/*
* Copyright (c) 2007-2013 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.data.cufflinks;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.renderer.ContinuousColorScale;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.track.DataTrack;
import org.broad.igv.track.Track;
import org.broad.igv.util.ResourceLocator;
import java.awt.*;
import java.util.List;
/**
* @author jrobinso
* Date: 3/8/13
* Time: 5:45 PM
*/
public class CufflinksTrack extends DataTrack {
CufflinksDataSource dataSource;
public CufflinksTrack(ResourceLocator locator, String id, String name, CufflinksDataSource dataSource) {
super(locator, id, name);
this.dataSource = dataSource;
}
@Override
public List<LocusScore> getSummaryScores(String chr, int startLocation, int endLocation, int zoom) {
return dataSource.getSummaryScoresForRange(chr, startLocation, endLocation, zoom);
}
// Bit of a hack
static boolean isExpDiff(String path) {
return path != null && path.toLowerCase().endsWith("_exp.diff");
}
public static void setCufflinksScale(Track inputTrack){
String path = inputTrack.getResourceLocator() != null ? inputTrack.getResourceLocator().getPath() : null;
if(isExpDiff(path)) {
// Make +/- scale symmetic
float range = Math.min(5, Math.abs(Math.max(inputTrack.getDataRange().getMinimum(), inputTrack.getDataRange().getMaximum())));
inputTrack.setDataRange(new DataRange(-range, 0, range));
inputTrack.setColor(Color.RED);
inputTrack.setAltColor(Color.BLUE);
inputTrack.setColorScale(new ContinuousColorScale(-range, 0, range, Color.RED, Color.WHITE, Color.BLUE));
}
else {
inputTrack.setDataRange(new DataRange(inputTrack.getDataRange().getMinimum(), 0, inputTrack.getDataRange().getMaximum()));
}
}
}