/*
* 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.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.FeatureRenderer;
import jalview.api.SequenceRenderer;
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,
String protocol)
{
super(pdbentry, seq, chains, protocol);
}
public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
super(viewer);
ap = alignPanel;
this.sequence = seqs;
notifyFileLoaded(null, null, null, null, 0);
}
public void updateColours(Object source)
{
// TODO Auto-generated method stub
}
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
}
public FeatureRenderer getFeatureRenderer()
{
if (ap.av.showSequenceFeatures)
{
return ap.getFeatureRenderer();
}
else
{
return null;
}
}
public SequenceRenderer getSequenceRenderer()
{
return ap.getSequenceRenderer();
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// ignore
}
public void sendConsoleEcho(String strEcho)
{
// ignore
}
public void sendConsoleMessage(String strStatus)
{
// ignore
}
public void showUrl(String url, String target)
{
ap.alignFrame.showURL(url, target);
}
public void refreshGUI()
{
// ignore
}
public void selectionChanged(BitSet arg0)
{
System.out.println(arg0);
}
public void refreshPdbEntries()
{
Vector pdbe = new Vector();
Hashtable fileids = new Hashtable();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
for (int s=0;s