X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e1aa9dc8970945f3568d06682a149c2821eb50da;hb=2026a420963f094072607c0495b6369ba96e60c0;hp=936f13916d3680f77617e23b9ce8bde3b31620ef;hpb=a90e0eeb2b61e962b86e9dcef586f9e4224405b0;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 936f139..e1aa9dc 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -22,23 +22,44 @@ import java.util.*; import MCview.*; import jalview.analysis.*; +import jalview.api.AlignmentViewPanel; +import jalview.api.StructureSelectionManagerProvider; import jalview.datamodel.*; public class StructureSelectionManager { - static StructureSelectionManager instance; + static IdentityHashMap instances; StructureMapping[] mappings; + /** + * debug function - write all mappings to stdout + */ + public void reportMapping() { + if (mappings==null) + { + System.err.println("reportMapping: No PDB/Sequence mappings."); + }else{ + System.err.println("reportMapping: There are "+mappings.length+" mappings."); + for (int m=0;m(); + } + StructureSelectionManager instance=instances.get(context); + if (instance==null) + { + instances.put(context, instance=new StructureSelectionManager()); } - return instance; } @@ -73,6 +94,10 @@ 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)) @@ -97,12 +122,18 @@ public class StructureSelectionManager } /** - * create sequence structure mappings between each sequence and the given pdbFile (retrieved via the given protocol). + * 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 + * @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, @@ -121,16 +152,32 @@ public class StructureSelectionManager ex.printStackTrace(); return null; } - + String targetChain; for (int s = 0; s < sequence.length; s++) { + boolean infChain = true; if (targetChains != null && targetChains[s] != null) + { + infChain = false; targetChain = targetChains[s]; + } else if (sequence[s].getName().indexOf("|") > -1) { targetChain = sequence[s].getName().substring( sequence[s].getName().lastIndexOf("|") + 1); + if (targetChain.length() > 1) + { + if (targetChain.trim().length() == 0) + { + targetChain = " "; + } + else + { + // not a valid chain identifier + targetChain = ""; + } + } } else targetChain = ""; @@ -139,35 +186,34 @@ public class StructureSelectionManager AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; - boolean first=true; + 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)) + if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain) { 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(); if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals(targetChain))) { - first=false; + first = false; maxChain = chain; max = as.maxscore; maxAlignseq = as; maxChainId = chain.id; } } - if (maxChain==null) + if (maxChain == null) { continue; } @@ -201,7 +247,9 @@ 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[sequence[s].findPosition(sequence[s].getLength()) + 2][2]; int resNum = -10000; int index = 0; @@ -233,8 +281,8 @@ 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]); } // /////// @@ -245,7 +293,18 @@ public class StructureSelectionManager public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl); - if (pdbfiles==null) + if (svl instanceof SequenceListener) + { + for (int i=0;i0 && mappings != null) + + if (pdbs.size() > 0 && mappings != null) { Vector tmp = new Vector(); for (int i = 0; i < mappings.length; i++) @@ -290,8 +349,15 @@ public class StructureSelectionManager public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) { + if (listeners==null) + { + // old or prematurely sent event + return; + } 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) @@ -300,31 +366,39 @@ 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); + } + } } + } } } } } - if (results.getSize() > 0) + if (results!=null) { for (int i = 0; i < listeners.size(); i++) { @@ -348,7 +422,8 @@ 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; @@ -361,7 +436,7 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - if (mappings==null) + if (mappings == null) { continue; } @@ -431,8 +506,11 @@ 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); + } + else if(listeners.elementAt(i) instanceof SecondaryStructureListener){ + ((SecondaryStructureListener) listeners.elementAt(i)).mouseOverSequence(seq,indexpos); } } } @@ -453,14 +531,15 @@ 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; } @@ -524,14 +603,16 @@ 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++) { @@ -621,7 +702,7 @@ public class StructureSelectionManager modifySeqMappingList(true, codonFrames); } - Vector sel_listeners = new Vector(); + Vector sel_listeners = new Vector(); public void addSelectionListener(SelectionListener selecter) { @@ -658,4 +739,78 @@ public class StructureSelectionManager } } } + + Vector view_listeners=new Vector(); + public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes, + int endRes, int startSeq, int endSeq) + { + + if (view_listeners != null && view_listeners.size() > 0) + { + Enumeration listeners = view_listeners.elements(); + while (listeners.hasMoreElements()) + { + AlignmentViewPanelListener slis = listeners + .nextElement(); + if (slis != source) + { + slis.viewPosition(startRes, endRes, startSeq, endSeq, source); + } + ; + } + } + } + + + public void finalize() throws Throwable { + if (listeners!=null) { + listeners.clear(); + listeners=null; + } + if (mappingData!=null) + { + mappingData.clear(); + mappingData=null; + } + if (sel_listeners!=null) + { + sel_listeners.clear(); + sel_listeners=null; + } + if (view_listeners!=null) + { + view_listeners.clear(); + view_listeners=null; + } + mappings=null; + seqmappingrefs=null; + } + + /** + * release all references associated with this manager provider + * @param jalviewLite + */ + public static void release(StructureSelectionManagerProvider jalviewLite) + { +// synchronized (instances) + { + if (instances == null) + { + return; + } + StructureSelectionManager mnger = (instances.get(jalviewLite)); + if (mnger != null) + { + instances.remove(jalviewLite); + try + { + mnger.finalize(); + } catch (Throwable x) + { + } + ; + } + } + } + }