Package 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 Object
implements FeatureCodec<T,PositionalBufferedStream>
Implements common methods of
FeatureCodec
s that read from PositionalBufferedStream
s.-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
close
(PositionalBufferedStream source) Adapter method that closes the providedFeatureCodec
.final TabixFormat
Marked as final because binary features could not be tabix indexedboolean
isDone
(PositionalBufferedStream source) Adapter method that assesses whether the providedFeatureCodec
has more data.makeIndexableSourceFromStream
(InputStream bufferedInputStream) PositionalBufferedStream
is alreadyLocationAware
.makeSourceFromStream
(InputStream bufferedInputStream) Generates a reader of typeFeatureCodec
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, getPathToDataFile, readHeader
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Constructor Details
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BinaryFeatureCodec
public BinaryFeatureCodec()
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Method Details
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makeSourceFromStream
Description copied from interface:FeatureCodec
Generates a reader of typeFeatureCodec
appropriate for use by this codec from the generic input stream. Implementers should assume the stream is buffered.- Specified by:
makeSourceFromStream
in interfaceFeatureCodec<T extends Feature,
PositionalBufferedStream>
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makeIndexableSourceFromStream
PositionalBufferedStream
is alreadyLocationAware
.- Specified by:
makeIndexableSourceFromStream
in interfaceFeatureCodec<T extends Feature,
PositionalBufferedStream>
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close
Description copied from interface:FeatureCodec
Adapter method that closes the providedFeatureCodec
.- Specified by:
close
in interfaceFeatureCodec<T extends Feature,
PositionalBufferedStream>
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isDone
Description copied from interface:FeatureCodec
Adapter method that assesses whether the providedFeatureCodec
has more data. True if it does, false otherwise.- Specified by:
isDone
in interfaceFeatureCodec<T extends Feature,
PositionalBufferedStream>
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getTabixFormat
Marked as final because binary features could not be tabix indexed- Specified by:
getTabixFormat
in interfaceFeatureCodec<T extends Feature,
PositionalBufferedStream> - Returns:
- the format to use with tabix
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