org.biojavax.bio.seq.io

Class HashedFastaIterator

java.lang.Object

org.biojavax.bio.seq.io.HashedFastaIterator

All Implemented Interfaces:

SequenceIterator, BioEntryIterator, RichSequenceIterator

public class HashedFastaIterator
extends java.lang.Object
implements RichSequenceIterator

Iterates over a Fasta file that is kept in memory for optimized access.

Since:

1.7

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
HashedFastaIterator(java.io.BufferedInputStream is, Alphabet alpha, Namespace ns)

Method Summary

Methods

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

HashedFastaIterator

public HashedFastaIterator(java.io.BufferedInputStream is,
                   Alphabet alpha,
                   Namespace ns)
                    throws BioException

Throws:

BioException

Method Detail

nextRichSequence

public RichSequence nextRichSequence()
                              throws java.util.NoSuchElementException,
                                     BioException

Specified by:

nextRichSequence in interface RichSequenceIterator

Throws:

java.util.NoSuchElementException

BioException

hasNext

public boolean hasNext()

Description copied from interface: BioEntryIterator

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

nextBioEntry

public BioEntry nextBioEntry()
                      throws java.util.NoSuchElementException,
                             BioException

Specified by:

nextBioEntry in interface BioEntryIterator

Throws:

java.util.NoSuchElementException

BioException

nextSequence

public Sequence nextSequence()
                      throws java.util.NoSuchElementException,
                             BioException

Description copied from interface: SequenceIterator

Returns the next sequence in the iterator.

Specified by:

nextSequence in interface SequenceIterator

Returns:

the next Sequence

Throws:

java.util.NoSuchElementException - if you call nextSequence when hasNext returns false

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