/*
* 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.data;
import org.apache.commons.lang.ArrayUtils;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.CodecFactory;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.FeatureCodec;
import org.junit.Test;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static junit.framework.Assert.assertEquals;
/**
* User: jacob
* Date: 2013-Mar-11
*/
public class GenomeSummaryDataTest extends AbstractHeadlessTest {
private static final String testDataPath = TestUtils.DATA_DIR + "bed/chr1-2_peaks.bed";
@Override
public void setUp() throws Exception {
super.setUp();
TestUtils.createIndex(testDataPath);
}
private Iterable getFeatures(String chr) throws Exception {
FeatureCodec codec = CodecFactory.getCodec(testDataPath, genome);
AbstractFeatureReader bfs = AbstractFeatureReader.getFeatureReader(testDataPath, codec, true);
if(chr == null) return bfs.iterator();
return bfs.query(chr, 0, Integer.MAX_VALUE);
}
/**
* Build GenomeSummaryData from sorted (by chromosome and start position) set of features
* @param genome
* @param trackId
* @param features
* @return
*/
private GenomeSummaryData buildGenomeSummaryData(Genome genome, String trackId, Iterable<BasicFeature> features, double scale){
GenomeSummaryData genomeSummaryData = new GenomeSummaryData(genome, new String[]{trackId});
if(scale > 0){
genomeSummaryData.setScale(scale);
}
List<Integer> startLocations = new ArrayList<Integer>();
List<Float> data = new ArrayList<Float>();
String lastChr = null;
for(BasicFeature feature: features){
String chr = feature.getChr();
//Finish off last chromosome
if(lastChr != null && !chr.equals(lastChr)){
Map<String, float[]> dMap = new HashMap<String, float[]>();
dMap.put(trackId, ArrayUtils.toPrimitive(data.toArray(new Float[data.size()])));
genomeSummaryData.addData(lastChr, ArrayUtils.toPrimitive(startLocations.toArray(new Integer[startLocations.size()])), dMap);
startLocations.clear();
data.clear();
}
startLocations.add(feature.getStart());
data.add(feature.getScore());
lastChr = chr;
}
Map<String, float[]> dMap = new HashMap<String, float[]>();
dMap.put(trackId, ArrayUtils.toPrimitive(data.toArray(new Float[data.size()])));
genomeSummaryData.addData(lastChr, ArrayUtils.toPrimitive(startLocations.toArray(new Integer[startLocations.size()])), dMap);
return genomeSummaryData;
}
@Test
public void testSinglePointsSingleChromo_01() throws Exception{
tstAccumulate("chr1", 6, 100.0);
}
@Test
public void testSinglePointsSingleChromo_02() throws Exception{
tstAccumulate("chr2", 8, 10.0);
}
@Test
public void testCombinePointsSingleChromo_01() throws Exception{
tstAccumulate("chr1", 3, 1000.0);
}
@Test
public void testCombinePointsSingleChromo_02() throws Exception{
tstAccumulate("chr2", 5, 1000.0);
}
@Test
public void testSinglePointsMultiChromo() throws Exception{
tstAccumulate(null, 14, 10.0);
}
@Test
public void testCombinePointsMultiChromo_01() throws Exception{
tstAccumulate(null, 13, 100.0);
}
@Test
public void testCombinePointsMultiChromo_02() throws Exception{
tstAccumulate(null, 7, -1);
}
private void tstAccumulate(String chr, int expLocations, double scale) throws Exception{
GenomeSummaryData genomeSummaryData = buildGenomeSummaryData(genome, testDataPath, getFeatures(chr), scale);
assertEquals(0, genomeSummaryData.skippedChromosomes.size());
assertEquals(expLocations, genomeSummaryData.nDataPts);
assertEquals(expLocations, genomeSummaryData.getLocations().length);
assertEquals(expLocations, genomeSummaryData.getData(testDataPath).length);
}
}