package jalview.appletgui;

import java.util.BitSet;
import java.util.Hashtable;
import java.util.Vector;

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<sq.length;s++)
    {
      Vector pdbids = sq[s].getPDBId();
      if (pdbids!=null)
      {
        for (int pe=0,peSize=pdbids.size(); pe<peSize; pe++)
        {
          PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
          if (!fileids.containsKey(pentry.getId())) {
            pdbe.addElement(pentry);
          }
        }
      }
    }
    pdbentry = new PDBEntry[pdbe.size()];
    for (int pe=0;pe<pdbe.size(); pe++)
    {
      pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
    }
  }
}