Class FastaWriterHelper
- java.lang.Object
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- org.biojava.nbio.core.sequence.io.FastaWriterHelper
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public class FastaWriterHelper extends Object
The class that should be used to write out fasta file of a sequence collection- Author:
- Scooter Willis
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Constructor Summary
Constructors Constructor Description FastaWriterHelper()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
writeGeneSequence(File file, Collection<GeneSequence> geneSequences, boolean showExonUppercase)
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequencestatic void
writeGeneSequence(OutputStream outputStream, Collection<GeneSequence> geneSequences, boolean showExonUppercase)
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequencestatic void
writeNucleotideSequence(File file, Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a filestatic void
writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a filestatic void
writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a filestatic void
writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a streamstatic void
writeSequence(File file, Sequence<?> sequence)
Write a sequence to a filestatic void
writeSequence(OutputStream outputStream, Sequence<?> sequence)
Write a sequence to OutputStreamstatic void
writeSequences(OutputStream outputStream, Collection<Sequence<?>> sequences)
Method which will write your given Sequences to the specifiedOutputStream
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Constructor Detail
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FastaWriterHelper
public FastaWriterHelper()
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Method Detail
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writeProteinSequence
public static void writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) throws Exception
Write collection of protein sequences to a file- Parameters:
file
-proteinSequences
-- Throws:
Exception
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writeProteinSequence
public static void writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) throws Exception
Write collection of protein sequences to a stream- Parameters:
outputStream
-proteinSequences
-- Throws:
Exception
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writeGeneSequence
public static void writeGeneSequence(File file, Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws Exception
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence- Parameters:
file
-geneSequences
-- Throws:
Exception
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writeGeneSequence
public static void writeGeneSequence(OutputStream outputStream, Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws Exception
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence- Parameters:
outputStream
-dnaSequences
-- Throws:
Exception
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writeNucleotideSequence
public static void writeNucleotideSequence(File file, Collection<DNASequence> dnaSequences) throws Exception
Write a collection of NucleotideSequences to a file- Parameters:
file
-dnaSequences
-- Throws:
Exception
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writeNucleotideSequence
public static void writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences) throws Exception
Write a collection of NucleotideSequences to a file- Parameters:
outputStream
-dnaSequences
-- Throws:
Exception
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writeSequence
public static void writeSequence(File file, Sequence<?> sequence) throws Exception
Write a sequence to a file- Parameters:
file
-sequence
-- Throws:
Exception
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writeSequence
public static void writeSequence(OutputStream outputStream, Sequence<?> sequence) throws Exception
Write a sequence to OutputStream- Parameters:
outputStream
-sequence
-- Throws:
Exception
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writeSequences
public static void writeSequences(OutputStream outputStream, Collection<Sequence<?>> sequences) throws Exception
Method which will write your given Sequences to the specifiedOutputStream
. This is a very generic method which writes just the AccessionID of the Sequence as the FASTA header.- Parameters:
outputStream
- Stream to write to; can be System.outsequences
- The sequences to write out- Throws:
Exception
- Thrown normally thanks to IO problems
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