X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=d1593df77746948e05c9fd25a0930da519a77de9;hb=27a5a96f40f4721c9b9024938547a997dbf16cf4;hp=678bf3bf26796890b657f9a7c1c648c4cfc90e50;hpb=e57ac4e703658ff81d7e172222e718ff7611e96e;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 678bf3b..d1593df 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -31,10 +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.io.AppletFormatAdapter; +import jalview.ext.jmol.JmolParser; +import jalview.gui.IProgressIndicator; +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; @@ -45,11 +50,10 @@ 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.LinkedHashSet; import java.util.List; import java.util.Map; -import java.util.Set; import java.util.Vector; import MCview.Atom; @@ -70,15 +74,24 @@ public class StructureSelectionManager private boolean addTempFacAnnot = false; + private IProgressIndicator progressIndicator; + + private SiftsClient siftsClient = null; + + private long progressSessionId; + + /* * Set of any registered mappings between (dataset) sequences. */ - public Set seqmappings = new LinkedHashSet(); + private List seqmappings = new ArrayList(); private List commandListeners = new ArrayList(); private List sel_listeners = new ArrayList(); + private Map phyre2ModelTemplates = new Hashtable(); + /** * @return true if will try to use external services for processing secondary * structure @@ -314,12 +327,15 @@ 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, - String[] targetChains, String pdbFile, String protocol) + synchronized public StructureFile setMapping(SequenceI[] sequence, + String[] targetChains, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) { - return setMapping(true, sequence, targetChains, pdbFile, protocol); + return computeMapping(true, sequence, targetChains, pdbFile, protocol, + progress); } + /** * create sequence structure mappings between each sequence and the given * pdbFile (retrieved via the given protocol). @@ -331,18 +347,27 @@ 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 * - 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) + 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 @@ -373,19 +398,20 @@ public class StructureSelectionManager } } } - PDBfile pdb = null; + StructureFile pdb = null; boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); - SiftsClient siftsClient = null; try { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); + pdb = new JmolParser(pdbFile, protocol); - if (pdb.id != null && pdb.id.trim().length() > 0 - && AppletFormatAdapter.FILE.equals(protocol)) + if (pdb.getId() != null && pdb.getId().trim().length() > 0 + && DataSourceType.FILE == protocol) { - registerPDBFile(pdb.id.trim(), pdbFile); + registerPDBFile(pdb.getId().trim(), pdbFile); } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + } catch (Exception ex) { ex.printStackTrace(); @@ -409,6 +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; @@ -422,7 +454,7 @@ public class StructureSelectionManager { if (targetChainId.trim().length() == 0) { - targetChainId = " "; + targetChainId = StructureMapping.NO_CHAIN; } else { @@ -442,10 +474,10 @@ public class StructureSelectionManager */ int max = -10; AlignSeq maxAlignseq = null; - String maxChainId = " "; + String maxChainId = StructureMapping.NO_CHAIN; // space PDBChain maxChain = null; boolean first = true; - for (PDBChain chain : pdb.chains) + for (PDBChain chain : pdb.getChains()) { if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) && !infChain) @@ -477,70 +509,175 @@ public class StructureSelectionManager continue; } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol.equals(DataSourceType.PASTE)) { - pdbFile = "INLINE" + pdb.id; + pdbFile = "INLINE" + pdb.getId(); } - - ArrayList seqToStrucMapping = null; - if (isMapUsingSIFTs) + boolean phyre2Template = isPhyre2Template(pdbFile); + List seqToStrucMapping = new ArrayList(); + if (!phyre2Template && isMapUsingSIFTs && seq.isProtein()) { - try + 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()) { - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - seqToStrucMapping = new ArrayList(); - if (targetChainId != null && !targetChainId.trim().isEmpty()) + 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) { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, targetChainId); - seqToStrucMapping.add(curChainMapping); - maxChainId = targetChainId; - PDBChain chain = pdb.findChain(targetChainId); - if (chain != null) + // 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)); + } catch (Exception e) + { + e.printStackTrace(); + } + } + else + { + List foundSiftsMappings = new ArrayList(); + for (PDBChain chain : pdb.getChains()) + { + try + { + StructureMapping siftsMapping = getStructureMapping(seq, + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); + foundSiftsMappings.add(siftsMapping); + } catch (SiftsException e) + { + System.err.println(e.getMessage()); + } catch (Exception e) { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + e.printStackTrace(); } } + 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 { - for (PDBChain chain : pdb.chains) - { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, chain.id); - seqToStrucMapping.add(curChainMapping); - maxChainId = chain.id; - chain.transferResidueAnnotation(curChainMapping, sqmpping); - } + 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)); } - } catch (SiftsException e) - { - e.printStackTrace(); - System.err - .