X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=14cef12766585973b6b792ee267f362ea42d103b;hb=a4d145722369877a3cb8bfe2f23c1c405891cb6b;hp=00b3143bf4585b979d7a78f9e538cf9f57c6d18e;hpb=4da7d6ec8ef5ff030c6d06d37a099da2d92d7246;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 00b3143..14cef12 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; @@ -61,7 +66,7 @@ public class StructureSelectionManager static IdentityHashMap instances; - private List mappings = new ArrayList(); + private List mappings = new ArrayList<>(); private boolean processSecondaryStructure = false; @@ -69,20 +74,16 @@ 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. */ - private List seqmappings = new ArrayList(); + private List seqmappings = new ArrayList<>(); - private List commandListeners = new ArrayList(); + private List commandListeners = new ArrayList<>(); - private List sel_listeners = new ArrayList(); + private List sel_listeners = new ArrayList<>(); /** * @return true if will try to use external services for processing secondary @@ -156,8 +157,8 @@ 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) { @@ -170,9 +171,9 @@ 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 */ - Map pdbIdFileName = new HashMap(); + Map pdbIdFileName = new HashMap<>(); - Map pdbFileNameId = new HashMap(); + Map pdbFileNameId = new HashMap<>(); public void registerPDBFile(String idForFile, String absoluteFile) { @@ -209,9 +210,8 @@ 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"))); } @@ -224,7 +224,7 @@ public class StructureSelectionManager } if (instances == null) { - instances = new java.util.IdentityHashMap(); + instances = new java.util.IdentityHashMap<>(); } StructureSelectionManager instance = instances.get(context); if (instance == null) @@ -319,15 +319,44 @@ 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, + IProgressIndicator progress) + { + return computeMapping(true, sequence, targetChains, pdbFile, protocol, + progress); + } + + /** + * Import a single structure file and register sequence structure mappings for + * broadcasting colouring, mouseovers and selection events (convenience + * wrapper). + * + * @param forStructureView + * when true, record the mapping for use in mouseOvers + * @param sequence + * - one or more sequences to be mapped to pdbFile + * @param targetChains + * - optional chain specification for mapping each sequence to pdb + * (may be nill, individual elements may be nill) + * @param pdbFile + * - structure data resource + * @param protocol + * - how to resolve data from resource + * @return null or the structure data parsed as a pdb file + */ + synchronized public StructureFile setMapping(boolean forStructureView, + SequenceI[] sequenceArray, String[] targetChainIds, + String pdbFile, DataSourceType sourceType) { - return setMapping(true, sequence, targetChains, pdbFile, protocol); + return computeMapping(forStructureView, sequenceArray, targetChainIds, + pdbFile, sourceType, null); } /** * create sequence structure mappings between each sequence and the given - * pdbFile (retrieved via the given protocol). + * pdbFile (retrieved via the given protocol). Either constructs a mapping + * using NW alignment or derives one from any available SIFTS mapping data. * * @param forStructureView * when true, record the mapping for use in mouseOvers @@ -336,21 +365,24 @@ 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 + * @param IProgressIndicator + * reference to UI component that maintains a progress bar for the + * mapping operation * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(boolean forStructureView, - SequenceI[] sequenceArray, String[] targetChainIds, - String pdbFile, - String protocol) + synchronized public StructureFile computeMapping( + boolean forStructureView, SequenceI[] sequenceArray, + String[] targetChainIds, String pdbFile, DataSourceType sourceType, + IProgressIndicator progress) { - /* - * There will be better ways of doing this in the future, for now we'll use - * the tried and tested MCview pdb mapping + long progressSessionId = System.currentTimeMillis() * 3; */ boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) @@ -378,18 +410,21 @@ public class StructureSelectionManager } } } - PDBfile pdb = null; + StructureFile pdb = null; boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); + sourceType = AppletFormatAdapter.checkProtocol(pdbFile); + pdb = new JmolParser(pdbFile, sourceType); if (pdb.getId() != null && pdb.getId().trim().length() > 0 - && AppletFormatAdapter.FILE.equals(protocol)) + && DataSourceType.FILE == sourceType) { registerPDBFile(pdb.getId().trim(), pdbFile); } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + } catch (Exception ex) { ex.printStackTrace(); @@ -413,6 +448,12 @@ 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; @@ -420,8 +461,8 @@ 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) @@ -444,7 +485,7 @@ 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; @@ -481,91 +522,159 @@ public class StructureSelectionManager continue; } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (sourceType == DataSourceType.PASTE) { pdbFile = "INLINE" + pdb.getId(); } - ArrayList seqToStrucMapping = new ArrayList(); - if (isMapUsingSIFTs) + List seqToStrucMapping = new ArrayList<>(); + if (isMapUsingSIFTs && seq.isProtein()) { - setProgressBar(null); - setProgressBar("Obtaining mapping with SIFTS"); + if (progress!