X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fstructure%2FStructureSelectionManager.js;h=cdbab5100c71edb0d61c942d079f8de4310627d1;hp=681a2a7e31d58f10f4769b872ce3073608fb7ded;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

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);
+});