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment"); - seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId, - maxChain, pdb, maxAlignseq); } } + else if (phyre2Template) + { + setProgressBar(null); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_phyre2_template_alignment")); + String fastaFile = getPhyre2FastaFileFor(pdbFile); + StructureMapping phyre2ModelMapping = new Phyre2Client(pdb) + .getStructureMapping(seq, pdbFile, fastaFile, + StructureMapping.NO_CHAIN); + 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 { - seqToStrucMapping = getNWMappings(seq, pdbFile, - maxChainId, maxChain, pdb, - maxAlignseq); + 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) { - // mappings.add(seqToStrucMapping); mappings.addAll(seqToStrucMapping); } } return pdb; } - private ArrayList getNWMappings(SequenceI seq, - String pdbFile, - String maxChainId, PDBChain maxChain, PDBfile pdb, + public void registerPhyre2Template(String phyre2Template, + String fastaMappingFile) + { + 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 Exception + { + 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; + } + + private StructureMapping getNWMappings(SequenceI seq, String pdbFile, + String maxChainId, PDBChain maxChain, StructureFile pdb, AlignSeq maxAlignseq) { final StringBuilder mappingDetails = new StringBuilder(128); @@ -591,17 +728,18 @@ public class StructureSelectionManager HashMap mapping = new HashMap(); int resNum = -10000; int index = 0; + char insCode = ' '; do { Atom tmp = maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + if ((resNum != tmp.resNumber || insCode != tmp.insCode) + && tmp.alignmentMapping != -1) { resNum = tmp.resNumber; + insCode = tmp.insCode; if (tmp.alignmentMapping >= -1) { - // TODO (JAL-1836) address root cause: negative residue no in PDB - // file mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber, tmp.atomIndex }); } @@ -611,11 +749,9 @@ public class StructureSelectionManager } while (index < maxChain.atoms.size()); StructureMapping nwMapping = new StructureMapping(seq, pdbFile, - pdb.id, maxChainId, mapping, mappingDetails.toString()); + pdb.getId(), maxChainId, mapping, mappingDetails.toString()); maxChain.transferResidueAnnotation(nwMapping, sqmpping); - ArrayList mappings = new ArrayList(); - mappings.add(nwMapping); - return mappings; + return nwMapping; } public void removeStructureViewerListener(Object svl, String[] pdbfiles) @@ -650,7 +786,7 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - for (String pdbfile : sl.getPdbFile()) + for (String pdbfile : sl.getStructureFiles()) { pdbs.remove(pdbfile); } @@ -715,7 +851,28 @@ public class StructureSelectionManager return; } - SearchResults results = new SearchResults(); + SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms); + for (Object li : listeners) + { + if (li instanceof SequenceListener) + { + ((SequenceListener) li).highlightSequence(results); + } + } + } + + /** + * Constructs a SearchResults object holding regions (if any) in the Jalview + * alignment which have a mapping to the structure viewer positions in the + * supplied list + * + * @param atoms + * @return + */ + public SearchResultsI findAlignmentPositionsForStructurePositions( + List atoms) + { + SearchResultsI results = new SearchResults(); for (AtomSpec atom : atoms) { SequenceI lastseq = null; @@ -740,13 +897,7 @@ public class StructureSelectionManager } } } - for (Object li : listeners) - { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } - } + return results; } /** @@ -756,19 +907,19 @@ public class StructureSelectionManager * the sequence that the mouse over occurred on * @param indexpos * the absolute position being mouseovered in seq (0 to seq.length()) - * @param index + * @param seqPos * the sequence position (if -1, seq.findPosition is called to * resolve the residue number) */ - public void mouseOverSequence(SequenceI seq, int indexpos, int index, + public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos, VamsasSource source) { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); - SearchResults results = null; - if (index == -1) + SearchResultsI results = null; + if (seqPos == -1) { - index = seq.findPosition(indexpos); + seqPos = seq.findPosition(indexpos); } for (int i = 0; i < listeners.size(); i++) { @@ -781,7 +932,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -795,12 +946,12 @@ public class StructureSelectionManager { if (results == null) { - results = MappingUtils.buildSearchResults(seq, index, + results = MappingUtils.buildSearchResults(seq, seqPos, seqmappings); } if (handlingVamsasMo) { - results.addResult(seq, index, index); + results.addResult(seq, seqPos, seqPos); } if (!results.isEmpty()) @@ -818,7 +969,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -826,14 +977,14 @@ public class StructureSelectionManager /** * Send suitable messages to a StructureListener to highlight atoms - * corresponding to the given sequence position. + * corresponding to the given sequence position(s) * * @param sl * @param seq - * @param index + * @param positions */ - protected void highlightStructure(StructureListener sl, SequenceI seq, - int index) + public void highlightStructure(StructureListener sl, SequenceI seq, + int... positions) { if (!sl.isListeningFor(seq)) { @@ -843,14 +994,20 @@ 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())) { - atomNo = sm.getAtomNum(index); - - if (atomNo > 0) + for (int index : positions) { - atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm - .getPDBResNum(index), atomNo)); + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm + .getPDBResNum(index), atomNo)); + } } } } @@ -1006,13 +1163,13 @@ public class StructureSelectionManager /** * Add each of the given codonFrames to the stored set, if not aready present. * - * @param set + * @param mappings */ - public void registerMappings(Set set) + public void registerMappings(List mappings) { - if (set != null) + if (mappings != null) { - for (AlignedCodonFrame acf : set) + for (AlignedCodonFrame acf : mappings) { registerMapping(acf); } @@ -1224,4 +1381,66 @@ public class StructureSelectionManager } return null; } + + public IProgressIndicator getProgressIndicator() + { + return progressIndicator; + } + + public void setProgressIndicator(IProgressIndicator progressIndicator) + { + this.progressIndicator = progressIndicator; + } + + public long getProgressSessionId() + { + return progressSessionId; + } + + public void setProgressSessionId(long progressSessionId) + { + this.progressSessionId = progressSessionId; + } + + public void setProgressBar(String message) + { + if (progressIndicator == null) + { + return; + } + progressIndicator.setProgressBar(message, progressSessionId); + } + + public List getSequenceMappings() + { + 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(); + } + + public void addStructureMapping(StructureMapping smapping) + { + mappings.add(smapping); + } + }