X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0e4ec2fa50fb609a8e07a0d4d5edb9ea6c98d4f9;hb=2f3b33ed7140d07e2bb31960ce5aedfed134dfeb;hp=d2b336d3dec563a2e30aa0640517da5e573a67a4;hpb=f8456d4c0b253ae32a4b569e12bb8bf7f7096d65;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index d2b336d..0e4ec2f 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. @@ -73,6 +73,10 @@ public class StructureSelectionManager Vector listeners = new Vector(); + /** + * register a listener for alignment sequence mouseover events + * @param svl + */ public void addStructureViewerListener(Object svl) { if (!listeners.contains(svl)) @@ -96,13 +100,28 @@ public class StructureSelectionManager return null; } - /* - * There will be better ways of doing this in the future, for now we'll use - * the tried and tested MCview pdb mapping + /** + * create sequence structure mappings between each sequence and the given + * pdbFile (retrieved via the given protocol). + * + * @param sequence + * - one or more sequences to be mapped to pdbFile + * @param targetChains + * - optional chain specification for mapping each sequence to pdb + * (may be nill, individual elements may be nill) + * @param pdbFile + * - structure data resource + * @param protocol + * - how to resolve data from resource + * @return null or the structure data parsed as a pdb file */ synchronized public MCview.PDBfile setMapping(SequenceI[] sequence, String[] targetChains, String pdbFile, String protocol) { + /* + * There will be better ways of doing this in the future, for now we'll use + * the tried and tested MCview pdb mapping + */ MCview.PDBfile pdb = null; try { @@ -130,29 +149,40 @@ public class StructureSelectionManager AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; - + boolean first = true; for (int i = 0; i < pdb.chains.size(); i++) { - + // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may + // need to be revoked + PDBChain chain = ((PDBChain) pdb.chains.elementAt(i)); + if (targetChain.length() > 0 && !targetChain.equals(chain.id)) + { + continue; // don't try to map chains don't match. + } + // end of patch for limiting computed mappings // TODO: correctly determine sequence type for mixed na/peptide // structures - AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains - .elementAt(i)).sequence, ((PDBChain) pdb.chains - .elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP); + AlignSeq as = new AlignSeq(sequence[s], + ((PDBChain) pdb.chains.elementAt(i)).sequence, + ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA + : AlignSeq.PEP); as.calcScoreMatrix(); as.traceAlignment(); - PDBChain chain = ((PDBChain) pdb.chains.elementAt(i)); - if (as.maxscore > max + if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals(targetChain))) { + first = false; maxChain = chain; max = as.maxscore; maxAlignseq = as; maxChainId = chain.id; } } - + if (maxChain == null) + { + continue; + } final StringBuffer mappingDetails = new StringBuffer(); mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + maxChain.sequence.getSequenceAsString()); @@ -183,7 +213,9 @@ public class StructureSelectionManager maxChain.transferRESNUMFeatures(sequence[s], null); - int[][] mapping = new int[sequence[s].getEnd() + 2][2]; + // allocate enough slots to store the mapping from positions in + // sequence[s] to the associated chain + int[][] mapping = new int[maxChain.sequence.getEnd() + 2][2]; int resNum = -10000; int index = 0; @@ -215,8 +247,8 @@ public class StructureSelectionManager pdbFile = "INLINE" + pdb.id; mappings[mappings.length - 1] = new StructureMapping(sequence[s], - pdbFile, pdb.id, maxChainId, mapping, mappingDetails - .toString()); + pdbFile, pdb.id, maxChainId, mapping, + mappingDetails.toString()); maxChain.transferResidueAnnotation(mappings[mappings.length - 1]); } // /////// @@ -227,7 +259,7 @@ public class StructureSelectionManager public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl); - if (pdbfiles==null) + if (pdbfiles == null) { return; } @@ -253,8 +285,8 @@ public class StructureSelectionManager } } - - if (pdbs.size()>0 && mappings != null) + + if (pdbs.size() > 0 && mappings != null) { Vector tmp = new Vector(); for (int i = 0; i < mappings.length; i++) @@ -274,6 +306,8 @@ public class StructureSelectionManager { boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null; SearchResults results = null; + SequenceI lastseq = null; + int lastipos = -1, indexpos; for (int i = 0; i < listeners.size(); i++) { if (listeners.elementAt(i) instanceof SequenceListener) @@ -282,25 +316,33 @@ public class StructureSelectionManager { results = new SearchResults(); } - int indexpos; - for (int j = 0; j < mappings.length; j++) + if (mappings != null) { - if (mappings[j].pdbfile.equals(pdbfile) - && mappings[j].pdbchain.equals(chain)) + for (int j = 0; j < mappings.length; j++) { - indexpos = mappings[j].getSeqPos(pdbResNum); - results.addResult(mappings[j].sequence, indexpos, indexpos); - // construct highlighted sequence list - if (seqmappings != null) + if (mappings[j].pdbfile.equals(pdbfile) + && mappings[j].pdbchain.equals(chain)) { + indexpos = mappings[j].getSeqPos(pdbResNum); + if (lastipos != indexpos && lastseq != mappings[j].sequence) + { + results.addResult(mappings[j].sequence, indexpos, indexpos); + lastipos = indexpos; + lastseq = mappings[j].sequence; + // construct highlighted sequence list + if (seqmappings != null) + { - Enumeration e = seqmappings.elements(); - while (e.hasMoreElements()) + Enumeration e = seqmappings.elements(); + while (e.hasMoreElements()) - { - ((AlignedCodonFrame) e.nextElement()).markMappedRegion( - mappings[j].sequence, indexpos, results); + { + ((AlignedCodonFrame) e.nextElement()).markMappedRegion( + mappings[j].sequence, indexpos, results); + } + } } + } } } @@ -330,7 +372,8 @@ public class StructureSelectionManager * 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 index, + VamsasSource source) { boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null; SearchResults results = null; @@ -343,7 +386,10 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - + if (mappings == null) + { + continue; + } for (int j = 0; j < mappings.length; j++) { if (mappings[j].sequence == seq @@ -410,8 +456,8 @@ public class StructureSelectionManager // index); // pass the mouse over and absolute position onto the // VamsasListener(s) - ((VamsasListener) listeners.elementAt(i)) - .mouseOver(seq, indexpos); + ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, + indexpos, source); } } } @@ -432,14 +478,15 @@ public class StructureSelectionManager * @param position * in an alignment sequence */ - public void mouseOverVamsasSequence(SequenceI sequenceI, int position) + public void mouseOverVamsasSequence(SequenceI sequenceI, int position, + VamsasSource source) { handlingVamsasMo = true; long msg = sequenceI.hashCode() * (1 + position); if (lastmsg != msg) { lastmsg = msg; - mouseOverSequence(sequenceI, position, -1); + mouseOverSequence(sequenceI, position, -1, source); } handlingVamsasMo = false; } @@ -503,14 +550,16 @@ public class StructureSelectionManager public StructureMapping[] getMapping(String pdbfile) { Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) + if (mappings != null) { - if (mappings[i].pdbfile.equals(pdbfile)) + for (int i = 0; i < mappings.length; i++) { - tmp.addElement(mappings[i]); + if (mappings[i].pdbfile.equals(pdbfile)) + { + tmp.addElement(mappings[i]); + } } } - StructureMapping[] ret = new StructureMapping[tmp.size()]; for (int i = 0; i < tmp.size(); i++) {