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

Class AbstractSampleSheetConverter

java.lang.Object

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

Direct Known Subclasses:

IlluminaSampleSheetConverter, NanoporeSampleSheetConverter

public abstract class AbstractSampleSheetConverter
extends Object

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

Since:

3.1

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
protected File	errorFile
protected File	inputFile
protected File	outputDir
protected File	outputFile
protected File	warningFile

Method Summary

Modifier and Type	Method	Description
protected abstract void	checkSampleSheet(List<String> warnings)	Check the samplesheet.
void	convert()	Convert the samplesheet.
File	defineErrorFile(File inputFile, File destDir)
File	defineOutputFile(File inputFile, File destDir)
File	defineWarningFile(File inputFile, File destDir)
protected abstract void	fixSampleSheet(List<String> warnings)	Fix the samplesheet.
protected abstract void	loadSampleSheet()	Load the samplesheet.
void	saveError(Aozan3Exception e)	Save error message.
protected static void	saveFile(String text, File inputFile, File outputFile)	Save file.
protected abstract void	saveSampleSheet()	Save the samplesheet.
protected static void	saveWarnings(List<String> warnings, File inputFile, File warningFile)	Save warning message.

Methods inherited from class java.lang.Object

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

Field Detail

inputFile

protected final File inputFile

outputDir

protected final File outputDir

outputFile

protected final File outputFile

errorFile

protected final File errorFile

warningFile

protected final File warningFile

Method Detail

convert

public void convert()
             throws Aozan3Exception

Convert the samplesheet.

Throws:

Aozan3Exception - if an error occurs while converting the samplesheet

loadSampleSheet

protected abstract void loadSampleSheet()
                                 throws Aozan3Exception

Load the samplesheet.

Throws:

Aozan3Exception - if an error occurs while loading the samplesheet

fixSampleSheet

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

Fix the samplesheet.

Throws:

Aozan3Exception - if an error occurs while fixing the samplesheet

checkSampleSheet

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

Check the samplesheet.

Throws:

Aozan3Exception - if an error occurs while checking the samplesheet

saveSampleSheet

protected abstract void saveSampleSheet()
                                 throws Aozan3Exception

Save the samplesheet.

Throws:

Aozan3Exception - if an error occurs while saving the samplesheet

defineOutputFile

public File defineOutputFile(File inputFile,
                             File destDir)

defineErrorFile

public File defineErrorFile(File inputFile,
                            File destDir)

defineWarningFile

public File defineWarningFile(File inputFile,
                              File destDir)

saveError

public void saveError(Aozan3Exception e)

Save error message.

Parameters:

e - exception

saveWarnings

protected static void saveWarnings(List<String> warnings,
                                   File inputFile,
                                   File warningFile)

Save warning message.

Parameters:

warnings - warnings

inputFile - input file

warningFile - warning file

saveFile

protected static void saveFile(String text,
                               File inputFile,
                               File outputFile)

Save file.

Parameters:

inputFile - input file

outputFile - output file