htsjdk.tribble

Class AsciiFeatureCodec<T extends Feature>

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>

htsjdk.tribble.AsciiFeatureCodec<T>

Type Parameters:

T - The feature type this codec reads

All Implemented Interfaces:

FeatureCodec<T,LineIterator>

Direct Known Subclasses:

AbstractVCFCodec, BEDCodec, IntervalListCodec

public abstract class AsciiFeatureCodec<T extends Feature>
extends AbstractFeatureCodec<T,LineIterator>

A convenience base class for codecs that want to read in features from ASCII lines.

This class overrides the general decode locs for streams and presents instead Strings to decode(String) and readHeader(LineReader) functions.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AsciiFeatureCodec(java.lang.Class<T> myClass)

Method Summary

Modifier and Type	Method and Description
void	close(LineIterator lineIterator) Adapter method that closes the provided SOURCE.
T	decode(LineIterator lineIterator) Convenience method.
abstract T	decode(java.lang.String s)
boolean	isDone(LineIterator lineIterator) Adapter method that assesses whether the provided SOURCE has more data.
LocationAware	makeIndexableSourceFromStream(java.io.InputStream inputStream) Return a SOURCE for this FeatureCodec that implements LocationAware, and is thus suitable for use during indexing.
LineIterator	makeSourceFromStream(java.io.InputStream bufferedInputStream) Generates a reader of type SOURCE appropriate for use by this codec from the generic input stream.
abstract java.lang.Object	readActualHeader(LineIterator reader) Read and return the header, or null if there is no header.
FeatureCodecHeader	readHeader(LineIterator lineIterator) Read and return the header, or null if there is no header.

Methods inherited from class htsjdk.tribble.AbstractFeatureCodec

decodeLoc, getFeatureType

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, getPathToDataFile, getTabixFormat

Constructor Detail

AsciiFeatureCodec

protected AsciiFeatureCodec(java.lang.Class<T> myClass)

Method Detail

close

public void close(LineIterator lineIterator)

Description copied from interface: FeatureCodec

Adapter method that closes the provided SOURCE.

isDone

public boolean isDone(LineIterator lineIterator)

Description copied from interface: FeatureCodec

Adapter method that assesses whether the provided SOURCE has more data. True if it does, false otherwise.

makeIndexableSourceFromStream

public LocationAware makeIndexableSourceFromStream(java.io.InputStream inputStream)

Description copied from interface: FeatureCodec

Return a SOURCE for this FeatureCodec that implements LocationAware, and is thus suitable for use during indexing. Like FeatureCodec.makeSourceFromStream(java.io.InputStream), except the LocationAware compatibility is required for creating indexes.

Implementers of this method must return a type that is both LocationAware as well as SOURCE. Note that this requirement cannot be enforced via the method signature due to limitations in Java's generic typing system. Instead, consumers should cast the call result into a SOURCE when applicable.

NOTE: During the indexing process, the indexer passes the SOURCE to the codec to consume Features from the underlying SOURCE, one at a time, recording the Feature location via the SOURCE's LocationAware interface. Therefore, it is essential that the SOURCE implementation, the FeatureCodec.readHeader(SOURCE) method, and the FeatureCodec.decodeLoc(SOURCE) method, which are used during indexing, not introduce any buffering that would that would advance the SOURCE more than a single feature (or the more than the size of the header, in the case of FeatureCodec.readHeader(SOURCE)).

makeSourceFromStream

public LineIterator makeSourceFromStream(java.io.InputStream bufferedInputStream)

Description copied from interface: FeatureCodec

Generates a reader of type SOURCE appropriate for use by this codec from the generic input stream. Implementers should assume the stream is buffered.

decode

public T decode(LineIterator lineIterator)

Convenience method. Decoding in ASCII files operates line-by-line, so obviate the need to call Iterator.next() in implementing classes and, instead, have them implement decode(String).

Parameters:

lineIterator - the input stream from which to decode the next record

Returns:

Return the Feature encoded by the line, or null if the line does not represent a feature (e.g. is a comment)

decode

public abstract T decode(java.lang.String s)

See Also:

decode(htsjdk.tribble.readers.LineIterator)

readHeader

public FeatureCodecHeader readHeader(LineIterator lineIterator)
                              throws java.io.IOException

Description copied from interface: FeatureCodec

Read and return the header, or null if there is no header. Note: Implementers of this method must be careful to read exactly as much from SOURCE as needed to parse the header, and no more. Otherwise, data that might otherwise be fed into parsing a Feature may be lost.

Parameters:

lineIterator - the source from which to decode the header

Returns:

header object

Throws:

java.io.IOException

readActualHeader

public abstract java.lang.Object readActualHeader(LineIterator reader)

Read and return the header, or null if there is no header.

Returns:

the actual header data in the file, or null if none is available