X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=83a055e7392ba1c5063701e20abd806ca54cf7dd;hb=f2eadfd123e9540bd9af1e5c0ff73f6080ec03c7;hp=b3b57083cbba8c9080131449dbdfa1413bedfcac;hpb=776ce4a23c079b7a4baf9f49c10a2e3776842bf0;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index b3b5708..83a055e 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -29,11 +29,16 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; import jalview.gui.IProgressIndicator; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.StructureFile; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.ws.sifts.SiftsClient; @@ -47,10 +52,8 @@ 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; @@ -73,12 +76,14 @@ public class StructureSelectionManager private IProgressIndicator progressIndicator; + private SiftsClient siftsClient = null; + private long progressSessionId; /* * Set of any registered mappings between (dataset) sequences. */ - public Set seqmappings = new LinkedHashSet(); + private List seqmappings = new ArrayList(); private List commandListeners = new ArrayList(); @@ -156,8 +161,8 @@ public class StructureSelectionManager } else { - System.err.println("reportMapping: There are " + mappings.size() - + " mappings."); + System.err.println( + "reportMapping: There are " + mappings.size() + " mappings."); int i = 0; for (StructureMapping sm : mappings) { @@ -209,9 +214,8 @@ public class StructureSelectionManager { if (instances != null) { - throw new Error( - MessageManager - .getString("error.implementation_error_structure_selection_manager_null"), + throw new Error(MessageManager.getString( + "error.implementation_error_structure_selection_manager_null"), new NullPointerException(MessageManager .getString("exception.ssm_context_is_null"))); } @@ -319,8 +323,8 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + synchronized public StructureFile setMapping(SequenceI[] sequence, + String[] targetChains, String pdbFile, DataSourceType protocol) { return setMapping(true, sequence, targetChains, pdbFile, protocol); } @@ -336,17 +340,18 @@ public class StructureSelectionManager * - one or more sequences to be mapped to pdbFile * @param targetChainIds * - optional chain specification for mapping each sequence to pdb - * (may be nill, individual elements may be nill) + * (may be nill, individual elements may be nill) - JBPNote: JAL-2693 + * - this should be List>, empty lists indicate no + * predefined mappings * @param pdbFile * - structure data resource - * @param protocol + * @param sourceType * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(boolean forStructureView, + synchronized public StructureFile setMapping(boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, - String pdbFile, - String protocol) + String pdbFile, DataSourceType sourceType) { /* * There will be better ways of doing this in the future, for now we'll use @@ -378,19 +383,21 @@ public class StructureSelectionManager } } } - PDBfile pdb = null; + StructureFile pdb = null; boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); - SiftsClient siftsClient = null; try { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); + sourceType = AppletFormatAdapter.checkProtocol(pdbFile); + pdb = new JmolParser(pdbFile, sourceType); - if (pdb.id != null && pdb.id.trim().length() > 0 - && AppletFormatAdapter.FILE.equals(protocol)) + if (pdb.getId() != null && pdb.getId().trim().length() > 0 + && DataSourceType.FILE == sourceType) { - registerPDBFile(pdb.id.trim(), pdbFile); + registerPDBFile(pdb.getId().trim(), pdbFile); } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + } catch (Exception ex) { ex.printStackTrace(); @@ -414,6 +421,12 @@ public class StructureSelectionManager { boolean infChain = true; final SequenceI seq = sequenceArray[s]; + SequenceI ds = seq; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + if (targetChainIds != null && targetChainIds[s] != null) { infChain = false; @@ -421,8 +434,8 @@ public class StructureSelectionManager } else if (seq.getName().indexOf("|") > -1) { - targetChainId = seq.getName().substring( - seq.getName().lastIndexOf("|") + 1); + targetChainId = seq.getName() + .substring(seq.getName().lastIndexOf("|") + 1); if (targetChainId.length() > 1) { if (targetChainId.trim().length() == 0) @@ -445,12 +458,15 @@ public class StructureSelectionManager * Attempt pairwise alignment of the sequence with each chain in the PDB, * and remember the highest scoring chain */ - int max = -10; + float max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; boolean first = true; - for (PDBChain chain : pdb.chains) + List maximalChain = new ArrayList<>(); + List maximalAlignseqs = new ArrayList<>(); + List maximalChainIds = new ArrayList<>(); + for (PDBChain chain : pdb.getChains()) { if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) && !infChain) @@ -467,14 +483,39 @@ public class StructureSelectionManager // as.calcScoreMatrix(); // as.traceAlignment(); - if (first || as.maxscore > max - || (as.maxscore == max && chain.id.equals(targetChainId))) + if (targetChainId.length() > 0 && chain.id.equals(targetChainId)) { - first = false; + // Don't care - just pick this chain as the mapping maxChain = chain; max = as.maxscore; maxAlignseq = as; maxChainId = chain.id; + // if targetChainId is specified then it is expected to be unique, so + // precisely one maximal chain will be added + maximalChainIds.add(chain.id); + maximalChain.add(chain); + maximalAlignseqs.add(as); + } + else + { + // select chains with maximal mappings to this sequence + if (first || as.maxscore > max) + { + // clear out old maximal mappings (if any) + max = as.maxscore; + maximalChain.clear(); + maxChain = chain; + max = as.maxscore; + maxAlignseq = as; + maxChainId = chain.id; + first = false; + } + if (as.maxscore == max) + { + maximalChainIds.add(chain.id); + maximalChain.add(chain); + maximalAlignseqs.add(as); + } } } if (maxChain == null) @@ -482,81 +523,164 @@ public class StructureSelectionManager continue; } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (sourceType == DataSourceType.PASTE) { - pdbFile = "INLINE" + pdb.id; + pdbFile = "INLINE" + pdb.getId(); } - ArrayList seqToStrucMapping = null; - if (isMapUsingSIFTs) + List seqToStrucMapping = new ArrayList<>(); + if (isMapUsingSIFTs && seq.isProtein()) { setProgressBar(null); - setProgressBar("Obtaining mapping with SIFTS"); - try + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts")); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + if (targetChainId != null && !targetChainId.trim().isEmpty()) + { + 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, + maximalChainIds, maximalChain, pdb, maximalAlignseqs) + .get(0); + 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)); + } + } + else { - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - seqToStrucMapping = new ArrayList(); - if (targetChainId != null && !targetChainId.trim().isEmpty()) + List foundSiftsMappings = new ArrayList<>(); + for (PDBChain chain : pdb.getChains()) { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, targetChainId); - seqToStrucMapping.add(curChainMapping); - maxChainId = targetChainId; - PDBChain chain = pdb.findChain(targetChainId); - if (chain != null) + try { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + 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 { - for (PDBChain chain : pdb.chains) - { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, chain.id); - seqToStrucMapping.add(curChainMapping); - maxChainId = chain.id; - chain.transferResidueAnnotation(curChainMapping, sqmpping); - } + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maximalChainIds, maximalChain, pdb, maximalAlignseqs) + .get(0); + seqToStrucMapping.add(nwMapping); + maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } - } 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..."); - seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId, - maxChain, pdb, maxAlignseq); } } else { setProgressBar(null); - setProgressBar("Obtaining mapping with NW alignment"); - seqToStrucMapping = getNWMappings(seq, pdbFile, - maxChainId, maxChain, pdb, - maxAlignseq); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment")); + List nwMapping = getNWMappings(seq, pdbFile, + maximalChainIds, maximalChain, pdb, maximalAlignseqs); + seqToStrucMapping.addAll(nwMapping); + for (PDBChain mc : maximalChain) + { + ds.addPDBId(mc.sequence.getAllPDBEntries().get(0)); + } + ; + } if (forStructureView) { - // mappings.add(seqToStrucMapping); mappings.addAll(seqToStrucMapping); } } return pdb; } - private ArrayList getNWMappings(SequenceI seq, + public void addStructureMapping(StructureMapping sm) + { + mappings.add(sm); + } + + /** + * 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; + } + + private List getNWMappings(SequenceI seq, String pdbFile, - String maxChainId, PDBChain maxChain, PDBfile pdb, - AlignSeq maxAlignseq) + List maximalChainId, List maximalChain, + StructureFile pdb, List maximalAlignseq) { + List nwMappings = new ArrayList(); + for (int ch = 0; ch < maximalChain.size(); ch++) + { + String maxChainId = maximalChainId.get(ch); + PDBChain maxChain = maximalChain.get(ch); + AlignSeq maxAlignseq = maximalAlignseq.get(ch); final StringBuilder mappingDetails = new StringBuilder(128); - mappingDetails.append(NEWLINE).append( - "Sequence \u27f7 Structure mapping details"); + mappingDetails.append(NEWLINE) + .append("Sequence \u27f7 Structure mapping details"); mappingDetails.append(NEWLINE); mappingDetails .append("Method: inferred with Needleman & Wunsch alignment"); @@ -588,11 +712,12 @@ public class StructureSelectionManager .append(" "); mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); mappingDetails.append(NEWLINE).append("SEQ start/end "); - mappingDetails.append( - String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1))) + mappingDetails + .append(String + .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1))) .append(" "); - mappingDetails.append(String.valueOf(maxAlignseq.seq1end - + (seq.getStart() - 1))); + mappingDetails.append( + String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1))); mappingDetails.append(NEWLINE); maxChain.makeExactMapping(maxAlignseq, seq); jalview.datamodel.Mapping sqmpping = maxAlignseq @@ -602,19 +727,21 @@ public class StructureSelectionManager HashMap mapping = new HashMap(); int resNum = -10000; int index = 0; + char insCode = ' '; do { Atom tmp = maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + if ((resNum != tmp.resNumber || insCode != tmp.insCode) + && tmp.alignmentMapping != -1) { resNum = tmp.resNumber; + insCode = tmp.insCode; 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 }); + mapping.put(tmp.alignmentMapping + 1, + new int[] + { tmp.resNumber, tmp.atomIndex }); } } @@ -622,11 +749,11 @@ public class StructureSelectionManager } while (index < maxChain.atoms.size()); StructureMapping nwMapping = new StructureMapping(seq, pdbFile, - pdb.id, maxChainId, mapping, mappingDetails.toString()); + pdb.getId(), maxChainId, mapping, mappingDetails.toString()); maxChain.transferResidueAnnotation(nwMapping, sqmpping); - ArrayList mappings = new ArrayList(); - mappings.add(nwMapping); - return mappings; + nwMappings.add(nwMapping); + } + return nwMappings; } public void removeStructureViewerListener(Object svl, String[] pdbfiles) @@ -661,7 +788,7 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - for (String pdbfile : sl.getPdbFile()) + for (String pdbfile : sl.getStructureFiles()) { pdbs.remove(pdbfile); } @@ -694,7 +821,8 @@ public class StructureSelectionManager * @param chain * @param pdbfile */ - public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) + public void mouseOverStructure(int pdbResNum, String chain, + String pdbfile) { AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0); List atoms = Collections.singletonList(atomSpec); @@ -726,7 +854,29 @@ public class StructureSelectionManager return; } - SearchResults results = new SearchResults(); + SearchResultsI results = findAlignmentPositionsForStructurePositions( + atoms); + for (Object li : listeners) + { + if (li instanceof SequenceListener) + { + ((SequenceListener) li).highlightSequence(results); + } + } + } + + /** + * Constructs a SearchResults object holding regions (if any) in the Jalview + * alignment which have a mapping to the structure viewer positions in the + * supplied list + * + * @param atoms + * @return + */ + public SearchResultsI findAlignmentPositionsForStructurePositions( + List atoms) + { + SearchResultsI results = new SearchResults(); for (AtomSpec atom : atoms) { SequenceI lastseq = null; @@ -751,13 +901,7 @@ public class StructureSelectionManager } } } - for (Object li : listeners) - { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } - } + return results; } /** @@ -767,19 +911,19 @@ public class StructureSelectionManager * 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.isEmpty(); - SearchResults results = null; - if (index == -1) + SearchResultsI results = null; + if (seqPos == -1) { - index = seq.findPosition(indexpos); + seqPos = seq.findPosition(indexpos); } for (int i = 0; i < listeners.size(); i++) { @@ -792,7 +936,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -806,12 +950,12 @@ public class StructureSelectionManager { if (results == null) { - results = MappingUtils.buildSearchResults(seq, index, + results = MappingUtils.buildSearchResults(seq, seqPos, seqmappings); } if (handlingVamsasMo) { - results.addResult(seq, index, index); + results.addResult(seq, seqPos, seqPos); } if (!results.isEmpty()) @@ -829,7 +973,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -837,14 +981,14 @@ public class StructureSelectionManager /** * Send suitable messages to a StructureListener to highlight atoms - * corresponding to the given sequence position. + * corresponding to the given sequence position(s) * * @param sl * @param seq - * @param index + * @param positions */ - protected void highlightStructure(StructureListener sl, SequenceI seq, - int index) + public void highlightStructure(StructureListener sl, SequenceI seq, + int... positions) { if (!sl.isListeningFor(seq)) { @@ -854,14 +998,19 @@ public class StructureSelectionManager List atoms = new ArrayList(); for (StructureMapping sm : mappings) { - if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()) + if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence() + || (sm.sequence.getDatasetSequence() != null && sm.sequence + .getDatasetSequence() == seq.getDatasetSequence())) { - atomNo = sm.getAtomNum(index); - - if (atomNo > 0) + for (int index : positions) { - atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm - .getPDBResNum(index), atomNo)); + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, + sm.getPDBResNum(index), atomNo)); + } } } } @@ -1017,13 +1166,13 @@ public class StructureSelectionManager /** * Add each of the given codonFrames to the stored set, if not aready present. * - * @param set + * @param mappings */ - public void registerMappings(Set set) + public void registerMappings(List mappings) { - if (set != null) + if (mappings != null) { - for (AlignedCodonFrame acf : set) + for (AlignedCodonFrame acf : mappings) { registerMapping(acf); } @@ -1102,13 +1251,14 @@ public class StructureSelectionManager public synchronized void sendSelection( jalview.datamodel.SequenceGroup selection, - jalview.datamodel.ColumnSelection colsel, SelectionSource source) + jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { for (SelectionListener slis : sel_listeners) { if (slis != source) { - slis.selection(selection, colsel, source); + slis.selection(selection, colsel, hidden, source); } } } @@ -1225,8 +1375,8 @@ public class StructureSelectionManager { if (command instanceof EditCommand) { - return MappingUtils.mapEditCommand((EditCommand) command, undo, - mapTo, gapChar, seqmappings); + return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo, + gapChar, seqmappings); } else if (command instanceof OrderCommand) { @@ -1258,7 +1408,16 @@ public class StructureSelectionManager public void setProgressBar(String message) { + if (progressIndicator == null) + { + return; + } progressIndicator.setProgressBar(message, progressSessionId); } + public List getSequenceMappings() + { + return seqmappings; + } + }