X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;fp=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=3d5a97576e2221e81a5ceb127302a9709b6ef74b;hb=605217afe6b4bb56ddd2e5925941ed8fa1bc9d32;hp=26b7d484c93411f0be4557e54a394d64ebd3eb2f;hpb=a7c333565f975ce40069334efe291d035580c253;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 26b7d48..3d5a975 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -35,6 +35,8 @@ import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.ws.sifts.SiftsClient; +import jalview.ws.sifts.SiftsException; import java.io.PrintStream; import java.util.ArrayList; @@ -324,7 +326,7 @@ public class StructureSelectionManager * @param forStructureView * when true, record the mapping for use in mouseOvers * - * @param sequence + * @param sequenceArray * - one or more sequences to be mapped to pdbFile * @param targetChains * - optional chain specification for mapping each sequence to pdb @@ -336,7 +338,7 @@ public class StructureSelectionManager * @return null or the structure data parsed as a pdb file */ synchronized public PDBfile setMapping(boolean forStructureView, - SequenceI[] sequence, String[] targetChains, String pdbFile, + SequenceI[] sequenceArray, String[] targetChains, String pdbFile, String protocol) { /* @@ -346,7 +348,7 @@ public class StructureSelectionManager boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) { - for (SequenceI sq : sequence) + for (SequenceI sq : sequenceArray) { SequenceI ds = sq; while (ds.getDatasetSequence() != null) @@ -370,15 +372,25 @@ public class StructureSelectionManager } } PDBfile pdb = null; + boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault( + "MAP_WITH_SIFTS", "false")); + SiftsClient siftsClient = null; try { pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, pdbFile, protocol); + if (isMapUsingSIFTs) + { + siftsClient = new SiftsClient(pdb); + } if (pdb.id != null && pdb.id.trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { registerPDBFile(pdb.id.trim(), pdbFile); } + } catch (SiftsException e) + { + e.printStackTrace(); } catch (Exception ex) { ex.printStackTrace(); @@ -386,10 +398,10 @@ public class StructureSelectionManager } String targetChain; - for (int s = 0; s < sequence.length; s++) + for (int s = 0; s < sequenceArray.length; s++) { boolean infChain = true; - final SequenceI seq = sequence[s]; + final SequenceI seq = sequenceArray[s]; if (targetChains != null && targetChains[s] != null) { infChain = false; @@ -457,90 +469,141 @@ public class StructureSelectionManager { continue; } - final StringBuilder mappingDetails = new StringBuilder(128); - mappingDetails.append(NEWLINE).append("PDB Sequence is :") - .append(NEWLINE).append("Sequence = ") - .append(maxChain.sequence.getSequenceAsString()); - mappingDetails.append(NEWLINE).append("No of residues = ") - .append(maxChain.residues.size()).append(NEWLINE) - .append(NEWLINE); - PrintStream ps = new PrintStream(System.out) + + if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) { - @Override - public void print(String x) - { - mappingDetails.append(x); - } + pdbFile = "INLINE" + pdb.id; + } - @Override - public void println() - { - mappingDetails.append(NEWLINE); - } - }; - - maxAlignseq.printAlignment(ps); - - mappingDetails.append(NEWLINE).append("PDB start/end "); - mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append( - " "); - mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); - - mappingDetails.append(NEWLINE).append("SEQ start/end "); - mappingDetails.append( - String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1)) - .append(" "); - mappingDetails.append(String.valueOf(maxAlignseq.seq1end - + seq.getEnd() - 1)); - - maxChain.makeExactMapping(maxAlignseq, seq); - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping( - sqmpping.getMap().getInverse()); - maxChain.transferRESNUMFeatures(seq, null); - - // allocate enough slots to store the mapping from positions in - // sequence[s] to the associated chain - int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2]; - int resNum = -10000; - int index = 0; - - do + ArrayList seqToStrucMapping = null; + if (isMapUsingSIFTs) { - Atom tmp = maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + try { - resNum = tmp.resNumber; - if (tmp.alignmentMapping >= -1) + seqToStrucMapping = new ArrayList(); + if (targetChain != null && !targetChain.trim().isEmpty()) { - // TODO (JAL-1836) address root cause: negative residue no in PDB - // file - mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; + maxChainId = targetChain; + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChain); + seqToStrucMapping.add(curChainMapping); } + else + { + for (PDBChain chain : pdb.chains) + { + maxChainId = chain.id; + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, chain.id); + seqToStrucMapping.add(curChainMapping); + } + } + } catch (SiftsException e) + { + System.err + .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment"); + seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq); } - - index++; - } while (index < maxChain.atoms.size()); - - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + } + else { - pdbFile = "INLINE" + pdb.id; + seqToStrucMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, + maxAlignseq); } - StructureMapping newMapping = new StructureMapping(seq, pdbFile, - pdb.id, maxChainId, mapping, mappingDetails.toString()); + if (forStructureView) { - mappings.add(newMapping); + // mappings.add(seqToStrucMapping); + mappings.addAll(seqToStrucMapping); } - maxChain.transferResidueAnnotation(newMapping, sqmpping); } - // /////// - return pdb; } + private ArrayList getNWMappings(SequenceI seq, + String pdbFile, + String maxChainId, PDBChain maxChain, PDBfile pdb, + AlignSeq maxAlignseq) + { + final StringBuilder mappingDetails = new StringBuilder(128); + mappingDetails.append(NEWLINE).append( + "Sequence \u27f7 Structure mapping details"); + mappingDetails.append(NEWLINE); + mappingDetails + .append("Method: inferred with Needleman & Wunsch alignment"); + mappingDetails.append(NEWLINE).append("PDB Sequence is :") + .append(NEWLINE).append("Sequence = ") + .append(maxChain.sequence.getSequenceAsString()); + mappingDetails.append(NEWLINE).append("No of residues = ") + .append(maxChain.residues.size()).append(NEWLINE) + .append(NEWLINE); + PrintStream ps = new PrintStream(System.out) + { + @Override + public void print(String x) + { + mappingDetails.append(x); + } + + @Override + public void println() + { + mappingDetails.append(NEWLINE); + } + }; + + maxAlignseq.printAlignment(ps); + + mappingDetails.append(NEWLINE).append("PDB start/end "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2start)) + .append(" "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); + mappingDetails.append(NEWLINE).append("SEQ start/end "); + mappingDetails.append( + String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1))) + .append(" "); + mappingDetails.append(String.valueOf(maxAlignseq.seq1end + + (seq.getStart() - 1))); + mappingDetails.append(NEWLINE); + maxChain.makeExactMapping(maxAlignseq, seq); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + maxChain.transferRESNUMFeatures(seq, null); + + // allocate enough slots to store the mapping from positions in + // sequence[s] to the associated chain + int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2]; + int resNum = -10000; + int index = 0; + + do + { + Atom tmp = maxChain.atoms.elementAt(index); + if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + { + resNum = tmp.resNumber; + if (tmp.alignmentMapping >= -1) + { + // TODO (JAL-1836) address root cause: negative residue no in PDB + // file + mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; + mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; + } + } + + index++; + } while (index < maxChain.atoms.size()); + + StructureMapping nwMapping = new StructureMapping(seq, pdbFile, + pdb.id, maxChainId, mapping, mappingDetails.toString()); + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ArrayList mappings = new ArrayList(); + mappings.add(nwMapping); + return mappings; + } + public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl);