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Another round of FindBugs fixes. Comparator doesn't implement Serializable.

This commit is contained in:
Ryan Poplin 2012-08-21 09:20:55 -04:00
parent 77fbaec044
commit 55b7949d68
6 changed files with 15 additions and 11 deletions
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3
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import org.jgrapht.graph.DefaultDirectedGraph;
import java.io.Serializable;
import java.util.Comparator;
/**
@ -55,7 +56,7 @@ public class DeBruijnEdge {
return (graph.getEdgeSource(this).equals(graph2.getEdgeSource(edge))) && (graph.getEdgeTarget(this).equals(graph2.getEdgeTarget(edge)));
}
public static class EdgeWeightComparator implements Comparator<DeBruijnEdge> {
public static class EdgeWeightComparator implements Comparator<DeBruijnEdge>, Serializable {
@Override
public int compare(final DeBruijnEdge edge1, final DeBruijnEdge edge2) {
return edge1.multiplicity - edge2.multiplicity;

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java
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@ -4,6 +4,7 @@ import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.jgrapht.graph.DefaultDirectedGraph;
import java.io.Serializable;
import java.util.*;
/**
@ -76,14 +77,14 @@ public class KBestPaths {
}
}
protected static class PathComparatorTotalScore implements Comparator<Path> {
protected static class PathComparatorTotalScore implements Comparator<Path>, Serializable {
@Override
public int compare(final Path path1, final Path path2) {
return path1.totalScore - path2.totalScore;
}
}
//protected static class PathComparatorLowestEdge implements Comparator<Path> {
//protected static class PathComparatorLowestEdge implements Comparator<Path>, Serializable {
// @Override
// public int compare(final Path path1, final Path path2) {
// return path2.lowestEdge - path1.lowestEdge;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -47,6 +47,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.Serializable;
import java.util.*;
/**
@ -103,7 +104,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
return map;
}
private static class HaplotypeComparator implements Comparator<Haplotype> {
private static class HaplotypeComparator implements Comparator<Haplotype>, Serializable {
public int compare(Haplotype a, Haplotype b) {
if (a.getQualitySum() < b.getQualitySum())

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
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@ -29,10 +29,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.io.*;
import java.util.*;
/**
@ -83,7 +80,7 @@ public class Tranche {
return accessibleTruthSites > 0 ? callsAtTruthSites / (1.0*accessibleTruthSites) : 0.0;
}
public static class TrancheTruthSensitivityComparator implements Comparator<Tranche> {
public static class TrancheTruthSensitivityComparator implements Comparator<Tranche>, Serializable {
@Override
public int compare(final Tranche tranche1, final Tranche tranche2) {
return Double.compare(tranche1.ts, tranche2.ts);

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.Serializable;
import java.util.Comparator;
/**
@ -54,7 +55,7 @@ public class VariantDatum {
public int worstAnnotation;
public MultivariateGaussian assignment; // used in K-means implementation
public static class VariantDatumLODComparator implements Comparator<VariantDatum> {
public static class VariantDatumLODComparator implements Comparator<VariantDatum>, Serializable {
@Override
public int compare(final VariantDatum datum1, final VariantDatum datum2) {
return Double.compare(datum1.lod, datum2.lod);

5
public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
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@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.Serializable;
import java.util.Comparator;
import java.util.TreeSet;
@ -434,12 +435,14 @@ public class MannWhitneyU {
* A comparator class which uses dithering on tie-breaking to ensure that the internal treeset drops no values
* and to ensure that rank ties are broken at random.
*/
private static class DitheringComparator implements Comparator<Pair<Number,USet>> {
private static class DitheringComparator implements Comparator<Pair<Number,USet>>, Serializable {
public DitheringComparator() {}
@Override
public boolean equals(Object other) { return false; }
@Override
public int compare(Pair<Number,USet> left, Pair<Number,USet> right) {
double comp = Double.compare(left.first.doubleValue(),right.first.doubleValue());
if ( comp > 0 ) { return 1; }