-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");\r
+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", "$.Vector"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.chains = null;\r
+this.id = null;\r
+this.visibleChainAnnotation = false;\r
+this.$predictSecondaryStructure = true;\r
+this.externalSecondaryStructure = false;\r
+Clazz.instantialize (this, arguments);\r
+}, MCview, "PDBfile", jalview.io.AlignFile);\r
+Clazz.makeConstructor (c$, \r
+function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr) {\r
+Clazz.superConstructor (this, MCview.PDBfile);\r
+this.visibleChainAnnotation = addAlignmentAnnotations;\r
+this.$predictSecondaryStructure = predictSecondaryStructure;\r
+this.externalSecondaryStructure = externalSecStr;\r
+}, "~B,~B,~B");\r
+Clazz.makeConstructor (c$, \r
+function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr, file, protocol) {\r
+Clazz.superConstructor (this, MCview.PDBfile, [false, file, protocol]);\r
+this.visibleChainAnnotation = addAlignmentAnnotations;\r
+this.$predictSecondaryStructure = predictSecondaryStructure;\r
+this.externalSecondaryStructure = externalSecStr;\r
+this.doParse ();\r
+}, "~B,~B,~B,~S,~S");\r
+Clazz.makeConstructor (c$, \r
+function (addAlignmentAnnotations, predictSecondaryStructure, externalSecStr, source) {\r
+Clazz.superConstructor (this, MCview.PDBfile, [false, source]);\r
+this.visibleChainAnnotation = addAlignmentAnnotations;\r
+this.$predictSecondaryStructure = predictSecondaryStructure;\r
+this.externalSecondaryStructure = externalSecStr;\r
+this.doParse ();\r
+}, "~B,~B,~B,jalview.io.FileParse");\r
+Clazz.overrideMethod (c$, "print", \r
+function () {\r
+return null;\r
+});\r
+Clazz.overrideMethod (c$, "parse", \r
+function () {\r
+this.id = this.safeName (this.getDataName ());\r
+this.chains = new java.util.Vector ();\r
+var rna = new java.util.ArrayList ();\r
+var prot = new java.util.ArrayList ();\r
+var tmpchain;\r
+var line = null;\r
+var modelFlag = false;\r
+var terFlag = false;\r
+var lastID = "";\r
+var indexx = 0;\r
+var atomnam = null;\r
+try {\r
+while ((line = this.nextLine ()) != null) {\r
+if (line.indexOf ("HEADER") == 0) {\r
+if (line.length > 62) {\r
+var tid;\r
+if (line.length > 67) {\r
+tid = line.substring (62, 67).trim ();\r
+} else {\r
+tid = line.substring (62).trim ();\r
+}if (tid.length > 0) {\r
+this.id = tid;\r
+}continue;\r
+}}if (line.indexOf ("SEQRES") == 0) {\r
+}if (line.indexOf ("MODEL") == 0) {\r
+modelFlag = true;\r
+}if (line.indexOf ("TER") == 0) {\r
+terFlag = true;\r
+}if (modelFlag && line.indexOf ("ENDMDL") == 0) {\r
+break;\r
+}if (line.indexOf ("ATOM") == 0 || (line.indexOf ("HETATM") == 0 && !terFlag)) {\r
+terFlag = false;\r
+atomnam = line.substring (12, 15).trim ();\r
+if (!atomnam.equals ("CA") && !atomnam.equals ("P")) {\r
+continue;\r
+}var tmpatom = new MCview.Atom (line);\r
+tmpchain = this.findChain (tmpatom.chain);\r
+if (tmpchain != null) {\r
+if (tmpatom.resNumIns.trim ().equals (lastID)) {\r
+continue;\r
+}tmpchain.atoms.addElement (tmpatom);\r
+} else {\r
+tmpchain = new MCview.PDBChain (this.id, tmpatom.chain);\r
+this.chains.addElement (tmpchain);\r
+tmpchain.atoms.addElement (tmpatom);\r
+}lastID = tmpatom.resNumIns.trim ();\r
+}this.index++;\r
+}\r
+this.makeResidueList ();\r
+this.makeCaBondList ();\r
+if (this.id == null) {\r
+this.id = this.inFile.getName ();\r
+}for (var chain, $chain = this.chains.iterator (); $chain.hasNext () && ((chain = $chain.next ()) || true);) {\r
+var chainseq = this.postProcessChain (chain);\r
+if (MCview.PDBfile.isRNA (chainseq)) {\r
+rna.add (chainseq);\r
+} else {\r
+prot.add (chainseq);\r
+}}\r
+if (this.$predictSecondaryStructure) {\r
+this.predictSecondaryStructure (rna, prot);\r
+}} catch (e$$) {\r
+if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {\r
+var er = e$$;\r
+{\r
+System.out.println ("OUT OF MEMORY LOADING PDB FILE");\r
+throw new java.io.IOException (jalview.util.MessageManager.getString ("exception.outofmemory_loading_pdb_file"));\r
+}\r
+} else if (Clazz.exceptionOf (e$$, NumberFormatException)) {\r
+var ex = e$$;\r
+{\r
+if (line != null) {\r
+System.err.println ("Couldn't read number from line:");\r
+System.err.println (line);\r
+}}\r
+} else {\r
+throw e$$;\r
+}\r
+}\r
+this.markCalcIds ();\r
+});\r
+Clazz.defineMethod (c$, "predictSecondaryStructure", \r
+function (rnaSequences, proteinSequences) {\r
+if (this.externalSecondaryStructure && rnaSequences.size () > 0) {\r
+try {\r
+this.processPdbFileWithAnnotate3d (rnaSequences);\r
+} catch (x) {\r
+if (Clazz.exceptionOf (x, Exception)) {\r
+System.err.println ("Exceptions when dealing with RNA in pdb file");\r
+x.printStackTrace ();\r
+} else {\r
+throw x;\r
+}\r
+}\r
+}if (proteinSequences.size () > 0) {\r
+try {\r
+this.processPdbFileWithJmol (proteinSequences);\r
+} catch (x) {\r
+if (Clazz.exceptionOf (x, Exception)) {\r
+System.err.println ("Exceptions from Jmol when processing data in pdb file");\r
+x.printStackTrace ();\r
+} else {\r
+throw x;\r
+}\r
+}\r
+}}, "java.util.List,java.util.List");\r
+Clazz.defineMethod (c$, "postProcessChain", \r
+function (chain) {\r
+var dataset = chain.sequence;\r
+dataset.setName (this.id + "|" + dataset.getName ());\r
+var entry = new jalview.datamodel.PDBEntry ();\r
+entry.setId (this.id);\r
+entry.setType (jalview.datamodel.PDBEntry.Type.PDB);\r
+entry.setProperty ( new java.util.Hashtable ());\r
+if (chain.id != null) {\r
+entry.setChainCode (String.valueOf (chain.id));\r
+}if (this.inFile != null) {\r
+entry.setFile (this.inFile.getAbsolutePath ());\r
+} else {\r
+entry.setFile (this.getDataName ());\r
+}dataset.addPDBId (entry);\r
+var chainseq = dataset.deriveSequence ();\r
+this.seqs.addElement (chainseq);\r
+var chainannot = chainseq.getAnnotation ();\r
+if (chainannot != null && this.visibleChainAnnotation) {\r
+for (var ai = 0; ai < chainannot.length; ai++) {\r
+chainannot[ai].visible = this.visibleChainAnnotation;\r
+this.annotations.addElement (chainannot[ai]);\r
+}\r
+}return chainseq;\r
+}, "MCview.PDBChain");\r
+c$.isCalcIdHandled = Clazz.defineMethod (c$, "isCalcIdHandled", \r
