X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=fb96b2218eb06e0db036eae5bbe9798009128f41;hb=4e3166c6b7348b10af5ee6526a83eaa78191b1b6;hp=2f962b5422e053a172a1e5800f59422fca76915a;hpb=8294bb03dcb1718915fe6ffa182d06b831352116;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 2f962b5..fb96b22 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; @@ -47,10 +48,8 @@ import java.util.Collections; import java.util.Enumeration; import java.util.HashMap; 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; @@ -73,12 +72,14 @@ public class StructureSelectionManager 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(); @@ -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) @@ -378,18 +380,26 @@ 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); - if (pdb.id != null && pdb.id.trim().length() > 0 + 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); + } + + if (pdb.getId() != null && pdb.getId().trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { - registerPDBFile(pdb.id.trim(), pdbFile); + registerPDBFile(pdb.getId().trim(), pdbFile); } } catch (Exception ex) { @@ -450,7 +460,7 @@ public class StructureSelectionManager String maxChainId = " "; 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) @@ -484,74 +494,117 @@ public class StructureSelectionManager if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) { - pdbFile = "INLINE" + pdb.id; + pdbFile = "INLINE" + pdb.getId(); } - ArrayList seqToStrucMapping = null; + ArrayList seqToStrucMapping = new ArrayList(); if (isMapUsingSIFTs) { setProgressBar(null); - setProgressBar("Obtaining mapping with SIFTS"); - try + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts")); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + 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); + maxChain.transferResidueAnnotation(siftsMapping, sqmpping); + } 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); + } + } + else { - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - seqToStrucMapping = new ArrayList(); - if (targetChainId != null && !targetChainId.trim().isEmpty()) + ArrayList foundSiftsMappings = new ArrayList(); + for (PDBChain chain : pdb.getChains()) { - StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, targetChainId); - seqToStrucMapping.add(curChainMapping); - maxChainId = targetChainId; - PDBChain chain = pdb.findChain(targetChainId); - if (chain != null) + try + { + StructureMapping siftsMapping = getStructureMapping(seq, + pdbFile, + chain.id, pdb, chain, sqmpping, maxAlignseq); + foundSiftsMappings.add(siftsMapping); + } catch (SiftsException e) { - chain.transferResidueAnnotation(curChainMapping, sqmpping); + System.err.println(e.getMessage()); } } + if (!foundSiftsMappings.isEmpty()) + { + seqToStrucMapping.addAll(foundSiftsMappings); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null); + maxChain.transferResidueAnnotation(foundSiftsMappings.get(0), + sqmpping); + } 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); } - } catch (SiftsException e) - { - e.printStackTrace(); - System.err - .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment"); - setProgressBar(null); - setProgressBar("SIFTs mapping could not be obtained... Now mapping with NW alignment"); - seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId, - maxChain, pdb, maxAlignseq); } } else { setProgressBar(null); - setProgressBar("Obtaining mapping with NW alignment"); - seqToStrucMapping = getNWMappings(seq, pdbFile, - maxChainId, maxChain, pdb, - maxAlignseq); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment")); + seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq)); } if (forStructureView) { - // mappings.add(seqToStrucMapping); mappings.addAll(seqToStrucMapping); } } return pdb; } - private ArrayList getNWMappings(SequenceI seq, + private boolean isCIFFile(String filename) + { + String fileExt = filename.substring(filename.lastIndexOf(".") + 1, + filename.length()); + return "cif".equalsIgnoreCase(fileExt); + } + + private StructureMapping getStructureMapping(SequenceI seq, + String pdbFile, String targetChainId, StructureFile pdb, + PDBChain maxChain, jalview.datamodel.Mapping sqmpping, + AlignSeq maxAlignseq) throws SiftsException + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(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, PDBfile pdb, + String maxChainId, PDBChain maxChain, StructureFile pdb, AlignSeq maxAlignseq) { final StringBuilder mappingDetails = new StringBuilder(128); @@ -602,17 +655,18 @@ 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 }); } @@ -622,11 +676,9 @@ 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) @@ -767,19 +819,19 @@ 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) + if (seqPos == -1) { - index = seq.findPosition(indexpos); + seqPos = seq.findPosition(indexpos); } for (int i = 0; i < listeners.size(); i++) { @@ -792,7 +844,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -806,12 +858,12 @@ 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()) @@ -829,7 +881,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -837,14 +889,14 @@ 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)) { @@ -854,14 +906,20 @@ 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)); + } } } } @@ -1017,13 +1075,13 @@ 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); } @@ -1258,7 +1316,16 @@ public class StructureSelectionManager public void setProgressBar(String message) { + if (progressIndicator == null) + { + return; + } progressIndicator.setProgressBar(message, progressSessionId); } + public List getSequenceMappings() + { + return seqmappings; + } + }