X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=a5d973649ae24f680dad7e6e43ebcee65b685207;hb=5585b4b0ed1f5dd85887ed6b76352947ce1be133;hp=4da715e7699ba0b1768d5475a733334cacaa5833;hpb=07f0cb34d94a87585e56f0128af5201699c1b1b4;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 4da715e..a5d9736 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) @@ -378,17 +380,26 @@ 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 + 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) { @@ -449,7 +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) @@ -483,7 +494,7 @@ public class StructureSelectionManager if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) { - pdbFile = "INLINE" + pdb.id; + pdbFile = "INLINE" + pdb.getId(); } ArrayList seqToStrucMapping = new ArrayList(); @@ -501,7 +512,7 @@ public class StructureSelectionManager } else { - for (PDBChain chain : pdb.chains) + for (PDBChain chain : pdb.getChains()) { StructureMapping mapping = getStructureMapping(seq, pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq); @@ -525,8 +536,15 @@ 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) { @@ -535,11 +553,17 @@ public class StructureSelectionManager { 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) { @@ -554,7 +578,7 @@ public class StructureSelectionManager 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); @@ -605,17 +629,18 @@ 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 }); } @@ -625,7 +650,7 @@ 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; } @@ -768,19 +793,19 @@ 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++) { @@ -793,7 +818,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -807,12 +832,12 @@ 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()) @@ -830,7 +855,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -838,14 +863,14 @@ 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)) { @@ -855,14 +880,20 @@ 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)); + } } } } @@ -1259,6 +1290,10 @@ public class StructureSelectionManager public void setProgressBar(String message) { + if (progressIndicator == null) + { + return; + } progressIndicator.setProgressBar(message, progressSessionId); }