X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=7e691be6ae7f87ddd1ee3b5b48ba368d036f91ed;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=af0079870b139f6d4230a701df32371c7729fc68;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index af00798..7e691be 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -22,32 +22,69 @@ package jalview.structure; import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; +import jalview.gui.IProgressIndicator; import jalview.io.AppletFormatAdapter; +import jalview.io.StructureFile; +import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.ws.sifts.SiftsClient; +import jalview.ws.sifts.SiftsException; +import jalview.ws.sifts.SiftsSettings; 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.List; +import java.util.Map; 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; - StructureMapping[] mappings; + private List mappings = new ArrayList(); + + private boolean processSecondaryStructure = false; + + private boolean secStructServices = false; + + private boolean addTempFacAnnot = false; + + private IProgressIndicator progressIndicator; + + private SiftsClient siftsClient = null; - private boolean processSecondaryStructure = false, - secStructServices = false, addTempFacAnnot = false; + private long progressSessionId; + + /* + * Set of any registered mappings between (dataset) sequences. + */ + private List seqmappings = new ArrayList(); + + private List commandListeners = new ArrayList(); + + private List sel_listeners = new ArrayList(); /** * @return true if will try to use external services for processing secondary @@ -115,17 +152,18 @@ public class StructureSelectionManager */ public void reportMapping() { - if (mappings == null) + if (mappings.isEmpty()) { System.err.println("reportMapping: No PDB/Sequence mappings."); } else { - System.err.println("reportMapping: There are " + mappings.length + System.err.println("reportMapping: There are " + mappings.size() + " mappings."); - for (int m = 0; m < mappings.length; m++) + int i = 0; + for (StructureMapping sm : mappings) { - System.err.println("mapping " + m + " : " + mappings[m].pdbfile); + System.err.println("mapping " + i++ + " : " + sm.pdbfile); } } } @@ -134,8 +172,9 @@ 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) { @@ -172,8 +211,11 @@ 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 { @@ -246,16 +288,19 @@ public class StructureSelectionManager } } + /** + * Returns the file name for a mapped PDB id (or null if not mapped). + * + * @param pdbid + * @return + */ public String alreadyMappedToFile(String pdbid) { - if (mappings != null) + for (StructureMapping sm : mappings) { - for (int i = 0; i < mappings.length; i++) + if (sm.getPdbId().equals(pdbid)) { - if (mappings[i].getPdbId().equals(pdbid)) - { - return mappings[i].pdbfile; - } + return sm.pdbfile; } } return null; @@ -276,7 +321,7 @@ 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 StructureFile setMapping(SequenceI[] sequence, String[] targetChains, String pdbFile, String protocol) { return setMapping(true, sequence, targetChains, pdbFile, protocol); @@ -289,9 +334,9 @@ public class StructureSelectionManager * @param forStructureView * when true, record the mapping for use in mouseOvers * - * @param sequence + * @param sequenceArray * - one or more sequences to be mapped to pdbFile - * @param targetChains + * @param targetChainIds * - optional chain specification for mapping each sequence to pdb * (may be nill, individual elements may be nill) * @param pdbFile @@ -300,19 +345,18 @@ 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 StructureFile setMapping(boolean forStructureView, + SequenceI[] sequenceArray, String[] targetChainIds, + 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)) { - for (SequenceI sq : sequence) + for (SequenceI sq : sequenceArray) { SequenceI ds = sq; while (ds.getDatasetSequence() != null) @@ -327,8 +371,7 @@ 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; } @@ -336,76 +379,104 @@ public class StructureSelectionManager } } } + StructureFile pdb = null; + boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr, - secStructServices, pdbFile, protocol); - if (pdb.id != null && pdb.id.trim().length() > 0 + pdb = new JmolParser(pdbFile, protocol); + + if (pdb.getId() != null && pdb.getId().trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { - registerPDBFile(pdb.id.trim(), pdbFile); + registerPDBFile(pdb.getId().trim(), pdbFile); } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = pdb.isPPDBIdAvailable(); + } catch (Exception ex) { ex.printStackTrace(); return