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

Packages that use Sample

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.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload	This package contain classes related to upload data to HDFS and Cloud.

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

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

Modifier and Type	Method	Description
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.

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

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

Modifier and Type	Method	Description
Sample	StepOutputDataFile.getSample()	Get the sample that produced the file.

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

Modifier and Type	Method	Description
static int	StepOutputDataFile.dataFileCount(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample, boolean existingFiles)	Get the count of files that exists for a step, a format and sample (case of multi-files data).
static String	StepOutputDataFile.newStandardFilename(Step step, String portName, DataFormat format, Sample sample, int fileIndex, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create a standard filename.
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.

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

Constructor	Description
StepOutputDataFile(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample)	Constructor.
StepOutputDataFile(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample, int fileIndex)	Constructor.

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

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

Modifier and Type	Method	Description
String	DataFormatRegistry.getSampleMetadataKeyForDataFormat(Sample sample, DataFormat dataformat)	Get the field name in a Sample object that correspond to a dataformat.

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

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

Modifier and Type	Method	Description
Sample	Design.getSample(String sampleId)	Get the name of a sample.
Sample	ExperimentSample.getSample()	Get the experiment sample name.
Sample	ExperimentSampleImpl.getSample()

Methods in fr.ens.biologie.genomique.eoulsan.design that return types with arguments of type Sample

Modifier and Type	Method	Description
List<Sample>	Design.getSamples()	Get the list of the samples.
List<Sample>	Experiment.getSamples()	Get the samples of the experiment.
List<Sample>	ExperimentImpl.getSamples()
List<Sample>	UnmodifiableExperiment.getSamples()

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

Modifier and Type	Method	Description
ExperimentSample	Experiment.addSample(Sample sample)	Add a sample.
ExperimentSample	ExperimentImpl.addSample(Sample sample)
ExperimentSample	UnmodifiableExperiment.addSample(Sample sample)
boolean	Experiment.containsSample(Sample sample)	Test if the experiment contains a sample.
boolean	ExperimentImpl.containsSample(Sample sample)
boolean	UnmodifiableExperiment.containsSample(Sample sample)
static String	DesignUtils.getCondition(Experiment experiment, Sample sample)	Get the Condition metadata value for an experimentSample.
ExperimentSample	Experiment.getExperimentSample(Sample sample)	Get the experiment sample related to the sample.
ExperimentSample	ExperimentImpl.getExperimentSample(Sample sample)
ExperimentSample	UnmodifiableExperiment.getExperimentSample(Sample sample)
List<Experiment>	Design.getExperimentsUsingASample(Sample sampleId)	Get all the experiments related to a sample.
static String	DesignUtils.getMetadata(Experiment experiment, Sample sample, String key)	Get a metadata value for an experiment and a sample.
static String	DesignUtils.getReference(Experiment experiment, Sample sample)	Get the reference of a sample.
static String	DesignUtils.getRepTechGroup(Experiment experiment, Sample sample)	Get the RepTechGroup metadata value for an experimentSample.
void	Experiment.removeSample(Sample sample)	Remove the sample.
void	ExperimentImpl.removeSample(Sample sample)
void	UnmodifiableExperiment.removeSample(Sample sample)

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

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.diffana with type arguments of type Sample

Modifier and Type	Method	Description
protected StringBuilder	Normalization.generateRnwpreamble(List<Sample> experimentSamplesList, String title, String filePrefix)	Write Rnw preamble.

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

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

Modifier and Type	Method	Description
protected DataFile	HadoopUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected DataFile	LocalUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
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