/*
 * 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 <http://www.gnu.org/licenses/>.
 * 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<AtomSpec> 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<PDBEntry> pdbe = new ArrayList<PDBEntry>();
//    List<String> fileids = new ArrayList<String>();
//    SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
//    for (int s = 0; s < sq.length; s++)
//    {
//      Vector<PDBEntry> 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<String, Object> getJSpecViewProperty(String arg0)
//  {
//    // TODO Auto-generated method stub
//    return null;
//  }
//
}