X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=678bf3bf26796890b657f9a7c1c648c4cfc90e50;hb=e57ac4e703658ff81d7e172222e718ff7611e96e;hp=9702159e713f550792fe44321109e55411aff26c;hpb=a7ea1ba47dae32481aa6390a29cef6c7c5a403c4;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 9702159..678bf3b 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -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; @@ -50,6 +35,26 @@ import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; 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.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 { @@ -68,13 +73,7 @@ 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(); @@ -166,8 +165,9 @@ 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) { @@ -204,8 +204,11 @@ 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 { @@ -311,7 +314,7 @@ 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); @@ -324,9 +327,9 @@ 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 @@ -335,19 +338,19 @@ 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[] 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) @@ -362,8 +365,7 @@ 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; } @@ -371,10 +373,14 @@ public class StructureSelectionManager } } } + PDBfile pdb = null; + boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); + SiftsClient siftsClient = 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)) { @@ -386,61 +392,78 @@ public class StructureSelectionManager 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]; + 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.chains) { - 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; @@ -453,79 +476,148 @@ 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.id; + } - @Override - public void println() - { - mappingDetails.append("\n"); - } - }; - - 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 + ArrayList seqToStrucMapping = null; + if (isMapUsingSIFTs) { - Atom tmp = maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + try { - resNum = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + seqToStrucMapping = new ArrayList(); + if (targetChainId != null && !targetChainId.trim().isEmpty()) + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChainId); + seqToStrucMapping.add(curChainMapping); + maxChainId = targetChainId; + PDBChain chain = pdb.findChain(targetChainId); + if (chain != null) + { + chain.transferResidueAnnotation(curChainMapping, sqmpping); + } + } + else + { + for (PDBChain chain : pdb.chains) + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, chain.id); + seqToStrucMapping.add(curChainMapping); + maxChainId = chain.id; + chain.transferResidueAnnotation(curChainMapping, sqmpping); + } + } + } catch (SiftsException e) + { + e.printStackTrace(); + System.err + .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment"); + seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq); } - - index++; - } while (index < maxChain.atoms.size()); - - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + } + else { - pdbFile = "INLINE" + pdb.id; + seqToStrucMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, + maxAlignseq); } - StructureMapping newMapping = new StructureMapping(sequence[s], - pdbFile, pdb.id, maxChainId, mapping, - mappingDetails.toString()); + if (forStructureView) { - mappings.add(newMapping); + // mappings.add(seqToStrucMapping); + mappings.addAll(seqToStrucMapping); } - maxChain.transferResidueAnnotation(newMapping, sqmpping); } - // /////// - return pdb; } + private ArrayList getNWMappings(SequenceI seq, + String pdbFile, + String maxChainId, PDBChain maxChain, PDBfile 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; + + do + { + Atom tmp = maxChain.atoms.elementAt(index); + if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + { + resNum = tmp.resNumber; + if (tmp.alignmentMapping >= -1) + { + // TODO (JAL-1836) address root cause: negative residue no in PDB + // file + mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber, + tmp.atomIndex }); + } + } + + index++; + } while (index < maxChain.atoms.size()); + + StructureMapping nwMapping = new StructureMapping(seq, pdbFile, + pdb.id, maxChainId, mapping, mappingDetails.toString()); + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ArrayList mappings = new ArrayList(); + mappings.add(nwMapping); + return mappings; + } + public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl); @@ -545,30 +637,30 @@ 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(); @@ -711,7 +803,10 @@ public class StructureSelectionManager results.addResult(seq, index, index); } - seqListener.highlightSequence(results); + if (!results.isEmpty()) + { + seqListener.highlightSequence(results); + } } } } @@ -723,7 +818,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos); + indexpos, index); } } } @@ -740,6 +835,10 @@ 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) @@ -846,11 +945,11 @@ 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()]); } @@ -888,80 +987,89 @@ public class StructureSelectionManager } /** - * 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(); } }