; +}} +if (index == 0) { +return null; +}if (!trim) { +return seqs; +}if (index < seqs.length) { +var dummy = seqs; +seqs = new Array (index); +while (--index >= 0) { +seqs[index] = dummy[index]; +dummy[index] = null; +} +}return seqs; +}}, "jalview.datamodel.AlignmentI,~B"); +Clazz.defineMethod (c$, "getIdColour", +function () { +return this.idColour; +}); +Clazz.defineMethod (c$, "setIdColour", +function (idColour) { +this.idColour = idColour; +}, "java.awt.Color"); +Clazz.overrideMethod (c$, "getSeqrep", +function () { +return this.seqrep; +}); +Clazz.overrideMethod (c$, "setSeqrep", +function (seqrep) { +this.seqrep = seqrep; +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "hasSeqrep", +function () { +return this.seqrep != null; +}); +Clazz.defineMethod (c$, "setHidereps", +function (visibility) { +this.hidereps = visibility; +}, "~B"); +Clazz.defineMethod (c$, "isHidereps", +function () { +return this.hidereps; +}); +Clazz.defineMethod (c$, "setHideCols", +function (visibility) { +this.hidecols = visibility; +}, "~B"); +Clazz.defineMethod (c$, "isHideCols", +function () { +return this.hidecols; +}); +Clazz.defineMethod (c$, "intersect", +function (alignment, map) { +var sgroup = new jalview.datamodel.SequenceGroup (this); +var insect = this.getSequencesInOrder (alignment); +sgroup.sequences = new java.util.ArrayList (); +for (var s = 0; insect != null && s < insect.length; s++) { +if (map == null || map.containsKey (insect[s])) { +sgroup.sequences.add (insect[s]); +}} +return sgroup; +}, "jalview.datamodel.AlignmentI,java.util.Map"); +Clazz.defineMethod (c$, "getShowNonconserved", +function () { +return this.showNonconserved; +}); +Clazz.defineMethod (c$, "setShowNonconserved", +function (displayNonconserved) { +this.showNonconserved = displayNonconserved; +}, "~B"); +Clazz.defineMethod (c$, "setConsensus", +function (aan) { +if (this.consensus == null) { +this.consensus = aan; +}}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "getConsensus", +function () { +var aWidth = this.getWidth (); +if (aWidth < 0) { +return null; +}if (this.consensus == null) { +this.consensus = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 100, 1); +this.consensus.hasText = true; +this.consensus.autoCalculated = true; +this.consensus.groupRef = this; +this.consensus.label = "Consensus for " + this.getName (); +this.consensus.description = "Percent Identity"; +}return this.consensus; +}); +Clazz.defineMethod (c$, "setConservationRow", +function (aan) { +if (this.conservation == null) { +this.conservation = aan; +}}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "getConservationRow", +function () { +if (this.conservation == null) { +this.conservation = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 11, 1); +}this.conservation.hasText = true; +this.conservation.autoCalculated = true; +this.conservation.groupRef = this; +this.conservation.label = "Conservation for " + this.getName (); +this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps"; +return this.conservation; +}); +Clazz.defineMethod (c$, "hasAnnotationRows", +function () { +return this.consensus != null || this.conservation != null; +}); +Clazz.defineMethod (c$, "getConsensusSeq", +function () { +this.getConsensus (); +var seqs = new StringBuffer (); +for (var i = 0; i < this.consensus.annotations.length; i++) { +if (this.consensus.annotations[i] != null) { +if (this.consensus.annotations[i].description.charAt (0) == '[') { +seqs.append (this.consensus.annotations[i].description.charAt (1)); +} else { +seqs.append (this.consensus.annotations[i].displayCharacter); +}}} +var sq = new jalview.datamodel.Sequence ("Group" + this.getName () + " Consensus", seqs.toString ()); +sq.setDescription ("Percentage Identity Consensus " + ((this.ignoreGapsInConsensus) ? " without gaps" : "")); +return sq; +}); +Clazz.defineMethod (c$, "setIgnoreGapsConsensus", +function (state) { +if (this.ignoreGapsInConsensus != state && this.consensus != null) { +this.ignoreGapsInConsensus = state; +this.recalcConservation (); +}this.ignoreGapsInConsensus = state; +}, "~B"); +Clazz.defineMethod (c$, "getIgnoreGapsConsensus", +function () { +return this.ignoreGapsInConsensus; +}); +Clazz.defineMethod (c$, "setshowSequenceLogo", +function (showSequenceLogo) { +if (this.showSequenceLogo != showSequenceLogo && this.consensus != null) { +this.showSequenceLogo = showSequenceLogo; +this.recalcConservation (); +}this.showSequenceLogo = showSequenceLogo; +}, "~B"); +Clazz.defineMethod (c$, "setShowConsensusHistogram", +function (showConsHist) { +if (this.showConsensusHistogram != showConsHist && this.consensus != null) { +this.showConsensusHistogram = showConsHist; +this.recalcConservation (); +}this.showConsensusHistogram = showConsHist; +}, "~B"); +Clazz.defineMethod (c$, "isShowConsensusHistogram", +function () { +return this.showConsensusHistogram; +}); +Clazz.defineMethod (c$, "setNormaliseSequenceLogo", +function (norm) { +this.normaliseSequenceLogo = norm; +}, "~B"); +Clazz.defineMethod (c$, "isNormaliseSequenceLogo", +function () { +return this.normaliseSequenceLogo; +}); +Clazz.overrideMethod (c$, "getAlignmentAnnotation", +function () { +var annot = new java.util.ArrayList (); +{ +for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +var aa = seq.getAnnotation (); +if (aa != null) { +for (var al, $al = 0, $$al = aa; $al < $$al.length && ((al = $$al[$al]) || true); $al++) { +if (al.groupRef === this) { +annot.add (al); +}} +}} +if (this.consensus != null) { +annot.add (this.consensus); +}if (this.conservation != null) { +annot.add (this.conservation); +}}return annot.toArray ( new Array (0)); +}); +Clazz.overrideMethod (c$, "findAnnotation", +function (calcId) { +var aa = new java.util.ArrayList (); +for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) { +if (a.getCalcId () === calcId) { +aa.add (a); +}} +return aa; +}, "~S"); +Clazz.overrideMethod (c$, "findAnnotations", +function (seq, calcId, label) { +var aa = new java.util.ArrayList (); +for (var ann, $ann = 0, $$ann = this.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { +if (ann.getCalcId () != null && ann.getCalcId ().equals (calcId) && ann.sequenceRef != null && ann.sequenceRef === seq && ann.label != null && ann.label.equals (label)) { +aa.add (ann); +}} +return aa; +}, "jalview.datamodel.SequenceI,~S,~S"); +Clazz.defineMethod (c$, "hasAnnotation", +function (calcId) { +if (calcId != null && !"".equals (calcId)) { +for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) { +if (a.getCalcId () === calcId) { +return true; +}} +}return false; +}, "~S"); +Clazz.defineMethod (c$, "clear", +function () { +{ +this.sequences.clear (); +}}); +Clazz.defineMethod (c$, "setContext", +function (context) { +this.context = context; +}, "jalview.datamodel.AnnotatedCollectionI"); +Clazz.overrideMethod (c$, "getContext", +function () { +return this.context; +}); +}); diff --git a/bin/jalview/datamodel/SequenceI.js b/bin/jalview/datamodel/SequenceI.js index 242d5a5..dcf0724 100644 --- a/bin/jalview/datamodel/SequenceI.js +++ b/bin/jalview/datamodel/SequenceI.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.ASequenceI"], "jalview.datamodel.SequenceI", null, function () { -Clazz.declareInterface (jalview.datamodel, "SequenceI", jalview.datamodel.ASequenceI); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.ASequenceI"], "jalview.datamodel.SequenceI", null, function () { +Clazz.declareInterface (jalview.datamodel, "SequenceI", jalview.datamodel.ASequenceI); +}); diff --git a/bin/jalview/datamodel/SequenceNode.js b/bin/jalview/datamodel/SequenceNode.js index 54cb491..2069471 100644 --- a/bin/jalview/datamodel/SequenceNode.js +++ b/bin/jalview/datamodel/SequenceNode.js @@ -1,64 +1,64 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["jalview.datamodel.BinaryNode", "java.awt.Color"], "jalview.datamodel.SequenceNode", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.dist = 0; -this.count = 0; -this.height = 0; -this.ycount = 0; -this.color = null; -this.dummy = false; -this.placeholder = false; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SequenceNode", jalview.datamodel.BinaryNode); -Clazz.prepareFields (c$, function () { -this.color = java.awt.Color.black; -}); -Clazz.makeConstructor (c$, -function (val, parent, dist, name) { -Clazz.superConstructor (this, jalview.datamodel.SequenceNode, [val, parent, name]); -this.dist = dist; -}, "~O,jalview.datamodel.SequenceNode,~N,~S"); -Clazz.makeConstructor (c$, -function (val, parent, name, dist, bootstrap, dummy) { -Clazz.superConstructor (this, jalview.datamodel.SequenceNode, [val, parent, name]); -this.dist = dist; -this.bootstrap = bootstrap; -this.dummy = dummy; -}, "~O,jalview.datamodel.SequenceNode,~S,~N,~N,~B"); -Clazz.defineMethod (c$, "isDummy", -function () { -return this.dummy; -}); -Clazz.defineMethod (c$, "isPlaceholder", -function () { -return this.placeholder; -}); -Clazz.defineMethod (c$, "setDummy", -function (newstate) { -var oldstate = this.dummy; -this.dummy = newstate; -return oldstate; -}, "~B"); -Clazz.defineMethod (c$, "setPlaceholder", -function (Placeholder) { -this.placeholder = Placeholder; -}, "~B"); -Clazz.defineMethod (c$, "AscendTree", -function () { -var c = this; -do { -c = c.parent (); -} while ((c != null) && c.dummy); -return c; -}); -Clazz.defineMethod (c$, "isSequenceLabel", -function () { -if (this.name != null && this.name.length > 0) { -for (var c = 0, s = this.name.length; c < s; c++) { -var q = this.name.charAt (c); -if ('0' <= q && q <= '9') continue; -return true; -} -}return false; -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["jalview.datamodel.BinaryNode", "java.awt.Color"], "jalview.datamodel.SequenceNode", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.dist = 0; +this.count = 0; +this.height = 0; +this.ycount = 0; +this.color = null; +this.dummy = false; +this.placeholder = false; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SequenceNode", jalview.datamodel.BinaryNode); +Clazz.prepareFields (c$, function () { +this.color = java.awt.Color.black; +}); +Clazz.makeConstructor (c$, +function (val, parent, dist, name) { +Clazz.superConstructor (this, jalview.datamodel.SequenceNode, [val, parent, name]); +this.dist = dist; +}, "~O,jalview.datamodel.SequenceNode,~N,~S"); +Clazz.makeConstructor (c$, +function (val, parent, name, dist, bootstrap, dummy) { +Clazz.superConstructor (this, jalview.datamodel.SequenceNode, [val, parent, name]); +this.dist = dist; +this.bootstrap = bootstrap; +this.dummy = dummy; +}, "~O,jalview.datamodel.SequenceNode,~S,~N,~N,~B"); +Clazz.defineMethod (c$, "isDummy", +function () { +return this.dummy; +}); +Clazz.defineMethod (c$, "isPlaceholder", +function () { +return this.placeholder; +}); +Clazz.defineMethod (c$, "setDummy", +function (newstate) { +var oldstate = this.dummy; +this.dummy = newstate; +return oldstate; +}, "~B"); +Clazz.defineMethod (c$, "setPlaceholder", +function (Placeholder) { +this.placeholder = Placeholder; +}, "~B"); +Clazz.defineMethod (c$, "AscendTree", +function () { +var c = this; +do { +c = c.parent (); +} while ((c != null) && c.dummy); +return c; +}); +Clazz.defineMethod (c$, "isSequenceLabel", +function () { +if (this.name != null && this.name.length > 0) { +for (var c = 0, s = this.name.length; c < s; c++) { +var q = this.name.charAt (c); +if ('0' <= q && q <= '9') continue; +return true; +} +}return false; +}); +}); diff --git a/bin/jalview/datamodel/SequencePoint.js b/bin/jalview/datamodel/SequencePoint.js index 0616692..549eae1 100644 --- a/bin/jalview/datamodel/SequencePoint.js +++ b/bin/jalview/datamodel/SequencePoint.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this.isPlaceholder = false; -this.sequence = null; -this.coord = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "SequencePoint"); -Clazz.makeConstructor (c$, -function (sequence, coord) { -this.sequence = sequence; -this.coord = coord; -}, "jalview.datamodel.SequenceI,~A"); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this.isPlaceholder = false; +this.sequence = null; +this.coord = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "SequencePoint"); +Clazz.makeConstructor (c$, +function (sequence, coord) { +this.sequence = sequence; +this.coord = coord; +}, "jalview.datamodel.SequenceI,~A"); diff --git a/bin/jalview/datamodel/StructureViewerModel.js b/bin/jalview/datamodel/StructureViewerModel.js index e21d3fc..cc11e43 100644 --- a/bin/jalview/datamodel/StructureViewerModel.js +++ b/bin/jalview/datamodel/StructureViewerModel.js @@ -1,156 +1,156 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (["java.util.HashMap"], "jalview.datamodel.StructureViewerModel", ["java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this.x = 0; -this.y = 0; -this.width = 0; -this.height = 0; -this.alignWithPanel = false; -this.colourWithAlignPanel = false; -this.colourByViewer = false; -this.stateData = ""; -this.viewId = null; -this.type = null; -this.fileData = null; -if (!Clazz.isClassDefined ("jalview.datamodel.StructureViewerModel.StructureData")) { -jalview.datamodel.StructureViewerModel.$StructureViewerModel$StructureData$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "StructureViewerModel"); -Clazz.prepareFields (c$, function () { -this.fileData = new java.util.HashMap (); -}); -Clazz.makeConstructor (c$, -function (x, y, width, height, alignWithPanel, colourWithAlignPanel, colourByViewer, viewId, type) { -this.x = x; -this.y = y; -this.width = width; -this.height = height; -this.alignWithPanel = alignWithPanel; -this.colourWithAlignPanel = colourWithAlignPanel; -this.colourByViewer = colourByViewer; -this.viewId = viewId; -this.type = type; -}, "~N,~N,~N,~N,~B,~B,~B,~S,~S"); -Clazz.defineMethod (c$, "getX", -function () { -return this.x; -}); -Clazz.defineMethod (c$, "setX", -function (x) { -this.x = x; -}, "~N"); -Clazz.defineMethod (c$, "getY", -function () { -return this.y; -}); -Clazz.defineMethod (c$, "setY", -function (y) { -this.y = y; -}, "~N"); -Clazz.defineMethod (c$, "getWidth", -function () { -return this.width; -}); -Clazz.defineMethod (c$, "setWidth", -function (width) { -this.width = width; -}, "~N"); -Clazz.defineMethod (c$, "getHeight", -function () { -return this.height; -}); -Clazz.defineMethod (c$, "setHeight", -function (height) { -this.height = height; -}, "~N"); -Clazz.defineMethod (c$, "isAlignWithPanel", -function () { -return this.alignWithPanel; -}); -Clazz.defineMethod (c$, "setAlignWithPanel", -function (alignWithPanel) { -this.alignWithPanel = alignWithPanel; -}, "~B"); -Clazz.defineMethod (c$, "isColourWithAlignPanel", -function () { -return this.colourWithAlignPanel; -}); -Clazz.defineMethod (c$, "setColourWithAlignPanel", -function (colourWithAlignPanel) { -this.colourWithAlignPanel = colourWithAlignPanel; -}, "~B"); -Clazz.defineMethod (c$, "isColourByViewer", -function () { -return this.colourByViewer; -}); -Clazz.defineMethod (c$, "setColourByViewer", -function (colourByViewer) { -this.colourByViewer = colourByViewer; -}, "~B"); -Clazz.defineMethod (c$, "getStateData", -function () { -return this.stateData; -}); -Clazz.defineMethod (c$, "setStateData", -function (stateData) { -this.stateData = stateData; -}, "~S"); -Clazz.defineMethod (c$, "getFileData", -function () { -return this.fileData; -}); -Clazz.defineMethod (c$, "setFileData", -function (fileData) { -this.fileData = fileData; -}, "java.util.Map"); -Clazz.defineMethod (c$, "getViewId", -function () { -return this.viewId; -}); -Clazz.defineMethod (c$, "getType", -function () { -return this.type; -}); -c$.$StructureViewerModel$StructureData$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.filePath = null; -this.pdbId = null; -this.seqList = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel.StructureViewerModel, "StructureData"); -Clazz.makeConstructor (c$, -function (a, b) { -this.filePath = a; -this.pdbId = b; -this.seqList = new java.util.ArrayList (); -}, "~S,~S"); -Clazz.defineMethod (c$, "getFilePath", -function () { -return this.filePath; -}); -Clazz.defineMethod (c$, "setFilePath", -function (a) { -this.filePath = a; -}, "~S"); -Clazz.defineMethod (c$, "getPdbId", -function () { -return this.pdbId; -}); -Clazz.defineMethod (c$, "setPdbId", -function (a) { -this.pdbId = a; -}, "~S"); -Clazz.defineMethod (c$, "getSeqList", -function () { -return this.seqList; -}); -Clazz.defineMethod (c$, "setSeqList", -function (a) { -this.seqList = a; -}, "java.util.List"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (["java.util.HashMap"], "jalview.datamodel.StructureViewerModel", ["java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this.x = 0; +this.y = 0; +this.width = 0; +this.height = 0; +this.alignWithPanel = false; +this.colourWithAlignPanel = false; +this.colourByViewer = false; +this.stateData = ""; +this.viewId = null; +this.type = null; +this.fileData = null; +if (!Clazz.isClassDefined ("jalview.datamodel.StructureViewerModel.StructureData")) { +jalview.datamodel.StructureViewerModel.$StructureViewerModel$StructureData$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "StructureViewerModel"); +Clazz.prepareFields (c$, function () { +this.fileData = new java.util.HashMap (); +}); +Clazz.makeConstructor (c$, +function (x, y, width, height, alignWithPanel, colourWithAlignPanel, colourByViewer, viewId, type) { +this.x = x; +this.y = y; +this.width = width; +this.height = height; +this.alignWithPanel = alignWithPanel; +this.colourWithAlignPanel = colourWithAlignPanel; +this.colourByViewer = colourByViewer; +this.viewId = viewId; +this.type = type; +}, "~N,~N,~N,~N,~B,~B,~B,~S,~S"); +Clazz.defineMethod (c$, "getX", +function () { +return this.x; +}); +Clazz.defineMethod (c$, "setX", +function (x) { +this.x = x; +}, "~N"); +Clazz.defineMethod (c$, "getY", +function () { +return this.y; +}); +Clazz.defineMethod (c$, "setY", +function (y) { +this.y = y; +}, "~N"); +Clazz.defineMethod (c$, "getWidth", +function () { +return this.width; +}); +Clazz.defineMethod (c$, "setWidth", +function (width) { +this.width = width; +}, "~N"); +Clazz.defineMethod (c$, "getHeight", +function () { +return this.height; +}); +Clazz.defineMethod (c$, "setHeight", +function (height) { +this.height = height; +}, "~N"); +Clazz.defineMethod (c$, "isAlignWithPanel", +function () { +return this.alignWithPanel; +}); +Clazz.defineMethod (c$, "setAlignWithPanel", +function (alignWithPanel) { +this.alignWithPanel = alignWithPanel; +}, "~B"); +Clazz.defineMethod (c$, "isColourWithAlignPanel", +function () { +return this.colourWithAlignPanel; +}); +Clazz.defineMethod (c$, "setColourWithAlignPanel", +function (colourWithAlignPanel) { +this.colourWithAlignPanel = colourWithAlignPanel; +}, "~B"); +Clazz.defineMethod (c$, "isColourByViewer", +function () { +return this.colourByViewer; +}); +Clazz.defineMethod (c$, "setColourByViewer", +function (colourByViewer) { +this.colourByViewer = colourByViewer; +}, "~B"); +Clazz.defineMethod (c$, "getStateData", +function () { +return this.stateData; +}); +Clazz.defineMethod (c$, "setStateData", +function (stateData) { +this.stateData = stateData; +}, "~S"); +Clazz.defineMethod (c$, "getFileData", +function () { +return this.fileData; +}); +Clazz.defineMethod (c$, "setFileData", +function (fileData) { +this.fileData = fileData; +}, "java.util.Map"); +Clazz.defineMethod (c$, "getViewId", +function () { +return this.viewId; +}); +Clazz.defineMethod (c$, "getType", +function () { +return this.type; +}); +c$.$StructureViewerModel$StructureData$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.filePath = null; +this.pdbId = null; +this.seqList = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel.StructureViewerModel, "StructureData"); +Clazz.makeConstructor (c$, +function (a, b) { +this.filePath = a; +this.pdbId = b; +this.seqList = new java.util.ArrayList (); +}, "~S,~S"); +Clazz.defineMethod (c$, "getFilePath", +function () { +return this.filePath; +}); +Clazz.defineMethod (c$, "setFilePath", +function (a) { +this.filePath = a; +}, "~S"); +Clazz.defineMethod (c$, "getPdbId", +function () { +return this.pdbId; +}); +Clazz.defineMethod (c$, "setPdbId", +function (a) { +this.pdbId = a; +}, "~S"); +Clazz.defineMethod (c$, "getSeqList", +function () { +return this.seqList; +}); +Clazz.defineMethod (c$, "setSeqList", +function (a) { +this.seqList = a; +}, "java.util.List"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/datamodel/UniprotEntry.js b/bin/jalview/datamodel/UniprotEntry.js index 24b3ce2..5b80f48 100644 --- a/bin/jalview/datamodel/UniprotEntry.js +++ b/bin/jalview/datamodel/UniprotEntry.js @@ -1,58 +1,58 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this.sequence = null; -this.name = null; -this.accession = null; -this.feature = null; -this.dbrefs = null; -this.protName = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "UniprotEntry"); -Clazz.defineMethod (c$, "setAccession", -function (items) { -this.accession = items; -}, "java.util.Vector"); -Clazz.defineMethod (c$, "setFeature", -function (items) { -this.feature = items; -}, "java.util.Vector"); -Clazz.defineMethod (c$, "getFeature", -function () { -return this.feature; -}); -Clazz.defineMethod (c$, "getAccession", -function () { -return this.accession; -}); -Clazz.defineMethod (c$, "setProtein", -function (names) { -this.protName = names; -}, "jalview.datamodel.UniprotProteinName"); -Clazz.defineMethod (c$, "getProtein", -function () { -return this.protName; -}); -Clazz.defineMethod (c$, "setName", -function (na) { -this.name = na; -}, "java.util.Vector"); -Clazz.defineMethod (c$, "getName", -function () { -return this.name; -}); -Clazz.defineMethod (c$, "getUniprotSequence", -function () { -return this.sequence; -}); -Clazz.defineMethod (c$, "setUniprotSequence", -function (seq) { -this.sequence = seq; -}, "jalview.datamodel.UniprotSequence"); -Clazz.defineMethod (c$, "getDbReference", -function () { -return this.dbrefs; -}); -Clazz.defineMethod (c$, "setDbReference", -function (dbref) { -this.dbrefs = dbref; -}, "java.util.Vector"); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this.sequence = null; +this.name = null; +this.accession = null; +this.feature = null; +this.dbrefs = null; +this.protName = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "UniprotEntry"); +Clazz.defineMethod (c$, "setAccession", +function (items) { +this.accession = items; +}, "java.util.Vector"); +Clazz.defineMethod (c$, "setFeature", +function (items) { +this.feature = items; +}, "java.util.Vector"); +Clazz.defineMethod (c$, "getFeature", +function () { +return this.feature; +}); +Clazz.defineMethod (c$, "getAccession", +function () { +return this.accession; +}); +Clazz.defineMethod (c$, "setProtein", +function (names) { +this.protName = names; +}, "jalview.datamodel.UniprotProteinName"); +Clazz.defineMethod (c$, "getProtein", +function () { +return this.protName; +}); +Clazz.defineMethod (c$, "setName", +function (na) { +this.name = na; +}, "java.util.Vector"); +Clazz.defineMethod (c$, "getName", +function () { +return this.name; +}); +Clazz.defineMethod (c$, "getUniprotSequence", +function () { +return this.sequence; +}); +Clazz.defineMethod (c$, "setUniprotSequence", +function (seq) { +this.sequence = seq; +}, "jalview.datamodel.UniprotSequence"); +Clazz.defineMethod (c$, "getDbReference", +function () { +return this.dbrefs; +}); +Clazz.defineMethod (c$, "setDbReference", +function (dbref) { +this.dbrefs = dbref; +}, "java.util.Vector"); diff --git a/bin/jalview/datamodel/UniprotFile.js b/bin/jalview/datamodel/UniprotFile.js index f779f79..e0f80f8 100644 --- a/bin/jalview/datamodel/UniprotFile.js +++ b/bin/jalview/datamodel/UniprotFile.js @@ -1,13 +1,13 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this._items = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "UniprotFile"); -Clazz.defineMethod (c$, "setUniprotEntries", -function (items) { -this._items = items; -}, "java.util.Vector"); -Clazz.defineMethod (c$, "getUniprotEntries", -function () { -return this._items; -}); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this._items = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "UniprotFile"); +Clazz.defineMethod (c$, "setUniprotEntries", +function (items) { +this._items = items; +}, "java.util.Vector"); +Clazz.defineMethod (c$, "getUniprotEntries", +function () { +return this._items; +}); diff --git a/bin/jalview/datamodel/UniprotProteinName.js b/bin/jalview/datamodel/UniprotProteinName.js index fd4ce5b..931e26c 100644 --- a/bin/jalview/datamodel/UniprotProteinName.js +++ b/bin/jalview/datamodel/UniprotProteinName.js @@ -1,13 +1,13 @@ -Clazz.declarePackage ("jalview.datamodel"); -c$ = Clazz.decorateAsClass (function () { -this.names = null; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "UniprotProteinName"); -Clazz.defineMethod (c$, "setName", -function (names) { -this.names = names; -}, "java.util.Vector"); -Clazz.defineMethod (c$, "getName", -function () { -return this.names; -}); +Clazz.declarePackage ("jalview.datamodel"); +c$ = Clazz.decorateAsClass (function () { +this.names = null; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "UniprotProteinName"); +Clazz.defineMethod (c$, "setName", +function (names) { +this.names = names; +}, "java.util.Vector"); +Clazz.defineMethod (c$, "getName", +function () { +return this.names; +}); diff --git a/bin/jalview/datamodel/UniprotSequence.js b/bin/jalview/datamodel/UniprotSequence.js index 039f1db..d6ae549 100644 --- a/bin/jalview/datamodel/UniprotSequence.js +++ b/bin/jalview/datamodel/UniprotSequence.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("jalview.datamodel"); -Clazz.load (null, "jalview.datamodel.UniprotSequence", ["java.lang.StringBuilder"], function () { -c$ = Clazz.decorateAsClass (function () { -this._content = ""; -Clazz.instantialize (this, arguments); -}, jalview.datamodel, "UniprotSequence"); -Clazz.defineMethod (c$, "setContent", -function (seq) { -if (seq != null) { -var sb = new StringBuilder (seq.length); -for (var i = 0; i < seq.length; i++) { -if (seq.charAt (i) != ' ') { -sb.append (seq.charAt (i)); -}} -this._content = sb.toString (); -}}, "~S"); -Clazz.defineMethod (c$, "getContent", -function () { -return this._content; -}); -}); +Clazz.declarePackage ("jalview.datamodel"); +Clazz.load (null, "jalview.datamodel.UniprotSequence", ["java.lang.StringBuilder"], function () { +c$ = Clazz.decorateAsClass (function () { +this._content = ""; +Clazz.instantialize (this, arguments); +}, jalview.datamodel, "UniprotSequence"); +Clazz.defineMethod (c$, "setContent", +function (seq) { +if (seq != null) { +var sb = new StringBuilder (seq.length); +for (var i = 0; i < seq.length; i++) { +if (seq.charAt (i) != ' ') { +sb.append (seq.charAt (i)); +}} +this._content = sb.toString (); +}}, "~S"); +Clazz.defineMethod (c$, "getContent", +function () { +return this._content; +}); +}); diff --git a/bin/jalview/ext/jmol/JmolCommands.class b/bin/jalview/ext/jmol/JmolCommands.class index 5debe8d..36f4b3f 100644 Binary files a/bin/jalview/ext/jmol/JmolCommands.class and b/bin/jalview/ext/jmol/JmolCommands.class differ diff --git a/bin/jalview/ext/jmol/JmolCommands.js b/bin/jalview/ext/jmol/JmolCommands.js index 495572c..b08a4e3 100644 --- a/bin/jalview/ext/jmol/JmolCommands.js +++ b/bin/jalview/ext/jmol/JmolCommands.js @@ -1,69 +1,69 @@ -Clazz.declarePackage ("jalview.ext.jmol"); -Clazz.load (null, "jalview.ext.jmol.JmolCommands", ["jalview.structure.StructureMappingcommandSet", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () { -c$ = Clazz.declareType (jalview.ext.jmol, "JmolCommands"); -c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", -function (ssm, files, sequence, sr, fr, alignment) { -var cset = new java.util.ArrayList (); -for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { -var mapping = ssm.getMapping (files[pdbfnum]); -var command = new StringBuffer (); -var smc; -var str = new java.util.ArrayList (); -if (mapping == null || mapping.length < 1) { -continue; -}var lastPos = -1; -for (var s = 0; s < sequence[pdbfnum].length; s++) { -for (var sp, m = 0; m < mapping.length; m++) { -if (mapping[m].getSequence () === sequence[pdbfnum][s] && (sp = alignment.findIndex (sequence[pdbfnum][s])) > -1) { -var asp = alignment.getSequenceAt (sp); -for (var r = 0; r < asp.getLength (); r++) { -if (jalview.util.Comparison.isGap (asp.getCharAt (r))) { -continue; -}var pos = mapping[m].getPDBResNum (asp.findPosition (r)); -if (pos < 1 || pos == lastPos) { -continue; -}lastPos = pos; -var col = sr.getResidueBoxColour (sequence[pdbfnum][s], r); -if (fr != null) { -col = fr.findFeatureColour (col, sequence[pdbfnum][s], r); -}var newSelcom = (mapping[m].getChain () !== " " ? ":" + mapping[m].getChain () : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" + col.getRed () + "," + col.getGreen () + "," + col.getBlue () + "]"; -if (command.length () > newSelcom.length && command.substring (command.length () - newSelcom.length).equals (newSelcom)) { -command = jalview.ext.jmol.JmolCommands.condenseCommand (command, pos); -continue; -}command.append (";"); -if (command.length () > 51200) { -str.add (command.toString ()); -command.setLength (0); -}command.append ("select " + pos); -command.append (newSelcom); -} -break; -}} -} -{ -str.add (command.toString ()); -command.setLength (0); -}cset.add ( new jalview.structure.StructureMappingcommandSet (jalview.ext.jmol.JmolCommands, files[pdbfnum], str.toArray ( new Array (str.size ())))); -} -return cset.toArray ( new Array (cset.size ())); -}, "jalview.structure.StructureSelectionManager,~A,~A,jalview.api.SequenceRenderer,jalview.api.FeatureRenderer,jalview.datamodel.AlignmentI"); -c$.condenseCommand = Clazz.defineMethod (c$, "condenseCommand", -function (command, pos) { -var p = command.length (); -var q = p; -do { -p -= 6; -if (p < 1) { -p = 0; -};} while ((q = command.indexOf ("select", p)) == -1 && p > 0); -var sb = new StringBuffer (command.substring (0, q + 7)); -command = command.$delete (0, q + 7); -var start; -if (command.indexOf ("-") > -1) { -start = command.substring (0, command.indexOf ("-")); -} else { -start = command.substring (0, command.indexOf (":")); -}sb.append (start + "-" + pos + command.substring (command.indexOf (":"))); -return sb; -}, "StringBuffer,~N"); -}); +Clazz.declarePackage ("jalview.ext.jmol"); +Clazz.load (null, "jalview.ext.jmol.JmolCommands", ["jalview.structure.StructureMappingcommandSet", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () { +c$ = Clazz.declareType (jalview.ext.jmol, "JmolCommands"); +c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", +function (ssm, files, sequence, sr, fr, alignment) { +var cset = new java.util.ArrayList (); +for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { +var mapping = ssm.getMapping (files[pdbfnum]); +var command = new StringBuffer (); +var smc; +var str = new java.util.ArrayList (); +if (mapping == null || mapping.length < 1) { +continue; +}var lastPos = -1; +for (var s = 0; s < sequence[pdbfnum].length; s++) { +for (var sp, m = 0; m < mapping.length; m++) { +if (mapping[m].getSequence () === sequence[pdbfnum][s] && (sp = alignment.findIndex (sequence[pdbfnum][s])) > -1) { +var asp = alignment.getSequenceAt (sp); +for (var r = 0; r < asp.getLength (); r++) { +if (jalview.util.Comparison.isGap (asp.getCharAt (r))) { +continue; +}var pos = mapping[m].getPDBResNum (asp.findPosition (r)); +if (pos < 1 || pos == lastPos) { +continue; +}lastPos = pos; +var col = sr.getResidueBoxColour (sequence[pdbfnum][s], r); +if (fr != null) { +col = fr.findFeatureColour (col, sequence[pdbfnum][s], r); +}var newSelcom = (mapping[m].getChain () !== " " ? ":" + mapping[m].getChain () : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" + col.getRed () + "," + col.getGreen () + "," + col.getBlue () + "]"; +if (command.length () > newSelcom.length && command.substring (command.length () - newSelcom.length).equals (newSelcom)) { +command = jalview.ext.jmol.JmolCommands.condenseCommand (command, pos); +continue; +}command.append (";"); +if (command.length () > 51200) { +str.add (command.toString ()); +command.setLength (0); +}command.append ("select " + pos); +command.append (newSelcom); +} +break; +}} +} +{ +str.add (command.toString ()); +command.setLength (0); +}cset.add ( new jalview.structure.StructureMappingcommandSet (jalview.ext.jmol.JmolCommands, files[pdbfnum], str.toArray ( new Array (str.size ())))); +} +return cset.toArray ( new Array (cset.size ())); +}, "jalview.structure.StructureSelectionManager,~A,~A,jalview.api.SequenceRenderer,jalview.api.FeatureRenderer,jalview.datamodel.AlignmentI"); +c$.condenseCommand = Clazz.defineMethod (c$, "condenseCommand", +function (command, pos) { +var p = command.length (); +var q = p; +do { +p -= 6; +if (p < 1) { +p = 0; +};} while ((q = command.indexOf ("select", p)) == -1 && p > 0); +var sb = new StringBuffer (command.substring (0, q + 7)); +command = command.$delete (0, q + 7); +var start; +if (command.indexOf ("-") > -1) { +start = command.substring (0, command.indexOf ("-")); +} else { +start = command.substring (0, command.indexOf (":")); +}sb.append (start + "-" + pos + command.substring (command.indexOf (":"))); +return sb; +}, "StringBuffer,~N"); +}); diff --git a/bin/jalview/ext/varna/JalviewVarnaBinding.js b/bin/jalview/ext/varna/JalviewVarnaBinding.js index f8bdf18..61bd3e7 100644 --- a/bin/jalview/ext/varna/JalviewVarnaBinding.js +++ b/bin/jalview/ext/varna/JalviewVarnaBinding.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.ext.varna"); -Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.structure.StructureListener", "jalview.structures.models.SequenceStructureBindingModel", "java.awt.event.ComponentListener"], "jalview.ext.varna.JalviewVarnaBinding", null, function () { -c$ = Clazz.declareType (jalview.ext.varna, "JalviewVarnaBinding", jalview.structures.models.SequenceStructureBindingModel, [jalview.structure.StructureListener, java.awt.event.ComponentListener, jalview.api.StructureSelectionManagerProvider]); -}); +Clazz.declarePackage ("jalview.ext.varna"); +Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.structure.StructureListener", "jalview.structures.models.SequenceStructureBindingModel", "java.awt.event.ComponentListener"], "jalview.ext.varna.JalviewVarnaBinding", null, function () { +c$ = Clazz.declareType (jalview.ext.varna, "JalviewVarnaBinding", jalview.structures.models.SequenceStructureBindingModel, [jalview.structure.StructureListener, java.awt.event.ComponentListener, jalview.api.StructureSelectionManagerProvider]); +}); diff --git a/bin/jalview/ext/varna/RnaModel.js b/bin/jalview/ext/varna/RnaModel.js index 9916e8e..f125256 100644 --- a/bin/jalview/ext/varna/RnaModel.js +++ b/bin/jalview/ext/varna/RnaModel.js @@ -1,17 +1,17 @@ -Clazz.declarePackage ("jalview.ext.varna"); -c$ = Clazz.decorateAsClass (function () { -this.title = null; -this.ann = null; -this.seq = null; -this.gapped = false; -this.rna = null; -Clazz.instantialize (this, arguments); -}, jalview.ext.varna, "RnaModel"); -Clazz.makeConstructor (c$, -function (t, aa, s, r, g) { -this.title = t; -this.ann = aa; -this.seq = s; -this.rna = r; -this.gapped = g; -}, "~S,jalview.datamodel.AlignmentAnnotation,jalview.datamodel.SequenceI,fr.orsay.lri.varna.models.rna.RNA,~B"); +Clazz.declarePackage ("jalview.ext.varna"); +c$ = Clazz.decorateAsClass (function () { +this.title = null; +this.ann = null; +this.seq = null; +this.gapped = false; +this.rna = null; +Clazz.instantialize (this, arguments); +}, jalview.ext.varna, "RnaModel"); +Clazz.makeConstructor (c$, +function (t, aa, s, r, g) { +this.title = t; +this.ann = aa; +this.seq = s; +this.rna = r; +this.gapped = g; +}, "~S,jalview.datamodel.AlignmentAnnotation,jalview.datamodel.SequenceI,fr.orsay.lri.varna.models.rna.RNA,~B"); diff --git a/bin/jalview/ext/varna/VarnaCommands.class b/bin/jalview/ext/varna/VarnaCommands.class index 7a0d88f..27a2330 100644 Binary files a/bin/jalview/ext/varna/VarnaCommands.class and b/bin/jalview/ext/varna/VarnaCommands.class differ diff --git a/bin/jalview/ext/varna/VarnaCommands.js b/bin/jalview/ext/varna/VarnaCommands.js index b609d09..6562f80 100644 --- a/bin/jalview/ext/varna/VarnaCommands.js +++ b/bin/jalview/ext/varna/VarnaCommands.js @@ -1,66 +1,66 @@ -Clazz.declarePackage ("jalview.ext.varna"); -Clazz.load (null, "jalview.ext.varna.VarnaCommands", ["jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () { -c$ = Clazz.declareType (jalview.ext.varna, "VarnaCommands"); -c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", -function (ssm, files, sequence, sr, fr, alignment) { -var str = new java.util.ArrayList (); -var command = new StringBuffer (); -for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { -var mapping = ssm.getMapping (files[pdbfnum]); -if (mapping == null || mapping.length < 1) { -continue; -}var lastPos = -1; -for (var s = 0; s < sequence[pdbfnum].length; s++) { -for (var sp, m = 0; m < mapping.length; m++) { -if (mapping[m].getSequence () === sequence[pdbfnum][s] && (sp = alignment.findIndex (sequence[pdbfnum][s])) > -1) { -var asp = alignment.getSequenceAt (sp); -for (var r = 0; r < asp.getLength (); r++) { -if (jalview.util.Comparison.isGap (asp.getCharAt (r))) { -continue; -}var pos = mapping[m].getPDBResNum (asp.findPosition (r)); -if (pos < 1 || pos == lastPos) { -continue; -}lastPos = pos; -var col = sr.getResidueBoxColour (sequence[pdbfnum][s], r); -if (fr != null) { -col = fr.findFeatureColour (col, sequence[pdbfnum][s], r); -}var newSelcom = (mapping[m].getChain () !== " " ? ":" + mapping[m].getChain () : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" + col.getRed () + "," + col.getGreen () + "," + col.getBlue () + "]"; -if (command.length () > newSelcom.length && command.substring (command.length () - newSelcom.length).equals (newSelcom)) { -command = jalview.ext.varna.VarnaCommands.condenseCommand (command, pos); -continue; -}command.append (";"); -if (command.length () > 51200) { -str.add (command.toString ()); -command.setLength (0); -}command.append ("select " + pos); -command.append (newSelcom); -} -break; -}} -} -} -{ -str.add (command.toString ()); -command.setLength (0); -}return str.toArray ( new Array (str.size ())); -}, "jalview.structure.StructureSelectionManager,~A,~A,jalview.api.SequenceRenderer,jalview.api.FeatureRenderer,jalview.datamodel.AlignmentI"); -c$.condenseCommand = Clazz.defineMethod (c$, "condenseCommand", -function (command, pos) { -var p = command.length (); -var q = p; -do { -p -= 6; -if (p < 1) { -p = 0; -};} while ((q = command.indexOf ("select", p)) == -1 && p > 0); -var sb = new StringBuffer (command.substring (0, q + 7)); -command = command.$delete (0, q + 7); -var start; -if (command.indexOf ("-") > -1) { -start = command.substring (0, command.indexOf ("-")); -} else { -start = command.substring (0, command.indexOf (":")); -}sb.append (start + "-" + pos + command.substring (command.indexOf (":"))); -return sb; -}, "StringBuffer,~N"); -}); +Clazz.declarePackage ("jalview.ext.varna"); +Clazz.load (null, "jalview.ext.varna.VarnaCommands", ["jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () { +c$ = Clazz.declareType (jalview.ext.varna, "VarnaCommands"); +c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", +function (ssm, files, sequence, sr, fr, alignment) { +var str = new java.util.ArrayList (); +var command = new StringBuffer (); +for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { +var mapping = ssm.getMapping (files[pdbfnum]); +if (mapping == null || mapping.length < 1) { +continue; +}var lastPos = -1; +for (var s = 0; s < sequence[pdbfnum].length; s++) { +for (var sp, m = 0; m < mapping.length; m++) { +if (mapping[m].getSequence () === sequence[pdbfnum][s] && (sp = alignment.findIndex (sequence[pdbfnum][s])) > -1) { +var asp = alignment.getSequenceAt (sp); +for (var r = 0; r < asp.getLength (); r++) { +if (jalview.util.Comparison.isGap (asp.getCharAt (r))) { +continue; +}var pos = mapping[m].getPDBResNum (asp.findPosition (r)); +if (pos < 1 || pos == lastPos) { +continue; +}lastPos = pos; +var col = sr.getResidueBoxColour (sequence[pdbfnum][s], r); +if (fr != null) { +col = fr.findFeatureColour (col, sequence[pdbfnum][s], r); +}var newSelcom = (mapping[m].getChain () !== " " ? ":" + mapping[m].getChain () : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" + col.getRed () + "," + col.getGreen () + "," + col.getBlue () + "]"; +if (command.length () > newSelcom.length && command.substring (command.length () - newSelcom.length).equals (newSelcom)) { +command = jalview.ext.varna.VarnaCommands.condenseCommand (command, pos); +continue; +}command.append (";"); +if (command.length () > 51200) { +str.add (command.toString ()); +command.setLength (0); +}command.append ("select " + pos); +command.append (newSelcom); +} +break; +}} +} +} +{ +str.add (command.toString ()); +command.setLength (0); +}return str.toArray ( new Array (str.size ())); +}, "jalview.structure.StructureSelectionManager,~A,~A,jalview.api.SequenceRenderer,jalview.api.FeatureRenderer,jalview.datamodel.AlignmentI"); +c$.condenseCommand = Clazz.defineMethod (c$, "condenseCommand", +function (command, pos) { +var p = command.length (); +var q = p; +do { +p -= 6; +if (p < 1) { +p = 0; +};} while ((q = command.indexOf ("select", p)) == -1 && p > 0); +var sb = new StringBuffer (command.substring (0, q + 7)); +command = command.$delete (0, q + 7); +var start; +if (command.indexOf ("-") > -1) { +start = command.substring (0, command.indexOf ("-")); +} else { +start = command.substring (0, command.indexOf (":")); +}sb.append (start + "-" + pos + command.substring (command.indexOf (":"))); +return sb; +}, "StringBuffer,~N"); +}); diff --git a/bin/jalview/io/AlignFile.js b/bin/jalview/io/AlignFile.js index f3247de..142c507 100644 --- a/bin/jalview/io/AlignFile.js +++ b/bin/jalview/io/AlignFile.js @@ -1,158 +1,158 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.FileParse"], "jalview.io.AlignFile", ["jalview.datamodel.Sequence", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Error", "java.util.ArrayList", "$.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.noSeqs = 0; -this.maxLength = 0; -this.seqs = null; -this.annotations = null; -this.seqGroups = null; -this.properties = null; -this.start = 0; -this.end = 0; -this.jvSuffix = true; -this.parseCalled = false; -this.newickStrings = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "AlignFile", jalview.io.FileParse); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.AlignFile, []); -this.initData (); -}); -Clazz.makeConstructor (c$, -function (inFile, type) { -this.construct (true, inFile, type); -}, "~S,~S"); -Clazz.makeConstructor (c$, -function (parseImmediately, inFile, type) { -Clazz.superConstructor (this, jalview.io.AlignFile, [inFile, type]); -this.initData (); -if (parseImmediately) { -this.doParse (); -}}, "~B,~S,~S"); -Clazz.makeConstructor (c$, -function (source) { -this.construct (true, source); -}, "jalview.io.FileParse"); -Clazz.makeConstructor (c$, -function (parseImmediately, source) { -Clazz.superConstructor (this, jalview.io.AlignFile, [source]); -this.initData (); -if (parseImmediately) { -this.doParse (); -}}, "~B,jalview.io.FileParse"); -Clazz.defineMethod (c$, "doParse", -function () { -if (this.parseCalled) { -throw new java.io.IOException ("Implementation error: Parser called twice for same data.\nNeed to call initData() again before parsing can be reattempted."); -}this.parseCalled = true; -this.parse (); -for (var i = 0, c = this.seqs.size (); i < c; i++) { -this.seqs.get (i).setIndex (i); -} -}); -Clazz.defineMethod (c$, "getSeqs", -function () { -return this.seqs; -}); -Clazz.defineMethod (c$, "getSeqGroups", -function () { -return this.seqGroups; -}); -Clazz.defineMethod (c$, "getSeqsAsArray", -function () { -var s = new Array (this.seqs.size ()); -for (var i = 0; i < this.seqs.size (); i++) { -s[i] = this.seqs.elementAt (i); -} -return s; -}); -Clazz.defineMethod (c$, "addAnnotations", -function (al) { -this.addProperties (al); -for (var i = 0; i < this.annotations.size (); i++) { -var an = this.annotations.elementAt (i); -an.validateRangeAndDisplay (); -al.addAnnotation (an); -} -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "addSeqGroups", -function (al) { -this.seqGroups = al.getGroups (); -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "addProperties", -function (al) { -if (this.properties != null && this.properties.size () > 0) { -var keys = this.properties.keys (); -var vals = this.properties.elements (); -while (keys.hasMoreElements ()) { -al.setProperty (keys.nextElement (), vals.nextElement ()); -} -}}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "setAlignmentProperty", -function (key, value) { -if (key == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_cannot_have_null_alignment")); -}if (value == null) { -return; -}if (this.properties == null) { -this.properties = new java.util.Hashtable (); -}this.properties.put (key, value); -}, "~O,~O"); -Clazz.defineMethod (c$, "getAlignmentProperty", -function (key) { -if (this.properties != null && key != null) { -return this.properties.get (key); -}return null; -}, "~O"); -Clazz.defineMethod (c$, "initData", -function () { -this.seqs = new java.util.Vector (); -this.annotations = new java.util.Vector (); -this.seqGroups = new java.util.ArrayList (); -this.parseCalled = false; -}); -Clazz.defineMethod (c$, "setSeqs", -function (s) { -this.seqs = new java.util.Vector (); -for (var i = 0; i < s.length; i++) { -this.seqs.addElement (s[i]); -} -}, "~A"); -Clazz.defineMethod (c$, "addJVSuffix", -function (b) { -this.jvSuffix = b; -}, "~B"); -Clazz.defineMethod (c$, "parseId", -function (id) { -var seq = null; -id = id.trim (); -var space = id.indexOf (" "); -if (space > -1) { -seq = new jalview.datamodel.Sequence (id.substring (0, space), ""); -seq.setDescription (id.substring (space + 1)); -} else { -seq = new jalview.datamodel.Sequence (id, ""); -}return seq; -}, "~S"); -Clazz.defineMethod (c$, "printId", -function (seq) { -return seq.getDisplayId (this.jvSuffix); -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "addNewickTree", -function (treeName, newickString) { -if (this.newickStrings == null) { -this.newickStrings = new java.util.Vector (); -}this.newickStrings.addElement ( Clazz.newArray (-1, [treeName, newickString])); -}, "~S,~S"); -Clazz.defineMethod (c$, "getTreeCount", -function () { -return this.newickStrings == null ? 0 : this.newickStrings.size (); -}); -Clazz.defineMethod (c$, "addGroups", -function (al) { -for (var sg, $sg = this.getSeqGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -al.addGroup (sg); -} -}, "jalview.datamodel.AlignmentI"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.FileParse"], "jalview.io.AlignFile", ["jalview.datamodel.Sequence", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Error", "java.util.ArrayList", "$.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.noSeqs = 0; +this.maxLength = 0; +this.seqs = null; +this.annotations = null; +this.seqGroups = null; +this.properties = null; +this.start = 0; +this.end = 0; +this.jvSuffix = true; +this.parseCalled = false; +this.newickStrings = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "AlignFile", jalview.io.FileParse); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.AlignFile, []); +this.initData (); +}); +Clazz.makeConstructor (c$, +function (inFile, type) { +this.construct (true, inFile, type); +}, "~S,~S"); +Clazz.makeConstructor (c$, +function (parseImmediately, inFile, type) { +Clazz.superConstructor (this, jalview.io.AlignFile, [inFile, type]); +this.initData (); +if (parseImmediately) { +this.doParse (); +}}, "~B,~S,~S"); +Clazz.makeConstructor (c$, +function (source) { +this.construct (true, source); +}, "jalview.io.FileParse"); +Clazz.makeConstructor (c$, +function (parseImmediately, source) { +Clazz.superConstructor (this, jalview.io.AlignFile, [source]); +this.initData (); +if (parseImmediately) { +this.doParse (); +}}, "~B,jalview.io.FileParse"); +Clazz.defineMethod (c$, "doParse", +function () { +if (this.parseCalled) { +throw new java.io.IOException ("Implementation error: Parser called twice for same data.\nNeed to call initData() again before parsing can be reattempted."); +}this.parseCalled = true; +this.parse (); +for (var i = 0, c = this.seqs.size (); i < c; i++) { +this.seqs.get (i).setIndex (i); +} +}); +Clazz.defineMethod (c$, "getSeqs", +function () { +return this.seqs; +}); +Clazz.defineMethod (c$, "getSeqGroups", +function () { +return this.seqGroups; +}); +Clazz.defineMethod (c$, "getSeqsAsArray", +function () { +var s = new Array (this.seqs.size ()); +for (var i = 0; i < this.seqs.size (); i++) { +s[i] = this.seqs.elementAt (i); +} +return s; +}); +Clazz.defineMethod (c$, "addAnnotations", +function (al) { +this.addProperties (al); +for (var i = 0; i < this.annotations.size (); i++) { +var an = this.annotations.elementAt (i); +an.validateRangeAndDisplay (); +al.addAnnotation (an); +} +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "addSeqGroups", +function (al) { +this.seqGroups = al.getGroups (); +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "addProperties", +function (al) { +if (this.properties != null && this.properties.size () > 0) { +var keys = this.properties.keys (); +var vals = this.properties.elements (); +while (keys.hasMoreElements ()) { +al.setProperty (keys.nextElement (), vals.nextElement ()); +} +}}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "setAlignmentProperty", +function (key, value) { +if (key == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_cannot_have_null_alignment")); +}if (value == null) { +return; +}if (this.properties == null) { +this.properties = new java.util.Hashtable (); +}this.properties.put (key, value); +}, "~O,~O"); +Clazz.defineMethod (c$, "getAlignmentProperty", +function (key) { +if (this.properties != null && key != null) { +return this.properties.get (key); +}return null; +}, "~O"); +Clazz.defineMethod (c$, "initData", +function () { +this.seqs = new java.util.Vector (); +this.annotations = new java.util.Vector (); +this.seqGroups = new java.util.ArrayList (); +this.parseCalled = false; +}); +Clazz.defineMethod (c$, "setSeqs", +function (s) { +this.seqs = new java.util.Vector (); +for (var i = 0; i < s.length; i++) { +this.seqs.addElement (s[i]); +} +}, "~A"); +Clazz.defineMethod (c$, "addJVSuffix", +function (b) { +this.jvSuffix = b; +}, "~B"); +Clazz.defineMethod (c$, "parseId", +function (id) { +var seq = null; +id = id.trim (); +var space = id.indexOf (" "); +if (space > -1) { +seq = new jalview.datamodel.Sequence (id.substring (0, space), ""); +seq.setDescription (id.substring (space + 1)); +} else { +seq = new jalview.datamodel.Sequence (id, ""); +}return seq; +}, "~S"); +Clazz.defineMethod (c$, "printId", +function (seq) { +return seq.getDisplayId (this.jvSuffix); +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "addNewickTree", +function (treeName, newickString) { +if (this.newickStrings == null) { +this.newickStrings = new java.util.Vector (); +}this.newickStrings.addElement ( Clazz.newArray (-1, [treeName, newickString])); +}, "~S,~S"); +Clazz.defineMethod (c$, "getTreeCount", +function () { +return this.newickStrings == null ? 0 : this.newickStrings.size (); +}); +Clazz.defineMethod (c$, "addGroups", +function (al) { +for (var sg, $sg = this.getSeqGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +al.addGroup (sg); +} +}, "jalview.datamodel.AlignmentI"); +}); diff --git a/bin/jalview/io/AlignmentProperties.js b/bin/jalview/io/AlignmentProperties.js index 0092589..6030bea 100644 --- a/bin/jalview/io/AlignmentProperties.js +++ b/bin/jalview/io/AlignmentProperties.js @@ -1,78 +1,78 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.AlignmentProperties", ["java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.alignment = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "AlignmentProperties"); -Clazz.makeConstructor (c$, -function (alignment) { -this.alignment = alignment; -}, "jalview.datamodel.AlignmentI"); -Clazz.defineMethod (c$, "writeProperties", -function (sb, html) { -var nl = html ? "
" : System.getProperty ("line.separator"); -var avg = 0; -var min = 2147483647; -var max = 0; -for (var i = 0; i < this.alignment.getHeight (); i++) { -var size = 1 + this.alignment.getSequenceAt (i).getEnd () - this.alignment.getSequenceAt (i).getStart (); -avg += size; -if (size > max) { -max = size; -}if (size < min) { -min = size; -}} -avg = avg / this.alignment.getHeight (); -sb.append (nl); -sb.append ("Sequences: " + this.alignment.getHeight ()); -sb.append (nl); -sb.append ("Minimum Sequence Length: " + min); -sb.append (nl); -sb.append ("Maximum Sequence Length: " + max); -sb.append (nl); -sb.append ("Average Length: " + Clazz.floatToInt (avg)); -if ((this.alignment).alignmentProperties != null) { -sb.append (nl); -sb.append (nl); -if (html) { -sb.append (""); -}var props = (this.alignment).alignmentProperties; -var en = props.keys (); -while (en.hasMoreElements ()) { -var key = en.nextElement ().toString (); -var vals = props.get (key).toString (); -if (html) { -var val = new StringBuffer (); -var pos = 0; -var npos; -do { -npos = vals.indexOf ("\n", pos); -if (npos == -1) { -val.append (vals.substring (pos)); -} else { -val.append (vals.substring (pos, npos)); -val.append ("
"); -}pos = npos + 1; -} while (npos != -1); -sb.append (""); -} else { -sb.append (nl + key + "\t" + vals); -}} -if (html) { -sb.append ("
" + key + "" + val + "
"); -}}}, "StringBuffer,~B"); -Clazz.defineMethod (c$, "formatAsString", -function () { -return this.formatReport (false); -}); -Clazz.defineMethod (c$, "formatReport", -function (html) { -var sb = new StringBuffer (); -this.writeProperties (sb, html); -return sb; -}, "~B"); -Clazz.defineMethod (c$, "formatAsHtml", -function () { -return this.formatReport (true); -}); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.AlignmentProperties", ["java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.alignment = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "AlignmentProperties"); +Clazz.makeConstructor (c$, +function (alignment) { +this.alignment = alignment; +}, "jalview.datamodel.AlignmentI"); +Clazz.defineMethod (c$, "writeProperties", +function (sb, html) { +var nl = html ? "
" : System.getProperty ("line.separator"); +var avg = 0; +var min = 2147483647; +var max = 0; +for (var i = 0; i < this.alignment.getHeight (); i++) { +var size = 1 + this.alignment.getSequenceAt (i).getEnd () - this.alignment.getSequenceAt (i).getStart (); +avg += size; +if (size > max) { +max = size; +}if (size < min) { +min = size; +}} +avg = avg / this.alignment.getHeight (); +sb.append (nl); +sb.append ("Sequences: " + this.alignment.getHeight ()); +sb.append (nl); +sb.append ("Minimum Sequence Length: " + min); +sb.append (nl); +sb.append ("Maximum Sequence Length: " + max); +sb.append (nl); +sb.append ("Average Length: " + Clazz.floatToInt (avg)); +if ((this.alignment).alignmentProperties != null) { +sb.append (nl); +sb.append (nl); +if (html) { +sb.append (""); +}var props = (this.alignment).alignmentProperties; +var en = props.keys (); +while (en.hasMoreElements ()) { +var key = en.nextElement ().toString (); +var vals = props.get (key).toString (); +if (html) { +var val = new StringBuffer (); +var pos = 0; +var npos; +do { +npos = vals.indexOf ("\n", pos); +if (npos == -1) { +val.append (vals.substring (pos)); +} else { +val.append (vals.substring (pos, npos)); +val.append ("
"); +}pos = npos + 1; +} while (npos != -1); +sb.append (""); +} else { +sb.append (nl + key + "\t" + vals); +}} +if (html) { +sb.append ("
" + key + "" + val + "
"); +}}}, "StringBuffer,~B"); +Clazz.defineMethod (c$, "formatAsString", +function () { +return this.formatReport (false); +}); +Clazz.defineMethod (c$, "formatReport", +function (html) { +var sb = new StringBuffer (); +this.writeProperties (sb, html); +return sb; +}, "~B"); +Clazz.defineMethod (c$, "formatAsHtml", +function () { +return this.formatReport (true); +}); +}); diff --git a/bin/jalview/io/AnnotationFile.class b/bin/jalview/io/AnnotationFile.class index 4aea77a..fd5b729 100644 Binary files a/bin/jalview/io/AnnotationFile.class and b/bin/jalview/io/AnnotationFile.class differ diff --git a/bin/jalview/io/AnnotationFile.js b/bin/jalview/io/AnnotationFile.js index 2aaf007..4c4c01e 100644 --- a/bin/jalview/io/AnnotationFile.js +++ b/bin/jalview/io/AnnotationFile.js @@ -1,1003 +1,1003 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.AnnotationFile", ["jalview.analysis.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.ColumnSelection", "$.GraphLine", "$.SequenceGroup", "jalview.io.AppletFormatAdapter", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Comparison", "$.Format", "java.awt.Color", "java.io.BufferedReader", "$.InputStreamReader", "$.StringReader", "java.lang.Boolean", "$.Float", "$.StringBuffer", "java.util.ArrayList", "$.BitSet", "$.Date", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.newline = null; -this.text = null; -if (!Clazz.isClassDefined ("jalview.io.AnnotationFile.ViewDef")) { -jalview.io.AnnotationFile.$AnnotationFile$ViewDef$ (); -} -this.refSeq = null; -this.refSeqId = null; -this.nlinesread = 0; -this.lastread = ""; -Clazz.instantialize (this, arguments); -}, jalview.io, "AnnotationFile"); -Clazz.prepareFields (c$, function () { -this.newline = System.getProperty ("line.separator"); -}); -Clazz.makeConstructor (c$, -function () { -this.init (); -}); -Clazz.defineMethod (c$, "setNewlineString", -function (nl) { -this.newline = nl; -this.init (); -}, "~S"); -Clazz.defineMethod (c$, "getNewlineString", -function () { -return this.newline; -}); -Clazz.defineMethod (c$, "init", -($fz = function () { -this.text = new StringBuffer ("JALVIEW_ANNOTATION" + this.newline + "# Created: " + new java.util.Date () + this.newline + this.newline); -this.refSeq = null; -this.refSeqId = null; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "printAnnotations", -function (annotations, list, properties) { -return this.printAnnotations (annotations, list, properties, null, null, null); -}, "~A,java.util.List,java.util.Hashtable"); -Clazz.defineMethod (c$, "printAnnotations", -function (annotations, list, properties, cs, al, view) { -if (view != null) { -if (view.viewname != null) { -this.text.append ("VIEW_DEF\t" + view.viewname + "\n"); -}if (list == null) { -list = view.visibleGroups; -}if (cs == null) { -cs = view.hiddencols; -}if (al == null) { -}}if (al != null && al.hasSeqrep ()) { -this.text.append ("VIEW_SETREF\t" + al.getSeqrep ().getName () + "\n"); -}if (cs != null && cs.hasHiddenColumns ()) { -this.text.append ("VIEW_HIDECOLS\t"); -var hc = cs.getHiddenColumns (); -var comma = false; -for (var r, $r = hc.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { -if (!comma) { -comma = true; -} else { -this.text.append (","); -}this.text.append (r[0]); -this.text.append ("-"); -this.text.append (r[1]); -} -this.text.append ("\n"); -}if (annotations != null) { -var oneColour = true; -var row; -var comma; -var refSeq = null; -var refGroup = null; -var colours = new StringBuffer (); -var graphLine = new StringBuffer (); -var rowprops = new StringBuffer (); -var graphGroup = new java.util.Hashtable (); -var graphGroup_refs = new java.util.Hashtable (); -var graphGroupSeen = new java.util.BitSet (); -var color; -for (var i = 0; i < annotations.length; i++) { -row = annotations[i]; -if (!row.visible && !row.hasScore () && !(row.graphGroup > -1 && graphGroupSeen.get (row.graphGroup))) { -continue; -}color = null; -oneColour = true; -this.writeSequence_Ref (refSeq, row.sequenceRef); -refSeq = row.sequenceRef; -this.writeGroup_Ref (refGroup, row.groupRef); -refGroup = row.groupRef; -var hasGlyphs = row.hasIcons; -var hasLabels = row.hasText; -var hasValues = row.$hasScore; -var hasText = false; -for (var j = 0; row.annotations != null && j < row.annotations.length && (!hasGlyphs || !hasLabels || !hasValues); j++) { -if (row.annotations[j] != null) { -hasLabels = new Boolean (hasLabels | (row.annotations[j].displayCharacter != null && row.annotations[j].displayCharacter.length > 0 && !row.annotations[j].displayCharacter.equals (" "))).valueOf (); -hasGlyphs = new Boolean (hasGlyphs | ((row.annotations[j].secondaryStructure).charCodeAt (0) != 0 && row.annotations[j].secondaryStructure != ' ')).valueOf (); -hasValues = new Boolean (hasValues | (!Float.isNaN (row.annotations[j].value))).valueOf (); -hasText = new Boolean (hasText | (row.annotations[j].description != null && row.annotations[j].description.length > 0)).valueOf (); -}} -if (row.graph == 0) { -this.text.append ("NO_GRAPH\t"); -hasValues = false; -} else { -if (row.graph == 1) { -this.text.append ("BAR_GRAPH\t"); -hasGlyphs = false; -} else if (row.graph == 2) { -hasGlyphs = false; -this.text.append ("LINE_GRAPH\t"); -}if (row.getThreshold () != null) { -graphLine.append ("GRAPHLINE\t"); -graphLine.append (row.label); -graphLine.append ("\t"); -graphLine.append (row.getThreshold ().value); -graphLine.append ("\t"); -graphLine.append (row.getThreshold ().label); -graphLine.append ("\t"); -graphLine.append (jalview.util.Format.getHexString (row.getThreshold ().colour)); -graphLine.append (this.newline); -}if (row.graphGroup > -1) { -graphGroupSeen.set (row.graphGroup); -var key = new Integer (row.graphGroup); -if (graphGroup.containsKey (key)) { -graphGroup.put (key, graphGroup.get (key) + "\t" + row.label); -} else { -graphGroup_refs.put (key, Clazz.newArray (-1, [refSeq, refGroup])); -graphGroup.put (key, row.label); -}}}this.text.append (row.label + "\t"); -if (row.description != null) { -this.text.append (row.description + "\t"); -}for (var j = 0; row.annotations != null && j < row.annotations.length; j++) { -if (refSeq != null && jalview.util.Comparison.isGap (refSeq.getCharAt (j))) { -continue; -}if (row.annotations[j] != null) { -comma = ""; -if (hasGlyphs) { -this.text.append (comma); -if (row.annotations[j].secondaryStructure != ' ') { -this.text.append (row.annotations[j].secondaryStructure); -}comma = ","; -}if (hasValues) { -if (!Float.isNaN (row.annotations[j].value)) { -this.text.append (comma + row.annotations[j].value); -} else { -System.err.println ("Skipping NaN - not valid value."); -this.text.append (comma + 0); -}comma = ","; -}if (hasLabels) { -if (row.annotations[j].displayCharacter != null && row.annotations[j].displayCharacter.length > 0 && !row.annotations[j].displayCharacter.equals (" ")) { -this.text.append (comma + row.annotations[j].displayCharacter); -comma = ","; -}}if (hasText) { -if (row.annotations[j].description != null && row.annotations[j].description.length > 0 && !row.annotations[j].description.equals (row.annotations[j].displayCharacter)) { -this.text.append (comma + row.annotations[j].description); -comma = ","; -}}if (color != null && !color.equals (row.annotations[j].colour)) { -oneColour = false; -}color = row.annotations[j].colour; -if (row.annotations[j].colour != null && row.annotations[j].colour !== java.awt.Color.black) { -this.text.append (comma + "[" + jalview.util.Format.getHexString (row.annotations[j].colour) + "]"); -comma = ","; -}}this.text.append ("|"); -} -if (row.hasScore ()) { -this.text.append ("\t" + row.score); -}this.text.append (this.newline); -if (color != null && color !== java.awt.Color.black && oneColour) { -colours.append ("COLOUR\t"); -colours.append (row.label); -colours.append ("\t"); -colours.append (jalview.util.Format.getHexString (color)); -colours.append (this.newline); -}if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels) { -rowprops.append ("ROWPROPERTIES\t"); -rowprops.append (row.label); -rowprops.append ("\tscaletofit="); -rowprops.append (row.scaleColLabel); -rowprops.append ("\tshowalllabs="); -rowprops.append (row.showAllColLabels); -rowprops.append ("\tcentrelabs="); -rowprops.append (row.centreColLabels); -rowprops.append (this.newline); -}if (graphLine.length () > 0) { -this.text.append (graphLine.toString ()); -graphLine.setLength (0); -}} -this.text.append (this.newline); -this.text.append (colours.toString ()); -if (graphGroup.size () > 0) { -var oldRefSeq = refSeq; -var oldRefGroup = refGroup; -for (var combine_statement, $combine_statement = graphGroup.entrySet ().iterator (); $combine_statement.hasNext () && ((combine_statement = $combine_statement.next ()) || true);) { -var seqRefAndGroup = graphGroup_refs.get (combine_statement.getKey ()); -this.writeSequence_Ref (refSeq, seqRefAndGroup[0]); -refSeq = seqRefAndGroup[0]; -this.writeGroup_Ref (refGroup, seqRefAndGroup[1]); -refGroup = seqRefAndGroup[1]; -this.text.append ("COMBINE\t"); -this.text.append (combine_statement.getValue ()); -this.text.append (this.newline); -} -this.writeSequence_Ref (refSeq, oldRefSeq); -refSeq = oldRefSeq; -this.writeGroup_Ref (refGroup, oldRefGroup); -refGroup = oldRefGroup; -}this.text.append (rowprops.toString ()); -}if (list != null) { -this.printGroups (list); -}if (properties != null) { -this.text.append (this.newline); -this.text.append (this.newline); -this.text.append ("ALIGNMENT"); -var en = properties.keys (); -while (en.hasMoreElements ()) { -var key = en.nextElement ().toString (); -this.text.append ("\t"); -this.text.append (key); -this.text.append ("="); -this.text.append (properties.get (key)); -} -}return this.text.toString (); -}, "~A,java.util.List,java.util.Hashtable,jalview.datamodel.ColumnSelection,jalview.datamodel.AlignmentI,jalview.io.AnnotationFile.ViewDef"); -Clazz.defineMethod (c$, "writeGroup_Ref", -($fz = function (refGroup, next_refGroup) { -if (next_refGroup == null) { -if (refGroup != null) { -this.text.append (this.newline); -this.text.append ("GROUP_REF\t"); -this.text.append ("ALIGNMENT"); -this.text.append (this.newline); -}return true; -} else { -if (refGroup == null || refGroup !== next_refGroup) { -this.text.append (this.newline); -this.text.append ("GROUP_REF\t"); -this.text.append (next_refGroup.getName ()); -this.text.append (this.newline); -return true; -}}return false; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceGroup,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "writeSequence_Ref", -($fz = function (refSeq, next_refSeq) { -if (next_refSeq == null) { -if (refSeq != null) { -this.text.append (this.newline); -this.text.append ("SEQUENCE_REF\t"); -this.text.append ("ALIGNMENT"); -this.text.append (this.newline); -return true; -}} else { -if (refSeq == null || refSeq !== next_refSeq) { -this.text.append (this.newline); -this.text.append ("SEQUENCE_REF\t"); -this.text.append (next_refSeq.getName ()); -this.text.append (this.newline); -return true; -}}return false; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "printGroups", -function (list) { -var seqrep = null; -for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (!sg.hasSeqrep ()) { -this.text.append ("SEQUENCE_GROUP\t" + sg.getName () + "\t" + (sg.getStartRes () + 1) + "\t" + (sg.getEndRes () + 1) + "\t" + "-1\t"); -seqrep = null; -} else { -seqrep = sg.getSeqrep (); -this.text.append ("SEQUENCE_REF\t"); -this.text.append (seqrep.getName ()); -this.text.append (this.newline); -this.text.append ("SEQUENCE_GROUP\t"); -this.text.append (sg.getName ()); -this.text.append ("\t"); -this.text.append ((seqrep.findPosition (sg.getStartRes ()))); -this.text.append ("\t"); -this.text.append ((seqrep.findPosition (sg.getEndRes ()))); -this.text.append ("\t"); -this.text.append ("-1\t"); -}for (var s = 0; s < sg.getSize (); s++) { -this.text.append (sg.getSequenceAt (s).getName ()); -this.text.append ("\t"); -} -this.text.append (this.newline); -this.text.append ("PROPERTIES\t"); -this.text.append (sg.getName ()); -this.text.append ("\t"); -if (sg.getDescription () != null) { -this.text.append ("description="); -this.text.append (sg.getDescription ()); -this.text.append ("\t"); -}if (sg.cs != null) { -this.text.append ("colour="); -this.text.append (jalview.schemes.ColourSchemeProperty.getColourName (sg.cs)); -this.text.append ("\t"); -if (sg.cs.getThreshold () != 0) { -this.text.append ("pidThreshold="); -this.text.append (sg.cs.getThreshold ()); -}if (sg.cs.conservationApplied ()) { -this.text.append ("consThreshold="); -this.text.append (sg.cs.getConservationInc ()); -this.text.append ("\t"); -}}this.text.append ("outlineColour="); -this.text.append (jalview.util.Format.getHexString (sg.getOutlineColour ())); -this.text.append ("\t"); -this.text.append ("displayBoxes="); -this.text.append (sg.getDisplayBoxes ()); -this.text.append ("\t"); -this.text.append ("displayText="); -this.text.append (sg.getDisplayText ()); -this.text.append ("\t"); -this.text.append ("colourText="); -this.text.append (sg.getColourText ()); -this.text.append ("\t"); -this.text.append ("showUnconserved="); -this.text.append (sg.getShowNonconserved ()); -this.text.append ("\t"); -if (sg.textColour !== java.awt.Color.black) { -this.text.append ("textCol1="); -this.text.append (jalview.util.Format.getHexString (sg.textColour)); -this.text.append ("\t"); -}if (sg.textColour2 !== java.awt.Color.white) { -this.text.append ("textCol2="); -this.text.append (jalview.util.Format.getHexString (sg.textColour2)); -this.text.append ("\t"); -}if (sg.thresholdTextColour != 0) { -this.text.append ("textColThreshold="); -this.text.append (sg.thresholdTextColour); -this.text.append ("\t"); -}if (sg.idColour != null) { -this.text.append ("idColour="); -this.text.append (jalview.util.Format.getHexString (sg.idColour)); -this.text.append ("\t"); -}if (sg.isHidereps ()) { -this.text.append ("hide=true\t"); -}if (sg.isHideCols ()) { -this.text.append ("hidecols=true\t"); -}if (seqrep != null) { -this.text.append (this.newline); -this.text.append ("SEQUENCE_REF"); -}this.text.append (this.newline); -this.text.append (this.newline); -} -}, "java.util.List"); -Clazz.defineMethod (c$, "annotateAlignmentView", -function (viewport, file, protocol) { -var colSel = viewport.getColumnSelection (); -if (colSel == null) { -colSel = new jalview.datamodel.ColumnSelection (); -}var rslt = this.readAnnotationFile (viewport.getAlignment (), colSel, file, protocol); -if (rslt && (colSel.hasSelectedColumns () || colSel.hasHiddenColumns ())) { -viewport.setColumnSelection (colSel); -}return rslt; -}, "jalview.api.AlignViewportI,~S,~S"); -Clazz.defineMethod (c$, "readAnnotationFile", -function (al, file, protocol) { -return this.readAnnotationFile (al, null, file, protocol); -}, "jalview.datamodel.AlignmentI,~S,~S"); -Clazz.defineMethod (c$, "readAnnotationFile", -function (al, colSel, file, protocol) { -var $in = null; -try { -if (protocol.equals (jalview.io.AppletFormatAdapter.FILE)) { -$in = jalview.jsdev.GenericFileAdapter.getReader (file, false); -} else if (protocol.equals (jalview.io.AppletFormatAdapter.URL)) { -$in = jalview.jsdev.GenericFileAdapter.getReader (file, true); -} else if (protocol.equals (jalview.io.AppletFormatAdapter.PASTE)) { -$in = new java.io.BufferedReader ( new java.io.StringReader (file)); -} else if (protocol.equals (jalview.io.AppletFormatAdapter.CLASSLOADER)) { -var is = this.getClass ().getResourceAsStream ("/" + file); -if (is != null) { -$in = new java.io.BufferedReader ( new java.io.InputStreamReader (is)); -}}if ($in != null) { -return this.parseAnnotationFrom (al, colSel, $in); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -System.out.println ("Problem reading annotation file: " + ex); -if (this.nlinesread > 0) { -System.out.println ("Last read line " + this.nlinesread + ": '" + this.lastread + "' (first 80 chars) ..."); -}return false; -} else { -throw ex; -} -} -return false; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,~S,~S"); -Clazz.defineMethod (c$, "parseAnnotationFrom", -function (al, colSel, $in) { -this.nlinesread = 0; -var combineAnnotation_calls = new java.util.ArrayList (); -var deferredAnnotation_calls = new java.util.ArrayList (); -var modified = false; -var groupRef = null; -var groupRefRows = new java.util.Hashtable (); -var autoAnnots = new java.util.Hashtable (); -{ -var line; -var label; -var description; -var token; -var graphStyle; -var index; -var refSeqIndex = 1; -var existingAnnotations = 0; -var overrideAutoAnnot = false; -if (al.getAlignmentAnnotation () != null) { -existingAnnotations = al.getAlignmentAnnotation ().length; -if (existingAnnotations > 0) { -var aa = al.getAlignmentAnnotation (); -for (var aai = 0; aai < aa.length; aai++) { -if (aa[aai].autoCalculated) { -autoAnnots.put (this.autoAnnotsKey (aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef == null ? null : aa[aai].groupRef.getName ())), new Integer (1)); -}} -}}var alWidth = al.getWidth (); -var st; -var annotations; -var annotation = null; -var jvAnnotationFile = false; -while ((line = $in.readLine ()) != null) { -this.nlinesread++; -this.lastread = String.instantialize (line); -if (line.indexOf ("#") == 0) { -continue; -}if (line.indexOf ("JALVIEW_ANNOTATION") > -1) { -jvAnnotationFile = true; -break; -}} -if (!jvAnnotationFile) { -$in.close (); -return false; -}while ((line = $in.readLine ()) != null) { -this.nlinesread++; -this.lastread = String.instantialize (line); -if (line.indexOf ("#") == 0 || line.indexOf ("JALVIEW_ANNOTATION") > -1 || line.length == 0) { -continue; -}st = new java.util.StringTokenizer (line, "\t"); -token = st.nextToken (); -if (token.equalsIgnoreCase ("COLOUR")) { -this.colourAnnotations (al, st.nextToken (), st.nextToken ()); -modified = true; -continue; -} else if (token.equalsIgnoreCase (jalview.io.AnnotationFile.COMBINE)) { -combineAnnotation_calls.add ( Clazz.newArray (-1, [st, this.refSeq, groupRef])); -modified = true; -continue; -} else if (token.equalsIgnoreCase ("ROWPROPERTIES")) { -this.addRowProperties (al, st); -modified = true; -continue; -} else if (token.equalsIgnoreCase (jalview.io.AnnotationFile.GRAPHLINE)) { -deferredAnnotation_calls.add ( Clazz.newArray (-1, [jalview.io.AnnotationFile.GRAPHLINE, st, this.refSeq, groupRef])); -modified = true; -continue; -} else if (token.equalsIgnoreCase ("SEQUENCE_REF")) { -if (st.hasMoreTokens ()) { -this.refSeq = al.findName (this.refSeqId = st.nextToken ()); -if (this.refSeq == null) { -this.refSeqId = null; -}try { -refSeqIndex = Integer.parseInt (st.nextToken ()); -if (refSeqIndex < 1) { -refSeqIndex = 1; -System.out.println ("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile"); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -refSeqIndex = 1; -} else { -throw ex; -} -} -} else { -this.refSeq = null; -this.refSeqId = null; -}continue; -} else if (token.equalsIgnoreCase ("GROUP_REF")) { -groupRef = null; -if (st.hasMoreTokens ()) { -groupRef = st.nextToken (); -if (groupRef.length < 1) { -groupRef = null; -} else { -if (groupRefRows.get (groupRef) == null) { -groupRefRows.put (groupRef, new java.util.Vector ()); -}}}continue; -} else if (token.equalsIgnoreCase ("SEQUENCE_GROUP")) { -this.addGroup (al, st); -modified = true; -continue; -} else if (token.equalsIgnoreCase ("PROPERTIES")) { -this.addProperties (al, st); -modified = true; -continue; -} else if (token.equalsIgnoreCase ("BELOW_ALIGNMENT")) { -this.setBelowAlignment (al, st); -modified = true; -continue; -} else if (token.equalsIgnoreCase ("ALIGNMENT")) { -this.addAlignmentDetails (al, st); -modified = true; -continue; -} else if (token.equalsIgnoreCase ("VIEW_SETREF")) { -if (this.refSeq != null) { -al.setSeqrep (this.refSeq); -}modified = true; -continue; -} else if (token.equalsIgnoreCase ("VIEW_HIDECOLS")) { -if (st.hasMoreTokens ()) { -if (colSel == null) { -colSel = new jalview.datamodel.ColumnSelection (); -}this.parseHideCols (colSel, st.nextToken ()); -}modified = true; -continue; -} else if (token.equalsIgnoreCase ("HIDE_INSERTIONS")) { -var sr = this.refSeq == null ? al.getSeqrep () : this.refSeq; -if (sr == null) { -sr = al.getSequenceAt (0); -}if (sr != null) { -if (colSel == null) { -System.err.println ("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: " + line); -} else { -colSel.hideInsertionsFor (sr); -}}modified = true; -continue; -}graphStyle = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString (token); -label = st.nextToken (); -index = 0; -annotations = new Array (alWidth); -description = null; -var score = NaN; -if (st.hasMoreTokens ()) { -line = st.nextToken (); -if (line.indexOf ("|") == -1) { -description = line; -if (st.hasMoreTokens ()) { -line = st.nextToken (); -}}if (st.hasMoreTokens ()) { -score = Float.$valueOf (st.nextToken ()).floatValue (); -}st = new java.util.StringTokenizer (line, "|", true); -var emptyColumn = true; -var onlyOneElement = (st.countTokens () == 1); -while (st.hasMoreElements () && index < alWidth) { -token = st.nextToken ().trim (); -if (onlyOneElement) { -try { -score = Float.$valueOf (token).floatValue (); -break; -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -}if (token.equals ("|")) { -if (emptyColumn) { -index++; -}emptyColumn = true; -} else { -annotations[index++] = this.parseAnnotation (token, graphStyle); -emptyColumn = false; -}} -}annotation = new jalview.datamodel.AlignmentAnnotation (label, description, (index == 0) ? null : annotations, 0, 0, graphStyle); -annotation.score = score; -if (!overrideAutoAnnot && autoAnnots.containsKey (this.autoAnnotsKey (annotation, this.refSeq, groupRef))) { -continue; -}if (this.refSeq != null) { -annotation.belowAlignment = false; -var referedSeq = this.refSeq; -do { -var ann = new jalview.datamodel.AlignmentAnnotation (annotation); -annotation.createSequenceMapping (referedSeq, refSeqIndex, false); -annotation.adjustForAlignment (); -referedSeq.addAlignmentAnnotation (annotation); -al.addAnnotation (annotation); -al.setAnnotationIndex (annotation, al.getAlignmentAnnotation ().length - existingAnnotations - 1); -if (groupRef != null) { -(groupRefRows.get (groupRef)).addElement (annotation); -}annotation = ann; -} while (this.refSeqId != null && (referedSeq = al.findName (referedSeq, this.refSeqId, true)) != null); -} else { -al.addAnnotation (annotation); -al.setAnnotationIndex (annotation, al.getAlignmentAnnotation ().length - existingAnnotations - 1); -if (groupRef != null) { -(groupRefRows.get (groupRef)).addElement (annotation); -}}modified = true; -} -var groupRefLookup = new java.util.Hashtable (); -var en = groupRefRows.keys (); -while (en.hasMoreElements ()) { -groupRef = en.nextElement (); -var matched = false; -for (var theGroup, $theGroup = al.getGroups ().iterator (); $theGroup.hasNext () && ((theGroup = $theGroup.next ()) || true);) { -if (theGroup.getName ().equals (groupRef)) { -if (matched) { -System.err.println ("Ignoring 1:many group reference mappings for group name '" + groupRef + "'"); -} else { -matched = true; -var rowset = groupRefRows.get (groupRef); -groupRefLookup.put (groupRef, theGroup); -if (rowset != null && rowset.size () > 0) { -var alan = null; -for (var elm = 0, elmSize = rowset.size (); elm < elmSize; elm++) { -alan = rowset.elementAt (elm); -alan.groupRef = theGroup; -} -}}}} -(groupRefRows.get (groupRef)).removeAllElements (); -} -for (var _deferred_args, $_deferred_args = deferredAnnotation_calls.iterator (); $_deferred_args.hasNext () && ((_deferred_args = $_deferred_args.next ()) || true);) { -if (_deferred_args[0] === jalview.io.AnnotationFile.GRAPHLINE) { -this.addLine (al, _deferred_args[1], _deferred_args[2], (_deferred_args[3] == null) ? null : groupRefLookup.get (_deferred_args[3])); -}} -var combinecount = 0; -for (var _combine_args, $_combine_args = combineAnnotation_calls.iterator (); $_combine_args.hasNext () && ((_combine_args = $_combine_args.next ()) || true);) { -this.combineAnnotations (al, ++combinecount, _combine_args[0], _combine_args[1], (_combine_args[2] == null) ? null : groupRefLookup.get (_combine_args[2])); -} -}return modified; -}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,java.io.BufferedReader"); -Clazz.defineMethod (c$, "parseHideCols", -($fz = function (colSel, nextToken) { -var inval = new java.util.StringTokenizer (nextToken, ","); -while (inval.hasMoreTokens ()) { -var range = inval.nextToken ().trim (); -var from; -var to = range.indexOf ("-"); -if (to == -1) { -from = to = Integer.parseInt (range); -if (from >= 0) { -colSel.hideColumns (from, to); -}} else { -from = Integer.parseInt (range.substring (0, to)); -if (to < range.length - 1) { -to = Integer.parseInt (range.substring (to + 1)); -} else { -to = from; -}if (from > 0 && to >= from) { -colSel.hideColumns (from, to); -}}} -}, $fz.isPrivate = true, $fz), "jalview.datamodel.ColumnSelection,~S"); -Clazz.defineMethod (c$, "autoAnnotsKey", -($fz = function (annotation, refSeq, groupRef) { -return annotation.graph + "\t" + annotation.label + "\t" + annotation.description + "\t" + (refSeq != null ? refSeq.getDisplayId (true) : ""); -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.SequenceI,~S"); -Clazz.defineMethod (c$, "parseAnnotation", -function (string, graphStyle) { -var hasSymbols = (graphStyle == 0); -var desc = null; -var displayChar = null; -var ss = ' '; -var value = 0; -var parsedValue = false; -var dcset = false; -var colour = null; -var i = string.indexOf ("["); -var j = string.indexOf ("]"); -if (i > -1 && j > -1) { -var ucs = new jalview.schemes.UserColourScheme (); -colour = ucs.getColourFromString (string.substring (i + 1, j)); -if (i > 0 && string.charAt (i - 1) == ',') { -i--; -}string = string.substring (0, i) + string.substring (j + 1); -}var st = new java.util.StringTokenizer (string, ",", true); -var token; -var seenContent = false; -var pass = 0; -while (st.hasMoreTokens ()) { -pass++; -token = st.nextToken ().trim (); -if (token.equals (",")) { -if (!seenContent && parsedValue && !dcset) { -dcset = true; -displayChar = " "; -}seenContent = false; -continue; -} else { -seenContent = true; -}if (!parsedValue) { -try { -displayChar = token; -value = new Float (token).floatValue (); -parsedValue = true; -continue; -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -} else { -if (token.length == 1) { -displayChar = token; -}}if (hasSymbols && (token.equals ("H") || token.equals ("E") || token.equals ("S") || token.equals (" "))) { -ss = token.charAt (0); -if (displayChar.equals (token.substring (0, 1))) { -displayChar = ""; -}} else if (desc == null || (parsedValue && pass > 2)) { -desc = token; -}} -if (displayChar != null && desc != null && desc.length == 1) { -if (displayChar.length > 1) { -var tmp = displayChar; -displayChar = desc; -desc = tmp; -} else { -if (displayChar.equals (desc)) { -desc = null; -}}}var anot = new jalview.datamodel.Annotation (displayChar, desc, ss, value); -anot.colour = colour; -return anot; -}, "~S,~N"); -Clazz.defineMethod (c$, "colourAnnotations", -function (al, label, colour) { -var ucs = new jalview.schemes.UserColourScheme (colour); -var annotations; -for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { -if (al.getAlignmentAnnotation ()[i].label.equalsIgnoreCase (label)) { -annotations = al.getAlignmentAnnotation ()[i].annotations; -for (var j = 0; j < annotations.length; j++) { -if (annotations[j] != null) { -annotations[j].colour = ucs.findColour ('A'); -}} -}} -}, "jalview.datamodel.AlignmentI,~S,~S"); -Clazz.defineMethod (c$, "combineAnnotations", -function (al, combineCount, st, seqRef, groupRef) { -var group = st.nextToken (); -var graphGroup = 0; -if (al.getAlignmentAnnotation () != null) { -for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { -var aa = al.getAlignmentAnnotation ()[i]; -if (aa.graphGroup > graphGroup) { -graphGroup = aa.graphGroup + 1; -}if (aa.sequenceRef === seqRef && aa.groupRef === groupRef && aa.label.equalsIgnoreCase (group)) { -if (aa.graphGroup > -1) { -graphGroup = aa.graphGroup; -} else { -if (graphGroup <= combineCount) { -graphGroup = combineCount + 1; -}aa.graphGroup = graphGroup; -}break; -}} -while (st.hasMoreTokens ()) { -group = st.nextToken (); -for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { -var aa = al.getAlignmentAnnotation ()[i]; -if (aa.sequenceRef === seqRef && aa.groupRef === groupRef && aa.label.equalsIgnoreCase (group)) { -aa.graphGroup = graphGroup; -break; -}} -} -} else { -System.err.println ("Couldn't combine annotations. None are added to alignment yet!"); -}}, "jalview.datamodel.AlignmentI,~N,java.util.StringTokenizer,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "addLine", -function (al, st, seqRef, groupRef) { -var group = st.nextToken (); -var annotation = null; -var alannot = al.getAlignmentAnnotation (); -var value = new Float (st.nextToken ()).floatValue (); -var label = st.hasMoreTokens () ? st.nextToken () : null; -var colour = null; -if (st.hasMoreTokens ()) { -var ucs = new jalview.schemes.UserColourScheme (st.nextToken ()); -colour = ucs.findColour ('A'); -}if (alannot != null) { -for (var i = 0; i < alannot.length; i++) { -if (alannot[i].label.equalsIgnoreCase (group) && (seqRef == null || alannot[i].sequenceRef === seqRef) && (groupRef == null || alannot[i].groupRef === groupRef)) { -alannot[i].setThreshold ( new jalview.datamodel.GraphLine (value, label, colour)); -}} -}if (annotation == null) { -return; -}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "addGroup", -function (al, st) { -var sg = new jalview.datamodel.SequenceGroup (); -sg.setName (st.nextToken ()); -var rng = ""; -try { -rng = st.nextToken (); -if (rng.length > 0 && !rng.startsWith ("*")) { -sg.setStartRes (Integer.parseInt (rng) - 1); -} else { -sg.setStartRes (0); -}rng = st.nextToken (); -if (rng.length > 0 && !rng.startsWith ("*")) { -sg.setEndRes (Integer.parseInt (rng) - 1); -} else { -sg.setEndRes (al.getWidth () - 1); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '" + rng + "' - assuming alignment width for group."); -sg.setStartRes (0); -sg.setEndRes (al.getWidth () - 1); -} else { -throw e; -} -} -var index = st.nextToken (); -if (index.equals ("-1")) { -while (st.hasMoreElements ()) { -sg.addSequence (al.findName (st.nextToken ()), false); -} -} else { -var st2 = new java.util.StringTokenizer (index, ","); -while (st2.hasMoreTokens ()) { -var tmp = st2.nextToken (); -if (tmp.equals ("*")) { -for (var i = 0; i < al.getHeight (); i++) { -sg.addSequence (al.getSequenceAt (i), false); -} -} else if (tmp.indexOf ("-") >= 0) { -var st3 = new java.util.StringTokenizer (tmp, "-"); -var start = (Integer.parseInt (st3.nextToken ())); -var end = (Integer.parseInt (st3.nextToken ())); -if (end > start) { -for (var i = start; i <= end; i++) { -sg.addSequence (al.getSequenceAt (i - 1), false); -} -}} else { -sg.addSequence (al.getSequenceAt (Integer.parseInt (tmp) - 1), false); -}} -}if (this.refSeq != null) { -sg.setStartRes (this.refSeq.findIndex (sg.getStartRes () + 1) - 1); -sg.setEndRes (this.refSeq.findIndex (sg.getEndRes () + 1) - 1); -sg.setSeqrep (this.refSeq); -}if (sg.getSize () > 0) { -al.addGroup (sg); -}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); -Clazz.defineMethod (c$, "addRowProperties", -function (al, st) { -var label = st.nextToken (); -var keyValue; -var key; -var value; -var scaletofit = false; -var centerlab = false; -var showalllabs = false; -while (st.hasMoreTokens ()) { -keyValue = st.nextToken (); -key = keyValue.substring (0, keyValue.indexOf ("=")); -value = keyValue.substring (keyValue.indexOf ("=") + 1); -if (key.equalsIgnoreCase ("scaletofit")) { -scaletofit = Boolean.$valueOf (value).booleanValue (); -}if (key.equalsIgnoreCase ("showalllabs")) { -showalllabs = Boolean.$valueOf (value).booleanValue (); -}if (key.equalsIgnoreCase ("centrelabs")) { -centerlab = Boolean.$valueOf (value).booleanValue (); -}var alr = al.getAlignmentAnnotation (); -if (alr != null) { -for (var i = 0; i < alr.length; i++) { -if (alr[i].label.equalsIgnoreCase (label)) { -alr[i].centreColLabels = centerlab; -alr[i].scaleColLabel = scaletofit; -alr[i].showAllColLabels = showalllabs; -}} -}} -}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); -Clazz.defineMethod (c$, "addProperties", -function (al, st) { -if (al.getGroups () == null) { -return; -}var name = st.nextToken (); -var sg = null; -for (var _sg, $_sg = al.getGroups ().iterator (); $_sg.hasNext () && ((_sg = $_sg.next ()) || true);) { -if ((sg = _sg).getName ().equals (name)) { -break; -} else { -sg = null; -}} -if (sg != null) { -var keyValue; -var key; -var value; -var def = sg.cs; -sg.cs = null; -while (st.hasMoreTokens ()) { -keyValue = st.nextToken (); -key = keyValue.substring (0, keyValue.indexOf ("=")); -value = keyValue.substring (keyValue.indexOf ("=") + 1); -if (key.equalsIgnoreCase ("description")) { -sg.setDescription (value); -} else if (key.equalsIgnoreCase ("colour")) { -sg.cs = jalview.schemes.ColourSchemeProperty.getColour (al, value); -} else if (key.equalsIgnoreCase ("pidThreshold")) { -sg.cs.setThreshold (Integer.parseInt (value), true); -} else if (key.equalsIgnoreCase ("consThreshold")) { -sg.cs.setConservationInc (Integer.parseInt (value)); -var c = new jalview.analysis.Conservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (null), sg.getStartRes (), sg.getEndRes () + 1); -c.calculate (); -c.verdict (false, 25); -sg.cs.setConservation (c); -} else if (key.equalsIgnoreCase ("outlineColour")) { -sg.setOutlineColour ( new jalview.schemes.UserColourScheme (value).findColour ('A')); -} else if (key.equalsIgnoreCase ("displayBoxes")) { -sg.setDisplayBoxes (Boolean.$valueOf (value).booleanValue ()); -} else if (key.equalsIgnoreCase ("showUnconserved")) { -sg.setShowNonconserved (Boolean.$valueOf (value).booleanValue ()); -} else if (key.equalsIgnoreCase ("displayText")) { -sg.setDisplayText (Boolean.$valueOf (value).booleanValue ()); -} else if (key.equalsIgnoreCase ("colourText")) { -sg.setColourText (Boolean.$valueOf (value).booleanValue ()); -} else if (key.equalsIgnoreCase ("textCol1")) { -sg.textColour = new jalview.schemes.UserColourScheme (value).findColour ('A'); -} else if (key.equalsIgnoreCase ("textCol2")) { -sg.textColour2 = new jalview.schemes.UserColourScheme (value).findColour ('A'); -} else if (key.equalsIgnoreCase ("textColThreshold")) { -sg.thresholdTextColour = Integer.parseInt (value); -} else if (key.equalsIgnoreCase ("idColour")) { -sg.setIdColour ((def = new jalview.schemes.UserColourScheme (value)).findColour ('A')); -} else if (key.equalsIgnoreCase ("hide")) { -sg.setHidereps (true); -} else if (key.equalsIgnoreCase ("hidecols")) { -sg.setHideCols (true); -}sg.recalcConservation (); -} -if (sg.cs == null) { -sg.cs = def; -}}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); -Clazz.defineMethod (c$, "setBelowAlignment", -function (al, st) { -var token; -var aa; -var ala = al.getAlignmentAnnotation (); -if (ala == null) { -System.err.print ("Warning - no annotation to set below for sequence associated annotation:"); -}while (st.hasMoreTokens ()) { -token = st.nextToken (); -if (ala == null) { -System.err.print (" " + token); -} else { -for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { -aa = al.getAlignmentAnnotation ()[i]; -if (aa.sequenceRef === this.refSeq && aa.label.equals (token)) { -aa.belowAlignment = true; -}} -}} -if (ala == null) { -System.err.print ("\n"); -}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); -Clazz.defineMethod (c$, "addAlignmentDetails", -function (al, st) { -var keyValue; -var key; -var value; -while (st.hasMoreTokens ()) { -keyValue = st.nextToken (); -key = keyValue.substring (0, keyValue.indexOf ("=")); -value = keyValue.substring (keyValue.indexOf ("=") + 1); -al.setProperty (key, value); -} -}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); -Clazz.defineMethod (c$, "printCSVAnnotations", -function (annotations) { -var sp = new StringBuffer (); -for (var i = 0; i < annotations.length; i++) { -var atos = annotations[i].toString (); -var p = 0; -do { -var cp = atos.indexOf ("\n", p); -sp.append (annotations[i].label); -sp.append (","); -if (cp > p) { -sp.append (atos.substring (p, cp + 1)); -} else { -sp.append (atos.substring (p)); -sp.append (this.newline); -}p = cp + 1; -} while (p > 0); -} -return sp.toString (); -}, "~A"); -Clazz.defineMethod (c$, "printAnnotationsForView", -function (viewport) { -return this.printAnnotations (viewport.isShowAnnotation () ? viewport.getAlignment ().getAlignmentAnnotation () : null, viewport.getAlignment ().getGroups (), viewport.getAlignment ().getProperties (), viewport.getColumnSelection (), viewport.getAlignment (), null); -}, "jalview.api.AlignViewportI"); -Clazz.defineMethod (c$, "printAnnotationsForAlignment", -function (al) { -return this.printAnnotations (al.getAlignmentAnnotation (), al.getGroups (), al.getProperties (), null, al, null); -}, "jalview.datamodel.AlignmentI"); -c$.$AnnotationFile$ViewDef$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.viewname = null; -this.hidseqs = null; -this.hiddencols = null; -this.visibleGroups = null; -this.hiddenRepSeqs = null; -Clazz.instantialize (this, arguments); -}, jalview.io.AnnotationFile, "ViewDef"); -Clazz.makeConstructor (c$, -function (a, b, c, d) { -this.viewname = a; -this.hidseqs = b; -this.hiddencols = c; -this.hiddenRepSeqs = d; -}, "~S,jalview.datamodel.HiddenSequences,jalview.datamodel.ColumnSelection,java.util.Hashtable"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"GRAPHLINE", "GRAPHLINE", -"COMBINE", "COMBINE"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.AnnotationFile", ["jalview.analysis.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.ColumnSelection", "$.GraphLine", "$.SequenceGroup", "jalview.io.AppletFormatAdapter", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Comparison", "$.Format", "java.awt.Color", "java.io.BufferedReader", "$.InputStreamReader", "$.StringReader", "java.lang.Boolean", "$.Float", "$.StringBuffer", "java.util.ArrayList", "$.BitSet", "$.Date", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.newline = null; +this.text = null; +if (!Clazz.isClassDefined ("jalview.io.AnnotationFile.ViewDef")) { +jalview.io.AnnotationFile.$AnnotationFile$ViewDef$ (); +} +this.refSeq = null; +this.refSeqId = null; +this.nlinesread = 0; +this.lastread = ""; +Clazz.instantialize (this, arguments); +}, jalview.io, "AnnotationFile"); +Clazz.prepareFields (c$, function () { +this.newline = System.getProperty ("line.separator"); +}); +Clazz.makeConstructor (c$, +function () { +this.init (); +}); +Clazz.defineMethod (c$, "setNewlineString", +function (nl) { +this.newline = nl; +this.init (); +}, "~S"); +Clazz.defineMethod (c$, "getNewlineString", +function () { +return this.newline; +}); +Clazz.defineMethod (c$, "init", +($fz = function () { +this.text = new StringBuffer ("JALVIEW_ANNOTATION" + this.newline + "# Created: " + new java.util.Date () + this.newline + this.newline); +this.refSeq = null; +this.refSeqId = null; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "printAnnotations", +function (annotations, list, properties) { +return this.printAnnotations (annotations, list, properties, null, null, null); +}, "~A,java.util.List,java.util.Hashtable"); +Clazz.defineMethod (c$, "printAnnotations", +function (annotations, list, properties, cs, al, view) { +if (view != null) { +if (view.viewname != null) { +this.text.append ("VIEW_DEF\t" + view.viewname + "\n"); +}if (list == null) { +list = view.visibleGroups; +}if (cs == null) { +cs = view.hiddencols; +}if (al == null) { +}}if (al != null && al.hasSeqrep ()) { +this.text.append ("VIEW_SETREF\t" + al.getSeqrep ().getName () + "\n"); +}if (cs != null && cs.hasHiddenColumns ()) { +this.text.append ("VIEW_HIDECOLS\t"); +var hc = cs.getHiddenColumns (); +var comma = false; +for (var r, $r = hc.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { +if (!comma) { +comma = true; +} else { +this.text.append (","); +}this.text.append ("" + r[0]); +this.text.append ("-"); +this.text.append ("" + r[1]); +} +this.text.append ("\n"); +}if (annotations != null) { +var oneColour = true; +var row; +var comma; +var refSeq = null; +var refGroup = null; +var colours = new StringBuffer (); +var graphLine = new StringBuffer (); +var rowprops = new StringBuffer (); +var graphGroup = new java.util.Hashtable (); +var graphGroup_refs = new java.util.Hashtable (); +var graphGroupSeen = new java.util.BitSet (); +var color; +for (var i = 0; i < annotations.length; i++) { +row = annotations[i]; +if (!row.visible && !row.hasScore () && !(row.graphGroup > -1 && graphGroupSeen.get (row.graphGroup))) { +continue; +}color = null; +oneColour = true; +this.writeSequence_Ref (refSeq, row.sequenceRef); +refSeq = row.sequenceRef; +this.writeGroup_Ref (refGroup, row.groupRef); +refGroup = row.groupRef; +var hasGlyphs = row.hasIcons; +var hasLabels = row.hasText; +var hasValues = row.$hasScore; +var hasText = false; +for (var j = 0; row.annotations != null && j < row.annotations.length && (!hasGlyphs || !hasLabels || !hasValues); j++) { +if (row.annotations[j] != null) { +hasLabels = new Boolean (hasLabels | (row.annotations[j].displayCharacter != null && row.annotations[j].displayCharacter.length > 0 && !row.annotations[j].displayCharacter.equals (" "))).valueOf (); +hasGlyphs = new Boolean (hasGlyphs | ((row.annotations[j].secondaryStructure).charCodeAt (0) != 0 && row.annotations[j].secondaryStructure != ' ')).valueOf (); +hasValues = new Boolean (hasValues | (!Float.isNaN (row.annotations[j].value))).valueOf (); +hasText = new Boolean (hasText | (row.annotations[j].description != null && row.annotations[j].description.length > 0)).valueOf (); +}} +if (row.graph == 0) { +this.text.append ("NO_GRAPH\t"); +hasValues = false; +} else { +if (row.graph == 1) { +this.text.append ("BAR_GRAPH\t"); +hasGlyphs = false; +} else if (row.graph == 2) { +hasGlyphs = false; +this.text.append ("LINE_GRAPH\t"); +}if (row.getThreshold () != null) { +graphLine.append ("GRAPHLINE\t"); +graphLine.append (row.label); +graphLine.append ("\t"); +graphLine.append (row.getThreshold ().value); +graphLine.append ("\t"); +graphLine.append (row.getThreshold ().label); +graphLine.append ("\t"); +graphLine.append (jalview.util.Format.getHexString (row.getThreshold ().colour)); +graphLine.append (this.newline); +}if (row.graphGroup > -1) { +graphGroupSeen.set (row.graphGroup); +var key = new Integer (row.graphGroup); +if (graphGroup.containsKey (key)) { +graphGroup.put (key, graphGroup.get (key) + "\t" + row.label); +} else { +graphGroup_refs.put (key, Clazz.newArray (-1, [refSeq, refGroup])); +graphGroup.put (key, row.label); +}}}this.text.append (row.label + "\t"); +if (row.description != null) { +this.text.append (row.description + "\t"); +}for (var j = 0; row.annotations != null && j < row.annotations.length; j++) { +if (refSeq != null && jalview.util.Comparison.isGap (refSeq.getCharAt (j))) { +continue; +}if (row.annotations[j] != null) { +comma = ""; +if (hasGlyphs) { +this.text.append (comma); +if (row.annotations[j].secondaryStructure != ' ') { +this.text.append (row.annotations[j].secondaryStructure); +}comma = ","; +}if (hasValues) { +if (!Float.isNaN (row.annotations[j].value)) { +this.text.append (comma + row.annotations[j].value); +} else { +System.err.println ("Skipping NaN - not valid value."); +this.text.append (comma + 0); +}comma = ","; +}if (hasLabels) { +if (row.annotations[j].displayCharacter != null && row.annotations[j].displayCharacter.length > 0 && !row.annotations[j].displayCharacter.equals (" ")) { +this.text.append (comma + row.annotations[j].displayCharacter); +comma = ","; +}}if (hasText) { +if (row.annotations[j].description != null && row.annotations[j].description.length > 0 && !row.annotations[j].description.equals (row.annotations[j].displayCharacter)) { +this.text.append (comma + row.annotations[j].description); +comma = ","; +}}if (color != null && !color.equals (row.annotations[j].colour)) { +oneColour = false; +}color = row.annotations[j].colour; +if (row.annotations[j].colour != null && row.annotations[j].colour !== java.awt.Color.black) { +this.text.append (comma + "[" + jalview.util.Format.getHexString (row.annotations[j].colour) + "]"); +comma = ","; +}}this.text.append ("|"); +} +if (row.hasScore ()) { +this.text.append ("\t" + row.score); +}this.text.append (this.newline); +if (color != null && color !== java.awt.Color.black && oneColour) { +colours.append ("COLOUR\t"); +colours.append (row.label); +colours.append ("\t"); +colours.append (jalview.util.Format.getHexString (color)); +colours.append (this.newline); +}if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels) { +rowprops.append ("ROWPROPERTIES\t"); +rowprops.append (row.label); +rowprops.append ("\tscaletofit="); +rowprops.append (row.scaleColLabel); +rowprops.append ("\tshowalllabs="); +rowprops.append (row.showAllColLabels); +rowprops.append ("\tcentrelabs="); +rowprops.append (row.centreColLabels); +rowprops.append (this.newline); +}if (graphLine.length () > 0) { +this.text.append (graphLine.toString ()); +graphLine.setLength (0); +}} +this.text.append (this.newline); +this.text.append (colours.toString ()); +if (graphGroup.size () > 0) { +var oldRefSeq = refSeq; +var oldRefGroup = refGroup; +for (var combine_statement, $combine_statement = graphGroup.entrySet ().iterator (); $combine_statement.hasNext () && ((combine_statement = $combine_statement.next ()) || true);) { +var seqRefAndGroup = graphGroup_refs.get (combine_statement.getKey ()); +this.writeSequence_Ref (refSeq, seqRefAndGroup[0]); +refSeq = seqRefAndGroup[0]; +this.writeGroup_Ref (refGroup, seqRefAndGroup[1]); +refGroup = seqRefAndGroup[1]; +this.text.append ("COMBINE\t"); +this.text.append (combine_statement.getValue ()); +this.text.append (this.newline); +} +this.writeSequence_Ref (refSeq, oldRefSeq); +refSeq = oldRefSeq; +this.writeGroup_Ref (refGroup, oldRefGroup); +refGroup = oldRefGroup; +}this.text.append (rowprops.toString ()); +}if (list != null) { +this.printGroups (list); +}if (properties != null) { +this.text.append (this.newline); +this.text.append (this.newline); +this.text.append ("ALIGNMENT"); +var en = properties.keys (); +while (en.hasMoreElements ()) { +var key = en.nextElement ().toString (); +this.text.append ("\t"); +this.text.append (key); +this.text.append ("="); +this.text.append (properties.get (key)); +} +}return this.text.toString (); +}, "~A,java.util.List,java.util.Hashtable,jalview.datamodel.ColumnSelection,jalview.datamodel.AlignmentI,jalview.io.AnnotationFile.ViewDef"); +Clazz.defineMethod (c$, "writeGroup_Ref", +($fz = function (refGroup, next_refGroup) { +if (next_refGroup == null) { +if (refGroup != null) { +this.text.append (this.newline); +this.text.append ("GROUP_REF\t"); +this.text.append ("ALIGNMENT"); +this.text.append (this.newline); +}return true; +} else { +if (refGroup == null || refGroup !== next_refGroup) { +this.text.append (this.newline); +this.text.append ("GROUP_REF\t"); +this.text.append (next_refGroup.getName ()); +this.text.append (this.newline); +return true; +}}return false; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceGroup,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "writeSequence_Ref", +($fz = function (refSeq, next_refSeq) { +if (next_refSeq == null) { +if (refSeq != null) { +this.text.append (this.newline); +this.text.append ("SEQUENCE_REF\t"); +this.text.append ("ALIGNMENT"); +this.text.append (this.newline); +return true; +}} else { +if (refSeq == null || refSeq !== next_refSeq) { +this.text.append (this.newline); +this.text.append ("SEQUENCE_REF\t"); +this.text.append (next_refSeq.getName ()); +this.text.append (this.newline); +return true; +}}return false; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "printGroups", +function (list) { +var seqrep = null; +for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (!sg.hasSeqrep ()) { +this.text.append ("SEQUENCE_GROUP\t" + sg.getName () + "\t" + (sg.getStartRes () + 1) + "\t" + (sg.getEndRes () + 1) + "\t" + "-1\t"); +seqrep = null; +} else { +seqrep = sg.getSeqrep (); +this.text.append ("SEQUENCE_REF\t"); +this.text.append (seqrep.getName ()); +this.text.append (this.newline); +this.text.append ("SEQUENCE_GROUP\t"); +this.text.append (sg.getName ()); +this.text.append ("\t"); +this.text.append ("" + (seqrep.findPosition (sg.getStartRes ()))); +this.text.append ("\t"); +this.text.append ((seqrep.findPosition (sg.getEndRes ()))); +this.text.append ("\t"); +this.text.append ("-1\t"); +}for (var s = 0; s < sg.getSize (); s++) { +this.text.append (sg.getSequenceAt (s).getName ()); +this.text.append ("\t"); +} +this.text.append (this.newline); +this.text.append ("PROPERTIES\t"); +this.text.append (sg.getName ()); +this.text.append ("\t"); +if (sg.getDescription () != null) { +this.text.append ("description="); +this.text.append (sg.getDescription ()); +this.text.append ("\t"); +}if (sg.cs != null) { +this.text.append ("colour="); +this.text.append (jalview.schemes.ColourSchemeProperty.getColourName (sg.cs)); +this.text.append ("\t"); +if (sg.cs.getThreshold () != 0) { +this.text.append ("pidThreshold="); +this.text.append (sg.cs.getThreshold ()); +}if (sg.cs.conservationApplied ()) { +this.text.append ("consThreshold="); +this.text.append (sg.cs.getConservationInc ()); +this.text.append ("\t"); +}}this.text.append ("outlineColour="); +this.text.append (jalview.util.Format.getHexString (sg.getOutlineColour ())); +this.text.append ("\t"); +this.text.append ("displayBoxes="); +this.text.append (sg.getDisplayBoxes ()); +this.text.append ("\t"); +this.text.append ("displayText="); +this.text.append (sg.getDisplayText ()); +this.text.append ("\t"); +this.text.append ("colourText="); +this.text.append (sg.getColourText ()); +this.text.append ("\t"); +this.text.append ("showUnconserved="); +this.text.append (sg.getShowNonconserved ()); +this.text.append ("\t"); +if (sg.textColour !== java.awt.Color.black) { +this.text.append ("textCol1="); +this.text.append (jalview.util.Format.getHexString (sg.textColour)); +this.text.append ("\t"); +}if (sg.textColour2 !== java.awt.Color.white) { +this.text.append ("textCol2="); +this.text.append (jalview.util.Format.getHexString (sg.textColour2)); +this.text.append ("\t"); +}if (sg.thresholdTextColour != 0) { +this.text.append ("textColThreshold="); +this.text.append (sg.thresholdTextColour); +this.text.append ("\t"); +}if (sg.idColour != null) { +this.text.append ("idColour="); +this.text.append (jalview.util.Format.getHexString (sg.idColour)); +this.text.append ("\t"); +}if (sg.isHidereps ()) { +this.text.append ("hide=true\t"); +}if (sg.isHideCols ()) { +this.text.append ("hidecols=true\t"); +}if (seqrep != null) { +this.text.append (this.newline); +this.text.append ("SEQUENCE_REF"); +}this.text.append (this.newline); +this.text.append (this.newline); +} +}, "java.util.List"); +Clazz.defineMethod (c$, "annotateAlignmentView", +function (viewport, file, protocol) { +var colSel = viewport.getColumnSelection (); +if (colSel == null) { +colSel = new jalview.datamodel.ColumnSelection (); +}var rslt = this.readAnnotationFile (viewport.getAlignment (), colSel, file, protocol); +if (rslt && (colSel.hasSelectedColumns () || colSel.hasHiddenColumns ())) { +viewport.setColumnSelection (colSel); +}return rslt; +}, "jalview.api.AlignViewportI,~S,~S"); +Clazz.defineMethod (c$, "readAnnotationFile", +function (al, file, protocol) { +return this.readAnnotationFile (al, null, file, protocol); +}, "jalview.datamodel.AlignmentI,~S,~S"); +Clazz.defineMethod (c$, "readAnnotationFile", +function (al, colSel, file, protocol) { +var $in = null; +try { +if (protocol.equals (jalview.io.AppletFormatAdapter.FILE)) { +$in = jalview.jsdev.GenericFileAdapter.getReader (file, false); +} else if (protocol.equals (jalview.io.AppletFormatAdapter.URL)) { +$in = jalview.jsdev.GenericFileAdapter.getReader (file, true); +} else if (protocol.equals (jalview.io.AppletFormatAdapter.PASTE)) { +$in = new java.io.BufferedReader ( new java.io.StringReader (file)); +} else if (protocol.equals (jalview.io.AppletFormatAdapter.CLASSLOADER)) { +var is = this.getClass ().getResourceAsStream ("/" + file); +if (is != null) { +$in = new java.io.BufferedReader ( new java.io.InputStreamReader (is)); +}}if ($in != null) { +return this.parseAnnotationFrom (al, colSel, $in); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +System.out.println ("Problem reading annotation file: " + ex); +if (this.nlinesread > 0) { +System.out.println ("Last read line " + this.nlinesread + ": '" + this.lastread + "' (first 80 chars) ..."); +}return false; +} else { +throw ex; +} +} +return false; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,~S,~S"); +Clazz.defineMethod (c$, "parseAnnotationFrom", +function (al, colSel, $in) { +this.nlinesread = 0; +var combineAnnotation_calls = new java.util.ArrayList (); +var deferredAnnotation_calls = new java.util.ArrayList (); +var modified = false; +var groupRef = null; +var groupRefRows = new java.util.Hashtable (); +var autoAnnots = new java.util.Hashtable (); +{ +var line; +var label; +var description; +var token; +var graphStyle; +var index; +var refSeqIndex = 1; +var existingAnnotations = 0; +var overrideAutoAnnot = false; +if (al.getAlignmentAnnotation () != null) { +existingAnnotations = al.getAlignmentAnnotation ().length; +if (existingAnnotations > 0) { +var aa = al.getAlignmentAnnotation (); +for (var aai = 0; aai < aa.length; aai++) { +if (aa[aai].autoCalculated) { +autoAnnots.put (this.autoAnnotsKey (aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef == null ? null : aa[aai].groupRef.getName ())), new Integer (1)); +}} +}}var alWidth = al.getWidth (); +var st; +var annotations; +var annotation = null; +var jvAnnotationFile = false; +while ((line = $in.readLine ()) != null) { +this.nlinesread++; +this.lastread = String.instantialize (line); +if (line.indexOf ("#") == 0) { +continue; +}if (line.indexOf ("JALVIEW_ANNOTATION") > -1) { +jvAnnotationFile = true; +break; +}} +if (!jvAnnotationFile) { +$in.close (); +return false; +}while ((line = $in.readLine ()) != null) { +this.nlinesread++; +this.lastread = String.instantialize (line); +if (line.indexOf ("#") == 0 || line.indexOf ("JALVIEW_ANNOTATION") > -1 || line.length == 0) { +continue; +}st = new java.util.StringTokenizer (line, "\t"); +token = st.nextToken (); +if (token.equalsIgnoreCase ("COLOUR")) { +this.colourAnnotations (al, st.nextToken (), st.nextToken ()); +modified = true; +continue; +} else if (token.equalsIgnoreCase (jalview.io.AnnotationFile.COMBINE)) { +combineAnnotation_calls.add ( Clazz.newArray (-1, [st, this.refSeq, groupRef])); +modified = true; +continue; +} else if (token.equalsIgnoreCase ("ROWPROPERTIES")) { +this.addRowProperties (al, st); +modified = true; +continue; +} else if (token.equalsIgnoreCase (jalview.io.AnnotationFile.GRAPHLINE)) { +deferredAnnotation_calls.add ( Clazz.newArray (-1, [jalview.io.AnnotationFile.GRAPHLINE, st, this.refSeq, groupRef])); +modified = true; +continue; +} else if (token.equalsIgnoreCase ("SEQUENCE_REF")) { +if (st.hasMoreTokens ()) { +this.refSeq = al.findName (this.refSeqId = st.nextToken ()); +if (this.refSeq == null) { +this.refSeqId = null; +}try { +refSeqIndex = Integer.parseInt (st.nextToken ()); +if (refSeqIndex < 1) { +refSeqIndex = 1; +System.out.println ("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile"); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +refSeqIndex = 1; +} else { +throw ex; +} +} +} else { +this.refSeq = null; +this.refSeqId = null; +}continue; +} else if (token.equalsIgnoreCase ("GROUP_REF")) { +groupRef = null; +if (st.hasMoreTokens ()) { +groupRef = st.nextToken (); +if (groupRef.length < 1) { +groupRef = null; +} else { +if (groupRefRows.get (groupRef) == null) { +groupRefRows.put (groupRef, new java.util.Vector ()); +}}}continue; +} else if (token.equalsIgnoreCase ("SEQUENCE_GROUP")) { +this.addGroup (al, st); +modified = true; +continue; +} else if (token.equalsIgnoreCase ("PROPERTIES")) { +this.addProperties (al, st); +modified = true; +continue; +} else if (token.equalsIgnoreCase ("BELOW_ALIGNMENT")) { +this.setBelowAlignment (al, st); +modified = true; +continue; +} else if (token.equalsIgnoreCase ("ALIGNMENT")) { +this.addAlignmentDetails (al, st); +modified = true; +continue; +} else if (token.equalsIgnoreCase ("VIEW_SETREF")) { +if (this.refSeq != null) { +al.setSeqrep (this.refSeq); +}modified = true; +continue; +} else if (token.equalsIgnoreCase ("VIEW_HIDECOLS")) { +if (st.hasMoreTokens ()) { +if (colSel == null) { +colSel = new jalview.datamodel.ColumnSelection (); +}this.parseHideCols (colSel, st.nextToken ()); +}modified = true; +continue; +} else if (token.equalsIgnoreCase ("HIDE_INSERTIONS")) { +var sr = this.refSeq == null ? al.getSeqrep () : this.refSeq; +if (sr == null) { +sr = al.getSequenceAt (0); +}if (sr != null) { +if (colSel == null) { +System.err.println ("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: " + line); +} else { +colSel.hideInsertionsFor (sr); +}}modified = true; +continue; +}graphStyle = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString (token); +label = st.nextToken (); +index = 0; +annotations = new Array (alWidth); +description = null; +var score = NaN; +if (st.hasMoreTokens ()) { +line = st.nextToken (); +if (line.indexOf ("|") == -1) { +description = line; +if (st.hasMoreTokens ()) { +line = st.nextToken (); +}}if (st.hasMoreTokens ()) { +score = Float.$valueOf (st.nextToken ()).floatValue (); +}st = new java.util.StringTokenizer (line, "|", true); +var emptyColumn = true; +var onlyOneElement = (st.countTokens () == 1); +while (st.hasMoreElements () && index < alWidth) { +token = st.nextToken ().trim (); +if (onlyOneElement) { +try { +score = Float.$valueOf (token).floatValue (); +break; +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +}if (token.equals ("|")) { +if (emptyColumn) { +index++; +}emptyColumn = true; +} else { +annotations[index++] = this.parseAnnotation (token, graphStyle); +emptyColumn = false; +}} +}annotation = new jalview.datamodel.AlignmentAnnotation (label, description, (index == 0) ? null : annotations, 0, 0, graphStyle); +annotation.score = score; +if (!overrideAutoAnnot && autoAnnots.containsKey (this.autoAnnotsKey (annotation, this.refSeq, groupRef))) { +continue; +}if (this.refSeq != null) { +annotation.belowAlignment = false; +var referedSeq = this.refSeq; +do { +var ann = new jalview.datamodel.AlignmentAnnotation (annotation); +annotation.createSequenceMapping (referedSeq, refSeqIndex, false); +annotation.adjustForAlignment (); +referedSeq.addAlignmentAnnotation (annotation); +al.addAnnotation (annotation); +al.setAnnotationIndex (annotation, al.getAlignmentAnnotation ().length - existingAnnotations - 1); +if (groupRef != null) { +(groupRefRows.get (groupRef)).addElement (annotation); +}annotation = ann; +} while (this.refSeqId != null && (referedSeq = al.findName (referedSeq, this.refSeqId, true)) != null); +} else { +al.addAnnotation (annotation); +al.setAnnotationIndex (annotation, al.getAlignmentAnnotation ().length - existingAnnotations - 1); +if (groupRef != null) { +(groupRefRows.get (groupRef)).addElement (annotation); +}}modified = true; +} +var groupRefLookup = new java.util.Hashtable (); +var en = groupRefRows.keys (); +while (en.hasMoreElements ()) { +groupRef = en.nextElement (); +var matched = false; +for (var theGroup, $theGroup = al.getGroups ().iterator (); $theGroup.hasNext () && ((theGroup = $theGroup.next ()) || true);) { +if (theGroup.getName ().equals (groupRef)) { +if (matched) { +System.err.println ("Ignoring 1:many group reference mappings for group name '" + groupRef + "'"); +} else { +matched = true; +var rowset = groupRefRows.get (groupRef); +groupRefLookup.put (groupRef, theGroup); +if (rowset != null && rowset.size () > 0) { +var alan = null; +for (var elm = 0, elmSize = rowset.size (); elm < elmSize; elm++) { +alan = rowset.elementAt (elm); +alan.groupRef = theGroup; +} +}}}} +(groupRefRows.get (groupRef)).removeAllElements (); +} +for (var _deferred_args, $_deferred_args = deferredAnnotation_calls.iterator (); $_deferred_args.hasNext () && ((_deferred_args = $_deferred_args.next ()) || true);) { +if (_deferred_args[0] === jalview.io.AnnotationFile.GRAPHLINE) { +this.addLine (al, _deferred_args[1], _deferred_args[2], (_deferred_args[3] == null) ? null : groupRefLookup.get (_deferred_args[3])); +}} +var combinecount = 0; +for (var _combine_args, $_combine_args = combineAnnotation_calls.iterator (); $_combine_args.hasNext () && ((_combine_args = $_combine_args.next ()) || true);) { +this.combineAnnotations (al, ++combinecount, _combine_args[0], _combine_args[1], (_combine_args[2] == null) ? null : groupRefLookup.get (_combine_args[2])); +} +}return modified; +}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,java.io.BufferedReader"); +Clazz.defineMethod (c$, "parseHideCols", +($fz = function (colSel, nextToken) { +var inval = new java.util.StringTokenizer (nextToken, ","); +while (inval.hasMoreTokens ()) { +var range = inval.nextToken ().trim (); +var from; +var to = range.indexOf ("-"); +if (to == -1) { +from = to = Integer.parseInt (range); +if (from >= 0) { +colSel.hideColumns (from, to); +}} else { +from = Integer.parseInt (range.substring (0, to)); +if (to < range.length - 1) { +to = Integer.parseInt (range.substring (to + 1)); +} else { +to = from; +}if (from > 0 && to >= from) { +colSel.hideColumns (from, to); +}}} +}, $fz.isPrivate = true, $fz), "jalview.datamodel.ColumnSelection,~S"); +Clazz.defineMethod (c$, "autoAnnotsKey", +($fz = function (annotation, refSeq, groupRef) { +return annotation.graph + "\t" + annotation.label + "\t" + annotation.description + "\t" + (refSeq != null ? refSeq.getDisplayId (true) : ""); +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,jalview.datamodel.SequenceI,~S"); +Clazz.defineMethod (c$, "parseAnnotation", +function (string, graphStyle) { +var hasSymbols = (graphStyle == 0); +var desc = null; +var displayChar = null; +var ss = ' '; +var value = 0; +var parsedValue = false; +var dcset = false; +var colour = null; +var i = string.indexOf ("["); +var j = string.indexOf ("]"); +if (i > -1 && j > -1) { +var ucs = new jalview.schemes.UserColourScheme (); +colour = ucs.getColourFromString (string.substring (i + 1, j)); +if (i > 0 && string.charAt (i - 1) == ',') { +i--; +}string = string.substring (0, i) + string.substring (j + 1); +}var st = new java.util.StringTokenizer (string, ",", true); +var token; +var seenContent = false; +var pass = 0; +while (st.hasMoreTokens ()) { +pass++; +token = st.nextToken ().trim (); +if (token.equals (",")) { +if (!seenContent && parsedValue && !dcset) { +dcset = true; +displayChar = " "; +}seenContent = false; +continue; +} else { +seenContent = true; +}if (!parsedValue) { +try { +displayChar = token; +value = new Float (token).floatValue (); +parsedValue = true; +continue; +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +} else { +if (token.length == 1) { +displayChar = token; +}}if (hasSymbols && (token.equals ("H") || token.equals ("E") || token.equals ("S") || token.equals (" "))) { +ss = token.charAt (0); +if (displayChar.equals (token.substring (0, 1))) { +displayChar = ""; +}} else if (desc == null || (parsedValue && pass > 2)) { +desc = token; +}} +if (displayChar != null && desc != null && desc.length == 1) { +if (displayChar.length > 1) { +var tmp = displayChar; +displayChar = desc; +desc = tmp; +} else { +if (displayChar.equals (desc)) { +desc = null; +}}}var anot = new jalview.datamodel.Annotation (displayChar, desc, ss, value); +anot.colour = colour; +return anot; +}, "~S,~N"); +Clazz.defineMethod (c$, "colourAnnotations", +function (al, label, colour) { +var ucs = new jalview.schemes.UserColourScheme (colour); +var annotations; +for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { +if (al.getAlignmentAnnotation ()[i].label.equalsIgnoreCase (label)) { +annotations = al.getAlignmentAnnotation ()[i].annotations; +for (var j = 0; j < annotations.length; j++) { +if (annotations[j] != null) { +annotations[j].colour = ucs.findColour ('A'); +}} +}} +}, "jalview.datamodel.AlignmentI,~S,~S"); +Clazz.defineMethod (c$, "combineAnnotations", +function (al, combineCount, st, seqRef, groupRef) { +var group = st.nextToken (); +var graphGroup = 0; +if (al.getAlignmentAnnotation () != null) { +for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { +var aa = al.getAlignmentAnnotation ()[i]; +if (aa.graphGroup > graphGroup) { +graphGroup = aa.graphGroup + 1; +}if (aa.sequenceRef === seqRef && aa.groupRef === groupRef && aa.label.equalsIgnoreCase (group)) { +if (aa.graphGroup > -1) { +graphGroup = aa.graphGroup; +} else { +if (graphGroup <= combineCount) { +graphGroup = combineCount + 1; +}aa.graphGroup = graphGroup; +}break; +}} +while (st.hasMoreTokens ()) { +group = st.nextToken (); +for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { +var aa = al.getAlignmentAnnotation ()[i]; +if (aa.sequenceRef === seqRef && aa.groupRef === groupRef && aa.label.equalsIgnoreCase (group)) { +aa.graphGroup = graphGroup; +break; +}} +} +} else { +System.err.println ("Couldn't combine annotations. None are added to alignment yet!"); +}}, "jalview.datamodel.AlignmentI,~N,java.util.StringTokenizer,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "addLine", +function (al, st, seqRef, groupRef) { +var group = st.nextToken (); +var annotation = null; +var alannot = al.getAlignmentAnnotation (); +var value = new Float (st.nextToken ()).floatValue (); +var label = st.hasMoreTokens () ? st.nextToken () : null; +var colour = null; +if (st.hasMoreTokens ()) { +var ucs = new jalview.schemes.UserColourScheme (st.nextToken ()); +colour = ucs.findColour ('A'); +}if (alannot != null) { +for (var i = 0; i < alannot.length; i++) { +if (alannot[i].label.equalsIgnoreCase (group) && (seqRef == null || alannot[i].sequenceRef === seqRef) && (groupRef == null || alannot[i].groupRef === groupRef)) { +alannot[i].setThreshold ( new jalview.datamodel.GraphLine (value, label, colour)); +}} +}if (annotation == null) { +return; +}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "addGroup", +function (al, st) { +var sg = new jalview.datamodel.SequenceGroup (); +sg.setName (st.nextToken ()); +var rng = ""; +try { +rng = st.nextToken (); +if (rng.length > 0 && !rng.startsWith ("*")) { +sg.setStartRes (Integer.parseInt (rng) - 1); +} else { +sg.setStartRes (0); +}rng = st.nextToken (); +if (rng.length > 0 && !rng.startsWith ("*")) { +sg.setEndRes (Integer.parseInt (rng) - 1); +} else { +sg.setEndRes (al.getWidth () - 1); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '" + rng + "' - assuming alignment width for group."); +sg.setStartRes (0); +sg.setEndRes (al.getWidth () - 1); +} else { +throw e; +} +} +var index = st.nextToken (); +if (index.equals ("-1")) { +while (st.hasMoreElements ()) { +sg.addSequence (al.findName (st.nextToken ()), false); +} +} else { +var st2 = new java.util.StringTokenizer (index, ","); +while (st2.hasMoreTokens ()) { +var tmp = st2.nextToken (); +if (tmp.equals ("*")) { +for (var i = 0; i < al.getHeight (); i++) { +sg.addSequence (al.getSequenceAt (i), false); +} +} else if (tmp.indexOf ("-") >= 0) { +var st3 = new java.util.StringTokenizer (tmp, "-"); +var start = (Integer.parseInt (st3.nextToken ())); +var end = (Integer.parseInt (st3.nextToken ())); +if (end > start) { +for (var i = start; i <= end; i++) { +sg.addSequence (al.getSequenceAt (i - 1), false); +} +}} else { +sg.addSequence (al.getSequenceAt (Integer.parseInt (tmp) - 1), false); +}} +}if (this.refSeq != null) { +sg.setStartRes (this.refSeq.findIndex (sg.getStartRes () + 1) - 1); +sg.setEndRes (this.refSeq.findIndex (sg.getEndRes () + 1) - 1); +sg.setSeqrep (this.refSeq); +}if (sg.getSize () > 0) { +al.addGroup (sg); +}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); +Clazz.defineMethod (c$, "addRowProperties", +function (al, st) { +var label = st.nextToken (); +var keyValue; +var key; +var value; +var scaletofit = false; +var centerlab = false; +var showalllabs = false; +while (st.hasMoreTokens ()) { +keyValue = st.nextToken (); +key = keyValue.substring (0, keyValue.indexOf ("=")); +value = keyValue.substring (keyValue.indexOf ("=") + 1); +if (key.equalsIgnoreCase ("scaletofit")) { +scaletofit = Boolean.$valueOf (value).booleanValue (); +}if (key.equalsIgnoreCase ("showalllabs")) { +showalllabs = Boolean.$valueOf (value).booleanValue (); +}if (key.equalsIgnoreCase ("centrelabs")) { +centerlab = Boolean.$valueOf (value).booleanValue (); +}var alr = al.getAlignmentAnnotation (); +if (alr != null) { +for (var i = 0; i < alr.length; i++) { +if (alr[i].label.equalsIgnoreCase (label)) { +alr[i].centreColLabels = centerlab; +alr[i].scaleColLabel = scaletofit; +alr[i].showAllColLabels = showalllabs; +}} +}} +}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); +Clazz.defineMethod (c$, "addProperties", +function (al, st) { +if (al.getGroups () == null) { +return; +}var name = st.nextToken (); +var sg = null; +for (var _sg, $_sg = al.getGroups ().iterator (); $_sg.hasNext () && ((_sg = $_sg.next ()) || true);) { +if ((sg = _sg).getName ().equals (name)) { +break; +} else { +sg = null; +}} +if (sg != null) { +var keyValue; +var key; +var value; +var def = sg.cs; +sg.cs = null; +while (st.hasMoreTokens ()) { +keyValue = st.nextToken (); +key = keyValue.substring (0, keyValue.indexOf ("=")); +value = keyValue.substring (keyValue.indexOf ("=") + 1); +if (key.equalsIgnoreCase ("description")) { +sg.setDescription (value); +} else if (key.equalsIgnoreCase ("colour")) { +sg.cs = jalview.schemes.ColourSchemeProperty.getColour (al, value); +} else if (key.equalsIgnoreCase ("pidThreshold")) { +sg.cs.setThreshold (Integer.parseInt (value), true); +} else if (key.equalsIgnoreCase ("consThreshold")) { +sg.cs.setConservationInc (Integer.parseInt (value)); +var c = new jalview.analysis.Conservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (null), sg.getStartRes (), sg.getEndRes () + 1); +c.calculate (); +c.verdict (false, 25); +sg.cs.setConservation (c); +} else if (key.equalsIgnoreCase ("outlineColour")) { +sg.setOutlineColour ( new jalview.schemes.UserColourScheme (value).findColour ('A')); +} else if (key.equalsIgnoreCase ("displayBoxes")) { +sg.setDisplayBoxes (Boolean.$valueOf (value).booleanValue ()); +} else if (key.equalsIgnoreCase ("showUnconserved")) { +sg.setShowNonconserved (Boolean.$valueOf (value).booleanValue ()); +} else if (key.equalsIgnoreCase ("displayText")) { +sg.setDisplayText (Boolean.$valueOf (value).booleanValue ()); +} else if (key.equalsIgnoreCase ("colourText")) { +sg.setColourText (Boolean.$valueOf (value).booleanValue ()); +} else if (key.equalsIgnoreCase ("textCol1")) { +sg.textColour = new jalview.schemes.UserColourScheme (value).findColour ('A'); +} else if (key.equalsIgnoreCase ("textCol2")) { +sg.textColour2 = new jalview.schemes.UserColourScheme (value).findColour ('A'); +} else if (key.equalsIgnoreCase ("textColThreshold")) { +sg.thresholdTextColour = Integer.parseInt (value); +} else if (key.equalsIgnoreCase ("idColour")) { +sg.setIdColour ((def = new jalview.schemes.UserColourScheme (value)).findColour ('A')); +} else if (key.equalsIgnoreCase ("hide")) { +sg.setHidereps (true); +} else if (key.equalsIgnoreCase ("hidecols")) { +sg.setHideCols (true); +}sg.recalcConservation (); +} +if (sg.cs == null) { +sg.cs = def; +}}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); +Clazz.defineMethod (c$, "setBelowAlignment", +function (al, st) { +var token; +var aa; +var ala = al.getAlignmentAnnotation (); +if (ala == null) { +System.err.print ("Warning - no annotation to set below for sequence associated annotation:"); +}while (st.hasMoreTokens ()) { +token = st.nextToken (); +if (ala == null) { +System.err.print (" " + token); +} else { +for (var i = 0; i < al.getAlignmentAnnotation ().length; i++) { +aa = al.getAlignmentAnnotation ()[i]; +if (aa.sequenceRef === this.refSeq && aa.label.equals (token)) { +aa.belowAlignment = true; +}} +}} +if (ala == null) { +System.err.print ("\n"); +}}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); +Clazz.defineMethod (c$, "addAlignmentDetails", +function (al, st) { +var keyValue; +var key; +var value; +while (st.hasMoreTokens ()) { +keyValue = st.nextToken (); +key = keyValue.substring (0, keyValue.indexOf ("=")); +value = keyValue.substring (keyValue.indexOf ("=") + 1); +al.setProperty (key, value); +} +}, "jalview.datamodel.AlignmentI,java.util.StringTokenizer"); +Clazz.defineMethod (c$, "printCSVAnnotations", +function (annotations) { +var sp = new StringBuffer (); +for (var i = 0; i < annotations.length; i++) { +var atos = annotations[i].toString (); +var p = 0; +do { +var cp = atos.indexOf ("\n", p); +sp.append (annotations[i].label); +sp.append (","); +if (cp > p) { +sp.append (atos.substring (p, cp + 1)); +} else { +sp.append (atos.substring (p)); +sp.append (this.newline); +}p = cp + 1; +} while (p > 0); +} +return sp.toString (); +}, "~A"); +Clazz.defineMethod (c$, "printAnnotationsForView", +function (viewport) { +return this.printAnnotations (viewport.isShowAnnotation () ? viewport.getAlignment ().getAlignmentAnnotation () : null, viewport.getAlignment ().getGroups (), viewport.getAlignment ().getProperties (), viewport.getColumnSelection (), viewport.getAlignment (), null); +}, "jalview.api.AlignViewportI"); +Clazz.defineMethod (c$, "printAnnotationsForAlignment", +function (al) { +return this.printAnnotations (al.getAlignmentAnnotation (), al.getGroups (), al.getProperties (), null, al, null); +}, "jalview.datamodel.AlignmentI"); +c$.$AnnotationFile$ViewDef$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.viewname = null; +this.hidseqs = null; +this.hiddencols = null; +this.visibleGroups = null; +this.hiddenRepSeqs = null; +Clazz.instantialize (this, arguments); +}, jalview.io.AnnotationFile, "ViewDef"); +Clazz.makeConstructor (c$, +function (a, b, c, d) { +this.viewname = a; +this.hidseqs = b; +this.hiddencols = c; +this.hiddenRepSeqs = d; +}, "~S,jalview.datamodel.HiddenSequences,jalview.datamodel.ColumnSelection,java.util.Hashtable"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"GRAPHLINE", "GRAPHLINE", +"COMBINE", "COMBINE"); +}); diff --git a/bin/jalview/io/AppletFormatAdapter.class b/bin/jalview/io/AppletFormatAdapter.class index 6c39b9d..2c63ec8 100644 Binary files a/bin/jalview/io/AppletFormatAdapter.class and b/bin/jalview/io/AppletFormatAdapter.class differ diff --git a/bin/jalview/io/AppletFormatAdapter.js b/bin/jalview/io/AppletFormatAdapter.js index 681a44d..f4dab9f 100644 --- a/bin/jalview/io/AppletFormatAdapter.js +++ b/bin/jalview/io/AppletFormatAdapter.js @@ -1,389 +1,389 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.AppletFormatAdapter", ["MCview.PDBfile", "jalview.datamodel.Alignment", "jalview.io.FileParse", "$.IdentifyFile", "jalview.jsdev.GenericFileAdapter", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Exception", "$.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.viewpanel = null; -this.annotFromStructure = false; -this.localSecondaryStruct = false; -this.serviceSecondaryStruct = false; -this.alignFile = null; -this.inFile = null; -this.newline = null; -this.exportSettings = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "AppletFormatAdapter"); -Clazz.prepareFields (c$, function () { -this.newline = System.getProperty ("line.separator"); -}); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (viewpanel) { -this.viewpanel = viewpanel; -}, "jalview.api.AlignmentViewPanel"); -Clazz.makeConstructor (c$, -function (alignPanel, settings) { -this.viewpanel = alignPanel; -this.exportSettings = settings; -}, "jalview.api.AlignmentViewPanel,jalview.api.AlignExportSettingI"); -c$.prettyPrint = Clazz.defineMethod (c$, "prettyPrint", -function (els) { -var list = new StringBuffer (); -for (var i = 0, iSize = els.length - 1; i < iSize; i++) { -list.append (els[i]); -list.append (", "); -} -list.append (" and " + els[els.length - 1] + "."); -return list.toString (); -}, "~A"); -Clazz.defineMethod (c$, "setNewlineString", -function (nl) { -this.newline = nl; -}, "~S"); -Clazz.defineMethod (c$, "getNewlineString", -function () { -return this.newline; -}); -c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", -function (format) { -return jalview.io.AppletFormatAdapter.isValidFormat (format, false); -}, "~S"); -c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", -function (format, forwriting) { -var valid = false; -var format_list = (forwriting) ? jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS : jalview.io.AppletFormatAdapter.READABLE_FORMATS; -for (var element, $element = 0, $$element = format_list; $element < $$element.length && ((element = $$element[$element]) || true); $element++) { -if (element.equalsIgnoreCase (format)) { -return true; -}} -return valid; -}, "~S,~B"); -Clazz.defineMethod (c$, "readFile", -function (inFile, type, format) { -this.inFile = inFile; -try { -if (format.equals ("FASTA")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [inFile, type]); -} else if (format.equals ("MSF")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [inFile, type]); -} else if (format.equals ("PileUp")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [inFile, type]); -} else if (format.equals ("CLUSTAL")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [inFile, type]); -} else if (format.equals ("BLC")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [inFile, type]); -} else if (format.equals ("PIR")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [inFile, type]); -} else if (format.equals ("PFAM")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [inFile, type]); -} else if (format.equals ("JnetFile")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [inFile, type]); -(this.alignFile).removeNonSequences (); -} else if (format.equals ("PDB")) { -this.alignFile = new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, inFile, type); -} else if (format.equals ("STH")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [inFile, type]); -} else if (format.equals ("SimpleBLAST")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [inFile, type]); -} else if (format.equals ("PHYLIP")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [inFile, type]); -} else if (format.equals ("JSON")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [inFile, type]); -} else if (format.equals ("HTML")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [inFile, type]); -} else if (format.equals ("RNAML")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [inFile, type]); -} else if (format.equals ("GFF v2 or v3")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [inFile, type]); -}return this.buildAlignmentFrom (this.alignFile); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e); -if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { -throw new java.io.IOException (e.getMessage ()); -}if (type.equalsIgnoreCase ("Paste")) { -try { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + inFile, "Paste"]); -return this.buildAlignmentFrom (this.alignFile); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { -throw new java.io.IOException (e.getMessage ()); -}ex.printStackTrace (); -} else { -throw ex; -} -} -}throw new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS); -} else { -throw e; -} -} -}, "~S,~S,~S"); -Clazz.defineMethod (c$, "readFromFile", -function (source, format) { -this.inFile = source.getInFile (); -var type = source.type; -try { -if (format.equals ("FASTA")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [source]); -} else if (format.equals ("MSF")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [source]); -} else if (format.equals ("PileUp")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [source]); -} else if (format.equals ("CLUSTAL")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [source]); -} else if (format.equals ("BLC")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [source]); -} else if (format.equals ("PIR")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [source]); -} else if (format.equals ("PFAM")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [source]); -} else if (format.equals ("JnetFile")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [source]); -(this.alignFile).removeNonSequences (); -} else if (format.equals ("PDB")) { -this.alignFile = new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, source); -} else if (format.equals ("STH")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [source]); -} else if (format.equals ("RNAML")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [source]); -} else if (format.equals ("SimpleBLAST")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [source]); -} else if (format.equals ("PHYLIP")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [source]); -} else if (format.equals ("GFF v2 or v3")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [this.inFile, type]); -} else if (format.equals ("JSON")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [source]); -} else if (format.equals ("HTML")) { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [source]); -}return this.buildAlignmentFrom (this.alignFile); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -e.printStackTrace (); -System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e); -if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { -throw new java.io.IOException (e.getMessage ()); -}if (type.equalsIgnoreCase ("Paste")) { -try { -this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + this.inFile, "Paste"]); -return this.buildAlignmentFrom (this.alignFile); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { -throw new java.io.IOException (e.getMessage ()); -}ex.printStackTrace (); -} else { -throw ex; -} -} -}throw new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS); -} else { -throw e; -} -} -}, "jalview.io.FileParse,~S"); -Clazz.defineMethod (c$, "buildAlignmentFrom", -($fz = function (alignFile2) { -var al = new jalview.datamodel.Alignment (this.alignFile.getSeqsAsArray ()); -this.alignFile.addAnnotations (al); -this.alignFile.addGroups (al); -return al; -}, $fz.isPrivate = true, $fz), "jalview.io.AlignFile"); -Clazz.defineMethod (c$, "formatSequences", -function (format, jvsuffix, ap, selectedOnly) { -var selvew = ap.getAlignViewport ().getAlignmentView (selectedOnly, false); -var aselview = selvew.getVisibleAlignment (ap.getAlignViewport ().getGapCharacter ()); -var ala = (ap.getAlignViewport ().getVisibleAlignmentAnnotation (selectedOnly)); -if (ala != null) { -for (var aa, $aa = ala.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { -aselview.addAnnotation (aa); -} -}this.viewpanel = ap; -return this.formatSequences (format, aselview, jvsuffix); -}, "~S,~B,jalview.api.AlignmentViewPanel,~B"); -Clazz.defineMethod (c$, "formatSequences", -function (format, alignment, jvsuffix) { -try { -var afile = null; -if (format.equalsIgnoreCase ("FASTA")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", []); -} else if (format.equalsIgnoreCase ("MSF")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", []); -} else if (format.equalsIgnoreCase ("PileUp")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", []); -} else if (format.equalsIgnoreCase ("CLUSTAL")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", []); -} else if (format.equalsIgnoreCase ("BLC")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", []); -} else if (format.equalsIgnoreCase ("PIR")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", []); -} else if (format.equalsIgnoreCase ("PFAM")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", []); -} else if (format.equalsIgnoreCase ("STH")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [alignment]); -} else if (format.equalsIgnoreCase ("AMSA")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("AMSAFile", [alignment]); -} else if (format.equalsIgnoreCase ("PHYLIP")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", []); -} else if (format.equalsIgnoreCase ("JSON")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", []); -} else if (format.equalsIgnoreCase ("RNAML")) { -afile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", []); -} else { -throw new Exception (jalview.util.MessageManager.getString ("error.implementation_error_unknown_file_format_string")); -}afile.setNewlineString (this.newline); -afile.addJVSuffix (jvsuffix); -afile.setExportSettings (this.exportSettings); -afile.configureForView (this.viewpanel); -if (this.viewpanel == null || this.viewpanel.getAlignment () == null || this.viewpanel.getAlignment () !== alignment) { -afile.setSeqs (alignment.getSequencesArray ()); -} else { -afile.setSeqs (this.viewpanel.getAlignment ().getSequencesArray ()); -}var afileresp = afile.print (); -if (afile.hasWarningMessage ()) { -System.err.println ("Warning raised when writing as " + format + " : " + afile.getWarningMessage ()); -}return afileresp; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Failed to write alignment as a '" + format + "' file\n"); -e.printStackTrace (); -} else { -throw e; -} -} -return null; -}, "~S,jalview.datamodel.AlignmentI,~B"); -c$.checkProtocol = Clazz.defineMethod (c$, "checkProtocol", -function (file) { -var protocol = jalview.io.AppletFormatAdapter.FILE; -var ft = file.toLowerCase ().trim (); -if (ft.indexOf ("http:") == 0 || ft.indexOf ("https:") == 0 || ft.indexOf ("file:") == 0) { -protocol = jalview.io.AppletFormatAdapter.URL; -}return protocol; -}, "~S"); -c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", -function (file, format) { -return jalview.io.AppletFormatAdapter.resolveProtocol (file, format, false); -}, "~S,~S"); -c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", -function (file, format, debug) { -var protocol = null; -if (debug) { -System.out.println ("resolving datasource started with:\n>>file\n" + file + ">>endfile"); -}try { -var rtn = false; -var is = System.getSecurityManager ().getClass ().getResourceAsStream ("/" + file); -if (is != null) { -rtn = true; -is.close (); -}if (debug) { -System.err.println ("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader."); -};if (rtn) { -protocol = jalview.io.AppletFormatAdapter.CLASSLOADER; -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Exception checking resources: " + file + " " + ex); -} else { -throw ex; -} -} -if (file.indexOf ("://") > -1) { -protocol = jalview.io.AppletFormatAdapter.URL; -} else { -protocol = jalview.io.AppletFormatAdapter.FILE; -}var fp = null; -try { -if (debug) { -System.out.println ("Trying to get contents of resource as " + protocol + ":"); -}fp = new jalview.io.FileParse (file, protocol); -if (!fp.isValid ()) { -fp = null; -} else { -if (debug) { -System.out.println ("Successful."); -}}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -if (debug) { -System.err.println ("Exception when accessing content: " + e); -}fp = null; -} else { -throw e; -} -} -if (fp == null) { -if (debug) { -System.out.println ("Accessing as paste."); -}protocol = jalview.io.AppletFormatAdapter.PASTE; -fp = null; -try { -fp = new jalview.io.FileParse (file, protocol); -if (!fp.isValid ()) { -fp = null; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Failed to access content as paste!"); -e.printStackTrace (); -fp = null; -} else { -throw e; -} -} -}if (fp == null) { -return null; -}if (format == null || format.length == 0) { -return protocol; -} else { -try { -var idformat = new jalview.io.IdentifyFile ().Identify (file, protocol); -if (idformat == null) { -if (debug) { -System.out.println ("Format not identified. Inaccessible file."); -}return null; -}if (debug) { -System.out.println ("Format identified as " + idformat + "and expected as " + format); -}if (idformat.equals (format)) { -if (debug) { -System.out.println ("Protocol identified as " + protocol); -}return protocol; -} else { -if (debug) { -System.out.println ("File deemed not accessible via " + protocol); -}fp.close (); -return null; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -if (debug) { -System.err.println ("File deemed not accessible via " + protocol); -e.printStackTrace (); -};} else { -throw e; -} -} -}return null; -}, "~S,~S,~B"); -Clazz.defineMethod (c$, "getAlignFile", -function () { -return this.alignFile; -}); -Clazz.defineMethod (c$, "setAlignFile", -function (alignFile) { -this.alignFile = alignFile; -}, "jalview.io.AlignFile"); -Clazz.defineStatics (c$, -"FILE", "File", -"URL", "URL", -"PASTE", "Paste", -"CLASSLOADER", "ClassLoader"); -c$.READABLE_FORMATS = c$.prototype.READABLE_FORMATS = Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "HTML"]); -c$.READABLE_EXTENSIONS = c$.prototype.READABLE_EXTENSIONS = Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp", "html"]); -c$.READABLE_FNAMES = c$.prototype.READABLE_FNAMES = Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "Jalview", "HTML"]); -c$.WRITEABLE_FORMATS = c$.prototype.WRITEABLE_FORMATS = Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH", "PHYLIP", "JSON"]); -c$.WRITABLE_EXTENSIONS = c$.prototype.WRITABLE_EXTENSIONS = Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "phy", "json", "jvp"]); -c$.WRITABLE_FNAMES = c$.prototype.WRITABLE_FNAMES = Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP", "JSON", "Jalview"]); -Clazz.defineStatics (c$, -"INVALID_CHARACTERS", "Contains invalid characters"); -c$.SUPPORTED_FORMATS = c$.prototype.SUPPORTED_FORMATS = "Formats currently supported are\n" + jalview.io.AppletFormatAdapter.prettyPrint (jalview.io.AppletFormatAdapter.READABLE_FORMATS); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.AppletFormatAdapter", ["MCview.PDBfile", "jalview.datamodel.Alignment", "jalview.io.FileParse", "$.IdentifyFile", "jalview.jsdev.GenericFileAdapter", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Exception", "$.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.viewpanel = null; +this.annotFromStructure = false; +this.localSecondaryStruct = false; +this.serviceSecondaryStruct = false; +this.alignFile = null; +this.inFile = null; +this.newline = null; +this.exportSettings = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "AppletFormatAdapter"); +Clazz.prepareFields (c$, function () { +this.newline = System.getProperty ("line.separator"); +}); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (viewpanel) { +this.viewpanel = viewpanel; +}, "jalview.api.AlignmentViewPanel"); +Clazz.makeConstructor (c$, +function (alignPanel, settings) { +this.viewpanel = alignPanel; +this.exportSettings = settings; +}, "jalview.api.AlignmentViewPanel,jalview.api.AlignExportSettingI"); +c$.prettyPrint = Clazz.defineMethod (c$, "prettyPrint", +function (els) { +var list = new StringBuffer (); +for (var i = 0, iSize = els.length - 1; i < iSize; i++) { +list.append (els[i]); +list.append (", "); +} +list.append (" and " + els[els.length - 1] + "."); +return list.toString (); +}, "~A"); +Clazz.defineMethod (c$, "setNewlineString", +function (nl) { +this.newline = nl; +}, "~S"); +Clazz.defineMethod (c$, "getNewlineString", +function () { +return this.newline; +}); +c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", +function (format) { +return jalview.io.AppletFormatAdapter.isValidFormat (format, false); +}, "~S"); +c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", +function (format, forwriting) { +var valid = false; +var format_list = (forwriting) ? jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS : jalview.io.AppletFormatAdapter.READABLE_FORMATS; +for (var element, $element = 0, $$element = format_list; $element < $$element.length && ((element = $$element[$element]) || true); $element++) { +if (element.equalsIgnoreCase (format)) { +return true; +}} +return valid; +}, "~S,~B"); +Clazz.defineMethod (c$, "readFile", +function (inFile, type, format) { +this.inFile = inFile; +try { +if (format.equals ("FASTA")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [inFile, type]); +} else if (format.equals ("MSF")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [inFile, type]); +} else if (format.equals ("PileUp")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [inFile, type]); +} else if (format.equals ("CLUSTAL")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [inFile, type]); +} else if (format.equals ("BLC")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [inFile, type]); +} else if (format.equals ("PIR")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [inFile, type]); +} else if (format.equals ("PFAM")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [inFile, type]); +} else if (format.equals ("JnetFile")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [inFile, type]); +(this.alignFile).removeNonSequences (); +} else if (format.equals ("PDB")) { +this.alignFile = new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, inFile, type); +} else if (format.equals ("STH")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [inFile, type]); +} else if (format.equals ("SimpleBLAST")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [inFile, type]); +} else if (format.equals ("PHYLIP")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [inFile, type]); +} else if (format.equals ("JSON")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [inFile, type]); +} else if (format.equals ("HTML")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [inFile, type]); +} else if (format.equals ("RNAML")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [inFile, type]); +} else if (format.equals ("GFF v2 or v3")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [inFile, type]); +}return this.buildAlignmentFrom (this.alignFile); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e); +if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { +throw new java.io.IOException (e.getMessage ()); +}if (type.equalsIgnoreCase ("Paste")) { +try { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + inFile, "Paste"]); +return this.buildAlignmentFrom (this.alignFile); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { +throw new java.io.IOException (e.getMessage ()); +}ex.printStackTrace (); +} else { +throw ex; +} +} +}throw new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS); +} else { +throw e; +} +} +}, "~S,~S,~S"); +Clazz.defineMethod (c$, "readFromFile", +function (source, format) { +this.inFile = source.getInFile (); +var type = source.type; +try { +if (format.equals ("FASTA")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [source]); +} else if (format.equals ("MSF")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [source]); +} else if (format.equals ("PileUp")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [source]); +} else if (format.equals ("CLUSTAL")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [source]); +} else if (format.equals ("BLC")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [source]); +} else if (format.equals ("PIR")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [source]); +} else if (format.equals ("PFAM")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [source]); +} else if (format.equals ("JnetFile")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [source]); +(this.alignFile).removeNonSequences (); +} else if (format.equals ("PDB")) { +this.alignFile = new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, source); +} else if (format.equals ("STH")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [source]); +} else if (format.equals ("RNAML")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [source]); +} else if (format.equals ("SimpleBLAST")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [source]); +} else if (format.equals ("PHYLIP")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [source]); +} else if (format.equals ("GFF v2 or v3")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [this.inFile, type]); +} else if (format.equals ("JSON")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [source]); +} else if (format.equals ("HTML")) { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [source]); +}return this.buildAlignmentFrom (this.alignFile); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +e.printStackTrace (); +System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e); +if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { +throw new java.io.IOException (e.getMessage ()); +}if (type.equalsIgnoreCase ("Paste")) { +try { +this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + this.inFile, "Paste"]); +return this.buildAlignmentFrom (this.alignFile); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) { +throw new java.io.IOException (e.getMessage ()); +}ex.printStackTrace (); +} else { +throw ex; +} +} +}throw new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS); +} else { +throw e; +} +} +}, "jalview.io.FileParse,~S"); +Clazz.defineMethod (c$, "buildAlignmentFrom", +($fz = function (alignFile2) { +var al = new jalview.datamodel.Alignment (this.alignFile.getSeqsAsArray ()); +this.alignFile.addAnnotations (al); +this.alignFile.addGroups (al); +return al; +}, $fz.isPrivate = true, $fz), "jalview.io.AlignFile"); +Clazz.defineMethod (c$, "formatSequences", +function (format, jvsuffix, ap, selectedOnly) { +var selvew = ap.getAlignViewport ().getAlignmentView (selectedOnly, false); +var aselview = selvew.getVisibleAlignment (ap.getAlignViewport ().getGapCharacter ()); +var ala = (ap.getAlignViewport ().getVisibleAlignmentAnnotation (selectedOnly)); +if (ala != null) { +for (var aa, $aa = ala.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { +aselview.addAnnotation (aa); +} +}this.viewpanel = ap; +return this.formatSequences (format, aselview, jvsuffix); +}, "~S,~B,jalview.api.AlignmentViewPanel,~B"); +Clazz.defineMethod (c$, "formatSequences", +function (format, alignment, jvsuffix) { +try { +var afile = null; +if (format.equalsIgnoreCase ("FASTA")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", []); +} else if (format.equalsIgnoreCase ("MSF")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", []); +} else if (format.equalsIgnoreCase ("PileUp")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", []); +} else if (format.equalsIgnoreCase ("CLUSTAL")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", []); +} else if (format.equalsIgnoreCase ("BLC")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", []); +} else if (format.equalsIgnoreCase ("PIR")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", []); +} else if (format.equalsIgnoreCase ("PFAM")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", []); +} else if (format.equalsIgnoreCase ("STH")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [alignment]); +} else if (format.equalsIgnoreCase ("AMSA")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("AMSAFile", [alignment]); +} else if (format.equalsIgnoreCase ("PHYLIP")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", []); +} else if (format.equalsIgnoreCase ("JSON")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", []); +} else if (format.equalsIgnoreCase ("RNAML")) { +afile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", []); +} else { +throw new Exception (jalview.util.MessageManager.getString ("error.implementation_error_unknown_file_format_string")); +}afile.setNewlineString (this.newline); +afile.addJVSuffix (jvsuffix); +afile.setExportSettings (this.exportSettings); +afile.configureForView (this.viewpanel); +if (this.viewpanel == null || this.viewpanel.getAlignment () == null || this.viewpanel.getAlignment () !== alignment) { +afile.setSeqs (alignment.getSequencesArray ()); +} else { +afile.setSeqs (this.viewpanel.getAlignment ().getSequencesArray ()); +}var afileresp = afile.print (); +if (afile.hasWarningMessage ()) { +System.err.println ("Warning raised when writing as " + format + " : " + afile.getWarningMessage ()); +}return afileresp; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Failed to write alignment as a '" + format + "' file\n"); +e.printStackTrace (); +} else { +throw e; +} +} +return null; +}, "~S,jalview.datamodel.AlignmentI,~B"); +c$.checkProtocol = Clazz.defineMethod (c$, "checkProtocol", +function (file) { +var protocol = jalview.io.AppletFormatAdapter.FILE; +var ft = file.toLowerCase ().trim (); +if (ft.indexOf ("http:") == 0 || ft.indexOf ("https:") == 0 || ft.indexOf ("file:") == 0) { +protocol = jalview.io.AppletFormatAdapter.URL; +}return protocol; +}, "~S"); +c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", +function (file, format) { +return jalview.io.AppletFormatAdapter.resolveProtocol (file, format, false); +}, "~S,~S"); +c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", +function (file, format, debug) { +var protocol = null; +if (debug) { +System.out.println ("resolving datasource started with:\n>>file\n" + file + ">>endfile"); +}try { +var rtn = false; +var is = System.getSecurityManager ().getClass ().getResourceAsStream ("/" + file); +if (is != null) { +rtn = true; +is.close (); +}if (debug) { +System.err.println ("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader."); +};if (rtn) { +protocol = jalview.io.AppletFormatAdapter.CLASSLOADER; +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Exception checking resources: " + file + " " + ex); +} else { +throw ex; +} +} +if (file.indexOf ("://") > -1) { +protocol = jalview.io.AppletFormatAdapter.URL; +} else { +protocol = jalview.io.AppletFormatAdapter.FILE; +}var fp = null; +try { +if (debug) { +System.out.println ("Trying to get contents of resource as " + protocol + ":"); +}fp = new jalview.io.FileParse (file, protocol); +if (!fp.isValid ()) { +fp = null; +} else { +if (debug) { +System.out.println ("Successful."); +}}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +if (debug) { +System.err.println ("Exception when accessing content: " + e); +}fp = null; +} else { +throw e; +} +} +if (fp == null) { +if (debug) { +System.out.println ("Accessing as paste."); +}protocol = jalview.io.AppletFormatAdapter.PASTE; +fp = null; +try { +fp = new jalview.io.FileParse (file, protocol); +if (!fp.isValid ()) { +fp = null; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Failed to access content as paste!"); +e.printStackTrace (); +fp = null; +} else { +throw e; +} +} +}if (fp == null) { +return null; +}if (format == null || format.length == 0) { +return protocol; +} else { +try { +var idformat = new jalview.io.IdentifyFile ().Identify (file, protocol); +if (idformat == null) { +if (debug) { +System.out.println ("Format not identified. Inaccessible file."); +}return null; +}if (debug) { +System.out.println ("Format identified as " + idformat + "and expected as " + format); +}if (idformat.equals (format)) { +if (debug) { +System.out.println ("Protocol identified as " + protocol); +}return protocol; +} else { +if (debug) { +System.out.println ("File deemed not accessible via " + protocol); +}fp.close (); +return null; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +if (debug) { +System.err.println ("File deemed not accessible via " + protocol); +e.printStackTrace (); +};} else { +throw e; +} +} +}return null; +}, "~S,~S,~B"); +Clazz.defineMethod (c$, "getAlignFile", +function () { +return this.alignFile; +}); +Clazz.defineMethod (c$, "setAlignFile", +function (alignFile) { +this.alignFile = alignFile; +}, "jalview.io.AlignFile"); +Clazz.defineStatics (c$, +"FILE", "File", +"URL", "URL", +"PASTE", "Paste", +"CLASSLOADER", "ClassLoader"); +c$.READABLE_FORMATS = c$.prototype.READABLE_FORMATS = Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "HTML"]); +c$.READABLE_EXTENSIONS = c$.prototype.READABLE_EXTENSIONS = Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp", "html"]); +c$.READABLE_FNAMES = c$.prototype.READABLE_FNAMES = Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "Jalview", "HTML"]); +c$.WRITEABLE_FORMATS = c$.prototype.WRITEABLE_FORMATS = Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH", "PHYLIP", "JSON"]); +c$.WRITABLE_EXTENSIONS = c$.prototype.WRITABLE_EXTENSIONS = Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "phy", "json", "jvp"]); +c$.WRITABLE_FNAMES = c$.prototype.WRITABLE_FNAMES = Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP", "JSON", "Jalview"]); +Clazz.defineStatics (c$, +"INVALID_CHARACTERS", "Contains invalid characters"); +c$.SUPPORTED_FORMATS = c$.prototype.SUPPORTED_FORMATS = "Formats currently supported are\n" + jalview.io.AppletFormatAdapter.prettyPrint (jalview.io.AppletFormatAdapter.READABLE_FORMATS); +}); diff --git a/bin/jalview/io/FastaFile.class b/bin/jalview/io/FastaFile.class index 8111432..d7fe1ef 100644 Binary files a/bin/jalview/io/FastaFile.class and b/bin/jalview/io/FastaFile.class differ diff --git a/bin/jalview/io/FastaFile.js b/bin/jalview/io/FastaFile.js index 38f827f..5dc3155 100644 --- a/bin/jalview/io/FastaFile.js +++ b/bin/jalview/io/FastaFile.js @@ -1,94 +1,94 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile"], "jalview.io.FastaFile", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.len = 72; -this.out = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "FastaFile", jalview.io.AlignFile); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.FastaFile, []); -}); -Clazz.overrideMethod (c$, "parse", -function () { -var sb = new StringBuffer (); -var firstLine = true; -var line; -var uline; -var seq = null; -var annotation = false; -while ((uline = this.nextLine ()) != null) { -line = uline.trim (); -if (line.length > 0) { -if (line.charAt (0) == '>') { -if (line.startsWith (">#_")) { -if (annotation) { -this.annotations.addElement (this.makeAnnotation (seq, sb)); -}} else { -annotation = false; -}if (!firstLine) { -seq.setSequence (sb.toString ()); -if (!annotation) { -this.seqs.addElement (seq); -}}seq = this.parseId (line.substring (1)); -firstLine = false; -sb = new StringBuffer (); -if (line.startsWith (">#_")) { -annotation = true; -}} else { -sb.append (annotation ? uline : line); -}}} -if (annotation) { -this.annotations.addElement (this.makeAnnotation (seq, sb)); -} else if (!firstLine) { -seq.setSequence (sb.toString ()); -this.seqs.addElement (seq); -}}); -Clazz.defineMethod (c$, "makeAnnotation", -($fz = function (seq, sb) { -var anots = new Array (sb.length ()); -var cb; -for (var i = 0; i < anots.length; i++) { -var cn = sb.charAt (i); -if (cn != ' ') { -anots[i] = new jalview.datamodel.Annotation ("" + cn, null, ' ', NaN); -}} -var aa = new jalview.datamodel.AlignmentAnnotation (seq.getName ().substring (2), seq.getDescription (), anots); -return aa; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,StringBuffer"); -Clazz.defineMethod (c$, "addAnnotations", -function (al) { -this.addProperties (al); -for (var i = 0; i < this.annotations.size (); i++) { -var aa = this.annotations.elementAt (i); -aa.setPadGaps (true, al.getGapCharacter ()); -al.addAnnotation (aa); -} -}, "jalview.datamodel.Alignment"); -Clazz.defineMethod (c$, "print", -function (s) { -this.out = new StringBuffer (); -var i = 0; -while ((i < s.length) && (s[i] != null)) { -this.out.append (">" + this.printId (s[i])); -if (s[i].getDescription () != null) { -this.out.append (" " + s[i].getDescription ()); -}this.out.append (this.newline); -var nochunks = (Clazz.doubleToInt (s[i].getLength () / this.len)) + 1; -for (var j = 0; j < nochunks; j++) { -var start = j * this.len; -var end = start + this.len; -if (end < s[i].getLength ()) { -this.out.append (s[i].getSequenceAsString (start, end) + this.newline); -} else if (start < s[i].getLength ()) { -this.out.append (s[i].getSequenceAsString (start, s[i].getLength ()) + this.newline); -}} -i++; -} -return this.out.toString (); -}, "~A"); -Clazz.defineMethod (c$, "print", -function () { -return this.print (this.getSeqsAsArray ()); -}); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile"], "jalview.io.FastaFile", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.len = 72; +this.out = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "FastaFile", jalview.io.AlignFile); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.FastaFile, []); +}); +Clazz.overrideMethod (c$, "parse", +function () { +var sb = new StringBuffer (); +var firstLine = true; +var line; +var uline; +var seq = null; +var annotation = false; +while ((uline = this.nextLine ()) != null) { +line = uline.trim (); +if (line.length > 0) { +if (line.charAt (0) == '>') { +if (line.startsWith (">#_")) { +if (annotation) { +this.annotations.addElement (this.makeAnnotation (seq, sb)); +}} else { +annotation = false; +}if (!firstLine) { +seq.setSequence (sb.toString ()); +if (!annotation) { +this.seqs.addElement (seq); +}}seq = this.parseId (line.substring (1)); +firstLine = false; +sb = new StringBuffer (); +if (line.startsWith (">#_")) { +annotation = true; +}} else { +sb.append (annotation ? uline : line); +}}} +if (annotation) { +this.annotations.addElement (this.makeAnnotation (seq, sb)); +} else if (!firstLine) { +seq.setSequence (sb.toString ()); +this.seqs.addElement (seq); +}}); +Clazz.defineMethod (c$, "makeAnnotation", +($fz = function (seq, sb) { +var anots = new Array (sb.length ()); +var cb; +for (var i = 0; i < anots.length; i++) { +var cn = sb.charAt (i); +if (cn != ' ') { +anots[i] = new jalview.datamodel.Annotation ("" + cn, null, ' ', NaN); +}} +var aa = new jalview.datamodel.AlignmentAnnotation (seq.getName ().substring (2), seq.getDescription (), anots); +return aa; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,StringBuffer"); +Clazz.defineMethod (c$, "addAnnotations", +function (al) { +this.addProperties (al); +for (var i = 0; i < this.annotations.size (); i++) { +var aa = this.annotations.elementAt (i); +aa.setPadGaps (true, al.getGapCharacter ()); +al.addAnnotation (aa); +} +}, "jalview.datamodel.Alignment"); +Clazz.defineMethod (c$, "print", +function (s) { +this.out = new StringBuffer (); +var i = 0; +while ((i < s.length) && (s[i] != null)) { +this.out.append (">" + this.printId (s[i])); +if (s[i].getDescription () != null) { +this.out.append (" " + s[i].getDescription ()); +}this.out.append (this.newline); +var nochunks = (Clazz.doubleToInt (s[i].getLength () / this.len)) + 1; +for (var j = 0; j < nochunks; j++) { +var start = j * this.len; +var end = start + this.len; +if (end < s[i].getLength ()) { +this.out.append (s[i].getSequenceAsString (start, end) + this.newline); +} else if (start < s[i].getLength ()) { +this.out.append (s[i].getSequenceAsString (start, s[i].getLength ()) + this.newline); +}} +i++; +} +return this.out.toString (); +}, "~A"); +Clazz.defineMethod (c$, "print", +function () { +return this.print (this.getSeqsAsArray ()); +}); +}); diff --git a/bin/jalview/io/FeaturesFile.class b/bin/jalview/io/FeaturesFile.class index 1efc2f6..2d37a41 100644 Binary files a/bin/jalview/io/FeaturesFile.class and b/bin/jalview/io/FeaturesFile.class differ diff --git a/bin/jalview/io/FeaturesFile.js b/bin/jalview/io/FeaturesFile.js index 7bdc9f9..458787b 100644 --- a/bin/jalview/io/FeaturesFile.js +++ b/bin/jalview/io/FeaturesFile.js @@ -1,772 +1,772 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile", "java.lang.Enum", "$.Exception"], "jalview.io.FeaturesFile", ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.AlignedCodonFrame", "$.SequenceDummy", "$.SequenceFeature", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.Format", "$.MapList", "$.ParseHtmlBodyAndLinks", "java.awt.Color", "java.lang.Float", "$.StringBuffer", "java.util.ArrayList", "$.Arrays", "$.HashMap", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.doGffSource = true; -this.gffversion = 0; -if (!Clazz.isClassDefined ("jalview.io.FeaturesFile.InvalidGFF3FieldException")) { -jalview.io.FeaturesFile.$FeaturesFile$InvalidGFF3FieldException$ (); -} -this.lastmatchedAl = null; -this.matcher = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "FeaturesFile", jalview.io.AlignFile); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.FeaturesFile, []); -}); -Clazz.defineMethod (c$, "parse", -function (align, colours, removeHTML) { -return this.parse (align, colours, null, removeHTML, false); -}, "jalview.datamodel.AlignmentI,java.util.Hashtable,~B"); -Clazz.defineMethod (c$, "parse", -function (align, colours, removeHTML, relaxedIdMatching) { -return this.parse (align, colours, null, removeHTML, relaxedIdMatching); -}, "jalview.datamodel.AlignmentI,java.util.Map,~B,~B"); -Clazz.defineMethod (c$, "parse", -function (align, colours, featureLink, removeHTML) { -return this.parse (align, colours, featureLink, removeHTML, false); -}, "jalview.datamodel.AlignmentI,java.util.Map,java.util.Map,~B"); -Clazz.defineMethod (c$, "parse", -function (align, colours, featureLink, removeHTML, relaxedIdmatching) { -var line = null; -try { -var seq = null; -var newseqs = new java.util.ArrayList (); -var type; -var desc; -var token = null; -var index; -var start; -var end; -var score; -var st; -var sf; -var featureGroup = null; -var groupLink = null; -var typeLink = new java.util.Hashtable (); -var GFFFile = true; -var gffProps = new java.util.HashMap (); -while ((line = this.nextLine ()) != null) { -if (line.startsWith ("#")) { -if (line.startsWith ("##")) { -this.processGffPragma (line, gffProps, align, newseqs); -line = ""; -}continue; -}st = new java.util.StringTokenizer (line, "\t"); -if (st.countTokens () == 1) { -if (line.trim ().equalsIgnoreCase ("GFF")) { -GFFFile = true; -continue; -}}if (st.countTokens () > 1 && st.countTokens () < 4) { -GFFFile = false; -type = st.nextToken (); -if (type.equalsIgnoreCase ("startgroup")) { -featureGroup = st.nextToken (); -if (st.hasMoreElements ()) { -groupLink = st.nextToken (); -featureLink.put (featureGroup, groupLink); -}} else if (type.equalsIgnoreCase ("endgroup")) { -st.nextToken (); -featureGroup = null; -groupLink = null; -} else { -var colour = null; -var colscheme = st.nextToken (); -if (colscheme.indexOf ("|") > -1 || colscheme.trim ().equalsIgnoreCase ("label")) { -var gcol = new java.util.StringTokenizer (colscheme, "|", true); -var threshtype = -1; -var min = 1.4E-45; -var max = 3.4028235E38; -var threshval = NaN; -var labelCol = false; -var mincol = gcol.nextToken (); -if (mincol === "|") { -System.err.println ("Expected either 'label' or a colour specification in the line: " + line); -continue; -}var maxcol = null; -if (mincol.toLowerCase ().indexOf ("label") == 0) { -labelCol = true; -mincol = (gcol.hasMoreTokens () ? gcol.nextToken () : null); -mincol = (gcol.hasMoreTokens () ? gcol.nextToken () : null); -}var abso = null; -var minval; -var maxval; -if (mincol != null) { -if (mincol.equals ("|")) { -mincol = ""; -} else { -gcol.nextToken (); -}maxcol = gcol.nextToken (); -if (maxcol.equals ("|")) { -maxcol = ""; -} else { -gcol.nextToken (); -}abso = gcol.nextToken (); -gcol.nextToken (); -if (abso.toLowerCase ().indexOf ("abso") != 0) { -minval = abso; -abso = null; -} else { -minval = gcol.nextToken (); -gcol.nextToken (); -}maxval = gcol.nextToken (); -if (gcol.hasMoreTokens ()) { -gcol.nextToken (); -}try { -if (minval.length > 0) { -min = new Float (minval).floatValue (); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Couldn't parse the minimum value for graduated colour for type (" + colscheme + ") - did you misspell 'auto' for the optional automatic colour switch ?"); -e.printStackTrace (); -} else { -throw e; -} -} -try { -if (maxval.length > 0) { -max = new Float (maxval).floatValue (); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Couldn't parse the maximum value for graduated colour for type (" + colscheme + ")"); -e.printStackTrace (); -} else { -throw e; -} -} -} else { -mincol = "FFFFFF"; -maxcol = "000000"; -}try { -colour = new jalview.schemes.GraduatedColor ( new jalview.schemes.UserColourScheme (mincol).findColour ('A'), new jalview.schemes.UserColourScheme (maxcol).findColour ('A'), min, max); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Couldn't parse the graduated colour scheme (" + colscheme + ")"); -e.printStackTrace (); -} else { -throw e; -} -} -if (colour != null) { -(colour).setColourByLabel (labelCol); -(colour).setAutoScaled (abso == null); -var ttype = null; -var tval = null; -if (gcol.hasMoreTokens ()) { -ttype = gcol.nextToken (); -if (ttype.toLowerCase ().startsWith ("below")) { -(colour).setThreshType (0); -} else if (ttype.toLowerCase ().startsWith ("above")) { -(colour).setThreshType (1); -} else { -(colour).setThreshType (-1); -if (!ttype.toLowerCase ().startsWith ("no")) { -System.err.println ("Ignoring unrecognised threshold type : " + ttype); -}}}if ((colour).getThreshType () != -1) { -try { -gcol.nextToken (); -tval = gcol.nextToken (); -(colour).setThresh ( new Float (tval).floatValue ()); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Couldn't parse threshold value as a float: (" + tval + ")"); -e.printStackTrace (); -} else { -throw e; -} -} -}if (gcol.hasMoreTokens ()) { -System.err.println ("Ignoring additional tokens in parameters in graduated colour specification\n"); -while (gcol.hasMoreTokens ()) { -System.err.println ("|" + gcol.nextToken ()); -} -System.err.println ("\n"); -}}} else { -var ucs = new jalview.schemes.UserColourScheme (colscheme); -colour = ucs.findColour ('A'); -}if (colour != null) { -colours.put (type, colour); -}if (st.hasMoreElements ()) { -var link = st.nextToken (); -typeLink.put (type, link); -if (featureLink == null) { -featureLink = new java.util.Hashtable (); -}featureLink.put (type, link); -}}continue; -}var seqId = ""; -while (st.hasMoreElements ()) { -if (GFFFile) { -seqId = token = st.nextToken (); -seq = this.findName (align, seqId, relaxedIdmatching, newseqs); -if (seq != null) { -desc = st.nextToken (); -var group = null; -if (this.doGffSource && desc.indexOf (' ') == -1) { -group = String.instantialize (desc); -}type = st.nextToken (); -try { -var stt = st.nextToken (); -if (stt.length == 0 || stt.equals ("-")) { -start = 0; -} else { -start = Integer.parseInt (stt); -}} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -start = 0; -} else { -throw ex; -} -} -try { -var stt = st.nextToken (); -if (stt.length == 0 || stt.equals ("-")) { -end = 0; -} else { -end = Integer.parseInt (stt); -}} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -end = 0; -} else { -throw ex; -} -} -if (end == 0) { -start = 0; -}try { -score = new Float (st.nextToken ()).floatValue (); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -score = 0; -} else { -throw ex; -} -} -sf = new jalview.datamodel.SequenceFeature (type, desc, start, end, score, group); -try { -sf.setValue ("STRAND", st.nextToken ()); -sf.setValue ("FRAME", st.nextToken ()); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -if (st.hasMoreTokens ()) { -var attributes = new StringBuffer (); -var sep = false; -while (st.hasMoreTokens ()) { -attributes.append ((sep ? "\t" : "") + st.nextElement ()); -sep = true; -} -sf.setValue ("ATTRIBUTES", attributes.toString ()); -}if (this.processOrAddSeqFeature (align, newseqs, seq, sf, GFFFile, relaxedIdmatching)) { -while ((seq = align.findName (seq, seqId, true)) != null) { -seq.addSequenceFeature ( new jalview.datamodel.SequenceFeature (sf)); -} -}break; -}}if (GFFFile && seq == null) { -desc = token; -} else { -desc = st.nextToken (); -}if (!st.hasMoreTokens ()) { -System.err.println ("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up."); -return false; -}token = st.nextToken (); -if (!token.equals ("ID_NOT_SPECIFIED")) { -seq = this.findName (align, seqId = token, relaxedIdmatching, null); -st.nextToken (); -} else { -seqId = null; -try { -index = Integer.parseInt (st.nextToken ()); -seq = align.getSequenceAt (index); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -seq = null; -} else { -throw ex; -} -} -}if (seq == null) { -System.out.println ("Sequence not found: " + line); -break; -}start = Integer.parseInt (st.nextToken ()); -end = Integer.parseInt (st.nextToken ()); -type = st.nextToken (); -if (!colours.containsKey (type)) { -var ucs = new jalview.schemes.UserColourScheme (type); -colours.put (type, ucs.findColour ('A')); -}sf = new jalview.datamodel.SequenceFeature (type, desc, "", start, end, featureGroup); -if (st.hasMoreTokens ()) { -try { -score = new Float (st.nextToken ()).floatValue (); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -score = 0; -} else { -throw ex; -} -} -sf.setScore (score); -}if (groupLink != null && removeHTML) { -sf.addLink (groupLink); -sf.description += "%LINK%"; -}if (typeLink.containsKey (type) && removeHTML) { -sf.addLink (typeLink.get (type).toString ()); -sf.description += "%LINK%"; -}this.parseDescriptionHTML (sf, removeHTML); -seq.addSequenceFeature (sf); -while (seqId != null && (seq = align.findName (seq, seqId, false)) != null) { -seq.addSequenceFeature ( new jalview.datamodel.SequenceFeature (sf)); -} -GFFFile = false; -} -} -this.resetMatcher (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -this.warningMessage = ((this.warningMessage == null) ? "" : this.warningMessage) + "Parsing error at\n" + line; -System.out.println ("Error parsing feature file: " + ex + "\n" + line); -ex.printStackTrace (System.err); -this.resetMatcher (); -return false; -} else { -throw ex; -} -} -return true; -}, "jalview.datamodel.AlignmentI,java.util.Map,java.util.Map,~B,~B"); -Clazz.defineMethod (c$, "processGffPragma", -($fz = function (line, gffProps, align, newseqs) { -var spacepos = line.indexOf (' '); -var pragma = spacepos == -1 ? line.substring (2).trim () : line.substring (2, spacepos); -var gffpragma = jalview.io.FeaturesFile.GFFPRAGMA.get (pragma.toLowerCase ()); -if (gffpragma == null) { -return; -}switch (gffpragma) { -case jalview.io.FeaturesFile.GffPragmas.gff_version: -try { -this.gffversion = Integer.parseInt (line.substring (spacepos + 1)); -} finally { -} -break; -case jalview.io.FeaturesFile.GffPragmas.feature_ontology: -break; -case jalview.io.FeaturesFile.GffPragmas.attribute_ontology: -break; -case jalview.io.FeaturesFile.GffPragmas.source_ontology: -break; -case jalview.io.FeaturesFile.GffPragmas.species_build: -break; -case jalview.io.FeaturesFile.GffPragmas.hash: -break; -case jalview.io.FeaturesFile.GffPragmas.fasta: -this.process_as_fasta (align, newseqs); -break; -default: -System.err.println ("Ignoring unknown pragma:\n" + line); -} -}, $fz.isPrivate = true, $fz), "~S,java.util.Map,jalview.datamodel.AlignmentI,java.util.ArrayList"); -Clazz.defineMethod (c$, "process_as_fasta", -($fz = function (align, newseqs) { -try { -this.mark (); -} catch (q) { -if (Clazz.exceptionOf (q, java.io.IOException)) { -} else { -throw q; -} -} -var parser = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", []); -var includedseqs = parser.getSeqs (); -var smatcher = new jalview.analysis.SequenceIdMatcher (newseqs); -for (var p = 0, pSize = includedseqs.size (); p < pSize; p++) { -var dummyseq = smatcher.findIdMatch (includedseqs.get (p)); -if (dummyseq != null) { -var mseq = includedseqs.get (p); -if (Clazz.instanceOf (dummyseq, jalview.datamodel.SequenceDummy)) { -(dummyseq).become (mseq); -includedseqs.set (p, dummyseq); -}}} -for (var seq, $seq = includedseqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -align.addSequence (seq); -} -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List"); -Clazz.defineMethod (c$, "processOrAddSeqFeature", -function (align, newseqs, seq, sf, gFFFile, relaxedIdMatching) { -var attr = sf.getValue ("ATTRIBUTES"); -var add = true; -if (gFFFile && attr != null) { -var nattr = 8; -for (var attset, $attset = 0, $$attset = attr.$plit ("\t"); $attset < $$attset.length && ((attset = $$attset[$attset]) || true); $attset++) { -if (attset == null || attset.trim ().length == 0) { -continue; -}nattr++; -var set = new java.util.HashMap (); -for (var pair, $pair = 0, $$pair = attset.trim ().$plit (";"); $pair < $$pair.length && ((pair = $$pair[$pair]) || true); $pair++) { -pair = pair.trim (); -if (pair.length == 0) { -continue; -}var eqpos = pair.indexOf ('='); -var sppos = pair.indexOf (' '); -var key = null; -var value = null; -if (sppos > -1 && (eqpos == -1 || sppos < eqpos)) { -key = pair.substring (0, sppos); -value = pair.substring (sppos + 1); -} else { -if (eqpos > -1 && (sppos == -1 || eqpos < sppos)) { -key = pair.substring (0, eqpos); -value = pair.substring (eqpos + 1); -} else { -key = pair; -}}if (key != null) { -var vals = set.get (key); -if (vals == null) { -vals = new java.util.ArrayList (); -set.put (key, vals); -}if (value != null) { -vals.add (value.trim ()); -}}} -try { -add = new Boolean (add & this.processGffKey (set, nattr, seq, sf, align, newseqs, relaxedIdMatching)).valueOf (); -} catch (ivfe) { -if (Clazz.exceptionOf (ivfe, jalview.io.FeaturesFile.InvalidGFF3FieldException)) { -System.err.println (ivfe); -} else { -throw ivfe; -} -} -} -}if (add) { -seq.addSequenceFeature (sf); -}return add; -}, "jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceI,jalview.datamodel.SequenceFeature,~B,~B"); -Clazz.defineMethod (c$, "processGffKey", -function (set, nattr, seq, sf, align, newseqs, relaxedIdMatching) { -var attr; -if (sf.getType ().equals ("similarity")) { -var strand = sf.getStrand (); -var querySeq = this.findNames (align, newseqs, relaxedIdMatching, set.get (attr = "Query")); -if (querySeq == null || querySeq.size () != 1) { -throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Expecting exactly one sequence in Query field (got " + set.get (attr) + ")"); -}if (set.containsKey (attr = "Align")) { -var alco = new jalview.datamodel.AlignedCodonFrame (); -var codonmapping = this.constructCodonMappingFromAlign (set, attr, strand); -alco.addMap (seq, querySeq.get (0), codonmapping); -align.addCodonFrame (alco); -return false; -}}return true; -}, "java.util.Map,~N,jalview.datamodel.SequenceI,jalview.datamodel.SequenceFeature,jalview.datamodel.AlignmentI,java.util.List,~B"); -Clazz.defineMethod (c$, "constructCodonMappingFromAlign", -($fz = function (set, attr, strand) { -if (strand == 0) { -throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Invalid strand for a codon mapping (cannot be 0)"); -}var fromrange = new java.util.ArrayList (); -var torange = new java.util.ArrayList (); -var lastppos = 0; -var lastpframe = 0; -for (var range, $range = set.get (attr).iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { -var ints = new java.util.ArrayList (); -var st = new java.util.StringTokenizer (range, " "); -while (st.hasMoreTokens ()) { -var num = st.nextToken (); -try { -ints.add ( new Integer (num)); -} catch (nfe) { -if (Clazz.exceptionOf (nfe, NumberFormatException)) { -throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Invalid number in field " + num); -} else { -throw nfe; -} -} -} -if (ints.size () != 3) { -throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Invalid number of fields for this attribute (" + ints.size () + ")"); -}fromrange.add ( new Integer (ints.get (0).intValue ())); -fromrange.add ( new Integer (ints.get (0).intValue () + strand * ints.get (2).intValue ())); -if (ints.get (1).equals (new Integer (lastppos)) && lastpframe > 0) { -lastppos += (ints.get (2)).intValue () / 3; -lastpframe = (ints.get (2)).intValue () % 3; -torange.set (torange.size () - 1, new Integer (lastppos)); -} else { -torange.add (ints.get (1)); -lastppos = (ints.get (1)).intValue () + (ints.get (2)).intValue () / 3; -lastpframe = (ints.get (2)).intValue () % 3; -torange.add ( new Integer (lastppos)); -}} -if (fromrange.size () % 2 == 1) { -throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Couldn't parse the DNA alignment range correctly"); -}if (torange.size () % 2 == 1) { -throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Couldn't parse the protein alignment range correctly"); -}var frommap = Clazz.newIntArray (fromrange.size (), 0); -var tomap = Clazz.newIntArray (torange.size (), 0); -var p = 0; -for (var ip, $ip = fromrange.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { -frommap[p++] = ip.intValue (); -} -p = 0; -for (var ip, $ip = torange.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { -tomap[p++] = ip.intValue (); -} -return new jalview.util.MapList (frommap, tomap, 3, 1); -}, $fz.isPrivate = true, $fz), "java.util.Map,~S,~N"); -Clazz.defineMethod (c$, "findNames", -($fz = function (align, newseqs, relaxedIdMatching, list) { -var found = new java.util.ArrayList (); -for (var seqId, $seqId = list.iterator (); $seqId.hasNext () && ((seqId = $seqId.next ()) || true);) { -var seq = this.findName (align, seqId, relaxedIdMatching, newseqs); -if (seq != null) { -found.add (seq); -}} -return found; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List,~B,java.util.List"); -Clazz.defineMethod (c$, "resetMatcher", -($fz = function () { -this.lastmatchedAl = null; -this.matcher = null; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "findName", -($fz = function (align, seqId, relaxedIdMatching, newseqs) { -var match = null; -if (relaxedIdMatching) { -if (this.lastmatchedAl !== align) { -this.matcher = new jalview.analysis.SequenceIdMatcher ((this.lastmatchedAl = align).getSequencesArray ()); -if (newseqs != null) { -this.matcher.addAll (newseqs); -}}match = this.matcher.findIdMatch (seqId); -} else { -match = align.findName (seqId, true); -if (match == null && newseqs != null) { -for (var m, $m = newseqs.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -if (seqId.equals (m.getName ())) { -return m; -}} -}}if (match == null && newseqs != null) { -match = new jalview.datamodel.SequenceDummy (seqId); -if (relaxedIdMatching) { -this.matcher.addAll (java.util.Arrays.asList ( Clazz.newArray (-1, [match]))); -}newseqs.add (match); -}return match; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~S,~B,java.util.List"); -Clazz.defineMethod (c$, "parseDescriptionHTML", -function (sf, removeHTML) { -if (sf.getDescription () == null) { -return; -}var parsed = new jalview.util.ParseHtmlBodyAndLinks (sf.getDescription (), removeHTML, this.newline); -sf.description = (removeHTML) ? parsed.getNonHtmlContent () : sf.description; -for (var link, $link = parsed.getLinks ().iterator (); $link.hasNext () && ((link = $link.next ()) || true);) { -sf.addLink (link); -} -}, "jalview.datamodel.SequenceFeature,~B"); -Clazz.defineMethod (c$, "printJalviewFormat", -function (seqs, visible) { -return this.printJalviewFormat (seqs, visible, true, true); -}, "~A,java.util.Map"); -Clazz.defineMethod (c$, "printJalviewFormat", -function (seqs, visible, visOnly, nonpos) { -var out = new StringBuffer (); -var next; -var featuresGen = false; -if (visOnly && !nonpos && (visible == null || visible.size () < 1)) { -return "No Features Visible"; -}if (visible != null && visOnly) { -var en = visible.keySet ().iterator (); -var type; -var color; -while (en.hasNext ()) { -type = en.next ().toString (); -if (Clazz.instanceOf (visible.get (type), jalview.schemes.GraduatedColor)) { -var gc = visible.get (type); -color = (gc.isColourByLabel () ? "label|" : "") + jalview.util.Format.getHexString (gc.getMinColor ()) + "|" + jalview.util.Format.getHexString (gc.getMaxColor ()) + (gc.isAutoScale () ? "|" : "|abso|") + gc.getMin () + "|" + gc.getMax () + "|"; -if (gc.getThreshType () != -1) { -if (gc.getThreshType () == 0) { -color += "below"; -} else { -if (gc.getThreshType () != 1) { -System.err.println ("WARNING: Unsupported threshold type (" + gc.getThreshType () + ") : Assuming 'above'"); -}color += "above"; -}color += "|" + gc.getThresh (); -} else { -color += "none"; -}} else if (Clazz.instanceOf (visible.get (type), java.awt.Color)) { -color = jalview.util.Format.getHexString (visible.get (type)); -} else { -color = jalview.util.Format.getHexString ( new java.awt.Color (Integer.parseInt (visible.get (type).toString ()))); -}out.append (type); -out.append ("\t"); -out.append (color); -out.append (this.newline); -} -}var groups = new java.util.Vector (); -var groupIndex = 0; -var isnonpos = false; -for (var i = 0; i < seqs.length; i++) { -next = seqs[i].getSequenceFeatures (); -if (next != null) { -for (var j = 0; j < next.length; j++) { -isnonpos = next[j].begin == 0 && next[j].end == 0; -if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible.containsKey (next[j].type))) { -continue; -}if (next[j].featureGroup != null && !groups.contains (next[j].featureGroup)) { -groups.addElement (next[j].featureGroup); -}} -}} -var group = null; -do { -if (groups.size () > 0 && groupIndex < groups.size ()) { -group = groups.elementAt (groupIndex).toString (); -out.append (this.newline); -out.append ("STARTGROUP\t"); -out.append (group); -out.append (this.newline); -} else { -group = null; -}for (var i = 0; i < seqs.length; i++) { -next = seqs[i].getSequenceFeatures (); -if (next != null) { -for (var j = 0; j < next.length; j++) { -isnonpos = next[j].begin == 0 && next[j].end == 0; -if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible.containsKey (next[j].type))) { -continue; -}if (group != null && (next[j].featureGroup == null || !next[j].featureGroup.equals (group))) { -continue; -}if (group == null && next[j].featureGroup != null) { -continue; -}featuresGen = true; -if (next[j].description == null || next[j].description.equals ("")) { -out.append (next[j].type + "\t"); -} else { -if (next[j].links != null && next[j].getDescription ().indexOf ("") == -1) { -out.append (""); -}out.append (next[j].description + " "); -if (next[j].links != null) { -for (var l = 0; l < next[j].links.size (); l++) { -var label = next[j].links.elementAt (l).toString (); -var href = label.substring (label.indexOf ("|") + 1); -label = label.substring (0, label.indexOf ("|")); -if (next[j].description.indexOf (href) == -1) { -out.append ("" + label + ""); -}} -if (next[j].getDescription ().indexOf ("") == -1) { -out.append (""); -}}out.append ("\t"); -}out.append (seqs[i].getName ()); -out.append ("\t-1\t"); -out.append (next[j].begin); -out.append ("\t"); -out.append (next[j].end); -out.append ("\t"); -out.append (next[j].type); -if (!Float.isNaN (next[j].score)) { -out.append ("\t"); -out.append (next[j].score); -}out.append (this.newline); -} -}} -if (group != null) { -out.append ("ENDGROUP\t"); -out.append (group); -out.append (this.newline); -groupIndex++; -} else { -break; -}} while (groupIndex < groups.size () + 1); -if (!featuresGen) { -return "No Features Visible"; -}return out.toString (); -}, "~A,java.util.Map,~B,~B"); -Clazz.defineMethod (c$, "printGFFFormat", -function (seqs, visible) { -return this.printGFFFormat (seqs, visible, true, true); -}, "~A,java.util.Map"); -Clazz.defineMethod (c$, "printGFFFormat", -function (seqs, visible, visOnly, nonpos) { -var out = new StringBuffer (); -var next; -var source; -var isnonpos; -for (var i = 0; i < seqs.length; i++) { -if (seqs[i].getSequenceFeatures () != null) { -next = seqs[i].getSequenceFeatures (); -for (var j = 0; j < next.length; j++) { -isnonpos = next[j].begin == 0 && next[j].end == 0; -if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible.containsKey (next[j].type))) { -continue; -}source = next[j].featureGroup; -if (source == null) { -source = next[j].getDescription (); -}out.append (seqs[i].getName ()); -out.append ("\t"); -out.append (source); -out.append ("\t"); -out.append (next[j].type); -out.append ("\t"); -out.append (next[j].begin); -out.append ("\t"); -out.append (next[j].end); -out.append ("\t"); -out.append (next[j].score); -out.append ("\t"); -if (next[j].getValue ("STRAND") != null) { -out.append (next[j].getValue ("STRAND")); -out.append ("\t"); -} else { -out.append (".\t"); -}if (next[j].getValue ("FRAME") != null) { -out.append (next[j].getValue ("FRAME")); -} else { -out.append ("."); -}if (next[j].getValue ("ATTRIBUTES") != null) { -out.append (next[j].getValue ("ATTRIBUTES")); -}out.append (this.newline); -} -}} -return out.toString (); -}, "~A,java.util.Map,~B,~B"); -Clazz.defineMethod (c$, "parse", -function () { -}); -Clazz.overrideMethod (c$, "print", -function () { -return "USE printGFFFormat() or printJalviewFormat()"; -}); -c$.$FeaturesFile$InvalidGFF3FieldException$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.field = null; -this.value = null; -Clazz.instantialize (this, arguments); -}, jalview.io.FeaturesFile, "InvalidGFF3FieldException", Exception); -Clazz.makeConstructor (c$, -function (a, b, c) { -Clazz.superConstructor (this, jalview.io.FeaturesFile.InvalidGFF3FieldException, [c + " (Field was " + a + " and value was " + b.get (a).toString ()]); -this.field = a; -this.value = b.get (a).toString (); -}, "~S,java.util.Map,~S"); -c$ = Clazz.p0p (); -}; -Clazz.pu$h (); -c$ = Clazz.declareType (jalview.io.FeaturesFile, "GffPragmas", Enum); -Clazz.defineEnumConstant (c$, "gff_version", 0, []); -Clazz.defineEnumConstant (c$, "sequence_region", 1, []); -Clazz.defineEnumConstant (c$, "feature_ontology", 2, []); -Clazz.defineEnumConstant (c$, "attribute_ontology", 3, []); -Clazz.defineEnumConstant (c$, "source_ontology", 4, []); -Clazz.defineEnumConstant (c$, "species_build", 5, []); -Clazz.defineEnumConstant (c$, "fasta", 6, []); -Clazz.defineEnumConstant (c$, "hash", 7, []); -c$ = Clazz.p0p (); -Clazz.defineStatics (c$, -"GFFPRAGMA", null); -{ -jalview.io.FeaturesFile.GFFPRAGMA = new java.util.HashMap (); -jalview.io.FeaturesFile.GFFPRAGMA.put ("sequence-region", jalview.io.FeaturesFile.GffPragmas.sequence_region); -jalview.io.FeaturesFile.GFFPRAGMA.put ("feature-ontology", jalview.io.FeaturesFile.GffPragmas.feature_ontology); -jalview.io.FeaturesFile.GFFPRAGMA.put ("#", jalview.io.FeaturesFile.GffPragmas.hash); -jalview.io.FeaturesFile.GFFPRAGMA.put ("fasta", jalview.io.FeaturesFile.GffPragmas.fasta); -jalview.io.FeaturesFile.GFFPRAGMA.put ("species-build", jalview.io.FeaturesFile.GffPragmas.species_build); -jalview.io.FeaturesFile.GFFPRAGMA.put ("source-ontology", jalview.io.FeaturesFile.GffPragmas.source_ontology); -jalview.io.FeaturesFile.GFFPRAGMA.put ("attribute-ontology", jalview.io.FeaturesFile.GffPragmas.attribute_ontology); -}}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile", "java.lang.Enum", "$.Exception"], "jalview.io.FeaturesFile", ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.AlignedCodonFrame", "$.SequenceDummy", "$.SequenceFeature", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.Format", "$.MapList", "$.ParseHtmlBodyAndLinks", "java.awt.Color", "java.lang.Float", "$.StringBuffer", "java.util.ArrayList", "$.Arrays", "$.HashMap", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.doGffSource = true; +this.gffversion = 0; +if (!Clazz.isClassDefined ("jalview.io.FeaturesFile.InvalidGFF3FieldException")) { +jalview.io.FeaturesFile.$FeaturesFile$InvalidGFF3FieldException$ (); +} +this.lastmatchedAl = null; +this.matcher = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "FeaturesFile", jalview.io.AlignFile); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.FeaturesFile, []); +}); +Clazz.defineMethod (c$, "parse", +function (align, colours, removeHTML) { +return this.parse (align, colours, null, removeHTML, false); +}, "jalview.datamodel.AlignmentI,java.util.Hashtable,~B"); +Clazz.defineMethod (c$, "parse", +function (align, colours, removeHTML, relaxedIdMatching) { +return this.parse (align, colours, null, removeHTML, relaxedIdMatching); +}, "jalview.datamodel.AlignmentI,java.util.Map,~B,~B"); +Clazz.defineMethod (c$, "parse", +function (align, colours, featureLink, removeHTML) { +return this.parse (align, colours, featureLink, removeHTML, false); +}, "jalview.datamodel.AlignmentI,java.util.Map,java.util.Map,~B"); +Clazz.defineMethod (c$, "parse", +function (align, colours, featureLink, removeHTML, relaxedIdmatching) { +var line = null; +try { +var seq = null; +var newseqs = new java.util.ArrayList (); +var type; +var desc; +var token = null; +var index; +var start; +var end; +var score; +var st; +var sf; +var featureGroup = null; +var groupLink = null; +var typeLink = new java.util.Hashtable (); +var GFFFile = true; +var gffProps = new java.util.HashMap (); +while ((line = this.nextLine ()) != null) { +if (line.startsWith ("#")) { +if (line.startsWith ("##")) { +this.processGffPragma (line, gffProps, align, newseqs); +line = ""; +}continue; +}st = new java.util.StringTokenizer (line, "\t"); +if (st.countTokens () == 1) { +if (line.trim ().equalsIgnoreCase ("GFF")) { +GFFFile = true; +continue; +}}if (st.countTokens () > 1 && st.countTokens () < 4) { +GFFFile = false; +type = st.nextToken (); +if (type.equalsIgnoreCase ("startgroup")) { +featureGroup = st.nextToken (); +if (st.hasMoreElements ()) { +groupLink = st.nextToken (); +featureLink.put (featureGroup, groupLink); +}} else if (type.equalsIgnoreCase ("endgroup")) { +st.nextToken (); +featureGroup = null; +groupLink = null; +} else { +var colour = null; +var colscheme = st.nextToken (); +if (colscheme.indexOf ("|") > -1 || colscheme.trim ().equalsIgnoreCase ("label")) { +var gcol = new java.util.StringTokenizer (colscheme, "|", true); +var threshtype = -1; +var min = 1.4E-45; +var max = 3.4028235E38; +var threshval = NaN; +var labelCol = false; +var mincol = gcol.nextToken (); +if (mincol === "|") { +System.err.println ("Expected either 'label' or a colour specification in the line: " + line); +continue; +}var maxcol = null; +if (mincol.toLowerCase ().indexOf ("label") == 0) { +labelCol = true; +mincol = (gcol.hasMoreTokens () ? gcol.nextToken () : null); +mincol = (gcol.hasMoreTokens () ? gcol.nextToken () : null); +}var abso = null; +var minval; +var maxval; +if (mincol != null) { +if (mincol.equals ("|")) { +mincol = ""; +} else { +gcol.nextToken (); +}maxcol = gcol.nextToken (); +if (maxcol.equals ("|")) { +maxcol = ""; +} else { +gcol.nextToken (); +}abso = gcol.nextToken (); +gcol.nextToken (); +if (abso.toLowerCase ().indexOf ("abso") != 0) { +minval = abso; +abso = null; +} else { +minval = gcol.nextToken (); +gcol.nextToken (); +}maxval = gcol.nextToken (); +if (gcol.hasMoreTokens ()) { +gcol.nextToken (); +}try { +if (minval.length > 0) { +min = new Float (minval).floatValue (); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Couldn't parse the minimum value for graduated colour for type (" + colscheme + ") - did you misspell 'auto' for the optional automatic colour switch ?"); +e.printStackTrace (); +} else { +throw e; +} +} +try { +if (maxval.length > 0) { +max = new Float (maxval).floatValue (); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Couldn't parse the maximum value for graduated colour for type (" + colscheme + ")"); +e.printStackTrace (); +} else { +throw e; +} +} +} else { +mincol = "FFFFFF"; +maxcol = "000000"; +}try { +colour = new jalview.schemes.GraduatedColor ( new jalview.schemes.UserColourScheme (mincol).findColour ('A'), new jalview.schemes.UserColourScheme (maxcol).findColour ('A'), min, max); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Couldn't parse the graduated colour scheme (" + colscheme + ")"); +e.printStackTrace (); +} else { +throw e; +} +} +if (colour != null) { +(colour).setColourByLabel (labelCol); +(colour).setAutoScaled (abso == null); +var ttype = null; +var tval = null; +if (gcol.hasMoreTokens ()) { +ttype = gcol.nextToken (); +if (ttype.toLowerCase ().startsWith ("below")) { +(colour).setThreshType (0); +} else if (ttype.toLowerCase ().startsWith ("above")) { +(colour).setThreshType (1); +} else { +(colour).setThreshType (-1); +if (!ttype.toLowerCase ().startsWith ("no")) { +System.err.println ("Ignoring unrecognised threshold type : " + ttype); +}}}if ((colour).getThreshType () != -1) { +try { +gcol.nextToken (); +tval = gcol.nextToken (); +(colour).setThresh ( new Float (tval).floatValue ()); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Couldn't parse threshold value as a float: (" + tval + ")"); +e.printStackTrace (); +} else { +throw e; +} +} +}if (gcol.hasMoreTokens ()) { +System.err.println ("Ignoring additional tokens in parameters in graduated colour specification\n"); +while (gcol.hasMoreTokens ()) { +System.err.println ("|" + gcol.nextToken ()); +} +System.err.println ("\n"); +}}} else { +var ucs = new jalview.schemes.UserColourScheme (colscheme); +colour = ucs.findColour ('A'); +}if (colour != null) { +colours.put (type, colour); +}if (st.hasMoreElements ()) { +var link = st.nextToken (); +typeLink.put (type, link); +if (featureLink == null) { +featureLink = new java.util.Hashtable (); +}featureLink.put (type, link); +}}continue; +}var seqId = ""; +while (st.hasMoreElements ()) { +if (GFFFile) { +seqId = token = st.nextToken (); +seq = this.findName (align, seqId, relaxedIdmatching, newseqs); +if (seq != null) { +desc = st.nextToken (); +var group = null; +if (this.doGffSource && desc.indexOf (' ') == -1) { +group = String.instantialize (desc); +}type = st.nextToken (); +try { +var stt = st.nextToken (); +if (stt.length == 0 || stt.equals ("-")) { +start = 0; +} else { +start = Integer.parseInt (stt); +}} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +start = 0; +} else { +throw ex; +} +} +try { +var stt = st.nextToken (); +if (stt.length == 0 || stt.equals ("-")) { +end = 0; +} else { +end = Integer.parseInt (stt); +}} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +end = 0; +} else { +throw ex; +} +} +if (end == 0) { +start = 0; +}try { +score = new Float (st.nextToken ()).floatValue (); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +score = 0; +} else { +throw ex; +} +} +sf = new jalview.datamodel.SequenceFeature (type, desc, start, end, score, group); +try { +sf.setValue ("STRAND", st.nextToken ()); +sf.setValue ("FRAME", st.nextToken ()); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +if (st.hasMoreTokens ()) { +var attributes = new StringBuffer (); +var sep = false; +while (st.hasMoreTokens ()) { +attributes.append ((sep ? "\t" : "") + st.nextElement ()); +sep = true; +} +sf.setValue ("ATTRIBUTES", attributes.toString ()); +}if (this.processOrAddSeqFeature (align, newseqs, seq, sf, GFFFile, relaxedIdmatching)) { +while ((seq = align.findName (seq, seqId, true)) != null) { +seq.addSequenceFeature ( new jalview.datamodel.SequenceFeature (sf)); +} +}break; +}}if (GFFFile && seq == null) { +desc = token; +} else { +desc = st.nextToken (); +}if (!st.hasMoreTokens ()) { +System.err.println ("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up."); +return false; +}token = st.nextToken (); +if (!token.equals ("ID_NOT_SPECIFIED")) { +seq = this.findName (align, seqId = token, relaxedIdmatching, null); +st.nextToken (); +} else { +seqId = null; +try { +index = Integer.parseInt (st.nextToken ()); +seq = align.getSequenceAt (index); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +seq = null; +} else { +throw ex; +} +} +}if (seq == null) { +System.out.println ("Sequence not found: " + line); +break; +}start = Integer.parseInt (st.nextToken ()); +end = Integer.parseInt (st.nextToken ()); +type = st.nextToken (); +if (!colours.containsKey (type)) { +var ucs = new jalview.schemes.UserColourScheme (type); +colours.put (type, ucs.findColour ('A')); +}sf = new jalview.datamodel.SequenceFeature (type, desc, "", start, end, featureGroup); +if (st.hasMoreTokens ()) { +try { +score = new Float (st.nextToken ()).floatValue (); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +score = 0; +} else { +throw ex; +} +} +sf.setScore (score); +}if (groupLink != null && removeHTML) { +sf.addLink (groupLink); +sf.description += "%LINK%"; +}if (typeLink.containsKey (type) && removeHTML) { +sf.addLink (typeLink.get (type).toString ()); +sf.description += "%LINK%"; +}this.parseDescriptionHTML (sf, removeHTML); +seq.addSequenceFeature (sf); +while (seqId != null && (seq = align.findName (seq, seqId, false)) != null) { +seq.addSequenceFeature ( new jalview.datamodel.SequenceFeature (sf)); +} +GFFFile = false; +} +} +this.resetMatcher (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +this.warningMessage = ((this.warningMessage == null) ? "" : this.warningMessage) + "Parsing error at\n" + line; +System.out.println ("Error parsing feature file: " + ex + "\n" + line); +ex.printStackTrace (System.err); +this.resetMatcher (); +return false; +} else { +throw ex; +} +} +return true; +}, "jalview.datamodel.AlignmentI,java.util.Map,java.util.Map,~B,~B"); +Clazz.defineMethod (c$, "processGffPragma", +($fz = function (line, gffProps, align, newseqs) { +var spacepos = line.indexOf (' '); +var pragma = spacepos == -1 ? line.substring (2).trim () : line.substring (2, spacepos); +var gffpragma = jalview.io.FeaturesFile.GFFPRAGMA.get (pragma.toLowerCase ()); +if (gffpragma == null) { +return; +}switch (gffpragma) { +case jalview.io.FeaturesFile.GffPragmas.gff_version: +try { +this.gffversion = Integer.parseInt (line.substring (spacepos + 1)); +} finally { +} +break; +case jalview.io.FeaturesFile.GffPragmas.feature_ontology: +break; +case jalview.io.FeaturesFile.GffPragmas.attribute_ontology: +break; +case jalview.io.FeaturesFile.GffPragmas.source_ontology: +break; +case jalview.io.FeaturesFile.GffPragmas.species_build: +break; +case jalview.io.FeaturesFile.GffPragmas.hash: +break; +case jalview.io.FeaturesFile.GffPragmas.fasta: +this.process_as_fasta (align, newseqs); +break; +default: +System.err.println ("Ignoring unknown pragma:\n" + line); +} +}, $fz.isPrivate = true, $fz), "~S,java.util.Map,jalview.datamodel.AlignmentI,java.util.ArrayList"); +Clazz.defineMethod (c$, "process_as_fasta", +($fz = function (align, newseqs) { +try { +this.mark (); +} catch (q) { +if (Clazz.exceptionOf (q, java.io.IOException)) { +} else { +throw q; +} +} +var parser = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", []); +var includedseqs = parser.getSeqs (); +var smatcher = new jalview.analysis.SequenceIdMatcher (newseqs); +for (var p = 0, pSize = includedseqs.size (); p < pSize; p++) { +var dummyseq = smatcher.findIdMatch (includedseqs.get (p)); +if (dummyseq != null) { +var mseq = includedseqs.get (p); +if (Clazz.instanceOf (dummyseq, jalview.datamodel.SequenceDummy)) { +(dummyseq).become (mseq); +includedseqs.set (p, dummyseq); +}}} +for (var seq, $seq = includedseqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +align.addSequence (seq); +} +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List"); +Clazz.defineMethod (c$, "processOrAddSeqFeature", +function (align, newseqs, seq, sf, gFFFile, relaxedIdMatching) { +var attr = sf.getValue ("ATTRIBUTES"); +var add = true; +if (gFFFile && attr != null) { +var nattr = 8; +for (var attset, $attset = 0, $$attset = attr.$plit ("\t"); $attset < $$attset.length && ((attset = $$attset[$attset]) || true); $attset++) { +if (attset == null || attset.trim ().length == 0) { +continue; +}nattr++; +var set = new java.util.HashMap (); +for (var pair, $pair = 0, $$pair = attset.trim ().$plit (";"); $pair < $$pair.length && ((pair = $$pair[$pair]) || true); $pair++) { +pair = pair.trim (); +if (pair.length == 0) { +continue; +}var eqpos = pair.indexOf ('='); +var sppos = pair.indexOf (' '); +var key = null; +var value = null; +if (sppos > -1 && (eqpos == -1 || sppos < eqpos)) { +key = pair.substring (0, sppos); +value = pair.substring (sppos + 1); +} else { +if (eqpos > -1 && (sppos == -1 || eqpos < sppos)) { +key = pair.substring (0, eqpos); +value = pair.substring (eqpos + 1); +} else { +key = pair; +}}if (key != null) { +var vals = set.get (key); +if (vals == null) { +vals = new java.util.ArrayList (); +set.put (key, vals); +}if (value != null) { +vals.add (value.trim ()); +}}} +try { +add = new Boolean (add & this.processGffKey (set, nattr, seq, sf, align, newseqs, relaxedIdMatching)).valueOf (); +} catch (ivfe) { +if (Clazz.exceptionOf (ivfe, jalview.io.FeaturesFile.InvalidGFF3FieldException)) { +System.err.println (ivfe); +} else { +throw ivfe; +} +} +} +}if (add) { +seq.addSequenceFeature (sf); +}return add; +}, "jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceI,jalview.datamodel.SequenceFeature,~B,~B"); +Clazz.defineMethod (c$, "processGffKey", +function (set, nattr, seq, sf, align, newseqs, relaxedIdMatching) { +var attr; +if (sf.getType ().equals ("similarity")) { +var strand = sf.getStrand (); +var querySeq = this.findNames (align, newseqs, relaxedIdMatching, set.get (attr = "Query")); +if (querySeq == null || querySeq.size () != 1) { +throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Expecting exactly one sequence in Query field (got " + set.get (attr) + ")"); +}if (set.containsKey (attr = "Align")) { +var alco = new jalview.datamodel.AlignedCodonFrame (); +var codonmapping = this.constructCodonMappingFromAlign (set, attr, strand); +alco.addMap (seq, querySeq.get (0), codonmapping); +align.addCodonFrame (alco); +return false; +}}return true; +}, "java.util.Map,~N,jalview.datamodel.SequenceI,jalview.datamodel.SequenceFeature,jalview.datamodel.AlignmentI,java.util.List,~B"); +Clazz.defineMethod (c$, "constructCodonMappingFromAlign", +($fz = function (set, attr, strand) { +if (strand == 0) { +throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Invalid strand for a codon mapping (cannot be 0)"); +}var fromrange = new java.util.ArrayList (); +var torange = new java.util.ArrayList (); +var lastppos = 0; +var lastpframe = 0; +for (var range, $range = set.get (attr).iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { +var ints = new java.util.ArrayList (); +var st = new java.util.StringTokenizer (range, " "); +while (st.hasMoreTokens ()) { +var num = st.nextToken (); +try { +ints.add ( new Integer (num)); +} catch (nfe) { +if (Clazz.exceptionOf (nfe, NumberFormatException)) { +throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Invalid number in field " + num); +} else { +throw nfe; +} +} +} +if (ints.size () != 3) { +throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Invalid number of fields for this attribute (" + ints.size () + ")"); +}fromrange.add ( new Integer (ints.get (0).intValue ())); +fromrange.add ( new Integer (ints.get (0).intValue () + strand * ints.get (2).intValue ())); +if (ints.get (1).equals (new Integer (lastppos)) && lastpframe > 0) { +lastppos += (ints.get (2)).intValue () / 3; +lastpframe = (ints.get (2)).intValue () % 3; +torange.set (torange.size () - 1, new Integer (lastppos)); +} else { +torange.add (ints.get (1)); +lastppos = (ints.get (1)).intValue () + (ints.get (2)).intValue () / 3; +lastpframe = (ints.get (2)).intValue () % 3; +torange.add ( new Integer (lastppos)); +}} +if (fromrange.size () % 2 == 1) { +throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Couldn't parse the DNA alignment range correctly"); +}if (torange.size () % 2 == 1) { +throw Clazz.innerTypeInstance (jalview.io.FeaturesFile.InvalidGFF3FieldException, this, null, attr, set, "Couldn't parse the protein alignment range correctly"); +}var frommap = Clazz.newIntArray (fromrange.size (), 0); +var tomap = Clazz.newIntArray (torange.size (), 0); +var p = 0; +for (var ip, $ip = fromrange.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { +frommap[p++] = ip.intValue (); +} +p = 0; +for (var ip, $ip = torange.iterator (); $ip.hasNext () && ((ip = $ip.next ()) || true);) { +tomap[p++] = ip.intValue (); +} +return new jalview.util.MapList (frommap, tomap, 3, 1); +}, $fz.isPrivate = true, $fz), "java.util.Map,~S,~N"); +Clazz.defineMethod (c$, "findNames", +($fz = function (align, newseqs, relaxedIdMatching, list) { +var found = new java.util.ArrayList (); +for (var seqId, $seqId = list.iterator (); $seqId.hasNext () && ((seqId = $seqId.next ()) || true);) { +var seq = this.findName (align, seqId, relaxedIdMatching, newseqs); +if (seq != null) { +found.add (seq); +}} +return found; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,java.util.List,~B,java.util.List"); +Clazz.defineMethod (c$, "resetMatcher", +($fz = function () { +this.lastmatchedAl = null; +this.matcher = null; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "findName", +($fz = function (align, seqId, relaxedIdMatching, newseqs) { +var match = null; +if (relaxedIdMatching) { +if (this.lastmatchedAl !== align) { +this.matcher = new jalview.analysis.SequenceIdMatcher ((this.lastmatchedAl = align).getSequencesArray ()); +if (newseqs != null) { +this.matcher.addAll (newseqs); +}}match = this.matcher.findIdMatch (seqId); +} else { +match = align.findName (seqId, true); +if (match == null && newseqs != null) { +for (var m, $m = newseqs.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +if (seqId.equals (m.getName ())) { +return m; +}} +}}if (match == null && newseqs != null) { +match = new jalview.datamodel.SequenceDummy (seqId); +if (relaxedIdMatching) { +this.matcher.addAll (java.util.Arrays.asList ( Clazz.newArray (-1, [match]))); +}newseqs.add (match); +}return match; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~S,~B,java.util.List"); +Clazz.defineMethod (c$, "parseDescriptionHTML", +function (sf, removeHTML) { +if (sf.getDescription () == null) { +return; +}var parsed = new jalview.util.ParseHtmlBodyAndLinks (sf.getDescription (), removeHTML, this.newline); +sf.description = (removeHTML) ? parsed.getNonHtmlContent () : sf.description; +for (var link, $link = parsed.getLinks ().iterator (); $link.hasNext () && ((link = $link.next ()) || true);) { +sf.addLink (link); +} +}, "jalview.datamodel.SequenceFeature,~B"); +Clazz.defineMethod (c$, "printJalviewFormat", +function (seqs, visible) { +return this.printJalviewFormat (seqs, visible, true, true); +}, "~A,java.util.Map"); +Clazz.defineMethod (c$, "printJalviewFormat", +function (seqs, visible, visOnly, nonpos) { +var out = new StringBuffer (); +var next; +var featuresGen = false; +if (visOnly && !nonpos && (visible == null || visible.size () < 1)) { +return "No Features Visible"; +}if (visible != null && visOnly) { +var en = visible.keySet ().iterator (); +var type; +var color; +while (en.hasNext ()) { +type = en.next ().toString (); +if (Clazz.instanceOf (visible.get (type), jalview.schemes.GraduatedColor)) { +var gc = visible.get (type); +color = (gc.isColourByLabel () ? "label|" : "") + jalview.util.Format.getHexString (gc.getMinColor ()) + "|" + jalview.util.Format.getHexString (gc.getMaxColor ()) + (gc.isAutoScale () ? "|" : "|abso|") + gc.getMin () + "|" + gc.getMax () + "|"; +if (gc.getThreshType () != -1) { +if (gc.getThreshType () == 0) { +color += "below"; +} else { +if (gc.getThreshType () != 1) { +System.err.println ("WARNING: Unsupported threshold type (" + gc.getThreshType () + ") : Assuming 'above'"); +}color += "above"; +}color += "|" + gc.getThresh (); +} else { +color += "none"; +}} else if (Clazz.instanceOf (visible.get (type), java.awt.Color)) { +color = jalview.util.Format.getHexString (visible.get (type)); +} else { +color = jalview.util.Format.getHexString ( new java.awt.Color (Integer.parseInt (visible.get (type).toString ()))); +}out.append (type); +out.append ("\t"); +out.append (color); +out.append (this.newline); +} +}var groups = new java.util.Vector (); +var groupIndex = 0; +var isnonpos = false; +for (var i = 0; i < seqs.length; i++) { +next = seqs[i].getSequenceFeatures (); +if (next != null) { +for (var j = 0; j < next.length; j++) { +isnonpos = next[j].begin == 0 && next[j].end == 0; +if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible.containsKey (next[j].type))) { +continue; +}if (next[j].featureGroup != null && !groups.contains (next[j].featureGroup)) { +groups.addElement (next[j].featureGroup); +}} +}} +var group = null; +do { +if (groups.size () > 0 && groupIndex < groups.size ()) { +group = groups.elementAt (groupIndex).toString (); +out.append (this.newline); +out.append ("STARTGROUP\t"); +out.append (group); +out.append (this.newline); +} else { +group = null; +}for (var i = 0; i < seqs.length; i++) { +next = seqs[i].getSequenceFeatures (); +if (next != null) { +for (var j = 0; j < next.length; j++) { +isnonpos = next[j].begin == 0 && next[j].end == 0; +if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible.containsKey (next[j].type))) { +continue; +}if (group != null && (next[j].featureGroup == null || !next[j].featureGroup.equals (group))) { +continue; +}if (group == null && next[j].featureGroup != null) { +continue; +}featuresGen = true; +if (next[j].description == null || next[j].description.equals ("")) { +out.append (next[j].type + "\t"); +} else { +if (next[j].links != null && next[j].getDescription ().indexOf ("") == -1) { +out.append (""); +}out.append (next[j].description + " "); +if (next[j].links != null) { +for (var l = 0; l < next[j].links.size (); l++) { +var label = next[j].links.elementAt (l).toString (); +var href = label.substring (label.indexOf ("|") + 1); +label = label.substring (0, label.indexOf ("|")); +if (next[j].description.indexOf (href) == -1) { +out.append ("" + label + ""); +}} +if (next[j].getDescription ().indexOf ("") == -1) { +out.append (""); +}}out.append ("\t"); +}out.append (seqs[i].getName ()); +out.append ("\t-1\t"); +out.append ("" + next[j].begin); +out.append ("\t"); +out.append ("" + next[j].end); +out.append ("\t"); +out.append (next[j].type); +if (!Float.isNaN (next[j].score)) { +out.append ("\t"); +out.append (next[j].score); +}out.append (this.newline); +} +}} +if (group != null) { +out.append ("ENDGROUP\t"); +out.append (group); +out.append (this.newline); +groupIndex++; +} else { +break; +}} while (groupIndex < groups.size () + 1); +if (!featuresGen) { +return "No Features Visible"; +}return out.toString (); +}, "~A,java.util.Map,~B,~B"); +Clazz.defineMethod (c$, "printGFFFormat", +function (seqs, visible) { +return this.printGFFFormat (seqs, visible, true, true); +}, "~A,java.util.Map"); +Clazz.defineMethod (c$, "printGFFFormat", +function (seqs, visible, visOnly, nonpos) { +var out = new StringBuffer (); +var next; +var source; +var isnonpos; +for (var i = 0; i < seqs.length; i++) { +if (seqs[i].getSequenceFeatures () != null) { +next = seqs[i].getSequenceFeatures (); +for (var j = 0; j < next.length; j++) { +isnonpos = next[j].begin == 0 && next[j].end == 0; +if ((!nonpos && isnonpos) || (!isnonpos && visOnly && !visible.containsKey (next[j].type))) { +continue; +}source = next[j].featureGroup; +if (source == null) { +source = next[j].getDescription (); +}out.append (seqs[i].getName ()); +out.append ("\t"); +out.append (source); +out.append ("\t"); +out.append (next[j].type); +out.append ("\t"); +out.append ("" + next[j].begin); +out.append ("\t"); +out.append ("" + next[j].end); +out.append ("\t"); +out.append (next[j].score); +out.append ("\t"); +if (next[j].getValue ("STRAND") != null) { +out.append (next[j].getValue ("STRAND")); +out.append ("\t"); +} else { +out.append (".\t"); +}if (next[j].getValue ("FRAME") != null) { +out.append (next[j].getValue ("FRAME")); +} else { +out.append ("."); +}if (next[j].getValue ("ATTRIBUTES") != null) { +out.append (next[j].getValue ("ATTRIBUTES")); +}out.append (this.newline); +} +}} +return out.toString (); +}, "~A,java.util.Map,~B,~B"); +Clazz.defineMethod (c$, "parse", +function () { +}); +Clazz.overrideMethod (c$, "print", +function () { +return "USE printGFFFormat() or printJalviewFormat()"; +}); +c$.$FeaturesFile$InvalidGFF3FieldException$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.field = null; +this.value = null; +Clazz.instantialize (this, arguments); +}, jalview.io.FeaturesFile, "InvalidGFF3FieldException", Exception); +Clazz.makeConstructor (c$, +function (a, b, c) { +Clazz.superConstructor (this, jalview.io.FeaturesFile.InvalidGFF3FieldException, [c + " (Field was " + a + " and value was " + b.get (a).toString ()]); +this.field = a; +this.value = b.get (a).toString (); +}, "~S,java.util.Map,~S"); +c$ = Clazz.p0p (); +}; +Clazz.pu$h (); +c$ = Clazz.declareType (jalview.io.FeaturesFile, "GffPragmas", Enum); +Clazz.defineEnumConstant (c$, "gff_version", 0, []); +Clazz.defineEnumConstant (c$, "sequence_region", 1, []); +Clazz.defineEnumConstant (c$, "feature_ontology", 2, []); +Clazz.defineEnumConstant (c$, "attribute_ontology", 3, []); +Clazz.defineEnumConstant (c$, "source_ontology", 4, []); +Clazz.defineEnumConstant (c$, "species_build", 5, []); +Clazz.defineEnumConstant (c$, "fasta", 6, []); +Clazz.defineEnumConstant (c$, "hash", 7, []); +c$ = Clazz.p0p (); +Clazz.defineStatics (c$, +"GFFPRAGMA", null); +{ +jalview.io.FeaturesFile.GFFPRAGMA = new java.util.HashMap (); +jalview.io.FeaturesFile.GFFPRAGMA.put ("sequence-region", jalview.io.FeaturesFile.GffPragmas.sequence_region); +jalview.io.FeaturesFile.GFFPRAGMA.put ("feature-ontology", jalview.io.FeaturesFile.GffPragmas.feature_ontology); +jalview.io.FeaturesFile.GFFPRAGMA.put ("#", jalview.io.FeaturesFile.GffPragmas.hash); +jalview.io.FeaturesFile.GFFPRAGMA.put ("fasta", jalview.io.FeaturesFile.GffPragmas.fasta); +jalview.io.FeaturesFile.GFFPRAGMA.put ("species-build", jalview.io.FeaturesFile.GffPragmas.species_build); +jalview.io.FeaturesFile.GFFPRAGMA.put ("source-ontology", jalview.io.FeaturesFile.GffPragmas.source_ontology); +jalview.io.FeaturesFile.GFFPRAGMA.put ("attribute-ontology", jalview.io.FeaturesFile.GffPragmas.attribute_ontology); +}}); diff --git a/bin/jalview/io/FileParse.class b/bin/jalview/io/FileParse.class index 86fbc3c..e2448f1 100644 Binary files a/bin/jalview/io/FileParse.class and b/bin/jalview/io/FileParse.class differ diff --git a/bin/jalview/io/FileParse.js b/bin/jalview/io/FileParse.js index 51d1e87..a16b90a 100644 --- a/bin/jalview/io/FileParse.js +++ b/bin/jalview/io/FileParse.js @@ -1,250 +1,250 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.FileParse", ["jalview.io.AppletFormatAdapter", "jalview.util.MessageManager", "java.io.BufferedReader", "$.IOException", "$.InputStreamReader", "$.StringReader", "java.lang.Error", "java.net.URL", "java.util.zip.GZIPInputStream"], function () { -c$ = Clazz.decorateAsClass (function () { -this.dataName = "unknown source"; -this.inFile = null; -this.viewport = null; -this.exportSettings = null; -this.index = 1; -this.suffixSeparator = '#'; -this.newline = null; -this.suffix = null; -this.type = null; -this.dataIn = null; -this.errormessage = "UNITIALISED SOURCE"; -this.error = true; -this.warningMessage = null; -this.READAHEAD_LIMIT = 2048; -Clazz.instantialize (this, arguments); -}, jalview.io, "FileParse"); -Clazz.prepareFields (c$, function () { -this.newline = System.getProperty ("line.separator"); -}); -Clazz.defineMethod (c$, "setNewlineString", -function (nl) { -this.newline = nl; -}, "~S"); -Clazz.defineMethod (c$, "getNewlineString", -function () { -return this.newline; -}); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.makeConstructor (c$, -function (from) { -if (from == null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_null_fileparse")); -}if (from === this) { -return; -}this.index = ++from.index; -this.inFile = from.inFile; -this.suffixSeparator = from.suffixSeparator; -this.suffix = from.suffix; -this.errormessage = from.errormessage; -this.error = false; -this.type = from.type; -this.dataIn = from.dataIn; -if (this.dataIn != null) { -this.mark (); -}this.dataName = from.dataName; -}, "jalview.io.FileParse"); -Clazz.defineMethod (c$, "tryAsGzipSource", -($fz = function (inputStream) { -var inData = new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.util.zip.GZIPInputStream (inputStream))); -inData.mark (2048); -inData.read (); -inData.reset (); -return inData; -}, $fz.isPrivate = true, $fz), "java.io.InputStream"); -Clazz.defineMethod (c$, "checkURLSource", -($fz = function (fileStr) { -this.errormessage = "URL NOT FOUND"; -var url = new java.net.URL (fileStr); -var e = null; -if (fileStr.toLowerCase ().endsWith (".gz")) { -try { -var inputStream = url.openStream (); -this.dataIn = this.tryAsGzipSource (inputStream); -this.dataName = fileStr; -return false; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -e = ex; -} else { -throw ex; -} -} -}try { -this.dataIn = new java.io.BufferedReader ( new java.io.InputStreamReader (url.openStream ())); -} catch (q) { -if (Clazz.exceptionOf (q, java.io.IOException)) { -if (e != null) { -throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.failed_to_resolve_gzip_stream"), e); -}throw q; -} else { -throw q; -} -} -this.dataName = fileStr; -return false; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "extractSuffix", -($fz = function (fileStr) { -var sfpos = fileStr.lastIndexOf (this.suffixSeparator); -if (sfpos > -1 && sfpos < fileStr.length - 1) { -this.suffix = fileStr.substring (sfpos + 1); -return fileStr.substring (0, sfpos); -}return null; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.makeConstructor (c$, -function (fileStr, type) { -this.type = type; -this.error = false; -if (type.equals (jalview.io.AppletFormatAdapter.FILE)) { -{ -}} else if (type.equals (jalview.io.AppletFormatAdapter.URL)) { -try { -try { -this.checkURLSource (fileStr); -if (this.suffixSeparator == '#') { -this.extractSuffix (fileStr); -}} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -var suffixLess = this.extractSuffix (fileStr); -if (suffixLess == null) { -throw (e); -} else { -try { -this.checkURLSource (suffixLess); -} catch (e2) { -if (Clazz.exceptionOf (e2, java.io.IOException)) { -this.errormessage = "BAD URL WITH OR WITHOUT SUFFIX"; -throw (e); -} else { -throw e2; -} -} -}} else { -throw e; -} -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -this.errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' (" + e.getMessage () + ")"; -this.error = true; -} else { -throw e; -} -} -} else if (type.equals (jalview.io.AppletFormatAdapter.PASTE)) { -this.errormessage = "PASTE INACCESSIBLE!"; -this.dataIn = new java.io.BufferedReader ( new java.io.StringReader (fileStr)); -this.dataName = "Paste"; -} else if (type.equals (jalview.io.AppletFormatAdapter.CLASSLOADER)) { -this.errormessage = "RESOURCE CANNOT BE LOCATED"; -var is = this.getClass ().getResourceAsStream ("/" + fileStr); -if (is == null) { -var suffixLess = this.extractSuffix (fileStr); -if (suffixLess != null) { -is = this.getClass ().getResourceAsStream ("/" + suffixLess); -}}if (is != null) { -this.dataIn = new java.io.BufferedReader ( new java.io.InputStreamReader (is)); -this.dataName = fileStr; -} else { -this.error = true; -}} else { -this.errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" + (type != null ? type : "null") + "'"; -this.error = true; -}if (this.dataIn == null || this.error) { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.failed_to_read_data_from_source", Clazz.newArray (-1, [this.errormessage]))); -}this.error = false; -this.dataIn.mark (2048); -}, "~S,~S"); -Clazz.defineMethod (c$, "mark", -function () { -if (this.dataIn != null) { -this.dataIn.mark (2048); -} else { -throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.no_init_source_stream")); -}}); -Clazz.defineMethod (c$, "nextLine", -function () { -if (!this.error) { -return this.dataIn.readLine (); -}throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.invalid_source_stream", Clazz.newArray (-1, [this.errormessage]))); -}); -Clazz.defineMethod (c$, "isExporting", -function () { -return !this.error && this.dataIn == null; -}); -Clazz.defineMethod (c$, "isValid", -function () { -return !this.error; -}); -Clazz.defineMethod (c$, "close", -function () { -this.errormessage = "EXCEPTION ON CLOSE"; -this.error = true; -this.dataIn.close (); -this.dataIn = null; -this.errormessage = "SOURCE IS CLOSED"; -}); -Clazz.defineMethod (c$, "reset", -function () { -if (this.dataIn != null && !this.error) { -this.dataIn.reset (); -} else { -throw new java.io.IOException (jalview.util.MessageManager.getString ("error.implementation_error_reset_called_for_invalid_source")); -}}); -Clazz.defineMethod (c$, "hasWarningMessage", -function () { -return (this.warningMessage != null && this.warningMessage.length > 0); -}); -Clazz.defineMethod (c$, "getWarningMessage", -function () { -return this.warningMessage; -}); -Clazz.defineMethod (c$, "getInFile", -function () { -if (this.inFile != null) { -return this.inFile.getAbsolutePath () + " (" + this.index + ")"; -} else { -return "From Paste + (" + this.index + ")"; -}}); -Clazz.defineMethod (c$, "getDataName", -function () { -return this.dataName; -}); -Clazz.defineMethod (c$, "setDataName", -function (dataname) { -this.dataName = dataname; -}, "~S"); -Clazz.defineMethod (c$, "getReader", -function () { -if (this.dataIn != null) { -return this.dataIn; -}return null; -}); -Clazz.defineMethod (c$, "getViewport", -function () { -return this.viewport; -}); -Clazz.defineMethod (c$, "setViewport", -function (viewport) { -this.viewport = viewport; -}, "jalview.api.AlignViewportI"); -Clazz.defineMethod (c$, "getExportSettings", -function () { -return this.exportSettings; -}); -Clazz.defineMethod (c$, "setExportSettings", -function (exportSettings) { -this.exportSettings = exportSettings; -}, "jalview.api.AlignExportSettingI"); -Clazz.defineMethod (c$, "configureForView", -function (avpanel) { -if (avpanel != null) { -this.setViewport (avpanel.getAlignViewport ()); -}}, "jalview.api.AlignmentViewPanel"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.FileParse", ["jalview.io.AppletFormatAdapter", "jalview.util.MessageManager", "java.io.BufferedReader", "$.IOException", "$.InputStreamReader", "$.StringReader", "java.lang.Error", "java.net.URL", "java.util.zip.GZIPInputStream"], function () { +c$ = Clazz.decorateAsClass (function () { +this.dataName = "unknown source"; +this.inFile = null; +this.viewport = null; +this.exportSettings = null; +this.index = 1; +this.suffixSeparator = '#'; +this.newline = null; +this.suffix = null; +this.type = null; +this.dataIn = null; +this.errormessage = "UNITIALISED SOURCE"; +this.error = true; +this.warningMessage = null; +this.READAHEAD_LIMIT = 2048; +Clazz.instantialize (this, arguments); +}, jalview.io, "FileParse"); +Clazz.prepareFields (c$, function () { +this.newline = System.getProperty ("line.separator"); +}); +Clazz.defineMethod (c$, "setNewlineString", +function (nl) { +this.newline = nl; +}, "~S"); +Clazz.defineMethod (c$, "getNewlineString", +function () { +return this.newline; +}); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.makeConstructor (c$, +function (from) { +if (from == null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_null_fileparse")); +}if (from === this) { +return; +}this.index = ++from.index; +this.inFile = from.inFile; +this.suffixSeparator = from.suffixSeparator; +this.suffix = from.suffix; +this.errormessage = from.errormessage; +this.error = false; +this.type = from.type; +this.dataIn = from.dataIn; +if (this.dataIn != null) { +this.mark (); +}this.dataName = from.dataName; +}, "jalview.io.FileParse"); +Clazz.defineMethod (c$, "tryAsGzipSource", +($fz = function (inputStream) { +var inData = new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.util.zip.GZIPInputStream (inputStream))); +inData.mark (2048); +inData.read (); +inData.reset (); +return inData; +}, $fz.isPrivate = true, $fz), "java.io.InputStream"); +Clazz.defineMethod (c$, "checkURLSource", +($fz = function (fileStr) { +this.errormessage = "URL NOT FOUND"; +var url = new java.net.URL (fileStr); +var e = null; +if (fileStr.toLowerCase ().endsWith (".gz")) { +try { +var inputStream = url.openStream (); +this.dataIn = this.tryAsGzipSource (inputStream); +this.dataName = fileStr; +return false; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +e = ex; +} else { +throw ex; +} +} +}try { +this.dataIn = new java.io.BufferedReader ( new java.io.InputStreamReader (url.openStream ())); +} catch (q) { +if (Clazz.exceptionOf (q, java.io.IOException)) { +if (e != null) { +throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.failed_to_resolve_gzip_stream"), e); +}throw q; +} else { +throw q; +} +} +this.dataName = fileStr; +return false; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "extractSuffix", +($fz = function (fileStr) { +var sfpos = fileStr.lastIndexOf (this.suffixSeparator); +if (sfpos > -1 && sfpos < fileStr.length - 1) { +this.suffix = fileStr.substring (sfpos + 1); +return fileStr.substring (0, sfpos); +}return null; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.makeConstructor (c$, +function (fileStr, type) { +this.type = type; +this.error = false; +if (type.equals (jalview.io.AppletFormatAdapter.FILE)) { +{ +}} else if (type.equals (jalview.io.AppletFormatAdapter.URL)) { +try { +try { +this.checkURLSource (fileStr); +if (this.suffixSeparator == '#') { +this.extractSuffix (fileStr); +}} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +var suffixLess = this.extractSuffix (fileStr); +if (suffixLess == null) { +throw (e); +} else { +try { +this.checkURLSource (suffixLess); +} catch (e2) { +if (Clazz.exceptionOf (e2, java.io.IOException)) { +this.errormessage = "BAD URL WITH OR WITHOUT SUFFIX"; +throw (e); +} else { +throw e2; +} +} +}} else { +throw e; +} +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +this.errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' (" + e.getMessage () + ")"; +this.error = true; +} else { +throw e; +} +} +} else if (type.equals (jalview.io.AppletFormatAdapter.PASTE)) { +this.errormessage = "PASTE INACCESSIBLE!"; +this.dataIn = new java.io.BufferedReader ( new java.io.StringReader (fileStr)); +this.dataName = "Paste"; +} else if (type.equals (jalview.io.AppletFormatAdapter.CLASSLOADER)) { +this.errormessage = "RESOURCE CANNOT BE LOCATED"; +var is = this.getClass ().getResourceAsStream ("/" + fileStr); +if (is == null) { +var suffixLess = this.extractSuffix (fileStr); +if (suffixLess != null) { +is = this.getClass ().getResourceAsStream ("/" + suffixLess); +}}if (is != null) { +this.dataIn = new java.io.BufferedReader ( new java.io.InputStreamReader (is)); +this.dataName = fileStr; +} else { +this.error = true; +}} else { +this.errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" + (type != null ? type : "null") + "'"; +this.error = true; +}if (this.dataIn == null || this.error) { +throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.failed_to_read_data_from_source", Clazz.newArray (-1, [this.errormessage]))); +}this.error = false; +this.dataIn.mark (2048); +}, "~S,~S"); +Clazz.defineMethod (c$, "mark", +function () { +if (this.dataIn != null) { +this.dataIn.mark (2048); +} else { +throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.no_init_source_stream")); +}}); +Clazz.defineMethod (c$, "nextLine", +function () { +if (!this.error) { +return this.dataIn.readLine (); +}throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.invalid_source_stream", Clazz.newArray (-1, [this.errormessage]))); +}); +Clazz.defineMethod (c$, "isExporting", +function () { +return !this.error && this.dataIn == null; +}); +Clazz.defineMethod (c$, "isValid", +function () { +return !this.error; +}); +Clazz.defineMethod (c$, "close", +function () { +this.errormessage = "EXCEPTION ON CLOSE"; +this.error = true; +this.dataIn.close (); +this.dataIn = null; +this.errormessage = "SOURCE IS CLOSED"; +}); +Clazz.defineMethod (c$, "reset", +function () { +if (this.dataIn != null && !this.error) { +this.dataIn.reset (); +} else { +throw new java.io.IOException (jalview.util.MessageManager.getString ("error.implementation_error_reset_called_for_invalid_source")); +}}); +Clazz.defineMethod (c$, "hasWarningMessage", +function () { +return (this.warningMessage != null && this.warningMessage.length > 0); +}); +Clazz.defineMethod (c$, "getWarningMessage", +function () { +return this.warningMessage; +}); +Clazz.defineMethod (c$, "getInFile", +function () { +if (this.inFile != null) { +return this.inFile.getAbsolutePath () + " (" + this.index + ")"; +} else { +return "From Paste + (" + this.index + ")"; +}}); +Clazz.defineMethod (c$, "getDataName", +function () { +return this.dataName; +}); +Clazz.defineMethod (c$, "setDataName", +function (dataname) { +this.dataName = dataname; +}, "~S"); +Clazz.defineMethod (c$, "getReader", +function () { +if (this.dataIn != null) { +return this.dataIn; +}return null; +}); +Clazz.defineMethod (c$, "getViewport", +function () { +return this.viewport; +}); +Clazz.defineMethod (c$, "setViewport", +function (viewport) { +this.viewport = viewport; +}, "jalview.api.AlignViewportI"); +Clazz.defineMethod (c$, "getExportSettings", +function () { +return this.exportSettings; +}); +Clazz.defineMethod (c$, "setExportSettings", +function (exportSettings) { +this.exportSettings = exportSettings; +}, "jalview.api.AlignExportSettingI"); +Clazz.defineMethod (c$, "configureForView", +function (avpanel) { +if (avpanel != null) { +this.setViewport (avpanel.getAlignViewport ()); +}}, "jalview.api.AlignmentViewPanel"); +}); diff --git a/bin/jalview/io/IdentifyFile.class b/bin/jalview/io/IdentifyFile.class index 7acd351..2b3d5d4 100644 Binary files a/bin/jalview/io/IdentifyFile.class and b/bin/jalview/io/IdentifyFile.class differ diff --git a/bin/jalview/io/IdentifyFile.js b/bin/jalview/io/IdentifyFile.js index 4d88cdd..cf35241 100644 --- a/bin/jalview/io/IdentifyFile.js +++ b/bin/jalview/io/IdentifyFile.js @@ -1,157 +1,157 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.IdentifyFile", ["jalview.io.FileParse"], function () { -c$ = Clazz.declareType (jalview.io, "IdentifyFile"); -Clazz.defineMethod (c$, "Identify", -function (file, protocol) { -var emessage = "UNIDENTIFIED FILE PARSING ERROR"; -var parser = null; -try { -parser = new jalview.io.FileParse (file, protocol); -if (parser.isValid ()) { -return this.Identify (parser); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Error whilst identifying"); -e.printStackTrace (System.err); -emessage = e.getMessage (); -} else { -throw e; -} -} -if (parser != null) { -return parser.errormessage; -}return emessage; -}, "~S,~S"); -Clazz.defineMethod (c$, "Identify", -function (source) { -return this.Identify (source, true); -}, "jalview.io.FileParse"); -Clazz.defineMethod (c$, "Identify", -function (source, closeSource) { -var reply = "PFAM"; -var data; -var length = 0; -var lineswereskipped = false; -var isBinary = false; -try { -if (!closeSource) { -source.mark (); -}while ((data = source.nextLine ()) != null) { -length += data.trim ().length; -if (!lineswereskipped) { -for (var i = 0; !isBinary && i < data.length; i++) { -var c = data.charAt (i); -isBinary = (c.charCodeAt (0) < 32 && c != '\t' && c != '\n' && c != '\r' && c.charCodeAt (0) != 5 && c.charCodeAt (0) != 27); -} -}if (isBinary) { -if (source.inFile != null) { -var fileStr = source.inFile.getName (); -if (fileStr.lastIndexOf (".jar") > -1 || fileStr.lastIndexOf (".zip") > -1) { -reply = "Jalview"; -}}if (!lineswereskipped && data.startsWith ("PK")) { -reply = "Jalview"; -break; -}}data = data.toUpperCase (); -if (data.startsWith ("##GFF-VERSION")) { -reply = "GFF v2 or v3"; -break; -}if (data.indexOf ("# STOCKHOLM") > -1) { -reply = "STH"; -break; -}if (data.matches ("])*>")) { -reply = "HTML"; -break; -}if (data.matches ("])*>")) { -reply = "RNAML"; -break; -}if (data.indexOf ("{\"") > -1) { -reply = "JSON"; -break; -}if ((data.length < 1) || (data.indexOf ("#") == 0)) { -lineswereskipped = true; -continue; -}if (data.indexOf ("PILEUP") > -1) { -reply = "PileUp"; -break; -}if ((data.indexOf ("//") == 0) || ((data.indexOf ("!!") > -1) && (data.indexOf ("!!") < data.indexOf ("_MULTIPLE_ALIGNMENT ")))) { -reply = "MSF"; -break; -} else if (data.indexOf ("CLUSTAL") > -1) { -reply = "CLUSTAL"; -break; -} else if (data.indexOf (">") > -1) { -var checkPIR = false; -var starterm = false; -if ((data.indexOf (">P1;") > -1) || (data.indexOf (">DL;") > -1)) { -checkPIR = true; -reply = "PIR"; -}data = source.nextLine (); -if (data.indexOf (">") > -1) { -reply = "BLC"; -} else { -var data1 = source.nextLine (); -var data2 = source.nextLine (); -var c1; -if (checkPIR) { -starterm = (data1 != null && data1.indexOf ("*") > -1) || (data2 != null && data2.indexOf ("*") > -1); -}if (data2 != null && (c1 = data.indexOf ("*")) > -1) { -if (c1 == 0 && c1 == data2.indexOf ("*")) { -reply = "BLC"; -} else { -reply = "FASTA"; -}} else { -reply = "FASTA"; -if (!checkPIR) { -break; -}}}if (checkPIR) { -var dta = null; -if (!starterm) { -do { -try { -dta = source.nextLine (); -} catch (ex) { -if (Clazz.exceptionOf (ex, java.io.IOException)) { -} else { -throw ex; -} -} -;if (dta != null && dta.indexOf ("*") > -1) { -starterm = true; -}} while (dta != null && !starterm); -}if (starterm) { -reply = "PIR"; -break; -} else { -reply = "FASTA"; -}}break; -} else if (data.indexOf ("HEADER") == 0 || data.indexOf ("ATOM") == 0) { -reply = "PDB"; -break; -} else if (data.matches ("\\s*\\d+\\s+\\d+\\s*")) { -reply = "PHYLIP"; -break; -} else if (!lineswereskipped && data.charAt (0) != '*' && data.charAt (0) != ' ' && data.indexOf (":") < data.indexOf (",")) { -reply = "JnetFile"; -break; -}lineswereskipped = true; -} -if (closeSource) { -source.close (); -} else { -source.reset (); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("File Identification failed!\n" + ex); -return source.errormessage; -} else { -throw ex; -} -} -if (length == 0) { -System.err.println ("File Identification failed! - Empty file was read."); -return "EMPTY DATA FILE"; -}return reply; -}, "jalview.io.FileParse,~B"); -Clazz.defineStatics (c$, -"GFF3File", "GFF v2 or v3"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.IdentifyFile", ["jalview.io.FileParse"], function () { +c$ = Clazz.declareType (jalview.io, "IdentifyFile"); +Clazz.defineMethod (c$, "Identify", +function (file, protocol) { +var emessage = "UNIDENTIFIED FILE PARSING ERROR"; +var parser = null; +try { +parser = new jalview.io.FileParse (file, protocol); +if (parser.isValid ()) { +return this.Identify (parser); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Error whilst identifying"); +e.printStackTrace (System.err); +emessage = e.getMessage (); +} else { +throw e; +} +} +if (parser != null) { +return parser.errormessage; +}return emessage; +}, "~S,~S"); +Clazz.defineMethod (c$, "Identify", +function (source) { +return this.Identify (source, true); +}, "jalview.io.FileParse"); +Clazz.defineMethod (c$, "Identify", +function (source, closeSource) { +var reply = "PFAM"; +var data; +var length = 0; +var lineswereskipped = false; +var isBinary = false; +try { +if (!closeSource) { +source.mark (); +}while ((data = source.nextLine ()) != null) { +length += data.trim ().length; +if (!lineswereskipped) { +for (var i = 0; !isBinary && i < data.length; i++) { +var c = data.charAt (i); +isBinary = (c.charCodeAt (0) < 32 && c != '\t' && c != '\n' && c != '\r' && c.charCodeAt (0) != 5 && c.charCodeAt (0) != 27); +} +}if (isBinary) { +if (source.inFile != null) { +var fileStr = source.inFile.getName (); +if (fileStr.lastIndexOf (".jar") > -1 || fileStr.lastIndexOf (".zip") > -1) { +reply = "Jalview"; +}}if (!lineswereskipped && data.startsWith ("PK")) { +reply = "Jalview"; +break; +}}data = data.toUpperCase (); +if (data.startsWith ("##GFF-VERSION")) { +reply = "GFF v2 or v3"; +break; +}if (data.indexOf ("# STOCKHOLM") > -1) { +reply = "STH"; +break; +}if (data.matches ("])*>")) { +reply = "HTML"; +break; +}if (data.matches ("])*>")) { +reply = "RNAML"; +break; +}if (data.indexOf ("{\"") > -1) { +reply = "JSON"; +break; +}if ((data.length < 1) || (data.indexOf ("#") == 0)) { +lineswereskipped = true; +continue; +}if (data.indexOf ("PILEUP") > -1) { +reply = "PileUp"; +break; +}if ((data.indexOf ("//") == 0) || ((data.indexOf ("!!") > -1) && (data.indexOf ("!!") < data.indexOf ("_MULTIPLE_ALIGNMENT ")))) { +reply = "MSF"; +break; +} else if (data.indexOf ("CLUSTAL") > -1) { +reply = "CLUSTAL"; +break; +} else if (data.indexOf (">") > -1) { +var checkPIR = false; +var starterm = false; +if ((data.indexOf (">P1;") > -1) || (data.indexOf (">DL;") > -1)) { +checkPIR = true; +reply = "PIR"; +}data = source.nextLine (); +if (data.indexOf (">") > -1) { +reply = "BLC"; +} else { +var data1 = source.nextLine (); +var data2 = source.nextLine (); +var c1; +if (checkPIR) { +starterm = (data1 != null && data1.indexOf ("*") > -1) || (data2 != null && data2.indexOf ("*") > -1); +}if (data2 != null && (c1 = data.indexOf ("*")) > -1) { +if (c1 == 0 && c1 == data2.indexOf ("*")) { +reply = "BLC"; +} else { +reply = "FASTA"; +}} else { +reply = "FASTA"; +if (!checkPIR) { +break; +}}}if (checkPIR) { +var dta = null; +if (!starterm) { +do { +try { +dta = source.nextLine (); +} catch (ex) { +if (Clazz.exceptionOf (ex, java.io.IOException)) { +} else { +throw ex; +} +} +;if (dta != null && dta.indexOf ("*") > -1) { +starterm = true; +}} while (dta != null && !starterm); +}if (starterm) { +reply = "PIR"; +break; +} else { +reply = "FASTA"; +}}break; +} else if (data.indexOf ("HEADER") == 0 || data.indexOf ("ATOM") == 0) { +reply = "PDB"; +break; +} else if (data.matches ("\\s*\\d+\\s+\\d+\\s*")) { +reply = "PHYLIP"; +break; +} else if (!lineswereskipped && data.charAt (0) != '*' && data.charAt (0) != ' ' && data.indexOf (":") < data.indexOf (",")) { +reply = "JnetFile"; +break; +}lineswereskipped = true; +} +if (closeSource) { +source.close (); +} else { +source.reset (); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("File Identification failed!\n" + ex); +return source.errormessage; +} else { +throw ex; +} +} +if (length == 0) { +System.err.println ("File Identification failed! - Empty file was read."); +return "EMPTY DATA FILE"; +}return reply; +}, "jalview.io.FileParse,~B"); +Clazz.defineStatics (c$, +"GFF3File", "GFF v2 or v3"); +}); diff --git a/bin/jalview/io/JPredFile.class b/bin/jalview/io/JPredFile.class index d668d00..a3812ce 100644 Binary files a/bin/jalview/io/JPredFile.class and b/bin/jalview/io/JPredFile.class differ diff --git a/bin/jalview/io/JPredFile.js b/bin/jalview/io/JPredFile.js index 9dc5044..1975edb 100644 --- a/bin/jalview/io/JPredFile.js +++ b/bin/jalview/io/JPredFile.js @@ -1,185 +1,185 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile"], "jalview.io.JPredFile", ["jalview.datamodel.Alignment", "$.Sequence", "jalview.io.JnetAnnotationMaker", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Float", "$.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ids = null; -this.conf = null; -this.Scores = null; -this.Symscores = null; -this.QuerySeqPosition = 0; -this.annotSeqs = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "JPredFile", jalview.io.AlignFile); -Clazz.defineMethod (c$, "setQuerySeqPosition", -function (QuerySeqPosition) { -this.QuerySeqPosition = QuerySeqPosition; -}, "~N"); -Clazz.defineMethod (c$, "getQuerySeqPosition", -function () { -return this.QuerySeqPosition; -}); -Clazz.defineMethod (c$, "getScores", -function () { -return this.Scores; -}); -Clazz.defineMethod (c$, "getSymscores", -function () { -return this.Symscores; -}); -Clazz.defineMethod (c$, "initData", -function () { -Clazz.superCall (this, jalview.io.JPredFile, "initData", []); -this.Scores = new java.util.Hashtable (); -this.ids = null; -this.conf = null; -}); -Clazz.overrideMethod (c$, "parse", -function () { -var line; -this.QuerySeqPosition = -1; -this.noSeqs = 0; -var seq_entries = new java.util.Vector (); -var ids = new java.util.Vector (); -var Symscores = new java.util.Hashtable (); -while ((line = this.nextLine ()) != null) { -var str = new java.util.StringTokenizer (line, ":"); -var id = ""; -if (!str.hasMoreTokens ()) { -continue; -}id = str.nextToken (); -var seqsym = str.nextToken (); -var symbols = new java.util.StringTokenizer (seqsym, ","); -var numSymbols = symbols.countTokens (); -if (numSymbols == 0) { -continue; -}if (seqsym.length != (2 * numSymbols)) { -if (this.Scores.containsKey (id)) { -var i = 1; -while (this.Scores.containsKey (id + "_" + i)) { -i++; -} -id = id + "_" + i; -}var scores = new java.util.Vector (); -var i = 0; -var ascore = "dead"; -try { -while (symbols.hasMoreTokens ()) { -ascore = symbols.nextToken (); -var score = new Float (ascore); -scores.addElement (score); -} -this.Scores.put (id, scores); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -i = scores.size (); -for (var j = 0; j < i; j++) { -scores.setElementAt ((scores.elementAt (j)).toString (), j); -} -scores.addElement (ascore); -while (symbols.hasMoreTokens ()) { -ascore = symbols.nextToken (); -scores.addElement (ascore); -} -this.Scores.put (id, scores); -} else { -throw e; -} -} -} else if (id.equals ("jnetconf")) { -id = "Prediction Confidence"; -this.conf = new java.util.Vector (numSymbols); -for (var i = 0; i < numSymbols; i++) { -this.conf.setElementAt (symbols.nextToken (), i); -} -} else { -var newseq = new StringBuffer (); -for (var i = 0; i < numSymbols; i++) { -newseq.append (symbols.nextToken ()); -} -if (id.indexOf (";") > -1) { -seq_entries.addElement (newseq); -var i = 1; -var name = id.substring (id.indexOf (";") + 1); -while (ids.lastIndexOf (name) > -1) { -name = id.substring (id.indexOf (";") + 1) + "_" + ++i; -} -if (this.QuerySeqPosition == -1) this.QuerySeqPosition = ids.size (); -ids.addElement (name); -this.noSeqs++; -} else { -if (id.equals ("JNETPRED")) { -id = "Predicted Secondary Structure"; -}seq_entries.addElement (newseq.toString ()); -ids.addElement (id); -Symscores.put (id, new Integer (ids.size () - 1)); -}}} -this.maxLength = seq_entries.elementAt (0).toString ().length; -for (var i = 0; i < ids.size (); i++) { -var newSeq = new jalview.datamodel.Sequence (ids.elementAt (i).toString (), seq_entries.elementAt (i).toString (), 1, seq_entries.elementAt (i).toString ().length); -if (this.maxLength != seq_entries.elementAt (i).toString ().length) { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.jpredconcide_entry_has_unexpected_number_of_columns", Clazz.newArray (-1, [ids.elementAt (i).toString ()]))); -}if ((newSeq.getName ().startsWith ("QUERY") || newSeq.getName ().startsWith ("align;")) && (this.QuerySeqPosition == -1)) { -this.QuerySeqPosition = this.seqs.size (); -}this.seqs.addElement (newSeq); -} -if (this.seqs.size () > 0 && this.QuerySeqPosition > -1) { -var tal = new jalview.datamodel.Alignment (this.getSeqsAsArray ()); -try { -jalview.io.JnetAnnotationMaker.add_annotation (this, tal, this.QuerySeqPosition, true); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -tal = null; -var ex = new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.couldnt_parse_concise_annotation_for_prediction", Clazz.newArray (-1, [e.getMessage ()]))); -e.printStackTrace (); -throw ex; -} else { -throw e; -} -} -this.annotations = new java.util.Vector (); -var aan = tal.getAlignmentAnnotation (); -for (var aai = 0; aan != null && aai < aan.length; aai++) { -this.annotations.addElement (aan[aai]); -} -}}); -Clazz.overrideMethod (c$, "print", -function () { -return "Not Supported"; -}); -c$.main = Clazz.defineMethod (c$, "main", -function (args) { -try { -var blc = new jalview.io.JPredFile (args[0], "File"); -for (var i = 0; i < blc.seqs.size (); i++) { -System.out.println ((blc.seqs.elementAt (i)).getName () + "\n" + (blc.seqs.elementAt (i)).getSequenceAsString () + "\n"); -} -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -System.err.println ("Exception " + e); -} else { -throw e; -} -} -}, "~A"); -Clazz.defineMethod (c$, "removeNonSequences", -function () { -if (this.annotSeqs != null) { -return; -}this.annotSeqs = new java.util.Vector (); -var newseqs = new java.util.Vector (); -var i = 0; -var j = this.seqs.size (); -for (; i < this.QuerySeqPosition; i++) { -this.annotSeqs.addElement (this.seqs.elementAt (i)); -} -{ -var sq = this.seqs.elementAt (j - 1); -if (sq.getName ().toUpperCase ().startsWith ("JPRED")) { -this.annotSeqs.addElement (sq); -this.seqs.removeElementAt (--j); -}}for (; i < j; i++) { -newseqs.addElement (this.seqs.elementAt (i)); -} -this.seqs.removeAllElements (); -this.seqs = newseqs; -}); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile"], "jalview.io.JPredFile", ["jalview.datamodel.Alignment", "$.Sequence", "jalview.io.JnetAnnotationMaker", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Float", "$.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ids = null; +this.conf = null; +this.Scores = null; +this.Symscores = null; +this.QuerySeqPosition = 0; +this.annotSeqs = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "JPredFile", jalview.io.AlignFile); +Clazz.defineMethod (c$, "setQuerySeqPosition", +function (QuerySeqPosition) { +this.QuerySeqPosition = QuerySeqPosition; +}, "~N"); +Clazz.defineMethod (c$, "getQuerySeqPosition", +function () { +return this.QuerySeqPosition; +}); +Clazz.defineMethod (c$, "getScores", +function () { +return this.Scores; +}); +Clazz.defineMethod (c$, "getSymscores", +function () { +return this.Symscores; +}); +Clazz.defineMethod (c$, "initData", +function () { +Clazz.superCall (this, jalview.io.JPredFile, "initData", []); +this.Scores = new java.util.Hashtable (); +this.ids = null; +this.conf = null; +}); +Clazz.overrideMethod (c$, "parse", +function () { +var line; +this.QuerySeqPosition = -1; +this.noSeqs = 0; +var seq_entries = new java.util.Vector (); +var ids = new java.util.Vector (); +var Symscores = new java.util.Hashtable (); +while ((line = this.nextLine ()) != null) { +var str = new java.util.StringTokenizer (line, ":"); +var id = ""; +if (!str.hasMoreTokens ()) { +continue; +}id = str.nextToken (); +var seqsym = str.nextToken (); +var symbols = new java.util.StringTokenizer (seqsym, ","); +var numSymbols = symbols.countTokens (); +if (numSymbols == 0) { +continue; +}if (seqsym.length != (2 * numSymbols)) { +if (this.Scores.containsKey (id)) { +var i = 1; +while (this.Scores.containsKey (id + "_" + i)) { +i++; +} +id = id + "_" + i; +}var scores = new java.util.Vector (); +var i = 0; +var ascore = "dead"; +try { +while (symbols.hasMoreTokens ()) { +ascore = symbols.nextToken (); +var score = new Float (ascore); +scores.addElement (score); +} +this.Scores.put (id, scores); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +i = scores.size (); +for (var j = 0; j < i; j++) { +scores.setElementAt ((scores.elementAt (j)).toString (), j); +} +scores.addElement (ascore); +while (symbols.hasMoreTokens ()) { +ascore = symbols.nextToken (); +scores.addElement (ascore); +} +this.Scores.put (id, scores); +} else { +throw e; +} +} +} else if (id.equals ("jnetconf")) { +id = "Prediction Confidence"; +this.conf = new java.util.Vector (numSymbols); +for (var i = 0; i < numSymbols; i++) { +this.conf.setElementAt (symbols.nextToken (), i); +} +} else { +var newseq = new StringBuffer (); +for (var i = 0; i < numSymbols; i++) { +newseq.append (symbols.nextToken ()); +} +if (id.indexOf (";") > -1) { +seq_entries.addElement (newseq); +var i = 1; +var name = id.substring (id.indexOf (";") + 1); +while (ids.lastIndexOf (name) > -1) { +name = id.substring (id.indexOf (";") + 1) + "_" + ++i; +} +if (this.QuerySeqPosition == -1) this.QuerySeqPosition = ids.size (); +ids.addElement (name); +this.noSeqs++; +} else { +if (id.equals ("JNETPRED")) { +id = "Predicted Secondary Structure"; +}seq_entries.addElement (newseq.toString ()); +ids.addElement (id); +Symscores.put (id, new Integer (ids.size () - 1)); +}}} +this.maxLength = seq_entries.elementAt (0).toString ().length; +for (var i = 0; i < ids.size (); i++) { +var newSeq = new jalview.datamodel.Sequence (ids.elementAt (i).toString (), seq_entries.elementAt (i).toString (), 1, seq_entries.elementAt (i).toString ().length); +if (this.maxLength != seq_entries.elementAt (i).toString ().length) { +throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.jpredconcide_entry_has_unexpected_number_of_columns", Clazz.newArray (-1, [ids.elementAt (i).toString ()]))); +}if ((newSeq.getName ().startsWith ("QUERY") || newSeq.getName ().startsWith ("align;")) && (this.QuerySeqPosition == -1)) { +this.QuerySeqPosition = this.seqs.size (); +}this.seqs.addElement (newSeq); +} +if (this.seqs.size () > 0 && this.QuerySeqPosition > -1) { +var tal = new jalview.datamodel.Alignment (this.getSeqsAsArray ()); +try { +jalview.io.JnetAnnotationMaker.add_annotation (this, tal, this.QuerySeqPosition, true); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +tal = null; +var ex = new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.couldnt_parse_concise_annotation_for_prediction", Clazz.newArray (-1, [e.getMessage ()]))); +e.printStackTrace (); +throw ex; +} else { +throw e; +} +} +this.annotations = new java.util.Vector (); +var aan = tal.getAlignmentAnnotation (); +for (var aai = 0; aan != null && aai < aan.length; aai++) { +this.annotations.addElement (aan[aai]); +} +}}); +Clazz.overrideMethod (c$, "print", +function () { +return "Not Supported"; +}); +c$.main = Clazz.defineMethod (c$, "main", +function (args) { +try { +var blc = new jalview.io.JPredFile (args[0], "File"); +for (var i = 0; i < blc.seqs.size (); i++) { +System.out.println ((blc.seqs.elementAt (i)).getName () + "\n" + (blc.seqs.elementAt (i)).getSequenceAsString () + "\n"); +} +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +System.err.println ("Exception " + e); +} else { +throw e; +} +} +}, "~A"); +Clazz.defineMethod (c$, "removeNonSequences", +function () { +if (this.annotSeqs != null) { +return; +}this.annotSeqs = new java.util.Vector (); +var newseqs = new java.util.Vector (); +var i = 0; +var j = this.seqs.size (); +for (; i < this.QuerySeqPosition; i++) { +this.annotSeqs.addElement (this.seqs.elementAt (i)); +} +{ +var sq = this.seqs.elementAt (j - 1); +if (sq.getName ().toUpperCase ().startsWith ("JPRED")) { +this.annotSeqs.addElement (sq); +this.seqs.removeElementAt (--j); +}}for (; i < j; i++) { +newseqs.addElement (this.seqs.elementAt (i)); +} +this.seqs.removeAllElements (); +this.seqs = newseqs; +}); +}); diff --git a/bin/jalview/io/JnetAnnotationMaker.class b/bin/jalview/io/JnetAnnotationMaker.class index 9724528..38b1701 100644 Binary files a/bin/jalview/io/JnetAnnotationMaker.class and b/bin/jalview/io/JnetAnnotationMaker.class differ diff --git a/bin/jalview/io/JnetAnnotationMaker.js b/bin/jalview/io/JnetAnnotationMaker.js index f39d55b..e2f51a5 100644 --- a/bin/jalview/io/JnetAnnotationMaker.js +++ b/bin/jalview/io/JnetAnnotationMaker.js @@ -1,90 +1,90 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.JnetAnnotationMaker", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "jalview.util.MessageManager", "java.lang.Exception", "$.Float"], function () { -c$ = Clazz.declareType (jalview.io, "JnetAnnotationMaker"); -c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", -function (prediction, al, firstSeq, noMsa) { -jalview.io.JnetAnnotationMaker.add_annotation (prediction, al, firstSeq, noMsa, Clazz.castNullAs ("Array")); -}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B"); -c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", -function (prediction, al, firstSeq, noMsa, delMap) { -var i = 0; -var preds = prediction.getSeqsAsArray (); -var seqRef = al.getSequenceAt (firstSeq); -var width = preds[0].getSequence ().length; -var gapmap = al.getSequenceAt (firstSeq).gapMap (); -if ((delMap != null && delMap.length > width) || (delMap == null && gapmap.length != width)) { -throw ( new Exception (jalview.util.MessageManager.formatMessage ("exception.number_of_residues_in_query_sequence_differ_from_prediction", Clazz.newArray (-1, [(delMap == null ? "" : jalview.util.MessageManager.getString ("label.mapped")), al.getSequenceAt (firstSeq).getName (), al.getSequenceAt (firstSeq).getSequenceAsString (), Integer.$valueOf (width).toString ()])))); -}var annot; -var annotations = null; -var existingAnnotations = 0; -if (al.getAlignmentAnnotation () != null) { -existingAnnotations = al.getAlignmentAnnotation ().length; -}var sol = new Array (al.getWidth ()); -var firstsol = true; -while (i < preds.length) { -var id = preds[i].getName ().toUpperCase (); -if (id.startsWith ("LUPAS") || id.startsWith ("JNET") || id.startsWith ("JPRED")) { -if (id.startsWith ("JNETSOL")) { -var amnt = (id.endsWith ("25") ? 3 : id.endsWith ("5") ? 6 : 9); -for (var spos = 0; spos < width; spos++) { -var sposw = (delMap == null) ? gapmap[spos] : gapmap[delMap[spos]]; -if (firstsol) { -sol[sposw] = new jalview.datamodel.Annotation (0); -}if (preds[i].getCharAt (spos) == 'B' && (sol[sposw].value == 0 || sol[sposw].value < amnt)) { -sol[sposw].value = amnt; -}} -firstsol = false; -} else { -annotations = new Array (al.getWidth ()); -if (id.equals ("JNETPRED") || id.equals ("JNETPSSM") || id.equals ("JNETFREQ") || id.equals ("JNETHMM") || id.equals ("JNETALIGN") || id.equals ("JPRED")) { -if (delMap == null) { -for (var j = 0; j < width; j++) { -annotations[gapmap[j]] = new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0); -} -} else { -for (var j = 0; j < width; j++) { -annotations[gapmap[delMap[j]]] = new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0); -} -}} else if (id.equals ("JNETCONF")) { -if (delMap == null) { -for (var j = 0; j < width; j++) { -var value = new Float (preds[i].getCharAt (j) + "").floatValue (); -annotations[gapmap[j]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value); -} -} else { -for (var j = 0; j < width; j++) { -var value = new Float (preds[i].getCharAt (j) + "").floatValue (); -annotations[gapmap[delMap[j]]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value); -} -}} else { -if (delMap == null) { -for (var j = 0; j < width; j++) { -annotations[gapmap[j]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0); -} -} else { -for (var j = 0; j < width; j++) { -annotations[gapmap[delMap[j]]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0); -} -}}if (id.equals ("JNETCONF")) { -annot = new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations, 0, 10, 1); -} else { -annot = new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations); -}if (seqRef != null) { -annot.createSequenceMapping (seqRef, 1, true); -seqRef.addAlignmentAnnotation (annot); -}al.addAnnotation (annot); -al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1); -}if (noMsa) { -al.deleteSequence (preds[i]); -}}i++; -} -if (!firstsol) { -annot = new jalview.datamodel.AlignmentAnnotation ("Jnet Burial", "Prediction of Solvent Accessibility
levels are
  • 0 - Exposed
  • 3 - 25% or more S.A. accessible
  • 6 - 5% or more S.A. accessible
  • 9 - Buried (<5% exposed)
", sol, 0, 9, 1); -annot.validateRangeAndDisplay (); -if (seqRef != null) { -annot.createSequenceMapping (seqRef, 1, true); -seqRef.addAlignmentAnnotation (annot); -}al.addAnnotation (annot); -al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1); -}}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B,~A"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.JnetAnnotationMaker", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "jalview.util.MessageManager", "java.lang.Exception", "$.Float"], function () { +c$ = Clazz.declareType (jalview.io, "JnetAnnotationMaker"); +c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", +function (prediction, al, firstSeq, noMsa) { +jalview.io.JnetAnnotationMaker.add_annotation (prediction, al, firstSeq, noMsa, Clazz.castNullAs ("Array")); +}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B"); +c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", +function (prediction, al, firstSeq, noMsa, delMap) { +var i = 0; +var preds = prediction.getSeqsAsArray (); +var seqRef = al.getSequenceAt (firstSeq); +var width = preds[0].getSequence ().length; +var gapmap = al.getSequenceAt (firstSeq).gapMap (); +if ((delMap != null && delMap.length > width) || (delMap == null && gapmap.length != width)) { +throw ( new Exception (jalview.util.MessageManager.formatMessage ("exception.number_of_residues_in_query_sequence_differ_from_prediction", Clazz.newArray (-1, [(delMap == null ? "" : jalview.util.MessageManager.getString ("label.mapped")), al.getSequenceAt (firstSeq).getName (), al.getSequenceAt (firstSeq).getSequenceAsString (), Integer.$valueOf (width).toString ()])))); +}var annot; +var annotations = null; +var existingAnnotations = 0; +if (al.getAlignmentAnnotation () != null) { +existingAnnotations = al.getAlignmentAnnotation ().length; +}var sol = new Array (al.getWidth ()); +var firstsol = true; +while (i < preds.length) { +var id = preds[i].getName ().toUpperCase (); +if (id.startsWith ("LUPAS") || id.startsWith ("JNET") || id.startsWith ("JPRED")) { +if (id.startsWith ("JNETSOL")) { +var amnt = (id.endsWith ("25") ? 3 : id.endsWith ("5") ? 6 : 9); +for (var spos = 0; spos < width; spos++) { +var sposw = (delMap == null) ? gapmap[spos] : gapmap[delMap[spos]]; +if (firstsol) { +sol[sposw] = new jalview.datamodel.Annotation (0); +}if (preds[i].getCharAt (spos) == 'B' && (sol[sposw].value == 0 || sol[sposw].value < amnt)) { +sol[sposw].value = amnt; +}} +firstsol = false; +} else { +annotations = new Array (al.getWidth ()); +if (id.equals ("JNETPRED") || id.equals ("JNETPSSM") || id.equals ("JNETFREQ") || id.equals ("JNETHMM") || id.equals ("JNETALIGN") || id.equals ("JPRED")) { +if (delMap == null) { +for (var j = 0; j < width; j++) { +annotations[gapmap[j]] = new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0); +} +} else { +for (var j = 0; j < width; j++) { +annotations[gapmap[delMap[j]]] = new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0); +} +}} else if (id.equals ("JNETCONF")) { +if (delMap == null) { +for (var j = 0; j < width; j++) { +var value = new Float (preds[i].getCharAt (j) + "").floatValue (); +annotations[gapmap[j]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value); +} +} else { +for (var j = 0; j < width; j++) { +var value = new Float (preds[i].getCharAt (j) + "").floatValue (); +annotations[gapmap[delMap[j]]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value); +} +}} else { +if (delMap == null) { +for (var j = 0; j < width; j++) { +annotations[gapmap[j]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0); +} +} else { +for (var j = 0; j < width; j++) { +annotations[gapmap[delMap[j]]] = new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0); +} +}}if (id.equals ("JNETCONF")) { +annot = new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations, 0, 10, 1); +} else { +annot = new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations); +}if (seqRef != null) { +annot.createSequenceMapping (seqRef, 1, true); +seqRef.addAlignmentAnnotation (annot); +}al.addAnnotation (annot); +al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1); +}if (noMsa) { +al.deleteSequence (preds[i]); +}}i++; +} +if (!firstsol) { +annot = new jalview.datamodel.AlignmentAnnotation ("Jnet Burial", "Prediction of Solvent Accessibility
levels are
  • 0 - Exposed
  • 3 - 25% or more S.A. accessible
  • 6 - 5% or more S.A. accessible
  • 9 - Buried (<5% exposed)
", sol, 0, 9, 1); +annot.validateRangeAndDisplay (); +if (seqRef != null) { +annot.createSequenceMapping (seqRef, 1, true); +seqRef.addAlignmentAnnotation (annot); +}al.addAnnotation (annot); +al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1); +}}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B,~A"); +}); diff --git a/bin/jalview/io/MSFfile.class b/bin/jalview/io/MSFfile.class index 264fda6..5173c4c 100644 Binary files a/bin/jalview/io/MSFfile.class and b/bin/jalview/io/MSFfile.class differ diff --git a/bin/jalview/io/MSFfile.js b/bin/jalview/io/MSFfile.js index d80fbdc..ee2e3af 100644 --- a/bin/jalview/io/MSFfile.js +++ b/bin/jalview/io/MSFfile.js @@ -1,190 +1,190 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile"], "jalview.io.MSFfile", ["jalview.datamodel.Sequence", "jalview.util.Comparison", "$.Format", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () { -c$ = Clazz.declareType (jalview.io, "MSFfile", jalview.io.AlignFile); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.MSFfile, []); -}); -Clazz.overrideMethod (c$, "parse", -function () { -var i = 0; -var seqFlag = false; -var key = String.instantialize (); -var headers = new java.util.Vector (); -var seqhash = new java.util.Hashtable (); -var line; -try { -while ((line = this.nextLine ()) != null) { -var str = new java.util.StringTokenizer (line); -while (str.hasMoreTokens ()) { -var inStr = str.nextToken (); -if (inStr.indexOf ("Name:") != -1) { -key = str.nextToken (); -headers.addElement (key); -}if (inStr.indexOf ("//") != -1) { -seqFlag = true; -}if ((inStr.indexOf ("//") == -1) && (seqFlag == true)) { -key = inStr; -var tempseq; -if (seqhash.containsKey (key)) { -tempseq = seqhash.get (key); -} else { -tempseq = new StringBuffer (); -seqhash.put (key, tempseq); -}while (str.hasMoreTokens ()) { -tempseq.append (str.nextToken ()); -} -}} -} -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -System.err.println ("Exception parsing MSFFile " + e); -e.printStackTrace (); -} else { -throw e; -} -} -this.noSeqs = headers.size (); -for (i = 0; i < headers.size (); i++) { -if (seqhash.get (headers.elementAt (i)) != null) { -var head = headers.elementAt (i).toString (); -var seq = seqhash.get (head).toString (); -if (this.maxLength < head.length) { -this.maxLength = head.length; -}seq = seq.$replace ('~', '-'); -var newSeq = this.parseId (head); -newSeq.setSequence (seq); -this.seqs.addElement (newSeq); -} else { -System.err.println ("MSFFile Parser: Can't find sequence for " + headers.elementAt (i)); -}} -}); -Clazz.defineMethod (c$, "checkSum", -function (seq) { -var check = 0; -var sequence = seq.toUpperCase (); -for (var i = 0; i < sequence.length; i++) { -try { -var value = sequence.charCodeAt (i); -if (value != -1) { -check += (i % 57 + 1) * value; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Exception during MSF Checksum calculation"); -e.printStackTrace (); -} else { -throw e; -} -} -} -return check % 10000; -}, "~S"); -Clazz.defineMethod (c$, "print", -function (seqs) { -var is_NA = jalview.util.Comparison.isNucleotide (seqs); -var s = new Array (seqs.length); -var out = new StringBuffer ("!!" + (is_NA ? "NA" : "AA") + "_MULTIPLE_ALIGNMENT 1.0"); -out.append (this.newline); -out.append (this.newline); -var max = 0; -var maxid = 0; -var i = 0; -while ((i < seqs.length) && (seqs[i] != null)) { -s[i] = new jalview.datamodel.Sequence (seqs[i].getName (), seqs[i].getSequenceAsString ().$replace ('-', '.'), seqs[i].getStart (), seqs[i].getEnd ()); -var sb = new StringBuffer (); -sb.append (s[i].getSequence ()); -for (var ii = 0; ii < sb.length (); ii++) { -if (sb.charAt (ii) == '.') { -sb.setCharAt (ii, '~'); -} else { -break; -}} -for (var ii = sb.length () - 1; ii > 0; ii--) { -if (sb.charAt (ii) == '.') { -sb.setCharAt (ii, '~'); -} else { -break; -}} -s[i].setSequence (sb.toString ()); -if (s[i].getSequence ().length > max) { -max = s[i].getSequence ().length; -}i++; -} -var maxLenpad = new jalview.util.Format ("%" + ( String.instantialize ("" + max)).length + "d"); -var maxChkpad = new jalview.util.Format ("%" + ( String.instantialize ("1" + max)).length + "d"); -i = 0; -var bigChecksum = 0; -var checksums = Clazz.newIntArray (s.length, 0); -while (i < s.length) { -checksums[i] = this.checkSum (s[i].getSequenceAsString ()); -bigChecksum += checksums[i]; -i++; -} -var maxNB = 0; -out.append (" MSF: " + s[0].getSequence ().length + " Type: " + (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) + " .."); -out.append (this.newline); -out.append (this.newline); -out.append (this.newline); -var nameBlock = new Array (s.length); -var idBlock = new Array (s.length); -i = 0; -while ((i < s.length) && (s[i] != null)) { -nameBlock[i] = String.instantialize (" Name: " + this.printId (s[i]) + " "); -idBlock[i] = String.instantialize ("Len: " + maxLenpad.formLong (s[i].getSequence ().length) + " Check: " + maxChkpad.formLong (checksums[i]) + " Weight: 1.00" + this.newline); -if (s[i].getName ().length > maxid) { -maxid = s[i].getName ().length; -}if (nameBlock[i].length > maxNB) { -maxNB = nameBlock[i].length; -}i++; -} -if (maxid < 10) { -maxid = 10; -}if (maxNB < 15) { -maxNB = 15; -}var nbFormat = new jalview.util.Format ("%-" + maxNB + "s"); -for (i = 0; (i < s.length) && (s[i] != null); i++) { -out.append (nbFormat.form (nameBlock[i]) + idBlock[i]); -} -maxid++; -out.append (this.newline); -out.append (this.newline); -out.append ("//"); -out.append (this.newline); -out.append (this.newline); -var len = 50; -var nochunks = (Clazz.doubleToInt (max / len)) + 1; -if ((max % len) == 0) { -nochunks--; -}for (i = 0; i < nochunks; i++) { -var j = 0; -while ((j < s.length) && (s[j] != null)) { -var name = this.printId (s[j]); -out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " ")); -for (var k = 0; k < 5; k++) { -var start = (i * 50) + (k * 10); -var end = start + 10; -if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) { -out.append (s[j].getSequence (start, end)); -if (k < 4) { -out.append (" "); -} else { -out.append (this.newline); -}} else { -if (start < s[j].getSequence ().length) { -out.append (s[j].getSequenceAsString ().substring (start)); -out.append (this.newline); -} else { -if (k == 0) { -out.append (this.newline); -}}}} -j++; -} -out.append (this.newline); -} -return out.toString (); -}, "~A"); -Clazz.defineMethod (c$, "print", -function () { -return this.print (this.getSeqsAsArray ()); -}); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile"], "jalview.io.MSFfile", ["jalview.datamodel.Sequence", "jalview.util.Comparison", "$.Format", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () { +c$ = Clazz.declareType (jalview.io, "MSFfile", jalview.io.AlignFile); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.MSFfile, []); +}); +Clazz.overrideMethod (c$, "parse", +function () { +var i = 0; +var seqFlag = false; +var key = String.instantialize (); +var headers = new java.util.Vector (); +var seqhash = new java.util.Hashtable (); +var line; +try { +while ((line = this.nextLine ()) != null) { +var str = new java.util.StringTokenizer (line); +while (str.hasMoreTokens ()) { +var inStr = str.nextToken (); +if (inStr.indexOf ("Name:") != -1) { +key = str.nextToken (); +headers.addElement (key); +}if (inStr.indexOf ("//") != -1) { +seqFlag = true; +}if ((inStr.indexOf ("//") == -1) && (seqFlag == true)) { +key = inStr; +var tempseq; +if (seqhash.containsKey (key)) { +tempseq = seqhash.get (key); +} else { +tempseq = new StringBuffer (); +seqhash.put (key, tempseq); +}while (str.hasMoreTokens ()) { +tempseq.append (str.nextToken ()); +} +}} +} +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +System.err.println ("Exception parsing MSFFile " + e); +e.printStackTrace (); +} else { +throw e; +} +} +this.noSeqs = headers.size (); +for (i = 0; i < headers.size (); i++) { +if (seqhash.get (headers.elementAt (i)) != null) { +var head = headers.elementAt (i).toString (); +var seq = seqhash.get (head).toString (); +if (this.maxLength < head.length) { +this.maxLength = head.length; +}seq = seq.$replace ('~', '-'); +var newSeq = this.parseId (head); +newSeq.setSequence (seq); +this.seqs.addElement (newSeq); +} else { +System.err.println ("MSFFile Parser: Can't find sequence for " + headers.elementAt (i)); +}} +}); +Clazz.defineMethod (c$, "checkSum", +function (seq) { +var check = 0; +var sequence = seq.toUpperCase (); +for (var i = 0; i < sequence.length; i++) { +try { +var value = sequence.charCodeAt (i); +if (value != -1) { +check += (i % 57 + 1) * value; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Exception during MSF Checksum calculation"); +e.printStackTrace (); +} else { +throw e; +} +} +} +return check % 10000; +}, "~S"); +Clazz.defineMethod (c$, "print", +function (seqs) { +var is_NA = jalview.util.Comparison.isNucleotide (seqs); +var s = new Array (seqs.length); +var out = new StringBuffer ("!!" + (is_NA ? "NA" : "AA") + "_MULTIPLE_ALIGNMENT 1.0"); +out.append (this.newline); +out.append (this.newline); +var max = 0; +var maxid = 0; +var i = 0; +while ((i < seqs.length) && (seqs[i] != null)) { +s[i] = new jalview.datamodel.Sequence (seqs[i].getName (), seqs[i].getSequenceAsString ().$replace ('-', '.'), seqs[i].getStart (), seqs[i].getEnd ()); +var sb = new StringBuffer (); +sb.append (s[i].getSequence ()); +for (var ii = 0; ii < sb.length (); ii++) { +if (sb.charAt (ii) == '.') { +sb.setCharAt (ii, '~'); +} else { +break; +}} +for (var ii = sb.length () - 1; ii > 0; ii--) { +if (sb.charAt (ii) == '.') { +sb.setCharAt (ii, '~'); +} else { +break; +}} +s[i].setSequence (sb.toString ()); +if (s[i].getSequence ().length > max) { +max = s[i].getSequence ().length; +}i++; +} +var maxLenpad = new jalview.util.Format ("%" + ( String.instantialize ("" + max)).length + "d"); +var maxChkpad = new jalview.util.Format ("%" + ( String.instantialize ("1" + max)).length + "d"); +i = 0; +var bigChecksum = 0; +var checksums = Clazz.newIntArray (s.length, 0); +while (i < s.length) { +checksums[i] = this.checkSum (s[i].getSequenceAsString ()); +bigChecksum += checksums[i]; +i++; +} +var maxNB = 0; +out.append (" MSF: " + s[0].getSequence ().length + " Type: " + (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) + " .."); +out.append (this.newline); +out.append (this.newline); +out.append (this.newline); +var nameBlock = new Array (s.length); +var idBlock = new Array (s.length); +i = 0; +while ((i < s.length) && (s[i] != null)) { +nameBlock[i] = String.instantialize (" Name: " + this.printId (s[i]) + " "); +idBlock[i] = String.instantialize ("Len: " + maxLenpad.formLong (s[i].getSequence ().length) + " Check: " + maxChkpad.formLong (checksums[i]) + " Weight: 1.00" + this.newline); +if (s[i].getName ().length > maxid) { +maxid = s[i].getName ().length; +}if (nameBlock[i].length > maxNB) { +maxNB = nameBlock[i].length; +}i++; +} +if (maxid < 10) { +maxid = 10; +}if (maxNB < 15) { +maxNB = 15; +}var nbFormat = new jalview.util.Format ("%-" + maxNB + "s"); +for (i = 0; (i < s.length) && (s[i] != null); i++) { +out.append (nbFormat.form (nameBlock[i]) + idBlock[i]); +} +maxid++; +out.append (this.newline); +out.append (this.newline); +out.append ("//"); +out.append (this.newline); +out.append (this.newline); +var len = 50; +var nochunks = (Clazz.doubleToInt (max / len)) + 1; +if ((max % len) == 0) { +nochunks--; +}for (i = 0; i < nochunks; i++) { +var j = 0; +while ((j < s.length) && (s[j] != null)) { +var name = this.printId (s[j]); +out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " ")); +for (var k = 0; k < 5; k++) { +var start = (i * 50) + (k * 10); +var end = start + 10; +if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) { +out.append (s[j].getSequence (start, end)); +if (k < 4) { +out.append (" "); +} else { +out.append (this.newline); +}} else { +if (start < s[j].getSequence ().length) { +out.append (s[j].getSequenceAsString ().substring (start)); +out.append (this.newline); +} else { +if (k == 0) { +out.append (this.newline); +}}}} +j++; +} +out.append (this.newline); +} +return out.toString (); +}, "~A"); +Clazz.defineMethod (c$, "print", +function () { +return this.print (this.getSeqsAsArray ()); +}); +}); diff --git a/bin/jalview/io/ModellerDescription.class b/bin/jalview/io/ModellerDescription.class index 9465d75..16bff0d 100644 Binary files a/bin/jalview/io/ModellerDescription.class and b/bin/jalview/io/ModellerDescription.class differ diff --git a/bin/jalview/io/ModellerDescription.js b/bin/jalview/io/ModellerDescription.js index 1232c05..c08736d 100644 --- a/bin/jalview/io/ModellerDescription.js +++ b/bin/jalview/io/ModellerDescription.js @@ -1,236 +1,236 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["java.util.Hashtable"], "jalview.io.ModellerDescription", ["jalview.datamodel.DBRefSource", "jalview.jsdev.RegExp", "java.util.StringTokenizer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.seqTypes = null; -this.Fields = null; -this.TYPE = 0; -this.LOCALID = 1; -this.START = 2; -this.START_CHAIN = 3; -this.END = 4; -this.END_CHAIN = 5; -this.DESCRIPTION1 = 6; -this.DESCRIPTION2 = 7; -this.RESOLUTION = 8; -this.TAIL = 9; -this.Types = null; -this.Padding = null; -this.fields = null; -if (!Clazz.isClassDefined ("jalview.io.ModellerDescription.resCode")) { -jalview.io.ModellerDescription.$ModellerDescription$resCode$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.io, "ModellerDescription"); -Clazz.prepareFields (c$, function () { -this.seqTypes = Clazz.newArray (-1, ["sequence", "structure", "structureX", "structureN"]); -this.Fields = Clazz.newArray (-1, ["objectType", "objectId", "startField", "startCode", "endField", "endCode", "description1", "description2", "resolutionField", "tailField"]); -this.Types = Clazz.newIntArray (-1, [0, 0, 1, 0, 1, 0, 0, 0, 0, 0]); -this.Padding = Clazz.newCharArray (-1, [' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.']); -this.fields = new java.util.Hashtable (); -}); -Clazz.makeConstructor (c$, -function () { -this.fields.put (this.Fields[9], ""); -}); -Clazz.defineMethod (c$, "validResidueCode", -($fz = function (field) { -var val = null; -var r = jalview.jsdev.RegExp.newRegex (["\\s*((([-0-9]+).?)|FIRST|LAST|@)"]); -if (!r.search (field)) { -return null; -}var value = r.stringMatchedI (3); -if (value == null) { -value = r.stringMatchedI (1); -}try { -val = Integer.$valueOf (value); -return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, val); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, null); -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "parseDescription", -($fz = function (desc) { -var fields = new java.util.Hashtable (); -var st = new java.util.StringTokenizer (desc, ":", true); -var field; -var type = -1; -if (st.countTokens () > 0) { -var i = 0; -field = st.nextToken (":"); -do { -if (this.seqTypes[i].equalsIgnoreCase (field)) { -break; -}} while (++i < this.seqTypes.length); -if (i < this.seqTypes.length) { -st.nextToken (); -type = i; -i = 1; -while (i < 9 && st.hasMoreTokens ()) { -if ((field = st.nextToken (":")) != null) { -if (!field.equals (":")) { -if (this.Types[i] == 1) { -var val = this.validResidueCode (field); -if (val != null) { -fields.put ( String.instantialize (this.Fields[i] + "num"), val); -} else { -type = -1; -};}fields.put (this.Fields[i++], field); -if (st.hasMoreTokens ()) { -st.nextToken (); -}} else { -i++; -}}} -if (i == 9) { -while (st.hasMoreTokens ()) { -var tl = st.nextToken (":"); -field += tl.equals (":") ? tl : (":" + tl); -} -fields.put (this.Fields[9], field); -}}}if (type == -1) { -fields = new java.util.Hashtable (); -fields.put (this.Fields[9], String.instantialize (desc)); -} else { -fields.put (this.Fields[0], this.seqTypes[type]); -}return fields; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.makeConstructor (c$, -function (desc) { -if (desc == null) { -desc = ""; -}this.fields = this.parseDescription (desc); -}, "~S"); -Clazz.defineMethod (c$, "setStartCode", -function (v) { -var r; -this.fields.put (this.Fields[2] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v)); -this.fields.put (this.Fields[2], r.field); -}, "~N"); -Clazz.defineMethod (c$, "setEndCode", -function (v) { -var r; -this.fields.put (this.Fields[4] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v)); -this.fields.put (this.Fields[4], r.field); -}, "~N"); -Clazz.makeConstructor (c$, -function (seq) { -if (seq.getDescription () != null) { -this.fields = this.parseDescription (seq.getDescription ()); -}if (this.isModellerFieldset ()) { -if (this.getStartCode () == null || (this.getStartNum () != seq.getStart () && this.getStartCode ().val != null)) { -this.setStartCode (seq.getStart ()); -}if (this.getEndCode () == null || (this.getEndNum () != seq.getEnd () && this.getStartCode () != null && this.getStartCode ().val != null)) { -this.setEndCode (seq.getEnd ()); -}} else { -this.setStartCode (seq.getStart ()); -this.setEndCode (seq.getEnd ()); -this.fields.put (this.Fields[1], seq.getName ()); -var t = 0; -if (seq.getDatasetSequence () != null && seq.getDatasetSequence ().getDBRef () != null) { -var dbr = seq.getDatasetSequence ().getDBRef (); -var i; -var j; -for (i = 0, j = dbr.length; i < j; i++) { -if (dbr[i] != null) { -if (dbr[i].getSource ().equals (jalview.datamodel.DBRefSource.PDB)) { -this.fields.put (this.Fields[1], dbr[i].getAccessionId ()); -t = 2; -break; -}}} -}this.fields.put (this.Fields[0], this.seqTypes[t]); -}}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "isModellerFieldset", -function () { -return (this.fields.containsKey (this.Fields[0])); -}); -Clazz.defineMethod (c$, "getDescriptionLine", -function () { -var desc = ""; -var lastfield = this.Fields.length - 1; -if (this.isModellerFieldset ()) { -var value; -for (; lastfield > 6; lastfield--) { -if (this.fields.containsKey (this.Fields[lastfield])) { -break; -}} -for (var i = 0; i < lastfield; i++) { -value = this.fields.get (this.Fields[i]); -if (value != null && value.length > 0) { -desc += (this.fields.get (this.Fields[i])) + ":"; -} else { -desc += this.Padding[i] + ":"; -}} -}if (this.fields.containsKey (this.Fields[lastfield])) { -desc += this.fields.get (this.Fields[lastfield]); -} else { -desc += "."; -}return desc; -}); -Clazz.defineMethod (c$, "getStartNum", -function () { -var start = 0; -var val = this.getStartCode (); -if (val != null && val.val != null) { -return val.val.intValue (); -}return start; -}); -Clazz.defineMethod (c$, "getStartCode", -function () { -if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[2] + "num")) { -return this.fields.get (this.Fields[2] + "num"); -}return null; -}); -Clazz.defineMethod (c$, "getEndCode", -function () { -if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[4] + "num")) { -return this.fields.get (this.Fields[4] + "num"); -}return null; -}); -Clazz.defineMethod (c$, "getEndNum", -function () { -var end = 0; -var val = this.getEndCode (); -if (val != null && val.val != null) { -return val.val.intValue (); -}return end; -}); -Clazz.defineMethod (c$, "updateSequenceI", -function (newSeq) { -if (this.isModellerFieldset ()) { -var rc = this.getStartCode (); -if (rc != null && rc.val != null) { -newSeq.setStart (this.getStartNum ()); -} else { -newSeq.setStart (1); -}rc = this.getEndCode (); -if (rc != null && rc.val != null) { -newSeq.setEnd (this.getEndNum ()); -} else { -newSeq.setEnd (newSeq.getStart () + newSeq.getLength ()); -}return true; -}return false; -}, "jalview.datamodel.SequenceI"); -c$.$ModellerDescription$resCode$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.val = null; -this.field = null; -Clazz.instantialize (this, arguments); -}, jalview.io.ModellerDescription, "resCode"); -Clazz.makeConstructor (c$, -function (a, b) { -this.val = b; -this.field = a; -}, "~S,Integer"); -Clazz.makeConstructor (c$, -function (a) { -this.val = new Integer (a); -this.field = this.val.toString (); -}, "~N"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["java.util.Hashtable"], "jalview.io.ModellerDescription", ["jalview.datamodel.DBRefSource", "jalview.jsdev.RegExp", "java.util.StringTokenizer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.seqTypes = null; +this.Fields = null; +this.TYPE = 0; +this.LOCALID = 1; +this.START = 2; +this.START_CHAIN = 3; +this.END = 4; +this.END_CHAIN = 5; +this.DESCRIPTION1 = 6; +this.DESCRIPTION2 = 7; +this.RESOLUTION = 8; +this.TAIL = 9; +this.Types = null; +this.Padding = null; +this.fields = null; +if (!Clazz.isClassDefined ("jalview.io.ModellerDescription.resCode")) { +jalview.io.ModellerDescription.$ModellerDescription$resCode$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.io, "ModellerDescription"); +Clazz.prepareFields (c$, function () { +this.seqTypes = Clazz.newArray (-1, ["sequence", "structure", "structureX", "structureN"]); +this.Fields = Clazz.newArray (-1, ["objectType", "objectId", "startField", "startCode", "endField", "endCode", "description1", "description2", "resolutionField", "tailField"]); +this.Types = Clazz.newIntArray (-1, [0, 0, 1, 0, 1, 0, 0, 0, 0, 0]); +this.Padding = Clazz.newCharArray (-1, [' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.']); +this.fields = new java.util.Hashtable (); +}); +Clazz.makeConstructor (c$, +function () { +this.fields.put (this.Fields[9], ""); +}); +Clazz.defineMethod (c$, "validResidueCode", +($fz = function (field) { +var val = null; +var r = jalview.jsdev.RegExp.newRegex (["\\s*((([-0-9]+).?)|FIRST|LAST|@)"]); +if (!r.search (field)) { +return null; +}var value = r.stringMatchedI (3); +if (value == null) { +value = r.stringMatchedI (1); +}try { +val = Integer.$valueOf (value); +return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, val); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, null); +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "parseDescription", +($fz = function (desc) { +var fields = new java.util.Hashtable (); +var st = new java.util.StringTokenizer (desc, ":", true); +var field; +var type = -1; +if (st.countTokens () > 0) { +var i = 0; +field = st.nextToken (":"); +do { +if (this.seqTypes[i].equalsIgnoreCase (field)) { +break; +}} while (++i < this.seqTypes.length); +if (i < this.seqTypes.length) { +st.nextToken (); +type = i; +i = 1; +while (i < 9 && st.hasMoreTokens ()) { +if ((field = st.nextToken (":")) != null) { +if (!field.equals (":")) { +if (this.Types[i] == 1) { +var val = this.validResidueCode (field); +if (val != null) { +fields.put ( String.instantialize (this.Fields[i] + "num"), val); +} else { +type = -1; +};}fields.put (this.Fields[i++], field); +if (st.hasMoreTokens ()) { +st.nextToken (); +}} else { +i++; +}}} +if (i == 9) { +while (st.hasMoreTokens ()) { +var tl = st.nextToken (":"); +field += tl.equals (":") ? tl : (":" + tl); +} +fields.put (this.Fields[9], field); +}}}if (type == -1) { +fields = new java.util.Hashtable (); +fields.put (this.Fields[9], String.instantialize (desc)); +} else { +fields.put (this.Fields[0], this.seqTypes[type]); +}return fields; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.makeConstructor (c$, +function (desc) { +if (desc == null) { +desc = ""; +}this.fields = this.parseDescription (desc); +}, "~S"); +Clazz.defineMethod (c$, "setStartCode", +function (v) { +var r; +this.fields.put (this.Fields[2] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v)); +this.fields.put (this.Fields[2], r.field); +}, "~N"); +Clazz.defineMethod (c$, "setEndCode", +function (v) { +var r; +this.fields.put (this.Fields[4] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v)); +this.fields.put (this.Fields[4], r.field); +}, "~N"); +Clazz.makeConstructor (c$, +function (seq) { +if (seq.getDescription () != null) { +this.fields = this.parseDescription (seq.getDescription ()); +}if (this.isModellerFieldset ()) { +if (this.getStartCode () == null || (this.getStartNum () != seq.getStart () && this.getStartCode ().val != null)) { +this.setStartCode (seq.getStart ()); +}if (this.getEndCode () == null || (this.getEndNum () != seq.getEnd () && this.getStartCode () != null && this.getStartCode ().val != null)) { +this.setEndCode (seq.getEnd ()); +}} else { +this.setStartCode (seq.getStart ()); +this.setEndCode (seq.getEnd ()); +this.fields.put (this.Fields[1], seq.getName ()); +var t = 0; +if (seq.getDatasetSequence () != null && seq.getDatasetSequence ().getDBRef () != null) { +var dbr = seq.getDatasetSequence ().getDBRef (); +var i; +var j; +for (i = 0, j = dbr.length; i < j; i++) { +if (dbr[i] != null) { +if (dbr[i].getSource ().equals (jalview.datamodel.DBRefSource.PDB)) { +this.fields.put (this.Fields[1], dbr[i].getAccessionId ()); +t = 2; +break; +}}} +}this.fields.put (this.Fields[0], this.seqTypes[t]); +}}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "isModellerFieldset", +function () { +return (this.fields.containsKey (this.Fields[0])); +}); +Clazz.defineMethod (c$, "getDescriptionLine", +function () { +var desc = ""; +var lastfield = this.Fields.length - 1; +if (this.isModellerFieldset ()) { +var value; +for (; lastfield > 6; lastfield--) { +if (this.fields.containsKey (this.Fields[lastfield])) { +break; +}} +for (var i = 0; i < lastfield; i++) { +value = this.fields.get (this.Fields[i]); +if (value != null && value.length > 0) { +desc += (this.fields.get (this.Fields[i])) + ":"; +} else { +desc += this.Padding[i] + ":"; +}} +}if (this.fields.containsKey (this.Fields[lastfield])) { +desc += this.fields.get (this.Fields[lastfield]); +} else { +desc += "."; +}return desc; +}); +Clazz.defineMethod (c$, "getStartNum", +function () { +var start = 0; +var val = this.getStartCode (); +if (val != null && val.val != null) { +return val.val.intValue (); +}return start; +}); +Clazz.defineMethod (c$, "getStartCode", +function () { +if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[2] + "num")) { +return this.fields.get (this.Fields[2] + "num"); +}return null; +}); +Clazz.defineMethod (c$, "getEndCode", +function () { +if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[4] + "num")) { +return this.fields.get (this.Fields[4] + "num"); +}return null; +}); +Clazz.defineMethod (c$, "getEndNum", +function () { +var end = 0; +var val = this.getEndCode (); +if (val != null && val.val != null) { +return val.val.intValue (); +}return end; +}); +Clazz.defineMethod (c$, "updateSequenceI", +function (newSeq) { +if (this.isModellerFieldset ()) { +var rc = this.getStartCode (); +if (rc != null && rc.val != null) { +newSeq.setStart (this.getStartNum ()); +} else { +newSeq.setStart (1); +}rc = this.getEndCode (); +if (rc != null && rc.val != null) { +newSeq.setEnd (this.getEndNum ()); +} else { +newSeq.setEnd (newSeq.getStart () + newSeq.getLength ()); +}return true; +}return false; +}, "jalview.datamodel.SequenceI"); +c$.$ModellerDescription$resCode$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.val = null; +this.field = null; +Clazz.instantialize (this, arguments); +}, jalview.io.ModellerDescription, "resCode"); +Clazz.makeConstructor (c$, +function (a, b) { +this.val = b; +this.field = a; +}, "~S,Integer"); +Clazz.makeConstructor (c$, +function (a) { +this.val = new Integer (a); +this.field = this.val.toString (); +}, "~N"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/io/NewickFile.class b/bin/jalview/io/NewickFile.class index 59a2362..2b1359c 100644 Binary files a/bin/jalview/io/NewickFile.class and b/bin/jalview/io/NewickFile.class differ diff --git a/bin/jalview/io/NewickFile.js b/bin/jalview/io/NewickFile.js index 886a07b..2975319 100644 --- a/bin/jalview/io/NewickFile.js +++ b/bin/jalview/io/NewickFile.js @@ -1,408 +1,408 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.FileParse", "jalview.jsdev.RegExp"], "jalview.io.NewickFile", ["jalview.datamodel.SequenceNode", "jalview.util.MessageManager", "java.io.BufferedReader", "$.IOException", "java.lang.Float", "$.StringBuffer", "java.util.StringTokenizer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.root = null; -this.$HasBootstrap = false; -this.$HasDistances = false; -this.RootHasDistance = false; -this.ReplaceUnderscores = false; -this.printRootInfo = true; -this.NodeSafeName = null; -this.QuoteChar = '\''; -Clazz.instantialize (this, arguments); -}, jalview.io, "NewickFile", jalview.io.FileParse); -Clazz.prepareFields (c$, function () { -this.NodeSafeName = Clazz.newArray (-1, [jalview.jsdev.RegExp.perlCode ("m/[\\[,:'()]/"), jalview.jsdev.RegExp.perlCode ("s/'/''/"), jalview.jsdev.RegExp.perlCode ("s/\\/w/_/")]); -}); -Clazz.makeConstructor (c$, -function (inStr) { -Clazz.superConstructor (this, jalview.io.NewickFile, [inStr, "Paste"]); -}, "~S"); -Clazz.makeConstructor (c$, -function (newtree) { -Clazz.superConstructor (this, jalview.io.NewickFile, []); -this.root = newtree; -}, "jalview.datamodel.SequenceNode"); -Clazz.makeConstructor (c$, -function (newtree, bootstrap) { -Clazz.superConstructor (this, jalview.io.NewickFile, []); -this.$HasBootstrap = bootstrap; -this.root = newtree; -}, "jalview.datamodel.SequenceNode,~B"); -Clazz.makeConstructor (c$, -function (newtree, bootstrap, distances) { -Clazz.superConstructor (this, jalview.io.NewickFile, []); -this.root = newtree; -this.$HasBootstrap = bootstrap; -this.$HasDistances = distances; -}, "jalview.datamodel.SequenceNode,~B,~B"); -Clazz.makeConstructor (c$, -function (newtree, bootstrap, distances, rootdistance) { -Clazz.superConstructor (this, jalview.io.NewickFile, []); -this.root = newtree; -this.$HasBootstrap = bootstrap; -this.$HasDistances = distances; -this.RootHasDistance = rootdistance; -}, "jalview.datamodel.SequenceNode,~B,~B,~B"); -Clazz.defineMethod (c$, "ErrorStringrange", -($fz = function (Error, Er, r, p, s) { -return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( " + s.substring (((p - r) < 0) ? 0 : (p - r), ((p + r) > s.length) ? s.length : (p + r)) + " )\n"; -}, $fz.isPrivate = true, $fz), "~S,~S,~N,~N,~S"); -Clazz.defineMethod (c$, "HasBootstrap", -function () { -return this.$HasBootstrap; -}); -Clazz.defineMethod (c$, "HasDistances", -function () { -return this.$HasDistances; -}); -Clazz.defineMethod (c$, "HasRootDistance", -function () { -return this.RootHasDistance; -}); -Clazz.defineMethod (c$, "parse", -function () { -var nf; -{ -var file = new StringBuffer (); -while ((nf = this.nextLine ()) != null) { -file.append (nf); -} -nf = file.toString (); -}this.root = new jalview.datamodel.SequenceNode (); -var realroot = null; -var c = this.root; -var d = -1; -var cp = 0; -var Error = null; -var nodename = null; -var commentString2 = null; -var DefDistance = 0.001; -var DefBootstrap = -1; -var distance = DefDistance; -var bootstrap = DefBootstrap; -var ascending = false; -var majorsyms = jalview.jsdev.RegExp.newRegex (["[(\\['),;]"]); -var nextcp = 0; -var ncp = cp; -var parsednodename = false; -while (majorsyms.searchFrom (nf, cp) && (Error == null)) { -var fcp = majorsyms.matchedFrom (); -var schar; -switch (schar = nf.charAt (fcp)) { -case '(': -if (ascending) { -Error = this.ErrorStringrange (Error, "Unexpected '('", 7, fcp, nf); -continue; -};d++; -if (c.right () == null) { -c.setRight ( new jalview.datamodel.SequenceNode (null, c, null, DefDistance, DefBootstrap, false)); -c = c.right (); -} else { -if (c.left () != null) { -var tmpn = new jalview.datamodel.SequenceNode (null, c, null, 0, 0, true); -tmpn.SetChildren (c.left (), c.right ()); -c.setRight (tmpn); -}c.setLeft ( new jalview.datamodel.SequenceNode (null, c, null, DefDistance, DefBootstrap, false)); -c = c.left (); -}if (realroot == null) { -realroot = c; -}nodename = null; -distance = DefDistance; -bootstrap = DefBootstrap; -cp = fcp + 1; -break; -case '\'': -var qnodename = jalview.jsdev.RegExp.newRegex (["'([^']|'')+'"]); -if (qnodename.searchFrom (nf, fcp)) { -var nl = qnodename.stringMatched ().length; -nodename = String.instantialize (qnodename.stringMatched ().substring (1, nl - 1)); -var xpandquotes = jalview.jsdev.RegExp.perlCode ("s/''/'/"); -var widernodename = xpandquotes.replaceAll (nodename); -nodename = widernodename; -nextcp = fcp + nl + 1; -parsednodename = true; -} else { -Error = this.ErrorStringrange (Error, "Unterminated quotes for nodename", 7, fcp, nf); -}break; -default: -if (schar == ';') { -if (d != -1) { -Error = this.ErrorStringrange (Error, "Wayward semicolon (depth=" + d + ")", 7, fcp, nf); -}}if (schar == '[') { -var comment = jalview.jsdev.RegExp.newRegex (["]"]); -if (comment.searchFrom (nf, fcp)) { -nextcp = comment.matchedFrom () + 1; -this.warningMessage = "Tree file contained comments which may confuse input algorithm."; -break; -} else { -Error = this.ErrorStringrange (Error, "Unterminated comment", 3, fcp, nf); -};}var fstring = nf.substring (ncp, fcp); -while (fstring.indexOf (']') > -1) { -var cstart = fstring.indexOf ('['); -var cend = fstring.indexOf (']'); -commentString2 = fstring.substring (cstart + 1, cend); -fstring = fstring.substring (0, cstart) + fstring.substring (cend + 1); -} -var uqnodename = jalview.jsdev.RegExp.newRegex (["\\b([^' :;\\](),]+)"]); -var nbootstrap = jalview.jsdev.RegExp.newRegex (["\\s*([0-9+]+)\\s*:"]); -var ndist = jalview.jsdev.RegExp.newRegex ([":([-0-9Ee.+]+)"]); -if (!parsednodename && uqnodename.search (fstring) && ((uqnodename.matchedFromI (1) == 0) || (fstring.charAt (uqnodename.matchedFromI (1) - 1) != ':'))) { -if (nodename == null) { -if (this.ReplaceUnderscores) { -nodename = uqnodename.stringMatchedI (1).$replace ('_', ' '); -} else { -nodename = uqnodename.stringMatchedI (1); -}} else { -Error = this.ErrorStringrange (Error, "File has broken algorithm - overwritten nodename", 10, fcp, nf); -}}if (nbootstrap.search (fstring)) { -if (nbootstrap.stringMatchedI (1).equals (uqnodename.stringMatchedI (1))) { -nodename = null; -}if (nodename == null || nodename.length == 0 || nbootstrap.matchedFromI (1) > (uqnodename.matchedFromI (1) + uqnodename.stringMatched ().length)) { -try { -bootstrap = ( new Integer (nbootstrap.stringMatchedI (1))).intValue (); -this.$HasBootstrap = true; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -Error = this.ErrorStringrange (Error, "Can't parse bootstrap value", 4, ncp + nbootstrap.matchedFrom (), nf); -} else { -throw e; -} -} -}}var nodehasdistance = false; -if (ndist.search (fstring)) { -try { -distance = ( new Float (ndist.stringMatchedI (1))).floatValue (); -this.$HasDistances = true; -nodehasdistance = true; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -Error = this.ErrorStringrange (Error, "Can't parse node distance value", 7, ncp + ndist.matchedFrom (), nf); -} else { -throw e; -} -} -}if (ascending) { -c.setName (nodename); -c.dist = (this.$HasDistances) ? distance : DefDistance; -c.setBootstrap ((this.$HasBootstrap) ? bootstrap : DefBootstrap); -if (c === realroot) { -this.RootHasDistance = nodehasdistance; -}this.parseNHXNodeProps (c, commentString2); -commentString2 = null; -} else { -var newnode = new jalview.datamodel.SequenceNode (null, c, nodename, (this.$HasDistances) ? distance : DefDistance, (this.$HasBootstrap) ? bootstrap : DefBootstrap, false); -this.parseNHXNodeProps (c, commentString2); -commentString2 = null; -if (c.right () == null) { -c.setRight (newnode); -} else { -if (c.left () == null) { -c.setLeft (newnode); -} else { -var newdummy = new jalview.datamodel.SequenceNode (null, c, null, (this.$HasDistances ? 0 : DefDistance), 0, true); -newdummy.SetChildren (c.left (), newnode); -c.setLeft (newdummy); -}}}if (ascending) { -c = c.AscendTree (); -if ((d > -1) && (c == null)) { -Error = this.ErrorStringrange (Error, "File broke algorithm: Lost place in tree (is there an extra ')' ?)", 7, fcp, nf); -}}if (nf.charAt (fcp) == ')') { -d--; -ascending = true; -} else { -if (nf.charAt (fcp) == ',') { -if (ascending) { -ascending = false; -} else { -if ((c.left () != null) && (!c.left ().isLeaf ())) { -c = c.left (); -}}}}nodename = null; -distance = DefDistance; -bootstrap = DefBootstrap; -commentString2 = null; -parsednodename = false; -} -if (nextcp == 0) { -ncp = cp = fcp + 1; -} else { -cp = nextcp; -nextcp = 0; -}} -if (Error != null) { -throw ( new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.newfile", Clazz.newArray (-1, [Error.toString ()])))); -}if (this.root == null) { -throw ( new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.newfile", Clazz.newArray (-1, [jalview.util.MessageManager.getString ("label.no_tree_read_in")])))); -}this.root = this.root.right ().detach (); -if (!this.RootHasDistance) { -this.root.dist = (this.$HasDistances) ? 0 : DefDistance; -}}); -Clazz.defineMethod (c$, "parseNHXNodeProps", -($fz = function (c, commentString) { -if (commentString != null && commentString.startsWith ("&&NHX")) { -var st = new java.util.StringTokenizer (commentString.substring (5), ":"); -while (st.hasMoreTokens ()) { -var tok = st.nextToken (); -var colpos = tok.indexOf ("="); -if (colpos > -1) { -var code = tok.substring (0, colpos); -var value = tok.substring (colpos + 1); -try { -if (code.toLowerCase ().equals ("b")) { -var v = -1; -var iv = new Float (value); -v = iv.intValue (); -c.setBootstrap (v); -this.$HasBootstrap = true; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.err.println ("Couldn't parse code '" + code + "' = '" + value + "'"); -e.printStackTrace (System.err); -} else { -throw e; -} -} -}} -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode,~S"); -Clazz.defineMethod (c$, "getTree", -function () { -return this.root; -}); -Clazz.defineMethod (c$, "print", -function () { -{ -var tf = new StringBuffer (); -this.print (tf, this.root); -return (tf.append (";").toString ()); -}}); -Clazz.defineMethod (c$, "print", -function (withbootstraps) { -{ -var boots = this.$HasBootstrap; -this.$HasBootstrap = withbootstraps; -var rv = this.print (); -this.$HasBootstrap = boots; -return rv; -}}, "~B"); -Clazz.defineMethod (c$, "print", -function (withbootstraps, withdists) { -{ -var dists = this.$HasDistances; -this.$HasDistances = withdists; -var rv = this.print (withbootstraps); -this.$HasDistances = dists; -return rv; -}}, "~B,~B"); -Clazz.defineMethod (c$, "print", -function (withbootstraps, withdists, printRootInfo) { -{ -var rootinfo = printRootInfo; -this.printRootInfo = printRootInfo; -var rv = this.print (withbootstraps, withdists); -this.printRootInfo = rootinfo; -return rv; -}}, "~B,~B,~B"); -Clazz.defineMethod (c$, "getQuoteChar", -function () { -return this.QuoteChar; -}); -Clazz.defineMethod (c$, "setQuoteChar", -function (c) { -var old = this.QuoteChar; -this.QuoteChar = c; -return old; -}, "~S"); -Clazz.defineMethod (c$, "nodeName", -($fz = function (name) { -if (this.NodeSafeName[0].search (name)) { -return this.QuoteChar + this.NodeSafeName[1].replaceAll (name) + this.QuoteChar; -} else { -return this.NodeSafeName[2].replaceAll (name); -}}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "printNodeField", -($fz = function (c) { -return ((c.getName () == null) ? "" : this.nodeName (c.getName ())) + ((this.$HasBootstrap) ? ((c.getBootstrap () > -1) ? ((c.getName () != null ? " " : "") + c.getBootstrap ()) : "") : "") + ((this.$HasDistances) ? (":" + c.dist) : ""); -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "printRootField", -($fz = function (root) { -return (this.printRootInfo) ? (((root.getName () == null) ? "" : this.nodeName (root.getName ())) + ((this.$HasBootstrap) ? ((root.getBootstrap () > -1) ? ((root.getName () != null ? " " : "") + +root.getBootstrap ()) : "") : "") + ((this.RootHasDistance) ? (":" + root.dist) : "")) : ""; -}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "print", -function (tf, root) { -if (root != null) { -if (root.isLeaf () && this.printRootInfo) { -tf.append (this.printRootField (root)); -} else { -if (root.isDummy ()) { -this._print (tf, root.right ()); -this._print (tf, root.left ()); -} else { -tf.append ("("); -this._print (tf, root.right ()); -if (root.left () != null) { -tf.append (","); -}this._print (tf, root.left ()); -tf.append (")" + this.printRootField (root)); -}}}}, "StringBuffer,jalview.datamodel.SequenceNode"); -Clazz.defineMethod (c$, "_print", -function (tf, c) { -if (c != null) { -if (c.isLeaf ()) { -tf.append (this.printNodeField (c)); -} else { -if (c.isDummy ()) { -this._print (tf, c.left ()); -if (c.left () != null) { -tf.append (","); -}this._print (tf, c.right ()); -} else { -tf.append ("("); -this._print (tf, c.right ()); -if (c.left () != null) { -tf.append (","); -}this._print (tf, c.left ()); -tf.append (")" + this.printNodeField (c)); -}}}}, "StringBuffer,jalview.datamodel.SequenceNode"); -c$.main = Clazz.defineMethod (c$, "main", -function (args) { -try { -if (args == null || args.length != 1) { -System.err.println ("Takes one argument - file name of a newick tree file."); -System.exit (0); -}var fn = new java.io.File (args[0]); -var newickfile = new StringBuffer (); -var treefile = new java.io.BufferedReader ( new java.io.FileReader (fn)); -var l; -while ((l = treefile.readLine ()) != null) { -newickfile.append (l); -} -treefile.close (); -System.out.println ("Read file :\n"); -var trf = new jalview.io.NewickFile (args[0], "File"); -trf.parse (); -System.out.println ("Original file :\n"); -var nonl = jalview.jsdev.RegExp.newRegex (["\n+", ""]); -System.out.println (nonl.replaceAll (newickfile.toString ()) + "\n"); -System.out.println ("Parsed file.\n"); -System.out.println ("Default output type for original input.\n"); -System.out.println (trf.print ()); -System.out.println ("Without bootstraps.\n"); -System.out.println (trf.print (false)); -System.out.println ("Without distances.\n"); -System.out.println (trf.print (true, false)); -System.out.println ("Without bootstraps but with distanecs.\n"); -System.out.println (trf.print (false, true)); -System.out.println ("Without bootstraps or distanecs.\n"); -System.out.println (trf.print (false, false)); -System.out.println ("With bootstraps and with distances.\n"); -System.out.println (trf.print (true, true)); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -System.err.println ("Exception\n" + e); -e.printStackTrace (); -} else { -throw e; -} -} -}, "~A"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.FileParse", "jalview.jsdev.RegExp"], "jalview.io.NewickFile", ["jalview.datamodel.SequenceNode", "jalview.util.MessageManager", "java.io.BufferedReader", "$.IOException", "java.lang.Float", "$.StringBuffer", "java.util.StringTokenizer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.root = null; +this.$HasBootstrap = false; +this.$HasDistances = false; +this.RootHasDistance = false; +this.ReplaceUnderscores = false; +this.printRootInfo = true; +this.NodeSafeName = null; +this.QuoteChar = '\''; +Clazz.instantialize (this, arguments); +}, jalview.io, "NewickFile", jalview.io.FileParse); +Clazz.prepareFields (c$, function () { +this.NodeSafeName = Clazz.newArray (-1, [jalview.jsdev.RegExp.perlCode ("m/[\\[,:'()]/"), jalview.jsdev.RegExp.perlCode ("s/'/''/"), jalview.jsdev.RegExp.perlCode ("s/\\/w/_/")]); +}); +Clazz.makeConstructor (c$, +function (inStr) { +Clazz.superConstructor (this, jalview.io.NewickFile, [inStr, "Paste"]); +}, "~S"); +Clazz.makeConstructor (c$, +function (newtree) { +Clazz.superConstructor (this, jalview.io.NewickFile, []); +this.root = newtree; +}, "jalview.datamodel.SequenceNode"); +Clazz.makeConstructor (c$, +function (newtree, bootstrap) { +Clazz.superConstructor (this, jalview.io.NewickFile, []); +this.$HasBootstrap = bootstrap; +this.root = newtree; +}, "jalview.datamodel.SequenceNode,~B"); +Clazz.makeConstructor (c$, +function (newtree, bootstrap, distances) { +Clazz.superConstructor (this, jalview.io.NewickFile, []); +this.root = newtree; +this.$HasBootstrap = bootstrap; +this.$HasDistances = distances; +}, "jalview.datamodel.SequenceNode,~B,~B"); +Clazz.makeConstructor (c$, +function (newtree, bootstrap, distances, rootdistance) { +Clazz.superConstructor (this, jalview.io.NewickFile, []); +this.root = newtree; +this.$HasBootstrap = bootstrap; +this.$HasDistances = distances; +this.RootHasDistance = rootdistance; +}, "jalview.datamodel.SequenceNode,~B,~B,~B"); +Clazz.defineMethod (c$, "ErrorStringrange", +($fz = function (Error, Er, r, p, s) { +return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( " + s.substring (((p - r) < 0) ? 0 : (p - r), ((p + r) > s.length) ? s.length : (p + r)) + " )\n"; +}, $fz.isPrivate = true, $fz), "~S,~S,~N,~N,~S"); +Clazz.defineMethod (c$, "HasBootstrap", +function () { +return this.$HasBootstrap; +}); +Clazz.defineMethod (c$, "HasDistances", +function () { +return this.$HasDistances; +}); +Clazz.defineMethod (c$, "HasRootDistance", +function () { +return this.RootHasDistance; +}); +Clazz.defineMethod (c$, "parse", +function () { +var nf; +{ +var file = new StringBuffer (); +while ((nf = this.nextLine ()) != null) { +file.append (nf); +} +nf = file.toString (); +}this.root = new jalview.datamodel.SequenceNode (); +var realroot = null; +var c = this.root; +var d = -1; +var cp = 0; +var Error = null; +var nodename = null; +var commentString2 = null; +var DefDistance = 0.001; +var DefBootstrap = -1; +var distance = DefDistance; +var bootstrap = DefBootstrap; +var ascending = false; +var majorsyms = jalview.jsdev.RegExp.newRegex (["[(\\['),;]"]); +var nextcp = 0; +var ncp = cp; +var parsednodename = false; +while (majorsyms.searchFrom (nf, cp) && (Error == null)) { +var fcp = majorsyms.matchedFrom (); +var schar; +switch (schar = nf.charAt (fcp)) { +case '(': +if (ascending) { +Error = this.ErrorStringrange (Error, "Unexpected '('", 7, fcp, nf); +continue; +};d++; +if (c.right () == null) { +c.setRight ( new jalview.datamodel.SequenceNode (null, c, null, DefDistance, DefBootstrap, false)); +c = c.right (); +} else { +if (c.left () != null) { +var tmpn = new jalview.datamodel.SequenceNode (null, c, null, 0, 0, true); +tmpn.SetChildren (c.left (), c.right ()); +c.setRight (tmpn); +}c.setLeft ( new jalview.datamodel.SequenceNode (null, c, null, DefDistance, DefBootstrap, false)); +c = c.left (); +}if (realroot == null) { +realroot = c; +}nodename = null; +distance = DefDistance; +bootstrap = DefBootstrap; +cp = fcp + 1; +break; +case '\'': +var qnodename = jalview.jsdev.RegExp.newRegex (["'([^']|'')+'"]); +if (qnodename.searchFrom (nf, fcp)) { +var nl = qnodename.stringMatched ().length; +nodename = String.instantialize (qnodename.stringMatched ().substring (1, nl - 1)); +var xpandquotes = jalview.jsdev.RegExp.perlCode ("s/''/'/"); +var widernodename = xpandquotes.replaceAll (nodename); +nodename = widernodename; +nextcp = fcp + nl + 1; +parsednodename = true; +} else { +Error = this.ErrorStringrange (Error, "Unterminated quotes for nodename", 7, fcp, nf); +}break; +default: +if (schar == ';') { +if (d != -1) { +Error = this.ErrorStringrange (Error, "Wayward semicolon (depth=" + d + ")", 7, fcp, nf); +}}if (schar == '[') { +var comment = jalview.jsdev.RegExp.newRegex (["]"]); +if (comment.searchFrom (nf, fcp)) { +nextcp = comment.matchedFrom () + 1; +this.warningMessage = "Tree file contained comments which may confuse input algorithm."; +break; +} else { +Error = this.ErrorStringrange (Error, "Unterminated comment", 3, fcp, nf); +};}var fstring = nf.substring (ncp, fcp); +while (fstring.indexOf (']') > -1) { +var cstart = fstring.indexOf ('['); +var cend = fstring.indexOf (']'); +commentString2 = fstring.substring (cstart + 1, cend); +fstring = fstring.substring (0, cstart) + fstring.substring (cend + 1); +} +var uqnodename = jalview.jsdev.RegExp.newRegex (["\\b([^' :;\\](),]+)"]); +var nbootstrap = jalview.jsdev.RegExp.newRegex (["\\s*([0-9+]+)\\s*:"]); +var ndist = jalview.jsdev.RegExp.newRegex ([":([-0-9Ee.+]+)"]); +if (!parsednodename && uqnodename.search (fstring) && ((uqnodename.matchedFromI (1) == 0) || (fstring.charAt (uqnodename.matchedFromI (1) - 1) != ':'))) { +if (nodename == null) { +if (this.ReplaceUnderscores) { +nodename = uqnodename.stringMatchedI (1).$replace ('_', ' '); +} else { +nodename = uqnodename.stringMatchedI (1); +}} else { +Error = this.ErrorStringrange (Error, "File has broken algorithm - overwritten nodename", 10, fcp, nf); +}}if (nbootstrap.search (fstring)) { +if (nbootstrap.stringMatchedI (1).equals (uqnodename.stringMatchedI (1))) { +nodename = null; +}if (nodename == null || nodename.length == 0 || nbootstrap.matchedFromI (1) > (uqnodename.matchedFromI (1) + uqnodename.stringMatched ().length)) { +try { +bootstrap = ( new Integer (nbootstrap.stringMatchedI (1))).intValue (); +this.$HasBootstrap = true; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +Error = this.ErrorStringrange (Error, "Can't parse bootstrap value", 4, ncp + nbootstrap.matchedFrom (), nf); +} else { +throw e; +} +} +}}var nodehasdistance = false; +if (ndist.search (fstring)) { +try { +distance = ( new Float (ndist.stringMatchedI (1))).floatValue (); +this.$HasDistances = true; +nodehasdistance = true; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +Error = this.ErrorStringrange (Error, "Can't parse node distance value", 7, ncp + ndist.matchedFrom (), nf); +} else { +throw e; +} +} +}if (ascending) { +c.setName (nodename); +c.dist = (this.$HasDistances) ? distance : DefDistance; +c.setBootstrap ((this.$HasBootstrap) ? bootstrap : DefBootstrap); +if (c === realroot) { +this.RootHasDistance = nodehasdistance; +}this.parseNHXNodeProps (c, commentString2); +commentString2 = null; +} else { +var newnode = new jalview.datamodel.SequenceNode (null, c, nodename, (this.$HasDistances) ? distance : DefDistance, (this.$HasBootstrap) ? bootstrap : DefBootstrap, false); +this.parseNHXNodeProps (c, commentString2); +commentString2 = null; +if (c.right () == null) { +c.setRight (newnode); +} else { +if (c.left () == null) { +c.setLeft (newnode); +} else { +var newdummy = new jalview.datamodel.SequenceNode (null, c, null, (this.$HasDistances ? 0 : DefDistance), 0, true); +newdummy.SetChildren (c.left (), newnode); +c.setLeft (newdummy); +}}}if (ascending) { +c = c.AscendTree (); +if ((d > -1) && (c == null)) { +Error = this.ErrorStringrange (Error, "File broke algorithm: Lost place in tree (is there an extra ')' ?)", 7, fcp, nf); +}}if (nf.charAt (fcp) == ')') { +d--; +ascending = true; +} else { +if (nf.charAt (fcp) == ',') { +if (ascending) { +ascending = false; +} else { +if ((c.left () != null) && (!c.left ().isLeaf ())) { +c = c.left (); +}}}}nodename = null; +distance = DefDistance; +bootstrap = DefBootstrap; +commentString2 = null; +parsednodename = false; +} +if (nextcp == 0) { +ncp = cp = fcp + 1; +} else { +cp = nextcp; +nextcp = 0; +}} +if (Error != null) { +throw ( new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.newfile", Clazz.newArray (-1, [Error.toString ()])))); +}if (this.root == null) { +throw ( new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.newfile", Clazz.newArray (-1, [jalview.util.MessageManager.getString ("label.no_tree_read_in")])))); +}this.root = this.root.right ().detach (); +if (!this.RootHasDistance) { +this.root.dist = (this.$HasDistances) ? 0 : DefDistance; +}}); +Clazz.defineMethod (c$, "parseNHXNodeProps", +($fz = function (c, commentString) { +if (commentString != null && commentString.startsWith ("&&NHX")) { +var st = new java.util.StringTokenizer (commentString.substring (5), ":"); +while (st.hasMoreTokens ()) { +var tok = st.nextToken (); +var colpos = tok.indexOf ("="); +if (colpos > -1) { +var code = tok.substring (0, colpos); +var value = tok.substring (colpos + 1); +try { +if (code.toLowerCase ().equals ("b")) { +var v = -1; +var iv = new Float (value); +v = iv.intValue (); +c.setBootstrap (v); +this.$HasBootstrap = true; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.err.println ("Couldn't parse code '" + code + "' = '" + value + "'"); +e.printStackTrace (System.err); +} else { +throw e; +} +} +}} +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode,~S"); +Clazz.defineMethod (c$, "getTree", +function () { +return this.root; +}); +Clazz.defineMethod (c$, "print", +function () { +{ +var tf = new StringBuffer (); +this.print (tf, this.root); +return (tf.append (";").toString ()); +}}); +Clazz.defineMethod (c$, "print", +function (withbootstraps) { +{ +var boots = this.$HasBootstrap; +this.$HasBootstrap = withbootstraps; +var rv = this.print (); +this.$HasBootstrap = boots; +return rv; +}}, "~B"); +Clazz.defineMethod (c$, "print", +function (withbootstraps, withdists) { +{ +var dists = this.$HasDistances; +this.$HasDistances = withdists; +var rv = this.print (withbootstraps); +this.$HasDistances = dists; +return rv; +}}, "~B,~B"); +Clazz.defineMethod (c$, "print", +function (withbootstraps, withdists, printRootInfo) { +{ +var rootinfo = printRootInfo; +this.printRootInfo = printRootInfo; +var rv = this.print (withbootstraps, withdists); +this.printRootInfo = rootinfo; +return rv; +}}, "~B,~B,~B"); +Clazz.defineMethod (c$, "getQuoteChar", +function () { +return this.QuoteChar; +}); +Clazz.defineMethod (c$, "setQuoteChar", +function (c) { +var old = this.QuoteChar; +this.QuoteChar = c; +return old; +}, "~S"); +Clazz.defineMethod (c$, "nodeName", +($fz = function (name) { +if (this.NodeSafeName[0].search (name)) { +return this.QuoteChar + this.NodeSafeName[1].replaceAll (name) + this.QuoteChar; +} else { +return this.NodeSafeName[2].replaceAll (name); +}}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "printNodeField", +($fz = function (c) { +return ((c.getName () == null) ? "" : this.nodeName (c.getName ())) + ((this.$HasBootstrap) ? ((c.getBootstrap () > -1) ? ((c.getName () != null ? " " : "") + c.getBootstrap ()) : "") : "") + ((this.$HasDistances) ? (":" + c.dist) : ""); +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "printRootField", +($fz = function (root) { +return (this.printRootInfo) ? (((root.getName () == null) ? "" : this.nodeName (root.getName ())) + ((this.$HasBootstrap) ? ((root.getBootstrap () > -1) ? ((root.getName () != null ? " " : "") + +root.getBootstrap ()) : "") : "") + ((this.RootHasDistance) ? (":" + root.dist) : "")) : ""; +}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "print", +function (tf, root) { +if (root != null) { +if (root.isLeaf () && this.printRootInfo) { +tf.append (this.printRootField (root)); +} else { +if (root.isDummy ()) { +this._print (tf, root.right ()); +this._print (tf, root.left ()); +} else { +tf.append ("("); +this._print (tf, root.right ()); +if (root.left () != null) { +tf.append (","); +}this._print (tf, root.left ()); +tf.append (")" + this.printRootField (root)); +}}}}, "StringBuffer,jalview.datamodel.SequenceNode"); +Clazz.defineMethod (c$, "_print", +function (tf, c) { +if (c != null) { +if (c.isLeaf ()) { +tf.append (this.printNodeField (c)); +} else { +if (c.isDummy ()) { +this._print (tf, c.left ()); +if (c.left () != null) { +tf.append (","); +}this._print (tf, c.right ()); +} else { +tf.append ("("); +this._print (tf, c.right ()); +if (c.left () != null) { +tf.append (","); +}this._print (tf, c.left ()); +tf.append (")" + this.printNodeField (c)); +}}}}, "StringBuffer,jalview.datamodel.SequenceNode"); +c$.main = Clazz.defineMethod (c$, "main", +function (args) { +try { +if (args == null || args.length != 1) { +System.err.println ("Takes one argument - file name of a newick tree file."); +System.exit (0); +}var fn = new java.io.File (args[0]); +var newickfile = new StringBuffer (); +var treefile = new java.io.BufferedReader ( new java.io.FileReader (fn)); +var l; +while ((l = treefile.readLine ()) != null) { +newickfile.append (l); +} +treefile.close (); +System.out.println ("Read file :\n"); +var trf = new jalview.io.NewickFile (args[0], "File"); +trf.parse (); +System.out.println ("Original file :\n"); +var nonl = jalview.jsdev.RegExp.newRegex (["\n+", ""]); +System.out.println (nonl.replaceAll (newickfile.toString ()) + "\n"); +System.out.println ("Parsed file.\n"); +System.out.println ("Default output type for original input.\n"); +System.out.println (trf.print ()); +System.out.println ("Without bootstraps.\n"); +System.out.println (trf.print (false)); +System.out.println ("Without distances.\n"); +System.out.println (trf.print (true, false)); +System.out.println ("Without bootstraps but with distanecs.\n"); +System.out.println (trf.print (false, true)); +System.out.println ("Without bootstraps or distanecs.\n"); +System.out.println (trf.print (false, false)); +System.out.println ("With bootstraps and with distances.\n"); +System.out.println (trf.print (true, true)); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +System.err.println ("Exception\n" + e); +e.printStackTrace (); +} else { +throw e; +} +} +}, "~A"); +}); diff --git a/bin/jalview/io/PIRFile.class b/bin/jalview/io/PIRFile.class index 939524f..6d17207 100644 Binary files a/bin/jalview/io/PIRFile.class and b/bin/jalview/io/PIRFile.class differ diff --git a/bin/jalview/io/PIRFile.js b/bin/jalview/io/PIRFile.js index fe50c34..f14a6ea 100644 --- a/bin/jalview/io/PIRFile.js +++ b/bin/jalview/io/PIRFile.js @@ -1,101 +1,101 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile", "java.util.Vector"], "jalview.io.PIRFile", ["jalview.io.ModellerDescription", "jalview.util.Comparison", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.words = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "PIRFile", jalview.io.AlignFile); -Clazz.prepareFields (c$, function () { -this.words = new java.util.Vector (); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.PIRFile, []); -}); -Clazz.overrideMethod (c$, "parse", -function () { -var sequence; -var line = null; -var md; -while ((line = this.nextLine ()) != null) { -if (line.length == 0) { -continue; -}if (line.indexOf ("C;") == 0 || line.indexOf ("#") == 0) { -continue; -}var newSeq = this.parseId (line.substring (line.indexOf (";") + 1)); -sequence = new StringBuffer (); -newSeq.setDescription (this.nextLine ()); -var starFound = false; -while (!starFound) { -line = this.nextLine (); -sequence.append (line); -if (line == null) { -break; -}if (line.indexOf ("*") > -1) { -starFound = true; -}} -if (sequence.length () > 0) { -sequence.setLength (sequence.length () - 1); -newSeq.setSequence (sequence.toString ()); -this.seqs.addElement (newSeq); -md = new jalview.io.ModellerDescription (newSeq.getDescription ()); -md.updateSequenceI (newSeq); -}} -}); -Clazz.defineMethod (c$, "print", -function () { -return this.print (this.getSeqsAsArray ()); -}); -Clazz.defineMethod (c$, "print", -function (s) { -var is_NA = jalview.util.Comparison.isNucleotide (s); -var len = 72; -var out = new StringBuffer (); -var i = 0; -var md; -while ((i < s.length) && (s[i] != null)) { -var seq = s[i].getSequenceAsString (); -seq = seq + "*"; -if (is_NA) { -out.append (">N1;" + s[i].getName ()); -out.append (this.newline); -if (s[i].getDescription () == null) { -out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1)); -out.append (is_NA ? " bases" : " residues"); -out.append (this.newline); -} else { -out.append (s[i].getDescription ()); -out.append (this.newline); -}} else { -if (jalview.io.PIRFile.useModellerOutput) { -out.append (">P1;" + s[i].getName ()); -out.append (this.newline); -md = new jalview.io.ModellerDescription (s[i]); -out.append (md.getDescriptionLine ()); -out.append (this.newline); -} else { -out.append (">P1;" + this.printId (s[i])); -out.append (this.newline); -if (s[i].getDescription () != null) { -out.append (s[i].getDescription ()); -out.append (this.newline); -} else { -out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1) + " residues"); -out.append (this.newline); -}}}var nochunks = (Clazz.doubleToInt (seq.length / len)) + 1; -for (var j = 0; j < nochunks; j++) { -var start = j * len; -var end = start + len; -if (end < seq.length) { -out.append (seq.substring (start, end)); -out.append (this.newline); -} else if (start < seq.length) { -out.append (seq.substring (start)); -out.append (this.newline); -}} -i++; -} -return out.toString (); -}, "~A"); -Clazz.defineStatics (c$, -"useModellerOutput", false); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile", "java.util.Vector"], "jalview.io.PIRFile", ["jalview.io.ModellerDescription", "jalview.util.Comparison", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.words = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "PIRFile", jalview.io.AlignFile); +Clazz.prepareFields (c$, function () { +this.words = new java.util.Vector (); +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.PIRFile, []); +}); +Clazz.overrideMethod (c$, "parse", +function () { +var sequence; +var line = null; +var md; +while ((line = this.nextLine ()) != null) { +if (line.length == 0) { +continue; +}if (line.indexOf ("C;") == 0 || line.indexOf ("#") == 0) { +continue; +}var newSeq = this.parseId (line.substring (line.indexOf (";") + 1)); +sequence = new StringBuffer (); +newSeq.setDescription (this.nextLine ()); +var starFound = false; +while (!starFound) { +line = this.nextLine (); +sequence.append (line); +if (line == null) { +break; +}if (line.indexOf ("*") > -1) { +starFound = true; +}} +if (sequence.length () > 0) { +sequence.setLength (sequence.length () - 1); +newSeq.setSequence (sequence.toString ()); +this.seqs.addElement (newSeq); +md = new jalview.io.ModellerDescription (newSeq.getDescription ()); +md.updateSequenceI (newSeq); +}} +}); +Clazz.defineMethod (c$, "print", +function () { +return this.print (this.getSeqsAsArray ()); +}); +Clazz.defineMethod (c$, "print", +function (s) { +var is_NA = jalview.util.Comparison.isNucleotide (s); +var len = 72; +var out = new StringBuffer (); +var i = 0; +var md; +while ((i < s.length) && (s[i] != null)) { +var seq = s[i].getSequenceAsString (); +seq = seq + "*"; +if (is_NA) { +out.append (">N1;" + s[i].getName ()); +out.append (this.newline); +if (s[i].getDescription () == null) { +out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1)); +out.append (is_NA ? " bases" : " residues"); +out.append (this.newline); +} else { +out.append (s[i].getDescription ()); +out.append (this.newline); +}} else { +if (jalview.io.PIRFile.useModellerOutput) { +out.append (">P1;" + s[i].getName ()); +out.append (this.newline); +md = new jalview.io.ModellerDescription (s[i]); +out.append (md.getDescriptionLine ()); +out.append (this.newline); +} else { +out.append (">P1;" + this.printId (s[i])); +out.append (this.newline); +if (s[i].getDescription () != null) { +out.append (s[i].getDescription ()); +out.append (this.newline); +} else { +out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1) + " residues"); +out.append (this.newline); +}}}var nochunks = (Clazz.doubleToInt (seq.length / len)) + 1; +for (var j = 0; j < nochunks; j++) { +var start = j * len; +var end = start + len; +if (end < seq.length) { +out.append (seq.substring (start, end)); +out.append (this.newline); +} else if (start < seq.length) { +out.append (seq.substring (start)); +out.append (this.newline); +}} +i++; +} +return out.toString (); +}, "~A"); +Clazz.defineStatics (c$, +"useModellerOutput", false); +}); diff --git a/bin/jalview/io/PfamFile.js b/bin/jalview/io/PfamFile.js index c094356..47e9cc1 100644 --- a/bin/jalview/io/PfamFile.js +++ b/bin/jalview/io/PfamFile.js @@ -1,76 +1,76 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile"], "jalview.io.PfamFile", ["jalview.util.Format", "$.MessageManager", "java.io.IOException", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () { -c$ = Clazz.declareType (jalview.io, "PfamFile", jalview.io.AlignFile); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.PfamFile, []); -}); -Clazz.overrideMethod (c$, "parse", -function () { -var i = 0; -var line; -var seqhash = new java.util.Hashtable (); -var headers = new java.util.Vector (); -while ((line = this.nextLine ()) != null) { -if (line.indexOf (" ") != 0) { -if (line.indexOf ("#") != 0) { -var str = new java.util.StringTokenizer (line, " "); -var id = ""; -if (str.hasMoreTokens ()) { -id = str.nextToken (); -var tempseq; -if (seqhash.containsKey (id)) { -tempseq = seqhash.get (id); -} else { -tempseq = new StringBuffer (); -seqhash.put (id, tempseq); -}if (!(headers.contains (id))) { -headers.addElement (id); -}if (str.hasMoreTokens ()) { -tempseq.append (str.nextToken ()); -}}}}} -this.noSeqs = headers.size (); -if (this.noSeqs < 1) { -throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.pfam_no_sequences_found")); -}for (i = 0; i < headers.size (); i++) { -if (seqhash.get (headers.elementAt (i)) != null) { -if (this.maxLength < seqhash.get (headers.elementAt (i)).toString ().length) { -this.maxLength = seqhash.get (headers.elementAt (i)).toString ().length; -}var newSeq = this.parseId (headers.elementAt (i).toString ()); -newSeq.setSequence (seqhash.get (headers.elementAt (i).toString ()).toString ()); -this.seqs.addElement (newSeq); -} else { -System.err.println ("PFAM File reader: Can't find sequence for " + headers.elementAt (i)); -}} -}); -Clazz.defineMethod (c$, "print", -function (s) { -var out = new StringBuffer (""); -var max = 0; -var maxid = 0; -var i = 0; -while ((i < s.length) && (s[i] != null)) { -var tmp = this.printId (s[i]); -if (s[i].getSequence ().length > max) { -max = s[i].getSequence ().length; -}if (tmp.length > maxid) { -maxid = tmp.length; -}i++; -} -if (maxid < 15) { -maxid = 15; -}var j = 0; -while ((j < s.length) && (s[j] != null)) { -out.append ( new jalview.util.Format ("%-" + maxid + "s").form (this.printId (s[j]) + " ")); -out.append (s[j].getSequenceAsString ()); -out.append (this.newline); -j++; -} -out.append (this.newline); -return out.toString (); -}, "~A"); -Clazz.defineMethod (c$, "print", -function () { -return this.print (this.getSeqsAsArray ()); -}); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile"], "jalview.io.PfamFile", ["jalview.util.Format", "$.MessageManager", "java.io.IOException", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () { +c$ = Clazz.declareType (jalview.io, "PfamFile", jalview.io.AlignFile); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.PfamFile, []); +}); +Clazz.overrideMethod (c$, "parse", +function () { +var i = 0; +var line; +var seqhash = new java.util.Hashtable (); +var headers = new java.util.Vector (); +while ((line = this.nextLine ()) != null) { +if (line.indexOf (" ") != 0) { +if (line.indexOf ("#") != 0) { +var str = new java.util.StringTokenizer (line, " "); +var id = ""; +if (str.hasMoreTokens ()) { +id = str.nextToken (); +var tempseq; +if (seqhash.containsKey (id)) { +tempseq = seqhash.get (id); +} else { +tempseq = new StringBuffer (); +seqhash.put (id, tempseq); +}if (!(headers.contains (id))) { +headers.addElement (id); +}if (str.hasMoreTokens ()) { +tempseq.append (str.nextToken ()); +}}}}} +this.noSeqs = headers.size (); +if (this.noSeqs < 1) { +throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.pfam_no_sequences_found")); +}for (i = 0; i < headers.size (); i++) { +if (seqhash.get (headers.elementAt (i)) != null) { +if (this.maxLength < seqhash.get (headers.elementAt (i)).toString ().length) { +this.maxLength = seqhash.get (headers.elementAt (i)).toString ().length; +}var newSeq = this.parseId (headers.elementAt (i).toString ()); +newSeq.setSequence (seqhash.get (headers.elementAt (i).toString ()).toString ()); +this.seqs.addElement (newSeq); +} else { +System.err.println ("PFAM File reader: Can't find sequence for " + headers.elementAt (i)); +}} +}); +Clazz.defineMethod (c$, "print", +function (s) { +var out = new StringBuffer (""); +var max = 0; +var maxid = 0; +var i = 0; +while ((i < s.length) && (s[i] != null)) { +var tmp = this.printId (s[i]); +if (s[i].getSequence ().length > max) { +max = s[i].getSequence ().length; +}if (tmp.length > maxid) { +maxid = tmp.length; +}i++; +} +if (maxid < 15) { +maxid = 15; +}var j = 0; +while ((j < s.length) && (s[j] != null)) { +out.append ( new jalview.util.Format ("%-" + maxid + "s").form (this.printId (s[j]) + " ")); +out.append (s[j].getSequenceAsString ()); +out.append (this.newline); +j++; +} +out.append (this.newline); +return out.toString (); +}, "~A"); +Clazz.defineMethod (c$, "print", +function () { +return this.print (this.getSeqsAsArray ()); +}); +}); diff --git a/bin/jalview/io/PhylipFile.js b/bin/jalview/io/PhylipFile.js index 74e851f..0cd22ea 100644 --- a/bin/jalview/io/PhylipFile.js +++ b/bin/jalview/io/PhylipFile.js @@ -1,103 +1,103 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile"], "jalview.io.PhylipFile", ["java.io.IOException", "java.lang.StringBuffer"], function () { -c$ = Clazz.declareType (jalview.io, "PhylipFile", jalview.io.AlignFile); -Clazz.overrideMethod (c$, "parse", -function () { -try { -var line = this.nextLine (); -var lineElements = line.trim ().$plit ("\\s+"); -if (lineElements.length < 2) { -throw new java.io.IOException ("First line must contain the number of specifies and number of characters"); -}var numberSpecies = Integer.parseInt (lineElements[0]); -var numberCharacters = Integer.parseInt (lineElements[1]); -if (numberSpecies <= 0) { -return; -}var sequenceElements = new Array (numberSpecies); -var sequences = new Array (numberSpecies); -for (var i = 0; i < numberSpecies; i++) { -line = this.nextLine (); -var potentialName = line.substring (0, 10); -var tabIndex = potentialName.indexOf ('\t'); -if (tabIndex == -1) { -sequenceElements[i] = this.parseId (this.validateName (potentialName)); -sequences[i] = new StringBuffer (this.removeWhitespace (line.substring (10))); -} else { -sequenceElements[i] = this.parseId (this.validateName (potentialName.substring (0, tabIndex))); -sequences[i] = new StringBuffer (this.removeWhitespace (line.substring (tabIndex))); -}} -if ((sequences[0]).length () != numberCharacters) { -var i = 0; -for (line = this.nextLine (); line != null; line = this.nextLine ()) { -if (line.length > 0) { -sequences[i++].append (this.removeWhitespace (line)); -}if (i == sequences.length) { -i = 0; -}} -}for (var i = 0; i < numberSpecies; i++) { -if (sequences[i].length () != numberCharacters) { -throw new java.io.IOException (sequenceElements[i].getName () + " sequence is incorrect length - should be " + numberCharacters + " but is " + sequences[i].length ()); -}sequenceElements[i].setSequence (sequences[i].toString ()); -this.seqs.add (sequenceElements[i]); -} -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -System.err.println ("Exception parsing PHYLIP file " + e); -e.printStackTrace (System.err); -throw e; -} else { -throw e; -} -} -}); -Clazz.defineMethod (c$, "removeWhitespace", -($fz = function (txt) { -return txt.replaceAll ("\\s*", ""); -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "validateName", -($fz = function (name) { -var invalidCharacters = Clazz.newCharArray (-1, ['(', ')', '[', ']', ':', ';', ',']); -for (var c, $c = 0, $$c = invalidCharacters; $c < $$c.length && ((c = $$c[$c]) || true); $c++) { -if (name.indexOf (c) > -1) { -throw new java.io.IOException ("Species name contains illegal character " + c); -}} -return name; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.overrideMethod (c$, "print", -function () { -var sb = new StringBuffer (Integer.toString (this.seqs.size ())); -sb.append (" "); -sb.append ((this.seqs.size () > 0) ? Integer.toString (this.seqs.get (0).getSequence ().length) : "0").append (this.newline); -var sequential = false; -var numInterleavedColumns = 60; -var sequenceLength = 0; -for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { -var name = s.getName (); -if (name.length > 10) { -name = name.substring (0, 10); -} else { -name = String.format ("%1$-10s", [s.getName ()]); -}sb.append (name); -if (sequential) { -sb.append (s.getSequence ()); -} else { -sequenceLength = s.getSequence ().length; -sb.append (s.getSequence (0, Math.min (numInterleavedColumns, sequenceLength))); -}sb.append (this.newline); -} -if (!sequential && sequenceLength > numInterleavedColumns) { -var numMatrics = Clazz.doubleToInt (sequenceLength / numInterleavedColumns); -if ((sequenceLength % numInterleavedColumns) > 0) { -numMatrics++; -}for (var i = 1; i < numMatrics; i++) { -sb.append (this.newline); -var start = i * numInterleavedColumns; -for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { -sb.append (s.getSequence (start, Math.min (start + numInterleavedColumns, sequenceLength))).append (this.newline); -} -} -}return sb.toString (); -}); -Clazz.defineStatics (c$, -"FILE_EXT", "phy", -"FILE_DESC", "PHYLIP"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile"], "jalview.io.PhylipFile", ["java.io.IOException", "java.lang.StringBuffer"], function () { +c$ = Clazz.declareType (jalview.io, "PhylipFile", jalview.io.AlignFile); +Clazz.overrideMethod (c$, "parse", +function () { +try { +var line = this.nextLine (); +var lineElements = line.trim ().$plit ("\\s+"); +if (lineElements.length < 2) { +throw new java.io.IOException ("First line must contain the number of specifies and number of characters"); +}var numberSpecies = Integer.parseInt (lineElements[0]); +var numberCharacters = Integer.parseInt (lineElements[1]); +if (numberSpecies <= 0) { +return; +}var sequenceElements = new Array (numberSpecies); +var sequences = new Array (numberSpecies); +for (var i = 0; i < numberSpecies; i++) { +line = this.nextLine (); +var potentialName = line.substring (0, 10); +var tabIndex = potentialName.indexOf ('\t'); +if (tabIndex == -1) { +sequenceElements[i] = this.parseId (this.validateName (potentialName)); +sequences[i] = new StringBuffer (this.removeWhitespace (line.substring (10))); +} else { +sequenceElements[i] = this.parseId (this.validateName (potentialName.substring (0, tabIndex))); +sequences[i] = new StringBuffer (this.removeWhitespace (line.substring (tabIndex))); +}} +if ((sequences[0]).length () != numberCharacters) { +var i = 0; +for (line = this.nextLine (); line != null; line = this.nextLine ()) { +if (line.length > 0) { +sequences[i++].append (this.removeWhitespace (line)); +}if (i == sequences.length) { +i = 0; +}} +}for (var i = 0; i < numberSpecies; i++) { +if (sequences[i].length () != numberCharacters) { +throw new java.io.IOException (sequenceElements[i].getName () + " sequence is incorrect length - should be " + numberCharacters + " but is " + sequences[i].length ()); +}sequenceElements[i].setSequence (sequences[i].toString ()); +this.seqs.add (sequenceElements[i]); +} +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +System.err.println ("Exception parsing PHYLIP file " + e); +e.printStackTrace (System.err); +throw e; +} else { +throw e; +} +} +}); +Clazz.defineMethod (c$, "removeWhitespace", +($fz = function (txt) { +return txt.replaceAll ("\\s*", ""); +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "validateName", +($fz = function (name) { +var invalidCharacters = Clazz.newCharArray (-1, ['(', ')', '[', ']', ':', ';', ',']); +for (var c, $c = 0, $$c = invalidCharacters; $c < $$c.length && ((c = $$c[$c]) || true); $c++) { +if (name.indexOf (c) > -1) { +throw new java.io.IOException ("Species name contains illegal character " + c); +}} +return name; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.overrideMethod (c$, "print", +function () { +var sb = new StringBuffer (Integer.toString (this.seqs.size ())); +sb.append (" "); +sb.append ((this.seqs.size () > 0) ? Integer.toString (this.seqs.get (0).getSequence ().length) : "0").append (this.newline); +var sequential = false; +var numInterleavedColumns = 60; +var sequenceLength = 0; +for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { +var name = s.getName (); +if (name.length > 10) { +name = name.substring (0, 10); +} else { +name = String.format ("%1$-10s", [s.getName ()]); +}sb.append (name); +if (sequential) { +sb.append (s.getSequence ()); +} else { +sequenceLength = s.getSequence ().length; +sb.append (s.getSequence (0, Math.min (numInterleavedColumns, sequenceLength))); +}sb.append (this.newline); +} +if (!sequential && sequenceLength > numInterleavedColumns) { +var numMatrics = Clazz.doubleToInt (sequenceLength / numInterleavedColumns); +if ((sequenceLength % numInterleavedColumns) > 0) { +numMatrics++; +}for (var i = 1; i < numMatrics; i++) { +sb.append (this.newline); +var start = i * numInterleavedColumns; +for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { +sb.append (s.getSequence (start, Math.min (start + numInterleavedColumns, sequenceLength))).append (this.newline); +} +} +}return sb.toString (); +}); +Clazz.defineStatics (c$, +"FILE_EXT", "phy", +"FILE_DESC", "PHYLIP"); +}); diff --git a/bin/jalview/io/PileUpfile.class b/bin/jalview/io/PileUpfile.class index 690574c..d75d06b 100644 Binary files a/bin/jalview/io/PileUpfile.class and b/bin/jalview/io/PileUpfile.class differ diff --git a/bin/jalview/io/PileUpfile.js b/bin/jalview/io/PileUpfile.js index b8bb68c..a6effa1 100644 --- a/bin/jalview/io/PileUpfile.js +++ b/bin/jalview/io/PileUpfile.js @@ -1,82 +1,82 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.MSFfile"], "jalview.io.PileUpfile", ["jalview.util.Format", "java.lang.StringBuffer"], function () { -c$ = Clazz.declareType (jalview.io, "PileUpfile", jalview.io.MSFfile); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.io.PileUpfile, []); -}); -Clazz.defineMethod (c$, "print", -function () { -return this.print (this.getSeqsAsArray ()); -}); -Clazz.defineMethod (c$, "print", -function (s) { -var out = new StringBuffer ("PileUp"); -out.append (this.newline); -out.append (this.newline); -var max = 0; -var maxid = 0; -var i = 0; -var bigChecksum = 0; -var checksums = Clazz.newIntArray (s.length, 0); -while (i < s.length) { -checksums[i] = this.checkSum (s[i].getSequenceAsString ()); -bigChecksum += checksums[i]; -i++; -} -out.append (" MSF: " + s[0].getSequence ().length + " Type: P Check: " + bigChecksum % 10000 + " .."); -out.append (this.newline); -out.append (this.newline); -out.append (this.newline); -i = 0; -while ((i < s.length) && (s[i] != null)) { -var seq = s[i].getSequenceAsString (); -out.append (" Name: " + this.printId (s[i]) + " oo Len: " + seq.length + " Check: " + checksums[i] + " Weight: 1.00"); -out.append (this.newline); -if (seq.length > max) { -max = seq.length; -}if (s[i].getName ().length > maxid) { -maxid = s[i].getName ().length; -}i++; -} -if (maxid < 10) { -maxid = 10; -}maxid++; -out.append (this.newline); -out.append (this.newline); -out.append ("//"); -out.append (this.newline); -out.append (this.newline); -var len = 50; -var nochunks = (Clazz.doubleToInt (max / len)) + 1; -if ((max % len) == 0) { -nochunks--; -}for (i = 0; i < nochunks; i++) { -var j = 0; -while ((j < s.length) && (s[j] != null)) { -var name = this.printId (s[j]); -out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " ")); -for (var k = 0; k < 5; k++) { -var start = (i * 50) + (k * 10); -var end = start + 10; -if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) { -out.append (s[j].getSequence (start, end)); -if (k < 4) { -out.append (" "); -} else { -out.append (this.newline); -}} else { -if (start < s[j].getSequence ().length) { -out.append (s[j].getSequenceAsString ().substring (start)); -out.append (this.newline); -} else { -if (k == 0) { -out.append (this.newline); -}}}} -j++; -} -out.append (this.newline); -} -return out.toString (); -}, "~A"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.MSFfile"], "jalview.io.PileUpfile", ["jalview.util.Format", "java.lang.StringBuffer"], function () { +c$ = Clazz.declareType (jalview.io, "PileUpfile", jalview.io.MSFfile); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.io.PileUpfile, []); +}); +Clazz.defineMethod (c$, "print", +function () { +return this.print (this.getSeqsAsArray ()); +}); +Clazz.defineMethod (c$, "print", +function (s) { +var out = new StringBuffer ("PileUp"); +out.append (this.newline); +out.append (this.newline); +var max = 0; +var maxid = 0; +var i = 0; +var bigChecksum = 0; +var checksums = Clazz.newIntArray (s.length, 0); +while (i < s.length) { +checksums[i] = this.checkSum (s[i].getSequenceAsString ()); +bigChecksum += checksums[i]; +i++; +} +out.append (" MSF: " + s[0].getSequence ().length + " Type: P Check: " + bigChecksum % 10000 + " .."); +out.append (this.newline); +out.append (this.newline); +out.append (this.newline); +i = 0; +while ((i < s.length) && (s[i] != null)) { +var seq = s[i].getSequenceAsString (); +out.append (" Name: " + this.printId (s[i]) + " oo Len: " + seq.length + " Check: " + checksums[i] + " Weight: 1.00"); +out.append (this.newline); +if (seq.length > max) { +max = seq.length; +}if (s[i].getName ().length > maxid) { +maxid = s[i].getName ().length; +}i++; +} +if (maxid < 10) { +maxid = 10; +}maxid++; +out.append (this.newline); +out.append (this.newline); +out.append ("//"); +out.append (this.newline); +out.append (this.newline); +var len = 50; +var nochunks = (Clazz.doubleToInt (max / len)) + 1; +if ((max % len) == 0) { +nochunks--; +}for (i = 0; i < nochunks; i++) { +var j = 0; +while ((j < s.length) && (s[j] != null)) { +var name = this.printId (s[j]); +out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " ")); +for (var k = 0; k < 5; k++) { +var start = (i * 50) + (k * 10); +var end = start + 10; +if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) { +out.append (s[j].getSequence (start, end)); +if (k < 4) { +out.append (" "); +} else { +out.append (this.newline); +}} else { +if (start < s[j].getSequence ().length) { +out.append (s[j].getSequenceAsString ().substring (start)); +out.append (this.newline); +} else { +if (k == 0) { +out.append (this.newline); +}}}} +j++; +} +out.append (this.newline); +} +return out.toString (); +}, "~A"); +}); diff --git a/bin/jalview/io/SequenceAnnotationReport.class b/bin/jalview/io/SequenceAnnotationReport.class index c84960c..53c67b0 100644 Binary files a/bin/jalview/io/SequenceAnnotationReport.class and b/bin/jalview/io/SequenceAnnotationReport.class differ diff --git a/bin/jalview/io/SequenceAnnotationReport.js b/bin/jalview/io/SequenceAnnotationReport.js index 4ab2aa6..889211b 100644 --- a/bin/jalview/io/SequenceAnnotationReport.js +++ b/bin/jalview/io/SequenceAnnotationReport.js @@ -1,181 +1,181 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (null, "jalview.io.SequenceAnnotationReport", ["jalview.util.DBRefUtils", "$.UrlLink", "java.lang.Float", "java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this.linkImageURL = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "SequenceAnnotationReport"); -Clazz.makeConstructor (c$, -function (linkImageURL) { -this.linkImageURL = linkImageURL; -}, "~S"); -Clazz.defineMethod (c$, "appendFeatures", -function (tooltipText2, rpos, features) { -this.appendFeatures (tooltipText2, rpos, features, null); -}, "StringBuffer,~N,java.util.List"); -Clazz.defineMethod (c$, "appendFeatures", -function (tooltipText2, rpos, features, minmax) { -var tmpString; -if (features != null) { -for (var feature, $feature = features.iterator (); $feature.hasNext () && ((feature = $feature.next ()) || true);) { -if (feature.getType ().equals ("disulfide bond")) { -if (feature.getBegin () == rpos || feature.getEnd () == rpos) { -if (tooltipText2.length () > 6) { -tooltipText2.append ("
"); -}tooltipText2.append ("disulfide bond " + feature.getBegin () + ":" + feature.getEnd ()); -}} else { -if (tooltipText2.length () > 6) { -tooltipText2.append ("
"); -}var linkOnly = feature.getValue ("linkonly") != null; -if (!linkOnly) { -tooltipText2.append (feature.getType () + " "); -if (rpos != 0) { -tooltipText2.append (feature.begin); -}if (feature.begin != feature.end) { -tooltipText2.append (" " + feature.end); -}if (feature.getDescription () != null && !feature.description.equals (feature.getType ())) { -tmpString = feature.getDescription (); -var tmp2up = tmpString.toUpperCase (); -var startTag = tmp2up.indexOf (""); -if (startTag > -1) { -tmpString = tmpString.substring (startTag + 6); -tmp2up = tmp2up.substring (startTag + 6); -}var endTag = tmp2up.indexOf (""); -if (endTag > -1) { -tmpString = tmpString.substring (0, endTag); -tmp2up = tmp2up.substring (0, endTag); -}endTag = tmp2up.indexOf (""); -if (endTag > -1) { -tmpString = tmpString.substring (0, endTag); -}if (startTag > -1) { -tooltipText2.append ("; " + tmpString); -} else { -if (tmpString.indexOf ("<") > -1 || tmpString.indexOf (">") > -1) { -tmpString = tmpString.replaceAll ("<", "<"); -tmpString = tmpString.replaceAll (">", ">"); -tooltipText2.append ("; "); -tooltipText2.append (tmpString); -} else { -tooltipText2.append ("; " + tmpString); -}}}if (!Float.isNaN (feature.getScore ())) { -var rng = (minmax == null) ? null : (minmax.get (feature.getType ())); -if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { -tooltipText2.append (" Score=" + feature.getScore ()); -}}if (feature.getValue ("status") != null) { -var status = feature.getValue ("status").toString (); -if (status.length > 0) { -tooltipText2.append ("; (" + feature.getValue ("status") + ")"); -}}}}if (feature.links != null) { -if (this.linkImageURL != null) { -tooltipText2.append (" "); -} else { -for (var urlstring, $urlstring = feature.links.iterator (); $urlstring.hasNext () && ((urlstring = $urlstring.next ()) || true);) { -try { -for (var urllink, $urllink = 0, $$urllink = this.createLinksFrom (null, urlstring); $urllink < $$urllink.length && ((urllink = $$urllink[$urllink]) || true); $urllink++) { -tooltipText2.append ("
" + (urllink[0].toLowerCase ().equals (urllink[1].toLowerCase ()) ? urllink[0] : (urllink[0] + ":" + urllink[1])) + "
"); -} -} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -System.err.println ("problem when creating links from " + urlstring); -x.printStackTrace (); -} else { -throw x; -} -} -} -}}} -}}, "StringBuffer,~N,java.util.List,java.util.Hashtable"); -Clazz.defineMethod (c$, "createLinksFrom", -function (seq, link) { -var urlSets = new java.util.ArrayList (); -var uniques = new java.util.ArrayList (); -var urlLink = new jalview.util.UrlLink (link); -if (!urlLink.isValid ()) { -System.err.println (urlLink.getInvalidMessage ()); -return null; -}var target = urlLink.getTarget (); -var label = urlLink.getLabel (); -if (seq != null && urlLink.isDynamic ()) { -var dbr = jalview.util.DBRefUtils.selectRefs (seq.getDBRef (), Clazz.newArray (-1, [target])); -var id = seq.getName (); -var descr = seq.getDescription (); -if (descr != null && descr.length < 1) { -descr = null; -}if (dbr != null) { -for (var r = 0; r < dbr.length; r++) { -if (id != null && dbr[r].getAccessionId ().equals (id)) { -id = null; -}var urls = urlLink.makeUrls (dbr[r].getAccessionId (), true); -if (urls != null) { -for (var u = 0; u < urls.length; u += 2) { -var unq = urls[u] + "|" + urls[u + 1]; -if (!uniques.contains (unq)) { -urlSets.add ( Clazz.newArray (-1, [target, label, urls[u], urls[u + 1]])); -uniques.add (unq); -}} -}} -}if (id != null) { -var urls = urlLink.makeUrls (id, true); -if (urls != null) { -for (var u = 0; u < urls.length; u += 2) { -var unq = urls[u] + "|" + urls[u + 1]; -if (!uniques.contains (unq)) { -urlSets.add ( Clazz.newArray (-1, [target, label, urls[u], urls[u + 1]])); -uniques.add (unq); -}} -}}if (descr != null && urlLink.getRegexReplace () != null) { -var urls = urlLink.makeUrls (descr, true); -if (urls != null) { -for (var u = 0; u < urls.length; u += 2) { -var unq = urls[u] + "|" + urls[u + 1]; -if (!uniques.contains (unq)) { -urlSets.add ( Clazz.newArray (-1, [target, label, urls[u], urls[u + 1]])); -uniques.add (unq); -}} -}}} else { -var unq = label + "|" + urlLink.getUrl_prefix (); -if (!uniques.contains (unq)) { -uniques.add (unq); -urlSets.add ( Clazz.newArray (-1, [target, label, null, urlLink.getUrl_prefix ()])); -}}return urlSets.toArray ( Clazz.newArray (-1, [])); -}, "jalview.datamodel.SequenceI,~S"); -Clazz.defineMethod (c$, "createSequenceAnnotationReport", -function (tip, sequence, showDbRefs, showNpFeats, minmax) { -this.createSequenceAnnotationReport (tip, sequence, showDbRefs, showNpFeats, true, minmax); -}, "StringBuffer,jalview.datamodel.SequenceI,~B,~B,java.util.Hashtable"); -Clazz.defineMethod (c$, "createSequenceAnnotationReport", -function (tip, sequence, showDbRefs, showNpFeats, tableWrap, minmax) { -var tmp; -tip.append (""); -var maxWidth = 0; -if (sequence.getDescription () != null) { -tmp = sequence.getDescription (); -tip.append ("
" + tmp); -maxWidth = Math.max (maxWidth, tmp.length); -}var ds = sequence; -while (ds.getDatasetSequence () != null) { -ds = ds.getDatasetSequence (); -} -var dbrefs = ds.getDBRef (); -if (showDbRefs && dbrefs != null) { -for (var i = 0; i < dbrefs.length; i++) { -tip.append ("
"); -tmp = dbrefs[i].getSource () + " " + dbrefs[i].getAccessionId (); -tip.append (tmp); -maxWidth = Math.max (maxWidth, tmp.length); -} -}var features = sequence.getSequenceFeatures (); -if (showNpFeats && features != null) { -for (var i = 0; i < features.length; i++) { -if (features[i].begin == 0 && features[i].end == 0) { -var sz = -tip.length (); -var tfeat = new java.util.ArrayList (); -tfeat.add (features[i]); -this.appendFeatures (tip, 0, tfeat, minmax); -sz += tip.length (); -maxWidth = Math.max (maxWidth, sz); -}} -}if (tableWrap && maxWidth > 60) { -tip.insert (0, "
"); -tip.append ("
"); -}}, "StringBuffer,jalview.datamodel.SequenceI,~B,~B,~B,java.util.Hashtable"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (null, "jalview.io.SequenceAnnotationReport", ["jalview.util.DBRefUtils", "$.UrlLink", "java.lang.Float", "java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this.linkImageURL = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "SequenceAnnotationReport"); +Clazz.makeConstructor (c$, +function (linkImageURL) { +this.linkImageURL = linkImageURL; +}, "~S"); +Clazz.defineMethod (c$, "appendFeatures", +function (tooltipText2, rpos, features) { +this.appendFeatures (tooltipText2, rpos, features, null); +}, "StringBuffer,~N,java.util.List"); +Clazz.defineMethod (c$, "appendFeatures", +function (tooltipText2, rpos, features, minmax) { +var tmpString; +if (features != null) { +for (var feature, $feature = features.iterator (); $feature.hasNext () && ((feature = $feature.next ()) || true);) { +if (feature.getType ().equals ("disulfide bond")) { +if (feature.getBegin () == rpos || feature.getEnd () == rpos) { +if (tooltipText2.length () > 6) { +tooltipText2.append ("
"); +}tooltipText2.append ("disulfide bond " + feature.getBegin () + ":" + feature.getEnd ()); +}} else { +if (tooltipText2.length () > 6) { +tooltipText2.append ("
"); +}var linkOnly = feature.getValue ("linkonly") != null; +if (!linkOnly) { +tooltipText2.append (feature.getType () + " "); +if (rpos != 0) { +tooltipText2.append ("" + feature.begin); +}if (feature.begin != feature.end) { +tooltipText2.append (" " + feature.end); +}if (feature.getDescription () != null && !feature.description.equals (feature.getType ())) { +tmpString = feature.getDescription (); +var tmp2up = tmpString.toUpperCase (); +var startTag = tmp2up.indexOf (""); +if (startTag > -1) { +tmpString = tmpString.substring (startTag + 6); +tmp2up = tmp2up.substring (startTag + 6); +}var endTag = tmp2up.indexOf (""); +if (endTag > -1) { +tmpString = tmpString.substring (0, endTag); +tmp2up = tmp2up.substring (0, endTag); +}endTag = tmp2up.indexOf (""); +if (endTag > -1) { +tmpString = tmpString.substring (0, endTag); +}if (startTag > -1) { +tooltipText2.append ("; " + tmpString); +} else { +if (tmpString.indexOf ("<") > -1 || tmpString.indexOf (">") > -1) { +tmpString = tmpString.replaceAll ("<", "<"); +tmpString = tmpString.replaceAll (">", ">"); +tooltipText2.append ("; "); +tooltipText2.append (tmpString); +} else { +tooltipText2.append ("; " + tmpString); +}}}if (!Float.isNaN (feature.getScore ())) { +var rng = (minmax == null) ? null : (minmax.get (feature.getType ())); +if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { +tooltipText2.append (" Score=" + feature.getScore ()); +}}if (feature.getValue ("status") != null) { +var status = feature.getValue ("status").toString (); +if (status.length > 0) { +tooltipText2.append ("; (" + feature.getValue ("status") + ")"); +}}}}if (feature.links != null) { +if (this.linkImageURL != null) { +tooltipText2.append (" "); +} else { +for (var urlstring, $urlstring = feature.links.iterator (); $urlstring.hasNext () && ((urlstring = $urlstring.next ()) || true);) { +try { +for (var urllink, $urllink = 0, $$urllink = this.createLinksFrom (null, urlstring); $urllink < $$urllink.length && ((urllink = $$urllink[$urllink]) || true); $urllink++) { +tooltipText2.append ("
" + (urllink[0].toLowerCase ().equals (urllink[1].toLowerCase ()) ? urllink[0] : (urllink[0] + ":" + urllink[1])) + "
"); +} +} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +System.err.println ("problem when creating links from " + urlstring); +x.printStackTrace (); +} else { +throw x; +} +} +} +}}} +}}, "StringBuffer,~N,java.util.List,java.util.Hashtable"); +Clazz.defineMethod (c$, "createLinksFrom", +function (seq, link) { +var urlSets = new java.util.ArrayList (); +var uniques = new java.util.ArrayList (); +var urlLink = new jalview.util.UrlLink (link); +if (!urlLink.isValid ()) { +System.err.println (urlLink.getInvalidMessage ()); +return null; +}var target = urlLink.getTarget (); +var label = urlLink.getLabel (); +if (seq != null && urlLink.isDynamic ()) { +var dbr = jalview.util.DBRefUtils.selectRefs (seq.getDBRef (), Clazz.newArray (-1, [target])); +var id = seq.getName (); +var descr = seq.getDescription (); +if (descr != null && descr.length < 1) { +descr = null; +}if (dbr != null) { +for (var r = 0; r < dbr.length; r++) { +if (id != null && dbr[r].getAccessionId ().equals (id)) { +id = null; +}var urls = urlLink.makeUrls (dbr[r].getAccessionId (), true); +if (urls != null) { +for (var u = 0; u < urls.length; u += 2) { +var unq = urls[u] + "|" + urls[u + 1]; +if (!uniques.contains (unq)) { +urlSets.add ( Clazz.newArray (-1, [target, label, urls[u], urls[u + 1]])); +uniques.add (unq); +}} +}} +}if (id != null) { +var urls = urlLink.makeUrls (id, true); +if (urls != null) { +for (var u = 0; u < urls.length; u += 2) { +var unq = urls[u] + "|" + urls[u + 1]; +if (!uniques.contains (unq)) { +urlSets.add ( Clazz.newArray (-1, [target, label, urls[u], urls[u + 1]])); +uniques.add (unq); +}} +}}if (descr != null && urlLink.getRegexReplace () != null) { +var urls = urlLink.makeUrls (descr, true); +if (urls != null) { +for (var u = 0; u < urls.length; u += 2) { +var unq = urls[u] + "|" + urls[u + 1]; +if (!uniques.contains (unq)) { +urlSets.add ( Clazz.newArray (-1, [target, label, urls[u], urls[u + 1]])); +uniques.add (unq); +}} +}}} else { +var unq = label + "|" + urlLink.getUrl_prefix (); +if (!uniques.contains (unq)) { +uniques.add (unq); +urlSets.add ( Clazz.newArray (-1, [target, label, null, urlLink.getUrl_prefix ()])); +}}return urlSets.toArray ( Clazz.newArray (-1, [])); +}, "jalview.datamodel.SequenceI,~S"); +Clazz.defineMethod (c$, "createSequenceAnnotationReport", +function (tip, sequence, showDbRefs, showNpFeats, minmax) { +this.createSequenceAnnotationReport (tip, sequence, showDbRefs, showNpFeats, true, minmax); +}, "StringBuffer,jalview.datamodel.SequenceI,~B,~B,java.util.Hashtable"); +Clazz.defineMethod (c$, "createSequenceAnnotationReport", +function (tip, sequence, showDbRefs, showNpFeats, tableWrap, minmax) { +var tmp; +tip.append (""); +var maxWidth = 0; +if (sequence.getDescription () != null) { +tmp = sequence.getDescription (); +tip.append ("
" + tmp); +maxWidth = Math.max (maxWidth, tmp.length); +}var ds = sequence; +while (ds.getDatasetSequence () != null) { +ds = ds.getDatasetSequence (); +} +var dbrefs = ds.getDBRef (); +if (showDbRefs && dbrefs != null) { +for (var i = 0; i < dbrefs.length; i++) { +tip.append ("
"); +tmp = dbrefs[i].getSource () + " " + dbrefs[i].getAccessionId (); +tip.append (tmp); +maxWidth = Math.max (maxWidth, tmp.length); +} +}var features = sequence.getSequenceFeatures (); +if (showNpFeats && features != null) { +for (var i = 0; i < features.length; i++) { +if (features[i].begin == 0 && features[i].end == 0) { +var sz = -tip.length (); +var tfeat = new java.util.ArrayList (); +tfeat.add (features[i]); +this.appendFeatures (tip, 0, tfeat, minmax); +sz += tip.length (); +maxWidth = Math.max (maxWidth, sz); +}} +}if (tableWrap && maxWidth > 60) { +tip.insert (0, "
"); +tip.append ("
"); +}}, "StringBuffer,jalview.datamodel.SequenceI,~B,~B,~B,java.util.Hashtable"); +}); diff --git a/bin/jalview/io/TCoffeeScoreFile.class b/bin/jalview/io/TCoffeeScoreFile.class index 71e39b1..6e9db73 100644 Binary files a/bin/jalview/io/TCoffeeScoreFile.class and b/bin/jalview/io/TCoffeeScoreFile.class differ diff --git a/bin/jalview/io/TCoffeeScoreFile.js b/bin/jalview/io/TCoffeeScoreFile.js index 1036432..7f2d629 100644 --- a/bin/jalview/io/TCoffeeScoreFile.js +++ b/bin/jalview/io/TCoffeeScoreFile.js @@ -1,274 +1,274 @@ -Clazz.declarePackage ("jalview.io"); -Clazz.load (["jalview.io.AlignFile", "java.awt.Color", "java.util.LinkedHashMap", "java.util.regex.Pattern"], "jalview.io.TCoffeeScoreFile", ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.Annotation", "jalview.util.Comparison", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.header = null; -this.scores = null; -this.fWidth = null; -Clazz.instantialize (this, arguments); -}, jalview.io, "TCoffeeScoreFile", jalview.io.AlignFile); -Clazz.defineMethod (c$, "getHeight", -function () { -return this.scores != null && this.scores.size () > 0 ? this.scores.size () - 1 : 0; -}); -Clazz.defineMethod (c$, "getWidth", -function () { -return this.fWidth != null ? this.fWidth : 0; -}); -Clazz.defineMethod (c$, "getScoresFor", -function (id) { -return this.scores != null && this.scores.containsKey (id) ? this.scores.get (id).toString () : ""; -}, "~S"); -Clazz.defineMethod (c$, "getScoresList", -function () { -if (this.scores == null) { -return null; -}var result = new java.util.ArrayList (this.scores.size ()); -for (var it, $it = this.scores.entrySet ().iterator (); $it.hasNext () && ((it = $it.next ()) || true);) { -result.add (it.getValue ().toString ()); -} -return result; -}); -Clazz.defineMethod (c$, "getScoresArray", -function () { -if (this.scores == null) { -return null; -}var result = Clazz.newByteArray (this.scores.size (), 0); -var rowCount = 0; -for (var it, $it = this.scores.entrySet ().iterator (); $it.hasNext () && ((it = $it.next ()) || true);) { -var line = it.getValue ().toString (); -var seqValues = Clazz.newByteArray (line.length, 0); -for (var j = 0, c = line.length; j < c; j++) { -var val = (line.charCodeAt (j) - 48); -seqValues[j] = (val >= 0 && val <= 9) ? val : -1; -} -result[rowCount++] = seqValues; -} -return result; -}); -Clazz.overrideMethod (c$, "parse", -function () { -this.header = jalview.io.TCoffeeScoreFile.readHeader (this); -if (this.header == null) { -this.error = true; -return; -}this.scores = new java.util.LinkedHashMap (); -for (var entry, $entry = this.header.scores.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) { -this.scores.put (entry.getKey (), new StringBuilder ()); -} -var block; -while ((block = jalview.io.TCoffeeScoreFile.readBlock (this, this.header.scores.size ())) != null) { -for (var entry, $entry = block.items.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) { -var scoreStringBuilder = this.scores.get (entry.getKey ()); -if (scoreStringBuilder == null) { -this.error = true; -this.errormessage = String.format ("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", [entry.getKey ()]); -return; -}scoreStringBuilder.append (entry.getValue ()); -} -} -for (var str, $str = this.scores.values ().iterator (); $str.hasNext () && ((str = $str.next ()) || true);) { -if (this.fWidth == null) { -this.fWidth = new Integer (str.length ()); -} else if ((this.fWidth).intValue () !== str.length ()) { -this.error = true; -this.errormessage = "Invalid T-Coffee score file: All the score sequences must have the same length"; -return; -}} -return; -}); -c$.parseInt = Clazz.defineMethod (c$, "parseInt", -function (str) { -try { -return Integer.parseInt (str); -} catch (e) { -if (Clazz.exceptionOf (e, NumberFormatException)) { -return 0; -} else { -throw e; -} -} -}, "~S"); -c$.readHeader = Clazz.defineMethod (c$, "readHeader", -function (reader) { -var result = null; -try { -result = new jalview.io.TCoffeeScoreFile.Header (); -result.head = reader.nextLine (); -var line; -while ((line = reader.nextLine ()) != null) { -if (line.startsWith ("SCORE=")) { -result.score = jalview.io.TCoffeeScoreFile.parseInt (line.substring (6).trim ()); -break; -}} -if ((line = reader.nextLine ()) == null || !"*".equals (line.trim ())) { -jalview.io.TCoffeeScoreFile.error (reader, "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); -return null; -}if ((line = reader.nextLine ()) == null || !"BAD AVG GOOD".equals (line.trim ())) { -jalview.io.TCoffeeScoreFile.error (reader, "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); -return null; -}if ((line = reader.nextLine ()) == null || !"*".equals (line.trim ())) { -jalview.io.TCoffeeScoreFile.error (reader, "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); -return null; -}while ((line = reader.nextLine ()) != null) { -if ("".equals (line)) { -break; -}var p = line.indexOf (":"); -if (p == -1) { -continue; -}var id = line.substring (0, p).trim (); -var val = jalview.io.TCoffeeScoreFile.parseInt (line.substring (p + 1).trim ()); -if ("".equals (id)) { -continue; -}result.scores.put (id, new Integer (val)); -} -if (result == null) { -jalview.io.TCoffeeScoreFile.error (reader, "T-COFFEE score file had no per-sequence scores"); -}} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -jalview.io.TCoffeeScoreFile.error (reader, "Unexpected problem parsing T-Coffee score ascii file"); -throw e; -} else { -throw e; -} -} -return result; -}, "jalview.io.FileParse"); -c$.error = Clazz.defineMethod (c$, "error", -($fz = function (reader, errm) { -reader.error = true; -if (reader.errormessage == null) { -reader.errormessage = errm; -} else { -reader.errormessage += "\n" + errm; -}}, $fz.isPrivate = true, $fz), "jalview.io.FileParse,~S"); -c$.readBlock = Clazz.defineMethod (c$, "readBlock", -function (reader, size) { -var result = new jalview.io.TCoffeeScoreFile.Block (size); -var line; -while ((line = reader.nextLine ()) != null && "".equals (line.trim ())) { -} -if (line == null) { -return null; -}do { -if ("".equals (line.trim ())) { -break; -}var p = line.indexOf (" "); -if (p == -1) { -if (reader.warningMessage == null) { -reader.warningMessage = ""; -}reader.warningMessage += "Possible parsing error - expected to find a space in line: '" + line + "'\n"; -continue; -}var id = line.substring (0, p).trim (); -var val = line.substring (p + 1).trim (); -var m = jalview.io.TCoffeeScoreFile.SCORES_WITH_RESIDUE_NUMS.matcher (val); -if (m.matches ()) { -val = m.group (1); -}result.items.put (id, val); -} while ((line = reader.nextLine ()) != null); -return result; -}, "jalview.io.FileParse,~N"); -Clazz.defineMethod (c$, "annotateAlignment", -function (al, matchids) { -if (al.getHeight () != this.getHeight () || al.getWidth () != this.getWidth ()) { -var info = String.format ("align w: %s, h: %s; score: w: %s; h: %s ", [new Integer (al.getWidth ()), new Integer (al.getHeight ()), new Integer (this.getWidth ()), new Integer (this.getHeight ())]); -this.warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info; -return false; -}var added = false; -var i = 0; -var sidmatcher = new jalview.analysis.SequenceIdMatcher (al.getSequencesArray ()); -var scoreMatrix = this.getScoresArray (); -for (var id, $id = this.scores.entrySet ().iterator (); $id.hasNext () && ((id = $id.next ()) || true);) { -var srow = scoreMatrix[i]; -var s; -if (matchids) { -s = sidmatcher.findIdMatch (id.getKey ()); -} else { -s = al.getSequenceAt (i); -}i++; -if (s == null && i != this.scores.size () && !id.getKey ().equals ("cons")) { -System.err.println ("No " + (matchids ? "match " : " sequences left ") + " for TCoffee score set : " + id.getKey ()); -continue; -}var jSize = al.getWidth () < srow.length ? al.getWidth () : srow.length; -var annotations = new Array (al.getWidth ()); -for (var j = 0; j < jSize; j++) { -var val = srow[j]; -if (s != null && jalview.util.Comparison.isGap (s.getCharAt (j))) { -annotations[j] = null; -if (val > 0) { -System.err.println ("Warning: non-zero value for positional T-COFFEE score for gap at " + j + " in sequence " + s.getName ()); -}} else { -annotations[j] = new jalview.datamodel.Annotation (s == null ? "" + val : null, s == null ? "" + val : null, '\0', val * 1, val >= 0 && val < jalview.io.TCoffeeScoreFile.colors.length ? jalview.io.TCoffeeScoreFile.colors[val] : java.awt.Color.white); -}} -var aa = al.findOrCreateAnnotation ("TCoffeeScore", "TCoffeeScore", false, s, null); -if (s != null) { -aa.label = "T-COFFEE"; -aa.description = "" + id.getKey (); -aa.annotations = annotations; -aa.visible = false; -aa.belowAlignment = false; -aa.setScore (this.header.getScoreFor (id.getKey ())); -aa.createSequenceMapping (s, s.getStart (), true); -s.addAlignmentAnnotation (aa); -aa.adjustForAlignment (); -} else { -aa.graph = 0; -aa.label = "T-COFFEE"; -aa.description = "TCoffee column reliability score"; -aa.annotations = annotations; -aa.belowAlignment = true; -aa.visible = true; -aa.setScore (this.header.getScoreAvg ()); -}aa.showAllColLabels = true; -aa.validateRangeAndDisplay (); -added = true; -} -return added; -}, "jalview.datamodel.AlignmentI,~B"); -Clazz.overrideMethod (c$, "print", -function () { -return "Not valid."; -}); -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.head = null; -this.score = 0; -this.scores = null; -Clazz.instantialize (this, arguments); -}, jalview.io.TCoffeeScoreFile, "Header"); -Clazz.prepareFields (c$, function () { -this.scores = new java.util.LinkedHashMap (); -}); -Clazz.defineMethod (c$, "getScoreAvg", -function () { -return this.score; -}); -Clazz.defineMethod (c$, "getScoreFor", -function (a) { -return this.scores.containsKey (a) ? this.scores.get (a) : -1; -}, "~S"); -c$ = Clazz.p0p (); -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.size = 0; -this.items = null; -Clazz.instantialize (this, arguments); -}, jalview.io.TCoffeeScoreFile, "Block"); -Clazz.makeConstructor (c$, -function (a) { -this.size = a; -this.items = new java.util.HashMap (a); -}, "~N"); -Clazz.defineMethod (c$, "getScoresFor", -function (a) { -return this.items.get (a); -}, "~S"); -Clazz.defineMethod (c$, "getConsensus", -function () { -return this.items.get ("cons"); -}); -c$ = Clazz.p0p (); -c$.SCORES_WITH_RESIDUE_NUMS = c$.prototype.SCORES_WITH_RESIDUE_NUMS = java.util.regex.Pattern.compile ("^\\d+\\s([^\\s]+)\\s+\\d+$"); -c$.colors = c$.prototype.colors = Clazz.newArray (-1, [ new java.awt.Color (102, 102, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (102, 255, 0), new java.awt.Color (204, 255, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 153, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 34, 0)]); -Clazz.defineStatics (c$, -"TCOFFEE_SCORE", "TCoffeeScore"); -}); +Clazz.declarePackage ("jalview.io"); +Clazz.load (["jalview.io.AlignFile", "java.awt.Color", "java.util.LinkedHashMap", "java.util.regex.Pattern"], "jalview.io.TCoffeeScoreFile", ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.Annotation", "jalview.util.Comparison", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.header = null; +this.scores = null; +this.fWidth = null; +Clazz.instantialize (this, arguments); +}, jalview.io, "TCoffeeScoreFile", jalview.io.AlignFile); +Clazz.defineMethod (c$, "getHeight", +function () { +return this.scores != null && this.scores.size () > 0 ? this.scores.size () - 1 : 0; +}); +Clazz.defineMethod (c$, "getWidth", +function () { +return this.fWidth != null ? this.fWidth : 0; +}); +Clazz.defineMethod (c$, "getScoresFor", +function (id) { +return this.scores != null && this.scores.containsKey (id) ? this.scores.get (id).toString () : ""; +}, "~S"); +Clazz.defineMethod (c$, "getScoresList", +function () { +if (this.scores == null) { +return null; +}var result = new java.util.ArrayList (this.scores.size ()); +for (var it, $it = this.scores.entrySet ().iterator (); $it.hasNext () && ((it = $it.next ()) || true);) { +result.add (it.getValue ().toString ()); +} +return result; +}); +Clazz.defineMethod (c$, "getScoresArray", +function () { +if (this.scores == null) { +return null; +}var result = Clazz.newByteArray (this.scores.size (), 0); +var rowCount = 0; +for (var it, $it = this.scores.entrySet ().iterator (); $it.hasNext () && ((it = $it.next ()) || true);) { +var line = it.getValue ().toString (); +var seqValues = Clazz.newByteArray (line.length, 0); +for (var j = 0, c = line.length; j < c; j++) { +var val = (line.charCodeAt (j) - 48); +seqValues[j] = (val >= 0 && val <= 9) ? val : -1; +} +result[rowCount++] = seqValues; +} +return result; +}); +Clazz.overrideMethod (c$, "parse", +function () { +this.header = jalview.io.TCoffeeScoreFile.readHeader (this); +if (this.header == null) { +this.error = true; +return; +}this.scores = new java.util.LinkedHashMap (); +for (var entry, $entry = this.header.scores.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) { +this.scores.put (entry.getKey (), new StringBuilder ()); +} +var block; +while ((block = jalview.io.TCoffeeScoreFile.readBlock (this, this.header.scores.size ())) != null) { +for (var entry, $entry = block.items.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) { +var scoreStringBuilder = this.scores.get (entry.getKey ()); +if (scoreStringBuilder == null) { +this.error = true; +this.errormessage = String.format ("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", [entry.getKey ()]); +return; +}scoreStringBuilder.append (entry.getValue ()); +} +} +for (var str, $str = this.scores.values ().iterator (); $str.hasNext () && ((str = $str.next ()) || true);) { +if (this.fWidth == null) { +this.fWidth = new Integer (str.length ()); +} else if ((this.fWidth).intValue () !== str.length ()) { +this.error = true; +this.errormessage = "Invalid T-Coffee score file: All the score sequences must have the same length"; +return; +}} +return; +}); +c$.parseInt = Clazz.defineMethod (c$, "parseInt", +function (str) { +try { +return Integer.parseInt (str); +} catch (e) { +if (Clazz.exceptionOf (e, NumberFormatException)) { +return 0; +} else { +throw e; +} +} +}, "~S"); +c$.readHeader = Clazz.defineMethod (c$, "readHeader", +function (reader) { +var result = null; +try { +result = new jalview.io.TCoffeeScoreFile.Header (); +result.head = reader.nextLine (); +var line; +while ((line = reader.nextLine ()) != null) { +if (line.startsWith ("SCORE=")) { +result.score = jalview.io.TCoffeeScoreFile.parseInt (line.substring (6).trim ()); +break; +}} +if ((line = reader.nextLine ()) == null || !"*".equals (line.trim ())) { +jalview.io.TCoffeeScoreFile.error (reader, "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); +return null; +}if ((line = reader.nextLine ()) == null || !"BAD AVG GOOD".equals (line.trim ())) { +jalview.io.TCoffeeScoreFile.error (reader, "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); +return null; +}if ((line = reader.nextLine ()) == null || !"*".equals (line.trim ())) { +jalview.io.TCoffeeScoreFile.error (reader, "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); +return null; +}while ((line = reader.nextLine ()) != null) { +if ("".equals (line)) { +break; +}var p = line.indexOf (":"); +if (p == -1) { +continue; +}var id = line.substring (0, p).trim (); +var val = jalview.io.TCoffeeScoreFile.parseInt (line.substring (p + 1).trim ()); +if ("".equals (id)) { +continue; +}result.scores.put (id, new Integer (val)); +} +if (result == null) { +jalview.io.TCoffeeScoreFile.error (reader, "T-COFFEE score file had no per-sequence scores"); +}} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +jalview.io.TCoffeeScoreFile.error (reader, "Unexpected problem parsing T-Coffee score ascii file"); +throw e; +} else { +throw e; +} +} +return result; +}, "jalview.io.FileParse"); +c$.error = Clazz.defineMethod (c$, "error", +($fz = function (reader, errm) { +reader.error = true; +if (reader.errormessage == null) { +reader.errormessage = errm; +} else { +reader.errormessage += "\n" + errm; +}}, $fz.isPrivate = true, $fz), "jalview.io.FileParse,~S"); +c$.readBlock = Clazz.defineMethod (c$, "readBlock", +function (reader, size) { +var result = new jalview.io.TCoffeeScoreFile.Block (size); +var line; +while ((line = reader.nextLine ()) != null && "".equals (line.trim ())) { +} +if (line == null) { +return null; +}do { +if ("".equals (line.trim ())) { +break; +}var p = line.indexOf (" "); +if (p == -1) { +if (reader.warningMessage == null) { +reader.warningMessage = ""; +}reader.warningMessage += "Possible parsing error - expected to find a space in line: '" + line + "'\n"; +continue; +}var id = line.substring (0, p).trim (); +var val = line.substring (p + 1).trim (); +var m = jalview.io.TCoffeeScoreFile.SCORES_WITH_RESIDUE_NUMS.matcher (val); +if (m.matches ()) { +val = m.group (1); +}result.items.put (id, val); +} while ((line = reader.nextLine ()) != null); +return result; +}, "jalview.io.FileParse,~N"); +Clazz.defineMethod (c$, "annotateAlignment", +function (al, matchids) { +if (al.getHeight () != this.getHeight () || al.getWidth () != this.getWidth ()) { +var info = String.format ("align w: %s, h: %s; score: w: %s; h: %s ", [new Integer (al.getWidth ()), new Integer (al.getHeight ()), new Integer (this.getWidth ()), new Integer (this.getHeight ())]); +this.warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info; +return false; +}var added = false; +var i = 0; +var sidmatcher = new jalview.analysis.SequenceIdMatcher (al.getSequencesArray ()); +var scoreMatrix = this.getScoresArray (); +for (var id, $id = this.scores.entrySet ().iterator (); $id.hasNext () && ((id = $id.next ()) || true);) { +var srow = scoreMatrix[i]; +var s; +if (matchids) { +s = sidmatcher.findIdMatch (id.getKey ()); +} else { +s = al.getSequenceAt (i); +}i++; +if (s == null && i != this.scores.size () && !id.getKey ().equals ("cons")) { +System.err.println ("No " + (matchids ? "match " : " sequences left ") + " for TCoffee score set : " + id.getKey ()); +continue; +}var jSize = al.getWidth () < srow.length ? al.getWidth () : srow.length; +var annotations = new Array (al.getWidth ()); +for (var j = 0; j < jSize; j++) { +var val = srow[j]; +if (s != null && jalview.util.Comparison.isGap (s.getCharAt (j))) { +annotations[j] = null; +if (val > 0) { +System.err.println ("Warning: non-zero value for positional T-COFFEE score for gap at " + j + " in sequence " + s.getName ()); +}} else { +annotations[j] = new jalview.datamodel.Annotation (s == null ? "" + val : null, s == null ? "" + val : null, '\0', val * 1, val >= 0 && val < jalview.io.TCoffeeScoreFile.colors.length ? jalview.io.TCoffeeScoreFile.colors[val] : java.awt.Color.white); +}} +var aa = al.findOrCreateAnnotation ("TCoffeeScore", "TCoffeeScore", false, s, null); +if (s != null) { +aa.label = "T-COFFEE"; +aa.description = "" + id.getKey (); +aa.annotations = annotations; +aa.visible = false; +aa.belowAlignment = false; +aa.setScore (this.header.getScoreFor (id.getKey ())); +aa.createSequenceMapping (s, s.getStart (), true); +s.addAlignmentAnnotation (aa); +aa.adjustForAlignment (); +} else { +aa.graph = 0; +aa.label = "T-COFFEE"; +aa.description = "TCoffee column reliability score"; +aa.annotations = annotations; +aa.belowAlignment = true; +aa.visible = true; +aa.setScore (this.header.getScoreAvg ()); +}aa.showAllColLabels = true; +aa.validateRangeAndDisplay (); +added = true; +} +return added; +}, "jalview.datamodel.AlignmentI,~B"); +Clazz.overrideMethod (c$, "print", +function () { +return "Not valid."; +}); +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.head = null; +this.score = 0; +this.scores = null; +Clazz.instantialize (this, arguments); +}, jalview.io.TCoffeeScoreFile, "Header"); +Clazz.prepareFields (c$, function () { +this.scores = new java.util.LinkedHashMap (); +}); +Clazz.defineMethod (c$, "getScoreAvg", +function () { +return this.score; +}); +Clazz.defineMethod (c$, "getScoreFor", +function (a) { +return this.scores.containsKey (a) ? this.scores.get (a) : -1; +}, "~S"); +c$ = Clazz.p0p (); +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.size = 0; +this.items = null; +Clazz.instantialize (this, arguments); +}, jalview.io.TCoffeeScoreFile, "Block"); +Clazz.makeConstructor (c$, +function (a) { +this.size = a; +this.items = new java.util.HashMap (a); +}, "~N"); +Clazz.defineMethod (c$, "getScoresFor", +function (a) { +return this.items.get (a); +}, "~S"); +Clazz.defineMethod (c$, "getConsensus", +function () { +return this.items.get ("cons"); +}); +c$ = Clazz.p0p (); +c$.SCORES_WITH_RESIDUE_NUMS = c$.prototype.SCORES_WITH_RESIDUE_NUMS = java.util.regex.Pattern.compile ("^\\d+\\s([^\\s]+)\\s+\\d+$"); +c$.colors = c$.prototype.colors = Clazz.newArray (-1, [ new java.awt.Color (102, 102, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (102, 255, 0), new java.awt.Color (204, 255, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 153, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 34, 0)]); +Clazz.defineStatics (c$, +"TCOFFEE_SCORE", "TCoffeeScore"); +}); diff --git a/bin/jalview/javascript/JSFunctionExec$1.class b/bin/jalview/javascript/JSFunctionExec$1.class index 5466a9b..1f39479 100644 Binary files a/bin/jalview/javascript/JSFunctionExec$1.class and b/bin/jalview/javascript/JSFunctionExec$1.class differ diff --git a/bin/jalview/javascript/JSFunctionExec.class b/bin/jalview/javascript/JSFunctionExec.class index c6607f6..d29244d 100644 Binary files a/bin/jalview/javascript/JSFunctionExec.class and b/bin/jalview/javascript/JSFunctionExec.class differ diff --git a/bin/jalview/javascript/JSFunctionExec.js b/bin/jalview/javascript/JSFunctionExec.js index 3296c72..43f56a2 100644 --- a/bin/jalview/javascript/JSFunctionExec.js +++ b/bin/jalview/javascript/JSFunctionExec.js @@ -1,166 +1,166 @@ -Clazz.declarePackage ("jalview.javascript"); -Clazz.load (null, "jalview.javascript.JSFunctionExec", ["jalview.bin.JalviewLite", "java.lang.StringBuffer", "$.Thread", "java.net.MalformedURLException", "$.URL", "netscape.javascript.JSException", "$.JSObject"], function () { -c$ = Clazz.decorateAsClass (function () { -this.jvlite = null; -this.jsExecQueue = null; -this.executor = null; -Clazz.instantialize (this, arguments); -}, jalview.javascript, "JSFunctionExec", null, Runnable); -Clazz.makeConstructor (c$, -function (applet) { -this.jvlite = applet; -this.jsExecQueue = this.jvlite.getJsExecQueue (); -this.jvlite.setExecutor (this); -}, "jalview.bin.JalviewLite"); -Clazz.overrideMethod (c$, "finalize", -function () { -this.jvlite = null; -this.executor = null; -if (this.jsExecQueue != null) { -this.jsExecQueue.clear (); -}this.jsExecQueue = null; -}); -Clazz.defineMethod (c$, "stopQueue", -function () { -if (this.jsExecQueue != null) { -var q = null; -{ -q = this.jsExecQueue; -this.jsExecQueue = null; -}if (q != null) { -for (var jx, $jx = q.iterator (); $jx.hasNext () && ((jx = $jx.next ()) || true);) { -jx.jvlite = null; -} -q.removeAllElements (); -{ -q.notifyAll (); -}}}this.jvlite = null; -this.executor = null; -}); -Clazz.defineMethod (c$, "run", -function () { -while (this.jsExecQueue != null) { -if (this.jsExecQueue.size () > 0) { -var r = this.jsExecQueue.elementAt (0); -this.jsExecQueue.removeElementAt (0); -try { -r.run (); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, Exception)) { -var ex = e$$; -{ -ex.printStackTrace (); -} -} else if (Clazz.exceptionOf (e$$, Error)) { -var ex = e$$; -{ -ex.printStackTrace (); -} -} else { -throw e$$; -} -} -} else { -try { -{ -this.jsExecQueue.wait (1000); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -;}} -}); -Clazz.defineMethod (c$, "executeJavascriptFunction", -function (_listener, objects) { -this.executeJavascriptFunction (false, _listener, objects); -}, "~S,~A"); -Clazz.defineMethod (c$, "executeJavascriptFunction", -function (async, _listener, $arguments) { -this.executeJavascriptFunction (async, _listener, $arguments, null); -}, "~B,~S,~A"); -Clazz.defineMethod (c$, "executeJavascriptFunction", -function (async, _listener, $arguments, dbgMsg) { -var objects = new Array ($arguments != null ? $arguments.length : 0); -if ($arguments != null) { -System.arraycopy ($arguments, 0, objects, 0, $arguments.length); -}var jsex = new Array (1); -var exec = ((Clazz.isClassDefined ("jalview.javascript.JSFunctionExec$1") ? 0 : jalview.javascript.JSFunctionExec.$JSFunctionExec$1$ ()), Clazz.innerTypeInstance (jalview.javascript.JSFunctionExec$1, this, Clazz.cloneFinals ("dbgMsg", dbgMsg, "_listener", _listener, "objects", objects, "jsex", jsex, "async", async))); -if (async) { -if (this.executor == null) { -this.executor = new Thread ( new jalview.javascript.JSFunctionExec (this.jvlite)); -this.executor.start (); -}{ -this.jsExecQueue.addElement (exec); -this.jsExecQueue.notify (); -}} else { -exec.run (); -if (jsex[0] != null) { -throw (jsex[0]); -}}}, "~B,~S,~A,~S"); -c$.$JSFunctionExec$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.javascript, "JSFunctionExec$1", null, Runnable); -Clazz.defineMethod (c$, "run", -function () { -try { -var scriptObject = null; -try { -scriptObject = netscape.javascript.JSObject.getWindow (this.b$["jalview.javascript.JSFunctionExec"].jvlite); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -;if (scriptObject != null) { -if (jalview.bin.JalviewLite.debug && this.f$.dbgMsg != null) { -System.err.println (this.f$.dbgMsg); -}scriptObject.call (this.f$._listener, this.f$.objects); -}} catch (jex) { -if (Clazz.exceptionOf (jex, Exception)) { -if (!(Clazz.instanceOf (jex, java.net.MalformedURLException))) { -if (jalview.bin.JalviewLite.debug) { -System.err.println (jex); -}if (Clazz.instanceOf (jex, netscape.javascript.JSException) && this.b$["jalview.javascript.JSFunctionExec"].jvlite.jsfallbackEnabled) { -this.f$.jsex[0] = jex; -if (jalview.bin.JalviewLite.debug) { -System.err.println ("Falling back to javascript: url call"); -}var sb = new StringBuffer ("javascript:" + this.f$._listener + "("); -for (var i = 0; this.f$.objects != null && i < this.f$.objects.length; i++) { -if (i > 0) { -sb.append (","); -}sb.append ("\""); -if (this.f$.objects[i] != null && !(this.f$.objects[i].getClass ().getName ().indexOf ("jalview") == 0)) { -sb.append (this.f$.objects[i].toString ()); -}sb.append ("\""); -} -sb.append (")"); -if (jalview.bin.JalviewLite.debug) { -System.err.println (sb.toString ()); -}var url = null; -try { -url = new java.net.URL (sb.toString ()); -this.b$["jalview.javascript.JSFunctionExec"].jvlite.getAppletContext ().showDocument (url); -jex = null; -} catch (uex) { -if (Clazz.exceptionOf (uex, Exception)) { -jex = uex; -} else { -throw uex; -} -} -}if (jex != null) { -if (this.f$.async) { -jex.printStackTrace (); -} else { -this.f$.jsex[0] = jex; -}};}} else { -throw jex; -} -} -}); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.javascript"); +Clazz.load (null, "jalview.javascript.JSFunctionExec", ["jalview.bin.JalviewLite", "java.lang.StringBuffer", "$.Thread", "java.net.MalformedURLException", "$.URL", "netscape.javascript.JSException", "$.JSObject"], function () { +c$ = Clazz.decorateAsClass (function () { +this.jvlite = null; +this.jsExecQueue = null; +this.executor = null; +Clazz.instantialize (this, arguments); +}, jalview.javascript, "JSFunctionExec", null, Runnable); +Clazz.makeConstructor (c$, +function (applet) { +this.jvlite = applet; +this.jsExecQueue = this.jvlite.getJsExecQueue (); +this.jvlite.setExecutor (this); +}, "jalview.bin.JalviewLite"); +Clazz.overrideMethod (c$, "finalize", +function () { +this.jvlite = null; +this.executor = null; +if (this.jsExecQueue != null) { +this.jsExecQueue.clear (); +}this.jsExecQueue = null; +}); +Clazz.defineMethod (c$, "stopQueue", +function () { +if (this.jsExecQueue != null) { +var q = null; +{ +q = this.jsExecQueue; +this.jsExecQueue = null; +}if (q != null) { +for (var jx, $jx = q.iterator (); $jx.hasNext () && ((jx = $jx.next ()) || true);) { +jx.jvlite = null; +} +q.removeAllElements (); +{ +q.notifyAll (); +}}}this.jvlite = null; +this.executor = null; +}); +Clazz.defineMethod (c$, "run", +function () { +while (this.jsExecQueue != null) { +if (this.jsExecQueue.size () > 0) { +var r = this.jsExecQueue.elementAt (0); +this.jsExecQueue.removeElementAt (0); +try { +r.run (); +} catch (e$$) { +if (Clazz.exceptionOf (e$$, Exception)) { +var ex = e$$; +{ +ex.printStackTrace (); +} +} else if (Clazz.exceptionOf (e$$, Error)) { +var ex = e$$; +{ +ex.printStackTrace (); +} +} else { +throw e$$; +} +} +} else { +try { +{ +this.jsExecQueue.wait (1000); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +;}} +}); +Clazz.defineMethod (c$, "executeJavascriptFunction", +function (_listener, objects) { +this.executeJavascriptFunction (false, _listener, objects); +}, "~S,~A"); +Clazz.defineMethod (c$, "executeJavascriptFunction", +function (async, _listener, $arguments) { +this.executeJavascriptFunction (async, _listener, $arguments, null); +}, "~B,~S,~A"); +Clazz.defineMethod (c$, "executeJavascriptFunction", +function (async, _listener, $arguments, dbgMsg) { +var objects = new Array ($arguments != null ? $arguments.length : 0); +if ($arguments != null) { +System.arraycopy ($arguments, 0, objects, 0, $arguments.length); +}var jsex = new Array (1); +var exec = ((Clazz.isClassDefined ("jalview.javascript.JSFunctionExec$1") ? 0 : jalview.javascript.JSFunctionExec.$JSFunctionExec$1$ ()), Clazz.innerTypeInstance (jalview.javascript.JSFunctionExec$1, this, Clazz.cloneFinals ("dbgMsg", dbgMsg, "_listener", _listener, "objects", objects, "jsex", jsex, "async", async))); +if (async) { +if (this.executor == null) { +this.executor = new Thread ( new jalview.javascript.JSFunctionExec (this.jvlite)); +this.executor.start (); +}{ +this.jsExecQueue.addElement (exec); +this.jsExecQueue.notify (); +}} else { +exec.run (); +if (jsex[0] != null) { +throw (jsex[0]); +}}}, "~B,~S,~A,~S"); +c$.$JSFunctionExec$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.javascript, "JSFunctionExec$1", null, Runnable); +Clazz.defineMethod (c$, "run", +function () { +try { +var scriptObject = null; +try { +scriptObject = netscape.javascript.JSObject.getWindow (this.b$["jalview.javascript.JSFunctionExec"].jvlite); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +;if (scriptObject != null) { +if (jalview.bin.JalviewLite.debug && this.f$.dbgMsg != null) { +System.err.println (this.f$.dbgMsg); +}scriptObject.call (this.f$._listener, this.f$.objects); +}} catch (jex) { +if (Clazz.exceptionOf (jex, Exception)) { +if (!(Clazz.instanceOf (jex, java.net.MalformedURLException))) { +if (jalview.bin.JalviewLite.debug) { +System.err.println (jex); +}if (Clazz.instanceOf (jex, netscape.javascript.JSException) && this.b$["jalview.javascript.JSFunctionExec"].jvlite.jsfallbackEnabled) { +this.f$.jsex[0] = jex; +if (jalview.bin.JalviewLite.debug) { +System.err.println ("Falling back to javascript: url call"); +}var sb = new StringBuffer ("javascript:" + this.f$._listener + "("); +for (var i = 0; this.f$.objects != null && i < this.f$.objects.length; i++) { +if (i > 0) { +sb.append (","); +}sb.append ("\""); +if (this.f$.objects[i] != null && !(this.f$.objects[i].getClass ().getName ().indexOf ("jalview") == 0)) { +sb.append (this.f$.objects[i].toString ()); +}sb.append ("\""); +} +sb.append (")"); +if (jalview.bin.JalviewLite.debug) { +System.err.println (sb.toString ()); +}var url = null; +try { +url = new java.net.URL (sb.toString ()); +this.b$["jalview.javascript.JSFunctionExec"].jvlite.getAppletContext ().showDocument (url); +jex = null; +} catch (uex) { +if (Clazz.exceptionOf (uex, Exception)) { +jex = uex; +} else { +throw uex; +} +} +}if (jex != null) { +if (this.f$.async) { +jex.printStackTrace (); +} else { +this.f$.jsex[0] = jex; +}};}} else { +throw jex; +} +} +}); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/javascript/JalviewLiteJsApi.js b/bin/jalview/javascript/JalviewLiteJsApi.js index ed4943e..bdd7529 100644 --- a/bin/jalview/javascript/JalviewLiteJsApi.js +++ b/bin/jalview/javascript/JalviewLiteJsApi.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.javascript"); -Clazz.declareInterface (jalview.javascript, "JalviewLiteJsApi"); +Clazz.declarePackage ("jalview.javascript"); +Clazz.declareInterface (jalview.javascript, "JalviewLiteJsApi"); diff --git a/bin/jalview/javascript/JsCallBack.js b/bin/jalview/javascript/JsCallBack.js index 1577e6b..85ac52a 100644 --- a/bin/jalview/javascript/JsCallBack.js +++ b/bin/jalview/javascript/JsCallBack.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.javascript"); -Clazz.declareInterface (jalview.javascript, "JsCallBack"); +Clazz.declarePackage ("jalview.javascript"); +Clazz.declareInterface (jalview.javascript, "JsCallBack"); diff --git a/bin/jalview/javascript/JsSelectionSender.js b/bin/jalview/javascript/JsSelectionSender.js index ad763f0..36703c5 100644 --- a/bin/jalview/javascript/JsSelectionSender.js +++ b/bin/jalview/javascript/JsSelectionSender.js @@ -1,70 +1,70 @@ -Clazz.declarePackage ("jalview.javascript"); -Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.SelectionListener"], "jalview.javascript.JsSelectionSender", ["jalview.appletgui.AlignViewport", "netscape.javascript.JSException"], function () { -c$ = Clazz.decorateAsClass (function () { -this._af = null; -this._listener = null; -Clazz.instantialize (this, arguments); -}, jalview.javascript, "JsSelectionSender", jalview.javascript.JSFunctionExec, [jalview.structure.SelectionListener, jalview.javascript.JsCallBack]); -Clazz.makeConstructor (c$, -function (jvlite, af, listener) { -Clazz.superConstructor (this, jalview.javascript.JsSelectionSender, [jvlite]); -this._af = af; -this._listener = listener; -}, "jalview.bin.JalviewLite,jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "selection", -function (seqsel, colsel, source) { -try { -var setid = ""; -var viewid = ""; -var src = this._af; -if (source != null) { -if (Clazz.instanceOf (source, jalview.appletgui.AlignViewport) && (source).applet.currentAlignFrame.viewport === source) { -src = (source).applet.currentAlignFrame; -}}var seqs = Clazz.newArray (-1, []); -var cols = Clazz.newArray (-1, []); -var strt = 0; -var end = (src == null) ? -1 : src.alignPanel.av.getAlignment ().getWidth (); -if (seqsel != null && seqsel.getSize () > 0) { -seqs = new Array (seqsel.getSize ()); -for (var i = 0; i < seqs.length; i++) { -seqs[i] = seqsel.getSequenceAt (i).getName (); -} -if (strt < seqsel.getStartRes ()) { -strt = seqsel.getStartRes (); -}if (end == -1 || end > seqsel.getEndRes ()) { -end = seqsel.getEndRes (); -}}if (colsel != null && colsel.size () > 0) { -if (end == -1) { -end = colsel.getMax () + 1; -}cols = new Array (colsel.getSelected ().size ()); -var d = 0; -var r = -1; -for (var i = 0; i < cols.length; i++) { -cols[i] = "" + (1 + colsel.getSelected ().elementAt (i).intValue ()); -} -} else { -if (seqsel != null && seqsel.getSize () > 0) { -cols = new Array (2); -cols[0] = "" + (1 + strt) + "-" + (1 + end); -};}System.err.println ("Relaying selection to jsfunction:" + this._listener); -this.executeJavascriptFunction (this._listener, Clazz.newArray (-1, [src, setid, this.jvlite.arrayToSeparatorList (seqs), this.jvlite.arrayToSeparatorList (cols)])); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Jalview Javascript exec error: Couldn't send selection message using function '" + this._listener + "'"); -ex.printStackTrace (); -if (Clazz.instanceOf (ex, netscape.javascript.JSException)) { -System.err.println ("Javascript Exception: " + (ex).getCause ().toString ()); -}} else { -throw ex; -} -} -}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); -Clazz.overrideMethod (c$, "getAlignFrame", -function () { -return this._af; -}); -Clazz.overrideMethod (c$, "getListenerFunction", -function () { -return this._listener; -}); -}); +Clazz.declarePackage ("jalview.javascript"); +Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.SelectionListener"], "jalview.javascript.JsSelectionSender", ["jalview.appletgui.AlignViewport", "netscape.javascript.JSException"], function () { +c$ = Clazz.decorateAsClass (function () { +this._af = null; +this._listener = null; +Clazz.instantialize (this, arguments); +}, jalview.javascript, "JsSelectionSender", jalview.javascript.JSFunctionExec, [jalview.structure.SelectionListener, jalview.javascript.JsCallBack]); +Clazz.makeConstructor (c$, +function (jvlite, af, listener) { +Clazz.superConstructor (this, jalview.javascript.JsSelectionSender, [jvlite]); +this._af = af; +this._listener = listener; +}, "jalview.bin.JalviewLite,jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "selection", +function (seqsel, colsel, source) { +try { +var setid = ""; +var viewid = ""; +var src = this._af; +if (source != null) { +if (Clazz.instanceOf (source, jalview.appletgui.AlignViewport) && (source).applet.currentAlignFrame.viewport === source) { +src = (source).applet.currentAlignFrame; +}}var seqs = Clazz.newArray (-1, []); +var cols = Clazz.newArray (-1, []); +var strt = 0; +var end = (src == null) ? -1 : src.alignPanel.av.getAlignment ().getWidth (); +if (seqsel != null && seqsel.getSize () > 0) { +seqs = new Array (seqsel.getSize ()); +for (var i = 0; i < seqs.length; i++) { +seqs[i] = seqsel.getSequenceAt (i).getName (); +} +if (strt < seqsel.getStartRes ()) { +strt = seqsel.getStartRes (); +}if (end == -1 || end > seqsel.getEndRes ()) { +end = seqsel.getEndRes (); +}}if (colsel != null && colsel.size () > 0) { +if (end == -1) { +end = colsel.getMax () + 1; +}cols = new Array (colsel.getSelected ().size ()); +var d = 0; +var r = -1; +for (var i = 0; i < cols.length; i++) { +cols[i] = "" + (1 + colsel.getSelected ().elementAt (i).intValue ()); +} +} else { +if (seqsel != null && seqsel.getSize () > 0) { +cols = new Array (2); +cols[0] = "" + (1 + strt) + "-" + (1 + end); +};}System.err.println ("Relaying selection to jsfunction:" + this._listener); +this.executeJavascriptFunction (this._listener, Clazz.newArray (-1, [src, setid, this.jvlite.arrayToSeparatorList (seqs), this.jvlite.arrayToSeparatorList (cols)])); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Jalview Javascript exec error: Couldn't send selection message using function '" + this._listener + "'"); +ex.printStackTrace (); +if (Clazz.instanceOf (ex, netscape.javascript.JSException)) { +System.err.println ("Javascript Exception: " + (ex).getCause ().toString ()); +}} else { +throw ex; +} +} +}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); +Clazz.overrideMethod (c$, "getAlignFrame", +function () { +return this._af; +}); +Clazz.overrideMethod (c$, "getListenerFunction", +function () { +return this._listener; +}); +}); diff --git a/bin/jalview/javascript/MouseOverListener.js b/bin/jalview/javascript/MouseOverListener.js index 39cb7bc..de59a3e 100644 --- a/bin/jalview/javascript/MouseOverListener.js +++ b/bin/jalview/javascript/MouseOverListener.js @@ -1,46 +1,46 @@ -Clazz.declarePackage ("jalview.javascript"); -Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.VamsasListener"], "jalview.javascript.MouseOverListener", ["jalview.appletgui.AlignViewport", "netscape.javascript.JSException"], function () { -c$ = Clazz.decorateAsClass (function () { -this._af = null; -this._listener = null; -this.last = null; -this.i = -1; -Clazz.instantialize (this, arguments); -}, jalview.javascript, "MouseOverListener", jalview.javascript.JSFunctionExec, [jalview.structure.VamsasListener, jalview.javascript.JsCallBack]); -Clazz.overrideMethod (c$, "mouseOverSequence", -function (seq, index, source) { -if (seq !== this.last || this.i != index) { -this.last = seq; -this.i = index; -var src = null; -try { -if (source != null) { -if (Clazz.instanceOf (source, jalview.appletgui.AlignViewport) && (source).applet.currentAlignFrame.viewport === source) { -src = (source).applet.currentAlignFrame; -}}this.executeJavascriptFunction (this._listener, Clazz.newArray (-1, [src, seq.getDisplayId (false), "" + (1 + this.i), "" + seq.findPosition (this.i)])); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("JalviewLite javascript error: Couldn't send mouseOver with handler '" + this._listener + "'"); -if (Clazz.instanceOf (ex, netscape.javascript.JSException)) { -System.err.println ("Javascript Exception: " + (ex).getMessage ()); -}ex.printStackTrace (); -} else { -throw ex; -} -} -}}, "jalview.datamodel.SequenceI,~N,jalview.structure.VamsasSource"); -Clazz.makeConstructor (c$, -function (applet, af, listener) { -Clazz.superConstructor (this, jalview.javascript.MouseOverListener, [applet]); -this._af = af; -this._listener = listener; -}, "jalview.bin.JalviewLite,jalview.appletgui.AlignFrame,~S"); -Clazz.overrideMethod (c$, "getAlignFrame", -function () { -return this._af; -}); -Clazz.overrideMethod (c$, "getListenerFunction", -function () { -return this._listener; -}); -}); +Clazz.declarePackage ("jalview.javascript"); +Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.VamsasListener"], "jalview.javascript.MouseOverListener", ["jalview.appletgui.AlignViewport", "netscape.javascript.JSException"], function () { +c$ = Clazz.decorateAsClass (function () { +this._af = null; +this._listener = null; +this.last = null; +this.i = -1; +Clazz.instantialize (this, arguments); +}, jalview.javascript, "MouseOverListener", jalview.javascript.JSFunctionExec, [jalview.structure.VamsasListener, jalview.javascript.JsCallBack]); +Clazz.overrideMethod (c$, "mouseOverSequence", +function (seq, index, source) { +if (seq !== this.last || this.i != index) { +this.last = seq; +this.i = index; +var src = null; +try { +if (source != null) { +if (Clazz.instanceOf (source, jalview.appletgui.AlignViewport) && (source).applet.currentAlignFrame.viewport === source) { +src = (source).applet.currentAlignFrame; +}}this.executeJavascriptFunction (this._listener, Clazz.newArray (-1, [src, seq.getDisplayId (false), "" + (1 + this.i), "" + seq.findPosition (this.i)])); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("JalviewLite javascript error: Couldn't send mouseOver with handler '" + this._listener + "'"); +if (Clazz.instanceOf (ex, netscape.javascript.JSException)) { +System.err.println ("Javascript Exception: " + (ex).getMessage ()); +}ex.printStackTrace (); +} else { +throw ex; +} +} +}}, "jalview.datamodel.SequenceI,~N,jalview.structure.VamsasSource"); +Clazz.makeConstructor (c$, +function (applet, af, listener) { +Clazz.superConstructor (this, jalview.javascript.MouseOverListener, [applet]); +this._af = af; +this._listener = listener; +}, "jalview.bin.JalviewLite,jalview.appletgui.AlignFrame,~S"); +Clazz.overrideMethod (c$, "getAlignFrame", +function () { +return this._af; +}); +Clazz.overrideMethod (c$, "getListenerFunction", +function () { +return this._listener; +}); +}); diff --git a/bin/jalview/javascript/MouseOverStructureListener.js b/bin/jalview/javascript/MouseOverStructureListener.js index 12d1e2f..c897252 100644 --- a/bin/jalview/javascript/MouseOverStructureListener.js +++ b/bin/jalview/javascript/MouseOverStructureListener.js @@ -1,143 +1,143 @@ -Clazz.declarePackage ("jalview.javascript"); -Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.StructureListener"], "jalview.javascript.MouseOverStructureListener", ["jalview.api.AlignmentViewPanel", "jalview.appletgui.FeatureRenderer", "jalview.ext.jmol.JmolCommands", "jalview.structure.StructureSelectionManager", "java.net.URL", "java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this._listenerfn = null; -this.modelSet = null; -Clazz.instantialize (this, arguments); -}, jalview.javascript, "MouseOverStructureListener", jalview.javascript.JSFunctionExec, [jalview.javascript.JsCallBack, jalview.structure.StructureListener]); -Clazz.makeConstructor (c$, -function (jalviewLite, listener, modelList) { -Clazz.superConstructor (this, jalview.javascript.MouseOverStructureListener, [jalviewLite]); -this._listenerfn = listener; -this.modelSet = modelList; -if (this.modelSet != null) { -for (var i = 0; i < this.modelSet.length; i++) { -try { -if ( new java.net.URL (this.modelSet[i]).openConnection () != null) { -continue; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -} else { -throw x; -} -} -;try { -var db = this.jvlite.getDocumentBase ().toString (); -db = db.substring (0, db.lastIndexOf ("/")); -if ( new java.net.URL (db + "/" + this.modelSet[i]).openConnection () != null) { -this.modelSet[i] = db + "/" + this.modelSet[i]; -continue; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -} else { -throw x; -} -} -;try { -if ( new java.net.URL (this.jvlite.getCodeBase () + this.modelSet[i]).openConnection () != null) { -this.modelSet[i] = this.jvlite.getCodeBase () + this.modelSet[i]; -continue; -}} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -} else { -throw x; -} -} -;} -}}, "jalview.bin.JalviewLite,~S,~A"); -Clazz.overrideMethod (c$, "getPdbFile", -function () { -return this.modelSet; -}); -Clazz.defineMethod (c$, "mouseOverStructure", -function (atomIndex, strInfo) { -}, "~N,~S"); -Clazz.overrideMethod (c$, "highlightAtoms", -function (atoms) { -for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { -try { -this.executeJavascriptFunction (this._listenerfn, Clazz.newArray (-1, ["mouseover", "" + atom.getPdbFile (), "" + atom.getChain (), "" + (atom.getPdbResNum ()), "" + atom.getAtomIndex ()])); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Couldn't execute callback with " + this._listenerfn + " for atomSpec: " + atom); -ex.printStackTrace (); -} else { -throw ex; -} -} -} -}, "java.util.List"); -Clazz.overrideMethod (c$, "updateColours", -function (srce) { -var source = srce; -var ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.jvlite); -if (Clazz.instanceOf (source, jalview.api.AlignmentViewPanel)) { -var sequence = new Array (this.modelSet.length); -for (var m = 0; m < this.modelSet.length; m++) { -var sm = ssm.getMapping (this.modelSet[m]); -if (sm != null && sm.length > 0) { -sequence[m] = new Array (sm.length); -for (var i = 0; i < sm.length; i++) { -sequence[m][i] = sm[i].getSequence (); -} -} else { -sequence[m] = new Array (0); -}} -var sr = (source).getSequenceRenderer (); -var fr = (source).av.isShowSequenceFeatures () ? new jalview.appletgui.FeatureRenderer ((source).av) : null; -if (fr != null) { -(fr).transferSettings ((source).getFeatureRenderer ()); -};var ccomands = new java.util.ArrayList (); -var pdbfn = new java.util.ArrayList (); -var colcommands = jalview.ext.jmol.JmolCommands.getColourBySequenceCommand (ssm, this.modelSet, sequence, sr, fr, (source).getAlignment ()); -if (colcommands == null) { -return; -}var sz = 0; -for (var ccset, $ccset = 0, $$ccset = colcommands; $ccset < $$ccset.length && ((ccset = $$ccset[$ccset]) || true); $ccset++) { -sz += ccset.commands.length; -ccomands.add (ccset.commands); -pdbfn.add (ccset.mapping); -} -var mclass; -var mhandle; -var ccomandset = new Array (sz); -sz = 0; -for (var ccset, $ccset = ccomands.iterator (); $ccset.hasNext () && ((ccset = $ccset.next ()) || true);) { -System.arraycopy (ccset, 0, ccomandset, sz, ccset.length); -sz += ccset.length; -} -if (this.jvlite.isJsMessageSetChanged (mclass = "colourstruct", mhandle = (source).av.getViewId (), ccomandset)) { -this.jvlite.setJsMessageSet (mclass, mhandle, ccomandset); -var st = Clazz.newArray (-1, ["colourstruct", "" + (source).av.getViewId (), "" + ccomandset.length, this.jvlite.arrayToSeparatorList (pdbfn.toArray ( new Array (pdbfn.size ())))]); -try { -this.executeJavascriptFunction (true, this._listenerfn, st); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.err.println ("Couldn't execute callback with " + this._listenerfn + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] + "}"); -ex.printStackTrace (); -} else { -throw ex; -} -} -}}}, "~O"); -Clazz.overrideMethod (c$, "getAlignFrame", -function () { -return null; -}); -Clazz.overrideMethod (c$, "getListenerFunction", -function () { -return this._listenerfn; -}); -Clazz.defineMethod (c$, "finalise", -function () { -this.jvlite = null; -Clazz.superCall (this, jalview.javascript.MouseOverStructureListener, "finalize", []); -}); -Clazz.overrideMethod (c$, "releaseReferences", -function (svl) { -}, "~O"); -Clazz.overrideMethod (c$, "isListeningFor", -function (seq) { -return true; -}, "jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.javascript"); +Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.StructureListener"], "jalview.javascript.MouseOverStructureListener", ["jalview.api.AlignmentViewPanel", "jalview.appletgui.FeatureRenderer", "jalview.ext.jmol.JmolCommands", "jalview.structure.StructureSelectionManager", "java.net.URL", "java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this._listenerfn = null; +this.modelSet = null; +Clazz.instantialize (this, arguments); +}, jalview.javascript, "MouseOverStructureListener", jalview.javascript.JSFunctionExec, [jalview.javascript.JsCallBack, jalview.structure.StructureListener]); +Clazz.makeConstructor (c$, +function (jalviewLite, listener, modelList) { +Clazz.superConstructor (this, jalview.javascript.MouseOverStructureListener, [jalviewLite]); +this._listenerfn = listener; +this.modelSet = modelList; +if (this.modelSet != null) { +for (var i = 0; i < this.modelSet.length; i++) { +try { +if ( new java.net.URL (this.modelSet[i]).openConnection () != null) { +continue; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +} else { +throw x; +} +} +;try { +var db = this.jvlite.getDocumentBase ().toString (); +db = db.substring (0, db.lastIndexOf ("/")); +if ( new java.net.URL (db + "/" + this.modelSet[i]).openConnection () != null) { +this.modelSet[i] = db + "/" + this.modelSet[i]; +continue; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +} else { +throw x; +} +} +;try { +if ( new java.net.URL (this.jvlite.getCodeBase () + this.modelSet[i]).openConnection () != null) { +this.modelSet[i] = this.jvlite.getCodeBase () + this.modelSet[i]; +continue; +}} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +} else { +throw x; +} +} +;} +}}, "jalview.bin.JalviewLite,~S,~A"); +Clazz.overrideMethod (c$, "getPdbFile", +function () { +return this.modelSet; +}); +Clazz.defineMethod (c$, "mouseOverStructure", +function (atomIndex, strInfo) { +}, "~N,~S"); +Clazz.overrideMethod (c$, "highlightAtoms", +function (atoms) { +for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { +try { +this.executeJavascriptFunction (this._listenerfn, Clazz.newArray (-1, ["mouseover", "" + atom.getPdbFile (), "" + atom.getChain (), "" + (atom.getPdbResNum ()), "" + atom.getAtomIndex ()])); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Couldn't execute callback with " + this._listenerfn + " for atomSpec: " + atom); +ex.printStackTrace (); +} else { +throw ex; +} +} +} +}, "java.util.List"); +Clazz.overrideMethod (c$, "updateColours", +function (srce) { +var source = srce; +var ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.jvlite); +if (Clazz.instanceOf (source, jalview.api.AlignmentViewPanel)) { +var sequence = new Array (this.modelSet.length); +for (var m = 0; m < this.modelSet.length; m++) { +var sm = ssm.getMapping (this.modelSet[m]); +if (sm != null && sm.length > 0) { +sequence[m] = new Array (sm.length); +for (var i = 0; i < sm.length; i++) { +sequence[m][i] = sm[i].getSequence (); +} +} else { +sequence[m] = new Array (0); +}} +var sr = (source).getSequenceRenderer (); +var fr = (source).av.isShowSequenceFeatures () ? new jalview.appletgui.FeatureRenderer ((source).av) : null; +if (fr != null) { +(fr).transferSettings ((source).getFeatureRenderer ()); +};var ccomands = new java.util.ArrayList (); +var pdbfn = new java.util.ArrayList (); +var colcommands = jalview.ext.jmol.JmolCommands.getColourBySequenceCommand (ssm, this.modelSet, sequence, sr, fr, (source).getAlignment ()); +if (colcommands == null) { +return; +}var sz = 0; +for (var ccset, $ccset = 0, $$ccset = colcommands; $ccset < $$ccset.length && ((ccset = $$ccset[$ccset]) || true); $ccset++) { +sz += ccset.commands.length; +ccomands.add (ccset.commands); +pdbfn.add (ccset.mapping); +} +var mclass; +var mhandle; +var ccomandset = new Array (sz); +sz = 0; +for (var ccset, $ccset = ccomands.iterator (); $ccset.hasNext () && ((ccset = $ccset.next ()) || true);) { +System.arraycopy (ccset, 0, ccomandset, sz, ccset.length); +sz += ccset.length; +} +if (this.jvlite.isJsMessageSetChanged (mclass = "colourstruct", mhandle = (source).av.getViewId (), ccomandset)) { +this.jvlite.setJsMessageSet (mclass, mhandle, ccomandset); +var st = Clazz.newArray (-1, ["colourstruct", "" + (source).av.getViewId (), "" + ccomandset.length, this.jvlite.arrayToSeparatorList (pdbfn.toArray ( new Array (pdbfn.size ())))]); +try { +this.executeJavascriptFunction (true, this._listenerfn, st); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.err.println ("Couldn't execute callback with " + this._listenerfn + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] + "}"); +ex.printStackTrace (); +} else { +throw ex; +} +} +}}}, "~O"); +Clazz.overrideMethod (c$, "getAlignFrame", +function () { +return null; +}); +Clazz.overrideMethod (c$, "getListenerFunction", +function () { +return this._listenerfn; +}); +Clazz.defineMethod (c$, "finalise", +function () { +this.jvlite = null; +Clazz.superCall (this, jalview.javascript.MouseOverStructureListener, "finalize", []); +}); +Clazz.overrideMethod (c$, "releaseReferences", +function (svl) { +}, "~O"); +Clazz.overrideMethod (c$, "isListeningFor", +function (seq) { +return true; +}, "jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/jsdev/Constants.js b/bin/jalview/jsdev/Constants.js index 9963449..64acea4 100644 --- a/bin/jalview/jsdev/Constants.js +++ b/bin/jalview/jsdev/Constants.js @@ -1,13 +1,13 @@ -Clazz.declarePackage ("jalview.jsdev"); -c$ = Clazz.declareType (jalview.jsdev, "Constants"); -Clazz.defineStatics (c$, -"TCOFFEE_SCORE", "TCoffeeScore", -"Phylip_FILE", 1, -"Phylip_FILE_EXT", "phy", -"Phylip_FILE_DESC", "PHYLIP", -"JSON_FILE", 2, -"JSON_FILE_EXT", "json", -"JSON_FILE_DESC", "JSON", -"Html_FILE", 3, -"Html_FILE_EXT", "html", -"Html_FILE_DESC", "HTML"); +Clazz.declarePackage ("jalview.jsdev"); +c$ = Clazz.declareType (jalview.jsdev, "Constants"); +Clazz.defineStatics (c$, +"TCOFFEE_SCORE", "TCoffeeScore", +"Phylip_FILE", 1, +"Phylip_FILE_EXT", "phy", +"Phylip_FILE_DESC", "PHYLIP", +"JSON_FILE", 2, +"JSON_FILE_EXT", "json", +"JSON_FILE_DESC", "JSON", +"Html_FILE", 3, +"Html_FILE_EXT", "html", +"Html_FILE_DESC", "HTML"); diff --git a/bin/jalview/jsdev/GenericFileAdapter.js b/bin/jalview/jsdev/GenericFileAdapter.js index 60cf065..9144c4b 100644 --- a/bin/jalview/jsdev/GenericFileAdapter.js +++ b/bin/jalview/jsdev/GenericFileAdapter.js @@ -1,85 +1,85 @@ -Clazz.declarePackage ("jalview.jsdev"); -Clazz.load (["jalview.io.AlignFile"], "jalview.jsdev.GenericFileAdapter", ["jalview.datamodel.AlignmentI", "jalview.io.FileParse", "java.io.BufferedReader", "$.InputStreamReader", "java.net.URL"], function () { -c$ = Clazz.declareType (jalview.jsdev, "GenericFileAdapter", jalview.io.AlignFile); -c$.getFile = Clazz.defineMethod (c$, "getFile", -function (fileType, params) { -var cl = null; -try { -cl = Class.forName ("jalview.io." + fileType); -} catch (e) { -if (Clazz.exceptionOf (e, ClassNotFoundException)) { -System.err.println ("did not find file jalview.io." + fileType); -return null; -} else { -throw e; -} -} -var m; -var ex = null; -try { -switch (params.length) { -case 0: -return cl.newInstance (); -case 1: -m = (Clazz.instanceOf (params[0], jalview.io.FileParse) ? cl.getConstructor ([jalview.io.FileParse]) : cl.getConstructor ([jalview.datamodel.AlignmentI])); -break; -case 2: -m = cl.getConstructor ([String, String]); -break; -default: -return null; -} -return m.newInstance (params); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, InstantiationException)) { -var e = e$$; -{ -ex = e; -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var e = e$$; -{ -ex = e; -} -} else if (Clazz.exceptionOf (e$$, NoSuchMethodException)) { -var e = e$$; -{ -ex = e; -} -} else if (Clazz.exceptionOf (e$$, SecurityException)) { -var e = e$$; -{ -ex = e; -} -} else if (Clazz.exceptionOf (e$$, IllegalArgumentException)) { -var e = e$$; -{ -ex = e; -} -} else if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var e = e$$; -{ -ex = e; -} -} else { -throw e$$; -} -} -if (ex != null) { -System.err.println ("Error in GenericFileAdapter: " + ex); -{ -alert(ex) -}}return null; -}, "~S,~A"); -c$.isJS = Clazz.defineMethod (c$, "isJS", -function () { -{ -return true; -}}); -c$.getReader = Clazz.defineMethod (c$, "getReader", -function (fileName, forceURL) { -if (!forceURL && !jalview.jsdev.GenericFileAdapter.isJS ()) return new java.io.BufferedReader ( new java.io.FileReader (fileName)); -if (fileName.indexOf ("//") < 0) fileName = "file://" + fileName; -return new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.net.URL (fileName).openStream ())); -}, "~S,~B"); -}); +Clazz.declarePackage ("jalview.jsdev"); +Clazz.load (["jalview.io.AlignFile"], "jalview.jsdev.GenericFileAdapter", ["jalview.datamodel.AlignmentI", "jalview.io.FileParse", "java.io.BufferedReader", "$.InputStreamReader", "java.net.URL"], function () { +c$ = Clazz.declareType (jalview.jsdev, "GenericFileAdapter", jalview.io.AlignFile); +c$.getFile = Clazz.defineMethod (c$, "getFile", +function (fileType, params) { +var cl = null; +try { +cl = Class.forName ("jalview.io." + fileType); +} catch (e) { +if (Clazz.exceptionOf (e, ClassNotFoundException)) { +System.err.println ("did not find file jalview.io." + fileType); +return null; +} else { +throw e; +} +} +var m; +var ex = null; +try { +switch (params.length) { +case 0: +return cl.newInstance (); +case 1: +m = (Clazz.instanceOf (params[0], jalview.io.FileParse) ? cl.getConstructor ([jalview.io.FileParse]) : cl.getConstructor ([jalview.datamodel.AlignmentI])); +break; +case 2: +m = cl.getConstructor ([String, String]); +break; +default: +return null; +} +return m.newInstance (params); +} catch (e$$) { +if (Clazz.exceptionOf (e$$, InstantiationException)) { +var e = e$$; +{ +ex = e; +} +} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { +var e = e$$; +{ +ex = e; +} +} else if (Clazz.exceptionOf (e$$, NoSuchMethodException)) { +var e = e$$; +{ +ex = e; +} +} else if (Clazz.exceptionOf (e$$, SecurityException)) { +var e = e$$; +{ +ex = e; +} +} else if (Clazz.exceptionOf (e$$, IllegalArgumentException)) { +var e = e$$; +{ +ex = e; +} +} else if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { +var e = e$$; +{ +ex = e; +} +} else { +throw e$$; +} +} +if (ex != null) { +System.err.println ("Error in GenericFileAdapter: " + ex); +{ +alert(ex) +}}return null; +}, "~S,~A"); +c$.isJS = Clazz.defineMethod (c$, "isJS", +function () { +{ +return true; +}}); +c$.getReader = Clazz.defineMethod (c$, "getReader", +function (fileName, forceURL) { +if (!forceURL && !jalview.jsdev.GenericFileAdapter.isJS ()) return new java.io.BufferedReader ( new java.io.FileReader (fileName)); +if (fileName.indexOf ("//") < 0) fileName = "file://" + fileName; +return new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.net.URL (fileName).openStream ())); +}, "~S,~B"); +}); diff --git a/bin/jalview/jsdev/JSRegex.js b/bin/jalview/jsdev/JSRegex.js index 4dcc13e..08e9c64 100644 --- a/bin/jalview/jsdev/JSRegex.js +++ b/bin/jalview/jsdev/JSRegex.js @@ -1,55 +1,55 @@ -Clazz.declarePackage ("jalview.jsdev"); -Clazz.load (["jalview.jsdev.api.RegExpInterface"], "jalview.jsdev.JSRegex", null, function () { -c$ = Clazz.declareType (jalview.jsdev, "JSRegex", null, jalview.jsdev.api.RegExpInterface); -Clazz.overrideMethod (c$, "charsMatched", -function () { -return 0; -}); -Clazz.overrideMethod (c$, "left", -function () { -return null; -}); -Clazz.overrideMethod (c$, "matchedFrom", -function () { -return 0; -}); -Clazz.overrideMethod (c$, "matchedFromI", -function (pos) { -return 0; -}, "~N"); -Clazz.overrideMethod (c$, "matchedTo", -function () { -return 0; -}); -Clazz.overrideMethod (c$, "matchedToI", -function (pos) { -return 0; -}, "~N"); -Clazz.overrideMethod (c$, "numSubs", -function () { -return 0; -}); -Clazz.overrideMethod (c$, "replaceAll", -function (string) { -return null; -}, "~S"); -Clazz.overrideMethod (c$, "search", -function (str) { -return false; -}, "~S"); -Clazz.overrideMethod (c$, "searchFrom", -function (string, rematchat) { -return false; -}, "~S,~N"); -Clazz.overrideMethod (c$, "setIgnoreCase", -function (b) { -}, "~B"); -Clazz.overrideMethod (c$, "stringMatched", -function () { -return null; -}); -Clazz.overrideMethod (c$, "stringMatchedI", -function (i) { -return null; -}, "~N"); -}); +Clazz.declarePackage ("jalview.jsdev"); +Clazz.load (["jalview.jsdev.api.RegExpInterface"], "jalview.jsdev.JSRegex", null, function () { +c$ = Clazz.declareType (jalview.jsdev, "JSRegex", null, jalview.jsdev.api.RegExpInterface); +Clazz.overrideMethod (c$, "charsMatched", +function () { +return 0; +}); +Clazz.overrideMethod (c$, "left", +function () { +return null; +}); +Clazz.overrideMethod (c$, "matchedFrom", +function () { +return 0; +}); +Clazz.overrideMethod (c$, "matchedFromI", +function (pos) { +return 0; +}, "~N"); +Clazz.overrideMethod (c$, "matchedTo", +function () { +return 0; +}); +Clazz.overrideMethod (c$, "matchedToI", +function (pos) { +return 0; +}, "~N"); +Clazz.overrideMethod (c$, "numSubs", +function () { +return 0; +}); +Clazz.overrideMethod (c$, "replaceAll", +function (string) { +return null; +}, "~S"); +Clazz.overrideMethod (c$, "search", +function (str) { +return false; +}, "~S"); +Clazz.overrideMethod (c$, "searchFrom", +function (string, rematchat) { +return false; +}, "~S,~N"); +Clazz.overrideMethod (c$, "setIgnoreCase", +function (b) { +}, "~B"); +Clazz.overrideMethod (c$, "stringMatched", +function () { +return null; +}); +Clazz.overrideMethod (c$, "stringMatchedI", +function (i) { +return null; +}, "~N"); +}); diff --git a/bin/jalview/jsdev/JavaScriptRegExp.js b/bin/jalview/jsdev/JavaScriptRegExp.js index 735a4b6..5d67e59 100644 --- a/bin/jalview/jsdev/JavaScriptRegExp.js +++ b/bin/jalview/jsdev/JavaScriptRegExp.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.jsdev"); -Clazz.declareInterface (jalview.jsdev, "JavaScriptRegExp"); +Clazz.declarePackage ("jalview.jsdev"); +Clazz.declareInterface (jalview.jsdev, "JavaScriptRegExp"); diff --git a/bin/jalview/jsdev/RegExp.js b/bin/jalview/jsdev/RegExp.js index ffb883f..8b2e026 100644 --- a/bin/jalview/jsdev/RegExp.js +++ b/bin/jalview/jsdev/RegExp.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("jalview.jsdev"); -Clazz.load (null, "jalview.jsdev.RegExp", ["com.stevesoft.pat.Regex"], function () { -c$ = Clazz.decorateAsClass (function () { -this.rg = null; -Clazz.instantialize (this, arguments); -}, jalview.jsdev, "RegExp"); -c$.newRegex = Clazz.defineMethod (c$, "newRegex", -function (params) { -return new com.stevesoft.pat.Regex (params.length < 1 ? null : params[0], params.length < 2 ? "" : params[1]); -}, "~A"); -c$.perlCode = Clazz.defineMethod (c$, "perlCode", -function (s) { -return com.stevesoft.pat.Regex.perlCode (s); -}, "~S"); -}); +Clazz.declarePackage ("jalview.jsdev"); +Clazz.load (null, "jalview.jsdev.RegExp", ["com.stevesoft.pat.Regex"], function () { +c$ = Clazz.decorateAsClass (function () { +this.rg = null; +Clazz.instantialize (this, arguments); +}, jalview.jsdev, "RegExp"); +c$.newRegex = Clazz.defineMethod (c$, "newRegex", +function (params) { +return new com.stevesoft.pat.Regex (params.length < 1 ? null : params[0], params.length < 2 ? "" : params[1]); +}, "~A"); +c$.perlCode = Clazz.defineMethod (c$, "perlCode", +function (s) { +return com.stevesoft.pat.Regex.perlCode (s); +}, "~S"); +}); diff --git a/bin/jalview/jsdev/api/RegExpInterface.js b/bin/jalview/jsdev/api/RegExpInterface.js index 5dfe0cd..48bb568 100644 --- a/bin/jalview/jsdev/api/RegExpInterface.js +++ b/bin/jalview/jsdev/api/RegExpInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.jsdev.api"); -Clazz.declareInterface (jalview.jsdev.api, "RegExpInterface"); +Clazz.declarePackage ("jalview.jsdev.api"); +Clazz.declareInterface (jalview.jsdev.api, "RegExpInterface"); diff --git a/bin/jalview/jsdev/api/VarnaRNA.js b/bin/jalview/jsdev/api/VarnaRNA.js index c2ec8a3..1fa65f5 100644 --- a/bin/jalview/jsdev/api/VarnaRNA.js +++ b/bin/jalview/jsdev/api/VarnaRNA.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.jsdev.api"); -Clazz.declareInterface (jalview.jsdev.api, "VarnaRNA"); +Clazz.declarePackage ("jalview.jsdev.api"); +Clazz.declareInterface (jalview.jsdev.api, "VarnaRNA"); diff --git a/bin/jalview/math/AlignmentDimension.js b/bin/jalview/math/AlignmentDimension.js index 178fe61..2a23983 100644 --- a/bin/jalview/math/AlignmentDimension.js +++ b/bin/jalview/math/AlignmentDimension.js @@ -1,27 +1,27 @@ -Clazz.declarePackage ("jalview.math"); -c$ = Clazz.decorateAsClass (function () { -this.width = 0; -this.height = 0; -Clazz.instantialize (this, arguments); -}, jalview.math, "AlignmentDimension"); -Clazz.makeConstructor (c$, -function (width, height) { -this.width = width; -this.height = height; -}, "~N,~N"); -Clazz.defineMethod (c$, "getWidth", -function () { -return this.width; -}); -Clazz.defineMethod (c$, "setWidth", -function (width) { -this.width = width; -}, "~N"); -Clazz.defineMethod (c$, "getHeight", -function () { -return this.height; -}); -Clazz.defineMethod (c$, "setHeight", -function (height) { -this.height = height; -}, "~N"); +Clazz.declarePackage ("jalview.math"); +c$ = Clazz.decorateAsClass (function () { +this.width = 0; +this.height = 0; +Clazz.instantialize (this, arguments); +}, jalview.math, "AlignmentDimension"); +Clazz.makeConstructor (c$, +function (width, height) { +this.width = width; +this.height = height; +}, "~N,~N"); +Clazz.defineMethod (c$, "getWidth", +function () { +return this.width; +}); +Clazz.defineMethod (c$, "setWidth", +function (width) { +this.width = width; +}, "~N"); +Clazz.defineMethod (c$, "getHeight", +function () { +return this.height; +}); +Clazz.defineMethod (c$, "setHeight", +function (height) { +this.height = height; +}, "~N"); diff --git a/bin/jalview/math/Matrix.class b/bin/jalview/math/Matrix.class index ff18c28..3bb0722 100644 Binary files a/bin/jalview/math/Matrix.class and b/bin/jalview/math/Matrix.class differ diff --git a/bin/jalview/math/Matrix.js b/bin/jalview/math/Matrix.js index e260277..22cb59d 100644 --- a/bin/jalview/math/Matrix.js +++ b/bin/jalview/math/Matrix.js @@ -1,423 +1,423 @@ -Clazz.declarePackage ("jalview.math"); -Clazz.load (null, "jalview.math.Matrix", ["jalview.util.Format", "$.MessageManager", "java.lang.Exception"], function () { -c$ = Clazz.decorateAsClass (function () { -this.value = null; -this.rows = 0; -this.cols = 0; -this.d = null; -this.e = null; -this.maxIter = 45; -Clazz.instantialize (this, arguments); -}, jalview.math, "Matrix"); -Clazz.makeConstructor (c$, -function (value, rows, cols) { -this.rows = rows; -this.cols = cols; -this.value = value; -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "transpose", -function () { -var out = Clazz.newDoubleArray (this.cols, this.rows, 0); -for (var i = 0; i < this.cols; i++) { -for (var j = 0; j < this.rows; j++) { -out[i][j] = this.value[j][i]; -} -} -return new jalview.math.Matrix (out, this.cols, this.rows); -}); -Clazz.defineMethod (c$, "print", -function (ps) { -for (var i = 0; i < this.rows; i++) { -for (var j = 0; j < this.cols; j++) { -jalview.util.Format.printDouble (ps, "%8.2f", this.value[i][j]); -} -ps.println (); -} -}, "java.io.PrintStream"); -Clazz.defineMethod (c$, "preMultiply", -function ($in) { -var tmp = Clazz.newDoubleArray ($in.rows, this.cols, 0); -for (var i = 0; i < $in.rows; i++) { -for (var j = 0; j < this.cols; j++) { -tmp[i][j] = 0.0; -for (var k = 0; k < $in.cols; k++) { -tmp[i][j] += ($in.value[i][k] * this.value[k][j]); -} -} -} -return new jalview.math.Matrix (tmp, $in.rows, this.cols); -}, "jalview.math.Matrix"); -Clazz.defineMethod (c$, "vectorPostMultiply", -function ($in) { -var out = Clazz.newDoubleArray ($in.length, 0); -for (var i = 0; i < $in.length; i++) { -out[i] = 0.0; -for (var k = 0; k < $in.length; k++) { -out[i] += (this.value[i][k] * $in[k]); -} -} -return out; -}, "~A"); -Clazz.defineMethod (c$, "postMultiply", -function ($in) { -var out = Clazz.newDoubleArray (this.rows, $in.cols, 0); -for (var i = 0; i < this.rows; i++) { -for (var j = 0; j < $in.cols; j++) { -out[i][j] = 0.0; -for (var k = 0; k < this.rows; k++) { -out[i][j] = out[i][j] + (this.value[i][k] * $in.value[k][j]); -} -} -} -return new jalview.math.Matrix (out, this.cols, $in.rows); -}, "jalview.math.Matrix"); -Clazz.defineMethod (c$, "copy", -function () { -var newmat = Clazz.newDoubleArray (this.rows, this.cols, 0); -for (var i = 0; i < this.rows; i++) { -for (var j = 0; j < this.cols; j++) { -newmat[i][j] = this.value[i][j]; -} -} -return new jalview.math.Matrix (newmat, this.rows, this.cols); -}); -Clazz.defineMethod (c$, "tred", -function () { -var n = this.rows; -var l; -var k; -var j; -var i; -var scale; -var hh; -var h; -var g; -var f; -this.d = Clazz.newDoubleArray (this.rows, 0); -this.e = Clazz.newDoubleArray (this.rows, 0); -for (i = n; i >= 2; i--) { -l = i - 1; -h = 0.0; -scale = 0.0; -if (l > 1) { -for (k = 1; k <= l; k++) { -scale += Math.abs (this.value[i - 1][k - 1]); -} -if (scale == 0.0) { -this.e[i - 1] = this.value[i - 1][l - 1]; -} else { -for (k = 1; k <= l; k++) { -this.value[i - 1][k - 1] /= scale; -h += (this.value[i - 1][k - 1] * this.value[i - 1][k - 1]); -} -f = this.value[i - 1][l - 1]; -if (f > 0) { -g = -1.0 * Math.sqrt (h); -} else { -g = Math.sqrt (h); -}this.e[i - 1] = scale * g; -h -= (f * g); -this.value[i - 1][l - 1] = f - g; -f = 0.0; -for (j = 1; j <= l; j++) { -this.value[j - 1][i - 1] = this.value[i - 1][j - 1] / h; -g = 0.0; -for (k = 1; k <= j; k++) { -g += (this.value[j - 1][k - 1] * this.value[i - 1][k - 1]); -} -for (k = j + 1; k <= l; k++) { -g += (this.value[k - 1][j - 1] * this.value[i - 1][k - 1]); -} -this.e[j - 1] = g / h; -f += (this.e[j - 1] * this.value[i - 1][j - 1]); -} -hh = f / (h + h); -for (j = 1; j <= l; j++) { -f = this.value[i - 1][j - 1]; -g = this.e[j - 1] - (hh * f); -this.e[j - 1] = g; -for (k = 1; k <= j; k++) { -this.value[j - 1][k - 1] -= ((f * this.e[k - 1]) + (g * this.value[i - 1][k - 1])); -} -} -}} else { -this.e[i - 1] = this.value[i - 1][l - 1]; -}this.d[i - 1] = h; -} -this.d[0] = 0.0; -this.e[0] = 0.0; -for (i = 1; i <= n; i++) { -l = i - 1; -if (this.d[i - 1] != 0.0) { -for (j = 1; j <= l; j++) { -g = 0.0; -for (k = 1; k <= l; k++) { -g += (this.value[i - 1][k - 1] * this.value[k - 1][j - 1]); -} -for (k = 1; k <= l; k++) { -this.value[k - 1][j - 1] -= (g * this.value[k - 1][i - 1]); -} -} -}this.d[i - 1] = this.value[i - 1][i - 1]; -this.value[i - 1][i - 1] = 1.0; -for (j = 1; j <= l; j++) { -this.value[j - 1][i - 1] = 0.0; -this.value[i - 1][j - 1] = 0.0; -} -} -}); -Clazz.defineMethod (c$, "tqli", -function () { -var n = this.rows; -var m; -var l; -var iter; -var i; -var k; -var s; -var r; -var p; -;var g; -var f; -var dd; -var c; -var b; -for (i = 2; i <= n; i++) { -this.e[i - 2] = this.e[i - 1]; -} -this.e[n - 1] = 0.0; -for (l = 1; l <= n; l++) { -iter = 0; -do { -for (m = l; m <= (n - 1); m++) { -dd = Math.abs (this.d[m - 1]) + Math.abs (this.d[m]); -if ((Math.abs (this.e[m - 1]) + dd) == dd) { -break; -}} -if (m != l) { -iter++; -if (iter == this.maxIter) { -throw new Exception (jalview.util.MessageManager.formatMessage ("exception.matrix_too_many_iteration", Clazz.newArray (-1, ["tqli", Integer.$valueOf (this.maxIter).toString ()]))); -} else { -}g = (this.d[l] - this.d[l - 1]) / (2.0 * this.e[l - 1]); -r = Math.sqrt ((g * g) + 1.0); -g = this.d[m - 1] - this.d[l - 1] + (this.e[l - 1] / (g + this.sign (r, g))); -c = 1.0; -s = c; -p = 0.0; -for (i = m - 1; i >= l; i--) { -f = s * this.e[i - 1]; -b = c * this.e[i - 1]; -if (Math.abs (f) >= Math.abs (g)) { -c = g / f; -r = Math.sqrt ((c * c) + 1.0); -this.e[i] = f * r; -s = 1.0 / r; -c *= s; -} else { -s = f / g; -r = Math.sqrt ((s * s) + 1.0); -this.e[i] = g * r; -c = 1.0 / r; -s *= c; -}g = this.d[i] - p; -r = ((this.d[i - 1] - g) * s) + (2.0 * c * b); -p = s * r; -this.d[i] = g + p; -g = (c * r) - b; -for (k = 1; k <= n; k++) { -f = this.value[k - 1][i]; -this.value[k - 1][i] = (s * this.value[k - 1][i - 1]) + (c * f); -this.value[k - 1][i - 1] = (c * this.value[k - 1][i - 1]) - (s * f); -} -} -this.d[l - 1] = this.d[l - 1] - p; -this.e[l - 1] = g; -this.e[m - 1] = 0.0; -}} while (m != l); -} -}); -Clazz.defineMethod (c$, "tred2", -function () { -var n = this.rows; -var l; -var k; -var j; -var i; -var scale; -var hh; -var h; -var g; -var f; -this.d = Clazz.newDoubleArray (this.rows, 0); -this.e = Clazz.newDoubleArray (this.rows, 0); -for (i = n - 1; i >= 1; i--) { -l = i - 1; -h = 0.0; -scale = 0.0; -if (l > 0) { -for (k = 0; k < l; k++) { -scale += Math.abs (this.value[i][k]); -} -if (scale == 0.0) { -this.e[i] = this.value[i][l]; -} else { -for (k = 0; k < l; k++) { -this.value[i][k] /= scale; -h += (this.value[i][k] * this.value[i][k]); -} -f = this.value[i][l]; -if (f > 0) { -g = -1.0 * Math.sqrt (h); -} else { -g = Math.sqrt (h); -}this.e[i] = scale * g; -h -= (f * g); -this.value[i][l] = f - g; -f = 0.0; -for (j = 0; j < l; j++) { -this.value[j][i] = this.value[i][j] / h; -g = 0.0; -for (k = 0; k < j; k++) { -g += (this.value[j][k] * this.value[i][k]); -} -for (k = j; k < l; k++) { -g += (this.value[k][j] * this.value[i][k]); -} -this.e[j] = g / h; -f += (this.e[j] * this.value[i][j]); -} -hh = f / (h + h); -for (j = 0; j < l; j++) { -f = this.value[i][j]; -g = this.e[j] - (hh * f); -this.e[j] = g; -for (k = 0; k < j; k++) { -this.value[j][k] -= ((f * this.e[k]) + (g * this.value[i][k])); -} -} -}} else { -this.e[i] = this.value[i][l]; -}this.d[i] = h; -} -this.d[0] = 0.0; -this.e[0] = 0.0; -for (i = 0; i < n; i++) { -l = i - 1; -if (this.d[i] != 0.0) { -for (j = 0; j < l; j++) { -g = 0.0; -for (k = 0; k < l; k++) { -g += (this.value[i][k] * this.value[k][j]); -} -for (k = 0; k < l; k++) { -this.value[k][j] -= (g * this.value[k][i]); -} -} -}this.d[i] = this.value[i][i]; -this.value[i][i] = 1.0; -for (j = 0; j < l; j++) { -this.value[j][i] = 0.0; -this.value[i][j] = 0.0; -} -} -}); -Clazz.defineMethod (c$, "tqli2", -function () { -var n = this.rows; -var m; -var l; -var iter; -var i; -var k; -var s; -var r; -var p; -;var g; -var f; -var dd; -var c; -var b; -for (i = 2; i <= n; i++) { -this.e[i - 2] = this.e[i - 1]; -} -this.e[n - 1] = 0.0; -for (l = 1; l <= n; l++) { -iter = 0; -do { -for (m = l; m <= (n - 1); m++) { -dd = Math.abs (this.d[m - 1]) + Math.abs (this.d[m]); -if ((Math.abs (this.e[m - 1]) + dd) == dd) { -break; -}} -if (m != l) { -iter++; -if (iter == this.maxIter) { -throw new Exception (jalview.util.MessageManager.formatMessage ("exception.matrix_too_many_iteration", Clazz.newArray (-1, ["tqli2", Integer.$valueOf (this.maxIter).toString ()]))); -} else { -}g = (this.d[l] - this.d[l - 1]) / (2.0 * this.e[l - 1]); -r = Math.sqrt ((g * g) + 1.0); -g = this.d[m - 1] - this.d[l - 1] + (this.e[l - 1] / (g + this.sign (r, g))); -c = 1.0; -s = c; -p = 0.0; -for (i = m - 1; i >= l; i--) { -f = s * this.e[i - 1]; -b = c * this.e[i - 1]; -if (Math.abs (f) >= Math.abs (g)) { -c = g / f; -r = Math.sqrt ((c * c) + 1.0); -this.e[i] = f * r; -s = 1.0 / r; -c *= s; -} else { -s = f / g; -r = Math.sqrt ((s * s) + 1.0); -this.e[i] = g * r; -c = 1.0 / r; -s *= c; -}g = this.d[i] - p; -r = ((this.d[i - 1] - g) * s) + (2.0 * c * b); -p = s * r; -this.d[i] = g + p; -g = (c * r) - b; -for (k = 1; k <= n; k++) { -f = this.value[k - 1][i]; -this.value[k - 1][i] = (s * this.value[k - 1][i - 1]) + (c * f); -this.value[k - 1][i - 1] = (c * this.value[k - 1][i - 1]) - (s * f); -} -} -this.d[l - 1] = this.d[l - 1] - p; -this.e[l - 1] = g; -this.e[m - 1] = 0.0; -}} while (m != l); -} -}); -Clazz.defineMethod (c$, "sign", -function (a, b) { -if (b < 0) { -return -Math.abs (a); -} else { -return Math.abs (a); -}}, "~N,~N"); -Clazz.defineMethod (c$, "getColumn", -function (n) { -var out = Clazz.newDoubleArray (this.rows, 0); -for (var i = 0; i < this.rows; i++) { -out[i] = this.value[i][n]; -} -return out; -}, "~N"); -Clazz.defineMethod (c$, "printD", -function (ps) { -for (var j = 0; j < this.rows; j++) { -jalview.util.Format.printDouble (ps, "%15.4e", this.d[j]); -} -}, "java.io.PrintStream"); -Clazz.defineMethod (c$, "printE", -function (ps) { -for (var j = 0; j < this.rows; j++) { -jalview.util.Format.printDouble (ps, "%15.4e", this.e[j]); -} -}, "java.io.PrintStream"); -}); +Clazz.declarePackage ("jalview.math"); +Clazz.load (null, "jalview.math.Matrix", ["jalview.util.Format", "$.MessageManager", "java.lang.Exception"], function () { +c$ = Clazz.decorateAsClass (function () { +this.value = null; +this.rows = 0; +this.cols = 0; +this.d = null; +this.e = null; +this.maxIter = 45; +Clazz.instantialize (this, arguments); +}, jalview.math, "Matrix"); +Clazz.makeConstructor (c$, +function (value, rows, cols) { +this.rows = rows; +this.cols = cols; +this.value = value; +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "transpose", +function () { +var out = Clazz.newDoubleArray (this.cols, this.rows, 0); +for (var i = 0; i < this.cols; i++) { +for (var j = 0; j < this.rows; j++) { +out[i][j] = this.value[j][i]; +} +} +return new jalview.math.Matrix (out, this.cols, this.rows); +}); +Clazz.defineMethod (c$, "print", +function (ps) { +for (var i = 0; i < this.rows; i++) { +for (var j = 0; j < this.cols; j++) { +jalview.util.Format.printDouble (ps, "%8.2f", this.value[i][j]); +} +ps.println (); +} +}, "java.io.PrintStream"); +Clazz.defineMethod (c$, "preMultiply", +function ($in) { +var tmp = Clazz.newDoubleArray ($in.rows, this.cols, 0); +for (var i = 0; i < $in.rows; i++) { +for (var j = 0; j < this.cols; j++) { +tmp[i][j] = 0.0; +for (var k = 0; k < $in.cols; k++) { +tmp[i][j] += ($in.value[i][k] * this.value[k][j]); +} +} +} +return new jalview.math.Matrix (tmp, $in.rows, this.cols); +}, "jalview.math.Matrix"); +Clazz.defineMethod (c$, "vectorPostMultiply", +function ($in) { +var out = Clazz.newDoubleArray ($in.length, 0); +for (var i = 0; i < $in.length; i++) { +out[i] = 0.0; +for (var k = 0; k < $in.length; k++) { +out[i] += (this.value[i][k] * $in[k]); +} +} +return out; +}, "~A"); +Clazz.defineMethod (c$, "postMultiply", +function ($in) { +var out = Clazz.newDoubleArray (this.rows, $in.cols, 0); +for (var i = 0; i < this.rows; i++) { +for (var j = 0; j < $in.cols; j++) { +out[i][j] = 0.0; +for (var k = 0; k < this.rows; k++) { +out[i][j] = out[i][j] + (this.value[i][k] * $in.value[k][j]); +} +} +} +return new jalview.math.Matrix (out, this.cols, $in.rows); +}, "jalview.math.Matrix"); +Clazz.defineMethod (c$, "copy", +function () { +var newmat = Clazz.newDoubleArray (this.rows, this.cols, 0); +for (var i = 0; i < this.rows; i++) { +for (var j = 0; j < this.cols; j++) { +newmat[i][j] = this.value[i][j]; +} +} +return new jalview.math.Matrix (newmat, this.rows, this.cols); +}); +Clazz.defineMethod (c$, "tred", +function () { +var n = this.rows; +var l; +var k; +var j; +var i; +var scale; +var hh; +var h; +var g; +var f; +this.d = Clazz.newDoubleArray (this.rows, 0); +this.e = Clazz.newDoubleArray (this.rows, 0); +for (i = n; i >= 2; i--) { +l = i - 1; +h = 0.0; +scale = 0.0; +if (l > 1) { +for (k = 1; k <= l; k++) { +scale += Math.abs (this.value[i - 1][k - 1]); +} +if (scale == 0.0) { +this.e[i - 1] = this.value[i - 1][l - 1]; +} else { +for (k = 1; k <= l; k++) { +this.value[i - 1][k - 1] /= scale; +h += (this.value[i - 1][k - 1] * this.value[i - 1][k - 1]); +} +f = this.value[i - 1][l - 1]; +if (f > 0) { +g = -1.0 * Math.sqrt (h); +} else { +g = Math.sqrt (h); +}this.e[i - 1] = scale * g; +h -= (f * g); +this.value[i - 1][l - 1] = f - g; +f = 0.0; +for (j = 1; j <= l; j++) { +this.value[j - 1][i - 1] = this.value[i - 1][j - 1] / h; +g = 0.0; +for (k = 1; k <= j; k++) { +g += (this.value[j - 1][k - 1] * this.value[i - 1][k - 1]); +} +for (k = j + 1; k <= l; k++) { +g += (this.value[k - 1][j - 1] * this.value[i - 1][k - 1]); +} +this.e[j - 1] = g / h; +f += (this.e[j - 1] * this.value[i - 1][j - 1]); +} +hh = f / (h + h); +for (j = 1; j <= l; j++) { +f = this.value[i - 1][j - 1]; +g = this.e[j - 1] - (hh * f); +this.e[j - 1] = g; +for (k = 1; k <= j; k++) { +this.value[j - 1][k - 1] -= ((f * this.e[k - 1]) + (g * this.value[i - 1][k - 1])); +} +} +}} else { +this.e[i - 1] = this.value[i - 1][l - 1]; +}this.d[i - 1] = h; +} +this.d[0] = 0.0; +this.e[0] = 0.0; +for (i = 1; i <= n; i++) { +l = i - 1; +if (this.d[i - 1] != 0.0) { +for (j = 1; j <= l; j++) { +g = 0.0; +for (k = 1; k <= l; k++) { +g += (this.value[i - 1][k - 1] * this.value[k - 1][j - 1]); +} +for (k = 1; k <= l; k++) { +this.value[k - 1][j - 1] -= (g * this.value[k - 1][i - 1]); +} +} +}this.d[i - 1] = this.value[i - 1][i - 1]; +this.value[i - 1][i - 1] = 1.0; +for (j = 1; j <= l; j++) { +this.value[j - 1][i - 1] = 0.0; +this.value[i - 1][j - 1] = 0.0; +} +} +}); +Clazz.defineMethod (c$, "tqli", +function () { +var n = this.rows; +var m; +var l; +var iter; +var i; +var k; +var s; +var r; +var p; +;var g; +var f; +var dd; +var c; +var b; +for (i = 2; i <= n; i++) { +this.e[i - 2] = this.e[i - 1]; +} +this.e[n - 1] = 0.0; +for (l = 1; l <= n; l++) { +iter = 0; +do { +for (m = l; m <= (n - 1); m++) { +dd = Math.abs (this.d[m - 1]) + Math.abs (this.d[m]); +if ((Math.abs (this.e[m - 1]) + dd) == dd) { +break; +}} +if (m != l) { +iter++; +if (iter == this.maxIter) { +throw new Exception (jalview.util.MessageManager.formatMessage ("exception.matrix_too_many_iteration", Clazz.newArray (-1, ["tqli", Integer.$valueOf (this.maxIter).toString ()]))); +} else { +}g = (this.d[l] - this.d[l - 1]) / (2.0 * this.e[l - 1]); +r = Math.sqrt ((g * g) + 1.0); +g = this.d[m - 1] - this.d[l - 1] + (this.e[l - 1] / (g + this.sign (r, g))); +c = 1.0; +s = c; +p = 0.0; +for (i = m - 1; i >= l; i--) { +f = s * this.e[i - 1]; +b = c * this.e[i - 1]; +if (Math.abs (f) >= Math.abs (g)) { +c = g / f; +r = Math.sqrt ((c * c) + 1.0); +this.e[i] = f * r; +s = 1.0 / r; +c *= s; +} else { +s = f / g; +r = Math.sqrt ((s * s) + 1.0); +this.e[i] = g * r; +c = 1.0 / r; +s *= c; +}g = this.d[i] - p; +r = ((this.d[i - 1] - g) * s) + (2.0 * c * b); +p = s * r; +this.d[i] = g + p; +g = (c * r) - b; +for (k = 1; k <= n; k++) { +f = this.value[k - 1][i]; +this.value[k - 1][i] = (s * this.value[k - 1][i - 1]) + (c * f); +this.value[k - 1][i - 1] = (c * this.value[k - 1][i - 1]) - (s * f); +} +} +this.d[l - 1] = this.d[l - 1] - p; +this.e[l - 1] = g; +this.e[m - 1] = 0.0; +}} while (m != l); +} +}); +Clazz.defineMethod (c$, "tred2", +function () { +var n = this.rows; +var l; +var k; +var j; +var i; +var scale; +var hh; +var h; +var g; +var f; +this.d = Clazz.newDoubleArray (this.rows, 0); +this.e = Clazz.newDoubleArray (this.rows, 0); +for (i = n - 1; i >= 1; i--) { +l = i - 1; +h = 0.0; +scale = 0.0; +if (l > 0) { +for (k = 0; k < l; k++) { +scale += Math.abs (this.value[i][k]); +} +if (scale == 0.0) { +this.e[i] = this.value[i][l]; +} else { +for (k = 0; k < l; k++) { +this.value[i][k] /= scale; +h += (this.value[i][k] * this.value[i][k]); +} +f = this.value[i][l]; +if (f > 0) { +g = -1.0 * Math.sqrt (h); +} else { +g = Math.sqrt (h); +}this.e[i] = scale * g; +h -= (f * g); +this.value[i][l] = f - g; +f = 0.0; +for (j = 0; j < l; j++) { +this.value[j][i] = this.value[i][j] / h; +g = 0.0; +for (k = 0; k < j; k++) { +g += (this.value[j][k] * this.value[i][k]); +} +for (k = j; k < l; k++) { +g += (this.value[k][j] * this.value[i][k]); +} +this.e[j] = g / h; +f += (this.e[j] * this.value[i][j]); +} +hh = f / (h + h); +for (j = 0; j < l; j++) { +f = this.value[i][j]; +g = this.e[j] - (hh * f); +this.e[j] = g; +for (k = 0; k < j; k++) { +this.value[j][k] -= ((f * this.e[k]) + (g * this.value[i][k])); +} +} +}} else { +this.e[i] = this.value[i][l]; +}this.d[i] = h; +} +this.d[0] = 0.0; +this.e[0] = 0.0; +for (i = 0; i < n; i++) { +l = i - 1; +if (this.d[i] != 0.0) { +for (j = 0; j < l; j++) { +g = 0.0; +for (k = 0; k < l; k++) { +g += (this.value[i][k] * this.value[k][j]); +} +for (k = 0; k < l; k++) { +this.value[k][j] -= (g * this.value[k][i]); +} +} +}this.d[i] = this.value[i][i]; +this.value[i][i] = 1.0; +for (j = 0; j < l; j++) { +this.value[j][i] = 0.0; +this.value[i][j] = 0.0; +} +} +}); +Clazz.defineMethod (c$, "tqli2", +function () { +var n = this.rows; +var m; +var l; +var iter; +var i; +var k; +var s; +var r; +var p; +;var g; +var f; +var dd; +var c; +var b; +for (i = 2; i <= n; i++) { +this.e[i - 2] = this.e[i - 1]; +} +this.e[n - 1] = 0.0; +for (l = 1; l <= n; l++) { +iter = 0; +do { +for (m = l; m <= (n - 1); m++) { +dd = Math.abs (this.d[m - 1]) + Math.abs (this.d[m]); +if ((Math.abs (this.e[m - 1]) + dd) == dd) { +break; +}} +if (m != l) { +iter++; +if (iter == this.maxIter) { +throw new Exception (jalview.util.MessageManager.formatMessage ("exception.matrix_too_many_iteration", Clazz.newArray (-1, ["tqli2", Integer.$valueOf (this.maxIter).toString ()]))); +} else { +}g = (this.d[l] - this.d[l - 1]) / (2.0 * this.e[l - 1]); +r = Math.sqrt ((g * g) + 1.0); +g = this.d[m - 1] - this.d[l - 1] + (this.e[l - 1] / (g + this.sign (r, g))); +c = 1.0; +s = c; +p = 0.0; +for (i = m - 1; i >= l; i--) { +f = s * this.e[i - 1]; +b = c * this.e[i - 1]; +if (Math.abs (f) >= Math.abs (g)) { +c = g / f; +r = Math.sqrt ((c * c) + 1.0); +this.e[i] = f * r; +s = 1.0 / r; +c *= s; +} else { +s = f / g; +r = Math.sqrt ((s * s) + 1.0); +this.e[i] = g * r; +c = 1.0 / r; +s *= c; +}g = this.d[i] - p; +r = ((this.d[i - 1] - g) * s) + (2.0 * c * b); +p = s * r; +this.d[i] = g + p; +g = (c * r) - b; +for (k = 1; k <= n; k++) { +f = this.value[k - 1][i]; +this.value[k - 1][i] = (s * this.value[k - 1][i - 1]) + (c * f); +this.value[k - 1][i - 1] = (c * this.value[k - 1][i - 1]) - (s * f); +} +} +this.d[l - 1] = this.d[l - 1] - p; +this.e[l - 1] = g; +this.e[m - 1] = 0.0; +}} while (m != l); +} +}); +Clazz.defineMethod (c$, "sign", +function (a, b) { +if (b < 0) { +return -Math.abs (a); +} else { +return Math.abs (a); +}}, "~N,~N"); +Clazz.defineMethod (c$, "getColumn", +function (n) { +var out = Clazz.newDoubleArray (this.rows, 0); +for (var i = 0; i < this.rows; i++) { +out[i] = this.value[i][n]; +} +return out; +}, "~N"); +Clazz.defineMethod (c$, "printD", +function (ps) { +for (var j = 0; j < this.rows; j++) { +jalview.util.Format.printDouble (ps, "%15.4e", this.d[j]); +} +}, "java.io.PrintStream"); +Clazz.defineMethod (c$, "printE", +function (ps) { +for (var j = 0; j < this.rows; j++) { +jalview.util.Format.printDouble (ps, "%15.4e", this.e[j]); +} +}, "java.io.PrintStream"); +}); diff --git a/bin/jalview/math/RotatableMatrix.js b/bin/jalview/math/RotatableMatrix.js index 12195ca..bec7c23 100644 --- a/bin/jalview/math/RotatableMatrix.js +++ b/bin/jalview/math/RotatableMatrix.js @@ -1,114 +1,114 @@ -Clazz.declarePackage ("jalview.math"); -c$ = Clazz.decorateAsClass (function () { -this.matrix = null; -this.temp = null; -this.rot = null; -Clazz.instantialize (this, arguments); -}, jalview.math, "RotatableMatrix"); -Clazz.makeConstructor (c$, -function (rows, cols) { -this.matrix = Clazz.newFloatArray (rows, cols, 0); -this.temp = Clazz.newFloatArray (3, 0); -this.rot = Clazz.newFloatArray (3, 3, 0); -}, "~N,~N"); -Clazz.defineMethod (c$, "addElement", -function (i, j, value) { -this.matrix[i][j] = value; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "print", -function () { -System.out.println (this.matrix[0][0] + " " + this.matrix[0][1] + " " + this.matrix[0][2]); -System.out.println (this.matrix[1][0] + " " + this.matrix[1][1] + " " + this.matrix[1][2]); -System.out.println (this.matrix[2][0] + " " + this.matrix[2][1] + " " + this.matrix[2][2]); -}); -Clazz.defineMethod (c$, "rotate", -function (degrees, axis) { -var costheta = Math.cos ((degrees * 3.141592653589793) / 180.0); -var sintheta = Math.sin ((degrees * 3.141592653589793) / 180.0); -if (axis == 'z') { -this.rot[0][0] = costheta; -this.rot[0][1] = -sintheta; -this.rot[0][2] = 0.0; -this.rot[1][0] = sintheta; -this.rot[1][1] = costheta; -this.rot[1][2] = 0.0; -this.rot[2][0] = 0.0; -this.rot[2][1] = 0.0; -this.rot[2][2] = 1.0; -this.preMultiply (this.rot); -}if (axis == 'x') { -this.rot[0][0] = 1.0; -this.rot[0][1] = 0.0; -this.rot[0][2] = 0.0; -this.rot[1][0] = 0.0; -this.rot[1][1] = costheta; -this.rot[1][2] = sintheta; -this.rot[2][0] = 0.0; -this.rot[2][1] = -sintheta; -this.rot[2][2] = costheta; -this.preMultiply (this.rot); -}if (axis == 'y') { -this.rot[0][0] = costheta; -this.rot[0][1] = 0.0; -this.rot[0][2] = -sintheta; -this.rot[1][0] = 0.0; -this.rot[1][1] = 1.0; -this.rot[1][2] = 0.0; -this.rot[2][0] = sintheta; -this.rot[2][1] = 0.0; -this.rot[2][2] = costheta; -this.preMultiply (this.rot); -}}, "~N,~S"); -Clazz.defineMethod (c$, "vectorMultiply", -function (vect) { -this.temp[0] = vect[0]; -this.temp[1] = vect[1]; -this.temp[2] = vect[2]; -for (var i = 0; i < 3; i++) { -this.temp[i] = (this.matrix[i][0] * vect[0]) + (this.matrix[i][1] * vect[1]) + (this.matrix[i][2] * vect[2]); -} -vect[0] = this.temp[0]; -vect[1] = this.temp[1]; -vect[2] = this.temp[2]; -return vect; -}, "~A"); -Clazz.defineMethod (c$, "preMultiply", -function (mat) { -var tmp = Clazz.newFloatArray (3, 3, 0); -for (var i = 0; i < 3; i++) { -for (var j = 0; j < 3; j++) { -tmp[i][j] = (mat[i][0] * this.matrix[0][j]) + (mat[i][1] * this.matrix[1][j]) + (mat[i][2] * this.matrix[2][j]); -} -} -for (var i = 0; i < 3; i++) { -for (var j = 0; j < 3; j++) { -this.matrix[i][j] = tmp[i][j]; -} -} -}, "~A"); -Clazz.defineMethod (c$, "postMultiply", -function (mat) { -var tmp = Clazz.newFloatArray (3, 3, 0); -for (var i = 0; i < 3; i++) { -for (var j = 0; j < 3; j++) { -tmp[i][j] = (this.matrix[i][0] * mat[0][j]) + (this.matrix[i][1] * mat[1][j]) + (this.matrix[i][2] * mat[2][j]); -} -} -for (var i = 0; i < 3; i++) { -for (var j = 0; j < 3; j++) { -this.matrix[i][j] = tmp[i][j]; -} -} -}, "~A"); -Clazz.defineMethod (c$, "setIdentity", -function () { -this.matrix[0][0] = 1.0; -this.matrix[1][1] = 1.0; -this.matrix[2][2] = 1.0; -this.matrix[0][1] = 0.0; -this.matrix[0][2] = 0.0; -this.matrix[1][0] = 0.0; -this.matrix[1][2] = 0.0; -this.matrix[2][0] = 0.0; -this.matrix[2][1] = 0.0; -}); +Clazz.declarePackage ("jalview.math"); +c$ = Clazz.decorateAsClass (function () { +this.matrix = null; +this.temp = null; +this.rot = null; +Clazz.instantialize (this, arguments); +}, jalview.math, "RotatableMatrix"); +Clazz.makeConstructor (c$, +function (rows, cols) { +this.matrix = Clazz.newFloatArray (rows, cols, 0); +this.temp = Clazz.newFloatArray (3, 0); +this.rot = Clazz.newFloatArray (3, 3, 0); +}, "~N,~N"); +Clazz.defineMethod (c$, "addElement", +function (i, j, value) { +this.matrix[i][j] = value; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "print", +function () { +System.out.println (this.matrix[0][0] + " " + this.matrix[0][1] + " " + this.matrix[0][2]); +System.out.println (this.matrix[1][0] + " " + this.matrix[1][1] + " " + this.matrix[1][2]); +System.out.println (this.matrix[2][0] + " " + this.matrix[2][1] + " " + this.matrix[2][2]); +}); +Clazz.defineMethod (c$, "rotate", +function (degrees, axis) { +var costheta = Math.cos ((degrees * 3.141592653589793) / 180.0); +var sintheta = Math.sin ((degrees * 3.141592653589793) / 180.0); +if (axis == 'z') { +this.rot[0][0] = costheta; +this.rot[0][1] = -sintheta; +this.rot[0][2] = 0.0; +this.rot[1][0] = sintheta; +this.rot[1][1] = costheta; +this.rot[1][2] = 0.0; +this.rot[2][0] = 0.0; +this.rot[2][1] = 0.0; +this.rot[2][2] = 1.0; +this.preMultiply (this.rot); +}if (axis == 'x') { +this.rot[0][0] = 1.0; +this.rot[0][1] = 0.0; +this.rot[0][2] = 0.0; +this.rot[1][0] = 0.0; +this.rot[1][1] = costheta; +this.rot[1][2] = sintheta; +this.rot[2][0] = 0.0; +this.rot[2][1] = -sintheta; +this.rot[2][2] = costheta; +this.preMultiply (this.rot); +}if (axis == 'y') { +this.rot[0][0] = costheta; +this.rot[0][1] = 0.0; +this.rot[0][2] = -sintheta; +this.rot[1][0] = 0.0; +this.rot[1][1] = 1.0; +this.rot[1][2] = 0.0; +this.rot[2][0] = sintheta; +this.rot[2][1] = 0.0; +this.rot[2][2] = costheta; +this.preMultiply (this.rot); +}}, "~N,~S"); +Clazz.defineMethod (c$, "vectorMultiply", +function (vect) { +this.temp[0] = vect[0]; +this.temp[1] = vect[1]; +this.temp[2] = vect[2]; +for (var i = 0; i < 3; i++) { +this.temp[i] = (this.matrix[i][0] * vect[0]) + (this.matrix[i][1] * vect[1]) + (this.matrix[i][2] * vect[2]); +} +vect[0] = this.temp[0]; +vect[1] = this.temp[1]; +vect[2] = this.temp[2]; +return vect; +}, "~A"); +Clazz.defineMethod (c$, "preMultiply", +function (mat) { +var tmp = Clazz.newFloatArray (3, 3, 0); +for (var i = 0; i < 3; i++) { +for (var j = 0; j < 3; j++) { +tmp[i][j] = (mat[i][0] * this.matrix[0][j]) + (mat[i][1] * this.matrix[1][j]) + (mat[i][2] * this.matrix[2][j]); +} +} +for (var i = 0; i < 3; i++) { +for (var j = 0; j < 3; j++) { +this.matrix[i][j] = tmp[i][j]; +} +} +}, "~A"); +Clazz.defineMethod (c$, "postMultiply", +function (mat) { +var tmp = Clazz.newFloatArray (3, 3, 0); +for (var i = 0; i < 3; i++) { +for (var j = 0; j < 3; j++) { +tmp[i][j] = (this.matrix[i][0] * mat[0][j]) + (this.matrix[i][1] * mat[1][j]) + (this.matrix[i][2] * mat[2][j]); +} +} +for (var i = 0; i < 3; i++) { +for (var j = 0; j < 3; j++) { +this.matrix[i][j] = tmp[i][j]; +} +} +}, "~A"); +Clazz.defineMethod (c$, "setIdentity", +function () { +this.matrix[0][0] = 1.0; +this.matrix[1][1] = 1.0; +this.matrix[2][2] = 1.0; +this.matrix[0][1] = 0.0; +this.matrix[0][2] = 0.0; +this.matrix[1][0] = 0.0; +this.matrix[1][2] = 0.0; +this.matrix[2][0] = 0.0; +this.matrix[2][1] = 0.0; +}); diff --git a/bin/jalview/renderer/AnnotationRenderer.class b/bin/jalview/renderer/AnnotationRenderer.class index 2cab4d6..446ba32 100644 Binary files a/bin/jalview/renderer/AnnotationRenderer.class and b/bin/jalview/renderer/AnnotationRenderer.class differ diff --git a/bin/jalview/renderer/AnnotationRenderer.js b/bin/jalview/renderer/AnnotationRenderer.js index 00d98e4..221e5d3 100644 --- a/bin/jalview/renderer/AnnotationRenderer.js +++ b/bin/jalview/renderer/AnnotationRenderer.js @@ -1,805 +1,805 @@ -Clazz.declarePackage ("jalview.renderer"); -Clazz.load (["jalview.util.Platform", "java.awt.Color"], "jalview.renderer.AnnotationRenderer", ["jalview.analysis.AAFrequency", "$.CodingUtils", "$.StructureFrequency", "jalview.jsdev.RegExp", "jalview.schemes.NucleotideColourScheme", "$.ResidueProperties", "$.ZappoColourScheme", "java.awt.BasicStroke", "java.awt.geom.AffineTransform", "java.util.BitSet"], function () { -c$ = Clazz.decorateAsClass (function () { -this.debugRedraw = false; -this.charWidth = 0; -this.endRes = 0; -this.charHeight = 0; -this.validCharWidth = false; -this.hasHiddenColumns = false; -this.fm = null; -this.MAC = false; -this.av_renderHistogram = true; -this.av_renderProfile = true; -this.av_normaliseProfile = false; -this.profcolour = null; -this.columnSelection = null; -this.hconsensus = null; -this.complementConsensus = null; -this.hStrucConsensus = null; -this.av_ignoreGapsConsensus = false; -this.fadedImage = null; -this.annotationPanel = null; -this.imgWidth = 0; -this.sOffset = 0; -this.visHeight = 0; -this.useClip = true; -this.canClip = false; -this.rna = false; -this.sdNOTCANONICAL_COLOUR = null; -Clazz.instantialize (this, arguments); -}, jalview.renderer, "AnnotationRenderer"); -Clazz.prepareFields (c$, function () { -this.MAC = jalview.util.Platform.isAMac (); -}); -Clazz.makeConstructor (c$, -function () { -this.construct (false); -}); -Clazz.makeConstructor (c$, -function (debugRedraw) { -this.debugRedraw = debugRedraw; -}, "~B"); -Clazz.defineMethod (c$, "drawStemAnnot", -function (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { -g.setColor (jalview.renderer.AnnotationRenderer.STEM_COLOUR); -var sCol = (Clazz.doubleToInt (lastSSX / this.charWidth)) + startRes; -var x1 = lastSSX; -var x2 = (x * this.charWidth); -var closeparen = jalview.jsdev.RegExp.newRegex (["(\\))"]); -var dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' : row_annotations[column - 1].secondaryStructure; -var diffupstream = sCol == 0 || row_annotations[sCol - 1] == null || dc != row_annotations[sCol - 1].secondaryStructure; -var diffdownstream = !validRes || !validEnd || row_annotations[column] == null || dc != row_annotations[column].secondaryStructure; -if (column > 0 && jalview.schemes.ResidueProperties.isCloseParenRNA (dc)) { -if (diffupstream) { -g.fillPolygon ( Clazz.newIntArray (-1, [lastSSX + 5, lastSSX + 5, lastSSX]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); -x1 += 5; -}if (diffdownstream) { -x2 -= 1; -}} else { -if (diffdownstream) { -g.fillPolygon ( Clazz.newIntArray (-1, [x2 - 5, x2 - 5, x2]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); -x2 -= 5; -}if (diffupstream) { -x1 += 1; -}}g.fillRect (x1, y + 4 + iconOffset, x2 - x1, 7); -}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); -Clazz.defineMethod (c$, "drawNotCanonicalAnnot", -function (g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { -g.setColor (nonCanColor); -var sCol = (Clazz.doubleToInt (lastSSX / this.charWidth)) + startRes; -var x1 = lastSSX; -var x2 = (x * this.charWidth); -var closeparen = jalview.jsdev.RegExp.newRegex (["}|]|<|[a-z]"]); -var dc = (column == 0 || row_annotations[column - 1] == null) ? "" : row_annotations[column - 1].displayCharacter; -var diffupstream = sCol == 0 || row_annotations[sCol - 1] == null || !dc.equals (row_annotations[sCol - 1].displayCharacter); -var diffdownstream = !validRes || !validEnd || row_annotations[column] == null || !dc.equals (row_annotations[column].displayCharacter); -if (column > 0 && closeparen.search (dc)) { -if (diffupstream) { -g.fillPolygon ( Clazz.newIntArray (-1, [lastSSX + 5, lastSSX + 5, lastSSX]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); -x1 += 5; -}if (diffdownstream) { -x2 -= 1; -}} else { -if (diffdownstream) { -g.fillPolygon ( Clazz.newIntArray (-1, [x2 - 5, x2 - 5, x2]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); -x2 -= 5; -}if (diffupstream) { -x1 += 1; -}}g.fillRect (x1, y + 4 + iconOffset, x2 - x1, 7); -}, "java.awt.Graphics,java.awt.Color,~A,~N,~N,~N,~N,~N,~N,~B,~B"); -Clazz.defineMethod (c$, "updateFromAwtRenderPanel", -function (annotPanel, av) { -this.fm = annotPanel.getFontMetrics (); -this.annotationPanel = annotPanel; -this.fadedImage = annotPanel.getFadedImage (); -this.imgWidth = annotPanel.getFadedImageWidth (); -var bounds = annotPanel.getVisibleVRange (); -if (bounds != null) { -this.sOffset = bounds[0]; -this.visHeight = bounds[1]; -if (this.visHeight == 0) { -this.useClip = false; -} else { -this.useClip = this.canClip; -}} else { -this.useClip = false; -}this.updateFromAlignViewport (av); -}, "jalview.renderer.AwtRenderPanelI,jalview.api.AlignViewportI"); -Clazz.defineMethod (c$, "updateFromAlignViewport", -function (av) { -this.charWidth = av.getCharWidth (); -this.endRes = av.getEndRes (); -this.charHeight = av.getCharHeight (); -this.hasHiddenColumns = av.hasHiddenColumns (); -this.validCharWidth = av.isValidCharWidth (); -this.av_renderHistogram = av.isShowConsensusHistogram (); -this.av_renderProfile = av.isShowSequenceLogo (); -this.av_normaliseProfile = av.isNormaliseSequenceLogo (); -this.profcolour = av.getGlobalColourScheme (); -if (this.profcolour == null) { -this.profcolour = av.getAlignment ().isNucleotide () ? new jalview.schemes.NucleotideColourScheme () : new jalview.schemes.ZappoColourScheme (); -}this.columnSelection = av.getColumnSelection (); -this.hconsensus = av.getSequenceConsensusHash (); -this.complementConsensus = av.getComplementConsensusHash (); -this.hStrucConsensus = av.getRnaStructureConsensusHash (); -this.av_ignoreGapsConsensus = av.isIgnoreGapsConsensus (); -}, "jalview.api.AlignViewportI"); -Clazz.defineMethod (c$, "getProfileFor", -function (aa, column) { -if (aa.autoCalculated && (aa.label.startsWith ("Consensus") || aa.label.startsWith ("cDNA Consensus"))) { -var forComplement = aa.label.startsWith ("cDNA Consensus"); -if (aa.groupRef != null && aa.groupRef.consensusData != null && aa.groupRef.isShowSequenceLogo ()) { -return jalview.analysis.AAFrequency.extractProfile (aa.groupRef.consensusData[column], aa.groupRef.getIgnoreGapsConsensus ()); -}if (aa.groupRef == null && aa.sequenceRef == null) { -if (forComplement) { -return jalview.analysis.AAFrequency.extractCdnaProfile (this.complementConsensus[column], this.av_ignoreGapsConsensus); -} else { -return jalview.analysis.AAFrequency.extractProfile (this.hconsensus[column], this.av_ignoreGapsConsensus); -}}} else { -if (aa.autoCalculated && aa.label.startsWith ("StrucConsensus")) { -if (aa.groupRef == null && aa.sequenceRef == null && this.hStrucConsensus != null && this.hStrucConsensus.length > column) { -return jalview.analysis.StructureFrequency.extractProfile (this.hStrucConsensus[column], this.av_ignoreGapsConsensus); -}}}return null; -}, "jalview.datamodel.AlignmentAnnotation,~N"); -Clazz.defineMethod (c$, "drawComponent", -function (annotPanel, av, g, activeRow, startRes, endRes) { -var stime = System.currentTimeMillis (); -var usedFaded = false; -this.updateFromAwtRenderPanel (annotPanel, av); -this.fm = g.getFontMetrics (); -var aa = av.getAlignment ().getAlignmentAnnotation (); -var temp = 0; -if (aa == null) { -return false; -}var x = 0; -var y = 0; -var column = 0; -var lastSS; -var lastSSX; -var iconOffset = 0; -var validRes = false; -var validEnd = false; -var labelAllCols = false; -var centreColLabels; -var centreColLabelsDef = av.isCentreColumnLabels (); -var scaleColLabel = false; -var consensusAnnot = av.getAlignmentConsensusAnnotation (); -var structConsensusAnnot = av.getAlignmentStrucConsensusAnnotation (); -var complementConsensusAnnot = av.getComplementConsensusAnnotation (); -var renderHistogram = true; -var renderProfile = true; -var normaliseProfile = false; -var isRNA = this.rna; -var graphGroupDrawn = new java.util.BitSet (); -var charOffset = 0; -var fmWidth; -var fmScaling = 1; -var ofont = g.getFont (); -var yfrom = 0; -var f_i = 0; -var yto = 0; -var f_to = 0; -var clipst = false; -var clipend = false; -for (var i = 0; i < aa.length; i++) { -var row = aa[i]; -isRNA = row.isRNA (); -{ -if (row.groupRef != null && row === row.groupRef.getConsensus ()) { -renderHistogram = row.groupRef.isShowConsensusHistogram (); -renderProfile = row.groupRef.isShowSequenceLogo (); -normaliseProfile = row.groupRef.isNormaliseSequenceLogo (); -} else if (row === consensusAnnot || row === structConsensusAnnot || row === complementConsensusAnnot) { -renderHistogram = this.av_renderHistogram; -renderProfile = this.av_renderProfile; -normaliseProfile = this.av_normaliseProfile; -} else { -renderHistogram = true; -}}var row_annotations = row.annotations; -if (!row.visible) { -continue; -}centreColLabels = row.centreColLabels || centreColLabelsDef; -labelAllCols = row.showAllColLabels; -scaleColLabel = row.scaleColLabel; -lastSS = ' '; -lastSSX = 0; -if (!this.useClip || ((y - this.charHeight) < this.visHeight && (y + row.height + this.charHeight * 2) >= this.sOffset)) { -if (!clipst) { -clipst = true; -yfrom = y; -f_i = i; -}yto = y; -f_to = i; -if (row.graph > 0) { -if (row.graphGroup > -1 && graphGroupDrawn.get (row.graphGroup)) { -continue; -}y += row.height; -if (row.hasText) { -iconOffset = this.charHeight - this.fm.getDescent (); -y -= this.charHeight; -}} else if (row.hasText) { -iconOffset = this.charHeight - this.fm.getDescent (); -} else { -iconOffset = 0; -}if (row.autoCalculated && av.isCalculationInProgress (row)) { -y += this.charHeight; -usedFaded = true; -g.drawImage (this.fadedImage, 0, y - row.height, this.imgWidth, y, 0, y - row.height, this.imgWidth, y, this.annotationPanel); -g.setColor (java.awt.Color.black); -continue; -}x = (startRes == 0) ? 0 : -1; -while (x < endRes - startRes) { -if (this.hasHiddenColumns) { -column = this.columnSelection.adjustForHiddenColumns (startRes + x); -if (column > row_annotations.length - 1) { -break; -}} else { -column = startRes + x; -}if ((row_annotations == null) || (row_annotations.length <= column) || (row_annotations[column] == null)) { -validRes = false; -} else { -validRes = true; -}var displayChar = validRes ? row_annotations[column].displayCharacter : null; -if (x > -1) { -if (activeRow == i) { -g.setColor (java.awt.Color.red); -if (this.columnSelection != null) { -for (var n = 0; n < this.columnSelection.size (); n++) { -var v = this.columnSelection.columnAt (n); -if (v == column) { -g.fillRect (x * this.charWidth, y, this.charWidth, this.charHeight); -}} -}}if (row.getInvalidStrucPos () > x) { -g.setColor (java.awt.Color.orange); -g.fillRect (x * this.charWidth, y, this.charWidth, this.charHeight); -} else if (row.getInvalidStrucPos () == x) { -g.setColor (java.awt.Color.orange.darker ()); -g.fillRect (x * this.charWidth, y, this.charWidth, this.charHeight); -}if (this.validCharWidth && validRes && displayChar != null && (displayChar.length > 0)) { -fmWidth = this.fm.charsWidth (displayChar.toCharArray (), 0, displayChar.length); -if (scaleColLabel) { -if (fmWidth > this.charWidth) { -fmScaling = this.charWidth; -fmScaling /= fmWidth; -g.setFont (ofont.deriveFont (java.awt.geom.AffineTransform.getScaleInstance (fmScaling, 1.0))); -fmWidth = this.charWidth; -}}charOffset = Clazz.floatToInt ((this.charWidth - fmWidth) / 2); -if (row_annotations[column].colour == null) { -g.setColor (java.awt.Color.black); -} else { -g.setColor (row_annotations[column].colour); -}if (column == 0 || row.graph > 0) { -g.drawString (displayChar, (x * this.charWidth) + charOffset, y + iconOffset); -} else if (row_annotations[column - 1] == null || (labelAllCols || !displayChar.equals (row_annotations[column - 1].displayCharacter) || (displayChar.length < 2 && row_annotations[column].secondaryStructure == ' '))) { -g.drawString (displayChar, x * this.charWidth + charOffset, y + iconOffset); -}g.setFont (ofont); -}}if (row.hasIcons) { -var ss = validRes ? row_annotations[column].secondaryStructure : '-'; -if (ss == '(') { -if (displayChar.indexOf (')') > -1) { -ss = ')'; -}}if (ss == '[') { -if ((displayChar.indexOf (']') > -1)) { -ss = ']'; -}}if (ss == '{') { -if (displayChar.indexOf ('}') > -1) { -ss = '}'; -}}if (ss == '<') { -if (displayChar.indexOf ('<') > -1) { -ss = '>'; -}}if (ss.charCodeAt (0) >= 65) { -if (displayChar.indexOf (ss.charCodeAt (0) + 32) > -1) { -ss = String.fromCharCode (ss.charCodeAt (0) + 32); -}}if (!validRes || (ss != lastSS)) { -if (x > -1) { -var nb_annot = x - temp; -switch (lastSS) { -case '(': -case ')': -this.drawStemAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -temp = x; -break; -case 'H': -if (!isRNA) { -this.drawHelixAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -}case 'E': -if (!isRNA) { -this.drawSheetAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -}case '{': -case '}': -case '[': -case ']': -case '>': -case '<': -case 'A': -case 'a': -case 'B': -case 'b': -case 'C': -case 'c': -case 'D': -case 'd': -case 'e': -case 'F': -case 'f': -case 'G': -case 'g': -case 'h': -case 'I': -case 'i': -case 'J': -case 'j': -case 'K': -case 'k': -case 'L': -case 'l': -case 'M': -case 'm': -case 'N': -case 'n': -case 'O': -case 'o': -case 'P': -case 'p': -case 'Q': -case 'q': -case 'R': -case 'r': -case 'S': -case 's': -case 'T': -case 't': -case 'U': -case 'u': -case 'V': -case 'v': -case 'W': -case 'w': -case 'X': -case 'x': -case 'Y': -case 'y': -case 'Z': -case 'z': -var nonCanColor = this.getNotCanonicalColor (lastSS); -this.drawNotCanonicalAnnot (g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -temp = x; -break; -default: -g.setColor (java.awt.Color.gray); -g.fillRect (lastSSX, y + 6 + iconOffset, (x * this.charWidth) - lastSSX, 2); -temp = x; -break; -} -}if (validRes) { -lastSS = ss; -} else { -lastSS = ' '; -}if (x > -1) { -lastSSX = (x * this.charWidth); -}}}column++; -x++; -} -if (column >= row_annotations.length) { -column = row_annotations.length - 1; -validEnd = false; -} else { -validEnd = true; -}if ((row_annotations == null) || (row_annotations.length <= column) || (row_annotations[column] == null)) { -validRes = false; -} else { -validRes = true; -}if (row.hasIcons) { -switch (lastSS) { -case 'H': -if (!isRNA) { -this.drawHelixAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -}case 'E': -if (!isRNA) { -this.drawSheetAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -}case '(': -case ')': -this.drawStemAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -case '{': -case '}': -case '[': -case ']': -case '>': -case '<': -case 'A': -case 'a': -case 'B': -case 'b': -case 'C': -case 'c': -case 'D': -case 'd': -case 'e': -case 'F': -case 'f': -case 'G': -case 'g': -case 'h': -case 'I': -case 'i': -case 'J': -case 'j': -case 'K': -case 'k': -case 'L': -case 'l': -case 'M': -case 'm': -case 'N': -case 'n': -case 'O': -case 'o': -case 'P': -case 'p': -case 'Q': -case 'q': -case 'R': -case 'r': -case 'T': -case 't': -case 'U': -case 'u': -case 'V': -case 'v': -case 'W': -case 'w': -case 'X': -case 'x': -case 'Y': -case 'y': -case 'Z': -case 'z': -var nonCanColor = this.getNotCanonicalColor (lastSS); -this.drawNotCanonicalAnnot (g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -default: -this.drawGlyphLine (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); -break; -} -}if (row.graph > 0 && row.graphHeight > 0) { -if (row.graph == 2) { -if (row.graphGroup > -1 && !graphGroupDrawn.get (row.graphGroup)) { -var groupmax = -999999; -var groupmin = 9999999; -for (var gg = 0; gg < aa.length; gg++) { -if (aa[gg].graphGroup != row.graphGroup) { -continue; -}if (aa[gg] !== row) { -aa[gg].visible = false; -}if (aa[gg].graphMax > groupmax) { -groupmax = aa[gg].graphMax; -}if (aa[gg].graphMin < groupmin) { -groupmin = aa[gg].graphMin; -}} -for (var gg = 0; gg < aa.length; gg++) { -if (aa[gg].graphGroup == row.graphGroup) { -this.drawLineGraph (g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin, groupmax, row.graphHeight); -}} -graphGroupDrawn.set (row.graphGroup); -} else { -this.drawLineGraph (g, row, row_annotations, startRes, endRes, y, row.graphMin, row.graphMax, row.graphHeight); -}} else if (row.graph == 1) { -this.drawBarGraph (g, row, row_annotations, startRes, endRes, row.graphMin, row.graphMax, y, renderHistogram, renderProfile, normaliseProfile); -}}} else { -if (clipst && !clipend) { -clipend = true; -}}if (row.graph > 0 && row.hasText) { -y += this.charHeight; -}if (row.graph == 0) { -y += aa[i].height; -}} -if (this.debugRedraw) { -if (this.canClip) { -if (clipst) { -System.err.println ("Start clip at : " + yfrom + " (index " + f_i + ")"); -}if (clipend) { -System.err.println ("End clip at : " + yto + " (index " + f_to + ")"); -}};System.err.println ("Annotation Rendering time:" + (System.currentTimeMillis () - stime)); -};return !usedFaded; -}, "jalview.renderer.AwtRenderPanelI,jalview.api.AlignViewportI,java.awt.Graphics,~N,~N,~N"); -Clazz.defineMethod (c$, "drawGlyphLine", -function (g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { -g.setColor (jalview.renderer.AnnotationRenderer.GLYPHLINE_COLOR); -g.fillRect (lastSSX, y + 6 + iconOffset, (x * this.charWidth) - lastSSX, 2); -}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); -Clazz.defineMethod (c$, "drawSheetAnnot", -function (g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { -g.setColor (jalview.renderer.AnnotationRenderer.SHEET_COLOUR); -if (!validEnd || !validRes || row == null || row[column] == null || row[column].secondaryStructure != 'E') { -g.fillRect (lastSSX, y + 4 + iconOffset, (x * this.charWidth) - lastSSX - 4, 7); -g.fillPolygon ( Clazz.newIntArray (-1, [(x * this.charWidth) - 4, (x * this.charWidth) - 4, (x * this.charWidth)]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset]), 3); -} else { -g.fillRect (lastSSX, y + 4 + iconOffset, (x + 1) * this.charWidth - lastSSX, 7); -}}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); -Clazz.defineMethod (c$, "drawHelixAnnot", -function (g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { -g.setColor (jalview.renderer.AnnotationRenderer.HELIX_COLOUR); -var sCol = (Clazz.doubleToInt (lastSSX / this.charWidth)) + startRes; -var x1 = lastSSX; -var x2 = (x * this.charWidth); -if (this.MAC) { -var ofs = Clazz.doubleToInt (this.charWidth / 2); -g.fillRoundRect (lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); -if (sCol == 0 || row[sCol - 1] == null || row[sCol - 1].secondaryStructure != 'H') { -} else { -g.fillRoundRect (lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, 0, 0); -}if (!validRes || row[column] == null || row[column].secondaryStructure != 'H') { -} else { -g.fillRoundRect (lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, 0, 0); -}return; -}if (sCol == 0 || row[sCol - 1] == null || row[sCol - 1].secondaryStructure != 'H') { -g.fillArc (lastSSX, y + 4 + iconOffset, this.charWidth, 8, 90, 180); -x1 += Clazz.doubleToInt (this.charWidth / 2); -}if (!validRes || row[column] == null || row[column].secondaryStructure != 'H') { -g.fillArc ((x * this.charWidth) - this.charWidth, y + 4 + iconOffset, this.charWidth, 8, 270, 180); -x2 -= Clazz.doubleToInt (this.charWidth / 2); -}g.fillRect (x1, y + 4 + iconOffset, x2 - x1, 8); -}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); -Clazz.defineMethod (c$, "drawLineGraph", -function (g, _aa, aa_annotations, sRes, eRes, y, min, max, graphHeight) { -if (sRes > aa_annotations.length) { -return; -}var x = 0; -if (eRes < this.endRes) { -eRes++; -}eRes = Math.min (eRes, aa_annotations.length); -if (sRes == 0) { -x++; -}var y1 = y; -var y2 = y; -var range = max - min; -if (min < 0) { -y2 = y - Clazz.floatToInt ((0 - min / range) * graphHeight); -}g.setColor (java.awt.Color.gray); -g.drawLine (x - this.charWidth, y2, (eRes - sRes + 1) * this.charWidth, y2); -eRes = Math.min (eRes, aa_annotations.length); -var column; -var aaMax = aa_annotations.length - 1; -while (x < eRes - sRes) { -column = sRes + x; -if (this.hasHiddenColumns) { -column = this.columnSelection.adjustForHiddenColumns (column); -}if (column > aaMax) { -break; -}if (aa_annotations[column] == null || aa_annotations[column - 1] == null) { -x++; -continue; -}if (aa_annotations[column].colour == null) { -g.setColor (java.awt.Color.black); -} else { -g.setColor (aa_annotations[column].colour); -}y1 = y - Clazz.floatToInt (((aa_annotations[column - 1].value - min) / range) * graphHeight); -y2 = y - Clazz.floatToInt (((aa_annotations[column].value - min) / range) * graphHeight); -g.drawLine (x * this.charWidth - Clazz.doubleToInt (this.charWidth / 2), y1, x * this.charWidth + Clazz.doubleToInt (this.charWidth / 2), y2); -x++; -} -if (_aa.threshold != null) { -g.setColor (_aa.threshold.colour); -var g2 = g; -g2.setStroke ( new java.awt.BasicStroke (1, 2, 1, 3, Clazz.newFloatArray (-1, [5, 3]), 0)); -y2 = Clazz.floatToInt (y - ((_aa.threshold.value - min) / range) * graphHeight); -g.drawLine (0, y2, (eRes - sRes) * this.charWidth, y2); -g2.setStroke ( new java.awt.BasicStroke ()); -}}, "java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "drawBarGraph", -function (g, _aa, aa_annotations, sRes, eRes, min, max, y, renderHistogram, renderProfile, normaliseProfile) { -if (sRes > aa_annotations.length) { -return; -}var ofont = g.getFont (); -eRes = Math.min (eRes, aa_annotations.length); -var x = 0; -var y1 = y; -var y2 = y; -var range = max - min; -if (min < 0) { -y2 = y - Clazz.floatToInt ((0 - min / (range)) * _aa.graphHeight); -}g.setColor (java.awt.Color.gray); -g.drawLine (x, y2, (eRes - sRes) * this.charWidth, y2); -var column; -var aaMax = aa_annotations.length - 1; -while (x < eRes - sRes) { -column = sRes + x; -if (this.hasHiddenColumns) { -column = this.columnSelection.adjustForHiddenColumns (column); -}if (column > aaMax) { -break; -}if (aa_annotations[column] == null) { -x++; -continue; -}if (aa_annotations[column].colour == null) { -g.setColor (java.awt.Color.black); -} else { -g.setColor (aa_annotations[column].colour); -}y1 = y - Clazz.floatToInt (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight); -if (renderHistogram) { -if (y1 - y2 > 0) { -g.fillRect (x * this.charWidth, y2, this.charWidth, y1 - y2); -} else { -g.fillRect (x * this.charWidth, y1, this.charWidth, y2 - y1); -}}if (renderProfile) { -var profl = this.getProfileFor (_aa, column); -if (profl != null && profl[2] != 0) { -var isStructureProfile = profl[0] == 1; -var isCdnaProfile = profl[0] == 2; -var ht = normaliseProfile ? y - _aa.graphHeight : y1; -var htn = normaliseProfile ? _aa.graphHeight : (y2 - y1); -var hght; -var wdth; -var ht2 = 0; -var dc; -dc = Clazz.newCharArray (isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1), '\0'); -var lm = g.getFontMetrics (ofont).getLineMetrics ("Q", g); -var scale = 1 / (normaliseProfile ? profl[2] : 100); -var ofontHeight = 1 / lm.getAscent (); -var scl = 0.0; -var c = 3; -var valuesProcessed = 0; -while (valuesProcessed < profl[1]) { -if (isStructureProfile) { -dc[0] = String.fromCharCode (profl[c++]); -dc[1] = String.fromCharCode (profl[c++]); -} else if (isCdnaProfile) { -dc = jalview.analysis.CodingUtils.decodeCodon (profl[c++]); -} else { -dc[0] = String.fromCharCode (profl[c++]); -}wdth = this.charWidth; -wdth /= this.fm.charsWidth (dc, 0, dc.length); -ht += scl; -scl = htn * scale * profl[c++]; -lm = ofont.getLineMetrics (dc, 0, 1, g.getFontMetrics ().getFontRenderContext ()); -g.setFont (ofont.deriveFont (java.awt.geom.AffineTransform.getScaleInstance (wdth, scl / lm.getAscent ()))); -lm = g.getFontMetrics ().getLineMetrics (dc, 0, 1, g); -var colour = null; -if (isCdnaProfile) { -var codonTranslation = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (dc)); -colour = this.profcolour.findColour (codonTranslation.charAt (0), column, null); -} else { -colour = this.profcolour.findColour (dc[0], column, null); -}g.setColor (colour === java.awt.Color.white ? java.awt.Color.lightGray : colour); -hght = (ht + (scl - lm.getDescent () - lm.getBaselineOffsets ()[lm.getBaselineIndex ()])); -g.drawChars (dc, 0, dc.length, x * this.charWidth, Clazz.doubleToInt (hght)); -valuesProcessed++; -} -g.setFont (ofont); -}}x++; -} -if (_aa.threshold != null) { -g.setColor (_aa.threshold.colour); -var g2 = g; -g2.setStroke ( new java.awt.BasicStroke (1, 2, 1, 3, Clazz.newFloatArray (-1, [5, 3]), 0)); -y2 = Clazz.floatToInt (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight); -g.drawLine (0, y2, (eRes - sRes) * this.charWidth, y2); -g2.setStroke ( new java.awt.BasicStroke ()); -}}, "java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N,~N,~B,~B,~B"); -Clazz.defineMethod (c$, "drawGraph", -function (g, _aa, aa_annotations, width, y, sRes, eRes) { -eRes = Math.min (eRes, aa_annotations.length); -g.setColor (java.awt.Color.white); -g.fillRect (0, 0, width, y); -g.setColor ( new java.awt.Color (0, 0, 180)); -var x = 0; -var height; -for (var j = sRes; j < eRes; j++) { -if (aa_annotations[j] != null) { -if (aa_annotations[j].colour == null) { -g.setColor (java.awt.Color.black); -} else { -g.setColor (aa_annotations[j].colour); -}height = Clazz.floatToInt ((aa_annotations[j].value / _aa.graphMax) * y); -if (height > y) { -height = y; -}g.fillRect (x, y - height, this.charWidth, height); -}x += this.charWidth; -} -}, "java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "getNotCanonicalColor", -function (lastss) { -switch (lastss) { -case '{': -case '}': -return new java.awt.Color (255, 125, 5); -case '[': -case ']': -return new java.awt.Color (245, 115, 10); -case '>': -case '<': -return new java.awt.Color (235, 135, 15); -case 'A': -case 'a': -return new java.awt.Color (225, 105, 20); -case 'B': -case 'b': -return new java.awt.Color (215, 145, 30); -case 'C': -case 'c': -return new java.awt.Color (205, 95, 35); -case 'D': -case 'd': -return new java.awt.Color (195, 155, 45); -case 'E': -case 'e': -return new java.awt.Color (185, 85, 55); -case 'F': -case 'f': -return new java.awt.Color (175, 165, 65); -case 'G': -case 'g': -return new java.awt.Color (170, 75, 75); -case 'H': -case 'h': -return new java.awt.Color (160, 175, 85); -case 'I': -case 'i': -return new java.awt.Color (150, 65, 95); -case 'J': -case 'j': -return new java.awt.Color (140, 185, 105); -case 'K': -case 'k': -return new java.awt.Color (130, 55, 110); -case 'L': -case 'l': -return new java.awt.Color (120, 195, 120); -case 'M': -case 'm': -return new java.awt.Color (110, 45, 130); -case 'N': -case 'n': -return new java.awt.Color (100, 205, 140); -case 'O': -case 'o': -return new java.awt.Color (90, 35, 150); -case 'P': -case 'p': -return new java.awt.Color (85, 215, 160); -case 'Q': -case 'q': -return new java.awt.Color (75, 25, 170); -case 'R': -case 'r': -return new java.awt.Color (65, 225, 180); -case 'S': -case 's': -return new java.awt.Color (55, 15, 185); -case 'T': -case 't': -return new java.awt.Color (45, 235, 195); -case 'U': -case 'u': -return new java.awt.Color (35, 5, 205); -case 'V': -case 'v': -return new java.awt.Color (25, 245, 215); -case 'W': -case 'w': -return new java.awt.Color (15, 0, 225); -case 'X': -case 'x': -return new java.awt.Color (10, 255, 235); -case 'Y': -case 'y': -return new java.awt.Color (5, 150, 245); -case 'Z': -case 'z': -return new java.awt.Color (0, 80, 255); -default: -System.out.println ("This is not a interaction : " + lastss); -return null; -} -}, "~S"); -c$.GLYPHLINE_COLOR = c$.prototype.GLYPHLINE_COLOR = java.awt.Color.gray; -c$.SHEET_COLOUR = c$.prototype.SHEET_COLOUR = java.awt.Color.green; -c$.HELIX_COLOUR = c$.prototype.HELIX_COLOUR = java.awt.Color.red; -c$.STEM_COLOUR = c$.prototype.STEM_COLOUR = java.awt.Color.blue; -}); +Clazz.declarePackage ("jalview.renderer"); +Clazz.load (["jalview.util.Platform", "java.awt.Color"], "jalview.renderer.AnnotationRenderer", ["jalview.analysis.AAFrequency", "$.CodingUtils", "$.StructureFrequency", "jalview.jsdev.RegExp", "jalview.schemes.NucleotideColourScheme", "$.ResidueProperties", "$.ZappoColourScheme", "java.awt.BasicStroke", "java.awt.geom.AffineTransform", "java.util.BitSet"], function () { +c$ = Clazz.decorateAsClass (function () { +this.debugRedraw = false; +this.charWidth = 0; +this.endRes = 0; +this.charHeight = 0; +this.validCharWidth = false; +this.hasHiddenColumns = false; +this.fm = null; +this.MAC = false; +this.av_renderHistogram = true; +this.av_renderProfile = true; +this.av_normaliseProfile = false; +this.profcolour = null; +this.columnSelection = null; +this.hconsensus = null; +this.complementConsensus = null; +this.hStrucConsensus = null; +this.av_ignoreGapsConsensus = false; +this.fadedImage = null; +this.annotationPanel = null; +this.imgWidth = 0; +this.sOffset = 0; +this.visHeight = 0; +this.useClip = true; +this.canClip = false; +this.rna = false; +this.sdNOTCANONICAL_COLOUR = null; +Clazz.instantialize (this, arguments); +}, jalview.renderer, "AnnotationRenderer"); +Clazz.prepareFields (c$, function () { +this.MAC = jalview.util.Platform.isAMac (); +}); +Clazz.makeConstructor (c$, +function () { +this.construct (false); +}); +Clazz.makeConstructor (c$, +function (debugRedraw) { +this.debugRedraw = debugRedraw; +}, "~B"); +Clazz.defineMethod (c$, "drawStemAnnot", +function (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { +g.setColor (jalview.renderer.AnnotationRenderer.STEM_COLOUR); +var sCol = (Clazz.doubleToInt (lastSSX / this.charWidth)) + startRes; +var x1 = lastSSX; +var x2 = (x * this.charWidth); +var closeparen = jalview.jsdev.RegExp.newRegex (["(\\))"]); +var dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' : row_annotations[column - 1].secondaryStructure; +var diffupstream = sCol == 0 || row_annotations[sCol - 1] == null || dc != row_annotations[sCol - 1].secondaryStructure; +var diffdownstream = !validRes || !validEnd || row_annotations[column] == null || dc != row_annotations[column].secondaryStructure; +if (column > 0 && jalview.schemes.ResidueProperties.isCloseParenRNA (dc)) { +if (diffupstream) { +g.fillPolygon ( Clazz.newIntArray (-1, [lastSSX + 5, lastSSX + 5, lastSSX]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); +x1 += 5; +}if (diffdownstream) { +x2 -= 1; +}} else { +if (diffdownstream) { +g.fillPolygon ( Clazz.newIntArray (-1, [x2 - 5, x2 - 5, x2]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); +x2 -= 5; +}if (diffupstream) { +x1 += 1; +}}g.fillRect (x1, y + 4 + iconOffset, x2 - x1, 7); +}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); +Clazz.defineMethod (c$, "drawNotCanonicalAnnot", +function (g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { +g.setColor (nonCanColor); +var sCol = (Clazz.doubleToInt (lastSSX / this.charWidth)) + startRes; +var x1 = lastSSX; +var x2 = (x * this.charWidth); +var closeparen = jalview.jsdev.RegExp.newRegex (["}|]|<|[a-z]"]); +var dc = (column == 0 || row_annotations[column - 1] == null) ? "" : row_annotations[column - 1].displayCharacter; +var diffupstream = sCol == 0 || row_annotations[sCol - 1] == null || !dc.equals (row_annotations[sCol - 1].displayCharacter); +var diffdownstream = !validRes || !validEnd || row_annotations[column] == null || !dc.equals (row_annotations[column].displayCharacter); +if (column > 0 && closeparen.search (dc)) { +if (diffupstream) { +g.fillPolygon ( Clazz.newIntArray (-1, [lastSSX + 5, lastSSX + 5, lastSSX]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); +x1 += 5; +}if (diffdownstream) { +x2 -= 1; +}} else { +if (diffdownstream) { +g.fillPolygon ( Clazz.newIntArray (-1, [x2 - 5, x2 - 5, x2]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset]), 3); +x2 -= 5; +}if (diffupstream) { +x1 += 1; +}}g.fillRect (x1, y + 4 + iconOffset, x2 - x1, 7); +}, "java.awt.Graphics,java.awt.Color,~A,~N,~N,~N,~N,~N,~N,~B,~B"); +Clazz.defineMethod (c$, "updateFromAwtRenderPanel", +function (annotPanel, av) { +this.fm = annotPanel.getFontMetrics (); +this.annotationPanel = annotPanel; +this.fadedImage = annotPanel.getFadedImage (); +this.imgWidth = annotPanel.getFadedImageWidth (); +var bounds = annotPanel.getVisibleVRange (); +if (bounds != null) { +this.sOffset = bounds[0]; +this.visHeight = bounds[1]; +if (this.visHeight == 0) { +this.useClip = false; +} else { +this.useClip = this.canClip; +}} else { +this.useClip = false; +}this.updateFromAlignViewport (av); +}, "jalview.renderer.AwtRenderPanelI,jalview.api.AlignViewportI"); +Clazz.defineMethod (c$, "updateFromAlignViewport", +function (av) { +this.charWidth = av.getCharWidth (); +this.endRes = av.getEndRes (); +this.charHeight = av.getCharHeight (); +this.hasHiddenColumns = av.hasHiddenColumns (); +this.validCharWidth = av.isValidCharWidth (); +this.av_renderHistogram = av.isShowConsensusHistogram (); +this.av_renderProfile = av.isShowSequenceLogo (); +this.av_normaliseProfile = av.isNormaliseSequenceLogo (); +this.profcolour = av.getGlobalColourScheme (); +if (this.profcolour == null) { +this.profcolour = av.getAlignment ().isNucleotide () ? new jalview.schemes.NucleotideColourScheme () : new jalview.schemes.ZappoColourScheme (); +}this.columnSelection = av.getColumnSelection (); +this.hconsensus = av.getSequenceConsensusHash (); +this.complementConsensus = av.getComplementConsensusHash (); +this.hStrucConsensus = av.getRnaStructureConsensusHash (); +this.av_ignoreGapsConsensus = av.isIgnoreGapsConsensus (); +}, "jalview.api.AlignViewportI"); +Clazz.defineMethod (c$, "getProfileFor", +function (aa, column) { +if (aa.autoCalculated && (aa.label.startsWith ("Consensus") || aa.label.startsWith ("cDNA Consensus"))) { +var forComplement = aa.label.startsWith ("cDNA Consensus"); +if (aa.groupRef != null && aa.groupRef.consensusData != null && aa.groupRef.isShowSequenceLogo ()) { +return jalview.analysis.AAFrequency.extractProfile (aa.groupRef.consensusData[column], aa.groupRef.getIgnoreGapsConsensus ()); +}if (aa.groupRef == null && aa.sequenceRef == null) { +if (forComplement) { +return jalview.analysis.AAFrequency.extractCdnaProfile (this.complementConsensus[column], this.av_ignoreGapsConsensus); +} else { +return jalview.analysis.AAFrequency.extractProfile (this.hconsensus[column], this.av_ignoreGapsConsensus); +}}} else { +if (aa.autoCalculated && aa.label.startsWith ("StrucConsensus")) { +if (aa.groupRef == null && aa.sequenceRef == null && this.hStrucConsensus != null && this.hStrucConsensus.length > column) { +return jalview.analysis.StructureFrequency.extractProfile (this.hStrucConsensus[column], this.av_ignoreGapsConsensus); +}}}return null; +}, "jalview.datamodel.AlignmentAnnotation,~N"); +Clazz.defineMethod (c$, "drawComponent", +function (annotPanel, av, g, activeRow, startRes, endRes) { +var stime = System.currentTimeMillis (); +var usedFaded = false; +this.updateFromAwtRenderPanel (annotPanel, av); +this.fm = g.getFontMetrics (); +var aa = av.getAlignment ().getAlignmentAnnotation (); +var temp = 0; +if (aa == null) { +return false; +}var x = 0; +var y = 0; +var column = 0; +var lastSS; +var lastSSX; +var iconOffset = 0; +var validRes = false; +var validEnd = false; +var labelAllCols = false; +var centreColLabels; +var centreColLabelsDef = av.isCentreColumnLabels (); +var scaleColLabel = false; +var consensusAnnot = av.getAlignmentConsensusAnnotation (); +var structConsensusAnnot = av.getAlignmentStrucConsensusAnnotation (); +var complementConsensusAnnot = av.getComplementConsensusAnnotation (); +var renderHistogram = true; +var renderProfile = true; +var normaliseProfile = false; +var isRNA = this.rna; +var graphGroupDrawn = new java.util.BitSet (); +var charOffset = 0; +var fmWidth; +var fmScaling = 1; +var ofont = g.getFont (); +var yfrom = 0; +var f_i = 0; +var yto = 0; +var f_to = 0; +var clipst = false; +var clipend = false; +for (var i = 0; i < aa.length; i++) { +var row = aa[i]; +isRNA = row.isRNA (); +{ +if (row.groupRef != null && row === row.groupRef.getConsensus ()) { +renderHistogram = row.groupRef.isShowConsensusHistogram (); +renderProfile = row.groupRef.isShowSequenceLogo (); +normaliseProfile = row.groupRef.isNormaliseSequenceLogo (); +} else if (row === consensusAnnot || row === structConsensusAnnot || row === complementConsensusAnnot) { +renderHistogram = this.av_renderHistogram; +renderProfile = this.av_renderProfile; +normaliseProfile = this.av_normaliseProfile; +} else { +renderHistogram = true; +}}var row_annotations = row.annotations; +if (!row.visible) { +continue; +}centreColLabels = row.centreColLabels || centreColLabelsDef; +labelAllCols = row.showAllColLabels; +scaleColLabel = row.scaleColLabel; +lastSS = ' '; +lastSSX = 0; +if (!this.useClip || ((y - this.charHeight) < this.visHeight && (y + row.height + this.charHeight * 2) >= this.sOffset)) { +if (!clipst) { +clipst = true; +yfrom = y; +f_i = i; +}yto = y; +f_to = i; +if (row.graph > 0) { +if (row.graphGroup > -1 && graphGroupDrawn.get (row.graphGroup)) { +continue; +}y += row.height; +if (row.hasText) { +iconOffset = this.charHeight - this.fm.getDescent (); +y -= this.charHeight; +}} else if (row.hasText) { +iconOffset = this.charHeight - this.fm.getDescent (); +} else { +iconOffset = 0; +}if (row.autoCalculated && av.isCalculationInProgress (row)) { +y += this.charHeight; +usedFaded = true; +g.drawImage (this.fadedImage, 0, y - row.height, this.imgWidth, y, 0, y - row.height, this.imgWidth, y, this.annotationPanel); +g.setColor (java.awt.Color.black); +continue; +}x = (startRes == 0) ? 0 : -1; +while (x < endRes - startRes) { +if (this.hasHiddenColumns) { +column = this.columnSelection.adjustForHiddenColumns (startRes + x); +if (column > row_annotations.length - 1) { +break; +}} else { +column = startRes + x; +}if ((row_annotations == null) || (row_annotations.length <= column) || (row_annotations[column] == null)) { +validRes = false; +} else { +validRes = true; +}var displayChar = validRes ? row_annotations[column].displayCharacter : null; +if (x > -1) { +if (activeRow == i) { +g.setColor (java.awt.Color.red); +if (this.columnSelection != null) { +for (var n = 0; n < this.columnSelection.size (); n++) { +var v = this.columnSelection.columnAt (n); +if (v == column) { +g.fillRect (x * this.charWidth, y, this.charWidth, this.charHeight); +}} +}}if (row.getInvalidStrucPos () > x) { +g.setColor (java.awt.Color.orange); +g.fillRect (x * this.charWidth, y, this.charWidth, this.charHeight); +} else if (row.getInvalidStrucPos () == x) { +g.setColor (java.awt.Color.orange.darker ()); +g.fillRect (x * this.charWidth, y, this.charWidth, this.charHeight); +}if (this.validCharWidth && validRes && displayChar != null && (displayChar.length > 0)) { +fmWidth = this.fm.charsWidth (displayChar.toCharArray (), 0, displayChar.length); +if (scaleColLabel) { +if (fmWidth > this.charWidth) { +fmScaling = this.charWidth; +fmScaling /= fmWidth; +g.setFont (ofont.deriveFont (java.awt.geom.AffineTransform.getScaleInstance (fmScaling, 1.0))); +fmWidth = this.charWidth; +}}charOffset = Clazz.floatToInt ((this.charWidth - fmWidth) / 2); +if (row_annotations[column].colour == null) { +g.setColor (java.awt.Color.black); +} else { +g.setColor (row_annotations[column].colour); +}if (column == 0 || row.graph > 0) { +g.drawString (displayChar, (x * this.charWidth) + charOffset, y + iconOffset); +} else if (row_annotations[column - 1] == null || (labelAllCols || !displayChar.equals (row_annotations[column - 1].displayCharacter) || (displayChar.length < 2 && row_annotations[column].secondaryStructure == ' '))) { +g.drawString (displayChar, x * this.charWidth + charOffset, y + iconOffset); +}g.setFont (ofont); +}}if (row.hasIcons) { +var ss = validRes ? row_annotations[column].secondaryStructure : '-'; +if (ss == '(') { +if (displayChar.indexOf (')') > -1) { +ss = ')'; +}}if (ss == '[') { +if ((displayChar.indexOf (']') > -1)) { +ss = ']'; +}}if (ss == '{') { +if (displayChar.indexOf ('}') > -1) { +ss = '}'; +}}if (ss == '<') { +if (displayChar.indexOf ('<') > -1) { +ss = '>'; +}}if (ss.charCodeAt (0) >= 65) { +if (displayChar.indexOf (ss.charCodeAt (0) + 32) > -1) { +ss = String.fromCharCode (ss.charCodeAt (0) + 32); +}}if (!validRes || (ss != lastSS)) { +if (x > -1) { +var nb_annot = x - temp; +switch (lastSS) { +case '(': +case ')': +this.drawStemAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +temp = x; +break; +case 'H': +if (!isRNA) { +this.drawHelixAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +}case 'E': +if (!isRNA) { +this.drawSheetAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +}case '{': +case '}': +case '[': +case ']': +case '>': +case '<': +case 'A': +case 'a': +case 'B': +case 'b': +case 'C': +case 'c': +case 'D': +case 'd': +case 'e': +case 'F': +case 'f': +case 'G': +case 'g': +case 'h': +case 'I': +case 'i': +case 'J': +case 'j': +case 'K': +case 'k': +case 'L': +case 'l': +case 'M': +case 'm': +case 'N': +case 'n': +case 'O': +case 'o': +case 'P': +case 'p': +case 'Q': +case 'q': +case 'R': +case 'r': +case 'S': +case 's': +case 'T': +case 't': +case 'U': +case 'u': +case 'V': +case 'v': +case 'W': +case 'w': +case 'X': +case 'x': +case 'Y': +case 'y': +case 'Z': +case 'z': +var nonCanColor = this.getNotCanonicalColor (lastSS); +this.drawNotCanonicalAnnot (g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +temp = x; +break; +default: +g.setColor (java.awt.Color.gray); +g.fillRect (lastSSX, y + 6 + iconOffset, (x * this.charWidth) - lastSSX, 2); +temp = x; +break; +} +}if (validRes) { +lastSS = ss; +} else { +lastSS = ' '; +}if (x > -1) { +lastSSX = (x * this.charWidth); +}}}column++; +x++; +} +if (column >= row_annotations.length) { +column = row_annotations.length - 1; +validEnd = false; +} else { +validEnd = true; +}if ((row_annotations == null) || (row_annotations.length <= column) || (row_annotations[column] == null)) { +validRes = false; +} else { +validRes = true; +}if (row.hasIcons) { +switch (lastSS) { +case 'H': +if (!isRNA) { +this.drawHelixAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +}case 'E': +if (!isRNA) { +this.drawSheetAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +}case '(': +case ')': +this.drawStemAnnot (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +case '{': +case '}': +case '[': +case ']': +case '>': +case '<': +case 'A': +case 'a': +case 'B': +case 'b': +case 'C': +case 'c': +case 'D': +case 'd': +case 'e': +case 'F': +case 'f': +case 'G': +case 'g': +case 'h': +case 'I': +case 'i': +case 'J': +case 'j': +case 'K': +case 'k': +case 'L': +case 'l': +case 'M': +case 'm': +case 'N': +case 'n': +case 'O': +case 'o': +case 'P': +case 'p': +case 'Q': +case 'q': +case 'R': +case 'r': +case 'T': +case 't': +case 'U': +case 'u': +case 'V': +case 'v': +case 'W': +case 'w': +case 'X': +case 'x': +case 'Y': +case 'y': +case 'Z': +case 'z': +var nonCanColor = this.getNotCanonicalColor (lastSS); +this.drawNotCanonicalAnnot (g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +default: +this.drawGlyphLine (g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +break; +} +}if (row.graph > 0 && row.graphHeight > 0) { +if (row.graph == 2) { +if (row.graphGroup > -1 && !graphGroupDrawn.get (row.graphGroup)) { +var groupmax = -999999; +var groupmin = 9999999; +for (var gg = 0; gg < aa.length; gg++) { +if (aa[gg].graphGroup != row.graphGroup) { +continue; +}if (aa[gg] !== row) { +aa[gg].visible = false; +}if (aa[gg].graphMax > groupmax) { +groupmax = aa[gg].graphMax; +}if (aa[gg].graphMin < groupmin) { +groupmin = aa[gg].graphMin; +}} +for (var gg = 0; gg < aa.length; gg++) { +if (aa[gg].graphGroup == row.graphGroup) { +this.drawLineGraph (g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin, groupmax, row.graphHeight); +}} +graphGroupDrawn.set (row.graphGroup); +} else { +this.drawLineGraph (g, row, row_annotations, startRes, endRes, y, row.graphMin, row.graphMax, row.graphHeight); +}} else if (row.graph == 1) { +this.drawBarGraph (g, row, row_annotations, startRes, endRes, row.graphMin, row.graphMax, y, renderHistogram, renderProfile, normaliseProfile); +}}} else { +if (clipst && !clipend) { +clipend = true; +}}if (row.graph > 0 && row.hasText) { +y += this.charHeight; +}if (row.graph == 0) { +y += aa[i].height; +}} +if (this.debugRedraw) { +if (this.canClip) { +if (clipst) { +System.err.println ("Start clip at : " + yfrom + " (index " + f_i + ")"); +}if (clipend) { +System.err.println ("End clip at : " + yto + " (index " + f_to + ")"); +}};System.err.println ("Annotation Rendering time:" + (System.currentTimeMillis () - stime)); +};return !usedFaded; +}, "jalview.renderer.AwtRenderPanelI,jalview.api.AlignViewportI,java.awt.Graphics,~N,~N,~N"); +Clazz.defineMethod (c$, "drawGlyphLine", +function (g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { +g.setColor (jalview.renderer.AnnotationRenderer.GLYPHLINE_COLOR); +g.fillRect (lastSSX, y + 6 + iconOffset, (x * this.charWidth) - lastSSX, 2); +}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); +Clazz.defineMethod (c$, "drawSheetAnnot", +function (g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { +g.setColor (jalview.renderer.AnnotationRenderer.SHEET_COLOUR); +if (!validEnd || !validRes || row == null || row[column] == null || row[column].secondaryStructure != 'E') { +g.fillRect (lastSSX, y + 4 + iconOffset, (x * this.charWidth) - lastSSX - 4, 7); +g.fillPolygon ( Clazz.newIntArray (-1, [(x * this.charWidth) - 4, (x * this.charWidth) - 4, (x * this.charWidth)]), Clazz.newIntArray (-1, [y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset]), 3); +} else { +g.fillRect (lastSSX, y + 4 + iconOffset, (x + 1) * this.charWidth - lastSSX, 7); +}}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); +Clazz.defineMethod (c$, "drawHelixAnnot", +function (g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd) { +g.setColor (jalview.renderer.AnnotationRenderer.HELIX_COLOUR); +var sCol = (Clazz.doubleToInt (lastSSX / this.charWidth)) + startRes; +var x1 = lastSSX; +var x2 = (x * this.charWidth); +if (this.MAC) { +var ofs = Clazz.doubleToInt (this.charWidth / 2); +g.fillRoundRect (lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); +if (sCol == 0 || row[sCol - 1] == null || row[sCol - 1].secondaryStructure != 'H') { +} else { +g.fillRoundRect (lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, 0, 0); +}if (!validRes || row[column] == null || row[column].secondaryStructure != 'H') { +} else { +g.fillRoundRect (lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, 0, 0); +}return; +}if (sCol == 0 || row[sCol - 1] == null || row[sCol - 1].secondaryStructure != 'H') { +g.fillArc (lastSSX, y + 4 + iconOffset, this.charWidth, 8, 90, 180); +x1 += Clazz.doubleToInt (this.charWidth / 2); +}if (!validRes || row[column] == null || row[column].secondaryStructure != 'H') { +g.fillArc ((x * this.charWidth) - this.charWidth, y + 4 + iconOffset, this.charWidth, 8, 270, 180); +x2 -= Clazz.doubleToInt (this.charWidth / 2); +}g.fillRect (x1, y + 4 + iconOffset, x2 - x1, 8); +}, "java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B"); +Clazz.defineMethod (c$, "drawLineGraph", +function (g, _aa, aa_annotations, sRes, eRes, y, min, max, graphHeight) { +if (sRes > aa_annotations.length) { +return; +}var x = 0; +if (eRes < this.endRes) { +eRes++; +}eRes = Math.min (eRes, aa_annotations.length); +if (sRes == 0) { +x++; +}var y1 = y; +var y2 = y; +var range = max - min; +if (min < 0) { +y2 = y - Clazz.floatToInt ((0 - min / range) * graphHeight); +}g.setColor (java.awt.Color.gray); +g.drawLine (x - this.charWidth, y2, (eRes - sRes + 1) * this.charWidth, y2); +eRes = Math.min (eRes, aa_annotations.length); +var column; +var aaMax = aa_annotations.length - 1; +while (x < eRes - sRes) { +column = sRes + x; +if (this.hasHiddenColumns) { +column = this.columnSelection.adjustForHiddenColumns (column); +}if (column > aaMax) { +break; +}if (aa_annotations[column] == null || aa_annotations[column - 1] == null) { +x++; +continue; +}if (aa_annotations[column].colour == null) { +g.setColor (java.awt.Color.black); +} else { +g.setColor (aa_annotations[column].colour); +}y1 = y - Clazz.floatToInt (((aa_annotations[column - 1].value - min) / range) * graphHeight); +y2 = y - Clazz.floatToInt (((aa_annotations[column].value - min) / range) * graphHeight); +g.drawLine (x * this.charWidth - Clazz.doubleToInt (this.charWidth / 2), y1, x * this.charWidth + Clazz.doubleToInt (this.charWidth / 2), y2); +x++; +} +if (_aa.threshold != null) { +g.setColor (_aa.threshold.colour); +var g2 = g; +g2.setStroke ( new java.awt.BasicStroke (1, 2, 1, 3, Clazz.newFloatArray (-1, [5, 3]), 0)); +y2 = Clazz.floatToInt (y - ((_aa.threshold.value - min) / range) * graphHeight); +g.drawLine (0, y2, (eRes - sRes) * this.charWidth, y2); +g2.setStroke ( new java.awt.BasicStroke ()); +}}, "java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "drawBarGraph", +function (g, _aa, aa_annotations, sRes, eRes, min, max, y, renderHistogram, renderProfile, normaliseProfile) { +if (sRes > aa_annotations.length) { +return; +}var ofont = g.getFont (); +eRes = Math.min (eRes, aa_annotations.length); +var x = 0; +var y1 = y; +var y2 = y; +var range = max - min; +if (min < 0) { +y2 = y - Clazz.floatToInt ((0 - min / (range)) * _aa.graphHeight); +}g.setColor (java.awt.Color.gray); +g.drawLine (x, y2, (eRes - sRes) * this.charWidth, y2); +var column; +var aaMax = aa_annotations.length - 1; +while (x < eRes - sRes) { +column = sRes + x; +if (this.hasHiddenColumns) { +column = this.columnSelection.adjustForHiddenColumns (column); +}if (column > aaMax) { +break; +}if (aa_annotations[column] == null) { +x++; +continue; +}if (aa_annotations[column].colour == null) { +g.setColor (java.awt.Color.black); +} else { +g.setColor (aa_annotations[column].colour); +}y1 = y - Clazz.floatToInt (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight); +if (renderHistogram) { +if (y1 - y2 > 0) { +g.fillRect (x * this.charWidth, y2, this.charWidth, y1 - y2); +} else { +g.fillRect (x * this.charWidth, y1, this.charWidth, y2 - y1); +}}if (renderProfile) { +var profl = this.getProfileFor (_aa, column); +if (profl != null && profl[2] != 0) { +var isStructureProfile = profl[0] == 1; +var isCdnaProfile = profl[0] == 2; +var ht = normaliseProfile ? y - _aa.graphHeight : y1; +var htn = normaliseProfile ? _aa.graphHeight : (y2 - y1); +var hght; +var wdth; +var ht2 = 0; +var dc; +dc = Clazz.newCharArray (isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1), '\0'); +var lm = g.getFontMetrics (ofont).getLineMetrics ("Q", g); +var scale = 1 / (normaliseProfile ? profl[2] : 100); +var ofontHeight = 1 / lm.getAscent (); +var scl = 0.0; +var c = 3; +var valuesProcessed = 0; +while (valuesProcessed < profl[1]) { +if (isStructureProfile) { +dc[0] = String.fromCharCode (profl[c++]); +dc[1] = String.fromCharCode (profl[c++]); +} else if (isCdnaProfile) { +dc = jalview.analysis.CodingUtils.decodeCodon (profl[c++]); +} else { +dc[0] = String.fromCharCode (profl[c++]); +}wdth = this.charWidth; +wdth /= this.fm.charsWidth (dc, 0, dc.length); +ht += scl; +scl = htn * scale * profl[c++]; +lm = ofont.getLineMetrics (dc, 0, 1, g.getFontMetrics ().getFontRenderContext ()); +g.setFont (ofont.deriveFont (java.awt.geom.AffineTransform.getScaleInstance (wdth, scl / lm.getAscent ()))); +lm = g.getFontMetrics ().getLineMetrics (dc, 0, 1, g); +var colour = null; +if (isCdnaProfile) { +var codonTranslation = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (dc)); +colour = this.profcolour.findColour (codonTranslation.charAt (0), column, null); +} else { +colour = this.profcolour.findColour (dc[0], column, null); +}g.setColor (colour === java.awt.Color.white ? java.awt.Color.lightGray : colour); +hght = (ht + (scl - lm.getDescent () - lm.getBaselineOffsets ()[lm.getBaselineIndex ()])); +g.drawChars (dc, 0, dc.length, x * this.charWidth, Clazz.doubleToInt (hght)); +valuesProcessed++; +} +g.setFont (ofont); +}}x++; +} +if (_aa.threshold != null) { +g.setColor (_aa.threshold.colour); +var g2 = g; +g2.setStroke ( new java.awt.BasicStroke (1, 2, 1, 3, Clazz.newFloatArray (-1, [5, 3]), 0)); +y2 = Clazz.floatToInt (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight); +g.drawLine (0, y2, (eRes - sRes) * this.charWidth, y2); +g2.setStroke ( new java.awt.BasicStroke ()); +}}, "java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N,~N,~B,~B,~B"); +Clazz.defineMethod (c$, "drawGraph", +function (g, _aa, aa_annotations, width, y, sRes, eRes) { +eRes = Math.min (eRes, aa_annotations.length); +g.setColor (java.awt.Color.white); +g.fillRect (0, 0, width, y); +g.setColor ( new java.awt.Color (0, 0, 180)); +var x = 0; +var height; +for (var j = sRes; j < eRes; j++) { +if (aa_annotations[j] != null) { +if (aa_annotations[j].colour == null) { +g.setColor (java.awt.Color.black); +} else { +g.setColor (aa_annotations[j].colour); +}height = Clazz.floatToInt ((aa_annotations[j].value / _aa.graphMax) * y); +if (height > y) { +height = y; +}g.fillRect (x, y - height, this.charWidth, height); +}x += this.charWidth; +} +}, "java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "getNotCanonicalColor", +function (lastss) { +switch (lastss) { +case '{': +case '}': +return new java.awt.Color (255, 125, 5); +case '[': +case ']': +return new java.awt.Color (245, 115, 10); +case '>': +case '<': +return new java.awt.Color (235, 135, 15); +case 'A': +case 'a': +return new java.awt.Color (225, 105, 20); +case 'B': +case 'b': +return new java.awt.Color (215, 145, 30); +case 'C': +case 'c': +return new java.awt.Color (205, 95, 35); +case 'D': +case 'd': +return new java.awt.Color (195, 155, 45); +case 'E': +case 'e': +return new java.awt.Color (185, 85, 55); +case 'F': +case 'f': +return new java.awt.Color (175, 165, 65); +case 'G': +case 'g': +return new java.awt.Color (170, 75, 75); +case 'H': +case 'h': +return new java.awt.Color (160, 175, 85); +case 'I': +case 'i': +return new java.awt.Color (150, 65, 95); +case 'J': +case 'j': +return new java.awt.Color (140, 185, 105); +case 'K': +case 'k': +return new java.awt.Color (130, 55, 110); +case 'L': +case 'l': +return new java.awt.Color (120, 195, 120); +case 'M': +case 'm': +return new java.awt.Color (110, 45, 130); +case 'N': +case 'n': +return new java.awt.Color (100, 205, 140); +case 'O': +case 'o': +return new java.awt.Color (90, 35, 150); +case 'P': +case 'p': +return new java.awt.Color (85, 215, 160); +case 'Q': +case 'q': +return new java.awt.Color (75, 25, 170); +case 'R': +case 'r': +return new java.awt.Color (65, 225, 180); +case 'S': +case 's': +return new java.awt.Color (55, 15, 185); +case 'T': +case 't': +return new java.awt.Color (45, 235, 195); +case 'U': +case 'u': +return new java.awt.Color (35, 5, 205); +case 'V': +case 'v': +return new java.awt.Color (25, 245, 215); +case 'W': +case 'w': +return new java.awt.Color (15, 0, 225); +case 'X': +case 'x': +return new java.awt.Color (10, 255, 235); +case 'Y': +case 'y': +return new java.awt.Color (5, 150, 245); +case 'Z': +case 'z': +return new java.awt.Color (0, 80, 255); +default: +System.out.println ("This is not a interaction : " + lastss); +return null; +} +}, "~S"); +c$.GLYPHLINE_COLOR = c$.prototype.GLYPHLINE_COLOR = java.awt.Color.gray; +c$.SHEET_COLOUR = c$.prototype.SHEET_COLOUR = java.awt.Color.green; +c$.HELIX_COLOUR = c$.prototype.HELIX_COLOUR = java.awt.Color.red; +c$.STEM_COLOUR = c$.prototype.STEM_COLOUR = java.awt.Color.blue; +}); diff --git a/bin/jalview/renderer/AwtRenderPanelI.js b/bin/jalview/renderer/AwtRenderPanelI.js index e3aa6c9..42dbcc3 100644 --- a/bin/jalview/renderer/AwtRenderPanelI.js +++ b/bin/jalview/renderer/AwtRenderPanelI.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.renderer"); -Clazz.load (["java.awt.image.ImageObserver"], "jalview.renderer.AwtRenderPanelI", null, function () { -Clazz.declareInterface (jalview.renderer, "AwtRenderPanelI", java.awt.image.ImageObserver); -}); +Clazz.declarePackage ("jalview.renderer"); +Clazz.load (["java.awt.image.ImageObserver"], "jalview.renderer.AwtRenderPanelI", null, function () { +Clazz.declareInterface (jalview.renderer, "AwtRenderPanelI", java.awt.image.ImageObserver); +}); diff --git a/bin/jalview/renderer/seqfeatures/FeatureRenderer.class b/bin/jalview/renderer/seqfeatures/FeatureRenderer.class index 04d500b..9f05aad 100644 Binary files a/bin/jalview/renderer/seqfeatures/FeatureRenderer.class and b/bin/jalview/renderer/seqfeatures/FeatureRenderer.class differ diff --git a/bin/jalview/renderer/seqfeatures/FeatureRenderer.js b/bin/jalview/renderer/seqfeatures/FeatureRenderer.js index 019d218..7dc84b1 100644 --- a/bin/jalview/renderer/seqfeatures/FeatureRenderer.js +++ b/bin/jalview/renderer/seqfeatures/FeatureRenderer.js @@ -1,187 +1,187 @@ -Clazz.declarePackage ("jalview.renderer.seqfeatures"); -Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fm = null; -this.charOffset = 0; -this.offscreenRender = false; -this.lastSeq = null; -this.s = '\0'; -this.i = 0; -this.av_charHeight = 0; -this.av_charWidth = 0; -this.av_validCharWidth = false; -this.av_isShowSeqFeatureHeight = false; -this.offscreenImage = null; -this.lastSequenceFeatures = null; -this.sfSize = 0; -this.sfindex = 0; -this.spos = 0; -this.epos = 0; -this.transparencyAvailable = true; -Clazz.instantialize (this, arguments); -}, jalview.renderer.seqfeatures, "FeatureRenderer", jalview.viewmodel.seqfeatures.FeatureRendererModel); -Clazz.defineMethod (c$, "updateAvConfig", -function () { -this.av_charHeight = this.av.getCharHeight (); -this.av_charWidth = this.av.getCharWidth (); -this.av_validCharWidth = this.av.isValidCharWidth (); -this.av_isShowSeqFeatureHeight = this.av.isShowSequenceFeaturesHeight (); -}); -Clazz.defineMethod (c$, "renderFeature", -function (g, seq, fstart, fend, featureColour, start, end, y1) { -this.updateAvConfig (); -if (((fstart <= end) && (fend >= start))) { -if (fstart < start) { -fstart = start; -}if (fend >= end) { -fend = end; -}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5); -for (this.i = fstart; this.i <= fend; this.i++) { -this.s = seq.getCharAt (this.i); -if (jalview.util.Comparison.isGap (this.s)) { -continue; -}g.setColor (featureColour); -g.fillRect ((this.i - start) * this.av_charWidth, y1, this.av_charWidth, this.av_charHeight); -if (this.offscreenRender || !this.av_validCharWidth) { -continue; -}g.setColor (java.awt.Color.white); -this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2); -g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); -} -}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N"); -Clazz.defineMethod (c$, "renderScoreFeature", -function (g, seq, fstart, fend, featureColour, start, end, y1, bs) { -this.updateAvConfig (); -if (((fstart <= end) && (fend >= start))) { -if (fstart < start) { -fstart = start; -}if (fend >= end) { -fend = end; -}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5); -var ystrt = 0; -var yend = this.av_charHeight; -if (bs[0] != 0) { -if (bs[1] < 128) { -yend = Clazz.doubleToInt (this.av_charHeight * (128 - bs[1]) / 512); -ystrt = this.av_charHeight - Clazz.doubleToInt (yend / 2); -} else { -ystrt = Clazz.doubleToInt (this.av_charHeight / 2); -yend = Clazz.doubleToInt (this.av_charHeight * (bs[1] - 128) / 512); -}} else { -yend = Clazz.doubleToInt (this.av_charHeight * bs[1] / 255); -ystrt = this.av_charHeight - yend; -}for (this.i = fstart; this.i <= fend; this.i++) { -this.s = seq.getCharAt (this.i); -if (jalview.util.Comparison.isGap (this.s)) { -continue; -}g.setColor (featureColour); -var x = (this.i - start) * this.av_charWidth; -g.drawRect (x, y1, this.av_charWidth, this.av_charHeight); -g.fillRect (x, y1 + ystrt, this.av_charWidth, yend); -if (this.offscreenRender || !this.av_validCharWidth) { -continue; -}g.setColor (java.awt.Color.black); -this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2); -g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); -} -}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A"); -Clazz.defineMethod (c$, "findFeatureColour", -function (initialCol, seq, res) { -return new java.awt.Color (this.findFeatureColour (initialCol.getRGB (), seq, res)); -}, "java.awt.Color,jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "findFeatureColour", -function (initialCol, seq, column) { -if (!this.av.isShowSequenceFeatures ()) { -return initialCol; -}var sequenceFeatures = seq.getSequenceFeatures (); -if (seq !== this.lastSeq) { -this.lastSeq = seq; -this.lastSequenceFeatures = sequenceFeatures; -if (this.lastSequenceFeatures != null) { -this.sfSize = this.lastSequenceFeatures.length; -}} else { -if (this.lastSequenceFeatures !== sequenceFeatures) { -this.lastSequenceFeatures = sequenceFeatures; -if (this.lastSequenceFeatures != null) { -this.sfSize = this.lastSequenceFeatures.length; -}}}if (this.lastSequenceFeatures == null || this.sfSize == 0) { -return initialCol; -}if (jalview.util.Comparison.isGap (this.lastSeq.getCharAt (column))) { -return java.awt.Color.white.getRGB (); -}if (this.transparency != 1.0 && this.offscreenImage == null) { -this.offscreenImage = new java.awt.image.BufferedImage (1, 1, 2); -}this.currentColour = null; -this.offscreenRender = true; -if (this.offscreenImage != null) { -this.offscreenImage.setRGB (0, 0, initialCol); -this.drawSequence (this.offscreenImage.getGraphics (), this.lastSeq, column, column, 0); -return this.offscreenImage.getRGB (0, 0); -} else { -this.drawSequence (null, this.lastSeq, this.lastSeq.findPosition (column), -1, -1); -if (this.currentColour == null) { -return initialCol; -} else { -return (this.currentColour).intValue (); -}}}, "~N,jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "drawSequence", -function (g, seq, start, end, y1) { -var sequenceFeatures = seq.getSequenceFeatures (); -if (sequenceFeatures == null || sequenceFeatures.length == 0) { -return; -}if (g != null) { -this.fm = g.getFontMetrics (); -}this.updateFeatures (); -if (this.lastSeq == null || seq !== this.lastSeq || sequenceFeatures !== this.lastSequenceFeatures) { -this.lastSeq = seq; -this.lastSequenceFeatures = sequenceFeatures; -}if (this.transparency != 1 && g != null) { -var g2 = g; -g2.setComposite (java.awt.AlphaComposite.getInstance (3, this.transparency)); -}if (!this.offscreenRender) { -this.spos = this.lastSeq.findPosition (start); -this.epos = this.lastSeq.findPosition (end); -}this.sfSize = this.lastSequenceFeatures.length; -var type; -for (var renderIndex = 0; renderIndex < this.renderOrder.length; renderIndex++) { -type = this.renderOrder[renderIndex]; -if (type == null || !this.showFeatureOfType (type)) { -continue; -}for (this.sfindex = 0; this.sfindex < this.sfSize; this.sfindex++) { -var sequenceFeature = this.lastSequenceFeatures[this.sfindex]; -if (!sequenceFeature.type.equals (type)) { -continue; -}if (this.featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length != 0 && this.featureGroups.containsKey (sequenceFeature.featureGroup) && !this.featureGroups.get (sequenceFeature.featureGroup).booleanValue ()) { -continue; -}if (!this.offscreenRender && (sequenceFeature.getBegin () > this.epos || sequenceFeature.getEnd () < this.spos)) { -continue; -}if (this.offscreenRender && this.offscreenImage == null) { -if (sequenceFeature.begin <= start && sequenceFeature.end >= start) { -this.currentColour = new Integer (this.getColour (sequenceFeature).getRGB ()); -}} else if (sequenceFeature.type.equals ("disulfide bond")) { -this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.begin) - 1, this.getColour (sequenceFeature), start, end, y1); -this.renderFeature (g, seq, seq.findIndex (sequenceFeature.end) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1); -} else if (this.showFeature (sequenceFeature)) { -if (this.av_isShowSeqFeatureHeight && !Float.isNaN (sequenceFeature.score)) { -this.renderScoreFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1, this.normaliseScore (sequenceFeature)); -} else { -this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1); -}}} -} -if (this.transparency != 1.0 && g != null && this.transparencyAvailable) { -var g2 = g; -g2.setComposite (java.awt.AlphaComposite.getInstance (3, 1.0)); -}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,~N"); -Clazz.defineMethod (c$, "setTransparencyAvailable", -function (isTransparencyAvailable) { -this.transparencyAvailable = isTransparencyAvailable; -}, "~B"); -Clazz.overrideMethod (c$, "isTransparencyAvailable", -function () { -return this.transparencyAvailable; -}); -Clazz.overrideMethod (c$, "featuresAdded", -function () { -this.lastSeq = null; -this.findAllFeatures (); -}); -}); +Clazz.declarePackage ("jalview.renderer.seqfeatures"); +Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fm = null; +this.charOffset = 0; +this.offscreenRender = false; +this.lastSeq = null; +this.s = '\0'; +this.i = 0; +this.av_charHeight = 0; +this.av_charWidth = 0; +this.av_validCharWidth = false; +this.av_isShowSeqFeatureHeight = false; +this.offscreenImage = null; +this.lastSequenceFeatures = null; +this.sfSize = 0; +this.sfindex = 0; +this.spos = 0; +this.epos = 0; +this.transparencyAvailable = true; +Clazz.instantialize (this, arguments); +}, jalview.renderer.seqfeatures, "FeatureRenderer", jalview.viewmodel.seqfeatures.FeatureRendererModel); +Clazz.defineMethod (c$, "updateAvConfig", +function () { +this.av_charHeight = this.av.getCharHeight (); +this.av_charWidth = this.av.getCharWidth (); +this.av_validCharWidth = this.av.isValidCharWidth (); +this.av_isShowSeqFeatureHeight = this.av.isShowSequenceFeaturesHeight (); +}); +Clazz.defineMethod (c$, "renderFeature", +function (g, seq, fstart, fend, featureColour, start, end, y1) { +this.updateAvConfig (); +if (((fstart <= end) && (fend >= start))) { +if (fstart < start) { +fstart = start; +}if (fend >= end) { +fend = end; +}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5); +for (this.i = fstart; this.i <= fend; this.i++) { +this.s = seq.getCharAt (this.i); +if (jalview.util.Comparison.isGap (this.s)) { +continue; +}g.setColor (featureColour); +g.fillRect ((this.i - start) * this.av_charWidth, y1, this.av_charWidth, this.av_charHeight); +if (this.offscreenRender || !this.av_validCharWidth) { +continue; +}g.setColor (java.awt.Color.white); +this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2); +g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); +} +}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N"); +Clazz.defineMethod (c$, "renderScoreFeature", +function (g, seq, fstart, fend, featureColour, start, end, y1, bs) { +this.updateAvConfig (); +if (((fstart <= end) && (fend >= start))) { +if (fstart < start) { +fstart = start; +}if (fend >= end) { +fend = end; +}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5); +var ystrt = 0; +var yend = this.av_charHeight; +if (bs[0] != 0) { +if (bs[1] < 128) { +yend = Clazz.doubleToInt (this.av_charHeight * (128 - bs[1]) / 512); +ystrt = this.av_charHeight - Clazz.doubleToInt (yend / 2); +} else { +ystrt = Clazz.doubleToInt (this.av_charHeight / 2); +yend = Clazz.doubleToInt (this.av_charHeight * (bs[1] - 128) / 512); +}} else { +yend = Clazz.doubleToInt (this.av_charHeight * bs[1] / 255); +ystrt = this.av_charHeight - yend; +}for (this.i = fstart; this.i <= fend; this.i++) { +this.s = seq.getCharAt (this.i); +if (jalview.util.Comparison.isGap (this.s)) { +continue; +}g.setColor (featureColour); +var x = (this.i - start) * this.av_charWidth; +g.drawRect (x, y1, this.av_charWidth, this.av_charHeight); +g.fillRect (x, y1 + ystrt, this.av_charWidth, yend); +if (this.offscreenRender || !this.av_validCharWidth) { +continue; +}g.setColor (java.awt.Color.black); +this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2); +g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); +} +}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A"); +Clazz.defineMethod (c$, "findFeatureColour", +function (initialCol, seq, res) { +return new java.awt.Color (this.findFeatureColour (initialCol.getRGB (), seq, res)); +}, "java.awt.Color,jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "findFeatureColour", +function (initialCol, seq, column) { +if (!this.av.isShowSequenceFeatures ()) { +return initialCol; +}var sequenceFeatures = seq.getSequenceFeatures (); +if (seq !== this.lastSeq) { +this.lastSeq = seq; +this.lastSequenceFeatures = sequenceFeatures; +if (this.lastSequenceFeatures != null) { +this.sfSize = this.lastSequenceFeatures.length; +}} else { +if (this.lastSequenceFeatures !== sequenceFeatures) { +this.lastSequenceFeatures = sequenceFeatures; +if (this.lastSequenceFeatures != null) { +this.sfSize = this.lastSequenceFeatures.length; +}}}if (this.lastSequenceFeatures == null || this.sfSize == 0) { +return initialCol; +}if (jalview.util.Comparison.isGap (this.lastSeq.getCharAt (column))) { +return java.awt.Color.white.getRGB (); +}if (this.transparency != 1.0 && this.offscreenImage == null) { +this.offscreenImage = new java.awt.image.BufferedImage (1, 1, 2); +}this.currentColour = null; +this.offscreenRender = true; +if (this.offscreenImage != null) { +this.offscreenImage.setRGB (0, 0, initialCol); +this.drawSequence (this.offscreenImage.getGraphics (), this.lastSeq, column, column, 0); +return this.offscreenImage.getRGB (0, 0); +} else { +this.drawSequence (null, this.lastSeq, this.lastSeq.findPosition (column), -1, -1); +if (this.currentColour == null) { +return initialCol; +} else { +return (this.currentColour).intValue (); +}}}, "~N,jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "drawSequence", +function (g, seq, start, end, y1) { +var sequenceFeatures = seq.getSequenceFeatures (); +if (sequenceFeatures == null || sequenceFeatures.length == 0) { +return; +}if (g != null) { +this.fm = g.getFontMetrics (); +}this.updateFeatures (); +if (this.lastSeq == null || seq !== this.lastSeq || sequenceFeatures !== this.lastSequenceFeatures) { +this.lastSeq = seq; +this.lastSequenceFeatures = sequenceFeatures; +}if (this.transparency != 1 && g != null) { +var g2 = g; +g2.setComposite (java.awt.AlphaComposite.getInstance (3, this.transparency)); +}if (!this.offscreenRender) { +this.spos = this.lastSeq.findPosition (start); +this.epos = this.lastSeq.findPosition (end); +}this.sfSize = this.lastSequenceFeatures.length; +var type; +for (var renderIndex = 0; renderIndex < this.renderOrder.length; renderIndex++) { +type = this.renderOrder[renderIndex]; +if (type == null || !this.showFeatureOfType (type)) { +continue; +}for (this.sfindex = 0; this.sfindex < this.sfSize; this.sfindex++) { +var sequenceFeature = this.lastSequenceFeatures[this.sfindex]; +if (!sequenceFeature.type.equals (type)) { +continue; +}if (this.featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length != 0 && this.featureGroups.containsKey (sequenceFeature.featureGroup) && !this.featureGroups.get (sequenceFeature.featureGroup).booleanValue ()) { +continue; +}if (!this.offscreenRender && (sequenceFeature.getBegin () > this.epos || sequenceFeature.getEnd () < this.spos)) { +continue; +}if (this.offscreenRender && this.offscreenImage == null) { +if (sequenceFeature.begin <= start && sequenceFeature.end >= start) { +this.currentColour = new Integer (this.getColour (sequenceFeature).getRGB ()); +}} else if (sequenceFeature.type.equals ("disulfide bond")) { +this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.begin) - 1, this.getColour (sequenceFeature), start, end, y1); +this.renderFeature (g, seq, seq.findIndex (sequenceFeature.end) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1); +} else if (this.showFeature (sequenceFeature)) { +if (this.av_isShowSeqFeatureHeight && !Float.isNaN (sequenceFeature.score)) { +this.renderScoreFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1, this.normaliseScore (sequenceFeature)); +} else { +this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1); +}}} +} +if (this.transparency != 1.0 && g != null && this.transparencyAvailable) { +var g2 = g; +g2.setComposite (java.awt.AlphaComposite.getInstance (3, 1.0)); +}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,~N"); +Clazz.defineMethod (c$, "setTransparencyAvailable", +function (isTransparencyAvailable) { +this.transparencyAvailable = isTransparencyAvailable; +}, "~B"); +Clazz.overrideMethod (c$, "isTransparencyAvailable", +function () { +return this.transparencyAvailable; +}); +Clazz.overrideMethod (c$, "featuresAdded", +function () { +this.lastSeq = null; +this.findAllFeatures (); +}); +}); diff --git a/bin/jalview/schemes/AnnotationColourGradient.class b/bin/jalview/schemes/AnnotationColourGradient.class index 65eb813..04210df 100644 Binary files a/bin/jalview/schemes/AnnotationColourGradient.class and b/bin/jalview/schemes/AnnotationColourGradient.class differ diff --git a/bin/jalview/schemes/AnnotationColourGradient.js b/bin/jalview/schemes/AnnotationColourGradient.js index 40ed8eb..0f29e11 100644 --- a/bin/jalview/schemes/AnnotationColourGradient.js +++ b/bin/jalview/schemes/AnnotationColourGradient.js @@ -1,200 +1,200 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.FollowerColourScheme"], "jalview.schemes.AnnotationColourGradient", ["jalview.datamodel.AlignmentI", "$.GraphLine", "jalview.renderer.AnnotationRenderer", "jalview.schemes.ColourSchemeProperty", "jalview.util.Comparison", "java.awt.Color", "java.util.IdentityHashMap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.annotation = null; -this.aboveAnnotationThreshold = -1; -this.thresholdIsMinMax = false; -this.annotationThreshold = null; -this.r1 = 0; -this.g1 = 0; -this.b1 = 0; -this.rr = 0; -this.gg = 0; -this.bb = 0; -this.predefinedColours = false; -this.seqAssociated = false; -this.noGradient = false; -this.seqannot = null; -this.aamin = 0; -this.aamax = 0; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "AnnotationColourGradient", jalview.schemes.FollowerColourScheme); -Clazz.overrideMethod (c$, "applyTo", -function (sg, hiddenRepSequences) { -var acg = new jalview.schemes.AnnotationColourGradient (this.annotation, this.colourScheme, this.aboveAnnotationThreshold); -acg.thresholdIsMinMax = this.thresholdIsMinMax; -acg.annotationThreshold = (this.annotationThreshold == null) ? null : new jalview.datamodel.GraphLine (this.annotationThreshold); -acg.r1 = this.r1; -acg.g1 = this.g1; -acg.b1 = this.b1; -acg.rr = this.rr; -acg.gg = this.gg; -acg.bb = this.bb; -acg.predefinedColours = this.predefinedColours; -acg.seqAssociated = this.seqAssociated; -acg.noGradient = this.noGradient; -return acg; -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.makeConstructor (c$, -function (annotation, originalColour, aboveThreshold) { -Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []); -if (Clazz.instanceOf (originalColour, jalview.schemes.AnnotationColourGradient)) { -this.colourScheme = (originalColour).colourScheme; -} else { -this.colourScheme = originalColour; -}this.annotation = annotation; -this.aboveAnnotationThreshold = aboveThreshold; -if (aboveThreshold != -1 && annotation.threshold != null) { -this.annotationThreshold = annotation.threshold; -}this.r1 = 254; -this.g1 = 254; -this.b1 = 254; -this.rr = 0; -this.gg = 0; -this.bb = 0; -this.noGradient = true; -}, "jalview.datamodel.AlignmentAnnotation,jalview.schemes.ColourSchemeI,~N"); -Clazz.makeConstructor (c$, -function (annotation, minColour, maxColour, aboveThreshold) { -Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []); -this.annotation = annotation; -this.aboveAnnotationThreshold = aboveThreshold; -if (aboveThreshold != -1 && annotation.threshold != null) { -this.annotationThreshold = annotation.threshold; -}this.r1 = minColour.getRed (); -this.g1 = minColour.getGreen (); -this.b1 = minColour.getBlue (); -this.rr = maxColour.getRed () - this.r1; -this.gg = maxColour.getGreen () - this.g1; -this.bb = maxColour.getBlue () - this.b1; -this.noGradient = false; -this.aamax = annotation.graphMax; -this.aamin = annotation.graphMin; -if (annotation.isRNA ()) { -jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax)); -}}, "jalview.datamodel.AlignmentAnnotation,java.awt.Color,java.awt.Color,~N"); -Clazz.defineMethod (c$, "alignmentChanged", -function (alignment, hiddenReps) { -Clazz.superCall (this, jalview.schemes.AnnotationColourGradient, "alignmentChanged", [alignment, hiddenReps]); -if (this.seqAssociated && this.annotation.getCalcId () != null) { -if (this.seqannot != null) { -this.seqannot.clear (); -} else { -this.seqannot = new java.util.IdentityHashMap (); -}var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext (); -var f = true; -var rna = false; -for (var alan, $alan = alcontext.findAnnotation (this.annotation.getCalcId ()).iterator (); $alan.hasNext () && ((alan = $alan.next ()) || true);) { -if (alan.sequenceRef != null && (alan.label != null && this.annotation != null && alan.label.equals (this.annotation.label))) { -if (!rna && alan.isRNA ()) { -rna = true; -}this.seqannot.put (alan.sequenceRef, alan); -if (f || alan.graphMax > this.aamax) { -this.aamax = alan.graphMax; -}if (f || alan.graphMin < this.aamin) { -this.aamin = alan.graphMin; -}f = false; -}} -if (rna) { -jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax)); -}}}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.defineMethod (c$, "getAnnotation", -function () { -return this.annotation.label; -}); -Clazz.defineMethod (c$, "getAboveThreshold", -function () { -return this.aboveAnnotationThreshold; -}); -Clazz.defineMethod (c$, "getAnnotationThreshold", -function () { -if (this.annotationThreshold == null) { -return 0; -} else { -return this.annotationThreshold.value; -}}); -Clazz.defineMethod (c$, "getMinColour", -function () { -return new java.awt.Color (Clazz.floatToInt (this.r1), Clazz.floatToInt (this.g1), Clazz.floatToInt (this.b1)); -}); -Clazz.defineMethod (c$, "getMaxColour", -function () { -return new java.awt.Color (Clazz.floatToInt (this.r1 + this.rr), Clazz.floatToInt (this.g1 + this.gg), Clazz.floatToInt (this.b1 + this.bb)); -}); -Clazz.defineMethod (c$, "findColour", -function (c) { -return java.awt.Color.red; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var currentColour = java.awt.Color.white; -var annotation = (this.seqAssociated && this.seqannot != null ? this.seqannot.get (seq) : this.annotation); -if (annotation == null) { -return currentColour; -}if ((this.threshold == 0) || this.aboveThreshold (c, j)) { -if (annotation.annotations != null && j < annotation.annotations.length && annotation.annotations[j] != null && !jalview.util.Comparison.isGap (c)) { -var aj = annotation.annotations[j]; -if (this.aboveAnnotationThreshold == -1 || (this.annotationThreshold != null && (this.aboveAnnotationThreshold == 1 ? aj.value >= this.annotationThreshold.value : aj.value <= this.annotationThreshold.value))) { -if (this.predefinedColours && aj.colour != null && !aj.colour.equals (java.awt.Color.black)) { -currentColour = aj.colour; -} else if (annotation.hasIcons && annotation.graph == 0) { -if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' && aj.secondaryStructure != '-') { -if (this.colourScheme != null) { -currentColour = this.colourScheme.findColour (c, j, seq); -} else { -if (annotation.isRNA ()) { -currentColour = jalview.schemes.ColourSchemeProperty.rnaHelices[Clazz.floatToInt (aj.value)]; -} else { -currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR : jalview.renderer.AnnotationRenderer.STEM_COLOUR; -}}} else { -return java.awt.Color.white; -}} else if (this.noGradient) { -if (this.colourScheme != null) { -currentColour = this.colourScheme.findColour (c, j, seq); -} else { -if (aj.colour != null) { -currentColour = aj.colour; -}}} else { -currentColour = this.shadeCalculation (annotation, j); -}}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}}}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "shadeCalculation", -($fz = function (annotation, j) { -var range = 1; -if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 1 && annotation.annotations[j].value >= annotation.threshold.value) { -range = (annotation.annotations[j].value - annotation.threshold.value) / (annotation.graphMax - annotation.threshold.value); -} else if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 0 && annotation.annotations[j].value >= annotation.graphMin) { -range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.threshold.value - annotation.graphMin); -} else { -if (annotation.graphMax != annotation.graphMin) { -range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.graphMax - annotation.graphMin); -} else { -range = 0; -}}var dr = Clazz.floatToInt (this.rr * range + this.r1); -var dg = Clazz.floatToInt (this.gg * range + this.g1); -var db = Clazz.floatToInt (this.bb * range + this.b1); -return new java.awt.Color (dr, dg, db); -}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,~N"); -Clazz.defineMethod (c$, "isPredefinedColours", -function () { -return this.predefinedColours; -}); -Clazz.defineMethod (c$, "setPredefinedColours", -function (predefinedColours) { -this.predefinedColours = predefinedColours; -}, "~B"); -Clazz.defineMethod (c$, "isSeqAssociated", -function () { -return this.seqAssociated; -}); -Clazz.defineMethod (c$, "setSeqAssociated", -function (sassoc) { -this.seqAssociated = sassoc; -}, "~B"); -Clazz.defineStatics (c$, -"NO_THRESHOLD", -1, -"BELOW_THRESHOLD", 0, -"ABOVE_THRESHOLD", 1); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.FollowerColourScheme"], "jalview.schemes.AnnotationColourGradient", ["jalview.datamodel.AlignmentI", "$.GraphLine", "jalview.renderer.AnnotationRenderer", "jalview.schemes.ColourSchemeProperty", "jalview.util.Comparison", "java.awt.Color", "java.util.IdentityHashMap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.annotation = null; +this.aboveAnnotationThreshold = -1; +this.thresholdIsMinMax = false; +this.annotationThreshold = null; +this.r1 = 0; +this.g1 = 0; +this.b1 = 0; +this.rr = 0; +this.gg = 0; +this.bb = 0; +this.predefinedColours = false; +this.seqAssociated = false; +this.noGradient = false; +this.seqannot = null; +this.aamin = 0; +this.aamax = 0; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "AnnotationColourGradient", jalview.schemes.FollowerColourScheme); +Clazz.overrideMethod (c$, "applyTo", +function (sg, hiddenRepSequences) { +var acg = new jalview.schemes.AnnotationColourGradient (this.annotation, this.colourScheme, this.aboveAnnotationThreshold); +acg.thresholdIsMinMax = this.thresholdIsMinMax; +acg.annotationThreshold = (this.annotationThreshold == null) ? null : new jalview.datamodel.GraphLine (this.annotationThreshold); +acg.r1 = this.r1; +acg.g1 = this.g1; +acg.b1 = this.b1; +acg.rr = this.rr; +acg.gg = this.gg; +acg.bb = this.bb; +acg.predefinedColours = this.predefinedColours; +acg.seqAssociated = this.seqAssociated; +acg.noGradient = this.noGradient; +return acg; +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.makeConstructor (c$, +function (annotation, originalColour, aboveThreshold) { +Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []); +if (Clazz.instanceOf (originalColour, jalview.schemes.AnnotationColourGradient)) { +this.colourScheme = (originalColour).colourScheme; +} else { +this.colourScheme = originalColour; +}this.annotation = annotation; +this.aboveAnnotationThreshold = aboveThreshold; +if (aboveThreshold != -1 && annotation.threshold != null) { +this.annotationThreshold = annotation.threshold; +}this.r1 = 254; +this.g1 = 254; +this.b1 = 254; +this.rr = 0; +this.gg = 0; +this.bb = 0; +this.noGradient = true; +}, "jalview.datamodel.AlignmentAnnotation,jalview.schemes.ColourSchemeI,~N"); +Clazz.makeConstructor (c$, +function (annotation, minColour, maxColour, aboveThreshold) { +Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []); +this.annotation = annotation; +this.aboveAnnotationThreshold = aboveThreshold; +if (aboveThreshold != -1 && annotation.threshold != null) { +this.annotationThreshold = annotation.threshold; +}this.r1 = minColour.getRed (); +this.g1 = minColour.getGreen (); +this.b1 = minColour.getBlue (); +this.rr = maxColour.getRed () - this.r1; +this.gg = maxColour.getGreen () - this.g1; +this.bb = maxColour.getBlue () - this.b1; +this.noGradient = false; +this.aamax = annotation.graphMax; +this.aamin = annotation.graphMin; +if (annotation.isRNA ()) { +jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax)); +}}, "jalview.datamodel.AlignmentAnnotation,java.awt.Color,java.awt.Color,~N"); +Clazz.defineMethod (c$, "alignmentChanged", +function (alignment, hiddenReps) { +Clazz.superCall (this, jalview.schemes.AnnotationColourGradient, "alignmentChanged", [alignment, hiddenReps]); +if (this.seqAssociated && this.annotation.getCalcId () != null) { +if (this.seqannot != null) { +this.seqannot.clear (); +} else { +this.seqannot = new java.util.IdentityHashMap (); +}var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext (); +var f = true; +var rna = false; +for (var alan, $alan = alcontext.findAnnotation (this.annotation.getCalcId ()).iterator (); $alan.hasNext () && ((alan = $alan.next ()) || true);) { +if (alan.sequenceRef != null && (alan.label != null && this.annotation != null && alan.label.equals (this.annotation.label))) { +if (!rna && alan.isRNA ()) { +rna = true; +}this.seqannot.put (alan.sequenceRef, alan); +if (f || alan.graphMax > this.aamax) { +this.aamax = alan.graphMax; +}if (f || alan.graphMin < this.aamin) { +this.aamin = alan.graphMin; +}f = false; +}} +if (rna) { +jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax)); +}}}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.defineMethod (c$, "getAnnotation", +function () { +return this.annotation.label; +}); +Clazz.defineMethod (c$, "getAboveThreshold", +function () { +return this.aboveAnnotationThreshold; +}); +Clazz.defineMethod (c$, "getAnnotationThreshold", +function () { +if (this.annotationThreshold == null) { +return 0; +} else { +return this.annotationThreshold.value; +}}); +Clazz.defineMethod (c$, "getMinColour", +function () { +return new java.awt.Color (Clazz.floatToInt (this.r1), Clazz.floatToInt (this.g1), Clazz.floatToInt (this.b1)); +}); +Clazz.defineMethod (c$, "getMaxColour", +function () { +return new java.awt.Color (Clazz.floatToInt (this.r1 + this.rr), Clazz.floatToInt (this.g1 + this.gg), Clazz.floatToInt (this.b1 + this.bb)); +}); +Clazz.defineMethod (c$, "findColour", +function (c) { +return java.awt.Color.red; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var currentColour = java.awt.Color.white; +var annotation = (this.seqAssociated && this.seqannot != null ? this.seqannot.get (seq) : this.annotation); +if (annotation == null) { +return currentColour; +}if ((this.threshold == 0) || this.aboveThreshold (c, j)) { +if (annotation.annotations != null && j < annotation.annotations.length && annotation.annotations[j] != null && !jalview.util.Comparison.isGap (c)) { +var aj = annotation.annotations[j]; +if (this.aboveAnnotationThreshold == -1 || (this.annotationThreshold != null && (this.aboveAnnotationThreshold == 1 ? aj.value >= this.annotationThreshold.value : aj.value <= this.annotationThreshold.value))) { +if (this.predefinedColours && aj.colour != null && !aj.colour.equals (java.awt.Color.black)) { +currentColour = aj.colour; +} else if (annotation.hasIcons && annotation.graph == 0) { +if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' && aj.secondaryStructure != '-') { +if (this.colourScheme != null) { +currentColour = this.colourScheme.findColour (c, j, seq); +} else { +if (annotation.isRNA ()) { +currentColour = jalview.schemes.ColourSchemeProperty.rnaHelices[Clazz.floatToInt (aj.value)]; +} else { +currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR : jalview.renderer.AnnotationRenderer.STEM_COLOUR; +}}} else { +return java.awt.Color.white; +}} else if (this.noGradient) { +if (this.colourScheme != null) { +currentColour = this.colourScheme.findColour (c, j, seq); +} else { +if (aj.colour != null) { +currentColour = aj.colour; +}}} else { +currentColour = this.shadeCalculation (annotation, j); +}}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}}}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "shadeCalculation", +($fz = function (annotation, j) { +var range = 1; +if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 1 && annotation.annotations[j].value >= annotation.threshold.value) { +range = (annotation.annotations[j].value - annotation.threshold.value) / (annotation.graphMax - annotation.threshold.value); +} else if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 0 && annotation.annotations[j].value >= annotation.graphMin) { +range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.threshold.value - annotation.graphMin); +} else { +if (annotation.graphMax != annotation.graphMin) { +range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.graphMax - annotation.graphMin); +} else { +range = 0; +}}var dr = Clazz.floatToInt (this.rr * range + this.r1); +var dg = Clazz.floatToInt (this.gg * range + this.g1); +var db = Clazz.floatToInt (this.bb * range + this.b1); +return new java.awt.Color (dr, dg, db); +}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation,~N"); +Clazz.defineMethod (c$, "isPredefinedColours", +function () { +return this.predefinedColours; +}); +Clazz.defineMethod (c$, "setPredefinedColours", +function (predefinedColours) { +this.predefinedColours = predefinedColours; +}, "~B"); +Clazz.defineMethod (c$, "isSeqAssociated", +function () { +return this.seqAssociated; +}); +Clazz.defineMethod (c$, "setSeqAssociated", +function (sassoc) { +this.seqAssociated = sassoc; +}, "~B"); +Clazz.defineStatics (c$, +"NO_THRESHOLD", -1, +"BELOW_THRESHOLD", 0, +"ABOVE_THRESHOLD", 1); +}); diff --git a/bin/jalview/schemes/Blosum62ColourScheme.class b/bin/jalview/schemes/Blosum62ColourScheme.class index f864598..17dd259 100644 Binary files a/bin/jalview/schemes/Blosum62ColourScheme.class and b/bin/jalview/schemes/Blosum62ColourScheme.class differ diff --git a/bin/jalview/schemes/Blosum62ColourScheme.js b/bin/jalview/schemes/Blosum62ColourScheme.js index 3268bc7..87c4a51 100644 --- a/bin/jalview/schemes/Blosum62ColourScheme.js +++ b/bin/jalview/schemes/Blosum62ColourScheme.js @@ -1,37 +1,37 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.Blosum62ColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "Blosum62ColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.defineMethod (c$, "findColour", -function (res, j, seq) { -if ('a' <= res && res <= 'z') { -res = String.fromCharCode (res.charCodeAt (0) - (32)); -}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null || (this.threshold != 0 && !this.aboveThreshold (res, j))) { -return java.awt.Color.white; -}var currentColour; -if (!jalview.util.Comparison.isGap (res)) { -var max = this.consensus[j].get ("R"); -if (max.indexOf (res) > -1) { -currentColour = new java.awt.Color (154, 154, 255); -} else { -var c = 0; -var max_aa = 0; -var n = max.length; -do { -c += jalview.schemes.ResidueProperties.getBLOSUM62 (max.charAt (max_aa), res); -} while (++max_aa < n); -if (c > 0) { -currentColour = new java.awt.Color (204, 204, 255); -} else { -currentColour = java.awt.Color.white; -}}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}} else { -return java.awt.Color.white; -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "applyTo", -function (sg, hiddenRepSequences) { -var newcs = Clazz.superCall (this, jalview.schemes.Blosum62ColourScheme, "applyTo", [sg, hiddenRepSequences]); -return newcs; -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.Blosum62ColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "Blosum62ColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.defineMethod (c$, "findColour", +function (res, j, seq) { +if ('a' <= res && res <= 'z') { +res = String.fromCharCode (res.charCodeAt (0) - (32)); +}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null || (this.threshold != 0 && !this.aboveThreshold (res, j))) { +return java.awt.Color.white; +}var currentColour; +if (!jalview.util.Comparison.isGap (res)) { +var max = this.consensus[j].get ("R"); +if (max.indexOf (res) > -1) { +currentColour = new java.awt.Color (154, 154, 255); +} else { +var c = 0; +var max_aa = 0; +var n = max.length; +do { +c += jalview.schemes.ResidueProperties.getBLOSUM62 (max.charAt (max_aa), res); +} while (++max_aa < n); +if (c > 0) { +currentColour = new java.awt.Color (204, 204, 255); +} else { +currentColour = java.awt.Color.white; +}}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}} else { +return java.awt.Color.white; +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "applyTo", +function (sg, hiddenRepSequences) { +var newcs = Clazz.superCall (this, jalview.schemes.Blosum62ColourScheme, "applyTo", [sg, hiddenRepSequences]); +return newcs; +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +}); diff --git a/bin/jalview/schemes/BuriedColourScheme.js b/bin/jalview/schemes/BuriedColourScheme.js index fa820e3..0ca91cd 100644 --- a/bin/jalview/schemes/BuriedColourScheme.js +++ b/bin/jalview/schemes/BuriedColourScheme.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.BuriedColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "BuriedColourScheme", jalview.schemes.ScoreColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.BuriedColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.buried, 0.05, 4.6]); -}); -Clazz.overrideMethod (c$, "makeColour", -function (c) { -return new java.awt.Color (0, (1.0 - c), c); -}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.BuriedColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "BuriedColourScheme", jalview.schemes.ScoreColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.BuriedColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.buried, 0.05, 4.6]); +}); +Clazz.overrideMethod (c$, "makeColour", +function (c) { +return new java.awt.Color (0, (1.0 - c), c); +}, "~N"); +}); diff --git a/bin/jalview/schemes/ClustalxColourScheme.js b/bin/jalview/schemes/ClustalxColourScheme.js index 3897463..0556777 100644 --- a/bin/jalview/schemes/ClustalxColourScheme.js +++ b/bin/jalview/schemes/ClustalxColourScheme.js @@ -1,237 +1,237 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.HashMap"], ["jalview.schemes.ConsensusColour", "$.ClustalxColourScheme"], ["jalview.schemes.Consensus", "$.