X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=688762fa38c44e9c7e8aecc9b4c4a246af709c9a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=53ed66371e47bd92e6e327ee5442feda53ababed;hpb=f2f654875a6eb5f4e90b2c5c545bfed3a70f2b5f;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 53ed663..688762f 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,21 +20,6 @@ */ package jalview.structure; -import java.io.PrintStream; -import java.util.ArrayList; -import java.util.Collections; -import java.util.Enumeration; -import java.util.HashMap; -import java.util.IdentityHashMap; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.Vector; - -import MCview.Atom; -import MCview.PDBChain; - import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; import jalview.commands.CommandI; @@ -51,8 +36,27 @@ import jalview.io.AppletFormatAdapter; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import java.io.PrintStream; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.IdentityHashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.Vector; + +import MCview.Atom; +import MCview.PDBChain; +import MCview.PDBfile; + public class StructureSelectionManager { + public final static String NEWLINE = System.lineSeparator(); + static IdentityHashMap instances; private List mappings = new ArrayList(); @@ -66,13 +70,7 @@ public class StructureSelectionManager /* * Set of any registered mappings between (dataset) sequences. */ - Set seqmappings = new LinkedHashSet(); - - /* - * Reference counters for the above mappings. Remove mappings when ref count - * goes to zero. - */ - Map seqMappingRefCounts = new HashMap(); + public Set seqmappings = new LinkedHashSet(); private List commandListeners = new ArrayList(); @@ -164,8 +162,9 @@ public class StructureSelectionManager * map between the PDB IDs (or structure identifiers) used by Jalview and the * absolute filenames for PDB data that corresponds to it */ - HashMap pdbIdFileName = new HashMap(), - pdbFileNameId = new HashMap(); + Map pdbIdFileName = new HashMap(); + + Map pdbFileNameId = new HashMap(); public void registerPDBFile(String idForFile, String absoluteFile) { @@ -202,8 +201,11 @@ public class StructureSelectionManager { if (instances != null) { - throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"), - new NullPointerException(MessageManager.getString("exception.ssm_context_is_null"))); + throw new Error( + MessageManager + .getString("error.implementation_error_structure_selection_manager_null"), + new NullPointerException(MessageManager + .getString("exception.ssm_context_is_null"))); } else { @@ -309,7 +311,7 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public MCview.PDBfile setMapping(SequenceI[] sequence, + synchronized public PDBfile setMapping(SequenceI[] sequence, String[] targetChains, String pdbFile, String protocol) { return setMapping(true, sequence, targetChains, pdbFile, protocol); @@ -333,15 +335,14 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public MCview.PDBfile setMapping(boolean forStructureView, - SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + synchronized public PDBfile setMapping(boolean forStructureView, + SequenceI[] sequence, String[] targetChains, String pdbFile, + String protocol) { /* * There will be better ways of doing this in the future, for now we'll use * the tried and tested MCview pdb mapping */ - MCview.PDBfile pdb = null; boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) { @@ -360,8 +361,7 @@ public class StructureSelectionManager // false if any annotation present from this structure // JBPNote this fails for jmol/chimera view because the *file* is // passed, not the structure data ID - - if (MCview.PDBfile.isCalcIdForFile(ala, - findIdForPDBFile(pdbFile))) + if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile))) { parseSecStr = false; } @@ -369,10 +369,11 @@ public class StructureSelectionManager } } } + PDBfile pdb = null; try { - pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr, - secStructServices, pdbFile, protocol); + pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, + pdbFile, protocol); if (pdb.id != null && pdb.id.trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { @@ -388,15 +389,16 @@ public class StructureSelectionManager for (int s = 0; s < sequence.length; s++) { boolean infChain = true; + final SequenceI seq = sequence[s]; if (targetChains != null && targetChains[s] != null) { infChain = false; targetChain = targetChains[s]; } - else if (sequence[s].getName().indexOf("|") > -1) + else if (seq.getName().indexOf("|") > -1) { - targetChain = sequence[s].getName().substring( - sequence[s].getName().lastIndexOf("|") + 1); + targetChain = seq.getName().substring( + seq.getName().lastIndexOf("|") + 1); if (targetChain.length() > 1) { if (targetChain.trim().length() == 0) @@ -415,14 +417,17 @@ public class StructureSelectionManager targetChain = ""; } + /* + * Attempt pairwise alignment of the sequence with each chain in the PDB, + * and remember the highest scoring chain + */ int max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; boolean first = true; - for (int i = 0; i < pdb.chains.size(); i++) + for (PDBChain chain : pdb.chains) { - PDBChain chain = (pdb.chains.elementAt(i)); if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain) { @@ -430,12 +435,13 @@ public class StructureSelectionManager } // TODO: correctly determine sequence type for mixed na/peptide // structures - AlignSeq as = new AlignSeq(sequence[s], - pdb.chains.elementAt(i).sequence, - pdb.chains.elementAt(i).isNa ? AlignSeq.DNA - : AlignSeq.PEP); - as.calcScoreMatrix(); - as.traceAlignment(); + final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP; + AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence, + type); + // equivalent to: + // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type); + // as.calcScoreMatrix(); + // as.traceAlignment(); if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals(targetChain))) @@ -451,11 +457,13 @@ public class StructureSelectionManager { continue; } - final StringBuffer mappingDetails = new StringBuffer(); - mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + maxChain.sequence.getSequenceAsString()); - mappingDetails.append("\nNo of residues = " - + maxChain.residues.size() + "\n\n"); + final StringBuilder mappingDetails = new StringBuilder(128); + mappingDetails.append(NEWLINE).append("PDB Sequence is :") + .append(NEWLINE).append("Sequence = ") + .append(maxChain.sequence.getSequenceAsString()); + mappingDetails.append(NEWLINE).append("No of residues = ") + .append(maxChain.residues.size()).append(NEWLINE) + .append(NEWLINE); PrintStream ps = new PrintStream(System.out) { @Override @@ -467,40 +475,50 @@ public class StructureSelectionManager @Override public void println() { - mappingDetails.append("\n"); + mappingDetails.append(NEWLINE); } }; maxAlignseq.printAlignment(ps); - mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start - + " " + maxAlignseq.seq2end); - mappingDetails.append("\nSEQ start/end " - + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + " " - + (maxAlignseq.seq1end + sequence[s].getEnd() - 1)); + mappingDetails.append(NEWLINE).append("PDB start/end "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append( + " "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); + + mappingDetails.append(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, sequence[s]); + maxChain.makeExactMapping(maxAlignseq, seq); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping( sqmpping.getMap().getInverse()); - maxChain.transferRESNUMFeatures(sequence[s], null); + maxChain.transferRESNUMFeatures(seq, null); // allocate enough slots to store the mapping from positions in // sequence[s] to the associated chain - int[][] mapping = new int[sequence[s].findPosition(sequence[s] - .getLength()) + 2][2]; + int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2]; int resNum = -10000; int index = 0; do { - Atom tmp = (Atom) maxChain.atoms.elementAt(index); + Atom 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; + if (tmp.alignmentMapping >= -1) + { + // TODO (JAL-1836) address root cause: negative residue no in PDB + // file + mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; + mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; + } } index++; @@ -510,9 +528,8 @@ public class StructureSelectionManager { pdbFile = "INLINE" + pdb.id; } - StructureMapping newMapping = new StructureMapping(sequence[s], - pdbFile, pdb.id, maxChainId, mapping, - mappingDetails.toString()); + StructureMapping newMapping = new StructureMapping(seq, pdbFile, + pdb.id, maxChainId, mapping, mappingDetails.toString()); if (forStructureView) { mappings.add(newMapping); @@ -543,30 +560,30 @@ public class StructureSelectionManager { return; } - String[] handlepdbs; - Vector pdbs = new Vector(); - for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++])) - { - ; - } + + /* + * Remove mappings to the closed listener's PDB files, but first check if + * another listener is still interested + */ + List pdbs = new ArrayList(Arrays.asList(pdbfiles)); + StructureListener sl; for (int i = 0; i < listeners.size(); i++) { if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - handlepdbs = sl.getPdbFile(); - for (int j = 0; j < handlepdbs.length; j++) + for (String pdbfile : sl.getPdbFile()) { - if (pdbs.contains(handlepdbs[j])) - { - pdbs.removeElement(handlepdbs[j]); - } + pdbs.remove(pdbfile); } - } } + /* + * Rebuild