X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=ae5431bc8d1b224ad807d08a50f3dfc3889114cc;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=7456304abc4a07b146f231a50932221341b01274;hpb=52cfe80caf018cf3cc6937304f0b20b57153278f;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 7456304..ae5431b 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -20,8 +20,12 @@ */ package jalview.structure; + import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.OrderCommand; @@ -41,6 +45,7 @@ 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; @@ -53,18 +58,18 @@ import java.util.Enumeration; import java.util.HashMap; import java.util.IdentityHashMap; import java.util.List; +import java.util.Locale; 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<>(); @@ -82,6 +87,111 @@ public class StructureSelectionManager private List commandListeners = new ArrayList<>(); 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; + } +/** Null provider in 2.11.2 + + + 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; + } +*/ /** * @return true if will try to use external services for processing secondary @@ -197,49 +307,6 @@ 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 +336,7 @@ public class StructureSelectionManager return relaySeqMappings; } - Vector listeners = new Vector(); + Vector listeners = new Vector<>(); /** * register a listener for alignment sequence mouseover events @@ -285,7 +352,8 @@ 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 @@ -294,7 +362,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -306,6 +374,8 @@ 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 @@ -330,8 +400,11 @@ 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 @@ -375,7 +448,7 @@ 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) @@ -397,15 +470,28 @@ public class StructureSelectionManager { // 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) { @@ -425,7 +511,8 @@ public class StructureSelectionManager } catch (SiftsException e) { isMapUsingSIFTs = false; - e.printStackTrace(); + Console.error("SIFTS mapping failed", e); + Console.error("Falling back on Needleman & Wunsch alignment"); siftsClient = null; } @@ -532,22 +619,23 @@ 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", + pdb.getId().toLowerCase(Locale.ROOT)); maxChain.transferResidueAnnotation(siftsMapping, null); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } catch (SiftsException e) { // fall back to NW alignment - System.err.println(e.getMessage()); + Console.error(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.transferRESNUMFeatures(seq, "IEA:Jalview", + pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is + // this + // "IEA:Jalview" ? maxChain.transferResidueAnnotation(nwMapping, sqmpping); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } @@ -565,7 +653,8 @@ public class StructureSelectionManager siftsClient); foundSiftsMappings.add(siftsMapping); chain.makeExactMapping(siftsMapping, seq); - chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this + chain.transferRESNUMFeatures(seq, "IEA: SIFTS", + pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this // "IEA:SIFTS" ? chain.transferResidueAnnotation(siftsMapping, null); } catch (SiftsException e) @@ -590,8 +679,9 @@ public class StructureSelectionManager StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); - maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this - // "IEA:Jalview" ? + maxChain.transferRESNUMFeatures(seq, null, + pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this + // "IEA:Jalview" ? maxChain.transferResidueAnnotation(nwMapping, sqmpping); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } @@ -612,7 +702,10 @@ public class StructureSelectionManager } if (forStructureView) { - mappings.addAll(seqToStrucMapping); + for (StructureMapping sm : seqToStrucMapping) + { + addStructureMapping(sm); // not addAll! + } } if (progress != null) { @@ -664,7 +757,10 @@ public class StructureSelectionManager public void addStructureMapping(StructureMapping sm) { - mappings.add(sm); + if (!mappings.contains(sm)) + { + mappings.add(sm); + } } /** @@ -752,7 +848,8 @@ public class StructureSelectionManager maxChain.makeExactMapping(maxAlignseq, seq); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); - maxChain.transferRESNUMFeatures(seq, null); + maxChain.transferRESNUMFeatures(seq, null, + pdb.getId().toLowerCase(Locale.ROOT)); HashMap mapping = new HashMap<>(); int resNum = -10000; @@ -848,13 +945,14 @@ 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); } /** @@ -862,12 +960,12 @@ 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++) @@ -879,18 +977,24 @@ 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; } /** @@ -1160,7 +1264,8 @@ 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); @@ -1222,8 +1327,11 @@ 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() { @@ -1261,7 +1369,11 @@ public class StructureSelectionManager } } - public void addSelectionListener(SelectionListener selecter) + public List getListeners() { + return sel_listeners; + } + + public void addSelectionListener(SelectionListener selecter) { if (!sel_listeners.contains(selecter)) { @@ -1314,31 +1426,15 @@ public class StructureSelectionManager } } + /** - * 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)