+function (calcId) {\r
+return calcId != null && (MCview.PDBfile.CALC_ID_PREFIX.equals (calcId));\r
+}, "~S");\r
+c$.isCalcIdForFile = Clazz.defineMethod (c$, "isCalcIdForFile", \r
+function (alan, pdbFile) {\r
+return alan.getCalcId () != null && MCview.PDBfile.CALC_ID_PREFIX.equals (alan.getCalcId ()) && pdbFile.equals (alan.getProperty ("PDBID"));\r
+}, "jalview.datamodel.AlignmentAnnotation,~S");\r
+c$.relocateCalcId = Clazz.defineMethod (c$, "relocateCalcId", \r
+function (calcId, alreadyLoadedPDB) {\r
+var s = MCview.PDBfile.CALC_ID_PREFIX.length;\r
+var end = calcId.indexOf (MCview.PDBfile.CALC_ID_PREFIX, s);\r
+var between = calcId.substring (s, end - 1);\r
+return MCview.PDBfile.CALC_ID_PREFIX + alreadyLoadedPDB.get (between) + ":" + calcId.substring (end);\r
+}, "~S,java.util.Hashtable");\r
+Clazz.defineMethod (c$, "markCalcIds", \r
+($fz = function () {\r
+for (var sq, $sq = this.seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
+if (sq.getAnnotation () != null) {\r
+for (var aa, $aa = 0, $$aa = sq.getAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) {\r
+var oldId = aa.getCalcId ();\r
+if (oldId == null) {\r
+oldId = "";\r
+}aa.setCalcId (MCview.PDBfile.CALC_ID_PREFIX);\r
+aa.setProperty ("PDBID", this.id);\r
+aa.setProperty ("oldCalcId", oldId);\r
+}\r
+}}\r
+}, $fz.isPrivate = true, $fz));\r
+Clazz.defineMethod (c$, "processPdbFileWithJmol", \r
+($fz = function (prot) {\r
+try {\r
+var cl = Class.forName ("jalview.ext.jmol.PDBFileWithJmol");\r
+if (cl != null) {\r
+var constructor = cl.getConstructor ( Clazz.newArray (-1, [jalview.io.FileParse]));\r
+var args = Clazz.newArray (-1, [ new jalview.io.FileParse (this.getDataName (), this.type)]);\r
+var jmf = constructor.newInstance (args);\r
+var al = new jalview.datamodel.Alignment (cl.getMethod ("getSeqsAsArray", Clazz.newArray (-1, [])).invoke (jmf, []));\r
+cl.getMethod ("addAnnotations", Clazz.newArray (-1, [jalview.datamodel.AlignmentI])).invoke (jmf, [al]);\r
+for (var sq, $sq = al.getSequences ().iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
+if (sq.getDatasetSequence () != null) {\r
+sq.getDatasetSequence ().getPDBId ().clear ();\r
+} else {\r
+sq.getPDBId ().clear ();\r
+}}\r
+this.replaceAndUpdateChains (prot, al, "pep", false);\r
+}} catch (q) {\r
+if (Clazz.exceptionOf (q, ClassNotFoundException)) {\r
+} else {\r
+throw q;\r
+}\r
+}\r
+}, $fz.isPrivate = true, $fz), "java.util.List");\r
+Clazz.defineMethod (c$, "replaceAndUpdateChains", \r
+($fz = function (prot, al, pep, b) {\r
+var replaced = jalview.analysis.AlignSeq.replaceMatchingSeqsWith (this.seqs, this.annotations, prot, al, pep, false);\r
+for (var ch, $ch = this.chains.iterator (); $ch.hasNext () && ((ch = $ch.next ()) || true);) {\r
+var p = 0;\r
+for (var sq, $sq = replaced.get (0).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
+p++;\r
+if (sq === ch.sequence || sq.getDatasetSequence () === ch.sequence) {\r
+p = -p;\r
+break;\r
+}}\r
+if (p < 0) {\r
+p = -p - 1;\r
+ch.shadow = replaced.get (1).get (p);\r
+ch.shadowMap = (replaced.get (2).get (p)).getMappingFromS1 (false);\r
+}}\r
+}, $fz.isPrivate = true, $fz), "java.util.List,jalview.datamodel.AlignmentI,~S,~B");\r
+Clazz.defineMethod (c$, "processPdbFileWithAnnotate3d", \r
+($fz = function (rna) {\r
+try {\r
+var cl = Class.forName ("jalview.ws.jws1.Annotate3D");\r
+if (cl != null) {\r
+var annotate3d = cl.getConstructor ( Clazz.newArray (-1, [])).newInstance ( Clazz.newArray (-1, []));\r
+var al = (cl.getMethod ("getRNAMLFor", Clazz.newArray (-1, [jalview.io.FileParse])).invoke (annotate3d, Clazz.newArray (-1, [ new jalview.io.FileParse (this.getDataName (), this.type)])));\r
+for (var sq, $sq = al.getSequences ().iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
+if (sq.getDatasetSequence () != null) {\r
+if (sq.getDatasetSequence ().getPDBId () != null) {\r
+sq.getDatasetSequence ().getPDBId ().clear ();\r
+}} else {\r
+if (sq.getPDBId () != null) {\r
+sq.getPDBId ().clear ();\r
+}}}\r
+this.replaceAndUpdateChains (rna, al, "dna", false);\r
+}} catch (x) {\r
+if (Clazz.exceptionOf (x, ClassNotFoundException)) {\r
+} else {\r
+throw x;\r
+}\r
+}\r
+;}, $fz.isPrivate = true, $fz), "java.util.List");\r
+Clazz.defineMethod (c$, "safeName", \r
+($fz = function (dataName) {\r
+var p = 0;\r
+while ((p = dataName.indexOf ("/")) > -1 && p < dataName.length) {\r
+dataName = dataName.substring (p + 1);\r
+}\r
+return dataName;\r
+}, $fz.isPrivate = true, $fz), "~S");\r
+Clazz.defineMethod (c$, "makeResidueList", \r
+function () {\r
+for (var i = 0; i < this.chains.size (); i++) {\r
+this.chains.elementAt (i).makeResidueList (this.visibleChainAnnotation);\r
+}\r
+});\r
+Clazz.defineMethod (c$, "makeCaBondList", \r
+function () {\r
+for (var i = 0; i < this.chains.size (); i++) {\r
+this.chains.elementAt (i).makeCaBondList ();\r
+}\r
+});\r
+Clazz.defineMethod (c$, "findChain", \r
+function (id) {\r
+for (var i = 0; i < this.chains.size (); i++) {\r
+if (this.chains.elementAt (i).id.equals (id)) {\r
+return this.chains.elementAt (i);\r
+}}\r
+return null;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "setChargeColours", \r
+function () {\r
+for (var i = 0; i < this.chains.size (); i++) {\r
+this.chains.elementAt (i).setChargeColours ();\r
+}\r
+});\r
+Clazz.defineMethod (c$, "setColours", \r
+function (cs) {\r
+for (var i = 0; i < this.chains.size (); i++) {\r
+this.chains.elementAt (i).setChainColours (cs);\r
+}\r
+}, "jalview.schemes.ColourSchemeI");\r
+Clazz.defineMethod (c$, "setChainColours", \r
+function () {\r
+for (var i = 0; i < this.chains.size (); i++) {\r
+this.chains.elementAt (i).setChainColours (java.awt.Color.getHSBColor (1.0 / i, .4, 1.0));\r
+}\r
+});\r
+c$.isRNA = Clazz.defineMethod (c$, "isRNA", \r
+function (seq) {\r
+for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) {\r
+if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U')) {\r
+return false;\r
+}}\r
+return true;\r
+}, "jalview.datamodel.SequenceI");\r
+Clazz.defineStatics (c$,\r
+"CALC_ID_PREFIX", "JalviewPDB");\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff