calhoun.seq
Class QualityIterator

java.lang.Object
  calhoun.seq.QualityIterator

All Implemented Interfaces:

java.util.Iterator

public class QualityIterator
extends java.lang.Object
implements java.util.Iterator

Constructor Summary

QualityIterator(java.io.BufferedReader reader)

QualityIterator(java.io.File file, boolean isGzipped)

QualityIterator(java.lang.String fileName)

QualityIterator(java.lang.String fileName, boolean isGzipped)

Method Summary

void	addNextQuality(SimpleFastaSequence input) Adds the next sequence of qualities in the file to the given FastaSequence.
boolean	hasNext()
java.lang.Object	next() Returns the next set of qualities in this file.
FastaSequence	nextQuality() Returns the next set of qualities in this file.
void	remove()

Methods inherited from class java.lang.Object

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

Constructor Detail

QualityIterator

public QualityIterator(java.lang.String fileName,
                       boolean isGzipped)
                throws java.io.IOException

Throws:

java.io.IOException

QualityIterator

public QualityIterator(java.lang.String fileName)
                throws java.io.IOException

Throws:

java.io.IOException

QualityIterator

public QualityIterator(java.io.BufferedReader reader)

QualityIterator

public QualityIterator(java.io.File file,
                       boolean isGzipped)
                throws java.io.IOException

Throws:

java.io.IOException

Method Detail

next

public java.lang.Object next()

Returns the next set of qualities in this file.

Specified by:

next in interface java.util.Iterator

nextQuality

public FastaSequence nextQuality()

Returns the next set of qualities in this file. Provides a detailed return type.

addNextQuality

public void addNextQuality(SimpleFastaSequence input)

Adds the next sequence of qualities in the file to the given FastaSequence. If the FastaSequence already has a sequence set, verifies that the quality matches the sequence (header and length).

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator

remove

public void remove()

Specified by:

remove in interface java.util.Iterator