-Clazz.declarePackage ("jalview.structure");\r
-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", "$.IdentityHashMap"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.mappings = null;\r
-this.processSecondaryStructure = false;\r
-this.secStructServices = false;\r
-this.addTempFacAnnot = false;\r
-this.seqmappings = null;\r
-this.seqMappingRefCounts = null;\r
-this.commandListeners = null;\r
-this.sel_listeners = null;\r
-this.pdbIdFileName = null;\r
-this.pdbFileNameId = null;\r
-this.relaySeqMappings = true;\r
-this.listeners = null;\r
-this.handlingVamsasMo = false;\r
-this.lastmsg = 0;\r
-this.view_listeners = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.structure, "StructureSelectionManager");\r
-Clazz.prepareFields (c$, function () {\r
-this.mappings = new java.util.ArrayList ();\r
-this.seqmappings = new java.util.LinkedHashSet ();\r
-this.seqMappingRefCounts = new java.util.HashMap ();\r
-this.commandListeners = new java.util.ArrayList ();\r
-this.sel_listeners = new java.util.ArrayList ();\r
-this.pdbIdFileName = new java.util.HashMap ();\r
-this.pdbFileNameId = new java.util.HashMap ();\r
-this.listeners = new java.util.Vector ();\r
-this.view_listeners = new java.util.Vector ();\r
-});\r
-Clazz.defineMethod (c$, "isSecStructServices", \r
-function () {\r
-return this.secStructServices;\r
-});\r
-Clazz.defineMethod (c$, "setSecStructServices", \r
-function (secStructServices) {\r
-this.secStructServices = secStructServices;\r
-}, "~B");\r
-Clazz.defineMethod (c$, "isAddTempFacAnnot", \r
-function () {\r
-return this.addTempFacAnnot;\r
-});\r
-Clazz.defineMethod (c$, "setAddTempFacAnnot", \r
-function (addTempFacAnnot) {\r
-this.addTempFacAnnot = addTempFacAnnot;\r
-}, "~B");\r
-Clazz.defineMethod (c$, "isProcessSecondaryStructure", \r
-function () {\r
-return this.processSecondaryStructure;\r
-});\r
-Clazz.defineMethod (c$, "setProcessSecondaryStructure", \r
-function (enable) {\r
-this.processSecondaryStructure = enable;\r
-}, "~B");\r
-Clazz.defineMethod (c$, "reportMapping", \r
-function () {\r
-if (this.mappings.isEmpty ()) {\r
-System.err.println ("reportMapping: No PDB/Sequence mappings.");\r
-} else {\r
-System.err.println ("reportMapping: There are " + this.mappings.size () + " mappings.");\r
-var i = 0;\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-System.err.println ("mapping " + i++ + " : " + sm.pdbfile);\r
-}\r
-}});\r
-Clazz.defineMethod (c$, "registerPDBFile", \r
-function (idForFile, absoluteFile) {\r
-this.pdbIdFileName.put (idForFile, absoluteFile);\r
-this.pdbFileNameId.put (absoluteFile, idForFile);\r
-}, "~S,~S");\r
-Clazz.defineMethod (c$, "findIdForPDBFile", \r
-function (idOrFile) {\r
-var id = this.pdbFileNameId.get (idOrFile);\r
-return id;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "findFileForPDBId", \r
-function (idOrFile) {\r
-var id = this.pdbIdFileName.get (idOrFile);\r
-return id;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "isPDBFileRegistered", \r
-function (idOrFile) {\r
-return this.pdbFileNameId.containsKey (idOrFile) || this.pdbIdFileName.containsKey (idOrFile);\r
-}, "~S");\r
-c$.getStructureSelectionManager = Clazz.defineMethod (c$, "getStructureSelectionManager", \r
-function (context) {\r
-if (context == null) {\r
-if (jalview.structure.StructureSelectionManager.nullProvider == null) {\r
-if (jalview.structure.StructureSelectionManager.instances != null) {\r
-throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_structure_selection_manager_null"), new NullPointerException (jalview.util.MessageManager.getString ("exception.ssm_context_is_null")));\r
-} else {\r
-jalview.structure.StructureSelectionManager.nullProvider = new jalview.structure.StructureSelectionManager ();\r
-}return jalview.structure.StructureSelectionManager.nullProvider;\r
-}}if (jalview.structure.StructureSelectionManager.instances == null) {\r
-jalview.structure.StructureSelectionManager.instances = new java.util.IdentityHashMap ();\r
-}var instance = jalview.structure.StructureSelectionManager.instances.get (context);\r
-if (instance == null) {\r
-if (jalview.structure.StructureSelectionManager.nullProvider != null) {\r
-instance = jalview.structure.StructureSelectionManager.nullProvider;\r
-} else {\r
-instance = new jalview.structure.StructureSelectionManager ();\r
-}jalview.structure.StructureSelectionManager.instances.put (context, instance);\r
-}return instance;\r
-}, "jalview.api.StructureSelectionManagerProvider");\r
-Clazz.defineMethod (c$, "setRelaySeqMappings", \r
-function (relay) {\r
-this.relaySeqMappings = relay;\r
-}, "~B");\r
-Clazz.defineMethod (c$, "isRelaySeqMappingsEnabled", \r
-function () {\r
-return this.relaySeqMappings;\r
-});\r
-Clazz.defineMethod (c$, "addStructureViewerListener", \r
-function (svl) {\r
-if (!this.listeners.contains (svl)) {\r
-this.listeners.addElement (svl);\r
-}}, "~O");\r
-Clazz.defineMethod (c$, "alreadyMappedToFile", \r
-function (pdbid) {\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-if (sm.getPdbId ().equals (pdbid)) {\r
-return sm.pdbfile;\r
-}}\r
-return null;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "setMapping", \r
-function (sequence, targetChains, pdbFile, protocol) {\r
-return this.setMapping (true, sequence, targetChains, pdbFile, protocol);\r
-}, "~A,~A,~S,~S");\r
-Clazz.defineMethod (c$, "setMapping", \r
-function (forStructureView, sequence, targetChains, pdbFile, protocol) {\r
-var parseSecStr = this.processSecondaryStructure;\r
-if (this.isPDBFileRegistered (pdbFile)) {\r
-for (var sq, $sq = 0, $$sq = sequence; $sq < $$sq.length && ((sq = $$sq[$sq]) || true); $sq++) {\r
-var ds = sq;\r
-while (ds.getDatasetSequence () != null) {\r
-ds = ds.getDatasetSequence ();\r
-}\r
-;if (ds.getAnnotation () != null) {\r
-for (var ala, $ala = 0, $$ala = ds.getAnnotation (); $ala < $$ala.length && ((ala = $$ala[$ala]) || true); $ala++) {\r
-if (MCview.PDBfile.isCalcIdForFile (ala, this.findIdForPDBFile (pdbFile))) {\r
-parseSecStr = false;\r
-}}\r
-}}\r
-}var pdb = null;\r
-try {\r
-pdb = new MCview.PDBfile (this.addTempFacAnnot, parseSecStr, this.secStructServices, pdbFile, protocol);\r
-if (pdb.id != null && pdb.id.trim ().length > 0 && jalview.io.AppletFormatAdapter.FILE.equals (protocol)) {\r
-this.registerPDBFile (pdb.id.trim (), pdbFile);\r
-}} catch (ex) {\r
-if (Clazz.exceptionOf (ex, Exception)) {\r
-ex.printStackTrace ();\r
-return null;\r
-} else {\r
-throw ex;\r
-}\r
-}\r
-var targetChain;\r
-for (var s = 0; s < sequence.length; s++) {\r
-var infChain = true;\r
-var seq = sequence[s];\r
-if (targetChains != null && targetChains[s] != null) {\r
-infChain = false;\r
-targetChain = targetChains[s];\r
-} else if (seq.getName ().indexOf ("|") > -1) {\r
-targetChain = seq.getName ().substring (seq.getName ().lastIndexOf ("|") + 1);\r
-if (targetChain.length > 1) {\r
-if (targetChain.trim ().length == 0) {\r
-targetChain = " ";\r
-} else {\r
-targetChain = "";\r
-}}} else {\r
-targetChain = "";\r
-}var max = -10;\r
-var maxAlignseq = null;\r
-var maxChainId = " ";\r
-var maxChain = null;\r
-var first = true;\r
-for (var chain, $chain = pdb.chains.iterator (); $chain.hasNext () && ((chain = $chain.next ()) || true);) {\r
-if (targetChain.length > 0 && !targetChain.equals (chain.id) && !infChain) {\r
-continue;\r
-}var type = chain.isNa ? "dna" : "pep";\r
-var as = jalview.analysis.AlignSeq.doGlobalNWAlignment (seq, chain.sequence, type);\r
-if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals (targetChain))) {\r
-first = false;\r
-maxChain = chain;\r
-max = as.maxscore;\r
-maxAlignseq = as;\r
-maxChainId = chain.id;\r
-}}\r
-if (maxChain == null) {\r
-continue;\r
-}var mappingDetails = new StringBuilder (128);\r
-mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("PDB Sequence is :").append (jalview.structure.StructureSelectionManager.NEWLINE).append ("Sequence = ").append (maxChain.sequence.getSequenceAsString ());\r
-mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("No of residues = ").append (maxChain.residues.size ()).append (jalview.structure.StructureSelectionManager.NEWLINE).append (jalview.structure.StructureSelectionManager.NEWLINE);\r
-var ps = ((Clazz.isClassDefined ("jalview.structure.StructureSelectionManager$1") ? 0 : jalview.structure.StructureSelectionManager.$StructureSelectionManager$1$ ()), Clazz.innerTypeInstance (jalview.structure.StructureSelectionManager$1, this, Clazz.cloneFinals ("mappingDetails", mappingDetails), System.out));\r
-maxAlignseq.printAlignment (ps);\r
-mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("PDB start/end ");\r
-mappingDetails.append (String.valueOf (maxAlignseq.seq2start)).append (" ");\r
-mappingDetails.append (String.valueOf (maxAlignseq.seq2end));\r
-mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE).append ("SEQ start/end ");\r
-mappingDetails.append (String.valueOf (maxAlignseq.seq1start + seq.getStart () - 1)).append (" ");\r
-mappingDetails.append (String.valueOf (maxAlignseq.seq1end + seq.getEnd () - 1));\r
-maxChain.makeExactMapping (maxAlignseq, seq);\r
-var sqmpping = maxAlignseq.getMappingFromS1 (false);\r
-var omap = new jalview.datamodel.Mapping (sqmpping.getMap ().getInverse ());\r
-maxChain.transferRESNUMFeatures (seq, null);\r
-var mapping = Clazz.newIntArray (seq.findPosition (seq.getLength ()) + 2, 2, 0);\r
-var resNum = -10000;\r
-var index = 0;\r
-do {\r
-var tmp = maxChain.atoms.elementAt (index);\r
-if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) {\r
-resNum = tmp.resNumber;\r
-mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;\r
-mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;\r
-}index++;\r
-} while (index < maxChain.atoms.size ());\r
-if (protocol.equals (jalview.io.AppletFormatAdapter.PASTE)) {\r
-pdbFile = "INLINE" + pdb.id;\r
-}var newMapping = new jalview.structure.StructureMapping (seq, pdbFile, pdb.id, maxChainId, mapping, mappingDetails.toString ());\r
-if (forStructureView) {\r
-this.mappings.add (newMapping);\r
-}maxChain.transferResidueAnnotation (newMapping, sqmpping);\r
-}\r
-return pdb;\r
-}, "~B,~A,~A,~S,~S");\r
-Clazz.defineMethod (c$, "removeStructureViewerListener", \r
-function (svl, pdbfiles) {\r
-this.listeners.removeElement (svl);\r
-if (Clazz.instanceOf (svl, jalview.structure.SequenceListener)) {\r
-for (var i = 0; i < this.listeners.size (); i++) {\r
-if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) {\r
-(this.listeners.elementAt (i)).releaseReferences (svl);\r
-}}\r
-}if (pdbfiles == null) {\r
-return;\r
-}var pdbs = new java.util.ArrayList (java.util.Arrays.asList (pdbfiles));\r
-var sl;\r
-for (var i = 0; i < this.listeners.size (); i++) {\r
-if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) {\r
-sl = this.listeners.elementAt (i);\r
-for (var pdbfile, $pdbfile = 0, $$pdbfile = sl.getPdbFile (); $pdbfile < $$pdbfile.length && ((pdbfile = $$pdbfile[$pdbfile]) || true); $pdbfile++) {\r
-pdbs.remove (pdbfile);\r
-}\r
-}}\r
-if (pdbs.size () > 0) {\r
-var tmp = new java.util.ArrayList ();\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-if (!pdbs.contains (sm.pdbfile)) {\r
