Uses of Class
fr.ens.biologie.genomique.eoulsan.data.DataFile

Packages that use DataFile

Package	Description
fr.ens.biologie.genomique.eoulsan.core	This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data	This package contains classes for data files, data types and data formats.
fr.ens.biologie.genomique.eoulsan.data.protocols	This package contains class for protocols used by the DataFile classes.
fr.ens.biologie.genomique.eoulsan.data.storages	This package contains and define data storages.
fr.ens.biologie.genomique.eoulsan.design	This package contains classes to handle experimental designs.
fr.ens.biologie.genomique.eoulsan.design.io	This package contains I/O classes to read and write design files.
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.expression	This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.fastqc	This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators	This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload	This package contain classes related to upload data to HDFS and Cloud.
fr.ens.biologie.genomique.eoulsan.splitermergers	This package contains splitter and merger used when running Eoulsan on a standard cluster to get more parallelization efficiency.
fr.ens.biologie.genomique.eoulsan.util	This package contain utility classes.
fr.ens.biologie.genomique.eoulsan.util.r	This package contain utility classes for R usage.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.core

Methods in fr.ens.biologie.genomique.eoulsan.core that return DataFile

Modifier and Type	Method	Description
DataFile	StepConfigurationContext.getDesignFile()	Get the design file path.
static DataFile	ContextUtils.getHadoopWorkingDirectory(TaskContext context)	Get the Hadoop working directory.
static DataFile	ContextUtils.getJarPathname(TaskContext context)	Get the application jar file.
static DataFile	ContextUtils.getJobDirectory(TaskContext context)	Get the job directory.
DataFile	StepConfigurationContext.getJobDirectory()	Get the job path.
static DataFile	ContextUtils.getLocalWorkingDirectory(TaskContext context)	Get the local working directory.
DataFile	StepConfigurationContext.getOutputDirectory()	Get the output path.
DataFile	StepConfigurationContext.getStepOutputDirectory()	Get the step working directory.
static DataFile	ContextUtils.getTaskOutputDirectory(TaskContext context)	Get the task output directory.
DataFile	StepConfigurationContext.getWorkflowFile()	Get the workflow file path.

Methods in fr.ens.biologie.genomique.eoulsan.core that return types with arguments of type DataFile

Modifier and Type	Method	Description
static List<DataFile>	DataUtils.getDataFiles(Data data)	Get the list of the DataFile objects in a Data object.

Methods in fr.ens.biologie.genomique.eoulsan.core with parameters of type DataFile

Modifier and Type	Method	Description
static boolean	FileNaming.dataEquals(DataFile file1, DataFile file2)	Test if two files are related to the same data.
void	Workflow.deleteOnExit(DataFile file)	Delete a file on the exit of the workflow.
static boolean	FileNaming.isFilenameValid(DataFile file)	Test if a filename is valid.
static FileNaming	FileNaming.parse(DataFile file)	Create a FileNaming object from a DataFile object.
static void	DataUtils.setDataFile(Data data, DataFile dataFile)	Change the DataFile in a Data object

Method parameters in fr.ens.biologie.genomique.eoulsan.core with type arguments of type DataFile

Modifier and Type	Method	Description
static void	DataUtils.setDataFiles(Data data, List<DataFile> dataFiles)	Change the DataFiles in a Data object

