/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program 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 2
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/

package jalview.appletgui;

import jalview.datamodel.*;
import jalview.jbappletgui.GPairwiseAlignPanel;
import jalview.analysis.*;
import java.awt.event.*;
import java.util.*;


public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
    Vector sequences = new Vector();
    AlignViewport av;

    public PairwiseAlignPanel(AlignViewport av)
    {
      super();
      this.av = av;
      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
      double totscore = 0;
      int count = av.getSelectionGroup().getSize();

      int acount = 0;
        for (int i = 1; i < count; i++)
        {
          for (int j = 0; j < i; j++)
          {
            acount++;
            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
                                       av.getSelectionGroup().getSequenceAt(j),"pep");

            as.calcScoreMatrix();
            as.traceAlignment();
            as.printAlignment();
            scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;
            totscore = totscore + scores[i][j];

            textarea.append(as.getOutput());
            sequences.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) );
            sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) );


          }
        }

        if (count > 2)
        {
          for (int i = 0; i < count;i++)
            for (int j = 0; j < i; j++)
              jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);
        }
      }


  protected void viewInEditorButton_actionPerformed(ActionEvent e)
  {

      Sequence [] seq = new Sequence[sequences.size()];

      for (int i=0;i<sequences.size();i++)
       seq[i] = (Sequence) sequences.elementAt(i);


      AlignFrame af = new AlignFrame(new Alignment(seq));
      jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
                               AlignFrame.NEW_WINDOW_WIDTH,
                               AlignFrame.NEW_WINDOW_HEIGHT);

  }

}