-tmp.add (sm);\r
-}}\r
-this.mappings = tmp;\r
-}}, "~O,~A");\r
-Clazz.defineMethod (c$, "mouseOverStructure", \r
-function (pdbResNum, chain, pdbfile) {\r
-var atomSpec = new jalview.structure.AtomSpec (pdbfile, chain, pdbResNum, 0);\r
-var atoms = java.util.Collections.singletonList (atomSpec);\r
-this.mouseOverStructure (atoms);\r
-}, "~N,~S,~S");\r
-Clazz.defineMethod (c$, "mouseOverStructure", \r
-function (atoms) {\r
-if (this.listeners == null) {\r
-return;\r
-}var hasSequenceListener = false;\r
-for (var i = 0; i < this.listeners.size (); i++) {\r
-if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.SequenceListener)) {\r
-hasSequenceListener = true;\r
-}}\r
-if (!hasSequenceListener) {\r
-return;\r
-}var results = new jalview.datamodel.SearchResults ();\r
-for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) {\r
-var lastseq = null;\r
-var lastipos = -1;\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-if (sm.pdbfile.equals (atom.getPdbFile ()) && sm.pdbchain.equals (atom.getChain ())) {\r
-var indexpos = sm.getSeqPos (atom.getPdbResNum ());\r
-if (lastipos != indexpos && lastseq !== sm.sequence) {\r
-results.addResult (sm.sequence, indexpos, indexpos);\r
-lastipos = indexpos;\r
-lastseq = sm.sequence;\r
-for (var acf, $acf = this.seqmappings.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) {\r
-acf.markMappedRegion (sm.sequence, indexpos, results);\r
-}\r
-}}}\r
-}\r
-for (var li, $li = this.listeners.iterator (); $li.hasNext () && ((li = $li.next ()) || true);) {\r
-if (Clazz.instanceOf (li, jalview.structure.SequenceListener)) {\r
-(li).highlightSequence (results);\r
-}}\r
-}, "java.util.List");\r
-Clazz.defineMethod (c$, "mouseOverSequence", \r
-function (seq, indexpos, index, source) {\r
-var hasSequenceListeners = this.handlingVamsasMo || !this.seqmappings.isEmpty ();\r
-var results = null;\r
-if (index == -1) {\r
-index = seq.findPosition (indexpos);\r
-}for (var i = 0; i < this.listeners.size (); i++) {\r
-var listener = this.listeners.elementAt (i);\r
-if (listener === source) {\r
-continue;\r
-}if (Clazz.instanceOf (listener, jalview.structure.StructureListener)) {\r
-this.highlightStructure (listener, seq, index);\r
-} else {\r
-if (Clazz.instanceOf (listener, jalview.structure.SequenceListener)) {\r
-var seqListener = listener;\r
-if (hasSequenceListeners && seqListener.getVamsasSource () !== source) {\r
-if (this.relaySeqMappings) {\r
-if (results == null) {\r
-results = jalview.util.MappingUtils.buildSearchResults (seq, index, this.seqmappings);\r
-}if (this.handlingVamsasMo) {\r
-results.addResult (seq, index, index);\r
-}seqListener.highlightSequence (results);\r
-}}} else if (Clazz.instanceOf (listener, jalview.structure.VamsasListener) && !this.handlingVamsasMo) {\r
-(listener).mouseOverSequence (seq, indexpos, source);\r
-} else if (Clazz.instanceOf (listener, jalview.structure.SecondaryStructureListener)) {\r
-(listener).mouseOverSequence (seq, indexpos, index);\r
-}}}\r
-}, "jalview.datamodel.SequenceI,~N,~N,jalview.structure.VamsasSource");\r
-Clazz.defineMethod (c$, "highlightStructure", \r
-function (sl, seq, index) {\r
-if (!sl.isListeningFor (seq)) {\r
-return;\r
-}var atomNo;\r
-var atoms = new java.util.ArrayList ();\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-if (sm.sequence === seq || sm.sequence === seq.getDatasetSequence ()) {\r
-atomNo = sm.getAtomNum (index);\r
-if (atomNo > 0) {\r
-atoms.add ( new jalview.structure.AtomSpec (sm.pdbfile, sm.pdbchain, sm.getPDBResNum (index), atomNo));\r
-}}}\r
-sl.highlightAtoms (atoms);\r
-}, "jalview.structure.StructureListener,jalview.datamodel.SequenceI,~N");\r
