Package htsjdk.variant.variantcontext.filter

Class FilteringVariantContextIterator

java.lang.Object

htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator

All Implemented Interfaces:

CloseableIterator<VariantContext>, Closeable, AutoCloseable, Iterable<VariantContext>, Iterator<VariantContext>

Direct Known Subclasses:

FilteringIterator

public class FilteringVariantContextIterator
extends Object
implements CloseableIterator<VariantContext>, Iterable<VariantContext>

A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter. The iterator returns all the variantcontexts for which the filter's function "test" returns true (and only those)

Constructor Summary

Constructors

Constructor	Description
FilteringVariantContextIterator(Iterator<VariantContext> iterator, VariantContextFilter filter)	Constructor of an iterator based on the provided iterator and predicate.

Method Summary

Modifier and Type	Method	Description
void	close()	Should be implemented to close/release any underlying resources.
boolean	hasNext()	Returns true if the iteration has more elements.
Iterator<VariantContext>	iterator()	function to satisfy the Iterable interface
VariantContext	next()	Returns the next element in the iteration.
void	remove()	Required method for Iterator API.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Details

FilteringVariantContextIterator

public FilteringVariantContextIterator(Iterator<VariantContext> iterator,
 VariantContextFilter filter)

Constructor of an iterator based on the provided iterator and predicate. The resulting records will be all those VariantContexts from iterator for which filter.test( . ) is true

Parameters:

iterator - the backing iterator

filter - the filter

Method Details

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface CloseableIterator<VariantContext>

hasNext

public boolean hasNext()

Returns true if the iteration has more elements.

Specified by:

hasNext in interface Iterator<VariantContext>

Returns:

true if the iteration has more elements. Otherwise returns false.

next

public VariantContext next()
                    throws NoSuchElementException

Returns the next element in the iteration.

Specified by:

next in interface Iterator<VariantContext>

Returns:

the next element in the iteration

Throws:

NoSuchElementException - if there are no more elements to return

remove

public void remove()

Required method for Iterator API.

Specified by:

remove in interface Iterator<VariantContext>

Throws:

UnsupportedOperationException - since it is unsupported here.

iterator

public Iterator<VariantContext> iterator()

function to satisfy the Iterable interface

Specified by:

iterator in interface Iterable<VariantContext>

Returns:

itself since the class inherits from Iterator