Uses of Interface
fr.ens.biologie.genomique.eoulsan.data.Data

Packages that use Data

Package	Description
fr.ens.biologie.genomique.eoulsan.checkers	This package contains and define checkers of DataFormat.
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.modules	This package define the steps for the Eoulsan workflow.
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.multiqc

Uses of Data in fr.ens.biologie.genomique.eoulsan.checkers

Methods in fr.ens.biologie.genomique.eoulsan.checkers with parameters of type Data

Modifier and Type	Method	Description
boolean	Checker.check(Data data, CheckStore checkInfo)	Launch the check.
boolean	DESeq2DesignChecker.check(Data data, CheckStore checkInfo)
boolean	GenomeChecker.check(Data data, CheckStore checkInfo)
boolean	GFFChecker.check(Data data, CheckStore checkInfo)
boolean	ReadsChecker.check(Data data, CheckStore checkInfo)

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

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

Modifier and Type	Method	Description
Data	TaskContext.getInputData(DataFormat format)	Get the input data for an input DataType and a Sample.
Data	TaskContext.getInputData(String portName)	Get the input data for a port name and a Sample.
Data	TaskContext.getOutputData(DataFormat format, Data origin)	Get the output data for an input DataType and a Sample.
Data	TaskContext.getOutputData(DataFormat format, String dataName)	Get the output data for an input DataType and a Sample.
Data	TaskContext.getOutputData(DataFormat format, String dataName, int part)	Get the output data for an input DataType and a Sample.
Data	TaskContext.getOutputData(String portName, Data origin)	Get the output data for a port name and a Sample.
Data	TaskContext.getOutputData(String portName, String dataName)	Get the output data for a port name and a Sample.
Data	TaskContext.getOutputData(String portName, String dataName, int part)	Get the output data for a port name and a Sample.

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

Modifier and Type	Method	Description
static List<DataFile>	DataUtils.getDataFiles(Data data)	Get the list of the DataFile objects in a Data object.
Data	TaskContext.getOutputData(DataFormat format, Data origin)	Get the output data for an input DataType and a Sample.
Data	TaskContext.getOutputData(String portName, Data origin)	Get the output data for a port name and a Sample.
protected void	FileNaming.set(Data data)	Set several field of the object from a Data object.
static void	DataUtils.setDataFile(Data data, DataFile dataFile)	Change the DataFile in a Data object
static void	DataUtils.setDataFiles(Data data, List<DataFile> dataFiles)	Change the DataFiles in a Data object
static void	DataUtils.setDataMetadata(Data data, Collection<Data> dataSourceOfMetadata)	Set the metadata of a data object from the information of another data object.
static void	DataUtils.setDataMetaData(Data data, Sample sample)	Set the metadata of a data object from the information of a Sample object from a Design.

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

Modifier and Type	Method	Description
static void	DataUtils.setDataMetadata(Data data, Collection<Data> dataSourceOfMetadata)	Set the metadata of a data object from the information of another data object.

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

Classes in fr.ens.biologie.genomique.eoulsan.core.workflow that implement Data

Modifier and Type	Class	Description
class	DataList	This class define a data list.
class	UnmodifiableData	This class define an unmodifiable data

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

Modifier and Type	Method	Description
Data	DataList.addDataToList(String name)
Data	DataList.addDataToList(String name, int part)
Data	UnmodifiableData.addDataToList(String name)
Data	UnmodifiableData.addDataToList(String name, int part)
Data	TaskContextImpl.getInputData(InputPort port)	Get raw access to input data stored in the object.
Data	TaskContextImpl.getInputData(DataFormat format)
Data	TaskContextImpl.getInputData(String portName)
Data	TaskContextImpl.getOutputData(DataFormat format, Data origin)
Data	TaskContextImpl.getOutputData(DataFormat format, String dataName)
Data	TaskContextImpl.getOutputData(DataFormat format, String dataName, int part)
Data	TaskContextImpl.getOutputData(String portName, Data origin)
Data	TaskContextImpl.getOutputData(String portName, String dataName)
Data	TaskContextImpl.getOutputData(String portName, String dataName, int part)

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

Modifier and Type	Method	Description
List<Data>	DataList.getListElements()
List<Data>	UnmodifiableData.getListElements()

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

Modifier and Type	Method	Description
static List<DataFile>	WorkflowDataUtils.getDataFiles(Data data)	Get the list of the DataFile objects in a Data object.
Data	TaskContextImpl.getOutputData(DataFormat format, Data origin)
Data	TaskContextImpl.getOutputData(String portName, Data origin)
boolean	DataMetadataStorage.loadMetadata(Data data)	Set the metadata of a data from the metadata storage.
boolean	DataMetadataStorage.loadMetadata(Data data, List<DataFile> files)	Set the metadata of a data from the metadata storage.
void	DataMetadataStorage.saveMetaData(Data data)	Save metadata of a Data object.
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
static void	WorkflowDataUtils.setDataFiles(Data data, List<DataFile> dataFiles)	Change the DataFiles in a Data object
static void	WorkflowDataUtils.setDataMetadata(Data data, Data dataSourceOfMetadata)	Set the metadata of a data object from the information of another data object.
static void	WorkflowDataUtils.setDataMetadata(Data data, Collection<Data> dataSourceOfMetadata)	Set the metadata of a data object from the information of another data object.
static void	WorkflowDataUtils.setDataMetaData(Data data, Sample sample)	Set the metadata of a data object from the information of a Sample object from a Design.

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

Modifier and Type	Method	Description
static void	WorkflowDataUtils.setDataMetadata(Data data, Collection<Data> dataSourceOfMetadata)	Set the metadata of a data object from the information of another data object.

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

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

Modifier and Type	Method	Description
Data	Data.addDataToList(String name)	Add a data to the list of data.
Data	Data.addDataToList(String name, int part)	Add a data to the list of data.

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

Modifier and Type	Method	Description
List<Data>	Data.getListElements()	Get the the list of data.

Uses of Data in fr.ens.biologie.genomique.eoulsan.modules

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

Modifier and Type	Method	Description
protected String	MergerModule.getMapKey(Data data)	Define the key to use for replicate merging.
protected String	TechnicalReplicateMergerModule.getMapKey(Data data)

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

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

Modifier and Type	Method	Description
void	Normalization.run(TaskContext context, Data data)	Run normalisation step
protected void	Normalization.runRExecutor(TaskContext context, Data data)	Execute Rnw script.

Uses of Data in fr.ens.biologie.genomique.eoulsan.modules.multiqc

Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc with parameters of type Data

Modifier and Type	Method	Description
void	ExpressionInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)
void	FastQCInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)
void	FeatureCountsInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)
void	InputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)	Preprocess data.
void	MapperInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)