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
FeatureCodecs that read from PositionalBufferedStreams.-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidclose(PositionalBufferedStream source) Adapter method that closes the providedFeatureCodec.final TabixFormatMarked as final because binary features could not be tabix indexedbooleanisDone(PositionalBufferedStream source) Adapter method that assesses whether the providedFeatureCodechas more data.makeIndexableSourceFromStream(InputStream bufferedInputStream) PositionalBufferedStreamis alreadyLocationAware.makeSourceFromStream(InputStream bufferedInputStream) Generates a reader of typeFeatureCodecappropriate 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, waitMethods 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:FeatureCodecGenerates a reader of typeFeatureCodecappropriate for use by this codec from the generic input stream. Implementers should assume the stream is buffered.- Specified by:
makeSourceFromStreamin interfaceFeatureCodec<T extends Feature,PositionalBufferedStream>
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makeIndexableSourceFromStream
PositionalBufferedStreamis alreadyLocationAware.- Specified by:
makeIndexableSourceFromStreamin interfaceFeatureCodec<T extends Feature,PositionalBufferedStream>
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close
Description copied from interface:FeatureCodecAdapter method that closes the providedFeatureCodec.- Specified by:
closein interfaceFeatureCodec<T extends Feature,PositionalBufferedStream>
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isDone
Description copied from interface:FeatureCodecAdapter method that assesses whether the providedFeatureCodechas more data. True if it does, false otherwise.- Specified by:
isDonein interfaceFeatureCodec<T extends Feature,PositionalBufferedStream>
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getTabixFormat
Marked as final because binary features could not be tabix indexed- Specified by:
getTabixFormatin interfaceFeatureCodec<T extends Feature,PositionalBufferedStream> - Returns:
- the format to use with tabix
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