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

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

Simple basic class providing much of the basic functionality of codecs

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractFeatureCodec(java.lang.Class<FEATURE_TYPE> myClass)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canDecode(java.lang.String path) This function returns true iff the File potentialInput can be parsed by this codec.
Feature	decodeLoc(SOURCE source) Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
java.lang.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

close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader

Constructor Detail

AbstractFeatureCodec

protected AbstractFeatureCodec(java.lang.Class<FEATURE_TYPE> myClass)

Method Detail

decodeLoc

public Feature decodeLoc(SOURCE source)
                  throws java.io.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:

java.io.IOException

getFeatureType

public java.lang.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.

canDecode

public boolean canDecode(java.lang.String path)

Description copied from interface: FeatureCodec

This function returns true iff the File potentialInput can be parsed by this codec.

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.

Specified by:

canDecode in interface FeatureCodec<FEATURE_TYPE extends Feature,SOURCE>

Parameters:

path - the file to test for parsability with this codec

Returns:

true if potentialInput can be parsed, false otherwise