the mappings set, retaining only those which are for 'other' PDB + * files + */ if (pdbs.size() > 0) { List tmp = new ArrayList(); @@ -646,14 +663,11 @@ public class StructureSelectionManager } } } - if (!results.isEmpty()) + for (Object li : listeners) { - for (Object li : listeners) + if (li instanceof SequenceListener) { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } + ((SequenceListener) li).highlightSequence(results); } } } @@ -712,7 +726,10 @@ public class StructureSelectionManager results.addResult(seq, index, index); } - seqListener.highlightSequence(results); + if (!results.isEmpty()) + { + seqListener.highlightSequence(results); + } } } } @@ -724,7 +741,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos); + indexpos, index); } } } @@ -741,6 +758,10 @@ public class StructureSelectionManager protected void highlightStructure(StructureListener sl, SequenceI seq, int index) { + if (!sl.isListeningFor(seq)) + { + return; + } int atomNo; List atoms = new ArrayList(); for (StructureMapping sm : mappings) @@ -847,104 +868,131 @@ public class StructureSelectionManager { List tmp = new ArrayList(); for (StructureMapping sm : mappings) - { + { if (sm.pdbfile.equals(pdbfile)) - { + { tmp.add(sm); - } + } } return tmp.toArray(new StructureMapping[tmp.size()]); } - public String printMapping(String pdbfile) + /** + * Returns a readable description of all mappings for the given pdbfile to any + * of the given sequences + * + * @param pdbfile + * @param seqs + * @return + */ + public String printMappings(String pdbfile, List seqs) { + if (pdbfile == null || seqs == null || seqs.isEmpty()) + { + return ""; + } + StringBuilder sb = new StringBuilder(64); for (StructureMapping sm : mappings) { - if (sm.pdbfile.equals(pdbfile)) + if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence)) { sb.append(sm.mappingDetails); + sb.append(NEWLINE); + // separator makes it easier to read multiple mappings + sb.append("====================="); + sb.append(NEWLINE); } } + sb.append(NEWLINE); return sb.toString(); } /** - * Decrement the reference counter for each of the given mappings, and remove - * it entirely if its reference counter reduces to zero. + * Remove the given mapping * - * @param set + * @param acf */ - public void removeMappings(Set set) + public void deregisterMapping(AlignedCodonFrame acf) { - if (set != null) + if (acf != null) { - for (AlignedCodonFrame acf : set) - { - removeMapping(acf); + boolean removed = seqmappings.remove(acf); + if (removed && seqmappings.isEmpty()) + { // debug + System.out.println("All mappings removed"); } } } /** - * Decrement the reference counter for the given mapping, and remove it - * entirely if its reference counter reduces to zero. + * Add each of the given codonFrames to the stored set, if not aready present. * - * @param acf + * @param set */ - public void removeMapping(AlignedCodonFrame acf) + public void registerMappings(Set set) { - if (acf != null && seqmappings.contains(acf)) + if (set != null) { - int count = seqMappingRefCounts.get(acf); - count--; - if (count > 0) - { - seqMappingRefCounts.put(acf, count); - } - else + for (AlignedCodonFrame acf : set) { - seqmappings.remove(acf); - seqMappingRefCounts.remove(acf); + registerMapping(acf); } } } /** - * Add each of the given codonFrames to the stored set. If not aready present, - * increments its reference count instead. - * - * @param set + * Add the given mapping to the stored set, unless already stored. */ - public void addMappings(Set set) + public void registerMapping(AlignedCodonFrame acf) { - if (set != null) + if (acf != null) { - for (AlignedCodonFrame acf : set) + if (!seqmappings.contains(acf)) { - addMapping(acf); + seqmappings.add(acf); } } } /** - * Add the given mapping to the stored set, or if already stored, increment - * its reference counter. + * Resets this object to its initial state by removing all registered + * listeners, codon mappings, PDB file mappings */ - public void addMapping(AlignedCodonFrame acf) + public void resetAll() { - if (acf != null) + if (mappings != null) { - if (seqmappings.contains(acf)) - { - seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1); - } - else - { - seqmappings.add(acf); - seqMappingRefCounts.put(acf, 1); - } + mappings.clear(); + } + if (seqmappings != null) + { + seqmappings.clear(); + } + if (sel_listeners != null) + { + sel_listeners.clear(); + } + if (listeners != null) + { + listeners.clear(); + } + if (commandListeners != null) + { + commandListeners.clear(); + } + if (view_listeners != null) + { + view_listeners.clear(); + } + if (pdbFileNameId != null) + { + pdbFileNameId.clear(); + } + if (pdbIdFileName != null) + { + pdbIdFileName.clear(); } }