X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=be042e6b6476a7491dc7494d89a138d6771662d9;hb=134291d04042b3d7252598a9f73753f40da08a18;hp=9d06aef88ff0dfd78a57460e1f76dfa5e0d70740;hpb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 9d06aef..be042e6 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; @@ -80,7 +79,7 @@ public class StructureSelectionManager /* * Set of any registered mappings between (dataset) sequences. */ - public Set seqmappings = new LinkedHashSet(); + private List seqmappings = new ArrayList(); private List commandListeners = new ArrayList(); @@ -321,12 +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). @@ -345,7 +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) @@ -380,17 +380,30 @@ public class StructureSelectionManager } } } - PDBfile pdb = null; + StructureFile pdb = null; boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); - if (pdb.id != null && pdb.id.trim().length() > 0 + 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)) { - registerPDBFile(pdb.id.trim(), pdbFile); + registerPDBFile(pdb.getId().trim(), pdbFile); } } catch (Exception ex) { @@ -451,7 +464,7 @@ 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) @@ -485,36 +498,74 @@ public class StructureSelectionManager if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) { - pdbFile = "INLINE" + pdb.id; + pdbFile = "INLINE" + pdb.getId(); } ArrayList seqToStrucMapping = new ArrayList(); if (isMapUsingSIFTs) { 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); + 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 { - for (PDBChain chain : pdb.chains) + 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); + maxChain.transferResidueAnnotation(foundSiftsMappings.get(0), + sqmpping); + } + else + { + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); } } } else { setProgressBar(null); - setProgressBar("Obtaining mapping with NW alignment"); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment")); seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq)); } @@ -527,36 +578,37 @@ public class StructureSelectionManager return pdb; } + 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, 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 + { PDBChain chain = pdb.findChain(targetChainId); if (chain != null) { chain.transferResidueAnnotation(curChainMapping, sqmpping); } + } catch (Exception e) + { + 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); @@ -628,7 +680,7 @@ 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); return nwMapping; } @@ -771,19 +823,19 @@ 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++) { @@ -796,7 +848,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -810,12 +862,12 @@ 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()) @@ -833,7 +885,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -841,14 +893,14 @@ 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)) { @@ -858,14 +910,20 @@ 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)); + } } } } @@ -1021,13 +1079,13 @@ 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); } @@ -1262,7 +1320,16 @@ public class StructureSelectionManager public void setProgressBar(String message) { + if (progressIndicator == null) + { + return; + } progressIndicator.setProgressBar(message, progressSessionId); } + public List getSequenceMappings() + { + return seqmappings; + } + }