/*
 * 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 jalview.datamodel.*;

import jalview.jbgui.*;

import java.awt.event.*;

import java.util.*;

import javax.swing.event.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class RedundancyPanel extends GSliderPanel
{
    AlignFrame af;
    AlignmentPanel ap;
    Stack historyList = new Stack(); // simpler than synching with alignFrame.

    /**
     * Creates a new RedundancyPanel object.
     *
     * @param ap DOCUMENT ME!
     * @param af DOCUMENT ME!
     */
    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);
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void applyButton_actionPerformed(ActionEvent e)
    {
        float threshold = slider.getValue();
        Vector del;
        historyList.push(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), true);
                }
            }
        }
        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());
        af.updateEditMenuBar();


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

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    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();
            }
        }
    }

    /**
     * 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() + "");
        }
    }
}