/*
* 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.track;
import org.broad.igv.data.seg.FreqData;
import org.broad.igv.feature.FeatureUtils;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.renderer.BarChartRenderer;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.renderer.Renderer;
import org.broad.igv.session.IGVSessionReader;
import org.broad.igv.session.SubtlyImportant;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ResourceLocator;
import javax.swing.*;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author jrobinso
* @date Oct 13, 2010
*/
@XmlType(factoryMethod = "getNextTrack")
public class CNFreqTrack extends AbstractTrack {
FreqData data;
BarChartRenderer renderer;
@XmlAttribute
float ampThreshold;
@XmlAttribute
float delThreshold;
public CNFreqTrack() {
}
public CNFreqTrack(ResourceLocator rl, String id, String name, FreqData fd) {
super(rl, id, name);
data = fd;
this.ampThreshold = PreferencesManager.getPreferences().getAsFloat(Constants.CN_FREQ_AMP_THRESHOLD);
this.delThreshold = PreferencesManager.getPreferences().getAsFloat(Constants.CN_FREQ_DEL_THRESHOLD);
float nSamples = data.getNumberOfSamples();
this.setDataRange(new DataRange(-nSamples, 0, nSamples));
this.posColor = Color.red;
this.altColor = Color.blue;
renderer = new BarChartRenderer();
this.setMinimumHeight(25);
this.setHeight(50);
this.setSortable(false);
}
@Override
public boolean isReadyToPaint(ReferenceFrame frame) {
return true; // Track is initialized with all data
}
@Override
public void load(ReferenceFrame frame) {
// Track is initialized with all data
}
@SubtlyImportant
public void setAmpThreshold(float ampThreshold) {
this.ampThreshold = ampThreshold;
}
@SubtlyImportant
public void setDelThreshold(float delThreshold) {
this.delThreshold = delThreshold;
}
@SubtlyImportant
public float getAmpThreshold() {
return ampThreshold;
}
@SubtlyImportant
public float getDelThreshold() {
return delThreshold;
}
public Map<String, String> getPersistentState() {
Map<String, String> map = new HashMap<String, String>();
map.put("ampThreshold", String.valueOf(ampThreshold));
map.put("delThreshold", String.valueOf(delThreshold));
return map;
}
public void render(RenderContext context, Rectangle rect) {
data.compute(ampThreshold, delThreshold);
renderer.render(data.getDelCounts(context.getChr()), context, rect, this);
renderer.render(data.getAmpCounts(context.getChr()), context, rect, this);
renderer.setMarginFraction(0);
renderer.renderBorder(this, context, rect);
context.getGraphic2DForColor(Color.black).drawRect(rect.x, rect.y, rect.width, rect.height - 1);
}
public String getValueStringAt(String chr, double position, int mouseX, int mouseY, ReferenceFrame frame) {
List<LocusScore> ampScores = data.getAmpCounts(chr);
List<LocusScore> delScores = data.getDelCounts(chr);
StringBuffer buf = new StringBuffer();
int startIdx = Math.max(0, FeatureUtils.getIndexBefore(position, ampScores));
for (int i = startIdx; i < ampScores.size(); i++) {
LocusScore ampScore = ampScores.get(i);
if (position >= ampScore.getStart() && position <= ampScore.getEnd()) {
buf.append("# of samples with log2(cn/2) > " + ampThreshold + ": ");
buf.append(ampScore.getValueString(position, mouseX, null));
buf.append("<br># of samples with log2(cn/2) < " + delThreshold + ": ");
buf.append(delScores.get(i).getValueString(position, mouseX, null));
}
}
return buf.length() == 0 ? null : buf.toString();
}
public Renderer getRenderer() {
return renderer;
}
public boolean isLogNormalized() {
return false;
}
public float getRegionScore(String chr, int start, int end, int zoom, RegionScoreType type, String frameName) {
return Integer.MIN_VALUE; //To change body of implemented methods use File | Settings | File Templates.
}
@Override
public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
IGVPopupMenu menu = new IGVPopupMenu();
final JMenuItem ampThresholdItem = new JMenuItem("Set amplification threshold (" + ampThreshold + ")");
ampThresholdItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String t = MessageUtils.showInputDialog("Amplification threshold (log2(cn)/2)", String.valueOf(ampThreshold));
if(t != null) {
try {
float threshold = Float.parseFloat(t);
setAmpThreshold(threshold);
IGV.getInstance().repaint();
} catch (NumberFormatException e1) {
MessageUtils.showErrorMessage("Amplification threshold must be a number", e1);
}
}
}
});
menu.add(ampThresholdItem);
final JMenuItem delThresholdItem = new JMenuItem("Set deletion threshold (" + delThreshold + ")");
delThresholdItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String t = MessageUtils.showInputDialog("Deletion threshold (log2(cn)/2)", String.valueOf(delThreshold));
try {
float threshold = Float.parseFloat(t);
setDelThreshold(threshold);
IGV.getInstance().repaint();
} catch (NumberFormatException e1) {
MessageUtils.showErrorMessage("Deletion threshold must be a number", e1);
}
}
});
menu.add(delThresholdItem);
menu.addSeparator();
List<Track> selfAsList = Arrays.asList((Track) this);
TrackMenuUtils.addSharedItems(menu, selfAsList, false, false);
return menu;
}
@SubtlyImportant
private static CNFreqTrack getNextTrack() {
return (CNFreqTrack) IGVSessionReader.getNextTrack();
}
}