org.irisa.genouest.logol.utils.converter
Class GFFConverter

java.lang.Object
  extended by org.irisa.genouest.logol.utils.converter.GFFConverter

public class GFFConverter
extends java.lang.Object

History: Fix 1659 O. Sallou 21/07/10: GFF output should start at position 1, add 1 to positions

Author:
osallou

Constructor Summary
GFFConverter()
           
 
Method Summary
 void convert2GFF(java.lang.String inputFile, java.lang.String outputFile)
          Read fasta file from results, load seq name from file Size will be min/max of matches
static void main(java.lang.String[] args)
          GFF converter from Logol result file
 void writeGFF(java.lang.String outputFile, org.biojava.bio.program.gff.GFFEntrySet gffSet)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GFFConverter

public GFFConverter()
Method Detail

main

public static void main(java.lang.String[] args)
GFF converter from Logol result file

Parameters:
args - input and output file

writeGFF

public void writeGFF(java.lang.String outputFile,
                     org.biojava.bio.program.gff.GFFEntrySet gffSet)
              throws java.io.IOException
Throws:
java.io.IOException

convert2GFF

public void convert2GFF(java.lang.String inputFile,
                        java.lang.String outputFile)
                 throws java.util.NoSuchElementException
Read fasta file from results, load seq name from file Size will be min/max of matches

Parameters:
inputFile - File of matches for a sequence
outputFile - File to write the GFF
Throws:
java.util.NoSuchElementException
org.biojava.bio.BioException