Package vcf

Class IntervalVcfIt<E extends MarkerContainer>

java.lang.Object

vcf.IntervalVcfIt<E>

Type Parameters:

E - the type parameter

All Implemented Interfaces:

FileIt<E>, SampleFileIt<E>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<E>

public final class IntervalVcfIt<E extends MarkerContainer>
extends java.lang.Object
implements SampleFileIt<E>

Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.

Constructor Summary

Constructors

Constructor	Description
IntervalVcfIt(SampleFileIt<E> it, ChromInterval interval)	Constructs a new IntervalVcfIterator instance.

Method Summary

Modifier and Type	Method	Description
void	close()	Terminates the iteration and releases any system resources that are held by this object.
java.io.File	file()	Returns the file from which the data are read, or null if the data are read from standard input or are computed data.
boolean	hasNext()	Returns true if the iteration has more elements.
E	next()	Returns the next element in the iteration.
void	remove()	The remove method is not supported by this iterator.
Samples	samples()	Returns the list of samples.

Methods inherited from interface blbutil.FileIt

toString

Methods inherited from interface java.util.Iterator

forEachRemaining

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalVcfIt

public IntervalVcfIt(SampleFileIt<E> it,
                     ChromInterval interval)

Constructs a new IntervalVcfIterator instance.

Parameters:

it - an iterator whose next() method returns a marker container

interval - a chromosome interval

Throws:

java.lang.NullPointerException - if it == null || interval == null

Method Detail

file

public java.io.File file()

Description copied from interface: FileIt

Returns the file from which the data are read, or null if the data are read from standard input or are computed data.

Specified by:

file in interface FileIt<E extends MarkerContainer>

Returns:

the file from which the data are read, or null if the data are read from standard input or are computed data

samples

public Samples samples()

Description copied from interface: SampleFileIt

Returns the list of samples.

Specified by:

samples in interface SampleFileIt<E extends MarkerContainer>

Returns:

the list of samples

hasNext

public boolean hasNext()

Returns true if the iteration has more elements.

Specified by:

hasNext in interface java.util.Iterator<E extends MarkerContainer>

Returns:

true if the iteration has more elements.

next

public E next()

Returns the next element in the iteration.

Specified by:

next in interface java.util.Iterator<E extends MarkerContainer>

Returns:

the next element in the iteration.

Throws:

java.util.NoSuchElementException - if the iteration has no more elements.

remove

public void remove()

The remove method is not supported by this iterator.

Specified by:

remove in interface java.util.Iterator<E extends MarkerContainer>

Throws:

java.lang.UnsupportedOperationException - if this method is invoked

close

public void close()

Description copied from interface: FileIt

Terminates the iteration and releases any system resources that are held by this object. After invoking close(), further invocations of close() have no effect.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface FileIt<E extends MarkerContainer>