/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package org.broad.igv.ui.panel;

import com.jidesoft.swing.JidePopupMenu;
import org.broad.igv.charts.ScatterPlotUtils;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.track.RegionScoreType;
import org.broad.igv.track.TrackType;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.action.MenuAction;

import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Set;

/**
 * @author jrobinso
 * @date Sep 18, 2010
 */
public class RegionMenu extends JPopupMenu {

    RegionOfInterest roi;
    ReferenceFrame frame;

    public RegionMenu(final RegionOfInterest roi, final ReferenceFrame frame) {
        this(roi, frame, null);
    }

    public RegionMenu(final RegionOfInterest roi, final ReferenceFrame frame, String title) {

        this.roi = roi;
        this.frame = frame;

        if (title != null) {
            JLabel heading = new JLabel("<html>&nbsp;<b>" + title);
            //heading.setFont(UIConstants.boldFont);
            add(heading);
            addSeparator();
        }


        Set<TrackType> loadedTypes = IGV.getInstance().getLoadedTypes();

        if (loadedTypes.contains(TrackType.COPY_NUMBER) ||
                loadedTypes.contains(TrackType.ALLELE_SPECIFIC_COPY_NUMBER) ||
                loadedTypes.contains(TrackType.CNV)) {
            JMenuItem item = new JMenuItem("Sort by amplification");
            item.addActionListener(new ActionListener() {
                public void actionPerformed(ActionEvent e) {

                    IGV.getInstance().sortByRegionScore(roi, RegionScoreType.AMPLIFICATION, frame);

                }
            });
            add(item);


            item = new JMenuItem("Sort by deletion");
            item.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {

                    IGV.getInstance().sortByRegionScore(roi, RegionScoreType.DELETION, frame);
                    IGV.getInstance().getContentPane().repaint();
                }
            });
            add(item);

            item = new JMenuItem("Sort by breakpoint amplitudes");
            item.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {

                    IGV.getInstance().sortByRegionScore(roi, RegionScoreType.FLUX, frame);
                    IGV.getInstance().getContentPane().repaint();
                }
            });
            add(item);
        }

        if (loadedTypes.contains(TrackType.GENE_EXPRESSION)) {
            JMenuItem item = new JMenuItem("Sort by expression");
            item.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {

                    IGV.getInstance().sortByRegionScore(roi, RegionScoreType.EXPRESSION, frame);
                    IGV.getInstance().getContentPane().repaint();

                }
            });

            add(item);
        }

        if (loadedTypes.contains(TrackType.MUTATION)) {
            JMenuItem item = new JMenuItem("Sort by mutation count");
            item.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {

                    IGV.getInstance().sortByRegionScore(roi, RegionScoreType.MUTATION_COUNT, frame);
                    IGV.getInstance().getContentPane().repaint();

                }
            });

            add(item);
        }

        JMenuItem item = new JMenuItem("Sort by value");
        item.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {

                IGV.getInstance().sortByRegionScore(roi, RegionScoreType.SCORE, frame);
                IGV.getInstance().getContentPane().repaint();

            }
        });
        add(item);

        if (ScatterPlotUtils.hasPlottableTracks()) {
            addSeparator();
            item = new JMenuItem("Scatter Plot ...");
            item.addActionListener(new ActionListener() {
                public void actionPerformed(ActionEvent e) {

                    String chr = roi.getChr();
                    int start = roi.getStart();
                    int end = roi.getEnd();
                    int zoom = frame.getZoom();
                    ScatterPlotUtils.openPlot(chr, start, end, zoom);
                }
            });
            add(item);
        }

    }


}

@@ -1187,49 +1187,8 @@
 l;%0A%0A
-import com.jidesoft.swing.JidePopupMenu;%0A
 impo
@@ -1390,51 +1390,8 @@
 IGV;
-%0Aimport org.broad.igv.ui.action.MenuAction;
 %0A%0Aim

remove unused imports