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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
HashedFastaIterator
public HashedFastaIterator(java.io.BufferedInputStream is,
Alphabet alpha,
Namespace ns)
throws BioException
- Throws:
BioException
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