X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=bd3d7b32c3848a3799e5eba7eaf8a76a124e04d9;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=b89fb42dcc62a3645ba84207043fa2b7e5da36c9;hpb=47018371de707a8932377aed95424b3090e0c944;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index b89fb42..bd3d7b32 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -22,6 +22,9 @@ package jalview.structure; import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.OrderCommand; @@ -41,6 +44,7 @@ import jalview.io.DataSourceType; import jalview.io.StructureFile; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.ws.sifts.SiftsClient; import jalview.ws.sifts.SiftsException; import jalview.ws.sifts.SiftsSettings; @@ -56,17 +60,15 @@ import java.util.List; import java.util.Map; import java.util.Vector; -import MCview.Atom; -import MCview.PDBChain; -import MCview.PDBfile; +import mc_view.Atom; +import mc_view.PDBChain; +import mc_view.PDBfile; -public class StructureSelectionManager +public class StructureSelectionManager implements ApplicationSingletonI { public final static String NEWLINE = System.lineSeparator(); - static IdentityHashMap instances; - - private List mappings = new ArrayList(); + private List mappings = new ArrayList<>(); private boolean processSecondaryStructure = false; @@ -74,20 +76,75 @@ public class StructureSelectionManager private boolean addTempFacAnnot = false; - private IProgressIndicator progressIndicator; + /* + * Set of any registered mappings between (dataset) sequences. + */ + private List seqmappings = new ArrayList<>(); - private SiftsClient siftsClient = null; + private List commandListeners = new ArrayList<>(); - private long progressSessionId; + private List sel_listeners = new ArrayList<>(); /* - * Set of any registered mappings between (dataset) sequences. + * instances of this class scoped by some context class + */ + private IdentityHashMap selectionManagers; + + /** + * Answers an instance of this class for the current application (Java or JS + * 'applet') scope + * + * @return */ - private List seqmappings = new ArrayList(); + private static StructureSelectionManager getInstance() + { + return (StructureSelectionManager) ApplicationSingletonProvider + .getInstance(StructureSelectionManager.class); + } - private List commandListeners = new ArrayList(); + /** + * Private constructor as all 'singleton' instances are managed here or by + * ApplicationSingletonProvider + */ + private StructureSelectionManager() + { + selectionManagers = new IdentityHashMap<>(); + } + + /** + * Answers an instance of this class for the current application (Java or JS + * 'applet') scope, and scoped to the specified context + * + * @param context + * @return + */ + public static StructureSelectionManager getStructureSelectionManager( + StructureSelectionManagerProvider context) + { + return getInstance().getInstanceForContext(context); + } + + /** + * Answers an instance of this class scoped to the given context. The instance + * is created on the first request for the context, thereafter the same + * instance is returned. Note that the context may be null (this is the case + * when running headless without a Desktop). + * + * @param context + * @return + */ + StructureSelectionManager getInstanceForContext( + StructureSelectionManagerProvider context) + { + StructureSelectionManager instance = selectionManagers.get(context); + if (instance == null) + { + instance = new StructureSelectionManager(); + selectionManagers.put(context, instance); + } + return instance; + } - private List sel_listeners = new ArrayList(); /** * @return true if will try to use external services for processing secondary @@ -175,9 +232,9 @@ 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) { @@ -203,49 +260,6 @@ public class StructureSelectionManager || pdbIdFileName.containsKey(idOrFile); } - private static StructureSelectionManager nullProvider = null; - - public static StructureSelectionManager getStructureSelectionManager( - StructureSelectionManagerProvider context) - { - if (context == null) - { - if (nullProvider == null) - { - if (instances != null) - { - throw new Error(MessageManager.getString( - "error.implementation_error_structure_selection_manager_null"), - new NullPointerException(MessageManager - .getString("exception.ssm_context_is_null"))); - } - else - { - nullProvider = new StructureSelectionManager(); - } - return nullProvider; - } - } - if (instances == null) - { - instances = new java.util.IdentityHashMap(); - } - StructureSelectionManager instance = instances.get(context); - if (instance == null) - { - if (nullProvider != null) - { - instance = nullProvider; - } - else - { - instance = new StructureSelectionManager(); - } - instances.put(context, instance); - } - return instance; - } - /** * flag controlling whether SeqMappings are relayed from received sequence * mouse over events to other sequences @@ -275,7 +289,7 @@ public class StructureSelectionManager return relaySeqMappings; } - Vector listeners = new Vector(); + Vector listeners = new Vector<>(); /** * register a listener for alignment sequence mouseover events @@ -291,7 +305,8 @@ 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 +315,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -312,6 +327,8 @@ public class StructureSelectionManager * Import structure data and register a structure mapping for broadcasting * colouring, mouseovers and selection events (convenience wrapper). * + * This is the standard entry point. + * * @param sequence * - one or more sequences to be mapped to pdbFile * @param targetChains @@ -324,14 +341,46 @@ 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 (testng only), record the mapping for use in mouseOvers + * (testng only) + * @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 @@ -347,63 +396,65 @@ public class StructureSelectionManager * - 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 private 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); - + 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 && DataSourceType.FILE == sourceType) { registerPDBFile(pdb.getId().trim(), pdbFile); } // if PDBId is unavailable then skip SIFTS mapping execution path - isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + // TODO: JAL-3868 need to know if structure is actually from + // PDB (has valid PDB ID and has provenance suggesting it + // actually came from PDB) + boolean isProtein = false; + for (SequenceI s:sequenceArray) { + if (s.isProtein()) { + isProtein = true; + break; + } + } + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein; } catch (Exception ex) { ex.printStackTrace(); return null; } - + /* + * sifts client - non null if SIFTS mappings are to be used + */ + SiftsClient siftsClient = null; try { if (isMapUsingSIFTs) @@ -413,7 +464,9 @@ public class StructureSelectionManager } catch (SiftsException e) { isMapUsingSIFTs = false; - e.printStackTrace(); + Cache.log.error("SIFTS mapping failed", e); + Cache.log.error("Falling back on Needleman & Wunsch alignment"); + siftsClient = null; } String targetChainId; @@ -500,12 +553,14 @@ 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()) @@ -514,23 +569,23 @@ 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 - // "IEA:SIFTS" ? - maxChain.transferResidueAnnotation(siftsMapping, sqmpping); + maxChain.makeExactMapping(siftsMapping, seq); + maxChain.transferRESNUMFeatures(seq, "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()); + Cache.log.error(e.getMessage()); StructureMapping nwMapping = getNWMappings(seq, pdbFile, 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)); @@ -538,27 +593,35 @@ 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 @@ -575,27 +638,77 @@ 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); + } } /** @@ -609,13 +722,15 @@ 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); @@ -624,7 +739,7 @@ public class StructureSelectionManager PDBChain chain = pdb.findChain(targetChainId); if (chain != null) { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + chain.transferResidueAnnotation(curChainMapping, null); } } catch (Exception e) { @@ -683,7 +798,7 @@ 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 = ' '; @@ -737,7 +852,7 @@ 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++) @@ -758,7 +873,7 @@ public class StructureSelectionManager */ if (pdbs.size() > 0) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (!pdbs.contains(sm.pdbfile)) @@ -777,13 +892,14 @@ public class StructureSelectionManager * @param pdbResNum * @param chain * @param pdbfile + * @return */ - public void mouseOverStructure(int pdbResNum, String chain, + public String mouseOverStructure(int pdbResNum, String chain, String pdbfile) { AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0); List atoms = Collections.singletonList(atomSpec); - mouseOverStructure(atoms); + return mouseOverStructure(atoms); } /** @@ -791,12 +907,12 @@ public class StructureSelectionManager * * @param atoms */ - public void mouseOverStructure(List atoms) + public String mouseOverStructure(List atoms) { if (listeners == null) { // old or prematurely sent event - return; + return null; } boolean hasSequenceListener = false; for (int i = 0; i < listeners.size(); i++) @@ -808,19 +924,25 @@ public class StructureSelectionManager } if (!hasSequenceListener) { - return; + return null; } SearchResultsI results = findAlignmentPositionsForStructurePositions( atoms); + String result = null; for (Object li : listeners) { if (li instanceof SequenceListener) { - ((SequenceListener) li).highlightSequence(results); + String s = ((SequenceListener) li).highlightSequence(results); + if (s != null) + { + result = s; } } } + return result; + } /** * Constructs a SearchResults object holding regions (if any) in the Jalview @@ -952,7 +1074,7 @@ 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() @@ -1060,7 +1182,7 @@ 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)) @@ -1089,7 +1211,8 @@ public class StructureSelectionManager StringBuilder sb = new StringBuilder(64); for (StructureMapping sm : mappings) { - if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence)) + if (Platform.pathEquals(sm.pdbfile, pdbfile) + && seqs.contains(sm.sequence)) { sb.append(sm.mappingDetails); sb.append(NEWLINE); @@ -1151,8 +1274,11 @@ public class StructureSelectionManager } /** - * Resets this object to its initial state by removing all registered - * listeners, codon mappings, PDB file mappings + * Reset this object to its initial state by removing all registered + * listeners, codon mappings, PDB file mappings. + * + * Called only by Desktop and testng. + * */ public void resetAll() { @@ -1190,7 +1316,11 @@ public class StructureSelectionManager } } - public void addSelectionListener(SelectionListener selecter) + public List getListeners() { + return sel_listeners; + } + + public void addSelectionListener(SelectionListener selecter) { if (!sel_listeners.contains(selecter)) { @@ -1220,7 +1350,7 @@ 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, @@ -1238,38 +1368,23 @@ public class StructureSelectionManager { slis.viewPosition(startRes, endRes, startSeq, endSeq, source); } - ; + } } } + /** - * release all references associated with this manager provider + * Removes the instance associated with this provider * - * @param jalviewLite + * @param provider */ - public static void release(StructureSelectionManagerProvider jalviewLite) + + public static void release(StructureSelectionManagerProvider provider) { - // synchronized (instances) - { - if (instances == null) - { - return; - } - StructureSelectionManager mnger = (instances.get(jalviewLite)); - if (mnger != null) - { - instances.remove(jalviewLite); - try - { - mnger.finalize(); - } catch (Throwable x) - { - } - } - } + getInstance().selectionManagers.remove(provider); } - + public void registerPDBEntry(PDBEntry pdbentry) { if (pdbentry.getFile() != null @@ -1343,35 +1458,6 @@ 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;