org.biojava3.core.sequence.io
Class FastaGeneWriter
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
-
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)