htsjdk.variant.variantcontext.filter

Class CompoundFilter

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<VariantContextFilter>

htsjdk.variant.variantcontext.filter.CompoundFilter

All Implemented Interfaces:

VariantContextFilter, java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<VariantContextFilter>, java.util.Collection<VariantContextFilter>, java.util.List<VariantContextFilter>, java.util.RandomAccess

public class CompoundFilter
extends java.util.ArrayList<VariantContextFilter>
implements VariantContextFilter

A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
CompoundFilter(boolean requireAll) A constructor that will determine if this compound filter will require that *all* the included filters pass or *some* of them pass (depending on the requireAll parameter in the constructor).

Method Summary

Modifier and Type	Method and Description
boolean	test(VariantContext variantContext) Determines whether a VariantContext matches this filter

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, forEach, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeIf, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode

Methods inherited from class java.util.AbstractCollection

containsAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode

Methods inherited from interface java.util.Collection

parallelStream, stream

Constructor Detail

CompoundFilter

public CompoundFilter(boolean requireAll)

A constructor that will determine if this compound filter will require that *all* the included filters pass or *some* of them pass (depending on the requireAll parameter in the constructor).

Parameters:

requireAll - a boolean parameter determining whether this filter requires all its elements to pass (true) for it to pass, or only one (false). If there are no variantfilters it will return true.

Method Detail

test

public boolean test(VariantContext variantContext)

Description copied from interface: VariantContextFilter

Determines whether a VariantContext matches this filter

Specified by:

test in interface VariantContextFilter

Parameters:

variantContext - the record to examine against the sub-filters

Returns:

true if variantContext either passes all the filters (when requireAll==true) or doesn't fail any of the filters (when requireAll==false)