/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
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.renderer.BarChartRenderer;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.renderer.Renderer;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.util.ResourceLocator;
import java.awt.*;
import java.util.Arrays;
import java.util.List;
/**
* @author jrobinso
* @date Oct 13, 2010
*/
public class CNFreqTrack extends AbstractTrack {
FreqData data;
BarChartRenderer renderer;
public CNFreqTrack(ResourceLocator rl, String id, String name, FreqData fd) {
super(rl, id, name);
data = fd;
float nSamples = data.getNumberOfSamples();
this.setDataRange(new DataRange(-nSamples, 0, nSamples));
this.setColor(Color.red);
this.setAltColor(Color.blue);
renderer = new BarChartRenderer();
this.setMinimumHeight(25);
this.setHeight(50);
this.setSortable(false);
}
public void render(RenderContext context, Rectangle rect) {
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 y, 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) > " + data.getAmpThreshold() + ": ");
buf.append(ampScore.getValueString(position, null));
buf.append("<br># of samples with log2(cn/2) < " + data.getDelThreshold() + ": ");
buf.append(delScores.get(i).getValueString(position, 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();
List<Track> selfAsList = Arrays.asList((Track) this);
TrackMenuUtils.addSharedItems(menu, selfAsList, false);
menu.addSeparator();
menu.add(TrackMenuUtils.getRemoveMenuItem(selfAsList));
return menu;
}
}