/*
* 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.tdf;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.Globals;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.ChromosomeCoordinate;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static junit.framework.Assert.assertEquals;
/**
* User: jacob
* Date: 2012-Dec-28
*/
public class TDFDataSourceTest extends AbstractHeadlessTest {
@Test
public void testWholeGenomeScores() throws Exception {
Map<String, Double> expectedValues = new HashMap<String, Double>();
String[] chrNames = {"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11",
"chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22",
"chrX", "chrY", "chrM"};
double value = 1;
for (String chr : chrNames) {
expectedValues.put(chr, value);
value++;
}
String testFile = TestUtils.DATA_DIR + "tdf/wholeGenomeTest.tdf";
TDFReader reader = new TDFReader(new ResourceLocator(testFile));
TDFDataSource ds = new TDFDataSource(reader, 0, "", genome);
List<LocusScore> wgScores = ds.getSummaryScores(Globals.CHR_ALL, 0, Integer.MAX_VALUE, 0);
for (LocusScore score : wgScores) {
int genomeStart = score.getStart();
ChromosomeCoordinate stCoord = genome.getChromosomeCoordinate(genomeStart);
ChromosomeCoordinate endCoord = genome.getChromosomeCoordinate(score.getEnd());
// Skip "edge" bins that include data from 2 chromosomes. We don't know the expected value for these.
if (stCoord.getChr().equals(endCoord.getChr())) {
String chrName = stCoord.getChr();
double ev = expectedValues.get(chrName);
assertEquals(ev, score.getScore(), 0.001);
}
}
}
}