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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
This commit is contained in:
chartl 2011-05-23 18:06:05 +00:00
parent f8f37a786d
commit 0b07373909
2 changed files with 5 additions and 7 deletions
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8
java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
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@ -305,8 +305,7 @@ public class MannWhitneyU {
* @return same as cpr * @return same as cpr
* @deprecated - for testing only (really) * @deprecated - for testing only (really)
*/ */
@Deprecated protected static double calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(int n, int m, long u) {
public static double calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(int n, int m, long u) {
return cpr(n,m,u); return cpr(n,m,u);
} }
@ -336,8 +335,7 @@ public class MannWhitneyU {
* @return observations * @return observations
* @deprecated - only for testing * @deprecated - only for testing
*/ */
@Deprecated protected TreeSet<Pair<Number,USet>> getObservations() {
public TreeSet<Pair<Number,USet>> getObservations() {
return observations; return observations;
} }
@ -346,7 +344,7 @@ public class MannWhitneyU {
* @return size set 1, size set 2 * @return size set 1, size set 2
* @deprecated - only for testing * @deprecated - only for testing
*/ */
public Pair<Integer,Integer> getSetSizes() { protected Pair<Integer,Integer> getSetSizes() {
return new Pair<Integer,Integer>(sizeSet1,sizeSet2); return new Pair<Integer,Integer>(sizeSet1,sizeSet2);
} }

4
java/test/org/broadinstitute/sting/oneoffprojects/walkers/RFAUnitTest.java → java/test/org/broadinstitute/sting/utils/MWUnitTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers; package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.oneoffprojects.walkers.newassociation.features.ReadFeatureAggregator; import org.broadinstitute.sting.oneoffprojects.walkers.newassociation.features.ReadFeatureAggregator;
@ -17,7 +17,7 @@ import org.testng.Assert;
* Time: 2:06 PM * Time: 2:06 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public class RFAUnitTest extends BaseTest { public class MWUnitTest extends BaseTest {
@BeforeClass @BeforeClass
public void init() { } public void init() { }