From 0b07373909f85e5092b98e5d2fb1cb1606ef53c3 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 May 2011 18:06:05 +0000
Subject: [PATCH] Incorporating old feedback from eric: @deprecated methods
 should not be @deprecated, but rather protected, and the test's package moved
 to where it can access those test methods.

Also allows for the slightly more awesome name "MWUnitTest"



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5850 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/MannWhitneyU.java | 8 +++-----
 .../walkers/RFAUnitTest.java => utils/MWUnitTest.java}    | 4 ++--
 2 files changed, 5 insertions(+), 7 deletions(-)
 rename java/test/org/broadinstitute/sting/{oneoffprojects/walkers/RFAUnitTest.java => utils/MWUnitTest.java} (97%)

diff --git a/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java b/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
index aab8a4c35..fac04db1d 100755
--- a/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
+++ b/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
@@ -305,8 +305,7 @@ public class MannWhitneyU {
      * @return same as cpr
      * @deprecated - for testing only (really)
      */
-    @Deprecated
-    public static double calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(int n, int m, long u) {
+    protected static double calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(int n, int m, long u) {
         return cpr(n,m,u);
     }
 
@@ -336,8 +335,7 @@ public class MannWhitneyU {
      * @return  observations
      * @deprecated - only for testing
      */
-    @Deprecated
-    public TreeSet<Pair<Number,USet>> getObservations() {
+    protected TreeSet<Pair<Number,USet>> getObservations() {
         return observations;
     }
 
@@ -346,7 +344,7 @@ public class MannWhitneyU {
      * @return size set 1, size set 2
      * @deprecated - only for testing
      */
-    public Pair<Integer,Integer> getSetSizes() {
+    protected Pair<Integer,Integer> getSetSizes() {
         return new Pair<Integer,Integer>(sizeSet1,sizeSet2);
     }
 
diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/RFAUnitTest.java b/java/test/org/broadinstitute/sting/utils/MWUnitTest.java
similarity index 97%
rename from java/test/org/broadinstitute/sting/oneoffprojects/walkers/RFAUnitTest.java
rename to java/test/org/broadinstitute/sting/utils/MWUnitTest.java
index 32b5e218a..72d67e8ff 100755
--- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/RFAUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/MWUnitTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.walkers;
+package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.oneoffprojects.walkers.newassociation.features.ReadFeatureAggregator;
@@ -17,7 +17,7 @@ import org.testng.Assert;
  * Time: 2:06 PM
  * To change this template use File | Settings | File Templates.
  */
-public class RFAUnitTest extends BaseTest {
+public class MWUnitTest extends BaseTest {
     @BeforeClass
     public void init() { }