/*
- * 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.
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;
}
Vector listeners = new Vector();
+ /**
+ * register a listener for alignment sequence mouseover events
+ * @param svl
+ */
public void addStructureViewerListener(Object svl)
{
if (!listeners.contains(svl))
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
{
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());
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;
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]);
}
// ///////
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
- if (pdbfiles==null)
+ 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;
}
}
}
-
- if (pdbs.size()>0 && mappings != null)
+
+ if (pdbs.size() > 0 && mappings != null)
{
Vector tmp = new Vector();
for (int i = 0; i < mappings.length; i++)
{
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;
- 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++)
{
* 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;
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- if (mappings==null)
+ if (mappings == null)
{
continue;
}
// 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);
}
}
}
* @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;
}
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++)
{
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)
+ {
+ StructureSelectionManager mnger=(instances.get(jalviewLite));
+ if (mnger!=null)
+ {
+ instances.remove(jalviewLite);
+ try {
+ mnger.finalize();
+ } catch (Throwable x){};
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff