Package org.biojava.nbio.core.sequence.io

Class FastaWriterHelper

java.lang.Object

org.biojava.nbio.core.sequence.io.FastaWriterHelper

public class FastaWriterHelper
extends Object

The class that should be used to write out fasta file of a sequence collection

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
FastaWriterHelper()

Method Summary

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 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

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FastaWriterHelper

public FastaWriterHelper()

Method Detail

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

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

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

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

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

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

writeSequence

public static void writeSequence(File file,
                                 Sequence<?> sequence)
                          throws Exception

Write a sequence to a file

Parameters:

file -

sequence -

Throws:

Exception

writeSequence

public static void writeSequence(OutputStream outputStream,
                                 Sequence<?> sequence)
                          throws Exception

Write a sequence to OutputStream

Parameters:

outputStream -

sequence -

Throws:

Exception

writeSequences

public static void writeSequences(OutputStream outputStream,
                                  Collection<Sequence<?>> sequences)
                           throws Exception

Method which will write your given Sequences to the specified OutputStream. 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.out

sequences - The sequences to write out

Throws:

Exception - Thrown normally thanks to IO problems