/*
* 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.feature;
import org.apache.log4j.Logger;
import org.broad.igv.exceptions.DataLoadException;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.TribbleIndexNotFoundException;
import org.broad.igv.feature.tribble.MUTCodec;
import org.broad.igv.track.*;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.Feature;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
/**
* Parses a mutation file, such as ".mut" or ".maf" (mutation annotation file)
*
* @author jrobinso
*/
public class MutationTrackLoader {
private static Logger log = Logger.getLogger(MutationTrackLoader.class);
private ResourceLocator locator = null;
private Genome genome = null;
MUTCodec codec;
public static boolean isMutationAnnotationFile(ResourceLocator locator) throws IOException {
return MUTCodec.isMutationAnnotationFile(locator);
}
public List<FeatureTrack> loadMutationTracks(ResourceLocator locator, Genome genome) throws IOException, TribbleIndexNotFoundException {
this.locator = locator;
this.genome = genome;
boolean indexed = isIndexed(locator, genome);
List<FeatureTrack> tracks = new ArrayList<FeatureTrack>();
if (indexed) {
String[] samples = getCodec().getSamples();
MutationFeatureSource.MutationDataManager dataManager = new MutationFeatureSource.MutationDataManager(locator, genome);
for (String sampleId : samples) {
String id = locator.getPath() + "_" + sampleId;
FeatureSource<Mutation> featureSource = new MutationFeatureSource(sampleId, dataManager);
MutationTrack track = new MutationTrack(locator, id, featureSource);
tracks.add(track);
track.setName(sampleId);
}
} else {
Map<String, List<htsjdk.tribble.Feature>> features = loadMutations();
for (String sampleId : features.keySet()) {
String id = locator.getPath() + "_" + sampleId;
MutationTrack track = new MutationTrack(locator, id, new FeatureCollectionSource(features.get(sampleId), genome));
tracks.add(track);
track.setName(sampleId);
}
}
for (FeatureTrack track : tracks) {
track.setSquishedRowHeight(5);
track.setExpandedRowHeight(15);
track.setHeight(15);
// Override default minimum height (10 for feature tracks).
track.setMinimumHeight(0);
}
//Just to make sure we have no memory
this.locator = null;
this.genome = null;
return tracks;
}
private MUTCodec getCodec() {
if (codec == null) codec = new MUTCodec(locator.getPath(), genome);
return codec;
}
/**
* Test to see if a usable index exists. In addition to the index, mutation files have an additional requirement
* that samples be specified in a header directive.
*
* @param locator
* @return
*/
private boolean isIndexed(ResourceLocator locator, Genome genome) {
if (!TrackLoader.isIndexed(locator, genome)) return false;
try {
String[] samples = getCodec().getSamples();
return samples != null && samples.length > 0;
} catch (Exception e) {
log.error("Error creating codec for: " + locator.getPath(), e);
return false;
}
}
/**
* Return a map of runId -> list of mutation objects. The "runId" field
* is the track identifier (name) for mutation files.
*
* @return
*/
private Map<String, List<htsjdk.tribble.Feature>> loadMutations() {
AsciiLineReader reader = null;
String nextLine = null;
try {
if (codec == null) codec = new MUTCodec(locator.getPath(), genome);
Map<String, List<htsjdk.tribble.Feature>> mutationMap = new LinkedHashMap();
reader = ParsingUtils.openAsciiReader(locator);
// Skip header - handled in codec
while ((nextLine = reader.readLine()) != null) {
if (nextLine.startsWith("#")) continue;
else break;
}
while ((nextLine = reader.readLine()) != null) {
Mutation mut = codec.decode(nextLine);
if (mut != null) {
String sampleId = mut.getSampleId();
List<htsjdk.tribble.Feature> features = mutationMap.get(sampleId);
if (features == null) {
features = new ArrayList<Feature>();
mutationMap.put(sampleId, features);
}
features.add(mut);
}
}
return mutationMap;
} catch (IOException e) {
log.error("Error loading mutation file", e);
throw new DataLoadException("IO Exception: " + e.toString(), locator.getPath());
} finally {
reader.close();
}
}
}