X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=9d06aef88ff0dfd78a57460e1f76dfa5e0d70740;hb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;hp=9dd730c223e7bf5ff02e29ba3adad69583ce1484;hpb=bd817b546aad8c7456fd5682a890eb79faeb5deb;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 9dd730c..9d06aef 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -21,7 +21,6 @@ package jalview.structure; import jalview.analysis.AlignSeq; -import jalview.api.AlignmentViewPanel; import jalview.api.StructureSelectionManagerProvider; import jalview.commands.CommandI; import jalview.commands.EditCommand; @@ -33,11 +32,13 @@ import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceI; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; +import jalview.gui.IProgressIndicator; 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; @@ -70,10 +71,16 @@ public class StructureSelectionManager private boolean addTempFacAnnot = false; + private IProgressIndicator progressIndicator; + + private SiftsClient siftsClient = null; + + private long progressSessionId; + /* * Set of any registered mappings between (dataset) sequences. */ - Set seqmappings = new LinkedHashSet(); + public Set seqmappings = new LinkedHashSet(); private List commandListeners = new ArrayList(); @@ -327,9 +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 @@ -339,7 +346,8 @@ public class StructureSelectionManager * @return null or the structure data parsed as a pdb file */ synchronized public PDBfile setMapping(boolean forStructureView, - SequenceI[] sequence, String[] targetChains, String pdbFile, + SequenceI[] sequenceArray, String[] targetChainIds, + String pdbFile, String protocol) { /* @@ -349,7 +357,7 @@ public class StructureSelectionManager boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) { - for (SequenceI sq : sequence) + for (SequenceI sq : sequenceArray) { SequenceI ds = sq; while (ds.getDatasetSequence() != null) @@ -373,10 +381,12 @@ public class StructureSelectionManager } } PDBfile pdb = null; + boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, pdbFile, protocol); + if (pdb.id != null && pdb.id.trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { @@ -388,36 +398,48 @@ 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; - final SequenceI seq = sequence[s]; - 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 (seq.getName().indexOf("|") > -1) { - targetChain = seq.getName().substring( + targetChainId = seq.getName().substring( seq.getName().lastIndexOf("|") + 1); - if (targetChain.length() > 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 = ""; } /* @@ -431,7 +453,7 @@ public class StructureSelectionManager boolean first = true; for (PDBChain chain : pdb.chains) { - 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. @@ -447,7 +469,7 @@ public class StructureSelectionManager // 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; @@ -460,89 +482,157 @@ public class StructureSelectionManager { continue; } - 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) + + if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) { - @Override - public void print(String x) - { - mappingDetails.append(x); - } + pdbFile = "INLINE" + pdb.id; + } - @Override - public void println() + ArrayList seqToStrucMapping = new ArrayList(); + if (isMapUsingSIFTs) + { + setProgressBar(null); + setProgressBar("Obtaining mapping with SIFTS"); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + if (targetChainId != null && !targetChainId.trim().isEmpty()) { - mappingDetails.append(NEWLINE); + StructureMapping mapping = getStructureMapping(seq, pdbFile, + targetChainId, pdb, maxChain, sqmpping, maxAlignseq); + seqToStrucMapping.add(mapping); } - }; - - 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.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(seq, null); - - // allocate enough slots to store the mapping from positions in - // sequence[s] to the associated chain - int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2]; - int resNum = -10000; - int index = 0; - - do - { - Atom tmp = maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + else { - resNum = tmp.resNumber; - if (tmp.alignmentMapping >= -1) + for (PDBChain chain : pdb.chains) { - // 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; + StructureMapping mapping = getStructureMapping(seq, pdbFile, + chain.id, pdb, chain, sqmpping, maxAlignseq); + seqToStrucMapping.add(mapping); } } - - index++; - } while (index < maxChain.atoms.size()); - - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + } + else { - pdbFile = "INLINE" + pdb.id; + setProgressBar(null); + setProgressBar("Obtaining mapping with NW alignment"); + seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq)); } - StructureMapping newMapping = new StructureMapping(seq, pdbFile, - pdb.id, maxChainId, mapping, mappingDetails.toString()); + if (forStructureView) { - mappings.add(newMapping); + mappings.addAll(seqToStrucMapping); } - maxChain.transferResidueAnnotation(newMapping, sqmpping); } - // /////// - return pdb; } + private StructureMapping getStructureMapping(SequenceI seq, + String pdbFile, String targetChainId, PDBfile pdb, + PDBChain maxChain, jalview.datamodel.Mapping sqmpping, + AlignSeq maxAlignseq) + { + String maxChainId = targetChainId; + try + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChainId); + PDBChain chain = pdb.findChain(targetChainId); + if (chain != null) + { + chain.transferResidueAnnotation(curChainMapping, sqmpping); + } + return curChainMapping; + } catch (SiftsException e) + { + System.err.println(e.getMessage()); + System.err.println(">>> Now switching mapping with NW alignment..."); + setProgressBar(null); + setProgressBar(">>> Now switching mapping with NW alignment..."); + return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, + maxAlignseq); + } + } + + private StructureMapping 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; + 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) + { + 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); + return nwMapping; + } + public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl); @@ -722,7 +812,7 @@ public class StructureSelectionManager { results = MappingUtils.buildSearchResults(seq, index, seqmappings); - } + } if (handlingVamsasMo) { results.addResult(seq, index, index); @@ -912,31 +1002,13 @@ public class StructureSelectionManager } /** - * Deregister each mapping in the set, unless there is still an alignment that - * holds a reference to it. Note we do not update the set itself, as it may be - * shared with an alignment view which is still open. - * - * @param set - */ - public void deregisterMappings(Set set) - { - if (set != null) - { - for (AlignedCodonFrame acf : set) - { - deregisterMapping(acf); - } - } - } - - /** - * Remove the given mapping provided no alignment holds a reference to it + * Remove the given mapping * * @param acf */ public void deregisterMapping(AlignedCodonFrame acf) { - if (noReferencesTo(acf)) + if (acf != null) { boolean removed = seqmappings.remove(acf); if (removed && seqmappings.isEmpty()) @@ -947,33 +1019,6 @@ public class StructureSelectionManager } /** - * Answers true if no alignment holds a reference to the given mapping - * - * @param acf - * @return - */ - protected boolean noReferencesTo(AlignedCodonFrame acf) - { - AlignFrame[] frames = Desktop.getAlignFrames(); - if (frames == null) - { - return true; - } - for (AlignFrame af : frames) - { - for (AlignmentViewPanel ap : af.getAlignPanels()) - { - AlignmentI al = ap.getAlignment(); - if (al != null && al.getCodonFrames().contains(acf)) - { - return false; - } - } - } - return true; - } - - /** * Add each of the given codonFrames to the stored set, if not aready present. * * @param set @@ -1194,4 +1239,30 @@ public class StructureSelectionManager } 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) + { + progressIndicator.setProgressBar(message, progressSessionId); + } + }