htsjdk.samtools.util

Class IntervalCodec

java.lang.Object

htsjdk.samtools.util.IntervalCodec

All Implemented Interfaces:

SortingCollection.Codec<Interval>, java.lang.Cloneable

public class IntervalCodec
extends java.lang.Object
implements SortingCollection.Codec<Interval>

Constructor Summary

Constructors

Constructor and Description
IntervalCodec(SAMSequenceDictionary dict) Creates a new binary codec to read or write.

Method Summary

Modifier and Type	Method and Description
IntervalCodec	clone() Must return a cloned copy of the codec that can be used independently of the original instance.
Interval	decode() Reads an interval from the input stream.
void	encode(Interval interval) Writes the interval to the output stream.
void	setInputStream(java.io.InputStream is) Sets the input stream that records will be read from.
void	setInputStream(java.io.InputStream is, java.lang.String filename) Sets the input stream that records will be read from.
void	setOutputStream(java.io.OutputStream os) Sets the output stream that records will be written to.
void	setOutputStream(java.io.OutputStream os, java.lang.String filename) Sets the output stream that records will be written to.

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalCodec

public IntervalCodec(SAMSequenceDictionary dict)

Creates a new binary codec to read or write.

Parameters:

dict - the sequence dictionary associated with the intervals.

Method Detail

clone

public IntervalCodec clone()

Description copied from interface: SortingCollection.Codec

Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.

Specified by:

clone in interface SortingCollection.Codec<Interval>

Overrides:

clone in class java.lang.Object

setOutputStream

public void setOutputStream(java.io.OutputStream os)

Sets the output stream that records will be written to.

Specified by:

setOutputStream in interface SortingCollection.Codec<Interval>

setOutputStream

public void setOutputStream(java.io.OutputStream os,
                            java.lang.String filename)

Sets the output stream that records will be written to.

setInputStream

public void setInputStream(java.io.InputStream is)

Sets the input stream that records will be read from.

Specified by:

setInputStream in interface SortingCollection.Codec<Interval>

setInputStream

public void setInputStream(java.io.InputStream is,
                           java.lang.String filename)

Sets the input stream that records will be read from.

encode

public void encode(Interval interval)

Writes the interval to the output stream.

Specified by:

encode in interface SortingCollection.Codec<Interval>

Parameters:

interval - the interval to write.

decode

public Interval decode()

Reads an interval from the input stream.

Specified by:

decode in interface SortingCollection.Codec<Interval>

Returns:

null if no more intervals, otherwise the next interval.