/*
* 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.methyl;
import org.broad.igv.Globals;
import org.broad.igv.bbfile.BBFileReader;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.renderer.GraphicUtils;
import org.broad.igv.renderer.PointsRenderer;
import org.broad.igv.renderer.Renderer;
import org.broad.igv.track.AbstractTrack;
import org.broad.igv.track.RenderContext;
import org.broad.igv.util.LongRunningTask;
import org.broad.igv.util.ResourceLocator;
import java.awt.*;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
/**
* Experimental class for specific dataset.
* <p/>
* if(locator.getPath().contains("RRBS_cpgMethylation") || locator.getPath().contains("")) {
*
* @author Jim Robinson
* @date 4/19/12
*/
public class MethylTrack extends AbstractTrack {
public static final int FIVE_MB = 5000000;
public static final int FIFTY_MB = 50000000;
private MethylDataSource dataSource;
private Range loadedRange;
private Renderer renderer;
private int resolutionThreshold;
private boolean loading = false;
public MethylTrack(ResourceLocator dataResourceLocator, BBFileReader reader, Genome genome) throws IOException {
super(dataResourceLocator);
setHeight(60);
renderer = new PointsRenderer();
boolean isWGBS;
if (reader.getAutoSql() != null && reader.getAutoSql().startsWith("table BisulfiteSeq")) {
resolutionThreshold = FIVE_MB;
dataSource = new CachingMethylSource(new BBMethylDataSource(reader, BBMethylDataSource.Type.USC, genome), resolutionThreshold);
//dataSource = new BBMethylDataSource(reader, BBMethylDataSource.Type.USC, genome);
} else {
isWGBS = dataResourceLocator.getPath().contains("BiSeq_cpgMethylation");
resolutionThreshold = isWGBS ? FIVE_MB : FIFTY_MB;
dataSource = new CachingMethylSource(new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome), resolutionThreshold);
//dataSource = new BBMethylDataSource(reader, BBMethylDataSource.Type.USC, genome);
}
loadedRange = new Range("", -1, -1, Collections.<MethylScore>emptyList());
setDataRange(new DataRange(0, 100));
}
/**
* Render the track in the supplied rectangle. It is the responsibility of the track to draw within the
* bounds of the rectangle.
*
* @param context the render context
* @param rect the track bounds, relative to the enclosing DataPanel bounds.
*/
public void render(final RenderContext context, final Rectangle rect) {
if (context.getChr().equals(Globals.CHR_ALL) || context.getScale() * rect.width > resolutionThreshold) {
Graphics2D g = context.getGraphic2DForColor(Color.gray);
Rectangle textRect = new Rectangle(rect);
// Keep text near the top of the track rectangle
textRect.height = Math.min(rect.height, 20);
textRect.height = Math.min(rect.height, 20);
String message = context.getChr().equals(Globals.CHR_ALL) ? "Zoom in to see features." :
"Zoom in to see features, or right-click to increase Feature Visibility Window.";
GraphicUtils.drawCenteredText(message, textRect, g);
return;
}
final String chr = context.getChr();
final int start = (int) context.getOrigin();
final int end = (int) context.getEndLocation();
if (loadedRange.contains(chr, start, end)) {
renderer.render(loadedRange.scores, context, rect, this);
} else {
if (!loading) {
loading = true;
Runnable runnable = new Runnable() {
public void run() {
try {
int width = (end - start) / 2;
int expandedStart = Math.max(0, start - width);
int expandedEnd = end + width;
List<MethylScore> scores = new ArrayList<MethylScore>(1000);
Iterator<MethylScore> iter = dataSource.query(chr, expandedStart, expandedEnd);
while (iter.hasNext()) {
scores.add(iter.next());
}
loadedRange = new Range(chr, expandedStart, expandedEnd, scores);
context.getPanel().repaint(); //rect);
} finally {
loading = false;
}
}
};
LongRunningTask.submit(runnable);
}
}
}
public Renderer getRenderer() {
return renderer;
}
static class Range extends org.broad.igv.feature.Range {
List<MethylScore> scores;
Range(String chr, int start, int end, List<MethylScore> scores) {
super(chr, start, end);
this.scores = scores;
}
}
}