-Clazz.defineMethod (c$, "mouseOverVamsasSequence", \r
-function (sequenceI, position, source) {\r
-this.handlingVamsasMo = true;\r
-var msg = sequenceI.hashCode () * (1 + position);\r
-if (this.lastmsg != msg) {\r
-this.lastmsg = msg;\r
-this.mouseOverSequence (sequenceI, position, -1, source);\r
-}this.handlingVamsasMo = false;\r
-}, "jalview.datamodel.SequenceI,~N,jalview.structure.VamsasSource");\r
-Clazz.defineMethod (c$, "colourSequenceFromStructure", \r
-function (seq, pdbid) {\r
-return null;\r
-}, "jalview.datamodel.SequenceI,~S");\r
-Clazz.defineMethod (c$, "structureSelectionChanged", \r
-function () {\r
-});\r
-Clazz.defineMethod (c$, "sequenceSelectionChanged", \r
-function () {\r
-});\r
-Clazz.defineMethod (c$, "sequenceColoursChanged", \r
-function (source) {\r
-var sl;\r
-for (var i = 0; i < this.listeners.size (); i++) {\r
-if (Clazz.instanceOf (this.listeners.elementAt (i), jalview.structure.StructureListener)) {\r
-sl = this.listeners.elementAt (i);\r
-sl.updateColours (source);\r
-}}\r
-}, "~O");\r
-Clazz.defineMethod (c$, "getMapping", \r
-function (pdbfile) {\r
-var tmp = new java.util.ArrayList ();\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-if (sm.pdbfile.equals (pdbfile)) {\r
-tmp.add (sm);\r
-}}\r
-return tmp.toArray ( new Array (tmp.size ()));\r
-}, "~S");\r
-Clazz.defineMethod (c$, "printMappings", \r
-function (pdbfile, seqs) {\r
-if (pdbfile == null || seqs == null || seqs.isEmpty ()) {\r
-return "";\r
-}var sb = new StringBuilder (64);\r
-for (var sm, $sm = this.mappings.iterator (); $sm.hasNext () && ((sm = $sm.next ()) || true);) {\r
-if (sm.pdbfile.equals (pdbfile) && seqs.contains (sm.sequence)) {\r
-sb.append (sm.mappingDetails);\r
-sb.append (jalview.structure.StructureSelectionManager.NEWLINE);\r
-sb.append ("=====================");\r
-sb.append (jalview.structure.StructureSelectionManager.NEWLINE);\r
-}}\r
-sb.append (jalview.structure.StructureSelectionManager.NEWLINE);\r
-return sb.toString ();\r
-}, "~S,java.util.List");\r
-Clazz.defineMethod (c$, "removeMappings", \r
-function (set) {\r
-if (set != null) {\r
-for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) {\r
-this.removeMapping (acf);\r
-}\r
-}}, "java.util.Set");\r
-Clazz.defineMethod (c$, "removeMapping", \r
-function (acf) {\r
-if (acf != null && this.seqmappings.contains (acf)) {\r
-var count = (this.seqMappingRefCounts.get (acf)).intValue ();\r
-count--;\r
-if (count > 0) {\r
-this.seqMappingRefCounts.put (acf, new Integer (count));\r
-} else {\r
-this.seqmappings.remove (acf);\r
-this.seqMappingRefCounts.remove (acf);\r
-}}}, "jalview.datamodel.AlignedCodonFrame");\r
-Clazz.defineMethod (c$, "addMappings", \r
-function (set) {\r
-if (set != null) {\r
-for (var acf, $acf = set.iterator (); $acf.hasNext () && ((acf = $acf.next ()) || true);) {\r
-this.addMapping (acf);\r
-}\r
-}}, "java.util.Set");\r
-Clazz.defineMethod (c$, "addMapping", \r
-function (acf) {\r
-if (acf != null) {\r
-if (this.seqmappings.contains (acf)) {\r
-this.seqMappingRefCounts.put (acf, new Integer ((this.seqMappingRefCounts.get (acf)).intValue () + 1));\r
-} else {\r
-this.seqmappings.add (acf);\r
-this.seqMappingRefCounts.put (acf, new Integer (1));\r
-}}}, "jalview.datamodel.AlignedCodonFrame");\r
-Clazz.defineMethod (c$, "addSelectionListener", \r
-function (selecter) {\r
-if (!this.sel_listeners.contains (selecter)) {\r
-this.sel_listeners.add (selecter);\r
-}}, "jalview.structure.SelectionListener");\r
-Clazz.defineMethod (c$, "removeSelectionListener", \r
-function (toremove) {\r
-if (this.sel_listeners.contains (toremove)) {\r
-this.sel_listeners.remove (toremove);\r
-}}, "jalview.structure.SelectionListener");\r
-Clazz.defineMethod (c$, "sendSelection", \r
-function (selection, colsel, source) {\r
-for (var slis, $slis = this.sel_listeners.iterator (); $slis.hasNext () && ((slis = $slis.next ()) || true);) {\r
-if (slis !== source) {\r
-slis.selection (selection, colsel, source);\r
-}}\r
-}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource");\r
-Clazz.defineMethod (c$, "sendViewPosition", \r
-function (source, startRes, endRes, startSeq, endSeq) {\r
-if (this.view_listeners != null && this.view_listeners.size () > 0) {\r
-var listeners = this.view_listeners.elements ();\r
-while (listeners.hasMoreElements ()) {\r
-var slis = listeners.nextElement ();\r
-if (slis !== source) {\r
-slis.viewPosition (startRes, endRes, startSeq, endSeq, source);\r
-};}\r
-}}, "jalview.api.AlignmentViewPanel,~N,~N,~N,~N");\r
-c$.release = Clazz.defineMethod (c$, "release", \r
-function (jalviewLite) {\r
-{\r
-if (jalview.structure.StructureSelectionManager.instances == null) {\r
-return;\r
-}var mnger = (jalview.structure.StructureSelectionManager.instances.get (jalviewLite));\r
-if (mnger != null) {\r
-jalview.structure.StructureSelectionManager.instances.remove (jalviewLite);\r
-try {\r
-mnger.finalize ();\r
-} catch (x) {\r
-}\r
-}}}, "jalview.api.StructureSelectionManagerProvider");\r
-Clazz.defineMethod (c$, "registerPDBEntry", \r
-function (pdbentry) {\r
-if (pdbentry.getFile () != null && pdbentry.getFile ().trim ().length > 0) {\r
-this.registerPDBFile (pdbentry.getId (), pdbentry.getFile ());\r
-}}, "jalview.datamodel.PDBEntry");\r
-Clazz.defineMethod (c$, "addCommandListener", \r
-function (cl) {\r
-if (!this.commandListeners.contains (cl)) {\r
-this.commandListeners.add (cl);\r
-}}, "jalview.structure.CommandListener");\r
-Clazz.defineMethod (c$, "hasCommandListener", \r
-function (cl) {\r
-return this.commandListeners.contains (cl);\r
-}, "jalview.structure.CommandListener");\r
-Clazz.defineMethod (c$, "removeCommandListener", \r
-function (l) {\r
-return this.commandListeners.remove (l);\r
-}, "jalview.structure.CommandListener");\r
-Clazz.defineMethod (c$, "commandPerformed", \r
-function (command, undo, source) {\r
-for (var listener, $listener = this.commandListeners.iterator (); $listener.hasNext () && ((listener = $listener.next ()) || true);) {\r
-listener.mirrorCommand (command, undo, this, source);\r
-}\r
-}, "jalview.commands.CommandI,~B,jalview.structure.VamsasSource");\r
-Clazz.defineMethod (c$, "mapCommand", \r
-function (command, undo, mapTo, gapChar) {\r
-if (Clazz.instanceOf (command, jalview.commands.EditCommand)) {\r
-return jalview.util.MappingUtils.mapEditCommand (command, undo, mapTo, gapChar, this.seqmappings);\r
-} else if (Clazz.instanceOf (command, jalview.commands.OrderCommand)) {\r
-return jalview.util.MappingUtils.mapOrderCommand (command, undo, mapTo, this.seqmappings);\r
-}return null;\r
-}, "jalview.commands.CommandI,~B,jalview.datamodel.AlignmentI,~S");\r
-c$.$StructureSelectionManager$1$ = function () {\r
-Clazz.pu$h(self.c$);\r
-c$ = Clazz.declareAnonymous (jalview.structure, "StructureSelectionManager$1", java.io.PrintStream);\r
-Clazz.defineMethod (c$, "print", \r
-function (x) {\r
-this.f$.mappingDetails.append (x);\r
-}, "~S");\r
-Clazz.defineMethod (c$, "println", \r
-function () {\r
-this.f$.mappingDetails.append (jalview.structure.StructureSelectionManager.NEWLINE);\r
-});\r
-c$ = Clazz.p0p ();\r
-};\r
-c$.NEWLINE = c$.prototype.NEWLINE = System.lineSeparator ();\r
-Clazz.defineStatics (c$,\r
-"instances", null,\r
-"nullProvider", null);\r
-});\r
+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$h(self.c$);
+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);
+});
git://source.jalview.org / jalviewjs.git / blobdiff