X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=ad259fd88d0e957830b429597a4c1209cad3f5f2;hb=083fb85bfa1be57c30db0ac1cb9f5f8ad08d1060;hp=fbfa486a6d9c3dbbac592005ea6fd2c084d4b53f;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index fbfa486..ad259fd 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -66,7 +66,7 @@ public class StructureSelectionManager static IdentityHashMap instances; - private List mappings = new ArrayList(); + private List mappings = new ArrayList<>(); private boolean processSecondaryStructure = false; @@ -74,20 +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 @@ -175,9 +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) { @@ -228,7 +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) @@ -291,7 +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 @@ -300,7 +295,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -324,14 +319,43 @@ public class StructureSelectionManager * @return null or the structure data parsed as a pdb file */ synchronized public StructureFile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, DataSourceType protocol) + String[] targetChains, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) { - return setMapping(true, sequence, targetChains, pdbFile, protocol); + 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 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 @@ -340,51 +364,39 @@ 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 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 setMapping(boolean forStructureView, - SequenceI[] sequenceArray, String[] targetChainIds, - String pdbFile, DataSourceType sourceType) + 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; + + /** + * 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 { + // FIXME if sourceType is not null, we've lost data here sourceType = AppletFormatAdapter.checkProtocol(pdbFile); pdb = new JmolParser(pdbFile, sourceType); @@ -401,7 +413,10 @@ public class StructureSelectionManager ex.printStackTrace(); return null; } - + /* + * sifts client - non null if SIFTS mappings are to be used + */ + SiftsClient siftsClient = null; try { if (isMapUsingSIFTs) @@ -412,6 +427,7 @@ public class StructureSelectionManager { isMapUsingSIFTs = false; e.printStackTrace(); + siftsClient = null; } String targetChainId; @@ -498,12 +514,14 @@ public class StructureSelectionManager pdbFile = "INLINE" + pdb.getId(); } - List 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()) @@ -512,12 +530,12 @@ 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) @@ -528,7 +546,8 @@ 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)); @@ -536,27 +555,35 @@ public class StructureSelectionManager } else { - List 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 @@ -573,27 +600,78 @@ public class StructureSelectionManager } else { - setProgressBar(null); - setProgressBar(MessageManager - .getString("status.obtaining_mapping_with_nw_alignment")); + 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; } + /** + * 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) { - mappings.add(sm); + if (!mappings.contains(sm)) + { + mappings.add(sm); + } } /** @@ -607,13 +685,15 @@ 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); @@ -622,7 +702,7 @@ public class StructureSelectionManager PDBChain chain = pdb.findChain(targetChainId); if (chain != null) { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + chain.transferResidueAnnotation(curChainMapping, null); } } catch (Exception e) { @@ -681,7 +761,7 @@ public class StructureSelectionManager .getMappingFromS1(false); maxChain.transferRESNUMFeatures(seq, null); - HashMap mapping = new HashMap(); + HashMap mapping = new HashMap<>(); int resNum = -10000; int index = 0; char insCode = ' '; @@ -735,7 +815,7 @@ 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++) @@ -756,7 +836,7 @@ public class StructureSelectionManager */ if (pdbs.size() > 0) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (!pdbs.contains(sm.pdbfile)) @@ -842,7 +922,7 @@ 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; @@ -950,7 +1030,7 @@ 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() @@ -1058,7 +1138,7 @@ 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)) @@ -1218,7 +1298,7 @@ public class StructureSelectionManager } } - Vector view_listeners = new Vector(); + Vector view_listeners = new Vector<>(); public synchronized void sendViewPosition( jalview.api.AlignmentViewPanel source, int startRes, int endRes, @@ -1341,35 +1421,6 @@ 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;