Class FastaGeneWriter
- java.lang.Object
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- org.biojava.nbio.core.sequence.io.FastaGeneWriter
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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
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Constructor Summary
Constructors Constructor Description 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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getLineLength()
void
process()
void
setLineLength(int lineLength)
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Constructor Detail
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FastaGeneWriter
public FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)
- Parameters:
os
-sequences
-headerFormat
-showExonUppercase
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FastaGeneWriter
public FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength)
- Parameters:
os
-sequences
-headerFormat
-showExonUppercase
-lineLength
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Method Detail
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getLineLength
public int getLineLength()
- Returns:
- the lineLength
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setLineLength
public void setLineLength(int lineLength)
- Parameters:
lineLength
- the lineLength to set
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