X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2FMCview%2FPDBChain.js;h=727e98e8cf1e142bee111fc1930772f8ca1e0a9c;hp=b58d3ddf64780b6f6406ed07e4d00fe864674ccf;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/MCview/PDBChain.js b/site/j2s/MCview/PDBChain.js
index b58d3dd..727e98e 100644
--- a/site/j2s/MCview/PDBChain.js
+++ b/site/j2s/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");
+});