Package fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter

Class IlluminaSampleSheetConverter

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter

fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.IlluminaSampleSheetConverter

public class IlluminaSampleSheetConverter
extends AbstractSampleSheetConverter

This class define a converter between an Illumina samplesheet in XLS format to CSV.

Since:

3.1

Author:

Laurent Jourdren

Field Summary

Fields inherited from class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter

errorFile, inputFile, outputDir, outputFile, warningFile

Constructor Summary

Constructors

Constructor	Description
IlluminaSampleSheetConverter(File inputFile, File outputDir)	Abstract constructor.

Method Summary

Modifier and Type	Method	Description
protected void	checkSampleSheet(List<String> warnings)	Check the samplesheet.
protected void	fixSampleSheet(List<String> warnings)	Fix the samplesheet.
protected void	loadSampleSheet()	Load the samplesheet.
protected void	saveSampleSheet()	Save the samplesheet.

Methods inherited from class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter

convert, defineErrorFile, defineOutputFile, defineWarningFile, saveError, saveFile, saveWarnings

Methods inherited from class java.lang.Object

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

Constructor Detail

IlluminaSampleSheetConverter

public IlluminaSampleSheetConverter(File inputFile,
                                    File outputDir)

Abstract constructor.

Parameters:

inputFile - input file

outputDir - output directory

Method Detail

loadSampleSheet

protected void loadSampleSheet()
                        throws Aozan3Exception

Description copied from class: AbstractSampleSheetConverter

Load the samplesheet.

Specified by:

loadSampleSheet in class AbstractSampleSheetConverter

Throws:

Aozan3Exception - if an error occurs while loading the samplesheet

fixSampleSheet

protected void fixSampleSheet(List<String> warnings)
                       throws Aozan3Exception

Description copied from class: AbstractSampleSheetConverter

Fix the samplesheet.

Specified by:

fixSampleSheet in class AbstractSampleSheetConverter

Throws:

Aozan3Exception - if an error occurs while fixing the samplesheet

checkSampleSheet

protected void checkSampleSheet(List<String> warnings)
                         throws Aozan3Exception

Description copied from class: AbstractSampleSheetConverter

Check the samplesheet.

Specified by:

checkSampleSheet in class AbstractSampleSheetConverter

Throws:

Aozan3Exception - if an error occurs while checking the samplesheet

saveSampleSheet

protected void saveSampleSheet()
                        throws Aozan3Exception

Description copied from class: AbstractSampleSheetConverter

Save the samplesheet.

Specified by:

saveSampleSheet in class AbstractSampleSheetConverter

Throws:

Aozan3Exception - if an error occurs while saving the samplesheet