=null) { + progress.setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts"), + progressSessionId); + } jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); if (targetChainId != null && !targetChainId.trim().isEmpty()) { - StructureMapping mapping = getStructureMapping(seq, pdbFile, - targetChainId, pdb, maxChain, sqmpping, maxAlignseq); - seqToStrucMapping.add(mapping); + StructureMapping siftsMapping; + try + { + siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, + pdb, maxChain, sqmpping, maxAlignseq); + seqToStrucMapping.add(siftsMapping); + maxChain.makeExactMapping(siftsMapping, seq); + maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this + // "IEA:SIFTS" ? + maxChain.transferResidueAnnotation(siftsMapping, null); + 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, "IEA:Jalview"); // FIXME: is + // this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } } else { + List foundSiftsMappings = new ArrayList<>(); for (PDBChain chain : pdb.getChains()) { - StructureMapping mapping = getStructureMapping(seq, pdbFile, - chain.id, pdb, chain, sqmpping, maxAlignseq); - seqToStrucMapping.add(mapping); + StructureMapping siftsMapping = null; + try + { + siftsMapping = getStructureMapping(seq, + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); + foundSiftsMappings.add(siftsMapping); + chain.makeExactMapping(siftsMapping, seq); + chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this + // "IEA:SIFTS" ? + chain.transferResidueAnnotation(siftsMapping, null); + } catch (SiftsException e) + { + System.err.println(e.getMessage()); + } + } + if (!foundSiftsMappings.isEmpty()) + { + seqToStrucMapping.addAll(foundSiftsMappings); + 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("Obtaining mapping with NW alignment"); - seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, - maxChain, pdb, maxAlignseq)); + if (progress != null) + { + progress.setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment"), + progressSessionId); + } + StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } - if (forStructureView) { mappings.addAll(seqToStrucMapping); } + if (progress != null) + { + progress.setProgressBar(null, progressSessionId); + } } return pdb; } + 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, PDBfile pdb, + String pdbFile, String targetChainId, StructureFile pdb, PDBChain maxChain, jalview.datamodel.Mapping sqmpping, - AlignSeq maxAlignseq) + AlignSeq maxAlignseq) throws SiftsException { - String maxChainId = targetChainId; + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChainId); try { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, targetChainId); - try - { PDBChain chain = pdb.findChain(targetChainId); if (chain != null) { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + chain.transferResidueAnnotation(curChainMapping, null); } - } catch (Exception e) - { - e.printStackTrace(); - } - return curChainMapping; - } catch (SiftsException e) + } catch (Exception 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); + e.printStackTrace(); } + return curChainMapping; } - private StructureMapping getNWMappings(SequenceI seq, - String pdbFile, - String maxChainId, PDBChain maxChain, PDBfile pdb, + 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) + .append("Sequence \u27f7 Structure mapping details"); mappingDetails.append(NEWLINE); mappingDetails .append("Method: inferred with Needleman & Wunsch alignment"); @@ -597,18 +706,19 @@ 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 .getMappingFromS1(false); maxChain.transferRESNUMFeatures(seq, null); - HashMap mapping = new HashMap(); + HashMap mapping = new HashMap<>(); int resNum = -10000; int index = 0; char insCode = ' '; @@ -623,8 +733,9 @@ public class StructureSelectionManager insCode = tmp.insCode; if (tmp.alignmentMapping >= -1) { - mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber, - tmp.atomIndex }); + mapping.put(tmp.alignmentMapping + 1, + new int[] + { tmp.resNumber, tmp.atomIndex }); } } @@ -661,7 +772,7 @@ public class StructureSelectionManager * 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)); + List pdbs = new ArrayList<>(Arrays.asList(pdbfiles)); StructureListener sl; for (int i = 0; i < listeners.size(); i++) @@ -669,7 +780,7 @@ 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); } @@ -682,7 +793,7 @@ public class StructureSelectionManager */ if (pdbs.size() > 0) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (!pdbs.contains(sm.pdbfile)) @@ -702,7 +813,8 @@ 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); @@ -734,7 +846,29 @@ 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; @@ -745,7 +879,7 @@ public class StructureSelectionManager && sm.pdbchain.equals(atom.getChain())) { int indexpos = sm.getSeqPos(atom.getPdbResNum()); - if (lastipos != indexpos && lastseq != sm.sequence) + if (lastipos != indexpos || lastseq != sm.sequence) { results.addResult(sm.sequence, indexpos, indexpos); lastipos = indexpos; @@ -759,13 +893,7 @@ public class StructureSelectionManager } } } - for (Object li : listeners) - { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } - } + return results; } /** @@ -784,7 +912,7 @@ public class StructureSelectionManager { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); - SearchResults results = null; + SearchResultsI results = null; if (seqPos == -1) { seqPos = seq.findPosition(indexpos); @@ -859,10 +987,12 @@ public class StructureSelectionManager return; } int atomNo; - List atoms = new ArrayList(); + 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())) { for (int index : positions) { @@ -870,8 +1000,8 @@ public class StructureSelectionManager if (atomNo > 0) { - atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm - .getPDBResNum(index), atomNo)); + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, + sm.getPDBResNum(index), atomNo)); } } } @@ -965,7 +1095,7 @@ public class StructureSelectionManager public StructureMapping[] getMapping(String pdbfile) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (sm.pdbfile.equals(pdbfile)) @@ -1113,18 +1243,19 @@ 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); } } } - Vector view_listeners = new Vector(); + Vector view_listeners = new Vector<>(); public synchronized void sendViewPosition( jalview.api.AlignmentViewPanel source, int startRes, int endRes, @@ -1236,8 +1367,8 @@ 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) { @@ -1247,31 +1378,6 @@ 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); - } - public List getSequenceMappings() { return seqmappings;