Package htsjdk.tribble

Class AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE>

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<FEATURE_TYPE,SOURCE>

All Implemented Interfaces:

FeatureCodec<FEATURE_TYPE,SOURCE>

Direct Known Subclasses:

AsciiFeatureCodec, Gff3Codec

public abstract class AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE>
extends Object
implements FeatureCodec<FEATURE_TYPE,SOURCE>

Simple basic class providing much of the basic functionality of codecs Every concrete subclass must implement FeatureCodec.canDecode(String) to indicate whether it can decode the file. Note that that method is the only way that the right codec for a file is identified and that only one codec is allowed to identify itself as being able to decode any given file.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractFeatureCodec(Class<FEATURE_TYPE> myClass)

Method Summary

Modifier and Type	Method	Description
Feature	decodeLoc(SOURCE source)	Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
Class<FEATURE_TYPE>	getFeatureType()	This function returns the object the codec generates.

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, close, decode, getPathToDataFile, getTabixFormat, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader

Constructor Details

AbstractFeatureCodec

protected AbstractFeatureCodec(Class<FEATURE_TYPE> myClass)

Method Details

decodeLoc

public Feature decodeLoc(SOURCE source)
                  throws IOException

Description copied from interface: FeatureCodec

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

Specified by:

decodeLoc in interface FeatureCodec<FEATURE_TYPE extends Feature,SOURCE>

Parameters:

source - 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

getFeatureType

public Class<FEATURE_TYPE> 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

Specified by:

getFeatureType in interface FeatureCodec<FEATURE_TYPE extends Feature,SOURCE>

Returns:

the feature type this codec generates.