/*
 * 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 java.util.*;

import java.awt.event.*;

import jalview.datamodel.*;
import jalview.jbappletgui.*;

public class RedundancyPanel
    extends GSliderPanel
{
  AlignmentPanel ap;

  SequenceI[] oldAlignment;

  public RedundancyPanel(AlignmentPanel ap)
  {
    this.ap = ap;

    label.setText("Enter the redundancy threshold");

    slider.addAdjustmentListener(new AdjustmentListener()
    {
      public void adjustmentValueChanged(AdjustmentEvent evt)
      {
        valueField.setText(slider.getValue() + "");
      }
    });

    slider.setMinimum(0);
    slider.setMaximum(100);
    slider.setValue(100);

  }

  public void applyButton_actionPerformed(ActionEvent e)
  {
    float threshold = slider.getValue();
    Vector del;

    oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
    for (int i = 0; i < ap.av.alignment.getHeight(); i++)
    {
      oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
                                     ap.av.alignment.getSequenceAt(i).
                                     getSequence());
    }

    undoButton.setEnabled(true);

    SequenceGroup sg = ap.av.getSelectionGroup();
    if (sg != null && sg.getSize() > 1)
    {

      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
      for (int i = 0; i < del.size(); i++)
      {
        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
        {
          sg.deleteSequence( (SequenceI) del.elementAt(i));
        }
      }

    }
    else
    {
      Vector s = new Vector();
      int i = 0;
      while (i < ap.av.alignment.getHeight())
      {
        s.addElement(ap.av.alignment.getSequenceAt(i));
        i++;
      }
      del = ap.av.alignment.removeRedundancy(threshold, s);
      for (int j = 0; j < del.size(); j++)
      {
        if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
        {
          sg.deleteSequence( (SequenceI) del.elementAt(j));
        }

      }
    }

    ap.repaint();

  }

  public void undoButton_actionPerformed(ActionEvent e)
  {
    undoButton.setEnabled(false);
    ap.av.setAlignment(new Alignment(oldAlignment));
    oldAlignment = null;
    ap.repaint();
  }

  public void valueField_actionPerformed(ActionEvent e)
  {
    try
    {
      int i = Integer.parseInt(valueField.getText());
      slider.setValue(i);
    }
    catch (Exception ex)
    {
      valueField.setText(slider.getValue() + "");
    }
  }
}