htsjdk.samtools

Interface CoordinateSortedPairInfoMap.Codec<KEY,REC>

Enclosing class:

CoordinateSortedPairInfoMap<KEY,REC>

public static interface CoordinateSortedPairInfoMap.Codec<KEY,REC>

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

Method Summary

Modifier and Type	Method and Description
java.util.Map.Entry<KEY,REC>	decode() Read the next key and record from the input stream and convert into a java object.
void	encode(KEY key, REC record) 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(KEY key,
            REC record)

Write object to output stream. If the key is part of the record, then there is no need to write it separately.

decode

java.util.Map.Entry<KEY,REC> decode()

Read the next key and 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.