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

Class GenbankWriterHelper

java.lang.Object

org.biojava.nbio.core.sequence.io.GenbankWriterHelper

public class GenbankWriterHelper
extends Object

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

Author:

mckeee1

Field Summary

Fields

Modifier and Type	Field	Description
static String	CIRCULAR_DNA
static String	LINEAR_DNA

Constructor Summary

Constructors

Constructor	Description
GenbankWriterHelper()

Method Summary

Modifier and Type	Method	Description
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	writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences, String seqType)	Write a collection of NucleotideSequences to a file
static void	writeNucleotideSequenceOriginal(OutputStream outputStream, Collection<DNASequence> dnaSequences)	Write a collection of NucleotideSequences to a file using the NucleotideSequences original header as the LOCUS line rather than generating it
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

Field Detail

LINEAR_DNA

public static final String LINEAR_DNA

See Also:

Constant Field Values

CIRCULAR_DNA

public static final String CIRCULAR_DNA

See Also:

Constant Field Values

Constructor Detail

GenbankWriterHelper

public GenbankWriterHelper()

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

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

writeNucleotideSequence

public static void writeNucleotideSequence(OutputStream outputStream,
                                           Collection<DNASequence> dnaSequences,
                                           String seqType)
                                    throws Exception

Write a collection of NucleotideSequences to a file

Parameters:

outputStream -

dnaSequences -

seqType -

Throws:

Exception

writeNucleotideSequenceOriginal

public static void writeNucleotideSequenceOriginal(OutputStream outputStream,
                                                   Collection<DNASequence> dnaSequences)
                                            throws Exception

Write a collection of NucleotideSequences to a file using the NucleotideSequences original header as the LOCUS line rather than generating it

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