public class GenbankWriterHelper
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
CIRCULAR_DNA |
static java.lang.String |
LINEAR_DNA |
Constructor and Description |
---|
GenbankWriterHelper() |
Modifier and Type | Method and Description |
---|---|
static void |
writeNucleotideSequence(java.io.File file,
java.util.Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a file
|
static void |
writeNucleotideSequence(java.io.OutputStream outputStream,
java.util.Collection<DNASequence> dnaSequences)
Write a collection of NucleotideSequences to a file
|
static void |
writeNucleotideSequence(java.io.OutputStream outputStream,
java.util.Collection<DNASequence> dnaSequences,
java.lang.String seqType)
Write a collection of NucleotideSequences to a file
|
static void |
writeProteinSequence(java.io.File file,
java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a file
|
static void |
writeProteinSequence(java.io.OutputStream outputStream,
java.util.Collection<ProteinSequence> proteinSequences)
Write collection of protein sequences to a stream
|
static void |
writeSequence(java.io.File file,
Sequence<?> sequence)
Write a sequence to a file
|
static void |
writeSequence(java.io.OutputStream outputStream,
Sequence<?> sequence)
Write a sequence to OutputStream
|
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 final java.lang.String LINEAR_DNA
public static final java.lang.String CIRCULAR_DNA
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 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 writeNucleotideSequence(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences, java.lang.String seqType) throws java.lang.Exception
outputStream
- dnaSequences
- seqType
- 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