/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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 jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.util.Comparison;
import jalview.commands.*;

import java.awt.event.*;

import java.util.*;

import javax.swing.event.*;

import javax.swing.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class RedundancyPanel extends GSliderPanel implements Runnable
{
    AlignFrame af;
    AlignmentPanel ap;
    Stack historyList = new Stack(); // simpler than synching with alignFrame.
    float [] redundancy;
    SequenceI [] originalSequences;
    JInternalFrame frame;
    Vector redundantSeqs;

    /**
     * Creates a new RedundancyPanel object.
     *
     * @param ap DOCUMENT ME!
     * @param af DOCUMENT ME!
     */
    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
    {
        this.ap = ap;
        this.af = af;
        redundantSeqs = new Vector();

        slider.addChangeListener(new ChangeListener()
            {
                public void stateChanged(ChangeEvent evt)
                {
                    valueField.setText(slider.getValue() + "");
                    sliderValueChanged();
                }
            });

        applyButton.setText("Remove");
        allGroupsCheck.setVisible(false);
        slider.setMinimum(0);
        slider.setMaximum(100);
        slider.setValue(100);

        Thread worker = new Thread(this);
        worker.start();

        frame = new JInternalFrame();
        frame.setContentPane(this);
        Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
                         100, false);
        frame.addInternalFrameListener(new InternalFrameAdapter()
            {
              public void internalFrameClosing(InternalFrameEvent evt)
              {
               ap.idPanel.idCanvas.setHighlighted(null);
              }
            }
            );

    }


    /**
     * This is a copy of remove redundancy in jalivew.datamodel.Alignment
     * except we dont want to remove redundancy, just calculate once
     * so we can use the slider to dynamically hide redundant sequences
     *
     * @param threshold DOCUMENT ME!
     * @param sel DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public void run()
    {
        JProgressBar progress = new JProgressBar();
        progress.setIndeterminate(true);
        southPanel.add(progress, java.awt.BorderLayout.SOUTH);

        label.setText("Calculating....");

        slider.setVisible(false);
        applyButton.setEnabled(false);
        valueField.setVisible(false);

        validate();

        String[] omitHidden = null;

        SequenceGroup sg = ap.av.getSelectionGroup();
        int height;

        int start, end;

        if ( (sg != null) && (sg.getSize(false) >= 1))
        {
           originalSequences = sg.getSequencesInOrder(ap.av.alignment);
           start = sg.getStartRes();
           end = sg.getEndRes();
        }
        else
        {
          originalSequences = ap.av.alignment.getSequencesArray();
          start = 0;
          end = ap.av.alignment.getWidth();
        }

        height = originalSequences.length;

        redundancy = new float[height];
        for (int i = 0; i < height; i++)
        {
          redundancy[i] = 0f;
        }

        if (ap.av.hasHiddenColumns)
        {
          omitHidden = ap.av.getViewAsString(sg!=null);
        }


       // long start = System.currentTimeMillis();

        float pid;
        String seqi, seqj;
        for (int i = 0; i < height; i++)
        {

            for (int j = 0; j < i; j++)
            {
              if(i==j)
                continue;

              if(omitHidden==null)
              {
                seqi = originalSequences[i].getSequence(start, end);
                seqj = originalSequences[j].getSequence(start, end);
              }
              else
              {
                seqi = omitHidden[i];
                seqj = omitHidden[j];
              }

              pid = Comparison.PID( seqi,  seqj );

              if(seqj.length() < seqi.length())
                redundancy[j] = Math.max(pid, redundancy[j]);
              else
                redundancy[i] = Math.max(pid, redundancy[i]);

            }
        }

        progress.setIndeterminate(false);
        progress.setVisible(false);
        progress = null;

        label.setText("Enter the redundancy threshold");
        slider.setVisible(true);
        applyButton.setEnabled(true);
        valueField.setVisible(true);

        validate();
       // System.out.println((System.currentTimeMillis()-start));
    }

    void sliderValueChanged()
    {
      if(redundancy==null)
        return;

      float value = slider.getValue();

      for(int i=0; i<redundancy.length; i++)
      {
        if (value > redundancy[i])
          redundantSeqs.remove(originalSequences[i]);
        else if(!redundantSeqs.contains(originalSequences[i]))
          redundantSeqs.add(originalSequences[i]);

      }

      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void applyButton_actionPerformed(ActionEvent e)
    {
        Vector del = new Vector();

        undoButton.setEnabled(true);

        float value = slider.getValue();
        SequenceGroup sg = ap.av.getSelectionGroup();

        for (int i = 0; i < redundancy.length; i++)
        {
          if (value <= redundancy[i])
          {
            del.addElement(originalSequences[i]);
          }
        }

        // This has to be done before the restoreHistoryItem method of alignFrame will
        // actually restore these sequences.
        if (del.size() > 0)
        {
          SequenceI [] deleted = new SequenceI[del.size()];

          int width = 0;
          for (int i = 0; i < del.size(); i++)
          {
            deleted[i] = (SequenceI)del.elementAt(i);
            if(deleted[i].getLength()>width)
              width = deleted[i].getLength();
          }

          EditCommand cut = new EditCommand("Remove Redundancy",
              EditCommand.CUT, deleted,0,width,ap.av.alignment);

          for (int i = 0; i < del.size(); i++)
          {
            ap.av.alignment.deleteSequence( deleted[i] );
            PaintRefresher.Refresh(this,
                                   ap.av.getSequenceSetId(),
                                   true,
                                   true);
            if (sg != null)
            {
              sg.deleteSequence(deleted[i], false);
            }
          }

          historyList.push(cut);

          ap.alignFrame.addHistoryItem(cut);

          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
        }


    }


    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void undoButton_actionPerformed(ActionEvent e)
    {
      CommandI command = (CommandI) historyList.pop();
      command.undoCommand();

      if (ap.av.historyList.contains(command))
      {
        ap.av.historyList.remove(command);
        af.updateEditMenuBar();
      }

      ap.repaint();

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

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


}