-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");\r
+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 () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.ssm = null;\r
+this.pdbEntry = null;\r
+this.sequence = null;\r
+this.chains = null;\r
+this.protocol = null;\r
+this.colourBySequence = true;\r
+this.nucleotide = false;\r
+if (!Clazz.isClassDefined ("jalview.structures.models.AAStructureBindingModel.SuperposeData")) {\r
+jalview.structures.models.AAStructureBindingModel.$AAStructureBindingModel$SuperposeData$ ();\r
+}\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.structures.models, "AAStructureBindingModel", jalview.structures.models.SequenceStructureBindingModel, [jalview.structure.StructureListener, jalview.api.StructureSelectionManagerProvider]);\r
+Clazz.makeConstructor (c$, \r
+function (ssm, seqs) {\r
+Clazz.superConstructor (this, jalview.structures.models.AAStructureBindingModel, []);\r
+this.ssm = ssm;\r
+this.sequence = seqs;\r
+}, "jalview.structure.StructureSelectionManager,~A");\r
+Clazz.makeConstructor (c$, \r
+function (ssm, pdbentry, sequenceIs, chains, protocol) {\r
+Clazz.superConstructor (this, jalview.structures.models.AAStructureBindingModel, []);\r
+this.ssm = ssm;\r
+this.sequence = sequenceIs;\r
+this.nucleotide = jalview.util.Comparison.isNucleotide2 (sequenceIs);\r
+this.chains = chains;\r
+this.pdbEntry = pdbentry;\r
+this.protocol = protocol;\r
+if (chains == null) {\r
+this.chains = new Array (pdbentry.length);\r
+}}, "jalview.structure.StructureSelectionManager,~A,~A,~A,~S");\r
+Clazz.defineMethod (c$, "getSsm", \r
+function () {\r
+return this.ssm;\r
+});\r
+Clazz.defineMethod (c$, "getPdbEntry", \r
+function (i) {\r
+return (this.pdbEntry != null && this.pdbEntry.length > i) ? this.pdbEntry[i] : null;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "hasPdbId", \r
+function (pdbId) {\r
+if (this.pdbEntry != null) {\r
+for (var pdb, $pdb = 0, $$pdb = this.pdbEntry; $pdb < $$pdb.length && ((pdb = $$pdb[$pdb]) || true); $pdb++) {\r
+if (pdb.getId ().equals (pdbId)) {\r
+return true;\r
+}}\r
+}return false;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "getPdbCount", \r
+function () {\r
+return this.pdbEntry == null ? 0 : this.pdbEntry.length;\r
+});\r
+Clazz.defineMethod (c$, "getSequence", \r
+function () {\r
+return this.sequence;\r
+});\r
+Clazz.defineMethod (c$, "getChains", \r
+function () {\r
+return this.chains;\r
+});\r
+Clazz.defineMethod (c$, "getProtocol", \r
+function () {\r
+return this.protocol;\r
+});\r
+Clazz.defineMethod (c$, "setPdbentry", \r
+function (pdbentry) {\r
+this.pdbEntry = pdbentry;\r
+}, "~A");\r
+Clazz.defineMethod (c$, "setSequence", \r
+function (sequence) {\r
+this.sequence = sequence;\r
+}, "~A");\r
+Clazz.defineMethod (c$, "setChains", \r
+function (chains) {\r
+this.chains = chains;\r
+}, "~A");\r
+Clazz.defineMethod (c$, "getViewerTitle", \r
+function (viewerName, verbose) {\r
+if (this.getSequence () == null || this.getSequence ().length < 1 || this.getPdbCount () < 1 || this.getSequence ()[0].length < 1) {\r
+return ("Jalview " + viewerName + " Window");\r
+}var title = new StringBuilder (64);\r
+var pdbEntry = this.getPdbEntry (0);\r
+title.append (viewerName + " view for " + this.getSequence ()[0][0].getName () + ":" + pdbEntry.getId ());\r
+if (verbose) {\r
+if (pdbEntry.getProperty () != null) {\r
+if (pdbEntry.getProperty ().get ("method") != null) {\r
+title.append (" Method: ");\r
+title.append (pdbEntry.getProperty ().get ("method"));\r
+}if (pdbEntry.getProperty ().get ("chains") != null) {\r
+title.append (" Chain:");\r
+title.append (pdbEntry.getProperty ().get ("chains"));\r
+}}}return title.toString ();\r
+}, "~S,~B");\r
+Clazz.defineMethod (c$, "releaseUIResources", \r
+function () {\r
+});\r
+Clazz.defineMethod (c$, "isColourBySequence", \r
+function () {\r
+return this.colourBySequence;\r
+});\r
+Clazz.defineMethod (c$, "setColourBySequence", \r
+function (colourBySequence) {\r
+this.colourBySequence = colourBySequence;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "addSequenceAndChain", \r
+function (pe, seq, tchain) {\r
+if (pe < 0 || pe >= this.getPdbCount ()) {\r
+throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_no_pdbentry_from_index", Clazz.newArray (-1, [Integer.$valueOf (pe).toString ()])));\r
+}var nullChain = "TheNullChain";\r
+var s = new java.util.ArrayList ();\r
+var c = new java.util.ArrayList ();\r
+if (this.getChains () == null) {\r
+this.setChains ( new Array (this.getPdbCount ()));\r
+}if (this.getSequence ()[pe] != null) {\r
+for (var i = 0; i < this.getSequence ()[pe].length; i++) {\r
+s.add (this.getSequence ()[pe][i]);\r
+if (this.getChains ()[pe] != null) {\r
+if (i < this.getChains ()[pe].length) {\r
+c.add (this.getChains ()[pe][i]);\r
+} else {\r
+c.add ("TheNullChain");\r
+}} else {\r
+if (tchain != null && tchain.length > 0) {\r
+c.add ("TheNullChain");\r
+}}}\r
+}for (var i = 0; i < seq.length; i++) {\r
+if (!s.contains (seq[i])) {\r
+s.add (seq[i]);\r
+if (tchain != null && i < tchain.length) {\r
+c.add (tchain[i] == null ? "TheNullChain" : tchain[i]);\r
+}}}\r
+var tmp = s.toArray ( new Array (s.size ()));\r
+this.getSequence ()[pe] = tmp;\r
+if (c.size () > 0) {\r
+var tch = c.toArray ( new Array (c.size ()));\r
+for (var i = 0; i < tch.length; i++) {\r
+if (tch[i] === "TheNullChain") {\r
+tch[i] = null;\r
+}}\r
+this.getChains ()[pe] = tch;\r
+} else {\r
+this.getChains ()[pe] = null;\r
+}}, "~N,~A,~A");\r
+Clazz.defineMethod (c$, "addSequenceAndChain", \r
+function (pdbe, seq, chns) {\r
+var v = new java.util.ArrayList ();\r
+var rtn = new java.util.ArrayList ();\r
+for (var i = 0; i < this.getPdbCount (); i++) {\r
+v.add (this.getPdbEntry (i));\r
+}\r
+for (var i = 0; i < pdbe.length; i++) {\r
+var r = v.indexOf (pdbe[i]);\r
+if (r == -1 || r >= this.getPdbCount ()) {\r
+rtn.add ( Clazz.newIntArray (-1, [v.size (), i]));\r
+v.add (pdbe[i]);\r
+} else {\r
+this.addSequenceAndChain (r, seq[i], chns[i]);\r
+}}\r
+pdbe = v.toArray ( new Array (v.size ()));\r
+this.setPdbentry (pdbe);\r
+if (rtn.size () > 0) {\r
+var sqs = new Array (this.getPdbCount ());\r
+var sch = new Array (this.getPdbCount ());\r
+System.arraycopy (this.getSequence (), 0, sqs, 0, this.getSequence ().length);\r
+System.arraycopy (this.getChains (), 0, sch, 0, this.getChains ().length);\r
+this.setSequence (sqs);\r
+this.setChains (sch);\r
+pdbe = new Array (rtn.size ());\r
+for (var r = 0; r < pdbe.length; r++) {\r
+var stri = (rtn.get (r));\r
+pdbe[r] = this.getPdbEntry (stri[0]);\r
+this.addSequenceAndChain (stri[0], seq[stri[1]], chns[stri[1]]);\r
+}\r
+} else {\r
+pdbe = null;\r
+}return pdbe;\r
+}, "~A,~A,~A");\r
+Clazz.defineMethod (c$, "addSequence", \r
+function (pe, seq) {\r
+this.addSequenceAndChain (pe, seq, null);\r
+}, "~N,~A");\r
+Clazz.defineMethod (c$, "addSequenceForStructFile", \r
+function (pdbFile, seq) {\r
+for (var pe = 0; pe < this.getPdbCount (); pe++) {\r
+if (this.getPdbEntry (pe).getFile ().equals (pdbFile)) {\r
+this.addSequence (pe, seq);\r
+}}\r
+}, "~S,~A");\r
+Clazz.defineMethod (c$, "isNucleotide", \r
+function () {\r
+return this.nucleotide;\r
+});\r
+Clazz.defineMethod (c$, "printMappings", \r
+function () {\r
+if (this.pdbEntry == null) {\r
+return "";\r
+}var sb = new StringBuilder (128);\r
+for (var pdbe = 0; pdbe < this.getPdbCount (); pdbe++) {\r
+var pdbfile = this.getPdbEntry (pdbe).getFile ();\r
+var seqs = java.util.Arrays.asList (this.getSequence ()[pdbe]);\r
+sb.append (this.getSsm ().printMappings (pdbfile, seqs));\r
+}\r
+return sb.toString ();\r
+});\r
+Clazz.defineMethod (c$, "getMappedPosition", \r
+function (seq, alignedPos, mapping) {\r
+if (alignedPos >= seq.getLength ()) {\r
+return -1;\r
+}if (jalview.util.Comparison.isGap (seq.getCharAt (alignedPos))) {\r
+return -1;\r
+}var seqPos = seq.findPosition (alignedPos);\r
+var pos = mapping.getPDBResNum (seqPos);\r
+return pos;\r
+}, "jalview.datamodel.SequenceI,~N,jalview.structure.StructureMapping");\r
+Clazz.defineMethod (c$, "findSuperposableResidues", \r
+function (alignment, matched, structures) {\r
+var refStructure = -1;\r
+var files = this.getPdbFile ();\r
+for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) {\r
+var mappings = this.getSsm ().getMapping (files[pdbfnum]);\r
+var lastPos = -1;\r
+var seqCountForPdbFile = this.getSequence ()[pdbfnum].length;\r
+for (var s = 0; s < seqCountForPdbFile; s++) {\r
+for (var mapping, $mapping = 0, $$mapping = mappings; $mapping < $$mapping.length && ((mapping = $$mapping[$mapping]) || true); $mapping++) {\r
+var theSequence = this.getSequence ()[pdbfnum][s];\r
+if (mapping.getSequence () === theSequence && alignment.findIndex (theSequence) > -1) {\r
+if (refStructure < 0) {\r
+refStructure = pdbfnum;\r
+}for (var r = 0; r < matched.length; r++) {\r
+if (!matched[r]) {\r
+continue;\r
+}var pos = this.getMappedPosition (theSequence, r, mapping);\r
+if (pos < 1 || pos == lastPos) {\r
+matched[r] = false;\r
+continue;\r
+}lastPos = pos;\r
+structures[pdbfnum].pdbResNo[r] = pos;\r
+}\r
+var chain = mapping.getChain ();\r
+if (chain != null && chain.trim ().length > 0) {\r
+structures[pdbfnum].chain = chain;\r
+}structures[pdbfnum].pdbId = mapping.getPdbId ();\r
+structures[pdbfnum].isRna = theSequence.getRNA () != null;\r
+s = seqCountForPdbFile;\r
+break;\r
+}}\r
+}\r
+}\r
+return refStructure;\r
+}, "jalview.datamodel.AlignmentI,~A,~A");\r
+Clazz.defineMethod (c$, "waitForFileLoad", \r
+function (files) {\r
+var starttime = System.currentTimeMillis ();\r
+var endTime = 10000 + 1000 * files.length + starttime;\r
+var notLoaded = null;\r
+var waiting = true;\r
+while (waiting && System.currentTimeMillis () < endTime) {\r
+waiting = false;\r
+for (var file, $file = 0, $$file = files; $file < $$file.length && ((file = $$file[$file]) || true); $file++) {\r
+notLoaded = file;\r
+try {\r
+var sm = this.getSsm ().getMapping (file);\r
+if (sm == null || sm.length == 0) {\r
+waiting = true;\r
+}} catch (x) {\r
+waiting = true;\r
+}\r
+}\r
+}\r
+if (waiting) {\r
+System.err.println ("Timed out waiting for structure viewer to load file " + notLoaded);\r
+return false;\r
+}return true;\r
+}, "~A");\r
+Clazz.overrideMethod (c$, "isListeningFor", \r
+function (seq) {\r
+if (this.sequence != null) {\r
+for (var seqs, $seqs = 0, $$seqs = this.sequence; $seqs < $$seqs.length && ((seqs = $$seqs[$seqs]) || true); $seqs++) {\r
+if (seqs != null) {\r
+for (var s, $s = 0, $$s = seqs; $s < $$s.length && ((s = $$s[$s]) || true); $s++) {\r
+if (s === seq) {\r
+return true;\r
+}}\r
+}}\r
+}return false;\r
+}, "jalview.datamodel.SequenceI");\r
+c$.$AAStructureBindingModel$SuperposeData$ = function () {\r
+Clazz.pu$h ();\r
+c$ = Clazz.decorateAsClass (function () {\r
+Clazz.prepareCallback (this, arguments);\r
+this.filename = null;\r
+this.pdbId = null;\r
+this.chain = "";\r
+this.isRna = false;\r
+this.pdbResNo = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.structures.models.AAStructureBindingModel, "SuperposeData");\r
+Clazz.makeConstructor (c$, \r
+function (a) {\r
+this.pdbResNo = Clazz.newIntArray (a, 0);\r
+}, "~N");\r
+c$ = Clazz.p0p ();\r
+};\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff