Package fr.ens.biologie.genomique.eoulsan.modules.expression

Class ExpressionCounterUtils

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils

public class ExpressionCounterUtils
extends Object

This class define some glue methods between Eoulsan and Kenetre.

Since:

2.6

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
static Map<String,Integer>	count(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile samFile, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer reporter, String counterGroup)	Count the the features.
static void	init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile genomeDescFile, DataFile annotationFile, boolean gtfFormat)	Initialize the counter.
static void	init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDesc, DataFile annotationFile, boolean gtfFormat)	Initialize the counter.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

init

public static void init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter,
                        fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDesc,
                        DataFile annotationFile,
                        boolean gtfFormat)
                 throws IOException,
                        fr.ens.biologie.genomique.kenetre.KenetreException

Initialize the counter.

Parameters:

counter - the counter

genomeDesc - genome description

annotationFile - annotation file

gtfFormat - true if the input format is in GTF format

Throws:

EoulsanException - if an error occurs while initialize the counter

fr.ens.biologie.genomique.kenetre.KenetreException - if an error occurs while reading input files

IOException

init

public static void init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter,
                        DataFile genomeDescFile,
                        DataFile annotationFile,
                        boolean gtfFormat)
                 throws IOException,
                        fr.ens.biologie.genomique.kenetre.KenetreException

Initialize the counter.

Parameters:

counter - the counter

genomeDescFile - genome description file

annotationFile - annotation file

gtfFormat - true if the input format is in GTF format

Throws:

fr.ens.biologie.genomique.kenetre.KenetreException - if an error occurs while initialize the counter

IOException - if an error occurs while reading input files

count

public static Map<String,Integer> count(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter,
                                              DataFile samFile,
                                              fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer reporter,
                                              String counterGroup)
                                       throws IOException,
                                              fr.ens.biologie.genomique.kenetre.KenetreException

Count the the features.

Parameters:

counter - the counter

samFile - SAM file

reporter - the reporter

counterGroup - the counter group of the reporter

Returns:

a map with the counts

Throws:

EoulsanException - if an error occurs while counting

IOException - if an error occurs while reading the input file

fr.ens.biologie.genomique.kenetre.KenetreException