From 8eeb87af2a66fad93026e18d51fe496d60b4b4e9 Mon Sep 17 00:00:00 2001
From: andrewk <andrewk@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 31 Jul 2009 00:09:35 +0000
Subject: [PATCH] Tests for downsampling related utilities in ListUtils class
 that didn't get checked in earlier

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1352 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/ListUtilsTest.java            | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 java/test/org/broadinstitute/sting/utils/ListUtilsTest.java

diff --git a/java/test/org/broadinstitute/sting/utils/ListUtilsTest.java b/java/test/org/broadinstitute/sting/utils/ListUtilsTest.java
new file mode 100644
index 000000000..723a16476
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/ListUtilsTest.java
@@ -0,0 +1,61 @@
+package org.broadinstitute.sting.utils;
+
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.MathUtils;
+
+
+import java.io.File;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Collections;
+
+/**
+ * Basic unit test for MathUtils
+ */
+public class ListUtilsTest extends BaseTest {
+    @BeforeClass
+    public static void init() { }
+
+    /**
+     * Tests that the random index selection is working correctly
+     */
+    @Test
+    public void testRandomIndicesWithReplacement() {
+        logger.warn("Executing testRandomIndicesWithReplacement");
+
+        // Check that the size of the list returned is correct
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(0, 5).size() == 0);
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(1, 5).size() == 1);
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(5, 5).size() == 5);
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(1000, 5).size() == 1000);
+
+        // Check that the list contains only the k element range that as asked for - no more, no less
+        List<Integer> Five = new ArrayList<Integer>();
+        Collections.addAll(Five, 0, 1, 2, 3, 4);
+        List<Integer> BigFive = ListUtils.sampleIndicesWithReplacement(10000, 5);
+        Assert.assertTrue(BigFive.containsAll(Five));
+        Assert.assertTrue(Five.containsAll(BigFive));
+    }
+
+    /**
+     * Tests that we get the right values from the multinomial distribution
+     */
+    @Test
+    public void testSliceListByIndices() {
+        logger.warn("Executing testSliceListByIndices");
+
+        // Check that the list contains only the k element range that as asked for - no more, no less but now
+        // use the index list to pull elements from another list using sliceListByIndices
+        List<Integer> Five = new ArrayList<Integer>();
+        Collections.addAll(Five, 0, 1, 2, 3, 4);
+        List<Character> FiveAlpha = new ArrayList<Character>();
+        Collections.addAll(FiveAlpha, 'a', 'b', 'c', 'd', 'e');
+        List<Integer> BigFive = ListUtils.sampleIndicesWithReplacement(10000, 5);
+        List<Character> BigFiveAlpha = ListUtils.sliceListByIndices(BigFive, FiveAlpha);
+        Assert.assertTrue(BigFiveAlpha.containsAll(FiveAlpha));
+        Assert.assertTrue(FiveAlpha.containsAll(BigFiveAlpha));
+    }
+}
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