public class StreamReader extends Object implements SequenceIterator, ParseErrorListenerParses 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.
- Matthew Pocock, Thomas Down
- See Also:
All Methods Instance Methods Concrete Methods Modifier and Type Method Description
BadLineParsed(ParseErrorEvent theEvent)This method determines the behaviour when a bad line is processed.
hasNext()Returns whether there are more sequences to iterate over.
nextSequence()Pull the next sequence out of the stream.
public Sequence nextSequence() throws NoSuchElementException, BioExceptionPull 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.
public boolean hasNext()Description copied from interface:
SequenceIteratorReturns whether there are more sequences to iterate over.
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.