htsjdk.samtools.util

Interface SortingCollection.Codec<T>

All Superinterfaces:

java.lang.Cloneable

All Known Implementing Classes:

BAMRecordCodec, VCFRecordCodec

Enclosing class:

SortingCollection<T>

public static interface SortingCollection.Codec<T>
extends java.lang.Cloneable

Client must implement this class, which defines the way in which records are written to and read from file.

Method Summary

Methods

Modifier and Type	Method and Description
SortingCollection.Codec<T>	clone() Must return a cloned copy of the codec that can be used independently of the original instance.
T	decode() Read the next record from the input stream and convert into a java object.
void	encode(T val) Write object to output stream
void	setInputStream(java.io.InputStream is) Where to read encoded input from
void	setOutputStream(java.io.OutputStream os) Where to write encoded output

Method Detail

setOutputStream

void setOutputStream(java.io.OutputStream os)

Where to write encoded output

Parameters:

os -

setInputStream

void setInputStream(java.io.InputStream is)

Where to read encoded input from

Parameters:

is -

encode

void encode(T val)

Write object to output stream

Parameters:

val - what to write

decode

T decode()

Read the next record from the input stream and convert into a java object.

Returns:

null if no more records. Should throw exception if EOF is encountered in the middle of a record.

clone

SortingCollection.Codec<T> clone()

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.