X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=760cab04aa674316447939ee8d0d749bc4e690b6;hb=8a43b8353b89a47002ef17c959ed61281fc4d826;hp=8380b19572d35591a57ef8855c79874f9ee56b5d;hpb=9e7b5a1d3af2af268d19b2f82c964ce2c27e9c3e;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 8380b19..760cab0 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -20,8 +20,20 @@ */ package jalview.structure; +import java.io.PrintStream; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.IdentityHashMap; +import java.util.List; +import java.util.Map; +import java.util.Vector; + import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.OrderCommand; @@ -41,24 +53,13 @@ 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; - -import java.io.PrintStream; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Enumeration; -import java.util.HashMap; -import java.util.IdentityHashMap; -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 { @@ -74,8 +75,6 @@ public class StructureSelectionManager private boolean addTempFacAnnot = false; - private SiftsClient siftsClient = null; - /* * Set of any registered mappings between (dataset) sequences. */ @@ -287,7 +286,8 @@ 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 @@ -296,7 +296,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -397,9 +397,13 @@ public class StructureSelectionManager 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) { @@ -413,7 +417,10 @@ public class StructureSelectionManager ex.printStackTrace(); return null; } - + /* + * sifts client - non null if SIFTS mappings are to be used + */ + SiftsClient siftsClient = null; try { if (isMapUsingSIFTs) @@ -423,7 +430,9 @@ 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; @@ -526,18 +535,17 @@ public class StructureSelectionManager try { siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, - pdb, maxChain, sqmpping, maxAlignseq); + 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); @@ -558,7 +566,8 @@ public class StructureSelectionManager try { siftsMapping = getStructureMapping(seq, - pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq, + siftsClient); foundSiftsMappings.add(siftsMapping); chain.makeExactMapping(siftsMapping, seq); chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this @@ -568,6 +577,13 @@ public class StructureSelectionManager { 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()) { @@ -601,7 +617,10 @@ public class StructureSelectionManager } if (forStructureView) { - mappings.addAll(seqToStrucMapping); + for (StructureMapping sm : seqToStrucMapping) + { + addStructureMapping(sm); // not addAll! + } } if (progress != null) { @@ -653,7 +672,10 @@ public class StructureSelectionManager public void addStructureMapping(StructureMapping sm) { - mappings.add(sm); + if (!mappings.contains(sm)) + { + mappings.add(sm); + } } /** @@ -667,13 +689,15 @@ 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); @@ -835,13 +859,14 @@ 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); } /** @@ -849,12 +874,12 @@ 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++) @@ -866,18 +891,24 @@ 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; } /** @@ -1130,6 +1161,28 @@ public class StructureSelectionManager } /** + * Answers a (possibly empty) list of structure to sequence mappings matching + * the given pdb and chain ids + * + * @param pdbId + * @param chain + * @return + */ + public List getMappingForChain(String pdbId, + String chain) + { + List result = new ArrayList<>(); + for (StructureMapping sm : mappings) + { + if (sm.pdbid.equals(pdbId) && sm.pdbchain.equals(chain)) + { + result.add(sm); + } + } + return result; + } + + /** * Returns a readable description of all mappings for the given pdbfile to any * of the given sequences * @@ -1147,7 +1200,8 @@ 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); @@ -1320,7 +1374,10 @@ public class StructureSelectionManager instances.remove(jalviewLite); try { - mnger.finalize(); + /* bsoares 2019-03-20 finalize deprecated, no apparent external + * resources to close + */ + // mnger.finalize(); } catch (Throwable x) { }