X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=cf604901294225357148143b1bca115e6325426b;hb=43d326c3a7616aedecfce6f7980b3831ec25243a;hp=ed5ee2d4cb4afb58a51d8695075c536cdc1f76f5;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index ed5ee2d..cf60490 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -38,6 +38,8 @@ 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; @@ -49,9 +51,12 @@ 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(); @@ -71,7 +76,7 @@ public class StructureSelectionManager * Reference counters for the above mappings. Remove mappings when ref count * goes to zero. */ - Map seqMappingRefCounts = new HashMap(); + private Map seqMappingRefCounts = new HashMap(); private List commandListeners = new ArrayList(); @@ -163,8 +168,9 @@ 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) { @@ -201,8 +207,11 @@ 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 { @@ -308,7 +317,7 @@ 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); @@ -332,15 +341,14 @@ 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)) { @@ -359,8 +367,7 @@ 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; } @@ -368,10 +375,11 @@ 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)) { @@ -387,15 +395,16 @@ 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) @@ -414,14 +423,17 @@ 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) { @@ -429,12 +441,13 @@ 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))) @@ -450,11 +463,13 @@ 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 @@ -466,35 +481,40 @@ 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)); - maxChain.makeExactMapping(maxAlignseq, sequence[s]); + 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, 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; @@ -509,9 +529,8 @@ 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); @@ -542,30 +561,30 @@ 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(); @@ -581,53 +600,75 @@ public class StructureSelectionManager } } + /** + * 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; } - 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(); - } - for (StructureMapping sm : mappings) + 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())) { - if (sm.pdbfile.equals(pdbfile) && sm.pdbchain.equals(chain)) + int indexpos = sm.getSeqPos(atom.getPdbResNum()); + if (lastipos != indexpos && lastseq != sm.sequence) { - indexpos = sm.getSeqPos(pdbResNum); - if (lastipos != indexpos && lastseq != sm.sequence) + results.addResult(sm.sequence, indexpos, indexpos); + lastipos = indexpos; + lastseq = sm.sequence; + // construct highlighted sequence list + for (AlignedCodonFrame acf : seqmappings) { - results.addResult(sm.sequence, indexpos, indexpos); - lastipos = indexpos; - lastseq = sm.sequence; - // construct highlighted sequence list - for (AlignedCodonFrame acf : seqmappings) - { - acf.markMappedRegion(sm.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); } } } @@ -680,13 +721,16 @@ public class StructureSelectionManager { results = MappingUtils.buildSearchResults(seq, index, seqmappings); - } + } if (handlingVamsasMo) { results.addResult(seq, index, index); } - seqListener.highlightSequence(results); + if (!results.isEmpty()) + { + seqListener.highlightSequence(results); + } } } } @@ -698,7 +742,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos); + indexpos, index); } } } @@ -715,6 +759,10 @@ 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) @@ -821,25 +869,43 @@ 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(); } @@ -881,6 +947,10 @@ public class StructureSelectionManager { seqmappings.remove(acf); seqMappingRefCounts.remove(acf); + if (seqmappings.isEmpty()) + { // debug + System.out.println("All mappings removed"); + } } } } @@ -922,6 +992,50 @@ public class StructureSelectionManager } } + /** + * Resets this object to its initial state by removing all registered + * listeners, codon mappings, PDB file mappings + */ + public void resetAll() + { + if (mappings != null) + { + mappings.clear(); + } + if (seqmappings != null) + { + seqmappings.clear(); + } + if (seqMappingRefCounts != null) + { + seqMappingRefCounts.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(); + } + } + public void addSelectionListener(SelectionListener selecter) { if (!sel_listeners.contains(selecter)) @@ -1073,4 +1187,20 @@ public class StructureSelectionManager } return null; } + + /** + * Returns the reference count for a mapping + * + * @param acf + * @return + */ + protected int getMappingReferenceCount(AlignedCodonFrame acf) + { + if (seqMappingRefCounts == null) + { + return 0; + } + Integer count = seqMappingRefCounts.get(acf); + return (count == null ? 0 : count.intValue()); + } }