public class FastaWriterHelper
extends java.lang.Object
Constructor and Description |
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FastaWriterHelper() |
Modifier and Type | Method and Description |
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static void |
writeGeneSequence(java.io.File file,
java.util.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 sequence
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static void |
writeGeneSequence(java.io.OutputStream outputStream,
java.util.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 sequence
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static void |
writeNucleotideSequence(java.io.File file,
java.util.Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a file
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static void |
writeNucleotideSequence(java.io.OutputStream outputStream,
java.util.Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a file
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static void |
writeProteinSequence(java.io.File file,
java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a file
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static void |
writeProteinSequence(java.io.OutputStream outputStream,
java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a stream
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static void |
writeSequence(java.io.File file,
Sequence<?> sequence)
Write a sequence to a file
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static void |
writeSequence(java.io.OutputStream outputStream,
Sequence<?> sequence)
Write a sequence to OutputStream
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static void |
writeSequences(java.io.OutputStream outputStream,
java.util.Collection<Sequence<?>> sequences)
Method which will write your given Sequences to the specified
OutputStream . |
public static void writeProteinSequence(java.io.File file, java.util.Collection<ProteinSequence> proteinSequences) throws java.lang.Exception
file
- proteinSequences
- java.lang.Exception
public static void writeProteinSequence(java.io.OutputStream outputStream, java.util.Collection<ProteinSequence> proteinSequences) throws java.lang.Exception
outputStream
- proteinSequences
- java.lang.Exception
public static void writeGeneSequence(java.io.File file, java.util.Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws java.lang.Exception
file
- geneSequences
- java.lang.Exception
public static void writeGeneSequence(java.io.OutputStream outputStream, java.util.Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws java.lang.Exception
outputStream
- dnaSequences
- java.lang.Exception
public static void writeNucleotideSequence(java.io.File file, java.util.Collection<DNASequence> dnaSequences) throws java.lang.Exception
file
- dnaSequences
- java.lang.Exception
public static void writeNucleotideSequence(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences) throws java.lang.Exception
outputStream
- dnaSequences
- java.lang.Exception
public static void writeSequence(java.io.File file, Sequence<?> sequence) throws java.lang.Exception
file
- sequence
- java.lang.Exception
public static void writeSequence(java.io.OutputStream outputStream, Sequence<?> sequence) throws java.lang.Exception
outputStream
- sequence
- java.lang.Exception
public static void writeSequences(java.io.OutputStream outputStream, java.util.Collection<Sequence<?>> sequences) throws java.lang.Exception
OutputStream
. This is a very generic method which writes just the
AccessionID of the Sequence as the FASTA header.outputStream
- Stream to write to; can be System.outsequences
- The sequences to write outjava.lang.Exception
- Thrown normally thanks to IO problems