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GenotypesContext no longer have immutability in constructor 

-- additional bug fixes throughout VariantContext and GenotypesContext objects
This commit is contained in:
Mark DePristo 2011-11-21 14:34:31 -05:00
parent e467b8e1ae
commit 2c501364b8
5 changed files with 55 additions and 23 deletions
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57
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
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@ -38,7 +38,7 @@ public class GenotypesContext implements List<Genotype> {
* static constant value for an empty GenotypesContext. Useful since so many VariantContexts have no genotypes
*/
public final static GenotypesContext NO_GENOTYPES =
new GenotypesContext(new ArrayList<Genotype>(0), new HashMap<String, Integer>(0), Collections.<String>emptyList(), true);
new GenotypesContext(new ArrayList<Genotype>(0), new HashMap<String, Integer>(0), Collections.<String>emptyList()).immutable();
/**
*sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order
@ -77,24 +77,23 @@ public class GenotypesContext implements List<Genotype> {
* Create an empty GenotypeContext
*/
protected GenotypesContext() {
this(10, false);
this(10);
}
/**
* Create an empty GenotypeContext, with initial capacity for n elements
*/
@Requires("n >= 0")
protected GenotypesContext(final int n, final boolean immutable) {
this(new ArrayList<Genotype>(n), immutable);
protected GenotypesContext(final int n) {
this(new ArrayList<Genotype>(n));
}
/**
* Create an GenotypeContext containing genotypes
*/
@Requires("genotypes != null")
protected GenotypesContext(final ArrayList<Genotype> genotypes, final boolean immutable) {
@Requires({"genotypes != null", "noDups(genotypes)"})
protected GenotypesContext(final ArrayList<Genotype> genotypes) {
this.notToBeDirectlyAccessedGenotypes = genotypes;
this.immutable = immutable;
this.sampleNameToOffset = null;
this.cacheIsInvalid = true;
}
@ -109,19 +108,16 @@ public class GenotypesContext implements List<Genotype> {
* genotype in the vector of genotypes
* @param sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical
* order.
* @param immutable
*/
@Requires({"genotypes != null",
@Requires({"genotypes != null", "noDups(genotypes)",
"sampleNameToOffset != null",
"sampleNamesInOrder != null",
"genotypes.size() == sampleNameToOffset.size()",
"genotypes.size() == sampleNamesInOrder.size()"})
protected GenotypesContext(final ArrayList<Genotype> genotypes,
final Map<String, Integer> sampleNameToOffset,
final List<String> sampleNamesInOrder,
final boolean immutable) {
final List<String> sampleNamesInOrder) {
this.notToBeDirectlyAccessedGenotypes = genotypes;
this.immutable = immutable;
this.sampleNameToOffset = sampleNameToOffset;
this.sampleNamesInOrder = sampleNamesInOrder;
this.cacheIsInvalid = false;
@ -149,7 +145,7 @@ public class GenotypesContext implements List<Genotype> {
@Requires("nGenotypes >= 0")
@Ensures({"result != null"})
public static final GenotypesContext create(final int nGenotypes) {
return new GenotypesContext(nGenotypes, false);
return new GenotypesContext(nGenotypes);
}
/**
@ -173,7 +169,7 @@ public class GenotypesContext implements List<Genotype> {
public static final GenotypesContext create(final ArrayList<Genotype> genotypes,
final Map<String, Integer> sampleNameToOffset,
final List<String> sampleNamesInOrder) {
return new GenotypesContext(genotypes, sampleNameToOffset, sampleNamesInOrder, false);
return new GenotypesContext(genotypes, sampleNameToOffset, sampleNamesInOrder);
}
/**
@ -185,7 +181,7 @@ public class GenotypesContext implements List<Genotype> {
@Requires({"genotypes != null"})
@Ensures({"result != null"})
public static final GenotypesContext create(final ArrayList<Genotype> genotypes) {
return genotypes == null ? NO_GENOTYPES : new GenotypesContext(genotypes, false);
return genotypes == null ? NO_GENOTYPES : new GenotypesContext(genotypes);
}
/**
@ -197,7 +193,7 @@ public class GenotypesContext implements List<Genotype> {
@Requires({"genotypes != null"})
@Ensures({"result != null"})
public static final GenotypesContext create(final Genotype... genotypes) {
return new GenotypesContext(new ArrayList<Genotype>(Arrays.asList(genotypes)), false);
return create(new ArrayList<Genotype>(Arrays.asList(genotypes)));
}
/**
@ -306,14 +302,16 @@ public class GenotypesContext implements List<Genotype> {
}
@Override
@Requires("genotype != null")
@Requires({"genotype != null", "get(genotype.getSampleName()) == null"})
@Ensures("noDups(getGenotypes())")
public boolean add(final Genotype genotype) {
checkImmutability();
invalidateCaches();
return getGenotypes().add(genotype);
}
@Requires("genotype != null")
@Requires({"genotype != null", "! containsAny(Arrays.asList(genotype))"})
@Ensures("noDups(getGenotypes())")
public boolean add(final Genotype ... genotype) {
checkImmutability();
invalidateCaches();
@ -321,11 +319,15 @@ public class GenotypesContext implements List<Genotype> {
}
@Override
@Requires("! contains(genotype)")
@Ensures("noDups(getGenotypes())")
public void add(final int i, final Genotype genotype) {
throw new UnsupportedOperationException();
}
@Override
@Requires("! containsAny(genotypes)")
@Ensures("noDups(getGenotypes())")
public boolean addAll(final Collection<? extends Genotype> genotypes) {
checkImmutability();
invalidateCaches();
@ -347,6 +349,13 @@ public class GenotypesContext implements List<Genotype> {
return getGenotypes().containsAll(objects);
}
private boolean containsAny(final Collection<? extends Genotype> genotypes) {
for ( final Genotype g : genotypes ) {
if ( contains(g) ) return true;
}
return false;
}
@Override
public Genotype get(final int i) {
return getGenotypes().get(i);
@ -421,6 +430,7 @@ public class GenotypesContext implements List<Genotype> {
}
@Override
@Ensures("noDups(getGenotypes())")
public Genotype set(final int i, final Genotype genotype) {
checkImmutability();
invalidateCaches();
@ -604,6 +614,17 @@ public class GenotypesContext implements List<Genotype> {
}
}
protected final static boolean noDups(Collection<Genotype> genotypes) {
Set<String> names = new HashSet<String>(genotypes.size());
for ( final Genotype g : genotypes ) {
if ( names.contains(g.getSampleName()) )
return false;
names.add(g.getSampleName());
}
return true;
}
protected final static boolean sameSamples(List<Genotype> genotypes, Collection<String> sampleNamesInOrder) {
Set<String> names = new HashSet<String>(sampleNamesInOrder);
if ( names.size() != sampleNamesInOrder.size() )

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
View File

@ -73,7 +73,7 @@ public class LazyGenotypesContext extends GenotypesContext {
/**
* Returns the data used in the full GenotypesContext constructor
*
* {@link GenotypesContext#GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List, boolean)}
* {@link GenotypesContext#GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)}
*/
public static class LazyData {
final ArrayList<Genotype> genotypes;
@ -102,7 +102,7 @@ public class LazyGenotypesContext extends GenotypesContext {
*/
@Requires({"parser != null", "unparsedGenotypeData != null", "nUnparsedGenotypes >= 0"})
public LazyGenotypesContext(final LazyParser parser, final Object unparsedGenotypeData, final int nUnparsedGenotypes) {
super(EMPTY, false);
super(EMPTY);
this.parser = parser;
this.unparsedGenotypeData = unparsedGenotypeData;
this.nUnparsedGenotypes = nUnparsedGenotypes;

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -58,7 +58,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
// they don't get reordered. It's a good test of the genotype ordering system.
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("0cc0ec59f0328792e6413b6ff3f71780"));
Arrays.asList("f2ddfa8105c290b1f34b7a261a02a1ac"));
executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
}

12
public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java
View File

@ -77,6 +77,11 @@ public class GenotypesContextUnitTest extends BaseTest {
public GenotypesContext make(final List<Genotype> initialSamples) {
return GenotypesContext.copy(initialSamples);
}
@Override
public String toString() {
return "GenotypesContext";
}
};
private final class lazyMaker implements LazyGenotypesContext.LazyParser, ContextMaker {
@ -91,6 +96,11 @@ public class GenotypesContextUnitTest extends BaseTest {
public GenotypesContext make(final List<Genotype> initialSamples) {
return new LazyGenotypesContext(this, initialSamples, initialSamples.size());
}
@Override
public String toString() {
return "LazyGenotypesContext";
}
}
private Collection<ContextMaker> allMakers = Arrays.asList(baseMaker, new lazyMaker());
@ -100,7 +110,7 @@ public class GenotypesContextUnitTest extends BaseTest {
final List<Genotype> initialSamples;
private GenotypesContextProvider(ContextMaker maker, List<Genotype> initialSamples) {
super(GenotypesContextProvider.class);
super(GenotypesContextProvider.class, String.format("%s with %d samples", maker.toString(), initialSamples.size()));
this.maker = maker;
this.initialSamples = initialSamples;
}

3
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
View File

@ -834,7 +834,8 @@ public class VariantContextUnitTest extends BaseTest {
for ( int j = 0; j < i; j++ ) {
nSamples++;
Genotype g = allGenotypes.get(j % allGenotypes.size());
gc.add(g);
final String name = String.format("%s_%d%d", g.getSampleName(), i, j);
gc.add(new Genotype(name, g.getAlleles()));
switch ( g.getType() ) {
case NO_CALL: nNoCall++; nNoCallAlleles++; break;
case HOM_REF: nA += 2; nHomRef++; break;