null; } - String targetChain; - for (int s = 0; s < sequence.length; s++) + try + { + if (isMapUsingSIFTs) + { + siftsClient = new SiftsClient(pdb); + } + } catch (SiftsException e) + { + isMapUsingSIFTs = false; + e.printStackTrace(); + } + + String targetChainId; + for (int s = 0; s < sequenceArray.length; s++) { boolean infChain = true; - if (targetChains != null && targetChains[s] != null) + final SequenceI seq = sequenceArray[s]; + SequenceI ds = seq; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + + if (targetChainIds != null && targetChainIds[s] != null) { infChain = false; - targetChain = targetChains[s]; + targetChainId = targetChainIds[s]; } - else if (sequence[s].getName().indexOf("|") > -1) + else if (seq.getName().indexOf("|") > -1) { - targetChain = sequence[s].getName().substring( - sequence[s].getName().lastIndexOf("|") + 1); - if (targetChain.length() > 1) + targetChainId = seq.getName().substring( + seq.getName().lastIndexOf("|") + 1); + if (targetChainId.length() > 1) { - if (targetChain.trim().length() == 0) + if (targetChainId.trim().length() == 0) { - targetChain = " "; + targetChainId = " "; } else { // not a valid chain identifier - targetChain = ""; + targetChainId = ""; } } } else { - targetChain = ""; + targetChainId = ""; } + /* + * 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.getChains()) { - PDBChain chain = (pdb.chains.elementAt(i)); - if (targetChain.length() > 0 && !targetChain.equals(chain.id) + if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) && !infChain) { continue; // don't try to map chains don't match. } // 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))) + || (as.maxscore == max && chain.id.equals(targetChainId))) { first = false; maxChain = chain; @@ -418,89 +489,223 @@ 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"); - PrintStream ps = new PrintStream(System.out) + + if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) { - @Override - public void print(String x) - { - mappingDetails.append(x); - } + pdbFile = "INLINE" + pdb.getId(); + } - @Override - public void println() + ArrayList seqToStrucMapping = new ArrayList(); + if (isMapUsingSIFTs && seq.isProtein()) + { + setProgressBar(null); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts")); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + if (targetChainId != null && !targetChainId.trim().isEmpty()) { - mappingDetails.append("\n"); + StructureMapping siftsMapping; + try + { + siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, + pdb, maxChain, sqmpping, maxAlignseq); + seqToStrucMapping.add(siftsMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this + // "IEA:SIFTS" ? + maxChain.transferResidueAnnotation(siftsMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + + } catch (SiftsException e) + { + // fall back to NW alignment + System.err.println(e.getMessage()); + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + targetChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } } - }; - - 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)); - - maxChain.makeExactMapping(maxAlignseq, sequence[s]); - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping( - sqmpping.getMap().getInverse()); - maxChain.transferRESNUMFeatures(sequence[s], 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 resNum = -10000; - int index = 0; - - do - { - Atom tmp = (Atom) maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + else { - resNum = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; + ArrayList foundSiftsMappings = new ArrayList(); + for (PDBChain chain : pdb.getChains()) + { + try + { + StructureMapping siftsMapping = getStructureMapping(seq, + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); + foundSiftsMappings.add(siftsMapping); + } catch (SiftsException e) + { + System.err.println(e.getMessage()); + } + } + if (!foundSiftsMappings.isEmpty()) + { + seqToStrucMapping.addAll(foundSiftsMappings); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this + // "IEA:SIFTS" ? + maxChain.transferResidueAnnotation(foundSiftsMappings.get(0), + sqmpping); + ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0)); + } + else + { + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } } + } + else + { + setProgressBar(null); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment")); + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); - index++; - } while (index < maxChain.atoms.size()); + } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (forStructureView) { - pdbFile = "INLINE" + pdb.id; + mappings.addAll(seqToStrucMapping); } - StructureMapping newMapping = new StructureMapping(sequence[s], - pdbFile, pdb.id, maxChainId, mapping, - mappingDetails.toString()); - if (forStructureView) + } + return pdb; + } + + private boolean isCIFFile(String filename) + { + String fileExt = filename.substring(filename.lastIndexOf(".") + 1, + filename.length()); + return "cif".equalsIgnoreCase(fileExt); + } + + /** + * retrieve a mapping for seq from SIFTs using associated DBRefEntry for + * uniprot or PDB + * + * @param seq + * @param pdbFile + * @param targetChainId + * @param pdb + * @param maxChain + * @param sqmpping + * @param maxAlignseq + * @return + * @throws SiftsException + */ + private StructureMapping getStructureMapping(SequenceI seq, + String pdbFile, String targetChainId, StructureFile pdb, + PDBChain maxChain, jalview.datamodel.Mapping sqmpping, + AlignSeq maxAlignseq) throws SiftsException + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChainId); + try + { + PDBChain chain = pdb.findChain(targetChainId); + if (chain != null) { + chain.transferResidueAnnotation(curChainMapping, sqmpping); + } + } catch (Exception e) + { + e.printStackTrace(); + } + return curChainMapping; + } - if (mappings == null) - { - mappings = new StructureMapping[1]; - } - else + private StructureMapping getNWMappings(SequenceI seq, String pdbFile, + String maxChainId, PDBChain maxChain, StructureFile pdb, + AlignSeq maxAlignseq) + { + final StringBuilder mappingDetails = new StringBuilder(128); + mappingDetails.append(NEWLINE).append( + "Sequence \u27f7 Structure mapping details"); + mappingDetails.append(NEWLINE); + mappingDetails + .append("Method: inferred with Needleman & Wunsch alignment"); + 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 + public void print(String x) + { + mappingDetails.append(x); + } + + @Override + public void println() + { + mappingDetails.append(NEWLINE); + } + }; + + maxAlignseq.printAlignment(ps); + + 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.getStart() - 1))); + mappingDetails.append(NEWLINE); + maxChain.makeExactMapping(maxAlignseq, seq); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + maxChain.transferRESNUMFeatures(seq, null); + + HashMap mapping = new HashMap(); + int resNum = -10000; + int index = 0; + char insCode = ' '; + + do + { + Atom tmp = maxChain.atoms.elementAt(index); + if ((resNum != tmp.resNumber || insCode != tmp.insCode) + && tmp.alignmentMapping != -1) + { + resNum = tmp.resNumber; + insCode = tmp.insCode; + if (tmp.alignmentMapping >= -1) { - StructureMapping[] tmp = new StructureMapping[mappings.length + 1]; - System.arraycopy(mappings, 0, tmp, 0, mappings.length); - mappings = tmp; + mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber, + tmp.atomIndex }); } - - mappings[mappings.length - 1] = newMapping; } - maxChain.transferResidueAnnotation(newMapping, sqmpping); - } - // /////// - return pdb; + index++; + } while (index < maxChain.atoms.size()); + + StructureMapping nwMapping = new StructureMapping(seq, pdbFile, + pdb.getId(), maxChainId, mapping, mappingDetails.toString()); + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + return nwMapping; } public void removeStructureViewerListener(Object svl, String[] pdbfiles) @@ -522,224 +727,233 @@ 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); } - } } - if (pdbs.size() > 0 && mappings != null) + /* + * Rebuild the mappings set, retaining only those which are for 'other' PDB + * files + */ + if (pdbs.size() > 0) { - Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) + List tmp = new ArrayList(); + for (StructureMapping sm : mappings) { - if (!pdbs.contains(mappings[i].pdbfile)) + if (!pdbs.contains(sm.pdbfile)) { - tmp.addElement(mappings[i]); + tmp.add(sm); } } - mappings = new StructureMapping[tmp.size()]; - tmp.copyInto(mappings); + mappings = tmp; } } + /** + * Propagate mouseover of a single position in a structure + * + * @param pdbResNum + * @param chain + * @param pdbfile + */ public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) { + AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0); + List atoms = Collections.singletonList(atomSpec); + mouseOverStructure(atoms); + } + + /** + * Propagate mouseover or selection of multiple positions in a structure + * + * @param atoms + */ + public void mouseOverStructure(List atoms) + { if (listeners == null) { // old or prematurely sent event return; } - boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null; - SearchResults results = null; - SequenceI lastseq = null; - int lastipos = -1, indexpos; + boolean hasSequenceListener = false; for (int i = 0; i < listeners.size(); i++) { if (listeners.elementAt(i) instanceof SequenceListener) { - if (results == null) - { - results = new SearchResults(); - } - if (mappings != null) + hasSequenceListener = true; + } + } + if (!hasSequenceListener) + { + return; + } + + SearchResults results = new SearchResults(); + for (AtomSpec atom : atoms) + { + SequenceI lastseq = null; + int lastipos = -1; + for (StructureMapping sm : mappings) + { + if (sm.pdbfile.equals(atom.getPdbFile()) + && sm.pdbchain.equals(atom.getChain())) { - for (int j = 0; j < mappings.length; j++) + int indexpos = sm.getSeqPos(atom.getPdbResNum()); + if (lastipos != indexpos && lastseq != sm.sequence) { - if (mappings[j].pdbfile.equals(pdbfile) - && mappings[j].pdbchain.equals(chain)) + results.addResult(sm.sequence, indexpos, indexpos); + lastipos = indexpos; + lastseq = sm.sequence; + // construct highlighted sequence list + for (AlignedCodonFrame acf : seqmappings) { - indexpos = mappings[j].getSeqPos(pdbResNum); - if (lastipos != indexpos && lastseq != mappings[j].sequence) - { - results.addResult(mappings[j].sequence, indexpos, indexpos); - lastipos = indexpos; - lastseq = mappings[j].sequence; - // construct highlighted sequence list - if (seqmappings != null) - { - - Enumeration e = seqmappings.elements(); - while (e.hasMoreElements()) - - { - ((AlignedCodonFrame) e.nextElement()).markMappedRegion( - mappings[j].sequence, indexpos, results); - } - } - } - + acf.markMappedRegion(sm.sequence, indexpos, results); } } } } } - if (results != null) + for (Object li : listeners) { - for (int i = 0; i < listeners.size(); i++) + if (li instanceof SequenceListener) { - Object li = listeners.elementAt(i); - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } + ((SequenceListener) li).highlightSequence(results); } } } - Vector seqmappings = null; // should be a simpler list of mapped seuqence - /** * highlight regions associated with a position (indexpos) in seq * * @param seq - * the sequeence that the mouse over occured on + * the sequence that the mouse over occurred on * @param indexpos * the absolute position being mouseovered in seq (0 to seq.length()) - * @param index + * @param seqPos * the sequence position (if -1, seq.findPosition is called to * resolve the residue number) */ - public void mouseOverSequence(SequenceI seq, int indexpos, int index, + public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos, VamsasSource source) { - boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null; + boolean hasSequenceListeners = handlingVamsasMo + || !seqmappings.isEmpty(); SearchResults results = null; - if (index == -1) + if (seqPos == -1) { - index = seq.findPosition(indexpos); + seqPos = seq.findPosition(indexpos); } - StructureListener sl; - int atomNo = 0; for (int i = 0; i < listeners.size(); i++) { Object listener = listeners.elementAt(i); if (listener == source) { + // TODO listener (e.g. SeqPanel) is never == source (AlignViewport) + // Temporary fudge with SequenceListener.getVamsasSource() continue; } if (listener instanceof StructureListener) { - sl = (StructureListener) listener; - if (mappings == null) - { - continue; - } - for (int j = 0; j < mappings.length; j++) - { - if (mappings[j].sequence == seq - || mappings[j].sequence == seq.getDatasetSequence()) - { - atomNo = mappings[j].getAtomNum(index); - - if (atomNo > 0) - { - sl.highlightAtom(atomNo, mappings[j].getPDBResNum(index), - mappings[j].pdbchain, mappings[j].pdbfile); - } - } - } + highlightStructure((StructureListener) listener, seq, seqPos); } else { - if (relaySeqMappings && hasSequenceListeners - && listener instanceof SequenceListener) + if (listener instanceof SequenceListener) { - // DEBUG - // System.err.println("relay Seq " + seq.getDisplayId(false) + " " + - // index); - - if (results == null) + final SequenceListener seqListener = (SequenceListener) listener; + if (hasSequenceListeners + && seqListener.getVamsasSource() != source) { - results = new SearchResults(); - if (index >= seq.getStart() && index <= seq.getEnd()) + if (relaySeqMappings) { - // construct highlighted sequence list - - if (seqmappings != null) + if (results == null) { - Enumeration e = seqmappings.elements(); - while (e.hasMoreElements()) - - { - ((AlignedCodonFrame) e.nextElement()).markMappedRegion( - seq, index, results); - } + results = MappingUtils.buildSearchResults(seq, seqPos, + seqmappings); } - // hasSequenceListeners = results.getSize() > 0; if (handlingVamsasMo) { - // maybe have to resolve seq to a dataset seqeunce... - // add in additional direct sequence and/or dataset sequence - // highlighting - results.addResult(seq, index, index); + results.addResult(seq, seqPos, seqPos); + + } + if (!results.isEmpty()) + { + seqListener.highlightSequence(results); } } } - if (hasSequenceListeners) - { - ((SequenceListener) listener).highlightSequence(results); - } } else if (listener instanceof VamsasListener && !handlingVamsasMo) { - // DEBUG - // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " - // " + - // index); - // pass the mouse over and absolute position onto the - // VamsasListener(s) - ((VamsasListener) listener).mouseOver(seq, indexpos, source); + ((VamsasListener) listener).mouseOverSequence(seq, indexpos, + source); } else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos); + indexpos, seqPos); } } } } /** + * Send suitable messages to a StructureListener to highlight atoms + * corresponding to the given sequence position(s) + * + * @param sl + * @param seq + * @param positions + */ + public void highlightStructure(StructureListener sl, SequenceI seq, + int... positions) + { + if (!sl.isListeningFor(seq)) + { + return; + } + int atomNo; + List atoms = new ArrayList(); + for (StructureMapping sm : mappings) + { + if (sm.sequence == seq + || sm.sequence == seq.getDatasetSequence() + || (sm.sequence.getDatasetSequence() != null && sm.sequence + .getDatasetSequence() == seq.getDatasetSequence())) + { + for (int index : positions) + { + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm + .getPDBResNum(index), atomNo)); + } + } + } + } + sl.highlightAtoms(atoms); + } + + /** * true if a mouse over event from an external (ie Vamsas) source is being * handled */ @@ -825,119 +1039,141 @@ public class StructureSelectionManager public StructureMapping[] getMapping(String pdbfile) { - Vector tmp = new Vector(); - if (mappings != null) + List tmp = new ArrayList(); + for (StructureMapping sm : mappings) { - for (int i = 0; i < mappings.length; i++) + if (sm.pdbfile.equals(pdbfile)) { - if (mappings[i].pdbfile.equals(pdbfile)) - { - tmp.addElement(mappings[i]); - } + tmp.add(sm); } } - StructureMapping[] ret = new StructureMapping[tmp.size()]; - for (int i = 0; i < tmp.size(); i++) - { - ret[i] = (StructureMapping) tmp.elementAt(i); - } - - return ret; + 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) { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < mappings.length; i++) + if (pdbfile == null || seqs == null || seqs.isEmpty()) + { + return ""; + } + + StringBuilder sb = new StringBuilder(64); + for (StructureMapping sm : mappings) { - if (mappings[i].pdbfile.equals(pdbfile)) + if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence)) { - sb.append(mappings[i].mappingDetails); + 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(); } - private int[] seqmappingrefs = null; // refcount for seqmappings elements - - private synchronized void modifySeqMappingList(boolean add, - AlignedCodonFrame[] codonFrames) + /** + * Remove the given mapping + * + * @param acf + */ + public void deregisterMapping(AlignedCodonFrame acf) { - if (!add && (seqmappings == null || seqmappings.size() == 0)) + if (acf != null) { - return; - } - if (seqmappings == null) - { - seqmappings = new Vector(); + boolean removed = seqmappings.remove(acf); + if (removed && seqmappings.isEmpty()) + { // debug + System.out.println("All mappings removed"); + } } - if (codonFrames != null && codonFrames.length > 0) + } + + /** + * Add each of the given codonFrames to the stored set, if not aready present. + * + * @param mappings + */ + public void registerMappings(List mappings) + { + if (mappings != null) { - for (int cf = 0; cf < codonFrames.length; cf++) + for (AlignedCodonFrame acf : mappings) { - if (seqmappings.contains(codonFrames[cf])) - { - if (add) - { - seqmappingrefs[seqmappings.indexOf(codonFrames[cf])]++; - } - else - { - if (--seqmappingrefs[seqmappings.indexOf(codonFrames[cf])] <= 0) - { - int pos = seqmappings.indexOf(codonFrames[cf]); - int[] nr = new int[seqmappingrefs.length - 1]; - if (pos > 0) - { - System.arraycopy(seqmappingrefs, 0, nr, 0, pos); - } - if (pos < seqmappingrefs.length - 1) - { - System.arraycopy(seqmappingrefs, pos + 1, nr, 0, - seqmappingrefs.length - pos - 2); - } - } - } - } - else - { - if (add) - { - seqmappings.addElement(codonFrames[cf]); - - int[] nsr = new int[(seqmappingrefs == null) ? 