org.biojavax.bio.seq.io
Class HashedFastaIterator

java.lang.Object
  extended by 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
HashedFastaIterator(java.io.BufferedInputStream is, Alphabet alpha, Namespace ns)
           
 
Method Summary
 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