Class StreamReader

  • All Implemented Interfaces:
    java.util.EventListener, SequenceIterator, ParseErrorListener

    public class StreamReader
    extends java.lang.Object
    implements SequenceIterator, ParseErrorListener
    Parses a stream into sequences.

    This object implements SequenceIterator, so you can loop over each sequence produced. It consumes a stream, and uses a SequenceFormat to extract each sequence from the stream.

    It is assumed that the stream contains sequences that can be handled by the one format, and that they are not seperated other than by delimiters that the format can handle.

    Sequences are instantiated when they are requested by nextSequence, not before, so it is safe to use this object to parse a gigabyte fasta file, and do sequence-by-sequence processing, while being guaranteed that StreamReader will not require you to keep any of the sequences in memory.

    More functionality is offered by RichStreamReader, Use of this interface is prefered.

    Author:
    Matthew Pocock, Thomas Down
    See Also:
    RichStreamReader
    • Method Detail

      • nextSequence

        public Sequence nextSequence()
                              throws java.util.NoSuchElementException,
                                     BioException
        Pull the next sequence out of the stream.

        This method will delegate parsing from the stream to a SequenceFormat object, and then return the resulting sequence.

        Specified by:
        nextSequence in interface SequenceIterator
        Returns:
        the next Sequence
        Throws:
        java.util.NoSuchElementException - if the end of the stream has been hit
        BioException - if for any reason the next sequence could not be read
      • hasNext

        public boolean hasNext()
        Description copied from interface: SequenceIterator
        Returns whether there are more sequences to iterate over.
        Specified by:
        hasNext in interface SequenceIterator
        Returns:
        true if there are more sequences to get and false otherwise
      • BadLineParsed

        public void BadLineParsed​(ParseErrorEvent theEvent)
        This method determines the behaviour when a bad line is processed. Some options are to log the error, throw an exception, ignore it completely, or pass the event through.

        This method should be overwritten when different behavior is desired.

        Specified by:
        BadLineParsed in interface ParseErrorListener
        Parameters:
        theEvent - The event that contains the bad line and token.