Class GenbankWriterHelper
- java.lang.Object
-
- org.biojava.nbio.core.sequence.io.GenbankWriterHelper
-
public class GenbankWriterHelper extends java.lang.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 java.lang.String
CIRCULAR_DNA
static java.lang.String
LINEAR_DNA
-
Constructor Summary
Constructors Constructor Description GenbankWriterHelper()
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
writeNucleotideSequence(java.io.File file, java.util.Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a filestatic void
writeNucleotideSequence(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a filestatic void
writeNucleotideSequence(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences, java.lang.String seqType)
Write a collection of NucleotideSequences to a filestatic void
writeProteinSequence(java.io.File file, java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a filestatic void
writeProteinSequence(java.io.OutputStream outputStream, java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a streamstatic void
writeSequence(java.io.File file, Sequence<?> sequence)
Write a sequence to a filestatic void
writeSequence(java.io.OutputStream outputStream, Sequence<?> sequence)
Write a sequence to OutputStreamstatic void
writeSequences(java.io.OutputStream outputStream, java.util.Collection<Sequence<?>> sequences)
Method which will write your given Sequences to the specifiedOutputStream
.
-
-
-
Field Detail
-
LINEAR_DNA
public static final java.lang.String LINEAR_DNA
- See Also:
- Constant Field Values
-
CIRCULAR_DNA
public static final java.lang.String CIRCULAR_DNA
- See Also:
- Constant Field Values
-
-
Method Detail
-
writeProteinSequence
public static void writeProteinSequence(java.io.File file, java.util.Collection<ProteinSequence> proteinSequences) throws java.lang.Exception
Write collection of protein sequences to a file- Parameters:
file
-proteinSequences
-- Throws:
java.lang.Exception
-
writeProteinSequence
public static void writeProteinSequence(java.io.OutputStream outputStream, java.util.Collection<ProteinSequence> proteinSequences) throws java.lang.Exception
Write collection of protein sequences to a stream- Parameters:
outputStream
-proteinSequences
-- Throws:
java.lang.Exception
-
writeNucleotideSequence
public static void writeNucleotideSequence(java.io.File file, java.util.Collection<DNASequence> dnaSequences) throws java.lang.Exception
Write a collection of NucleotideSequences to a file- Parameters:
file
-dnaSequences
-- Throws:
java.lang.Exception
-
writeNucleotideSequence
public static void writeNucleotideSequence(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences) throws java.lang.Exception
Write a collection of NucleotideSequences to a file- Parameters:
outputStream
-dnaSequences
-- Throws:
java.lang.Exception
-
writeNucleotideSequence
public static void writeNucleotideSequence(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences, java.lang.String seqType) throws java.lang.Exception
Write a collection of NucleotideSequences to a file- Parameters:
outputStream
-dnaSequences
-seqType
-- Throws:
java.lang.Exception
-
writeSequence
public static void writeSequence(java.io.File file, Sequence<?> sequence) throws java.lang.Exception
Write a sequence to a file- Parameters:
file
-sequence
-- Throws:
java.lang.Exception
-
writeSequence
public static void writeSequence(java.io.OutputStream outputStream, Sequence<?> sequence) throws java.lang.Exception
Write a sequence to OutputStream- Parameters:
outputStream
-sequence
-- Throws:
java.lang.Exception
-
writeSequences
public static void writeSequences(java.io.OutputStream outputStream, java.util.Collection<Sequence<?>> sequences) throws java.lang.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:
java.lang.Exception
- Thrown normally thanks to IO problems
-
-