X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=cd986c0550cecca569f19e213f22cd26e3aacbbc;hb=df0734bbe3c42eb4e1d2e6471040888c85801ba5;hp=ccd106c543531e723dbb36cc0b406f2a35b0f5df;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index ccd106c..cd986c0 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -29,12 +29,15 @@ 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; @@ -63,7 +66,7 @@ public class StructureSelectionManager static IdentityHashMap instances; - private List mappings = new ArrayList(); + private List mappings = new ArrayList<>(); private boolean processSecondaryStructure = false; @@ -71,20 +74,14 @@ 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 @@ -158,8 +155,8 @@ 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) { @@ -172,9 +169,9 @@ 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) { @@ -211,9 +208,8 @@ 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"))); } @@ -226,7 +222,7 @@ public class StructureSelectionManager } if (instances == null) { - instances = new java.util.IdentityHashMap(); + instances = new java.util.IdentityHashMap<>(); } StructureSelectionManager instance = instances.get(context); if (instance == null) @@ -289,7 +285,8 @@ public class StructureSelectionManager } /** - * Returns the file name for a mapped PDB id (or null if not mapped). + * Returns the filename the PDB id is already mapped to if known, or null if + * it is not mapped * * @param pdbid * @return @@ -298,7 +295,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -322,21 +319,23 @@ public class StructureSelectionManager * @return null or the structure data parsed as a pdb file */ synchronized public StructureFile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + String[] targetChains, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) { - return setMapping(true, sequence, targetChains, pdbFile, protocol); + return computeMapping(true, sequence, targetChains, pdbFile, protocol, + progress); } /** - * create sequence structure mappings between each sequence and the given - * pdbFile (retrieved via the given protocol). + * 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 sequenceArray + * @param sequence * - one or more sequences to be mapped to pdbFile - * @param targetChainIds + * @param targetChains * - optional chain specification for mapping each sequence to pdb * (may be nill, individual elements may be nill) * @param pdbFile @@ -347,55 +346,80 @@ public class StructureSelectionManager */ 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 - * the tried and tested MCview pdb mapping + return computeMapping(forStructureView, sequenceArray, targetChainIds, + pdbFile, sourceType, null); + } + + /** + * create sequence structure mappings between each sequence and the given + * 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 + * + * @param sequenceArray + * - 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) - JBPNote: JAL-2693 + * - this should be List>, empty lists indicate no + * predefined mappings + * @param pdbFile + * - structure data resource + * @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 StructureFile computeMapping( + boolean forStructureView, SequenceI[] sequenceArray, + String[] targetChainIds, String pdbFile, DataSourceType sourceType, + IProgressIndicator progress) + { + long progressSessionId = System.currentTimeMillis() * 3; + + /** + * do we extract and transfer annotation from 3D data ? */ - boolean parseSecStr = processSecondaryStructure; - if (isPDBFileRegistered(pdbFile)) - { - for (SequenceI sq : sequenceArray) - { - SequenceI ds = sq; - while (ds.getDatasetSequence() != null) - { - ds = ds.getDatasetSequence(); - } - ; - if (ds.getAnnotation() != null) - { - for (AlignmentAnnotation ala : ds.getAnnotation()) - { - // 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 (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile))) - { - parseSecStr = false; - } - } - } - } - } + // FIXME: possibly should just delete + + boolean parseSecStr = processSecondaryStructure + ? isStructureFileProcessed(pdbFile, sequenceArray) + : false; + StructureFile pdb = null; boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - pdb = new JmolParser(pdbFile, protocol); - + // FIXME if sourceType is not null, we've lost data here + sourceType = AppletFormatAdapter.checkProtocol(pdbFile); + pdb = new JmolParser(false, pdbFile, sourceType); + pdb.addSettings(parseSecStr && processSecondaryStructure, + parseSecStr && addTempFacAnnot, + parseSecStr && secStructServices); + pdb.doParse(); 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(); return null; } - + /* + * sifts client - non null if SIFTS mappings are to be used + */ + SiftsClient siftsClient = null; try { if (isMapUsingSIFTs) @@ -406,6 +430,7 @@ public class StructureSelectionManager { isMapUsingSIFTs = false; e.printStackTrace(); + siftsClient = null; } String targetChainId; @@ -426,8 +451,8 @@ 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) @@ -450,7 +475,7 @@ 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; @@ -487,17 +512,19 @@ public class StructureSelectionManager continue; } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (sourceType == DataSourceType.PASTE) { pdbFile = "INLINE" + pdb.getId(); } - ArrayList seqToStrucMapping = new ArrayList(); + List seqToStrucMapping = new ArrayList<>(); if (isMapUsingSIFTs && seq.isProtein()) { - setProgressBar(null); - setProgressBar(MessageManager - .getString("status.