X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e4dc137908b459ec26345310e5251d8ac5e69098;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=2b429d797ea0b911a261990366256d069d49be94;hpb=602686d713d7b4554b96d09847a77a675dae3aab;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 2b429d7..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 { @@ -74,8 +76,6 @@ public class StructureSelectionManager private boolean addTempFacAnnot = false; - private SiftsClient siftsClient = null; - /* * Set of any registered mappings between (dataset) sequences. */ @@ -287,7 +287,8 @@ 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 +297,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -328,22 +329,20 @@ public class StructureSelectionManager } /** - * create sequence structure mappings between each sequence and the given - * pdbFile (retrieved via the given protocol). + * Import a single structure file and register sequence structure mappings for + * broadcasting colouring, mouseovers and selection events (convenience + * wrapper). * * @param forStructureView * when true, record the mapping for use in mouseOvers - * - * @param sequenceArray + * @param sequence * - one or more sequences to be mapped to pdbFile - * @param targetChainIds + * @param targetChains * - optional chain specification for mapping each sequence to pdb - * (may be nill, individual elements may be nill) - JBPNote: JAL-2693 - * - this should be List>, empty lists indicate no - * predefined mappings + * (may be nill, individual elements may be nill) * @param pdbFile * - structure data resource - * @param sourceType + * @param protocol * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ @@ -355,63 +354,84 @@ public class StructureSelectionManager pdbFile, sourceType, null); } + /** + * create sequence structure mappings between each sequence and the given + * 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 + * + * @param sequenceArray + * - one or more sequences to be mapped to pdbFile + * @param targetChainIds + * - optional chain specification for mapping each sequence to pdb + * (may be nill, individual elements may be nill) - JBPNote: JAL-2693 + * - this should be List>, empty lists indicate no + * predefined mappings + * @param pdbFile + * - 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 computeMapping( boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, String pdbFile, DataSourceType sourceType, IProgressIndicator progress) { long progressSessionId = System.currentTimeMillis() * 3; - /* - * There will be better ways of doing this in the future, for now we'll use - * the tried and tested MCview pdb mapping + + /** + * 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) @@ -421,7 +441,9 @@ 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; } String targetChainId; @@ -524,23 +546,22 @@ 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",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); @@ -556,16 +577,24 @@ 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 + 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()) { @@ -577,7 +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)); @@ -599,7 +628,10 @@ public class StructureSelectionManager } if (forStructureView) { - mappings.addAll(seqToStrucMapping); + for (StructureMapping sm : seqToStrucMapping) + { + addStructureMapping(sm); // not addAll! + } } if (progress != null) { @@ -609,9 +641,52 @@ public class StructureSelectionManager 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); + } } /** @@ -625,13 +700,15 @@ 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); @@ -697,7 +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; @@ -793,13 +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); } /** @@ -807,12 +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++) @@ -824,18 +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; } /** @@ -1105,7 +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); @@ -1278,7 +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) { }