Uses of Interface
fr.ens.biologie.genomique.eoulsan.design.Design

Packages that use Design

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.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	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.

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

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

Modifier and Type	Method	Description
Design	Workflow.getDesign()	Get the design used by the workflow.

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

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

Modifier and Type	Method	Description
Design	AbstractWorkflow.getDesign()

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

Constructor	Description
AbstractWorkflow(ExecutorArguments executionArguments, Design design)	Protected constructor.
CommandWorkflow(ExecutorArguments executionArguments, CommandWorkflowModel workflowCommand, List<Module> firstSteps, List<Module> endSteps, Design design)	Public constructor.

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

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

Modifier and Type	Method	Description
String	DataFormatRegistry.getDesignMetadataKeyForDataFormat(Design design, DataFormat dataformat)	Get the field name in a Design object that correspond to a dataformat.

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

Methods in fr.ens.biologie.genomique.eoulsan.design that return Design

Modifier and Type	Method	Description
static Design	DesignFactory.createEmptyDesign()	Create a design without targets.
Design	DesignBuilder.getDesign(boolean pairedEndMode)	Create design object.
Design	Experiment.getDesign()	Get the design related to the experiment.
Design	ExperimentImpl.getDesign()
Design	Sample.getDesign()	Get the design related to the sample.
Design	UnmodifiableExperiment.getDesign()
static Design	DesignUtils.readAndCheckDesign(InputStream is)	Read and Check design
static Design	DesignFactory.unmodifiableDesign(Design design)	Create an unmodifiable wrapper around an existing design.

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

Modifier and Type	Method	Description
static boolean	DesignUtils.checkAnnotations(Design design)	Check if there is more than one annotation in the design
static boolean	DesignUtils.checkGenomes(Design design)	Check if there is more than one genome in the design
static boolean	DesignUtils.checkSamples(Design design)	Check if there are duplicate samples in the design.
static List<String>	DesignUtils.getAllSamplesMetadataKeys(Design design)	Get all the sample metadata keys of the samples of a design.
static void	DesignUtils.obfuscate(Design design, boolean removeReplicateInformation)	Remove optional description fields and obfuscate condition field.
static void	DesignUtils.replaceLocalPathBySymlinks(Design design, DataFile symlinksDir)	Replace the local paths in the design by paths to symbolic links in a directory.
static void	DesignUtils.showDesign(Design design)	Show a design
static Design	DesignFactory.unmodifiableDesign(Design design)	Create an unmodifiable wrapper around an existing design.

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

Methods in fr.ens.biologie.genomique.eoulsan.design.io that return Design

Modifier and Type	Method	Description
Design	DefaultDesignReader.read()
Design	DesignReader.read()	Read the design.
Design	Eoulsan1DesignReader.read()
Design	Eoulsan2DesignReader.read()

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

Modifier and Type	Method	Description
void	DesignWriter.write(Design design)
void	Eoulsan1DesignWriter.write(Design design)
void	Eoulsan2DesignWriter.write(Design design)

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

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

Constructor	Description
DesignModule(Design design, CheckerModule checkeModule)	Constructor.

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

Fields in fr.ens.biologie.genomique.eoulsan.modules.diffana declared as Design

Modifier and Type	Field	Description
protected Design	Normalization.design

Constructors in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type Design

Constructor	Description
DESeq2(RExecutor executor, String stepId, Design design, Experiment experiment, Map<String,File> sampleFiles, boolean normFig, boolean diffanaFig, boolean normDiffana, boolean diffana, DESeq2.SizeFactorsType sizeFactorsType, DESeq2.FitType fitType, DESeq2.StatisticTest statisticTest, boolean saveRScripts)	Public constructor.
DiffAna(RExecutor executor, Design design, DiffAna.DispersionMethod dispEstMethod, DiffAna.DispersionSharingMode dispEstSharingMode, DiffAna.DispersionFitType dispEstFitType)	Public constructor.
Normalization(RExecutor executor, Design design)	Public constructor.