calhoun.seq
Class FastaIterator

java.lang.Object
  calhoun.seq.FastaIterator

All Implemented Interfaces:

java.util.Iterator<FastaSequence>

public class FastaIterator
extends java.lang.Object
implements java.util.Iterator<FastaSequence>

This class implements iterator and allows a fasta file to be iterated through without having to read anything. Can also take a second file containing quality. You can now use new FastaReader().iterator() instead.

Nested Class Summary

static class

FastaIterator.ReaderSequence A minimal sequence class that slurps its sequence in immediately.

Field Summary

static java.lang.String

HEADER_START

Constructor Summary

FastaIterator(java.io.File file)

FastaIterator(java.io.File sequence, java.io.File quality)
Creates an iterator over a sequence file and also possibly a quality file

FastaIterator(java.lang.String file)

FastaIterator(java.lang.String sequence, java.lang.String quality)

Method Summary

boolean	hasNext()
FastaSequence	next()
void	remove() Throws an UnsupportedOperationException.

Methods inherited from class java.lang.Object

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

Field Detail

HEADER_START

public static final java.lang.String HEADER_START

See Also:

Constant Field Values

Constructor Detail

FastaIterator

public FastaIterator(java.lang.String file)
              throws java.io.IOException

Throws:

java.io.IOException

FastaIterator

public FastaIterator(java.io.File file)
              throws java.io.IOException

Throws:

java.io.IOException

FastaIterator

public FastaIterator(java.lang.String sequence,
                     java.lang.String quality)
              throws java.io.IOException

Throws:

java.io.IOException

FastaIterator

public FastaIterator(java.io.File sequence,
                     java.io.File quality)
              throws java.io.IOException

Creates an iterator over a sequence file and also possibly a quality file

Throws:

java.io.IOException

Method Detail

remove

public void remove()

Throws an UnsupportedOperationException.

Specified by:

remove in interface java.util.Iterator<FastaSequence>

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<FastaSequence>

next

public FastaSequence next()

Specified by:

next in interface java.util.Iterator<FastaSequence>