Package htsjdk.tribble
Class BinaryFeatureCodec<T extends Feature>
- java.lang.Object
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- htsjdk.tribble.BinaryFeatureCodec<T>
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- 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 ofFeatureCodec
s that read fromPositionalBufferedStream
s.
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Constructor Summary
Constructors Constructor Description BinaryFeatureCodec()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close(PositionalBufferedStream source)
Adapter method that closes the providedFeatureCodec
.TabixFormat
getTabixFormat()
Marked as final because binary features could not be tabix indexedboolean
isDone(PositionalBufferedStream source)
Adapter method that assesses whether the providedFeatureCodec
has more data.LocationAware
makeIndexableSourceFromStream(InputStream bufferedInputStream)
PositionalBufferedStream
is alreadyLocationAware
.PositionalBufferedStream
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
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Methods inherited from interface htsjdk.tribble.FeatureCodec
canDecode, decode, decodeLoc, getFeatureType, getPathToDataFile, readHeader
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Method Detail
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makeSourceFromStream
public PositionalBufferedStream makeSourceFromStream(InputStream bufferedInputStream)
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
public LocationAware makeIndexableSourceFromStream(InputStream bufferedInputStream)
PositionalBufferedStream
is alreadyLocationAware
.- Specified by:
makeIndexableSourceFromStream
in interfaceFeatureCodec<T extends Feature,PositionalBufferedStream>
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close
public void close(PositionalBufferedStream source)
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
public boolean isDone(PositionalBufferedStream source)
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
public final TabixFormat 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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