X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=478706a74f6c98d7c970b36ed50552362f6dc869;hb=2c6965c96b057296981403f3394a4c180ed60ea4;hp=d33c380cf3109ffabb543ee02ce092c3b3da57b4;hpb=95bf0ccfad1458a77d30394f4b60b40a9794dd9c;p=jalview.git
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index d33c380..478706a 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 2.5)
+ * 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;
@@ -259,6 +258,7 @@ 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++)
{
@@ -267,41 +267,61 @@ public class StructureSelectionManager
if (results == null)
{
results = new SearchResults();
-
- for (int j = 0; j < mappings.length; j++)
+ }
+ int indexpos;
+ for (int j = 0; j < mappings.length; j++)
+ {
+ if (mappings[j].pdbfile.equals(pdbfile)
+ && mappings[j].pdbchain.equals(chain))
{
- if (mappings[j].pdbfile.equals(pdbfile)
- && mappings[j].pdbchain.equals(chain))
+ indexpos = mappings[j].getSeqPos(pdbResNum);
+ results.addResult(mappings[j].sequence, indexpos, indexpos);
+ // construct highlighted sequence list
+ if (seqmappings != null)
{
- results.addResult(mappings[j].sequence, mappings[j]
- .getSeqPos(pdbResNum), mappings[j]
- .getSeqPos(pdbResNum));
+
+ 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
+
/**
* 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)
+ *
+ * @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);
+ if (index == -1)
+ index = seq.findPosition(indexpos);
StructureListener sl;
int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
@@ -312,7 +332,8 @@ public class StructureSelectionManager
for (int j = 0; j < mappings.length; j++)
{
- if (mappings[j].sequence == seq || mappings[j].sequence==seq.getDatasetSequence())
+ if (mappings[j].sequence == seq
+ || mappings[j].sequence == seq.getDatasetSequence())
{
atomNo = mappings[j].getAtomNum(index);
@@ -329,9 +350,9 @@ 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)
{
@@ -340,7 +361,7 @@ public class StructureSelectionManager
{
// construct highlighted sequence list
- if (seqmappings!=null)
+ if (seqmappings != null)
{
Enumeration e = seqmappings.elements();
while (e.hasMoreElements())
@@ -369,11 +390,14 @@ 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 and absolute position onto the VamsasListener(s)
- ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, indexpos);
+ // pass the mouse over and absolute position onto the
+ // VamsasListener(s)
+ ((VamsasListener) listeners.elementAt(i))
+ .mouseOver(seq, indexpos);
}
}
}
@@ -384,23 +408,26 @@ public class StructureSelectionManager
* handled
*/
boolean handlingVamsasMo = false;
- long lastmsg=0;
+
+ long lastmsg = 0;
+
/**
* as mouseOverSequence but only route event to SequenceListeners
*
* @param sequenceI
- * @param position in an alignment sequence
+ * @param position
+ * in an alignment sequence
*/
public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
{
handlingVamsasMo = true;
- long msg = sequenceI.hashCode()*(1+position);
- if (lastmsg!=msg)
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
{
lastmsg = msg;
mouseOverSequence(sequenceI, position, -1);
}
- handlingVamsasMo = false;
+ handlingVamsasMo = false;
}
public Annotation[] colourSequenceFromStructure(SequenceI seq,
@@ -418,9 +445,10 @@ 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);
+ }
+ ;
+ }
+ }
+ }
}