1 - : seqmappingrefs.length + 1]; - if (seqmappingrefs != null && seqmappingrefs.length > 0) - { - System.arraycopy(seqmappingrefs, 0, nsr, 0, - seqmappingrefs.length); - } - nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1; - seqmappingrefs = nsr; - } - } + registerMapping(acf); } } } - public void removeMappings(AlignedCodonFrame[] codonFrames) + /** + * Add the given mapping to the stored set, unless already stored. + */ + public void registerMapping(AlignedCodonFrame acf) { - modifySeqMappingList(false, codonFrames); + if (acf != null) + { + if (!seqmappings.contains(acf)) + { + seqmappings.add(acf); + } + } } - public void addMappings(AlignedCodonFrame[] codonFrames) + /** + * Resets this object to its initial state by removing all registered + * listeners, codon mappings, PDB file mappings + */ + public void resetAll() { - modifySeqMappingList(true, codonFrames); + if (mappings != null) + { + 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(); + } } - Vector sel_listeners = new Vector(); - public void addSelectionListener(SelectionListener selecter) { if (!sel_listeners.contains(selecter)) { - sel_listeners.addElement(selecter); + sel_listeners.add(selecter); } } @@ -945,7 +1181,7 @@ public class StructureSelectionManager { if (sel_listeners.contains(toremove)) { - sel_listeners.removeElement(toremove); + sel_listeners.remove(toremove); } } @@ -953,18 +1189,11 @@ public class StructureSelectionManager jalview.datamodel.SequenceGroup selection, jalview.datamodel.ColumnSelection colsel, SelectionSource source) { - if (sel_listeners != null && sel_listeners.size() > 0) + for (SelectionListener slis : sel_listeners) { - Enumeration listeners = sel_listeners.elements(); - while (listeners.hasMoreElements()) + if (slis != source) { - SelectionListener slis = ((SelectionListener) listeners - .nextElement()); - if (slis != source) - { - slis.selection(selection, colsel, source); - } - ; + slis.selection(selection, colsel, source); } } } @@ -992,32 +1221,6 @@ public class StructureSelectionManager } } - public void finalize() throws Throwable - { - if (listeners != null) - { - listeners.clear(); - listeners = null; - } - if (pdbIdFileName != null) - { - pdbIdFileName.clear(); - pdbIdFileName = null; - } - if (sel_listeners != null) - { - sel_listeners.clear(); - sel_listeners = null; - } - if (view_listeners != null) - { - view_listeners.clear(); - view_listeners = null; - } - mappings = null; - seqmappingrefs = null; - } - /** * release all references associated with this manager provider * @@ -1041,7 +1244,6 @@ public class StructureSelectionManager } catch (Throwable x) { } - ; } } } @@ -1055,4 +1257,102 @@ public class StructureSelectionManager } } + public void addCommandListener(CommandListener cl) + { + if (!commandListeners.contains(cl)) + { + commandListeners.add(cl); + } + } + + public boolean hasCommandListener(CommandListener cl) + { + return this.commandListeners.contains(cl); + } + + public boolean removeCommandListener(CommandListener l) + { + return commandListeners.remove(l); + } + + /** + * Forward a command to any command listeners (except for the command's + * source). + * + * @param command + * the command to be broadcast (in its form after being performed) + * @param undo + * if true, the command was being 'undone' + * @param source + */ + public void commandPerformed(CommandI command, boolean undo, + VamsasSource source) + { + for (CommandListener listener : commandListeners) + { + listener.mirrorCommand(command, undo, this, source); + } + } + + /** + * Returns a new CommandI representing the given command as mapped to the + * given sequences. If no mapping could be made, or the command is not of a + * mappable kind, returns null. + * + * @param command + * @param undo + * @param mapTo + * @param gapChar + * @return + */ + public CommandI mapCommand(CommandI command, boolean undo, + final AlignmentI mapTo, char gapChar) + { + if (command instanceof EditCommand) + { + return MappingUtils.mapEditCommand((EditCommand) command, undo, + mapTo, gapChar, seqmappings); + } + else if (command instanceof OrderCommand) + { + return MappingUtils.mapOrderCommand((OrderCommand) command, undo, + mapTo, seqmappings); + } + return null; + } + + public IProgressIndicator getProgressIndicator() + { + return progressIndicator; + } + + public void setProgressIndicator(IProgressIndicator progressIndicator) + { + this.progressIndicator = progressIndicator; + } + + public long getProgressSessionId() + { + return progressSessionId; + } + + public void setProgressSessionId(long progressSessionId) + { + this.progressSessionId = progressSessionId; + } + + public void setProgressBar(String message) + { + if (progressIndicator == null) + { + return; + } + progressIndicator.setProgressBar(message, progressSessionId); + } + + public List getSequenceMappings() + { + return seqmappings; + } + }