X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=32241a5c3de536c2ec9dc700cbd276e0c86691cd;hb=ce89ec35928a6cb2f05a655c44c39a0249beb2d6;hp=5a2ac7036d58cd6c2944ff9ef877688c923f4a28;hpb=9f3f8923d63c90a045c1ecefa0197a2acf6c7167;p=jalview.git
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 5a2ac70..32241a5 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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 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;
@@ -23,23 +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;
}
@@ -74,6 +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))
@@ -97,13 +121,28 @@ 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
{
@@ -113,16 +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 = "";
@@ -131,25 +186,37 @@ 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);
+ PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
+ if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
+ {
+ continue; // don't try to map chains don't match.
+ }
+ // 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 +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;
@@ -212,8 +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]);
}
// ///////
@@ -221,32 +290,53 @@ public class StructureSelectionManager
return pdb;
}
- public void removeStructureViewerListener(Object svl, String pdbfile)
+ public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
-
+ if (svl instanceof SequenceListener)
+ {
+ for (int i=0;i 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 +351,8 @@ 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)
@@ -269,31 +361,39 @@ 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++)
{
@@ -310,15 +410,15 @@ 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 +431,10 @@ 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 +501,8 @@ 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 +521,17 @@ 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 +551,10 @@ 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 sel_listeners = new Vector();
+
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
@@ -595,25 +703,95 @@ public class StructureSelectionManager
sel_listeners.addElement(selecter);
}
}
+
public void removeSelectionListener(SelectionListener toremove)
{
if (sel_listeners.contains(toremove))
{
- sel_listeners.remove(toremove);
+ sel_listeners.removeElement(toremove);
}
}
- public synchronized void sendSelection(jalview.datamodel.SequenceGroup selection, jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+
+ public synchronized void sendSelection(
+ jalview.datamodel.SequenceGroup selection,
+ jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
- if (sel_listeners!=null && sel_listeners.size()>0)
+ if (sel_listeners != null && sel_listeners.size() > 0)
{
Enumeration listeners = sel_listeners.elements();
while (listeners.hasMoreElements())
{
- SelectionListener slis = ((SelectionListener) listeners.nextElement());
- if (slis!=source) {
- slis.selection(selection, colsel, source);
- };
+ SelectionListener slis = ((SelectionListener) listeners
+ .nextElement());
+ if (slis != source)
+ {
+ slis.selection(selection, colsel, source);
+ }
+ ;
+ }
+ }
+ }
+
+ 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)
+ {
+ StructureSelectionManager mnger=(instances.get(jalviewLite));
+ if (mnger!=null)
+ {
+ instances.remove(jalviewLite);
+ try {
+ mnger.finalize();
+ } catch (Throwable x){};
+ }
+ }
+
}