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.core.workflow

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return DataFile

Modifier and Type	Method	Description
static DataFile	WorkflowFileNaming.file(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port, fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data, int fileIndex)	Create a DataFile object for a file of the workflow.
DataFile	DataList.getDataFile()
DataFile	DataList.getDataFile(int fileIndex)
DataFile	StepOutputDataFile.getDataFile()	Get the file as a DataFile.
DataFile	UnmodifiableData.getDataFile()
DataFile	UnmodifiableData.getDataFile(int fileIndex)
DataFile	TaskContextImpl.getDataRepositoryDirectory()	Get the data repository directory.
DataFile	WorkflowContext.getDataRepositoryDirectory()	Get the data repository directory.
DataFile	StepConfigurationContextImpl.getDesignFile()
DataFile	TaskContextImpl.getDesignFile()
DataFile	WorkflowContext.getDesignFile()	Get the design file.
DataFile	StepConfigurationContextImpl.getHadoopWorkingDirectory()	Get the Hadoop working directory.
DataFile	WorkflowContext.getHadoopWorkingDirectory()	Get the local working directory.
DataFile	TaskContextImpl.getHadoopWorkingPathname()	Get the Hadoop working directory.
DataFile	WorkflowContext.getJarFile()	Get the application jar file.
DataFile	StepConfigurationContextImpl.getJarPathname()	Get the application jar file.
DataFile	TaskContextImpl.getJarPathname()	Get the application jar path.
DataFile	StepConfigurationContextImpl.getJobDirectory()	Get the job directory.
DataFile	TaskContextImpl.getJobDirectory()	Get the job directory.
DataFile	WorkflowContext.getJobDirectory()	Get the job path.
DataFile	StepConfigurationContextImpl.getLocalWorkingDirectory()	Get the local working directory.
DataFile	WorkflowContext.getLocalWorkingDirectory()	Get the local working directory.
DataFile	TaskContextImpl.getLocalWorkingPathname()	Get the local working directory.
DataFile	StepConfigurationContextImpl.getOutputDirectory()
DataFile	TaskContextImpl.getOutputDirectory()
DataFile	WorkflowContext.getOutputDirectory()	Get the output directory.
DataFile	AbstractStep.getStepOutputDirectory()	Get step output directory (where output file of the step will be written).
DataFile	StepConfigurationContextImpl.getStepOutputDirectory()
DataFile	TaskContextImpl.getStepOutputDirectory()
DataFile	WorkflowContext.getTaskDirectory()	Get the task directory.
DataFile	StepConfigurationContextImpl.getTaskOutputDirectory()	Get the task output directory.
DataFile	TaskContextImpl.getTaskOutputDirectory()	Get the task output directory.
DataFile	StepConfigurationContextImpl.getWorkflowFile()
DataFile	TaskContextImpl.getWorkflowFile()
DataFile	WorkflowContext.getWorkflowFile()	Get the workflow file.

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return types with arguments of type DataFile

Modifier and Type	Method	Description
static List<DataFile>	WorkflowDataUtils.getDataFiles(Data data)	Get the list of the DataFile objects in a Data object.

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type DataFile

Modifier and Type	Method	Description
void	AbstractWorkflow.deleteOnExit(DataFile file)
static TaskContextImpl	TaskContextImpl.deserialize(DataFile file)	Deserialize the TaskContext object.
static TaskResultImpl	TaskResultImpl.deserialize(DataFile file)	Deserialize the TaskResult object.
void	TaskContextImpl.deserializeOutputData(DataFile file)	Deserialize output data.
static TaskResultImpl	TaskSerializationUtils.execute(DataFile taskContextFile)	Execute a task context serialization file.
static TaskResultImpl	TaskSerializationUtils.execute(DataFile taskContextFile, DataFile outputDir)	Execute a task context serialization file.
static DataMetadataStorage	DataMetadataStorage.getInstance(DataFile metadataDir)	Get the singleton.
Map<String,String>	DataMetadataStorage.getMetadata(DataFile file)	Get the metadata of a file.
void	StepResult.read(DataFile file)	Read a step result file.
void	TaskContextImpl.serialize(DataFile file)	Serialize the TaskContext object.
void	TaskResultImpl.serialize(DataFile file)	Serialize the TaskResult object.
void	TaskContextImpl.serializeOutputData(DataFile file)	Serialize output data.
static void	WorkflowDataUtils.setDataFile(Data data, int fileIndex, DataFile dataFile)	Change the DataFile in a Data object
static void	WorkflowDataUtils.setDataFile(Data data, DataFile dataFile)	Change the DataFile in a Data object
void	WorkflowContext.setDesignFile(DataFile designFile)	Set the design file.
void	WorkflowContext.setJarFile(DataFile jarFile)	Set the jar file.
void	WorkflowContext.setWorkflowFile(DataFile workflowFile)	Set the workflow file.
void	StepResult.write(DataFile file, boolean oldFormat)	Write the result.