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.decorateAsClass (function () { -this.cons2 = null; -this.colours = null; -this.residueColour = null; -this.size = 0; -this.conses = null; -this.includeGaps = true; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "ClustalxColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.prepareFields (c$, function () { -this.conses = new Array (32); -}); -Clazz.makeConstructor (c$, -function (alignment, hiddenReps) { -Clazz.superConstructor (this, jalview.schemes.ClustalxColourScheme, []); -this.alignmentChanged (alignment, hiddenReps); -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.overrideMethod (c$, "alignmentChanged", -function (alignment, hiddenReps) { -var maxWidth = alignment.getWidth (); -var seqs = alignment.getSequences (hiddenReps); -this.cons2 = Clazz.newIntArray (maxWidth, 24, 0); -this.includeGaps = this.isIncludeGaps (); -var start = 0; -for (var j = 0; j < 24; j++) { -for (var i = 0; i < maxWidth; i++) { -this.cons2[i][j] = 0; -} -} -var res; -var i; -var j = 0; -var seq; -for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { -seq = sq.getSequence (); -var end_j = seq.length - 1; -for (i = start; i <= end_j; i++) { -if ((seq.length - 1) < i) { -res = 23; -} else { -res = jalview.schemes.ResidueProperties.aaIndex[seq[i].charCodeAt (0)]; -}this.cons2[i][res]++; -} -j++; -} -this.size = seqs.size (); -this.makeColours (); -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.defineMethod (c$, "makeColours", -function () { -this.conses[0] = new jalview.schemes.Consensus ("WLVIMAFCYHP", 60); -this.conses[1] = new jalview.schemes.Consensus ("WLVIMAFCYHP", 80); -this.conses[2] = new jalview.schemes.Consensus ("ED", 50); -this.conses[3] = new jalview.schemes.Consensus ("KR", 60); -this.conses[4] = new jalview.schemes.Consensus ("G", 50); -this.conses[5] = new jalview.schemes.Consensus ("N", 50); -this.conses[6] = new jalview.schemes.Consensus ("QE", 50); -this.conses[7] = new jalview.schemes.Consensus ("P", 50); -this.conses[8] = new jalview.schemes.Consensus ("TS", 50); -this.conses[26] = new jalview.schemes.Consensus ("A", 85); -this.conses[27] = new jalview.schemes.Consensus ("C", 85); -this.conses[10] = new jalview.schemes.Consensus ("E", 85); -this.conses[11] = new jalview.schemes.Consensus ("F", 85); -this.conses[12] = new jalview.schemes.Consensus ("G", 85); -this.conses[13] = new jalview.schemes.Consensus ("H", 85); -this.conses[14] = new jalview.schemes.Consensus ("I", 85); -this.conses[15] = new jalview.schemes.Consensus ("L", 85); -this.conses[16] = new jalview.schemes.Consensus ("M", 85); -this.conses[17] = new jalview.schemes.Consensus ("N", 85); -this.conses[18] = new jalview.schemes.Consensus ("P", 85); -this.conses[19] = new jalview.schemes.Consensus ("Q", 85); -this.conses[20] = new jalview.schemes.Consensus ("R", 85); -this.conses[21] = new jalview.schemes.Consensus ("S", 85); -this.conses[22] = new jalview.schemes.Consensus ("T", 85); -this.conses[23] = new jalview.schemes.Consensus ("V", 85); -this.conses[24] = new jalview.schemes.Consensus ("W", 85); -this.conses[25] = new jalview.schemes.Consensus ("Y", 85); -this.conses[28] = new jalview.schemes.Consensus ("K", 85); -this.conses[29] = new jalview.schemes.Consensus ("D", 85); -this.conses[30] = new jalview.schemes.Consensus ("G", 0); -this.conses[31] = new jalview.schemes.Consensus ("P", 0); -this.colours = new Array (11); -var tmp8 = new Array (1); -tmp8[0] = this.conses[30]; -this.colours[7] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.ORANGE), tmp8); -var tmp9 = new Array (1); -tmp9[0] = this.conses[31]; -this.colours[8] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.YELLOW), tmp9); -var tmp10 = new Array (1); -tmp10[0] = this.conses[27]; -this.colours[9] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK), tmp8); -var tmp1 = new Array (14); -tmp1[0] = this.conses[0]; -tmp1[1] = this.conses[1]; -tmp1[2] = this.conses[26]; -tmp1[3] = this.conses[27]; -tmp1[4] = this.conses[11]; -tmp1[5] = this.conses[13]; -tmp1[6] = this.conses[14]; -tmp1[7] = this.conses[15]; -tmp1[8] = this.conses[16]; -tmp1[9] = this.conses[23]; -tmp1[10] = this.conses[24]; -tmp1[11] = this.conses[25]; -tmp1[12] = this.conses[18]; -tmp1[13] = this.conses[19]; -this.colours[0] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.BLUE), tmp1); -this.colours[10] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.CYAN), tmp1); -var tmp2 = new Array (5); -tmp2[0] = this.conses[8]; -tmp2[1] = this.conses[21]; -tmp2[2] = this.conses[22]; -tmp2[3] = this.conses[0]; -tmp2[4] = this.conses[1]; -this.colours[1] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp2); -var tmp3 = new Array (3); -tmp3[0] = this.conses[17]; -tmp3[1] = this.conses[29]; -tmp3[2] = this.conses[5]; -this.colours[2] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp3); -var tmp4 = new Array (6); -tmp4[0] = this.conses[6]; -tmp4[1] = this.conses[19]; -tmp4[2] = this.conses[22]; -tmp4[3] = this.conses[3]; -tmp4[4] = this.conses[28]; -tmp4[5] = this.conses[20]; -this.colours[3] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp4); -var tmp5 = new Array (4); -tmp5[0] = this.conses[3]; -tmp5[1] = this.conses[28]; -tmp5[2] = this.conses[20]; -tmp5[3] = this.conses[19]; -this.colours[4] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.RED), tmp5); -var tmp6 = new Array (6); -tmp6[0] = this.conses[3]; -tmp6[1] = this.conses[29]; -tmp6[2] = this.conses[10]; -tmp6[3] = this.conses[6]; -tmp6[4] = this.conses[19]; -tmp6[5] = this.conses[2]; -this.colours[5] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp6); -var tmp7 = new Array (5); -tmp7[0] = this.conses[3]; -tmp7[1] = this.conses[29]; -tmp7[2] = this.conses[10]; -tmp7[3] = this.conses[17]; -tmp7[4] = this.conses[2]; -this.colours[6] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp7); -this.residueColour = new Array (20); -this.residueColour[0] = this.colours[0]; -this.residueColour[1] = this.colours[4]; -this.residueColour[2] = this.colours[2]; -this.residueColour[3] = this.colours[6]; -this.residueColour[4] = this.colours[0]; -this.residueColour[5] = this.colours[3]; -this.residueColour[6] = this.colours[5]; -this.residueColour[7] = this.colours[7]; -this.residueColour[8] = this.colours[10]; -this.residueColour[9] = this.colours[0]; -this.residueColour[10] = this.colours[0]; -this.residueColour[11] = this.colours[4]; -this.residueColour[12] = this.colours[0]; -this.residueColour[13] = this.colours[0]; -this.residueColour[14] = this.colours[8]; -this.residueColour[15] = this.colours[1]; -this.residueColour[16] = this.colours[1]; -this.residueColour[17] = this.colours[0]; -this.residueColour[18] = this.colours[10]; -this.residueColour[19] = this.colours[0]; -}); -Clazz.defineMethod (c$, "findColour", -function (c) { -return java.awt.Color.pink; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var currentColour; -if (this.cons2.length <= j || (this.includeGaps && this.threshold != 0 && !this.aboveThreshold (c, j))) { -return java.awt.Color.white; -}var i = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; -currentColour = java.awt.Color.white; -if (i > 19) { -return currentColour; -}for (var k = 0; k < this.residueColour[i].conses.length; k++) { -if (this.residueColour[i].conses[k].isConserved (this.cons2, j, this.size, this.includeGaps)) { -currentColour = this.residueColour[i].c; -}} -if (i == 4) { -if (this.conses[27].isConserved (this.cons2, j, this.size, this.includeGaps)) { -currentColour = jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK); -}}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "isIncludeGaps", -function () { -return this.includeGaps; -}); -Clazz.defineMethod (c$, "setIncludeGaps", -function (includeGaps) { -this.includeGaps = includeGaps; -}, "~B"); -Clazz.overrideMethod (c$, "applyTo", -function (sg, hiddenRepSequences) { -var css = new jalview.schemes.ClustalxColourScheme (sg, hiddenRepSequences); -css.includeGaps = this.includeGaps; -return css; -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.defineStatics (c$, -"EIGHTY_FIVE", 85, -"FIFTY", 50, -"EIGHTY", 80, -"SIXTY", 60); -c$.colhash = c$.prototype.colhash = new java.util.HashMap (); -{ -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.RED, new java.awt.Color (0.9, 0.2, 0.1)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.BLUE, new java.awt.Color (0.5, 0.7, 0.9)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.GREEN, new java.awt.Color (0.1, 0.8, 0.1)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.ORANGE, new java.awt.Color (0.9, 0.6, 0.3)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.CYAN, new java.awt.Color (0.1, 0.7, 0.7)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.PINK, new java.awt.Color (0.9, 0.5, 0.5)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.MAGENTA, new java.awt.Color (0.8, 0.3, 0.8)); -jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.YELLOW, new java.awt.Color (0.8, 0.8, 0.0)); -}c$ = Clazz.decorateAsClass (function () { -this.conses = null; -this.c = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "ConsensusColour"); -Clazz.makeConstructor (c$, -function (c, conses) { -this.conses = conses; -this.c = c; -}, "java.awt.Color,~A"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.HashMap"], ["jalview.schemes.ConsensusColour", "$.ClustalxColourScheme"], ["jalview.schemes.Consensus", "$.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.decorateAsClass (function () { +this.cons2 = null; +this.colours = null; +this.residueColour = null; +this.size = 0; +this.conses = null; +this.includeGaps = true; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "ClustalxColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.prepareFields (c$, function () { +this.conses = new Array (32); +}); +Clazz.makeConstructor (c$, +function (alignment, hiddenReps) { +Clazz.superConstructor (this, jalview.schemes.ClustalxColourScheme, []); +this.alignmentChanged (alignment, hiddenReps); +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.overrideMethod (c$, "alignmentChanged", +function (alignment, hiddenReps) { +var maxWidth = alignment.getWidth (); +var seqs = alignment.getSequences (hiddenReps); +this.cons2 = Clazz.newIntArray (maxWidth, 24, 0); +this.includeGaps = this.isIncludeGaps (); +var start = 0; +for (var j = 0; j < 24; j++) { +for (var i = 0; i < maxWidth; i++) { +this.cons2[i][j] = 0; +} +} +var res; +var i; +var j = 0; +var seq; +for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) { +seq = sq.getSequence (); +var end_j = seq.length - 1; +for (i = start; i <= end_j; i++) { +if ((seq.length - 1) < i) { +res = 23; +} else { +res = jalview.schemes.ResidueProperties.aaIndex[seq[i].charCodeAt (0)]; +}this.cons2[i][res]++; +} +j++; +} +this.size = seqs.size (); +this.makeColours (); +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.defineMethod (c$, "makeColours", +function () { +this.conses[0] = new jalview.schemes.Consensus ("WLVIMAFCYHP", 60); +this.conses[1] = new jalview.schemes.Consensus ("WLVIMAFCYHP", 80); +this.conses[2] = new jalview.schemes.Consensus ("ED", 50); +this.conses[3] = new jalview.schemes.Consensus ("KR", 60); +this.conses[4] = new jalview.schemes.Consensus ("G", 50); +this.conses[5] = new jalview.schemes.Consensus ("N", 50); +this.conses[6] = new jalview.schemes.Consensus ("QE", 50); +this.conses[7] = new jalview.schemes.Consensus ("P", 50); +this.conses[8] = new jalview.schemes.Consensus ("TS", 50); +this.conses[26] = new jalview.schemes.Consensus ("A", 85); +this.conses[27] = new jalview.schemes.Consensus ("C", 85); +this.conses[10] = new jalview.schemes.Consensus ("E", 85); +this.conses[11] = new jalview.schemes.Consensus ("F", 85); +this.conses[12] = new jalview.schemes.Consensus ("G", 85); +this.conses[13] = new jalview.schemes.Consensus ("H", 85); +this.conses[14] = new jalview.schemes.Consensus ("I", 85); +this.conses[15] = new jalview.schemes.Consensus ("L", 85); +this.conses[16] = new jalview.schemes.Consensus ("M", 85); +this.conses[17] = new jalview.schemes.Consensus ("N", 85); +this.conses[18] = new jalview.schemes.Consensus ("P", 85); +this.conses[19] = new jalview.schemes.Consensus ("Q", 85); +this.conses[20] = new jalview.schemes.Consensus ("R", 85); +this.conses[21] = new jalview.schemes.Consensus ("S", 85); +this.conses[22] = new jalview.schemes.Consensus ("T", 85); +this.conses[23] = new jalview.schemes.Consensus ("V", 85); +this.conses[24] = new jalview.schemes.Consensus ("W", 85); +this.conses[25] = new jalview.schemes.Consensus ("Y", 85); +this.conses[28] = new jalview.schemes.Consensus ("K", 85); +this.conses[29] = new jalview.schemes.Consensus ("D", 85); +this.conses[30] = new jalview.schemes.Consensus ("G", 0); +this.conses[31] = new jalview.schemes.Consensus ("P", 0); +this.colours = new Array (11); +var tmp8 = new Array (1); +tmp8[0] = this.conses[30]; +this.colours[7] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.ORANGE), tmp8); +var tmp9 = new Array (1); +tmp9[0] = this.conses[31]; +this.colours[8] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.YELLOW), tmp9); +var tmp10 = new Array (1); +tmp10[0] = this.conses[27]; +this.colours[9] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK), tmp8); +var tmp1 = new Array (14); +tmp1[0] = this.conses[0]; +tmp1[1] = this.conses[1]; +tmp1[2] = this.conses[26]; +tmp1[3] = this.conses[27]; +tmp1[4] = this.conses[11]; +tmp1[5] = this.conses[13]; +tmp1[6] = this.conses[14]; +tmp1[7] = this.conses[15]; +tmp1[8] = this.conses[16]; +tmp1[9] = this.conses[23]; +tmp1[10] = this.conses[24]; +tmp1[11] = this.conses[25]; +tmp1[12] = this.conses[18]; +tmp1[13] = this.conses[19]; +this.colours[0] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.BLUE), tmp1); +this.colours[10] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.CYAN), tmp1); +var tmp2 = new Array (5); +tmp2[0] = this.conses[8]; +tmp2[1] = this.conses[21]; +tmp2[2] = this.conses[22]; +tmp2[3] = this.conses[0]; +tmp2[4] = this.conses[1]; +this.colours[1] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp2); +var tmp3 = new Array (3); +tmp3[0] = this.conses[17]; +tmp3[1] = this.conses[29]; +tmp3[2] = this.conses[5]; +this.colours[2] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp3); +var tmp4 = new Array (6); +tmp4[0] = this.conses[6]; +tmp4[1] = this.conses[19]; +tmp4[2] = this.conses[22]; +tmp4[3] = this.conses[3]; +tmp4[4] = this.conses[28]; +tmp4[5] = this.conses[20]; +this.colours[3] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp4); +var tmp5 = new Array (4); +tmp5[0] = this.conses[3]; +tmp5[1] = this.conses[28]; +tmp5[2] = this.conses[20]; +tmp5[3] = this.conses[19]; +this.colours[4] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.RED), tmp5); +var tmp6 = new Array (6); +tmp6[0] = this.conses[3]; +tmp6[1] = this.conses[29]; +tmp6[2] = this.conses[10]; +tmp6[3] = this.conses[6]; +tmp6[4] = this.conses[19]; +tmp6[5] = this.conses[2]; +this.colours[5] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp6); +var tmp7 = new Array (5); +tmp7[0] = this.conses[3]; +tmp7[1] = this.conses[29]; +tmp7[2] = this.conses[10]; +tmp7[3] = this.conses[17]; +tmp7[4] = this.conses[2]; +this.colours[6] = new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp7); +this.residueColour = new Array (20); +this.residueColour[0] = this.colours[0]; +this.residueColour[1] = this.colours[4]; +this.residueColour[2] = this.colours[2]; +this.residueColour[3] = this.colours[6]; +this.residueColour[4] = this.colours[0]; +this.residueColour[5] = this.colours[3]; +this.residueColour[6] = this.colours[5]; +this.residueColour[7] = this.colours[7]; +this.residueColour[8] = this.colours[10]; +this.residueColour[9] = this.colours[0]; +this.residueColour[10] = this.colours[0]; +this.residueColour[11] = this.colours[4]; +this.residueColour[12] = this.colours[0]; +this.residueColour[13] = this.colours[0]; +this.residueColour[14] = this.colours[8]; +this.residueColour[15] = this.colours[1]; +this.residueColour[16] = this.colours[1]; +this.residueColour[17] = this.colours[0]; +this.residueColour[18] = this.colours[10]; +this.residueColour[19] = this.colours[0]; +}); +Clazz.defineMethod (c$, "findColour", +function (c) { +return java.awt.Color.pink; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var currentColour; +if (this.cons2.length <= j || (this.includeGaps && this.threshold != 0 && !this.aboveThreshold (c, j))) { +return java.awt.Color.white; +}var i = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; +currentColour = java.awt.Color.white; +if (i > 19) { +return currentColour; +}for (var k = 0; k < this.residueColour[i].conses.length; k++) { +if (this.residueColour[i].conses[k].isConserved (this.cons2, j, this.size, this.includeGaps)) { +currentColour = this.residueColour[i].c; +}} +if (i == 4) { +if (this.conses[27].isConserved (this.cons2, j, this.size, this.includeGaps)) { +currentColour = jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK); +}}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "isIncludeGaps", +function () { +return this.includeGaps; +}); +Clazz.defineMethod (c$, "setIncludeGaps", +function (includeGaps) { +this.includeGaps = includeGaps; +}, "~B"); +Clazz.overrideMethod (c$, "applyTo", +function (sg, hiddenRepSequences) { +var css = new jalview.schemes.ClustalxColourScheme (sg, hiddenRepSequences); +css.includeGaps = this.includeGaps; +return css; +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.defineStatics (c$, +"EIGHTY_FIVE", 85, +"FIFTY", 50, +"EIGHTY", 80, +"SIXTY", 60); +c$.colhash = c$.prototype.colhash = new java.util.HashMap (); +{ +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.RED, new java.awt.Color (0.9, 0.2, 0.1)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.BLUE, new java.awt.Color (0.5, 0.7, 0.9)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.GREEN, new java.awt.Color (0.1, 0.8, 0.1)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.ORANGE, new java.awt.Color (0.9, 0.6, 0.3)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.CYAN, new java.awt.Color (0.1, 0.7, 0.7)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.PINK, new java.awt.Color (0.9, 0.5, 0.5)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.MAGENTA, new java.awt.Color (0.8, 0.3, 0.8)); +jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.YELLOW, new java.awt.Color (0.8, 0.8, 0.0)); +}c$ = Clazz.decorateAsClass (function () { +this.conses = null; +this.c = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "ConsensusColour"); +Clazz.makeConstructor (c$, +function (c, conses) { +this.conses = conses; +this.c = c; +}, "java.awt.Color,~A"); +}); diff --git a/bin/jalview/schemes/ColourSchemeI.js b/bin/jalview/schemes/ColourSchemeI.js index 9777117..b82090d 100644 --- a/bin/jalview/schemes/ColourSchemeI.js +++ b/bin/jalview/schemes/ColourSchemeI.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.declareInterface (jalview.schemes, "ColourSchemeI"); +Clazz.declarePackage ("jalview.schemes"); +Clazz.declareInterface (jalview.schemes, "ColourSchemeI"); diff --git a/bin/jalview/schemes/ColourSchemeProperty.js b/bin/jalview/schemes/ColourSchemeProperty.js index 352a373..eb55454 100644 --- a/bin/jalview/schemes/ColourSchemeProperty.js +++ b/bin/jalview/schemes/ColourSchemeProperty.js @@ -1,292 +1,292 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (null, "jalview.schemes.ColourSchemeProperty", ["jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColour", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.UserColourScheme", "$.ZappoColourScheme", "jalview.util.ColorUtils", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "ColourSchemeProperty"); -c$.getColourIndexFromName = Clazz.defineMethod (c$, "getColourIndexFromName", -function (name) { -var ret = -1; -if (name.equalsIgnoreCase ("Clustal")) { -ret = 2; -} else if (name.equalsIgnoreCase ("Blosum62")) { -ret = 3; -} else if (name.equalsIgnoreCase ("% Identity")) { -ret = 4; -} else if (name.equalsIgnoreCase ("Zappo")) { -ret = 5; -} else if (name.equalsIgnoreCase ("Taylor")) { -ret = 6; -} else if (name.equalsIgnoreCase ("Hydrophobic")) { -ret = 7; -} else if (name.equalsIgnoreCase ("Helix Propensity")) { -ret = 8; -} else if (name.equalsIgnoreCase ("Strand Propensity")) { -ret = 9; -} else if (name.equalsIgnoreCase ("Turn Propensity")) { -ret = 10; -} else if (name.equalsIgnoreCase ("Buried Index")) { -ret = 11; -} else if (name.equalsIgnoreCase ("Nucleotide")) { -ret = 12; -} else if (name.equalsIgnoreCase ("T-Coffee Scores")) { -ret = 15; -} else if (name.equalsIgnoreCase ("User Defined")) { -ret = 0; -} else if (name.equalsIgnoreCase ("None")) { -ret = 1; -} else if (name.equalsIgnoreCase ("Purine/Pyrimidine")) { -ret = 13; -} else if (name.equalsIgnoreCase ("RNA Interaction type")) { -ret = 17; -} else if (name.equalsIgnoreCase ("RNA Helices")) { -ret = 16; -}return ret; -}, "~S"); -c$.getColourName = Clazz.defineMethod (c$, "getColourName", -function (cs) { -var index = 1; -if (Clazz.instanceOf (cs, jalview.schemes.ClustalxColourScheme)) { -index = 2; -} else if (Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) { -index = 3; -} else if (Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme)) { -index = 4; -} else if (Clazz.instanceOf (cs, jalview.schemes.ZappoColourScheme)) { -index = 5; -} else if (Clazz.instanceOf (cs, jalview.schemes.TaylorColourScheme)) { -index = 6; -} else if (Clazz.instanceOf (cs, jalview.schemes.HydrophobicColourScheme)) { -index = 7; -} else if (Clazz.instanceOf (cs, jalview.schemes.HelixColourScheme)) { -index = 8; -} else if (Clazz.instanceOf (cs, jalview.schemes.StrandColourScheme)) { -index = 9; -} else if (Clazz.instanceOf (cs, jalview.schemes.TurnColourScheme)) { -index = 10; -} else if (Clazz.instanceOf (cs, jalview.schemes.BuriedColourScheme)) { -index = 11; -} else if (Clazz.instanceOf (cs, jalview.schemes.NucleotideColourScheme)) { -index = 12; -} else if (Clazz.instanceOf (cs, jalview.schemes.PurinePyrimidineColourScheme)) { -index = 13; -} else if (Clazz.instanceOf (cs, jalview.schemes.TCoffeeColourScheme)) { -index = 15; -} else if (Clazz.instanceOf (cs, jalview.schemes.RNAHelicesColour)) { -index = 16; -} else if (Clazz.instanceOf (cs, jalview.schemes.UserColourScheme)) { -if (((cs).getName () != null) && ((cs).getName ().length > 0)) { -return (cs).getName (); -}index = 0; -}return jalview.schemes.ColourSchemeProperty.getColourName (index); -}, "jalview.schemes.ColourSchemeI"); -c$.getColourName = Clazz.defineMethod (c$, "getColourName", -function (index) { -var ret = null; -switch (index) { -case 2: -ret = "Clustal"; -break; -case 3: -ret = "Blosum62"; -break; -case 4: -ret = "% Identity"; -break; -case 5: -ret = "Zappo"; -break; -case 6: -ret = "Taylor"; -break; -case 7: -ret = "Hydrophobic"; -break; -case 8: -ret = "Helix Propensity"; -break; -case 9: -ret = "Strand Propensity"; -break; -case 10: -ret = "Turn Propensity"; -break; -case 11: -ret = "Buried Index"; -break; -case 12: -ret = "Nucleotide"; -break; -case 13: -ret = "Purine/Pyrimidine"; -break; -case 15: -ret = "T-Coffee Scores"; -break; -case 17: -ret = "RNA Interaction type"; -break; -case 16: -ret = "RNA Helices"; -break; -case 0: -ret = "User Defined"; -break; -default: -ret = "None"; -break; -} -return ret; -}, "~N"); -c$.getColour = Clazz.defineMethod (c$, "getColour", -function (alignment, name) { -var colindex = jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name); -if (colindex == -1) { -if (name.indexOf ('=') == -1) { -try { -return new jalview.schemes.UserColourScheme (name); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -} else { -try { -var ucs = new jalview.schemes.UserColourScheme ("white"); -ucs.parseAppletParameter (name); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -}}return jalview.schemes.ColourSchemeProperty.getColour (alignment, jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name)); -}, "jalview.datamodel.AnnotatedCollectionI,~S"); -c$.getColour = Clazz.defineMethod (c$, "getColour", -function (coll, index) { -var cs = null; -switch (index) { -case 2: -cs = new jalview.schemes.ClustalxColourScheme (coll, null); -break; -case 3: -cs = new jalview.schemes.Blosum62ColourScheme (); -break; -case 4: -cs = new jalview.schemes.PIDColourScheme (); -break; -case 5: -cs = new jalview.schemes.ZappoColourScheme (); -break; -case 6: -cs = new jalview.schemes.TaylorColourScheme (); -break; -case 7: -cs = new jalview.schemes.HydrophobicColourScheme (); -break; -case 8: -cs = new jalview.schemes.HelixColourScheme (); -break; -case 9: -cs = new jalview.schemes.StrandColourScheme (); -break; -case 10: -cs = new jalview.schemes.TurnColourScheme (); -break; -case 11: -cs = new jalview.schemes.BuriedColourScheme (); -break; -case 12: -cs = new jalview.schemes.NucleotideColourScheme (); -break; -case 13: -cs = new jalview.schemes.PurinePyrimidineColourScheme (); -break; -case 15: -cs = new jalview.schemes.TCoffeeColourScheme (coll); -break; -case 16: -cs = new jalview.schemes.RNAHelicesColour (coll); -break; -case 0: -var col = new Array (24); -for (var i = 0; i < 24; i++) { -col[i] = java.awt.Color.white; -} -cs = new jalview.schemes.UserColourScheme (col); -break; -default: -break; -} -return cs; -}, "jalview.datamodel.AnnotatedCollectionI,~N"); -c$.getAWTColorFromName = Clazz.defineMethod (c$, "getAWTColorFromName", -function (name) { -var col = null; -name = name.toLowerCase (); -if (name.equals ("black")) { -col = java.awt.Color.black; -} else if (name.equals ("blue")) { -col = java.awt.Color.blue; -} else if (name.equals ("cyan")) { -col = java.awt.Color.cyan; -} else if (name.equals ("darkGray")) { -col = java.awt.Color.darkGray; -} else if (name.equals ("gray")) { -col = java.awt.Color.gray; -} else if (name.equals ("green")) { -col = java.awt.Color.green; -} else if (name.equals ("lightGray")) { -col = java.awt.Color.lightGray; -} else if (name.equals ("magenta")) { -col = java.awt.Color.magenta; -} else if (name.equals ("orange")) { -col = java.awt.Color.orange; -} else if (name.equals ("pink")) { -col = java.awt.Color.pink; -} else if (name.equals ("red")) { -col = java.awt.Color.red; -} else if (name.equals ("white")) { -col = java.awt.Color.white; -} else if (name.equals ("yellow")) { -col = java.awt.Color.yellow; -}return col; -}, "~S"); -c$.initRnaHelicesShading = Clazz.defineMethod (c$, "initRnaHelicesShading", -function (n) { -var j = 0; -if (jalview.schemes.ColourSchemeProperty.rnaHelices == null) { -jalview.schemes.ColourSchemeProperty.rnaHelices = new Array (n + 1); -} else if (jalview.schemes.ColourSchemeProperty.rnaHelices != null && jalview.schemes.ColourSchemeProperty.rnaHelices.length <= n) { -var t = new Array (n + 1); -System.arraycopy (jalview.schemes.ColourSchemeProperty.rnaHelices, 0, t, 0, jalview.schemes.ColourSchemeProperty.rnaHelices.length); -j = jalview.schemes.ColourSchemeProperty.rnaHelices.length; -jalview.schemes.ColourSchemeProperty.rnaHelices = t; -} else { -return; -}for (; j <= n; j++) { -jalview.schemes.ColourSchemeProperty.rnaHelices[j] = jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white); -} -}, "~N"); -Clazz.defineStatics (c$, -"UNDEFINED", -1, -"USER_DEFINED", 0, -"NONE", 1, -"CLUSTAL", 2, -"BLOSUM", 3, -"PID", 4, -"ZAPPO", 5, -"TAYLOR", 6, -"HYDROPHOBIC", 7, -"HELIX", 8, -"STRAND", 9, -"TURN", 10, -"BURIED", 11, -"NUCLEOTIDE", 12, -"PURINEPYRIMIDINE", 13, -"COVARIATION", 14, -"TCOFFEE", 15, -"RNAHELIX", 16, -"RNAINTERACTION", 17, -"FIRST_COLOUR", 1, -"LAST_COLOUR", 17, -"rnaHelices", null); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (null, "jalview.schemes.ColourSchemeProperty", ["jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColour", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.UserColourScheme", "$.ZappoColourScheme", "jalview.util.ColorUtils", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "ColourSchemeProperty"); +c$.getColourIndexFromName = Clazz.defineMethod (c$, "getColourIndexFromName", +function (name) { +var ret = -1; +if (name.equalsIgnoreCase ("Clustal")) { +ret = 2; +} else if (name.equalsIgnoreCase ("Blosum62")) { +ret = 3; +} else if (name.equalsIgnoreCase ("% Identity")) { +ret = 4; +} else if (name.equalsIgnoreCase ("Zappo")) { +ret = 5; +} else if (name.equalsIgnoreCase ("Taylor")) { +ret = 6; +} else if (name.equalsIgnoreCase ("Hydrophobic")) { +ret = 7; +} else if (name.equalsIgnoreCase ("Helix Propensity")) { +ret = 8; +} else if (name.equalsIgnoreCase ("Strand Propensity")) { +ret = 9; +} else if (name.equalsIgnoreCase ("Turn Propensity")) { +ret = 10; +} else if (name.equalsIgnoreCase ("Buried Index")) { +ret = 11; +} else if (name.equalsIgnoreCase ("Nucleotide")) { +ret = 12; +} else if (name.equalsIgnoreCase ("T-Coffee Scores")) { +ret = 15; +} else if (name.equalsIgnoreCase ("User Defined")) { +ret = 0; +} else if (name.equalsIgnoreCase ("None")) { +ret = 1; +} else if (name.equalsIgnoreCase ("Purine/Pyrimidine")) { +ret = 13; +} else if (name.equalsIgnoreCase ("RNA Interaction type")) { +ret = 17; +} else if (name.equalsIgnoreCase ("RNA Helices")) { +ret = 16; +}return ret; +}, "~S"); +c$.getColourName = Clazz.defineMethod (c$, "getColourName", +function (cs) { +var index = 1; +if (Clazz.instanceOf (cs, jalview.schemes.ClustalxColourScheme)) { +index = 2; +} else if (Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) { +index = 3; +} else if (Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme)) { +index = 4; +} else if (Clazz.instanceOf (cs, jalview.schemes.ZappoColourScheme)) { +index = 5; +} else if (Clazz.instanceOf (cs, jalview.schemes.TaylorColourScheme)) { +index = 6; +} else if (Clazz.instanceOf (cs, jalview.schemes.HydrophobicColourScheme)) { +index = 7; +} else if (Clazz.instanceOf (cs, jalview.schemes.HelixColourScheme)) { +index = 8; +} else if (Clazz.instanceOf (cs, jalview.schemes.StrandColourScheme)) { +index = 9; +} else if (Clazz.instanceOf (cs, jalview.schemes.TurnColourScheme)) { +index = 10; +} else if (Clazz.instanceOf (cs, jalview.schemes.BuriedColourScheme)) { +index = 11; +} else if (Clazz.instanceOf (cs, jalview.schemes.NucleotideColourScheme)) { +index = 12; +} else if (Clazz.instanceOf (cs, jalview.schemes.PurinePyrimidineColourScheme)) { +index = 13; +} else if (Clazz.instanceOf (cs, jalview.schemes.TCoffeeColourScheme)) { +index = 15; +} else if (Clazz.instanceOf (cs, jalview.schemes.RNAHelicesColour)) { +index = 16; +} else if (Clazz.instanceOf (cs, jalview.schemes.UserColourScheme)) { +if (((cs).getName () != null) && ((cs).getName ().length > 0)) { +return (cs).getName (); +}index = 0; +}return jalview.schemes.ColourSchemeProperty.getColourName (index); +}, "jalview.schemes.ColourSchemeI"); +c$.getColourName = Clazz.defineMethod (c$, "getColourName", +function (index) { +var ret = null; +switch (index) { +case 2: +ret = "Clustal"; +break; +case 3: +ret = "Blosum62"; +break; +case 4: +ret = "% Identity"; +break; +case 5: +ret = "Zappo"; +break; +case 6: +ret = "Taylor"; +break; +case 7: +ret = "Hydrophobic"; +break; +case 8: +ret = "Helix Propensity"; +break; +case 9: +ret = "Strand Propensity"; +break; +case 10: +ret = "Turn Propensity"; +break; +case 11: +ret = "Buried Index"; +break; +case 12: +ret = "Nucleotide"; +break; +case 13: +ret = "Purine/Pyrimidine"; +break; +case 15: +ret = "T-Coffee Scores"; +break; +case 17: +ret = "RNA Interaction type"; +break; +case 16: +ret = "RNA Helices"; +break; +case 0: +ret = "User Defined"; +break; +default: +ret = "None"; +break; +} +return ret; +}, "~N"); +c$.getColour = Clazz.defineMethod (c$, "getColour", +function (alignment, name) { +var colindex = jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name); +if (colindex == -1) { +if (name.indexOf ('=') == -1) { +try { +return new jalview.schemes.UserColourScheme (name); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +} else { +try { +var ucs = new jalview.schemes.UserColourScheme ("white"); +ucs.parseAppletParameter (name); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +}}return jalview.schemes.ColourSchemeProperty.getColour (alignment, jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name)); +}, "jalview.datamodel.AnnotatedCollectionI,~S"); +c$.getColour = Clazz.defineMethod (c$, "getColour", +function (coll, index) { +var cs = null; +switch (index) { +case 2: +cs = new jalview.schemes.ClustalxColourScheme (coll, null); +break; +case 3: +cs = new jalview.schemes.Blosum62ColourScheme (); +break; +case 4: +cs = new jalview.schemes.PIDColourScheme (); +break; +case 5: +cs = new jalview.schemes.ZappoColourScheme (); +break; +case 6: +cs = new jalview.schemes.TaylorColourScheme (); +break; +case 7: +cs = new jalview.schemes.HydrophobicColourScheme (); +break; +case 8: +cs = new jalview.schemes.HelixColourScheme (); +break; +case 9: +cs = new jalview.schemes.StrandColourScheme (); +break; +case 10: +cs = new jalview.schemes.TurnColourScheme (); +break; +case 11: +cs = new jalview.schemes.BuriedColourScheme (); +break; +case 12: +cs = new jalview.schemes.NucleotideColourScheme (); +break; +case 13: +cs = new jalview.schemes.PurinePyrimidineColourScheme (); +break; +case 15: +cs = new jalview.schemes.TCoffeeColourScheme (coll); +break; +case 16: +cs = new jalview.schemes.RNAHelicesColour (coll); +break; +case 0: +var col = new Array (24); +for (var i = 0; i < 24; i++) { +col[i] = java.awt.Color.white; +} +cs = new jalview.schemes.UserColourScheme (col); +break; +default: +break; +} +return cs; +}, "jalview.datamodel.AnnotatedCollectionI,~N"); +c$.getAWTColorFromName = Clazz.defineMethod (c$, "getAWTColorFromName", +function (name) { +var col = null; +name = name.toLowerCase (); +if (name.equals ("black")) { +col = java.awt.Color.black; +} else if (name.equals ("blue")) { +col = java.awt.Color.blue; +} else if (name.equals ("cyan")) { +col = java.awt.Color.cyan; +} else if (name.equals ("darkGray")) { +col = java.awt.Color.darkGray; +} else if (name.equals ("gray")) { +col = java.awt.Color.gray; +} else if (name.equals ("green")) { +col = java.awt.Color.green; +} else if (name.equals ("lightGray")) { +col = java.awt.Color.lightGray; +} else if (name.equals ("magenta")) { +col = java.awt.Color.magenta; +} else if (name.equals ("orange")) { +col = java.awt.Color.orange; +} else if (name.equals ("pink")) { +col = java.awt.Color.pink; +} else if (name.equals ("red")) { +col = java.awt.Color.red; +} else if (name.equals ("white")) { +col = java.awt.Color.white; +} else if (name.equals ("yellow")) { +col = java.awt.Color.yellow; +}return col; +}, "~S"); +c$.initRnaHelicesShading = Clazz.defineMethod (c$, "initRnaHelicesShading", +function (n) { +var j = 0; +if (jalview.schemes.ColourSchemeProperty.rnaHelices == null) { +jalview.schemes.ColourSchemeProperty.rnaHelices = new Array (n + 1); +} else if (jalview.schemes.ColourSchemeProperty.rnaHelices != null && jalview.schemes.ColourSchemeProperty.rnaHelices.length <= n) { +var t = new Array (n + 1); +System.arraycopy (jalview.schemes.ColourSchemeProperty.rnaHelices, 0, t, 0, jalview.schemes.ColourSchemeProperty.rnaHelices.length); +j = jalview.schemes.ColourSchemeProperty.rnaHelices.length; +jalview.schemes.ColourSchemeProperty.rnaHelices = t; +} else { +return; +}for (; j <= n; j++) { +jalview.schemes.ColourSchemeProperty.rnaHelices[j] = jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white); +} +}, "~N"); +Clazz.defineStatics (c$, +"UNDEFINED", -1, +"USER_DEFINED", 0, +"NONE", 1, +"CLUSTAL", 2, +"BLOSUM", 3, +"PID", 4, +"ZAPPO", 5, +"TAYLOR", 6, +"HYDROPHOBIC", 7, +"HELIX", 8, +"STRAND", 9, +"TURN", 10, +"BURIED", 11, +"NUCLEOTIDE", 12, +"PURINEPYRIMIDINE", 13, +"COVARIATION", 14, +"TCOFFEE", 15, +"RNAHELIX", 16, +"RNAINTERACTION", 17, +"FIRST_COLOUR", 1, +"LAST_COLOUR", 17, +"rnaHelices", null); +}); diff --git a/bin/jalview/schemes/Consensus.js b/bin/jalview/schemes/Consensus.js index 39d8ac9..45c3c6a 100644 --- a/bin/jalview/schemes/Consensus.js +++ b/bin/jalview/schemes/Consensus.js @@ -1,45 +1,45 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (null, "jalview.schemes.Consensus", ["jalview.schemes.ResidueProperties"], function () { -c$ = Clazz.decorateAsClass (function () { -this.mask = null; -this.threshold = 0; -this.maskstr = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "Consensus"); -Clazz.makeConstructor (c$, -function (mask, threshold) { -this.maskstr = mask; -this.setMask (mask); -this.threshold = threshold; -}, "~S,~N"); -Clazz.defineMethod (c$, "setMask", -function (s) { -this.mask = this.setNums (s); -}, "~S"); -Clazz.defineMethod (c$, "isConserved", -function (cons2, col, size) { -return this.isConserved (cons2, col, size, true); -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "isConserved", -function (cons2, col, size, includeGaps) { -var tot = 0; -if (!includeGaps) { -size -= cons2[col][cons2[col].length - 1]; -}for (var i = 0; i < this.mask.length; i++) { -tot += cons2[col][this.mask[i]]; -} -if (tot > ((this.threshold * size) / 100)) { -return true; -}return false; -}, "~A,~N,~N,~B"); -Clazz.defineMethod (c$, "setNums", -function (s) { -var out = Clazz.newIntArray (s.length, 0); -var i = 0; -while (i < s.length) { -out[i] = jalview.schemes.ResidueProperties.aaIndex[s.charCodeAt (i)]; -i++; -} -return out; -}, "~S"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (null, "jalview.schemes.Consensus", ["jalview.schemes.ResidueProperties"], function () { +c$ = Clazz.decorateAsClass (function () { +this.mask = null; +this.threshold = 0; +this.maskstr = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "Consensus"); +Clazz.makeConstructor (c$, +function (mask, threshold) { +this.maskstr = mask; +this.setMask (mask); +this.threshold = threshold; +}, "~S,~N"); +Clazz.defineMethod (c$, "setMask", +function (s) { +this.mask = this.setNums (s); +}, "~S"); +Clazz.defineMethod (c$, "isConserved", +function (cons2, col, size) { +return this.isConserved (cons2, col, size, true); +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "isConserved", +function (cons2, col, size, includeGaps) { +var tot = 0; +if (!includeGaps) { +size -= cons2[col][cons2[col].length - 1]; +}for (var i = 0; i < this.mask.length; i++) { +tot += cons2[col][this.mask[i]]; +} +if (tot > ((this.threshold * size) / 100)) { +return true; +}return false; +}, "~A,~N,~N,~B"); +Clazz.defineMethod (c$, "setNums", +function (s) { +var out = Clazz.newIntArray (s.length, 0); +var i = 0; +while (i < s.length) { +out[i] = jalview.schemes.ResidueProperties.aaIndex[s.charCodeAt (i)]; +i++; +} +return out; +}, "~S"); +}); diff --git a/bin/jalview/schemes/CovariationColourScheme.js b/bin/jalview/schemes/CovariationColourScheme.js index 3d75e42..68c8f15 100644 --- a/bin/jalview/schemes/CovariationColourScheme.js +++ b/bin/jalview/schemes/CovariationColourScheme.js @@ -1,41 +1,41 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.CovariationColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () { -c$ = Clazz.decorateAsClass (function () { -this.helixcolorhash = null; -this.positionsToHelix = null; -this.numHelix = 0; -this.annotation = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "CovariationColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.prepareFields (c$, function () { -this.helixcolorhash = new java.util.Hashtable (); -this.positionsToHelix = new java.util.Hashtable (); -}); -Clazz.makeConstructor (c$, -function (annotation) { -Clazz.superConstructor (this, jalview.schemes.CovariationColourScheme, []); -this.annotation = annotation; -for (var x = 0; x < this.annotation._rnasecstr.length; x++) { -this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ()); -this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ()); -if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) { -this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()); -}} -for (var j = 0; j <= this.numHelix; j++) { -this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white)); -} -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "findColour", -function (c) { -return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j) { -var currentColour = java.awt.Color.white; -var currentHelix = null; -currentHelix = this.positionsToHelix.get (new Integer (j)); -if (currentHelix != null) { -currentColour = this.helixcolorhash.get (currentHelix); -}return currentColour; -}, "~S,~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.CovariationColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () { +c$ = Clazz.decorateAsClass (function () { +this.helixcolorhash = null; +this.positionsToHelix = null; +this.numHelix = 0; +this.annotation = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "CovariationColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.prepareFields (c$, function () { +this.helixcolorhash = new java.util.Hashtable (); +this.positionsToHelix = new java.util.Hashtable (); +}); +Clazz.makeConstructor (c$, +function (annotation) { +Clazz.superConstructor (this, jalview.schemes.CovariationColourScheme, []); +this.annotation = annotation; +for (var x = 0; x < this.annotation._rnasecstr.length; x++) { +this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ()); +this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ()); +if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) { +this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()); +}} +for (var j = 0; j <= this.numHelix; j++) { +this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white)); +} +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "findColour", +function (c) { +return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j) { +var currentColour = java.awt.Color.white; +var currentHelix = null; +currentHelix = this.positionsToHelix.get (new Integer (j)); +if (currentHelix != null) { +currentColour = this.helixcolorhash.get (currentHelix); +}return currentColour; +}, "~S,~N"); +}); diff --git a/bin/jalview/schemes/FollowerColourScheme.js b/bin/jalview/schemes/FollowerColourScheme.js index e73b3d9..e71f907 100644 --- a/bin/jalview/schemes/FollowerColourScheme.js +++ b/bin/jalview/schemes/FollowerColourScheme.js @@ -1,26 +1,26 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.FollowerColourScheme", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.colourScheme = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "FollowerColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.defineMethod (c$, "getBaseColour", -function () { -return this.colourScheme; -}); -Clazz.overrideMethod (c$, "setConsensus", -function (consensus) { -if (this.colourScheme != null) { -this.colourScheme.setConsensus (consensus); -}}, "~A"); -Clazz.overrideMethod (c$, "setConservation", -function (cons) { -if (this.colourScheme != null) { -this.colourScheme.setConservation (cons); -}}, "jalview.analysis.Conservation"); -Clazz.overrideMethod (c$, "setConservationInc", -function (i) { -if (this.colourScheme != null) { -this.colourScheme.setConservationInc (i); -}}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.FollowerColourScheme", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.colourScheme = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "FollowerColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.defineMethod (c$, "getBaseColour", +function () { +return this.colourScheme; +}); +Clazz.overrideMethod (c$, "setConsensus", +function (consensus) { +if (this.colourScheme != null) { +this.colourScheme.setConsensus (consensus); +}}, "~A"); +Clazz.overrideMethod (c$, "setConservation", +function (cons) { +if (this.colourScheme != null) { +this.colourScheme.setConservation (cons); +}}, "jalview.analysis.Conservation"); +Clazz.overrideMethod (c$, "setConservationInc", +function (i) { +if (this.colourScheme != null) { +this.colourScheme.setConservationInc (i); +}}, "~N"); +}); diff --git a/bin/jalview/schemes/GraduatedColor.js b/bin/jalview/schemes/GraduatedColor.js index 5daa0fb..e9998a1 100644 --- a/bin/jalview/schemes/GraduatedColor.js +++ b/bin/jalview/schemes/GraduatedColor.js @@ -1,160 +1,160 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (null, "jalview.schemes.GraduatedColor", ["jalview.schemes.UserColourScheme", "java.awt.Color", "java.lang.Float"], function () { -c$ = Clazz.decorateAsClass (function () { -this.thresholdState = -1; -this.lr = 0; -this.lg = 0; -this.lb = 0; -this.dr = 0; -this.dg = 0; -this.db = 0; -this.base = 0; -this.range = 0; -this.thrsh = 0; -this.tolow = false; -this.autoScale = true; -this.ucs = null; -this.colourByLabel = false; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "GraduatedColor"); -Clazz.makeConstructor (c$, -function (low, high, min, max) { -this.thrsh = NaN; -this.tolow = min >= max; -this.lr = low.getRed () / 255; -this.lg = low.getGreen () / 255; -this.lb = low.getBlue () / 255; -this.dr = (high.getRed () / 255) - this.lr; -this.dg = (high.getGreen () / 255) - this.lg; -this.db = (high.getBlue () / 255) - this.lb; -if (this.tolow) { -this.base = max; -this.range = min - max; -} else { -this.base = min; -this.range = max - min; -}}, "java.awt.Color,java.awt.Color,~N,~N"); -Clazz.makeConstructor (c$, -function (oldcs) { -this.lr = oldcs.lr; -this.lg = oldcs.lg; -this.lb = oldcs.lb; -this.dr = oldcs.dr; -this.dg = oldcs.dg; -this.db = oldcs.db; -this.base = oldcs.base; -this.range = oldcs.range; -this.tolow = oldcs.tolow; -this.thresholdState = oldcs.thresholdState; -this.thrsh = oldcs.thrsh; -this.autoScale = oldcs.autoScale; -this.colourByLabel = oldcs.colourByLabel; -}, "jalview.schemes.GraduatedColor"); -Clazz.makeConstructor (c$, -function (oldcs, min, max) { -this.construct (oldcs); -this.updateBounds (min, max); -}, "jalview.schemes.GraduatedColor,~N,~N"); -Clazz.defineMethod (c$, "getMinColor", -function () { -return new java.awt.Color (this.lr, this.lg, this.lb); -}); -Clazz.defineMethod (c$, "getMaxColor", -function () { -return new java.awt.Color (this.lr + this.dr, this.lg + this.dg, this.lb + this.db); -}); -Clazz.defineMethod (c$, "getTolow", -function () { -return this.tolow; -}); -Clazz.defineMethod (c$, "setTolow", -function (tolower) { -this.tolow = tolower; -}, "~B"); -Clazz.defineMethod (c$, "isColored", -function (feature) { -var val = feature.getScore (); -if (Float.isNaN (val)) { -return true; -}if (this.thresholdState == -1) { -return true; -}if (Float.isNaN (this.thrsh)) { -return true; -}var rtn = this.thresholdState == 1; -if (val <= this.thrsh) { -return !rtn; -} else { -return rtn; -}}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "isColourByLabel", -function () { -return this.colourByLabel; -}); -Clazz.defineMethod (c$, "setColourByLabel", -function (colourByLabel) { -this.colourByLabel = colourByLabel; -}, "~B"); -Clazz.defineMethod (c$, "findColor", -function (feature) { -if (this.colourByLabel) { -if (this.ucs == null) { -this.ucs = new jalview.schemes.UserColourScheme (); -}return this.ucs.createColourFromName (feature.getDescription ()); -}if (this.range == 0.0) { -return this.getMaxColor (); -}var scr = feature.getScore (); -if (Float.isNaN (scr)) { -return this.getMinColor (); -}var scl = (scr - this.base) / this.range; -if (this.tolow) { -scl = -scl; -}if (scl < 0) { -scl = 0; -}if (scl > 1) { -scl = 1; -}return new java.awt.Color (this.lr + scl * this.dr, this.lg + scl * this.dg, this.lb + scl * this.db); -}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "setThresh", -function (value) { -this.thrsh = value; -}, "~N"); -Clazz.defineMethod (c$, "getThresh", -function () { -return this.thrsh; -}); -Clazz.defineMethod (c$, "setThreshType", -function (aboveThreshold) { -this.thresholdState = aboveThreshold; -}, "~N"); -Clazz.defineMethod (c$, "getThreshType", -function () { -return this.thresholdState; -}); -Clazz.defineMethod (c$, "getMax", -function () { -return (this.tolow) ? this.base : (this.base + this.range); -}); -Clazz.defineMethod (c$, "getMin", -function () { -return (this.tolow) ? (this.base + this.range) : this.base; -}); -Clazz.defineMethod (c$, "isAutoScale", -function () { -return this.autoScale; -}); -Clazz.defineMethod (c$, "setAutoScaled", -function (autoscale) { -this.autoScale = autoscale; -}, "~B"); -Clazz.defineMethod (c$, "updateBounds", -function (min, max) { -if (max < min) { -this.base = max; -this.range = min - max; -this.tolow = true; -} else { -this.base = min; -this.range = max - min; -this.tolow = false; -}}, "~N,~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (null, "jalview.schemes.GraduatedColor", ["jalview.schemes.UserColourScheme", "java.awt.Color", "java.lang.Float"], function () { +c$ = Clazz.decorateAsClass (function () { +this.thresholdState = -1; +this.lr = 0; +this.lg = 0; +this.lb = 0; +this.dr = 0; +this.dg = 0; +this.db = 0; +this.base = 0; +this.range = 0; +this.thrsh = 0; +this.tolow = false; +this.autoScale = true; +this.ucs = null; +this.colourByLabel = false; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "GraduatedColor"); +Clazz.makeConstructor (c$, +function (low, high, min, max) { +this.thrsh = NaN; +this.tolow = min >= max; +this.lr = low.getRed () / 255; +this.lg = low.getGreen () / 255; +this.lb = low.getBlue () / 255; +this.dr = (high.getRed () / 255) - this.lr; +this.dg = (high.getGreen () / 255) - this.lg; +this.db = (high.getBlue () / 255) - this.lb; +if (this.tolow) { +this.base = max; +this.range = min - max; +} else { +this.base = min; +this.range = max - min; +}}, "java.awt.Color,java.awt.Color,~N,~N"); +Clazz.makeConstructor (c$, +function (oldcs) { +this.lr = oldcs.lr; +this.lg = oldcs.lg; +this.lb = oldcs.lb; +this.dr = oldcs.dr; +this.dg = oldcs.dg; +this.db = oldcs.db; +this.base = oldcs.base; +this.range = oldcs.range; +this.tolow = oldcs.tolow; +this.thresholdState = oldcs.thresholdState; +this.thrsh = oldcs.thrsh; +this.autoScale = oldcs.autoScale; +this.colourByLabel = oldcs.colourByLabel; +}, "jalview.schemes.GraduatedColor"); +Clazz.makeConstructor (c$, +function (oldcs, min, max) { +this.construct (oldcs); +this.updateBounds (min, max); +}, "jalview.schemes.GraduatedColor,~N,~N"); +Clazz.defineMethod (c$, "getMinColor", +function () { +return new java.awt.Color (this.lr, this.lg, this.lb); +}); +Clazz.defineMethod (c$, "getMaxColor", +function () { +return new java.awt.Color (this.lr + this.dr, this.lg + this.dg, this.lb + this.db); +}); +Clazz.defineMethod (c$, "getTolow", +function () { +return this.tolow; +}); +Clazz.defineMethod (c$, "setTolow", +function (tolower) { +this.tolow = tolower; +}, "~B"); +Clazz.defineMethod (c$, "isColored", +function (feature) { +var val = feature.getScore (); +if (Float.isNaN (val)) { +return true; +}if (this.thresholdState == -1) { +return true; +}if (Float.isNaN (this.thrsh)) { +return true; +}var rtn = this.thresholdState == 1; +if (val <= this.thrsh) { +return !rtn; +} else { +return rtn; +}}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "isColourByLabel", +function () { +return this.colourByLabel; +}); +Clazz.defineMethod (c$, "setColourByLabel", +function (colourByLabel) { +this.colourByLabel = colourByLabel; +}, "~B"); +Clazz.defineMethod (c$, "findColor", +function (feature) { +if (this.colourByLabel) { +if (this.ucs == null) { +this.ucs = new jalview.schemes.UserColourScheme (); +}return this.ucs.createColourFromName (feature.getDescription ()); +}if (this.range == 0.0) { +return this.getMaxColor (); +}var scr = feature.getScore (); +if (Float.isNaN (scr)) { +return this.getMinColor (); +}var scl = (scr - this.base) / this.range; +if (this.tolow) { +scl = -scl; +}if (scl < 0) { +scl = 0; +}if (scl > 1) { +scl = 1; +}return new java.awt.Color (this.lr + scl * this.dr, this.lg + scl * this.dg, this.lb + scl * this.db); +}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "setThresh", +function (value) { +this.thrsh = value; +}, "~N"); +Clazz.defineMethod (c$, "getThresh", +function () { +return this.thrsh; +}); +Clazz.defineMethod (c$, "setThreshType", +function (aboveThreshold) { +this.thresholdState = aboveThreshold; +}, "~N"); +Clazz.defineMethod (c$, "getThreshType", +function () { +return this.thresholdState; +}); +Clazz.defineMethod (c$, "getMax", +function () { +return (this.tolow) ? this.base : (this.base + this.range); +}); +Clazz.defineMethod (c$, "getMin", +function () { +return (this.tolow) ? (this.base + this.range) : this.base; +}); +Clazz.defineMethod (c$, "isAutoScale", +function () { +return this.autoScale; +}); +Clazz.defineMethod (c$, "setAutoScaled", +function (autoscale) { +this.autoScale = autoscale; +}, "~B"); +Clazz.defineMethod (c$, "updateBounds", +function (min, max) { +if (max < min) { +this.base = max; +this.range = min - max; +this.tolow = true; +} else { +this.base = min; +this.range = max - min; +this.tolow = false; +}}, "~N,~N"); +}); diff --git a/bin/jalview/schemes/HelixColourScheme.js b/bin/jalview/schemes/HelixColourScheme.js index 4768a33..64e88e9 100644 --- a/bin/jalview/schemes/HelixColourScheme.js +++ b/bin/jalview/schemes/HelixColourScheme.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.HelixColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "HelixColourScheme", jalview.schemes.ScoreColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.HelixColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.helix, 0.57, 1.51]); -}); -Clazz.overrideMethod (c$, "makeColour", -function (c) { -return new java.awt.Color (c, 1.0 - c, c); -}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.HelixColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "HelixColourScheme", jalview.schemes.ScoreColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.HelixColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.helix, 0.57, 1.51]); +}); +Clazz.overrideMethod (c$, "makeColour", +function (c) { +return new java.awt.Color (c, 1.0 - c, c); +}, "~N"); +}); diff --git a/bin/jalview/schemes/HydrophobicColourScheme.js b/bin/jalview/schemes/HydrophobicColourScheme.js index 02e1bbd..224f202 100644 --- a/bin/jalview/schemes/HydrophobicColourScheme.js +++ b/bin/jalview/schemes/HydrophobicColourScheme.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.HydrophobicColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "HydrophobicColourScheme", jalview.schemes.ScoreColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.HydrophobicColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.hyd, -3.9, 4.5]); -}); -Clazz.overrideMethod (c$, "makeColour", -function (c) { -return new java.awt.Color (c, 0.0, 1.0 - c); -}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.HydrophobicColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "HydrophobicColourScheme", jalview.schemes.ScoreColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.HydrophobicColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.hyd, -3.9, 4.5]); +}); +Clazz.overrideMethod (c$, "makeColour", +function (c) { +return new java.awt.Color (c, 0.0, 1.0 - c); +}, "~N"); +}); diff --git a/bin/jalview/schemes/NucleotideColourScheme.js b/bin/jalview/schemes/NucleotideColourScheme.js index 1345bc6..abdfb5e 100644 --- a/bin/jalview/schemes/NucleotideColourScheme.js +++ b/bin/jalview/schemes/NucleotideColourScheme.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.NucleotideColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "NucleotideColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.NucleotideColourScheme, [jalview.schemes.ResidueProperties.nucleotideIndex, jalview.schemes.ResidueProperties.nucleotide, 0]); -}); -Clazz.defineMethod (c$, "findColour", -function (c) { -return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var currentColour; -if ((this.threshold == 0) || this.aboveThreshold (c, j)) { -try { -currentColour = this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -return java.awt.Color.white; -} else { -throw ex; -} -} -} else { -return java.awt.Color.white; -}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.NucleotideColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "NucleotideColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.NucleotideColourScheme, [jalview.schemes.ResidueProperties.nucleotideIndex, jalview.schemes.ResidueProperties.nucleotide, 0]); +}); +Clazz.defineMethod (c$, "findColour", +function (c) { +return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var currentColour; +if ((this.threshold == 0) || this.aboveThreshold (c, j)) { +try { +currentColour = this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +return java.awt.Color.white; +} else { +throw ex; +} +} +} else { +return java.awt.Color.white; +}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/schemes/PIDColourScheme.js b/bin/jalview/schemes/PIDColourScheme.js index 093328c..bdf6f24 100644 --- a/bin/jalview/schemes/PIDColourScheme.js +++ b/bin/jalview/schemes/PIDColourScheme.js @@ -1,39 +1,39 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PIDColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { -c$ = Clazz.decorateAsClass (function () { -this.pidColours = null; -this.thresholds = null; -this.group = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "PIDColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.PIDColourScheme, []); -this.pidColours = jalview.schemes.ResidueProperties.pidColours; -this.thresholds = jalview.schemes.ResidueProperties.pidThresholds; -}); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -if ('a' <= c && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) - (32)); -}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null) { -return java.awt.Color.white; -}if ((this.threshold != 0) && !this.aboveThreshold (c, j)) { -return java.awt.Color.white; -}var currentColour = java.awt.Color.white; -var sc = 0; -if (this.consensus.length <= j) { -return java.awt.Color.white; -}if ((Integer.parseInt (this.consensus[j].get ("C").toString ()) != -1) && this.consensus[j].contains (String.valueOf (c))) { -sc = (this.consensus[j].get (this.ignoreGaps)).floatValue (); -if (!jalview.util.Comparison.isGap (c)) { -for (var i = 0; i < this.thresholds.length; i++) { -if (sc > this.thresholds[i]) { -currentColour = this.pidColours[i]; -break; -}} -}}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PIDColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { +c$ = Clazz.decorateAsClass (function () { +this.pidColours = null; +this.thresholds = null; +this.group = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "PIDColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.PIDColourScheme, []); +this.pidColours = jalview.schemes.ResidueProperties.pidColours; +this.thresholds = jalview.schemes.ResidueProperties.pidThresholds; +}); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +if ('a' <= c && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) - (32)); +}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null) { +return java.awt.Color.white; +}if ((this.threshold != 0) && !this.aboveThreshold (c, j)) { +return java.awt.Color.white; +}var currentColour = java.awt.Color.white; +var sc = 0; +if (this.consensus.length <= j) { +return java.awt.Color.white; +}if ((Integer.parseInt (this.consensus[j].get ("C").toString ()) != -1) && this.consensus[j].contains (String.valueOf (c))) { +sc = (this.consensus[j].get (this.ignoreGaps)).floatValue (); +if (!jalview.util.Comparison.isGap (c)) { +for (var i = 0; i < this.thresholds.length; i++) { +if (sc > this.thresholds[i]) { +currentColour = this.pidColours[i]; +break; +}} +}}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/schemes/PurinePyrimidineColourScheme.js b/bin/jalview/schemes/PurinePyrimidineColourScheme.js index be4e523..514d31b 100644 --- a/bin/jalview/schemes/PurinePyrimidineColourScheme.js +++ b/bin/jalview/schemes/PurinePyrimidineColourScheme.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PurinePyrimidineColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "PurinePyrimidineColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.PurinePyrimidineColourScheme, [jalview.schemes.ResidueProperties.purinepyrimidineIndex, jalview.schemes.ResidueProperties.purinepyrimidine, 0]); -}); -Clazz.defineMethod (c$, "findColour", -function (c) { -return this.colors[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j) { -var currentColour; -if ((this.threshold == 0) || this.aboveThreshold (c, j)) { -try { -currentColour = this.colors[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -return java.awt.Color.white; -} else { -throw ex; -} -} -} else { -return java.awt.Color.white; -}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PurinePyrimidineColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "PurinePyrimidineColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.PurinePyrimidineColourScheme, [jalview.schemes.ResidueProperties.purinepyrimidineIndex, jalview.schemes.ResidueProperties.purinepyrimidine, 0]); +}); +Clazz.defineMethod (c$, "findColour", +function (c) { +return this.colors[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j) { +var currentColour; +if ((this.threshold == 0) || this.aboveThreshold (c, j)) { +try { +currentColour = this.colors[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +return java.awt.Color.white; +} else { +throw ex; +} +} +} else { +return java.awt.Color.white; +}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N"); +}); diff --git a/bin/jalview/schemes/RNAHelicesColour.js b/bin/jalview/schemes/RNAHelicesColour.js index 5023c90..c7d3af2 100644 --- a/bin/jalview/schemes/RNAHelicesColour.js +++ b/bin/jalview/schemes/RNAHelicesColour.js @@ -1,68 +1,68 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.RNAHelicesColour", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () { -c$ = Clazz.decorateAsClass (function () { -this.helixcolorhash = null; -this.positionsToHelix = null; -this.numHelix = 0; -this.annotation = null; -this.lastrefresh = -1; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "RNAHelicesColour", jalview.schemes.ResidueColourScheme); -Clazz.prepareFields (c$, function () { -this.helixcolorhash = new java.util.Hashtable (); -this.positionsToHelix = new java.util.Hashtable (); -}); -Clazz.makeConstructor (c$, -function (annotation) { -Clazz.superConstructor (this, jalview.schemes.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]); -this.annotation = annotation; -this.refresh (); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.makeConstructor (c$, -function (alignment) { -Clazz.superConstructor (this, jalview.schemes.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]); -this.alignmentChanged (alignment, null); -}, "jalview.datamodel.AnnotatedCollectionI"); -Clazz.overrideMethod (c$, "alignmentChanged", -function (alignment, hiddenReps) { -var annotations = alignment.getAlignmentAnnotation (); -for (var i = 0; i < annotations.length; i++) { -if (annotations[i].getRNAStruc () != null) { -this.annotation = annotations[i]; -break; -}} -this.refresh (); -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.defineMethod (c$, "refresh", -function () { -if (this.annotation != null && ((this.annotation._rnasecstr == null || this.lastrefresh != this.annotation._rnasecstr.hashCode ()) && this.annotation.isValidStruc ())) { -this.annotation.getRNAStruc (); -this.lastrefresh = this.annotation._rnasecstr.hashCode (); -this.numHelix = 0; -this.positionsToHelix = new java.util.Hashtable (); -for (var x = 0; x < this.annotation._rnasecstr.length; x++) { -this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ()); -this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ()); -if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) { -this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()); -}} -for (var j = 0; j <= this.numHelix; j++) { -if (!this.helixcolorhash.containsKey (Integer.toString (j))) { -this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white)); -}} -}}); -Clazz.defineMethod (c$, "findColour", -function (c) { -return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -this.refresh (); -var currentColour = java.awt.Color.white; -var currentHelix = null; -currentHelix = this.positionsToHelix.get (new Integer (j)); -if (currentHelix != null) { -currentColour = this.helixcolorhash.get (currentHelix); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.RNAHelicesColour", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () { +c$ = Clazz.decorateAsClass (function () { +this.helixcolorhash = null; +this.positionsToHelix = null; +this.numHelix = 0; +this.annotation = null; +this.lastrefresh = -1; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "RNAHelicesColour", jalview.schemes.ResidueColourScheme); +Clazz.prepareFields (c$, function () { +this.helixcolorhash = new java.util.Hashtable (); +this.positionsToHelix = new java.util.Hashtable (); +}); +Clazz.makeConstructor (c$, +function (annotation) { +Clazz.superConstructor (this, jalview.schemes.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]); +this.annotation = annotation; +this.refresh (); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.makeConstructor (c$, +function (alignment) { +Clazz.superConstructor (this, jalview.schemes.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]); +this.alignmentChanged (alignment, null); +}, "jalview.datamodel.AnnotatedCollectionI"); +Clazz.overrideMethod (c$, "alignmentChanged", +function (alignment, hiddenReps) { +var annotations = alignment.getAlignmentAnnotation (); +for (var i = 0; i < annotations.length; i++) { +if (annotations[i].getRNAStruc () != null) { +this.annotation = annotations[i]; +break; +}} +this.refresh (); +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.defineMethod (c$, "refresh", +function () { +if (this.annotation != null && ((this.annotation._rnasecstr == null || this.lastrefresh != this.annotation._rnasecstr.hashCode ()) && this.annotation.isValidStruc ())) { +this.annotation.getRNAStruc (); +this.lastrefresh = this.annotation._rnasecstr.hashCode (); +this.numHelix = 0; +this.positionsToHelix = new java.util.Hashtable (); +for (var x = 0; x < this.annotation._rnasecstr.length; x++) { +this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ()); +this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ()); +if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) { +this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()); +}} +for (var j = 0; j <= this.numHelix; j++) { +if (!this.helixcolorhash.containsKey (Integer.toString (j))) { +this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white)); +}} +}}); +Clazz.defineMethod (c$, "findColour", +function (c) { +return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +this.refresh (); +var currentColour = java.awt.Color.white; +var currentHelix = null; +currentHelix = this.positionsToHelix.get (new Integer (j)); +if (currentHelix != null) { +currentColour = this.helixcolorhash.get (currentHelix); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/schemes/RNAHelicesColourChooser.js b/bin/jalview/schemes/RNAHelicesColourChooser.js index 27a0f25..0d9cf26 100644 --- a/bin/jalview/schemes/RNAHelicesColourChooser.js +++ b/bin/jalview/schemes/RNAHelicesColourChooser.js @@ -1,63 +1,63 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (null, "jalview.schemes.RNAHelicesColourChooser", ["jalview.schemes.RNAHelicesColour", "java.util.Hashtable", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.av = null; -this.ap = null; -this.oldcs = null; -this.oldgroupColours = null; -this.currentAnnotation = null; -this.adjusting = false; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "RNAHelicesColourChooser"); -Clazz.makeConstructor (c$, -function (av, ap) { -this.oldcs = av.getGlobalColourScheme (); -if (av.getAlignment ().getGroups () != null) { -this.oldgroupColours = new java.util.Hashtable (); -for (var sg, $sg = ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.cs != null) { -this.oldgroupColours.put (sg, sg.cs); -}} -}this.av = av; -this.ap = ap; -if (Clazz.instanceOf (this.oldcs, jalview.schemes.RNAHelicesColour)) { -var rhc = this.oldcs; -}this.adjusting = true; -var list = new java.util.Vector (); -var index = 1; -for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) { -var label = av.getAlignment ().getAlignmentAnnotation ()[i].label; -if (!list.contains (label)) list.addElement (label); - else list.addElement (label + "_" + (index++)); -} -this.adjusting = false; -this.changeColour (); -}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "changeColour", -function () { -if (this.adjusting) { -return; -}var rhc = null; -rhc = new jalview.schemes.RNAHelicesColour (this.av.getAlignment ()); -this.av.setGlobalColourScheme (rhc); -if (this.av.getAlignment ().getGroups () != null) { -for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.cs == null) { -continue; -}sg.cs = new jalview.schemes.RNAHelicesColour (sg); -} -}this.ap.paintAlignment (false); -}); -Clazz.defineMethod (c$, "reset", -function () { -this.av.setGlobalColourScheme (this.oldcs); -if (this.av.getAlignment ().getGroups () != null) { -for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -sg.cs = this.oldgroupColours.get (sg); -} -}}); -Clazz.defineMethod (c$, "annotations_actionPerformed", -function (e) { -this.changeColour (); -}, "java.awt.event.ActionEvent"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (null, "jalview.schemes.RNAHelicesColourChooser", ["jalview.schemes.RNAHelicesColour", "java.util.Hashtable", "$.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.av = null; +this.ap = null; +this.oldcs = null; +this.oldgroupColours = null; +this.currentAnnotation = null; +this.adjusting = false; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "RNAHelicesColourChooser"); +Clazz.makeConstructor (c$, +function (av, ap) { +this.oldcs = av.getGlobalColourScheme (); +if (av.getAlignment ().getGroups () != null) { +this.oldgroupColours = new java.util.Hashtable (); +for (var sg, $sg = ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.cs != null) { +this.oldgroupColours.put (sg, sg.cs); +}} +}this.av = av; +this.ap = ap; +if (Clazz.instanceOf (this.oldcs, jalview.schemes.RNAHelicesColour)) { +var rhc = this.oldcs; +}this.adjusting = true; +var list = new java.util.Vector (); +var index = 1; +for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) { +var label = av.getAlignment ().getAlignmentAnnotation ()[i].label; +if (!list.contains (label)) list.addElement (label); + else list.addElement (label + "_" + (index++)); +} +this.adjusting = false; +this.changeColour (); +}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "changeColour", +function () { +if (this.adjusting) { +return; +}var rhc = null; +rhc = new jalview.schemes.RNAHelicesColour (this.av.getAlignment ()); +this.av.setGlobalColourScheme (rhc); +if (this.av.getAlignment ().getGroups () != null) { +for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.cs == null) { +continue; +}sg.cs = new jalview.schemes.RNAHelicesColour (sg); +} +}this.ap.paintAlignment (false); +}); +Clazz.defineMethod (c$, "reset", +function () { +this.av.setGlobalColourScheme (this.oldcs); +if (this.av.getAlignment ().getGroups () != null) { +for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +sg.cs = this.oldgroupColours.get (sg); +} +}}); +Clazz.defineMethod (c$, "annotations_actionPerformed", +function (e) { +this.changeColour (); +}, "java.awt.event.ActionEvent"); +}); diff --git a/bin/jalview/schemes/RNAInteractionColourScheme.js b/bin/jalview/schemes/RNAInteractionColourScheme.js index 9c2e946..6935253 100644 --- a/bin/jalview/schemes/RNAInteractionColourScheme.js +++ b/bin/jalview/schemes/RNAInteractionColourScheme.js @@ -1,27 +1,27 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.RNAInteractionColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "RNAInteractionColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.defineMethod (c$, "findColour", -function (c) { -return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var currentColour; -if ((this.threshold == 0) || this.aboveThreshold (c, j)) { -try { -currentColour = this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -return java.awt.Color.white; -} else { -throw ex; -} -} -} else { -return java.awt.Color.white; -}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.RNAInteractionColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "RNAInteractionColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.defineMethod (c$, "findColour", +function (c) { +return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var currentColour; +if ((this.threshold == 0) || this.aboveThreshold (c, j)) { +try { +currentColour = this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +return java.awt.Color.white; +} else { +throw ex; +} +} +} else { +return java.awt.Color.white; +}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +}); diff --git a/bin/jalview/schemes/ResidueColourScheme.js b/bin/jalview/schemes/ResidueColourScheme.js index aaf6ef5..9b2382f 100644 --- a/bin/jalview/schemes/ResidueColourScheme.js +++ b/bin/jalview/schemes/ResidueColourScheme.js @@ -1,146 +1,146 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ColourSchemeI"], "jalview.schemes.ResidueColourScheme", ["jalview.util.Comparison", "$.MessageManager", "java.awt.Color", "java.lang.Error"], function () { -c$ = Clazz.decorateAsClass (function () { -this.symbolIndex = null; -this.conservationColouring = false; -this.colors = null; -this.threshold = 0; -this.ignoreGaps = "G"; -this.consensus = null; -this.conservation = null; -this.conservationLength = 0; -this.inc = 30; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "ResidueColourScheme", null, jalview.schemes.ColourSchemeI); -Clazz.makeConstructor (c$, -function (aaOrnaIndex, colours, threshold) { -this.symbolIndex = aaOrnaIndex; -this.colors = colours; -this.threshold = threshold; -}, "~A,~A,~N"); -Clazz.makeConstructor (c$, -function (aaOrNaIndex) { -this.symbolIndex = aaOrNaIndex; -}, "~A"); -Clazz.makeConstructor (c$, -function () { -this.symbolIndex = null; -}); -Clazz.defineMethod (c$, "findColour", -function (c) { -return this.colors == null ? java.awt.Color.white : this.colors[this.symbolIndex[c.charCodeAt (0)]]; -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var currentColour; -if (this.colors != null && this.symbolIndex != null && (this.threshold == 0) || this.aboveThreshold (c, j)) { -currentColour = this.colors[this.symbolIndex[c.charCodeAt (0)]]; -} else { -currentColour = java.awt.Color.white; -}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "getThreshold", -function () { -return this.threshold; -}); -Clazz.overrideMethod (c$, "setThreshold", -function (ct, ignoreGaps) { -this.threshold = ct; -if (ignoreGaps) { -this.ignoreGaps = "N"; -} else { -this.ignoreGaps = "G"; -}}, "~N,~B"); -Clazz.defineMethod (c$, "aboveThreshold", -function (c, j) { -if ('a' <= c && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) - (32)); -}if (this.consensus == null || this.consensus.length < j || this.consensus[j] == null) { -return false; -}if (((this.consensus[j].get ("C")).intValue () != -1) && this.consensus[j].contains (String.valueOf (c))) { -if ((this.consensus[j].get (this.ignoreGaps)).floatValue () >= this.threshold) { -return true; -}}return false; -}, "~S,~N"); -Clazz.overrideMethod (c$, "conservationApplied", -function () { -return this.conservationColouring; -}); -Clazz.overrideMethod (c$, "setConservationApplied", -function (conservationApplied) { -this.conservationColouring = conservationApplied; -}, "~B"); -Clazz.overrideMethod (c$, "setConservationInc", -function (i) { -this.inc = i; -}, "~N"); -Clazz.overrideMethod (c$, "getConservationInc", -function () { -return this.inc; -}); -Clazz.overrideMethod (c$, "setConsensus", -function (consensus) { -if (consensus == null) { -return; -}this.consensus = consensus; -}, "~A"); -Clazz.overrideMethod (c$, "setConservation", -function (cons) { -if (cons == null) { -this.conservationColouring = false; -this.conservation = null; -} else { -this.conservationColouring = true; -var i; -var iSize = cons.getConsSequence ().getLength (); -this.conservation = Clazz.newCharArray (iSize, '\0'); -for (i = 0; i < iSize; i++) { -this.conservation[i] = cons.getConsSequence ().getCharAt (i); -} -this.conservationLength = this.conservation.length; -}}, "jalview.analysis.Conservation"); -Clazz.defineMethod (c$, "applyConservation", -function (currentColour, i) { -if ((this.conservationLength > i) && (this.conservation[i] != '*') && (this.conservation[i] != '+')) { -if (jalview.util.Comparison.isGap (this.conservation[i])) { -currentColour = java.awt.Color.white; -} else { -var t = 11 - ((this.conservation[i]).charCodeAt (0) - 48); -if (t == 0) { -return java.awt.Color.white; -}var red = currentColour.getRed (); -var green = currentColour.getGreen (); -var blue = currentColour.getBlue (); -var dr = 255 - red; -var dg = 255 - green; -var db = 255 - blue; -dr *= t / 10; -dg *= t / 10; -db *= t / 10; -red += (this.inc / 20) * dr; -green += (this.inc / 20) * dg; -blue += (this.inc / 20) * db; -if (red > 255 || green > 255 || blue > 255) { -currentColour = java.awt.Color.white; -} else { -currentColour = new java.awt.Color (red, green, blue); -}}}return currentColour; -}, "java.awt.Color,~N"); -Clazz.overrideMethod (c$, "alignmentChanged", -function (alignment, hiddenReps) { -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.overrideMethod (c$, "applyTo", -function (sg, hiddenRepSequences) { -try { -return this.getClass ().newInstance (); -} catch (q) { -if (Clazz.exceptionOf (q, Exception)) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_cannot_duplicate_colour_scheme", Clazz.newArray (-1, [this.getClass ().getName ()])), q); -} else { -throw q; -} -} -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ColourSchemeI"], "jalview.schemes.ResidueColourScheme", ["jalview.util.Comparison", "$.MessageManager", "java.awt.Color", "java.lang.Error"], function () { +c$ = Clazz.decorateAsClass (function () { +this.symbolIndex = null; +this.conservationColouring = false; +this.colors = null; +this.threshold = 0; +this.ignoreGaps = "G"; +this.consensus = null; +this.conservation = null; +this.conservationLength = 0; +this.inc = 30; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "ResidueColourScheme", null, jalview.schemes.ColourSchemeI); +Clazz.makeConstructor (c$, +function (aaOrnaIndex, colours, threshold) { +this.symbolIndex = aaOrnaIndex; +this.colors = colours; +this.threshold = threshold; +}, "~A,~A,~N"); +Clazz.makeConstructor (c$, +function (aaOrNaIndex) { +this.symbolIndex = aaOrNaIndex; +}, "~A"); +Clazz.makeConstructor (c$, +function () { +this.symbolIndex = null; +}); +Clazz.defineMethod (c$, "findColour", +function (c) { +return this.colors == null ? java.awt.Color.white : this.colors[this.symbolIndex[c.charCodeAt (0)]]; +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var currentColour; +if (this.colors != null && this.symbolIndex != null && (this.threshold == 0) || this.aboveThreshold (c, j)) { +currentColour = this.colors[this.symbolIndex[c.charCodeAt (0)]]; +} else { +currentColour = java.awt.Color.white; +}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "getThreshold", +function () { +return this.threshold; +}); +Clazz.overrideMethod (c$, "setThreshold", +function (ct, ignoreGaps) { +this.threshold = ct; +if (ignoreGaps) { +this.ignoreGaps = "N"; +} else { +this.ignoreGaps = "G"; +}}, "~N,~B"); +Clazz.defineMethod (c$, "aboveThreshold", +function (c, j) { +if ('a' <= c && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) - (32)); +}if (this.consensus == null || this.consensus.length < j || this.consensus[j] == null) { +return false; +}if (((this.consensus[j].get ("C")).intValue () != -1) && this.consensus[j].contains (String.valueOf (c))) { +if ((this.consensus[j].get (this.ignoreGaps)).floatValue () >= this.threshold) { +return true; +}}return false; +}, "~S,~N"); +Clazz.overrideMethod (c$, "conservationApplied", +function () { +return this.conservationColouring; +}); +Clazz.overrideMethod (c$, "setConservationApplied", +function (conservationApplied) { +this.conservationColouring = conservationApplied; +}, "~B"); +Clazz.overrideMethod (c$, "setConservationInc", +function (i) { +this.inc = i; +}, "~N"); +Clazz.overrideMethod (c$, "getConservationInc", +function () { +return this.inc; +}); +Clazz.overrideMethod (c$, "setConsensus", +function (consensus) { +if (consensus == null) { +return; +}this.consensus = consensus; +}, "~A"); +Clazz.overrideMethod (c$, "setConservation", +function (cons) { +if (cons == null) { +this.conservationColouring = false; +this.conservation = null; +} else { +this.conservationColouring = true; +var i; +var iSize = cons.getConsSequence ().getLength (); +this.conservation = Clazz.newCharArray (iSize, '\0'); +for (i = 0; i < iSize; i++) { +this.conservation[i] = cons.getConsSequence ().getCharAt (i); +} +this.conservationLength = this.conservation.length; +}}, "jalview.analysis.Conservation"); +Clazz.defineMethod (c$, "applyConservation", +function (currentColour, i) { +if ((this.conservationLength > i) && (this.conservation[i] != '*') && (this.conservation[i] != '+')) { +if (jalview.util.Comparison.isGap (this.conservation[i])) { +currentColour = java.awt.Color.white; +} else { +var t = 11 - ((this.conservation[i]).charCodeAt (0) - 48); +if (t == 0) { +return java.awt.Color.white; +}var red = currentColour.getRed (); +var green = currentColour.getGreen (); +var blue = currentColour.getBlue (); +var dr = 255 - red; +var dg = 255 - green; +var db = 255 - blue; +dr *= t / 10; +dg *= t / 10; +db *= t / 10; +red += (this.inc / 20) * dr; +green += (this.inc / 20) * dg; +blue += (this.inc / 20) * db; +if (red > 255 || green > 255 || blue > 255) { +currentColour = java.awt.Color.white; +} else { +currentColour = new java.awt.Color (red, green, blue); +}}}return currentColour; +}, "java.awt.Color,~N"); +Clazz.overrideMethod (c$, "alignmentChanged", +function (alignment, hiddenReps) { +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.overrideMethod (c$, "applyTo", +function (sg, hiddenRepSequences) { +try { +return this.getClass ().newInstance (); +} catch (q) { +if (Clazz.exceptionOf (q, Exception)) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_cannot_duplicate_colour_scheme", Clazz.newArray (-1, [this.getClass ().getName ()])), q); +} else { +throw q; +} +} +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +}); diff --git a/bin/jalview/schemes/ResidueProperties.class b/bin/jalview/schemes/ResidueProperties.class index c98cf35..539dcc8 100644 Binary files a/bin/jalview/schemes/ResidueProperties.class and b/bin/jalview/schemes/ResidueProperties.class differ diff --git a/bin/jalview/schemes/ResidueProperties.js b/bin/jalview/schemes/ResidueProperties.js index 612edb4..2a81845 100644 --- a/bin/jalview/schemes/ResidueProperties.js +++ b/bin/jalview/schemes/ResidueProperties.js @@ -1,1090 +1,1090 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.analysis.scoremodels.FeatureScoreModel", "$.PIDScoreModel", "jalview.schemes.ScoreMatrix", "java.awt.Color", "java.util.ArrayList", "$.HashMap", "$.Hashtable", "$.Vector"], "jalview.schemes.ResidueProperties", ["java.lang.StringBuffer"], function () { -c$ = Clazz.declareType (jalview.schemes, "ResidueProperties"); -c$.buildAmbiguityCodonSet = Clazz.defineMethod (c$, "buildAmbiguityCodonSet", -function () { -if (jalview.schemes.ResidueProperties._ambiguityCodes.size () > 0) { -System.err.println ("Ignoring multiple calls to buildAmbiguityCodonSet"); -return; -}for (var acode, $acode = jalview.schemes.ResidueProperties.ambiguityCodes.entrySet ().iterator (); $acode.hasNext () && ((acode = $acode.next ()) || true);) { -for (var r, $r = 0, $$r = acode.getValue (); $r < $$r.length && ((r = $$r[$r]) || true); $r++) { -var codesfor = jalview.schemes.ResidueProperties._ambiguityCodes.get (r); -if (codesfor == null) { -jalview.schemes.ResidueProperties._ambiguityCodes.put (r, codesfor = new java.util.ArrayList ()); -}if (!codesfor.contains (acode.getKey ())) { -codesfor.add (acode.getKey ()); -} else { -System.err.println ("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey () + " in residue " + r); -}} -} -var unambcodons = jalview.schemes.ResidueProperties.codonHash2.keySet ().toArray ( new Array (jalview.schemes.ResidueProperties.codonHash2.size ())); -for (var codon, $codon = 0, $$codon = unambcodons; $codon < $$codon.length && ((codon = $$codon[$codon]) || true); $codon++) { -var residue = jalview.schemes.ResidueProperties.codonHash2.get (codon); -var acodon = new Array (codon.length); -for (var i = 0, iSize = codon.length; i < iSize; i++) { -var _ac = "" + codon.charAt (i); -var acodes = jalview.schemes.ResidueProperties._ambiguityCodes.get (_ac); -if (acodes != null) { -acodon[i] = acodes.toArray ( new Array (acodes.size ())); -} else { -acodon[i] = Clazz.newArray (-1, []); -}} -var tpos = Clazz.newIntArray (codon.length, 0); -var cpos = Clazz.newIntArray (codon.length, 0); -for (var i = 0; i < tpos.length; i++) { -tpos[i] = -1; -} -tpos[acodon.length - 1] = 0; -var ipos; -var j; -while (tpos[0] < acodon[0].length) { -var allres = Clazz.newCharArray (tpos.length, '\0'); -var _acodon = ""; -var _anuc; -for (ipos = 0; ipos < tpos.length; ipos++) { -if (acodon[ipos].length == 0 || tpos[ipos] < 0) { -_acodon += codon.charAt (ipos); -allres[ipos] = Clazz.newCharArray (-1, [codon.charAt (ipos)]); -} else { -_acodon += acodon[ipos][tpos[ipos]]; -var altbase = jalview.schemes.ResidueProperties.ambiguityCodes.get (acodon[ipos][tpos[ipos]]); -allres[ipos] = Clazz.newCharArray (altbase.length, '\0'); -j = 0; -for (var ab, $ab = 0, $$ab = altbase; $ab < $$ab.length && ((ab = $$ab[$ab]) || true); $ab++) { -allres[ipos][j++] = ab.charAt (0); -} -}} -for (ipos = 0; ipos < cpos.length; ipos++) { -cpos[ipos] = 0; -} -var valid = true; -do { -var _codon = ""; -for (j = 0; j < cpos.length; j++) { -_codon += allres[j][cpos[j]]; -} -var tr = jalview.schemes.ResidueProperties.codonHash2.get (_codon); -if (valid = (tr != null && tr.equals (residue))) { -ipos = acodon.length - 1; -while (++cpos[ipos] >= allres[ipos].length && ipos > 0) { -cpos[ipos] = 0; -ipos--; -} -}} while (valid && cpos[0] < allres[0].length); -if (valid) { -jalview.schemes.ResidueProperties.codonHash2.put (_acodon, residue); -} else { -}ipos = acodon.length - 1; -while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) { -tpos[ipos] = -1; -ipos--; -} -} -} -}); -c$.getHydmax = Clazz.defineMethod (c$, "getHydmax", -function () { -return 4.5; -}); -c$.getHydmin = Clazz.defineMethod (c$, "getHydmin", -function () { -return -3.9; -}); -c$.getHyd = Clazz.defineMethod (c$, "getHyd", -function () { -return jalview.schemes.ResidueProperties.hyd; -}); -c$.getAA3Hash = Clazz.defineMethod (c$, "getAA3Hash", -function () { -return jalview.schemes.ResidueProperties.aa3Hash; -}); -c$.getDNA = Clazz.defineMethod (c$, "getDNA", -function () { -return jalview.schemes.ResidueProperties.DNA; -}); -c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", -function () { -return jalview.schemes.ResidueProperties.BLOSUM62; -}); -c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", -function (A1, A2) { -return jalview.schemes.ResidueProperties.getPAM250 (A1.charAt (0), A2.charAt (0)); -}, "~S,~S"); -c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", -function (c1, c2) { -var pog = 0; -try { -var a = jalview.schemes.ResidueProperties.aaIndex[c1.charCodeAt (0)]; -var b = jalview.schemes.ResidueProperties.aaIndex[c2.charCodeAt (0)]; -pog = jalview.schemes.ResidueProperties.BLOSUM62[a][b]; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -return pog; -}, "~S,~S"); -c$.getCodons = Clazz.defineMethod (c$, "getCodons", -function (res) { -if (jalview.schemes.ResidueProperties.codonHash.containsKey (res)) { -return jalview.schemes.ResidueProperties.codonHash.get (res); -}return null; -}, "~S"); -c$.codonTranslate = Clazz.defineMethod (c$, "codonTranslate", -function (lccodon) { -if (false) { -return jalview.schemes.ResidueProperties._codonTranslate (lccodon); -}var cdn = jalview.schemes.ResidueProperties.codonHash2.get (lccodon.toUpperCase ()); -if (cdn != null && cdn.equals ("*")) { -return "STOP"; -}return cdn; -}, "~S"); -c$._codonTranslate = Clazz.defineMethod (c$, "_codonTranslate", -function (lccodon) { -var codon = lccodon.toUpperCase (); -if (codon.indexOf ('X') > -1 || codon.indexOf ('N') > -1) { -return "X"; -}for (var key, $key = jalview.schemes.ResidueProperties.codonHash.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { -if (jalview.schemes.ResidueProperties.codonHash.get (key).contains (codon)) { -return key; -}} -return null; -}, "~S"); -c$.getDefaultPeptideMatrix = Clazz.defineMethod (c$, "getDefaultPeptideMatrix", -function () { -return jalview.schemes.ResidueProperties.getBLOSUM62 (); -}); -c$.getDefaultDnaMatrix = Clazz.defineMethod (c$, "getDefaultDnaMatrix", -function () { -return jalview.schemes.ResidueProperties.getDNA (); -}); -c$.getScoreMatrix = Clazz.defineMethod (c$, "getScoreMatrix", -function (pwtype) { -var val = jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype); -if (val != null && Clazz.instanceOf (val, jalview.schemes.ScoreMatrix)) { -return val; -}return null; -}, "~S"); -c$.getScoreModel = Clazz.defineMethod (c$, "getScoreModel", -function (pwtype) { -return jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype); -}, "~S"); -c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", -function (c, d) { -var a = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; -var b = jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)]; -var pog = jalview.schemes.ResidueProperties.PAM250[a][b]; -return pog; -}, "~S,~S"); -c$.getDssp3state = Clazz.defineMethod (c$, "getDssp3state", -function (ssstring) { -if (ssstring == null) { -return null; -}var ss = new StringBuffer (); -for (var i = 0; i < ssstring.length; i++) { -var ssc = ssstring.substring (i, i + 1); -if (jalview.schemes.ResidueProperties.toDssp3State.containsKey (ssc)) { -ss.append (jalview.schemes.ResidueProperties.toDssp3State.get (ssc)); -} else { -ss.append (" "); -}} -return ss.toString (); -}, "~S"); -c$.getRNASecStrucState = Clazz.defineMethod (c$, "getRNASecStrucState", -function (ssstring) { -if (ssstring == null) { -return null; -}var ss = new StringBuffer (); -for (var i = 0; i < ssstring.length; i++) { -var ssc = ssstring.substring (i, i + 1); -if (jalview.schemes.ResidueProperties.toRNAssState.containsKey (ssc)) { -ss.append (ssc); -} else { -ss.append (" "); -}} -return ss.toString (); -}, "~S"); -c$.isCloseParenRNA = Clazz.defineMethod (c$, "isCloseParenRNA", -function (dc) { -return jalview.schemes.ResidueProperties.RNAcloseParen[dc.charCodeAt (0)]; -}, "~S"); -c$.getResidues = Clazz.defineMethod (c$, "getResidues", -function (nucleotide, includeAmbiguous) { -var result = new java.util.ArrayList (); -if (nucleotide) { -for (var nuc, $nuc = jalview.schemes.ResidueProperties.nucleotideName.keySet ().iterator (); $nuc.hasNext () && ((nuc = $nuc.next ()) || true);) { -var val = jalview.schemes.ResidueProperties.nucleotideIndex[nuc.charCodeAt (0)]; -if ((!includeAmbiguous && val > 4) || (val >= 10)) { -continue; -}nuc = nuc.toUpperCase (); -if (!result.contains (nuc)) { -result.add (nuc); -}} -} else { -for (var res, $res = jalview.schemes.ResidueProperties.aa3Hash.keySet ().iterator (); $res.hasNext () && ((res = $res.next ()) || true);) { -var index = jalview.schemes.ResidueProperties.aa3Hash.get (res).intValue (); -if ((!includeAmbiguous && index >= 20) || index >= 23) { -continue; -}res = res.toUpperCase (); -if (!result.contains (res)) { -result.add (res); -}} -}return result; -}, "~B,~B"); -c$.scoreMatrices = c$.prototype.scoreMatrices = new java.util.Hashtable (); -Clazz.defineStatics (c$, -"aaIndex", null, -"nucleotideIndex", null, -"purinepyrimidineIndex", null); -c$.aa3Hash = c$.prototype.aa3Hash = new java.util.HashMap (); -c$.aa2Triplet = c$.prototype.aa2Triplet = new java.util.HashMap (); -c$.nucleotideName = c$.prototype.nucleotideName = new java.util.HashMap (); -{ -jalview.schemes.ResidueProperties.aaIndex = Clazz.newIntArray (255, 0); -for (var i = 0; i < 255; i++) { -jalview.schemes.ResidueProperties.aaIndex[i] = 23; -} -jalview.schemes.ResidueProperties.aaIndex['A'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.aaIndex['R'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.aaIndex['N'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)] = 3; -jalview.schemes.ResidueProperties.aaIndex['C'.charCodeAt (0)] = 4; -jalview.schemes.ResidueProperties.aaIndex['Q'.charCodeAt (0)] = 5; -jalview.schemes.ResidueProperties.aaIndex['E'.charCodeAt (0)] = 6; -jalview.schemes.ResidueProperties.aaIndex['G'.charCodeAt (0)] = 7; -jalview.schemes.ResidueProperties.aaIndex['H'.charCodeAt (0)] = 8; -jalview.schemes.ResidueProperties.aaIndex['I'.charCodeAt (0)] = 9; -jalview.schemes.ResidueProperties.aaIndex['L'.charCodeAt (0)] = 10; -jalview.schemes.ResidueProperties.aaIndex['K'.charCodeAt (0)] = 11; -jalview.schemes.ResidueProperties.aaIndex['M'.charCodeAt (0)] = 12; -jalview.schemes.ResidueProperties.aaIndex['F'.charCodeAt (0)] = 13; -jalview.schemes.ResidueProperties.aaIndex['P'.charCodeAt (0)] = 14; -jalview.schemes.ResidueProperties.aaIndex['S'.charCodeAt (0)] = 15; -jalview.schemes.ResidueProperties.aaIndex['T'.charCodeAt (0)] = 16; -jalview.schemes.ResidueProperties.aaIndex['W'.charCodeAt (0)] = 17; -jalview.schemes.ResidueProperties.aaIndex['Y'.charCodeAt (0)] = 18; -jalview.schemes.ResidueProperties.aaIndex['V'.charCodeAt (0)] = 19; -jalview.schemes.ResidueProperties.aaIndex['B'.charCodeAt (0)] = 20; -jalview.schemes.ResidueProperties.aaIndex['Z'.charCodeAt (0)] = 21; -jalview.schemes.ResidueProperties.aaIndex['X'.charCodeAt (0)] = 22; -jalview.schemes.ResidueProperties.aaIndex['U'.charCodeAt (0)] = 22; -jalview.schemes.ResidueProperties.aaIndex['a'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.aaIndex['r'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.aaIndex['n'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.aaIndex['d'.charCodeAt (0)] = 3; -jalview.schemes.ResidueProperties.aaIndex['c'.charCodeAt (0)] = 4; -jalview.schemes.ResidueProperties.aaIndex['q'.charCodeAt (0)] = 5; -jalview.schemes.ResidueProperties.aaIndex['e'.charCodeAt (0)] = 6; -jalview.schemes.ResidueProperties.aaIndex['g'.charCodeAt (0)] = 7; -jalview.schemes.ResidueProperties.aaIndex['h'.charCodeAt (0)] = 8; -jalview.schemes.ResidueProperties.aaIndex['i'.charCodeAt (0)] = 9; -jalview.schemes.ResidueProperties.aaIndex['l'.charCodeAt (0)] = 10; -jalview.schemes.ResidueProperties.aaIndex['k'.charCodeAt (0)] = 11; -jalview.schemes.ResidueProperties.aaIndex['m'.charCodeAt (0)] = 12; -jalview.schemes.ResidueProperties.aaIndex['f'.charCodeAt (0)] = 13; -jalview.schemes.ResidueProperties.aaIndex['p'.charCodeAt (0)] = 14; -jalview.schemes.ResidueProperties.aaIndex['s'.charCodeAt (0)] = 15; -jalview.schemes.ResidueProperties.aaIndex['t'.charCodeAt (0)] = 16; -jalview.schemes.ResidueProperties.aaIndex['w'.charCodeAt (0)] = 17; -jalview.schemes.ResidueProperties.aaIndex['y'.charCodeAt (0)] = 18; -jalview.schemes.ResidueProperties.aaIndex['v'.charCodeAt (0)] = 19; -jalview.schemes.ResidueProperties.aaIndex['b'.charCodeAt (0)] = 20; -jalview.schemes.ResidueProperties.aaIndex['z'.charCodeAt (0)] = 21; -jalview.schemes.ResidueProperties.aaIndex['x'.charCodeAt (0)] = 22; -jalview.schemes.ResidueProperties.aaIndex['u'.charCodeAt (0)] = 22; -}Clazz.defineStatics (c$, -"maxProteinIndex", 23, -"maxNucleotideIndex", 10); -{ -jalview.schemes.ResidueProperties.nucleotideIndex = Clazz.newIntArray (255, 0); -for (var i = 0; i < 255; i++) { -jalview.schemes.ResidueProperties.nucleotideIndex[i] = 10; -} -jalview.schemes.ResidueProperties.nucleotideIndex['A'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.nucleotideIndex['a'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.nucleotideIndex['C'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.nucleotideIndex['c'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.nucleotideIndex['G'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.nucleotideIndex['g'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.nucleotideIndex['T'.charCodeAt (0)] = 3; -jalview.schemes.ResidueProperties.nucleotideIndex['t'.charCodeAt (0)] = 3; -jalview.schemes.ResidueProperties.nucleotideIndex['U'.charCodeAt (0)] = 4; -jalview.schemes.ResidueProperties.nucleotideIndex['u'.charCodeAt (0)] = 4; -jalview.schemes.ResidueProperties.nucleotideIndex['I'.charCodeAt (0)] = 5; -jalview.schemes.ResidueProperties.nucleotideIndex['i'.charCodeAt (0)] = 5; -jalview.schemes.ResidueProperties.nucleotideIndex['X'.charCodeAt (0)] = 6; -jalview.schemes.ResidueProperties.nucleotideIndex['x'.charCodeAt (0)] = 6; -jalview.schemes.ResidueProperties.nucleotideIndex['R'.charCodeAt (0)] = 7; -jalview.schemes.ResidueProperties.nucleotideIndex['r'.charCodeAt (0)] = 7; -jalview.schemes.ResidueProperties.nucleotideIndex['Y'.charCodeAt (0)] = 8; -jalview.schemes.ResidueProperties.nucleotideIndex['y'.charCodeAt (0)] = 8; -jalview.schemes.ResidueProperties.nucleotideIndex['N'.charCodeAt (0)] = 9; -jalview.schemes.ResidueProperties.nucleotideIndex['n'.charCodeAt (0)] = 9; -jalview.schemes.ResidueProperties.nucleotideName.put ("A", "Adenine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("a", "Adenine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("G", "Guanine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("g", "Guanine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("C", "Cytosine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("c", "Cytosine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("T", "Thymine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("t", "Thymine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("U", "Uracil"); -jalview.schemes.ResidueProperties.nucleotideName.put ("u", "Uracil"); -jalview.schemes.ResidueProperties.nucleotideName.put ("I", "Inosine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("i", "Inosine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("X", "Xanthine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("x", "Xanthine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("R", "Unknown Purine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("r", "Unknown Purine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("Y", "Unknown Pyrimidine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("y", "Unknown Pyrimidine"); -jalview.schemes.ResidueProperties.nucleotideName.put ("N", "Unknown"); -jalview.schemes.ResidueProperties.nucleotideName.put ("n", "Unknown"); -jalview.schemes.ResidueProperties.nucleotideName.put ("W", "Weak nucleotide (A or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("w", "Weak nucleotide (A or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("S", "Strong nucleotide (G or C)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("s", "Strong nucleotide (G or C)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("M", "Amino (A or C)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("m", "Amino (A or C)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("K", "Keto (G or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("k", "Keto (G or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("B", "Not A (G or C or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("b", "Not A (G or C or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("H", "Not G (A or C or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("h", "Not G (A or C or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("D", "Not C (A or G or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("d", "Not C (A or G or T)"); -jalview.schemes.ResidueProperties.nucleotideName.put ("V", "Not T (A or G or C"); -jalview.schemes.ResidueProperties.nucleotideName.put ("v", "Not T (A or G or C"); -}{ -jalview.schemes.ResidueProperties.purinepyrimidineIndex = Clazz.newIntArray (255, 0); -for (var i = 0; i < 255; i++) { -jalview.schemes.ResidueProperties.purinepyrimidineIndex[i] = 3; -} -jalview.schemes.ResidueProperties.purinepyrimidineIndex['A'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['a'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['C'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['c'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['G'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['g'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['T'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['t'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['U'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['u'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['I'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['i'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['X'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['x'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['R'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['r'.charCodeAt (0)] = 0; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['Y'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['y'.charCodeAt (0)] = 1; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['N'.charCodeAt (0)] = 2; -jalview.schemes.ResidueProperties.purinepyrimidineIndex['n'.charCodeAt (0)] = 2; -}{ -jalview.schemes.ResidueProperties.aa3Hash.put ("ALA", new Integer (0)); -jalview.schemes.ResidueProperties.aa3Hash.put ("ARG", new Integer (1)); -jalview.schemes.ResidueProperties.aa3Hash.put ("ASN", new Integer (2)); -jalview.schemes.ResidueProperties.aa3Hash.put ("ASP", new Integer (3)); -jalview.schemes.ResidueProperties.aa3Hash.put ("CYS", new Integer (4)); -jalview.schemes.ResidueProperties.aa3Hash.put ("GLN", new Integer (5)); -jalview.schemes.ResidueProperties.aa3Hash.put ("GLU", new Integer (6)); -jalview.schemes.ResidueProperties.aa3Hash.put ("GLY", new Integer (7)); -jalview.schemes.ResidueProperties.aa3Hash.put ("HIS", new Integer (8)); -jalview.schemes.ResidueProperties.aa3Hash.put ("ILE", new Integer (9)); -jalview.schemes.ResidueProperties.aa3Hash.put ("LEU", new Integer (10)); -jalview.schemes.ResidueProperties.aa3Hash.put ("LYS", new Integer (11)); -jalview.schemes.ResidueProperties.aa3Hash.put ("MET", new Integer (12)); -jalview.schemes.ResidueProperties.aa3Hash.put ("PHE", new Integer (13)); -jalview.schemes.ResidueProperties.aa3Hash.put ("PRO", new Integer (14)); -jalview.schemes.ResidueProperties.aa3Hash.put ("SER", new Integer (15)); -jalview.schemes.ResidueProperties.aa3Hash.put ("THR", new Integer (16)); -jalview.schemes.ResidueProperties.aa3Hash.put ("TRP", new Integer (17)); -jalview.schemes.ResidueProperties.aa3Hash.put ("TYR", new Integer (18)); -jalview.schemes.ResidueProperties.aa3Hash.put ("VAL", new Integer (19)); -jalview.schemes.ResidueProperties.aa3Hash.put ("ASX", new Integer (20)); -jalview.schemes.ResidueProperties.aa3Hash.put ("GLX", new Integer (21)); -jalview.schemes.ResidueProperties.aa3Hash.put ("XAA", new Integer (22)); -jalview.schemes.ResidueProperties.aa3Hash.put ("-", new Integer (23)); -jalview.schemes.ResidueProperties.aa3Hash.put ("*", new Integer (23)); -jalview.schemes.ResidueProperties.aa3Hash.put (".", new Integer (23)); -jalview.schemes.ResidueProperties.aa3Hash.put (" ", new Integer (23)); -jalview.schemes.ResidueProperties.aa3Hash.put ("Gap", new Integer (23)); -}{ -jalview.schemes.ResidueProperties.aa2Triplet.put ("A", "ALA"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("a", "ALA"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("R", "ARG"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("r", "ARG"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("N", "ASN"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("n", "ASN"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("D", "ASP"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("d", "ASP"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("C", "CYS"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("c", "CYS"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("Q", "GLN"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("q", "GLN"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("E", "GLU"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("e", "GLU"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("G", "GLY"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("g", "GLY"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("H", "HIS"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("h", "HIS"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("I", "ILE"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("i", "ILE"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("L", "LEU"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("l", "LEU"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("K", "LYS"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("k", "LYS"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("M", "MET"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("m", "MET"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("F", "PHE"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("f", "PHE"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("P", "PRO"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("p", "PRO"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("S", "SER"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("s", "SER"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("T", "THR"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("t", "THR"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("W", "TRP"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("w", "TRP"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("Y", "TYR"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("y", "TYR"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("V", "VAL"); -jalview.schemes.ResidueProperties.aa2Triplet.put ("v", "VAL"); -}Clazz.defineStatics (c$, -"aa", Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "])); -c$.midBlue = c$.prototype.midBlue = new java.awt.Color (100, 100, 255); -c$.scaleColours = c$.prototype.scaleColours = new java.util.Vector (); -{ -jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (114, 0, 147)); -jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (156, 0, 98)); -jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (190, 0, 0)); -jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.red); -jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 125, 0)); -jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.orange); -jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 194, 85)); -jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.yellow); -jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 255, 181)); -jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.white); -}c$.taylor = c$.prototype.taylor = Clazz.newArray (-1, [ new java.awt.Color (204, 255, 0), new java.awt.Color (0, 0, 255), new java.awt.Color (204, 0, 255), new java.awt.Color (255, 0, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 0, 204), new java.awt.Color (255, 0, 102), new java.awt.Color (255, 153, 0), new java.awt.Color (0, 102, 255), new java.awt.Color (102, 255, 0), new java.awt.Color (51, 255, 0), new java.awt.Color (102, 0, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (0, 255, 102), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (0, 204, 255), new java.awt.Color (0, 255, 204), new java.awt.Color (153, 255, 0), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]); -c$.nucleotide = c$.prototype.nucleotide = Clazz.newArray (-1, [ new java.awt.Color (100, 247, 63), new java.awt.Color (255, 179, 64), new java.awt.Color (235, 65, 60), new java.awt.Color (60, 136, 238), new java.awt.Color (60, 136, 238), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]); -c$.purinepyrimidine = c$.prototype.purinepyrimidine = Clazz.newArray (-1, [ new java.awt.Color (255, 131, 250), new java.awt.Color (64, 224, 208), java.awt.Color.white, java.awt.Color.white]); -c$.zappo = c$.prototype.zappo = Clazz.newArray (-1, [java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.green, java.awt.Color.red, java.awt.Color.yellow, java.awt.Color.green, java.awt.Color.red, java.awt.Color.magenta, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.orange, java.awt.Color.magenta, java.awt.Color.green, java.awt.Color.green, java.awt.Color.orange, java.awt.Color.orange, java.awt.Color.pink, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]); -Clazz.defineStatics (c$, -"hyd2", Clazz.newDoubleArray (-1, [0.62, 0.29, -0.9, -0.74, 1.19, 0.48, -0.4, 1.38, -1.5, 1.06, 0.64, -0.78, 0.12, -0.85, -2.53, -0.18, -0.05, 1.08, 0.81, 0.0, 0.26, 0.0, 0.0]), -"helix", Clazz.newDoubleArray (-1, [1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0]), -"helixmin", 0.57, -"helixmax", 1.51, -"strand", Clazz.newDoubleArray (-1, [0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0]), -"strandmin", 0.37, -"strandmax", 1.7, -"turn", Clazz.newDoubleArray (-1, [0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0]), -"turnmin", 0.47, -"turnmax", 1.56, -"buried", Clazz.newDoubleArray (-1, [1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00]), -"buriedmin", 0.05, -"buriedmax", 4.6, -"hyd", Clazz.newDoubleArray (-1, [1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0]), -"hydmax", 4.5, -"hydmin", -3.9, -"BLOSUM62", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4]), Clazz.newIntArray (-1, [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4]), Clazz.newIntArray (-1, [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4]), Clazz.newIntArray (-1, [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4]), Clazz.newIntArray (-1, [0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4]), Clazz.newIntArray (-1, [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4]), Clazz.newIntArray (-1, [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]), Clazz.newIntArray (-1, [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4]), Clazz.newIntArray (-1, [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4]), Clazz.newIntArray (-1, [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4]), Clazz.newIntArray (-1, [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4]), Clazz.newIntArray (-1, [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4]), Clazz.newIntArray (-1, [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4]), Clazz.newIntArray (-1, [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4]), Clazz.newIntArray (-1, [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4]), Clazz.newIntArray (-1, [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4]), Clazz.newIntArray (-1, [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4]), Clazz.newIntArray (-1, [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4]), Clazz.newIntArray (-1, [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4]), Clazz.newIntArray (-1, [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4]), Clazz.newIntArray (-1, [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4]), Clazz.newIntArray (-1, [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]), Clazz.newIntArray (-1, [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4]), Clazz.newIntArray (-1, [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1])]), -"PAM250", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8]), Clazz.newIntArray (-1, [-2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8]), Clazz.newIntArray (-1, [0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8]), Clazz.newIntArray (-1, [0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]), Clazz.newIntArray (-1, [-2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8]), Clazz.newIntArray (-1, [0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8]), Clazz.newIntArray (-1, [0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]), Clazz.newIntArray (-1, [1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8]), Clazz.newIntArray (-1, [-1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8]), Clazz.newIntArray (-1, [-1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8]), Clazz.newIntArray (-1, [-2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8]), Clazz.newIntArray (-1, [-1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8]), Clazz.newIntArray (-1, [-1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8]), Clazz.newIntArray (-1, [-3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8]), Clazz.newIntArray (-1, [1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8]), Clazz.newIntArray (-1, [1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8]), Clazz.newIntArray (-1, [1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8]), Clazz.newIntArray (-1, [-6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8]), Clazz.newIntArray (-1, [-3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8]), Clazz.newIntArray (-1, [0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8]), Clazz.newIntArray (-1, [0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8]), Clazz.newIntArray (-1, [0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8]), Clazz.newIntArray (-1, [0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8]), Clazz.newIntArray (-1, [-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1])])); -c$.ssHash = c$.prototype.ssHash = new java.util.Hashtable (); -{ -jalview.schemes.ResidueProperties.ssHash.put ("H", java.awt.Color.magenta); -jalview.schemes.ResidueProperties.ssHash.put ("E", java.awt.Color.yellow); -jalview.schemes.ResidueProperties.ssHash.put ("-", java.awt.Color.white); -jalview.schemes.ResidueProperties.ssHash.put (".", java.awt.Color.white); -jalview.schemes.ResidueProperties.ssHash.put ("S", java.awt.Color.cyan); -jalview.schemes.ResidueProperties.ssHash.put ("T", java.awt.Color.blue); -jalview.schemes.ResidueProperties.ssHash.put ("G", java.awt.Color.pink); -jalview.schemes.ResidueProperties.ssHash.put ("I", java.awt.Color.pink); -jalview.schemes.ResidueProperties.ssHash.put ("B", java.awt.Color.yellow); -}Clazz.defineStatics (c$, -"DNA", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1]), Clazz.newIntArray (-1, [-8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [-8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1]), Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1]), Clazz.newIntArray (-1, [1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1]), Clazz.newIntArray (-1, [-8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])])); -{ -jalview.schemes.ResidueProperties.scoreMatrices.put ("BLOSUM62", new jalview.schemes.ScoreMatrix ("BLOSUM62", jalview.schemes.ResidueProperties.BLOSUM62, 0)); -jalview.schemes.ResidueProperties.scoreMatrices.put ("PAM250", new jalview.schemes.ScoreMatrix ("PAM250", jalview.schemes.ResidueProperties.PAM250, 0)); -jalview.schemes.ResidueProperties.scoreMatrices.put ("DNA", new jalview.schemes.ScoreMatrix ("DNA", jalview.schemes.ResidueProperties.DNA, 1)); -}c$.pidColours = c$.prototype.pidColours = Clazz.newArray (-1, [jalview.schemes.ResidueProperties.midBlue, new java.awt.Color (153, 153, 255), new java.awt.Color (204, 204, 255)]); -Clazz.defineStatics (c$, -"pidThresholds", Clazz.newFloatArray (-1, [80, 60, 40])); -c$.codonHash = c$.prototype.codonHash = new java.util.HashMap (); -c$.Lys = c$.prototype.Lys = new java.util.ArrayList (); -c$.Asn = c$.prototype.Asn = new java.util.ArrayList (); -c$.Gln = c$.prototype.Gln = new java.util.ArrayList (); -c$.His = c$.prototype.His = new java.util.ArrayList (); -c$.Glu = c$.prototype.Glu = new java.util.ArrayList (); -c$.Asp = c$.prototype.Asp = new java.util.ArrayList (); -c$.Tyr = c$.prototype.Tyr = new java.util.ArrayList (); -c$.Thr = c$.prototype.Thr = new java.util.ArrayList (); -c$.Pro = c$.prototype.Pro = new java.util.ArrayList (); -c$.Ala = c$.prototype.Ala = new java.util.ArrayList (); -c$.Ser = c$.prototype.Ser = new java.util.ArrayList (); -c$.Arg = c$.prototype.Arg = new java.util.ArrayList (); -c$.Gly = c$.prototype.Gly = new java.util.ArrayList (); -c$.Trp = c$.prototype.Trp = new java.util.ArrayList (); -c$.Cys = c$.prototype.Cys = new java.util.ArrayList (); -c$.Ile = c$.prototype.Ile = new java.util.ArrayList (); -c$.Met = c$.prototype.Met = new java.util.ArrayList (); -c$.Leu = c$.prototype.Leu = new java.util.ArrayList (); -c$.Val = c$.prototype.Val = new java.util.ArrayList (); -c$.Phe = c$.prototype.Phe = new java.util.ArrayList (); -c$.STOP = c$.prototype.STOP = new java.util.ArrayList (); -Clazz.defineStatics (c$, -"START", "ATG"); -{ -jalview.schemes.ResidueProperties.codonHash.put ("K", jalview.schemes.ResidueProperties.Lys); -jalview.schemes.ResidueProperties.codonHash.put ("N", jalview.schemes.ResidueProperties.Asn); -jalview.schemes.ResidueProperties.codonHash.put ("Q", jalview.schemes.ResidueProperties.Gln); -jalview.schemes.ResidueProperties.codonHash.put ("H", jalview.schemes.ResidueProperties.His); -jalview.schemes.ResidueProperties.codonHash.put ("E", jalview.schemes.ResidueProperties.Glu); -jalview.schemes.ResidueProperties.codonHash.put ("D", jalview.schemes.ResidueProperties.Asp); -jalview.schemes.ResidueProperties.codonHash.put ("Y", jalview.schemes.ResidueProperties.Tyr); -jalview.schemes.ResidueProperties.codonHash.put ("T", jalview.schemes.ResidueProperties.Thr); -jalview.schemes.ResidueProperties.codonHash.put ("P", jalview.schemes.ResidueProperties.Pro); -jalview.schemes.ResidueProperties.codonHash.put ("A", jalview.schemes.ResidueProperties.Ala); -jalview.schemes.ResidueProperties.codonHash.put ("S", jalview.schemes.ResidueProperties.Ser); -jalview.schemes.ResidueProperties.codonHash.put ("R", jalview.schemes.ResidueProperties.Arg); -jalview.schemes.ResidueProperties.codonHash.put ("G", jalview.schemes.ResidueProperties.Gly); -jalview.schemes.ResidueProperties.codonHash.put ("W", jalview.schemes.ResidueProperties.Trp); -jalview.schemes.ResidueProperties.codonHash.put ("C", jalview.schemes.ResidueProperties.Cys); -jalview.schemes.ResidueProperties.codonHash.put ("I", jalview.schemes.ResidueProperties.Ile); -jalview.schemes.ResidueProperties.codonHash.put ("M", jalview.schemes.ResidueProperties.Met); -jalview.schemes.ResidueProperties.codonHash.put ("L", jalview.schemes.ResidueProperties.Leu); -jalview.schemes.ResidueProperties.codonHash.put ("V", jalview.schemes.ResidueProperties.Val); -jalview.schemes.ResidueProperties.codonHash.put ("F", jalview.schemes.ResidueProperties.Phe); -jalview.schemes.ResidueProperties.codonHash.put ("STOP", jalview.schemes.ResidueProperties.STOP); -}c$.ambiguityCodes = c$.prototype.ambiguityCodes = new java.util.Hashtable (); -c$.codonHash2 = c$.prototype.codonHash2 = new java.util.Hashtable (); -c$._ambiguityCodes = c$.prototype._ambiguityCodes = new java.util.Hashtable (); -{ -jalview.schemes.ResidueProperties.ambiguityCodes.put ("R", Clazz.newArray (-1, ["A", "G"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("Y", Clazz.newArray (-1, ["T", "C"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("W", Clazz.newArray (-1, ["A", "T"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("S", Clazz.newArray (-1, ["G", "C"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("M", Clazz.newArray (-1, ["A", "C"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("K", Clazz.newArray (-1, ["G", "T"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("H", Clazz.newArray (-1, ["A", "T", "C"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("B", Clazz.newArray (-1, ["G", "T", "C"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("V", Clazz.newArray (-1, ["G", "A", "C"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("D", Clazz.newArray (-1, ["G", "A", "T"])); -jalview.schemes.ResidueProperties.ambiguityCodes.put ("N", Clazz.newArray (-1, ["G", "A", "T", "C"])); -jalview.schemes.ResidueProperties.codonHash2.put ("AAA", "K"); -jalview.schemes.ResidueProperties.codonHash2.put ("AAG", "K"); -jalview.schemes.ResidueProperties.codonHash2.put ("AAC", "N"); -jalview.schemes.ResidueProperties.codonHash2.put ("AAT", "N"); -jalview.schemes.ResidueProperties.codonHash2.put ("CAA", "Q"); -jalview.schemes.ResidueProperties.codonHash2.put ("CAG", "Q"); -jalview.schemes.ResidueProperties.codonHash2.put ("CAC", "H"); -jalview.schemes.ResidueProperties.codonHash2.put ("CAT", "H"); -jalview.schemes.ResidueProperties.codonHash2.put ("GAA", "E"); -jalview.schemes.ResidueProperties.codonHash2.put ("GAG", "E"); -jalview.schemes.ResidueProperties.codonHash2.put ("GAC", "D"); -jalview.schemes.ResidueProperties.codonHash2.put ("GAT", "D"); -jalview.schemes.ResidueProperties.codonHash2.put ("TAC", "Y"); -jalview.schemes.ResidueProperties.codonHash2.put ("TAT", "Y"); -jalview.schemes.ResidueProperties.codonHash2.put ("ACA", "T"); -jalview.schemes.ResidueProperties.codonHash2.put ("ACC", "T"); -jalview.schemes.ResidueProperties.codonHash2.put ("ACT", "T"); -jalview.schemes.ResidueProperties.codonHash2.put ("ACG", "T"); -jalview.schemes.ResidueProperties.codonHash2.put ("CCA", "P"); -jalview.schemes.ResidueProperties.codonHash2.put ("CCG", "P"); -jalview.schemes.ResidueProperties.codonHash2.put ("CCC", "P"); -jalview.schemes.ResidueProperties.codonHash2.put ("CCT", "P"); -jalview.schemes.ResidueProperties.codonHash2.put ("GCA", "A"); -jalview.schemes.ResidueProperties.codonHash2.put ("GCG", "A"); -jalview.schemes.ResidueProperties.codonHash2.put ("GCC", "A"); -jalview.schemes.ResidueProperties.codonHash2.put ("GCT", "A"); -jalview.schemes.ResidueProperties.codonHash2.put ("TCA", "S"); -jalview.schemes.ResidueProperties.codonHash2.put ("TCG", "S"); -jalview.schemes.ResidueProperties.codonHash2.put ("TCC", "S"); -jalview.schemes.ResidueProperties.codonHash2.put ("TCT", "S"); -jalview.schemes.ResidueProperties.codonHash2.put ("AGC", "S"); -jalview.schemes.ResidueProperties.codonHash2.put ("AGT", "S"); -jalview.schemes.ResidueProperties.codonHash2.put ("AGA", "R"); -jalview.schemes.ResidueProperties.codonHash2.put ("AGG", "R"); -jalview.schemes.ResidueProperties.codonHash2.put ("CGA", "R"); -jalview.schemes.ResidueProperties.codonHash2.put ("CGG", "R"); -jalview.schemes.ResidueProperties.codonHash2.put ("CGC", "R"); -jalview.schemes.ResidueProperties.codonHash2.put ("CGT", "R"); -jalview.schemes.ResidueProperties.codonHash2.put ("GGA", "G"); -jalview.schemes.ResidueProperties.codonHash2.put ("GGG", "G"); -jalview.schemes.ResidueProperties.codonHash2.put ("GGC", "G"); -jalview.schemes.ResidueProperties.codonHash2.put ("GGT", "G"); -jalview.schemes.ResidueProperties.codonHash2.put ("TGA", "*"); -jalview.schemes.ResidueProperties.codonHash2.put ("TAA", "*"); -jalview.schemes.ResidueProperties.codonHash2.put ("TAG", "*"); -jalview.schemes.ResidueProperties.codonHash2.put ("TGG", "W"); -jalview.schemes.ResidueProperties.codonHash2.put ("TGC", "C"); -jalview.schemes.ResidueProperties.codonHash2.put ("TGT", "C"); -jalview.schemes.ResidueProperties.codonHash2.put ("ATA", "I"); -jalview.schemes.ResidueProperties.codonHash2.put ("ATC", "I"); -jalview.schemes.ResidueProperties.codonHash2.put ("ATT", "I"); -jalview.schemes.ResidueProperties.codonHash2.put ("ATG", "M"); -jalview.schemes.ResidueProperties.codonHash2.put ("CTA", "L"); -jalview.schemes.ResidueProperties.codonHash2.put ("CTG", "L"); -jalview.schemes.ResidueProperties.codonHash2.put ("CTC", "L"); -jalview.schemes.ResidueProperties.codonHash2.put ("CTT", "L"); -jalview.schemes.ResidueProperties.codonHash2.put ("TTA", "L"); -jalview.schemes.ResidueProperties.codonHash2.put ("TTG", "L"); -jalview.schemes.ResidueProperties.codonHash2.put ("GTA", "V"); -jalview.schemes.ResidueProperties.codonHash2.put ("GTG", "V"); -jalview.schemes.ResidueProperties.codonHash2.put ("GTC", "V"); -jalview.schemes.ResidueProperties.codonHash2.put ("GTT", "V"); -jalview.schemes.ResidueProperties.codonHash2.put ("TTC", "F"); -jalview.schemes.ResidueProperties.codonHash2.put ("TTT", "F"); -jalview.schemes.ResidueProperties.buildAmbiguityCodonSet (); -}{ -jalview.schemes.ResidueProperties.Lys.add ("AAA"); -jalview.schemes.ResidueProperties.Lys.add ("AAG"); -jalview.schemes.ResidueProperties.Asn.add ("AAC"); -jalview.schemes.ResidueProperties.Asn.add ("AAT"); -jalview.schemes.ResidueProperties.Gln.add ("CAA"); -jalview.schemes.ResidueProperties.Gln.add ("CAG"); -jalview.schemes.ResidueProperties.His.add ("CAC"); -jalview.schemes.ResidueProperties.His.add ("CAT"); -jalview.schemes.ResidueProperties.Glu.add ("GAA"); -jalview.schemes.ResidueProperties.Glu.add ("GAG"); -jalview.schemes.ResidueProperties.Asp.add ("GAC"); -jalview.schemes.ResidueProperties.Asp.add ("GAT"); -jalview.schemes.ResidueProperties.Tyr.add ("TAC"); -jalview.schemes.ResidueProperties.Tyr.add ("TAT"); -jalview.schemes.ResidueProperties.Thr.add ("ACA"); -jalview.schemes.ResidueProperties.Thr.add ("ACG"); -jalview.schemes.ResidueProperties.Thr.add ("ACC"); -jalview.schemes.ResidueProperties.Thr.add ("ACT"); -jalview.schemes.ResidueProperties.Pro.add ("CCA"); -jalview.schemes.ResidueProperties.Pro.add ("CCG"); -jalview.schemes.ResidueProperties.Pro.add ("CCC"); -jalview.schemes.ResidueProperties.Pro.add ("CCT"); -jalview.schemes.ResidueProperties.Ala.add ("GCA"); -jalview.schemes.ResidueProperties.Ala.add ("GCG"); -jalview.schemes.ResidueProperties.Ala.add ("GCC"); -jalview.schemes.ResidueProperties.Ala.add ("GCT"); -jalview.schemes.ResidueProperties.Ser.add ("TCA"); -jalview.schemes.ResidueProperties.Ser.add ("TCG"); -jalview.schemes.ResidueProperties.Ser.add ("TCC"); -jalview.schemes.ResidueProperties.Ser.add ("TCT"); -jalview.schemes.ResidueProperties.Ser.add ("AGC"); -jalview.schemes.ResidueProperties.Ser.add ("AGT"); -jalview.schemes.ResidueProperties.Arg.add ("AGA"); -jalview.schemes.ResidueProperties.Arg.add ("AGG"); -jalview.schemes.ResidueProperties.Arg.add ("CGA"); -jalview.schemes.ResidueProperties.Arg.add ("CGG"); -jalview.schemes.ResidueProperties.Arg.add ("CGC"); -jalview.schemes.ResidueProperties.Arg.add ("CGT"); -jalview.schemes.ResidueProperties.Gly.add ("GGA"); -jalview.schemes.ResidueProperties.Gly.add ("GGG"); -jalview.schemes.ResidueProperties.Gly.add ("GGC"); -jalview.schemes.ResidueProperties.Gly.add ("GGT"); -jalview.schemes.ResidueProperties.STOP.add ("TGA"); -jalview.schemes.ResidueProperties.STOP.add ("TAA"); -jalview.schemes.ResidueProperties.STOP.add ("TAG"); -jalview.schemes.ResidueProperties.Trp.add ("TGG"); -jalview.schemes.ResidueProperties.Cys.add ("TGC"); -jalview.schemes.ResidueProperties.Cys.add ("TGT"); -jalview.schemes.ResidueProperties.Ile.add ("ATA"); -jalview.schemes.ResidueProperties.Ile.add ("ATC"); -jalview.schemes.ResidueProperties.Ile.add ("ATT"); -jalview.schemes.ResidueProperties.Met.add ("ATG"); -jalview.schemes.ResidueProperties.Leu.add ("CTA"); -jalview.schemes.ResidueProperties.Leu.add ("CTG"); -jalview.schemes.ResidueProperties.Leu.add ("CTC"); -jalview.schemes.ResidueProperties.Leu.add ("CTT"); -jalview.schemes.ResidueProperties.Leu.add ("TTA"); -jalview.schemes.ResidueProperties.Leu.add ("TTG"); -jalview.schemes.ResidueProperties.Val.add ("GTA"); -jalview.schemes.ResidueProperties.Val.add ("GTG"); -jalview.schemes.ResidueProperties.Val.add ("GTC"); -jalview.schemes.ResidueProperties.Val.add ("GTT"); -jalview.schemes.ResidueProperties.Phe.add ("TTC"); -jalview.schemes.ResidueProperties.Phe.add ("TTT"); -}c$.propHash = c$.prototype.propHash = new java.util.Hashtable (); -c$.hydrophobic = c$.prototype.hydrophobic = new java.util.Hashtable (); -c$.polar = c$.prototype.polar = new java.util.Hashtable (); -c$.small = c$.prototype.small = new java.util.Hashtable (); -c$.positive = c$.prototype.positive = new java.util.Hashtable (); -c$.negative = c$.prototype.negative = new java.util.Hashtable (); -c$.charged = c$.prototype.charged = new java.util.Hashtable (); -c$.aromatic = c$.prototype.aromatic = new java.util.Hashtable (); -c$.aliphatic = c$.prototype.aliphatic = new java.util.Hashtable (); -c$.tiny = c$.prototype.tiny = new java.util.Hashtable (); -c$.proline = c$.prototype.proline = new java.util.Hashtable (); -{ -jalview.schemes.ResidueProperties.hydrophobic.put ("I", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("L", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("V", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("C", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("A", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("G", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("M", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("F", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("Y", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("W", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("H", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("K", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("X", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("*", new Integer (1)); -jalview.schemes.ResidueProperties.hydrophobic.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("D", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.hydrophobic.put ("P", new Integer (0)); -}{ -jalview.schemes.ResidueProperties.polar.put ("Y", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("W", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("H", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("K", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("R", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("E", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("Q", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("D", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("N", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("S", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("T", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("X", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("*", new Integer (1)); -jalview.schemes.ResidueProperties.polar.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.polar.put ("P", new Integer (0)); -}{ -jalview.schemes.ResidueProperties.small.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("V", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("C", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("A", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("G", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("H", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("K", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.small.put ("D", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("N", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("S", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("T", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("P", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.small.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.positive.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("H", new Integer (1)); -jalview.schemes.ResidueProperties.positive.put ("K", new Integer (1)); -jalview.schemes.ResidueProperties.positive.put ("R", new Integer (1)); -jalview.schemes.ResidueProperties.positive.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("D", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("P", new Integer (0)); -jalview.schemes.ResidueProperties.positive.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.positive.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.negative.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("H", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("K", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("E", new Integer (1)); -jalview.schemes.ResidueProperties.negative.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("D", new Integer (1)); -jalview.schemes.ResidueProperties.negative.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("P", new Integer (0)); -jalview.schemes.ResidueProperties.negative.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.negative.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.charged.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("H", new Integer (1)); -jalview.schemes.ResidueProperties.charged.put ("K", new Integer (1)); -jalview.schemes.ResidueProperties.charged.put ("R", new Integer (1)); -jalview.schemes.ResidueProperties.charged.put ("E", new Integer (1)); -jalview.schemes.ResidueProperties.charged.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("D", new Integer (1)); -jalview.schemes.ResidueProperties.charged.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("P", new Integer (0)); -jalview.schemes.ResidueProperties.charged.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.charged.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.aromatic.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("F", new Integer (1)); -jalview.schemes.ResidueProperties.aromatic.put ("Y", new Integer (1)); -jalview.schemes.ResidueProperties.aromatic.put ("W", new Integer (1)); -jalview.schemes.ResidueProperties.aromatic.put ("H", new Integer (1)); -jalview.schemes.ResidueProperties.aromatic.put ("K", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("D", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("P", new Integer (0)); -jalview.schemes.ResidueProperties.aromatic.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.aromatic.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.aliphatic.put ("I", new Integer (1)); -jalview.schemes.ResidueProperties.aliphatic.put ("L", new Integer (1)); -jalview.schemes.ResidueProperties.aliphatic.put ("V", new Integer (1)); -jalview.schemes.ResidueProperties.aliphatic.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("H", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("K", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("D", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("P", new Integer (0)); -jalview.schemes.ResidueProperties.aliphatic.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.aliphatic.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.tiny.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("A", new Integer (1)); -jalview.schemes.ResidueProperties.tiny.put ("G", new Integer (1)); -jalview.schemes.ResidueProperties.tiny.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("H", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("K", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("D", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("S", new Integer (1)); -jalview.schemes.ResidueProperties.tiny.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("P", new Integer (0)); -jalview.schemes.ResidueProperties.tiny.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.tiny.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.proline.put ("I", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("L", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("V", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("C", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("A", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("G", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("M", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("F", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("Y", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("W", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("H", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("K", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("R", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("E", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("Q", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("D", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("N", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("S", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("T", new Integer (0)); -jalview.schemes.ResidueProperties.proline.put ("P", new Integer (1)); -jalview.schemes.ResidueProperties.proline.put ("-", new Integer (1)); -jalview.schemes.ResidueProperties.proline.put ("*", new Integer (1)); -}{ -jalview.schemes.ResidueProperties.propHash.put ("hydrophobic", jalview.schemes.ResidueProperties.hydrophobic); -jalview.schemes.ResidueProperties.propHash.put ("small", jalview.schemes.ResidueProperties.small); -jalview.schemes.ResidueProperties.propHash.put ("positive", jalview.schemes.ResidueProperties.positive); -jalview.schemes.ResidueProperties.propHash.put ("negative", jalview.schemes.ResidueProperties.negative); -jalview.schemes.ResidueProperties.propHash.put ("charged", jalview.schemes.ResidueProperties.charged); -jalview.schemes.ResidueProperties.propHash.put ("aromatic", jalview.schemes.ResidueProperties.aromatic); -jalview.schemes.ResidueProperties.propHash.put ("aliphatic", jalview.schemes.ResidueProperties.aliphatic); -jalview.schemes.ResidueProperties.propHash.put ("tiny", jalview.schemes.ResidueProperties.tiny); -jalview.schemes.ResidueProperties.propHash.put ("proline", jalview.schemes.ResidueProperties.proline); -jalview.schemes.ResidueProperties.propHash.put ("polar", jalview.schemes.ResidueProperties.polar); -}{ -var propMatrixF = Clazz.newIntArray (23, 23, 0); -var propMatrixPos = Clazz.newIntArray (23, 23, 0); -var propMatrixEpos = Clazz.newIntArray (23, 23, 0); -for (var i = 0; i < 23; i++) { -var maxF = 0; -var maxP = 0; -var maxEP = 0; -var ic = ""; -if (jalview.schemes.ResidueProperties.aa.length > i) { -ic += jalview.schemes.ResidueProperties.aa[i]; -} else { -ic = "-"; -}for (var j = i + 1; j < 23; j++) { -var jc = ""; -if (jalview.schemes.ResidueProperties.aa.length > j) { -jc += jalview.schemes.ResidueProperties.aa[j]; -} else { -jc = "-"; -}propMatrixF[i][j] = 0; -propMatrixPos[i][j] = 0; -propMatrixEpos[i][j] = 0; -for (var en = jalview.schemes.ResidueProperties.propHash.keys (); en.hasMoreElements (); ) { -var ph = en.nextElement (); -var pph = jalview.schemes.ResidueProperties.propHash.get (ph); -if (pph.get (ic) != null && pph.get (jc) != null) { -var icp = pph.get (ic).intValue (); -var jcp = pph.get (jc).intValue (); -propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0; -propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0; -propMatrixF[i][j] += icp == jcp ? 2 : 0; -propMatrixF[j][i] += icp == jcp ? 2 : 0; -propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0; -propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0; -}} -if (maxF < propMatrixF[i][j]) { -maxF = propMatrixF[i][j]; -}if (maxP < propMatrixPos[i][j]) { -maxP = propMatrixPos[i][j]; -}if (maxEP < propMatrixEpos[i][j]) { -maxEP = propMatrixEpos[i][j]; -}} -propMatrixF[i][i] = maxF; -propMatrixPos[i][i] = maxP; -propMatrixEpos[i][i] = maxEP; -} -jalview.schemes.ResidueProperties.scoreMatrices.put ("PID", new jalview.analysis.scoremodels.PIDScoreModel ()); -jalview.schemes.ResidueProperties.scoreMatrices.put ("Displayed Features", new jalview.analysis.scoremodels.FeatureScoreModel ()); -}Clazz.defineStatics (c$, -"toDssp3State", null); -{ -jalview.schemes.ResidueProperties.toDssp3State = new java.util.Hashtable (); -jalview.schemes.ResidueProperties.toDssp3State.put ("H", "H"); -jalview.schemes.ResidueProperties.toDssp3State.put ("E", "E"); -jalview.schemes.ResidueProperties.toDssp3State.put ("C", " "); -jalview.schemes.ResidueProperties.toDssp3State.put (" ", " "); -jalview.schemes.ResidueProperties.toDssp3State.put ("T", " "); -jalview.schemes.ResidueProperties.toDssp3State.put ("B", "E"); -jalview.schemes.ResidueProperties.toDssp3State.put ("G", "H"); -jalview.schemes.ResidueProperties.toDssp3State.put ("I", "H"); -jalview.schemes.ResidueProperties.toDssp3State.put ("X", " "); -}Clazz.defineStatics (c$, -"toRNAssState", null, -"RNAcloseParen", Clazz.newBooleanArray (255, false)); -{ -jalview.schemes.ResidueProperties.toRNAssState = new java.util.Hashtable (); -jalview.schemes.ResidueProperties.toRNAssState.put (")", "("); -jalview.schemes.ResidueProperties.toRNAssState.put ("(", "("); -jalview.schemes.ResidueProperties.toRNAssState.put ("]", "["); -jalview.schemes.ResidueProperties.toRNAssState.put ("[", "["); -jalview.schemes.ResidueProperties.toRNAssState.put ("{", "{"); -jalview.schemes.ResidueProperties.toRNAssState.put ("}", "{"); -jalview.schemes.ResidueProperties.toRNAssState.put (">", ">"); -jalview.schemes.ResidueProperties.toRNAssState.put ("<", ">"); -jalview.schemes.ResidueProperties.toRNAssState.put ("A", "A"); -jalview.schemes.ResidueProperties.toRNAssState.put ("a", "A"); -jalview.schemes.ResidueProperties.toRNAssState.put ("B", "B"); -jalview.schemes.ResidueProperties.toRNAssState.put ("b", "B"); -jalview.schemes.ResidueProperties.toRNAssState.put ("C", "C"); -jalview.schemes.ResidueProperties.toRNAssState.put ("c", "C"); -jalview.schemes.ResidueProperties.toRNAssState.put ("D", "D"); -jalview.schemes.ResidueProperties.toRNAssState.put ("d", "D"); -jalview.schemes.ResidueProperties.toRNAssState.put ("E", "E"); -jalview.schemes.ResidueProperties.toRNAssState.put ("e", "E"); -jalview.schemes.ResidueProperties.toRNAssState.put ("F", "F"); -jalview.schemes.ResidueProperties.toRNAssState.put ("f", "F"); -jalview.schemes.ResidueProperties.toRNAssState.put ("G", "G"); -jalview.schemes.ResidueProperties.toRNAssState.put ("g", "G"); -jalview.schemes.ResidueProperties.toRNAssState.put ("H", "H"); -jalview.schemes.ResidueProperties.toRNAssState.put ("h", "H"); -jalview.schemes.ResidueProperties.toRNAssState.put ("I", "I"); -jalview.schemes.ResidueProperties.toRNAssState.put ("i", "I"); -jalview.schemes.ResidueProperties.toRNAssState.put ("J", "J"); -jalview.schemes.ResidueProperties.toRNAssState.put ("j", "J"); -jalview.schemes.ResidueProperties.toRNAssState.put ("K", "K"); -jalview.schemes.ResidueProperties.toRNAssState.put ("k", "K"); -jalview.schemes.ResidueProperties.toRNAssState.put ("L", "L"); -jalview.schemes.ResidueProperties.toRNAssState.put ("l", "L"); -jalview.schemes.ResidueProperties.toRNAssState.put ("M", "M"); -jalview.schemes.ResidueProperties.toRNAssState.put ("m", "M"); -jalview.schemes.ResidueProperties.toRNAssState.put ("N", "N"); -jalview.schemes.ResidueProperties.toRNAssState.put ("n", "N"); -jalview.schemes.ResidueProperties.toRNAssState.put ("O", "O"); -jalview.schemes.ResidueProperties.toRNAssState.put ("o", "O"); -jalview.schemes.ResidueProperties.toRNAssState.put ("P", "P"); -jalview.schemes.ResidueProperties.toRNAssState.put ("p", "P"); -jalview.schemes.ResidueProperties.toRNAssState.put ("Q", "Q"); -jalview.schemes.ResidueProperties.toRNAssState.put ("q", "Q"); -jalview.schemes.ResidueProperties.toRNAssState.put ("R", "R"); -jalview.schemes.ResidueProperties.toRNAssState.put ("r", "R"); -jalview.schemes.ResidueProperties.toRNAssState.put ("S", "S"); -jalview.schemes.ResidueProperties.toRNAssState.put ("s", "S"); -jalview.schemes.ResidueProperties.toRNAssState.put ("T", "T"); -jalview.schemes.ResidueProperties.toRNAssState.put ("t", "T"); -jalview.schemes.ResidueProperties.toRNAssState.put ("U", "U"); -jalview.schemes.ResidueProperties.toRNAssState.put ("u", "U"); -jalview.schemes.ResidueProperties.toRNAssState.put ("V", "V"); -jalview.schemes.ResidueProperties.toRNAssState.put ("v", "V"); -jalview.schemes.ResidueProperties.toRNAssState.put ("W", "W"); -jalview.schemes.ResidueProperties.toRNAssState.put ("w", "W"); -jalview.schemes.ResidueProperties.toRNAssState.put ("X", "X"); -jalview.schemes.ResidueProperties.toRNAssState.put ("x", "X"); -jalview.schemes.ResidueProperties.toRNAssState.put ("Y", "Y"); -jalview.schemes.ResidueProperties.toRNAssState.put ("y", "Y"); -jalview.schemes.ResidueProperties.toRNAssState.put ("Z", "Z"); -jalview.schemes.ResidueProperties.toRNAssState.put ("z", "Z"); -for (var p = 0; p < jalview.schemes.ResidueProperties.RNAcloseParen.length; p++) { -jalview.schemes.ResidueProperties.RNAcloseParen[p] = false; -} -for (var k, $k = jalview.schemes.ResidueProperties.toRNAssState.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) { -jalview.schemes.ResidueProperties.RNAcloseParen[k.charCodeAt (0)] = k.charAt (0) != jalview.schemes.ResidueProperties.toRNAssState.get (k).charAt (0); -} -}}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.analysis.scoremodels.FeatureScoreModel", "$.PIDScoreModel", "jalview.schemes.ScoreMatrix", "java.awt.Color", "java.util.ArrayList", "$.HashMap", "$.Hashtable", "$.Vector"], "jalview.schemes.ResidueProperties", ["java.lang.StringBuffer"], function () { +c$ = Clazz.declareType (jalview.schemes, "ResidueProperties"); +c$.buildAmbiguityCodonSet = Clazz.defineMethod (c$, "buildAmbiguityCodonSet", +function () { +if (jalview.schemes.ResidueProperties._ambiguityCodes.size () > 0) { +System.err.println ("Ignoring multiple calls to buildAmbiguityCodonSet"); +return; +}for (var acode, $acode = jalview.schemes.ResidueProperties.ambiguityCodes.entrySet ().iterator (); $acode.hasNext () && ((acode = $acode.next ()) || true);) { +for (var r, $r = 0, $$r = acode.getValue (); $r < $$r.length && ((r = $$r[$r]) || true); $r++) { +var codesfor = jalview.schemes.ResidueProperties._ambiguityCodes.get (r); +if (codesfor == null) { +jalview.schemes.ResidueProperties._ambiguityCodes.put (r, codesfor = new java.util.ArrayList ()); +}if (!codesfor.contains (acode.getKey ())) { +codesfor.add (acode.getKey ()); +} else { +System.err.println ("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey () + " in residue " + r); +}} +} +var unambcodons = jalview.schemes.ResidueProperties.codonHash2.keySet ().toArray ( new Array (jalview.schemes.ResidueProperties.codonHash2.size ())); +for (var codon, $codon = 0, $$codon = unambcodons; $codon < $$codon.length && ((codon = $$codon[$codon]) || true); $codon++) { +var residue = jalview.schemes.ResidueProperties.codonHash2.get (codon); +var acodon = new Array (codon.length); +for (var i = 0, iSize = codon.length; i < iSize; i++) { +var _ac = "" + codon.charAt (i); +var acodes = jalview.schemes.ResidueProperties._ambiguityCodes.get (_ac); +if (acodes != null) { +acodon[i] = acodes.toArray ( new Array (acodes.size ())); +} else { +acodon[i] = Clazz.newArray (-1, []); +}} +var tpos = Clazz.newIntArray (codon.length, 0); +var cpos = Clazz.newIntArray (codon.length, 0); +for (var i = 0; i < tpos.length; i++) { +tpos[i] = -1; +} +tpos[acodon.length - 1] = 0; +var ipos; +var j; +while (tpos[0] < acodon[0].length) { +var allres = Clazz.newCharArray (tpos.length, '\0'); +var _acodon = ""; +var _anuc; +for (ipos = 0; ipos < tpos.length; ipos++) { +if (acodon[ipos].length == 0 || tpos[ipos] < 0) { +_acodon += codon.charAt (ipos); +allres[ipos] = Clazz.newCharArray (-1, [codon.charAt (ipos)]); +} else { +_acodon += acodon[ipos][tpos[ipos]]; +var altbase = jalview.schemes.ResidueProperties.ambiguityCodes.get (acodon[ipos][tpos[ipos]]); +allres[ipos] = Clazz.newCharArray (altbase.length, '\0'); +j = 0; +for (var ab, $ab = 0, $$ab = altbase; $ab < $$ab.length && ((ab = $$ab[$ab]) || true); $ab++) { +allres[ipos][j++] = ab.charAt (0); +} +}} +for (ipos = 0; ipos < cpos.length; ipos++) { +cpos[ipos] = 0; +} +var valid = true; +do { +var _codon = ""; +for (j = 0; j < cpos.length; j++) { +_codon += allres[j][cpos[j]]; +} +var tr = jalview.schemes.ResidueProperties.codonHash2.get (_codon); +if (valid = (tr != null && tr.equals (residue))) { +ipos = acodon.length - 1; +while (++cpos[ipos] >= allres[ipos].length && ipos > 0) { +cpos[ipos] = 0; +ipos--; +} +}} while (valid && cpos[0] < allres[0].length); +if (valid) { +jalview.schemes.ResidueProperties.codonHash2.put (_acodon, residue); +} else { +}ipos = acodon.length - 1; +while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) { +tpos[ipos] = -1; +ipos--; +} +} +} +}); +c$.getHydmax = Clazz.defineMethod (c$, "getHydmax", +function () { +return 4.5; +}); +c$.getHydmin = Clazz.defineMethod (c$, "getHydmin", +function () { +return -3.9; +}); +c$.getHyd = Clazz.defineMethod (c$, "getHyd", +function () { +return jalview.schemes.ResidueProperties.hyd; +}); +c$.getAA3Hash = Clazz.defineMethod (c$, "getAA3Hash", +function () { +return jalview.schemes.ResidueProperties.aa3Hash; +}); +c$.getDNA = Clazz.defineMethod (c$, "getDNA", +function () { +return jalview.schemes.ResidueProperties.DNA; +}); +c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", +function () { +return jalview.schemes.ResidueProperties.BLOSUM62; +}); +c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", +function (A1, A2) { +return jalview.schemes.ResidueProperties.getPAM250 (A1.charAt (0), A2.charAt (0)); +}, "~S,~S"); +c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", +function (c1, c2) { +var pog = 0; +try { +var a = jalview.schemes.ResidueProperties.aaIndex[c1.charCodeAt (0)]; +var b = jalview.schemes.ResidueProperties.aaIndex[c2.charCodeAt (0)]; +pog = jalview.schemes.ResidueProperties.BLOSUM62[a][b]; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +return pog; +}, "~S,~S"); +c$.getCodons = Clazz.defineMethod (c$, "getCodons", +function (res) { +if (jalview.schemes.ResidueProperties.codonHash.containsKey (res)) { +return jalview.schemes.ResidueProperties.codonHash.get (res); +}return null; +}, "~S"); +c$.codonTranslate = Clazz.defineMethod (c$, "codonTranslate", +function (lccodon) { +if (false) { +return jalview.schemes.ResidueProperties._codonTranslate (lccodon); +}var cdn = jalview.schemes.ResidueProperties.codonHash2.get (lccodon.toUpperCase ()); +if (cdn != null && cdn.equals ("*")) { +return "STOP"; +}return cdn; +}, "~S"); +c$._codonTranslate = Clazz.defineMethod (c$, "_codonTranslate", +function (lccodon) { +var codon = lccodon.toUpperCase (); +if (codon.indexOf ('X') > -1 || codon.indexOf ('N') > -1) { +return "X"; +}for (var key, $key = jalview.schemes.ResidueProperties.codonHash.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { +if (jalview.schemes.ResidueProperties.codonHash.get (key).contains (codon)) { +return key; +}} +return null; +}, "~S"); +c$.getDefaultPeptideMatrix = Clazz.defineMethod (c$, "getDefaultPeptideMatrix", +function () { +return jalview.schemes.ResidueProperties.getBLOSUM62 (); +}); +c$.getDefaultDnaMatrix = Clazz.defineMethod (c$, "getDefaultDnaMatrix", +function () { +return jalview.schemes.ResidueProperties.getDNA (); +}); +c$.getScoreMatrix = Clazz.defineMethod (c$, "getScoreMatrix", +function (pwtype) { +var val = jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype); +if (val != null && Clazz.instanceOf (val, jalview.schemes.ScoreMatrix)) { +return val; +}return null; +}, "~S"); +c$.getScoreModel = Clazz.defineMethod (c$, "getScoreModel", +function (pwtype) { +return jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype); +}, "~S"); +c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", +function (c, d) { +var a = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; +var b = jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)]; +var pog = jalview.schemes.ResidueProperties.PAM250[a][b]; +return pog; +}, "~S,~S"); +c$.getDssp3state = Clazz.defineMethod (c$, "getDssp3state", +function (ssstring) { +if (ssstring == null) { +return null; +}var ss = new StringBuffer (); +for (var i = 0; i < ssstring.length; i++) { +var ssc = ssstring.substring (i, i + 1); +if (jalview.schemes.ResidueProperties.toDssp3State.containsKey (ssc)) { +ss.append (jalview.schemes.ResidueProperties.toDssp3State.get (ssc)); +} else { +ss.append (" "); +}} +return ss.toString (); +}, "~S"); +c$.getRNASecStrucState = Clazz.defineMethod (c$, "getRNASecStrucState", +function (ssstring) { +if (ssstring == null) { +return null; +}var ss = new StringBuffer (); +for (var i = 0; i < ssstring.length; i++) { +var ssc = ssstring.substring (i, i + 1); +if (jalview.schemes.ResidueProperties.toRNAssState.containsKey (ssc)) { +ss.append (ssc); +} else { +ss.append (" "); +}} +return ss.toString (); +}, "~S"); +c$.isCloseParenRNA = Clazz.defineMethod (c$, "isCloseParenRNA", +function (dc) { +return jalview.schemes.ResidueProperties.RNAcloseParen[dc.charCodeAt (0)]; +}, "~S"); +c$.getResidues = Clazz.defineMethod (c$, "getResidues", +function (nucleotide, includeAmbiguous) { +var result = new java.util.ArrayList (); +if (nucleotide) { +for (var nuc, $nuc = jalview.schemes.ResidueProperties.nucleotideName.keySet ().iterator (); $nuc.hasNext () && ((nuc = $nuc.next ()) || true);) { +var val = jalview.schemes.ResidueProperties.nucleotideIndex[nuc.charCodeAt (0)]; +if ((!includeAmbiguous && val > 4) || (val >= 10)) { +continue; +}nuc = nuc.toUpperCase (); +if (!result.contains (nuc)) { +result.add (nuc); +}} +} else { +for (var res, $res = jalview.schemes.ResidueProperties.aa3Hash.keySet ().iterator (); $res.hasNext () && ((res = $res.next ()) || true);) { +var index = jalview.schemes.ResidueProperties.aa3Hash.get (res).intValue (); +if ((!includeAmbiguous && index >= 20) || index >= 23) { +continue; +}res = res.toUpperCase (); +if (!result.contains (res)) { +result.add (res); +}} +}return result; +}, "~B,~B"); +c$.scoreMatrices = c$.prototype.scoreMatrices = new java.util.Hashtable (); +Clazz.defineStatics (c$, +"aaIndex", null, +"nucleotideIndex", null, +"purinepyrimidineIndex", null); +c$.aa3Hash = c$.prototype.aa3Hash = new java.util.HashMap (); +c$.aa2Triplet = c$.prototype.aa2Triplet = new java.util.HashMap (); +c$.nucleotideName = c$.prototype.nucleotideName = new java.util.HashMap (); +{ +jalview.schemes.ResidueProperties.aaIndex = Clazz.newIntArray (255, 0); +for (var i = 0; i < 255; i++) { +jalview.schemes.ResidueProperties.aaIndex[i] = 23; +} +jalview.schemes.ResidueProperties.aaIndex['A'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.aaIndex['R'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.aaIndex['N'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)] = 3; +jalview.schemes.ResidueProperties.aaIndex['C'.charCodeAt (0)] = 4; +jalview.schemes.ResidueProperties.aaIndex['Q'.charCodeAt (0)] = 5; +jalview.schemes.ResidueProperties.aaIndex['E'.charCodeAt (0)] = 6; +jalview.schemes.ResidueProperties.aaIndex['G'.charCodeAt (0)] = 7; +jalview.schemes.ResidueProperties.aaIndex['H'.charCodeAt (0)] = 8; +jalview.schemes.ResidueProperties.aaIndex['I'.charCodeAt (0)] = 9; +jalview.schemes.ResidueProperties.aaIndex['L'.charCodeAt (0)] = 10; +jalview.schemes.ResidueProperties.aaIndex['K'.charCodeAt (0)] = 11; +jalview.schemes.ResidueProperties.aaIndex['M'.charCodeAt (0)] = 12; +jalview.schemes.ResidueProperties.aaIndex['F'.charCodeAt (0)] = 13; +jalview.schemes.ResidueProperties.aaIndex['P'.charCodeAt (0)] = 14; +jalview.schemes.ResidueProperties.aaIndex['S'.charCodeAt (0)] = 15; +jalview.schemes.ResidueProperties.aaIndex['T'.charCodeAt (0)] = 16; +jalview.schemes.ResidueProperties.aaIndex['W'.charCodeAt (0)] = 17; +jalview.schemes.ResidueProperties.aaIndex['Y'.charCodeAt (0)] = 18; +jalview.schemes.ResidueProperties.aaIndex['V'.charCodeAt (0)] = 19; +jalview.schemes.ResidueProperties.aaIndex['B'.charCodeAt (0)] = 20; +jalview.schemes.ResidueProperties.aaIndex['Z'.charCodeAt (0)] = 21; +jalview.schemes.ResidueProperties.aaIndex['X'.charCodeAt (0)] = 22; +jalview.schemes.ResidueProperties.aaIndex['U'.charCodeAt (0)] = 22; +jalview.schemes.ResidueProperties.aaIndex['a'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.aaIndex['r'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.aaIndex['n'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.aaIndex['d'.charCodeAt (0)] = 3; +jalview.schemes.ResidueProperties.aaIndex['c'.charCodeAt (0)] = 4; +jalview.schemes.ResidueProperties.aaIndex['q'.charCodeAt (0)] = 5; +jalview.schemes.ResidueProperties.aaIndex['e'.charCodeAt (0)] = 6; +jalview.schemes.ResidueProperties.aaIndex['g'.charCodeAt (0)] = 7; +jalview.schemes.ResidueProperties.aaIndex['h'.charCodeAt (0)] = 8; +jalview.schemes.ResidueProperties.aaIndex['i'.charCodeAt (0)] = 9; +jalview.schemes.ResidueProperties.aaIndex['l'.charCodeAt (0)] = 10; +jalview.schemes.ResidueProperties.aaIndex['k'.charCodeAt (0)] = 11; +jalview.schemes.ResidueProperties.aaIndex['m'.charCodeAt (0)] = 12; +jalview.schemes.ResidueProperties.aaIndex['f'.charCodeAt (0)] = 13; +jalview.schemes.ResidueProperties.aaIndex['p'.charCodeAt (0)] = 14; +jalview.schemes.ResidueProperties.aaIndex['s'.charCodeAt (0)] = 15; +jalview.schemes.ResidueProperties.aaIndex['t'.charCodeAt (0)] = 16; +jalview.schemes.ResidueProperties.aaIndex['w'.charCodeAt (0)] = 17; +jalview.schemes.ResidueProperties.aaIndex['y'.charCodeAt (0)] = 18; +jalview.schemes.ResidueProperties.aaIndex['v'.charCodeAt (0)] = 19; +jalview.schemes.ResidueProperties.aaIndex['b'.charCodeAt (0)] = 20; +jalview.schemes.ResidueProperties.aaIndex['z'.charCodeAt (0)] = 21; +jalview.schemes.ResidueProperties.aaIndex['x'.charCodeAt (0)] = 22; +jalview.schemes.ResidueProperties.aaIndex['u'.charCodeAt (0)] = 22; +}Clazz.defineStatics (c$, +"maxProteinIndex", 23, +"maxNucleotideIndex", 10); +{ +jalview.schemes.ResidueProperties.nucleotideIndex = Clazz.newIntArray (255, 0); +for (var i = 0; i < 255; i++) { +jalview.schemes.ResidueProperties.nucleotideIndex[i] = 10; +} +jalview.schemes.ResidueProperties.nucleotideIndex['A'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.nucleotideIndex['a'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.nucleotideIndex['C'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.nucleotideIndex['c'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.nucleotideIndex['G'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.nucleotideIndex['g'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.nucleotideIndex['T'.charCodeAt (0)] = 3; +jalview.schemes.ResidueProperties.nucleotideIndex['t'.charCodeAt (0)] = 3; +jalview.schemes.ResidueProperties.nucleotideIndex['U'.charCodeAt (0)] = 4; +jalview.schemes.ResidueProperties.nucleotideIndex['u'.charCodeAt (0)] = 4; +jalview.schemes.ResidueProperties.nucleotideIndex['I'.charCodeAt (0)] = 5; +jalview.schemes.ResidueProperties.nucleotideIndex['i'.charCodeAt (0)] = 5; +jalview.schemes.ResidueProperties.nucleotideIndex['X'.charCodeAt (0)] = 6; +jalview.schemes.ResidueProperties.nucleotideIndex['x'.charCodeAt (0)] = 6; +jalview.schemes.ResidueProperties.nucleotideIndex['R'.charCodeAt (0)] = 7; +jalview.schemes.ResidueProperties.nucleotideIndex['r'.charCodeAt (0)] = 7; +jalview.schemes.ResidueProperties.nucleotideIndex['Y'.charCodeAt (0)] = 8; +jalview.schemes.ResidueProperties.nucleotideIndex['y'.charCodeAt (0)] = 8; +jalview.schemes.ResidueProperties.nucleotideIndex['N'.charCodeAt (0)] = 9; +jalview.schemes.ResidueProperties.nucleotideIndex['n'.charCodeAt (0)] = 9; +jalview.schemes.ResidueProperties.nucleotideName.put ("A", "Adenine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("a", "Adenine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("G", "Guanine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("g", "Guanine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("C", "Cytosine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("c", "Cytosine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("T", "Thymine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("t", "Thymine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("U", "Uracil"); +jalview.schemes.ResidueProperties.nucleotideName.put ("u", "Uracil"); +jalview.schemes.ResidueProperties.nucleotideName.put ("I", "Inosine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("i", "Inosine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("X", "Xanthine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("x", "Xanthine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("R", "Unknown Purine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("r", "Unknown Purine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("Y", "Unknown Pyrimidine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("y", "Unknown Pyrimidine"); +jalview.schemes.ResidueProperties.nucleotideName.put ("N", "Unknown"); +jalview.schemes.ResidueProperties.nucleotideName.put ("n", "Unknown"); +jalview.schemes.ResidueProperties.nucleotideName.put ("W", "Weak nucleotide (A or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("w", "Weak nucleotide (A or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("S", "Strong nucleotide (G or C)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("s", "Strong nucleotide (G or C)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("M", "Amino (A or C)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("m", "Amino (A or C)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("K", "Keto (G or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("k", "Keto (G or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("B", "Not A (G or C or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("b", "Not A (G or C or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("H", "Not G (A or C or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("h", "Not G (A or C or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("D", "Not C (A or G or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("d", "Not C (A or G or T)"); +jalview.schemes.ResidueProperties.nucleotideName.put ("V", "Not T (A or G or C"); +jalview.schemes.ResidueProperties.nucleotideName.put ("v", "Not T (A or G or C"); +}{ +jalview.schemes.ResidueProperties.purinepyrimidineIndex = Clazz.newIntArray (255, 0); +for (var i = 0; i < 255; i++) { +jalview.schemes.ResidueProperties.purinepyrimidineIndex[i] = 3; +} +jalview.schemes.ResidueProperties.purinepyrimidineIndex['A'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['a'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['C'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['c'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['G'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['g'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['T'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['t'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['U'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['u'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['I'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['i'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['X'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['x'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['R'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['r'.charCodeAt (0)] = 0; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['Y'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['y'.charCodeAt (0)] = 1; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['N'.charCodeAt (0)] = 2; +jalview.schemes.ResidueProperties.purinepyrimidineIndex['n'.charCodeAt (0)] = 2; +}{ +jalview.schemes.ResidueProperties.aa3Hash.put ("ALA", new Integer (0)); +jalview.schemes.ResidueProperties.aa3Hash.put ("ARG", new Integer (1)); +jalview.schemes.ResidueProperties.aa3Hash.put ("ASN", new Integer (2)); +jalview.schemes.ResidueProperties.aa3Hash.put ("ASP", new Integer (3)); +jalview.schemes.ResidueProperties.aa3Hash.put ("CYS", new Integer (4)); +jalview.schemes.ResidueProperties.aa3Hash.put ("GLN", new Integer (5)); +jalview.schemes.ResidueProperties.aa3Hash.put ("GLU", new Integer (6)); +jalview.schemes.ResidueProperties.aa3Hash.put ("GLY", new Integer (7)); +jalview.schemes.ResidueProperties.aa3Hash.put ("HIS", new Integer (8)); +jalview.schemes.ResidueProperties.aa3Hash.put ("ILE", new Integer (9)); +jalview.schemes.ResidueProperties.aa3Hash.put ("LEU", new Integer (10)); +jalview.schemes.ResidueProperties.aa3Hash.put ("LYS", new Integer (11)); +jalview.schemes.ResidueProperties.aa3Hash.put ("MET", new Integer (12)); +jalview.schemes.ResidueProperties.aa3Hash.put ("PHE", new Integer (13)); +jalview.schemes.ResidueProperties.aa3Hash.put ("PRO", new Integer (14)); +jalview.schemes.ResidueProperties.aa3Hash.put ("SER", new Integer (15)); +jalview.schemes.ResidueProperties.aa3Hash.put ("THR", new Integer (16)); +jalview.schemes.ResidueProperties.aa3Hash.put ("TRP", new Integer (17)); +jalview.schemes.ResidueProperties.aa3Hash.put ("TYR", new Integer (18)); +jalview.schemes.ResidueProperties.aa3Hash.put ("VAL", new Integer (19)); +jalview.schemes.ResidueProperties.aa3Hash.put ("ASX", new Integer (20)); +jalview.schemes.ResidueProperties.aa3Hash.put ("GLX", new Integer (21)); +jalview.schemes.ResidueProperties.aa3Hash.put ("XAA", new Integer (22)); +jalview.schemes.ResidueProperties.aa3Hash.put ("-", new Integer (23)); +jalview.schemes.ResidueProperties.aa3Hash.put ("*", new Integer (23)); +jalview.schemes.ResidueProperties.aa3Hash.put (".", new Integer (23)); +jalview.schemes.ResidueProperties.aa3Hash.put (" ", new Integer (23)); +jalview.schemes.ResidueProperties.aa3Hash.put ("Gap", new Integer (23)); +}{ +jalview.schemes.ResidueProperties.aa2Triplet.put ("A", "ALA"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("a", "ALA"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("R", "ARG"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("r", "ARG"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("N", "ASN"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("n", "ASN"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("D", "ASP"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("d", "ASP"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("C", "CYS"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("c", "CYS"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("Q", "GLN"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("q", "GLN"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("E", "GLU"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("e", "GLU"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("G", "GLY"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("g", "GLY"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("H", "HIS"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("h", "HIS"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("I", "ILE"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("i", "ILE"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("L", "LEU"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("l", "LEU"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("K", "LYS"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("k", "LYS"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("M", "MET"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("m", "MET"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("F", "PHE"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("f", "PHE"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("P", "PRO"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("p", "PRO"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("S", "SER"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("s", "SER"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("T", "THR"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("t", "THR"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("W", "TRP"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("w", "TRP"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("Y", "TYR"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("y", "TYR"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("V", "VAL"); +jalview.schemes.ResidueProperties.aa2Triplet.put ("v", "VAL"); +}Clazz.defineStatics (c$, +"aa", Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "])); +c$.midBlue = c$.prototype.midBlue = new java.awt.Color (100, 100, 255); +c$.scaleColours = c$.prototype.scaleColours = new java.util.Vector (); +{ +jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (114, 0, 147)); +jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (156, 0, 98)); +jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (190, 0, 0)); +jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.red); +jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 125, 0)); +jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.orange); +jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 194, 85)); +jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.yellow); +jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 255, 181)); +jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.white); +}c$.taylor = c$.prototype.taylor = Clazz.newArray (-1, [ new java.awt.Color (204, 255, 0), new java.awt.Color (0, 0, 255), new java.awt.Color (204, 0, 255), new java.awt.Color (255, 0, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 0, 204), new java.awt.Color (255, 0, 102), new java.awt.Color (255, 153, 0), new java.awt.Color (0, 102, 255), new java.awt.Color (102, 255, 0), new java.awt.Color (51, 255, 0), new java.awt.Color (102, 0, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (0, 255, 102), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (0, 204, 255), new java.awt.Color (0, 255, 204), new java.awt.Color (153, 255, 0), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]); +c$.nucleotide = c$.prototype.nucleotide = Clazz.newArray (-1, [ new java.awt.Color (100, 247, 63), new java.awt.Color (255, 179, 64), new java.awt.Color (235, 65, 60), new java.awt.Color (60, 136, 238), new java.awt.Color (60, 136, 238), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]); +c$.purinepyrimidine = c$.prototype.purinepyrimidine = Clazz.newArray (-1, [ new java.awt.Color (255, 131, 250), new java.awt.Color (64, 224, 208), java.awt.Color.white, java.awt.Color.white]); +c$.zappo = c$.prototype.zappo = Clazz.newArray (-1, [java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.green, java.awt.Color.red, java.awt.Color.yellow, java.awt.Color.green, java.awt.Color.red, java.awt.Color.magenta, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.orange, java.awt.Color.magenta, java.awt.Color.green, java.awt.Color.green, java.awt.Color.orange, java.awt.Color.orange, java.awt.Color.pink, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]); +Clazz.defineStatics (c$, +"hyd2", Clazz.newDoubleArray (-1, [0.62, 0.29, -0.9, -0.74, 1.19, 0.48, -0.4, 1.38, -1.5, 1.06, 0.64, -0.78, 0.12, -0.85, -2.53, -0.18, -0.05, 1.08, 0.81, 0.0, 0.26, 0.0, 0.0]), +"helix", Clazz.newDoubleArray (-1, [1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0]), +"helixmin", 0.57, +"helixmax", 1.51, +"strand", Clazz.newDoubleArray (-1, [0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0]), +"strandmin", 0.37, +"strandmax", 1.7, +"turn", Clazz.newDoubleArray (-1, [0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0]), +"turnmin", 0.47, +"turnmax", 1.56, +"buried", Clazz.newDoubleArray (-1, [1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00]), +"buriedmin", 0.05, +"buriedmax", 4.6, +"hyd", Clazz.newDoubleArray (-1, [1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0]), +"hydmax", 4.5, +"hydmin", -3.9, +"BLOSUM62", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4]), Clazz.newIntArray (-1, [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4]), Clazz.newIntArray (-1, [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4]), Clazz.newIntArray (-1, [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4]), Clazz.newIntArray (-1, [0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4]), Clazz.newIntArray (-1, [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4]), Clazz.newIntArray (-1, [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]), Clazz.newIntArray (-1, [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4]), Clazz.newIntArray (-1, [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4]), Clazz.newIntArray (-1, [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4]), Clazz.newIntArray (-1, [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4]), Clazz.newIntArray (-1, [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4]), Clazz.newIntArray (-1, [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4]), Clazz.newIntArray (-1, [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4]), Clazz.newIntArray (-1, [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4]), Clazz.newIntArray (-1, [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4]), Clazz.newIntArray (-1, [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4]), Clazz.newIntArray (-1, [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4]), Clazz.newIntArray (-1, [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4]), Clazz.newIntArray (-1, [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4]), Clazz.newIntArray (-1, [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4]), Clazz.newIntArray (-1, [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]), Clazz.newIntArray (-1, [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4]), Clazz.newIntArray (-1, [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1])]), +"PAM250", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8]), Clazz.newIntArray (-1, [-2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8]), Clazz.newIntArray (-1, [0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8]), Clazz.newIntArray (-1, [0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]), Clazz.newIntArray (-1, [-2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8]), Clazz.newIntArray (-1, [0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8]), Clazz.newIntArray (-1, [0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]), Clazz.newIntArray (-1, [1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8]), Clazz.newIntArray (-1, [-1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8]), Clazz.newIntArray (-1, [-1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8]), Clazz.newIntArray (-1, [-2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8]), Clazz.newIntArray (-1, [-1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8]), Clazz.newIntArray (-1, [-1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8]), Clazz.newIntArray (-1, [-3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8]), Clazz.newIntArray (-1, [1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8]), Clazz.newIntArray (-1, [1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8]), Clazz.newIntArray (-1, [1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8]), Clazz.newIntArray (-1, [-6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8]), Clazz.newIntArray (-1, [-3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8]), Clazz.newIntArray (-1, [0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8]), Clazz.newIntArray (-1, [0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8]), Clazz.newIntArray (-1, [0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8]), Clazz.newIntArray (-1, [0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8]), Clazz.newIntArray (-1, [-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1])])); +c$.ssHash = c$.prototype.ssHash = new java.util.Hashtable (); +{ +jalview.schemes.ResidueProperties.ssHash.put ("H", java.awt.Color.magenta); +jalview.schemes.ResidueProperties.ssHash.put ("E", java.awt.Color.yellow); +jalview.schemes.ResidueProperties.ssHash.put ("-", java.awt.Color.white); +jalview.schemes.ResidueProperties.ssHash.put (".", java.awt.Color.white); +jalview.schemes.ResidueProperties.ssHash.put ("S", java.awt.Color.cyan); +jalview.schemes.ResidueProperties.ssHash.put ("T", java.awt.Color.blue); +jalview.schemes.ResidueProperties.ssHash.put ("G", java.awt.Color.pink); +jalview.schemes.ResidueProperties.ssHash.put ("I", java.awt.Color.pink); +jalview.schemes.ResidueProperties.ssHash.put ("B", java.awt.Color.yellow); +}Clazz.defineStatics (c$, +"DNA", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1]), Clazz.newIntArray (-1, [-8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [-8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1]), Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1]), Clazz.newIntArray (-1, [1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1]), Clazz.newIntArray (-1, [-8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])])); +{ +jalview.schemes.ResidueProperties.scoreMatrices.put ("BLOSUM62", new jalview.schemes.ScoreMatrix ("BLOSUM62", jalview.schemes.ResidueProperties.BLOSUM62, 0)); +jalview.schemes.ResidueProperties.scoreMatrices.put ("PAM250", new jalview.schemes.ScoreMatrix ("PAM250", jalview.schemes.ResidueProperties.PAM250, 0)); +jalview.schemes.ResidueProperties.scoreMatrices.put ("DNA", new jalview.schemes.ScoreMatrix ("DNA", jalview.schemes.ResidueProperties.DNA, 1)); +}c$.pidColours = c$.prototype.pidColours = Clazz.newArray (-1, [jalview.schemes.ResidueProperties.midBlue, new java.awt.Color (153, 153, 255), new java.awt.Color (204, 204, 255)]); +Clazz.defineStatics (c$, +"pidThresholds", Clazz.newFloatArray (-1, [80, 60, 40])); +c$.codonHash = c$.prototype.codonHash = new java.util.HashMap (); +c$.Lys = c$.prototype.Lys = new java.util.ArrayList (); +c$.Asn = c$.prototype.Asn = new java.util.ArrayList (); +c$.Gln = c$.prototype.Gln = new java.util.ArrayList (); +c$.His = c$.prototype.His = new java.util.ArrayList (); +c$.Glu = c$.prototype.Glu = new java.util.ArrayList (); +c$.Asp = c$.prototype.Asp = new java.util.ArrayList (); +c$.Tyr = c$.prototype.Tyr = new java.util.ArrayList (); +c$.Thr = c$.prototype.Thr = new java.util.ArrayList (); +c$.Pro = c$.prototype.Pro = new java.util.ArrayList (); +c$.Ala = c$.prototype.Ala = new java.util.ArrayList (); +c$.Ser = c$.prototype.Ser = new java.util.ArrayList (); +c$.Arg = c$.prototype.Arg = new java.util.ArrayList (); +c$.Gly = c$.prototype.Gly = new java.util.ArrayList (); +c$.Trp = c$.prototype.Trp = new java.util.ArrayList (); +c$.Cys = c$.prototype.Cys = new java.util.ArrayList (); +c$.Ile = c$.prototype.Ile = new java.util.ArrayList (); +c$.Met = c$.prototype.Met = new java.util.ArrayList (); +c$.Leu = c$.prototype.Leu = new java.util.ArrayList (); +c$.Val = c$.prototype.Val = new java.util.ArrayList (); +c$.Phe = c$.prototype.Phe = new java.util.ArrayList (); +c$.STOP = c$.prototype.STOP = new java.util.ArrayList (); +Clazz.defineStatics (c$, +"START", "ATG"); +{ +jalview.schemes.ResidueProperties.codonHash.put ("K", jalview.schemes.ResidueProperties.Lys); +jalview.schemes.ResidueProperties.codonHash.put ("N", jalview.schemes.ResidueProperties.Asn); +jalview.schemes.ResidueProperties.codonHash.put ("Q", jalview.schemes.ResidueProperties.Gln); +jalview.schemes.ResidueProperties.codonHash.put ("H", jalview.schemes.ResidueProperties.His); +jalview.schemes.ResidueProperties.codonHash.put ("E", jalview.schemes.ResidueProperties.Glu); +jalview.schemes.ResidueProperties.codonHash.put ("D", jalview.schemes.ResidueProperties.Asp); +jalview.schemes.ResidueProperties.codonHash.put ("Y", jalview.schemes.ResidueProperties.Tyr); +jalview.schemes.ResidueProperties.codonHash.put ("T", jalview.schemes.ResidueProperties.Thr); +jalview.schemes.ResidueProperties.codonHash.put ("P", jalview.schemes.ResidueProperties.Pro); +jalview.schemes.ResidueProperties.codonHash.put ("A", jalview.schemes.ResidueProperties.Ala); +jalview.schemes.ResidueProperties.codonHash.put ("S", jalview.schemes.ResidueProperties.Ser); +jalview.schemes.ResidueProperties.codonHash.put ("R", jalview.schemes.ResidueProperties.Arg); +jalview.schemes.ResidueProperties.codonHash.put ("G", jalview.schemes.ResidueProperties.Gly); +jalview.schemes.ResidueProperties.codonHash.put ("W", jalview.schemes.ResidueProperties.Trp); +jalview.schemes.ResidueProperties.codonHash.put ("C", jalview.schemes.ResidueProperties.Cys); +jalview.schemes.ResidueProperties.codonHash.put ("I", jalview.schemes.ResidueProperties.Ile); +jalview.schemes.ResidueProperties.codonHash.put ("M", jalview.schemes.ResidueProperties.Met); +jalview.schemes.ResidueProperties.codonHash.put ("L", jalview.schemes.ResidueProperties.Leu); +jalview.schemes.ResidueProperties.codonHash.put ("V", jalview.schemes.ResidueProperties.Val); +jalview.schemes.ResidueProperties.codonHash.put ("F", jalview.schemes.ResidueProperties.Phe); +jalview.schemes.ResidueProperties.codonHash.put ("STOP", jalview.schemes.ResidueProperties.STOP); +}c$.ambiguityCodes = c$.prototype.ambiguityCodes = new java.util.Hashtable (); +c$.codonHash2 = c$.prototype.codonHash2 = new java.util.Hashtable (); +c$._ambiguityCodes = c$.prototype._ambiguityCodes = new java.util.Hashtable (); +{ +jalview.schemes.ResidueProperties.ambiguityCodes.put ("R", Clazz.newArray (-1, ["A", "G"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("Y", Clazz.newArray (-1, ["T", "C"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("W", Clazz.newArray (-1, ["A", "T"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("S", Clazz.newArray (-1, ["G", "C"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("M", Clazz.newArray (-1, ["A", "C"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("K", Clazz.newArray (-1, ["G", "T"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("H", Clazz.newArray (-1, ["A", "T", "C"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("B", Clazz.newArray (-1, ["G", "T", "C"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("V", Clazz.newArray (-1, ["G", "A", "C"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("D", Clazz.newArray (-1, ["G", "A", "T"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put ("N", Clazz.newArray (-1, ["G", "A", "T", "C"])); +jalview.schemes.ResidueProperties.codonHash2.put ("AAA", "K"); +jalview.schemes.ResidueProperties.codonHash2.put ("AAG", "K"); +jalview.schemes.ResidueProperties.codonHash2.put ("AAC", "N"); +jalview.schemes.ResidueProperties.codonHash2.put ("AAT", "N"); +jalview.schemes.ResidueProperties.codonHash2.put ("CAA", "Q"); +jalview.schemes.ResidueProperties.codonHash2.put ("CAG", "Q"); +jalview.schemes.ResidueProperties.codonHash2.put ("CAC", "H"); +jalview.schemes.ResidueProperties.codonHash2.put ("CAT", "H"); +jalview.schemes.ResidueProperties.codonHash2.put ("GAA", "E"); +jalview.schemes.ResidueProperties.codonHash2.put ("GAG", "E"); +jalview.schemes.ResidueProperties.codonHash2.put ("GAC", "D"); +jalview.schemes.ResidueProperties.codonHash2.put ("GAT", "D"); +jalview.schemes.ResidueProperties.codonHash2.put ("TAC", "Y"); +jalview.schemes.ResidueProperties.codonHash2.put ("TAT", "Y"); +jalview.schemes.ResidueProperties.codonHash2.put ("ACA", "T"); +jalview.schemes.ResidueProperties.codonHash2.put ("ACC", "T"); +jalview.schemes.ResidueProperties.codonHash2.put ("ACT", "T"); +jalview.schemes.ResidueProperties.codonHash2.put ("ACG", "T"); +jalview.schemes.ResidueProperties.codonHash2.put ("CCA", "P"); +jalview.schemes.ResidueProperties.codonHash2.put ("CCG", "P"); +jalview.schemes.ResidueProperties.codonHash2.put ("CCC", "P"); +jalview.schemes.ResidueProperties.codonHash2.put ("CCT", "P"); +jalview.schemes.ResidueProperties.codonHash2.put ("GCA", "A"); +jalview.schemes.ResidueProperties.codonHash2.put ("GCG", "A"); +jalview.schemes.ResidueProperties.codonHash2.put ("GCC", "A"); +jalview.schemes.ResidueProperties.codonHash2.put ("GCT", "A"); +jalview.schemes.ResidueProperties.codonHash2.put ("TCA", "S"); +jalview.schemes.ResidueProperties.codonHash2.put ("TCG", "S"); +jalview.schemes.ResidueProperties.codonHash2.put ("TCC", "S"); +jalview.schemes.ResidueProperties.codonHash2.put ("TCT", "S"); +jalview.schemes.ResidueProperties.codonHash2.put ("AGC", "S"); +jalview.schemes.ResidueProperties.codonHash2.put ("AGT", "S"); +jalview.schemes.ResidueProperties.codonHash2.put ("AGA", "R"); +jalview.schemes.ResidueProperties.codonHash2.put ("AGG", "R"); +jalview.schemes.ResidueProperties.codonHash2.put ("CGA", "R"); +jalview.schemes.ResidueProperties.codonHash2.put ("CGG", "R"); +jalview.schemes.ResidueProperties.codonHash2.put ("CGC", "R"); +jalview.schemes.ResidueProperties.codonHash2.put ("CGT", "R"); +jalview.schemes.ResidueProperties.codonHash2.put ("GGA", "G"); +jalview.schemes.ResidueProperties.codonHash2.put ("GGG", "G"); +jalview.schemes.ResidueProperties.codonHash2.put ("GGC", "G"); +jalview.schemes.ResidueProperties.codonHash2.put ("GGT", "G"); +jalview.schemes.ResidueProperties.codonHash2.put ("TGA", "*"); +jalview.schemes.ResidueProperties.codonHash2.put ("TAA", "*"); +jalview.schemes.ResidueProperties.codonHash2.put ("TAG", "*"); +jalview.schemes.ResidueProperties.codonHash2.put ("TGG", "W"); +jalview.schemes.ResidueProperties.codonHash2.put ("TGC", "C"); +jalview.schemes.ResidueProperties.codonHash2.put ("TGT", "C"); +jalview.schemes.ResidueProperties.codonHash2.put ("ATA", "I"); +jalview.schemes.ResidueProperties.codonHash2.put ("ATC", "I"); +jalview.schemes.ResidueProperties.codonHash2.put ("ATT", "I"); +jalview.schemes.ResidueProperties.codonHash2.put ("ATG", "M"); +jalview.schemes.ResidueProperties.codonHash2.put ("CTA", "L"); +jalview.schemes.ResidueProperties.codonHash2.put ("CTG", "L"); +jalview.schemes.ResidueProperties.codonHash2.put ("CTC", "L"); +jalview.schemes.ResidueProperties.codonHash2.put ("CTT", "L"); +jalview.schemes.ResidueProperties.codonHash2.put ("TTA", "L"); +jalview.schemes.ResidueProperties.codonHash2.put ("TTG", "L"); +jalview.schemes.ResidueProperties.codonHash2.put ("GTA", "V"); +jalview.schemes.ResidueProperties.codonHash2.put ("GTG", "V"); +jalview.schemes.ResidueProperties.codonHash2.put ("GTC", "V"); +jalview.schemes.ResidueProperties.codonHash2.put ("GTT", "V"); +jalview.schemes.ResidueProperties.codonHash2.put ("TTC", "F"); +jalview.schemes.ResidueProperties.codonHash2.put ("TTT", "F"); +jalview.schemes.ResidueProperties.buildAmbiguityCodonSet (); +}{ +jalview.schemes.ResidueProperties.Lys.add ("AAA"); +jalview.schemes.ResidueProperties.Lys.add ("AAG"); +jalview.schemes.ResidueProperties.Asn.add ("AAC"); +jalview.schemes.ResidueProperties.Asn.add ("AAT"); +jalview.schemes.ResidueProperties.Gln.add ("CAA"); +jalview.schemes.ResidueProperties.Gln.add ("CAG"); +jalview.schemes.ResidueProperties.His.add ("CAC"); +jalview.schemes.ResidueProperties.His.add ("CAT"); +jalview.schemes.ResidueProperties.Glu.add ("GAA"); +jalview.schemes.ResidueProperties.Glu.add ("GAG"); +jalview.schemes.ResidueProperties.Asp.add ("GAC"); +jalview.schemes.ResidueProperties.Asp.add ("GAT"); +jalview.schemes.ResidueProperties.Tyr.add ("TAC"); +jalview.schemes.ResidueProperties.Tyr.add ("TAT"); +jalview.schemes.ResidueProperties.Thr.add ("ACA"); +jalview.schemes.ResidueProperties.Thr.add ("ACG"); +jalview.schemes.ResidueProperties.Thr.add ("ACC"); +jalview.schemes.ResidueProperties.Thr.add ("ACT"); +jalview.schemes.ResidueProperties.Pro.add ("CCA"); +jalview.schemes.ResidueProperties.Pro.add ("CCG"); +jalview.schemes.ResidueProperties.Pro.add ("CCC"); +jalview.schemes.ResidueProperties.Pro.add ("CCT"); +jalview.schemes.ResidueProperties.Ala.add ("GCA"); +jalview.schemes.ResidueProperties.Ala.add ("GCG"); +jalview.schemes.ResidueProperties.Ala.add ("GCC"); +jalview.schemes.ResidueProperties.Ala.add ("GCT"); +jalview.schemes.ResidueProperties.Ser.add ("TCA"); +jalview.schemes.ResidueProperties.Ser.add ("TCG"); +jalview.schemes.ResidueProperties.Ser.add ("TCC"); +jalview.schemes.ResidueProperties.Ser.add ("TCT"); +jalview.schemes.ResidueProperties.Ser.add ("AGC"); +jalview.schemes.ResidueProperties.Ser.add ("AGT"); +jalview.schemes.ResidueProperties.Arg.add ("AGA"); +jalview.schemes.ResidueProperties.Arg.add ("AGG"); +jalview.schemes.ResidueProperties.Arg.add ("CGA"); +jalview.schemes.ResidueProperties.Arg.add ("CGG"); +jalview.schemes.ResidueProperties.Arg.add ("CGC"); +jalview.schemes.ResidueProperties.Arg.add ("CGT"); +jalview.schemes.ResidueProperties.Gly.add ("GGA"); +jalview.schemes.ResidueProperties.Gly.add ("GGG"); +jalview.schemes.ResidueProperties.Gly.add ("GGC"); +jalview.schemes.ResidueProperties.Gly.add ("GGT"); +jalview.schemes.ResidueProperties.STOP.add ("TGA"); +jalview.schemes.ResidueProperties.STOP.add ("TAA"); +jalview.schemes.ResidueProperties.STOP.add ("TAG"); +jalview.schemes.ResidueProperties.Trp.add ("TGG"); +jalview.schemes.ResidueProperties.Cys.add ("TGC"); +jalview.schemes.ResidueProperties.Cys.add ("TGT"); +jalview.schemes.ResidueProperties.Ile.add ("ATA"); +jalview.schemes.ResidueProperties.Ile.add ("ATC"); +jalview.schemes.ResidueProperties.Ile.add ("ATT"); +jalview.schemes.ResidueProperties.Met.add ("ATG"); +jalview.schemes.ResidueProperties.Leu.add ("CTA"); +jalview.schemes.ResidueProperties.Leu.add ("CTG"); +jalview.schemes.ResidueProperties.Leu.add ("CTC"); +jalview.schemes.ResidueProperties.Leu.add ("CTT"); +jalview.schemes.ResidueProperties.Leu.add ("TTA"); +jalview.schemes.ResidueProperties.Leu.add ("TTG"); +jalview.schemes.ResidueProperties.Val.add ("GTA"); +jalview.schemes.ResidueProperties.Val.add ("GTG"); +jalview.schemes.ResidueProperties.Val.add ("GTC"); +jalview.schemes.ResidueProperties.Val.add ("GTT"); +jalview.schemes.ResidueProperties.Phe.add ("TTC"); +jalview.schemes.ResidueProperties.Phe.add ("TTT"); +}c$.propHash = c$.prototype.propHash = new java.util.Hashtable (); +c$.hydrophobic = c$.prototype.hydrophobic = new java.util.Hashtable (); +c$.polar = c$.prototype.polar = new java.util.Hashtable (); +c$.small = c$.prototype.small = new java.util.Hashtable (); +c$.positive = c$.prototype.positive = new java.util.Hashtable (); +c$.negative = c$.prototype.negative = new java.util.Hashtable (); +c$.charged = c$.prototype.charged = new java.util.Hashtable (); +c$.aromatic = c$.prototype.aromatic = new java.util.Hashtable (); +c$.aliphatic = c$.prototype.aliphatic = new java.util.Hashtable (); +c$.tiny = c$.prototype.tiny = new java.util.Hashtable (); +c$.proline = c$.prototype.proline = new java.util.Hashtable (); +{ +jalview.schemes.ResidueProperties.hydrophobic.put ("I", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("L", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("V", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("C", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("A", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("G", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("M", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("F", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("Y", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("W", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("H", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("K", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("X", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("*", new Integer (1)); +jalview.schemes.ResidueProperties.hydrophobic.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("D", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.hydrophobic.put ("P", new Integer (0)); +}{ +jalview.schemes.ResidueProperties.polar.put ("Y", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("W", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("H", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("K", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("R", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("E", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("Q", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("D", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("N", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("S", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("T", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("X", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("*", new Integer (1)); +jalview.schemes.ResidueProperties.polar.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.polar.put ("P", new Integer (0)); +}{ +jalview.schemes.ResidueProperties.small.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("V", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("C", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("A", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("G", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("H", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("K", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.small.put ("D", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("N", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("S", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("T", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("P", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.small.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.positive.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("H", new Integer (1)); +jalview.schemes.ResidueProperties.positive.put ("K", new Integer (1)); +jalview.schemes.ResidueProperties.positive.put ("R", new Integer (1)); +jalview.schemes.ResidueProperties.positive.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("D", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("P", new Integer (0)); +jalview.schemes.ResidueProperties.positive.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.positive.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.negative.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("H", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("K", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("E", new Integer (1)); +jalview.schemes.ResidueProperties.negative.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("D", new Integer (1)); +jalview.schemes.ResidueProperties.negative.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("P", new Integer (0)); +jalview.schemes.ResidueProperties.negative.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.negative.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.charged.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("H", new Integer (1)); +jalview.schemes.ResidueProperties.charged.put ("K", new Integer (1)); +jalview.schemes.ResidueProperties.charged.put ("R", new Integer (1)); +jalview.schemes.ResidueProperties.charged.put ("E", new Integer (1)); +jalview.schemes.ResidueProperties.charged.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("D", new Integer (1)); +jalview.schemes.ResidueProperties.charged.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("P", new Integer (0)); +jalview.schemes.ResidueProperties.charged.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.charged.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.aromatic.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("F", new Integer (1)); +jalview.schemes.ResidueProperties.aromatic.put ("Y", new Integer (1)); +jalview.schemes.ResidueProperties.aromatic.put ("W", new Integer (1)); +jalview.schemes.ResidueProperties.aromatic.put ("H", new Integer (1)); +jalview.schemes.ResidueProperties.aromatic.put ("K", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("D", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("P", new Integer (0)); +jalview.schemes.ResidueProperties.aromatic.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.aromatic.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.aliphatic.put ("I", new Integer (1)); +jalview.schemes.ResidueProperties.aliphatic.put ("L", new Integer (1)); +jalview.schemes.ResidueProperties.aliphatic.put ("V", new Integer (1)); +jalview.schemes.ResidueProperties.aliphatic.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("H", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("K", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("D", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("P", new Integer (0)); +jalview.schemes.ResidueProperties.aliphatic.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.aliphatic.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.tiny.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("A", new Integer (1)); +jalview.schemes.ResidueProperties.tiny.put ("G", new Integer (1)); +jalview.schemes.ResidueProperties.tiny.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("H", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("K", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("D", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("S", new Integer (1)); +jalview.schemes.ResidueProperties.tiny.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("P", new Integer (0)); +jalview.schemes.ResidueProperties.tiny.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.tiny.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.proline.put ("I", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("L", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("V", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("C", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("A", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("G", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("M", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("F", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("Y", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("W", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("H", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("K", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("R", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("E", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("Q", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("D", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("N", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("S", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("T", new Integer (0)); +jalview.schemes.ResidueProperties.proline.put ("P", new Integer (1)); +jalview.schemes.ResidueProperties.proline.put ("-", new Integer (1)); +jalview.schemes.ResidueProperties.proline.put ("*", new Integer (1)); +}{ +jalview.schemes.ResidueProperties.propHash.put ("hydrophobic", jalview.schemes.ResidueProperties.hydrophobic); +jalview.schemes.ResidueProperties.propHash.put ("small", jalview.schemes.ResidueProperties.small); +jalview.schemes.ResidueProperties.propHash.put ("positive", jalview.schemes.ResidueProperties.positive); +jalview.schemes.ResidueProperties.propHash.put ("negative", jalview.schemes.ResidueProperties.negative); +jalview.schemes.ResidueProperties.propHash.put ("charged", jalview.schemes.ResidueProperties.charged); +jalview.schemes.ResidueProperties.propHash.put ("aromatic", jalview.schemes.ResidueProperties.aromatic); +jalview.schemes.ResidueProperties.propHash.put ("aliphatic", jalview.schemes.ResidueProperties.aliphatic); +jalview.schemes.ResidueProperties.propHash.put ("tiny", jalview.schemes.ResidueProperties.tiny); +jalview.schemes.ResidueProperties.propHash.put ("proline", jalview.schemes.ResidueProperties.proline); +jalview.schemes.ResidueProperties.propHash.put ("polar", jalview.schemes.ResidueProperties.polar); +}{ +var propMatrixF = Clazz.newIntArray (23, 23, 0); +var propMatrixPos = Clazz.newIntArray (23, 23, 0); +var propMatrixEpos = Clazz.newIntArray (23, 23, 0); +for (var i = 0; i < 23; i++) { +var maxF = 0; +var maxP = 0; +var maxEP = 0; +var ic = ""; +if (jalview.schemes.ResidueProperties.aa.length > i) { +ic += jalview.schemes.ResidueProperties.aa[i]; +} else { +ic = "-"; +}for (var j = i + 1; j < 23; j++) { +var jc = ""; +if (jalview.schemes.ResidueProperties.aa.length > j) { +jc += jalview.schemes.ResidueProperties.aa[j]; +} else { +jc = "-"; +}propMatrixF[i][j] = 0; +propMatrixPos[i][j] = 0; +propMatrixEpos[i][j] = 0; +for (var en = jalview.schemes.ResidueProperties.propHash.keys (); en.hasMoreElements (); ) { +var ph = en.nextElement (); +var pph = jalview.schemes.ResidueProperties.propHash.get (ph); +if (pph.get (ic) != null && pph.get (jc) != null) { +var icp = pph.get (ic).intValue (); +var jcp = pph.get (jc).intValue (); +propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0; +propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0; +propMatrixF[i][j] += icp == jcp ? 2 : 0; +propMatrixF[j][i] += icp == jcp ? 2 : 0; +propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0; +propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0; +}} +if (maxF < propMatrixF[i][j]) { +maxF = propMatrixF[i][j]; +}if (maxP < propMatrixPos[i][j]) { +maxP = propMatrixPos[i][j]; +}if (maxEP < propMatrixEpos[i][j]) { +maxEP = propMatrixEpos[i][j]; +}} +propMatrixF[i][i] = maxF; +propMatrixPos[i][i] = maxP; +propMatrixEpos[i][i] = maxEP; +} +jalview.schemes.ResidueProperties.scoreMatrices.put ("PID", new jalview.analysis.scoremodels.PIDScoreModel ()); +jalview.schemes.ResidueProperties.scoreMatrices.put ("Displayed Features", new jalview.analysis.scoremodels.FeatureScoreModel ()); +}Clazz.defineStatics (c$, +"toDssp3State", null); +{ +jalview.schemes.ResidueProperties.toDssp3State = new java.util.Hashtable (); +jalview.schemes.ResidueProperties.toDssp3State.put ("H", "H"); +jalview.schemes.ResidueProperties.toDssp3State.put ("E", "E"); +jalview.schemes.ResidueProperties.toDssp3State.put ("C", " "); +jalview.schemes.ResidueProperties.toDssp3State.put (" ", " "); +jalview.schemes.ResidueProperties.toDssp3State.put ("T", " "); +jalview.schemes.ResidueProperties.toDssp3State.put ("B", "E"); +jalview.schemes.ResidueProperties.toDssp3State.put ("G", "H"); +jalview.schemes.ResidueProperties.toDssp3State.put ("I", "H"); +jalview.schemes.ResidueProperties.toDssp3State.put ("X", " "); +}Clazz.defineStatics (c$, +"toRNAssState", null, +"RNAcloseParen", Clazz.newBooleanArray (255, false)); +{ +jalview.schemes.ResidueProperties.toRNAssState = new java.util.Hashtable (); +jalview.schemes.ResidueProperties.toRNAssState.put (")", "("); +jalview.schemes.ResidueProperties.toRNAssState.put ("(", "("); +jalview.schemes.ResidueProperties.toRNAssState.put ("]", "["); +jalview.schemes.ResidueProperties.toRNAssState.put ("[", "["); +jalview.schemes.ResidueProperties.toRNAssState.put ("{", "{"); +jalview.schemes.ResidueProperties.toRNAssState.put ("}", "{"); +jalview.schemes.ResidueProperties.toRNAssState.put (">", ">"); +jalview.schemes.ResidueProperties.toRNAssState.put ("<", ">"); +jalview.schemes.ResidueProperties.toRNAssState.put ("A", "A"); +jalview.schemes.ResidueProperties.toRNAssState.put ("a", "A"); +jalview.schemes.ResidueProperties.toRNAssState.put ("B", "B"); +jalview.schemes.ResidueProperties.toRNAssState.put ("b", "B"); +jalview.schemes.ResidueProperties.toRNAssState.put ("C", "C"); +jalview.schemes.ResidueProperties.toRNAssState.put ("c", "C"); +jalview.schemes.ResidueProperties.toRNAssState.put ("D", "D"); +jalview.schemes.ResidueProperties.toRNAssState.put ("d", "D"); +jalview.schemes.ResidueProperties.toRNAssState.put ("E", "E"); +jalview.schemes.ResidueProperties.toRNAssState.put ("e", "E"); +jalview.schemes.ResidueProperties.toRNAssState.put ("F", "F"); +jalview.schemes.ResidueProperties.toRNAssState.put ("f", "F"); +jalview.schemes.ResidueProperties.toRNAssState.put ("G", "G"); +jalview.schemes.ResidueProperties.toRNAssState.put ("g", "G"); +jalview.schemes.ResidueProperties.toRNAssState.put ("H", "H"); +jalview.schemes.ResidueProperties.toRNAssState.put ("h", "H"); +jalview.schemes.ResidueProperties.toRNAssState.put ("I", "I"); +jalview.schemes.ResidueProperties.toRNAssState.put ("i", "I"); +jalview.schemes.ResidueProperties.toRNAssState.put ("J", "J"); +jalview.schemes.ResidueProperties.toRNAssState.put ("j", "J"); +jalview.schemes.ResidueProperties.toRNAssState.put ("K", "K"); +jalview.schemes.ResidueProperties.toRNAssState.put ("k", "K"); +jalview.schemes.ResidueProperties.toRNAssState.put ("L", "L"); +jalview.schemes.ResidueProperties.toRNAssState.put ("l", "L"); +jalview.schemes.ResidueProperties.toRNAssState.put ("M", "M"); +jalview.schemes.ResidueProperties.toRNAssState.put ("m", "M"); +jalview.schemes.ResidueProperties.toRNAssState.put ("N", "N"); +jalview.schemes.ResidueProperties.toRNAssState.put ("n", "N"); +jalview.schemes.ResidueProperties.toRNAssState.put ("O", "O"); +jalview.schemes.ResidueProperties.toRNAssState.put ("o", "O"); +jalview.schemes.ResidueProperties.toRNAssState.put ("P", "P"); +jalview.schemes.ResidueProperties.toRNAssState.put ("p", "P"); +jalview.schemes.ResidueProperties.toRNAssState.put ("Q", "Q"); +jalview.schemes.ResidueProperties.toRNAssState.put ("q", "Q"); +jalview.schemes.ResidueProperties.toRNAssState.put ("R", "R"); +jalview.schemes.ResidueProperties.toRNAssState.put ("r", "R"); +jalview.schemes.ResidueProperties.toRNAssState.put ("S", "S"); +jalview.schemes.ResidueProperties.toRNAssState.put ("s", "S"); +jalview.schemes.ResidueProperties.toRNAssState.put ("T", "T"); +jalview.schemes.ResidueProperties.toRNAssState.put ("t", "T"); +jalview.schemes.ResidueProperties.toRNAssState.put ("U", "U"); +jalview.schemes.ResidueProperties.toRNAssState.put ("u", "U"); +jalview.schemes.ResidueProperties.toRNAssState.put ("V", "V"); +jalview.schemes.ResidueProperties.toRNAssState.put ("v", "V"); +jalview.schemes.ResidueProperties.toRNAssState.put ("W", "W"); +jalview.schemes.ResidueProperties.toRNAssState.put ("w", "W"); +jalview.schemes.ResidueProperties.toRNAssState.put ("X", "X"); +jalview.schemes.ResidueProperties.toRNAssState.put ("x", "X"); +jalview.schemes.ResidueProperties.toRNAssState.put ("Y", "Y"); +jalview.schemes.ResidueProperties.toRNAssState.put ("y", "Y"); +jalview.schemes.ResidueProperties.toRNAssState.put ("Z", "Z"); +jalview.schemes.ResidueProperties.toRNAssState.put ("z", "Z"); +for (var p = 0; p < jalview.schemes.ResidueProperties.RNAcloseParen.length; p++) { +jalview.schemes.ResidueProperties.RNAcloseParen[p] = false; +} +for (var k, $k = jalview.schemes.ResidueProperties.toRNAssState.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) { +jalview.schemes.ResidueProperties.RNAcloseParen[k.charCodeAt (0)] = k.charAt (0) != jalview.schemes.ResidueProperties.toRNAssState.get (k).charAt (0); +} +}}); diff --git a/bin/jalview/schemes/ScoreColourScheme.js b/bin/jalview/schemes/ScoreColourScheme.js index 5027bdf..f097a40 100644 --- a/bin/jalview/schemes/ScoreColourScheme.js +++ b/bin/jalview/schemes/ScoreColourScheme.js @@ -1,43 +1,43 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.ScoreColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { -c$ = Clazz.decorateAsClass (function () { -this.min = 0; -this.max = 0; -this.scores = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "ScoreColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function (symbolIndex, scores, min, max) { -Clazz.superConstructor (this, jalview.schemes.ScoreColourScheme, [symbolIndex]); -this.scores = scores; -this.min = min; -this.max = max; -var i; -var iSize = scores.length; -this.colors = new Array (scores.length); -for (i = 0; i < iSize; i++) { -var red = (scores[i] - min) / (max - min); -if (red > 1.0) { -red = 1.0; -}if (red < 0.0) { -red = 0.0; -}this.colors[i] = this.makeColour (red); -} -}, "~A,~A,~N,~N"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -if (this.threshold > 0) { -if (!this.aboveThreshold (c, j)) { -return java.awt.Color.white; -}}if (jalview.util.Comparison.isGap (c)) { -return java.awt.Color.white; -}var currentColour = this.colors[jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]]; -if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "makeColour", -function (c) { -return new java.awt.Color (c, 0.0, 1.0 - c); -}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.ScoreColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { +c$ = Clazz.decorateAsClass (function () { +this.min = 0; +this.max = 0; +this.scores = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "ScoreColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function (symbolIndex, scores, min, max) { +Clazz.superConstructor (this, jalview.schemes.ScoreColourScheme, [symbolIndex]); +this.scores = scores; +this.min = min; +this.max = max; +var i; +var iSize = scores.length; +this.colors = new Array (scores.length); +for (i = 0; i < iSize; i++) { +var red = (scores[i] - min) / (max - min); +if (red > 1.0) { +red = 1.0; +}if (red < 0.0) { +red = 0.0; +}this.colors[i] = this.makeColour (red); +} +}, "~A,~A,~N,~N"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +if (this.threshold > 0) { +if (!this.aboveThreshold (c, j)) { +return java.awt.Color.white; +}}if (jalview.util.Comparison.isGap (c)) { +return java.awt.Color.white; +}var currentColour = this.colors[jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]]; +if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "makeColour", +function (c) { +return new java.awt.Color (c, 0.0, 1.0 - c); +}, "~N"); +}); diff --git a/bin/jalview/schemes/ScoreMatrix.js b/bin/jalview/schemes/ScoreMatrix.js index a12c842..401ab41 100644 --- a/bin/jalview/schemes/ScoreMatrix.js +++ b/bin/jalview/schemes/ScoreMatrix.js @@ -1,86 +1,86 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.analysis.scoremodels.PairwiseSeqScoreModel", "jalview.api.analysis.ScoreModelI"], "jalview.schemes.ScoreMatrix", ["jalview.schemes.ResidueProperties", "java.lang.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.name = null; -this.matrix = null; -this.type = 0; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "ScoreMatrix", jalview.analysis.scoremodels.PairwiseSeqScoreModel, jalview.api.analysis.ScoreModelI); -Clazz.overrideMethod (c$, "getName", -function () { -return this.name; -}); -Clazz.makeConstructor (c$, -function (name, matrix, type) { -Clazz.superConstructor (this, jalview.schemes.ScoreMatrix, []); -this.matrix = matrix; -this.type = type; -this.name = name; -}, "~S,~A,~N"); -Clazz.overrideMethod (c$, "isDNA", -function () { -return this.type == 1; -}); -Clazz.overrideMethod (c$, "isProtein", -function () { -return this.type == 0; -}); -Clazz.overrideMethod (c$, "getMatrix", -function () { -return this.matrix; -}); -Clazz.defineMethod (c$, "getPairwiseScore", -function (A1, A2) { -return this.getPairwiseScore (A1.charAt (0), A2.charAt (0)); -}, "~S,~S"); -Clazz.defineMethod (c$, "getPairwiseScore", -function (c, d) { -var pog = 0; -try { -var a = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]; -var b = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[d.charCodeAt (0)]; -pog = this.matrix[a][b]; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -return pog; -}, "~S,~S"); -Clazz.overrideMethod (c$, "toString", -function () { -return this.outputMatrix (false); -}); -Clazz.defineMethod (c$, "outputMatrix", -function (html) { -var sb = new StringBuffer (); -var symbols = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex : jalview.schemes.ResidueProperties.nucleotideIndex; -var symMax = (this.type == 0) ? 23 : 10; -var header = true; -if (html) { -sb.append (""); -}for (var sym = 'A'; sym <= 'Z'; sym = String.fromCharCode (sym.charCodeAt (0) + 1)) { -if (symbols[sym.charCodeAt (0)] >= 0 && symbols[sym.charCodeAt (0)] < symMax) { -if (header) { -sb.append (html ? "" : ""); -for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) { -if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) { -sb.append ((html ? "" : "")); -}} -header = false; -sb.append (html ? "\n" : "\n"); -}if (html) { -sb.append (""); -}sb.append ((html ? "" : "")); -for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) { -if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) { -sb.append ((html ? "" : "")); -}} -sb.append (html ? "\n" : "\n"); -}} -if (html) { -sb.append ("
 " : "\t") + sym2 + (html ? " 
" : "") + sym + (html ? "" : "\t") + this.matrix[symbols[sym.charCodeAt (0)]][symbols[sym2.charCodeAt (0)]] + (html ? "
"); -}return sb.toString (); -}, "~B"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.analysis.scoremodels.PairwiseSeqScoreModel", "jalview.api.analysis.ScoreModelI"], "jalview.schemes.ScoreMatrix", ["jalview.schemes.ResidueProperties", "java.lang.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.name = null; +this.matrix = null; +this.type = 0; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "ScoreMatrix", jalview.analysis.scoremodels.PairwiseSeqScoreModel, jalview.api.analysis.ScoreModelI); +Clazz.overrideMethod (c$, "getName", +function () { +return this.name; +}); +Clazz.makeConstructor (c$, +function (name, matrix, type) { +Clazz.superConstructor (this, jalview.schemes.ScoreMatrix, []); +this.matrix = matrix; +this.type = type; +this.name = name; +}, "~S,~A,~N"); +Clazz.overrideMethod (c$, "isDNA", +function () { +return this.type == 1; +}); +Clazz.overrideMethod (c$, "isProtein", +function () { +return this.type == 0; +}); +Clazz.overrideMethod (c$, "getMatrix", +function () { +return this.matrix; +}); +Clazz.defineMethod (c$, "getPairwiseScore", +function (A1, A2) { +return this.getPairwiseScore (A1.charAt (0), A2.charAt (0)); +}, "~S,~S"); +Clazz.defineMethod (c$, "getPairwiseScore", +function (c, d) { +var pog = 0; +try { +var a = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]; +var b = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[d.charCodeAt (0)]; +pog = this.matrix[a][b]; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +return pog; +}, "~S,~S"); +Clazz.overrideMethod (c$, "toString", +function () { +return this.outputMatrix (false); +}); +Clazz.defineMethod (c$, "outputMatrix", +function (html) { +var sb = new StringBuffer (); +var symbols = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex : jalview.schemes.ResidueProperties.nucleotideIndex; +var symMax = (this.type == 0) ? 23 : 10; +var header = true; +if (html) { +sb.append (""); +}for (var sym = 'A'; sym <= 'Z'; sym = String.fromCharCode (sym.charCodeAt (0) + 1)) { +if (symbols[sym.charCodeAt (0)] >= 0 && symbols[sym.charCodeAt (0)] < symMax) { +if (header) { +sb.append (html ? "" : ""); +for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) { +if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) { +sb.append ((html ? "" : "")); +}} +header = false; +sb.append (html ? "\n" : "\n"); +}if (html) { +sb.append (""); +}sb.append ((html ? "" : "")); +for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) { +if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) { +sb.append ((html ? "" : "")); +}} +sb.append (html ? "\n" : "\n"); +}} +if (html) { +sb.append ("
 " : "\t") + sym2 + (html ? " 
" : "") + sym + (html ? "" : "\t") + this.matrix[symbols[sym.charCodeAt (0)]][symbols[sym2.charCodeAt (0)]] + (html ? "
"); +}return sb.toString (); +}, "~B"); +}); diff --git a/bin/jalview/schemes/StrandColourScheme.js b/bin/jalview/schemes/StrandColourScheme.js index cf2f6bf..7ccf062 100644 --- a/bin/jalview/schemes/StrandColourScheme.js +++ b/bin/jalview/schemes/StrandColourScheme.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.StrandColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "StrandColourScheme", jalview.schemes.ScoreColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.StrandColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.strand, 0.37, 1.7]); -}); -Clazz.overrideMethod (c$, "makeColour", -function (c) { -return new java.awt.Color (c, c, 1.0 - c); -}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.StrandColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "StrandColourScheme", jalview.schemes.ScoreColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.StrandColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.strand, 0.37, 1.7]); +}); +Clazz.overrideMethod (c$, "makeColour", +function (c) { +return new java.awt.Color (c, c, 1.0 - c); +}, "~N"); +}); diff --git a/bin/jalview/schemes/TCoffeeColourScheme.js b/bin/jalview/schemes/TCoffeeColourScheme.js index 0952425..6350ad9 100644 --- a/bin/jalview/schemes/TCoffeeColourScheme.js +++ b/bin/jalview/schemes/TCoffeeColourScheme.js @@ -1,45 +1,45 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme", "java.awt.Color"], "jalview.schemes.TCoffeeColourScheme", ["jalview.datamodel.AlignmentI", "java.util.ArrayList", "$.IdentityHashMap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.seqMap = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "TCoffeeColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function (alignment) { -Clazz.superConstructor (this, jalview.schemes.TCoffeeColourScheme, []); -this.alignmentChanged (alignment, null); -}, "jalview.datamodel.AnnotatedCollectionI"); -Clazz.overrideMethod (c$, "alignmentChanged", -function (alignment, hiddenReps) { -var annots = new java.util.ArrayList (); -this.seqMap = new java.util.IdentityHashMap (); -var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext (); -var w = 0; -for (var al, $al = alcontext.findAnnotation ("TCoffeeScore").iterator (); $al.hasNext () && ((al = $al.next ()) || true);) { -if (al.sequenceRef != null && !al.belowAlignment) { -annots.add (al); -if (w < al.annotations.length) { -w = al.annotations.length; -}var scores = new Array (al.annotations.length); -var i = 0; -for (var an, $an = 0, $$an = al.annotations; $an < $$an.length && ((an = $$an[$an]) || true); $an++) { -scores[i++] = (an != null) ? an.colour : java.awt.Color.white; -} -this.seqMap.put (al.sequenceRef, scores); -}} -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var cols; -if (this.seqMap == null || (cols = this.seqMap.get (seq)) == null) { -return java.awt.Color.white; -}if (j < 0 || j >= cols.length) { -return java.awt.Color.white; -}return cols[j]; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "applyTo", -function (sg, hiddenRepSequences) { -return new jalview.schemes.TCoffeeColourScheme (sg); -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -c$.$colors = c$.prototype.$colors = Clazz.newArray (-1, [ new java.awt.Color (102, 102, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (102, 255, 0), new java.awt.Color (204, 255, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 153, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 34, 0)]); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme", "java.awt.Color"], "jalview.schemes.TCoffeeColourScheme", ["jalview.datamodel.AlignmentI", "java.util.ArrayList", "$.IdentityHashMap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.seqMap = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "TCoffeeColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function (alignment) { +Clazz.superConstructor (this, jalview.schemes.TCoffeeColourScheme, []); +this.alignmentChanged (alignment, null); +}, "jalview.datamodel.AnnotatedCollectionI"); +Clazz.overrideMethod (c$, "alignmentChanged", +function (alignment, hiddenReps) { +var annots = new java.util.ArrayList (); +this.seqMap = new java.util.IdentityHashMap (); +var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext (); +var w = 0; +for (var al, $al = alcontext.findAnnotation ("TCoffeeScore").iterator (); $al.hasNext () && ((al = $al.next ()) || true);) { +if (al.sequenceRef != null && !al.belowAlignment) { +annots.add (al); +if (w < al.annotations.length) { +w = al.annotations.length; +}var scores = new Array (al.annotations.length); +var i = 0; +for (var an, $an = 0, $$an = al.annotations; $an < $$an.length && ((an = $$an[$an]) || true); $an++) { +scores[i++] = (an != null) ? an.colour : java.awt.Color.white; +} +this.seqMap.put (al.sequenceRef, scores); +}} +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var cols; +if (this.seqMap == null || (cols = this.seqMap.get (seq)) == null) { +return java.awt.Color.white; +}if (j < 0 || j >= cols.length) { +return java.awt.Color.white; +}return cols[j]; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "applyTo", +function (sg, hiddenRepSequences) { +return new jalview.schemes.TCoffeeColourScheme (sg); +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +c$.$colors = c$.prototype.$colors = Clazz.newArray (-1, [ new java.awt.Color (102, 102, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (102, 255, 0), new java.awt.Color (204, 255, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 153, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 34, 0)]); +}); diff --git a/bin/jalview/schemes/TaylorColourScheme.js b/bin/jalview/schemes/TaylorColourScheme.js index 156c6fc..65bba75 100644 --- a/bin/jalview/schemes/TaylorColourScheme.js +++ b/bin/jalview/schemes/TaylorColourScheme.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.TaylorColourScheme", ["jalview.schemes.ResidueProperties"], function () { -c$ = Clazz.declareType (jalview.schemes, "TaylorColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.TaylorColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.taylor, 0]); -}); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.TaylorColourScheme", ["jalview.schemes.ResidueProperties"], function () { +c$ = Clazz.declareType (jalview.schemes, "TaylorColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.TaylorColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.taylor, 0]); +}); +}); diff --git a/bin/jalview/schemes/TurnColourScheme.js b/bin/jalview/schemes/TurnColourScheme.js index 74fe374..7e440d8 100644 --- a/bin/jalview/schemes/TurnColourScheme.js +++ b/bin/jalview/schemes/TurnColourScheme.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.TurnColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { -c$ = Clazz.declareType (jalview.schemes, "TurnColourScheme", jalview.schemes.ScoreColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.TurnColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.turn, 0.47, 1.56]); -}); -Clazz.overrideMethod (c$, "makeColour", -function (c) { -return new java.awt.Color (c, 1 - c, 1 - c); -}, "~N"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ScoreColourScheme"], "jalview.schemes.TurnColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { +c$ = Clazz.declareType (jalview.schemes, "TurnColourScheme", jalview.schemes.ScoreColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.TurnColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.turn, 0.47, 1.56]); +}); +Clazz.overrideMethod (c$, "makeColour", +function (c) { +return new java.awt.Color (c, 1 - c, 1 - c); +}, "~N"); +}); diff --git a/bin/jalview/schemes/UserColourScheme.class b/bin/jalview/schemes/UserColourScheme.class index c6ab601..5ca8ca9 100644 Binary files a/bin/jalview/schemes/UserColourScheme.class and b/bin/jalview/schemes/UserColourScheme.class differ diff --git a/bin/jalview/schemes/UserColourScheme.js b/bin/jalview/schemes/UserColourScheme.js index dcf5f86..ee83987 100644 --- a/bin/jalview/schemes/UserColourScheme.js +++ b/bin/jalview/schemes/UserColourScheme.js @@ -1,165 +1,165 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.UserColourScheme", ["jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "java.awt.Color", "java.util.StringTokenizer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.lowerCaseColours = null; -this.schemeName = null; -Clazz.instantialize (this, arguments); -}, jalview.schemes, "UserColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]); -}); -Clazz.makeConstructor (c$, -function (newColors) { -Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]); -this.colors = newColors; -}, "~A"); -Clazz.overrideMethod (c$, "applyTo", -function (sg, hiddenRepSequences) { -var usc = new jalview.schemes.UserColourScheme (this.colors); -if (this.lowerCaseColours != null) { -usc.schemeName = String.instantialize (this.schemeName); -usc.lowerCaseColours = new Array (this.lowerCaseColours.length); -System.arraycopy (this.lowerCaseColours, 0, usc.lowerCaseColours, 0, this.lowerCaseColours.length); -}return usc; -}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.makeConstructor (c$, -function (colour) { -Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]); -var col = this.getColourFromString (colour); -if (col == null) { -System.out.println ("Unknown colour!! " + colour); -col = this.createColourFromName (colour); -}this.colors = new Array (24); -for (var i = 0; i < 24; i++) { -this.colors[i] = col; -} -this.schemeName = colour; -}, "~S"); -Clazz.defineMethod (c$, "getColours", -function () { -return this.colors; -}); -Clazz.defineMethod (c$, "getLowerCaseColours", -function () { -return this.lowerCaseColours; -}); -Clazz.defineMethod (c$, "setName", -function (name) { -this.schemeName = name; -}, "~S"); -Clazz.defineMethod (c$, "getName", -function () { -return this.schemeName; -}); -Clazz.defineMethod (c$, "getColourFromString", -function (colour) { -colour = colour.trim (); -var col = null; -try { -var value = Integer.parseInt (colour, 16); -col = new java.awt.Color (value); -} catch (ex) { -if (Clazz.exceptionOf (ex, NumberFormatException)) { -} else { -throw ex; -} -} -if (col == null) { -col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName (colour); -}if (col == null) { -try { -var st = new java.util.StringTokenizer (colour, ","); -var r = Integer.parseInt (st.nextToken ()); -var g = Integer.parseInt (st.nextToken ()); -var b = Integer.parseInt (st.nextToken ()); -col = new java.awt.Color (r, g, b); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}return col; -}, "~S"); -Clazz.defineMethod (c$, "createColourFromName", -function (name) { -var r; -var g; -var b; -var lsize = name.length; -var start = 0; -var end = Clazz.doubleToInt (lsize / 3); -var rgbOffset = Math.abs (name.hashCode () % 10) * 15; -r = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20; -start = end; -end += Clazz.doubleToInt (lsize / 3); -if (end > lsize) { -end = lsize; -}g = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20; -b = Math.abs (name.substring (end).hashCode () + rgbOffset) % 210 + 20; -var color = new java.awt.Color (r, g, b); -return color; -}, "~S"); -Clazz.defineMethod (c$, "parseAppletParameter", -function (paramValue) { -var st = new java.util.StringTokenizer (paramValue, ";"); -var st2; -var token = null; -var colour; -var residues; -try { -while (st.hasMoreElements ()) { -token = st.nextToken ().trim (); -residues = token.substring (0, token.indexOf ("=")); -colour = token.substring (token.indexOf ("=") + 1); -st2 = new java.util.StringTokenizer (residues, " ,"); -while (st2.hasMoreTokens ()) { -token = st2.nextToken (); -if (jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)] == -1) { -continue; -}var colIndex = jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)]; -if (token.equalsIgnoreCase ("lowerCase")) { -if (this.lowerCaseColours == null) { -this.lowerCaseColours = new Array (23); -}for (var i = 0; i < 23; i++) { -if (this.lowerCaseColours[i] == null) { -this.lowerCaseColours[i] = this.getColourFromString (colour); -}} -continue; -}if (token.equals (token.toLowerCase ())) { -if (this.lowerCaseColours == null) { -this.lowerCaseColours = new Array (23); -}this.lowerCaseColours[colIndex] = this.getColourFromString (colour); -} else { -this.colors[colIndex] = this.getColourFromString (colour); -}} -} -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -System.out.println ("Error parsing userDefinedColours:\n" + token + "\n" + ex); -} else { -throw ex; -} -} -}, "~S"); -Clazz.defineMethod (c$, "findColour", -function (c, j, seq) { -var currentColour; -var index = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; -if ((this.threshold == 0) || this.aboveThreshold (c, j)) { -if (this.lowerCaseColours != null && 'a' <= c && c <= 'z') { -currentColour = this.lowerCaseColours[index]; -} else { -currentColour = this.colors[index]; -}} else { -currentColour = java.awt.Color.white; -}if (this.conservationColouring) { -currentColour = this.applyConservation (currentColour, j); -}return currentColour; -}, "~S,~N,jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "setLowerCaseColours", -function (lcolours) { -this.lowerCaseColours = lcolours; -}, "~A"); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.UserColourScheme", ["jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "java.awt.Color", "java.util.StringTokenizer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.lowerCaseColours = null; +this.schemeName = null; +Clazz.instantialize (this, arguments); +}, jalview.schemes, "UserColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]); +}); +Clazz.makeConstructor (c$, +function (newColors) { +Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]); +this.colors = newColors; +}, "~A"); +Clazz.overrideMethod (c$, "applyTo", +function (sg, hiddenRepSequences) { +var usc = new jalview.schemes.UserColourScheme (this.colors); +if (this.lowerCaseColours != null) { +usc.schemeName = String.instantialize (this.schemeName); +usc.lowerCaseColours = new Array (this.lowerCaseColours.length); +System.arraycopy (this.lowerCaseColours, 0, usc.lowerCaseColours, 0, this.lowerCaseColours.length); +}return usc; +}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); +Clazz.makeConstructor (c$, +function (colour) { +Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]); +var col = this.getColourFromString (colour); +if (col == null) { +System.out.println ("Unknown colour!! " + colour); +col = this.createColourFromName (colour); +}this.colors = new Array (24); +for (var i = 0; i < 24; i++) { +this.colors[i] = col; +} +this.schemeName = colour; +}, "~S"); +Clazz.defineMethod (c$, "getColours", +function () { +return this.colors; +}); +Clazz.defineMethod (c$, "getLowerCaseColours", +function () { +return this.lowerCaseColours; +}); +Clazz.defineMethod (c$, "setName", +function (name) { +this.schemeName = name; +}, "~S"); +Clazz.defineMethod (c$, "getName", +function () { +return this.schemeName; +}); +Clazz.defineMethod (c$, "getColourFromString", +function (colour) { +colour = colour.trim (); +var col = null; +try { +var value = Integer.parseInt (colour, 16); +col = new java.awt.Color (value); +} catch (ex) { +if (Clazz.exceptionOf (ex, NumberFormatException)) { +} else { +throw ex; +} +} +if (col == null) { +col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName (colour); +}if (col == null) { +try { +var st = new java.util.StringTokenizer (colour, ","); +var r = Integer.parseInt (st.nextToken ()); +var g = Integer.parseInt (st.nextToken ()); +var b = Integer.parseInt (st.nextToken ()); +col = new java.awt.Color (r, g, b); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}return col; +}, "~S"); +Clazz.defineMethod (c$, "createColourFromName", +function (name) { +var r; +var g; +var b; +var lsize = name.length; +var start = 0; +var end = Clazz.doubleToInt (lsize / 3); +var rgbOffset = Math.abs (name.hashCode () % 10) * 15; +r = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20; +start = end; +end += Clazz.doubleToInt (lsize / 3); +if (end > lsize) { +end = lsize; +}g = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20; +b = Math.abs (name.substring (end).hashCode () + rgbOffset) % 210 + 20; +var color = new java.awt.Color (r, g, b); +return color; +}, "~S"); +Clazz.defineMethod (c$, "parseAppletParameter", +function (paramValue) { +var st = new java.util.StringTokenizer (paramValue, ";"); +var st2; +var token = null; +var colour; +var residues; +try { +while (st.hasMoreElements ()) { +token = st.nextToken ().trim (); +residues = token.substring (0, token.indexOf ("=")); +colour = token.substring (token.indexOf ("=") + 1); +st2 = new java.util.StringTokenizer (residues, " ,"); +while (st2.hasMoreTokens ()) { +token = st2.nextToken (); +if (jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)] == -1) { +continue; +}var colIndex = jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)]; +if (token.equalsIgnoreCase ("lowerCase")) { +if (this.lowerCaseColours == null) { +this.lowerCaseColours = new Array (23); +}for (var i = 0; i < 23; i++) { +if (this.lowerCaseColours[i] == null) { +this.lowerCaseColours[i] = this.getColourFromString (colour); +}} +continue; +}if (token.equals (token.toLowerCase ())) { +if (this.lowerCaseColours == null) { +this.lowerCaseColours = new Array (23); +}this.lowerCaseColours[colIndex] = this.getColourFromString (colour); +} else { +this.colors[colIndex] = this.getColourFromString (colour); +}} +} +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +System.out.println ("Error parsing userDefinedColours:\n" + token + "\n" + ex); +} else { +throw ex; +} +} +}, "~S"); +Clazz.defineMethod (c$, "findColour", +function (c, j, seq) { +var currentColour; +var index = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; +if ((this.threshold == 0) || this.aboveThreshold (c, j)) { +if (this.lowerCaseColours != null && 'a' <= c && c <= 'z') { +currentColour = this.lowerCaseColours[index]; +} else { +currentColour = this.colors[index]; +}} else { +currentColour = java.awt.Color.white; +}if (this.conservationColouring) { +currentColour = this.applyConservation (currentColour, j); +}return currentColour; +}, "~S,~N,jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "setLowerCaseColours", +function (lcolours) { +this.lowerCaseColours = lcolours; +}, "~A"); +}); diff --git a/bin/jalview/schemes/ZappoColourScheme.js b/bin/jalview/schemes/ZappoColourScheme.js index fc253d3..b63064e 100644 --- a/bin/jalview/schemes/ZappoColourScheme.js +++ b/bin/jalview/schemes/ZappoColourScheme.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("jalview.schemes"); -Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.ZappoColourScheme", ["jalview.schemes.ResidueProperties"], function () { -c$ = Clazz.declareType (jalview.schemes, "ZappoColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.schemes.ZappoColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.zappo, 0]); -}); -}); +Clazz.declarePackage ("jalview.schemes"); +Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.ZappoColourScheme", ["jalview.schemes.ResidueProperties"], function () { +c$ = Clazz.declareType (jalview.schemes, "ZappoColourScheme", jalview.schemes.ResidueColourScheme); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.schemes.ZappoColourScheme, [jalview.schemes.ResidueProperties.aaIndex, jalview.schemes.ResidueProperties.zappo, 0]); +}); +}); diff --git a/bin/jalview/schemes/package.js b/bin/jalview/schemes/package.js index 045573a..5891eb2 100644 --- a/bin/jalview/schemes/package.js +++ b/bin/jalview/schemes/package.js @@ -1,5 +1,5 @@ -var path = ClazzLoader.getClasspathFor ("jalview.schemes.package"); -path = path.substring (0, path.lastIndexOf ("package.js")); -ClazzLoader.jarClasspath (path + "ClustalxColourScheme.js", [ -"jalview.schemes.ConsensusColour", -"$.ClustalxColourScheme"]); +var path = ClazzLoader.getClasspathFor ("jalview.schemes.package"); +path = path.substring (0, path.lastIndexOf ("package.js")); +ClazzLoader.jarClasspath (path + "ClustalxColourScheme.js", [ +"jalview.schemes.ConsensusColour", +"$.ClustalxColourScheme"]); diff --git a/bin/jalview/structure/AlignmentViewPanelListener.js b/bin/jalview/structure/AlignmentViewPanelListener.js index 979d03f..d293108 100644 --- a/bin/jalview/structure/AlignmentViewPanelListener.js +++ b/bin/jalview/structure/AlignmentViewPanelListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "AlignmentViewPanelListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "AlignmentViewPanelListener"); diff --git a/bin/jalview/structure/AtomSpec.js b/bin/jalview/structure/AtomSpec.js index 3e50bc2..0023fdc 100644 --- a/bin/jalview/structure/AtomSpec.js +++ b/bin/jalview/structure/AtomSpec.js @@ -1,35 +1,35 @@ -Clazz.declarePackage ("jalview.structure"); -c$ = Clazz.decorateAsClass (function () { -this.pdbFile = null; -this.chain = null; -this.pdbResNum = 0; -this.atomIndex = 0; -Clazz.instantialize (this, arguments); -}, jalview.structure, "AtomSpec"); -Clazz.makeConstructor (c$, -function (pdbFile, chain, resNo, atomNo) { -this.pdbFile = pdbFile; -this.chain = chain; -this.pdbResNum = resNo; -this.atomIndex = atomNo; -}, "~S,~S,~N,~N"); -Clazz.defineMethod (c$, "getPdbFile", -function () { -return this.pdbFile; -}); -Clazz.defineMethod (c$, "getChain", -function () { -return this.chain; -}); -Clazz.defineMethod (c$, "getPdbResNum", -function () { -return this.pdbResNum; -}); -Clazz.defineMethod (c$, "getAtomIndex", -function () { -return this.atomIndex; -}); -Clazz.overrideMethod (c$, "toString", -function () { -return "pdbFile: " + this.pdbFile + ", chain: " + this.chain + ", res: " + this.pdbResNum + ", atom: " + this.atomIndex; -}); +Clazz.declarePackage ("jalview.structure"); +c$ = Clazz.decorateAsClass (function () { +this.pdbFile = null; +this.chain = null; +this.pdbResNum = 0; +this.atomIndex = 0; +Clazz.instantialize (this, arguments); +}, jalview.structure, "AtomSpec"); +Clazz.makeConstructor (c$, +function (pdbFile, chain, resNo, atomNo) { +this.pdbFile = pdbFile; +this.chain = chain; +this.pdbResNum = resNo; +this.atomIndex = atomNo; +}, "~S,~S,~N,~N"); +Clazz.defineMethod (c$, "getPdbFile", +function () { +return this.pdbFile; +}); +Clazz.defineMethod (c$, "getChain", +function () { +return this.chain; +}); +Clazz.defineMethod (c$, "getPdbResNum", +function () { +return this.pdbResNum; +}); +Clazz.defineMethod (c$, "getAtomIndex", +function () { +return this.atomIndex; +}); +Clazz.overrideMethod (c$, "toString", +function () { +return "pdbFile: " + this.pdbFile + ", chain: " + this.chain + ", res: " + this.pdbResNum + ", atom: " + this.atomIndex; +}); diff --git a/bin/jalview/structure/CommandListener.js b/bin/jalview/structure/CommandListener.js index 5f0c290..8901ca3 100644 --- a/bin/jalview/structure/CommandListener.js +++ b/bin/jalview/structure/CommandListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "CommandListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "CommandListener"); diff --git a/bin/jalview/structure/SecondaryStructureListener.js b/bin/jalview/structure/SecondaryStructureListener.js index d9e73f4..b16a9bc 100644 --- a/bin/jalview/structure/SecondaryStructureListener.js +++ b/bin/jalview/structure/SecondaryStructureListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "SecondaryStructureListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "SecondaryStructureListener"); diff --git a/bin/jalview/structure/SelectionListener.js b/bin/jalview/structure/SelectionListener.js index f7ce6dc..6dc17bd 100644 --- a/bin/jalview/structure/SelectionListener.js +++ b/bin/jalview/structure/SelectionListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "SelectionListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "SelectionListener"); diff --git a/bin/jalview/structure/SelectionSource.js b/bin/jalview/structure/SelectionSource.js index 995ec35..7bb91f3 100644 --- a/bin/jalview/structure/SelectionSource.js +++ b/bin/jalview/structure/SelectionSource.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "SelectionSource"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "SelectionSource"); diff --git a/bin/jalview/structure/SequenceListener.js b/bin/jalview/structure/SequenceListener.js index 026c9c1..6ff05ae 100644 --- a/bin/jalview/structure/SequenceListener.js +++ b/bin/jalview/structure/SequenceListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "SequenceListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "SequenceListener"); diff --git a/bin/jalview/structure/StructureListener.js b/bin/jalview/structure/StructureListener.js index 47bde4f..e5ea9ef 100644 --- a/bin/jalview/structure/StructureListener.js +++ b/bin/jalview/structure/StructureListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "StructureListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "StructureListener"); diff --git a/bin/jalview/structure/StructureMapping.js b/bin/jalview/structure/StructureMapping.js index 8cf2f33..40c774f 100644 --- a/bin/jalview/structure/StructureMapping.js +++ b/bin/jalview/structure/StructureMapping.js @@ -1,69 +1,69 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.load (null, "jalview.structure.StructureMapping", ["jalview.datamodel.AlignmentAnnotation"], function () { -c$ = Clazz.decorateAsClass (function () { -this.mappingDetails = null; -this.sequence = null; -this.pdbfile = null; -this.pdbid = null; -this.pdbchain = null; -this.mapping = null; -Clazz.instantialize (this, arguments); -}, jalview.structure, "StructureMapping"); -Clazz.makeConstructor (c$, -function (seq, pdbfile, pdbid, chain, mapping, mappingDetails) { -this.sequence = seq; -this.pdbfile = pdbfile; -this.pdbid = pdbid; -this.pdbchain = chain; -this.mapping = mapping; -this.mappingDetails = mappingDetails; -}, "jalview.datamodel.SequenceI,~S,~S,~S,~A,~S"); -Clazz.defineMethod (c$, "getSequence", -function () { -return this.sequence; -}); -Clazz.defineMethod (c$, "getChain", -function () { -return this.pdbchain; -}); -Clazz.defineMethod (c$, "getPdbId", -function () { -return this.pdbid; -}); -Clazz.defineMethod (c$, "getAtomNum", -function (seqpos) { -if (this.mapping.length > seqpos) { -return this.mapping[seqpos][1]; -} else { -return 0; -}}, "~N"); -Clazz.defineMethod (c$, "getPDBResNum", -function (seqpos) { -if (this.mapping.length > seqpos) { -return this.mapping[seqpos][0]; -} else { -return 0; -}}, "~N"); -Clazz.defineMethod (c$, "getSeqPos", -function (pdbResNum) { -for (var i = 0; i < this.mapping.length; i++) { -if (this.mapping[i][0] == pdbResNum) { -return i; -}} -return -1; -}, "~N"); -Clazz.defineMethod (c$, "transfer", -function (ana) { -var ala_copy = new jalview.datamodel.AlignmentAnnotation (ana); -var ds = this.sequence; -while (ds.getDatasetSequence () != null) { -ds = ds.getDatasetSequence (); -} -ala_copy.remap (ds, this.mapping, -1, -1, 0); -ds.addAlignmentAnnotation (ala_copy); -if (ds !== this.sequence) { -ala_copy = new jalview.datamodel.AlignmentAnnotation (ala_copy); -this.sequence.addAlignmentAnnotation (ala_copy); -}return ala_copy; -}, "jalview.datamodel.AlignmentAnnotation"); -}); +Clazz.declarePackage ("jalview.structure"); +Clazz.load (null, "jalview.structure.StructureMapping", ["jalview.datamodel.AlignmentAnnotation"], function () { +c$ = Clazz.decorateAsClass (function () { +this.mappingDetails = null; +this.sequence = null; +this.pdbfile = null; +this.pdbid = null; +this.pdbchain = null; +this.mapping = null; +Clazz.instantialize (this, arguments); +}, jalview.structure, "StructureMapping"); +Clazz.makeConstructor (c$, +function (seq, pdbfile, pdbid, chain, mapping, mappingDetails) { +this.sequence = seq; +this.pdbfile = pdbfile; +this.pdbid = pdbid; +this.pdbchain = chain; +this.mapping = mapping; +this.mappingDetails = mappingDetails; +}, "jalview.datamodel.SequenceI,~S,~S,~S,~A,~S"); +Clazz.defineMethod (c$, "getSequence", +function () { +return this.sequence; +}); +Clazz.defineMethod (c$, "getChain", +function () { +return this.pdbchain; +}); +Clazz.defineMethod (c$, "getPdbId", +function () { +return this.pdbid; +}); +Clazz.defineMethod (c$, "getAtomNum", +function (seqpos) { +if (this.mapping.length > seqpos) { +return this.mapping[seqpos][1]; +} else { +return 0; +}}, "~N"); +Clazz.defineMethod (c$, "getPDBResNum", +function (seqpos) { +if (this.mapping.length > seqpos) { +return this.mapping[seqpos][0]; +} else { +return 0; +}}, "~N"); +Clazz.defineMethod (c$, "getSeqPos", +function (pdbResNum) { +for (var i = 0; i < this.mapping.length; i++) { +if (this.mapping[i][0] == pdbResNum) { +return i; +}} +return -1; +}, "~N"); +Clazz.defineMethod (c$, "transfer", +function (ana) { +var ala_copy = new jalview.datamodel.AlignmentAnnotation (ana); +var ds = this.sequence; +while (ds.getDatasetSequence () != null) { +ds = ds.getDatasetSequence (); +} +ala_copy.remap (ds, this.mapping, -1, -1, 0); +ds.addAlignmentAnnotation (ala_copy); +if (ds !== this.sequence) { +ala_copy = new jalview.datamodel.AlignmentAnnotation (ala_copy); +this.sequence.addAlignmentAnnotation (ala_copy); +}return ala_copy; +}, "jalview.datamodel.AlignmentAnnotation"); +}); diff --git a/bin/jalview/structure/StructureMappingcommandSet.js b/bin/jalview/structure/StructureMappingcommandSet.js index 2f615c6..97ef9f5 100644 --- a/bin/jalview/structure/StructureMappingcommandSet.js +++ b/bin/jalview/structure/StructureMappingcommandSet.js @@ -1,13 +1,13 @@ -Clazz.declarePackage ("jalview.structure"); -c$ = Clazz.decorateAsClass (function () { -this.mapping = null; -this.commands = null; -this.handledBy = null; -Clazz.instantialize (this, arguments); -}, jalview.structure, "StructureMappingcommandSet"); -Clazz.makeConstructor (c$, -function (handledBy, files, commands) { -this.mapping = files; -this.handledBy = handledBy; -this.commands = commands; -}, "~O,~S,~A"); +Clazz.declarePackage ("jalview.structure"); +c$ = Clazz.decorateAsClass (function () { +this.mapping = null; +this.commands = null; +this.handledBy = null; +Clazz.instantialize (this, arguments); +}, jalview.structure, "StructureMappingcommandSet"); +Clazz.makeConstructor (c$, +function (handledBy, files, commands) { +this.mapping = files; +this.handledBy = handledBy; +this.commands = commands; +}, "~O,~S,~A"); diff --git a/bin/jalview/structure/StructureSelectionManager.class b/bin/jalview/structure/StructureSelectionManager.class index bd3d0d7..837803e 100644 Binary files a/bin/jalview/structure/StructureSelectionManager.class and b/bin/jalview/structure/StructureSelectionManager.class differ diff --git a/bin/jalview/structure/StructureSelectionManager.js b/bin/jalview/structure/StructureSelectionManager.js index 681a2a7..cdbab51 100644 --- a/bin/jalview/structure/StructureSelectionManager.js +++ b/bin/jalview/structure/StructureSelectionManager.js @@ -1,511 +1,511 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.load (["java.util.ArrayList", "$.HashMap", "$.LinkedHashSet", "$.Vector"], "jalview.structure.StructureSelectionManager", ["MCview.PDBfile", "jalview.analysis.AlignSeq", "jalview.commands.EditCommand", "$.OrderCommand", "jalview.datamodel.Mapping", "$.SearchResults", "jalview.io.AppletFormatAdapter", "jalview.structure.AtomSpec", "$.SecondaryStructureListener", "$.SequenceListener", "$.StructureListener", "$.StructureMapping", "$.VamsasListener", "jalview.util.MappingUtils", "$.MessageManager", "java.lang.Error", "$.NullPointerException", "$.StringBuilder", "java.util.Arrays", "$.Collections", "$.IdentityHashMap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.mappings = null; -this.processSecondaryStructure = false; -this.secStructServices = false; -this.addTempFacAnnot = false; -this.seqmappings = null; -this.seqMappingRefCounts = null; -this.commandListeners = null; -this.sel_listeners = null; -this.pdbIdFileName = null; -this.pdbFileNameId = null; -this.relaySeqMappings = true; -this.listeners = null; -this.handlingVamsasMo = false; -this.lastmsg = 0; -this.view_listeners = null; -Clazz.instantialize (this, arguments); -}, jalview.structure, "StructureSelectionManager"); -Clazz.prepareFields (c$, function () { -this.mappings = new java.util.ArrayList (); -this.seqmappings = new java.util.LinkedHashSet (); -this.seqMappingRefCounts = new java.util.HashMap (); -this.commandListeners = new java.util.ArrayList (); -this.sel_listeners = new java.util.ArrayList (); -this.pdbIdFileName = new java.util.HashMap (); -this.pdbFileNameId = new java.util.HashMap (); -this.listeners = new java.util.Vector (); -this.view_listeners = new java.util.Vector (); -}); -Clazz.defineMethod (c$, "isSecStructServices", -function () { -return this.secStructServices; -}); -Clazz.defineMethod (c$, "setSecStructServices", -function (secStructServices) { -this.secStructServices = secStructServices; -}, "~B"); -Clazz.defineMethod (c$, "isAddTempFacAnnot", -function () { -return this.addTempFacAnnot; -}); -Clazz.defineMethod (c$, "setAddTempFacAnnot", -function (addTempFacAnnot) { -this.addTempFacAnnot = addTempFacAnnot; -}, "~B"); -Clazz.defineMethod (c$, "isProcessSecondaryStructure", -function () { -return this.processSecondaryStructure; -}); -Clazz.defineMethod (c$, "setProcessSecondaryStructure", -function (enable) { -this.processSecondaryStructure = enable; -}, "~B"); -Clazz.defineMethod (c$, "reportMapping", -function () { -if (this.mappings.isEmpty ()) { -System.err.println ("reportMapping: No PDB/Sequence mappings."); -} else { -System.err.println ("reportMapping: There are " + this.mappings.size () + " mappings."); -var i = 0; -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -System.err.println ("mapping " + i++ + " : " + sm.pdbfile); -} -}}); -Clazz.defineMethod (c$, "registerPDBFile", -function (idForFile, absoluteFile) { -this.pdbIdFileName.put (idForFile, absoluteFile); -this.pdbFileNameId.put (absoluteFile, idForFile); -}, "~S,~S"); -Clazz.defineMethod (c$, "findIdForPDBFile", -function (idOrFile) { -var id = this.pdbFileNameId.get (idOrFile); -return id; -}, "~S"); -Clazz.defineMethod (c$, "findFileForPDBId", -function (idOrFile) { -var id = this.pdbIdFileName.get (idOrFile); -return id; -}, "~S"); -Clazz.defineMethod (c$, "isPDBFileRegistered", -function (idOrFile) { -return this.pdbFileNameId.containsKey (idOrFile) || this.pdbIdFileName.containsKey (idOrFile); -}, "~S"); -c$.getStructureSelectionManager = Clazz.defineMethod (c$, "getStructureSelectionManager", -function (context) { -if (context == null) { -if (jalview.structure.StructureSelectionManager.nullProvider == null) { -if (jalview.structure.StructureSelectionManager.instances != null) { -throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_structure_selection_manager_null"), new NullPointerException (jalview.util.MessageManager.getString ("exception.ssm_context_is_null"))); -} else { -jalview.structure.StructureSelectionManager.nullProvider = new jalview.structure.StructureSelectionManager (); -}return jalview.structure.StructureSelectionManager.nullProvider; -}}if (jalview.structure.StructureSelectionManager.instances == null) { -jalview.structure.StructureSelectionManager.instances = new java.util.IdentityHashMap (); -}var instance = jalview.structure.StructureSelectionManager.instances.get (context); -if (instance == null) { -if (jalview.structure.StructureSelectionManager.nullProvider != null) { -instance = jalview.structure.StructureSelectionManager.nullProvider; -} else { -instance = new jalview.structure.StructureSelectionManager (); -}jalview.structure.StructureSelectionManager.instances.put (context, instance); -}return instance; -}, "jalview.api.StructureSelectionManagerProvider"); -Clazz.defineMethod (c$, "setRelaySeqMappings", -function (relay) { -this.relaySeqMappings = relay; -}, "~B"); -Clazz.defineMethod (c$, "isRelaySeqMappingsEnabled", -function () { -return this.relaySeqMappings; -}); -Clazz.defineMethod (c$, "addStructureViewerListener", -function (svl) { -if (!this.listeners.contains (svl)) { -this.listeners.addElement (svl); -}}, "~O"); -Clazz.defineMethod (c$, "alreadyMappedToFile", -function (pdbid) { -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -if (sm.getPdbId ().equals (pdbid)) { -return sm.pdbfile; -}} -return null; -}, "~S"); -Clazz.defineMethod (c$, "setMapping", -function (sequence, targetChains, pdbFile, protocol) { -return this.setMapping (true, sequence, targetChains, pdbFile, protocol); -}, "~A,~A,~S,~S"); -Clazz.defineMethod (c$, "setMapping", -function (forStructureView, sequence, targetChains, pdbFile, protocol) { -var parseSecStr = this.processSecondaryStructure; -if (this.isPDBFileRegistered (pdbFile)) { -for (var sq, $sq = 0, $$sq = sequence; $sq < $$sq.length && ((sq = $$sq[$sq]) || true); $sq++) { -var ds = sq; -while (ds.getDatasetSequence () != null) { -ds = ds.getDatasetSequence (); -} -;if (ds.getAnnotation () != null) { -for (var ala, $ala = 0, $$ala = ds.getAnnotation (); $ala < $$ala.length && ((ala = $$ala[$ala]) || true); $ala++) { -if (MCview.PDBfile.isCalcIdForFile (ala, this.findIdForPDBFile (pdbFile))) { -parseSecStr = false; -}} -}} -}var pdb = null; -try { -pdb = new MCview.PDBfile (this.addTempFacAnnot, parseSecStr, this.secStructServices, pdbFile, protocol); -if (pdb.id != null && pdb.id.trim ().length > 0 && jalview.io.AppletFormatAdapter.FILE.equals (protocol)) { -this.registerPDBFile (pdb.id.trim (), pdbFile); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -return null; -} else { -throw ex; -} -} -var targetChain; -for (var s = 0; s < sequence.length; s++) { -var infChain = true; -var seq = sequence[s]; -if (targetChains != null && targetChains[s] != null) { -infChain = false; -targetChain = targetChains[s]; -} else if (seq.getName ().indexOf ("|") > -1) { -targetChain = seq.getName ().substring (seq.getName ().lastIndexOf ("|") + 1); -if (targetChain.length > 1) { -if (targetChain.trim ().length == 0) { -targetChain = " "; -} else { -targetChain = ""; -}}} else { -targetChain = ""; -}var max = -10; -var maxAlignseq = null; -var maxChainId = " "; -var maxChain = null; -var first = true; -for (var chain, $chain = pdb.chains.iterator (); $chain.hasNext () && ((chain = $chain.next ()) || true);) { -if (targetChain.length > 0 && !targetChain.equals (chain.id) && !infChain) { -continue; -}var type = chain.isNa ? "dna" : "pep"; -var as = jalview.analysis.AlignSeq.doGlobalNWAlignment (seq, chain.sequence, type); -if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals (targetChain))) { -first = false; -maxChain = chain; -max = as.maxscore; -maxAlignseq = as; -maxChainId = chain.id; -}} -if (maxChain == null) { -continue; -}var mappingDetails = new StringBuilder (128); -mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("PDB Sequence is :").append (jalview.structure.StructureSelectionManager.NEWLINE).append ("Sequence = ").append (maxChain.sequence.getSequenceAsString ()); -mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("No of residues = ").append (maxChain.residues.size ()).append (jalview.structure.StructureSelectionManager.NEWLINE).append (jalview.structure.StructureSelectionManager.NEWLINE); -var ps = ((Clazz.isClassDefined ("jalview.structure.StructureSelectionManager$1") ? 0 : jalview.structure.StructureSelectionManager.$StructureSelectionManager$1$ ()), Clazz.innerTypeInstance (jalview.structure.StructureSelectionManager$1, this, Clazz.cloneFinals ("mappingDetails", mappingDetails), System.out)); -maxAlignseq.printAlignment (ps); -mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("PDB start/end "); -mappingDetails.append (String.valueOf (maxAlignseq.seq2start)).append (" "); -mappingDetails.append (String.valueOf (maxAlignseq.seq2end)); -mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("SEQ start/end "); -mappingDetails.append (String.valueOf (maxAlignseq.seq1start + seq.getStart () - 1)).append (" "); -mappingDetails.append (String.valueOf (maxAlignseq.seq1end + seq.getEnd () - 1)); -maxChain.makeExactMapping (maxAlignseq, seq); -var sqmpping = maxAlignseq.getMappingFromS1 (false); -var omap = new jalview.datamodel.Mapping (sqmpping.getMap ().getInverse ()); -maxChain.transferRESNUMFeatures (seq, null); -var mapping = Clazz.newIntArray (seq.findPosition (seq.getLength ()) + 2, 2, 0); -var resNum = -10000; -var index = 0; -do { -var tmp = maxChain.atoms.elementAt (index); -if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) { -resNum = tmp.resNumber; -mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; -mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; -}index++; -} while (index < maxChain.atoms.size ()); -if (protocol.equals (jalview.io.AppletFormatAdapter.PASTE)) { -pdbFile = "INLINE" + pdb.id; -}var newMapping = new jalview.structure.StructureMapping (seq, pdbFile, pdb.id, maxChainId, mapping, mappingDetails.toString ()); -if (forStructureView) { -this.mappings.add (newMapping); -}maxChain.transferResidueAnnotation (newMapping, sqmpping); -} -return pdb; -}, "~B,~A,~A,~S,~S"); -Clazz.defineMethod (c$, "removeStructureViewerListener", -function (svl, pdbfiles) { -this.listeners.removeElement (svl); -if (Clazz.instanceOf (svl, jalview.structure.SequenceListener)) { -for (var i = 0; i < this.listeners.size (); i++) { -if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) { -(this.listeners.elementAt (i)).releaseReferences (svl); -}} -}if (pdbfiles == null) { -return; -}var pdbs = new java.util.ArrayList (java.util.Arrays.asList (pdbfiles)); -var sl; -for (var i = 0; i < this.listeners.size (); i++) { -if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) { -sl = this.listeners.elementAt (i); -for (var pdbfile, $pdbfile = 0, $$pdbfile = sl.getPdbFile (); $pdbfile < $$pdbfile.length && ((pdbfile = $$pdbfile[$pdbfile]) || true); $pdbfile++) { -pdbs.remove (pdbfile); -} -}} -if (pdbs.size () > 0) { -var tmp = new java.util.ArrayList (); -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -if (!pdbs.contains (sm.pdbfile)) { -tmp.add (sm); -}} -this.mappings = tmp; -}}, "~O,~A"); -Clazz.defineMethod (c$, "mouseOverStructure", -function (pdbResNum, chain, pdbfile) { -var atomSpec = new jalview.structure.AtomSpec (pdbfile, chain, pdbResNum, 0); -var atoms = java.util.Collections.singletonList (atomSpec); -this.mouseOverStructure (atoms); -}, "~N,~S,~S"); -Clazz.defineMethod (c$, "mouseOverStructure", -function (atoms) { -if (this.listeners == null) { -return; -}var hasSequenceListener = false; -for (var i = 0; i < this.listeners.size (); i++) { -if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.SequenceListener)) { -hasSequenceListener = true; -}} -if (!hasSequenceListener) { -return; -}var results = new jalview.datamodel.SearchResults (); -for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { -var lastseq = null; -var lastipos = -1; -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -if (sm.pdbfile.equals (atom.getPdbFile ()) && sm.pdbchain.equals (atom.getChain ())) { -var indexpos = sm.getSeqPos (atom.getPdbResNum ()); -if (lastipos != indexpos && lastseq !== sm.sequence) { -results.addResult (sm.sequence, indexpos, indexpos); -lastipos = indexpos; -lastseq = sm.sequence; -for (var acf, $acf = this.seqmappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -acf.markMappedRegion (sm.sequence, indexpos, results); -} -}}} -} -for (var li, $li = this.listeners.iterator (); $li.hasNext () && ((li = $li.next ()) || true);) { -if (Clazz.instanceOf (li, jalview.structure.SequenceListener)) { -(li).highlightSequence (results); -}} -}, "java.util.List"); -Clazz.defineMethod (c$, "mouseOverSequence", -function (seq, indexpos, index, source) { -var hasSequenceListeners = this.handlingVamsasMo || !this.seqmappings.isEmpty (); -var results = null; -if (index == -1) { -index = seq.findPosition (indexpos); -}for (var i = 0; i < this.listeners.size (); i++) { -var listener = this.listeners.elementAt (i); -if (listener === source) { -continue; -}if (Clazz.instanceOf (listener, jalview.structure.StructureListener)) { -this.highlightStructure (listener, seq, index); -} else { -if (Clazz.instanceOf (listener, jalview.structure.SequenceListener)) { -var seqListener = listener; -if (hasSequenceListeners && seqListener.getVamsasSource () !== source) { -if (this.relaySeqMappings) { -if (results == null) { -results = jalview.util.MappingUtils.buildSearchResults (seq, index, this.seqmappings); -}if (this.handlingVamsasMo) { -results.addResult (seq, index, index); -}seqListener.highlightSequence (results); -}}} else if (Clazz.instanceOf (listener, jalview.structure.VamsasListener) && !this.handlingVamsasMo) { -(listener).mouseOverSequence (seq, indexpos, source); -} else if (Clazz.instanceOf (listener, jalview.structure.SecondaryStructureListener)) { -(listener).mouseOverSequence (seq, indexpos, index); -}}} -}, "jalview.datamodel.SequenceI,~N,~N,jalview.structure.VamsasSource"); -Clazz.defineMethod (c$, "highlightStructure", -function (sl, seq, index) { -if (!sl.isListeningFor (seq)) { -return; -}var atomNo; -var atoms = new java.util.ArrayList (); -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -if (sm.sequence === seq || sm.sequence === seq.getDatasetSequence ()) { -atomNo = sm.getAtomNum (index); -if (atomNo > 0) { -atoms.add ( new jalview.structure.AtomSpec (sm.pdbfile, sm.pdbchain, sm.getPDBResNum (index), atomNo)); -}}} -sl.highlightAtoms (atoms); -}, "jalview.structure.StructureListener,jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "mouseOverVamsasSequence", -function (sequenceI, position, source) { -this.handlingVamsasMo = true; -var msg = sequenceI.hashCode () * (1 + position); -if (this.lastmsg != msg) { -this.lastmsg = msg; -this.mouseOverSequence (sequenceI, position, -1, source); -}this.handlingVamsasMo = false; -}, "jalview.datamodel.SequenceI,~N,jalview.structure.VamsasSource"); -Clazz.defineMethod (c$, "colourSequenceFromStructure", -function (seq, pdbid) { -return null; -}, "jalview.datamodel.SequenceI,~S"); -Clazz.defineMethod (c$, "structureSelectionChanged", -function () { -}); -Clazz.defineMethod (c$, "sequenceSelectionChanged", -function () { -}); -Clazz.defineMethod (c$, "sequenceColoursChanged", -function (source) { -var sl; -for (var i = 0; i < this.listeners.size (); i++) { -if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) { -sl = this.listeners.elementAt (i); -sl.updateColours (source); -}} -}, "~O"); -Clazz.defineMethod (c$, "getMapping", -function (pdbfile) { -var tmp = new java.util.ArrayList (); -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -if (sm.pdbfile.equals (pdbfile)) { -tmp.add (sm); -}} -return tmp.toArray ( new Array (tmp.size ())); -}, "~S"); -Clazz.defineMethod (c$, "printMappings", -function (pdbfile, seqs) { -if (pdbfile == null || seqs == null || seqs.isEmpty ()) { -return ""; -}var sb = new StringBuilder (64); -for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { -if (sm.pdbfile.equals (pdbfile) && seqs.contains (sm.sequence)) { -sb.append (sm.mappingDetails); -sb.append (jalview.structure.StructureSelectionManager.NEWLINE); -sb.append ("====================="); -sb.append (jalview.structure.StructureSelectionManager.NEWLINE); -}} -sb.append (jalview.structure.StructureSelectionManager.NEWLINE); -return sb.toString (); -}, "~S,java.util.List"); -Clazz.defineMethod (c$, "removeMappings", -function (set) { -if (set != null) { -for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -this.removeMapping (acf); -} -}}, "java.util.Set"); -Clazz.defineMethod (c$, "removeMapping", -function (acf) { -if (acf != null && this.seqmappings.contains (acf)) { -var count = (this.seqMappingRefCounts.get (acf)).intValue (); -count--; -if (count > 0) { -this.seqMappingRefCounts.put (acf, new Integer (count)); -} else { -this.seqmappings.remove (acf); -this.seqMappingRefCounts.remove (acf); -}}}, "jalview.datamodel.AlignedCodonFrame"); -Clazz.defineMethod (c$, "addMappings", -function (set) { -if (set != null) { -for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -this.addMapping (acf); -} -}}, "java.util.Set"); -Clazz.defineMethod (c$, "addMapping", -function (acf) { -if (acf != null) { -if (this.seqmappings.contains (acf)) { -this.seqMappingRefCounts.put (acf, new Integer ((this.seqMappingRefCounts.get (acf)).intValue () + 1)); -} else { -this.seqmappings.add (acf); -this.seqMappingRefCounts.put (acf, new Integer (1)); -}}}, "jalview.datamodel.AlignedCodonFrame"); -Clazz.defineMethod (c$, "addSelectionListener", -function (selecter) { -if (!this.sel_listeners.contains (selecter)) { -this.sel_listeners.add (selecter); -}}, "jalview.structure.SelectionListener"); -Clazz.defineMethod (c$, "removeSelectionListener", -function (toremove) { -if (this.sel_listeners.contains (toremove)) { -this.sel_listeners.remove (toremove); -}}, "jalview.structure.SelectionListener"); -Clazz.defineMethod (c$, "sendSelection", -function (selection, colsel, source) { -for (var slis, $slis = this.sel_listeners.iterator (); $slis.hasNext () && ((slis = $slis.next ()) || true);) { -if (slis !== source) { -slis.selection (selection, colsel, source); -}} -}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); -Clazz.defineMethod (c$, "sendViewPosition", -function (source, startRes, endRes, startSeq, endSeq) { -if (this.view_listeners != null && this.view_listeners.size () > 0) { -var listeners = this.view_listeners.elements (); -while (listeners.hasMoreElements ()) { -var slis = listeners.nextElement (); -if (slis !== source) { -slis.viewPosition (startRes, endRes, startSeq, endSeq, source); -};} -}}, "jalview.api.AlignmentViewPanel,~N,~N,~N,~N"); -c$.release = Clazz.defineMethod (c$, "release", -function (jalviewLite) { -{ -if (jalview.structure.StructureSelectionManager.instances == null) { -return; -}var mnger = (jalview.structure.StructureSelectionManager.instances.get (jalviewLite)); -if (mnger != null) { -jalview.structure.StructureSelectionManager.instances.remove (jalviewLite); -try { -mnger.finalize (); -} catch (x) { -} -}}}, "jalview.api.StructureSelectionManagerProvider"); -Clazz.defineMethod (c$, "registerPDBEntry", -function (pdbentry) { -if (pdbentry.getFile () != null && pdbentry.getFile ().trim ().length > 0) { -this.registerPDBFile (pdbentry.getId (), pdbentry.getFile ()); -}}, "jalview.datamodel.PDBEntry"); -Clazz.defineMethod (c$, "addCommandListener", -function (cl) { -if (!this.commandListeners.contains (cl)) { -this.commandListeners.add (cl); -}}, "jalview.structure.CommandListener"); -Clazz.defineMethod (c$, "hasCommandListener", -function (cl) { -return this.commandListeners.contains (cl); -}, "jalview.structure.CommandListener"); -Clazz.defineMethod (c$, "removeCommandListener", -function (l) { -return this.commandListeners.remove (l); -}, "jalview.structure.CommandListener"); -Clazz.defineMethod (c$, "commandPerformed", -function (command, undo, source) { -for (var listener, $listener = this.commandListeners.iterator (); $listener.hasNext () && ((listener = $listener.next ()) || true);) { -listener.mirrorCommand (command, undo, this, source); -} -}, "jalview.commands.CommandI,~B,jalview.structure.VamsasSource"); -Clazz.defineMethod (c$, "mapCommand", -function (command, undo, mapTo, gapChar) { -if (Clazz.instanceOf (command, jalview.commands.EditCommand)) { -return jalview.util.MappingUtils.mapEditCommand (command, undo, mapTo, gapChar, this.seqmappings); -} else if (Clazz.instanceOf (command, jalview.commands.OrderCommand)) { -return jalview.util.MappingUtils.mapOrderCommand (command, undo, mapTo, this.seqmappings); -}return null; -}, "jalview.commands.CommandI,~B,jalview.datamodel.AlignmentI,~S"); -c$.$StructureSelectionManager$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.structure, "StructureSelectionManager$1", java.io.PrintStream); -Clazz.defineMethod (c$, "print", -function (x) { -this.f$.mappingDetails.append (x); -}, "~S"); -Clazz.defineMethod (c$, "println", -function () { -this.f$.mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE); -}); -c$ = Clazz.p0p (); -}; -c$.NEWLINE = c$.prototype.NEWLINE = System.lineSeparator (); -Clazz.defineStatics (c$, -"instances", null, -"nullProvider", null); -}); +Clazz.declarePackage ("jalview.structure"); +Clazz.load (["java.util.ArrayList", "$.HashMap", "$.LinkedHashSet", "$.Vector"], "jalview.structure.StructureSelectionManager", ["MCview.PDBfile", "jalview.analysis.AlignSeq", "jalview.commands.EditCommand", "$.OrderCommand", "jalview.datamodel.Mapping", "$.SearchResults", "jalview.io.AppletFormatAdapter", "jalview.structure.AtomSpec", "$.SecondaryStructureListener", "$.SequenceListener", "$.StructureListener", "$.StructureMapping", "$.VamsasListener", "jalview.util.MappingUtils", "$.MessageManager", "java.lang.Error", "$.NullPointerException", "$.StringBuilder", "java.util.Arrays", "$.Collections", "$.IdentityHashMap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.mappings = null; +this.processSecondaryStructure = false; +this.secStructServices = false; +this.addTempFacAnnot = false; +this.seqmappings = null; +this.seqMappingRefCounts = null; +this.commandListeners = null; +this.sel_listeners = null; +this.pdbIdFileName = null; +this.pdbFileNameId = null; +this.relaySeqMappings = true; +this.listeners = null; +this.handlingVamsasMo = false; +this.lastmsg = 0; +this.view_listeners = null; +Clazz.instantialize (this, arguments); +}, jalview.structure, "StructureSelectionManager"); +Clazz.prepareFields (c$, function () { +this.mappings = new java.util.ArrayList (); +this.seqmappings = new java.util.LinkedHashSet (); +this.seqMappingRefCounts = new java.util.HashMap (); +this.commandListeners = new java.util.ArrayList (); +this.sel_listeners = new java.util.ArrayList (); +this.pdbIdFileName = new java.util.HashMap (); +this.pdbFileNameId = new java.util.HashMap (); +this.listeners = new java.util.Vector (); +this.view_listeners = new java.util.Vector (); +}); +Clazz.defineMethod (c$, "isSecStructServices", +function () { +return this.secStructServices; +}); +Clazz.defineMethod (c$, "setSecStructServices", +function (secStructServices) { +this.secStructServices = secStructServices; +}, "~B"); +Clazz.defineMethod (c$, "isAddTempFacAnnot", +function () { +return this.addTempFacAnnot; +}); +Clazz.defineMethod (c$, "setAddTempFacAnnot", +function (addTempFacAnnot) { +this.addTempFacAnnot = addTempFacAnnot; +}, "~B"); +Clazz.defineMethod (c$, "isProcessSecondaryStructure", +function () { +return this.processSecondaryStructure; +}); +Clazz.defineMethod (c$, "setProcessSecondaryStructure", +function (enable) { +this.processSecondaryStructure = enable; +}, "~B"); +Clazz.defineMethod (c$, "reportMapping", +function () { +if (this.mappings.isEmpty ()) { +System.err.println ("reportMapping: No PDB/Sequence mappings."); +} else { +System.err.println ("reportMapping: There are " + this.mappings.size () + " mappings."); +var i = 0; +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +System.err.println ("mapping " + i++ + " : " + sm.pdbfile); +} +}}); +Clazz.defineMethod (c$, "registerPDBFile", +function (idForFile, absoluteFile) { +this.pdbIdFileName.put (idForFile, absoluteFile); +this.pdbFileNameId.put (absoluteFile, idForFile); +}, "~S,~S"); +Clazz.defineMethod (c$, "findIdForPDBFile", +function (idOrFile) { +var id = this.pdbFileNameId.get (idOrFile); +return id; +}, "~S"); +Clazz.defineMethod (c$, "findFileForPDBId", +function (idOrFile) { +var id = this.pdbIdFileName.get (idOrFile); +return id; +}, "~S"); +Clazz.defineMethod (c$, "isPDBFileRegistered", +function (idOrFile) { +return this.pdbFileNameId.containsKey (idOrFile) || this.pdbIdFileName.containsKey (idOrFile); +}, "~S"); +c$.getStructureSelectionManager = Clazz.defineMethod (c$, "getStructureSelectionManager", +function (context) { +if (context == null) { +if (jalview.structure.StructureSelectionManager.nullProvider == null) { +if (jalview.structure.StructureSelectionManager.instances != null) { +throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_structure_selection_manager_null"), new NullPointerException (jalview.util.MessageManager.getString ("exception.ssm_context_is_null"))); +} else { +jalview.structure.StructureSelectionManager.nullProvider = new jalview.structure.StructureSelectionManager (); +}return jalview.structure.StructureSelectionManager.nullProvider; +}}if (jalview.structure.StructureSelectionManager.instances == null) { +jalview.structure.StructureSelectionManager.instances = new java.util.IdentityHashMap (); +}var instance = jalview.structure.StructureSelectionManager.instances.get (context); +if (instance == null) { +if (jalview.structure.StructureSelectionManager.nullProvider != null) { +instance = jalview.structure.StructureSelectionManager.nullProvider; +} else { +instance = new jalview.structure.StructureSelectionManager (); +}jalview.structure.StructureSelectionManager.instances.put (context, instance); +}return instance; +}, "jalview.api.StructureSelectionManagerProvider"); +Clazz.defineMethod (c$, "setRelaySeqMappings", +function (relay) { +this.relaySeqMappings = relay; +}, "~B"); +Clazz.defineMethod (c$, "isRelaySeqMappingsEnabled", +function () { +return this.relaySeqMappings; +}); +Clazz.defineMethod (c$, "addStructureViewerListener", +function (svl) { +if (!this.listeners.contains (svl)) { +this.listeners.addElement (svl); +}}, "~O"); +Clazz.defineMethod (c$, "alreadyMappedToFile", +function (pdbid) { +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +if (sm.getPdbId ().equals (pdbid)) { +return sm.pdbfile; +}} +return null; +}, "~S"); +Clazz.defineMethod (c$, "setMapping", +function (sequence, targetChains, pdbFile, protocol) { +return this.setMapping (true, sequence, targetChains, pdbFile, protocol); +}, "~A,~A,~S,~S"); +Clazz.defineMethod (c$, "setMapping", +function (forStructureView, sequence, targetChains, pdbFile, protocol) { +var parseSecStr = this.processSecondaryStructure; +if (this.isPDBFileRegistered (pdbFile)) { +for (var sq, $sq = 0, $$sq = sequence; $sq < $$sq.length && ((sq = $$sq[$sq]) || true); $sq++) { +var ds = sq; +while (ds.getDatasetSequence () != null) { +ds = ds.getDatasetSequence (); +} +;if (ds.getAnnotation () != null) { +for (var ala, $ala = 0, $$ala = ds.getAnnotation (); $ala < $$ala.length && ((ala = $$ala[$ala]) || true); $ala++) { +if (MCview.PDBfile.isCalcIdForFile (ala, this.findIdForPDBFile (pdbFile))) { +parseSecStr = false; +}} +}} +}var pdb = null; +try { +pdb = new MCview.PDBfile (this.addTempFacAnnot, parseSecStr, this.secStructServices, pdbFile, protocol); +if (pdb.id != null && pdb.id.trim ().length > 0 && jalview.io.AppletFormatAdapter.FILE.equals (protocol)) { +this.registerPDBFile (pdb.id.trim (), pdbFile); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +return null; +} else { +throw ex; +} +} +var targetChain; +for (var s = 0; s < sequence.length; s++) { +var infChain = true; +var seq = sequence[s]; +if (targetChains != null && targetChains[s] != null) { +infChain = false; +targetChain = targetChains[s]; +} else if (seq.getName ().indexOf ("|") > -1) { +targetChain = seq.getName ().substring (seq.getName ().lastIndexOf ("|") + 1); +if (targetChain.length > 1) { +if (targetChain.trim ().length == 0) { +targetChain = " "; +} else { +targetChain = ""; +}}} else { +targetChain = ""; +}var max = -10; +var maxAlignseq = null; +var maxChainId = " "; +var maxChain = null; +var first = true; +for (var chain, $chain = pdb.chains.iterator (); $chain.hasNext () && ((chain = $chain.next ()) || true);) { +if (targetChain.length > 0 && !targetChain.equals (chain.id) && !infChain) { +continue; +}var type = chain.isNa ? "dna" : "pep"; +var as = jalview.analysis.AlignSeq.doGlobalNWAlignment (seq, chain.sequence, type); +if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals (targetChain))) { +first = false; +maxChain = chain; +max = as.maxscore; +maxAlignseq = as; +maxChainId = chain.id; +}} +if (maxChain == null) { +continue; +}var mappingDetails = new StringBuilder (128); +mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("PDB Sequence is :").append (jalview.structure.StructureSelectionManager.NEWLINE).append ("Sequence = ").append (maxChain.sequence.getSequenceAsString ()); +mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("No of residues = ").append (maxChain.residues.size ()).append (jalview.structure.StructureSelectionManager.NEWLINE).append (jalview.structure.StructureSelectionManager.NEWLINE); +var ps = ((Clazz.isClassDefined ("jalview.structure.StructureSelectionManager$1") ? 0 : jalview.structure.StructureSelectionManager.$StructureSelectionManager$1$ ()), Clazz.innerTypeInstance (jalview.structure.StructureSelectionManager$1, this, Clazz.cloneFinals ("mappingDetails", mappingDetails), System.out)); +maxAlignseq.printAlignment (ps); +mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("PDB start/end "); +mappingDetails.append (String.valueOf (maxAlignseq.seq2start)).append (" "); +mappingDetails.append (String.valueOf (maxAlignseq.seq2end)); +mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("SEQ start/end "); +mappingDetails.append (String.valueOf (maxAlignseq.seq1start + seq.getStart () - 1)).append (" "); +mappingDetails.append (String.valueOf (maxAlignseq.seq1end + seq.getEnd () - 1)); +maxChain.makeExactMapping (maxAlignseq, seq); +var sqmpping = maxAlignseq.getMappingFromS1 (false); +var omap = new jalview.datamodel.Mapping (sqmpping.getMap ().getInverse ()); +maxChain.transferRESNUMFeatures (seq, null); +var mapping = Clazz.newIntArray (seq.findPosition (seq.getLength ()) + 2, 2, 0); +var resNum = -10000; +var index = 0; +do { +var tmp = maxChain.atoms.elementAt (index); +if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) { +resNum = tmp.resNumber; +mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; +mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; +}index++; +} while (index < maxChain.atoms.size ()); +if (protocol.equals (jalview.io.AppletFormatAdapter.PASTE)) { +pdbFile = "INLINE" + pdb.id; +}var newMapping = new jalview.structure.StructureMapping (seq, pdbFile, pdb.id, maxChainId, mapping, mappingDetails.toString ()); +if (forStructureView) { +this.mappings.add (newMapping); +}maxChain.transferResidueAnnotation (newMapping, sqmpping); +} +return pdb; +}, "~B,~A,~A,~S,~S"); +Clazz.defineMethod (c$, "removeStructureViewerListener", +function (svl, pdbfiles) { +this.listeners.removeElement (svl); +if (Clazz.instanceOf (svl, jalview.structure.SequenceListener)) { +for (var i = 0; i < this.listeners.size (); i++) { +if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) { +(this.listeners.elementAt (i)).releaseReferences (svl); +}} +}if (pdbfiles == null) { +return; +}var pdbs = new java.util.ArrayList (java.util.Arrays.asList (pdbfiles)); +var sl; +for (var i = 0; i < this.listeners.size (); i++) { +if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) { +sl = this.listeners.elementAt (i); +for (var pdbfile, $pdbfile = 0, $$pdbfile = sl.getPdbFile (); $pdbfile < $$pdbfile.length && ((pdbfile = $$pdbfile[$pdbfile]) || true); $pdbfile++) { +pdbs.remove (pdbfile); +} +}} +if (pdbs.size () > 0) { +var tmp = new java.util.ArrayList (); +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +if (!pdbs.contains (sm.pdbfile)) { +tmp.add (sm); +}} +this.mappings = tmp; +}}, "~O,~A"); +Clazz.defineMethod (c$, "mouseOverStructure", +function (pdbResNum, chain, pdbfile) { +var atomSpec = new jalview.structure.AtomSpec (pdbfile, chain, pdbResNum, 0); +var atoms = java.util.Collections.singletonList (atomSpec); +this.mouseOverStructure (atoms); +}, "~N,~S,~S"); +Clazz.defineMethod (c$, "mouseOverStructure", +function (atoms) { +if (this.listeners == null) { +return; +}var hasSequenceListener = false; +for (var i = 0; i < this.listeners.size (); i++) { +if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.SequenceListener)) { +hasSequenceListener = true; +}} +if (!hasSequenceListener) { +return; +}var results = new jalview.datamodel.SearchResults (); +for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) { +var lastseq = null; +var lastipos = -1; +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +if (sm.pdbfile.equals (atom.getPdbFile ()) && sm.pdbchain.equals (atom.getChain ())) { +var indexpos = sm.getSeqPos (atom.getPdbResNum ()); +if (lastipos != indexpos && lastseq !== sm.sequence) { +results.addResult (sm.sequence, indexpos, indexpos); +lastipos = indexpos; +lastseq = sm.sequence; +for (var acf, $acf = this.seqmappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +acf.markMappedRegion (sm.sequence, indexpos, results); +} +}}} +} +for (var li, $li = this.listeners.iterator (); $li.hasNext () && ((li = $li.next ()) || true);) { +if (Clazz.instanceOf (li, jalview.structure.SequenceListener)) { +(li).highlightSequence (results); +}} +}, "java.util.List"); +Clazz.defineMethod (c$, "mouseOverSequence", +function (seq, indexpos, index, source) { +var hasSequenceListeners = this.handlingVamsasMo || !this.seqmappings.isEmpty (); +var results = null; +if (index == -1) { +index = seq.findPosition (indexpos); +}for (var i = 0; i < this.listeners.size (); i++) { +var listener = this.listeners.elementAt (i); +if (listener === source) { +continue; +}if (Clazz.instanceOf (listener, jalview.structure.StructureListener)) { +this.highlightStructure (listener, seq, index); +} else { +if (Clazz.instanceOf (listener, jalview.structure.SequenceListener)) { +var seqListener = listener; +if (hasSequenceListeners && seqListener.getVamsasSource () !