X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=678bf3bf26796890b657f9a7c1c648c4cfc90e50;hb=e57ac4e703658ff81d7e172222e718ff7611e96e;hp=e9d736f1dafd1cb17f769af265fa2783a4540776;hpb=a21b84a669a9620f6943b9b5054e8756cb6f0687;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index e9d736f..678bf3b 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -33,9 +33,11 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; -import jalview.io.SiftsClient; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.ws.sifts.SiftsClient; +import jalview.ws.sifts.SiftsException; +import jalview.ws.sifts.SiftsSettings; import java.io.PrintStream; import java.util.ArrayList; @@ -325,9 +327,9 @@ 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 + * @param targetChainIds * - optional chain specification for mapping each sequence to pdb * (may be nill, individual elements may be nill) * @param pdbFile @@ -337,7 +339,8 @@ 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[] targetChainIds, + String pdbFile, String protocol) { /* @@ -347,7 +350,7 @@ public class StructureSelectionManager boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) { - for (SequenceI sq : sequence) + for (SequenceI sq : sequenceArray) { SequenceI ds = sq; while (ds.getDatasetSequence() != null) @@ -371,10 +374,13 @@ public class StructureSelectionManager } } PDBfile 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 && AppletFormatAdapter.FILE.equals(protocol)) { @@ -386,36 +392,48 @@ public class StructureSelectionManager return null; } - String targetChain; - for (int s = 0; s < sequence.length; s++) + try + { + if (isMapUsingSIFTs) + { + siftsClient = new SiftsClient(pdb); + } + } catch (SiftsException e) + { + isMapUsingSIFTs = false; + e.printStackTrace(); + } + + String targetChainId; + for (int s = 0; s < sequenceArray.length; s++) { boolean infChain = true; - final SequenceI seq = sequence[s]; - if (targetChains != null && targetChains[s] != null) + final SequenceI seq = sequenceArray[s]; + if (targetChainIds != null && targetChainIds[s] != null) { infChain = false; - targetChain = targetChains[s]; + targetChainId = targetChainIds[s]; } else if (seq.getName().indexOf("|") > -1) { - targetChain = seq.getName().substring( + targetChainId = seq.getName().substring( seq.getName().lastIndexOf("|") + 1); - if (targetChain.length() > 1) + if (targetChainId.length() > 1) { - if (targetChain.trim().length() == 0) + if (targetChainId.trim().length() == 0) { - targetChain = " "; + targetChainId = " "; } else { // not a valid chain identifier - targetChain = ""; + targetChainId = ""; } } } else { - targetChain = ""; + targetChainId = ""; } /* @@ -429,7 +447,7 @@ public class StructureSelectionManager boolean first = true; for (PDBChain chain : pdb.chains) { - if (targetChain.length() > 0 && !targetChain.equals(chain.id) + if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) && !infChain) { continue; // don't try to map chains don't match. @@ -445,7 +463,7 @@ public class StructureSelectionManager // as.traceAlignment(); if (first || as.maxscore > max - || (as.maxscore == max && chain.id.equals(targetChain))) + || (as.maxscore == max && chain.id.equals(targetChainId))) { first = false; maxChain = chain; @@ -458,98 +476,100 @@ 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); - } - }; - - // mapWithNWAlignment(); - // mapWithSIFTS(); - 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 "); - // TODO JAL-1887 should be fixed from here - 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) + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + seqToStrucMapping = new ArrayList(); + if (targetChainId != null && !targetChainId.trim().isEmpty()) + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChainId); + seqToStrucMapping.add(curChainMapping); + maxChainId = targetChainId; + PDBChain chain = pdb.findChain(targetChainId); + if (chain != null) + { + chain.transferResidueAnnotation(curChainMapping, sqmpping); + } + } + else { - // 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; + for (PDBChain chain : pdb.chains) + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, chain.id); + seqToStrucMapping.add(curChainMapping); + maxChainId = chain.id; + chain.transferResidueAnnotation(curChainMapping, sqmpping); + } } + } 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); } - - 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()); - StructureMapping newMapping = new SiftsClient(pdb.id) - .getSiftsMappingsFor(seq, pdbFile, maxChainId); + if (forStructureView) { - mappings.add(newMapping); + // mappings.add(seqToStrucMapping); + mappings.addAll(seqToStrucMapping); } - maxChain.transferResidueAnnotation(newMapping, sqmpping); } - // /////// - return pdb; } - private StructureMapping mapWithNWAlignment(StringBuilder mappingDetails, - PDBChain maxChain, AlignSeq maxAlignseq, SequenceI seq, - PrintStream ps) + 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 "); @@ -557,23 +577,18 @@ public class StructureSelectionManager .append(" "); mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); mappingDetails.append(NEWLINE).append("SEQ start/end "); - // TODO JAL-1887 should be fixed from here mappingDetails.append( - String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1)) + String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1))) .append(" "); - mappingDetails.append(String.valueOf(maxAlignseq.seq1end + seq.getEnd() - - 1)); - + mappingDetails.append(String.valueOf(maxAlignseq.seq1end + + (seq.getStart() - 1))); + mappingDetails.append(NEWLINE); 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]; + HashMap mapping = new HashMap(); int resNum = -10000; int index = 0; @@ -587,15 +602,20 @@ public class StructureSelectionManager { // 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; + mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber, + tmp.atomIndex }); } } index++; } while (index < maxChain.atoms.size()); - return null; + 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)