org.biojava3.core.sequence.io
Class FastaGeneWriter

java.lang.Object
  extended by org.biojava3.core.sequence.io.FastaGeneWriter

public class FastaGeneWriter
extends 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
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)
           
FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength)
           
 
Method Summary
 int getLineLength()
           
static void main(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(OutputStream os,
                       Collection<GeneSequence> sequences,
                       FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat,
                       boolean showExonUppercase)
Parameters:
os -
sequences -
headerFormat -
showExonUppercase -

FastaGeneWriter

public FastaGeneWriter(OutputStream os,
                       Collection<GeneSequence> sequences,
                       FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat,
                       boolean showExonUppercase,
                       int lineLength)
Parameters:
os -
sequences -
headerFormat -
showExonUppercase -
lineLength -
Method Detail

process

public void process()
             throws Exception
Throws:
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(String[] args)