/*
* 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 JidePopupMenu {
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> <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);
}
}
}