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Adding VariantContext.hasAlternateAllele functionality

This commit is contained in:
Eric Banks 2012-04-24 11:07:46 -04:00
parent 66f3315548
commit 74ad008163
1 changed files with 16 additions and 4 deletions
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20
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -592,15 +592,27 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/**
* @return True if this context contains Allele allele, or false otherwise
*/
public boolean hasAllele(Allele allele) {
return hasAllele(allele, false);
public boolean hasAllele(final Allele allele) {
return hasAllele(allele, false, getAlleles());
}
public boolean hasAllele(Allele allele, boolean ignoreRefState) {
public boolean hasAllele(final Allele allele, final boolean ignoreRefState) {
return hasAllele(allele, ignoreRefState, getAlleles());
}
public boolean hasAlternateAllele(final Allele allele) {
return hasAllele(allele, false, getAlternateAlleles());
}
public boolean hasAlternateAllele(final Allele allele, final boolean ignoreRefState) {
return hasAllele(allele, ignoreRefState, getAlternateAlleles());
}
private boolean hasAllele(final Allele allele, final boolean ignoreRefState, final List<Allele> allelesToConsider) {
if ( allele == REF || allele == ALT ) // optimization for cached cases
return true;
for ( Allele a : getAlleles() ) {
for ( Allele a : allelesToConsider ) {
if ( a.equals(allele, ignoreRefState) )
return true;
}