diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileResultTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileResultTest.java new file mode 100644 index 000000000..d131666fa --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileResultTest.java @@ -0,0 +1,98 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.activeregion; + +import net.sf.picard.reference.ReferenceSequenceFile; +import net.sf.samtools.SAMFileHeader; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.Arrays; +import java.util.EnumSet; +import java.util.LinkedList; +import java.util.List; + +/** + * Created with IntelliJ IDEA. + * User: depristo + * Date: 1/17/13 + * Time: 2:30 PM + * To change this template use File | Settings | File Templates. + */ +public class ActivityProfileResultTest { + private GenomeLocParser genomeLocParser; + + @BeforeClass + public void init() throws FileNotFoundException { + // sequence + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 100); + genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + } + + @DataProvider(name = "ActiveProfileResultProvider") + public Object[][] makeActiveProfileResultProvider() { + final List tests = new LinkedList(); + + final String chr = genomeLocParser.getContigs().getSequence(0).getSequenceName(); + for ( final GenomeLoc loc : Arrays.asList( + genomeLocParser.createGenomeLoc(chr, 10, 10), + genomeLocParser.createGenomeLoc(chr, 100, 100) )) { + for ( final double prob : Arrays.asList(0.0, 0.5, 1.0) ) { + for ( final ActivityProfileResult.ActivityProfileResultState state : ActivityProfileResult.ActivityProfileResultState.values() ) { + for ( final Number value : Arrays.asList(1, 2, 4) ) { + tests.add(new Object[]{ loc, prob, state, value}); + } + } + tests.add(new Object[]{ loc, prob, null, null}); + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "ActiveProfileResultProvider") + public void testActiveProfileResultProvider(GenomeLoc loc, final double prob, ActivityProfileResult.ActivityProfileResultState maybeState, final Number maybeNumber) { + final ActivityProfileResult apr = maybeState == null + ? new ActivityProfileResult(loc, prob) + : new ActivityProfileResult(loc, prob, maybeState, maybeNumber); + + Assert.assertEquals(apr.getLoc(), loc); + Assert.assertNotNull(apr.toString()); + Assert.assertEquals(apr.isActiveProb, prob); + Assert.assertEquals(apr.resultState, maybeState == null ? ActivityProfileResult.ActivityProfileResultState.NONE : maybeState); + Assert.assertEquals(apr.resultValue, maybeState == null ? null : maybeNumber); + } +}