Method parameters in fr.ens.biologie.genomique.eoulsan.core.workflow with type arguments of type DataFile

Modifier and Type	Method	Description
boolean	DataMetadataStorage.loadMetadata(Data data, List<DataFile> files)	Set the metadata of a data from the metadata storage.
static void	WorkflowDataUtils.setDataFiles(Data data, List<DataFile> dataFiles)	Change the DataFiles in a Data object

Constructors in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type DataFile

Constructor	Description
CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct, DataFile outputDirectory)	Create a step for a standard step.
CommandWorkflowParser(DataFile file)	Public constructor.
Workflow2Graphviz(AbstractWorkflow workflow, DataFile dotFile, DataFile imageFile)	Public constructor.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.data

Methods in fr.ens.biologie.genomique.eoulsan.data that return DataFile

Modifier and Type	Method	Description
DataFile	Data.getDataFile()	Get the DataFile for an input DataType and a Sample.
DataFile	Data.getDataFile(int fileIndex)	Get the DataFile for an input DataType and a Sample.
DataFile	DataFileMetadata.getLinkTarget()	Get the symbolic link target.
DataFile	DataFile.getParent()	Get the parent of this DataFile.
DataFile	DataFile.toAbsoluteDataFile()	Convert the the DataFile to a absolute DataFile.
DataFile	DataFile.toRealDataFile()	Convert the the DataFile to a DataFile where all the indirection has been solved.

Methods in fr.ens.biologie.genomique.eoulsan.data that return types with arguments of type DataFile

Modifier and Type	Method	Description
List<DataFile>	DataFile.list()	List the content of a directory.

Methods in fr.ens.biologie.genomique.eoulsan.data with parameters of type DataFile

Modifier and Type	Method	Description
int	DataFile.compareTo(DataFile o)
static void	DataFiles.copy(DataFile input, DataFile output)	Copy a file, if input data is compressed, data will be uncompressed and if output require to be compressed output will be compressed.
void	DataFile.copyTo(DataFile dest)	Copy this DataFile in a other DataFile.
static void	DataFiles.rawCopy(DataFile input, DataFile output)	Copy a file.
void	DataFile.renameTo(DataFile dest)	Rename the DataFile.
void	DataFile.symlink(DataFile link)	Create a symbolic link that target is the current file.
void	DataFile.symlink(DataFile link, boolean relativize)	Create a symbolic link that target is the current file.
static void	DataFiles.symlinkOrCopy(DataFile input, DataFile output)	Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.
static void	DataFiles.symlinkOrCopy(DataFile input, DataFile output, boolean relativize)	Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.

Constructors in fr.ens.biologie.genomique.eoulsan.data with parameters of type DataFile

Constructor	Description
DataFile(DataFile parentFile, String filename)	Public constructor.
DataFormatConverter(DataFile inFile, DataFile outFile)	Constructor
DataFormatConverter(DataFile inFile, DataFile outFile, DataFormat outFormat, OutputStream os)	Constructor
DataFormatConverter(DataFile inFile, DataFile outFile, OutputStream os)	Constructor

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.data.protocols

Methods in fr.ens.biologie.genomique.eoulsan.data.protocols that return DataFile

Modifier and Type	Method	Description
DataFile	DataProtocol.getDataFileParent(DataFile src)	Get the parent source of the source.
DataFile	StorageDataProtocol.getUnderLyingData(DataFile src)	Get the underlying Data.

Methods in fr.ens.biologie.genomique.eoulsan.data.protocols that return types with arguments of type DataFile

Modifier and Type	Method	Description
List<DataFile>	DataProtocol.list(DataFile dir)	List a directory.
List<DataFile>	FileDataProtocol.list(DataFile file)
List<DataFile>	HDFSPathDataProtocol.list(DataFile file)

Methods in fr.ens.biologie.genomique.eoulsan.data.protocols with parameters of type DataFile

Modifier and Type	Method	Description
void	DataProtocol.delete(DataFile file, boolean recursive)	Delete a file.
void	FileDataProtocol.delete(DataFile file, boolean recursive)
void	HDFSPathDataProtocol.delete(DataFile file, boolean recursive)
boolean	DataProtocol.exists(DataFile src, boolean followLink)	Test a source exists.
boolean	DeprecatedDataProtocol.exists(DataFile src, boolean followLink)
boolean	FileDataProtocol.exists(DataFile src, boolean followLink)
boolean	PathDataProtocol.exists(DataFile src, boolean followLink)
boolean	StorageDataProtocol.exists(DataFile src, boolean followLink)
boolean	URLDataProtocol.exists(DataFile src, boolean followLink)
InputStream	DataProtocol.getData(DataFile src)	Create an InputStream from the source.
InputStream	DeprecatedDataProtocol.getData(DataFile src)
InputStream	FileDataProtocol.getData(DataFile src)
InputStream	HDFSPathDataProtocol.getData(DataFile src)
InputStream	PathDataProtocol.getData(DataFile src)
InputStream	StorageDataProtocol.getData(DataFile src)
InputStream	URLDataProtocol.getData(DataFile src)
DataFile	DataProtocol.getDataFileParent(DataFile src)	Get the parent source of the source.
DataFileMetadata	DataProtocol.getMetadata(DataFile src)	Get the metadata for the source.
DataFileMetadata	DeprecatedDataProtocol.getMetadata(DataFile src)
DataFileMetadata	FileDataProtocol.getMetadata(DataFile src)
DataFileMetadata	PathDataProtocol.getMetadata(DataFile src)
DataFileMetadata	StorageDataProtocol.getMetadata(DataFile src)
DataFileMetadata	URLDataProtocol.getMetadata(DataFile src)
org.apache.hadoop.fs.Path	PathDataProtocol.getPath(DataFile dataFile)	Get Convert a DataFile object to a Path object.
File	DataProtocol.getSourceAsFile(DataFile src)	Get the underlying File object for the DataFile if the protocol allow it.
File	FileDataProtocol.getSourceAsFile(DataFile dataFile)
File	StorageDataProtocol.getSourceAsFile(DataFile src)
DataFile	StorageDataProtocol.getUnderLyingData(DataFile src)	Get the underlying Data.
List<DataFile>	DataProtocol.list(DataFile dir)	List a directory.
List<DataFile>	FileDataProtocol.list(DataFile file)
List<DataFile>	HDFSPathDataProtocol.list(DataFile file)
void	DataProtocol.mkdir(DataFile dir)	Create a directory.
void	FileDataProtocol.mkdir(DataFile dir)
void	HDFSPathDataProtocol.mkdir(DataFile dir)
void	DataProtocol.mkdirs(DataFile dir)	Create a directory and its parents if not exists.
void	FileDataProtocol.mkdirs(DataFile dir)
void	HDFSPathDataProtocol.mkdirs(DataFile dir)
OutputStream	DataProtocol.putData(DataFile dest)	Create an OutputStream from the source.
void	DataProtocol.putData(DataFile src, DataFile dest)	Copy data from a source to a destination source
OutputStream	DataProtocol.putData(DataFile dest, DataFileMetadata md)	Create an OutputStream from the source.
OutputStream	DeprecatedDataProtocol.putData(DataFile dest)
OutputStream	FileDataProtocol.putData(DataFile src)
OutputStream	PathDataProtocol.putData(DataFile src)
OutputStream	StorageDataProtocol.putData(DataFile dest)
OutputStream	URLDataProtocol.putData(DataFile src)
void	DataProtocol.rename(DataFile file, DataFile dest)	Rename a file.
void	FileDataProtocol.rename(DataFile src, DataFile dest)
void	HDFSPathDataProtocol.rename(DataFile file, DataFile dest)
void	DataProtocol.symlink(DataFile target, DataFile link)	Create a symbolic link.
void	FileDataProtocol.symlink(DataFile target, DataFile link)

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.data.storages

Methods in fr.ens.biologie.genomique.eoulsan.data.storages that return DataFile

Modifier and Type	Method	Description
DataFile	DataFileDataPath.getDataFile()
DataFile	DataFileGenomeIndexStorage.getDataFile(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription)	Get the DataFile that corresponds to a mapper and a genome
DataFile	DataFileStorage.getDataFile(String shortName)	Get a Datafile related to a short name

Methods in fr.ens.biologie.genomique.eoulsan.data.storages with parameters of type DataFile

Modifier and Type	Method	Description
void	DataFileGenomeMapperIndexer.createIndex(DataFile genomeDataFile, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDescription, DataFile mapperIndexDataFile)	Create an archived genome index.
static fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage	DataFileGenomeDescStorage.getInstance(DataFile dir, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Create a GenomeDescStorage
void	DataFileGenomeIndexStorage.put(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription, DataFile indexArchive)	Put the index archive in the storage.

