X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=c27289c468bdc1a396b6b78e9cd92cf410c38b3d;hb=3f12f4932226512316ec113e600695150431fd0a;hp=00b3143bf4585b979d7a78f9e538cf9f57c6d18e;hpb=4da7d6ec8ef5ff030c6d06d37a099da2d92d7246;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 00b3143..c27289c 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -34,6 +34,7 @@ import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceI; import jalview.gui.IProgressIndicator; import jalview.io.AppletFormatAdapter; +import jalview.io.StructureFile; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.ws.sifts.SiftsClient; @@ -319,12 +320,13 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(SequenceI[] sequence, + synchronized public StructureFile setMapping(SequenceI[] sequence, String[] targetChains, String pdbFile, String protocol) { return setMapping(true, sequence, targetChains, pdbFile, protocol); } + /** * create sequence structure mappings between each sequence and the given * pdbFile (retrieved via the given protocol). @@ -343,7 +345,7 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(boolean forStructureView, + synchronized public StructureFile setMapping(boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, String pdbFile, String protocol) @@ -378,12 +380,25 @@ public class StructureSelectionManager } } } - PDBfile pdb = null; + StructureFile pdb = null; boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); + + boolean isParseWithJMOL = StructureImportSettings + .getDefaultPDBFileParser().equalsIgnoreCase( + StructureImportSettings.StructureParser.JMOL_PARSER + .toString()); + if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile))) + { + pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr, + secStructServices, pdbFile, protocol); + } + else + { + pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, + pdbFile, protocol); + } if (pdb.getId() != null && pdb.getId().trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) @@ -413,6 +428,12 @@ public class StructureSelectionManager { boolean infChain = true; final SequenceI seq = sequenceArray[s]; + SequenceI ds = seq; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + if (targetChainIds != null && targetChainIds[s] != null) { infChain = false; @@ -487,34 +508,89 @@ public class StructureSelectionManager } ArrayList seqToStrucMapping = new ArrayList(); - if (isMapUsingSIFTs) + if (isMapUsingSIFTs && seq.isProtein()) { setProgressBar(null); - setProgressBar("Obtaining mapping with SIFTS"); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts")); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); if (targetChainId != null && !targetChainId.trim().isEmpty()) { - StructureMapping mapping = getStructureMapping(seq, pdbFile, - targetChainId, pdb, maxChain, sqmpping, maxAlignseq); - seqToStrucMapping.add(mapping); + StructureMapping siftsMapping; + try + { + siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, + pdb, maxChain, sqmpping, maxAlignseq); + seqToStrucMapping.add(siftsMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this + // "IEA:SIFTS" ? + maxChain.transferResidueAnnotation(siftsMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + + } catch (SiftsException e) + { + // fall back to NW alignment + System.err.println(e.getMessage()); + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + targetChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } } else { + ArrayList foundSiftsMappings = new ArrayList(); for (PDBChain chain : pdb.getChains()) { - StructureMapping mapping = getStructureMapping(seq, pdbFile, - chain.id, pdb, chain, sqmpping, maxAlignseq); - seqToStrucMapping.add(mapping); + try + { + StructureMapping siftsMapping = getStructureMapping(seq, + pdbFile, + chain.id, pdb, chain, sqmpping, maxAlignseq); + foundSiftsMappings.add(siftsMapping); + } catch (SiftsException e) + { + System.err.println(e.getMessage()); + } + } + if (!foundSiftsMappings.isEmpty()) + { + seqToStrucMapping.addAll(foundSiftsMappings); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this + // "IEA:SIFTS" ? + maxChain.transferResidueAnnotation(foundSiftsMappings.get(0), + sqmpping); + ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0)); + } + else + { + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } } } else { setProgressBar(null); - setProgressBar("Obtaining mapping with NW alignment"); - seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, - maxChain, pdb, maxAlignseq)); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment")); + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } if (forStructureView) @@ -525,14 +601,32 @@ public class StructureSelectionManager return pdb; } + private boolean isCIFFile(String filename) + { + String fileExt = filename.substring(filename.lastIndexOf(".") + 1, + filename.length()); + return "cif".equalsIgnoreCase(fileExt); + } + + /** + * retrieve a mapping for seq from SIFTs using associated DBRefEntry for + * uniprot or PDB + * + * @param seq + * @param pdbFile + * @param targetChainId + * @param pdb + * @param maxChain + * @param sqmpping + * @param maxAlignseq + * @return + * @throws SiftsException + */ private StructureMapping getStructureMapping(SequenceI seq, - String pdbFile, String targetChainId, PDBfile pdb, + String pdbFile, String targetChainId, StructureFile pdb, PDBChain maxChain, jalview.datamodel.Mapping sqmpping, - AlignSeq maxAlignseq) + AlignSeq maxAlignseq) throws SiftsException { - String maxChainId = targetChainId; - try - { StructureMapping curChainMapping = siftsClient .getSiftsStructureMapping(seq, pdbFile, targetChainId); try @@ -547,20 +641,11 @@ public class StructureSelectionManager e.printStackTrace(); } return curChainMapping; - } catch (SiftsException e) - { - System.err.println(e.getMessage()); - System.err.println(">>> Now switching mapping with NW alignment..."); - setProgressBar(null); - setProgressBar(">>> Now switching mapping with NW alignment..."); - return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, - maxAlignseq); - } } private StructureMapping getNWMappings(SequenceI seq, String pdbFile, - String maxChainId, PDBChain maxChain, PDBfile pdb, + String maxChainId, PDBChain maxChain, StructureFile pdb, AlignSeq maxAlignseq) { final StringBuilder mappingDetails = new StringBuilder(128); @@ -862,7 +947,10 @@ public class StructureSelectionManager List atoms = new ArrayList(); for (StructureMapping sm : mappings) { - if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()) + if (sm.sequence == seq + || sm.sequence == seq.getDatasetSequence() + || (sm.sequence.getDatasetSequence() != null && sm.sequence + .getDatasetSequence() == seq.getDatasetSequence())) { for (int index : positions) { @@ -1269,6 +1357,10 @@ public class StructureSelectionManager public void setProgressBar(String message) { + if (progressIndicator == null) + { + return; + } progressIndicator.setProgressBar(message, progressSessionId); }