== source) { +if (this.relaySeqMappings) { +if (results == null) { +results = jalview.util.MappingUtils.buildSearchResults (seq, index, this.seqmappings); +}if (this.handlingVamsasMo) { +results.addResult (seq, index, index); +}seqListener.highlightSequence (results); +}}} else if (Clazz.instanceOf (listener, jalview.structure.VamsasListener) && !this.handlingVamsasMo) { +(listener).mouseOverSequence (seq, indexpos, source); +} else if (Clazz.instanceOf (listener, jalview.structure.SecondaryStructureListener)) { +(listener).mouseOverSequence (seq, indexpos, index); +}}} +}, "jalview.datamodel.SequenceI,~N,~N,jalview.structure.VamsasSource"); +Clazz.defineMethod (c$, "highlightStructure", +function (sl, seq, index) { +if (!sl.isListeningFor (seq)) { +return; +}var atomNo; +var atoms = new java.util.ArrayList (); +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +if (sm.sequence === seq || sm.sequence === seq.getDatasetSequence ()) { +atomNo = sm.getAtomNum (index); +if (atomNo > 0) { +atoms.add ( new jalview.structure.AtomSpec (sm.pdbfile, sm.pdbchain, sm.getPDBResNum (index), atomNo)); +}}} +sl.highlightAtoms (atoms); +}, "jalview.structure.StructureListener,jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "mouseOverVamsasSequence", +function (sequenceI, position, source) { +this.handlingVamsasMo = true; +var msg = sequenceI.hashCode () * (1 + position); +if (this.lastmsg != msg) { +this.lastmsg = msg; +this.mouseOverSequence (sequenceI, position, -1, source); +}this.handlingVamsasMo = false; +}, "jalview.datamodel.SequenceI,~N,jalview.structure.VamsasSource"); +Clazz.defineMethod (c$, "colourSequenceFromStructure", +function (seq, pdbid) { +return null; +}, "jalview.datamodel.SequenceI,~S"); +Clazz.defineMethod (c$, "structureSelectionChanged", +function () { +}); +Clazz.defineMethod (c$, "sequenceSelectionChanged", +function () { +}); +Clazz.defineMethod (c$, "sequenceColoursChanged", +function (source) { +var sl; +for (var i = 0; i < this.listeners.size (); i++) { +if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) { +sl = this.listeners.elementAt (i); +sl.updateColours (source); +}} +}, "~O"); +Clazz.defineMethod (c$, "getMapping", +function (pdbfile) { +var tmp = new java.util.ArrayList (); +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +if (sm.pdbfile.equals (pdbfile)) { +tmp.add (sm); +}} +return tmp.toArray ( new Array (tmp.size ())); +}, "~S"); +Clazz.defineMethod (c$, "printMappings", +function (pdbfile, seqs) { +if (pdbfile == null || seqs == null || seqs.isEmpty ()) { +return ""; +}var sb = new StringBuilder (64); +for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) { +if (sm.pdbfile.equals (pdbfile) && seqs.contains (sm.sequence)) { +sb.append (sm.mappingDetails); +sb.append (jalview.structure.StructureSelectionManager.NEWLINE); +sb.append ("====================="); +sb.append (jalview.structure.StructureSelectionManager.NEWLINE); +}} +sb.append (jalview.structure.StructureSelectionManager.NEWLINE); +return sb.toString (); +}, "~S,java.util.List"); +Clazz.defineMethod (c$, "removeMappings", +function (set) { +if (set != null) { +for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +this.removeMapping (acf); +} +}}, "java.util.Set"); +Clazz.defineMethod (c$, "removeMapping", +function (acf) { +if (acf != null && this.seqmappings.contains (acf)) { +var count = (this.seqMappingRefCounts.get (acf)).intValue (); +count--; +if (count > 0) { +this.seqMappingRefCounts.put (acf, new Integer (count)); +} else { +this.seqmappings.remove (acf); +this.seqMappingRefCounts.remove (acf); +}}}, "jalview.datamodel.AlignedCodonFrame"); +Clazz.defineMethod (c$, "addMappings", +function (set) { +if (set != null) { +for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +this.addMapping (acf); +} +}}, "java.util.Set"); +Clazz.defineMethod (c$, "addMapping", +function (acf) { +if (acf != null) { +if (this.seqmappings.contains (acf)) { +this.seqMappingRefCounts.put (acf, new Integer ((this.seqMappingRefCounts.get (acf)).intValue () + 1)); +} else { +this.seqmappings.add (acf); +this.seqMappingRefCounts.put (acf, new Integer (1)); +}}}, "jalview.datamodel.AlignedCodonFrame"); +Clazz.defineMethod (c$, "addSelectionListener", +function (selecter) { +if (!this.sel_listeners.contains (selecter)) { +this.sel_listeners.add (selecter); +}}, "jalview.structure.SelectionListener"); +Clazz.defineMethod (c$, "removeSelectionListener", +function (toremove) { +if (this.sel_listeners.contains (toremove)) { +this.sel_listeners.remove (toremove); +}}, "jalview.structure.SelectionListener"); +Clazz.defineMethod (c$, "sendSelection", +function (selection, colsel, source) { +for (var slis, $slis = this.sel_listeners.iterator (); $slis.hasNext () && ((slis = $slis.next ()) || true);) { +if (slis !== source) { +slis.selection (selection, colsel, source); +}} +}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource"); +Clazz.defineMethod (c$, "sendViewPosition", +function (source, startRes, endRes, startSeq, endSeq) { +if (this.view_listeners != null && this.view_listeners.size () > 0) { +var listeners = this.view_listeners.elements (); +while (listeners.hasMoreElements ()) { +var slis = listeners.nextElement (); +if (slis !== source) { +slis.viewPosition (startRes, endRes, startSeq, endSeq, source); +};} +}}, "jalview.api.AlignmentViewPanel,~N,~N,~N,~N"); +c$.release = Clazz.defineMethod (c$, "release", +function (jalviewLite) { +{ +if (jalview.structure.StructureSelectionManager.instances == null) { +return; +}var mnger = (jalview.structure.StructureSelectionManager.instances.get (jalviewLite)); +if (mnger != null) { +jalview.structure.StructureSelectionManager.instances.remove (jalviewLite); +try { +mnger.finalize (); +} catch (x) { +} +}}}, "jalview.api.StructureSelectionManagerProvider"); +Clazz.defineMethod (c$, "registerPDBEntry", +function (pdbentry) { +if (pdbentry.getFile () != null && pdbentry.getFile ().trim ().length > 0) { +this.registerPDBFile (pdbentry.getId (), pdbentry.getFile ()); +}}, "jalview.datamodel.PDBEntry"); +Clazz.defineMethod (c$, "addCommandListener", +function (cl) { +if (!this.commandListeners.contains (cl)) { +this.commandListeners.add (cl); +}}, "jalview.structure.CommandListener"); +Clazz.defineMethod (c$, "hasCommandListener", +function (cl) { +return this.commandListeners.contains (cl); +}, "jalview.structure.CommandListener"); +Clazz.defineMethod (c$, "removeCommandListener", +function (l) { +return this.commandListeners.remove (l); +}, "jalview.structure.CommandListener"); +Clazz.defineMethod (c$, "commandPerformed", +function (command, undo, source) { +for (var listener, $listener = this.commandListeners.iterator (); $listener.hasNext () && ((listener = $listener.next ()) || true);) { +listener.mirrorCommand (command, undo, this, source); +} +}, "jalview.commands.CommandI,~B,jalview.structure.VamsasSource"); +Clazz.defineMethod (c$, "mapCommand", +function (command, undo, mapTo, gapChar) { +if (Clazz.instanceOf (command, jalview.commands.EditCommand)) { +return jalview.util.MappingUtils.mapEditCommand (command, undo, mapTo, gapChar, this.seqmappings); +} else if (Clazz.instanceOf (command, jalview.commands.OrderCommand)) { +return jalview.util.MappingUtils.mapOrderCommand (command, undo, mapTo, this.seqmappings); +}return null; +}, "jalview.commands.CommandI,~B,jalview.datamodel.AlignmentI,~S"); +c$.$StructureSelectionManager$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.structure, "StructureSelectionManager$1", java.io.PrintStream); +Clazz.defineMethod (c$, "print", +function (x) { +this.f$.mappingDetails.append (x); +}, "~S"); +Clazz.defineMethod (c$, "println", +function () { +this.f$.mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE); +}); +c$ = Clazz.p0p (); +}; +c$.NEWLINE = c$.prototype.NEWLINE = System.lineSeparator (); +Clazz.defineStatics (c$, +"instances", null, +"nullProvider", null); +}); diff --git a/bin/jalview/structure/VamsasListener.js b/bin/jalview/structure/VamsasListener.js index 4d4fcbc..3e2c764 100644 --- a/bin/jalview/structure/VamsasListener.js +++ b/bin/jalview/structure/VamsasListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "VamsasListener"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "VamsasListener"); diff --git a/bin/jalview/structure/VamsasSource.js b/bin/jalview/structure/VamsasSource.js index a910ac7..6654402 100644 --- a/bin/jalview/structure/VamsasSource.js +++ b/bin/jalview/structure/VamsasSource.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("jalview.structure"); -Clazz.declareInterface (jalview.structure, "VamsasSource"); +Clazz.declarePackage ("jalview.structure"); +Clazz.declareInterface (jalview.structure, "VamsasSource"); diff --git a/bin/jalview/structures/models/AAStructureBindingModel.class b/bin/jalview/structures/models/AAStructureBindingModel.class index 41ab261..db598fb 100644 Binary files a/bin/jalview/structures/models/AAStructureBindingModel.class and b/bin/jalview/structures/models/AAStructureBindingModel.class differ diff --git a/bin/jalview/structures/models/AAStructureBindingModel.js b/bin/jalview/structures/models/AAStructureBindingModel.js index f64bb34..a66cb14 100644 --- a/bin/jalview/structures/models/AAStructureBindingModel.js +++ b/bin/jalview/structures/models/AAStructureBindingModel.js @@ -1,306 +1,306 @@ -Clazz.declarePackage ("jalview.structures.models"); -Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.structure.StructureListener", "jalview.structures.models.SequenceStructureBindingModel"], "jalview.structures.models.AAStructureBindingModel", ["jalview.util.Comparison", "$.MessageManager", "java.lang.Error", "$.StringBuilder", "java.util.ArrayList", "$.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ssm = null; -this.pdbEntry = null; -this.sequence = null; -this.chains = null; -this.protocol = null; -this.colourBySequence = true; -this.nucleotide = false; -if (!Clazz.isClassDefined ("jalview.structures.models.AAStructureBindingModel.SuperposeData")) { -jalview.structures.models.AAStructureBindingModel.$AAStructureBindingModel$SuperposeData$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.structures.models, "AAStructureBindingModel", jalview.structures.models.SequenceStructureBindingModel, [jalview.structure.StructureListener, jalview.api.StructureSelectionManagerProvider]); -Clazz.makeConstructor (c$, -function (ssm, seqs) { -Clazz.superConstructor (this, jalview.structures.models.AAStructureBindingModel, []); -this.ssm = ssm; -this.sequence = seqs; -}, "jalview.structure.StructureSelectionManager,~A"); -Clazz.makeConstructor (c$, -function (ssm, pdbentry, sequenceIs, chains, protocol) { -Clazz.superConstructor (this, jalview.structures.models.AAStructureBindingModel, []); -this.ssm = ssm; -this.sequence = sequenceIs; -this.nucleotide = jalview.util.Comparison.isNucleotide2 (sequenceIs); -this.chains = chains; -this.pdbEntry = pdbentry; -this.protocol = protocol; -if (chains == null) { -this.chains = new Array (pdbentry.length); -}}, "jalview.structure.StructureSelectionManager,~A,~A,~A,~S"); -Clazz.defineMethod (c$, "getSsm", -function () { -return this.ssm; -}); -Clazz.defineMethod (c$, "getPdbEntry", -function (i) { -return (this.pdbEntry != null && this.pdbEntry.length > i) ? this.pdbEntry[i] : null; -}, "~N"); -Clazz.defineMethod (c$, "hasPdbId", -function (pdbId) { -if (this.pdbEntry != null) { -for (var pdb, $pdb = 0, $$pdb = this.pdbEntry; $pdb < $$pdb.length && ((pdb = $$pdb[$pdb]) || true); $pdb++) { -if (pdb.getId ().equals (pdbId)) { -return true; -}} -}return false; -}, "~S"); -Clazz.defineMethod (c$, "getPdbCount", -function () { -return this.pdbEntry == null ? 0 : this.pdbEntry.length; -}); -Clazz.defineMethod (c$, "getSequence", -function () { -return this.sequence; -}); -Clazz.defineMethod (c$, "getChains", -function () { -return this.chains; -}); -Clazz.defineMethod (c$, "getProtocol", -function () { -return this.protocol; -}); -Clazz.defineMethod (c$, "setPdbentry", -function (pdbentry) { -this.pdbEntry = pdbentry; -}, "~A"); -Clazz.defineMethod (c$, "setSequence", -function (sequence) { -this.sequence = sequence; -}, "~A"); -Clazz.defineMethod (c$, "setChains", -function (chains) { -this.chains = chains; -}, "~A"); -Clazz.defineMethod (c$, "getViewerTitle", -function (viewerName, verbose) { -if (this.getSequence () == null || this.getSequence ().length < 1 || this.getPdbCount () < 1 || this.getSequence ()[0].length < 1) { -return ("Jalview " + viewerName + " Window"); -}var title = new StringBuilder (64); -var pdbEntry = this.getPdbEntry (0); -title.append (viewerName + " view for " + this.getSequence ()[0][0].getName () + ":" + pdbEntry.getId ()); -if (verbose) { -if (pdbEntry.getProperty () != null) { -if (pdbEntry.getProperty ().get ("method") != null) { -title.append (" Method: "); -title.append (pdbEntry.getProperty ().get ("method")); -}if (pdbEntry.getProperty ().get ("chains") != null) { -title.append (" Chain:"); -title.append (pdbEntry.getProperty ().get ("chains")); -}}}return title.toString (); -}, "~S,~B"); -Clazz.defineMethod (c$, "releaseUIResources", -function () { -}); -Clazz.defineMethod (c$, "isColourBySequence", -function () { -return this.colourBySequence; -}); -Clazz.defineMethod (c$, "setColourBySequence", -function (colourBySequence) { -this.colourBySequence = colourBySequence; -}, "~B"); -Clazz.defineMethod (c$, "addSequenceAndChain", -function (pe, seq, tchain) { -if (pe < 0 || pe >= this.getPdbCount ()) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_no_pdbentry_from_index", Clazz.newArray (-1, [Integer.$valueOf (pe).toString ()]))); -}var nullChain = "TheNullChain"; -var s = new java.util.ArrayList (); -var c = new java.util.ArrayList (); -if (this.getChains () == null) { -this.setChains ( new Array (this.getPdbCount ())); -}if (this.getSequence ()[pe] != null) { -for (var i = 0; i < this.getSequence ()[pe].length; i++) { -s.add (this.getSequence ()[pe][i]); -if (this.getChains ()[pe] != null) { -if (i < this.getChains ()[pe].length) { -c.add (this.getChains ()[pe][i]); -} else { -c.add ("TheNullChain"); -}} else { -if (tchain != null && tchain.length > 0) { -c.add ("TheNullChain"); -}}} -}for (var i = 0; i < seq.length; i++) { -if (!s.contains (seq[i])) { -s.add (seq[i]); -if (tchain != null && i < tchain.length) { -c.add (tchain[i] == null ? "TheNullChain" : tchain[i]); -}}} -var tmp = s.toArray ( new Array (s.size ())); -this.getSequence ()[pe] = tmp; -if (c.size () > 0) { -var tch = c.toArray ( new Array (c.size ())); -for (var i = 0; i < tch.length; i++) { -if (tch[i] === "TheNullChain") { -tch[i] = null; -}} -this.getChains ()[pe] = tch; -} else { -this.getChains ()[pe] = null; -}}, "~N,~A,~A"); -Clazz.defineMethod (c$, "addSequenceAndChain", -function (pdbe, seq, chns) { -var v = new java.util.ArrayList (); -var rtn = new java.util.ArrayList (); -for (var i = 0; i < this.getPdbCount (); i++) { -v.add (this.getPdbEntry (i)); -} -for (var i = 0; i < pdbe.length; i++) { -var r = v.indexOf (pdbe[i]); -if (r == -1 || r >= this.getPdbCount ()) { -rtn.add ( Clazz.newIntArray (-1, [v.size (), i])); -v.add (pdbe[i]); -} else { -this.addSequenceAndChain (r, seq[i], chns[i]); -}} -pdbe = v.toArray ( new Array (v.size ())); -this.setPdbentry (pdbe); -if (rtn.size () > 0) { -var sqs = new Array (this.getPdbCount ()); -var sch = new Array (this.getPdbCount ()); -System.arraycopy (this.getSequence (), 0, sqs, 0, this.getSequence ().length); -System.arraycopy (this.getChains (), 0, sch, 0, this.getChains ().length); -this.setSequence (sqs); -this.setChains (sch); -pdbe = new Array (rtn.size ()); -for (var r = 0; r < pdbe.length; r++) { -var stri = (rtn.get (r)); -pdbe[r] = this.getPdbEntry (stri[0]); -this.addSequenceAndChain (stri[0], seq[stri[1]], chns[stri[1]]); -} -} else { -pdbe = null; -}return pdbe; -}, "~A,~A,~A"); -Clazz.defineMethod (c$, "addSequence", -function (pe, seq) { -this.addSequenceAndChain (pe, seq, null); -}, "~N,~A"); -Clazz.defineMethod (c$, "addSequenceForStructFile", -function (pdbFile, seq) { -for (var pe = 0; pe < this.getPdbCount (); pe++) { -if (this.getPdbEntry (pe).getFile ().equals (pdbFile)) { -this.addSequence (pe, seq); -}} -}, "~S,~A"); -Clazz.defineMethod (c$, "isNucleotide", -function () { -return this.nucleotide; -}); -Clazz.defineMethod (c$, "printMappings", -function () { -if (this.pdbEntry == null) { -return ""; -}var sb = new StringBuilder (128); -for (var pdbe = 0; pdbe < this.getPdbCount (); pdbe++) { -var pdbfile = this.getPdbEntry (pdbe).getFile (); -var seqs = java.util.Arrays.asList (this.getSequence ()[pdbe]); -sb.append (this.getSsm ().printMappings (pdbfile, seqs)); -} -return sb.toString (); -}); -Clazz.defineMethod (c$, "getMappedPosition", -function (seq, alignedPos, mapping) { -if (alignedPos >= seq.getLength ()) { -return -1; -}if (jalview.util.Comparison.isGap (seq.getCharAt (alignedPos))) { -return -1; -}var seqPos = seq.findPosition (alignedPos); -var pos = mapping.getPDBResNum (seqPos); -return pos; -}, "jalview.datamodel.SequenceI,~N,jalview.structure.StructureMapping"); -Clazz.defineMethod (c$, "findSuperposableResidues", -function (alignment, matched, structures) { -var refStructure = -1; -var files = this.getPdbFile (); -for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { -var mappings = this.getSsm ().getMapping (files[pdbfnum]); -var lastPos = -1; -var seqCountForPdbFile = this.getSequence ()[pdbfnum].length; -for (var s = 0; s < seqCountForPdbFile; s++) { -for (var mapping, $mapping = 0, $$mapping = mappings; $mapping < $$mapping.length && ((mapping = $$mapping[$mapping]) || true); $mapping++) { -var theSequence = this.getSequence ()[pdbfnum][s]; -if (mapping.getSequence () === theSequence && alignment.findIndex (theSequence) > -1) { -if (refStructure < 0) { -refStructure = pdbfnum; -}for (var r = 0; r < matched.length; r++) { -if (!matched[r]) { -continue; -}var pos = this.getMappedPosition (theSequence, r, mapping); -if (pos < 1 || pos == lastPos) { -matched[r] = false; -continue; -}lastPos = pos; -structures[pdbfnum].pdbResNo[r] = pos; -} -var chain = mapping.getChain (); -if (chain != null && chain.trim ().length > 0) { -structures[pdbfnum].chain = chain; -}structures[pdbfnum].pdbId = mapping.getPdbId (); -structures[pdbfnum].isRna = theSequence.getRNA () != null; -s = seqCountForPdbFile; -break; -}} -} -} -return refStructure; -}, "jalview.datamodel.AlignmentI,~A,~A"); -Clazz.defineMethod (c$, "waitForFileLoad", -function (files) { -var starttime = System.currentTimeMillis (); -var endTime = 10000 + 1000 * files.length + starttime; -var notLoaded = null; -var waiting = true; -while (waiting && System.currentTimeMillis () < endTime) { -waiting = false; -for (var file, $file = 0, $$file = files; $file < $$file.length && ((file = $$file[$file]) || true); $file++) { -notLoaded = file; -try { -var sm = this.getSsm ().getMapping (file); -if (sm == null || sm.length == 0) { -waiting = true; -}} catch (x) { -waiting = true; -} -} -} -if (waiting) { -System.err.println ("Timed out waiting for structure viewer to load file " + notLoaded); -return false; -}return true; -}, "~A"); -Clazz.overrideMethod (c$, "isListeningFor", -function (seq) { -if (this.sequence != null) { -for (var seqs, $seqs = 0, $$seqs = this.sequence; $seqs < $$seqs.length && ((seqs = $$seqs[$seqs]) || true); $seqs++) { -if (seqs != null) { -for (var s, $s = 0, $$s = seqs; $s < $$s.length && ((s = $$s[$s]) || true); $s++) { -if (s === seq) { -return true; -}} -}} -}return false; -}, "jalview.datamodel.SequenceI"); -c$.$AAStructureBindingModel$SuperposeData$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.filename = null; -this.pdbId = null; -this.chain = ""; -this.isRna = false; -this.pdbResNo = null; -Clazz.instantialize (this, arguments); -}, jalview.structures.models.AAStructureBindingModel, "SuperposeData"); -Clazz.makeConstructor (c$, -function (a) { -this.pdbResNo = Clazz.newIntArray (a, 0); -}, "~N"); -c$ = Clazz.p0p (); -}; -}); +Clazz.declarePackage ("jalview.structures.models"); +Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.structure.StructureListener", "jalview.structures.models.SequenceStructureBindingModel"], "jalview.structures.models.AAStructureBindingModel", ["jalview.util.Comparison", "$.MessageManager", "java.lang.Error", "$.StringBuilder", "java.util.ArrayList", "$.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ssm = null; +this.pdbEntry = null; +this.sequence = null; +this.chains = null; +this.protocol = null; +this.colourBySequence = true; +this.nucleotide = false; +if (!Clazz.isClassDefined ("jalview.structures.models.AAStructureBindingModel.SuperposeData")) { +jalview.structures.models.AAStructureBindingModel.$AAStructureBindingModel$SuperposeData$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.structures.models, "AAStructureBindingModel", jalview.structures.models.SequenceStructureBindingModel, [jalview.structure.StructureListener, jalview.api.StructureSelectionManagerProvider]); +Clazz.makeConstructor (c$, +function (ssm, seqs) { +Clazz.superConstructor (this, jalview.structures.models.AAStructureBindingModel, []); +this.ssm = ssm; +this.sequence = seqs; +}, "jalview.structure.StructureSelectionManager,~A"); +Clazz.makeConstructor (c$, +function (ssm, pdbentry, sequenceIs, chains, protocol) { +Clazz.superConstructor (this, jalview.structures.models.AAStructureBindingModel, []); +this.ssm = ssm; +this.sequence = sequenceIs; +this.nucleotide = jalview.util.Comparison.isNucleotide2 (sequenceIs); +this.chains = chains; +this.pdbEntry = pdbentry; +this.protocol = protocol; +if (chains == null) { +this.chains = new Array (pdbentry.length); +}}, "jalview.structure.StructureSelectionManager,~A,~A,~A,~S"); +Clazz.defineMethod (c$, "getSsm", +function () { +return this.ssm; +}); +Clazz.defineMethod (c$, "getPdbEntry", +function (i) { +return (this.pdbEntry != null && this.pdbEntry.length > i) ? this.pdbEntry[i] : null; +}, "~N"); +Clazz.defineMethod (c$, "hasPdbId", +function (pdbId) { +if (this.pdbEntry != null) { +for (var pdb, $pdb = 0, $$pdb = this.pdbEntry; $pdb < $$pdb.length && ((pdb = $$pdb[$pdb]) || true); $pdb++) { +if (pdb.getId ().equals (pdbId)) { +return true; +}} +}return false; +}, "~S"); +Clazz.defineMethod (c$, "getPdbCount", +function () { +return this.pdbEntry == null ? 0 : this.pdbEntry.length; +}); +Clazz.defineMethod (c$, "getSequence", +function () { +return this.sequence; +}); +Clazz.defineMethod (c$, "getChains", +function () { +return this.chains; +}); +Clazz.defineMethod (c$, "getProtocol", +function () { +return this.protocol; +}); +Clazz.defineMethod (c$, "setPdbentry", +function (pdbentry) { +this.pdbEntry = pdbentry; +}, "~A"); +Clazz.defineMethod (c$, "setSequence", +function (sequence) { +this.sequence = sequence; +}, "~A"); +Clazz.defineMethod (c$, "setChains", +function (chains) { +this.chains = chains; +}, "~A"); +Clazz.defineMethod (c$, "getViewerTitle", +function (viewerName, verbose) { +if (this.getSequence () == null || this.getSequence ().length < 1 || this.getPdbCount () < 1 || this.getSequence ()[0].length < 1) { +return ("Jalview " + viewerName + " Window"); +}var title = new StringBuilder (64); +var pdbEntry = this.getPdbEntry (0); +title.append (viewerName + " view for " + this.getSequence ()[0][0].getName () + ":" + pdbEntry.getId ()); +if (verbose) { +if (pdbEntry.getProperty () != null) { +if (pdbEntry.getProperty ().get ("method") != null) { +title.append (" Method: "); +title.append (pdbEntry.getProperty ().get ("method")); +}if (pdbEntry.getProperty ().get ("chains") != null) { +title.append (" Chain:"); +title.append (pdbEntry.getProperty ().get ("chains")); +}}}return title.toString (); +}, "~S,~B"); +Clazz.defineMethod (c$, "releaseUIResources", +function () { +}); +Clazz.defineMethod (c$, "isColourBySequence", +function () { +return this.colourBySequence; +}); +Clazz.defineMethod (c$, "setColourBySequence", +function (colourBySequence) { +this.colourBySequence = colourBySequence; +}, "~B"); +Clazz.defineMethod (c$, "addSequenceAndChain", +function (pe, seq, tchain) { +if (pe < 0 || pe >= this.getPdbCount ()) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_no_pdbentry_from_index", Clazz.newArray (-1, [Integer.$valueOf (pe).toString ()]))); +}var nullChain = "TheNullChain"; +var s = new java.util.ArrayList (); +var c = new java.util.ArrayList (); +if (this.getChains () == null) { +this.setChains ( new Array (this.getPdbCount ())); +}if (this.getSequence ()[pe] != null) { +for (var i = 0; i < this.getSequence ()[pe].length; i++) { +s.add (this.getSequence ()[pe][i]); +if (this.getChains ()[pe] != null) { +if (i < this.getChains ()[pe].length) { +c.add (this.getChains ()[pe][i]); +} else { +c.add ("TheNullChain"); +}} else { +if (tchain != null && tchain.length > 0) { +c.add ("TheNullChain"); +}}} +}for (var i = 0; i < seq.length; i++) { +if (!s.contains (seq[i])) { +s.add (seq[i]); +if (tchain != null && i < tchain.length) { +c.add (tchain[i] == null ? "TheNullChain" : tchain[i]); +}}} +var tmp = s.toArray ( new Array (s.size ())); +this.getSequence ()[pe] = tmp; +if (c.size () > 0) { +var tch = c.toArray ( new Array (c.size ())); +for (var i = 0; i < tch.length; i++) { +if (tch[i] === "TheNullChain") { +tch[i] = null; +}} +this.getChains ()[pe] = tch; +} else { +this.getChains ()[pe] = null; +}}, "~N,~A,~A"); +Clazz.defineMethod (c$, "addSequenceAndChain", +function (pdbe, seq, chns) { +var v = new java.util.ArrayList (); +var rtn = new java.util.ArrayList (); +for (var i = 0; i < this.getPdbCount (); i++) { +v.add (this.getPdbEntry (i)); +} +for (var i = 0; i < pdbe.length; i++) { +var r = v.indexOf (pdbe[i]); +if (r == -1 || r >= this.getPdbCount ()) { +rtn.add ( Clazz.newIntArray (-1, [v.size (), i])); +v.add (pdbe[i]); +} else { +this.addSequenceAndChain (r, seq[i], chns[i]); +}} +pdbe = v.toArray ( new Array (v.size ())); +this.setPdbentry (pdbe); +if (rtn.size () > 0) { +var sqs = new Array (this.getPdbCount ()); +var sch = new Array (this.getPdbCount ()); +System.arraycopy (this.getSequence (), 0, sqs, 0, this.getSequence ().length); +System.arraycopy (this.getChains (), 0, sch, 0, this.getChains ().length); +this.setSequence (sqs); +this.setChains (sch); +pdbe = new Array (rtn.size ()); +for (var r = 0; r < pdbe.length; r++) { +var stri = (rtn.get (r)); +pdbe[r] = this.getPdbEntry (stri[0]); +this.addSequenceAndChain (stri[0], seq[stri[1]], chns[stri[1]]); +} +} else { +pdbe = null; +}return pdbe; +}, "~A,~A,~A"); +Clazz.defineMethod (c$, "addSequence", +function (pe, seq) { +this.addSequenceAndChain (pe, seq, null); +}, "~N,~A"); +Clazz.defineMethod (c$, "addSequenceForStructFile", +function (pdbFile, seq) { +for (var pe = 0; pe < this.getPdbCount (); pe++) { +if (this.getPdbEntry (pe).getFile ().equals (pdbFile)) { +this.addSequence (pe, seq); +}} +}, "~S,~A"); +Clazz.defineMethod (c$, "isNucleotide", +function () { +return this.nucleotide; +}); +Clazz.defineMethod (c$, "printMappings", +function () { +if (this.pdbEntry == null) { +return ""; +}var sb = new StringBuilder (128); +for (var pdbe = 0; pdbe < this.getPdbCount (); pdbe++) { +var pdbfile = this.getPdbEntry (pdbe).getFile (); +var seqs = java.util.Arrays.asList (this.getSequence ()[pdbe]); +sb.append (this.getSsm ().printMappings (pdbfile, seqs)); +} +return sb.toString (); +}); +Clazz.defineMethod (c$, "getMappedPosition", +function (seq, alignedPos, mapping) { +if (alignedPos >= seq.getLength ()) { +return -1; +}if (jalview.util.Comparison.isGap (seq.getCharAt (alignedPos))) { +return -1; +}var seqPos = seq.findPosition (alignedPos); +var pos = mapping.getPDBResNum (seqPos); +return pos; +}, "jalview.datamodel.SequenceI,~N,jalview.structure.StructureMapping"); +Clazz.defineMethod (c$, "findSuperposableResidues", +function (alignment, matched, structures) { +var refStructure = -1; +var files = this.getPdbFile (); +for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { +var mappings = this.getSsm ().getMapping (files[pdbfnum]); +var lastPos = -1; +var seqCountForPdbFile = this.getSequence ()[pdbfnum].length; +for (var s = 0; s < seqCountForPdbFile; s++) { +for (var mapping, $mapping = 0, $$mapping = mappings; $mapping < $$mapping.length && ((mapping = $$mapping[$mapping]) || true); $mapping++) { +var theSequence = this.getSequence ()[pdbfnum][s]; +if (mapping.getSequence () === theSequence && alignment.findIndex (theSequence) > -1) { +if (refStructure < 0) { +refStructure = pdbfnum; +}for (var r = 0; r < matched.length; r++) { +if (!matched[r]) { +continue; +}var pos = this.getMappedPosition (theSequence, r, mapping); +if (pos < 1 || pos == lastPos) { +matched[r] = false; +continue; +}lastPos = pos; +structures[pdbfnum].pdbResNo[r] = pos; +} +var chain = mapping.getChain (); +if (chain != null && chain.trim ().length > 0) { +structures[pdbfnum].chain = chain; +}structures[pdbfnum].pdbId = mapping.getPdbId (); +structures[pdbfnum].isRna = theSequence.getRNA () != null; +s = seqCountForPdbFile; +break; +}} +} +} +return refStructure; +}, "jalview.datamodel.AlignmentI,~A,~A"); +Clazz.defineMethod (c$, "waitForFileLoad", +function (files) { +var starttime = System.currentTimeMillis (); +var endTime = 10000 + 1000 * files.length + starttime; +var notLoaded = null; +var waiting = true; +while (waiting && System.currentTimeMillis () < endTime) { +waiting = false; +for (var file, $file = 0, $$file = files; $file < $$file.length && ((file = $$file[$file]) || true); $file++) { +notLoaded = file; +try { +var sm = this.getSsm ().getMapping (file); +if (sm == null || sm.length == 0) { +waiting = true; +}} catch (x) { +waiting = true; +} +} +} +if (waiting) { +System.err.println ("Timed out waiting for structure viewer to load file " + notLoaded); +return false; +}return true; +}, "~A"); +Clazz.overrideMethod (c$, "isListeningFor", +function (seq) { +if (this.sequence != null) { +for (var seqs, $seqs = 0, $$seqs = this.sequence; $seqs < $$seqs.length && ((seqs = $$seqs[$seqs]) || true); $seqs++) { +if (seqs != null) { +for (var s, $s = 0, $$s = seqs; $s < $$s.length && ((s = $$s[$s]) || true); $s++) { +if (s === seq) { +return true; +}} +}} +}return false; +}, "jalview.datamodel.SequenceI"); +c$.$AAStructureBindingModel$SuperposeData$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.filename = null; +this.pdbId = null; +this.chain = ""; +this.isRna = false; +this.pdbResNo = null; +Clazz.instantialize (this, arguments); +}, jalview.structures.models.AAStructureBindingModel, "SuperposeData"); +Clazz.makeConstructor (c$, +function (a) { +this.pdbResNo = Clazz.newIntArray (a, 0); +}, "~N"); +c$ = Clazz.p0p (); +}; +}); diff --git a/bin/jalview/structures/models/SequenceStructureBindingModel.js b/bin/jalview/structures/models/SequenceStructureBindingModel.js index 98e8875..f9d2e7a 100644 --- a/bin/jalview/structures/models/SequenceStructureBindingModel.js +++ b/bin/jalview/structures/models/SequenceStructureBindingModel.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("jalview.structures.models"); -Clazz.load (["jalview.api.SequenceStructureBinding"], "jalview.structures.models.SequenceStructureBindingModel", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.loadingFromArchive = false; -this.loadingFinished = true; -Clazz.instantialize (this, arguments); -}, jalview.structures.models, "SequenceStructureBindingModel", null, jalview.api.SequenceStructureBinding); -Clazz.overrideMethod (c$, "setLoadingFromArchive", -function (loadingFromArchive) { -this.loadingFromArchive = loadingFromArchive; -}, "~B"); -Clazz.overrideMethod (c$, "isLoadingFromArchive", -function () { -return this.loadingFromArchive && !this.loadingFinished; -}); -Clazz.overrideMethod (c$, "isLoadingFinished", -function () { -return this.loadingFinished; -}); -Clazz.overrideMethod (c$, "setFinishedLoadingFromArchive", -function (finishedLoading) { -this.loadingFinished = finishedLoading; -}, "~B"); -}); +Clazz.declarePackage ("jalview.structures.models"); +Clazz.load (["jalview.api.SequenceStructureBinding"], "jalview.structures.models.SequenceStructureBindingModel", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.loadingFromArchive = false; +this.loadingFinished = true; +Clazz.instantialize (this, arguments); +}, jalview.structures.models, "SequenceStructureBindingModel", null, jalview.api.SequenceStructureBinding); +Clazz.overrideMethod (c$, "setLoadingFromArchive", +function (loadingFromArchive) { +this.loadingFromArchive = loadingFromArchive; +}, "~B"); +Clazz.overrideMethod (c$, "isLoadingFromArchive", +function () { +return this.loadingFromArchive && !this.loadingFinished; +}); +Clazz.overrideMethod (c$, "isLoadingFinished", +function () { +return this.loadingFinished; +}); +Clazz.overrideMethod (c$, "setFinishedLoadingFromArchive", +function (finishedLoading) { +this.loadingFinished = finishedLoading; +}, "~B"); +}); diff --git a/bin/jalview/util/AWTConsole.js b/bin/jalview/util/AWTConsole.js deleted file mode 100644 index d03b9fa..0000000 --- a/bin/jalview/util/AWTConsole.js +++ /dev/null @@ -1,187 +0,0 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.awt.event.ActionListener", "$.WindowAdapter", "$.WindowListener", "java.io.PipedInputStream"], "jalview.util.AWTConsole", ["jalview.util.MessageManager", "java.awt.BorderLayout", "$.Button", "$.Dimension", "$.Frame", "$.GraphicsEnvironment", "$.Panel", "$.TextArea", "$.Toolkit", "java.io.PipedOutputStream", "java.lang.NullPointerException", "$.Thread"], function () { -c$ = Clazz.decorateAsClass (function () { -this.frame = null; -this.textArea = null; -this.reader = null; -this.reader2 = null; -this.quit = false; -this.pin = null; -this.pin2 = null; -this.errorThrower = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "AWTConsole", java.awt.event.WindowAdapter, [java.awt.event.WindowListener, java.awt.event.ActionListener, Runnable]); -Clazz.prepareFields (c$, function () { -this.pin = new java.io.PipedInputStream (); -this.pin2 = new java.io.PipedInputStream (); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.util.AWTConsole, []); -this.frame = new java.awt.Frame ("Java Console"); -var screenSize = java.awt.Toolkit.getDefaultToolkit ().getScreenSize (); -var frameSize = new java.awt.Dimension ((Clazz.doubleToInt (screenSize.width / 2)), (Clazz.doubleToInt (screenSize.height / 2))); -var x = (Clazz.doubleToInt (frameSize.width / 2)); -var y = (Clazz.doubleToInt (frameSize.height / 2)); -this.frame.setBounds (x, y, frameSize.width, frameSize.height); -this.textArea = new java.awt.TextArea (); -this.textArea.setEditable (false); -var button = new java.awt.Button ("clear"); -var panel = new java.awt.Panel (); -panel.setLayout ( new java.awt.BorderLayout ()); -panel.add (this.textArea, "Center"); -panel.add (button, "South"); -this.frame.add (panel); -this.frame.setVisible (true); -this.frame.addWindowListener (this); -button.addActionListener (this); -try { -var pout = new java.io.PipedOutputStream (this.pin); -System.setOut ( new java.io.PrintStream (pout, true)); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, java.io.IOException)) { -var io = e$$; -{ -this.textArea.append ("Couldn't redirect STDOUT to this console\n" + io.getMessage ()); -} -} else if (Clazz.exceptionOf (e$$, SecurityException)) { -var se = e$$; -{ -this.textArea.append ("Couldn't redirect STDOUT to this console\n" + se.getMessage ()); -} -} else { -throw e$$; -} -} -try { -var pout2 = new java.io.PipedOutputStream (this.pin2); -System.setErr ( new java.io.PrintStream (pout2, true)); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, java.io.IOException)) { -var io = e$$; -{ -this.textArea.append ("Couldn't redirect STDERR to this console\n" + io.getMessage ()); -} -} else if (Clazz.exceptionOf (e$$, SecurityException)) { -var se = e$$; -{ -this.textArea.append ("Couldn't redirect STDERR to this console\n" + se.getMessage ()); -} -} else { -throw e$$; -} -} -this.quit = false; -this.reader = new Thread (this); -this.reader.setDaemon (true); -this.reader.start (); -this.reader2 = new Thread (this); -this.reader2.setDaemon (true); -this.reader2.start (); -System.out.println ("Hello World 2"); -System.out.println ("All fonts available to Graphic2D:\n"); -var ge = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment (); -var fontNames = ge.getAvailableFontFamilyNames (); -for (var n = 0; n < fontNames.length; n++) System.out.println (fontNames[n]); - -System.out.println ("\nLets throw an error on this console"); -this.errorThrower = new Thread (this); -this.errorThrower.setDaemon (true); -this.errorThrower.start (); -}); -Clazz.overrideMethod (c$, "windowClosed", -function (evt) { -this.quit = true; -this.notifyAll (); -try { -this.reader.join (1000); -this.pin.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -try { -this.reader2.join (1000); -this.pin2.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -System.exit (0); -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowClosing", -function (evt) { -this.frame.setVisible (false); -this.frame.dispose (); -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -this.textArea.setText (""); -}, "java.awt.event.ActionEvent"); -Clazz.overrideMethod (c$, "run", -function () { -try { -while (Thread.currentThread () === this.reader) { -try { -this.wait (100); -} catch (ie) { -if (Clazz.exceptionOf (ie, InterruptedException)) { -} else { -throw ie; -} -} -if (this.pin.available () != 0) { -var input = this.readLine (this.pin); -this.textArea.append (input); -}if (this.quit) return; -} -while (Thread.currentThread () === this.reader2) { -try { -this.wait (100); -} catch (ie) { -if (Clazz.exceptionOf (ie, InterruptedException)) { -} else { -throw ie; -} -} -if (this.pin2.available () != 0) { -var input = this.readLine (this.pin2); -this.textArea.append (input); -}if (this.quit) return; -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -this.textArea.append ("\nConsole reports an Internal error."); -this.textArea.append ("The error is: " + e); -} else { -throw e; -} -} -if (Thread.currentThread () === this.errorThrower) { -try { -this.wait (1000); -} catch (ie) { -if (Clazz.exceptionOf (ie, InterruptedException)) { -} else { -throw ie; -} -} -throw new NullPointerException (jalview.util.MessageManager.getString ("exception.application_test_npe")); -}}); -Clazz.defineMethod (c$, "readLine", -function ($in) { -var input = ""; -do { -var available = $in.available (); -if (available == 0) break; -var b = Clazz.newByteArray (available, 0); -$in.read (b); -input = input + String.instantialize (b, 0, b.length); -} while (!input.endsWith ("\n") && !input.endsWith ("\r\n") && !this.quit); -return input; -}, "java.io.PipedInputStream"); -}); diff --git a/bin/jalview/util/BrowserLauncher.js b/bin/jalview/util/BrowserLauncher.js deleted file mode 100644 index 0b28b4c..0000000 --- a/bin/jalview/util/BrowserLauncher.js +++ /dev/null @@ -1,487 +0,0 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.BrowserLauncher", ["jalview.bin.Cache", "jalview.util.MessageManager", "java.io.File", "$.IOException", "java.lang.Double", "$.Runtime"], function () { -c$ = Clazz.declareType (jalview.util, "BrowserLauncher"); -c$.loadClasses = Clazz.defineMethod (c$, "loadClasses", -($fz = function () { -switch (jalview.util.BrowserLauncher.jvm) { -case 0: -try { -var aeTargetClass = Class.forName ("com.apple.MacOS.AETarget"); -var osUtilsClass = Class.forName ("com.apple.MacOS.OSUtils"); -var appleEventClass = Class.forName ("com.apple.MacOS.AppleEvent"); -var aeClass = Class.forName ("com.apple.MacOS.ae"); -jalview.util.BrowserLauncher.aeDescClass = Class.forName ("com.apple.MacOS.AEDesc"); -jalview.util.BrowserLauncher.aeTargetConstructor = aeTargetClass.getDeclaredConstructor ( Clazz.newArray (-1, [Number])); -jalview.util.BrowserLauncher.appleEventConstructor = appleEventClass.getDeclaredConstructor ( Clazz.newArray (-1, [Number, Number, aeTargetClass, Number, Number])); -jalview.util.BrowserLauncher.aeDescConstructor = jalview.util.BrowserLauncher.aeDescClass.getDeclaredConstructor ( Clazz.newArray (-1, [String])); -jalview.util.BrowserLauncher.makeOSType = osUtilsClass.getDeclaredMethod ("makeOSType", Clazz.newArray (-1, [String])); -jalview.util.BrowserLauncher.putParameter = appleEventClass.getDeclaredMethod ("putParameter", Clazz.newArray (-1, [Number, jalview.util.BrowserLauncher.aeDescClass])); -jalview.util.BrowserLauncher.sendNoReply = appleEventClass.getDeclaredMethod ("sendNoReply", Clazz.newArray (-1, [])); -var keyDirectObjectField = aeClass.getDeclaredField ("keyDirectObject"); -jalview.util.BrowserLauncher.keyDirectObject = keyDirectObjectField.get (null); -var autoGenerateReturnIDField = appleEventClass.getDeclaredField ("kAutoGenerateReturnID"); -jalview.util.BrowserLauncher.kAutoGenerateReturnID = autoGenerateReturnIDField.get (null); -var anyTransactionIDField = appleEventClass.getDeclaredField ("kAnyTransactionID"); -jalview.util.BrowserLauncher.kAnyTransactionID = anyTransactionIDField.get (null); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, ClassNotFoundException)) { -var cnfe = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = cnfe.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, NoSuchMethodException)) { -var nsme = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = nsme.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, NoSuchFieldException)) { -var nsfe = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = nsfe.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = iae.getMessage (); -return false; -} -} else { -throw e$$; -} -} -break; -case 1: -try { -jalview.util.BrowserLauncher.mrjFileUtilsClass = Class.forName ("com.apple.mrj.MRJFileUtils"); -jalview.util.BrowserLauncher.mrjOSTypeClass = Class.forName ("com.apple.mrj.MRJOSType"); -var systemFolderField = jalview.util.BrowserLauncher.mrjFileUtilsClass.getDeclaredField ("kSystemFolderType"); -jalview.util.BrowserLauncher.kSystemFolderType = systemFolderField.get (null); -jalview.util.BrowserLauncher.findFolder = jalview.util.BrowserLauncher.mrjFileUtilsClass.getDeclaredMethod ("findFolder", Clazz.newArray (-1, [jalview.util.BrowserLauncher.mrjOSTypeClass])); -jalview.util.BrowserLauncher.getFileCreator = jalview.util.BrowserLauncher.mrjFileUtilsClass.getDeclaredMethod ("getFileCreator", Clazz.newArray (-1, [java.io.File])); -jalview.util.BrowserLauncher.getFileType = jalview.util.BrowserLauncher.mrjFileUtilsClass.getDeclaredMethod ("getFileType", Clazz.newArray (-1, [java.io.File])); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, ClassNotFoundException)) { -var cnfe = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = cnfe.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, NoSuchFieldException)) { -var nsfe = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = nsfe.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, NoSuchMethodException)) { -var nsme = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = nsme.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, SecurityException)) { -var se = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = se.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = iae.getMessage (); -return false; -} -} else { -throw e$$; -} -} -break; -case 3: -try { -var linker = Class.forName ("com.apple.mrj.jdirect.Linker"); -var constructor = linker.getConstructor ( Clazz.newArray (-1, [Class])); -jalview.util.BrowserLauncher.linkage = constructor.newInstance ( Clazz.newArray (-1, [jalview.util.BrowserLauncher])); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, ClassNotFoundException)) { -var cnfe = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = cnfe.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, NoSuchMethodException)) { -var nsme = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = nsme.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var ite = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = ite.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, InstantiationException)) { -var ie = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = ie.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = iae.getMessage (); -return false; -} -} else { -throw e$$; -} -} -break; -case 4: -try { -jalview.util.BrowserLauncher.mrjFileUtilsClass = Class.forName ("com.apple.mrj.MRJFileUtils"); -jalview.util.BrowserLauncher.$openURL = jalview.util.BrowserLauncher.mrjFileUtilsClass.getDeclaredMethod ("openURL", Clazz.newArray (-1, [String])); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, ClassNotFoundException)) { -var cnfe = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = cnfe.getMessage (); -return false; -} -} else if (Clazz.exceptionOf (e$$, NoSuchMethodException)) { -var nsme = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = nsme.getMessage (); -return false; -} -} else { -throw e$$; -} -} -break; -default: -break; -} -return true; -}, $fz.isPrivate = true, $fz)); -c$.locateBrowser = Clazz.defineMethod (c$, "locateBrowser", -($fz = function () { -if (jalview.util.BrowserLauncher.browser != null) { -return jalview.util.BrowserLauncher.browser; -}switch (jalview.util.BrowserLauncher.jvm) { -case 0: -try { -var finderCreatorCode = jalview.util.BrowserLauncher.makeOSType.invoke (null, Clazz.newArray (-1, ["MACS"])); -var aeTarget = jalview.util.BrowserLauncher.aeTargetConstructor.newInstance ( Clazz.newArray (-1, [finderCreatorCode])); -var gurlType = jalview.util.BrowserLauncher.makeOSType.invoke (null, Clazz.newArray (-1, ["GURL"])); -var appleEvent = jalview.util.BrowserLauncher.appleEventConstructor.newInstance ( Clazz.newArray (-1, [gurlType, gurlType, aeTarget, jalview.util.BrowserLauncher.kAutoGenerateReturnID, jalview.util.BrowserLauncher.kAnyTransactionID])); -return appleEvent; -} catch (e$$) { -if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = iae.getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else if (Clazz.exceptionOf (e$$, InstantiationException)) { -var ie = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = ie.getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var ite = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = ite.getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else { -throw e$$; -} -} -case 1: -var systemFolder; -try { -systemFolder = jalview.util.BrowserLauncher.findFolder.invoke (null, Clazz.newArray (-1, [jalview.util.BrowserLauncher.kSystemFolderType])); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, IllegalArgumentException)) { -var iare = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = iare.getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = iae.getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var ite = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = ite.getTargetException ().getClass () + ": " + ite.getTargetException ().getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else { -throw e$$; -} -} -var systemFolderFiles = systemFolder.list (); -for (var i = 0; i < systemFolderFiles.length; i++) { -try { -var file = new java.io.File (systemFolder, systemFolderFiles[i]); -if (!file.isFile ()) { -continue; -}var fileType = jalview.util.BrowserLauncher.getFileType.invoke (null, Clazz.newArray (-1, [file])); -if ("FNDR".equals (fileType.toString ())) { -var fileCreator = jalview.util.BrowserLauncher.getFileCreator.invoke (null, Clazz.newArray (-1, [file])); -if ("MACS".equals (fileCreator.toString ())) { -jalview.util.BrowserLauncher.browser = file.toString (); -return jalview.util.BrowserLauncher.browser; -}}} catch (e$$) { -if (Clazz.exceptionOf (e$$, IllegalArgumentException)) { -var iare = e$$; -{ -jalview.util.BrowserLauncher.errorMessage = iare.getMessage (); -return null; -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = iae.getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var ite = e$$; -{ -jalview.util.BrowserLauncher.browser = null; -jalview.util.BrowserLauncher.errorMessage = ite.getTargetException ().getClass () + ": " + ite.getTargetException ().getMessage (); -return jalview.util.BrowserLauncher.browser; -} -} else { -throw e$$; -} -} -} -jalview.util.BrowserLauncher.browser = null; -break; -case 3: -case 4: -jalview.util.BrowserLauncher.browser = ""; -break; -case 5: -jalview.util.BrowserLauncher.browser = "cmd.exe"; -break; -case 6: -jalview.util.BrowserLauncher.browser = "command.com"; -break; -case -1: -default: -jalview.util.BrowserLauncher.browser = jalview.bin.Cache.getDefault ("DEFAULT_BROWSER", "firefox"); -break; -} -return jalview.util.BrowserLauncher.browser; -}, $fz.isPrivate = true, $fz)); -c$.resetBrowser = Clazz.defineMethod (c$, "resetBrowser", -function () { -jalview.util.BrowserLauncher.browser = null; -}); -c$.openURL = Clazz.defineMethod (c$, "openURL", -function (url) { -if (!jalview.util.BrowserLauncher.loadedWithoutErrors) { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.browser_not_found", Clazz.newArray (-1, [jalview.util.BrowserLauncher.errorMessage]))); -}var browser = jalview.util.BrowserLauncher.locateBrowser (); -if (browser == null) { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.browser_unable_to_locate", Clazz.newArray (-1, [jalview.util.BrowserLauncher.errorMessage]))); -}switch (jalview.util.BrowserLauncher.jvm) { -case 0: -var aeDesc = null; -try { -aeDesc = jalview.util.BrowserLauncher.aeDescConstructor.newInstance ( Clazz.newArray (-1, [url])); -jalview.util.BrowserLauncher.putParameter.invoke (browser, Clazz.newArray (-1, [jalview.util.BrowserLauncher.keyDirectObject, aeDesc])); -jalview.util.BrowserLauncher.sendNoReply.invoke (browser, Clazz.newArray (-1, [])); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var ite = e$$; -{ -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.invocation_target_exception_creating_aedesc", Clazz.newArray (-1, [ite.getMessage ()]))); -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.illegal_access_building_apple_evt", Clazz.newArray (-1, [iae.getMessage ()]))); -} -} else if (Clazz.exceptionOf (e$$, InstantiationException)) { -var ie = e$$; -{ -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.illegal_access_building_apple_evt", Clazz.newArray (-1, [ie.getMessage ()]))); -} -} else { -throw e$$; -} -} finally { -aeDesc = null; -browser = null; -} -break; -case 1: -Runtime.getRuntime ().exec ( Clazz.newArray (-1, [browser, url])); -break; -case 3: -var instance = Clazz.newIntArray (1, 0); -var result = jalview.util.BrowserLauncher.ICStart (instance, 0); -if (result == 0) { -var selectionStart = Clazz.newIntArray (-1, [0]); -var urlBytes = url.getBytes (); -var selectionEnd = Clazz.newIntArray (-1, [urlBytes.length]); -result = jalview.util.BrowserLauncher.ICLaunchURL (instance[0], Clazz.newByteArray (-1, [0]), urlBytes, urlBytes.length, selectionStart, selectionEnd); -if (result == 0) { -jalview.util.BrowserLauncher.ICStop (instance); -} else { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.unable_to_launch_url", Clazz.newArray (-1, [Integer.$valueOf (result).toString ()]))); -}} else { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.unable_to_create_internet_config", Clazz.newArray (-1, [Integer.$valueOf (result).toString ()]))); -}break; -case 4: -try { -jalview.util.BrowserLauncher.$openURL.invoke (null, Clazz.newArray (-1, [url])); -} catch (e$$) { -if (Clazz.exceptionOf (e$$, java.lang.reflect.InvocationTargetException)) { -var ite = e$$; -{ -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.invocation_target_calling_url", Clazz.newArray (-1, [ite.getMessage ()]))); -} -} else if (Clazz.exceptionOf (e$$, IllegalAccessException)) { -var iae = e$$; -{ -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.illegal_access_calling_url", Clazz.newArray (-1, [iae.getMessage ()]))); -} -} else { -throw e$$; -} -} -break; -case 5: -case 6: -var process = Runtime.getRuntime ().exec ( Clazz.newArray (-1, [browser, "/c", "start", "\"\"", '"' + url + '"'])); -try { -process.waitFor (); -process.exitValue (); -} catch (ie) { -if (Clazz.exceptionOf (ie, InterruptedException)) { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.interrupted_launching_browser", Clazz.newArray (-1, [ie.getMessage ()]))); -} else { -throw ie; -} -} -break; -case -1: -process = Runtime.getRuntime ().exec ( Clazz.newArray (-1, [browser, "-remote", "openURL(" + url + ", new-window" + ")"])); -try { -var exitCode = process.waitFor (); -if (exitCode != 0) { -Runtime.getRuntime ().exec ( Clazz.newArray (-1, [browser, url])); -}} catch (ie) { -if (Clazz.exceptionOf (ie, InterruptedException)) { -throw new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.interrupted_launching_browser", Clazz.newArray (-1, [ie.getMessage ()]))); -} else { -throw ie; -} -} -break; -default: -Runtime.getRuntime ().exec ( Clazz.newArray (-1, [browser, url])); -break; -} -}, "~S"); -Clazz.defineStatics (c$, -"jvm", 0, -"browser", null, -"loadedWithoutErrors", false, -"mrjFileUtilsClass", null, -"mrjOSTypeClass", null, -"aeDescClass", null, -"aeTargetConstructor", null, -"appleEventConstructor", null, -"aeDescConstructor", null, -"findFolder", null, -"getFileCreator", null, -"getFileType", null, -"$openURL", null, -"makeOSType", null, -"putParameter", null, -"sendNoReply", null, -"kSystemFolderType", null, -"keyDirectObject", null, -"kAutoGenerateReturnID", null, -"kAnyTransactionID", null, -"linkage", null, -"JDirect_MacOSX", "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox", -"MRJ_2_0", 0, -"MRJ_2_1", 1, -"MRJ_3_0", 3, -"MRJ_3_1", 4, -"WINDOWS_NT", 5, -"WINDOWS_9x", 6, -"OTHER", -1, -"FINDER_TYPE", "FNDR", -"FINDER_CREATOR", "MACS", -"GURL_EVENT", "GURL", -"FIRST_WINDOWS_PARAMETER", "/c", -"SECOND_WINDOWS_PARAMETER", "start", -"THIRD_WINDOWS_PARAMETER", "\"\"", -"NETSCAPE_REMOTE_PARAMETER", "-remote", -"NETSCAPE_OPEN_PARAMETER_START", "openURL(", -"NETSCAPE_OPEN_NEW_WINDOW", ", new-window", -"NETSCAPE_OPEN_PARAMETER_END", ")", -"errorMessage", null); -{ -jalview.util.BrowserLauncher.loadedWithoutErrors = true; -var osName = System.getProperty ("os.name"); -if (osName.startsWith ("Mac OS")) { -var mrjVersion = System.getProperty ("mrj.version"); -var majorMRJVersion; -if (mrjVersion == null) { -majorMRJVersion = "3.1"; -} else { -majorMRJVersion = mrjVersion.substring (0, 3); -}try { -var version = Double.$valueOf (majorMRJVersion).doubleValue (); -if (version == 2) { -jalview.util.BrowserLauncher.jvm = 0; -} else if ((version >= 2.1) && (version < 3)) { -jalview.util.BrowserLauncher.jvm = 1; -} else if (version == 3.0) { -jalview.util.BrowserLauncher.jvm = 3; -} else if (version >= 3.1) { -jalview.util.BrowserLauncher.jvm = 4; -} else { -jalview.util.BrowserLauncher.loadedWithoutErrors = false; -jalview.util.BrowserLauncher.errorMessage = "Unsupported MRJ version: " + version; -}} catch (nfe) { -if (Clazz.exceptionOf (nfe, NumberFormatException)) { -jalview.util.BrowserLauncher.loadedWithoutErrors = false; -jalview.util.BrowserLauncher.errorMessage = "Invalid MRJ version: " + mrjVersion; -} else { -throw nfe; -} -} -} else if (osName.startsWith ("Windows")) { -if (osName.indexOf ("9") != -1) { -jalview.util.BrowserLauncher.jvm = 6; -} else { -jalview.util.BrowserLauncher.jvm = 5; -}} else { -jalview.util.BrowserLauncher.jvm = -1; -}if (jalview.util.BrowserLauncher.loadedWithoutErrors) { -jalview.util.BrowserLauncher.loadedWithoutErrors = jalview.util.BrowserLauncher.loadClasses (); -}}}); diff --git a/bin/jalview/util/ColorUtils.js b/bin/jalview/util/ColorUtils.js index 129c265..ed016da 100644 --- a/bin/jalview/util/ColorUtils.js +++ b/bin/jalview/util/ColorUtils.js @@ -1,30 +1,30 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.ColorUtils", ["java.awt.Color", "java.util.Random"], function () { -c$ = Clazz.declareType (jalview.util, "ColorUtils"); -c$.generateRandomColor = Clazz.defineMethod (c$, "generateRandomColor", -function (mix) { -var random = new java.util.Random (); -var red = random.nextInt (256); -var green = random.nextInt (256); -var blue = random.nextInt (256); -if (mix != null) { -red = Clazz.doubleToInt ((red + mix.getRed ()) / 2); -green = Clazz.doubleToInt ((green + mix.getGreen ()) / 2); -blue = Clazz.doubleToInt ((blue + mix.getBlue ()) / 2); -}var color = new java.awt.Color (red, green, blue); -return color; -}, "java.awt.Color"); -c$.toTkCode = Clazz.defineMethod (c$, "toTkCode", -function (colour) { -var colstring = "#" + ((colour.getRed () < 16) ? "0" : "") + Integer.toHexString (colour.getRed ()) + ((colour.getGreen () < 16) ? "0" : "") + Integer.toHexString (colour.getGreen ()) + ((colour.getBlue () < 16) ? "0" : "") + Integer.toHexString (colour.getBlue ()); -return colstring; -}, "java.awt.Color"); -c$.darkerThan = Clazz.defineMethod (c$, "darkerThan", -function (col) { -return col == null ? null : col.darker ().darker ().darker (); -}, "java.awt.Color"); -c$.brighterThan = Clazz.defineMethod (c$, "brighterThan", -function (col) { -return col == null ? null : col.brighter ().brighter ().brighter (); -}, "java.awt.Color"); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.ColorUtils", ["java.awt.Color", "java.util.Random"], function () { +c$ = Clazz.declareType (jalview.util, "ColorUtils"); +c$.generateRandomColor = Clazz.defineMethod (c$, "generateRandomColor", +function (mix) { +var random = new java.util.Random (); +var red = random.nextInt (256); +var green = random.nextInt (256); +var blue = random.nextInt (256); +if (mix != null) { +red = Clazz.doubleToInt ((red + mix.getRed ()) / 2); +green = Clazz.doubleToInt ((green + mix.getGreen ()) / 2); +blue = Clazz.doubleToInt ((blue + mix.getBlue ()) / 2); +}var color = new java.awt.Color (red, green, blue); +return color; +}, "java.awt.Color"); +c$.toTkCode = Clazz.defineMethod (c$, "toTkCode", +function (colour) { +var colstring = "#" + ((colour.getRed () < 16) ? "0" : "") + Integer.toHexString (colour.getRed ()) + ((colour.getGreen () < 16) ? "0" : "") + Integer.toHexString (colour.getGreen ()) + ((colour.getBlue () < 16) ? "0" : "") + Integer.toHexString (colour.getBlue ()); +return colstring; +}, "java.awt.Color"); +c$.darkerThan = Clazz.defineMethod (c$, "darkerThan", +function (col) { +return col == null ? null : col.darker ().darker ().darker (); +}, "java.awt.Color"); +c$.brighterThan = Clazz.defineMethod (c$, "brighterThan", +function (col) { +return col == null ? null : col.brighter ().brighter ().brighter (); +}, "java.awt.Color"); +}); diff --git a/bin/jalview/util/Comparison.class b/bin/jalview/util/Comparison.class index 096f532..590a80c 100644 Binary files a/bin/jalview/util/Comparison.class and b/bin/jalview/util/Comparison.class differ diff --git a/bin/jalview/util/Comparison.js b/bin/jalview/util/Comparison.js index e46a616..29499bb 100644 --- a/bin/jalview/util/Comparison.js +++ b/bin/jalview/util/Comparison.js @@ -1,131 +1,131 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.Comparison", ["java.util.ArrayList"], function () { -c$ = Clazz.declareType (jalview.util, "Comparison"); -c$.compare = Clazz.defineMethod (c$, "compare", -function (ii, jj) { -return jalview.util.Comparison.compare (ii, jj, 0, ii.getLength () - 1); -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); -c$.compare = Clazz.defineMethod (c$, "compare", -function (ii, jj, start, end) { -var si = ii.getSequenceAsString (); -var sj = jj.getSequenceAsString (); -var ilen = si.length - 1; -var jlen = sj.length - 1; -while (jalview.util.Comparison.isGap (si.charAt (start + ilen))) { -ilen--; -} -while (jalview.util.Comparison.isGap (sj.charAt (start + jlen))) { -jlen--; -} -var count = 0; -var match = 0; -var pid = -1; -if (ilen > jlen) { -for (var j = 0; j < jlen; j++) { -if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) { -match++; -}count++; -} -pid = match / ilen * 100; -} else { -for (var j = 0; j < jlen; j++) { -if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) { -match++; -}count++; -} -pid = match / jlen * 100; -}return pid; -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N,~N"); -c$.PID = Clazz.defineMethod (c$, "PID", -function (seq1, seq2) { -return jalview.util.Comparison.PID (seq1, seq2, 0, seq1.length); -}, "~S,~S"); -c$.PID = Clazz.defineMethod (c$, "PID", -function (seq1, seq2, start, end) { -return jalview.util.Comparison.PID (seq1, seq2, start, end, true, false); -}, "~S,~S,~N,~N"); -c$.PID = Clazz.defineMethod (c$, "PID", -function (seq1, seq2, start, end, wcGaps, ungappedOnly) { -var s1len = seq1.length; -var s2len = seq2.length; -var len = Math.min (s1len, s2len); -if (end < len) { -len = end; -}if (len < start) { -start = len - 1; -}var elen = len - start; -var bad = 0; -var chr1; -var chr2; -var agap; -for (var i = start; i < len; i++) { -chr1 = seq1.charAt (i); -chr2 = seq2.charAt (i); -agap = jalview.util.Comparison.isGap (chr1) || jalview.util.Comparison.isGap (chr2); -if ('a' <= chr1 && chr1 <= 'z') { -chr1 = String.fromCharCode (chr1.charCodeAt (0) - 32); -}if ('a' <= chr2 && chr2 <= 'z') { -chr2 = String.fromCharCode (chr2.charCodeAt (0) - 32); -}if (chr1 != chr2) { -if (agap) { -if (ungappedOnly) { -elen--; -} else if (!wcGaps) { -bad++; -}} else { -bad++; -}}} -if (elen < 1) { -return 0; -}return (100 * (elen - bad)) / elen; -}, "~S,~S,~N,~N,~B,~B"); -c$.isGap = Clazz.defineMethod (c$, "isGap", -function (c) { -return (c == '-' || c == '.' || c == ' ') ? true : false; -}, "~S"); -c$.isNucleotide = Clazz.defineMethod (c$, "isNucleotide", -function (seqs) { -if (seqs == null) { -return false; -}var ntCount = 0; -var aaCount = 0; -for (var seq, $seq = 0, $$seq = seqs; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { -if (seq == null) { -continue; -}for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) { -if ('a' <= c && c <= 'z') { -c = String.fromCharCode (c.charCodeAt (0) - 32); -}if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U') { -ntCount++; -} else if (!jalview.util.Comparison.isGap (c)) { -aaCount++; -}} -} -if (ntCount * 100 > 85 * (ntCount + aaCount)) { -return true; -} else { -return false; -}}, "~A"); -c$.isNucleotide2 = Clazz.defineMethod (c$, "isNucleotide2", -function (seqs) { -if (seqs == null) { -return false; -}var flattened = new java.util.ArrayList (); -for (var ss, $ss = 0, $$ss = seqs; $ss < $$ss.length && ((ss = $$ss[$ss]) || true); $ss++) { -for (var s, $s = 0, $$s = ss; $s < $$s.length && ((s = $$s[$s]) || true); $s++) { -flattened.add (s); -} -} -var oneDArray = flattened.toArray ( new Array (flattened.size ())); -return jalview.util.Comparison.isNucleotide (oneDArray); -}, "~A"); -Clazz.defineStatics (c$, -"EIGHTY_FIVE", 85, -"TO_UPPER_CASE", 32, -"GAP_SPACE", ' ', -"GAP_DOT", '.', -"GAP_DASH", '-'); -c$.GapChars = c$.prototype.GapChars = String.instantialize ( Clazz.newCharArray (-1, [' ', '.', '-'])); -Clazz.defineStatics (c$, -"caseShift", 32); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.Comparison", ["java.util.ArrayList"], function () { +c$ = Clazz.declareType (jalview.util, "Comparison"); +c$.compare = Clazz.defineMethod (c$, "compare", +function (ii, jj) { +return jalview.util.Comparison.compare (ii, jj, 0, ii.getLength () - 1); +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI"); +c$.compare = Clazz.defineMethod (c$, "compare", +function (ii, jj, start, end) { +var si = ii.getSequenceAsString (); +var sj = jj.getSequenceAsString (); +var ilen = si.length - 1; +var jlen = sj.length - 1; +while (jalview.util.Comparison.isGap (si.charAt (start + ilen))) { +ilen--; +} +while (jalview.util.Comparison.isGap (sj.charAt (start + jlen))) { +jlen--; +} +var count = 0; +var match = 0; +var pid = -1; +if (ilen > jlen) { +for (var j = 0; j < jlen; j++) { +if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) { +match++; +}count++; +} +pid = match / ilen * 100; +} else { +for (var j = 0; j < jlen; j++) { +if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) { +match++; +}count++; +} +pid = match / jlen * 100; +}return pid; +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N,~N"); +c$.PID = Clazz.defineMethod (c$, "PID", +function (seq1, seq2) { +return jalview.util.Comparison.PID (seq1, seq2, 0, seq1.length); +}, "~S,~S"); +c$.PID = Clazz.defineMethod (c$, "PID", +function (seq1, seq2, start, end) { +return jalview.util.Comparison.PID (seq1, seq2, start, end, true, false); +}, "~S,~S,~N,~N"); +c$.PID = Clazz.defineMethod (c$, "PID", +function (seq1, seq2, start, end, wcGaps, ungappedOnly) { +var s1len = seq1.length; +var s2len = seq2.length; +var len = Math.min (s1len, s2len); +if (end < len) { +len = end; +}if (len < start) { +start = len - 1; +}var elen = len - start; +var bad = 0; +var chr1; +var chr2; +var agap; +for (var i = start; i < len; i++) { +chr1 = seq1.charAt (i); +chr2 = seq2.charAt (i); +agap = jalview.util.Comparison.isGap (chr1) || jalview.util.Comparison.isGap (chr2); +if ('a' <= chr1 && chr1 <= 'z') { +chr1 = String.fromCharCode (chr1.charCodeAt (0) - 32); +}if ('a' <= chr2 && chr2 <= 'z') { +chr2 = String.fromCharCode (chr2.charCodeAt (0) - 32); +}if (chr1 != chr2) { +if (agap) { +if (ungappedOnly) { +elen--; +} else if (!wcGaps) { +bad++; +}} else { +bad++; +}}} +if (elen < 1) { +return 0; +}return (100 * (elen - bad)) / elen; +}, "~S,~S,~N,~N,~B,~B"); +c$.isGap = Clazz.defineMethod (c$, "isGap", +function (c) { +return (c == '-' || c == '.' || c == ' ') ? true : false; +}, "~S"); +c$.isNucleotide = Clazz.defineMethod (c$, "isNucleotide", +function (seqs) { +if (seqs == null) { +return false; +}var ntCount = 0; +var aaCount = 0; +for (var seq, $seq = 0, $$seq = seqs; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { +if (seq == null) { +continue; +}for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) { +if ('a' <= c && c <= 'z') { +c = String.fromCharCode (c.charCodeAt (0) - 32); +}if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U') { +ntCount++; +} else if (!jalview.util.Comparison.isGap (c)) { +aaCount++; +}} +} +if (ntCount * 100 > 85 * (ntCount + aaCount)) { +return true; +} else { +return false; +}}, "~A"); +c$.isNucleotide2 = Clazz.defineMethod (c$, "isNucleotide2", +function (seqs) { +if (seqs == null) { +return false; +}var flattened = new java.util.ArrayList (); +for (var ss, $ss = 0, $$ss = seqs; $ss < $$ss.length && ((ss = $$ss[$ss]) || true); $ss++) { +for (var s, $s = 0, $$s = ss; $s < $$s.length && ((s = $$s[$s]) || true); $s++) { +flattened.add (s); +} +} +var oneDArray = flattened.toArray ( new Array (flattened.size ())); +return jalview.util.Comparison.isNucleotide (oneDArray); +}, "~A"); +Clazz.defineStatics (c$, +"EIGHTY_FIVE", 85, +"TO_UPPER_CASE", 32, +"GAP_SPACE", ' ', +"GAP_DOT", '.', +"GAP_DASH", '-'); +c$.GapChars = c$.prototype.GapChars = String.instantialize ( Clazz.newCharArray (-1, [' ', '.', '-'])); +Clazz.defineStatics (c$, +"caseShift", 32); +}); diff --git a/bin/jalview/util/DBRefUtils.class b/bin/jalview/util/DBRefUtils.class index fae2024..0686bf2 100644 Binary files a/bin/jalview/util/DBRefUtils.class and b/bin/jalview/util/DBRefUtils.class differ diff --git a/bin/jalview/util/DBRefUtils.js b/bin/jalview/util/DBRefUtils.js index 051cde7..b27f196 100644 --- a/bin/jalview/util/DBRefUtils.js +++ b/bin/jalview/util/DBRefUtils.js @@ -1,184 +1,184 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.util.HashMap"], "jalview.util.DBRefUtils", ["jalview.datamodel.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "jalview.jsdev.RegExp", "java.util.ArrayList", "$.Hashtable"], function () { -c$ = Clazz.declareType (jalview.util, "DBRefUtils"); -c$.selectRefs = Clazz.defineMethod (c$, "selectRefs", -function (dbrefs, sources) { -if (dbrefs == null) { -return null; -}if (sources == null) { -return dbrefs; -}var srcs = new java.util.HashMap (); -var res = new java.util.ArrayList (); -for (var i = 0; i < sources.length; i++) { -srcs.put ( String.instantialize (sources[i]), new Integer (i)); -} -for (var i = 0, j = dbrefs.length; i < j; i++) { -if (srcs.containsKey (dbrefs[i].getSource ())) { -res.add (dbrefs[i]); -}} -if (res.size () > 0) { -var reply = new Array (res.size ()); -return res.toArray (reply); -}res = null; -return null; -}, "~A,~A"); -c$.isDasCoordinateSystem = Clazz.defineMethod (c$, "isDasCoordinateSystem", -function (string, dBRefEntry) { -if (string == null || dBRefEntry == null) { -return false; -}var coordsys = jalview.util.DBRefUtils.dasCoordinateSystemsLookup.get (string.toLowerCase ()); -return coordsys == null ? false : coordsys.equals (dBRefEntry.getSource ()); -}, "~S,jalview.datamodel.DBRefEntry"); -c$.getCanonicalName = Clazz.defineMethod (c$, "getCanonicalName", -function (source) { -if (source == null) { -return null; -}var canonical = jalview.util.DBRefUtils.canonicalSourceNameLookup.get (source.toLowerCase ()); -return canonical == null ? source : canonical; -}, "~S"); -c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", -function (ref, entry) { -return jalview.util.DBRefUtils.searchRefs (ref, entry, jalview.util.DBRefUtils.matchDbAndIdAndEitherMapOrEquivalentMapList); -}, "~A,jalview.datamodel.DBRefEntry"); -c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", -function (refs, entry, comparator) { -if (refs == null || entry == null) { -return null; -}var rfs = new java.util.ArrayList (); -for (var i = 0; i < refs.length; i++) { -if (comparator.matches (entry, refs[i])) { -rfs.add (refs[i]); -}} -return rfs.size () == 0 ? null : rfs.toArray ( new Array (rfs.size ())); -}, "~A,jalview.datamodel.DBRefEntry,jalview.util.DBRefUtils.DbRefComp"); -c$.parseToDbRef = Clazz.defineMethod (c$, "parseToDbRef", -function (seq, dbname, version, acn) { -var ref = null; -if (dbname != null) { -var locsrc = jalview.util.DBRefUtils.getCanonicalName (dbname); -if (locsrc.equals (jalview.datamodel.DBRefSource.PDB)) { -var r = jalview.jsdev.RegExp.newRegex (["([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)"]); -if (r.search (acn.trim ())) { -var pdbid = r.stringMatchedI (1); -var chaincode = r.stringMatchedI (2); -if (chaincode == null) { -chaincode = " "; -}if (chaincode.equals (" ")) { -chaincode = "_"; -}ref = new jalview.datamodel.DBRefEntry (locsrc, version, pdbid + chaincode); -var pdbr = new jalview.datamodel.PDBEntry (); -pdbr.setId (pdbid); -pdbr.setType (jalview.datamodel.PDBEntry.Type.PDB); -pdbr.setProperty ( new java.util.Hashtable ()); -pdbr.setChainCode (chaincode); -seq.addPDBId (pdbr); -} else { -System.err.println ("Malformed PDB DR line:" + acn); -}} else { -ref = new jalview.datamodel.DBRefEntry (locsrc, version, acn); -}}if (ref != null) { -seq.addDBRef (ref); -}return ref; -}, "jalview.datamodel.SequenceI,~S,~S,~S"); -c$.$DBRefUtils$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$1", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () == null || refb.getSource ().equals (refa.getSource ())) { -if (refa.getVersion () == null || refb.getVersion ().equals (refa.getVersion ())) { -if (refa.getAccessionId () == null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if (refa.getMap () == null || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { -return true; -}}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$2", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if ((refa.getSource () == null || refb.getSource () == null) || refb.getSource ().equals (refa.getSource ())) { -if ((refa.getVersion () == null || refb.getVersion () == null) || refb.getVersion ().equals (refa.getVersion ())) { -if ((refa.getAccessionId () == null || refb.getAccessionId () == null) || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if ((refa.getMap () == null || refb.getMap () == null) || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { -return true; -}}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$3$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$3", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if ((refa.getMap () == null || refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { -return true; -}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$4$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$4", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if ((refa.getMap () == null && refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null)) { -if ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().getInverse ().equals (refa.getMap ().getMap ()))) { -return true; -}}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$5$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$5", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if (refa.getMap () == null && refb.getMap () == null) { -return true; -}if (refa.getMap () != null && refb.getMap () != null && ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { -return true; -}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$6$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$6", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null && refb.getAccessionId ().equals (refa.getAccessionId ())) { -if (refa.getMap () == null || refb.getMap () == null) { -return true; -}if ((refa.getMap () != null && refb.getMap () != null) && (refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && (refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { -return true; -}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -Clazz.declareInterface (jalview.util.DBRefUtils, "DbRefComp"); -c$.canonicalSourceNameLookup = c$.prototype.canonicalSourceNameLookup = new java.util.HashMap (); -c$.dasCoordinateSystemsLookup = c$.prototype.dasCoordinateSystemsLookup = new java.util.HashMap (); -{ -jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT); -jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT); -jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("pdb", jalview.datamodel.DBRefSource.PDB); -jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("pdbresnum", jalview.datamodel.DBRefSource.PDB); -jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("uniprot", jalview.datamodel.DBRefSource.UNIPROT); -jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("embl", jalview.datamodel.DBRefSource.EMBL); -}c$.matchNonNullonA = c$.prototype.matchNonNullonA = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$1") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$1$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$1, this, null)); -c$.matchEitherNonNull = c$.prototype.matchEitherNonNull = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$2") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$2$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$2, this, null)); -c$.matchDbAndIdAndEitherMap = c$.prototype.matchDbAndIdAndEitherMap = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$3") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$3$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$3, this, null)); -c$.matchDbAndIdAndComplementaryMapList = c$.prototype.matchDbAndIdAndComplementaryMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$4") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$4$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$4, this, null)); -c$.matchDbAndIdAndEquivalentMapList = c$.prototype.matchDbAndIdAndEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$5") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$5$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$5, this, null)); -c$.matchDbAndIdAndEitherMapOrEquivalentMapList = c$.prototype.matchDbAndIdAndEitherMapOrEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$6") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$6$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$6, this, null)); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.util.HashMap"], "jalview.util.DBRefUtils", ["jalview.datamodel.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "jalview.jsdev.RegExp", "java.util.ArrayList", "$.Hashtable"], function () { +c$ = Clazz.declareType (jalview.util, "DBRefUtils"); +c$.selectRefs = Clazz.defineMethod (c$, "selectRefs", +function (dbrefs, sources) { +if (dbrefs == null) { +return null; +}if (sources == null) { +return dbrefs; +}var srcs = new java.util.HashMap (); +var res = new java.util.ArrayList (); +for (var i = 0; i < sources.length; i++) { +srcs.put ( String.instantialize (sources[i]), new Integer (i)); +} +for (var i = 0, j = dbrefs.length; i < j; i++) { +if (srcs.containsKey (dbrefs[i].getSource ())) { +res.add (dbrefs[i]); +}} +if (res.size () > 0) { +var reply = new Array (res.size ()); +return res.toArray (reply); +}res = null; +return null; +}, "~A,~A"); +c$.isDasCoordinateSystem = Clazz.defineMethod (c$, "isDasCoordinateSystem", +function (string, dBRefEntry) { +if (string == null || dBRefEntry == null) { +return false; +}var coordsys = jalview.util.DBRefUtils.dasCoordinateSystemsLookup.get (string.toLowerCase ()); +return coordsys == null ? false : coordsys.equals (dBRefEntry.getSource ()); +}, "~S,jalview.datamodel.DBRefEntry"); +c$.getCanonicalName = Clazz.defineMethod (c$, "getCanonicalName", +function (source) { +if (source == null) { +return null; +}var canonical = jalview.util.DBRefUtils.canonicalSourceNameLookup.get (source.toLowerCase ()); +return canonical == null ? source : canonical; +}, "~S"); +c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", +function (ref, entry) { +return jalview.util.DBRefUtils.searchRefs (ref, entry, jalview.util.DBRefUtils.matchDbAndIdAndEitherMapOrEquivalentMapList); +}, "~A,jalview.datamodel.DBRefEntry"); +c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", +function (refs, entry, comparator) { +if (refs == null || entry == null) { +return null; +}var rfs = new java.util.ArrayList (); +for (var i = 0; i < refs.length; i++) { +if (comparator.matches (entry, refs[i])) { +rfs.add (refs[i]); +}} +return rfs.size () == 0 ? null : rfs.toArray ( new Array (rfs.size ())); +}, "~A,jalview.datamodel.DBRefEntry,jalview.util.DBRefUtils.DbRefComp"); +c$.parseToDbRef = Clazz.defineMethod (c$, "parseToDbRef", +function (seq, dbname, version, acn) { +var ref = null; +if (dbname != null) { +var locsrc = jalview.util.DBRefUtils.getCanonicalName (dbname); +if (locsrc.equals (jalview.datamodel.DBRefSource.PDB)) { +var r = jalview.jsdev.RegExp.newRegex (["([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)"]); +if (r.search (acn.trim ())) { +var pdbid = r.stringMatchedI (1); +var chaincode = r.stringMatchedI (2); +if (chaincode == null) { +chaincode = " "; +}if (chaincode.equals (" ")) { +chaincode = "_"; +}ref = new jalview.datamodel.DBRefEntry (locsrc, version, pdbid + chaincode); +var pdbr = new jalview.datamodel.PDBEntry (); +pdbr.setId (pdbid); +pdbr.setType (jalview.datamodel.PDBEntry.Type.PDB); +pdbr.setProperty ( new java.util.Hashtable ()); +pdbr.setChainCode (chaincode); +seq.addPDBId (pdbr); +} else { +System.err.println ("Malformed PDB DR line:" + acn); +}} else { +ref = new jalview.datamodel.DBRefEntry (locsrc, version, acn); +}}if (ref != null) { +seq.addDBRef (ref); +}return ref; +}, "jalview.datamodel.SequenceI,~S,~S,~S"); +c$.$DBRefUtils$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$1", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () == null || refb.getSource ().equals (refa.getSource ())) { +if (refa.getVersion () == null || refb.getVersion ().equals (refa.getVersion ())) { +if (refa.getAccessionId () == null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if (refa.getMap () == null || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { +return true; +}}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$2", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if ((refa.getSource () == null || refb.getSource () == null) || refb.getSource ().equals (refa.getSource ())) { +if ((refa.getVersion () == null || refb.getVersion () == null) || refb.getVersion ().equals (refa.getVersion ())) { +if ((refa.getAccessionId () == null || refb.getAccessionId () == null) || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if ((refa.getMap () == null || refb.getMap () == null) || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { +return true; +}}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$3$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$3", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if ((refa.getMap () == null || refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { +return true; +}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$4$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$4", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if ((refa.getMap () == null && refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null)) { +if ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().getInverse ().equals (refa.getMap ().getMap ()))) { +return true; +}}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$5$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$5", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if (refa.getMap () == null && refb.getMap () == null) { +return true; +}if (refa.getMap () != null && refb.getMap () != null && ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { +return true; +}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$6$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$6", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null && refb.getAccessionId ().equals (refa.getAccessionId ())) { +if (refa.getMap () == null || refb.getMap () == null) { +return true; +}if ((refa.getMap () != null && refb.getMap () != null) && (refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && (refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { +return true; +}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +Clazz.declareInterface (jalview.util.DBRefUtils, "DbRefComp"); +c$.canonicalSourceNameLookup = c$.prototype.canonicalSourceNameLookup = new java.util.HashMap (); +c$.dasCoordinateSystemsLookup = c$.prototype.dasCoordinateSystemsLookup = new java.util.HashMap (); +{ +jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT); +jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT); +jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("pdb", jalview.datamodel.DBRefSource.PDB); +jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("pdbresnum", jalview.datamodel.DBRefSource.PDB); +jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("uniprot", jalview.datamodel.DBRefSource.UNIPROT); +jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("embl", jalview.datamodel.DBRefSource.EMBL); +}c$.matchNonNullonA = c$.prototype.matchNonNullonA = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$1") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$1$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$1, this, null)); +c$.matchEitherNonNull = c$.prototype.matchEitherNonNull = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$2") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$2$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$2, this, null)); +c$.matchDbAndIdAndEitherMap = c$.prototype.matchDbAndIdAndEitherMap = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$3") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$3$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$3, this, null)); +c$.matchDbAndIdAndComplementaryMapList = c$.prototype.matchDbAndIdAndComplementaryMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$4") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$4$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$4, this, null)); +c$.matchDbAndIdAndEquivalentMapList = c$.prototype.matchDbAndIdAndEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$5") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$5$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$5, this, null)); +c$.matchDbAndIdAndEitherMapOrEquivalentMapList = c$.prototype.matchDbAndIdAndEitherMapOrEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$6") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$6$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$6, this, null)); +}); diff --git a/bin/jalview/util/Format.class b/bin/jalview/util/Format.class index 43f3a99..c8b23d7 100644 Binary files a/bin/jalview/util/Format.class and b/bin/jalview/util/Format.class differ diff --git a/bin/jalview/util/Format.js b/bin/jalview/util/Format.js index 739add8..95a3560 100644 --- a/bin/jalview/util/Format.js +++ b/bin/jalview/util/Format.js @@ -1,389 +1,389 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.Format", ["java.lang.Character", "$.IllegalArgumentException", "$.StringBuffer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.width = 0; -this.precision = 0; -this.pre = null; -this.post = null; -this.leading_zeroes = false; -this.show_plus = false; -this.alternate = false; -this.show_space = false; -this.left_align = false; -this.fmt = '\0'; -this.formatString = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "Format"); -Clazz.makeConstructor (c$, -function (s) { -this.formatString = s; -this.width = 0; -this.precision = -1; -this.pre = ""; -this.post = ""; -this.leading_zeroes = false; -this.show_plus = false; -this.alternate = false; -this.show_space = false; -this.left_align = false; -this.fmt = ' '; -var length = s.length; -var parse_state = 0; -var i = 0; -while (parse_state == 0) { -if (i >= length) { -parse_state = 5; -} else if (s.charAt (i) == '%') { -if (i < (length - 1)) { -if (s.charAt (i + 1) == '%') { -this.pre = this.pre + '%'; -i++; -} else { -parse_state = 1; -}} else { -throw new IllegalArgumentException (); -}} else { -this.pre = this.pre + s.charAt (i); -}i++; -} -while (parse_state == 1) { -if (i >= length) { -parse_state = 5; -} else if (s.charAt (i) == ' ') { -this.show_space = true; -} else if (s.charAt (i) == '-') { -this.left_align = true; -} else if (s.charAt (i) == '+') { -this.show_plus = true; -} else if (s.charAt (i) == '0') { -this.leading_zeroes = true; -} else if (s.charAt (i) == '#') { -this.alternate = true; -} else { -parse_state = 2; -i--; -}i++; -} -while (parse_state == 2) { -if (i >= length) { -parse_state = 5; -} else if (('0' <= s.charAt (i)) && (s.charAt (i) <= '9')) { -this.width = ((this.width * 10) + s.charCodeAt (i)) - 48; -i++; -} else if (s.charAt (i) == '.') { -parse_state = 3; -this.precision = 0; -i++; -} else { -parse_state = 4; -}} -while (parse_state == 3) { -if (i >= length) { -parse_state = 5; -} else if (('0' <= s.charAt (i)) && (s.charAt (i) <= '9')) { -this.precision = ((this.precision * 10) + s.charCodeAt (i)) - 48; -i++; -} else { -parse_state = 4; -}} -if (parse_state == 4) { -if (i >= length) { -parse_state = 5; -} else { -this.fmt = s.charAt (i); -}i++; -}if (i < length) { -this.post = s.substring (i, length); -}}, "~S"); -c$.getHexString = Clazz.defineMethod (c$, "getHexString", -function (color) { -var r; -var g; -var b; -r = Integer.toHexString (color.getRed ()); -if (r.length < 2) { -r = "0" + r; -}g = Integer.toHexString (color.getGreen ()); -if (g.length < 2) { -g = "0" + g; -}b = Integer.toHexString (color.getBlue ()); -if (b.length < 2) { -b = "0" + b; -}return r + g + b; -}, "java.awt.Color"); -c$.printDouble = Clazz.defineMethod (c$, "printDouble", -function (s, fmt, x) { -s.print ( new jalview.util.Format (fmt).formDouble (x)); -}, "java.io.PrintStream,~S,~N"); -c$.printLong = Clazz.defineMethod (c$, "printLong", -function (s, fmt, x) { -s.print ( new jalview.util.Format (fmt).formLong (x)); -}, "java.io.PrintStream,~S,~N"); -c$.printChar = Clazz.defineMethod (c$, "printChar", -function (s, fmt, x) { -s.print ( new jalview.util.Format (fmt).formChar (x)); -}, "java.io.PrintStream,~S,~S"); -c$.print = Clazz.defineMethod (c$, "print", -function (s, fmt, x) { -s.print ( new jalview.util.Format (fmt).form (x)); -}, "java.io.PrintStream,~S,~S"); -c$.atoi = Clazz.defineMethod (c$, "atoi", -function (s) { -return jalview.util.Format.atol (s); -}, "~S"); -c$.atol = Clazz.defineMethod (c$, "atol", -function (s) { -var i = 0; -while ((i < s.length) && Character.isWhitespace (s.charAt (i))) { -i++; -} -if ((i < s.length) && (s.charAt (i) == '0')) { -if (((i + 1) < s.length) && ((s.charAt (i + 1) == 'x') || (s.charAt (i + 1) == 'X'))) { -return jalview.util.Format.parseLong (s.substring (i + 2), 16); -} else { -return jalview.util.Format.parseLong (s, 8); -}} else { -return jalview.util.Format.parseLong (s, 10); -}}, "~S"); -c$.parseLong = Clazz.defineMethod (c$, "parseLong", -($fz = function (s, base) { -var i = 0; -var sign = 1; -var r = 0; -while ((i < s.length) && Character.isWhitespace (s.charAt (i))) { -i++; -} -if ((i < s.length) && (s.charAt (i) == '-')) { -sign = -1; -i++; -} else if ((i < s.length) && (s.charAt (i) == '+')) { -i++; -}while (i < s.length) { -var ch = s.charAt (i); -if (('0' <= ch) && (ch.charCodeAt (0) < (48 + base))) { -r = ((r * base) + ch.charCodeAt (0)) - 48; -} else if (('A' <= ch) && (ch.charCodeAt (0) < ((65 + base) - 10))) { -r = ((r * base) + ch.charCodeAt (0)) - 65 + 10; -} else if (('a' <= ch) && (ch.charCodeAt (0) < ((97 + base) - 10))) { -r = ((r * base) + ch.charCodeAt (0)) - 97 + 10; -} else { -return r * sign; -}i++; -} -return r * sign; -}, $fz.isPrivate = true, $fz), "~S,~N"); -c$.atof = Clazz.defineMethod (c$, "atof", -function (s) { -var i = 0; -var sign = 1; -var r = 0; -var p = 1; -var state = 0; -while ((i < s.length) && Character.isWhitespace (s.charAt (i))) { -i++; -} -if ((i < s.length) && (s.charAt (i) == '-')) { -sign = -1; -i++; -} else if ((i < s.length) && (s.charAt (i) == '+')) { -i++; -}while (i < s.length) { -var ch = s.charAt (i); -if (('0' <= ch) && (ch <= '9')) { -if (state == 0) { -r = ((r * 10) + ch.charCodeAt (0)) - 48; -} else if (state == 1) { -p = p / 10; -r = r + (p * (ch.charCodeAt (0) - 48)); -}} else if (ch == '.') { -if (state == 0) { -state = 1; -} else { -return sign * r; -}} else if ((ch == 'e') || (ch == 'E')) { -var e = jalview.util.Format.parseLong (s.substring (i + 1), 10); -return sign * r * Math.pow (10, e); -} else { -return sign * r; -}i++; -} -return sign * r; -}, "~S"); -Clazz.defineMethod (c$, "formDouble", -function (x) { -var r; -if (this.precision < 0) { -this.precision = 6; -}var s = 1; -if (x < 0) { -x = -x; -s = -1; -}if (this.fmt == 'f') { -r = this.fixed_format (x); -} else if ((this.fmt == 'e') || (this.fmt == 'E') || (this.fmt == 'g') || (this.fmt == 'G')) { -r = this.exp_format (x); -} else { -throw new IllegalArgumentException (); -}return this.pad (this.sign (s, r)); -}, "~N"); -Clazz.defineMethod (c$, "formLong", -function (x) { -var r; -var s = 0; -if ((this.fmt == 'd') || (this.fmt == 'i')) { -if (x < 0) { -r = ("" + x).substring (1); -s = -1; -} else { -r = "" + x; -s = 1; -}} else if (this.fmt == 'o') { -r = jalview.util.Format.convert (x, 3, 7, "01234567"); -} else if (this.fmt == 'x') { -r = jalview.util.Format.convert (x, 4, 15, "0123456789abcdef"); -} else if (this.fmt == 'X') { -r = jalview.util.Format.convert (x, 4, 15, "0123456789ABCDEF"); -} else { -throw new IllegalArgumentException (); -}return this.pad (this.sign (s, r)); -}, "~N"); -Clazz.defineMethod (c$, "formChar", -function (c) { -if (this.fmt != 'c') { -throw new IllegalArgumentException (); -}var r = "" + c; -return this.pad (r); -}, "~S"); -Clazz.defineMethod (c$, "form", -function (s) { -if (this.fmt != 's') { -throw new IllegalArgumentException (); -}if (this.precision >= 0) { -s = s.substring (0, this.precision); -}return this.pad (s); -}, "~S"); -c$.repeat = Clazz.defineMethod (c$, "repeat", -($fz = function (c, n) { -if (n <= 0) { -return ""; -}var s = new StringBuffer (n); -for (var i = 0; i < n; i++) { -s.append (c); -} -return s.toString (); -}, $fz.isPrivate = true, $fz), "~S,~N"); -c$.convert = Clazz.defineMethod (c$, "convert", -($fz = function (x, n, m, d) { -if (x == 0) { -return "0"; -}var r = ""; -while (x != 0) { -r = d.charAt ((x & m)) + r; -x = x >>> n; -} -return r; -}, $fz.isPrivate = true, $fz), "~N,~N,~N,~S"); -Clazz.defineMethod (c$, "pad", -($fz = function (r) { -var p = jalview.util.Format.repeat (' ', this.width - r.length); -if (this.left_align) { -return this.pre + r + p + this.post; -} else { -return this.pre + p + r + this.post; -}}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "sign", -($fz = function (s, r) { -var p = ""; -if (s < 0) { -p = "-"; -} else if (s > 0) { -if (this.show_plus) { -p = "+"; -} else if (this.show_space) { -p = " "; -}} else { -if ((this.fmt == 'o') && this.alternate && (r.length > 0) && (r.charAt (0) != '0')) { -p = "0"; -} else if ((this.fmt == 'x') && this.alternate) { -p = "0x"; -} else if ((this.fmt == 'X') && this.alternate) { -p = "0X"; -}}var w = 0; -if (this.leading_zeroes) { -w = this.width; -} else if (((this.fmt == 'd') || (this.fmt == 'i') || (this.fmt == 'x') || (this.fmt == 'X') || (this.fmt == 'o')) && (this.precision > 0)) { -w = this.precision; -}return p + jalview.util.Format.repeat ('0', w - p.length - r.length) + r; -}, $fz.isPrivate = true, $fz), "~N,~S"); -Clazz.defineMethod (c$, "fixed_format", -($fz = function (d) { -var removeTrailing = ((this.fmt == 'G') || (this.fmt == 'g')) && !this.alternate; -if (d > 0x7FFFFFFFFFFFFFFF) { -return this.exp_format (d); -}if (this.precision == 0) { -return Clazz.doubleToLong (d + 0.5) + (removeTrailing ? "" : "."); -}var whole = Clazz.doubleToLong (d); -var fr = d - whole; -if ((fr >= 1) || (fr < 0)) { -return this.exp_format (d); -}var factor = 1; -var leading_zeroes = ""; -for (var i = 1; (i <= this.precision) && (factor <= 0x7FFFFFFFFFFFFFFF); i++) { -factor *= 10; -leading_zeroes = leading_zeroes + "0"; -} -var l = Clazz.doubleToLong ((factor * fr) + 0.5); -if (l >= factor) { -l = 0; -whole++; -}var z = leading_zeroes + l; -z = "." + z.substring (z.length - this.precision, z.length); -if (removeTrailing) { -var t = z.length - 1; -while ((t >= 0) && (z.charAt (t) == '0')) { -t--; -} -if ((t >= 0) && (z.charAt (t) == '.')) { -t--; -}z = z.substring (0, t + 1); -}return whole + z; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "exp_format", -($fz = function (d) { -var f = ""; -var e = 0; -var dd = d; -var factor = 1; -if (d != 0) { -while (dd > 10) { -e++; -factor /= 10; -dd = dd / 10; -} -while (dd < 1) { -e--; -factor *= 10; -dd = dd * 10; -} -}if (((this.fmt == 'g') || (this.fmt == 'G')) && (e >= -4) && (e < this.precision)) { -return this.fixed_format (d); -}d = d * factor; -f = f + this.fixed_format (d); -if ((this.fmt == 'e') || (this.fmt == 'g')) { -f = f + "e"; -} else { -f = f + "E"; -}var p = "000"; -if (e >= 0) { -f = f + "+"; -p = p + e; -} else { -f = f + "-"; -p = p + (-e); -}return f + p.substring (p.length - 3, p.length); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -return this.formatString; -}); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.Format", ["java.lang.Character", "$.IllegalArgumentException", "$.StringBuffer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.width = 0; +this.precision = 0; +this.pre = null; +this.post = null; +this.leading_zeroes = false; +this.show_plus = false; +this.alternate = false; +this.show_space = false; +this.left_align = false; +this.fmt = '\0'; +this.formatString = null; +Clazz.instantialize (this, arguments); +}, jalview.util, "Format"); +Clazz.makeConstructor (c$, +function (s) { +this.formatString = s; +this.width = 0; +this.precision = -1; +this.pre = ""; +this.post = ""; +this.leading_zeroes = false; +this.show_plus = false; +this.alternate = false; +this.show_space = false; +this.left_align = false; +this.fmt = ' '; +var length = s.length; +var parse_state = 0; +var i = 0; +while (parse_state == 0) { +if (i >= length) { +parse_state = 5; +} else if (s.charAt (i) == '%') { +if (i < (length - 1)) { +if (s.charAt (i + 1) == '%') { +this.pre = this.pre + '%'; +i++; +} else { +parse_state = 1; +}} else { +throw new IllegalArgumentException (); +}} else { +this.pre = this.pre + s.charAt (i); +}i++; +} +while (parse_state == 1) { +if (i >= length) { +parse_state = 5; +} else if (s.charAt (i) == ' ') { +this.show_space = true; +} else if (s.charAt (i) == '-') { +this.left_align = true; +} else if (s.charAt (i) == '+') { +this.show_plus = true; +} else if (s.charAt (i) == '0') { +this.leading_zeroes = true; +} else if (s.charAt (i) == '#') { +this.alternate = true; +} else { +parse_state = 2; +i--; +}i++; +} +while (parse_state == 2) { +if (i >= length) { +parse_state = 5; +} else if (('0' <= s.charAt (i)) && (s.charAt (i) <= '9')) { +this.width = ((this.width * 10) + s.charCodeAt (i)) - 48; +i++; +} else if (s.charAt (i) == '.') { +parse_state = 3; +this.precision = 0; +i++; +} else { +parse_state = 4; +}} +while (parse_state == 3) { +if (i >= length) { +parse_state = 5; +} else if (('0' <= s.charAt (i)) && (s.charAt (i) <= '9')) { +this.precision = ((this.precision * 10) + s.charCodeAt (i)) - 48; +i++; +} else { +parse_state = 4; +}} +if (parse_state == 4) { +if (i >= length) { +parse_state = 5; +} else { +this.fmt = s.charAt (i); +}i++; +}if (i < length) { +this.post = s.substring (i, length); +}}, "~S"); +c$.getHexString = Clazz.defineMethod (c$, "getHexString", +function (color) { +var r; +var g; +var b; +r = Integer.toHexString (color.getRed ()); +if (r.length < 2) { +r = "0" + r; +}g = Integer.toHexString (color.getGreen ()); +if (g.length < 2) { +g = "0" + g; +}b = Integer.toHexString (color.getBlue ()); +if (b.length < 2) { +b = "0" + b; +}return r + g + b; +}, "java.awt.Color"); +c$.printDouble = Clazz.defineMethod (c$, "printDouble", +function (s, fmt, x) { +s.print ( new jalview.util.Format (fmt).formDouble (x)); +}, "java.io.PrintStream,~S,~N"); +c$.printLong = Clazz.defineMethod (c$, "printLong", +function (s, fmt, x) { +s.print ( new jalview.util.Format (fmt).formLong (x)); +}, "java.io.PrintStream,~S,~N"); +c$.printChar = Clazz.defineMethod (c$, "printChar", +function (s, fmt, x) { +s.print ( new jalview.util.Format (fmt).formChar (x)); +}, "java.io.PrintStream,~S,~S"); +c$.print = Clazz.defineMethod (c$, "print", +function (s, fmt, x) { +s.print ( new jalview.util.Format (fmt).form (x)); +}, "java.io.PrintStream,~S,~S"); +c$.atoi = Clazz.defineMethod (c$, "atoi", +function (s) { +return jalview.util.Format.atol (s); +}, "~S"); +c$.atol = Clazz.defineMethod (c$, "atol", +function (s) { +var i = 0; +while ((i < s.length) && Character.isWhitespace (s.charAt (i))) { +i++; +} +if ((i < s.length) && (s.charAt (i) == '0')) { +if (((i + 1) < s.length) && ((s.charAt (i + 1) == 'x') || (s.charAt (i + 1) == 'X'))) { +return jalview.util.Format.parseLong (s.substring (i + 2), 16); +} else { +return jalview.util.Format.parseLong (s, 8); +}} else { +return jalview.util.Format.parseLong (s, 10); +}}, "~S"); +c$.parseLong = Clazz.defineMethod (c$, "parseLong", +($fz = function (s, base) { +var i = 0; +var sign = 1; +var r = 0; +while ((i < s.length) && Character.isWhitespace (s.charAt (i))) { +i++; +} +if ((i < s.length) && (s.charAt (i) == '-')) { +sign = -1; +i++; +} else if ((i < s.length) && (s.charAt (i) == '+')) { +i++; +}while (i < s.length) { +var ch = s.charAt (i); +if (('0' <= ch) && (ch.charCodeAt (0) < (48 + base))) { +r = ((r * base) + ch.charCodeAt (0)) - 48; +} else if (('A' <= ch) && (ch.charCodeAt (0) < ((65 + base) - 10))) { +r = ((r * base) + ch.charCodeAt (0)) - 65 + 10; +} else if (('a' <= ch) && (ch.charCodeAt (0) < ((97 + base) - 10))) { +r = ((r * base) + ch.charCodeAt (0)) - 97 + 10; +} else { +return r * sign; +}i++; +} +return r * sign; +}, $fz.isPrivate = true, $fz), "~S,~N"); +c$.atof = Clazz.defineMethod (c$, "atof", +function (s) { +var i = 0; +var sign = 1; +var r = 0; +var p = 1; +var state = 0; +while ((i < s.length) && Character.isWhitespace (s.charAt (i))) { +i++; +} +if ((i < s.length) && (s.charAt (i) == '-')) { +sign = -1; +i++; +} else if ((i < s.length) && (s.charAt (i) == '+')) { +i++; +}while (i < s.length) { +var ch = s.charAt (i); +if (('0' <= ch) && (ch <= '9')) { +if (state == 0) { +r = ((r * 10) + ch.charCodeAt (0)) - 48; +} else if (state == 1) { +p = p / 10; +r = r + (p * (ch.charCodeAt (0) - 48)); +}} else if (ch == '.') { +if (state == 0) { +state = 1; +} else { +return sign * r; +}} else if ((ch == 'e') || (ch == 'E')) { +var e = jalview.util.Format.parseLong (s.substring (i + 1), 10); +return sign * r * Math.pow (10, e); +} else { +return sign * r; +}i++; +} +return sign * r; +}, "~S"); +Clazz.defineMethod (c$, "formDouble", +function (x) { +var r; +if (this.precision < 0) { +this.precision = 6; +}var s = 1; +if (x < 0) { +x = -x; +s = -1; +}if (this.fmt == 'f') { +r = this.fixed_format (x); +} else if ((this.fmt == 'e') || (this.fmt == 'E') || (this.fmt == 'g') || (this.fmt == 'G')) { +r = this.exp_format (x); +} else { +throw new IllegalArgumentException (); +}return this.pad (this.sign (s, r)); +}, "~N"); +Clazz.defineMethod (c$, "formLong", +function (x) { +var r; +var s = 0; +if ((this.fmt == 'd') || (this.fmt == 'i')) { +if (x < 0) { +r = ("" + x).substring (1); +s = -1; +} else { +r = "" + x; +s = 1; +}} else if (this.fmt == 'o') { +r = jalview.util.Format.convert (x, 3, 7, "01234567"); +} else if (this.fmt == 'x') { +r = jalview.util.Format.convert (x, 4, 15, "0123456789abcdef"); +} else if (this.fmt == 'X') { +r = jalview.util.Format.convert (x, 4, 15, "0123456789ABCDEF"); +} else { +throw new IllegalArgumentException (); +}return this.pad (this.sign (s, r)); +}, "~N"); +Clazz.defineMethod (c$, "formChar", +function (c) { +if (this.fmt != 'c') { +throw new IllegalArgumentException (); +}var r = "" + c; +return this.pad (r); +}, "~S"); +Clazz.defineMethod (c$, "form", +function (s) { +if (this.fmt != 's') { +throw new IllegalArgumentException (); +}if (this.precision >= 0) { +s = s.substring (0, this.precision); +}return this.pad (s); +}, "~S"); +c$.repeat = Clazz.defineMethod (c$, "repeat", +($fz = function (c, n) { +if (n <= 0) { +return ""; +}var s = new StringBuffer (n); +for (var i = 0; i < n; i++) { +s.append (c); +} +return s.toString (); +}, $fz.isPrivate = true, $fz), "~S,~N"); +c$.convert = Clazz.defineMethod (c$, "convert", +($fz = function (x, n, m, d) { +if (x == 0) { +return "0"; +}var r = ""; +while (x != 0) { +r = d.charAt ((x & m)) + r; +x = x >>> n; +} +return r; +}, $fz.isPrivate = true, $fz), "~N,~N,~N,~S"); +Clazz.defineMethod (c$, "pad", +($fz = function (r) { +var p = jalview.util.Format.repeat (' ', this.width - r.length); +if (this.left_align) { +return this.pre + r + p + this.post; +} else { +return this.pre + p + r + this.post; +}}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "sign", +($fz = function (s, r) { +var p = ""; +if (s < 0) { +p = "-"; +} else if (s > 0) { +if (this.show_plus) { +p = "+"; +} else if (this.show_space) { +p = " "; +}} else { +if ((this.fmt == 'o') && this.alternate && (r.length > 0) && (r.charAt (0) != '0')) { +p = "0"; +} else if ((this.fmt == 'x') && this.alternate) { +p = "0x"; +} else if ((this.fmt == 'X') && this.alternate) { +p = "0X"; +}}var w = 0; +if (this.leading_zeroes) { +w = this.width; +} else if (((this.fmt == 'd') || (this.fmt == 'i') || (this.fmt == 'x') || (this.fmt == 'X') || (this.fmt == 'o')) && (this.precision > 0)) { +w = this.precision; +}return p + jalview.util.Format.repeat ('0', w - p.length - r.length) + r; +}, $fz.isPrivate = true, $fz), "~N,~S"); +Clazz.defineMethod (c$, "fixed_format", +($fz = function (d) { +var removeTrailing = ((this.fmt == 'G') || (this.fmt == 'g')) && !this.alternate; +if (d > 0x7FFFFFFFFFFFFFFF) { +return this.exp_format (d); +}if (this.precision == 0) { +return Clazz.doubleToLong (d + 0.5) + (removeTrailing ? "" : "."); +}var whole = Clazz.doubleToLong (d); +var fr = d - whole; +if ((fr >= 1) || (fr < 0)) { +return this.exp_format (d); +}var factor = 1; +var leading_zeroes = ""; +for (var i = 1; (i <= this.precision) && (factor <= 0x7FFFFFFFFFFFFFFF); i++) { +factor *= 10; +leading_zeroes = leading_zeroes + "0"; +} +var l = Clazz.doubleToLong ((factor * fr) + 0.5); +if (l >= factor) { +l = 0; +whole++; +}var z = leading_zeroes + l; +z = "." + z.substring (z.length - this.precision, z.length); +if (removeTrailing) { +var t = z.length - 1; +while ((t >= 0) && (z.charAt (t) == '0')) { +t--; +} +if ((t >= 0) && (z.charAt (t) == '.')) { +t--; +}z = z.substring (0, t + 1); +}return whole + z; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "exp_format", +($fz = function (d) { +var f = ""; +var e = 0; +var dd = d; +var factor = 1; +if (d != 0) { +while (dd > 10) { +e++; +factor /= 10; +dd = dd / 10; +} +while (dd < 1) { +e--; +factor *= 10; +dd = dd * 10; +} +}if (((this.fmt == 'g') || (this.fmt == 'G')) && (e >= -4) && (e < this.precision)) { +return this.fixed_format (d); +}d = d * factor; +f = f + this.fixed_format (d); +if ((this.fmt == 'e') || (this.fmt == 'g')) { +f = f + "e"; +} else { +f = f + "E"; +}var p = "000"; +if (e >= 0) { +f = f + "+"; +p = p + e; +} else { +f = f + "-"; +p = p + (-e); +}return f + p.substring (p.length - 3, p.length); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +return this.formatString; +}); +}); diff --git a/bin/jalview/util/GroupUrlLink.class b/bin/jalview/util/GroupUrlLink.class index 8eab61a..c9f543d 100644 Binary files a/bin/jalview/util/GroupUrlLink.class and b/bin/jalview/util/GroupUrlLink.class differ diff --git a/bin/jalview/util/GroupUrlLink.js b/bin/jalview/util/GroupUrlLink.js index c6f0e7e..5535c1f 100644 --- a/bin/jalview/util/GroupUrlLink.js +++ b/bin/jalview/util/GroupUrlLink.js @@ -1,363 +1,363 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.lang.Exception"], "jalview.util.GroupUrlLink", ["jalview.jsdev.RegExp", "jalview.util.MessageManager", "$.Platform", "$.QuickSort", "java.lang.Error", "$.StringBuffer", "java.util.Hashtable"], function () { -c$ = Clazz.decorateAsClass (function () { -if (!Clazz.isClassDefined ("jalview.util.GroupUrlLink.UrlStringTooLongException")) { -jalview.util.GroupUrlLink.$GroupUrlLink$UrlStringTooLongException$ (); -} -this.url_prefix = null; -this.target = null; -this.label = null; -this.url_suffix = null; -this.separators = null; -this.regexReplace = null; -this.invalidMessage = null; -this.segs = null; -this.mtch = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "GroupUrlLink"); -Clazz.makeConstructor (c$, -function (link) { -var sep = link.indexOf ("|"); -this.segs = Clazz.newIntArray (jalview.util.GroupUrlLink.tokens.length, 0); -var ntoks = 0; -for (var i = 0; i < this.segs.length; i++) { -if ((this.segs[i] = link.indexOf ("$" + jalview.util.GroupUrlLink.tokens[i])) > -1) { -ntoks++; -}} -if (ntoks == 0) { -this.invalidMessage = "Group URL string must contain at least one of "; -for (var i = 0; i < this.segs.length; i++) { -this.invalidMessage += " '$" + jalview.util.GroupUrlLink.tokens[i] + "[=/regex=/]$'"; -} -return; -}var ptok = Clazz.newIntArray (ntoks + 1, 0); -var tmtch = new Array (ntoks + 1); -this.mtch = new Array (ntoks); -for (var i = 0, t = 0; i < this.segs.length; i++) { -if (this.segs[i] > -1) { -ptok[t] = this.segs[i]; -tmtch[t++] = jalview.util.GroupUrlLink.tokens[i]; -}} -ptok[ntoks] = link.length; -tmtch[ntoks] = "$$$$$$$$$"; -jalview.util.QuickSort.sortInt (ptok, tmtch); -for (var i = 0; i < ntoks; i++) { -this.mtch[i] = tmtch[i]; -} -var p = sep; -do { -sep = p; -p = link.indexOf ("|", sep + 1); -} while (p > sep && p < ptok[0]); -this.label = link.substring (0, sep); -if (this.label.indexOf ("|") > -1) { -this.target = this.label.substring (0, this.label.indexOf ("|")); -} else if (this.label.indexOf (" ") > 2) { -this.target = this.label.substring (0, this.label.indexOf (" ")); -} else { -this.target = this.label; -}this.url_prefix = link.substring (sep + 1, ptok[0]); -this.url_suffix = new Array (this.mtch.length); -this.regexReplace = new Array (this.mtch.length); -for (var pass = 0; pass < this.mtch.length; pass++) { -var mlength = 3 + this.mtch[pass].length; -if (link.indexOf ("$" + this.mtch[pass] + "=/") == ptok[pass] && (p = link.indexOf ("/=$", ptok[pass] + mlength)) > ptok[pass] + mlength) { -if (ptok[pass + 1] < p + 3) { -this.invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $" + this.mtch[pass] + " regex with a '/=$' ?"; -return; -}this.url_suffix[pass] = link.substring (p + 3, ptok[pass + 1]); -this.regexReplace[pass] = link.substring (ptok[pass] + mlength, p); -try { -var rg = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace[pass] + "/"); -if (rg == null) { -this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace[pass] + "'\n"; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace[pass] + "'\n"; -} else { -throw e; -} -} -} else { -this.regexReplace[pass] = null; -if ((p = link.indexOf ("$" + this.mtch[pass] + "$")) == ptok[pass]) { -this.url_suffix[pass] = link.substring (p + this.mtch[pass].length + 2, ptok[pass + 1]); -} else { -this.invalidMessage = "Warning: invalid regex structure (after '" + this.mtch[0] + "') for URL link : " + link; -}}} -var pass = 0; -this.separators = new Array (this.url_suffix.length); -var suffices = this.url_suffix[this.url_suffix.length - 1]; -var lastsep = ","; -while ((p = suffices.indexOf ('|')) > -1) { -this.separators[pass] = suffices.substring (p + 1); -if (pass == 0) { -this.url_suffix[this.url_suffix.length - 1] = suffices.substring (0, p); -} else { -lastsep = (this.separators[pass - 1] = this.separators[pass - 1].substring (0, p)); -}suffices = this.separators[pass]; -pass++; -} -if (pass > 0) { -lastsep = this.separators[pass - 1]; -}while (pass < this.separators.length) { -this.separators[pass++] = lastsep; -} -}, "~S"); -Clazz.defineMethod (c$, "getUrl_suffix", -function () { -return this.url_suffix[this.url_suffix.length - 1]; -}); -Clazz.defineMethod (c$, "getUrl_prefix", -function () { -return this.url_prefix; -}); -Clazz.defineMethod (c$, "getTarget", -function () { -return this.target; -}); -Clazz.defineMethod (c$, "getLabel", -function () { -return this.label; -}); -Clazz.defineMethod (c$, "getIDRegexReplace", -function () { -return this._replaceFor (jalview.util.GroupUrlLink.tokens[0]); -}); -Clazz.defineMethod (c$, "_replaceFor", -($fz = function (token) { -for (var i = 0; i < this.mtch.length; i++) { -if (this.segs[i] > -1 && this.mtch[i].equals (token)) { -return this.regexReplace[i]; -}} -return null; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "getSeqRegexReplace", -function () { -return this._replaceFor (jalview.util.GroupUrlLink.tokens[1]); -}); -Clazz.defineMethod (c$, "getInvalidMessage", -function () { -return this.invalidMessage; -}); -Clazz.defineMethod (c$, "isValid", -function () { -return this.invalidMessage == null; -}); -Clazz.defineMethod (c$, "makeUrls", -function (idstrings, seqstrings, dsstring, onlyIfMatches) { -var rstrings = this.replacementArgs (idstrings, seqstrings, dsstring); -return this.makeUrls (rstrings, onlyIfMatches); -}, "~A,~A,~S,~B"); -Clazz.defineMethod (c$, "replacementArgs", -($fz = function (idstrings, seqstrings, dsstring) { -var rstrings = new java.util.Hashtable (); -rstrings.put (jalview.util.GroupUrlLink.tokens[0], idstrings); -rstrings.put (jalview.util.GroupUrlLink.tokens[1], seqstrings); -rstrings.put (jalview.util.GroupUrlLink.tokens[2], Clazz.newArray (-1, [dsstring])); -if (idstrings.length != seqstrings.length) { -throw new Error (jalview.util.MessageManager.getString ("error.idstring_seqstrings_only_one_per_sequence")); -}return rstrings; -}, $fz.isPrivate = true, $fz), "~A,~A,~S"); -Clazz.defineMethod (c$, "makeUrls", -function (repstrings, onlyIfMatches) { -return this.makeUrlsIf (true, repstrings, onlyIfMatches); -}, "java.util.Hashtable,~B"); -Clazz.defineMethod (c$, "makeUrlStubs", -function (ids, seqstr, string, b) { -var rstrings = this.replacementArgs (ids, seqstr, string); -var stubs = this.makeUrlsIf (false, rstrings, b); -if (stubs != null) { -return Clazz.newArray (-1, [stubs[0], stubs[1], rstrings, Clazz.newBooleanArray (-1, [b])]); -}return null; -}, "~A,~A,~S,~B"); -Clazz.defineMethod (c$, "constructFrom", -function (stubs) { -var results = this.makeUrlsIf (true, stubs[2], (stubs[3])[0]); -return (results[3])[0]; -}, "~A"); -Clazz.defineMethod (c$, "makeUrlsIf", -function (createFullUrl, repstrings, onlyIfMatches) { -var pass = 0; -var idseq = new Array (this.mtch.length); -var mins = 0; -var maxs = 0; -for (var i = 0; i < this.mtch.length; i++) { -idseq[i] = repstrings.get (this.mtch[i]); -if (idseq[i].length >= 1) { -if (mins == 0 && idseq[i].length == 1) { -mins = 1; -}if (maxs < 2) { -maxs = idseq[i].length; -} else { -if (maxs != idseq[i].length) { -throw new Error (jalview.util.MessageManager.formatMessage ("error.cannot_have_mixed_length_replacement_vectors", Clazz.newArray (-1, [(this.mtch[i]), Integer.$valueOf (idseq[i].length).toString (), Integer.$valueOf (maxs).toString ()]))); -}}} else { -throw new Error (jalview.util.MessageManager.getString ("error.cannot_have_zero_length_vector_replacement_strings")); -}} -var matched = new Array (idseq.length); -var rgxs = new Array (matched.length); -for (pass = 0; pass < matched.length; pass++) { -matched[pass] = new StringBuffer (); -if (this.regexReplace[pass] != null) { -rgxs[pass] = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace[pass] + "/"); -} else { -rgxs[pass] = null; -}} -var urllength = this.url_prefix.length; -for (pass = 0; pass < matched.length; pass++) { -urllength += this.url_suffix[pass].length; -} -var thismatched = Clazz.newBooleanArray (maxs, false); -var seqsmatched = 0; -for (var sq = 0; sq < maxs; sq++) { -thismatched[sq] = false; -var thematches = new Array (rgxs.length); -for (pass = 0; pass < rgxs.length; pass++) { -thematches[pass] = new StringBuffer (); -if (idseq[pass].length <= sq) { -continue; -}if (rgxs[pass] != null) { -var rg = rgxs[pass]; -var rematchat = 0; -while (rg.searchFrom (idseq[pass][sq], rematchat)) { -rematchat = rg.matchedTo (); -thismatched[sq] = new Boolean (thismatched[sq] | true).valueOf (); -urllength += rg.charsMatched (); -if ((urllength + 32) > jalview.util.Platform.getMaxCommandLineLength ()) { -throw Clazz.innerTypeInstance (jalview.util.GroupUrlLink.UrlStringTooLongException, this, null, urllength); -}if (!createFullUrl) { -continue; -}var ns = rg.numSubs (); -if (ns == 0) { -thematches[pass].append (rg.stringMatched ()); -} else { -var subs = new StringBuffer (); -var s = 0; -while (s <= ns) { -if (s + 1 <= ns && rg.matchedToI (s) > -1 && rg.matchedToI (s + 1) > -1 && rg.matchedToI (s + 1) < rg.matchedToI (s)) { -var r = s + 1; -var rmtch = new StringBuffer (); -while (r <= ns && rg.matchedToI (r) <= rg.matchedToI (s)) { -if (rg.matchedFromI (r) > -1) { -rmtch.append (rg.stringMatchedI (r)); -}r++; -} -if (rmtch.length () > 0) { -subs.append (rmtch); -}s = r; -} else { -if (rg.matchedFromI (s) > -1) { -subs.append (rg.stringMatchedI (s)); -}s++; -}} -thematches[pass].append (subs); -}} -} else { -if (!onlyIfMatches) { -thismatched[sq] = new Boolean (thismatched[sq] | true).valueOf (); -urllength += idseq[pass][sq].length; -if (createFullUrl) { -thematches[pass] = new StringBuffer (idseq[pass][sq]); -}}}} -if (thismatched[sq]) { -if (createFullUrl) { -for (pass = 0; pass < matched.length; pass++) { -if (idseq[pass].length > 1 && matched[pass].length () > 0) { -matched[pass].append (this.separators[pass]); -}matched[pass].append (thematches[pass]); -} -}seqsmatched++; -}} -if (seqsmatched == 0 || (createFullUrl && matched[0].length () == 0)) { -return null; -}if ((urllength + 32) > jalview.util.Platform.getMaxCommandLineLength ()) { -throw Clazz.innerTypeInstance (jalview.util.GroupUrlLink.UrlStringTooLongException, this, null, urllength); -}if (!createFullUrl) { -return Clazz.newArray (-1, [ Clazz.newIntArray (-1, [seqsmatched]), thismatched]); -}var submiturl = new StringBuffer (); -submiturl.append (this.url_prefix); -for (pass = 0; pass < matched.length; pass++) { -submiturl.append (matched[pass]); -if (this.url_suffix[pass] != null) { -submiturl.append (this.url_suffix[pass]); -}} -return Clazz.newArray (-1, [ Clazz.newIntArray (-1, [seqsmatched]), thismatched, matched, Clazz.newArray (-1, [submiturl.toString ()])]); -}, "~B,java.util.Hashtable,~B"); -Clazz.defineMethod (c$, "getNumberInvolved", -function (urlstub) { -return (urlstub[0])[0]; -}, "~A"); -Clazz.defineMethod (c$, "getGroupURLType", -function () { -var r = 0; -for (var pass = 0; pass < jalview.util.GroupUrlLink.tokens.length; pass++) { -for (var i = 0; i < this.mtch.length; i++) { -if (this.mtch[i].equals (jalview.util.GroupUrlLink.tokens[pass])) { -r += 1 << pass; -}} -} -return r; -}); -Clazz.overrideMethod (c$, "toString", -function () { -var result = new StringBuffer (); -result.append (this.label + "|" + this.url_prefix); -var r; -for (r = 0; r < this.url_suffix.length; r++) { -result.append ("$"); -result.append (this.mtch[r]); -if (this.regexReplace[r] != null) { -result.append ("=/"); -result.append (this.regexReplace[r]); -result.append ("/="); -}result.append ("$"); -result.append (this.url_suffix[r]); -} -for (r = 0; r < this.separators.length; r++) { -result.append ("|"); -result.append (this.separators[r]); -} -return result.toString (); -}); -c$.formStrings = Clazz.defineMethod (c$, "formStrings", -function (seqs) { -var idset = Clazz.newArray (2, seqs.length, null); -for (var i = 0; i < seqs.length; i++) { -idset[0][i] = seqs[i].getName (); -idset[1][i] = seqs[i].getSequenceAsString (); -} -return idset; -}, "~A"); -Clazz.defineMethod (c$, "setLabel", -function (newlabel) { -this.label = newlabel; -}, "~S"); -c$.$GroupUrlLink$UrlStringTooLongException$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.urlLength = 0; -Clazz.instantialize (this, arguments); -}, jalview.util.GroupUrlLink, "UrlStringTooLongException", Exception); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, jalview.util.GroupUrlLink.UrlStringTooLongException, []); -this.urlLength = a; -}, "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -return "Generated url is estimated to be too long (" + this.urlLength + ")"; -}); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"tokens", null); -{ -if (jalview.util.GroupUrlLink.tokens == null) { -jalview.util.GroupUrlLink.tokens = Clazz.newArray (-1, ["SEQUENCEIDS", "SEQUENCES", "DATASETID"]); -}}Clazz.defineStatics (c$, -"SEQUENCEIDS", 1, -"SEQUENCES", 2, -"DATASETID", 4); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.lang.Exception"], "jalview.util.GroupUrlLink", ["jalview.jsdev.RegExp", "jalview.util.MessageManager", "$.Platform", "$.QuickSort", "java.lang.Error", "$.StringBuffer", "java.util.Hashtable"], function () { +c$ = Clazz.decorateAsClass (function () { +if (!Clazz.isClassDefined ("jalview.util.GroupUrlLink.UrlStringTooLongException")) { +jalview.util.GroupUrlLink.$GroupUrlLink$UrlStringTooLongException$ (); +} +this.url_prefix = null; +this.target = null; +this.label = null; +this.url_suffix = null; +this.separators = null; +this.regexReplace = null; +this.invalidMessage = null; +this.segs = null; +this.mtch = null; +Clazz.instantialize (this, arguments); +}, jalview.util, "GroupUrlLink"); +Clazz.makeConstructor (c$, +function (link) { +var sep = link.indexOf ("|"); +this.segs = Clazz.newIntArray (jalview.util.GroupUrlLink.tokens.length, 0); +var ntoks = 0; +for (var i = 0; i < this.segs.length; i++) { +if ((this.segs[i] = link.indexOf ("$" + jalview.util.GroupUrlLink.tokens[i])) > -1) { +ntoks++; +}} +if (ntoks == 0) { +this.invalidMessage = "Group URL string must contain at least one of "; +for (var i = 0; i < this.segs.length; i++) { +this.invalidMessage += " '$" + jalview.util.GroupUrlLink.tokens[i] + "[=/regex=/]$'"; +} +return; +}var ptok = Clazz.newIntArray (ntoks + 1, 0); +var tmtch = new Array (ntoks + 1); +this.mtch = new Array (ntoks); +for (var i = 0, t = 0; i < this.segs.length; i++) { +if (this.segs[i] > -1) { +ptok[t] = this.segs[i]; +tmtch[t++] = jalview.util.GroupUrlLink.tokens[i]; +}} +ptok[ntoks] = link.length; +tmtch[ntoks] = "$$$$$$$$$"; +jalview.util.QuickSort.sortInt (ptok, tmtch); +for (var i = 0; i < ntoks; i++) { +this.mtch[i] = tmtch[i]; +} +var p = sep; +do { +sep = p; +p = link.indexOf ("|", sep + 1); +} while (p > sep && p < ptok[0]); +this.label = link.substring (0, sep); +if (this.label.indexOf ("|") > -1) { +this.target = this.label.substring (0, this.label.indexOf ("|")); +} else if (this.label.indexOf (" ") > 2) { +this.target = this.label.substring (0, this.label.indexOf (" ")); +} else { +this.target = this.label; +}this.url_prefix = link.substring (sep + 1, ptok[0]); +this.url_suffix = new Array (this.mtch.length); +this.regexReplace = new Array (this.mtch.length); +for (var pass = 0; pass < this.mtch.length; pass++) { +var mlength = 3 + this.mtch[pass].length; +if (link.indexOf ("$" + this.mtch[pass] + "=/") == ptok[pass] && (p = link.indexOf ("/=$", ptok[pass] + mlength)) > ptok[pass] + mlength) { +if (ptok[pass + 1] < p + 3) { +this.invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $" + this.mtch[pass] + " regex with a '/=$' ?"; +return; +}this.url_suffix[pass] = link.substring (p + 3, ptok[pass + 1]); +this.regexReplace[pass] = link.substring (ptok[pass] + mlength, p); +try { +var rg = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace[pass] + "/"); +if (rg == null) { +this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace[pass] + "'\n"; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace[pass] + "'\n"; +} else { +throw e; +} +} +} else { +this.regexReplace[pass] = null; +if ((p = link.indexOf ("$" + this.mtch[pass] + "$")) == ptok[pass]) { +this.url_suffix[pass] = link.substring (p + this.mtch[pass].length + 2, ptok[pass + 1]); +} else { +this.invalidMessage = "Warning: invalid regex structure (after '" + this.mtch[0] + "') for URL link : " + link; +}}} +var pass = 0; +this.separators = new Array (this.url_suffix.length); +var suffices = this.url_suffix[this.url_suffix.length - 1]; +var lastsep = ","; +while ((p = suffices.indexOf ('|')) > -1) { +this.separators[pass] = suffices.substring (p + 1); +if (pass == 0) { +this.url_suffix[this.url_suffix.length - 1] = suffices.substring (0, p); +} else { +lastsep = (this.separators[pass - 1] = this.separators[pass - 1].substring (0, p)); +}suffices = this.separators[pass]; +pass++; +} +if (pass > 0) { +lastsep = this.separators[pass - 1]; +}while (pass < this.separators.length) { +this.separators[pass++] = lastsep; +} +}, "~S"); +Clazz.defineMethod (c$, "getUrl_suffix", +function () { +return this.url_suffix[this.url_suffix.length - 1]; +}); +Clazz.defineMethod (c$, "getUrl_prefix", +function () { +return this.url_prefix; +}); +Clazz.defineMethod (c$, "getTarget", +function () { +return this.target; +}); +Clazz.defineMethod (c$, "getLabel", +function () { +return this.label; +}); +Clazz.defineMethod (c$, "getIDRegexReplace", +function () { +return this._replaceFor (jalview.util.GroupUrlLink.tokens[0]); +}); +Clazz.defineMethod (c$, "_replaceFor", +($fz = function (token) { +for (var i = 0; i < this.mtch.length; i++) { +if (this.segs[i] > -1 && this.mtch[i].equals (token)) { +return this.regexReplace[i]; +}} +return null; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "getSeqRegexReplace", +function () { +return this._replaceFor (jalview.util.GroupUrlLink.tokens[1]); +}); +Clazz.defineMethod (c$, "getInvalidMessage", +function () { +return this.invalidMessage; +}); +Clazz.defineMethod (c$, "isValid", +function () { +return this.invalidMessage == null; +}); +Clazz.defineMethod (c$, "makeUrls", +function (idstrings, seqstrings, dsstring, onlyIfMatches) { +var rstrings = this.replacementArgs (idstrings, seqstrings, dsstring); +return this.makeUrls (rstrings, onlyIfMatches); +}, "~A,~A,~S,~B"); +Clazz.defineMethod (c$, "replacementArgs", +($fz = function (idstrings, seqstrings, dsstring) { +var rstrings = new java.util.Hashtable (); +rstrings.put (jalview.util.GroupUrlLink.tokens[0], idstrings); +rstrings.put (jalview.util.GroupUrlLink.tokens[1], seqstrings); +rstrings.put (jalview.util.GroupUrlLink.tokens[2], Clazz.newArray (-1, [dsstring])); +if (idstrings.length != seqstrings.length) { +throw new Error (jalview.util.MessageManager.getString ("error.idstring_seqstrings_only_one_per_sequence")); +}return rstrings; +}, $fz.isPrivate = true, $fz), "~A,~A,~S"); +Clazz.defineMethod (c$, "makeUrls", +function (repstrings, onlyIfMatches) { +return this.makeUrlsIf (true, repstrings, onlyIfMatches); +}, "java.util.Hashtable,~B"); +Clazz.defineMethod (c$, "makeUrlStubs", +function (ids, seqstr, string, b) { +var rstrings = this.replacementArgs (ids, seqstr, string); +var stubs = this.makeUrlsIf (false, rstrings, b); +if (stubs != null) { +return Clazz.newArray (-1, [stubs[0], stubs[1], rstrings, Clazz.newBooleanArray (-1, [b])]); +}return null; +}, "~A,~A,~S,~B"); +Clazz.defineMethod (c$, "constructFrom", +function (stubs) { +var results = this.makeUrlsIf (true, stubs[2], (stubs[3])[0]); +return (results[3])[0]; +}, "~A"); +Clazz.defineMethod (c$, "makeUrlsIf", +function (createFullUrl, repstrings, onlyIfMatches) { +var pass = 0; +var idseq = new Array (this.mtch.length); +var mins = 0; +var maxs = 0; +for (var i = 0; i < this.mtch.length; i++) { +idseq[i] = repstrings.get (this.mtch[i]); +if (idseq[i].length >= 1) { +if (mins == 0 && idseq[i].length == 1) { +mins = 1; +}if (maxs < 2) { +maxs = idseq[i].length; +} else { +if (maxs != idseq[i].length) { +throw new Error (jalview.util.MessageManager.formatMessage ("error.cannot_have_mixed_length_replacement_vectors", Clazz.newArray (-1, [(this.mtch[i]), Integer.$valueOf (idseq[i].length).toString (), Integer.$valueOf (maxs).toString ()]))); +}}} else { +throw new Error (jalview.util.MessageManager.getString ("error.cannot_have_zero_length_vector_replacement_strings")); +}} +var matched = new Array (idseq.length); +var rgxs = new Array (matched.length); +for (pass = 0; pass < matched.length; pass++) { +matched[pass] = new StringBuffer (); +if (this.regexReplace[pass] != null) { +rgxs[pass] = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace[pass] + "/"); +} else { +rgxs[pass] = null; +}} +var urllength = this.url_prefix.length; +for (pass = 0; pass < matched.length; pass++) { +urllength += this.url_suffix[pass].length; +} +var thismatched = Clazz.newBooleanArray (maxs, false); +var seqsmatched = 0; +for (var sq = 0; sq < maxs; sq++) { +thismatched[sq] = false; +var thematches = new Array (rgxs.length); +for (pass = 0; pass < rgxs.length; pass++) { +thematches[pass] = new StringBuffer (); +if (idseq[pass].length <= sq) { +continue; +}if (rgxs[pass] != null) { +var rg = rgxs[pass]; +var rematchat = 0; +while (rg.searchFrom (idseq[pass][sq], rematchat)) { +rematchat = rg.matchedTo (); +thismatched[sq] = new Boolean (thismatched[sq] | true).valueOf (); +urllength += rg.charsMatched (); +if ((urllength + 32) > jalview.util.Platform.getMaxCommandLineLength ()) { +throw Clazz.innerTypeInstance (jalview.util.GroupUrlLink.UrlStringTooLongException, this, null, urllength); +}if (!createFullUrl) { +continue; +}var ns = rg.numSubs (); +if (ns == 0) { +thematches[pass].append (rg.stringMatched ()); +} else { +var subs = new StringBuffer (); +var s = 0; +while (s <= ns) { +if (s + 1 <= ns && rg.matchedToI (s) > -1 && rg.matchedToI (s + 1) > -1 && rg.matchedToI (s + 1) < rg.matchedToI (s)) { +var r = s + 1; +var rmtch = new StringBuffer (); +while (r <= ns && rg.matchedToI (r) <= rg.matchedToI (s)) { +if (rg.matchedFromI (r) > -1) { +rmtch.append (rg.stringMatchedI (r)); +}r++; +} +if (rmtch.length () > 0) { +subs.append (rmtch); +}s = r; +} else { +if (rg.matchedFromI (s) > -1) { +subs.append (rg.stringMatchedI (s)); +}s++; +}} +thematches[pass].append (subs); +}} +} else { +if (!onlyIfMatches) { +thismatched[sq] = new Boolean (thismatched[sq] | true).valueOf (); +urllength += idseq[pass][sq].length; +if (createFullUrl) { +thematches[pass] = new StringBuffer (idseq[pass][sq]); +}}}} +if (thismatched[sq]) { +if (createFullUrl) { +for (pass = 0; pass < matched.length; pass++) { +if (idseq[pass].length > 1 && matched[pass].length () > 0) { +matched[pass].append (this.separators[pass]); +}matched[pass].append (thematches[pass]); +} +}seqsmatched++; +}} +if (seqsmatched == 0 || (createFullUrl && matched[0].length () == 0)) { +return null; +}if ((urllength + 32) > jalview.util.Platform.getMaxCommandLineLength ()) { +throw Clazz.innerTypeInstance (jalview.util.GroupUrlLink.UrlStringTooLongException, this, null, urllength); +}if (!createFullUrl) { +return Clazz.newArray (-1, [ Clazz.newIntArray (-1, [seqsmatched]), thismatched]); +}var submiturl = new StringBuffer (); +submiturl.append (this.url_prefix); +for (pass = 0; pass < matched.length; pass++) { +submiturl.append (matched[pass]); +if (this.url_suffix[pass] != null) { +submiturl.append (this.url_suffix[pass]); +}} +return Clazz.newArray (-1, [ Clazz.newIntArray (-1, [seqsmatched]), thismatched, matched, Clazz.newArray (-1, [submiturl.toString ()])]); +}, "~B,java.util.Hashtable,~B"); +Clazz.defineMethod (c$, "getNumberInvolved", +function (urlstub) { +return (urlstub[0])[0]; +}, "~A"); +Clazz.defineMethod (c$, "getGroupURLType", +function () { +var r = 0; +for (var pass = 0; pass < jalview.util.GroupUrlLink.tokens.length; pass++) { +for (var i = 0; i < this.mtch.length; i++) { +if (this.mtch[i].equals (jalview.util.GroupUrlLink.tokens[pass])) { +r += 1 << pass; +}} +} +return r; +}); +Clazz.overrideMethod (c$, "toString", +function () { +var result = new StringBuffer (); +result.append (this.label + "|" + this.url_prefix); +var r; +for (r = 0; r < this.url_suffix.length; r++) { +result.append ("$"); +result.append (this.mtch[r]); +if (this.regexReplace[r] != null) { +result.append ("=/"); +result.append (this.regexReplace[r]); +result.append ("/="); +}result.append ("$"); +result.append (this.url_suffix[r]); +} +for (r = 0; r < this.separators.length; r++) { +result.append ("|"); +result.append (this.separators[r]); +} +return result.toString (); +}); +c$.formStrings = Clazz.defineMethod (c$, "formStrings", +function (seqs) { +var idset = Clazz.newArray (2, seqs.length, null); +for (var i = 0; i < seqs.length; i++) { +idset[0][i] = seqs[i].getName (); +idset[1][i] = seqs[i].getSequenceAsString (); +} +return idset; +}, "~A"); +Clazz.defineMethod (c$, "setLabel", +function (newlabel) { +this.label = newlabel; +}, "~S"); +c$.$GroupUrlLink$UrlStringTooLongException$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.urlLength = 0; +Clazz.instantialize (this, arguments); +}, jalview.util.GroupUrlLink, "UrlStringTooLongException", Exception); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, jalview.util.GroupUrlLink.UrlStringTooLongException, []); +this.urlLength = a; +}, "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +return "Generated url is estimated to be too long (" + this.urlLength + ")"; +}); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"tokens", null); +{ +if (jalview.util.GroupUrlLink.tokens == null) { +jalview.util.GroupUrlLink.tokens = Clazz.newArray (-1, ["SEQUENCEIDS", "SEQUENCES", "DATASETID"]); +}}Clazz.defineStatics (c$, +"SEQUENCEIDS", 1, +"SEQUENCES", 2, +"DATASETID", 4); +}); diff --git a/bin/jalview/util/MapList.class b/bin/jalview/util/MapList.class index 8c02e1a..d5fddbf 100644 Binary files a/bin/jalview/util/MapList.class and b/bin/jalview/util/MapList.class differ diff --git a/bin/jalview/util/MapList.js b/bin/jalview/util/MapList.js index ff777cc..e7281ac 100644 --- a/bin/jalview/util/MapList.js +++ b/bin/jalview/util/MapList.js @@ -1,409 +1,409 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.util.ArrayList"], "jalview.util.MapList", ["java.lang.StringBuilder", "java.util.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fromShifts = null; -this.toShifts = null; -this.fromRatio = 0; -this.toRatio = 0; -this.fromLowest = 0; -this.fromHighest = 0; -this.toLowest = 0; -this.toHighest = 0; -Clazz.instantialize (this, arguments); -}, jalview.util, "MapList"); -Clazz.prepareFields (c$, function () { -this.fromShifts = new java.util.ArrayList (); -this.toShifts = new java.util.ArrayList (); -}); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (o == null || !(Clazz.instanceOf (o, jalview.util.MapList))) { -return false; -}var obj = o; -if (obj === this) { -return true; -}if (obj.fromRatio != this.fromRatio || obj.toRatio != this.toRatio || obj.fromShifts == null || obj.toShifts == null) { -return false; -}return java.util.Arrays.deepEquals (this.fromShifts.toArray (), obj.fromShifts.toArray ()) && java.util.Arrays.deepEquals (this.toShifts.toArray (), obj.toShifts.toArray ()); -}, "~O"); -Clazz.defineMethod (c$, "getFromRanges", -function () { -return this.fromShifts; -}); -Clazz.defineMethod (c$, "getToRanges", -function () { -return this.toShifts; -}); -c$.getRanges = Clazz.defineMethod (c$, "getRanges", -function (shifts) { -var rnges = Clazz.newIntArray (2 * shifts.size (), 0); -var i = 0; -for (var r, $r = shifts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { -rnges[i++] = r[0]; -rnges[i++] = r[1]; -} -return rnges; -}, "java.util.List"); -Clazz.defineMethod (c$, "getFromRatio", -function () { -return this.fromRatio; -}); -Clazz.defineMethod (c$, "getToRatio", -function () { -return this.toRatio; -}); -Clazz.defineMethod (c$, "getFromLowest", -function () { -return this.fromLowest; -}); -Clazz.defineMethod (c$, "getFromHighest", -function () { -return this.fromHighest; -}); -Clazz.defineMethod (c$, "getToLowest", -function () { -return this.toLowest; -}); -Clazz.defineMethod (c$, "getToHighest", -function () { -return this.toHighest; -}); -Clazz.makeConstructor (c$, -function (from, to, fromRatio, toRatio) { -this.fromRatio = fromRatio; -this.toRatio = toRatio; -this.fromLowest = from[0]; -this.fromHighest = from[1]; -for (var i = 0; i < from.length; i += 2) { -this.fromLowest = Math.min (this.fromLowest, from[i]); -this.fromHighest = Math.max (this.fromHighest, from[i + 1]); -this.fromShifts.add ( Clazz.newIntArray (-1, [from[i], from[i + 1]])); -} -this.toLowest = to[0]; -this.toHighest = to[1]; -for (var i = 0; i < to.length; i += 2) { -this.toLowest = Math.min (this.toLowest, to[i]); -this.toHighest = Math.max (this.toHighest, to[i + 1]); -this.toShifts.add ( Clazz.newIntArray (-1, [to[i], to[i + 1]])); -} -}, "~A,~A,~N,~N"); -Clazz.makeConstructor (c$, -function (map) { -this.fromLowest = map.fromLowest; -this.fromHighest = map.fromHighest; -this.toLowest = map.toLowest; -this.toHighest = map.toHighest; -this.fromRatio = map.fromRatio; -this.toRatio = map.toRatio; -if (map.fromShifts != null) { -for (var r, $r = map.fromShifts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { -this.fromShifts.add ( Clazz.newIntArray (-1, [r[0], r[1]])); -} -}if (map.toShifts != null) { -for (var r, $r = map.toShifts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { -this.toShifts.add ( Clazz.newIntArray (-1, [r[0], r[1]])); -} -}}, "jalview.util.MapList"); -Clazz.makeConstructor (c$, -function (fromRange, toRange, fromRatio, toRatio) { -this.fromShifts = fromRange; -this.toShifts = toRange; -this.fromRatio = fromRatio; -this.toRatio = toRatio; -this.fromLowest = 2147483647; -this.fromHighest = 0; -for (var range, $range = fromRange.iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { -this.fromLowest = Math.min (this.fromLowest, range[0]); -this.fromHighest = Math.max (this.fromHighest, range[1]); -} -this.toLowest = 2147483647; -this.toHighest = 0; -for (var range, $range = toRange.iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { -this.toLowest = Math.min (this.toLowest, range[0]); -this.toHighest = Math.max (this.toHighest, range[1]); -} -}, "java.util.List,java.util.List,~N,~N"); -Clazz.defineMethod (c$, "makeFromMap", -function () { -return this.posMap (this.fromShifts, this.fromRatio, this.toShifts, this.toRatio); -}); -Clazz.defineMethod (c$, "makeToMap", -function () { -return this.posMap (this.toShifts, this.toRatio, this.fromShifts, this.fromRatio); -}); -Clazz.defineMethod (c$, "posMap", -($fz = function (shiftTo, ratio, shiftFrom, toRatio) { -var iv = 0; -var ivSize = shiftTo.size (); -if (iv >= ivSize) { -return null; -}var intv = shiftTo.get (iv++); -var from = intv[0]; -var to = intv[1]; -if (from > to) { -from = intv[1]; -to = intv[0]; -}while (iv < ivSize) { -intv = shiftTo.get (iv++); -if (intv[0] < from) { -from = intv[0]; -}if (intv[1] < from) { -from = intv[1]; -}if (intv[0] > to) { -to = intv[0]; -}if (intv[1] > to) { -to = intv[1]; -}} -var tF = 0; -var tT = 0; -var mp = Clazz.newIntArray (to - from + 2, 0); -for (var i = 0; i < mp.length; i++) { -var m = jalview.util.MapList.shift (i + from, shiftTo, ratio, shiftFrom, toRatio); -if (m != null) { -if (i == 0) { -tF = tT = m[0]; -} else { -if (m[0] < tF) { -tF = m[0]; -}if (m[0] > tT) { -tT = m[0]; -}}}mp[i] = m; -} -var map = Clazz.newArray (-1, [ Clazz.newIntArray (-1, [from, to, tF, tT]), Clazz.newIntArray (to - from + 2, 0)]); -map[0][2] = tF; -map[0][3] = tT; -for (var i = 0; i < mp.length; i++) { -if (mp[i] != null) { -map[1][i] = mp[i][0] - tF; -} else { -map[1][i] = -1; -}} -return map; -}, $fz.isPrivate = true, $fz), "java.util.List,~N,java.util.List,~N"); -Clazz.defineMethod (c$, "shiftFrom", -function (pos) { -return jalview.util.MapList.shift (pos, this.fromShifts, this.fromRatio, this.toShifts, this.toRatio); -}, "~N"); -Clazz.defineMethod (c$, "shiftTo", -function (pos) { -return jalview.util.MapList.shift (pos, this.toShifts, this.toRatio, this.fromShifts, this.fromRatio); -}, "~N"); -c$.shift = Clazz.defineMethod (c$, "shift", -function (pos, shiftTo, fromRatio, shiftFrom, toRatio) { -var fromCount = jalview.util.MapList.countPos (shiftTo, pos); -if (fromCount == null) { -return null; -}var fromRemainder = (fromCount[0] - 1) % fromRatio; -var toCount = 1 + ((Clazz.doubleToInt ((fromCount[0] - 1) / fromRatio)) * toRatio); -var toPos = jalview.util.MapList.countToPos (shiftFrom, toCount); -if (toPos == null) { -return null; -}return Clazz.newIntArray (-1, [toPos[0], fromRemainder, toPos[1]]); -}, "~N,java.util.List,~N,java.util.List,~N"); -c$.countPos = Clazz.defineMethod (c$, "countPos", -function (shiftTo, pos) { -var count = 0; -var intv; -var iv = 0; -var ivSize = shiftTo.size (); -while (iv < ivSize) { -intv = shiftTo.get (iv++); -if (intv[0] <= intv[1]) { -if (pos >= intv[0] && pos <= intv[1]) { -return Clazz.newIntArray (-1, [count + pos - intv[0] + 1, 1]); -} else { -count += intv[1] - intv[0] + 1; -}} else { -if (pos >= intv[1] && pos <= intv[0]) { -return Clazz.newIntArray (-1, [count + intv[0] - pos + 1, -1]); -} else { -count += intv[0] - intv[1] + 1; -}}} -return null; -}, "java.util.List,~N"); -c$.countToPos = Clazz.defineMethod (c$, "countToPos", -function (shiftFrom, pos) { -var count = 0; -var diff = 0; -var iv = 0; -var ivSize = shiftFrom.size (); -var intv = Clazz.newIntArray (-1, [0, 0]); -while (iv < ivSize) { -intv = shiftFrom.get (iv++); -diff = intv[1] - intv[0]; -if (diff >= 0) { -if (pos <= count + 1 + diff) { -return Clazz.newIntArray (-1, [pos - count - 1 + intv[0], 1]); -} else { -count += 1 + diff; -}} else { -if (pos <= count + 1 - diff) { -return Clazz.newIntArray (-1, [intv[0] - (pos - count - 1), -1]); -} else { -count += 1 - diff; -}}} -return null; -}, "java.util.List,~N"); -Clazz.defineMethod (c$, "locateInFrom", -function (start, end) { -var fromStart = this.shiftTo (start); -var fromEnd = this.shiftTo (end); -return jalview.util.MapList.getIntervals (this.fromShifts, fromStart, fromEnd, this.fromRatio); -}, "~N,~N"); -Clazz.defineMethod (c$, "locateInTo", -function (start, end) { -var toStart = this.shiftFrom (start); -var toEnd = this.shiftFrom (end); -return jalview.util.MapList.getIntervals (this.toShifts, toStart, toEnd, this.toRatio); -}, "~N,~N"); -c$.getIntervals = Clazz.defineMethod (c$, "getIntervals", -function (shiftFrom, fromStart, fromEnd, fromRatio2) { -if (fromStart == null || fromEnd == null) { -return null; -}var startpos; -var endpos; -startpos = fromStart[0]; -endpos = fromEnd[0]; -var endindx = (fromRatio2 - 1); -var intv = 0; -var intvSize = shiftFrom.size (); -var iv; -var i = 0; -var fs = -1; -var fe_s = -1; -var fe = -1; -while (intv < intvSize && (fs == -1 || fe == -1)) { -iv = shiftFrom.get (intv++); -if (fe_s > -1) { -endpos = iv[0]; -endindx--; -}if (iv[0] <= iv[1]) { -if (fs == -1 && startpos >= iv[0] && startpos <= iv[1]) { -fs = i; -}if (endpos >= iv[0] && endpos <= iv[1]) { -if (fe_s == -1) { -fe_s = i; -}if (fe_s != -1) { -if (endpos + endindx <= iv[1]) { -fe = i; -endpos = endpos + endindx; -} else { -endindx -= iv[1] - endpos; -}}}} else { -if (fs == -1 && startpos <= iv[0] && startpos >= iv[1]) { -fs = i; -}if (endpos <= iv[0] && endpos >= iv[1]) { -if (fe_s == -1) { -fe_s = i; -}if (fe_s != -1) { -if (endpos - endindx >= iv[1]) { -fe = i; -endpos = endpos - endindx; -} else { -endindx -= endpos - iv[1]; -}}}}i++; -} -if (fs == fe && fe == -1) { -return null; -}var ranges = new java.util.ArrayList (); -if (fs <= fe) { -intv = fs; -i = fs; -iv = shiftFrom.get (intv++); -iv = Clazz.newIntArray (-1, [iv[0], iv[1]]); -if (i == fs) { -iv[0] = startpos; -}while (i != fe) { -ranges.add (iv); -iv = shiftFrom.get (intv++); -iv = Clazz.newIntArray (-1, [iv[0], iv[1]]); -i++; -} -if (i == fe) { -iv[1] = endpos; -}ranges.add (iv); -} else { -i = shiftFrom.size () - 1; -while (i > fs) { -i--; -} -iv = shiftFrom.get (i); -iv = Clazz.newIntArray (-1, [iv[1], iv[0]]); -if (i == fs) { -iv[0] = startpos; -}while (--i != fe) { -ranges.add (iv); -iv = shiftFrom.get (i); -iv = Clazz.newIntArray (-1, [iv[1], iv[0]]); -} -if (i == fe) { -iv[1] = endpos; -}ranges.add (iv); -}var range = null; -if (ranges != null && ranges.size () > 0) { -range = Clazz.newIntArray (ranges.size () * 2, 0); -intv = 0; -intvSize = ranges.size (); -i = 0; -while (intv < intvSize) { -iv = ranges.get (intv); -range[i++] = iv[0]; -range[i++] = iv[1]; -ranges.set (intv++, null); -} -}return range; -}, "java.util.List,~A,~A,~N"); -Clazz.defineMethod (c$, "getToPosition", -function (mpos) { -var mp = this.shiftTo (mpos); -if (mp != null) { -return mp[0]; -}return mpos; -}, "~N"); -Clazz.defineMethod (c$, "getToWord", -function (mpos) { -var mp = this.shiftTo (mpos); -if (mp != null) { -return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.getFromRatio () - 1)]); -}return null; -}, "~N"); -Clazz.defineMethod (c$, "getMappedPosition", -function (pos) { -var mp = this.shiftFrom (pos); -if (mp != null) { -return mp[0]; -}return pos; -}, "~N"); -Clazz.defineMethod (c$, "getMappedWord", -function (pos) { -var mp = this.shiftFrom (pos); -if (mp != null) { -return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.getToRatio () - 1)]); -}return null; -}, "~N"); -Clazz.defineMethod (c$, "getInverse", -function () { -return new jalview.util.MapList (this.getToRanges (), this.getFromRanges (), this.getToRatio (), this.getFromRatio ()); -}); -Clazz.defineMethod (c$, "containsEither", -function (local, map) { -if (local) { -return ((this.getFromLowest () >= map.getFromLowest () && this.getFromHighest () <= map.getFromHighest ()) || (this.getFromLowest () <= map.getFromLowest () && this.getFromHighest () >= map.getFromHighest ())); -} else { -return ((this.getToLowest () >= map.getToLowest () && this.getToHighest () <= map.getToHighest ()) || (this.getToLowest () <= map.getToLowest () && this.getToHighest () >= map.getToHighest ())); -}}, "~B,jalview.util.MapList"); -Clazz.overrideMethod (c$, "toString", -function () { -var sb = new StringBuilder (64); -sb.append ("From (").append (this.fromRatio).append (":").append (this.toRatio).append (") ["); -for (var shift, $shift = this.fromShifts.iterator (); $shift.hasNext () && ((shift = $shift.next ()) || true);) { -sb.append (" ").append (java.util.Arrays.toString (shift)); -} -sb.append (" ] To ["); -for (var shift, $shift = this.toShifts.iterator (); $shift.hasNext () && ((shift = $shift.next ()) || true);) { -sb.append (" ").append (java.util.Arrays.toString (shift)); -} -sb.append (" ]"); -return sb.toString (); -}); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.util.ArrayList"], "jalview.util.MapList", ["java.lang.StringBuilder", "java.util.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fromShifts = null; +this.toShifts = null; +this.fromRatio = 0; +this.toRatio = 0; +this.fromLowest = 0; +this.fromHighest = 0; +this.toLowest = 0; +this.toHighest = 0; +Clazz.instantialize (this, arguments); +}, jalview.util, "MapList"); +Clazz.prepareFields (c$, function () { +this.fromShifts = new java.util.ArrayList (); +this.toShifts = new java.util.ArrayList (); +}); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (o == null || !(Clazz.instanceOf (o, jalview.util.MapList))) { +return false; +}var obj = o; +if (obj === this) { +return true; +}if (obj.fromRatio != this.fromRatio || obj.toRatio != this.toRatio || obj.fromShifts == null || obj.toShifts == null) { +return false; +}return java.util.Arrays.deepEquals (this.fromShifts.toArray (), obj.fromShifts.toArray ()) && java.util.Arrays.deepEquals (this.toShifts.toArray (), obj.toShifts.toArray ()); +}, "~O"); +Clazz.defineMethod (c$, "getFromRanges", +function () { +return this.fromShifts; +}); +Clazz.defineMethod (c$, "getToRanges", +function () { +return this.toShifts; +}); +c$.getRanges = Clazz.defineMethod (c$, "getRanges", +function (shifts) { +var rnges = Clazz.newIntArray (2 * shifts.size (), 0); +var i = 0; +for (var r, $r = shifts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { +rnges[i++] = r[0]; +rnges[i++] = r[1]; +} +return rnges; +}, "java.util.List"); +Clazz.defineMethod (c$, "getFromRatio", +function () { +return this.fromRatio; +}); +Clazz.defineMethod (c$, "getToRatio", +function () { +return this.toRatio; +}); +Clazz.defineMethod (c$, "getFromLowest", +function () { +return this.fromLowest; +}); +Clazz.defineMethod (c$, "getFromHighest", +function () { +return this.fromHighest; +}); +Clazz.defineMethod (c$, "getToLowest", +function () { +return this.toLowest; +}); +Clazz.defineMethod (c$, "getToHighest", +function () { +return this.toHighest; +}); +Clazz.makeConstructor (c$, +function (from, to, fromRatio, toRatio) { +this.fromRatio = fromRatio; +this.toRatio = toRatio; +this.fromLowest = from[0]; +this.fromHighest = from[1]; +for (var i = 0; i < from.length; i += 2) { +this.fromLowest = Math.min (this.fromLowest, from[i]); +this.fromHighest = Math.max (this.fromHighest, from[i + 1]); +this.fromShifts.add ( Clazz.newIntArray (-1, [from[i], from[i + 1]])); +} +this.toLowest = to[0]; +this.toHighest = to[1]; +for (var i = 0; i < to.length; i += 2) { +this.toLowest = Math.min (this.toLowest, to[i]); +this.toHighest = Math.max (this.toHighest, to[i + 1]); +this.toShifts.add ( Clazz.newIntArray (-1, [to[i], to[i + 1]])); +} +}, "~A,~A,~N,~N"); +Clazz.makeConstructor (c$, +function (map) { +this.fromLowest = map.fromLowest; +this.fromHighest = map.fromHighest; +this.toLowest = map.toLowest; +this.toHighest = map.toHighest; +this.fromRatio = map.fromRatio; +this.toRatio = map.toRatio; +if (map.fromShifts != null) { +for (var r, $r = map.fromShifts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { +this.fromShifts.add ( Clazz.newIntArray (-1, [r[0], r[1]])); +} +}if (map.toShifts != null) { +for (var r, $r = map.toShifts.iterator (); $r.hasNext () && ((r = $r.next ()) || true);) { +this.toShifts.add ( Clazz.newIntArray (-1, [r[0], r[1]])); +} +}}, "jalview.util.MapList"); +Clazz.makeConstructor (c$, +function (fromRange, toRange, fromRatio, toRatio) { +this.fromShifts = fromRange; +this.toShifts = toRange; +this.fromRatio = fromRatio; +this.toRatio = toRatio; +this.fromLowest = 2147483647; +this.fromHighest = 0; +for (var range, $range = fromRange.iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { +this.fromLowest = Math.min (this.fromLowest, range[0]); +this.fromHighest = Math.max (this.fromHighest, range[1]); +} +this.toLowest = 2147483647; +this.toHighest = 0; +for (var range, $range = toRange.iterator (); $range.hasNext () && ((range = $range.next ()) || true);) { +this.toLowest = Math.min (this.toLowest, range[0]); +this.toHighest = Math.max (this.toHighest, range[1]); +} +}, "java.util.List,java.util.List,~N,~N"); +Clazz.defineMethod (c$, "makeFromMap", +function () { +return this.posMap (this.fromShifts, this.fromRatio, this.toShifts, this.toRatio); +}); +Clazz.defineMethod (c$, "makeToMap", +function () { +return this.posMap (this.toShifts, this.toRatio, this.fromShifts, this.fromRatio); +}); +Clazz.defineMethod (c$, "posMap", +($fz = function (shiftTo, ratio, shiftFrom, toRatio) { +var iv = 0; +var ivSize = shiftTo.size (); +if (iv >= ivSize) { +return null; +}var intv = shiftTo.get (iv++); +var from = intv[0]; +var to = intv[1]; +if (from > to) { +from = intv[1]; +to = intv[0]; +}while (iv < ivSize) { +intv = shiftTo.get (iv++); +if (intv[0] < from) { +from = intv[0]; +}if (intv[1] < from) { +from = intv[1]; +}if (intv[0] > to) { +to = intv[0]; +}if (intv[1] > to) { +to = intv[1]; +}} +var tF = 0; +var tT = 0; +var mp = Clazz.newIntArray (to - from + 2, 0); +for (var i = 0; i < mp.length; i++) { +var m = jalview.util.MapList.shift (i + from, shiftTo, ratio, shiftFrom, toRatio); +if (m != null) { +if (i == 0) { +tF = tT = m[0]; +} else { +if (m[0] < tF) { +tF = m[0]; +}if (m[0] > tT) { +tT = m[0]; +}}}mp[i] = m; +} +var map = Clazz.newArray (-1, [ Clazz.newIntArray (-1, [from, to, tF, tT]), Clazz.newIntArray (to - from + 2, 0)]); +map[0][2] = tF; +map[0][3] = tT; +for (var i = 0; i < mp.length; i++) { +if (mp[i] != null) { +map[1][i] = mp[i][0] - tF; +} else { +map[1][i] = -1; +}} +return map; +}, $fz.isPrivate = true, $fz), "java.util.List,~N,java.util.List,~N"); +Clazz.defineMethod (c$, "shiftFrom", +function (pos) { +return jalview.util.MapList.shift (pos, this.fromShifts, this.fromRatio, this.toShifts, this.toRatio); +}, "~N"); +Clazz.defineMethod (c$, "shiftTo", +function (pos) { +return jalview.util.MapList.shift (pos, this.toShifts, this.toRatio, this.fromShifts, this.fromRatio); +}, "~N"); +c$.shift = Clazz.defineMethod (c$, "shift", +function (pos, shiftTo, fromRatio, shiftFrom, toRatio) { +var fromCount = jalview.util.MapList.countPos (shiftTo, pos); +if (fromCount == null) { +return null; +}var fromRemainder = (fromCount[0] - 1) % fromRatio; +var toCount = 1 + ((Clazz.doubleToInt ((fromCount[0] - 1) / fromRatio)) * toRatio); +var toPos = jalview.util.MapList.countToPos (shiftFrom, toCount); +if (toPos == null) { +return null; +}return Clazz.newIntArray (-1, [toPos[0], fromRemainder, toPos[1]]); +}, "~N,java.util.List,~N,java.util.List,~N"); +c$.countPos = Clazz.defineMethod (c$, "countPos", +function (shiftTo, pos) { +var count = 0; +var intv; +var iv = 0; +var ivSize = shiftTo.size (); +while (iv < ivSize) { +intv = shiftTo.get (iv++); +if (intv[0] <= intv[1]) { +if (pos >= intv[0] && pos <= intv[1]) { +return Clazz.newIntArray (-1, [count + pos - intv[0] + 1, 1]); +} else { +count += intv[1] - intv[0] + 1; +}} else { +if (pos >= intv[1] && pos <= intv[0]) { +return Clazz.newIntArray (-1, [count + intv[0] - pos + 1, -1]); +} else { +count += intv[0] - intv[1] + 1; +}}} +return null; +}, "java.util.List,~N"); +c$.countToPos = Clazz.defineMethod (c$, "countToPos", +function (shiftFrom, pos) { +var count = 0; +var diff = 0; +var iv = 0; +var ivSize = shiftFrom.size (); +var intv = Clazz.newIntArray (-1, [0, 0]); +while (iv < ivSize) { +intv = shiftFrom.get (iv++); +diff = intv[1] - intv[0]; +if (diff >= 0) { +if (pos <= count + 1 + diff) { +return Clazz.newIntArray (-1, [pos - count - 1 + intv[0], 1]); +} else { +count += 1 + diff; +}} else { +if (pos <= count + 1 - diff) { +return Clazz.newIntArray (-1, [intv[0] - (pos - count - 1), -1]); +} else { +count += 1 - diff; +}}} +return null; +}, "java.util.List,~N"); +Clazz.defineMethod (c$, "locateInFrom", +function (start, end) { +var fromStart = this.shiftTo (start); +var fromEnd = this.shiftTo (end); +return jalview.util.MapList.getIntervals (this.fromShifts, fromStart, fromEnd, this.fromRatio); +}, "~N,~N"); +Clazz.defineMethod (c$, "locateInTo", +function (start, end) { +var toStart = this.shiftFrom (start); +var toEnd = this.shiftFrom (end); +return jalview.util.MapList.getIntervals (this.toShifts, toStart, toEnd, this.toRatio); +}, "~N,~N"); +c$.getIntervals = Clazz.defineMethod (c$, "getIntervals", +function (shiftFrom, fromStart, fromEnd, fromRatio2) { +if (fromStart == null || fromEnd == null) { +return null; +}var startpos; +var endpos; +startpos = fromStart[0]; +endpos = fromEnd[0]; +var endindx = (fromRatio2 - 1); +var intv = 0; +var intvSize = shiftFrom.size (); +var iv; +var i = 0; +var fs = -1; +var fe_s = -1; +var fe = -1; +while (intv < intvSize && (fs == -1 || fe == -1)) { +iv = shiftFrom.get (intv++); +if (fe_s > -1) { +endpos = iv[0]; +endindx--; +}if (iv[0] <= iv[1]) { +if (fs == -1 && startpos >= iv[0] && startpos <= iv[1]) { +fs = i; +}if (endpos >= iv[0] && endpos <= iv[1]) { +if (fe_s == -1) { +fe_s = i; +}if (fe_s != -1) { +if (endpos + endindx <= iv[1]) { +fe = i; +endpos = endpos + endindx; +} else { +endindx -= iv[1] - endpos; +}}}} else { +if (fs == -1 && startpos <= iv[0] && startpos >= iv[1]) { +fs = i; +}if (endpos <= iv[0] && endpos >= iv[1]) { +if (fe_s == -1) { +fe_s = i; +}if (fe_s != -1) { +if (endpos - endindx >= iv[1]) { +fe = i; +endpos = endpos - endindx; +} else { +endindx -= endpos - iv[1]; +}}}}i++; +} +if (fs == fe && fe == -1) { +return null; +}var ranges = new java.util.ArrayList (); +if (fs <= fe) { +intv = fs; +i = fs; +iv = shiftFrom.get (intv++); +iv = Clazz.newIntArray (-1, [iv[0], iv[1]]); +if (i == fs) { +iv[0] = startpos; +}while (i != fe) { +ranges.add (iv); +iv = shiftFrom.get (intv++); +iv = Clazz.newIntArray (-1, [iv[0], iv[1]]); +i++; +} +if (i == fe) { +iv[1] = endpos; +}ranges.add (iv); +} else { +i = shiftFrom.size () - 1; +while (i > fs) { +i--; +} +iv = shiftFrom.get (i); +iv = Clazz.newIntArray (-1, [iv[1], iv[0]]); +if (i == fs) { +iv[0] = startpos; +}while (--i != fe) { +ranges.add (iv); +iv = shiftFrom.get (i); +iv = Clazz.newIntArray (-1, [iv[1], iv[0]]); +} +if (i == fe) { +iv[1] = endpos; +}ranges.add (iv); +}var range = null; +if (ranges != null && ranges.size () > 0) { +range = Clazz.newIntArray (ranges.size () * 2, 0); +intv = 0; +intvSize = ranges.size (); +i = 0; +while (intv < intvSize) { +iv = ranges.get (intv); +range[i++] = iv[0]; +range[i++] = iv[1]; +ranges.set (intv++, null); +} +}return range; +}, "java.util.List,~A,~A,~N"); +Clazz.defineMethod (c$, "getToPosition", +function (mpos) { +var mp = this.shiftTo (mpos); +if (mp != null) { +return mp[0]; +}return mpos; +}, "~N"); +Clazz.defineMethod (c$, "getToWord", +function (mpos) { +var mp = this.shiftTo (mpos); +if (mp != null) { +return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.getFromRatio () - 1)]); +}return null; +}, "~N"); +Clazz.defineMethod (c$, "getMappedPosition", +function (pos) { +var mp = this.shiftFrom (pos); +if (mp != null) { +return mp[0]; +}return pos; +}, "~N"); +Clazz.defineMethod (c$, "getMappedWord", +function (pos) { +var mp = this.shiftFrom (pos); +if (mp != null) { +return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.getToRatio () - 1)]); +}return null; +}, "~N"); +Clazz.defineMethod (c$, "getInverse", +function () { +return new jalview.util.MapList (this.getToRanges (), this.getFromRanges (), this.getToRatio (), this.getFromRatio ()); +}); +Clazz.defineMethod (c$, "containsEither", +function (local, map) { +if (local) { +return ((this.getFromLowest () >= map.getFromLowest () && this.getFromHighest () <= map.getFromHighest ()) || (this.getFromLowest () <= map.getFromLowest () && this.getFromHighest () >= map.getFromHighest ())); +} else { +return ((this.getToLowest () >= map.getToLowest () && this.getToHighest () <= map.getToHighest ()) || (this.getToLowest () <= map.getToLowest () && this.getToHighest () >= map.getToHighest ())); +}}, "~B,jalview.util.MapList"); +Clazz.overrideMethod (c$, "toString", +function () { +var sb = new StringBuilder (64); +sb.append ("From (").append (this.fromRatio).append (":").append (this.toRatio).append (") ["); +for (var shift, $shift = this.fromShifts.iterator (); $shift.hasNext () && ((shift = $shift.next ()) || true);) { +sb.append (" ").append (java.util.Arrays.toString (shift)); +} +sb.append (" ] To ["); +for (var shift, $shift = this.toShifts.iterator (); $shift.hasNext () && ((shift = $shift.next ()) || true);) { +sb.append (" ").append (java.util.Arrays.toString (shift)); +} +sb.append (" ]"); +return sb.toString (); +}); +}); diff --git a/bin/jalview/util/MappingUtils.js b/bin/jalview/util/MappingUtils.js index e5f76b9..487e30d 100644 --- a/bin/jalview/util/MappingUtils.js +++ b/bin/jalview/util/MappingUtils.js @@ -1,245 +1,245 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.MappingUtils", ["jalview.analysis.AlignmentSorter", "jalview.commands.EditCommand", "$.OrderCommand", "jalview.datamodel.AlignmentOrder", "$.ColumnSelection", "$.SearchResults", "$.Sequence", "$.SequenceGroup", "jalview.util.Comparison", "$.StringUtils", "java.util.ArrayList", "$.Collections", "$.HashMap"], function () { -c$ = Clazz.declareType (jalview.util, "MappingUtils"); -c$.mapCutOrPaste = Clazz.defineMethod (c$, "mapCutOrPaste", -function (edit, undo, targetSeqs, result, mappings) { -var action = edit.getAction (); -if (undo) { -action = action.getUndoAction (); -}System.err.println ("MappingUtils.mapCutOrPaste not yet implemented"); -}, "jalview.commands.EditCommand.Edit,~B,java.util.List,jalview.commands.EditCommand,java.util.Set"); -c$.mapEditCommand = Clazz.defineMethod (c$, "mapEditCommand", -function (command, undo, mapTo, gapChar, mappings) { -if (!mapTo.isNucleotide ()) { -return null; -}var targetCopies = new java.util.HashMap (); -for (var seq, $seq = mapTo.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -var ds = seq.getDatasetSequence (); -if (ds != null) { -var copy = new jalview.datamodel.Sequence (seq); -copy.setDatasetSequence (ds); -targetCopies.put (ds, copy); -}} -var originalSequences = command.priorState (undo); -var result = new jalview.commands.EditCommand (); -var edits = command.getEditIterator (!undo); -while (edits.hasNext ()) { -var edit = edits.next (); -if (edit.getAction () === jalview.commands.EditCommand.Action.CUT || edit.getAction () === jalview.commands.EditCommand.Action.PASTE) { -jalview.util.MappingUtils.mapCutOrPaste (edit, undo, mapTo.getSequences (), result, mappings); -} else if (edit.getAction () === jalview.commands.EditCommand.Action.INSERT_GAP || edit.getAction () === jalview.commands.EditCommand.Action.DELETE_GAP) { -jalview.util.MappingUtils.mapInsertOrDelete (edit, undo, originalSequences, mapTo.getSequences (), targetCopies, gapChar, result, mappings); -}} -return result.getSize () > 0 ? result : null; -}, "jalview.commands.EditCommand,~B,jalview.datamodel.AlignmentI,~S,java.util.Set"); -c$.mapInsertOrDelete = Clazz.defineMethod (c$, "mapInsertOrDelete", -function (edit, undo, originalSequences, targetSeqs, targetCopies, gapChar, result, mappings) { -var action = edit.getAction (); -if (undo) { -action = action.getUndoAction (); -}var count = edit.getNumber (); -var editPos = edit.getPosition (); -for (var seq, $seq = 0, $$seq = edit.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { -var ds = seq.getDatasetSequence (); -if (ds == null) { -continue; -}var actedOn = originalSequences.get (ds); -var seqpos = actedOn.findPosition (editPos); -var sr = jalview.util.MappingUtils.buildSearchResults (seq, seqpos, mappings); -if (!sr.isEmpty ()) { -for (var targetSeq, $targetSeq = targetSeqs.iterator (); $targetSeq.hasNext () && ((targetSeq = $targetSeq.next ()) || true);) { -ds = targetSeq.getDatasetSequence (); -if (ds == null) { -continue; -}var copyTarget = targetCopies.get (ds); -var match = sr.getResults (copyTarget, 0, copyTarget.getLength ()); -if (match != null) { -var ratio = 3; -var mappedCount = count * 3; -var mappedEditPos = action === jalview.commands.EditCommand.Action.DELETE_GAP ? match[0] - mappedCount : match[0]; -var e = resultClazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, action, Clazz.newArray (-1, [targetSeq]), mappedEditPos, mappedCount, gapChar); -result.addEdit (e); -if (action === jalview.commands.EditCommand.Action.INSERT_GAP) { -copyTarget.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (copyTarget.getSequence (), mappedEditPos, mappedCount, gapChar))); -} else if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { -copyTarget.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (copyTarget.getSequence (), mappedEditPos, mappedEditPos + mappedCount))); -}}} -}if (action === jalview.commands.EditCommand.Action.INSERT_GAP) { -actedOn.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (actedOn.getSequence (), editPos, count, gapChar))); -} else if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { -actedOn.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (actedOn.getSequence (), editPos, editPos + count))); -}} -}, "jalview.commands.EditCommand.Edit,~B,java.util.Map,java.util.List,java.util.Map,~S,jalview.commands.EditCommand,java.util.Set"); -c$.buildSearchResults = Clazz.defineMethod (c$, "buildSearchResults", -function (seq, index, seqmappings) { -var results = new jalview.datamodel.SearchResults (); -jalview.util.MappingUtils.addSearchResults (results, seq, index, seqmappings); -return results; -}, "jalview.datamodel.SequenceI,~N,java.util.Set"); -c$.addSearchResults = Clazz.defineMethod (c$, "addSearchResults", -function (results, seq, index, seqmappings) { -if (index >= seq.getStart () && index <= seq.getEnd ()) { -for (var acf, $acf = seqmappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -acf.markMappedRegion (seq, index, results); -} -}}, "jalview.datamodel.SearchResults,jalview.datamodel.SequenceI,~N,java.util.Set"); -c$.mapSequenceGroup = Clazz.defineMethod (c$, "mapSequenceGroup", -function (sg, mapFrom, mapTo) { -var targetIsNucleotide = mapTo.isNucleotide (); -var protein = targetIsNucleotide ? mapFrom : mapTo; -var codonFrames = protein.getAlignment ().getCodonFrames (); -var mappedGroup = new jalview.datamodel.SequenceGroup (sg); -mappedGroup.cs = mapTo.getGlobalColourScheme (); -mappedGroup.clear (); -var minStartCol = -1; -var maxEndCol = -1; -var selectionStartRes = sg.getStartRes (); -var selectionEndRes = sg.getEndRes (); -for (var selected, $selected = sg.getSequences ().iterator (); $selected.hasNext () && ((selected = $selected.next ()) || true);) { -var firstUngappedPos = selectionStartRes; -while (firstUngappedPos <= selectionEndRes && jalview.util.Comparison.isGap (selected.getCharAt (firstUngappedPos))) { -firstUngappedPos++; -} -if (firstUngappedPos > selectionEndRes) { -continue; -}var lastUngappedPos = selectionEndRes; -while (lastUngappedPos >= selectionStartRes && jalview.util.Comparison.isGap (selected.getCharAt (lastUngappedPos))) { -lastUngappedPos--; -} -var startResiduePos = selected.findPosition (firstUngappedPos); -var endResiduePos = selected.findPosition (lastUngappedPos); -for (var acf, $acf = codonFrames.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -var mappedSequence = targetIsNucleotide ? acf.getDnaForAaSeq (selected) : acf.getAaForDnaSeq (selected); -if (mappedSequence != null) { -for (var seq, $seq = mapTo.getAlignment ().getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -var mappedStartResidue = 0; -var mappedEndResidue = 0; -if (seq.getDatasetSequence () === mappedSequence) { -var sr = jalview.util.MappingUtils.buildSearchResults (selected, startResiduePos, java.util.Collections.singleton (acf)); -for (var m, $m = sr.getResults ().iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -mappedStartResidue = m.getStart (); -mappedEndResidue = m.getEnd (); -} -sr = jalview.util.MappingUtils.buildSearchResults (selected, endResiduePos, java.util.Collections.singleton (acf)); -for (var m, $m = sr.getResults ().iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -mappedStartResidue = Math.min (mappedStartResidue, m.getStart ()); -mappedEndResidue = Math.max (mappedEndResidue, m.getEnd ()); -} -var mappedStartCol = seq.findIndex (mappedStartResidue) - 1; -minStartCol = minStartCol == -1 ? mappedStartCol : Math.min (minStartCol, mappedStartCol); -var mappedEndCol = seq.findIndex (mappedEndResidue) - 1; -maxEndCol = maxEndCol == -1 ? mappedEndCol : Math.max (maxEndCol, mappedEndCol); -mappedGroup.addSequence (seq, false); -break; -}} -}} -} -mappedGroup.setStartRes (minStartCol < 0 ? 0 : minStartCol); -mappedGroup.setEndRes (maxEndCol < 0 ? 0 : maxEndCol); -return mappedGroup; -}, "jalview.datamodel.SequenceGroup,jalview.api.AlignViewportI,jalview.api.AlignViewportI"); -c$.mapOrderCommand = Clazz.defineMethod (c$, "mapOrderCommand", -function (command, undo, mapTo, mappings) { -var sortOrder = command.getSequenceOrder (undo); -var mappedOrder = new java.util.ArrayList (); -var j = 0; -var mappingToNucleotide = mapTo.isNucleotide (); -for (var seq, $seq = 0, $$seq = sortOrder; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { -for (var acf, $acf = mappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { -var mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq (seq) : acf.getAaForDnaSeq (seq); -if (mappedSeq != null) { -for (var seq2, $seq2 = mapTo.getSequences ().iterator (); $seq2.hasNext () && ((seq2 = $seq2.next ()) || true);) { -if (seq2.getDatasetSequence () === mappedSeq) { -mappedOrder.add (seq2); -j++; -break; -}} -}} -} -if (j == 0) { -return null; -}if (j < mapTo.getHeight ()) { -for (var seq, $seq = mapTo.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -if (!mappedOrder.contains (seq)) { -mappedOrder.add (seq); -}} -}var mappedOrderArray = mappedOrder.toArray ( new Array (mappedOrder.size ())); -var oldOrder = mapTo.getSequencesArray (); -jalview.analysis.AlignmentSorter.sortBy (mapTo, new jalview.datamodel.AlignmentOrder (mappedOrderArray)); -var result = new jalview.commands.OrderCommand (command.getDescription (), oldOrder, mapTo); -return result; -}, "jalview.commands.OrderCommand,~B,jalview.datamodel.AlignmentI,java.util.Set"); -c$.mapColumnSelection = Clazz.defineMethod (c$, "mapColumnSelection", -function (colsel, mapFrom, mapTo) { -var targetIsNucleotide = mapTo.isNucleotide (); -var protein = targetIsNucleotide ? mapFrom : mapTo; -var codonFrames = protein.getAlignment ().getCodonFrames (); -var mappedColumns = new jalview.datamodel.ColumnSelection (); -if (colsel == null) { -return mappedColumns; -}var fromGapChar = mapFrom.getAlignment ().getGapCharacter (); -for (var obj, $obj = colsel.getSelected ().iterator (); $obj.hasNext () && ((obj = $obj.next ()) || true);) { -var col = (obj).intValue (); -var mappedToMin = 2147483647; -var mappedToMax = -2147483648; -for (var fromSeq, $fromSeq = mapFrom.getAlignment ().getSequences ().iterator (); $fromSeq.hasNext () && ((fromSeq = $fromSeq.next ()) || true);) { -if (fromSeq.getCharAt (col) == fromGapChar) { -continue; -}var residuePos = fromSeq.findPosition (col); -var sr = jalview.util.MappingUtils.buildSearchResults (fromSeq, residuePos, codonFrames); -for (var m, $m = sr.getResults ().iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { -var mappedStartResidue = m.getStart (); -var mappedEndResidue = m.getEnd (); -var mappedSeq = m.getSequence (); -for (var toSeq, $toSeq = mapTo.getAlignment ().getSequences ().iterator (); $toSeq.hasNext () && ((toSeq = $toSeq.next ()) || true);) { -if (toSeq.getDatasetSequence () === mappedSeq) { -var mappedStartCol = toSeq.findIndex (mappedStartResidue); -var mappedEndCol = toSeq.findIndex (mappedEndResidue); -mappedToMin = Math.min (mappedToMin, mappedStartCol); -mappedToMax = Math.max (mappedToMax, mappedEndCol); -break; -}} -} -} -for (var i = mappedToMin; i <= mappedToMax; i++) { -mappedColumns.addElement (i - 1); -} -} -return mappedColumns; -}, "jalview.datamodel.ColumnSelection,jalview.api.AlignViewportI,jalview.api.AlignViewportI"); -c$.findCodonFor = Clazz.defineMethod (c$, "findCodonFor", -function (seq, col, mappings) { -var dsPos = seq.findPosition (col); -for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { -if (mapping.involvesSequence (seq)) { -return mapping.getMappedCodon (seq.getDatasetSequence (), dsPos); -}} -return null; -}, "jalview.datamodel.SequenceI,~N,java.util.Set"); -c$.flattenRanges = Clazz.defineMethod (c$, "flattenRanges", -function (ranges) { -var count = 0; -for (var i = 0; i < ranges.length - 1; i += 2) { -count += ranges[i + 1] - ranges[i] + 1; -} -var result = Clazz.newIntArray (count, 0); -var k = 0; -for (var i = 0; i < ranges.length - 1; i += 2) { -for (var j = ranges[i]; j <= ranges[i + 1]; j++) { -result[k++] = j; -} -} -return result; -}, "~A"); -c$.findMappingsForSequence = Clazz.defineMethod (c$, "findMappingsForSequence", -function (sequence, mappings) { -var result = new java.util.ArrayList (); -if (sequence == null || mappings == null) { -return result; -}for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { -if (mapping.involvesSequence (sequence)) { -result.add (mapping); -}} -return result; -}, "jalview.datamodel.SequenceI,java.util.Set"); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.MappingUtils", ["jalview.analysis.AlignmentSorter", "jalview.commands.EditCommand", "$.OrderCommand", "jalview.datamodel.AlignmentOrder", "$.ColumnSelection", "$.SearchResults", "$.Sequence", "$.SequenceGroup", "jalview.util.Comparison", "$.StringUtils", "java.util.ArrayList", "$.Collections", "$.HashMap"], function () { +c$ = Clazz.declareType (jalview.util, "MappingUtils"); +c$.mapCutOrPaste = Clazz.defineMethod (c$, "mapCutOrPaste", +function (edit, undo, targetSeqs, result, mappings) { +var action = edit.getAction (); +if (undo) { +action = action.getUndoAction (); +}System.err.println ("MappingUtils.mapCutOrPaste not yet implemented"); +}, "jalview.commands.EditCommand.Edit,~B,java.util.List,jalview.commands.EditCommand,java.util.Set"); +c$.mapEditCommand = Clazz.defineMethod (c$, "mapEditCommand", +function (command, undo, mapTo, gapChar, mappings) { +if (!mapTo.isNucleotide ()) { +return null; +}var targetCopies = new java.util.HashMap (); +for (var seq, $seq = mapTo.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +var ds = seq.getDatasetSequence (); +if (ds != null) { +var copy = new jalview.datamodel.Sequence (seq); +copy.setDatasetSequence (ds); +targetCopies.put (ds, copy); +}} +var originalSequences = command.priorState (undo); +var result = new jalview.commands.EditCommand (); +var edits = command.getEditIterator (!undo); +while (edits.hasNext ()) { +var edit = edits.next (); +if (edit.getAction () === jalview.commands.EditCommand.Action.CUT || edit.getAction () === jalview.commands.EditCommand.Action.PASTE) { +jalview.util.MappingUtils.mapCutOrPaste (edit, undo, mapTo.getSequences (), result, mappings); +} else if (edit.getAction () === jalview.commands.EditCommand.Action.INSERT_GAP || edit.getAction () === jalview.commands.EditCommand.Action.DELETE_GAP) { +jalview.util.MappingUtils.mapInsertOrDelete (edit, undo, originalSequences, mapTo.getSequences (), targetCopies, gapChar, result, mappings); +}} +return result.getSize () > 0 ? result : null; +}, "jalview.commands.EditCommand,~B,jalview.datamodel.AlignmentI,~S,java.util.Set"); +c$.mapInsertOrDelete = Clazz.defineMethod (c$, "mapInsertOrDelete", +function (edit, undo, originalSequences, targetSeqs, targetCopies, gapChar, result, mappings) { +var action = edit.getAction (); +if (undo) { +action = action.getUndoAction (); +}var count = edit.getNumber (); +var editPos = edit.getPosition (); +for (var seq, $seq = 0, $$seq = edit.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { +var ds = seq.getDatasetSequence (); +if (ds == null) { +continue; +}var actedOn = originalSequences.get (ds); +var seqpos = actedOn.findPosition (editPos); +var sr = jalview.util.MappingUtils.buildSearchResults (seq, seqpos, mappings); +if (!sr.isEmpty ()) { +for (var targetSeq, $targetSeq = targetSeqs.iterator (); $targetSeq.hasNext () && ((targetSeq = $targetSeq.next ()) || true);) { +ds = targetSeq.getDatasetSequence (); +if (ds == null) { +continue; +}var copyTarget = targetCopies.get (ds); +var match = sr.getResults (copyTarget, 0, copyTarget.getLength ()); +if (match != null) { +var ratio = 3; +var mappedCount = count * 3; +var mappedEditPos = action === jalview.commands.EditCommand.Action.DELETE_GAP ? match[0] - mappedCount : match[0]; +var e = resultClazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, action, Clazz.newArray (-1, [targetSeq]), mappedEditPos, mappedCount, gapChar); +result.addEdit (e); +if (action === jalview.commands.EditCommand.Action.INSERT_GAP) { +copyTarget.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (copyTarget.getSequence (), mappedEditPos, mappedCount, gapChar))); +} else if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { +copyTarget.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (copyTarget.getSequence (), mappedEditPos, mappedEditPos + mappedCount))); +}}} +}if (action === jalview.commands.EditCommand.Action.INSERT_GAP) { +actedOn.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (actedOn.getSequence (), editPos, count, gapChar))); +} else if (action === jalview.commands.EditCommand.Action.DELETE_GAP) { +actedOn.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (actedOn.getSequence (), editPos, editPos + count))); +}} +}, "jalview.commands.EditCommand.Edit,~B,java.util.Map,java.util.List,java.util.Map,~S,jalview.commands.EditCommand,java.util.Set"); +c$.buildSearchResults = Clazz.defineMethod (c$, "buildSearchResults", +function (seq, index, seqmappings) { +var results = new jalview.datamodel.SearchResults (); +jalview.util.MappingUtils.addSearchResults (results, seq, index, seqmappings); +return results; +}, "jalview.datamodel.SequenceI,~N,java.util.Set"); +c$.addSearchResults = Clazz.defineMethod (c$, "addSearchResults", +function (results, seq, index, seqmappings) { +if (index >= seq.getStart () && index <= seq.getEnd ()) { +for (var acf, $acf = seqmappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +acf.markMappedRegion (seq, index, results); +} +}}, "jalview.datamodel.SearchResults,jalview.datamodel.SequenceI,~N,java.util.Set"); +c$.mapSequenceGroup = Clazz.defineMethod (c$, "mapSequenceGroup", +function (sg, mapFrom, mapTo) { +var targetIsNucleotide = mapTo.isNucleotide (); +var protein = targetIsNucleotide ? mapFrom : mapTo; +var codonFrames = protein.getAlignment ().getCodonFrames (); +var mappedGroup = new jalview.datamodel.SequenceGroup (sg); +mappedGroup.cs = mapTo.getGlobalColourScheme (); +mappedGroup.clear (); +var minStartCol = -1; +var maxEndCol = -1; +var selectionStartRes = sg.getStartRes (); +var selectionEndRes = sg.getEndRes (); +for (var selected, $selected = sg.getSequences ().iterator (); $selected.hasNext () && ((selected = $selected.next ()) || true);) { +var firstUngappedPos = selectionStartRes; +while (firstUngappedPos <= selectionEndRes && jalview.util.Comparison.isGap (selected.getCharAt (firstUngappedPos))) { +firstUngappedPos++; +} +if (firstUngappedPos > selectionEndRes) { +continue; +}var lastUngappedPos = selectionEndRes; +while (lastUngappedPos >= selectionStartRes && jalview.util.Comparison.isGap (selected.getCharAt (lastUngappedPos))) { +lastUngappedPos--; +} +var startResiduePos = selected.findPosition (firstUngappedPos); +var endResiduePos = selected.findPosition (lastUngappedPos); +for (var acf, $acf = codonFrames.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +var mappedSequence = targetIsNucleotide ? acf.getDnaForAaSeq (selected) : acf.getAaForDnaSeq (selected); +if (mappedSequence != null) { +for (var seq, $seq = mapTo.getAlignment ().getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +var mappedStartResidue = 0; +var mappedEndResidue = 0; +if (seq.getDatasetSequence () === mappedSequence) { +var sr = jalview.util.MappingUtils.buildSearchResults (selected, startResiduePos, java.util.Collections.singleton (acf)); +for (var m, $m = sr.getResults ().iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +mappedStartResidue = m.getStart (); +mappedEndResidue = m.getEnd (); +} +sr = jalview.util.MappingUtils.buildSearchResults (selected, endResiduePos, java.util.Collections.singleton (acf)); +for (var m, $m = sr.getResults ().iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +mappedStartResidue = Math.min (mappedStartResidue, m.getStart ()); +mappedEndResidue = Math.max (mappedEndResidue, m.getEnd ()); +} +var mappedStartCol = seq.findIndex (mappedStartResidue) - 1; +minStartCol = minStartCol == -1 ? mappedStartCol : Math.min (minStartCol, mappedStartCol); +var mappedEndCol = seq.findIndex (mappedEndResidue) - 1; +maxEndCol = maxEndCol == -1 ? mappedEndCol : Math.max (maxEndCol, mappedEndCol); +mappedGroup.addSequence (seq, false); +break; +}} +}} +} +mappedGroup.setStartRes (minStartCol < 0 ? 0 : minStartCol); +mappedGroup.setEndRes (maxEndCol < 0 ? 0 : maxEndCol); +return mappedGroup; +}, "jalview.datamodel.SequenceGroup,jalview.api.AlignViewportI,jalview.api.AlignViewportI"); +c$.mapOrderCommand = Clazz.defineMethod (c$, "mapOrderCommand", +function (command, undo, mapTo, mappings) { +var sortOrder = command.getSequenceOrder (undo); +var mappedOrder = new java.util.ArrayList (); +var j = 0; +var mappingToNucleotide = mapTo.isNucleotide (); +for (var seq, $seq = 0, $$seq = sortOrder; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) { +for (var acf, $acf = mappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) { +var mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq (seq) : acf.getAaForDnaSeq (seq); +if (mappedSeq != null) { +for (var seq2, $seq2 = mapTo.getSequences ().iterator (); $seq2.hasNext () && ((seq2 = $seq2.next ()) || true);) { +if (seq2.getDatasetSequence () === mappedSeq) { +mappedOrder.add (seq2); +j++; +break; +}} +}} +} +if (j == 0) { +return null; +}if (j < mapTo.getHeight ()) { +for (var seq, $seq = mapTo.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +if (!mappedOrder.contains (seq)) { +mappedOrder.add (seq); +}} +}var mappedOrderArray = mappedOrder.toArray ( new Array (mappedOrder.size ())); +var oldOrder = mapTo.getSequencesArray (); +jalview.analysis.AlignmentSorter.sortBy (mapTo, new jalview.datamodel.AlignmentOrder (mappedOrderArray)); +var result = new jalview.commands.OrderCommand (command.getDescription (), oldOrder, mapTo); +return result; +}, "jalview.commands.OrderCommand,~B,jalview.datamodel.AlignmentI,java.util.Set"); +c$.mapColumnSelection = Clazz.defineMethod (c$, "mapColumnSelection", +function (colsel, mapFrom, mapTo) { +var targetIsNucleotide = mapTo.isNucleotide (); +var protein = targetIsNucleotide ? mapFrom : mapTo; +var codonFrames = protein.getAlignment ().getCodonFrames (); +var mappedColumns = new jalview.datamodel.ColumnSelection (); +if (colsel == null) { +return mappedColumns; +}var fromGapChar = mapFrom.getAlignment ().getGapCharacter (); +for (var obj, $obj = colsel.getSelected ().iterator (); $obj.hasNext () && ((obj = $obj.next ()) || true);) { +var col = (obj).intValue (); +var mappedToMin = 2147483647; +var mappedToMax = -2147483648; +for (var fromSeq, $fromSeq = mapFrom.getAlignment ().getSequences ().iterator (); $fromSeq.hasNext () && ((fromSeq = $fromSeq.next ()) || true);) { +if (fromSeq.getCharAt (col) == fromGapChar) { +continue; +}var residuePos = fromSeq.findPosition (col); +var sr = jalview.util.MappingUtils.buildSearchResults (fromSeq, residuePos, codonFrames); +for (var m, $m = sr.getResults ().iterator (); $m.hasNext () && ((m = $m.next ()) || true);) { +var mappedStartResidue = m.getStart (); +var mappedEndResidue = m.getEnd (); +var mappedSeq = m.getSequence (); +for (var toSeq, $toSeq = mapTo.getAlignment ().getSequences ().iterator (); $toSeq.hasNext () && ((toSeq = $toSeq.next ()) || true);) { +if (toSeq.getDatasetSequence () === mappedSeq) { +var mappedStartCol = toSeq.findIndex (mappedStartResidue); +var mappedEndCol = toSeq.findIndex (mappedEndResidue); +mappedToMin = Math.min (mappedToMin, mappedStartCol); +mappedToMax = Math.max (mappedToMax, mappedEndCol); +break; +}} +} +} +for (var i = mappedToMin; i <= mappedToMax; i++) { +mappedColumns.addElement (i - 1); +} +} +return mappedColumns; +}, "jalview.datamodel.ColumnSelection,jalview.api.AlignViewportI,jalview.api.AlignViewportI"); +c$.findCodonFor = Clazz.defineMethod (c$, "findCodonFor", +function (seq, col, mappings) { +var dsPos = seq.findPosition (col); +for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { +if (mapping.involvesSequence (seq)) { +return mapping.getMappedCodon (seq.getDatasetSequence (), dsPos); +}} +return null; +}, "jalview.datamodel.SequenceI,~N,java.util.Set"); +c$.flattenRanges = Clazz.defineMethod (c$, "flattenRanges", +function (ranges) { +var count = 0; +for (var i = 0; i < ranges.length - 1; i += 2) { +count += ranges[i + 1] - ranges[i] + 1; +} +var result = Clazz.newIntArray (count, 0); +var k = 0; +for (var i = 0; i < ranges.length - 1; i += 2) { +for (var j = ranges[i]; j <= ranges[i + 1]; j++) { +result[k++] = j; +} +} +return result; +}, "~A"); +c$.findMappingsForSequence = Clazz.defineMethod (c$, "findMappingsForSequence", +function (sequence, mappings) { +var result = new java.util.ArrayList (); +if (sequence == null || mappings == null) { +return result; +}for (var mapping, $mapping = mappings.iterator (); $mapping.hasNext () && ((mapping = $mapping.next ()) || true);) { +if (mapping.involvesSequence (sequence)) { +result.add (mapping); +}} +return result; +}, "jalview.datamodel.SequenceI,java.util.Set"); +}); diff --git a/bin/jalview/util/MessageManager.class b/bin/jalview/util/MessageManager.class index be41395..c37487c 100644 Binary files a/bin/jalview/util/MessageManager.class and b/bin/jalview/util/MessageManager.class differ diff --git a/bin/jalview/util/MessageManager.js b/bin/jalview/util/MessageManager.js index 44350e0..4283582 100644 --- a/bin/jalview/util/MessageManager.js +++ b/bin/jalview/util/MessageManager.js @@ -1,73 +1,73 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.text.MessageFormat", "java.util.logging.Logger"], "jalview.util.MessageManager", ["java.util.Locale", "$.ResourceBundle", "java.util.logging.Level"], function () { -c$ = Clazz.declareType (jalview.util, "MessageManager"); -c$.getString = Clazz.defineMethod (c$, "getString", -function (key) { -var value = "[missing key] " + key; -try { -value = jalview.util.MessageManager.rb.getString (key); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -jalview.util.MessageManager.log.warning ("I18N missing: " + jalview.util.MessageManager.loc + "\t" + key); -} else { -throw e; -} -} -return value; -}, "~S"); -c$.getLocale = Clazz.defineMethod (c$, "getLocale", -function () { -return jalview.util.MessageManager.loc; -}); -c$.formatMessage = Clazz.defineMethod (c$, "formatMessage", -function (key, params) { -return java.text.MessageFormat.format (jalview.util.MessageManager.getString (key), params); -}, "~S,~A"); -c$.formatMessage = Clazz.defineMethod (c$, "formatMessage", -function (key, params) { -return java.text.MessageFormat.format (jalview.util.MessageManager.getString (key), params); -}, "~S,~A"); -c$.getStringOrReturn = Clazz.defineMethod (c$, "getStringOrReturn", -function (keyroot, name) { -var smkey = keyroot + name.toLowerCase ().replaceAll (" ", ""); -try { -name = jalview.util.MessageManager.rb.getString (smkey); -} catch (x) { -if (Clazz.exceptionOf (x, Exception)) { -jalview.util.MessageManager.log.finest ("I18N missing key with root " + keyroot + ": " + jalview.util.MessageManager.loc + "\t" + smkey); -} else { -throw x; -} -} -return name; -}, "~S,~S"); -Clazz.defineStatics (c$, -"rb", null); -c$.log = c$.prototype.log = java.util.logging.Logger.getLogger (jalview.util.MessageManager.getCanonicalName ()); -Clazz.defineStatics (c$, -"loc", null); -{ -try { -jalview.util.MessageManager.loc = java.util.Locale.getDefault (); -jalview.util.MessageManager.log.info ("Getting messages for lang: " + jalview.util.MessageManager.loc); -jalview.util.MessageManager.rb = java.util.ResourceBundle.getBundle ("lang.Messages", jalview.util.MessageManager.loc); -if (jalview.util.MessageManager.rb == null || jalview.util.MessageManager.log.isLoggable (java.util.logging.Level.FINEST)) { -jalview.util.MessageManager.log.finest ("Language keys: " + jalview.util.MessageManager.rb.keySet ()); -}} catch (e$$) { -if (Clazz.exceptionOf (e$$, Exception)) { -var q = e$$; -{ -jalview.util.MessageManager.log.warning ("Exception when initting Locale for i18n messages\n" + q.getMessage ()); -q.printStackTrace (); -} -} else if (Clazz.exceptionOf (e$$, Error)) { -var v = e$$; -{ -jalview.util.MessageManager.log.warning ("Error when initting Locale for i18n messages\n" + v.getMessage ()); -v.printStackTrace (); -} -} else { -throw e$$; -} -} -}}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.text.MessageFormat", "java.util.logging.Logger"], "jalview.util.MessageManager", ["java.util.Locale", "$.ResourceBundle", "java.util.logging.Level"], function () { +c$ = Clazz.declareType (jalview.util, "MessageManager"); +c$.getString = Clazz.defineMethod (c$, "getString", +function (key) { +var value = "[missing key] " + key; +try { +value = jalview.util.MessageManager.rb.getString (key); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +jalview.util.MessageManager.log.warning ("I18N missing: " + jalview.util.MessageManager.loc + "\t" + key); +} else { +throw e; +} +} +return value; +}, "~S"); +c$.getLocale = Clazz.defineMethod (c$, "getLocale", +function () { +return jalview.util.MessageManager.loc; +}); +c$.formatMessage = Clazz.defineMethod (c$, "formatMessage", +function (key, params) { +return java.text.MessageFormat.format (jalview.util.MessageManager.getString (key), params); +}, "~S,~A"); +c$.formatMessage = Clazz.defineMethod (c$, "formatMessage", +function (key, params) { +return java.text.MessageFormat.format (jalview.util.MessageManager.getString (key), params); +}, "~S,~A"); +c$.getStringOrReturn = Clazz.defineMethod (c$, "getStringOrReturn", +function (keyroot, name) { +var smkey = keyroot + name.toLowerCase ().replaceAll (" ", ""); +try { +name = jalview.util.MessageManager.rb.getString (smkey); +} catch (x) { +if (Clazz.exceptionOf (x, Exception)) { +jalview.util.MessageManager.log.finest ("I18N missing key with root " + keyroot + ": " + jalview.util.MessageManager.loc + "\t" + smkey); +} else { +throw x; +} +} +return name; +}, "~S,~S"); +Clazz.defineStatics (c$, +"rb", null); +c$.log = c$.prototype.log = java.util.logging.Logger.getLogger (jalview.util.MessageManager.getCanonicalName ()); +Clazz.defineStatics (c$, +"loc", null); +{ +try { +jalview.util.MessageManager.loc = java.util.Locale.getDefault (); +jalview.util.MessageManager.log.info ("Getting messages for lang: " + jalview.util.MessageManager.loc); +jalview.util.MessageManager.rb = java.util.ResourceBundle.getBundle ("lang.Messages", jalview.util.MessageManager.loc); +if (jalview.util.MessageManager.rb == null || jalview.util.MessageManager.log.isLoggable (java.util.logging.Level.FINEST)) { +jalview.util.MessageManager.log.finest ("Language keys: " + jalview.util.MessageManager.rb.keySet ()); +}} catch (e$$) { +if (Clazz.exceptionOf (e$$, Exception)) { +var q = e$$; +{ +jalview.util.MessageManager.log.warning ("Exception when initting Locale for i18n messages\n" + q.getMessage ()); +q.printStackTrace (); +} +} else if (Clazz.exceptionOf (e$$, Error)) { +var v = e$$; +{ +jalview.util.MessageManager.log.warning ("Error when initting Locale for i18n messages\n" + v.getMessage ()); +v.printStackTrace (); +} +} else { +throw e$$; +} +} +}}); diff --git a/bin/jalview/util/ParseHtmlBodyAndLinks.class b/bin/jalview/util/ParseHtmlBodyAndLinks.class index 4160bc9..3c62b7d 100644 Binary files a/bin/jalview/util/ParseHtmlBodyAndLinks.class and b/bin/jalview/util/ParseHtmlBodyAndLinks.class differ diff --git a/bin/jalview/util/ParseHtmlBodyAndLinks.js b/bin/jalview/util/ParseHtmlBodyAndLinks.js index bf67f6a..8e41548 100644 --- a/bin/jalview/util/ParseHtmlBodyAndLinks.js +++ b/bin/jalview/util/ParseHtmlBodyAndLinks.js @@ -1,78 +1,78 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.lang.StringBuffer", "java.util.ArrayList", "java.util.regex.Pattern"], "jalview.util.ParseHtmlBodyAndLinks", ["java.util.StringTokenizer"], function () { -c$ = Clazz.decorateAsClass (function () { -this.orig = null; -this.htmlContent = true; -this.links = null; -this.sb = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "ParseHtmlBodyAndLinks"); -Clazz.prepareFields (c$, function () { -this.links = new java.util.ArrayList (); -this.sb = new StringBuffer (); -}); -Clazz.defineMethod (c$, "getOrig", -function () { -return this.orig; -}); -Clazz.defineMethod (c$, "isHtmlContent", -function () { -return this.htmlContent; -}); -Clazz.defineMethod (c$, "getContent", -function () { -return this.sb.toString (); -}); -Clazz.defineMethod (c$, "getLinks", -function () { -return this.links; -}); -Clazz.makeConstructor (c$, -function (description, removeHTML, newline) { -if (description == null || description.length == 0) { -this.htmlContent = false; -return; -}if (description.toUpperCase ().indexOf ("") == -1) { -this.htmlContent = false; -}this.orig = description; -var st = new java.util.StringTokenizer (description, "<"); -var token; -var link; -var startTag; -var tag = null; -while (st.hasMoreElements ()) { -token = st.nextToken ("&>"); -if (token.equalsIgnoreCase ("html") || token.startsWith ("/")) { -continue; -}tag = null; -startTag = token.indexOf ("<"); -if (startTag > -1) { -tag = token.substring (startTag + 1); -token = token.substring (0, startTag); -}if (tag != null && tag.toUpperCase ().startsWith ("A HREF=")) { -if (token.length > 0) { -this.sb.append (token); -}link = tag.substring (tag.indexOf ("\"") + 1, tag.length - 1); -var label = st.nextToken ("<>"); -this.links.add (label + "|" + link); -this.sb.append (label + "%LINK%"); -} else if (tag != null && tag.equalsIgnoreCase ("br")) { -this.sb.append (newline); -} else if (token.startsWith ("lt;")) { -this.sb.append ("<" + token.substring (3)); -} else if (token.startsWith ("gt;")) { -this.sb.append (">" + token.substring (3)); -} else if (token.startsWith ("amp;")) { -this.sb.append ("&" + token.substring (4)); -} else { -this.sb.append (token); -}} -if (removeHTML && !this.htmlContent) { -this.sb = new StringBuffer (jalview.util.ParseHtmlBodyAndLinks.LEFT_ANGLE_BRACKET_PATTERN.matcher (description).replaceAll ("<")); -}}, "~S,~B,~S"); -Clazz.defineMethod (c$, "getNonHtmlContent", -function () { -return this.isHtmlContent () ? this.sb.toString () : this.orig; -}); -c$.LEFT_ANGLE_BRACKET_PATTERN = c$.prototype.LEFT_ANGLE_BRACKET_PATTERN = java.util.regex.Pattern.compile ("<"); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.lang.StringBuffer", "java.util.ArrayList", "java.util.regex.Pattern"], "jalview.util.ParseHtmlBodyAndLinks", ["java.util.StringTokenizer"], function () { +c$ = Clazz.decorateAsClass (function () { +this.orig = null; +this.htmlContent = true; +this.links = null; +this.sb = null; +Clazz.instantialize (this, arguments); +}, jalview.util, "ParseHtmlBodyAndLinks"); +Clazz.prepareFields (c$, function () { +this.links = new java.util.ArrayList (); +this.sb = new StringBuffer (); +}); +Clazz.defineMethod (c$, "getOrig", +function () { +return this.orig; +}); +Clazz.defineMethod (c$, "isHtmlContent", +function () { +return this.htmlContent; +}); +Clazz.defineMethod (c$, "getContent", +function () { +return this.sb.toString (); +}); +Clazz.defineMethod (c$, "getLinks", +function () { +return this.links; +}); +Clazz.makeConstructor (c$, +function (description, removeHTML, newline) { +if (description == null || description.length == 0) { +this.htmlContent = false; +return; +}if (description.toUpperCase ().indexOf ("") == -1) { +this.htmlContent = false; +}this.orig = description; +var st = new java.util.StringTokenizer (description, "<"); +var token; +var link; +var startTag; +var tag = null; +while (st.hasMoreElements ()) { +token = st.nextToken ("&>"); +if (token.equalsIgnoreCase ("html") || token.startsWith ("/")) { +continue; +}tag = null; +startTag = token.indexOf ("<"); +if (startTag > -1) { +tag = token.substring (startTag + 1); +token = token.substring (0, startTag); +}if (tag != null && tag.toUpperCase ().startsWith ("A HREF=")) { +if (token.length > 0) { +this.sb.append (token); +}link = tag.substring (tag.indexOf ("\"") + 1, tag.length - 1); +var label = st.nextToken ("<>"); +this.links.add (label + "|" + link); +this.sb.append (label + "%LINK%"); +} else if (tag != null && tag.equalsIgnoreCase ("br")) { +this.sb.append (newline); +} else if (token.startsWith ("lt;")) { +this.sb.append ("<" + token.substring (3)); +} else if (token.startsWith ("gt;")) { +this.sb.append (">" + token.substring (3)); +} else if (token.startsWith ("amp;")) { +this.sb.append ("&" + token.substring (4)); +} else { +this.sb.append (token); +}} +if (removeHTML && !this.htmlContent) { +this.sb = new StringBuffer (jalview.util.ParseHtmlBodyAndLinks.LEFT_ANGLE_BRACKET_PATTERN.matcher (description).replaceAll ("<")); +}}, "~S,~B,~S"); +Clazz.defineMethod (c$, "getNonHtmlContent", +function () { +return this.isHtmlContent () ? this.sb.toString () : this.orig; +}); +c$.LEFT_ANGLE_BRACKET_PATTERN = c$.prototype.LEFT_ANGLE_BRACKET_PATTERN = java.util.regex.Pattern.compile ("<"); +}); diff --git a/bin/jalview/util/Platform.js b/bin/jalview/util/Platform.js index d349bdb..e599669 100644 --- a/bin/jalview/util/Platform.js +++ b/bin/jalview/util/Platform.js @@ -1,30 +1,30 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.Platform", ["java.lang.StringBuffer"], function () { -c$ = Clazz.declareType (jalview.util, "Platform"); -c$.isAMac = Clazz.defineMethod (c$, "isAMac", -function () { -return java.lang.System.getProperty ("os.name").indexOf ("Mac") > -1; -}); -c$.isHeadless = Clazz.defineMethod (c$, "isHeadless", -function () { -var hdls = java.lang.System.getProperty ("java.awt.headless"); -return hdls != null && hdls.equals ("true"); -}); -c$.getMaxCommandLineLength = Clazz.defineMethod (c$, "getMaxCommandLineLength", -function () { -return 2046; -}); -c$.escapeString = Clazz.defineMethod (c$, "escapeString", -function (file) { -var f = new StringBuffer (); -var p = 0; -var lastp = 0; -while ((p = file.indexOf ('\\', lastp)) > -1) { -f.append (file.subSequence (lastp, p)); -f.append ("\\\\"); -lastp = p + 1; -} -f.append (file.substring (lastp)); -return f.toString (); -}, "~S"); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.Platform", ["java.lang.StringBuffer"], function () { +c$ = Clazz.declareType (jalview.util, "Platform"); +c$.isAMac = Clazz.defineMethod (c$, "isAMac", +function () { +return java.lang.System.getProperty ("os.name").indexOf ("Mac") > -1; +}); +c$.isHeadless = Clazz.defineMethod (c$, "isHeadless", +function () { +var hdls = java.lang.System.getProperty ("java.awt.headless"); +return hdls != null && hdls.equals ("true"); +}); +c$.getMaxCommandLineLength = Clazz.defineMethod (c$, "getMaxCommandLineLength", +function () { +return 2046; +}); +c$.escapeString = Clazz.defineMethod (c$, "escapeString", +function (file) { +var f = new StringBuffer (); +var p = 0; +var lastp = 0; +while ((p = file.indexOf ('\\', lastp)) > -1) { +f.append (file.subSequence (lastp, p)); +f.append ("\\\\"); +lastp = p + 1; +} +f.append (file.substring (lastp)); +return f.toString (); +}, "~S"); +}); diff --git a/bin/jalview/util/QuickSort.js b/bin/jalview/util/QuickSort.js index a0960b5..f8fb52f 100644 --- a/bin/jalview/util/QuickSort.js +++ b/bin/jalview/util/QuickSort.js @@ -1,231 +1,231 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.QuickSort", ["java.lang.Float", "java.util.Arrays"], function () { -c$ = Clazz.declareType (jalview.util, "QuickSort"); -c$.sortInt = Clazz.defineMethod (c$, "sortInt", -function (arr, s) { -jalview.util.QuickSort.sortInt (arr, 0, arr.length - 1, s); -}, "~A,~A"); -c$.sortFloatObject = Clazz.defineMethod (c$, "sortFloatObject", -function (arr, s) { -jalview.util.QuickSort.sortFloat (arr, 0, arr.length - 1, s); -}, "~A,~A"); -c$.sortDouble = Clazz.defineMethod (c$, "sortDouble", -function (arr, s) { -jalview.util.QuickSort.sortDouble (arr, 0, arr.length - 1, s); -}, "~A,~A"); -c$.sort = Clazz.defineMethod (c$, "sort", -function (arr, s) { -jalview.util.QuickSort.stringSort (arr, 0, arr.length - 1, s); -}, "~A,~A"); -c$.stringSort = Clazz.defineMethod (c$, "stringSort", -($fz = function (arr, p, r, s) { -var q; -if (p < r) { -q = jalview.util.QuickSort.stringPartition (arr, p, r, s); -jalview.util.QuickSort.stringSort (arr, p, q, s); -jalview.util.QuickSort.stringSort (arr, q + 1, r, s); -}}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); -c$.sortFloat = Clazz.defineMethod (c$, "sortFloat", -($fz = function (arr, p, r, s) { -var q; -if (p < r) { -q = jalview.util.QuickSort.partitionFloat (arr, p, r, s); -jalview.util.QuickSort.sortFloat (arr, p, q, s); -jalview.util.QuickSort.sortFloat (arr, q + 1, r, s); -}}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); -c$.sortInt = Clazz.defineMethod (c$, "sortInt", -($fz = function (arr, p, r, s) { -var q; -if (p < r) { -q = jalview.util.QuickSort.partitionInt (arr, p, r, s); -jalview.util.QuickSort.sortInt (arr, p, q, s); -jalview.util.QuickSort.sortInt (arr, q + 1, r, s); -}}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); -c$.partitionFloat = Clazz.defineMethod (c$, "partitionFloat", -($fz = function (arr, p, r, s) { -var x = arr[p]; -var i = p - 1; -var j = r + 1; -while (true) { -do { -j = j - 1; -} while (arr[j] > x); -do { -i = i + 1; -} while (arr[i] < x); -if (i < j) { -var tmp = arr[i]; -arr[i] = arr[j]; -arr[j] = tmp; -var tmp2 = s[i]; -s[i] = s[j]; -s[j] = tmp2; -} else { -return j; -}} -}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); -c$.partitionInt = Clazz.defineMethod (c$, "partitionInt", -($fz = function (arr, p, r, s) { -var x = arr[p]; -var i = p - 1; -var j = r + 1; -while (true) { -do { -j = j - 1; -} while (arr[j] > x); -do { -i = i + 1; -} while (arr[i] < x); -if (i < j) { -var tmp = arr[i]; -arr[i] = arr[j]; -arr[j] = tmp; -var tmp2 = s[i]; -s[i] = s[j]; -s[j] = tmp2; -} else { -return j; -}} -}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); -c$.stringPartition = Clazz.defineMethod (c$, "stringPartition", -($fz = function (arr, p, r, s) { -var x = arr[p]; -var i = p - 1; -var j = r + 1; -while (true) { -do { -j = j - 1; -} while (arr[j].compareTo (x) < 0); -do { -i = i + 1; -} while (arr[i].compareTo (x) > 0); -if (i < j) { -var tmp = arr[i]; -arr[i] = arr[j]; -arr[j] = tmp; -var tmp2 = s[i]; -s[i] = s[j]; -s[j] = tmp2; -} else { -return j; -}} -}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); -c$.sortFloatChar = Clazz.defineMethod (c$, "sortFloatChar", -function (arr, s) { -var f1 = Clazz.newFloatArray (arr.length, 0); -var s1 = Clazz.newCharArray (s.length, '\0'); -var nextZeroValue = 0; -var nextNonZeroValue = arr.length - 1; -for (var i = 0; i < arr.length; i++) { -var val = arr[i]; -if (val > 0) { -f1[nextNonZeroValue] = val; -s1[nextNonZeroValue] = s[i]; -nextNonZeroValue--; -} else { -f1[nextZeroValue] = val; -s1[nextZeroValue] = s[i]; -nextZeroValue++; -}} -System.arraycopy (f1, 0, arr, 0, nextZeroValue); -System.arraycopy (s1, 0, s, 0, nextZeroValue); -if (nextZeroValue == arr.length) { -return; -}var nonZeroFloats = java.util.Arrays.copyOfRange (f1, nextZeroValue, f1.length); -var nonZeroChars = java.util.Arrays.copyOfRange (s1, nextZeroValue, s1.length); -jalview.util.QuickSort.externalSortFloat (nonZeroFloats, nonZeroChars); -System.arraycopy (nonZeroFloats, 0, arr, nextZeroValue, nonZeroFloats.length); -System.arraycopy (nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length); -}, "~A,~A"); -c$.externalSortFloat = Clazz.defineMethod (c$, "externalSortFloat", -($fz = function (arr, s) { -var length = arr.length; -var indices = jalview.util.QuickSort.makeIndexArray (length); -java.util.Arrays.sort (indices, new jalview.util.QuickSort.FloatComparator (arr)); -var sortedFloats = Clazz.newFloatArray (length, 0); -var sortedChars = Clazz.newCharArray (s.length, '\0'); -for (var i = 0; i < length; i++) { -sortedFloats[i] = arr[indices[i]]; -sortedChars[i] = s[indices[i]]; -} -System.arraycopy (sortedFloats, 0, arr, 0, length); -System.arraycopy (sortedChars, 0, s, 0, s.length); -}, $fz.isPrivate = true, $fz), "~A,~A"); -c$.makeIndexArray = Clazz.defineMethod (c$, "makeIndexArray", -($fz = function (length) { -var indices = new Array (length); -for (var i = 0; i < length; i++) { -indices[i] = new Integer (i); -} -return indices; -}, $fz.isPrivate = true, $fz), "~N"); -c$.sortIntChar = Clazz.defineMethod (c$, "sortIntChar", -function (arr, s) { -var f1 = Clazz.newIntArray (arr.length, 0); -var s1 = Clazz.newCharArray (s.length, '\0'); -var nextZeroValue = 0; -var nextNonZeroValue = arr.length - 1; -for (var i = 0; i < arr.length; i++) { -var val = arr[i]; -if (val > 0) { -f1[nextNonZeroValue] = val; -s1[nextNonZeroValue] = s[i]; -nextNonZeroValue--; -} else { -f1[nextZeroValue] = val; -s1[nextZeroValue] = s[i]; -nextZeroValue++; -}} -System.arraycopy (f1, 0, arr, 0, nextZeroValue); -System.arraycopy (s1, 0, s, 0, nextZeroValue); -if (nextZeroValue == arr.length) { -return; -}var nonZeroInts = java.util.Arrays.copyOfRange (f1, nextZeroValue, f1.length); -var nonZeroChars = java.util.Arrays.copyOfRange (s1, nextZeroValue, s1.length); -jalview.util.QuickSort.externalSortInt (nonZeroInts, nonZeroChars); -System.arraycopy (nonZeroInts, 0, arr, nextZeroValue, nonZeroInts.length); -System.arraycopy (nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length); -}, "~A,~A"); -c$.externalSortInt = Clazz.defineMethod (c$, "externalSortInt", -($fz = function (arr, s) { -var length = arr.length; -var indices = jalview.util.QuickSort.makeIndexArray (length); -java.util.Arrays.sort (indices, new jalview.util.QuickSort.IntComparator (arr)); -var sortedInts = Clazz.newIntArray (length, 0); -var sortedChars = Clazz.newCharArray (s.length, '\0'); -for (var i = 0; i < length; i++) { -sortedInts[i] = arr[indices[i]]; -sortedChars[i] = s[indices[i]]; -} -System.arraycopy (sortedInts, 0, arr, 0, length); -System.arraycopy (sortedChars, 0, s, 0, s.length); -}, $fz.isPrivate = true, $fz), "~A,~A"); -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.values = null; -Clazz.instantialize (this, arguments); -}, jalview.util.QuickSort, "FloatComparator", null, java.util.Comparator); -Clazz.makeConstructor (c$, -function (a) { -this.values = a; -}, "~A"); -Clazz.overrideMethod (c$, "compare", -function (a, b) { -return Float.compare (this.values[a.intValue ()], this.values[b]); -}, "Integer,Integer"); -c$ = Clazz.p0p (); -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.values = null; -Clazz.instantialize (this, arguments); -}, jalview.util.QuickSort, "IntComparator", null, java.util.Comparator); -Clazz.makeConstructor (c$, -function (a) { -this.values = a; -}, "~A"); -Clazz.overrideMethod (c$, "compare", -function (a, b) { -return Integer.compare (this.values[a], this.values[b]); -}, "Integer,Integer"); -c$ = Clazz.p0p (); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.QuickSort", ["java.lang.Float", "java.util.Arrays"], function () { +c$ = Clazz.declareType (jalview.util, "QuickSort"); +c$.sortInt = Clazz.defineMethod (c$, "sortInt", +function (arr, s) { +jalview.util.QuickSort.sortInt (arr, 0, arr.length - 1, s); +}, "~A,~A"); +c$.sortFloatObject = Clazz.defineMethod (c$, "sortFloatObject", +function (arr, s) { +jalview.util.QuickSort.sortFloat (arr, 0, arr.length - 1, s); +}, "~A,~A"); +c$.sortDouble = Clazz.defineMethod (c$, "sortDouble", +function (arr, s) { +jalview.util.QuickSort.sortDouble (arr, 0, arr.length - 1, s); +}, "~A,~A"); +c$.sort = Clazz.defineMethod (c$, "sort", +function (arr, s) { +jalview.util.QuickSort.stringSort (arr, 0, arr.length - 1, s); +}, "~A,~A"); +c$.stringSort = Clazz.defineMethod (c$, "stringSort", +($fz = function (arr, p, r, s) { +var q; +if (p < r) { +q = jalview.util.QuickSort.stringPartition (arr, p, r, s); +jalview.util.QuickSort.stringSort (arr, p, q, s); +jalview.util.QuickSort.stringSort (arr, q + 1, r, s); +}}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); +c$.sortFloat = Clazz.defineMethod (c$, "sortFloat", +($fz = function (arr, p, r, s) { +var q; +if (p < r) { +q = jalview.util.QuickSort.partitionFloat (arr, p, r, s); +jalview.util.QuickSort.sortFloat (arr, p, q, s); +jalview.util.QuickSort.sortFloat (arr, q + 1, r, s); +}}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); +c$.sortInt = Clazz.defineMethod (c$, "sortInt", +($fz = function (arr, p, r, s) { +var q; +if (p < r) { +q = jalview.util.QuickSort.partitionInt (arr, p, r, s); +jalview.util.QuickSort.sortInt (arr, p, q, s); +jalview.util.QuickSort.sortInt (arr, q + 1, r, s); +}}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); +c$.partitionFloat = Clazz.defineMethod (c$, "partitionFloat", +($fz = function (arr, p, r, s) { +var x = arr[p]; +var i = p - 1; +var j = r + 1; +while (true) { +do { +j = j - 1; +} while (arr[j] > x); +do { +i = i + 1; +} while (arr[i] < x); +if (i < j) { +var tmp = arr[i]; +arr[i] = arr[j]; +arr[j] = tmp; +var tmp2 = s[i]; +s[i] = s[j]; +s[j] = tmp2; +} else { +return j; +}} +}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); +c$.partitionInt = Clazz.defineMethod (c$, "partitionInt", +($fz = function (arr, p, r, s) { +var x = arr[p]; +var i = p - 1; +var j = r + 1; +while (true) { +do { +j = j - 1; +} while (arr[j] > x); +do { +i = i + 1; +} while (arr[i] < x); +if (i < j) { +var tmp = arr[i]; +arr[i] = arr[j]; +arr[j] = tmp; +var tmp2 = s[i]; +s[i] = s[j]; +s[j] = tmp2; +} else { +return j; +}} +}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); +c$.stringPartition = Clazz.defineMethod (c$, "stringPartition", +($fz = function (arr, p, r, s) { +var x = arr[p]; +var i = p - 1; +var j = r + 1; +while (true) { +do { +j = j - 1; +} while (arr[j].compareTo (x) < 0); +do { +i = i + 1; +} while (arr[i].compareTo (x) > 0); +if (i < j) { +var tmp = arr[i]; +arr[i] = arr[j]; +arr[j] = tmp; +var tmp2 = s[i]; +s[i] = s[j]; +s[j] = tmp2; +} else { +return j; +}} +}, $fz.isPrivate = true, $fz), "~A,~N,~N,~A"); +c$.sortFloatChar = Clazz.defineMethod (c$, "sortFloatChar", +function (arr, s) { +var f1 = Clazz.newFloatArray (arr.length, 0); +var s1 = Clazz.newCharArray (s.length, '\0'); +var nextZeroValue = 0; +var nextNonZeroValue = arr.length - 1; +for (var i = 0; i < arr.length; i++) { +var val = arr[i]; +if (val > 0) { +f1[nextNonZeroValue] = val; +s1[nextNonZeroValue] = s[i]; +nextNonZeroValue--; +} else { +f1[nextZeroValue] = val; +s1[nextZeroValue] = s[i]; +nextZeroValue++; +}} +System.arraycopy (f1, 0, arr, 0, nextZeroValue); +System.arraycopy (s1, 0, s, 0, nextZeroValue); +if (nextZeroValue == arr.length) { +return; +}var nonZeroFloats = java.util.Arrays.copyOfRange (f1, nextZeroValue, f1.length); +var nonZeroChars = java.util.Arrays.copyOfRange (s1, nextZeroValue, s1.length); +jalview.util.QuickSort.externalSortFloat (nonZeroFloats, nonZeroChars); +System.arraycopy (nonZeroFloats, 0, arr, nextZeroValue, nonZeroFloats.length); +System.arraycopy (nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length); +}, "~A,~A"); +c$.externalSortFloat = Clazz.defineMethod (c$, "externalSortFloat", +($fz = function (arr, s) { +var length = arr.length; +var indices = jalview.util.QuickSort.makeIndexArray (length); +java.util.Arrays.sort (indices, new jalview.util.QuickSort.FloatComparator (arr)); +var sortedFloats = Clazz.newFloatArray (length, 0); +var sortedChars = Clazz.newCharArray (s.length, '\0'); +for (var i = 0; i < length; i++) { +sortedFloats[i] = arr[indices[i]]; +sortedChars[i] = s[indices[i]]; +} +System.arraycopy (sortedFloats, 0, arr, 0, length); +System.arraycopy (sortedChars, 0, s, 0, s.length); +}, $fz.isPrivate = true, $fz), "~A,~A"); +c$.makeIndexArray = Clazz.defineMethod (c$, "makeIndexArray", +($fz = function (length) { +var indices = new Array (length); +for (var i = 0; i < length; i++) { +indices[i] = new Integer (i); +} +return indices; +}, $fz.isPrivate = true, $fz), "~N"); +c$.sortIntChar = Clazz.defineMethod (c$, "sortIntChar", +function (arr, s) { +var f1 = Clazz.newIntArray (arr.length, 0); +var s1 = Clazz.newCharArray (s.length, '\0'); +var nextZeroValue = 0; +var nextNonZeroValue = arr.length - 1; +for (var i = 0; i < arr.length; i++) { +var val = arr[i]; +if (val > 0) { +f1[nextNonZeroValue] = val; +s1[nextNonZeroValue] = s[i]; +nextNonZeroValue--; +} else { +f1[nextZeroValue] = val; +s1[nextZeroValue] = s[i]; +nextZeroValue++; +}} +System.arraycopy (f1, 0, arr, 0, nextZeroValue); +System.arraycopy (s1, 0, s, 0, nextZeroValue); +if (nextZeroValue == arr.length) { +return; +}var nonZeroInts = java.util.Arrays.copyOfRange (f1, nextZeroValue, f1.length); +var nonZeroChars = java.util.Arrays.copyOfRange (s1, nextZeroValue, s1.length); +jalview.util.QuickSort.externalSortInt (nonZeroInts, nonZeroChars); +System.arraycopy (nonZeroInts, 0, arr, nextZeroValue, nonZeroInts.length); +System.arraycopy (nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length); +}, "~A,~A"); +c$.externalSortInt = Clazz.defineMethod (c$, "externalSortInt", +($fz = function (arr, s) { +var length = arr.length; +var indices = jalview.util.QuickSort.makeIndexArray (length); +java.util.Arrays.sort (indices, new jalview.util.QuickSort.IntComparator (arr)); +var sortedInts = Clazz.newIntArray (length, 0); +var sortedChars = Clazz.newCharArray (s.length, '\0'); +for (var i = 0; i < length; i++) { +sortedInts[i] = arr[indices[i]]; +sortedChars[i] = s[indices[i]]; +} +System.arraycopy (sortedInts, 0, arr, 0, length); +System.arraycopy (sortedChars, 0, s, 0, s.length); +}, $fz.isPrivate = true, $fz), "~A,~A"); +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.values = null; +Clazz.instantialize (this, arguments); +}, jalview.util.QuickSort, "FloatComparator", null, java.util.Comparator); +Clazz.makeConstructor (c$, +function (a) { +this.values = a; +}, "~A"); +Clazz.overrideMethod (c$, "compare", +function (a, b) { +return Float.compare (this.values[a.intValue ()], this.values[b]); +}, "Integer,Integer"); +c$ = Clazz.p0p (); +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.values = null; +Clazz.instantialize (this, arguments); +}, jalview.util.QuickSort, "IntComparator", null, java.util.Comparator); +Clazz.makeConstructor (c$, +function (a) { +this.values = a; +}, "~A"); +Clazz.overrideMethod (c$, "compare", +function (a, b) { +return Integer.compare (this.values[a], this.values[b]); +}, "Integer,Integer"); +c$ = Clazz.p0p (); +}); diff --git a/bin/jalview/util/ReverseListIterator.js b/bin/jalview/util/ReverseListIterator.js index f9edbc8..66e861f 100644 --- a/bin/jalview/util/ReverseListIterator.js +++ b/bin/jalview/util/ReverseListIterator.js @@ -1,23 +1,23 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.util.Iterator"], "jalview.util.ReverseListIterator", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.iterator = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "ReverseListIterator", null, java.util.Iterator); -Clazz.makeConstructor (c$, -function (stuff) { -this.iterator = stuff.listIterator (stuff.size ()); -}, "java.util.List"); -Clazz.overrideMethod (c$, "hasNext", -function () { -return this.iterator.hasPrevious (); -}); -Clazz.overrideMethod (c$, "next", -function () { -return this.iterator.previous (); -}); -Clazz.overrideMethod (c$, "remove", -function () { -this.iterator.remove (); -}); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.util.Iterator"], "jalview.util.ReverseListIterator", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.iterator = null; +Clazz.instantialize (this, arguments); +}, jalview.util, "ReverseListIterator", null, java.util.Iterator); +Clazz.makeConstructor (c$, +function (stuff) { +this.iterator = stuff.listIterator (stuff.size ()); +}, "java.util.List"); +Clazz.overrideMethod (c$, "hasNext", +function () { +return this.iterator.hasPrevious (); +}); +Clazz.overrideMethod (c$, "next", +function () { +return this.iterator.previous (); +}); +Clazz.overrideMethod (c$, "remove", +function () { +this.iterator.remove (); +}); +}); diff --git a/bin/jalview/util/ShiftList.js b/bin/jalview/util/ShiftList.js index 29a9645..258fe14 100644 --- a/bin/jalview/util/ShiftList.js +++ b/bin/jalview/util/ShiftList.js @@ -1,67 +1,67 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.ShiftList", ["java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this.shifts = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "ShiftList"); -Clazz.makeConstructor (c$, -function () { -this.shifts = new java.util.ArrayList (); -}); -Clazz.defineMethod (c$, "addShift", -function (pos, shift) { -{ -var sidx = 0; -var rshift = null; -while (sidx < this.shifts.size () && (rshift = this.shifts.get (sidx))[0] < pos) { -sidx++; -} -if (sidx == this.shifts.size ()) { -this.shifts.add (sidx, Clazz.newIntArray (-1, [pos, shift])); -} else { -rshift[1] += shift; -}}}, "~N,~N"); -Clazz.defineMethod (c$, "shift", -function (pos) { -if (this.shifts.size () == 0) { -return pos; -}var shifted = pos; -var sidx = 0; -var rshift; -while (sidx < this.shifts.size () && (rshift = (this.shifts.get (sidx++)))[0] <= pos) { -shifted += rshift[1]; -} -return shifted; -}, "~N"); -Clazz.defineMethod (c$, "clear", -function () { -this.shifts.clear (); -}); -Clazz.defineMethod (c$, "getInverse", -function () { -var inverse = new jalview.util.ShiftList (); -{ -if (this.shifts != null) { -for (var sh, $sh = this.shifts.iterator (); $sh.hasNext () && ((sh = $sh.next ()) || true);) { -if (sh != null) { -inverse.shifts.add ( Clazz.newIntArray (-1, [sh[0], -sh[1]])); -}} -}}return inverse; -}); -c$.parseMap = Clazz.defineMethod (c$, "parseMap", -function (gapMap) { -var shiftList = null; -if (gapMap != null && gapMap.length > 0) { -shiftList = new jalview.util.ShiftList (); -for (var i = 0, p = 0; i < gapMap.length; p++, i++) { -if (p != gapMap[i]) { -shiftList.addShift (p, gapMap[i] - p); -p = gapMap[i]; -}} -}return shiftList; -}, "~A"); -Clazz.defineMethod (c$, "getShifts", -function () { -return this.shifts; -}); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.ShiftList", ["java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this.shifts = null; +Clazz.instantialize (this, arguments); +}, jalview.util, "ShiftList"); +Clazz.makeConstructor (c$, +function () { +this.shifts = new java.util.ArrayList (); +}); +Clazz.defineMethod (c$, "addShift", +function (pos, shift) { +{ +var sidx = 0; +var rshift = null; +while (sidx < this.shifts.size () && (rshift = this.shifts.get (sidx))[0] < pos) { +sidx++; +} +if (sidx == this.shifts.size ()) { +this.shifts.add (sidx, Clazz.newIntArray (-1, [pos, shift])); +} else { +rshift[1] += shift; +}}}, "~N,~N"); +Clazz.defineMethod (c$, "shift", +function (pos) { +if (this.shifts.size () == 0) { +return pos; +}var shifted = pos; +var sidx = 0; +var rshift; +while (sidx < this.shifts.size () && (rshift = (this.shifts.get (sidx++)))[0] <= pos) { +shifted += rshift[1]; +} +return shifted; +}, "~N"); +Clazz.defineMethod (c$, "clear", +function () { +this.shifts.clear (); +}); +Clazz.defineMethod (c$, "getInverse", +function () { +var inverse = new jalview.util.ShiftList (); +{ +if (this.shifts != null) { +for (var sh, $sh = this.shifts.iterator (); $sh.hasNext () && ((sh = $sh.next ()) || true);) { +if (sh != null) { +inverse.shifts.add ( Clazz.newIntArray (-1, [sh[0], -sh[1]])); +}} +}}return inverse; +}); +c$.parseMap = Clazz.defineMethod (c$, "parseMap", +function (gapMap) { +var shiftList = null; +if (gapMap != null && gapMap.length > 0) { +shiftList = new jalview.util.ShiftList (); +for (var i = 0, p = 0; i < gapMap.length; p++, i++) { +if (p != gapMap[i]) { +shiftList.addShift (p, gapMap[i] - p); +p = gapMap[i]; +}} +}return shiftList; +}, "~A"); +Clazz.defineMethod (c$, "getShifts", +function () { +return this.shifts; +}); +}); diff --git a/bin/jalview/util/StringUtils.js b/bin/jalview/util/StringUtils.js index fd878bf..0b21437 100644 --- a/bin/jalview/util/StringUtils.js +++ b/bin/jalview/util/StringUtils.js @@ -1,108 +1,108 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.util.regex.Pattern"], "jalview.util.StringUtils", ["java.lang.StringBuffer", "java.util.ArrayList"], function () { -c$ = Clazz.declareType (jalview.util, "StringUtils"); -c$.insertCharAt = Clazz.defineMethod (c$, "insertCharAt", -function ($in, position, count, ch) { -var tmp = Clazz.newCharArray ($in.length + count, '\0'); -if (position >= $in.length) { -System.arraycopy ($in, 0, tmp, 0, $in.length); -position = $in.length; -} else { -System.arraycopy ($in, 0, tmp, 0, position); -}var index = position; -while (count > 0) { -tmp[index++] = ch; -count--; -} -if (position < $in.length) { -System.arraycopy ($in, position, tmp, index, $in.length - position); -}return tmp; -}, "~A,~N,~N,~S"); -c$.deleteChars = Clazz.defineMethod (c$, "deleteChars", -function ($in, from, to) { -if (from >= $in.length || from < 0) { -return $in; -}var tmp; -if (to >= $in.length) { -tmp = Clazz.newCharArray (from, '\0'); -System.arraycopy ($in, 0, tmp, 0, from); -to = $in.length; -} else { -tmp = Clazz.newCharArray ($in.length - to + from, '\0'); -System.arraycopy ($in, 0, tmp, 0, from); -System.arraycopy ($in, to, tmp, from, $in.length - to); -}return tmp; -}, "~A,~N,~N"); -c$.getLastToken = Clazz.defineMethod (c$, "getLastToken", -function (input, token) { -if (input == null) { -return null; -}if (token == null) { -return input; -}var st = input.$plit (token); -return st[st.length - 1]; -}, "~S,~S"); -c$.separatorListToArray = Clazz.defineMethod (c$, "separatorListToArray", -function (input, delimiter) { -var seplen = delimiter.length; -if (input == null || input.equals ("") || input.equals (delimiter)) { -return null; -}var jv = new java.util.ArrayList (); -var cp = 0; -var pos; -var escape; -var wasescaped = false; -var wasquoted = false; -var lstitem = null; -while ((pos = input.indexOf (delimiter, cp)) >= cp) { -escape = (pos > 0 && input.charAt (pos - 1) == '\\') ? -1 : 0; -if (wasescaped || wasquoted) { -jv.set (jv.size () - 1, lstitem = lstitem + delimiter + input.substring (cp, pos + escape)); -} else { -jv.add (lstitem = input.substring (cp, pos + escape)); -}cp = pos + seplen; -wasescaped = escape == -1; -wasquoted = jalview.util.StringUtils.DELIMITERS_PATTERN.matcher (lstitem).matches (); -} -if (cp < input.length) { -var c = input.substring (cp); -if (wasescaped || wasquoted) { -jv.set (jv.size () - 1, lstitem + delimiter + c); -} else { -if (!c.equals (delimiter)) { -jv.add (c); -}}}if (jv.size () > 0) { -var v = jv.toArray ( new Array (jv.size ())); -jv.clear (); -if (false) { -System.err.println ("Array from '" + delimiter + "' separated List:\n" + v.length); -for (var i = 0; i < v.length; i++) { -System.err.println ("item " + i + " '" + v[i] + "'"); -} -}return v; -}if (false) { -System.err.println ("Empty Array from '" + delimiter + "' separated List"); -}return null; -}, "~S,~S"); -c$.arrayToSeparatorList = Clazz.defineMethod (c$, "arrayToSeparatorList", -function (list, separator) { -var v = new StringBuffer (); -if (list != null && list.length > 0) { -for (var i = 0, iSize = list.length; i < iSize; i++) { -if (list[i] != null) { -if (v.length () > 0) { -v.append (separator); -}v.append (list[i]); -}} -if (false) { -System.err.println ("Returning '" + separator + "' separated List:\n"); -System.err.println (v); -}return v.toString (); -}if (false) { -System.err.println ("Returning empty '" + separator + "' separated List\n"); -}return "" + separator; -}, "~A,~S"); -c$.DELIMITERS_PATTERN = c$.prototype.DELIMITERS_PATTERN = java.util.regex.Pattern.compile (".*='[^']*(?!')"); -Clazz.defineStatics (c$, -"DEBUG", false); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.util.regex.Pattern"], "jalview.util.StringUtils", ["java.lang.StringBuffer", "java.util.ArrayList"], function () { +c$ = Clazz.declareType (jalview.util, "StringUtils"); +c$.insertCharAt = Clazz.defineMethod (c$, "insertCharAt", +function ($in, position, count, ch) { +var tmp = Clazz.newCharArray ($in.length + count, '\0'); +if (position >= $in.length) { +System.arraycopy ($in, 0, tmp, 0, $in.length); +position = $in.length; +} else { +System.arraycopy ($in, 0, tmp, 0, position); +}var index = position; +while (count > 0) { +tmp[index++] = ch; +count--; +} +if (position < $in.length) { +System.arraycopy ($in, position, tmp, index, $in.length - position); +}return tmp; +}, "~A,~N,~N,~S"); +c$.deleteChars = Clazz.defineMethod (c$, "deleteChars", +function ($in, from, to) { +if (from >= $in.length || from < 0) { +return $in; +}var tmp; +if (to >= $in.length) { +tmp = Clazz.newCharArray (from, '\0'); +System.arraycopy ($in, 0, tmp, 0, from); +to = $in.length; +} else { +tmp = Clazz.newCharArray ($in.length - to + from, '\0'); +System.arraycopy ($in, 0, tmp, 0, from); +System.arraycopy ($in, to, tmp, from, $in.length - to); +}return tmp; +}, "~A,~N,~N"); +c$.getLastToken = Clazz.defineMethod (c$, "getLastToken", +function (input, token) { +if (input == null) { +return null; +}if (token == null) { +return input; +}var st = input.$plit (token); +return st[st.length - 1]; +}, "~S,~S"); +c$.separatorListToArray = Clazz.defineMethod (c$, "separatorListToArray", +function (input, delimiter) { +var seplen = delimiter.length; +if (input == null || input.equals ("") || input.equals (delimiter)) { +return null; +}var jv = new java.util.ArrayList (); +var cp = 0; +var pos; +var escape; +var wasescaped = false; +var wasquoted = false; +var lstitem = null; +while ((pos = input.indexOf (delimiter, cp)) >= cp) { +escape = (pos > 0 && input.charAt (pos - 1) == '\\') ? -1 : 0; +if (wasescaped || wasquoted) { +jv.set (jv.size () - 1, lstitem = lstitem + delimiter + input.substring (cp, pos + escape)); +} else { +jv.add (lstitem = input.substring (cp, pos + escape)); +}cp = pos + seplen; +wasescaped = escape == -1; +wasquoted = jalview.util.StringUtils.DELIMITERS_PATTERN.matcher (lstitem).matches (); +} +if (cp < input.length) { +var c = input.substring (cp); +if (wasescaped || wasquoted) { +jv.set (jv.size () - 1, lstitem + delimiter + c); +} else { +if (!c.equals (delimiter)) { +jv.add (c); +}}}if (jv.size () > 0) { +var v = jv.toArray ( new Array (jv.size ())); +jv.clear (); +if (false) { +System.err.println ("Array from '" + delimiter + "' separated List:\n" + v.length); +for (var i = 0; i < v.length; i++) { +System.err.println ("item " + i + " '" + v[i] + "'"); +} +}return v; +}if (false) { +System.err.println ("Empty Array from '" + delimiter + "' separated List"); +}return null; +}, "~S,~S"); +c$.arrayToSeparatorList = Clazz.defineMethod (c$, "arrayToSeparatorList", +function (list, separator) { +var v = new StringBuffer (); +if (list != null && list.length > 0) { +for (var i = 0, iSize = list.length; i < iSize; i++) { +if (list[i] != null) { +if (v.length () > 0) { +v.append (separator); +}v.append (list[i]); +}} +if (false) { +System.err.println ("Returning '" + separator + "' separated List:\n"); +System.err.println (v); +}return v.toString (); +}if (false) { +System.err.println ("Returning empty '" + separator + "' separated List\n"); +}return "" + separator; +}, "~A,~S"); +c$.DELIMITERS_PATTERN = c$.prototype.DELIMITERS_PATTERN = java.util.regex.Pattern.compile (".*='[^']*(?!')"); +Clazz.defineStatics (c$, +"DEBUG", false); +}); diff --git a/bin/jalview/util/TableSorter.js b/bin/jalview/util/TableSorter.js index 44ff978..dcc7fea 100644 --- a/bin/jalview/util/TableSorter.js +++ b/bin/jalview/util/TableSorter.js @@ -1,387 +1,387 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.awt.event.MouseAdapter", "javax.swing.Icon", "javax.swing.event.TableModelListener", "javax.swing.table.AbstractTableModel", "$.TableCellRenderer", "java.util.ArrayList", "$.HashMap"], "jalview.util.TableSorter", ["java.awt.Color", "java.util.Arrays", "javax.swing.JLabel", "javax.swing.event.TableModelEvent"], function () { -c$ = Clazz.decorateAsClass (function () { -this.tableModel = null; -this.viewToModel = null; -this.modelToView = null; -this.tableHeader = null; -this.mouseListener = null; -this.tableModelListener = null; -this.columnComparators = null; -this.sortingColumns = null; -if (!Clazz.isClassDefined ("jalview.util.TableSorter.Row")) { -jalview.util.TableSorter.$TableSorter$Row$ (); -} -if (!Clazz.isClassDefined ("jalview.util.TableSorter.TableModelHandler")) { -jalview.util.TableSorter.$TableSorter$TableModelHandler$ (); -} -if (!Clazz.isClassDefined ("jalview.util.TableSorter.MouseHandler")) { -jalview.util.TableSorter.$TableSorter$MouseHandler$ (); -} -if (!Clazz.isClassDefined ("jalview.util.TableSorter.SortableHeaderRenderer")) { -jalview.util.TableSorter.$TableSorter$SortableHeaderRenderer$ (); -} -Clazz.instantialize (this, arguments); -}, jalview.util, "TableSorter", javax.swing.table.AbstractTableModel); -Clazz.prepareFields (c$, function () { -this.columnComparators = new java.util.HashMap (); -this.sortingColumns = new java.util.ArrayList (); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, jalview.util.TableSorter, []); -this.mouseListener = Clazz.innerTypeInstance (jalview.util.TableSorter.MouseHandler, this, null); -this.tableModelListener = Clazz.innerTypeInstance (jalview.util.TableSorter.TableModelHandler, this, null); -}); -Clazz.makeConstructor (c$, -function (tableModel) { -this.construct (); -this.setTableModel (tableModel); -}, "javax.swing.table.TableModel"); -Clazz.makeConstructor (c$, -function (tableModel, tableHeader) { -this.construct (); -this.setTableHeader (tableHeader); -this.setTableModel (tableModel); -}, "javax.swing.table.TableModel,javax.swing.table.JTableHeader"); -Clazz.defineMethod (c$, "clearSortingState", -($fz = function () { -this.viewToModel = null; -this.modelToView = null; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getTableModel", -function () { -return this.tableModel; -}); -Clazz.defineMethod (c$, "setTableModel", -function (tableModel) { -if (this.tableModel != null) { -this.tableModel.removeTableModelListener (this.tableModelListener); -}this.tableModel = tableModel; -if (this.tableModel != null) { -this.tableModel.addTableModelListener (this.tableModelListener); -}this.clearSortingState (); -this.fireTableStructureChanged (); -}, "javax.swing.table.TableModel"); -Clazz.defineMethod (c$, "getTableHeader", -function () { -return this.tableHeader; -}); -Clazz.defineMethod (c$, "setTableHeader", -function (tableHeader) { -if (this.tableHeader != null) { -this.tableHeader.removeMouseListener (this.mouseListener); -var defaultRenderer = this.tableHeader.getDefaultRenderer (); -if (Clazz.instanceOf (defaultRenderer, jalview.util.TableSorter.SortableHeaderRenderer)) { -this.tableHeader.setDefaultRenderer ((defaultRenderer).tableCellRenderer); -}}this.tableHeader = tableHeader; -if (this.tableHeader != null) { -this.tableHeader.addMouseListener (this.mouseListener); -this.tableHeader.setDefaultRenderer (Clazz.innerTypeInstance (jalview.util.TableSorter.SortableHeaderRenderer, this, null, this.tableHeader.getDefaultRenderer ())); -}}, "javax.swing.table.JTableHeader"); -Clazz.defineMethod (c$, "isSorting", -function () { -return this.sortingColumns.size () != 0; -}); -Clazz.defineMethod (c$, "getDirective", -($fz = function (column) { -for (var i = 0; i < this.sortingColumns.size (); i++) { -var directive = this.sortingColumns.get (i); -if (directive.column == column) { -return directive; -}} -return jalview.util.TableSorter.EMPTY_DIRECTIVE; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "getSortingStatus", -function (column) { -return this.getDirective (column).direction; -}, "~N"); -Clazz.defineMethod (c$, "sortingStatusChanged", -($fz = function () { -this.clearSortingState (); -this.fireTableDataChanged (); -if (this.tableHeader != null) { -this.tableHeader.repaint (); -}}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "setSortingStatus", -function (column, status) { -var directive = this.getDirective (column); -if (directive !== jalview.util.TableSorter.EMPTY_DIRECTIVE) { -this.sortingColumns.remove (directive); -}if (status != 0) { -this.sortingColumns.add ( new jalview.util.TableSorter.Directive (column, status)); -}this.sortingStatusChanged (); -}, "~N,~N"); -Clazz.defineMethod (c$, "getHeaderRendererIcon", -function (column, size) { -var directive = this.getDirective (column); -if (directive === jalview.util.TableSorter.EMPTY_DIRECTIVE) { -return null; -}return new jalview.util.TableSorter.Arrow (directive.direction == -1, size, this.sortingColumns.indexOf (directive)); -}, "~N,~N"); -Clazz.defineMethod (c$, "cancelSorting", -($fz = function () { -this.sortingColumns.clear (); -this.sortingStatusChanged (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "setColumnComparator", -function (type, comparator) { -if (comparator == null) { -this.columnComparators.remove (type); -} else { -this.columnComparators.put (type, comparator); -}}, "Class,java.util.Comparator"); -Clazz.defineMethod (c$, "getComparator", -function (column) { -var columnType = this.tableModel.getColumnClass (column); -var comparator = this.columnComparators.get (columnType); -if (comparator != null) { -return comparator; -}if (Comparable.isAssignableFrom (columnType)) { -return jalview.util.TableSorter.COMPARABLE_COMAPRATOR; -}return jalview.util.TableSorter.LEXICAL_COMPARATOR; -}, "~N"); -Clazz.defineMethod (c$, "getViewToModel", -($fz = function () { -if (this.viewToModel == null) { -var tableModelRowCount = this.tableModel.getRowCount (); -this.viewToModel = new Array (tableModelRowCount); -for (var row = 0; row < tableModelRowCount; row++) { -this.viewToModel[row] = Clazz.innerTypeInstance (jalview.util.TableSorter.Row, this, null, row); -} -if (this.isSorting ()) { -java.util.Arrays.sort (this.viewToModel); -}}return this.viewToModel; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "modelIndex", -function (viewIndex) { -return this.getViewToModel ()[viewIndex].modelIndex; -}, "~N"); -Clazz.defineMethod (c$, "getModelToView", -($fz = function () { -if (this.modelToView == null) { -var n = this.getViewToModel ().length; -this.modelToView = Clazz.newIntArray (n, 0); -for (var i = 0; i < n; i++) { -this.modelToView[this.modelIndex (i)] = i; -} -}return this.modelToView; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getRowCount", -function () { -return (this.tableModel == null) ? 0 : this.tableModel.getRowCount (); -}); -Clazz.defineMethod (c$, "getColumnCount", -function () { -return (this.tableModel == null) ? 0 : this.tableModel.getColumnCount (); -}); -Clazz.overrideMethod (c$, "getColumnName", -function (column) { -return this.tableModel.getColumnName (column); -}, "~N"); -Clazz.overrideMethod (c$, "getColumnClass", -function (column) { -return this.tableModel.getColumnClass (column); -}, "~N"); -Clazz.overrideMethod (c$, "isCellEditable", -function (row, column) { -return this.tableModel.isCellEditable (this.modelIndex (row), column); -}, "~N,~N"); -Clazz.defineMethod (c$, "getValueAt", -function (row, column) { -return this.tableModel.getValueAt (this.modelIndex (row), column); -}, "~N,~N"); -Clazz.overrideMethod (c$, "setValueAt", -function (aValue, row, column) { -this.tableModel.setValueAt (aValue, this.modelIndex (row), column); -}, "~O,~N,~N"); -c$.$TableSorter$Row$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.modelIndex = 0; -Clazz.instantialize (this, arguments); -}, jalview.util.TableSorter, "Row", null, Comparable); -Clazz.makeConstructor (c$, -function (a) { -this.modelIndex = a; -}, "~N"); -Clazz.overrideMethod (c$, "compareTo", -function (a) { -var b = this.modelIndex; -var c = (a).modelIndex; -for (var d = this.b$["jalview.util.TableSorter"].sortingColumns.iterator (); d.hasNext (); ) { -var e = d.next (); -var f = e.column; -var g = this.b$["jalview.util.TableSorter"].tableModel.getValueAt (b, f); -var h = this.b$["jalview.util.TableSorter"].tableModel.getValueAt (c, f); -var i = 0; -if (g == null && h == null) { -i = 0; -} else if (g == null) { -i = -1; -} else if (h == null) { -i = 1; -} else { -i = this.b$["jalview.util.TableSorter"].getComparator (f).compare (g, h); -}if (i != 0) { -return e.direction == -1 ? -i : i; -}} -return 0; -}, "~O"); -c$ = Clazz.p0p (); -}; -c$.$TableSorter$TableModelHandler$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -Clazz.instantialize (this, arguments); -}, jalview.util.TableSorter, "TableModelHandler", null, javax.swing.event.TableModelListener); -Clazz.overrideMethod (c$, "tableChanged", -function (a) { -if (!this.b$["jalview.util.TableSorter"].isSorting ()) { -this.b$["jalview.util.TableSorter"].clearSortingState (); -this.b$["jalview.util.TableSorter"].fireTableChanged (a); -return; -}if (a.getFirstRow () == -1) { -this.b$["jalview.util.TableSorter"].cancelSorting (); -this.b$["jalview.util.TableSorter"].fireTableChanged (a); -return; -}var b = a.getColumn (); -if (a.getFirstRow () == a.getLastRow () && b != -1 && this.b$["jalview.util.TableSorter"].getSortingStatus (b) == 0 && this.b$["jalview.util.TableSorter"].modelToView != null) { -var c = this.b$["jalview.util.TableSorter"].getModelToView ()[a.getFirstRow ()]; -this.b$["jalview.util.TableSorter"].fireTableChanged ( new javax.swing.event.TableModelEvent (this.b$["jalview.util.TableSorter"], c, c, b, a.getType ())); -return; -}this.b$["jalview.util.TableSorter"].clearSortingState (); -this.b$["jalview.util.TableSorter"].fireTableDataChanged (); -return; -}, "javax.swing.event.TableModelEvent"); -c$ = Clazz.p0p (); -}; -c$.$TableSorter$MouseHandler$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -Clazz.instantialize (this, arguments); -}, jalview.util.TableSorter, "MouseHandler", java.awt.event.MouseAdapter); -Clazz.overrideMethod (c$, "mouseClicked", -function (a) { -var b = a.getSource (); -var c = b.getColumnModel (); -var d = c.getColumnIndexAtX (a.getX ()); -var e = c.getColumn (d).getModelIndex (); -if (e != -1) { -var f = this.b$["jalview.util.TableSorter"].getSortingStatus (e); -if (!a.isControlDown ()) { -this.b$["jalview.util.TableSorter"].cancelSorting (); -}f = f + (a.isShiftDown () ? -1 : 1); -f = (f + 4) % 3 - 1; -this.b$["jalview.util.TableSorter"].setSortingStatus (e, f); -}}, "java.awt.event.MouseEvent"); -c$ = Clazz.p0p (); -}; -c$.$TableSorter$SortableHeaderRenderer$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.tableCellRenderer = null; -Clazz.instantialize (this, arguments); -}, jalview.util.TableSorter, "SortableHeaderRenderer", null, javax.swing.table.TableCellRenderer); -Clazz.makeConstructor (c$, -function (a) { -this.tableCellRenderer = a; -}, "javax.swing.table.TableCellRenderer"); -Clazz.defineMethod (c$, "getTableCellRendererComponent", -function (a, b, c, d, e, f) { -var g = this.tableCellRenderer.getTableCellRendererComponent (a, b, c, d, e, f); -if (Clazz.instanceOf (g, javax.swing.JLabel)) { -var h = g; -h.setHorizontalTextPosition (2); -var i = a.convertColumnIndexToModel (f); -h.setIcon (this.b$["jalview.util.TableSorter"].getHeaderRendererIcon (i, h.getFont ().getSize ())); -}return g; -}, "javax.swing.JTable,~O,~B,~B,~N,~N"); -c$ = Clazz.p0p (); -}; -c$.$TableSorter$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "TableSorter$1", null, java.util.Comparator); -Clazz.defineMethod (c$, "compare", -function (o1, o2) { -return (o1).compareTo (o2); -}, "~O,~O"); -c$ = Clazz.p0p (); -}; -c$.$TableSorter$2$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (jalview.util, "TableSorter$2", null, java.util.Comparator); -Clazz.defineMethod (c$, "compare", -function (o1, o2) { -return o1.toString ().compareTo (o2.toString ()); -}, "~O,~O"); -c$ = Clazz.p0p (); -}; -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.descending = false; -this.size = 0; -this.priority = 0; -Clazz.instantialize (this, arguments); -}, jalview.util.TableSorter, "Arrow", null, javax.swing.Icon); -Clazz.makeConstructor (c$, -function (a, b, c) { -this.descending = a; -this.size = b; -this.priority = c; -}, "~B,~N,~N"); -Clazz.overrideMethod (c$, "paintIcon", -function (a, b, c, d) { -var e = a == null ? java.awt.Color.GRAY : a.getBackground (); -var f = Clazz.doubleToInt (Clazz.doubleToInt (this.size / 2) * Math.pow (0.8, this.priority)); -var g = this.descending ? f : -f; -d = d + Clazz.doubleToInt (5 * this.size / 6) + (this.descending ? -g : 0); -var h = this.descending ? 1 : -1; -b.translate (c, d); -b.setColor (e.darker ()); -b.drawLine (Clazz.doubleToInt (f / 2), g, 0, 0); -b.drawLine (Clazz.doubleToInt (f / 2), g + h, 0, h); -b.setColor (e.brighter ()); -b.drawLine (Clazz.doubleToInt (f / 2), g, f, 0); -b.drawLine (Clazz.doubleToInt (f / 2), g + h, f, h); -if (this.descending) { -b.setColor (e.darker ().darker ()); -} else { -b.setColor (e.brighter ().brighter ()); -}b.drawLine (f, 0, 0, 0); -b.setColor (e); -b.translate (-c, -d); -}, "java.awt.Component,java.awt.Graphics,~N,~N"); -Clazz.overrideMethod (c$, "getIconWidth", -function () { -return this.size; -}); -Clazz.overrideMethod (c$, "getIconHeight", -function () { -return this.size; -}); -c$ = Clazz.p0p (); -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -this.column = 0; -this.direction = 0; -Clazz.instantialize (this, arguments); -}, jalview.util.TableSorter, "Directive"); -Clazz.makeConstructor (c$, -function (a, b) { -this.column = a; -this.direction = b; -}, "~N,~N"); -c$ = Clazz.p0p (); -Clazz.defineStatics (c$, -"DESCENDING", -1, -"NOT_SORTED", 0, -"ASCENDING", 1); -c$.EMPTY_DIRECTIVE = c$.prototype.EMPTY_DIRECTIVE = new jalview.util.TableSorter.Directive (-1, 0); -c$.COMPARABLE_COMAPRATOR = c$.prototype.COMPARABLE_COMAPRATOR = ((Clazz.isClassDefined ("jalview.util.TableSorter$1") ? 0 : jalview.util.TableSorter.$TableSorter$1$ ()), Clazz.innerTypeInstance (jalview.util.TableSorter$1, this, null)); -c$.LEXICAL_COMPARATOR = c$.prototype.LEXICAL_COMPARATOR = ((Clazz.isClassDefined ("jalview.util.TableSorter$2") ? 0 : jalview.util.TableSorter.$TableSorter$2$ ()), Clazz.innerTypeInstance (jalview.util.TableSorter$2, this, null)); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.awt.event.MouseAdapter", "javax.swing.Icon", "javax.swing.event.TableModelListener", "javax.swing.table.AbstractTableModel", "$.TableCellRenderer", "java.util.ArrayList", "$.HashMap"], "jalview.util.TableSorter", ["java.awt.Color", "java.util.Arrays", "javax.swing.JLabel", "javax.swing.event.TableModelEvent"], function () { +c$ = Clazz.decorateAsClass (function () { +this.tableModel = null; +this.viewToModel = null; +this.modelToView = null; +this.tableHeader = null; +this.mouseListener = null; +this.tableModelListener = null; +this.columnComparators = null; +this.sortingColumns = null; +if (!Clazz.isClassDefined ("jalview.util.TableSorter.Row")) { +jalview.util.TableSorter.$TableSorter$Row$ (); +} +if (!Clazz.isClassDefined ("jalview.util.TableSorter.TableModelHandler")) { +jalview.util.TableSorter.$TableSorter$TableModelHandler$ (); +} +if (!Clazz.isClassDefined ("jalview.util.TableSorter.MouseHandler")) { +jalview.util.TableSorter.$TableSorter$MouseHandler$ (); +} +if (!Clazz.isClassDefined ("jalview.util.TableSorter.SortableHeaderRenderer")) { +jalview.util.TableSorter.$TableSorter$SortableHeaderRenderer$ (); +} +Clazz.instantialize (this, arguments); +}, jalview.util, "TableSorter", javax.swing.table.AbstractTableModel); +Clazz.prepareFields (c$, function () { +this.columnComparators = new java.util.HashMap (); +this.sortingColumns = new java.util.ArrayList (); +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, jalview.util.TableSorter, []); +this.mouseListener = Clazz.innerTypeInstance (jalview.util.TableSorter.MouseHandler, this, null); +this.tableModelListener = Clazz.innerTypeInstance (jalview.util.TableSorter.TableModelHandler, this, null); +}); +Clazz.makeConstructor (c$, +function (tableModel) { +this.construct (); +this.setTableModel (tableModel); +}, "javax.swing.table.TableModel"); +Clazz.makeConstructor (c$, +function (tableModel, tableHeader) { +this.construct (); +this.setTableHeader (tableHeader); +this.setTableModel (tableModel); +}, "javax.swing.table.TableModel,javax.swing.table.JTableHeader"); +Clazz.defineMethod (c$, "clearSortingState", +($fz = function () { +this.viewToModel = null; +this.modelToView = null; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getTableModel", +function () { +return this.tableModel; +}); +Clazz.defineMethod (c$, "setTableModel", +function (tableModel) { +if (this.tableModel != null) { +this.tableModel.removeTableModelListener (this.tableModelListener); +}this.tableModel = tableModel; +if (this.tableModel != null) { +this.tableModel.addTableModelListener (this.tableModelListener); +}this.clearSortingState (); +this.fireTableStructureChanged (); +}, "javax.swing.table.TableModel"); +Clazz.defineMethod (c$, "getTableHeader", +function () { +return this.tableHeader; +}); +Clazz.defineMethod (c$, "setTableHeader", +function (tableHeader) { +if (this.tableHeader != null) { +this.tableHeader.removeMouseListener (this.mouseListener); +var defaultRenderer = this.tableHeader.getDefaultRenderer (); +if (Clazz.instanceOf (defaultRenderer, jalview.util.TableSorter.SortableHeaderRenderer)) { +this.tableHeader.setDefaultRenderer ((defaultRenderer).tableCellRenderer); +}}this.tableHeader = tableHeader; +if (this.tableHeader != null) { +this.tableHeader.addMouseListener (this.mouseListener); +this.tableHeader.setDefaultRenderer (Clazz.innerTypeInstance (jalview.util.TableSorter.SortableHeaderRenderer, this, null, this.tableHeader.getDefaultRenderer ())); +}}, "javax.swing.table.JTableHeader"); +Clazz.defineMethod (c$, "isSorting", +function () { +return this.sortingColumns.size () != 0; +}); +Clazz.defineMethod (c$, "getDirective", +($fz = function (column) { +for (var i = 0; i < this.sortingColumns.size (); i++) { +var directive = this.sortingColumns.get (i); +if (directive.column == column) { +return directive; +}} +return jalview.util.TableSorter.EMPTY_DIRECTIVE; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "getSortingStatus", +function (column) { +return this.getDirective (column).direction; +}, "~N"); +Clazz.defineMethod (c$, "sortingStatusChanged", +($fz = function () { +this.clearSortingState (); +this.fireTableDataChanged (); +if (this.tableHeader != null) { +this.tableHeader.repaint (); +}}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "setSortingStatus", +function (column, status) { +var directive = this.getDirective (column); +if (directive !== jalview.util.TableSorter.EMPTY_DIRECTIVE) { +this.sortingColumns.remove (directive); +}if (status != 0) { +this.sortingColumns.add ( new jalview.util.TableSorter.Directive (column, status)); +}this.sortingStatusChanged (); +}, "~N,~N"); +Clazz.defineMethod (c$, "getHeaderRendererIcon", +function (column, size) { +var directive = this.getDirective (column); +if (directive === jalview.util.TableSorter.EMPTY_DIRECTIVE) { +return null; +}return new jalview.util.TableSorter.Arrow (directive.direction == -1, size, this.sortingColumns.indexOf (directive)); +}, "~N,~N"); +Clazz.defineMethod (c$, "cancelSorting", +($fz = function () { +this.sortingColumns.clear (); +this.sortingStatusChanged (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "setColumnComparator", +function (type, comparator) { +if (comparator == null) { +this.columnComparators.remove (type); +} else { +this.columnComparators.put (type, comparator); +}}, "Class,java.util.Comparator"); +Clazz.defineMethod (c$, "getComparator", +function (column) { +var columnType = this.tableModel.getColumnClass (column); +var comparator = this.columnComparators.get (columnType); +if (comparator != null) { +return comparator; +}if (Comparable.isAssignableFrom (columnType)) { +return jalview.util.TableSorter.COMPARABLE_COMAPRATOR; +}return jalview.util.TableSorter.LEXICAL_COMPARATOR; +}, "~N"); +Clazz.defineMethod (c$, "getViewToModel", +($fz = function () { +if (this.viewToModel == null) { +var tableModelRowCount = this.tableModel.getRowCount (); +this.viewToModel = new Array (tableModelRowCount); +for (var row = 0; row < tableModelRowCount; row++) { +this.viewToModel[row] = Clazz.innerTypeInstance (jalview.util.TableSorter.Row, this, null, row); +} +if (this.isSorting ()) { +java.util.Arrays.sort (this.viewToModel); +}}return this.viewToModel; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "modelIndex", +function (viewIndex) { +return this.getViewToModel ()[viewIndex].modelIndex; +}, "~N"); +Clazz.defineMethod (c$, "getModelToView", +($fz = function () { +if (this.modelToView == null) { +var n = this.getViewToModel ().length; +this.modelToView = Clazz.newIntArray (n, 0); +for (var i = 0; i < n; i++) { +this.modelToView[this.modelIndex (i)] = i; +} +}return this.modelToView; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getRowCount", +function () { +return (this.tableModel == null) ? 0 : this.tableModel.getRowCount (); +}); +Clazz.defineMethod (c$, "getColumnCount", +function () { +return (this.tableModel == null) ? 0 : this.tableModel.getColumnCount (); +}); +Clazz.overrideMethod (c$, "getColumnName", +function (column) { +return this.tableModel.getColumnName (column); +}, "~N"); +Clazz.overrideMethod (c$, "getColumnClass", +function (column) { +return this.tableModel.getColumnClass (column); +}, "~N"); +Clazz.overrideMethod (c$, "isCellEditable", +function (row, column) { +return this.tableModel.isCellEditable (this.modelIndex (row), column); +}, "~N,~N"); +Clazz.defineMethod (c$, "getValueAt", +function (row, column) { +return this.tableModel.getValueAt (this.modelIndex (row), column); +}, "~N,~N"); +Clazz.overrideMethod (c$, "setValueAt", +function (aValue, row, column) { +this.tableModel.setValueAt (aValue, this.modelIndex (row), column); +}, "~O,~N,~N"); +c$.$TableSorter$Row$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.modelIndex = 0; +Clazz.instantialize (this, arguments); +}, jalview.util.TableSorter, "Row", null, Comparable); +Clazz.makeConstructor (c$, +function (a) { +this.modelIndex = a; +}, "~N"); +Clazz.overrideMethod (c$, "compareTo", +function (a) { +var b = this.modelIndex; +var c = (a).modelIndex; +for (var d = this.b$["jalview.util.TableSorter"].sortingColumns.iterator (); d.hasNext (); ) { +var e = d.next (); +var f = e.column; +var g = this.b$["jalview.util.TableSorter"].tableModel.getValueAt (b, f); +var h = this.b$["jalview.util.TableSorter"].tableModel.getValueAt (c, f); +var i = 0; +if (g == null && h == null) { +i = 0; +} else if (g == null) { +i = -1; +} else if (h == null) { +i = 1; +} else { +i = this.b$["jalview.util.TableSorter"].getComparator (f).compare (g, h); +}if (i != 0) { +return e.direction == -1 ? -i : i; +}} +return 0; +}, "~O"); +c$ = Clazz.p0p (); +}; +c$.$TableSorter$TableModelHandler$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +Clazz.instantialize (this, arguments); +}, jalview.util.TableSorter, "TableModelHandler", null, javax.swing.event.TableModelListener); +Clazz.overrideMethod (c$, "tableChanged", +function (a) { +if (!this.b$["jalview.util.TableSorter"].isSorting ()) { +this.b$["jalview.util.TableSorter"].clearSortingState (); +this.b$["jalview.util.TableSorter"].fireTableChanged (a); +return; +}if (a.getFirstRow () == -1) { +this.b$["jalview.util.TableSorter"].cancelSorting (); +this.b$["jalview.util.TableSorter"].fireTableChanged (a); +return; +}var b = a.getColumn (); +if (a.getFirstRow () == a.getLastRow () && b != -1 && this.b$["jalview.util.TableSorter"].getSortingStatus (b) == 0 && this.b$["jalview.util.TableSorter"].modelToView != null) { +var c = this.b$["jalview.util.TableSorter"].getModelToView ()[a.getFirstRow ()]; +this.b$["jalview.util.TableSorter"].fireTableChanged ( new javax.swing.event.TableModelEvent (this.b$["jalview.util.TableSorter"], c, c, b, a.getType ())); +return; +}this.b$["jalview.util.TableSorter"].clearSortingState (); +this.b$["jalview.util.TableSorter"].fireTableDataChanged (); +return; +}, "javax.swing.event.TableModelEvent"); +c$ = Clazz.p0p (); +}; +c$.$TableSorter$MouseHandler$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +Clazz.instantialize (this, arguments); +}, jalview.util.TableSorter, "MouseHandler", java.awt.event.MouseAdapter); +Clazz.overrideMethod (c$, "mouseClicked", +function (a) { +var b = a.getSource (); +var c = b.getColumnModel (); +var d = c.getColumnIndexAtX (a.getX ()); +var e = c.getColumn (d).getModelIndex (); +if (e != -1) { +var f = this.b$["jalview.util.TableSorter"].getSortingStatus (e); +if (!a.isControlDown ()) { +this.b$["jalview.util.TableSorter"].cancelSorting (); +}f = f + (a.isShiftDown () ? -1 : 1); +f = (f + 4) % 3 - 1; +this.b$["jalview.util.TableSorter"].setSortingStatus (e, f); +}}, "java.awt.event.MouseEvent"); +c$ = Clazz.p0p (); +}; +c$.$TableSorter$SortableHeaderRenderer$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.tableCellRenderer = null; +Clazz.instantialize (this, arguments); +}, jalview.util.TableSorter, "SortableHeaderRenderer", null, javax.swing.table.TableCellRenderer); +Clazz.makeConstructor (c$, +function (a) { +this.tableCellRenderer = a; +}, "javax.swing.table.TableCellRenderer"); +Clazz.defineMethod (c$, "getTableCellRendererComponent", +function (a, b, c, d, e, f) { +var g = this.tableCellRenderer.getTableCellRendererComponent (a, b, c, d, e, f); +if (Clazz.instanceOf (g, javax.swing.JLabel)) { +var h = g; +h.setHorizontalTextPosition (2); +var i = a.convertColumnIndexToModel (f); +h.setIcon (this.b$["jalview.util.TableSorter"].getHeaderRendererIcon (i, h.getFont ().getSize ())); +}return g; +}, "javax.swing.JTable,~O,~B,~B,~N,~N"); +c$ = Clazz.p0p (); +}; +c$.$TableSorter$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "TableSorter$1", null, java.util.Comparator); +Clazz.defineMethod (c$, "compare", +function (o1, o2) { +return (o1).compareTo (o2); +}, "~O,~O"); +c$ = Clazz.p0p (); +}; +c$.$TableSorter$2$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (jalview.util, "TableSorter$2", null, java.util.Comparator); +Clazz.defineMethod (c$, "compare", +function (o1, o2) { +return o1.toString ().compareTo (o2.toString ()); +}, "~O,~O"); +c$ = Clazz.p0p (); +}; +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.descending = false; +this.size = 0; +this.priority = 0; +Clazz.instantialize (this, arguments); +}, jalview.util.TableSorter, "Arrow", null, javax.swing.Icon); +Clazz.makeConstructor (c$, +function (a, b, c) { +this.descending = a; +this.size = b; +this.priority = c; +}, "~B,~N,~N"); +Clazz.overrideMethod (c$, "paintIcon", +function (a, b, c, d) { +var e = a == null ? java.awt.Color.GRAY : a.getBackground (); +var f = Clazz.doubleToInt (Clazz.doubleToInt (this.size / 2) * Math.pow (0.8, this.priority)); +var g = this.descending ? f : -f; +d = d + Clazz.doubleToInt (5 * this.size / 6) + (this.descending ? -g : 0); +var h = this.descending ? 1 : -1; +b.translate (c, d); +b.setColor (e.darker ()); +b.drawLine (Clazz.doubleToInt (f / 2), g, 0, 0); +b.drawLine (Clazz.doubleToInt (f / 2), g + h, 0, h); +b.setColor (e.brighter ()); +b.drawLine (Clazz.doubleToInt (f / 2), g, f, 0); +b.drawLine (Clazz.doubleToInt (f / 2), g + h, f, h); +if (this.descending) { +b.setColor (e.darker ().darker ()); +} else { +b.setColor (e.brighter ().brighter ()); +}b.drawLine (f, 0, 0, 0); +b.setColor (e); +b.translate (-c, -d); +}, "java.awt.Component,java.awt.Graphics,~N,~N"); +Clazz.overrideMethod (c$, "getIconWidth", +function () { +return this.size; +}); +Clazz.overrideMethod (c$, "getIconHeight", +function () { +return this.size; +}); +c$ = Clazz.p0p (); +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +this.column = 0; +this.direction = 0; +Clazz.instantialize (this, arguments); +}, jalview.util.TableSorter, "Directive"); +Clazz.makeConstructor (c$, +function (a, b) { +this.column = a; +this.direction = b; +}, "~N,~N"); +c$ = Clazz.p0p (); +Clazz.defineStatics (c$, +"DESCENDING", -1, +"NOT_SORTED", 0, +"ASCENDING", 1); +c$.EMPTY_DIRECTIVE = c$.prototype.EMPTY_DIRECTIVE = new jalview.util.TableSorter.Directive (-1, 0); +c$.COMPARABLE_COMAPRATOR = c$.prototype.COMPARABLE_COMAPRATOR = ((Clazz.isClassDefined ("jalview.util.TableSorter$1") ? 0 : jalview.util.TableSorter.$TableSorter$1$ ()), Clazz.innerTypeInstance (jalview.util.TableSorter$1, this, null)); +c$.LEXICAL_COMPARATOR = c$.prototype.LEXICAL_COMPARATOR = ((Clazz.isClassDefined ("jalview.util.TableSorter$2") ? 0 : jalview.util.TableSorter.$TableSorter$2$ ()), Clazz.innerTypeInstance (jalview.util.TableSorter$2, this, null)); +}); diff --git a/bin/jalview/util/UrlLink.class b/bin/jalview/util/UrlLink.class index da2ea87..0e8bcb6 100644 Binary files a/bin/jalview/util/UrlLink.class and b/bin/jalview/util/UrlLink.class differ diff --git a/bin/jalview/util/UrlLink.js b/bin/jalview/util/UrlLink.js index c50c6ae..a28894b 100644 --- a/bin/jalview/util/UrlLink.js +++ b/bin/jalview/util/UrlLink.js @@ -1,148 +1,148 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (null, "jalview.util.UrlLink", ["jalview.jsdev.RegExp", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.url_suffix = null; -this.url_prefix = null; -this.target = null; -this.label = null; -this.regexReplace = null; -this.dynamic = false; -this.invalidMessage = null; -Clazz.instantialize (this, arguments); -}, jalview.util, "UrlLink"); -Clazz.makeConstructor (c$, -function (link) { -var sep = link.indexOf ("|"); -var psqid = link.indexOf ("$SEQUENCE_ID"); -if (psqid > -1) { -this.dynamic = true; -var p = sep; -do { -sep = p; -p = link.indexOf ("|", sep + 1); -} while (p > sep && p < psqid); -this.label = link.substring (0, sep); -if (this.label.indexOf ("|") > -1) { -this.target = this.label.substring (0, this.label.indexOf ("|")); -} else if (this.label.indexOf (" ") > 2) { -this.target = this.label.substring (0, this.label.indexOf (" ")); -} else { -this.target = this.label; -}this.url_prefix = link.substring (sep + 1, psqid); -if (link.indexOf ("$SEQUENCE_ID=/") == psqid && (p = link.indexOf ("/=$", psqid + 14)) > psqid + 14) { -this.url_suffix = link.substring (p + 3); -this.regexReplace = link.substring (psqid + 14, p); -try { -var rg = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace + "/"); -if (rg == null) { -this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace + "'\n"; -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace + "'\n"; -} else { -throw e; -} -} -} else { -this.regexReplace = null; -if (link.indexOf ("$SEQUENCE_ID$") == psqid) { -this.url_suffix = link.substring (psqid + 13); -this.regexReplace = null; -} else { -this.invalidMessage = "Warning: invalid regex structure for URL link : " + link; -}}} else { -this.target = link.substring (0, sep); -this.label = link.substring (0, sep = link.lastIndexOf ("|")); -this.url_prefix = link.substring (sep + 1); -this.regexReplace = null; -this.url_suffix = null; -}}, "~S"); -Clazz.defineMethod (c$, "getUrl_suffix", -function () { -return this.url_suffix; -}); -Clazz.defineMethod (c$, "getUrl_prefix", -function () { -return this.url_prefix; -}); -Clazz.defineMethod (c$, "getTarget", -function () { -return this.target; -}); -Clazz.defineMethod (c$, "getLabel", -function () { -return this.label; -}); -Clazz.defineMethod (c$, "getRegexReplace", -function () { -return this.regexReplace; -}); -Clazz.defineMethod (c$, "getInvalidMessage", -function () { -return this.invalidMessage; -}); -Clazz.defineMethod (c$, "isValid", -function () { -return this.invalidMessage == null; -}); -Clazz.defineMethod (c$, "makeUrls", -function (idstring, onlyIfMatches) { -if (this.dynamic) { -if (this.regexReplace != null) { -var rg = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace + "/"); -if (rg.search (idstring)) { -var ns = rg.numSubs (); -if (ns == 0) { -return Clazz.newArray (-1, [rg.stringMatchedI (ns), this.url_prefix + rg.stringMatched () + this.url_suffix]); -} else { -for (var s = 0; s <= rg.numSubs (); s++) { -System.err.println ("Sub " + s + " : " + rg.matchedFromI (s) + " : " + rg.matchedToI (s) + " : '" + rg.stringMatchedI (s) + "'"); -} -var subs = new java.util.Vector (); -var s = 0; -while (s <= ns) { -if (s + 1 <= ns && rg.matchedToI (s) > -1 && rg.matchedToI (s + 1) > -1 && rg.matchedToI (s + 1) < rg.matchedToI (s)) { -var r = s + 1; -var mtch = ""; -while (r <= ns && rg.matchedToI (r) <= rg.matchedToI (s)) { -if (rg.matchedFromI (r) > -1) { -mtch += rg.stringMatchedI (r); -}r++; -} -if (mtch.length > 0) { -subs.addElement (mtch); -subs.addElement (this.url_prefix + mtch + this.url_suffix); -}s = r; -} else { -if (rg.matchedFromI (s) > -1) { -subs.addElement (rg.stringMatchedI (s)); -subs.addElement (this.url_prefix + rg.stringMatchedI (s) + this.url_suffix); -}s++; -}} -var res = new Array (subs.size ()); -for (var r = 0, rs = subs.size (); r < rs; r++) { -res[r] = subs.elementAt (r); -} -subs.removeAllElements (); -return res; -}}if (onlyIfMatches) { -return null; -}}if (idstring.indexOf ("|") > -1) { -idstring = idstring.substring (idstring.lastIndexOf ("|") + 1); -}return Clazz.newArray (-1, [idstring, this.url_prefix + idstring + this.url_suffix]); -} else { -return Clazz.newArray (-1, ["", this.url_prefix]); -}}, "~S,~B"); -Clazz.overrideMethod (c$, "toString", -function () { -return this.label + "|" + this.url_prefix + (this.dynamic ? ("$SEQUENCE_ID" + ((this.regexReplace != null) ? "=" + this.regexReplace + "=$" : "$")) : "") + ((this.url_suffix == null) ? "" : this.url_suffix); -}); -Clazz.defineMethod (c$, "isDynamic", -function () { -return this.dynamic; -}); -Clazz.defineMethod (c$, "setLabel", -function (newlabel) { -this.label = newlabel; -}, "~S"); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (null, "jalview.util.UrlLink", ["jalview.jsdev.RegExp", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.url_suffix = null; +this.url_prefix = null; +this.target = null; +this.label = null; +this.regexReplace = null; +this.dynamic = false; +this.invalidMessage = null; +Clazz.instantialize (this, arguments); +}, jalview.util, "UrlLink"); +Clazz.makeConstructor (c$, +function (link) { +var sep = link.indexOf ("|"); +var psqid = link.indexOf ("$SEQUENCE_ID"); +if (psqid > -1) { +this.dynamic = true; +var p = sep; +do { +sep = p; +p = link.indexOf ("|", sep + 1); +} while (p > sep && p < psqid); +this.label = link.substring (0, sep); +if (this.label.indexOf ("|") > -1) { +this.target = this.label.substring (0, this.label.indexOf ("|")); +} else if (this.label.indexOf (" ") > 2) { +this.target = this.label.substring (0, this.label.indexOf (" ")); +} else { +this.target = this.label; +}this.url_prefix = link.substring (sep + 1, psqid); +if (link.indexOf ("$SEQUENCE_ID=/") == psqid && (p = link.indexOf ("/=$", psqid + 14)) > psqid + 14) { +this.url_suffix = link.substring (p + 3); +this.regexReplace = link.substring (psqid + 14, p); +try { +var rg = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace + "/"); +if (rg == null) { +this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace + "'\n"; +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +this.invalidMessage = "Invalid Regular Expression : '" + this.regexReplace + "'\n"; +} else { +throw e; +} +} +} else { +this.regexReplace = null; +if (link.indexOf ("$SEQUENCE_ID$") == psqid) { +this.url_suffix = link.substring (psqid + 13); +this.regexReplace = null; +} else { +this.invalidMessage = "Warning: invalid regex structure for URL link : " + link; +}}} else { +this.target = link.substring (0, sep); +this.label = link.substring (0, sep = link.lastIndexOf ("|")); +this.url_prefix = link.substring (sep + 1); +this.regexReplace = null; +this.url_suffix = null; +}}, "~S"); +Clazz.defineMethod (c$, "getUrl_suffix", +function () { +return this.url_suffix; +}); +Clazz.defineMethod (c$, "getUrl_prefix", +function () { +return this.url_prefix; +}); +Clazz.defineMethod (c$, "getTarget", +function () { +return this.target; +}); +Clazz.defineMethod (c$, "getLabel", +function () { +return this.label; +}); +Clazz.defineMethod (c$, "getRegexReplace", +function () { +return this.regexReplace; +}); +Clazz.defineMethod (c$, "getInvalidMessage", +function () { +return this.invalidMessage; +}); +Clazz.defineMethod (c$, "isValid", +function () { +return this.invalidMessage == null; +}); +Clazz.defineMethod (c$, "makeUrls", +function (idstring, onlyIfMatches) { +if (this.dynamic) { +if (this.regexReplace != null) { +var rg = jalview.jsdev.RegExp.perlCode ("/" + this.regexReplace + "/"); +if (rg.search (idstring)) { +var ns = rg.numSubs (); +if (ns == 0) { +return Clazz.newArray (-1, [rg.stringMatchedI (ns), this.url_prefix + rg.stringMatched () + this.url_suffix]); +} else { +for (var s = 0; s <= rg.numSubs (); s++) { +System.err.println ("Sub " + s + " : " + rg.matchedFromI (s) + " : " + rg.matchedToI (s) + " : '" + rg.stringMatchedI (s) + "'"); +} +var subs = new java.util.Vector (); +var s = 0; +while (s <= ns) { +if (s + 1 <= ns && rg.matchedToI (s) > -1 && rg.matchedToI (s + 1) > -1 && rg.matchedToI (s + 1) < rg.matchedToI (s)) { +var r = s + 1; +var mtch = ""; +while (r <= ns && rg.matchedToI (r) <= rg.matchedToI (s)) { +if (rg.matchedFromI (r) > -1) { +mtch += rg.stringMatchedI (r); +}r++; +} +if (mtch.length > 0) { +subs.addElement (mtch); +subs.addElement (this.url_prefix + mtch + this.url_suffix); +}s = r; +} else { +if (rg.matchedFromI (s) > -1) { +subs.addElement (rg.stringMatchedI (s)); +subs.addElement (this.url_prefix + rg.stringMatchedI (s) + this.url_suffix); +}s++; +}} +var res = new Array (subs.size ()); +for (var r = 0, rs = subs.size (); r < rs; r++) { +res[r] = subs.elementAt (r); +} +subs.removeAllElements (); +return res; +}}if (onlyIfMatches) { +return null; +}}if (idstring.indexOf ("|") > -1) { +idstring = idstring.substring (idstring.lastIndexOf ("|") + 1); +}return Clazz.newArray (-1, [idstring, this.url_prefix + idstring + this.url_suffix]); +} else { +return Clazz.newArray (-1, ["", this.url_prefix]); +}}, "~S,~B"); +Clazz.overrideMethod (c$, "toString", +function () { +return this.label + "|" + this.url_prefix + (this.dynamic ? ("$SEQUENCE_ID" + ((this.regexReplace != null) ? "=" + this.regexReplace + "=$" : "$")) : "") + ((this.url_suffix == null) ? "" : this.url_suffix); +}); +Clazz.defineMethod (c$, "isDynamic", +function () { +return this.dynamic; +}); +Clazz.defineMethod (c$, "setLabel", +function (newlabel) { +this.label = newlabel; +}, "~S"); +}); diff --git a/bin/jalview/util/jarInputStreamProvider.js b/bin/jalview/util/jarInputStreamProvider.js deleted file mode 100644 index 536a4ea..0000000 --- a/bin/jalview/util/jarInputStreamProvider.js +++ /dev/null @@ -1,2 +0,0 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.declareInterface (jalview.util, "jarInputStreamProvider"); diff --git a/bin/jalview/viewmodel/AlignmentViewport.js b/bin/jalview/viewmodel/AlignmentViewport.js index 6f07731..cdbd489 100644 --- a/bin/jalview/viewmodel/AlignmentViewport.js +++ b/bin/jalview/viewmodel/AlignmentViewport.js @@ -1,1254 +1,1254 @@ -Clazz.declarePackage ("jalview.viewmodel"); -Clazz.load (["jalview.api.AlignViewportI", "jalview.structure.CommandListener", "$.VamsasSource", "jalview.datamodel.ColumnSelection", "jalview.viewmodel.styles.ViewStyle", "jalview.workers.AlignCalcManager", "java.beans.PropertyChangeSupport", "java.util.ArrayDeque", "$.HashMap"], "jalview.viewmodel.AlignmentViewport", ["jalview.analysis.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.AlignmentView", "$.CigarArray", "$.Sequence", "$.SequenceGroup", "jalview.schemes.Blosum62ColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "jalview.util.Comparison", "$.MappingUtils", "jalview.workers.ComplementConsensusThread", "$.ConsensusThread", "$.ConservationThread", "$.StrucConsensusThread", "java.awt.Color", "java.util.ArrayList", "$.BitSet", "$.Hashtable"], function () { -c$ = Clazz.decorateAsClass (function () { -this.viewStyle = null; -this.codingComplement = null; -this.featuresDisplayed = null; -this.historyList = null; -this.redoList = null; -this.alignment = null; -this.sequenceSetID = null; -this.$isDataset = false; -this.hiddenRepSequences = null; -this.colSel = null; -this.autoCalculateConsensus = true; -this.autoCalculateStrucConsensus = true; -this.ignoreGapsInConsensusCalculation = false; -this.globalColourScheme = null; -this.consensus = null; -this.complementConsensus = null; -this.strucConsensus = null; -this.conservation = null; -this.quality = null; -this.groupConsensus = null; -this.groupConservation = null; -this.hconsensus = null; -this.hcomplementConsensus = null; -this.hStrucConsensus = null; -this.hconservation = null; -this.ConsPercGaps = 25; -this.calculator = null; -this.showGroupConservation = false; -this.showGroupConsensus = false; -this.showSequenceLogo = false; -this.normaliseSequenceLogo = false; -this.showConsensusHistogram = true; -this.padGaps = false; -this.sortByTree = false; -this.selectionGroup = null; -this.viewId = null; -this.sgrouphash = -1; -this.colselhash = -1; -this.changeSupport = null; -this.showConservation = true; -this.showQuality = true; -this.showConsensus = true; -this.sequenceColours = null; -this.sortAnnotationsBy = null; -this.showAutocalculatedAbove = false; -this.followHighlight = true; -this.startRes = 0; -this.endRes = 0; -this.startSeq = 0; -this.endSeq = 0; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel, "AlignmentViewport", null, [jalview.api.AlignViewportI, jalview.structure.CommandListener, jalview.structure.VamsasSource]); -Clazz.prepareFields (c$, function () { -this.viewStyle = new jalview.viewmodel.styles.ViewStyle (); -this.historyList = new java.util.ArrayDeque (); -this.redoList = new java.util.ArrayDeque (); -this.colSel = new jalview.datamodel.ColumnSelection (); -this.calculator = new jalview.workers.AlignCalcManager (); -this.changeSupport = new java.beans.PropertyChangeSupport (this); -this.sequenceColours = new java.util.HashMap (); -}); -Clazz.defineMethod (c$, "setFontName", -function (name) { -this.viewStyle.setFontName (name); -}, "~S"); -Clazz.defineMethod (c$, "setFontStyle", -function (style) { -this.viewStyle.setFontStyle (style); -}, "~N"); -Clazz.defineMethod (c$, "setFontSize", -function (size) { -this.viewStyle.setFontSize (size); -}, "~N"); -Clazz.defineMethod (c$, "getFontStyle", -function () { -return this.viewStyle.getFontStyle (); -}); -Clazz.defineMethod (c$, "getFontName", -function () { -return this.viewStyle.getFontName (); -}); -Clazz.defineMethod (c$, "getFontSize", -function () { -return this.viewStyle.getFontSize (); -}); -Clazz.defineMethod (c$, "setUpperCasebold", -function (upperCasebold) { -this.viewStyle.setUpperCasebold (upperCasebold); -}, "~B"); -Clazz.defineMethod (c$, "isUpperCasebold", -function () { -return this.viewStyle.isUpperCasebold (); -}); -Clazz.defineMethod (c$, "isSeqNameItalics", -function () { -return this.viewStyle.isSeqNameItalics (); -}); -Clazz.defineMethod (c$, "setColourByReferenceSeq", -function (colourByReferenceSeq) { -this.viewStyle.setColourByReferenceSeq (colourByReferenceSeq); -}, "~B"); -Clazz.defineMethod (c$, "setColourAppliesToAllGroups", -function (b) { -this.viewStyle.setColourAppliesToAllGroups (b); -}, "~B"); -Clazz.defineMethod (c$, "getColourAppliesToAllGroups", -function () { -return this.viewStyle.getColourAppliesToAllGroups (); -}); -Clazz.defineMethod (c$, "getAbovePIDThreshold", -function () { -return this.viewStyle.getAbovePIDThreshold (); -}); -Clazz.defineMethod (c$, "setIncrement", -function (inc) { -this.viewStyle.setIncrement (inc); -}, "~N"); -Clazz.defineMethod (c$, "getIncrement", -function () { -return this.viewStyle.getIncrement (); -}); -Clazz.defineMethod (c$, "setConservationSelected", -function (b) { -this.viewStyle.setConservationSelected (b); -}, "~B"); -Clazz.defineMethod (c$, "setShowHiddenMarkers", -function (show) { -this.viewStyle.setShowHiddenMarkers (show); -}, "~B"); -Clazz.defineMethod (c$, "getShowHiddenMarkers", -function () { -return this.viewStyle.getShowHiddenMarkers (); -}); -Clazz.defineMethod (c$, "setScaleRightWrapped", -function (b) { -this.viewStyle.setScaleRightWrapped (b); -}, "~B"); -Clazz.defineMethod (c$, "setScaleLeftWrapped", -function (b) { -this.viewStyle.setScaleLeftWrapped (b); -}, "~B"); -Clazz.defineMethod (c$, "setScaleAboveWrapped", -function (b) { -this.viewStyle.setScaleAboveWrapped (b); -}, "~B"); -Clazz.defineMethod (c$, "getScaleLeftWrapped", -function () { -return this.viewStyle.getScaleLeftWrapped (); -}); -Clazz.defineMethod (c$, "getScaleAboveWrapped", -function () { -return this.viewStyle.getScaleAboveWrapped (); -}); -Clazz.defineMethod (c$, "getScaleRightWrapped", -function () { -return this.viewStyle.getScaleRightWrapped (); -}); -Clazz.defineMethod (c$, "setAbovePIDThreshold", -function (b) { -this.viewStyle.setAbovePIDThreshold (b); -}, "~B"); -Clazz.defineMethod (c$, "setThreshold", -function (thresh) { -this.viewStyle.setThreshold (thresh); -}, "~N"); -Clazz.defineMethod (c$, "getThreshold", -function () { -return this.viewStyle.getThreshold (); -}); -Clazz.defineMethod (c$, "getShowJVSuffix", -function () { -return this.viewStyle.getShowJVSuffix (); -}); -Clazz.defineMethod (c$, "setShowJVSuffix", -function (b) { -this.viewStyle.setShowJVSuffix (b); -}, "~B"); -Clazz.defineMethod (c$, "setWrapAlignment", -function (state) { -this.viewStyle.setWrapAlignment (state); -}, "~B"); -Clazz.defineMethod (c$, "setShowText", -function (state) { -this.viewStyle.setShowText (state); -}, "~B"); -Clazz.defineMethod (c$, "setRenderGaps", -function (state) { -this.viewStyle.setRenderGaps (state); -}, "~B"); -Clazz.defineMethod (c$, "getColourText", -function () { -return this.viewStyle.getColourText (); -}); -Clazz.defineMethod (c$, "setColourText", -function (state) { -this.viewStyle.setColourText (state); -}, "~B"); -Clazz.defineMethod (c$, "getWrapAlignment", -function () { -return this.viewStyle.getWrapAlignment (); -}); -Clazz.defineMethod (c$, "getShowText", -function () { -return this.viewStyle.getShowText (); -}); -Clazz.defineMethod (c$, "getWrappedWidth", -function () { -return this.viewStyle.getWrappedWidth (); -}); -Clazz.defineMethod (c$, "setWrappedWidth", -function (w) { -this.viewStyle.setWrappedWidth (w); -}, "~N"); -Clazz.defineMethod (c$, "getCharHeight", -function () { -return this.viewStyle.getCharHeight (); -}); -Clazz.defineMethod (c$, "setCharHeight", -function (h) { -this.viewStyle.setCharHeight (h); -}, "~N"); -Clazz.defineMethod (c$, "getCharWidth", -function () { -return this.viewStyle.getCharWidth (); -}); -Clazz.defineMethod (c$, "setCharWidth", -function (w) { -this.viewStyle.setCharWidth (w); -}, "~N"); -Clazz.defineMethod (c$, "getShowBoxes", -function () { -return this.viewStyle.getShowBoxes (); -}); -Clazz.defineMethod (c$, "getShowUnconserved", -function () { -return this.viewStyle.getShowUnconserved (); -}); -Clazz.defineMethod (c$, "setShowUnconserved", -function (showunconserved) { -this.viewStyle.setShowUnconserved (showunconserved); -}, "~B"); -Clazz.defineMethod (c$, "setSeqNameItalics", -function (default1) { -this.viewStyle.setSeqNameItalics (default1); -}, "~B"); -Clazz.defineMethod (c$, "getAlignment", -function () { -return this.alignment; -}); -Clazz.overrideMethod (c$, "getGapCharacter", -function () { -return this.alignment.getGapCharacter (); -}); -Clazz.defineMethod (c$, "setDataset", -function (b) { -this.$isDataset = b; -}, "~B"); -Clazz.defineMethod (c$, "isDataset", -function () { -return this.$isDataset; -}); -Clazz.overrideMethod (c$, "setGlobalColourScheme", -function (cs) { -this.globalColourScheme = cs; -var recalc = false; -if (cs != null) { -cs.setConservationApplied (recalc = this.getConservationSelected ()); -if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) { -recalc = true; -cs.setThreshold (this.viewStyle.getThreshold (), this.ignoreGapsInConsensusCalculation); -} else { -cs.setThreshold (0, this.ignoreGapsInConsensusCalculation); -}if (recalc) { -cs.setConsensus (this.hconsensus); -cs.setConservation (this.hconservation); -}cs.alignmentChanged (this.alignment, this.hiddenRepSequences); -}if (this.getColourAppliesToAllGroups ()) { -for (var sg, $sg = this.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (cs == null) { -sg.cs = null; -continue; -}sg.cs = cs.applyTo (sg, this.getHiddenRepSequences ()); -sg.setConsPercGaps (this.ConsPercGaps); -if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) { -sg.cs.setThreshold (this.viewStyle.getThreshold (), this.isIgnoreGapsConsensus ()); -recalc = true; -} else { -sg.cs.setThreshold (0, this.isIgnoreGapsConsensus ()); -}if (this.getConservationSelected ()) { -sg.cs.setConservationApplied (true); -recalc = true; -} else { -sg.cs.setConservation (null); -}if (recalc) { -sg.recalcConservation (); -} else { -sg.cs.alignmentChanged (sg, this.hiddenRepSequences); -}} -}}, "jalview.schemes.ColourSchemeI"); -Clazz.overrideMethod (c$, "getGlobalColourScheme", -function () { -return this.globalColourScheme; -}); -Clazz.overrideMethod (c$, "setConservation", -function (cons) { -this.hconservation = cons; -}, "jalview.analysis.Conservation"); -Clazz.overrideMethod (c$, "getConsPercGaps", -function () { -return this.ConsPercGaps; -}); -Clazz.overrideMethod (c$, "setSequenceConsensusHash", -function (hconsensus) { -this.hconsensus = hconsensus; -}, "~A"); -Clazz.overrideMethod (c$, "setComplementConsensusHash", -function (hconsensus) { -this.hcomplementConsensus = hconsensus; -}, "~A"); -Clazz.overrideMethod (c$, "getSequenceConsensusHash", -function () { -return this.hconsensus; -}); -Clazz.overrideMethod (c$, "getComplementConsensusHash", -function () { -return this.hcomplementConsensus; -}); -Clazz.overrideMethod (c$, "getRnaStructureConsensusHash", -function () { -return this.hStrucConsensus; -}); -Clazz.overrideMethod (c$, "setRnaStructureConsensusHash", -function (hStrucConsensus) { -this.hStrucConsensus = hStrucConsensus; -}, "~A"); -Clazz.overrideMethod (c$, "getAlignmentQualityAnnot", -function () { -return this.quality; -}); -Clazz.overrideMethod (c$, "getAlignmentConservationAnnotation", -function () { -return this.conservation; -}); -Clazz.overrideMethod (c$, "getAlignmentConsensusAnnotation", -function () { -return this.consensus; -}); -Clazz.overrideMethod (c$, "getComplementConsensusAnnotation", -function () { -return this.complementConsensus; -}); -Clazz.overrideMethod (c$, "getAlignmentStrucConsensusAnnotation", -function () { -return this.strucConsensus; -}); -Clazz.defineMethod (c$, "updateConservation", -function (ap) { -if (this.alignment.isNucleotide () || this.conservation == null || !this.autoCalculateConsensus) { -return; -}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConservationThread) == null) { -this.calculator.registerWorker ( new jalview.workers.ConservationThread (this, ap)); -}}, "jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "updateConsensus", -function (ap) { -if (this.consensus == null || !this.autoCalculateConsensus) { -return; -}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConsensusThread) == null) { -this.calculator.registerWorker ( new jalview.workers.ConsensusThread (this, ap)); -}var al = this.getAlignment (); -if (!al.isNucleotide () && al.getCodonFrames () != null && !al.getCodonFrames ().isEmpty ()) { -if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ComplementConsensusThread) == null) { -this.calculator.registerWorker ( new jalview.workers.ComplementConsensusThread (this, ap)); -}}}, "jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "updateStrucConsensus", -function (ap) { -if (this.autoCalculateStrucConsensus && this.strucConsensus == null && this.alignment.isNucleotide () && this.alignment.hasRNAStructure ()) { -this.initRNAStructure (); -}if (this.strucConsensus == null || !this.autoCalculateStrucConsensus) { -return; -}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.StrucConsensusThread) == null) { -this.calculator.registerWorker ( new jalview.workers.StrucConsensusThread (this, ap)); -}}, "jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "isCalcInProgress", -function () { -return this.calculator.isWorking (); -}); -Clazz.overrideMethod (c$, "isCalculationInProgress", -function (alignmentAnnotation) { -if (!alignmentAnnotation.autoCalculated) { -return false; -}if (this.calculator.workingInvolvedWith (alignmentAnnotation)) { -return true; -}return false; -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.overrideMethod (c$, "isClosed", -function () { -return this.alignment == null; -}); -Clazz.overrideMethod (c$, "getCalcManager", -function () { -return this.calculator; -}); -Clazz.overrideMethod (c$, "isShowSequenceLogo", -function () { -return this.showSequenceLogo; -}); -Clazz.defineMethod (c$, "setShowSequenceLogo", -function (showSequenceLogo) { -if (showSequenceLogo != this.showSequenceLogo) { -this.showSequenceLogo = showSequenceLogo; -this.calculator.updateAnnotationFor (jalview.workers.ConsensusThread); -this.calculator.updateAnnotationFor (jalview.workers.ComplementConsensusThread); -this.calculator.updateAnnotationFor (jalview.workers.StrucConsensusThread); -}this.showSequenceLogo = showSequenceLogo; -}, "~B"); -Clazz.defineMethod (c$, "setShowConsensusHistogram", -function (showConsensusHistogram) { -this.showConsensusHistogram = showConsensusHistogram; -}, "~B"); -Clazz.defineMethod (c$, "isShowGroupConservation", -function () { -return this.showGroupConservation; -}); -Clazz.defineMethod (c$, "setShowGroupConservation", -function (showGroupConservation) { -this.showGroupConservation = showGroupConservation; -}, "~B"); -Clazz.defineMethod (c$, "isShowGroupConsensus", -function () { -return this.showGroupConsensus; -}); -Clazz.defineMethod (c$, "setShowGroupConsensus", -function (showGroupConsensus) { -this.showGroupConsensus = showGroupConsensus; -}, "~B"); -Clazz.overrideMethod (c$, "isShowConsensusHistogram", -function () { -return this.showConsensusHistogram; -}); -Clazz.overrideMethod (c$, "getSelectionGroup", -function () { -return this.selectionGroup; -}); -Clazz.overrideMethod (c$, "setSelectionGroup", -function (sg) { -this.selectionGroup = sg; -}, "jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "setHiddenColumns", -function (colsel) { -this.colSel = colsel; -}, "jalview.datamodel.ColumnSelection"); -Clazz.overrideMethod (c$, "getColumnSelection", -function () { -return this.colSel; -}); -Clazz.overrideMethod (c$, "setColumnSelection", -function (colSel) { -this.colSel = colSel; -if (colSel != null) { -this.updateHiddenColumns (); -}}, "jalview.datamodel.ColumnSelection"); -Clazz.overrideMethod (c$, "getHiddenRepSequences", -function () { -return this.hiddenRepSequences; -}); -Clazz.overrideMethod (c$, "setHiddenRepSequences", -function (hiddenRepSequences) { -this.hiddenRepSequences = hiddenRepSequences; -}, "java.util.Map"); -Clazz.overrideMethod (c$, "hasHiddenColumns", -function () { -return this.colSel != null && this.colSel.hasHiddenColumns (); -}); -Clazz.defineMethod (c$, "updateHiddenColumns", -function () { -}); -Clazz.overrideMethod (c$, "hasHiddenRows", -function () { -return this.alignment.getHiddenSequences ().getSize () > 0; -}); -Clazz.defineMethod (c$, "setSequenceSetId", -function (newid) { -if (this.sequenceSetID != null) { -System.err.println ("Warning - overwriting a sequenceSetId for a viewport!"); -}this.sequenceSetID = String.instantialize (newid); -}, "~S"); -Clazz.overrideMethod (c$, "getSequenceSetId", -function () { -if (this.sequenceSetID == null) { -this.sequenceSetID = this.alignment.hashCode () + ""; -}return this.sequenceSetID; -}); -Clazz.overrideMethod (c$, "getViewId", -function () { -if (this.viewId == null) { -this.viewId = this.getSequenceSetId () + "." + this.hashCode () + ""; -}return this.viewId; -}); -Clazz.defineMethod (c$, "setIgnoreGapsConsensus", -function (b, ap) { -this.ignoreGapsInConsensusCalculation = b; -if (ap != null) { -this.updateConsensus (ap); -if (this.globalColourScheme != null) { -this.globalColourScheme.setThreshold (this.globalColourScheme.getThreshold (), this.ignoreGapsInConsensusCalculation); -}}}, "~B,jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "isSelectionGroupChanged", -function (b) { -var hc = (this.selectionGroup == null || this.selectionGroup.getSize () == 0) ? -1 : this.selectionGroup.hashCode (); -if (hc != -1 && hc != this.sgrouphash) { -if (b) { -this.sgrouphash = hc; -}return true; -}return false; -}, "~B"); -Clazz.defineMethod (c$, "isColSelChanged", -function (b) { -var hc = (this.colSel == null || this.colSel.size () == 0) ? -1 : this.colSel.hashCode (); -if (hc != -1 && hc != this.colselhash) { -if (b) { -this.colselhash = hc; -}return true; -}return false; -}, "~B"); -Clazz.overrideMethod (c$, "isIgnoreGapsConsensus", -function () { -return this.ignoreGapsInConsensusCalculation; -}); -Clazz.defineMethod (c$, "addPropertyChangeListener", -function (listener) { -this.changeSupport.addPropertyChangeListener (listener); -}, "java.beans.PropertyChangeListener"); -Clazz.defineMethod (c$, "removePropertyChangeListener", -function (listener) { -this.changeSupport.removePropertyChangeListener (listener); -}, "java.beans.PropertyChangeListener"); -Clazz.defineMethod (c$, "firePropertyChange", -function (prop, oldvalue, newvalue) { -this.changeSupport.firePropertyChange (prop, oldvalue, newvalue); -}, "~S,~O,~O"); -Clazz.defineMethod (c$, "hideSelectedColumns", -function () { -if (this.colSel.size () < 1) { -return; -}this.colSel.hideSelectedColumns (); -this.setSelectionGroup (null); -}); -Clazz.defineMethod (c$, "hideColumns", -function (start, end) { -if (start == end) { -this.colSel.hideColumns (start); -} else { -this.colSel.hideColumns (start, end); -}}, "~N,~N"); -Clazz.defineMethod (c$, "showColumn", -function (col) { -this.colSel.revealHiddenColumns (col); -}, "~N"); -Clazz.defineMethod (c$, "showAllHiddenColumns", -function () { -this.colSel.revealAllHiddenColumns (); -}); -Clazz.defineMethod (c$, "showAllHiddenSeqs", -function () { -if (this.alignment.getHiddenSequences ().getSize () > 0) { -if (this.selectionGroup == null) { -this.selectionGroup = new jalview.datamodel.SequenceGroup (); -this.selectionGroup.setEndRes (this.alignment.getWidth () - 1); -}var tmp = this.alignment.getHiddenSequences ().showAll (this.hiddenRepSequences); -for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -this.selectionGroup.addSequence (seq, false); -this.setSequenceAnnotationsVisible (seq, true); -} -this.hiddenRepSequences = null; -this.firePropertyChange ("alignment", null, this.alignment.getSequences ()); -this.sendSelection (); -}}); -Clazz.defineMethod (c$, "showSequence", -function (index) { -var tmp = this.alignment.getHiddenSequences ().showSequence (index, this.hiddenRepSequences); -if (tmp.size () > 0) { -if (this.selectionGroup == null) { -this.selectionGroup = new jalview.datamodel.SequenceGroup (); -this.selectionGroup.setEndRes (this.alignment.getWidth () - 1); -}for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { -this.selectionGroup.addSequence (seq, false); -this.setSequenceAnnotationsVisible (seq, true); -} -this.firePropertyChange ("alignment", null, this.alignment.getSequences ()); -this.sendSelection (); -}}, "~N"); -Clazz.defineMethod (c$, "hideAllSelectedSeqs", -function () { -if (this.selectionGroup == null || this.selectionGroup.getSize () < 1) { -return; -}var seqs = this.selectionGroup.getSequencesInOrder (this.alignment); -this.hideSequence (seqs); -this.setSelectionGroup (null); -}); -Clazz.defineMethod (c$, "hideSequence", -function (seq) { -if (seq != null) { -for (var i = 0; i < seq.length; i++) { -this.alignment.getHiddenSequences ().hideSequence (seq[i]); -this.setSequenceAnnotationsVisible (seq[i], false); -} -this.firePropertyChange ("alignment", null, this.alignment.getSequences ()); -}}, "~A"); -Clazz.defineMethod (c$, "setSequenceAnnotationsVisible", -function (sequenceI, visible) { -for (var ann, $ann = 0, $$ann = this.alignment.