org.irisa.genouest.logol.utils
Class FastaConverter
java.lang.Object
org.irisa.genouest.logol.utils.FastaConverter
Deprecated.
@Deprecated
public class FastaConverter
- extends java.lang.Object
Method Summary |
static void |
main(java.lang.String[] args)
Deprecated. |
static 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)
Deprecated. Writes Sequence s from a SequenceIterator to an OutputStream in
Fasta Format. |
static void |
writeFasta(java.io.OutputStream os,
org.biojava.bio.seq.Sequence seq,
org.biojavax.Namespace ns)
Deprecated. 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 |
FastaConverter
public FastaConverter()
- Deprecated.
main
public static void main(java.lang.String[] args)
- Deprecated.
- Parameters:
args
-
writeFasta
public static 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
- Deprecated.
- Writes
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.
- Parameters:
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.
- Throws:
java.io.IOException
- if there is an IO problem
writeFasta
public static void writeFasta(java.io.OutputStream os,
org.biojava.bio.seq.Sequence seq,
org.biojavax.Namespace ns)
throws java.io.IOException
- Deprecated.
- Writes a single
Sequence
to an OutputStream
in Fasta format.
- Parameters:
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.
- Throws:
java.io.IOException
- if there is an IO problem