/*
* 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.cli_plugin;
import org.apache.log4j.Logger;
import org.broad.igv.feature.Locus;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.AlignmentTrack;
import org.broad.igv.session.SubtlyImportant;
import org.broad.igv.track.FeatureSource;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.Track;
import htsjdk.tribble.Feature;
import javax.xml.bind.annotation.XmlAttribute;
import java.io.IOException;
import java.util.Arrays;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
/**
* A feature source which derives its information
* from a command line cli_plugin
* User: jacob
* Date: 2012/05/01
*/
public class PluginFeatureSource<E extends Feature, D extends Feature> extends PluginSource implements FeatureSource{
private static Logger log = Logger.getLogger(PluginFeatureSource.class);
@XmlAttribute
private boolean forbidEmptyOutput;
@SubtlyImportant
private PluginFeatureSource(){}
public PluginFeatureSource(List<String> commands, LinkedHashMap<Argument, Object> arguments, PluginSpecReader.Output outputAttrs, String specPath) {
this(commands, arguments, outputAttrs, specPath, false);
}
public PluginFeatureSource(List<String> commands, LinkedHashMap<Argument, Object> arguments, PluginSpecReader.Output outputAttrs, String specPath, boolean forbidEmptyOutput) {
super(commands, arguments, outputAttrs, specPath);
this.forbidEmptyOutput = forbidEmptyOutput;
}
@Override
protected String createTempFile(Track track, Argument argument, String chr, int start, int end, int zoom) throws IOException {
if(track instanceof AlignmentTrack){
List<Alignment> alignments = getAlignmentsForRange((AlignmentTrack) track, chr, start, end, zoom);
return super.createTempFile(alignments, argument);
}
FeatureTrack fTrack = (FeatureTrack) track;
List<Feature> features = fTrack.getFeatures(chr, start, end);
//Workaround for BEDTools bug, github #88, it can't read an empty file
if(features.size() == 0 && forbidEmptyOutput){
features = Arrays.<Feature>asList(new Locus("XXXchr0XXX", 0, 1));
}
return super.createTempFile(features, argument);
}
/**
* Perform the actual combination operation between the constituent data
* sources. This implementation re-runs the operation each call.
*
* @param chr
* @param start
* @param end
* @return
* @throws java.io.IOException
*/
@Override
public final Iterator<D> getFeatures(String chr, int start, int end) throws IOException {
return super.getFeatures(chr, start, end, -1);
}
@Override
public List<LocusScore> getCoverageScores(String chr, int start, int end, int zoom) {
return null;
}
/**
* If this track has not had it's feature window size set,
* we use the minimum of the sources
*
* @return
*/
@Override
public final int getFeatureWindowSize() {
int featureWindowSize = getMinSizeFromTracks(arguments.values());
return featureWindowSize;
}
private int getMinSizeFromTracks(Iterable tracks) {
int featureWindowSize = Integer.MAX_VALUE;
for (Object val : tracks) {
int tmpSize = Integer.MAX_VALUE;
if (val instanceof FeatureTrack) {
FeatureTrack track = ((FeatureTrack) val);
tmpSize = track.getFeatureWindowSize();
} else if (val instanceof List) {
featureWindowSize = getMinSizeFromTracks((List) val);
}
featureWindowSize = Math.min(featureWindowSize, tmpSize);
}
return featureWindowSize;
}
@Override
public final void setFeatureWindowSize(int size) {
//no-op
}
}