Unit tests for ActivityProfileResult

public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileResultTest.java

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+/*
+ * 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<Object[]> tests = new LinkedList<Object[]>();
+
+        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);
+    }
+}