org.irisa.genouest.logol.utils
Class FastaConverter

java.lang.Object
  extended by org.irisa.genouest.logol.utils.FastaConverter

Deprecated.

@Deprecated
public class FastaConverter
extends java.lang.Object


Constructor Summary
FastaConverter()
          Deprecated.  
 
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 Sequences 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
 

Constructor Detail

FastaConverter

public FastaConverter()
Deprecated. 
Method Detail

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 Sequences 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 to
in - The source of input RichSequences
ns - a Namespace to write the RichSequences 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