/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import MCview.*;
import jalview.analysis.*;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.*;
public class StructureSelectionManager
{
- static StructureSelectionManager instance;
+ static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
StructureMapping[] mappings;
+ /**
+ * debug function - write all mappings to stdout
+ */
+ public void reportMapping() {\r
+ if (mappings==null)\r
+ {\r
+ System.err.println("reportMapping: No PDB/Sequence mappings.");\r
+ }else{\r
+ System.err.println("reportMapping: There are "+mappings.length+" mappings.");\r
+ for (int m=0;m<mappings.length;m++)\r
+ {\r
+ System.err.println("mapping "+m+" : "+mappings[m].pdbfile);\r
+ }\r
+ }\r
+ }\r
Hashtable mappingData = new Hashtable();
- public static StructureSelectionManager getStructureSelectionManager()
+ public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
{
- if (instance == null)
+ if (instances == null)
{
- instance = new StructureSelectionManager();
+ instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+ }
+ StructureSelectionManager instance=instances.get(context);
+ if (instance==null)
+ {
+ instances.put(context, instance=new StructureSelectionManager());
}
-
return instance;
}
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 = "";
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],
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;
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
+ if (svl instanceof SequenceListener)
+ {
+ for (int i=0;i<listeners.size();i++)
+ {
+ if (listeners.elementAt(i) instanceof StructureListener)
+ {
+ ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+ }
+ }
+ }
+
if (pdbfiles == null)
{
return;
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)
{
results = new SearchResults();
}
- int indexpos;
if (mappings != null)
{
for (int j = 0; j < mappings.length; j++)
&& mappings[j].pdbchain.equals(chain))
{
indexpos = mappings[j].getSeqPos(pdbResNum);
- results.addResult(mappings[j].sequence, indexpos, indexpos);
- // construct highlighted sequence list
- if (seqmappings != null)
+ 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++)
{
* 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;
// 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);
}
}
}
* @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;
}
modifySeqMappingList(true, codonFrames);
}
- Vector sel_listeners = new Vector();
+ Vector<SelectionListener> sel_listeners = new Vector<SelectionListener>();
public void addSelectionListener(SelectionListener selecter)
{
}
}
}
+
+ Vector<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
+ 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<AlignmentViewPanelListener> 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)
+ {
+ }
+ ;
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff