X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e4dc137908b459ec26345310e5251d8ac5e69098;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=d68f3463875272b8965f318920b86e82a1357401;hpb=2459e383f02f6ef9b15a1d6312fff89f74947a6e;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index d68f346..e4dc137 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -20,8 +20,21 @@ */ 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.Locale; +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 +54,13 @@ 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 { @@ -398,15 +400,28 @@ 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) { @@ -426,7 +441,8 @@ public class StructureSelectionManager } catch (SiftsException e) { isMapUsingSIFTs = false; - e.printStackTrace(); + Cache.error("SIFTS mapping failed", e); + Cache.error("Falling back on Needleman & Wunsch alignment"); siftsClient = null; } @@ -533,20 +549,19 @@ 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()); + Cache.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 + maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is // this // "IEA:Jalview" ? maxChain.transferResidueAnnotation(nwMapping, sqmpping); @@ -566,13 +581,20 @@ 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) { 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()) { @@ -584,7 +606,7 @@ public class StructureSelectionManager StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); - maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + 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)); @@ -752,7 +774,7 @@ 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 +870,14 @@ 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 +885,12 @@ 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 +902,24 @@ 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 +1189,8 @@ 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); @@ -1333,7 +1363,10 @@ 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) { }