/*
- * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.structure;
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
-
- 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++)
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);
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())
// 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);
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);
}
}
}
*/
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;
}
*
* 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<seq.getLength(); index++) {
* if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
{
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