X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=bd3d7b32c3848a3799e5eba7eaf8a76a124e04d9;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=6261e7454d6bd5e1b92db46c2ff01434130aa878;hpb=b879c4a2d32d3489e63ac06917e81637e6bb4068;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 6261e74..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; @@ -60,12 +64,10 @@ 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 boolean processSecondaryStructure = false; @@ -83,6 +85,67 @@ public class StructureSelectionManager private List sel_listeners = new ArrayList<>(); + /* + * 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 static StructureSelectionManager getInstance() + { + return (StructureSelectionManager) ApplicationSingletonProvider + .getInstance(StructureSelectionManager.class); + } + + /** + * 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; + } + + /** * @return true if will try to use external services for processing secondary * structure @@ -197,49 +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 @@ -269,7 +289,7 @@ public class StructureSelectionManager return relaySeqMappings; } - Vector listeners = new Vector(); + Vector listeners = new Vector<>(); /** * register a listener for alignment sequence mouseover events @@ -307,6 +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 @@ -331,8 +353,11 @@ public class StructureSelectionManager * broadcasting colouring, mouseovers and selection events (convenience * wrapper). * + * + * * @param forStructureView - * when true, record the mapping for use in mouseOvers + * 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 @@ -376,7 +401,7 @@ public class StructureSelectionManager * mapping operation * @return null or the structure data parsed as a pdb file */ - synchronized public StructureFile computeMapping( + synchronized private StructureFile computeMapping( boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, String pdbFile, DataSourceType sourceType, IProgressIndicator progress) @@ -409,7 +434,17 @@ public class StructureSelectionManager 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) { @@ -429,7 +464,8 @@ 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; } @@ -536,15 +572,14 @@ public class StructureSelectionManager pdb, maxChain, sqmpping, maxAlignseq, siftsClient); seqToStrucMapping.add(siftsMapping); maxChain.makeExactMapping(siftsMapping, seq); - maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this - // "IEA:SIFTS" ? + 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); @@ -650,7 +685,6 @@ public class StructureSelectionManager { ds = ds.getDatasetSequence(); } - ; if (ds.getAnnotation() != null) { for (AlignmentAnnotation ala : ds.getAnnotation()) @@ -858,13 +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); } /** @@ -872,12 +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++) @@ -889,19 +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 @@ -1170,7 +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); @@ -1232,8 +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() { @@ -1271,7 +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)) { @@ -1319,38 +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