X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=5ff2da4cc02e3ee049f862a0e6bdff07c67ab175;hb=refs%2Fheads%2Fmerge%2FJAL-2136_phyre2_integration;hp=33c566d2d1e68d5796b12639c5694d19b7ebd00a;hpb=cbf0b72e90f4c719dff345e467b5c9b9873247ed;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 33c566d..5ff2da4 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -31,12 +31,15 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; import jalview.gui.IProgressIndicator; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.StructureFile; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.ws.phyre2.Phyre2Client; import jalview.ws.sifts.SiftsClient; import jalview.ws.sifts.SiftsException; import jalview.ws.sifts.SiftsSettings; @@ -47,6 +50,7 @@ import java.util.Arrays; import java.util.Collections; import java.util.Enumeration; import java.util.HashMap; +import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.List; import java.util.Map; @@ -76,6 +80,7 @@ public class StructureSelectionManager private long progressSessionId; + /* * Set of any registered mappings between (dataset) sequences. */ @@ -85,6 +90,8 @@ public class StructureSelectionManager private List sel_listeners = new ArrayList(); + private Map phyre2ModelTemplates = new Hashtable(); + /** * @return true if will try to use external services for processing secondary * structure @@ -321,9 +328,11 @@ public class StructureSelectionManager * @return null or the structure data parsed as a pdb file */ synchronized public StructureFile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + String[] targetChains, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) { - return setMapping(true, sequence, targetChains, pdbFile, protocol); + return computeMapping(true, sequence, targetChains, pdbFile, protocol, + progress); } @@ -338,7 +347,7 @@ public class StructureSelectionManager * - 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) + * (may be null, individual elements may be null) * @param pdbFile * - structure data resource * @param protocol @@ -347,9 +356,18 @@ public class StructureSelectionManager */ synchronized public StructureFile setMapping(boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, - String pdbFile, - String protocol) + String pdbFile, DataSourceType protocol) + { + return computeMapping(forStructureView, sequenceArray, targetChainIds, + pdbFile, protocol, null); + } + + synchronized public StructureFile computeMapping( + boolean forStructureView, SequenceI[] sequenceArray, + String[] targetChainIds, String pdbFile, DataSourceType protocol, + 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 @@ -384,23 +402,16 @@ public class StructureSelectionManager boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - - if (pdbFile != null && isCIFFile(pdbFile)) - { - pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr, - secStructServices, pdbFile, protocol); - } - else - { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); - } + pdb = new JmolParser(pdbFile, protocol); if (pdb.getId() != null && pdb.getId().trim().length() > 0 - && AppletFormatAdapter.FILE.equals(protocol)) + && DataSourceType.FILE == protocol) { registerPDBFile(pdb.getId().trim(), pdbFile); } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + } catch (Exception ex) { ex.printStackTrace(); @@ -424,6 +435,12 @@ 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; @@ -492,16 +509,19 @@ public class StructureSelectionManager continue; } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol.equals(DataSourceType.PASTE)) { pdbFile = "INLINE" + pdb.getId(); } - - ArrayList seqToStrucMapping = new ArrayList(); - if (isMapUsingSIFTs) + boolean phyre2Template = isPhyre2Template(pdbFile); + List seqToStrucMapping = new ArrayList(); + if (!phyre2Template && isMapUsingSIFTs && seq.isProtein()) { - setProgressBar(null); - setProgressBar("Obtaining mapping with SIFTS"); + if (progress!