Class FastaGeneWriter
java.lang.Object
org.biojava.nbio.core.sequence.io.FastaGeneWriter
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
ConstructorsConstructorDescriptionFastaGeneWriter(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
Modifier and TypeMethodDescriptionintstatic voidvoidprocess()voidsetLineLength(int lineLength)
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Constructor Details
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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 Details
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process
- Throws:
Exception
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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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main
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