Package org.biojava.nbio.core.sequence.io

Class FastaGeneWriter

java.lang.Object

org.biojava.nbio.core.sequence.io.FastaGeneWriter

public class FastaGeneWriter
extends java.lang.Object

A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version. It is also an option to write out the gene sequence where the exon regions are upper case 6/22/2010 FastaWriter needs to be sequence aware to handle writing out a GeneSequence which is negative Strand with the proper sequence

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
FastaGeneWriter(java.io.OutputStream os, java.util.Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)
FastaGeneWriter(java.io.OutputStream os, java.util.Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength)

Method Summary

Modifier and Type	Method	Description
int	getLineLength()
static void	main(java.lang.String[] args)
void	process()
void	setLineLength(int lineLength)

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaGeneWriter

public FastaGeneWriter(java.io.OutputStream os,
                       java.util.Collection<GeneSequence> sequences,
                       FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat,
                       boolean showExonUppercase)

Parameters:

os -

sequences -

headerFormat -

showExonUppercase -

FastaGeneWriter

public FastaGeneWriter(java.io.OutputStream os,
                       java.util.Collection<GeneSequence> sequences,
                       FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat,
                       boolean showExonUppercase,
                       int lineLength)

Parameters:

os -

sequences -

headerFormat -

showExonUppercase -

lineLength -

Method Detail

process

public void process()
             throws java.lang.Exception

Throws:

java.lang.Exception

getLineLength

public int getLineLength()

Returns:

the lineLength

setLineLength

public void setLineLength(int lineLength)

Parameters:

lineLength - the lineLength to set

main

public static void main(java.lang.String[] args)