BinaryFeatureCodec (htsjdk 2.14.3 API)

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
Constructor Description

BinaryFeatureCodec()

Constructors
Constructor	Description
`BinaryFeatureCodec()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close(PositionalBufferedStream source)`	Adapter method that closes the provided `FeatureCodec`.
`TabixFormat`	`getTabixFormat()`	Marked as final because binary features could not be tabix indexed
`boolean`	`isDone(PositionalBufferedStream source)`	Adapter method that assesses whether the provided `FeatureCodec` has more data.
`LocationAware`	`makeIndexableSourceFromStream(InputStream bufferedInputStream)`	`PositionalBufferedStream` is already `LocationAware`.
`PositionalBufferedStream`	`makeSourceFromStream(InputStream bufferedInputStream)`	Generates a reader of type `FeatureCodec` appropriate for use by this codec from the generic input stream.

Methods inherited from interface htsjdk.tribble.FeatureCodec
canDecode, decode, decodeLoc, getFeatureType, readHeader

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BinaryFeatureCodec
```
public BinaryFeatureCodec()
```
- Method Detail
  - makeSourceFromStream
```
public PositionalBufferedStream makeSourceFromStream(InputStream bufferedInputStream)
```
    Description copied from interface: FeatureCodec
    
    Generates a reader of type FeatureCodec appropriate for use by this codec from the generic input stream. Implementers should assume the stream is buffered.
    
    Specified by:
    
    makeSourceFromStream in interface FeatureCodec<T extends Feature,PositionalBufferedStream>
  - makeIndexableSourceFromStream
```
public LocationAware makeIndexableSourceFromStream(InputStream bufferedInputStream)
```
    PositionalBufferedStream is already LocationAware.
    
    Specified by:
    
    makeIndexableSourceFromStream in interface FeatureCodec<T extends Feature,PositionalBufferedStream>
  - close
```
public void close(PositionalBufferedStream source)
```
    Description copied from interface: FeatureCodec
    
    Adapter method that closes the provided FeatureCodec.
    
    Specified by:
    
    close in interface FeatureCodec<T extends Feature,PositionalBufferedStream>
  - isDone
```
public boolean isDone(PositionalBufferedStream source)
```
    Description copied from interface: FeatureCodec
    
    Adapter method that assesses whether the provided FeatureCodec has more data. True if it does, false otherwise.
    
    Specified by:
    
    isDone in interface FeatureCodec<T extends Feature,PositionalBufferedStream>
  - getTabixFormat
```
public final TabixFormat getTabixFormat()
```
    Marked as final because binary features could not be tabix indexed
    
    Specified by:
    
    getTabixFormat in interface FeatureCodec<T extends Feature,PositionalBufferedStream>
    
    Returns:
    
    the format to use with tabix

Class BinaryFeatureCodec<T extends Feature>

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.tribble.FeatureCodec

Methods inherited from class java.lang.Object

Constructor Detail

BinaryFeatureCodec

Method Detail

makeSourceFromStream

makeIndexableSourceFromStream

close

isDone

getTabixFormat