nct.parsers
Class FastaProteinParser

java.lang.Object
  extended by nct.parsers.FastaProteinParser

public class FastaProteinParser
extends java.lang.Object

A simple class that provides a method to parse a multiple FASTA file.


Constructor Summary
FastaProteinParser()
           
 
Method Summary
static org.biojava.bio.seq.SequenceIterator parseFile(java.lang.String FASTAFileName)
          A simple method that parses a multiple FASTA file and returns a BioJava SequenceIterator.
static org.biojava.bio.seq.SequenceIterator parseString(java.lang.String sequenceString)
          A simple method that parses a multiple FASTA file and returns a BioJava SequenceIterator.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FastaProteinParser

public FastaProteinParser()
Method Detail

parseFile

public static org.biojava.bio.seq.SequenceIterator parseFile(java.lang.String FASTAFileName)
                                                      throws org.biojava.bio.BioException,
                                                             java.util.NoSuchElementException,
                                                             java.io.FileNotFoundException
A simple method that parses a multiple FASTA file and returns a BioJava SequenceIterator.

Parameters:
FASTAFileName - The name of the multiple Fasta file to parse.
Returns:
A BioJava SequenceIterator.
Throws:
org.biojava.bio.BioException
java.util.NoSuchElementException
java.io.FileNotFoundException

parseString

public static org.biojava.bio.seq.SequenceIterator parseString(java.lang.String sequenceString)
                                                        throws org.biojava.bio.BioException,
                                                               java.util.NoSuchElementException,
                                                               java.io.FileNotFoundException
A simple method that parses a multiple FASTA file and returns a BioJava SequenceIterator.

Parameters:
sequenceString - A string containing fasta sequence data.
Returns:
A BioJava SequenceIterator.
Throws:
org.biojava.bio.BioException
java.util.NoSuchElementException
java.io.FileNotFoundException