/*
* 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;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.data.seg.SegmentFileParser;
import org.broad.igv.data.seg.SegmentedAsciiDataSet;
import org.broad.igv.data.seg.SegmentedDataSet;
import org.broad.igv.data.seg.SegmentedDataSource;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.DataSourceTrack;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.util.List;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertNotNull;
/**
* @author jacob
* @date 2013-Apr-25
*/
public class CombinedDataSourceTest extends AbstractHeadlessTest {
/**
* Just test that nothing crashes
* @throws Exception
*/
@Test
public void testNoExceptions() throws Exception{
String chr = "chr1";
int start = 0;
int end = (int) 100e6;
int zoom = 0;
CombinedDataSource combinedSource = getDataSource(CombinedDataSource.Operation.ADD);
List<LocusScore> combinedScores = combinedSource.getSummaryScoresForRange(chr, start, end, zoom);
for(LocusScore score: combinedScores){
assertNotNull(score);
}
}
/**
* Test combination when the two data sources have the same tiling boundaries
* shouldn't need to split anything up, easy case
* @throws Exception
*/
@Test
public void testSameBoundaries() throws Exception{
String chr = "chr1";
int start = 0;
int end = 1000;
int zoom = 0;
CombinedDataSource combinedSource = getDataSource(CombinedDataSource.Operation.ADD);
List<LocusScore> combinedScores = combinedSource.getSummaryScoresForRange(chr, start, end, zoom);
int[] expStarts = new int[]{0,100,200,300};
int[] expEnds = new int[]{100,200,300,400};
float[] expScores = new float[]{1,2,3,4};
int expCount = expStarts.length;
assertEquals(expCount, combinedScores.size());
int idx = 0;
for(LocusScore score: combinedScores){
assertEquals(expStarts[idx], score.getStart());
assertEquals(expEnds[idx], score.getEnd());
assertEquals(expScores[idx++], score.getScore());
}
}
@Test
public void testDifferentBoundaries() throws Exception{
String chr = "chr2";
int start = 0;
int end = 1000;
int zoom = 0;
CombinedDataSource combinedSource = getDataSource(CombinedDataSource.Operation.ADD);
List<LocusScore> combinedScores = combinedSource.getSummaryScoresForRange(chr, start, end, zoom);
int[] expStarts = new int[]{100,150,200,250,300,350,400,450,500,550};
int[] expEnds = new int[]{150,200,250,300,350,400,450,500,550,650};
float[] expScores = new float[]{1, 2, 3, 3, 4, 4, 5, 5, 1, 1};
int expCount = expStarts.length;
assertEquals(expCount, combinedScores.size());
int idx = 0;
for(LocusScore score: combinedScores){
assertEquals(expStarts[idx], score.getStart());
assertEquals(expEnds[idx], score.getEnd());
assertEquals(expScores[idx++], score.getScore());
}
}
private CombinedDataSource getDataSource(CombinedDataSource.Operation operation){
String pathA = TestUtils.DATA_DIR + "seg/toCombine_a.seg";
String pathB = TestUtils.DATA_DIR + "seg/toCombine_b.seg";
SegmentedDataSet dsA = getSegDataSet(pathA);
SegmentedDataSet dsB = getSegDataSet(pathB);
SegmentedDataSource sourceA = new SegmentedDataSource("0123-A", dsA);
SegmentedDataSource sourceB = new SegmentedDataSource("0123-B-1", dsB);
DataSourceTrack trackA = new DataSourceTrack(null, sourceA.getTrackIdentifier(), sourceA.getTrackIdentifier(), sourceA);
DataSourceTrack trackB = new DataSourceTrack(null, sourceB.getTrackIdentifier(), sourceB.getTrackIdentifier(), sourceB);
return new CombinedDataSource(trackA, trackB, operation);
}
private SegmentedAsciiDataSet getSegDataSet(String path){
ResourceLocator locator = new ResourceLocator(path);
SegmentFileParser parser = new SegmentFileParser(locator);
return parser.loadSegments(locator, genome);
}
}