/*
* 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.peaks;
import org.apache.log4j.Logger;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackClickEvent;
import org.broad.igv.track.TrackMenuUtils;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.lang.ref.SoftReference;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/**
* @author jrobinso
* @date Apr 23, 2011
*/
public class PeakTrackMenu extends IGVPopupMenu {
private static Logger log = Logger.getLogger(PeakTrackMenu.class);
private PeakTrack track;
private JRadioButtonMenuItem colorByScoreMI;
private JRadioButtonMenuItem colorByFoldMI;
public PeakTrackMenu(PeakTrack track, TrackClickEvent te) {
super();
// TODO -- what if multiple tracks are selected?
this.track = track;
init(te);
}
private void init(final TrackClickEvent trackClickEvent) {
Collection<Track> tracks = IGV.getInstance().getSelectedTracks(); //Arrays.asList(new Track[] {track});
//Title
JLabel popupTitle = new JLabel("<html><b>" + track.getName(), JLabel.LEFT);
Font newFont = getFont().deriveFont(Font.BOLD, 12);
popupTitle.setFont(newFont);
add(popupTitle);
addSeparator();
add(TrackMenuUtils.getTrackRenameItem(tracks));
add(TrackMenuUtils.getChangeTrackHeightItem(tracks));
add(TrackMenuUtils.getChangeFontSizeItem(tracks));
//Change Track Settings
addDisplayModeItems();
addSeparator();
JMenuItem plotItem = new JMenuItem("Open Trend Plot...");
plotItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
openTimeSeriesPlot(trackClickEvent);
}
});
add(plotItem);
if (track.isShowSignals()) {
add(TrackMenuUtils.getDataRangeItem(tracks));
add(TrackMenuUtils.getLogScaleItem(tracks));
add(TrackMenuUtils.getShowDataRangeItem(tracks));
}
}
public void addDisplayModeItems() {
addSeparator();
ButtonGroup group = new ButtonGroup();
Track.DisplayMode displayMode = track.getDisplayMode();
JRadioButtonMenuItem m1 = new JRadioButtonMenuItem("Compressed");
m1.setSelected(displayMode == Track.DisplayMode.COLLAPSED);
m1.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setDisplayMode(Track.DisplayMode.COLLAPSED);
PeakTrack.setAnimate(false);
IGV.getInstance().doRefresh();
}
});
JRadioButtonMenuItem m3 = new JRadioButtonMenuItem("Time Series");
m3.setSelected(displayMode == Track.DisplayMode.EXPANDED);
m3.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setDisplayMode(Track.DisplayMode.EXPANDED);
PeakTrack.setAnimate(false);
IGV.getInstance().doRefresh();
}
});
JRadioButtonMenuItem m4 = new JRadioButtonMenuItem("Animate");
m4.setSelected(PeakTrack.animate);
m4.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setDisplayMode(Track.DisplayMode.COLLAPSED);
PeakTrack.setAnimate(true);
}
});
add(m1);
add(m3);
add(m4);
group.add(m1);
group.add(m3);
group.add(m4);
}
public void addColorByItems() {
addSeparator();
add(new JLabel("Color by"));
ButtonGroup group = new ButtonGroup();
colorByScoreMI = new JRadioButtonMenuItem("Score");
colorByScoreMI.setSelected(PeakTrack.getColorOption() == PeakTrack.ColorOption.SCORE);
colorByScoreMI.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
PeakTrack.setShadeOption(PeakTrack.ColorOption.SCORE);
IGV.getInstance().repaint();
}
});
colorByFoldMI = new JRadioButtonMenuItem("Fold change");
colorByFoldMI.setSelected(PeakTrack.getColorOption() == PeakTrack.ColorOption.FOLD_CHANGE);
colorByFoldMI.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
PeakTrack.setShadeOption(PeakTrack.ColorOption.FOLD_CHANGE);
IGV.getInstance().repaint();
}
});
add(colorByScoreMI);
add(colorByFoldMI);
group.add(colorByScoreMI);
group.add(colorByFoldMI);
}
void openTimeSeriesPlot(TrackClickEvent trackClickEvent) {
if (trackClickEvent == null) return;
ReferenceFrame referenceFrame = trackClickEvent.getFrame();
if (referenceFrame == null) return;
String chr = referenceFrame.getChrName();
double position = trackClickEvent.getChromosomePosition();
XYSeriesCollection data = new XYSeriesCollection();
List<Color> colors = new ArrayList();
for (SoftReference<PeakTrack> ref : PeakTrack.instances) {
PeakTrack track = ref.get();
if (track != null) {
Peak peak = track.getFilteredPeakNearest(chr, position);
if (peak != null) {
XYSeries series = new XYSeries(track.getName());
float[] scores = peak.getTimeScores();
if (scores.length == 4) {
float t0 = scores[0] + 10;
series.add(0, (scores[0] + 10) / t0);
series.add(30, (scores[1] + 10) / t0);
series.add(60, (scores[2] + 10) / t0);
series.add(120, (scores[3] + 10) / t0);
}
data.addSeries(series);
Color c = track.getName().contains("Pol") ? Color.black : track.getColor();
colors.add(c);
}
}
}
final JFreeChart chart = ChartFactory.createXYLineChart(
"",
"Time",
"Score",
data,
PlotOrientation.VERTICAL,
true,
true,
false
);
NumberAxis axis = (NumberAxis) chart.getXYPlot().getDomainAxis(0);
axis.setTickUnit(new NumberTickUnit(30));
final ChartPanel chartPanel = new ChartPanel(chart);
chartPanel.setPreferredSize(new java.awt.Dimension(400, 400));
chartPanel.setSize(new java.awt.Dimension(400, 400));
XYItemRenderer renderer = chart.getXYPlot().getRenderer();
for (int i = 0; i < colors.size(); i++) {
renderer.setSeriesPaint(i, colors.get(i));
}
chartPanel.setBackground(Color.white);
chart.getXYPlot().setBackgroundPaint(Color.white);
chart.getXYPlot().setRangeGridlinePaint(Color.black);
PeakTimePlotFrame frame = new PeakTimePlotFrame(chartPanel);
frame.setVisible(true);
}
}