package jalview.gui;

import jalview.jbgui.*;
import jalview.datamodel.*;
import java.awt.event.*;
import java.util.*;
import javax.swing.event.*;

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;
    historyList.push(new HistoryItem("Remove redundancy (" + threshold + "%)",
                                      ap.av.alignment, HistoryItem.HIDE));

    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);
  }

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