|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.irisa.genouest.logol.utils.converter.FastaConverter
public class FastaConverter
Constructor Summary | |
---|---|
FastaConverter()
|
Method Summary | |
---|---|
void |
convert2Fasta(java.lang.String inputFile,
java.lang.String outputFile)
Convert a Logol output XML file to fasta format |
static void |
main(java.lang.String[] args)
Fasta conversion from Logol result file |
void |
writeFasta(java.io.OutputStream os,
org.biojava.bio.seq.SequenceIterator in,
org.biojavax.Namespace ns,
org.biojavax.bio.seq.io.FastaHeader header,
int length)
Writes Sequence s from a SequenceIterator to an OutputStream in
Fasta Format. |
void |
writeFasta(java.io.OutputStream os,
org.biojava.bio.seq.Sequence seq,
org.biojavax.Namespace ns)
Writes a single Sequence to an OutputStream in Fasta format. |
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public FastaConverter()
Method Detail |
---|
public static void main(java.lang.String[] args)
args
- input and output file namespublic void convert2Fasta(java.lang.String inputFile, java.lang.String outputFile)
inputFile
- Logol outputoutputFile
- New fasta result filepublic void writeFasta(java.io.OutputStream os, org.biojava.bio.seq.SequenceIterator in, org.biojavax.Namespace ns, org.biojavax.bio.seq.io.FastaHeader header, int length) throws java.io.IOException
Sequence
s from a SequenceIterator
to an OutputStream
in
Fasta Format. This makes for a useful format filter where a
StreamReader
can be sent to the RichStreamWriter
after formatting.
os
- The stream to write fasta formatted data toin
- The source of input RichSequence
sns
- a Namespace
to write the RichSequence
s to. Null
implies that it should
use the namespace specified in the individual sequence.length
- Size of the sequence line.
java.io.IOException
- if there is an IO problempublic void writeFasta(java.io.OutputStream os, org.biojava.bio.seq.Sequence seq, org.biojavax.Namespace ns) throws java.io.IOException
Sequence
to an OutputStream
in Fasta format.
os
- the OutputStream
.seq
- the Sequence
.ns
- a Namespace
to write the sequences to. Null implies that it should
use the namespace specified in the individual sequence.
java.io.IOException
- if there is an IO problem
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |