org.biojavax.bio.seq.io

Class RichStreamReader

java.lang.Object

org.biojavax.bio.seq.io.RichStreamReader

All Implemented Interfaces:

SequenceIterator, BioEntryIterator, RichSequenceIterator

public class RichStreamReader
extends Object
implements RichSequenceIterator

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 RichStreamReader will not require you to keep any of the sequences in memory.

Since:

1.5

Author:

Matthew Pocock, Thomas Down, Richard Holland

Constructor Summary

Constructors

Constructor and Description
RichStreamReader(BufferedReader reader, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns) Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.
RichStreamReader(InputStream is, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns) Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.

Method Summary

Modifier and Type	Method and Description
boolean	hasNext() Returns whether there are more sequences to iterate over.
BioEntry	nextBioEntry()
RichSequence	nextRichSequence()
Sequence	nextSequence() Returns the next sequence in the iterator.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RichStreamReader

public RichStreamReader(InputStream is,
                        RichSequenceFormat format,
                        SymbolTokenization symParser,
                        RichSequenceBuilderFactory sf,
                        Namespace ns)

Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.

Parameters:

is - the input stream to read from

format - the input file format

symParser - the tokenizer that understands the sequence symbols in the file

sf - the factory that will build the sequences

ns - the namespace the sequences will be loaded into.

RichStreamReader

public RichStreamReader(BufferedReader reader,
                        RichSequenceFormat format,
                        SymbolTokenization symParser,
                        RichSequenceBuilderFactory sf,
                        Namespace ns)

Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.

Parameters:

reader - the reader to read from

format - the input file format

symParser - the tokenizer that understands the sequence symbols in the file

sf - the factory that will build the sequences

ns - the namespace the sequences will be loaded into.

Method Detail

nextSequence

public Sequence nextSequence()
                      throws NoSuchElementException,
                             BioException

Returns the next sequence in the iterator.

Specified by:

nextSequence in interface SequenceIterator

Returns:

the next Sequence

Throws:

NoSuchElementException - if you call nextSequence when hasNext returns false

BioException - if for any reason the sequence could not be retrieved

nextBioEntry

public BioEntry nextBioEntry()
                      throws NoSuchElementException,
                             BioException

Specified by:

nextBioEntry in interface BioEntryIterator

Throws:

NoSuchElementException

BioException

nextRichSequence

public RichSequence nextRichSequence()
                              throws NoSuchElementException,
                                     BioException

Specified by:

nextRichSequence in interface RichSequenceIterator

Throws:

NoSuchElementException

BioException

hasNext

public boolean hasNext()

Returns whether there are more sequences to iterate over.

Specified by:

hasNext in interface SequenceIterator

Specified by:

hasNext in interface BioEntryIterator

Returns:

true if there are more sequences to get and false otherwise