htsjdk.tribble

Class BinaryFeatureCodec<T extends Feature>

java.lang.Object

htsjdk.tribble.BinaryFeatureCodec<T>

All Implemented Interfaces:

FeatureCodec<T,PositionalBufferedStream>

Direct Known Subclasses:

BCF2Codec, ExampleBinaryCodec

public abstract class BinaryFeatureCodec<T extends Feature>
extends java.lang.Object
implements FeatureCodec<T,PositionalBufferedStream>

Implements common methods of FeatureCodecs that read from PositionalBufferedStreams.

Constructor Summary

Constructors

Constructor and Description
BinaryFeatureCodec()

Method Summary

Modifier and Type	Method and Description
void	close(PositionalBufferedStream source) Adapter method that closes the provided SOURCE.
TabixFormat	getTabixFormat() Marked as final because binary features could not be tabix indexed
boolean	isDone(PositionalBufferedStream source) Adapter method that assesses whether the provided SOURCE has more data.
LocationAware	makeIndexableSourceFromStream(java.io.InputStream bufferedInputStream) PositionalBufferedStream is already LocationAware.
PositionalBufferedStream	makeSourceFromStream(java.io.InputStream bufferedInputStream) Generates a reader of type SOURCE appropriate for use by this codec from the generic input stream.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.FeatureCodec

canDecode, decode, decodeLoc, getFeatureType, readHeader

Constructor Detail

BinaryFeatureCodec

public BinaryFeatureCodec()

Method Detail

makeSourceFromStream

public PositionalBufferedStream makeSourceFromStream(java.io.InputStream bufferedInputStream)

Description copied from interface: FeatureCodec

Generates a reader of type SOURCE appropriate for use by this codec from the generic input stream. Implementers should assume the stream is buffered.

Specified by:

makeSourceFromStream in interface FeatureCodec<T extends Feature,PositionalBufferedStream>

makeIndexableSourceFromStream

public LocationAware makeIndexableSourceFromStream(java.io.InputStream bufferedInputStream)

PositionalBufferedStream is already LocationAware.

Specified by:

makeIndexableSourceFromStream in interface FeatureCodec<T extends Feature,PositionalBufferedStream>

close

public void close(PositionalBufferedStream source)

Description copied from interface: FeatureCodec

Adapter method that closes the provided SOURCE.

Specified by:

close in interface FeatureCodec<T extends Feature,PositionalBufferedStream>

isDone

public boolean isDone(PositionalBufferedStream source)

Description copied from interface: FeatureCodec

Adapter method that assesses whether the provided SOURCE has more data. True if it does, false otherwise.

Specified by:

isDone in interface FeatureCodec<T extends Feature,PositionalBufferedStream>

getTabixFormat

public final TabixFormat getTabixFormat()

Marked as final because binary features could not be tabix indexed

Specified by:

getTabixFormat in interface FeatureCodec<T extends Feature,PositionalBufferedStream>

Returns:

the format to use with tabix