org.broadinstitute.hellbender.tools.walkers.varianteval.util

Class EvaluationContext

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext

public class EvaluationContext
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext.EvaluationContextCombiner	COMBINER

Constructor Summary

Constructors

Constructor and Description
EvaluationContext(VariantEval walker, java.util.Set<java.lang.Class<? extends VariantEvaluator>> evaluationClasses)

Method Summary

Modifier and Type	Method and Description
void	apply(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext, htsjdk.variant.variantcontext.VariantContext comp, htsjdk.variant.variantcontext.VariantContext eval)
void	combine(EvaluationContext rhs)
java.util.Set<java.lang.Class<? extends VariantEvaluator>>	getEvaluationClasses() Returns a set of VariantEvaluator classes to be used
java.util.List<VariantEvaluator>	getEvaluationInstances() Return a list of instances of each VariantEvaluator (see getEvaluationClasses).
java.util.TreeSet<VariantEvaluator>	getVariantEvaluators() Returns a sorted set of VariantEvaluators

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

COMBINER

public static final org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext.EvaluationContextCombiner COMBINER

Constructor Detail

EvaluationContext

public EvaluationContext(VariantEval walker,
                         java.util.Set<java.lang.Class<? extends VariantEvaluator>> evaluationClasses)

Method Detail

getEvaluationInstances

public java.util.List<VariantEvaluator> getEvaluationInstances()

Return a list of instances of each VariantEvaluator (see getEvaluationClasses). Note: elements of this list can be null.

Returns:

The list of VariantEvaluator instances

getEvaluationClasses

public java.util.Set<java.lang.Class<? extends VariantEvaluator>> getEvaluationClasses()

Returns a set of VariantEvaluator classes to be used

Returns:

The set of VariantEvaluator classes to be used

getVariantEvaluators

public final java.util.TreeSet<VariantEvaluator> getVariantEvaluators()

Returns a sorted set of VariantEvaluators

Returns:

A sorted set of VariantEvaluator instances

apply

public final void apply(ReferenceContext referenceContext,
                        ReadsContext readsContext,
                        FeatureContext featureContext,
                        htsjdk.variant.variantcontext.VariantContext comp,
                        htsjdk.variant.variantcontext.VariantContext eval)

combine

public void combine(EvaluationContext rhs)