Constructors in fr.ens.biologie.genomique.eoulsan.data.storages with parameters of type DataFile

Constructor	Description
DataFileDataPath(DataFile file)	Constructor.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.design

Methods in fr.ens.biologie.genomique.eoulsan.design with parameters of type DataFile

Modifier and Type	Method	Description
void	DesignBuilder.addFile(DataFile file)	Add a file to the design builder
static void	DesignUtils.replaceLocalPathBySymlinks(Design design, DataFile symlinksDir)	Replace the local paths in the design by paths to symbolic links in a directory.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.design.io

Constructors in fr.ens.biologie.genomique.eoulsan.design.io with parameters of type DataFile

Constructor	Description
DefaultDesignReader(DataFile file)	Public constructor.
Eoulsan1DesignReader(DataFile file)	Public constructor.
Eoulsan1DesignWriter(DataFile file)	Public constructor.
Eoulsan2DesignReader(DataFile file)	Public constructor.
Eoulsan2DesignWriter(DataFile file)	Public constructor.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.diffana

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type DataFile

Modifier and Type	Method	Description
void	DESeq2.runDEseq2(DataFile workflowOutputDir)	Method to run DESeq2.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.expression

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression with parameters of type DataFile

Modifier and Type	Method	Description
static Map<String,Integer>	ExpressionCounterUtils.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	ExpressionCounterUtils.init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile genomeDescFile, DataFile annotationFile, boolean gtfFormat)	Initialize the counter.
static void	ExpressionCounterUtils.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.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.fastqc

Constructors in fr.ens.biologie.genomique.eoulsan.modules.fastqc with parameters of type DataFile

Constructor	Description
EmptyFileQC(DataFile file)	Constructor.
FastqSequenceFile(DataFile fastqFile)	Public constructor.
SAMSequenceFile(DataFile inFile)	Public constructor.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.generators

Methods in fr.ens.biologie.genomique.eoulsan.modules.generators with parameters of type DataFile

Modifier and Type	Method	Description
fr.ens.biologie.genomique.kenetre.bio.GenomeDescription	GenomeDescriptionCreator.createGenomeDescription(DataFile genomeDataFile)	Create genome description object from the storage if already exists or compute it from the genome.
fr.ens.biologie.genomique.kenetre.bio.GenomeDescription	GenomeDescriptionCreator.createGenomeDescriptionFromAnnotation(DataFile annotationDataFile)	Create genome description object from the storage if already exists or compute it from the genome.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop with parameters of type DataFile

Modifier and Type	Method	Description
static org.apache.hadoop.mapreduce.Job	PairedEndFastqToTfq.convert(org.apache.hadoop.conf.Configuration parentConf, DataFile fastqFile1, DataFile fastqFile2, DataFile outputFile, int reducerTaskCount)	Create the job to convert FASTQ files in a TFQ file.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload that return DataFile

Modifier and Type	Method	Description
protected DataFile	UploadModule.getDest()
protected DataFile	HadoopUploadModule.getUploadedDataFile(DataFile file)
protected DataFile	HadoopUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected DataFile	LocalUploadModule.getUploadedDataFile(DataFile file)
protected DataFile	LocalUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected abstract DataFile	UploadModule.getUploadedDataFile(DataFile file)	Generate the DataFile Object for the uploaded DataFile
protected abstract DataFile	UploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)	Generate the DataFile Object for the uploaded DataFile

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type DataFile

Modifier and Type	Method	Description
protected DataFile	HadoopUploadModule.getUploadedDataFile(DataFile file)
protected DataFile	HadoopUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected DataFile	LocalUploadModule.getUploadedDataFile(DataFile file)
protected DataFile	LocalUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected abstract DataFile	UploadModule.getUploadedDataFile(DataFile file)	Generate the DataFile Object for the uploaded DataFile
protected abstract DataFile	UploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)	Generate the DataFile Object for the uploaded DataFile

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with type arguments of type DataFile

Modifier and Type	Method	Description
void	DataFileDistCp.copy(Map<DataFile,DataFile> entries)
void	DataFileDistCp.copy(Map<DataFile,DataFile> entries)
protected void	HadoopUploadModule.copy(Map<DataFile,DataFile> files)
protected void	HadoopUploadModule.copy(Map<DataFile,DataFile> files)
protected void	LocalUploadModule.copy(Map<DataFile,DataFile> files)
protected void	LocalUploadModule.copy(Map<DataFile,DataFile> files)
protected abstract void	UploadModule.copy(Map<DataFile,DataFile> files)	Copy files to destinations.
protected abstract void	UploadModule.copy(Map<DataFile,DataFile> files)	Copy files to destinations.

Constructors in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type DataFile

Constructor	Description
HadoopUploadModule(DataFile dest, org.apache.hadoop.conf.Configuration conf)	Public constructor.
LocalUploadModule(DataFile dest)	Public constructor.
UploadModule(DataFile destination)	Public constructor.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.splitermergers

Methods in fr.ens.biologie.genomique.eoulsan.splitermergers with parameters of type DataFile

Modifier and Type	Method	Description
void	BAMMerger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void	ExpressionMerger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void	FastqMerger.merge(Iterator<DataFile> inDataFileIterator, DataFile outFile)
void	Merger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)	Merger data.
void	SAMMerger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void	BAMSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	ExpressionSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	FastqSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	SAMSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	Splitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)	Split data.
void	BAMSplitter.splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)	Split BAM file by chromosomes.
void	SAMSplitter.splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)	Split SAM file by chromosomes.

Method parameters in fr.ens.biologie.genomique.eoulsan.splitermergers with type arguments of type DataFile

Modifier and Type	Method	Description
void	BAMMerger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void	ExpressionMerger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void	FastqMerger.merge(Iterator<DataFile> inDataFileIterator, DataFile outFile)
void	Merger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)	Merger data.
void	SAMMerger.merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void	BAMSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	ExpressionSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	FastqSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	SAMSplitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)
void	Splitter.split(DataFile inFile, Iterator<DataFile> outFileIterator)	Split data.
void	BAMSplitter.splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)	Split BAM file by chromosomes.
void	SAMSplitter.splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)	Split SAM file by chromosomes.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.util

Methods in fr.ens.biologie.genomique.eoulsan.util that return DataFile

Modifier and Type	Method	Description
static DataFile	EoulsanTranslatorUtils.getLinksFileFromSettings(Settings settings)	Get the links file from the settings.

Methods in fr.ens.biologie.genomique.eoulsan.util with parameters of type DataFile

Modifier and Type	Method	Description
void	FileResourceLoader.addResourcePath(DataFile resourcePath)	Add a resource path.
static fr.ens.biologie.genomique.kenetre.translator.Translator	EoulsanTranslatorUtils.loadTranslator(DataFile linksFile)	Create a translator annotation from a link file.
static fr.ens.biologie.genomique.kenetre.translator.Translator	EoulsanTranslatorUtils.loadTranslator(DataFile annotationFile, DataFile linksFile)	Create a translator annotation from an additional annotation file and a link file.
boolean	FileResourceLoader.removeResourcePath(DataFile resourcePath)	Add a resource path.

Constructors in fr.ens.biologie.genomique.eoulsan.util with parameters of type DataFile

Constructor	Description
FileResourceLoader(Class<S> clazz, DataFile resourcePath)	Public constructor.

Uses of DataFile in fr.ens.biologie.genomique.eoulsan.util.r

Methods in fr.ens.biologie.genomique.eoulsan.util.r with parameters of type DataFile

Modifier and Type	Method	Description
void	AbstractRExecutor.executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)
void	RExecutor.executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)	Execute a R script.
protected static boolean	ProcessRExecutor.isSameLocalPath(DataFile a, DataFile b)	Check if two file have the same local path
protected abstract void	AbstractRExecutor.putFile(DataFile inputFile, String outputFilename)	Put a file for the analysis.
protected void	DockerRExecutor.putFile(DataFile inputFile, String outputFilename)
protected void	ProcessRExecutor.putFile(DataFile inputFile, String outputFilename)
protected void	RserveRExecutor.putFile(DataFile inputFile, String inputFilename)
void	AbstractRExecutor.putInputFile(DataFile inputFile)
void	AbstractRExecutor.putInputFile(DataFile inputFile, String outputFilename)
void	RExecutor.putInputFile(DataFile inputFile)	Put a file for the analysis.
void	RExecutor.putInputFile(DataFile inputFile, String outputFilename)	Put a file.