calhoun.seq
Class FastaIterator.ReaderSequence

java.lang.Object
  calhoun.seq.SimpleFastaSequence
      calhoun.seq.FastaIterator.ReaderSequence

All Implemented Interfaces:

FastaSequence, java.io.Serializable

Enclosing class:

FastaIterator

public static class FastaIterator.ReaderSequence
extends SimpleFastaSequence

A minimal sequence class that slurps its sequence in immediately.

See Also:

Serialized Form

Constructor Summary

FastaIterator.ReaderSequence(java.io.File file, java.lang.String header)

Method Summary

java.io.File	getFile()
java.lang.String	loadSequence(java.io.BufferedReader reader)

Methods inherited from class calhoun.seq.SimpleFastaSequence

getHeader, getLength, getQuality, getSequence, getSequence, hasQuality, hasSequence, setHeader, setQuality, setSequence

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaIterator.ReaderSequence

public FastaIterator.ReaderSequence(java.io.File file,
                                    java.lang.String header)

Method Detail

getFile

public java.io.File getFile()

loadSequence

public java.lang.String loadSequence(java.io.BufferedReader reader)
                              throws java.io.IOException

Throws:

java.io.IOException