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()) @@ -506,12 +533,12 @@ public class StructureSelectionManager try { siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, - pdb, maxChain, sqmpping, maxAlignseq); + pdb, maxChain, sqmpping, maxAlignseq, siftsClient); seqToStrucMapping.add(siftsMapping); - maxChain.makeExactMapping(maxAlignseq, seq); - maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this + maxChain.makeExactMapping(siftsMapping, seq); + maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this // "IEA:SIFTS" ? - maxChain.transferResidueAnnotation(siftsMapping, sqmpping); + maxChain.transferResidueAnnotation(siftsMapping, null); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } catch (SiftsException e) @@ -522,7 +549,8 @@ public class StructureSelectionManager targetChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); maxChain.makeExactMapping(maxAlignseq, seq); - maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is + // this // "IEA:Jalview" ? maxChain.transferResidueAnnotation(nwMapping, sqmpping); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); @@ -530,27 +558,35 @@ public class StructureSelectionManager } else { - ArrayList foundSiftsMappings = new ArrayList(); + List foundSiftsMappings = new ArrayList<>(); for (PDBChain chain : pdb.getChains()) { + StructureMapping siftsMapping = null; try { - StructureMapping siftsMapping = getStructureMapping(seq, - pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); + siftsMapping = getStructureMapping(seq, + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq, + siftsClient); 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()); } + catch (Exception e) + { + System.err + .println( + "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair"); + 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 @@ -567,29 +603,78 @@ public class StructureSelectionManager } else { - setProgressBar(null); - setProgressBar(MessageManager - .getString("status.obtaining_mapping_with_nw_alignment")); - StructureMapping nwMapping = 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); + for (StructureMapping sm : seqToStrucMapping) + { + addStructureMapping(sm); // not addAll! + } + } + if (progress != null) + { + progress.setProgressBar(null, progressSessionId); } } return pdb; } - private boolean isCIFFile(String filename) + /** + * check if we need to extract secondary structure from given pdbFile and + * transfer to sequences + * + * @param pdbFile + * @param sequenceArray + * @return + */ + private boolean isStructureFileProcessed(String pdbFile, + SequenceI[] sequenceArray) + { + boolean parseSecStr = true; + if (isPDBFileRegistered(pdbFile)) + { + for (SequenceI sq : sequenceArray) + { + SequenceI ds = sq; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + ; + if (ds.getAnnotation() != null) + { + for (AlignmentAnnotation ala : ds.getAnnotation()) + { + // 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 (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile))) + { + parseSecStr = false; + } + } + } + } + } + return parseSecStr; + } + + public void addStructureMapping(StructureMapping sm) { - String fileExt = filename.substring(filename.lastIndexOf(".") + 1, - filename.length()); - return "cif".equalsIgnoreCase(fileExt); + if (!mappings.contains(sm)) + { + mappings.add(sm); + } } /** @@ -603,13 +688,15 @@ public class StructureSelectionManager * @param maxChain * @param sqmpping * @param maxAlignseq + * @param siftsClient + * client for retrieval of SIFTS mappings for this structure * @return * @throws SiftsException */ private StructureMapping getStructureMapping(SequenceI seq, String pdbFile, String targetChainId, StructureFile pdb, PDBChain maxChain, jalview.datamodel.Mapping sqmpping, - AlignSeq maxAlignseq) throws SiftsException + AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException { StructureMapping curChainMapping = siftsClient .getSiftsStructureMapping(seq, pdbFile, targetChainId); @@ -618,7 +705,7 @@ public class StructureSelectionManager PDBChain chain = pdb.findChain(targetChainId); if (chain != null) { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + chain.transferResidueAnnotation(curChainMapping, null); } } catch (Exception e) { @@ -632,8 +719,8 @@ public class StructureSelectionManager 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"); @@ -665,18 +752,19 @@ 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 = ' '; @@ -691,8 +779,9 @@ 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 }); } } @@ -729,7 +818,7 @@ 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++) @@ -737,7 +826,7 @@ 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); } @@ -750,7 +839,7 @@ public class StructureSelectionManager */ if (pdbs.size() > 0) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (!pdbs.contains(sm.pdbfile)) @@ -770,7 +859,8 @@ 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); @@ -802,7 +892,29 @@ 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; @@ -813,7 +925,7 @@ 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; @@ -827,13 +939,7 @@ public class StructureSelectionManager } } } - for (Object li : listeners) - { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } - } + return results; } /** @@ -852,7 +958,7 @@ public class StructureSelectionManager { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); - SearchResults results = null; + SearchResultsI results = null; if (seqPos == -1) { seqPos = seq.findPosition(indexpos); @@ -927,11 +1033,10 @@ 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())) { @@ -941,8 +1046,8 @@ 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)); } } } @@ -1036,7 +1141,7 @@ 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)) @@ -1184,18 +1289,19 @@ 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, @@ -1307,8 +1413,8 @@ 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) { @@ -1318,35 +1424,6 @@ 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) - { - if (progressIndicator == null) - { - return; - } - progressIndicator.setProgressBar(message, progressSessionId); - } - public List getSequenceMappings() { return seqmappings;