/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
//import jalview.ext.jmol.JalviewJmolBinding;
import jalview.structure.AtomSpec;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import java.awt.Container;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Vector;
//import org.jmol.api.JmolAppConsoleInterface;
//import org.jmol.java.BS;
import org.jmol.viewer.Viewer;
/**
* bind an alignment view to an external Jmol instance.
*
* @author JimP
*
*/
public class ExtJmol extends AAStructureBindingModel //extends JalviewJmolBinding
{
public ExtJmol(StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, String[][] chains, String protocol) {
super(ssm, pdbentry, sequenceIs, chains, protocol);
// TODO Auto-generated constructor stub
}
@Override
public String[] getPdbFile() {
// TODO Auto-generated method stub
return null;
}
@Override
public void updateColours(Object source) {
// TODO Auto-generated method stub
}
@Override
public void releaseReferences(Object svl) {
// TODO Auto-generated method stub
}
@Override
public void highlightAtoms(List atoms) {
// TODO Auto-generated method stub
}
// private AlignmentPanel ap;
//
// protected ExtJmol(jalview.appletgui.AlignFrame alframe,
// PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
// String protocol)
// {
// super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
// chains, protocol);
// }
//
// public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
// SequenceI[][] seqs)
// {
// super(alignPanel.getStructureSelectionManager(), seqs, viewer);
// ap = alignPanel;
// notifyFileLoaded(null, null, null, null, 0);
// }
//
// public void updateColours(Object source)
// {
//
// // TODO Auto-generated method stub
//
// }
//
// public void showUrl(String arg0)
// {
// showUrl(arg0, "jmol");
// }
//
// @Override
// public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
// {
// AlignmentPanel ap = (AlignmentPanel) alignment;
// if (ap.av.isShowSequenceFeatures())
// {
// return ap.getFeatureRenderer();
// }
// else
// {
// return null;
// }
// }
//
// @Override
// public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
// {
// return ((AlignmentPanel) alignment).getSequenceRenderer();
// }
//
// @Override
// public void notifyScriptTermination(String strStatus, int msWalltime)
// {
// // ignore
// }
//
// @Override
// public void sendConsoleEcho(String strEcho)
// {
// // ignore
// }
//
// @Override
// public void sendConsoleMessage(String strStatus)
// {
// // ignore
// }
//
// @Override
// public void showUrl(String url, String target)
// {
// ap.alignFrame.showURL(url, target);
// }
//
// @Override
// public void refreshGUI()
// {
// // ignore
// }
//
// public void selectionChanged(BS arg0)
// {
// System.out.println(arg0);
// }
//
// @Override
// public void refreshPdbEntries()
// {
// List pdbe = new ArrayList();
// List fileids = new ArrayList();
// SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
// for (int s = 0; s < sq.length; s++)
// {
// Vector pdbids = sq[s].getPDBId();
// if (pdbids != null)
// {
// for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
// {
// PDBEntry pentry = pdbids.elementAt(pe);
// if (!fileids.contains(pentry.getId()))
// {
// pdbe.add(pentry);
// }
// else
// {
// fileids.add(pentry.getId());
// }
// }
// }
// }
// PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
// for (int pe = 0; pe < pdbe.size(); pe++)
// {
// newEntries[pe] = pdbe.get(pe);
// }
// setPdbentry(newEntries);
// }
//
// @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(
// Container consolePanel, String buttonsToShow)
// {
// // TODO Auto-generated method stub
// return null;
// }
//
// @Override
// protected void releaseUIResources()
// {
// ap = null;
// closeConsole();
//
// }
//
// @Override
// public void releaseReferences(Object svl)
// {
// // TODO Auto-generated method stub
//
// }
//
// @Override
// public Map getJSpecViewProperty(String arg0)
// {
// // TODO Auto-generated method stub
// return null;
// }
//
}