/*
 * 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.gui;

import java.util.*;

import java.awt.event.*;
import javax.swing.event.*;

import jalview.datamodel.*;
import jalview.jbgui.*;

public class RedundancyPanel
    extends GSliderPanel
{
  AlignFrame af;
  AlignmentPanel ap;
  Stack historyList = new Stack(); // simpler than synching with alignFrame.

  public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
  {
    this.ap = ap;
    this.af = af;
    label.setText("Enter the redundancy threshold");

    slider.addChangeListener(new ChangeListener()
    {
      public void stateChanged(ChangeEvent 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;
    HistoryItem it;
    historyList.push(it = new HistoryItem("Remove redundancy",
                                          ap.av.alignment, HistoryItem.HIDE));

    if ( (historyList.size() == 1) ||
        !af.historyList.contains(historyList.firstElement()))
    {
      af.addHistoryItem( (HistoryItem) historyList.firstElement());
      af.updateEditMenuBar();
    }

    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);
    }

    // This has to be done before the restoreHistoryItem method of alignFrame will
    // actually restore these sequences.
    if (del.size() > 0)
    {
      for (int i = 0, j = del.size(); i < j; i++)
      {
        SequenceI sq = (SequenceI) del.elementAt(i);
        sq.deleteChars(0, sq.getLength());
      }
    }

    ap.av.firePropertyChange("alignment", null,
                             ap.av.getAlignment().getSequences());
    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());

    if (ap.av.getAlignment().getHeight() < 1)
    {
      try
      {
        af.setClosed(true);
      }
      catch (Exception ex)
      {
      }
    }

    ap.av.updateConservation();
    ap.av.updateConsensus();
    af.updateEditMenuBar();
    ap.repaint();
  }

  public void undoButton_actionPerformed(ActionEvent e)
  {
    HistoryItem hi = (HistoryItem) historyList.pop();
    af.restoreHistoryItem(hi);

    if (historyList.size() == 0)
    {
      undoButton.setEnabled(false);

      if (af.historyList.contains(hi))
      {
        af.historyList.remove(hi);
        af.updateEditMenuBar();
      }
    }
  }

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