/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.data;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
/**
* @author jrobinso
*/
public class IGVDatasetTest extends AbstractHeadlessTest {
String cnFile = TestUtils.DATA_DIR + "igv/MIP_44.cn";
/**
* Test loading a dataset and accessing some random data cells
*/
@Test
public void testDataset() {
IGVDataset ds = new IGVDataset(new ResourceLocator(cnFile), genome);
// Get the start locations and data from sample yw280-4_44 on chr 1
int[] startLocations = ds.getStartLocations("chr1");
float[] data = ds.getData("yw280-4_44", "chr1");
assertEquals(startLocations.length, data.length);
// Check the first data point
assertEquals(794055, startLocations[0]);
assertEquals(1.86971, data[0], 1.0e-4);
// Check the last data point
int end = startLocations.length - 1;
assertEquals(245171540, startLocations[end]);
assertEquals(3.7871208, data[end], 1.0e-4);
}
/**
* Test of the parser getHeadings method
*/
@Test
public void testGetHeadings() {
String firstHeading = "yw280-4_44";
String secondHeading = "yw280-4_48";
String lastHeading = "DN30_3_03";
String headingsLine = "SNP Chromosome PhysicalPosition yw280-4_44 yw280-4_48 yw280-5_40 yw280-5_41 yw280-5_42 yw280-5_43 yw280-5_44 yw280-5_46 yw280-5_47 yw280-5_48 yw280-5_45 DN30_01 DN30_02 DN30_03 DN30_04 DN30_06 DN30_07 DN30_09 DN30_10 DN30_11 DN30_13 DN30_14 DN30_15 DN30_16 DN30_17 DN30_18 DN30_19 DN30_20 DN30_21 DN30_32 DN30_33 DN30_34 DN30_35 DN30_36 DN30_41 DN30_42 DN30_43 DN30_44 DN30_45 DN30_46 DN30_47 DN30_48 DN30_3_02 DN30_3_03";
String[] tokens = headingsLine.split("\t");
IGVDataset ds = new IGVDataset(new ResourceLocator(cnFile), genome);
IGVDatasetParser parser = new IGVDatasetParser(new ResourceLocator(cnFile), genome);
//parser.scan necessary to set values needed in getHeadings
List<ChromosomeSummary> summaries = parser.scan(ds);
String[] headings = parser.getHeadings(tokens, 1);
assertEquals(firstHeading, headings[0]);
assertEquals(secondHeading, headings[1]);
assertEquals(lastHeading, headings[headings.length - 1]);
}
/**
* Test of scan method. Test that we find
* all chromosomes we expect
*/
@Test
public void testScanDataset() {
IGVDataset ds = new IGVDataset(new ResourceLocator(cnFile), genome);
IGVDatasetParser parser = new IGVDatasetParser(new ResourceLocator(cnFile), genome);
List<ChromosomeSummary> summaries = parser.scan(ds);
assertEquals(24, summaries.size());
Set<String> chromos = new TreeSet<String>();
ArrayList<String> chromos_L = new ArrayList<String>(24);
for (int ii = 1; ii <= 22; ii++) {
chromos_L.add("chr" + ii);
}
chromos_L.add("chrX");
chromos_L.add("chrY");
chromos.addAll(chromos_L);
for (ChromosomeSummary cSum : summaries) {
assertTrue(chromos.contains(cSum.getName()));
}
}
}