X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e2cf3c9940f1085e9f1dd0449ed74badfb7ae683;hb=d0e72629ac2b7d5d35f151fc8cbec6365a4c1660;hp=b07b7a4f487dc0ad919e16d239f6d0dea40d8c7d;hpb=bc510a49947e32b3886275b869749cd3f42bde08;p=jalview.git
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index b07b7a4..e2cf3c9 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;
@@ -97,13 +96,28 @@ 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 +145,40 @@ 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());
@@ -212,8 +241,8 @@ 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 +250,42 @@ 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]);
}
@@ -259,6 +298,7 @@ public class StructureSelectionManager
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
+ boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
for (int i = 0; i < listeners.size(); i++)
{
@@ -267,36 +307,64 @@ public class StructureSelectionManager
if (results == null)
{
results = new SearchResults();
-
+ }
+ int indexpos;
+ if (mappings != null)
+ {
for (int j = 0; j < mappings.length; j++)
{
if (mappings[j].pdbfile.equals(pdbfile)
&& mappings[j].pdbchain.equals(chain))
{
- results.addResult(mappings[j].sequence, mappings[j]
- .getSeqPos(pdbResNum), mappings[j]
- .getSeqPos(pdbResNum));
+ indexpos = mappings[j].getSeqPos(pdbResNum);
+ results.addResult(mappings[j].sequence, indexpos, indexpos);
+ // construct highlighted sequence list
+ if (seqmappings != null)
+ {
+
+ Enumeration e = seqmappings.elements();
+ while (e.hasMoreElements())
+
+ {
+ ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+ mappings[j].sequence, indexpos, results);
+ }
+ }
}
}
}
- if (results.getSize() > 0)
- {
- ((SequenceListener) listeners.elementAt(i))
- .highlightSequence(results);
- }
-
+ }
+ }
+ if (results.getSize() > 0)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object li = listeners.elementAt(i);
+ if (li instanceof SequenceListener)
+ ((SequenceListener) li).highlightSequence(results);
}
}
}
Vector seqmappings = null; // should be a simpler list of mapped seuqence
- // pairs
-
- public void mouseOverSequence(SequenceI seq, int index)
+ /**
+ * highlight regions associated with a position (indexpos) in seq
+ *
+ * @param seq
+ * the sequeence that the mouse over occured on
+ * @param indexpos
+ * 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)
+ */
+ public void mouseOverSequence(SequenceI seq, int indexpos, int index)
{
boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
+ if (index == -1)
+ index = seq.findPosition(indexpos);
StructureListener sl;
int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
@@ -304,10 +372,14 @@ 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)
+ if (mappings[j].sequence == seq
+ || mappings[j].sequence == seq.getDatasetSequence())
{
atomNo = mappings[j].getAtomNum(index);
@@ -324,9 +396,9 @@ public class StructureSelectionManager
if (relaySeqMappings && hasSequenceListeners
&& listeners.elementAt(i) instanceof SequenceListener)
{
- // DEBUG
- //System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
- // index);
+ // DEBUG
+ // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
+ // index);
if (results == null)
{
@@ -335,7 +407,7 @@ public class StructureSelectionManager
{
// construct highlighted sequence list
- if (seqmappings!=null)
+ if (seqmappings != null)
{
Enumeration e = seqmappings.elements();
while (e.hasMoreElements())
@@ -348,6 +420,7 @@ public class StructureSelectionManager
// hasSequenceListeners = results.getSize() > 0;
if (handlingVamsasMo)
{
+ // maybe have to resolve seq to a dataset seqeunce...
// add in additional direct sequence and/or dataset sequence
// highlighting
results.addResult(seq, index, index);
@@ -363,11 +436,14 @@ public class StructureSelectionManager
else if (listeners.elementAt(i) instanceof VamsasListener
&& !handlingVamsasMo)
{
- // DEBUG
- //System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " +
+ // DEBUG
+ // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
+ // " +
// index);
- // pass the mouse over onto the VamsasListener(s)
- ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, index);
+ // pass the mouse over and absolute position onto the
+ // VamsasListener(s)
+ ((VamsasListener) listeners.elementAt(i))
+ .mouseOver(seq, indexpos);
}
}
}
@@ -379,16 +455,24 @@ public class StructureSelectionManager
*/
boolean handlingVamsasMo = false;
+ long lastmsg = 0;
+
/**
* as mouseOverSequence but only route event to SequenceListeners
*
* @param sequenceI
* @param position
+ * in an alignment sequence
*/
public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
{
handlingVamsasMo = true;
- mouseOverSequence(sequenceI, position);
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
+ {
+ lastmsg = msg;
+ mouseOverSequence(sequenceI, position, -1);
+ }
handlingVamsasMo = false;
}
@@ -407,9 +491,10 @@ 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);
+ }
+ ;
+ }
+ }
+ }
}