## org.irisa.genouest.logol.utils.converter
Class FastaConverter

    java.lang.Object
      org.irisa.genouest.logol.utils.converter.FastaConverter

    public class FastaConverter

extends java.lang.Object

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

### FastaConverter

    public FastaConverter()

Method Detail

### main

    public static void main(java.lang.String[] args)

  Fasta conversion from Logol result file

  Parameters:
    `args` - input and output file names

### convert2Fasta

    public void convert2Fasta(java.lang.String inputFile,
                              java.lang.String outputFile)

  Convert a Logol output XML file to fasta format

  Parameters:
    `inputFile` - Logol output
    `outputFile` - New fasta result file

### writeFasta

    public 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

  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 to
    `in` - The source of input `RichSequence`s
    `ns` - 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 void writeFasta(java.io.OutputStream os,
                           org.biojava.bio.seq.Sequence seq,
                           org.biojavax.Namespace ns)
                    throws java.io.IOException

  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