X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0e4ec2fa50fb609a8e07a0d4d5edb9ea6c98d4f9;hb=d038c9702429f76a1556c7d2b282f26d9feb22f6;hp=e12e3abfa2ea14833f3dd85ed4928b339b203db5;hpb=30fbdf1d58c59dff55b3ba29c6135b2ad223383c;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index e12e3ab..0e4ec2f 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.structure; @@ -74,6 +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)) @@ -97,13 +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 { @@ -131,25 +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++) { - AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains - .elementAt(i)).sequence, AlignSeq.PEP); + // 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); 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()); @@ -180,7 +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; @@ -212,8 +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]); } // /////// @@ -221,32 +256,42 @@ public class StructureSelectionManager return pdb; } - public void removeStructureViewerListener(Object svl, String pdbfile) + public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl); - + if (pdbfiles == null) + { + return; + } boolean removeMapping = true; - + String[] handlepdbs; + Vector pdbs = new Vector(); + for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++])) + ; StructureListener sl; for (int i = 0; i < listeners.size(); i++) { if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - if (sl.getPdbFile().equals(pdbfile)) + handlepdbs = sl.getPdbFile(); + for (int j = 0; j < handlepdbs.length; j++) { - removeMapping = false; - break; + if (pdbs.contains(handlepdbs[j])) + { + pdbs.removeElement(handlepdbs[j]); + } } + } } - if (removeMapping && mappings != null) + if (pdbs.size() > 0 && mappings != null) { Vector tmp = new Vector(); for (int i = 0; i < mappings.length; i++) { - if (!mappings[i].pdbfile.equals(pdbfile)) + if (!pdbs.contains(mappings[i].pdbfile)) { tmp.addElement(mappings[i]); } @@ -261,6 +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) @@ -269,25 +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)) { - - Enumeration e = seqmappings.elements(); - while (e.hasMoreElements()) - + indexpos = mappings[j].getSeqPos(pdbResNum); + if (lastipos != indexpos && lastseq != mappings[j].sequence) { - ((AlignedCodonFrame) e.nextElement()).markMappedRegion( - mappings[j].sequence, indexpos, results); + 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()) + + { + ((AlignedCodonFrame) e.nextElement()).markMappedRegion( + mappings[j].sequence, indexpos, results); + } + } } + } } } @@ -310,15 +365,15 @@ public class StructureSelectionManager * highlight regions associated with a position (indexpos) in seq * * @param seq - * the sequeence that the mouse over occured on + * the sequeence that the mouse over occured on * @param indexpos - * the absolute position being mouseovered in seq (0 to - * seq.length()) + * the absolute position being mouseovered in seq (0 to seq.length()) * @param index - * the sequence position (if -1, seq.findPosition is called to - * resolve the residue number) + * 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; @@ -331,7 +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 @@ -398,8 +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); } } } @@ -418,16 +476,17 @@ public class StructureSelectionManager * * @param sequenceI * @param position - * in an alignment sequence + * 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; } @@ -447,9 +506,10 @@ public class StructureSelectionManager * * for (int j = 0; j < mappings.length; j++) { * - * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid) && - * mappings[j].pdbfile.equals(sl.getPdbFile())) { System.out.println(pdbid+" - * "+mappings[j].getPdbId() +" "+mappings[j].pdbfile); + * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid) + * && mappings[j].pdbfile.equals(sl.getPdbFile())) { + * System.out.println(pdbid+" "+mappings[j].getPdbId() +" + * "+mappings[j].pdbfile); * * java.awt.Color col; for(int index=0; index 0) + { + Enumeration listeners = sel_listeners.elements(); + while (listeners.hasMoreElements()) + { + SelectionListener slis = ((SelectionListener) listeners + .nextElement()); + if (slis != source) + { + slis.selection(selection, colsel, source); + } + ; + } + } + } }