Package 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 Details

    • AsciiFeatureCodec

      protected AsciiFeatureCodec(Class<T> myClass)

  • Method Details

    • close

      public void close(LineIterator lineIterator)
      Description copied from interface: FeatureCodec
      Adapter method that closes the provided FeatureCodec.

    • isDone

      public boolean isDone(LineIterator lineIterator)
      Description copied from interface: FeatureCodec
      Adapter method that assesses whether the provided FeatureCodec has more data. True if it does, false otherwise.

    • makeIndexableSourceFromStream

      public LocationAware makeIndexableSourceFromStream(InputStream inputStream)
      Description copied from interface: FeatureCodec
      Return a FeatureCodec 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 FeatureCodec. 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 FeatureCodec when applicable.

      NOTE: During the indexing process, the indexer passes the FeatureCodec to the codec to consume Features from the underlying FeatureCodec, one at a time, recording the Feature location via the FeatureCodec's LocationAware interface. Therefore, it is essential that the FeatureCodec 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 FeatureCodec 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(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.

    • 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(String s)
      See Also:

    • readHeader

      public FeatureCodecHeader readHeader(LineIterator lineIterator) throws 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 FeatureCodec 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:
      IOException

    • readActualHeader

      public abstract 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