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Make DiploidGenotype enum private to walkers.genotyper

This commit is contained in:
Mark DePristo 2011-09-24 08:48:33 -04:00
parent b66841f179
commit c0bb0cb465
7 changed files with 4 additions and 8 deletions
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4
public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java → public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE. * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.utils.genotype; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
* Time: 6:46:09 PM * Time: 6:46:09 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public enum DiploidGenotype { enum DiploidGenotype {
AA ('A', 'A'), AA ('A', 'A'),
AC ('A', 'C'), AC ('A', 'C'),
AG ('A', 'G'), AG ('A', 'G'),

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel; import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -30,7 +30,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.FragmentPileup; import org.broadinstitute.sting.utils.pileup.FragmentPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypePriors.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import java.util.Arrays; import java.util.Arrays;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;

3
public/java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeUnitTest.java → public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.utils.genotype; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
import org.testng.Assert; import org.testng.Assert;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;

1
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.testng.Assert; import org.testng.Assert;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.testng.annotations.Test; import org.testng.annotations.Test;