Package htsjdk.tribble.example

Class ExampleBinaryCodec

java.lang.Object

htsjdk.tribble.BinaryFeatureCodec<Feature>

htsjdk.tribble.example.ExampleBinaryCodec

All Implemented Interfaces:

FeatureCodec<Feature,PositionalBufferedStream>

public class ExampleBinaryCodec
extends BinaryFeatureCodec<Feature>

An example binary codec that encodes / decodes contig / start / stop values via DataInputStreams

Field Summary

Fields

Modifier and Type	Field	Description
static final String	HEADER_LINE

Constructor Summary

Constructors

Constructor	Description
ExampleBinaryCodec()

Method Summary

Modifier and Type	Method	Description
boolean	canDecode(String path)	This function returns true iff the File potentialInput can be parsed by this codec.
static <FEATURE_TYPE extends Feature> void	convertToBinaryTest(FeatureReader<FEATURE_TYPE> reader, OutputStream out)	Convenience method that creates an ExampleBinaryCodec file from another feature file.
static <FEATURE_TYPE extends Feature> void	convertToBinaryTest(File source, File dest, FeatureCodec<FEATURE_TYPE,LineIterator> codec)	Convenience method that creates an ExampleBinaryCodec file from another feature file.
Feature	decode(PositionalBufferedStream stream)	Decode a single Feature from the FeatureCodec, reading no further in the underlying source than beyond that feature.
Feature	decodeLoc(PositionalBufferedStream stream)	Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
Class<Feature>	getFeatureType()	This function returns the object the codec generates.
FeatureCodecHeader	readHeader(PositionalBufferedStream stream)	Read and return the header, or null if there is no header.

Methods inherited from class htsjdk.tribble.BinaryFeatureCodec

close, getTabixFormat, isDone, makeIndexableSourceFromStream, makeSourceFromStream

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

getPathToDataFile

Field Details

HEADER_LINE

public static final String HEADER_LINE

See Also:

• Constant Field Values

Constructor Details

ExampleBinaryCodec

public ExampleBinaryCodec()

Method Details

decodeLoc

public Feature decodeLoc(PositionalBufferedStream stream)
                  throws IOException

Description copied from interface: FeatureCodec

Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.

Parameters:

stream - the input stream from which to decode the next record

Returns:

Return the FeatureLoc encoded by the line, or null if the line does not represent a feature (e.g. is a comment)

Throws:

IOException

decode

public Feature decode(PositionalBufferedStream stream)
               throws IOException

Description copied from interface: FeatureCodec

Decode a single Feature from the FeatureCodec, reading no further in the underlying source than beyond that feature.

Parameters:

stream - the input stream from which to decode the next record

Returns:

Return the Feature encoded by the line, or null if the line does not represent a feature (e.g. is a comment)

Throws:

IOException

readHeader

public FeatureCodecHeader readHeader(PositionalBufferedStream stream)
                              throws IOException

Description copied from interface: FeatureCodec

Read and return the header, or null if there is no header. Note: Implementers of this method must be careful to read exactly as much from FeatureCodec as needed to parse the header, and no more. Otherwise, data that might otherwise be fed into parsing a Feature may be lost.

Parameters:

stream - the source from which to decode the header

Returns:

header object

Throws:

IOException

getFeatureType

public Class<Feature> getFeatureType()

Description copied from interface: FeatureCodec

This function returns the object the codec generates. This is allowed to be Feature in the case where conditionally different types are generated. Be as specific as you can though.

This function is used by reflections based tools, so we can know the underlying type

Returns:

the feature type this codec generates.

canDecode

public boolean canDecode(String path)

Description copied from interface: FeatureCodec

This function returns true iff the File potentialInput can be parsed by this codec. Note that checking the file's extension is a perfectly acceptable implementation of this method and file contents only rarely need to be checked.

There is an assumption that there's never a situation where two different Codecs return true for the same file. If this occurs, the recommendation would be to error out.

Note this function must never throw an error. All errors should be trapped and false returned.

Parameters:

path - the file to test for parsability with this codec

Returns:

true if potentialInput can be parsed, false otherwise

convertToBinaryTest

public static <FEATURE_TYPE extends Feature> void convertToBinaryTest(File source,
 File dest,
 FeatureCodec<FEATURE_TYPE,LineIterator> codec)
                                                               throws IOException

Convenience method that creates an ExampleBinaryCodec file from another feature file. For testing purposes really

Parameters:

source - file containing the features

dest - the place to write the binary features

codec - of the source file features

Throws:

IOException

convertToBinaryTest

public static <FEATURE_TYPE extends Feature> void convertToBinaryTest(FeatureReader<FEATURE_TYPE> reader,
 OutputStream out)
                                                               throws IOException

Convenience method that creates an ExampleBinaryCodec file from another feature file. For testing purposes really

Throws:

IOException