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { -if (ann.sequenceRef === sequenceI) { -ann.visible = visible; -}} -}, "jalview.datamodel.SequenceI,~B"); -Clazz.defineMethod (c$, "hideRepSequences", -function (repSequence, sg) { -var sSize = sg.getSize (); -if (sSize < 2) { -return; -}if (this.hiddenRepSequences == null) { -this.hiddenRepSequences = new java.util.Hashtable (); -}this.hiddenRepSequences.put (repSequence, sg); -var seqs = new Array (sSize - 1); -var index = 0; -for (var i = 0; i < sSize; i++) { -if (sg.getSequenceAt (i) !== repSequence) { -if (index == sSize - 1) { -return; -}seqs[index++] = sg.getSequenceAt (i); -}} -sg.setSeqrep (repSequence); -sg.setHidereps (true); -this.hideSequence (seqs); -}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); -Clazz.defineMethod (c$, "isHiddenRepSequence", -function (seq) { -return this.alignment.getSeqrep () === seq || (this.hiddenRepSequences != null && this.hiddenRepSequences.containsKey (seq)); -}, "jalview.datamodel.SequenceI"); -Clazz.defineMethod (c$, "getRepresentedSequences", -function (seq) { -return (this.hiddenRepSequences == null ? null : this.hiddenRepSequences.get (seq)); -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "adjustForHiddenSeqs", -function (alignmentIndex) { -return this.alignment.getHiddenSequences ().adjustForHiddenSeqs (alignmentIndex); -}, "~N"); -Clazz.overrideMethod (c$, "invertColumnSelection", -function () { -this.colSel.invertColumnSelection (0, this.alignment.getWidth ()); -}); -Clazz.overrideMethod (c$, "getSelectionAsNewSequence", -function () { -var sequences; -if (this.selectionGroup == null || this.selectionGroup.getSize () == 0) { -sequences = this.alignment.getSequencesArray (); -var annots = this.alignment.getAlignmentAnnotation (); -for (var i = 0; i < sequences.length; i++) { -sequences[i] = new jalview.datamodel.Sequence (sequences[i], annots); -} -} else { -sequences = this.selectionGroup.getSelectionAsNewSequences (this.alignment); -}return sequences; -}); -Clazz.overrideMethod (c$, "getSequenceSelection", -function () { -var sequences = null; -if (this.selectionGroup != null) { -sequences = this.selectionGroup.getSequencesInOrder (this.alignment); -}if (sequences == null) { -sequences = this.alignment.getSequencesArray (); -}return sequences; -}); -Clazz.overrideMethod (c$, "getViewAsCigars", -function (selectedRegionOnly) { -return new jalview.datamodel.CigarArray (this.alignment, this.colSel, (selectedRegionOnly ? this.selectionGroup : null)); -}, "~B"); -Clazz.defineMethod (c$, "getAlignmentView", -function (selectedOnly) { -return this.getAlignmentView (selectedOnly, false); -}, "~B"); -Clazz.defineMethod (c$, "getAlignmentView", -function (selectedOnly, markGroups) { -return new jalview.datamodel.AlignmentView (this.alignment, this.colSel, this.selectionGroup, this.colSel != null && this.colSel.hasHiddenColumns (), selectedOnly, markGroups); -}, "~B,~B"); -Clazz.overrideMethod (c$, "getViewAsString", -function (selectedRegionOnly) { -var selection = null; -var seqs = null; -var i; -var iSize; -var start = 0; -var end = 0; -if (selectedRegionOnly && this.selectionGroup != null) { -iSize = this.selectionGroup.getSize (); -seqs = this.selectionGroup.getSequencesInOrder (this.alignment); -start = this.selectionGroup.getStartRes (); -end = this.selectionGroup.getEndRes () + 1; -} else { -iSize = this.alignment.getHeight (); -seqs = this.alignment.getSequencesArray (); -end = this.alignment.getWidth (); -}selection = new Array (iSize); -if (this.colSel != null && this.colSel.hasHiddenColumns ()) { -selection = this.colSel.getVisibleSequenceStrings (start, end, seqs); -} else { -for (i = 0; i < iSize; i++) { -selection[i] = seqs[i].getSequenceAsString (start, end); -} -}return selection; -}, "~B"); -Clazz.overrideMethod (c$, "getVisibleRegionBoundaries", -function (min, max) { -var regions = new java.util.ArrayList (); -var start = min; -var end = max; -do { -if (this.colSel != null && this.colSel.hasHiddenColumns ()) { -if (start == 0) { -start = this.colSel.adjustForHiddenColumns (start); -}end = this.colSel.getHiddenBoundaryRight (start); -if (start == end) { -end = max; -}if (end > max) { -end = max; -}}regions.add ( Clazz.newIntArray (-1, [start, end])); -if (this.colSel != null && this.colSel.hasHiddenColumns ()) { -start = this.colSel.adjustForHiddenColumns (end); -start = this.colSel.getHiddenBoundaryLeft (start) + 1; -}} while (end < max); -var startEnd = Clazz.newIntArray (regions.size (), 2, 0); -return regions; -}, "~N,~N"); -Clazz.overrideMethod (c$, "getVisibleAlignmentAnnotation", -function (selectedOnly) { -var ala = new java.util.ArrayList (); -var aa; -if ((aa = this.alignment.getAlignmentAnnotation ()) != null) { -for (var annot, $annot = 0, $$annot = aa; $annot < $$annot.length && ((annot = $$annot[$annot]) || true); $annot++) { -var clone = new jalview.datamodel.AlignmentAnnotation (annot); -if (selectedOnly && this.selectionGroup != null) { -this.colSel.makeVisibleAnnotation (this.selectionGroup.getStartRes (), this.selectionGroup.getEndRes (), clone); -} else { -this.colSel.makeVisibleAnnotation (clone); -}ala.add (clone); -} -}return ala; -}, "~B"); -Clazz.overrideMethod (c$, "isPadGaps", -function () { -return this.padGaps; -}); -Clazz.overrideMethod (c$, "setPadGaps", -function (padGaps) { -this.padGaps = padGaps; -}, "~B"); -Clazz.overrideMethod (c$, "alignmentChanged", -function (ap) { -if (this.isPadGaps ()) { -this.alignment.padGaps (); -}if (this.autoCalculateConsensus) { -this.updateConsensus (ap); -}if (this.hconsensus != null && this.autoCalculateConsensus) { -this.updateConservation (ap); -}if (this.autoCalculateStrucConsensus) { -this.updateStrucConsensus (ap); -}var alWidth = this.alignment.getWidth (); -var groups = this.alignment.getGroups (); -if (groups != null) { -for (var sg, $sg = groups.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.getEndRes () > alWidth) { -sg.setEndRes (alWidth - 1); -}} -}if (this.selectionGroup != null && this.selectionGroup.getEndRes () > alWidth) { -this.selectionGroup.setEndRes (alWidth - 1); -}this.resetAllColourSchemes (); -this.calculator.restartWorkers (); -}, "jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "resetAllColourSchemes", -function () { -var cs = this.globalColourScheme; -if (cs != null) { -cs.alignmentChanged (this.alignment, this.hiddenRepSequences); -cs.setConsensus (this.hconsensus); -if (cs.conservationApplied ()) { -cs.setConservation (jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.alignment.getWidth (), false, this.getConsPercGaps (), false)); -}}for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.cs != null) { -sg.cs.alignmentChanged (sg, this.hiddenRepSequences); -}sg.recalcConservation (); -} -}); -Clazz.defineMethod (c$, "initAutoAnnotation", -function () { -if (this.hconsensus == null && !this.$isDataset) { -if (!this.alignment.isNucleotide ()) { -this.initConservation (); -this.initQuality (); -} else { -this.initRNAStructure (); -}this.consensus = new jalview.datamodel.AlignmentAnnotation ("Consensus", "PID", new Array (1), 0, 100, 1); -this.initConsensus (this.consensus); -this.initComplementConsensus (); -}}); -Clazz.defineMethod (c$, "initComplementConsensus", -function () { -if (!this.alignment.isNucleotide ()) { -var codonMappings = this.alignment.getCodonFrames (); -if (codonMappings != null && !codonMappings.isEmpty ()) { -this.complementConsensus = new jalview.datamodel.AlignmentAnnotation ("cDNA Consensus", "PID for cDNA", new Array (1), 0, 100, 1); -this.initConsensus (this.complementConsensus); -}}}); -Clazz.defineMethod (c$, "initConsensus", -($fz = function (aa) { -aa.hasText = true; -aa.autoCalculated = true; -if (this.showConsensus) { -this.alignment.addAnnotation (aa); -}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation"); -Clazz.defineMethod (c$, "initConservation", -($fz = function () { -if (this.showConservation) { -if (this.conservation == null) { -this.conservation = new jalview.datamodel.AlignmentAnnotation ("Conservation", "Conservation of total alignment less than " + this.getConsPercGaps () + "% gaps", new Array (1), 0, 11, 1); -this.conservation.hasText = true; -this.conservation.autoCalculated = true; -this.alignment.addAnnotation (this.conservation); -}}}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "initQuality", -($fz = function () { -if (this.showQuality) { -if (this.quality == null) { -this.quality = new jalview.datamodel.AlignmentAnnotation ("Quality", "Alignment Quality based on Blosum62 scores", new Array (1), 0, 11, 1); -this.quality.hasText = true; -this.quality.autoCalculated = true; -this.alignment.addAnnotation (this.quality); -}}}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "initRNAStructure", -($fz = function () { -if (this.alignment.hasRNAStructure () && this.strucConsensus == null) { -this.strucConsensus = new jalview.datamodel.AlignmentAnnotation ("StrucConsensus", "PID", new Array (1), 0, 100, 1); -this.strucConsensus.hasText = true; -this.strucConsensus.autoCalculated = true; -if (this.showConsensus) { -this.alignment.addAnnotation (this.strucConsensus); -}}}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "calcPanelHeight", -function () { -var anns = this.getAlignment ().getAlignmentAnnotation (); -var height = 0; -var charHeight = this.getCharHeight (); -if (anns != null) { -var graphgrp = new java.util.BitSet (); -for (var aa, $aa = 0, $$aa = anns; $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { -if (aa == null) { -System.err.println ("Null annotation row: ignoring."); -continue; -}if (!aa.visible) { -continue; -}if (aa.graphGroup > -1) { -if (graphgrp.get (aa.graphGroup)) { -continue; -} else { -graphgrp.set (aa.graphGroup); -}}aa.height = 0; -if (aa.hasText) { -aa.height += charHeight; -}if (aa.hasIcons) { -aa.height += 16; -}if (aa.graph > 0) { -aa.height += aa.graphHeight; -}if (aa.height == 0) { -aa.height = 20; -}height += aa.height; -} -}if (height == 0) { -height = 20; -}return height; -}); -Clazz.overrideMethod (c$, "updateGroupAnnotationSettings", -function (applyGlobalSettings, preserveNewGroupSettings) { -var updateCalcs = false; -var conv = this.isShowGroupConservation (); -var cons = this.isShowGroupConsensus (); -var showprf = this.isShowSequenceLogo (); -var showConsHist = this.isShowConsensusHistogram (); -var normLogo = this.isNormaliseSequenceLogo (); -var sortg = true; -var aan = this.alignment.getAlignmentAnnotation (); -var oldrfs = new java.util.ArrayList (); -if (aan != null) { -for (var an = 0; an < aan.length; an++) { -if (aan[an].autoCalculated && aan[an].groupRef != null) { -oldrfs.add (aan[an].groupRef); -this.alignment.deleteAnnotation (aan[an], false); -}} -}if (this.alignment.getGroups () != null) { -for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -updateCalcs = false; -if (applyGlobalSettings || (!preserveNewGroupSettings && !oldrfs.contains (sg))) { -sg.setshowSequenceLogo (showprf); -sg.setShowConsensusHistogram (showConsHist); -sg.setNormaliseSequenceLogo (normLogo); -}if (conv) { -updateCalcs = true; -this.alignment.addAnnotation (sg.getConservationRow (), 0); -}if (cons) { -updateCalcs = true; -this.alignment.addAnnotation (sg.getConsensus (), 0); -}if (updateCalcs) { -sg.recalcConservation (); -}} -}oldrfs.clear (); -}, "~B,~B"); -Clazz.defineMethod (c$, "isDisplayReferenceSeq", -function () { -return this.alignment.hasSeqrep () && this.viewStyle.isDisplayReferenceSeq (); -}); -Clazz.defineMethod (c$, "setDisplayReferenceSeq", -function (displayReferenceSeq) { -this.viewStyle.setDisplayReferenceSeq (displayReferenceSeq); -}, "~B"); -Clazz.defineMethod (c$, "isColourByReferenceSeq", -function () { -return this.alignment.hasSeqrep () && this.viewStyle.isColourByReferenceSeq (); -}); -Clazz.overrideMethod (c$, "getSequenceColour", -function (seq) { -var sqc = this.sequenceColours.get (seq); -return (sqc == null ? java.awt.Color.white : sqc); -}, "jalview.datamodel.SequenceI"); -Clazz.overrideMethod (c$, "setSequenceColour", -function (seq, col) { -if (col == null) { -this.sequenceColours.remove (seq); -} else { -this.sequenceColours.put (seq, col); -}}, "jalview.datamodel.SequenceI,java.awt.Color"); -Clazz.overrideMethod (c$, "updateSequenceIdColours", -function () { -for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if (sg.idColour != null) { -for (var s, $s = sg.getSequences (this.getHiddenRepSequences ()).iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { -this.sequenceColours.put (s, sg.idColour); -} -}} -}); -Clazz.overrideMethod (c$, "clearSequenceColours", -function () { -this.sequenceColours.clear (); -}); -Clazz.defineMethod (c$, "getCodingComplement", -function () { -return this.codingComplement; -}); -Clazz.defineMethod (c$, "setCodingComplement", -function (av) { -if (this === av) { -System.err.println ("Ignoring recursive setCodingComplement request"); -} else { -this.codingComplement = av; -if (av.getCodingComplement () !== this) { -av.setCodingComplement (this); -}}}, "jalview.api.AlignViewportI"); -Clazz.overrideMethod (c$, "isNucleotide", -function () { -return this.getAlignment () == null ? false : this.getAlignment ().isNucleotide (); -}); -Clazz.overrideMethod (c$, "getFeaturesDisplayed", -function () { -return this.featuresDisplayed; -}); -Clazz.overrideMethod (c$, "setFeaturesDisplayed", -function (featuresDisplayedI) { -this.featuresDisplayed = featuresDisplayedI; -}, "jalview.api.FeaturesDisplayedI"); -Clazz.overrideMethod (c$, "areFeaturesDisplayed", -function () { -return this.featuresDisplayed != null && this.featuresDisplayed.getRegisterdFeaturesCount () > 0; -}); -Clazz.defineMethod (c$, "setShowSequenceFeatures", -function (b) { -this.viewStyle.setShowSequenceFeatures (b); -}, "~B"); -Clazz.defineMethod (c$, "isShowSequenceFeatures", -function () { -return this.viewStyle.isShowSequenceFeatures (); -}); -Clazz.defineMethod (c$, "setShowSequenceFeaturesHeight", -function (selected) { -this.viewStyle.setShowSequenceFeaturesHeight (selected); -}, "~B"); -Clazz.defineMethod (c$, "isShowSequenceFeaturesHeight", -function () { -return this.viewStyle.isShowSequenceFeaturesHeight (); -}); -Clazz.defineMethod (c$, "setShowAnnotation", -function (b) { -this.viewStyle.setShowAnnotation (b); -}, "~B"); -Clazz.defineMethod (c$, "isShowAnnotation", -function () { -return this.viewStyle.isShowAnnotation (); -}); -Clazz.defineMethod (c$, "isRightAlignIds", -function () { -return this.viewStyle.isRightAlignIds (); -}); -Clazz.defineMethod (c$, "setRightAlignIds", -function (rightAlignIds) { -this.viewStyle.setRightAlignIds (rightAlignIds); -}, "~B"); -Clazz.defineMethod (c$, "getConservationSelected", -function () { -return this.viewStyle.getConservationSelected (); -}); -Clazz.defineMethod (c$, "setShowBoxes", -function (state) { -this.viewStyle.setShowBoxes (state); -}, "~B"); -Clazz.defineMethod (c$, "getTextColour", -function () { -return this.viewStyle.getTextColour (); -}); -Clazz.defineMethod (c$, "getTextColour2", -function () { -return this.viewStyle.getTextColour2 (); -}); -Clazz.defineMethod (c$, "getThresholdTextColour", -function () { -return this.viewStyle.getThresholdTextColour (); -}); -Clazz.defineMethod (c$, "isConservationColourSelected", -function () { -return this.viewStyle.isConservationColourSelected (); -}); -Clazz.defineMethod (c$, "isRenderGaps", -function () { -return this.viewStyle.isRenderGaps (); -}); -Clazz.defineMethod (c$, "isShowColourText", -function () { -return this.viewStyle.isShowColourText (); -}); -Clazz.defineMethod (c$, "setConservationColourSelected", -function (conservationColourSelected) { -this.viewStyle.setConservationColourSelected (conservationColourSelected); -}, "~B"); -Clazz.defineMethod (c$, "setShowColourText", -function (showColourText) { -this.viewStyle.setShowColourText (showColourText); -}, "~B"); -Clazz.defineMethod (c$, "setTextColour", -function (textColour) { -this.viewStyle.setTextColour (textColour); -}, "java.awt.Color"); -Clazz.defineMethod (c$, "setThresholdTextColour", -function (thresholdTextColour) { -this.viewStyle.setThresholdTextColour (thresholdTextColour); -}, "~N"); -Clazz.defineMethod (c$, "setTextColour2", -function (textColour2) { -this.viewStyle.setTextColour2 (textColour2); -}, "java.awt.Color"); -Clazz.overrideMethod (c$, "getViewStyle", -function () { -return new jalview.viewmodel.styles.ViewStyle (this.viewStyle); -}); -Clazz.overrideMethod (c$, "setViewStyle", -function (settingsForView) { -this.viewStyle = new jalview.viewmodel.styles.ViewStyle (settingsForView); -}, "jalview.api.ViewStyleI"); -Clazz.defineMethod (c$, "sameStyle", -function (them) { -return this.viewStyle.sameStyle (them); -}, "jalview.api.ViewStyleI"); -Clazz.defineMethod (c$, "getIdWidth", -function () { -return this.viewStyle.getIdWidth (); -}); -Clazz.defineMethod (c$, "setIdWidth", -function (i) { -this.viewStyle.setIdWidth (i); -}, "~N"); -Clazz.defineMethod (c$, "isCentreColumnLabels", -function () { -return this.viewStyle.isCentreColumnLabels (); -}); -Clazz.defineMethod (c$, "setCentreColumnLabels", -function (centreColumnLabels) { -this.viewStyle.setCentreColumnLabels (centreColumnLabels); -}, "~B"); -Clazz.defineMethod (c$, "setShowDBRefs", -function (showdbrefs) { -this.viewStyle.setShowDBRefs (showdbrefs); -}, "~B"); -Clazz.defineMethod (c$, "isShowDBRefs", -function () { -return this.viewStyle.isShowDBRefs (); -}); -Clazz.defineMethod (c$, "isShowNPFeats", -function () { -return this.viewStyle.isShowNPFeats (); -}); -Clazz.defineMethod (c$, "setShowNPFeats", -function (shownpfeats) { -this.viewStyle.setShowNPFeats (shownpfeats); -}, "~B"); -Clazz.defineMethod (c$, "addToHistoryList", -function (command) { -if (this.historyList != null) { -this.historyList.push (command); -this.broadcastCommand (command, false); -}}, "jalview.commands.CommandI"); -Clazz.defineMethod (c$, "broadcastCommand", -function (command, undo) { -this.getStructureSelectionManager ().commandPerformed (command, undo, this.getVamsasSource ()); -}, "jalview.commands.CommandI,~B"); -Clazz.defineMethod (c$, "addToRedoList", -function (command) { -if (this.redoList != null) { -this.redoList.push (command); -}this.broadcastCommand (command, true); -}, "jalview.commands.CommandI"); -Clazz.defineMethod (c$, "clearRedoList", -function () { -if (this.redoList != null) { -this.redoList.clear (); -}}); -Clazz.defineMethod (c$, "setHistoryList", -function (list) { -this.historyList = list; -}, "java.util.Deque"); -Clazz.defineMethod (c$, "getHistoryList", -function () { -return this.historyList; -}); -Clazz.defineMethod (c$, "setRedoList", -function (list) { -this.redoList = list; -}, "java.util.Deque"); -Clazz.defineMethod (c$, "getRedoList", -function () { -return this.redoList; -}); -Clazz.overrideMethod (c$, "getVamsasSource", -function () { -return this; -}); -Clazz.defineMethod (c$, "getSortAnnotationsBy", -function () { -return this.sortAnnotationsBy; -}); -Clazz.defineMethod (c$, "setSortAnnotationsBy", -function (sortAnnotationsBy) { -this.sortAnnotationsBy = sortAnnotationsBy; -}, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); -Clazz.defineMethod (c$, "isShowAutocalculatedAbove", -function () { -return this.showAutocalculatedAbove; -}); -Clazz.defineMethod (c$, "setShowAutocalculatedAbove", -function (showAutocalculatedAbove) { -this.showAutocalculatedAbove = showAutocalculatedAbove; -}, "~B"); -Clazz.defineMethod (c$, "isScaleProteinAsCdna", -function () { -return this.viewStyle.isScaleProteinAsCdna (); -}); -Clazz.defineMethod (c$, "setScaleProteinAsCdna", -function (b) { -this.viewStyle.setScaleProteinAsCdna (b); -}, "~B"); -Clazz.defineMethod (c$, "isFollowHighlight", -function () { -return this.followHighlight; -}); -Clazz.overrideMethod (c$, "setFollowHighlight", -function (b) { -this.followHighlight = b; -}, "~B"); -Clazz.defineMethod (c$, "getStartRes", -function () { -return this.startRes; -}); -Clazz.overrideMethod (c$, "getEndRes", -function () { -return this.endRes; -}); -Clazz.defineMethod (c$, "getStartSeq", -function () { -return this.startSeq; -}); -Clazz.defineMethod (c$, "setStartRes", -function (res) { -this.startRes = res; -}, "~N"); -Clazz.defineMethod (c$, "setStartSeq", -function (seq) { -this.startSeq = seq; -}, "~N"); -Clazz.defineMethod (c$, "setEndRes", -function (res) { -if (res > this.alignment.getWidth () - 1) { -res = this.alignment.getWidth () - 1; -}if (res < 0) { -res = 0; -}this.endRes = res; -}, "~N"); -Clazz.defineMethod (c$, "setEndSeq", -function (seq) { -if (seq > this.alignment.getHeight ()) { -seq = this.alignment.getHeight (); -}if (seq < 0) { -seq = 0; -}this.endSeq = seq; -}, "~N"); -Clazz.defineMethod (c$, "getEndSeq", -function () { -return this.endSeq; -}); -Clazz.defineMethod (c$, "findComplementScrollTarget", -function (sr) { -var complement = this.getCodingComplement (); -if (complement == null || !complement.isFollowHighlight ()) { -return 0; -}var iAmProtein = !this.getAlignment ().isNucleotide (); -var proteinAlignment = iAmProtein ? this.getAlignment () : complement.getAlignment (); -if (proteinAlignment == null) { -return 0; -}var mappings = proteinAlignment.getCodonFrames (); -var seqOffset = 0; -var sequence = null; -var middleColumn = this.getStartRes () + Clazz.doubleToInt ((this.getEndRes () - this.getStartRes ()) / 2); -var hiddenSequences = this.getAlignment ().getHiddenSequences (); -for (var seqNo = this.getStartSeq (); seqNo < this.getEndSeq (); seqNo++, seqOffset++) { -sequence = this.getAlignment ().getSequenceAt (seqNo); -if (hiddenSequences != null && hiddenSequences.isHidden (sequence)) { -continue; -}if (jalview.util.Comparison.isGap (sequence.getCharAt (middleColumn))) { -continue; -}var seqMappings = jalview.util.MappingUtils.findMappingsForSequence (sequence, mappings); -if (!seqMappings.isEmpty ()) { -break; -}} -if (sequence == null) { -return 0; -}jalview.util.MappingUtils.addSearchResults (sr, sequence, sequence.findPosition (middleColumn), mappings); -return seqOffset; -}, "jalview.datamodel.SearchResults"); -}); +Clazz.declarePackage ("jalview.viewmodel"); +Clazz.load (["jalview.api.AlignViewportI", "jalview.structure.CommandListener", "$.VamsasSource", "jalview.datamodel.ColumnSelection", "jalview.viewmodel.styles.ViewStyle", "jalview.workers.AlignCalcManager", "java.beans.PropertyChangeSupport", "java.util.ArrayDeque", "$.HashMap"], "jalview.viewmodel.AlignmentViewport", ["jalview.analysis.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.AlignmentView", "$.CigarArray", "$.Sequence", "$.SequenceGroup", "jalview.schemes.Blosum62ColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "jalview.util.Comparison", "$.MappingUtils", "jalview.workers.ComplementConsensusThread", "$.ConsensusThread", "$.ConservationThread", "$.StrucConsensusThread", "java.awt.Color", "java.util.ArrayList", "$.BitSet", "$.Hashtable"], function () { +c$ = Clazz.decorateAsClass (function () { +this.viewStyle = null; +this.codingComplement = null; +this.featuresDisplayed = null; +this.historyList = null; +this.redoList = null; +this.alignment = null; +this.sequenceSetID = null; +this.$isDataset = false; +this.hiddenRepSequences = null; +this.colSel = null; +this.autoCalculateConsensus = true; +this.autoCalculateStrucConsensus = true; +this.ignoreGapsInConsensusCalculation = false; +this.globalColourScheme = null; +this.consensus = null; +this.complementConsensus = null; +this.strucConsensus = null; +this.conservation = null; +this.quality = null; +this.groupConsensus = null; +this.groupConservation = null; +this.hconsensus = null; +this.hcomplementConsensus = null; +this.hStrucConsensus = null; +this.hconservation = null; +this.ConsPercGaps = 25; +this.calculator = null; +this.showGroupConservation = false; +this.showGroupConsensus = false; +this.showSequenceLogo = false; +this.normaliseSequenceLogo = false; +this.showConsensusHistogram = true; +this.padGaps = false; +this.sortByTree = false; +this.selectionGroup = null; +this.viewId = null; +this.sgrouphash = -1; +this.colselhash = -1; +this.changeSupport = null; +this.showConservation = true; +this.showQuality = true; +this.showConsensus = true; +this.sequenceColours = null; +this.sortAnnotationsBy = null; +this.showAutocalculatedAbove = false; +this.followHighlight = true; +this.startRes = 0; +this.endRes = 0; +this.startSeq = 0; +this.endSeq = 0; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel, "AlignmentViewport", null, [jalview.api.AlignViewportI, jalview.structure.CommandListener, jalview.structure.VamsasSource]); +Clazz.prepareFields (c$, function () { +this.viewStyle = new jalview.viewmodel.styles.ViewStyle (); +this.historyList = new java.util.ArrayDeque (); +this.redoList = new java.util.ArrayDeque (); +this.colSel = new jalview.datamodel.ColumnSelection (); +this.calculator = new jalview.workers.AlignCalcManager (); +this.changeSupport = new java.beans.PropertyChangeSupport (this); +this.sequenceColours = new java.util.HashMap (); +}); +Clazz.defineMethod (c$, "setFontName", +function (name) { +this.viewStyle.setFontName (name); +}, "~S"); +Clazz.defineMethod (c$, "setFontStyle", +function (style) { +this.viewStyle.setFontStyle (style); +}, "~N"); +Clazz.defineMethod (c$, "setFontSize", +function (size) { +this.viewStyle.setFontSize (size); +}, "~N"); +Clazz.defineMethod (c$, "getFontStyle", +function () { +return this.viewStyle.getFontStyle (); +}); +Clazz.defineMethod (c$, "getFontName", +function () { +return this.viewStyle.getFontName (); +}); +Clazz.defineMethod (c$, "getFontSize", +function () { +return this.viewStyle.getFontSize (); +}); +Clazz.defineMethod (c$, "setUpperCasebold", +function (upperCasebold) { +this.viewStyle.setUpperCasebold (upperCasebold); +}, "~B"); +Clazz.defineMethod (c$, "isUpperCasebold", +function () { +return this.viewStyle.isUpperCasebold (); +}); +Clazz.defineMethod (c$, "isSeqNameItalics", +function () { +return this.viewStyle.isSeqNameItalics (); +}); +Clazz.defineMethod (c$, "setColourByReferenceSeq", +function (colourByReferenceSeq) { +this.viewStyle.setColourByReferenceSeq (colourByReferenceSeq); +}, "~B"); +Clazz.defineMethod (c$, "setColourAppliesToAllGroups", +function (b) { +this.viewStyle.setColourAppliesToAllGroups (b); +}, "~B"); +Clazz.defineMethod (c$, "getColourAppliesToAllGroups", +function () { +return this.viewStyle.getColourAppliesToAllGroups (); +}); +Clazz.defineMethod (c$, "getAbovePIDThreshold", +function () { +return this.viewStyle.getAbovePIDThreshold (); +}); +Clazz.defineMethod (c$, "setIncrement", +function (inc) { +this.viewStyle.setIncrement (inc); +}, "~N"); +Clazz.defineMethod (c$, "getIncrement", +function () { +return this.viewStyle.getIncrement (); +}); +Clazz.defineMethod (c$, "setConservationSelected", +function (b) { +this.viewStyle.setConservationSelected (b); +}, "~B"); +Clazz.defineMethod (c$, "setShowHiddenMarkers", +function (show) { +this.viewStyle.setShowHiddenMarkers (show); +}, "~B"); +Clazz.defineMethod (c$, "getShowHiddenMarkers", +function () { +return this.viewStyle.getShowHiddenMarkers (); +}); +Clazz.defineMethod (c$, "setScaleRightWrapped", +function (b) { +this.viewStyle.setScaleRightWrapped (b); +}, "~B"); +Clazz.defineMethod (c$, "setScaleLeftWrapped", +function (b) { +this.viewStyle.setScaleLeftWrapped (b); +}, "~B"); +Clazz.defineMethod (c$, "setScaleAboveWrapped", +function (b) { +this.viewStyle.setScaleAboveWrapped (b); +}, "~B"); +Clazz.defineMethod (c$, "getScaleLeftWrapped", +function () { +return this.viewStyle.getScaleLeftWrapped (); +}); +Clazz.defineMethod (c$, "getScaleAboveWrapped", +function () { +return this.viewStyle.getScaleAboveWrapped (); +}); +Clazz.defineMethod (c$, "getScaleRightWrapped", +function () { +return this.viewStyle.getScaleRightWrapped (); +}); +Clazz.defineMethod (c$, "setAbovePIDThreshold", +function (b) { +this.viewStyle.setAbovePIDThreshold (b); +}, "~B"); +Clazz.defineMethod (c$, "setThreshold", +function (thresh) { +this.viewStyle.setThreshold (thresh); +}, "~N"); +Clazz.defineMethod (c$, "getThreshold", +function () { +return this.viewStyle.getThreshold (); +}); +Clazz.defineMethod (c$, "getShowJVSuffix", +function () { +return this.viewStyle.getShowJVSuffix (); +}); +Clazz.defineMethod (c$, "setShowJVSuffix", +function (b) { +this.viewStyle.setShowJVSuffix (b); +}, "~B"); +Clazz.defineMethod (c$, "setWrapAlignment", +function (state) { +this.viewStyle.setWrapAlignment (state); +}, "~B"); +Clazz.defineMethod (c$, "setShowText", +function (state) { +this.viewStyle.setShowText (state); +}, "~B"); +Clazz.defineMethod (c$, "setRenderGaps", +function (state) { +this.viewStyle.setRenderGaps (state); +}, "~B"); +Clazz.defineMethod (c$, "getColourText", +function () { +return this.viewStyle.getColourText (); +}); +Clazz.defineMethod (c$, "setColourText", +function (state) { +this.viewStyle.setColourText (state); +}, "~B"); +Clazz.defineMethod (c$, "getWrapAlignment", +function () { +return this.viewStyle.getWrapAlignment (); +}); +Clazz.defineMethod (c$, "getShowText", +function () { +return this.viewStyle.getShowText (); +}); +Clazz.defineMethod (c$, "getWrappedWidth", +function () { +return this.viewStyle.getWrappedWidth (); +}); +Clazz.defineMethod (c$, "setWrappedWidth", +function (w) { +this.viewStyle.setWrappedWidth (w); +}, "~N"); +Clazz.defineMethod (c$, "getCharHeight", +function () { +return this.viewStyle.getCharHeight (); +}); +Clazz.defineMethod (c$, "setCharHeight", +function (h) { +this.viewStyle.setCharHeight (h); +}, "~N"); +Clazz.defineMethod (c$, "getCharWidth", +function () { +return this.viewStyle.getCharWidth (); +}); +Clazz.defineMethod (c$, "setCharWidth", +function (w) { +this.viewStyle.setCharWidth (w); +}, "~N"); +Clazz.defineMethod (c$, "getShowBoxes", +function () { +return this.viewStyle.getShowBoxes (); +}); +Clazz.defineMethod (c$, "getShowUnconserved", +function () { +return this.viewStyle.getShowUnconserved (); +}); +Clazz.defineMethod (c$, "setShowUnconserved", +function (showunconserved) { +this.viewStyle.setShowUnconserved (showunconserved); +}, "~B"); +Clazz.defineMethod (c$, "setSeqNameItalics", +function (default1) { +this.viewStyle.setSeqNameItalics (default1); +}, "~B"); +Clazz.defineMethod (c$, "getAlignment", +function () { +return this.alignment; +}); +Clazz.overrideMethod (c$, "getGapCharacter", +function () { +return this.alignment.getGapCharacter (); +}); +Clazz.defineMethod (c$, "setDataset", +function (b) { +this.$isDataset = b; +}, "~B"); +Clazz.defineMethod (c$, "isDataset", +function () { +return this.$isDataset; +}); +Clazz.overrideMethod (c$, "setGlobalColourScheme", +function (cs) { +this.globalColourScheme = cs; +var recalc = false; +if (cs != null) { +cs.setConservationApplied (recalc = this.getConservationSelected ()); +if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) { +recalc = true; +cs.setThreshold (this.viewStyle.getThreshold (), this.ignoreGapsInConsensusCalculation); +} else { +cs.setThreshold (0, this.ignoreGapsInConsensusCalculation); +}if (recalc) { +cs.setConsensus (this.hconsensus); +cs.setConservation (this.hconservation); +}cs.alignmentChanged (this.alignment, this.hiddenRepSequences); +}if (this.getColourAppliesToAllGroups ()) { +for (var sg, $sg = this.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (cs == null) { +sg.cs = null; +continue; +}sg.cs = cs.applyTo (sg, this.getHiddenRepSequences ()); +sg.setConsPercGaps (this.ConsPercGaps); +if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) { +sg.cs.setThreshold (this.viewStyle.getThreshold (), this.isIgnoreGapsConsensus ()); +recalc = true; +} else { +sg.cs.setThreshold (0, this.isIgnoreGapsConsensus ()); +}if (this.getConservationSelected ()) { +sg.cs.setConservationApplied (true); +recalc = true; +} else { +sg.cs.setConservation (null); +}if (recalc) { +sg.recalcConservation (); +} else { +sg.cs.alignmentChanged (sg, this.hiddenRepSequences); +}} +}}, "jalview.schemes.ColourSchemeI"); +Clazz.overrideMethod (c$, "getGlobalColourScheme", +function () { +return this.globalColourScheme; +}); +Clazz.overrideMethod (c$, "setConservation", +function (cons) { +this.hconservation = cons; +}, "jalview.analysis.Conservation"); +Clazz.overrideMethod (c$, "getConsPercGaps", +function () { +return this.ConsPercGaps; +}); +Clazz.overrideMethod (c$, "setSequenceConsensusHash", +function (hconsensus) { +this.hconsensus = hconsensus; +}, "~A"); +Clazz.overrideMethod (c$, "setComplementConsensusHash", +function (hconsensus) { +this.hcomplementConsensus = hconsensus; +}, "~A"); +Clazz.overrideMethod (c$, "getSequenceConsensusHash", +function () { +return this.hconsensus; +}); +Clazz.overrideMethod (c$, "getComplementConsensusHash", +function () { +return this.hcomplementConsensus; +}); +Clazz.overrideMethod (c$, "getRnaStructureConsensusHash", +function () { +return this.hStrucConsensus; +}); +Clazz.overrideMethod (c$, "setRnaStructureConsensusHash", +function (hStrucConsensus) { +this.hStrucConsensus = hStrucConsensus; +}, "~A"); +Clazz.overrideMethod (c$, "getAlignmentQualityAnnot", +function () { +return this.quality; +}); +Clazz.overrideMethod (c$, "getAlignmentConservationAnnotation", +function () { +return this.conservation; +}); +Clazz.overrideMethod (c$, "getAlignmentConsensusAnnotation", +function () { +return this.consensus; +}); +Clazz.overrideMethod (c$, "getComplementConsensusAnnotation", +function () { +return this.complementConsensus; +}); +Clazz.overrideMethod (c$, "getAlignmentStrucConsensusAnnotation", +function () { +return this.strucConsensus; +}); +Clazz.defineMethod (c$, "updateConservation", +function (ap) { +if (this.alignment.isNucleotide () || this.conservation == null || !this.autoCalculateConsensus) { +return; +}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConservationThread) == null) { +this.calculator.registerWorker ( new jalview.workers.ConservationThread (this, ap)); +}}, "jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "updateConsensus", +function (ap) { +if (this.consensus == null || !this.autoCalculateConsensus) { +return; +}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConsensusThread) == null) { +this.calculator.registerWorker ( new jalview.workers.ConsensusThread (this, ap)); +}var al = this.getAlignment (); +if (!al.isNucleotide () && al.getCodonFrames () != null && !al.getCodonFrames ().isEmpty ()) { +if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ComplementConsensusThread) == null) { +this.calculator.registerWorker ( new jalview.workers.ComplementConsensusThread (this, ap)); +}}}, "jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "updateStrucConsensus", +function (ap) { +if (this.autoCalculateStrucConsensus && this.strucConsensus == null && this.alignment.isNucleotide () && this.alignment.hasRNAStructure ()) { +this.initRNAStructure (); +}if (this.strucConsensus == null || !this.autoCalculateStrucConsensus) { +return; +}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.StrucConsensusThread) == null) { +this.calculator.registerWorker ( new jalview.workers.StrucConsensusThread (this, ap)); +}}, "jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "isCalcInProgress", +function () { +return this.calculator.isWorking (); +}); +Clazz.overrideMethod (c$, "isCalculationInProgress", +function (alignmentAnnotation) { +if (!alignmentAnnotation.autoCalculated) { +return false; +}if (this.calculator.workingInvolvedWith (alignmentAnnotation)) { +return true; +}return false; +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.overrideMethod (c$, "isClosed", +function () { +return this.alignment == null; +}); +Clazz.overrideMethod (c$, "getCalcManager", +function () { +return this.calculator; +}); +Clazz.overrideMethod (c$, "isShowSequenceLogo", +function () { +return this.showSequenceLogo; +}); +Clazz.defineMethod (c$, "setShowSequenceLogo", +function (showSequenceLogo) { +if (showSequenceLogo != this.showSequenceLogo) { +this.showSequenceLogo = showSequenceLogo; +this.calculator.updateAnnotationFor (jalview.workers.ConsensusThread); +this.calculator.updateAnnotationFor (jalview.workers.ComplementConsensusThread); +this.calculator.updateAnnotationFor (jalview.workers.StrucConsensusThread); +}this.showSequenceLogo = showSequenceLogo; +}, "~B"); +Clazz.defineMethod (c$, "setShowConsensusHistogram", +function (showConsensusHistogram) { +this.showConsensusHistogram = showConsensusHistogram; +}, "~B"); +Clazz.defineMethod (c$, "isShowGroupConservation", +function () { +return this.showGroupConservation; +}); +Clazz.defineMethod (c$, "setShowGroupConservation", +function (showGroupConservation) { +this.showGroupConservation = showGroupConservation; +}, "~B"); +Clazz.defineMethod (c$, "isShowGroupConsensus", +function () { +return this.showGroupConsensus; +}); +Clazz.defineMethod (c$, "setShowGroupConsensus", +function (showGroupConsensus) { +this.showGroupConsensus = showGroupConsensus; +}, "~B"); +Clazz.overrideMethod (c$, "isShowConsensusHistogram", +function () { +return this.showConsensusHistogram; +}); +Clazz.overrideMethod (c$, "getSelectionGroup", +function () { +return this.selectionGroup; +}); +Clazz.overrideMethod (c$, "setSelectionGroup", +function (sg) { +this.selectionGroup = sg; +}, "jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "setHiddenColumns", +function (colsel) { +this.colSel = colsel; +}, "jalview.datamodel.ColumnSelection"); +Clazz.overrideMethod (c$, "getColumnSelection", +function () { +return this.colSel; +}); +Clazz.overrideMethod (c$, "setColumnSelection", +function (colSel) { +this.colSel = colSel; +if (colSel != null) { +this.updateHiddenColumns (); +}}, "jalview.datamodel.ColumnSelection"); +Clazz.overrideMethod (c$, "getHiddenRepSequences", +function () { +return this.hiddenRepSequences; +}); +Clazz.overrideMethod (c$, "setHiddenRepSequences", +function (hiddenRepSequences) { +this.hiddenRepSequences = hiddenRepSequences; +}, "java.util.Map"); +Clazz.overrideMethod (c$, "hasHiddenColumns", +function () { +return this.colSel != null && this.colSel.hasHiddenColumns (); +}); +Clazz.defineMethod (c$, "updateHiddenColumns", +function () { +}); +Clazz.overrideMethod (c$, "hasHiddenRows", +function () { +return this.alignment.getHiddenSequences ().getSize () > 0; +}); +Clazz.defineMethod (c$, "setSequenceSetId", +function (newid) { +if (this.sequenceSetID != null) { +System.err.println ("Warning - overwriting a sequenceSetId for a viewport!"); +}this.sequenceSetID = String.instantialize (newid); +}, "~S"); +Clazz.overrideMethod (c$, "getSequenceSetId", +function () { +if (this.sequenceSetID == null) { +this.sequenceSetID = this.alignment.hashCode () + ""; +}return this.sequenceSetID; +}); +Clazz.overrideMethod (c$, "getViewId", +function () { +if (this.viewId == null) { +this.viewId = this.getSequenceSetId () + "." + this.hashCode () + ""; +}return this.viewId; +}); +Clazz.defineMethod (c$, "setIgnoreGapsConsensus", +function (b, ap) { +this.ignoreGapsInConsensusCalculation = b; +if (ap != null) { +this.updateConsensus (ap); +if (this.globalColourScheme != null) { +this.globalColourScheme.setThreshold (this.globalColourScheme.getThreshold (), this.ignoreGapsInConsensusCalculation); +}}}, "~B,jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "isSelectionGroupChanged", +function (b) { +var hc = (this.selectionGroup == null || this.selectionGroup.getSize () == 0) ? -1 : this.selectionGroup.hashCode (); +if (hc != -1 && hc != this.sgrouphash) { +if (b) { +this.sgrouphash = hc; +}return true; +}return false; +}, "~B"); +Clazz.defineMethod (c$, "isColSelChanged", +function (b) { +var hc = (this.colSel == null || this.colSel.size () == 0) ? -1 : this.colSel.hashCode (); +if (hc != -1 && hc != this.colselhash) { +if (b) { +this.colselhash = hc; +}return true; +}return false; +}, "~B"); +Clazz.overrideMethod (c$, "isIgnoreGapsConsensus", +function () { +return this.ignoreGapsInConsensusCalculation; +}); +Clazz.defineMethod (c$, "addPropertyChangeListener", +function (listener) { +this.changeSupport.addPropertyChangeListener (listener); +}, "java.beans.PropertyChangeListener"); +Clazz.defineMethod (c$, "removePropertyChangeListener", +function (listener) { +this.changeSupport.removePropertyChangeListener (listener); +}, "java.beans.PropertyChangeListener"); +Clazz.defineMethod (c$, "firePropertyChange", +function (prop, oldvalue, newvalue) { +this.changeSupport.firePropertyChange (prop, oldvalue, newvalue); +}, "~S,~O,~O"); +Clazz.defineMethod (c$, "hideSelectedColumns", +function () { +if (this.colSel.size () < 1) { +return; +}this.colSel.hideSelectedColumns (); +this.setSelectionGroup (null); +}); +Clazz.defineMethod (c$, "hideColumns", +function (start, end) { +if (start == end) { +this.colSel.hideColumns (start); +} else { +this.colSel.hideColumns (start, end); +}}, "~N,~N"); +Clazz.defineMethod (c$, "showColumn", +function (col) { +this.colSel.revealHiddenColumns (col); +}, "~N"); +Clazz.defineMethod (c$, "showAllHiddenColumns", +function () { +this.colSel.revealAllHiddenColumns (); +}); +Clazz.defineMethod (c$, "showAllHiddenSeqs", +function () { +if (this.alignment.getHiddenSequences ().getSize () > 0) { +if (this.selectionGroup == null) { +this.selectionGroup = new jalview.datamodel.SequenceGroup (); +this.selectionGroup.setEndRes (this.alignment.getWidth () - 1); +}var tmp = this.alignment.getHiddenSequences ().showAll (this.hiddenRepSequences); +for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +this.selectionGroup.addSequence (seq, false); +this.setSequenceAnnotationsVisible (seq, true); +} +this.hiddenRepSequences = null; +this.firePropertyChange ("alignment", null, this.alignment.getSequences ()); +this.sendSelection (); +}}); +Clazz.defineMethod (c$, "showSequence", +function (index) { +var tmp = this.alignment.getHiddenSequences ().showSequence (index, this.hiddenRepSequences); +if (tmp.size () > 0) { +if (this.selectionGroup == null) { +this.selectionGroup = new jalview.datamodel.SequenceGroup (); +this.selectionGroup.setEndRes (this.alignment.getWidth () - 1); +}for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) { +this.selectionGroup.addSequence (seq, false); +this.setSequenceAnnotationsVisible (seq, true); +} +this.firePropertyChange ("alignment", null, this.alignment.getSequences ()); +this.sendSelection (); +}}, "~N"); +Clazz.defineMethod (c$, "hideAllSelectedSeqs", +function () { +if (this.selectionGroup == null || this.selectionGroup.getSize () < 1) { +return; +}var seqs = this.selectionGroup.getSequencesInOrder (this.alignment); +this.hideSequence (seqs); +this.setSelectionGroup (null); +}); +Clazz.defineMethod (c$, "hideSequence", +function (seq) { +if (seq != null) { +for (var i = 0; i < seq.length; i++) { +this.alignment.getHiddenSequences ().hideSequence (seq[i]); +this.setSequenceAnnotationsVisible (seq[i], false); +} +this.firePropertyChange ("alignment", null, this.alignment.getSequences ()); +}}, "~A"); +Clazz.defineMethod (c$, "setSequenceAnnotationsVisible", +function (sequenceI, visible) { +for (var ann, $ann = 0, $$ann = this.alignment.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) { +if (ann.sequenceRef === sequenceI) { +ann.visible = visible; +}} +}, "jalview.datamodel.SequenceI,~B"); +Clazz.defineMethod (c$, "hideRepSequences", +function (repSequence, sg) { +var sSize = sg.getSize (); +if (sSize < 2) { +return; +}if (this.hiddenRepSequences == null) { +this.hiddenRepSequences = new java.util.Hashtable (); +}this.hiddenRepSequences.put (repSequence, sg); +var seqs = new Array (sSize - 1); +var index = 0; +for (var i = 0; i < sSize; i++) { +if (sg.getSequenceAt (i) !== repSequence) { +if (index == sSize - 1) { +return; +}seqs[index++] = sg.getSequenceAt (i); +}} +sg.setSeqrep (repSequence); +sg.setHidereps (true); +this.hideSequence (seqs); +}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup"); +Clazz.defineMethod (c$, "isHiddenRepSequence", +function (seq) { +return this.alignment.getSeqrep () === seq || (this.hiddenRepSequences != null && this.hiddenRepSequences.containsKey (seq)); +}, "jalview.datamodel.SequenceI"); +Clazz.defineMethod (c$, "getRepresentedSequences", +function (seq) { +return (this.hiddenRepSequences == null ? null : this.hiddenRepSequences.get (seq)); +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "adjustForHiddenSeqs", +function (alignmentIndex) { +return this.alignment.getHiddenSequences ().adjustForHiddenSeqs (alignmentIndex); +}, "~N"); +Clazz.overrideMethod (c$, "invertColumnSelection", +function () { +this.colSel.invertColumnSelection (0, this.alignment.getWidth ()); +}); +Clazz.overrideMethod (c$, "getSelectionAsNewSequence", +function () { +var sequences; +if (this.selectionGroup == null || this.selectionGroup.getSize () == 0) { +sequences = this.alignment.getSequencesArray (); +var annots = this.alignment.getAlignmentAnnotation (); +for (var i = 0; i < sequences.length; i++) { +sequences[i] = new jalview.datamodel.Sequence (sequences[i], annots); +} +} else { +sequences = this.selectionGroup.getSelectionAsNewSequences (this.alignment); +}return sequences; +}); +Clazz.overrideMethod (c$, "getSequenceSelection", +function () { +var sequences = null; +if (this.selectionGroup != null) { +sequences = this.selectionGroup.getSequencesInOrder (this.alignment); +}if (sequences == null) { +sequences = this.alignment.getSequencesArray (); +}return sequences; +}); +Clazz.overrideMethod (c$, "getViewAsCigars", +function (selectedRegionOnly) { +return new jalview.datamodel.CigarArray (this.alignment, this.colSel, (selectedRegionOnly ? this.selectionGroup : null)); +}, "~B"); +Clazz.defineMethod (c$, "getAlignmentView", +function (selectedOnly) { +return this.getAlignmentView (selectedOnly, false); +}, "~B"); +Clazz.defineMethod (c$, "getAlignmentView", +function (selectedOnly, markGroups) { +return new jalview.datamodel.AlignmentView (this.alignment, this.colSel, this.selectionGroup, this.colSel != null && this.colSel.hasHiddenColumns (), selectedOnly, markGroups); +}, "~B,~B"); +Clazz.overrideMethod (c$, "getViewAsString", +function (selectedRegionOnly) { +var selection = null; +var seqs = null; +var i; +var iSize; +var start = 0; +var end = 0; +if (selectedRegionOnly && this.selectionGroup != null) { +iSize = this.selectionGroup.getSize (); +seqs = this.selectionGroup.getSequencesInOrder (this.alignment); +start = this.selectionGroup.getStartRes (); +end = this.selectionGroup.getEndRes () + 1; +} else { +iSize = this.alignment.getHeight (); +seqs = this.alignment.getSequencesArray (); +end = this.alignment.getWidth (); +}selection = new Array (iSize); +if (this.colSel != null && this.colSel.hasHiddenColumns ()) { +selection = this.colSel.getVisibleSequenceStrings (start, end, seqs); +} else { +for (i = 0; i < iSize; i++) { +selection[i] = seqs[i].getSequenceAsString (start, end); +} +}return selection; +}, "~B"); +Clazz.overrideMethod (c$, "getVisibleRegionBoundaries", +function (min, max) { +var regions = new java.util.ArrayList (); +var start = min; +var end = max; +do { +if (this.colSel != null && this.colSel.hasHiddenColumns ()) { +if (start == 0) { +start = this.colSel.adjustForHiddenColumns (start); +}end = this.colSel.getHiddenBoundaryRight (start); +if (start == end) { +end = max; +}if (end > max) { +end = max; +}}regions.add ( Clazz.newIntArray (-1, [start, end])); +if (this.colSel != null && this.colSel.hasHiddenColumns ()) { +start = this.colSel.adjustForHiddenColumns (end); +start = this.colSel.getHiddenBoundaryLeft (start) + 1; +}} while (end < max); +var startEnd = Clazz.newIntArray (regions.size (), 2, 0); +return regions; +}, "~N,~N"); +Clazz.overrideMethod (c$, "getVisibleAlignmentAnnotation", +function (selectedOnly) { +var ala = new java.util.ArrayList (); +var aa; +if ((aa = this.alignment.getAlignmentAnnotation ()) != null) { +for (var annot, $annot = 0, $$annot = aa; $annot < $$annot.length && ((annot = $$annot[$annot]) || true); $annot++) { +var clone = new jalview.datamodel.AlignmentAnnotation (annot); +if (selectedOnly && this.selectionGroup != null) { +this.colSel.makeVisibleAnnotation (this.selectionGroup.getStartRes (), this.selectionGroup.getEndRes (), clone); +} else { +this.colSel.makeVisibleAnnotation (clone); +}ala.add (clone); +} +}return ala; +}, "~B"); +Clazz.overrideMethod (c$, "isPadGaps", +function () { +return this.padGaps; +}); +Clazz.overrideMethod (c$, "setPadGaps", +function (padGaps) { +this.padGaps = padGaps; +}, "~B"); +Clazz.overrideMethod (c$, "alignmentChanged", +function (ap) { +if (this.isPadGaps ()) { +this.alignment.padGaps (); +}if (this.autoCalculateConsensus) { +this.updateConsensus (ap); +}if (this.hconsensus != null && this.autoCalculateConsensus) { +this.updateConservation (ap); +}if (this.autoCalculateStrucConsensus) { +this.updateStrucConsensus (ap); +}var alWidth = this.alignment.getWidth (); +var groups = this.alignment.getGroups (); +if (groups != null) { +for (var sg, $sg = groups.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.getEndRes () > alWidth) { +sg.setEndRes (alWidth - 1); +}} +}if (this.selectionGroup != null && this.selectionGroup.getEndRes () > alWidth) { +this.selectionGroup.setEndRes (alWidth - 1); +}this.resetAllColourSchemes (); +this.calculator.restartWorkers (); +}, "jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "resetAllColourSchemes", +function () { +var cs = this.globalColourScheme; +if (cs != null) { +cs.alignmentChanged (this.alignment, this.hiddenRepSequences); +cs.setConsensus (this.hconsensus); +if (cs.conservationApplied ()) { +cs.setConservation (jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.alignment.getWidth (), false, this.getConsPercGaps (), false)); +}}for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.cs != null) { +sg.cs.alignmentChanged (sg, this.hiddenRepSequences); +}sg.recalcConservation (); +} +}); +Clazz.defineMethod (c$, "initAutoAnnotation", +function () { +if (this.hconsensus == null && !this.$isDataset) { +if (!this.alignment.isNucleotide ()) { +this.initConservation (); +this.initQuality (); +} else { +this.initRNAStructure (); +}this.consensus = new jalview.datamodel.AlignmentAnnotation ("Consensus", "PID", new Array (1), 0, 100, 1); +this.initConsensus (this.consensus); +this.initComplementConsensus (); +}}); +Clazz.defineMethod (c$, "initComplementConsensus", +function () { +if (!this.alignment.isNucleotide ()) { +var codonMappings = this.alignment.getCodonFrames (); +if (codonMappings != null && !codonMappings.isEmpty ()) { +this.complementConsensus = new jalview.datamodel.AlignmentAnnotation ("cDNA Consensus", "PID for cDNA", new Array (1), 0, 100, 1); +this.initConsensus (this.complementConsensus); +}}}); +Clazz.defineMethod (c$, "initConsensus", +($fz = function (aa) { +aa.hasText = true; +aa.autoCalculated = true; +if (this.showConsensus) { +this.alignment.addAnnotation (aa); +}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation"); +Clazz.defineMethod (c$, "initConservation", +($fz = function () { +if (this.showConservation) { +if (this.conservation == null) { +this.conservation = new jalview.datamodel.AlignmentAnnotation ("Conservation", "Conservation of total alignment less than " + this.getConsPercGaps () + "% gaps", new Array (1), 0, 11, 1); +this.conservation.hasText = true; +this.conservation.autoCalculated = true; +this.alignment.addAnnotation (this.conservation); +}}}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "initQuality", +($fz = function () { +if (this.showQuality) { +if (this.quality == null) { +this.quality = new jalview.datamodel.AlignmentAnnotation ("Quality", "Alignment Quality based on Blosum62 scores", new Array (1), 0, 11, 1); +this.quality.hasText = true; +this.quality.autoCalculated = true; +this.alignment.addAnnotation (this.quality); +}}}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "initRNAStructure", +($fz = function () { +if (this.alignment.hasRNAStructure () && this.strucConsensus == null) { +this.strucConsensus = new jalview.datamodel.AlignmentAnnotation ("StrucConsensus", "PID", new Array (1), 0, 100, 1); +this.strucConsensus.hasText = true; +this.strucConsensus.autoCalculated = true; +if (this.showConsensus) { +this.alignment.addAnnotation (this.strucConsensus); +}}}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "calcPanelHeight", +function () { +var anns = this.getAlignment ().getAlignmentAnnotation (); +var height = 0; +var charHeight = this.getCharHeight (); +if (anns != null) { +var graphgrp = new java.util.BitSet (); +for (var aa, $aa = 0, $$aa = anns; $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { +if (aa == null) { +System.err.println ("Null annotation row: ignoring."); +continue; +}if (!aa.visible) { +continue; +}if (aa.graphGroup > -1) { +if (graphgrp.get (aa.graphGroup)) { +continue; +} else { +graphgrp.set (aa.graphGroup); +}}aa.height = 0; +if (aa.hasText) { +aa.height += charHeight; +}if (aa.hasIcons) { +aa.height += 16; +}if (aa.graph > 0) { +aa.height += aa.graphHeight; +}if (aa.height == 0) { +aa.height = 20; +}height += aa.height; +} +}if (height == 0) { +height = 20; +}return height; +}); +Clazz.overrideMethod (c$, "updateGroupAnnotationSettings", +function (applyGlobalSettings, preserveNewGroupSettings) { +var updateCalcs = false; +var conv = this.isShowGroupConservation (); +var cons = this.isShowGroupConsensus (); +var showprf = this.isShowSequenceLogo (); +var showConsHist = this.isShowConsensusHistogram (); +var normLogo = this.isNormaliseSequenceLogo (); +var sortg = true; +var aan = this.alignment.getAlignmentAnnotation (); +var oldrfs = new java.util.ArrayList (); +if (aan != null) { +for (var an = 0; an < aan.length; an++) { +if (aan[an].autoCalculated && aan[an].groupRef != null) { +oldrfs.add (aan[an].groupRef); +this.alignment.deleteAnnotation (aan[an], false); +}} +}if (this.alignment.getGroups () != null) { +for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +updateCalcs = false; +if (applyGlobalSettings || (!preserveNewGroupSettings && !oldrfs.contains (sg))) { +sg.setshowSequenceLogo (showprf); +sg.setShowConsensusHistogram (showConsHist); +sg.setNormaliseSequenceLogo (normLogo); +}if (conv) { +updateCalcs = true; +this.alignment.addAnnotation (sg.getConservationRow (), 0); +}if (cons) { +updateCalcs = true; +this.alignment.addAnnotation (sg.getConsensus (), 0); +}if (updateCalcs) { +sg.recalcConservation (); +}} +}oldrfs.clear (); +}, "~B,~B"); +Clazz.defineMethod (c$, "isDisplayReferenceSeq", +function () { +return this.alignment.hasSeqrep () && this.viewStyle.isDisplayReferenceSeq (); +}); +Clazz.defineMethod (c$, "setDisplayReferenceSeq", +function (displayReferenceSeq) { +this.viewStyle.setDisplayReferenceSeq (displayReferenceSeq); +}, "~B"); +Clazz.defineMethod (c$, "isColourByReferenceSeq", +function () { +return this.alignment.hasSeqrep () && this.viewStyle.isColourByReferenceSeq (); +}); +Clazz.overrideMethod (c$, "getSequenceColour", +function (seq) { +var sqc = this.sequenceColours.get (seq); +return (sqc == null ? java.awt.Color.white : sqc); +}, "jalview.datamodel.SequenceI"); +Clazz.overrideMethod (c$, "setSequenceColour", +function (seq, col) { +if (col == null) { +this.sequenceColours.remove (seq); +} else { +this.sequenceColours.put (seq, col); +}}, "jalview.datamodel.SequenceI,java.awt.Color"); +Clazz.overrideMethod (c$, "updateSequenceIdColours", +function () { +for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if (sg.idColour != null) { +for (var s, $s = sg.getSequences (this.getHiddenRepSequences ()).iterator (); $s.hasNext () && ((s = $s.next ()) || true);) { +this.sequenceColours.put (s, sg.idColour); +} +}} +}); +Clazz.overrideMethod (c$, "clearSequenceColours", +function () { +this.sequenceColours.clear (); +}); +Clazz.defineMethod (c$, "getCodingComplement", +function () { +return this.codingComplement; +}); +Clazz.defineMethod (c$, "setCodingComplement", +function (av) { +if (this === av) { +System.err.println ("Ignoring recursive setCodingComplement request"); +} else { +this.codingComplement = av; +if (av.getCodingComplement () !== this) { +av.setCodingComplement (this); +}}}, "jalview.api.AlignViewportI"); +Clazz.overrideMethod (c$, "isNucleotide", +function () { +return this.getAlignment () == null ? false : this.getAlignment ().isNucleotide (); +}); +Clazz.overrideMethod (c$, "getFeaturesDisplayed", +function () { +return this.featuresDisplayed; +}); +Clazz.overrideMethod (c$, "setFeaturesDisplayed", +function (featuresDisplayedI) { +this.featuresDisplayed = featuresDisplayedI; +}, "jalview.api.FeaturesDisplayedI"); +Clazz.overrideMethod (c$, "areFeaturesDisplayed", +function () { +return this.featuresDisplayed != null && this.featuresDisplayed.getRegisterdFeaturesCount () > 0; +}); +Clazz.defineMethod (c$, "setShowSequenceFeatures", +function (b) { +this.viewStyle.setShowSequenceFeatures (b); +}, "~B"); +Clazz.defineMethod (c$, "isShowSequenceFeatures", +function () { +return this.viewStyle.isShowSequenceFeatures (); +}); +Clazz.defineMethod (c$, "setShowSequenceFeaturesHeight", +function (selected) { +this.viewStyle.setShowSequenceFeaturesHeight (selected); +}, "~B"); +Clazz.defineMethod (c$, "isShowSequenceFeaturesHeight", +function () { +return this.viewStyle.isShowSequenceFeaturesHeight (); +}); +Clazz.defineMethod (c$, "setShowAnnotation", +function (b) { +this.viewStyle.setShowAnnotation (b); +}, "~B"); +Clazz.defineMethod (c$, "isShowAnnotation", +function () { +return this.viewStyle.isShowAnnotation (); +}); +Clazz.defineMethod (c$, "isRightAlignIds", +function () { +return this.viewStyle.isRightAlignIds (); +}); +Clazz.defineMethod (c$, "setRightAlignIds", +function (rightAlignIds) { +this.viewStyle.setRightAlignIds (rightAlignIds); +}, "~B"); +Clazz.defineMethod (c$, "getConservationSelected", +function () { +return this.viewStyle.getConservationSelected (); +}); +Clazz.defineMethod (c$, "setShowBoxes", +function (state) { +this.viewStyle.setShowBoxes (state); +}, "~B"); +Clazz.defineMethod (c$, "getTextColour", +function () { +return this.viewStyle.getTextColour (); +}); +Clazz.defineMethod (c$, "getTextColour2", +function () { +return this.viewStyle.getTextColour2 (); +}); +Clazz.defineMethod (c$, "getThresholdTextColour", +function () { +return this.viewStyle.getThresholdTextColour (); +}); +Clazz.defineMethod (c$, "isConservationColourSelected", +function () { +return this.viewStyle.isConservationColourSelected (); +}); +Clazz.defineMethod (c$, "isRenderGaps", +function () { +return this.viewStyle.isRenderGaps (); +}); +Clazz.defineMethod (c$, "isShowColourText", +function () { +return this.viewStyle.isShowColourText (); +}); +Clazz.defineMethod (c$, "setConservationColourSelected", +function (conservationColourSelected) { +this.viewStyle.setConservationColourSelected (conservationColourSelected); +}, "~B"); +Clazz.defineMethod (c$, "setShowColourText", +function (showColourText) { +this.viewStyle.setShowColourText (showColourText); +}, "~B"); +Clazz.defineMethod (c$, "setTextColour", +function (textColour) { +this.viewStyle.setTextColour (textColour); +}, "java.awt.Color"); +Clazz.defineMethod (c$, "setThresholdTextColour", +function (thresholdTextColour) { +this.viewStyle.setThresholdTextColour (thresholdTextColour); +}, "~N"); +Clazz.defineMethod (c$, "setTextColour2", +function (textColour2) { +this.viewStyle.setTextColour2 (textColour2); +}, "java.awt.Color"); +Clazz.overrideMethod (c$, "getViewStyle", +function () { +return new jalview.viewmodel.styles.ViewStyle (this.viewStyle); +}); +Clazz.overrideMethod (c$, "setViewStyle", +function (settingsForView) { +this.viewStyle = new jalview.viewmodel.styles.ViewStyle (settingsForView); +}, "jalview.api.ViewStyleI"); +Clazz.defineMethod (c$, "sameStyle", +function (them) { +return this.viewStyle.sameStyle (them); +}, "jalview.api.ViewStyleI"); +Clazz.defineMethod (c$, "getIdWidth", +function () { +return this.viewStyle.getIdWidth (); +}); +Clazz.defineMethod (c$, "setIdWidth", +function (i) { +this.viewStyle.setIdWidth (i); +}, "~N"); +Clazz.defineMethod (c$, "isCentreColumnLabels", +function () { +return this.viewStyle.isCentreColumnLabels (); +}); +Clazz.defineMethod (c$, "setCentreColumnLabels", +function (centreColumnLabels) { +this.viewStyle.setCentreColumnLabels (centreColumnLabels); +}, "~B"); +Clazz.defineMethod (c$, "setShowDBRefs", +function (showdbrefs) { +this.viewStyle.setShowDBRefs (showdbrefs); +}, "~B"); +Clazz.defineMethod (c$, "isShowDBRefs", +function () { +return this.viewStyle.isShowDBRefs (); +}); +Clazz.defineMethod (c$, "isShowNPFeats", +function () { +return this.viewStyle.isShowNPFeats (); +}); +Clazz.defineMethod (c$, "setShowNPFeats", +function (shownpfeats) { +this.viewStyle.setShowNPFeats (shownpfeats); +}, "~B"); +Clazz.defineMethod (c$, "addToHistoryList", +function (command) { +if (this.historyList != null) { +this.historyList.push (command); +this.broadcastCommand (command, false); +}}, "jalview.commands.CommandI"); +Clazz.defineMethod (c$, "broadcastCommand", +function (command, undo) { +this.getStructureSelectionManager ().commandPerformed (command, undo, this.getVamsasSource ()); +}, "jalview.commands.CommandI,~B"); +Clazz.defineMethod (c$, "addToRedoList", +function (command) { +if (this.redoList != null) { +this.redoList.push (command); +}this.broadcastCommand (command, true); +}, "jalview.commands.CommandI"); +Clazz.defineMethod (c$, "clearRedoList", +function () { +if (this.redoList != null) { +this.redoList.clear (); +}}); +Clazz.defineMethod (c$, "setHistoryList", +function (list) { +this.historyList = list; +}, "java.util.Deque"); +Clazz.defineMethod (c$, "getHistoryList", +function () { +return this.historyList; +}); +Clazz.defineMethod (c$, "setRedoList", +function (list) { +this.redoList = list; +}, "java.util.Deque"); +Clazz.defineMethod (c$, "getRedoList", +function () { +return this.redoList; +}); +Clazz.overrideMethod (c$, "getVamsasSource", +function () { +return this; +}); +Clazz.defineMethod (c$, "getSortAnnotationsBy", +function () { +return this.sortAnnotationsBy; +}); +Clazz.defineMethod (c$, "setSortAnnotationsBy", +function (sortAnnotationsBy) { +this.sortAnnotationsBy = sortAnnotationsBy; +}, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); +Clazz.defineMethod (c$, "isShowAutocalculatedAbove", +function () { +return this.showAutocalculatedAbove; +}); +Clazz.defineMethod (c$, "setShowAutocalculatedAbove", +function (showAutocalculatedAbove) { +this.showAutocalculatedAbove = showAutocalculatedAbove; +}, "~B"); +Clazz.defineMethod (c$, "isScaleProteinAsCdna", +function () { +return this.viewStyle.isScaleProteinAsCdna (); +}); +Clazz.defineMethod (c$, "setScaleProteinAsCdna", +function (b) { +this.viewStyle.setScaleProteinAsCdna (b); +}, "~B"); +Clazz.defineMethod (c$, "isFollowHighlight", +function () { +return this.followHighlight; +}); +Clazz.overrideMethod (c$, "setFollowHighlight", +function (b) { +this.followHighlight = b; +}, "~B"); +Clazz.defineMethod (c$, "getStartRes", +function () { +return this.startRes; +}); +Clazz.overrideMethod (c$, "getEndRes", +function () { +return this.endRes; +}); +Clazz.defineMethod (c$, "getStartSeq", +function () { +return this.startSeq; +}); +Clazz.defineMethod (c$, "setStartRes", +function (res) { +this.startRes = res; +}, "~N"); +Clazz.defineMethod (c$, "setStartSeq", +function (seq) { +this.startSeq = seq; +}, "~N"); +Clazz.defineMethod (c$, "setEndRes", +function (res) { +if (res > this.alignment.getWidth () - 1) { +res = this.alignment.getWidth () - 1; +}if (res < 0) { +res = 0; +}this.endRes = res; +}, "~N"); +Clazz.defineMethod (c$, "setEndSeq", +function (seq) { +if (seq > this.alignment.getHeight ()) { +seq = this.alignment.getHeight (); +}if (seq < 0) { +seq = 0; +}this.endSeq = seq; +}, "~N"); +Clazz.defineMethod (c$, "getEndSeq", +function () { +return this.endSeq; +}); +Clazz.defineMethod (c$, "findComplementScrollTarget", +function (sr) { +var complement = this.getCodingComplement (); +if (complement == null || !complement.isFollowHighlight ()) { +return 0; +}var iAmProtein = !this.getAlignment ().isNucleotide (); +var proteinAlignment = iAmProtein ? this.getAlignment () : complement.getAlignment (); +if (proteinAlignment == null) { +return 0; +}var mappings = proteinAlignment.getCodonFrames (); +var seqOffset = 0; +var sequence = null; +var middleColumn = this.getStartRes () + Clazz.doubleToInt ((this.getEndRes () - this.getStartRes ()) / 2); +var hiddenSequences = this.getAlignment ().getHiddenSequences (); +for (var seqNo = this.getStartSeq (); seqNo < this.getEndSeq (); seqNo++, seqOffset++) { +sequence = this.getAlignment ().getSequenceAt (seqNo); +if (hiddenSequences != null && hiddenSequences.isHidden (sequence)) { +continue; +}if (jalview.util.Comparison.isGap (sequence.getCharAt (middleColumn))) { +continue; +}var seqMappings = jalview.util.MappingUtils.findMappingsForSequence (sequence, mappings); +if (!seqMappings.isEmpty ()) { +break; +}} +if (sequence == null) { +return 0; +}jalview.util.MappingUtils.addSearchResults (sr, sequence, sequence.findPosition (middleColumn), mappings); +return seqOffset; +}, "jalview.datamodel.SearchResults"); +}); diff --git a/bin/jalview/viewmodel/PCAModel.class b/bin/jalview/viewmodel/PCAModel.class index 25ba04c..47bb240 100644 Binary files a/bin/jalview/viewmodel/PCAModel.class and b/bin/jalview/viewmodel/PCAModel.class differ diff --git a/bin/jalview/viewmodel/PCAModel.js b/bin/jalview/viewmodel/PCAModel.js index cdb9868..7527935 100644 --- a/bin/jalview/viewmodel/PCAModel.js +++ b/bin/jalview/viewmodel/PCAModel.js @@ -1,134 +1,134 @@ -Clazz.declarePackage ("jalview.viewmodel"); -Clazz.load (null, "jalview.viewmodel.PCAModel", ["jalview.analysis.PCA", "jalview.datamodel.SequencePoint", "java.lang.StringBuffer", "java.util.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.pca = null; -this.top = 0; -this.seqstrings = null; -this.seqs = null; -this.score_matrix = null; -this.nucleotide = false; -this.points = null; -this.jvCalcMode = true; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel, "PCAModel"); -Clazz.makeConstructor (c$, -function (seqstrings2, seqs2, nucleotide2) { -this.seqstrings = seqstrings2; -this.seqs = seqs2; -this.nucleotide = nucleotide2; -this.score_matrix = nucleotide2 ? "PID" : "BLOSUM62"; -}, "jalview.datamodel.AlignmentView,~A,~B"); -Clazz.defineMethod (c$, "isJvCalcMode", -function () { -return this.jvCalcMode; -}); -Clazz.defineMethod (c$, "run", -function () { -this.pca = new jalview.analysis.PCA (this.seqstrings.getSequenceStrings (' '), this.nucleotide, this.score_matrix); -this.pca.setJvCalcMode (this.jvCalcMode); -this.pca.run (); -var ii = 0; -while ((ii < this.seqs.length) && (this.seqs[ii] != null)) { -ii++; -} -var comps = Clazz.newDoubleArray (ii, ii, 0); -for (var i = 0; i < ii; i++) { -if (this.pca.getEigenvalue (i) > 1e-4) { -comps[i] = this.pca.component (i); -}} -this.top = this.pca.getM ().rows - 1; -this.points = new java.util.Vector (); -var scores = this.pca.getComponents (this.top - 1, this.top - 2, this.top - 3, 100); -for (var i = 0; i < this.pca.getM ().rows; i++) { -var sp = new jalview.datamodel.SequencePoint (this.seqs[i], scores[i]); -this.points.addElement (sp); -} -}); -Clazz.defineMethod (c$, "updateRc", -function (rc) { -rc.setPoints (this.points, this.pca.getM ().rows); -}, "jalview.api.RotatableCanvasI"); -Clazz.defineMethod (c$, "isNucleotide", -function () { -return this.nucleotide; -}); -Clazz.defineMethod (c$, "setNucleotide", -function (nucleotide) { -this.nucleotide = nucleotide; -}, "~B"); -Clazz.defineMethod (c$, "getTop", -function () { -return this.top; -}); -Clazz.defineMethod (c$, "updateRcView", -function (dim1, dim2, dim3) { -var scores = this.pca.getComponents (dim1 - 1, dim2 - 1, dim3 - 1, 100); -for (var i = 0; i < this.pca.getM ().rows; i++) { -(this.points.elementAt (i)).coord = scores[i]; -} -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "getDetails", -function () { -return this.pca.getDetails (); -}); -Clazz.defineMethod (c$, "getSeqtrings", -function () { -return this.seqstrings; -}); -Clazz.defineMethod (c$, "getPointsasCsv", -function (transformed, xdim, ydim, zdim) { -var csv = new StringBuffer (); -csv.append ("\"Sequence\""); -if (transformed) { -csv.append (","); -csv.append (xdim); -csv.append (","); -csv.append (ydim); -csv.append (","); -csv.append (zdim); -} else { -for (var d = 1, dmax = this.pca.component (1).length; d <= dmax; d++) { -csv.append ("," + d); -} -}csv.append ("\n"); -for (var s = 0; s < this.seqs.length; s++) { -csv.append ("\"" + this.seqs[s].getName () + "\""); -var fl; -if (!transformed) { -fl = this.pca.component (s); -for (var d = fl.length - 1; d >= 0; d--) { -csv.append (","); -csv.append (fl[d]); -} -} else { -fl = this.getPointPosition (s); -for (var d = 0; d < fl.length; d++) { -csv.append (","); -csv.append (fl[d]); -} -}csv.append ("\n"); -} -return csv.toString (); -}, "~B,~N,~N,~N"); -Clazz.defineMethod (c$, "getPointPosition", -function (s) { -var pts = Clazz.newDoubleArray (3, 0); -var p = this.points.elementAt (s).coord; -pts[0] = p[0]; -pts[1] = p[1]; -pts[2] = p[2]; -return pts; -}, "~N"); -Clazz.defineMethod (c$, "setJvCalcMode", -function (state) { -this.jvCalcMode = state; -}, "~B"); -Clazz.defineMethod (c$, "getScore_matrix", -function () { -return this.score_matrix; -}); -Clazz.defineMethod (c$, "setScore_matrix", -function (score_matrix) { -this.score_matrix = score_matrix; -}, "~S"); -}); +Clazz.declarePackage ("jalview.viewmodel"); +Clazz.load (null, "jalview.viewmodel.PCAModel", ["jalview.analysis.PCA", "jalview.datamodel.SequencePoint", "java.lang.StringBuffer", "java.util.Vector"], function () { +c$ = Clazz.decorateAsClass (function () { +this.pca = null; +this.top = 0; +this.seqstrings = null; +this.seqs = null; +this.score_matrix = null; +this.nucleotide = false; +this.points = null; +this.jvCalcMode = true; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel, "PCAModel"); +Clazz.makeConstructor (c$, +function (seqstrings2, seqs2, nucleotide2) { +this.seqstrings = seqstrings2; +this.seqs = seqs2; +this.nucleotide = nucleotide2; +this.score_matrix = nucleotide2 ? "PID" : "BLOSUM62"; +}, "jalview.datamodel.AlignmentView,~A,~B"); +Clazz.defineMethod (c$, "isJvCalcMode", +function () { +return this.jvCalcMode; +}); +Clazz.defineMethod (c$, "run", +function () { +this.pca = new jalview.analysis.PCA (this.seqstrings.getSequenceStrings (' '), this.nucleotide, this.score_matrix); +this.pca.setJvCalcMode (this.jvCalcMode); +this.pca.run (); +var ii = 0; +while ((ii < this.seqs.length) && (this.seqs[ii] != null)) { +ii++; +} +var comps = Clazz.newDoubleArray (ii, ii, 0); +for (var i = 0; i < ii; i++) { +if (this.pca.getEigenvalue (i) > 1e-4) { +comps[i] = this.pca.component (i); +}} +this.top = this.pca.getM ().rows - 1; +this.points = new java.util.Vector (); +var scores = this.pca.getComponents (this.top - 1, this.top - 2, this.top - 3, 100); +for (var i = 0; i < this.pca.getM ().rows; i++) { +var sp = new jalview.datamodel.SequencePoint (this.seqs[i], scores[i]); +this.points.addElement (sp); +} +}); +Clazz.defineMethod (c$, "updateRc", +function (rc) { +rc.setPoints (this.points, this.pca.getM ().rows); +}, "jalview.api.RotatableCanvasI"); +Clazz.defineMethod (c$, "isNucleotide", +function () { +return this.nucleotide; +}); +Clazz.defineMethod (c$, "setNucleotide", +function (nucleotide) { +this.nucleotide = nucleotide; +}, "~B"); +Clazz.defineMethod (c$, "getTop", +function () { +return this.top; +}); +Clazz.defineMethod (c$, "updateRcView", +function (dim1, dim2, dim3) { +var scores = this.pca.getComponents (dim1 - 1, dim2 - 1, dim3 - 1, 100); +for (var i = 0; i < this.pca.getM ().rows; i++) { +(this.points.elementAt (i)).coord = scores[i]; +} +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "getDetails", +function () { +return this.pca.getDetails (); +}); +Clazz.defineMethod (c$, "getSeqtrings", +function () { +return this.seqstrings; +}); +Clazz.defineMethod (c$, "getPointsasCsv", +function (transformed, xdim, ydim, zdim) { +var csv = new StringBuffer (); +csv.append ("\"Sequence\""); +if (transformed) { +csv.append (","); +csv.append ("" + xdim); +csv.append (","); +csv.append ("" + ydim); +csv.append (","); +csv.append ("" + zdim); +} else { +for (var d = 1, dmax = this.pca.component (1).length; d <= dmax; d++) { +csv.append ("," + d); +} +}csv.append ("\n"); +for (var s = 0; s < this.seqs.length; s++) { +csv.append ("\"" + this.seqs[s].getName () + "\""); +var fl; +if (!transformed) { +fl = this.pca.component (s); +for (var d = fl.length - 1; d >= 0; d--) { +csv.append (","); +csv.append (fl[d]); +} +} else { +fl = this.getPointPosition (s); +for (var d = 0; d < fl.length; d++) { +csv.append (","); +csv.append (fl[d]); +} +}csv.append ("\n"); +} +return csv.toString (); +}, "~B,~N,~N,~N"); +Clazz.defineMethod (c$, "getPointPosition", +function (s) { +var pts = Clazz.newDoubleArray (3, 0); +var p = this.points.elementAt (s).coord; +pts[0] = p[0]; +pts[1] = p[1]; +pts[2] = p[2]; +return pts; +}, "~N"); +Clazz.defineMethod (c$, "setJvCalcMode", +function (state) { +this.jvCalcMode = state; +}, "~B"); +Clazz.defineMethod (c$, "getScore_matrix", +function () { +return this.score_matrix; +}); +Clazz.defineMethod (c$, "setScore_matrix", +function (score_matrix) { +this.score_matrix = score_matrix; +}, "~S"); +}); diff --git a/bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js b/bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js index 7daaad4..5fd34a4 100644 --- a/bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js +++ b/bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js @@ -1,83 +1,83 @@ -Clazz.declarePackage ("jalview.viewmodel.annotationfilter"); -Clazz.load (["java.lang.Enum", "java.util.ArrayList"], "jalview.viewmodel.annotationfilter.AnnotationFilterParameter", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.thresholdType = null; -this.thresholdValue = 0; -this.filterAlphaHelix = false; -this.filterBetaSheet = false; -this.filterTurn = false; -this.regexString = null; -this.regexSearchFields = null; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel.annotationfilter, "AnnotationFilterParameter"); -Clazz.prepareFields (c$, function () { -this.regexSearchFields = new java.util.ArrayList (); -}); -Clazz.defineMethod (c$, "getThresholdType", -function () { -return this.thresholdType; -}); -Clazz.defineMethod (c$, "setThresholdType", -function (thresholdType) { -this.thresholdType = thresholdType; -}, "jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType"); -Clazz.defineMethod (c$, "getThresholdValue", -function () { -return this.thresholdValue; -}); -Clazz.defineMethod (c$, "setThresholdValue", -function (thresholdValue) { -this.thresholdValue = thresholdValue; -}, "~N"); -Clazz.defineMethod (c$, "getRegexString", -function () { -return this.regexString; -}); -Clazz.defineMethod (c$, "setRegexString", -function (regexString) { -this.regexString = regexString; -}, "~S"); -Clazz.defineMethod (c$, "getRegexSearchFields", -function () { -return this.regexSearchFields; -}); -Clazz.defineMethod (c$, "addRegexSearchField", -function (regexSearchField) { -this.regexSearchFields.add (regexSearchField); -}, "jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField"); -Clazz.defineMethod (c$, "isFilterAlphaHelix", -function () { -return this.filterAlphaHelix; -}); -Clazz.defineMethod (c$, "setFilterAlphaHelix", -function (alphaHelix) { -this.filterAlphaHelix = alphaHelix; -}, "~B"); -Clazz.defineMethod (c$, "isFilterBetaSheet", -function () { -return this.filterBetaSheet; -}); -Clazz.defineMethod (c$, "setFilterBetaSheet", -function (betaSheet) { -this.filterBetaSheet = betaSheet; -}, "~B"); -Clazz.defineMethod (c$, "isFilterTurn", -function () { -return this.filterTurn; -}); -Clazz.defineMethod (c$, "setFilterTurn", -function (turn) { -this.filterTurn = turn; -}, "~B"); -Clazz.pu$h (); -c$ = Clazz.declareType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter, "ThresholdType", Enum); -Clazz.defineEnumConstant (c$, "NO_THRESHOLD", 0, []); -Clazz.defineEnumConstant (c$, "BELOW_THRESHOLD", 1, []); -Clazz.defineEnumConstant (c$, "ABOVE_THRESHOLD", 2, []); -c$ = Clazz.p0p (); -Clazz.pu$h (); -c$ = Clazz.declareType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter, "SearchableAnnotationField", Enum); -Clazz.defineEnumConstant (c$, "DISPLAY_STRING", 0, []); -Clazz.defineEnumConstant (c$, "DESCRIPTION", 1, []); -c$ = Clazz.p0p (); -}); +Clazz.declarePackage ("jalview.viewmodel.annotationfilter"); +Clazz.load (["java.lang.Enum", "java.util.ArrayList"], "jalview.viewmodel.annotationfilter.AnnotationFilterParameter", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.thresholdType = null; +this.thresholdValue = 0; +this.filterAlphaHelix = false; +this.filterBetaSheet = false; +this.filterTurn = false; +this.regexString = null; +this.regexSearchFields = null; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel.annotationfilter, "AnnotationFilterParameter"); +Clazz.prepareFields (c$, function () { +this.regexSearchFields = new java.util.ArrayList (); +}); +Clazz.defineMethod (c$, "getThresholdType", +function () { +return this.thresholdType; +}); +Clazz.defineMethod (c$, "setThresholdType", +function (thresholdType) { +this.thresholdType = thresholdType; +}, "jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType"); +Clazz.defineMethod (c$, "getThresholdValue", +function () { +return this.thresholdValue; +}); +Clazz.defineMethod (c$, "setThresholdValue", +function (thresholdValue) { +this.thresholdValue = thresholdValue; +}, "~N"); +Clazz.defineMethod (c$, "getRegexString", +function () { +return this.regexString; +}); +Clazz.defineMethod (c$, "setRegexString", +function (regexString) { +this.regexString = regexString; +}, "~S"); +Clazz.defineMethod (c$, "getRegexSearchFields", +function () { +return this.regexSearchFields; +}); +Clazz.defineMethod (c$, "addRegexSearchField", +function (regexSearchField) { +this.regexSearchFields.add (regexSearchField); +}, "jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField"); +Clazz.defineMethod (c$, "isFilterAlphaHelix", +function () { +return this.filterAlphaHelix; +}); +Clazz.defineMethod (c$, "setFilterAlphaHelix", +function (alphaHelix) { +this.filterAlphaHelix = alphaHelix; +}, "~B"); +Clazz.defineMethod (c$, "isFilterBetaSheet", +function () { +return this.filterBetaSheet; +}); +Clazz.defineMethod (c$, "setFilterBetaSheet", +function (betaSheet) { +this.filterBetaSheet = betaSheet; +}, "~B"); +Clazz.defineMethod (c$, "isFilterTurn", +function () { +return this.filterTurn; +}); +Clazz.defineMethod (c$, "setFilterTurn", +function (turn) { +this.filterTurn = turn; +}, "~B"); +Clazz.pu$h (); +c$ = Clazz.declareType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter, "ThresholdType", Enum); +Clazz.defineEnumConstant (c$, "NO_THRESHOLD", 0, []); +Clazz.defineEnumConstant (c$, "BELOW_THRESHOLD", 1, []); +Clazz.defineEnumConstant (c$, "ABOVE_THRESHOLD", 2, []); +c$ = Clazz.p0p (); +Clazz.pu$h (); +c$ = Clazz.declareType (jalview.viewmodel.annotationfilter.AnnotationFilterParameter, "SearchableAnnotationField", Enum); +Clazz.defineEnumConstant (c$, "DISPLAY_STRING", 0, []); +Clazz.defineEnumConstant (c$, "DESCRIPTION", 1, []); +c$ = Clazz.p0p (); +}); diff --git a/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.class b/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.class index 5f33a88..cd148bd 100644 Binary files a/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.class and b/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.class differ diff --git a/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js b/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js index cd53bbe..985bdda 100644 --- a/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js +++ b/bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js @@ -1,481 +1,481 @@ -Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); -Clazz.load (["jalview.api.FeatureRenderer", "java.beans.PropertyChangeSupport", "java.lang.Boolean", "java.util.Hashtable", "java.util.concurrent.ConcurrentHashMap"], "jalview.viewmodel.seqfeatures.FeatureRendererModel", ["jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.QuickSort", "jalview.viewmodel.seqfeatures.FeatureRendererSettings", "$.FeaturesDisplayed", "java.awt.Color", "java.lang.Error", "$.Float", "java.util.ArrayList", "$.Arrays"], function () { -c$ = Clazz.decorateAsClass (function () { -this.transparency = 1.0; -this.featureColours = null; -this.featureGroups = null; -this.currentColour = null; -this.renderOrder = null; -this.changeSupport = null; -this.av = null; -this.minmax = null; -this.newFeatureAdded = false; -this.findingFeatures = false; -this.firing = null; -this.featureOrder = null; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel.seqfeatures, "FeatureRendererModel", null, jalview.api.FeatureRenderer); -Clazz.prepareFields (c$, function () { -this.featureColours = new java.util.concurrent.ConcurrentHashMap (); -this.featureGroups = new java.util.concurrent.ConcurrentHashMap (); -this.changeSupport = new java.beans.PropertyChangeSupport (this); -this.minmax = new java.util.Hashtable (); -this.firing = Boolean.FALSE; -}); -Clazz.overrideMethod (c$, "getViewport", -function () { -return this.av; -}); -Clazz.defineMethod (c$, "getSettings", -function () { -return new jalview.viewmodel.seqfeatures.FeatureRendererSettings (this); -}); -Clazz.defineMethod (c$, "transferSettings", -function (fr) { -this.renderOrder = fr.renderOrder; -this.featureGroups = fr.featureGroups; -this.featureColours = fr.featureColours; -this.transparency = fr.transparency; -this.featureOrder = fr.featureOrder; -}, "jalview.viewmodel.seqfeatures.FeatureRendererSettings"); -Clazz.defineMethod (c$, "transferSettings", -function (_fr) { -var fr = _fr; -var frs = new jalview.viewmodel.seqfeatures.FeatureRendererSettings (fr); -this.renderOrder = frs.renderOrder; -this.featureGroups = frs.featureGroups; -this.featureColours = frs.featureColours; -this.transparency = frs.transparency; -this.featureOrder = frs.featureOrder; -if (this.av != null && this.av !== fr.getViewport ()) { -if (_fr.getFeaturesDisplayed () != null) { -var fd = this.getFeaturesDisplayed (); -if (fd == null) { -this.setFeaturesDisplayedFrom (_fr.getFeaturesDisplayed ()); -} else { -{ -fd.clear (); -var fdisp = _fr.getFeaturesDisplayed ().getVisibleFeatures (); -while (fdisp.hasNext ()) { -fd.setVisible (fdisp.next ()); -} -}}}}}, "jalview.api.FeatureRenderer"); -Clazz.defineMethod (c$, "setFeaturesDisplayedFrom", -function (featuresDisplayed) { -this.av.setFeaturesDisplayed ( new jalview.viewmodel.seqfeatures.FeaturesDisplayed (featuresDisplayed)); -}, "jalview.api.FeaturesDisplayedI"); -Clazz.overrideMethod (c$, "setVisible", -function (featureType) { -var fdi = this.av.getFeaturesDisplayed (); -if (fdi == null) { -this.av.setFeaturesDisplayed (fdi = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); -}if (!fdi.isRegistered (featureType)) { -this.pushFeatureType (java.util.Arrays.asList ( Clazz.newArray (-1, [featureType]))); -}fdi.setVisible (featureType); -}, "~S"); -Clazz.overrideMethod (c$, "setAllVisible", -function (featureTypes) { -var fdi = this.av.getFeaturesDisplayed (); -if (fdi == null) { -this.av.setFeaturesDisplayed (fdi = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); -}var nft = new java.util.ArrayList (); -for (var featureType, $featureType = featureTypes.iterator (); $featureType.hasNext () && ((featureType = $featureType.next ()) || true);) { -if (!fdi.isRegistered (featureType)) { -nft.add (featureType); -}} -if (nft.size () > 0) { -this.pushFeatureType (nft); -}fdi.setAllVisible (featureTypes); -}, "java.util.List"); -Clazz.defineMethod (c$, "pushFeatureType", -($fz = function (types) { -var ts = types.size (); -var neworder = new Array ((this.renderOrder == null ? 0 : this.renderOrder.length) + ts); -types.toArray (neworder); -if (this.renderOrder != null) { -System.arraycopy (neworder, 0, neworder, this.renderOrder.length, ts); -System.arraycopy (this.renderOrder, 0, neworder, 0, this.renderOrder.length); -}this.renderOrder = neworder; -}, $fz.isPrivate = true, $fz), "java.util.List"); -Clazz.defineMethod (c$, "getMinMax", -function () { -return this.minmax; -}); -Clazz.defineMethod (c$, "normaliseScore", -function (sequenceFeature) { -var mm = (this.minmax.get (sequenceFeature.type))[0]; -var r = Clazz.newByteArray (-1, [0, 255]); -if (mm != null) { -if (r[0] != 0 || mm[0] < 0.0) { -r[0] = 1; -r[1] = Clazz.doubleToByte (Clazz.doubleToInt (128.0) + 127.0 * (sequenceFeature.score / mm[1])); -} else { -r[1] = Clazz.floatToByte (Clazz.doubleToInt (255.0) * (sequenceFeature.score / mm[1])); -}}return r; -}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "updateFeatures", -function () { -if (this.av.getFeaturesDisplayed () == null || this.renderOrder == null || this.newFeatureAdded) { -this.findAllFeatures (); -if (this.av.getFeaturesDisplayed ().getVisibleFeatureCount () < 1) { -return false; -}}return true; -}); -Clazz.defineMethod (c$, "findAllFeatures", -function () { -{ -if (this.firing.equals (Boolean.FALSE)) { -this.firing = Boolean.TRUE; -this.findAllFeatures (true); -this.changeSupport.firePropertyChange ("changeSupport", null, null); -this.firing = Boolean.FALSE; -}}}); -Clazz.overrideMethod (c$, "findFeaturesAtRes", -function (sequence, res) { -var tmp = new java.util.ArrayList (); -var features = sequence.getSequenceFeatures (); -if (features != null) { -for (var i = 0; i < features.length; i++) { -if (!this.av.areFeaturesDisplayed () || !this.av.getFeaturesDisplayed ().isVisible (features[i].getType ())) { -continue; -}if (features[i].featureGroup != null && this.featureGroups != null && this.featureGroups.containsKey (features[i].featureGroup) && !this.featureGroups.get (features[i].featureGroup).booleanValue ()) { -continue; -}if ((features[i].getBegin () <= res) && (features[i].getEnd () >= res)) { -tmp.add (features[i]); -}} -}return tmp; -}, "jalview.datamodel.SequenceI,~N"); -Clazz.defineMethod (c$, "findAllFeatures", -function (newMadeVisible) { -this.newFeatureAdded = false; -if (this.findingFeatures) { -this.newFeatureAdded = true; -return; -}this.findingFeatures = true; -if (this.av.getFeaturesDisplayed () == null) { -this.av.setFeaturesDisplayed ( new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); -}var featuresDisplayed = this.av.getFeaturesDisplayed (); -var allfeatures = new java.util.ArrayList (); -var oldfeatures = new java.util.ArrayList (); -if (this.renderOrder != null) { -for (var i = 0; i < this.renderOrder.length; i++) { -if (this.renderOrder[i] != null) { -oldfeatures.add (this.renderOrder[i]); -}} -}if (this.minmax == null) { -this.minmax = new java.util.Hashtable (); -}var alignment = this.av.getAlignment (); -for (var i = 0; i < alignment.getHeight (); i++) { -var asq = alignment.getSequenceAt (i); -var features = asq.getSequenceFeatures (); -if (features == null) { -continue; -}var index = 0; -while (index < features.length) { -if (!featuresDisplayed.isRegistered (features[index].getType ())) { -var fgrp = features[index].getFeatureGroup (); -if (fgrp != null) { -var groupDisplayed = this.featureGroups.get (fgrp); -if (groupDisplayed == null) { -groupDisplayed = Boolean.$valueOf (newMadeVisible); -this.featureGroups.put (fgrp, groupDisplayed); -}if (!groupDisplayed.booleanValue ()) { -index++; -continue; -}}if (!(features[index].begin == 0 && features[index].end == 0)) { -if (newMadeVisible && !oldfeatures.contains (features[index].getType ())) { -featuresDisplayed.setVisible (features[index].getType ()); -this.setOrder (features[index].getType (), 0); -}}}if (!allfeatures.contains (features[index].getType ())) { -allfeatures.add (features[index].getType ()); -}if (!Float.isNaN (features[index].score)) { -var nonpos = features[index].getBegin () >= 1 ? 0 : 1; -var mm = this.minmax.get (features[index].getType ()); -if (mm == null) { -mm = Clazz.newArray (-1, [null, null]); -this.minmax.put (features[index].getType (), mm); -}if (mm[nonpos] == null) { -mm[nonpos] = Clazz.newFloatArray (-1, [features[index].score, features[index].score]); -} else { -if (mm[nonpos][0] > features[index].score) { -mm[nonpos][0] = features[index].score; -}if (mm[nonpos][1] < features[index].score) { -mm[nonpos][1] = features[index].score; -}}}index++; -} -} -this.updateRenderOrder (allfeatures); -this.findingFeatures = false; -}, "~B"); -Clazz.defineMethod (c$, "updateRenderOrder", -($fz = function (allFeatures) { -var allfeatures = new java.util.ArrayList (allFeatures); -var oldRender = this.renderOrder; -this.renderOrder = new Array (allfeatures.size ()); -var mmrange; -var fc = null; -var initOrders = (this.featureOrder == null); -var opos = 0; -if (oldRender != null && oldRender.length > 0) { -for (var j = 0; j < oldRender.length; j++) { -if (oldRender[j] != null) { -if (initOrders) { -this.setOrder (oldRender[j], (1 - (1 + j) / oldRender.length)); -}if (allfeatures.contains (oldRender[j])) { -this.renderOrder[opos++] = oldRender[j]; -allfeatures.remove (oldRender[j]); -if (this.minmax != null) { -mmrange = this.minmax.get (oldRender[j]); -if (mmrange != null) { -fc = this.featureColours.get (oldRender[j]); -if (fc != null && Clazz.instanceOf (fc, jalview.schemes.GraduatedColor) && (fc).isAutoScale ()) { -(fc).updateBounds ((mmrange)[0][0], (mmrange)[0][1]); -}}}}}} -}if (allfeatures.size () == 0) { -return; -}var i = allfeatures.size () - 1; -var iSize = i; -var sort = false; -var newf = new Array (allfeatures.size ()); -var sortOrder = Clazz.newFloatArray (allfeatures.size (), 0); -for (var newfeat, $newfeat = allfeatures.iterator (); $newfeat.hasNext () && ((newfeat = $newfeat.next ()) || true);) { -newf[i] = newfeat; -if (this.minmax != null) { -mmrange = this.minmax.get (newf[i]); -if (mmrange != null) { -fc = this.featureColours.get (newf[i]); -if (fc != null && Clazz.instanceOf (fc, jalview.schemes.GraduatedColor) && (fc).isAutoScale ()) { -(fc).updateBounds ((mmrange)[0][0], (mmrange)[0][1]); -}}}if (initOrders || !this.featureOrder.containsKey (newf[i])) { -var denom = initOrders ? allfeatures.size () : this.featureOrder.size (); -this.setOrder (newf[i], i / denom); -}sortOrder[i] = 2 - (this.featureOrder.get (newf[i])).floatValue (); -if (i < iSize) { -sort = sort || sortOrder[i] > sortOrder[i + 1]; -}i--; -} -if (iSize > 1 && sort) { -jalview.util.QuickSort.sortFloatObject (sortOrder, newf); -}sortOrder = null; -System.arraycopy (newf, 0, this.renderOrder, opos, newf.length); -}, $fz.isPrivate = true, $fz), "java.util.List"); -Clazz.overrideMethod (c$, "getFeatureStyle", -function (featureType) { -var fc = this.featureColours.get (featureType); -if (fc == null) { -var ucs = new jalview.schemes.UserColourScheme (); -var col = ucs.createColourFromName (featureType); -this.featureColours.put (featureType, fc = col); -}return fc; -}, "~S"); -Clazz.defineMethod (c$, "getColour", -function (featureType) { -var fc = this.getFeatureStyle (featureType); -if (Clazz.instanceOf (fc, java.awt.Color)) { -return fc; -} else { -if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) { -return (fc).getMaxColor (); -}}throw new Error ("Implementation Error: Unrecognised render object " + fc.getClass () + " for features of type " + featureType); -}, "~S"); -Clazz.defineMethod (c$, "getColour", -function (feature) { -var fc = this.getFeatureStyle (feature.getType ()); -if (Clazz.instanceOf (fc, java.awt.Color)) { -return fc; -} else { -if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) { -return (fc).findColor (feature); -}}throw new Error ("Implementation Error: Unrecognised render object " + fc.getClass () + " for features of type " + feature.getType ()); -}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "showFeature", -function (sequenceFeature) { -var fc = this.getFeatureStyle (sequenceFeature.type); -if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) { -return (fc).isColored (sequenceFeature); -} else { -return true; -}}, "jalview.datamodel.SequenceFeature"); -Clazz.defineMethod (c$, "showFeatureOfType", -function (type) { -return this.av.getFeaturesDisplayed ().isVisible (type); -}, "~S"); -Clazz.overrideMethod (c$, "setColour", -function (featureType, col) { -{ -this.featureColours.put (featureType, col); -}}, "~S,~O"); -Clazz.defineMethod (c$, "setTransparency", -function (value) { -this.transparency = value; -}, "~N"); -Clazz.defineMethod (c$, "getTransparency", -function () { -return this.transparency; -}); -Clazz.defineMethod (c$, "setOrder", -function (type, position) { -if (this.featureOrder == null) { -this.featureOrder = new java.util.Hashtable (); -}this.featureOrder.put (type, new Float (position)); -return position; -}, "~S,~N"); -Clazz.defineMethod (c$, "getOrder", -function (type) { -if (this.featureOrder != null) { -if (this.featureOrder.containsKey (type)) { -return (this.featureOrder.get (type)).floatValue (); -}}return -1; -}, "~S"); -Clazz.overrideMethod (c$, "getFeatureColours", -function () { -return new java.util.concurrent.ConcurrentHashMap (this.featureColours); -}); -Clazz.defineMethod (c$, "setFeaturePriority", -function (data) { -this.setFeaturePriority (data, true); -}, "~A"); -Clazz.defineMethod (c$, "setFeaturePriority", -function (data, visibleNew) { -var av_featuresdisplayed = null; -if (visibleNew) { -if ((av_featuresdisplayed = this.av.getFeaturesDisplayed ()) != null) { -this.av.getFeaturesDisplayed ().clear (); -} else { -this.av.setFeaturesDisplayed (av_featuresdisplayed = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); -}} else { -av_featuresdisplayed = this.av.getFeaturesDisplayed (); -}if (data == null) { -return; -}this.renderOrder = new Array (data.length); -if (data.length > 0) { -for (var i = 0; i < data.length; i++) { -var type = data[i][0].toString (); -this.setColour (type, data[i][1]); -if ((data[i][2]).booleanValue ()) { -av_featuresdisplayed.setVisible (type); -}this.renderOrder[data.length - i - 1] = type; -} -}}, "~A,~B"); -Clazz.defineMethod (c$, "addPropertyChangeListener", -function (listener) { -this.changeSupport.addPropertyChangeListener (listener); -}, "java.beans.PropertyChangeListener"); -Clazz.defineMethod (c$, "removePropertyChangeListener", -function (listener) { -this.changeSupport.removePropertyChangeListener (listener); -}, "java.beans.PropertyChangeListener"); -Clazz.defineMethod (c$, "getAllFeatureColours", -function () { -return this.featureColours.keySet (); -}); -Clazz.defineMethod (c$, "clearRenderOrder", -function () { -this.renderOrder = null; -}); -Clazz.defineMethod (c$, "hasRenderOrder", -function () { -return this.renderOrder != null; -}); -Clazz.defineMethod (c$, "getRenderOrder", -function () { -if (this.renderOrder == null) { -return java.util.Arrays.asList ( Clazz.newArray (-1, [])); -}return java.util.Arrays.asList (this.renderOrder); -}); -Clazz.defineMethod (c$, "getFeatureGroupsSize", -function () { -return this.featureGroups != null ? 0 : this.featureGroups.size (); -}); -Clazz.overrideMethod (c$, "getFeatureGroups", -function () { -return (this.featureGroups == null) ? java.util.Arrays.asList ( new Array (0)) : java.util.Arrays.asList (this.featureGroups.keySet ().toArray ( new Array (0))); -}); -Clazz.defineMethod (c$, "checkGroupVisibility", -function (group, newGroupsVisible) { -if (this.featureGroups == null) { -}if (this.featureGroups.containsKey (group)) { -return this.featureGroups.get (group).booleanValue (); -}if (newGroupsVisible) { -this.featureGroups.put (group, new Boolean (true)); -return true; -}return false; -}, "~S,~B"); -Clazz.overrideMethod (c$, "getGroups", -function (visible) { -if (this.featureGroups != null) { -var gp = new java.util.ArrayList (); -for (var grp, $grp = this.featureGroups.keySet ().iterator (); $grp.hasNext () && ((grp = $grp.next ()) || true);) { -var state = this.featureGroups.get (grp); -if (state.booleanValue () == visible) { -gp.add (grp); -}} -return gp; -}return null; -}, "~B"); -Clazz.defineMethod (c$, "setGroupVisibility", -function (group, visible) { -this.featureGroups.put (group, new Boolean (visible)); -}, "~S,~B"); -Clazz.defineMethod (c$, "setGroupVisibility", -function (toset, visible) { -if (toset != null && toset.size () > 0 && this.featureGroups != null) { -var rdrw = false; -for (var gst, $gst = toset.iterator (); $gst.hasNext () && ((gst = $gst.next ()) || true);) { -var st = this.featureGroups.get (gst); -this.featureGroups.put (gst, new Boolean (visible)); -if (st != null) { -rdrw = rdrw || (visible != st.booleanValue ()); -}} -if (rdrw) { -}}}, "java.util.List,~B"); -Clazz.overrideMethod (c$, "getDisplayedFeatureCols", -function () { -var fcols = new java.util.Hashtable (); -if (this.getViewport ().getFeaturesDisplayed () == null) { -return fcols; -}var en = this.getViewport ().getFeaturesDisplayed ().getVisibleFeatures (); -while (en.hasNext ()) { -var col = en.next (); -fcols.put (col, this.getColour (col)); -} -return fcols; -}); -Clazz.defineMethod (c$, "getFeaturesDisplayed", -function () { -return this.av.getFeaturesDisplayed (); -}); -Clazz.overrideMethod (c$, "getDisplayedFeatureTypes", -function () { -var typ = null; -typ = this.getRenderOrder ().toArray ( new Array (0)); -var feature_disp = this.av.getFeaturesDisplayed (); -if (feature_disp != null) { -{ -for (var i = 0; i < typ.length; i++) { -if (!feature_disp.isVisible (typ[i])) { -typ[i] = null; -}} -}}return typ; -}); -Clazz.overrideMethod (c$, "getDisplayedFeatureGroups", -function () { -var gps = null; -var _gps = new java.util.ArrayList (); -var en = this.getFeatureGroups ().iterator (); -var g = 0; -var valid = false; -while (en.hasNext ()) { -var gp = en.next (); -if (this.checkGroupVisibility (gp, false)) { -valid = true; -_gps.add (gp); -}if (!valid) { -return null; -} else { -gps = new Array (_gps.size ()); -_gps.toArray (gps); -}} -return gps; -}); -}); +Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); +Clazz.load (["jalview.api.FeatureRenderer", "java.beans.PropertyChangeSupport", "java.lang.Boolean", "java.util.Hashtable", "java.util.concurrent.ConcurrentHashMap"], "jalview.viewmodel.seqfeatures.FeatureRendererModel", ["jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.QuickSort", "jalview.viewmodel.seqfeatures.FeatureRendererSettings", "$.FeaturesDisplayed", "java.awt.Color", "java.lang.Error", "$.Float", "java.util.ArrayList", "$.Arrays"], function () { +c$ = Clazz.decorateAsClass (function () { +this.transparency = 1.0; +this.featureColours = null; +this.featureGroups = null; +this.currentColour = null; +this.renderOrder = null; +this.changeSupport = null; +this.av = null; +this.minmax = null; +this.newFeatureAdded = false; +this.findingFeatures = false; +this.firing = null; +this.featureOrder = null; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel.seqfeatures, "FeatureRendererModel", null, jalview.api.FeatureRenderer); +Clazz.prepareFields (c$, function () { +this.featureColours = new java.util.concurrent.ConcurrentHashMap (); +this.featureGroups = new java.util.concurrent.ConcurrentHashMap (); +this.changeSupport = new java.beans.PropertyChangeSupport (this); +this.minmax = new java.util.Hashtable (); +this.firing = Boolean.FALSE; +}); +Clazz.overrideMethod (c$, "getViewport", +function () { +return this.av; +}); +Clazz.defineMethod (c$, "getSettings", +function () { +return new jalview.viewmodel.seqfeatures.FeatureRendererSettings (this); +}); +Clazz.defineMethod (c$, "transferSettings", +function (fr) { +this.renderOrder = fr.renderOrder; +this.featureGroups = fr.featureGroups; +this.featureColours = fr.featureColours; +this.transparency = fr.transparency; +this.featureOrder = fr.featureOrder; +}, "jalview.viewmodel.seqfeatures.FeatureRendererSettings"); +Clazz.defineMethod (c$, "transferSettings", +function (_fr) { +var fr = _fr; +var frs = new jalview.viewmodel.seqfeatures.FeatureRendererSettings (fr); +this.renderOrder = frs.renderOrder; +this.featureGroups = frs.featureGroups; +this.featureColours = frs.featureColours; +this.transparency = frs.transparency; +this.featureOrder = frs.featureOrder; +if (this.av != null && this.av !== fr.getViewport ()) { +if (_fr.getFeaturesDisplayed () != null) { +var fd = this.getFeaturesDisplayed (); +if (fd == null) { +this.setFeaturesDisplayedFrom (_fr.getFeaturesDisplayed ()); +} else { +{ +fd.clear (); +var fdisp = _fr.getFeaturesDisplayed ().getVisibleFeatures (); +while (fdisp.hasNext ()) { +fd.setVisible (fdisp.next ()); +} +}}}}}, "jalview.api.FeatureRenderer"); +Clazz.defineMethod (c$, "setFeaturesDisplayedFrom", +function (featuresDisplayed) { +this.av.setFeaturesDisplayed ( new jalview.viewmodel.seqfeatures.FeaturesDisplayed (featuresDisplayed)); +}, "jalview.api.FeaturesDisplayedI"); +Clazz.overrideMethod (c$, "setVisible", +function (featureType) { +var fdi = this.av.getFeaturesDisplayed (); +if (fdi == null) { +this.av.setFeaturesDisplayed (fdi = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); +}if (!fdi.isRegistered (featureType)) { +this.pushFeatureType (java.util.Arrays.asList ( Clazz.newArray (-1, [featureType]))); +}fdi.setVisible (featureType); +}, "~S"); +Clazz.overrideMethod (c$, "setAllVisible", +function (featureTypes) { +var fdi = this.av.getFeaturesDisplayed (); +if (fdi == null) { +this.av.setFeaturesDisplayed (fdi = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); +}var nft = new java.util.ArrayList (); +for (var featureType, $featureType = featureTypes.iterator (); $featureType.hasNext () && ((featureType = $featureType.next ()) || true);) { +if (!fdi.isRegistered (featureType)) { +nft.add (featureType); +}} +if (nft.size () > 0) { +this.pushFeatureType (nft); +}fdi.setAllVisible (featureTypes); +}, "java.util.List"); +Clazz.defineMethod (c$, "pushFeatureType", +($fz = function (types) { +var ts = types.size (); +var neworder = new Array ((this.renderOrder == null ? 0 : this.renderOrder.length) + ts); +types.toArray (neworder); +if (this.renderOrder != null) { +System.arraycopy (neworder, 0, neworder, this.renderOrder.length, ts); +System.arraycopy (this.renderOrder, 0, neworder, 0, this.renderOrder.length); +}this.renderOrder = neworder; +}, $fz.isPrivate = true, $fz), "java.util.List"); +Clazz.defineMethod (c$, "getMinMax", +function () { +return this.minmax; +}); +Clazz.defineMethod (c$, "normaliseScore", +function (sequenceFeature) { +var mm = (this.minmax.get (sequenceFeature.type))[0]; +var r = Clazz.newByteArray (-1, [0, 255]); +if (mm != null) { +if (r[0] != 0 || mm[0] < 0.0) { +r[0] = 1; +r[1] = Clazz.doubleToByte (Clazz.doubleToInt (128.0) + 127.0 * (sequenceFeature.score / mm[1])); +} else { +r[1] = Clazz.floatToByte (Clazz.doubleToInt (255.0) * (sequenceFeature.score / mm[1])); +}}return r; +}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "updateFeatures", +function () { +if (this.av.getFeaturesDisplayed () == null || this.renderOrder == null || this.newFeatureAdded) { +this.findAllFeatures (); +if (this.av.getFeaturesDisplayed ().getVisibleFeatureCount () < 1) { +return false; +}}return true; +}); +Clazz.defineMethod (c$, "findAllFeatures", +function () { +{ +if (this.firing.equals (Boolean.FALSE)) { +this.firing = Boolean.TRUE; +this.findAllFeatures (true); +this.changeSupport.firePropertyChange ("changeSupport", null, null); +this.firing = Boolean.FALSE; +}}}); +Clazz.overrideMethod (c$, "findFeaturesAtRes", +function (sequence, res) { +var tmp = new java.util.ArrayList (); +var features = sequence.getSequenceFeatures (); +if (features != null) { +for (var i = 0; i < features.length; i++) { +if (!this.av.areFeaturesDisplayed () || !this.av.getFeaturesDisplayed ().isVisible (features[i].getType ())) { +continue; +}if (features[i].featureGroup != null && this.featureGroups != null && this.featureGroups.containsKey (features[i].featureGroup) && !this.featureGroups.get (features[i].featureGroup).booleanValue ()) { +continue; +}if ((features[i].getBegin () <= res) && (features[i].getEnd () >= res)) { +tmp.add (features[i]); +}} +}return tmp; +}, "jalview.datamodel.SequenceI,~N"); +Clazz.defineMethod (c$, "findAllFeatures", +function (newMadeVisible) { +this.newFeatureAdded = false; +if (this.findingFeatures) { +this.newFeatureAdded = true; +return; +}this.findingFeatures = true; +if (this.av.getFeaturesDisplayed () == null) { +this.av.setFeaturesDisplayed ( new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); +}var featuresDisplayed = this.av.getFeaturesDisplayed (); +var allfeatures = new java.util.ArrayList (); +var oldfeatures = new java.util.ArrayList (); +if (this.renderOrder != null) { +for (var i = 0; i < this.renderOrder.length; i++) { +if (this.renderOrder[i] != null) { +oldfeatures.add (this.renderOrder[i]); +}} +}if (this.minmax == null) { +this.minmax = new java.util.Hashtable (); +}var alignment = this.av.getAlignment (); +for (var i = 0; i < alignment.getHeight (); i++) { +var asq = alignment.getSequenceAt (i); +var features = asq.getSequenceFeatures (); +if (features == null) { +continue; +}var index = 0; +while (index < features.length) { +if (!featuresDisplayed.isRegistered (features[index].getType ())) { +var fgrp = features[index].getFeatureGroup (); +if (fgrp != null) { +var groupDisplayed = this.featureGroups.get (fgrp); +if (groupDisplayed == null) { +groupDisplayed = Boolean.$valueOf (newMadeVisible); +this.featureGroups.put (fgrp, groupDisplayed); +}if (!groupDisplayed.booleanValue ()) { +index++; +continue; +}}if (!(features[index].begin == 0 && features[index].end == 0)) { +if (newMadeVisible && !oldfeatures.contains (features[index].getType ())) { +featuresDisplayed.setVisible (features[index].getType ()); +this.setOrder (features[index].getType (), 0); +}}}if (!allfeatures.contains (features[index].getType ())) { +allfeatures.add (features[index].getType ()); +}if (!Float.isNaN (features[index].score)) { +var nonpos = features[index].getBegin () >= 1 ? 0 : 1; +var mm = this.minmax.get (features[index].getType ()); +if (mm == null) { +mm = Clazz.newArray (-1, [null, null]); +this.minmax.put (features[index].getType (), mm); +}if (mm[nonpos] == null) { +mm[nonpos] = Clazz.newFloatArray (-1, [features[index].score, features[index].score]); +} else { +if (mm[nonpos][0] > features[index].score) { +mm[nonpos][0] = features[index].score; +}if (mm[nonpos][1] < features[index].score) { +mm[nonpos][1] = features[index].score; +}}}index++; +} +} +this.updateRenderOrder (allfeatures); +this.findingFeatures = false; +}, "~B"); +Clazz.defineMethod (c$, "updateRenderOrder", +($fz = function (allFeatures) { +var allfeatures = new java.util.ArrayList (allFeatures); +var oldRender = this.renderOrder; +this.renderOrder = new Array (allfeatures.size ()); +var mmrange; +var fc = null; +var initOrders = (this.featureOrder == null); +var opos = 0; +if (oldRender != null && oldRender.length > 0) { +for (var j = 0; j < oldRender.length; j++) { +if (oldRender[j] != null) { +if (initOrders) { +this.setOrder (oldRender[j], (1 - (1 + j) / oldRender.length)); +}if (allfeatures.contains (oldRender[j])) { +this.renderOrder[opos++] = oldRender[j]; +allfeatures.remove (oldRender[j]); +if (this.minmax != null) { +mmrange = this.minmax.get (oldRender[j]); +if (mmrange != null) { +fc = this.featureColours.get (oldRender[j]); +if (fc != null && Clazz.instanceOf (fc, jalview.schemes.GraduatedColor) && (fc).isAutoScale ()) { +(fc).updateBounds ((mmrange)[0][0], (mmrange)[0][1]); +}}}}}} +}if (allfeatures.size () == 0) { +return; +}var i = allfeatures.size () - 1; +var iSize = i; +var sort = false; +var newf = new Array (allfeatures.size ()); +var sortOrder = Clazz.newFloatArray (allfeatures.size (), 0); +for (var newfeat, $newfeat = allfeatures.iterator (); $newfeat.hasNext () && ((newfeat = $newfeat.next ()) || true);) { +newf[i] = newfeat; +if (this.minmax != null) { +mmrange = this.minmax.get (newf[i]); +if (mmrange != null) { +fc = this.featureColours.get (newf[i]); +if (fc != null && Clazz.instanceOf (fc, jalview.schemes.GraduatedColor) && (fc).isAutoScale ()) { +(fc).updateBounds ((mmrange)[0][0], (mmrange)[0][1]); +}}}if (initOrders || !this.featureOrder.containsKey (newf[i])) { +var denom = initOrders ? allfeatures.size () : this.featureOrder.size (); +this.setOrder (newf[i], i / denom); +}sortOrder[i] = 2 - (this.featureOrder.get (newf[i])).floatValue (); +if (i < iSize) { +sort = sort || sortOrder[i] > sortOrder[i + 1]; +}i--; +} +if (iSize > 1 && sort) { +jalview.util.QuickSort.sortFloatObject (sortOrder, newf); +}sortOrder = null; +System.arraycopy (newf, 0, this.renderOrder, opos, newf.length); +}, $fz.isPrivate = true, $fz), "java.util.List"); +Clazz.overrideMethod (c$, "getFeatureStyle", +function (featureType) { +var fc = this.featureColours.get (featureType); +if (fc == null) { +var ucs = new jalview.schemes.UserColourScheme (); +var col = ucs.createColourFromName (featureType); +this.featureColours.put (featureType, fc = col); +}return fc; +}, "~S"); +Clazz.defineMethod (c$, "getColour", +function (featureType) { +var fc = this.getFeatureStyle (featureType); +if (Clazz.instanceOf (fc, java.awt.Color)) { +return fc; +} else { +if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) { +return (fc).getMaxColor (); +}}throw new Error ("Implementation Error: Unrecognised render object " + fc.getClass () + " for features of type " + featureType); +}, "~S"); +Clazz.defineMethod (c$, "getColour", +function (feature) { +var fc = this.getFeatureStyle (feature.getType ()); +if (Clazz.instanceOf (fc, java.awt.Color)) { +return fc; +} else { +if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) { +return (fc).findColor (feature); +}}throw new Error ("Implementation Error: Unrecognised render object " + fc.getClass () + " for features of type " + feature.getType ()); +}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "showFeature", +function (sequenceFeature) { +var fc = this.getFeatureStyle (sequenceFeature.type); +if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) { +return (fc).isColored (sequenceFeature); +} else { +return true; +}}, "jalview.datamodel.SequenceFeature"); +Clazz.defineMethod (c$, "showFeatureOfType", +function (type) { +return this.av.getFeaturesDisplayed ().isVisible (type); +}, "~S"); +Clazz.overrideMethod (c$, "setColour", +function (featureType, col) { +{ +this.featureColours.put (featureType, col); +}}, "~S,~O"); +Clazz.defineMethod (c$, "setTransparency", +function (value) { +this.transparency = value; +}, "~N"); +Clazz.defineMethod (c$, "getTransparency", +function () { +return this.transparency; +}); +Clazz.defineMethod (c$, "setOrder", +function (type, position) { +if (this.featureOrder == null) { +this.featureOrder = new java.util.Hashtable (); +}this.featureOrder.put (type, new Float (position)); +return position; +}, "~S,~N"); +Clazz.defineMethod (c$, "getOrder", +function (type) { +if (this.featureOrder != null) { +if (this.featureOrder.containsKey (type)) { +return (this.featureOrder.get (type)).floatValue (); +}}return -1; +}, "~S"); +Clazz.overrideMethod (c$, "getFeatureColours", +function () { +return new java.util.concurrent.ConcurrentHashMap (this.featureColours); +}); +Clazz.defineMethod (c$, "setFeaturePriority", +function (data) { +this.setFeaturePriority (data, true); +}, "~A"); +Clazz.defineMethod (c$, "setFeaturePriority", +function (data, visibleNew) { +var av_featuresdisplayed = null; +if (visibleNew) { +if ((av_featuresdisplayed = this.av.getFeaturesDisplayed ()) != null) { +this.av.getFeaturesDisplayed ().clear (); +} else { +this.av.setFeaturesDisplayed (av_featuresdisplayed = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ()); +}} else { +av_featuresdisplayed = this.av.getFeaturesDisplayed (); +}if (data == null) { +return; +}this.renderOrder = new Array (data.length); +if (data.length > 0) { +for (var i = 0; i < data.length; i++) { +var type = data[i][0].toString (); +this.setColour (type, data[i][1]); +if ((data[i][2]).booleanValue ()) { +av_featuresdisplayed.setVisible (type); +}this.renderOrder[data.length - i - 1] = type; +} +}}, "~A,~B"); +Clazz.defineMethod (c$, "addPropertyChangeListener", +function (listener) { +this.changeSupport.addPropertyChangeListener (listener); +}, "java.beans.PropertyChangeListener"); +Clazz.defineMethod (c$, "removePropertyChangeListener", +function (listener) { +this.changeSupport.removePropertyChangeListener (listener); +}, "java.beans.PropertyChangeListener"); +Clazz.defineMethod (c$, "getAllFeatureColours", +function () { +return this.featureColours.keySet (); +}); +Clazz.defineMethod (c$, "clearRenderOrder", +function () { +this.renderOrder = null; +}); +Clazz.defineMethod (c$, "hasRenderOrder", +function () { +return this.renderOrder != null; +}); +Clazz.defineMethod (c$, "getRenderOrder", +function () { +if (this.renderOrder == null) { +return java.util.Arrays.asList ( Clazz.newArray (-1, [])); +}return java.util.Arrays.asList (this.renderOrder); +}); +Clazz.defineMethod (c$, "getFeatureGroupsSize", +function () { +return this.featureGroups != null ? 0 : this.featureGroups.size (); +}); +Clazz.overrideMethod (c$, "getFeatureGroups", +function () { +return (this.featureGroups == null) ? java.util.Arrays.asList ( new Array (0)) : java.util.Arrays.asList (this.featureGroups.keySet ().toArray ( new Array (0))); +}); +Clazz.defineMethod (c$, "checkGroupVisibility", +function (group, newGroupsVisible) { +if (this.featureGroups == null) { +}if (this.featureGroups.containsKey (group)) { +return this.featureGroups.get (group).booleanValue (); +}if (newGroupsVisible) { +this.featureGroups.put (group, new Boolean (true)); +return true; +}return false; +}, "~S,~B"); +Clazz.overrideMethod (c$, "getGroups", +function (visible) { +if (this.featureGroups != null) { +var gp = new java.util.ArrayList (); +for (var grp, $grp = this.featureGroups.keySet ().iterator (); $grp.hasNext () && ((grp = $grp.next ()) || true);) { +var state = this.featureGroups.get (grp); +if (state.booleanValue () == visible) { +gp.add (grp); +}} +return gp; +}return null; +}, "~B"); +Clazz.defineMethod (c$, "setGroupVisibility", +function (group, visible) { +this.featureGroups.put (group, new Boolean (visible)); +}, "~S,~B"); +Clazz.defineMethod (c$, "setGroupVisibility", +function (toset, visible) { +if (toset != null && toset.size () > 0 && this.featureGroups != null) { +var rdrw = false; +for (var gst, $gst = toset.iterator (); $gst.hasNext () && ((gst = $gst.next ()) || true);) { +var st = this.featureGroups.get (gst); +this.featureGroups.put (gst, new Boolean (visible)); +if (st != null) { +rdrw = rdrw || (visible != st.booleanValue ()); +}} +if (rdrw) { +}}}, "java.util.List,~B"); +Clazz.overrideMethod (c$, "getDisplayedFeatureCols", +function () { +var fcols = new java.util.Hashtable (); +if (this.getViewport ().getFeaturesDisplayed () == null) { +return fcols; +}var en = this.getViewport ().getFeaturesDisplayed ().getVisibleFeatures (); +while (en.hasNext ()) { +var col = en.next (); +fcols.put (col, this.getColour (col)); +} +return fcols; +}); +Clazz.defineMethod (c$, "getFeaturesDisplayed", +function () { +return this.av.getFeaturesDisplayed (); +}); +Clazz.overrideMethod (c$, "getDisplayedFeatureTypes", +function () { +var typ = null; +typ = this.getRenderOrder ().toArray ( new Array (0)); +var feature_disp = this.av.getFeaturesDisplayed (); +if (feature_disp != null) { +{ +for (var i = 0; i < typ.length; i++) { +if (!feature_disp.isVisible (typ[i])) { +typ[i] = null; +}} +}}return typ; +}); +Clazz.overrideMethod (c$, "getDisplayedFeatureGroups", +function () { +var gps = null; +var _gps = new java.util.ArrayList (); +var en = this.getFeatureGroups ().iterator (); +var g = 0; +var valid = false; +while (en.hasNext ()) { +var gp = en.next (); +if (this.checkGroupVisibility (gp, false)) { +valid = true; +_gps.add (gp); +}if (!valid) { +return null; +} else { +gps = new Array (_gps.size ()); +_gps.toArray (gps); +}} +return gps; +}); +}); diff --git a/bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js b/bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js index f166a1b..187a380 100644 --- a/bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js +++ b/bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js @@ -1,43 +1,43 @@ -Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); -Clazz.load (null, "jalview.viewmodel.seqfeatures.FeatureRendererSettings", ["jalview.schemes.GraduatedColor", "java.util.Arrays", "java.util.concurrent.ConcurrentHashMap"], function () { -c$ = Clazz.decorateAsClass (function () { -this.renderOrder = null; -this.featureGroups = null; -this.featureColours = null; -this.transparency = 0; -this.featureOrder = null; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel.seqfeatures, "FeatureRendererSettings", null, Cloneable); -Clazz.makeConstructor (c$, -function (renderOrder, featureGroups, featureColours, transparency, featureOrder) { -this.renderOrder = java.util.Arrays.copyOf (renderOrder, renderOrder.length); -this.featureGroups = new java.util.concurrent.ConcurrentHashMap (featureGroups); -this.featureColours = new java.util.concurrent.ConcurrentHashMap (featureColours); -this.transparency = transparency; -this.featureOrder = new java.util.concurrent.ConcurrentHashMap (featureOrder); -}, "~A,java.util.Hashtable,java.util.Hashtable,~N,java.util.Hashtable"); -Clazz.makeConstructor (c$, -function (fr) { -this.renderOrder = null; -this.featureGroups = new java.util.concurrent.ConcurrentHashMap (); -this.featureColours = new java.util.concurrent.ConcurrentHashMap (); -this.featureOrder = new java.util.concurrent.ConcurrentHashMap (); -if (fr.renderOrder != null) { -this.renderOrder = new Array (fr.renderOrder.length); -System.arraycopy (fr.renderOrder, 0, this.renderOrder, 0, fr.renderOrder.length); -}if (fr.featureGroups != null) { -this.featureGroups = new java.util.concurrent.ConcurrentHashMap (fr.featureGroups); -}if (fr.featureColours != null) { -this.featureColours = new java.util.concurrent.ConcurrentHashMap (fr.featureColours); -}var en = fr.featureColours.keySet ().iterator (); -while (en.hasNext ()) { -var next = en.next (); -var val = this.featureColours.get (next); -if (Clazz.instanceOf (val, jalview.schemes.GraduatedColor)) { -this.featureColours.put (next, new jalview.schemes.GraduatedColor (val)); -}} -this.transparency = fr.transparency; -if (fr.featureOrder != null) { -this.featureOrder = new java.util.concurrent.ConcurrentHashMap (fr.featureOrder); -}}, "jalview.viewmodel.seqfeatures.FeatureRendererModel"); -}); +Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); +Clazz.load (null, "jalview.viewmodel.seqfeatures.FeatureRendererSettings", ["jalview.schemes.GraduatedColor", "java.util.Arrays", "java.util.concurrent.ConcurrentHashMap"], function () { +c$ = Clazz.decorateAsClass (function () { +this.renderOrder = null; +this.featureGroups = null; +this.featureColours = null; +this.transparency = 0; +this.featureOrder = null; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel.seqfeatures, "FeatureRendererSettings", null, Cloneable); +Clazz.makeConstructor (c$, +function (renderOrder, featureGroups, featureColours, transparency, featureOrder) { +this.renderOrder = java.util.Arrays.copyOf (renderOrder, renderOrder.length); +this.featureGroups = new java.util.concurrent.ConcurrentHashMap (featureGroups); +this.featureColours = new java.util.concurrent.ConcurrentHashMap (featureColours); +this.transparency = transparency; +this.featureOrder = new java.util.concurrent.ConcurrentHashMap (featureOrder); +}, "~A,java.util.Hashtable,java.util.Hashtable,~N,java.util.Hashtable"); +Clazz.makeConstructor (c$, +function (fr) { +this.renderOrder = null; +this.featureGroups = new java.util.concurrent.ConcurrentHashMap (); +this.featureColours = new java.util.concurrent.ConcurrentHashMap (); +this.featureOrder = new java.util.concurrent.ConcurrentHashMap (); +if (fr.renderOrder != null) { +this.renderOrder = new Array (fr.renderOrder.length); +System.arraycopy (fr.renderOrder, 0, this.renderOrder, 0, fr.renderOrder.length); +}if (fr.featureGroups != null) { +this.featureGroups = new java.util.concurrent.ConcurrentHashMap (fr.featureGroups); +}if (fr.featureColours != null) { +this.featureColours = new java.util.concurrent.ConcurrentHashMap (fr.featureColours); +}var en = fr.featureColours.keySet ().iterator (); +while (en.hasNext ()) { +var next = en.next (); +var val = this.featureColours.get (next); +if (Clazz.instanceOf (val, jalview.schemes.GraduatedColor)) { +this.featureColours.put (next, new jalview.schemes.GraduatedColor (val)); +}} +this.transparency = fr.transparency; +if (fr.featureOrder != null) { +this.featureOrder = new java.util.concurrent.ConcurrentHashMap (fr.featureOrder); +}}, "jalview.viewmodel.seqfeatures.FeatureRendererModel"); +}); diff --git a/bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js b/bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js index 72b72b5..6623fc4 100644 --- a/bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js +++ b/bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); -Clazz.load (["jalview.api.FeatureSettingsModelI"], "jalview.viewmodel.seqfeatures.FeatureSettingsModel", null, function () { -c$ = Clazz.declareType (jalview.viewmodel.seqfeatures, "FeatureSettingsModel", null, jalview.api.FeatureSettingsModelI); -}); +Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); +Clazz.load (["jalview.api.FeatureSettingsModelI"], "jalview.viewmodel.seqfeatures.FeatureSettingsModel", null, function () { +c$ = Clazz.declareType (jalview.viewmodel.seqfeatures, "FeatureSettingsModel", null, jalview.api.FeatureSettingsModelI); +}); diff --git a/bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js b/bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js index 8f0de99..32ddafc 100644 --- a/bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js +++ b/bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js @@ -1,68 +1,68 @@ -Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); -Clazz.load (["jalview.api.FeaturesDisplayedI", "java.util.HashSet"], "jalview.viewmodel.seqfeatures.FeaturesDisplayed", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.featuresDisplayed = null; -this.featuresRegistered = null; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel.seqfeatures, "FeaturesDisplayed", null, jalview.api.FeaturesDisplayedI); -Clazz.prepareFields (c$, function () { -this.featuresDisplayed = new java.util.HashSet (); -this.featuresRegistered = new java.util.HashSet (); -}); -Clazz.makeConstructor (c$, -function (featuresDisplayed2) { -var fdisp = featuresDisplayed2.getVisibleFeatures (); -var ftype; -while (fdisp.hasNext ()) { -ftype = fdisp.next (); -this.featuresDisplayed.add (ftype); -this.featuresRegistered.add (ftype); -} -}, "jalview.api.FeaturesDisplayedI"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "getVisibleFeatures", -function () { -return this.featuresDisplayed.iterator (); -}); -Clazz.overrideMethod (c$, "isVisible", -function (featureType) { -return this.featuresDisplayed.contains (featureType); -}, "~S"); -Clazz.overrideMethod (c$, "areVisible", -function (featureTypes) { -return this.featuresDisplayed.containsAll (featureTypes); -}, "java.util.Collection"); -Clazz.overrideMethod (c$, "clear", -function () { -this.featuresDisplayed.clear (); -this.featuresRegistered.clear (); -}); -Clazz.overrideMethod (c$, "setAllVisible", -function (makeVisible) { -this.featuresDisplayed.addAll (makeVisible); -this.featuresRegistered.addAll (makeVisible); -}, "java.util.Collection"); -Clazz.overrideMethod (c$, "setAllRegisteredVisible", -function () { -this.featuresDisplayed.addAll (this.featuresRegistered); -}); -Clazz.overrideMethod (c$, "setVisible", -function (featureType) { -this.featuresDisplayed.add (featureType); -this.featuresRegistered.add (featureType); -}, "~S"); -Clazz.overrideMethod (c$, "isRegistered", -function (type) { -return this.featuresRegistered.contains (type); -}, "~S"); -Clazz.overrideMethod (c$, "getVisibleFeatureCount", -function () { -return this.featuresDisplayed.size (); -}); -Clazz.overrideMethod (c$, "getRegisterdFeaturesCount", -function () { -return this.featuresRegistered.size (); -}); -}); +Clazz.declarePackage ("jalview.viewmodel.seqfeatures"); +Clazz.load (["jalview.api.FeaturesDisplayedI", "java.util.HashSet"], "jalview.viewmodel.seqfeatures.FeaturesDisplayed", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.featuresDisplayed = null; +this.featuresRegistered = null; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel.seqfeatures, "FeaturesDisplayed", null, jalview.api.FeaturesDisplayedI); +Clazz.prepareFields (c$, function () { +this.featuresDisplayed = new java.util.HashSet (); +this.featuresRegistered = new java.util.HashSet (); +}); +Clazz.makeConstructor (c$, +function (featuresDisplayed2) { +var fdisp = featuresDisplayed2.getVisibleFeatures (); +var ftype; +while (fdisp.hasNext ()) { +ftype = fdisp.next (); +this.featuresDisplayed.add (ftype); +this.featuresRegistered.add (ftype); +} +}, "jalview.api.FeaturesDisplayedI"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "getVisibleFeatures", +function () { +return this.featuresDisplayed.iterator (); +}); +Clazz.overrideMethod (c$, "isVisible", +function (featureType) { +return this.featuresDisplayed.contains (featureType); +}, "~S"); +Clazz.overrideMethod (c$, "areVisible", +function (featureTypes) { +return this.featuresDisplayed.containsAll (featureTypes); +}, "java.util.Collection"); +Clazz.overrideMethod (c$, "clear", +function () { +this.featuresDisplayed.clear (); +this.featuresRegistered.clear (); +}); +Clazz.overrideMethod (c$, "setAllVisible", +function (makeVisible) { +this.featuresDisplayed.addAll (makeVisible); +this.featuresRegistered.addAll (makeVisible); +}, "java.util.Collection"); +Clazz.overrideMethod (c$, "setAllRegisteredVisible", +function () { +this.featuresDisplayed.addAll (this.featuresRegistered); +}); +Clazz.overrideMethod (c$, "setVisible", +function (featureType) { +this.featuresDisplayed.add (featureType); +this.featuresRegistered.add (featureType); +}, "~S"); +Clazz.overrideMethod (c$, "isRegistered", +function (type) { +return this.featuresRegistered.contains (type); +}, "~S"); +Clazz.overrideMethod (c$, "getVisibleFeatureCount", +function () { +return this.featuresDisplayed.size (); +}); +Clazz.overrideMethod (c$, "getRegisterdFeaturesCount", +function () { +return this.featuresRegistered.size (); +}); +}); diff --git a/bin/jalview/viewmodel/styles/ViewStyle.js b/bin/jalview/viewmodel/styles/ViewStyle.js index f41fe5d..8ec10fa 100644 --- a/bin/jalview/viewmodel/styles/ViewStyle.js +++ b/bin/jalview/viewmodel/styles/ViewStyle.js @@ -1,457 +1,457 @@ -Clazz.declarePackage ("jalview.viewmodel.styles"); -Clazz.load (["jalview.api.ViewStyleI", "java.awt.Color"], "jalview.viewmodel.styles.ViewStyle", ["java.lang.Boolean"], function () { -c$ = Clazz.decorateAsClass (function () { -this.abovePIDThreshold = false; -this.charHeight = 0; -this.charWidth = 0; -this.idWidth = -1; -this.colourAppliesToAllGroups = false; -this.centreColumnLabels = false; -this.showdbrefs = false; -this.shownpfeats = false; -this.colourByReferenceSeq = false; -this.conservationColourSelected = false; -this.displayReferenceSeq = false; -this.increment = 0; -this.renderGaps = true; -this.rightAlignIds = false; -this.scaleAboveWrapped = false; -this.scaleLeftWrapped = true; -this.scaleRightWrapped = true; -this.seqNameItalics = false; -this.showAnnotation = true; -this.showBoxes = true; -this.showColourText = false; -this.showHiddenMarkers = true; -this.showJVSuffix = true; -this.showSeqFeaturesHeight = false; -this.showSequenceFeatures = false; -this.showText = true; -this.showUnconserved = false; -this.textColour = null; -this.textColour2 = null; -this.threshold = 0; -this.thresholdTextColour = 0; -this.upperCasebold = false; -this.fontName = null; -this.fontSize = 0; -this.scaleProteinAsCdna = true; -this.wrapAlignment = false; -this.wrappedWidth = 0; -this.fontStyle = 0; -Clazz.instantialize (this, arguments); -}, jalview.viewmodel.styles, "ViewStyle", null, jalview.api.ViewStyleI); -Clazz.prepareFields (c$, function () { -this.textColour = java.awt.Color.black; -this.textColour2 = java.awt.Color.white; -}); -Clazz.makeConstructor (c$, -function (vs) { -this.setAbovePIDThreshold (vs.getAbovePIDThreshold ()); -this.setCentreColumnLabels (vs.isCentreColumnLabels ()); -this.setCharHeight (vs.getCharHeight ()); -this.setCharWidth (vs.getCharWidth ()); -this.setColourAppliesToAllGroups (vs.getColourAppliesToAllGroups ()); -this.setColourByReferenceSeq (vs.isColourByReferenceSeq ()); -this.setColourText (vs.getColourText ()); -this.setConservationColourSelected (vs.isConservationColourSelected ()); -this.setConservationSelected (vs.getConservationSelected ()); -this.setDisplayReferenceSeq (vs.isDisplayReferenceSeq ()); -this.setFontName (vs.getFontName ()); -this.setFontSize (vs.getFontSize ()); -this.setFontStyle (vs.getFontStyle ()); -this.setIdWidth (vs.getIdWidth ()); -this.setIncrement (vs.getIncrement ()); -this.setRenderGaps (vs.isRenderGaps ()); -this.setRightAlignIds (vs.isRightAlignIds ()); -this.setScaleAboveWrapped (vs.getScaleAboveWrapped ()); -this.setScaleLeftWrapped (vs.getScaleLeftWrapped ()); -this.setScaleProteinAsCdna (vs.isScaleProteinAsCdna ()); -this.setScaleRightWrapped (vs.getScaleRightWrapped ()); -this.setSeqNameItalics (vs.isSeqNameItalics ()); -this.setShowAnnotation (vs.isShowAnnotation ()); -this.setShowBoxes (vs.getShowBoxes ()); -this.setShowColourText (vs.isShowColourText ()); -this.setShowDBRefs (vs.isShowDBRefs ()); -this.setShowHiddenMarkers (vs.getShowHiddenMarkers ()); -this.setShowJVSuffix (vs.getShowJVSuffix ()); -this.setShowNPFeats (vs.isShowNPFeats ()); -this.setShowSequenceFeaturesHeight (vs.isShowSequenceFeaturesHeight ()); -this.setShowSequenceFeatures (vs.isShowSequenceFeatures ()); -this.setShowText (vs.getShowText ()); -this.setShowUnconserved (vs.getShowUnconserved ()); -this.setTextColour (vs.getTextColour ()); -this.setTextColour2 (vs.getTextColour2 ()); -this.setThreshold (vs.getThreshold ()); -this.setThresholdTextColour (vs.getThresholdTextColour ()); -this.setUpperCasebold (vs.isUpperCasebold ()); -this.setWrapAlignment (vs.getWrapAlignment ()); -this.setWrappedWidth (vs.getWrappedWidth ()); -}, "jalview.api.ViewStyleI"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.overrideMethod (c$, "equals", -function (other) { -if (other == null || !(Clazz.instanceOf (other, jalview.viewmodel.styles.ViewStyle))) { -return false; -}var vs = other; -var match = (this.getAbovePIDThreshold () == vs.getAbovePIDThreshold () && this.isCentreColumnLabels () == vs.isCentreColumnLabels () && this.getCharHeight () == vs.getCharHeight () && this.getCharWidth () == vs.getCharWidth () && this.getColourAppliesToAllGroups () == vs.getColourAppliesToAllGroups () && this.isColourByReferenceSeq () == vs.isColourByReferenceSeq () && this.getColourText () == vs.getColourText () && this.isConservationColourSelected () == vs.isConservationColourSelected () && this.getConservationSelected () == vs.getConservationSelected () && this.isDisplayReferenceSeq () == vs.isDisplayReferenceSeq () && this.getFontSize () == vs.getFontSize () && this.getFontStyle () == vs.getFontStyle () && this.getIdWidth () == vs.getIdWidth () && this.getIncrement () == vs.getIncrement () && this.isRenderGaps () == vs.isRenderGaps () && this.isRightAlignIds () == vs.isRightAlignIds () && this.getScaleAboveWrapped () == vs.getScaleAboveWrapped () && this.getScaleLeftWrapped () == vs.getScaleLeftWrapped () && this.isScaleProteinAsCdna () == vs.isScaleProteinAsCdna () && this.getScaleRightWrapped () == vs.getScaleRightWrapped () && this.isSeqNameItalics () == vs.isSeqNameItalics () && this.isShowAnnotation () == vs.isShowAnnotation () && this.getShowBoxes () == vs.getShowBoxes () && this.isShowColourText () == vs.isShowColourText () && this.isShowDBRefs () == vs.isShowDBRefs () && this.getShowHiddenMarkers () == vs.getShowHiddenMarkers () && this.getShowJVSuffix () == vs.getShowJVSuffix () && this.isShowNPFeats () == vs.isShowNPFeats () && this.isShowSequenceFeaturesHeight () == vs.isShowSequenceFeaturesHeight () && this.isShowSequenceFeatures () == vs.isShowSequenceFeatures () && this.getShowText () == vs.getShowText () && this.getShowUnconserved () == vs.getShowUnconserved () && this.getThreshold () == vs.getThreshold () && this.getThresholdTextColour () == vs.getThresholdTextColour () && this.isUpperCasebold () == vs.isUpperCasebold () && this.getWrapAlignment () == vs.getWrapAlignment () && this.getWrappedWidth () == vs.getWrappedWidth ()); -match = match && String.valueOf (this.getFontName ()).equals (String.valueOf (vs.getFontName ())); -match = match && String.valueOf (this.getTextColour ()).equals (String.valueOf (vs.getTextColour ())); -match = match && String.valueOf (this.getTextColour2 ()).equals (String.valueOf (vs.getTextColour2 ())); -return match; -}, "~O"); -Clazz.overrideMethod (c$, "hashCode", -function () { -var hash = 0; -var m = 1; -hash += m++ * Boolean.$valueOf (this.abovePIDThreshold).hashCode (); -hash += m++ * Boolean.$valueOf (this.centreColumnLabels).hashCode (); -hash += m++ * Boolean.$valueOf (this.colourAppliesToAllGroups).hashCode (); -hash += m++ * Boolean.$valueOf (this.displayReferenceSeq).hashCode (); -hash += m++ * Boolean.$valueOf (this.renderGaps).hashCode (); -hash += m++ * Boolean.$valueOf (this.rightAlignIds).hashCode (); -hash += m++ * Boolean.$valueOf (this.scaleProteinAsCdna).hashCode (); -hash += m++ * Boolean.$valueOf (this.scaleRightWrapped).hashCode (); -hash += m++ * Boolean.$valueOf (this.seqNameItalics).hashCode (); -hash += m++ * Boolean.$valueOf (this.showAnnotation).hashCode (); -hash += m++ * Boolean.$valueOf (this.showBoxes).hashCode (); -hash += m++ * Boolean.$valueOf (this.showdbrefs).hashCode (); -hash += m++ * Boolean.$valueOf (this.showJVSuffix).hashCode (); -hash += m++ * Boolean.$valueOf (this.showSequenceFeatures).hashCode (); -hash += m++ * Boolean.$valueOf (this.showUnconserved).hashCode (); -hash += m++ * Boolean.$valueOf (this.wrapAlignment).hashCode (); -hash += m++ * this.charHeight; -hash += m++ * this.charWidth; -hash += m++ * this.fontSize; -hash += m++ * this.fontStyle; -hash += m++ * this.idWidth; -hash += String.valueOf (this.fontName).hashCode (); -return hash; -}); -Clazz.defineMethod (c$, "isUpperCasebold", -function () { -return this.upperCasebold; -}); -Clazz.overrideMethod (c$, "setUpperCasebold", -function (upperCasebold) { -this.upperCasebold = upperCasebold; -}, "~B"); -Clazz.defineMethod (c$, "getAbovePIDThreshold", -function () { -return this.abovePIDThreshold; -}); -Clazz.defineMethod (c$, "getCharHeight", -function () { -return this.charHeight; -}); -Clazz.defineMethod (c$, "getCharWidth", -function () { -return this.charWidth; -}); -Clazz.defineMethod (c$, "getColourAppliesToAllGroups", -function () { -return this.colourAppliesToAllGroups; -}); -Clazz.defineMethod (c$, "getColourText", -function () { -return this.showColourText; -}); -Clazz.defineMethod (c$, "getConservationSelected", -function () { -return this.conservationColourSelected; -}); -Clazz.defineMethod (c$, "getIncrement", -function () { -return this.increment; -}); -Clazz.defineMethod (c$, "getScaleAboveWrapped", -function () { -return this.scaleAboveWrapped; -}); -Clazz.defineMethod (c$, "getScaleLeftWrapped", -function () { -return this.scaleLeftWrapped; -}); -Clazz.defineMethod (c$, "getScaleRightWrapped", -function () { -return this.scaleRightWrapped; -}); -Clazz.defineMethod (c$, "getShowBoxes", -function () { -return this.showBoxes; -}); -Clazz.defineMethod (c$, "getShowHiddenMarkers", -function () { -return this.showHiddenMarkers; -}); -Clazz.defineMethod (c$, "getShowJVSuffix", -function () { -return this.showJVSuffix; -}); -Clazz.defineMethod (c$, "getShowText", -function () { -return this.showText; -}); -Clazz.defineMethod (c$, "getShowUnconserved", -function () { -return this.showUnconserved; -}); -Clazz.defineMethod (c$, "getTextColour", -function () { -return this.textColour; -}); -Clazz.defineMethod (c$, "getTextColour2", -function () { -return this.textColour2; -}); -Clazz.defineMethod (c$, "getThreshold", -function () { -return this.threshold; -}); -Clazz.defineMethod (c$, "getThresholdTextColour", -function () { -return this.thresholdTextColour; -}); -Clazz.defineMethod (c$, "getWrapAlignment", -function () { -return this.wrapAlignment; -}); -Clazz.defineMethod (c$, "getWrappedWidth", -function () { -return this.wrappedWidth; -}); -Clazz.defineMethod (c$, "isColourByReferenceSeq", -function () { -return this.colourByReferenceSeq; -}); -Clazz.defineMethod (c$, "isConservationColourSelected", -function () { -return this.conservationColourSelected; -}); -Clazz.defineMethod (c$, "isDisplayReferenceSeq", -function () { -return this.displayReferenceSeq; -}); -Clazz.defineMethod (c$, "isRenderGaps", -function () { -return this.renderGaps; -}); -Clazz.defineMethod (c$, "isRightAlignIds", -function () { -return this.rightAlignIds; -}); -Clazz.defineMethod (c$, "isSeqNameItalics", -function () { -return this.seqNameItalics; -}); -Clazz.defineMethod (c$, "isShowAnnotation", -function () { -return this.showAnnotation; -}); -Clazz.defineMethod (c$, "isShowColourText", -function () { -return this.showColourText; -}); -Clazz.defineMethod (c$, "isShowSequenceFeaturesHeight", -function () { -return this.showSeqFeaturesHeight; -}); -Clazz.defineMethod (c$, "isShowSequenceFeatures", -function () { -return this.showSequenceFeatures; -}); -Clazz.overrideMethod (c$, "setAbovePIDThreshold", -function (b) { -this.abovePIDThreshold = b; -}, "~B"); -Clazz.overrideMethod (c$, "setCharHeight", -function (h) { -this.charHeight = h; -}, "~N"); -Clazz.overrideMethod (c$, "setCharWidth", -function (w) { -this.charWidth = w; -}, "~N"); -Clazz.overrideMethod (c$, "setColourAppliesToAllGroups", -function (b) { -this.colourAppliesToAllGroups = b; -}, "~B"); -Clazz.overrideMethod (c$, "setColourByReferenceSeq", -function (colourByReferenceSeq) { -this.colourByReferenceSeq = colourByReferenceSeq; -}, "~B"); -Clazz.overrideMethod (c$, "setColourText", -function (state) { -this.showColourText = state; -}, "~B"); -Clazz.overrideMethod (c$, "setConservationColourSelected", -function (conservationColourSelected) { -this.conservationColourSelected = conservationColourSelected; -}, "~B"); -Clazz.overrideMethod (c$, "setConservationSelected", -function (b) { -this.conservationColourSelected = b; -}, "~B"); -Clazz.overrideMethod (c$, "setDisplayReferenceSeq", -function (displayReferenceSeq) { -this.displayReferenceSeq = displayReferenceSeq; -}, "~B"); -Clazz.overrideMethod (c$, "setIncrement", -function (inc) { -this.increment = inc; -}, "~N"); -Clazz.overrideMethod (c$, "setRenderGaps", -function (state) { -this.renderGaps = state; -}, "~B"); -Clazz.overrideMethod (c$, "setRightAlignIds", -function (rightAlignIds) { -this.rightAlignIds = rightAlignIds; -}, "~B"); -Clazz.overrideMethod (c$, "setScaleAboveWrapped", -function (b) { -this.scaleAboveWrapped = b; -}, "~B"); -Clazz.overrideMethod (c$, "setScaleLeftWrapped", -function (b) { -this.scaleLeftWrapped = b; -}, "~B"); -Clazz.overrideMethod (c$, "setScaleRightWrapped", -function (b) { -this.scaleRightWrapped = b; -}, "~B"); -Clazz.overrideMethod (c$, "setSeqNameItalics", -function (italics) { -this.seqNameItalics = italics; -}, "~B"); -Clazz.overrideMethod (c$, "setShowAnnotation", -function (b) { -this.showAnnotation = b; -}, "~B"); -Clazz.overrideMethod (c$, "setShowBoxes", -function (state) { -this.showBoxes = state; -}, "~B"); -Clazz.overrideMethod (c$, "setShowColourText", -function (showColourText) { -this.showColourText = showColourText; -}, "~B"); -Clazz.overrideMethod (c$, "setShowHiddenMarkers", -function (show) { -this.showHiddenMarkers = show; -}, "~B"); -Clazz.overrideMethod (c$, "setShowJVSuffix", -function (b) { -this.showJVSuffix = b; -}, "~B"); -Clazz.overrideMethod (c$, "setShowSequenceFeaturesHeight", -function (selected) { -this.showSeqFeaturesHeight = selected; -}, "~B"); -Clazz.overrideMethod (c$, "setShowSequenceFeatures", -function (b) { -this.showSequenceFeatures = b; -}, "~B"); -Clazz.overrideMethod (c$, "setShowText", -function (state) { -this.showText = state; -}, "~B"); -Clazz.overrideMethod (c$, "setShowUnconserved", -function (showunconserved) { -this.showUnconserved = showunconserved; -}, "~B"); -Clazz.overrideMethod (c$, "setTextColour", -function (textColour) { -this.textColour = textColour; -}, "java.awt.Color"); -Clazz.overrideMethod (c$, "setTextColour2", -function (textColour2) { -this.textColour2 = textColour2; -}, "java.awt.Color"); -Clazz.overrideMethod (c$, "setThreshold", -function (thresh) { -this.threshold = thresh; -}, "~N"); -Clazz.overrideMethod (c$, "setThresholdTextColour", -function (thresholdTextColour) { -this.thresholdTextColour = thresholdTextColour; -}, "~N"); -Clazz.overrideMethod (c$, "setWrapAlignment", -function (state) { -this.wrapAlignment = state; -}, "~B"); -Clazz.overrideMethod (c$, "setWrappedWidth", -function (w) { -this.wrappedWidth = w; -}, "~N"); -Clazz.overrideMethod (c$, "sameStyle", -function (that) { -return this.equals (that); -}, "jalview.api.ViewStyleI"); -Clazz.defineMethod (c$, "getFontName", -function () { -return this.fontName; -}); -Clazz.defineMethod (c$, "getFontSize", -function () { -return this.fontSize; -}); -Clazz.defineMethod (c$, "getFontStyle", -function () { -return this.fontStyle; -}); -Clazz.overrideMethod (c$, "setFontName", -function (name) { -this.fontName = name; -}, "~S"); -Clazz.overrideMethod (c$, "setFontSize", -function (size) { -this.fontSize = size; -}, "~N"); -Clazz.overrideMethod (c$, "setFontStyle", -function (style) { -this.fontStyle = style; -}, "~N"); -Clazz.defineMethod (c$, "getIdWidth", -function () { -return this.idWidth; -}); -Clazz.overrideMethod (c$, "setIdWidth", -function (idWidth) { -this.idWidth = idWidth; -}, "~N"); -Clazz.defineMethod (c$, "isCentreColumnLabels", -function () { -return this.centreColumnLabels; -}); -Clazz.overrideMethod (c$, "setCentreColumnLabels", -function (centreColumnLabels) { -this.centreColumnLabels = centreColumnLabels; -}, "~B"); -Clazz.defineMethod (c$, "isShowDBRefs", -function () { -return this.showdbrefs; -}); -Clazz.overrideMethod (c$, "setShowDBRefs", -function (showdbrefs) { -this.showdbrefs = showdbrefs; -}, "~B"); -Clazz.defineMethod (c$, "isShowNPFeats", -function () { -return this.shownpfeats; -}); -Clazz.overrideMethod (c$, "setShowNPFeats", -function (shownpfeats) { -this.shownpfeats = shownpfeats; -}, "~B"); -Clazz.defineMethod (c$, "isScaleProteinAsCdna", -function () { -return this.scaleProteinAsCdna; -}); -Clazz.overrideMethod (c$, "setScaleProteinAsCdna", -function (b) { -this.scaleProteinAsCdna = b; -}, "~B"); -}); +Clazz.declarePackage ("jalview.viewmodel.styles"); +Clazz.load (["jalview.api.ViewStyleI", "java.awt.Color"], "jalview.viewmodel.styles.ViewStyle", ["java.lang.Boolean"], function () { +c$ = Clazz.decorateAsClass (function () { +this.abovePIDThreshold = false; +this.charHeight = 0; +this.charWidth = 0; +this.idWidth = -1; +this.colourAppliesToAllGroups = false; +this.centreColumnLabels = false; +this.showdbrefs = false; +this.shownpfeats = false; +this.colourByReferenceSeq = false; +this.conservationColourSelected = false; +this.displayReferenceSeq = false; +this.increment = 0; +this.renderGaps = true; +this.rightAlignIds = false; +this.scaleAboveWrapped = false; +this.scaleLeftWrapped = true; +this.scaleRightWrapped = true; +this.seqNameItalics = false; +this.showAnnotation = true; +this.showBoxes = true; +this.showColourText = false; +this.showHiddenMarkers = true; +this.showJVSuffix = true; +this.showSeqFeaturesHeight = false; +this.showSequenceFeatures = false; +this.showText = true; +this.showUnconserved = false; +this.textColour = null; +this.textColour2 = null; +this.threshold = 0; +this.thresholdTextColour = 0; +this.upperCasebold = false; +this.fontName = null; +this.fontSize = 0; +this.scaleProteinAsCdna = true; +this.wrapAlignment = false; +this.wrappedWidth = 0; +this.fontStyle = 0; +Clazz.instantialize (this, arguments); +}, jalview.viewmodel.styles, "ViewStyle", null, jalview.api.ViewStyleI); +Clazz.prepareFields (c$, function () { +this.textColour = java.awt.Color.black; +this.textColour2 = java.awt.Color.white; +}); +Clazz.makeConstructor (c$, +function (vs) { +this.setAbovePIDThreshold (vs.getAbovePIDThreshold ()); +this.setCentreColumnLabels (vs.isCentreColumnLabels ()); +this.setCharHeight (vs.getCharHeight ()); +this.setCharWidth (vs.getCharWidth ()); +this.setColourAppliesToAllGroups (vs.getColourAppliesToAllGroups ()); +this.setColourByReferenceSeq (vs.isColourByReferenceSeq ()); +this.setColourText (vs.getColourText ()); +this.setConservationColourSelected (vs.isConservationColourSelected ()); +this.setConservationSelected (vs.getConservationSelected ()); +this.setDisplayReferenceSeq (vs.isDisplayReferenceSeq ()); +this.setFontName (vs.getFontName ()); +this.setFontSize (vs.getFontSize ()); +this.setFontStyle (vs.getFontStyle ()); +this.setIdWidth (vs.getIdWidth ()); +this.setIncrement (vs.getIncrement ()); +this.setRenderGaps (vs.isRenderGaps ()); +this.setRightAlignIds (vs.isRightAlignIds ()); +this.setScaleAboveWrapped (vs.getScaleAboveWrapped ()); +this.setScaleLeftWrapped (vs.getScaleLeftWrapped ()); +this.setScaleProteinAsCdna (vs.isScaleProteinAsCdna ()); +this.setScaleRightWrapped (vs.getScaleRightWrapped ()); +this.setSeqNameItalics (vs.isSeqNameItalics ()); +this.setShowAnnotation (vs.isShowAnnotation ()); +this.setShowBoxes (vs.getShowBoxes ()); +this.setShowColourText (vs.isShowColourText ()); +this.setShowDBRefs (vs.isShowDBRefs ()); +this.setShowHiddenMarkers (vs.getShowHiddenMarkers ()); +this.setShowJVSuffix (vs.getShowJVSuffix ()); +this.setShowNPFeats (vs.isShowNPFeats ()); +this.setShowSequenceFeaturesHeight (vs.isShowSequenceFeaturesHeight ()); +this.setShowSequenceFeatures (vs.isShowSequenceFeatures ()); +this.setShowText (vs.getShowText ()); +this.setShowUnconserved (vs.getShowUnconserved ()); +this.setTextColour (vs.getTextColour ()); +this.setTextColour2 (vs.getTextColour2 ()); +this.setThreshold (vs.getThreshold ()); +this.setThresholdTextColour (vs.getThresholdTextColour ()); +this.setUpperCasebold (vs.isUpperCasebold ()); +this.setWrapAlignment (vs.getWrapAlignment ()); +this.setWrappedWidth (vs.getWrappedWidth ()); +}, "jalview.api.ViewStyleI"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.overrideMethod (c$, "equals", +function (other) { +if (other == null || !(Clazz.instanceOf (other, jalview.viewmodel.styles.ViewStyle))) { +return false; +}var vs = other; +var match = (this.getAbovePIDThreshold () == vs.getAbovePIDThreshold () && this.isCentreColumnLabels () == vs.isCentreColumnLabels () && this.getCharHeight () == vs.getCharHeight () && this.getCharWidth () == vs.getCharWidth () && this.getColourAppliesToAllGroups () == vs.getColourAppliesToAllGroups () && this.isColourByReferenceSeq () == vs.isColourByReferenceSeq () && this.getColourText () == vs.getColourText () && this.isConservationColourSelected () == vs.isConservationColourSelected () && this.getConservationSelected () == vs.getConservationSelected () && this.isDisplayReferenceSeq () == vs.isDisplayReferenceSeq () && this.getFontSize () == vs.getFontSize () && this.getFontStyle () == vs.getFontStyle () && this.getIdWidth () == vs.getIdWidth () && this.getIncrement () == vs.getIncrement () && this.isRenderGaps () == vs.isRenderGaps () && this.isRightAlignIds () == vs.isRightAlignIds () && this.getScaleAboveWrapped () == vs.getScaleAboveWrapped () && this.getScaleLeftWrapped () == vs.getScaleLeftWrapped () && this.isScaleProteinAsCdna () == vs.isScaleProteinAsCdna () && this.getScaleRightWrapped () == vs.getScaleRightWrapped () && this.isSeqNameItalics () == vs.isSeqNameItalics () && this.isShowAnnotation () == vs.isShowAnnotation () && this.getShowBoxes () == vs.getShowBoxes () && this.isShowColourText () == vs.isShowColourText () && this.isShowDBRefs () == vs.isShowDBRefs () && this.getShowHiddenMarkers () == vs.getShowHiddenMarkers () && this.getShowJVSuffix () == vs.getShowJVSuffix () && this.isShowNPFeats () == vs.isShowNPFeats () && this.isShowSequenceFeaturesHeight () == vs.isShowSequenceFeaturesHeight () && this.isShowSequenceFeatures () == vs.isShowSequenceFeatures () && this.getShowText () == vs.getShowText () && this.getShowUnconserved () == vs.getShowUnconserved () && this.getThreshold () == vs.getThreshold () && this.getThresholdTextColour () == vs.getThresholdTextColour () && this.isUpperCasebold () == vs.isUpperCasebold () && this.getWrapAlignment () == vs.getWrapAlignment () && this.getWrappedWidth () == vs.getWrappedWidth ()); +match = match && String.valueOf (this.getFontName ()).equals (String.valueOf (vs.getFontName ())); +match = match && String.valueOf (this.getTextColour ()).equals (String.valueOf (vs.getTextColour ())); +match = match && String.valueOf (this.getTextColour2 ()).equals (String.valueOf (vs.getTextColour2 ())); +return match; +}, "~O"); +Clazz.overrideMethod (c$, "hashCode", +function () { +var hash = 0; +var m = 1; +hash += m++ * Boolean.$valueOf (this.abovePIDThreshold).hashCode (); +hash += m++ * Boolean.$valueOf (this.centreColumnLabels).hashCode (); +hash += m++ * Boolean.$valueOf (this.colourAppliesToAllGroups).hashCode (); +hash += m++ * Boolean.$valueOf (this.displayReferenceSeq).hashCode (); +hash += m++ * Boolean.$valueOf (this.renderGaps).hashCode (); +hash += m++ * Boolean.$valueOf (this.rightAlignIds).hashCode (); +hash += m++ * Boolean.$valueOf (this.scaleProteinAsCdna).hashCode (); +hash += m++ * Boolean.$valueOf (this.scaleRightWrapped).hashCode (); +hash += m++ * Boolean.$valueOf (this.seqNameItalics).hashCode (); +hash += m++ * Boolean.$valueOf (this.showAnnotation).hashCode (); +hash += m++ * Boolean.$valueOf (this.showBoxes).hashCode (); +hash += m++ * Boolean.$valueOf (this.showdbrefs).hashCode (); +hash += m++ * Boolean.$valueOf (this.showJVSuffix).hashCode (); +hash += m++ * Boolean.$valueOf (this.showSequenceFeatures).hashCode (); +hash += m++ * Boolean.$valueOf (this.showUnconserved).hashCode (); +hash += m++ * Boolean.$valueOf (this.wrapAlignment).hashCode (); +hash += m++ * this.charHeight; +hash += m++ * this.charWidth; +hash += m++ * this.fontSize; +hash += m++ * this.fontStyle; +hash += m++ * this.idWidth; +hash += String.valueOf (this.fontName).hashCode (); +return hash; +}); +Clazz.defineMethod (c$, "isUpperCasebold", +function () { +return this.upperCasebold; +}); +Clazz.overrideMethod (c$, "setUpperCasebold", +function (upperCasebold) { +this.upperCasebold = upperCasebold; +}, "~B"); +Clazz.defineMethod (c$, "getAbovePIDThreshold", +function () { +return this.abovePIDThreshold; +}); +Clazz.defineMethod (c$, "getCharHeight", +function () { +return this.charHeight; +}); +Clazz.defineMethod (c$, "getCharWidth", +function () { +return this.charWidth; +}); +Clazz.defineMethod (c$, "getColourAppliesToAllGroups", +function () { +return this.colourAppliesToAllGroups; +}); +Clazz.defineMethod (c$, "getColourText", +function () { +return this.showColourText; +}); +Clazz.defineMethod (c$, "getConservationSelected", +function () { +return this.conservationColourSelected; +}); +Clazz.defineMethod (c$, "getIncrement", +function () { +return this.increment; +}); +Clazz.defineMethod (c$, "getScaleAboveWrapped", +function () { +return this.scaleAboveWrapped; +}); +Clazz.defineMethod (c$, "getScaleLeftWrapped", +function () { +return this.scaleLeftWrapped; +}); +Clazz.defineMethod (c$, "getScaleRightWrapped", +function () { +return this.scaleRightWrapped; +}); +Clazz.defineMethod (c$, "getShowBoxes", +function () { +return this.showBoxes; +}); +Clazz.defineMethod (c$, "getShowHiddenMarkers", +function () { +return this.showHiddenMarkers; +}); +Clazz.defineMethod (c$, "getShowJVSuffix", +function () { +return this.showJVSuffix; +}); +Clazz.defineMethod (c$, "getShowText", +function () { +return this.showText; +}); +Clazz.defineMethod (c$, "getShowUnconserved", +function () { +return this.showUnconserved; +}); +Clazz.defineMethod (c$, "getTextColour", +function () { +return this.textColour; +}); +Clazz.defineMethod (c$, "getTextColour2", +function () { +return this.textColour2; +}); +Clazz.defineMethod (c$, "getThreshold", +function () { +return this.threshold; +}); +Clazz.defineMethod (c$, "getThresholdTextColour", +function () { +return this.thresholdTextColour; +}); +Clazz.defineMethod (c$, "getWrapAlignment", +function () { +return this.wrapAlignment; +}); +Clazz.defineMethod (c$, "getWrappedWidth", +function () { +return this.wrappedWidth; +}); +Clazz.defineMethod (c$, "isColourByReferenceSeq", +function () { +return this.colourByReferenceSeq; +}); +Clazz.defineMethod (c$, "isConservationColourSelected", +function () { +return this.conservationColourSelected; +}); +Clazz.defineMethod (c$, "isDisplayReferenceSeq", +function () { +return this.displayReferenceSeq; +}); +Clazz.defineMethod (c$, "isRenderGaps", +function () { +return this.renderGaps; +}); +Clazz.defineMethod (c$, "isRightAlignIds", +function () { +return this.rightAlignIds; +}); +Clazz.defineMethod (c$, "isSeqNameItalics", +function () { +return this.seqNameItalics; +}); +Clazz.defineMethod (c$, "isShowAnnotation", +function () { +return this.showAnnotation; +}); +Clazz.defineMethod (c$, "isShowColourText", +function () { +return this.showColourText; +}); +Clazz.defineMethod (c$, "isShowSequenceFeaturesHeight", +function () { +return this.showSeqFeaturesHeight; +}); +Clazz.defineMethod (c$, "isShowSequenceFeatures", +function () { +return this.showSequenceFeatures; +}); +Clazz.overrideMethod (c$, "setAbovePIDThreshold", +function (b) { +this.abovePIDThreshold = b; +}, "~B"); +Clazz.overrideMethod (c$, "setCharHeight", +function (h) { +this.charHeight = h; +}, "~N"); +Clazz.overrideMethod (c$, "setCharWidth", +function (w) { +this.charWidth = w; +}, "~N"); +Clazz.overrideMethod (c$, "setColourAppliesToAllGroups", +function (b) { +this.colourAppliesToAllGroups = b; +}, "~B"); +Clazz.overrideMethod (c$, "setColourByReferenceSeq", +function (colourByReferenceSeq) { +this.colourByReferenceSeq = colourByReferenceSeq; +}, "~B"); +Clazz.overrideMethod (c$, "setColourText", +function (state) { +this.showColourText = state; +}, "~B"); +Clazz.overrideMethod (c$, "setConservationColourSelected", +function (conservationColourSelected) { +this.conservationColourSelected = conservationColourSelected; +}, "~B"); +Clazz.overrideMethod (c$, "setConservationSelected", +function (b) { +this.conservationColourSelected = b; +}, "~B"); +Clazz.overrideMethod (c$, "setDisplayReferenceSeq", +function (displayReferenceSeq) { +this.displayReferenceSeq = displayReferenceSeq; +}, "~B"); +Clazz.overrideMethod (c$, "setIncrement", +function (inc) { +this.increment = inc; +}, "~N"); +Clazz.overrideMethod (c$, "setRenderGaps", +function (state) { +this.renderGaps = state; +}, "~B"); +Clazz.overrideMethod (c$, "setRightAlignIds", +function (rightAlignIds) { +this.rightAlignIds = rightAlignIds; +}, "~B"); +Clazz.overrideMethod (c$, "setScaleAboveWrapped", +function (b) { +this.scaleAboveWrapped = b; +}, "~B"); +Clazz.overrideMethod (c$, "setScaleLeftWrapped", +function (b) { +this.scaleLeftWrapped = b; +}, "~B"); +Clazz.overrideMethod (c$, "setScaleRightWrapped", +function (b) { +this.scaleRightWrapped = b; +}, "~B"); +Clazz.overrideMethod (c$, "setSeqNameItalics", +function (italics) { +this.seqNameItalics = italics; +}, "~B"); +Clazz.overrideMethod (c$, "setShowAnnotation", +function (b) { +this.showAnnotation = b; +}, "~B"); +Clazz.overrideMethod (c$, "setShowBoxes", +function (state) { +this.showBoxes = state; +}, "~B"); +Clazz.overrideMethod (c$, "setShowColourText", +function (showColourText) { +this.showColourText = showColourText; +}, "~B"); +Clazz.overrideMethod (c$, "setShowHiddenMarkers", +function (show) { +this.showHiddenMarkers = show; +}, "~B"); +Clazz.overrideMethod (c$, "setShowJVSuffix", +function (b) { +this.showJVSuffix = b; +}, "~B"); +Clazz.overrideMethod (c$, "setShowSequenceFeaturesHeight", +function (selected) { +this.showSeqFeaturesHeight = selected; +}, "~B"); +Clazz.overrideMethod (c$, "setShowSequenceFeatures", +function (b) { +this.showSequenceFeatures = b; +}, "~B"); +Clazz.overrideMethod (c$, "setShowText", +function (state) { +this.showText = state; +}, "~B"); +Clazz.overrideMethod (c$, "setShowUnconserved", +function (showunconserved) { +this.showUnconserved = showunconserved; +}, "~B"); +Clazz.overrideMethod (c$, "setTextColour", +function (textColour) { +this.textColour = textColour; +}, "java.awt.Color"); +Clazz.overrideMethod (c$, "setTextColour2", +function (textColour2) { +this.textColour2 = textColour2; +}, "java.awt.Color"); +Clazz.overrideMethod (c$, "setThreshold", +function (thresh) { +this.threshold = thresh; +}, "~N"); +Clazz.overrideMethod (c$, "setThresholdTextColour", +function (thresholdTextColour) { +this.thresholdTextColour = thresholdTextColour; +}, "~N"); +Clazz.overrideMethod (c$, "setWrapAlignment", +function (state) { +this.wrapAlignment = state; +}, "~B"); +Clazz.overrideMethod (c$, "setWrappedWidth", +function (w) { +this.wrappedWidth = w; +}, "~N"); +Clazz.overrideMethod (c$, "sameStyle", +function (that) { +return this.equals (that); +}, "jalview.api.ViewStyleI"); +Clazz.defineMethod (c$, "getFontName", +function () { +return this.fontName; +}); +Clazz.defineMethod (c$, "getFontSize", +function () { +return this.fontSize; +}); +Clazz.defineMethod (c$, "getFontStyle", +function () { +return this.fontStyle; +}); +Clazz.overrideMethod (c$, "setFontName", +function (name) { +this.fontName = name; +}, "~S"); +Clazz.overrideMethod (c$, "setFontSize", +function (size) { +this.fontSize = size; +}, "~N"); +Clazz.overrideMethod (c$, "setFontStyle", +function (style) { +this.fontStyle = style; +}, "~N"); +Clazz.defineMethod (c$, "getIdWidth", +function () { +return this.idWidth; +}); +Clazz.overrideMethod (c$, "setIdWidth", +function (idWidth) { +this.idWidth = idWidth; +}, "~N"); +Clazz.defineMethod (c$, "isCentreColumnLabels", +function () { +return this.centreColumnLabels; +}); +Clazz.overrideMethod (c$, "setCentreColumnLabels", +function (centreColumnLabels) { +this.centreColumnLabels = centreColumnLabels; +}, "~B"); +Clazz.defineMethod (c$, "isShowDBRefs", +function () { +return this.showdbrefs; +}); +Clazz.overrideMethod (c$, "setShowDBRefs", +function (showdbrefs) { +this.showdbrefs = showdbrefs; +}, "~B"); +Clazz.defineMethod (c$, "isShowNPFeats", +function () { +return this.shownpfeats; +}); +Clazz.overrideMethod (c$, "setShowNPFeats", +function (shownpfeats) { +this.shownpfeats = shownpfeats; +}, "~B"); +Clazz.defineMethod (c$, "isScaleProteinAsCdna", +function () { +return this.scaleProteinAsCdna; +}); +Clazz.overrideMethod (c$, "setScaleProteinAsCdna", +function (b) { +this.scaleProteinAsCdna = b; +}, "~B"); +}); diff --git a/bin/jalview/workers/AlignCalcManager.js b/bin/jalview/workers/AlignCalcManager.js index 7f25a9c..39105f8 100644 --- a/bin/jalview/workers/AlignCalcManager.js +++ b/bin/jalview/workers/AlignCalcManager.js @@ -1,192 +1,192 @@ -Clazz.declarePackage ("jalview.workers"); -Clazz.load (["jalview.api.AlignCalcManagerI", "java.util.ArrayList", "$.Collections", "$.HashSet", "$.Hashtable"], "jalview.workers.AlignCalcManager", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.restartable = null; -this.blackList = null; -this.inProgress = null; -this.updating = null; -this.canUpdate = null; -Clazz.instantialize (this, arguments); -}, jalview.workers, "AlignCalcManager", null, jalview.api.AlignCalcManagerI); -Clazz.prepareFields (c$, function () { -this.restartable = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); -this.blackList = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); -this.inProgress = java.util.Collections.synchronizedMap ( new java.util.Hashtable ()); -this.updating = java.util.Collections.synchronizedMap ( new java.util.Hashtable ()); -this.canUpdate = new java.util.HashSet (); -}); -Clazz.overrideMethod (c$, "notifyStart", -function (worker) { -{ -var upd = this.updating.get (worker.getClass ()); -if (upd == null) { -this.updating.put (worker.getClass (), upd = java.util.Collections.synchronizedList ( new java.util.ArrayList ())); -}{ -upd.add (worker); -}}}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "alreadyDoing", -function (worker) { -{ -return this.inProgress.containsKey (worker.getClass ()); -}}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "isPending", -function (workingClass) { -var upd; -{ -upd = this.updating.get (workingClass.getClass ()); -if (upd == null) { -return false; -}{ -if (upd.size () > 1) { -return true; -}}return false; -}}, "jalview.api.AlignCalcWorkerI"); -Clazz.defineMethod (c$, "numberLive", -function (worker) { -{ -var upd = this.updating.get (worker.getClass ()); -if (upd == null) { -return 0; -};return upd.size (); -}}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "notifyWorking", -function (worker) { -{ -if (this.inProgress.get (worker.getClass ()) != null) { -if (false) { -System.err.println ("Warning: Multiple workers are running of type " + worker.getClass ()); -}return false; -}this.inProgress.put (worker.getClass (), worker); -}return true; -}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "workerComplete", -function (worker) { -{ -this.inProgress.remove (worker.getClass ()); -var upd = this.updating.get (worker.getClass ()); -if (upd != null) { -{ -upd.remove (worker); -}this.canUpdate.add (worker); -}}}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "workerCannotRun", -function (worker) { -{ -this.blackList.add (worker.getClass ()); -}}, "jalview.api.AlignCalcWorkerI"); -Clazz.defineMethod (c$, "isBlackListed", -function (workerType) { -{ -return this.blackList.contains (workerType); -}}, "Class"); -Clazz.overrideMethod (c$, "startWorker", -function (worker) { -var workerAsThread = worker; -if (workerAsThread.isAlive ()) { -workerAsThread.interrupt (); -worker = worker.getNewWorker (); -}worker.setName (worker.getClass ().getName ()); -worker.start (); -}, "jalview.api.AlignCalcWorkerI"); -Clazz.defineMethod (c$, "isWorking", -function (worker) { -{ -return worker != null && this.inProgress.get (worker.getClass ()) === worker; -}}, "jalview.api.AlignCalcWorkerI"); -Clazz.defineMethod (c$, "isWorking", -function () { -{ -return this.inProgress.size () > 0; -}}); -Clazz.overrideMethod (c$, "registerWorker", -function (worker) { -{ -if (!this.restartable.contains (worker)) { -this.restartable.add (worker); -}this.startWorker (worker); -}}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "restartWorkers", -function () { -{ -for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { -this.startWorker (worker); -} -}}); -Clazz.overrideMethod (c$, "workingInvolvedWith", -function (alignmentAnnotation) { -{ -for (var worker, $worker = this.inProgress.values ().iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { -if (worker.involves (alignmentAnnotation)) { -return true; -}} -}{ -for (var workers, $workers = this.updating.values ().iterator (); $workers.hasNext () && ((workers = $workers.next ()) || true);) { -for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { -if (worker.involves (alignmentAnnotation)) { -return true; -}} -} -}return false; -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.overrideMethod (c$, "updateAnnotationFor", -function (workerClass) { -var workers; -{ -workers = this.canUpdate.toArray ( new Array (0)); -}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) { -if (workerClass.equals (worker.getClass ())) { -worker.updateAnnotation (); -}} -}, "Class"); -Clazz.overrideMethod (c$, "getRegisteredWorkersOfClass", -function (workerClass) { -var workingClass = new java.util.ArrayList (); -var workers; -{ -workers = this.canUpdate.toArray ( new Array (this.canUpdate.size ())); -}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) { -if (workerClass.equals (worker.getClass ())) { -workingClass.add (worker); -}} -return (workingClass.size () == 0) ? null : workingClass; -}, "Class"); -Clazz.overrideMethod (c$, "startRegisteredWorkersOfClass", -function (workerClass) { -var workers = this.getRegisteredWorkersOfClass (workerClass); -if (workers == null) { -return false; -}for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { -if (!this.isPending (worker)) { -this.startWorker (worker); -} else { -System.err.println ("Pending exists for " + workerClass); -}} -return true; -}, "Class"); -Clazz.overrideMethod (c$, "workerMayRun", -function (worker) { -{ -if (this.blackList.contains (worker.getClass ())) { -this.blackList.remove (worker.getClass ()); -}}}, "jalview.api.AlignCalcWorkerI"); -Clazz.overrideMethod (c$, "removeRegisteredWorkersOfClass", -function (typeToRemove) { -var workers = this.getRegisteredWorkersOfClass (typeToRemove); -var removable = new java.util.ArrayList (); -var toremovannot = new java.util.HashSet (); -{ -for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { -if (typeToRemove.equals (worker.getClass ())) { -removable.add (worker); -toremovannot.add (worker); -}} -this.restartable.removeAll (removable); -}{ -for (var worker, $worker = this.canUpdate.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { -if (typeToRemove.equals (worker.getClass ())) { -removable.add (worker); -toremovannot.add (worker); -}} -this.canUpdate.removeAll (removable); -}}, "Class"); -}); +Clazz.declarePackage ("jalview.workers"); +Clazz.load (["jalview.api.AlignCalcManagerI", "java.util.ArrayList", "$.Collections", "$.HashSet", "$.Hashtable"], "jalview.workers.AlignCalcManager", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.restartable = null; +this.blackList = null; +this.inProgress = null; +this.updating = null; +this.canUpdate = null; +Clazz.instantialize (this, arguments); +}, jalview.workers, "AlignCalcManager", null, jalview.api.AlignCalcManagerI); +Clazz.prepareFields (c$, function () { +this.restartable = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); +this.blackList = java.util.Collections.synchronizedList ( new java.util.ArrayList ()); +this.inProgress = java.util.Collections.synchronizedMap ( new java.util.Hashtable ()); +this.updating = java.util.Collections.synchronizedMap ( new java.util.Hashtable ()); +this.canUpdate = new java.util.HashSet (); +}); +Clazz.overrideMethod (c$, "notifyStart", +function (worker) { +{ +var upd = this.updating.get (worker.getClass ()); +if (upd == null) { +this.updating.put (worker.getClass (), upd = java.util.Collections.synchronizedList ( new java.util.ArrayList ())); +}{ +upd.add (worker); +}}}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "alreadyDoing", +function (worker) { +{ +return this.inProgress.containsKey (worker.getClass ()); +}}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "isPending", +function (workingClass) { +var upd; +{ +upd = this.updating.get (workingClass.getClass ()); +if (upd == null) { +return false; +}{ +if (upd.size () > 1) { +return true; +}}return false; +}}, "jalview.api.AlignCalcWorkerI"); +Clazz.defineMethod (c$, "numberLive", +function (worker) { +{ +var upd = this.updating.get (worker.getClass ()); +if (upd == null) { +return 0; +};return upd.size (); +}}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "notifyWorking", +function (worker) { +{ +if (this.inProgress.get (worker.getClass ()) != null) { +if (false) { +System.err.println ("Warning: Multiple workers are running of type " + worker.getClass ()); +}return false; +}this.inProgress.put (worker.getClass (), worker); +}return true; +}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "workerComplete", +function (worker) { +{ +this.inProgress.remove (worker.getClass ()); +var upd = this.updating.get (worker.getClass ()); +if (upd != null) { +{ +upd.remove (worker); +}this.canUpdate.add (worker); +}}}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "workerCannotRun", +function (worker) { +{ +this.blackList.add (worker.getClass ()); +}}, "jalview.api.AlignCalcWorkerI"); +Clazz.defineMethod (c$, "isBlackListed", +function (workerType) { +{ +return this.blackList.contains (workerType); +}}, "Class"); +Clazz.overrideMethod (c$, "startWorker", +function (worker) { +var workerAsThread = worker; +if (workerAsThread.isAlive ()) { +workerAsThread.interrupt (); +worker = worker.getNewWorker (); +}worker.setName (worker.getClass ().getName ()); +worker.start (); +}, "jalview.api.AlignCalcWorkerI"); +Clazz.defineMethod (c$, "isWorking", +function (worker) { +{ +return worker != null && this.inProgress.get (worker.getClass ()) === worker; +}}, "jalview.api.AlignCalcWorkerI"); +Clazz.defineMethod (c$, "isWorking", +function () { +{ +return this.inProgress.size () > 0; +}}); +Clazz.overrideMethod (c$, "registerWorker", +function (worker) { +{ +if (!this.restartable.contains (worker)) { +this.restartable.add (worker); +}this.startWorker (worker); +}}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "restartWorkers", +function () { +{ +for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { +this.startWorker (worker); +} +}}); +Clazz.overrideMethod (c$, "workingInvolvedWith", +function (alignmentAnnotation) { +{ +for (var worker, $worker = this.inProgress.values ().iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { +if (worker.involves (alignmentAnnotation)) { +return true; +}} +}{ +for (var workers, $workers = this.updating.values ().iterator (); $workers.hasNext () && ((workers = $workers.next ()) || true);) { +for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { +if (worker.involves (alignmentAnnotation)) { +return true; +}} +} +}return false; +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.overrideMethod (c$, "updateAnnotationFor", +function (workerClass) { +var workers; +{ +workers = this.canUpdate.toArray ( new Array (0)); +}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) { +if (workerClass.equals (worker.getClass ())) { +worker.updateAnnotation (); +}} +}, "Class"); +Clazz.overrideMethod (c$, "getRegisteredWorkersOfClass", +function (workerClass) { +var workingClass = new java.util.ArrayList (); +var workers; +{ +workers = this.canUpdate.toArray ( new Array (this.canUpdate.size ())); +}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) { +if (workerClass.equals (worker.getClass ())) { +workingClass.add (worker); +}} +return (workingClass.size () == 0) ? null : workingClass; +}, "Class"); +Clazz.overrideMethod (c$, "startRegisteredWorkersOfClass", +function (workerClass) { +var workers = this.getRegisteredWorkersOfClass (workerClass); +if (workers == null) { +return false; +}for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { +if (!this.isPending (worker)) { +this.startWorker (worker); +} else { +System.err.println ("Pending exists for " + workerClass); +}} +return true; +}, "Class"); +Clazz.overrideMethod (c$, "workerMayRun", +function (worker) { +{ +if (this.blackList.contains (worker.getClass ())) { +this.blackList.remove (worker.getClass ()); +}}}, "jalview.api.AlignCalcWorkerI"); +Clazz.overrideMethod (c$, "removeRegisteredWorkersOfClass", +function (typeToRemove) { +var workers = this.getRegisteredWorkersOfClass (typeToRemove); +var removable = new java.util.ArrayList (); +var toremovannot = new java.util.HashSet (); +{ +for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { +if (typeToRemove.equals (worker.getClass ())) { +removable.add (worker); +toremovannot.add (worker); +}} +this.restartable.removeAll (removable); +}{ +for (var worker, $worker = this.canUpdate.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) { +if (typeToRemove.equals (worker.getClass ())) { +removable.add (worker); +toremovannot.add (worker); +}} +this.canUpdate.removeAll (removable); +}}, "Class"); +}); diff --git a/bin/jalview/workers/AlignCalcWorker.js b/bin/jalview/workers/AlignCalcWorker.js index 43b690b..6636e6d 100644 --- a/bin/jalview/workers/AlignCalcWorker.js +++ b/bin/jalview/workers/AlignCalcWorker.js @@ -1,54 +1,54 @@ -Clazz.declarePackage ("jalview.workers"); -Clazz.load (["jalview.api.AlignCalcWorkerI", "swingjs.JSThread"], "jalview.workers.AlignCalcWorker", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.iFirst = 0; -this.iLast = 0; -this.nPer = 2; -this.started = 0; -this.alignment = null; -this.aWidth = 0; -this.alignViewport = null; -this.calcMan = null; -this.ap = null; -this.ourAnnots = null; -Clazz.instantialize (this, arguments); -}, jalview.workers, "AlignCalcWorker", swingjs.JSThread, jalview.api.AlignCalcWorkerI); -Clazz.makeConstructor (c$, -function (alignViewport, alignPanel) { -Clazz.superConstructor (this, jalview.workers.AlignCalcWorker, [null, "AlignCalcWorker"]); -this.alignViewport = alignViewport; -this.calcMan = alignViewport.getCalcManager (); -this.ap = alignPanel; -}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); -Clazz.defineMethod (c$, "abortAndDestroy", -function () { -if (this.calcMan != null) { -this.calcMan.workerComplete (this); -}this.alignViewport = null; -this.calcMan = null; -this.ap = null; -}); -Clazz.overrideMethod (c$, "involves", -function (i) { -return this.ourAnnots != null && this.ourAnnots.contains (i); -}, "jalview.datamodel.AlignmentAnnotation"); -Clazz.overrideMethod (c$, "removeOurAnnotation", -function () { -if (this.ourAnnots != null && this.alignViewport != null) { -var alignment = this.alignViewport.getAlignment (); -{ -for (var aa, $aa = this.ourAnnots.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { -alignment.deleteAnnotation (aa, true); -} -}}}); -Clazz.defineMethod (c$, "notifyDone", -function () { -if (this.ap != null) { -this.ap.paintAlignment (true); -}this.calcMan.workerComplete (this); -}); -Clazz.defineStatics (c$, -"LOOP_STANDBY", 3, -"LOOP_CALCULATE", 4, -"MS_MAX", 500); -}); +Clazz.declarePackage ("jalview.workers"); +Clazz.load (["jalview.api.AlignCalcWorkerI", "swingjs.JSThread"], "jalview.workers.AlignCalcWorker", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.iFirst = 0; +this.iLast = 0; +this.nPer = 2; +this.started = 0; +this.alignment = null; +this.aWidth = 0; +this.alignViewport = null; +this.calcMan = null; +this.ap = null; +this.ourAnnots = null; +Clazz.instantialize (this, arguments); +}, jalview.workers, "AlignCalcWorker", swingjs.JSThread, jalview.api.AlignCalcWorkerI); +Clazz.makeConstructor (c$, +function (alignViewport, alignPanel) { +Clazz.superConstructor (this, jalview.workers.AlignCalcWorker, [null, "AlignCalcWorker"]); +this.alignViewport = alignViewport; +this.calcMan = alignViewport.getCalcManager (); +this.ap = alignPanel; +}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); +Clazz.defineMethod (c$, "abortAndDestroy", +function () { +if (this.calcMan != null) { +this.calcMan.workerComplete (this); +}this.alignViewport = null; +this.calcMan = null; +this.ap = null; +}); +Clazz.overrideMethod (c$, "involves", +function (i) { +return this.ourAnnots != null && this.ourAnnots.contains (i); +}, "jalview.datamodel.AlignmentAnnotation"); +Clazz.overrideMethod (c$, "removeOurAnnotation", +function () { +if (this.ourAnnots != null && this.alignViewport != null) { +var alignment = this.alignViewport.getAlignment (); +{ +for (var aa, $aa = this.ourAnnots.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) { +alignment.deleteAnnotation (aa, true); +} +}}}); +Clazz.defineMethod (c$, "notifyDone", +function () { +if (this.ap != null) { +this.ap.paintAlignment (true); +}this.calcMan.workerComplete (this); +}); +Clazz.defineStatics (c$, +"LOOP_STANDBY", 3, +"LOOP_CALCULATE", 4, +"MS_MAX", 500); +}); diff --git a/bin/jalview/workers/ComplementConsensusThread.js b/bin/jalview/workers/ComplementConsensusThread.js index 641c3ba..17ece7f 100644 --- a/bin/jalview/workers/ComplementConsensusThread.js +++ b/bin/jalview/workers/ComplementConsensusThread.js @@ -1,46 +1,46 @@ -Clazz.declarePackage ("jalview.workers"); -Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () { -c$ = Clazz.decorateAsClass (function () { -this.mappings = null; -Clazz.instantialize (this, arguments); -}, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread); -Clazz.overrideMethod (c$, "getNewWorker", -function () { -return new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap); -}); -Clazz.overrideMethod (c$, "getConsensusAnnotation", -function () { -return this.alignViewport.getComplementConsensusAnnotation (); -}); -Clazz.overrideMethod (c$, "getViewportConsensus", -function () { -return this.alignViewport.getComplementConsensusHash (); -}); -Clazz.defineMethod (c$, "initializeCalc", -function () { -this.mappings = this.alignment.getCodonFrames (); -return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", [])); -}); -Clazz.overrideMethod (c$, "computeConsensus", -function () { -for (var i = 0; i < 3; i++) { -try { -jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast); -break; -} catch (e) { -if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) { -} else { -throw e; -} -} -} -}); -Clazz.overrideMethod (c$, "finalizeCalc", -function () { -this.alignViewport.setComplementConsensusHash (this.hconsensus); -}); -Clazz.overrideMethod (c$, "deriveConsensus", -function (consensusAnnotation, consensusData) { -jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length); -}, "jalview.datamodel.AlignmentAnnotation,~A"); -}); +Clazz.declarePackage ("jalview.workers"); +Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () { +c$ = Clazz.decorateAsClass (function () { +this.mappings = null; +Clazz.instantialize (this, arguments); +}, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread); +Clazz.overrideMethod (c$, "getNewWorker", +function () { +return new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap); +}); +Clazz.overrideMethod (c$, "getConsensusAnnotation", +function () { +return this.alignViewport.getComplementConsensusAnnotation (); +}); +Clazz.overrideMethod (c$, "getViewportConsensus", +function () { +return this.alignViewport.getComplementConsensusHash (); +}); +Clazz.defineMethod (c$, "initializeCalc", +function () { +this.mappings = this.alignment.getCodonFrames (); +return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", [])); +}); +Clazz.overrideMethod (c$, "computeConsensus", +function () { +for (var i = 0; i < 3; i++) { +try { +jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast); +break; +} catch (e) { +if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) { +} else { +throw e; +} +} +} +}); +Clazz.overrideMethod (c$, "finalizeCalc", +function () { +this.alignViewport.setComplementConsensusHash (this.hconsensus); +}); +Clazz.overrideMethod (c$, "deriveConsensus", +function (consensusAnnotation, consensusData) { +jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length); +}, "jalview.datamodel.AlignmentAnnotation,~A"); +}); diff --git a/bin/jalview/workers/ConsensusThread.js b/bin/jalview/workers/ConsensusThread.js index 3f62035..089a18e 100644 --- a/bin/jalview/workers/ConsensusThread.js +++ b/bin/jalview/workers/ConsensusThread.js @@ -1,149 +1,149 @@ -Clazz.declarePackage ("jalview.workers"); -Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConsensusThread", ["jalview.analysis.AAFrequency"], function () { -c$ = Clazz.decorateAsClass (function () { -this.hconsensus = null; -this.aseqs = null; -Clazz.instantialize (this, arguments); -}, jalview.workers, "ConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI); -Clazz.overrideMethod (c$, "getNewWorker", -function () { -return new jalview.workers.ConsensusThread (this.alignViewport, this.ap); -}); -Clazz.overrideMethod (c$, "run1", -function (state) { -while (!Thread.interrupted ()) { -if (this.alignViewport.isClosed ()) { -this.abortAndDestroy (); -return; -}try { -switch (state) { -case 0: -if (this.calcMan.isPending (this)) return; -this.calcMan.notifyStart (this); -var consensus = this.getConsensusAnnotation (); -if (consensus == null || this.calcMan.isPending (this)) { -this.calcMan.workerComplete (this); -return; -}state = 3; -break; -case 3: -while (!this.calcMan.notifyWorking (this)) { -if (this.ap != null) { -this.ap.paintAlignment (false); -}try { -if (this.sleepAndReturn (200, state)) return; -} catch (e) { -if (Clazz.exceptionOf (e, InterruptedException)) { -state = 2; -break; -} else { -throw e; -} -} -} -if (this.alignViewport.isClosed ()) { -this.abortAndDestroy (); -state = 2; -break; -}this.alignment = this.alignViewport.getAlignment (); -this.aWidth = -1; -if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) { -state = 2; -}this.eraseConsensus (this.aWidth); -state = (this.initializeCalc () ? 4 : 2); -break; -case 4: -this.iFirst = this.iLast; -this.iLast = Math.min (this.iLast + this.nPer, this.aWidth); -if (this.iLast == this.iFirst) { -state = 2; -} else { -this.computeConsensus (); -if (this.sleepAndReturn (0, state)) return; -}break; -case 2: -this.finalizeCalc (); -this.updateAlignment (); -this.notifyDone (); -return; -} -} catch (e$$) { -if (Clazz.exceptionOf (e$$, OutOfMemoryError)) { -var error = e$$; -{ -this.calcMan.workerCannotRun (this); -this.ap.raiseOOMWarning ("calculating consensus", error); -} -} else { -var e = e$$; -{ -System.out.println ("Error in ConsensusThread: " + e); -e.printStackTrace (); -this.calcMan.workerComplete (this); -} -} -} -} -}, "~N"); -Clazz.defineMethod (c$, "initializeCalc", -function () { -this.iLast = 0; -this.hconsensus = new Array (this.aWidth); -this.aseqs = this.getSequences (); -return true; -}); -Clazz.defineMethod (c$, "computeConsensus", -function () { -this.started = System.currentTimeMillis (); -jalview.analysis.AAFrequency.calculate (this.aseqs, this.iFirst, this.iLast, this.hconsensus, true); -if (System.currentTimeMillis () - this.started < 500) this.nPer *= 2; -}); -Clazz.defineMethod (c$, "finalizeCalc", -function () { -this.alignViewport.setSequenceConsensusHash (this.hconsensus); -}); -Clazz.defineMethod (c$, "updateAlignment", -function () { -this.setColourSchemeConsensus (this.hconsensus); -this.updateResultAnnotation (true); -}); -Clazz.defineMethod (c$, "eraseConsensus", -function (aWidth) { -var consensus = this.getConsensusAnnotation (); -consensus.annotations = new Array (aWidth); -}, "~N"); -Clazz.defineMethod (c$, "getSequences", -function () { -return this.alignViewport.getAlignment ().getSequencesArray (); -}); -Clazz.defineMethod (c$, "setColourSchemeConsensus", -function (hconsensus) { -var globalColourScheme = this.alignViewport.getGlobalColourScheme (); -if (globalColourScheme != null) { -globalColourScheme.setConsensus (hconsensus); -}}, "~A"); -Clazz.defineMethod (c$, "getConsensusAnnotation", -function () { -return this.alignViewport.getAlignmentConsensusAnnotation (); -}); -Clazz.overrideMethod (c$, "updateAnnotation", -function () { -this.updateResultAnnotation (false); -}); -Clazz.defineMethod (c$, "updateResultAnnotation", -function (immediate) { -var consensus = this.getConsensusAnnotation (); -var hconsensus = this.getViewportConsensus (); -if (immediate || !this.calcMan.isWorking (this) && consensus != null && hconsensus != null) { -this.deriveConsensus (consensus, hconsensus); -}}, "~B"); -Clazz.defineMethod (c$, "deriveConsensus", -function (consensusAnnotation, consensusData) { -var nseq = this.getSequences ().length; -jalview.analysis.AAFrequency.completeConsensus (consensusAnnotation, consensusData, 0, consensusData.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), nseq); -}, "jalview.datamodel.AlignmentAnnotation,~A"); -Clazz.defineMethod (c$, "getViewportConsensus", -function () { -return this.alignViewport.getSequenceConsensusHash (); -}); -}); +Clazz.declarePackage ("jalview.workers"); +Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConsensusThread", ["jalview.analysis.AAFrequency"], function () { +c$ = Clazz.decorateAsClass (function () { +this.hconsensus = null; +this.aseqs = null; +Clazz.instantialize (this, arguments); +}, jalview.workers, "ConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI); +Clazz.overrideMethod (c$, "getNewWorker", +function () { +return new jalview.workers.ConsensusThread (this.alignViewport, this.ap); +}); +Clazz.overrideMethod (c$, "run1", +function (state) { +while (!Thread.interrupted ()) { +if (this.alignViewport.isClosed ()) { +this.abortAndDestroy (); +return; +}try { +switch (state) { +case 0: +if (this.calcMan.isPending (this)) return; +this.calcMan.notifyStart (this); +var consensus = this.getConsensusAnnotation (); +if (consensus == null || this.calcMan.isPending (this)) { +this.calcMan.workerComplete (this); +return; +}state = 3; +break; +case 3: +while (!this.calcMan.notifyWorking (this)) { +if (this.ap != null) { +this.ap.paintAlignment (false); +}try { +if (this.sleepAndReturn (200, state)) return; +} catch (e) { +if (Clazz.exceptionOf (e, InterruptedException)) { +state = 2; +break; +} else { +throw e; +} +} +} +if (this.alignViewport.isClosed ()) { +this.abortAndDestroy (); +state = 2; +break; +}this.alignment = this.alignViewport.getAlignment (); +this.aWidth = -1; +if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) { +state = 2; +}this.eraseConsensus (this.aWidth); +state = (this.initializeCalc () ? 4 : 2); +break; +case 4: +this.iFirst = this.iLast; +this.iLast = Math.min (this.iLast + this.nPer, this.aWidth); +if (this.iLast == this.iFirst) { +state = 2; +} else { +this.computeConsensus (); +if (this.sleepAndReturn (0, state)) return; +}break; +case 2: +this.finalizeCalc (); +this.updateAlignment (); +this.notifyDone (); +return; +} +} catch (e$$) { +if (Clazz.exceptionOf (e$$, OutOfMemoryError)) { +var error = e$$; +{ +this.calcMan.workerCannotRun (this); +this.ap.raiseOOMWarning ("calculating consensus", error); +} +} else { +var e = e$$; +{ +System.out.println ("Error in ConsensusThread: " + e); +e.printStackTrace (); +this.calcMan.workerComplete (this); +} +} +} +} +}, "~N"); +Clazz.defineMethod (c$, "initializeCalc", +function () { +this.iLast = 0; +this.hconsensus = new Array (this.aWidth); +this.aseqs = this.getSequences (); +return true; +}); +Clazz.defineMethod (c$, "computeConsensus", +function () { +this.started = System.currentTimeMillis (); +jalview.analysis.AAFrequency.calculate (this.aseqs, this.iFirst, this.iLast, this.hconsensus, true); +if (System.currentTimeMillis () - this.started < 500) this.nPer *= 2; +}); +Clazz.defineMethod (c$, "finalizeCalc", +function () { +this.alignViewport.setSequenceConsensusHash (this.hconsensus); +}); +Clazz.defineMethod (c$, "updateAlignment", +function () { +this.setColourSchemeConsensus (this.hconsensus); +this.updateResultAnnotation (true); +}); +Clazz.defineMethod (c$, "eraseConsensus", +function (aWidth) { +var consensus = this.getConsensusAnnotation (); +consensus.annotations = new Array (aWidth); +}, "~N"); +Clazz.defineMethod (c$, "getSequences", +function () { +return this.alignViewport.getAlignment ().getSequencesArray (); +}); +Clazz.defineMethod (c$, "setColourSchemeConsensus", +function (hconsensus) { +var globalColourScheme = this.alignViewport.getGlobalColourScheme (); +if (globalColourScheme != null) { +globalColourScheme.setConsensus (hconsensus); +}}, "~A"); +Clazz.defineMethod (c$, "getConsensusAnnotation", +function () { +return this.alignViewport.getAlignmentConsensusAnnotation (); +}); +Clazz.overrideMethod (c$, "updateAnnotation", +function () { +this.updateResultAnnotation (false); +}); +Clazz.defineMethod (c$, "updateResultAnnotation", +function (immediate) { +var consensus = this.getConsensusAnnotation (); +var hconsensus = this.getViewportConsensus (); +if (immediate || !this.calcMan.isWorking (this) && consensus != null && hconsensus != null) { +this.deriveConsensus (consensus, hconsensus); +}}, "~B"); +Clazz.defineMethod (c$, "deriveConsensus", +function (consensusAnnotation, consensusData) { +var nseq = this.getSequences ().length; +jalview.analysis.AAFrequency.completeConsensus (consensusAnnotation, consensusData, 0, consensusData.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), nseq); +}, "jalview.datamodel.AlignmentAnnotation,~A"); +Clazz.defineMethod (c$, "getViewportConsensus", +function () { +return this.alignViewport.getSequenceConsensusHash (); +}); +}); diff --git a/bin/jalview/workers/ConservationThread.js b/bin/jalview/workers/ConservationThread.js index dc839a9..d790876 100644 --- a/bin/jalview/workers/ConservationThread.js +++ b/bin/jalview/workers/ConservationThread.js @@ -1,108 +1,108 @@ -Clazz.declarePackage ("jalview.workers"); -Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConservationThread", ["jalview.analysis.Conservation", "jalview.schemes.ResidueProperties", "java.util.ArrayList"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ConsPercGaps = 25; -this.cons = null; -this.conservation = null; -this.quality = null; -Clazz.instantialize (this, arguments); -}, jalview.workers, "ConservationThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI); -Clazz.overrideMethod (c$, "getNewWorker", -function () { -return new jalview.workers.ConservationThread (this.alignViewport, this.ap); -}); -Clazz.makeConstructor (c$, -function (alignViewport, alignPanel) { -Clazz.superConstructor (this, jalview.workers.ConservationThread, [alignViewport, alignPanel]); -this.ConsPercGaps = alignViewport.getConsPercGaps (); -}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); -Clazz.overrideMethod (c$, "run1", -function (state) { -while (!Thread.interrupted ()) { -try { -switch (state) { -case 0: -if (this.calcMan.isPending (this)) return; -this.calcMan.notifyStart (this); -state = 3; -break; -case 3: -while (!this.calcMan.notifyWorking (this)) { -if (this.ap != null) { -this.ap.paintAlignment (false); -}try { -if (this.sleepAndReturn (200, state)) return; -} catch (e) { -if (Clazz.exceptionOf (e, InterruptedException)) { -state = 2; -break; -} else { -throw e; -} -} -} -if (this.alignViewport.isClosed ()) { -this.abortAndDestroy (); -state = 2; -break; -}var ourAnnot = new java.util.ArrayList (); -this.alignment = this.alignViewport.getAlignment (); -this.conservation = this.alignViewport.getAlignmentConservationAnnotation (); -this.quality = this.alignViewport.getAlignmentQualityAnnot (); -ourAnnot.add (this.conservation); -ourAnnot.add (this.quality); -this.ourAnnots = ourAnnot; -this.ConsPercGaps = this.alignViewport.getConsPercGaps (); -if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) { -this.calcMan.workerComplete (this); -return; -}state = 4; -break; -case 4: -this.iFirst = this.iLast; -this.nPer = this.aWidth + 1; -this.iLast = Math.min (this.iLast + this.nPer, this.aWidth); -if (this.iLast == this.iFirst) { -state = 2; -} else { -this.computeConsensus (); -if (this.sleepAndReturn (0, state)) return; -}break; -case 2: -this.updateResultAnnotation (true); -this.notifyDone (); -return; -} -} catch (e$$) { -if (Clazz.exceptionOf (e$$, OutOfMemoryError)) { -var error = e$$; -{ -this.calcMan.workerCannotRun (this); -this.ap.raiseOOMWarning ("calculating conservation", error); -} -} else { -var e = e$$; -{ -System.out.println ("Error in ConsensusThread: " + e); -e.printStackTrace (); -this.calcMan.workerComplete (this); -} -} -} -} -}, "~N"); -Clazz.defineMethod (c$, "computeConsensus", -($fz = function () { -this.cons = jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.aWidth - 1, false, this.ConsPercGaps, this.quality != null); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "updateResultAnnotation", -($fz = function (b) { -if (b || !this.calcMan.isWorking (this) && this.cons != null && this.conservation != null && this.quality != null) { -this.alignViewport.setConservation (this.cons); -this.cons.completeAnnotations (this.conservation, this.quality, 0, this.aWidth); -}}, $fz.isPrivate = true, $fz), "~B"); -Clazz.overrideMethod (c$, "updateAnnotation", -function () { -this.updateResultAnnotation (false); -}); -}); +Clazz.declarePackage ("jalview.workers"); +Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConservationThread", ["jalview.analysis.Conservation", "jalview.schemes.ResidueProperties", "java.util.ArrayList"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ConsPercGaps = 25; +this.cons = null; +this.conservation = null; +this.quality = null; +Clazz.instantialize (this, arguments); +}, jalview.workers, "ConservationThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI); +Clazz.overrideMethod (c$, "getNewWorker", +function () { +return new jalview.workers.ConservationThread (this.alignViewport, this.ap); +}); +Clazz.makeConstructor (c$, +function (alignViewport, alignPanel) { +Clazz.superConstructor (this, jalview.workers.ConservationThread, [alignViewport, alignPanel]); +this.ConsPercGaps = alignViewport.getConsPercGaps (); +}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel"); +Clazz.overrideMethod (c$, "run1", +function (state) { +while (!Thread.interrupted ()) { +try { +switch (state) { +case 0: +if (this.calcMan.isPending (this)) return; +this.calcMan.notifyStart (this); +state = 3; +break; +case 3: +while (!this.calcMan.notifyWorking (this)) { +if (this.ap != null) { +this.ap.paintAlignment (false); +}try { +if (this.sleepAndReturn (200, state)) return; +} catch (e) { +if (Clazz.exceptionOf (e, InterruptedException)) { +state = 2; +break; +} else { +throw e; +} +} +} +if (this.alignViewport.isClosed ()) { +this.abortAndDestroy (); +state = 2; +break; +}var ourAnnot = new java.util.ArrayList (); +this.alignment = this.alignViewport.getAlignment (); +this.conservation = this.alignViewport.getAlignmentConservationAnnotation (); +this.quality = this.alignViewport.getAlignmentQualityAnnot (); +ourAnnot.add (this.conservation); +ourAnnot.add (this.quality); +this.ourAnnots = ourAnnot; +this.ConsPercGaps = this.alignViewport.getConsPercGaps (); +if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) { +this.calcMan.workerComplete (this); +return; +}state = 4; +break; +case 4: +this.iFirst = this.iLast; +this.nPer = this.aWidth + 1; +this.iLast = Math.min (this.iLast + this.nPer, this.aWidth); +if (this.iLast == this.iFirst) { +state = 2; +} else { +this.computeConsensus (); +if (this.sleepAndReturn (0, state)) return; +}break; +case 2: +this.updateResultAnnotation (true); +this.notifyDone (); +return; +} +} catch (e$$) { +if (Clazz.exceptionOf (e$$, OutOfMemoryError)) { +var error = e$$; +{ +this.calcMan.workerCannotRun (this); +this.ap.raiseOOMWarning ("calculating conservation", error); +} +} else { +var e = e$$; +{ +System.out.println ("Error in ConsensusThread: " + e); +e.printStackTrace (); +this.calcMan.workerComplete (this); +} +} +} +} +}, "~N"); +Clazz.defineMethod (c$, "computeConsensus", +($fz = function () { +this.cons = jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.aWidth - 1, false, this.ConsPercGaps, this.quality != null); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "updateResultAnnotation", +($fz = function (b) { +if (b || !this.calcMan.isWorking (this) && this.cons != null && this.conservation != null && this.quality != null) { +this.alignViewport.setConservation (this.cons); +this.cons.completeAnnotations (this.conservation, this.quality, 0, this.aWidth); +}}, $fz.isPrivate = true, $fz), "~B"); +Clazz.overrideMethod (c$, "updateAnnotation", +function () { +this.updateResultAnnotation (false); +}); +}); diff --git a/bin/jalview/workers/StrucConsensusThread.class b/bin/jalview/workers/StrucConsensusThread.class index 48b83a5..419bb43 100644 Binary files a/bin/jalview/workers/StrucConsensusThread.class and b/bin/jalview/workers/StrucConsensusThread.class differ diff --git a/bin/jalview/workers/StrucConsensusThread.js b/bin/jalview/workers/StrucConsensusThread.js index 4010f84..dbe6d50 100644 --- a/bin/jalview/workers/StrucConsensusThread.js +++ b/bin/jalview/workers/StrucConsensusThread.js @@ -1,95 +1,95 @@ -Clazz.declarePackage ("jalview.workers"); -Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency", "java.lang.Thread"], function () { -c$ = Clazz.decorateAsClass (function () { -this.strucConsensus = null; -this.hStrucConsensus = null; -this.nseq = -1; -Clazz.instantialize (this, arguments); -}, jalview.workers, "StrucConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI); -Clazz.overrideMethod (c$, "getNewWorker", -function () { -return new jalview.workers.StrucConsensusThread (this.alignViewport, this.ap); -}); -Clazz.overrideMethod (c$, "run", -function () { -try { -if (this.calcMan.isPending (this)) { -return; -}this.calcMan.notifyStart (this); -while (!this.calcMan.notifyWorking (this)) { -try { -if (this.ap != null) { -}Thread.sleep (200); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -} -if (this.alignViewport.isClosed ()) { -this.abortAndDestroy (); -return; -}var alignment = this.alignViewport.getAlignment (); -var aWidth = -1; -if (alignment == null || (aWidth = alignment.getWidth ()) < 0) { -this.calcMan.workerComplete (this); -return; -}this.strucConsensus = this.alignViewport.getAlignmentStrucConsensusAnnotation (); -this.hStrucConsensus = this.alignViewport.getRnaStructureConsensusHash (); -this.strucConsensus.annotations = null; -this.strucConsensus.annotations = new Array (aWidth); -this.hStrucConsensus = new Array (aWidth); -var aa = this.alignViewport.getAlignment ().getAlignmentAnnotation (); -var rnaStruc = null; -for (var i = 0; i < aa.length; i++) { -if (aa[i].getRNAStruc () != null && aa[i].isValidStruc ()) { -rnaStruc = aa[i]; -break; -}} -if (rnaStruc == null || !rnaStruc.isValidStruc ()) { -this.calcMan.workerComplete (this); -return; -}try { -var arr = alignment.getSequencesArray (); -this.nseq = arr.length; -jalview.analysis.StructureFrequency.calculate (arr, 0, alignment.getWidth (), this.hStrucConsensus, true, rnaStruc); -} catch (x) { -if (Clazz.exceptionOf (x, ArrayIndexOutOfBoundsException)) { -this.calcMan.workerComplete (this); -return; -} else { -throw x; -} -} -this.alignViewport.setRnaStructureConsensusHash (this.hStrucConsensus); -this.updateResultAnnotation (true); -if (this.alignViewport.getGlobalColourScheme () != null) { -this.alignViewport.getGlobalColourScheme ().setConsensus (this.hStrucConsensus); -}} catch (error) { -if (Clazz.exceptionOf (error, OutOfMemoryError)) { -this.calcMan.workerCannotRun (this); -this.ap.raiseOOMWarning ("calculating RNA structure consensus", error); -} else { -throw error; -} -} finally { -this.calcMan.workerComplete (this); -if (this.ap != null) { -this.ap.paintAlignment (true); -}} -}); -Clazz.overrideMethod (c$, "updateAnnotation", -function () { -this.updateResultAnnotation (false); -}); -Clazz.defineMethod (c$, "updateResultAnnotation", -function (immediate) { -if (immediate || !this.calcMan.isWorking (this) && this.strucConsensus != null && this.hStrucConsensus != null) { -jalview.analysis.StructureFrequency.completeConsensus (this.strucConsensus, this.hStrucConsensus, 0, this.hStrucConsensus.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), this.nseq); -}}, "~B"); -Clazz.overrideMethod (c$, "run1", -function (state) { -}, "~N"); -}); +Clazz.declarePackage ("jalview.workers"); +Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency", "java.lang.Thread"], function () { +c$ = Clazz.decorateAsClass (function () { +this.strucConsensus = null; +this.hStrucConsensus = null; +this.nseq = -1; +Clazz.instantialize (this, arguments); +}, jalview.workers, "StrucConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI); +Clazz.overrideMethod (c$, "getNewWorker", +function () { +return new jalview.workers.StrucConsensusThread (this.alignViewport, this.ap); +}); +Clazz.overrideMethod (c$, "run", +function () { +try { +if (this.calcMan.isPending (this)) { +return; +}this.calcMan.notifyStart (this); +while (!this.calcMan.notifyWorking (this)) { +try { +if (this.ap != null) { +}Thread.sleep (200); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +} +if (this.alignViewport.isClosed ()) { +this.abortAndDestroy (); +return; +}var alignment = this.alignViewport.getAlignment (); +var aWidth = -1; +if (alignment == null || (aWidth = alignment.getWidth ()) < 0) { +this.calcMan.workerComplete (this); +return; +}this.strucConsensus = this.alignViewport.getAlignmentStrucConsensusAnnotation (); +this.hStrucConsensus = this.alignViewport.getRnaStructureConsensusHash (); +this.strucConsensus.annotations = null; +this.strucConsensus.annotations = new Array (aWidth); +this.hStrucConsensus = new Array (aWidth); +var aa = this.alignViewport.getAlignment ().getAlignmentAnnotation (); +var rnaStruc = null; +for (var i = 0; i < aa.length; i++) { +if (aa[i].getRNAStruc () != null && aa[i].isValidStruc ()) { +rnaStruc = aa[i]; +break; +}} +if (rnaStruc == null || !rnaStruc.isValidStruc ()) { +this.calcMan.workerComplete (this); +return; +}try { +var arr = alignment.getSequencesArray (); +this.nseq = arr.length; +jalview.analysis.StructureFrequency.calculate (arr, 0, alignment.getWidth (), this.hStrucConsensus, true, rnaStruc); +} catch (x) { +if (Clazz.exceptionOf (x, ArrayIndexOutOfBoundsException)) { +this.calcMan.workerComplete (this); +return; +} else { +throw x; +} +} +this.alignViewport.setRnaStructureConsensusHash (this.hStrucConsensus); +this.updateResultAnnotation (true); +if (this.alignViewport.getGlobalColourScheme () != null) { +this.alignViewport.getGlobalColourScheme ().setConsensus (this.hStrucConsensus); +}} catch (error) { +if (Clazz.exceptionOf (error, OutOfMemoryError)) { +this.calcMan.workerCannotRun (this); +this.ap.raiseOOMWarning ("calculating RNA structure consensus", error); +} else { +throw error; +} +} finally { +this.calcMan.workerComplete (this); +if (this.ap != null) { +this.ap.paintAlignment (true); +}} +}); +Clazz.overrideMethod (c$, "updateAnnotation", +function () { +this.updateResultAnnotation (false); +}); +Clazz.defineMethod (c$, "updateResultAnnotation", +function (immediate) { +if (immediate || !this.calcMan.isWorking (this) && this.strucConsensus != null && this.hStrucConsensus != null) { +jalview.analysis.StructureFrequency.completeConsensus (this.strucConsensus, this.hStrucConsensus, 0, this.hStrucConsensus.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), this.nseq); +}}, "~B"); +Clazz.overrideMethod (c$, "run1", +function (state) { +}, "~N"); +}); diff --git a/bin/java.policy.applet b/bin/java.policy.applet deleted file mode 100644 index 35527af..0000000 --- a/bin/java.policy.applet +++ /dev/null @@ -1,7 +0,0 @@ -/* AUTOMATICALLY GENERATED ON Tue Apr 16 17:20:59 EDT 2002*/ -/* DO NOT EDIT */ - -grant { - permission java.security.AllPermission; -}; - diff --git a/bin/javajs/J2SIgnoreImport.js b/bin/javajs/J2SIgnoreImport.js index 5b4de23..bd94c0d 100644 --- a/bin/javajs/J2SIgnoreImport.js +++ b/bin/javajs/J2SIgnoreImport.js @@ -1 +1 @@ -Clazz.declarePackage ("javajs"); +Clazz.declarePackage ("javajs"); diff --git a/bin/javajs/J2SRequireImport.js b/bin/javajs/J2SRequireImport.js index 5b4de23..bd94c0d 100644 --- a/bin/javajs/J2SRequireImport.js +++ b/bin/javajs/J2SRequireImport.js @@ -1 +1 @@ -Clazz.declarePackage ("javajs"); +Clazz.declarePackage ("javajs"); diff --git a/bin/javajs/api/BytePoster.js b/bin/javajs/api/BytePoster.js index c97ddaf..1fb861c 100644 --- a/bin/javajs/api/BytePoster.js +++ b/bin/javajs/api/BytePoster.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "BytePoster"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "BytePoster"); diff --git a/bin/javajs/api/EigenInterface.js b/bin/javajs/api/EigenInterface.js index b5d1d99..b6e97f1 100644 --- a/bin/javajs/api/EigenInterface.js +++ b/bin/javajs/api/EigenInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "EigenInterface"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "EigenInterface"); diff --git a/bin/javajs/api/EventManager.js b/bin/javajs/api/EventManager.js index c5a4fa9..a80b250 100644 --- a/bin/javajs/api/EventManager.js +++ b/bin/javajs/api/EventManager.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "EventManager"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "EventManager"); diff --git a/bin/javajs/api/FontManager.js b/bin/javajs/api/FontManager.js index a809538..f458d89 100644 --- a/bin/javajs/api/FontManager.js +++ b/bin/javajs/api/FontManager.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "FontManager"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "FontManager"); diff --git a/bin/javajs/api/GenericBinaryDocument.js b/bin/javajs/api/GenericBinaryDocument.js index 0da5b99..8a2bbf9 100644 --- a/bin/javajs/api/GenericBinaryDocument.js +++ b/bin/javajs/api/GenericBinaryDocument.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericBinaryDocument"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericBinaryDocument"); diff --git a/bin/javajs/api/GenericCifDataParser.js b/bin/javajs/api/GenericCifDataParser.js index 2696094..6127596 100644 --- a/bin/javajs/api/GenericCifDataParser.js +++ b/bin/javajs/api/GenericCifDataParser.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.api"); -c$ = Clazz.declareInterface (javajs.api, "GenericCifDataParser"); -Clazz.defineStatics (c$, -"NONE", -1); +Clazz.declarePackage ("javajs.api"); +c$ = Clazz.declareInterface (javajs.api, "GenericCifDataParser"); +Clazz.defineStatics (c$, +"NONE", -1); diff --git a/bin/javajs/api/GenericColor.js b/bin/javajs/api/GenericColor.js index c5d0d77..ed0a0ee 100644 --- a/bin/javajs/api/GenericColor.js +++ b/bin/javajs/api/GenericColor.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericColor"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericColor"); diff --git a/bin/javajs/api/GenericFileInterface.js b/bin/javajs/api/GenericFileInterface.js index 9a09815..deae68e 100644 --- a/bin/javajs/api/GenericFileInterface.js +++ b/bin/javajs/api/GenericFileInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericFileInterface"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericFileInterface"); diff --git a/bin/javajs/api/GenericImageDialog.js b/bin/javajs/api/GenericImageDialog.js index 16c01cb..fa18c18 100644 --- a/bin/javajs/api/GenericImageDialog.js +++ b/bin/javajs/api/GenericImageDialog.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericImageDialog"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericImageDialog"); diff --git a/bin/javajs/api/GenericImageEncoder.js b/bin/javajs/api/GenericImageEncoder.js index f6a2e95..a7313d0 100644 --- a/bin/javajs/api/GenericImageEncoder.js +++ b/bin/javajs/api/GenericImageEncoder.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericImageEncoder"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericImageEncoder"); diff --git a/bin/javajs/api/GenericLineReader.js b/bin/javajs/api/GenericLineReader.js index f4d2aad..787a669 100644 --- a/bin/javajs/api/GenericLineReader.js +++ b/bin/javajs/api/GenericLineReader.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericLineReader"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericLineReader"); diff --git a/bin/javajs/api/GenericMenuInterface.js b/bin/javajs/api/GenericMenuInterface.js index d35fda0..8636834 100644 --- a/bin/javajs/api/GenericMenuInterface.js +++ b/bin/javajs/api/GenericMenuInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericMenuInterface"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericMenuInterface"); diff --git a/bin/javajs/api/GenericMouseInterface.js b/bin/javajs/api/GenericMouseInterface.js index d40a3a0..dad99c3 100644 --- a/bin/javajs/api/GenericMouseInterface.js +++ b/bin/javajs/api/GenericMouseInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericMouseInterface"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericMouseInterface"); diff --git a/bin/javajs/api/GenericPlatform.js b/bin/javajs/api/GenericPlatform.js index 00504e7..ae3869f 100644 --- a/bin/javajs/api/GenericPlatform.js +++ b/bin/javajs/api/GenericPlatform.js @@ -1,11 +1,11 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.load (["javajs.api.FontManager"], "javajs.api.GenericPlatform", null, function () { -c$ = Clazz.declareInterface (javajs.api, "GenericPlatform", javajs.api.FontManager); -Clazz.defineStatics (c$, -"CURSOR_DEFAULT", 0, -"CURSOR_CROSSHAIR", 1, -"CURSOR_WAIT", 3, -"CURSOR_ZOOM", 8, -"CURSOR_HAND", 12, -"CURSOR_MOVE", 13); -}); +Clazz.declarePackage ("javajs.api"); +Clazz.load (["javajs.api.FontManager"], "javajs.api.GenericPlatform", null, function () { +c$ = Clazz.declareInterface (javajs.api, "GenericPlatform", javajs.api.FontManager); +Clazz.defineStatics (c$, +"CURSOR_DEFAULT", 0, +"CURSOR_CROSSHAIR", 1, +"CURSOR_WAIT", 3, +"CURSOR_ZOOM", 8, +"CURSOR_HAND", 12, +"CURSOR_MOVE", 13); +}); diff --git a/bin/javajs/api/GenericZipInputStream.js b/bin/javajs/api/GenericZipInputStream.js index 9e55715..d74cfea 100644 --- a/bin/javajs/api/GenericZipInputStream.js +++ b/bin/javajs/api/GenericZipInputStream.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.load (["java.util.zip.ZipInputStream", "javajs.api.ZInputStream"], "javajs.api.GenericZipInputStream", null, function () { -c$ = Clazz.declareType (javajs.api, "GenericZipInputStream", java.util.zip.ZipInputStream, javajs.api.ZInputStream); -}); +Clazz.declarePackage ("javajs.api"); +Clazz.load (["java.util.zip.ZipInputStream", "javajs.api.ZInputStream"], "javajs.api.GenericZipInputStream", null, function () { +c$ = Clazz.declareType (javajs.api, "GenericZipInputStream", java.util.zip.ZipInputStream, javajs.api.ZInputStream); +}); diff --git a/bin/javajs/api/GenericZipTools.js b/bin/javajs/api/GenericZipTools.js index 00e6edf..902f592 100644 --- a/bin/javajs/api/GenericZipTools.js +++ b/bin/javajs/api/GenericZipTools.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "GenericZipTools"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "GenericZipTools"); diff --git a/bin/javajs/api/HTMLElement.js b/bin/javajs/api/HTMLElement.js index b305eae..97473c7 100644 --- a/bin/javajs/api/HTMLElement.js +++ b/bin/javajs/api/HTMLElement.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "HTMLElement"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "HTMLElement"); diff --git a/bin/javajs/api/HTMLWindowEvent.js b/bin/javajs/api/HTMLWindowEvent.js index 47438ca..538a5c1 100644 --- a/bin/javajs/api/HTMLWindowEvent.js +++ b/bin/javajs/api/HTMLWindowEvent.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "HTMLWindowEvent"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "HTMLWindowEvent"); diff --git a/bin/javajs/api/Interface.js b/bin/javajs/api/Interface.js index 024bf74..8887be8 100644 --- a/bin/javajs/api/Interface.js +++ b/bin/javajs/api/Interface.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("javajs.api"); -c$ = Clazz.declareType (javajs.api, "Interface"); -c$.getInterface = Clazz.defineMethod (c$, "getInterface", -function (name) { -try { -var x = Class.forName (name); -return (x == null ? null : x.newInstance ()); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println ("Interface.java Error creating instance for " + name + ": \n" + e); -return null; -} else { -throw e; -} -} -}, "~S"); +Clazz.declarePackage ("javajs.api"); +c$ = Clazz.declareType (javajs.api, "Interface"); +c$.getInterface = Clazz.defineMethod (c$, "getInterface", +function (name) { +try { +var x = Class.forName (name); +return (x == null ? null : x.newInstance ()); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println ("Interface.java Error creating instance for " + name + ": \n" + e); +return null; +} else { +throw e; +} +} +}, "~S"); diff --git a/bin/javajs/api/JSInterface.js b/bin/javajs/api/JSInterface.js index 1086b93..ce34ecc 100644 --- a/bin/javajs/api/JSInterface.js +++ b/bin/javajs/api/JSInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "JSInterface"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "JSInterface"); diff --git a/bin/javajs/api/JSONEncodable.js b/bin/javajs/api/JSONEncodable.js index 9f5778f..e94f4b8 100644 --- a/bin/javajs/api/JSONEncodable.js +++ b/bin/javajs/api/JSONEncodable.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "JSONEncodable"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "JSONEncodable"); diff --git a/bin/javajs/api/JmolObjectInterface.js b/bin/javajs/api/JmolObjectInterface.js index a499b01..0f1e805 100644 --- a/bin/javajs/api/JmolObjectInterface.js +++ b/bin/javajs/api/JmolObjectInterface.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "JmolObjectInterface"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "JmolObjectInterface"); diff --git a/bin/javajs/api/PlatformViewer.js b/bin/javajs/api/PlatformViewer.js index 8cad055..32ed2dc 100644 --- a/bin/javajs/api/PlatformViewer.js +++ b/bin/javajs/api/PlatformViewer.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "PlatformViewer"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "PlatformViewer"); diff --git a/bin/javajs/api/SC.js b/bin/javajs/api/SC.js index 0edd956..01512cd 100644 --- a/bin/javajs/api/SC.js +++ b/bin/javajs/api/SC.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "SC"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "SC"); diff --git a/bin/javajs/api/SwingController.js b/bin/javajs/api/SwingController.js index 75f1f05..277bc34 100644 --- a/bin/javajs/api/SwingController.js +++ b/bin/javajs/api/SwingController.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "SwingController"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "SwingController"); diff --git a/bin/javajs/api/ZInputStream.js b/bin/javajs/api/ZInputStream.js index abc5bb9..7a79598 100644 --- a/bin/javajs/api/ZInputStream.js +++ b/bin/javajs/api/ZInputStream.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.api"); -Clazz.declareInterface (javajs.api, "ZInputStream"); +Clazz.declarePackage ("javajs.api"); +Clazz.declareInterface (javajs.api, "ZInputStream"); diff --git a/bin/javajs/awt/BorderLayout.js b/bin/javajs/awt/BorderLayout.js index 875b476..1686394 100644 --- a/bin/javajs/awt/BorderLayout.js +++ b/bin/javajs/awt/BorderLayout.js @@ -1,10 +1,10 @@ -Clazz.declarePackage ("javajs.awt"); -Clazz.load (["javajs.awt.LayoutManager"], "javajs.awt.BorderLayout", null, function () { -c$ = Clazz.declareType (javajs.awt, "BorderLayout", javajs.awt.LayoutManager); -Clazz.defineStatics (c$, -"CENTER", "Center", -"NORTH", "North", -"SOUTH", "South", -"EAST", "East", -"WEST", "West"); -}); +Clazz.declarePackage ("javajs.awt"); +Clazz.load (["javajs.awt.LayoutManager"], "javajs.awt.BorderLayout", null, function () { +c$ = Clazz.declareType (javajs.awt, "BorderLayout", javajs.awt.LayoutManager); +Clazz.defineStatics (c$, +"CENTER", "Center", +"NORTH", "North", +"SOUTH", "South", +"EAST", "East", +"WEST", "West"); +}); diff --git a/bin/javajs/awt/Color.js b/bin/javajs/awt/Color.js index 1f168d2..725aa31 100644 --- a/bin/javajs/awt/Color.js +++ b/bin/javajs/awt/Color.js @@ -1,43 +1,43 @@ -Clazz.declarePackage ("javajs.awt"); -Clazz.load (["javajs.api.GenericColor"], "javajs.awt.Color", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.argb = 0; -Clazz.instantialize (this, arguments); -}, javajs.awt, "Color", null, javajs.api.GenericColor); -Clazz.overrideMethod (c$, "getRGB", -function () { -return this.argb & 0x00FFFFFF; -}); -Clazz.overrideMethod (c$, "getOpacity255", -function () { -return ((this.argb >> 24) & 0xFF); -}); -Clazz.overrideMethod (c$, "setOpacity255", -function (a) { -this.argb = this.argb & 0xFFFFFF | ((a & 0xFF) << 24); -}, "~N"); -c$.get1 = Clazz.defineMethod (c$, "get1", -function (rgb) { -var c = new javajs.awt.Color (); -c.argb = rgb | 0xFF000000; -return c; -}, "~N"); -c$.get3 = Clazz.defineMethod (c$, "get3", -function (r, g, b) { -return new javajs.awt.Color ().set4 (r, g, b, 0xFF); -}, "~N,~N,~N"); -c$.get4 = Clazz.defineMethod (c$, "get4", -function (r, g, b, a) { -return new javajs.awt.Color ().set4 (r, g, b, a); -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "set4", -($fz = function (r, g, b, a) { -this.argb = ((a << 24) | (r << 16) | (g << 8) | b) & 0xFFFFFFFF; -return this; -}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N"); -Clazz.overrideMethod (c$, "toString", -function () { -var s = ("00000000" + Integer.toHexString (this.argb)); -return "[0x" + s.substring (s.length - 8, s.length) + "]"; -}); -}); +Clazz.declarePackage ("javajs.awt"); +Clazz.load (["javajs.api.GenericColor"], "javajs.awt.Color", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.argb = 0; +Clazz.instantialize (this, arguments); +}, javajs.awt, "Color", null, javajs.api.GenericColor); +Clazz.overrideMethod (c$, "getRGB", +function () { +return this.argb & 0x00FFFFFF; +}); +Clazz.overrideMethod (c$, "getOpacity255", +function () { +return ((this.argb >> 24) & 0xFF); +}); +Clazz.overrideMethod (c$, "setOpacity255", +function (a) { +this.argb = this.argb & 0xFFFFFF | ((a & 0xFF) << 24); +}, "~N"); +c$.get1 = Clazz.defineMethod (c$, "get1", +function (rgb) { +var c = new javajs.awt.Color (); +c.argb = rgb | 0xFF000000; +return c; +}, "~N"); +c$.get3 = Clazz.defineMethod (c$, "get3", +function (r, g, b) { +return new javajs.awt.Color ().set4 (r, g, b, 0xFF); +}, "~N,~N,~N"); +c$.get4 = Clazz.defineMethod (c$, "get4", +function (r, g, b, a) { +return new javajs.awt.Color ().set4 (r, g, b, a); +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "set4", +($fz = function (r, g, b, a) { +this.argb = ((a << 24) | (r << 16) | (g << 8) | b) & 0xFFFFFFFF; +return this; +}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N"); +Clazz.overrideMethod (c$, "toString", +function () { +var s = ("00000000" + Integer.toHexString (this.argb)); +return "[0x" + s.substring (s.length - 8, s.length) + "]"; +}); +}); diff --git a/bin/javajs/awt/Component.js b/bin/javajs/awt/Component.js index f17a3eb..20f1f1a 100644 --- a/bin/javajs/awt/Component.js +++ b/bin/javajs/awt/Component.js @@ -1,120 +1,120 @@ -Clazz.declarePackage ("javajs.awt"); -Clazz.load (null, "javajs.awt.Component", ["javajs.util.CU"], function () { -c$ = Clazz.decorateAsClass (function () { -this.visible = false; -this.enabled = true; -this.text = null; -this.name = null; -this.width = 0; -this.height = 0; -this.id = null; -this.parent = null; -this.mouseListener = null; -this.bgcolor = null; -this.minWidth = 30; -this.minHeight = 30; -this.renderWidth = 0; -this.renderHeight = 0; -Clazz.instantialize (this, arguments); -}, javajs.awt, "Component"); -Clazz.defineMethod (c$, "setParent", -function (p) { -this.parent = p; -}, "~O"); -Clazz.makeConstructor (c$, -function (type) { -this.id = javajs.awt.Component.newID (type); -if (type == null) return; -{ -SwingController.register(this, type); -}}, "~S"); -c$.newID = Clazz.defineMethod (c$, "newID", -function (type) { -return type + ("" + Math.random ()).substring (3, 10); -}, "~S"); -Clazz.defineMethod (c$, "setBackground", -function (color) { -this.bgcolor = color; -}, "javajs.api.GenericColor"); -Clazz.defineMethod (c$, "setText", -function (text) { -this.text = text; -{ -SwingController.setText(this); -}}, "~S"); -Clazz.defineMethod (c$, "setName", -function (name) { -this.name = name; -}, "~S"); -Clazz.defineMethod (c$, "getName", -function () { -return this.name; -}); -Clazz.defineMethod (c$, "getParent", -function () { -return this.parent; -}); -Clazz.defineMethod (c$, "setPreferredSize", -function (dimension) { -this.width = dimension.width; -this.height = dimension.height; -}, "javajs.awt.Dimension"); -Clazz.defineMethod (c$, "addMouseListener", -function (listener) { -this.mouseListener = listener; -}, "~O"); -Clazz.defineMethod (c$, "getText", -function () { -return this.text; -}); -Clazz.defineMethod (c$, "isEnabled", -function () { -return this.enabled; -}); -Clazz.defineMethod (c$, "setEnabled", -function (enabled) { -this.enabled = enabled; -{ -SwingController.setEnabled(this); -}}, "~B"); -Clazz.defineMethod (c$, "isVisible", -function () { -return this.visible; -}); -Clazz.defineMethod (c$, "setVisible", -function (visible) { -this.visible = visible; -{ -SwingController.setVisible(this); -}}, "~B"); -Clazz.defineMethod (c$, "getHeight", -function () { -return this.height; -}); -Clazz.defineMethod (c$, "getWidth", -function () { -return this.width; -}); -Clazz.defineMethod (c$, "setMinimumSize", -function (d) { -this.minWidth = d.width; -this.minHeight = d.height; -}, "javajs.awt.Dimension"); -Clazz.defineMethod (c$, "getSubcomponentWidth", -function () { -return this.width; -}); -Clazz.defineMethod (c$, "getSubcomponentHeight", -function () { -return this.height; -}); -Clazz.defineMethod (c$, "getCSSstyle", -function (defaultPercentW, defaultPercentH) { -var width = (this.renderWidth > 0 ? this.renderWidth : this.getSubcomponentWidth ()); -var height = (this.renderHeight > 0 ? this.renderHeight : this.getSubcomponentHeight ()); -return (width > 0 ? "width:" + width + "px;" : defaultPercentW > 0 ? "width:" + defaultPercentW + "%;" : "") + (height > 0 ? "height:" + height + "px;" : defaultPercentH > 0 ? "height:" + defaultPercentH + "%;" : "") + (this.bgcolor == null ? "" : "background-color:" + javajs.util.CU.toCSSString (this.bgcolor) + ";"); -}, "~N,~N"); -Clazz.defineMethod (c$, "repaint", -function () { -}); -}); +Clazz.declarePackage ("javajs.awt"); +Clazz.load (null, "javajs.awt.Component", ["javajs.util.CU"], function () { +c$ = Clazz.decorateAsClass (function () { +this.visible = false; +this.enabled = true; +this.text = null; +this.name = null; +this.width = 0; +this.height = 0; +this.id = null; +this.parent = null; +this.mouseListener = null; +this.bgcolor = null; +this.minWidth = 30; +this.minHeight = 30; +this.renderWidth = 0; +this.renderHeight = 0; +Clazz.instantialize (this, arguments); +}, javajs.awt, "Component"); +Clazz.defineMethod (c$, "setParent", +function (p) { +this.parent = p; +}, "~O"); +Clazz.makeConstructor (c$, +function (type) { +this.id = javajs.awt.Component.newID (type); +if (type == null) return; +{ +SwingController.register(this, type); +}}, "~S"); +c$.newID = Clazz.defineMethod (c$, "newID", +function (type) { +return type + ("" + Math.random ()).substring (3, 10); +}, "~S"); +Clazz.defineMethod (c$, "setBackground", +function (color) { +this.bgcolor = color; +}, "javajs.api.GenericColor"); +Clazz.defineMethod (c$, "setText", +function (text) { +this.text = text; +{ +SwingController.setText(this); +}}, "~S"); +Clazz.defineMethod (c$, "setName", +function (name) { +this.name = name; +}, "~S"); +Clazz.defineMethod (c$, "getName", +function () { +return this.name; +}); +Clazz.defineMethod (c$, "getParent", +function () { +return this.parent; +}); +Clazz.defineMethod (c$, "setPreferredSize", +function (dimension) { +this.width = dimension.width; +this.height = dimension.height; +}, "javajs.awt.Dimension"); +Clazz.defineMethod (c$, "addMouseListener", +function (listener) { +this.mouseListener = listener; +}, "~O"); +Clazz.defineMethod (c$, "getText", +function () { +return this.text; +}); +Clazz.defineMethod (c$, "isEnabled", +function () { +return this.enabled; +}); +Clazz.defineMethod (c$, "setEnabled", +function (enabled) { +this.enabled = enabled; +{ +SwingController.setEnabled(this); +}}, "~B"); +Clazz.defineMethod (c$, "isVisible", +function () { +return this.visible; +}); +Clazz.defineMethod (c$, "setVisible", +function (visible) { +this.visible = visible; +{ +SwingController.setVisible(this); +}}, "~B"); +Clazz.defineMethod (c$, "getHeight", +function () { +return this.height; +}); +Clazz.defineMethod (c$, "getWidth", +function () { +return this.width; +}); +Clazz.defineMethod (c$, "setMinimumSize", +function (d) { +this.minWidth = d.width; +this.minHeight = d.height; +}, "javajs.awt.Dimension"); +Clazz.defineMethod (c$, "getSubcomponentWidth", +function () { +return this.width; +}); +Clazz.defineMethod (c$, "getSubcomponentHeight", +function () { +return this.height; +}); +Clazz.defineMethod (c$, "getCSSstyle", +function (defaultPercentW, defaultPercentH) { +var width = (this.renderWidth > 0 ? this.renderWidth : this.getSubcomponentWidth ()); +var height = (this.renderHeight > 0 ? this.renderHeight : this.getSubcomponentHeight ()); +return (width > 0 ? "width:" + width + "px;" : defaultPercentW > 0 ? "width:" + defaultPercentW + "%;" : "") + (height > 0 ? "height:" + height + "px;" : defaultPercentH > 0 ? "height:" + defaultPercentH + "%;" : "") + (this.bgcolor == null ? "" : "background-color:" + javajs.util.CU.toCSSString (this.bgcolor) + ";"); +}, "~N,~N"); +Clazz.defineMethod (c$, "repaint", +function () { +}); +}); diff --git a/bin/javajs/awt/Container.js b/bin/javajs/awt/Container.js index fe3fb75..5bb85ea 100644 --- a/bin/javajs/awt/Container.js +++ b/bin/javajs/awt/Container.js @@ -1,65 +1,65 @@ -Clazz.declarePackage ("javajs.awt"); -Clazz.load (["javajs.awt.Component"], "javajs.awt.Container", ["javajs.util.Lst"], function () { -c$ = Clazz.decorateAsClass (function () { -this.list = null; -this.cList = null; -Clazz.instantialize (this, arguments); -}, javajs.awt, "Container", javajs.awt.Component); -Clazz.defineMethod (c$, "getComponent", -function (i) { -return this.list.get (i); -}, "~N"); -Clazz.defineMethod (c$, "getComponentCount", -function () { -return (this.list == null ? 0 : this.list.size ()); -}); -Clazz.defineMethod (c$, "getComponents", -function () { -if (this.cList == null) { -if (this.list == null) return new Array (0); -this.cList = this.list.toArray (); -}return this.cList; -}); -Clazz.defineMethod (c$, "add", -function (component) { -return this.addComponent (component); -}, "javajs.awt.Component"); -Clazz.defineMethod (c$, "addComponent", -function (component) { -if (this.list == null) this.list = new javajs.util.Lst (); -this.list.addLast (component); -this.cList = null; -component.parent = this; -return component; -}, "javajs.awt.Component"); -Clazz.defineMethod (c$, "insertComponent", -function (component, index) { -if (this.list == null) return this.addComponent (component); -this.list.add (index, component); -this.cList = null; -component.parent = this; -return component; -}, "javajs.awt.Component,~N"); -Clazz.defineMethod (c$, "remove", -function (i) { -var c = this.list.remove (i); -c.parent = null; -this.cList = null; -}, "~N"); -Clazz.defineMethod (c$, "removeAll", -function () { -if (this.list != null) { -for (var i = this.list.size (); --i >= 0; ) this.list.get (i).parent = null; - -this.list.clear (); -}this.cList = null; -}); -Clazz.defineMethod (c$, "getSubcomponentWidth", -function () { -return (this.list != null && this.list.size () == 1 ? this.list.get (0).getSubcomponentWidth () : 0); -}); -Clazz.defineMethod (c$, "getSubcomponentHeight", -function () { -return (this.list != null && this.list.size () == 1 ? this.list.get (0).getSubcomponentHeight () : 0); -}); -}); +Clazz.declarePackage ("javajs.awt"); +Clazz.load (["javajs.awt.Component"], "javajs.awt.Container", ["javajs.util.Lst"], function () { +c$ = Clazz.decorateAsClass (function () { +this.list = null; +this.cList = null; +Clazz.instantialize (this, arguments); +}, javajs.awt, "Container", javajs.awt.Component); +Clazz.defineMethod (c$, "getComponent", +function (i) { +return this.list.get (i); +}, "~N"); +Clazz.defineMethod (c$, "getComponentCount", +function () { +return (this.list == null ? 0 : this.list.size ()); +}); +Clazz.defineMethod (c$, "getComponents", +function () { +if (this.cList == null) { +if (this.list == null) return new Array (0); +this.cList = this.list.toArray (); +}return this.cList; +}); +Clazz.defineMethod (c$, "add", +function (component) { +return this.addComponent (component); +}, "javajs.awt.Component"); +Clazz.defineMethod (c$, "addComponent", +function (component) { +if (this.list == null) this.list = new javajs.util.Lst (); +this.list.addLast (component); +this.cList = null; +component.parent = this; +return component; +}, "javajs.awt.Component"); +Clazz.defineMethod (c$, "insertComponent", +function (component, index) { +if (this.list == null) return this.addComponent (component); +this.list.add (index, component); +this.cList = null; +component.parent = this; +return component; +}, "javajs.awt.Component,~N"); +Clazz.defineMethod (c$, "remove", +function (i) { +var c = this.list.remove (i); +c.parent = null; +this.cList = null; +}, "~N"); +Clazz.defineMethod (c$, "removeAll", +function () { +if (this.list != null) { +for (var i = this.list.size (); --i >= 0; ) this.list.get (i).parent = null; + +this.list.clear (); +}this.cList = null; +}); +Clazz.defineMethod (c$, "getSubcomponentWidth", +function () { +return (this.list != null && this.list.size () == 1 ? this.list.get (0).getSubcomponentWidth () : 0); +}); +Clazz.defineMethod (c$, "getSubcomponentHeight", +function () { +return (this.list != null && this.list.size () == 1 ? this.list.get (0).getSubcomponentHeight () : 0); +}); +}); diff --git a/bin/javajs/awt/Dimension.js b/bin/javajs/awt/Dimension.js index 4d21384..448d107 100644 --- a/bin/javajs/awt/Dimension.js +++ b/bin/javajs/awt/Dimension.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("javajs.awt"); -c$ = Clazz.decorateAsClass (function () { -this.width = 0; -this.height = 0; -Clazz.instantialize (this, arguments); -}, javajs.awt, "Dimension"); -Clazz.makeConstructor (c$, -function (w, h) { -this.set (w, h); -}, "~N,~N"); -Clazz.defineMethod (c$, "set", -function (w, h) { -this.width = w; -this.height = h; -return this; -}, "~N,~N"); +Clazz.declarePackage ("javajs.awt"); +c$ = Clazz.decorateAsClass (function () { +this.width = 0; +this.height = 0; +Clazz.instantialize (this, arguments); +}, javajs.awt, "Dimension"); +Clazz.makeConstructor (c$, +function (w, h) { +this.set (w, h); +}, "~N,~N"); +Clazz.defineMethod (c$, "set", +function (w, h) { +this.width = w; +this.height = h; +return this; +}, "~N,~N"); diff --git a/bin/javajs/awt/Font.js b/bin/javajs/awt/Font.js index a5f2df9..809c862 100644 --- a/bin/javajs/awt/Font.js +++ b/bin/javajs/awt/Font.js @@ -1,105 +1,105 @@ -Clazz.declarePackage ("javajs.awt"); -Clazz.load (null, "javajs.awt.Font", ["javajs.util.AU"], function () { -c$ = Clazz.decorateAsClass (function () { -this.fid = 0; -this.fontFace = null; -this.fontStyle = null; -this.fontSizeNominal = 0; -this.idFontFace = 0; -this.idFontStyle = 0; -this.fontSize = 0; -this.font = null; -this.fontMetrics = null; -this.manager = null; -this.ascent = 0; -this.descent = 0; -this.isBold = false; -this.isItalic = false; -Clazz.instantialize (this, arguments); -}, javajs.awt, "Font"); -Clazz.makeConstructor (c$, -($fz = function (manager, fid, idFontFace, idFontStyle, fontSize, fontSizeNominal, graphics) { -this.manager = manager; -this.fid = fid; -this.fontFace = javajs.awt.Font.fontFaces[idFontFace]; -this.fontStyle = javajs.awt.Font.fontStyles[idFontStyle]; -this.idFontFace = idFontFace; -this.idFontStyle = idFontStyle; -this.fontSize = fontSize; -this.isBold = (idFontStyle & 1) == 1; -this.isItalic = (idFontStyle & 2) == 2; -this.fontSizeNominal = fontSizeNominal; -this.font = manager.newFont (javajs.awt.Font.fontFaces[idFontFace], this.isBold, this.isItalic, fontSize); -this.fontMetrics = manager.getFontMetrics (this, graphics); -this.descent = manager.getFontDescent (this.fontMetrics); -this.ascent = manager.getFontAscent (this.fontMetrics); -}, $fz.isPrivate = true, $fz), "javajs.api.FontManager,~N,~N,~N,~N,~N,~O"); -c$.getFont3D = Clazz.defineMethod (c$, "getFont3D", -function (fontID) { -return javajs.awt.Font.font3ds[fontID & 0xFF]; -}, "~N"); -c$.createFont3D = Clazz.defineMethod (c$, "createFont3D", -function (fontface, fontstyle, fontsize, fontsizeNominal, manager, graphicsForMetrics) { -if (fontsize > 0xFF) fontsize = 0xFF; -var fontsizeX16 = (Clazz.floatToInt (fontsize)) << 4; -var fontkey = ((fontface & 3) | ((fontstyle & 3) << 2) | (fontsizeX16 << 4)); -for (var i = javajs.awt.Font.fontkeyCount; --i > 0; ) if (fontkey == javajs.awt.Font.fontkeys[i] && javajs.awt.Font.font3ds[i].fontSizeNominal == fontsizeNominal) return javajs.awt.Font.font3ds[i]; - -var fontIndexNext = javajs.awt.Font.fontkeyCount++; -if (fontIndexNext == javajs.awt.Font.fontkeys.length) javajs.awt.Font.fontkeys = javajs.util.AU.arrayCopyI (javajs.awt.Font.fontkeys, fontIndexNext + 8); -javajs.awt.Font.font3ds = javajs.util.AU.arrayCopyObject (javajs.awt.Font.font3ds, fontIndexNext + 8); -var font3d = new javajs.awt.Font (manager, fontIndexNext, fontface, fontstyle, fontsize, fontsizeNominal, graphicsForMetrics); -javajs.awt.Font.font3ds[fontIndexNext] = font3d; -javajs.awt.Font.fontkeys[fontIndexNext] = fontkey; -return font3d; -}, "~N,~N,~N,~N,javajs.api.FontManager,~O"); -c$.getFontFaceID = Clazz.defineMethod (c$, "getFontFaceID", -function (fontface) { -return ("Monospaced".equalsIgnoreCase (fontface) ? 2 : "Serif".equalsIgnoreCase (fontface) ? 1 : 0); -}, "~S"); -c$.getFontStyleID = Clazz.defineMethod (c$, "getFontStyleID", -function (fontstyle) { -for (var i = 4; --i >= 0; ) if (javajs.awt.Font.fontStyles[i].equalsIgnoreCase (fontstyle)) return i; - -return -1; -}, "~S"); -Clazz.defineMethod (c$, "getAscent", -function () { -return this.ascent; -}); -Clazz.defineMethod (c$, "getDescent", -function () { -return this.descent; -}); -Clazz.defineMethod (c$, "getHeight", -function () { -return this.getAscent () + this.getDescent (); -}); -Clazz.defineMethod (c$, "getFontMetrics", -function () { -return this.fontMetrics; -}); -Clazz.defineMethod (c$, "stringWidth", -function (text) { -return this.manager.fontStringWidth (this, text); -}, "~S"); -Clazz.defineMethod (c$, "getInfo", -function () { -return this.fontSizeNominal + " " + this.fontFace + " " + this.fontStyle; -}); -Clazz.defineStatics (c$, -"FONT_ALLOCATION_UNIT", 8, -"fontkeyCount", 1, -"fontkeys", Clazz.newIntArray (8, 0)); -c$.font3ds = c$.prototype.font3ds = new Array (8); -Clazz.defineStatics (c$, -"FONT_FACE_SANS", 0, -"FONT_FACE_SERIF", 1, -"FONT_FACE_MONO", 2, -"fontFaces", Clazz.newArray (-1, ["SansSerif", "Serif", "Monospaced", ""]), -"FONT_STYLE_PLAIN", 0, -"FONT_STYLE_BOLD", 1, -"FONT_STYLE_ITALIC", 2, -"FONT_STYLE_BOLDITALIC", 3, -"fontStyles", Clazz.newArray (-1, ["Plain", "Bold", "Italic", "BoldItalic"])); -}); +Clazz.declarePackage ("javajs.awt"); +Clazz.load (null, "javajs.awt.Font", ["javajs.util.AU"], function () { +c$ = Clazz.decorateAsClass (function () { +this.fid = 0; +this.fontFace = null; +this.fontStyle = null; +this.fontSizeNominal = 0; +this.idFontFace = 0; +this.idFontStyle = 0; +this.fontSize = 0; +this.font = null; +this.fontMetrics = null; +this.manager = null; +this.ascent = 0; +this.descent = 0; +this.isBold = false; +this.isItalic = false; +Clazz.instantialize (this, arguments); +}, javajs.awt, "Font"); +Clazz.makeConstructor (c$, +($fz = function (manager, fid, idFontFace, idFontStyle, fontSize, fontSizeNominal, graphics) { +this.manager = manager; +this.fid = fid; +this.fontFace = javajs.awt.Font.fontFaces[idFontFace]; +this.fontStyle = javajs.awt.Font.fontStyles[idFontStyle]; +this.idFontFace = idFontFace; +this.idFontStyle = idFontStyle; +this.fontSize = fontSize; +this.isBold = (idFontStyle & 1) == 1; +this.isItalic = (idFontStyle & 2) == 2; +this.fontSizeNominal = fontSizeNominal; +this.font = manager.newFont (javajs.awt.Font.fontFaces[idFontFace], this.isBold, this.isItalic, fontSize); +this.fontMetrics = manager.getFontMetrics (this, graphics); +this.descent = manager.getFontDescent (this.fontMetrics); +this.ascent = manager.getFontAscent (this.fontMetrics); +}, $fz.isPrivate = true, $fz), "javajs.api.FontManager,~N,~N,~N,~N,~N,~O"); +c$.getFont3D = Clazz.defineMethod (c$, "getFont3D", +function (fontID) { +return javajs.awt.Font.font3ds[fontID & 0xFF]; +}, "~N"); +c$.createFont3D = Clazz.defineMethod (c$, "createFont3D", +function (fontface, fontstyle, fontsize, fontsizeNominal, manager, graphicsForMetrics) { +if (fontsize > 0xFF) fontsize = 0xFF; +var fontsizeX16 = (Clazz.floatToInt (fontsize)) << 4; +var fontkey = ((fontface & 3) | ((fontstyle & 3) << 2) | (fontsizeX16 << 4)); +for (var i = javajs.awt.Font.fontkeyCount; --i > 0; ) if (fontkey == javajs.awt.Font.fontkeys[i] && javajs.awt.Font.font3ds[i].fontSizeNominal == fontsizeNominal) return javajs.awt.Font.font3ds[i]; + +var fontIndexNext = javajs.awt.Font.fontkeyCount++; +if (fontIndexNext == javajs.awt.Font.fontkeys.length) javajs.awt.Font.fontkeys = javajs.util.AU.arrayCopyI (javajs.awt.Font.fontkeys, fontIndexNext + 8); +javajs.awt.Font.font3ds = javajs.util.AU.arrayCopyObject (javajs.awt.Font.font3ds, fontIndexNext + 8); +var font3d = new javajs.awt.Font (manager, fontIndexNext, fontface, fontstyle, fontsize, fontsizeNominal, graphicsForMetrics); +javajs.awt.Font.font3ds[fontIndexNext] = font3d; +javajs.awt.Font.fontkeys[fontIndexNext] = fontkey; +return font3d; +}, "~N,~N,~N,~N,javajs.api.FontManager,~O"); +c$.getFontFaceID = Clazz.defineMethod (c$, "getFontFaceID", +function (fontface) { +return ("Monospaced".equalsIgnoreCase (fontface) ? 2 : "Serif".equalsIgnoreCase (fontface) ? 1 : 0); +}, "~S"); +c$.getFontStyleID = Clazz.defineMethod (c$, "getFontStyleID", +function (fontstyle) { +for (var i = 4; --i >= 0; ) if (javajs.awt.Font.fontStyles[i].equalsIgnoreCase (fontstyle)) return i; + +return -1; +}, "~S"); +Clazz.defineMethod (c$, "getAscent", +function () { +return this.ascent; +}); +Clazz.defineMethod (c$, "getDescent", +function () { +return this.descent; +}); +Clazz.defineMethod (c$, "getHeight", +function () { +return this.getAscent () + this.getDescent (); +}); +Clazz.defineMethod (c$, "getFontMetrics", +function () { +return this.fontMetrics; +}); +Clazz.defineMethod (c$, "stringWidth", +function (text) { +return this.manager.fontStringWidth (this, text); +}, "~S"); +Clazz.defineMethod (c$, "getInfo", +function () { +return this.fontSizeNominal + " " + this.fontFace + " " + this.fontStyle; +}); +Clazz.defineStatics (c$, +"FONT_ALLOCATION_UNIT", 8, +"fontkeyCount", 1, +"fontkeys", Clazz.newIntArray (8, 0)); +c$.font3ds = c$.prototype.font3ds = new Array (8); +Clazz.defineStatics (c$, +"FONT_FACE_SANS", 0, +"FONT_FACE_SERIF", 1, +"FONT_FACE_MONO", 2, +"fontFaces", Clazz.newArray (-1, ["SansSerif", "Serif", "Monospaced", ""]), +"FONT_STYLE_PLAIN", 0, +"FONT_STYLE_BOLD", 1, +"FONT_STYLE_ITALIC", 2, +"FONT_STYLE_BOLDITALIC", 3, +"fontStyles", Clazz.newArray (-1, ["Plain", "Bold", "Italic", "BoldItalic"])); +}); diff --git a/bin/javajs/awt/LayoutManager.js b/bin/javajs/awt/LayoutManager.js index 49c8b3a..93d4055 100644 --- a/bin/javajs/awt/LayoutManager.js +++ b/bin/javajs/awt/LayoutManager.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.awt"); -c$ = Clazz.declareType (javajs.awt, "LayoutManager"); +Clazz.declarePackage ("javajs.awt"); +c$ = Clazz.declareType (javajs.awt, "LayoutManager"); diff --git a/bin/javajs/awt/event/ActionEvent.js b/bin/javajs/awt/event/ActionEvent.js index 11f0d44..5ff2dcc 100644 --- a/bin/javajs/awt/event/ActionEvent.js +++ b/bin/javajs/awt/event/ActionEvent.js @@ -1,11 +1,11 @@ -Clazz.declarePackage ("javajs.awt.event"); -Clazz.load (["javajs.awt.event.Event"], "javajs.awt.event.ActionEvent", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.actionCommand = null; -Clazz.instantialize (this, arguments); -}, javajs.awt.event, "ActionEvent", javajs.awt.event.Event); -Clazz.defineMethod (c$, "getActionCommand", -function () { -return this.actionCommand; -}); -}); +Clazz.declarePackage ("javajs.awt.event"); +Clazz.load (["javajs.awt.event.Event"], "javajs.awt.event.ActionEvent", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.actionCommand = null; +Clazz.instantialize (this, arguments); +}, javajs.awt.event, "ActionEvent", javajs.awt.event.Event); +Clazz.defineMethod (c$, "getActionCommand", +function () { +return this.actionCommand; +}); +}); diff --git a/bin/javajs/awt/event/ActionListener.js b/bin/javajs/awt/event/ActionListener.js index c41017a..09f483e 100644 --- a/bin/javajs/awt/event/ActionListener.js +++ b/bin/javajs/awt/event/ActionListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.awt.event"); -Clazz.declareInterface (javajs.awt.event, "ActionListener"); +Clazz.declarePackage ("javajs.awt.event"); +Clazz.declareInterface (javajs.awt.event, "ActionListener"); diff --git a/bin/javajs/awt/event/Event.js b/bin/javajs/awt/event/Event.js index 795e48f..522ac2f 100644 --- a/bin/javajs/awt/event/Event.js +++ b/bin/javajs/awt/event/Event.js @@ -1,49 +1,49 @@ -Clazz.declarePackage ("javajs.awt.event"); -c$ = Clazz.decorateAsClass (function () { -this.source = null; -Clazz.instantialize (this, arguments); -}, javajs.awt.event, "Event"); -Clazz.defineMethod (c$, "getSource", -function () { -return this.source; -}); -Clazz.defineStatics (c$, -"MOUSE_LEFT", 16, -"MOUSE_MIDDLE", 8, -"MOUSE_RIGHT", 4, -"MOUSE_WHEEL", 32, -"MAC_COMMAND", 20, -"BUTTON_MASK", 28, -"MOUSE_DOWN", 501, -"MOUSE_UP", 502, -"MOUSE_MOVE", 503, -"MOUSE_ENTER", 504, -"MOUSE_EXIT", 505, -"MOUSE_DRAG", 506, -"SHIFT_MASK", 1, -"ALT_MASK", 8, -"CTRL_MASK", 2, -"CTRL_ALT", 10, -"CTRL_SHIFT", 3, -"META_MASK", 4, -"VK_SHIFT", 16, -"VK_ALT", 18, -"VK_CONTROL", 17, -"VK_META", 157, -"VK_LEFT", 37, -"VK_RIGHT", 39, -"VK_PERIOD", 46, -"VK_SPACE", 32, -"VK_DOWN", 40, -"VK_UP", 38, -"VK_ESCAPE", 27, -"VK_DELETE", 127, -"VK_BACK_SPACE", 8, -"VK_PAGE_DOWN", 34, -"VK_PAGE_UP", 33, -"MOVED", 0, -"DRAGGED", 1, -"CLICKED", 2, -"WHEELED", 3, -"PRESSED", 4, -"RELEASED", 5); +Clazz.declarePackage ("javajs.awt.event"); +c$ = Clazz.decorateAsClass (function () { +this.source = null; +Clazz.instantialize (this, arguments); +}, javajs.awt.event, "Event"); +Clazz.defineMethod (c$, "getSource", +function () { +return this.source; +}); +Clazz.defineStatics (c$, +"MOUSE_LEFT", 16, +"MOUSE_MIDDLE", 8, +"MOUSE_RIGHT", 4, +"MOUSE_WHEEL", 32, +"MAC_COMMAND", 20, +"BUTTON_MASK", 28, +"MOUSE_DOWN", 501, +"MOUSE_UP", 502, +"MOUSE_MOVE", 503, +"MOUSE_ENTER", 504, +"MOUSE_EXIT", 505, +"MOUSE_DRAG", 506, +"SHIFT_MASK", 1, +"ALT_MASK", 8, +"CTRL_MASK", 2, +"CTRL_ALT", 10, +"CTRL_SHIFT", 3, +"META_MASK", 4, +"VK_SHIFT", 16, +"VK_ALT", 18, +"VK_CONTROL", 17, +"VK_META", 157, +"VK_LEFT", 37, +"VK_RIGHT", 39, +"VK_PERIOD", 46, +"VK_SPACE", 32, +"VK_DOWN", 40, +"VK_UP", 38, +"VK_ESCAPE", 27, +"VK_DELETE", 127, +"VK_BACK_SPACE", 8, +"VK_PAGE_DOWN", 34, +"VK_PAGE_UP", 33, +"MOVED", 0, +"DRAGGED", 1, +"CLICKED", 2, +"WHEELED", 3, +"PRESSED", 4, +"RELEASED", 5); diff --git a/bin/javajs/awt/event/ItemEvent.js b/bin/javajs/awt/event/ItemEvent.js index 8aa944f..b2722ab 100644 --- a/bin/javajs/awt/event/ItemEvent.js +++ b/bin/javajs/awt/event/ItemEvent.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.awt.event"); -Clazz.load (["javajs.awt.event.Event"], "javajs.awt.event.ItemEvent", null, function () { -c$ = Clazz.declareType (javajs.awt.event, "ItemEvent", javajs.awt.event.Event); -}); +Clazz.declarePackage ("javajs.awt.event"); +Clazz.load (["javajs.awt.event.Event"], "javajs.awt.event.ItemEvent", null, function () { +c$ = Clazz.declareType (javajs.awt.event, "ItemEvent", javajs.awt.event.Event); +}); diff --git a/bin/javajs/awt/event/WindowEvent.js b/bin/javajs/awt/event/WindowEvent.js index efa578b..0017c88 100644 --- a/bin/javajs/awt/event/WindowEvent.js +++ b/bin/javajs/awt/event/WindowEvent.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.awt.event"); -Clazz.load (["javajs.awt.event.Event"], "javajs.awt.event.WindowEvent", null, function () { -c$ = Clazz.declareType (javajs.awt.event, "WindowEvent", javajs.awt.event.Event); -}); +Clazz.declarePackage ("javajs.awt.event"); +Clazz.load (["javajs.awt.event.Event"], "javajs.awt.event.WindowEvent", null, function () { +c$ = Clazz.declareType (javajs.awt.event, "WindowEvent", javajs.awt.event.Event); +}); diff --git a/bin/javajs/awt/event/WindowListener.js b/bin/javajs/awt/event/WindowListener.js index bb9e9c5..7656d2f 100644 --- a/bin/javajs/awt/event/WindowListener.js +++ b/bin/javajs/awt/event/WindowListener.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.awt.event"); -Clazz.declareInterface (javajs.awt.event, "WindowListener"); +Clazz.declarePackage ("javajs.awt.event"); +Clazz.declareInterface (javajs.awt.event, "WindowListener"); diff --git a/bin/javajs/export/PDFCreator.js b/bin/javajs/export/PDFCreator.js index 7f5c820..3442530 100644 --- a/bin/javajs/export/PDFCreator.js +++ b/bin/javajs/export/PDFCreator.js @@ -1,300 +1,300 @@ -Clazz.declarePackage ("javajs.export"); -Clazz.load (null, "javajs.export.PDFCreator", ["java.lang.Double", "java.util.Hashtable", "javajs.export.PDFObject", "javajs.util.Lst", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.os = null; -this.indirectObjects = null; -this.root = null; -this.graphics = null; -this.pt = 0; -this.xrefPt = 0; -this.count = 0; -this.height = 0; -this.width = 0; -this.fonts = null; -this.images = null; -Clazz.instantialize (this, arguments); -}, javajs["export"], "PDFCreator"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "setOutputStream", -function (os) { -this.os = os; -}, "java.io.OutputStream"); -Clazz.defineMethod (c$, "newDocument", -function (paperWidth, paperHeight, isLandscape) { -this.width = (isLandscape ? paperHeight : paperWidth); -this.height = (isLandscape ? paperWidth : paperHeight); -System.out.println ("Creating PDF with width=" + this.width + " and height=" + this.height); -this.fonts = new java.util.Hashtable (); -this.indirectObjects = new javajs.util.Lst (); -this.root = this.newObject ("Catalog"); -var pages = this.newObject ("Pages"); -var page = this.newObject ("Page"); -var pageContents = this.newObject (null); -this.graphics = this.newObject ("XObject"); -this.root.addDef ("Pages", pages.getRef ()); -pages.addDef ("Count", "1"); -pages.addDef ("Kids", "[ " + page.getRef () + " ]"); -page.addDef ("Parent", pages.getRef ()); -page.addDef ("MediaBox", "[ 0 0 " + paperWidth + " " + paperHeight + " ]"); -if (isLandscape) page.addDef ("Rotate", "90"); -pageContents.addDef ("Length", "?"); -pageContents.append ((isLandscape ? "q 0 1 1 0 0 0 " : "q 1 0 0 -1 0 " + (paperHeight)) + " cm /" + this.graphics.getID () + " Do Q"); -page.addDef ("Contents", pageContents.getRef ()); -this.addProcSet (page); -this.addProcSet (this.graphics); -this.graphics.addDef ("Subtype", "/Form"); -this.graphics.addDef ("FormType", "1"); -this.graphics.addDef ("BBox", "[0 0 " + this.width + " " + this.height + "]"); -this.graphics.addDef ("Matrix", "[1 0 0 1 0 0]"); -this.graphics.addDef ("Length", "?"); -page.addResource ("XObject", this.graphics.getID (), this.graphics.getRef ()); -this.g ("q 1 w 1 J 1 j 10 M []0 d q "); -this.clip (0, 0, this.width, this.height); -}, "~N,~N,~B"); -Clazz.defineMethod (c$, "addProcSet", -($fz = function (o) { -o.addResource (null, "ProcSet", "[/PDF /Text /ImageB /ImageC /ImageI]"); -}, $fz.isPrivate = true, $fz), "javajs.export.PDFObject"); -Clazz.defineMethod (c$, "clip", -($fz = function (x1, y1, x2, y2) { -this.moveto (x1, y1); -this.lineto (x2, y1); -this.lineto (x2, y2); -this.lineto (x1, y2); -this.g ("h W n"); -}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "moveto", -function (x, y) { -this.g (x + " " + y + " m"); -}, "~N,~N"); -Clazz.defineMethod (c$, "lineto", -function (x, y) { -this.g (x + " " + y + " l"); -}, "~N,~N"); -Clazz.defineMethod (c$, "newObject", -($fz = function (type) { -var o = new javajs["export"].PDFObject (++this.count); -if (type != null) o.addDef ("Type", "/" + type); -this.indirectObjects.addLast (o); -return o; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "addInfo", -function (data) { -var info = new java.util.Hashtable (); -for (var e, $e = data.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) { -var value = "(" + e.getValue ().$replace (')', '_').$replace ('(', '_') + ")"; -info.put (e.getKey (), value); -} -this.root.addDef ("Info", info); -}, "java.util.Map"); -Clazz.defineMethod (c$, "addFontResource", -($fz = function (fname) { -var f = this.newObject ("Font"); -this.fonts.put (fname, f); -f.addDef ("BaseFont", fname); -f.addDef ("Encoding", "/WinAnsiEncoding"); -f.addDef ("Subtype", "/Type1"); -this.graphics.addResource ("Font", f.getID (), f.getRef ()); -return f; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "addImageResource", -function (newImage, width, height, buffer, isRGB) { -var imageObj = this.newObject ("XObject"); -if (this.images == null) this.images = new java.util.Hashtable (); -this.images.put (newImage, imageObj); -imageObj.addDef ("Subtype", "/Image"); -imageObj.addDef ("Length", "?"); -imageObj.addDef ("ColorSpace", isRGB ? "/DeviceRGB" : "/DeviceGray"); -imageObj.addDef ("BitsPerComponent", "8"); -imageObj.addDef ("Width", "" + width); -imageObj.addDef ("Height", "" + height); -this.graphics.addResource ("XObject", imageObj.getID (), imageObj.getRef ()); -var n = buffer.length; -var stream = Clazz.newByteArray (n * (isRGB ? 3 : 1), 0); -if (isRGB) { -for (var i = 0, pt = 0; i < n; i++) { -stream[pt++] = ((buffer[i] >> 16) & 0xFF); -stream[pt++] = ((buffer[i] >> 8) & 0xFF); -stream[pt++] = (buffer[i] & 0xFF); -} -} else { -for (var i = 0; i < n; i++) stream[i] = buffer[i]; - -}imageObj.setStream (stream); -this.graphics.addResource ("XObject", imageObj.getID (), imageObj.getRef ()); -}, "~O,~N,~N,~A,~B"); -Clazz.defineMethod (c$, "g", -function (cmd) { -this.graphics.append (cmd).appendC ('\n'); -}, "~S"); -Clazz.defineMethod (c$, "output", -($fz = function (s) { -var b = s.getBytes (); -this.os.write (b, 0, b.length); -this.pt += b.length; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "closeDocument", -function () { -this.g ("Q Q"); -this.outputHeader (); -this.writeObjects (); -this.writeXRefTable (); -this.writeTrailer (); -this.os.flush (); -this.os.close (); -}); -Clazz.defineMethod (c$, "outputHeader", -($fz = function () { -this.output ("%PDF-1.3\n%"); -var b = Clazz.newByteArray (-1, [-1, -1, -1, -1]); -this.os.write (b, 0, b.length); -this.pt += 4; -this.output ("\n"); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeTrailer", -($fz = function () { -var trailer = new javajs["export"].PDFObject (-2); -this.output ("trailer"); -trailer.addDef ("Size", "" + this.indirectObjects.size ()); -trailer.addDef ("Root", this.root.getRef ()); -trailer.output (this.os); -this.output ("startxref\n"); -this.output ("" + this.xrefPt + "\n"); -this.output ("%%EOF\n"); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeObjects", -($fz = function () { -var nObj = this.indirectObjects.size (); -for (var i = 0; i < nObj; i++) { -var o = this.indirectObjects.get (i); -if (!o.isFont ()) continue; -o.pt = this.pt; -this.pt += o.output (this.os); -} -for (var i = 0; i < nObj; i++) { -var o = this.indirectObjects.get (i); -if (o.isFont ()) continue; -o.pt = this.pt; -this.pt += o.output (this.os); -} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeXRefTable", -($fz = function () { -this.xrefPt = this.pt; -var nObj = this.indirectObjects.size (); -var sb = new javajs.util.SB (); -sb.append ("xref\n0 " + (nObj + 1) + "\n0000000000 65535 f\r\n"); -for (var i = 0; i < nObj; i++) { -var o = this.indirectObjects.get (i); -var s = "0000000000" + o.pt; -sb.append (s.substring (s.length - 10)); -sb.append (" 00000 n\r\n"); -} -this.output (sb.toString ()); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "canDoLineTo", -function () { -return true; -}); -Clazz.defineMethod (c$, "fill", -function () { -this.g ("f"); -}); -Clazz.defineMethod (c$, "stroke", -function () { -this.g ("S"); -}); -Clazz.defineMethod (c$, "doCircle", -function (x, y, r, doFill) { -var d = r * 4 * (Math.sqrt (2) - 1) / 3; -var dx = x; -var dy = y; -this.g ((dx + r) + " " + dy + " m"); -this.g ((dx + r) + " " + (dy + d) + " " + (dx + d) + " " + (dy + r) + " " + (dx) + " " + (dy + r) + " " + " c"); -this.g ((dx - d) + " " + (dy + r) + " " + (dx - r) + " " + (dy + d) + " " + (dx - r) + " " + (dy) + " c"); -this.g ((dx - r) + " " + (dy - d) + " " + (dx - d) + " " + (dy - r) + " " + (dx) + " " + (dy - r) + " c"); -this.g ((dx + d) + " " + (dy - r) + " " + (dx + r) + " " + (dy - d) + " " + (dx + r) + " " + (dy) + " c"); -this.g (doFill ? "f" : "s"); -}, "~N,~N,~N,~B"); -Clazz.defineMethod (c$, "doPolygon", -function (axPoints, ayPoints, nPoints, doFill) { -this.moveto (axPoints[0], ayPoints[0]); -for (var i = 1; i < nPoints; i++) this.lineto (axPoints[i], ayPoints[i]); - -this.g (doFill ? "f" : "s"); -}, "~A,~A,~N,~B"); -Clazz.defineMethod (c$, "doRect", -function (x, y, width, height, doFill) { -this.g (x + " " + y + " " + width + " " + height + " re " + (doFill ? "f" : "s")); -}, "~N,~N,~N,~N,~B"); -Clazz.defineMethod (c$, "drawImage", -function (image, destX0, destY0, destX1, destY1, srcX0, srcY0, srcX1, srcY1) { -var imageObj = this.images.get (image); -if (imageObj == null) return; -this.g ("q"); -this.clip (destX0, destY0, destX1, destY1); -var iw = Double.parseDouble (imageObj.getDef ("Width")); -var ih = Double.parseDouble (imageObj.getDef ("Height")); -var dw = (destX1 - destX0 + 1); -var dh = (destY1 - destY0 + 1); -var sw = (srcX1 - srcX0 + 1); -var sh = (srcY1 - srcY0 + 1); -var scaleX = dw / sw; -var scaleY = dh / sh; -var transX = destX0 - srcX0 * scaleX; -var transY = destY0 + (ih - srcY0) * scaleY; -this.g (scaleX * iw + " 0 0 " + -scaleY * ih + " " + transX + " " + transY + " cm"); -this.g ("/" + imageObj.getID () + " Do"); -this.g ("Q"); -}, "~O,~N,~N,~N,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "drawStringRotated", -function (s, x, y, angle) { -this.g ("q " + this.getRotation (angle) + " " + x + " " + y + " cm BT(" + s + ")Tj ET Q"); -}, "~S,~N,~N,~N"); -Clazz.defineMethod (c$, "getRotation", -function (angle) { -var cos = 0; -var sin = 0; -switch (angle) { -case 0: -cos = 1; -break; -case 90: -sin = 1; -break; -case -90: -sin = -1; -break; -case 180: -cos = -1; -break; -default: -var a = (angle / 180.0 * 3.141592653589793); -cos = Math.cos (a); -sin = Math.sin (a); -if (Math.abs (cos) < 0.0001) cos = 0; -if (Math.abs (sin) < 0.0001) sin = 0; -} -return cos + " " + sin + " " + sin + " " + -cos; -}, "~N"); -Clazz.defineMethod (c$, "setColor", -function (rgb, isFill) { -this.g (rgb[0] + " " + rgb[1] + " " + rgb[2] + (isFill ? " rg" : " RG")); -}, "~A,~B"); -Clazz.defineMethod (c$, "setFont", -function (fname, size) { -var f = this.fonts.get (fname); -if (f == null) f = this.addFontResource (fname); -this.g ("/" + f.getID () + " " + size + " Tf"); -}, "~S,~N"); -Clazz.defineMethod (c$, "setLineWidth", -function (width) { -this.g (width + " w"); -}, "~N"); -Clazz.defineMethod (c$, "translateScale", -function (x, y, scale) { -this.g (scale + " 0 0 " + scale + " " + x + " " + y + " cm"); -}, "~N,~N,~N"); -}); +Clazz.declarePackage ("javajs.export"); +Clazz.load (null, "javajs.export.PDFCreator", ["java.lang.Double", "java.util.Hashtable", "javajs.export.PDFObject", "javajs.util.Lst", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.os = null; +this.indirectObjects = null; +this.root = null; +this.graphics = null; +this.pt = 0; +this.xrefPt = 0; +this.count = 0; +this.height = 0; +this.width = 0; +this.fonts = null; +this.images = null; +Clazz.instantialize (this, arguments); +}, javajs["export"], "PDFCreator"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "setOutputStream", +function (os) { +this.os = os; +}, "java.io.OutputStream"); +Clazz.defineMethod (c$, "newDocument", +function (paperWidth, paperHeight, isLandscape) { +this.width = (isLandscape ? paperHeight : paperWidth); +this.height = (isLandscape ? paperWidth : paperHeight); +System.out.println ("Creating PDF with width=" + this.width + " and height=" + this.height); +this.fonts = new java.util.Hashtable (); +this.indirectObjects = new javajs.util.Lst (); +this.root = this.newObject ("Catalog"); +var pages = this.newObject ("Pages"); +var page = this.newObject ("Page"); +var pageContents = this.newObject (null); +this.graphics = this.newObject ("XObject"); +this.root.addDef ("Pages", pages.getRef ()); +pages.addDef ("Count", "1"); +pages.addDef ("Kids", "[ " + page.getRef () + " ]"); +page.addDef ("Parent", pages.getRef ()); +page.addDef ("MediaBox", "[ 0 0 " + paperWidth + " " + paperHeight + " ]"); +if (isLandscape) page.addDef ("Rotate", "90"); +pageContents.addDef ("Length", "?"); +pageContents.append ((isLandscape ? "q 0 1 1 0 0 0 " : "q 1 0 0 -1 0 " + (paperHeight)) + " cm /" + this.graphics.getID () + " Do Q"); +page.addDef ("Contents", pageContents.getRef ()); +this.addProcSet (page); +this.addProcSet (this.graphics); +this.graphics.addDef ("Subtype", "/Form"); +this.graphics.addDef ("FormType", "1"); +this.graphics.addDef ("BBox", "[0 0 " + this.width + " " + this.height + "]"); +this.graphics.addDef ("Matrix", "[1 0 0 1 0 0]"); +this.graphics.addDef ("Length", "?"); +page.addResource ("XObject", this.graphics.getID (), this.graphics.getRef ()); +this.g ("q 1 w 1 J 1 j 10 M []0 d q "); +this.clip (0, 0, this.width, this.height); +}, "~N,~N,~B"); +Clazz.defineMethod (c$, "addProcSet", +($fz = function (o) { +o.addResource (null, "ProcSet", "[/PDF /Text /ImageB /ImageC /ImageI]"); +}, $fz.isPrivate = true, $fz), "javajs.export.PDFObject"); +Clazz.defineMethod (c$, "clip", +($fz = function (x1, y1, x2, y2) { +this.moveto (x1, y1); +this.lineto (x2, y1); +this.lineto (x2, y2); +this.lineto (x1, y2); +this.g ("h W n"); +}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "moveto", +function (x, y) { +this.g (x + " " + y + " m"); +}, "~N,~N"); +Clazz.defineMethod (c$, "lineto", +function (x, y) { +this.g (x + " " + y + " l"); +}, "~N,~N"); +Clazz.defineMethod (c$, "newObject", +($fz = function (type) { +var o = new javajs["export"].PDFObject (++this.count); +if (type != null) o.addDef ("Type", "/" + type); +this.indirectObjects.addLast (o); +return o; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "addInfo", +function (data) { +var info = new java.util.Hashtable (); +for (var e, $e = data.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) { +var value = "(" + e.getValue ().$replace (')', '_').$replace ('(', '_') + ")"; +info.put (e.getKey (), value); +} +this.root.addDef ("Info", info); +}, "java.util.Map"); +Clazz.defineMethod (c$, "addFontResource", +($fz = function (fname) { +var f = this.newObject ("Font"); +this.fonts.put (fname, f); +f.addDef ("BaseFont", fname); +f.addDef ("Encoding", "/WinAnsiEncoding"); +f.addDef ("Subtype", "/Type1"); +this.graphics.addResource ("Font", f.getID (), f.getRef ()); +return f; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "addImageResource", +function (newImage, width, height, buffer, isRGB) { +var imageObj = this.newObject ("XObject"); +if (this.images == null) this.images = new java.util.Hashtable (); +this.images.put (newImage, imageObj); +imageObj.addDef ("Subtype", "/Image"); +imageObj.addDef ("Length", "?"); +imageObj.addDef ("ColorSpace", isRGB ? "/DeviceRGB" : "/DeviceGray"); +imageObj.addDef ("BitsPerComponent", "8"); +imageObj.addDef ("Width", "" + width); +imageObj.addDef ("Height", "" + height); +this.graphics.addResource ("XObject", imageObj.getID (), imageObj.getRef ()); +var n = buffer.length; +var stream = Clazz.newByteArray (n * (isRGB ? 3 : 1), 0); +if (isRGB) { +for (var i = 0, pt = 0; i < n; i++) { +stream[pt++] = ((buffer[i] >> 16) & 0xFF); +stream[pt++] = ((buffer[i] >> 8) & 0xFF); +stream[pt++] = (buffer[i] & 0xFF); +} +} else { +for (var i = 0; i < n; i++) stream[i] = buffer[i]; + +}imageObj.setStream (stream); +this.graphics.addResource ("XObject", imageObj.getID (), imageObj.getRef ()); +}, "~O,~N,~N,~A,~B"); +Clazz.defineMethod (c$, "g", +function (cmd) { +this.graphics.append (cmd).appendC ('\n'); +}, "~S"); +Clazz.defineMethod (c$, "output", +($fz = function (s) { +var b = s.getBytes (); +this.os.write (b, 0, b.length); +this.pt += b.length; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "closeDocument", +function () { +this.g ("Q Q"); +this.outputHeader (); +this.writeObjects (); +this.writeXRefTable (); +this.writeTrailer (); +this.os.flush (); +this.os.close (); +}); +Clazz.defineMethod (c$, "outputHeader", +($fz = function () { +this.output ("%PDF-1.3\n%"); +var b = Clazz.newByteArray (-1, [-1, -1, -1, -1]); +this.os.write (b, 0, b.length); +this.pt += 4; +this.output ("\n"); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeTrailer", +($fz = function () { +var trailer = new javajs["export"].PDFObject (-2); +this.output ("trailer"); +trailer.addDef ("Size", "" + this.indirectObjects.size ()); +trailer.addDef ("Root", this.root.getRef ()); +trailer.output (this.os); +this.output ("startxref\n"); +this.output ("" + this.xrefPt + "\n"); +this.output ("%%EOF\n"); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeObjects", +($fz = function () { +var nObj = this.indirectObjects.size (); +for (var i = 0; i < nObj; i++) { +var o = this.indirectObjects.get (i); +if (!o.isFont ()) continue; +o.pt = this.pt; +this.pt += o.output (this.os); +} +for (var i = 0; i < nObj; i++) { +var o = this.indirectObjects.get (i); +if (o.isFont ()) continue; +o.pt = this.pt; +this.pt += o.output (this.os); +} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeXRefTable", +($fz = function () { +this.xrefPt = this.pt; +var nObj = this.indirectObjects.size (); +var sb = new javajs.util.SB (); +sb.append ("xref\n0 " + (nObj + 1) + "\n0000000000 65535 f\r\n"); +for (var i = 0; i < nObj; i++) { +var o = this.indirectObjects.get (i); +var s = "0000000000" + o.pt; +sb.append (s.substring (s.length - 10)); +sb.append (" 00000 n\r\n"); +} +this.output (sb.toString ()); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "canDoLineTo", +function () { +return true; +}); +Clazz.defineMethod (c$, "fill", +function () { +this.g ("f"); +}); +Clazz.defineMethod (c$, "stroke", +function () { +this.g ("S"); +}); +Clazz.defineMethod (c$, "doCircle", +function (x, y, r, doFill) { +var d = r * 4 * (Math.sqrt (2) - 1) / 3; +var dx = x; +var dy = y; +this.g ((dx + r) + " " + dy + " m"); +this.g ((dx + r) + " " + (dy + d) + " " + (dx + d) + " " + (dy + r) + " " + (dx) + " " + (dy + r) + " " + " c"); +this.g ((dx - d) + " " + (dy + r) + " " + (dx - r) + " " + (dy + d) + " " + (dx - r) + " " + (dy) + " c"); +this.g ((dx - r) + " " + (dy - d) + " " + (dx - d) + " " + (dy - r) + " " + (dx) + " " + (dy - r) + " c"); +this.g ((dx + d) + " " + (dy - r) + " " + (dx + r) + " " + (dy - d) + " " + (dx + r) + " " + (dy) + " c"); +this.g (doFill ? "f" : "s"); +}, "~N,~N,~N,~B"); +Clazz.defineMethod (c$, "doPolygon", +function (axPoints, ayPoints, nPoints, doFill) { +this.moveto (axPoints[0], ayPoints[0]); +for (var i = 1; i < nPoints; i++) this.lineto (axPoints[i], ayPoints[i]); + +this.g (doFill ? "f" : "s"); +}, "~A,~A,~N,~B"); +Clazz.defineMethod (c$, "doRect", +function (x, y, width, height, doFill) { +this.g (x + " " + y + " " + width + " " + height + " re " + (doFill ? "f" : "s")); +}, "~N,~N,~N,~N,~B"); +Clazz.defineMethod (c$, "drawImage", +function (image, destX0, destY0, destX1, destY1, srcX0, srcY0, srcX1, srcY1) { +var imageObj = this.images.get (image); +if (imageObj == null) return; +this.g ("q"); +this.clip (destX0, destY0, destX1, destY1); +var iw = Double.parseDouble (imageObj.getDef ("Width")); +var ih = Double.parseDouble (imageObj.getDef ("Height")); +var dw = (destX1 - destX0 + 1); +var dh = (destY1 - destY0 + 1); +var sw = (srcX1 - srcX0 + 1); +var sh = (srcY1 - srcY0 + 1); +var scaleX = dw / sw; +var scaleY = dh / sh; +var transX = destX0 - srcX0 * scaleX; +var transY = destY0 + (ih - srcY0) * scaleY; +this.g (scaleX * iw + " 0 0 " + -scaleY * ih + " " + transX + " " + transY + " cm"); +this.g ("/" + imageObj.getID () + " Do"); +this.g ("Q"); +}, "~O,~N,~N,~N,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "drawStringRotated", +function (s, x, y, angle) { +this.g ("q " + this.getRotation (angle) + " " + x + " " + y + " cm BT(" + s + ")Tj ET Q"); +}, "~S,~N,~N,~N"); +Clazz.defineMethod (c$, "getRotation", +function (angle) { +var cos = 0; +var sin = 0; +switch (angle) { +case 0: +cos = 1; +break; +case 90: +sin = 1; +break; +case -90: +sin = -1; +break; +case 180: +cos = -1; +break; +default: +var a = (angle / 180.0 * 3.141592653589793); +cos = Math.cos (a); +sin = Math.sin (a); +if (Math.abs (cos) < 0.0001) cos = 0; +if (Math.abs (sin) < 0.0001) sin = 0; +} +return cos + " " + sin + " " + sin + " " + -cos; +}, "~N"); +Clazz.defineMethod (c$, "setColor", +function (rgb, isFill) { +this.g (rgb[0] + " " + rgb[1] + " " + rgb[2] + (isFill ? " rg" : " RG")); +}, "~A,~B"); +Clazz.defineMethod (c$, "setFont", +function (fname, size) { +var f = this.fonts.get (fname); +if (f == null) f = this.addFontResource (fname); +this.g ("/" + f.getID () + " " + size + " Tf"); +}, "~S,~N"); +Clazz.defineMethod (c$, "setLineWidth", +function (width) { +this.g (width + " w"); +}, "~N"); +Clazz.defineMethod (c$, "translateScale", +function (x, y, scale) { +this.g (scale + " 0 0 " + scale + " " + x + " " + y + " cm"); +}, "~N,~N,~N"); +}); diff --git a/bin/javajs/export/PDFObject.class b/bin/javajs/export/PDFObject.class index c270a41..9a6e8fe 100644 Binary files a/bin/javajs/export/PDFObject.class and b/bin/javajs/export/PDFObject.class differ diff --git a/bin/javajs/export/PDFObject.js b/bin/javajs/export/PDFObject.js index 2752622..ad20c61 100644 --- a/bin/javajs/export/PDFObject.js +++ b/bin/javajs/export/PDFObject.js @@ -1,115 +1,115 @@ -Clazz.declarePackage ("javajs.export"); -Clazz.load (["javajs.util.SB"], "javajs.export.PDFObject", ["java.io.ByteArrayOutputStream", "java.util.Hashtable", "$.Map", "java.util.zip.Deflater", "$.DeflaterOutputStream"], function () { -c$ = Clazz.decorateAsClass (function () { -this.dictionary = null; -this.stream = null; -this.index = 0; -this.type = null; -this.len = 0; -this.pt = 0; -Clazz.instantialize (this, arguments); -}, javajs["export"], "PDFObject", javajs.util.SB); -Clazz.makeConstructor (c$, -function (index) { -Clazz.superConstructor (this, javajs["export"].PDFObject, []); -this.index = index; -}, "~N"); -Clazz.defineMethod (c$, "getRef", -function () { -return this.index + " 0 R"; -}); -Clazz.defineMethod (c$, "getID", -function () { -return this.type.substring (0, 1) + this.index; -}); -Clazz.defineMethod (c$, "isFont", -function () { -return "Font".equals (this.type); -}); -Clazz.defineMethod (c$, "setStream", -function (stream) { -this.stream = stream; -}, "~A"); -Clazz.defineMethod (c$, "getDef", -function (key) { -return this.dictionary.get (key); -}, "~S"); -Clazz.defineMethod (c$, "addDef", -function (key, value) { -if (this.dictionary == null) this.dictionary = new java.util.Hashtable (); -this.dictionary.put (key, value); -if (key.equals ("Type")) this.type = (value).substring (1); -}, "~S,~O"); -Clazz.defineMethod (c$, "setAsStream", -function () { -this.stream = this.toBytes (0, -1); -this.setLength (0); -}); -Clazz.defineMethod (c$, "output", -function (os) { -if (this.index > 0) { -var s = this.index + " 0 obj\n"; -this.write (os, s.getBytes (), 0); -}var streamLen = 0; -if (this.dictionary != null) { -if (this.dictionary.containsKey ("Length")) { -if (this.stream == null) this.setAsStream (); -streamLen = this.stream.length; -var doDeflate = (streamLen > 1000); -if (doDeflate) { -var deflater = new java.util.zip.Deflater (9); -var outBytes = new java.io.ByteArrayOutputStream (1024); -var compBytes = new java.util.zip.DeflaterOutputStream (outBytes, deflater); -compBytes.write (this.stream, 0, streamLen); -compBytes.finish (); -this.stream = outBytes.toByteArray (); -this.dictionary.put ("Filter", "/FlateDecode"); -streamLen = this.stream.length; -}this.dictionary.put ("Length", "" + streamLen); -}this.write (os, this.getDictionaryText (this.dictionary, "\n").getBytes (), 0); -}if (this.length () > 0) this.write (os, this.toString ().getBytes (), 0); -if (this.stream != null) { -this.write (os, "stream\r\n".getBytes (), 0); -this.write (os, this.stream, streamLen); -this.write (os, "\r\nendstream\r\n".getBytes (), 0); -}if (this.index > 0) this.write (os, "endobj\n".getBytes (), 0); -return this.len; -}, "java.io.OutputStream"); -Clazz.defineMethod (c$, "write", -($fz = function (os, bytes, nBytes) { -if (nBytes == 0) nBytes = bytes.length; -this.len += nBytes; -os.write (bytes, 0, nBytes); -}, $fz.isPrivate = true, $fz), "java.io.OutputStream,~A,~N"); -Clazz.defineMethod (c$, "getDictionaryText", -($fz = function (d, nl) { -var sb = new javajs.util.SB (); -sb.append ("<<"); -if (d.containsKey ("Type")) sb.append ("/Type").appendO (d.get ("Type")); -for (var e, $e = d.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) { -var s = e.getKey (); -if (s.equals ("Type") || s.startsWith ("!")) continue; -sb.append ("/" + s); -var o = e.getValue (); -if (Clazz.instanceOf (o, java.util.Map)) { -sb.append ((this.getDictionaryText (o, ""))); -continue; -}s = e.getValue (); -if (!s.startsWith ("/")) sb.append (" "); -sb.appendO (s); -} -return (sb.length () > 3 ? sb.append (">>").append (nl).toString () : ""); -}, $fz.isPrivate = true, $fz), "java.util.Map,~S"); -Clazz.defineMethod (c$, "createSubdict", -($fz = function (d0, dict) { -var d = d0.get (dict); -if (d == null) d0.put (dict, d = new java.util.Hashtable ()); -return d; -}, $fz.isPrivate = true, $fz), "java.util.Map,~S"); -Clazz.defineMethod (c$, "addResource", -function (type, key, value) { -var r = this.createSubdict (this.dictionary, "Resources"); -if (type != null) r = this.createSubdict (r, type); -r.put (key, value); -}, "~S,~S,~S"); -}); +Clazz.declarePackage ("javajs.export"); +Clazz.load (["javajs.util.SB"], "javajs.export.PDFObject", ["java.io.ByteArrayOutputStream", "java.util.Hashtable", "$.Map", "java.util.zip.Deflater", "$.DeflaterOutputStream"], function () { +c$ = Clazz.decorateAsClass (function () { +this.dictionary = null; +this.stream = null; +this.index = 0; +this.type = null; +this.len = 0; +this.pt = 0; +Clazz.instantialize (this, arguments); +}, javajs["export"], "PDFObject", javajs.util.SB); +Clazz.makeConstructor (c$, +function (index) { +Clazz.superConstructor (this, javajs["export"].PDFObject, []); +this.index = index; +}, "~N"); +Clazz.defineMethod (c$, "getRef", +function () { +return this.index + " 0 R"; +}); +Clazz.defineMethod (c$, "getID", +function () { +return this.type.substring (0, 1) + this.index; +}); +Clazz.defineMethod (c$, "isFont", +function () { +return "Font".equals (this.type); +}); +Clazz.defineMethod (c$, "setStream", +function (stream) { +this.stream = stream; +}, "~A"); +Clazz.defineMethod (c$, "getDef", +function (key) { +return this.dictionary.get (key); +}, "~S"); +Clazz.defineMethod (c$, "addDef", +function (key, value) { +if (this.dictionary == null) this.dictionary = new java.util.Hashtable (); +this.dictionary.put (key, value); +if (key.equals ("Type")) this.type = (value).substring (1); +}, "~S,~O"); +Clazz.defineMethod (c$, "setAsStream", +function () { +this.stream = this.toBytes (0, -1); +this.setLength (0); +}); +Clazz.defineMethod (c$, "output", +function (os) { +if (this.index > 0) { +var s = this.index + " 0 obj\n"; +this.write (os, s.getBytes (), 0); +}var streamLen = 0; +if (this.dictionary != null) { +if (this.dictionary.containsKey ("Length")) { +if (this.stream == null) this.setAsStream (); +streamLen = this.stream.length; +var doDeflate = (streamLen > 1000); +if (doDeflate) { +var deflater = new java.util.zip.Deflater (9); +var outBytes = new java.io.ByteArrayOutputStream (1024); +var compBytes = new java.util.zip.DeflaterOutputStream (outBytes, deflater); +compBytes.write (this.stream, 0, streamLen); +compBytes.finish (); +this.stream = outBytes.toByteArray (); +this.dictionary.put ("Filter", "/FlateDecode"); +streamLen = this.stream.length; +}this.dictionary.put ("Length", "" + streamLen); +}this.write (os, this.getDictionaryText (this.dictionary, "\n").getBytes (), 0); +}if (this.length () > 0) this.write (os, this.toString ().getBytes (), 0); +if (this.stream != null) { +this.write (os, "stream\r\n".getBytes (), 0); +this.write (os, this.stream, streamLen); +this.write (os, "\r\nendstream\r\n".getBytes (), 0); +}if (this.index > 0) this.write (os, "endobj\n".getBytes (), 0); +return this.len; +}, "java.io.OutputStream"); +Clazz.defineMethod (c$, "write", +($fz = function (os, bytes, nBytes) { +if (nBytes == 0) nBytes = bytes.length; +this.len += nBytes; +os.write (bytes, 0, nBytes); +}, $fz.isPrivate = true, $fz), "java.io.OutputStream,~A,~N"); +Clazz.defineMethod (c$, "getDictionaryText", +($fz = function (d, nl) { +var sb = new javajs.util.SB (); +sb.append ("<<"); +if (d.containsKey ("Type")) sb.append ("/Type").appendO (d.get ("Type")); +for (var e, $e = d.