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java.lang.Objectorg.biojava3.core.sequence.io.FastaWriterHelper
public class FastaWriterHelper
The class that should be used to write out fasta file of a sequence collection
Constructor Summary | |
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FastaWriterHelper()
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Method Summary | |
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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 sequence |
static 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 sequence |
static void |
writeNucleotideSequence(File file,
Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a file |
static void |
writeNucleotideSequence(OutputStream outputStream,
Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a file |
static void |
writeProteinSequence(File file,
Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a file |
static void |
writeProteinSequence(OutputStream outputStream,
Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a stream |
static void |
writeSequence(File file,
Sequence<?> sequence)
Write a sequence to a file |
static void |
writeSequence(OutputStream outputStream,
Sequence<?> sequence)
Write a sequence to OutputStream |
static void |
writeSequences(OutputStream outputStream,
Collection<Sequence<?>> sequences)
Method which will write your given Sequences to the specified OutputStream . |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FastaWriterHelper()
Method Detail |
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public static void writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) throws Exception
file
- proteinSequences
-
Exception
public static void writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) throws Exception
outputStream
- proteinSequences
-
Exception
public static void writeGeneSequence(File file, Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws Exception
file
- geneSequences
-
Exception
public static void writeGeneSequence(OutputStream outputStream, Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws Exception
outputStream
- dnaSequences
-
Exception
public static void writeNucleotideSequence(File file, Collection<DNASequence> dnaSequences) throws Exception
file
- dnaSequences
-
Exception
public static void writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences) throws Exception
outputStream
- dnaSequences
-
Exception
public static void writeSequence(File file, Sequence<?> sequence) throws Exception
file
- sequence
-
Exception
public static void writeSequence(OutputStream outputStream, Sequence<?> sequence) throws Exception
outputStream
- sequence
-
Exception
public static void writeSequences(OutputStream outputStream, Collection<Sequence<?>> sequences) throws 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 out
Exception
- Thrown normally thanks to IO problems
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