=null) { + progress.setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts"), + progressSessionId); + } jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); if (targetChainId != null && !targetChainId.trim().isEmpty()) @@ -513,8 +533,11 @@ public class StructureSelectionManager pdb, maxChain, sqmpping, maxAlignseq); seqToStrucMapping.add(siftsMapping); maxChain.makeExactMapping(maxAlignseq, seq); - maxChain.transferRESNUMFeatures(seq, null); + 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 @@ -522,46 +545,85 @@ public class StructureSelectionManager 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)); + } catch (Exception e) + { + e.printStackTrace(); } } else { - ArrayList foundSiftsMappings = new ArrayList(); + List foundSiftsMappings = new ArrayList(); for (PDBChain chain : pdb.getChains()) { try { StructureMapping siftsMapping = getStructureMapping(seq, - pdbFile, - chain.id, pdb, chain, sqmpping, maxAlignseq); + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); foundSiftsMappings.add(siftsMapping); } catch (SiftsException e) { System.err.println(e.getMessage()); + } catch (Exception e) + { + e.printStackTrace(); } } if (!foundSiftsMappings.isEmpty()) { seqToStrucMapping.addAll(foundSiftsMappings); maxChain.makeExactMapping(maxAlignseq, seq); - maxChain.transferRESNUMFeatures(seq, null); + 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 + else if (phyre2Template) { setProgressBar(null); - setProgressBar("Obtaining mapping with NW alignment"); - seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, - maxChain, pdb, maxAlignseq)); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_phyre2_template_alignment")); + String fastaFile = getPhyre2FastaFileFor(pdbFile); + StructureMapping phyre2ModelMapping = new Phyre2Client(pdb) + .getStructureMapping(seq, pdbFile, fastaFile, " "); + seqToStrucMapping.add(phyre2ModelMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } + else + { + if (progress != null) + { + progress.setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment"), + progressSessionId); + } + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } if (forStructureView) @@ -572,36 +634,48 @@ public class StructureSelectionManager return pdb; } - private boolean isCIFFile(String filename) + public void registerPhyre2Template(String phyre2Template, + String fastaMappingFile) { - String fileExt = filename.substring(filename.lastIndexOf(".") + 1, - filename.length()); - return "cif".equalsIgnoreCase(fileExt); + phyre2ModelTemplates.put(phyre2Template, fastaMappingFile); } + /** + * 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, StructureFile pdb, PDBChain maxChain, jalview.datamodel.Mapping sqmpping, - AlignSeq maxAlignseq) throws SiftsException + AlignSeq maxAlignseq) throws Exception { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, targetChainId); - try - { + StructureMapping curChainMapping = siftsClient + .getStructureMapping(seq, pdbFile, targetChainId); + try + { PDBChain chain = pdb.findChain(targetChainId); if (chain != null) { chain.transferResidueAnnotation(curChainMapping, sqmpping); } - } catch (Exception e) - { - e.printStackTrace(); - } - return curChainMapping; + } catch (Exception e) + { + e.printStackTrace(); + } + return curChainMapping; } - private StructureMapping getNWMappings(SequenceI seq, - String pdbFile, + private StructureMapping getNWMappings(SequenceI seq, String pdbFile, String maxChainId, PDBChain maxChain, StructureFile pdb, AlignSeq maxAlignseq) { @@ -776,7 +850,7 @@ public class StructureSelectionManager return; } - SearchResults results = new SearchResults(); + SearchResultsI results = new SearchResults(); for (AtomSpec atom : atoms) { SequenceI lastseq = null; @@ -826,7 +900,7 @@ public class StructureSelectionManager { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); - SearchResults results = null; + SearchResultsI results = null; if (seqPos == -1) { seqPos = seq.findPosition(indexpos); @@ -1326,4 +1400,26 @@ public class StructureSelectionManager return seqmappings; } + public boolean isPhyre2Template(String structureFile) + { + if (structureFile == null || phyre2ModelTemplates == null + || phyre2ModelTemplates.isEmpty()) + { + return false; + } + return phyre2ModelTemplates.get(structureFile) != null + && !phyre2ModelTemplates.get(structureFile).isEmpty(); + } + + public String getPhyre2FastaFileFor(String structureFile) + { + return phyre2ModelTemplates.get(structureFile); + } + + + public static StructureSelectionManager getStructureSelectionManager() + { + return instances.values().iterator().next(); + } + }