+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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.appletgui;
+import java.awt.Container;
import java.util.BitSet;
import java.util.Hashtable;
import java.util.Vector;
+import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
/**
* bind an alignment view to an external Jmol instance.
+ *
* @author JimP
- *
+ *
*/
public class ExtJmol extends JalviewJmolBinding
{
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+ protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+ PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq, chains, protocol);
}
public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
- super(viewer);
+ super(alignPanel.getStructureSelectionManager(), viewer);
ap = alignPanel;
this.sequence = seqs;
notifyFileLoaded(null, null, null, null, 0);
public void updateColours(Object source)
{
-
+
// TODO Auto-generated method stub
}
showUrl(arg0, "jmol");
}
- public FeatureRenderer getFeatureRenderer()
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
+ AlignmentPanel ap = (AlignmentPanel)alignment;
if (ap.av.showSequenceFeatures)
{
return ap.getFeatureRenderer();
}
}
- public SequenceRenderer getSequenceRenderer()
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return ap.getSequenceRenderer();
+ return ((AlignmentPanel)alignment).getSequenceRenderer();
}
public void notifyScriptTermination(String strStatus, int msWalltime)
Vector pdbe = new Vector();
Hashtable fileids = new Hashtable();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s=0;s<sq.length;s++)
+ for (int s = 0; s < sq.length; s++)
{
Vector pdbids = sq[s].getPDBId();
- if (pdbids!=null)
+ if (pdbids != null)
{
- for (int pe=0,peSize=pdbids.size(); pe<peSize; pe++)
+ for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
- if (!fileids.containsKey(pentry.getId())) {
+ if (!fileids.containsKey(pentry.getId()))
+ {
pdbe.addElement(pentry);
}
}
}
}
pdbentry = new PDBEntry[pdbe.size()];
- for (int pe=0;pe<pdbe.size(); pe++)
+ for (int pe = 0; pe < pdbe.size(); pe++)
{
pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
}
}
+
+ @Override
+ public void showConsole(boolean show)
+ {
+ // This never gets called because we haven't overriden the associated Jmol's
+ // console
+ System.err
+ .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ + show);
+ }
+
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ Container consolePanel, String buttonsToShow)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ ap = null;
+ if (console != null)
+ {
+ try
+ {
+ console.setVisible(false);
+ } catch (Error e)
+ {
+ } catch (Exception x)
+ {
+ }
+ ;
+ console = null;
+ }
+
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}