-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");\r
+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 () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.id = null;\r
+this.bonds = null;\r
+this.atoms = null;\r
+this.residues = null;\r
+this.offset = 0;\r
+this.sequence = null;\r
+this.shadow = null;\r
+this.isNa = false;\r
+this.isVisible = true;\r
+this.pdbstart = 0;\r
+this.pdbend = 0;\r
+this.seqstart = 0;\r
+this.seqend = 0;\r
+this.pdbid = "";\r
+this.newline = null;\r
+this.shadowMap = null;\r
+Clazz.instantialize (this, arguments);\r
+}, MCview, "PDBChain");\r
+Clazz.prepareFields (c$, function () {\r
+this.bonds = new java.util.Vector ();\r
+this.atoms = new java.util.Vector ();\r
+this.residues = new java.util.Vector ();\r
+this.newline = System.getProperty ("line.separator");\r
+});\r
+Clazz.makeConstructor (c$, \r
+function (pdbid, id) {\r
+this.pdbid = pdbid.toLowerCase ();\r
+this.id = id;\r
+}, "~S,~S");\r
+Clazz.defineMethod (c$, "setNewlineString", \r
+function (nl) {\r
+this.newline = nl;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "getNewlineString", \r
+function () {\r
+return this.newline;\r
+});\r
+Clazz.defineMethod (c$, "print", \r
+function () {\r
+var tmp = new StringBuilder (256);\r
+for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) {\r
+tmp.append (b.at1.resName).append (" ").append (b.at1.resNumber).append (" ").append (this.offset).append (this.newline);\r
+}\r
+return tmp.toString ();\r
+});\r
+Clazz.defineMethod (c$, "makeExactMapping", \r
+function (as, s1) {\r
+var pdbpos = as.getSeq2Start () - 2;\r
+var alignpos = s1.getStart () + as.getSeq1Start () - 3;\r
+for (var atom, $atom = this.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) {\r
+atom.alignmentMapping = -1;\r
+}\r
+for (var i = 0; i < as.astr1.length; i++) {\r
+if (as.astr1.charAt (i) != '-') {\r
+alignpos++;\r
+}if (as.astr2.charAt (i) != '-') {\r
+pdbpos++;\r
+}if (as.astr1.charAt (i) == as.astr2.charAt (i)) {\r
+var res = this.residues.elementAt (pdbpos);\r
+for (var atom, $atom = res.atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) {\r
+atom.alignmentMapping = alignpos;\r
+}\r
+}}\r
+}, "jalview.analysis.AlignSeq,jalview.datamodel.SequenceI");\r
+Clazz.defineMethod (c$, "transferRESNUMFeatures", \r
+function (seq, status) {\r
+var sq = seq;\r
+while (sq != null && sq.getDatasetSequence () != null) {\r
+sq = sq.getDatasetSequence ();\r
+if (sq === this.sequence) {\r
+return null;\r
+}}\r
+if (status == null) {\r
+status = "IEA:jalview";\r
+}var features = this.sequence.getSequenceFeatures ();\r
+for (var i = 0; i < features.length; i++) {\r
+if (features[i].getFeatureGroup ().equals (this.pdbid)) {\r
+var tx = new jalview.datamodel.SequenceFeature (features[i]);\r
+tx.setBegin (1 + this.residues.elementAt (tx.getBegin () - this.offset).atoms.elementAt (0).alignmentMapping);\r
+tx.setEnd (1 + this.residues.elementAt (tx.getEnd () - this.offset).atoms.elementAt (0).alignmentMapping);\r
+tx.setStatus (status + ((tx.getStatus () == null || tx.getStatus ().length == 0) ? "" : ":" + tx.getStatus ()));\r
+if (tx.begin != 0 && tx.end != 0) {\r
+sq.addSequenceFeature (tx);\r
+}}}\r
+return features;\r
+}, "jalview.datamodel.SequenceI,~S");\r
+Clazz.defineMethod (c$, "makeCaBondList", \r
+function () {\r
+var na = false;\r
+var numNa = 0;\r
+for (var i = 0; i < (this.residues.size () - 1); i++) {\r
+var tmpres = this.residues.elementAt (i);\r
+var tmpres2 = this.residues.elementAt (i + 1);\r
+var at1 = tmpres.findAtom ("CA");\r
+var at2 = tmpres2.findAtom ("CA");\r
+na = false;\r
+if ((at1 == null) && (at2 == null)) {\r
+na = true;\r
+at1 = tmpres.findAtom ("P");\r
+at2 = tmpres2.findAtom ("P");\r
+}if ((at1 != null) && (at2 != null)) {\r
+if (at1.chain.equals (at2.chain)) {\r
+if (na) {\r
+numNa++;\r
+}this.makeBond (at1, at2);\r
+}} else {\r
+System.out.println ("not found " + i);\r
+}}\r
+if (this.residues.size () > 0 && (Clazz.doubleToInt (numNa / (this.residues.size () - 1)) > 0.99)) {\r
+this.isNa = true;\r
+}});\r
+Clazz.defineMethod (c$, "makeBond", \r
+function (at1, at2) {\r
+this.bonds.addElement ( new MCview.Bond (at1, at2));\r
+}, "MCview.Atom,MCview.Atom");\r
+Clazz.defineMethod (c$, "makeResidueList", \r
+function (visibleChainAnnotation) {\r
+var count = 0;\r
+var symbol;\r
+var deoxyn = false;\r
+var nucleotide = false;\r
+var seq = new StringBuilder (256);\r
+var resFeatures = new java.util.Vector ();\r
+var resAnnotation = new java.util.Vector ();\r
+var i;\r
+var iSize = this.atoms.size () - 1;\r
+var resNumber = -1;\r
+for (i = 0; i <= iSize; i++) {\r
+var tmp = this.atoms.elementAt (i);\r
+resNumber = tmp.resNumber;\r
+var res = resNumber;\r
+if (i == 0) {\r
+this.offset = resNumber;\r
+}var resAtoms = new java.util.Vector ();\r
+while ((resNumber == res) && (i < this.atoms.size ())) {\r
+resAtoms.add (this.atoms.elementAt (i));\r
+i++;\r
+if (i < this.atoms.size ()) {\r
+resNumber = this.atoms.elementAt (i).resNumber;\r
+} else {\r
+resNumber++;\r
+}}\r
+i--;\r
+this.residues.addElement ( new MCview.Residue (resAtoms, resNumber - 1, count));\r
+var tmpres = this.residues.lastElement ();\r
+var tmpat = tmpres.atoms.get (0);\r
+var sf = new jalview.datamodel.SequenceFeature ("RESNUM", tmpat.resName + ":" + tmpat.resNumIns + " " + this.pdbid + this.id, "", this.offset + count, this.offset + count, this.pdbid);\r
+resFeatures.addElement (sf);\r
+resAnnotation.addElement ( new jalview.datamodel.Annotation (tmpat.tfactor));\r
+if ((symbol = jalview.schemes.ResidueProperties.getAA3Hash ().get (tmpat.resName)) == null) {\r
+var nucname = tmpat.resName.trim ();\r
+deoxyn = nucname.length == 2 && jalview.schemes.ResidueProperties.aaIndex[nucname.charCodeAt (0)] == jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)];\r
+if (tmpat.name.equalsIgnoreCase ("CA") || jalview.schemes.ResidueProperties.nucleotideIndex[nucname.charCodeAt ((deoxyn ? 1 : 0))] == -1) {\r
+seq.append ("X");\r
+} else {\r
+nucleotide = true;\r
+seq.append (nucname.charAt ((deoxyn ? 1 : 0)));\r
+}} else {\r
+if (nucleotide) {\r
+System.err.println ("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");\r
+}seq.append (jalview.schemes.ResidueProperties.aa[(symbol).intValue ()]);\r
+}count++;\r
+}\r
+if (this.id.length < 1) {\r
+this.id = " ";\r
+}this.isNa = nucleotide;\r
+this.sequence = new jalview.datamodel.Sequence (this.id, seq.toString (), this.offset, resNumber - 1);\r
+for (i = 0, iSize = resFeatures.size (); i < iSize; i++) {\r
+this.sequence.addSequenceFeature (resFeatures.elementAt (i));\r
+resFeatures.setElementAt (null, i);\r
+}\r
+if (visibleChainAnnotation) {\r
+var annots = new Array (resAnnotation.size ());\r
+var max = 0;\r
+for (i = 0, iSize = annots.length; i < iSize; i++) {\r
+annots[i] = resAnnotation.elementAt (i);\r
+if (annots[i].value > max) {\r
+max = annots[i].value;\r
+}resAnnotation.setElementAt (null, i);\r
+}\r
+var tfactorann = new jalview.datamodel.AlignmentAnnotation ("Temperature Factor", "Temperature Factor for " + this.pdbid + this.id, annots, 0, max, 2);\r
+tfactorann.setSequenceRef (this.sequence);\r
+this.sequence.addAlignmentAnnotation (tfactorann);\r
+}}, "~B");\r
+Clazz.defineMethod (c$, "setChargeColours", \r
+function () {\r
+for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) {\r
+if (b.at1 != null && b.at2 != null) {\r
+b.startCol = MCview.PDBChain.getChargeColour (b.at1.resName);\r
+b.endCol = MCview.PDBChain.getChargeColour (b.at2.resName);\r
+} else {\r
+b.startCol = java.awt.Color.gray;\r
+b.endCol = java.awt.Color.gray;\r
+}}\r
+});\r
+c$.getChargeColour = Clazz.defineMethod (c$, "getChargeColour", \r
+function (resName) {\r
+var result = java.awt.Color.lightGray;\r
+if ("ASP".equals (resName) || "GLU".equals (resName)) {\r
+result = java.awt.Color.red;\r
+} else if ("LYS".equals (resName) || "ARG".equals (resName)) {\r
+result = java.awt.Color.blue;\r
+} else if ("CYS".equals (resName)) {\r
+result = java.awt.Color.yellow;\r
+}return result;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "setChainColours", \r
+function (cs) {\r
+var index;\r
+for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) {\r
+try {\r
+index = jalview.schemes.ResidueProperties.aa3Hash.get (b.at1.resName).intValue ();\r
+b.startCol = cs.findColour (jalview.schemes.ResidueProperties.aa[index].charAt (0));\r
+index = jalview.schemes.ResidueProperties.aa3Hash.get (b.at2.resName).intValue ();\r
+b.endCol = cs.findColour (jalview.schemes.ResidueProperties.aa[index].charAt (0));\r
+} catch (e) {\r
+if (Clazz.exceptionOf (e, Exception)) {\r
+b.startCol = java.awt.Color.gray;\r
+b.endCol = java.awt.Color.gray;\r
+} else {\r
+throw e;\r
+}\r
+}\r
+}\r
+}, "jalview.schemes.ColourSchemeI");\r
+Clazz.defineMethod (c$, "setChainColours", \r
+function (col) {\r
+for (var b, $b = this.bonds.iterator (); $b.hasNext () && ((b = $b.next ()) || true);) {\r
+b.startCol = col;\r
+b.endCol = col;\r
+}\r
+}, "java.awt.Color");\r
+Clazz.defineMethod (c$, "transferResidueAnnotation", \r
+function (mapping, sqmpping) {\r
+var sq = mapping.getSequence ();\r
+var dsq = sq;\r
+if (sq != null) {\r
+while (dsq.getDatasetSequence () != null) {\r
+dsq = dsq.getDatasetSequence ();\r
+}\r
+if (this.shadow != null && this.shadow.getAnnotation () != null) {\r
+for (var ana, $ana = 0, $$ana = this.shadow.getAnnotation (); $ana < $$ana.length && ((ana = $$ana[$ana]) || true); $ana++) {\r
+var transfer = sq.getAlignmentAnnotations (ana.getCalcId (), ana.label);\r
+if (transfer == null || transfer.size () == 0) {\r
+ana = new jalview.datamodel.AlignmentAnnotation (ana);\r
+ana.liftOver (this.sequence, this.shadowMap);\r
+ana.liftOver (dsq, sqmpping);\r
+dsq.addAlignmentAnnotation (ana);\r
+} else {\r
+continue;\r
+}}\r
+} else {\r
+if (this.sequence != null && this.sequence.getAnnotation () != null) {\r
+for (var ana, $ana = 0, $$ana = this.sequence.getAnnotation (); $ana < $$ana.length && ((ana = $$ana[$ana]) || true); $ana++) {\r
+var transfer = sq.getAlignmentAnnotations (ana.getCalcId (), ana.label);\r
+if (transfer == null || transfer.size () == 0) {\r
+ana = new jalview.datamodel.AlignmentAnnotation (ana);\r
+ana.liftOver (dsq, sqmpping);\r
+} else {\r
+continue;\r
+}}\r
+}}if (false) {\r
+var min = -1;\r
+var max = 0;\r
+var an = new Array (sq.getEnd () - sq.getStart () + 1);\r
+for (var i = sq.getStart (), j = sq.getEnd (), k = 0; i <= j; i++, k++) {\r
+var prn = mapping.getPDBResNum (k + 1);\r
+an[k] = new jalview.datamodel.Annotation (prn);\r
+if (min == -1) {\r
+min = k;\r
+max = k;\r
+} else {\r
+if (min > k) {\r
+min = k;\r
+} else if (max < k) {\r
+max = k;\r
+}}}\r
+sq.addAlignmentAnnotation ( new jalview.datamodel.AlignmentAnnotation ("PDB.RESNUM", "PDB Residue Numbering for " + this.pdbid + ":" + this.id, an, min, max, 2));\r
+}}}, "jalview.structure.StructureMapping,jalview.datamodel.Mapping");\r
+Clazz.defineStatics (c$,\r
+"PDBFILEFEATURE", "PDBFile",\r
+"IEASTATUS", "IEA:jalview");\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff