CompoundFilter (htsjdk 5.0.0 API)

java.lang.Object

java.util.AbstractCollection<VariantContextFilter>

java.util.AbstractList<VariantContextFilter>

java.util.ArrayList<VariantContextFilter>

htsjdk.variant.variantcontext.filter.CompoundFilter

All Implemented Interfaces:: VariantContextFilter, Serializable, Cloneable, Iterable<VariantContextFilter>, Collection<VariantContextFilter>, Predicate<VariantContext>, List<VariantContextFilter>, RandomAccess, SequencedCollection<VariantContextFilter>

public class CompoundFilter extends 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:

Field Summary

Fields inherited from class AbstractList
modCount
Constructor Summary

Constructors

Constructor

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

Description

boolean

test(VariantContext variantContext)

Methods inherited from class ArrayList
add, add, addAll, addAll, addFirst, addLast, clear, clone, contains, ensureCapacity, equals, forEach, get, getFirst, getLast, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeFirst, removeIf, removeLast, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class AbstractCollection
containsAll, toString

Methods inherited from class Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface Collection
parallelStream, stream, toArray

Methods inherited from interface List
containsAll, reversed

Methods inherited from interface Predicate
and, negate, or

Constructor Details
- 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 Details
- test
  
  public boolean test(VariantContext variantContext)
  
  Specified by:
  
  test in interface Predicate<VariantContext>
  
  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)