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) { +var s = e.getKey (); +if (s.equals ("Type") || s.startsWith ("!")) continue; +sb.append ("/" + s); +var o = e.getValue (); +if (Clazz.instanceOf (o, java.util.Map)) { +sb.append ((this.getDictionaryText (o, ""))); +continue; +}s = e.getValue (); +if (!s.startsWith ("/")) sb.append (" "); +sb.appendO (s); +} +return (sb.length () > 3 ? sb.append (">>").append (nl).toString () : ""); +}, $fz.isPrivate = true, $fz), "java.util.Map,~S"); +Clazz.defineMethod (c$, "createSubdict", +($fz = function (d0, dict) { +var d = d0.get (dict); +if (d == null) d0.put (dict, d = new java.util.Hashtable ()); +return d; +}, $fz.isPrivate = true, $fz), "java.util.Map,~S"); +Clazz.defineMethod (c$, "addResource", +function (type, key, value) { +var r = this.createSubdict (this.dictionary, "Resources"); +if (type != null) r = this.createSubdict (r, type); +r.put (key, value); +}, "~S,~S,~S"); +}); diff --git a/bin/javajs/img/BMPDecoder.js b/bin/javajs/img/BMPDecoder.js index b32016b..c3b4dc7 100644 --- a/bin/javajs/img/BMPDecoder.js +++ b/bin/javajs/img/BMPDecoder.js @@ -1,144 +1,144 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (null, "javajs.img.BMPDecoder", ["javajs.util.Rdr"], function () { -c$ = Clazz.decorateAsClass (function () { -this.bis = null; -this.temp = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "BMPDecoder"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "decodeWindowsBMP", -function (bytes) { -try { -this.bis = javajs.util.Rdr.getBIS (bytes); -this.temp = Clazz.newByteArray (4, 0); -if (this.readByte () != 66 || this.readByte () != 77) return null; -this.readInt (); -this.readShort (); -this.readShort (); -this.readInt (); -var imageWidth; -var imageHeight; -var bitsPerPixel; -var nColors = 0; -var imageSize = 0; -var headerSize = this.readInt (); -switch (headerSize) { -case 12: -imageWidth = this.readShort (); -imageHeight = this.readShort (); -this.readShort (); -bitsPerPixel = this.readShort (); -break; -case 40: -imageWidth = this.readInt (); -imageHeight = this.readInt (); -this.readShort (); -bitsPerPixel = this.readShort (); -var ncompression = this.readInt (); -if (ncompression != 0) { -System.out.println ("BMP Compression is :" + ncompression + " -- aborting"); -return null; -}imageSize = this.readInt (); -this.readInt (); -this.readInt (); -nColors = this.readInt (); -this.readInt (); -break; -default: -System.out.println ("BMP Header unrecognized, length=" + headerSize + " -- aborting"); -return null; -} -var isYReversed = (imageHeight < 0); -if (isYReversed) imageHeight = -imageHeight; -var nPixels = imageHeight * imageWidth; -var bytesPerPixel = Clazz.doubleToInt (bitsPerPixel / 8); -nColors = (nColors > 0 ? nColors : 1 << bitsPerPixel); -var npad = (bytesPerPixel == 4 ? 0 : imageSize == 0 ? 4 - (imageWidth % 4) : (Clazz.doubleToInt (imageSize / imageHeight)) - imageWidth * bytesPerPixel) % 4; -var palette; -var buf = Clazz.newIntArray (nPixels, 0); -var dpt = (isYReversed ? imageWidth : -imageWidth); -var pt0 = (isYReversed ? 0 : nPixels + dpt); -var pt1 = (isYReversed ? nPixels : dpt); -switch (bitsPerPixel) { -case 32: -case 24: -for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0; i < imageWidth; i++) buf[pt + i] = this.readColor (bytesPerPixel); - - -break; -case 8: -palette = Clazz.newIntArray (nColors, 0); -for (var i = 0; i < nColors; i++) palette[i] = this.readColor (4); - -for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0; i < imageWidth; i++) buf[pt + i] = palette[this.readByte ()]; - - -break; -case 4: -npad = (4 - ((Clazz.doubleToInt ((imageWidth + 1) / 2)) % 4)) % 4; -palette = Clazz.newIntArray (nColors, 0); -for (var i = 0; i < nColors; i++) palette[i] = this.readColor (4); - -var b4 = 0; -for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0, shift = 4; i < imageWidth; i++, shift = 4 - shift) buf[pt + i] = palette[((shift == 4 ? (b4 = this.readByte ()) : b4) >> shift) & 0xF]; - - -break; -case 1: -var color1 = this.readColor (3); -var color2 = this.readColor (3); -npad = (4 - ((Clazz.doubleToInt ((imageWidth + 7) / 8)) % 4)) % 4; -var b = 0; -for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0, bpt = -1; i < imageWidth; i++, bpt--) { -if (bpt < 0) { -b = this.readByte (); -bpt = 7; -}buf[pt + i] = ((b & (1 << bpt)) == 0 ? color1 : color2); -} - -break; -case 64: -case 2: -default: -System.out.println ("Not a 32-, 24-, 8-, 4-, or 1-bit Windows Bitmap, aborting..."); -return null; -} -return Clazz.newArray (-1, [buf, Integer.$valueOf (imageWidth), Integer.$valueOf (imageHeight)]); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println ("Caught exception in loadbitmap!"); -} else { -throw e; -} -} -return null; -}, "~A"); -Clazz.defineMethod (c$, "pad", -($fz = function (npad) { -for (var i = 0; i < npad; i++) this.readByte (); - -return true; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "readColor", -($fz = function (n) { -this.bis.read (this.temp, 0, n); -return -16777216 | ((this.temp[2] & 0xff) << 16) | ((this.temp[1] & 0xff) << 8) | this.temp[0] & 0xff; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "readInt", -($fz = function () { -this.bis.read (this.temp, 0, 4); -return ((this.temp[3] & 0xff) << 24) | ((this.temp[2] & 0xff) << 16) | ((this.temp[1] & 0xff) << 8) | this.temp[0] & 0xff; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "readShort", -($fz = function () { -this.bis.read (this.temp, 0, 2); -return ((this.temp[1] & 0xff) << 8) | this.temp[0] & 0xff; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "readByte", -($fz = function () { -this.bis.read (this.temp, 0, 1); -return this.temp[0] & 0xff; -}, $fz.isPrivate = true, $fz)); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (null, "javajs.img.BMPDecoder", ["javajs.util.Rdr"], function () { +c$ = Clazz.decorateAsClass (function () { +this.bis = null; +this.temp = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "BMPDecoder"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "decodeWindowsBMP", +function (bytes) { +try { +this.bis = javajs.util.Rdr.getBIS (bytes); +this.temp = Clazz.newByteArray (4, 0); +if (this.readByte () != 66 || this.readByte () != 77) return null; +this.readInt (); +this.readShort (); +this.readShort (); +this.readInt (); +var imageWidth; +var imageHeight; +var bitsPerPixel; +var nColors = 0; +var imageSize = 0; +var headerSize = this.readInt (); +switch (headerSize) { +case 12: +imageWidth = this.readShort (); +imageHeight = this.readShort (); +this.readShort (); +bitsPerPixel = this.readShort (); +break; +case 40: +imageWidth = this.readInt (); +imageHeight = this.readInt (); +this.readShort (); +bitsPerPixel = this.readShort (); +var ncompression = this.readInt (); +if (ncompression != 0) { +System.out.println ("BMP Compression is :" + ncompression + " -- aborting"); +return null; +}imageSize = this.readInt (); +this.readInt (); +this.readInt (); +nColors = this.readInt (); +this.readInt (); +break; +default: +System.out.println ("BMP Header unrecognized, length=" + headerSize + " -- aborting"); +return null; +} +var isYReversed = (imageHeight < 0); +if (isYReversed) imageHeight = -imageHeight; +var nPixels = imageHeight * imageWidth; +var bytesPerPixel = Clazz.doubleToInt (bitsPerPixel / 8); +nColors = (nColors > 0 ? nColors : 1 << bitsPerPixel); +var npad = (bytesPerPixel == 4 ? 0 : imageSize == 0 ? 4 - (imageWidth % 4) : (Clazz.doubleToInt (imageSize / imageHeight)) - imageWidth * bytesPerPixel) % 4; +var palette; +var buf = Clazz.newIntArray (nPixels, 0); +var dpt = (isYReversed ? imageWidth : -imageWidth); +var pt0 = (isYReversed ? 0 : nPixels + dpt); +var pt1 = (isYReversed ? nPixels : dpt); +switch (bitsPerPixel) { +case 32: +case 24: +for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0; i < imageWidth; i++) buf[pt + i] = this.readColor (bytesPerPixel); + + +break; +case 8: +palette = Clazz.newIntArray (nColors, 0); +for (var i = 0; i < nColors; i++) palette[i] = this.readColor (4); + +for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0; i < imageWidth; i++) buf[pt + i] = palette[this.readByte ()]; + + +break; +case 4: +npad = (4 - ((Clazz.doubleToInt ((imageWidth + 1) / 2)) % 4)) % 4; +palette = Clazz.newIntArray (nColors, 0); +for (var i = 0; i < nColors; i++) palette[i] = this.readColor (4); + +var b4 = 0; +for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0, shift = 4; i < imageWidth; i++, shift = 4 - shift) buf[pt + i] = palette[((shift == 4 ? (b4 = this.readByte ()) : b4) >> shift) & 0xF]; + + +break; +case 1: +var color1 = this.readColor (3); +var color2 = this.readColor (3); +npad = (4 - ((Clazz.doubleToInt ((imageWidth + 7) / 8)) % 4)) % 4; +var b = 0; +for (var pt = pt0; pt != pt1; pt += dpt, this.pad (npad)) for (var i = 0, bpt = -1; i < imageWidth; i++, bpt--) { +if (bpt < 0) { +b = this.readByte (); +bpt = 7; +}buf[pt + i] = ((b & (1 << bpt)) == 0 ? color1 : color2); +} + +break; +case 64: +case 2: +default: +System.out.println ("Not a 32-, 24-, 8-, 4-, or 1-bit Windows Bitmap, aborting..."); +return null; +} +return Clazz.newArray (-1, [buf, Integer.$valueOf (imageWidth), Integer.$valueOf (imageHeight)]); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println ("Caught exception in loadbitmap!"); +} else { +throw e; +} +} +return null; +}, "~A"); +Clazz.defineMethod (c$, "pad", +($fz = function (npad) { +for (var i = 0; i < npad; i++) this.readByte (); + +return true; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "readColor", +($fz = function (n) { +this.bis.read (this.temp, 0, n); +return -16777216 | ((this.temp[2] & 0xff) << 16) | ((this.temp[1] & 0xff) << 8) | this.temp[0] & 0xff; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "readInt", +($fz = function () { +this.bis.read (this.temp, 0, 4); +return ((this.temp[3] & 0xff) << 24) | ((this.temp[2] & 0xff) << 16) | ((this.temp[1] & 0xff) << 8) | this.temp[0] & 0xff; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "readShort", +($fz = function () { +this.bis.read (this.temp, 0, 2); +return ((this.temp[1] & 0xff) << 8) | this.temp[0] & 0xff; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "readByte", +($fz = function () { +this.bis.read (this.temp, 0, 1); +return this.temp[0] & 0xff; +}, $fz.isPrivate = true, $fz)); +}); diff --git a/bin/javajs/img/CRCEncoder.js b/bin/javajs/img/CRCEncoder.js index 3a7582e..2dca50d 100644 --- a/bin/javajs/img/CRCEncoder.js +++ b/bin/javajs/img/CRCEncoder.js @@ -1,74 +1,74 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.ImageEncoder"], "javajs.img.CRCEncoder", ["java.util.zip.CRC32", "javajs.util.AU"], function () { -c$ = Clazz.decorateAsClass (function () { -this.startPos = 0; -this.bytePos = 0; -this.crc = null; -this.pngBytes = null; -this.dataLen = 0; -this.int2 = null; -this.int4 = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "CRCEncoder", javajs.img.ImageEncoder); -Clazz.prepareFields (c$, function () { -this.int2 = Clazz.newByteArray (2, 0); -this.int4 = Clazz.newByteArray (4, 0); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.img.CRCEncoder, []); -this.pngBytes = Clazz.newByteArray (250, 0); -this.crc = new java.util.zip.CRC32 (); -}); -Clazz.defineMethod (c$, "setData", -function (b, pt) { -this.pngBytes = b; -this.dataLen = b.length; -this.startPos = this.bytePos = pt; -}, "~A,~N"); -Clazz.defineMethod (c$, "getBytes", -function () { -return (this.dataLen == this.pngBytes.length ? this.pngBytes : javajs.util.AU.arrayCopyByte (this.pngBytes, this.dataLen)); -}); -Clazz.defineMethod (c$, "writeCRC", -function () { -this.crc.reset (); -this.crc.update (this.pngBytes, this.startPos, this.bytePos - this.startPos); -this.writeInt4 (this.crc.getValue ()); -}); -Clazz.defineMethod (c$, "writeInt2", -function (n) { -this.int2[0] = ((n >> 8) & 0xff); -this.int2[1] = (n & 0xff); -this.writeBytes (this.int2); -}, "~N"); -Clazz.defineMethod (c$, "writeInt4", -function (n) { -javajs.img.CRCEncoder.getInt4 (n, this.int4); -this.writeBytes (this.int4); -}, "~N"); -c$.getInt4 = Clazz.defineMethod (c$, "getInt4", -function (n, int4) { -int4[0] = ((n >> 24) & 0xff); -int4[1] = ((n >> 16) & 0xff); -int4[2] = ((n >> 8) & 0xff); -int4[3] = (n & 0xff); -}, "~N,~A"); -Clazz.defineMethod (c$, "writeByte", -function (b) { -var temp = Clazz.newByteArray (-1, [b]); -this.writeBytes (temp); -}, "~N"); -Clazz.defineMethod (c$, "writeString", -function (s) { -this.writeBytes (s.getBytes ()); -}, "~S"); -Clazz.defineMethod (c$, "writeBytes", -function (data) { -var newPos = this.bytePos + data.length; -this.dataLen = Math.max (this.dataLen, newPos); -if (newPos > this.pngBytes.length) this.pngBytes = javajs.util.AU.arrayCopyByte (this.pngBytes, newPos + 16); -System.arraycopy (data, 0, this.pngBytes, this.bytePos, data.length); -this.bytePos = newPos; -}, "~A"); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.ImageEncoder"], "javajs.img.CRCEncoder", ["java.util.zip.CRC32", "javajs.util.AU"], function () { +c$ = Clazz.decorateAsClass (function () { +this.startPos = 0; +this.bytePos = 0; +this.crc = null; +this.pngBytes = null; +this.dataLen = 0; +this.int2 = null; +this.int4 = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "CRCEncoder", javajs.img.ImageEncoder); +Clazz.prepareFields (c$, function () { +this.int2 = Clazz.newByteArray (2, 0); +this.int4 = Clazz.newByteArray (4, 0); +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.img.CRCEncoder, []); +this.pngBytes = Clazz.newByteArray (250, 0); +this.crc = new java.util.zip.CRC32 (); +}); +Clazz.defineMethod (c$, "setData", +function (b, pt) { +this.pngBytes = b; +this.dataLen = b.length; +this.startPos = this.bytePos = pt; +}, "~A,~N"); +Clazz.defineMethod (c$, "getBytes", +function () { +return (this.dataLen == this.pngBytes.length ? this.pngBytes : javajs.util.AU.arrayCopyByte (this.pngBytes, this.dataLen)); +}); +Clazz.defineMethod (c$, "writeCRC", +function () { +this.crc.reset (); +this.crc.update (this.pngBytes, this.startPos, this.bytePos - this.startPos); +this.writeInt4 (this.crc.getValue ()); +}); +Clazz.defineMethod (c$, "writeInt2", +function (n) { +this.int2[0] = ((n >> 8) & 0xff); +this.int2[1] = (n & 0xff); +this.writeBytes (this.int2); +}, "~N"); +Clazz.defineMethod (c$, "writeInt4", +function (n) { +javajs.img.CRCEncoder.getInt4 (n, this.int4); +this.writeBytes (this.int4); +}, "~N"); +c$.getInt4 = Clazz.defineMethod (c$, "getInt4", +function (n, int4) { +int4[0] = ((n >> 24) & 0xff); +int4[1] = ((n >> 16) & 0xff); +int4[2] = ((n >> 8) & 0xff); +int4[3] = (n & 0xff); +}, "~N,~A"); +Clazz.defineMethod (c$, "writeByte", +function (b) { +var temp = Clazz.newByteArray (-1, [b]); +this.writeBytes (temp); +}, "~N"); +Clazz.defineMethod (c$, "writeString", +function (s) { +this.writeBytes (s.getBytes ()); +}, "~S"); +Clazz.defineMethod (c$, "writeBytes", +function (data) { +var newPos = this.bytePos + data.length; +this.dataLen = Math.max (this.dataLen, newPos); +if (newPos > this.pngBytes.length) this.pngBytes = javajs.util.AU.arrayCopyByte (this.pngBytes, newPos + 16); +System.arraycopy (data, 0, this.pngBytes, this.bytePos, data.length); +this.bytePos = newPos; +}, "~A"); +}); diff --git a/bin/javajs/img/GifEncoder$ColorCell.class b/bin/javajs/img/GifEncoder$ColorCell.class index 738eed0..305c142 100644 Binary files a/bin/javajs/img/GifEncoder$ColorCell.class and b/bin/javajs/img/GifEncoder$ColorCell.class differ diff --git a/bin/javajs/img/GifEncoder.class b/bin/javajs/img/GifEncoder.class index ee78a46..a2954d3 100644 Binary files a/bin/javajs/img/GifEncoder.class and b/bin/javajs/img/GifEncoder.class differ diff --git a/bin/javajs/img/GifEncoder.js b/bin/javajs/img/GifEncoder.js index dd22f43..9170951 100644 --- a/bin/javajs/img/GifEncoder.js +++ b/bin/javajs/img/GifEncoder.js @@ -1,627 +1,627 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.ImageEncoder", "javajs.util.Lst", "$.P3"], "javajs.img.GifEncoder", ["java.lang.Boolean", "java.util.Hashtable", "javajs.util.CU", "$.M3"], function () { -c$ = Clazz.decorateAsClass (function () { -this.params = null; -this.palette = null; -this.backgroundColor = 0; -this.interlaced = false; -this.addHeader = true; -this.addImage = true; -this.addTrailer = true; -this.isTransparent = false; -this.floydSteinberg = true; -this.capturing = false; -this.looping = false; -this.delayTime100ths = -1; -this.bitsPerPixel = 1; -this.byteCount = 0; -if (!Clazz.isClassDefined ("javajs.img.GifEncoder.ColorItem")) { -javajs.img.GifEncoder.$GifEncoder$ColorItem$ (); -} -if (!Clazz.isClassDefined ("javajs.img.GifEncoder.ColorCell")) { -javajs.img.GifEncoder.$GifEncoder$ColorCell$ (); -} -this.initCodeSize = 0; -this.curpt = 0; -this.nBits = 0; -this.maxbits = 12; -this.maxcode = 0; -this.maxmaxcode = 4096; -this.htab = null; -this.codetab = null; -this.hsize = 5003; -this.freeEnt = 0; -this.clearFlag = false; -this.clearCode = 0; -this.EOFCode = 0; -this.countDown = 0; -this.pass = 0; -this.curx = 0; -this.cury = 0; -this.curAccum = 0; -this.curBits = 0; -this.masks = null; -this.bufPt = 0; -this.buf = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "GifEncoder", javajs.img.ImageEncoder); -Clazz.prepareFields (c$, function () { -this.htab = Clazz.newIntArray (5003, 0); -this.codetab = Clazz.newIntArray (5003, 0); -this.masks = Clazz.newIntArray (-1, [0x0000, 0x0001, 0x0003, 0x0007, 0x000F, 0x001F, 0x003F, 0x007F, 0x00FF, 0x01FF, 0x03FF, 0x07FF, 0x0FFF, 0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF]); -this.buf = Clazz.newByteArray (256, 0); -}); -Clazz.overrideMethod (c$, "setParams", -function (params) { -this.params = params; -var ic = params.get ("transparentColor"); -if (ic == null) { -ic = params.get ("backgroundColor"); -if (ic != null) this.backgroundColor = ic.intValue (); -} else { -this.backgroundColor = ic.intValue (); -this.isTransparent = true; -}this.interlaced = (Boolean.TRUE === params.get ("interlaced")); -if (params.containsKey ("captureRootExt") || !params.containsKey ("captureMode")) return; -this.interlaced = false; -this.capturing = true; -try { -this.byteCount = (params.get ("captureByteCount")).intValue (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -switch ("maec".indexOf ((params.get ("captureMode")).substring (0, 1))) { -case 0: -params.put ("captureMode", "add"); -this.addImage = false; -this.addTrailer = false; -break; -case 1: -this.addHeader = false; -this.addTrailer = false; -var fps = Math.abs ((params.get ("captureFps")).intValue ()); -this.delayTime100ths = (fps == 0 ? 0 : Clazz.doubleToInt (100 / fps)); -this.looping = (Boolean.FALSE !== params.get ("captureLooping")); -break; -case 2: -this.addHeader = false; -this.addImage = false; -break; -case 3: -this.addHeader = false; -this.addImage = false; -this.out.cancel (); -break; -} -}, "java.util.Map"); -Clazz.overrideMethod (c$, "generate", -function () { -if (this.addHeader) this.writeHeader (); -this.addHeader = false; -if (this.addImage) { -this.createPalette (); -this.writeGraphicControlExtension (); -if (this.delayTime100ths >= 0 && this.looping) this.writeNetscapeLoopExtension (); -this.writeImage (); -}}); -Clazz.overrideMethod (c$, "close", -function () { -if (this.addTrailer) { -this.writeTrailer (); -} else { -this.doClose = false; -}if (this.capturing) this.params.put ("captureByteCount", Integer.$valueOf (this.byteCount)); -}); -Clazz.defineMethod (c$, "createPalette", -($fz = function () { -var tempColors = new javajs.util.Lst (); -var ciHash = new java.util.Hashtable (); -for (var i = 0, n = this.pixels.length; i < n; i++) { -var rgb = this.pixels[i]; -var key = Integer.$valueOf (rgb); -var item = ciHash.get (key); -if (item == null) { -item = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorItem, this, null, rgb, rgb == this.backgroundColor); -ciHash.put (key, item); -tempColors.addLast (item); -}} -var nColors = tempColors.size (); -System.out.println ("GIF total image colors: " + nColors); -ciHash = null; -var cells = this.quantizeColors (tempColors); -nColors = cells.size (); -System.out.println ("GIF final color count: " + nColors); -var colorMap = new java.util.Hashtable (); -this.bitsPerPixel = (nColors <= 2 ? 1 : nColors <= 4 ? 2 : nColors <= 16 ? 4 : 8); -this.palette = new Array (1 << this.bitsPerPixel); -for (var i = 0; i < nColors; i++) { -var c = cells.get (i); -colorMap.put (Integer.$valueOf (javajs.util.CU.colorPtToFFRGB (this.palette[i] = c.setColor ())), c); -} -this.pixels = this.indexPixels (cells, colorMap); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "quantizeColors", -($fz = function (tempColors) { -var n = tempColors.size (); -var cells = new javajs.util.Lst (); -var cc = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, 0); -cc.addLast (Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorItem, this, null, this.backgroundColor, true)); -cells.addLast (cc); -cc = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, 1); -if (n > 256) cells.addLast (cc); -for (var i = 0; i < n; i++) { -var c = tempColors.get (i); -if (c.isBackground) continue; -cc.addLast (c); -if (n <= 256) { -cells.addLast (cc); -cc = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, cells.size ()); -}} -tempColors.clear (); -if (n > 256) while ((n = cells.size ()) < 256) { -var maxVol = 0; -var maxCell = null; -for (var i = n; --i >= 1; ) { -var c = cells.get (i); -var v = c.getVolume (false); -if (v > maxVol) { -maxVol = v; -maxCell = c; -}} -if (maxCell == null || !maxCell.splitCell (cells)) break; -} -return cells; -}, $fz.isPrivate = true, $fz), "javajs.util.Lst"); -Clazz.defineMethod (c$, "indexPixels", -($fz = function (cells, colorMap) { -var w2 = this.width + 2; -var errors = new Array (w2); -var newPixels = Clazz.newIntArray (this.pixels.length, 0); -var err = new javajs.util.P3 (); -var lab; -var rgb; -var nearestCell = new java.util.Hashtable (); -for (var i = 0, p = 0; i < this.height; ++i) { -var notLastRow = (i != this.height - 1); -for (var j = 0; j < this.width; ++j, p++) { -if (this.pixels[p] == this.backgroundColor) { -continue; -}var pe = errors[p % w2]; -if (pe == null || pe.x == 3.4028235E38) { -lab = null; -rgb = this.pixels[p]; -} else { -lab = this.toLABnorm (this.pixels[p]); -err = pe; -err.x = this.clamp (err.x, -75, 75); -err.y = this.clamp (err.y, -75, 75); -err.z = this.clamp (err.z, -75, 75); -lab.add (err); -rgb = javajs.util.CU.colorPtToFFRGB (this.toRGB (lab)); -}var key = Integer.$valueOf (rgb); -var cell = colorMap.get (key); -if (cell == null) { -lab = this.toLABnorm (rgb); -cell = nearestCell.get (key); -if (cell == null) { -var maxerr = 3.4028235E38; -for (var ib = cells.size (); --ib >= 1; ) { -var c = cells.get (ib); -err.sub2 (lab, c.center); -var d = err.lengthSquared (); -if (d < maxerr) { -maxerr = d; -cell = c; -}} -nearestCell.put (key, cell); -}if (this.floydSteinberg) { -err.sub2 (lab, cell.center); -var notLastCol = (j < this.width - 1); -if (notLastCol) this.addError (err, 7, errors, p + 1, w2); -if (notLastRow) { -if (j > 0) this.addError (err, 3, errors, p + this.width - 1, w2); -this.addError (err, 5, errors, p + this.width, w2); -if (notLastCol) this.addError (err, 1, errors, p + this.width + 1, w2); -}}err.x = 3.4028235E38; -}newPixels[p] = cell.index; -} -} -return newPixels; -}, $fz.isPrivate = true, $fz), "javajs.util.Lst,java.util.Map"); -Clazz.defineMethod (c$, "addError", -($fz = function (err, f, errors, p, w2) { -if (this.pixels[p] == this.backgroundColor) return; -p %= w2; -var errp = errors[p]; -if (errp == null) errp = errors[p] = new javajs.util.P3 (); - else if (errp.x == 3.4028235E38) errp.set (0, 0, 0); -errp.scaleAdd2 (f / 16, err, errp); -}, $fz.isPrivate = true, $fz), "javajs.util.P3,~N,~A,~N,~N"); -Clazz.defineMethod (c$, "toLABnorm", -function (rgb) { -var lab = javajs.util.CU.colorPtFromInt (rgb, null); -this.rgbToXyz (lab, lab); -this.xyzToLab (lab, lab); -lab.y = (lab.y + 86.185) / (184.439) * 100; -lab.z = (lab.z + 107.863) / (202.345) * 100; -return lab; -}, "~N"); -Clazz.defineMethod (c$, "toRGB", -function (lab) { -var xyz = javajs.util.P3.newP (lab); -xyz.y = xyz.y / 100 * (184.439) - 86.185; -xyz.z = xyz.z / 100 * (202.345) - 107.863; -this.labToXyz (xyz, xyz); -return this.xyzToRgb (xyz, xyz); -}, "javajs.util.P3"); -Clazz.defineMethod (c$, "rgbToXyz", -function (rgb, xyz) { -if (xyz == null) xyz = new javajs.util.P3 (); -xyz.x = this.sxyz (rgb.x); -xyz.y = this.sxyz (rgb.y); -xyz.z = this.sxyz (rgb.z); -javajs.img.GifEncoder.rgb2xyz.rotate (xyz); -return xyz; -}, "javajs.util.P3,javajs.util.P3"); -Clazz.defineMethod (c$, "sxyz", -($fz = function (x) { -x /= 255; -return (x <= 0.04045 ? x / 12.92 : Math.pow (((x + 0.055) / 1.055), 2.4)) * 100; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "xyzToRgb", -function (xyz, rgb) { -if (rgb == null) rgb = new javajs.util.P3 (); -rgb.setT (xyz); -rgb.scale (0.01); -javajs.img.GifEncoder.xyz2rgb.rotate (rgb); -rgb.x = this.clamp (this.srgb (rgb.x), 0, 255); -rgb.y = this.clamp (this.srgb (rgb.y), 0, 255); -rgb.z = this.clamp (this.srgb (rgb.z), 0, 255); -return rgb; -}, "javajs.util.P3,javajs.util.P3"); -Clazz.defineMethod (c$, "srgb", -($fz = function (x) { -return (x > 0.0031308 ? (1.055 * Math.pow (x, 0.4166666666666667)) - 0.055 : x * 12.92) * 255; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "xyzToLab", -function (xyz, lab) { -if (lab == null) lab = new javajs.util.P3 (); -var x = this.flab (xyz.x / 95.0429); -var y = this.flab (xyz.y / 100); -var z = this.flab (xyz.z / 108.89); -lab.x = (116 * y) - 16; -lab.y = 500 * (x - y); -lab.z = 200 * (y - z); -return lab; -}, "javajs.util.P3,javajs.util.P3"); -Clazz.defineMethod (c$, "flab", -($fz = function (t) { -return (t > 8.85645168E-3 ? Math.pow (t, 0.333333333) : 7.78703704 * t + 0.137931034); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "labToXyz", -function (lab, xyz) { -if (xyz == null) xyz = new javajs.util.P3 (); -xyz.setT (lab); -var y = (xyz.x + 16) / 116; -var x = xyz.y / 500 + y; -var z = y - xyz.z / 200; -xyz.x = this.fxyz (x) * 95.0429; -xyz.y = this.fxyz (y) * 100; -xyz.z = this.fxyz (z) * 108.89; -return xyz; -}, "javajs.util.P3,javajs.util.P3"); -Clazz.defineMethod (c$, "fxyz", -($fz = function (t) { -return (t > 0.206896552 ? t * t * t : 0.128418549 * (t - 0.137931034)); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "clamp", -($fz = function (c, min, max) { -c = (c < min ? min : c > max ? max : c); -return (min == 0 ? Math.round (c) : c); -}, $fz.isPrivate = true, $fz), "~N,~N,~N"); -Clazz.defineMethod (c$, "writeHeader", -($fz = function () { -this.putString ("GIF89a"); -this.putWord (this.width); -this.putWord (this.height); -this.putByte (0); -this.putByte (0); -this.putByte (0); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeGraphicControlExtension", -($fz = function () { -if (this.isTransparent || this.delayTime100ths >= 0) { -this.putByte (0x21); -this.putByte (0xf9); -this.putByte (4); -this.putByte ((this.isTransparent ? 9 : 0) | (this.delayTime100ths > 0 ? 2 : 0)); -this.putWord (this.delayTime100ths > 0 ? this.delayTime100ths : 0); -this.putByte (0); -this.putByte (0); -}}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeNetscapeLoopExtension", -($fz = function () { -this.putByte (0x21); -this.putByte (0xff); -this.putByte (0x0B); -this.putString ("NETSCAPE2.0"); -this.putByte (3); -this.putByte (1); -this.putWord (0); -this.putByte (0); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeImage", -($fz = function () { -this.putByte (0x2C); -this.putWord (0); -this.putWord (0); -this.putWord (this.width); -this.putWord (this.height); -var packedFields = 0x80 | (this.interlaced ? 0x40 : 0) | (this.bitsPerPixel - 1); -this.putByte (packedFields); -var colorMapSize = 1 << this.bitsPerPixel; -var p = new javajs.util.P3 (); -for (var i = 0; i < colorMapSize; i++) { -if (this.palette[i] != null) p = this.palette[i]; -this.putByte (Clazz.floatToInt (p.x)); -this.putByte (Clazz.floatToInt (p.y)); -this.putByte (Clazz.floatToInt (p.z)); -} -this.putByte (this.initCodeSize = (this.bitsPerPixel <= 1 ? 2 : this.bitsPerPixel)); -this.compress (); -this.putByte (0); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeTrailer", -($fz = function () { -this.putByte (0x3B); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "nextPixel", -($fz = function () { -if (this.countDown-- == 0) return -1; -var colorIndex = this.pixels[this.curpt]; -++this.curx; -if (this.curx == this.width) { -this.curx = 0; -if (this.interlaced) this.updateY (javajs.img.GifEncoder.INTERLACE_PARAMS[this.pass], javajs.img.GifEncoder.INTERLACE_PARAMS[this.pass + 4]); - else ++this.cury; -}this.curpt = this.cury * this.width + this.curx; -return colorIndex & 0xff; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "updateY", -($fz = function (yNext, yNew) { -this.cury += yNext; -if (yNew >= 0 && this.cury >= this.height) { -this.cury = yNew; -++this.pass; -}}, $fz.isPrivate = true, $fz), "~N,~N"); -Clazz.defineMethod (c$, "putWord", -($fz = function (w) { -this.putByte (w); -this.putByte (w >> 8); -}, $fz.isPrivate = true, $fz), "~N"); -c$.MAXCODE = Clazz.defineMethod (c$, "MAXCODE", -($fz = function (nBits) { -return (1 << nBits) - 1; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "compress", -($fz = function () { -this.countDown = this.width * this.height; -this.pass = 0; -this.curx = 0; -this.cury = 0; -this.clearFlag = false; -this.nBits = this.initCodeSize + 1; -this.maxcode = javajs.img.GifEncoder.MAXCODE (this.nBits); -this.clearCode = 1 << this.initCodeSize; -this.EOFCode = this.clearCode + 1; -this.freeEnt = this.clearCode + 2; -this.bufPt = 0; -var ent = this.nextPixel (); -var hshift = 0; -var fcode; -for (fcode = this.hsize; fcode < 65536; fcode *= 2) ++hshift; - -hshift = 8 - hshift; -var hsizeReg = this.hsize; -this.clearHash (hsizeReg); -this.output (this.clearCode); -var c; -outer_loop : while ((c = this.nextPixel ()) != -1) { -fcode = (c << this.maxbits) + ent; -var i = (c << hshift) ^ ent; -if (this.htab[i] == fcode) { -ent = this.codetab[i]; -continue; -} else if (this.htab[i] >= 0) { -var disp = hsizeReg - i; -if (i == 0) disp = 1; -do { -if ((i -= disp) < 0) i += hsizeReg; -if (this.htab[i] == fcode) { -ent = this.codetab[i]; -continue outer_loop; -}} while (this.htab[i] >= 0); -}this.output (ent); -ent = c; -if (this.freeEnt < this.maxmaxcode) { -this.codetab[i] = this.freeEnt++; -this.htab[i] = fcode; -} else { -this.clearBlock (); -}} -this.output (ent); -this.output (this.EOFCode); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "output", -($fz = function (code) { -this.curAccum &= this.masks[this.curBits]; -if (this.curBits > 0) this.curAccum |= (code << this.curBits); - else this.curAccum = code; -this.curBits += this.nBits; -while (this.curBits >= 8) { -this.byteOut ((this.curAccum & 0xff)); -this.curAccum >>= 8; -this.curBits -= 8; -} -if (this.freeEnt > this.maxcode || this.clearFlag) { -if (this.clearFlag) { -this.maxcode = javajs.img.GifEncoder.MAXCODE (this.nBits = this.initCodeSize + 1); -this.clearFlag = false; -} else { -++this.nBits; -if (this.nBits == this.maxbits) this.maxcode = this.maxmaxcode; - else this.maxcode = javajs.img.GifEncoder.MAXCODE (this.nBits); -}}if (code == this.EOFCode) { -while (this.curBits > 0) { -this.byteOut ((this.curAccum & 0xff)); -this.curAccum >>= 8; -this.curBits -= 8; -} -this.flushBytes (); -}}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "clearBlock", -($fz = function () { -this.clearHash (this.hsize); -this.freeEnt = this.clearCode + 2; -this.clearFlag = true; -this.output (this.clearCode); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "clearHash", -($fz = function (hsize) { -for (var i = 0; i < hsize; ++i) this.htab[i] = -1; - -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "byteOut", -($fz = function (c) { -this.buf[this.bufPt++] = c; -if (this.bufPt >= 254) this.flushBytes (); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "flushBytes", -function () { -if (this.bufPt > 0) { -this.putByte (this.bufPt); -this.out.write (this.buf, 0, this.bufPt); -this.byteCount += this.bufPt; -this.bufPt = 0; -}}); -c$.$GifEncoder$ColorItem$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.isBackground = false; -Clazz.instantialize (this, arguments); -}, javajs.img.GifEncoder, "ColorItem", javajs.util.P3); -Clazz.makeConstructor (c$, -function (a, b) { -Clazz.superConstructor (this, javajs.img.GifEncoder.ColorItem, []); -this.isBackground = b; -this.setT (this.b$["javajs.img.GifEncoder"].toLABnorm (a)); -}, "~N,~B"); -c$ = Clazz.p0p (); -}; -c$.$GifEncoder$ColorCell$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.index = 0; -this.center = null; -this.volume = 0; -Clazz.instantialize (this, arguments); -}, javajs.img.GifEncoder, "ColorCell", javajs.util.Lst); -Clazz.makeConstructor (c$, -function (a) { -Clazz.superConstructor (this, javajs.img.GifEncoder.ColorCell, []); -this.index = a; -}, "~N"); -Clazz.defineMethod (c$, "getVolume", -function (a) { -if (this.volume != 0) return this.volume; -if (this.size () < 2) return -1; -var b = -2147483647; -var c = 2147483647; -var d = -2147483647; -var e = 2147483647; -var f = -2147483647; -var g = 2147483647; -var h = this.size (); -for (var i = h; --i >= 0; ) { -var j = this.get (i); -if (j.x < c) c = j.x; -if (j.y < e) e = j.y; -if (j.z < g) g = j.z; -if (j.x > b) b = j.x; -if (j.y > d) d = j.y; -if (j.z > f) f = j.z; -} -var j = (b - c); -var k = (d - e); -var l = (f - g); -return this.volume = j * j + k * k + l * l; -}, "~B"); -Clazz.defineMethod (c$, "setColor", -function () { -var a = this.size (); -this.center = new javajs.util.P3 (); -for (var b = a; --b >= 0; ) this.center.add (this.get (b)); - -this.center.scale (1 / a); -return this.b$["javajs.img.GifEncoder"].toRGB (this.center); -}); -Clazz.defineMethod (c$, "splitCell", -function (a) { -var b = this.size (); -if (b < 2) return false; -var c = a.size (); -var d = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, c); -a.addLast (d); -var e = Clazz.newFloatArray (3, 3, 0); -for (var f = 0; f < 3; f++) { -var g = 3.4028235E38; -var h = -3.4028235E38; -for (var i = b; --i >= 0; ) { -var j = this.get (i); -var k = (f == 0 ? j.x : f == 1 ? j.y : j.z); -if (g > k) g = k; -if (h < k) h = k; -} -e[0][f] = g; -e[1][f] = h; -e[2][f] = h - g; -} -var g = e[2]; -var h = (g[0] >= g[1] ? (g[0] >= g[2] ? 0 : 2) : g[1] >= g[2] ? 1 : 2); -var i = e[0][h] + e[2][h] / 2; -this.volume = 0; -switch (h) { -case 0: -for (var j = b; --j >= 0; ) if (this.get (j).x >= i) d.addLast (this.remove (j)); - -break; -case 1: -for (var k = b; --k >= 0; ) if (this.get (k).y >= i) d.addLast (this.remove (k)); - -break; -case 2: -for (var l = this.size (); --l >= 0; ) if (this.get (l).z >= i) d.addLast (this.remove (l)); - -break; -} -return true; -}, "javajs.util.Lst"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"xyz2rgb", null, -"rgb2xyz", null); -{ -javajs.img.GifEncoder.rgb2xyz = javajs.util.M3.newA9 ( Clazz.newFloatArray (-1, [0.4124, 0.3576, 0.1805, 0.2126, 0.7152, 0.0722, 0.0193, 0.1192, 0.9505])); -javajs.img.GifEncoder.xyz2rgb = javajs.util.M3.newA9 ( Clazz.newFloatArray (-1, [3.2406, -1.5372, -0.4986, -0.9689, 1.8758, 0.0415, 0.0557, -0.204, 1.0570])); -}Clazz.defineStatics (c$, -"EOF", -1, -"INTERLACE_PARAMS", Clazz.newIntArray (-1, [8, 8, 4, 2, 4, 2, 1, 0]), -"BITS", 12, -"HSIZE", 5003); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.ImageEncoder", "javajs.util.Lst", "$.P3"], "javajs.img.GifEncoder", ["java.lang.Boolean", "java.util.Hashtable", "javajs.util.CU", "$.M3"], function () { +c$ = Clazz.decorateAsClass (function () { +this.params = null; +this.palette = null; +this.backgroundColor = 0; +this.interlaced = false; +this.addHeader = true; +this.addImage = true; +this.addTrailer = true; +this.isTransparent = false; +this.floydSteinberg = true; +this.capturing = false; +this.looping = false; +this.delayTime100ths = -1; +this.bitsPerPixel = 1; +this.byteCount = 0; +if (!Clazz.isClassDefined ("javajs.img.GifEncoder.ColorItem")) { +javajs.img.GifEncoder.$GifEncoder$ColorItem$ (); +} +if (!Clazz.isClassDefined ("javajs.img.GifEncoder.ColorCell")) { +javajs.img.GifEncoder.$GifEncoder$ColorCell$ (); +} +this.initCodeSize = 0; +this.curpt = 0; +this.nBits = 0; +this.maxbits = 12; +this.maxcode = 0; +this.maxmaxcode = 4096; +this.htab = null; +this.codetab = null; +this.hsize = 5003; +this.freeEnt = 0; +this.clearFlag = false; +this.clearCode = 0; +this.EOFCode = 0; +this.countDown = 0; +this.pass = 0; +this.curx = 0; +this.cury = 0; +this.curAccum = 0; +this.curBits = 0; +this.masks = null; +this.bufPt = 0; +this.buf = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "GifEncoder", javajs.img.ImageEncoder); +Clazz.prepareFields (c$, function () { +this.htab = Clazz.newIntArray (5003, 0); +this.codetab = Clazz.newIntArray (5003, 0); +this.masks = Clazz.newIntArray (-1, [0x0000, 0x0001, 0x0003, 0x0007, 0x000F, 0x001F, 0x003F, 0x007F, 0x00FF, 0x01FF, 0x03FF, 0x07FF, 0x0FFF, 0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF]); +this.buf = Clazz.newByteArray (256, 0); +}); +Clazz.overrideMethod (c$, "setParams", +function (params) { +this.params = params; +var ic = params.get ("transparentColor"); +if (ic == null) { +ic = params.get ("backgroundColor"); +if (ic != null) this.backgroundColor = ic.intValue (); +} else { +this.backgroundColor = ic.intValue (); +this.isTransparent = true; +}this.interlaced = (Boolean.TRUE === params.get ("interlaced")); +if (params.containsKey ("captureRootExt") || !params.containsKey ("captureMode")) return; +this.interlaced = false; +this.capturing = true; +try { +this.byteCount = (params.get ("captureByteCount")).intValue (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +switch ("maec".indexOf ((params.get ("captureMode")).substring (0, 1))) { +case 0: +params.put ("captureMode", "add"); +this.addImage = false; +this.addTrailer = false; +break; +case 1: +this.addHeader = false; +this.addTrailer = false; +var fps = Math.abs ((params.get ("captureFps")).intValue ()); +this.delayTime100ths = (fps == 0 ? 0 : Clazz.doubleToInt (100 / fps)); +this.looping = (Boolean.FALSE !== params.get ("captureLooping")); +break; +case 2: +this.addHeader = false; +this.addImage = false; +break; +case 3: +this.addHeader = false; +this.addImage = false; +this.out.cancel (); +break; +} +}, "java.util.Map"); +Clazz.overrideMethod (c$, "generate", +function () { +if (this.addHeader) this.writeHeader (); +this.addHeader = false; +if (this.addImage) { +this.createPalette (); +this.writeGraphicControlExtension (); +if (this.delayTime100ths >= 0 && this.looping) this.writeNetscapeLoopExtension (); +this.writeImage (); +}}); +Clazz.overrideMethod (c$, "close", +function () { +if (this.addTrailer) { +this.writeTrailer (); +} else { +this.doClose = false; +}if (this.capturing) this.params.put ("captureByteCount", Integer.$valueOf (this.byteCount)); +}); +Clazz.defineMethod (c$, "createPalette", +($fz = function () { +var tempColors = new javajs.util.Lst (); +var ciHash = new java.util.Hashtable (); +for (var i = 0, n = this.pixels.length; i < n; i++) { +var rgb = this.pixels[i]; +var key = Integer.$valueOf (rgb); +var item = ciHash.get (key); +if (item == null) { +item = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorItem, this, null, rgb, rgb == this.backgroundColor); +ciHash.put (key, item); +tempColors.addLast (item); +}} +var nColors = tempColors.size (); +System.out.println ("GIF total image colors: " + nColors); +ciHash = null; +var cells = this.quantizeColors (tempColors); +nColors = cells.size (); +System.out.println ("GIF final color count: " + nColors); +var colorMap = new java.util.Hashtable (); +this.bitsPerPixel = (nColors <= 2 ? 1 : nColors <= 4 ? 2 : nColors <= 16 ? 4 : 8); +this.palette = new Array (1 << this.bitsPerPixel); +for (var i = 0; i < nColors; i++) { +var c = cells.get (i); +colorMap.put (Integer.$valueOf (javajs.util.CU.colorPtToFFRGB (this.palette[i] = c.setColor ())), c); +} +this.pixels = this.indexPixels (cells, colorMap); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "quantizeColors", +($fz = function (tempColors) { +var n = tempColors.size (); +var cells = new javajs.util.Lst (); +var cc = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, 0); +cc.addLast (Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorItem, this, null, this.backgroundColor, true)); +cells.addLast (cc); +cc = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, 1); +if (n > 256) cells.addLast (cc); +for (var i = 0; i < n; i++) { +var c = tempColors.get (i); +if (c.isBackground) continue; +cc.addLast (c); +if (n <= 256) { +cells.addLast (cc); +cc = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, cells.size ()); +}} +tempColors.clear (); +if (n > 256) while ((n = cells.size ()) < 256) { +var maxVol = 0; +var maxCell = null; +for (var i = n; --i >= 1; ) { +var c = cells.get (i); +var v = c.getVolume (false); +if (v > maxVol) { +maxVol = v; +maxCell = c; +}} +if (maxCell == null || !maxCell.splitCell (cells)) break; +} +return cells; +}, $fz.isPrivate = true, $fz), "javajs.util.Lst"); +Clazz.defineMethod (c$, "indexPixels", +($fz = function (cells, colorMap) { +var w2 = this.width + 2; +var errors = new Array (w2); +var newPixels = Clazz.newIntArray (this.pixels.length, 0); +var err = new javajs.util.P3 (); +var lab; +var rgb; +var nearestCell = new java.util.Hashtable (); +for (var i = 0, p = 0; i < this.height; ++i) { +var notLastRow = (i != this.height - 1); +for (var j = 0; j < this.width; ++j, p++) { +if (this.pixels[p] == this.backgroundColor) { +continue; +}var pe = errors[p % w2]; +if (pe == null || pe.x == 3.4028235E38) { +lab = null; +rgb = this.pixels[p]; +} else { +lab = this.toLABnorm (this.pixels[p]); +err = pe; +err.x = this.clamp (err.x, -75, 75); +err.y = this.clamp (err.y, -75, 75); +err.z = this.clamp (err.z, -75, 75); +lab.add (err); +rgb = javajs.util.CU.colorPtToFFRGB (this.toRGB (lab)); +}var key = Integer.$valueOf (rgb); +var cell = colorMap.get (key); +if (cell == null) { +lab = this.toLABnorm (rgb); +cell = nearestCell.get (key); +if (cell == null) { +var maxerr = 3.4028235E38; +for (var ib = cells.size (); --ib >= 1; ) { +var c = cells.get (ib); +err.sub2 (lab, c.center); +var d = err.lengthSquared (); +if (d < maxerr) { +maxerr = d; +cell = c; +}} +nearestCell.put (key, cell); +}if (this.floydSteinberg) { +err.sub2 (lab, cell.center); +var notLastCol = (j < this.width - 1); +if (notLastCol) this.addError (err, 7, errors, p + 1, w2); +if (notLastRow) { +if (j > 0) this.addError (err, 3, errors, p + this.width - 1, w2); +this.addError (err, 5, errors, p + this.width, w2); +if (notLastCol) this.addError (err, 1, errors, p + this.width + 1, w2); +}}err.x = 3.4028235E38; +}newPixels[p] = cell.index; +} +} +return newPixels; +}, $fz.isPrivate = true, $fz), "javajs.util.Lst,java.util.Map"); +Clazz.defineMethod (c$, "addError", +($fz = function (err, f, errors, p, w2) { +if (this.pixels[p] == this.backgroundColor) return; +p %= w2; +var errp = errors[p]; +if (errp == null) errp = errors[p] = new javajs.util.P3 (); + else if (errp.x == 3.4028235E38) errp.set (0, 0, 0); +errp.scaleAdd2 (f / 16, err, errp); +}, $fz.isPrivate = true, $fz), "javajs.util.P3,~N,~A,~N,~N"); +Clazz.defineMethod (c$, "toLABnorm", +function (rgb) { +var lab = javajs.util.CU.colorPtFromInt (rgb, null); +this.rgbToXyz (lab, lab); +this.xyzToLab (lab, lab); +lab.y = (lab.y + 86.185) / (184.439) * 100; +lab.z = (lab.z + 107.863) / (202.345) * 100; +return lab; +}, "~N"); +Clazz.defineMethod (c$, "toRGB", +function (lab) { +var xyz = javajs.util.P3.newP (lab); +xyz.y = xyz.y / 100 * (184.439) - 86.185; +xyz.z = xyz.z / 100 * (202.345) - 107.863; +this.labToXyz (xyz, xyz); +return this.xyzToRgb (xyz, xyz); +}, "javajs.util.P3"); +Clazz.defineMethod (c$, "rgbToXyz", +function (rgb, xyz) { +if (xyz == null) xyz = new javajs.util.P3 (); +xyz.x = this.sxyz (rgb.x); +xyz.y = this.sxyz (rgb.y); +xyz.z = this.sxyz (rgb.z); +javajs.img.GifEncoder.rgb2xyz.rotate (xyz); +return xyz; +}, "javajs.util.P3,javajs.util.P3"); +Clazz.defineMethod (c$, "sxyz", +($fz = function (x) { +x /= 255; +return (x <= 0.04045 ? x / 12.92 : Math.pow (((x + 0.055) / 1.055), 2.4)) * 100; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "xyzToRgb", +function (xyz, rgb) { +if (rgb == null) rgb = new javajs.util.P3 (); +rgb.setT (xyz); +rgb.scale (0.01); +javajs.img.GifEncoder.xyz2rgb.rotate (rgb); +rgb.x = this.clamp (this.srgb (rgb.x), 0, 255); +rgb.y = this.clamp (this.srgb (rgb.y), 0, 255); +rgb.z = this.clamp (this.srgb (rgb.z), 0, 255); +return rgb; +}, "javajs.util.P3,javajs.util.P3"); +Clazz.defineMethod (c$, "srgb", +($fz = function (x) { +return (x > 0.0031308 ? (1.055 * Math.pow (x, 0.4166666666666667)) - 0.055 : x * 12.92) * 255; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "xyzToLab", +function (xyz, lab) { +if (lab == null) lab = new javajs.util.P3 (); +var x = this.flab (xyz.x / 95.0429); +var y = this.flab (xyz.y / 100); +var z = this.flab (xyz.z / 108.89); +lab.x = (116 * y) - 16; +lab.y = 500 * (x - y); +lab.z = 200 * (y - z); +return lab; +}, "javajs.util.P3,javajs.util.P3"); +Clazz.defineMethod (c$, "flab", +($fz = function (t) { +return (t > 8.85645168E-3 ? Math.pow (t, 0.333333333) : 7.78703704 * t + 0.137931034); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "labToXyz", +function (lab, xyz) { +if (xyz == null) xyz = new javajs.util.P3 (); +xyz.setT (lab); +var y = (xyz.x + 16) / 116; +var x = xyz.y / 500 + y; +var z = y - xyz.z / 200; +xyz.x = this.fxyz (x) * 95.0429; +xyz.y = this.fxyz (y) * 100; +xyz.z = this.fxyz (z) * 108.89; +return xyz; +}, "javajs.util.P3,javajs.util.P3"); +Clazz.defineMethod (c$, "fxyz", +($fz = function (t) { +return (t > 0.206896552 ? t * t * t : 0.128418549 * (t - 0.137931034)); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "clamp", +($fz = function (c, min, max) { +c = (c < min ? min : c > max ? max : c); +return (min == 0 ? Math.round (c) : c); +}, $fz.isPrivate = true, $fz), "~N,~N,~N"); +Clazz.defineMethod (c$, "writeHeader", +($fz = function () { +this.putString ("GIF89a"); +this.putWord (this.width); +this.putWord (this.height); +this.putByte (0); +this.putByte (0); +this.putByte (0); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeGraphicControlExtension", +($fz = function () { +if (this.isTransparent || this.delayTime100ths >= 0) { +this.putByte (0x21); +this.putByte (0xf9); +this.putByte (4); +this.putByte ((this.isTransparent ? 9 : 0) | (this.delayTime100ths > 0 ? 2 : 0)); +this.putWord (this.delayTime100ths > 0 ? this.delayTime100ths : 0); +this.putByte (0); +this.putByte (0); +}}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeNetscapeLoopExtension", +($fz = function () { +this.putByte (0x21); +this.putByte (0xff); +this.putByte (0x0B); +this.putString ("NETSCAPE2.0"); +this.putByte (3); +this.putByte (1); +this.putWord (0); +this.putByte (0); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeImage", +($fz = function () { +this.putByte (0x2C); +this.putWord (0); +this.putWord (0); +this.putWord (this.width); +this.putWord (this.height); +var packedFields = 0x80 | (this.interlaced ? 0x40 : 0) | (this.bitsPerPixel - 1); +this.putByte (packedFields); +var colorMapSize = 1 << this.bitsPerPixel; +var p = new javajs.util.P3 (); +for (var i = 0; i < colorMapSize; i++) { +if (this.palette[i] != null) p = this.palette[i]; +this.putByte (Clazz.floatToInt (p.x)); +this.putByte (Clazz.floatToInt (p.y)); +this.putByte (Clazz.floatToInt (p.z)); +} +this.putByte (this.initCodeSize = (this.bitsPerPixel <= 1 ? 2 : this.bitsPerPixel)); +this.compress (); +this.putByte (0); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeTrailer", +($fz = function () { +this.putByte (0x3B); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "nextPixel", +($fz = function () { +if (this.countDown-- == 0) return -1; +var colorIndex = this.pixels[this.curpt]; +++this.curx; +if (this.curx == this.width) { +this.curx = 0; +if (this.interlaced) this.updateY (javajs.img.GifEncoder.INTERLACE_PARAMS[this.pass], javajs.img.GifEncoder.INTERLACE_PARAMS[this.pass + 4]); + else ++this.cury; +}this.curpt = this.cury * this.width + this.curx; +return colorIndex & 0xff; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "updateY", +($fz = function (yNext, yNew) { +this.cury += yNext; +if (yNew >= 0 && this.cury >= this.height) { +this.cury = yNew; +++this.pass; +}}, $fz.isPrivate = true, $fz), "~N,~N"); +Clazz.defineMethod (c$, "putWord", +($fz = function (w) { +this.putByte (w); +this.putByte (w >> 8); +}, $fz.isPrivate = true, $fz), "~N"); +c$.MAXCODE = Clazz.defineMethod (c$, "MAXCODE", +($fz = function (nBits) { +return (1 << nBits) - 1; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "compress", +($fz = function () { +this.countDown = this.width * this.height; +this.pass = 0; +this.curx = 0; +this.cury = 0; +this.clearFlag = false; +this.nBits = this.initCodeSize + 1; +this.maxcode = javajs.img.GifEncoder.MAXCODE (this.nBits); +this.clearCode = 1 << this.initCodeSize; +this.EOFCode = this.clearCode + 1; +this.freeEnt = this.clearCode + 2; +this.bufPt = 0; +var ent = this.nextPixel (); +var hshift = 0; +var fcode; +for (fcode = this.hsize; fcode < 65536; fcode *= 2) ++hshift; + +hshift = 8 - hshift; +var hsizeReg = this.hsize; +this.clearHash (hsizeReg); +this.output (this.clearCode); +var c; +outer_loop : while ((c = this.nextPixel ()) != -1) { +fcode = (c << this.maxbits) + ent; +var i = (c << hshift) ^ ent; +if (this.htab[i] == fcode) { +ent = this.codetab[i]; +continue; +} else if (this.htab[i] >= 0) { +var disp = hsizeReg - i; +if (i == 0) disp = 1; +do { +if ((i -= disp) < 0) i += hsizeReg; +if (this.htab[i] == fcode) { +ent = this.codetab[i]; +continue outer_loop; +}} while (this.htab[i] >= 0); +}this.output (ent); +ent = c; +if (this.freeEnt < this.maxmaxcode) { +this.codetab[i] = this.freeEnt++; +this.htab[i] = fcode; +} else { +this.clearBlock (); +}} +this.output (ent); +this.output (this.EOFCode); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "output", +($fz = function (code) { +this.curAccum &= this.masks[this.curBits]; +if (this.curBits > 0) this.curAccum |= (code << this.curBits); + else this.curAccum = code; +this.curBits += this.nBits; +while (this.curBits >= 8) { +this.byteOut ((this.curAccum & 0xff)); +this.curAccum >>= 8; +this.curBits -= 8; +} +if (this.freeEnt > this.maxcode || this.clearFlag) { +if (this.clearFlag) { +this.maxcode = javajs.img.GifEncoder.MAXCODE (this.nBits = this.initCodeSize + 1); +this.clearFlag = false; +} else { +++this.nBits; +if (this.nBits == this.maxbits) this.maxcode = this.maxmaxcode; + else this.maxcode = javajs.img.GifEncoder.MAXCODE (this.nBits); +}}if (code == this.EOFCode) { +while (this.curBits > 0) { +this.byteOut ((this.curAccum & 0xff)); +this.curAccum >>= 8; +this.curBits -= 8; +} +this.flushBytes (); +}}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "clearBlock", +($fz = function () { +this.clearHash (this.hsize); +this.freeEnt = this.clearCode + 2; +this.clearFlag = true; +this.output (this.clearCode); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "clearHash", +($fz = function (hsize) { +for (var i = 0; i < hsize; ++i) this.htab[i] = -1; + +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "byteOut", +($fz = function (c) { +this.buf[this.bufPt++] = c; +if (this.bufPt >= 254) this.flushBytes (); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "flushBytes", +function () { +if (this.bufPt > 0) { +this.putByte (this.bufPt); +this.out.write (this.buf, 0, this.bufPt); +this.byteCount += this.bufPt; +this.bufPt = 0; +}}); +c$.$GifEncoder$ColorItem$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.isBackground = false; +Clazz.instantialize (this, arguments); +}, javajs.img.GifEncoder, "ColorItem", javajs.util.P3); +Clazz.makeConstructor (c$, +function (a, b) { +Clazz.superConstructor (this, javajs.img.GifEncoder.ColorItem, []); +this.isBackground = b; +this.setT (this.b$["javajs.img.GifEncoder"].toLABnorm (a)); +}, "~N,~B"); +c$ = Clazz.p0p (); +}; +c$.$GifEncoder$ColorCell$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.index = 0; +this.center = null; +this.volume = 0; +Clazz.instantialize (this, arguments); +}, javajs.img.GifEncoder, "ColorCell", javajs.util.Lst); +Clazz.makeConstructor (c$, +function (a) { +Clazz.superConstructor (this, javajs.img.GifEncoder.ColorCell, []); +this.index = a; +}, "~N"); +Clazz.defineMethod (c$, "getVolume", +function (a) { +if (this.volume != 0) return this.volume; +if (this.size () < 2) return -1; +var b = -2147483647; +var c = 2147483647; +var d = -2147483647; +var e = 2147483647; +var f = -2147483647; +var g = 2147483647; +var h = this.size (); +for (var i = h; --i >= 0; ) { +var j = this.get (i); +if (j.x < c) c = j.x; +if (j.y < e) e = j.y; +if (j.z < g) g = j.z; +if (j.x > b) b = j.x; +if (j.y > d) d = j.y; +if (j.z > f) f = j.z; +} +var j = (b - c); +var k = (d - e); +var l = (f - g); +return this.volume = j * j + k * k + l * l; +}, "~B"); +Clazz.defineMethod (c$, "setColor", +function () { +var a = this.size (); +this.center = new javajs.util.P3 (); +for (var b = a; --b >= 0; ) this.center.add (this.get (b)); + +this.center.scale (1 / a); +return this.b$["javajs.img.GifEncoder"].toRGB (this.center); +}); +Clazz.defineMethod (c$, "splitCell", +function (a) { +var b = this.size (); +if (b < 2) return false; +var c = a.size (); +var d = Clazz.innerTypeInstance (javajs.img.GifEncoder.ColorCell, this, null, c); +a.addLast (d); +var e = Clazz.newFloatArray (3, 3, 0); +for (var f = 0; f < 3; f++) { +var g = 3.4028235E38; +var h = -3.4028235E38; +for (var i = b; --i >= 0; ) { +var j = this.get (i); +var k = (f == 0 ? j.x : f == 1 ? j.y : j.z); +if (g > k) g = k; +if (h < k) h = k; +} +e[0][f] = g; +e[1][f] = h; +e[2][f] = h - g; +} +var g = e[2]; +var h = (g[0] >= g[1] ? (g[0] >= g[2] ? 0 : 2) : g[1] >= g[2] ? 1 : 2); +var i = e[0][h] + e[2][h] / 2; +this.volume = 0; +switch (h) { +case 0: +for (var j = b; --j >= 0; ) if (this.get (j).x >= i) d.addLast (this.remove (j)); + +break; +case 1: +for (var k = b; --k >= 0; ) if (this.get (k).y >= i) d.addLast (this.remove (k)); + +break; +case 2: +for (var l = this.size (); --l >= 0; ) if (this.get (l).z >= i) d.addLast (this.remove (l)); + +break; +} +return true; +}, "javajs.util.Lst"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"xyz2rgb", null, +"rgb2xyz", null); +{ +javajs.img.GifEncoder.rgb2xyz = javajs.util.M3.newA9 ( Clazz.newFloatArray (-1, [0.4124, 0.3576, 0.1805, 0.2126, 0.7152, 0.0722, 0.0193, 0.1192, 0.9505])); +javajs.img.GifEncoder.xyz2rgb = javajs.util.M3.newA9 ( Clazz.newFloatArray (-1, [3.2406, -1.5372, -0.4986, -0.9689, 1.8758, 0.0415, 0.0557, -0.204, 1.0570])); +}Clazz.defineStatics (c$, +"EOF", -1, +"INTERLACE_PARAMS", Clazz.newIntArray (-1, [8, 8, 4, 2, 4, 2, 1, 0]), +"BITS", 12, +"HSIZE", 5003); +}); diff --git a/bin/javajs/img/ImageEncoder.js b/bin/javajs/img/ImageEncoder.js index 79e2086..a0fc4c0 100644 --- a/bin/javajs/img/ImageEncoder.js +++ b/bin/javajs/img/ImageEncoder.js @@ -1,41 +1,41 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.api.GenericImageEncoder"], "javajs.img.ImageEncoder", ["java.lang.Boolean"], function () { -c$ = Clazz.decorateAsClass (function () { -this.out = null; -this.width = -1; -this.height = -1; -this.quality = -1; -this.date = null; -this.logging = false; -this.doClose = true; -this.pixels = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "ImageEncoder", null, javajs.api.GenericImageEncoder); -Clazz.overrideMethod (c$, "createImage", -function (type, out, params) { -this.out = out; -this.logging = (Boolean.TRUE === params.get ("logging")); -this.width = (params.get ("imageWidth")).intValue (); -this.height = (params.get ("imageHeight")).intValue (); -this.pixels = params.get ("imagePixels"); -this.date = params.get ("date"); -var q = params.get ("quality"); -this.quality = (q == null ? -1 : q.intValue ()); -this.setParams (params); -this.generate (); -this.close (); -return this.doClose; -}, "~S,javajs.util.OC,java.util.Map"); -Clazz.defineMethod (c$, "putString", -function (s) { -var b = s.getBytes (); -this.out.write (b, 0, b.length); -}, "~S"); -Clazz.defineMethod (c$, "putByte", -function (b) { -this.out.writeByteAsInt (b); -}, "~N"); -Clazz.defineMethod (c$, "close", -function () { -}); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.api.GenericImageEncoder"], "javajs.img.ImageEncoder", ["java.lang.Boolean"], function () { +c$ = Clazz.decorateAsClass (function () { +this.out = null; +this.width = -1; +this.height = -1; +this.quality = -1; +this.date = null; +this.logging = false; +this.doClose = true; +this.pixels = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "ImageEncoder", null, javajs.api.GenericImageEncoder); +Clazz.overrideMethod (c$, "createImage", +function (type, out, params) { +this.out = out; +this.logging = (Boolean.TRUE === params.get ("logging")); +this.width = (params.get ("imageWidth")).intValue (); +this.height = (params.get ("imageHeight")).intValue (); +this.pixels = params.get ("imagePixels"); +this.date = params.get ("date"); +var q = params.get ("quality"); +this.quality = (q == null ? -1 : q.intValue ()); +this.setParams (params); +this.generate (); +this.close (); +return this.doClose; +}, "~S,javajs.util.OC,java.util.Map"); +Clazz.defineMethod (c$, "putString", +function (s) { +var b = s.getBytes (); +this.out.write (b, 0, b.length); +}, "~S"); +Clazz.defineMethod (c$, "putByte", +function (b) { +this.out.writeByteAsInt (b); +}, "~N"); +Clazz.defineMethod (c$, "close", +function () { +}); +}); diff --git a/bin/javajs/img/Jpg64Encoder.js b/bin/javajs/img/Jpg64Encoder.js index 2ef2678..c8eb5d1 100644 --- a/bin/javajs/img/Jpg64Encoder.js +++ b/bin/javajs/img/Jpg64Encoder.js @@ -1,23 +1,23 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.JpgEncoder"], "javajs.img.Jpg64Encoder", ["javajs.util.Base64"], function () { -c$ = Clazz.decorateAsClass (function () { -this.outTemp = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "Jpg64Encoder", javajs.img.JpgEncoder); -Clazz.defineMethod (c$, "setParams", -function (params) { -this.defaultQuality = 75; -this.outTemp = params.remove ("outputChannelTemp"); -Clazz.superCall (this, javajs.img.Jpg64Encoder, "setParams", [params]); -}, "java.util.Map"); -Clazz.defineMethod (c$, "generate", -function () { -var out0 = this.out; -this.out = this.outTemp; -Clazz.superCall (this, javajs.img.Jpg64Encoder, "generate", []); -var bytes = javajs.util.Base64.getBytes64 (this.out.toByteArray ()); -this.outTemp = null; -this.out = out0; -this.out.write (bytes, 0, bytes.length); -}); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.JpgEncoder"], "javajs.img.Jpg64Encoder", ["javajs.util.Base64"], function () { +c$ = Clazz.decorateAsClass (function () { +this.outTemp = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "Jpg64Encoder", javajs.img.JpgEncoder); +Clazz.defineMethod (c$, "setParams", +function (params) { +this.defaultQuality = 75; +this.outTemp = params.remove ("outputChannelTemp"); +Clazz.superCall (this, javajs.img.Jpg64Encoder, "setParams", [params]); +}, "java.util.Map"); +Clazz.defineMethod (c$, "generate", +function () { +var out0 = this.out; +this.out = this.outTemp; +Clazz.superCall (this, javajs.img.Jpg64Encoder, "generate", []); +var bytes = javajs.util.Base64.getBytes64 (this.out.toByteArray ()); +this.outTemp = null; +this.out = out0; +this.out.write (bytes, 0, bytes.length); +}); +}); diff --git a/bin/javajs/img/JpgEncoder.js b/bin/javajs/img/JpgEncoder.js index 9edf3b2..b13c26f 100644 --- a/bin/javajs/img/JpgEncoder.js +++ b/bin/javajs/img/JpgEncoder.js @@ -1,753 +1,753 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.ImageEncoder", "javajs.util.AU"], ["javajs.img.DCT", "$.JpgEncoder", "$.JpegObj", "$.Huffman"], null, function () { -c$ = Clazz.decorateAsClass (function () { -this.jpegObj = null; -this.huf = null; -this.dct = null; -this.defaultQuality = 100; -this.applicationTag = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "JpgEncoder", javajs.img.ImageEncoder); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.img.JpgEncoder, []); -}); -Clazz.overrideMethod (c$, "setParams", -function (params) { -if (this.quality <= 0) this.quality = (params.containsKey ("qualityJPG") ? (params.get ("qualityJPG")).intValue () : this.defaultQuality); -this.jpegObj = new javajs.img.JpegObj (); -this.jpegObj.comment = params.get ("comment"); -this.applicationTag = params.get ("jpgAppTag"); -}, "java.util.Map"); -Clazz.overrideMethod (c$, "generate", -function () { -this.jpegObj.imageWidth = this.width; -this.jpegObj.imageHeight = this.height; -this.dct = new javajs.img.DCT (this.quality); -this.huf = new javajs.img.Huffman (this.width, this.height); -if (this.jpegObj == null) return; -this.jpegObj.getYCCArray (this.pixels); -var longState = this.writeHeaders (this.jpegObj, this.dct); -this.writeCompressedData (this.jpegObj, this.dct, this.huf); -this.writeMarker (javajs.img.JpgEncoder.eoi); -if (longState != null) { -var b = longState.getBytes (); -this.out.write (b, 0, b.length); -}}); -Clazz.defineMethod (c$, "writeCompressedData", -($fz = function (jpegObj, dct, huf) { -var i; -var j; -var r; -var c; -var a; -var b; -var comp; -var xpos; -var ypos; -var xblockoffset; -var yblockoffset; -var inputArray; -var dctArray1 = Clazz.newFloatArray (8, 8, 0); -var dctArray2 = Clazz.newDoubleArray (8, 8, 0); -var dctArray3 = Clazz.newIntArray (64, 0); -var lastDCvalue = Clazz.newIntArray (jpegObj.numberOfComponents, 0); -var minBlockWidth; -var minBlockHeight; -minBlockWidth = ((huf.imageWidth % 8 != 0) ? Clazz.doubleToInt (Math.floor (huf.imageWidth / 8.0) + 1) * 8 : huf.imageWidth); -minBlockHeight = ((huf.imageHeight % 8 != 0) ? Clazz.doubleToInt (Math.floor (huf.imageHeight / 8.0) + 1) * 8 : huf.imageHeight); -for (comp = 0; comp < jpegObj.numberOfComponents; comp++) { -minBlockWidth = Math.min (minBlockWidth, jpegObj.blockWidth[comp]); -minBlockHeight = Math.min (minBlockHeight, jpegObj.blockHeight[comp]); -} -xpos = 0; -for (r = 0; r < minBlockHeight; r++) { -for (c = 0; c < minBlockWidth; c++) { -xpos = c * 8; -ypos = r * 8; -for (comp = 0; comp < jpegObj.numberOfComponents; comp++) { -inputArray = jpegObj.components[comp]; -var vsampF = jpegObj.vsampFactor[comp]; -var hsampF = jpegObj.hsampFactor[comp]; -var qNumber = jpegObj.qtableNumber[comp]; -var dcNumber = jpegObj.dctableNumber[comp]; -var acNumber = jpegObj.actableNumber[comp]; -for (i = 0; i < vsampF; i++) { -for (j = 0; j < hsampF; j++) { -xblockoffset = j * 8; -yblockoffset = i * 8; -for (a = 0; a < 8; a++) { -for (b = 0; b < 8; b++) { -dctArray1[a][b] = inputArray[ypos + yblockoffset + a][xpos + xblockoffset + b]; -} -} -dctArray2 = javajs.img.DCT.forwardDCT (dctArray1); -dctArray3 = javajs.img.DCT.quantizeBlock (dctArray2, dct.divisors[qNumber]); -huf.HuffmanBlockEncoder (this.out, dctArray3, lastDCvalue[comp], dcNumber, acNumber); -lastDCvalue[comp] = dctArray3[0]; -} -} -} -} -} -huf.flushBuffer (this.out); -}, $fz.isPrivate = true, $fz), "javajs.img.JpegObj,javajs.img.DCT,javajs.img.Huffman"); -Clazz.defineMethod (c$, "writeHeaders", -($fz = function (jpegObj, dct) { -var i; -var j; -var index; -var offset; -var tempArray; -this.writeMarker (javajs.img.JpgEncoder.soi); -this.writeArray (javajs.img.JpgEncoder.jfif); -var comment = null; -if (jpegObj.comment.length > 0) this.writeString (jpegObj.comment, 0xE1); -this.writeString ("JPEG Encoder Copyright 1998, James R. Weeks and BioElectroMech.\n\n", 0xFE); -var dqt = Clazz.newByteArray (134, 0); -dqt[0] = 0xFF; -dqt[1] = 0xDB; -dqt[2] = 0; -dqt[3] = 132; -offset = 4; -for (i = 0; i < 2; i++) { -dqt[offset++] = ((0) + i); -tempArray = dct.quantum[i]; -for (j = 0; j < 64; j++) { -dqt[offset++] = tempArray[javajs.img.Huffman.jpegNaturalOrder[j]]; -} -} -this.writeArray (dqt); -var sof = Clazz.newByteArray (19, 0); -sof[0] = 0xFF; -sof[1] = 0xC0; -sof[2] = 0; -sof[3] = 17; -sof[4] = jpegObj.precision; -sof[5] = ((jpegObj.imageHeight >> 8) & 0xFF); -sof[6] = ((jpegObj.imageHeight) & 0xFF); -sof[7] = ((jpegObj.imageWidth >> 8) & 0xFF); -sof[8] = ((jpegObj.imageWidth) & 0xFF); -sof[9] = jpegObj.numberOfComponents; -index = 10; -for (i = 0; i < sof[9]; i++) { -sof[index++] = jpegObj.compID[i]; -sof[index++] = ((jpegObj.hsampFactor[i] << 4) + jpegObj.vsampFactor[i]); -sof[index++] = jpegObj.qtableNumber[i]; -} -this.writeArray (sof); -this.WriteDHTHeader (javajs.img.Huffman.bitsDCluminance, javajs.img.Huffman.valDCluminance); -this.WriteDHTHeader (javajs.img.Huffman.bitsACluminance, javajs.img.Huffman.valACluminance); -this.WriteDHTHeader (javajs.img.Huffman.bitsDCchrominance, javajs.img.Huffman.valDCchrominance); -this.WriteDHTHeader (javajs.img.Huffman.bitsACchrominance, javajs.img.Huffman.valACchrominance); -var sos = Clazz.newByteArray (14, 0); -sos[0] = 0xFF; -sos[1] = 0xDA; -sos[2] = 0; -sos[3] = 12; -sos[4] = jpegObj.numberOfComponents; -index = 5; -for (i = 0; i < sos[4]; i++) { -sos[index++] = jpegObj.compID[i]; -sos[index++] = ((jpegObj.dctableNumber[i] << 4) + jpegObj.actableNumber[i]); -} -sos[index++] = jpegObj.ss; -sos[index++] = jpegObj.se; -sos[index++] = ((jpegObj.ah << 4) + jpegObj.al); -this.writeArray (sos); -return comment; -}, $fz.isPrivate = true, $fz), "javajs.img.JpegObj,javajs.img.DCT"); -Clazz.defineMethod (c$, "writeString", -($fz = function (s, id) { -var len = s.length; -var i0 = 0; -var suffix = this.applicationTag; -while (i0 < len) { -var nBytes = len - i0; -if (nBytes > 65510) { -nBytes = 65500; -var pt = s.lastIndexOf ('\n', i0 + nBytes); -if (pt > i0 + 1) nBytes = pt - i0; -}if (i0 + nBytes == len) suffix = ""; -this.writeTag (nBytes + suffix.length, id); -this.writeArray (s.substring (i0, i0 + nBytes).getBytes ()); -if (suffix.length > 0) this.writeArray (suffix.getBytes ()); -i0 += nBytes; -} -}, $fz.isPrivate = true, $fz), "~S,~N"); -Clazz.defineMethod (c$, "writeTag", -($fz = function (length, id) { -length += 2; -var com = Clazz.newByteArray (4, 0); -com[0] = 0xFF; -com[1] = id; -com[2] = ((length >> 8) & 0xFF); -com[3] = (length & 0xFF); -this.writeArray (com); -}, $fz.isPrivate = true, $fz), "~N,~N"); -Clazz.defineMethod (c$, "WriteDHTHeader", -function (bits, val) { -var dht; -var bytes = 0; -for (var j = 1; j < 17; j++) bytes += bits[j]; - -dht = Clazz.newByteArray (21 + bytes, 0); -dht[0] = 0xFF; -dht[1] = 0xC4; -var index = 4; -for (var j = 0; j < 17; j++) dht[index++] = bits[j]; - -for (var j = 0; j < bytes; j++) dht[index++] = val[j]; - -dht[2] = (((index - 2) >> 8) & 0xFF); -dht[3] = ((index - 2) & 0xFF); -this.writeArray (dht); -}, "~A,~A"); -Clazz.defineMethod (c$, "writeMarker", -function (data) { -this.out.write (data, 0, 2); -}, "~A"); -Clazz.defineMethod (c$, "writeArray", -function (data) { -this.out.write (data, 0, data.length); -}, "~A"); -Clazz.defineStatics (c$, -"CONTINUE_MAX", 65500, -"CONTINUE_MAX_BUFFER", 65510, -"eoi", Clazz.newByteArray (-1, [0xFF, 0xD9]), -"jfif", Clazz.newByteArray (-1, [0xff, 0xe0, 0, 16, 0x4a, 0x46, 0x49, 0x46, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0]), -"soi", Clazz.newByteArray (-1, [0xFF, 0xD8])); -c$ = Clazz.decorateAsClass (function () { -this.quantum = null; -this.divisors = null; -this.quantum_luminance = null; -this.DivisorsLuminance = null; -this.quantum_chrominance = null; -this.DivisorsChrominance = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "DCT"); -Clazz.prepareFields (c$, function () { -this.quantum = javajs.util.AU.newInt2 (2); -this.divisors = javajs.util.AU.newDouble2 (2); -this.quantum_luminance = Clazz.newIntArray (64, 0); -this.DivisorsLuminance = Clazz.newDoubleArray (64, 0); -this.quantum_chrominance = Clazz.newIntArray (64, 0); -this.DivisorsChrominance = Clazz.newDoubleArray (64, 0); -}); -Clazz.makeConstructor (c$, -function (quality) { -this.initMatrix (quality); -}, "~N"); -Clazz.defineMethod (c$, "initMatrix", -($fz = function (quality) { -quality = (quality < 1 ? 1 : quality > 100 ? 100 : quality); -quality = (quality < 50 ? Clazz.doubleToInt (5000 / quality) : 200 - quality * 2); -this.quantum_luminance[0] = 16; -this.quantum_luminance[1] = 11; -this.quantum_luminance[2] = 10; -this.quantum_luminance[3] = 16; -this.quantum_luminance[4] = 24; -this.quantum_luminance[5] = 40; -this.quantum_luminance[6] = 51; -this.quantum_luminance[7] = 61; -this.quantum_luminance[8] = 12; -this.quantum_luminance[9] = 12; -this.quantum_luminance[10] = 14; -this.quantum_luminance[11] = 19; -this.quantum_luminance[12] = 26; -this.quantum_luminance[13] = 58; -this.quantum_luminance[14] = 60; -this.quantum_luminance[15] = 55; -this.quantum_luminance[16] = 14; -this.quantum_luminance[17] = 13; -this.quantum_luminance[18] = 16; -this.quantum_luminance[19] = 24; -this.quantum_luminance[20] = 40; -this.quantum_luminance[21] = 57; -this.quantum_luminance[22] = 69; -this.quantum_luminance[23] = 56; -this.quantum_luminance[24] = 14; -this.quantum_luminance[25] = 17; -this.quantum_luminance[26] = 22; -this.quantum_luminance[27] = 29; -this.quantum_luminance[28] = 51; -this.quantum_luminance[29] = 87; -this.quantum_luminance[30] = 80; -this.quantum_luminance[31] = 62; -this.quantum_luminance[32] = 18; -this.quantum_luminance[33] = 22; -this.quantum_luminance[34] = 37; -this.quantum_luminance[35] = 56; -this.quantum_luminance[36] = 68; -this.quantum_luminance[37] = 109; -this.quantum_luminance[38] = 103; -this.quantum_luminance[39] = 77; -this.quantum_luminance[40] = 24; -this.quantum_luminance[41] = 35; -this.quantum_luminance[42] = 55; -this.quantum_luminance[43] = 64; -this.quantum_luminance[44] = 81; -this.quantum_luminance[45] = 104; -this.quantum_luminance[46] = 113; -this.quantum_luminance[47] = 92; -this.quantum_luminance[48] = 49; -this.quantum_luminance[49] = 64; -this.quantum_luminance[50] = 78; -this.quantum_luminance[51] = 87; -this.quantum_luminance[52] = 103; -this.quantum_luminance[53] = 121; -this.quantum_luminance[54] = 120; -this.quantum_luminance[55] = 101; -this.quantum_luminance[56] = 72; -this.quantum_luminance[57] = 92; -this.quantum_luminance[58] = 95; -this.quantum_luminance[59] = 98; -this.quantum_luminance[60] = 112; -this.quantum_luminance[61] = 100; -this.quantum_luminance[62] = 103; -this.quantum_luminance[63] = 99; -javajs.img.DCT.AANscale (this.DivisorsLuminance, this.quantum_luminance, quality); -for (var i = 4; i < 64; i++) this.quantum_chrominance[i] = 99; - -this.quantum_chrominance[0] = 17; -this.quantum_chrominance[1] = 18; -this.quantum_chrominance[2] = 24; -this.quantum_chrominance[3] = 47; -this.quantum_chrominance[8] = 18; -this.quantum_chrominance[9] = 21; -this.quantum_chrominance[10] = 26; -this.quantum_chrominance[11] = 66; -this.quantum_chrominance[16] = 24; -this.quantum_chrominance[17] = 26; -this.quantum_chrominance[18] = 56; -this.quantum_chrominance[24] = 47; -this.quantum_chrominance[25] = 66; -javajs.img.DCT.AANscale (this.DivisorsChrominance, this.quantum_chrominance, quality); -this.quantum[0] = this.quantum_luminance; -this.quantum[1] = this.quantum_chrominance; -this.divisors[0] = this.DivisorsLuminance; -this.divisors[1] = this.DivisorsChrominance; -}, $fz.isPrivate = true, $fz), "~N"); -c$.AANscale = Clazz.defineMethod (c$, "AANscale", -($fz = function (divisors, values, quality) { -for (var j = 0; j < 64; j++) { -var temp = Clazz.doubleToInt ((values[j] * quality + 50) / 100); -values[j] = (temp < 1 ? 1 : temp > 255 ? 255 : temp); -} -for (var i = 0, index = 0; i < 8; i++) for (var j = 0; j < 8; j++, index++) divisors[index] = (0.125 / (values[index] * javajs.img.DCT.AANscaleFactor[i] * javajs.img.DCT.AANscaleFactor[j])); - - -}, $fz.isPrivate = true, $fz), "~A,~A,~N"); -c$.forwardDCT = Clazz.defineMethod (c$, "forwardDCT", -function (input) { -var output = Clazz.newDoubleArray (8, 8, 0); -var tmp0; -var tmp1; -var tmp2; -var tmp3; -var tmp4; -var tmp5; -var tmp6; -var tmp7; -var tmp10; -var tmp11; -var tmp12; -var tmp13; -var z1; -var z2; -var z3; -var z4; -var z5; -var z11; -var z13; -for (var i = 0; i < 8; i++) for (var j = 0; j < 8; j++) output[i][j] = (input[i][j] - 128.0); - - -for (var i = 0; i < 8; i++) { -tmp0 = output[i][0] + output[i][7]; -tmp7 = output[i][0] - output[i][7]; -tmp1 = output[i][1] + output[i][6]; -tmp6 = output[i][1] - output[i][6]; -tmp2 = output[i][2] + output[i][5]; -tmp5 = output[i][2] - output[i][5]; -tmp3 = output[i][3] + output[i][4]; -tmp4 = output[i][3] - output[i][4]; -tmp10 = tmp0 + tmp3; -tmp13 = tmp0 - tmp3; -tmp11 = tmp1 + tmp2; -tmp12 = tmp1 - tmp2; -output[i][0] = tmp10 + tmp11; -output[i][4] = tmp10 - tmp11; -z1 = (tmp12 + tmp13) * 0.707106781; -output[i][2] = tmp13 + z1; -output[i][6] = tmp13 - z1; -tmp10 = tmp4 + tmp5; -tmp11 = tmp5 + tmp6; -tmp12 = tmp6 + tmp7; -z5 = (tmp10 - tmp12) * 0.382683433; -z2 = 0.541196100 * tmp10 + z5; -z4 = 1.306562965 * tmp12 + z5; -z3 = tmp11 * 0.707106781; -z11 = tmp7 + z3; -z13 = tmp7 - z3; -output[i][5] = z13 + z2; -output[i][3] = z13 - z2; -output[i][1] = z11 + z4; -output[i][7] = z11 - z4; -} -for (var i = 0; i < 8; i++) { -tmp0 = output[0][i] + output[7][i]; -tmp7 = output[0][i] - output[7][i]; -tmp1 = output[1][i] + output[6][i]; -tmp6 = output[1][i] - output[6][i]; -tmp2 = output[2][i] + output[5][i]; -tmp5 = output[2][i] - output[5][i]; -tmp3 = output[3][i] + output[4][i]; -tmp4 = output[3][i] - output[4][i]; -tmp10 = tmp0 + tmp3; -tmp13 = tmp0 - tmp3; -tmp11 = tmp1 + tmp2; -tmp12 = tmp1 - tmp2; -output[0][i] = tmp10 + tmp11; -output[4][i] = tmp10 - tmp11; -z1 = (tmp12 + tmp13) * 0.707106781; -output[2][i] = tmp13 + z1; -output[6][i] = tmp13 - z1; -tmp10 = tmp4 + tmp5; -tmp11 = tmp5 + tmp6; -tmp12 = tmp6 + tmp7; -z5 = (tmp10 - tmp12) * 0.382683433; -z2 = 0.541196100 * tmp10 + z5; -z4 = 1.306562965 * tmp12 + z5; -z3 = tmp11 * 0.707106781; -z11 = tmp7 + z3; -z13 = tmp7 - z3; -output[5][i] = z13 + z2; -output[3][i] = z13 - z2; -output[1][i] = z11 + z4; -output[7][i] = z11 - z4; -} -return output; -}, "~A"); -c$.quantizeBlock = Clazz.defineMethod (c$, "quantizeBlock", -function (inputData, divisorsCode) { -var outputData = Clazz.newIntArray (64, 0); -for (var i = 0, index = 0; i < 8; i++) for (var j = 0; j < 8; j++, index++) outputData[index] = (Math.round (inputData[i][j] * divisorsCode[index])); - - -return outputData; -}, "~A,~A"); -Clazz.defineStatics (c$, -"N", 8, -"NN", 64, -"AANscaleFactor", Clazz.newDoubleArray (-1, [1.0, 1.387039845, 1.306562965, 1.175875602, 1.0, 0.785694958, 0.541196100, 0.275899379])); -c$ = Clazz.decorateAsClass (function () { -this.bufferPutBits = 0; -this.bufferPutBuffer = 0; -this.imageHeight = 0; -this.imageWidth = 0; -this.dc_matrix0 = null; -this.ac_matrix0 = null; -this.dc_matrix1 = null; -this.ac_matrix1 = null; -this.dc_matrix = null; -this.ac_matrix = null; -this.numOfDCTables = 0; -this.numOfACTables = 0; -Clazz.instantialize (this, arguments); -}, javajs.img, "Huffman"); -Clazz.makeConstructor (c$, -function (width, height) { -this.initHuf (); -this.imageWidth = width; -this.imageHeight = height; -}, "~N,~N"); -Clazz.defineMethod (c$, "HuffmanBlockEncoder", -function (out, zigzag, prec, dcCode, acCode) { -var temp; -var temp2; -var nbits; -var k; -var r; -var i; -this.numOfDCTables = 2; -this.numOfACTables = 2; -var matrixDC = this.dc_matrix[dcCode]; -var matrixAC = this.ac_matrix[acCode]; -temp = temp2 = zigzag[0] - prec; -if (temp < 0) { -temp = -temp; -temp2--; -}nbits = 0; -while (temp != 0) { -nbits++; -temp >>= 1; -} -this.bufferIt (out, matrixDC[nbits][0], matrixDC[nbits][1]); -if (nbits != 0) { -this.bufferIt (out, temp2, nbits); -}r = 0; -for (k = 1; k < 64; k++) { -if ((temp = zigzag[javajs.img.Huffman.jpegNaturalOrder[k]]) == 0) { -r++; -} else { -while (r > 15) { -this.bufferIt (out, matrixAC[0xF0][0], matrixAC[0xF0][1]); -r -= 16; -} -temp2 = temp; -if (temp < 0) { -temp = -temp; -temp2--; -}nbits = 1; -while ((temp >>= 1) != 0) { -nbits++; -} -i = (r << 4) + nbits; -this.bufferIt (out, matrixAC[i][0], matrixAC[i][1]); -this.bufferIt (out, temp2, nbits); -r = 0; -}} -if (r > 0) { -this.bufferIt (out, matrixAC[0][0], matrixAC[0][1]); -}}, "javajs.util.OC,~A,~N,~N,~N"); -Clazz.defineMethod (c$, "bufferIt", -function (out, code, size) { -var putBuffer = code; -var putBits = this.bufferPutBits; -putBuffer &= (1 << size) - 1; -putBits += size; -putBuffer <<= 24 - putBits; -putBuffer |= this.bufferPutBuffer; -while (putBits >= 8) { -var c = ((putBuffer >> 16) & 0xFF); -out.writeByteAsInt (c); -if (c == 0xFF) { -out.writeByteAsInt (0); -}putBuffer <<= 8; -putBits -= 8; -} -this.bufferPutBuffer = putBuffer; -this.bufferPutBits = putBits; -}, "javajs.util.OC,~N,~N"); -Clazz.defineMethod (c$, "flushBuffer", -function (out) { -var putBuffer = this.bufferPutBuffer; -var putBits = this.bufferPutBits; -while (putBits >= 8) { -var c = ((putBuffer >> 16) & 0xFF); -out.writeByteAsInt (c); -if (c == 0xFF) { -out.writeByteAsInt (0); -}putBuffer <<= 8; -putBits -= 8; -} -if (putBits > 0) { -var c = ((putBuffer >> 16) & 0xFF); -out.writeByteAsInt (c); -}}, "javajs.util.OC"); -Clazz.defineMethod (c$, "initHuf", -($fz = function () { -this.dc_matrix0 = Clazz.newIntArray (12, 2, 0); -this.dc_matrix1 = Clazz.newIntArray (12, 2, 0); -this.ac_matrix0 = Clazz.newIntArray (255, 2, 0); -this.ac_matrix1 = Clazz.newIntArray (255, 2, 0); -this.dc_matrix = javajs.util.AU.newInt3 (2, -1); -this.ac_matrix = javajs.util.AU.newInt3 (2, -1); -var p; -var l; -var i; -var lastp; -var si; -var code; -var huffsize = Clazz.newIntArray (257, 0); -var huffcode = Clazz.newIntArray (257, 0); -p = 0; -for (l = 1; l <= 16; l++) { -for (i = javajs.img.Huffman.bitsDCchrominance[l]; --i >= 0; ) { -huffsize[p++] = l; -} -} -huffsize[p] = 0; -lastp = p; -code = 0; -si = huffsize[0]; -p = 0; -while (huffsize[p] != 0) { -while (huffsize[p] == si) { -huffcode[p++] = code; -code++; -} -code <<= 1; -si++; -} -for (p = 0; p < lastp; p++) { -this.dc_matrix1[javajs.img.Huffman.valDCchrominance[p]][0] = huffcode[p]; -this.dc_matrix1[javajs.img.Huffman.valDCchrominance[p]][1] = huffsize[p]; -} -p = 0; -for (l = 1; l <= 16; l++) { -for (i = javajs.img.Huffman.bitsACchrominance[l]; --i >= 0; ) { -huffsize[p++] = l; -} -} -huffsize[p] = 0; -lastp = p; -code = 0; -si = huffsize[0]; -p = 0; -while (huffsize[p] != 0) { -while (huffsize[p] == si) { -huffcode[p++] = code; -code++; -} -code <<= 1; -si++; -} -for (p = 0; p < lastp; p++) { -this.ac_matrix1[javajs.img.Huffman.valACchrominance[p]][0] = huffcode[p]; -this.ac_matrix1[javajs.img.Huffman.valACchrominance[p]][1] = huffsize[p]; -} -p = 0; -for (l = 1; l <= 16; l++) { -for (i = javajs.img.Huffman.bitsDCluminance[l]; --i >= 0; ) { -huffsize[p++] = l; -} -} -huffsize[p] = 0; -lastp = p; -code = 0; -si = huffsize[0]; -p = 0; -while (huffsize[p] != 0) { -while (huffsize[p] == si) { -huffcode[p++] = code; -code++; -} -code <<= 1; -si++; -} -for (p = 0; p < lastp; p++) { -this.dc_matrix0[javajs.img.Huffman.valDCluminance[p]][0] = huffcode[p]; -this.dc_matrix0[javajs.img.Huffman.valDCluminance[p]][1] = huffsize[p]; -} -p = 0; -for (l = 1; l <= 16; l++) { -for (i = javajs.img.Huffman.bitsACluminance[l]; --i >= 0; ) { -huffsize[p++] = l; -} -} -huffsize[p] = 0; -lastp = p; -code = 0; -si = huffsize[0]; -p = 0; -while (huffsize[p] != 0) { -while (huffsize[p] == si) { -huffcode[p++] = code; -code++; -} -code <<= 1; -si++; -} -for (var q = 0; q < lastp; q++) { -this.ac_matrix0[javajs.img.Huffman.valACluminance[q]][0] = huffcode[q]; -this.ac_matrix0[javajs.img.Huffman.valACluminance[q]][1] = huffsize[q]; -} -this.dc_matrix[0] = this.dc_matrix0; -this.dc_matrix[1] = this.dc_matrix1; -this.ac_matrix[0] = this.ac_matrix0; -this.ac_matrix[1] = this.ac_matrix1; -}, $fz.isPrivate = true, $fz)); -Clazz.defineStatics (c$, -"bitsDCluminance", Clazz.newIntArray (-1, [0x00, 0, 1, 5, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0]), -"valDCluminance", Clazz.newIntArray (-1, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]), -"bitsDCchrominance", Clazz.newIntArray (-1, [0x01, 0, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0]), -"valDCchrominance", Clazz.newIntArray (-1, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]), -"bitsACluminance", Clazz.newIntArray (-1, [0x10, 0, 2, 1, 3, 3, 2, 4, 3, 5, 5, 4, 4, 0, 0, 1, 0x7d]), -"valACluminance", Clazz.newIntArray (-1, [0x01, 0x02, 0x03, 0x00, 0x04, 0x11, 0x05, 0x12, 0x21, 0x31, 0x41, 0x06, 0x13, 0x51, 0x61, 0x07, 0x22, 0x71, 0x14, 0x32, 0x81, 0x91, 0xa1, 0x08, 0x23, 0x42, 0xb1, 0xc1, 0x15, 0x52, 0xd1, 0xf0, 0x24, 0x33, 0x62, 0x72, 0x82, 0x09, 0x0a, 0x16, 0x17, 0x18, 0x19, 0x1a, 0x25, 0x26, 0x27, 0x28, 0x29, 0x2a, 0x34, 0x35, 0x36, 0x37, 0x38, 0x39, 0x3a, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4a, 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5a, 0x63, 0x64, 0x65, 0x66, 0x67, 0x68, 0x69, 0x6a, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7a, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8a, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98, 0x99, 0x9a, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7, 0xa8, 0xa9, 0xaa, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 0xb8, 0xb9, 0xba, 0xc2, 0xc3, 0xc4, 0xc5, 0xc6, 0xc7, 0xc8, 0xc9, 0xca, 0xd2, 0xd3, 0xd4, 0xd5, 0xd6, 0xd7, 0xd8, 0xd9, 0xda, 0xe1, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7, 0xe8, 0xe9, 0xea, 0xf1, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 0xf8, 0xf9, 0xfa]), -"bitsACchrominance", Clazz.newIntArray (-1, [0x11, 0, 2, 1, 2, 4, 4, 3, 4, 7, 5, 4, 4, 0, 1, 2, 0x77]), -"valACchrominance", Clazz.newIntArray (-1, [0x00, 0x01, 0x02, 0x03, 0x11, 0x04, 0x05, 0x21, 0x31, 0x06, 0x12, 0x41, 0x51, 0x07, 0x61, 0x71, 0x13, 0x22, 0x32, 0x81, 0x08, 0x14, 0x42, 0x91, 0xa1, 0xb1, 0xc1, 0x09, 0x23, 0x33, 0x52, 0xf0, 0x15, 0x62, 0x72, 0xd1, 0x0a, 0x16, 0x24, 0x34, 0xe1, 0x25, 0xf1, 0x17, 0x18, 0x19, 0x1a, 0x26, 0x27, 0x28, 0x29, 0x2a, 0x35, 0x36, 0x37, 0x38, 0x39, 0x3a, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4a, 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5a, 0x63, 0x64, 0x65, 0x66, 0x67, 0x68, 0x69, 0x6a, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7a, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8a, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98, 0x99, 0x9a, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7, 0xa8, 0xa9, 0xaa, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 0xb8, 0xb9, 0xba, 0xc2, 0xc3, 0xc4, 0xc5, 0xc6, 0xc7, 0xc8, 0xc9, 0xca, 0xd2, 0xd3, 0xd4, 0xd5, 0xd6, 0xd7, 0xd8, 0xd9, 0xda, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7, 0xe8, 0xe9, 0xea, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 0xf8, 0xf9, 0xfa]), -"jpegNaturalOrder", Clazz.newIntArray (-1, [0, 1, 8, 16, 9, 2, 3, 10, 17, 24, 32, 25, 18, 11, 4, 5, 12, 19, 26, 33, 40, 48, 41, 34, 27, 20, 13, 6, 7, 14, 21, 28, 35, 42, 49, 56, 57, 50, 43, 36, 29, 22, 15, 23, 30, 37, 44, 51, 58, 59, 52, 45, 38, 31, 39, 46, 53, 60, 61, 54, 47, 55, 62, 63])); -c$ = Clazz.decorateAsClass (function () { -this.comment = null; -this.imageHeight = 0; -this.imageWidth = 0; -this.blockWidth = null; -this.blockHeight = null; -this.precision = 8; -this.numberOfComponents = 3; -this.components = null; -this.compID = null; -this.hsampFactor = null; -this.vsampFactor = null; -this.qtableNumber = null; -this.dctableNumber = null; -this.actableNumber = null; -this.lastColumnIsDummy = null; -this.lastRowIsDummy = null; -this.ss = 0; -this.se = 63; -this.ah = 0; -this.al = 0; -this.compWidth = null; -this.compHeight = null; -this.maxHsampFactor = 0; -this.maxVsampFactor = 0; -Clazz.instantialize (this, arguments); -}, javajs.img, "JpegObj"); -Clazz.prepareFields (c$, function () { -this.compID = Clazz.newIntArray (-1, [1, 2, 3]); -this.hsampFactor = Clazz.newIntArray (-1, [1, 1, 1]); -this.vsampFactor = Clazz.newIntArray (-1, [1, 1, 1]); -this.qtableNumber = Clazz.newIntArray (-1, [0, 1, 1]); -this.dctableNumber = Clazz.newIntArray (-1, [0, 1, 1]); -this.actableNumber = Clazz.newIntArray (-1, [0, 1, 1]); -this.lastColumnIsDummy = Clazz.newBooleanArray (-1, [false, false, false]); -this.lastRowIsDummy = Clazz.newBooleanArray (-1, [false, false, false]); -}); -Clazz.makeConstructor (c$, -function () { -this.components = javajs.util.AU.newFloat3 (this.numberOfComponents, -1); -this.compWidth = Clazz.newIntArray (this.numberOfComponents, 0); -this.compHeight = Clazz.newIntArray (this.numberOfComponents, 0); -this.blockWidth = Clazz.newIntArray (this.numberOfComponents, 0); -this.blockHeight = Clazz.newIntArray (this.numberOfComponents, 0); -}); -Clazz.defineMethod (c$, "getYCCArray", -function (pixels) { -this.maxHsampFactor = 1; -this.maxVsampFactor = 1; -for (var y = 0; y < this.numberOfComponents; y++) { -this.maxHsampFactor = Math.max (this.maxHsampFactor, this.hsampFactor[y]); -this.maxVsampFactor = Math.max (this.maxVsampFactor, this.vsampFactor[y]); -} -for (var y = 0; y < this.numberOfComponents; y++) { -this.compWidth[y] = (Clazz.doubleToInt (((this.imageWidth % 8 != 0) ? (Clazz.doubleToInt (Math.ceil (this.imageWidth / 8.0))) * 8 : this.imageWidth) / this.maxHsampFactor)) * this.hsampFactor[y]; -if (this.compWidth[y] != ((Clazz.doubleToInt (this.imageWidth / this.maxHsampFactor)) * this.hsampFactor[y])) { -this.lastColumnIsDummy[y] = true; -}this.blockWidth[y] = Clazz.doubleToInt (Math.ceil (this.compWidth[y] / 8.0)); -this.compHeight[y] = (Clazz.doubleToInt (((this.imageHeight % 8 != 0) ? (Clazz.doubleToInt (Math.ceil (this.imageHeight / 8.0))) * 8 : this.imageHeight) / this.maxVsampFactor)) * this.vsampFactor[y]; -if (this.compHeight[y] != ((Clazz.doubleToInt (this.imageHeight / this.maxVsampFactor)) * this.vsampFactor[y])) { -this.lastRowIsDummy[y] = true; -}this.blockHeight[y] = Clazz.doubleToInt (Math.ceil (this.compHeight[y] / 8.0)); -} -var Y = Clazz.newFloatArray (this.compHeight[0], this.compWidth[0], 0); -var Cr1 = Clazz.newFloatArray (this.compHeight[0], this.compWidth[0], 0); -var Cb1 = Clazz.newFloatArray (this.compHeight[0], this.compWidth[0], 0); -for (var pt = 0, y = 0; y < this.imageHeight; ++y) { -for (var x = 0; x < this.imageWidth; ++x, pt++) { -var p = pixels[pt]; -var r = ((p >> 16) & 0xff); -var g = ((p >> 8) & 0xff); -var b = (p & 0xff); -Y[y][x] = ((0.299 * r + 0.587 * g + 0.114 * b)); -Cb1[y][x] = 128 + ((-0.16874 * r - 0.33126 * g + 0.5 * b)); -Cr1[y][x] = 128 + ((0.5 * r - 0.41869 * g - 0.08131 * b)); -} -} -this.components[0] = Y; -this.components[1] = Cb1; -this.components[2] = Cr1; -}, "~A"); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.ImageEncoder", "javajs.util.AU"], ["javajs.img.DCT", "$.JpgEncoder", "$.JpegObj", "$.Huffman"], null, function () { +c$ = Clazz.decorateAsClass (function () { +this.jpegObj = null; +this.huf = null; +this.dct = null; +this.defaultQuality = 100; +this.applicationTag = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "JpgEncoder", javajs.img.ImageEncoder); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.img.JpgEncoder, []); +}); +Clazz.overrideMethod (c$, "setParams", +function (params) { +if (this.quality <= 0) this.quality = (params.containsKey ("qualityJPG") ? (params.get ("qualityJPG")).intValue () : this.defaultQuality); +this.jpegObj = new javajs.img.JpegObj (); +this.jpegObj.comment = params.get ("comment"); +this.applicationTag = params.get ("jpgAppTag"); +}, "java.util.Map"); +Clazz.overrideMethod (c$, "generate", +function () { +this.jpegObj.imageWidth = this.width; +this.jpegObj.imageHeight = this.height; +this.dct = new javajs.img.DCT (this.quality); +this.huf = new javajs.img.Huffman (this.width, this.height); +if (this.jpegObj == null) return; +this.jpegObj.getYCCArray (this.pixels); +var longState = this.writeHeaders (this.jpegObj, this.dct); +this.writeCompressedData (this.jpegObj, this.dct, this.huf); +this.writeMarker (javajs.img.JpgEncoder.eoi); +if (longState != null) { +var b = longState.getBytes (); +this.out.write (b, 0, b.length); +}}); +Clazz.defineMethod (c$, "writeCompressedData", +($fz = function (jpegObj, dct, huf) { +var i; +var j; +var r; +var c; +var a; +var b; +var comp; +var xpos; +var ypos; +var xblockoffset; +var yblockoffset; +var inputArray; +var dctArray1 = Clazz.newFloatArray (8, 8, 0); +var dctArray2 = Clazz.newDoubleArray (8, 8, 0); +var dctArray3 = Clazz.newIntArray (64, 0); +var lastDCvalue = Clazz.newIntArray (jpegObj.numberOfComponents, 0); +var minBlockWidth; +var minBlockHeight; +minBlockWidth = ((huf.imageWidth % 8 != 0) ? Clazz.doubleToInt (Math.floor (huf.imageWidth / 8.0) + 1) * 8 : huf.imageWidth); +minBlockHeight = ((huf.imageHeight % 8 != 0) ? Clazz.doubleToInt (Math.floor (huf.imageHeight / 8.0) + 1) * 8 : huf.imageHeight); +for (comp = 0; comp < jpegObj.numberOfComponents; comp++) { +minBlockWidth = Math.min (minBlockWidth, jpegObj.blockWidth[comp]); +minBlockHeight = Math.min (minBlockHeight, jpegObj.blockHeight[comp]); +} +xpos = 0; +for (r = 0; r < minBlockHeight; r++) { +for (c = 0; c < minBlockWidth; c++) { +xpos = c * 8; +ypos = r * 8; +for (comp = 0; comp < jpegObj.numberOfComponents; comp++) { +inputArray = jpegObj.components[comp]; +var vsampF = jpegObj.vsampFactor[comp]; +var hsampF = jpegObj.hsampFactor[comp]; +var qNumber = jpegObj.qtableNumber[comp]; +var dcNumber = jpegObj.dctableNumber[comp]; +var acNumber = jpegObj.actableNumber[comp]; +for (i = 0; i < vsampF; i++) { +for (j = 0; j < hsampF; j++) { +xblockoffset = j * 8; +yblockoffset = i * 8; +for (a = 0; a < 8; a++) { +for (b = 0; b < 8; b++) { +dctArray1[a][b] = inputArray[ypos + yblockoffset + a][xpos + xblockoffset + b]; +} +} +dctArray2 = javajs.img.DCT.forwardDCT (dctArray1); +dctArray3 = javajs.img.DCT.quantizeBlock (dctArray2, dct.divisors[qNumber]); +huf.HuffmanBlockEncoder (this.out, dctArray3, lastDCvalue[comp], dcNumber, acNumber); +lastDCvalue[comp] = dctArray3[0]; +} +} +} +} +} +huf.flushBuffer (this.out); +}, $fz.isPrivate = true, $fz), "javajs.img.JpegObj,javajs.img.DCT,javajs.img.Huffman"); +Clazz.defineMethod (c$, "writeHeaders", +($fz = function (jpegObj, dct) { +var i; +var j; +var index; +var offset; +var tempArray; +this.writeMarker (javajs.img.JpgEncoder.soi); +this.writeArray (javajs.img.JpgEncoder.jfif); +var comment = null; +if (jpegObj.comment.length > 0) this.writeString (jpegObj.comment, 0xE1); +this.writeString ("JPEG Encoder Copyright 1998, James R. Weeks and BioElectroMech.\n\n", 0xFE); +var dqt = Clazz.newByteArray (134, 0); +dqt[0] = 0xFF; +dqt[1] = 0xDB; +dqt[2] = 0; +dqt[3] = 132; +offset = 4; +for (i = 0; i < 2; i++) { +dqt[offset++] = ((0) + i); +tempArray = dct.quantum[i]; +for (j = 0; j < 64; j++) { +dqt[offset++] = tempArray[javajs.img.Huffman.jpegNaturalOrder[j]]; +} +} +this.writeArray (dqt); +var sof = Clazz.newByteArray (19, 0); +sof[0] = 0xFF; +sof[1] = 0xC0; +sof[2] = 0; +sof[3] = 17; +sof[4] = jpegObj.precision; +sof[5] = ((jpegObj.imageHeight >> 8) & 0xFF); +sof[6] = ((jpegObj.imageHeight) & 0xFF); +sof[7] = ((jpegObj.imageWidth >> 8) & 0xFF); +sof[8] = ((jpegObj.imageWidth) & 0xFF); +sof[9] = jpegObj.numberOfComponents; +index = 10; +for (i = 0; i < sof[9]; i++) { +sof[index++] = jpegObj.compID[i]; +sof[index++] = ((jpegObj.hsampFactor[i] << 4) + jpegObj.vsampFactor[i]); +sof[index++] = jpegObj.qtableNumber[i]; +} +this.writeArray (sof); +this.WriteDHTHeader (javajs.img.Huffman.bitsDCluminance, javajs.img.Huffman.valDCluminance); +this.WriteDHTHeader (javajs.img.Huffman.bitsACluminance, javajs.img.Huffman.valACluminance); +this.WriteDHTHeader (javajs.img.Huffman.bitsDCchrominance, javajs.img.Huffman.valDCchrominance); +this.WriteDHTHeader (javajs.img.Huffman.bitsACchrominance, javajs.img.Huffman.valACchrominance); +var sos = Clazz.newByteArray (14, 0); +sos[0] = 0xFF; +sos[1] = 0xDA; +sos[2] = 0; +sos[3] = 12; +sos[4] = jpegObj.numberOfComponents; +index = 5; +for (i = 0; i < sos[4]; i++) { +sos[index++] = jpegObj.compID[i]; +sos[index++] = ((jpegObj.dctableNumber[i] << 4) + jpegObj.actableNumber[i]); +} +sos[index++] = jpegObj.ss; +sos[index++] = jpegObj.se; +sos[index++] = ((jpegObj.ah << 4) + jpegObj.al); +this.writeArray (sos); +return comment; +}, $fz.isPrivate = true, $fz), "javajs.img.JpegObj,javajs.img.DCT"); +Clazz.defineMethod (c$, "writeString", +($fz = function (s, id) { +var len = s.length; +var i0 = 0; +var suffix = this.applicationTag; +while (i0 < len) { +var nBytes = len - i0; +if (nBytes > 65510) { +nBytes = 65500; +var pt = s.lastIndexOf ('\n', i0 + nBytes); +if (pt > i0 + 1) nBytes = pt - i0; +}if (i0 + nBytes == len) suffix = ""; +this.writeTag (nBytes + suffix.length, id); +this.writeArray (s.substring (i0, i0 + nBytes).getBytes ()); +if (suffix.length > 0) this.writeArray (suffix.getBytes ()); +i0 += nBytes; +} +}, $fz.isPrivate = true, $fz), "~S,~N"); +Clazz.defineMethod (c$, "writeTag", +($fz = function (length, id) { +length += 2; +var com = Clazz.newByteArray (4, 0); +com[0] = 0xFF; +com[1] = id; +com[2] = ((length >> 8) & 0xFF); +com[3] = (length & 0xFF); +this.writeArray (com); +}, $fz.isPrivate = true, $fz), "~N,~N"); +Clazz.defineMethod (c$, "WriteDHTHeader", +function (bits, val) { +var dht; +var bytes = 0; +for (var j = 1; j < 17; j++) bytes += bits[j]; + +dht = Clazz.newByteArray (21 + bytes, 0); +dht[0] = 0xFF; +dht[1] = 0xC4; +var index = 4; +for (var j = 0; j < 17; j++) dht[index++] = bits[j]; + +for (var j = 0; j < bytes; j++) dht[index++] = val[j]; + +dht[2] = (((index - 2) >> 8) & 0xFF); +dht[3] = ((index - 2) & 0xFF); +this.writeArray (dht); +}, "~A,~A"); +Clazz.defineMethod (c$, "writeMarker", +function (data) { +this.out.write (data, 0, 2); +}, "~A"); +Clazz.defineMethod (c$, "writeArray", +function (data) { +this.out.write (data, 0, data.length); +}, "~A"); +Clazz.defineStatics (c$, +"CONTINUE_MAX", 65500, +"CONTINUE_MAX_BUFFER", 65510, +"eoi", Clazz.newByteArray (-1, [0xFF, 0xD9]), +"jfif", Clazz.newByteArray (-1, [0xff, 0xe0, 0, 16, 0x4a, 0x46, 0x49, 0x46, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0]), +"soi", Clazz.newByteArray (-1, [0xFF, 0xD8])); +c$ = Clazz.decorateAsClass (function () { +this.quantum = null; +this.divisors = null; +this.quantum_luminance = null; +this.DivisorsLuminance = null; +this.quantum_chrominance = null; +this.DivisorsChrominance = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "DCT"); +Clazz.prepareFields (c$, function () { +this.quantum = javajs.util.AU.newInt2 (2); +this.divisors = javajs.util.AU.newDouble2 (2); +this.quantum_luminance = Clazz.newIntArray (64, 0); +this.DivisorsLuminance = Clazz.newDoubleArray (64, 0); +this.quantum_chrominance = Clazz.newIntArray (64, 0); +this.DivisorsChrominance = Clazz.newDoubleArray (64, 0); +}); +Clazz.makeConstructor (c$, +function (quality) { +this.initMatrix (quality); +}, "~N"); +Clazz.defineMethod (c$, "initMatrix", +($fz = function (quality) { +quality = (quality < 1 ? 1 : quality > 100 ? 100 : quality); +quality = (quality < 50 ? Clazz.doubleToInt (5000 / quality) : 200 - quality * 2); +this.quantum_luminance[0] = 16; +this.quantum_luminance[1] = 11; +this.quantum_luminance[2] = 10; +this.quantum_luminance[3] = 16; +this.quantum_luminance[4] = 24; +this.quantum_luminance[5] = 40; +this.quantum_luminance[6] = 51; +this.quantum_luminance[7] = 61; +this.quantum_luminance[8] = 12; +this.quantum_luminance[9] = 12; +this.quantum_luminance[10] = 14; +this.quantum_luminance[11] = 19; +this.quantum_luminance[12] = 26; +this.quantum_luminance[13] = 58; +this.quantum_luminance[14] = 60; +this.quantum_luminance[15] = 55; +this.quantum_luminance[16] = 14; +this.quantum_luminance[17] = 13; +this.quantum_luminance[18] = 16; +this.quantum_luminance[19] = 24; +this.quantum_luminance[20] = 40; +this.quantum_luminance[21] = 57; +this.quantum_luminance[22] = 69; +this.quantum_luminance[23] = 56; +this.quantum_luminance[24] = 14; +this.quantum_luminance[25] = 17; +this.quantum_luminance[26] = 22; +this.quantum_luminance[27] = 29; +this.quantum_luminance[28] = 51; +this.quantum_luminance[29] = 87; +this.quantum_luminance[30] = 80; +this.quantum_luminance[31] = 62; +this.quantum_luminance[32] = 18; +this.quantum_luminance[33] = 22; +this.quantum_luminance[34] = 37; +this.quantum_luminance[35] = 56; +this.quantum_luminance[36] = 68; +this.quantum_luminance[37] = 109; +this.quantum_luminance[38] = 103; +this.quantum_luminance[39] = 77; +this.quantum_luminance[40] = 24; +this.quantum_luminance[41] = 35; +this.quantum_luminance[42] = 55; +this.quantum_luminance[43] = 64; +this.quantum_luminance[44] = 81; +this.quantum_luminance[45] = 104; +this.quantum_luminance[46] = 113; +this.quantum_luminance[47] = 92; +this.quantum_luminance[48] = 49; +this.quantum_luminance[49] = 64; +this.quantum_luminance[50] = 78; +this.quantum_luminance[51] = 87; +this.quantum_luminance[52] = 103; +this.quantum_luminance[53] = 121; +this.quantum_luminance[54] = 120; +this.quantum_luminance[55] = 101; +this.quantum_luminance[56] = 72; +this.quantum_luminance[57] = 92; +this.quantum_luminance[58] = 95; +this.quantum_luminance[59] = 98; +this.quantum_luminance[60] = 112; +this.quantum_luminance[61] = 100; +this.quantum_luminance[62] = 103; +this.quantum_luminance[63] = 99; +javajs.img.DCT.AANscale (this.DivisorsLuminance, this.quantum_luminance, quality); +for (var i = 4; i < 64; i++) this.quantum_chrominance[i] = 99; + +this.quantum_chrominance[0] = 17; +this.quantum_chrominance[1] = 18; +this.quantum_chrominance[2] = 24; +this.quantum_chrominance[3] = 47; +this.quantum_chrominance[8] = 18; +this.quantum_chrominance[9] = 21; +this.quantum_chrominance[10] = 26; +this.quantum_chrominance[11] = 66; +this.quantum_chrominance[16] = 24; +this.quantum_chrominance[17] = 26; +this.quantum_chrominance[18] = 56; +this.quantum_chrominance[24] = 47; +this.quantum_chrominance[25] = 66; +javajs.img.DCT.AANscale (this.DivisorsChrominance, this.quantum_chrominance, quality); +this.quantum[0] = this.quantum_luminance; +this.quantum[1] = this.quantum_chrominance; +this.divisors[0] = this.DivisorsLuminance; +this.divisors[1] = this.DivisorsChrominance; +}, $fz.isPrivate = true, $fz), "~N"); +c$.AANscale = Clazz.defineMethod (c$, "AANscale", +($fz = function (divisors, values, quality) { +for (var j = 0; j < 64; j++) { +var temp = Clazz.doubleToInt ((values[j] * quality + 50) / 100); +values[j] = (temp < 1 ? 1 : temp > 255 ? 255 : temp); +} +for (var i = 0, index = 0; i < 8; i++) for (var j = 0; j < 8; j++, index++) divisors[index] = (0.125 / (values[index] * javajs.img.DCT.AANscaleFactor[i] * javajs.img.DCT.AANscaleFactor[j])); + + +}, $fz.isPrivate = true, $fz), "~A,~A,~N"); +c$.forwardDCT = Clazz.defineMethod (c$, "forwardDCT", +function (input) { +var output = Clazz.newDoubleArray (8, 8, 0); +var tmp0; +var tmp1; +var tmp2; +var tmp3; +var tmp4; +var tmp5; +var tmp6; +var tmp7; +var tmp10; +var tmp11; +var tmp12; +var tmp13; +var z1; +var z2; +var z3; +var z4; +var z5; +var z11; +var z13; +for (var i = 0; i < 8; i++) for (var j = 0; j < 8; j++) output[i][j] = (input[i][j] - 128.0); + + +for (var i = 0; i < 8; i++) { +tmp0 = output[i][0] + output[i][7]; +tmp7 = output[i][0] - output[i][7]; +tmp1 = output[i][1] + output[i][6]; +tmp6 = output[i][1] - output[i][6]; +tmp2 = output[i][2] + output[i][5]; +tmp5 = output[i][2] - output[i][5]; +tmp3 = output[i][3] + output[i][4]; +tmp4 = output[i][3] - output[i][4]; +tmp10 = tmp0 + tmp3; +tmp13 = tmp0 - tmp3; +tmp11 = tmp1 + tmp2; +tmp12 = tmp1 - tmp2; +output[i][0] = tmp10 + tmp11; +output[i][4] = tmp10 - tmp11; +z1 = (tmp12 + tmp13) * 0.707106781; +output[i][2] = tmp13 + z1; +output[i][6] = tmp13 - z1; +tmp10 = tmp4 + tmp5; +tmp11 = tmp5 + tmp6; +tmp12 = tmp6 + tmp7; +z5 = (tmp10 - tmp12) * 0.382683433; +z2 = 0.541196100 * tmp10 + z5; +z4 = 1.306562965 * tmp12 + z5; +z3 = tmp11 * 0.707106781; +z11 = tmp7 + z3; +z13 = tmp7 - z3; +output[i][5] = z13 + z2; +output[i][3] = z13 - z2; +output[i][1] = z11 + z4; +output[i][7] = z11 - z4; +} +for (var i = 0; i < 8; i++) { +tmp0 = output[0][i] + output[7][i]; +tmp7 = output[0][i] - output[7][i]; +tmp1 = output[1][i] + output[6][i]; +tmp6 = output[1][i] - output[6][i]; +tmp2 = output[2][i] + output[5][i]; +tmp5 = output[2][i] - output[5][i]; +tmp3 = output[3][i] + output[4][i]; +tmp4 = output[3][i] - output[4][i]; +tmp10 = tmp0 + tmp3; +tmp13 = tmp0 - tmp3; +tmp11 = tmp1 + tmp2; +tmp12 = tmp1 - tmp2; +output[0][i] = tmp10 + tmp11; +output[4][i] = tmp10 - tmp11; +z1 = (tmp12 + tmp13) * 0.707106781; +output[2][i] = tmp13 + z1; +output[6][i] = tmp13 - z1; +tmp10 = tmp4 + tmp5; +tmp11 = tmp5 + tmp6; +tmp12 = tmp6 + tmp7; +z5 = (tmp10 - tmp12) * 0.382683433; +z2 = 0.541196100 * tmp10 + z5; +z4 = 1.306562965 * tmp12 + z5; +z3 = tmp11 * 0.707106781; +z11 = tmp7 + z3; +z13 = tmp7 - z3; +output[5][i] = z13 + z2; +output[3][i] = z13 - z2; +output[1][i] = z11 + z4; +output[7][i] = z11 - z4; +} +return output; +}, "~A"); +c$.quantizeBlock = Clazz.defineMethod (c$, "quantizeBlock", +function (inputData, divisorsCode) { +var outputData = Clazz.newIntArray (64, 0); +for (var i = 0, index = 0; i < 8; i++) for (var j = 0; j < 8; j++, index++) outputData[index] = (Math.round (inputData[i][j] * divisorsCode[index])); + + +return outputData; +}, "~A,~A"); +Clazz.defineStatics (c$, +"N", 8, +"NN", 64, +"AANscaleFactor", Clazz.newDoubleArray (-1, [1.0, 1.387039845, 1.306562965, 1.175875602, 1.0, 0.785694958, 0.541196100, 0.275899379])); +c$ = Clazz.decorateAsClass (function () { +this.bufferPutBits = 0; +this.bufferPutBuffer = 0; +this.imageHeight = 0; +this.imageWidth = 0; +this.dc_matrix0 = null; +this.ac_matrix0 = null; +this.dc_matrix1 = null; +this.ac_matrix1 = null; +this.dc_matrix = null; +this.ac_matrix = null; +this.numOfDCTables = 0; +this.numOfACTables = 0; +Clazz.instantialize (this, arguments); +}, javajs.img, "Huffman"); +Clazz.makeConstructor (c$, +function (width, height) { +this.initHuf (); +this.imageWidth = width; +this.imageHeight = height; +}, "~N,~N"); +Clazz.defineMethod (c$, "HuffmanBlockEncoder", +function (out, zigzag, prec, dcCode, acCode) { +var temp; +var temp2; +var nbits; +var k; +var r; +var i; +this.numOfDCTables = 2; +this.numOfACTables = 2; +var matrixDC = this.dc_matrix[dcCode]; +var matrixAC = this.ac_matrix[acCode]; +temp = temp2 = zigzag[0] - prec; +if (temp < 0) { +temp = -temp; +temp2--; +}nbits = 0; +while (temp != 0) { +nbits++; +temp >>= 1; +} +this.bufferIt (out, matrixDC[nbits][0], matrixDC[nbits][1]); +if (nbits != 0) { +this.bufferIt (out, temp2, nbits); +}r = 0; +for (k = 1; k < 64; k++) { +if ((temp = zigzag[javajs.img.Huffman.jpegNaturalOrder[k]]) == 0) { +r++; +} else { +while (r > 15) { +this.bufferIt (out, matrixAC[0xF0][0], matrixAC[0xF0][1]); +r -= 16; +} +temp2 = temp; +if (temp < 0) { +temp = -temp; +temp2--; +}nbits = 1; +while ((temp >>= 1) != 0) { +nbits++; +} +i = (r << 4) + nbits; +this.bufferIt (out, matrixAC[i][0], matrixAC[i][1]); +this.bufferIt (out, temp2, nbits); +r = 0; +}} +if (r > 0) { +this.bufferIt (out, matrixAC[0][0], matrixAC[0][1]); +}}, "javajs.util.OC,~A,~N,~N,~N"); +Clazz.defineMethod (c$, "bufferIt", +function (out, code, size) { +var putBuffer = code; +var putBits = this.bufferPutBits; +putBuffer &= (1 << size) - 1; +putBits += size; +putBuffer <<= 24 - putBits; +putBuffer |= this.bufferPutBuffer; +while (putBits >= 8) { +var c = ((putBuffer >> 16) & 0xFF); +out.writeByteAsInt (c); +if (c == 0xFF) { +out.writeByteAsInt (0); +}putBuffer <<= 8; +putBits -= 8; +} +this.bufferPutBuffer = putBuffer; +this.bufferPutBits = putBits; +}, "javajs.util.OC,~N,~N"); +Clazz.defineMethod (c$, "flushBuffer", +function (out) { +var putBuffer = this.bufferPutBuffer; +var putBits = this.bufferPutBits; +while (putBits >= 8) { +var c = ((putBuffer >> 16) & 0xFF); +out.writeByteAsInt (c); +if (c == 0xFF) { +out.writeByteAsInt (0); +}putBuffer <<= 8; +putBits -= 8; +} +if (putBits > 0) { +var c = ((putBuffer >> 16) & 0xFF); +out.writeByteAsInt (c); +}}, "javajs.util.OC"); +Clazz.defineMethod (c$, "initHuf", +($fz = function () { +this.dc_matrix0 = Clazz.newIntArray (12, 2, 0); +this.dc_matrix1 = Clazz.newIntArray (12, 2, 0); +this.ac_matrix0 = Clazz.newIntArray (255, 2, 0); +this.ac_matrix1 = Clazz.newIntArray (255, 2, 0); +this.dc_matrix = javajs.util.AU.newInt3 (2, -1); +this.ac_matrix = javajs.util.AU.newInt3 (2, -1); +var p; +var l; +var i; +var lastp; +var si; +var code; +var huffsize = Clazz.newIntArray (257, 0); +var huffcode = Clazz.newIntArray (257, 0); +p = 0; +for (l = 1; l <= 16; l++) { +for (i = javajs.img.Huffman.bitsDCchrominance[l]; --i >= 0; ) { +huffsize[p++] = l; +} +} +huffsize[p] = 0; +lastp = p; +code = 0; +si = huffsize[0]; +p = 0; +while (huffsize[p] != 0) { +while (huffsize[p] == si) { +huffcode[p++] = code; +code++; +} +code <<= 1; +si++; +} +for (p = 0; p < lastp; p++) { +this.dc_matrix1[javajs.img.Huffman.valDCchrominance[p]][0] = huffcode[p]; +this.dc_matrix1[javajs.img.Huffman.valDCchrominance[p]][1] = huffsize[p]; +} +p = 0; +for (l = 1; l <= 16; l++) { +for (i = javajs.img.Huffman.bitsACchrominance[l]; --i >= 0; ) { +huffsize[p++] = l; +} +} +huffsize[p] = 0; +lastp = p; +code = 0; +si = huffsize[0]; +p = 0; +while (huffsize[p] != 0) { +while (huffsize[p] == si) { +huffcode[p++] = code; +code++; +} +code <<= 1; +si++; +} +for (p = 0; p < lastp; p++) { +this.ac_matrix1[javajs.img.Huffman.valACchrominance[p]][0] = huffcode[p]; +this.ac_matrix1[javajs.img.Huffman.valACchrominance[p]][1] = huffsize[p]; +} +p = 0; +for (l = 1; l <= 16; l++) { +for (i = javajs.img.Huffman.bitsDCluminance[l]; --i >= 0; ) { +huffsize[p++] = l; +} +} +huffsize[p] = 0; +lastp = p; +code = 0; +si = huffsize[0]; +p = 0; +while (huffsize[p] != 0) { +while (huffsize[p] == si) { +huffcode[p++] = code; +code++; +} +code <<= 1; +si++; +} +for (p = 0; p < lastp; p++) { +this.dc_matrix0[javajs.img.Huffman.valDCluminance[p]][0] = huffcode[p]; +this.dc_matrix0[javajs.img.Huffman.valDCluminance[p]][1] = huffsize[p]; +} +p = 0; +for (l = 1; l <= 16; l++) { +for (i = javajs.img.Huffman.bitsACluminance[l]; --i >= 0; ) { +huffsize[p++] = l; +} +} +huffsize[p] = 0; +lastp = p; +code = 0; +si = huffsize[0]; +p = 0; +while (huffsize[p] != 0) { +while (huffsize[p] == si) { +huffcode[p++] = code; +code++; +} +code <<= 1; +si++; +} +for (var q = 0; q < lastp; q++) { +this.ac_matrix0[javajs.img.Huffman.valACluminance[q]][0] = huffcode[q]; +this.ac_matrix0[javajs.img.Huffman.valACluminance[q]][1] = huffsize[q]; +} +this.dc_matrix[0] = this.dc_matrix0; +this.dc_matrix[1] = this.dc_matrix1; +this.ac_matrix[0] = this.ac_matrix0; +this.ac_matrix[1] = this.ac_matrix1; +}, $fz.isPrivate = true, $fz)); +Clazz.defineStatics (c$, +"bitsDCluminance", Clazz.newIntArray (-1, [0x00, 0, 1, 5, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0]), +"valDCluminance", Clazz.newIntArray (-1, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]), +"bitsDCchrominance", Clazz.newIntArray (-1, [0x01, 0, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0]), +"valDCchrominance", Clazz.newIntArray (-1, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]), +"bitsACluminance", Clazz.newIntArray (-1, [0x10, 0, 2, 1, 3, 3, 2, 4, 3, 5, 5, 4, 4, 0, 0, 1, 0x7d]), +"valACluminance", Clazz.newIntArray (-1, [0x01, 0x02, 0x03, 0x00, 0x04, 0x11, 0x05, 0x12, 0x21, 0x31, 0x41, 0x06, 0x13, 0x51, 0x61, 0x07, 0x22, 0x71, 0x14, 0x32, 0x81, 0x91, 0xa1, 0x08, 0x23, 0x42, 0xb1, 0xc1, 0x15, 0x52, 0xd1, 0xf0, 0x24, 0x33, 0x62, 0x72, 0x82, 0x09, 0x0a, 0x16, 0x17, 0x18, 0x19, 0x1a, 0x25, 0x26, 0x27, 0x28, 0x29, 0x2a, 0x34, 0x35, 0x36, 0x37, 0x38, 0x39, 0x3a, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4a, 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5a, 0x63, 0x64, 0x65, 0x66, 0x67, 0x68, 0x69, 0x6a, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7a, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8a, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98, 0x99, 0x9a, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7, 0xa8, 0xa9, 0xaa, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 0xb8, 0xb9, 0xba, 0xc2, 0xc3, 0xc4, 0xc5, 0xc6, 0xc7, 0xc8, 0xc9, 0xca, 0xd2, 0xd3, 0xd4, 0xd5, 0xd6, 0xd7, 0xd8, 0xd9, 0xda, 0xe1, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7, 0xe8, 0xe9, 0xea, 0xf1, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 0xf8, 0xf9, 0xfa]), +"bitsACchrominance", Clazz.newIntArray (-1, [0x11, 0, 2, 1, 2, 4, 4, 3, 4, 7, 5, 4, 4, 0, 1, 2, 0x77]), +"valACchrominance", Clazz.newIntArray (-1, [0x00, 0x01, 0x02, 0x03, 0x11, 0x04, 0x05, 0x21, 0x31, 0x06, 0x12, 0x41, 0x51, 0x07, 0x61, 0x71, 0x13, 0x22, 0x32, 0x81, 0x08, 0x14, 0x42, 0x91, 0xa1, 0xb1, 0xc1, 0x09, 0x23, 0x33, 0x52, 0xf0, 0x15, 0x62, 0x72, 0xd1, 0x0a, 0x16, 0x24, 0x34, 0xe1, 0x25, 0xf1, 0x17, 0x18, 0x19, 0x1a, 0x26, 0x27, 0x28, 0x29, 0x2a, 0x35, 0x36, 0x37, 0x38, 0x39, 0x3a, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4a, 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5a, 0x63, 0x64, 0x65, 0x66, 0x67, 0x68, 0x69, 0x6a, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7a, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8a, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98, 0x99, 0x9a, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7, 0xa8, 0xa9, 0xaa, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 0xb8, 0xb9, 0xba, 0xc2, 0xc3, 0xc4, 0xc5, 0xc6, 0xc7, 0xc8, 0xc9, 0xca, 0xd2, 0xd3, 0xd4, 0xd5, 0xd6, 0xd7, 0xd8, 0xd9, 0xda, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7, 0xe8, 0xe9, 0xea, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 0xf8, 0xf9, 0xfa]), +"jpegNaturalOrder", Clazz.newIntArray (-1, [0, 1, 8, 16, 9, 2, 3, 10, 17, 24, 32, 25, 18, 11, 4, 5, 12, 19, 26, 33, 40, 48, 41, 34, 27, 20, 13, 6, 7, 14, 21, 28, 35, 42, 49, 56, 57, 50, 43, 36, 29, 22, 15, 23, 30, 37, 44, 51, 58, 59, 52, 45, 38, 31, 39, 46, 53, 60, 61, 54, 47, 55, 62, 63])); +c$ = Clazz.decorateAsClass (function () { +this.comment = null; +this.imageHeight = 0; +this.imageWidth = 0; +this.blockWidth = null; +this.blockHeight = null; +this.precision = 8; +this.numberOfComponents = 3; +this.components = null; +this.compID = null; +this.hsampFactor = null; +this.vsampFactor = null; +this.qtableNumber = null; +this.dctableNumber = null; +this.actableNumber = null; +this.lastColumnIsDummy = null; +this.lastRowIsDummy = null; +this.ss = 0; +this.se = 63; +this.ah = 0; +this.al = 0; +this.compWidth = null; +this.compHeight = null; +this.maxHsampFactor = 0; +this.maxVsampFactor = 0; +Clazz.instantialize (this, arguments); +}, javajs.img, "JpegObj"); +Clazz.prepareFields (c$, function () { +this.compID = Clazz.newIntArray (-1, [1, 2, 3]); +this.hsampFactor = Clazz.newIntArray (-1, [1, 1, 1]); +this.vsampFactor = Clazz.newIntArray (-1, [1, 1, 1]); +this.qtableNumber = Clazz.newIntArray (-1, [0, 1, 1]); +this.dctableNumber = Clazz.newIntArray (-1, [0, 1, 1]); +this.actableNumber = Clazz.newIntArray (-1, [0, 1, 1]); +this.lastColumnIsDummy = Clazz.newBooleanArray (-1, [false, false, false]); +this.lastRowIsDummy = Clazz.newBooleanArray (-1, [false, false, false]); +}); +Clazz.makeConstructor (c$, +function () { +this.components = javajs.util.AU.newFloat3 (this.numberOfComponents, -1); +this.compWidth = Clazz.newIntArray (this.numberOfComponents, 0); +this.compHeight = Clazz.newIntArray (this.numberOfComponents, 0); +this.blockWidth = Clazz.newIntArray (this.numberOfComponents, 0); +this.blockHeight = Clazz.newIntArray (this.numberOfComponents, 0); +}); +Clazz.defineMethod (c$, "getYCCArray", +function (pixels) { +this.maxHsampFactor = 1; +this.maxVsampFactor = 1; +for (var y = 0; y < this.numberOfComponents; y++) { +this.maxHsampFactor = Math.max (this.maxHsampFactor, this.hsampFactor[y]); +this.maxVsampFactor = Math.max (this.maxVsampFactor, this.vsampFactor[y]); +} +for (var y = 0; y < this.numberOfComponents; y++) { +this.compWidth[y] = (Clazz.doubleToInt (((this.imageWidth % 8 != 0) ? (Clazz.doubleToInt (Math.ceil (this.imageWidth / 8.0))) * 8 : this.imageWidth) / this.maxHsampFactor)) * this.hsampFactor[y]; +if (this.compWidth[y] != ((Clazz.doubleToInt (this.imageWidth / this.maxHsampFactor)) * this.hsampFactor[y])) { +this.lastColumnIsDummy[y] = true; +}this.blockWidth[y] = Clazz.doubleToInt (Math.ceil (this.compWidth[y] / 8.0)); +this.compHeight[y] = (Clazz.doubleToInt (((this.imageHeight % 8 != 0) ? (Clazz.doubleToInt (Math.ceil (this.imageHeight / 8.0))) * 8 : this.imageHeight) / this.maxVsampFactor)) * this.vsampFactor[y]; +if (this.compHeight[y] != ((Clazz.doubleToInt (this.imageHeight / this.maxVsampFactor)) * this.vsampFactor[y])) { +this.lastRowIsDummy[y] = true; +}this.blockHeight[y] = Clazz.doubleToInt (Math.ceil (this.compHeight[y] / 8.0)); +} +var Y = Clazz.newFloatArray (this.compHeight[0], this.compWidth[0], 0); +var Cr1 = Clazz.newFloatArray (this.compHeight[0], this.compWidth[0], 0); +var Cb1 = Clazz.newFloatArray (this.compHeight[0], this.compWidth[0], 0); +for (var pt = 0, y = 0; y < this.imageHeight; ++y) { +for (var x = 0; x < this.imageWidth; ++x, pt++) { +var p = pixels[pt]; +var r = ((p >> 16) & 0xff); +var g = ((p >> 8) & 0xff); +var b = (p & 0xff); +Y[y][x] = ((0.299 * r + 0.587 * g + 0.114 * b)); +Cb1[y][x] = 128 + ((-0.16874 * r - 0.33126 * g + 0.5 * b)); +Cr1[y][x] = 128 + ((0.5 * r - 0.41869 * g - 0.08131 * b)); +} +} +this.components[0] = Y; +this.components[1] = Cb1; +this.components[2] = Cr1; +}, "~A"); +}); diff --git a/bin/javajs/img/PdfEncoder.js b/bin/javajs/img/PdfEncoder.js index 0a468dc..664879f 100644 --- a/bin/javajs/img/PdfEncoder.js +++ b/bin/javajs/img/PdfEncoder.js @@ -1,58 +1,58 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.ImageEncoder"], "javajs.img.PdfEncoder", ["java.util.Hashtable", "javajs.export.PDFCreator"], function () { -c$ = Clazz.decorateAsClass (function () { -this.isLandscape = false; -this.pdf = null; -this.comment = null; -Clazz.instantialize (this, arguments); -}, javajs.img, "PdfEncoder", javajs.img.ImageEncoder); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.img.PdfEncoder, []); -}); -Clazz.overrideMethod (c$, "setParams", -function (params) { -this.isLandscape = (this.quality > 1); -this.comment = "Jmol " + params.get ("comment"); -}, "java.util.Map"); -Clazz.overrideMethod (c$, "generate", -function () { -this.pdf = new javajs["export"].PDFCreator (); -var pageWidth = 576; -var pageHeight = 792; -this.pdf.setOutputStream (this.out); -this.pdf.newDocument (pageWidth, pageHeight, this.isLandscape); -this.addMyImage (pageWidth, pageHeight); -var ht = new java.util.Hashtable (); -if (this.comment != null) ht.put ("Producer", this.comment); -ht.put ("Author", "JMol"); -ht.put ("CreationDate", this.date); -this.pdf.addInfo (ht); -this.pdf.closeDocument (); -}); -Clazz.defineMethod (c$, "addMyImage", -($fz = function (pageWidth, pageHeight) { -this.pdf.addImageResource ("img1", this.width, this.height, this.pixels, true); -var w = (this.isLandscape ? pageHeight : pageWidth); -var h = (this.isLandscape ? pageWidth : pageHeight); -var iw = this.width; -var ih = this.height; -if (iw > 0.9 * w) { -ih = Clazz.doubleToInt (ih * 0.9 * w / iw); -iw = Clazz.doubleToInt (w * 0.9); -}if (ih > 0.9 * h) { -iw = Clazz.doubleToInt (iw * 0.9 * h / ih); -ih = Clazz.doubleToInt (h * 0.9); -}var x = 0; -var y = 0; -var x1 = iw; -var y1 = ih; -if (w > iw) { -x = Clazz.doubleToInt ((w - iw) / 2); -x1 = iw + x; -}if (h > ih) { -y = Clazz.doubleToInt ((h - ih) / 2); -y1 = ih + y; -}this.pdf.drawImage ("img1", x, y, x1, y1, 0, 0, this.width, this.height); -}, $fz.isPrivate = true, $fz), "~N,~N"); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.ImageEncoder"], "javajs.img.PdfEncoder", ["java.util.Hashtable", "javajs.export.PDFCreator"], function () { +c$ = Clazz.decorateAsClass (function () { +this.isLandscape = false; +this.pdf = null; +this.comment = null; +Clazz.instantialize (this, arguments); +}, javajs.img, "PdfEncoder", javajs.img.ImageEncoder); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.img.PdfEncoder, []); +}); +Clazz.overrideMethod (c$, "setParams", +function (params) { +this.isLandscape = (this.quality > 1); +this.comment = "Jmol " + params.get ("comment"); +}, "java.util.Map"); +Clazz.overrideMethod (c$, "generate", +function () { +this.pdf = new javajs["export"].PDFCreator (); +var pageWidth = 576; +var pageHeight = 792; +this.pdf.setOutputStream (this.out); +this.pdf.newDocument (pageWidth, pageHeight, this.isLandscape); +this.addMyImage (pageWidth, pageHeight); +var ht = new java.util.Hashtable (); +if (this.comment != null) ht.put ("Producer", this.comment); +ht.put ("Author", "JMol"); +ht.put ("CreationDate", this.date); +this.pdf.addInfo (ht); +this.pdf.closeDocument (); +}); +Clazz.defineMethod (c$, "addMyImage", +($fz = function (pageWidth, pageHeight) { +this.pdf.addImageResource ("img1", this.width, this.height, this.pixels, true); +var w = (this.isLandscape ? pageHeight : pageWidth); +var h = (this.isLandscape ? pageWidth : pageHeight); +var iw = this.width; +var ih = this.height; +if (iw > 0.9 * w) { +ih = Clazz.doubleToInt (ih * 0.9 * w / iw); +iw = Clazz.doubleToInt (w * 0.9); +}if (ih > 0.9 * h) { +iw = Clazz.doubleToInt (iw * 0.9 * h / ih); +ih = Clazz.doubleToInt (h * 0.9); +}var x = 0; +var y = 0; +var x1 = iw; +var y1 = ih; +if (w > iw) { +x = Clazz.doubleToInt ((w - iw) / 2); +x1 = iw + x; +}if (h > ih) { +y = Clazz.doubleToInt ((h - ih) / 2); +y1 = ih + y; +}this.pdf.drawImage ("img1", x, y, x1, y1, 0, 0, this.width, this.height); +}, $fz.isPrivate = true, $fz), "~N,~N"); +}); diff --git a/bin/javajs/img/PngEncoder.js b/bin/javajs/img/PngEncoder.js index 8c07dbd..0accd9e 100644 --- a/bin/javajs/img/PngEncoder.js +++ b/bin/javajs/img/PngEncoder.js @@ -1,173 +1,173 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.CRCEncoder"], "javajs.img.PngEncoder", ["java.io.ByteArrayOutputStream", "java.util.zip.Deflater", "$.DeflaterOutputStream"], function () { -c$ = Clazz.decorateAsClass (function () { -this.encodeAlpha = false; -this.filter = 0; -this.bytesPerPixel = 0; -this.compressionLevel = 0; -this.type = null; -this.transparentColor = null; -this.appData = null; -this.appPrefix = null; -this.comment = null; -this.bytes = null; -this.scanLines = null; -this.byteWidth = 0; -Clazz.instantialize (this, arguments); -}, javajs.img, "PngEncoder", javajs.img.CRCEncoder); -Clazz.overrideMethod (c$, "setParams", -function (params) { -if (this.quality < 0) this.quality = (params.containsKey ("qualityPNG") ? (params.get ("qualityPNG")).intValue () : 2); -if (this.quality > 9) this.quality = 9; -this.encodeAlpha = false; -this.filter = 0; -this.compressionLevel = this.quality; -this.transparentColor = params.get ("transparentColor"); -this.comment = params.get ("comment"); -this.type = (params.get ("type") + "0000").substring (0, 4); -this.bytes = params.get ("pngImgData"); -this.appData = params.get ("pngAppData"); -this.appPrefix = params.get ("pngAppPrefix"); -}, "java.util.Map"); -Clazz.overrideMethod (c$, "generate", -function () { -if (this.bytes == null) { -if (!this.pngEncode ()) { -this.out.cancel (); -return; -}this.bytes = this.getBytes (); -} else { -this.dataLen = this.bytes.length; -}var len = this.dataLen; -if (this.appData != null) { -javajs.img.PngEncoder.setJmolTypeText (this.appPrefix, this.bytes, len, this.appData.length, this.type); -this.out.write (this.bytes, 0, len); -len = (this.bytes = this.appData).length; -}this.out.write (this.bytes, 0, len); -}); -Clazz.defineMethod (c$, "pngEncode", -($fz = function () { -var pngIdBytes = Clazz.newByteArray (-1, [-119, 80, 78, 71, 13, 10, 26, 10]); -this.writeBytes (pngIdBytes); -this.writeHeader (); -this.writeText (javajs.img.PngEncoder.getApplicationText (this.appPrefix, this.type, 0, 0)); -this.writeText ("Software\0Jmol " + this.comment); -this.writeText ("Creation Time\0" + this.date); -if (!this.encodeAlpha && this.transparentColor != null) this.writeTransparentColor (this.transparentColor.intValue ()); -return this.writeImageData (); -}, $fz.isPrivate = true, $fz)); -c$.setJmolTypeText = Clazz.defineMethod (c$, "setJmolTypeText", -($fz = function (prefix, b, nPNG, nState, type) { -var s = "tEXt" + javajs.img.PngEncoder.getApplicationText (prefix, type, nPNG, nState); -var encoder = new javajs.img.PngEncoder (); -var test = s.substring (0, 4 + prefix.length).getBytes (); -for (var i = test.length; --i >= 0; ) if (b[i + 37] != test[i]) { -System.out.println ("image is not of the right form; appending data, but not adding tEXt tag."); -return; -} -encoder.setData (b, 37); -encoder.writeString (s); -encoder.writeCRC (); -}, $fz.isPrivate = true, $fz), "~S,~A,~N,~N,~S"); -c$.getApplicationText = Clazz.defineMethod (c$, "getApplicationText", -($fz = function (prefix, type, nPNG, nState) { -var sPNG = "000000000" + nPNG; -sPNG = sPNG.substring (sPNG.length - 9); -var sState = "000000000" + nState; -sState = sState.substring (sState.length - 9); -return prefix + "\0" + type + (type.equals ("PNG") ? "0" : "") + sPNG + "+" + sState; -}, $fz.isPrivate = true, $fz), "~S,~S,~N,~N"); -Clazz.defineMethod (c$, "writeHeader", -($fz = function () { -this.writeInt4 (13); -this.startPos = this.bytePos; -this.writeString ("IHDR"); -this.writeInt4 (this.width); -this.writeInt4 (this.height); -this.writeByte (8); -this.writeByte (this.encodeAlpha ? 6 : 2); -this.writeByte (0); -this.writeByte (0); -this.writeByte (0); -this.writeCRC (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeText", -($fz = function (msg) { -this.writeInt4 (msg.length); -this.startPos = this.bytePos; -this.writeString ("tEXt" + msg); -this.writeCRC (); -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "writeTransparentColor", -($fz = function (icolor) { -this.writeInt4 (6); -this.startPos = this.bytePos; -this.writeString ("tRNS"); -this.writeInt2 ((icolor >> 16) & 0xFF); -this.writeInt2 ((icolor >> 8) & 0xFF); -this.writeInt2 (icolor & 0xFF); -this.writeCRC (); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "writeImageData", -($fz = function () { -this.bytesPerPixel = (this.encodeAlpha ? 4 : 3); -this.byteWidth = this.width * this.bytesPerPixel; -var scanWidth = this.byteWidth + 1; -var rowsLeft = this.height; -var nRows; -var scanPos; -var deflater = new java.util.zip.Deflater (this.compressionLevel); -var outBytes = new java.io.ByteArrayOutputStream (1024); -var compBytes = new java.util.zip.DeflaterOutputStream (outBytes, deflater); -var pt = 0; -try { -while (rowsLeft > 0) { -nRows = Math.max (1, Math.min (Clazz.doubleToInt (32767 / scanWidth), rowsLeft)); -this.scanLines = Clazz.newByteArray (scanWidth * nRows, 0); -var nPixels = this.width * nRows; -scanPos = 0; -for (var i = 0; i < nPixels; i++, pt++) { -if (i % this.width == 0) { -this.scanLines[scanPos++] = this.filter; -}this.scanLines[scanPos++] = ((this.pixels[pt] >> 16) & 0xff); -this.scanLines[scanPos++] = ((this.pixels[pt] >> 8) & 0xff); -this.scanLines[scanPos++] = ((this.pixels[pt]) & 0xff); -if (this.encodeAlpha) { -this.scanLines[scanPos++] = ((this.pixels[pt] >> 24) & 0xff); -}} -compBytes.write (this.scanLines, 0, scanPos); -rowsLeft -= nRows; -} -compBytes.close (); -var compressedLines = outBytes.toByteArray (); -this.writeInt4 (compressedLines.length); -this.startPos = this.bytePos; -this.writeString ("IDAT"); -this.writeBytes (compressedLines); -this.writeCRC (); -this.writeEnd (); -deflater.finish (); -return true; -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -System.err.println (e.toString ()); -return false; -} else { -throw e; -} -} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeEnd", -($fz = function () { -this.writeInt4 (0); -this.startPos = this.bytePos; -this.writeString ("IEND"); -this.writeCRC (); -}, $fz.isPrivate = true, $fz)); -Clazz.defineStatics (c$, -"FILTER_NONE", 0, -"FILTER_SUB", 1, -"FILTER_UP", 2, -"FILTER_LAST", 2, -"PT_FIRST_TAG", 37); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.CRCEncoder"], "javajs.img.PngEncoder", ["java.io.ByteArrayOutputStream", "java.util.zip.Deflater", "$.DeflaterOutputStream"], function () { +c$ = Clazz.decorateAsClass (function () { +this.encodeAlpha = false; +this.filter = 0; +this.bytesPerPixel = 0; +this.compressionLevel = 0; +this.type = null; +this.transparentColor = null; +this.appData = null; +this.appPrefix = null; +this.comment = null; +this.bytes = null; +this.scanLines = null; +this.byteWidth = 0; +Clazz.instantialize (this, arguments); +}, javajs.img, "PngEncoder", javajs.img.CRCEncoder); +Clazz.overrideMethod (c$, "setParams", +function (params) { +if (this.quality < 0) this.quality = (params.containsKey ("qualityPNG") ? (params.get ("qualityPNG")).intValue () : 2); +if (this.quality > 9) this.quality = 9; +this.encodeAlpha = false; +this.filter = 0; +this.compressionLevel = this.quality; +this.transparentColor = params.get ("transparentColor"); +this.comment = params.get ("comment"); +this.type = (params.get ("type") + "0000").substring (0, 4); +this.bytes = params.get ("pngImgData"); +this.appData = params.get ("pngAppData"); +this.appPrefix = params.get ("pngAppPrefix"); +}, "java.util.Map"); +Clazz.overrideMethod (c$, "generate", +function () { +if (this.bytes == null) { +if (!this.pngEncode ()) { +this.out.cancel (); +return; +}this.bytes = this.getBytes (); +} else { +this.dataLen = this.bytes.length; +}var len = this.dataLen; +if (this.appData != null) { +javajs.img.PngEncoder.setJmolTypeText (this.appPrefix, this.bytes, len, this.appData.length, this.type); +this.out.write (this.bytes, 0, len); +len = (this.bytes = this.appData).length; +}this.out.write (this.bytes, 0, len); +}); +Clazz.defineMethod (c$, "pngEncode", +($fz = function () { +var pngIdBytes = Clazz.newByteArray (-1, [-119, 80, 78, 71, 13, 10, 26, 10]); +this.writeBytes (pngIdBytes); +this.writeHeader (); +this.writeText (javajs.img.PngEncoder.getApplicationText (this.appPrefix, this.type, 0, 0)); +this.writeText ("Software\0Jmol " + this.comment); +this.writeText ("Creation Time\0" + this.date); +if (!this.encodeAlpha && this.transparentColor != null) this.writeTransparentColor (this.transparentColor.intValue ()); +return this.writeImageData (); +}, $fz.isPrivate = true, $fz)); +c$.setJmolTypeText = Clazz.defineMethod (c$, "setJmolTypeText", +($fz = function (prefix, b, nPNG, nState, type) { +var s = "tEXt" + javajs.img.PngEncoder.getApplicationText (prefix, type, nPNG, nState); +var encoder = new javajs.img.PngEncoder (); +var test = s.substring (0, 4 + prefix.length).getBytes (); +for (var i = test.length; --i >= 0; ) if (b[i + 37] != test[i]) { +System.out.println ("image is not of the right form; appending data, but not adding tEXt tag."); +return; +} +encoder.setData (b, 37); +encoder.writeString (s); +encoder.writeCRC (); +}, $fz.isPrivate = true, $fz), "~S,~A,~N,~N,~S"); +c$.getApplicationText = Clazz.defineMethod (c$, "getApplicationText", +($fz = function (prefix, type, nPNG, nState) { +var sPNG = "000000000" + nPNG; +sPNG = sPNG.substring (sPNG.length - 9); +var sState = "000000000" + nState; +sState = sState.substring (sState.length - 9); +return prefix + "\0" + type + (type.equals ("PNG") ? "0" : "") + sPNG + "+" + sState; +}, $fz.isPrivate = true, $fz), "~S,~S,~N,~N"); +Clazz.defineMethod (c$, "writeHeader", +($fz = function () { +this.writeInt4 (13); +this.startPos = this.bytePos; +this.writeString ("IHDR"); +this.writeInt4 (this.width); +this.writeInt4 (this.height); +this.writeByte (8); +this.writeByte (this.encodeAlpha ? 6 : 2); +this.writeByte (0); +this.writeByte (0); +this.writeByte (0); +this.writeCRC (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeText", +($fz = function (msg) { +this.writeInt4 (msg.length); +this.startPos = this.bytePos; +this.writeString ("tEXt" + msg); +this.writeCRC (); +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "writeTransparentColor", +($fz = function (icolor) { +this.writeInt4 (6); +this.startPos = this.bytePos; +this.writeString ("tRNS"); +this.writeInt2 ((icolor >> 16) & 0xFF); +this.writeInt2 ((icolor >> 8) & 0xFF); +this.writeInt2 (icolor & 0xFF); +this.writeCRC (); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "writeImageData", +($fz = function () { +this.bytesPerPixel = (this.encodeAlpha ? 4 : 3); +this.byteWidth = this.width * this.bytesPerPixel; +var scanWidth = this.byteWidth + 1; +var rowsLeft = this.height; +var nRows; +var scanPos; +var deflater = new java.util.zip.Deflater (this.compressionLevel); +var outBytes = new java.io.ByteArrayOutputStream (1024); +var compBytes = new java.util.zip.DeflaterOutputStream (outBytes, deflater); +var pt = 0; +try { +while (rowsLeft > 0) { +nRows = Math.max (1, Math.min (Clazz.doubleToInt (32767 / scanWidth), rowsLeft)); +this.scanLines = Clazz.newByteArray (scanWidth * nRows, 0); +var nPixels = this.width * nRows; +scanPos = 0; +for (var i = 0; i < nPixels; i++, pt++) { +if (i % this.width == 0) { +this.scanLines[scanPos++] = this.filter; +}this.scanLines[scanPos++] = ((this.pixels[pt] >> 16) & 0xff); +this.scanLines[scanPos++] = ((this.pixels[pt] >> 8) & 0xff); +this.scanLines[scanPos++] = ((this.pixels[pt]) & 0xff); +if (this.encodeAlpha) { +this.scanLines[scanPos++] = ((this.pixels[pt] >> 24) & 0xff); +}} +compBytes.write (this.scanLines, 0, scanPos); +rowsLeft -= nRows; +} +compBytes.close (); +var compressedLines = outBytes.toByteArray (); +this.writeInt4 (compressedLines.length); +this.startPos = this.bytePos; +this.writeString ("IDAT"); +this.writeBytes (compressedLines); +this.writeCRC (); +this.writeEnd (); +deflater.finish (); +return true; +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +System.err.println (e.toString ()); +return false; +} else { +throw e; +} +} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeEnd", +($fz = function () { +this.writeInt4 (0); +this.startPos = this.bytePos; +this.writeString ("IEND"); +this.writeCRC (); +}, $fz.isPrivate = true, $fz)); +Clazz.defineStatics (c$, +"FILTER_NONE", 0, +"FILTER_SUB", 1, +"FILTER_UP", 2, +"FILTER_LAST", 2, +"PT_FIRST_TAG", 37); +}); diff --git a/bin/javajs/img/PpmEncoder.js b/bin/javajs/img/PpmEncoder.js index 7cb6943..1769c71 100644 --- a/bin/javajs/img/PpmEncoder.js +++ b/bin/javajs/img/PpmEncoder.js @@ -1,23 +1,23 @@ -Clazz.declarePackage ("javajs.img"); -Clazz.load (["javajs.img.ImageEncoder"], "javajs.img.PpmEncoder", null, function () { -c$ = Clazz.declareType (javajs.img, "PpmEncoder", javajs.img.ImageEncoder); -Clazz.overrideMethod (c$, "setParams", -function (params) { -}, "java.util.Map"); -Clazz.overrideMethod (c$, "generate", -function () { -this.putString ("P6\n"); -this.putString (this.width + " " + this.height + "\n"); -this.putString ("255\n"); -var ppmPixels = Clazz.newByteArray (this.width * 3, 0); -for (var pt = 0, row = 0; row < this.height; ++row) { -for (var col = 0, j = 0; col < this.width; ++col, pt++) { -var p = this.pixels[pt]; -ppmPixels[j++] = ((p >> 16) & 0xff); -ppmPixels[j++] = ((p >> 8) & 0xff); -ppmPixels[j++] = (p & 0xff); -} -this.out.write (ppmPixels, 0, ppmPixels.length); -} -}); -}); +Clazz.declarePackage ("javajs.img"); +Clazz.load (["javajs.img.ImageEncoder"], "javajs.img.PpmEncoder", null, function () { +c$ = Clazz.declareType (javajs.img, "PpmEncoder", javajs.img.ImageEncoder); +Clazz.overrideMethod (c$, "setParams", +function (params) { +}, "java.util.Map"); +Clazz.overrideMethod (c$, "generate", +function () { +this.putString ("P6\n"); +this.putString (this.width + " " + this.height + "\n"); +this.putString ("255\n"); +var ppmPixels = Clazz.newByteArray (this.width * 3, 0); +for (var pt = 0, row = 0; row < this.height; ++row) { +for (var col = 0, j = 0; col < this.width; ++col, pt++) { +var p = this.pixels[pt]; +ppmPixels[j++] = ((p >> 16) & 0xff); +ppmPixels[j++] = ((p >> 8) & 0xff); +ppmPixels[j++] = (p & 0xff); +} +this.out.write (ppmPixels, 0, ppmPixels.length); +} +}); +}); diff --git a/bin/javajs/img/package.js b/bin/javajs/img/package.js index 0982066..4086dd3 100644 --- a/bin/javajs/img/package.js +++ b/bin/javajs/img/package.js @@ -1,7 +1,7 @@ -var path = ClazzLoader.getClasspathFor ("javajs.img.package"); -path = path.substring (0, path.lastIndexOf ("package.js")); -ClazzLoader.jarClasspath (path + "JpgEncoder.js", [ -"javajs.img.DCT", -"$.JpgEncoder", -"$.JpegObj", -"$.Huffman"]); +var path = ClazzLoader.getClasspathFor ("javajs.img.package"); +path = path.substring (0, path.lastIndexOf ("package.js")); +ClazzLoader.jarClasspath (path + "JpgEncoder.js", [ +"javajs.img.DCT", +"$.JpgEncoder", +"$.JpegObj", +"$.Huffman"]); diff --git a/bin/javajs/swing/AbstractButton.js b/bin/javajs/swing/AbstractButton.js index 7a53af7..f97cb2f 100644 --- a/bin/javajs/swing/AbstractButton.js +++ b/bin/javajs/swing/AbstractButton.js @@ -1,82 +1,82 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.api.SC", "javajs.swing.JComponent"], "javajs.swing.AbstractButton", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.itemListener = null; -this.applet = null; -this.htmlName = null; -this.selected = false; -this.popupMenu = null; -this.icon = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "AbstractButton", javajs.swing.JComponent, javajs.api.SC); -Clazz.makeConstructor (c$, -function (type) { -Clazz.superConstructor (this, javajs.swing.AbstractButton, [type]); -this.enabled = true; -}, "~S"); -Clazz.overrideMethod (c$, "setSelected", -function (selected) { -this.selected = selected; -{ -SwingController.setSelected(this); -}}, "~B"); -Clazz.overrideMethod (c$, "isSelected", -function () { -return this.selected; -}); -Clazz.overrideMethod (c$, "addItemListener", -function (listener) { -this.itemListener = listener; -}, "~O"); -Clazz.overrideMethod (c$, "getIcon", -function () { -return this.icon; -}); -Clazz.overrideMethod (c$, "setIcon", -function (icon) { -this.icon = icon; -}, "~O"); -Clazz.overrideMethod (c$, "init", -function (text, icon, actionCommand, popupMenu) { -this.text = text; -this.icon = icon; -this.actionCommand = actionCommand; -this.popupMenu = popupMenu; -{ -SwingController.initMenuItem(this); -}}, "~S,~O,~S,javajs.api.SC"); -Clazz.defineMethod (c$, "getTopPopupMenu", -function () { -return this.popupMenu; -}); -Clazz.defineMethod (c$, "add", -function (item) { -this.addComponent (item); -}, "javajs.api.SC"); -Clazz.overrideMethod (c$, "insert", -function (subMenu, index) { -this.insertComponent (subMenu, index); -}, "javajs.api.SC,~N"); -Clazz.overrideMethod (c$, "getPopupMenu", -function () { -return null; -}); -Clazz.defineMethod (c$, "getMenuHTML", -function () { -var label = (this.icon != null ? this.icon : this.text != null ? this.text : null); -var s = (label == null ? "" : "
  • " + label + "" + this.htmlMenuOpener ("ul")); -var n = this.getComponentCount (); -if (n > 0) for (var i = 0; i < n; i++) s += this.getComponent (i).toHTML (); - -if (label != null) s += "
    • "; -return s; -}); -Clazz.defineMethod (c$, "htmlMenuOpener", -function (type) { -return "<" + type + " id=\"" + this.id + "\"" + (this.enabled ? "" : this.getHtmlDisabled ()) + ">"; -}, "~S"); -Clazz.defineMethod (c$, "getHtmlDisabled", -function () { -return " disabled=\"disabled\""; -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.api.SC", "javajs.swing.JComponent"], "javajs.swing.AbstractButton", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.itemListener = null; +this.applet = null; +this.htmlName = null; +this.selected = false; +this.popupMenu = null; +this.icon = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "AbstractButton", javajs.swing.JComponent, javajs.api.SC); +Clazz.makeConstructor (c$, +function (type) { +Clazz.superConstructor (this, javajs.swing.AbstractButton, [type]); +this.enabled = true; +}, "~S"); +Clazz.overrideMethod (c$, "setSelected", +function (selected) { +this.selected = selected; +{ +SwingController.setSelected(this); +}}, "~B"); +Clazz.overrideMethod (c$, "isSelected", +function () { +return this.selected; +}); +Clazz.overrideMethod (c$, "addItemListener", +function (listener) { +this.itemListener = listener; +}, "~O"); +Clazz.overrideMethod (c$, "getIcon", +function () { +return this.icon; +}); +Clazz.overrideMethod (c$, "setIcon", +function (icon) { +this.icon = icon; +}, "~O"); +Clazz.overrideMethod (c$, "init", +function (text, icon, actionCommand, popupMenu) { +this.text = text; +this.icon = icon; +this.actionCommand = actionCommand; +this.popupMenu = popupMenu; +{ +SwingController.initMenuItem(this); +}}, "~S,~O,~S,javajs.api.SC"); +Clazz.defineMethod (c$, "getTopPopupMenu", +function () { +return this.popupMenu; +}); +Clazz.defineMethod (c$, "add", +function (item) { +this.addComponent (item); +}, "javajs.api.SC"); +Clazz.overrideMethod (c$, "insert", +function (subMenu, index) { +this.insertComponent (subMenu, index); +}, "javajs.api.SC,~N"); +Clazz.overrideMethod (c$, "getPopupMenu", +function () { +return null; +}); +Clazz.defineMethod (c$, "getMenuHTML", +function () { +var label = (this.icon != null ? this.icon : this.text != null ? this.text : null); +var s = (label == null ? "" : "
  • " + label + "" + this.htmlMenuOpener ("ul")); +var n = this.getComponentCount (); +if (n > 0) for (var i = 0; i < n; i++) s += this.getComponent (i).toHTML (); + +if (label != null) s += "
    • "; +return s; +}); +Clazz.defineMethod (c$, "htmlMenuOpener", +function (type) { +return "<" + type + " id=\"" + this.id + "\"" + (this.enabled ? "" : this.getHtmlDisabled ()) + ">"; +}, "~S"); +Clazz.defineMethod (c$, "getHtmlDisabled", +function () { +return " disabled=\"disabled\""; +}); +}); diff --git a/bin/javajs/swing/AbstractTableModel.js b/bin/javajs/swing/AbstractTableModel.js index 1f7382c..c17cd4a 100644 --- a/bin/javajs/swing/AbstractTableModel.js +++ b/bin/javajs/swing/AbstractTableModel.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.TableColumn"], "javajs.swing.AbstractTableModel", null, function () { -Clazz.declareInterface (javajs.swing, "AbstractTableModel", javajs.swing.TableColumn); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.TableColumn"], "javajs.swing.AbstractTableModel", null, function () { +Clazz.declareInterface (javajs.swing, "AbstractTableModel", javajs.swing.TableColumn); +}); diff --git a/bin/javajs/swing/ButtonGroup.js b/bin/javajs/swing/ButtonGroup.js index dbeaf88..ebd1ca6 100644 --- a/bin/javajs/swing/ButtonGroup.js +++ b/bin/javajs/swing/ButtonGroup.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (null, "javajs.swing.ButtonGroup", ["javajs.awt.Component"], function () { -c$ = Clazz.decorateAsClass (function () { -this.id = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "ButtonGroup"); -Clazz.makeConstructor (c$, -function () { -this.id = javajs.awt.Component.newID ("bg"); -}); -Clazz.defineMethod (c$, "add", -function (item) { -(item).htmlName = this.id; -}, "javajs.api.SC"); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (null, "javajs.swing.ButtonGroup", ["javajs.awt.Component"], function () { +c$ = Clazz.decorateAsClass (function () { +this.id = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "ButtonGroup"); +Clazz.makeConstructor (c$, +function () { +this.id = javajs.awt.Component.newID ("bg"); +}); +Clazz.defineMethod (c$, "add", +function (item) { +(item).htmlName = this.id; +}, "javajs.api.SC"); +}); diff --git a/bin/javajs/swing/Cell.js b/bin/javajs/swing/Cell.js index 2fc85c8..5ac8a90 100644 --- a/bin/javajs/swing/Cell.js +++ b/bin/javajs/swing/Cell.js @@ -1,21 +1,21 @@ -Clazz.declarePackage ("javajs.swing"); -c$ = Clazz.decorateAsClass (function () { -this.component = null; -this.colspan = 0; -this.rowspan = 0; -this.textAlign = 0; -this.c = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "Cell"); -Clazz.makeConstructor (c$, -function (btn, c) { -this.component = btn; -this.colspan = c.gridwidth; -this.rowspan = c.gridheight; -this.c = c; -}, "javajs.swing.JComponent,javajs.swing.GridBagConstraints"); -Clazz.defineMethod (c$, "toHTML", -function (id) { -var style = this.c.getStyle (false); -return "" + this.component.toHTML () + ""; -}, "~S"); +Clazz.declarePackage ("javajs.swing"); +c$ = Clazz.decorateAsClass (function () { +this.component = null; +this.colspan = 0; +this.rowspan = 0; +this.textAlign = 0; +this.c = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "Cell"); +Clazz.makeConstructor (c$, +function (btn, c) { +this.component = btn; +this.colspan = c.gridwidth; +this.rowspan = c.gridheight; +this.c = c; +}, "javajs.swing.JComponent,javajs.swing.GridBagConstraints"); +Clazz.defineMethod (c$, "toHTML", +function (id) { +var style = this.c.getStyle (false); +return "" + this.component.toHTML () + ""; +}, "~S"); diff --git a/bin/javajs/swing/ColumnSelectionModel.js b/bin/javajs/swing/ColumnSelectionModel.js index f9395b7..4ce0290 100644 --- a/bin/javajs/swing/ColumnSelectionModel.js +++ b/bin/javajs/swing/ColumnSelectionModel.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.declareInterface (javajs.swing, "ColumnSelectionModel"); +Clazz.declarePackage ("javajs.swing"); +Clazz.declareInterface (javajs.swing, "ColumnSelectionModel"); diff --git a/bin/javajs/swing/Document.js b/bin/javajs/swing/Document.js index 90cf95a..243ba05 100644 --- a/bin/javajs/swing/Document.js +++ b/bin/javajs/swing/Document.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.declareInterface (javajs.swing, "Document"); +Clazz.declarePackage ("javajs.swing"); +Clazz.declareInterface (javajs.swing, "Document"); diff --git a/bin/javajs/swing/FlowLayout.js b/bin/javajs/swing/FlowLayout.js index 8989304..6ed7d37 100644 --- a/bin/javajs/swing/FlowLayout.js +++ b/bin/javajs/swing/FlowLayout.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.awt.LayoutManager"], "javajs.swing.FlowLayout", null, function () { -c$ = Clazz.declareType (javajs.swing, "FlowLayout", javajs.awt.LayoutManager); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.awt.LayoutManager"], "javajs.swing.FlowLayout", null, function () { +c$ = Clazz.declareType (javajs.swing, "FlowLayout", javajs.awt.LayoutManager); +}); diff --git a/bin/javajs/swing/Grid.js b/bin/javajs/swing/Grid.js index 2551964..d0b179f 100644 --- a/bin/javajs/swing/Grid.js +++ b/bin/javajs/swing/Grid.js @@ -1,46 +1,46 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (null, "javajs.swing.Grid", ["javajs.swing.Cell", "javajs.util.AU", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.nrows = 0; -this.ncols = 0; -this.grid = null; -this.renderer = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "Grid"); -Clazz.makeConstructor (c$, -function (rows, cols) { -this.grid = Clazz.newArray (0, 0, null); -}, "~N,~N"); -Clazz.defineMethod (c$, "add", -function (btn, c) { -if (c.gridx >= this.ncols) { -this.ncols = c.gridx + 1; -for (var i = 0; i < this.nrows; i++) { -this.grid[i] = javajs.util.AU.ensureLength (this.grid[i], this.ncols * 2); -} -}if (c.gridy >= this.nrows) { -var g = new Array (c.gridy * 2 + 1); -for (var i = 0; i < this.nrows; i++) g[i] = this.grid[i]; - -for (var i = g.length; --i >= this.nrows; ) g[i] = new Array (this.ncols * 2 + 1); - -this.grid = g; -this.nrows = c.gridy + 1; -}this.grid[c.gridy][c.gridx] = new javajs.swing.Cell (btn, c); -}, "javajs.swing.JComponent,javajs.swing.GridBagConstraints"); -Clazz.defineMethod (c$, "toHTML", -function (id) { -var sb = new javajs.util.SB (); -id += "_grid"; -sb.append ("\n"); -for (var i = 0; i < this.nrows; i++) { -var rowid = id + "_" + i; -sb.append ("\n"); -for (var j = 0; j < this.ncols; j++) if (this.grid[i][j] != null) sb.append (this.grid[i][j].toHTML (rowid + "_" + j)); - -sb.append (""); -} -sb.append ("\n
    \n"); -return sb.toString (); -}, "~S"); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (null, "javajs.swing.Grid", ["javajs.swing.Cell", "javajs.util.AU", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.nrows = 0; +this.ncols = 0; +this.grid = null; +this.renderer = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "Grid"); +Clazz.makeConstructor (c$, +function (rows, cols) { +this.grid = Clazz.newArray (0, 0, null); +}, "~N,~N"); +Clazz.defineMethod (c$, "add", +function (btn, c) { +if (c.gridx >= this.ncols) { +this.ncols = c.gridx + 1; +for (var i = 0; i < this.nrows; i++) { +this.grid[i] = javajs.util.AU.ensureLength (this.grid[i], this.ncols * 2); +} +}if (c.gridy >= this.nrows) { +var g = new Array (c.gridy * 2 + 1); +for (var i = 0; i < this.nrows; i++) g[i] = this.grid[i]; + +for (var i = g.length; --i >= this.nrows; ) g[i] = new Array (this.ncols * 2 + 1); + +this.grid = g; +this.nrows = c.gridy + 1; +}this.grid[c.gridy][c.gridx] = new javajs.swing.Cell (btn, c); +}, "javajs.swing.JComponent,javajs.swing.GridBagConstraints"); +Clazz.defineMethod (c$, "toHTML", +function (id) { +var sb = new javajs.util.SB (); +id += "_grid"; +sb.append ("\n"); +for (var i = 0; i < this.nrows; i++) { +var rowid = id + "_" + i; +sb.append ("\n"); +for (var j = 0; j < this.ncols; j++) if (this.grid[i][j] != null) sb.append (this.grid[i][j].toHTML (rowid + "_" + j)); + +sb.append (""); +} +sb.append ("\n
    \n"); +return sb.toString (); +}, "~S"); +}); diff --git a/bin/javajs/swing/GridBagConstraints.js b/bin/javajs/swing/GridBagConstraints.js index 31cf45c..f631d92 100644 --- a/bin/javajs/swing/GridBagConstraints.js +++ b/bin/javajs/swing/GridBagConstraints.js @@ -1,41 +1,41 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (null, "javajs.swing.GridBagConstraints", ["javajs.swing.Insets"], function () { -c$ = Clazz.decorateAsClass (function () { -this.gridx = 0; -this.gridy = 0; -this.gridwidth = 0; -this.gridheight = 0; -this.weightx = 0; -this.weighty = 0; -this.anchor = 0; -this.fill = 0; -this.insets = null; -this.ipadx = 0; -this.ipady = 0; -Clazz.instantialize (this, arguments); -}, javajs.swing, "GridBagConstraints"); -Clazz.makeConstructor (c$, -function (gridx, gridy, gridwidth, gridheight, weightx, weighty, anchor, fill, insets, ipadx, ipady) { -this.gridx = gridx; -this.gridy = gridy; -this.gridwidth = gridwidth; -this.gridheight = gridheight; -this.weightx = weightx; -this.weighty = weighty; -this.anchor = anchor; -this.fill = fill; -if (insets == null) insets = new javajs.swing.Insets (0, 0, 0, 0); -this.insets = insets; -this.ipadx = ipadx; -this.ipady = ipady; -}, "~N,~N,~N,~N,~N,~N,~N,~N,javajs.swing.Insets,~N,~N"); -Clazz.defineMethod (c$, "getStyle", -function (margins) { -return "style='" + (margins ? "margin:" + this.insets.top + "px " + (this.ipady + this.insets.right) + "px " + this.insets.bottom + "px " + (this.ipadx + this.insets.left) + "px;" : "text-align:" + (this.anchor == 13 ? "right" : this.anchor == 17 ? "left" : "center")) + "'"; -}, "~B"); -Clazz.defineStatics (c$, -"NONE", 0, -"CENTER", 10, -"WEST", 17, -"EAST", 13); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (null, "javajs.swing.GridBagConstraints", ["javajs.swing.Insets"], function () { +c$ = Clazz.decorateAsClass (function () { +this.gridx = 0; +this.gridy = 0; +this.gridwidth = 0; +this.gridheight = 0; +this.weightx = 0; +this.weighty = 0; +this.anchor = 0; +this.fill = 0; +this.insets = null; +this.ipadx = 0; +this.ipady = 0; +Clazz.instantialize (this, arguments); +}, javajs.swing, "GridBagConstraints"); +Clazz.makeConstructor (c$, +function (gridx, gridy, gridwidth, gridheight, weightx, weighty, anchor, fill, insets, ipadx, ipady) { +this.gridx = gridx; +this.gridy = gridy; +this.gridwidth = gridwidth; +this.gridheight = gridheight; +this.weightx = weightx; +this.weighty = weighty; +this.anchor = anchor; +this.fill = fill; +if (insets == null) insets = new javajs.swing.Insets (0, 0, 0, 0); +this.insets = insets; +this.ipadx = ipadx; +this.ipady = ipady; +}, "~N,~N,~N,~N,~N,~N,~N,~N,javajs.swing.Insets,~N,~N"); +Clazz.defineMethod (c$, "getStyle", +function (margins) { +return "style='" + (margins ? "margin:" + this.insets.top + "px " + (this.ipady + this.insets.right) + "px " + this.insets.bottom + "px " + (this.ipadx + this.insets.left) + "px;" : "text-align:" + (this.anchor == 13 ? "right" : this.anchor == 17 ? "left" : "center")) + "'"; +}, "~B"); +Clazz.defineStatics (c$, +"NONE", 0, +"CENTER", 10, +"WEST", 17, +"EAST", 13); +}); diff --git a/bin/javajs/swing/GridBagLayout.js b/bin/javajs/swing/GridBagLayout.js index e2a6b72..f2d3d43 100644 --- a/bin/javajs/swing/GridBagLayout.js +++ b/bin/javajs/swing/GridBagLayout.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.awt.LayoutManager"], "javajs.swing.GridBagLayout", null, function () { -c$ = Clazz.declareType (javajs.swing, "GridBagLayout", javajs.awt.LayoutManager); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.awt.LayoutManager"], "javajs.swing.GridBagLayout", null, function () { +c$ = Clazz.declareType (javajs.swing, "GridBagLayout", javajs.awt.LayoutManager); +}); diff --git a/bin/javajs/swing/Insets.js b/bin/javajs/swing/Insets.js index c9338fd..989e644 100644 --- a/bin/javajs/swing/Insets.js +++ b/bin/javajs/swing/Insets.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("javajs.swing"); -c$ = Clazz.decorateAsClass (function () { -this.top = 0; -this.left = 0; -this.bottom = 0; -this.right = 0; -Clazz.instantialize (this, arguments); -}, javajs.swing, "Insets"); -Clazz.makeConstructor (c$, -function (top, left, bottom, right) { -this.top = top; -this.left = left; -this.bottom = bottom; -this.right = right; -}, "~N,~N,~N,~N"); +Clazz.declarePackage ("javajs.swing"); +c$ = Clazz.decorateAsClass (function () { +this.top = 0; +this.left = 0; +this.bottom = 0; +this.right = 0; +Clazz.instantialize (this, arguments); +}, javajs.swing, "Insets"); +Clazz.makeConstructor (c$, +function (top, left, bottom, right) { +this.top = top; +this.left = left; +this.bottom = bottom; +this.right = right; +}, "~N,~N,~N,~N"); diff --git a/bin/javajs/swing/JButton.js b/bin/javajs/swing/JButton.js index 6fa242d..b1f5cc2 100644 --- a/bin/javajs/swing/JButton.js +++ b/bin/javajs/swing/JButton.js @@ -1,14 +1,14 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JButton", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JButton", javajs.swing.AbstractButton); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JButton, ["btnJB"]); -}); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append (""); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JButton", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JButton", javajs.swing.AbstractButton); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JButton, ["btnJB"]); +}); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append (""); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JCheckBox.js b/bin/javajs/swing/JCheckBox.js index f4697cb..bae9b88 100644 --- a/bin/javajs/swing/JCheckBox.js +++ b/bin/javajs/swing/JCheckBox.js @@ -1,13 +1,13 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JCheckBox", null, function () { -c$ = Clazz.declareType (javajs.swing, "JCheckBox", javajs.swing.AbstractButton); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JCheckBox, ["chkJCB"]); -}); -Clazz.overrideMethod (c$, "toHTML", -function () { -var s = ""; -return s; -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JCheckBox", null, function () { +c$ = Clazz.declareType (javajs.swing, "JCheckBox", javajs.swing.AbstractButton); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JCheckBox, ["chkJCB"]); +}); +Clazz.overrideMethod (c$, "toHTML", +function () { +var s = ""; +return s; +}); +}); diff --git a/bin/javajs/swing/JCheckBoxMenuItem.js b/bin/javajs/swing/JCheckBoxMenuItem.js index 7f50135..0b6f970 100644 --- a/bin/javajs/swing/JCheckBoxMenuItem.js +++ b/bin/javajs/swing/JCheckBoxMenuItem.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JMenuItem"], "javajs.swing.JCheckBoxMenuItem", null, function () { -c$ = Clazz.declareType (javajs.swing, "JCheckBoxMenuItem", javajs.swing.JMenuItem); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JCheckBoxMenuItem, ["chk", 2]); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JMenuItem"], "javajs.swing.JCheckBoxMenuItem", null, function () { +c$ = Clazz.declareType (javajs.swing, "JCheckBoxMenuItem", javajs.swing.JMenuItem); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JCheckBoxMenuItem, ["chk", 2]); +}); +}); diff --git a/bin/javajs/swing/JComboBox.js b/bin/javajs/swing/JComboBox.js index 3e829b4..088b19f 100644 --- a/bin/javajs/swing/JComboBox.js +++ b/bin/javajs/swing/JComboBox.js @@ -1,36 +1,36 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JComboBox", ["javajs.util.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.info = null; -this.selectedIndex = 0; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JComboBox", javajs.swing.AbstractButton); -Clazz.makeConstructor (c$, -function (info) { -Clazz.superConstructor (this, javajs.swing.JComboBox, ["cmbJCB"]); -this.info = info; -}, "~A"); -Clazz.defineMethod (c$, "setSelectedIndex", -function (i) { -this.selectedIndex = i; -{ -SwingController.setSelectedIndex(this); -}}, "~N"); -Clazz.defineMethod (c$, "getSelectedIndex", -function () { -return this.selectedIndex; -}); -Clazz.defineMethod (c$, "getSelectedItem", -function () { -return (this.selectedIndex < 0 ? null : this.info[this.selectedIndex]); -}); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append ("\n\n"); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JComboBox", ["javajs.util.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.info = null; +this.selectedIndex = 0; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JComboBox", javajs.swing.AbstractButton); +Clazz.makeConstructor (c$, +function (info) { +Clazz.superConstructor (this, javajs.swing.JComboBox, ["cmbJCB"]); +this.info = info; +}, "~A"); +Clazz.defineMethod (c$, "setSelectedIndex", +function (i) { +this.selectedIndex = i; +{ +SwingController.setSelectedIndex(this); +}}, "~N"); +Clazz.defineMethod (c$, "getSelectedIndex", +function () { +return this.selectedIndex; +}); +Clazz.defineMethod (c$, "getSelectedItem", +function () { +return (this.selectedIndex < 0 ? null : this.info[this.selectedIndex]); +}); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append ("\n\n"); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JComponent.js b/bin/javajs/swing/JComponent.js index 28b137e..aca8bfd 100644 --- a/bin/javajs/swing/JComponent.js +++ b/bin/javajs/swing/JComponent.js @@ -1,25 +1,25 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.awt.Container"], "javajs.swing.JComponent", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.autoScrolls = false; -this.actionCommand = null; -this.actionListener = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JComponent", javajs.awt.Container); -Clazz.defineMethod (c$, "setAutoscrolls", -function (b) { -this.autoScrolls = b; -}, "~B"); -Clazz.defineMethod (c$, "addActionListener", -function (listener) { -this.actionListener = listener; -}, "~O"); -Clazz.defineMethod (c$, "getActionCommand", -function () { -return this.actionCommand; -}); -Clazz.defineMethod (c$, "setActionCommand", -function (actionCommand) { -this.actionCommand = actionCommand; -}, "~S"); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.awt.Container"], "javajs.swing.JComponent", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.autoScrolls = false; +this.actionCommand = null; +this.actionListener = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JComponent", javajs.awt.Container); +Clazz.defineMethod (c$, "setAutoscrolls", +function (b) { +this.autoScrolls = b; +}, "~B"); +Clazz.defineMethod (c$, "addActionListener", +function (listener) { +this.actionListener = listener; +}, "~O"); +Clazz.defineMethod (c$, "getActionCommand", +function () { +return this.actionCommand; +}); +Clazz.defineMethod (c$, "setActionCommand", +function (actionCommand) { +this.actionCommand = actionCommand; +}, "~S"); +}); diff --git a/bin/javajs/swing/JComponentImp.js b/bin/javajs/swing/JComponentImp.js index 2158688..a19f4ee 100644 --- a/bin/javajs/swing/JComponentImp.js +++ b/bin/javajs/swing/JComponentImp.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JComponentImp", null, function () { -c$ = Clazz.declareType (javajs.swing, "JComponentImp", javajs.swing.JComponent); -Clazz.overrideMethod (c$, "toHTML", -function () { -return null; -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JComponentImp", null, function () { +c$ = Clazz.declareType (javajs.swing, "JComponentImp", javajs.swing.JComponent); +Clazz.overrideMethod (c$, "toHTML", +function () { +return null; +}); +}); diff --git a/bin/javajs/swing/JContentPane.js b/bin/javajs/swing/JContentPane.js index 5f822fa..5cd86e3 100644 --- a/bin/javajs/swing/JContentPane.js +++ b/bin/javajs/swing/JContentPane.js @@ -1,17 +1,17 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JContentPane", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JContentPane", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JContentPane, ["JCP"]); -}); -Clazz.defineMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append ("\n
    \n"); -if (this.list != null) for (var i = 0; i < this.list.size (); i++) sb.append (this.list.get (i).toHTML ()); - -sb.append ("\n
    \n"); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JContentPane", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JContentPane", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JContentPane, ["JCP"]); +}); +Clazz.defineMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append ("\n
    \n"); +if (this.list != null) for (var i = 0; i < this.list.size (); i++) sb.append (this.list.get (i).toHTML ()); + +sb.append ("\n
    \n"); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JDialog.js b/bin/javajs/swing/JDialog.js index 16bacd5..6b11856 100644 --- a/bin/javajs/swing/JDialog.js +++ b/bin/javajs/swing/JDialog.js @@ -1,82 +1,82 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.awt.Container"], "javajs.swing.JDialog", ["javajs.awt.Color", "javajs.swing.JContentPane", "javajs.util.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.defaultWidth = 600; -this.defaultHeight = 300; -this.contentPane = null; -this.title = null; -this.html = null; -this.zIndex = 9000; -this.loc = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JDialog", javajs.awt.Container); -Clazz.defineMethod (c$, "setZIndex", -function (zIndex) { -this.zIndex = zIndex; -}, "~N"); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JDialog, ["JD"]); -this.add (this.contentPane = new javajs.swing.JContentPane ()); -this.setBackground (javajs.awt.Color.get3 (210, 210, 240)); -this.contentPane.setBackground (javajs.awt.Color.get3 (230, 230, 230)); -}); -Clazz.defineMethod (c$, "setLocation", -function (loc) { -this.loc = loc; -}, "~A"); -Clazz.defineMethod (c$, "getContentPane", -function () { -return this.contentPane; -}); -Clazz.defineMethod (c$, "setTitle", -function (title) { -this.title = title; -}, "~S"); -Clazz.defineMethod (c$, "pack", -function () { -this.html = null; -}); -Clazz.defineMethod (c$, "validate", -function () { -this.html = null; -}); -Clazz.defineMethod (c$, "setVisible", -function (tf) { -if (tf && this.html == null) this.setDialog (); -Clazz.superCall (this, javajs.swing.JDialog, "setVisible", [tf]); -}, "~B"); -Clazz.defineMethod (c$, "dispose", -function () { -{ -{ -SwingController.dispose(this); -}}}); -Clazz.overrideMethod (c$, "repaint", -function () { -this.setDialog (); -}); -Clazz.defineMethod (c$, "setDialog", -($fz = function () { -this.html = this.toHTML (); -{ -SwingController.setDialog(this); -}}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "toHTML", -function () { -this.renderWidth = this.getSubcomponentWidth (); -if (this.renderWidth == 0) this.renderWidth = this.defaultWidth; -this.renderHeight = this.contentPane.getSubcomponentHeight (); -if (this.renderHeight == 0) this.renderHeight = this.defaultHeight; -var h = this.renderHeight - 25; -var sb = new javajs.util.SB (); -sb.append ("\n
    \n"); -sb.append ("\n
    " + "" + this.title + "" + "
    \n"); -sb.append ("\n
    \n"); -sb.append (this.contentPane.toHTML ()); -sb.append ("\n
    \n"); -return sb.toString (); -}); -Clazz.defineStatics (c$, -"headerHeight", 25); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.awt.Container"], "javajs.swing.JDialog", ["javajs.awt.Color", "javajs.swing.JContentPane", "javajs.util.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.defaultWidth = 600; +this.defaultHeight = 300; +this.contentPane = null; +this.title = null; +this.html = null; +this.zIndex = 9000; +this.loc = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JDialog", javajs.awt.Container); +Clazz.defineMethod (c$, "setZIndex", +function (zIndex) { +this.zIndex = zIndex; +}, "~N"); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JDialog, ["JD"]); +this.add (this.contentPane = new javajs.swing.JContentPane ()); +this.setBackground (javajs.awt.Color.get3 (210, 210, 240)); +this.contentPane.setBackground (javajs.awt.Color.get3 (230, 230, 230)); +}); +Clazz.defineMethod (c$, "setLocation", +function (loc) { +this.loc = loc; +}, "~A"); +Clazz.defineMethod (c$, "getContentPane", +function () { +return this.contentPane; +}); +Clazz.defineMethod (c$, "setTitle", +function (title) { +this.title = title; +}, "~S"); +Clazz.defineMethod (c$, "pack", +function () { +this.html = null; +}); +Clazz.defineMethod (c$, "validate", +function () { +this.html = null; +}); +Clazz.defineMethod (c$, "setVisible", +function (tf) { +if (tf && this.html == null) this.setDialog (); +Clazz.superCall (this, javajs.swing.JDialog, "setVisible", [tf]); +}, "~B"); +Clazz.defineMethod (c$, "dispose", +function () { +{ +{ +SwingController.dispose(this); +}}}); +Clazz.overrideMethod (c$, "repaint", +function () { +this.setDialog (); +}); +Clazz.defineMethod (c$, "setDialog", +($fz = function () { +this.html = this.toHTML (); +{ +SwingController.setDialog(this); +}}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "toHTML", +function () { +this.renderWidth = this.getSubcomponentWidth (); +if (this.renderWidth == 0) this.renderWidth = this.defaultWidth; +this.renderHeight = this.contentPane.getSubcomponentHeight (); +if (this.renderHeight == 0) this.renderHeight = this.defaultHeight; +var h = this.renderHeight - 25; +var sb = new javajs.util.SB (); +sb.append ("\n
    \n"); +sb.append ("\n
    " + "" + this.title + "" + "
    \n"); +sb.append ("\n
    \n"); +sb.append (this.contentPane.toHTML ()); +sb.append ("\n
    \n"); +return sb.toString (); +}); +Clazz.defineStatics (c$, +"headerHeight", 25); +}); diff --git a/bin/javajs/swing/JEditorPane.js b/bin/javajs/swing/JEditorPane.js index 4f40aab..f8dcf8c 100644 --- a/bin/javajs/swing/JEditorPane.js +++ b/bin/javajs/swing/JEditorPane.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JEditorPane", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JEditorPane", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JEditorPane, ["txtJEP"]); -this.text = ""; -}); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append (""); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JEditorPane", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JEditorPane", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JEditorPane, ["txtJEP"]); +this.text = ""; +}); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append (""); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JLabel.js b/bin/javajs/swing/JLabel.js index 778976c..2146a5e 100644 --- a/bin/javajs/swing/JLabel.js +++ b/bin/javajs/swing/JLabel.js @@ -1,17 +1,17 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JLabel", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JLabel", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function (text) { -Clazz.superConstructor (this, javajs.swing.JLabel, ["lblJL"]); -this.text = text; -}, "~S"); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append (""); -sb.append (this.text); -sb.append (""); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JLabel", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JLabel", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function (text) { +Clazz.superConstructor (this, javajs.swing.JLabel, ["lblJL"]); +this.text = text; +}, "~S"); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append (""); +sb.append (this.text); +sb.append (""); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JMenu.js b/bin/javajs/swing/JMenu.js index f887330..4dae0ad 100644 --- a/bin/javajs/swing/JMenu.js +++ b/bin/javajs/swing/JMenu.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JMenuItem"], "javajs.swing.JMenu", null, function () { -c$ = Clazz.declareType (javajs.swing, "JMenu", javajs.swing.JMenuItem); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JMenu, ["mnu", 4]); -}); -Clazz.defineMethod (c$, "getItemCount", -function () { -return this.getComponentCount (); -}); -Clazz.defineMethod (c$, "getItem", -function (i) { -return this.getComponent (i); -}, "~N"); -Clazz.overrideMethod (c$, "getPopupMenu", -function () { -return this; -}); -Clazz.overrideMethod (c$, "toHTML", -function () { -return this.getMenuHTML (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JMenuItem"], "javajs.swing.JMenu", null, function () { +c$ = Clazz.declareType (javajs.swing, "JMenu", javajs.swing.JMenuItem); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JMenu, ["mnu", 4]); +}); +Clazz.defineMethod (c$, "getItemCount", +function () { +return this.getComponentCount (); +}); +Clazz.defineMethod (c$, "getItem", +function (i) { +return this.getComponent (i); +}, "~N"); +Clazz.overrideMethod (c$, "getPopupMenu", +function () { +return this; +}); +Clazz.overrideMethod (c$, "toHTML", +function () { +return this.getMenuHTML (); +}); +}); diff --git a/bin/javajs/swing/JMenuItem.js b/bin/javajs/swing/JMenuItem.js index 36e3220..b1183cc 100644 --- a/bin/javajs/swing/JMenuItem.js +++ b/bin/javajs/swing/JMenuItem.js @@ -1,36 +1,36 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JMenuItem", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.btnType = 0; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JMenuItem", javajs.swing.AbstractButton); -Clazz.makeConstructor (c$, -function (text) { -Clazz.superConstructor (this, javajs.swing.JMenuItem, ["btn"]); -this.setText (text); -this.btnType = (text == null ? 0 : 1); -}, "~S"); -Clazz.makeConstructor (c$, -function (type, i) { -Clazz.superConstructor (this, javajs.swing.JMenuItem, [type]); -this.btnType = i; -}, "~S,~N"); -Clazz.overrideMethod (c$, "toHTML", -function () { -return this.htmlMenuOpener ("li") + (this.text == null ? "" : "" + this.htmlLabel () + "") + ""; -}); -Clazz.overrideMethod (c$, "getHtmlDisabled", -function () { -return " class=\"ui-state-disabled\""; -}); -Clazz.defineMethod (c$, "htmlLabel", -($fz = function () { -return (this.btnType == 1 ? this.text : ""); -}, $fz.isPrivate = true, $fz)); -Clazz.defineStatics (c$, -"TYPE_SEPARATOR", 0, -"TYPE_BUTTON", 1, -"TYPE_CHECKBOX", 2, -"TYPE_RADIO", 3, -"TYPE_MENU", 4); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JMenuItem", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.btnType = 0; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JMenuItem", javajs.swing.AbstractButton); +Clazz.makeConstructor (c$, +function (text) { +Clazz.superConstructor (this, javajs.swing.JMenuItem, ["btn"]); +this.setText (text); +this.btnType = (text == null ? 0 : 1); +}, "~S"); +Clazz.makeConstructor (c$, +function (type, i) { +Clazz.superConstructor (this, javajs.swing.JMenuItem, [type]); +this.btnType = i; +}, "~S,~N"); +Clazz.overrideMethod (c$, "toHTML", +function () { +return this.htmlMenuOpener ("li") + (this.text == null ? "" : "" + this.htmlLabel () + "") + ""; +}); +Clazz.overrideMethod (c$, "getHtmlDisabled", +function () { +return " class=\"ui-state-disabled\""; +}); +Clazz.defineMethod (c$, "htmlLabel", +($fz = function () { +return (this.btnType == 1 ? this.text : ""); +}, $fz.isPrivate = true, $fz)); +Clazz.defineStatics (c$, +"TYPE_SEPARATOR", 0, +"TYPE_BUTTON", 1, +"TYPE_CHECKBOX", 2, +"TYPE_RADIO", 3, +"TYPE_MENU", 4); +}); diff --git a/bin/javajs/swing/JPanel.js b/bin/javajs/swing/JPanel.js index a7a7ef9..76bb933 100644 --- a/bin/javajs/swing/JPanel.js +++ b/bin/javajs/swing/JPanel.js @@ -1,39 +1,39 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JPanel", ["javajs.swing.Grid", "$.GridBagConstraints", "javajs.util.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.grid = null; -this.nElements = 0; -this.last = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JPanel", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function (manager) { -Clazz.superConstructor (this, javajs.swing.JPanel, ["JP"]); -this.grid = new javajs.swing.Grid (10, 10); -}, "javajs.awt.LayoutManager"); -Clazz.defineMethod (c$, "add", -function (btn, c) { -this.last = (++this.nElements == 1 ? btn : null); -if (Clazz.instanceOf (c, String)) { -if (c.equals ("North")) c = new javajs.swing.GridBagConstraints (0, 0, 3, 1, 0, 0, 10, 0, null, 0, 0); - else if (c.equals ("South")) c = new javajs.swing.GridBagConstraints (0, 2, 3, 1, 0, 0, 10, 0, null, 0, 0); - else if (c.equals ("East")) c = new javajs.swing.GridBagConstraints (2, 1, 1, 1, 0, 0, 13, 0, null, 0, 0); - else if (c.equals ("West")) c = new javajs.swing.GridBagConstraints (0, 1, 1, 1, 0, 0, 17, 0, null, 0, 0); - else c = new javajs.swing.GridBagConstraints (1, 1, 1, 1, 0, 0, 10, 0, null, 0, 0); -}this.grid.add (btn, c); -}, "javajs.swing.JComponent,~O"); -Clazz.overrideMethod (c$, "toHTML", -function () { -if (this.last != null) { -this.grid = new javajs.swing.Grid (1, 1); -this.grid.add (this.last, new javajs.swing.GridBagConstraints (0, 0, 1, 1, 0, 0, 10, 0, null, 0, 0)); -this.last = null; -}var sb = new javajs.util.SB (); -sb.append ("\n
    \n"); -sb.append ("\n"); -sb.append (this.grid.toHTML (this.id)); -sb.append (""); -sb.append ("\n
    \n"); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JPanel", ["javajs.swing.Grid", "$.GridBagConstraints", "javajs.util.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.grid = null; +this.nElements = 0; +this.last = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JPanel", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function (manager) { +Clazz.superConstructor (this, javajs.swing.JPanel, ["JP"]); +this.grid = new javajs.swing.Grid (10, 10); +}, "javajs.awt.LayoutManager"); +Clazz.defineMethod (c$, "add", +function (btn, c) { +this.last = (++this.nElements == 1 ? btn : null); +if (Clazz.instanceOf (c, String)) { +if (c.equals ("North")) c = new javajs.swing.GridBagConstraints (0, 0, 3, 1, 0, 0, 10, 0, null, 0, 0); + else if (c.equals ("South")) c = new javajs.swing.GridBagConstraints (0, 2, 3, 1, 0, 0, 10, 0, null, 0, 0); + else if (c.equals ("East")) c = new javajs.swing.GridBagConstraints (2, 1, 1, 1, 0, 0, 13, 0, null, 0, 0); + else if (c.equals ("West")) c = new javajs.swing.GridBagConstraints (0, 1, 1, 1, 0, 0, 17, 0, null, 0, 0); + else c = new javajs.swing.GridBagConstraints (1, 1, 1, 1, 0, 0, 10, 0, null, 0, 0); +}this.grid.add (btn, c); +}, "javajs.swing.JComponent,~O"); +Clazz.overrideMethod (c$, "toHTML", +function () { +if (this.last != null) { +this.grid = new javajs.swing.Grid (1, 1); +this.grid.add (this.last, new javajs.swing.GridBagConstraints (0, 0, 1, 1, 0, 0, 10, 0, null, 0, 0)); +this.last = null; +}var sb = new javajs.util.SB (); +sb.append ("\n
    \n"); +sb.append ("\n"); +sb.append (this.grid.toHTML (this.id)); +sb.append (""); +sb.append ("\n
    \n"); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JPopupMenu.js b/bin/javajs/swing/JPopupMenu.js index 855df96..95cbc1f 100644 --- a/bin/javajs/swing/JPopupMenu.js +++ b/bin/javajs/swing/JPopupMenu.js @@ -1,37 +1,37 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JPopupMenu", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.tainted = true; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JPopupMenu", javajs.swing.AbstractButton); -Clazz.makeConstructor (c$, -function (name) { -Clazz.superConstructor (this, javajs.swing.JPopupMenu, ["mnu"]); -this.name = name; -}, "~S"); -Clazz.defineMethod (c$, "setInvoker", -function (applet) { -this.applet = applet; -{ -SwingController.setMenu(this); -}}, "~O"); -Clazz.defineMethod (c$, "show", -function (applet, x, y) { -{ -if (applet != null) -this.tainted = true; -SwingController.showMenu(this, x, y); -}}, "javajs.awt.Component,~N,~N"); -Clazz.defineMethod (c$, "disposeMenu", -function () { -{ -SwingController.disposeMenu(this); -}}); -Clazz.overrideMethod (c$, "toHTML", -function () { -return this.getMenuHTML (); -}); -{ -{ -SwingController.setDraggable(javajs.swing.JPopupMenu); -}}}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.AbstractButton"], "javajs.swing.JPopupMenu", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.tainted = true; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JPopupMenu", javajs.swing.AbstractButton); +Clazz.makeConstructor (c$, +function (name) { +Clazz.superConstructor (this, javajs.swing.JPopupMenu, ["mnu"]); +this.name = name; +}, "~S"); +Clazz.defineMethod (c$, "setInvoker", +function (applet) { +this.applet = applet; +{ +SwingController.setMenu(this); +}}, "~O"); +Clazz.defineMethod (c$, "show", +function (applet, x, y) { +{ +if (applet != null) +this.tainted = true; +SwingController.showMenu(this, x, y); +}}, "javajs.awt.Component,~N,~N"); +Clazz.defineMethod (c$, "disposeMenu", +function () { +{ +SwingController.disposeMenu(this); +}}); +Clazz.overrideMethod (c$, "toHTML", +function () { +return this.getMenuHTML (); +}); +{ +{ +SwingController.setDraggable(javajs.swing.JPopupMenu); +}}}); diff --git a/bin/javajs/swing/JRadioButtonMenuItem.js b/bin/javajs/swing/JRadioButtonMenuItem.js index 1ba2401..8388819 100644 --- a/bin/javajs/swing/JRadioButtonMenuItem.js +++ b/bin/javajs/swing/JRadioButtonMenuItem.js @@ -1,11 +1,11 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JMenuItem"], "javajs.swing.JRadioButtonMenuItem", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.isRadio = true; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JRadioButtonMenuItem", javajs.swing.JMenuItem); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JRadioButtonMenuItem, ["rad", 3]); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JMenuItem"], "javajs.swing.JRadioButtonMenuItem", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.isRadio = true; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JRadioButtonMenuItem", javajs.swing.JMenuItem); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JRadioButtonMenuItem, ["rad", 3]); +}); +}); diff --git a/bin/javajs/swing/JScrollPane.js b/bin/javajs/swing/JScrollPane.js index 64c766a..2ba9959 100644 --- a/bin/javajs/swing/JScrollPane.js +++ b/bin/javajs/swing/JScrollPane.js @@ -1,22 +1,22 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JScrollPane", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JScrollPane", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function (component) { -Clazz.superConstructor (this, javajs.swing.JScrollPane, ["JScP"]); -this.add (component); -}, "javajs.swing.JComponent"); -Clazz.defineMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append ("\n
    \n"); -if (this.list != null) { -var c = this.list.get (0); -sb.append (c.toHTML ()); -}sb.append ("\n
    \n"); -return sb.toString (); -}); -Clazz.overrideMethod (c$, "setMinimumSize", -function (dimension) { -}, "javajs.awt.Dimension"); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JScrollPane", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JScrollPane", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function (component) { +Clazz.superConstructor (this, javajs.swing.JScrollPane, ["JScP"]); +this.add (component); +}, "javajs.swing.JComponent"); +Clazz.defineMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append ("\n
    \n"); +if (this.list != null) { +var c = this.list.get (0); +sb.append (c.toHTML ()); +}sb.append ("\n
    \n"); +return sb.toString (); +}); +Clazz.overrideMethod (c$, "setMinimumSize", +function (dimension) { +}, "javajs.awt.Dimension"); +}); diff --git a/bin/javajs/swing/JSplitPane.js b/bin/javajs/swing/JSplitPane.js index 11f99e2..08969e2 100644 --- a/bin/javajs/swing/JSplitPane.js +++ b/bin/javajs/swing/JSplitPane.js @@ -1,67 +1,67 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JSplitPane", ["javajs.swing.JComponentImp", "javajs.util.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.isH = true; -this.split = 1; -this.right = null; -this.left = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JSplitPane", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function (split) { -Clazz.superConstructor (this, javajs.swing.JSplitPane, ["JSpP"]); -this.split = split; -this.isH = (split == 1); -}, "~N"); -Clazz.defineMethod (c$, "setRightComponent", -function (r) { -this.right = new javajs.swing.JComponentImp (null); -this.right.add (r); -}, "javajs.swing.JComponent"); -Clazz.defineMethod (c$, "setLeftComponent", -function (l) { -this.left = new javajs.swing.JComponentImp (null); -this.left.add (l); -}, "javajs.swing.JComponent"); -Clazz.defineMethod (c$, "getSubcomponentWidth", -function () { -var w = this.width; -if (w == 0) { -var wleft = this.left.getSubcomponentWidth (); -var wright = this.right.getSubcomponentWidth (); -if (wleft > 0 && wright > 0) { -if (this.isH) w = wleft + wright; - else w = Math.max (wleft, wright); -}}return w; -}); -Clazz.defineMethod (c$, "getSubcomponentHeight", -function () { -var h = this.height; -if (h == 0) { -var hleft = this.left.getSubcomponentHeight (); -var hright = this.right.getSubcomponentHeight (); -if (hleft > 0 && hright > 0) { -if (this.isH) h = Math.max (hleft, hright); - else h = hleft + hright; -}}return h; -}); -Clazz.defineMethod (c$, "toHTML", -function () { -if (this.left == null || this.right == null) return ""; -var isH = (this.split == 1); -if (this.width == 0) this.width = this.getSubcomponentWidth (); -if (this.height == 0) this.height = this.getSubcomponentHeight (); -var sb = new javajs.util.SB (); -sb.append ("
    "); -if (isH) sb.append ("
    "); - else sb.append ("
    "); -sb.append (this.left.getComponents ()[0].toHTML ()); -if (isH) sb.append ("
    "); - else sb.append ("
    "); -sb.append (this.right.getComponents ()[0].toHTML ()); -sb.append ("
    \n"); -return sb.toString (); -}); -Clazz.defineStatics (c$, -"HORIZONTAL_SPLIT", 1); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JSplitPane", ["javajs.swing.JComponentImp", "javajs.util.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.isH = true; +this.split = 1; +this.right = null; +this.left = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JSplitPane", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function (split) { +Clazz.superConstructor (this, javajs.swing.JSplitPane, ["JSpP"]); +this.split = split; +this.isH = (split == 1); +}, "~N"); +Clazz.defineMethod (c$, "setRightComponent", +function (r) { +this.right = new javajs.swing.JComponentImp (null); +this.right.add (r); +}, "javajs.swing.JComponent"); +Clazz.defineMethod (c$, "setLeftComponent", +function (l) { +this.left = new javajs.swing.JComponentImp (null); +this.left.add (l); +}, "javajs.swing.JComponent"); +Clazz.defineMethod (c$, "getSubcomponentWidth", +function () { +var w = this.width; +if (w == 0) { +var wleft = this.left.getSubcomponentWidth (); +var wright = this.right.getSubcomponentWidth (); +if (wleft > 0 && wright > 0) { +if (this.isH) w = wleft + wright; + else w = Math.max (wleft, wright); +}}return w; +}); +Clazz.defineMethod (c$, "getSubcomponentHeight", +function () { +var h = this.height; +if (h == 0) { +var hleft = this.left.getSubcomponentHeight (); +var hright = this.right.getSubcomponentHeight (); +if (hleft > 0 && hright > 0) { +if (this.isH) h = Math.max (hleft, hright); + else h = hleft + hright; +}}return h; +}); +Clazz.defineMethod (c$, "toHTML", +function () { +if (this.left == null || this.right == null) return ""; +var isH = (this.split == 1); +if (this.width == 0) this.width = this.getSubcomponentWidth (); +if (this.height == 0) this.height = this.getSubcomponentHeight (); +var sb = new javajs.util.SB (); +sb.append ("
    "); +if (isH) sb.append ("
    "); + else sb.append ("
    "); +sb.append (this.left.getComponents ()[0].toHTML ()); +if (isH) sb.append ("
    "); + else sb.append ("
    "); +sb.append (this.right.getComponents ()[0].toHTML ()); +sb.append ("
    \n"); +return sb.toString (); +}); +Clazz.defineStatics (c$, +"HORIZONTAL_SPLIT", 1); +}); diff --git a/bin/javajs/swing/JTable.js b/bin/javajs/swing/JTable.js index a281668..b8f4499 100644 --- a/bin/javajs/swing/JTable.js +++ b/bin/javajs/swing/JTable.js @@ -1,67 +1,67 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.ColumnSelectionModel", "$.JComponent", "$.ListSelectionModel"], "javajs.swing.JTable", ["javajs.util.BS", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.tableModel = null; -this.bsSelectedCells = null; -this.bsSelectedRows = null; -this.rowSelectionAllowed = false; -this.cellSelectionEnabled = false; -this.selectionListener = null; -Clazz.instantialize (this, arguments); -}, javajs.swing, "JTable", javajs.swing.JComponent, [javajs.swing.ListSelectionModel, javajs.swing.ColumnSelectionModel]); -Clazz.makeConstructor (c$, -function (tableModel) { -Clazz.superConstructor (this, javajs.swing.JTable, ["JT"]); -this.tableModel = tableModel; -this.bsSelectedCells = new javajs.util.BS (); -this.bsSelectedRows = new javajs.util.BS (); -}, "javajs.swing.AbstractTableModel"); -Clazz.overrideMethod (c$, "getSelectionModel", -function () { -return this; -}); -Clazz.defineMethod (c$, "getColumnModel", -function () { -return this; -}); -Clazz.defineMethod (c$, "setPreferredScrollableViewportSize", -function (dimension) { -this.width = dimension.width; -this.height = dimension.height; -}, "javajs.awt.Dimension"); -Clazz.defineMethod (c$, "clearSelection", -function () { -this.bsSelectedCells.clearAll (); -this.bsSelectedRows.clearAll (); -}); -Clazz.defineMethod (c$, "setRowSelectionAllowed", -function (b) { -this.rowSelectionAllowed = b; -}, "~B"); -Clazz.defineMethod (c$, "setRowSelectionInterval", -function (i, j) { -this.bsSelectedRows.clearAll (); -this.bsSelectedRows.setBits (i, j); -this.bsSelectedCells.clearAll (); -}, "~N,~N"); -Clazz.defineMethod (c$, "setCellSelectionEnabled", -function (enabled) { -this.cellSelectionEnabled = enabled; -}, "~B"); -Clazz.overrideMethod (c$, "addListSelectionListener", -function (listener) { -this.selectionListener = listener; -}, "~O"); -Clazz.overrideMethod (c$, "getColumn", -function (i) { -return this.tableModel.getColumn (i); -}, "~N"); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append ("\n"); -this.tableModel.toHTML (sb, this.id, this.bsSelectedRows); -sb.append ("\n
    \n"); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.ColumnSelectionModel", "$.JComponent", "$.ListSelectionModel"], "javajs.swing.JTable", ["javajs.util.BS", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.tableModel = null; +this.bsSelectedCells = null; +this.bsSelectedRows = null; +this.rowSelectionAllowed = false; +this.cellSelectionEnabled = false; +this.selectionListener = null; +Clazz.instantialize (this, arguments); +}, javajs.swing, "JTable", javajs.swing.JComponent, [javajs.swing.ListSelectionModel, javajs.swing.ColumnSelectionModel]); +Clazz.makeConstructor (c$, +function (tableModel) { +Clazz.superConstructor (this, javajs.swing.JTable, ["JT"]); +this.tableModel = tableModel; +this.bsSelectedCells = new javajs.util.BS (); +this.bsSelectedRows = new javajs.util.BS (); +}, "javajs.swing.AbstractTableModel"); +Clazz.overrideMethod (c$, "getSelectionModel", +function () { +return this; +}); +Clazz.defineMethod (c$, "getColumnModel", +function () { +return this; +}); +Clazz.defineMethod (c$, "setPreferredScrollableViewportSize", +function (dimension) { +this.width = dimension.width; +this.height = dimension.height; +}, "javajs.awt.Dimension"); +Clazz.defineMethod (c$, "clearSelection", +function () { +this.bsSelectedCells.clearAll (); +this.bsSelectedRows.clearAll (); +}); +Clazz.defineMethod (c$, "setRowSelectionAllowed", +function (b) { +this.rowSelectionAllowed = b; +}, "~B"); +Clazz.defineMethod (c$, "setRowSelectionInterval", +function (i, j) { +this.bsSelectedRows.clearAll (); +this.bsSelectedRows.setBits (i, j); +this.bsSelectedCells.clearAll (); +}, "~N,~N"); +Clazz.defineMethod (c$, "setCellSelectionEnabled", +function (enabled) { +this.cellSelectionEnabled = enabled; +}, "~B"); +Clazz.overrideMethod (c$, "addListSelectionListener", +function (listener) { +this.selectionListener = listener; +}, "~O"); +Clazz.overrideMethod (c$, "getColumn", +function (i) { +return this.tableModel.getColumn (i); +}, "~N"); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append ("\n"); +this.tableModel.toHTML (sb, this.id, this.bsSelectedRows); +sb.append ("\n
    \n"); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JTextField.js b/bin/javajs/swing/JTextField.js index 9cc639f..88b08a6 100644 --- a/bin/javajs/swing/JTextField.js +++ b/bin/javajs/swing/JTextField.js @@ -1,15 +1,15 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JTextField", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JTextField", javajs.swing.JComponent); -Clazz.makeConstructor (c$, -function (value) { -Clazz.superConstructor (this, javajs.swing.JTextField, ["txtJT"]); -this.text = value; -}, "~S"); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append (""); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.JComponent"], "javajs.swing.JTextField", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JTextField", javajs.swing.JComponent); +Clazz.makeConstructor (c$, +function (value) { +Clazz.superConstructor (this, javajs.swing.JTextField, ["txtJT"]); +this.text = value; +}, "~S"); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append (""); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/JTextPane.js b/bin/javajs/swing/JTextPane.js index 23d5a22..25d3764 100644 --- a/bin/javajs/swing/JTextPane.js +++ b/bin/javajs/swing/JTextPane.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.load (["javajs.swing.Document", "$.JComponent"], "javajs.swing.JTextPane", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.swing, "JTextPane", javajs.swing.JComponent, javajs.swing.Document); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.swing.JTextPane, ["txtJTP"]); -this.text = ""; -}); -Clazz.defineMethod (c$, "getDocument", -function () { -return this; -}); -Clazz.overrideMethod (c$, "insertString", -function (i, s, object) { -i = Math.min (i, this.text.length); -this.text = this.text.substring (0, i) + s + this.text.substring (i); -}, "~N,~S,~O"); -Clazz.overrideMethod (c$, "toHTML", -function () { -var sb = new javajs.util.SB (); -sb.append (""); -return sb.toString (); -}); -}); +Clazz.declarePackage ("javajs.swing"); +Clazz.load (["javajs.swing.Document", "$.JComponent"], "javajs.swing.JTextPane", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.swing, "JTextPane", javajs.swing.JComponent, javajs.swing.Document); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.swing.JTextPane, ["txtJTP"]); +this.text = ""; +}); +Clazz.defineMethod (c$, "getDocument", +function () { +return this; +}); +Clazz.overrideMethod (c$, "insertString", +function (i, s, object) { +i = Math.min (i, this.text.length); +this.text = this.text.substring (0, i) + s + this.text.substring (i); +}, "~N,~S,~O"); +Clazz.overrideMethod (c$, "toHTML", +function () { +var sb = new javajs.util.SB (); +sb.append (""); +return sb.toString (); +}); +}); diff --git a/bin/javajs/swing/ListSelectionModel.js b/bin/javajs/swing/ListSelectionModel.js index 5cb1d3a..c5fd420 100644 --- a/bin/javajs/swing/ListSelectionModel.js +++ b/bin/javajs/swing/ListSelectionModel.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.declareInterface (javajs.swing, "ListSelectionModel"); +Clazz.declarePackage ("javajs.swing"); +Clazz.declareInterface (javajs.swing, "ListSelectionModel"); diff --git a/bin/javajs/swing/SwingConstants.js b/bin/javajs/swing/SwingConstants.js index f10e094..2298d0a 100644 --- a/bin/javajs/swing/SwingConstants.js +++ b/bin/javajs/swing/SwingConstants.js @@ -1,6 +1,6 @@ -Clazz.declarePackage ("javajs.swing"); -c$ = Clazz.declareType (javajs.swing, "SwingConstants"); -Clazz.defineStatics (c$, -"LEFT", 2, -"CENTER", 0, -"RIGHT", 4); +Clazz.declarePackage ("javajs.swing"); +c$ = Clazz.declareType (javajs.swing, "SwingConstants"); +Clazz.defineStatics (c$, +"LEFT", 2, +"CENTER", 0, +"RIGHT", 4); diff --git a/bin/javajs/swing/TableCellRenderer.js b/bin/javajs/swing/TableCellRenderer.js index 94b3f9f..6b1942e 100644 --- a/bin/javajs/swing/TableCellRenderer.js +++ b/bin/javajs/swing/TableCellRenderer.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.declareInterface (javajs.swing, "TableCellRenderer"); +Clazz.declarePackage ("javajs.swing"); +Clazz.declareInterface (javajs.swing, "TableCellRenderer"); diff --git a/bin/javajs/swing/TableColumn.js b/bin/javajs/swing/TableColumn.js index e2fa800..19d5394 100644 --- a/bin/javajs/swing/TableColumn.js +++ b/bin/javajs/swing/TableColumn.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("javajs.swing"); -Clazz.declareInterface (javajs.swing, "TableColumn"); +Clazz.declarePackage ("javajs.swing"); +Clazz.declareInterface (javajs.swing, "TableColumn"); diff --git a/bin/javajs/util/A4.js b/bin/javajs/util/A4.js index d3d3a66..b3f66b8 100644 --- a/bin/javajs/util/A4.js +++ b/bin/javajs/util/A4.js @@ -1,89 +1,89 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.JSONEncodable"], "javajs.util.A4", ["javajs.util.T3"], function () { -c$ = Clazz.decorateAsClass (function () { -this.x = 0; -this.y = 0; -this.z = 0; -this.angle = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "A4", null, [javajs.api.JSONEncodable, java.io.Serializable]); -Clazz.makeConstructor (c$, -function () { -this.z = 1.0; -}); -c$.new4 = Clazz.defineMethod (c$, "new4", -function (x, y, z, angle) { -var a = new javajs.util.A4 (); -a.set4 (x, y, z, angle); -return a; -}, "~N,~N,~N,~N"); -c$.newAA = Clazz.defineMethod (c$, "newAA", -function (a1) { -var a = new javajs.util.A4 (); -a.set4 (a1.x, a1.y, a1.z, a1.angle); -return a; -}, "javajs.util.A4"); -c$.newVA = Clazz.defineMethod (c$, "newVA", -function (axis, angle) { -var a = new javajs.util.A4 (); -a.setVA (axis, angle); -return a; -}, "javajs.util.V3,~N"); -Clazz.defineMethod (c$, "setVA", -function (axis, angle) { -this.x = axis.x; -this.y = axis.y; -this.z = axis.z; -this.angle = angle; -}, "javajs.util.V3,~N"); -Clazz.defineMethod (c$, "set4", -function (x, y, z, angle) { -this.x = x; -this.y = y; -this.z = z; -this.angle = angle; -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "setAA", -function (a) { -this.x = a.x; -this.y = a.y; -this.z = a.z; -this.angle = a.angle; -}, "javajs.util.A4"); -Clazz.defineMethod (c$, "setM", -function (m1) { -this.setFromMat (m1.m00, m1.m01, m1.m02, m1.m10, m1.m11, m1.m12, m1.m20, m1.m21, m1.m22); -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "setFromMat", -($fz = function (m00, m01, m02, m10, m11, m12, m20, m21, m22) { -var cos = (m00 + m11 + m22 - 1.0) * 0.5; -this.x = (m21 - m12); -this.y = (m02 - m20); -this.z = (m10 - m01); -var sin = 0.5 * Math.sqrt (this.x * this.x + this.y * this.y + this.z * this.z); -if (sin == 0 && cos == 1) { -this.x = this.y = 0; -this.z = 1; -this.angle = 0; -} else { -this.angle = Math.atan2 (sin, cos); -}}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N,~N,~N,~N,~N,~N"); -Clazz.overrideMethod (c$, "hashCode", -function () { -return javajs.util.T3.floatToIntBits0 (this.x) ^ javajs.util.T3.floatToIntBits0 (this.y) ^ javajs.util.T3.floatToIntBits0 (this.z) ^ javajs.util.T3.floatToIntBits0 (this.angle); -}); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (!(Clazz.instanceOf (o, javajs.util.A4))) return false; -var a1 = o; -return this.x == a1.x && this.y == a1.y && this.z == a1.z && this.angle == a1.angle; -}, "~O"); -Clazz.overrideMethod (c$, "toString", -function () { -return "(" + this.x + ", " + this.y + ", " + this.z + ", " + this.angle + ")"; -}); -Clazz.overrideMethod (c$, "toJSON", -function () { -return "[" + this.x + "," + this.y + "," + this.z + "," + (this.angle * 180.0 / 3.141592653589793) + "]"; -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.JSONEncodable"], "javajs.util.A4", ["javajs.util.T3"], function () { +c$ = Clazz.decorateAsClass (function () { +this.x = 0; +this.y = 0; +this.z = 0; +this.angle = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "A4", null, [javajs.api.JSONEncodable, java.io.Serializable]); +Clazz.makeConstructor (c$, +function () { +this.z = 1.0; +}); +c$.new4 = Clazz.defineMethod (c$, "new4", +function (x, y, z, angle) { +var a = new javajs.util.A4 (); +a.set4 (x, y, z, angle); +return a; +}, "~N,~N,~N,~N"); +c$.newAA = Clazz.defineMethod (c$, "newAA", +function (a1) { +var a = new javajs.util.A4 (); +a.set4 (a1.x, a1.y, a1.z, a1.angle); +return a; +}, "javajs.util.A4"); +c$.newVA = Clazz.defineMethod (c$, "newVA", +function (axis, angle) { +var a = new javajs.util.A4 (); +a.setVA (axis, angle); +return a; +}, "javajs.util.V3,~N"); +Clazz.defineMethod (c$, "setVA", +function (axis, angle) { +this.x = axis.x; +this.y = axis.y; +this.z = axis.z; +this.angle = angle; +}, "javajs.util.V3,~N"); +Clazz.defineMethod (c$, "set4", +function (x, y, z, angle) { +this.x = x; +this.y = y; +this.z = z; +this.angle = angle; +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "setAA", +function (a) { +this.x = a.x; +this.y = a.y; +this.z = a.z; +this.angle = a.angle; +}, "javajs.util.A4"); +Clazz.defineMethod (c$, "setM", +function (m1) { +this.setFromMat (m1.m00, m1.m01, m1.m02, m1.m10, m1.m11, m1.m12, m1.m20, m1.m21, m1.m22); +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "setFromMat", +($fz = function (m00, m01, m02, m10, m11, m12, m20, m21, m22) { +var cos = (m00 + m11 + m22 - 1.0) * 0.5; +this.x = (m21 - m12); +this.y = (m02 - m20); +this.z = (m10 - m01); +var sin = 0.5 * Math.sqrt (this.x * this.x + this.y * this.y + this.z * this.z); +if (sin == 0 && cos == 1) { +this.x = this.y = 0; +this.z = 1; +this.angle = 0; +} else { +this.angle = Math.atan2 (sin, cos); +}}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N,~N,~N,~N,~N,~N"); +Clazz.overrideMethod (c$, "hashCode", +function () { +return javajs.util.T3.floatToIntBits0 (this.x) ^ javajs.util.T3.floatToIntBits0 (this.y) ^ javajs.util.T3.floatToIntBits0 (this.z) ^ javajs.util.T3.floatToIntBits0 (this.angle); +}); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (!(Clazz.instanceOf (o, javajs.util.A4))) return false; +var a1 = o; +return this.x == a1.x && this.y == a1.y && this.z == a1.z && this.angle == a1.angle; +}, "~O"); +Clazz.overrideMethod (c$, "toString", +function () { +return "(" + this.x + ", " + this.y + ", " + this.z + ", " + this.angle + ")"; +}); +Clazz.overrideMethod (c$, "toJSON", +function () { +return "[" + this.x + "," + this.y + "," + this.z + "," + (this.angle * 180.0 / 3.141592653589793) + "]"; +}); +}); diff --git a/bin/javajs/util/AU.js b/bin/javajs/util/AU.js index f7f0201..080d17c 100644 --- a/bin/javajs/util/AU.js +++ b/bin/javajs/util/AU.js @@ -1,351 +1,351 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.AU", ["java.util.Arrays", "javajs.util.Lst"], function () { -c$ = Clazz.declareType (javajs.util, "AU"); -c$.ensureLength = Clazz.defineMethod (c$, "ensureLength", -function (array, minimumLength) { -if (array != null && javajs.util.AU.getLength (array) >= minimumLength) return array; -return javajs.util.AU.arrayCopyObject (array, minimumLength); -}, "~O,~N"); -c$.ensureLengthS = Clazz.defineMethod (c$, "ensureLengthS", -function (array, minimumLength) { -if (array != null && array.length >= minimumLength) return array; -return javajs.util.AU.arrayCopyS (array, minimumLength); -}, "~A,~N"); -c$.ensureLengthA = Clazz.defineMethod (c$, "ensureLengthA", -function (array, minimumLength) { -if (array != null && array.length >= minimumLength) return array; -return javajs.util.AU.arrayCopyF (array, minimumLength); -}, "~A,~N"); -c$.ensureLengthI = Clazz.defineMethod (c$, "ensureLengthI", -function (array, minimumLength) { -if (array != null && array.length >= minimumLength) return array; -return javajs.util.AU.arrayCopyI (array, minimumLength); -}, "~A,~N"); -c$.ensureLengthShort = Clazz.defineMethod (c$, "ensureLengthShort", -function (array, minimumLength) { -if (array != null && array.length >= minimumLength) return array; -return javajs.util.AU.arrayCopyShort (array, minimumLength); -}, "~A,~N"); -c$.ensureLengthByte = Clazz.defineMethod (c$, "ensureLengthByte", -function (array, minimumLength) { -if (array != null && array.length >= minimumLength) return array; -return javajs.util.AU.arrayCopyByte (array, minimumLength); -}, "~A,~N"); -c$.doubleLength = Clazz.defineMethod (c$, "doubleLength", -function (array) { -return javajs.util.AU.arrayCopyObject (array, (array == null ? 16 : 2 * javajs.util.AU.getLength (array))); -}, "~O"); -c$.doubleLengthS = Clazz.defineMethod (c$, "doubleLengthS", -function (array) { -return javajs.util.AU.arrayCopyS (array, (array == null ? 16 : 2 * array.length)); -}, "~A"); -c$.doubleLengthF = Clazz.defineMethod (c$, "doubleLengthF", -function (array) { -return javajs.util.AU.arrayCopyF (array, (array == null ? 16 : 2 * array.length)); -}, "~A"); -c$.doubleLengthI = Clazz.defineMethod (c$, "doubleLengthI", -function (array) { -return javajs.util.AU.arrayCopyI (array, (array == null ? 16 : 2 * array.length)); -}, "~A"); -c$.doubleLengthShort = Clazz.defineMethod (c$, "doubleLengthShort", -function (array) { -return javajs.util.AU.arrayCopyShort (array, (array == null ? 16 : 2 * array.length)); -}, "~A"); -c$.doubleLengthByte = Clazz.defineMethod (c$, "doubleLengthByte", -function (array) { -return javajs.util.AU.arrayCopyByte (array, (array == null ? 16 : 2 * array.length)); -}, "~A"); -c$.doubleLengthBool = Clazz.defineMethod (c$, "doubleLengthBool", -function (array) { -return javajs.util.AU.arrayCopyBool (array, (array == null ? 16 : 2 * array.length)); -}, "~A"); -c$.deleteElements = Clazz.defineMethod (c$, "deleteElements", -function (array, firstElement, nElements) { -if (nElements == 0 || array == null) return array; -var oldLength = javajs.util.AU.getLength (array); -if (firstElement >= oldLength) return array; -var n = oldLength - (firstElement + nElements); -if (n < 0) n = 0; -var t = javajs.util.AU.newInstanceO (array, firstElement + n); -if (firstElement > 0) System.arraycopy (array, 0, t, 0, firstElement); -if (n > 0) System.arraycopy (array, firstElement + nElements, t, firstElement, n); -return t; -}, "~O,~N,~N"); -c$.arrayCopyObject = Clazz.defineMethod (c$, "arrayCopyObject", -function (array, newLength) { -if (array == null) { -return null; -}var oldLength = javajs.util.AU.getLength (array); -if (newLength == oldLength) return array; -var t = javajs.util.AU.newInstanceO (array, newLength); -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -return t; -}, "~O,~N"); -c$.newInstanceO = Clazz.defineMethod (c$, "newInstanceO", -($fz = function (array, n) { -{ -if (!array.getClass().getComponentType) -return new Array(n); -}}, $fz.isPrivate = true, $fz), "~O,~N"); -c$.getLength = Clazz.defineMethod (c$, "getLength", -function (array) { -{ -return array.length -}}, "~O"); -c$.arrayCopyS = Clazz.defineMethod (c$, "arrayCopyS", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = new Array (newLength); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyII = Clazz.defineMethod (c$, "arrayCopyII", -function (array, newLength) { -var t = javajs.util.AU.newInt2 (newLength); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyPt = Clazz.defineMethod (c$, "arrayCopyPt", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = new Array (newLength); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyF = Clazz.defineMethod (c$, "arrayCopyF", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = Clazz.newFloatArray (newLength, 0); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyI = Clazz.defineMethod (c$, "arrayCopyI", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = Clazz.newIntArray (newLength, 0); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyRangeI = Clazz.defineMethod (c$, "arrayCopyRangeI", -function (array, i0, n) { -if (array == null) return null; -var oldLength = array.length; -if (n == -1) n = oldLength; -if (n == -2) n = Clazz.doubleToInt (oldLength / 2); -n = n - i0; -var t = Clazz.newIntArray (n, 0); -System.arraycopy (array, i0, t, 0, n); -return t; -}, "~A,~N,~N"); -c$.arrayCopyRangeRevI = Clazz.defineMethod (c$, "arrayCopyRangeRevI", -function (array, i0, n) { -if (array == null) return null; -var t = javajs.util.AU.arrayCopyRangeI (array, i0, n); -if (n < 0) n = array.length; -for (var i = Clazz.doubleToInt (n / 2); --i >= 0; ) javajs.util.AU.swapInt (t, i, n - 1 - i); - -return t; -}, "~A,~N,~N"); -c$.arrayCopyShort = Clazz.defineMethod (c$, "arrayCopyShort", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = Clazz.newShortArray (newLength, 0); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyByte = Clazz.defineMethod (c$, "arrayCopyByte", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = Clazz.newByteArray (newLength, 0); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.arrayCopyBool = Clazz.defineMethod (c$, "arrayCopyBool", -function (array, newLength) { -if (newLength < 0) newLength = array.length; -var t = Clazz.newBooleanArray (newLength, false); -if (array != null) { -var oldLength = array.length; -System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); -}return t; -}, "~A,~N"); -c$.swapInt = Clazz.defineMethod (c$, "swapInt", -function (array, indexA, indexB) { -var t = array[indexA]; -array[indexA] = array[indexB]; -array[indexB] = t; -}, "~A,~N,~N"); -c$.dumpArray = Clazz.defineMethod (c$, "dumpArray", -function (msg, A, x1, x2, y1, y2) { -var s = "dumpArray: " + msg + "\n"; -for (var x = x1; x <= x2; x++) s += "\t*" + x + "*"; - -for (var y = y2; y >= y1; y--) { -s += "\n*" + y + "*"; -for (var x = x1; x <= x2; x++) s += "\t" + (x < A.length && y < A[x].length ? A[x][y] : NaN); - -} -return s; -}, "~S,~A,~N,~N,~N,~N"); -c$.dumpIntArray = Clazz.defineMethod (c$, "dumpIntArray", -function (A, n) { -var str = ""; -for (var i = 0; i < n; i++) str += " " + A[i]; - -return str; -}, "~A,~N"); -c$.sortedItem = Clazz.defineMethod (c$, "sortedItem", -function (v, n) { -if (v.size () == 0) return null; -if (v.size () == 1) return v.get (0); -var keys = v.toArray ( new Array (v.size ())); -java.util.Arrays.sort (keys); -return keys[n % keys.length]; -}, "javajs.util.Lst,~N"); -c$.createArrayOfArrayList = Clazz.defineMethod (c$, "createArrayOfArrayList", -function (size) { -return new Array (size); -}, "~N"); -c$.createArrayOfHashtable = Clazz.defineMethod (c$, "createArrayOfHashtable", -function (size) { -return new Array (size); -}, "~N"); -c$.swap = Clazz.defineMethod (c$, "swap", -function (o, i, j) { -var oi = o[i]; -o[i] = o[j]; -o[j] = oi; -}, "~A,~N,~N"); -c$.newFloat2 = Clazz.defineMethod (c$, "newFloat2", -function (n) { -{ -return Clazz.newArray(n, null); -}}, "~N"); -c$.newInt2 = Clazz.defineMethod (c$, "newInt2", -function (n) { -{ -return Clazz.newArray(n, null); -}}, "~N"); -c$.newInt3 = Clazz.defineMethod (c$, "newInt3", -function (nx, ny) { -{ -return Clazz.newArray(nx, null); -}}, "~N,~N"); -c$.newFloat3 = Clazz.defineMethod (c$, "newFloat3", -function (nx, ny) { -{ -return Clazz.newArray(nx, null); -}}, "~N,~N"); -c$.newInt4 = Clazz.defineMethod (c$, "newInt4", -function (n) { -{ -return Clazz.newArray(n, null); -}}, "~N"); -c$.newShort2 = Clazz.defineMethod (c$, "newShort2", -function (n) { -{ -return Clazz.newArray(n, null); -}}, "~N"); -c$.newByte2 = Clazz.defineMethod (c$, "newByte2", -function (n) { -{ -return Clazz.newArray(n, null); -}}, "~N"); -c$.newDouble2 = Clazz.defineMethod (c$, "newDouble2", -function (n) { -{ -return Clazz.newArray(n, null); -}}, "~N"); -c$.removeMapKeys = Clazz.defineMethod (c$, "removeMapKeys", -function (map, root) { -var list = new javajs.util.Lst (); -for (var key, $key = map.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) if (key.startsWith (root)) list.addLast (key); - -for (var i = list.size (); --i >= 0; ) map.remove (list.get (i)); - -return list.size (); -}, "java.util.Map,~S"); -c$.isAS = Clazz.defineMethod (c$, "isAS", -function (x) { -{ -return Clazz.isAS(x); -}}, "~O"); -c$.isASS = Clazz.defineMethod (c$, "isASS", -function (x) { -{ -return Clazz.isASS(x); -}}, "~O"); -c$.isAP = Clazz.defineMethod (c$, "isAP", -function (x) { -{ -return Clazz.isAP(x); -}}, "~O"); -c$.isAF = Clazz.defineMethod (c$, "isAF", -function (x) { -{ -return Clazz.isAF(x); -}}, "~O"); -c$.isAFloat = Clazz.defineMethod (c$, "isAFloat", -function (x) { -{ -return Clazz.isAFloat(x); -}}, "~O"); -c$.isAD = Clazz.defineMethod (c$, "isAD", -function (x) { -{ -return Clazz.isAF(x); -}}, "~O"); -c$.isADD = Clazz.defineMethod (c$, "isADD", -function (x) { -{ -return Clazz.isAFF(x); -}}, "~O"); -c$.isAB = Clazz.defineMethod (c$, "isAB", -function (x) { -{ -return Clazz.isAI(x); -}}, "~O"); -c$.isAI = Clazz.defineMethod (c$, "isAI", -function (x) { -{ -return Clazz.isAI(x); -}}, "~O"); -c$.isAII = Clazz.defineMethod (c$, "isAII", -function (x) { -{ -return Clazz.isAII(x); -}}, "~O"); -c$.isAFF = Clazz.defineMethod (c$, "isAFF", -function (x) { -{ -return Clazz.isAFF(x); -}}, "~O"); -c$.isAFFF = Clazz.defineMethod (c$, "isAFFF", -function (x) { -{ -return Clazz.isAFFF(x); -}}, "~O"); -c$.ensureSignedBytes = Clazz.defineMethod (c$, "ensureSignedBytes", -function (b) { -{ -for (var i = b.length; --i >= 0;) { -var j = b[i] & 0xFF; -if (j >= 0x80) j -= 0x100; -b[i] = j; -} -}}, "~A"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.AU", ["java.util.Arrays", "javajs.util.Lst"], function () { +c$ = Clazz.declareType (javajs.util, "AU"); +c$.ensureLength = Clazz.defineMethod (c$, "ensureLength", +function (array, minimumLength) { +if (array != null && javajs.util.AU.getLength (array) >= minimumLength) return array; +return javajs.util.AU.arrayCopyObject (array, minimumLength); +}, "~O,~N"); +c$.ensureLengthS = Clazz.defineMethod (c$, "ensureLengthS", +function (array, minimumLength) { +if (array != null && array.length >= minimumLength) return array; +return javajs.util.AU.arrayCopyS (array, minimumLength); +}, "~A,~N"); +c$.ensureLengthA = Clazz.defineMethod (c$, "ensureLengthA", +function (array, minimumLength) { +if (array != null && array.length >= minimumLength) return array; +return javajs.util.AU.arrayCopyF (array, minimumLength); +}, "~A,~N"); +c$.ensureLengthI = Clazz.defineMethod (c$, "ensureLengthI", +function (array, minimumLength) { +if (array != null && array.length >= minimumLength) return array; +return javajs.util.AU.arrayCopyI (array, minimumLength); +}, "~A,~N"); +c$.ensureLengthShort = Clazz.defineMethod (c$, "ensureLengthShort", +function (array, minimumLength) { +if (array != null && array.length >= minimumLength) return array; +return javajs.util.AU.arrayCopyShort (array, minimumLength); +}, "~A,~N"); +c$.ensureLengthByte = Clazz.defineMethod (c$, "ensureLengthByte", +function (array, minimumLength) { +if (array != null && array.length >= minimumLength) return array; +return javajs.util.AU.arrayCopyByte (array, minimumLength); +}, "~A,~N"); +c$.doubleLength = Clazz.defineMethod (c$, "doubleLength", +function (array) { +return javajs.util.AU.arrayCopyObject (array, (array == null ? 16 : 2 * javajs.util.AU.getLength (array))); +}, "~O"); +c$.doubleLengthS = Clazz.defineMethod (c$, "doubleLengthS", +function (array) { +return javajs.util.AU.arrayCopyS (array, (array == null ? 16 : 2 * array.length)); +}, "~A"); +c$.doubleLengthF = Clazz.defineMethod (c$, "doubleLengthF", +function (array) { +return javajs.util.AU.arrayCopyF (array, (array == null ? 16 : 2 * array.length)); +}, "~A"); +c$.doubleLengthI = Clazz.defineMethod (c$, "doubleLengthI", +function (array) { +return javajs.util.AU.arrayCopyI (array, (array == null ? 16 : 2 * array.length)); +}, "~A"); +c$.doubleLengthShort = Clazz.defineMethod (c$, "doubleLengthShort", +function (array) { +return javajs.util.AU.arrayCopyShort (array, (array == null ? 16 : 2 * array.length)); +}, "~A"); +c$.doubleLengthByte = Clazz.defineMethod (c$, "doubleLengthByte", +function (array) { +return javajs.util.AU.arrayCopyByte (array, (array == null ? 16 : 2 * array.length)); +}, "~A"); +c$.doubleLengthBool = Clazz.defineMethod (c$, "doubleLengthBool", +function (array) { +return javajs.util.AU.arrayCopyBool (array, (array == null ? 16 : 2 * array.length)); +}, "~A"); +c$.deleteElements = Clazz.defineMethod (c$, "deleteElements", +function (array, firstElement, nElements) { +if (nElements == 0 || array == null) return array; +var oldLength = javajs.util.AU.getLength (array); +if (firstElement >= oldLength) return array; +var n = oldLength - (firstElement + nElements); +if (n < 0) n = 0; +var t = javajs.util.AU.newInstanceO (array, firstElement + n); +if (firstElement > 0) System.arraycopy (array, 0, t, 0, firstElement); +if (n > 0) System.arraycopy (array, firstElement + nElements, t, firstElement, n); +return t; +}, "~O,~N,~N"); +c$.arrayCopyObject = Clazz.defineMethod (c$, "arrayCopyObject", +function (array, newLength) { +if (array == null) { +return null; +}var oldLength = javajs.util.AU.getLength (array); +if (newLength == oldLength) return array; +var t = javajs.util.AU.newInstanceO (array, newLength); +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +return t; +}, "~O,~N"); +c$.newInstanceO = Clazz.defineMethod (c$, "newInstanceO", +($fz = function (array, n) { +{ +if (!array.getClass().getComponentType) +return new Array(n); +}}, $fz.isPrivate = true, $fz), "~O,~N"); +c$.getLength = Clazz.defineMethod (c$, "getLength", +function (array) { +{ +return array.length +}}, "~O"); +c$.arrayCopyS = Clazz.defineMethod (c$, "arrayCopyS", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = new Array (newLength); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyII = Clazz.defineMethod (c$, "arrayCopyII", +function (array, newLength) { +var t = javajs.util.AU.newInt2 (newLength); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyPt = Clazz.defineMethod (c$, "arrayCopyPt", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = new Array (newLength); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyF = Clazz.defineMethod (c$, "arrayCopyF", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = Clazz.newFloatArray (newLength, 0); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyI = Clazz.defineMethod (c$, "arrayCopyI", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = Clazz.newIntArray (newLength, 0); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyRangeI = Clazz.defineMethod (c$, "arrayCopyRangeI", +function (array, i0, n) { +if (array == null) return null; +var oldLength = array.length; +if (n == -1) n = oldLength; +if (n == -2) n = Clazz.doubleToInt (oldLength / 2); +n = n - i0; +var t = Clazz.newIntArray (n, 0); +System.arraycopy (array, i0, t, 0, n); +return t; +}, "~A,~N,~N"); +c$.arrayCopyRangeRevI = Clazz.defineMethod (c$, "arrayCopyRangeRevI", +function (array, i0, n) { +if (array == null) return null; +var t = javajs.util.AU.arrayCopyRangeI (array, i0, n); +if (n < 0) n = array.length; +for (var i = Clazz.doubleToInt (n / 2); --i >= 0; ) javajs.util.AU.swapInt (t, i, n - 1 - i); + +return t; +}, "~A,~N,~N"); +c$.arrayCopyShort = Clazz.defineMethod (c$, "arrayCopyShort", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = Clazz.newShortArray (newLength, 0); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyByte = Clazz.defineMethod (c$, "arrayCopyByte", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = Clazz.newByteArray (newLength, 0); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.arrayCopyBool = Clazz.defineMethod (c$, "arrayCopyBool", +function (array, newLength) { +if (newLength < 0) newLength = array.length; +var t = Clazz.newBooleanArray (newLength, false); +if (array != null) { +var oldLength = array.length; +System.arraycopy (array, 0, t, 0, oldLength < newLength ? oldLength : newLength); +}return t; +}, "~A,~N"); +c$.swapInt = Clazz.defineMethod (c$, "swapInt", +function (array, indexA, indexB) { +var t = array[indexA]; +array[indexA] = array[indexB]; +array[indexB] = t; +}, "~A,~N,~N"); +c$.dumpArray = Clazz.defineMethod (c$, "dumpArray", +function (msg, A, x1, x2, y1, y2) { +var s = "dumpArray: " + msg + "\n"; +for (var x = x1; x <= x2; x++) s += "\t*" + x + "*"; + +for (var y = y2; y >= y1; y--) { +s += "\n*" + y + "*"; +for (var x = x1; x <= x2; x++) s += "\t" + (x < A.length && y < A[x].length ? A[x][y] : NaN); + +} +return s; +}, "~S,~A,~N,~N,~N,~N"); +c$.dumpIntArray = Clazz.defineMethod (c$, "dumpIntArray", +function (A, n) { +var str = ""; +for (var i = 0; i < n; i++) str += " " + A[i]; + +return str; +}, "~A,~N"); +c$.sortedItem = Clazz.defineMethod (c$, "sortedItem", +function (v, n) { +if (v.size () == 0) return null; +if (v.size () == 1) return v.get (0); +var keys = v.toArray ( new Array (v.size ())); +java.util.Arrays.sort (keys); +return keys[n % keys.length]; +}, "javajs.util.Lst,~N"); +c$.createArrayOfArrayList = Clazz.defineMethod (c$, "createArrayOfArrayList", +function (size) { +return new Array (size); +}, "~N"); +c$.createArrayOfHashtable = Clazz.defineMethod (c$, "createArrayOfHashtable", +function (size) { +return new Array (size); +}, "~N"); +c$.swap = Clazz.defineMethod (c$, "swap", +function (o, i, j) { +var oi = o[i]; +o[i] = o[j]; +o[j] = oi; +}, "~A,~N,~N"); +c$.newFloat2 = Clazz.defineMethod (c$, "newFloat2", +function (n) { +{ +return Clazz.newArray(n, null); +}}, "~N"); +c$.newInt2 = Clazz.defineMethod (c$, "newInt2", +function (n) { +{ +return Clazz.newArray(n, null); +}}, "~N"); +c$.newInt3 = Clazz.defineMethod (c$, "newInt3", +function (nx, ny) { +{ +return Clazz.newArray(nx, null); +}}, "~N,~N"); +c$.newFloat3 = Clazz.defineMethod (c$, "newFloat3", +function (nx, ny) { +{ +return Clazz.newArray(nx, null); +}}, "~N,~N"); +c$.newInt4 = Clazz.defineMethod (c$, "newInt4", +function (n) { +{ +return Clazz.newArray(n, null); +}}, "~N"); +c$.newShort2 = Clazz.defineMethod (c$, "newShort2", +function (n) { +{ +return Clazz.newArray(n, null); +}}, "~N"); +c$.newByte2 = Clazz.defineMethod (c$, "newByte2", +function (n) { +{ +return Clazz.newArray(n, null); +}}, "~N"); +c$.newDouble2 = Clazz.defineMethod (c$, "newDouble2", +function (n) { +{ +return Clazz.newArray(n, null); +}}, "~N"); +c$.removeMapKeys = Clazz.defineMethod (c$, "removeMapKeys", +function (map, root) { +var list = new javajs.util.Lst (); +for (var key, $key = map.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) if (key.startsWith (root)) list.addLast (key); + +for (var i = list.size (); --i >= 0; ) map.remove (list.get (i)); + +return list.size (); +}, "java.util.Map,~S"); +c$.isAS = Clazz.defineMethod (c$, "isAS", +function (x) { +{ +return Clazz.isAS(x); +}}, "~O"); +c$.isASS = Clazz.defineMethod (c$, "isASS", +function (x) { +{ +return Clazz.isASS(x); +}}, "~O"); +c$.isAP = Clazz.defineMethod (c$, "isAP", +function (x) { +{ +return Clazz.isAP(x); +}}, "~O"); +c$.isAF = Clazz.defineMethod (c$, "isAF", +function (x) { +{ +return Clazz.isAF(x); +}}, "~O"); +c$.isAFloat = Clazz.defineMethod (c$, "isAFloat", +function (x) { +{ +return Clazz.isAFloat(x); +}}, "~O"); +c$.isAD = Clazz.defineMethod (c$, "isAD", +function (x) { +{ +return Clazz.isAF(x); +}}, "~O"); +c$.isADD = Clazz.defineMethod (c$, "isADD", +function (x) { +{ +return Clazz.isAFF(x); +}}, "~O"); +c$.isAB = Clazz.defineMethod (c$, "isAB", +function (x) { +{ +return Clazz.isAI(x); +}}, "~O"); +c$.isAI = Clazz.defineMethod (c$, "isAI", +function (x) { +{ +return Clazz.isAI(x); +}}, "~O"); +c$.isAII = Clazz.defineMethod (c$, "isAII", +function (x) { +{ +return Clazz.isAII(x); +}}, "~O"); +c$.isAFF = Clazz.defineMethod (c$, "isAFF", +function (x) { +{ +return Clazz.isAFF(x); +}}, "~O"); +c$.isAFFF = Clazz.defineMethod (c$, "isAFFF", +function (x) { +{ +return Clazz.isAFFF(x); +}}, "~O"); +c$.ensureSignedBytes = Clazz.defineMethod (c$, "ensureSignedBytes", +function (b) { +{ +for (var i = b.length; --i >= 0;) { +var j = b[i] & 0xFF; +if (j >= 0x80) j -= 0x100; +b[i] = j; +} +}}, "~A"); +}); diff --git a/bin/javajs/util/AjaxURLConnection.js b/bin/javajs/util/AjaxURLConnection.js index 41e35ef..50f227d 100644 --- a/bin/javajs/util/AjaxURLConnection.js +++ b/bin/javajs/util/AjaxURLConnection.js @@ -1,39 +1,39 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.net.URLConnection"], "javajs.util.AjaxURLConnection", ["javajs.util.AU", "$.Rdr", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.bytesOut = null; -this.postOut = ""; -Clazz.instantialize (this, arguments); -}, javajs.util, "AjaxURLConnection", java.net.URLConnection); -Clazz.defineMethod (c$, "doAjax", -($fz = function () { -var jmol = null; -{ -jmol = Jmol; -}return jmol._doAjax (this.url, this.postOut, this.bytesOut); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "connect", -function () { -}); -Clazz.defineMethod (c$, "outputBytes", -function (bytes) { -this.bytesOut = bytes; -}, "~A"); -Clazz.defineMethod (c$, "outputString", -function (post) { -this.postOut = post; -}, "~S"); -Clazz.overrideMethod (c$, "getInputStream", -function () { -var is = null; -var o = this.doAjax (); -if (javajs.util.AU.isAB (o)) is = javajs.util.Rdr.getBIS (o); - else if (Clazz.instanceOf (o, javajs.util.SB)) is = javajs.util.Rdr.getBIS (javajs.util.Rdr.getBytesFromSB (o)); - else if (Clazz.instanceOf (o, String)) is = javajs.util.Rdr.getBIS ((o).getBytes ()); -return is; -}); -Clazz.defineMethod (c$, "getContents", -function () { -return this.doAjax (); -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.net.URLConnection"], "javajs.util.AjaxURLConnection", ["javajs.util.AU", "$.Rdr", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.bytesOut = null; +this.postOut = ""; +Clazz.instantialize (this, arguments); +}, javajs.util, "AjaxURLConnection", java.net.URLConnection); +Clazz.defineMethod (c$, "doAjax", +($fz = function () { +var jmol = null; +{ +jmol = Jmol; +}return jmol._doAjax (this.url, this.postOut, this.bytesOut); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "connect", +function () { +}); +Clazz.defineMethod (c$, "outputBytes", +function (bytes) { +this.bytesOut = bytes; +}, "~A"); +Clazz.defineMethod (c$, "outputString", +function (post) { +this.postOut = post; +}, "~S"); +Clazz.overrideMethod (c$, "getInputStream", +function () { +var is = null; +var o = this.doAjax (); +if (javajs.util.AU.isAB (o)) is = javajs.util.Rdr.getBIS (o); + else if (Clazz.instanceOf (o, javajs.util.SB)) is = javajs.util.Rdr.getBIS (javajs.util.Rdr.getBytesFromSB (o)); + else if (Clazz.instanceOf (o, String)) is = javajs.util.Rdr.getBIS ((o).getBytes ()); +return is; +}); +Clazz.defineMethod (c$, "getContents", +function () { +return this.doAjax (); +}); +}); diff --git a/bin/javajs/util/AjaxURLStreamHandler.js b/bin/javajs/util/AjaxURLStreamHandler.js index 600c417..59628d6 100644 --- a/bin/javajs/util/AjaxURLStreamHandler.js +++ b/bin/javajs/util/AjaxURLStreamHandler.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.net.URLStreamHandler"], "javajs.util.AjaxURLStreamHandler", ["javajs.util.AjaxURLConnection", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.protocol = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "AjaxURLStreamHandler", java.net.URLStreamHandler); -Clazz.makeConstructor (c$, -function (protocol) { -Clazz.superConstructor (this, javajs.util.AjaxURLStreamHandler, []); -this.protocol = protocol; -}, "~S"); -Clazz.defineMethod (c$, "openConnection", -function (url) { -return new javajs.util.AjaxURLConnection (url); -}, "java.net.URL"); -Clazz.overrideMethod (c$, "toExternalForm", -function (u) { -var result = new javajs.util.SB (); -result.append (u.getProtocol ()); -result.append (":"); -if (u.getAuthority () != null && u.getAuthority ().length > 0) { -result.append ("//"); -result.append (u.getAuthority ()); -}if (u.getPath () != null) { -result.append (u.getPath ()); -}if (u.getQuery () != null) { -result.append ("?"); -result.append (u.getQuery ()); -}if (u.getRef () != null) { -result.append ("#"); -result.append (u.getRef ()); -}return result.toString (); -}, "java.net.URL"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.net.URLStreamHandler"], "javajs.util.AjaxURLStreamHandler", ["javajs.util.AjaxURLConnection", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.protocol = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "AjaxURLStreamHandler", java.net.URLStreamHandler); +Clazz.makeConstructor (c$, +function (protocol) { +Clazz.superConstructor (this, javajs.util.AjaxURLStreamHandler, []); +this.protocol = protocol; +}, "~S"); +Clazz.defineMethod (c$, "openConnection", +function (url) { +return new javajs.util.AjaxURLConnection (url); +}, "java.net.URL"); +Clazz.overrideMethod (c$, "toExternalForm", +function (u) { +var result = new javajs.util.SB (); +result.append (u.getProtocol ()); +result.append (":"); +if (u.getAuthority () != null && u.getAuthority ().length > 0) { +result.append ("//"); +result.append (u.getAuthority ()); +}if (u.getPath () != null) { +result.append (u.getPath ()); +}if (u.getQuery () != null) { +result.append ("?"); +result.append (u.getQuery ()); +}if (u.getRef () != null) { +result.append ("#"); +result.append (u.getRef ()); +}return result.toString (); +}, "java.net.URL"); +}); diff --git a/bin/javajs/util/AjaxURLStreamHandlerFactory.js b/bin/javajs/util/AjaxURLStreamHandlerFactory.js index 88452ce..e51bb4e 100644 --- a/bin/javajs/util/AjaxURLStreamHandlerFactory.js +++ b/bin/javajs/util/AjaxURLStreamHandlerFactory.js @@ -1,16 +1,16 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.net.URLStreamHandlerFactory", "java.util.Hashtable"], "javajs.util.AjaxURLStreamHandlerFactory", ["javajs.util.AjaxURLStreamHandler"], function () { -c$ = Clazz.decorateAsClass (function () { -this.htFactories = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "AjaxURLStreamHandlerFactory", null, java.net.URLStreamHandlerFactory); -Clazz.prepareFields (c$, function () { -this.htFactories = new java.util.Hashtable (); -}); -Clazz.overrideMethod (c$, "createURLStreamHandler", -function (protocol) { -var fac = this.htFactories.get (protocol); -if (fac == null) this.htFactories.put (protocol, fac = new javajs.util.AjaxURLStreamHandler (protocol)); -return (fac.protocol == null ? null : fac); -}, "~S"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.net.URLStreamHandlerFactory", "java.util.Hashtable"], "javajs.util.AjaxURLStreamHandlerFactory", ["javajs.util.AjaxURLStreamHandler"], function () { +c$ = Clazz.decorateAsClass (function () { +this.htFactories = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "AjaxURLStreamHandlerFactory", null, java.net.URLStreamHandlerFactory); +Clazz.prepareFields (c$, function () { +this.htFactories = new java.util.Hashtable (); +}); +Clazz.overrideMethod (c$, "createURLStreamHandler", +function (protocol) { +var fac = this.htFactories.get (protocol); +if (fac == null) this.htFactories.put (protocol, fac = new javajs.util.AjaxURLStreamHandler (protocol)); +return (fac.protocol == null ? null : fac); +}, "~S"); +}); diff --git a/bin/javajs/util/ArrayDataReader.js b/bin/javajs/util/ArrayDataReader.js index 89f64c3..532e8a9 100644 --- a/bin/javajs/util/ArrayDataReader.js +++ b/bin/javajs/util/ArrayDataReader.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.DataReader"], "javajs.util.ArrayDataReader", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.data = null; -this.pt = 0; -this.len = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "ArrayDataReader", javajs.util.DataReader); -Clazz.overrideMethod (c$, "setData", -function (data) { -this.data = data; -this.len = this.data.length; -return this; -}, "~O"); -Clazz.defineMethod (c$, "read", -function (buf, off, len) { -return this.readBuf (buf, off, len); -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "readLine", -function () { -return (this.pt < this.len ? this.data[this.pt++] : null); -}); -Clazz.defineMethod (c$, "mark", -function (ptr) { -this.ptMark = this.pt; -}, "~N"); -Clazz.overrideMethod (c$, "reset", -function () { -this.pt = this.ptMark; -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.DataReader"], "javajs.util.ArrayDataReader", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.data = null; +this.pt = 0; +this.len = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "ArrayDataReader", javajs.util.DataReader); +Clazz.overrideMethod (c$, "setData", +function (data) { +this.data = data; +this.len = this.data.length; +return this; +}, "~O"); +Clazz.defineMethod (c$, "read", +function (buf, off, len) { +return this.readBuf (buf, off, len); +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "readLine", +function () { +return (this.pt < this.len ? this.data[this.pt++] : null); +}); +Clazz.defineMethod (c$, "mark", +function (ptr) { +this.ptMark = this.pt; +}, "~N"); +Clazz.overrideMethod (c$, "reset", +function () { +this.pt = this.ptMark; +}); +}); diff --git a/bin/javajs/util/BArray.js b/bin/javajs/util/BArray.js index 33ba55d..866e432 100644 --- a/bin/javajs/util/BArray.js +++ b/bin/javajs/util/BArray.js @@ -1,27 +1,27 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.data = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "BArray"); -Clazz.makeConstructor (c$, -function (data) { -this.data = data; -}, "~A"); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (Clazz.instanceOf (o, javajs.util.BArray)) { -var d = (o).data; -if (d.length == this.data.length) { -for (var i = 0; i < d.length; i++) if (d[i] != this.data[i]) return false; - -return true; -}}return false; -}, "~O"); -Clazz.defineMethod (c$, "hashCode", -function () { -return this.data.hashCode (); -}); -Clazz.overrideMethod (c$, "toString", -function () { -return String.instantialize (this.data); -}); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.data = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "BArray"); +Clazz.makeConstructor (c$, +function (data) { +this.data = data; +}, "~A"); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (Clazz.instanceOf (o, javajs.util.BArray)) { +var d = (o).data; +if (d.length == this.data.length) { +for (var i = 0; i < d.length; i++) if (d[i] != this.data[i]) return false; + +return true; +}}return false; +}, "~O"); +Clazz.defineMethod (c$, "hashCode", +function () { +return this.data.hashCode (); +}); +Clazz.overrideMethod (c$, "toString", +function () { +return String.instantialize (this.data); +}); diff --git a/bin/javajs/util/BC.js b/bin/javajs/util/BC.js index ec20ff4..cc5ed5a 100644 --- a/bin/javajs/util/BC.js +++ b/bin/javajs/util/BC.js @@ -1,65 +1,65 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.declareType (javajs.util, "BC"); -Clazz.makeConstructor (c$, -function () { -}); -c$.bytesToFloat = Clazz.defineMethod (c$, "bytesToFloat", -function (bytes, j, isBigEndian) { -return javajs.util.BC.intToFloat (javajs.util.BC.bytesToInt (bytes, j, isBigEndian)); -}, "~A,~N,~B"); -c$.bytesToInt = Clazz.defineMethod (c$, "bytesToInt", -function (bytes, j, isBigEndian) { -var n = (isBigEndian ? (bytes[j + 3] & 0xff) | (bytes[j + 2] & 0xff) << 8 | (bytes[j + 1] & 0xff) << 16 | (bytes[j] & 0xff) << 24 : (bytes[j++] & 0xff) | (bytes[j++] & 0xff) << 8 | (bytes[j++] & 0xff) << 16 | (bytes[j++] & 0xff) << 24); -{ -return (n > 0x7FFFFFFF ? n - 0x100000000 : n); -}}, "~A,~N,~B"); -c$.intToFloat = Clazz.defineMethod (c$, "intToFloat", -function (x) { -{ -if (x == 0) return 0; -var o = javajs.util.BC; -if (o.fracIEEE == null) -o.setFracIEEE(); -var m = ((x & 0x7F800000) >> 23); -return ((x & 0x80000000) == 0 ? 1 : -1) * o.shiftIEEE((x & 0x7FFFFF) | 0x800000, m - 149); -}}, "~N"); -c$.bytesToDoubleToFloat = Clazz.defineMethod (c$, "bytesToDoubleToFloat", -function (bytes, j, isBigEndian) { -{ -if (javajs.util.BC.fracIEEE == null) javajs.util.BC.setFracIEEE (); -{ -var o = javajs.util.BC; -var b1, b2, b3, b4, b5; -if (isBigEndian) { -b1 = bytes[j] & 0xFF; -b2 = bytes[j + 1] & 0xFF; -b3 = bytes[j + 2] & 0xFF; -b4 = bytes[j + 3] & 0xFF; -b5 = bytes[j + 4] & 0xFF; -} else { -b1 = bytes[j + 7] & 0xFF; -b2 = bytes[j + 6] & 0xFF; -b3 = bytes[j + 5] & 0xFF; -b4 = bytes[j + 4] & 0xFF; -b5 = bytes[j + 3] & 0xFF; -} -var s = ((b1 & 0x80) == 0 ? 1 : -1); -var e = (((b1 & 0x7F) << 4) | (b2 >> 4)) - 1026; -b2 = (b2 & 0xF) | 0x10; -return s * (o.shiftIEEE(b2, e) + o.shiftIEEE(b3, e - 8) + o.shiftIEEE(b4, e - 16) -+ o.shiftIEEE(b5, e - 24)); -}}}, "~A,~N,~B"); -c$.setFracIEEE = Clazz.defineMethod (c$, "setFracIEEE", -($fz = function () { -javajs.util.BC.fracIEEE = Clazz.newFloatArray (270, 0); -for (var i = 0; i < 270; i++) javajs.util.BC.fracIEEE[i] = Math.pow (2, i - 141); - -}, $fz.isPrivate = true, $fz)); -c$.shiftIEEE = Clazz.defineMethod (c$, "shiftIEEE", -function (f, i) { -if (f == 0 || i < -140) return 0; -if (i > 128) return 3.4028235E38; -return f * javajs.util.BC.fracIEEE[i + 140]; -}, "~N,~N"); -Clazz.defineStatics (c$, -"fracIEEE", null); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.declareType (javajs.util, "BC"); +Clazz.makeConstructor (c$, +function () { +}); +c$.bytesToFloat = Clazz.defineMethod (c$, "bytesToFloat", +function (bytes, j, isBigEndian) { +return javajs.util.BC.intToFloat (javajs.util.BC.bytesToInt (bytes, j, isBigEndian)); +}, "~A,~N,~B"); +c$.bytesToInt = Clazz.defineMethod (c$, "bytesToInt", +function (bytes, j, isBigEndian) { +var n = (isBigEndian ? (bytes[j + 3] & 0xff) | (bytes[j + 2] & 0xff) << 8 | (bytes[j + 1] & 0xff) << 16 | (bytes[j] & 0xff) << 24 : (bytes[j++] & 0xff) | (bytes[j++] & 0xff) << 8 | (bytes[j++] & 0xff) << 16 | (bytes[j++] & 0xff) << 24); +{ +return (n > 0x7FFFFFFF ? n - 0x100000000 : n); +}}, "~A,~N,~B"); +c$.intToFloat = Clazz.defineMethod (c$, "intToFloat", +function (x) { +{ +if (x == 0) return 0; +var o = javajs.util.BC; +if (o.fracIEEE == null) +o.setFracIEEE(); +var m = ((x & 0x7F800000) >> 23); +return ((x & 0x80000000) == 0 ? 1 : -1) * o.shiftIEEE((x & 0x7FFFFF) | 0x800000, m - 149); +}}, "~N"); +c$.bytesToDoubleToFloat = Clazz.defineMethod (c$, "bytesToDoubleToFloat", +function (bytes, j, isBigEndian) { +{ +if (javajs.util.BC.fracIEEE == null) javajs.util.BC.setFracIEEE (); +{ +var o = javajs.util.BC; +var b1, b2, b3, b4, b5; +if (isBigEndian) { +b1 = bytes[j] & 0xFF; +b2 = bytes[j + 1] & 0xFF; +b3 = bytes[j + 2] & 0xFF; +b4 = bytes[j + 3] & 0xFF; +b5 = bytes[j + 4] & 0xFF; +} else { +b1 = bytes[j + 7] & 0xFF; +b2 = bytes[j + 6] & 0xFF; +b3 = bytes[j + 5] & 0xFF; +b4 = bytes[j + 4] & 0xFF; +b5 = bytes[j + 3] & 0xFF; +} +var s = ((b1 & 0x80) == 0 ? 1 : -1); +var e = (((b1 & 0x7F) << 4) | (b2 >> 4)) - 1026; +b2 = (b2 & 0xF) | 0x10; +return s * (o.shiftIEEE(b2, e) + o.shiftIEEE(b3, e - 8) + o.shiftIEEE(b4, e - 16) ++ o.shiftIEEE(b5, e - 24)); +}}}, "~A,~N,~B"); +c$.setFracIEEE = Clazz.defineMethod (c$, "setFracIEEE", +($fz = function () { +javajs.util.BC.fracIEEE = Clazz.newFloatArray (270, 0); +for (var i = 0; i < 270; i++) javajs.util.BC.fracIEEE[i] = Math.pow (2, i - 141); + +}, $fz.isPrivate = true, $fz)); +c$.shiftIEEE = Clazz.defineMethod (c$, "shiftIEEE", +function (f, i) { +if (f == 0 || i < -140) return 0; +if (i > 128) return 3.4028235E38; +return f * javajs.util.BC.fracIEEE[i + 140]; +}, "~N,~N"); +Clazz.defineStatics (c$, +"fracIEEE", null); diff --git a/bin/javajs/util/BS.js b/bin/javajs/util/BS.js index bc34911..5677631 100644 --- a/bin/javajs/util/BS.js +++ b/bin/javajs/util/BS.js @@ -1,357 +1,357 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.JSONEncodable"], "javajs.util.BS", ["java.lang.IndexOutOfBoundsException", "$.NegativeArraySizeException", "javajs.util.PT", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.words = null; -this.wordsInUse = 0; -this.sizeIsSticky = false; -Clazz.instantialize (this, arguments); -}, javajs.util, "BS", null, [Cloneable, javajs.api.JSONEncodable]); -c$.wordIndex = Clazz.defineMethod (c$, "wordIndex", -($fz = function (bitIndex) { -return bitIndex >> 5; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "recalculateWordsInUse", -($fz = function () { -var i; -for (i = this.wordsInUse - 1; i >= 0; i--) if (this.words[i] != 0) break; - -this.wordsInUse = i + 1; -}, $fz.isPrivate = true, $fz)); -Clazz.makeConstructor (c$, -function () { -this.initWords (32); -this.sizeIsSticky = false; -}); -c$.newN = Clazz.defineMethod (c$, "newN", -function (nbits) { -var bs = new javajs.util.BS (); -bs.init (nbits); -return bs; -}, "~N"); -Clazz.defineMethod (c$, "init", -($fz = function (nbits) { -if (nbits < 0) throw new NegativeArraySizeException ("nbits < 0: " + nbits); -this.initWords (nbits); -this.sizeIsSticky = true; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "initWords", -($fz = function (nbits) { -this.words = Clazz.newIntArray (javajs.util.BS.wordIndex (nbits - 1) + 1, 0); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "ensureCapacity", -($fz = function (wordsRequired) { -if (this.words.length < wordsRequired) { -var request = Math.max (2 * this.words.length, wordsRequired); -this.setLength (request); -this.sizeIsSticky = false; -}}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "expandTo", -($fz = function (wordIndex) { -var wordsRequired = wordIndex + 1; -if (this.wordsInUse < wordsRequired) { -this.ensureCapacity (wordsRequired); -this.wordsInUse = wordsRequired; -}}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "set", -function (bitIndex) { -if (bitIndex < 0) throw new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex); -var wordIndex = javajs.util.BS.wordIndex (bitIndex); -this.expandTo (wordIndex); -this.words[wordIndex] |= (1 << bitIndex); -}, "~N"); -Clazz.defineMethod (c$, "setBitTo", -function (bitIndex, value) { -if (value) this.set (bitIndex); - else this.clear (bitIndex); -}, "~N,~B"); -Clazz.defineMethod (c$, "setBits", -function (fromIndex, toIndex) { -if (fromIndex == toIndex) return; -var startWordIndex = javajs.util.BS.wordIndex (fromIndex); -var endWordIndex = javajs.util.BS.wordIndex (toIndex - 1); -this.expandTo (endWordIndex); -var firstWordMask = -1 << fromIndex; -var lastWordMask = -1 >>> -toIndex; -if (startWordIndex == endWordIndex) { -this.words[startWordIndex] |= (firstWordMask & lastWordMask); -} else { -this.words[startWordIndex] |= firstWordMask; -for (var i = startWordIndex + 1; i < endWordIndex; i++) this.words[i] = -1; - -this.words[endWordIndex] |= lastWordMask; -}}, "~N,~N"); -Clazz.defineMethod (c$, "clear", -function (bitIndex) { -if (bitIndex < 0) throw new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex); -var wordIndex = javajs.util.BS.wordIndex (bitIndex); -if (wordIndex >= this.wordsInUse) return; -this.words[wordIndex] &= ~(1 << bitIndex); -this.recalculateWordsInUse (); -}, "~N"); -Clazz.defineMethod (c$, "clearBits", -function (fromIndex, toIndex) { -if (fromIndex == toIndex) return; -var startWordIndex = javajs.util.BS.wordIndex (fromIndex); -if (startWordIndex >= this.wordsInUse) return; -var endWordIndex = javajs.util.BS.wordIndex (toIndex - 1); -if (endWordIndex >= this.wordsInUse) { -toIndex = this.length (); -endWordIndex = this.wordsInUse - 1; -}var firstWordMask = -1 << fromIndex; -var lastWordMask = -1 >>> -toIndex; -if (startWordIndex == endWordIndex) { -this.words[startWordIndex] &= ~(firstWordMask & lastWordMask); -} else { -this.words[startWordIndex] &= ~firstWordMask; -for (var i = startWordIndex + 1; i < endWordIndex; i++) this.words[i] = 0; - -this.words[endWordIndex] &= ~lastWordMask; -}this.recalculateWordsInUse (); -}, "~N,~N"); -Clazz.defineMethod (c$, "clearAll", -function () { -while (this.wordsInUse > 0) this.words[--this.wordsInUse] = 0; - -}); -Clazz.defineMethod (c$, "get", -function (bitIndex) { -if (bitIndex < 0) throw new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex); -var wordIndex = javajs.util.BS.wordIndex (bitIndex); -return (wordIndex < this.wordsInUse) && ((this.words[wordIndex] & (1 << bitIndex)) != 0); -}, "~N"); -Clazz.defineMethod (c$, "nextSetBit", -function (fromIndex) { -if (fromIndex < 0) throw new IndexOutOfBoundsException ("fromIndex < 0: " + fromIndex); -var u = javajs.util.BS.wordIndex (fromIndex); -if (u >= this.wordsInUse) return -1; -var word = this.words[u] & (-1 << fromIndex); -while (true) { -if (word != 0) return (u * 32) + Integer.numberOfTrailingZeros (word); -if (++u == this.wordsInUse) return -1; -word = this.words[u]; -} -}, "~N"); -Clazz.defineMethod (c$, "nextClearBit", -function (fromIndex) { -if (fromIndex < 0) throw new IndexOutOfBoundsException ("fromIndex < 0: " + fromIndex); -var u = javajs.util.BS.wordIndex (fromIndex); -if (u >= this.wordsInUse) return fromIndex; -var word = ~this.words[u] & (-1 << fromIndex); -while (true) { -if (word != 0) return (u * 32) + Integer.numberOfTrailingZeros (word); -if (++u == this.wordsInUse) return this.wordsInUse * 32; -word = ~this.words[u]; -} -}, "~N"); -Clazz.defineMethod (c$, "length", -function () { -if (this.wordsInUse == 0) return 0; -return 32 * (this.wordsInUse - 1) + (32 - Integer.numberOfLeadingZeros (this.words[this.wordsInUse - 1])); -}); -Clazz.defineMethod (c$, "isEmpty", -function () { -return this.wordsInUse == 0; -}); -Clazz.defineMethod (c$, "intersects", -function (set) { -for (var i = Math.min (this.wordsInUse, set.wordsInUse) - 1; i >= 0; i--) if ((this.words[i] & set.words[i]) != 0) return true; - -return false; -}, "javajs.util.BS"); -Clazz.defineMethod (c$, "cardinality", -function () { -var sum = 0; -for (var i = 0; i < this.wordsInUse; i++) sum += Integer.bitCount (this.words[i]); - -return sum; -}); -Clazz.defineMethod (c$, "and", -function (set) { -if (this === set) return; -while (this.wordsInUse > set.wordsInUse) this.words[--this.wordsInUse] = 0; - -for (var i = 0; i < this.wordsInUse; i++) this.words[i] &= set.words[i]; - -this.recalculateWordsInUse (); -}, "javajs.util.BS"); -Clazz.defineMethod (c$, "or", -function (set) { -if (this === set) return; -var wordsInCommon = Math.min (this.wordsInUse, set.wordsInUse); -if (this.wordsInUse < set.wordsInUse) { -this.ensureCapacity (set.wordsInUse); -this.wordsInUse = set.wordsInUse; -}for (var i = 0; i < wordsInCommon; i++) this.words[i] |= set.words[i]; - -if (wordsInCommon < set.wordsInUse) System.arraycopy (set.words, wordsInCommon, this.words, wordsInCommon, this.wordsInUse - wordsInCommon); -}, "javajs.util.BS"); -Clazz.defineMethod (c$, "xor", -function (set) { -var wordsInCommon = Math.min (this.wordsInUse, set.wordsInUse); -if (this.wordsInUse < set.wordsInUse) { -this.ensureCapacity (set.wordsInUse); -this.wordsInUse = set.wordsInUse; -}for (var i = 0; i < wordsInCommon; i++) this.words[i] ^= set.words[i]; - -if (wordsInCommon < set.wordsInUse) System.arraycopy (set.words, wordsInCommon, this.words, wordsInCommon, set.wordsInUse - wordsInCommon); -this.recalculateWordsInUse (); -}, "javajs.util.BS"); -Clazz.defineMethod (c$, "andNot", -function (set) { -for (var i = Math.min (this.wordsInUse, set.wordsInUse) - 1; i >= 0; i--) this.words[i] &= ~set.words[i]; - -this.recalculateWordsInUse (); -}, "javajs.util.BS"); -Clazz.overrideMethod (c$, "hashCode", -function () { -var h = 1234; -for (var i = this.wordsInUse; --i >= 0; ) h ^= this.words[i] * (i + 1); - -return ((h >> 32) ^ h); -}); -Clazz.defineMethod (c$, "size", -function () { -return this.words.length * 32; -}); -Clazz.overrideMethod (c$, "equals", -function (obj) { -if (!(Clazz.instanceOf (obj, javajs.util.BS))) return false; -if (this === obj) return true; -var set = obj; -if (this.wordsInUse != set.wordsInUse) return false; -for (var i = 0; i < this.wordsInUse; i++) if (this.words[i] != set.words[i]) return false; - -return true; -}, "~O"); -Clazz.overrideMethod (c$, "clone", -function () { -if (!this.sizeIsSticky && this.wordsInUse != this.words.length) this.setLength (this.wordsInUse); -return javajs.util.BS.copy (this); -}); -Clazz.defineMethod (c$, "setLength", -($fz = function (n) { -var a = Clazz.newIntArray (n, 0); -System.arraycopy (this.words, 0, a, 0, Math.min (this.wordsInUse, n)); -this.words = a; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.overrideMethod (c$, "toString", -function () { -return javajs.util.BS.escape (this, '{', '}'); -}); -c$.copy = Clazz.defineMethod (c$, "copy", -function (bitsetToCopy) { -var bs; -{ -bs = Clazz.clone(bitsetToCopy); -}var wordCount = bitsetToCopy.wordsInUse; -if (wordCount == 0) { -bs.words = javajs.util.BS.emptyBitmap; -} else { -bs.words = Clazz.newIntArray (bs.wordsInUse = wordCount, 0); -System.arraycopy (bitsetToCopy.words, 0, bs.words, 0, wordCount); -}return bs; -}, "javajs.util.BS"); -Clazz.defineMethod (c$, "cardinalityN", -function (max) { -var n = this.cardinality (); -for (var i = this.length (); --i >= max; ) if (this.get (i)) n--; - -return n; -}, "~N"); -Clazz.overrideMethod (c$, "toJSON", -function () { -var numBits = (this.wordsInUse > 128) ? this.cardinality () : this.wordsInUse * 32; -var b = javajs.util.SB.newN (6 * numBits + 2); -b.appendC ('['); -var i = this.nextSetBit (0); -if (i != -1) { -b.appendI (i); -for (i = this.nextSetBit (i + 1); i >= 0; i = this.nextSetBit (i + 1)) { -var endOfRun = this.nextClearBit (i); -do { -b.append (", ").appendI (i); -} while (++i < endOfRun); -} -}b.appendC (']'); -return b.toString (); -}); -c$.escape = Clazz.defineMethod (c$, "escape", -function (bs, chOpen, chClose) { -if (bs == null) return chOpen + "{}" + chClose; -var s = new javajs.util.SB (); -s.append (chOpen + "{"); -var imax = bs.length (); -var iLast = -1; -var iFirst = -2; -var i = -1; -while (++i <= imax) { -var isSet = bs.get (i); -if (i == imax || iLast >= 0 && !isSet) { -if (iLast >= 0 && iFirst != iLast) s.append ((iFirst == iLast - 1 ? " " : ":") + iLast); -if (i == imax) break; -iLast = -1; -}if (bs.get (i)) { -if (iLast < 0) { -s.append ((iFirst == -2 ? "" : " ") + i); -iFirst = i; -}iLast = i; -}} -s.append ("}").appendC (chClose); -return s.toString (); -}, "javajs.util.BS,~S,~S"); -c$.unescape = Clazz.defineMethod (c$, "unescape", -function (str) { -var ch; -var len; -if (str == null || (len = (str = str.trim ()).length) < 4 || str.equalsIgnoreCase ("({null})") || (ch = str.charAt (0)) != '(' && ch != '[' || str.charAt (len - 1) != (ch == '(' ? ')' : ']') || str.charAt (1) != '{' || str.indexOf ('}') != len - 2) return null; -len -= 2; -for (var i = len; --i >= 2; ) if (!javajs.util.PT.isDigit (ch = str.charAt (i)) && ch != ' ' && ch != '\t' && ch != ':') return null; - -var lastN = len; -while (javajs.util.PT.isDigit (str.charAt (--lastN))) { -} -if (++lastN == len) lastN = 0; - else try { -lastN = Integer.parseInt (str.substring (lastN, len)); -} catch (e) { -if (Clazz.exceptionOf (e, NumberFormatException)) { -return null; -} else { -throw e; -} -} -var bs = javajs.util.BS.newN (lastN); -lastN = -1; -var iPrev = -1; -var iThis = -2; -for (var i = 2; i <= len; i++) { -switch (ch = str.charAt (i)) { -case '\t': -case ' ': -case '}': -if (iThis < 0) break; -if (iThis < lastN) return null; -lastN = iThis; -if (iPrev < 0) iPrev = iThis; -bs.setBits (iPrev, iThis + 1); -iPrev = -1; -iThis = -2; -break; -case ':': -iPrev = lastN = iThis; -iThis = -2; -break; -default: -if (javajs.util.PT.isDigit (ch)) { -if (iThis < 0) iThis = 0; -iThis = (iThis * 10) + (ch.charCodeAt (0) - 48); -}} -} -return (iPrev >= 0 ? null : bs); -}, "~S"); -Clazz.defineStatics (c$, -"ADDRESS_BITS_PER_WORD", 5, -"BITS_PER_WORD", 32, -"WORD_MASK", 0xffffffff, -"emptyBitmap", Clazz.newIntArray (0, 0)); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.JSONEncodable"], "javajs.util.BS", ["java.lang.IndexOutOfBoundsException", "$.NegativeArraySizeException", "javajs.util.PT", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.words = null; +this.wordsInUse = 0; +this.sizeIsSticky = false; +Clazz.instantialize (this, arguments); +}, javajs.util, "BS", null, [Cloneable, javajs.api.JSONEncodable]); +c$.wordIndex = Clazz.defineMethod (c$, "wordIndex", +($fz = function (bitIndex) { +return bitIndex >> 5; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "recalculateWordsInUse", +($fz = function () { +var i; +for (i = this.wordsInUse - 1; i >= 0; i--) if (this.words[i] != 0) break; + +this.wordsInUse = i + 1; +}, $fz.isPrivate = true, $fz)); +Clazz.makeConstructor (c$, +function () { +this.initWords (32); +this.sizeIsSticky = false; +}); +c$.newN = Clazz.defineMethod (c$, "newN", +function (nbits) { +var bs = new javajs.util.BS (); +bs.init (nbits); +return bs; +}, "~N"); +Clazz.defineMethod (c$, "init", +($fz = function (nbits) { +if (nbits < 0) throw new NegativeArraySizeException ("nbits < 0: " + nbits); +this.initWords (nbits); +this.sizeIsSticky = true; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "initWords", +($fz = function (nbits) { +this.words = Clazz.newIntArray (javajs.util.BS.wordIndex (nbits - 1) + 1, 0); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "ensureCapacity", +($fz = function (wordsRequired) { +if (this.words.length < wordsRequired) { +var request = Math.max (2 * this.words.length, wordsRequired); +this.setLength (request); +this.sizeIsSticky = false; +}}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "expandTo", +($fz = function (wordIndex) { +var wordsRequired = wordIndex + 1; +if (this.wordsInUse < wordsRequired) { +this.ensureCapacity (wordsRequired); +this.wordsInUse = wordsRequired; +}}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "set", +function (bitIndex) { +if (bitIndex < 0) throw new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex); +var wordIndex = javajs.util.BS.wordIndex (bitIndex); +this.expandTo (wordIndex); +this.words[wordIndex] |= (1 << bitIndex); +}, "~N"); +Clazz.defineMethod (c$, "setBitTo", +function (bitIndex, value) { +if (value) this.set (bitIndex); + else this.clear (bitIndex); +}, "~N,~B"); +Clazz.defineMethod (c$, "setBits", +function (fromIndex, toIndex) { +if (fromIndex == toIndex) return; +var startWordIndex = javajs.util.BS.wordIndex (fromIndex); +var endWordIndex = javajs.util.BS.wordIndex (toIndex - 1); +this.expandTo (endWordIndex); +var firstWordMask = -1 << fromIndex; +var lastWordMask = -1 >>> -toIndex; +if (startWordIndex == endWordIndex) { +this.words[startWordIndex] |= (firstWordMask & lastWordMask); +} else { +this.words[startWordIndex] |= firstWordMask; +for (var i = startWordIndex + 1; i < endWordIndex; i++) this.words[i] = -1; + +this.words[endWordIndex] |= lastWordMask; +}}, "~N,~N"); +Clazz.defineMethod (c$, "clear", +function (bitIndex) { +if (bitIndex < 0) throw new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex); +var wordIndex = javajs.util.BS.wordIndex (bitIndex); +if (wordIndex >= this.wordsInUse) return; +this.words[wordIndex] &= ~(1 << bitIndex); +this.recalculateWordsInUse (); +}, "~N"); +Clazz.defineMethod (c$, "clearBits", +function (fromIndex, toIndex) { +if (fromIndex == toIndex) return; +var startWordIndex = javajs.util.BS.wordIndex (fromIndex); +if (startWordIndex >= this.wordsInUse) return; +var endWordIndex = javajs.util.BS.wordIndex (toIndex - 1); +if (endWordIndex >= this.wordsInUse) { +toIndex = this.length (); +endWordIndex = this.wordsInUse - 1; +}var firstWordMask = -1 << fromIndex; +var lastWordMask = -1 >>> -toIndex; +if (startWordIndex == endWordIndex) { +this.words[startWordIndex] &= ~(firstWordMask & lastWordMask); +} else { +this.words[startWordIndex] &= ~firstWordMask; +for (var i = startWordIndex + 1; i < endWordIndex; i++) this.words[i] = 0; + +this.words[endWordIndex] &= ~lastWordMask; +}this.recalculateWordsInUse (); +}, "~N,~N"); +Clazz.defineMethod (c$, "clearAll", +function () { +while (this.wordsInUse > 0) this.words[--this.wordsInUse] = 0; + +}); +Clazz.defineMethod (c$, "get", +function (bitIndex) { +if (bitIndex < 0) throw new IndexOutOfBoundsException ("bitIndex < 0: " + bitIndex); +var wordIndex = javajs.util.BS.wordIndex (bitIndex); +return (wordIndex < this.wordsInUse) && ((this.words[wordIndex] & (1 << bitIndex)) != 0); +}, "~N"); +Clazz.defineMethod (c$, "nextSetBit", +function (fromIndex) { +if (fromIndex < 0) throw new IndexOutOfBoundsException ("fromIndex < 0: " + fromIndex); +var u = javajs.util.BS.wordIndex (fromIndex); +if (u >= this.wordsInUse) return -1; +var word = this.words[u] & (-1 << fromIndex); +while (true) { +if (word != 0) return (u * 32) + Integer.numberOfTrailingZeros (word); +if (++u == this.wordsInUse) return -1; +word = this.words[u]; +} +}, "~N"); +Clazz.defineMethod (c$, "nextClearBit", +function (fromIndex) { +if (fromIndex < 0) throw new IndexOutOfBoundsException ("fromIndex < 0: " + fromIndex); +var u = javajs.util.BS.wordIndex (fromIndex); +if (u >= this.wordsInUse) return fromIndex; +var word = ~this.words[u] & (-1 << fromIndex); +while (true) { +if (word != 0) return (u * 32) + Integer.numberOfTrailingZeros (word); +if (++u == this.wordsInUse) return this.wordsInUse * 32; +word = ~this.words[u]; +} +}, "~N"); +Clazz.defineMethod (c$, "length", +function () { +if (this.wordsInUse == 0) return 0; +return 32 * (this.wordsInUse - 1) + (32 - Integer.numberOfLeadingZeros (this.words[this.wordsInUse - 1])); +}); +Clazz.defineMethod (c$, "isEmpty", +function () { +return this.wordsInUse == 0; +}); +Clazz.defineMethod (c$, "intersects", +function (set) { +for (var i = Math.min (this.wordsInUse, set.wordsInUse) - 1; i >= 0; i--) if ((this.words[i] & set.words[i]) != 0) return true; + +return false; +}, "javajs.util.BS"); +Clazz.defineMethod (c$, "cardinality", +function () { +var sum = 0; +for (var i = 0; i < this.wordsInUse; i++) sum += Integer.bitCount (this.words[i]); + +return sum; +}); +Clazz.defineMethod (c$, "and", +function (set) { +if (this === set) return; +while (this.wordsInUse > set.wordsInUse) this.words[--this.wordsInUse] = 0; + +for (var i = 0; i < this.wordsInUse; i++) this.words[i] &= set.words[i]; + +this.recalculateWordsInUse (); +}, "javajs.util.BS"); +Clazz.defineMethod (c$, "or", +function (set) { +if (this === set) return; +var wordsInCommon = Math.min (this.wordsInUse, set.wordsInUse); +if (this.wordsInUse < set.wordsInUse) { +this.ensureCapacity (set.wordsInUse); +this.wordsInUse = set.wordsInUse; +}for (var i = 0; i < wordsInCommon; i++) this.words[i] |= set.words[i]; + +if (wordsInCommon < set.wordsInUse) System.arraycopy (set.words, wordsInCommon, this.words, wordsInCommon, this.wordsInUse - wordsInCommon); +}, "javajs.util.BS"); +Clazz.defineMethod (c$, "xor", +function (set) { +var wordsInCommon = Math.min (this.wordsInUse, set.wordsInUse); +if (this.wordsInUse < set.wordsInUse) { +this.ensureCapacity (set.wordsInUse); +this.wordsInUse = set.wordsInUse; +}for (var i = 0; i < wordsInCommon; i++) this.words[i] ^= set.words[i]; + +if (wordsInCommon < set.wordsInUse) System.arraycopy (set.words, wordsInCommon, this.words, wordsInCommon, set.wordsInUse - wordsInCommon); +this.recalculateWordsInUse (); +}, "javajs.util.BS"); +Clazz.defineMethod (c$, "andNot", +function (set) { +for (var i = Math.min (this.wordsInUse, set.wordsInUse) - 1; i >= 0; i--) this.words[i] &= ~set.words[i]; + +this.recalculateWordsInUse (); +}, "javajs.util.BS"); +Clazz.overrideMethod (c$, "hashCode", +function () { +var h = 1234; +for (var i = this.wordsInUse; --i >= 0; ) h ^= this.words[i] * (i + 1); + +return ((h >> 32) ^ h); +}); +Clazz.defineMethod (c$, "size", +function () { +return this.words.length * 32; +}); +Clazz.overrideMethod (c$, "equals", +function (obj) { +if (!(Clazz.instanceOf (obj, javajs.util.BS))) return false; +if (this === obj) return true; +var set = obj; +if (this.wordsInUse != set.wordsInUse) return false; +for (var i = 0; i < this.wordsInUse; i++) if (this.words[i] != set.words[i]) return false; + +return true; +}, "~O"); +Clazz.overrideMethod (c$, "clone", +function () { +if (!this.sizeIsSticky && this.wordsInUse != this.words.length) this.setLength (this.wordsInUse); +return javajs.util.BS.copy (this); +}); +Clazz.defineMethod (c$, "setLength", +($fz = function (n) { +var a = Clazz.newIntArray (n, 0); +System.arraycopy (this.words, 0, a, 0, Math.min (this.wordsInUse, n)); +this.words = a; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.overrideMethod (c$, "toString", +function () { +return javajs.util.BS.escape (this, '{', '}'); +}); +c$.copy = Clazz.defineMethod (c$, "copy", +function (bitsetToCopy) { +var bs; +{ +bs = Clazz.clone(bitsetToCopy); +}var wordCount = bitsetToCopy.wordsInUse; +if (wordCount == 0) { +bs.words = javajs.util.BS.emptyBitmap; +} else { +bs.words = Clazz.newIntArray (bs.wordsInUse = wordCount, 0); +System.arraycopy (bitsetToCopy.words, 0, bs.words, 0, wordCount); +}return bs; +}, "javajs.util.BS"); +Clazz.defineMethod (c$, "cardinalityN", +function (max) { +var n = this.cardinality (); +for (var i = this.length (); --i >= max; ) if (this.get (i)) n--; + +return n; +}, "~N"); +Clazz.overrideMethod (c$, "toJSON", +function () { +var numBits = (this.wordsInUse > 128) ? this.cardinality () : this.wordsInUse * 32; +var b = javajs.util.SB.newN (6 * numBits + 2); +b.appendC ('['); +var i = this.nextSetBit (0); +if (i != -1) { +b.appendI (i); +for (i = this.nextSetBit (i + 1); i >= 0; i = this.nextSetBit (i + 1)) { +var endOfRun = this.nextClearBit (i); +do { +b.append (", ").appendI (i); +} while (++i < endOfRun); +} +}b.appendC (']'); +return b.toString (); +}); +c$.escape = Clazz.defineMethod (c$, "escape", +function (bs, chOpen, chClose) { +if (bs == null) return chOpen + "{}" + chClose; +var s = new javajs.util.SB (); +s.append (chOpen + "{"); +var imax = bs.length (); +var iLast = -1; +var iFirst = -2; +var i = -1; +while (++i <= imax) { +var isSet = bs.get (i); +if (i == imax || iLast >= 0 && !isSet) { +if (iLast >= 0 && iFirst != iLast) s.append ((iFirst == iLast - 1 ? " " : ":") + iLast); +if (i == imax) break; +iLast = -1; +}if (bs.get (i)) { +if (iLast < 0) { +s.append ((iFirst == -2 ? "" : " ") + i); +iFirst = i; +}iLast = i; +}} +s.append ("}").appendC (chClose); +return s.toString (); +}, "javajs.util.BS,~S,~S"); +c$.unescape = Clazz.defineMethod (c$, "unescape", +function (str) { +var ch; +var len; +if (str == null || (len = (str = str.trim ()).length) < 4 || str.equalsIgnoreCase ("({null})") || (ch = str.charAt (0)) != '(' && ch != '[' || str.charAt (len - 1) != (ch == '(' ? ')' : ']') || str.charAt (1) != '{' || str.indexOf ('}') != len - 2) return null; +len -= 2; +for (var i = len; --i >= 2; ) if (!javajs.util.PT.isDigit (ch = str.charAt (i)) && ch != ' ' && ch != '\t' && ch != ':') return null; + +var lastN = len; +while (javajs.util.PT.isDigit (str.charAt (--lastN))) { +} +if (++lastN == len) lastN = 0; + else try { +lastN = Integer.parseInt (str.substring (lastN, len)); +} catch (e) { +if (Clazz.exceptionOf (e, NumberFormatException)) { +return null; +} else { +throw e; +} +} +var bs = javajs.util.BS.newN (lastN); +lastN = -1; +var iPrev = -1; +var iThis = -2; +for (var i = 2; i <= len; i++) { +switch (ch = str.charAt (i)) { +case '\t': +case ' ': +case '}': +if (iThis < 0) break; +if (iThis < lastN) return null; +lastN = iThis; +if (iPrev < 0) iPrev = iThis; +bs.setBits (iPrev, iThis + 1); +iPrev = -1; +iThis = -2; +break; +case ':': +iPrev = lastN = iThis; +iThis = -2; +break; +default: +if (javajs.util.PT.isDigit (ch)) { +if (iThis < 0) iThis = 0; +iThis = (iThis * 10) + (ch.charCodeAt (0) - 48); +}} +} +return (iPrev >= 0 ? null : bs); +}, "~S"); +Clazz.defineStatics (c$, +"ADDRESS_BITS_PER_WORD", 5, +"BITS_PER_WORD", 32, +"WORD_MASK", 0xffffffff, +"emptyBitmap", Clazz.newIntArray (0, 0)); +}); diff --git a/bin/javajs/util/Base64.js b/bin/javajs/util/Base64.js index 15f1a5f..e513e54 100644 --- a/bin/javajs/util/Base64.js +++ b/bin/javajs/util/Base64.js @@ -1,54 +1,54 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.Base64", ["javajs.util.SB"], function () { -c$ = Clazz.declareType (javajs.util, "Base64"); -c$.getBytes64 = Clazz.defineMethod (c$, "getBytes64", -function (bytes) { -return javajs.util.Base64.getBase64 (bytes).toBytes (0, -1); -}, "~A"); -c$.getBase64 = Clazz.defineMethod (c$, "getBase64", -function (bytes) { -var nBytes = bytes.length; -var sout = new javajs.util.SB (); -if (nBytes == 0) return sout; -for (var i = 0, nPad = 0; i < nBytes && nPad == 0; ) { -if (i % 75 == 0 && i != 0) sout.append ("\r\n"); -nPad = (i + 2 == nBytes ? 1 : i + 1 == nBytes ? 2 : 0); -var outbytes = ((bytes[i++] << 16) & 0xFF0000) | ((nPad == 2 ? 0 : bytes[i++] << 8) & 0x00FF00) | ((nPad >= 1 ? 0 : bytes[i++]) & 0x0000FF); -sout.appendC (javajs.util.Base64.base64.charAt ((outbytes >> 18) & 0x3F)); -sout.appendC (javajs.util.Base64.base64.charAt ((outbytes >> 12) & 0x3F)); -sout.appendC (nPad == 2 ? '=' : javajs.util.Base64.base64.charAt ((outbytes >> 6) & 0x3F)); -sout.appendC (nPad >= 1 ? '=' : javajs.util.Base64.base64.charAt (outbytes & 0x3F)); -} -return sout; -}, "~A"); -c$.decodeBase64 = Clazz.defineMethod (c$, "decodeBase64", -function (strBase64) { -var nBytes = 0; -var ch; -var pt0 = strBase64.indexOf (";base64,") + 1; -if (pt0 > 0) pt0 += 7; -var chars64 = strBase64.toCharArray (); -var len64 = chars64.length; -if (len64 == 0) return Clazz.newByteArray (0, 0); -for (var i = len64; --i >= pt0; ) nBytes += ((ch = (chars64[i]).charCodeAt (0) & 0x7F) == 65 || javajs.util.Base64.decode64[ch] > 0 ? 3 : 0); - -nBytes = nBytes >> 2; -var bytes = Clazz.newByteArray (nBytes, 0); -var offset = 18; -for (var i = pt0, pt = 0, b = 0; i < len64; i++) { -if (javajs.util.Base64.decode64[ch = (chars64[i]).charCodeAt (0) & 0x7F] > 0 || ch == 65 || ch == 61) { -b |= javajs.util.Base64.decode64[ch] << offset; -offset -= 6; -if (offset < 0) { -bytes[pt++] = ((b & 0xFF0000) >> 16); -if (pt < nBytes) bytes[pt++] = ((b & 0xFF00) >> 8); -if (pt < nBytes) bytes[pt++] = (b & 0xFF); -offset = 18; -b = 0; -}}} -return bytes; -}, "~S"); -Clazz.defineStatics (c$, -"base64", "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/", -"decode64", Clazz.newIntArray (-1, [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 62, 0, 62, 0, 63, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 0, 0, 0, 0, 63, 0, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 0, 0, 0, 0, 0])); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.Base64", ["javajs.util.SB"], function () { +c$ = Clazz.declareType (javajs.util, "Base64"); +c$.getBytes64 = Clazz.defineMethod (c$, "getBytes64", +function (bytes) { +return javajs.util.Base64.getBase64 (bytes).toBytes (0, -1); +}, "~A"); +c$.getBase64 = Clazz.defineMethod (c$, "getBase64", +function (bytes) { +var nBytes = bytes.length; +var sout = new javajs.util.SB (); +if (nBytes == 0) return sout; +for (var i = 0, nPad = 0; i < nBytes && nPad == 0; ) { +if (i % 75 == 0 && i != 0) sout.append ("\r\n"); +nPad = (i + 2 == nBytes ? 1 : i + 1 == nBytes ? 2 : 0); +var outbytes = ((bytes[i++] << 16) & 0xFF0000) | ((nPad == 2 ? 0 : bytes[i++] << 8) & 0x00FF00) | ((nPad >= 1 ? 0 : bytes[i++]) & 0x0000FF); +sout.appendC (javajs.util.Base64.base64.charAt ((outbytes >> 18) & 0x3F)); +sout.appendC (javajs.util.Base64.base64.charAt ((outbytes >> 12) & 0x3F)); +sout.appendC (nPad == 2 ? '=' : javajs.util.Base64.base64.charAt ((outbytes >> 6) & 0x3F)); +sout.appendC (nPad >= 1 ? '=' : javajs.util.Base64.base64.charAt (outbytes & 0x3F)); +} +return sout; +}, "~A"); +c$.decodeBase64 = Clazz.defineMethod (c$, "decodeBase64", +function (strBase64) { +var nBytes = 0; +var ch; +var pt0 = strBase64.indexOf (";base64,") + 1; +if (pt0 > 0) pt0 += 7; +var chars64 = strBase64.toCharArray (); +var len64 = chars64.length; +if (len64 == 0) return Clazz.newByteArray (0, 0); +for (var i = len64; --i >= pt0; ) nBytes += ((ch = (chars64[i]).charCodeAt (0) & 0x7F) == 65 || javajs.util.Base64.decode64[ch] > 0 ? 3 : 0); + +nBytes = nBytes >> 2; +var bytes = Clazz.newByteArray (nBytes, 0); +var offset = 18; +for (var i = pt0, pt = 0, b = 0; i < len64; i++) { +if (javajs.util.Base64.decode64[ch = (chars64[i]).charCodeAt (0) & 0x7F] > 0 || ch == 65 || ch == 61) { +b |= javajs.util.Base64.decode64[ch] << offset; +offset -= 6; +if (offset < 0) { +bytes[pt++] = ((b & 0xFF0000) >> 16); +if (pt < nBytes) bytes[pt++] = ((b & 0xFF00) >> 8); +if (pt < nBytes) bytes[pt++] = (b & 0xFF); +offset = 18; +b = 0; +}}} +return bytes; +}, "~S"); +Clazz.defineStatics (c$, +"base64", "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/", +"decode64", Clazz.newIntArray (-1, [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 62, 0, 62, 0, 63, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 0, 0, 0, 0, 63, 0, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 0, 0, 0, 0, 0])); +}); diff --git a/bin/javajs/util/BinaryDocument.js b/bin/javajs/util/BinaryDocument.js index 420db0b..a0edf33 100644 --- a/bin/javajs/util/BinaryDocument.js +++ b/bin/javajs/util/BinaryDocument.js @@ -1,218 +1,218 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.GenericBinaryDocument", "javajs.util.BC"], "javajs.util.BinaryDocument", ["java.io.DataInputStream", "java.lang.Double"], function () { -c$ = Clazz.decorateAsClass (function () { -this.stream = null; -this.isRandom = false; -this.isBigEndian = true; -this.jzt = null; -this.t8 = null; -this.nBytes = 0; -this.out = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "BinaryDocument", javajs.util.BC, javajs.api.GenericBinaryDocument); -Clazz.prepareFields (c$, function () { -this.t8 = Clazz.newByteArray (8, 0); -}); -Clazz.overrideMethod (c$, "close", -function () { -if (this.stream != null) try { -this.stream.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -if (this.out != null) this.out.closeChannel (); -}); -Clazz.overrideMethod (c$, "setStream", -function (jzt, bis, isBigEndian) { -if (jzt != null) this.jzt = jzt; -if (bis != null) this.stream = new java.io.DataInputStream (bis); -this.isBigEndian = isBigEndian; -}, "javajs.api.GenericZipTools,java.io.BufferedInputStream,~B"); -Clazz.overrideMethod (c$, "setStreamData", -function (stream, isBigEndian) { -if (stream != null) this.stream = stream; -this.isBigEndian = isBigEndian; -}, "java.io.DataInputStream,~B"); -Clazz.defineMethod (c$, "setRandom", -function (TF) { -this.isRandom = TF; -}, "~B"); -Clazz.overrideMethod (c$, "readByte", -function () { -this.nBytes++; -return this.ioReadByte (); -}); -Clazz.defineMethod (c$, "ioReadByte", -($fz = function () { -var b = this.stream.readByte (); -if (this.out != null) this.out.writeByteAsInt (b); -return b; -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "readByteArray", -function (b, off, len) { -var n = this.ioRead (b, off, len); -this.nBytes += n; -return n; -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "ioRead", -($fz = function (b, off, len) { -var m = 0; -while (len > 0) { -var n = this.stream.read (b, off, len); -m += n; -if (n > 0 && this.out != null) this.writeBytes (b, off, n); -if (n >= len) break; -off += n; -len -= n; -} -return m; -}, $fz.isPrivate = true, $fz), "~A,~N,~N"); -Clazz.defineMethod (c$, "writeBytes", -function (b, off, n) { -this.out.write (b, off, n); -}, "~A,~N,~N"); -Clazz.overrideMethod (c$, "readString", -function (nChar) { -var temp = Clazz.newByteArray (nChar, 0); -var n = this.readByteArray (temp, 0, nChar); -return String.instantialize (temp, 0, n, "UTF-8"); -}, "~N"); -Clazz.overrideMethod (c$, "readShort", -function () { -this.nBytes += 2; -var n = (this.isBigEndian ? this.ioReadShort () : ((this.ioReadByte () & 0xff) | (this.ioReadByte () & 0xff) << 8)); -{ -return (n > 0x7FFF ? n - 0x10000 : n); -}}); -Clazz.defineMethod (c$, "ioReadShort", -($fz = function () { -var b = this.stream.readShort (); -if (this.out != null) this.writeShort (b); -return b; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeShort", -function (i) { -this.out.writeByteAsInt (i >> 8); -this.out.writeByteAsInt (i); -}, "~N"); -Clazz.overrideMethod (c$, "readIntLE", -function () { -this.nBytes += 4; -return this.readLEInt (); -}); -Clazz.overrideMethod (c$, "readInt", -function () { -this.nBytes += 4; -return (this.isBigEndian ? this.ioReadInt () : this.readLEInt ()); -}); -Clazz.defineMethod (c$, "ioReadInt", -($fz = function () { -var i = this.stream.readInt (); -if (this.out != null) this.writeInt (i); -return i; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeInt", -function (i) { -this.out.writeByteAsInt (i >> 24); -this.out.writeByteAsInt (i >> 16); -this.out.writeByteAsInt (i >> 8); -this.out.writeByteAsInt (i); -}, "~N"); -Clazz.overrideMethod (c$, "swapBytesI", -function (n) { -return (((n >> 24) & 0xff) | ((n >> 16) & 0xff) << 8 | ((n >> 8) & 0xff) << 16 | (n & 0xff) << 24); -}, "~N"); -Clazz.overrideMethod (c$, "swapBytesS", -function (n) { -return ((((n >> 8) & 0xff) | (n & 0xff) << 8)); -}, "~N"); -Clazz.overrideMethod (c$, "readUnsignedShort", -function () { -this.nBytes += 2; -var a = (this.ioReadByte () & 0xff); -var b = (this.ioReadByte () & 0xff); -return (this.isBigEndian ? (a << 8) + b : (b << 8) + a); -}); -Clazz.overrideMethod (c$, "readLong", -function () { -this.nBytes += 8; -return (this.isBigEndian ? this.ioReadLong () : (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 54)); -}); -Clazz.defineMethod (c$, "ioReadLong", -($fz = function () { -var b = this.stream.readLong (); -if (this.out != null) this.writeLong (b); -return b; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "writeLong", -function (b) { -this.writeInt (((b >> 32) & 0xFFFFFFFF)); -this.writeInt ((b & 0xFFFFFFFF)); -}, "~N"); -Clazz.defineMethod (c$, "readLEInt", -($fz = function () { -this.ioRead (this.t8, 0, 4); -return javajs.util.BC.bytesToInt (this.t8, 0, false); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "readFloat", -function () { -return javajs.util.BC.intToFloat (this.readInt ()); -}); -Clazz.overrideMethod (c$, "readDouble", -function () { -{ -this.readByteArray(this.t8, 0, 8); -return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian); -}}); -Clazz.defineMethod (c$, "ioReadDouble", -($fz = function () { -var d = this.stream.readDouble (); -if (this.out != null) this.writeLong (Double.doubleToRawLongBits (d)); -return d; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "readLELong", -($fz = function () { -return (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 56); -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "seek", -function (offset) { -try { -if (offset == this.nBytes) return; -if (offset < this.nBytes) { -this.stream.reset (); -if (this.out != null && this.nBytes != 0) this.out.reset (); -this.nBytes = 0; -} else { -offset -= this.nBytes; -}if (this.out == null) { -this.stream.skipBytes (offset); -} else { -this.readByteArray ( Clazz.newByteArray (offset, 0), 0, offset); -}this.nBytes += offset; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -}, "~N"); -Clazz.overrideMethod (c$, "getPosition", -function () { -return this.nBytes; -}); -Clazz.overrideMethod (c$, "setOutputChannel", -function (out) { -this.out = out; -}, "javajs.util.OC"); -Clazz.overrideMethod (c$, "getAllDataFiles", -function (binaryFileList, firstFile) { -return null; -}, "~S,~S"); -Clazz.overrideMethod (c$, "getAllDataMapped", -function (replace, string, fileData) { -}, "~S,~S,java.util.Map"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.GenericBinaryDocument", "javajs.util.BC"], "javajs.util.BinaryDocument", ["java.io.DataInputStream", "java.lang.Double"], function () { +c$ = Clazz.decorateAsClass (function () { +this.stream = null; +this.isRandom = false; +this.isBigEndian = true; +this.jzt = null; +this.t8 = null; +this.nBytes = 0; +this.out = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "BinaryDocument", javajs.util.BC, javajs.api.GenericBinaryDocument); +Clazz.prepareFields (c$, function () { +this.t8 = Clazz.newByteArray (8, 0); +}); +Clazz.overrideMethod (c$, "close", +function () { +if (this.stream != null) try { +this.stream.close (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +if (this.out != null) this.out.closeChannel (); +}); +Clazz.overrideMethod (c$, "setStream", +function (jzt, bis, isBigEndian) { +if (jzt != null) this.jzt = jzt; +if (bis != null) this.stream = new java.io.DataInputStream (bis); +this.isBigEndian = isBigEndian; +}, "javajs.api.GenericZipTools,java.io.BufferedInputStream,~B"); +Clazz.overrideMethod (c$, "setStreamData", +function (stream, isBigEndian) { +if (stream != null) this.stream = stream; +this.isBigEndian = isBigEndian; +}, "java.io.DataInputStream,~B"); +Clazz.defineMethod (c$, "setRandom", +function (TF) { +this.isRandom = TF; +}, "~B"); +Clazz.overrideMethod (c$, "readByte", +function () { +this.nBytes++; +return this.ioReadByte (); +}); +Clazz.defineMethod (c$, "ioReadByte", +($fz = function () { +var b = this.stream.readByte (); +if (this.out != null) this.out.writeByteAsInt (b); +return b; +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "readByteArray", +function (b, off, len) { +var n = this.ioRead (b, off, len); +this.nBytes += n; +return n; +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "ioRead", +($fz = function (b, off, len) { +var m = 0; +while (len > 0) { +var n = this.stream.read (b, off, len); +m += n; +if (n > 0 && this.out != null) this.writeBytes (b, off, n); +if (n >= len) break; +off += n; +len -= n; +} +return m; +}, $fz.isPrivate = true, $fz), "~A,~N,~N"); +Clazz.defineMethod (c$, "writeBytes", +function (b, off, n) { +this.out.write (b, off, n); +}, "~A,~N,~N"); +Clazz.overrideMethod (c$, "readString", +function (nChar) { +var temp = Clazz.newByteArray (nChar, 0); +var n = this.readByteArray (temp, 0, nChar); +return String.instantialize (temp, 0, n, "UTF-8"); +}, "~N"); +Clazz.overrideMethod (c$, "readShort", +function () { +this.nBytes += 2; +var n = (this.isBigEndian ? this.ioReadShort () : ((this.ioReadByte () & 0xff) | (this.ioReadByte () & 0xff) << 8)); +{ +return (n > 0x7FFF ? n - 0x10000 : n); +}}); +Clazz.defineMethod (c$, "ioReadShort", +($fz = function () { +var b = this.stream.readShort (); +if (this.out != null) this.writeShort (b); +return b; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeShort", +function (i) { +this.out.writeByteAsInt (i >> 8); +this.out.writeByteAsInt (i); +}, "~N"); +Clazz.overrideMethod (c$, "readIntLE", +function () { +this.nBytes += 4; +return this.readLEInt (); +}); +Clazz.overrideMethod (c$, "readInt", +function () { +this.nBytes += 4; +return (this.isBigEndian ? this.ioReadInt () : this.readLEInt ()); +}); +Clazz.defineMethod (c$, "ioReadInt", +($fz = function () { +var i = this.stream.readInt (); +if (this.out != null) this.writeInt (i); +return i; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeInt", +function (i) { +this.out.writeByteAsInt (i >> 24); +this.out.writeByteAsInt (i >> 16); +this.out.writeByteAsInt (i >> 8); +this.out.writeByteAsInt (i); +}, "~N"); +Clazz.overrideMethod (c$, "swapBytesI", +function (n) { +return (((n >> 24) & 0xff) | ((n >> 16) & 0xff) << 8 | ((n >> 8) & 0xff) << 16 | (n & 0xff) << 24); +}, "~N"); +Clazz.overrideMethod (c$, "swapBytesS", +function (n) { +return ((((n >> 8) & 0xff) | (n & 0xff) << 8)); +}, "~N"); +Clazz.overrideMethod (c$, "readUnsignedShort", +function () { +this.nBytes += 2; +var a = (this.ioReadByte () & 0xff); +var b = (this.ioReadByte () & 0xff); +return (this.isBigEndian ? (a << 8) + b : (b << 8) + a); +}); +Clazz.overrideMethod (c$, "readLong", +function () { +this.nBytes += 8; +return (this.isBigEndian ? this.ioReadLong () : (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 54)); +}); +Clazz.defineMethod (c$, "ioReadLong", +($fz = function () { +var b = this.stream.readLong (); +if (this.out != null) this.writeLong (b); +return b; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "writeLong", +function (b) { +this.writeInt (((b >> 32) & 0xFFFFFFFF)); +this.writeInt ((b & 0xFFFFFFFF)); +}, "~N"); +Clazz.defineMethod (c$, "readLEInt", +($fz = function () { +this.ioRead (this.t8, 0, 4); +return javajs.util.BC.bytesToInt (this.t8, 0, false); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "readFloat", +function () { +return javajs.util.BC.intToFloat (this.readInt ()); +}); +Clazz.overrideMethod (c$, "readDouble", +function () { +{ +this.readByteArray(this.t8, 0, 8); +return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian); +}}); +Clazz.defineMethod (c$, "ioReadDouble", +($fz = function () { +var d = this.stream.readDouble (); +if (this.out != null) this.writeLong (Double.doubleToRawLongBits (d)); +return d; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "readLELong", +($fz = function () { +return (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 56); +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "seek", +function (offset) { +try { +if (offset == this.nBytes) return; +if (offset < this.nBytes) { +this.stream.reset (); +if (this.out != null && this.nBytes != 0) this.out.reset (); +this.nBytes = 0; +} else { +offset -= this.nBytes; +}if (this.out == null) { +this.stream.skipBytes (offset); +} else { +this.readByteArray ( Clazz.newByteArray (offset, 0), 0, offset); +}this.nBytes += offset; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +}, "~N"); +Clazz.overrideMethod (c$, "getPosition", +function () { +return this.nBytes; +}); +Clazz.overrideMethod (c$, "setOutputChannel", +function (out) { +this.out = out; +}, "javajs.util.OC"); +Clazz.overrideMethod (c$, "getAllDataFiles", +function (binaryFileList, firstFile) { +return null; +}, "~S,~S"); +Clazz.overrideMethod (c$, "getAllDataMapped", +function (replace, string, fileData) { +}, "~S,~S,java.util.Map"); +}); diff --git a/bin/javajs/util/CU.js b/bin/javajs/util/CU.js index f6b3020..edd8bdd 100644 --- a/bin/javajs/util/CU.js +++ b/bin/javajs/util/CU.js @@ -1,135 +1,135 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.util.Hashtable"], "javajs.util.CU", ["javajs.util.P3", "$.PT"], function () { -c$ = Clazz.declareType (javajs.util, "CU"); -c$.toRGBHexString = Clazz.defineMethod (c$, "toRGBHexString", -function (c) { -var rgb = c.getRGB (); -if (rgb == 0) return "000000"; -var r = "00" + Integer.toHexString ((rgb >> 16) & 0xFF); -r = r.substring (r.length - 2); -var g = "00" + Integer.toHexString ((rgb >> 8) & 0xFF); -g = g.substring (g.length - 2); -var b = "00" + Integer.toHexString (rgb & 0xFF); -b = b.substring (b.length - 2); -return r + g + b; -}, "javajs.api.GenericColor"); -c$.toCSSString = Clazz.defineMethod (c$, "toCSSString", -function (c) { -var opacity = c.getOpacity255 (); -if (opacity == 255) return "#" + javajs.util.CU.toRGBHexString (c); -var rgb = c.getRGB (); -return "rgba(" + ((rgb >> 16) & 0xFF) + "," + ((rgb >> 8) & 0xff) + "," + (rgb & 0xff) + "," + opacity / 255 + ")"; -}, "javajs.api.GenericColor"); -c$.getArgbFromString = Clazz.defineMethod (c$, "getArgbFromString", -function (strColor) { -var len = 0; -if (strColor == null || (len = strColor.length) == 0) return 0; -if (strColor.charAt (0) == '[' && strColor.charAt (len - 1) == ']') { -var check; -if (strColor.indexOf (",") >= 0) { -var tokens = javajs.util.PT.split (strColor.substring (1, strColor.length - 1), ","); -if (tokens.length != 3) return 0; -var red = javajs.util.PT.parseFloat (tokens[0]); -var grn = javajs.util.PT.parseFloat (tokens[1]); -var blu = javajs.util.PT.parseFloat (tokens[2]); -return javajs.util.CU.colorTriadToFFRGB (red, grn, blu); -}switch (len) { -case 9: -check = "x"; -break; -case 10: -check = "0x"; -break; -default: -return 0; -} -if (strColor.indexOf (check) != 1) return 0; -strColor = "#" + strColor.substring (len - 7, len - 1); -len = 7; -}if (len == 7 && strColor.charAt (0) == '#') { -try { -return javajs.util.PT.parseIntRadix (strColor.substring (1, 7), 16) | 0xFF000000; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -return 0; -} else { -throw e; -} -} -}var boxedArgb = javajs.util.CU.mapJavaScriptColors.get (strColor.toLowerCase ()); -return (boxedArgb == null ? 0 : boxedArgb.intValue ()); -}, "~S"); -c$.colorTriadToFFRGB = Clazz.defineMethod (c$, "colorTriadToFFRGB", -function (x, y, z) { -if (x <= 1 && y <= 1 && z <= 1) { -if (x > 0) x = x * 256 - 1; -if (y > 0) y = y * 256 - 1; -if (z > 0) z = z * 256 - 1; -}return javajs.util.CU.rgb (Clazz.floatToInt (x), Clazz.floatToInt (y), Clazz.floatToInt (z)); -}, "~N,~N,~N"); -c$.rgb = Clazz.defineMethod (c$, "rgb", -function (red, grn, blu) { -return 0xFF000000 | (red << 16) | (grn << 8) | blu; -}, "~N,~N,~N"); -c$.colorPtFromString = Clazz.defineMethod (c$, "colorPtFromString", -function (colorName) { -return javajs.util.CU.colorPtFromInt (javajs.util.CU.getArgbFromString (colorName), null); -}, "~S"); -c$.colorPtFromInt = Clazz.defineMethod (c$, "colorPtFromInt", -function (color, pt) { -if (pt == null) pt = new javajs.util.P3 (); -pt.set ((color >> 16) & 0xFF, (color >> 8) & 0xFF, color & 0xFF); -return pt; -}, "~N,javajs.util.P3"); -c$.colorPtToFFRGB = Clazz.defineMethod (c$, "colorPtToFFRGB", -function (pt) { -return javajs.util.CU.colorTriadToFFRGB (pt.x, pt.y, pt.z); -}, "javajs.util.T3"); -c$.toRGB3f = Clazz.defineMethod (c$, "toRGB3f", -function (c, f) { -f[0] = ((c >> 16) & 0xFF) / 255; -f[1] = ((c >> 8) & 0xFF) / 255; -f[2] = (c & 0xFF) / 255; -}, "~N,~A"); -c$.toFFGGGfromRGB = Clazz.defineMethod (c$, "toFFGGGfromRGB", -function (rgb) { -var grey = (Clazz.doubleToInt (((2989 * ((rgb >> 16) & 0xFF)) + (5870 * ((rgb >> 8) & 0xFF)) + (1140 * (rgb & 0xFF)) + 5000) / 10000)) & 0xFFFFFF; -return javajs.util.CU.rgb (grey, grey, grey); -}, "~N"); -c$.rgbToHSL = Clazz.defineMethod (c$, "rgbToHSL", -function (rgb, doRound) { -var r = rgb.x / 255; -var g = rgb.y / 255; -var b = rgb.z / 255; -var min = Math.min (r, Math.min (g, b)); -var max = Math.max (r, Math.max (g, b)); -var p = (max + min); -var q = (max - min); -var h = (60 * ((q == 0 ? 0 : max == r ? ((g - b) / q + 6) : max == g ? (b - r) / q + 2 : (r - g) / q + 4))) % 360; -var s = q / (q == 0 ? 1 : p <= 1 ? p : 2 - p); -return (doRound ? javajs.util.P3.new3 (Math.round (h * 10) / 10, Math.round (s * 1000) / 10, Math.round (p * 500) / 10) : javajs.util.P3.new3 (h, s * 100, p * 50)); -}, "javajs.util.P3,~B"); -c$.hslToRGB = Clazz.defineMethod (c$, "hslToRGB", -function (hsl) { -var h = Math.max (0, Math.min (360, hsl.x)) / 60; -var s = Math.max (0, Math.min (100, hsl.y)) / 100; -var l = Math.max (0, Math.min (100, hsl.z)) / 100; -var p = l - (l < 0.5 ? l : 1 - l) * s; -var q = 2 * (l - p); -var r = javajs.util.CU.toRGB (p, q, h + 2); -var g = javajs.util.CU.toRGB (p, q, h); -var b = javajs.util.CU.toRGB (p, q, h - 2); -return javajs.util.P3.new3 (Math.round (r * 255), Math.round (g * 255), Math.round (b * 255)); -}, "javajs.util.P3"); -c$.toRGB = Clazz.defineMethod (c$, "toRGB", -($fz = function (p, q, h) { -return ((h = (h + (h < 0 ? 6 : h > 6 ? -6 : 0))) < 1 ? p + q * h : h < 3 ? p + q : h < 4 ? p + q * (4 - h) : p); -}, $fz.isPrivate = true, $fz), "~N,~N,~N"); -Clazz.defineStatics (c$, -"colorNames", Clazz.newArray (-1, ["black", "pewhite", "pecyan", "pepurple", "pegreen", "peblue", "peviolet", "pebrown", "pepink", "peyellow", "pedarkgreen", "peorange", "pelightblue", "pedarkcyan", "pedarkgray", "aliceblue", "antiquewhite", "aqua", "aquamarine", "azure", "beige", "bisque", "blanchedalmond", "blue", "blueviolet", "brown", "burlywood", "cadetblue", "chartreuse", "chocolate", "coral", "cornflowerblue", "cornsilk", "crimson", "cyan", "darkblue", "darkcyan", "darkgoldenrod", "darkgray", "darkgreen", "darkkhaki", "darkmagenta", "darkolivegreen", "darkorange", "darkorchid", "darkred", "darksalmon", "darkseagreen", "darkslateblue", "darkslategray", "darkturquoise", "darkviolet", "deeppink", "deepskyblue", "dimgray", "dodgerblue", "firebrick", "floralwhite", "forestgreen", "fuchsia", "gainsboro", "ghostwhite", "gold", "goldenrod", "gray", "green", "greenyellow", "honeydew", "hotpink", "indianred", "indigo", "ivory", "khaki", "lavender", "lavenderblush", "lawngreen", "lemonchiffon", "lightblue", "lightcoral", "lightcyan", "lightgoldenrodyellow", "lightgreen", "lightgrey", "lightpink", "lightsalmon", "lightseagreen", "lightskyblue", "lightslategray", "lightsteelblue", "lightyellow", "lime", "limegreen", "linen", "magenta", "maroon", "mediumaquamarine", "mediumblue", "mediumorchid", "mediumpurple", "mediumseagreen", "mediumslateblue", "mediumspringgreen", "mediumturquoise", "mediumvioletred", "midnightblue", "mintcream", "mistyrose", "moccasin", "navajowhite", "navy", "oldlace", "olive", "olivedrab", "orange", "orangered", "orchid", "palegoldenrod", "palegreen", "paleturquoise", "palevioletred", "papayawhip", "peachpuff", "peru", "pink", "plum", "powderblue", "purple", "red", "rosybrown", "royalblue", "saddlebrown", "salmon", "sandybrown", "seagreen", "seashell", "sienna", "silver", "skyblue", "slateblue", "slategray", "snow", "springgreen", "steelblue", "tan", "teal", "thistle", "tomato", "turquoise", "violet", "wheat", "white", "whitesmoke", "yellow", "yellowgreen", "bluetint", "greenblue", "greentint", "grey", "pinktint", "redorange", "yellowtint"]), -"colorArgbs", Clazz.newIntArray (-1, [0xFF000000, 0xFFffffff, 0xFF00ffff, 0xFFd020ff, 0xFF00ff00, 0xFF6060ff, 0xFFff80c0, 0xFFa42028, 0xFFffd8d8, 0xFFffff00, 0xFF00c000, 0xFFffb000, 0xFFb0b0ff, 0xFF00a0a0, 0xFF606060, 0xFFF0F8FF, 0xFFFAEBD7, 0xFF00FFFF, 0xFF7FFFD4, 0xFFF0FFFF, 0xFFF5F5DC, 0xFFFFE4C4, 0xFFFFEBCD, 0xFF0000FF, 0xFF8A2BE2, 0xFFA52A2A, 0xFFDEB887, 0xFF5F9EA0, 0xFF7FFF00, 0xFFD2691E, 0xFFFF7F50, 0xFF6495ED, 0xFFFFF8DC, 0xFFDC143C, 0xFF00FFFF, 0xFF00008B, 0xFF008B8B, 0xFFB8860B, 0xFFA9A9A9, 0xFF006400, 0xFFBDB76B, 0xFF8B008B, 0xFF556B2F, 0xFFFF8C00, 0xFF9932CC, 0xFF8B0000, 0xFFE9967A, 0xFF8FBC8F, 0xFF483D8B, 0xFF2F4F4F, 0xFF00CED1, 0xFF9400D3, 0xFFFF1493, 0xFF00BFFF, 0xFF696969, 0xFF1E90FF, 0xFFB22222, 0xFFFFFAF0, 0xFF228B22, 0xFFFF00FF, 0xFFDCDCDC, 0xFFF8F8FF, 0xFFFFD700, 0xFFDAA520, 0xFF808080, 0xFF008000, 0xFFADFF2F, 0xFFF0FFF0, 0xFFFF69B4, 0xFFCD5C5C, 0xFF4B0082, 0xFFFFFFF0, 0xFFF0E68C, 0xFFE6E6FA, 0xFFFFF0F5, 0xFF7CFC00, 0xFFFFFACD, 0xFFADD8E6, 0xFFF08080, 0xFFE0FFFF, 0xFFFAFAD2, 0xFF90EE90, 0xFFD3D3D3, 0xFFFFB6C1, 0xFFFFA07A, 0xFF20B2AA, 0xFF87CEFA, 0xFF778899, 0xFFB0C4DE, 0xFFFFFFE0, 0xFF00FF00, 0xFF32CD32, 0xFFFAF0E6, 0xFFFF00FF, 0xFF800000, 0xFF66CDAA, 0xFF0000CD, 0xFFBA55D3, 0xFF9370DB, 0xFF3CB371, 0xFF7B68EE, 0xFF00FA9A, 0xFF48D1CC, 0xFFC71585, 0xFF191970, 0xFFF5FFFA, 0xFFFFE4E1, 0xFFFFE4B5, 0xFFFFDEAD, 0xFF000080, 0xFFFDF5E6, 0xFF808000, 0xFF6B8E23, 0xFFFFA500, 0xFFFF4500, 0xFFDA70D6, 0xFFEEE8AA, 0xFF98FB98, 0xFFAFEEEE, 0xFFDB7093, 0xFFFFEFD5, 0xFFFFDAB9, 0xFFCD853F, 0xFFFFC0CB, 0xFFDDA0DD, 0xFFB0E0E6, 0xFF800080, 0xFFFF0000, 0xFFBC8F8F, 0xFF4169E1, 0xFF8B4513, 0xFFFA8072, 0xFFF4A460, 0xFF2E8B57, 0xFFFFF5EE, 0xFFA0522D, 0xFFC0C0C0, 0xFF87CEEB, 0xFF6A5ACD, 0xFF708090, 0xFFFFFAFA, 0xFF00FF7F, 0xFF4682B4, 0xFFD2B48C, 0xFF008080, 0xFFD8BFD8, 0xFFFF6347, 0xFF40E0D0, 0xFFEE82EE, 0xFFF5DEB3, 0xFFFFFFFF, 0xFFF5F5F5, 0xFFFFFF00, 0xFF9ACD32, 0xFFAFD7FF, 0xFF2E8B57, 0xFF98FFB3, 0xFF808080, 0xFFFFABBB, 0xFFFF4500, 0xFFF6F675])); -c$.mapJavaScriptColors = c$.prototype.mapJavaScriptColors = new java.util.Hashtable (); -{ -for (var i = javajs.util.CU.colorNames.length; --i >= 0; ) javajs.util.CU.mapJavaScriptColors.put (javajs.util.CU.colorNames[i], Integer.$valueOf (javajs.util.CU.colorArgbs[i])); - -}}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.util.Hashtable"], "javajs.util.CU", ["javajs.util.P3", "$.PT"], function () { +c$ = Clazz.declareType (javajs.util, "CU"); +c$.toRGBHexString = Clazz.defineMethod (c$, "toRGBHexString", +function (c) { +var rgb = c.getRGB (); +if (rgb == 0) return "000000"; +var r = "00" + Integer.toHexString ((rgb >> 16) & 0xFF); +r = r.substring (r.length - 2); +var g = "00" + Integer.toHexString ((rgb >> 8) & 0xFF); +g = g.substring (g.length - 2); +var b = "00" + Integer.toHexString (rgb & 0xFF); +b = b.substring (b.length - 2); +return r + g + b; +}, "javajs.api.GenericColor"); +c$.toCSSString = Clazz.defineMethod (c$, "toCSSString", +function (c) { +var opacity = c.getOpacity255 (); +if (opacity == 255) return "#" + javajs.util.CU.toRGBHexString (c); +var rgb = c.getRGB (); +return "rgba(" + ((rgb >> 16) & 0xFF) + "," + ((rgb >> 8) & 0xff) + "," + (rgb & 0xff) + "," + opacity / 255 + ")"; +}, "javajs.api.GenericColor"); +c$.getArgbFromString = Clazz.defineMethod (c$, "getArgbFromString", +function (strColor) { +var len = 0; +if (strColor == null || (len = strColor.length) == 0) return 0; +if (strColor.charAt (0) == '[' && strColor.charAt (len - 1) == ']') { +var check; +if (strColor.indexOf (",") >= 0) { +var tokens = javajs.util.PT.split (strColor.substring (1, strColor.length - 1), ","); +if (tokens.length != 3) return 0; +var red = javajs.util.PT.parseFloat (tokens[0]); +var grn = javajs.util.PT.parseFloat (tokens[1]); +var blu = javajs.util.PT.parseFloat (tokens[2]); +return javajs.util.CU.colorTriadToFFRGB (red, grn, blu); +}switch (len) { +case 9: +check = "x"; +break; +case 10: +check = "0x"; +break; +default: +return 0; +} +if (strColor.indexOf (check) != 1) return 0; +strColor = "#" + strColor.substring (len - 7, len - 1); +len = 7; +}if (len == 7 && strColor.charAt (0) == '#') { +try { +return javajs.util.PT.parseIntRadix (strColor.substring (1, 7), 16) | 0xFF000000; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +return 0; +} else { +throw e; +} +} +}var boxedArgb = javajs.util.CU.mapJavaScriptColors.get (strColor.toLowerCase ()); +return (boxedArgb == null ? 0 : boxedArgb.intValue ()); +}, "~S"); +c$.colorTriadToFFRGB = Clazz.defineMethod (c$, "colorTriadToFFRGB", +function (x, y, z) { +if (x <= 1 && y <= 1 && z <= 1) { +if (x > 0) x = x * 256 - 1; +if (y > 0) y = y * 256 - 1; +if (z > 0) z = z * 256 - 1; +}return javajs.util.CU.rgb (Clazz.floatToInt (x), Clazz.floatToInt (y), Clazz.floatToInt (z)); +}, "~N,~N,~N"); +c$.rgb = Clazz.defineMethod (c$, "rgb", +function (red, grn, blu) { +return 0xFF000000 | (red << 16) | (grn << 8) | blu; +}, "~N,~N,~N"); +c$.colorPtFromString = Clazz.defineMethod (c$, "colorPtFromString", +function (colorName) { +return javajs.util.CU.colorPtFromInt (javajs.util.CU.getArgbFromString (colorName), null); +}, "~S"); +c$.colorPtFromInt = Clazz.defineMethod (c$, "colorPtFromInt", +function (color, pt) { +if (pt == null) pt = new javajs.util.P3 (); +pt.set ((color >> 16) & 0xFF, (color >> 8) & 0xFF, color & 0xFF); +return pt; +}, "~N,javajs.util.P3"); +c$.colorPtToFFRGB = Clazz.defineMethod (c$, "colorPtToFFRGB", +function (pt) { +return javajs.util.CU.colorTriadToFFRGB (pt.x, pt.y, pt.z); +}, "javajs.util.T3"); +c$.toRGB3f = Clazz.defineMethod (c$, "toRGB3f", +function (c, f) { +f[0] = ((c >> 16) & 0xFF) / 255; +f[1] = ((c >> 8) & 0xFF) / 255; +f[2] = (c & 0xFF) / 255; +}, "~N,~A"); +c$.toFFGGGfromRGB = Clazz.defineMethod (c$, "toFFGGGfromRGB", +function (rgb) { +var grey = (Clazz.doubleToInt (((2989 * ((rgb >> 16) & 0xFF)) + (5870 * ((rgb >> 8) & 0xFF)) + (1140 * (rgb & 0xFF)) + 5000) / 10000)) & 0xFFFFFF; +return javajs.util.CU.rgb (grey, grey, grey); +}, "~N"); +c$.rgbToHSL = Clazz.defineMethod (c$, "rgbToHSL", +function (rgb, doRound) { +var r = rgb.x / 255; +var g = rgb.y / 255; +var b = rgb.z / 255; +var min = Math.min (r, Math.min (g, b)); +var max = Math.max (r, Math.max (g, b)); +var p = (max + min); +var q = (max - min); +var h = (60 * ((q == 0 ? 0 : max == r ? ((g - b) / q + 6) : max == g ? (b - r) / q + 2 : (r - g) / q + 4))) % 360; +var s = q / (q == 0 ? 1 : p <= 1 ? p : 2 - p); +return (doRound ? javajs.util.P3.new3 (Math.round (h * 10) / 10, Math.round (s * 1000) / 10, Math.round (p * 500) / 10) : javajs.util.P3.new3 (h, s * 100, p * 50)); +}, "javajs.util.P3,~B"); +c$.hslToRGB = Clazz.defineMethod (c$, "hslToRGB", +function (hsl) { +var h = Math.max (0, Math.min (360, hsl.x)) / 60; +var s = Math.max (0, Math.min (100, hsl.y)) / 100; +var l = Math.max (0, Math.min (100, hsl.z)) / 100; +var p = l - (l < 0.5 ? l : 1 - l) * s; +var q = 2 * (l - p); +var r = javajs.util.CU.toRGB (p, q, h + 2); +var g = javajs.util.CU.toRGB (p, q, h); +var b = javajs.util.CU.toRGB (p, q, h - 2); +return javajs.util.P3.new3 (Math.round (r * 255), Math.round (g * 255), Math.round (b * 255)); +}, "javajs.util.P3"); +c$.toRGB = Clazz.defineMethod (c$, "toRGB", +($fz = function (p, q, h) { +return ((h = (h + (h < 0 ? 6 : h > 6 ? -6 : 0))) < 1 ? p + q * h : h < 3 ? p + q : h < 4 ? p + q * (4 - h) : p); +}, $fz.isPrivate = true, $fz), "~N,~N,~N"); +Clazz.defineStatics (c$, +"colorNames", Clazz.newArray (-1, ["black", "pewhite", "pecyan", "pepurple", "pegreen", "peblue", "peviolet", "pebrown", "pepink", "peyellow", "pedarkgreen", "peorange", "pelightblue", "pedarkcyan", "pedarkgray", "aliceblue", "antiquewhite", "aqua", "aquamarine", "azure", "beige", "bisque", "blanchedalmond", "blue", "blueviolet", "brown", "burlywood", "cadetblue", "chartreuse", "chocolate", "coral", "cornflowerblue", "cornsilk", "crimson", "cyan", "darkblue", "darkcyan", "darkgoldenrod", "darkgray", "darkgreen", "darkkhaki", "darkmagenta", "darkolivegreen", "darkorange", "darkorchid", "darkred", "darksalmon", "darkseagreen", "darkslateblue", "darkslategray", "darkturquoise", "darkviolet", "deeppink", "deepskyblue", "dimgray", "dodgerblue", "firebrick", "floralwhite", "forestgreen", "fuchsia", "gainsboro", "ghostwhite", "gold", "goldenrod", "gray", "green", "greenyellow", "honeydew", "hotpink", "indianred", "indigo", "ivory", "khaki", "lavender", "lavenderblush", "lawngreen", "lemonchiffon", "lightblue", "lightcoral", "lightcyan", "lightgoldenrodyellow", "lightgreen", "lightgrey", "lightpink", "lightsalmon", "lightseagreen", "lightskyblue", "lightslategray", "lightsteelblue", "lightyellow", "lime", "limegreen", "linen", "magenta", "maroon", "mediumaquamarine", "mediumblue", "mediumorchid", "mediumpurple", "mediumseagreen", "mediumslateblue", "mediumspringgreen", "mediumturquoise", "mediumvioletred", "midnightblue", "mintcream", "mistyrose", "moccasin", "navajowhite", "navy", "oldlace", "olive", "olivedrab", "orange", "orangered", "orchid", "palegoldenrod", "palegreen", "paleturquoise", "palevioletred", "papayawhip", "peachpuff", "peru", "pink", "plum", "powderblue", "purple", "red", "rosybrown", "royalblue", "saddlebrown", "salmon", "sandybrown", "seagreen", "seashell", "sienna", "silver", "skyblue", "slateblue", "slategray", "snow", "springgreen", "steelblue", "tan", "teal", "thistle", "tomato", "turquoise", "violet", "wheat", "white", "whitesmoke", "yellow", "yellowgreen", "bluetint", "greenblue", "greentint", "grey", "pinktint", "redorange", "yellowtint"]), +"colorArgbs", Clazz.newIntArray (-1, [0xFF000000, 0xFFffffff, 0xFF00ffff, 0xFFd020ff, 0xFF00ff00, 0xFF6060ff, 0xFFff80c0, 0xFFa42028, 0xFFffd8d8, 0xFFffff00, 0xFF00c000, 0xFFffb000, 0xFFb0b0ff, 0xFF00a0a0, 0xFF606060, 0xFFF0F8FF, 0xFFFAEBD7, 0xFF00FFFF, 0xFF7FFFD4, 0xFFF0FFFF, 0xFFF5F5DC, 0xFFFFE4C4, 0xFFFFEBCD, 0xFF0000FF, 0xFF8A2BE2, 0xFFA52A2A, 0xFFDEB887, 0xFF5F9EA0, 0xFF7FFF00, 0xFFD2691E, 0xFFFF7F50, 0xFF6495ED, 0xFFFFF8DC, 0xFFDC143C, 0xFF00FFFF, 0xFF00008B, 0xFF008B8B, 0xFFB8860B, 0xFFA9A9A9, 0xFF006400, 0xFFBDB76B, 0xFF8B008B, 0xFF556B2F, 0xFFFF8C00, 0xFF9932CC, 0xFF8B0000, 0xFFE9967A, 0xFF8FBC8F, 0xFF483D8B, 0xFF2F4F4F, 0xFF00CED1, 0xFF9400D3, 0xFFFF1493, 0xFF00BFFF, 0xFF696969, 0xFF1E90FF, 0xFFB22222, 0xFFFFFAF0, 0xFF228B22, 0xFFFF00FF, 0xFFDCDCDC, 0xFFF8F8FF, 0xFFFFD700, 0xFFDAA520, 0xFF808080, 0xFF008000, 0xFFADFF2F, 0xFFF0FFF0, 0xFFFF69B4, 0xFFCD5C5C, 0xFF4B0082, 0xFFFFFFF0, 0xFFF0E68C, 0xFFE6E6FA, 0xFFFFF0F5, 0xFF7CFC00, 0xFFFFFACD, 0xFFADD8E6, 0xFFF08080, 0xFFE0FFFF, 0xFFFAFAD2, 0xFF90EE90, 0xFFD3D3D3, 0xFFFFB6C1, 0xFFFFA07A, 0xFF20B2AA, 0xFF87CEFA, 0xFF778899, 0xFFB0C4DE, 0xFFFFFFE0, 0xFF00FF00, 0xFF32CD32, 0xFFFAF0E6, 0xFFFF00FF, 0xFF800000, 0xFF66CDAA, 0xFF0000CD, 0xFFBA55D3, 0xFF9370DB, 0xFF3CB371, 0xFF7B68EE, 0xFF00FA9A, 0xFF48D1CC, 0xFFC71585, 0xFF191970, 0xFFF5FFFA, 0xFFFFE4E1, 0xFFFFE4B5, 0xFFFFDEAD, 0xFF000080, 0xFFFDF5E6, 0xFF808000, 0xFF6B8E23, 0xFFFFA500, 0xFFFF4500, 0xFFDA70D6, 0xFFEEE8AA, 0xFF98FB98, 0xFFAFEEEE, 0xFFDB7093, 0xFFFFEFD5, 0xFFFFDAB9, 0xFFCD853F, 0xFFFFC0CB, 0xFFDDA0DD, 0xFFB0E0E6, 0xFF800080, 0xFFFF0000, 0xFFBC8F8F, 0xFF4169E1, 0xFF8B4513, 0xFFFA8072, 0xFFF4A460, 0xFF2E8B57, 0xFFFFF5EE, 0xFFA0522D, 0xFFC0C0C0, 0xFF87CEEB, 0xFF6A5ACD, 0xFF708090, 0xFFFFFAFA, 0xFF00FF7F, 0xFF4682B4, 0xFFD2B48C, 0xFF008080, 0xFFD8BFD8, 0xFFFF6347, 0xFF40E0D0, 0xFFEE82EE, 0xFFF5DEB3, 0xFFFFFFFF, 0xFFF5F5F5, 0xFFFFFF00, 0xFF9ACD32, 0xFFAFD7FF, 0xFF2E8B57, 0xFF98FFB3, 0xFF808080, 0xFFFFABBB, 0xFFFF4500, 0xFFF6F675])); +c$.mapJavaScriptColors = c$.prototype.mapJavaScriptColors = new java.util.Hashtable (); +{ +for (var i = javajs.util.CU.colorNames.length; --i >= 0; ) javajs.util.CU.mapJavaScriptColors.put (javajs.util.CU.colorNames[i], Integer.$valueOf (javajs.util.CU.colorArgbs[i])); + +}}); diff --git a/bin/javajs/util/CifDataParser.class b/bin/javajs/util/CifDataParser.class index cf79e99..56f6075 100644 Binary files a/bin/javajs/util/CifDataParser.class and b/bin/javajs/util/CifDataParser.class differ diff --git a/bin/javajs/util/CifDataParser.js b/bin/javajs/util/CifDataParser.js index c00c5e1..07e1495 100644 --- a/bin/javajs/util/CifDataParser.js +++ b/bin/javajs/util/CifDataParser.js @@ -1,303 +1,303 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.GenericCifDataParser", "java.util.Hashtable", "javajs.util.SB"], "javajs.util.CifDataParser", ["javajs.util.Lst", "$.PT"], function () { -c$ = Clazz.decorateAsClass (function () { -this.reader = null; -this.br = null; -this.line = null; -this.str = null; -this.ich = 0; -this.cch = 0; -this.wasUnQuoted = false; -this.strPeeked = null; -this.ichPeeked = 0; -this.fieldCount = 0; -this.loopData = null; -this.fileHeader = null; -this.isHeader = true; -this.nullString = "\0"; -this.fields = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "CifDataParser", null, javajs.api.GenericCifDataParser); -Clazz.prepareFields (c$, function () { -this.fileHeader = new javajs.util.SB (); -}); -Clazz.defineMethod (c$, "setNullValue", -function (nullString) { -this.nullString = nullString; -}, "~S"); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.overrideMethod (c$, "getLoopData", -function (i) { -return this.loopData[i]; -}, "~N"); -Clazz.overrideMethod (c$, "getFieldCount", -function () { -return this.fieldCount; -}); -Clazz.overrideMethod (c$, "getField", -function (i) { -return this.fields[i]; -}, "~N"); -Clazz.overrideMethod (c$, "set", -function (reader, br) { -this.reader = reader; -this.br = br; -return this; -}, "javajs.api.GenericLineReader,java.io.BufferedReader"); -Clazz.overrideMethod (c$, "getFileHeader", -function () { -return this.fileHeader.toString (); -}); -Clazz.overrideMethod (c$, "getAllCifData", -function () { -this.line = ""; -var key; -var data = null; -var allData = new java.util.Hashtable (); -var models = new javajs.util.Lst (); -allData.put ("models", models); -try { -while ((key = this.getNextToken ()) != null) { -if (key.startsWith ("global_") || key.startsWith ("data_")) { -models.addLast (data = new java.util.Hashtable ()); -data.put ("name", key); -continue; -}if (key.startsWith ("loop_")) { -this.getAllCifLoopData (data); -continue; -}if (key.charAt (0) != '_') { -System.out.println ("CIF ERROR ? should be an underscore: " + key); -} else { -var value = this.getNextToken (); -if (value == null) { -System.out.println ("CIF ERROR ? end of file; data missing: " + key); -} else { -data.put (this.fixKey (key), value); -}}} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -try { -if (this.br != null) this.br.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -return allData; -}); -Clazz.defineMethod (c$, "getAllCifLoopData", -($fz = function (data) { -var key; -var keyWords = new javajs.util.Lst (); -while ((key = this.peekToken ()) != null && key.charAt (0) == '_') { -key = this.fixKey (this.getTokenPeeked ()); -keyWords.addLast (key); -data.put (key, new javajs.util.Lst ()); -} -this.fieldCount = keyWords.size (); -if (this.fieldCount == 0) return; -this.loopData = new Array (this.fieldCount); -while (this.getData ()) for (var i = 0; i < this.fieldCount; i++) (data.get (keyWords.get (i))).addLast (this.loopData[i]); - - -}, $fz.isPrivate = true, $fz), "java.util.Map"); -Clazz.overrideMethod (c$, "readLine", -function () { -try { -this.line = (this.reader == null ? this.br.readLine () : this.reader.readNextLine ()); -if (this.line == null) return null; -if (this.isHeader) { -if (this.line.startsWith ("#")) this.fileHeader.append (this.line).appendC ('\n'); - else this.isHeader = false; -}return this.line; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -return null; -} else { -throw e; -} -} -}); -Clazz.overrideMethod (c$, "getData", -function () { -for (var i = 0; i < this.fieldCount; ++i) if ((this.loopData[i] = this.getNextDataToken ()) == null) return false; - -return (this.fieldCount > 0); -}); -Clazz.overrideMethod (c$, "skipLoop", -function (doReport) { -var str; -var ret = (doReport ? new javajs.util.SB () : null); -var n = 0; -while ((str = this.peekToken ()) != null && str.charAt (0) == '_') { -if (ret != null) ret.append (str).append ("\n"); -this.getTokenPeeked (); -n++; -} -var m = 0; -while ((str = this.getNextDataToken ()) != null) { -if (ret == null) continue; -ret.append (str).append (" "); -if ((++m % n) == 0) ret.append ("\n"); -} -return (ret == null ? null : ret.toString ()); -}, "~B"); -Clazz.overrideMethod (c$, "getNextToken", -function () { -while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null; - -return this.nextStrToken (); -}); -Clazz.overrideMethod (c$, "getNextDataToken", -function () { -var str = this.peekToken (); -if (str == null) return null; -if (this.wasUnQuoted) if (str.charAt (0) == '_' || str.startsWith ("loop_") || str.startsWith ("data_") || str.startsWith ("stop_") || str.startsWith ("global_")) return null; -return this.getTokenPeeked (); -}); -Clazz.overrideMethod (c$, "peekToken", -function () { -while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null; - -var ich = this.ich; -this.strPeeked = this.nextStrToken (); -this.ichPeeked = this.ich; -this.ich = ich; -return this.strPeeked; -}); -Clazz.overrideMethod (c$, "getTokenPeeked", -function () { -this.ich = this.ichPeeked; -return this.strPeeked; -}); -Clazz.overrideMethod (c$, "fullTrim", -function (str) { -var pt0 = -1; -var pt1 = str.length; -while (++pt0 < pt1 && javajs.util.PT.isWhitespace (str.charAt (pt0))) { -} -while (--pt1 > pt0 && javajs.util.PT.isWhitespace (str.charAt (pt1))) { -} -return str.substring (pt0, pt1 + 1); -}, "~S"); -Clazz.overrideMethod (c$, "toUnicode", -function (data) { -var pt; -try { -while ((pt = data.indexOf ('\\')) >= 0) { -var c = data.charCodeAt (pt + 1); -var ch = (c >= 65 && c <= 90 ? "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z".substring (c - 65, c - 64) : c >= 97 && c <= 122 ? "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6".substring (c - 97, c - 96) : "_"); -data = data.substring (0, pt) + ch + data.substring (pt + 2); -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -return data; -}, "~S"); -Clazz.overrideMethod (c$, "parseLoopParameters", -function (fields, fieldOf, propertyOf) { -var propertyCount = 0; -if (fields == null) { -this.fields = new Array (100); -} else { -if (!javajs.util.CifDataParser.htFields.containsKey (fields[0])) for (var i = fields.length; --i >= 0; ) javajs.util.CifDataParser.htFields.put (fields[i], Integer.$valueOf (i)); - -for (var i = fields.length; --i >= 0; ) fieldOf[i] = -1; - -propertyCount = fields.length; -}this.fieldCount = 0; -while (true) { -var str = this.peekToken (); -if (str == null) { -this.fieldCount = 0; -break; -}if (str.charAt (0) != '_') break; -var pt = this.fieldCount++; -str = this.fixKey (this.getTokenPeeked ()); -if (fields == null) { -this.fields[propertyOf[pt] = fieldOf[pt] = pt] = str; -continue; -}var iField = javajs.util.CifDataParser.htFields.get (str); -var i = (iField == null ? -1 : iField.intValue ()); -if ((propertyOf[pt] = i) != -1) fieldOf[i] = pt; -} -if (this.fieldCount > 0) this.loopData = new Array (this.fieldCount); -return propertyCount; -}, "~A,~A,~A"); -Clazz.overrideMethod (c$, "fixKey", -function (key) { -return (javajs.util.PT.rep (key.startsWith ("_magnetic") ? key.substring (9) : key.startsWith ("_jana") ? key.substring (5) : key, ".", "_").toLowerCase ()); -}, "~S"); -Clazz.defineMethod (c$, "setString", -($fz = function (str) { -this.str = this.line = str; -this.cch = (str == null ? 0 : str.length); -this.ich = 0; -}, $fz.isPrivate = true, $fz), "~S"); -Clazz.defineMethod (c$, "setStringNextLine", -($fz = function () { -this.setString (this.readLine ()); -if (this.line == null || this.line.length == 0) return this.line; -if (this.line.charAt (0) != ';') { -if (this.str.startsWith ("###non-st#")) this.ich = 10; -return this.line; -}this.ich = 1; -var str = '\1' + this.line.substring (1) + '\n'; -while (this.readLine () != null) { -if (this.line.startsWith (";")) { -str = str.substring (0, str.length - 1) + '\1' + this.line.substring (1); -break; -}str += this.line + '\n'; -} -this.setString (str); -return str; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "strHasMoreTokens", -($fz = function () { -if (this.str == null) return false; -var ch = '#'; -while (this.ich < this.cch && ((ch = this.str.charAt (this.ich)) == ' ' || ch == '\t')) ++this.ich; - -return (this.ich < this.cch && ch != '#'); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "nextStrToken", -($fz = function () { -if (this.ich == this.cch) return null; -var ichStart = this.ich; -var ch = this.str.charAt (ichStart); -if (ch != '\'' && ch != '"' && ch != '\1') { -this.wasUnQuoted = true; -while (this.ich < this.cch && (ch = this.str.charAt (this.ich)) != ' ' && ch != '\t') ++this.ich; - -if (this.ich == ichStart + 1) if (this.nullString != null && (this.str.charAt (ichStart) == '.' || this.str.charAt (ichStart) == '?')) return this.nullString; -var s = this.str.substring (ichStart, this.ich); -return s; -}this.wasUnQuoted = false; -var chOpeningQuote = ch; -var previousCharacterWasQuote = false; -while (++this.ich < this.cch) { -ch = this.str.charAt (this.ich); -if (previousCharacterWasQuote && (ch == ' ' || ch == '\t')) break; -previousCharacterWasQuote = (ch == chOpeningQuote); -} -if (this.ich == this.cch) { -if (previousCharacterWasQuote) return this.str.substring (ichStart + 1, this.ich - 1); -return this.str.substring (ichStart, this.ich); -}++this.ich; -return this.str.substring (ichStart + 1, this.ich - 2); -}, $fz.isPrivate = true, $fz)); -c$.htFields = c$.prototype.htFields = new java.util.Hashtable (); -Clazz.defineStatics (c$, -"grABC", "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z", -"grabc", "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.GenericCifDataParser", "java.util.Hashtable", "javajs.util.SB"], "javajs.util.CifDataParser", ["javajs.util.Lst", "$.PT"], function () { +c$ = Clazz.decorateAsClass (function () { +this.reader = null; +this.br = null; +this.line = null; +this.str = null; +this.ich = 0; +this.cch = 0; +this.wasUnQuoted = false; +this.strPeeked = null; +this.ichPeeked = 0; +this.fieldCount = 0; +this.loopData = null; +this.fileHeader = null; +this.isHeader = true; +this.nullString = "\0"; +this.fields = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "CifDataParser", null, javajs.api.GenericCifDataParser); +Clazz.prepareFields (c$, function () { +this.fileHeader = new javajs.util.SB (); +}); +Clazz.defineMethod (c$, "setNullValue", +function (nullString) { +this.nullString = nullString; +}, "~S"); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.overrideMethod (c$, "getLoopData", +function (i) { +return this.loopData[i]; +}, "~N"); +Clazz.overrideMethod (c$, "getFieldCount", +function () { +return this.fieldCount; +}); +Clazz.overrideMethod (c$, "getField", +function (i) { +return this.fields[i]; +}, "~N"); +Clazz.overrideMethod (c$, "set", +function (reader, br) { +this.reader = reader; +this.br = br; +return this; +}, "javajs.api.GenericLineReader,java.io.BufferedReader"); +Clazz.overrideMethod (c$, "getFileHeader", +function () { +return this.fileHeader.toString (); +}); +Clazz.overrideMethod (c$, "getAllCifData", +function () { +this.line = ""; +var key; +var data = null; +var allData = new java.util.Hashtable (); +var models = new javajs.util.Lst (); +allData.put ("models", models); +try { +while ((key = this.getNextToken ()) != null) { +if (key.startsWith ("global_") || key.startsWith ("data_")) { +models.addLast (data = new java.util.Hashtable ()); +data.put ("name", key); +continue; +}if (key.startsWith ("loop_")) { +this.getAllCifLoopData (data); +continue; +}if (key.charAt (0) != '_') { +System.out.println ("CIF ERROR ? should be an underscore: " + key); +} else { +var value = this.getNextToken (); +if (value == null) { +System.out.println ("CIF ERROR ? end of file; data missing: " + key); +} else { +data.put (this.fixKey (key), value); +}}} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +try { +if (this.br != null) this.br.close (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +return allData; +}); +Clazz.defineMethod (c$, "getAllCifLoopData", +($fz = function (data) { +var key; +var keyWords = new javajs.util.Lst (); +while ((key = this.peekToken ()) != null && key.charAt (0) == '_') { +key = this.fixKey (this.getTokenPeeked ()); +keyWords.addLast (key); +data.put (key, new javajs.util.Lst ()); +} +this.fieldCount = keyWords.size (); +if (this.fieldCount == 0) return; +this.loopData = new Array (this.fieldCount); +while (this.getData ()) for (var i = 0; i < this.fieldCount; i++) (data.get (keyWords.get (i))).addLast (this.loopData[i]); + + +}, $fz.isPrivate = true, $fz), "java.util.Map"); +Clazz.overrideMethod (c$, "readLine", +function () { +try { +this.line = (this.reader == null ? this.br.readLine () : this.reader.readNextLine ()); +if (this.line == null) return null; +if (this.isHeader) { +if (this.line.startsWith ("#")) this.fileHeader.append (this.line).appendC ('\n'); + else this.isHeader = false; +}return this.line; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +return null; +} else { +throw e; +} +} +}); +Clazz.overrideMethod (c$, "getData", +function () { +for (var i = 0; i < this.fieldCount; ++i) if ((this.loopData[i] = this.getNextDataToken ()) == null) return false; + +return (this.fieldCount > 0); +}); +Clazz.overrideMethod (c$, "skipLoop", +function (doReport) { +var str; +var ret = (doReport ? new javajs.util.SB () : null); +var n = 0; +while ((str = this.peekToken ()) != null && str.charAt (0) == '_') { +if (ret != null) ret.append (str).append ("\n"); +this.getTokenPeeked (); +n++; +} +var m = 0; +while ((str = this.getNextDataToken ()) != null) { +if (ret == null) continue; +ret.append (str).append (" "); +if ((++m % n) == 0) ret.append ("\n"); +} +return (ret == null ? null : ret.toString ()); +}, "~B"); +Clazz.overrideMethod (c$, "getNextToken", +function () { +while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null; + +return this.nextStrToken (); +}); +Clazz.overrideMethod (c$, "getNextDataToken", +function () { +var str = this.peekToken (); +if (str == null) return null; +if (this.wasUnQuoted) if (str.charAt (0) == '_' || str.startsWith ("loop_") || str.startsWith ("data_") || str.startsWith ("stop_") || str.startsWith ("global_")) return null; +return this.getTokenPeeked (); +}); +Clazz.overrideMethod (c$, "peekToken", +function () { +while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null; + +var ich = this.ich; +this.strPeeked = this.nextStrToken (); +this.ichPeeked = this.ich; +this.ich = ich; +return this.strPeeked; +}); +Clazz.overrideMethod (c$, "getTokenPeeked", +function () { +this.ich = this.ichPeeked; +return this.strPeeked; +}); +Clazz.overrideMethod (c$, "fullTrim", +function (str) { +var pt0 = -1; +var pt1 = str.length; +while (++pt0 < pt1 && javajs.util.PT.isWhitespace (str.charAt (pt0))) { +} +while (--pt1 > pt0 && javajs.util.PT.isWhitespace (str.charAt (pt1))) { +} +return str.substring (pt0, pt1 + 1); +}, "~S"); +Clazz.overrideMethod (c$, "toUnicode", +function (data) { +var pt; +try { +while ((pt = data.indexOf ('\\')) >= 0) { +var c = data.charCodeAt (pt + 1); +var ch = (c >= 65 && c <= 90 ? "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z".substring (c - 65, c - 64) : c >= 97 && c <= 122 ? "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6".substring (c - 97, c - 96) : "_"); +data = data.substring (0, pt) + ch + data.substring (pt + 2); +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +return data; +}, "~S"); +Clazz.overrideMethod (c$, "parseLoopParameters", +function (fields, fieldOf, propertyOf) { +var propertyCount = 0; +if (fields == null) { +this.fields = new Array (100); +} else { +if (!javajs.util.CifDataParser.htFields.containsKey (fields[0])) for (var i = fields.length; --i >= 0; ) javajs.util.CifDataParser.htFields.put (fields[i], Integer.$valueOf (i)); + +for (var i = fields.length; --i >= 0; ) fieldOf[i] = -1; + +propertyCount = fields.length; +}this.fieldCount = 0; +while (true) { +var str = this.peekToken (); +if (str == null) { +this.fieldCount = 0; +break; +}if (str.charAt (0) != '_') break; +var pt = this.fieldCount++; +str = this.fixKey (this.getTokenPeeked ()); +if (fields == null) { +this.fields[propertyOf[pt] = fieldOf[pt] = pt] = str; +continue; +}var iField = javajs.util.CifDataParser.htFields.get (str); +var i = (iField == null ? -1 : iField.intValue ()); +if ((propertyOf[pt] = i) != -1) fieldOf[i] = pt; +} +if (this.fieldCount > 0) this.loopData = new Array (this.fieldCount); +return propertyCount; +}, "~A,~A,~A"); +Clazz.overrideMethod (c$, "fixKey", +function (key) { +return (javajs.util.PT.rep (key.startsWith ("_magnetic") ? key.substring (9) : key.startsWith ("_jana") ? key.substring (5) : key, ".", "_").toLowerCase ()); +}, "~S"); +Clazz.defineMethod (c$, "setString", +($fz = function (str) { +this.str = this.line = str; +this.cch = (str == null ? 0 : str.length); +this.ich = 0; +}, $fz.isPrivate = true, $fz), "~S"); +Clazz.defineMethod (c$, "setStringNextLine", +($fz = function () { +this.setString (this.readLine ()); +if (this.line == null || this.line.length == 0) return this.line; +if (this.line.charAt (0) != ';') { +if (this.str.startsWith ("###non-st#")) this.ich = 10; +return this.line; +}this.ich = 1; +var str = '\1' + this.line.substring (1) + '\n'; +while (this.readLine () != null) { +if (this.line.startsWith (";")) { +str = str.substring (0, str.length - 1) + '\1' + this.line.substring (1); +break; +}str += this.line + '\n'; +} +this.setString (str); +return str; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "strHasMoreTokens", +($fz = function () { +if (this.str == null) return false; +var ch = '#'; +while (this.ich < this.cch && ((ch = this.str.charAt (this.ich)) == ' ' || ch == '\t')) ++this.ich; + +return (this.ich < this.cch && ch != '#'); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "nextStrToken", +($fz = function () { +if (this.ich == this.cch) return null; +var ichStart = this.ich; +var ch = this.str.charAt (ichStart); +if (ch != '\'' && ch != '"' && ch != '\1') { +this.wasUnQuoted = true; +while (this.ich < this.cch && (ch = this.str.charAt (this.ich)) != ' ' && ch != '\t') ++this.ich; + +if (this.ich == ichStart + 1) if (this.nullString != null && (this.str.charAt (ichStart) == '.' || this.str.charAt (ichStart) == '?')) return this.nullString; +var s = this.str.substring (ichStart, this.ich); +return s; +}this.wasUnQuoted = false; +var chOpeningQuote = ch; +var previousCharacterWasQuote = false; +while (++this.ich < this.cch) { +ch = this.str.charAt (this.ich); +if (previousCharacterWasQuote && (ch == ' ' || ch == '\t')) break; +previousCharacterWasQuote = (ch == chOpeningQuote); +} +if (this.ich == this.cch) { +if (previousCharacterWasQuote) return this.str.substring (ichStart + 1, this.ich - 1); +return this.str.substring (ichStart, this.ich); +}++this.ich; +return this.str.substring (ichStart + 1, this.ich - 2); +}, $fz.isPrivate = true, $fz)); +c$.htFields = c$.prototype.htFields = new java.util.Hashtable (); +Clazz.defineStatics (c$, +"grABC", "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z", +"grabc", "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6"); +}); diff --git a/bin/javajs/util/CompoundDocDirEntry.js b/bin/javajs/util/CompoundDocDirEntry.js index d792190..5c3ab43 100644 --- a/bin/javajs/util/CompoundDocDirEntry.js +++ b/bin/javajs/util/CompoundDocDirEntry.js @@ -1,58 +1,58 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.cd = null; -this.unicodeName64 = null; -this.nBytesUnicodeName = 0; -this.entryType = 0; -this.uniqueID16 = null; -this.userflags4 = null; -this.SIDfirstSector = 0; -this.lenStream = 0; -this.unused = null; -this.entryName = null; -this.isStandard = false; -this.isEmpty = false; -Clazz.instantialize (this, arguments); -}, javajs.util, "CompoundDocDirEntry"); -Clazz.prepareFields (c$, function () { -this.unicodeName64 = Clazz.newByteArray (64, 0); -this.uniqueID16 = Clazz.newByteArray (16, 0); -this.userflags4 = Clazz.newByteArray (4, 0); -this.unused = Clazz.newByteArray (8, 0); -}); -Clazz.makeConstructor (c$, -function (compoundDocument) { -this.cd = compoundDocument; -}, "javajs.util.CompoundDocument"); -Clazz.defineMethod (c$, "readData", -function () { -try { -this.cd.readByteArray (this.unicodeName64, 0, 64); -this.nBytesUnicodeName = this.cd.readShort (); -this.entryType = this.cd.readByte (); -this.cd.readByte (); -this.cd.readInt (); -this.cd.readInt (); -this.cd.readInt (); -this.cd.readByteArray (this.uniqueID16, 0, 16); -this.cd.readByteArray (this.userflags4, 0, 4); -this.cd.readByteArray (this.unused, 0, 8); -this.cd.readByteArray (this.unused, 0, 8); -this.SIDfirstSector = this.cd.readInt (); -this.lenStream = this.cd.readInt (); -this.cd.readByteArray (this.unused, 0, 4); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -return false; -} else { -throw e; -} -} -this.entryName = ""; -for (var i = 0; i < this.nBytesUnicodeName - 2; i += 2) this.entryName += String.fromCharCode (this.unicodeName64[i]); - -this.isStandard = (this.entryType == 5 || this.lenStream >= this.cd.header.minBytesStandardStream); -this.isEmpty = (this.entryType == 0 || this.lenStream <= 0); -return true; -}); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.cd = null; +this.unicodeName64 = null; +this.nBytesUnicodeName = 0; +this.entryType = 0; +this.uniqueID16 = null; +this.userflags4 = null; +this.SIDfirstSector = 0; +this.lenStream = 0; +this.unused = null; +this.entryName = null; +this.isStandard = false; +this.isEmpty = false; +Clazz.instantialize (this, arguments); +}, javajs.util, "CompoundDocDirEntry"); +Clazz.prepareFields (c$, function () { +this.unicodeName64 = Clazz.newByteArray (64, 0); +this.uniqueID16 = Clazz.newByteArray (16, 0); +this.userflags4 = Clazz.newByteArray (4, 0); +this.unused = Clazz.newByteArray (8, 0); +}); +Clazz.makeConstructor (c$, +function (compoundDocument) { +this.cd = compoundDocument; +}, "javajs.util.CompoundDocument"); +Clazz.defineMethod (c$, "readData", +function () { +try { +this.cd.readByteArray (this.unicodeName64, 0, 64); +this.nBytesUnicodeName = this.cd.readShort (); +this.entryType = this.cd.readByte (); +this.cd.readByte (); +this.cd.readInt (); +this.cd.readInt (); +this.cd.readInt (); +this.cd.readByteArray (this.uniqueID16, 0, 16); +this.cd.readByteArray (this.userflags4, 0, 4); +this.cd.readByteArray (this.unused, 0, 8); +this.cd.readByteArray (this.unused, 0, 8); +this.SIDfirstSector = this.cd.readInt (); +this.lenStream = this.cd.readInt (); +this.cd.readByteArray (this.unused, 0, 4); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +return false; +} else { +throw e; +} +} +this.entryName = ""; +for (var i = 0; i < this.nBytesUnicodeName - 2; i += 2) this.entryName += String.fromCharCode (this.unicodeName64[i]); + +this.isStandard = (this.entryType == 5 || this.lenStream >= this.cd.header.minBytesStandardStream); +this.isEmpty = (this.entryType == 0 || this.lenStream <= 0); +return true; +}); diff --git a/bin/javajs/util/CompoundDocHeader.js b/bin/javajs/util/CompoundDocHeader.js index 14d9c45..30d7fd1 100644 --- a/bin/javajs/util/CompoundDocHeader.js +++ b/bin/javajs/util/CompoundDocHeader.js @@ -1,66 +1,66 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.cd = null; -this.magicNumbers = null; -this.uniqueID16 = null; -this.revNumber = 0; -this.verNumber = 0; -this.sectorPower = 0; -this.shortSectorPower = 0; -this.unused = null; -this.nSATsectors = 0; -this.SID_DIR_start = 0; -this.minBytesStandardStream = 0; -this.SID_SSAT_start = 0; -this.nSSATsectors = 0; -this.SID_MSAT_next = 0; -this.nAdditionalMATsectors = 0; -this.MSAT0 = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "CompoundDocHeader"); -Clazz.prepareFields (c$, function () { -this.magicNumbers = Clazz.newByteArray (8, 0); -this.uniqueID16 = Clazz.newByteArray (16, 0); -this.unused = Clazz.newByteArray (10, 0); -this.MSAT0 = Clazz.newIntArray (109, 0); -}); -Clazz.makeConstructor (c$, -function (compoundDocument) { -this.cd = compoundDocument; -}, "javajs.util.CompoundDocument"); -Clazz.defineMethod (c$, "readData", -function () { -try { -this.cd.readByteArray (this.magicNumbers, 0, 8); -if (this.magicNumbers[0] != 0xD0 || this.magicNumbers[1] != 0xCF || this.magicNumbers[2] != 0x11 || this.magicNumbers[3] != 0xE0 || this.magicNumbers[4] != 0xA1 || this.magicNumbers[5] != 0xB1 || this.magicNumbers[6] != 0x1A || this.magicNumbers[7] != 0xE1) return false; -this.cd.readByteArray (this.uniqueID16, 0, 16); -this.revNumber = this.cd.readByte (); -this.cd.readByte (); -this.verNumber = this.cd.readByte (); -this.cd.readByte (); -var b1 = this.cd.readByte (); -var b2 = this.cd.readByte (); -this.cd.isBigEndian = (b1 == -1 && b2 == -2); -this.sectorPower = this.cd.readShort (); -this.shortSectorPower = this.cd.readShort (); -this.cd.readByteArray (this.unused, 0, 10); -this.nSATsectors = this.cd.readInt (); -this.SID_DIR_start = this.cd.readInt (); -this.cd.readByteArray (this.unused, 0, 4); -this.minBytesStandardStream = this.cd.readInt (); -this.SID_SSAT_start = this.cd.readInt (); -this.nSSATsectors = this.cd.readInt (); -this.SID_MSAT_next = this.cd.readInt (); -this.nAdditionalMATsectors = this.cd.readInt (); -for (var i = 0; i < 109; i++) this.MSAT0[i] = this.cd.readInt (); - -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -return false; -} else { -throw e; -} -} -return true; -}); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.cd = null; +this.magicNumbers = null; +this.uniqueID16 = null; +this.revNumber = 0; +this.verNumber = 0; +this.sectorPower = 0; +this.shortSectorPower = 0; +this.unused = null; +this.nSATsectors = 0; +this.SID_DIR_start = 0; +this.minBytesStandardStream = 0; +this.SID_SSAT_start = 0; +this.nSSATsectors = 0; +this.SID_MSAT_next = 0; +this.nAdditionalMATsectors = 0; +this.MSAT0 = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "CompoundDocHeader"); +Clazz.prepareFields (c$, function () { +this.magicNumbers = Clazz.newByteArray (8, 0); +this.uniqueID16 = Clazz.newByteArray (16, 0); +this.unused = Clazz.newByteArray (10, 0); +this.MSAT0 = Clazz.newIntArray (109, 0); +}); +Clazz.makeConstructor (c$, +function (compoundDocument) { +this.cd = compoundDocument; +}, "javajs.util.CompoundDocument"); +Clazz.defineMethod (c$, "readData", +function () { +try { +this.cd.readByteArray (this.magicNumbers, 0, 8); +if (this.magicNumbers[0] != 0xD0 || this.magicNumbers[1] != 0xCF || this.magicNumbers[2] != 0x11 || this.magicNumbers[3] != 0xE0 || this.magicNumbers[4] != 0xA1 || this.magicNumbers[5] != 0xB1 || this.magicNumbers[6] != 0x1A || this.magicNumbers[7] != 0xE1) return false; +this.cd.readByteArray (this.uniqueID16, 0, 16); +this.revNumber = this.cd.readByte (); +this.cd.readByte (); +this.verNumber = this.cd.readByte (); +this.cd.readByte (); +var b1 = this.cd.readByte (); +var b2 = this.cd.readByte (); +this.cd.isBigEndian = (b1 == -1 && b2 == -2); +this.sectorPower = this.cd.readShort (); +this.shortSectorPower = this.cd.readShort (); +this.cd.readByteArray (this.unused, 0, 10); +this.nSATsectors = this.cd.readInt (); +this.SID_DIR_start = this.cd.readInt (); +this.cd.readByteArray (this.unused, 0, 4); +this.minBytesStandardStream = this.cd.readInt (); +this.SID_SSAT_start = this.cd.readInt (); +this.nSSATsectors = this.cd.readInt (); +this.SID_MSAT_next = this.cd.readInt (); +this.nAdditionalMATsectors = this.cd.readInt (); +for (var i = 0; i < 109; i++) this.MSAT0[i] = this.cd.readInt (); + +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +return false; +} else { +throw e; +} +} +return true; +}); diff --git a/bin/javajs/util/CompoundDocument.class b/bin/javajs/util/CompoundDocument.class index ef31fcf..d2a24d4 100644 Binary files a/bin/javajs/util/CompoundDocument.class and b/bin/javajs/util/CompoundDocument.class differ diff --git a/bin/javajs/util/CompoundDocument.js b/bin/javajs/util/CompoundDocument.js index 7e480bc..a37c69e 100644 --- a/bin/javajs/util/CompoundDocument.js +++ b/bin/javajs/util/CompoundDocument.js @@ -1,286 +1,286 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.BinaryDocument", "$.CompoundDocHeader", "$.Lst"], "javajs.util.CompoundDocument", ["java.io.DataInputStream", "javajs.util.CompoundDocDirEntry", "$.SB", "$.ZipData"], function () { -c$ = Clazz.decorateAsClass (function () { -this.header = null; -this.directory = null; -this.rootEntry = null; -this.SAT = null; -this.SSAT = null; -this.sectorSize = 0; -this.shortSectorSize = 0; -this.nShortSectorsPerStandardSector = 0; -this.nIntPerSector = 0; -this.nDirEntriesperSector = 0; -this.data = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "CompoundDocument", javajs.util.BinaryDocument); -Clazz.prepareFields (c$, function () { -this.header = new javajs.util.CompoundDocHeader (this); -this.directory = new javajs.util.Lst (); -}); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.util.CompoundDocument); -this.isBigEndian = true; -}); -Clazz.overrideMethod (c$, "setStream", -function (jzt, bis, isBigEndian) { -this.jzt = jzt; -if (!this.isRandom) { -this.stream = new java.io.DataInputStream (bis); -}this.stream.mark (2147483647); -if (!this.readHeader ()) return; -this.getSectorAllocationTable (); -this.getShortSectorAllocationTable (); -this.getDirectoryTable (); -}, "javajs.api.GenericZipTools,java.io.BufferedInputStream,~B"); -Clazz.defineMethod (c$, "getDirectory", -function () { -return this.directory; -}); -Clazz.defineMethod (c$, "getDirectoryListing", -function (separator) { -var str = ""; -for (var i = 0; i < this.directory.size (); i++) { -var thisEntry = this.directory.get (i); -if (!thisEntry.isEmpty) str += separator + thisEntry.entryName + "\tlen=" + thisEntry.lenStream + "\tSID=" + thisEntry.SIDfirstSector + (thisEntry.isStandard ? "\tfileOffset=" + this.getOffset (thisEntry.SIDfirstSector) : ""); -} -return str; -}, "~S"); -Clazz.defineMethod (c$, "getAllData", -function () { -return this.getAllDataFiles (null, null); -}); -Clazz.overrideMethod (c$, "getAllDataMapped", -function (prefix, binaryFileList, fileData) { -fileData.put ("#Directory_Listing", this.getDirectoryListing ("|")); -binaryFileList = "|" + binaryFileList + "|"; -for (var i = 0; i < this.directory.size (); i++) { -var thisEntry = this.directory.get (i); -if (!thisEntry.isEmpty && thisEntry.entryType != 5) { -var name = thisEntry.entryName; -System.out.println ("CompoundDocument file " + name); -var isBinary = (binaryFileList.indexOf ("|" + name + "|") >= 0); -if (isBinary) name += ":asBinaryString"; -var data = new javajs.util.SB (); -data.append ("BEGIN Directory Entry ").append (name).append ("\n"); -data.appendSB (this.getEntryAsString (thisEntry, isBinary)); -data.append ("\nEND Directory Entry ").append (name).append ("\n"); -fileData.put (prefix + "/" + name, data.toString ()); -}} -this.close (); -}, "~S,~S,java.util.Map"); -Clazz.overrideMethod (c$, "getAllDataFiles", -function (binaryFileList, firstFile) { -if (firstFile != null) { -for (var i = 0; i < this.directory.size (); i++) { -var thisEntry = this.directory.get (i); -if (thisEntry.entryName.equals (firstFile)) { -this.directory.remove (i); -this.directory.add (1, thisEntry); -break; -}} -}this.data = new javajs.util.SB (); -this.data.append ("Compound Document File Directory: "); -this.data.append (this.getDirectoryListing ("|")); -this.data.append ("\n"); -binaryFileList = "|" + binaryFileList + "|"; -for (var i = 0; i < this.directory.size (); i++) { -var thisEntry = this.directory.get (i); -if (!thisEntry.isEmpty && thisEntry.entryType != 5) { -var name = thisEntry.entryName; -if (name.endsWith (".gz")) name = name.substring (0, name.length - 3); -this.data.append ("BEGIN Directory Entry ").append (name).append ("\n"); -this.data.appendSB (this.getEntryAsString (thisEntry, binaryFileList.indexOf ("|" + thisEntry.entryName + "|") >= 0)); -this.data.append ("\n"); -this.data.append ("END Directory Entry ").append (thisEntry.entryName).append ("\n"); -}} -this.close (); -return this.data; -}, "~S,~S"); -Clazz.defineMethod (c$, "getFileAsString", -function (entryName) { -for (var i = 0; i < this.directory.size (); i++) { -var thisEntry = this.directory.get (i); -if (thisEntry.entryName.equals (entryName)) return this.getEntryAsString (thisEntry, false); -} -return new javajs.util.SB (); -}, "~S"); -Clazz.defineMethod (c$, "getOffset", -($fz = function (SID) { -return (SID + 1) * this.sectorSize; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "gotoSector", -($fz = function (SID) { -this.seek (this.getOffset (SID)); -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "readHeader", -($fz = function () { -if (!this.header.readData ()) return false; -this.sectorSize = 1 << this.header.sectorPower; -this.shortSectorSize = 1 << this.header.shortSectorPower; -this.nShortSectorsPerStandardSector = Clazz.doubleToInt (this.sectorSize / this.shortSectorSize); -this.nIntPerSector = Clazz.doubleToInt (this.sectorSize / 4); -this.nDirEntriesperSector = Clazz.doubleToInt (this.sectorSize / 128); -return true; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getSectorAllocationTable", -($fz = function () { -var nSID = 0; -var thisSID; -this.SAT = Clazz.newIntArray (this.header.nSATsectors * this.nIntPerSector + 109, 0); -try { -for (var i = 0; i < 109; i++) { -thisSID = this.header.MSAT0[i]; -if (thisSID < 0) break; -this.gotoSector (thisSID); -for (var j = 0; j < this.nIntPerSector; j++) { -this.SAT[nSID++] = this.readInt (); -} -} -var nMaster = this.header.nAdditionalMATsectors; -thisSID = this.header.SID_MSAT_next; -var MSAT = Clazz.newIntArray (this.nIntPerSector, 0); -out : while (nMaster-- > 0 && thisSID >= 0) { -this.gotoSector (thisSID); -for (var i = 0; i < this.nIntPerSector; i++) MSAT[i] = this.readInt (); - -for (var i = 0; i < this.nIntPerSector - 1; i++) { -thisSID = MSAT[i]; -if (thisSID < 0) break out; -this.gotoSector (thisSID); -for (var j = this.nIntPerSector; --j >= 0; ) this.SAT[nSID++] = this.readInt (); - -} -thisSID = MSAT[this.nIntPerSector - 1]; -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getShortSectorAllocationTable", -($fz = function () { -var nSSID = 0; -var thisSID = this.header.SID_SSAT_start; -var nMax = this.header.nSSATsectors * this.nIntPerSector; -this.SSAT = Clazz.newIntArray (nMax, 0); -try { -while (thisSID > 0 && nSSID < nMax) { -this.gotoSector (thisSID); -for (var j = 0; j < this.nIntPerSector; j++) { -this.SSAT[nSSID++] = this.readInt (); -} -thisSID = this.SAT[thisSID]; -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getDirectoryTable", -($fz = function () { -var thisSID = this.header.SID_DIR_start; -var thisEntry; -this.rootEntry = null; -try { -while (thisSID > 0) { -this.gotoSector (thisSID); -for (var j = this.nDirEntriesperSector; --j >= 0; ) { -thisEntry = new javajs.util.CompoundDocDirEntry (this); -thisEntry.readData (); -if (thisEntry.lenStream > 0) { -this.directory.addLast (thisEntry); -}if (thisEntry.entryType == 5) this.rootEntry = thisEntry; -} -thisSID = this.SAT[thisSID]; -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getEntryAsString", -($fz = function (thisEntry, asBinaryString) { -if (thisEntry.isEmpty) return new javajs.util.SB (); -return (thisEntry.isStandard ? this.getStandardStringData (thisEntry.SIDfirstSector, thisEntry.lenStream, asBinaryString) : this.getShortStringData (thisEntry.SIDfirstSector, thisEntry.lenStream, asBinaryString)); -}, $fz.isPrivate = true, $fz), "javajs.util.CompoundDocDirEntry,~B"); -Clazz.defineMethod (c$, "getStandardStringData", -($fz = function (thisSID, nBytes, asBinaryString) { -var data = new javajs.util.SB (); -var byteBuf = Clazz.newByteArray (this.sectorSize, 0); -var gzipData = new javajs.util.ZipData (nBytes); -try { -while (thisSID > 0 && nBytes > 0) { -this.gotoSector (thisSID); -nBytes = this.getSectorData (data, byteBuf, this.sectorSize, nBytes, asBinaryString, gzipData); -thisSID = this.SAT[thisSID]; -} -if (nBytes == -9999) return new javajs.util.SB (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -if (gzipData.isEnabled) gzipData.addTo (this.jzt, data); -return data; -}, $fz.isPrivate = true, $fz), "~N,~N,~B"); -Clazz.defineMethod (c$, "getSectorData", -($fz = function (data, byteBuf, nSectorBytes, nBytes, asBinaryString, gzipData) { -this.readByteArray (byteBuf, 0, byteBuf.length); -var n = gzipData.addBytes (byteBuf, nSectorBytes, nBytes); -if (n >= 0) return n; -if (asBinaryString) { -for (var i = 0; i < nSectorBytes; i++) { -data.append (Integer.toHexString (byteBuf[i] & 0xFF)).appendC (' '); -if (--nBytes < 1) break; -} -} else { -for (var i = 0; i < nSectorBytes; i++) { -if (byteBuf[i] == 0) return -9999; -data.appendC (String.fromCharCode (byteBuf[i])); -if (--nBytes < 1) break; -} -}return nBytes; -}, $fz.isPrivate = true, $fz), "javajs.util.SB,~A,~N,~N,~B,javajs.util.ZipData"); -Clazz.defineMethod (c$, "getShortStringData", -($fz = function (shortSID, nBytes, asBinaryString) { -var data = new javajs.util.SB (); -if (this.rootEntry == null) return data; -var thisSID = this.rootEntry.SIDfirstSector; -var ptShort = 0; -var byteBuf = Clazz.newByteArray (this.shortSectorSize, 0); -var gzipData = new javajs.util.ZipData (nBytes); -try { -while (thisSID >= 0 && shortSID >= 0 && nBytes > 0) { -while (shortSID - ptShort >= this.nShortSectorsPerStandardSector) { -ptShort += this.nShortSectorsPerStandardSector; -thisSID = this.SAT[thisSID]; -} -this.seek (this.getOffset (thisSID) + (shortSID - ptShort) * this.shortSectorSize); -nBytes = this.getSectorData (data, byteBuf, this.shortSectorSize, nBytes, asBinaryString, gzipData); -shortSID = this.SSAT[shortSID]; -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (data.toString ()); -System.out.println ("reader error in CompoundDocument " + e.toString ()); -} else { -throw e; -} -} -if (gzipData.isEnabled) gzipData.addTo (this.jzt, data); -return data; -}, $fz.isPrivate = true, $fz), "~N,~N,~B"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.BinaryDocument", "$.CompoundDocHeader", "$.Lst"], "javajs.util.CompoundDocument", ["java.io.DataInputStream", "javajs.util.CompoundDocDirEntry", "$.SB", "$.ZipData"], function () { +c$ = Clazz.decorateAsClass (function () { +this.header = null; +this.directory = null; +this.rootEntry = null; +this.SAT = null; +this.SSAT = null; +this.sectorSize = 0; +this.shortSectorSize = 0; +this.nShortSectorsPerStandardSector = 0; +this.nIntPerSector = 0; +this.nDirEntriesperSector = 0; +this.data = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "CompoundDocument", javajs.util.BinaryDocument); +Clazz.prepareFields (c$, function () { +this.header = new javajs.util.CompoundDocHeader (this); +this.directory = new javajs.util.Lst (); +}); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.util.CompoundDocument); +this.isBigEndian = true; +}); +Clazz.overrideMethod (c$, "setStream", +function (jzt, bis, isBigEndian) { +this.jzt = jzt; +if (!this.isRandom) { +this.stream = new java.io.DataInputStream (bis); +}this.stream.mark (2147483647); +if (!this.readHeader ()) return; +this.getSectorAllocationTable (); +this.getShortSectorAllocationTable (); +this.getDirectoryTable (); +}, "javajs.api.GenericZipTools,java.io.BufferedInputStream,~B"); +Clazz.defineMethod (c$, "getDirectory", +function () { +return this.directory; +}); +Clazz.defineMethod (c$, "getDirectoryListing", +function (separator) { +var str = ""; +for (var i = 0; i < this.directory.size (); i++) { +var thisEntry = this.directory.get (i); +if (!thisEntry.isEmpty) str += separator + thisEntry.entryName + "\tlen=" + thisEntry.lenStream + "\tSID=" + thisEntry.SIDfirstSector + (thisEntry.isStandard ? "\tfileOffset=" + this.getOffset (thisEntry.SIDfirstSector) : ""); +} +return str; +}, "~S"); +Clazz.defineMethod (c$, "getAllData", +function () { +return this.getAllDataFiles (null, null); +}); +Clazz.overrideMethod (c$, "getAllDataMapped", +function (prefix, binaryFileList, fileData) { +fileData.put ("#Directory_Listing", this.getDirectoryListing ("|")); +binaryFileList = "|" + binaryFileList + "|"; +for (var i = 0; i < this.directory.size (); i++) { +var thisEntry = this.directory.get (i); +if (!thisEntry.isEmpty && thisEntry.entryType != 5) { +var name = thisEntry.entryName; +System.out.println ("CompoundDocument file " + name); +var isBinary = (binaryFileList.indexOf ("|" + name + "|") >= 0); +if (isBinary) name += ":asBinaryString"; +var data = new javajs.util.SB (); +data.append ("BEGIN Directory Entry ").append (name).append ("\n"); +data.appendSB (this.getEntryAsString (thisEntry, isBinary)); +data.append ("\nEND Directory Entry ").append (name).append ("\n"); +fileData.put (prefix + "/" + name, data.toString ()); +}} +this.close (); +}, "~S,~S,java.util.Map"); +Clazz.overrideMethod (c$, "getAllDataFiles", +function (binaryFileList, firstFile) { +if (firstFile != null) { +for (var i = 0; i < this.directory.size (); i++) { +var thisEntry = this.directory.get (i); +if (thisEntry.entryName.equals (firstFile)) { +this.directory.remove (i); +this.directory.add (1, thisEntry); +break; +}} +}this.data = new javajs.util.SB (); +this.data.append ("Compound Document File Directory: "); +this.data.append (this.getDirectoryListing ("|")); +this.data.append ("\n"); +binaryFileList = "|" + binaryFileList + "|"; +for (var i = 0; i < this.directory.size (); i++) { +var thisEntry = this.directory.get (i); +if (!thisEntry.isEmpty && thisEntry.entryType != 5) { +var name = thisEntry.entryName; +if (name.endsWith (".gz")) name = name.substring (0, name.length - 3); +this.data.append ("BEGIN Directory Entry ").append (name).append ("\n"); +this.data.appendSB (this.getEntryAsString (thisEntry, binaryFileList.indexOf ("|" + thisEntry.entryName + "|") >= 0)); +this.data.append ("\n"); +this.data.append ("END Directory Entry ").append (thisEntry.entryName).append ("\n"); +}} +this.close (); +return this.data; +}, "~S,~S"); +Clazz.defineMethod (c$, "getFileAsString", +function (entryName) { +for (var i = 0; i < this.directory.size (); i++) { +var thisEntry = this.directory.get (i); +if (thisEntry.entryName.equals (entryName)) return this.getEntryAsString (thisEntry, false); +} +return new javajs.util.SB (); +}, "~S"); +Clazz.defineMethod (c$, "getOffset", +($fz = function (SID) { +return (SID + 1) * this.sectorSize; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "gotoSector", +($fz = function (SID) { +this.seek (this.getOffset (SID)); +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "readHeader", +($fz = function () { +if (!this.header.readData ()) return false; +this.sectorSize = 1 << this.header.sectorPower; +this.shortSectorSize = 1 << this.header.shortSectorPower; +this.nShortSectorsPerStandardSector = Clazz.doubleToInt (this.sectorSize / this.shortSectorSize); +this.nIntPerSector = Clazz.doubleToInt (this.sectorSize / 4); +this.nDirEntriesperSector = Clazz.doubleToInt (this.sectorSize / 128); +return true; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getSectorAllocationTable", +($fz = function () { +var nSID = 0; +var thisSID; +this.SAT = Clazz.newIntArray (this.header.nSATsectors * this.nIntPerSector + 109, 0); +try { +for (var i = 0; i < 109; i++) { +thisSID = this.header.MSAT0[i]; +if (thisSID < 0) break; +this.gotoSector (thisSID); +for (var j = 0; j < this.nIntPerSector; j++) { +this.SAT[nSID++] = this.readInt (); +} +} +var nMaster = this.header.nAdditionalMATsectors; +thisSID = this.header.SID_MSAT_next; +var MSAT = Clazz.newIntArray (this.nIntPerSector, 0); +out : while (nMaster-- > 0 && thisSID >= 0) { +this.gotoSector (thisSID); +for (var i = 0; i < this.nIntPerSector; i++) MSAT[i] = this.readInt (); + +for (var i = 0; i < this.nIntPerSector - 1; i++) { +thisSID = MSAT[i]; +if (thisSID < 0) break out; +this.gotoSector (thisSID); +for (var j = this.nIntPerSector; --j >= 0; ) this.SAT[nSID++] = this.readInt (); + +} +thisSID = MSAT[this.nIntPerSector - 1]; +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getShortSectorAllocationTable", +($fz = function () { +var nSSID = 0; +var thisSID = this.header.SID_SSAT_start; +var nMax = this.header.nSSATsectors * this.nIntPerSector; +this.SSAT = Clazz.newIntArray (nMax, 0); +try { +while (thisSID > 0 && nSSID < nMax) { +this.gotoSector (thisSID); +for (var j = 0; j < this.nIntPerSector; j++) { +this.SSAT[nSSID++] = this.readInt (); +} +thisSID = this.SAT[thisSID]; +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getDirectoryTable", +($fz = function () { +var thisSID = this.header.SID_DIR_start; +var thisEntry; +this.rootEntry = null; +try { +while (thisSID > 0) { +this.gotoSector (thisSID); +for (var j = this.nDirEntriesperSector; --j >= 0; ) { +thisEntry = new javajs.util.CompoundDocDirEntry (this); +thisEntry.readData (); +if (thisEntry.lenStream > 0) { +this.directory.addLast (thisEntry); +}if (thisEntry.entryType == 5) this.rootEntry = thisEntry; +} +thisSID = this.SAT[thisSID]; +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getEntryAsString", +($fz = function (thisEntry, asBinaryString) { +if (thisEntry.isEmpty) return new javajs.util.SB (); +return (thisEntry.isStandard ? this.getStandardStringData (thisEntry.SIDfirstSector, thisEntry.lenStream, asBinaryString) : this.getShortStringData (thisEntry.SIDfirstSector, thisEntry.lenStream, asBinaryString)); +}, $fz.isPrivate = true, $fz), "javajs.util.CompoundDocDirEntry,~B"); +Clazz.defineMethod (c$, "getStandardStringData", +($fz = function (thisSID, nBytes, asBinaryString) { +var data = new javajs.util.SB (); +var byteBuf = Clazz.newByteArray (this.sectorSize, 0); +var gzipData = new javajs.util.ZipData (nBytes); +try { +while (thisSID > 0 && nBytes > 0) { +this.gotoSector (thisSID); +nBytes = this.getSectorData (data, byteBuf, this.sectorSize, nBytes, asBinaryString, gzipData); +thisSID = this.SAT[thisSID]; +} +if (nBytes == -9999) return new javajs.util.SB (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +if (gzipData.isEnabled) gzipData.addTo (this.jzt, data); +return data; +}, $fz.isPrivate = true, $fz), "~N,~N,~B"); +Clazz.defineMethod (c$, "getSectorData", +($fz = function (data, byteBuf, nSectorBytes, nBytes, asBinaryString, gzipData) { +this.readByteArray (byteBuf, 0, byteBuf.length); +var n = gzipData.addBytes (byteBuf, nSectorBytes, nBytes); +if (n >= 0) return n; +if (asBinaryString) { +for (var i = 0; i < nSectorBytes; i++) { +data.append (Integer.toHexString (byteBuf[i] & 0xFF)).appendC (' '); +if (--nBytes < 1) break; +} +} else { +for (var i = 0; i < nSectorBytes; i++) { +if (byteBuf[i] == 0) return -9999; +data.appendC (String.fromCharCode (byteBuf[i])); +if (--nBytes < 1) break; +} +}return nBytes; +}, $fz.isPrivate = true, $fz), "javajs.util.SB,~A,~N,~N,~B,javajs.util.ZipData"); +Clazz.defineMethod (c$, "getShortStringData", +($fz = function (shortSID, nBytes, asBinaryString) { +var data = new javajs.util.SB (); +if (this.rootEntry == null) return data; +var thisSID = this.rootEntry.SIDfirstSector; +var ptShort = 0; +var byteBuf = Clazz.newByteArray (this.shortSectorSize, 0); +var gzipData = new javajs.util.ZipData (nBytes); +try { +while (thisSID >= 0 && shortSID >= 0 && nBytes > 0) { +while (shortSID - ptShort >= this.nShortSectorsPerStandardSector) { +ptShort += this.nShortSectorsPerStandardSector; +thisSID = this.SAT[thisSID]; +} +this.seek (this.getOffset (thisSID) + (shortSID - ptShort) * this.shortSectorSize); +nBytes = this.getSectorData (data, byteBuf, this.shortSectorSize, nBytes, asBinaryString, gzipData); +shortSID = this.SSAT[shortSID]; +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (data.toString ()); +System.out.println ("reader error in CompoundDocument " + e.toString ()); +} else { +throw e; +} +} +if (gzipData.isEnabled) gzipData.addTo (this.jzt, data); +return data; +}, $fz.isPrivate = true, $fz), "~N,~N,~B"); +}); diff --git a/bin/javajs/util/DF.js b/bin/javajs/util/DF.js index 9247146..6122352 100644 --- a/bin/javajs/util/DF.js +++ b/bin/javajs/util/DF.js @@ -1,78 +1,78 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.lang.Boolean"], "javajs.util.DF", ["java.lang.Double", "$.Float", "javajs.util.PT", "$.SB"], function () { -c$ = Clazz.declareType (javajs.util, "DF"); -c$.setUseNumberLocalization = Clazz.defineMethod (c$, "setUseNumberLocalization", -function (TF) { -javajs.util.DF.useNumberLocalization[0] = (TF ? Boolean.TRUE : Boolean.FALSE); -}, "~B"); -c$.formatDecimalDbl = Clazz.defineMethod (c$, "formatDecimalDbl", -function (value, decimalDigits) { -if (decimalDigits == 2147483647 || value == -Infinity || value == Infinity || Double.isNaN (value)) return "" + value; -return javajs.util.DF.formatDecimal (value, decimalDigits); -}, "~N,~N"); -c$.formatDecimal = Clazz.defineMethod (c$, "formatDecimal", -function (value, decimalDigits) { -if (decimalDigits == 2147483647 || value == -Infinity || value == Infinity || Float.isNaN (value)) return "" + value; -var n; -if (decimalDigits < 0) { -decimalDigits = -decimalDigits; -if (decimalDigits > javajs.util.DF.formattingStrings.length) decimalDigits = javajs.util.DF.formattingStrings.length; -if (value == 0) return javajs.util.DF.formattingStrings[decimalDigits] + "E+0"; -n = 0; -var d; -if (Math.abs (value) < 1) { -n = 10; -d = value * 1e-10; -} else { -n = -10; -d = value * 1e10; -}var s = ("" + d).toUpperCase (); -var i = s.indexOf ("E"); -n = javajs.util.PT.parseInt (s.substring (i + 1)) + n; -return (i < 0 ? "" + value : javajs.util.DF.formatDecimal (javajs.util.PT.parseFloat (s.substring (0, i)), decimalDigits - 1) + "E" + (n >= 0 ? "+" : "") + n); -}if (decimalDigits >= javajs.util.DF.formattingStrings.length) decimalDigits = javajs.util.DF.formattingStrings.length - 1; -var s1 = ("" + value).toUpperCase (); -var pt = s1.indexOf ("."); -if (pt < 0) return s1 + javajs.util.DF.formattingStrings[decimalDigits].substring (1); -var isNeg = s1.startsWith ("-"); -if (isNeg) { -s1 = s1.substring (1); -pt--; -}var pt1 = s1.indexOf ("E-"); -if (pt1 > 0) { -n = javajs.util.PT.parseInt (s1.substring (pt1 + 1)); -s1 = "0." + "0000000000000000000000000000000000000000".substring (0, -n - 1) + s1.substring (0, 1) + s1.substring (2, pt1); -pt = 1; -}pt1 = s1.indexOf ("E"); -if (pt1 > 0) { -n = javajs.util.PT.parseInt (s1.substring (pt1 + 1)); -s1 = s1.substring (0, 1) + s1.substring (2, pt1) + "0000000000000000000000000000000000000000"; -s1 = s1.substring (0, n + 1) + "." + s1.substring (n + 1); -pt = s1.indexOf ("."); -}var len = s1.length; -var pt2 = decimalDigits + pt + 1; -if (pt2 < len && s1.charAt (pt2) >= '5') { -return javajs.util.DF.formatDecimal (value + (isNeg ? -1 : 1) * javajs.util.DF.formatAdds[decimalDigits], decimalDigits); -}var sb = javajs.util.SB.newS (s1.substring (0, (decimalDigits == 0 ? pt : ++pt))); -for (var i = 0; i < decimalDigits; i++, pt++) { -if (pt < len) sb.appendC (s1.charAt (pt)); - else sb.appendC ('0'); -} -s1 = (isNeg ? "-" : "") + sb; -return (Boolean.TRUE.equals (javajs.util.DF.useNumberLocalization[0]) ? s1 : s1.$replace (',', '.')); -}, "~N,~N"); -c$.formatDecimalTrimmed = Clazz.defineMethod (c$, "formatDecimalTrimmed", -function (x, precision) { -var str = javajs.util.DF.formatDecimalDbl (x, precision); -var m = str.length - 1; -var zero = '0'; -while (m >= 0 && str.charAt (m) == zero) m--; - -return str.substring (0, m + 1); -}, "~N,~N"); -Clazz.defineStatics (c$, -"formattingStrings", Clazz.newArray (-1, ["0", "0.0", "0.00", "0.000", "0.0000", "0.00000", "0.000000", "0.0000000", "0.00000000", "0.000000000"]), -"zeros", "0000000000000000000000000000000000000000", -"formatAdds", Clazz.newFloatArray (-1, [0.5, 0.05, 0.005, 0.0005, 0.00005, 0.000005, 0.0000005, 0.00000005, 0.000000005, 0.0000000005])); -c$.useNumberLocalization = c$.prototype.useNumberLocalization = Clazz.newArray (-1, [Boolean.TRUE]); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.lang.Boolean"], "javajs.util.DF", ["java.lang.Double", "$.Float", "javajs.util.PT", "$.SB"], function () { +c$ = Clazz.declareType (javajs.util, "DF"); +c$.setUseNumberLocalization = Clazz.defineMethod (c$, "setUseNumberLocalization", +function (TF) { +javajs.util.DF.useNumberLocalization[0] = (TF ? Boolean.TRUE : Boolean.FALSE); +}, "~B"); +c$.formatDecimalDbl = Clazz.defineMethod (c$, "formatDecimalDbl", +function (value, decimalDigits) { +if (decimalDigits == 2147483647 || value == -Infinity || value == Infinity || Double.isNaN (value)) return "" + value; +return javajs.util.DF.formatDecimal (value, decimalDigits); +}, "~N,~N"); +c$.formatDecimal = Clazz.defineMethod (c$, "formatDecimal", +function (value, decimalDigits) { +if (decimalDigits == 2147483647 || value == -Infinity || value == Infinity || Float.isNaN (value)) return "" + value; +var n; +if (decimalDigits < 0) { +decimalDigits = -decimalDigits; +if (decimalDigits > javajs.util.DF.formattingStrings.length) decimalDigits = javajs.util.DF.formattingStrings.length; +if (value == 0) return javajs.util.DF.formattingStrings[decimalDigits] + "E+0"; +n = 0; +var d; +if (Math.abs (value) < 1) { +n = 10; +d = value * 1e-10; +} else { +n = -10; +d = value * 1e10; +}var s = ("" + d).toUpperCase (); +var i = s.indexOf ("E"); +n = javajs.util.PT.parseInt (s.substring (i + 1)) + n; +return (i < 0 ? "" + value : javajs.util.DF.formatDecimal (javajs.util.PT.parseFloat (s.substring (0, i)), decimalDigits - 1) + "E" + (n >= 0 ? "+" : "") + n); +}if (decimalDigits >= javajs.util.DF.formattingStrings.length) decimalDigits = javajs.util.DF.formattingStrings.length - 1; +var s1 = ("" + value).toUpperCase (); +var pt = s1.indexOf ("."); +if (pt < 0) return s1 + javajs.util.DF.formattingStrings[decimalDigits].substring (1); +var isNeg = s1.startsWith ("-"); +if (isNeg) { +s1 = s1.substring (1); +pt--; +}var pt1 = s1.indexOf ("E-"); +if (pt1 > 0) { +n = javajs.util.PT.parseInt (s1.substring (pt1 + 1)); +s1 = "0." + "0000000000000000000000000000000000000000".substring (0, -n - 1) + s1.substring (0, 1) + s1.substring (2, pt1); +pt = 1; +}pt1 = s1.indexOf ("E"); +if (pt1 > 0) { +n = javajs.util.PT.parseInt (s1.substring (pt1 + 1)); +s1 = s1.substring (0, 1) + s1.substring (2, pt1) + "0000000000000000000000000000000000000000"; +s1 = s1.substring (0, n + 1) + "." + s1.substring (n + 1); +pt = s1.indexOf ("."); +}var len = s1.length; +var pt2 = decimalDigits + pt + 1; +if (pt2 < len && s1.charAt (pt2) >= '5') { +return javajs.util.DF.formatDecimal (value + (isNeg ? -1 : 1) * javajs.util.DF.formatAdds[decimalDigits], decimalDigits); +}var sb = javajs.util.SB.newS (s1.substring (0, (decimalDigits == 0 ? pt : ++pt))); +for (var i = 0; i < decimalDigits; i++, pt++) { +if (pt < len) sb.appendC (s1.charAt (pt)); + else sb.appendC ('0'); +} +s1 = (isNeg ? "-" : "") + sb; +return (Boolean.TRUE.equals (javajs.util.DF.useNumberLocalization[0]) ? s1 : s1.$replace (',', '.')); +}, "~N,~N"); +c$.formatDecimalTrimmed = Clazz.defineMethod (c$, "formatDecimalTrimmed", +function (x, precision) { +var str = javajs.util.DF.formatDecimalDbl (x, precision); +var m = str.length - 1; +var zero = '0'; +while (m >= 0 && str.charAt (m) == zero) m--; + +return str.substring (0, m + 1); +}, "~N,~N"); +Clazz.defineStatics (c$, +"formattingStrings", Clazz.newArray (-1, ["0", "0.0", "0.00", "0.000", "0.0000", "0.00000", "0.000000", "0.0000000", "0.00000000", "0.000000000"]), +"zeros", "0000000000000000000000000000000000000000", +"formatAdds", Clazz.newFloatArray (-1, [0.5, 0.05, 0.005, 0.0005, 0.00005, 0.000005, 0.0000005, 0.00000005, 0.000000005, 0.0000000005])); +c$.useNumberLocalization = c$.prototype.useNumberLocalization = Clazz.newArray (-1, [Boolean.TRUE]); +}); diff --git a/bin/javajs/util/DataReader.js b/bin/javajs/util/DataReader.js index 3be547c..ea8774f 100644 --- a/bin/javajs/util/DataReader.js +++ b/bin/javajs/util/DataReader.js @@ -1,34 +1,34 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.io.BufferedReader"], "javajs.util.DataReader", ["java.io.StringReader"], function () { -c$ = Clazz.decorateAsClass (function () { -this.ptMark = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "DataReader", java.io.BufferedReader); -Clazz.makeConstructor (c$, -function () { -Clazz.superConstructor (this, javajs.util.DataReader, [ new java.io.StringReader ("")]); -}); -Clazz.defineMethod (c$, "getBufferedReader", -function () { -return this; -}); -Clazz.defineMethod (c$, "readBuf", -function (buf, off, len) { -var nRead = 0; -var line = this.readLine (); -if (line == null) return 0; -var linept = 0; -var linelen = line.length; -for (var i = off; i < len && linelen >= 0; i++) { -if (linept >= linelen) { -linept = 0; -buf[i] = '\n'; -line = this.readLine (); -linelen = (line == null ? -1 : line.length); -} else { -buf[i] = line.charAt (linept++); -}nRead++; -} -return nRead; -}, "~A,~N,~N"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.io.BufferedReader"], "javajs.util.DataReader", ["java.io.StringReader"], function () { +c$ = Clazz.decorateAsClass (function () { +this.ptMark = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "DataReader", java.io.BufferedReader); +Clazz.makeConstructor (c$, +function () { +Clazz.superConstructor (this, javajs.util.DataReader, [ new java.io.StringReader ("")]); +}); +Clazz.defineMethod (c$, "getBufferedReader", +function () { +return this; +}); +Clazz.defineMethod (c$, "readBuf", +function (buf, off, len) { +var nRead = 0; +var line = this.readLine (); +if (line == null) return 0; +var linept = 0; +var linelen = line.length; +for (var i = off; i < len && linelen >= 0; i++) { +if (linept >= linelen) { +linept = 0; +buf[i] = '\n'; +line = this.readLine (); +linelen = (line == null ? -1 : line.length); +} else { +buf[i] = line.charAt (linept++); +}nRead++; +} +return nRead; +}, "~A,~N,~N"); +}); diff --git a/bin/javajs/util/Eigen.js b/bin/javajs/util/Eigen.js index b08955b..4d28a61 100644 --- a/bin/javajs/util/Eigen.js +++ b/bin/javajs/util/Eigen.js @@ -1,254 +1,254 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.EigenInterface"], "javajs.util.Eigen", ["javajs.util.V3"], function () { -c$ = Clazz.decorateAsClass (function () { -this.n = 3; -this.d = null; -this.e = null; -this.V = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "Eigen", null, javajs.api.EigenInterface); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "set", -function (n) { -this.n = n; -this.V = Clazz.newDoubleArray (n, n, 0); -this.d = Clazz.newDoubleArray (n, 0); -this.e = Clazz.newDoubleArray (n, 0); -return this; -}, "~N"); -Clazz.overrideMethod (c$, "setM", -function (m) { -this.set (m.length); -this.calc (m); -return this; -}, "~A"); -Clazz.overrideMethod (c$, "getEigenvalues", -function () { -return this.d; -}); -Clazz.overrideMethod (c$, "fillFloatArrays", -function (eigenVectors, eigenValues) { -for (var i = 0; i < 3; i++) { -if (eigenVectors != null) { -if (eigenVectors[i] == null) eigenVectors[i] = new javajs.util.V3 (); -eigenVectors[i].set (this.V[0][i], this.V[1][i], this.V[2][i]); -}if (eigenValues != null) eigenValues[i] = this.d[i]; -} -}, "~A,~A"); -Clazz.overrideMethod (c$, "getEigenvectorsFloatTransposed", -function () { -var f = Clazz.newFloatArray (this.n, this.n, 0); -for (var i = this.n; --i >= 0; ) for (var j = this.n; --j >= 0; ) f[j][i] = this.V[i][j]; - - -return f; -}); -Clazz.defineMethod (c$, "calc", -function (A) { -for (var i = 0; i < this.n; i++) { -for (var j = 0; j < this.n; j++) { -this.V[i][j] = A[i][j]; -} -} -this.tred2 (); -this.tql2 (); -}, "~A"); -Clazz.defineMethod (c$, "getRealEigenvalues", -function () { -return this.d; -}); -Clazz.defineMethod (c$, "getImagEigenvalues", -function () { -return this.e; -}); -Clazz.defineMethod (c$, "tred2", -($fz = function () { -for (var j = 0; j < this.n; j++) { -this.d[j] = this.V[this.n - 1][j]; -} -for (var i = this.n - 1; i > 0; i--) { -var scale = 0.0; -var h = 0.0; -for (var k = 0; k < i; k++) { -scale = scale + Math.abs (this.d[k]); -} -if (scale == 0.0) { -this.e[i] = this.d[i - 1]; -for (var j = 0; j < i; j++) { -this.d[j] = this.V[i - 1][j]; -this.V[i][j] = 0.0; -this.V[j][i] = 0.0; -} -} else { -for (var k = 0; k < i; k++) { -this.d[k] /= scale; -h += this.d[k] * this.d[k]; -} -var f = this.d[i - 1]; -var g = Math.sqrt (h); -if (f > 0) { -g = -g; -}this.e[i] = scale * g; -h = h - f * g; -this.d[i - 1] = f - g; -for (var j = 0; j < i; j++) { -this.e[j] = 0.0; -} -for (var j = 0; j < i; j++) { -f = this.d[j]; -this.V[j][i] = f; -g = this.e[j] + this.V[j][j] * f; -for (var k = j + 1; k <= i - 1; k++) { -g += this.V[k][j] * this.d[k]; -this.e[k] += this.V[k][j] * f; -} -this.e[j] = g; -} -f = 0.0; -for (var j = 0; j < i; j++) { -this.e[j] /= h; -f += this.e[j] * this.d[j]; -} -var hh = f / (h + h); -for (var j = 0; j < i; j++) { -this.e[j] -= hh * this.d[j]; -} -for (var j = 0; j < i; j++) { -f = this.d[j]; -g = this.e[j]; -for (var k = j; k <= i - 1; k++) { -this.V[k][j] -= (f * this.e[k] + g * this.d[k]); -} -this.d[j] = this.V[i - 1][j]; -this.V[i][j] = 0.0; -} -}this.d[i] = h; -} -for (var i = 0; i < this.n - 1; i++) { -this.V[this.n - 1][i] = this.V[i][i]; -this.V[i][i] = 1.0; -var h = this.d[i + 1]; -if (h != 0.0) { -for (var k = 0; k <= i; k++) { -this.d[k] = this.V[k][i + 1] / h; -} -for (var j = 0; j <= i; j++) { -var g = 0.0; -for (var k = 0; k <= i; k++) { -g += this.V[k][i + 1] * this.V[k][j]; -} -for (var k = 0; k <= i; k++) { -this.V[k][j] -= g * this.d[k]; -} -} -}for (var k = 0; k <= i; k++) { -this.V[k][i + 1] = 0.0; -} -} -for (var j = 0; j < this.n; j++) { -this.d[j] = this.V[this.n - 1][j]; -this.V[this.n - 1][j] = 0.0; -} -this.V[this.n - 1][this.n - 1] = 1.0; -this.e[0] = 0.0; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "tql2", -($fz = function () { -for (var i = 1; i < this.n; i++) { -this.e[i - 1] = this.e[i]; -} -this.e[this.n - 1] = 0.0; -var f = 0.0; -var tst1 = 0.0; -var eps = Math.pow (2.0, -52.0); -for (var l = 0; l < this.n; l++) { -tst1 = Math.max (tst1, Math.abs (this.d[l]) + Math.abs (this.e[l])); -var m = l; -while (m < this.n) { -if (Math.abs (this.e[m]) <= eps * tst1) { -break; -}m++; -} -if (m > l) { -var iter = 0; -do { -iter = iter + 1; -var g = this.d[l]; -var p = (this.d[l + 1] - g) / (2.0 * this.e[l]); -var r = javajs.util.Eigen.hypot (p, 1.0); -if (p < 0) { -r = -r; -}this.d[l] = this.e[l] / (p + r); -this.d[l + 1] = this.e[l] * (p + r); -var dl1 = this.d[l + 1]; -var h = g - this.d[l]; -for (var i = l + 2; i < this.n; i++) { -this.d[i] -= h; -} -f = f + h; -p = this.d[m]; -var c = 1.0; -var c2 = c; -var c3 = c; -var el1 = this.e[l + 1]; -var s = 0.0; -var s2 = 0.0; -for (var i = m - 1; i >= l; i--) { -c3 = c2; -c2 = c; -s2 = s; -g = c * this.e[i]; -h = c * p; -r = javajs.util.Eigen.hypot (p, this.e[i]); -this.e[i + 1] = s * r; -s = this.e[i] / r; -c = p / r; -p = c * this.d[i] - s * g; -this.d[i + 1] = h + s * (c * g + s * this.d[i]); -for (var k = 0; k < this.n; k++) { -h = this.V[k][i + 1]; -this.V[k][i + 1] = s * this.V[k][i] + c * h; -this.V[k][i] = c * this.V[k][i] - s * h; -} -} -p = -s * s2 * c3 * el1 * this.e[l] / dl1; -this.e[l] = s * p; -this.d[l] = c * p; -} while (Math.abs (this.e[l]) > eps * tst1); -}this.d[l] = this.d[l] + f; -this.e[l] = 0.0; -} -for (var i = 0; i < this.n - 1; i++) { -var k = i; -var p = this.d[i]; -for (var j = i + 1; j < this.n; j++) { -if (this.d[j] < p) { -k = j; -p = this.d[j]; -}} -if (k != i) { -this.d[k] = this.d[i]; -this.d[i] = p; -for (var j = 0; j < this.n; j++) { -p = this.V[j][i]; -this.V[j][i] = this.V[j][k]; -this.V[j][k] = p; -} -}} -}, $fz.isPrivate = true, $fz)); -c$.hypot = Clazz.defineMethod (c$, "hypot", -($fz = function (a, b) { -var r; -if (Math.abs (a) > Math.abs (b)) { -r = b / a; -r = Math.abs (a) * Math.sqrt (1 + r * r); -} else if (b != 0) { -r = a / b; -r = Math.abs (b) * Math.sqrt (1 + r * r); -} else { -r = 0.0; -}return r; -}, $fz.isPrivate = true, $fz), "~N,~N"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.EigenInterface"], "javajs.util.Eigen", ["javajs.util.V3"], function () { +c$ = Clazz.decorateAsClass (function () { +this.n = 3; +this.d = null; +this.e = null; +this.V = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "Eigen", null, javajs.api.EigenInterface); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "set", +function (n) { +this.n = n; +this.V = Clazz.newDoubleArray (n, n, 0); +this.d = Clazz.newDoubleArray (n, 0); +this.e = Clazz.newDoubleArray (n, 0); +return this; +}, "~N"); +Clazz.overrideMethod (c$, "setM", +function (m) { +this.set (m.length); +this.calc (m); +return this; +}, "~A"); +Clazz.overrideMethod (c$, "getEigenvalues", +function () { +return this.d; +}); +Clazz.overrideMethod (c$, "fillFloatArrays", +function (eigenVectors, eigenValues) { +for (var i = 0; i < 3; i++) { +if (eigenVectors != null) { +if (eigenVectors[i] == null) eigenVectors[i] = new javajs.util.V3 (); +eigenVectors[i].set (this.V[0][i], this.V[1][i], this.V[2][i]); +}if (eigenValues != null) eigenValues[i] = this.d[i]; +} +}, "~A,~A"); +Clazz.overrideMethod (c$, "getEigenvectorsFloatTransposed", +function () { +var f = Clazz.newFloatArray (this.n, this.n, 0); +for (var i = this.n; --i >= 0; ) for (var j = this.n; --j >= 0; ) f[j][i] = this.V[i][j]; + + +return f; +}); +Clazz.defineMethod (c$, "calc", +function (A) { +for (var i = 0; i < this.n; i++) { +for (var j = 0; j < this.n; j++) { +this.V[i][j] = A[i][j]; +} +} +this.tred2 (); +this.tql2 (); +}, "~A"); +Clazz.defineMethod (c$, "getRealEigenvalues", +function () { +return this.d; +}); +Clazz.defineMethod (c$, "getImagEigenvalues", +function () { +return this.e; +}); +Clazz.defineMethod (c$, "tred2", +($fz = function () { +for (var j = 0; j < this.n; j++) { +this.d[j] = this.V[this.n - 1][j]; +} +for (var i = this.n - 1; i > 0; i--) { +var scale = 0.0; +var h = 0.0; +for (var k = 0; k < i; k++) { +scale = scale + Math.abs (this.d[k]); +} +if (scale == 0.0) { +this.e[i] = this.d[i - 1]; +for (var j = 0; j < i; j++) { +this.d[j] = this.V[i - 1][j]; +this.V[i][j] = 0.0; +this.V[j][i] = 0.0; +} +} else { +for (var k = 0; k < i; k++) { +this.d[k] /= scale; +h += this.d[k] * this.d[k]; +} +var f = this.d[i - 1]; +var g = Math.sqrt (h); +if (f > 0) { +g = -g; +}this.e[i] = scale * g; +h = h - f * g; +this.d[i - 1] = f - g; +for (var j = 0; j < i; j++) { +this.e[j] = 0.0; +} +for (var j = 0; j < i; j++) { +f = this.d[j]; +this.V[j][i] = f; +g = this.e[j] + this.V[j][j] * f; +for (var k = j + 1; k <= i - 1; k++) { +g += this.V[k][j] * this.d[k]; +this.e[k] += this.V[k][j] * f; +} +this.e[j] = g; +} +f = 0.0; +for (var j = 0; j < i; j++) { +this.e[j] /= h; +f += this.e[j] * this.d[j]; +} +var hh = f / (h + h); +for (var j = 0; j < i; j++) { +this.e[j] -= hh * this.d[j]; +} +for (var j = 0; j < i; j++) { +f = this.d[j]; +g = this.e[j]; +for (var k = j; k <= i - 1; k++) { +this.V[k][j] -= (f * this.e[k] + g * this.d[k]); +} +this.d[j] = this.V[i - 1][j]; +this.V[i][j] = 0.0; +} +}this.d[i] = h; +} +for (var i = 0; i < this.n - 1; i++) { +this.V[this.n - 1][i] = this.V[i][i]; +this.V[i][i] = 1.0; +var h = this.d[i + 1]; +if (h != 0.0) { +for (var k = 0; k <= i; k++) { +this.d[k] = this.V[k][i + 1] / h; +} +for (var j = 0; j <= i; j++) { +var g = 0.0; +for (var k = 0; k <= i; k++) { +g += this.V[k][i + 1] * this.V[k][j]; +} +for (var k = 0; k <= i; k++) { +this.V[k][j] -= g * this.d[k]; +} +} +}for (var k = 0; k <= i; k++) { +this.V[k][i + 1] = 0.0; +} +} +for (var j = 0; j < this.n; j++) { +this.d[j] = this.V[this.n - 1][j]; +this.V[this.n - 1][j] = 0.0; +} +this.V[this.n - 1][this.n - 1] = 1.0; +this.e[0] = 0.0; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "tql2", +($fz = function () { +for (var i = 1; i < this.n; i++) { +this.e[i - 1] = this.e[i]; +} +this.e[this.n - 1] = 0.0; +var f = 0.0; +var tst1 = 0.0; +var eps = Math.pow (2.0, -52.0); +for (var l = 0; l < this.n; l++) { +tst1 = Math.max (tst1, Math.abs (this.d[l]) + Math.abs (this.e[l])); +var m = l; +while (m < this.n) { +if (Math.abs (this.e[m]) <= eps * tst1) { +break; +}m++; +} +if (m > l) { +var iter = 0; +do { +iter = iter + 1; +var g = this.d[l]; +var p = (this.d[l + 1] - g) / (2.0 * this.e[l]); +var r = javajs.util.Eigen.hypot (p, 1.0); +if (p < 0) { +r = -r; +}this.d[l] = this.e[l] / (p + r); +this.d[l + 1] = this.e[l] * (p + r); +var dl1 = this.d[l + 1]; +var h = g - this.d[l]; +for (var i = l + 2; i < this.n; i++) { +this.d[i] -= h; +} +f = f + h; +p = this.d[m]; +var c = 1.0; +var c2 = c; +var c3 = c; +var el1 = this.e[l + 1]; +var s = 0.0; +var s2 = 0.0; +for (var i = m - 1; i >= l; i--) { +c3 = c2; +c2 = c; +s2 = s; +g = c * this.e[i]; +h = c * p; +r = javajs.util.Eigen.hypot (p, this.e[i]); +this.e[i + 1] = s * r; +s = this.e[i] / r; +c = p / r; +p = c * this.d[i] - s * g; +this.d[i + 1] = h + s * (c * g + s * this.d[i]); +for (var k = 0; k < this.n; k++) { +h = this.V[k][i + 1]; +this.V[k][i + 1] = s * this.V[k][i] + c * h; +this.V[k][i] = c * this.V[k][i] - s * h; +} +} +p = -s * s2 * c3 * el1 * this.e[l] / dl1; +this.e[l] = s * p; +this.d[l] = c * p; +} while (Math.abs (this.e[l]) > eps * tst1); +}this.d[l] = this.d[l] + f; +this.e[l] = 0.0; +} +for (var i = 0; i < this.n - 1; i++) { +var k = i; +var p = this.d[i]; +for (var j = i + 1; j < this.n; j++) { +if (this.d[j] < p) { +k = j; +p = this.d[j]; +}} +if (k != i) { +this.d[k] = this.d[i]; +this.d[i] = p; +for (var j = 0; j < this.n; j++) { +p = this.V[j][i]; +this.V[j][i] = this.V[j][k]; +this.V[j][k] = p; +} +}} +}, $fz.isPrivate = true, $fz)); +c$.hypot = Clazz.defineMethod (c$, "hypot", +($fz = function (a, b) { +var r; +if (Math.abs (a) > Math.abs (b)) { +r = b / a; +r = Math.abs (a) * Math.sqrt (1 + r * r); +} else if (b != 0) { +r = a / b; +r = Math.abs (b) * Math.sqrt (1 + r * r); +} else { +r = 0.0; +}return r; +}, $fz.isPrivate = true, $fz), "~N,~N"); +}); diff --git a/bin/javajs/util/Encoding.js b/bin/javajs/util/Encoding.js index aecf019..d7abfc0 100644 --- a/bin/javajs/util/Encoding.js +++ b/bin/javajs/util/Encoding.js @@ -1,10 +1,10 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.lang.Enum"], "javajs.util.Encoding", null, function () { -c$ = Clazz.declareType (javajs.util, "Encoding", Enum); -Clazz.defineEnumConstant (c$, "NONE", 0, []); -Clazz.defineEnumConstant (c$, "UTF8", 1, []); -Clazz.defineEnumConstant (c$, "UTF_16BE", 2, []); -Clazz.defineEnumConstant (c$, "UTF_16LE", 3, []); -Clazz.defineEnumConstant (c$, "UTF_32BE", 4, []); -Clazz.defineEnumConstant (c$, "UTF_32LE", 5, []); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.lang.Enum"], "javajs.util.Encoding", null, function () { +c$ = Clazz.declareType (javajs.util, "Encoding", Enum); +Clazz.defineEnumConstant (c$, "NONE", 0, []); +Clazz.defineEnumConstant (c$, "UTF8", 1, []); +Clazz.defineEnumConstant (c$, "UTF_16BE", 2, []); +Clazz.defineEnumConstant (c$, "UTF_16LE", 3, []); +Clazz.defineEnumConstant (c$, "UTF_32BE", 4, []); +Clazz.defineEnumConstant (c$, "UTF_32LE", 5, []); +}); diff --git a/bin/javajs/util/LimitedLineReader.js b/bin/javajs/util/LimitedLineReader.js index c8c7764..95d0741 100644 --- a/bin/javajs/util/LimitedLineReader.js +++ b/bin/javajs/util/LimitedLineReader.js @@ -1,33 +1,33 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.buf = null; -this.cchBuf = 0; -this.ichCurrent = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "LimitedLineReader"); -Clazz.makeConstructor (c$, -function (bufferedReader, readLimit) { -bufferedReader.mark (readLimit + 1); -this.buf = Clazz.newCharArray (readLimit, '\0'); -this.cchBuf = Math.max (bufferedReader.read (this.buf, 0, readLimit), 0); -this.ichCurrent = 0; -bufferedReader.reset (); -}, "java.io.BufferedReader,~N"); -Clazz.defineMethod (c$, "getHeader", -function (n) { -return (n == 0 ? String.instantialize (this.buf) : String.instantialize (this.buf, 0, Math.min (this.cchBuf, n))); -}, "~N"); -Clazz.defineMethod (c$, "readLineWithNewline", -function () { -while (this.ichCurrent < this.cchBuf) { -var ichBeginningOfLine = this.ichCurrent; -var ch = String.fromCharCode (0); -while (this.ichCurrent < this.cchBuf && (ch = this.buf[this.ichCurrent++]) != '\r' && ch != '\n') { -} -if (ch == '\r' && this.ichCurrent < this.cchBuf && this.buf[this.ichCurrent] == '\n') ++this.ichCurrent; -var cchLine = this.ichCurrent - ichBeginningOfLine; -if (this.buf[ichBeginningOfLine] == '#') continue; -return String.instantialize (this.buf, ichBeginningOfLine, cchLine); -} -return ""; -}); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.buf = null; +this.cchBuf = 0; +this.ichCurrent = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "LimitedLineReader"); +Clazz.makeConstructor (c$, +function (bufferedReader, readLimit) { +bufferedReader.mark (readLimit + 1); +this.buf = Clazz.newCharArray (readLimit, '\0'); +this.cchBuf = Math.max (bufferedReader.read (this.buf, 0, readLimit), 0); +this.ichCurrent = 0; +bufferedReader.reset (); +}, "java.io.BufferedReader,~N"); +Clazz.defineMethod (c$, "getHeader", +function (n) { +return (n == 0 ? String.instantialize (this.buf) : String.instantialize (this.buf, 0, Math.min (this.cchBuf, n))); +}, "~N"); +Clazz.defineMethod (c$, "readLineWithNewline", +function () { +while (this.ichCurrent < this.cchBuf) { +var ichBeginningOfLine = this.ichCurrent; +var ch = String.fromCharCode (0); +while (this.ichCurrent < this.cchBuf && (ch = this.buf[this.ichCurrent++]) != '\r' && ch != '\n') { +} +if (ch == '\r' && this.ichCurrent < this.cchBuf && this.buf[this.ichCurrent] == '\n') ++this.ichCurrent; +var cchLine = this.ichCurrent - ichBeginningOfLine; +if (this.buf[ichBeginningOfLine] == '#') continue; +return String.instantialize (this.buf, ichBeginningOfLine, cchLine); +} +return ""; +}); diff --git a/bin/javajs/util/ListDataReader.js b/bin/javajs/util/ListDataReader.js index 54d8d69..dbd859d 100644 --- a/bin/javajs/util/ListDataReader.js +++ b/bin/javajs/util/ListDataReader.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.DataReader"], "javajs.util.ListDataReader", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.data = null; -this.pt = 0; -this.len = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "ListDataReader", javajs.util.DataReader); -Clazz.overrideMethod (c$, "setData", -function (data) { -this.data = data; -this.len = this.data.size (); -return this; -}, "~O"); -Clazz.defineMethod (c$, "read", -function (buf, off, len) { -return this.readBuf (buf, off, len); -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "readLine", -function () { -return (this.pt < this.len ? this.data.get (this.pt++) : null); -}); -Clazz.defineMethod (c$, "mark", -function (ptr) { -this.ptMark = this.pt; -}, "~N"); -Clazz.overrideMethod (c$, "reset", -function () { -this.pt = this.ptMark; -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.DataReader"], "javajs.util.ListDataReader", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.data = null; +this.pt = 0; +this.len = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "ListDataReader", javajs.util.DataReader); +Clazz.overrideMethod (c$, "setData", +function (data) { +this.data = data; +this.len = this.data.size (); +return this; +}, "~O"); +Clazz.defineMethod (c$, "read", +function (buf, off, len) { +return this.readBuf (buf, off, len); +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "readLine", +function () { +return (this.pt < this.len ? this.data.get (this.pt++) : null); +}); +Clazz.defineMethod (c$, "mark", +function (ptr) { +this.ptMark = this.pt; +}, "~N"); +Clazz.overrideMethod (c$, "reset", +function () { +this.pt = this.ptMark; +}); +}); diff --git a/bin/javajs/util/Lst.js b/bin/javajs/util/Lst.js index 414e59d..f809b5a 100644 --- a/bin/javajs/util/Lst.js +++ b/bin/javajs/util/Lst.js @@ -1,14 +1,14 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.util.ArrayList"], "javajs.util.Lst", null, function () { -c$ = Clazz.declareType (javajs.util, "Lst", java.util.ArrayList); -Clazz.defineMethod (c$, "addLast", -function (v) { -{ -return this.add1(v); -}}, "~O"); -Clazz.defineMethod (c$, "removeObj", -function (v) { -{ -return this.removeObject(v); -}}, "~O"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.util.ArrayList"], "javajs.util.Lst", null, function () { +c$ = Clazz.declareType (javajs.util, "Lst", java.util.ArrayList); +Clazz.defineMethod (c$, "addLast", +function (v) { +{ +return this.add1(v); +}}, "~O"); +Clazz.defineMethod (c$, "removeObj", +function (v) { +{ +return this.removeObject(v); +}}, "~O"); +}); diff --git a/bin/javajs/util/M3.js b/bin/javajs/util/M3.js index a395f3f..8461118 100644 --- a/bin/javajs/util/M3.js +++ b/bin/javajs/util/M3.js @@ -1,298 +1,298 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.M34"], "javajs.util.M3", ["javajs.util.T3"], function () { -c$ = Clazz.declareType (javajs.util, "M3", javajs.util.M34, java.io.Serializable); -c$.newA9 = Clazz.defineMethod (c$, "newA9", -function (v) { -var m = new javajs.util.M3 (); -m.setA (v); -return m; -}, "~A"); -c$.newM3 = Clazz.defineMethod (c$, "newM3", -function (m1) { -var m = new javajs.util.M3 (); -if (m1 == null) { -m.setScale (1); -return m; -}m.m00 = m1.m00; -m.m01 = m1.m01; -m.m02 = m1.m02; -m.m10 = m1.m10; -m.m11 = m1.m11; -m.m12 = m1.m12; -m.m20 = m1.m20; -m.m21 = m1.m21; -m.m22 = m1.m22; -return m; -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "setScale", -function (scale) { -this.clear33 (); -this.m00 = this.m11 = this.m22 = scale; -}, "~N"); -Clazz.defineMethod (c$, "setM3", -function (m1) { -this.setM33 (m1); -}, "javajs.util.M34"); -Clazz.defineMethod (c$, "setA", -function (m) { -this.m00 = m[0]; -this.m01 = m[1]; -this.m02 = m[2]; -this.m10 = m[3]; -this.m11 = m[4]; -this.m12 = m[5]; -this.m20 = m[6]; -this.m21 = m[7]; -this.m22 = m[8]; -}, "~A"); -Clazz.defineMethod (c$, "setElement", -function (row, col, v) { -this.set33 (row, col, v); -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "getElement", -function (row, col) { -return this.get33 (row, col); -}, "~N,~N"); -Clazz.defineMethod (c$, "setRow", -function (row, x, y, z) { -switch (row) { -case 0: -this.m00 = x; -this.m01 = y; -this.m02 = z; -return; -case 1: -this.m10 = x; -this.m11 = y; -this.m12 = z; -return; -case 2: -this.m20 = x; -this.m21 = y; -this.m22 = z; -return; -default: -this.err (); -} -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "setRowV", -function (row, v) { -switch (row) { -case 0: -this.m00 = v.x; -this.m01 = v.y; -this.m02 = v.z; -return; -case 1: -this.m10 = v.x; -this.m11 = v.y; -this.m12 = v.z; -return; -case 2: -this.m20 = v.x; -this.m21 = v.y; -this.m22 = v.z; -return; -default: -this.err (); -} -}, "~N,javajs.util.T3"); -Clazz.defineMethod (c$, "setRowA", -function (row, v) { -this.setRow33 (row, v); -}, "~N,~A"); -Clazz.overrideMethod (c$, "getRow", -function (row, v) { -this.getRow33 (row, v); -}, "~N,~A"); -Clazz.defineMethod (c$, "setColumn3", -function (column, x, y, z) { -switch (column) { -case 0: -this.m00 = x; -this.m10 = y; -this.m20 = z; -break; -case 1: -this.m01 = x; -this.m11 = y; -this.m21 = z; -break; -case 2: -this.m02 = x; -this.m12 = y; -this.m22 = z; -break; -default: -this.err (); -} -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "setColumnV", -function (column, v) { -switch (column) { -case 0: -this.m00 = v.x; -this.m10 = v.y; -this.m20 = v.z; -break; -case 1: -this.m01 = v.x; -this.m11 = v.y; -this.m21 = v.z; -break; -case 2: -this.m02 = v.x; -this.m12 = v.y; -this.m22 = v.z; -break; -default: -this.err (); -} -}, "~N,javajs.util.T3"); -Clazz.defineMethod (c$, "getColumnV", -function (column, v) { -switch (column) { -case 0: -v.x = this.m00; -v.y = this.m10; -v.z = this.m20; -break; -case 1: -v.x = this.m01; -v.y = this.m11; -v.z = this.m21; -break; -case 2: -v.x = this.m02; -v.y = this.m12; -v.z = this.m22; -break; -default: -this.err (); -} -}, "~N,javajs.util.T3"); -Clazz.defineMethod (c$, "setColumnA", -function (column, v) { -this.setColumn33 (column, v); -}, "~N,~A"); -Clazz.defineMethod (c$, "getColumn", -function (column, v) { -this.getColumn33 (column, v); -}, "~N,~A"); -Clazz.defineMethod (c$, "add", -function (m1) { -this.add33 (m1); -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "sub", -function (m1) { -this.sub33 (m1); -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "transpose", -function () { -this.transpose33 (); -}); -Clazz.defineMethod (c$, "transposeM", -function (m1) { -this.setM33 (m1); -this.transpose33 (); -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "invertM", -function (m1) { -this.setM33 (m1); -this.invert (); -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "invert", -function () { -var s = this.determinant3 (); -if (s == 0.0) return; -s = 1 / s; -this.set9 (this.m11 * this.m22 - this.m12 * this.m21, this.m02 * this.m21 - this.m01 * this.m22, this.m01 * this.m12 - this.m02 * this.m11, this.m12 * this.m20 - this.m10 * this.m22, this.m00 * this.m22 - this.m02 * this.m20, this.m02 * this.m10 - this.m00 * this.m12, this.m10 * this.m21 - this.m11 * this.m20, this.m01 * this.m20 - this.m00 * this.m21, this.m00 * this.m11 - this.m01 * this.m10); -this.scale (s); -}); -Clazz.defineMethod (c$, "setAsXRotation", -function (angle) { -this.setXRot (angle); -return this; -}, "~N"); -Clazz.defineMethod (c$, "setAsYRotation", -function (angle) { -this.setYRot (angle); -return this; -}, "~N"); -Clazz.defineMethod (c$, "setAsZRotation", -function (angle) { -this.setZRot (angle); -return this; -}, "~N"); -Clazz.defineMethod (c$, "scale", -function (scalar) { -this.mul33 (scalar); -}, "~N"); -Clazz.defineMethod (c$, "mul", -function (m1) { -this.mul2 (this, m1); -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "mul2", -function (m1, m2) { -this.set9 (m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20, m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21, m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22, m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20, m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21, m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22, m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20, m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21, m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22); -}, "javajs.util.M3,javajs.util.M3"); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (!(Clazz.instanceOf (o, javajs.util.M3))) return false; -var m = o; -return this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02 && this.m10 == m.m10 && this.m11 == m.m11 && this.m12 == m.m12 && this.m20 == m.m20 && this.m21 == m.m21 && this.m22 == m.m22; -}, "~O"); -Clazz.overrideMethod (c$, "hashCode", -function () { -return javajs.util.T3.floatToIntBits0 (this.m00) ^ javajs.util.T3.floatToIntBits0 (this.m01) ^ javajs.util.T3.floatToIntBits0 (this.m02) ^ javajs.util.T3.floatToIntBits0 (this.m10) ^ javajs.util.T3.floatToIntBits0 (this.m11) ^ javajs.util.T3.floatToIntBits0 (this.m12) ^ javajs.util.T3.floatToIntBits0 (this.m20) ^ javajs.util.T3.floatToIntBits0 (this.m21) ^ javajs.util.T3.floatToIntBits0 (this.m22); -}); -Clazz.defineMethod (c$, "setZero", -function () { -this.clear33 (); -}); -Clazz.defineMethod (c$, "set9", -($fz = function (m00, m01, m02, m10, m11, m12, m20, m21, m22) { -this.m00 = m00; -this.m01 = m01; -this.m02 = m02; -this.m10 = m10; -this.m11 = m11; -this.m12 = m12; -this.m20 = m20; -this.m21 = m21; -this.m22 = m22; -}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N,~N,~N,~N,~N,~N"); -Clazz.overrideMethod (c$, "toString", -function () { -return "[\n [" + this.m00 + "\t" + this.m01 + "\t" + this.m02 + "]" + "\n [" + this.m10 + "\t" + this.m11 + "\t" + this.m12 + "]" + "\n [" + this.m20 + "\t" + this.m21 + "\t" + this.m22 + "] ]"; -}); -Clazz.defineMethod (c$, "setAA", -function (a) { -this.setAA33 (a); -return this; -}, "javajs.util.A4"); -Clazz.defineMethod (c$, "setAsBallRotation", -function (responseFactor, dx, dy) { -var r = Math.sqrt (dx * dx + dy * dy); -var th = r * responseFactor; -if (th == 0) { -this.setScale (1); -return false; -}var c = Math.cos (th); -var s = Math.sin (th); -var nx = -dy / r; -var ny = dx / r; -var c1 = c - 1; -this.m00 = 1 + c1 * nx * nx; -this.m01 = this.m10 = c1 * nx * ny; -this.m20 = -(this.m02 = s * nx); -this.m11 = 1 + c1 * ny * ny; -this.m21 = -(this.m12 = s * ny); -this.m22 = c; -return true; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "isRotation", -function () { -return (Math.abs (this.determinant3 () - 1) < 0.001); -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.M34"], "javajs.util.M3", ["javajs.util.T3"], function () { +c$ = Clazz.declareType (javajs.util, "M3", javajs.util.M34, java.io.Serializable); +c$.newA9 = Clazz.defineMethod (c$, "newA9", +function (v) { +var m = new javajs.util.M3 (); +m.setA (v); +return m; +}, "~A"); +c$.newM3 = Clazz.defineMethod (c$, "newM3", +function (m1) { +var m = new javajs.util.M3 (); +if (m1 == null) { +m.setScale (1); +return m; +}m.m00 = m1.m00; +m.m01 = m1.m01; +m.m02 = m1.m02; +m.m10 = m1.m10; +m.m11 = m1.m11; +m.m12 = m1.m12; +m.m20 = m1.m20; +m.m21 = m1.m21; +m.m22 = m1.m22; +return m; +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "setScale", +function (scale) { +this.clear33 (); +this.m00 = this.m11 = this.m22 = scale; +}, "~N"); +Clazz.defineMethod (c$, "setM3", +function (m1) { +this.setM33 (m1); +}, "javajs.util.M34"); +Clazz.defineMethod (c$, "setA", +function (m) { +this.m00 = m[0]; +this.m01 = m[1]; +this.m02 = m[2]; +this.m10 = m[3]; +this.m11 = m[4]; +this.m12 = m[5]; +this.m20 = m[6]; +this.m21 = m[7]; +this.m22 = m[8]; +}, "~A"); +Clazz.defineMethod (c$, "setElement", +function (row, col, v) { +this.set33 (row, col, v); +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "getElement", +function (row, col) { +return this.get33 (row, col); +}, "~N,~N"); +Clazz.defineMethod (c$, "setRow", +function (row, x, y, z) { +switch (row) { +case 0: +this.m00 = x; +this.m01 = y; +this.m02 = z; +return; +case 1: +this.m10 = x; +this.m11 = y; +this.m12 = z; +return; +case 2: +this.m20 = x; +this.m21 = y; +this.m22 = z; +return; +default: +this.err (); +} +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "setRowV", +function (row, v) { +switch (row) { +case 0: +this.m00 = v.x; +this.m01 = v.y; +this.m02 = v.z; +return; +case 1: +this.m10 = v.x; +this.m11 = v.y; +this.m12 = v.z; +return; +case 2: +this.m20 = v.x; +this.m21 = v.y; +this.m22 = v.z; +return; +default: +this.err (); +} +}, "~N,javajs.util.T3"); +Clazz.defineMethod (c$, "setRowA", +function (row, v) { +this.setRow33 (row, v); +}, "~N,~A"); +Clazz.overrideMethod (c$, "getRow", +function (row, v) { +this.getRow33 (row, v); +}, "~N,~A"); +Clazz.defineMethod (c$, "setColumn3", +function (column, x, y, z) { +switch (column) { +case 0: +this.m00 = x; +this.m10 = y; +this.m20 = z; +break; +case 1: +this.m01 = x; +this.m11 = y; +this.m21 = z; +break; +case 2: +this.m02 = x; +this.m12 = y; +this.m22 = z; +break; +default: +this.err (); +} +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "setColumnV", +function (column, v) { +switch (column) { +case 0: +this.m00 = v.x; +this.m10 = v.y; +this.m20 = v.z; +break; +case 1: +this.m01 = v.x; +this.m11 = v.y; +this.m21 = v.z; +break; +case 2: +this.m02 = v.x; +this.m12 = v.y; +this.m22 = v.z; +break; +default: +this.err (); +} +}, "~N,javajs.util.T3"); +Clazz.defineMethod (c$, "getColumnV", +function (column, v) { +switch (column) { +case 0: +v.x = this.m00; +v.y = this.m10; +v.z = this.m20; +break; +case 1: +v.x = this.m01; +v.y = this.m11; +v.z = this.m21; +break; +case 2: +v.x = this.m02; +v.y = this.m12; +v.z = this.m22; +break; +default: +this.err (); +} +}, "~N,javajs.util.T3"); +Clazz.defineMethod (c$, "setColumnA", +function (column, v) { +this.setColumn33 (column, v); +}, "~N,~A"); +Clazz.defineMethod (c$, "getColumn", +function (column, v) { +this.getColumn33 (column, v); +}, "~N,~A"); +Clazz.defineMethod (c$, "add", +function (m1) { +this.add33 (m1); +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "sub", +function (m1) { +this.sub33 (m1); +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "transpose", +function () { +this.transpose33 (); +}); +Clazz.defineMethod (c$, "transposeM", +function (m1) { +this.setM33 (m1); +this.transpose33 (); +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "invertM", +function (m1) { +this.setM33 (m1); +this.invert (); +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "invert", +function () { +var s = this.determinant3 (); +if (s == 0.0) return; +s = 1 / s; +this.set9 (this.m11 * this.m22 - this.m12 * this.m21, this.m02 * this.m21 - this.m01 * this.m22, this.m01 * this.m12 - this.m02 * this.m11, this.m12 * this.m20 - this.m10 * this.m22, this.m00 * this.m22 - this.m02 * this.m20, this.m02 * this.m10 - this.m00 * this.m12, this.m10 * this.m21 - this.m11 * this.m20, this.m01 * this.m20 - this.m00 * this.m21, this.m00 * this.m11 - this.m01 * this.m10); +this.scale (s); +}); +Clazz.defineMethod (c$, "setAsXRotation", +function (angle) { +this.setXRot (angle); +return this; +}, "~N"); +Clazz.defineMethod (c$, "setAsYRotation", +function (angle) { +this.setYRot (angle); +return this; +}, "~N"); +Clazz.defineMethod (c$, "setAsZRotation", +function (angle) { +this.setZRot (angle); +return this; +}, "~N"); +Clazz.defineMethod (c$, "scale", +function (scalar) { +this.mul33 (scalar); +}, "~N"); +Clazz.defineMethod (c$, "mul", +function (m1) { +this.mul2 (this, m1); +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "mul2", +function (m1, m2) { +this.set9 (m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20, m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21, m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22, m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20, m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21, m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22, m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20, m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21, m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22); +}, "javajs.util.M3,javajs.util.M3"); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (!(Clazz.instanceOf (o, javajs.util.M3))) return false; +var m = o; +return this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02 && this.m10 == m.m10 && this.m11 == m.m11 && this.m12 == m.m12 && this.m20 == m.m20 && this.m21 == m.m21 && this.m22 == m.m22; +}, "~O"); +Clazz.overrideMethod (c$, "hashCode", +function () { +return javajs.util.T3.floatToIntBits0 (this.m00) ^ javajs.util.T3.floatToIntBits0 (this.m01) ^ javajs.util.T3.floatToIntBits0 (this.m02) ^ javajs.util.T3.floatToIntBits0 (this.m10) ^ javajs.util.T3.floatToIntBits0 (this.m11) ^ javajs.util.T3.floatToIntBits0 (this.m12) ^ javajs.util.T3.floatToIntBits0 (this.m20) ^ javajs.util.T3.floatToIntBits0 (this.m21) ^ javajs.util.T3.floatToIntBits0 (this.m22); +}); +Clazz.defineMethod (c$, "setZero", +function () { +this.clear33 (); +}); +Clazz.defineMethod (c$, "set9", +($fz = function (m00, m01, m02, m10, m11, m12, m20, m21, m22) { +this.m00 = m00; +this.m01 = m01; +this.m02 = m02; +this.m10 = m10; +this.m11 = m11; +this.m12 = m12; +this.m20 = m20; +this.m21 = m21; +this.m22 = m22; +}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N,~N,~N,~N,~N,~N"); +Clazz.overrideMethod (c$, "toString", +function () { +return "[\n [" + this.m00 + "\t" + this.m01 + "\t" + this.m02 + "]" + "\n [" + this.m10 + "\t" + this.m11 + "\t" + this.m12 + "]" + "\n [" + this.m20 + "\t" + this.m21 + "\t" + this.m22 + "] ]"; +}); +Clazz.defineMethod (c$, "setAA", +function (a) { +this.setAA33 (a); +return this; +}, "javajs.util.A4"); +Clazz.defineMethod (c$, "setAsBallRotation", +function (responseFactor, dx, dy) { +var r = Math.sqrt (dx * dx + dy * dy); +var th = r * responseFactor; +if (th == 0) { +this.setScale (1); +return false; +}var c = Math.cos (th); +var s = Math.sin (th); +var nx = -dy / r; +var ny = dx / r; +var c1 = c - 1; +this.m00 = 1 + c1 * nx * nx; +this.m01 = this.m10 = c1 * nx * ny; +this.m20 = -(this.m02 = s * nx); +this.m11 = 1 + c1 * ny * ny; +this.m21 = -(this.m12 = s * ny); +this.m22 = c; +return true; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "isRotation", +function () { +return (Math.abs (this.determinant3 () - 1) < 0.001); +}); +}); diff --git a/bin/javajs/util/M34.js b/bin/javajs/util/M34.js index 47c6a34..ae3f33d 100644 --- a/bin/javajs/util/M34.js +++ b/bin/javajs/util/M34.js @@ -1,336 +1,336 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.M34", ["java.lang.ArrayIndexOutOfBoundsException"], function () { -c$ = Clazz.decorateAsClass (function () { -this.m00 = 0; -this.m01 = 0; -this.m02 = 0; -this.m10 = 0; -this.m11 = 0; -this.m12 = 0; -this.m20 = 0; -this.m21 = 0; -this.m22 = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "M34"); -Clazz.defineMethod (c$, "setAA33", -function (a) { -var x = a.x; -var y = a.y; -var z = a.z; -var angle = a.angle; -var n = Math.sqrt (x * x + y * y + z * z); -n = 1 / n; -x *= n; -y *= n; -z *= n; -var c = Math.cos (angle); -var s = Math.sin (angle); -var omc = 1.0 - c; -this.m00 = (c + x * x * omc); -this.m11 = (c + y * y * omc); -this.m22 = (c + z * z * omc); -var tmp1 = x * y * omc; -var tmp2 = z * s; -this.m01 = (tmp1 - tmp2); -this.m10 = (tmp1 + tmp2); -tmp1 = x * z * omc; -tmp2 = y * s; -this.m02 = (tmp1 + tmp2); -this.m20 = (tmp1 - tmp2); -tmp1 = y * z * omc; -tmp2 = x * s; -this.m12 = (tmp1 - tmp2); -this.m21 = (tmp1 + tmp2); -}, "javajs.util.A4"); -Clazz.defineMethod (c$, "rotate", -function (t) { -this.rotate2 (t, t); -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "rotate2", -function (t, result) { -result.set (this.m00 * t.x + this.m01 * t.y + this.m02 * t.z, this.m10 * t.x + this.m11 * t.y + this.m12 * t.z, this.m20 * t.x + this.m21 * t.y + this.m22 * t.z); -}, "javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "setM33", -function (m1) { -this.m00 = m1.m00; -this.m01 = m1.m01; -this.m02 = m1.m02; -this.m10 = m1.m10; -this.m11 = m1.m11; -this.m12 = m1.m12; -this.m20 = m1.m20; -this.m21 = m1.m21; -this.m22 = m1.m22; -}, "javajs.util.M34"); -Clazz.defineMethod (c$, "clear33", -function () { -this.m00 = this.m01 = this.m02 = this.m10 = this.m11 = this.m12 = this.m20 = this.m21 = this.m22 = 0.0; -}); -Clazz.defineMethod (c$, "set33", -function (row, col, v) { -switch (row) { -case 0: -switch (col) { -case 0: -this.m00 = v; -return; -case 1: -this.m01 = v; -return; -case 2: -this.m02 = v; -return; -} -break; -case 1: -switch (col) { -case 0: -this.m10 = v; -return; -case 1: -this.m11 = v; -return; -case 2: -this.m12 = v; -return; -} -break; -case 2: -switch (col) { -case 0: -this.m20 = v; -return; -case 1: -this.m21 = v; -return; -case 2: -this.m22 = v; -return; -} -break; -} -this.err (); -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "get33", -function (row, col) { -switch (row) { -case 0: -switch (col) { -case 0: -return this.m00; -case 1: -return this.m01; -case 2: -return this.m02; -} -break; -case 1: -switch (col) { -case 0: -return this.m10; -case 1: -return this.m11; -case 2: -return this.m12; -} -break; -case 2: -switch (col) { -case 0: -return this.m20; -case 1: -return this.m21; -case 2: -return this.m22; -} -break; -} -this.err (); -return 0; -}, "~N,~N"); -Clazz.defineMethod (c$, "setRow33", -function (row, v) { -switch (row) { -case 0: -this.m00 = v[0]; -this.m01 = v[1]; -this.m02 = v[2]; -return; -case 1: -this.m10 = v[0]; -this.m11 = v[1]; -this.m12 = v[2]; -return; -case 2: -this.m20 = v[0]; -this.m21 = v[1]; -this.m22 = v[2]; -return; -default: -this.err (); -} -}, "~N,~A"); -Clazz.defineMethod (c$, "getRow33", -function (row, v) { -switch (row) { -case 0: -v[0] = this.m00; -v[1] = this.m01; -v[2] = this.m02; -return; -case 1: -v[0] = this.m10; -v[1] = this.m11; -v[2] = this.m12; -return; -case 2: -v[0] = this.m20; -v[1] = this.m21; -v[2] = this.m22; -return; -} -this.err (); -}, "~N,~A"); -Clazz.defineMethod (c$, "setColumn33", -function (column, v) { -switch (column) { -case 0: -this.m00 = v[0]; -this.m10 = v[1]; -this.m20 = v[2]; -break; -case 1: -this.m01 = v[0]; -this.m11 = v[1]; -this.m21 = v[2]; -break; -case 2: -this.m02 = v[0]; -this.m12 = v[1]; -this.m22 = v[2]; -break; -default: -this.err (); -} -}, "~N,~A"); -Clazz.defineMethod (c$, "getColumn33", -function (column, v) { -switch (column) { -case 0: -v[0] = this.m00; -v[1] = this.m10; -v[2] = this.m20; -break; -case 1: -v[0] = this.m01; -v[1] = this.m11; -v[2] = this.m21; -break; -case 2: -v[0] = this.m02; -v[1] = this.m12; -v[2] = this.m22; -break; -default: -this.err (); -} -}, "~N,~A"); -Clazz.defineMethod (c$, "add33", -function (m1) { -this.m00 += m1.m00; -this.m01 += m1.m01; -this.m02 += m1.m02; -this.m10 += m1.m10; -this.m11 += m1.m11; -this.m12 += m1.m12; -this.m20 += m1.m20; -this.m21 += m1.m21; -this.m22 += m1.m22; -}, "javajs.util.M34"); -Clazz.defineMethod (c$, "sub33", -function (m1) { -this.m00 -= m1.m00; -this.m01 -= m1.m01; -this.m02 -= m1.m02; -this.m10 -= m1.m10; -this.m11 -= m1.m11; -this.m12 -= m1.m12; -this.m20 -= m1.m20; -this.m21 -= m1.m21; -this.m22 -= m1.m22; -}, "javajs.util.M34"); -Clazz.defineMethod (c$, "mul33", -function (x) { -this.m00 *= x; -this.m01 *= x; -this.m02 *= x; -this.m10 *= x; -this.m11 *= x; -this.m12 *= x; -this.m20 *= x; -this.m21 *= x; -this.m22 *= x; -}, "~N"); -Clazz.defineMethod (c$, "transpose33", -function () { -var tmp = this.m01; -this.m01 = this.m10; -this.m10 = tmp; -tmp = this.m02; -this.m02 = this.m20; -this.m20 = tmp; -tmp = this.m12; -this.m12 = this.m21; -this.m21 = tmp; -}); -Clazz.defineMethod (c$, "setXRot", -function (angle) { -var c = Math.cos (angle); -var s = Math.sin (angle); -this.m00 = 1.0; -this.m01 = 0.0; -this.m02 = 0.0; -this.m10 = 0.0; -this.m11 = c; -this.m12 = -s; -this.m20 = 0.0; -this.m21 = s; -this.m22 = c; -}, "~N"); -Clazz.defineMethod (c$, "setYRot", -function (angle) { -var c = Math.cos (angle); -var s = Math.sin (angle); -this.m00 = c; -this.m01 = 0.0; -this.m02 = s; -this.m10 = 0.0; -this.m11 = 1.0; -this.m12 = 0.0; -this.m20 = -s; -this.m21 = 0.0; -this.m22 = c; -}, "~N"); -Clazz.defineMethod (c$, "setZRot", -function (angle) { -var c = Math.cos (angle); -var s = Math.sin (angle); -this.m00 = c; -this.m01 = -s; -this.m02 = 0.0; -this.m10 = s; -this.m11 = c; -this.m12 = 0.0; -this.m20 = 0.0; -this.m21 = 0.0; -this.m22 = 1.0; -}, "~N"); -Clazz.defineMethod (c$, "determinant3", -function () { -return this.m00 * (this.m11 * this.m22 - this.m21 * this.m12) - this.m01 * (this.m10 * this.m22 - this.m20 * this.m12) + this.m02 * (this.m10 * this.m21 - this.m20 * this.m11); -}); -Clazz.defineMethod (c$, "err", -function () { -throw new ArrayIndexOutOfBoundsException ("matrix column/row out of bounds"); -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.M34", ["java.lang.ArrayIndexOutOfBoundsException"], function () { +c$ = Clazz.decorateAsClass (function () { +this.m00 = 0; +this.m01 = 0; +this.m02 = 0; +this.m10 = 0; +this.m11 = 0; +this.m12 = 0; +this.m20 = 0; +this.m21 = 0; +this.m22 = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "M34"); +Clazz.defineMethod (c$, "setAA33", +function (a) { +var x = a.x; +var y = a.y; +var z = a.z; +var angle = a.angle; +var n = Math.sqrt (x * x + y * y + z * z); +n = 1 / n; +x *= n; +y *= n; +z *= n; +var c = Math.cos (angle); +var s = Math.sin (angle); +var omc = 1.0 - c; +this.m00 = (c + x * x * omc); +this.m11 = (c + y * y * omc); +this.m22 = (c + z * z * omc); +var tmp1 = x * y * omc; +var tmp2 = z * s; +this.m01 = (tmp1 - tmp2); +this.m10 = (tmp1 + tmp2); +tmp1 = x * z * omc; +tmp2 = y * s; +this.m02 = (tmp1 + tmp2); +this.m20 = (tmp1 - tmp2); +tmp1 = y * z * omc; +tmp2 = x * s; +this.m12 = (tmp1 - tmp2); +this.m21 = (tmp1 + tmp2); +}, "javajs.util.A4"); +Clazz.defineMethod (c$, "rotate", +function (t) { +this.rotate2 (t, t); +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "rotate2", +function (t, result) { +result.set (this.m00 * t.x + this.m01 * t.y + this.m02 * t.z, this.m10 * t.x + this.m11 * t.y + this.m12 * t.z, this.m20 * t.x + this.m21 * t.y + this.m22 * t.z); +}, "javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "setM33", +function (m1) { +this.m00 = m1.m00; +this.m01 = m1.m01; +this.m02 = m1.m02; +this.m10 = m1.m10; +this.m11 = m1.m11; +this.m12 = m1.m12; +this.m20 = m1.m20; +this.m21 = m1.m21; +this.m22 = m1.m22; +}, "javajs.util.M34"); +Clazz.defineMethod (c$, "clear33", +function () { +this.m00 = this.m01 = this.m02 = this.m10 = this.m11 = this.m12 = this.m20 = this.m21 = this.m22 = 0.0; +}); +Clazz.defineMethod (c$, "set33", +function (row, col, v) { +switch (row) { +case 0: +switch (col) { +case 0: +this.m00 = v; +return; +case 1: +this.m01 = v; +return; +case 2: +this.m02 = v; +return; +} +break; +case 1: +switch (col) { +case 0: +this.m10 = v; +return; +case 1: +this.m11 = v; +return; +case 2: +this.m12 = v; +return; +} +break; +case 2: +switch (col) { +case 0: +this.m20 = v; +return; +case 1: +this.m21 = v; +return; +case 2: +this.m22 = v; +return; +} +break; +} +this.err (); +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "get33", +function (row, col) { +switch (row) { +case 0: +switch (col) { +case 0: +return this.m00; +case 1: +return this.m01; +case 2: +return this.m02; +} +break; +case 1: +switch (col) { +case 0: +return this.m10; +case 1: +return this.m11; +case 2: +return this.m12; +} +break; +case 2: +switch (col) { +case 0: +return this.m20; +case 1: +return this.m21; +case 2: +return this.m22; +} +break; +} +this.err (); +return 0; +}, "~N,~N"); +Clazz.defineMethod (c$, "setRow33", +function (row, v) { +switch (row) { +case 0: +this.m00 = v[0]; +this.m01 = v[1]; +this.m02 = v[2]; +return; +case 1: +this.m10 = v[0]; +this.m11 = v[1]; +this.m12 = v[2]; +return; +case 2: +this.m20 = v[0]; +this.m21 = v[1]; +this.m22 = v[2]; +return; +default: +this.err (); +} +}, "~N,~A"); +Clazz.defineMethod (c$, "getRow33", +function (row, v) { +switch (row) { +case 0: +v[0] = this.m00; +v[1] = this.m01; +v[2] = this.m02; +return; +case 1: +v[0] = this.m10; +v[1] = this.m11; +v[2] = this.m12; +return; +case 2: +v[0] = this.m20; +v[1] = this.m21; +v[2] = this.m22; +return; +} +this.err (); +}, "~N,~A"); +Clazz.defineMethod (c$, "setColumn33", +function (column, v) { +switch (column) { +case 0: +this.m00 = v[0]; +this.m10 = v[1]; +this.m20 = v[2]; +break; +case 1: +this.m01 = v[0]; +this.m11 = v[1]; +this.m21 = v[2]; +break; +case 2: +this.m02 = v[0]; +this.m12 = v[1]; +this.m22 = v[2]; +break; +default: +this.err (); +} +}, "~N,~A"); +Clazz.defineMethod (c$, "getColumn33", +function (column, v) { +switch (column) { +case 0: +v[0] = this.m00; +v[1] = this.m10; +v[2] = this.m20; +break; +case 1: +v[0] = this.m01; +v[1] = this.m11; +v[2] = this.m21; +break; +case 2: +v[0] = this.m02; +v[1] = this.m12; +v[2] = this.m22; +break; +default: +this.err (); +} +}, "~N,~A"); +Clazz.defineMethod (c$, "add33", +function (m1) { +this.m00 += m1.m00; +this.m01 += m1.m01; +this.m02 += m1.m02; +this.m10 += m1.m10; +this.m11 += m1.m11; +this.m12 += m1.m12; +this.m20 += m1.m20; +this.m21 += m1.m21; +this.m22 += m1.m22; +}, "javajs.util.M34"); +Clazz.defineMethod (c$, "sub33", +function (m1) { +this.m00 -= m1.m00; +this.m01 -= m1.m01; +this.m02 -= m1.m02; +this.m10 -= m1.m10; +this.m11 -= m1.m11; +this.m12 -= m1.m12; +this.m20 -= m1.m20; +this.m21 -= m1.m21; +this.m22 -= m1.m22; +}, "javajs.util.M34"); +Clazz.defineMethod (c$, "mul33", +function (x) { +this.m00 *= x; +this.m01 *= x; +this.m02 *= x; +this.m10 *= x; +this.m11 *= x; +this.m12 *= x; +this.m20 *= x; +this.m21 *= x; +this.m22 *= x; +}, "~N"); +Clazz.defineMethod (c$, "transpose33", +function () { +var tmp = this.m01; +this.m01 = this.m10; +this.m10 = tmp; +tmp = this.m02; +this.m02 = this.m20; +this.m20 = tmp; +tmp = this.m12; +this.m12 = this.m21; +this.m21 = tmp; +}); +Clazz.defineMethod (c$, "setXRot", +function (angle) { +var c = Math.cos (angle); +var s = Math.sin (angle); +this.m00 = 1.0; +this.m01 = 0.0; +this.m02 = 0.0; +this.m10 = 0.0; +this.m11 = c; +this.m12 = -s; +this.m20 = 0.0; +this.m21 = s; +this.m22 = c; +}, "~N"); +Clazz.defineMethod (c$, "setYRot", +function (angle) { +var c = Math.cos (angle); +var s = Math.sin (angle); +this.m00 = c; +this.m01 = 0.0; +this.m02 = s; +this.m10 = 0.0; +this.m11 = 1.0; +this.m12 = 0.0; +this.m20 = -s; +this.m21 = 0.0; +this.m22 = c; +}, "~N"); +Clazz.defineMethod (c$, "setZRot", +function (angle) { +var c = Math.cos (angle); +var s = Math.sin (angle); +this.m00 = c; +this.m01 = -s; +this.m02 = 0.0; +this.m10 = s; +this.m11 = c; +this.m12 = 0.0; +this.m20 = 0.0; +this.m21 = 0.0; +this.m22 = 1.0; +}, "~N"); +Clazz.defineMethod (c$, "determinant3", +function () { +return this.m00 * (this.m11 * this.m22 - this.m21 * this.m12) - this.m01 * (this.m10 * this.m22 - this.m20 * this.m12) + this.m02 * (this.m10 * this.m21 - this.m20 * this.m11); +}); +Clazz.defineMethod (c$, "err", +function () { +throw new ArrayIndexOutOfBoundsException ("matrix column/row out of bounds"); +}); +}); diff --git a/bin/javajs/util/M4.js b/bin/javajs/util/M4.js index 211ae5d..59c23db 100644 --- a/bin/javajs/util/M4.js +++ b/bin/javajs/util/M4.js @@ -1,486 +1,486 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.M34"], "javajs.util.M4", ["javajs.util.T3"], function () { -c$ = Clazz.decorateAsClass (function () { -this.m03 = 0; -this.m13 = 0; -this.m23 = 0; -this.m30 = 0; -this.m31 = 0; -this.m32 = 0; -this.m33 = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "M4", javajs.util.M34); -c$.newA16 = Clazz.defineMethod (c$, "newA16", -function (v) { -var m = new javajs.util.M4 (); -m.m00 = v[0]; -m.m01 = v[1]; -m.m02 = v[2]; -m.m03 = v[3]; -m.m10 = v[4]; -m.m11 = v[5]; -m.m12 = v[6]; -m.m13 = v[7]; -m.m20 = v[8]; -m.m21 = v[9]; -m.m22 = v[10]; -m.m23 = v[11]; -m.m30 = v[12]; -m.m31 = v[13]; -m.m32 = v[14]; -m.m33 = v[15]; -return m; -}, "~A"); -c$.newM4 = Clazz.defineMethod (c$, "newM4", -function (m1) { -var m = new javajs.util.M4 (); -if (m1 == null) { -m.setIdentity (); -return m; -}m.setToM3 (m1); -m.m03 = m1.m03; -m.m13 = m1.m13; -m.m23 = m1.m23; -m.m30 = m1.m30; -m.m31 = m1.m31; -m.m32 = m1.m32; -m.m33 = m1.m33; -return m; -}, "javajs.util.M4"); -c$.newMV = Clazz.defineMethod (c$, "newMV", -function (m1, t) { -var m = new javajs.util.M4 (); -m.setMV (m1, t); -return m; -}, "javajs.util.M3,javajs.util.T3"); -Clazz.defineMethod (c$, "setZero", -function () { -this.clear33 (); -this.m03 = this.m13 = this.m23 = this.m30 = this.m31 = this.m32 = this.m33 = 0.0; -}); -Clazz.defineMethod (c$, "setIdentity", -function () { -this.setZero (); -this.m00 = this.m11 = this.m22 = this.m33 = 1.0; -}); -Clazz.defineMethod (c$, "setM4", -function (m1) { -this.setM33 (m1); -this.m03 = m1.m03; -this.m13 = m1.m13; -this.m23 = m1.m23; -this.m30 = m1.m30; -this.m31 = m1.m31; -this.m32 = m1.m32; -this.m33 = m1.m33; -return this; -}, "javajs.util.M4"); -Clazz.defineMethod (c$, "setMV", -function (m1, t) { -this.setM33 (m1); -this.setTranslation (t); -this.m33 = 1; -}, "javajs.util.M3,javajs.util.T3"); -Clazz.defineMethod (c$, "setToM3", -function (m1) { -this.setM33 (m1); -this.m03 = this.m13 = this.m23 = this.m30 = this.m31 = this.m32 = 0.0; -this.m33 = 1.0; -}, "javajs.util.M34"); -Clazz.defineMethod (c$, "setToAA", -function (a) { -this.setIdentity (); -this.setAA33 (a); -}, "javajs.util.A4"); -Clazz.defineMethod (c$, "setA", -function (m) { -this.m00 = m[0]; -this.m01 = m[1]; -this.m02 = m[2]; -this.m03 = m[3]; -this.m10 = m[4]; -this.m11 = m[5]; -this.m12 = m[6]; -this.m13 = m[7]; -this.m20 = m[8]; -this.m21 = m[9]; -this.m22 = m[10]; -this.m23 = m[11]; -this.m30 = m[12]; -this.m31 = m[13]; -this.m32 = m[14]; -this.m33 = m[15]; -}, "~A"); -Clazz.defineMethod (c$, "setTranslation", -function (trans) { -this.m03 = trans.x; -this.m13 = trans.y; -this.m23 = trans.z; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "setElement", -function (row, col, v) { -if (row < 3 && col < 3) { -this.set33 (row, col, v); -return; -}if (row > 3 || col > 3) this.err (); -switch (row) { -case 0: -this.m03 = v; -return; -case 1: -this.m13 = v; -return; -case 2: -this.m23 = v; -return; -} -switch (col) { -case 0: -this.m30 = v; -return; -case 1: -this.m31 = v; -return; -case 2: -this.m32 = v; -return; -case 3: -this.m33 = v; -return; -} -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "getElement", -function (row, col) { -if (row < 3 && col < 3) return this.get33 (row, col); -if (row > 3 || col > 3) { -this.err (); -return 0; -}switch (row) { -case 0: -return this.m03; -case 1: -return this.m13; -case 2: -return this.m23; -default: -switch (col) { -case 0: -return this.m30; -case 1: -return this.m31; -case 2: -return this.m32; -default: -return this.m33; -} -} -}, "~N,~N"); -Clazz.defineMethod (c$, "getTranslation", -function (trans) { -trans.x = this.m03; -trans.y = this.m13; -trans.z = this.m23; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "getRotationScale", -function (m1) { -m1.m00 = this.m00; -m1.m01 = this.m01; -m1.m02 = this.m02; -m1.m10 = this.m10; -m1.m11 = this.m11; -m1.m12 = this.m12; -m1.m20 = this.m20; -m1.m21 = this.m21; -m1.m22 = this.m22; -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "setRotationScale", -function (m1) { -this.m00 = m1.m00; -this.m01 = m1.m01; -this.m02 = m1.m02; -this.m10 = m1.m10; -this.m11 = m1.m11; -this.m12 = m1.m12; -this.m20 = m1.m20; -this.m21 = m1.m21; -this.m22 = m1.m22; -}, "javajs.util.M3"); -Clazz.defineMethod (c$, "setRowA", -function (row, v) { -if (row < 3) this.setRow33 (row, v); -switch (row) { -case 0: -this.m03 = v[3]; -return; -case 1: -this.m13 = v[3]; -return; -case 2: -this.m23 = v[3]; -return; -case 3: -this.m30 = v[0]; -this.m31 = v[1]; -this.m32 = v[2]; -this.m33 = v[3]; -return; -} -this.err (); -}, "~N,~A"); -Clazz.overrideMethod (c$, "getRow", -function (row, v) { -if (row < 3) this.getRow33 (row, v); -switch (row) { -case 0: -v[3] = this.m03; -return; -case 1: -v[3] = this.m13; -return; -case 2: -v[3] = this.m23; -return; -case 3: -v[0] = this.m30; -v[1] = this.m31; -v[2] = this.m32; -v[3] = this.m33; -return; -} -this.err (); -}, "~N,~A"); -Clazz.defineMethod (c$, "setColumn4", -function (column, x, y, z, w) { -if (column == 0) { -this.m00 = x; -this.m10 = y; -this.m20 = z; -this.m30 = w; -} else if (column == 1) { -this.m01 = x; -this.m11 = y; -this.m21 = z; -this.m31 = w; -} else if (column == 2) { -this.m02 = x; -this.m12 = y; -this.m22 = z; -this.m32 = w; -} else if (column == 3) { -this.m03 = x; -this.m13 = y; -this.m23 = z; -this.m33 = w; -} else { -this.err (); -}}, "~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "setColumnA", -function (column, v) { -if (column < 3) this.setColumn33 (column, v); -switch (column) { -case 0: -this.m30 = v[3]; -return; -case 1: -this.m31 = v[3]; -return; -case 2: -this.m32 = v[3]; -return; -case 3: -this.m03 = v[0]; -this.m13 = v[1]; -this.m23 = v[2]; -this.m33 = v[3]; -return; -default: -this.err (); -} -}, "~N,~A"); -Clazz.defineMethod (c$, "getColumn", -function (column, v) { -if (column < 3) this.getColumn33 (column, v); -switch (column) { -case 0: -v[3] = this.m30; -return; -case 1: -v[3] = this.m31; -return; -case 2: -v[3] = this.m32; -return; -case 3: -v[0] = this.m03; -v[1] = this.m13; -v[2] = this.m23; -v[3] = this.m33; -return; -default: -this.err (); -} -}, "~N,~A"); -Clazz.defineMethod (c$, "sub", -function (m1) { -this.sub33 (m1); -this.m03 -= m1.m03; -this.m13 -= m1.m13; -this.m23 -= m1.m23; -this.m30 -= m1.m30; -this.m31 -= m1.m31; -this.m32 -= m1.m32; -this.m33 -= m1.m33; -}, "javajs.util.M4"); -Clazz.defineMethod (c$, "transpose", -function () { -this.transpose33 (); -var tmp = this.m03; -this.m03 = this.m30; -this.m30 = tmp; -tmp = this.m13; -this.m13 = this.m31; -this.m31 = tmp; -tmp = this.m23; -this.m23 = this.m32; -this.m32 = tmp; -}); -Clazz.defineMethod (c$, "invert", -function () { -var s = this.determinant4 (); -if (s == 0.0) return this; -s = 1 / s; -this.set (this.m11 * (this.m22 * this.m33 - this.m23 * this.m32) + this.m12 * (this.m23 * this.m31 - this.m21 * this.m33) + this.m13 * (this.m21 * this.m32 - this.m22 * this.m31), this.m21 * (this.m02 * this.m33 - this.m03 * this.m32) + this.m22 * (this.m03 * this.m31 - this.m01 * this.m33) + this.m23 * (this.m01 * this.m32 - this.m02 * this.m31), this.m31 * (this.m02 * this.m13 - this.m03 * this.m12) + this.m32 * (this.m03 * this.m11 - this.m01 * this.m13) + this.m33 * (this.m01 * this.m12 - this.m02 * this.m11), this.m01 * (this.m13 * this.m22 - this.m12 * this.m23) + this.m02 * (this.m11 * this.m23 - this.m13 * this.m21) + this.m03 * (this.m12 * this.m21 - this.m11 * this.m22), this.m12 * (this.m20 * this.m33 - this.m23 * this.m30) + this.m13 * (this.m22 * this.m30 - this.m20 * this.m32) + this.m10 * (this.m23 * this.m32 - this.m22 * this.m33), this.m22 * (this.m00 * this.m33 - this.m03 * this.m30) + this.m23 * (this.m02 * this.m30 - this.m00 * this.m32) + this.m20 * (this.m03 * this.m32 - this.m02 * this.m33), this.m32 * (this.m00 * this.m13 - this.m03 * this.m10) + this.m33 * (this.m02 * this.m10 - this.m00 * this.m12) + this.m30 * (this.m03 * this.m12 - this.m02 * this.m13), this.m02 * (this.m13 * this.m20 - this.m10 * this.m23) + this.m03 * (this.m10 * this.m22 - this.m12 * this.m20) + this.m00 * (this.m12 * this.m23 - this.m13 * this.m22), this.m13 * (this.m20 * this.m31 - this.m21 * this.m30) + this.m10 * (this.m21 * this.m33 - this.m23 * this.m31) + this.m11 * (this.m23 * this.m30 - this.m20 * this.m33), this.m23 * (this.m00 * this.m31 - this.m01 * this.m30) + this.m20 * (this.m01 * this.m33 - this.m03 * this.m31) + this.m21 * (this.m03 * this.m30 - this.m00 * this.m33), this.m33 * (this.m00 * this.m11 - this.m01 * this.m10) + this.m30 * (this.m01 * this.m13 - this.m03 * this.m11) + this.m31 * (this.m03 * this.m10 - this.m00 * this.m13), this.m03 * (this.m11 * this.m20 - this.m10 * this.m21) + this.m00 * (this.m13 * this.m21 - this.m11 * this.m23) + this.m01 * (this.m10 * this.m23 - this.m13 * this.m20), this.m10 * (this.m22 * this.m31 - this.m21 * this.m32) + this.m11 * (this.m20 * this.m32 - this.m22 * this.m30) + this.m12 * (this.m21 * this.m30 - this.m20 * this.m31), this.m20 * (this.m02 * this.m31 - this.m01 * this.m32) + this.m21 * (this.m00 * this.m32 - this.m02 * this.m30) + this.m22 * (this.m01 * this.m30 - this.m00 * this.m31), this.m30 * (this.m02 * this.m11 - this.m01 * this.m12) + this.m31 * (this.m00 * this.m12 - this.m02 * this.m10) + this.m32 * (this.m01 * this.m10 - this.m00 * this.m11), this.m00 * (this.m11 * this.m22 - this.m12 * this.m21) + this.m01 * (this.m12 * this.m20 - this.m10 * this.m22) + this.m02 * (this.m10 * this.m21 - this.m11 * this.m20)); -this.scale (s); -return this; -}); -Clazz.defineMethod (c$, "set", -($fz = function (m00, m01, m02, m03, m10, m11, m12, m13, m20, m21, m22, m23, m30, m31, m32, m33) { -this.m00 = m00; -this.m01 = m01; -this.m02 = m02; -this.m03 = m03; -this.m10 = m10; -this.m11 = m11; -this.m12 = m12; -this.m13 = m13; -this.m20 = m20; -this.m21 = m21; -this.m22 = m22; -this.m23 = m23; -this.m30 = m30; -this.m31 = m31; -this.m32 = m32; -this.m33 = m33; -}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N"); -Clazz.defineMethod (c$, "determinant4", -function () { -return (this.m00 * this.m11 - this.m01 * this.m10) * (this.m22 * this.m33 - this.m23 * this.m32) - (this.m00 * this.m12 - this.m02 * this.m10) * (this.m21 * this.m33 - this.m23 * this.m31) + (this.m00 * this.m13 - this.m03 * this.m10) * (this.m21 * this.m32 - this.m22 * this.m31) + (this.m01 * this.m12 - this.m02 * this.m11) * (this.m20 * this.m33 - this.m23 * this.m30) - (this.m01 * this.m13 - this.m03 * this.m11) * (this.m20 * this.m32 - this.m22 * this.m30) + (this.m02 * this.m13 - this.m03 * this.m12) * (this.m20 * this.m31 - this.m21 * this.m30); -}); -Clazz.defineMethod (c$, "scale", -($fz = function (scalar) { -this.mul33 (scalar); -this.m03 *= scalar; -this.m13 *= scalar; -this.m23 *= scalar; -this.m30 *= scalar; -this.m31 *= scalar; -this.m32 *= scalar; -this.m33 *= scalar; -}, $fz.isPrivate = true, $fz), "~N"); -Clazz.defineMethod (c$, "mul", -function (m1) { -this.mul2 (this, m1); -}, "javajs.util.M4"); -Clazz.defineMethod (c$, "mul2", -function (m1, m2) { -this.set (m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20 + m1.m03 * m2.m30, m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21 + m1.m03 * m2.m31, m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22 + m1.m03 * m2.m32, m1.m00 * m2.m03 + m1.m01 * m2.m13 + m1.m02 * m2.m23 + m1.m03 * m2.m33, m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20 + m1.m13 * m2.m30, m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21 + m1.m13 * m2.m31, m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22 + m1.m13 * m2.m32, m1.m10 * m2.m03 + m1.m11 * m2.m13 + m1.m12 * m2.m23 + m1.m13 * m2.m33, m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20 + m1.m23 * m2.m30, m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21 + m1.m23 * m2.m31, m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22 + m1.m23 * m2.m32, m1.m20 * m2.m03 + m1.m21 * m2.m13 + m1.m22 * m2.m23 + m1.m23 * m2.m33, m1.m30 * m2.m00 + m1.m31 * m2.m10 + m1.m32 * m2.m20 + m1.m33 * m2.m30, m1.m30 * m2.m01 + m1.m31 * m2.m11 + m1.m32 * m2.m21 + m1.m33 * m2.m31, m1.m30 * m2.m02 + m1.m31 * m2.m12 + m1.m32 * m2.m22 + m1.m33 * m2.m32, m1.m30 * m2.m03 + m1.m31 * m2.m13 + m1.m32 * m2.m23 + m1.m33 * m2.m33); -}, "javajs.util.M4,javajs.util.M4"); -Clazz.defineMethod (c$, "transform", -function (vec) { -this.transform2 (vec, vec); -}, "javajs.util.T4"); -Clazz.defineMethod (c$, "transform2", -function (vec, vecOut) { -vecOut.set4 (this.m00 * vec.x + this.m01 * vec.y + this.m02 * vec.z + this.m03 * vec.w, this.m10 * vec.x + this.m11 * vec.y + this.m12 * vec.z + this.m13 * vec.w, this.m20 * vec.x + this.m21 * vec.y + this.m22 * vec.z + this.m23 * vec.w, this.m30 * vec.x + this.m31 * vec.y + this.m32 * vec.z + this.m33 * vec.w); -}, "javajs.util.T4,javajs.util.T4"); -Clazz.defineMethod (c$, "rotTrans", -function (point) { -this.rotTrans2 (point, point); -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "rotTrans2", -function (point, pointOut) { -pointOut.set (this.m00 * point.x + this.m01 * point.y + this.m02 * point.z + this.m03, this.m10 * point.x + this.m11 * point.y + this.m12 * point.z + this.m13, this.m20 * point.x + this.m21 * point.y + this.m22 * point.z + this.m23); -return pointOut; -}, "javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "setAsXYRotation", -function (angle) { -this.setIdentity (); -var c = Math.cos (angle); -var s = Math.sin (angle); -this.m22 = c; -this.m23 = -s; -this.m32 = s; -this.m33 = c; -return this; -}, "~N"); -Clazz.defineMethod (c$, "setAsYZRotation", -function (angle) { -this.setIdentity (); -var c = Math.cos (angle); -var s = Math.sin (angle); -this.m00 = c; -this.m03 = -s; -this.m30 = s; -this.m33 = c; -return this; -}, "~N"); -Clazz.defineMethod (c$, "setAsXZRotation", -function (angle) { -this.setIdentity (); -var c = Math.cos (angle); -var s = Math.sin (angle); -this.m11 = c; -this.m13 = -s; -this.m31 = s; -this.m33 = c; -return this; -}, "~N"); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (!(Clazz.instanceOf (o, javajs.util.M4))) return false; -var m = o; -return (this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02 && this.m03 == m.m03 && this.m10 == m.m10 && this.m11 == m.m11 && this.m12 == m.m12 && this.m13 == m.m13 && this.m20 == m.m20 && this.m21 == m.m21 && this.m22 == m.m22 && this.m23 == m.m23 && this.m30 == m.m30 && this.m31 == m.m31 && this.m32 == m.m32 && this.m33 == m.m33); -}, "~O"); -Clazz.overrideMethod (c$, "hashCode", -function () { -return javajs.util.T3.floatToIntBits0 (this.m00) ^ javajs.util.T3.floatToIntBits0 (this.m01) ^ javajs.util.T3.floatToIntBits0 (this.m02) ^ javajs.util.T3.floatToIntBits0 (this.m03) ^ javajs.util.T3.floatToIntBits0 (this.m10) ^ javajs.util.T3.floatToIntBits0 (this.m11) ^ javajs.util.T3.floatToIntBits0 (this.m12) ^ javajs.util.T3.floatToIntBits0 (this.m13) ^ javajs.util.T3.floatToIntBits0 (this.m20) ^ javajs.util.T3.floatToIntBits0 (this.m21) ^ javajs.util.T3.floatToIntBits0 (this.m22) ^ javajs.util.T3.floatToIntBits0 (this.m23) ^ javajs.util.T3.floatToIntBits0 (this.m30) ^ javajs.util.T3.floatToIntBits0 (this.m31) ^ javajs.util.T3.floatToIntBits0 (this.m32) ^ javajs.util.T3.floatToIntBits0 (this.m33); -}); -Clazz.overrideMethod (c$, "toString", -function () { -return "[\n [" + this.m00 + "\t" + this.m01 + "\t" + this.m02 + "\t" + this.m03 + "]" + "\n [" + this.m10 + "\t" + this.m11 + "\t" + this.m12 + "\t" + this.m13 + "]" + "\n [" + this.m20 + "\t" + this.m21 + "\t" + this.m22 + "\t" + this.m23 + "]" + "\n [" + this.m30 + "\t" + this.m31 + "\t" + this.m32 + "\t" + this.m33 + "] ]"; -}); -Clazz.defineMethod (c$, "round", -function (f) { -this.m00 = this.rnd (this.m00, f); -this.m01 = this.rnd (this.m01, f); -this.m02 = this.rnd (this.m02, f); -this.m03 = this.rnd (this.m03, f); -this.m10 = this.rnd (this.m10, f); -this.m11 = this.rnd (this.m11, f); -this.m12 = this.rnd (this.m12, f); -this.m13 = this.rnd (this.m13, f); -this.m20 = this.rnd (this.m20, f); -this.m21 = this.rnd (this.m21, f); -this.m22 = this.rnd (this.m22, f); -this.m23 = this.rnd (this.m23, f); -this.m30 = this.rnd (this.m30, f); -this.m31 = this.rnd (this.m31, f); -this.m32 = this.rnd (this.m32, f); -this.m33 = this.rnd (this.m33, f); -return this; -}, "~N"); -Clazz.defineMethod (c$, "rnd", -($fz = function (n, f) { -return (Math.abs (n) < f ? 0 : n); -}, $fz.isPrivate = true, $fz), "~N,~N"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.M34"], "javajs.util.M4", ["javajs.util.T3"], function () { +c$ = Clazz.decorateAsClass (function () { +this.m03 = 0; +this.m13 = 0; +this.m23 = 0; +this.m30 = 0; +this.m31 = 0; +this.m32 = 0; +this.m33 = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "M4", javajs.util.M34); +c$.newA16 = Clazz.defineMethod (c$, "newA16", +function (v) { +var m = new javajs.util.M4 (); +m.m00 = v[0]; +m.m01 = v[1]; +m.m02 = v[2]; +m.m03 = v[3]; +m.m10 = v[4]; +m.m11 = v[5]; +m.m12 = v[6]; +m.m13 = v[7]; +m.m20 = v[8]; +m.m21 = v[9]; +m.m22 = v[10]; +m.m23 = v[11]; +m.m30 = v[12]; +m.m31 = v[13]; +m.m32 = v[14]; +m.m33 = v[15]; +return m; +}, "~A"); +c$.newM4 = Clazz.defineMethod (c$, "newM4", +function (m1) { +var m = new javajs.util.M4 (); +if (m1 == null) { +m.setIdentity (); +return m; +}m.setToM3 (m1); +m.m03 = m1.m03; +m.m13 = m1.m13; +m.m23 = m1.m23; +m.m30 = m1.m30; +m.m31 = m1.m31; +m.m32 = m1.m32; +m.m33 = m1.m33; +return m; +}, "javajs.util.M4"); +c$.newMV = Clazz.defineMethod (c$, "newMV", +function (m1, t) { +var m = new javajs.util.M4 (); +m.setMV (m1, t); +return m; +}, "javajs.util.M3,javajs.util.T3"); +Clazz.defineMethod (c$, "setZero", +function () { +this.clear33 (); +this.m03 = this.m13 = this.m23 = this.m30 = this.m31 = this.m32 = this.m33 = 0.0; +}); +Clazz.defineMethod (c$, "setIdentity", +function () { +this.setZero (); +this.m00 = this.m11 = this.m22 = this.m33 = 1.0; +}); +Clazz.defineMethod (c$, "setM4", +function (m1) { +this.setM33 (m1); +this.m03 = m1.m03; +this.m13 = m1.m13; +this.m23 = m1.m23; +this.m30 = m1.m30; +this.m31 = m1.m31; +this.m32 = m1.m32; +this.m33 = m1.m33; +return this; +}, "javajs.util.M4"); +Clazz.defineMethod (c$, "setMV", +function (m1, t) { +this.setM33 (m1); +this.setTranslation (t); +this.m33 = 1; +}, "javajs.util.M3,javajs.util.T3"); +Clazz.defineMethod (c$, "setToM3", +function (m1) { +this.setM33 (m1); +this.m03 = this.m13 = this.m23 = this.m30 = this.m31 = this.m32 = 0.0; +this.m33 = 1.0; +}, "javajs.util.M34"); +Clazz.defineMethod (c$, "setToAA", +function (a) { +this.setIdentity (); +this.setAA33 (a); +}, "javajs.util.A4"); +Clazz.defineMethod (c$, "setA", +function (m) { +this.m00 = m[0]; +this.m01 = m[1]; +this.m02 = m[2]; +this.m03 = m[3]; +this.m10 = m[4]; +this.m11 = m[5]; +this.m12 = m[6]; +this.m13 = m[7]; +this.m20 = m[8]; +this.m21 = m[9]; +this.m22 = m[10]; +this.m23 = m[11]; +this.m30 = m[12]; +this.m31 = m[13]; +this.m32 = m[14]; +this.m33 = m[15]; +}, "~A"); +Clazz.defineMethod (c$, "setTranslation", +function (trans) { +this.m03 = trans.x; +this.m13 = trans.y; +this.m23 = trans.z; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "setElement", +function (row, col, v) { +if (row < 3 && col < 3) { +this.set33 (row, col, v); +return; +}if (row > 3 || col > 3) this.err (); +switch (row) { +case 0: +this.m03 = v; +return; +case 1: +this.m13 = v; +return; +case 2: +this.m23 = v; +return; +} +switch (col) { +case 0: +this.m30 = v; +return; +case 1: +this.m31 = v; +return; +case 2: +this.m32 = v; +return; +case 3: +this.m33 = v; +return; +} +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "getElement", +function (row, col) { +if (row < 3 && col < 3) return this.get33 (row, col); +if (row > 3 || col > 3) { +this.err (); +return 0; +}switch (row) { +case 0: +return this.m03; +case 1: +return this.m13; +case 2: +return this.m23; +default: +switch (col) { +case 0: +return this.m30; +case 1: +return this.m31; +case 2: +return this.m32; +default: +return this.m33; +} +} +}, "~N,~N"); +Clazz.defineMethod (c$, "getTranslation", +function (trans) { +trans.x = this.m03; +trans.y = this.m13; +trans.z = this.m23; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "getRotationScale", +function (m1) { +m1.m00 = this.m00; +m1.m01 = this.m01; +m1.m02 = this.m02; +m1.m10 = this.m10; +m1.m11 = this.m11; +m1.m12 = this.m12; +m1.m20 = this.m20; +m1.m21 = this.m21; +m1.m22 = this.m22; +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "setRotationScale", +function (m1) { +this.m00 = m1.m00; +this.m01 = m1.m01; +this.m02 = m1.m02; +this.m10 = m1.m10; +this.m11 = m1.m11; +this.m12 = m1.m12; +this.m20 = m1.m20; +this.m21 = m1.m21; +this.m22 = m1.m22; +}, "javajs.util.M3"); +Clazz.defineMethod (c$, "setRowA", +function (row, v) { +if (row < 3) this.setRow33 (row, v); +switch (row) { +case 0: +this.m03 = v[3]; +return; +case 1: +this.m13 = v[3]; +return; +case 2: +this.m23 = v[3]; +return; +case 3: +this.m30 = v[0]; +this.m31 = v[1]; +this.m32 = v[2]; +this.m33 = v[3]; +return; +} +this.err (); +}, "~N,~A"); +Clazz.overrideMethod (c$, "getRow", +function (row, v) { +if (row < 3) this.getRow33 (row, v); +switch (row) { +case 0: +v[3] = this.m03; +return; +case 1: +v[3] = this.m13; +return; +case 2: +v[3] = this.m23; +return; +case 3: +v[0] = this.m30; +v[1] = this.m31; +v[2] = this.m32; +v[3] = this.m33; +return; +} +this.err (); +}, "~N,~A"); +Clazz.defineMethod (c$, "setColumn4", +function (column, x, y, z, w) { +if (column == 0) { +this.m00 = x; +this.m10 = y; +this.m20 = z; +this.m30 = w; +} else if (column == 1) { +this.m01 = x; +this.m11 = y; +this.m21 = z; +this.m31 = w; +} else if (column == 2) { +this.m02 = x; +this.m12 = y; +this.m22 = z; +this.m32 = w; +} else if (column == 3) { +this.m03 = x; +this.m13 = y; +this.m23 = z; +this.m33 = w; +} else { +this.err (); +}}, "~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "setColumnA", +function (column, v) { +if (column < 3) this.setColumn33 (column, v); +switch (column) { +case 0: +this.m30 = v[3]; +return; +case 1: +this.m31 = v[3]; +return; +case 2: +this.m32 = v[3]; +return; +case 3: +this.m03 = v[0]; +this.m13 = v[1]; +this.m23 = v[2]; +this.m33 = v[3]; +return; +default: +this.err (); +} +}, "~N,~A"); +Clazz.defineMethod (c$, "getColumn", +function (column, v) { +if (column < 3) this.getColumn33 (column, v); +switch (column) { +case 0: +v[3] = this.m30; +return; +case 1: +v[3] = this.m31; +return; +case 2: +v[3] = this.m32; +return; +case 3: +v[0] = this.m03; +v[1] = this.m13; +v[2] = this.m23; +v[3] = this.m33; +return; +default: +this.err (); +} +}, "~N,~A"); +Clazz.defineMethod (c$, "sub", +function (m1) { +this.sub33 (m1); +this.m03 -= m1.m03; +this.m13 -= m1.m13; +this.m23 -= m1.m23; +this.m30 -= m1.m30; +this.m31 -= m1.m31; +this.m32 -= m1.m32; +this.m33 -= m1.m33; +}, "javajs.util.M4"); +Clazz.defineMethod (c$, "transpose", +function () { +this.transpose33 (); +var tmp = this.m03; +this.m03 = this.m30; +this.m30 = tmp; +tmp = this.m13; +this.m13 = this.m31; +this.m31 = tmp; +tmp = this.m23; +this.m23 = this.m32; +this.m32 = tmp; +}); +Clazz.defineMethod (c$, "invert", +function () { +var s = this.determinant4 (); +if (s == 0.0) return this; +s = 1 / s; +this.set (this.m11 * (this.m22 * this.m33 - this.m23 * this.m32) + this.m12 * (this.m23 * this.m31 - this.m21 * this.m33) + this.m13 * (this.m21 * this.m32 - this.m22 * this.m31), this.m21 * (this.m02 * this.m33 - this.m03 * this.m32) + this.m22 * (this.m03 * this.m31 - this.m01 * this.m33) + this.m23 * (this.m01 * this.m32 - this.m02 * this.m31), this.m31 * (this.m02 * this.m13 - this.m03 * this.m12) + this.m32 * (this.m03 * this.m11 - this.m01 * this.m13) + this.m33 * (this.m01 * this.m12 - this.m02 * this.m11), this.m01 * (this.m13 * this.m22 - this.m12 * this.m23) + this.m02 * (this.m11 * this.m23 - this.m13 * this.m21) + this.m03 * (this.m12 * this.m21 - this.m11 * this.m22), this.m12 * (this.m20 * this.m33 - this.m23 * this.m30) + this.m13 * (this.m22 * this.m30 - this.m20 * this.m32) + this.m10 * (this.m23 * this.m32 - this.m22 * this.m33), this.m22 * (this.m00 * this.m33 - this.m03 * this.m30) + this.m23 * (this.m02 * this.m30 - this.m00 * this.m32) + this.m20 * (this.m03 * this.m32 - this.m02 * this.m33), this.m32 * (this.m00 * this.m13 - this.m03 * this.m10) + this.m33 * (this.m02 * this.m10 - this.m00 * this.m12) + this.m30 * (this.m03 * this.m12 - this.m02 * this.m13), this.m02 * (this.m13 * this.m20 - this.m10 * this.m23) + this.m03 * (this.m10 * this.m22 - this.m12 * this.m20) + this.m00 * (this.m12 * this.m23 - this.m13 * this.m22), this.m13 * (this.m20 * this.m31 - this.m21 * this.m30) + this.m10 * (this.m21 * this.m33 - this.m23 * this.m31) + this.m11 * (this.m23 * this.m30 - this.m20 * this.m33), this.m23 * (this.m00 * this.m31 - this.m01 * this.m30) + this.m20 * (this.m01 * this.m33 - this.m03 * this.m31) + this.m21 * (this.m03 * this.m30 - this.m00 * this.m33), this.m33 * (this.m00 * this.m11 - this.m01 * this.m10) + this.m30 * (this.m01 * this.m13 - this.m03 * this.m11) + this.m31 * (this.m03 * this.m10 - this.m00 * this.m13), this.m03 * (this.m11 * this.m20 - this.m10 * this.m21) + this.m00 * (this.m13 * this.m21 - this.m11 * this.m23) + this.m01 * (this.m10 * this.m23 - this.m13 * this.m20), this.m10 * (this.m22 * this.m31 - this.m21 * this.m32) + this.m11 * (this.m20 * this.m32 - this.m22 * this.m30) + this.m12 * (this.m21 * this.m30 - this.m20 * this.m31), this.m20 * (this.m02 * this.m31 - this.m01 * this.m32) + this.m21 * (this.m00 * this.m32 - this.m02 * this.m30) + this.m22 * (this.m01 * this.m30 - this.m00 * this.m31), this.m30 * (this.m02 * this.m11 - this.m01 * this.m12) + this.m31 * (this.m00 * this.m12 - this.m02 * this.m10) + this.m32 * (this.m01 * this.m10 - this.m00 * this.m11), this.m00 * (this.m11 * this.m22 - this.m12 * this.m21) + this.m01 * (this.m12 * this.m20 - this.m10 * this.m22) + this.m02 * (this.m10 * this.m21 - this.m11 * this.m20)); +this.scale (s); +return this; +}); +Clazz.defineMethod (c$, "set", +($fz = function (m00, m01, m02, m03, m10, m11, m12, m13, m20, m21, m22, m23, m30, m31, m32, m33) { +this.m00 = m00; +this.m01 = m01; +this.m02 = m02; +this.m03 = m03; +this.m10 = m10; +this.m11 = m11; +this.m12 = m12; +this.m13 = m13; +this.m20 = m20; +this.m21 = m21; +this.m22 = m22; +this.m23 = m23; +this.m30 = m30; +this.m31 = m31; +this.m32 = m32; +this.m33 = m33; +}, $fz.isPrivate = true, $fz), "~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N"); +Clazz.defineMethod (c$, "determinant4", +function () { +return (this.m00 * this.m11 - this.m01 * this.m10) * (this.m22 * this.m33 - this.m23 * this.m32) - (this.m00 * this.m12 - this.m02 * this.m10) * (this.m21 * this.m33 - this.m23 * this.m31) + (this.m00 * this.m13 - this.m03 * this.m10) * (this.m21 * this.m32 - this.m22 * this.m31) + (this.m01 * this.m12 - this.m02 * this.m11) * (this.m20 * this.m33 - this.m23 * this.m30) - (this.m01 * this.m13 - this.m03 * this.m11) * (this.m20 * this.m32 - this.m22 * this.m30) + (this.m02 * this.m13 - this.m03 * this.m12) * (this.m20 * this.m31 - this.m21 * this.m30); +}); +Clazz.defineMethod (c$, "scale", +($fz = function (scalar) { +this.mul33 (scalar); +this.m03 *= scalar; +this.m13 *= scalar; +this.m23 *= scalar; +this.m30 *= scalar; +this.m31 *= scalar; +this.m32 *= scalar; +this.m33 *= scalar; +}, $fz.isPrivate = true, $fz), "~N"); +Clazz.defineMethod (c$, "mul", +function (m1) { +this.mul2 (this, m1); +}, "javajs.util.M4"); +Clazz.defineMethod (c$, "mul2", +function (m1, m2) { +this.set (m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20 + m1.m03 * m2.m30, m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21 + m1.m03 * m2.m31, m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22 + m1.m03 * m2.m32, m1.m00 * m2.m03 + m1.m01 * m2.m13 + m1.m02 * m2.m23 + m1.m03 * m2.m33, m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20 + m1.m13 * m2.m30, m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21 + m1.m13 * m2.m31, m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22 + m1.m13 * m2.m32, m1.m10 * m2.m03 + m1.m11 * m2.m13 + m1.m12 * m2.m23 + m1.m13 * m2.m33, m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20 + m1.m23 * m2.m30, m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21 + m1.m23 * m2.m31, m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22 + m1.m23 * m2.m32, m1.m20 * m2.m03 + m1.m21 * m2.m13 + m1.m22 * m2.m23 + m1.m23 * m2.m33, m1.m30 * m2.m00 + m1.m31 * m2.m10 + m1.m32 * m2.m20 + m1.m33 * m2.m30, m1.m30 * m2.m01 + m1.m31 * m2.m11 + m1.m32 * m2.m21 + m1.m33 * m2.m31, m1.m30 * m2.m02 + m1.m31 * m2.m12 + m1.m32 * m2.m22 + m1.m33 * m2.m32, m1.m30 * m2.m03 + m1.m31 * m2.m13 + m1.m32 * m2.m23 + m1.m33 * m2.m33); +}, "javajs.util.M4,javajs.util.M4"); +Clazz.defineMethod (c$, "transform", +function (vec) { +this.transform2 (vec, vec); +}, "javajs.util.T4"); +Clazz.defineMethod (c$, "transform2", +function (vec, vecOut) { +vecOut.set4 (this.m00 * vec.x + this.m01 * vec.y + this.m02 * vec.z + this.m03 * vec.w, this.m10 * vec.x + this.m11 * vec.y + this.m12 * vec.z + this.m13 * vec.w, this.m20 * vec.x + this.m21 * vec.y + this.m22 * vec.z + this.m23 * vec.w, this.m30 * vec.x + this.m31 * vec.y + this.m32 * vec.z + this.m33 * vec.w); +}, "javajs.util.T4,javajs.util.T4"); +Clazz.defineMethod (c$, "rotTrans", +function (point) { +this.rotTrans2 (point, point); +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "rotTrans2", +function (point, pointOut) { +pointOut.set (this.m00 * point.x + this.m01 * point.y + this.m02 * point.z + this.m03, this.m10 * point.x + this.m11 * point.y + this.m12 * point.z + this.m13, this.m20 * point.x + this.m21 * point.y + this.m22 * point.z + this.m23); +return pointOut; +}, "javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "setAsXYRotation", +function (angle) { +this.setIdentity (); +var c = Math.cos (angle); +var s = Math.sin (angle); +this.m22 = c; +this.m23 = -s; +this.m32 = s; +this.m33 = c; +return this; +}, "~N"); +Clazz.defineMethod (c$, "setAsYZRotation", +function (angle) { +this.setIdentity (); +var c = Math.cos (angle); +var s = Math.sin (angle); +this.m00 = c; +this.m03 = -s; +this.m30 = s; +this.m33 = c; +return this; +}, "~N"); +Clazz.defineMethod (c$, "setAsXZRotation", +function (angle) { +this.setIdentity (); +var c = Math.cos (angle); +var s = Math.sin (angle); +this.m11 = c; +this.m13 = -s; +this.m31 = s; +this.m33 = c; +return this; +}, "~N"); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (!(Clazz.instanceOf (o, javajs.util.M4))) return false; +var m = o; +return (this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02 && this.m03 == m.m03 && this.m10 == m.m10 && this.m11 == m.m11 && this.m12 == m.m12 && this.m13 == m.m13 && this.m20 == m.m20 && this.m21 == m.m21 && this.m22 == m.m22 && this.m23 == m.m23 && this.m30 == m.m30 && this.m31 == m.m31 && this.m32 == m.m32 && this.m33 == m.m33); +}, "~O"); +Clazz.overrideMethod (c$, "hashCode", +function () { +return javajs.util.T3.floatToIntBits0 (this.m00) ^ javajs.util.T3.floatToIntBits0 (this.m01) ^ javajs.util.T3.floatToIntBits0 (this.m02) ^ javajs.util.T3.floatToIntBits0 (this.m03) ^ javajs.util.T3.floatToIntBits0 (this.m10) ^ javajs.util.T3.floatToIntBits0 (this.m11) ^ javajs.util.T3.floatToIntBits0 (this.m12) ^ javajs.util.T3.floatToIntBits0 (this.m13) ^ javajs.util.T3.floatToIntBits0 (this.m20) ^ javajs.util.T3.floatToIntBits0 (this.m21) ^ javajs.util.T3.floatToIntBits0 (this.m22) ^ javajs.util.T3.floatToIntBits0 (this.m23) ^ javajs.util.T3.floatToIntBits0 (this.m30) ^ javajs.util.T3.floatToIntBits0 (this.m31) ^ javajs.util.T3.floatToIntBits0 (this.m32) ^ javajs.util.T3.floatToIntBits0 (this.m33); +}); +Clazz.overrideMethod (c$, "toString", +function () { +return "[\n [" + this.m00 + "\t" + this.m01 + "\t" + this.m02 + "\t" + this.m03 + "]" + "\n [" + this.m10 + "\t" + this.m11 + "\t" + this.m12 + "\t" + this.m13 + "]" + "\n [" + this.m20 + "\t" + this.m21 + "\t" + this.m22 + "\t" + this.m23 + "]" + "\n [" + this.m30 + "\t" + this.m31 + "\t" + this.m32 + "\t" + this.m33 + "] ]"; +}); +Clazz.defineMethod (c$, "round", +function (f) { +this.m00 = this.rnd (this.m00, f); +this.m01 = this.rnd (this.m01, f); +this.m02 = this.rnd (this.m02, f); +this.m03 = this.rnd (this.m03, f); +this.m10 = this.rnd (this.m10, f); +this.m11 = this.rnd (this.m11, f); +this.m12 = this.rnd (this.m12, f); +this.m13 = this.rnd (this.m13, f); +this.m20 = this.rnd (this.m20, f); +this.m21 = this.rnd (this.m21, f); +this.m22 = this.rnd (this.m22, f); +this.m23 = this.rnd (this.m23, f); +this.m30 = this.rnd (this.m30, f); +this.m31 = this.rnd (this.m31, f); +this.m32 = this.rnd (this.m32, f); +this.m33 = this.rnd (this.m33, f); +return this; +}, "~N"); +Clazz.defineMethod (c$, "rnd", +($fz = function (n, f) { +return (Math.abs (n) < f ? 0 : n); +}, $fz.isPrivate = true, $fz), "~N,~N"); +}); diff --git a/bin/javajs/util/Matrix.js b/bin/javajs/util/Matrix.js index 50972a4..cadc683 100644 --- a/bin/javajs/util/Matrix.js +++ b/bin/javajs/util/Matrix.js @@ -1,223 +1,223 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.a = null; -this.m = 0; -this.n = 0; -if (!Clazz.isClassDefined ("javajs.util.Matrix.LUDecomp")) { -javajs.util.Matrix.$Matrix$LUDecomp$ (); -} -Clazz.instantialize (this, arguments); -}, javajs.util, "Matrix", null, Cloneable); -Clazz.makeConstructor (c$, -function (a, m, n) { -this.a = (a == null ? Clazz.newDoubleArray (m, n, 0) : a); -this.m = m; -this.n = n; -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "getRowDimension", -function () { -return this.m; -}); -Clazz.defineMethod (c$, "getColumnDimension", -function () { -return this.n; -}); -Clazz.defineMethod (c$, "getArray", -function () { -return this.a; -}); -Clazz.defineMethod (c$, "getArrayCopy", -function () { -var x = Clazz.newDoubleArray (this.m, this.n, 0); -for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) x[i][j] = this.a[i][j]; - - -return x; -}); -Clazz.defineMethod (c$, "copy", -function () { -var x = new javajs.util.Matrix (null, this.m, this.n); -var c = x.a; -for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) c[i][j] = this.a[i][j]; - - -return x; -}); -Clazz.overrideMethod (c$, "clone", -function () { -return this.copy (); -}); -Clazz.defineMethod (c$, "getSubmatrix", -function (i0, j0, nrows, ncols) { -var x = new javajs.util.Matrix (null, nrows, ncols); -var xa = x.a; -for (var i = nrows; --i >= 0; ) for (var j = ncols; --j >= 0; ) xa[i][j] = this.a[i0 + i][j0 + j]; - - -return x; -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "getMatrixSelected", -function (r, n) { -var x = new javajs.util.Matrix (null, r.length, n); -var xa = x.a; -for (var i = r.length; --i >= 0; ) { -var b = this.a[r[i]]; -for (var j = n; --j >= 0; ) xa[i][j] = b[j]; - -} -return x; -}, "~A,~N"); -Clazz.defineMethod (c$, "transpose", -function () { -var x = new javajs.util.Matrix (null, this.n, this.m); -var c = x.a; -for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) c[j][i] = this.a[i][j]; - - -return x; -}); -Clazz.defineMethod (c$, "add", -function (b) { -return this.scaleAdd (b, 1); -}, "javajs.util.Matrix"); -Clazz.defineMethod (c$, "sub", -function (b) { -return this.scaleAdd (b, -1); -}, "javajs.util.Matrix"); -Clazz.defineMethod (c$, "scaleAdd", -function (b, scale) { -var x = new javajs.util.Matrix (null, this.m, this.n); -var xa = x.a; -var ba = b.a; -for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) xa[i][j] = ba[i][j] * scale + this.a[i][j]; - - -return x; -}, "javajs.util.Matrix,~N"); -Clazz.defineMethod (c$, "mul", -function (b) { -if (b.m != this.n) return null; -var x = new javajs.util.Matrix (null, this.m, b.n); -var xa = x.a; -var ba = b.a; -for (var j = b.n; --j >= 0; ) for (var i = this.m; --i >= 0; ) { -var arowi = this.a[i]; -var s = 0; -for (var k = this.n; --k >= 0; ) s += arowi[k] * ba[k][j]; - -xa[i][j] = s; -} - -return x; -}, "javajs.util.Matrix"); -Clazz.defineMethod (c$, "inverse", -function () { -return Clazz.innerTypeInstance (javajs.util.Matrix.LUDecomp, this, null, this.m, this.n).solve (javajs.util.Matrix.identity (this.m, this.m), this.n); -}); -Clazz.defineMethod (c$, "trace", -function () { -var t = 0; -for (var i = Math.min (this.m, this.n); --i >= 0; ) t += this.a[i][i]; - -return t; -}); -c$.identity = Clazz.defineMethod (c$, "identity", -function (m, n) { -var x = new javajs.util.Matrix (null, m, n); -var xa = x.a; -for (var i = Math.min (m, n); --i >= 0; ) xa[i][i] = 1; - -return x; -}, "~N,~N"); -Clazz.defineMethod (c$, "getRotation", -function () { -return this.getSubmatrix (0, 0, this.m - 1, this.n - 1); -}); -Clazz.defineMethod (c$, "getTranslation", -function () { -return this.getSubmatrix (0, this.n - 1, this.m - 1, 1); -}); -c$.newT = Clazz.defineMethod (c$, "newT", -function (r, asColumn) { -return (asColumn ? new javajs.util.Matrix ( Clazz.newArray (-1, [ Clazz.newDoubleArray (-1, [r.x]), Clazz.newDoubleArray (-1, [r.y]), Clazz.newDoubleArray (-1, [r.z])]), 3, 1) : new javajs.util.Matrix ( Clazz.newArray (-1, [ Clazz.newDoubleArray (-1, [r.x, r.y, r.z])]), 1, 3)); -}, "javajs.util.T3,~B"); -Clazz.overrideMethod (c$, "toString", -function () { -var s = "[\n"; -for (var i = 0; i < this.m; i++) { -s += " ["; -for (var j = 0; j < this.n; j++) s += " " + this.a[i][j]; - -s += "]\n"; -} -s += "]"; -return s; -}); -c$.$Matrix$LUDecomp$ = function () { -Clazz.pu$h (); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.LU = null; -this.piv = null; -this.pivsign = 0; -Clazz.instantialize (this, arguments); -}, javajs.util.Matrix, "LUDecomp"); -Clazz.makeConstructor (c$, -function (a, b) { -this.LU = this.b$["javajs.util.Matrix"].getArrayCopy (); -this.piv = Clazz.newIntArray (a, 0); -for (var c = a; --c >= 0; ) this.piv[c] = c; - -this.pivsign = 1; -var d; -var e = Clazz.newDoubleArray (a, 0); -for (var f = 0; f < b; f++) { -for (var g = a; --g >= 0; ) e[g] = this.LU[g][f]; - -for (var h = a; --h >= 0; ) { -d = this.LU[h]; -var i = Math.min (h, f); -var j = 0.0; -for (var k = i; --k >= 0; ) j += d[k] * e[k]; - -d[f] = e[h] -= j; -} -var i = f; -for (var j = a; --j > f; ) if (Math.abs (e[j]) > Math.abs (e[i])) i = j; - -if (i != f) { -for (var k = b; --k >= 0; ) { -var l = this.LU[i][k]; -this.LU[i][k] = this.LU[f][k]; -this.LU[f][k] = l; -} -var l = this.piv[i]; -this.piv[i] = this.piv[f]; -this.piv[f] = l; -this.pivsign = -this.pivsign; -}if ( new Boolean (f < a & this.LU[f][f] != 0.0).valueOf ()) for (var k = a; --k > f; ) this.LU[k][f] /= this.LU[f][f]; - -} -}, "~N,~N"); -Clazz.defineMethod (c$, "solve", -function (a, b) { -for (var c = 0; c < b; c++) if (this.LU[c][c] == 0) return null; - -var d = a.n; -var e = a.getMatrixSelected (this.piv, d); -var f = e.a; -for (var g = 0; g < b; g++) for (var h = g + 1; h < b; h++) for (var i = 0; i < d; i++) f[h][i] -= f[g][i] * this.LU[h][g]; - - - -for (var j = b; --j >= 0; ) { -for (var k = d; --k >= 0; ) f[j][k] /= this.LU[j][j]; - -for (var l = j; --l >= 0; ) for (var m = d; --m >= 0; ) f[l][m] -= f[j][m] * this.LU[l][j]; - - -} -return e; -}, "javajs.util.Matrix,~N"); -c$ = Clazz.p0p (); -}; +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.a = null; +this.m = 0; +this.n = 0; +if (!Clazz.isClassDefined ("javajs.util.Matrix.LUDecomp")) { +javajs.util.Matrix.$Matrix$LUDecomp$ (); +} +Clazz.instantialize (this, arguments); +}, javajs.util, "Matrix", null, Cloneable); +Clazz.makeConstructor (c$, +function (a, m, n) { +this.a = (a == null ? Clazz.newDoubleArray (m, n, 0) : a); +this.m = m; +this.n = n; +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "getRowDimension", +function () { +return this.m; +}); +Clazz.defineMethod (c$, "getColumnDimension", +function () { +return this.n; +}); +Clazz.defineMethod (c$, "getArray", +function () { +return this.a; +}); +Clazz.defineMethod (c$, "getArrayCopy", +function () { +var x = Clazz.newDoubleArray (this.m, this.n, 0); +for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) x[i][j] = this.a[i][j]; + + +return x; +}); +Clazz.defineMethod (c$, "copy", +function () { +var x = new javajs.util.Matrix (null, this.m, this.n); +var c = x.a; +for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) c[i][j] = this.a[i][j]; + + +return x; +}); +Clazz.overrideMethod (c$, "clone", +function () { +return this.copy (); +}); +Clazz.defineMethod (c$, "getSubmatrix", +function (i0, j0, nrows, ncols) { +var x = new javajs.util.Matrix (null, nrows, ncols); +var xa = x.a; +for (var i = nrows; --i >= 0; ) for (var j = ncols; --j >= 0; ) xa[i][j] = this.a[i0 + i][j0 + j]; + + +return x; +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "getMatrixSelected", +function (r, n) { +var x = new javajs.util.Matrix (null, r.length, n); +var xa = x.a; +for (var i = r.length; --i >= 0; ) { +var b = this.a[r[i]]; +for (var j = n; --j >= 0; ) xa[i][j] = b[j]; + +} +return x; +}, "~A,~N"); +Clazz.defineMethod (c$, "transpose", +function () { +var x = new javajs.util.Matrix (null, this.n, this.m); +var c = x.a; +for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) c[j][i] = this.a[i][j]; + + +return x; +}); +Clazz.defineMethod (c$, "add", +function (b) { +return this.scaleAdd (b, 1); +}, "javajs.util.Matrix"); +Clazz.defineMethod (c$, "sub", +function (b) { +return this.scaleAdd (b, -1); +}, "javajs.util.Matrix"); +Clazz.defineMethod (c$, "scaleAdd", +function (b, scale) { +var x = new javajs.util.Matrix (null, this.m, this.n); +var xa = x.a; +var ba = b.a; +for (var i = this.m; --i >= 0; ) for (var j = this.n; --j >= 0; ) xa[i][j] = ba[i][j] * scale + this.a[i][j]; + + +return x; +}, "javajs.util.Matrix,~N"); +Clazz.defineMethod (c$, "mul", +function (b) { +if (b.m != this.n) return null; +var x = new javajs.util.Matrix (null, this.m, b.n); +var xa = x.a; +var ba = b.a; +for (var j = b.n; --j >= 0; ) for (var i = this.m; --i >= 0; ) { +var arowi = this.a[i]; +var s = 0; +for (var k = this.n; --k >= 0; ) s += arowi[k] * ba[k][j]; + +xa[i][j] = s; +} + +return x; +}, "javajs.util.Matrix"); +Clazz.defineMethod (c$, "inverse", +function () { +return Clazz.innerTypeInstance (javajs.util.Matrix.LUDecomp, this, null, this.m, this.n).solve (javajs.util.Matrix.identity (this.m, this.m), this.n); +}); +Clazz.defineMethod (c$, "trace", +function () { +var t = 0; +for (var i = Math.min (this.m, this.n); --i >= 0; ) t += this.a[i][i]; + +return t; +}); +c$.identity = Clazz.defineMethod (c$, "identity", +function (m, n) { +var x = new javajs.util.Matrix (null, m, n); +var xa = x.a; +for (var i = Math.min (m, n); --i >= 0; ) xa[i][i] = 1; + +return x; +}, "~N,~N"); +Clazz.defineMethod (c$, "getRotation", +function () { +return this.getSubmatrix (0, 0, this.m - 1, this.n - 1); +}); +Clazz.defineMethod (c$, "getTranslation", +function () { +return this.getSubmatrix (0, this.n - 1, this.m - 1, 1); +}); +c$.newT = Clazz.defineMethod (c$, "newT", +function (r, asColumn) { +return (asColumn ? new javajs.util.Matrix ( Clazz.newArray (-1, [ Clazz.newDoubleArray (-1, [r.x]), Clazz.newDoubleArray (-1, [r.y]), Clazz.newDoubleArray (-1, [r.z])]), 3, 1) : new javajs.util.Matrix ( Clazz.newArray (-1, [ Clazz.newDoubleArray (-1, [r.x, r.y, r.z])]), 1, 3)); +}, "javajs.util.T3,~B"); +Clazz.overrideMethod (c$, "toString", +function () { +var s = "[\n"; +for (var i = 0; i < this.m; i++) { +s += " ["; +for (var j = 0; j < this.n; j++) s += " " + this.a[i][j]; + +s += "]\n"; +} +s += "]"; +return s; +}); +c$.$Matrix$LUDecomp$ = function () { +Clazz.pu$h (); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.LU = null; +this.piv = null; +this.pivsign = 0; +Clazz.instantialize (this, arguments); +}, javajs.util.Matrix, "LUDecomp"); +Clazz.makeConstructor (c$, +function (a, b) { +this.LU = this.b$["javajs.util.Matrix"].getArrayCopy (); +this.piv = Clazz.newIntArray (a, 0); +for (var c = a; --c >= 0; ) this.piv[c] = c; + +this.pivsign = 1; +var d; +var e = Clazz.newDoubleArray (a, 0); +for (var f = 0; f < b; f++) { +for (var g = a; --g >= 0; ) e[g] = this.LU[g][f]; + +for (var h = a; --h >= 0; ) { +d = this.LU[h]; +var i = Math.min (h, f); +var j = 0.0; +for (var k = i; --k >= 0; ) j += d[k] * e[k]; + +d[f] = e[h] -= j; +} +var i = f; +for (var j = a; --j > f; ) if (Math.abs (e[j]) > Math.abs (e[i])) i = j; + +if (i != f) { +for (var k = b; --k >= 0; ) { +var l = this.LU[i][k]; +this.LU[i][k] = this.LU[f][k]; +this.LU[f][k] = l; +} +var l = this.piv[i]; +this.piv[i] = this.piv[f]; +this.piv[f] = l; +this.pivsign = -this.pivsign; +}if ( new Boolean (f < a & this.LU[f][f] != 0.0).valueOf ()) for (var k = a; --k > f; ) this.LU[k][f] /= this.LU[f][f]; + +} +}, "~N,~N"); +Clazz.defineMethod (c$, "solve", +function (a, b) { +for (var c = 0; c < b; c++) if (this.LU[c][c] == 0) return null; + +var d = a.n; +var e = a.getMatrixSelected (this.piv, d); +var f = e.a; +for (var g = 0; g < b; g++) for (var h = g + 1; h < b; h++) for (var i = 0; i < d; i++) f[h][i] -= f[g][i] * this.LU[h][g]; + + + +for (var j = b; --j >= 0; ) { +for (var k = d; --k >= 0; ) f[j][k] /= this.LU[j][j]; + +for (var l = j; --l >= 0; ) for (var m = d; --m >= 0; ) f[l][m] -= f[j][m] * this.LU[l][j]; + + +} +return e; +}, "javajs.util.Matrix,~N"); +c$ = Clazz.p0p (); +}; diff --git a/bin/javajs/util/Measure.class b/bin/javajs/util/Measure.class index 9d2f979..e478913 100644 Binary files a/bin/javajs/util/Measure.class and b/bin/javajs/util/Measure.class differ diff --git a/bin/javajs/util/Measure.js b/bin/javajs/util/Measure.js index 14e6410..bbcd327 100644 --- a/bin/javajs/util/Measure.js +++ b/bin/javajs/util/Measure.js @@ -1,394 +1,394 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.V3"], "javajs.util.Measure", ["java.lang.Float", "javajs.api.Interface", "javajs.util.Lst", "$.P3", "$.P4", "$.Quat"], function () { -c$ = Clazz.declareType (javajs.util, "Measure"); -c$.computeAngle = Clazz.defineMethod (c$, "computeAngle", -function (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees) { -vectorBA.sub2 (pointA, pointB); -vectorBC.sub2 (pointC, pointB); -var angle = vectorBA.angle (vectorBC); -return (asDegrees ? angle / 0.017453292 : angle); -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,~B"); -c$.computeAngleABC = Clazz.defineMethod (c$, "computeAngleABC", -function (pointA, pointB, pointC, asDegrees) { -var vectorBA = new javajs.util.V3 (); -var vectorBC = new javajs.util.V3 (); -return javajs.util.Measure.computeAngle (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees); -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,~B"); -c$.computeTorsion = Clazz.defineMethod (c$, "computeTorsion", -function (p1, p2, p3, p4, asDegrees) { -var ijx = p1.x - p2.x; -var ijy = p1.y - p2.y; -var ijz = p1.z - p2.z; -var kjx = p3.x - p2.x; -var kjy = p3.y - p2.y; -var kjz = p3.z - p2.z; -var klx = p3.x - p4.x; -var kly = p3.y - p4.y; -var klz = p3.z - p4.z; -var ax = ijy * kjz - ijz * kjy; -var ay = ijz * kjx - ijx * kjz; -var az = ijx * kjy - ijy * kjx; -var cx = kjy * klz - kjz * kly; -var cy = kjz * klx - kjx * klz; -var cz = kjx * kly - kjy * klx; -var ai2 = 1 / (ax * ax + ay * ay + az * az); -var ci2 = 1 / (cx * cx + cy * cy + cz * cz); -var ai = Math.sqrt (ai2); -var ci = Math.sqrt (ci2); -var denom = ai * ci; -var cross = ax * cx + ay * cy + az * cz; -var cosang = cross * denom; -if (cosang > 1) { -cosang = 1; -}if (cosang < -1) { -cosang = -1; -}var torsion = Math.acos (cosang); -var dot = ijx * cx + ijy * cy + ijz * cz; -var absDot = Math.abs (dot); -torsion = (dot / absDot > 0) ? torsion : -torsion; -return (asDegrees ? torsion / 0.017453292 : torsion); -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,~B"); -c$.computeHelicalAxis = Clazz.defineMethod (c$, "computeHelicalAxis", -function (a, b, dq) { -var vab = new javajs.util.V3 (); -vab.sub2 (b, a); -var theta = dq.getTheta (); -var n = dq.getNormal (); -var v_dot_n = vab.dot (n); -if (Math.abs (v_dot_n) < 0.0001) v_dot_n = 0; -var va_prime_d = new javajs.util.V3 (); -va_prime_d.cross (vab, n); -if (va_prime_d.dot (va_prime_d) != 0) va_prime_d.normalize (); -var vda = new javajs.util.V3 (); -var vcb = javajs.util.V3.newV (n); -if (v_dot_n == 0) v_dot_n = 1.4E-45; -vcb.scale (v_dot_n); -vda.sub2 (vcb, vab); -vda.scale (0.5); -va_prime_d.scale (theta == 0 ? 0 : (vda.length () / Math.tan (theta / 2 / 180 * 3.141592653589793))); -var r = javajs.util.V3.newV (va_prime_d); -if (theta != 0) r.add (vda); -var pt_a_prime = javajs.util.P3.newP (a); -pt_a_prime.sub (r); -if (v_dot_n != 1.4E-45) n.scale (v_dot_n); -var pt_b_prime = javajs.util.P3.newP (pt_a_prime); -pt_b_prime.add (n); -theta = javajs.util.Measure.computeTorsion (a, pt_a_prime, pt_b_prime, b, true); -if (Float.isNaN (theta) || r.length () < 0.0001) theta = dq.getThetaDirectedV (n); -var residuesPerTurn = Math.abs (theta == 0 ? 0 : 360 / theta); -var pitch = Math.abs (v_dot_n == 1.4E-45 ? 0 : n.length () * (theta == 0 ? 1 : 360 / theta)); -return Clazz.newArray (-1, [pt_a_prime, n, r, javajs.util.P3.new3 (theta, pitch, residuesPerTurn), pt_b_prime]); -}, "javajs.util.P3,javajs.util.P3,javajs.util.Quat"); -c$.getPlaneThroughPoints = Clazz.defineMethod (c$, "getPlaneThroughPoints", -function (pointA, pointB, pointC, vNorm, vAB, plane) { -var w = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB); -plane.set4 (vNorm.x, vNorm.y, vNorm.z, w); -return plane; -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,javajs.util.P4"); -c$.getPlaneThroughPoint = Clazz.defineMethod (c$, "getPlaneThroughPoint", -function (pt, normal, plane) { -plane.set4 (normal.x, normal.y, normal.z, -normal.dot (pt)); -}, "javajs.util.T3,javajs.util.V3,javajs.util.P4"); -c$.distanceToPlane = Clazz.defineMethod (c$, "distanceToPlane", -function (plane, pt) { -return (plane == null ? NaN : (plane.dot (pt) + plane.w) / Math.sqrt (plane.dot (plane))); -}, "javajs.util.P4,javajs.util.T3"); -c$.directedDistanceToPlane = Clazz.defineMethod (c$, "directedDistanceToPlane", -function (pt, plane, ptref) { -var f = plane.dot (pt) + plane.w; -var f1 = plane.dot (ptref) + plane.w; -return Math.signum (f1) * f / Math.sqrt (plane.dot (plane)); -}, "javajs.util.P3,javajs.util.P4,javajs.util.P3"); -c$.distanceToPlaneD = Clazz.defineMethod (c$, "distanceToPlaneD", -function (plane, d, pt) { -return (plane == null ? NaN : (plane.dot (pt) + plane.w) / d); -}, "javajs.util.P4,~N,javajs.util.P3"); -c$.distanceToPlaneV = Clazz.defineMethod (c$, "distanceToPlaneV", -function (norm, w, pt) { -return (norm == null ? NaN : (norm.dot (pt) + w) / Math.sqrt (norm.dot (norm))); -}, "javajs.util.V3,~N,javajs.util.P3"); -c$.calcNormalizedNormal = Clazz.defineMethod (c$, "calcNormalizedNormal", -function (pointA, pointB, pointC, vNormNorm, vAB) { -vAB.sub2 (pointB, pointA); -vNormNorm.sub2 (pointC, pointA); -vNormNorm.cross (vAB, vNormNorm); -vNormNorm.normalize (); -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3"); -c$.getDirectedNormalThroughPoints = Clazz.defineMethod (c$, "getDirectedNormalThroughPoints", -function (pointA, pointB, pointC, ptRef, vNorm, vAB) { -var nd = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB); -if (ptRef != null) { -var pt0 = javajs.util.P3.newP (pointA); -pt0.add (vNorm); -var d = pt0.distance (ptRef); -pt0.sub2 (pointA, vNorm); -if (d > pt0.distance (ptRef)) { -vNorm.scale (-1); -nd = -nd; -}}return nd; -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3"); -c$.getNormalThroughPoints = Clazz.defineMethod (c$, "getNormalThroughPoints", -function (pointA, pointB, pointC, vNorm, vTemp) { -javajs.util.Measure.calcNormalizedNormal (pointA, pointB, pointC, vNorm, vTemp); -vTemp.setT (pointA); -return -vTemp.dot (vNorm); -}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3"); -c$.getPlaneProjection = Clazz.defineMethod (c$, "getPlaneProjection", -function (pt, plane, ptProj, vNorm) { -var dist = javajs.util.Measure.distanceToPlane (plane, pt); -vNorm.set (plane.x, plane.y, plane.z); -vNorm.normalize (); -vNorm.scale (-dist); -ptProj.add2 (pt, vNorm); -}, "javajs.util.P3,javajs.util.P4,javajs.util.P3,javajs.util.V3"); -c$.getNormalToLine = Clazz.defineMethod (c$, "getNormalToLine", -function (pointA, pointB, vNormNorm) { -vNormNorm.sub2 (pointA, pointB); -vNormNorm.cross (vNormNorm, javajs.util.Measure.axisY); -vNormNorm.normalize (); -if (Float.isNaN (vNormNorm.x)) vNormNorm.set (1, 0, 0); -}, "javajs.util.P3,javajs.util.P3,javajs.util.V3"); -c$.getBisectingPlane = Clazz.defineMethod (c$, "getBisectingPlane", -function (pointA, vAB, ptTemp, vTemp, plane) { -ptTemp.scaleAdd2 (0.5, vAB, pointA); -vTemp.setT (vAB); -vTemp.normalize (); -javajs.util.Measure.getPlaneThroughPoint (ptTemp, vTemp, plane); -}, "javajs.util.P3,javajs.util.V3,javajs.util.T3,javajs.util.V3,javajs.util.P4"); -c$.projectOntoAxis = Clazz.defineMethod (c$, "projectOntoAxis", -function (point, axisA, axisUnitVector, vectorProjection) { -vectorProjection.sub2 (point, axisA); -var projectedLength = vectorProjection.dot (axisUnitVector); -point.scaleAdd2 (projectedLength, axisUnitVector, axisA); -vectorProjection.sub2 (point, axisA); -}, "javajs.util.P3,javajs.util.P3,javajs.util.V3,javajs.util.V3"); -c$.calcBestAxisThroughPoints = Clazz.defineMethod (c$, "calcBestAxisThroughPoints", -function (points, axisA, axisUnitVector, vectorProjection, nTriesMax) { -var nPoints = points.length; -axisA.setT (points[0]); -axisUnitVector.sub2 (points[nPoints - 1], axisA); -axisUnitVector.normalize (); -javajs.util.Measure.calcAveragePointN (points, nPoints, axisA); -var nTries = 0; -while (nTries++ < nTriesMax && javajs.util.Measure.findAxis (points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) { -} -var tempA = javajs.util.P3.newP (points[0]); -javajs.util.Measure.projectOntoAxis (tempA, axisA, axisUnitVector, vectorProjection); -axisA.setT (tempA); -}, "~A,javajs.util.P3,javajs.util.V3,javajs.util.V3,~N"); -c$.findAxis = Clazz.defineMethod (c$, "findAxis", -function (points, nPoints, axisA, axisUnitVector, vectorProjection) { -var sumXiYi = new javajs.util.V3 (); -var vTemp = new javajs.util.V3 (); -var pt = new javajs.util.P3 (); -var ptProj = new javajs.util.P3 (); -var a = javajs.util.V3.newV (axisUnitVector); -var sum_Xi2 = 0; -for (var i = nPoints; --i >= 0; ) { -pt.setT (points[i]); -ptProj.setT (pt); -javajs.util.Measure.projectOntoAxis (ptProj, axisA, axisUnitVector, vectorProjection); -vTemp.sub2 (pt, ptProj); -vTemp.cross (vectorProjection, vTemp); -sumXiYi.add (vTemp); -sum_Xi2 += vectorProjection.lengthSquared (); -} -var m = javajs.util.V3.newV (sumXiYi); -m.scale (1 / sum_Xi2); -vTemp.cross (m, axisUnitVector); -axisUnitVector.add (vTemp); -axisUnitVector.normalize (); -vTemp.sub2 (axisUnitVector, a); -return vTemp.length (); -}, "~A,~N,javajs.util.P3,javajs.util.V3,javajs.util.V3"); -c$.calcAveragePoint = Clazz.defineMethod (c$, "calcAveragePoint", -function (pointA, pointB, pointC) { -pointC.set ((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2, (pointA.z + pointB.z) / 2); -}, "javajs.util.P3,javajs.util.P3,javajs.util.P3"); -c$.calcAveragePointN = Clazz.defineMethod (c$, "calcAveragePointN", -function (points, nPoints, averagePoint) { -averagePoint.setT (points[0]); -for (var i = 1; i < nPoints; i++) averagePoint.add (points[i]); - -averagePoint.scale (1 / nPoints); -}, "~A,~N,javajs.util.P3"); -c$.transformPoints = Clazz.defineMethod (c$, "transformPoints", -function (vPts, m4, center) { -var v = new javajs.util.Lst (); -for (var i = 0; i < vPts.size (); i++) { -var pt = javajs.util.P3.newP (vPts.get (i)); -pt.sub (center); -m4.rotTrans (pt); -pt.add (center); -v.addLast (pt); -} -return v; -}, "javajs.util.Lst,javajs.util.M4,javajs.util.P3"); -c$.isInTetrahedron = Clazz.defineMethod (c$, "isInTetrahedron", -function (pt, ptA, ptB, ptC, ptD, plane, vTemp, vTemp2, fullyEnclosed) { -var b = (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptC, ptD, ptA, vTemp, vTemp2, plane), pt) >= 0); -if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptD, ptB, vTemp, vTemp2, plane), pt) >= 0)) return false; -if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptB, ptD, ptC, vTemp, vTemp2, plane), pt) >= 0)) return false; -var d = javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptB, ptC, vTemp, vTemp2, plane), pt); -if (fullyEnclosed) return (b == (d >= 0)); -var d1 = javajs.util.Measure.distanceToPlane (plane, ptD); -return d1 * d <= 0 || Math.abs (d1) > Math.abs (d); -}, "javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P4,javajs.util.V3,javajs.util.V3,~B"); -c$.getIntersectionPP = Clazz.defineMethod (c$, "getIntersectionPP", -function (plane1, plane2) { -var a1 = plane1.x; -var b1 = plane1.y; -var c1 = plane1.z; -var d1 = plane1.w; -var a2 = plane2.x; -var b2 = plane2.y; -var c2 = plane2.z; -var d2 = plane2.w; -var norm1 = javajs.util.V3.new3 (a1, b1, c1); -var norm2 = javajs.util.V3.new3 (a2, b2, c2); -var nxn = new javajs.util.V3 (); -nxn.cross (norm1, norm2); -var ax = Math.abs (nxn.x); -var ay = Math.abs (nxn.y); -var az = Math.abs (nxn.z); -var x; -var y; -var z; -var diff; -var type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3); -switch (type) { -case 1: -x = 0; -diff = (b1 * c2 - b2 * c1); -if (Math.abs (diff) < 0.01) return null; -y = (c1 * d2 - c2 * d1) / diff; -z = (b2 * d1 - d2 * b1) / diff; -break; -case 2: -diff = (a1 * c2 - a2 * c1); -if (Math.abs (diff) < 0.01) return null; -x = (c1 * d2 - c2 * d1) / diff; -y = 0; -z = (a2 * d1 - d2 * a1) / diff; -break; -case 3: -default: -diff = (a1 * b2 - a2 * b1); -if (Math.abs (diff) < 0.01) return null; -x = (b1 * d2 - b2 * d1) / diff; -y = (a2 * d1 - d2 * a1) / diff; -z = 0; -} -var list = new javajs.util.Lst (); -list.addLast (javajs.util.P3.new3 (x, y, z)); -nxn.normalize (); -list.addLast (nxn); -return list; -}, "javajs.util.P4,javajs.util.P4"); -c$.getIntersection = Clazz.defineMethod (c$, "getIntersection", -function (pt1, v, plane, ptRet, tempNorm, vTemp) { -javajs.util.Measure.getPlaneProjection (pt1, plane, ptRet, tempNorm); -tempNorm.set (plane.x, plane.y, plane.z); -tempNorm.normalize (); -if (v == null) v = javajs.util.V3.newV (tempNorm); -var l_dot_n = v.dot (tempNorm); -if (Math.abs (l_dot_n) < 0.01) return null; -vTemp.sub2 (ptRet, pt1); -ptRet.scaleAdd2 (vTemp.dot (tempNorm) / l_dot_n, v, pt1); -return ptRet; -}, "javajs.util.P3,javajs.util.V3,javajs.util.P4,javajs.util.P3,javajs.util.V3,javajs.util.V3"); -c$.calculateQuaternionRotation = Clazz.defineMethod (c$, "calculateQuaternionRotation", -function (centerAndPoints, retStddev) { -retStddev[1] = NaN; -var q = new javajs.util.Quat (); -if (centerAndPoints[0].length == 1 || centerAndPoints[0].length != centerAndPoints[1].length) return q; -var n = centerAndPoints[0].length - 1; -if (n < 2) return q; -var Sxx = 0; -var Sxy = 0; -var Sxz = 0; -var Syx = 0; -var Syy = 0; -var Syz = 0; -var Szx = 0; -var Szy = 0; -var Szz = 0; -var ptA = new javajs.util.P3 (); -var ptB = new javajs.util.P3 (); -for (var i = n + 1; --i >= 1; ) { -var aij = centerAndPoints[0][i]; -var bij = centerAndPoints[1][i]; -ptA.sub2 (aij, centerAndPoints[0][0]); -ptB.sub2 (bij, centerAndPoints[0][1]); -Sxx += ptA.x * ptB.x; -Sxy += ptA.x * ptB.y; -Sxz += ptA.x * ptB.z; -Syx += ptA.y * ptB.x; -Syy += ptA.y * ptB.y; -Syz += ptA.y * ptB.z; -Szx += ptA.z * ptB.x; -Szy += ptA.z * ptB.y; -Szz += ptA.z * ptB.z; -} -retStddev[0] = javajs.util.Measure.getRmsd (centerAndPoints, q); -var N = Clazz.newDoubleArray (4, 4, 0); -N[0][0] = Sxx + Syy + Szz; -N[0][1] = N[1][0] = Syz - Szy; -N[0][2] = N[2][0] = Szx - Sxz; -N[0][3] = N[3][0] = Sxy - Syx; -N[1][1] = Sxx - Syy - Szz; -N[1][2] = N[2][1] = Sxy + Syx; -N[1][3] = N[3][1] = Szx + Sxz; -N[2][2] = -Sxx + Syy - Szz; -N[2][3] = N[3][2] = Syz + Szy; -N[3][3] = -Sxx - Syy + Szz; -var v = (javajs.api.Interface.getInterface ("javajs.util.Eigen")).setM (N).getEigenvectorsFloatTransposed ()[3]; -q = javajs.util.Quat.newP4 (javajs.util.P4.new4 (v[1], v[2], v[3], v[0])); -retStddev[1] = javajs.util.Measure.getRmsd (centerAndPoints, q); -return q; -}, "~A,~A"); -c$.getTransformMatrix4 = Clazz.defineMethod (c$, "getTransformMatrix4", -function (ptsA, ptsB, m, centerA) { -var cptsA = javajs.util.Measure.getCenterAndPoints (ptsA); -var cptsB = javajs.util.Measure.getCenterAndPoints (ptsB); -var retStddev = Clazz.newFloatArray (2, 0); -var q = javajs.util.Measure.calculateQuaternionRotation ( Clazz.newArray (-1, [cptsA, cptsB]), retStddev); -var r = q.getMatrix (); -if (centerA == null) r.rotate (cptsA[0]); - else centerA.setT (cptsA[0]); -var t = javajs.util.V3.newVsub (cptsB[0], cptsA[0]); -m.setMV (r, t); -return retStddev[1]; -}, "javajs.util.Lst,javajs.util.Lst,javajs.util.M4,javajs.util.P3"); -c$.getCenterAndPoints = Clazz.defineMethod (c$, "getCenterAndPoints", -function (vPts) { -var n = vPts.size (); -var pts = new Array (n + 1); -pts[0] = new javajs.util.P3 (); -if (n > 0) { -for (var i = 0; i < n; i++) { -pts[0].add (pts[i + 1] = vPts.get (i)); -} -pts[0].scale (1 / n); -}return pts; -}, "javajs.util.Lst"); -c$.getRmsd = Clazz.defineMethod (c$, "getRmsd", -function (centerAndPoints, q) { -var sum2 = 0; -var ptsA = centerAndPoints[0]; -var ptsB = centerAndPoints[1]; -var cA = ptsA[0]; -var cB = ptsB[0]; -var n = ptsA.length - 1; -var ptAnew = new javajs.util.P3 (); -for (var i = n + 1; --i >= 1; ) { -ptAnew.sub2 (ptsA[i], cA); -q.transform2 (ptAnew, ptAnew).add (cB); -sum2 += ptAnew.distanceSquared (ptsB[i]); -} -return Math.sqrt (sum2 / n); -}, "~A,javajs.util.Quat"); -Clazz.defineStatics (c$, -"radiansPerDegree", (0.017453292519943295)); -c$.axisY = c$.prototype.axisY = javajs.util.V3.new3 (0, 1, 0); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.V3"], "javajs.util.Measure", ["java.lang.Float", "javajs.api.Interface", "javajs.util.Lst", "$.P3", "$.P4", "$.Quat"], function () { +c$ = Clazz.declareType (javajs.util, "Measure"); +c$.computeAngle = Clazz.defineMethod (c$, "computeAngle", +function (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees) { +vectorBA.sub2 (pointA, pointB); +vectorBC.sub2 (pointC, pointB); +var angle = vectorBA.angle (vectorBC); +return (asDegrees ? angle / 0.017453292 : angle); +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,~B"); +c$.computeAngleABC = Clazz.defineMethod (c$, "computeAngleABC", +function (pointA, pointB, pointC, asDegrees) { +var vectorBA = new javajs.util.V3 (); +var vectorBC = new javajs.util.V3 (); +return javajs.util.Measure.computeAngle (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees); +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,~B"); +c$.computeTorsion = Clazz.defineMethod (c$, "computeTorsion", +function (p1, p2, p3, p4, asDegrees) { +var ijx = p1.x - p2.x; +var ijy = p1.y - p2.y; +var ijz = p1.z - p2.z; +var kjx = p3.x - p2.x; +var kjy = p3.y - p2.y; +var kjz = p3.z - p2.z; +var klx = p3.x - p4.x; +var kly = p3.y - p4.y; +var klz = p3.z - p4.z; +var ax = ijy * kjz - ijz * kjy; +var ay = ijz * kjx - ijx * kjz; +var az = ijx * kjy - ijy * kjx; +var cx = kjy * klz - kjz * kly; +var cy = kjz * klx - kjx * klz; +var cz = kjx * kly - kjy * klx; +var ai2 = 1 / (ax * ax + ay * ay + az * az); +var ci2 = 1 / (cx * cx + cy * cy + cz * cz); +var ai = Math.sqrt (ai2); +var ci = Math.sqrt (ci2); +var denom = ai * ci; +var cross = ax * cx + ay * cy + az * cz; +var cosang = cross * denom; +if (cosang > 1) { +cosang = 1; +}if (cosang < -1) { +cosang = -1; +}var torsion = Math.acos (cosang); +var dot = ijx * cx + ijy * cy + ijz * cz; +var absDot = Math.abs (dot); +torsion = (dot / absDot > 0) ? torsion : -torsion; +return (asDegrees ? torsion / 0.017453292 : torsion); +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,~B"); +c$.computeHelicalAxis = Clazz.defineMethod (c$, "computeHelicalAxis", +function (a, b, dq) { +var vab = new javajs.util.V3 (); +vab.sub2 (b, a); +var theta = dq.getTheta (); +var n = dq.getNormal (); +var v_dot_n = vab.dot (n); +if (Math.abs (v_dot_n) < 0.0001) v_dot_n = 0; +var va_prime_d = new javajs.util.V3 (); +va_prime_d.cross (vab, n); +if (va_prime_d.dot (va_prime_d) != 0) va_prime_d.normalize (); +var vda = new javajs.util.V3 (); +var vcb = javajs.util.V3.newV (n); +if (v_dot_n == 0) v_dot_n = 1.4E-45; +vcb.scale (v_dot_n); +vda.sub2 (vcb, vab); +vda.scale (0.5); +va_prime_d.scale (theta == 0 ? 0 : (vda.length () / Math.tan (theta / 2 / 180 * 3.141592653589793))); +var r = javajs.util.V3.newV (va_prime_d); +if (theta != 0) r.add (vda); +var pt_a_prime = javajs.util.P3.newP (a); +pt_a_prime.sub (r); +if (v_dot_n != 1.4E-45) n.scale (v_dot_n); +var pt_b_prime = javajs.util.P3.newP (pt_a_prime); +pt_b_prime.add (n); +theta = javajs.util.Measure.computeTorsion (a, pt_a_prime, pt_b_prime, b, true); +if (Float.isNaN (theta) || r.length () < 0.0001) theta = dq.getThetaDirectedV (n); +var residuesPerTurn = Math.abs (theta == 0 ? 0 : 360 / theta); +var pitch = Math.abs (v_dot_n == 1.4E-45 ? 0 : n.length () * (theta == 0 ? 1 : 360 / theta)); +return Clazz.newArray (-1, [pt_a_prime, n, r, javajs.util.P3.new3 (theta, pitch, residuesPerTurn), pt_b_prime]); +}, "javajs.util.P3,javajs.util.P3,javajs.util.Quat"); +c$.getPlaneThroughPoints = Clazz.defineMethod (c$, "getPlaneThroughPoints", +function (pointA, pointB, pointC, vNorm, vAB, plane) { +var w = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB); +plane.set4 (vNorm.x, vNorm.y, vNorm.z, w); +return plane; +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,javajs.util.P4"); +c$.getPlaneThroughPoint = Clazz.defineMethod (c$, "getPlaneThroughPoint", +function (pt, normal, plane) { +plane.set4 (normal.x, normal.y, normal.z, -normal.dot (pt)); +}, "javajs.util.T3,javajs.util.V3,javajs.util.P4"); +c$.distanceToPlane = Clazz.defineMethod (c$, "distanceToPlane", +function (plane, pt) { +return (plane == null ? NaN : (plane.dot (pt) + plane.w) / Math.sqrt (plane.dot (plane))); +}, "javajs.util.P4,javajs.util.T3"); +c$.directedDistanceToPlane = Clazz.defineMethod (c$, "directedDistanceToPlane", +function (pt, plane, ptref) { +var f = plane.dot (pt) + plane.w; +var f1 = plane.dot (ptref) + plane.w; +return Math.signum (f1) * f / Math.sqrt (plane.dot (plane)); +}, "javajs.util.P3,javajs.util.P4,javajs.util.P3"); +c$.distanceToPlaneD = Clazz.defineMethod (c$, "distanceToPlaneD", +function (plane, d, pt) { +return (plane == null ? NaN : (plane.dot (pt) + plane.w) / d); +}, "javajs.util.P4,~N,javajs.util.P3"); +c$.distanceToPlaneV = Clazz.defineMethod (c$, "distanceToPlaneV", +function (norm, w, pt) { +return (norm == null ? NaN : (norm.dot (pt) + w) / Math.sqrt (norm.dot (norm))); +}, "javajs.util.V3,~N,javajs.util.P3"); +c$.calcNormalizedNormal = Clazz.defineMethod (c$, "calcNormalizedNormal", +function (pointA, pointB, pointC, vNormNorm, vAB) { +vAB.sub2 (pointB, pointA); +vNormNorm.sub2 (pointC, pointA); +vNormNorm.cross (vAB, vNormNorm); +vNormNorm.normalize (); +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3"); +c$.getDirectedNormalThroughPoints = Clazz.defineMethod (c$, "getDirectedNormalThroughPoints", +function (pointA, pointB, pointC, ptRef, vNorm, vAB) { +var nd = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB); +if (ptRef != null) { +var pt0 = javajs.util.P3.newP (pointA); +pt0.add (vNorm); +var d = pt0.distance (ptRef); +pt0.sub2 (pointA, vNorm); +if (d > pt0.distance (ptRef)) { +vNorm.scale (-1); +nd = -nd; +}}return nd; +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3"); +c$.getNormalThroughPoints = Clazz.defineMethod (c$, "getNormalThroughPoints", +function (pointA, pointB, pointC, vNorm, vTemp) { +javajs.util.Measure.calcNormalizedNormal (pointA, pointB, pointC, vNorm, vTemp); +vTemp.setT (pointA); +return -vTemp.dot (vNorm); +}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3"); +c$.getPlaneProjection = Clazz.defineMethod (c$, "getPlaneProjection", +function (pt, plane, ptProj, vNorm) { +var dist = javajs.util.Measure.distanceToPlane (plane, pt); +vNorm.set (plane.x, plane.y, plane.z); +vNorm.normalize (); +vNorm.scale (-dist); +ptProj.add2 (pt, vNorm); +}, "javajs.util.P3,javajs.util.P4,javajs.util.P3,javajs.util.V3"); +c$.getNormalToLine = Clazz.defineMethod (c$, "getNormalToLine", +function (pointA, pointB, vNormNorm) { +vNormNorm.sub2 (pointA, pointB); +vNormNorm.cross (vNormNorm, javajs.util.Measure.axisY); +vNormNorm.normalize (); +if (Float.isNaN (vNormNorm.x)) vNormNorm.set (1, 0, 0); +}, "javajs.util.P3,javajs.util.P3,javajs.util.V3"); +c$.getBisectingPlane = Clazz.defineMethod (c$, "getBisectingPlane", +function (pointA, vAB, ptTemp, vTemp, plane) { +ptTemp.scaleAdd2 (0.5, vAB, pointA); +vTemp.setT (vAB); +vTemp.normalize (); +javajs.util.Measure.getPlaneThroughPoint (ptTemp, vTemp, plane); +}, "javajs.util.P3,javajs.util.V3,javajs.util.T3,javajs.util.V3,javajs.util.P4"); +c$.projectOntoAxis = Clazz.defineMethod (c$, "projectOntoAxis", +function (point, axisA, axisUnitVector, vectorProjection) { +vectorProjection.sub2 (point, axisA); +var projectedLength = vectorProjection.dot (axisUnitVector); +point.scaleAdd2 (projectedLength, axisUnitVector, axisA); +vectorProjection.sub2 (point, axisA); +}, "javajs.util.P3,javajs.util.P3,javajs.util.V3,javajs.util.V3"); +c$.calcBestAxisThroughPoints = Clazz.defineMethod (c$, "calcBestAxisThroughPoints", +function (points, axisA, axisUnitVector, vectorProjection, nTriesMax) { +var nPoints = points.length; +axisA.setT (points[0]); +axisUnitVector.sub2 (points[nPoints - 1], axisA); +axisUnitVector.normalize (); +javajs.util.Measure.calcAveragePointN (points, nPoints, axisA); +var nTries = 0; +while (nTries++ < nTriesMax && javajs.util.Measure.findAxis (points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) { +} +var tempA = javajs.util.P3.newP (points[0]); +javajs.util.Measure.projectOntoAxis (tempA, axisA, axisUnitVector, vectorProjection); +axisA.setT (tempA); +}, "~A,javajs.util.P3,javajs.util.V3,javajs.util.V3,~N"); +c$.findAxis = Clazz.defineMethod (c$, "findAxis", +function (points, nPoints, axisA, axisUnitVector, vectorProjection) { +var sumXiYi = new javajs.util.V3 (); +var vTemp = new javajs.util.V3 (); +var pt = new javajs.util.P3 (); +var ptProj = new javajs.util.P3 (); +var a = javajs.util.V3.newV (axisUnitVector); +var sum_Xi2 = 0; +for (var i = nPoints; --i >= 0; ) { +pt.setT (points[i]); +ptProj.setT (pt); +javajs.util.Measure.projectOntoAxis (ptProj, axisA, axisUnitVector, vectorProjection); +vTemp.sub2 (pt, ptProj); +vTemp.cross (vectorProjection, vTemp); +sumXiYi.add (vTemp); +sum_Xi2 += vectorProjection.lengthSquared (); +} +var m = javajs.util.V3.newV (sumXiYi); +m.scale (1 / sum_Xi2); +vTemp.cross (m, axisUnitVector); +axisUnitVector.add (vTemp); +axisUnitVector.normalize (); +vTemp.sub2 (axisUnitVector, a); +return vTemp.length (); +}, "~A,~N,javajs.util.P3,javajs.util.V3,javajs.util.V3"); +c$.calcAveragePoint = Clazz.defineMethod (c$, "calcAveragePoint", +function (pointA, pointB, pointC) { +pointC.set ((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2, (pointA.z + pointB.z) / 2); +}, "javajs.util.P3,javajs.util.P3,javajs.util.P3"); +c$.calcAveragePointN = Clazz.defineMethod (c$, "calcAveragePointN", +function (points, nPoints, averagePoint) { +averagePoint.setT (points[0]); +for (var i = 1; i < nPoints; i++) averagePoint.add (points[i]); + +averagePoint.scale (1 / nPoints); +}, "~A,~N,javajs.util.P3"); +c$.transformPoints = Clazz.defineMethod (c$, "transformPoints", +function (vPts, m4, center) { +var v = new javajs.util.Lst (); +for (var i = 0; i < vPts.size (); i++) { +var pt = javajs.util.P3.newP (vPts.get (i)); +pt.sub (center); +m4.rotTrans (pt); +pt.add (center); +v.addLast (pt); +} +return v; +}, "javajs.util.Lst,javajs.util.M4,javajs.util.P3"); +c$.isInTetrahedron = Clazz.defineMethod (c$, "isInTetrahedron", +function (pt, ptA, ptB, ptC, ptD, plane, vTemp, vTemp2, fullyEnclosed) { +var b = (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptC, ptD, ptA, vTemp, vTemp2, plane), pt) >= 0); +if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptD, ptB, vTemp, vTemp2, plane), pt) >= 0)) return false; +if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptB, ptD, ptC, vTemp, vTemp2, plane), pt) >= 0)) return false; +var d = javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptB, ptC, vTemp, vTemp2, plane), pt); +if (fullyEnclosed) return (b == (d >= 0)); +var d1 = javajs.util.Measure.distanceToPlane (plane, ptD); +return d1 * d <= 0 || Math.abs (d1) > Math.abs (d); +}, "javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P4,javajs.util.V3,javajs.util.V3,~B"); +c$.getIntersectionPP = Clazz.defineMethod (c$, "getIntersectionPP", +function (plane1, plane2) { +var a1 = plane1.x; +var b1 = plane1.y; +var c1 = plane1.z; +var d1 = plane1.w; +var a2 = plane2.x; +var b2 = plane2.y; +var c2 = plane2.z; +var d2 = plane2.w; +var norm1 = javajs.util.V3.new3 (a1, b1, c1); +var norm2 = javajs.util.V3.new3 (a2, b2, c2); +var nxn = new javajs.util.V3 (); +nxn.cross (norm1, norm2); +var ax = Math.abs (nxn.x); +var ay = Math.abs (nxn.y); +var az = Math.abs (nxn.z); +var x; +var y; +var z; +var diff; +var type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3); +switch (type) { +case 1: +x = 0; +diff = (b1 * c2 - b2 * c1); +if (Math.abs (diff) < 0.01) return null; +y = (c1 * d2 - c2 * d1) / diff; +z = (b2 * d1 - d2 * b1) / diff; +break; +case 2: +diff = (a1 * c2 - a2 * c1); +if (Math.abs (diff) < 0.01) return null; +x = (c1 * d2 - c2 * d1) / diff; +y = 0; +z = (a2 * d1 - d2 * a1) / diff; +break; +case 3: +default: +diff = (a1 * b2 - a2 * b1); +if (Math.abs (diff) < 0.01) return null; +x = (b1 * d2 - b2 * d1) / diff; +y = (a2 * d1 - d2 * a1) / diff; +z = 0; +} +var list = new javajs.util.Lst (); +list.addLast (javajs.util.P3.new3 (x, y, z)); +nxn.normalize (); +list.addLast (nxn); +return list; +}, "javajs.util.P4,javajs.util.P4"); +c$.getIntersection = Clazz.defineMethod (c$, "getIntersection", +function (pt1, v, plane, ptRet, tempNorm, vTemp) { +javajs.util.Measure.getPlaneProjection (pt1, plane, ptRet, tempNorm); +tempNorm.set (plane.x, plane.y, plane.z); +tempNorm.normalize (); +if (v == null) v = javajs.util.V3.newV (tempNorm); +var l_dot_n = v.dot (tempNorm); +if (Math.abs (l_dot_n) < 0.01) return null; +vTemp.sub2 (ptRet, pt1); +ptRet.scaleAdd2 (vTemp.dot (tempNorm) / l_dot_n, v, pt1); +return ptRet; +}, "javajs.util.P3,javajs.util.V3,javajs.util.P4,javajs.util.P3,javajs.util.V3,javajs.util.V3"); +c$.calculateQuaternionRotation = Clazz.defineMethod (c$, "calculateQuaternionRotation", +function (centerAndPoints, retStddev) { +retStddev[1] = NaN; +var q = new javajs.util.Quat (); +if (centerAndPoints[0].length == 1 || centerAndPoints[0].length != centerAndPoints[1].length) return q; +var n = centerAndPoints[0].length - 1; +if (n < 2) return q; +var Sxx = 0; +var Sxy = 0; +var Sxz = 0; +var Syx = 0; +var Syy = 0; +var Syz = 0; +var Szx = 0; +var Szy = 0; +var Szz = 0; +var ptA = new javajs.util.P3 (); +var ptB = new javajs.util.P3 (); +for (var i = n + 1; --i >= 1; ) { +var aij = centerAndPoints[0][i]; +var bij = centerAndPoints[1][i]; +ptA.sub2 (aij, centerAndPoints[0][0]); +ptB.sub2 (bij, centerAndPoints[0][1]); +Sxx += ptA.x * ptB.x; +Sxy += ptA.x * ptB.y; +Sxz += ptA.x * ptB.z; +Syx += ptA.y * ptB.x; +Syy += ptA.y * ptB.y; +Syz += ptA.y * ptB.z; +Szx += ptA.z * ptB.x; +Szy += ptA.z * ptB.y; +Szz += ptA.z * ptB.z; +} +retStddev[0] = javajs.util.Measure.getRmsd (centerAndPoints, q); +var N = Clazz.newDoubleArray (4, 4, 0); +N[0][0] = Sxx + Syy + Szz; +N[0][1] = N[1][0] = Syz - Szy; +N[0][2] = N[2][0] = Szx - Sxz; +N[0][3] = N[3][0] = Sxy - Syx; +N[1][1] = Sxx - Syy - Szz; +N[1][2] = N[2][1] = Sxy + Syx; +N[1][3] = N[3][1] = Szx + Sxz; +N[2][2] = -Sxx + Syy - Szz; +N[2][3] = N[3][2] = Syz + Szy; +N[3][3] = -Sxx - Syy + Szz; +var v = (javajs.api.Interface.getInterface ("javajs.util.Eigen")).setM (N).getEigenvectorsFloatTransposed ()[3]; +q = javajs.util.Quat.newP4 (javajs.util.P4.new4 (v[1], v[2], v[3], v[0])); +retStddev[1] = javajs.util.Measure.getRmsd (centerAndPoints, q); +return q; +}, "~A,~A"); +c$.getTransformMatrix4 = Clazz.defineMethod (c$, "getTransformMatrix4", +function (ptsA, ptsB, m, centerA) { +var cptsA = javajs.util.Measure.getCenterAndPoints (ptsA); +var cptsB = javajs.util.Measure.getCenterAndPoints (ptsB); +var retStddev = Clazz.newFloatArray (2, 0); +var q = javajs.util.Measure.calculateQuaternionRotation ( Clazz.newArray (-1, [cptsA, cptsB]), retStddev); +var r = q.getMatrix (); +if (centerA == null) r.rotate (cptsA[0]); + else centerA.setT (cptsA[0]); +var t = javajs.util.V3.newVsub (cptsB[0], cptsA[0]); +m.setMV (r, t); +return retStddev[1]; +}, "javajs.util.Lst,javajs.util.Lst,javajs.util.M4,javajs.util.P3"); +c$.getCenterAndPoints = Clazz.defineMethod (c$, "getCenterAndPoints", +function (vPts) { +var n = vPts.size (); +var pts = new Array (n + 1); +pts[0] = new javajs.util.P3 (); +if (n > 0) { +for (var i = 0; i < n; i++) { +pts[0].add (pts[i + 1] = vPts.get (i)); +} +pts[0].scale (1 / n); +}return pts; +}, "javajs.util.Lst"); +c$.getRmsd = Clazz.defineMethod (c$, "getRmsd", +function (centerAndPoints, q) { +var sum2 = 0; +var ptsA = centerAndPoints[0]; +var ptsB = centerAndPoints[1]; +var cA = ptsA[0]; +var cB = ptsB[0]; +var n = ptsA.length - 1; +var ptAnew = new javajs.util.P3 (); +for (var i = n + 1; --i >= 1; ) { +ptAnew.sub2 (ptsA[i], cA); +q.transform2 (ptAnew, ptAnew).add (cB); +sum2 += ptAnew.distanceSquared (ptsB[i]); +} +return Math.sqrt (sum2 / n); +}, "~A,javajs.util.Quat"); +Clazz.defineStatics (c$, +"radiansPerDegree", (0.017453292519943295)); +c$.axisY = c$.prototype.axisY = javajs.util.V3.new3 (0, 1, 0); +}); diff --git a/bin/javajs/util/OC.class b/bin/javajs/util/OC.class index 962e240..1ff4f42 100644 Binary files a/bin/javajs/util/OC.class and b/bin/javajs/util/OC.class differ diff --git a/bin/javajs/util/OC.js b/bin/javajs/util/OC.js index 76f148a..f720165 100644 --- a/bin/javajs/util/OC.js +++ b/bin/javajs/util/OC.js @@ -1,236 +1,236 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["java.io.OutputStream"], "javajs.util.OC", ["java.io.BufferedWriter", "$.ByteArrayOutputStream", "$.OutputStreamWriter", "javajs.util.Base64", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.bytePoster = null; -this.fileName = null; -this.bw = null; -this.isLocalFile = false; -this.byteCount = 0; -this.isCanceled = false; -this.closed = false; -this.os = null; -this.sb = null; -this.type = null; -this.$isBase64 = false; -this.os0 = null; -this.bytes = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "OC", java.io.OutputStream); -Clazz.defineMethod (c$, "setParams", -function (bytePoster, fileName, asWriter, os) { -this.bytePoster = bytePoster; -this.fileName = fileName; -this.$isBase64 = ";base64,".equals (fileName); -if (this.$isBase64) { -fileName = null; -this.os0 = os; -os = null; -}this.os = os; -this.isLocalFile = (fileName != null && !javajs.util.OC.isRemote (fileName)); -if (asWriter && !this.$isBase64 && os != null) this.bw = new java.io.BufferedWriter ( new java.io.OutputStreamWriter (os)); -return this; -}, "javajs.api.BytePoster,~S,~B,java.io.OutputStream"); -Clazz.defineMethod (c$, "setBytes", -function (b) { -this.bytes = b; -return this; -}, "~A"); -Clazz.defineMethod (c$, "getFileName", -function () { -return this.fileName; -}); -Clazz.defineMethod (c$, "getName", -function () { -return (this.fileName == null ? null : this.fileName.substring (this.fileName.lastIndexOf ("/") + 1)); -}); -Clazz.defineMethod (c$, "getByteCount", -function () { -return this.byteCount; -}); -Clazz.defineMethod (c$, "setType", -function (type) { -this.type = type; -}, "~S"); -Clazz.defineMethod (c$, "getType", -function () { -return this.type; -}); -Clazz.defineMethod (c$, "append", -function (s) { -try { -if (this.bw != null) { -this.bw.write (s); -} else if (this.os == null) { -if (this.sb == null) this.sb = new javajs.util.SB (); -this.sb.append (s); -} else { -var b = s.getBytes (); -this.os.write (b, 0, b.length); -this.byteCount += b.length; -return this; -}} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -this.byteCount += s.length; -return this; -}, "~S"); -Clazz.defineMethod (c$, "reset", -function () { -this.sb = null; -this.initOS (); -}); -Clazz.defineMethod (c$, "initOS", -($fz = function () { -if (this.sb != null) { -var s = this.sb.toString (); -this.reset (); -this.append (s); -return; -}try { -{ -this.os = null; -}if (this.os == null) this.os = new java.io.ByteArrayOutputStream (); -if (this.bw != null) { -this.bw.close (); -this.bw = new java.io.BufferedWriter ( new java.io.OutputStreamWriter (this.os)); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -this.byteCount = 0; -}, $fz.isPrivate = true, $fz)); -Clazz.overrideMethod (c$, "write", -function (buf, i, len) { -if (this.os == null) this.initOS (); -try { -this.os.write (buf, i, len); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -this.byteCount += len; -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "writeByteAsInt", -function (b) { -if (this.os == null) this.initOS (); -{ -this.os.writeByteAsInt(b); -}this.byteCount++; -}, "~N"); -Clazz.defineMethod (c$, "cancel", -function () { -this.isCanceled = true; -this.closeChannel (); -}); -Clazz.defineMethod (c$, "closeChannel", -function () { -if (this.closed) return null; -try { -if (this.bw != null) { -this.bw.flush (); -this.bw.close (); -} else if (this.os != null) { -this.os.flush (); -this.os.close (); -}if (this.os0 != null && this.isCanceled) { -this.os0.flush (); -this.os0.close (); -}} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -if (this.isCanceled) { -this.closed = true; -return null; -}if (this.fileName == null) { -if (this.$isBase64) { -var s = this.getBase64 (); -if (this.os0 != null) { -this.os = this.os0; -this.append (s); -}this.sb = new javajs.util.SB (); -this.sb.append (s); -this.$isBase64 = false; -return this.closeChannel (); -}return (this.sb == null ? null : this.sb.toString ()); -}this.closed = true; -var jmol = null; -var _function = null; -{ -jmol = Jmol; _function = (typeof this.fileName == "function" ? -this.fileName : null); -}if (jmol != null) { -var data = (this.sb == null ? this.toByteArray () : this.sb.toString ()); -if (_function == null) jmol._doAjax (this.fileName, null, data); - else jmol._apply (this.fileName, data); -}return null; -}); -Clazz.defineMethod (c$, "isBase64", -function () { -return this.$isBase64; -}); -Clazz.defineMethod (c$, "getBase64", -function () { -return javajs.util.Base64.getBase64 (this.toByteArray ()).toString (); -}); -Clazz.defineMethod (c$, "toByteArray", -function () { -return (this.bytes != null ? this.bytes : Clazz.instanceOf (this.os, java.io.ByteArrayOutputStream) ? (this.os).toByteArray () : null); -}); -Clazz.defineMethod (c$, "close", -function () { -this.closeChannel (); -}); -Clazz.overrideMethod (c$, "toString", -function () { -if (this.bw != null) try { -this.bw.flush (); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -if (this.sb != null) return this.closeChannel (); -return this.byteCount + " bytes"; -}); -Clazz.defineMethod (c$, "postByteArray", -($fz = function () { -var bytes = (this.sb == null ? this.toByteArray () : this.sb.toString ().getBytes ()); -return this.bytePoster.postByteArray (this.fileName, bytes); -}, $fz.isPrivate = true, $fz)); -c$.isRemote = Clazz.defineMethod (c$, "isRemote", -function (fileName) { -if (fileName == null) return false; -var itype = javajs.util.OC.urlTypeIndex (fileName); -return (itype >= 0 && itype != 4); -}, "~S"); -c$.isLocal = Clazz.defineMethod (c$, "isLocal", -function (fileName) { -if (fileName == null) return false; -var itype = javajs.util.OC.urlTypeIndex (fileName); -return (itype < 0 || itype == 4); -}, "~S"); -c$.urlTypeIndex = Clazz.defineMethod (c$, "urlTypeIndex", -function (name) { -if (name == null) return -2; -for (var i = 0; i < javajs.util.OC.urlPrefixes.length; ++i) { -if (name.startsWith (javajs.util.OC.urlPrefixes[i])) { -return i; -}} -return -1; -}, "~S"); -Clazz.defineStatics (c$, -"urlPrefixes", Clazz.newArray (-1, ["http:", "https:", "sftp:", "ftp:", "file:"]), -"URL_LOCAL", 4); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["java.io.OutputStream"], "javajs.util.OC", ["java.io.BufferedWriter", "$.ByteArrayOutputStream", "$.OutputStreamWriter", "javajs.util.Base64", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.bytePoster = null; +this.fileName = null; +this.bw = null; +this.isLocalFile = false; +this.byteCount = 0; +this.isCanceled = false; +this.closed = false; +this.os = null; +this.sb = null; +this.type = null; +this.$isBase64 = false; +this.os0 = null; +this.bytes = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "OC", java.io.OutputStream); +Clazz.defineMethod (c$, "setParams", +function (bytePoster, fileName, asWriter, os) { +this.bytePoster = bytePoster; +this.fileName = fileName; +this.$isBase64 = ";base64,".equals (fileName); +if (this.$isBase64) { +fileName = null; +this.os0 = os; +os = null; +}this.os = os; +this.isLocalFile = (fileName != null && !javajs.util.OC.isRemote (fileName)); +if (asWriter && !this.$isBase64 && os != null) this.bw = new java.io.BufferedWriter ( new java.io.OutputStreamWriter (os)); +return this; +}, "javajs.api.BytePoster,~S,~B,java.io.OutputStream"); +Clazz.defineMethod (c$, "setBytes", +function (b) { +this.bytes = b; +return this; +}, "~A"); +Clazz.defineMethod (c$, "getFileName", +function () { +return this.fileName; +}); +Clazz.defineMethod (c$, "getName", +function () { +return (this.fileName == null ? null : this.fileName.substring (this.fileName.lastIndexOf ("/") + 1)); +}); +Clazz.defineMethod (c$, "getByteCount", +function () { +return this.byteCount; +}); +Clazz.defineMethod (c$, "setType", +function (type) { +this.type = type; +}, "~S"); +Clazz.defineMethod (c$, "getType", +function () { +return this.type; +}); +Clazz.defineMethod (c$, "append", +function (s) { +try { +if (this.bw != null) { +this.bw.write (s); +} else if (this.os == null) { +if (this.sb == null) this.sb = new javajs.util.SB (); +this.sb.append (s); +} else { +var b = s.getBytes (); +this.os.write (b, 0, b.length); +this.byteCount += b.length; +return this; +}} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +this.byteCount += s.length; +return this; +}, "~S"); +Clazz.defineMethod (c$, "reset", +function () { +this.sb = null; +this.initOS (); +}); +Clazz.defineMethod (c$, "initOS", +($fz = function () { +if (this.sb != null) { +var s = this.sb.toString (); +this.reset (); +this.append (s); +return; +}try { +{ +this.os = null; +}if (this.os == null) this.os = new java.io.ByteArrayOutputStream (); +if (this.bw != null) { +this.bw.close (); +this.bw = new java.io.BufferedWriter ( new java.io.OutputStreamWriter (this.os)); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +this.byteCount = 0; +}, $fz.isPrivate = true, $fz)); +Clazz.overrideMethod (c$, "write", +function (buf, i, len) { +if (this.os == null) this.initOS (); +try { +this.os.write (buf, i, len); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +this.byteCount += len; +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "writeByteAsInt", +function (b) { +if (this.os == null) this.initOS (); +{ +this.os.writeByteAsInt(b); +}this.byteCount++; +}, "~N"); +Clazz.defineMethod (c$, "cancel", +function () { +this.isCanceled = true; +this.closeChannel (); +}); +Clazz.defineMethod (c$, "closeChannel", +function () { +if (this.closed) return null; +try { +if (this.bw != null) { +this.bw.flush (); +this.bw.close (); +} else if (this.os != null) { +this.os.flush (); +this.os.close (); +}if (this.os0 != null && this.isCanceled) { +this.os0.flush (); +this.os0.close (); +}} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +if (this.isCanceled) { +this.closed = true; +return null; +}if (this.fileName == null) { +if (this.$isBase64) { +var s = this.getBase64 (); +if (this.os0 != null) { +this.os = this.os0; +this.append (s); +}this.sb = new javajs.util.SB (); +this.sb.append (s); +this.$isBase64 = false; +return this.closeChannel (); +}return (this.sb == null ? null : this.sb.toString ()); +}this.closed = true; +var jmol = null; +var _function = null; +{ +jmol = Jmol; _function = (typeof this.fileName == "function" ? +this.fileName : null); +}if (jmol != null) { +var data = (this.sb == null ? this.toByteArray () : this.sb.toString ()); +if (_function == null) jmol._doAjax (this.fileName, null, data); + else jmol._apply (this.fileName, data); +}return null; +}); +Clazz.defineMethod (c$, "isBase64", +function () { +return this.$isBase64; +}); +Clazz.defineMethod (c$, "getBase64", +function () { +return javajs.util.Base64.getBase64 (this.toByteArray ()).toString (); +}); +Clazz.defineMethod (c$, "toByteArray", +function () { +return (this.bytes != null ? this.bytes : Clazz.instanceOf (this.os, java.io.ByteArrayOutputStream) ? (this.os).toByteArray () : null); +}); +Clazz.defineMethod (c$, "close", +function () { +this.closeChannel (); +}); +Clazz.overrideMethod (c$, "toString", +function () { +if (this.bw != null) try { +this.bw.flush (); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +if (this.sb != null) return this.closeChannel (); +return this.byteCount + " bytes"; +}); +Clazz.defineMethod (c$, "postByteArray", +($fz = function () { +var bytes = (this.sb == null ? this.toByteArray () : this.sb.toString ().getBytes ()); +return this.bytePoster.postByteArray (this.fileName, bytes); +}, $fz.isPrivate = true, $fz)); +c$.isRemote = Clazz.defineMethod (c$, "isRemote", +function (fileName) { +if (fileName == null) return false; +var itype = javajs.util.OC.urlTypeIndex (fileName); +return (itype >= 0 && itype != 4); +}, "~S"); +c$.isLocal = Clazz.defineMethod (c$, "isLocal", +function (fileName) { +if (fileName == null) return false; +var itype = javajs.util.OC.urlTypeIndex (fileName); +return (itype < 0 || itype == 4); +}, "~S"); +c$.urlTypeIndex = Clazz.defineMethod (c$, "urlTypeIndex", +function (name) { +if (name == null) return -2; +for (var i = 0; i < javajs.util.OC.urlPrefixes.length; ++i) { +if (name.startsWith (javajs.util.OC.urlPrefixes[i])) { +return i; +}} +return -1; +}, "~S"); +Clazz.defineStatics (c$, +"urlPrefixes", Clazz.newArray (-1, ["http:", "https:", "sftp:", "ftp:", "file:"]), +"URL_LOCAL", 4); +}); diff --git a/bin/javajs/util/P3.js b/bin/javajs/util/P3.js index cc292cd..b44211d 100644 --- a/bin/javajs/util/P3.js +++ b/bin/javajs/util/P3.js @@ -1,26 +1,26 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.T3"], "javajs.util.P3", null, function () { -c$ = Clazz.declareType (javajs.util, "P3", javajs.util.T3); -c$.newP = Clazz.defineMethod (c$, "newP", -function (t) { -var p = new javajs.util.P3 (); -p.x = t.x; -p.y = t.y; -p.z = t.z; -return p; -}, "javajs.util.T3"); -c$.getUnlikely = Clazz.defineMethod (c$, "getUnlikely", -function () { -return (javajs.util.P3.unlikely == null ? javajs.util.P3.unlikely = javajs.util.P3.new3 (3.141592653589793, 2.718281828459045, (8.539734222673566)) : javajs.util.P3.unlikely); -}); -c$.new3 = Clazz.defineMethod (c$, "new3", -function (x, y, z) { -var p = new javajs.util.P3 (); -p.x = x; -p.y = y; -p.z = z; -return p; -}, "~N,~N,~N"); -Clazz.defineStatics (c$, -"unlikely", null); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.T3"], "javajs.util.P3", null, function () { +c$ = Clazz.declareType (javajs.util, "P3", javajs.util.T3); +c$.newP = Clazz.defineMethod (c$, "newP", +function (t) { +var p = new javajs.util.P3 (); +p.x = t.x; +p.y = t.y; +p.z = t.z; +return p; +}, "javajs.util.T3"); +c$.getUnlikely = Clazz.defineMethod (c$, "getUnlikely", +function () { +return (javajs.util.P3.unlikely == null ? javajs.util.P3.unlikely = javajs.util.P3.new3 (3.141592653589793, 2.718281828459045, (8.539734222673566)) : javajs.util.P3.unlikely); +}); +c$.new3 = Clazz.defineMethod (c$, "new3", +function (x, y, z) { +var p = new javajs.util.P3 (); +p.x = x; +p.y = y; +p.z = z; +return p; +}, "~N,~N,~N"); +Clazz.defineStatics (c$, +"unlikely", null); +}); diff --git a/bin/javajs/util/P3i.js b/bin/javajs/util/P3i.js index 4888909..e4e31b5 100644 --- a/bin/javajs/util/P3i.js +++ b/bin/javajs/util/P3i.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.T3i"], "javajs.util.P3i", null, function () { -c$ = Clazz.declareType (javajs.util, "P3i", javajs.util.T3i); -c$.new3 = Clazz.defineMethod (c$, "new3", -function (x, y, z) { -var pt = new javajs.util.P3i (); -pt.x = x; -pt.y = y; -pt.z = z; -return pt; -}, "~N,~N,~N"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.T3i"], "javajs.util.P3i", null, function () { +c$ = Clazz.declareType (javajs.util, "P3i", javajs.util.T3i); +c$.new3 = Clazz.defineMethod (c$, "new3", +function (x, y, z) { +var pt = new javajs.util.P3i (); +pt.x = x; +pt.y = y; +pt.z = z; +return pt; +}, "~N,~N,~N"); +}); diff --git a/bin/javajs/util/P4.js b/bin/javajs/util/P4.js index c317cd6..2afde3c 100644 --- a/bin/javajs/util/P4.js +++ b/bin/javajs/util/P4.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.T4"], "javajs.util.P4", null, function () { -c$ = Clazz.declareType (javajs.util, "P4", javajs.util.T4); -c$.new4 = Clazz.defineMethod (c$, "new4", -function (x, y, z, w) { -var pt = new javajs.util.P4 (); -pt.set4 (x, y, z, w); -return pt; -}, "~N,~N,~N,~N"); -c$.newPt = Clazz.defineMethod (c$, "newPt", -function (value) { -var pt = new javajs.util.P4 (); -pt.set4 (value.x, value.y, value.z, value.w); -return pt; -}, "javajs.util.P4"); -Clazz.defineMethod (c$, "distance4", -function (p1) { -var dx = this.x - p1.x; -var dy = this.y - p1.y; -var dz = this.z - p1.z; -var dw = this.w - p1.w; -return Math.sqrt (dx * dx + dy * dy + dz * dz + dw * dw); -}, "javajs.util.P4"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.T4"], "javajs.util.P4", null, function () { +c$ = Clazz.declareType (javajs.util, "P4", javajs.util.T4); +c$.new4 = Clazz.defineMethod (c$, "new4", +function (x, y, z, w) { +var pt = new javajs.util.P4 (); +pt.set4 (x, y, z, w); +return pt; +}, "~N,~N,~N,~N"); +c$.newPt = Clazz.defineMethod (c$, "newPt", +function (value) { +var pt = new javajs.util.P4 (); +pt.set4 (value.x, value.y, value.z, value.w); +return pt; +}, "javajs.util.P4"); +Clazz.defineMethod (c$, "distance4", +function (p1) { +var dx = this.x - p1.x; +var dy = this.y - p1.y; +var dz = this.z - p1.z; +var dw = this.w - p1.w; +return Math.sqrt (dx * dx + dy * dy + dz * dz + dw * dw); +}, "javajs.util.P4"); +}); diff --git a/bin/javajs/util/PT.class b/bin/javajs/util/PT.class index c3955d6..280974d 100644 Binary files a/bin/javajs/util/PT.class and b/bin/javajs/util/PT.class differ diff --git a/bin/javajs/util/PT.js b/bin/javajs/util/PT.js index b20715c..2bfe06d 100644 --- a/bin/javajs/util/PT.js +++ b/bin/javajs/util/PT.js @@ -1,945 +1,945 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.PT", ["java.lang.Boolean", "$.Double", "$.Float", "$.Number", "java.util.Map", "javajs.api.JSONEncodable", "javajs.util.AU", "$.DF", "$.Lst", "$.M34", "$.M4", "$.SB"], function () { -c$ = Clazz.declareType (javajs.util, "PT"); -c$.parseInt = Clazz.defineMethod (c$, "parseInt", -function (str) { -return javajs.util.PT.parseIntNext (str, Clazz.newIntArray (-1, [0])); -}, "~S"); -c$.parseIntNext = Clazz.defineMethod (c$, "parseIntNext", -function (str, next) { -var cch = str.length; -if (next[0] < 0 || next[0] >= cch) return -2147483648; -return javajs.util.PT.parseIntChecked (str, cch, next); -}, "~S,~A"); -c$.parseIntChecked = Clazz.defineMethod (c$, "parseIntChecked", -function (str, ichMax, next) { -var digitSeen = false; -var value = 0; -var ich = next[0]; -if (ich < 0) return -2147483648; -var ch; -while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; - -var negative = false; -if (ich < ichMax && str.charCodeAt (ich) == 45) { -negative = true; -++ich; -}while (ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) { -value = value * 10 + (ch - 48); -digitSeen = true; -++ich; -} -if (!digitSeen) value = -2147483648; - else if (negative) value = -value; -next[0] = ich; -return value; -}, "~S,~N,~A"); -c$.isWhiteSpace = Clazz.defineMethod (c$, "isWhiteSpace", -function (str, ich) { -var ch; -return (ich >= 0 && ((ch = str.charAt (ich)) == ' ' || ch == '\t' || ch == '\n')); -}, "~S,~N"); -c$.parseFloatChecked = Clazz.defineMethod (c$, "parseFloatChecked", -function (str, ichMax, next, isStrict) { -var digitSeen = false; -var ich = next[0]; -if (isStrict && str.indexOf ('\n') != str.lastIndexOf ('\n')) return NaN; -while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; - -var negative = false; -if (ich < ichMax && str.charAt (ich) == '-') { -++ich; -negative = true; -}var ch = 0; -var ival = 0; -var ival2 = 0; -while (ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) { -ival = (ival * 10) + (ch - 48) * 1; -++ich; -digitSeen = true; -} -var isDecimal = false; -var iscale = 0; -var nzero = (ival == 0 ? -1 : 0); -if (ch == 46) { -isDecimal = true; -while (++ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) { -digitSeen = true; -if (nzero < 0) { -if (ch == 48) { -nzero--; -continue; -}nzero = -nzero; -}if (iscale < javajs.util.PT.decimalScale.length) { -ival2 = (ival2 * 10) + (ch - 48) * 1; -iscale++; -}} -}var value; -if (!digitSeen) { -value = NaN; -} else if (ival2 > 0) { -value = ival2 * javajs.util.PT.decimalScale[iscale - 1]; -if (nzero > 1) { -if (nzero - 2 < javajs.util.PT.decimalScale.length) { -value *= javajs.util.PT.decimalScale[nzero - 2]; -} else { -value *= Math.pow (10, 1 - nzero); -}} else { -value += ival; -}} else { -value = ival; -}var isExponent = false; -if (ich < ichMax && (ch == 69 || ch == 101 || ch == 68)) { -isExponent = true; -if (++ich >= ichMax) return NaN; -ch = str.charCodeAt (ich); -if ((ch == 43) && (++ich >= ichMax)) return NaN; -next[0] = ich; -var exponent = javajs.util.PT.parseIntChecked (str, ichMax, next); -if (exponent == -2147483648) return NaN; -if (exponent > 0 && exponent <= javajs.util.PT.tensScale.length) value *= javajs.util.PT.tensScale[exponent - 1]; - else if (exponent < 0 && -exponent <= javajs.util.PT.decimalScale.length) value *= javajs.util.PT.decimalScale[-exponent - 1]; - else if (exponent != 0) value *= Math.pow (10, exponent); -} else { -next[0] = ich; -}if (negative) value = -value; -if (value == Infinity) value = 3.4028235E38; -return (!isStrict || (!isExponent || isDecimal) && javajs.util.PT.checkTrailingText (str, next[0], ichMax) ? value : NaN); -}, "~S,~N,~A,~B"); -c$.checkTrailingText = Clazz.defineMethod (c$, "checkTrailingText", -function (str, ich, ichMax) { -var ch; -while (ich < ichMax && (javajs.util.PT.isWhitespace (ch = str.charAt (ich)) || ch == ';')) ++ich; - -return (ich == ichMax); -}, "~S,~N,~N"); -c$.parseFloatArray = Clazz.defineMethod (c$, "parseFloatArray", -function (str) { -return javajs.util.PT.parseFloatArrayNext (str, Clazz.newIntArray (1, 0), null, null, null); -}, "~S"); -c$.parseFloatArrayInfested = Clazz.defineMethod (c$, "parseFloatArrayInfested", -function (tokens, data) { -var len = data.length; -var nTokens = tokens.length; -var n = 0; -var max = 0; -for (var i = 0; i >= 0 && i < len && n < nTokens; i++) { -var f; -while (Float.isNaN (f = javajs.util.PT.parseFloat (tokens[n++])) && n < nTokens) { -} -if (!Float.isNaN (f)) data[(max = i)] = f; -if (n == nTokens) break; -} -return max + 1; -}, "~A,~A"); -c$.parseFloatArrayNext = Clazz.defineMethod (c$, "parseFloatArrayNext", -function (str, next, f, strStart, strEnd) { -var n = 0; -var pt = next[0]; -if (pt >= 0) { -if (strStart != null) { -var p = str.indexOf (strStart, pt); -if (p >= 0) next[0] = p + strStart.length; -}str = str.substring (next[0]); -pt = (strEnd == null ? -1 : str.indexOf (strEnd)); -if (pt < 0) pt = str.length; - else str = str.substring (0, pt); -next[0] += pt + 1; -var tokens = javajs.util.PT.getTokens (str); -if (f == null) f = Clazz.newFloatArray (tokens.length, 0); -n = javajs.util.PT.parseFloatArrayInfested (tokens, f); -}if (f == null) return Clazz.newFloatArray (0, 0); -for (var i = n; i < f.length; i++) f[i] = NaN; - -return f; -}, "~S,~A,~A,~S,~S"); -c$.parseFloatRange = Clazz.defineMethod (c$, "parseFloatRange", -function (str, ichMax, next) { -var cch = str.length; -if (ichMax > cch) ichMax = cch; -if (next[0] < 0 || next[0] >= ichMax) return NaN; -return javajs.util.PT.parseFloatChecked (str, ichMax, next, false); -}, "~S,~N,~A"); -c$.parseFloatNext = Clazz.defineMethod (c$, "parseFloatNext", -function (str, next) { -var cch = (str == null ? -1 : str.length); -return (next[0] < 0 || next[0] >= cch ? NaN : javajs.util.PT.parseFloatChecked (str, cch, next, false)); -}, "~S,~A"); -c$.parseFloatStrict = Clazz.defineMethod (c$, "parseFloatStrict", -function (str) { -var cch = str.length; -if (cch == 0) return NaN; -return javajs.util.PT.parseFloatChecked (str, cch, Clazz.newIntArray (-1, [0]), true); -}, "~S"); -c$.parseFloat = Clazz.defineMethod (c$, "parseFloat", -function (str) { -return javajs.util.PT.parseFloatNext (str, Clazz.newIntArray (-1, [0])); -}, "~S"); -c$.parseIntRadix = Clazz.defineMethod (c$, "parseIntRadix", -function (s, i) { -{ -return Integer.parseIntRadix(s, i); -}}, "~S,~N"); -c$.getTokens = Clazz.defineMethod (c$, "getTokens", -function (line) { -return javajs.util.PT.getTokensAt (line, 0); -}, "~S"); -c$.parseToken = Clazz.defineMethod (c$, "parseToken", -function (str) { -return javajs.util.PT.parseTokenNext (str, Clazz.newIntArray (-1, [0])); -}, "~S"); -c$.parseTrimmed = Clazz.defineMethod (c$, "parseTrimmed", -function (str) { -return javajs.util.PT.parseTrimmedRange (str, 0, str.length); -}, "~S"); -c$.parseTrimmedAt = Clazz.defineMethod (c$, "parseTrimmedAt", -function (str, ichStart) { -return javajs.util.PT.parseTrimmedRange (str, ichStart, str.length); -}, "~S,~N"); -c$.parseTrimmedRange = Clazz.defineMethod (c$, "parseTrimmedRange", -function (str, ichStart, ichMax) { -var cch = str.length; -if (ichMax < cch) cch = ichMax; -if (cch < ichStart) return ""; -return javajs.util.PT.parseTrimmedChecked (str, ichStart, cch); -}, "~S,~N,~N"); -c$.getTokensAt = Clazz.defineMethod (c$, "getTokensAt", -function (line, ich) { -if (line == null) return null; -var cchLine = line.length; -if (ich < 0 || ich > cchLine) return null; -var tokenCount = javajs.util.PT.countTokens (line, ich); -var tokens = new Array (tokenCount); -var next = Clazz.newIntArray (1, 0); -next[0] = ich; -for (var i = 0; i < tokenCount; ++i) tokens[i] = javajs.util.PT.parseTokenChecked (line, cchLine, next); - -return tokens; -}, "~S,~N"); -c$.countChar = Clazz.defineMethod (c$, "countChar", -function (line, c) { -var tokenCount = 0; -var pt = -1; -while ((pt = line.indexOf (c, pt + 1)) >= 0) tokenCount++; - -return tokenCount; -}, "~S,~S"); -c$.countTokens = Clazz.defineMethod (c$, "countTokens", -function (line, ich) { -var tokenCount = 0; -if (line != null) { -var ichMax = line.length; -while (true) { -while (ich < ichMax && javajs.util.PT.isWhiteSpace (line, ich)) ++ich; - -if (ich == ichMax) break; -++tokenCount; -do { -++ich; -} while (ich < ichMax && !javajs.util.PT.isWhiteSpace (line, ich)); -} -}return tokenCount; -}, "~S,~N"); -c$.parseTokenNext = Clazz.defineMethod (c$, "parseTokenNext", -function (str, next) { -var cch = str.length; -return (next[0] < 0 || next[0] >= cch ? null : javajs.util.PT.parseTokenChecked (str, cch, next)); -}, "~S,~A"); -c$.parseTokenRange = Clazz.defineMethod (c$, "parseTokenRange", -function (str, ichMax, next) { -var cch = str.length; -if (ichMax > cch) ichMax = cch; -return (next[0] < 0 || next[0] >= ichMax ? null : javajs.util.PT.parseTokenChecked (str, ichMax, next)); -}, "~S,~N,~A"); -c$.parseTokenChecked = Clazz.defineMethod (c$, "parseTokenChecked", -function (str, ichMax, next) { -var ich = next[0]; -while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; - -var ichNonWhite = ich; -while (ich < ichMax && !javajs.util.PT.isWhiteSpace (str, ich)) ++ich; - -next[0] = ich; -return (ichNonWhite == ich ? null : str.substring (ichNonWhite, ich)); -}, "~S,~N,~A"); -c$.parseTrimmedChecked = Clazz.defineMethod (c$, "parseTrimmedChecked", -function (str, ich, ichMax) { -while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; - -var ichLast = ichMax - 1; -while (ichLast >= ich && javajs.util.PT.isWhiteSpace (str, ichLast)) --ichLast; - -return (ichLast < ich ? "" : str.substring (ich, ichLast + 1)); -}, "~S,~N,~N"); -c$.dVal = Clazz.defineMethod (c$, "dVal", -function (s) { -{ -if(s==null) -throw new NumberFormatException("null"); -var d=parseFloat(s); -if(isNaN(d)) -throw new NumberFormatException("Not a Number : "+s); -return d -}}, "~S"); -c$.fVal = Clazz.defineMethod (c$, "fVal", -function (s) { -{ -return this.dVal(s); -}}, "~S"); -c$.parseIntRange = Clazz.defineMethod (c$, "parseIntRange", -function (str, ichMax, next) { -var cch = str.length; -if (ichMax > cch) ichMax = cch; -return (next[0] < 0 || next[0] >= ichMax ? -2147483648 : javajs.util.PT.parseIntChecked (str, ichMax, next)); -}, "~S,~N,~A"); -c$.parseFloatArrayData = Clazz.defineMethod (c$, "parseFloatArrayData", -function (tokens, data) { -javajs.util.PT.parseFloatArrayDataN (tokens, data, data.length); -}, "~A,~A"); -c$.parseFloatArrayDataN = Clazz.defineMethod (c$, "parseFloatArrayDataN", -function (tokens, data, nData) { -for (var i = nData; --i >= 0; ) data[i] = (i >= tokens.length ? NaN : javajs.util.PT.parseFloat (tokens[i])); - -}, "~A,~A,~N"); -c$.split = Clazz.defineMethod (c$, "split", -function (text, run) { -if (text.length == 0) return new Array (0); -var n = 1; -var i = text.indexOf (run); -var lines; -var runLen = run.length; -if (i < 0 || runLen == 0) { -lines = new Array (1); -lines[0] = text; -return lines; -}var len = text.length - runLen; -for (; i >= 0 && i < len; n++) i = text.indexOf (run, i + runLen); - -lines = new Array (n); -i = 0; -var ipt = 0; -var pt = 0; -for (; (ipt = text.indexOf (run, i)) >= 0 && pt + 1 < n; ) { -lines[pt++] = text.substring (i, ipt); -i = ipt + runLen; -} -if (text.indexOf (run, len) != len) len += runLen; -lines[pt] = text.substring (i, len); -return lines; -}, "~S,~S"); -c$.getQuotedStringAt = Clazz.defineMethod (c$, "getQuotedStringAt", -function (line, ipt0) { -var next = Clazz.newIntArray (-1, [ipt0]); -return javajs.util.PT.getQuotedStringNext (line, next); -}, "~S,~N"); -c$.getQuotedStringNext = Clazz.defineMethod (c$, "getQuotedStringNext", -function (line, next) { -var i = next[0]; -if (i < 0 || (i = line.indexOf ("\"", i)) < 0) return ""; -var pt = i + 1; -var len = line.length; -while (++i < len && line.charAt (i) != '"') if (line.charAt (i) == '\\') i++; - -next[0] = i + 1; -return line.substring (pt, i); -}, "~S,~A"); -c$.getCSVString = Clazz.defineMethod (c$, "getCSVString", -function (line, next) { -var i = next[1]; -if (i < 0 || (i = line.indexOf ("\"", i)) < 0) return null; -var pt = next[0] = i; -var len = line.length; -var escaped = false; -var haveEscape = false; -while (++i < len && (line.charAt (i) != '"' || (escaped = (i + 1 < len && line.charAt (i + 1) == '"')))) if (escaped) { -escaped = false; -haveEscape = true; -i++; -} -if (i >= len) { -next[1] = -1; -return null; -}next[1] = i + 1; -var s = line.substring (pt + 1, i); -return (haveEscape ? javajs.util.PT.rep (javajs.util.PT.rep (s, "\"\"", "\0"), "\0", "\"") : s); -}, "~S,~A"); -c$.isOneOf = Clazz.defineMethod (c$, "isOneOf", -function (key, semiList) { -if (semiList.length == 0) return false; -if (semiList.charAt (0) != ';') semiList = ";" + semiList + ";"; -return key.indexOf (";") < 0 && semiList.indexOf (';' + key + ';') >= 0; -}, "~S,~S"); -c$.getQuotedAttribute = Clazz.defineMethod (c$, "getQuotedAttribute", -function (info, name) { -var i = info.indexOf (name + "="); -return (i < 0 ? null : javajs.util.PT.getQuotedStringAt (info, i)); -}, "~S,~S"); -c$.approx = Clazz.defineMethod (c$, "approx", -function (f, n) { -return Math.round (f * n) / n; -}, "~N,~N"); -c$.rep = Clazz.defineMethod (c$, "rep", -function (str, strFrom, strTo) { -if (str == null || strFrom.length == 0 || str.indexOf (strFrom) < 0) return str; -var isOnce = (strTo.indexOf (strFrom) >= 0); -do { -str = str.$replace (strFrom, strTo); -} while (!isOnce && str.indexOf (strFrom) >= 0); -return str; -}, "~S,~S,~S"); -c$.formatF = Clazz.defineMethod (c$, "formatF", -function (value, width, precision, alignLeft, zeroPad) { -return javajs.util.PT.formatS (javajs.util.DF.formatDecimal (value, precision), width, 0, alignLeft, zeroPad); -}, "~N,~N,~N,~B,~B"); -c$.formatD = Clazz.defineMethod (c$, "formatD", -function (value, width, precision, alignLeft, zeroPad, allowOverflow) { -return javajs.util.PT.formatS (javajs.util.DF.formatDecimal (value, -1 - precision), width, 0, alignLeft, zeroPad); -}, "~N,~N,~N,~B,~B,~B"); -c$.formatS = Clazz.defineMethod (c$, "formatS", -function (value, width, precision, alignLeft, zeroPad) { -if (value == null) return ""; -var len = value.length; -if (precision != 2147483647 && precision > 0 && precision < len) value = value.substring (0, precision); - else if (precision < 0 && len + precision >= 0) value = value.substring (len + precision + 1); -var padLength = width - value.length; -if (padLength <= 0) return value; -var isNeg = (zeroPad && !alignLeft && value.charAt (0) == '-'); -var padChar = (zeroPad ? '0' : ' '); -var padChar0 = (isNeg ? '-' : padChar); -var sb = new javajs.util.SB (); -if (alignLeft) sb.append (value); -sb.appendC (padChar0); -for (var i = padLength; --i > 0; ) sb.appendC (padChar); - -if (!alignLeft) sb.append (isNeg ? padChar + value.substring (1) : value); -return sb.toString (); -}, "~S,~N,~N,~B,~B"); -c$.replaceWithCharacter = Clazz.defineMethod (c$, "replaceWithCharacter", -function (str, strFrom, chTo) { -if (str == null) return null; -for (var i = strFrom.length; --i >= 0; ) str = str.$replace (strFrom.charAt (i), chTo); - -return str; -}, "~S,~S,~S"); -c$.replaceAllCharacters = Clazz.defineMethod (c$, "replaceAllCharacters", -function (str, strFrom, strTo) { -for (var i = strFrom.length; --i >= 0; ) { -var chFrom = strFrom.substring (i, i + 1); -str = javajs.util.PT.rep (str, chFrom, strTo); -} -return str; -}, "~S,~S,~S"); -c$.trim = Clazz.defineMethod (c$, "trim", -function (str, chars) { -if (str == null || str.length == 0) return str; -if (chars.length == 0) return str.trim (); -var len = str.length; -var k = 0; -while (k < len && chars.indexOf (str.charAt (k)) >= 0) k++; - -var m = str.length - 1; -while (m > k && chars.indexOf (str.charAt (m)) >= 0) m--; - -return str.substring (k, m + 1); -}, "~S,~S"); -c$.trimQuotes = Clazz.defineMethod (c$, "trimQuotes", -function (value) { -return (value != null && value.length > 1 && value.startsWith ("\"") && value.endsWith ("\"") ? value.substring (1, value.length - 1) : value); -}, "~S"); -c$.isNonStringPrimitive = Clazz.defineMethod (c$, "isNonStringPrimitive", -function (info) { -return Clazz.instanceOf (info, Number) || Clazz.instanceOf (info, Boolean); -}, "~O"); -c$.arrayGet = Clazz.defineMethod (c$, "arrayGet", -($fz = function (info, i) { -{ -return info[i]; -}}, $fz.isPrivate = true, $fz), "~O,~N"); -c$.toJSON = Clazz.defineMethod (c$, "toJSON", -function (infoType, info) { -if (info == null) return javajs.util.PT.packageJSON (infoType, null); -if (javajs.util.PT.isNonStringPrimitive (info)) return javajs.util.PT.packageJSON (infoType, info.toString ()); -var s = null; -var sb = null; -while (true) { -if (Clazz.instanceOf (info, String)) { -s = info; -{ -if (typeof s == "undefined") s = "null" -}if (s.indexOf ("{\"") != 0) { -s = javajs.util.PT.rep (s, "\"", "\\\""); -s = javajs.util.PT.rep (s, "\n", "\\n"); -s = "\"" + s + "\""; -}break; -}if (Clazz.instanceOf (info, javajs.api.JSONEncodable)) { -if ((s = (info).toJSON ()) == null) s = "null"; -break; -}sb = new javajs.util.SB (); -if (Clazz.instanceOf (info, java.util.Map)) { -sb.append ("{ "); -var sep = ""; -for (var key, $key = (info).keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { -sb.append (sep).append (javajs.util.PT.packageJSON (key, javajs.util.PT.toJSON (null, (info).get (key)))); -sep = ","; -} -sb.append (" }"); -break; -}if (Clazz.instanceOf (info, javajs.util.Lst)) { -sb.append ("[ "); -var n = (info).size (); -for (var i = 0; i < n; i++) { -if (i > 0) sb.appendC (','); -sb.append (javajs.util.PT.toJSON (null, (info).get (i))); -} -sb.append (" ]"); -break; -}if (Clazz.instanceOf (info, javajs.util.M34)) { -var len = (Clazz.instanceOf (info, javajs.util.M4) ? 4 : 3); -var x = Clazz.newFloatArray (len, 0); -var m = info; -sb.appendC ('['); -for (var i = 0; i < len; i++) { -if (i > 0) sb.appendC (','); -m.getRow (i, x); -sb.append (javajs.util.PT.toJSON (null, x)); -} -sb.appendC (']'); -break; -}s = javajs.util.PT.nonArrayString (info); -if (s == null) { -sb.append ("["); -var n = javajs.util.AU.getLength (info); -for (var i = 0; i < n; i++) { -if (i > 0) sb.appendC (','); -sb.append (javajs.util.PT.toJSON (null, javajs.util.PT.arrayGet (info, i))); -} -sb.append ("]"); -break; -}info = info.toString (); -} -return javajs.util.PT.packageJSON (infoType, (s == null ? sb.toString () : s)); -}, "~S,~O"); -c$.nonArrayString = Clazz.defineMethod (c$, "nonArrayString", -function (x) { -{ -var s = x.toString(); return (s.startsWith("[object") && -s.endsWith("Array]") ? null : s); -}}, "~O"); -c$.byteArrayToJSON = Clazz.defineMethod (c$, "byteArrayToJSON", -function (data) { -var sb = new javajs.util.SB (); -sb.append ("["); -var n = data.length; -for (var i = 0; i < n; i++) { -if (i > 0) sb.appendC (','); -sb.appendI (data[i] & 0xFF); -} -sb.append ("]"); -return sb.toString (); -}, "~A"); -c$.packageJSON = Clazz.defineMethod (c$, "packageJSON", -function (infoType, info) { -return (infoType == null ? info : "\"" + infoType + "\": " + info); -}, "~S,~S"); -c$.escapeUrl = Clazz.defineMethod (c$, "escapeUrl", -function (url) { -url = javajs.util.PT.rep (url, "\n", ""); -url = javajs.util.PT.rep (url, "%", "%25"); -url = javajs.util.PT.rep (url, "#", "%23"); -url = javajs.util.PT.rep (url, "[", "%5B"); -url = javajs.util.PT.rep (url, "]", "%5D"); -url = javajs.util.PT.rep (url, " ", "%20"); -return url; -}, "~S"); -c$.esc = Clazz.defineMethod (c$, "esc", -function (str) { -if (str == null || str.length == 0) return "\"\""; -var haveEscape = false; -var i = 0; -for (; i < "\\\\\tt\rr\nn\"\"".length; i += 2) if (str.indexOf ("\\\\\tt\rr\nn\"\"".charAt (i)) >= 0) { -haveEscape = true; -break; -} -if (haveEscape) while (i < "\\\\\tt\rr\nn\"\"".length) { -var pt = -1; -var ch = "\\\\\tt\rr\nn\"\"".charAt (i++); -var ch2 = "\\\\\tt\rr\nn\"\"".charAt (i++); -var sb = new javajs.util.SB (); -var pt0 = 0; -while ((pt = str.indexOf (ch, pt + 1)) >= 0) { -sb.append (str.substring (pt0, pt)).appendC ('\\').appendC (ch2); -pt0 = pt + 1; -} -sb.append (str.substring (pt0, str.length)); -str = sb.toString (); -} -return "\"" + javajs.util.PT.escUnicode (str) + "\""; -}, "~S"); -c$.escUnicode = Clazz.defineMethod (c$, "escUnicode", -function (str) { -for (var i = str.length; --i >= 0; ) if (str.charCodeAt (i) > 0x7F) { -var s = "0000" + Integer.toHexString (str.charCodeAt (i)); -str = str.substring (0, i) + "\\u" + s.substring (s.length - 4) + str.substring (i + 1); -} -return str; -}, "~S"); -c$.escF = Clazz.defineMethod (c$, "escF", -function (f) { -var sf = "" + f; -{ -if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0) -sf += ".0"; -}return sf; -}, "~N"); -c$.join = Clazz.defineMethod (c$, "join", -function (s, c, i0) { -if (s.length < i0) return null; -var sb = new javajs.util.SB (); -sb.append (s[i0++]); -for (var i = i0; i < s.length; i++) sb.appendC (c).append (s[i]); - -return sb.toString (); -}, "~A,~S,~N"); -c$.isLike = Clazz.defineMethod (c$, "isLike", -function (a, b) { -var areEqual = a.equals (b); -if (areEqual) return true; -var isStart = b.startsWith ("*"); -var isEnd = b.endsWith ("*"); -return (!isStart && !isEnd) ? areEqual : isStart && isEnd ? b.length == 1 || a.contains (b.substring (1, b.length - 1)) : isStart ? a.endsWith (b.substring (1)) : a.startsWith (b.substring (0, b.length - 1)); -}, "~S,~S"); -c$.getMapValueNoCase = Clazz.defineMethod (c$, "getMapValueNoCase", -function (h, key) { -if ("this".equals (key)) return h; -var val = h.get (key); -if (val == null) for (var e, $e = h.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) if (e.getKey ().equalsIgnoreCase (key)) return e.getValue (); - -return val; -}, "java.util.Map,~S"); -c$.clean = Clazz.defineMethod (c$, "clean", -function (s) { -return javajs.util.PT.rep (javajs.util.PT.replaceAllCharacters (s, " \t\n\r", " "), " ", " ").trim (); -}, "~S"); -c$.fdup = Clazz.defineMethod (c$, "fdup", -function (f, pt, n) { -var ch; -var count = 0; -for (var i = pt; --i >= 1; ) { -if (javajs.util.PT.isDigit (ch = f.charAt (i))) continue; -switch (ch) { -case '.': -if (count++ != 0) return f; -continue; -case '-': -if (i != 1 && f.charAt (i - 1) != '.') return f; -continue; -default: -return f; -} -} -var s = f.substring (0, pt + 1); -var sb = new javajs.util.SB (); -for (var i = 0; i < n; i++) sb.append (s); - -sb.append (f.substring (pt + 1)); -return sb.toString (); -}, "~S,~N,~N"); -c$.formatString = Clazz.defineMethod (c$, "formatString", -function (strFormat, key, strT, floatT, doubleT, doOne) { -if (strFormat == null) return null; -if ("".equals (strFormat)) return ""; -var len = key.length; -if (strFormat.indexOf ("%") < 0 || len == 0 || strFormat.indexOf (key) < 0) return strFormat; -var strLabel = ""; -var ich; -var ichPercent; -var ichKey; -for (ich = 0; (ichPercent = strFormat.indexOf ('%', ich)) >= 0 && (ichKey = strFormat.indexOf (key, ichPercent + 1)) >= 0; ) { -if (ich != ichPercent) strLabel += strFormat.substring (ich, ichPercent); -ich = ichPercent + 1; -if (ichKey > ichPercent + 6) { -strLabel += '%'; -continue; -}try { -var alignLeft = false; -if (strFormat.charAt (ich) == '-') { -alignLeft = true; -++ich; -}var zeroPad = false; -if (strFormat.charAt (ich) == '0') { -zeroPad = true; -++ich; -}var ch; -var width = 0; -while ((ch = strFormat.charAt (ich)) >= '0' && (ch <= '9')) { -width = (10 * width) + (ch.charCodeAt (0) - 48); -++ich; -} -var precision = 2147483647; -var isExponential = false; -if (strFormat.charAt (ich) == '.') { -++ich; -if ((ch = strFormat.charAt (ich)) == '-') { -isExponential = true; -++ich; -}if ((ch = strFormat.charAt (ich)) >= '0' && ch <= '9') { -precision = ch.charCodeAt (0) - 48; -++ich; -}if (isExponential) precision = -precision - (strT == null ? 1 : 0); -}var st = strFormat.substring (ich, ich + len); -if (!st.equals (key)) { -ich = ichPercent + 1; -strLabel += '%'; -continue; -}ich += len; -if (!Float.isNaN (floatT)) strLabel += javajs.util.PT.formatF (floatT, width, precision, alignLeft, zeroPad); - else if (strT != null) strLabel += javajs.util.PT.formatS (strT, width, precision, alignLeft, zeroPad); - else if (!Double.isNaN (doubleT)) strLabel += javajs.util.PT.formatD (doubleT, width, precision, alignLeft, zeroPad, true); -if (doOne) break; -} catch (ioobe) { -if (Clazz.exceptionOf (ioobe, IndexOutOfBoundsException)) { -ich = ichPercent; -break; -} else { -throw ioobe; -} -} -} -strLabel += strFormat.substring (ich); -return strLabel; -}, "~S,~S,~S,~N,~N,~B"); -c$.formatStringS = Clazz.defineMethod (c$, "formatStringS", -function (strFormat, key, strT) { -return javajs.util.PT.formatString (strFormat, key, strT, NaN, NaN, false); -}, "~S,~S,~S"); -c$.formatStringF = Clazz.defineMethod (c$, "formatStringF", -function (strFormat, key, floatT) { -return javajs.util.PT.formatString (strFormat, key, null, floatT, NaN, false); -}, "~S,~S,~N"); -c$.formatStringI = Clazz.defineMethod (c$, "formatStringI", -function (strFormat, key, intT) { -return javajs.util.PT.formatString (strFormat, key, "" + intT, NaN, NaN, false); -}, "~S,~S,~N"); -c$.sprintf = Clazz.defineMethod (c$, "sprintf", -function (strFormat, list, values) { -if (values == null) return strFormat; -var n = list.length; -if (n == values.length) try { -for (var o = 0; o < n; o++) { -if (values[o] == null) continue; -switch (list.charAt (o)) { -case 's': -strFormat = javajs.util.PT.formatString (strFormat, "s", values[o], NaN, NaN, true); -break; -case 'f': -strFormat = javajs.util.PT.formatString (strFormat, "f", null, (values[o]).floatValue (), NaN, true); -break; -case 'i': -strFormat = javajs.util.PT.formatString (strFormat, "d", "" + values[o], NaN, NaN, true); -strFormat = javajs.util.PT.formatString (strFormat, "i", "" + values[o], NaN, NaN, true); -break; -case 'd': -strFormat = javajs.util.PT.formatString (strFormat, "e", null, NaN, (values[o]).doubleValue (), true); -break; -case 'p': -var pVal = values[o]; -strFormat = javajs.util.PT.formatString (strFormat, "p", null, pVal.x, NaN, true); -strFormat = javajs.util.PT.formatString (strFormat, "p", null, pVal.y, NaN, true); -strFormat = javajs.util.PT.formatString (strFormat, "p", null, pVal.z, NaN, true); -break; -case 'q': -var qVal = values[o]; -strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.x, NaN, true); -strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.y, NaN, true); -strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.z, NaN, true); -strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.w, NaN, true); -break; -case 'S': -var sVal = values[o]; -for (var i = 0; i < sVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "s", sVal[i], NaN, NaN, true); - -break; -case 'F': -var fVal = values[o]; -for (var i = 0; i < fVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "f", null, fVal[i], NaN, true); - -break; -case 'I': -var iVal = values[o]; -for (var i = 0; i < iVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "d", "" + iVal[i], NaN, NaN, true); - -for (var i = 0; i < iVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "i", "" + iVal[i], NaN, NaN, true); - -break; -case 'D': -var dVal = values[o]; -for (var i = 0; i < dVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "e", null, NaN, dVal[i], true); - -} -} -return javajs.util.PT.rep (strFormat, "%%", "%"); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -System.out.println ("TextFormat.sprintf error " + list + " " + strFormat); -return javajs.util.PT.rep (strFormat, "%", "?"); -}, "~S,~S,~A"); -c$.formatCheck = Clazz.defineMethod (c$, "formatCheck", -function (strFormat) { -if (strFormat == null || strFormat.indexOf ('p') < 0 && strFormat.indexOf ('q') < 0) return strFormat; -strFormat = javajs.util.PT.rep (strFormat, "%%", "\1"); -strFormat = javajs.util.PT.rep (strFormat, "%p", "%6.2p"); -strFormat = javajs.util.PT.rep (strFormat, "%q", "%6.2q"); -var format = javajs.util.PT.split (strFormat, "%"); -var sb = new javajs.util.SB (); -sb.append (format[0]); -for (var i = 1; i < format.length; i++) { -var f = "%" + format[i]; -var pt; -if (f.length >= 3) { -if ((pt = f.indexOf ('p')) >= 0) f = javajs.util.PT.fdup (f, pt, 3); -if ((pt = f.indexOf ('q')) >= 0) f = javajs.util.PT.fdup (f, pt, 4); -}sb.append (f); -} -return sb.toString ().$replace ('\1', '%'); -}, "~S"); -c$.leftJustify = Clazz.defineMethod (c$, "leftJustify", -function (s, s1, s2) { -s.append (s2); -var n = s1.length - s2.length; -if (n > 0) s.append (s1.substring (0, n)); -}, "javajs.util.SB,~S,~S"); -c$.rightJustify = Clazz.defineMethod (c$, "rightJustify", -function (s, s1, s2) { -var n = s1.length - s2.length; -if (n > 0) s.append (s1.substring (0, n)); -s.append (s2); -}, "javajs.util.SB,~S,~S"); -c$.safeTruncate = Clazz.defineMethod (c$, "safeTruncate", -function (f, n) { -if (f > -0.001 && f < 0.001) f = 0; -return (f + " ").substring (0, n); -}, "~N,~N"); -c$.isWild = Clazz.defineMethod (c$, "isWild", -function (s) { -return s != null && (s.indexOf ("*") >= 0 || s.indexOf ("?") >= 0); -}, "~S"); -c$.isMatch = Clazz.defineMethod (c$, "isMatch", -function (search, match, checkStar, allowInitialStar) { -if (search.equals (match)) return true; -var mLen = match.length; -if (mLen == 0) return false; -var isStar0 = (checkStar && allowInitialStar ? match.charAt (0) == '*' : false); -if (mLen == 1 && isStar0) return true; -var isStar1 = (checkStar && match.endsWith ("*")); -var haveQ = (match.indexOf ('?') >= 0); -if (!haveQ) { -if (isStar0) return (isStar1 ? (mLen < 3 || search.indexOf (match.substring (1, mLen - 1)) >= 0) : search.endsWith (match.substring (1))); - else if (isStar1) return search.startsWith (match.substring (0, mLen - 1)); -}var sLen = search.length; -var qqqq = "????"; -var nq = 4; -while (nq < sLen) { -qqqq += qqqq; -nq += 4; -} -if (checkStar) { -if (isStar0) { -match = qqqq + match.substring (1); -mLen += nq - 1; -}if (isStar1) { -match = match.substring (0, mLen - 1) + qqqq; -mLen += nq - 1; -}}if (mLen < sLen) return false; -var ich = 0; -while (mLen > sLen) { -if (allowInitialStar && match.charAt (ich) == '?') { -++ich; -} else if (match.charAt (ich + mLen - 1) != '?') { -return false; -}--mLen; -} -for (var i = sLen; --i >= 0; ) { -var chm = match.charAt (ich + i); -if (chm == '?') continue; -var chs = search.charAt (i); -if (chm != chs && (chm != '\1' || chs != '?')) return false; -} -return true; -}, "~S,~S,~B,~B"); -c$.replaceQuotedStrings = Clazz.defineMethod (c$, "replaceQuotedStrings", -function (s, list, newList) { -var n = list.size (); -for (var i = 0; i < n; i++) { -var name = list.get (i); -var newName = newList.get (i); -if (!newName.equals (name)) s = javajs.util.PT.rep (s, "\"" + name + "\"", "\"" + newName + "\""); -} -return s; -}, "~S,javajs.util.Lst,javajs.util.Lst"); -c$.replaceStrings = Clazz.defineMethod (c$, "replaceStrings", -function (s, list, newList) { -var n = list.size (); -for (var i = 0; i < n; i++) { -var name = list.get (i); -var newName = newList.get (i); -if (!newName.equals (name)) s = javajs.util.PT.rep (s, name, newName); -} -return s; -}, "~S,javajs.util.Lst,javajs.util.Lst"); -c$.isDigit = Clazz.defineMethod (c$, "isDigit", -function (ch) { -var c = (ch).charCodeAt (0); -return (48 <= c && c <= 57); -}, "~S"); -c$.isUpperCase = Clazz.defineMethod (c$, "isUpperCase", -function (ch) { -var c = (ch).charCodeAt (0); -return (65 <= c && c <= 90); -}, "~S"); -c$.isLowerCase = Clazz.defineMethod (c$, "isLowerCase", -function (ch) { -var c = (ch).charCodeAt (0); -return (97 <= c && c <= 122); -}, "~S"); -c$.isLetter = Clazz.defineMethod (c$, "isLetter", -function (ch) { -var c = (ch).charCodeAt (0); -return (65 <= c && c <= 90 || 97 <= c && c <= 122); -}, "~S"); -c$.isLetterOrDigit = Clazz.defineMethod (c$, "isLetterOrDigit", -function (ch) { -var c = (ch).charCodeAt (0); -return (65 <= c && c <= 90 || 97 <= c && c <= 122 || 48 <= c && c <= 57); -}, "~S"); -c$.isWhitespace = Clazz.defineMethod (c$, "isWhitespace", -function (ch) { -var c = (ch).charCodeAt (0); -return (c >= 0x1c && c <= 0x20 || c >= 0x9 && c <= 0xd); -}, "~S"); -c$.fixPtFloats = Clazz.defineMethod (c$, "fixPtFloats", -function (pt, f) { -pt.x = Math.round (pt.x * f) / f; -pt.y = Math.round (pt.y * f) / f; -pt.z = Math.round (pt.z * f) / f; -}, "javajs.util.T3,~N"); -c$.fixDouble = Clazz.defineMethod (c$, "fixDouble", -function (d, f) { -return Math.round (d * f) / f; -}, "~N,~N"); -c$.parseFloatFraction = Clazz.defineMethod (c$, "parseFloatFraction", -function (s) { -var pt = s.indexOf ("/"); -return (pt < 0 ? javajs.util.PT.parseFloat (s) : javajs.util.PT.parseFloat (s.substring (0, pt)) / javajs.util.PT.parseFloat (s.substring (pt + 1))); -}, "~S"); -Clazz.defineStatics (c$, -"tensScale", Clazz.newFloatArray (-1, [10, 100, 1000, 10000, 100000, 1000000]), -"decimalScale", Clazz.newFloatArray (-1, [0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001, 0.0000001, 0.00000001, 0.000000001]), -"FLOAT_MIN_SAFE", 2E-45, -"escapable", "\\\\\tt\rr\nn\"\"", -"FRACTIONAL_PRECISION", 100000, -"CARTESIAN_PRECISION", 10000); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.PT", ["java.lang.Boolean", "$.Double", "$.Float", "$.Number", "java.util.Map", "javajs.api.JSONEncodable", "javajs.util.AU", "$.DF", "$.Lst", "$.M34", "$.M4", "$.SB"], function () { +c$ = Clazz.declareType (javajs.util, "PT"); +c$.parseInt = Clazz.defineMethod (c$, "parseInt", +function (str) { +return javajs.util.PT.parseIntNext (str, Clazz.newIntArray (-1, [0])); +}, "~S"); +c$.parseIntNext = Clazz.defineMethod (c$, "parseIntNext", +function (str, next) { +var cch = str.length; +if (next[0] < 0 || next[0] >= cch) return -2147483648; +return javajs.util.PT.parseIntChecked (str, cch, next); +}, "~S,~A"); +c$.parseIntChecked = Clazz.defineMethod (c$, "parseIntChecked", +function (str, ichMax, next) { +var digitSeen = false; +var value = 0; +var ich = next[0]; +if (ich < 0) return -2147483648; +var ch; +while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; + +var negative = false; +if (ich < ichMax && str.charCodeAt (ich) == 45) { +negative = true; +++ich; +}while (ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) { +value = value * 10 + (ch - 48); +digitSeen = true; +++ich; +} +if (!digitSeen) value = -2147483648; + else if (negative) value = -value; +next[0] = ich; +return value; +}, "~S,~N,~A"); +c$.isWhiteSpace = Clazz.defineMethod (c$, "isWhiteSpace", +function (str, ich) { +var ch; +return (ich >= 0 && ((ch = str.charAt (ich)) == ' ' || ch == '\t' || ch == '\n')); +}, "~S,~N"); +c$.parseFloatChecked = Clazz.defineMethod (c$, "parseFloatChecked", +function (str, ichMax, next, isStrict) { +var digitSeen = false; +var ich = next[0]; +if (isStrict && str.indexOf ('\n') != str.lastIndexOf ('\n')) return NaN; +while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; + +var negative = false; +if (ich < ichMax && str.charAt (ich) == '-') { +++ich; +negative = true; +}var ch = 0; +var ival = 0; +var ival2 = 0; +while (ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) { +ival = (ival * 10) + (ch - 48) * 1; +++ich; +digitSeen = true; +} +var isDecimal = false; +var iscale = 0; +var nzero = (ival == 0 ? -1 : 0); +if (ch == 46) { +isDecimal = true; +while (++ich < ichMax && (ch = str.charCodeAt (ich)) >= 48 && ch <= 57) { +digitSeen = true; +if (nzero < 0) { +if (ch == 48) { +nzero--; +continue; +}nzero = -nzero; +}if (iscale < javajs.util.PT.decimalScale.length) { +ival2 = (ival2 * 10) + (ch - 48) * 1; +iscale++; +}} +}var value; +if (!digitSeen) { +value = NaN; +} else if (ival2 > 0) { +value = ival2 * javajs.util.PT.decimalScale[iscale - 1]; +if (nzero > 1) { +if (nzero - 2 < javajs.util.PT.decimalScale.length) { +value *= javajs.util.PT.decimalScale[nzero - 2]; +} else { +value *= Math.pow (10, 1 - nzero); +}} else { +value += ival; +}} else { +value = ival; +}var isExponent = false; +if (ich < ichMax && (ch == 69 || ch == 101 || ch == 68)) { +isExponent = true; +if (++ich >= ichMax) return NaN; +ch = str.charCodeAt (ich); +if ((ch == 43) && (++ich >= ichMax)) return NaN; +next[0] = ich; +var exponent = javajs.util.PT.parseIntChecked (str, ichMax, next); +if (exponent == -2147483648) return NaN; +if (exponent > 0 && exponent <= javajs.util.PT.tensScale.length) value *= javajs.util.PT.tensScale[exponent - 1]; + else if (exponent < 0 && -exponent <= javajs.util.PT.decimalScale.length) value *= javajs.util.PT.decimalScale[-exponent - 1]; + else if (exponent != 0) value *= Math.pow (10, exponent); +} else { +next[0] = ich; +}if (negative) value = -value; +if (value == Infinity) value = 3.4028235E38; +return (!isStrict || (!isExponent || isDecimal) && javajs.util.PT.checkTrailingText (str, next[0], ichMax) ? value : NaN); +}, "~S,~N,~A,~B"); +c$.checkTrailingText = Clazz.defineMethod (c$, "checkTrailingText", +function (str, ich, ichMax) { +var ch; +while (ich < ichMax && (javajs.util.PT.isWhitespace (ch = str.charAt (ich)) || ch == ';')) ++ich; + +return (ich == ichMax); +}, "~S,~N,~N"); +c$.parseFloatArray = Clazz.defineMethod (c$, "parseFloatArray", +function (str) { +return javajs.util.PT.parseFloatArrayNext (str, Clazz.newIntArray (1, 0), null, null, null); +}, "~S"); +c$.parseFloatArrayInfested = Clazz.defineMethod (c$, "parseFloatArrayInfested", +function (tokens, data) { +var len = data.length; +var nTokens = tokens.length; +var n = 0; +var max = 0; +for (var i = 0; i >= 0 && i < len && n < nTokens; i++) { +var f; +while (Float.isNaN (f = javajs.util.PT.parseFloat (tokens[n++])) && n < nTokens) { +} +if (!Float.isNaN (f)) data[(max = i)] = f; +if (n == nTokens) break; +} +return max + 1; +}, "~A,~A"); +c$.parseFloatArrayNext = Clazz.defineMethod (c$, "parseFloatArrayNext", +function (str, next, f, strStart, strEnd) { +var n = 0; +var pt = next[0]; +if (pt >= 0) { +if (strStart != null) { +var p = str.indexOf (strStart, pt); +if (p >= 0) next[0] = p + strStart.length; +}str = str.substring (next[0]); +pt = (strEnd == null ? -1 : str.indexOf (strEnd)); +if (pt < 0) pt = str.length; + else str = str.substring (0, pt); +next[0] += pt + 1; +var tokens = javajs.util.PT.getTokens (str); +if (f == null) f = Clazz.newFloatArray (tokens.length, 0); +n = javajs.util.PT.parseFloatArrayInfested (tokens, f); +}if (f == null) return Clazz.newFloatArray (0, 0); +for (var i = n; i < f.length; i++) f[i] = NaN; + +return f; +}, "~S,~A,~A,~S,~S"); +c$.parseFloatRange = Clazz.defineMethod (c$, "parseFloatRange", +function (str, ichMax, next) { +var cch = str.length; +if (ichMax > cch) ichMax = cch; +if (next[0] < 0 || next[0] >= ichMax) return NaN; +return javajs.util.PT.parseFloatChecked (str, ichMax, next, false); +}, "~S,~N,~A"); +c$.parseFloatNext = Clazz.defineMethod (c$, "parseFloatNext", +function (str, next) { +var cch = (str == null ? -1 : str.length); +return (next[0] < 0 || next[0] >= cch ? NaN : javajs.util.PT.parseFloatChecked (str, cch, next, false)); +}, "~S,~A"); +c$.parseFloatStrict = Clazz.defineMethod (c$, "parseFloatStrict", +function (str) { +var cch = str.length; +if (cch == 0) return NaN; +return javajs.util.PT.parseFloatChecked (str, cch, Clazz.newIntArray (-1, [0]), true); +}, "~S"); +c$.parseFloat = Clazz.defineMethod (c$, "parseFloat", +function (str) { +return javajs.util.PT.parseFloatNext (str, Clazz.newIntArray (-1, [0])); +}, "~S"); +c$.parseIntRadix = Clazz.defineMethod (c$, "parseIntRadix", +function (s, i) { +{ +return Integer.parseIntRadix(s, i); +}}, "~S,~N"); +c$.getTokens = Clazz.defineMethod (c$, "getTokens", +function (line) { +return javajs.util.PT.getTokensAt (line, 0); +}, "~S"); +c$.parseToken = Clazz.defineMethod (c$, "parseToken", +function (str) { +return javajs.util.PT.parseTokenNext (str, Clazz.newIntArray (-1, [0])); +}, "~S"); +c$.parseTrimmed = Clazz.defineMethod (c$, "parseTrimmed", +function (str) { +return javajs.util.PT.parseTrimmedRange (str, 0, str.length); +}, "~S"); +c$.parseTrimmedAt = Clazz.defineMethod (c$, "parseTrimmedAt", +function (str, ichStart) { +return javajs.util.PT.parseTrimmedRange (str, ichStart, str.length); +}, "~S,~N"); +c$.parseTrimmedRange = Clazz.defineMethod (c$, "parseTrimmedRange", +function (str, ichStart, ichMax) { +var cch = str.length; +if (ichMax < cch) cch = ichMax; +if (cch < ichStart) return ""; +return javajs.util.PT.parseTrimmedChecked (str, ichStart, cch); +}, "~S,~N,~N"); +c$.getTokensAt = Clazz.defineMethod (c$, "getTokensAt", +function (line, ich) { +if (line == null) return null; +var cchLine = line.length; +if (ich < 0 || ich > cchLine) return null; +var tokenCount = javajs.util.PT.countTokens (line, ich); +var tokens = new Array (tokenCount); +var next = Clazz.newIntArray (1, 0); +next[0] = ich; +for (var i = 0; i < tokenCount; ++i) tokens[i] = javajs.util.PT.parseTokenChecked (line, cchLine, next); + +return tokens; +}, "~S,~N"); +c$.countChar = Clazz.defineMethod (c$, "countChar", +function (line, c) { +var tokenCount = 0; +var pt = -1; +while ((pt = line.indexOf (c, pt + 1)) >= 0) tokenCount++; + +return tokenCount; +}, "~S,~S"); +c$.countTokens = Clazz.defineMethod (c$, "countTokens", +function (line, ich) { +var tokenCount = 0; +if (line != null) { +var ichMax = line.length; +while (true) { +while (ich < ichMax && javajs.util.PT.isWhiteSpace (line, ich)) ++ich; + +if (ich == ichMax) break; +++tokenCount; +do { +++ich; +} while (ich < ichMax && !javajs.util.PT.isWhiteSpace (line, ich)); +} +}return tokenCount; +}, "~S,~N"); +c$.parseTokenNext = Clazz.defineMethod (c$, "parseTokenNext", +function (str, next) { +var cch = str.length; +return (next[0] < 0 || next[0] >= cch ? null : javajs.util.PT.parseTokenChecked (str, cch, next)); +}, "~S,~A"); +c$.parseTokenRange = Clazz.defineMethod (c$, "parseTokenRange", +function (str, ichMax, next) { +var cch = str.length; +if (ichMax > cch) ichMax = cch; +return (next[0] < 0 || next[0] >= ichMax ? null : javajs.util.PT.parseTokenChecked (str, ichMax, next)); +}, "~S,~N,~A"); +c$.parseTokenChecked = Clazz.defineMethod (c$, "parseTokenChecked", +function (str, ichMax, next) { +var ich = next[0]; +while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; + +var ichNonWhite = ich; +while (ich < ichMax && !javajs.util.PT.isWhiteSpace (str, ich)) ++ich; + +next[0] = ich; +return (ichNonWhite == ich ? null : str.substring (ichNonWhite, ich)); +}, "~S,~N,~A"); +c$.parseTrimmedChecked = Clazz.defineMethod (c$, "parseTrimmedChecked", +function (str, ich, ichMax) { +while (ich < ichMax && javajs.util.PT.isWhiteSpace (str, ich)) ++ich; + +var ichLast = ichMax - 1; +while (ichLast >= ich && javajs.util.PT.isWhiteSpace (str, ichLast)) --ichLast; + +return (ichLast < ich ? "" : str.substring (ich, ichLast + 1)); +}, "~S,~N,~N"); +c$.dVal = Clazz.defineMethod (c$, "dVal", +function (s) { +{ +if(s==null) +throw new NumberFormatException("null"); +var d=parseFloat(s); +if(isNaN(d)) +throw new NumberFormatException("Not a Number : "+s); +return d +}}, "~S"); +c$.fVal = Clazz.defineMethod (c$, "fVal", +function (s) { +{ +return this.dVal(s); +}}, "~S"); +c$.parseIntRange = Clazz.defineMethod (c$, "parseIntRange", +function (str, ichMax, next) { +var cch = str.length; +if (ichMax > cch) ichMax = cch; +return (next[0] < 0 || next[0] >= ichMax ? -2147483648 : javajs.util.PT.parseIntChecked (str, ichMax, next)); +}, "~S,~N,~A"); +c$.parseFloatArrayData = Clazz.defineMethod (c$, "parseFloatArrayData", +function (tokens, data) { +javajs.util.PT.parseFloatArrayDataN (tokens, data, data.length); +}, "~A,~A"); +c$.parseFloatArrayDataN = Clazz.defineMethod (c$, "parseFloatArrayDataN", +function (tokens, data, nData) { +for (var i = nData; --i >= 0; ) data[i] = (i >= tokens.length ? NaN : javajs.util.PT.parseFloat (tokens[i])); + +}, "~A,~A,~N"); +c$.split = Clazz.defineMethod (c$, "split", +function (text, run) { +if (text.length == 0) return new Array (0); +var n = 1; +var i = text.indexOf (run); +var lines; +var runLen = run.length; +if (i < 0 || runLen == 0) { +lines = new Array (1); +lines[0] = text; +return lines; +}var len = text.length - runLen; +for (; i >= 0 && i < len; n++) i = text.indexOf (run, i + runLen); + +lines = new Array (n); +i = 0; +var ipt = 0; +var pt = 0; +for (; (ipt = text.indexOf (run, i)) >= 0 && pt + 1 < n; ) { +lines[pt++] = text.substring (i, ipt); +i = ipt + runLen; +} +if (text.indexOf (run, len) != len) len += runLen; +lines[pt] = text.substring (i, len); +return lines; +}, "~S,~S"); +c$.getQuotedStringAt = Clazz.defineMethod (c$, "getQuotedStringAt", +function (line, ipt0) { +var next = Clazz.newIntArray (-1, [ipt0]); +return javajs.util.PT.getQuotedStringNext (line, next); +}, "~S,~N"); +c$.getQuotedStringNext = Clazz.defineMethod (c$, "getQuotedStringNext", +function (line, next) { +var i = next[0]; +if (i < 0 || (i = line.indexOf ("\"", i)) < 0) return ""; +var pt = i + 1; +var len = line.length; +while (++i < len && line.charAt (i) != '"') if (line.charAt (i) == '\\') i++; + +next[0] = i + 1; +return line.substring (pt, i); +}, "~S,~A"); +c$.getCSVString = Clazz.defineMethod (c$, "getCSVString", +function (line, next) { +var i = next[1]; +if (i < 0 || (i = line.indexOf ("\"", i)) < 0) return null; +var pt = next[0] = i; +var len = line.length; +var escaped = false; +var haveEscape = false; +while (++i < len && (line.charAt (i) != '"' || (escaped = (i + 1 < len && line.charAt (i + 1) == '"')))) if (escaped) { +escaped = false; +haveEscape = true; +i++; +} +if (i >= len) { +next[1] = -1; +return null; +}next[1] = i + 1; +var s = line.substring (pt + 1, i); +return (haveEscape ? javajs.util.PT.rep (javajs.util.PT.rep (s, "\"\"", "\0"), "\0", "\"") : s); +}, "~S,~A"); +c$.isOneOf = Clazz.defineMethod (c$, "isOneOf", +function (key, semiList) { +if (semiList.length == 0) return false; +if (semiList.charAt (0) != ';') semiList = ";" + semiList + ";"; +return key.indexOf (";") < 0 && semiList.indexOf (';' + key + ';') >= 0; +}, "~S,~S"); +c$.getQuotedAttribute = Clazz.defineMethod (c$, "getQuotedAttribute", +function (info, name) { +var i = info.indexOf (name + "="); +return (i < 0 ? null : javajs.util.PT.getQuotedStringAt (info, i)); +}, "~S,~S"); +c$.approx = Clazz.defineMethod (c$, "approx", +function (f, n) { +return Math.round (f * n) / n; +}, "~N,~N"); +c$.rep = Clazz.defineMethod (c$, "rep", +function (str, strFrom, strTo) { +if (str == null || strFrom.length == 0 || str.indexOf (strFrom) < 0) return str; +var isOnce = (strTo.indexOf (strFrom) >= 0); +do { +str = str.$replace (strFrom, strTo); +} while (!isOnce && str.indexOf (strFrom) >= 0); +return str; +}, "~S,~S,~S"); +c$.formatF = Clazz.defineMethod (c$, "formatF", +function (value, width, precision, alignLeft, zeroPad) { +return javajs.util.PT.formatS (javajs.util.DF.formatDecimal (value, precision), width, 0, alignLeft, zeroPad); +}, "~N,~N,~N,~B,~B"); +c$.formatD = Clazz.defineMethod (c$, "formatD", +function (value, width, precision, alignLeft, zeroPad, allowOverflow) { +return javajs.util.PT.formatS (javajs.util.DF.formatDecimal (value, -1 - precision), width, 0, alignLeft, zeroPad); +}, "~N,~N,~N,~B,~B,~B"); +c$.formatS = Clazz.defineMethod (c$, "formatS", +function (value, width, precision, alignLeft, zeroPad) { +if (value == null) return ""; +var len = value.length; +if (precision != 2147483647 && precision > 0 && precision < len) value = value.substring (0, precision); + else if (precision < 0 && len + precision >= 0) value = value.substring (len + precision + 1); +var padLength = width - value.length; +if (padLength <= 0) return value; +var isNeg = (zeroPad && !alignLeft && value.charAt (0) == '-'); +var padChar = (zeroPad ? '0' : ' '); +var padChar0 = (isNeg ? '-' : padChar); +var sb = new javajs.util.SB (); +if (alignLeft) sb.append (value); +sb.appendC (padChar0); +for (var i = padLength; --i > 0; ) sb.appendC (padChar); + +if (!alignLeft) sb.append (isNeg ? padChar + value.substring (1) : value); +return sb.toString (); +}, "~S,~N,~N,~B,~B"); +c$.replaceWithCharacter = Clazz.defineMethod (c$, "replaceWithCharacter", +function (str, strFrom, chTo) { +if (str == null) return null; +for (var i = strFrom.length; --i >= 0; ) str = str.$replace (strFrom.charAt (i), chTo); + +return str; +}, "~S,~S,~S"); +c$.replaceAllCharacters = Clazz.defineMethod (c$, "replaceAllCharacters", +function (str, strFrom, strTo) { +for (var i = strFrom.length; --i >= 0; ) { +var chFrom = strFrom.substring (i, i + 1); +str = javajs.util.PT.rep (str, chFrom, strTo); +} +return str; +}, "~S,~S,~S"); +c$.trim = Clazz.defineMethod (c$, "trim", +function (str, chars) { +if (str == null || str.length == 0) return str; +if (chars.length == 0) return str.trim (); +var len = str.length; +var k = 0; +while (k < len && chars.indexOf (str.charAt (k)) >= 0) k++; + +var m = str.length - 1; +while (m > k && chars.indexOf (str.charAt (m)) >= 0) m--; + +return str.substring (k, m + 1); +}, "~S,~S"); +c$.trimQuotes = Clazz.defineMethod (c$, "trimQuotes", +function (value) { +return (value != null && value.length > 1 && value.startsWith ("\"") && value.endsWith ("\"") ? value.substring (1, value.length - 1) : value); +}, "~S"); +c$.isNonStringPrimitive = Clazz.defineMethod (c$, "isNonStringPrimitive", +function (info) { +return Clazz.instanceOf (info, Number) || Clazz.instanceOf (info, Boolean); +}, "~O"); +c$.arrayGet = Clazz.defineMethod (c$, "arrayGet", +($fz = function (info, i) { +{ +return info[i]; +}}, $fz.isPrivate = true, $fz), "~O,~N"); +c$.toJSON = Clazz.defineMethod (c$, "toJSON", +function (infoType, info) { +if (info == null) return javajs.util.PT.packageJSON (infoType, null); +if (javajs.util.PT.isNonStringPrimitive (info)) return javajs.util.PT.packageJSON (infoType, info.toString ()); +var s = null; +var sb = null; +while (true) { +if (Clazz.instanceOf (info, String)) { +s = info; +{ +if (typeof s == "undefined") s = "null" +}if (s.indexOf ("{\"") != 0) { +s = javajs.util.PT.rep (s, "\"", "\\\""); +s = javajs.util.PT.rep (s, "\n", "\\n"); +s = "\"" + s + "\""; +}break; +}if (Clazz.instanceOf (info, javajs.api.JSONEncodable)) { +if ((s = (info).toJSON ()) == null) s = "null"; +break; +}sb = new javajs.util.SB (); +if (Clazz.instanceOf (info, java.util.Map)) { +sb.append ("{ "); +var sep = ""; +for (var key, $key = (info).keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) { +sb.append (sep).append (javajs.util.PT.packageJSON (key, javajs.util.PT.toJSON (null, (info).get (key)))); +sep = ","; +} +sb.append (" }"); +break; +}if (Clazz.instanceOf (info, javajs.util.Lst)) { +sb.append ("[ "); +var n = (info).size (); +for (var i = 0; i < n; i++) { +if (i > 0) sb.appendC (','); +sb.append (javajs.util.PT.toJSON (null, (info).get (i))); +} +sb.append (" ]"); +break; +}if (Clazz.instanceOf (info, javajs.util.M34)) { +var len = (Clazz.instanceOf (info, javajs.util.M4) ? 4 : 3); +var x = Clazz.newFloatArray (len, 0); +var m = info; +sb.appendC ('['); +for (var i = 0; i < len; i++) { +if (i > 0) sb.appendC (','); +m.getRow (i, x); +sb.append (javajs.util.PT.toJSON (null, x)); +} +sb.appendC (']'); +break; +}s = javajs.util.PT.nonArrayString (info); +if (s == null) { +sb.append ("["); +var n = javajs.util.AU.getLength (info); +for (var i = 0; i < n; i++) { +if (i > 0) sb.appendC (','); +sb.append (javajs.util.PT.toJSON (null, javajs.util.PT.arrayGet (info, i))); +} +sb.append ("]"); +break; +}info = info.toString (); +} +return javajs.util.PT.packageJSON (infoType, (s == null ? sb.toString () : s)); +}, "~S,~O"); +c$.nonArrayString = Clazz.defineMethod (c$, "nonArrayString", +function (x) { +{ +var s = x.toString(); return (s.startsWith("[object") && +s.endsWith("Array]") ? null : s); +}}, "~O"); +c$.byteArrayToJSON = Clazz.defineMethod (c$, "byteArrayToJSON", +function (data) { +var sb = new javajs.util.SB (); +sb.append ("["); +var n = data.length; +for (var i = 0; i < n; i++) { +if (i > 0) sb.appendC (','); +sb.appendI (data[i] & 0xFF); +} +sb.append ("]"); +return sb.toString (); +}, "~A"); +c$.packageJSON = Clazz.defineMethod (c$, "packageJSON", +function (infoType, info) { +return (infoType == null ? info : "\"" + infoType + "\": " + info); +}, "~S,~S"); +c$.escapeUrl = Clazz.defineMethod (c$, "escapeUrl", +function (url) { +url = javajs.util.PT.rep (url, "\n", ""); +url = javajs.util.PT.rep (url, "%", "%25"); +url = javajs.util.PT.rep (url, "#", "%23"); +url = javajs.util.PT.rep (url, "[", "%5B"); +url = javajs.util.PT.rep (url, "]", "%5D"); +url = javajs.util.PT.rep (url, " ", "%20"); +return url; +}, "~S"); +c$.esc = Clazz.defineMethod (c$, "esc", +function (str) { +if (str == null || str.length == 0) return "\"\""; +var haveEscape = false; +var i = 0; +for (; i < "\\\\\tt\rr\nn\"\"".length; i += 2) if (str.indexOf ("\\\\\tt\rr\nn\"\"".charAt (i)) >= 0) { +haveEscape = true; +break; +} +if (haveEscape) while (i < "\\\\\tt\rr\nn\"\"".length) { +var pt = -1; +var ch = "\\\\\tt\rr\nn\"\"".charAt (i++); +var ch2 = "\\\\\tt\rr\nn\"\"".charAt (i++); +var sb = new javajs.util.SB (); +var pt0 = 0; +while ((pt = str.indexOf (ch, pt + 1)) >= 0) { +sb.append (str.substring (pt0, pt)).appendC ('\\').appendC (ch2); +pt0 = pt + 1; +} +sb.append (str.substring (pt0, str.length)); +str = sb.toString (); +} +return "\"" + javajs.util.PT.escUnicode (str) + "\""; +}, "~S"); +c$.escUnicode = Clazz.defineMethod (c$, "escUnicode", +function (str) { +for (var i = str.length; --i >= 0; ) if (str.charCodeAt (i) > 0x7F) { +var s = "0000" + Integer.toHexString (str.charCodeAt (i)); +str = str.substring (0, i) + "\\u" + s.substring (s.length - 4) + str.substring (i + 1); +} +return str; +}, "~S"); +c$.escF = Clazz.defineMethod (c$, "escF", +function (f) { +var sf = "" + f; +{ +if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0) +sf += ".0"; +}return sf; +}, "~N"); +c$.join = Clazz.defineMethod (c$, "join", +function (s, c, i0) { +if (s.length < i0) return null; +var sb = new javajs.util.SB (); +sb.append (s[i0++]); +for (var i = i0; i < s.length; i++) sb.appendC (c).append (s[i]); + +return sb.toString (); +}, "~A,~S,~N"); +c$.isLike = Clazz.defineMethod (c$, "isLike", +function (a, b) { +var areEqual = a.equals (b); +if (areEqual) return true; +var isStart = b.startsWith ("*"); +var isEnd = b.endsWith ("*"); +return (!isStart && !isEnd) ? areEqual : isStart && isEnd ? b.length == 1 || a.contains (b.substring (1, b.length - 1)) : isStart ? a.endsWith (b.substring (1)) : a.startsWith (b.substring (0, b.length - 1)); +}, "~S,~S"); +c$.getMapValueNoCase = Clazz.defineMethod (c$, "getMapValueNoCase", +function (h, key) { +if ("this".equals (key)) return h; +var val = h.get (key); +if (val == null) for (var e, $e = h.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) if (e.getKey ().equalsIgnoreCase (key)) return e.getValue (); + +return val; +}, "java.util.Map,~S"); +c$.clean = Clazz.defineMethod (c$, "clean", +function (s) { +return javajs.util.PT.rep (javajs.util.PT.replaceAllCharacters (s, " \t\n\r", " "), " ", " ").trim (); +}, "~S"); +c$.fdup = Clazz.defineMethod (c$, "fdup", +function (f, pt, n) { +var ch; +var count = 0; +for (var i = pt; --i >= 1; ) { +if (javajs.util.PT.isDigit (ch = f.charAt (i))) continue; +switch (ch) { +case '.': +if (count++ != 0) return f; +continue; +case '-': +if (i != 1 && f.charAt (i - 1) != '.') return f; +continue; +default: +return f; +} +} +var s = f.substring (0, pt + 1); +var sb = new javajs.util.SB (); +for (var i = 0; i < n; i++) sb.append (s); + +sb.append (f.substring (pt + 1)); +return sb.toString (); +}, "~S,~N,~N"); +c$.formatString = Clazz.defineMethod (c$, "formatString", +function (strFormat, key, strT, floatT, doubleT, doOne) { +if (strFormat == null) return null; +if ("".equals (strFormat)) return ""; +var len = key.length; +if (strFormat.indexOf ("%") < 0 || len == 0 || strFormat.indexOf (key) < 0) return strFormat; +var strLabel = ""; +var ich; +var ichPercent; +var ichKey; +for (ich = 0; (ichPercent = strFormat.indexOf ('%', ich)) >= 0 && (ichKey = strFormat.indexOf (key, ichPercent + 1)) >= 0; ) { +if (ich != ichPercent) strLabel += strFormat.substring (ich, ichPercent); +ich = ichPercent + 1; +if (ichKey > ichPercent + 6) { +strLabel += '%'; +continue; +}try { +var alignLeft = false; +if (strFormat.charAt (ich) == '-') { +alignLeft = true; +++ich; +}var zeroPad = false; +if (strFormat.charAt (ich) == '0') { +zeroPad = true; +++ich; +}var ch; +var width = 0; +while ((ch = strFormat.charAt (ich)) >= '0' && (ch <= '9')) { +width = (10 * width) + (ch.charCodeAt (0) - 48); +++ich; +} +var precision = 2147483647; +var isExponential = false; +if (strFormat.charAt (ich) == '.') { +++ich; +if ((ch = strFormat.charAt (ich)) == '-') { +isExponential = true; +++ich; +}if ((ch = strFormat.charAt (ich)) >= '0' && ch <= '9') { +precision = ch.charCodeAt (0) - 48; +++ich; +}if (isExponential) precision = -precision - (strT == null ? 1 : 0); +}var st = strFormat.substring (ich, ich + len); +if (!st.equals (key)) { +ich = ichPercent + 1; +strLabel += '%'; +continue; +}ich += len; +if (!Float.isNaN (floatT)) strLabel += javajs.util.PT.formatF (floatT, width, precision, alignLeft, zeroPad); + else if (strT != null) strLabel += javajs.util.PT.formatS (strT, width, precision, alignLeft, zeroPad); + else if (!Double.isNaN (doubleT)) strLabel += javajs.util.PT.formatD (doubleT, width, precision, alignLeft, zeroPad, true); +if (doOne) break; +} catch (ioobe) { +if (Clazz.exceptionOf (ioobe, IndexOutOfBoundsException)) { +ich = ichPercent; +break; +} else { +throw ioobe; +} +} +} +strLabel += strFormat.substring (ich); +return strLabel; +}, "~S,~S,~S,~N,~N,~B"); +c$.formatStringS = Clazz.defineMethod (c$, "formatStringS", +function (strFormat, key, strT) { +return javajs.util.PT.formatString (strFormat, key, strT, NaN, NaN, false); +}, "~S,~S,~S"); +c$.formatStringF = Clazz.defineMethod (c$, "formatStringF", +function (strFormat, key, floatT) { +return javajs.util.PT.formatString (strFormat, key, null, floatT, NaN, false); +}, "~S,~S,~N"); +c$.formatStringI = Clazz.defineMethod (c$, "formatStringI", +function (strFormat, key, intT) { +return javajs.util.PT.formatString (strFormat, key, "" + intT, NaN, NaN, false); +}, "~S,~S,~N"); +c$.sprintf = Clazz.defineMethod (c$, "sprintf", +function (strFormat, list, values) { +if (values == null) return strFormat; +var n = list.length; +if (n == values.length) try { +for (var o = 0; o < n; o++) { +if (values[o] == null) continue; +switch (list.charAt (o)) { +case 's': +strFormat = javajs.util.PT.formatString (strFormat, "s", values[o], NaN, NaN, true); +break; +case 'f': +strFormat = javajs.util.PT.formatString (strFormat, "f", null, (values[o]).floatValue (), NaN, true); +break; +case 'i': +strFormat = javajs.util.PT.formatString (strFormat, "d", "" + values[o], NaN, NaN, true); +strFormat = javajs.util.PT.formatString (strFormat, "i", "" + values[o], NaN, NaN, true); +break; +case 'd': +strFormat = javajs.util.PT.formatString (strFormat, "e", null, NaN, (values[o]).doubleValue (), true); +break; +case 'p': +var pVal = values[o]; +strFormat = javajs.util.PT.formatString (strFormat, "p", null, pVal.x, NaN, true); +strFormat = javajs.util.PT.formatString (strFormat, "p", null, pVal.y, NaN, true); +strFormat = javajs.util.PT.formatString (strFormat, "p", null, pVal.z, NaN, true); +break; +case 'q': +var qVal = values[o]; +strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.x, NaN, true); +strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.y, NaN, true); +strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.z, NaN, true); +strFormat = javajs.util.PT.formatString (strFormat, "q", null, qVal.w, NaN, true); +break; +case 'S': +var sVal = values[o]; +for (var i = 0; i < sVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "s", sVal[i], NaN, NaN, true); + +break; +case 'F': +var fVal = values[o]; +for (var i = 0; i < fVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "f", null, fVal[i], NaN, true); + +break; +case 'I': +var iVal = values[o]; +for (var i = 0; i < iVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "d", "" + iVal[i], NaN, NaN, true); + +for (var i = 0; i < iVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "i", "" + iVal[i], NaN, NaN, true); + +break; +case 'D': +var dVal = values[o]; +for (var i = 0; i < dVal.length; i++) strFormat = javajs.util.PT.formatString (strFormat, "e", null, NaN, dVal[i], true); + +} +} +return javajs.util.PT.rep (strFormat, "%%", "%"); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +System.out.println ("TextFormat.sprintf error " + list + " " + strFormat); +return javajs.util.PT.rep (strFormat, "%", "?"); +}, "~S,~S,~A"); +c$.formatCheck = Clazz.defineMethod (c$, "formatCheck", +function (strFormat) { +if (strFormat == null || strFormat.indexOf ('p') < 0 && strFormat.indexOf ('q') < 0) return strFormat; +strFormat = javajs.util.PT.rep (strFormat, "%%", "\1"); +strFormat = javajs.util.PT.rep (strFormat, "%p", "%6.2p"); +strFormat = javajs.util.PT.rep (strFormat, "%q", "%6.2q"); +var format = javajs.util.PT.split (strFormat, "%"); +var sb = new javajs.util.SB (); +sb.append (format[0]); +for (var i = 1; i < format.length; i++) { +var f = "%" + format[i]; +var pt; +if (f.length >= 3) { +if ((pt = f.indexOf ('p')) >= 0) f = javajs.util.PT.fdup (f, pt, 3); +if ((pt = f.indexOf ('q')) >= 0) f = javajs.util.PT.fdup (f, pt, 4); +}sb.append (f); +} +return sb.toString ().$replace ('\1', '%'); +}, "~S"); +c$.leftJustify = Clazz.defineMethod (c$, "leftJustify", +function (s, s1, s2) { +s.append (s2); +var n = s1.length - s2.length; +if (n > 0) s.append (s1.substring (0, n)); +}, "javajs.util.SB,~S,~S"); +c$.rightJustify = Clazz.defineMethod (c$, "rightJustify", +function (s, s1, s2) { +var n = s1.length - s2.length; +if (n > 0) s.append (s1.substring (0, n)); +s.append (s2); +}, "javajs.util.SB,~S,~S"); +c$.safeTruncate = Clazz.defineMethod (c$, "safeTruncate", +function (f, n) { +if (f > -0.001 && f < 0.001) f = 0; +return (f + " ").substring (0, n); +}, "~N,~N"); +c$.isWild = Clazz.defineMethod (c$, "isWild", +function (s) { +return s != null && (s.indexOf ("*") >= 0 || s.indexOf ("?") >= 0); +}, "~S"); +c$.isMatch = Clazz.defineMethod (c$, "isMatch", +function (search, match, checkStar, allowInitialStar) { +if (search.equals (match)) return true; +var mLen = match.length; +if (mLen == 0) return false; +var isStar0 = (checkStar && allowInitialStar ? match.charAt (0) == '*' : false); +if (mLen == 1 && isStar0) return true; +var isStar1 = (checkStar && match.endsWith ("*")); +var haveQ = (match.indexOf ('?') >= 0); +if (!haveQ) { +if (isStar0) return (isStar1 ? (mLen < 3 || search.indexOf (match.substring (1, mLen - 1)) >= 0) : search.endsWith (match.substring (1))); + else if (isStar1) return search.startsWith (match.substring (0, mLen - 1)); +}var sLen = search.length; +var qqqq = "????"; +var nq = 4; +while (nq < sLen) { +qqqq += qqqq; +nq += 4; +} +if (checkStar) { +if (isStar0) { +match = qqqq + match.substring (1); +mLen += nq - 1; +}if (isStar1) { +match = match.substring (0, mLen - 1) + qqqq; +mLen += nq - 1; +}}if (mLen < sLen) return false; +var ich = 0; +while (mLen > sLen) { +if (allowInitialStar && match.charAt (ich) == '?') { +++ich; +} else if (match.charAt (ich + mLen - 1) != '?') { +return false; +}--mLen; +} +for (var i = sLen; --i >= 0; ) { +var chm = match.charAt (ich + i); +if (chm == '?') continue; +var chs = search.charAt (i); +if (chm != chs && (chm != '\1' || chs != '?')) return false; +} +return true; +}, "~S,~S,~B,~B"); +c$.replaceQuotedStrings = Clazz.defineMethod (c$, "replaceQuotedStrings", +function (s, list, newList) { +var n = list.size (); +for (var i = 0; i < n; i++) { +var name = list.get (i); +var newName = newList.get (i); +if (!newName.equals (name)) s = javajs.util.PT.rep (s, "\"" + name + "\"", "\"" + newName + "\""); +} +return s; +}, "~S,javajs.util.Lst,javajs.util.Lst"); +c$.replaceStrings = Clazz.defineMethod (c$, "replaceStrings", +function (s, list, newList) { +var n = list.size (); +for (var i = 0; i < n; i++) { +var name = list.get (i); +var newName = newList.get (i); +if (!newName.equals (name)) s = javajs.util.PT.rep (s, name, newName); +} +return s; +}, "~S,javajs.util.Lst,javajs.util.Lst"); +c$.isDigit = Clazz.defineMethod (c$, "isDigit", +function (ch) { +var c = (ch).charCodeAt (0); +return (48 <= c && c <= 57); +}, "~S"); +c$.isUpperCase = Clazz.defineMethod (c$, "isUpperCase", +function (ch) { +var c = (ch).charCodeAt (0); +return (65 <= c && c <= 90); +}, "~S"); +c$.isLowerCase = Clazz.defineMethod (c$, "isLowerCase", +function (ch) { +var c = (ch).charCodeAt (0); +return (97 <= c && c <= 122); +}, "~S"); +c$.isLetter = Clazz.defineMethod (c$, "isLetter", +function (ch) { +var c = (ch).charCodeAt (0); +return (65 <= c && c <= 90 || 97 <= c && c <= 122); +}, "~S"); +c$.isLetterOrDigit = Clazz.defineMethod (c$, "isLetterOrDigit", +function (ch) { +var c = (ch).charCodeAt (0); +return (65 <= c && c <= 90 || 97 <= c && c <= 122 || 48 <= c && c <= 57); +}, "~S"); +c$.isWhitespace = Clazz.defineMethod (c$, "isWhitespace", +function (ch) { +var c = (ch).charCodeAt (0); +return (c >= 0x1c && c <= 0x20 || c >= 0x9 && c <= 0xd); +}, "~S"); +c$.fixPtFloats = Clazz.defineMethod (c$, "fixPtFloats", +function (pt, f) { +pt.x = Math.round (pt.x * f) / f; +pt.y = Math.round (pt.y * f) / f; +pt.z = Math.round (pt.z * f) / f; +}, "javajs.util.T3,~N"); +c$.fixDouble = Clazz.defineMethod (c$, "fixDouble", +function (d, f) { +return Math.round (d * f) / f; +}, "~N,~N"); +c$.parseFloatFraction = Clazz.defineMethod (c$, "parseFloatFraction", +function (s) { +var pt = s.indexOf ("/"); +return (pt < 0 ? javajs.util.PT.parseFloat (s) : javajs.util.PT.parseFloat (s.substring (0, pt)) / javajs.util.PT.parseFloat (s.substring (pt + 1))); +}, "~S"); +Clazz.defineStatics (c$, +"tensScale", Clazz.newFloatArray (-1, [10, 100, 1000, 10000, 100000, 1000000]), +"decimalScale", Clazz.newFloatArray (-1, [0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001, 0.0000001, 0.00000001, 0.000000001]), +"FLOAT_MIN_SAFE", 2E-45, +"escapable", "\\\\\tt\rr\nn\"\"", +"FRACTIONAL_PRECISION", 100000, +"CARTESIAN_PRECISION", 10000); +}); diff --git a/bin/javajs/util/Quat.js b/bin/javajs/util/Quat.js index 0db2469..bfc5444 100644 --- a/bin/javajs/util/Quat.js +++ b/bin/javajs/util/Quat.js @@ -1,427 +1,427 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.P4"], "javajs.util.Quat", ["java.lang.Float", "javajs.util.A4", "$.M3", "$.V3"], function () { -c$ = Clazz.decorateAsClass (function () { -this.q0 = 0; -this.q1 = 0; -this.q2 = 0; -this.q3 = 0; -this.mat = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "Quat"); -Clazz.makeConstructor (c$, -function () { -this.q0 = 1; -}); -c$.newQ = Clazz.defineMethod (c$, "newQ", -function (q) { -var q1 = new javajs.util.Quat (); -q1.set (q); -return q1; -}, "javajs.util.Quat"); -c$.newVA = Clazz.defineMethod (c$, "newVA", -function (v, theta) { -var q = new javajs.util.Quat (); -q.setTA (v, theta); -return q; -}, "javajs.util.T3,~N"); -c$.newM = Clazz.defineMethod (c$, "newM", -function (mat) { -var q = new javajs.util.Quat (); -q.setM (javajs.util.M3.newM3 (mat)); -return q; -}, "javajs.util.M3"); -c$.newAA = Clazz.defineMethod (c$, "newAA", -function (a) { -var q = new javajs.util.Quat (); -q.setAA (a); -return q; -}, "javajs.util.A4"); -c$.newP4 = Clazz.defineMethod (c$, "newP4", -function (pt) { -var q = new javajs.util.Quat (); -q.setP4 (pt); -return q; -}, "javajs.util.P4"); -c$.new4 = Clazz.defineMethod (c$, "new4", -function (q1, q2, q3, q0) { -var q = new javajs.util.Quat (); -if (q0 < -1) { -q.q0 = -1; -return q; -}if (q0 > 1) { -q.q0 = 1; -return q; -}q.q0 = q0; -q.q1 = q1; -q.q2 = q2; -q.q3 = q3; -return q; -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "set", -function (q) { -this.q0 = q.q0; -this.q1 = q.q1; -this.q2 = q.q2; -this.q3 = q.q3; -}, "javajs.util.Quat"); -Clazz.defineMethod (c$, "setP4", -($fz = function (pt) { -var factor = (pt == null ? 0 : pt.distance4 (javajs.util.Quat.qZero)); -if (factor == 0) { -this.q0 = 1; -return; -}this.q0 = pt.w / factor; -this.q1 = pt.x / factor; -this.q2 = pt.y / factor; -this.q3 = pt.z / factor; -}, $fz.isPrivate = true, $fz), "javajs.util.P4"); -Clazz.defineMethod (c$, "setTA", -function (pt, theta) { -if (pt.x == 0 && pt.y == 0 && pt.z == 0) { -this.q0 = 1; -return; -}var fact = (Math.sin (theta / 2 * 0.017453292519943295) / Math.sqrt (pt.x * pt.x + pt.y * pt.y + pt.z * pt.z)); -this.q0 = (Math.cos (theta / 2 * 0.017453292519943295)); -this.q1 = (pt.x * fact); -this.q2 = (pt.y * fact); -this.q3 = (pt.z * fact); -}, "javajs.util.T3,~N"); -Clazz.defineMethod (c$, "setAA", -function (a) { -var aa = javajs.util.A4.newAA (a); -if (aa.angle == 0) aa.y = 1; -this.setM ( new javajs.util.M3 ().setAA (aa)); -}, "javajs.util.A4"); -Clazz.defineMethod (c$, "setM", -($fz = function (mat) { -this.mat = mat; -var trace = mat.m00 + mat.m11 + mat.m22; -var temp; -var w; -var x; -var y; -var z; -if (trace >= 0.5) { -w = Math.sqrt (1.0 + trace); -x = (mat.m21 - mat.m12) / w; -y = (mat.m02 - mat.m20) / w; -z = (mat.m10 - mat.m01) / w; -} else if ((temp = mat.m00 + mat.m00 - trace) >= 0.5) { -x = Math.sqrt (1.0 + temp); -w = (mat.m21 - mat.m12) / x; -y = (mat.m10 + mat.m01) / x; -z = (mat.m20 + mat.m02) / x; -} else if ((temp = mat.m11 + mat.m11 - trace) >= 0.5 || mat.m11 > mat.m22) { -y = Math.sqrt (1.0 + temp); -w = (mat.m02 - mat.m20) / y; -x = (mat.m10 + mat.m01) / y; -z = (mat.m21 + mat.m12) / y; -} else { -z = Math.sqrt (1.0 + mat.m22 + mat.m22 - trace); -w = (mat.m10 - mat.m01) / z; -x = (mat.m20 + mat.m02) / z; -y = (mat.m21 + mat.m12) / z; -}this.q0 = (w * 0.5); -this.q1 = (x * 0.5); -this.q2 = (y * 0.5); -this.q3 = (z * 0.5); -}, $fz.isPrivate = true, $fz), "javajs.util.M3"); -Clazz.defineMethod (c$, "setRef", -function (qref) { -if (qref == null) { -this.mul (this.getFixFactor ()); -return; -}if (this.dot (qref) >= 0) return; -this.q0 *= -1; -this.q1 *= -1; -this.q2 *= -1; -this.q3 *= -1; -}, "javajs.util.Quat"); -c$.getQuaternionFrame = Clazz.defineMethod (c$, "getQuaternionFrame", -function (center, x, xy) { -var vA = javajs.util.V3.newV (x); -var vB = javajs.util.V3.newV (xy); -if (center != null) { -vA.sub (center); -vB.sub (center); -}return javajs.util.Quat.getQuaternionFrameV (vA, vB, null, false); -}, "javajs.util.P3,javajs.util.T3,javajs.util.T3"); -c$.getQuaternionFrameV = Clazz.defineMethod (c$, "getQuaternionFrameV", -function (vA, vB, vC, yBased) { -if (vC == null) { -vC = new javajs.util.V3 (); -vC.cross (vA, vB); -if (yBased) vA.cross (vB, vC); -}var vBprime = new javajs.util.V3 (); -vBprime.cross (vC, vA); -vA.normalize (); -vBprime.normalize (); -vC.normalize (); -var mat = new javajs.util.M3 (); -mat.setColumnV (0, vA); -mat.setColumnV (1, vBprime); -mat.setColumnV (2, vC); -var q = javajs.util.Quat.newM (mat); -return q; -}, "javajs.util.V3,javajs.util.V3,javajs.util.V3,~B"); -Clazz.defineMethod (c$, "getMatrix", -function () { -if (this.mat == null) this.setMatrix (); -return this.mat; -}); -Clazz.defineMethod (c$, "setMatrix", -($fz = function () { -this.mat = new javajs.util.M3 (); -this.mat.m00 = this.q0 * this.q0 + this.q1 * this.q1 - this.q2 * this.q2 - this.q3 * this.q3; -this.mat.m01 = 2 * this.q1 * this.q2 - 2 * this.q0 * this.q3; -this.mat.m02 = 2 * this.q1 * this.q3 + 2 * this.q0 * this.q2; -this.mat.m10 = 2 * this.q1 * this.q2 + 2 * this.q0 * this.q3; -this.mat.m11 = this.q0 * this.q0 - this.q1 * this.q1 + this.q2 * this.q2 - this.q3 * this.q3; -this.mat.m12 = 2 * this.q2 * this.q3 - 2 * this.q0 * this.q1; -this.mat.m20 = 2 * this.q1 * this.q3 - 2 * this.q0 * this.q2; -this.mat.m21 = 2 * this.q2 * this.q3 + 2 * this.q0 * this.q1; -this.mat.m22 = this.q0 * this.q0 - this.q1 * this.q1 - this.q2 * this.q2 + this.q3 * this.q3; -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "add", -function (x) { -return javajs.util.Quat.newVA (this.getNormal (), this.getTheta () + x); -}, "~N"); -Clazz.defineMethod (c$, "mul", -function (x) { -return (x == 1 ? javajs.util.Quat.new4 (this.q1, this.q2, this.q3, this.q0) : javajs.util.Quat.newVA (this.getNormal (), this.getTheta () * x)); -}, "~N"); -Clazz.defineMethod (c$, "mulQ", -function (p) { -return javajs.util.Quat.new4 (this.q0 * p.q1 + this.q1 * p.q0 + this.q2 * p.q3 - this.q3 * p.q2, this.q0 * p.q2 + this.q2 * p.q0 + this.q3 * p.q1 - this.q1 * p.q3, this.q0 * p.q3 + this.q3 * p.q0 + this.q1 * p.q2 - this.q2 * p.q1, this.q0 * p.q0 - this.q1 * p.q1 - this.q2 * p.q2 - this.q3 * p.q3); -}, "javajs.util.Quat"); -Clazz.defineMethod (c$, "div", -function (p) { -return this.mulQ (p.inv ()); -}, "javajs.util.Quat"); -Clazz.defineMethod (c$, "divLeft", -function (p) { -return this.inv ().mulQ (p); -}, "javajs.util.Quat"); -Clazz.defineMethod (c$, "dot", -function (q) { -return this.q0 * q.q0 + this.q1 * q.q1 + this.q2 * q.q2 + this.q3 * q.q3; -}, "javajs.util.Quat"); -Clazz.defineMethod (c$, "inv", -function () { -return javajs.util.Quat.new4 (-this.q1, -this.q2, -this.q3, this.q0); -}); -Clazz.defineMethod (c$, "negate", -function () { -return javajs.util.Quat.new4 (-this.q1, -this.q2, -this.q3, -this.q0); -}); -Clazz.defineMethod (c$, "getFixFactor", -($fz = function () { -return (this.q0 < 0 || this.q0 == 0 && (this.q1 < 0 || this.q1 == 0 && (this.q2 < 0 || this.q2 == 0 && this.q3 < 0)) ? -1 : 1); -}, $fz.isPrivate = true, $fz)); -Clazz.defineMethod (c$, "getVector", -function (i) { -return this.getVectorScaled (i, 1); -}, "~N"); -Clazz.defineMethod (c$, "getVectorScaled", -function (i, scale) { -if (i == -1) { -scale *= this.getFixFactor (); -return javajs.util.V3.new3 (this.q1 * scale, this.q2 * scale, this.q3 * scale); -}if (this.mat == null) this.setMatrix (); -var v = new javajs.util.V3 (); -this.mat.getColumnV (i, v); -if (scale != 1) v.scale (scale); -return v; -}, "~N,~N"); -Clazz.defineMethod (c$, "getNormal", -function () { -var v = javajs.util.Quat.getRawNormal (this); -v.scale (this.getFixFactor ()); -return v; -}); -c$.getRawNormal = Clazz.defineMethod (c$, "getRawNormal", -($fz = function (q) { -var v = javajs.util.V3.new3 (q.q1, q.q2, q.q3); -if (v.length () == 0) return javajs.util.V3.new3 (0, 0, 1); -v.normalize (); -return v; -}, $fz.isPrivate = true, $fz), "javajs.util.Quat"); -Clazz.defineMethod (c$, "getTheta", -function () { -return (Math.acos (Math.abs (this.q0)) * 2 * 180 / 3.141592653589793); -}); -Clazz.defineMethod (c$, "getThetaRadians", -function () { -return (Math.acos (Math.abs (this.q0)) * 2); -}); -Clazz.defineMethod (c$, "getNormalDirected", -function (v0) { -var v = this.getNormal (); -if (v.x * v0.x + v.y * v0.y + v.z * v0.z < 0) { -v.scale (-1); -}return v; -}, "javajs.util.V3"); -Clazz.defineMethod (c$, "get3dProjection", -function (v3d) { -v3d.set (this.q1, this.q2, this.q3); -return v3d; -}, "javajs.util.V3"); -Clazz.defineMethod (c$, "getThetaDirected", -function (axisAngle) { -var theta = this.getTheta (); -var v = this.getNormal (); -if (axisAngle.x * this.q1 + axisAngle.y * this.q2 + axisAngle.z * this.q3 < 0) { -v.scale (-1); -theta = -theta; -}axisAngle.set4 (v.x, v.y, v.z, theta); -return axisAngle; -}, "javajs.util.P4"); -Clazz.defineMethod (c$, "getThetaDirectedV", -function (vector) { -var theta = this.getTheta (); -var v = this.getNormal (); -if (vector.x * this.q1 + vector.y * this.q2 + vector.z * this.q3 < 0) { -v.scale (-1); -theta = -theta; -}return theta; -}, "javajs.util.V3"); -Clazz.defineMethod (c$, "toPoint4f", -function () { -return javajs.util.P4.new4 (this.q1, this.q2, this.q3, this.q0); -}); -Clazz.defineMethod (c$, "toAxisAngle4f", -function () { -var theta = 2 * Math.acos (Math.abs (this.q0)); -var sinTheta2 = Math.sin (theta / 2); -var v = this.getNormal (); -if (sinTheta2 < 0) { -v.scale (-1); -theta = 3.141592653589793 - theta; -}return javajs.util.A4.newVA (v, theta); -}); -Clazz.defineMethod (c$, "transform2", -function (pt, ptNew) { -if (this.mat == null) this.setMatrix (); -this.mat.rotate2 (pt, ptNew); -return ptNew; -}, "javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "leftDifference", -function (q2) { -var q2adjusted = (this.dot (q2) < 0 ? q2.negate () : q2); -return this.inv ().mulQ (q2adjusted); -}, "javajs.util.Quat"); -Clazz.defineMethod (c$, "rightDifference", -function (q2) { -var q2adjusted = (this.dot (q2) < 0 ? q2.negate () : q2); -return this.mulQ (q2adjusted.inv ()); -}, "javajs.util.Quat"); -Clazz.overrideMethod (c$, "toString", -function () { -return "{" + this.q1 + " " + this.q2 + " " + this.q3 + " " + this.q0 + "}"; -}); -c$.div = Clazz.defineMethod (c$, "div", -function (data1, data2, nMax, isRelative) { -var n; -if (data1 == null || data2 == null || (n = Math.min (data1.length, data2.length)) == 0) return null; -if (nMax > 0 && n > nMax) n = nMax; -var dqs = new Array (n); -for (var i = 0; i < n; i++) { -if (data1[i] == null || data2[i] == null) return null; -dqs[i] = (isRelative ? data1[i].divLeft (data2[i]) : data1[i].div (data2[i])); -} -return dqs; -}, "~A,~A,~N,~B"); -c$.sphereMean = Clazz.defineMethod (c$, "sphereMean", -function (data, retStddev, criterion) { -if (data == null || data.length == 0) return new javajs.util.Quat (); -if (retStddev == null) retStddev = Clazz.newFloatArray (1, 0); -if (data.length == 1) { -retStddev[0] = 0; -return javajs.util.Quat.newQ (data[0]); -}var diff = 3.4028235E38; -var lastStddev = 3.4028235E38; -var qMean = javajs.util.Quat.simpleAverage (data); -var maxIter = 100; -var iter = 0; -while (diff > criterion && lastStddev != 0 && iter < maxIter) { -qMean = javajs.util.Quat.newMean (data, qMean); -retStddev[0] = javajs.util.Quat.stdDev (data, qMean); -diff = Math.abs (retStddev[0] - lastStddev); -lastStddev = retStddev[0]; -} -return qMean; -}, "~A,~A,~N"); -c$.simpleAverage = Clazz.defineMethod (c$, "simpleAverage", -($fz = function (ndata) { -var mean = javajs.util.V3.new3 (0, 0, 1); -var v = ndata[0].getNormal (); -mean.add (v); -for (var i = ndata.length; --i >= 0; ) mean.add (ndata[i].getNormalDirected (mean)); - -mean.sub (v); -mean.normalize (); -var f = 0; -for (var i = ndata.length; --i >= 0; ) f += Math.abs (ndata[i].get3dProjection (v).dot (mean)); - -if (f != 0) mean.scale (f / ndata.length); -f = Math.sqrt (1 - mean.lengthSquared ()); -if (Float.isNaN (f)) f = 0; -return javajs.util.Quat.newP4 (javajs.util.P4.new4 (mean.x, mean.y, mean.z, f)); -}, $fz.isPrivate = true, $fz), "~A"); -c$.newMean = Clazz.defineMethod (c$, "newMean", -($fz = function (data, mean) { -var sum = new javajs.util.V3 (); -var v; -var q; -var dq; -for (var i = data.length; --i >= 0; ) { -q = data[i]; -dq = q.div (mean); -v = dq.getNormal (); -v.scale (dq.getTheta ()); -sum.add (v); -} -sum.scale (1 / data.length); -var dqMean = javajs.util.Quat.newVA (sum, sum.length ()); -return dqMean.mulQ (mean); -}, $fz.isPrivate = true, $fz), "~A,javajs.util.Quat"); -c$.stdDev = Clazz.defineMethod (c$, "stdDev", -($fz = function (data, mean) { -var sum2 = 0; -var n = data.length; -for (var i = n; --i >= 0; ) { -var theta = data[i].div (mean).getTheta (); -sum2 += theta * theta; -} -return Math.sqrt (sum2 / n); -}, $fz.isPrivate = true, $fz), "~A,javajs.util.Quat"); -Clazz.defineMethod (c$, "getEulerZYZ", -function () { -var rA; -var rB; -var rG; -if (this.q1 == 0 && this.q2 == 0) { -var theta = this.getTheta (); -return Clazz.newFloatArray (-1, [this.q3 < 0 ? -theta : theta, 0, 0]); -}rA = Math.atan2 (2 * (this.q2 * this.q3 + this.q0 * this.q1), 2 * (-this.q1 * this.q3 + this.q0 * this.q2)); -rB = Math.acos (this.q3 * this.q3 - this.q2 * this.q2 - this.q1 * this.q1 + this.q0 * this.q0); -rG = Math.atan2 (2 * (this.q2 * this.q3 - this.q0 * this.q1), 2 * (this.q0 * this.q2 + this.q1 * this.q3)); -return Clazz.newFloatArray (-1, [(rA / 0.017453292519943295), (rB / 0.017453292519943295), (rG / 0.017453292519943295)]); -}); -Clazz.defineMethod (c$, "getEulerZXZ", -function () { -var rA; -var rB; -var rG; -if (this.q1 == 0 && this.q2 == 0) { -var theta = this.getTheta (); -return Clazz.newFloatArray (-1, [this.q3 < 0 ? -theta : theta, 0, 0]); -}rA = Math.atan2 (2 * (this.q1 * this.q3 - this.q0 * this.q2), 2 * (this.q0 * this.q1 + this.q2 * this.q3)); -rB = Math.acos (this.q3 * this.q3 - this.q2 * this.q2 - this.q1 * this.q1 + this.q0 * this.q0); -rG = Math.atan2 (2 * (this.q1 * this.q3 + this.q0 * this.q2), 2 * (-this.q2 * this.q3 + this.q0 * this.q1)); -return Clazz.newFloatArray (-1, [(rA / 0.017453292519943295), (rB / 0.017453292519943295), (rG / 0.017453292519943295)]); -}); -c$.qZero = c$.prototype.qZero = new javajs.util.P4 (); -Clazz.defineStatics (c$, -"RAD_PER_DEG", 0.017453292519943295); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.P4"], "javajs.util.Quat", ["java.lang.Float", "javajs.util.A4", "$.M3", "$.V3"], function () { +c$ = Clazz.decorateAsClass (function () { +this.q0 = 0; +this.q1 = 0; +this.q2 = 0; +this.q3 = 0; +this.mat = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "Quat"); +Clazz.makeConstructor (c$, +function () { +this.q0 = 1; +}); +c$.newQ = Clazz.defineMethod (c$, "newQ", +function (q) { +var q1 = new javajs.util.Quat (); +q1.set (q); +return q1; +}, "javajs.util.Quat"); +c$.newVA = Clazz.defineMethod (c$, "newVA", +function (v, theta) { +var q = new javajs.util.Quat (); +q.setTA (v, theta); +return q; +}, "javajs.util.T3,~N"); +c$.newM = Clazz.defineMethod (c$, "newM", +function (mat) { +var q = new javajs.util.Quat (); +q.setM (javajs.util.M3.newM3 (mat)); +return q; +}, "javajs.util.M3"); +c$.newAA = Clazz.defineMethod (c$, "newAA", +function (a) { +var q = new javajs.util.Quat (); +q.setAA (a); +return q; +}, "javajs.util.A4"); +c$.newP4 = Clazz.defineMethod (c$, "newP4", +function (pt) { +var q = new javajs.util.Quat (); +q.setP4 (pt); +return q; +}, "javajs.util.P4"); +c$.new4 = Clazz.defineMethod (c$, "new4", +function (q1, q2, q3, q0) { +var q = new javajs.util.Quat (); +if (q0 < -1) { +q.q0 = -1; +return q; +}if (q0 > 1) { +q.q0 = 1; +return q; +}q.q0 = q0; +q.q1 = q1; +q.q2 = q2; +q.q3 = q3; +return q; +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "set", +function (q) { +this.q0 = q.q0; +this.q1 = q.q1; +this.q2 = q.q2; +this.q3 = q.q3; +}, "javajs.util.Quat"); +Clazz.defineMethod (c$, "setP4", +($fz = function (pt) { +var factor = (pt == null ? 0 : pt.distance4 (javajs.util.Quat.qZero)); +if (factor == 0) { +this.q0 = 1; +return; +}this.q0 = pt.w / factor; +this.q1 = pt.x / factor; +this.q2 = pt.y / factor; +this.q3 = pt.z / factor; +}, $fz.isPrivate = true, $fz), "javajs.util.P4"); +Clazz.defineMethod (c$, "setTA", +function (pt, theta) { +if (pt.x == 0 && pt.y == 0 && pt.z == 0) { +this.q0 = 1; +return; +}var fact = (Math.sin (theta / 2 * 0.017453292519943295) / Math.sqrt (pt.x * pt.x + pt.y * pt.y + pt.z * pt.z)); +this.q0 = (Math.cos (theta / 2 * 0.017453292519943295)); +this.q1 = (pt.x * fact); +this.q2 = (pt.y * fact); +this.q3 = (pt.z * fact); +}, "javajs.util.T3,~N"); +Clazz.defineMethod (c$, "setAA", +function (a) { +var aa = javajs.util.A4.newAA (a); +if (aa.angle == 0) aa.y = 1; +this.setM ( new javajs.util.M3 ().setAA (aa)); +}, "javajs.util.A4"); +Clazz.defineMethod (c$, "setM", +($fz = function (mat) { +this.mat = mat; +var trace = mat.m00 + mat.m11 + mat.m22; +var temp; +var w; +var x; +var y; +var z; +if (trace >= 0.5) { +w = Math.sqrt (1.0 + trace); +x = (mat.m21 - mat.m12) / w; +y = (mat.m02 - mat.m20) / w; +z = (mat.m10 - mat.m01) / w; +} else if ((temp = mat.m00 + mat.m00 - trace) >= 0.5) { +x = Math.sqrt (1.0 + temp); +w = (mat.m21 - mat.m12) / x; +y = (mat.m10 + mat.m01) / x; +z = (mat.m20 + mat.m02) / x; +} else if ((temp = mat.m11 + mat.m11 - trace) >= 0.5 || mat.m11 > mat.m22) { +y = Math.sqrt (1.0 + temp); +w = (mat.m02 - mat.m20) / y; +x = (mat.m10 + mat.m01) / y; +z = (mat.m21 + mat.m12) / y; +} else { +z = Math.sqrt (1.0 + mat.m22 + mat.m22 - trace); +w = (mat.m10 - mat.m01) / z; +x = (mat.m20 + mat.m02) / z; +y = (mat.m21 + mat.m12) / z; +}this.q0 = (w * 0.5); +this.q1 = (x * 0.5); +this.q2 = (y * 0.5); +this.q3 = (z * 0.5); +}, $fz.isPrivate = true, $fz), "javajs.util.M3"); +Clazz.defineMethod (c$, "setRef", +function (qref) { +if (qref == null) { +this.mul (this.getFixFactor ()); +return; +}if (this.dot (qref) >= 0) return; +this.q0 *= -1; +this.q1 *= -1; +this.q2 *= -1; +this.q3 *= -1; +}, "javajs.util.Quat"); +c$.getQuaternionFrame = Clazz.defineMethod (c$, "getQuaternionFrame", +function (center, x, xy) { +var vA = javajs.util.V3.newV (x); +var vB = javajs.util.V3.newV (xy); +if (center != null) { +vA.sub (center); +vB.sub (center); +}return javajs.util.Quat.getQuaternionFrameV (vA, vB, null, false); +}, "javajs.util.P3,javajs.util.T3,javajs.util.T3"); +c$.getQuaternionFrameV = Clazz.defineMethod (c$, "getQuaternionFrameV", +function (vA, vB, vC, yBased) { +if (vC == null) { +vC = new javajs.util.V3 (); +vC.cross (vA, vB); +if (yBased) vA.cross (vB, vC); +}var vBprime = new javajs.util.V3 (); +vBprime.cross (vC, vA); +vA.normalize (); +vBprime.normalize (); +vC.normalize (); +var mat = new javajs.util.M3 (); +mat.setColumnV (0, vA); +mat.setColumnV (1, vBprime); +mat.setColumnV (2, vC); +var q = javajs.util.Quat.newM (mat); +return q; +}, "javajs.util.V3,javajs.util.V3,javajs.util.V3,~B"); +Clazz.defineMethod (c$, "getMatrix", +function () { +if (this.mat == null) this.setMatrix (); +return this.mat; +}); +Clazz.defineMethod (c$, "setMatrix", +($fz = function () { +this.mat = new javajs.util.M3 (); +this.mat.m00 = this.q0 * this.q0 + this.q1 * this.q1 - this.q2 * this.q2 - this.q3 * this.q3; +this.mat.m01 = 2 * this.q1 * this.q2 - 2 * this.q0 * this.q3; +this.mat.m02 = 2 * this.q1 * this.q3 + 2 * this.q0 * this.q2; +this.mat.m10 = 2 * this.q1 * this.q2 + 2 * this.q0 * this.q3; +this.mat.m11 = this.q0 * this.q0 - this.q1 * this.q1 + this.q2 * this.q2 - this.q3 * this.q3; +this.mat.m12 = 2 * this.q2 * this.q3 - 2 * this.q0 * this.q1; +this.mat.m20 = 2 * this.q1 * this.q3 - 2 * this.q0 * this.q2; +this.mat.m21 = 2 * this.q2 * this.q3 + 2 * this.q0 * this.q1; +this.mat.m22 = this.q0 * this.q0 - this.q1 * this.q1 - this.q2 * this.q2 + this.q3 * this.q3; +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "add", +function (x) { +return javajs.util.Quat.newVA (this.getNormal (), this.getTheta () + x); +}, "~N"); +Clazz.defineMethod (c$, "mul", +function (x) { +return (x == 1 ? javajs.util.Quat.new4 (this.q1, this.q2, this.q3, this.q0) : javajs.util.Quat.newVA (this.getNormal (), this.getTheta () * x)); +}, "~N"); +Clazz.defineMethod (c$, "mulQ", +function (p) { +return javajs.util.Quat.new4 (this.q0 * p.q1 + this.q1 * p.q0 + this.q2 * p.q3 - this.q3 * p.q2, this.q0 * p.q2 + this.q2 * p.q0 + this.q3 * p.q1 - this.q1 * p.q3, this.q0 * p.q3 + this.q3 * p.q0 + this.q1 * p.q2 - this.q2 * p.q1, this.q0 * p.q0 - this.q1 * p.q1 - this.q2 * p.q2 - this.q3 * p.q3); +}, "javajs.util.Quat"); +Clazz.defineMethod (c$, "div", +function (p) { +return this.mulQ (p.inv ()); +}, "javajs.util.Quat"); +Clazz.defineMethod (c$, "divLeft", +function (p) { +return this.inv ().mulQ (p); +}, "javajs.util.Quat"); +Clazz.defineMethod (c$, "dot", +function (q) { +return this.q0 * q.q0 + this.q1 * q.q1 + this.q2 * q.q2 + this.q3 * q.q3; +}, "javajs.util.Quat"); +Clazz.defineMethod (c$, "inv", +function () { +return javajs.util.Quat.new4 (-this.q1, -this.q2, -this.q3, this.q0); +}); +Clazz.defineMethod (c$, "negate", +function () { +return javajs.util.Quat.new4 (-this.q1, -this.q2, -this.q3, -this.q0); +}); +Clazz.defineMethod (c$, "getFixFactor", +($fz = function () { +return (this.q0 < 0 || this.q0 == 0 && (this.q1 < 0 || this.q1 == 0 && (this.q2 < 0 || this.q2 == 0 && this.q3 < 0)) ? -1 : 1); +}, $fz.isPrivate = true, $fz)); +Clazz.defineMethod (c$, "getVector", +function (i) { +return this.getVectorScaled (i, 1); +}, "~N"); +Clazz.defineMethod (c$, "getVectorScaled", +function (i, scale) { +if (i == -1) { +scale *= this.getFixFactor (); +return javajs.util.V3.new3 (this.q1 * scale, this.q2 * scale, this.q3 * scale); +}if (this.mat == null) this.setMatrix (); +var v = new javajs.util.V3 (); +this.mat.getColumnV (i, v); +if (scale != 1) v.scale (scale); +return v; +}, "~N,~N"); +Clazz.defineMethod (c$, "getNormal", +function () { +var v = javajs.util.Quat.getRawNormal (this); +v.scale (this.getFixFactor ()); +return v; +}); +c$.getRawNormal = Clazz.defineMethod (c$, "getRawNormal", +($fz = function (q) { +var v = javajs.util.V3.new3 (q.q1, q.q2, q.q3); +if (v.length () == 0) return javajs.util.V3.new3 (0, 0, 1); +v.normalize (); +return v; +}, $fz.isPrivate = true, $fz), "javajs.util.Quat"); +Clazz.defineMethod (c$, "getTheta", +function () { +return (Math.acos (Math.abs (this.q0)) * 2 * 180 / 3.141592653589793); +}); +Clazz.defineMethod (c$, "getThetaRadians", +function () { +return (Math.acos (Math.abs (this.q0)) * 2); +}); +Clazz.defineMethod (c$, "getNormalDirected", +function (v0) { +var v = this.getNormal (); +if (v.x * v0.x + v.y * v0.y + v.z * v0.z < 0) { +v.scale (-1); +}return v; +}, "javajs.util.V3"); +Clazz.defineMethod (c$, "get3dProjection", +function (v3d) { +v3d.set (this.q1, this.q2, this.q3); +return v3d; +}, "javajs.util.V3"); +Clazz.defineMethod (c$, "getThetaDirected", +function (axisAngle) { +var theta = this.getTheta (); +var v = this.getNormal (); +if (axisAngle.x * this.q1 + axisAngle.y * this.q2 + axisAngle.z * this.q3 < 0) { +v.scale (-1); +theta = -theta; +}axisAngle.set4 (v.x, v.y, v.z, theta); +return axisAngle; +}, "javajs.util.P4"); +Clazz.defineMethod (c$, "getThetaDirectedV", +function (vector) { +var theta = this.getTheta (); +var v = this.getNormal (); +if (vector.x * this.q1 + vector.y * this.q2 + vector.z * this.q3 < 0) { +v.scale (-1); +theta = -theta; +}return theta; +}, "javajs.util.V3"); +Clazz.defineMethod (c$, "toPoint4f", +function () { +return javajs.util.P4.new4 (this.q1, this.q2, this.q3, this.q0); +}); +Clazz.defineMethod (c$, "toAxisAngle4f", +function () { +var theta = 2 * Math.acos (Math.abs (this.q0)); +var sinTheta2 = Math.sin (theta / 2); +var v = this.getNormal (); +if (sinTheta2 < 0) { +v.scale (-1); +theta = 3.141592653589793 - theta; +}return javajs.util.A4.newVA (v, theta); +}); +Clazz.defineMethod (c$, "transform2", +function (pt, ptNew) { +if (this.mat == null) this.setMatrix (); +this.mat.rotate2 (pt, ptNew); +return ptNew; +}, "javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "leftDifference", +function (q2) { +var q2adjusted = (this.dot (q2) < 0 ? q2.negate () : q2); +return this.inv ().mulQ (q2adjusted); +}, "javajs.util.Quat"); +Clazz.defineMethod (c$, "rightDifference", +function (q2) { +var q2adjusted = (this.dot (q2) < 0 ? q2.negate () : q2); +return this.mulQ (q2adjusted.inv ()); +}, "javajs.util.Quat"); +Clazz.overrideMethod (c$, "toString", +function () { +return "{" + this.q1 + " " + this.q2 + " " + this.q3 + " " + this.q0 + "}"; +}); +c$.div = Clazz.defineMethod (c$, "div", +function (data1, data2, nMax, isRelative) { +var n; +if (data1 == null || data2 == null || (n = Math.min (data1.length, data2.length)) == 0) return null; +if (nMax > 0 && n > nMax) n = nMax; +var dqs = new Array (n); +for (var i = 0; i < n; i++) { +if (data1[i] == null || data2[i] == null) return null; +dqs[i] = (isRelative ? data1[i].divLeft (data2[i]) : data1[i].div (data2[i])); +} +return dqs; +}, "~A,~A,~N,~B"); +c$.sphereMean = Clazz.defineMethod (c$, "sphereMean", +function (data, retStddev, criterion) { +if (data == null || data.length == 0) return new javajs.util.Quat (); +if (retStddev == null) retStddev = Clazz.newFloatArray (1, 0); +if (data.length == 1) { +retStddev[0] = 0; +return javajs.util.Quat.newQ (data[0]); +}var diff = 3.4028235E38; +var lastStddev = 3.4028235E38; +var qMean = javajs.util.Quat.simpleAverage (data); +var maxIter = 100; +var iter = 0; +while (diff > criterion && lastStddev != 0 && iter < maxIter) { +qMean = javajs.util.Quat.newMean (data, qMean); +retStddev[0] = javajs.util.Quat.stdDev (data, qMean); +diff = Math.abs (retStddev[0] - lastStddev); +lastStddev = retStddev[0]; +} +return qMean; +}, "~A,~A,~N"); +c$.simpleAverage = Clazz.defineMethod (c$, "simpleAverage", +($fz = function (ndata) { +var mean = javajs.util.V3.new3 (0, 0, 1); +var v = ndata[0].getNormal (); +mean.add (v); +for (var i = ndata.length; --i >= 0; ) mean.add (ndata[i].getNormalDirected (mean)); + +mean.sub (v); +mean.normalize (); +var f = 0; +for (var i = ndata.length; --i >= 0; ) f += Math.abs (ndata[i].get3dProjection (v).dot (mean)); + +if (f != 0) mean.scale (f / ndata.length); +f = Math.sqrt (1 - mean.lengthSquared ()); +if (Float.isNaN (f)) f = 0; +return javajs.util.Quat.newP4 (javajs.util.P4.new4 (mean.x, mean.y, mean.z, f)); +}, $fz.isPrivate = true, $fz), "~A"); +c$.newMean = Clazz.defineMethod (c$, "newMean", +($fz = function (data, mean) { +var sum = new javajs.util.V3 (); +var v; +var q; +var dq; +for (var i = data.length; --i >= 0; ) { +q = data[i]; +dq = q.div (mean); +v = dq.getNormal (); +v.scale (dq.getTheta ()); +sum.add (v); +} +sum.scale (1 / data.length); +var dqMean = javajs.util.Quat.newVA (sum, sum.length ()); +return dqMean.mulQ (mean); +}, $fz.isPrivate = true, $fz), "~A,javajs.util.Quat"); +c$.stdDev = Clazz.defineMethod (c$, "stdDev", +($fz = function (data, mean) { +var sum2 = 0; +var n = data.length; +for (var i = n; --i >= 0; ) { +var theta = data[i].div (mean).getTheta (); +sum2 += theta * theta; +} +return Math.sqrt (sum2 / n); +}, $fz.isPrivate = true, $fz), "~A,javajs.util.Quat"); +Clazz.defineMethod (c$, "getEulerZYZ", +function () { +var rA; +var rB; +var rG; +if (this.q1 == 0 && this.q2 == 0) { +var theta = this.getTheta (); +return Clazz.newFloatArray (-1, [this.q3 < 0 ? -theta : theta, 0, 0]); +}rA = Math.atan2 (2 * (this.q2 * this.q3 + this.q0 * this.q1), 2 * (-this.q1 * this.q3 + this.q0 * this.q2)); +rB = Math.acos (this.q3 * this.q3 - this.q2 * this.q2 - this.q1 * this.q1 + this.q0 * this.q0); +rG = Math.atan2 (2 * (this.q2 * this.q3 - this.q0 * this.q1), 2 * (this.q0 * this.q2 + this.q1 * this.q3)); +return Clazz.newFloatArray (-1, [(rA / 0.017453292519943295), (rB / 0.017453292519943295), (rG / 0.017453292519943295)]); +}); +Clazz.defineMethod (c$, "getEulerZXZ", +function () { +var rA; +var rB; +var rG; +if (this.q1 == 0 && this.q2 == 0) { +var theta = this.getTheta (); +return Clazz.newFloatArray (-1, [this.q3 < 0 ? -theta : theta, 0, 0]); +}rA = Math.atan2 (2 * (this.q1 * this.q3 - this.q0 * this.q2), 2 * (this.q0 * this.q1 + this.q2 * this.q3)); +rB = Math.acos (this.q3 * this.q3 - this.q2 * this.q2 - this.q1 * this.q1 + this.q0 * this.q0); +rG = Math.atan2 (2 * (this.q1 * this.q3 + this.q0 * this.q2), 2 * (-this.q2 * this.q3 + this.q0 * this.q1)); +return Clazz.newFloatArray (-1, [(rA / 0.017453292519943295), (rB / 0.017453292519943295), (rG / 0.017453292519943295)]); +}); +c$.qZero = c$.prototype.qZero = new javajs.util.P4 (); +Clazz.defineStatics (c$, +"RAD_PER_DEG", 0.017453292519943295); +}); diff --git a/bin/javajs/util/Rdr.class b/bin/javajs/util/Rdr.class index 2611f4e..0617f27 100644 Binary files a/bin/javajs/util/Rdr.class and b/bin/javajs/util/Rdr.class differ diff --git a/bin/javajs/util/Rdr.js b/bin/javajs/util/Rdr.js index 6f65dc5..45a14ab 100644 --- a/bin/javajs/util/Rdr.js +++ b/bin/javajs/util/Rdr.js @@ -1,311 +1,311 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.GenericLineReader"], "javajs.util.Rdr", ["java.io.BufferedInputStream", "$.BufferedReader", "$.ByteArrayInputStream", "$.InputStreamReader", "$.StringReader", "javajs.util.AU", "$.Base64", "$.Encoding", "$.SB"], function () { -c$ = Clazz.decorateAsClass (function () { -this.reader = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "Rdr", null, javajs.api.GenericLineReader); -Clazz.makeConstructor (c$, -function (reader) { -this.reader = reader; -}, "java.io.BufferedReader"); -Clazz.overrideMethod (c$, "readNextLine", -function () { -return this.reader.readLine (); -}); -c$.readCifData = Clazz.defineMethod (c$, "readCifData", -function (parser, br) { -return parser.set (null, br).getAllCifData (); -}, "javajs.api.GenericCifDataParser,java.io.BufferedReader"); -c$.fixUTF = Clazz.defineMethod (c$, "fixUTF", -function (bytes) { -var encoding = javajs.util.Rdr.getUTFEncoding (bytes); -if (encoding !== javajs.util.Encoding.NONE) try { -var s = String.instantialize (bytes, encoding.name ().$replace ('_', '-')); -switch (encoding) { -case javajs.util.Encoding.UTF8: -case javajs.util.Encoding.UTF_16BE: -case javajs.util.Encoding.UTF_16LE: -s = s.substring (1); -break; -default: -break; -} -return s; -} catch (e) { -if (Clazz.exceptionOf (e, java.io.UnsupportedEncodingException)) { -System.out.println (e); -} else { -throw e; -} -} -return String.instantialize (bytes); -}, "~A"); -c$.getUTFEncoding = Clazz.defineMethod (c$, "getUTFEncoding", -($fz = function (bytes) { -if (bytes.length >= 3 && bytes[0] == 0xEF && bytes[1] == 0xBB && bytes[2] == 0xBF) return javajs.util.Encoding.UTF8; -if (bytes.length >= 4 && bytes[0] == 0 && bytes[1] == 0 && bytes[2] == 0xFE && bytes[3] == 0xFF) return javajs.util.Encoding.UTF_32BE; -if (bytes.length >= 4 && bytes[0] == 0xFF && bytes[1] == 0xFE && bytes[2] == 0 && bytes[3] == 0) return javajs.util.Encoding.UTF_32LE; -if (bytes.length >= 2 && bytes[0] == 0xFF && bytes[1] == 0xFE) return javajs.util.Encoding.UTF_16LE; -if (bytes.length >= 2 && bytes[0] == 0xFE && bytes[1] == 0xFF) return javajs.util.Encoding.UTF_16BE; -return javajs.util.Encoding.NONE; -}, $fz.isPrivate = true, $fz), "~A"); -c$.getUTFEncodingForStream = Clazz.defineMethod (c$, "getUTFEncodingForStream", -($fz = function (is) { -{ -is.resetStream(); -}var abMagic = Clazz.newByteArray (4, 0); -abMagic[3] = 1; -try { -is.mark (5); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -return javajs.util.Encoding.NONE; -} else { -throw e; -} -} -is.read (abMagic, 0, 4); -is.reset (); -return javajs.util.Rdr.getUTFEncoding (abMagic); -}, $fz.isPrivate = true, $fz), "java.io.BufferedInputStream"); -c$.isBase64 = Clazz.defineMethod (c$, "isBase64", -function (sb) { -return (sb.indexOf (";base64,") == 0); -}, "javajs.util.SB"); -c$.isCompoundDocumentS = Clazz.defineMethod (c$, "isCompoundDocumentS", -function (is) { -return javajs.util.Rdr.isCompoundDocumentB (javajs.util.Rdr.getMagic (is, 8)); -}, "java.io.InputStream"); -c$.isCompoundDocumentB = Clazz.defineMethod (c$, "isCompoundDocumentB", -function (bytes) { -return (bytes.length >= 8 && bytes[0] == 0xD0 && bytes[1] == 0xCF && bytes[2] == 0x11 && bytes[3] == 0xE0 && bytes[4] == 0xA1 && bytes[5] == 0xB1 && bytes[6] == 0x1A && bytes[7] == 0xE1); -}, "~A"); -c$.isGzipS = Clazz.defineMethod (c$, "isGzipS", -function (is) { -return javajs.util.Rdr.isGzipB (javajs.util.Rdr.getMagic (is, 2)); -}, "java.io.InputStream"); -c$.isGzipB = Clazz.defineMethod (c$, "isGzipB", -function (bytes) { -return (bytes != null && bytes.length >= 2 && bytes[0] == 0x1F && bytes[1] == 0x8B); -}, "~A"); -c$.isPickleS = Clazz.defineMethod (c$, "isPickleS", -function (is) { -return javajs.util.Rdr.isPickleB (javajs.util.Rdr.getMagic (is, 2)); -}, "java.io.InputStream"); -c$.isPickleB = Clazz.defineMethod (c$, "isPickleB", -function (bytes) { -return (bytes != null && bytes.length >= 2 && bytes[0] == 0x7D && bytes[1] == 0x71); -}, "~A"); -c$.isPngZipStream = Clazz.defineMethod (c$, "isPngZipStream", -function (is) { -return javajs.util.Rdr.isPngZipB (javajs.util.Rdr.getMagic (is, 55)); -}, "java.io.InputStream"); -c$.isPngZipB = Clazz.defineMethod (c$, "isPngZipB", -function (bytes) { -return (bytes[50] == 0 && bytes[51] == 0x50 && bytes[52] == 0x4E && bytes[53] == 0x47 && bytes[54] == 0x4A); -}, "~A"); -c$.isZipS = Clazz.defineMethod (c$, "isZipS", -function (is) { -return javajs.util.Rdr.isZipB (javajs.util.Rdr.getMagic (is, 4)); -}, "java.io.InputStream"); -c$.isZipB = Clazz.defineMethod (c$, "isZipB", -function (bytes) { -return (bytes.length >= 4 && bytes[0] == 0x50 && bytes[1] == 0x4B && bytes[2] == 0x03 && bytes[3] == 0x04); -}, "~A"); -c$.getMagic = Clazz.defineMethod (c$, "getMagic", -($fz = function (is, n) { -var abMagic = Clazz.newByteArray (n, 0); -{ -is.resetStream(); -}try { -is.mark (n + 1); -is.read (abMagic, 0, n); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -try { -is.reset (); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -return abMagic; -}, $fz.isPrivate = true, $fz), "java.io.InputStream,~N"); -c$.guessMimeTypeForBytes = Clazz.defineMethod (c$, "guessMimeTypeForBytes", -function (bytes) { -switch (bytes.length < 2 ? -1 : bytes[1]) { -case 0: -return "image/jpg"; -case 0x49: -return "image/gif"; -case 0x4D: -return "image/BMP"; -case 0x50: -return "image/png"; -default: -return "image/unknown"; -} -}, "~A"); -c$.getBIS = Clazz.defineMethod (c$, "getBIS", -function (bytes) { -return new java.io.BufferedInputStream ( new java.io.ByteArrayInputStream (bytes)); -}, "~A"); -c$.getBR = Clazz.defineMethod (c$, "getBR", -function (string) { -return new java.io.BufferedReader ( new java.io.StringReader (string)); -}, "~S"); -c$.getUnzippedInputStream = Clazz.defineMethod (c$, "getUnzippedInputStream", -function (jzt, bis) { -while (javajs.util.Rdr.isGzipS (bis)) bis = new java.io.BufferedInputStream (jzt.newGZIPInputStream (bis)); - -return bis; -}, "javajs.api.GenericZipTools,java.io.BufferedInputStream"); -c$.getBytesFromSB = Clazz.defineMethod (c$, "getBytesFromSB", -function (sb) { -return (javajs.util.Rdr.isBase64 (sb) ? javajs.util.Base64.decodeBase64 (sb.substring (8)) : sb.toBytes (0, -1)); -}, "javajs.util.SB"); -c$.getStreamAsBytes = Clazz.defineMethod (c$, "getStreamAsBytes", -function (bis, out) { -var buf = Clazz.newByteArray (1024, 0); -var bytes = (out == null ? Clazz.newByteArray (4096, 0) : null); -var len = 0; -var totalLen = 0; -while ((len = bis.read (buf, 0, 1024)) > 0) { -totalLen += len; -if (out == null) { -if (totalLen >= bytes.length) bytes = javajs.util.AU.ensureLengthByte (bytes, totalLen * 2); -System.arraycopy (buf, 0, bytes, totalLen - len, len); -} else { -out.write (buf, 0, len); -}} -bis.close (); -if (out == null) { -return javajs.util.AU.arrayCopyByte (bytes, totalLen); -}return totalLen + " bytes"; -}, "java.io.BufferedInputStream,javajs.util.OC"); -c$.getBufferedReader = Clazz.defineMethod (c$, "getBufferedReader", -function (bis, charSet) { -if (javajs.util.Rdr.getUTFEncodingForStream (bis) === javajs.util.Encoding.NONE) return new java.io.BufferedReader ( new java.io.InputStreamReader (bis, (charSet == null ? "UTF-8" : charSet))); -var bytes = javajs.util.Rdr.getLimitedStreamBytes (bis, -1); -bis.close (); -return javajs.util.Rdr.getBR (charSet == null ? javajs.util.Rdr.fixUTF (bytes) : String.instantialize (bytes, charSet)); -}, "java.io.BufferedInputStream,~S"); -c$.getLimitedStreamBytes = Clazz.defineMethod (c$, "getLimitedStreamBytes", -function (is, n) { -var buflen = (n > 0 && n < 1024 ? n : 1024); -var buf = Clazz.newByteArray (buflen, 0); -var bytes = Clazz.newByteArray (n < 0 ? 4096 : n, 0); -var len = 0; -var totalLen = 0; -if (n < 0) n = 2147483647; -while (totalLen < n && (len = is.read (buf, 0, buflen)) > 0) { -totalLen += len; -if (totalLen > bytes.length) bytes = javajs.util.AU.ensureLengthByte (bytes, totalLen * 2); -System.arraycopy (buf, 0, bytes, totalLen - len, len); -if (n != 2147483647 && totalLen + buflen > bytes.length) buflen = bytes.length - totalLen; -} -if (totalLen == bytes.length) return bytes; -buf = Clazz.newByteArray (totalLen, 0); -System.arraycopy (bytes, 0, buf, 0, totalLen); -return buf; -}, "java.io.InputStream,~N"); -c$.StreamToUTF8String = Clazz.defineMethod (c$, "StreamToUTF8String", -function (bis) { -var data = new Array (1); -try { -javajs.util.Rdr.readAllAsString (javajs.util.Rdr.getBufferedReader (bis, "UTF-8"), -1, true, data, 0); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -} else { -throw e; -} -} -return data[0]; -}, "java.io.BufferedInputStream"); -c$.readAllAsString = Clazz.defineMethod (c$, "readAllAsString", -function (br, nBytesMax, allowBinary, data, i) { -try { -var sb = javajs.util.SB.newN (8192); -var line; -if (nBytesMax < 0) { -line = br.readLine (); -if (allowBinary || line != null && line.indexOf ('\0') < 0 && (line.length != 4 || line.charCodeAt (0) != 65533 || line.indexOf ("PNG") != 1)) { -sb.append (line).appendC ('\n'); -while ((line = br.readLine ()) != null) sb.append (line).appendC ('\n'); - -}} else { -var n = 0; -var len; -while (n < nBytesMax && (line = br.readLine ()) != null) { -if (nBytesMax - n < (len = line.length) + 1) line = line.substring (0, nBytesMax - n - 1); -sb.append (line).appendC ('\n'); -n += len + 1; -} -}br.close (); -data[i] = sb.toString (); -return true; -} catch (ioe) { -if (Clazz.exceptionOf (ioe, Exception)) { -data[i] = ioe.toString (); -return false; -} else { -throw ioe; -} -} -}, "java.io.BufferedReader,~N,~B,~A,~N"); -c$.getPngZipPointAndCount = Clazz.defineMethod (c$, "getPngZipPointAndCount", -function (bis, pt_count) { -bis.mark (75); -try { -var data = javajs.util.Rdr.getLimitedStreamBytes (bis, 74); -bis.reset (); -var pt = 0; -for (var i = 64, f = 1; --i > 54; f *= 10) pt += (data[i] - 48) * f; - -var n = 0; -for (var i = 74, f = 1; --i > 64; f *= 10) n += (data[i] - 48) * f; - -pt_count[0] = pt; -pt_count[1] = n; -} catch (e) { -pt_count[1] = 0; -} -}, "java.io.BufferedInputStream,~A"); -c$.getPngZipStream = Clazz.defineMethod (c$, "getPngZipStream", -function (bis, asNewStream) { -if (!javajs.util.Rdr.isPngZipStream (bis)) return bis; -var data = Clazz.newByteArray (0, 0); -bis.mark (75); -try { -var pt_count = Clazz.newIntArray (2, 0); -javajs.util.Rdr.getPngZipPointAndCount (bis, pt_count); -if (pt_count[1] != 0) { -var pt = pt_count[0]; -while (pt > 0) pt -= bis.skip (pt); - -if (!asNewStream) return bis; -data = javajs.util.Rdr.getLimitedStreamBytes (bis, pt_count[1]); -}} catch (e) { -} finally { -try { -if (asNewStream) bis.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -} -return javajs.util.Rdr.getBIS (data); -}, "java.io.BufferedInputStream,~B"); -c$.getZipRoot = Clazz.defineMethod (c$, "getZipRoot", -function (fileName) { -var pt = fileName.indexOf ("|"); -return (pt < 0 ? fileName : fileName.substring (0, pt)); -}, "~S"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.GenericLineReader"], "javajs.util.Rdr", ["java.io.BufferedInputStream", "$.BufferedReader", "$.ByteArrayInputStream", "$.InputStreamReader", "$.StringReader", "javajs.util.AU", "$.Base64", "$.Encoding", "$.SB"], function () { +c$ = Clazz.decorateAsClass (function () { +this.reader = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "Rdr", null, javajs.api.GenericLineReader); +Clazz.makeConstructor (c$, +function (reader) { +this.reader = reader; +}, "java.io.BufferedReader"); +Clazz.overrideMethod (c$, "readNextLine", +function () { +return this.reader.readLine (); +}); +c$.readCifData = Clazz.defineMethod (c$, "readCifData", +function (parser, br) { +return parser.set (null, br).getAllCifData (); +}, "javajs.api.GenericCifDataParser,java.io.BufferedReader"); +c$.fixUTF = Clazz.defineMethod (c$, "fixUTF", +function (bytes) { +var encoding = javajs.util.Rdr.getUTFEncoding (bytes); +if (encoding !== javajs.util.Encoding.NONE) try { +var s = String.instantialize (bytes, encoding.name ().$replace ('_', '-')); +switch (encoding) { +case javajs.util.Encoding.UTF8: +case javajs.util.Encoding.UTF_16BE: +case javajs.util.Encoding.UTF_16LE: +s = s.substring (1); +break; +default: +break; +} +return s; +} catch (e) { +if (Clazz.exceptionOf (e, java.io.UnsupportedEncodingException)) { +System.out.println (e); +} else { +throw e; +} +} +return String.instantialize (bytes); +}, "~A"); +c$.getUTFEncoding = Clazz.defineMethod (c$, "getUTFEncoding", +($fz = function (bytes) { +if (bytes.length >= 3 && bytes[0] == 0xEF && bytes[1] == 0xBB && bytes[2] == 0xBF) return javajs.util.Encoding.UTF8; +if (bytes.length >= 4 && bytes[0] == 0 && bytes[1] == 0 && bytes[2] == 0xFE && bytes[3] == 0xFF) return javajs.util.Encoding.UTF_32BE; +if (bytes.length >= 4 && bytes[0] == 0xFF && bytes[1] == 0xFE && bytes[2] == 0 && bytes[3] == 0) return javajs.util.Encoding.UTF_32LE; +if (bytes.length >= 2 && bytes[0] == 0xFF && bytes[1] == 0xFE) return javajs.util.Encoding.UTF_16LE; +if (bytes.length >= 2 && bytes[0] == 0xFE && bytes[1] == 0xFF) return javajs.util.Encoding.UTF_16BE; +return javajs.util.Encoding.NONE; +}, $fz.isPrivate = true, $fz), "~A"); +c$.getUTFEncodingForStream = Clazz.defineMethod (c$, "getUTFEncodingForStream", +($fz = function (is) { +{ +is.resetStream(); +}var abMagic = Clazz.newByteArray (4, 0); +abMagic[3] = 1; +try { +is.mark (5); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +return javajs.util.Encoding.NONE; +} else { +throw e; +} +} +is.read (abMagic, 0, 4); +is.reset (); +return javajs.util.Rdr.getUTFEncoding (abMagic); +}, $fz.isPrivate = true, $fz), "java.io.BufferedInputStream"); +c$.isBase64 = Clazz.defineMethod (c$, "isBase64", +function (sb) { +return (sb.indexOf (";base64,") == 0); +}, "javajs.util.SB"); +c$.isCompoundDocumentS = Clazz.defineMethod (c$, "isCompoundDocumentS", +function (is) { +return javajs.util.Rdr.isCompoundDocumentB (javajs.util.Rdr.getMagic (is, 8)); +}, "java.io.InputStream"); +c$.isCompoundDocumentB = Clazz.defineMethod (c$, "isCompoundDocumentB", +function (bytes) { +return (bytes.length >= 8 && bytes[0] == 0xD0 && bytes[1] == 0xCF && bytes[2] == 0x11 && bytes[3] == 0xE0 && bytes[4] == 0xA1 && bytes[5] == 0xB1 && bytes[6] == 0x1A && bytes[7] == 0xE1); +}, "~A"); +c$.isGzipS = Clazz.defineMethod (c$, "isGzipS", +function (is) { +return javajs.util.Rdr.isGzipB (javajs.util.Rdr.getMagic (is, 2)); +}, "java.io.InputStream"); +c$.isGzipB = Clazz.defineMethod (c$, "isGzipB", +function (bytes) { +return (bytes != null && bytes.length >= 2 && bytes[0] == 0x1F && bytes[1] == 0x8B); +}, "~A"); +c$.isPickleS = Clazz.defineMethod (c$, "isPickleS", +function (is) { +return javajs.util.Rdr.isPickleB (javajs.util.Rdr.getMagic (is, 2)); +}, "java.io.InputStream"); +c$.isPickleB = Clazz.defineMethod (c$, "isPickleB", +function (bytes) { +return (bytes != null && bytes.length >= 2 && bytes[0] == 0x7D && bytes[1] == 0x71); +}, "~A"); +c$.isPngZipStream = Clazz.defineMethod (c$, "isPngZipStream", +function (is) { +return javajs.util.Rdr.isPngZipB (javajs.util.Rdr.getMagic (is, 55)); +}, "java.io.InputStream"); +c$.isPngZipB = Clazz.defineMethod (c$, "isPngZipB", +function (bytes) { +return (bytes[50] == 0 && bytes[51] == 0x50 && bytes[52] == 0x4E && bytes[53] == 0x47 && bytes[54] == 0x4A); +}, "~A"); +c$.isZipS = Clazz.defineMethod (c$, "isZipS", +function (is) { +return javajs.util.Rdr.isZipB (javajs.util.Rdr.getMagic (is, 4)); +}, "java.io.InputStream"); +c$.isZipB = Clazz.defineMethod (c$, "isZipB", +function (bytes) { +return (bytes.length >= 4 && bytes[0] == 0x50 && bytes[1] == 0x4B && bytes[2] == 0x03 && bytes[3] == 0x04); +}, "~A"); +c$.getMagic = Clazz.defineMethod (c$, "getMagic", +($fz = function (is, n) { +var abMagic = Clazz.newByteArray (n, 0); +{ +is.resetStream(); +}try { +is.mark (n + 1); +is.read (abMagic, 0, n); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +try { +is.reset (); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +return abMagic; +}, $fz.isPrivate = true, $fz), "java.io.InputStream,~N"); +c$.guessMimeTypeForBytes = Clazz.defineMethod (c$, "guessMimeTypeForBytes", +function (bytes) { +switch (bytes.length < 2 ? -1 : bytes[1]) { +case 0: +return "image/jpg"; +case 0x49: +return "image/gif"; +case 0x4D: +return "image/BMP"; +case 0x50: +return "image/png"; +default: +return "image/unknown"; +} +}, "~A"); +c$.getBIS = Clazz.defineMethod (c$, "getBIS", +function (bytes) { +return new java.io.BufferedInputStream ( new java.io.ByteArrayInputStream (bytes)); +}, "~A"); +c$.getBR = Clazz.defineMethod (c$, "getBR", +function (string) { +return new java.io.BufferedReader ( new java.io.StringReader (string)); +}, "~S"); +c$.getUnzippedInputStream = Clazz.defineMethod (c$, "getUnzippedInputStream", +function (jzt, bis) { +while (javajs.util.Rdr.isGzipS (bis)) bis = new java.io.BufferedInputStream (jzt.newGZIPInputStream (bis)); + +return bis; +}, "javajs.api.GenericZipTools,java.io.BufferedInputStream"); +c$.getBytesFromSB = Clazz.defineMethod (c$, "getBytesFromSB", +function (sb) { +return (javajs.util.Rdr.isBase64 (sb) ? javajs.util.Base64.decodeBase64 (sb.substring (8)) : sb.toBytes (0, -1)); +}, "javajs.util.SB"); +c$.getStreamAsBytes = Clazz.defineMethod (c$, "getStreamAsBytes", +function (bis, out) { +var buf = Clazz.newByteArray (1024, 0); +var bytes = (out == null ? Clazz.newByteArray (4096, 0) : null); +var len = 0; +var totalLen = 0; +while ((len = bis.read (buf, 0, 1024)) > 0) { +totalLen += len; +if (out == null) { +if (totalLen >= bytes.length) bytes = javajs.util.AU.ensureLengthByte (bytes, totalLen * 2); +System.arraycopy (buf, 0, bytes, totalLen - len, len); +} else { +out.write (buf, 0, len); +}} +bis.close (); +if (out == null) { +return javajs.util.AU.arrayCopyByte (bytes, totalLen); +}return totalLen + " bytes"; +}, "java.io.BufferedInputStream,javajs.util.OC"); +c$.getBufferedReader = Clazz.defineMethod (c$, "getBufferedReader", +function (bis, charSet) { +if (javajs.util.Rdr.getUTFEncodingForStream (bis) === javajs.util.Encoding.NONE) return new java.io.BufferedReader ( new java.io.InputStreamReader (bis, (charSet == null ? "UTF-8" : charSet))); +var bytes = javajs.util.Rdr.getLimitedStreamBytes (bis, -1); +bis.close (); +return javajs.util.Rdr.getBR (charSet == null ? javajs.util.Rdr.fixUTF (bytes) : String.instantialize (bytes, charSet)); +}, "java.io.BufferedInputStream,~S"); +c$.getLimitedStreamBytes = Clazz.defineMethod (c$, "getLimitedStreamBytes", +function (is, n) { +var buflen = (n > 0 && n < 1024 ? n : 1024); +var buf = Clazz.newByteArray (buflen, 0); +var bytes = Clazz.newByteArray (n < 0 ? 4096 : n, 0); +var len = 0; +var totalLen = 0; +if (n < 0) n = 2147483647; +while (totalLen < n && (len = is.read (buf, 0, buflen)) > 0) { +totalLen += len; +if (totalLen > bytes.length) bytes = javajs.util.AU.ensureLengthByte (bytes, totalLen * 2); +System.arraycopy (buf, 0, bytes, totalLen - len, len); +if (n != 2147483647 && totalLen + buflen > bytes.length) buflen = bytes.length - totalLen; +} +if (totalLen == bytes.length) return bytes; +buf = Clazz.newByteArray (totalLen, 0); +System.arraycopy (bytes, 0, buf, 0, totalLen); +return buf; +}, "java.io.InputStream,~N"); +c$.StreamToUTF8String = Clazz.defineMethod (c$, "StreamToUTF8String", +function (bis) { +var data = new Array (1); +try { +javajs.util.Rdr.readAllAsString (javajs.util.Rdr.getBufferedReader (bis, "UTF-8"), -1, true, data, 0); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +} else { +throw e; +} +} +return data[0]; +}, "java.io.BufferedInputStream"); +c$.readAllAsString = Clazz.defineMethod (c$, "readAllAsString", +function (br, nBytesMax, allowBinary, data, i) { +try { +var sb = javajs.util.SB.newN (8192); +var line; +if (nBytesMax < 0) { +line = br.readLine (); +if (allowBinary || line != null && line.indexOf ('\0') < 0 && (line.length != 4 || line.charCodeAt (0) != 65533 || line.indexOf ("PNG") != 1)) { +sb.append (line).appendC ('\n'); +while ((line = br.readLine ()) != null) sb.append (line).appendC ('\n'); + +}} else { +var n = 0; +var len; +while (n < nBytesMax && (line = br.readLine ()) != null) { +if (nBytesMax - n < (len = line.length) + 1) line = line.substring (0, nBytesMax - n - 1); +sb.append (line).appendC ('\n'); +n += len + 1; +} +}br.close (); +data[i] = sb.toString (); +return true; +} catch (ioe) { +if (Clazz.exceptionOf (ioe, Exception)) { +data[i] = ioe.toString (); +return false; +} else { +throw ioe; +} +} +}, "java.io.BufferedReader,~N,~B,~A,~N"); +c$.getPngZipPointAndCount = Clazz.defineMethod (c$, "getPngZipPointAndCount", +function (bis, pt_count) { +bis.mark (75); +try { +var data = javajs.util.Rdr.getLimitedStreamBytes (bis, 74); +bis.reset (); +var pt = 0; +for (var i = 64, f = 1; --i > 54; f *= 10) pt += (data[i] - 48) * f; + +var n = 0; +for (var i = 74, f = 1; --i > 64; f *= 10) n += (data[i] - 48) * f; + +pt_count[0] = pt; +pt_count[1] = n; +} catch (e) { +pt_count[1] = 0; +} +}, "java.io.BufferedInputStream,~A"); +c$.getPngZipStream = Clazz.defineMethod (c$, "getPngZipStream", +function (bis, asNewStream) { +if (!javajs.util.Rdr.isPngZipStream (bis)) return bis; +var data = Clazz.newByteArray (0, 0); +bis.mark (75); +try { +var pt_count = Clazz.newIntArray (2, 0); +javajs.util.Rdr.getPngZipPointAndCount (bis, pt_count); +if (pt_count[1] != 0) { +var pt = pt_count[0]; +while (pt > 0) pt -= bis.skip (pt); + +if (!asNewStream) return bis; +data = javajs.util.Rdr.getLimitedStreamBytes (bis, pt_count[1]); +}} catch (e) { +} finally { +try { +if (asNewStream) bis.close (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +} +return javajs.util.Rdr.getBIS (data); +}, "java.io.BufferedInputStream,~B"); +c$.getZipRoot = Clazz.defineMethod (c$, "getZipRoot", +function (fileName) { +var pt = fileName.indexOf ("|"); +return (pt < 0 ? fileName : fileName.substring (0, pt)); +}, "~S"); +}); diff --git a/bin/javajs/util/SB.js b/bin/javajs/util/SB.js index daa1518..b597d0f 100644 --- a/bin/javajs/util/SB.js +++ b/bin/javajs/util/SB.js @@ -1,151 +1,151 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.sb = null; -this.s = null; -Clazz.instantialize (this, arguments); -}, javajs.util, "SB"); -Clazz.makeConstructor (c$, -function () { -{ -this.s = ""; -}}); -c$.newN = Clazz.defineMethod (c$, "newN", -function (n) { -{ -return new javajs.util.SB(); -}}, "~N"); -c$.newS = Clazz.defineMethod (c$, "newS", -function (s) { -{ -var sb = new javajs.util.SB(); -sb.s = s; -return sb; -}}, "~S"); -Clazz.defineMethod (c$, "append", -function (s) { -{ -this.s += s -}return this; -}, "~S"); -Clazz.defineMethod (c$, "appendC", -function (c) { -{ -this.s += c; -}return this; -}, "~S"); -Clazz.defineMethod (c$, "appendI", -function (i) { -{ -this.s += i -}return this; -}, "~N"); -Clazz.defineMethod (c$, "appendB", -function (b) { -{ -this.s += b -}return this; -}, "~B"); -Clazz.defineMethod (c$, "appendF", -function (f) { -{ -var sf = "" + f; -if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0) -sf += ".0" ; -this.s += sf; -}return this; -}, "~N"); -Clazz.defineMethod (c$, "appendD", -function (d) { -{ -var sf = "" + d; -if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0) -sf += ".0" ; -this.s += sf; -}return this; -}, "~N"); -Clazz.defineMethod (c$, "appendSB", -function (buf) { -{ -this.s += buf.s; -}return this; -}, "javajs.util.SB"); -Clazz.defineMethod (c$, "appendO", -function (data) { -if (data != null) { -{ -this.s += data.toString(); -}}return this; -}, "~O"); -Clazz.defineMethod (c$, "appendCB", -function (cb, off, len) { -{ -for (var i = len,j=off; --i >= 0;) -this.s += cb[j++]; -}}, "~A,~N,~N"); -Clazz.overrideMethod (c$, "toString", -function () { -{ -return this.s; -}}); -Clazz.defineMethod (c$, "length", -function () { -{ -return this.s.length; -}}); -Clazz.defineMethod (c$, "indexOf", -function (s) { -{ -return this.s.indexOf(s); -}}, "~S"); -Clazz.defineMethod (c$, "charAt", -function (i) { -{ -return this.s.charAt(i); -}}, "~N"); -Clazz.defineMethod (c$, "charCodeAt", -function (i) { -{ -return this.s.charCodeAt(i); -}}, "~N"); -Clazz.defineMethod (c$, "setLength", -function (n) { -{ -this.s = this.s.substring(0, n); -}}, "~N"); -Clazz.defineMethod (c$, "lastIndexOf", -function (s) { -{ -return this.s.lastIndexOf(s); -}}, "~S"); -Clazz.defineMethod (c$, "indexOf2", -function (s, i) { -{ -return this.s.indexOf(s, i); -}}, "~S,~N"); -Clazz.defineMethod (c$, "substring", -function (i) { -{ -return this.s.substring(i); -}}, "~N"); -Clazz.defineMethod (c$, "substring2", -function (i, j) { -{ -return this.s.substring(i, j); -}}, "~N,~N"); -Clazz.defineMethod (c$, "toBytes", -function (off, len) { -if (len < 0) len = this.length () - off; -var b = Clazz.newByteArray (len, 0); -for (var i = off + len, j = i - off; --i >= off; ) b[--j] = (this.charAt (i)).charCodeAt (0); - -return b; -}, "~N,~N"); -Clazz.defineMethod (c$, "replace", -function (start, end, str) { -{ -this.s = this.s.substring(0, start) + str + this.s.substring(end); -}}, "~N,~N,~S"); -Clazz.defineMethod (c$, "insert", -function (offset, str) { -this.replace (offset, offset, str); -}, "~N,~S"); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.sb = null; +this.s = null; +Clazz.instantialize (this, arguments); +}, javajs.util, "SB"); +Clazz.makeConstructor (c$, +function () { +{ +this.s = ""; +}}); +c$.newN = Clazz.defineMethod (c$, "newN", +function (n) { +{ +return new javajs.util.SB(); +}}, "~N"); +c$.newS = Clazz.defineMethod (c$, "newS", +function (s) { +{ +var sb = new javajs.util.SB(); +sb.s = s; +return sb; +}}, "~S"); +Clazz.defineMethod (c$, "append", +function (s) { +{ +this.s += s +}return this; +}, "~S"); +Clazz.defineMethod (c$, "appendC", +function (c) { +{ +this.s += c; +}return this; +}, "~S"); +Clazz.defineMethod (c$, "appendI", +function (i) { +{ +this.s += i +}return this; +}, "~N"); +Clazz.defineMethod (c$, "appendB", +function (b) { +{ +this.s += b +}return this; +}, "~B"); +Clazz.defineMethod (c$, "appendF", +function (f) { +{ +var sf = "" + f; +if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0) +sf += ".0" ; +this.s += sf; +}return this; +}, "~N"); +Clazz.defineMethod (c$, "appendD", +function (d) { +{ +var sf = "" + d; +if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0) +sf += ".0" ; +this.s += sf; +}return this; +}, "~N"); +Clazz.defineMethod (c$, "appendSB", +function (buf) { +{ +this.s += buf.s; +}return this; +}, "javajs.util.SB"); +Clazz.defineMethod (c$, "appendO", +function (data) { +if (data != null) { +{ +this.s += data.toString(); +}}return this; +}, "~O"); +Clazz.defineMethod (c$, "appendCB", +function (cb, off, len) { +{ +for (var i = len,j=off; --i >= 0;) +this.s += cb[j++]; +}}, "~A,~N,~N"); +Clazz.overrideMethod (c$, "toString", +function () { +{ +return this.s; +}}); +Clazz.defineMethod (c$, "length", +function () { +{ +return this.s.length; +}}); +Clazz.defineMethod (c$, "indexOf", +function (s) { +{ +return this.s.indexOf(s); +}}, "~S"); +Clazz.defineMethod (c$, "charAt", +function (i) { +{ +return this.s.charAt(i); +}}, "~N"); +Clazz.defineMethod (c$, "charCodeAt", +function (i) { +{ +return this.s.charCodeAt(i); +}}, "~N"); +Clazz.defineMethod (c$, "setLength", +function (n) { +{ +this.s = this.s.substring(0, n); +}}, "~N"); +Clazz.defineMethod (c$, "lastIndexOf", +function (s) { +{ +return this.s.lastIndexOf(s); +}}, "~S"); +Clazz.defineMethod (c$, "indexOf2", +function (s, i) { +{ +return this.s.indexOf(s, i); +}}, "~S,~N"); +Clazz.defineMethod (c$, "substring", +function (i) { +{ +return this.s.substring(i); +}}, "~N"); +Clazz.defineMethod (c$, "substring2", +function (i, j) { +{ +return this.s.substring(i, j); +}}, "~N,~N"); +Clazz.defineMethod (c$, "toBytes", +function (off, len) { +if (len < 0) len = this.length () - off; +var b = Clazz.newByteArray (len, 0); +for (var i = off + len, j = i - off; --i >= off; ) b[--j] = (this.charAt (i)).charCodeAt (0); + +return b; +}, "~N,~N"); +Clazz.defineMethod (c$, "replace", +function (start, end, str) { +{ +this.s = this.s.substring(0, start) + str + this.s.substring(end); +}}, "~N,~N,~S"); +Clazz.defineMethod (c$, "insert", +function (offset, str) { +this.replace (offset, offset, str); +}, "~N,~S"); diff --git a/bin/javajs/util/StringDataReader.js b/bin/javajs/util/StringDataReader.js index 691fb2c..229c2ac 100644 --- a/bin/javajs/util/StringDataReader.js +++ b/bin/javajs/util/StringDataReader.js @@ -1,12 +1,12 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.DataReader"], "javajs.util.StringDataReader", ["java.io.StringReader"], function () { -c$ = Clazz.declareType (javajs.util, "StringDataReader", javajs.util.DataReader); -Clazz.makeConstructor (c$, -function (data) { -Clazz.superConstructor (this, javajs.util.StringDataReader, [ new java.io.StringReader (data)]); -}, "~S"); -Clazz.overrideMethod (c$, "setData", -function (data) { -return new javajs.util.StringDataReader (data); -}, "~O"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.DataReader"], "javajs.util.StringDataReader", ["java.io.StringReader"], function () { +c$ = Clazz.declareType (javajs.util, "StringDataReader", javajs.util.DataReader); +Clazz.makeConstructor (c$, +function (data) { +Clazz.superConstructor (this, javajs.util.StringDataReader, [ new java.io.StringReader (data)]); +}, "~S"); +Clazz.overrideMethod (c$, "setData", +function (data) { +return new javajs.util.StringDataReader (data); +}, "~O"); +}); diff --git a/bin/javajs/util/T3.js b/bin/javajs/util/T3.js index a914fe2..81c591c 100644 --- a/bin/javajs/util/T3.js +++ b/bin/javajs/util/T3.js @@ -1,141 +1,141 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.JSONEncodable"], "javajs.util.T3", ["java.lang.Float"], function () { -c$ = Clazz.decorateAsClass (function () { -this.x = 0; -this.y = 0; -this.z = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "T3", null, [javajs.api.JSONEncodable, java.io.Serializable]); -Clazz.defineMethod (c$, "set", -function (x, y, z) { -this.x = x; -this.y = y; -this.z = z; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "setA", -function (t) { -this.x = t[0]; -this.y = t[1]; -this.z = t[2]; -}, "~A"); -Clazz.defineMethod (c$, "setT", -function (t1) { -this.x = t1.x; -this.y = t1.y; -this.z = t1.z; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "add2", -function (t1, t2) { -this.x = t1.x + t2.x; -this.y = t1.y + t2.y; -this.z = t1.z + t2.z; -}, "javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "add", -function (t1) { -this.x += t1.x; -this.y += t1.y; -this.z += t1.z; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "distanceSquared", -function (p1) { -var dx = this.x - p1.x; -var dy = this.y - p1.y; -var dz = this.z - p1.z; -return (dx * dx + dy * dy + dz * dz); -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "distance", -function (p1) { -return Math.sqrt (this.distanceSquared (p1)); -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "sub2", -function (t1, t2) { -this.x = t1.x - t2.x; -this.y = t1.y - t2.y; -this.z = t1.z - t2.z; -}, "javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "sub", -function (t1) { -this.x -= t1.x; -this.y -= t1.y; -this.z -= t1.z; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "scale", -function (s) { -this.x *= s; -this.y *= s; -this.z *= s; -}, "~N"); -Clazz.defineMethod (c$, "add3", -function (a, b, c) { -this.x += a; -this.y += b; -this.z += c; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "scaleT", -function (p) { -this.x *= p.x; -this.y *= p.y; -this.z *= p.z; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "scaleAdd2", -function (s, t1, t2) { -this.x = s * t1.x + t2.x; -this.y = s * t1.y + t2.y; -this.z = s * t1.z + t2.z; -}, "~N,javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "ave", -function (a, b) { -this.x = (a.x + b.x) / 2; -this.y = (a.y + b.y) / 2; -this.z = (a.z + b.z) / 2; -}, "javajs.util.T3,javajs.util.T3"); -Clazz.defineMethod (c$, "dot", -function (v) { -return this.x * v.x + this.y * v.y + this.z * v.z; -}, "javajs.util.T3"); -Clazz.defineMethod (c$, "lengthSquared", -function () { -return this.x * this.x + this.y * this.y + this.z * this.z; -}); -Clazz.defineMethod (c$, "length", -function () { -return Math.sqrt (this.lengthSquared ()); -}); -Clazz.defineMethod (c$, "normalize", -function () { -var d = this.length (); -this.x /= d; -this.y /= d; -this.z /= d; -}); -Clazz.defineMethod (c$, "cross", -function (v1, v2) { -this.set (v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y - v1.y * v2.x); -}, "javajs.util.T3,javajs.util.T3"); -Clazz.overrideMethod (c$, "hashCode", -function () { -var bits = 1; -bits = 31 * bits + javajs.util.T3.floatToIntBits0 (this.x); -bits = 31 * bits + javajs.util.T3.floatToIntBits0 (this.y); -bits = 31 * bits + javajs.util.T3.floatToIntBits0 (this.z); -return (bits ^ (bits >> 32)); -}); -c$.floatToIntBits0 = Clazz.defineMethod (c$, "floatToIntBits0", -function (f) { -return (f == 0 ? 0 : Float.floatToIntBits (f)); -}, "~N"); -Clazz.overrideMethod (c$, "equals", -function (t1) { -if (!(Clazz.instanceOf (t1, javajs.util.T3))) return false; -var t2 = t1; -return (this.x == t2.x && this.y == t2.y && this.z == t2.z); -}, "~O"); -Clazz.overrideMethod (c$, "toString", -function () { -return "{" + this.x + ", " + this.y + ", " + this.z + "}"; -}); -Clazz.overrideMethod (c$, "toJSON", -function () { -return "[" + this.x + "," + this.y + "," + this.z + "]"; -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.JSONEncodable"], "javajs.util.T3", ["java.lang.Float"], function () { +c$ = Clazz.decorateAsClass (function () { +this.x = 0; +this.y = 0; +this.z = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "T3", null, [javajs.api.JSONEncodable, java.io.Serializable]); +Clazz.defineMethod (c$, "set", +function (x, y, z) { +this.x = x; +this.y = y; +this.z = z; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "setA", +function (t) { +this.x = t[0]; +this.y = t[1]; +this.z = t[2]; +}, "~A"); +Clazz.defineMethod (c$, "setT", +function (t1) { +this.x = t1.x; +this.y = t1.y; +this.z = t1.z; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "add2", +function (t1, t2) { +this.x = t1.x + t2.x; +this.y = t1.y + t2.y; +this.z = t1.z + t2.z; +}, "javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "add", +function (t1) { +this.x += t1.x; +this.y += t1.y; +this.z += t1.z; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "distanceSquared", +function (p1) { +var dx = this.x - p1.x; +var dy = this.y - p1.y; +var dz = this.z - p1.z; +return (dx * dx + dy * dy + dz * dz); +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "distance", +function (p1) { +return Math.sqrt (this.distanceSquared (p1)); +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "sub2", +function (t1, t2) { +this.x = t1.x - t2.x; +this.y = t1.y - t2.y; +this.z = t1.z - t2.z; +}, "javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "sub", +function (t1) { +this.x -= t1.x; +this.y -= t1.y; +this.z -= t1.z; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "scale", +function (s) { +this.x *= s; +this.y *= s; +this.z *= s; +}, "~N"); +Clazz.defineMethod (c$, "add3", +function (a, b, c) { +this.x += a; +this.y += b; +this.z += c; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "scaleT", +function (p) { +this.x *= p.x; +this.y *= p.y; +this.z *= p.z; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "scaleAdd2", +function (s, t1, t2) { +this.x = s * t1.x + t2.x; +this.y = s * t1.y + t2.y; +this.z = s * t1.z + t2.z; +}, "~N,javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "ave", +function (a, b) { +this.x = (a.x + b.x) / 2; +this.y = (a.y + b.y) / 2; +this.z = (a.z + b.z) / 2; +}, "javajs.util.T3,javajs.util.T3"); +Clazz.defineMethod (c$, "dot", +function (v) { +return this.x * v.x + this.y * v.y + this.z * v.z; +}, "javajs.util.T3"); +Clazz.defineMethod (c$, "lengthSquared", +function () { +return this.x * this.x + this.y * this.y + this.z * this.z; +}); +Clazz.defineMethod (c$, "length", +function () { +return Math.sqrt (this.lengthSquared ()); +}); +Clazz.defineMethod (c$, "normalize", +function () { +var d = this.length (); +this.x /= d; +this.y /= d; +this.z /= d; +}); +Clazz.defineMethod (c$, "cross", +function (v1, v2) { +this.set (v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y - v1.y * v2.x); +}, "javajs.util.T3,javajs.util.T3"); +Clazz.overrideMethod (c$, "hashCode", +function () { +var bits = 1; +bits = 31 * bits + javajs.util.T3.floatToIntBits0 (this.x); +bits = 31 * bits + javajs.util.T3.floatToIntBits0 (this.y); +bits = 31 * bits + javajs.util.T3.floatToIntBits0 (this.z); +return (bits ^ (bits >> 32)); +}); +c$.floatToIntBits0 = Clazz.defineMethod (c$, "floatToIntBits0", +function (f) { +return (f == 0 ? 0 : Float.floatToIntBits (f)); +}, "~N"); +Clazz.overrideMethod (c$, "equals", +function (t1) { +if (!(Clazz.instanceOf (t1, javajs.util.T3))) return false; +var t2 = t1; +return (this.x == t2.x && this.y == t2.y && this.z == t2.z); +}, "~O"); +Clazz.overrideMethod (c$, "toString", +function () { +return "{" + this.x + ", " + this.y + ", " + this.z + "}"; +}); +Clazz.overrideMethod (c$, "toJSON", +function () { +return "[" + this.x + "," + this.y + "," + this.z + "]"; +}); +}); diff --git a/bin/javajs/util/T3d.js b/bin/javajs/util/T3d.js index 4040423..984370c 100644 --- a/bin/javajs/util/T3d.js +++ b/bin/javajs/util/T3d.js @@ -1,87 +1,87 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.T3d", ["java.lang.Double"], function () { -c$ = Clazz.decorateAsClass (function () { -this.x = 0; -this.y = 0; -this.z = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "T3d", null, java.io.Serializable); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "set", -function (x, y, z) { -this.x = x; -this.y = y; -this.z = z; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "setA", -function (t) { -this.x = t[0]; -this.y = t[1]; -this.z = t[2]; -}, "~A"); -Clazz.defineMethod (c$, "setT", -function (t1) { -this.x = t1.x; -this.y = t1.y; -this.z = t1.z; -}, "javajs.util.T3d"); -Clazz.defineMethod (c$, "add2", -function (t1, t2) { -this.x = t1.x + t2.x; -this.y = t1.y + t2.y; -this.z = t1.z + t2.z; -}, "javajs.util.T3d,javajs.util.T3d"); -Clazz.defineMethod (c$, "add", -function (t1) { -this.x += t1.x; -this.y += t1.y; -this.z += t1.z; -}, "javajs.util.T3d"); -Clazz.defineMethod (c$, "sub2", -function (t1, t2) { -this.x = t1.x - t2.x; -this.y = t1.y - t2.y; -this.z = t1.z - t2.z; -}, "javajs.util.T3d,javajs.util.T3d"); -Clazz.defineMethod (c$, "sub", -function (t1) { -this.x -= t1.x; -this.y -= t1.y; -this.z -= t1.z; -}, "javajs.util.T3d"); -Clazz.defineMethod (c$, "scale", -function (s) { -this.x *= s; -this.y *= s; -this.z *= s; -}, "~N"); -Clazz.defineMethod (c$, "scaleAdd", -function (s, t1, t2) { -this.x = s * t1.x + t2.x; -this.y = s * t1.y + t2.y; -this.z = s * t1.z + t2.z; -}, "~N,javajs.util.T3d,javajs.util.T3d"); -Clazz.overrideMethod (c$, "hashCode", -function () { -var xbits = javajs.util.T3d.doubleToLongBits0 (this.x); -var ybits = javajs.util.T3d.doubleToLongBits0 (this.y); -var zbits = javajs.util.T3d.doubleToLongBits0 (this.z); -return (xbits ^ (xbits >> 32) ^ ybits ^ (ybits >> 32) ^ zbits ^ (zbits >> 32)); -}); -c$.doubleToLongBits0 = Clazz.defineMethod (c$, "doubleToLongBits0", -function (d) { -return (d == 0 ? 0 : Double.doubleToLongBits (d)); -}, "~N"); -Clazz.overrideMethod (c$, "equals", -function (t1) { -if (!(Clazz.instanceOf (t1, javajs.util.T3d))) return false; -var t2 = t1; -return (this.x == t2.x && this.y == t2.y && this.z == t2.z); -}, "~O"); -Clazz.overrideMethod (c$, "toString", -function () { -return "{" + this.x + ", " + this.y + ", " + this.z + "}"; -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.T3d", ["java.lang.Double"], function () { +c$ = Clazz.decorateAsClass (function () { +this.x = 0; +this.y = 0; +this.z = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "T3d", null, java.io.Serializable); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "set", +function (x, y, z) { +this.x = x; +this.y = y; +this.z = z; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "setA", +function (t) { +this.x = t[0]; +this.y = t[1]; +this.z = t[2]; +}, "~A"); +Clazz.defineMethod (c$, "setT", +function (t1) { +this.x = t1.x; +this.y = t1.y; +this.z = t1.z; +}, "javajs.util.T3d"); +Clazz.defineMethod (c$, "add2", +function (t1, t2) { +this.x = t1.x + t2.x; +this.y = t1.y + t2.y; +this.z = t1.z + t2.z; +}, "javajs.util.T3d,javajs.util.T3d"); +Clazz.defineMethod (c$, "add", +function (t1) { +this.x += t1.x; +this.y += t1.y; +this.z += t1.z; +}, "javajs.util.T3d"); +Clazz.defineMethod (c$, "sub2", +function (t1, t2) { +this.x = t1.x - t2.x; +this.y = t1.y - t2.y; +this.z = t1.z - t2.z; +}, "javajs.util.T3d,javajs.util.T3d"); +Clazz.defineMethod (c$, "sub", +function (t1) { +this.x -= t1.x; +this.y -= t1.y; +this.z -= t1.z; +}, "javajs.util.T3d"); +Clazz.defineMethod (c$, "scale", +function (s) { +this.x *= s; +this.y *= s; +this.z *= s; +}, "~N"); +Clazz.defineMethod (c$, "scaleAdd", +function (s, t1, t2) { +this.x = s * t1.x + t2.x; +this.y = s * t1.y + t2.y; +this.z = s * t1.z + t2.z; +}, "~N,javajs.util.T3d,javajs.util.T3d"); +Clazz.overrideMethod (c$, "hashCode", +function () { +var xbits = javajs.util.T3d.doubleToLongBits0 (this.x); +var ybits = javajs.util.T3d.doubleToLongBits0 (this.y); +var zbits = javajs.util.T3d.doubleToLongBits0 (this.z); +return (xbits ^ (xbits >> 32) ^ ybits ^ (ybits >> 32) ^ zbits ^ (zbits >> 32)); +}); +c$.doubleToLongBits0 = Clazz.defineMethod (c$, "doubleToLongBits0", +function (d) { +return (d == 0 ? 0 : Double.doubleToLongBits (d)); +}, "~N"); +Clazz.overrideMethod (c$, "equals", +function (t1) { +if (!(Clazz.instanceOf (t1, javajs.util.T3d))) return false; +var t2 = t1; +return (this.x == t2.x && this.y == t2.y && this.z == t2.z); +}, "~O"); +Clazz.overrideMethod (c$, "toString", +function () { +return "{" + this.x + ", " + this.y + ", " + this.z + "}"; +}); +}); diff --git a/bin/javajs/util/T3i.js b/bin/javajs/util/T3i.js index bc24bf4..43b9910 100644 --- a/bin/javajs/util/T3i.js +++ b/bin/javajs/util/T3i.js @@ -1,48 +1,48 @@ -Clazz.declarePackage ("javajs.util"); -c$ = Clazz.decorateAsClass (function () { -this.x = 0; -this.y = 0; -this.z = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "T3i", null, java.io.Serializable); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.defineMethod (c$, "set", -function (x, y, z) { -this.x = x; -this.y = y; -this.z = z; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "setT", -function (t1) { -this.x = t1.x; -this.y = t1.y; -this.z = t1.z; -}, "javajs.util.T3i"); -Clazz.defineMethod (c$, "add", -function (t) { -this.x += t.x; -this.y += t.y; -this.z += t.z; -}, "javajs.util.T3i"); -Clazz.defineMethod (c$, "scaleAdd", -function (s, t1, t2) { -this.x = s * t1.x + t2.x; -this.y = s * t1.y + t2.y; -this.z = s * t1.z + t2.z; -}, "~N,javajs.util.T3i,javajs.util.T3i"); -Clazz.overrideMethod (c$, "hashCode", -function () { -return this.x ^ this.y ^ this.z; -}); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (!(Clazz.instanceOf (o, javajs.util.T3i))) return false; -var t = o; -return (this.x == t.x && this.y == t.y && this.z == t.z); -}, "~O"); -Clazz.overrideMethod (c$, "toString", -function () { -return "(" + this.x + ", " + this.y + ", " + this.z + ")"; -}); +Clazz.declarePackage ("javajs.util"); +c$ = Clazz.decorateAsClass (function () { +this.x = 0; +this.y = 0; +this.z = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "T3i", null, java.io.Serializable); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.defineMethod (c$, "set", +function (x, y, z) { +this.x = x; +this.y = y; +this.z = z; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "setT", +function (t1) { +this.x = t1.x; +this.y = t1.y; +this.z = t1.z; +}, "javajs.util.T3i"); +Clazz.defineMethod (c$, "add", +function (t) { +this.x += t.x; +this.y += t.y; +this.z += t.z; +}, "javajs.util.T3i"); +Clazz.defineMethod (c$, "scaleAdd", +function (s, t1, t2) { +this.x = s * t1.x + t2.x; +this.y = s * t1.y + t2.y; +this.z = s * t1.z + t2.z; +}, "~N,javajs.util.T3i,javajs.util.T3i"); +Clazz.overrideMethod (c$, "hashCode", +function () { +return this.x ^ this.y ^ this.z; +}); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (!(Clazz.instanceOf (o, javajs.util.T3i))) return false; +var t = o; +return (this.x == t.x && this.y == t.y && this.z == t.z); +}, "~O"); +Clazz.overrideMethod (c$, "toString", +function () { +return "(" + this.x + ", " + this.y + ", " + this.z + ")"; +}); diff --git a/bin/javajs/util/T4.js b/bin/javajs/util/T4.js index 3ea8edd..d33a2c7 100644 --- a/bin/javajs/util/T4.js +++ b/bin/javajs/util/T4.js @@ -1,37 +1,37 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.T3"], "javajs.util.T4", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.w = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "T4", javajs.util.T3); -Clazz.defineMethod (c$, "set4", -function (x, y, z, w) { -this.x = x; -this.y = y; -this.z = z; -this.w = w; -}, "~N,~N,~N,~N"); -Clazz.defineMethod (c$, "scale4", -function (s) { -this.scale (s); -this.w *= s; -}, "~N"); -Clazz.overrideMethod (c$, "hashCode", -function () { -return javajs.util.T3.floatToIntBits0 (this.x) ^ javajs.util.T3.floatToIntBits0 (this.y) ^ javajs.util.T3.floatToIntBits0 (this.z) ^ javajs.util.T3.floatToIntBits0 (this.w); -}); -Clazz.overrideMethod (c$, "equals", -function (o) { -if (!(Clazz.instanceOf (o, javajs.util.T4))) return false; -var t = o; -return (this.x == t.x && this.y == t.y && this.z == t.z && this.w == t.w); -}, "~O"); -Clazz.overrideMethod (c$, "toString", -function () { -return "(" + this.x + ", " + this.y + ", " + this.z + ", " + this.w + ")"; -}); -Clazz.overrideMethod (c$, "toJSON", -function () { -return "[" + this.x + ", " + this.y + ", " + this.z + ", " + this.w + "]"; -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.T3"], "javajs.util.T4", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.w = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "T4", javajs.util.T3); +Clazz.defineMethod (c$, "set4", +function (x, y, z, w) { +this.x = x; +this.y = y; +this.z = z; +this.w = w; +}, "~N,~N,~N,~N"); +Clazz.defineMethod (c$, "scale4", +function (s) { +this.scale (s); +this.w *= s; +}, "~N"); +Clazz.overrideMethod (c$, "hashCode", +function () { +return javajs.util.T3.floatToIntBits0 (this.x) ^ javajs.util.T3.floatToIntBits0 (this.y) ^ javajs.util.T3.floatToIntBits0 (this.z) ^ javajs.util.T3.floatToIntBits0 (this.w); +}); +Clazz.overrideMethod (c$, "equals", +function (o) { +if (!(Clazz.instanceOf (o, javajs.util.T4))) return false; +var t = o; +return (this.x == t.x && this.y == t.y && this.z == t.z && this.w == t.w); +}, "~O"); +Clazz.overrideMethod (c$, "toString", +function () { +return "(" + this.x + ", " + this.y + ", " + this.z + ", " + this.w + ")"; +}); +Clazz.overrideMethod (c$, "toJSON", +function () { +return "[" + this.x + ", " + this.y + ", " + this.z + ", " + this.w + "]"; +}); +}); diff --git a/bin/javajs/util/V3.js b/bin/javajs/util/V3.js index 37591c1..28f7077 100644 --- a/bin/javajs/util/V3.js +++ b/bin/javajs/util/V3.js @@ -1,31 +1,31 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.T3"], "javajs.util.V3", null, function () { -c$ = Clazz.declareType (javajs.util, "V3", javajs.util.T3); -Clazz.makeConstructor (c$, -function () { -}); -c$.newV = Clazz.defineMethod (c$, "newV", -function (t) { -return javajs.util.V3.new3 (t.x, t.y, t.z); -}, "javajs.util.T3"); -c$.newVsub = Clazz.defineMethod (c$, "newVsub", -function (t1, t2) { -return javajs.util.V3.new3 (t1.x - t2.x, t1.y - t2.y, t1.z - t2.z); -}, "javajs.util.T3,javajs.util.T3"); -c$.new3 = Clazz.defineMethod (c$, "new3", -function (x, y, z) { -var v = new javajs.util.V3 (); -v.x = x; -v.y = y; -v.z = z; -return v; -}, "~N,~N,~N"); -Clazz.defineMethod (c$, "angle", -function (v1) { -var xx = this.y * v1.z - this.z * v1.y; -var yy = this.z * v1.x - this.x * v1.z; -var zz = this.x * v1.y - this.y * v1.x; -var cross = Math.sqrt (xx * xx + yy * yy + zz * zz); -return Math.abs (Math.atan2 (cross, this.dot (v1))); -}, "javajs.util.V3"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.T3"], "javajs.util.V3", null, function () { +c$ = Clazz.declareType (javajs.util, "V3", javajs.util.T3); +Clazz.makeConstructor (c$, +function () { +}); +c$.newV = Clazz.defineMethod (c$, "newV", +function (t) { +return javajs.util.V3.new3 (t.x, t.y, t.z); +}, "javajs.util.T3"); +c$.newVsub = Clazz.defineMethod (c$, "newVsub", +function (t1, t2) { +return javajs.util.V3.new3 (t1.x - t2.x, t1.y - t2.y, t1.z - t2.z); +}, "javajs.util.T3,javajs.util.T3"); +c$.new3 = Clazz.defineMethod (c$, "new3", +function (x, y, z) { +var v = new javajs.util.V3 (); +v.x = x; +v.y = y; +v.z = z; +return v; +}, "~N,~N,~N"); +Clazz.defineMethod (c$, "angle", +function (v1) { +var xx = this.y * v1.z - this.z * v1.y; +var yy = this.z * v1.x - this.x * v1.z; +var zz = this.x * v1.y - this.y * v1.x; +var cross = Math.sqrt (xx * xx + yy * yy + zz * zz); +return Math.abs (Math.atan2 (cross, this.dot (v1))); +}, "javajs.util.V3"); +}); diff --git a/bin/javajs/util/V3d.js b/bin/javajs/util/V3d.js index 729c5a3..c3a166e 100644 --- a/bin/javajs/util/V3d.js +++ b/bin/javajs/util/V3d.js @@ -1,27 +1,27 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.util.T3d"], "javajs.util.V3d", null, function () { -c$ = Clazz.declareType (javajs.util, "V3d", javajs.util.T3d); -Clazz.defineMethod (c$, "cross", -function (v1, v2) { -this.set (v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y - v1.y * v2.x); -}, "javajs.util.V3d,javajs.util.V3d"); -Clazz.defineMethod (c$, "normalize", -function () { -var d = this.length (); -this.x /= d; -this.y /= d; -this.z /= d; -}); -Clazz.defineMethod (c$, "dot", -function (v) { -return this.x * v.x + this.y * v.y + this.z * v.z; -}, "javajs.util.V3d"); -Clazz.defineMethod (c$, "lengthSquared", -function () { -return this.x * this.x + this.y * this.y + this.z * this.z; -}); -Clazz.defineMethod (c$, "length", -function () { -return Math.sqrt (this.lengthSquared ()); -}); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.util.T3d"], "javajs.util.V3d", null, function () { +c$ = Clazz.declareType (javajs.util, "V3d", javajs.util.T3d); +Clazz.defineMethod (c$, "cross", +function (v1, v2) { +this.set (v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y - v1.y * v2.x); +}, "javajs.util.V3d,javajs.util.V3d"); +Clazz.defineMethod (c$, "normalize", +function () { +var d = this.length (); +this.x /= d; +this.y /= d; +this.z /= d; +}); +Clazz.defineMethod (c$, "dot", +function (v) { +return this.x * v.x + this.y * v.y + this.z * v.z; +}, "javajs.util.V3d"); +Clazz.defineMethod (c$, "lengthSquared", +function () { +return this.x * this.x + this.y * this.y + this.z * this.z; +}); +Clazz.defineMethod (c$, "length", +function () { +return Math.sqrt (this.lengthSquared ()); +}); +}); diff --git a/bin/javajs/util/XmlUtil.js b/bin/javajs/util/XmlUtil.js index ee4fff9..68b0ce4 100644 --- a/bin/javajs/util/XmlUtil.js +++ b/bin/javajs/util/XmlUtil.js @@ -1,73 +1,73 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.XmlUtil", ["javajs.util.PT"], function () { -c$ = Clazz.declareType (javajs.util, "XmlUtil"); -Clazz.makeConstructor (c$, -function () { -}); -c$.openDocument = Clazz.defineMethod (c$, "openDocument", -function (data) { -data.append ("\n"); -}, "javajs.util.SB"); -c$.openTag = Clazz.defineMethod (c$, "openTag", -function (sb, name) { -sb.append ("<").append (name).append (">\n"); -}, "javajs.util.SB,~S"); -c$.openTagAttr = Clazz.defineMethod (c$, "openTagAttr", -function (sb, name, attributes) { -javajs.util.XmlUtil.appendTagAll (sb, name, attributes, null, false, false); -sb.append ("\n"); -}, "javajs.util.SB,~S,~A"); -c$.closeTag = Clazz.defineMethod (c$, "closeTag", -function (sb, name) { -sb.append ("\n"); -}, "javajs.util.SB,~S"); -c$.appendTagAll = Clazz.defineMethod (c$, "appendTagAll", -function (sb, name, attributes, data, isCdata, doClose) { -var closer = ">"; -if (name.endsWith ("/")) { -name = name.substring (0, name.length - 1); -if (data == null) { -closer = "/>\n"; -doClose = false; -}}sb.append ("<").append (name); -if (attributes != null) for (var i = 0; i < attributes.length; i++) { -var o = attributes[i]; -if (o == null) continue; -if (Clazz.instanceOf (o, Array)) for (var j = 0; j < (o).length; j += 2) javajs.util.XmlUtil.appendAttrib (sb, (o)[j], (o)[j + 1]); - - else javajs.util.XmlUtil.appendAttrib (sb, o, attributes[++i]); -} -sb.append (closer); -if (data != null) { -if (isCdata) data = javajs.util.XmlUtil.wrapCdata (data); -sb.appendO (data); -}if (doClose) javajs.util.XmlUtil.closeTag (sb, name); -}, "javajs.util.SB,~S,~A,~O,~B,~B"); -c$.wrapCdata = Clazz.defineMethod (c$, "wrapCdata", -function (data) { -var s = "" + data; -return (s.indexOf ("&") < 0 && s.indexOf ("<") < 0 ? (s.startsWith ("\n") ? "" : "\n") + s : "", "]]]]>") + "]]>"); -}, "~O"); -c$.unwrapCdata = Clazz.defineMethod (c$, "unwrapCdata", -function (s) { -return (s.startsWith ("") ? javajs.util.PT.rep (s.substring (9, s.length - 3), "]]]]>", "]]>") : s); -}, "~S"); -c$.appendTagObj = Clazz.defineMethod (c$, "appendTagObj", -function (sb, name, attributes, data) { -javajs.util.XmlUtil.appendTagAll (sb, name, attributes, data, false, true); -}, "javajs.util.SB,~S,~A,~O"); -c$.appendTag = Clazz.defineMethod (c$, "appendTag", -function (sb, name, data) { -if (Clazz.instanceOf (data, Array)) javajs.util.XmlUtil.appendTagAll (sb, name, data, null, false, true); - else javajs.util.XmlUtil.appendTagAll (sb, name, null, data, false, true); -}, "javajs.util.SB,~S,~O"); -c$.appendCdata = Clazz.defineMethod (c$, "appendCdata", -function (sb, name, attributes, data) { -javajs.util.XmlUtil.appendTagAll (sb, name, attributes, data, true, true); -}, "javajs.util.SB,~S,~A,~S"); -c$.appendAttrib = Clazz.defineMethod (c$, "appendAttrib", -function (sb, name, value) { -if (value == null) return; -sb.append (" ").appendO (name).append ("=\"").appendO (value).append ("\""); -}, "javajs.util.SB,~O,~O"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.XmlUtil", ["javajs.util.PT"], function () { +c$ = Clazz.declareType (javajs.util, "XmlUtil"); +Clazz.makeConstructor (c$, +function () { +}); +c$.openDocument = Clazz.defineMethod (c$, "openDocument", +function (data) { +data.append ("\n"); +}, "javajs.util.SB"); +c$.openTag = Clazz.defineMethod (c$, "openTag", +function (sb, name) { +sb.append ("<").append (name).append (">\n"); +}, "javajs.util.SB,~S"); +c$.openTagAttr = Clazz.defineMethod (c$, "openTagAttr", +function (sb, name, attributes) { +javajs.util.XmlUtil.appendTagAll (sb, name, attributes, null, false, false); +sb.append ("\n"); +}, "javajs.util.SB,~S,~A"); +c$.closeTag = Clazz.defineMethod (c$, "closeTag", +function (sb, name) { +sb.append ("\n"); +}, "javajs.util.SB,~S"); +c$.appendTagAll = Clazz.defineMethod (c$, "appendTagAll", +function (sb, name, attributes, data, isCdata, doClose) { +var closer = ">"; +if (name.endsWith ("/")) { +name = name.substring (0, name.length - 1); +if (data == null) { +closer = "/>\n"; +doClose = false; +}}sb.append ("<").append (name); +if (attributes != null) for (var i = 0; i < attributes.length; i++) { +var o = attributes[i]; +if (o == null) continue; +if (Clazz.instanceOf (o, Array)) for (var j = 0; j < (o).length; j += 2) javajs.util.XmlUtil.appendAttrib (sb, (o)[j], (o)[j + 1]); + + else javajs.util.XmlUtil.appendAttrib (sb, o, attributes[++i]); +} +sb.append (closer); +if (data != null) { +if (isCdata) data = javajs.util.XmlUtil.wrapCdata (data); +sb.appendO (data); +}if (doClose) javajs.util.XmlUtil.closeTag (sb, name); +}, "javajs.util.SB,~S,~A,~O,~B,~B"); +c$.wrapCdata = Clazz.defineMethod (c$, "wrapCdata", +function (data) { +var s = "" + data; +return (s.indexOf ("&") < 0 && s.indexOf ("<") < 0 ? (s.startsWith ("\n") ? "" : "\n") + s : "", "]]]]>") + "]]>"); +}, "~O"); +c$.unwrapCdata = Clazz.defineMethod (c$, "unwrapCdata", +function (s) { +return (s.startsWith ("") ? javajs.util.PT.rep (s.substring (9, s.length - 3), "]]]]>", "]]>") : s); +}, "~S"); +c$.appendTagObj = Clazz.defineMethod (c$, "appendTagObj", +function (sb, name, attributes, data) { +javajs.util.XmlUtil.appendTagAll (sb, name, attributes, data, false, true); +}, "javajs.util.SB,~S,~A,~O"); +c$.appendTag = Clazz.defineMethod (c$, "appendTag", +function (sb, name, data) { +if (Clazz.instanceOf (data, Array)) javajs.util.XmlUtil.appendTagAll (sb, name, data, null, false, true); + else javajs.util.XmlUtil.appendTagAll (sb, name, null, data, false, true); +}, "javajs.util.SB,~S,~O"); +c$.appendCdata = Clazz.defineMethod (c$, "appendCdata", +function (sb, name, attributes, data) { +javajs.util.XmlUtil.appendTagAll (sb, name, attributes, data, true, true); +}, "javajs.util.SB,~S,~A,~S"); +c$.appendAttrib = Clazz.defineMethod (c$, "appendAttrib", +function (sb, name, value) { +if (value == null) return; +sb.append (" ").appendO (name).append ("=\"").appendO (value).append ("\""); +}, "javajs.util.SB,~O,~O"); +}); diff --git a/bin/javajs/util/ZipData.js b/bin/javajs/util/ZipData.js index 8f318ca..8d9db8e 100644 --- a/bin/javajs/util/ZipData.js +++ b/bin/javajs/util/ZipData.js @@ -1,45 +1,45 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (null, "javajs.util.ZipData", ["javajs.util.Rdr", "$.ZipTools"], function () { -c$ = Clazz.decorateAsClass (function () { -this.isEnabled = true; -this.buf = null; -this.pt = 0; -this.nBytes = 0; -Clazz.instantialize (this, arguments); -}, javajs.util, "ZipData"); -Clazz.makeConstructor (c$, -function (nBytes) { -this.nBytes = nBytes; -}, "~N"); -Clazz.defineMethod (c$, "addBytes", -function (byteBuf, nSectorBytes, nBytesRemaining) { -if (this.pt == 0) { -if (!javajs.util.Rdr.isGzipB (byteBuf)) { -this.isEnabled = false; -return -1; -}this.buf = Clazz.newByteArray (nBytesRemaining, 0); -}var nToAdd = Math.min (nSectorBytes, nBytesRemaining); -System.arraycopy (byteBuf, 0, this.buf, this.pt, nToAdd); -this.pt += nToAdd; -return nBytesRemaining - nToAdd; -}, "~A,~N,~N"); -Clazz.defineMethod (c$, "addTo", -function (jzt, data) { -data.append (javajs.util.ZipData.getGzippedBytesAsString (jzt, this.buf)); -}, "javajs.api.GenericZipTools,javajs.util.SB"); -c$.getGzippedBytesAsString = Clazz.defineMethod (c$, "getGzippedBytesAsString", -function (jzt, bytes) { -try { -var bis = jzt.getUnGzippedInputStream (bytes); -var s = javajs.util.ZipTools.getStreamAsString (bis); -bis.close (); -return s; -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -return ""; -} else { -throw e; -} -} -}, "javajs.api.GenericZipTools,~A"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (null, "javajs.util.ZipData", ["javajs.util.Rdr", "$.ZipTools"], function () { +c$ = Clazz.decorateAsClass (function () { +this.isEnabled = true; +this.buf = null; +this.pt = 0; +this.nBytes = 0; +Clazz.instantialize (this, arguments); +}, javajs.util, "ZipData"); +Clazz.makeConstructor (c$, +function (nBytes) { +this.nBytes = nBytes; +}, "~N"); +Clazz.defineMethod (c$, "addBytes", +function (byteBuf, nSectorBytes, nBytesRemaining) { +if (this.pt == 0) { +if (!javajs.util.Rdr.isGzipB (byteBuf)) { +this.isEnabled = false; +return -1; +}this.buf = Clazz.newByteArray (nBytesRemaining, 0); +}var nToAdd = Math.min (nSectorBytes, nBytesRemaining); +System.arraycopy (byteBuf, 0, this.buf, this.pt, nToAdd); +this.pt += nToAdd; +return nBytesRemaining - nToAdd; +}, "~A,~N,~N"); +Clazz.defineMethod (c$, "addTo", +function (jzt, data) { +data.append (javajs.util.ZipData.getGzippedBytesAsString (jzt, this.buf)); +}, "javajs.api.GenericZipTools,javajs.util.SB"); +c$.getGzippedBytesAsString = Clazz.defineMethod (c$, "getGzippedBytesAsString", +function (jzt, bytes) { +try { +var bis = jzt.getUnGzippedInputStream (bytes); +var s = javajs.util.ZipTools.getStreamAsString (bis); +bis.close (); +return s; +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +return ""; +} else { +throw e; +} +} +}, "javajs.api.GenericZipTools,~A"); +}); diff --git a/bin/javajs/util/ZipTools.class b/bin/javajs/util/ZipTools.class index ee31ca7..6d95ca3 100644 Binary files a/bin/javajs/util/ZipTools.class and b/bin/javajs/util/ZipTools.class differ diff --git a/bin/javajs/util/ZipTools.js b/bin/javajs/util/ZipTools.js index 5e0ad7b..fba24e6 100644 --- a/bin/javajs/util/ZipTools.js +++ b/bin/javajs/util/ZipTools.js @@ -1,308 +1,308 @@ -Clazz.declarePackage ("javajs.util"); -Clazz.load (["javajs.api.GenericZipTools"], "javajs.util.ZipTools", ["java.io.BufferedInputStream", "$.IOException", "java.lang.Boolean", "java.util.zip.CRC32", "$.GZIPInputStream", "$.ZipEntry", "$.ZipInputStream", "javajs.api.GenericZipInputStream", "$.ZInputStream", "javajs.util.BArray", "$.Lst", "$.PT", "$.Rdr", "$.SB"], function () { -c$ = Clazz.declareType (javajs.util, "ZipTools", null, javajs.api.GenericZipTools); -Clazz.makeConstructor (c$, -function () { -}); -Clazz.overrideMethod (c$, "newZipInputStream", -function (is) { -return javajs.util.ZipTools.newZIS (is); -}, "java.io.InputStream"); -c$.newZIS = Clazz.defineMethod (c$, "newZIS", -($fz = function (is) { -return (Clazz.instanceOf (is, javajs.api.ZInputStream) ? is : Clazz.instanceOf (is, java.io.BufferedInputStream) ? new javajs.api.GenericZipInputStream (is) : new javajs.api.GenericZipInputStream ( new java.io.BufferedInputStream (is))); -}, $fz.isPrivate = true, $fz), "java.io.InputStream"); -Clazz.overrideMethod (c$, "getAllZipData", -function (is, subfileList, name0, binaryFileList, fileData) { -var zis = javajs.util.ZipTools.newZIS (is); -var ze; -var listing = new javajs.util.SB (); -binaryFileList = "|" + binaryFileList + "|"; -var prefix = javajs.util.PT.join (subfileList, '/', 1); -var prefixd = null; -if (prefix != null) { -prefixd = prefix.substring (0, prefix.indexOf ("/") + 1); -if (prefixd.length == 0) prefixd = null; -}try { -while ((ze = zis.getNextEntry ()) != null) { -var name = ze.getName (); -if (prefix != null && prefixd != null && !(name.equals (prefix) || name.startsWith (prefixd))) continue; -listing.append (name).appendC ('\n'); -var sname = "|" + name.substring (name.lastIndexOf ("/") + 1) + "|"; -var asBinaryString = (binaryFileList.indexOf (sname) >= 0); -var bytes = javajs.util.Rdr.getLimitedStreamBytes (zis, ze.getSize ()); -var str; -if (asBinaryString) { -str = this.getBinaryStringForBytes (bytes); -name += ":asBinaryString"; -} else { -str = javajs.util.Rdr.fixUTF (bytes); -}str = "BEGIN Directory Entry " + name + "\n" + str + "\nEND Directory Entry " + name + "\n"; -fileData.put (name0 + "|" + name, str); -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -fileData.put ("#Directory_Listing", listing.toString ()); -}, "java.io.InputStream,~A,~S,~S,java.util.Map"); -Clazz.defineMethod (c$, "getBinaryStringForBytes", -($fz = function (bytes) { -var ret = new javajs.util.SB (); -for (var i = 0; i < bytes.length; i++) ret.append (Integer.toHexString (bytes[i] & 0xFF)).appendC (' '); - -return ret.toString (); -}, $fz.isPrivate = true, $fz), "~A"); -Clazz.overrideMethod (c$, "getZipFileDirectory", -function (bis, list, listPtr, asBufferedInputStream) { -var ret; -if (list == null || listPtr >= list.length) return this.getZipDirectoryAsStringAndClose (bis); -bis = javajs.util.Rdr.getPngZipStream (bis, true); -var fileName = list[listPtr]; -var zis = new java.util.zip.ZipInputStream (bis); -var ze; -try { -var isAll = (fileName.equals (".")); -if (isAll || fileName.lastIndexOf ("/") == fileName.length - 1) { -ret = new javajs.util.SB (); -while ((ze = zis.getNextEntry ()) != null) { -var name = ze.getName (); -if (isAll || name.startsWith (fileName)) ret.append (name).appendC ('\n'); -} -var str = ret.toString (); -return (asBufferedInputStream ? javajs.util.Rdr.getBIS (str.getBytes ()) : str); -}var pt = fileName.indexOf (":asBinaryString"); -var asBinaryString = (pt > 0); -if (asBinaryString) fileName = fileName.substring (0, pt); -fileName = fileName.$replace ('\\', '/'); -while ((ze = zis.getNextEntry ()) != null && !fileName.equals (ze.getName ())) { -} -var bytes = (ze == null ? null : javajs.util.Rdr.getLimitedStreamBytes (zis, ze.getSize ())); -ze = null; -zis.close (); -if (bytes == null) return ""; -if (javajs.util.Rdr.isZipB (bytes) || javajs.util.Rdr.isPngZipB (bytes)) return this.getZipFileDirectory (javajs.util.Rdr.getBIS (bytes), list, ++listPtr, asBufferedInputStream); -if (asBufferedInputStream) return javajs.util.Rdr.getBIS (bytes); -if (asBinaryString) { -ret = new javajs.util.SB (); -for (var i = 0; i < bytes.length; i++) ret.append (Integer.toHexString (bytes[i] & 0xFF)).appendC (' '); - -return ret.toString (); -}if (javajs.util.Rdr.isGzipB (bytes)) bytes = javajs.util.Rdr.getLimitedStreamBytes (this.getUnGzippedInputStream (bytes), -1); -return javajs.util.Rdr.fixUTF (bytes); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -return ""; -} else { -throw e; -} -} -}, "java.io.BufferedInputStream,~A,~N,~B"); -Clazz.overrideMethod (c$, "getZipFileContentsAsBytes", -function (bis, list, listPtr) { -var ret = Clazz.newByteArray (0, 0); -var fileName = list[listPtr]; -if (fileName.lastIndexOf ("/") == fileName.length - 1) return ret; -try { -bis = javajs.util.Rdr.getPngZipStream (bis, true); -var zis = new java.util.zip.ZipInputStream (bis); -var ze; -while ((ze = zis.getNextEntry ()) != null) { -if (!fileName.equals (ze.getName ())) continue; -var bytes = javajs.util.Rdr.getLimitedStreamBytes (zis, ze.getSize ()); -return ((javajs.util.Rdr.isZipB (bytes) || javajs.util.Rdr.isPngZipB (bytes)) && ++listPtr < list.length ? this.getZipFileContentsAsBytes (javajs.util.Rdr.getBIS (bytes), list, listPtr) : bytes); -} -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -} else { -throw e; -} -} -return ret; -}, "java.io.BufferedInputStream,~A,~N"); -Clazz.overrideMethod (c$, "getZipDirectoryAsStringAndClose", -function (bis) { -var sb = new javajs.util.SB (); -var s = new Array (0); -try { -s = this.getZipDirectoryOrErrorAndClose (bis, null); -bis.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -for (var i = 0; i < s.length; i++) sb.append (s[i]).appendC ('\n'); - -return sb.toString (); -}, "java.io.BufferedInputStream"); -Clazz.overrideMethod (c$, "getZipDirectoryAndClose", -function (bis, manifestID) { -var s = new Array (0); -try { -s = this.getZipDirectoryOrErrorAndClose (bis, manifestID); -bis.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -System.out.println (e.toString ()); -} else { -throw e; -} -} -return s; -}, "java.io.BufferedInputStream,~S"); -Clazz.defineMethod (c$, "getZipDirectoryOrErrorAndClose", -($fz = function (bis, manifestID) { -bis = javajs.util.Rdr.getPngZipStream (bis, true); -var v = new javajs.util.Lst (); -var zis = new java.util.zip.ZipInputStream (bis); -var ze; -var manifest = null; -while ((ze = zis.getNextEntry ()) != null) { -var fileName = ze.getName (); -if (manifestID != null && fileName.startsWith (manifestID)) manifest = javajs.util.ZipTools.getStreamAsString (zis); - else if (!fileName.startsWith ("__MACOS")) v.addLast (fileName); -} -zis.close (); -if (manifestID != null) v.add (0, manifest == null ? "" : manifest + "\n############\n"); -return v.toArray ( new Array (v.size ())); -}, $fz.isPrivate = true, $fz), "java.io.BufferedInputStream,~S"); -c$.getStreamAsString = Clazz.defineMethod (c$, "getStreamAsString", -function (is) { -return javajs.util.Rdr.fixUTF (javajs.util.Rdr.getLimitedStreamBytes (is, -1)); -}, "java.io.InputStream"); -Clazz.overrideMethod (c$, "newGZIPInputStream", -function (is) { -return new java.io.BufferedInputStream ( new java.util.zip.GZIPInputStream (is, 512)); -}, "java.io.InputStream"); -Clazz.overrideMethod (c$, "getUnGzippedInputStream", -function (bytes) { -try { -return javajs.util.Rdr.getUnzippedInputStream (this, javajs.util.Rdr.getBIS (bytes)); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -return null; -} else { -throw e; -} -} -}, "~A"); -Clazz.overrideMethod (c$, "addZipEntry", -function (zos, fileName) { -(zos).putNextEntry ( new java.util.zip.ZipEntry (fileName)); -}, "~O,~S"); -Clazz.overrideMethod (c$, "closeZipEntry", -function (zos) { -(zos).closeEntry (); -}, "~O"); -Clazz.overrideMethod (c$, "getZipOutputStream", -function (bos) { -{ -return javajs.api.Interface.getInterface( -"java.util.zip.ZipOutputStream").setZOS(bos); -}}, "~O"); -Clazz.overrideMethod (c$, "getCrcValue", -function (bytes) { -var crc = new java.util.zip.CRC32 (); -crc.update (bytes, 0, bytes.length); -return crc.getValue (); -}, "~A"); -Clazz.overrideMethod (c$, "readFileAsMap", -function (bis, bdata, name) { -var pt = (name == null ? -1 : name.indexOf ("|")); -name = (pt >= 0 ? name.substring (pt + 1) : null); -try { -if (javajs.util.Rdr.isPngZipStream (bis)) { -var isImage = "_IMAGE_".equals (name); -if (name == null || isImage) bdata.put ((isImage ? "_DATA_" : "_IMAGE_"), new javajs.util.BArray (javajs.util.ZipTools.getPngImageBytes (bis))); -if (!isImage) this.cacheZipContents (bis, name, bdata, true); -} else if (javajs.util.Rdr.isZipS (bis)) { -this.cacheZipContents (bis, name, bdata, true); -} else if (name == null) { -bdata.put ("_DATA_", new javajs.util.BArray (javajs.util.Rdr.getLimitedStreamBytes (bis, -1))); -} else { -throw new java.io.IOException ("ZIP file " + name + " not found"); -}bdata.put ("$_BINARY_$", Boolean.TRUE); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -bdata.clear (); -bdata.put ("_ERROR_", e.getMessage ()); -} else { -throw e; -} -} -}, "java.io.BufferedInputStream,java.util.Map,~S"); -Clazz.overrideMethod (c$, "cacheZipContents", -function (bis, fileName, cache, asByteArray) { -var zis = javajs.util.ZipTools.newZIS (bis); -var ze; -var listing = new javajs.util.SB (); -var n = 0; -var oneFile = (asByteArray && fileName != null); -var pt = (oneFile ? fileName.indexOf ("|") : -1); -var file0 = (pt >= 0 ? fileName : null); -if (pt >= 0) fileName = fileName.substring (0, pt); -try { -while ((ze = zis.getNextEntry ()) != null) { -var name = ze.getName (); -if (fileName != null) { -if (oneFile) { -if (!name.equalsIgnoreCase (fileName)) continue; -} else { -listing.append (name).appendC ('\n'); -}}var nBytes = ze.getSize (); -var bytes = javajs.util.Rdr.getLimitedStreamBytes (zis, nBytes); -if (file0 != null) { -this.readFileAsMap (javajs.util.Rdr.getBIS (bytes), cache, file0); -return null; -}n += bytes.length; -var o = (asByteArray ? new javajs.util.BArray (bytes) : bytes); -cache.put ((oneFile ? "_DATA_" : (fileName == null ? "" : fileName + "|") + name), o); -if (oneFile) break; -} -zis.close (); -} catch (e) { -if (Clazz.exceptionOf (e, Exception)) { -try { -zis.close (); -} catch (e1) { -if (Clazz.exceptionOf (e1, java.io.IOException)) { -} else { -throw e1; -} -} -return null; -} else { -throw e; -} -} -if (n == 0 || fileName == null) return null; -System.out.println ("ZipTools cached " + n + " bytes from " + fileName); -return listing.toString (); -}, "java.io.BufferedInputStream,~S,java.util.Map,~B"); -c$.getPngImageBytes = Clazz.defineMethod (c$, "getPngImageBytes", -($fz = function (bis) { -try { -if (javajs.util.Rdr.isPngZipStream (bis)) { -var pt_count = Clazz.newIntArray (2, 0); -javajs.util.Rdr.getPngZipPointAndCount (bis, pt_count); -if (pt_count[1] != 0) return javajs.util.ZipTools.deActivatePngZipB (javajs.util.Rdr.getLimitedStreamBytes (bis, pt_count[0])); -}return javajs.util.Rdr.getLimitedStreamBytes (bis, -1); -} catch (e) { -if (Clazz.exceptionOf (e, java.io.IOException)) { -return null; -} else { -throw e; -} -} -}, $fz.isPrivate = true, $fz), "java.io.BufferedInputStream"); -c$.deActivatePngZipB = Clazz.defineMethod (c$, "deActivatePngZipB", -($fz = function (bytes) { -if (javajs.util.Rdr.isPngZipB (bytes)) bytes[51] = 32; -return bytes; -}, $fz.isPrivate = true, $fz), "~A"); -}); +Clazz.declarePackage ("javajs.util"); +Clazz.load (["javajs.api.GenericZipTools"], "javajs.util.ZipTools", ["java.io.BufferedInputStream", "$.IOException", "java.lang.Boolean", "java.util.zip.CRC32", "$.GZIPInputStream", "$.ZipEntry", "$.ZipInputStream", "javajs.api.GenericZipInputStream", "$.ZInputStream", "javajs.util.BArray", "$.Lst", "$.PT", "$.Rdr", "$.SB"], function () { +c$ = Clazz.declareType (javajs.util, "ZipTools", null, javajs.api.GenericZipTools); +Clazz.makeConstructor (c$, +function () { +}); +Clazz.overrideMethod (c$, "newZipInputStream", +function (is) { +return javajs.util.ZipTools.newZIS (is); +}, "java.io.InputStream"); +c$.newZIS = Clazz.defineMethod (c$, "newZIS", +($fz = function (is) { +return (Clazz.instanceOf (is, javajs.api.ZInputStream) ? is : Clazz.instanceOf (is, java.io.BufferedInputStream) ? new javajs.api.GenericZipInputStream (is) : new javajs.api.GenericZipInputStream ( new java.io.BufferedInputStream (is))); +}, $fz.isPrivate = true, $fz), "java.io.InputStream"); +Clazz.overrideMethod (c$, "getAllZipData", +function (is, subfileList, name0, binaryFileList, fileData) { +var zis = javajs.util.ZipTools.newZIS (is); +var ze; +var listing = new javajs.util.SB (); +binaryFileList = "|" + binaryFileList + "|"; +var prefix = javajs.util.PT.join (subfileList, '/', 1); +var prefixd = null; +if (prefix != null) { +prefixd = prefix.substring (0, prefix.indexOf ("/") + 1); +if (prefixd.length == 0) prefixd = null; +}try { +while ((ze = zis.getNextEntry ()) != null) { +var name = ze.getName (); +if (prefix != null && prefixd != null && !(name.equals (prefix) || name.startsWith (prefixd))) continue; +listing.append (name).appendC ('\n'); +var sname = "|" + name.substring (name.lastIndexOf ("/") + 1) + "|"; +var asBinaryString = (binaryFileList.indexOf (sname) >= 0); +var bytes = javajs.util.Rdr.getLimitedStreamBytes (zis, ze.getSize ()); +var str; +if (asBinaryString) { +str = this.getBinaryStringForBytes (bytes); +name += ":asBinaryString"; +} else { +str = javajs.util.Rdr.fixUTF (bytes); +}str = "BEGIN Directory Entry " + name + "\n" + str + "\nEND Directory Entry " + name + "\n"; +fileData.put (name0 + "|" + name, str); +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +fileData.put ("#Directory_Listing", listing.toString ()); +}, "java.io.InputStream,~A,~S,~S,java.util.Map"); +Clazz.defineMethod (c$, "getBinaryStringForBytes", +($fz = function (bytes) { +var ret = new javajs.util.SB (); +for (var i = 0; i < bytes.length; i++) ret.append (Integer.toHexString (bytes[i] & 0xFF)).appendC (' '); + +return ret.toString (); +}, $fz.isPrivate = true, $fz), "~A"); +Clazz.overrideMethod (c$, "getZipFileDirectory", +function (bis, list, listPtr, asBufferedInputStream) { +var ret; +if (list == null || listPtr >= list.length) return this.getZipDirectoryAsStringAndClose (bis); +bis = javajs.util.Rdr.getPngZipStream (bis, true); +var fileName = list[listPtr]; +var zis = new java.util.zip.ZipInputStream (bis); +var ze; +try { +var isAll = (fileName.equals (".")); +if (isAll || fileName.lastIndexOf ("/") == fileName.length - 1) { +ret = new javajs.util.SB (); +while ((ze = zis.getNextEntry ()) != null) { +var name = ze.getName (); +if (isAll || name.startsWith (fileName)) ret.append (name).appendC ('\n'); +} +var str = ret.toString (); +return (asBufferedInputStream ? javajs.util.Rdr.getBIS (str.getBytes ()) : str); +}var pt = fileName.indexOf (":asBinaryString"); +var asBinaryString = (pt > 0); +if (asBinaryString) fileName = fileName.substring (0, pt); +fileName = fileName.$replace ('\\', '/'); +while ((ze = zis.getNextEntry ()) != null && !fileName.equals (ze.getName ())) { +} +var bytes = (ze == null ? null : javajs.util.Rdr.getLimitedStreamBytes (zis, ze.getSize ())); +ze = null; +zis.close (); +if (bytes == null) return ""; +if (javajs.util.Rdr.isZipB (bytes) || javajs.util.Rdr.isPngZipB (bytes)) return this.getZipFileDirectory (javajs.util.Rdr.getBIS (bytes), list, ++listPtr, asBufferedInputStream); +if (asBufferedInputStream) return javajs.util.Rdr.getBIS (bytes); +if (asBinaryString) { +ret = new javajs.util.SB (); +for (var i = 0; i < bytes.length; i++) ret.append (Integer.toHexString (bytes[i] & 0xFF)).appendC (' '); + +return ret.toString (); +}if (javajs.util.Rdr.isGzipB (bytes)) bytes = javajs.util.Rdr.getLimitedStreamBytes (this.getUnGzippedInputStream (bytes), -1); +return javajs.util.Rdr.fixUTF (bytes); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +return ""; +} else { +throw e; +} +} +}, "java.io.BufferedInputStream,~A,~N,~B"); +Clazz.overrideMethod (c$, "getZipFileContentsAsBytes", +function (bis, list, listPtr) { +var ret = Clazz.newByteArray (0, 0); +var fileName = list[listPtr]; +if (fileName.lastIndexOf ("/") == fileName.length - 1) return ret; +try { +bis = javajs.util.Rdr.getPngZipStream (bis, true); +var zis = new java.util.zip.ZipInputStream (bis); +var ze; +while ((ze = zis.getNextEntry ()) != null) { +if (!fileName.equals (ze.getName ())) continue; +var bytes = javajs.util.Rdr.getLimitedStreamBytes (zis, ze.getSize ()); +return ((javajs.util.Rdr.isZipB (bytes) || javajs.util.Rdr.isPngZipB (bytes)) && ++listPtr < list.length ? this.getZipFileContentsAsBytes (javajs.util.Rdr.getBIS (bytes), list, listPtr) : bytes); +} +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +} else { +throw e; +} +} +return ret; +}, "java.io.BufferedInputStream,~A,~N"); +Clazz.overrideMethod (c$, "getZipDirectoryAsStringAndClose", +function (bis) { +var sb = new javajs.util.SB (); +var s = new Array (0); +try { +s = this.getZipDirectoryOrErrorAndClose (bis, null); +bis.close (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +for (var i = 0; i < s.length; i++) sb.append (s[i]).appendC ('\n'); + +return sb.toString (); +}, "java.io.BufferedInputStream"); +Clazz.overrideMethod (c$, "getZipDirectoryAndClose", +function (bis, manifestID) { +var s = new Array (0); +try { +s = this.getZipDirectoryOrErrorAndClose (bis, manifestID); +bis.close (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +System.out.println (e.toString ()); +} else { +throw e; +} +} +return s; +}, "java.io.BufferedInputStream,~S"); +Clazz.defineMethod (c$, "getZipDirectoryOrErrorAndClose", +($fz = function (bis, manifestID) { +bis = javajs.util.Rdr.getPngZipStream (bis, true); +var v = new javajs.util.Lst (); +var zis = new java.util.zip.ZipInputStream (bis); +var ze; +var manifest = null; +while ((ze = zis.getNextEntry ()) != null) { +var fileName = ze.getName (); +if (manifestID != null && fileName.startsWith (manifestID)) manifest = javajs.util.ZipTools.getStreamAsString (zis); + else if (!fileName.startsWith ("__MACOS")) v.addLast (fileName); +} +zis.close (); +if (manifestID != null) v.add (0, manifest == null ? "" : manifest + "\n############\n"); +return v.toArray ( new Array (v.size ())); +}, $fz.isPrivate = true, $fz), "java.io.BufferedInputStream,~S"); +c$.getStreamAsString = Clazz.defineMethod (c$, "getStreamAsString", +function (is) { +return javajs.util.Rdr.fixUTF (javajs.util.Rdr.getLimitedStreamBytes (is, -1)); +}, "java.io.InputStream"); +Clazz.overrideMethod (c$, "newGZIPInputStream", +function (is) { +return new java.io.BufferedInputStream ( new java.util.zip.GZIPInputStream (is, 512)); +}, "java.io.InputStream"); +Clazz.overrideMethod (c$, "getUnGzippedInputStream", +function (bytes) { +try { +return javajs.util.Rdr.getUnzippedInputStream (this, javajs.util.Rdr.getBIS (bytes)); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +return null; +} else { +throw e; +} +} +}, "~A"); +Clazz.overrideMethod (c$, "addZipEntry", +function (zos, fileName) { +(zos).putNextEntry ( new java.util.zip.ZipEntry (fileName)); +}, "~O,~S"); +Clazz.overrideMethod (c$, "closeZipEntry", +function (zos) { +(zos).closeEntry (); +}, "~O"); +Clazz.overrideMethod (c$, "getZipOutputStream", +function (bos) { +{ +return javajs.api.Interface.getInterface( +"java.util.zip.ZipOutputStream").setZOS(bos); +}}, "~O"); +Clazz.overrideMethod (c$, "getCrcValue", +function (bytes) { +var crc = new java.util.zip.CRC32 (); +crc.update (bytes, 0, bytes.length); +return crc.getValue (); +}, "~A"); +Clazz.overrideMethod (c$, "readFileAsMap", +function (bis, bdata, name) { +var pt = (name == null ? -1 : name.indexOf ("|")); +name = (pt >= 0 ? name.substring (pt + 1) : null); +try { +if (javajs.util.Rdr.isPngZipStream (bis)) { +var isImage = "_IMAGE_".equals (name); +if (name == null || isImage) bdata.put ((isImage ? "_DATA_" : "_IMAGE_"), new javajs.util.BArray (javajs.util.ZipTools.getPngImageBytes (bis))); +if (!isImage) this.cacheZipContents (bis, name, bdata, true); +} else if (javajs.util.Rdr.isZipS (bis)) { +this.cacheZipContents (bis, name, bdata, true); +} else if (name == null) { +bdata.put ("_DATA_", new javajs.util.BArray (javajs.util.Rdr.getLimitedStreamBytes (bis, -1))); +} else { +throw new java.io.IOException ("ZIP file " + name + " not found"); +}bdata.put ("$_BINARY_$", Boolean.TRUE); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +bdata.clear (); +bdata.put ("_ERROR_", e.getMessage ()); +} else { +throw e; +} +} +}, "java.io.BufferedInputStream,java.util.Map,~S"); +Clazz.overrideMethod (c$, "cacheZipContents", +function (bis, fileName, cache, asByteArray) { +var zis = javajs.util.ZipTools.newZIS (bis); +var ze; +var listing = new javajs.util.SB (); +var n = 0; +var oneFile = (asByteArray && fileName != null); +var pt = (oneFile ? fileName.indexOf ("|") : -1); +var file0 = (pt >= 0 ? fileName : null); +if (pt >= 0) fileName = fileName.substring (0, pt); +try { +while ((ze = zis.getNextEntry ()) != null) { +var name = ze.getName (); +if (fileName != null) { +if (oneFile) { +if (!name.equalsIgnoreCase (fileName)) continue; +} else { +listing.append (name).appendC ('\n'); +}}var nBytes = ze.getSize (); +var bytes = javajs.util.Rdr.getLimitedStreamBytes (zis, nBytes); +if (file0 != null) { +this.readFileAsMap (javajs.util.Rdr.getBIS (bytes), cache, file0); +return null; +}n += bytes.length; +var o = (asByteArray ? new javajs.util.BArray (bytes) : bytes); +cache.put ((oneFile ? "_DATA_" : (fileName == null ? "" : fileName + "|") + name), o); +if (oneFile) break; +} +zis.close (); +} catch (e) { +if (Clazz.exceptionOf (e, Exception)) { +try { +zis.close (); +} catch (e1) { +if (Clazz.exceptionOf (e1, java.io.IOException)) { +} else { +throw e1; +} +} +return null; +} else { +throw e; +} +} +if (n == 0 || fileName == null) return null; +System.out.println ("ZipTools cached " + n + " bytes from " + fileName); +return listing.toString (); +}, "java.io.BufferedInputStream,~S,java.util.Map,~B"); +c$.getPngImageBytes = Clazz.defineMethod (c$, "getPngImageBytes", +($fz = function (bis) { +try { +if (javajs.util.Rdr.isPngZipStream (bis)) { +var pt_count = Clazz.newIntArray (2, 0); +javajs.util.Rdr.getPngZipPointAndCount (bis, pt_count); +if (pt_count[1] != 0) return javajs.util.ZipTools.deActivatePngZipB (javajs.util.Rdr.getLimitedStreamBytes (bis, pt_count[0])); +}return javajs.util.Rdr.getLimitedStreamBytes (bis, -1); +} catch (e) { +if (Clazz.exceptionOf (e, java.io.IOException)) { +return null; +} else { +throw e; +} +} +}, $fz.isPrivate = true, $fz), "java.io.BufferedInputStream"); +c$.deActivatePngZipB = Clazz.defineMethod (c$, "deActivatePngZipB", +($fz = function (bytes) { +if (javajs.util.Rdr.isPngZipB (bytes)) bytes[51] = 32; +return bytes; +}, $fz.isPrivate = true, $fz), "~A"); +}); diff --git a/bin/lang/Messages.properties b/bin/lang/Messages.properties deleted file mode 100644 index b2bf58b..0000000 --- a/bin/lang/Messages.properties +++ /dev/null @@ -1,1247 +0,0 @@ -action.refresh_services = Refresh Services -action.reset_services = Reset Services -action.merge_results = Merge Results -action.load_scheme = Load scheme -action.save_scheme = Save scheme -action.save_image = Save Image -action.paste = Paste -action.show_html_source = Show HTML Source -action.print = Print -action.web_service = Web Service -action.cancel_job = Cancel Job -action.start_job = Start Job -action.revert = Revert -action.move_down = Move Down -action.move_up = Move Up -action.remove_return_datatype = Remove return datatype -action.add_return_datatype = Add return datatype -action.remove_input_parameter = Remove selected input parameter -action.add_input_parameter = Add input parameter -action.edit = Edit -action.new = New -action.open_file = Open file -action.show_unconserved = Show Unconserved -action.open_new_alignment = Open new alignment -action.raise_associated_windows = Raise Associated Windows -action.minimize_associated_windows = Minimize Associated Windows -action.close_all = Close all -action.load_project = Load Project -action.save_project = Save Project -action.quit = Quit -action.expand_views = Expand Views -action.gather_views = Gather Views -action.page_setup = Page Setup -action.reload = Reload -action.load = Load -action.open = Open -action.cancel = Cancel -action.create = Create -action.update = Update -action.delete = Delete -action.snapshot = Snapshot -action.clear = Clear -action.accept = Accept -action.select_ddbb = --- Select Database --- -action.undo = Undo -action.redo = Redo -action.reset = Reset -action.remove_left = Remove left -action.remove_right = Remove right -action.remove_empty_columns = Remove Empty Columns -action.remove_all_gaps = Remove All Gaps -action.left_justify_alignment = Left Justify Alignment -action.right_justify_alignment = Right Justify Alignment -action.boxes = Boxes -action.text = Text -action.by_pairwise_id = by Pairwise Identity -action.by_id = by Id -action.by_length = by Length -action.by_group = by Group -action.unmark_as_reference = Unmark as Reference -action.set_as_reference = Set as Reference -action.remove = Remove -action.remove_redundancy = Remove Redundancy... -action.pairwise_alignment = Pairwise Alignments... -action.by_rna_helixes = by RNA Helices -action.user_defined = User Defined... -action.by_conservation = By Conservation -action.wrap = Wrap -action.show_gaps = Show Gaps -action.show_hidden_markers = Show Hidden Markers -action.find = Find -action.undefine_groups = Undefine Groups -action.create_groups = Create Groups -action.make_groups_selection = Make Groups For Selection -action.copy = Copy -action.cut = Cut -action.font = Font... -action.scale_above = Scale Above -action.scale_left = Scale Left -action.scale_right = Scale Right -action.by_tree_order = By Tree Order -action.sort = Sort -action.calculate_tree = Calculate Tree -action.help = Help -action.by_annotation = by Annotation... -action.invert_sequence_selection = Invert Sequence Selection -action.invert_column_selection = Invert Column Selection -action.show = Show -action.hide = Hide -action.ok = OK -action.set_defaults = Defaults -action.create_group = Create Group -action.remove_group = Remove Group -action.edit_group = Edit Group -action.border_colour = Border colour -action.edit_new_group = Edit New Group -action.hide_sequences = Hide Sequences -action.sequences = Sequences -action.ids = IDS -action.ids_sequences = IDS and sequences -action.reveal_all = Reveal All -action.reveal_sequences = Reveal Sequences -action.find_all = Find all -action.find_next = Find next -action.file = File -action.view = View -action.annotations = Annotations -action.change_params = Change Parameters -action.apply = Apply -action.apply_threshold_all_groups = Apply threshold to all groups -action.apply_all_groups = Apply to all Groups -action.by_chain = By Chain -action.by_sequence = By Sequence -action.paste_annotations = Paste Annotations -action.format = Format -action.select = Select -action.new_view = New View -action.close = Close -action.add = Add -action.save_as_default = Save as default -action.save_as = Save as -action.save = Save -action.cancel_fetch = Cancel Fetch -action.save_omit_hidden_columns = Save / Omit Hidden Regions -action.change_font = Change Font -action.change_font_tree_panel = Change Font (Tree Panel) -action.colour = Colour -action.calculate = Calculate -action.select_all = Select all -action.deselect_all = Deselect all -action.invert_selection = Invert selection -action.using_jmol = Using Jmol -action.link = Link -action.group_link = Group Link -action.show_chain = Show Chain -action.show_group = Show Group -action.fetch_db_references = Fetch DB References -action.view_flanking_regions = Show flanking regions -label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment -label.str = Str: -label.seq = Seq: -label.structures_manager = Structures Manager -label.nickname = Nickname: -label.url = URL: -label.input_file_url = Enter URL or Input File -label.select_feature = Select feature: -label.name = Name -label.name_param = Name: {0} -label.group = Group -label.group_name = Group Name -label.group_description = Group Description -label.edit_group_name_description = Edit Group Name/Description -label.colour = Colour: -label.description = Description: -label.start = Start: -label.end = End: -label.current_parameter_set_name = Current parameter set name: -label.service_action = Service Action: -label.post_url = POST URL: -label.url_suffix = URL Suffix -label.sequence_source = Sequence Source -label.per_seq = per Sequence -label.result_vertically_separable = Results are vertically separable -label.amend = Amend -label.undo_command = Undo {0} -label.redo_command = Redo {0} -label.principal_component_analysis = Principal Component Analysis -label.average_distance_identity = Average Distance Using % Identity -label.neighbour_joining_identity = Neighbour Joining Using % Identity -label.treecalc_title = {0} Using {1} -label.tree_calc_av = Average Distance -label.tree_calc_nj = Neighbour Joining -label.select_score_model = Select score model -label.score_model_pid = % Identity -label.score_model_blosum62 = BLOSUM62 -label.score_model_pam250 = PAM 250 -label.score_model_conservation = Physicochemical property conservation -label.score_model_enhconservation = Physicochemical property conservation -label.status_bar = Status bar -label.out_to_textbox = Output to Textbox -label.clustalx = Clustalx -label.clustal = Clustal -label.zappo = Zappo -label.taylor = Taylor -label.blc = BLC -label.fasta = Fasta -label.msf = MSF -label.pfam = PFAM -label.pileup = Pileup -label.pir = PIR -label.hydrophobicity = Hydrophobicity -label.helix_propensity = Helix Propensity -label.strand_propensity = Strand Propensity -label.turn_propensity = Turn Propensity -label.buried_index = Buried Index -label.purine_pyrimidine = Purine/Pyrimidine -label.percentage_identity = Percentage Identity -label.blosum62 = BLOSUM62 -label.blosum62_score = BLOSUM62 Score -label.tcoffee_scores = T-Coffee Scores -label.average_distance_bloslum62 = Average Distance Using BLOSUM62 -label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62 -label.show_annotations = Show annotations -label.hide_annotations = Hide annotations -label.show_all_seq_annotations = Show sequence related -label.hide_all_seq_annotations = Hide sequence related -label.show_all_al_annotations = Show alignment related -label.hide_all_al_annotations = Hide alignment related -label.hide_all = Hide all -label.add_reference_annotations = Add reference annotations -label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).
    Accepts regular expressions - search Help for 'regex' for details. -label.colour_text = Colour Text -label.show_non_conversed = Show nonconserved -label.overview_window = Overview Window -label.none = None -label.above_identity_threshold = Above Identity Threshold -label.show_sequence_features = Show Sequence Features -label.nucleotide = Nucleotide -label.protein = Protein -label.to_new_alignment = To New Alignment -label.to_this_alignment = Add To This Alignment -label.apply_colour_to_all_groups = Apply Colour To All Groups -label.modify_identity_thereshold = Modify Identity Threshold... -label.modify_conservation_thereshold = Modify Conservation Threshold... -label.input_from_textbox = Input from textbox -label.centre_column_labels = Centre column labels -label.automatic_scrolling = Automatic Scrolling -label.documentation = Documentation -label.about = About... -label.show_sequence_limits = Show Sequence Limits -label.feature_settings = Feature Settings... -label.all_columns = All Columns -label.all_sequences = All Sequences -label.selected_columns = Selected Columns -label.selected_sequences = Selected Sequences -label.except_selected_sequences = All except selected sequences -label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H) -label.selected_region = Selected Region -label.all_sequences_columns = All Sequences and Columns -label.hide_insertions = Hide columns gapped for selection -label.hide_selected_annotations = Hide selected annotations -label.show_selected_annotations = Show selected annotations -label.group_consensus = Group Consensus -label.group_conservation = Group Conservation -label.show_consensus_histogram = Show Consensus Histogram -label.show_consensus_logo = Show Consensus Logo -label.norm_consensus_logo = Normalise Consensus Logo -label.apply_all_groups = Apply to all groups -label.autocalculated_annotation = Autocalculated Annotation -label.show_first = Show first -label.show_last = Show last -label.struct_from_pdb = Process secondary structure from PDB -label.use_rnaview = Use RNAView for secondary structure -label.autoadd_secstr = Add secondary structure annotation to alignment -label.autoadd_temp = Add Temperature Factor annotation to alignment -label.structure_viewer = Default structure viewer -label.chimera_path = Path to Chimera program -label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.
    Double-click to browse for file. -label.invalid_chimera_path = Chimera path not found or not executable -label.chimera_missing = Chimera structure viewer not found.
    Please enter the path to Chimera (if installed),
    or download and install UCSF Chimera. -label.chimera_failed = Error opening Chimera - is it installed?\nCheck path in Preferences, Structure -label.min_colour = Minimum Colour -label.max_colour = Maximum Colour -label.use_original_colours = Use Original Colours -label.threshold_minmax = Threshold is min/max -label.represent_group_with = Represent Group with {0} -label.selection = Selection -label.group_colour = Group Colour -label.sequence = Sequence -label.view_pdb_structure = View PDB Structure -label.min = Min: -label.max = Max: -label.colour_by_label = Colour by label -label.new_feature = New Feature -label.match_case = Match Case -label.view_alignment_editor = View in alignment editor -label.labels = Labels -label.output_values = Output Values... -label.output_points = Output points... -label.output_transformed_points = Output transformed points -label.input_data = Input Data... -label.nucleotide_matrix = Nucleotide matrix -label.protein_matrix = Protein matrix -label.show_bootstrap_values = Show Bootstrap Values -label.show_distances = Show distances -label.mark_unassociated_leaves = Mark Unassociated Leaves -label.fit_to_window = Fit To Window -label.newick_format = Newick Format -label.select_newick_like_tree_file = Select a newick-like tree file -label.colours = Colours -label.view_mapping = View Mapping -label.wireframe = Wireframe -label.depthcue = Depthcue -label.z_buffering = Z Buffering -label.charge_cysteine = Charge & Cysteine -label.all_chains_visible = All Chains Visible -label.successfully_added_features_alignment = Successfully added features to alignment -label.keyboard_editing_mode = Keyboard editing mode is {0} -label.paste_features_annotations_Tcoffee_here = Paste your features / annotations / T-coffee score file here. -label.removed_columns = Removed {0} columns. -label.removed_empty_columns = Removed {0} empty columns. -label.paste_newick_tree_file = Paste your Newick tree file here. -label.order_by_params = Order by {0} -label.html_content = {0} -label.paste_pdb_file= Paste your PDB file here. -label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0} -label.could_not_parse_newick_file = Could not parse Newick file\!\n {0} -label.successfully_pasted_tcoffee_scores_to_alignment= Successfully pasted T-Coffee scores to alignment. -label.failed_add_tcoffee_scores = Failed to add T-Coffee scores: -label.successfully_pasted_annotation_to_alignment= Successfully pasted annotation to alignment. -label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file = Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file -label.successfully_pasted_alignment_file = Successfully pasted alignment file -label.paste_your_alignment_file = Paste your alignment file here -label.paste_your = Paste your -label.finished_searching = Finished searching -label.search_results= Search results {0} : {1} -label.found_match_for = Found match for {0} -label.font = Font: -label.size = Size: -label.style = Style: -label.enter_redundancy_threshold = Enter the redundancy threshold -label.calculating = Calculating.... -label.modify_conservation_visibility = Modify conservation visibility -label.colour_residues_above_occurence = Colour residues above % occurence -label.set_this_label_text = set this label text -label.sequences_from = Sequences from {0} -label.successfully_loaded_file = Successfully loaded file {0} -label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format. -label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard. -label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment. -label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file -label.source_to_target = {0} ... {1} -label.per_sequence_only= Per-sequence only -label.to_file = to File -label.to_textbox = to Textbox -label.jalview = Jalview -label.csv_spreadsheet = CSV (Spreadsheet) -label.status = Status -label.channels = Channels -label.channel_title_item_count = {0} ({1}) -label.blog_item_published_on_date = {0} {1} -label.select_das_service_from_table = Select a DAS service from the table to read a full description here. -label.session_update = Session Update -label.new_vamsas_session = New Vamsas Session -label.load_vamsas_session = Load Vamsas Session -label.save_vamsas_session = Save Vamsas Session -label.select_vamsas_session_opened_as_new_vamsas_session= Select a vamsas session to be opened as a new vamsas session. -label.open_saved_vamsas_session = Open a saved VAMSAS session -label.groovy_console = Groovy Console... -label.lineart = Lineart -label.dont_ask_me_again = Don't ask me again -label.select_eps_character_rendering_style = Select EPS character rendering style -label.invert_selection = Invert Selection -label.optimise_order = Optimise Order -label.seq_sort_by_score = Sequence sort by Score -label.load_colours = Load Colours -label.save_colours = Save Colours -label.fetch_das_features = Fetch DAS Features -label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} -label.database_param = Database: {0} -label.example = Example -label.example_param = Example: {0} -label.select_file_format_before_saving = You must select a file format before saving! -label.file_format_not_specified = File format not specified -label.alignment_contains_hidden_columns = The Alignment contains hidden regions (hidden sequences/columns).\nDo you want to save only the visible alignment? -label.couldnt_save_file = Couldn't save file: {0} -label.error_saving_file = Error Saving File -label.remove_from_default_list = Remove from default list? -label.remove_user_defined_colour = Remove user defined colour -label.you_must_select_least_two_sequences = You must select at least 2 sequences. -label.invalid_selection = Invalid Selection -label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences. -label.sequence_selection_insufficient = Sequence selection insufficient -label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree! -label.not_enough_sequences = Not enough sequences -label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services. -label.sequences_selection_not_aligned = Sequences in selection are not aligned -label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services. -label.sequences_not_aligned = Sequences not aligned -label.problem_reading_tree_file = Problem reading tree file -label.possible_problem_with_tree_file = Possible problem with tree file -label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation. -label.translation_failed = Translation Failed -label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace. -label.implementation_error = Implementation error: -label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name? -label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name -label.ignore_unmatched_dropped_files_info = Do you want to ignore the {0} files whose names did not match any sequence IDs ? -label.ignore_unmatched_dropped_files = Ignore unmatched dropped files? -label.view_name_original = Original -label.enter_view_name = Enter View Name -label.enter_label = Enter label -label.enter_label_for_the_structure = Enter a label for the structure? -label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ? -label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0} -label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n -label.align_to_existing_structure_view = Align to existing structure view -label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease retry, or try downloading them manually. -label.couldnt_load_file = Couldn't load file -label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure. -label.no_pdb_id_in_file = No PDB Id in File -label.couldnt_read_pasted_text = Couldn't read the pasted text {0} -label.error_parsing_text = Error parsing text -label.enter_local_das_source = Enter Nickname & URL of Local DAS Source -label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources! -label.public_das_source = Public DAS source - not editable -label.input_alignment_from_url = Input Alignment From URL -label.input_alignment = Input Alignment -label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session. -label.vamsas_document_import_failed = Vamsas Document Import Failed -label.couldnt_locate = Couldn't locate {0} -label.url_not_found = URL not found -label.no_link_selected = No link selected -label.new_sequence_url_link = New sequence URL link -label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view -label.wrapped_view_no_edit = Wrapped view - no edit -label.error_retrieving_data = Error Retrieving Data -label.user_colour_scheme_must_have_name = User colour scheme must have a name -label.no_name_colour_scheme = No name for colour scheme -label.invalid_url = Invalid URL ! -label.error_loading_file = Error loading file -label.problems_opening_file = Encountered problems opening {0}!! -label.file_open_error = File open error -label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again. -label.no_das_sources_selected_title = No DAS Sources Selected -label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?" -label.duplicate_scheme_name = Duplicate scheme name -label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n -label.jalview_user_survey = Jalview User Survey -label.alignment_properties = Alignment Properties: {0} -label.alignment_props = Alignment Properties -label.input_cut_paste = Cut & Paste Input -label.input_cut_paste_params = Cut & Paste Input - {0} -label.alignment_output_command = Alignment output - {0} -label.annotations = Annotations -label.structure_options = Structure Options -label.features = Features -label.overview_params = Overview {0} -label.paste_newick_file = Paste Newick file -label.load_tree_from_file = From File - -label.colour_by_annotation = Colour by Annotation -label.selection_output_command = Selection output - {0} -label.annotation_for_displayid =

    Annotation for {0}

    -label.pdb_sequence_mapping = PDB - Sequence Mapping -label.pca_details = PCA details -label.redundancy_threshold_selection = Redundancy threshold selection -label.user_defined_colours = User defined colours -label.jalviewLite_release = JalviewLite - Release {0} -label.jaview_build_date = Build date: {0} -label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt, -label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton. -label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK. -label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list -label.jalview_please_cite = If you use Jalview, please cite: -label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) -label.jalview_cite_1_title = Jalview Version 2 - a multiple sequence alignment editor and analysis workbench -label.jalview_cite_1_ref = Bioinformatics doi: 10.1093/bioinformatics/btp033 -label.right_click = Right click -label.to_add_annotation = to add annotation -label.alignment_has_no_annotations = Alignment has no annotations -label.retrieving_pdb_data = Retrieving PDB data... -label.label = Label -label.no_features_added_to_this_alignment = No Features added to this alignment!! -label.features_can_be_added_from_searches_1 = (Features can be added from searches or -label.features_can_be_added_from_searches_2 = from Jalview / GFF features files) -label.calculating_pca= Calculating PCA -label.reveal_columns = Reveal Columns -label.jalview_cannot_open_file = Jalview can't open file -label.jalview_applet = Jalview applet -label.loading_data = Loading data -label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} % -label.calculating_tree = Calculating tree -label.state_queueing = queuing -label.state_running = running -label.state_complete = complete -label.state_completed = finished -label.state_job_cancelled = job cancelled!! -label.state_job_error = job error! -label.server_error_try_later = Server Error! (try later) -label.error_loading_pdb_data = Error loading PDB data!! -label.fetching_pdb_data = Fetching PDB data... -label.structure_type = Structure type -label.settings_for_type = Settings for {0} -label.view_full_application = View in Full Application -label.load_associated_tree = Load Associated Tree ... -label.load_features_annotations = Load Features/Annotations ... -label.export_features = Export Features ... -label.export_annotations = Export Annotations ... -label.to_upper_case = To Upper Case -label.to_lower_case = To Lower Case -label.toggle_case = Toggle Case -label.edit_name_description = Edit Name/Description ... -label.create_sequence_feature = Create Sequence Feature ... -label.edit_sequence = Edit Sequence -label.edit_sequences = Edit Sequences -label.sequence_details = Sequence Details -label.jmol_help = Jmol Help -label.chimera_help = Chimera Help -label.close_viewer = Close Viewer -label.confirm_close_chimera = This will close Jalview''s connection to {0}.
    Do you want to close the Chimera window as well? -label.chimera_help = Chimera Help -label.all = All -label.sort_by = Sort alignment by -label.sort_by_score = Sort by Score -label.sort_by_density = Sort by Density -label.sequence_sort_by_density = Sequence sort by Density -label.sort_ann_by = Sort annotations by -label.sort_annotations_by_sequence = Sort by sequence -label.sort_annotations_by_label = Sort by label -label.reveal = Reveal -label.hide_columns = Hide Columns -label.load_jalview_annotations = Load Jalview Annotations or Features File -label.load_tree_file = Load a tree file -label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences -label.standard_databases = Standard Databases -label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources -label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences. -label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views -label.connect_to_session = Connect to session {0} -label.threshold_feature_display_by_score = Threshold the feature display by score. -label.threshold_feature_no_thereshold = No Threshold -label.threshold_feature_above_thereshold = Above Threshold -label.threshold_feature_below_thereshold = Below Threshold -label.adjust_thereshold = Adjust threshold -label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold. -label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features) -label.select_colour_minimum_value = Select Colour for Minimum Value -label.select_colour_maximum_value = Select Colour for Maximum Value -label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new structure viewer with all structures associated with the current selection and superimpose them using the alignment. -label.open_url_param = Open URL {0} -label.open_url_seqs_param = Open URL ({0}..) ({1} seqs) -label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0} -label.reveal_hidden_columns = Reveal Hidden Columns with Right Mouse Button -label.dark_colour = Dark Colour -label.light_colour = Light Colour -label.highlightnode = Left click to select leaves.
    Double-click to invert leaves.
    Right click to change colour. -label.load_colour_scheme = Load colour scheme -label.copy_format_from = Copy format from -label.toggle_enabled_views = When enabled, allows many views to be selected. -label.select_all_views = Select all views -label.select_many_views = Select many views -label.edit_notes_parameter_set = Click to edit the notes for this parameter set. -label.open_local_file = Open local file -label.enable_automatically_sort_alignment_when_open_new_tree = Enable this to automatically sort
    the alignment when you open
    a new tree. -label.listen_for_selections = Listen for selections -label.selections_mirror_selections_made_same_sequences_other_views = When selected, selections in this view will mirror
    selections made on the same sequences in other views. -label.toggle_sequence_visibility = Shift+H toggles sequence visiblity -label.toggle_columns_visibility = Ctrl+H toggles column visiblity. -label.toggles_visibility_hidden_selected_regions = H toggles visibility of hidden or selected regions -label.rename_tab_eXpand_reGroup= Right-click to rename tab
    Press X to eXpand tabs, G to reGroup. -label.right_align_sequence_id = Right Align Sequence Id -label.sequence_id_tooltip = Sequence ID Tooltip -label.no_services = -label.select_copy_raw_html = Select this if you want to copy raw html -label.share_data_vamsas_applications = Share data with other vamsas applications -label.connect_to = Connect to -label.join_existing_vamsas_session = Join an existing vamsas session -label.from_url = from URL -label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment -label.sort_with_new_tree = Sort With New Tree -label.from_textbox = from Textbox -label.window = Window -label.preferences = Preferences -label.tools = Tools -label.fetch_sequences = Fetch Sequence(s) -label.stop_vamsas_session = Stop Vamsas Session -label.collect_garbage = Collect Garbage -label.show_memory_usage = Show Memory Usage -label.show_java_console = Show Java Console -label.show_jalview_news = Show Jalview News -label.take_snapshot = Take snapshot -label.monospaced_fonts_faster_to_render = Monospaced fonts are faster to render -label.anti_alias_fonts = Anti-alias Fonts (Slower to render) -label.monospaced_font= Monospaced -label.quality = Quality -label.maximize_window = Maximize Window -label.conservation = Conservation -label.consensus = Consensus -label.histogram = Histogram -label.logo = Logo -label.non_positional_features = List Non-positional Features -label.database_references = List Database References -label.share_selection_across_views = Share selection across views -label.scroll_highlighted_regions = Scroll to highlighted regions -label.gap_symbol = Gap Symbol -label.prot_alignment_colour = Protein Alignment Colour -label.nuc_alignment_colour = Nucleotide Alignment Colour -label.address = Address -label.port = Port -label.default_browser_unix = Default Browser (Unix) -label.send_usage_statistics = Send usage statistics -label.check_for_questionnaires = Check for questionnaires -label.check_for_latest_version = Check for latest version -label.url_linkfrom_sequence_id = URL link from Sequence ID -label.use_proxy_server = Use a proxy server -label.eps_rendering_style = EPS rendering style -label.append_start_end = Append /start-end (/15-380) -label.full_sequence_id = Full Sequence Id -label.smooth_font = Smooth Font -label.autocalculate_consensus = AutoCalculate Consensus -label.pad_gaps = Pad Gaps -label.pad_gaps_when_editing = Pad Gaps When Editing -label.automatically_set_id_width = Automatically set ID width -label.figure_id_column_width = Figure ID column width -label.use_modeller_output = Use Modeller Output -label.wrap_alignment = Wrap Alignment -label.right_align_ids = Right Align Ids -label.sequence_name_italics = Italic Sequence Ids -label.open_overview = Open Overview -label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment -label.annotation_shading_default = Annotation Shading Default -label.default_minimum_colour_annotation_shading = Default Minimum Colour for annotation shading -label.default_maximum_colour_annotation_shading = Default Maximum Colour for annotation shading -label.visual = Visual -label.connections = Connections -label.output = Output -label.editing = Editing -label.das_settings = DAS Settings -label.web_services = Web Services -label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter. -label.let_jmol_manage_structure_colours = Let Jmol manage structure colours -label.let_chimera_manage_structure_colours = Let Chimera manage structure colours -label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence -label.index_web_services_menu_by_host_site = Index web services in menu by the host site -label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed
    when a web service URL cannot be accessed by Jalview
    when it starts up -label.new_service_url = New Service URL -label.edit_service_url = Edit Service URL -label.delete_service_url = Delete Service URL -label.details = Details -label.options = Options -label.parameters = Parameters -label.available_das_sources = Available DAS Sources -label.full_details = Full Details -label.authority = Authority -label.type = Type -label.proxy_server = Proxy Server -label.file_output = File Output -label.select_input_type = Select input type -label.set_options_for_type = Set options for type -label.data_input_parameters = Data input parameters -label.data_returned_by_service = Data returned by service -label.rsbs_encoded_service = RSBS Encoded Service -label.parsing_errors = Parsing errors -label.simple_bioinformatics_rest_services = Simple Bioinformatics Rest Services -label.web_service_discovery_urls = Web Service Discovery URLS -label.input_parameter_name = Input Parameter name -label.short_descriptive_name_for_service = Short descriptive name for service -label.function_service_performs = What kind of function the service performs (e.g. alignment, analysis, search, etc). -label.brief_description_service = Brief description of service -label.url_post_data_service = URL to post data to service. Include any special parameters needed here -label.optional_suffix = Optional suffix added to URL when retrieving results from service -label.preferred_gap_character = Which gap character does this service prefer? -label.gap_character = Gap character -label.move_return_type_up_order= Move return type up order -label.move_return_type_down_order= Move return type down order -label.update_user_parameter_set = Update this existing user parameter set -label.delete_user_parameter_set = Delete the currently selected user parameter set -label.create_user_parameter_set = Create a new parameter set with the current settings. -label.revert_changes_user_parameter_set = Undo all changes to the current parameter set -label.start_job_current_settings = Start Job with current settings -label.cancel_job_close_dialog = Close this dialog and cancel job -label.input_output = Input/Output -label.cut_paste = Cut'n'Paste -label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation -label.2d_rna_structure_line = 2D RNA {0} (alignment) -label.2d_rna_sequence_name = 2D RNA - {0} -label.edit_name_and_description_current_group = Edit name and description of current group. -label.view_structure_for = View structure for {0} -label.view_all_structures = View all {0} structures. -label.view_all_representative_structures = View all {0} representative structures. -label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment. -label.associate_structure_with_sequence = Associate Structure with Sequence -label.from_file = from file -label.enter_pdb_id = Enter PDB Id -label.discover_pdb_ids = Discover PDB ids -label.text_colour = Text Colour -label.structure = Structure -label.view_structure = View Structure -label.view_protein_structure = View Protein Structure -label.view_rna_structure = View Nucleotide Structure -label.clustalx_colours = Clustalx colours -label.above_identity_percentage = Above % Identity -label.create_sequence_details_report_annotation_for = Annotation for {0} -label.sequence_details_for = Sequence Details for {0} -label.sequence_name = Sequence Name -label.sequence_description = Sequence Description -label.edit_sequence_name_description = Edit Sequence Name/Description -label.spaces_converted_to_backslashes = Spaces have been converted to _ -label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name -label.select_outline_colour = Select Outline Colour -label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences." -label.web_browser_not_found = Web browser not found -label.select_pdb_file_for = Select a PDB file for {0} -label.html = HTML -label.wrap = Wrap -label.show_database_refs = Show Database Refs -label.show_non_positional_features = Show Non-Positional Features -label.save_png_image = Save As PNG Image -label.load_tree_for_sequence_set = Load a tree for this sequence set -label.export_image = Export Image -label.vamsas_store = VAMSAS store -label.translate_cDNA = Translate as cDNA -label.linked_view_title = Linked cDNA and protein view -label.align = Align -label.extract_scores = Extract Scores -label.get_cross_refs = Get Cross-References -label.sort_alignment_new_tree = Sort Alignment With New Tree -label.add_sequences = Add Sequences -label.new_window = New Window -label.split_window = Split Window -label.refresh_available_sources = Refresh Available Sources -label.use_registry = Use Registry -label.add_local_source = Add Local Source -label.set_as_default = Set as Default -label.show_labels = Show labels -label.background_colour = Background Colour -label.associate_nodes_with = Associate Nodes With -label.jalview_pca_calculation = Jalview PCA Calculation -label.link_name = Link Name -label.pdb_file = PDB file -label.colour_with_jmol = Colour with Jmol -label.colour_with_chimera = Colour with Chimera -label.align_structures = Align structures -label.jmol = Jmol -label.chimera = Chimera -label.sort_alignment_by_tree = Sort Alignment By Tree -label.mark_unlinked_leaves = Mark Unlinked Leaves -label.associate_leaves_with = Associate Leaves With -label.save_colour_scheme_with_unique_name_added_to_colour_menu = Save your colour scheme with a unique name and it will be added to the Colour menu -label.case_sensitive = Case Sensitive -label.lower_case_colour = Lower Case Colour -label.index_by_host = Index by host -label.index_by_type = Index by type -label.enable_jabaws_services = Enable JABAWS Services -label.display_warnings = Display warnings -label.move_url_up = Move URL up -label.move_url_down = Move URL down -label.add_sbrs_definition = Add a SBRS definition -label.edit_sbrs_definition = Edit SBRS definition -label.delete_sbrs_definition = Delete SBRS definition -label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n -label.sequence_names_updated = Sequence names updated -label.dbref_search_completed = DBRef search completed -label.show_all_chains = Show all chains -label.fetch_all_param = Fetch all {0} -label.paste_new_window = Paste To New Window -label.settings_for_param = Settings for {0} -label.view_params = View {0} -label.all_views = All Views -label.align_sequences_to_existing_alignment = Align sequences to an existing alignment -label.realign_with_params = Realign with {0} -label.calcname_with_default_settings = {0} with Defaults -label.action_with_default_settings = {0} with default settings -label.edit_settings_and_run = Edit settings and run... -label.view_and_change_parameters_before_alignment = View and change the parameters before alignment -label.run_with_preset_params = Run {0} with preset -label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation -label.view_documentation = View documentation -label.select_return_type = Select return type -label.translation_of_params = Translation of {0} -label.features_for_params = Features for - {0} -label.annotations_for_params = Annotations for - {0} -label.generating_features_for_params = Generating features for - {0} -label.generating_annotations_for_params = Generating annotations for - {0} -label.varna_params = VARNA - {0} -label.sequence_feature_settings = Sequence Feature Settings -label.pairwise_aligned_sequences = Pairwise Aligned Sequences -label.original_data_for_params = Original Data for {0} -label.points_for_params = Points for {0} -label.transformed_points_for_params = Transformed points for {0} -label.graduated_color_for_params = Graduated Feature Colour for {0} -label.select_backgroud_colour = Select Background Colour -label.invalid_font = Invalid Font -label.separate_multiple_accession_ids = Enter one or more PDB Ids -label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";" -label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire PDB database) -label.replace_commas_semicolons = Replace commas with semi-colons -label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0} -label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0} -label.example_query_param = Example query: {0} -label.enter_value_increase_conservation_visibility = Enter value to increase conservation visibility -label.enter_percentage_identity_above_which_colour_residues = Enter % identity above which to colour residues -label.wswublast_client_credits = To display sequence features an exact Uniprot id with 100% sequence identity match must be entered.\nIn order to display these features, try changing the names of your sequences to the ids suggested below.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1)\:W25-W28 (2005)); -label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences -label.select_columns_containing = Select columns containing -label.select_columns_not_containing = Select columns that do not contain -option.trim_retrieved_seqs = Trim retrieved sequences -label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences. -label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=//=$ -label.use_sequence_id_2 = \nto embed sequence id in URL -label.ws_parameters_for = Parameters for {0} -label.switch_server = Switch server -label.choose_jabaws_server = Choose a server for running this service -label.services_at = Services at {0} -label.rest_client_submit = {0} using {1} -label.fetch_retrieve_from =Retrieve from {0} -label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}
    First is :{2} -#label.feature_settings_click_drag = Click/drag feature types up or down to change render order.
    Double click to select columns containing feature in alignment/current selection
    Pressing Alt will select columns outside features rather than inside
    Pressing Shift to modify current selection (rather than clear current selection)
    Press CTRL or Command/Meta to toggle columns in/outside features
    -label.feature_settings_click_drag = Drag up or down to change render order.
    Double click to select columns containing feature. -label.transparency_tip = Adjust transparency to 'see through' feature colours. -label.opt_and_params_further_details = see further details by right-clicking -label.opt_and_params_show_brief_desc_image_link = Click to show brief description
    Right click for further information. -label.opt_and_params_show_brief_desc = Click to show brief description
    -label.adjusts_width_generated_eps_png = Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed -label.manually_specify_width_left_column = Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set -label.job_created_when_checked = When checked, a job is created for every sequence in the current selection. -label.when_checked_job_visible_region_and_results = When checked, a single job is created for the visible region and results mapped back onto their location in the alignment. Otherwise, a job would be created for every contiguous region visible in the alignment or current selection (e.g. a multiple alignment). -label.flat_file_representation = Flat file representation of this rest service using the Really Simple Bioinformatics Service formalism -label.result_of_parsing_rsbs = Results of parsing the RSBS representation -label.user_preset = User Preset -label.service_preset = Service Preset -label.run_with_preset = Run {0} with preset -label.view_service_doc_url = View {1} -label.submit_sequence = Submit {0} {1} {2} {3} to
    {4} -action.by_title_param = by {0} -label.alignment = Alignment -label.secondary_structure_prediction = Secondary Structure Prediction -label.sequence_database_search = Sequence Database Search -label.analysis = Analysis -label.protein_disorder = Protein Disorder -label.source_from_db_source = Sources from {0} -label.from_msname = from {0} -label.superpose_with = Superpose with ... -action.do = Do -label.scale_label_to_column = Scale Label to Column -label.add_new_row = Add New Row -label.edit_label_description = Edit Label/Description -label.hide_row = Hide This Row -label.delete_row = Delete This Row -label.show_all_hidden_rows = Show All Hidden Rows -label.export_annotation = Export Annotation -label.copy_consensus_sequence = Copy Consensus Sequence -label.helix = Helix -label.sheet = Sheet -label.rna_helix = RNA Helix -label.remove_annotation = Remove Annotation -label.colour_by = Colour by... -label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment -label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment -label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment -label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction -label.multiharmony = Multi-Harmony -label.unable_start_web_service_analysis = Unable to start web service analysis -label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages. -label.prompt_each_time = Prompt each time -label.use_source = Use Source -label.couldnt_save_project = Couldn't save project -label.error_whilst_saving_current_state_to = Error whilst saving current state to {0} -label.error_whilst_loading_project_from = Error whilst loading project from {0} -label.couldnt_load_project = Couldn't load project -label.pca_sequences_not_aligned = The sequences must be aligned before calculating PCA.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services. -label.invalid_name_preset_exists = Invalid name - preset already exists. -label.invalid_name = Invalid name -label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window -label.proxy_authorization_failed = Proxy Authorization Failed -label.internal_jalview_error = Internal Jalview Error -label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located. -label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\! -label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown -label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\! -label.seq_search_service_is_unknown = The Sequence Search Service named {0} is unknown -label.feature_type = Feature Type -label.display = Display -label.service_url = Service URL -label.copied_sequences = Copied sequences -label.cut_sequences = Cut Sequences -label.conservation_colour_increment = Conservation Colour Increment ({0}) -label.percentage_identity_thereshold = Percentage Identity Threshold ({0}) -label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User Colour scheme dialog -label.save_alignment_to_file = Save Alignment to file -label.save_features_to_file = Save Features to File -label.save_annotation_to_file = Save Annotation to File -label.no_features_on_alignment = No features found on alignment -label.save_pdb_file = Save PDB File -label.save_text_to_file = Save Text to File -label.save_state = Save State -label.restore_state = Restore State -label.saving_jalview_project = Saving jalview project {0} -label.loading_jalview_project = Loading jalview project {0} -label.save_vamsas_document_archive = Save Vamsas Document Archive -label.saving_vamsas_doc = Saving VAMSAS Document to {0} -label.load_feature_colours = Load Feature Colours -label.save_feature_colours = Save Feature Colour Scheme -label.dataset_for = {0} Dataset for {1} -label.select_startup_file = Select startup file -label.select_default_browser = Select default web browser -label.save_tree_as_newick = Save tree as newick file -label.create_eps_from_tree = Create EPS file from tree -label.create_png_from_tree = Create PNG image from tree -label.save_colour_scheme = Save colour scheme -label.edit_params_for = Edit parameters for {0} -label.choose_filename_for_param_file = Choose a filename for this parameter file -label.save_as_html = Save as HTML -label.recently_opened = Recently Opened -label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0} jobs running. -label.tree_from = Tree from {0} -label.webservice_job_title = {0} using {1} -label.select_visible_region_of = selected {0} region of {1} -label.visible = Visible -label.select_unselect_visible_regions_from = select and unselected {0} regions from {1} -label.visible_region_of = visible region of -label.webservice_job_title_on = {0} using {1} on {2} -label.updating_vamsas_session = Updating vamsas session -label.loading_file = Loading File: {0} -label.edit_params = Edit {0} -error.not_implemented = Not implemented -error.no_such_method_as_clone1_for = No such method as clone1 for {0} -error.null_from_clone1 = Null from clone1! -error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY. -error.not_yet_implemented = Not yet implemented -error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values. -error.implementation_error_dont_know_thereshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient. -error.implementation_error_embeddedpopup_not_null = Implementation error - embeddedPopup must be non-null -error.invalid_colour_for_mycheckbox = Invalid color for MyCheckBox -error.implementation_error_unrecognised_render_object_for_features_type = Implementation Error: Unrecognised render object {0} for features of type {1} -error.implementation_error_unsupported_feature_colour_object = Implementation error: Unsupported feature colour object. -error.invalid_separator_parameter = Invalid separator parameter - must be non-zero length -error.alignment_cigararray_not_implemented = Alignment(CigarArray) not yet implemented -error.weak_sequencei_equivalence_not_yet_implemented = Weak sequenceI equivalence not yet implemented. -error.implementation_error_can_only_make_alignmnet_from_cigararray = Implementation Error - can only make an alignment view from a CigarArray of sequences. -error.empty_view_cannot_be_updated = empty view cannot be updated. -error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2}) -error.padding_not_yet_implemented = Padding not yet implemented -error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view = Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks={0}) -error.unknown_seq_cigar_operation = Unknown SeqCigar operation {0} -error.implementation_bug_parse_cigar_string = Implementation bug in parseCigarString -error.implementation_error_invalid_operation_string = Implementation error. Invalid operation string. -error.invalid_range_string = Invalid range string (must be zero or positive number) -error.implementation_error_delete_range_out_of_bounds = Implementation Error: deleteRange out of bounds: start must be non-negative and less than end. -error.implementation_error = Implementation error -error.implementation_error_unknown_operation = Implementation Error! Unknown operation {0} -error.implementation_error_unexpected_null_from_get_sequence_and_deletions = Implementation Error - unexpected null from getSequenceAndDeletions -error.implementation_error_set_seq_null = Implementation Error - _setSeq(null,...) -error.implementation_error_s = Implementation Error: _s= {0} -error.implementation_error_seqcigar_possible = SeqCigar: Possible implementation error: sequence is longer than dataset sequence -error.implmentation_bug_seq_null = Implementation Bug. Null seq -error.implementation_bug_cigar_operation_list_range_list = Implementation Bug. Cigar Operation list!= range list -error.not_yet_implemented_cigar_object_from_cigar_string = NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence. -error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation {0} {1} not one of {2}, {3}, or {4}. -error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI) -error.implementation_error_cigar_seq_no_operations = Implementation error: {0}th sequence Cigar has no operations. -error.implementation_error_jmol_getting_data = Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016 -error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to -error.jmol_version_not_compatible_with_jalview_version = Jmol version {0} is not compatible with this version of Jalview. Report this problem at issues.jalview.org -error.not_implemented_remove = Remove: Not implemented -error.not_implemented_clone = Clone: Not implemented -error.implementation_error_chimera_getting_data = Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016 -error.call_setprogressbar_before_registering_handler = call setProgressBar before registering the progress bar's handler. -label.cancelled_params = Cancelled {0} -error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame. -error.implementation_error_dont_know_about_thereshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient. -error.eps_generation_not_implemented = EPS Generation not yet implemented -error.png_generation_not_implemented = PNG Generation not yet implemented -error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected -error.invalid_vamsas_session_id = Invalid vamsas session id -error.implementation_error_cannot_create_groovyshell = Implementation Error. Cannot create groovyShell without Groovy on the classpath! -label.groovy_support_failed = Jalview Groovy Support Failed -label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong. -error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0} -error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode. -error.invalid_value_for_option = Invalid value {0} for option {1} -error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet! -label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another -error.implementation_error_vamsas_operation_not_init = Impementation error! Vamsas Operations when client not initialised and connected -error.jalview_no_connected_vamsas_session = Jalview not connected to Vamsas session -error.implementation_error_cannot_recover_vamsas_object_mappings = IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made -error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0} -error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set -error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0}) -error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2}) -error.implementation_error_jalview_class_should_bind_to_type = Implementation Error: Jalview Class {0} should bind to a {1} (found a {2}) -error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice! -error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType. -error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key -error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor -error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document. -error.implementation_error_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0} -error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null' -exception.ssm_context_is_null = SSM context is null -error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence -error.cannot_have_mixed_length_replacement_vectors = Cannot have mixed length replacement vectors. Replacement vector for {0} is {1} strings long, and have already seen a {2} length vector. -error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero length vector of replacement strings - either 1 value or n values. -error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported -error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object! -error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0} -error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented -label.job_never_ran = Job never ran - input returned to user. -error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more -error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0} -error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference! -error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet -error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range! -error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0} -error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters -error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments -error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1}) -error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0} -error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset! -error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!" -error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore -error.cannot_set_source_file_for = Cannot set source file for {0} -error.mismatch_service_instance_preset = Probable mismatch between service instance and preset! -error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web service's preset -error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets -error.no_aacon_service_found = No AACon service found -error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain! -error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8. -error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented -error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process -error.dbrefsource_implementation_exception =DBRefSource Implementation Exception -error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0}) -error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources -label.view_controller_toggled_marked = {0} {1} columns {2} containing features of type {3} across {4} sequence(s) -label.toggled = Toggled -label.marked = Marked -label.not = not -label.no_feature_of_type_found = No features of type {0} found. -label.submission_params = Submission {0} -label.empty_alignment_job = Empty Alignment Job -label.add_new_sbrs_service = Add a new Simple Bioinformatics Rest Service -label.edit_sbrs_entry = Edit Simple Bioinformatics Rest Service entry -label.pca_recalculating = Recalculating PCA -label.pca_calculating = Calculating PCA -label.select_foreground_colour = Choose foreground colour -label.select_colour_for_text = Select Colour for Text -label.adjunst_foreground_text_colour_thereshold = Adjust Foreground Text Colour Threshold -label.select_subtree_colour = Select Sub-Tree Colour -label.create_new_sequence_features = Create New Sequence Feature(s) -label.amend_delete_features = Amend/Delete Features for {0} -exception.out_of_bounds_for_file = Out of bounds for file: i={0}, Final Buffer: i0={1} iend={2} -exception.null_string_given_to_regex_search = Null String Given to Regex.search -exception.null_string_like_given_to_regex_search = Null StringLike Given to Regex.search -exception.null_string_given_to_regex_reverse_search = Null String Given to Regex.reverseSearch -exception.null_string_like_given_to_regex_reverse_search = Null StringLike Given to Regex.reverseSearch -exception.null_string_like_given_to_regex_search_from = Null String Given to Regex.searchFrom -exception.null_string_like_given_to_regex_search_region = Null String Given to Regex.searchRegion -exception.replace_null_regex_pointer = Replacer has null Regex pointer -exception.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0} -exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0} -exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0} -exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0} -exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0} -exception.mismatched_closing_char = Mismatched closing character {0} -exception.mismatched_opening_char = Mismatched opening character {0} at {1} -exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader -exception.index_value_not_in_range = {0}: Index value {1} not in range [0..{2}] -exception.unterminated_cigar_string = Unterminated cigar string -exception.unexpected_operation_cigar_string_pos = Unexpected operation {0} in cigar string (position {1} in {2} -exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server -exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console -exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding -exception.overwriting_jalview_id_binding = Overwriting jalview id binding -error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string -exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream -exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2} -exception.problem_opening_file = Problem opening {0} : {1} -exception.failed_to_read_data_from_source = Failed to read data from source: {0} -exception.no_init_source_stream = Unitialised Source Stream -exception.invalid_source_stream = Invalid Source Stream: {0} -error.implementation_error_reset_called_for_invalid_source = Implementation Error: Reset called for invalid source. -exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3}) -label.mapped = mapped -exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns -exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0} -exception.newfile = NewickFile\: {0}\n -label.no_tree_read_in = No Tree read in -exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0}) -exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0}) -exception.ranml_invalid_file = Invalid RNAML file ({0}) -exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0}) -exception.pfam_no_sequences_found = No sequences found (PFAM input) -exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM' -exception.couldnt_parse_sequence_line = Could not parse sequence line: {0} -exception.error_parsing_line = Error parsing {0} -exception.unknown_annotation_detected = Unknown annotation detected: {0} {1} -exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0} -exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1}) -exception.browser_not_found = Exception in finding browser: {0} -exception.browser_unable_to_locate = Unable to locate browser: {0} -exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0} -exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0} -exception.instantiation_creating_aedesc = InstantiationException while creating AEDesc: {0} -exception.unable_to_launch_url = Unable to launch URL: {0} -exception.unable_to_create_internet_config = Unable to create an Internet Config instance: {0} -exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0} -exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0} -exception.interrupted_launching_browser = InterruptedException while launching browser: {0} -exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command. -exception.invalid_das_source = Invalid das source: {0} -exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1} -label.no_embl_record_found = # No EMBL record retrieved for {0}:{1} -label.embl_successfully_parsed = # Successfully parsed the {0} queries into an Alignment -exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1} -exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data -exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment -exception.unknown_format_for_file = Unknown format {0} for file \: \n{1} -label.remove_gaps = Remove Gaps -exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence! -exception.server_timeout_try_later = Server timed out - try again later\n -exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later. -exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0} -error.implementation_error_cannot_find_service_url_in_given_set = Implementation error: Cannot find service url in the given url set! -error.implementation_error_cannot_find_service_url_in_given_set_param_store = Implementation error: Cannot find service url in the given url set for this service parameter store ({0}} -exception.jobsubmission_invalid_params_set = Invalid parameter set. Check Jalview implementation -exception.notvaliddata_group_contains_less_than_min_seqs = Group contains less than {0} sequences. -exception.outofmemory_loading_pdb_file = Out of memory loading PDB File -exception.eps_coudnt_write_output_file = Could not write to the output file: {0} -exception.eps_method_not_supported = Method not currently supported by EpsGraphics2D version {0} -exception.eps_unable_to_get_inverse_matrix = Unable to get inverse of matrix: {0} -warn.job_cannot_be_cancelled_close_window = This job cannot be cancelled.\nJust close the window. -warn.service_not_supported = Service not supported! -warn.input_is_too_big = Input is too big! -warn.invalid_job_param_set = Invalid job parameter set! -warn.oneseq_msainput_selection = The current selection only contains a single sequence. Do you want to submit all sequences for alignment instead ? -info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0} -info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0} -info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n -info.no_jobs_ran = No jobs ran -info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1} -info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2} -info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n -info.alignment_object_method_notes = \nAlignment Object Method Notes\n -info.server_exception = \n{0} Server exception\!\n{1} -info.invalid_msa_input_mininfo = Need at least two sequences with at least 3 residues each, with no hidden regions between them. -info.invalid_msa_notenough = Not enough sequence data to align -status.processing_commandline_args = Processing commandline arguments... -status.das_features_being_retrived = DAS features being retrieved... -status.searching_for_sequences_from = Searching for sequences from {0} -status.finished_searching_for_sequences_from = Finished searching for sequences from {0} -label.eps_file = EPS file -label.png_image = PNG image -status.saving_file = Saving {0} -status.export_complete = Export complete. -status.fetching_pdb = Fetching PDB {0} -status.refreshing_news = Refreshing news -status.importing_vamsas_session_from = Importing VAMSAS session from {0} -status.opening_params = Opening {0} -status.waiting_sequence_database_fetchers_init = Waiting for Sequence Database Fetchers to initialise -status.init_sequence_database_fetchers = Initialising Sequence Database Fetchers -status.fetching_sequence_queries_from = Fetching {0} sequence queries from {1} -status.finshed_querying = Finished querying -status.parsing_results = Parsing results. -status.processing = Processing... -status.refreshing_web_service_menus = Refreshing Web Service Menus -status.collecting_job_results = Collecting job results. -status.fetching_das_sequence_features = Fetching DAS Sequence Features -status.no_das_sources_active = No DAS Sources Active -status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled -status.das_feature_fetching_complete = DAS Feature Fetching Complete -status.fetching_db_refs = Fetching db refs -status.loading_cached_pdb_entries = Loading Cached PDB Entries -status.searching_for_pdb_structures = Searching for PDB Structures -status.opening_file = opening file -status.colouring_chimera = Colouring Chimera -label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data -label.font_too_small = Font size is too small -label.error_loading_file_params = Error loading file {0} -label.error_loading_jalview_file = Error loading Jalview file -warn.out_of_memory_when_action = Out of memory when {0}\!\!\nSee help files for increasing Java Virtual Machine memory. -warn.out_of_memory_loading_file = Out of memory loading file {0}\!\!\nSee help files for increasing Java Virtual Machine memory. -label.out_of_memory = Out of memory -label.invalid_id_column_width = Invalid ID Column width -warn.user_defined_width_requirements = The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide. -label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher -warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details. -warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details. -warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=//=$ -info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results) -label.test_server = Test Server? -info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names? -label.find_uniprot_accession_ids = Find Uniprot Accession Ids -label.new_sequence_fetcher = New Sequence Fetcher -label.additional_sequence_fetcher = Additional Sequence Fetcher -label.select_database_retrieval_source = Select Database Retrieval Source -label.overwrite_existing_file = Overwrite existing file? -label.file_already_exists = File exists -label.edit_jabaws_url = Edit JABAWS URL -label.add_jabaws_url = Add new JABAWS URL -label.news_from_jalview = News from http://www.jalview.org -label.cut_paste_alignmen_file = Cut & Paste Alignment File -label.enter_redundancy_thereshold = Enter the redundancy threshold -label.select_dark_light_set_thereshold = Select a dark and light text colour, then set the threshold to
    switch between colours, based on background colour     -label.select_feature_colour = Select Feature Colour -label.delete_all = Delete all sequences -warn.delete_all = Deleting all sequences will close the alignment window.
    Confirm deletion or Cancel. -label.add_annotations_for = Add annotations for -label.choose_annotations = Choose annotations -label.find = Find -label.invalid_search = Search string invalid -error.invalid_regex = Invalid regular expression -label.ignore_gaps_consensus = Ignore Gaps In Consensus -label.show_group_histogram = Show Group Histogram -label.show_group_logo = Show Group Logo -label.normalise_group_logo = Normalise Group Logo -label.show_histogram = Show Histogram -label.show_logo = Show Logo -label.normalise_logo = Normalise Logo -label.no_colour_selection_in_scheme = Please make a colour selection before applying colour scheme -label.no_colour_selection_warn = Error saving colour scheme -label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked? -label.open_split_window = Open split window -label.no_mappings = No mappings found -label.mapping_failed = No sequence mapping could be made between the alignments.
    A mapping requires sequence names to match, and equivalent sequence lengths. -action.no = No -action.yes = Yes -label.for = for -label.select_by_annotation = Select/Hide Columns by Annotation -action.select_by_annotation = Select/Hide Columns by Annotation... -label.threshold_filter = Threshold Filter -action.hide = Hide -action.select = Select -label.alpha_helix = Alpha Helix -label.beta_strand = Beta Strand -label.turn = Turn -label.select_all = Select All -label.structures_filter = Structures Filter -label.search_filter = Search Filter -label.description = Description -label.include_description= Include Description -action.back = Back -label.hide_insertions = Hide Insertions -label.mark_as_representative = Mark as representative -label.open_jabaws_web_page = Open JABAWS web page -label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser -label.pdb_sequence_getcher = PDB Sequence Fetcher -label.result = result -label.results = results -label.structure_chooser = Structure Chooser -label.select = Select : -label.invert = Invert -label.select_pdb_file = Select PDB File -info.select_filter_option = Select Filter Option/Manual Entry -info.associate_wit_sequence = Associate with Sequence -label.search_result = Search Result -label.found_structures_summary = Found Structures Summary -label.configure_displayed_columns = Configure Displayed Columns -label.start_jalview = Start Jalview -label.biojs_html_export = BioJS -label.scale_as_cdna = Scale protein residues to codons -label.scale_protein_to_cdna = Scale Protein to cDNA -label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views -info.select_annotation_row = Select Annotation Row -info.enter_search_text_here = Enter Search Text Here -info.enter_search_text_to_enable = Enter Search Text to Enable -info.search_in_annotation_label = Search in {0} Label -info.search_in_annotation_description = Search in {0} Description -info.change_threshold_mode_to_enable = Change Threshold Mode to Enable diff --git a/bin/lang/Messages_es.properties b/bin/lang/Messages_es.properties deleted file mode 100644 index 6db40cf..0000000 --- a/bin/lang/Messages_es.properties +++ /dev/null @@ -1,1136 +0,0 @@ -action.refresh_services = Refrescar servicios -action.reset_services = Reiniciar servicios -action.merge_results = Unificar resultados -action.load_scheme = Cargar esquema -action.save_scheme = Guardar esquema -action.save_image = Guardar imagen -action.paste = Pegar -action.show_html_source = Mostrar código HTML -action.print = Imprimir -action.web_service = Servicio web -action.cancel_job = Cancelar trabajo -action.start_job = Arrancar trabajo -action.revert = Deshacer -action.move_down = Mover hacia abajo -action.move_up = Mover hacia arriba -action.remove_return_datatype = Borrar tipo de datos de retorno -action.add_return_datatype = Añadir tipo de datos de retorno -action.remove_input_parameter = Borrar el parámetro de entrada seleccionado -action.add_input_parameter = Añadir parámetro de entrada seleccionado -action.edit = Editar -action.new = Nuevo -action.open_file = Abrir fichero -action.show_unconserved = Mostrar regiones no conservadas -action.open_new_alignment = Abrir nuevo alineamiento -action.raise_associated_windows = Destacar ventanas asociadas -action.minimize_associated_windows = Minimizar ventanas asociadas -action.close_all = Cerrar todo -action.load_project = Cargar proyecto -action.save_project = Guardar proyecto -action.quit = Salir -action.expand_views = Expandir vistas -action.gather_views = Capturar vistas -action.page_setup = Configuración de la página -action.reload = Recargar -action.load = Cargar -action.open = Abrir -action.cancel = Cancelar -action.create = Crear -action.update = Actualizar -action.delete = Borrar -action.snapshot = Imagen -action.clear = Limpiar -action.accept = Aceptar -action.select_ddbb = --- Seleccionar base de datos --- -action.undo = Deshacer -action.redo = Rehacer -action.reset = Reiniciar -action.remove_left = Eliminar parte izquierda -action.remove_right = Eliminar parte derecha -action.remove_empty_columns = Eliminar las columnas vacías -action.remove_all_gaps = Eliminar todos los huecos -action.left_justify_alignment = Ajustar el alineamiento a la izquierda -action.right_justify_alignment = Ajustar el alineamiento a la derecha -action.boxes = Casillas -action.text = Texto -action.by_pairwise_id = Identificar por parejas -action.by_id = Por identificador -action.by_length = Por longitud -action.by_group = Por grupo -action.remove = Eliminar -action.remove_redundancy = Eliminar redundancia... -action.pairwise_alignment = Alineamiento de pares... -action.by_rna_helixes = Por hélices de RNA -action.user_defined = Definido por el usuario... -action.by_conservation = Por conservación -action.wrap = Envolver -action.show_gaps = Mostrar huecos -action.show_hidden_markers = Mostrar marcadores ocultos -action.find = Buscar -action.undefine_groups = Grupos sin definir -action.create_groups = Crear grupos -action.make_groups_selection = Hacer grupos para seleccionar -action.copy = Copiar -action.cut = Cortar -action.font = Fuente... -action.scale_above = Escala superior -action.scale_left = Escala izquierda -action.scale_right = Escala derecha -action.by_tree_order = Por orden del árbol -action.sort = Ordenar -action.calculate_tree = Calcular árbol -action.help = Ayuda -action.by_annotation = Por anotación... -action.invert_sequence_selection = Invertir selección de secuencias -action.invert_column_selection = Invertir selección de columnas -action.show = Mostrar -action.hide = Ocultar -action.ok = OK -action.set_defaults = Defecto -action.create_group = Crear grupo -action.remove_group = Eliminar grupo -action.edit_group = Editar grupo -action.border_colour = Color del borde -action.edit_new_group = Editar nuevo grupo -action.hide_sequences = Ocultar secuencias -action.sequences = Secuencias -action.ids = IDS -action.ids_sequences = IDS y secuencias -action.reveal_all = Revelar todo -action.reveal_sequences = Revelar secuencias -action.find_all = Buscar todo -action.find_next = Buscar siguiente -action.file = Archivo -action.view = Ver -action.change_params = Cambiar parámetros -action.apply = Aplicar -action.apply_threshold_all_groups = Aplicar umbral a todos los grupos -action.apply_all_groups = Aplicar a todos los grupos -action.by_chain = Por cadena -action.by_sequence = Por secuencia -action.paste_annotations = Pegar anotaciones -action.format = Formato -action.select = Seleccionar -action.new_view = Nueva vista -action.close = Cerrar -action.add = Añadir -action.save_as_default = Guardar como por defecto -action.save_as = Guardar como -action.save = Guardar -action.cancel_fetch = Cancelar búsqueda -action.save_omit_hidden_columns = Guardar / Omitir las columnas ocultas -action.change_font = Cambiar Fuente -action.change_font_tree_panel = Cambiar fuente (panel del árbol) -action.colour = Color -action.calculate = Calcular -action.select_all = Seleccionar Todo -action.deselect_all = Deseleccionar Todo -action.invert_selection = Invertir selección -action.using_jmol = Usar Jmol -action.link = Enlazar -action.group_link = Enlazar grupo -action.show_chain = Mostrar cadena -action.show_group = Mostrar grupo -action.fetch_db_references = Recuperar referencias a base de datos -action.view_flanking_regions = Mostrar flancos -label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento -label.str = Str: -label.seq = Seq: -label.structures_manager = Administrar estructuras -label.nickname = Sobrenombre: -label.url = URL: -label.input_file_url = Introducir URL en el fichero de entrada -label.select_feature = Seleccionar función: -label.name = Nombre: -label.name_param = Nombre: {0} -label.group = Grupo: -label.group_name = Nombre del grupo -label.group_description = Descripción del grupo -label.edit_group_name_description = Editar nombre/descripción del grupo -label.colour = Color: -label.description = Descripción: -label.start = Comenzar: -label.end = Terminar: -label.current_parameter_set_name = Nombre actual del conjunto de parámetros: -label.service_action = Acción de servicio: -label.post_url = POST URL: -label.url_suffix = URL Sufijo -label.sequence_source = Fuente de la secuencia -label.per_seq = por secuencia -label.result_vertically_separable = Los resultados son separables verticalmente -label.amend = Modificar -label.undo_command = Deshacer {0} -label.redo_command = Rehacer {0} -label.principal_component_analysis = Análisis del Componente Principal -label.average_distance_identity = Distancia Media Usando % de Identidad -label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad -label.treecalc_title = {0} utilizando {1} -label.tree_calc_av = Distancia media -label.tree_calc_nj = Unir vecinos -label.select_score_model = Selecciones modelo de puntuación -label.score_model_pid = % Identidad -label.score_model_blosum62 = BLOSUM62 -label.score_model_pam250 = PAM 250 -label.score_model_conservation = Conservación de las propiedades físico-químicas -label.score_model_enhconservation = Conservación de las propiedades físico-químicas -label.status_bar = Barra de estado -label.out_to_textbox = Generar cuadro de texto -label.clustalx = Clustalx -label.clustal = Clustal -label.zappo = Zappo -label.taylor = Taylor -label.blc = BLC -label.fasta = Fasta -label.msf = MSF -label.pfam = PFAM -label.pileup = Pileup -label.pir = PIR -label.hydrophobicity = Hidrofobicidad -label.helix_propensity = Tendencia de la hélice -label.strand_propensity = Tendencia de la hebra -label.turn_propensity = Tendencia de giro -label.buried_index = Índice de encubrimiento -label.purine_pyrimidine = Purina/Pirimidina -label.percentage_identity = Porcentaje de identidad -label.blosum62 = BLOSUM62 -label.blosum62_score = Puntuación del BLOSUM62 -label.tcoffee_scores = Puntuación del T-Coffee -label.average_distance_bloslum62 = Distancia Media Usando BLOSUM62 -label.neighbour_blosum62 = Neighbour Joining usando BLOSUM62 -label.show_annotations = Mostrar anotaciones -label.colour_text = Color del texto -label.show_non_conversed = Mostrar no conservadas -label.overview_window = Ventana resumen -label.none = Ninguno -label.above_identity_threshold = Por encima del umbral de identidad -label.show_sequence_features = Mostrar las características de las secuencias -label.nucleotide = Nucleótido -label.to_new_alignment = A nuevo alineamiento -label.to_this_alignment = Añadir a este alineamiento -label.apply_colour_to_all_groups = Aplicar color a todos los grupos -label.modify_identity_thereshold = Modificar el umbral de identidad... -label.modify_conservation_thereshold = Modificar el umbral de conservación... -label.input_from_textbox = Introducir desde el cuadro de texto -label.centre_column_labels = Centrar las etiquetas de las columnas -label.automatic_scrolling = Desplazamiento automático -label.documentation = Documentación -label.about = Acerca de... -label.show_sequence_limits = Mostrar los límites de la secuencia -label.feature_settings = Ajustar funciones... -label.sequence_features = Funciones de la secuencia -label.all_columns = Todas las columnas -label.all_sequences = Todas las secuencias -label.selected_columns = Columnas seleccionadas -label.selected_sequences = Secuencias seleccionadas -label.all_but_selected_region = Todo menos la región seleccionada (Shift+Ctrl+H) -label.selected_region = Región seleccionada -label.all_sequences_columns = Todas las secuencias y columnas -label.group_consensus = Consenso de grupo -label.group_conservation = Conservación de grupo -label.show_consensus_histogram = Mostrar el histograma de consenso -label.show_consensus_logo = Mostrar el logo de consenso -label.norm_consensus_logo = Normalizar el logo de consenso -label.apply_all_groups = Aplicar a todos los grupos -label.autocalculated_annotation = Anotación autocalculada -label.min_colour = Color mínimo -label.max_colour = Color máximo -label.use_original_colours = Usar colores originales -label.threshold_minmax = El umbral es mín/máx -label.represent_group_with = Representar al grupo con -label.selection = Seleccionar -label.group_colour = Color del grupo -label.sequence = Secuencia -label.view_pdb_structure = Ver estructura PDB -label.min = Mín: -label.max = Máx: -label.colour_by_label = Color por etiquetas -label.new_feature = Nueva función -label.match_case = Hacer corresponder mayúsculas y minúsculas -label.view_alignment_editor = Ver en el editor de alineamientos -label.labels = Etiquetas -label.output_values = Valores de salida... -label.output_points = Puntos de salida... -label.output_transformed_points = Puntos de salida transformados -label.input_data = Datos de entrada... -label.nucleotide_matrix = Matriz nucleotídica -label.protein_matrix = Matriz proteica -label.show_bootstrap_values = Mostrar valores de Bootstrap -label.show_distances = Mostrar distancias -label.mark_unassociated_leaves = Marcar hojas no asociadas -label.fit_to_window = Ajustar a la ventana -label.newick_format = Formato Newick -label.select_newick_like_tree_file = Seleccione un fichero de árbol tipo Newick -label.colours = Colores -label.view_mapping = Ver mapeado -label.wireframe = Estructura metálica -label.depthcue = Clave de profundidad -label.z_buffering = Tamponamiento Z -label.charge_cysteine = Carga & Cisteína -label.all_chains_visible = Todas las cadenas visibles -label.successfully_added_features_alignment = Funciones añadidas exitosamente al alineamiento -label.keyboard_editing_mode = El modo de editar teclado es {0} -label.paste_features_annotations_Tcoffee_here = Pegar tus funciones / anotaciones / puntuación del fichero T-coffee aquí. -label.removed_columns = {0} columnas eliminadas. -label.removed_empty_columns = {0} columnas vacías eliminadas. -label.paste_newick_tree_file = Pegar su fichero árbol Newick aquí. -label.order_by_params = Ordenar por {0} -label.html_content = {0} -label.paste_pdb_file= Pegar tu fichero PDB aquí. -label.paste_pdb_file_for_sequence = Pegar fichero PDB para la secuencia {0} -label.could_not_parse_newick_file = No se pudo analizar el fichero Newick\\\!\\n {0} -label.successfully_pasted_tcoffee_scores_to_alignment= Pegada exitosamente la puntuación T-Coffee al alineamiento. -label.failed_add_tcoffee_scores = Fallo al añadir las puntuaciones T-Coffee: -label.successfully_pasted_annotation_to_alignment = Anotación pegada exitosamente al alineamiento. -label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file = No es posible parsear el texto pegado como una anotación características, GFF, o fichero T-Coffee válidos -label.successfully_pasted_alignment_file = Fichero de alineamiento pegado exitosamente -label.paste_your_alignment_file = Pegar su fichero de alineamiento aquí -label.paste_your = Pegar su -label.finished_searching = Búsqueda finalizada -label.search_results= Buscar Resultados {0} : {1} -label.found_match_for = Buscar coincidencia para {0} -label.font = Fuente: -label.size = Talla: -label.style = Estilo: -label.enter_redundancy_threshold = Introducir el umbral de redundancia -label.calculating = Calculando.... -label.modify_conservation_visibility = Modificar la visibilidad de conservación -label.colour_residues_above_occurence = Residuos de color por encima del % de aparición -label.set_this_label_text = fijar como etiqueta -label.sequences_from = Secuencias de {0} -label.successfully_loaded_file = Fichero cargado exitosamente {0} -label.successfully_saved_to_file_in_format = Guardado exitosamente en el fichero: {0} en formato {1}. -label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles. -label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento. -label.problem_reading_tcoffee_score_file = Problema de lectura del fichero de puntuaciones T-COFFEE -label.source_to_target = {0} a {1} -label.per_sequence_only= Sólo por secuencia -label.to_file = a fichero -label.to_textbox = a cuadro de texto -label.jalview = Jalview -label.csv_spreadsheet = CSV (Hoja de cálculo) -label.status = [Estado] -label.channels = Canales -label.channel_title_item_count = {0} ({1}) -label.blog_item_published_on_date = {0} {1} -label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí. -label.session_update = Actualizar sesión -label.new_vamsas_session = Nueva sesión Vamsas -label.load_vamsas_session = Cargar sesión Vamsas -label.save_vamsas_session = Guardar sesión Vamsas -label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión. -label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada -label.groovy_console = Consola Groovy -label.lineart = lineart -label.dont_ask_me_again = No volver a preguntar -label.select_eps_character_rendering_style = Seleccionar el carácter EPS como estilo de visualización -label.invert_selection = Invertir selección -label.optimise_order = Optimizar orden -label.seq_sort_by_score = Ordenar las secuencias por puntuación -label.load_colours = Cargar colores -label.save_colours = Guardar colores -label.fetch_das_features = Recuperar funciones DAS -label.selected_database_to_fetch_from = Seleccionada {0} Base de datos {1} para buscar de {2} -label.database_param = Base de datos: {0} -label.example = Ejemplo -label.example_param = Ejemplo: {0} -label.select_file_format_before_saving = Debe seleccionar un formato de fichero antes de guardar! -label.file_format_not_specified = Formato de fichero no especificado -label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\\nQuieres guardar s\u00F3lo el alineamiento visible? -label.couldnt_save_file = No se pudo guardar el fichero: {0} -label.error_saving_file = Error guardando el fichero -label.remove_from_default_list = eliminar de la lista de defectuosos? -label.remove_user_defined_colour = Eliminar el color definido por el usuario -label.you_must_select_least_two_sequences = Debes seleccionar al menos 2 secuencias. -label.invalid_selection = Selección inválida -label.principal_component_analysis_must_take_least_four_input_sequences = El an\u00E1lisis de la componente principal debe tomar\\nal menos 4 secuencias de entrada. -label.sequence_selection_insufficient = Selección de secuencias insuficiente -label.you_need_more_two_sequences_selected_build_tree = necesitas seleccionar más de dos secuencias para construir un árbol! -label.not_enough_sequences = No suficientes secuencias -label.selected_region_to_tree_may_only_contain_residues_or_gaps = La regi\u00F3n seleccionada para construir un \u00E1rbol puede\\ncontener s\u00F3lo residuos o espacios.\\nPrueba usando la funci\u00F3n Pad en el men\u00FA de edici\u00F3n,\\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias. -label.sequences_selection_not_aligned = Las secuencias seleccionadas no están alineadas -label.sequences_must_be_aligned_before_creating_tree = Las secuencias deben estar alineadas antes de crear el \u00E1rbol.\\nPrueba usando la funci\u00F3n Pad en el men\u00FA de editar,\\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias. -label.sequences_not_aligned = Secuencias no alineadas -label.problem_reading_tree_file = Problema al leer el fichero del árbol -label.possible_problem_with_tree_file = Posible problema con el fichero del árbol -label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Por favor seleccionar al menos tres bases de al menos una secuencia para poder realizar la traducción de cDNA. -label.translation_failed = Translation Failed -label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\\nPor favor, revisa la consola Jalview java \\ny presenta un informe de error que incluya el seguimiento. -label.implementation_error = Error de implementación: -label.automatically_associate_pdb_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros PDB con las secuencias del alineamiento que tengan el mismo nombre? -label.automatically_associate_pdb_files_by_name = Asociar los ficheros PDB por nombre automáticamente -label.ignore_unmatched_dropped_files_info = Quieres ignorar los {0} ficheros cuyos nombres no coincidan con ningún IDs de las secuencias ? -label.ignore_unmatched_dropped_files = Ignorar los ficheros sin coincidencias? -label.enter_view_name = Introducir nombre visible (¿?) -label.enter_label = Introducir etiqueta -label.enter_label_for_the_structure = Introducir una etiqueta para la estructura? -label.pdb_entry_is_already_displayed = {0} Ya est\u00E1 mostrado.\\nQuieres volver a usar este visor? -label.map_sequences_to_visible_window = Mapa de secuencias en ventana visible: {0} -label.add_pdbentry_to_view = Quieres a\u00F1adir {0} a la vista llamada\\n{1}\\n -label.align_to_existing_structure_view = Alinear a una estructura ya existente -label.pdb_entries_couldnt_be_retrieved = Las siguientes entradas pdb no pueden ser extra\u00EDdas del PDB\\\:\\n{0}\\nPor favor, prueba descarg\u00E1ndolas manualmente. -label.couldnt_load_file = No se pudo cargar el fichero -label.couldnt_find_pdb_id_in_file = No se pudo encontrar un Id PDB en el fichero suministrado. Por favor, introduzca un Id para identificar esta estructura. -label.no_pdb_id_in_file = No hay un Id PDB en el fichero -label.couldnt_read_pasted_text = No se pudo leer el texto pegado {0} -label.error_parsing_text = Error analizando el texto -label.enter_local_das_source = Intruduzca el Nickname & URL de la fuente DAS local -label.you_can_only_edit_or_remove_local_das_sources = Sólo puedes editar o eliminar fuentes DAS locales! -label.public_das_source = Fuente pública DAS - no editable -label.input_alignment_from_url = Alineamiento de entrada desde URL -label.input_alignment = Alineamiento de entrada -label.couldnt_import_as_vamsas_session = No se pudo importar {0} como una nueva sesión Vamsas. -label.vamsas_document_import_failed = Fallo en la importación del documento Vamsas -label.couldnt_locate = No se pudo localizar {0} -label.url_not_found = URL no encontrada -label.no_link_selected = Enlace no seleccionado -label.new_sequence_url_link = Enlace a una nueva secuencia URL -label.cannot_edit_annotations_in_wrapped_view = No se pueden editar anotaciones en vista envolvente -label.wrapped_view_no_edit = Vista envolvente - no editar -label.error_retrieving_data = Error en la recuperación de datos -label.user_colour_scheme_must_have_name = El esquema de colores del usuario debe tener un nombre -label.no_name_colour_scheme = No hay nombre para el esquema de colores -label.invalid_url = URL Invalido! -label.error_loading_file = Error al cargar el fichero -label.problems_opening_file = Encontrados problemas al abrir el fichero {0}!! -label.file_open_error = Error al abrir el fichero -label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\\nPor favor, seleccione algunas fuentes y\\npruebe de nuevo. -label.no_das_sources_selected_title = No han sido seleccionadas fuentes DAS -label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\\nContinuar guardando el esquema de colores como {1}? -label.duplicate_scheme_name = Duplicar nombre de esquema -label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\\n -label.jalview_user_survey = Encuesta de usuario Jalview -label.alignment_properties = Propiedades del alineamiento: {0} -label.alignment_props = Propiedades del alineamiento -label.input_cut_paste = Cortar y pegar la entrada -label.input_cut_paste_params = Cortar y pegar la entrada - {0} -label.alignment_output_command = Alineamiento de salida - {0} -label.annotations = Anotaciones -label.features = Funciones -label.overview_params = Visión general {0} -label.paste_newick_file = Pegar nuevo fichero Newick -label.load_tree_from_file = desde fichero - -label.colour_by_annotation = Color por anotación -label.selection_output_command = Seleccionar salida - {0} -label.annotation_for_displayid =

    Anotación para {0}

    -label.pdb_sequence_mapping = PDB - Mapeado de secuencia -label.pca_details = detalles de la PCA -label.redundancy_threshold_selection = Selección del umbral de redundancia -label.user_defined_colours = Colores definidos del usuario -label.jalviewLite_release = JalviewLite - versión {0} -label.jaview_build_date = Fecha de creación: {0} -label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt, -label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton. -label.jalview_dev_managers = Desarrollo gestionado por The Barton Group, University of Dundee, Scotland, UK. -label.jalview_distribution_lists = Para ayuda, ver el FAQ at www.jalview.org y/o adjuntar la lista de envío jalview-discuss@jalview.org -label.jalview_please_cite = Si usa Jalview incluya la siguiente cita, por favor: -label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) -label.jalview_cite_1_title = Jalview Version 2 - un editor de alineamiento múltiple de secuencias y banco de trabajo de análisis -label.jalview_cite_1_ref = Bioinformaticos doi: 10.1093/bioinformatics/btp033 -label.right_click = clic en el botón derecho -label.to_add_annotation = para añadir anotación -label.alignment_has_no_annotations = El alineamiento no tiene anotaciones -label.retrieving_pdb_data = Recuperación de datos PDB... -label.label = Etiqueta -label.no_features_added_to_this_alignment = No hay funciones asociadas a este alineamiento!! -label.features_can_be_added_from_searches_1 = (Las funciones pueden ser añadidas de búsquedas o -label.features_can_be_added_from_searches_2 = de ficheros de funciones Jalview / GFF) -label.calculating_pca= Calculando PCA -label.reveal_columns = Mostrar Columnas -label.jalview_cannot_open_file = Jalview no puede abrir el fichero -label.jalview_applet = Aplicación Jalview -label.loading_data = Cargando datos -label.memory_stats = Memoria libre total: {0} MB; Memoria máxima: {1} MB; {2} % -label.calculating_tree = Calculando árbol -label.state_queueing = En cola -label.state_running = Procesando -label.state_complete = Completar -label.state_completed = Finalizado -label.state_job_cancelled = ¡Trabajo cancelado! -label.state_job_error = Error del trabajo! -label.server_error_try_later = ¡Error del servidor! (Intentar más tarde) -label.error_loading_pdb_data = ¡Error cargando los datos PDB! -label.fetching_pdb_data = Buscando los datos PDB... -label.structure_type = Estructura_tipo -label.settings_for_type = Ajustes para {0} -label.view_full_application = Ver en la aplicación completa -label.load_associated_tree = Cargar árbol asociado ... -label.load_features_annotations = Cargar características/anotaciones ... -label.export_features = Exportar características... -label.export_annotations = Exportar anotaciones ... -label.jalview_copy = Copiar (sólo Jalview) -label.jalview_cut = Cortar (sólo Jalview) -label.to_upper_case = Pasar a mayúsculas -label.to_lower_case = Pasar a minúsculas -label.toggle_case = Alternar mayúsculas y minúsculas -label.edit_name_description = Editar nombre/descripción -label.create_sequence_feature = Crear función de secuencia -label.edit_sequence = Editar secuencia -label.edit_sequences = Editar secuencias -label.sequence_details = Detalles de la secuencia -label.jmol_help = Ayuda de Jmol -label.all = Todo -label.sort_by = Ordenar por -label.sort_by_score = Ordenar por puntuación -label.sort_by_density = Ordenar por densidad -label.sequence_sort_by_density = Ordenar las secuencias por densidad -label.reveal = Revelar -label.hide_columns = Ocultar columnas -label.load_jalview_annotations = Cargar un fichero de anotación de Jalivew o un fichero de características -label.load_tree_file = Cargar un fichero de árbol -label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Recuperar y parsear un registro de secuencia de base de datos para el alineamiento o secuencias actualmente seleccionados -label.standard_databases = Bases de datos estándar -label.fetch_embl_uniprot = Recuperar de EMBL/EMBLCDS o Uniprot/PDB y de cualquier fuente DAS seleccionada -label.reset_min_max_colours_to_defaults = Reiniciar los colores min y max colours a los valores por defecto establecidos en las preferencias de usuario -label.align_structures_using_linked_alignment_views = Alinear las estructuras utlizando las {0} vistas de alineamiento enlazadas -label.connect_to_session = Conectar a la sesión {0} -label.threshold_feature_display_by_score = Filtrar la característica mostrada por puntuación. -label.threshold_feature_no_thereshold = Sin umbral -label.threshold_feature_above_thereshold = Por encima del umbral -label.threshold_feature_below_thereshold = Por debajo del umbral -label.adjust_thereshold = Ajustar umbral -label.toggle_absolute_relative_display_threshold = Cambiar entre mostrar el umbral absoluto y el relativo. -label.display_features_same_type_different_label_using_different_colour = Mostrar las características del mismo tipo con una etiqueta diferente y empleando un color distinto (p.e. características del dominio) -label.select_colour_minimum_value = Seleccionar el color para el valor mínimo -label.select_colour_maximum_value = Seleccionar el color para el valor máximo -label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista Jmol con todas las estructuras asociadas con la selección acxtual y superponer las utilizando el alineamiento. -label.open_url_param = Abrir URL {0} -label.open_url_seqs_param = Abrir URL ({0}..) ({1} secuencias) -label.load_pdb_file_associate_with_sequence = Cargar un fichero PDB y asociarlo con la secuencia {0} -label.reveal_hidden_columns = Revelar las columnas ocultas con el botón derecho del ratón -label.dark_colour = Oscurecer color -label.light_colour = Aclarar color -label.highlightnode = Pulse el botón izquierdo para seleccionar las hojas.
    Haga doble clic para invertir las hojas.
    Pulse el botón derecho para cambiar el color. -label.load_colour_scheme = Cargar esquema cromático -label.toggle_enabled_views = Cuando está habilitado, permite que se seleccionen varias vistas. -label.edit_notes_parameter_set = Haga clic para editar las notas de este conjunto de parámetros. -label.open_local_file = Abrir fichero local -label.enable_automatically_sort_alignment_when_open_new_tree = Habilite esta opción para ordenar automáticamente
    el alineamiento cuando abra
    un nuevo árbol. -label.listen_for_selections = Atención a las selecciones -label.selections_mirror_selections_made_same_sequences_other_views = Cuando está habilitado, las selecciones de esta vista serán un reflejo
    de las selecciones realizadas en las mismas secuencias de otras vistas. -label.toggle_sequence_visibility = Shift+H cambia la visibilidad de la secuencia -label.toggle_columns_visibility = Ctrl+H cambia la visibilidad de la columna -label.toggles_visibility_hidden_selected_regions = H cambiar la visibilidad de las regiones ocultas o seleccionadas -label.rename_tab_eXpand_reGroup= Haga clic en el botón derecho para renombrar la pestaña
    Presione X para expandir las tablas y G para reagrupar. -label.right_align_sequence_id = Alinear a la derecha el ID de la secuencia -label.sequence_id_tooltip = Ayuda del ID de la secuencia -label.no_services = -label.select_copy_raw_html = Seleccione esta opción si desea copiar el html en bruto -label.share_data_vamsas_applications = Compartir datos con otras aplicaciones vamsas -label.connect_to = Conectar a -label.join_existing_vamsas_session = Unirse a una sesión vamsas existente -label.from_url = desde una URL -label.any_trees_calculated_or_loaded_alignment_automatically_sort = Cuando está habilitado, cualquier árbol calculado o cargado en el alineamiento lo ordenará -label.sort_with_new_tree = Ordenar con el nuevo árbol -label.from_textbox = desde un área de texto -label.window = Ventana -label.preferences = Preferencias -label.tools = Herramientas -label.fetch_sequences = Recuperar secuencia(s) -label.stop_vamsas_session = Parar sesión vamsas -label.collect_garbage = Recolector de basura -label.show_memory_usage = Mostrar uso de memoria -label.show_java_console = Mostrar consola de Java -label.show_jalview_news = Mostrar las noticias de Jalview -label.take_snapshot = Tomar captura -label.monospaced_fonts_faster_to_render = Las fuentes monoespaciadas son más rápidas de pintar -label.anti_alias_fonts = Fuentes anti-alias (más lentas de pintar) -label.monospaced_font= Monoespaciadas -label.quality = Calidad -label.maximize_window = Maximizar ventana -label.conservation = Conservación -label.consensus = Consenso -label.histogram = Histograma -label.logo = Logo -label.non_positional_features = Características no posicionales -label.database_references = Referencias a base de datos -label.share_selection_across_views = Compartir la selección en todas las vistas -label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas -label.gap_symbol = Símbolo del hueco -label.alignment_colour = Color del alineamiento -label.address = Dirección -label.port = Puerto -label.default_browser_unix = Navegador por defecto (Unix) -label.send_usage_statistics = Enviar estadísticas de uso -label.check_for_questionnaires = Comprobar los cuestionarios -label.check_for_latest_version = Comprobar la última versión -label.url_linkfrom_sequence_id = URL del enlace del ID de la secuencia -label.use_proxy_server = Utilizar un servidor proxy -label.eps_rendering_style = Estilo de visualización EPS -label.append_start_end = Añadir /inicio-fin (/15-380) -label.full_sequence_id = ID de la secuencia completo -label.smooth_font = Fuente alargada -label.autocalculate_consensus = Autocalcular consenso -label.pad_gaps = Rellenar huecos -label.pad_gaps_when_editing = Rellenar huecos al editar -label.automatically_set_id_width = Establecer automáticamente al anchura del ID -label.figure_id_column_width = Anchura de la columna del ID de la Figura -label.use_modeller_output = Utilizar la salidad del Modeller -label.wrap_alignment = Envolver alineamiento -label.right_align_ids = Alinear IDs a la derecha -label.sequence_name_italics = Nombre de la secuencia en cursiva -label.open_overview = Abrir resumen -label.default_colour_scheme_for_alignment = Esquema cromático por defecto para el alineamiento -label.annotation_shading_default = Sombreado por defecto de la anotación -label.default_minimum_colour_annotation_shading = Por mínimo por defecto para el sombreado de la anotación -label.default_maximum_colour_annotation_shading = Por máximo por defecto para el sombreado de la anotación -label.visual = Visual -label.connections = Conexiones -label.output = Salida -label.editing = Edición -label.das_settings = Configuración DAS -label.web_services = Servicios web -label.right_click_to_edit_currently_selected_parameter = Haga clic en el botón derecho para editar el parámetro seleccionado actualmente. -label.let_jmol_manage_structure_colours = Permitir que Jmol gestione la estructuras cromáticas -label.marks_leaves_tree_not_associated_with_sequence = Marcar las hojas del árbol que no están asociadas a una secuencia -label.index_web_services_menu_by_host_site = Indizar los servicios web en el menú por el host que los aloja -label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Marque esta opción si desea ser informado
    cuando no se pueda acceder a la URL de un servicio web
    al arrancar Jalview. -label.new_service_url = Nueva URL del servicio -label.edit_service_url = Editar la URL del servicio -label.delete_service_url = Borrar la URL del servicio -label.details = Detalles -label.options = Opciones -label.parameters = Paramétros -label.available_das_sources = Fuentes DAS disponibles -label.full_details = Detalles completos -label.authority = Autoridad -label.type = Tipo -label.proxy_server = Servidor proxy -label.file_output = Fichero de salida -label.select_input_type = Seleccionar el tipo de entrada -label.set_options_for_type = Establecer opciones para el tipo -label.data_input_parameters = Datos de los parámetros de entrada -label.data_returned_by_service = Datos devueltos por el servicio -label.rsbs_encoded_service = Servicio RSBS codificado -label.parsing_errors = Errores de parseo -label.simple_bioinformatics_rest_services = Simple Bioinformatics Rest Services -label.web_service_discovery_urls = URL de descubrimiento de servicios web -label.input_parameter_name = Nombre del parámetro de entrada -label.short_descriptive_name_for_service = Nombre corto descriptivo del servicio -label.function_service_performs = Tipo de función que realiza el servicio (p.e. alineamiento, análisis, búsqueda, etc). -label.brief_description_service = Descripción breve del servicio -label.url_post_data_service = URL a la que enviar los datos del servicio. Incluya cualquier parámetro especial que se necesite aquí -label.optional_suffix = Sufijo opcional añadido a la URL al recuperar los resultados del servicio -label.preferred_gap_character = ¿Qué caracter para el hueco prefiere el servicio? -label.gap_character = Carácter para hueco -label.move_return_type_up_order= Mover el tipo de returno hacia arriba en el orden -label.move_return_type_down_order= Mover el tipo de returno hacia abajo en el orden -label.update_user_parameter_set = Actualizar el conjunto de parámetros de usuario existente -label.delete_user_parameter_set = Borrar el conjunto de parámetros de usuario existente -label.create_user_parameter_set = Crear un nuevo conjunto de parámetro con la configuración actual. -label.revert_changes_user_parameter_set = Deshacer todos los cambios en el conjunto de parámetros actual -label.start_job_current_settings = Arrancar trabajo con la configuración actual -label.cancel_job_close_dialog = Cerrar este diálogo y cancelar el trabajo -label.input_output = Entrada/Salida -label.cut_paste = Cortar y pegar -label.adjusting_parameters_for_calculation = Ajustar los parámetros para el cálculo existente -label.2d_rna_structure_line = 2D RNA {0} -label.2d_rna_sequence_name = 2D RNA - {0} -label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual. -label.view_structure_for = Visualizar la estructura para {0} -label.view_all_structures = Visualizar todas las {0} estructuras. -label.view_all_representative_structures = Visualizar todas las {0} estructuras representativas. -label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista de Jmol con todas las estructuras representativas\nasociadas con la selecci\u00F3n actual\nsuperpuesta con el alineamiento actual. -label.associate_structure_with_sequence = Asociar estructura con la secuencia -label.from_file = desde fichero -label.enter_pdb_id = Introducir PDB Id -label.discover_pdb_ids = Buscar PDB ids -label.text_colour = Color del texto -label.structure = Estructura -label.view_structure = Visualizar estructura -label.clustalx_colours = Colores de Clustalx -label.above_identity_percentage = Sobre % identidad -label.create_sequence_details_report_annotation_for = Anotación para {0} -label.sequece_details_for = Detalles de la secuencia para {0} -label.sequence_name = Nombre de la secuencia -label.sequence_description = Descripción de la secuencia -label.edit_sequence_name_description = Editar el nombre/descripción de la secuencia -label.spaces_converted_to_backslashes = Los espacios se han convertido en _ -label.no_spaces_allowed_sequence_name = No se permiten espacios en el nombre de la secuencia -label.select_outline_colour = Seleccionar el color del límite -label.web_browser_not_found_unix = Unixers\: No es posible encontrar el navegador web por defecto.\nA\u00F1ada la ruta completa de su navegador en la pesta\u00F1a de Preferencias. -label.web_browser_not_found = No se encuentra el navegador web -label.select_pdb_file_for = Seleccione un fichero PDB para {0} -label.html = HTML -label.wrap = Envolver -label.show_database_refs = Mostrar las referencias en base de datos -label.show_non_positional_features = Mostrar las características no posicionales -label.save_png_image = Guardar como imagen PNG -label.load_tree_for_sequence_set = Cargar un árbol para este conjunto de secuencias -label.export_image = Exportar imagen -label.vamsas_store = Almacén VAMSAS -label.translate_cDNA = Traducir cDNA -label.extract_scores = Extraer puntuaciones -label.get_cross_refs = Obtener referencias cruzadas -label.sort_alignment_new_tree = Alinear el alineamiento con el nuevo árbol -label.add_sequences = Añadir secuencias -label.new_window = Nueva ventana -label.refresh_available_sources = Refrescar las fuentes disponibles -label.use_registry = Utilizar el registro -label.add_local_source = Añadir fuente local -label.set_as_default = Establecer por defecto -label.show_labels = Mostrar etiquetas -label.background_colour = Color de fondo -label.associate_nodes_with = Asociar nodos con -label.jalview_pca_calculation = Cálculo del PCA por Jalview -label.link_name = Nombre del enalce -label.pdb_file = Fichero PDB -label.colour_with_jmol = Colorear con Jmol -label.align_structures = Alinear estructuras -label.jmol = Jmol -label.sort_alignment_by_tree = Ordenar alineamiento por árbol -label.mark_unlinked_leaves = Marcar las hojas como no enlazadas -label.associate_leaves_with = Asociar hojas con -label.save_colour_scheme_with_unique_name_added_to_colour_menu = Guarde el esquema cromáticos con un nombre único y se añadirá al menú de colores -label.case_sensitive = Sensible a mayúsculas -label.lower_case_colour = Color para las minúsculas -label.index_by_host = Indizar por host -label.index_by_type = Indizar por tipo -label.enable_jabaws_services = Habilitar servicios JABAWS -label.display_warnings = Mostrar advertencias -label.move_url_up = Mover la URL hacia arriba -label.move_url_down = Mover la URL hacia abajo -label.add_sbrs_definition = Añadir una definición SBRS -label.edit_sbrs_definition = Editar una definición SBRS -label.delete_sbrs_definition = Borrar una definición SBRS -label.your_sequences_have_been_verified = Sus secuencias has sido verificadas en una base de datos de secuencias conocidas. Algunos de sus ID se han alterado y\n, probablemente, el residuo de inicio/fin se haya actualizado.\nGuarde su alineamiento para mantener el ID actualizado.\n\n -label.sequence_names_updated = Nombres de secuencia actualizados -label.dbref_search_completed = Búsqueda de DBRef terminada -label.show_all_chains = Mostrar todas las cadenas -label.fetch_all_param = Recuperar todas {0} -label.paste_new_window = Pegar en una nueva ventana -label.settings_for_param = Configuración para {0} -label.view_params = Visualizar {0} -label.select_all_views = Seleccionar todas las vistas -label.align_sequences_to_existing_alignment = Alinear las secuencias con el alineamiento existente -label.realign_with_params = Realinear con {0} -label.calcname_with_default_settings = {0} por defecto -label.action_with_default_settings = {0} con la configuración por defecto -label.edit_settings_and_run = Editar la configuración y ejecutar... -label.view_and_change_parameters_before_alignment = Ver y cambiar los parámetros antes del alineamiento -label.run_with_preset_params = Ejecutar {0} con preconfiguración -label.view_and_change_parameters_before_running_calculation = Ver y cambiar los parámetros antes de lanzar el cálculo -label.view_documentation = Ver documentación -label.select_return_type = Seleccionar el tipo de retorno -label.translation_of_params = Traducción de {0} -label.features_for_params = Características de - {0} -label.annotations_for_params = Anotaciones de - {0} -label.generating_features_for_params = Generando características de - {0} -label.generating_annotations_for_params = Generando anotaciones de - {0} -label.varna_params = VARNA - {0} -label.sequence_feature_settings = Configuración de las características de la secuencia -label.pairwise_aligned_sequences = Secuencias alineadas a pares -label.original_data_for_params = Datos originales de {0} -label.points_for_params = Puntos de {0} -label.transformed_points_for_params = Puntos transformados de {0} -label.graduated_color_for_params = Color graduado para la característica de {0} -label.select_backgroud_colour = Seleccionar color de fondo -label.invalid_font = Fuente no válida -label.separate_multiple_accession_ids = Separar los accession id con un punto y coma ";" -label.replace_commas_semicolons = Cambiar comas por puntos y comas -label.parsing_failed_syntax_errors_shown_below_param = Parseo erróneo. A continuación, se muestras los errores de sintaxis {0} -label.parsing_failed_unrecoverable_exception_thrown_param = \nParseo err\u00F3neo. Se ha lanzado una excepci\u00F3n fatal\:\n {0} -label.example_query_param = Consulta de ejemplo: {0} -label.enter_value_increase_conservation_visibility = Introduzca un valor para incrementar la visibilidad de la conservación -label.enter_percentage_identity_above_which_colour_residues = Introduza un % de identidad por encima del cual se colorearán los residuos -label.wswublast_client_credits = Para mostrar las caracter\u00EDsticas de una secuencia, debe indicarse un id de Uniprot cuya secuencia se corresponda al 100 % con la introducida.\nPara mostrar estas caracter\u00EDsticas, prueba a cambar los nombre de sus secuencia con los ID que se sugieren a continuaci\u00F3n.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1)\:W25-W28 (2005)); -label.blasting_for_unidentified_sequence = Ejecutar BLAST para la secuencias sin identificar -label.select_columns_containing = Seleccione las columnas que contengan -label.select_columns_not_containing = Seleccione las columnas que no contengan -option.trim_retrieved_seqs = Ajustar las secuencias recuperadas -label.trim_retrieved_sequences = Cuando la secuencia de referencia es más larga que la secuencia con la que está trabajando, sólo se mantienen las subsecuencias relevantes. -label.use_sequence_id_1 = Utilice $SEQUENCE_ID$ o $SEQUENCE_ID=//=$ -label.use_sequence_id_2 = \nto para embeber el id de la secuencia en una URL -label.ws_parameters_for = Parámetros para {0} -label.switch_server = Cambiar servidor -label.open_jabaws_web_page = Abra el página principal del servidor JABAWS en un navegador web -label.choose_jabaws_server = Escoja un servidor para ejecutar este servicio -label.services_at = Servicios en {0} -label.rest_client_submit = {0} utilizando {1} -label.fetch_retrieve_from =Recuperar de {0} -label.fetch_retrieve_from_all_sources = Recuperar de todas las fuentes {0} en {1}
    La primera es :{2} -label.feature_settings_click_drag = Haga clic o arrastre los tipos de las características hacia arriba o hacia abajo para cambiar el orden de visualización.
    Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual.
    -label.opt_and_params_further_details = ver los detalles adicionales haciendo clic en el botón derecho -label.opt_and_params_show_brief_desc_image_link = Haga clic para ver una descripción breve
    Haga clic en el botón derecho para obtener información adicional. -label.opt_and_params_show_brief_desc = Haga clic para ver una descripción breve
    -label.adjusts_width_generated_eps_png = Ajusta la anchura del fichero EPS o PNG generado para asegurar incluso que el ID de la secuencia más larga o las etiquetas de anotación se muestran -label.manually_specify_width_left_column = Especificar manualmente la anchura de la columna izquierda en las etiquetas de los ID de la secuencia y las anotaciones se mostrar en las figuras del alineamiento exportado.Esta configuraicón se ignorará si está marcada la opción 'Establecer automáticamente al anchura del ID' -label.job_created_when_checked = Cuando está habilitado, se crea un trabajo para cada secuencia de la selección actual -label.when_checked_job_visible_region_and_results = Cuando está habilitado, se crea un único trabajo para la región visible y los resultados de mapean en su ubicación dentro del alineamiento. En caso contrario, se creará un trabajo para cada región visible y contigua en el alineamiento o selección actual (p.e. un alineamiento múlitple). -label.flat_file_representation = La representación del fichero plano de este servicio utilizando el formalismo Really Simple Bioinformatics Service -label.result_of_parsing_rsbs = Resultados de parsear la representación RSBS -label.user_preset = Preselección de usuario -label.service_preset = Preselección del servicio -label.run_with_preset = Ejecutar {0} con preselección -label.view_service_doc_url = Visualizar {1} -label.submit_sequence = Enviar {0} {1} {2} {3} a
    {4} -action.by_title_param = por {0} -label.alignment = Alineamiento -label.secondary_structure_prediction = Predicción de la estructura secundaria -label.sequence_database_search = Búsqueda en base de datos de secuencias -label.analysis = Análisis -label.protein_disorder = Desorden en la proteína -label.source_from_db_source = Fuentes de {0} -label.from_msname = de {0} -label.superpose_with = Superponer con... -action.do = Hacer -label.scale_label_to_column = Ajustar la etiqueta a la columna -label.add_new_row = Añadir nuevo fila -label.edit_label_description = Editar etiqueta/descripción -label.hide_row = Ocultar esta fila -label.delete_row = Borrar esta fila -label.show_all_hidden_rows = Mostrar todas las filas ocultas -label.export_annotation = Exportar anotación -label.copy_consensus_sequence = Copiar secuencia de consenso -label.helix = Hélice -label.sheet = Hoja -label.rna_helix = Hélice de ARN -label.remove_annotation = Borrar anotación -label.colour_by = Colorear por... -label.muscle_multiple_protein_sequence_alignment = Alineamiento múltiple de secuencias de proteínas con Muscle -label.mafft_multiple_sequence_alignment = Alineamiento múltiple de secuencias con MAFFT -label.clustalw_multiple_sequence_alignment = Alineamiento múltiple de secuencias con ClustalW -label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JNet -label.multiharmony = Multi-Harmony -label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis -label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview. -label.prompt_each_time = Preguntar siempre -label.use_source = Fuente -label.couldnt_save_project = No es posible guardar el proyecto -label.error_whilst_saving_current_state_to = Error mientras se guardaba el estado a {0} -label.error_whilst_loading_project_from = Error cargando el proyecto desde {0} -label.couldnt_load_project = No es posible cargar el proyecto -label.pca_sequences_not_aligned = Las secuencias deben estar alineadas antes de calcular el PCA.\nPruebe a utilizar la funci\u00F3n de rellenar huecos en el men\u00FA Editar,\no cualquiera de los servicios web de alineamiento m\u00FAltiple. -label.invalid_name_preset_exists = Nombre no válido - esta preconfiguración ya existe. -label.invalid_name = Nombre no válido -label.set_proxy_settings = Por favor, configure su proxy en la pestaña 'Conexiones' de la ventana de Preferencia -label.proxy_authorization_failed = Autorización del proxy fallida -label.internal_jalview_error = Error interno de Jalview -label.secondary_structure_prediction_service_couldnt_be_located = No se ha podido encontrar el Servicio de Predicciónd de la Estructura Secudaria {0} en {1}. -label.service_called_is_not_msa_service = El Servicio llamado \n{0}\nno es un \nServicio de Alineamiento M\u00FAltiple de Secuencias\! -label.msa_service_is_unknown = El Servicio de Alineamiento Múltiple llamado {0} es desconocido -label.service_called_is_not_seq_search_service = El Servicio llamando \n{0}\nno es un \nServicio de B\u00FAsqueda de Secuencias\! -label.seq_search_service_is_unknown = El Servicio de Búsqueda de Sencuencias llamado {0} es desconocido -label.feature_type = Tipo de característisca -label.display = Representación -label.service_url = URL del servicio -label.copied_sequences = Secuencias copiadas -label.cut_sequences = Cortar secuencias -label.conservation_colour_increment = Incremento de Conservación del Color ({0}) -label.percentage_identity_thereshold = Umbral del Porcentaje de Identidad ({0}) -label.error_unsupported_owwner_user_colour_scheme = Propietario no soportado para el diálogo del Esquema Cromático del Usuario -label.save_alignment_to_file = Guardar Alineamiento en fichero -label.save_features_to_file = Guardar Características en un fichero -label.save_annotation_to_file = Guardar Anotación en un fichero -label.no_features_on_alignment = No se han encontrado características en el alineamiento -label.save_pdb_file = Guardar fichero PDB -label.save_text_to_file = Guardar Texto en un fichero -label.save_state = Guardar estado -label.restore_state = Restaurar estado -label.saving_jalview_project = Guardando el proyecto de Jalview {0} -label.loading_jalview_project = Cargando el proyecto de Jalview {0} -label.save_vamsas_document_archive = Guardar el archivo de documento Vamsas -label.saving_vamsas_doc = Guardando el documento VAMSAS en {0} -label.load_feature_colours = Cargar colores de características -label.save_feature_colours = Guardar esquema cromático de características -label.dataset_for = {0} conjunto de datos para {1} -label.select_startup_file = Seleccionar fichero de arranque -label.select_default_browser = Seleccionar navegador web por defecto -label.save_tree_as_newick = Guardar árbol como fichero newick -label.create_eps_from_tree = Crear un fichero EPS a partir de un árbol -label.create_png_from_tree = Crear una imagen PNG a partir de un árbol -label.save_colour_scheme = Guardar esquema cromático -label.edit_params_for = Editar los parámetros de {0} -label.choose_filename_for_param_file = Escoja un nombre de fichero para este fichero de parámetros -label.save_as_html = Guardar como HTML -label.recently_opened = Abiertos recientemente -label.blasting_for_unidentified_sequence_jobs_running = Ejecutando BLAST de las secuencias no indentificadas - {0} trabajos en marcha. -label.tree_from = Árbol de {0} -label.webservice_job_title = {0} usando {1} -label.select_visible_region_of = seleccionada {0} región de {1} -label.visible = Visible -label.select_unselect_visible_regions_from = seleccionada y deseleccionadas {0} regiones de {1} -label.visible_region_of = región visible de -label.webservice_job_title_on = {0} usando {1} de {2} -label.updating_vamsas_session = Actualizando sesión VAMSAS -label.loading_file = Cargando fichero: {0} -label.edit_params = Editar {0} -error.not_implemented = No implementado -error.no_such_method_as_clone1_for = No existe ese método como un clone1 de {0} -error.null_from_clone1 = Nulo de clone1! -error.implementation_error_sortbyfeature = Error de implementación - sortByFeature debe ser uno de FEATURE_SCORE, FEATURE_LABEL o FEATURE_DENSITY. -error.not_yet_implemented = No se ha implementado todavía -error.unknown_type_dna_or_pep = Tipo desconocido {0} - dna o pep son los únicos valores permitidos -error.implementation_error_dont_know_thereshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual. -error.implementation_error_embeddedpopup_not_null = Error de implementación - embeddedPopup debe ser no nulo. -error.invalid_colour_for_mycheckbox = Color no válido para MyCheckBox -error.implementation_error_unrecognised_render_object_for_features_type = Error de implementación: no se reconoce el objeto de representación {0} para las características de tipo {1} -error.implementation_error_unsupported_feature_colour_object = Error de implementación: objeto de color de características no soportado. -error.invalid_separator_parameter = Separador de parámetros no válido - debe tener longitud mayor que cero -error.alignment_cigararray_not_implemented = Alignment(CigarArray) no se ha implementado todavía -error.weak_sequencei_equivalence_not_yet_implemented = Equivalencia débil sequenceI no se ha implementado todavía. -error.implementation_error_can_only_make_alignmnet_from_cigararray = Error de implementación - sólo se puede construir un vista de alineamiento a partir de una CigarArray de secuencias. -error.empty_view_cannot_be_updated = una vista vacía no se puede actualizar. -error.mismatch_between_number_of_sequences_in_block = No hay coincidencia entre el número de secuencias en el bloque {0} ({1}) y la vista original ({2}) -error.padding_not_yet_implemented = El relleno no se ha implementado todavía -error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view = No hay coincidencia entre los bloques visibles para actualizar y el número de contigs en la vista (contigs=0,blocks={0}) -error.unknown_seq_cigar_operation = Operación SeqCigar {0} desconocida -error.implementation_bug_parse_cigar_string = Bug de implementación en parseCigarString -error.implementation_error_invalid_operation_string = Error de implementación. Cadena de operación no válida. -error.invalid_range_string = Rango de la cadena no válido (debe ser cero o un número positivo) -error.implementation_error_delete_range_out_of_bounds = Error de implementación: deleteRange fuera de rango: el comienzo debe ser cero o positivo y menor que el final. -error.implementation_error = Error de implementación -error.implementation_error_unknown_operation = ¡Error de implementación! Operación desconocida {0} -error.implementation_error_unexpected_null_from_get_sequence_and_deletions = Error de implementación - valor nulo no esperado en getSequenceAndDeletions -error.implementation_error_set_seq_null = Error de implementación - _setSeq(null,...) -error.implementation_error_s = Error de implementación: _s= {0} -error.implementation_error_seqcigar_possible = SeqCigar: posible error de implementación: la secuencia es más larga de el conjunto de datos de la secuencia -error.implmentation_bug_seq_null = Bug de implementación. Seq nula -error.implementation_bug_cigar_operation_list_range_list = Bug de implementación: Cigar Operation list!= range list -error.not_yet_implemented_cigar_object_from_cigar_string = No implementado todavía: construcción de un objeto Cigar desde una cadena y una secuencia con huecos. -error.implementation_bug_cigar_operation = Bug de implementación. La operación Cigar {0} {1} no es ni {2}, ni {3} ni {4}. -error.implementation_error_for_new_cigar = Error de implementación en new Cigar(SequenceI) -error.implementation_error_cigar_seq_no_operations = Error de implementación: la {0}a secuencia Cigar no tiene operaciones. -error.implementation_error_jmol_getting_data = Error de implementación - Jmol parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016 -error.implementation_error_no_pdbentry_from_index = Error de implementación - no existe la correspondiente entrada pdb (para el índice {0}) para añadir el mapeo de secuencias a -error.jmol_version_not_compatible_with_jalview_version = La versión {0} de Jmol no es compatible con esta versión de Jalview. Informe de este problema en http://issues.jalview.org -error.not_implemented_remove = Borrar: no implementado -error.not_implemented_clone = Clonar: no implementado -error.implementation_error_chimera_getting_data = Error de implementación - Chimera parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016 -error.call_setprogressbar_before_registering_handler = llamada a setProgressBar antes de registrar el manejador de la barra de estado -label.cancelled_params = {0} cancelado -error.implementation_error_cannot_show_view_alignment_frame = Error de implementación: no es posible mostrar una vista de otro alineamiento en un AlignFrame. -error.implementation_error_dont_know_about_thereshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual. -error.eps_generation_not_implemented = La generación de EPS no se ha implementado todavía -error.png_generation_not_implemented = La generación de PNG no se ha implementado todavía -error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya había otra conectada -error.invalid_vamsas_session_id = Identificador de sesión VAMSAS no válido -error.implementation_error_cannot_create_groovyshell = Error de implementación:no se puede crear groovyShell sin Groovy en el classpath -label.groovy_support_failed = El soporte Groovy de Jalview ha fallado -label.couldnt_create_groovy_shell = No es posible crear el shell de Groovy. Compruebe el fichero de log para conocer los detalles. -error.unsupported_version_calcIdparam = Versión no soportada de {0} -error.implementation_error_cant_reorder_tree = Error de implementación: no es posible reordenar este árbol. No DefaultMutableTreeNode. -error.invalid_value_for_option = Valor no válido de {0} para la opción {1} -error.implementation_error_cannot_import_vamsas_doc = Error de implementación - todavía no es posible importar el documento VAMSAS existente en una sesión existente. -label.vamsas_doc_couldnt_be_opened_as_new_session = El documento VAMSAS no ha podido abrirse como una nueva sesión. Por favor, escoja otra. -error.implementation_error_vamsas_operation_not_init = ¡Error de implementación! Operaciones VAMSAS cuando el cliente no estaba inicializado ni conectado -error.jalview_no_connected_vamsas_session = Jalview está conectado a una sesión VAMSAS -error.implementation_error_cannot_recover_vamsas_object_mappings = Error de implementación: no es posible recuperar los mapeos del objeto VAMSAS - no se ha hecho ningún backup -error.setstatus_called_non_existent_job_pane = se lllamado a setStatus para el panel de trabajo {0} no existente -error.implementation_error_cannot_find_marshaller_for_param_set =Error de implementación: no puede encontrar un marshaller para el conjunto de parámetros -error.implementation_error_old_jalview_object_not_bound =Error de implementación: ¡el objeto Jalview antiguo no está enlazado! ({0}) -error.implementation_error_vamsas_doc_class_should_bind_to_type = Error de implementación: la clase de documento VAMSAS {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2}) -error.implementation_error_jalview_class_should_bind_to_type = Error de implementación: la clase Jalview {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2}) -error.invalid_vamsas_rangetype_cannot_resolve_lists = RangeType VAMSAS no válido - ¡no es posible resolver ambas listas de Pos y Seg con los valores elegidos! -error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType. -error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento -error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia -error.implementation_error_cannot_map_alignment_sequences = Error de implementación: no es posible maper un alineamiento de secuencias desde distintos conjuntos de datos en un único alineamiento en el documento VAMSAS. -error.implementation_error_cannot_duplicate_colour_scheme = Error grave de implementación: no es posible duplicar el esquema cromático {0} -error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo -exception.ssm_context_is_null = El contexto SSM es nulo -error.idstring_seqstrings_only_one_per_sequence = idstrings y seqstrings contienen una cadena por cada secuencia -error.cannot_have_mixed_length_replacement_vectors = No es posible tener vectores de reemplazo de distinta longitud. El vector de reemplazo para {0} es de {1} cadenas de largo, pero se ha considerado ya como un vector de longitud {2}. -error.cannot_have_zero_length_vector_replacement_strings = No es posible tener un vector de cadenas de reemplazo de longitud cero - debe ser uno o n. -error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = ¡Error de implementación! Todavía no se soportan varios trabajos de predicción asociados a una única secuencia. -error.implementation_error_invalid_msa_index_for_job = ¡Error de implementación! Valor msaIndex no válido para JPredJob en el objeto de entrada MSA padre! -error.implementation_error_startjob_called = Error de implementación - StartJob(JpredJob) invocado en {0} -error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JNet conjuntos. -label.job_never_ran = El trabajo nunca se ejecutó - entrada devuelta al usuario. -error.implementation_error_minlen_must_be_greater_zero = Error de implementación: minlen debe ser cero o más -error.implementation_error_msawbjob_called = Error de implementación - StartJob(MsaWSJob) invocado en un WSJobInstance {0} -error.implementation_error_cannot_attach_ws_menu_entry = Error de implementación: ¡no es posible adjunto una WS Menu Entry sin una referencia a un manejador del servicio! -error.parameter_migration_not_implemented_yet = La migración de parámetros no se ha implementado todavía -error.implementation_error_cannot_set_jaba_option = Error de implementación: no es posible establecer el valor de Jaba Option a un valor fuera de su rango permitido -error.implementation_error_valuetype_doesnt_support_jabaws_type = Error de implementación: jalview.ws.params.ValueConstrainI.ValueType no soporta el tipo JABAWS: {0} -error.cannot_create_jabaws_param_set = No es posible crear un JabaWSParamSet con parámetros no JabaWS -error.cannot_set_arguments_to_jabaws_param_set = No es posible establecer argumentos en JabaWSParamSet que no sean argumentos JabaWS -error.implementation_error_runner_config_not_available = Error de implementación: Runner Config no está disponible para un servicio JABAWS de tipo {0} ({1}) -error.implementation_error_cannot_handle_jaba_param = Error de implementación: no es posible manejar el objeto del parámetro Jaba {0} -error.implementation_error_attempt_to_delete_service_preset = Error de implementación: intento de borrar un servicio preestablecido -error.implementation_error_cannot_locate_oldname_presetname = Error de implementación: no es posible localizar ni el nombre antiguo ({0}) ni el presetName ({1} en el almacén de datos. -error.implementation_error_jabaws_param_set_only_handled_by = Error de implementación: JabaWsParamSets sólo puede ser manejado por JabaParamStore -error.cannot_set_source_file_for = No es posible establecer el fichero fuente para {0} -error.mismatch_service_instance_preset = Posible desajuste entre la instancia del servicio y la prestablecida -error.cannot_set_params_for_ws_preset = No es posible establecer los parámetros para el servicio web JABA presestablecido -error.implementation_error_can_only_instantiate_jaba_param_sets = Error de implementación: sólo se puede instanciar conjuntos de parámetros Jaba -error.no_aacon_service_found = No se ha encontrado ningún servicio AACon -error.implementation_error_couldnt_copy_value_constraint = Error de implementación: ¡no se puede copiar ValueConstrain! -error.couldnt_encode_as_utf8 = No se ha podido codificar {0} como UTF-8. -error.tree_inputtype_not_yet_implemented = No se ha implementado todavía el árbol como InputType -error.implementation_error_need_to_have_httpresponse = Error de implementación: se necesita tener un HttpResponse que procesar -error.dbrefsource_implementation_exception = Excepción de implementación DBRefSource -error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0}) -error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources -label.view_controller_toggled_marked = {0} {1} columnas {2} conteniendo características del tipo {3} en {4} secuencia(s) -label.toggled = Invertida -label.marked = Marcada -label.not = no -label.no_feature_of_type_found = No se han encontrado características del tipo {0}. -label.submission_params = Envío {0} -label.empty_alignment_job = Trabajo de alineamiento vacío -label.add_new_sbrs_service = Añadir un nuevo SBRS -label.edit_sbrs_entry = Editar entrada SBRS -label.pca_recalculating = Recalculando PCA -label.pca_calculating = Calculando PCA -label.select_foreground_colour = Escoger color del primer plano -label.select_colour_for_text = Seleccione el color del texto -label.adjunst_foreground_text_colour_thereshold = Ajustar el umbral del color del texto en primer plano -label.select_subtree_colour = Seleccioanr el color del sub-árbol -label.create_new_sequence_features = Crear nueva(s) característica(s) de secuencia -label.amend_delete_features = Arrelgar/Borrar características de {0} -exception.out_of_bounds_for_file = Fuera de rango para el fichero: i={0}, Buffer final: i0={1} iend={2} -exception.null_string_given_to_regex_search = Cadena nula enviada a Regex.search -exception.null_string_like_given_to_regex_search = StringLike nula enviada a Regex.search -exception.null_string_given_to_regex_reverse_search = Cadena nula enviada a Regex.reverseSearch -exception.null_string_like_given_to_regex_reverse_search = StringLike nula enviada a Regex.reverseSearch -exception.null_string_like_given_to_regex_search_from = Cadena nula enviada a Regex.searchFrom -exception.null_string_like_given_to_regex_search_region = Cadena nula enviada a Regex.searchRegion -exception.replace_null_regex_pointer = Reemplazador tiene un puntero Regex nulo -exception.bad_pattern_to_regex_perl_code = patrón erróneo en Regex.perlCode: {0} -exception.no_stub_implementation_for_interface = No existe una implementación del stub para la interfaz: {0} -exception.cannot_set_endpoint_address_unknown_port = No es posible estabelcer la dirección de punto final para el puerto desconocido {0} -exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Consultando la coincidencia de apertura de paréntesis para paréntesis sin cerrar (?) -exception.mismatched_unseen_closing_char = Discordancia (no vista) en el carácter de cierre {0} -exception.mismatched_closing_char = Carácter de cierre discordante {0} -exception.mismatched_opening_char = Carácter de apertura discordante {0} en {1} -exception.invalid_datasource_couldnt_obtain_reader = Fuente de datos no válida. No es posible obtener el Reader -exception.index_value_not_in_range = {0}: el valor del índice {1} en se encuentra en el rango [0..{2}] -exception.unterminated_cigar_string = Cadena cigar sin terminar -exception.unexpected_operation_cigar_string_pos = Operación no esperada {0} en una cadena cigar (posición {1} en {2}) -exception.couldnt_parse_responde_from_annotated3d_server = No es posible parsear la respuesta procedente del servidor Annotate3d -exception.application_test_npe = Prueba de aplicación: lanzando un NullPointerException que debe aparecer en la consola -exception.overwriting_vamsas_id_binding = Sobreescribiendo la asociación al VAMSAS id -exception.overwriting_jalview_id_binding = Sobreescribiendo la asociación al Jalview id -error.implementation_error_unknown_file_format_string = Error de implementación: cadena de formato de fichero desconocido -exception.failed_to_resolve_gzip_stream = Fallo al resolver el flujo GZIP -exception.problem_opening_file_also_tried = Problema abriendo {0} (también se intentó {1}) : {2} -exception.problem_opening_file = Problema abriendo {0} : {1} -exception.failed_to_read_data_from_source = Error al leer datos de la fuente: {0} -exception.no_init_source_stream = Flujo de fuente sin inicializar -exception.invalid_source_stream = Flujo de fuente no válida: {0} -error.implementation_error_reset_called_for_invalid_source = Error de implementación: se ha invocado un Reset en una fuente no válida. -exception.number_of_residues_in_query_sequence_differ_from_prediction = El n\u00FAmero de residuos en la supuesta secuencia consultada {0} ({1}\n{2})\ndifiere del n\u00FAmero de sitios de predicci\u00F3n en la predicci\u00F3n ({3}) -label.mapped = mapeado -exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: La entrada ({0}) tiene un número inesperado de columnas -exception.couldnt_parse_concise_annotation_for_prediction = No es posible parsear la anotaci\u00F3n concisa para el perfil de predicci\u00F3n.\n{0} -exception.newfile = Fichero Newick\: {0}\n -label.no_tree_read_in = No hay lectura de árbol en -exception.rnaml_couldnt_access_datasource = No ha sido posible acceder la fuente de datos ({0}) -exception.ranml_couldnt_process_data = No ha sido posible procesar los datos como un fichero RNAML ({0}) -exception.ranml_invalid_file = Fichero RNAML no válido ({0}) -exception.ranml_problem_parsing_data = Problema parseando los datos como RNAML ({0}) -exception.pfam_no_sequences_found = No se han encontrado secuencias (entrada PFAM) -exception.stockholm_invalid_format = Este fichero no es tiene un formato STOCKHOLM válido: la primera línea no contiene '# STOCKHOLM' -exception.couldnt_parse_sequence_line = No es posible parse la línea de secuencia: {0} -exception.error_parsing_line = Error parseando {0} -exception.unknown_annotation_detected = Anotación desconocida detectada: {0} {1} -exception.couldnt_store_sequence_mappings = No es posible almacenar los mapeos de secuencia para {0} -exception.matrix_too_many_iteration = Demasiadas iteraciones en {0} (el máximo es {1}) -exception.browser_not_found = Excepción al buscar el navegador: {0} -exception.browser_unable_to_locate = Imposible encontrar el navegador: {0} -exception.invocation_target_exception_creating_aedesc = InvocationTargetException mientras se creaba AEDesc: {0} -exception.illegal_access_building_apple_evt= IllegalAccessException mientras se construía AppleEvent: {0} -exception.instantiation_creating_aedesc = InstantiationException mientras se creaba AEDesc: {0} -exception.unable_to_launch_url = Imposible lanzar la URL: {0} -exception.unable_to_create_internet_config = Imposible crear una instancia de configuración de Internet: {0} -exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0} -exception.illegal_access_calling_url = IllegalAccessException mientras se invocaba openURL: {0} -exception.interrupted_launching_browser = InterruptedException mientras se lanzaba el navegador: {0} -exception.das_source_doesnt_support_sequence_command = La fuente {0} no soporta el comando sequence. -exception.invalid_das_source = Fuente DAS no válida: {0} -exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1} -label.no_embl_record_found = # No se ha recuperado ningún registro EMBL de {0}:{1} -label.embl_successfully_parsed = # Se han parseado con éxito las consultas {0} en un alineamiento -exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1} -exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB -exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento -exception.unknown_format_for_file = Formato desconocido {0} para el fichero \: \n{1} -label.remove_gaps = Eliminar huecos -exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JNet Query! -exception.server_timeout_try_later = Tiempo de conexi\u00F3n ha expirado - int\u00E9ntelo de nuevo m\u00E1s tarde\n -exception.web_service_returned_null_try_later= El servidor {0} ha devuelto un objeto nulo, por lo que probablemente no se haya podido contactar con él. Inténtelo de nuevo más tarde. -exception.cannot_contact_service_endpoint_at = No es posible contactar por el punto de acceso al servicio en {0} -error.implementation_error_cannot_find_service_url_in_given_set = Error de implementación: no es posible encontrar la URL del servicio en el conjunto de URL proporcionado -error.implementation_error_cannot_find_service_url_in_given_set_param_store = Error de implementación: la URL del servicio en el conjunto de URL para este almacén de parámetros del servicio({0}) -exception.jobsubmission_invalid_params_set = Conjunto de parámetros no válido. Comprueba la implementación de Jalview -exception.notvaliddata_group_contains_less_than_min_seqs = El grupo contiene menos de {0} secuencias. -exception.outofmemory_loading_pdb_file = Sin menoria al cargar el fichero PDB -exception.eps_coudnt_write_output_file = No es posible escribir el fichero de salida: {0} -exception.eps_method_not_supported = Método actualmente no suportado por la versión {0} de EpsGraphics2D -exception.eps_unable_to_get_inverse_matrix = Imposible obtener la inversa de la matrix: {0} -warn.job_cannot_be_cancelled_close_window = Este trabajo no se puede cancelar.\nSimplemente, cierre la ventana. -warn.service_not_supported = ¡Servicio no soportado! -warn.input_is_too_big = ¡El tamaño de la entrada es demasiado grande! -warn.invalid_job_param_set = ¡Conjunto de parámetros del trabajo no válido! -info.job_couldnt_be_run_server_doesnt_support_program = No es posible ejecutar el trabajo porque el servidor no soporta este programa.\n{0} -info.job_couldnt_be_run_exceeded_hard_limit = No es posible ejecutar el trabajo porque excede los l\u00EDmites del servidor.\n{0} -info.job_couldnt_be_run_incorrect_param_setting = No es posible ejecutar el trabjao porque el servidor no soporta algunos de los par\u00E1metros.\n{0}\nPor favor, aseg\u00FArese de que ha usado los par\u00E1metros adecuados para este servicio\n -info.no_jobs_ran = No se ha ejecutado ningún trabajo -info.failed_to_submit_prediction = Error al enviar la predicci\u00F3n\:\n{0} {1} -info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JNet no v\u00E1lidos\!\n{2} -info.failed_to_submit_sequences_for_alignment = Error al enviar la secuencias para el alineamiento.\nLo m\u00E1s probable es que haya un problema en el servidor.\nSimplemente, cierre la ventana\n -info.alignment_object_method_notes = \nNotas sobre los m\u00E9todos del objeto alineamiento\n -info.server_exception = \n{0} Excepci\u00F3n del servidor\!\n{1} -status.processing_commandline_args = Procesando los argumentos de la línea de comandos... -status.das_features_being_retrived = Recuperando características DAS... -status.searching_for_sequences_from = Buscando secuencias en {0} -status.finished_searching_for_sequences_from = Finalizada la búsqueda de secuencias en {0} -label.eps_file = Fichero EPS -label.png_image = Imagen PNG -status.saving_file = Guardando {0} -status.export_complete = Exportación completada. -status.fetching_pdb = Recuperando PDB {0} -status.refreshing_news = Refrescando noticias -status.importing_vamsas_session_from = Importando sesión VAMSAS de {0} -status.opening_params = Abriendo {0} -status.waiting_sequence_database_fetchers_init = Esperando la inicialización de los recuperadores de bases de datos de secuencias -status.init_sequence_database_fetchers = Inicializando recuperadores de bases de datos de secuencias -status.fetching_sequence_queries_from = Recuperando {0} consultas de secuencias de {1} -status.finshed_querying = Consulta finalizada -status.parsing_results = Parseando resultados. -status.processing = Procesando... -status.refreshing_web_service_menus = Refrescando los menús de servicios web -status.collecting_job_results = Recolectando los resultados de los trabajos. -status.fetching_das_sequence_features = Recuperando las características DAS de las secuencias -status.no_das_sources_active = No existe ninguna fuente DAS activa -status.das_feature_fetching_cancelled = Recuperación de características DAS cancelada -status.das_feature_fetching_complete = Recuperación de características DAS completada -status.fetching_db_refs = Recuperando db refs -label.font_doesnt_have_letters_defined = La fuente no tiene letras definidas\npor lo que no puede emplease\ncon datos de alineamientos -label.font_too_small = Tamaño de la letra es demasiado pequeña -label.error_loading_file_params = Error cargando el fichero {0} -label.error_loading_jalview_file = Error cargando el fichero Jalview -warn.out_of_memory_when_action = Sin memoria al {0}\!\!\nConsulte los ficheros de ayuda para ajustar la memoria de la m\u00E1quina virtual de Java. -warn.out_of_memory_loading_file = Sin memoria al cargar el fichero {0}\!\!\nConsulte los ficheros de ayuda para ajustar la memoria de la m\u00E1quina virtual de Java. -label.out_of_memory = Sin memoria -label.invalid_id_column_width = Identificador de anchura de columna no válido -warn.user_defined_width_requirements = La anchura definida por el usuario para la \nlas columnas de anotaci\u00F3n e identificador de secuencias\nen figuras exportadas debe ser\na, al menos, de 12 p\u00EDxels -label.couldnt_create_sequence_fetcher = No es posible crear SequenceFetcher -warn.couldnt_create_sequence_fetcher_client = No es posible crear el cliente de recuperador de secuencias. Comprueba el fichero de log para más detalles. -warn.server_didnt_pass_validation = El servicio no ha pasado la validaci\u00F3n.\nCompruebe la consola de Jalview para m\u00E1s detalles. -warn.url_must_contain = La URL de la secuencia debe contener $SEQUENCE_ID$ o un regex $SEQUENCE_ID=//=$ -info.validate_jabaws_server = \u00BFValidar el servidor JabaWS?\n(Consulte la consola de salida para obtener los resultados) -label.test_server = ¿Probar servidor? -info.you_want_jalview_to_find_uniprot_accessions = \u00BFDesea que Jalview encuentre\nUniprot Accession ids para los nombres de secuencias dados? -label.find_uniprot_accession_ids = Buscar Uniprot Accession Ids -label.new_sequence_fetcher = Añadir recuperador de secuencias -label.additional_sequence_fetcher = Recuperador de secuencia adicional -label.select_database_retrieval_source = Seleccionar fuente de recuperación de bases de datos -label.overwrite_existing_file = ¿Sobreescribir el fichero existente? -label.file_already_exists = El fichero existe -label.edit_jabaws_url = Editar JABAWS URL -label.add_jabaws_url = Añadir nueva JABAWS URL -label.news_from_jalview = Noticias de http://www.jalview.org -label.cut_paste_alignmen_file = Cortar & Pegar fichero de alineamiento -label.enter_redundancy_thereshold = Introducir el umbral de redundancia -label.select_dark_light_set_thereshold = Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que
    cambiar entre colores, basándose en el color de fondo     -label.select_feature_colour = Seleccionar color de las características -label.ignore_gaps_consensus = Ignorar huecos en el consenso -label.show_group_histogram = Mostrar histograma de grupo -label.show_group_logo = Mostrar logo de grupo -label.normalise_group_logo = Normalizar el logo de grupo -label.show_histogram = Mostrar histograma -label.show_logo = Mostrar logo -label.normalise_logo = Normalizar logo -label.no_colour_selection_in_scheme = Por favor, seleccione un color antes de aplicar el esquema cromático -label.no_colour_selection_warn = Error guardando el esquema cromático \ No newline at end of file diff --git a/bin/netscape/javascript/JSException.js b/bin/netscape/javascript/JSException.js index 41d9f27..8033210 100644 --- a/bin/netscape/javascript/JSException.js +++ b/bin/netscape/javascript/JSException.js @@ -1,4 +1,4 @@ -Clazz.declarePackage ("netscape.javascript"); -Clazz.load (["java.lang.Exception"], "netscape.javascript.JSException", null, function () { -c$ = Clazz.declareType (netscape.javascript, "JSException", Exception); -}); +Clazz.declarePackage ("netscape.javascript"); +Clazz.load (["java.lang.Exception"], "netscape.javascript.JSException", null, function () { +c$ = Clazz.declareType (netscape.javascript, "JSException", Exception); +}); diff --git a/bin/netscape/javascript/JSObject.js b/bin/netscape/javascript/JSObject.js index 661d426..e43f247 100644 --- a/bin/netscape/javascript/JSObject.js +++ b/bin/netscape/javascript/JSObject.js @@ -1,19 +1,19 @@ -Clazz.declarePackage ("netscape.javascript"); -c$ = Clazz.declareType (netscape.javascript, "JSObject"); -c$.getWindow = Clazz.defineMethod (c$, "getWindow", -function (jvlite) { -{ -return window; -}}, "jalview.bin.JalviewLite"); -Clazz.defineMethod (c$, "call", -function (func, params) { -{ -alert("call " + func); -func.apply(null, params); -}}, "~S,~A"); -Clazz.defineMethod (c$, "eval", -function (string) { -{ -alert("evval " + string); -}return this.eval (string); -}, "~S"); +Clazz.declarePackage ("netscape.javascript"); +c$ = Clazz.declareType (netscape.javascript, "JSObject"); +c$.getWindow = Clazz.defineMethod (c$, "getWindow", +function (jvlite) { +{ +return window; +}}, "jalview.bin.JalviewLite"); +Clazz.defineMethod (c$, "call", +function (func, params) { +{ +alert("call " + func); +func.apply(null, params); +}}, "~S,~A"); +Clazz.defineMethod (c$, "eval", +function (string) { +{ +alert("evval " + string); +}return this.eval (string); +}, "~S"); diff --git a/bin/org/exolab/castor/mapping/Mapping.js b/bin/org/exolab/castor/mapping/Mapping.js index d15a01d..b4a3c0f 100644 --- a/bin/org/exolab/castor/mapping/Mapping.js +++ b/bin/org/exolab/castor/mapping/Mapping.js @@ -1,8 +1,8 @@ -Clazz.declarePackage ("org.exolab.castor.mapping"); -c$ = Clazz.declareType (org.exolab.castor.mapping, "Mapping"); -Clazz.makeConstructor (c$, -function (classLoader) { -}, "ClassLoader"); -Clazz.defineMethod (c$, "loadMapping", -function (url) { -}, "java.net.URL"); +Clazz.declarePackage ("org.exolab.castor.mapping"); +c$ = Clazz.declareType (org.exolab.castor.mapping, "Mapping"); +Clazz.makeConstructor (c$, +function (classLoader) { +}, "ClassLoader"); +Clazz.defineMethod (c$, "loadMapping", +function (url) { +}, "java.net.URL"); diff --git a/bin/org/exolab/castor/xml/Unmarshaller.js b/bin/org/exolab/castor/xml/Unmarshaller.js index 09f0175..70aff82 100644 --- a/bin/org/exolab/castor/xml/Unmarshaller.js +++ b/bin/org/exolab/castor/xml/Unmarshaller.js @@ -1,24 +1,24 @@ -Clazz.declarePackage ("org.exolab.castor.xml"); -c$ = Clazz.declareType (org.exolab.castor.xml, "Unmarshaller"); -Clazz.makeConstructor (c$, -function (record) { -}, "~O"); -Clazz.defineMethod (c$, "setIgnoreExtraElements", -function (b) { -}, "~B"); -Clazz.defineMethod (c$, "setIgnoreExtraAttributes", -function (b) { -}, "~B"); -Clazz.defineMethod (c$, "setMapping", -function (map) { -}, "org.exolab.castor.mapping.Mapping"); -Clazz.defineMethod (c$, "setLogWriter", -function (printWriter) { -}, "java.io.PrintWriter"); -Clazz.defineMethod (c$, "unmarshal", -function (file) { -return null; -}, "java.io.Reader"); -Clazz.defineMethod (c$, "setDebug", -function (debugEnabled) { -}, "~B"); +Clazz.declarePackage ("org.exolab.castor.xml"); +c$ = Clazz.declareType (org.exolab.castor.xml, "Unmarshaller"); +Clazz.makeConstructor (c$, +function (record) { +}, "~O"); +Clazz.defineMethod (c$, "setIgnoreExtraElements", +function (b) { +}, "~B"); +Clazz.defineMethod (c$, "setIgnoreExtraAttributes", +function (b) { +}, "~B"); +Clazz.defineMethod (c$, "setMapping", +function (map) { +}, "org.exolab.castor.mapping.Mapping"); +Clazz.defineMethod (c$, "setLogWriter", +function (printWriter) { +}, "java.io.PrintWriter"); +Clazz.defineMethod (c$, "unmarshal", +function (file) { +return null; +}, "java.io.Reader"); +Clazz.defineMethod (c$, "setDebug", +function (debugEnabled) { +}, "~B"); diff --git a/bin/org/jmol/viewer/Viewer.js b/bin/org/jmol/viewer/Viewer.js index 42c1406..078e834 100644 --- a/bin/org/jmol/viewer/Viewer.js +++ b/bin/org/jmol/viewer/Viewer.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("org.jmol.viewer"); -c$ = Clazz.declareType (org.jmol.viewer, "Viewer"); +Clazz.declarePackage ("org.jmol.viewer"); +c$ = Clazz.declareType (org.jmol.viewer, "Viewer"); diff --git a/bin/swingjs/JSEvent.js b/bin/swingjs/JSEvent.js deleted file mode 100644 index 35812e3..0000000 --- a/bin/swingjs/JSEvent.js +++ /dev/null @@ -1,4 +0,0 @@ -Clazz.declarePackage ("swingjs"); -Clazz.load (["java.awt.event.InvocationEvent"], "swingjs.JSEvent", null, function () { -c$ = Clazz.declareType (swingjs, "JSEvent", java.awt.event.InvocationEvent); -}); diff --git a/bin/swingjs/JSThread.js b/bin/swingjs/JSThread.js index 5c12398..92f41fb 100644 --- a/bin/swingjs/JSThread.js +++ b/bin/swingjs/JSThread.js @@ -1,49 +1,49 @@ -Clazz.declarePackage ("swingjs"); -Clazz.load (["java.lang.Thread", "swingjs.api.JSFunction"], "swingjs.JSThread", null, function () { -c$ = Clazz.decorateAsClass (function () { -this.isJS = false; -Clazz.instantialize (this, arguments); -}, swingjs, "JSThread", Thread, swingjs.api.JSFunction); -Clazz.makeConstructor (c$, -function (group, name) { -Clazz.superConstructor (this, swingjs.JSThread, [group, name]); -{ -this.isJS = true; -}}, "ThreadGroup,~S"); -Clazz.overrideMethod (c$, "run", -function () { -this.run1 (0); -}); -Clazz.defineMethod (c$, "start", -function () { -{ -swingjs.JSToolkit.setTimeout(this, 1, 0); -}}); -Clazz.defineMethod (c$, "sleepAndReturn", -function (delay, state) { -if (!this.isJS) { -Thread.sleep (delay); -return false; -}var me = this; -var r = ((Clazz.isClassDefined ("swingjs.JSThread$1") ? 0 : swingjs.JSThread.$JSThread$1$ ()), Clazz.innerTypeInstance (swingjs.JSThread$1, this, Clazz.cloneFinals ("me", me, "state", state))); -{ -setTimeout( -function() {java.awt.Toolkit.getDefaultToolkit().getSystemEventQueue().postEvent(new java.awt.event.InvocationEvent(me, r))}, -delay -); -}return true; -}, "~N,~N"); -c$.$JSThread$1$ = function () { -Clazz.pu$h (); -c$ = Clazz.declareAnonymous (swingjs, "JSThread$1", null, Runnable); -Clazz.overrideMethod (c$, "run", -function () { -this.f$.me.run1 (this.f$.state); -}); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"INIT", 0, -"LOOP", 1, -"DONE", 2); -}); +Clazz.declarePackage ("swingjs"); +Clazz.load (["java.lang.Thread", "swingjs.api.JSFunction"], "swingjs.JSThread", null, function () { +c$ = Clazz.decorateAsClass (function () { +this.isJS = false; +Clazz.instantialize (this, arguments); +}, swingjs, "JSThread", Thread, swingjs.api.JSFunction); +Clazz.makeConstructor (c$, +function (group, name) { +Clazz.superConstructor (this, swingjs.JSThread, [group, name]); +{ +this.isJS = true; +}}, "ThreadGroup,~S"); +Clazz.overrideMethod (c$, "run", +function () { +this.run1 (0); +}); +Clazz.defineMethod (c$, "start", +function () { +{ +swingjs.JSToolkit.setTimeout(this, 1, 0); +}}); +Clazz.defineMethod (c$, "sleepAndReturn", +function (delay, state) { +if (!this.isJS) { +Thread.sleep (delay); +return false; +}var me = this; +var r = ((Clazz.isClassDefined ("swingjs.JSThread$1") ? 0 : swingjs.JSThread.$JSThread$1$ ()), Clazz.innerTypeInstance (swingjs.JSThread$1, this, Clazz.cloneFinals ("me", me, "state", state))); +{ +setTimeout( +function() {java.awt.Toolkit.getDefaultToolkit().getSystemEventQueue().postEvent(new java.awt.event.InvocationEvent(me, r))}, +delay +); +}return true; +}, "~N,~N"); +c$.$JSThread$1$ = function () { +Clazz.pu$h (); +c$ = Clazz.declareAnonymous (swingjs, "JSThread$1", null, Runnable); +Clazz.overrideMethod (c$, "run", +function () { +this.f$.me.run1 (this.f$.state); +}); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"INIT", 0, +"LOOP", 1, +"DONE", 2); +}); diff --git a/bin/swingjs/api/DOMNode.js b/bin/swingjs/api/DOMNode.js index f518093..ad28942 100644 --- a/bin/swingjs/api/DOMNode.js +++ b/bin/swingjs/api/DOMNode.js @@ -1,58 +1,58 @@ -Clazz.declarePackage ("swingjs.api"); -c$ = Clazz.declareType (swingjs.api, "DOMNode"); -c$.createElement = Clazz.defineMethod (c$, "createElement", -function (key, id) { -var obj = null; -{ -obj = document.createElement(key); -obj.id = id; -}return obj; -}, "~S,~S"); -c$.getParent = Clazz.defineMethod (c$, "getParent", -function (obj) { -{ -return obj.parentNode; -}}, "swingjs.api.DOMNode"); -c$.remove = Clazz.defineMethod (c$, "remove", -function (obj) { -{ -try { -var p = obj.parentNode; -p.removeNode(obj); -} catch(e) {}; -return p; -}}, "swingjs.api.DOMNode"); -c$.add = Clazz.defineMethod (c$, "add", -function (parent, child) { -{ -parent && parent.appendChild(child); -}}, "swingjs.api.DOMNode,swingjs.api.DOMNode"); -c$.getAttr = Clazz.defineMethod (c$, "getAttr", -function (obj, attr) { -{ -if (obj)return obj[attr]; -}}, "swingjs.api.DOMNode,~S"); -Clazz.defineMethod (c$, "getStyle", -function (style) { -{ -if (obj)return obj.style[style]; -}}, "~S"); -c$.setAttr = Clazz.defineMethod (c$, "setAttr", -function (obj, attr, val) { -{ -obj[attr] = (val == "TRUE" ? true : val); -}return obj; -}, "swingjs.api.DOMNode,~S,~O"); -c$.setStyles = Clazz.defineMethod (c$, "setStyles", -function (obj, attr) { -{ -for (var i = 0; i < attr.length;) { -//System.out.println(["DOMNode.setStyles ",attr[i],attr[i+1]]) -; -obj.style[attr[i++]] = attr[i++]; } -}return obj; -}, "swingjs.api.DOMNode,~A"); -c$.setSize = Clazz.defineMethod (c$, "setSize", -function (obj, width, height) { -return swingjs.api.DOMNode.setStyles (obj, ["width", width + "px", "height", height + "px"]); -}, "swingjs.api.DOMNode,~N,~N"); +Clazz.declarePackage ("swingjs.api"); +c$ = Clazz.declareType (swingjs.api, "DOMNode"); +c$.createElement = Clazz.defineMethod (c$, "createElement", +function (key, id) { +var obj = null; +{ +obj = document.createElement(key); +obj.id = id; +}return obj; +}, "~S,~S"); +c$.getParent = Clazz.defineMethod (c$, "getParent", +function (obj) { +{ +return obj.parentNode; +}}, "swingjs.api.DOMNode"); +c$.remove = Clazz.defineMethod (c$, "remove", +function (obj) { +{ +try { +var p = obj.parentNode; +p.removeNode(obj); +} catch(e) {}; +return p; +}}, "swingjs.api.DOMNode"); +c$.add = Clazz.defineMethod (c$, "add", +function (parent, child) { +{ +parent && parent.appendChild(child); +}}, "swingjs.api.DOMNode,swingjs.api.DOMNode"); +c$.getAttr = Clazz.defineMethod (c$, "getAttr", +function (obj, attr) { +{ +if (obj)return obj[attr]; +}}, "swingjs.api.DOMNode,~S"); +Clazz.defineMethod (c$, "getStyle", +function (style) { +{ +if (obj)return obj.style[style]; +}}, "~S"); +c$.setAttr = Clazz.defineMethod (c$, "setAttr", +function (obj, attr, val) { +{ +obj[attr] = (val == "TRUE" ? true : val); +}return obj; +}, "swingjs.api.DOMNode,~S,~O"); +c$.setStyles = Clazz.defineMethod (c$, "setStyles", +function (obj, attr) { +{ +for (var i = 0; i < attr.length;) { +//System.out.println(["DOMNode.setStyles ",attr[i],attr[i+1]]) +; +obj.style[attr[i++]] = attr[i++]; } +}return obj; +}, "swingjs.api.DOMNode,~A"); +c$.setSize = Clazz.defineMethod (c$, "setSize", +function (obj, width, height) { +return swingjs.api.DOMNode.setStyles (obj, ["width", width + "px", "height", height + "px"]); +}, "swingjs.api.DOMNode,~N,~N"); diff --git a/bin/swingjs/api/JSFunction.js b/bin/swingjs/api/JSFunction.js index 4923079..1c8077b 100644 --- a/bin/swingjs/api/JSFunction.js +++ b/bin/swingjs/api/JSFunction.js @@ -1,2 +1,2 @@ -Clazz.declarePackage ("swingjs.api"); -Clazz.declareInterface (swingjs.api, "JSFunction"); +Clazz.declarePackage ("swingjs.api"); +Clazz.declareInterface (swingjs.api, "JSFunction"); diff --git a/src/fr/orsay/lri/varna/models/rna/RNA.java b/src/fr/orsay/lri/varna/models/rna/RNA.java index 9df0400..589dc74 100644 --- a/src/fr/orsay/lri/varna/models/rna/RNA.java +++ b/src/fr/orsay/lri/varna/models/rna/RNA.java @@ -1,15 +1,21 @@ -package fr.orsay.lri.varna.models.rna; - -public class RNA { - - public int getSize() { - // TODO Auto-generated method stub - return 0; - } - - public String getStructDBN(boolean b) { - // TODO Auto-generated method stub - return null; - } - -} +package fr.orsay.lri.varna.models.rna; + +/** + * unused in applet? + * + * + */ + +public class RNA { + + public int getSize() { + // TODO Auto-generated method stub + return 0; + } + + public String getStructDBN(boolean b) { + // TODO Auto-generated method stub + return null; + } + +}