/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
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++)
{
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
- // pairs
-
+ /**
+ * 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);
+ if (index == -1)
+ index = seq.findPosition(indexpos);
StructureListener sl;
int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
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);
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)
{
{
// construct highlighted sequence list
- if (seqmappings!=null)
+ if (seqmappings != null)
{
Enumeration e = seqmappings.elements();
while (e.hasMoreElements())
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);
}
}
}
* 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,
{
modifySeqMappingList(true, codonFrames);
}
+
+ Vector sel_listeners = new Vector();
+ public void addSelectionListener(SelectionListener selecter)
+ {
+ if (!sel_listeners.contains(selecter))
+ {
+ sel_listeners.addElement(selecter);
+ }
+ }
+ public void removeSelectionListener(SelectionListener toremove)
+ {
+ if (sel_listeners.contains(toremove))
+ {
+ sel_listeners.removeElement(toremove);
+ }
+ }
+ public synchronized void sendSelection(jalview.datamodel.SequenceGroup selection, jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ {
+ 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);
+ };
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff