Index (Eoulsan 2.6.1 API)

A B C D E F G H I J K L M N O P R S T U V W X Z
All Classes All Packages

A

ABORTED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
ABOUT_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: About string, plain text version.
AbstractAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an abstract Action
AbstractAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
AbstractBAM2SAMModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting BAM files into SAM.
AbstractBAM2SAMModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
AbstractClusterTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class is a scheduler for task running on a cluster.
AbstractClusterTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
AbstractClusterTaskScheduler.ProcessThreadOutput - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class allow to fetch standard output or standard error.
AbstractConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define an InputStream that concatenate InputStream.
AbstractConcatInputStream() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
AbstractEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan: This class define an abstract EoulsanRuntime.
AbstractEoulsanRuntime(Settings) - Constructor for class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
AbstractEoulsanRuntime.EoulsanExecMode - Enum in fr.ens.biologie.genomique.eoulsan: This Enum define the Eoulsan execution mode.
AbstractExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define an abstract executor interpreter that contains the default implementation of the execute() method that use a ProcessBuilder.
AbstractExecutorInterpreter() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
AbstractExpressionModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This abstract class define and parse arguments for the expression module.
AbstractExpressionModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
AbstractFilterAndMapReadsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for read filtering, mapping and alignments filtering.
AbstractFilterAndMapReadsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
AbstractInfoAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an abstract action that show the some Eoulsan configuration and available modules
AbstractInfoAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
AbstractMetadata - Class in fr.ens.biologie.genomique.eoulsan.design: This abstract class defines methods for metadata.
AbstractMetadata() - Constructor for class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
AbstractModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define an abstract Module.
AbstractModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
AbstractParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an abstract class for tool element parameters.
AbstractParameterToolElement(Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement: Protected constructor.
AbstractPort - Class in fr.ens.biologie.genomique.eoulsan.core: Abstract class that define a port.
AbstractPorts<E extends Port> - Class in fr.ens.biologie.genomique.eoulsan.core: This class define a basic implementation of a Ports class.
AbstractPorts(Set<E>) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts: Constructor.
AbstractReadsFilterModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for read filtering.
AbstractReadsFilterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
AbstractReadsMapperModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for read mapping.
AbstractReadsMapperModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
AbstractRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define an abstract requirement.
AbstractRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
AbstractResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util: This class define an abstract resource loader.
AbstractResourceLoader() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
AbstractRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define an abstract RExecutor.
AbstractRExecutor(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Constructor.
AbstractSAM2BAMModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting SAM files into BAM.
AbstractSAM2BAMModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
AbstractSAM2FASTQModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting SAM files into BAM.
AbstractSAM2FASTQModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
AbstractSAMFilterModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for alignments filtering.
AbstractSAMFilterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
AbstractSplice2BEDModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting SAM files into BED.
AbstractSplice2BEDModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
AbstractStep - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a step of the workflow.
AbstractTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class define an abstract task scheduler.
AbstractTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Protected constructor.
AbstractToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an abstract tool element.
AbstractToolElement(Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Instantiates a new abstract tool element.
AbstractToolElement(Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Instantiates a new abstract tool element.
AbstractWorkflow - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a Workflow.
AbstractWorkflow(ExecutorArguments, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Protected constructor.
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
accept(Class<?>, boolean) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Check that annotation of a class is compatible with the Eoulsan mode (local or Hadoop).
accept(Path) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter
accept(Path) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
action(List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Execute action.
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
Action - Interface in fr.ens.biologie.genomique.eoulsan.actions: This interface define an action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction: Name of this action.
ActionService - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define a service to retrieve an Action
ActionService() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ActionService: Private constructor.
add(EmergencyStopTask) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks: Add an emergency task.
add(String, Object) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Store some data.
addBcl2FastqSamplesheetProject(SampleSheet, String, File) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add all the sample from a Bclfastq samplesheet.
addBcl2FastqSamplesheetProject(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add all the samples from a Bcl2Fastq samplesheet.
addConstant(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Add a constant.
addConstant(String, String, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Add a constant.
addConstants(ExecutorArguments) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Add job arguments information to constants.
addDataToList(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
addDataToList(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
addDataToList(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Add a data to the list of data.
addDataToList(String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
addDataToList(String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
addDataToList(String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Add a data to the list of data.
addDependency(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Add a dependency for this step.
addDependency(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Add a dependency.
addDependency(StepInputPort, StepOutputPort) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Add a dependency for this step.
addExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Add an experiment.
addFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add a file to the design builder
addFile(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.JarRepack: Add a file to the jar file.
addFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add a filename to the design builder
addFiles(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add filenames to the design builder
addFiles(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add filenames to the design builder
addHadoopJobEmergencyStopTask(ClusterTaskScheduler, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask: Add a cluster Job to the EmergencyStopTasks.
addHadoopJobEmergencyStopTask(Job) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask: Add an Hadoop Job to the EmergencyStopTasks.
addHandler(Handler) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler: Add an Handler.
ADDITIONAL_ANNOTATION_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
ADDITIONAL_ANNOTATION_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Additional annotation data format.
AdditionalAnnotationDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a additional annotation protocol.
AdditionalAnnotationDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
additionalScriptEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler: Define additional environment variable for bpipe scripts.
additionalScriptEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler
addObserver(StepObserver) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Add a listener.
addPort(String, boolean, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, boolean, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, boolean, DataFormat, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, boolean, DataFormat, CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, boolean, DataFormat, EnumSet<CompressionType>) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, boolean, DataFormat, EnumSet<CompressionType>, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, DataFormat, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat, CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, DataFormat, EnumSet<CompressionType>) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat, EnumSet<CompressionType>, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addResource(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Add a resource.
addResourcePath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Add a resource path.
addResourcePaths(Collection<String>) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Add a resource paths.
addResult(TaskContextImpl, TaskResultImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Add a task result to the step result.
addSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Add a sample.
addSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
addSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
addSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Add a sample.
afterExecute(Runnable, Throwable) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
afterExecuteTask(TaskContextImpl, TaskResultImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Set the state of the context after executing a task.
ALIGNMENTS_REJECTED_BY_FILTERS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
ALIGNMENTS_WITH_INVALID_SAM_FORMAT - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
ALIGNMENTS_WITH_MORE_ONE_HIT_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
allPortsRequiredInWorkingDirectory(InputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Set all ports of an existing input ports to be required in working directory.
AMAZON - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
AMBIGUOUS_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
ANNOTATED_EXPRESSION_RESULTS_ODS - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: ODS Annotated expression results data format.
ANNOTATED_EXPRESSION_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: TSV Annotated expression results data format.
ANNOTATED_EXPRESSION_RESULTS_XLSX - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: XLSX Annotated expression results data format.
ANNOTATION_GFF - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: GFF data format.
ANNOTATION_GTF - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: GTF data format.
AnnotationDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a annotation protocol.
AnnotationDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
ANY_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock: The magic version number that allows any mutation to always succeed regardless of actual version number.
ApacheCommonCompressionCodecs - Class in fr.ens.biologie.genomique.eoulsan.io: This class allow to create input and output stream for compression codecs of the Apache Common Compression library.
ApacheCommonCompressionCodecs() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs
APP_BUILD_COMMIT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The built commit of the application.
APP_BUILD_DATE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The build date of the application.
APP_BUILD_HOST - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The built host of the application.
APP_BUILD_NUMBER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The built number of the application.
APP_BUILD_YEAR - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The build year of the application.
APP_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The name of the application.
APP_NAME_LOWER_CASE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The name of the application.
APP_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The version of the application.
APP_VERSION_STRING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The version of the application.
ASAP - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
ASCII_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: Ascii charset.
ASCII_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: Ascii file encoding.
ASCII_LETTER_OR_DIGIT - Static variable in class fr.ens.biologie.genomique.eoulsan.core.Naming
AVAILABLE_BINARY_ARCH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Platforms where the application is available.
AVAILABLE_BINARY_ARCH_ALIAS - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Platforms alias.
AVAILABLE_PROCESSORS_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Available processor constant name.
AWS_S3_ACCESS_KEY_ID_PARAM_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
AWS_S3_SECRET_ACCESS_KEY_PARAM_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop

B

badParameterValue(StepConfigurationContext, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for bad parameter value.
badParameterValue(String, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for bad parameter value.
BAM2SAMLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for converting BAM files into SAM.
BAM2SAMLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.BAM2SAMLocalModule
BAMMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for SAM files.
BAMMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
BAMSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for BAM files.
BAMSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
base64ForIcon(String, Class) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher: This method replace the HTMLReportArchive.base64ForIcon() method.
BasicUI - Class in fr.ens.biologie.genomique.eoulsan.ui: This class define a basic UI for Eoulsan.
BasicUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
BedToolsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This class uses tools from the BEDTools suite.
BedToolsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
beforeExecute(Thread, Runnable) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
beforeExecuteTask(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Set the state of the context before executing a task.
BIGBED - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BigBed format.
BIGWIG - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BigWig format.
BLIND - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
BooleanParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a boolean tool element parameter.
BooleanParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement: Instantiates a new boolean tool parameter.
BooleanParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement: Instantiates a new boolean tool parameter.
BOWTIE_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Bowtie index data format.
BOWTIE2_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Bowtie2 index data format.
BpipeTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.
BpipeTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
BufferedHandler - Class in fr.ens.biologie.genomique.eoulsan: This class define a buffered handler.
BufferedHandler() - Constructor for class fr.ens.biologie.genomique.eoulsan.BufferedHandler
BUILD_CONTRAST_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
BUILD_DATE_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Build date constant name.
BUILD_NUMBER_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Build number constant name.
BundledScriptBpipeTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define an abstract scheduler that use a bpipe script bundled in Eoulsan distribution.
BundledScriptBpipeTaskScheduler(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler: Constructor.
BWA_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BWA index data format.
BYPASS_PLATFORM_CHECKING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Bypass platform checking.
ByteCountInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This filter class allow to count the number of bytes read by an inputStream.
ByteCountInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream: Public constructor
ByteCountInputStream(InputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream: Public constructor
ByteCountOutputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define a filter that count the number of written bytes by an InputStream.
ByteCountOutputStream(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream: Public constructor.
ByteCountOutputStream(OutputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream: Public constructor.

C

CALL_METHOD - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: The Constant CALL_METHOD.
canDelete() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the delete() method is available with this protocol.
canDelete() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canDelete() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canList() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the list() method is available with this protocol.
canList() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canList() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canMkdir() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the mkdir() and mkdirs() methods are available with this protocol.
canMkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canMkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canonicalize() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
canRead() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if source is readable with this protocol.
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
canRename() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the renameTo() method is available with this protocol.
canRename() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canRename() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canSymlink() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the symlink() method is available with this protocol.
canSymlink() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canWrite() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if source is writable with this protocol.
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
changeFileExtension(File, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Change the extendsion of a file
check(Data, CheckStore) - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Launch the check.
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
CHECK_COMPLETION_TIME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
checkAnnotations(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Check if there is more than one annotation in the design
checkDirectories() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Check directories needed by the workflow.
Checker - Interface in fr.ens.biologie.genomique.eoulsan.checkers: This interface define a checker.
CHECKER_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
CheckerModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class is a module that launch checkers.
CheckerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule: Public constructor.
checkExistingDirectoryFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a directory exists
checkExistingFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
checkExistingStandardFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
checkExistingStandardFileOrDirectory(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
checkExperimentDesign(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker: Check experiment design.
checkForPartDuplicates() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
checkForPartDuplicates() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
checkGenomes(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Check if there is more than one genome in the design
checkOutputSpecs(JobContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
checkRepTechGroupCoherence(List<String>, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Check if there is a problem in the repTechGroup coherence.
checkSamples(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Check if there are duplicate samples in the design.
CheckStore - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a storage where some results of the checker can be save for later reuse by other checkers.
CheetahInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: This class create a Cheetah interpreter, it can build a command line tool from command tag from Galaxy tool XML file.
CheetahInterpreter(String, Map<String, String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: Instantiates a new tool Cheetah script interpreter.
ChIPSeqDataFormats - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq: This class contains the definition of some DataFormats for ChiP-Seq.
ClassLoaderObjectInputStream - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to use ObjectInputStream with a ClassLoader that is not the default bootstrap ClassLoader.
ClassLoaderObjectInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream: Constructor, use the thread ClassLoader to load classes of objects to instantiate.
ClassLoaderObjectInputStream(ClassLoader, InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream: Constructor.
ClassPathResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to define a resource loader for resources in the class path.
ClassPathResourceLoader(Class<S>, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader: Constructor.
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
cleanupJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
cleanupJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Cleanup after a job.
clear() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Clear the content of the CheckStore.
clear() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Clear the entries of the object.
CLIMergingAnySAMOutputFormat<K> - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
CLIMergingAnySAMOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
close() - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
close() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.util.JarRepack: Close the repackaged file.
close(JobContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter: Close the SAM file header.
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
closeConnection() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Close the connection.
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
cloudInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with cloud configuration informations.
CLUSTER - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
CLUSTER_TASK - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
ClusterCombinedTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class defined a combined task scheduler for cluster mode.
ClusterCombinedTaskScheduler(int, ClusterTaskScheduler) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler: Constructor.
ClusterExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define the cluster exec Action.
ClusterExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
clusterInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with cluster configuration informations.
ClusterJobEmergencyStopTask - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define an EmergencyStopTask for cluster Jobs.
ClusterJobEmergencyStopTask(ClusterTaskScheduler, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask: Public constructor.
ClusterTaskAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define a action to launch a task on a cluster.
ClusterTaskAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
ClusterTaskScheduler - Interface in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This interface define a cluster task scheduler.
ClusterTaskScheduler.StatusResult - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a Status result return by the statusJob() method of the interface.
ClusterTaskScheduler.StatusValue - Enum in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This enum define the values of the status of a job.
ClusterTaskSchedulerService - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a service to retrieve a ClusterTaskScheduler.
CollectionUtils - Class in fr.ens.biologie.genomique.eoulsan.util: This class define an utility class that contains useful methods for collections.
CombinedTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class defined a combined task scheduler that use several context schedulers according to the parallelization mode of the step.
CombinedTaskScheduler(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler: Constructor.
COMMA - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: SPLITTER.
commandLineInfo(Main) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with command line informations.
CommandStep - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a step based on a Command object (workflow file).
CommandStep(AbstractWorkflow, Module) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow, Module, Set<Parameter>) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow, Step.StepType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.
CommandStep(AbstractWorkflow, DataFormat) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a Generator Workflow step.
CommandStep(AbstractWorkflow, String, String, String, Set<Parameter>, boolean, Step.DiscardOutput, int, int, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step.
CommandStep(AbstractWorkflow, String, String, String, Set<Parameter>, boolean, Step.DiscardOutput, int, int, String, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step.
CommandWorkflow - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a workflow based on a Command object (workflow file).
CommandWorkflow(ExecutorArguments, CommandWorkflowModel, List<Module>, List<Module>, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow: Public constructor.
CommandWorkflowModel - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define the workflow model object of Eoulsan.
CommandWorkflowModel() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Public constructor.
CommandWorkflowModel(boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Public constructor.
CommandWorkflowParser - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class allow parse the workflow file.
CommandWorkflowParser(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Public constructor.
CommandWorkflowParser(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Public constructor.
CommandWorkflowParser(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Public constructor.
CommandWorkflowParser.StepOutputPort - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
COMMENT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Common - Class in fr.ens.biologie.genomique.eoulsan: This class define common constants.
CommonHadoop - Class in fr.ens.biologie.genomique.eoulsan: This class define common constants and other methods specific to Hadoop mode.
CommonHadoop() - Constructor for class fr.ens.biologie.genomique.eoulsan.CommonHadoop
compareTo(Parameter) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
compareTo(StepOutputDataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
compareTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
compareTo(DataFileDataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
compareTo(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
COMPARISONS_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
compatibilityFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the filename using Eoulsan 1.x naming.
COMPLETE - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
CompressedSplitFastqLineReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
CompressedSplitFastqLineReader(SplitCompressionInputStream, Configuration, byte[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
computeMD5Sum(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
concat(List<Path>, Path, boolean, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy all files in a directory to one output file (merge).
concat(List<Path>, Path, boolean, boolean, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy all files in a directory to one output file (merge).
concat(List<Path>, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy all files in a directory to one output file (merge).
CONDITION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
CONDITION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
ConditionalToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a conditional tool element.
ConditionalToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: Instantiates a new tool conditional element.
conf - Variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
configure() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Set the parameters of the step to configure the module.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Set IDR parameters to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
configure(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
configure(Settings) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Configure the scheduler.
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Set the parameters of the checker to configure the checker.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Parse tool file to extract useful data to run tool.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Configure the requirement.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger: Configure the merger.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter: Configure the splitter.
configureChecker(DataFormat, Set<Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule: This method allow to configure a checker from the configure method of other steps, that's why this method is static.
CONFIGURED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
configureLog4J(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.OtherLogConfigurator: Configure Log4J.
configureSampling(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
CONTACT_EMAIL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Project email.
contains(E) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
contains(E) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Test if a port exists by testing if port name exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Test if a data exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
contains(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Test if a port exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
contains(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Test if the key is in md.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsAdditionalAnnotationFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the additional annotation file field exists.
containsAdditionalAnnotationFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsBuildContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the buildContrast option exists.
containsBuildContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsComment() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the comment field exists.
containsComparisons() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the comparisons option exists.
containsComparisons() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Test if the condition field exists.
containsCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
containsCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the condition field exists.
containsCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the contrast option exists.
containsContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsContrastFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the contrastFile option exists.
containsContrastFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsDate() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the date field exists.
containsDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the description field exists.
containsDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the designFile option exists.
containsDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Test if the experiment exists.
containsExperimentName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
containsFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the fastq format field exists.
containsGenomeFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the genomeFile field exists.
containsGenomeFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsGffFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the gffFile field exists.
containsGffFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsGtfFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the gtfFile field exists.
containsGtfFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsKey(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Test if a key exists.
containsModel() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the model option exists.
containsModel() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsOperator() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the operator field exists.
containsParameter(Set<Parameter>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: test if a set of parameters contains a parameter.
containsReads() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the reads field exists.
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the reference option exists.
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Test if the reference field exists.
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the reference field exists.
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsReferenceField(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Test if an experiment contains reference fields
containsRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Test if the RepTechGroup field exists.
containsRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
containsRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the RepTechGroup field exists.
containsRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Test if the experiment contains a sample.
containsSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
containsSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
containsSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Test if the sample exists.
containsSampleName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
containsSerialNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the serial number field exists.
containsSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the skip option exists.
containsSkip() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the UUID field exists.
ContextUtil - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli: Utility methods to allow applications to deal with inconsistencies between MapReduce Context Objects API between hadoop-0.20 and later versions.
ContextUtil() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
ContextUtils - Class in fr.ens.biologie.genomique.eoulsan.core: This class define utility methods on Context.
CONTRAST_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
CONTRAST_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
convert() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter
convert(Configuration, DataFile, DataFile, DataFile, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq: Create the job to convert FASTQ files in a TFQ file.
convert(Configuration, Path, Path, Path, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq: Create the job to convert FASTQ files in a TFQ file.
copy(InputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Convenient method to create a defensive copy of an InputPorts object.
copy(OutputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Convenient method to create a defensive copy of an OutputPorts object.
copy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles: Copy a file, if input data is compressed, data will be uncompressed and if output require to be compressed output will be compressed.
copy(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule: Copy files to destinations.
copy(Configuration, String, String, Path, boolean, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp: Deprecated.
copy(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy file from a path to another path.
copy(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy file from a path to another path.
copyAndCompressInputStreamToPath(InputStream, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy bytes from an InputStream to a path.
copyAndCompressLocalFileToPath(File, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
copyAndCompressLocalFileToPath(File, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
CopyDesignAndWorkflowFilesToOutputModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: This module copy design and workflow file to output directory.
CopyDesignAndWorkflowFilesToOutputModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
copyFromPathToLocalFile(Path, File, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a file from a path to a local file
copyFromPathToLocalFile(Path, File, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a file from a path to a local file.
CopyInputDataModule - Class in fr.ens.biologie.genomique.eoulsan.modules: Copy input files of a format in another location or in different compression format.
CopyInputDataModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
copyInputStreamToPath(InputStream, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy bytes from an InputStream to a path.
copyLocalFileToPath(File, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
copyLocalFileToPath(File, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
copyMerge(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Merge several file of a directory into one file.
copyMerge(Path, Path, boolean, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Merge several file of a directory into one file.
copyMerge(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Merge several file of a directory into one file.
CopyOutputDataModule - Class in fr.ens.biologie.genomique.eoulsan.modules: Copy output files of a step with a specified format to the output directory.
CopyOutputDataModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
copyTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Copy this DataFile in a other DataFile.
correctSAMRecordForMerging(SAMRecord, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
count(ExpressionCounter, DataFile, ReporterIncrementer, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils: Count the the features.
countDataFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
countDataFormat(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Count the number of occurrences of a format in the port.
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Group for hadoop counters.
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
COUNTER_GROUP_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
COUNTER_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
counterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get the name of the counter.
counterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters: Get the name of the counter.
Counters - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define the counters names used in this package.
Counters() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
CounterSequenceFile - Interface in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This interface extends SequenceFile to add a getCount() method that allow to get the count of the read entries.
CountSplicedReadsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc: This step computes how many spliced alignments there are in a SAM file.
CountSplicedReadsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
cpuInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with CPU informations.
create() - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Create the ports.
create() - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Create the ports.
create() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create an OutputStream for the DataFile.
create() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
createBZip2InputStream(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs: Create a bzip2 input stream.
createBZip2InputStream(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs: Create a bzip2 input stream.
createBZip2OutputStream(OutputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs: Create a bzip2 output stream.
createBZip2OutputStream(OutputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs: Create a bzip2 output stream.
createCommand(File, boolean, String, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Create R command.
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
createCommandLine(String) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter: Create the command line for the the argument of the interpreter.
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
createConfiguration() - Static method in class fr.ens.biologie.genomique.eoulsan.CommonHadoop: Create a new Configuration object from Eoulsan runtime settings.
createConfiguration(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.CommonHadoop: Create a new Configuration object from settings.
CREATED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
CreateDesignAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action to create design file.
CreateDesignAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
createEmptyDesign() - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignFactory: Create a design without targets.
createEoulsanDataDirectoryIfRequired() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Create an "eoulsan-data" directory if mapper indexes or genome description storage has not been defined.
createFileInTempDir(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a file in the temporary directory.
createGenomeDescription(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator: Create genome description object from the storage if already exists or compute it from the genome.
createGenomeDescriptionFromAnnotation(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator: Create genome description object from the storage if already exists or compute it from the genome.
CreateHadoopJarAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action to create hadoop jar file.
CreateHadoopJarAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
createIndex(DataFile, GenomeDescription, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer: Create an archived genome index.
createInputStream(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create an input stream from a path.
createLogFileAndFlushLog(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create a new log file and flush log.
createLogFiles(URI, URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create the log file for Eoulsan and additional log file for dependencies that use their own logging system.
createOtherLog(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create the additional log file for dependencies that use their own logging system.
createOutputStream(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create an output stream from a path.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
createSAMSequenceDictionaryFromSAMHeader(List<String>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils: Create a SAMSequenceDictionary from the SAM header in a list of String.
createShutdownHookThread() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Create a shutdown hook thread.
createSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
createSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Create the process that will execute the R Script.
createStepResult(TaskContextImpl, Throwable) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Create a step result for an exception.
createStepResult(TaskContextImpl, Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Create a step result for an exception.
createTaskResult() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object for a successful result.
createTaskResult() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTaskResult(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object.
createTaskResult(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTaskResult(Throwable) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object.
createTaskResult(Throwable) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTaskResult(Throwable, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object.
createTaskResult(Throwable, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTempDir() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a new temporary directory.
createTempDir(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a new temporary directory.
createTempFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a new temporary file.
createTempPath(Path, String, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create a new temporary path.
CUTADAPT_ADAPTER_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Cutadapt adapters format.

D

Data - Interface in fr.ens.biologie.genomique.eoulsan.data: This interface define data used by ports.
DATA_FORMAT_PATH_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
dataEquals(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if two files are related to the same data.
dataEquals(File, File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if two files are related to the same data.
dataEquals(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if two filenames are related to the same data.
DataFile - Class in fr.ens.biologie.genomique.eoulsan.data: This class define a DataFile.
DataFile(DataFile, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(URI) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(Path) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(Path, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
dataFileCount(StepOutputPort, Sample, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the count of files that exists for a step, a format and sample (case of multi-files data).
DataFileDataPath - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a bridge between Kenetre DataPath objects and Eoulsan DataFile objects.
DataFileDataPath(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath: Constructor.
DataFileDataPath(DataPath, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath: Constructor.
DataFileDataPath(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath: Constructor.
DataFileDistCp - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This class allow to copy and transform data in a distributed manner.
DataFileDistCp(Configuration, Path) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp: Public constructor.
DataFileDistCp.DistCpMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This inner class define the mapper class for DataSourceDistCp map-reduce job.
DataFileGenomeDescStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a storage for genome description files using DataFile API.
DataFileGenomeDescStorage(DataPath, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage: Protected constructor.
DataFileGenomeIndexStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a storage for genome indexes using DataFile API.
DataFileGenomeIndexStorage(DataPath, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Constructor.
DataFileGenomeMapperIndexer - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a genome mapper indexer.
DataFileGenomeMapperIndexer(MapperInstance, String, Map<String, String>, int, GenomeIndexStorage, File, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer: Public constructor.
DataFileMetadata - Interface in fr.ens.biologie.genomique.eoulsan.data: This class define source metadata
DataFiles - Class in fr.ens.biologie.genomique.eoulsan.data: This class contains utility methods on DataFile objects.
DataFiles() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFiles
DataFileStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a storage using DataFile API.
DataFileStorage(String, List<String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage: Constructor.
DataFormat - Interface in fr.ens.biologie.genomique.eoulsan.data: This interface define a DataFormat.
DataFormatConverter - Class in fr.ens.biologie.genomique.eoulsan.data: This class allow to copy and transform data while copying.
DataFormatConverter(DataFile, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter: Constructor
DataFormatConverter(DataFile, DataFile, DataFormat, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter: Constructor
DataFormatConverter(DataFile, DataFile, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter: Constructor
DataFormatRegistry - Class in fr.ens.biologie.genomique.eoulsan.data: this class register DataFormat to allow get the DataFormat of a file from its filename.
DataFormats - Class in fr.ens.biologie.genomique.eoulsan.data: This class contains the definition of some DataFormats.
DataFormats() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormats
DATAFORMATS_TO_DOWNLOAD_SETTING - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule: Key in the settings to use to save the list of DataFormat of the files to download.
DataList - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a data list.
DataMetadata - Interface in fr.ens.biologie.genomique.eoulsan.data: This interface define metadata of data objects.
DataMetadataStorage - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a storage for data metadata of all files generated by the workflow.
DataProtocol - Interface in fr.ens.biologie.genomique.eoulsan.data.protocols: This interface define a protocol.
DataProtocolService - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a service to retrieve a DataProtocol.
DataToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: The Class ToolOutputsData.
DataToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement: Instantiates a new tool outputs data.
DataUtils - Class in fr.ens.biologie.genomique.eoulsan.core: This class define an utility on data object.
DATE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
deadEvent(DeadEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus
DEBUG - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Set the debug mode.
decompressInputStreamIsNeeded(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Decompress an inputStream if needed.
DeepToolsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This class uses tools from the DeepTools suite.
DeepToolsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
DEFAULT_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default charset.
DEFAULT_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default file encoding.
DEFAULT_LOCALE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default locale of the application.
DEFAULT_R_LANG - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
DEFAULT_SINGLE_INPUT_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Default single input port name.
DEFAULT_SINGLE_OUTPUT_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Default single output port name.
DefaultDesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class allow to read a design file whatever the underlying design format.
DefaultDesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor.
DefaultDesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor.
DefaultDesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor
DefaultDesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor
DefaultExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define the default executor interpreter.
DefaultExecutorInterpreter() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
DefineDataFormatToDownload - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.
DefineDataFormatToDownload() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
defineSampleSubDirName(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Get the sample sub directory.
delete() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Delete the DataFile.
delete(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Delete the DataFile.
delete(DataFile, boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Delete a file.
delete(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
delete(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
deleteOnExit(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
deleteOnExit(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Delete a file on the exit of the workflow.
DeprecatedDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a deprecated protocol.
DeprecatedDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol: Constructor.
DeprecatedDataProtocol(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol: Constructor.
deprecatedParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters.
deprecatedParameter(StepConfigurationContext, Parameter, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters.
deprecatedParameter(String, Parameter, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters.
description() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
DESCRIPTION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
DESeq2 - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class contains methods to run the differential analysis module DESeq2.
DESeq2(RExecutor, String, Design, Experiment, Map<String, File>, boolean, boolean, boolean, boolean, DESeq2.SizeFactorsType, DESeq2.FitType, DESeq2.StatisticTest, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2: Public constructor.
DESeq2.FitType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Enum for the fitType option in DESeq2 related to the dispersion estimation.
DESeq2.SizeFactorsType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.
DESeq2.StatisticTest - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysis
DESeq2DesignChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a Checker on the design for DESeq2 analyzes.
DESeq2DesignChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
DESeq2Module - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: Class to run the differential analysis with DEseq2
DESeq2Module() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
deserialize(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize the TaskContext object.
deserialize(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Deserialize the TaskResult object.
deserialize(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize the TaskContext object.
deserialize(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Deserialize the TaskResult object.
deserialize(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize the TaskContext object.
deserialize(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Deserialize the TaskResult object.
deserializeOutputData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize output data.
deserializeOutputData(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize output data.
deserializeOutputData(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize output data.
design - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Design - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the design.
DESIGN_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
DESIGN_FILE_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Design file path constant name.
DESIGN_FILE_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Design file version.
DESIGN_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
DesignBuilder - Class in fr.ens.biologie.genomique.eoulsan.design: This class allow to easily build Design object from files paths.
DesignBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Public constructor.
DesignBuilder(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Public constructor.
DesignFactory - Class in fr.ens.biologie.genomique.eoulsan.design: This class is a factory for experimental design.
DesignFormatFinderInputStream - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class allow to automatically detect the format of a design file.
DesignFormatFinderInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream: Public constructor.
DesignMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the design metadata.
DesignMetadataImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of the design metadata.
DesignModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a design module.
DesignModule(Design, CheckerModule) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.DesignModule: Constructor.
DesignReader - Interface in fr.ens.biologie.genomique.eoulsan.design.io: This interface define a DesignReader.
DesignUtils - Class in fr.ens.biologie.genomique.eoulsan.design: Utils methods for Design.
DesignWriter - Interface in fr.ens.biologie.genomique.eoulsan.design.io: This interface define a writer for designs.
DiffAna - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class create and launch a R script to compute differential analysis.
DiffAna(RExecutor, Design, DiffAna.DispersionMethod, DiffAna.DispersionSharingMode, DiffAna.DispersionFitType) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna: Public constructor.
DIFFANA_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Diffana results data format.
DiffAna.DispersionFitType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Dispersion estimation fitType enum for DESeq differential analysis
DiffAna.DispersionMethod - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Dispersion estimation method enum for DESeq differential analysis
DiffAna.DispersionSharingMode - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Dispersion estimation sharingMode enum for DESeq differential analysis
DiffAnaModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class define the module of differential analysis in local mode.
DiffAnaModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
DiffanaResultsAnnotationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class define a module that create annotated expression files in TSV, ODS or XLSX format.
DiffanaResultsAnnotationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
disConnect() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Destroy the connection to the Rserve server.
DISCUSSION_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Project discussion group.
diskFreeInfo(File) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Get information about the partition of a file.
DistCp - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: A Map-reduce program to recursively copy directories between different file-systems.
DistCp(Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
DistCp.DuplicationException - Exception in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: An exception class for duplicated source files.
DistCpMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
DistributedLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker: Distributed locking via ZooKeeper.
DistributedLock(ZooKeeper, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
DistributedLock(ZooKeeper, String, Iterable<ACL>) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock: Creates a distributed lock using the given zkClient to coordinate locking.
DistributedLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class implements a locker using Zookeeper based on Twiter's DistributedLock class.
DistributedLocker(String, int, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker: Public constructor.
DOCKER - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
DOCKER_IMAGE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
DockerExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define a Docker executor interpreter.
DockerExecutorInterpreter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter: Constructor.
dockerInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with Docker configuration informations.
DockerRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define a Docker requirement.
DockerRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
DockerRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define a Docker RExecutor.
DockerRExecutor(File, File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor: Constructor.
DONE - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
DUMMY_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Dummy format.
DummyGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class implements a dummy generator module that create an empty file.
DummyGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
DummyTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a Dummy cluster scheduler.
DummyTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler: Constructor.

E

elapsed(TimeUnit) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
ELIMINATED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
EmergencyStopTask - Interface in fr.ens.biologie.genomique.eoulsan.core.workflow: This interface define a task that will executed if the execution of the workflow fail.
EmergencyStopTasks - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a class where the emergency tasks are stored
EMPTY_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
EmptyFileQC - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: Empty file FastQC module.
EmptyFileQC(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC: Constructor.
EmptyToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an empty tool element.
EmptyToolElement() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement: Public constructor.
EmptyToolElement(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement: Public constructor.
EmptyToolElement(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement: Public constructor.
encodeAllowedCompressionsParameterValue(EnumSet<CompressionType>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule: Method to encode an EnumSet of the allowed compressions parameter in a string.
endWork(Ticket) - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.TicketScheduler: Inform the scheduler that the ticket job has been finished.
endWork(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
ENTRIES_READ - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
ENTRIES_WRITTEN - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
entrySet() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get an entry set of the metadata.
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
EOULSAN_CLASSPATH_JVM_ARG - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_MEMORY - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_PATH - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_SCRIPT - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_TOOLS_WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Eoulsan tools website URL.
Eoulsan1DesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class define a design reader for limma design files.
Eoulsan1DesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignWriter - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class implements a writer for limma design files.
Eoulsan1DesignWriter(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan1DesignWriter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan1DesignWriter(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan1DesignWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan2DesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class define a design reader for Eoulsan 2 design file.
Eoulsan2DesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignWriter - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class implements a writer for Eoulsan 2 design files.
Eoulsan2DesignWriter(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
Eoulsan2DesignWriter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
Eoulsan2DesignWriter(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
Eoulsan2DesignWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
EoulsanAnnotationUtils - Class in fr.ens.biologie.genomique.eoulsan.annotations: This class contains annotation utilities.
EoulsanDockerManager - Class in fr.ens.biologie.genomique.eoulsan.util: This class define a Docker manager configurated with Eoulsan settings.
EoulsanError - Error in fr.ens.biologie.genomique.eoulsan: A nestable Eoulsan error.
EoulsanError() - Constructor for error fr.ens.biologie.genomique.eoulsan.EoulsanError: Create a new EoulsanError.
EoulsanError(String) - Constructor for error fr.ens.biologie.genomique.eoulsan.EoulsanError: Create a new EoulsanError with a message.
EoulsanException - Exception in fr.ens.biologie.genomique.eoulsan: A nestable Eoulsan exception.
EoulsanException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException.
EoulsanException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException with a message.
EoulsanException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException with a message and a cause.
EoulsanException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException with a cause.
EoulsanITRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan: This class define a runtime exception for integration tests.
EoulsanITRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException.
EoulsanITRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException with a message.
EoulsanITRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException with a message and a cause.
EoulsanITRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException with a cause.
EoulsanLogger - Class in fr.ens.biologie.genomique.eoulsan: This class allow to change the logger name for all Eoulsan classes.
EoulsanLogger() - Constructor for class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
EoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan: This class store the only Eoulsan runtime instance.
EoulsanRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan: A nestable Eoulsan exception.
EoulsanRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanRuntimeException.
EoulsanRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanRuntimeException with a message.
EoulsanRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanException with a message and a cause.
EoulsanRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanException with a cause.
EoulsanTranslatorUtils - Class in fr.ens.biologie.genomique.eoulsan.util: This class define Kenetre translator utility glue methods for Eoulsan.
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
equals(Object) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
ERROR_CODE - Static variable in exception fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException: Error code for this exception
errorExit(Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and exits the application.
errorExit(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and exits the application.
errorHalt(Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and halts the application.
errorHalt(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and halts the application.
escapeUnderScore(String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Escape underscore for LaTeX title.
exceptionMessage - Variable in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
exec(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS.
ExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define the Local exec Action.
ExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
ExecFileLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a lock file.
ExecFileLock(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock: Public constructor.
ExecJarHadoopAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action that allow to execute a jar on an Hadoop cluster.
ExecJarHadoopAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
ExecLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a lock to prevent execution of a process simultaneously on multiples JVM.
ExecLock(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock: Public constructor.
ExecLock(String, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock: Public constructor.
execThreadOutput(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command and write the content of the standard output and error to System.out and System.err.
execThreadOutput(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command and write the content of the standard output and error to System.out and System.err.
execToString(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS and return the output in a string.
execToString(String, boolean, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS and return the output in a string.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Execute the workflow.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor: run Eoulsan.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: Execute script by Python interpreter and replace variable name by value.
execute(TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Convert command tag from tool file in string, variable are replace by value.
execute(TaskContext, TaskStatus) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Execute a task step.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Merge input replicates.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule: Run bedtools multiinter.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule: Run deeptools.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module: Run macs2.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Install all the files necessary in the tmp folder, then run idr.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Install all the files necessary in the tmp folder, then run idr.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule: Run trackhub generator.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.local.ExpressionLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.BAM2SAMLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsFilterLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2BAMLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2FASTQLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAMFilterLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.Splice2BEDModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
execute(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils: Execute a task context serialization file.
execute(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils: Execute a task context serialization file.
execute(List<Module>, List<Module>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor: run Eoulsan.
execute(List<String>, File, File, File, File, File...) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
execute(List<String>, File, File, File, File, File...) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter: Execute a command line.
executeRCode(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Execute a R code.
executeRnwCode(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Execute a R Sweave code.
executeRnwCode(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Execute a R Sweave code.
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Execute a R script.
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
executeRScript(String, boolean, String, boolean, String, DataFile, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
executeRScript(String, boolean, String, boolean, String, DataFile, String...) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Execute a R script.
executeTask(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Default executing context method.
EXECUTION_MODE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
ExecutionMode - Enum in fr.ens.biologie.genomique.eoulsan.annotations: This class define an enum for the execution mode of Eoulsan.
executor - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Executor - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class is the executor for running all the steps of an analysis.
Executor(ExecutorArguments) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor: Constructor.
ExecutorArguments - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class contains arguments for the Executor.
ExecutorArguments() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Public constructor.
ExecutorArguments(long) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Public constructor.
ExecutorArguments(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Public constructor.
ExecutorInterpreter - Interface in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This interface define a executor interpreter for Galaxy tools.
execWriteOutput(String, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS and save the output in file.
exists() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Check if this DataFile exists.
exists() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
exists(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Check if this DataFile exists.
exists(DataFile, boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test a source exists.
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
exists(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Test if a path exists
exit(int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Exit the application.
Experiment - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines an experiment.
ExperimentImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of an experiment.
ExperimentMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the experiment metadata.
ExperimentSample - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the experiment sample.
ExperimentSampleImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of the experiment sample.
ExperimentSampleMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This inteface defines the experiment sample metadata.
ExperimentSampleMetadataImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of the experiment sample metadata.
EXPRESSION_MATRIX_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Expression matrix.
EXPRESSION_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Expression results data format.
ExpressionCounterCounter - Enum in fr.ens.biologie.genomique.eoulsan.modules.expression: This enum define counters for the expression step.
ExpressionCounterUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This class define some glue methods between Eoulsan and Kenetre.
expressionFilesPrefix - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
expressionFilesSuffix - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
ExpressionHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: This class is the main class for the expression program of the reads in hadoop mode.
ExpressionHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
ExpressionInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for expression reports.
ExpressionInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
ExpressionLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.local: This class is the module to compute expression in local mode
ExpressionLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.local.ExpressionLocalModule
ExpressionMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: Mapper for the expression estimation.
ExpressionMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
ExpressionMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for expression files.
ExpressionMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
ExpressionOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a expression output format.
ExpressionOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionOutputFormat
ExpressionRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordWriter for expression files.
ExpressionRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter: Public constructor.
ExpressionReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: Reducer for the expression estimation.
ExpressionReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionReducer
ExpressionResultsAnnotationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This class define a module that create annotated expression files in TSV, ODS or XLSX format.
ExpressionResultsAnnotationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
ExpressionSAMOutputMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: Mapper for the expression estimation with a SAM output.
ExpressionSAMOutputMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
ExpressionSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for expression files.
ExpressionSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
ExpressionToMatrixModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell: This class define a class that allow to merge expression file into a matrix file.
ExpressionToMatrixModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
EXTERNAL_APP - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
extractCheetahScript(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract command tag in string.
extractChildElementsByTagName(Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract child elements by tag name.
extractConditionalParamElement(ToolInfo, Element) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract conditional param element.
extractConditionalParamElement(ToolInfo, Element, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract conditional param element.
extractDescription(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract description tag in string.
extractDockerImage(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract docker image attribute in string.
extractElementsByTagName(ToolInfo, Document, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractElementsByTagName(ToolInfo, Document, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractElementsByTagName(Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractElementsByTagName(Element, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractInputs(ToolInfo, Document, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract all input parameters define in document.
extractInterpreters(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract interpreter attribute in string.
extractOutputs(ToolInfo, Document, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract all output parameters define in document.
extractParamElement(ToolInfo, Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract parameter elements.
extractParamElement(ToolInfo, Element, String, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract parameter elements.
extractToolID(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract tool id tag in string.
extractToolName(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract tool name tag in string.
extractToolVersion(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract tool version attribute in string.
extractValueFromElement(Document, String, int, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract text from DOM from tag name, at the index place.

F

FAILED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
FailModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This module is a module that always fails.
FailModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FailModule
FakeModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This module is a fake module.
FakeModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
FASTA_FILE_WIDTH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: FASTA file width.
FASTQ_FORMAT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
FASTQ_FORMAT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
FASTQC_CASAVA_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Format fastq type casava/Illumina
FASTQC_EXPGROUP_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Use exponential base groups in graph
FASTQC_KMER_SIZE_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Collector FastQC kmer size
FASTQC_NOFILTER_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Option for filter fastq file if casava=true for all modules
FASTQC_NOGROUP_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Collector FastQC nogroup
FASTQC_REPORT_HTML - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: FastQC HTML report format.
FASTQC_REPORT_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: FastQC ZIP report format.
FastQCInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for FastQC reports.
FastQCInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
FastQCModule - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class define a module that compute QC report using FastQC.
FastQCModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
FastQCRuntimePatcher - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class to patch FastQC to be compatible with Hadoop.
FastQCRuntimePatcher() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher
FastqInputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define an InputFormat for FASTQ files for the Hadoop MapReduce framework.
FastqInputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
FastqLineRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: Treats keys as offset in file and value as line.
FastqLineRecordReader() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
FastqLineRecordReader(byte[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
FastqMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for FASTQ files.
FastqMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
FastqOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a FASTQ output format.
FastqOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqOutputFormat
FastqPairedEndReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq.FastqPairedEndReducer
FastqRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordReader for FASTQ files for the Hadoop MapReduce framework.
FastqRecordReader(TaskAttemptContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader: Public constructor.
FastqRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordWriter for FASTQ files.
FastqRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter: Public constructor.
FastqSequenceFile - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class define a SequenceFile for FASTQ files.
FastqSequenceFile(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile: Public constructor.
FastqSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for FASTQ files.
FastqSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
FEATURECOUNTS_SUMMARY_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: FeatureCounts summary format.
FeatureCountsInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for FeatureCounts reports.
FeatureCountsInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
FEATURES_FILE_FORMAT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
file(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create a DataFile object for a file of the workflow.
FileCharsets - Class in fr.ens.biologie.genomique.eoulsan.io: This class define default charsets.
FileConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define an InputStream that concatenate files in an InputStream.
FileConcatInputStream(List<File>) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream: Constructor.
FileDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class implements a File Protocol.
FileDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
fileMiddle() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the middle string of the filename.
fileMiddle(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the middle of a filename.
fileMiddle(StepOutputPort, String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the middle of a filename.
fileMiddle(String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the middle of a filename.
filename() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the filename.
filename(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the name of a data file of the workflow.
filename(String, String, DataFormat, String, int, int, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the filename from several parameters.
FileNaming - Class in fr.ens.biologie.genomique.eoulsan.core: This class contains methods to create workflow data file names.
FileNaming() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Private constructor.
FileNamingParsingRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan.core: This class define a runtime exception for filename parsing errors.
FileNamingParsingRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException: Create a new FileNamingParsingRuntimeException.
FileNamingParsingRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException: Create a new FileNamingParsingRuntimeException with a message.
filePrefix() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the file prefix.
filePrefix(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the prefix of a filename.
filePrefix(String, String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the prefix of a filename.
filePrefix(String, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the prefix of a filename.
FileResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to define a resource loader for files.
FileResourceLoader(Class<S>, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Public constructor.
fileSuffix() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the file suffix.
fileSuffix(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the suffix of a filename.
fileSuffix(DataFormat, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the suffix of a file.
fileSuffix(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the suffix of a file.
fillBuffer(InputStream, byte[], boolean) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
FilterAndMapReadsHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define a Step that filter and map read in Hadoop mode.
FilterAndMapReadsHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
FinalExpressionFeaturesCreator - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This class generates the final expression file after counting the alignments for each feature with HTSeq-count.
FinalExpressionFeaturesCreator(ExpressionCounter) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Public constructor.
FIRST_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
FirstModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a first module that do nothing.
FirstModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
FIT_ONLY - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
FloatParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a float tool element parameter.
FloatParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement: Instantiates a new float tool parameter.
FloatParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement: Instantiates a new float tool parameter.
flush() - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
flush() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
flushLog() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Flush log.
FORMAT_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
FORMATS_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
FormatsAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action that show the list of available formats.
FormatsAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
fr.ens.biologie.genomique.eoulsan - package fr.ens.biologie.genomique.eoulsan: Root package of Eoulsan.
fr.ens.biologie.genomique.eoulsan.actions - package fr.ens.biologie.genomique.eoulsan.actions: This package contains all the commands (actions) available through the Eoulsan command line.
fr.ens.biologie.genomique.eoulsan.annotations - package fr.ens.biologie.genomique.eoulsan.annotations: This package define the annotations on Eoulsan classes plug-ins.
fr.ens.biologie.genomique.eoulsan.bio.io.hadoop - package fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This package contains I/O classes for reading objects of the fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters package from Hadoop.
fr.ens.biologie.genomique.eoulsan.checkers - package fr.ens.biologie.genomique.eoulsan.checkers: This package contains and define checkers of DataFormat.
fr.ens.biologie.genomique.eoulsan.core - package fr.ens.biologie.genomique.eoulsan.core: This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.schedulers - package fr.ens.biologie.genomique.eoulsan.core.schedulers: This package contains classes for schedulers.
fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters - package fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This package contains classes for cluster schedulers.
fr.ens.biologie.genomique.eoulsan.core.workflow - package fr.ens.biologie.genomique.eoulsan.core.workflow: This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data - package 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 - package 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 - package fr.ens.biologie.genomique.eoulsan.data.storages: This package contains and define data storages.
fr.ens.biologie.genomique.eoulsan.design - package fr.ens.biologie.genomique.eoulsan.design: This package contains classes to handle experimental designs.
fr.ens.biologie.genomique.eoulsan.design.io - package fr.ens.biologie.genomique.eoulsan.design.io: This package contains I/O classes to read and write design files.
fr.ens.biologie.genomique.eoulsan.galaxytools - package fr.ens.biologie.genomique.eoulsan.galaxytools: This package contain classes related to read tool xml file from galaxy.
fr.ens.biologie.genomique.eoulsan.galaxytools.elements - package fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This package contain classes related to parameter extractions from XML Galaxy tool xml files.
fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters - package fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This package contain classes related to the Galaxy tool executor interpreters.
fr.ens.biologie.genomique.eoulsan.io - package fr.ens.biologie.genomique.eoulsan.io: This package contains general I/O classes for Eoulsan (not dedicated to fr.ens.biologie.genomique.eoulsan.bio package).
fr.ens.biologie.genomique.eoulsan.modules - package fr.ens.biologie.genomique.eoulsan.modules: This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq - package fr.ens.biologie.genomique.eoulsan.modules.chipseq: This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling - package fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc - package fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc: This packages contains all the quality check modules for ChIP-Seq.
fr.ens.biologie.genomique.eoulsan.modules.diffana - package 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 - package fr.ens.biologie.genomique.eoulsan.modules.expression: This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop - package fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: This package contain all the classes related to the expression step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.expression.local - package fr.ens.biologie.genomique.eoulsan.modules.expression.local: This package contain all the classes related to the expression step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc - package fr.ens.biologie.genomique.eoulsan.modules.fastqc: This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators - package fr.ens.biologie.genomique.eoulsan.modules.generators: This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping - package fr.ens.biologie.genomique.eoulsan.modules.mapping: This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop - package 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.mapping.hadoop.hadoopbamcli - package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
fr.ens.biologie.genomique.eoulsan.modules.mapping.local - package fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt - package fr.ens.biologie.genomique.eoulsan.modules.mgmt: This package contain classes related data management (e.g.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop - package fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: This package contain classes related data management in Hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload - package 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.modules.multiqc - package fr.ens.biologie.genomique.eoulsan.modules.multiqc
fr.ens.biologie.genomique.eoulsan.modules.singlecell - package fr.ens.biologie.genomique.eoulsan.modules.singlecell
fr.ens.biologie.genomique.eoulsan.requirements - package fr.ens.biologie.genomique.eoulsan.requirements: This package contains requirement classes for Eoulsan.
fr.ens.biologie.genomique.eoulsan.splitermergers - package 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.ui - package fr.ens.biologie.genomique.eoulsan.ui: This package contains Eoulsan user interface classes.
fr.ens.biologie.genomique.eoulsan.util - package fr.ens.biologie.genomique.eoulsan.util: This package contain utility classes.
fr.ens.biologie.genomique.eoulsan.util.hadoop - package fr.ens.biologie.genomique.eoulsan.util.hadoop: This package contains utility classes for hadoopS.
fr.ens.biologie.genomique.eoulsan.util.locker - package fr.ens.biologie.genomique.eoulsan.util.locker: This package contain an advanced multi JVM lock system.
fr.ens.biologie.genomique.eoulsan.util.r - package fr.ens.biologie.genomique.eoulsan.util.r: This package contain utility classes for R usage.
FTPPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the FTP protocol in Hadoop mode.
FTPPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
FTPURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the ftp protocol in local mode.
FTPURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
fullyDelete(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Fully delete a file of the content of a directory

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GALAXY_TOOL_PATH_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
GalaxyToolInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: This class create an interpreter to tool xml file from Galaxy.
GalaxyToolInterpreter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Public constructor.
GalaxyToolInterpreter(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Public constructor.
GalaxyToolModule - Class in fr.ens.biologie.genomique.eoulsan.modules: The Class GalaxyToolStep.
GalaxyToolModule(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule: Constructor.
GalaxyToolModule(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule: Constructor.
GalaxyToolXMLParserUtils - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: This class define static utils methods to extract data in Galaxy tool XML file.
GalaxyToolXMLParserUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
GAPPED_PEAK - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats: Gapped peak format.
GENE_EST_ONLY - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
generalConf(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with general configuration informations.
generateConditionPart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add condition vector to R script.
generateExpressionFileNamesPart(StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add expression file name vector to R script.
generateRepTechGroupPart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Write the section of the script that handle technical replicate groups.
generateRnwpreamble(List<Sample>, String, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Write Rnw preamble.
generateSampleIdsPart(List<Integer>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add SampleIds vector to R script.
generateSampleNamePart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add sampleNames vector to R script.
generateScript(Experiment, TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna
generateScript(Experiment, TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Generate the R script.
Generator - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that is a generator with user custom parameters.
GENERATOR_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
GenericExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define a generic executor interpreter.
GenericExecutorInterpreter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter: Constructor.
GenericStorageGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This module allow to easily store output of generator to avoid computation at each Eoulsan startup.
GenericStorageGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
GENOME_DESC_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Genome data format.
GENOME_DESCRIPTION - Static variable in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
GENOME_DESCRIPTION_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
GENOME_DESCRIPTION_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
GENOME_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Genome data format.
GENOME_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
GenomeChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a Checker on genome FASTA files.
GenomeChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
GenomeDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a genome protocol.
GenomeDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
GenomeDescriptionCreator - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class define a genome description creator.
GenomeDescriptionCreator() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator: Public constructor.
GenomeDescriptionGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class implements a genome description generator module.
GenomeDescriptionGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
GenomeMapperIndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class define a module that generate a genome mapper index.
GenomeMapperIndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
get(Parameter) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType: Get the size factors type to be used in DESeq2.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Get some data.
get(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the value of metadata entry.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
get(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the value according the key.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
get(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType: Get the fit type to be used in DESeq2.
get(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest: Get the statistic test to be used in DESeq2.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo: Get the value for a key
getAction() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the action.
getActionArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the action arguments.
getActions() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService: Get the list of actions available.
getAdditionalAnnotationFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the additional annotation file.
getAdditionalAnnotationFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getAdditionalAnnotationHypertextLinksPath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the additional annotation hypertext links path.
getAdditionalAnnotationStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the additional annotation storage path.
getAlias() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the alias of the name of the format.
getAlias() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getAlias() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getAlignmentFilter(GenericLogger, ReporterIncrementer, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule: Get the ReadAlignmentsFilter object.
getAlignmentsFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the parameters of the read alignments filters.
getAlignmentsFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule: Get the parameters of the alignments filter.
getAllDefaultStepId() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Return the available default step ids of the step types.
getAllFiles(File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get all the file on the Rserve server.
getAllFormats() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get all the registered formats.
getAllModules() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry: Get all the modules.
getAllSamplesMetadataKeys(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get all the sample metadata keys of the samples of a design.
getAnnotationClass() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Get the Eoulsan annotation class that corresponds to the Eoulsan mode.
getArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get command line arguments.
getArgv0() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
getAsBoolean(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the value according the key as a boolean.
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
getAsList(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the value according the key as a list.
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get Author.
getAWSAccessKey() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the AWS access key.
getAWSSecretKey() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the AWS secret key.
getBasename() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the base name of this DataFile without all its extensions.
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the path where searching the files.
getBogoMips() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get processor bogomips.
getBooleanSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the value of the setting as a boolean value
getBooleanValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a boolean value.
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler: Get the path to the Bpipe command wrapper.
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
getBytesNumberWritten() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream: Get the number of bytes written.
getBytesRead() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream: Get the number of bytes read.
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the checker for the module
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get Checker.
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the checker needed to check data of this type.
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getCheckersRequired() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Get the list of Checker required to run before this checker.
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
getCheckerStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Get checker step.
getCheckStore() - Static method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Get the instance of the CheckStore.
getCheetahScript() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the Cheetah script.
getClassPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan classpath.
getClusterSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the name of the cluster scheduler.
getCommandAuthor() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the command author.
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the command author.
getCommandDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get command description.
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get command description.
getCommandLine() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Get the context command line.
getCommandLine() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getCommandLine() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the command line as a list of string arguments.
getCommandLineAsString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the command line as a String.
getCommandLineSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the command line settings arguments.
getCommandName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the command name.
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the command name.
getComment() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the comment.
getComparisons() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the comparisons DEseq2 option.
getComparisons() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getCompression() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the compression.
getCompression() - Method in interface fr.ens.biologie.genomique.eoulsan.core.OutputPort: Get the compression format of the port.
getCompression() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
getCompressionExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the compression extension of this DataFile.
getCompressionLevel() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule: Get the compression level to use.
getCompressionsAccepted() - Method in interface fr.ens.biologie.genomique.eoulsan.core.InputPort: Test if the port accept a compressed input format.
getCompressionsAccepted() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
getCompressionType() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the compression Type of this DataFile.
getCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the condition.
getCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
getCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the condition.
getCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getCondition(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the Condition metadata value for an experimentSample.
getCondition(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the Condition metadata value for an experimentSample.
getConf() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
getConfiguration() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime: Get Hadoop configuration.
getConfiguration(JobContext) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil: Invoke getConfiguration() method on JobContext.
getConfigurationFileArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the configuration file argument.
getConfigurationFilePath() - Static method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the configuration file path.
getContentEncoding() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content type of the file.
getContentLength() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content length of the file.
getContentLength() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getContentMD5() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content MD5 of the file.
getContentType() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content type of the file.
getContentType() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the content type.
getContentType() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getContentType() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getContextCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager: Get the number of context created by the token manager.
getContextCounters(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the contextName counters.
getContextCreationTime() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the creation time of the context.
getContextCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getContextCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the creation time of the context.
getContextId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the context id.
getContextMessage(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get a context message.
getContextName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the context name.
getContextName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getContextName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the context name.
getContrastFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the contrastFile DEseq2 option.
getContrastFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getCores() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get the number of cores of the processor.
getCount() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.fastqc.CounterSequenceFile: Get the count of the read entries.
getCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
getCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
getCounter(TaskInputOutputContext, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
getCounterFromEoulsanName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get an counter from its HTSeq-count name
getCounterFromHTSeqCountName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get an counter from its HTSeq-count name
getCounterGroup() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the counter group to use for this module.
getCounterGroups() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
getCounterNames(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
getCounters() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Get the sample counters.
getCounters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getCounterValue(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
getCPUMHz() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get CPU MHz.
getCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the creation time of the job.
getCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
getCurrentStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the current step.
getCurrentStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCurrentStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
getData(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create an InputStream from the source.
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the file as a DataFile.
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFile() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the DataFile for an input DataType and a Sample.
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getDataFile(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFile(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFile(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the DataFile for an input DataType and a Sample.
getDataFile(MapperInstance, GenomeDescription, Map<String, String>) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Get the DataFile that corresponds to a mapper and a genome
getDataFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage: Get a Datafile related to a short name
getDataFileCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFileCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFileCount() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Count the number for DataFile available for a multi-file DataFormat and a Sample.
getDataFileCount(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFileCount(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFileCount(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Count the number for DataFile available for a multi-file DataFormat and a Sample.
getDataFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFilename() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the pathname for the data.
getDataFilename(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFilename(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFilename(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the pathname for the data.
getDataFileParent(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the parent source of the source.
getDataFiles(Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils: Get the list of the DataFile objects in a Data object.
getDataFiles(Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Get the list of the DataFile objects in a Data object.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the DataFormat of the DataFile.
getDataFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the DataFormat of the file.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement: Get the data format of the tool element.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
getDataFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor: Get the DataFormat handled by the preprocessor.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
getDataFormatForDesignMetadata(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the DataFormat that define a metadata entry in the design file.
getDataFormatForSampleMetadata(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the DataFormat that define a metadata entry of a sample in the design file.
getDataFormatFromAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its alias.
getDataFormatFromFilename(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the DataFormat of a file from its filename
getDataFormatFromFilename(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat From a file prefix and extension
getDataFormatFromGalaxyFormatName(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get DataFormat from an Galaxy format name.
getDataFormatFromGalaxyFormatNameOrNameOrAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its Galaxy format name or its name or alias.
getDataFormatFromName(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its name.
getDataFormatFromNameOrAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its alias.
getDataFormatPaths() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the format paths.
getDataFormatsFromExtension(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get DataFormats from an extension.
getDataName() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the data name.
getDataPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the data directory path.
getDataRepositoryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the data repository directory.
getDataRepositoryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the data repository directory.
getDate() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the date.
getDefaultClusterMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the default memory required for the steps in cluster mode.
getDefaultExtension() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the default extension of the DataType.
getDefaultExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getDefaultExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getDefaultFastqFormat() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the default fastq format.
getDefaultProtocol() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService: Get the default protocol.
getDefaultStepId() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Get default step id.
getDefaultWorkFile(TaskAttemptContext, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Get action description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the description of the module
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Get the context description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the description of the format.
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the tool description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the design used by the workflow.
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the design related to the experiment.
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the design related to the sample.
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getDesign(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Create design object.
getDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the design file path.
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the design file.
getDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the designFile DEseq2 option.
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getDesignFormatVersion() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream: Get the format of the data to read.
getDesignMetadataKeyForDataFormat(Design, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the field name in a Design object that correspond to a dataformat.
getDesignMetadataKeyName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the name of the design metadata key of the design file that can provide the DataFile.
getDesignMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getDesignMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getDesignPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the design file path.
getDesignReader() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream: Get the DesignReader for the data.
getDesignStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getDesignStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the design step of the workflow.
getDest() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
getDiscardOutput() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the discard output value.
getDispEstFitTypeFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType: Get the Dispersion estimation fit type form its name
getDispEstMethodFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod: Get the Dispersion estimation method form its name
getDispEstSharingModeFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode: Get the Dispersion estimation sharing mode form its name
getDockerBackend() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker backend name.
getDockerConnection() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker connection string.
getDockerConnectionURI() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker connection URI.
getDockerImage() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get Docker image.
getDockerSingularityStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker singularity storage path.
getDoubleSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the value of the setting as a double value
getDoubleValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a double value.
getDuration() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Get the duration of the step.
getDuration() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the duration of the step.
getDuration() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
getEoulsanDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan directory.
getEoulsanMemory() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan memory requirement.
getEoulsanMode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the Eoulsan mode of the step.
getEoulsanScriptPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan script path.
getErrorMessage() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Get the error message.
getErrorMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the error message.
getErrorMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
getException() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Get the exception.
getException() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the exception.
getException() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
getException() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the exception.
getExecutablePids(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Return a set withs pid of existing executable.
getExecutablesTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the temporary directory for executables.
getExecutablesTempDirectoryFile() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the temporary directory File for executables.
getExecutionMode(Class<?>) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Get the execution mode related to an annotation class.
getExitCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult: Return the exit code.
getExitValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the exit value.
getExitValue() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult: Get the exit value of the process.
getExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the name of an experiment.
getExperiments() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the list of the experiments.
getExperimentSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment sample related to the sample.
getExperimentSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getExperimentSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getExperimentSampleAllMetadataKeys(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get all the experiment metadata keys of the samples of a design.
getExperimentSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get experiment samples list.
getExperimentSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getExperimentSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getExperimentsUsingASample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get all the experiments related to a sample.
getExpressionCounter() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule: Get the counter.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the extension of this DataFile without compression extension.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the file extensions of the files to search.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Get the extension of the files to load.
getExtensions() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the extensions for the DataType
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the list of the file extensions of the files to search.
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the FastqFormat.
getFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the fastq format.
getFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the FastqFormat.
getFile() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
getFile() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
getFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage: Get a file related to a short name
getFile(String, File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get a file from the RServer.
getFileAsArray(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get a file as a byte array.
getFileIndex() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the file index.
getFileIndex() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get file index.
getFileInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Create an inputStream on a file on RServer.
getFileOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Create an outputStream on a file on RServer.
getFilesIntoZip(List<String>, File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get a list of files from the RServer.
getFirstPort() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getFirstPort() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get the first port.
getFirstStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getFirstStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the first step of the workflow (after generator steps).
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Get format related to the checker.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the format.
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Get the data format of the port.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the format of the output
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the data format of the data.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger: Get the format related to the splitter.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter: Get the format related to the splitter.
getFullExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the base name of this DataFile with all its extensions (include compression extension).
getGalaxyFormatNames() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the extension from Galaxy tool file of the DataType.
getGalaxyFormatNames() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getGalaxyFormatNames() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getGalaxyToolPaths() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Galaxy tool path.
getGenerator() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the step needed to generate the DataType from DataTypes provided by the Design file.
getGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getGenericLogger() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the generic logger.
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the generic logger.
getGenericLogger() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
getGenomeDescStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the genome description storage path.
getGenomeFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the genome file.
getGenomeFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getGenomeMapperIndexStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the genome mapper index storage path.
getGenomeStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the genome storage path.
getGffFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the GFF file.
getGffFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getGFFStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the GFF storage path.
getGlobalParameters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the globals parameters.
getGtfFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the GTF file.
getGtfFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getGTFStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the GTF storage path.
getHadoopLogLevel() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Hadoop log level.
getHadoopWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the Hadoop working directory.
getHadoopWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the local working directory.
getHadoopWorkingDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the Hadoop working directory.
getHadoopWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the Hadoop working path.
getHadoopWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the Hadoop working directory.
getHelp() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the help.
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the command used to launch Eoulsan.
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get step id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: get the experiment id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo: Get the file to parse.
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo
getInputData(InputPort) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get raw access to input data stored in the object.
getInputData(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the input data for an input DataType and a Sample.
getInputData(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getInputData(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the input data for a port name and a Sample.
getInputData(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getInputDataElements() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the in data format expected associated with variable found in command line.
getInputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the input data format.
getInputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the input ports of the step.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Define input port.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Define input ports.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Define input ports.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Define input port.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getInputs() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the inputs.
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create an InputStream to load data.
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService: Retrieve the singleton static instance of an ActionService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService: Retrieve the singleton static instance of an ClusterTaskSchedulerService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks: Get the singleton instance of the class.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry: Retrieve the singleton static instance of ModuleRegistry.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Singleton method.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Get the singleton instance of WorkflowStepObserverRegistry.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus: Get the singleton instance of WorkflowBusEvent.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the singleton instance of DataFormatRegistry
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService: Retrieve the singleton static instance of DataProtocolService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.Main: Get the instance of the Main class.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService: Retrieve the singleton static instance of an AlignmentsFilter.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService: Retrieve the singleton static instance of a RequirementService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.ui.UIService: Retrieve the singleton static instance of UIService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanDockerManager: Get the instance of the DockerManager.
getInstance(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Get the singleton.
getInstance(DataFile, GenericLogger) - Static method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage: Create a GenomeDescStorage
getInstance(String, GenericLogger) - Static method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Create a GenomeIndexStorage
getInterpreter(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the interpreter.
getInterpreterPath() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter: Get the interpreter path.
getIntSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the value of the setting as a integer value
getIntValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a integer value.
getIntValueGreaterOrEqualsTo(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: * Get the value of the parameter as a integer value and check if this value is greater or equals to the min parameter value.
getIntValueInRange(int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a integer value and check if this value is in the correct range.
getJarFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the application jar file.
getJarPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the application jar file.
getJarPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the application jar path.
getJarPathname(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the application jar file.
getJavaExecutablePath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get java executable path.
getJavaMailSMTPProperties() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Create a property object for javamail smtp configuration from the settings.
getJobDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job description.
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job description.
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job description.
getJobDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job path.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the job directory.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the job directory.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job path.
getJobDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the job directory.
getJobEnvironment() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job environment.
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job environment.
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job environment.
getJobHost() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the host of the job.
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the host of the job.
getJobId() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job id.
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job id.
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job id.
getJobPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job path.
getJobUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the UUID of the job.
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the UUID of the job.
getJVMArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get JVM arguments.
getJVMsPIDs() - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.LockerUtils: Return a set withs pid of existing JVMs.
getLabel() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the label.
getLastActiveTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getLastModified() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the date of the last modification of the file.
getLastModified() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getLaunchMode() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the launch mode of the application.
getLaunchScriptPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the path to the launch script.
getLinkedSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
getLinkedSteps() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Get the steps linked to this port.
getLinksFileFromSettings(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils: Get the links file from the settings.
getLinkTarget() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the symbolic link target.
getListElements() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getListElements() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getListElements() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the the list of data.
getLocalTempDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get local temporary directory.
getLocalTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getLocalTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getLocalThreadsNumber() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the number of threads to use in Steps computation in local mode.
getLocalWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the local working directory.
getLocalWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the local working directory.
getLocalWorkingDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the local working directory.
getLocalWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the local working path.
getLocalWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the local working directory.
getLogFileArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the log file argument.
getLogger() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the logger.
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the logger.
getLogger() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Get the logger object.
getLoggerName() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Get the logger name.
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the Handler to create the log file.
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
getLogLevelArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the log level arguments.
getLowerStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a lower case String value.
getMapKey(Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule: Define the key to use for replicate merging.
getMapKey(Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
getMapper() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the mapper.
getMapper() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the mapper object.
getMapperArguments() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the name of the mapper to use.
getMapperArguments() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the arguments of the mapper to use.
getMapperDockerImage() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the mapper Docker image to use.
getMapperFlavor() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the flavor of the mapper to use.
getMapperFlavor() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the flavor of the mapper to use.
getMapperHadoopMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the amount in MB of memory required to execute the mapper.
getMapperHadoopMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the amount in MB of memory required to execute the mapper.
getMapperHadoopThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the name of the mapper to use.
getMapperHadoopThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the number of threads to use in local mode.
getMapperLocalThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the number of threads to use in local mode.
getMapperName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the name of the mapper to use.
getMapperName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the name of the mapper to use.
getMapperVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the version of the mapper to use.
getMapperVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the version of the mapper to use.
getMaxFilesCount() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the maximal number of files used to store data of this format.
getMaxFilesCount() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getMaxFilesCount() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getMaxRecordsInRam() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule: Get the maximum records in RAM.
getMemTotal() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo: Get the total memory of the system.
getMergeableWorkFile(Path, String, String, TaskAttemptContext, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Returns a name that mergeInto() will recognize as a file to be merged.
getMerger() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the merger class related to this type.
getMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent: Get the message of the event.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get metadata about the data.
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the design Metadata.
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSample: Get the experiment sample metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Get the metadata of a file.
getMetadata(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the metadata for the source.
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
getMetadata(Experiment, Sample, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get a metadata value for an experiment and a sample.
getMetadata(ExperimentSample, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get a metadata value for an experimentSample.
getMetaData() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the metadata for this DataFile.
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Get Eoulsan mode.
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getModel() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the model DEseq2 option.
getModel() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getModelColumns(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the column names used in DESeq2 model.
getModelName() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get the model of processor
getModule() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the underlying Module object.
getModule(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Get a module instance.
getModule(Step, String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Get a step instance.
getModuleName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the module name.
getModuleName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getModuleName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the module name of the step.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Get the name of the action.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Get the name of the checker.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GTFChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the name of the module.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the name of the parameter.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Get the name of the port.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get data name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the name of this DataFile.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the name of the format.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get Protocol name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get design name.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Gets the name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter: Get the name of the interpreter.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
getName() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info: Get the name of the information
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule: Methods
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType: Get the dispersion estimation fitType name
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod: Get the dispersion estimation method
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode: Get the dispersion estimation sharingMode name
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: The name of the requirement.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.ui.UI: Get the name of the UI.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Get the name of the RExecutor.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
getNote() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the note.
getNote() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the note.
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the unique numerical identifier of the step.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get design number.
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment number.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample number.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getOperator() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the operator.
getOutputData(DataFormat, Data) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(DataFormat, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(DataFormat, String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(String, Data) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for a port name and a Sample.
getOutputData(String, Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for a port name and a Sample.
getOutputData(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(String, String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for a port name and a Sample.
getOutputData(String, String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputDataElements() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the out data format expected associated with variable found in command line.
getOutputDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the output path.
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the output directory.
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Get the output directory of the analysis.
getOutputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
getOutputFiles() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Get the output files of the analysis
getOutputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
getOutputPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the output path.
getOutputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the output data format.
getOutputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the output ports of the step.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Define output port.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Define output port.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getOutputs() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the outputs.
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create an OutputStream to load data.
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getOutputTreeType() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the output tree type.
getParallelizationMode() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the parallelization mode of the module.
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the parallelization mode of the step.
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
getParameter(Set<Parameter>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Get the last parameter which name match for a parameter set.
getParameters() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the parameter of the step.
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
getParameters() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Get the parameters of the requirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
getParent() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the parent of this DataFile.
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the file part.
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getPart() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the part of the data.
getPath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol: Get Convert a DataFile object to a Path object.
getPercentComplete() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
getPercentComplete() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
getPid() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getPort(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getPort(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get a port.
getPortName() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the port name.
getPortName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the port name that produced the file.
getPortNames() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getPortNames() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get the names of the ports
getPortsWithDataFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getPortsWithDataFormat(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get a list with all the ports that format is the specified format.
getPrefix() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get DataFormat prefix.
getPrefix() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getPrefix() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getPriority() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Get the priority of the step.
getProcessesWaiting() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock: Get the number of processes waiting.
getProcessor() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get the processor name.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader: Get the progress within the split
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
getProgress() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Get the progress of the context processing.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the progress of the step.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the progress.
getProgressMessage() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Get the progress message.
getProgressMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getProtocol() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the protocol of this DataFile.
getProtocolPrefixInSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the prefix of the protocol in the source name of the DataFile.
getRandomId() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a raw InputStream (without decompression of input data) to load data.
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getRConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get the R connection.
getReadFilter(GenericLogger, ReporterIncrementer, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule: Get the ReadFilter object.
getReadFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the parameters of the read filters.
getReadFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule: Get the parameters of the read filter.
getReads() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the reads as a list.
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule: Get the reducer task count.
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the reference option.
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the reference.
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the reference.
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getReference(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the reference of a sample.
getReference(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the reference of a sample.
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
getReportName() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor: Get the name of the report.
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
getRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the RepTechGroup.
getRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
getRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the RepTechGroup.
getRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getRepTechGroup(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the RepTechGroup metadata value for an experimentSample.
getRepTechGroup(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the Condition metadata value for an experimentSample.
getRequiredEoulsanVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the required Version of the application to run the Module.
getRequiredEoulsanVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getRequiredMemory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the required memory for the step.
getRequiredMemory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getRequiredProcessors() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the required processors for the step.
getRequiredProcessors() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getRequiredSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Get the required steps.
getRequirements() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the requirements of the module.
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Get the input stream related to a resource.
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
getResourceName(S) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Get the resource name.
getResult() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Get the context result.
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getResult(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the result related to a step.
getResultMail() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the mail address for eoulsan results.
getResultsPanel() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
getRootStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getRootStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the first steps of the workflow.
getRServeServerName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the RServe server name.
getRuntime() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get EoulsanRuntime.
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get EoulsanRuntime.
getRuntime() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime: Get the Eoulsan runtime instance.
getSAMHeaderMerger(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSAMHeaderMerger(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils: Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSample() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the sample that produced the file.
getSample() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSample: Get the experiment sample name.
getSample() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
getSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the name of a sample.
getSampleId() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the sample id related to the data.
getSampleMetadataKeyForDataFormat(Sample, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the field name in a Sample object that correspond to a dataformat.
getSampleMetadataKeyName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the name of the sample metadata key of the design file that can provide the DataFile.
getSampleMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getSampleMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getSampleName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the sample name related to the data.
getSampleNumber() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the sample number related to the data.
getSampleNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the sample number related to the data.
getSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the list of the samples.
getSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the samples of the experiment.
getSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getScheduler() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskSchedulerFactory: Get the scheduler
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
getSchedulerName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Get the scheduler name.
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
getSerialNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the serial number.
getServerName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get the name of the Rserve server.
getServiceClasses() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
getSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get a setting value.
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Get Settings.
getSettings() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get Eoulsan settings.
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get Eoulsan settings.
getSettings() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime: Get instance settings.
getSettingsKeyToObfuscated() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get a set with the names of the settings to obfuscate.
getSettingsNames() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get a set of settings names.
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the short name.
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
getShortName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Gets the short name.
getSize(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Get the length of a file.
getSMTPHost() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the name of the SMTP server host.
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the source of this DataFile.
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule: Get the source the Galaxy tool.
getSourceAsFile(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the underlying File object for the DataFile if the protocol allow it.
getSourceAsFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getSourceAsFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
getSourceFilename(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the name of the filename that correspond to the source.
getSplitter() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the splitter class related to this type.
getSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getState() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the state of the step.
getState() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getState() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Get the state of the step.
getStatus() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the message type
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getStatus(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the status related to a step.
getStatusValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult: Get status value.
getStderr() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult: Get the standard error of the process
getStdout() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult: Get the standard output of the process
getStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the workflow step that produced the file.
getStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the step.
getStep(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Get the step related to a context.
getStep(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Get the step related to a context.
getStepCounters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the step counters.
getStepDataProduct(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the data product for the step.
getStepDiscardOutput(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the discard output value.
getStepId() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get Step Id.
getStepIds() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the list of step ids.
getStepInputs(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the inputs of a step
getStepMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get step message.
getStepOutputDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the step working directory.
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get step output directory (where output file of the step will be written).
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getStepParameters(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the parameters of a step
getStepRequiredMemory(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the required memory for the step.
getStepRequiredProcessors(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the required processors for the step.
getSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getSteps() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the steps of the workflow.
getStepVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the step version required by user.
getStepVersion() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getStepVersion(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the required version of the step.
getStringencyOptHelp() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
getStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a String value.
getSubmittedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the number of submitted tasks.
getSubmittedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the number of submitted tasks.
getTaskDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the task directory.
getTaskDoneCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getTaskDoneCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getTaskDoneCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getTaskDoneCount(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the count of done task contexts of a step.
getTaskFilePrefix() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Create the prefix of a related task file.
getTaskName(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the name of a task.
getTaskOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the task output directory.
getTaskOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the task output directory.
getTaskOutputDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the task output directory.
getTaskPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the task path.
getTaskProgress(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the progress of a task.
getTaskRunningCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getTaskRunningCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getTaskRunningCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getTaskRunningCount(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the count of running task contexts of a step.
getTaskSubmittedCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getTaskSubmittedCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getTaskSubmittedCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getTaskSubmittedCount(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the count of submitted task contexts of a step.
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Get the temporary directory.
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the temporary directory.
getTempDirectoryFile() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the temporary directory File.
getTemporaryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Get the temporary directory.
getTemporaryPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the temporary directory path.
getTerminatedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the number of terminated tasks.
getTerminatedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the number of terminated tasks.
getThreadId() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getThreadsNumber(int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Get the number of threads to use from localThreads, maxLocalThreads and global threads number.
getTickets(Ticket) - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.TicketScheduler: Update a ticket by the TicketScheduler and get all the valid tickets.
getTickets(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
getToolElementSelected() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: Gets the tool parameter selected.
getToolElementsResult() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: Gets the tool parameters result.
getToolID() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the tool Id.
getToolInfo() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the tool information.
getToolName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the tool name.
getToolSource() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the tool source.
getToolVersion() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the tool version.
getTotalTaskDoneCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getTotalTaskDoneCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getTotalTaskDoneCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getTotalTaskDoneCount() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the count of done task contexts for the workflow.
getTotalTaskRunningCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getTotalTaskRunningCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getTotalTaskRunningCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getTotalTaskRunningCount() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the count of running task contexts for the workflow.
getTotalTaskSubmittedCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getTotalTaskSubmittedCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getTotalTaskSubmittedCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getTotalTaskSubmittedCount() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the count of submitted task contexts for the workflow.
getTrimmed(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
getTrimmed(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the trimmed value according the key.
getTrimmed(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getTrimmed(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getType() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the type of the step.
getType() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getType() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the type.
getUIName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the UI name.
getUnderLyingData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the underlying Data.
getUploadedDataFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
getUploadedDataFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
getUploadedDataFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule: Generate the DataFile Object for the uploaded DataFile
getUploadedDataFile(DataFile, Step, Sample, String, DataFormat, int) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
getUploadedDataFile(DataFile, Step, Sample, String, DataFormat, int) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
getUploadedDataFile(DataFile, Step, Sample, String, DataFormat, int) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule: Generate the DataFile Object for the uploaded DataFile
getUpperStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a upper case String value.
getUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the UUID.
getValidatedName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
getValidatedName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
getValidatedName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
getValidatedName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Gets the name which respect Eoulsan's syntax.
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter.
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
getValue() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Gets the value.
getValues() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info: Get the value of the information
getVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get version of the Module.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
getWorkflow() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the workflow of the step.
getWorkflow() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the workflow description
getWorkflow() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getWorkflow() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getWorkflow() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the workflow description.
getWorkflowContext() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Get the real Context object.
getWorkflowFile() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the workflow file path.
getWorkflowFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getWorkflowFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getWorkflowFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the workflow file.
getWorkflowPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the workflow file path.
getZooKeeperConnectString() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the ZooKeeper connect string.
getZooKeeperDefaultPort() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the ZooKeeper default port.
getZooKeeperSessionTimeout() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the ZooKeeper session timeout.
GFF_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
GFFChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a Checker on GFF annotation.
GFFChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker: Public constructor.
GFFChecker(boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker: Protected constructor.
GFFDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a annotation protocol.
GFFDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
GFFFastaGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This generator allow to generate a genome fasta file from the fasta section of a GFF file.
GFFFastaGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
glob() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get a glob for the filename.
glob(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the glob for the port.
Globals - Class in fr.ens.biologie.genomique.eoulsan: This class contains globals constants for the application.
GOOD_QUALITY_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
GSNAP_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Gmap index data format.
GTF_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
GTFChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a Checker on GTF annotation.
GTFChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GTFChecker: Public constructor.
GTFDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a annotation protocol.
GTFDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol

H

HADOOP - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
HADOOP_COMPATIBLE - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
HADOOP_ONLY - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
HADOOP_PARAMETER_PREFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
HADOOP_REDUCER_TASK_COUNT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
HADOOP_TASK - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
HADOOP_THREADS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
HADOOP_TIMEOUT - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
HADOOP_TIMEOUT - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
HadoopBamUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
HadoopBamUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils
HadoopCompatible - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a plug-in class as usable in hadoop mode and local mode.
HadoopCompatibleMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
HadoopCompatibleTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class is a scheduler for tasks from step with the @HadoopComptible annotation in Hadoop mode.
HadoopCompatibleTaskScheduler.HadoopCompatibleMapper - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
HadoopCompressionCodecs - Class in fr.ens.biologie.genomique.eoulsan.io: This class allow to create input and output stream for compression codec of Hadoop.
HadoopCompressionCodecs() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs
HadoopEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan: This class define the Runtime to execute low level IO operation for Eoulsan in Hadoop mode.
HadoopExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class launch Eoulsan in hadoop mode.
HadoopExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
hadoopInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with Hadoop configuration informations.
HadoopInfo - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class show in log some Hadoop information.
HadoopInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopInfo
HadoopJarRepackager - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class allow to repackage the application.
HadoopJobEmergencyStopTask - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class define an EmergencyStopTask for Hadoop Jobs.
HadoopJobEmergencyStopTask(Job) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask: Public constructor.
HadoopMappingUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class contains utility methods for the Hadoop mapping package classes.
HadoopOnly - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a plug-in class as usable in hadoop mode only.
HadoopReporter - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class define a Hadoop reporter.
HadoopReporter(Counters) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter: Constructor.
HadoopReporter(TaskInputOutputContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter: Constructor.
HadoopReporterIncrementer - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class define a Hadoop reporter.
HadoopReporterIncrementer(TaskInputOutputContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporterIncrementer: Constructor.
HadoopUploadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This class define a module for Hadoop file uploading.
HadoopUploadModule(DataFile, Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule: Public constructor.
halt(int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Exit the application.
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
hashCode(Object...) - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
hasNext() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
hasNext() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
hasNextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream: Test if there is an other InputStream to concatenate
hasNextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream
hasNextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.PathConcatInputStream
HDFSDataDownloadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This class define a download module that retrieve data from HDFS at the end of an analysis.
HDFSDataDownloadModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
HDFSPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the HDFS protocol in Hadoop mode.
HDFSPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
HEADERMERGER_INPUTS_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
help(Options) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Show command line help.
HTCondorTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a HTCondor cluster scheduler using a Bpipe script.
HTCondorTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler: Constructor.
HTMLReportArchiveNeigborClass - Class in uk.ac.babraham.FastQC.Report: Empty class for patching the HTMLReportArchive class of FastQC.
HTMLReportArchiveNeigborClass() - Constructor for class uk.ac.babraham.FastQC.Report.HTMLReportArchiveNeigborClass
htSeqCountCounterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get the HTSeq-count name of the counter.
HTTPPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the HTTP protocol in Hadoop mode.
HTTPPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol
HTTPSPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the HTTP protocol in Hadoop mode.
HTTPSPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol
HTTPSURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the http protocol in local mode.
HTTPSURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol
HTTPURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the http protocol in local mode.
HTTPURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol

I

IDRModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc: This class defines the IDR quality check step.
IDRModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
ignoreFilteredSequences() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
ignoreInReport() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
ImportModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a import step.
ImportModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
incrCounter(String, String, long) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
incrCounter(String, String, long) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporterIncrementer
incrementCounter(Counter, long) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
Info(String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info: Constructor.
Info(String, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info: Constructor.
Info(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info: Constructor.
Info(String, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info: Constructor.
Info(String, List<String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info: Constructor.
Info(String, List<String>, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info: Constructor.
InfoAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action that show the Eoulsan configuration
InfoAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
Infos - Class in fr.ens.biologie.genomique.eoulsan: This class gathers information about Eoulsan configuration and system environment.
Infos() - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos
Infos.Info - Class in fr.ens.biologie.genomique.eoulsan: This class define an info.
init(Workflow) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
init(Workflow) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
init(Workflow) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
init(Workflow) - Method in interface fr.ens.biologie.genomique.eoulsan.ui.UI: Initialize the UI.
init(ExpressionCounter, DataFile, DataFile, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils: Initialize the counter.
init(ExpressionCounter, GenomeDescription, DataFile, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils: Initialize the counter.
initConsoleHandler() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Initialize the console logger handler for Hadoop mappers and reducers.
initConsoleHandler(Level) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Initialize the console logger handler for Hadoop mappers and reducers.
initEoulsanRuntimeForExternalApp() - Static method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime: Initialization Eoulsan runtime for external application who needed Eoulsan
initialize() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskSchedulerFactory
initialize(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
initializeExpressionResults() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Clear.
initializeRuntime(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Initialize the Eoulsan runtime.
initializeRuntime(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
initializeRuntime(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
INPUT_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
INPUT_ENTRIES - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
INPUT_RAW_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
InputPort - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define an input port of a step.
InputPorts - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a group of input ports.
InputPortsBuilder - Class in fr.ens.biologie.genomique.eoulsan.core: This class allow to easily create input ports for a step.
InputPortsBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
InputPreprocessor - Interface in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This interface define a preprocessor for MultiQC input data.
InputPreprocessorService - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a service to retrieve a InputPreprocessor.
install(Progress) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
install(Progress) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
install(Progress) - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Install the requirement.
install(Progress) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
INSTALLABLE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
IntegerParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an integer tool element parameter.
IntegerParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement: Instantiates a new integer tool element parameter.
IntegerParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement: Instantiates a new integer tool element parameter.
IntegrationTestAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class launch integration test with Testng class.
IntegrationTestAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
INTERNET_CHECK_PORT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Port of the server to check internet connection
INTERNET_CHECK_SERVER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Server name to check internet connection.
INTERPRETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
INTERPRETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
INVALID_CHROMOSOME_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
INVALID_INPUT_PRETREATMENT_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
INVALID_SAM_ENTRIES_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
invalidConfiguration(StepConfigurationContext, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for an invalid configuration.
invalidConfiguration(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for an invalid configuration.
isApplicationAvailableForCurrentArch() - Static method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction: Check if the application is available for current platform.
isAvailable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
isAvailable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
isAvailable() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Test if the requirement is available.
isAvailable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
isBuildContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the buildContrast DEseq2 option.
isBuildContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
isBypassPlatformChecking() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if the platform checking must be avoided at Eoulsan startup.
isCache() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
isChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Test if a checker is available for this DataFormat.
isChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
isChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
isColorspace() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
isColorspace() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
isContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the contrast DEseq2 option.
isContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
isCopyResultsToOutput() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput: Test if result must be copied to output.
isCurrentArchCompatible() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
isCurrentArchCompatible() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Test if the action can be executed with current platform.
isCurrentArchCompatible() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
isCurrentArchCompatible() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
isDataFormatFromDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Test if the DataFormat is provided by the design file.
isDataFormatFromDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
isDataFormatFromDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
isDataNameValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a data name is valid.
isDebug() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test is the debug mode is enabled.
isDesignChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Test if the Checker is a design checker
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
isDir() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Test if the file is a directory.
isDockerBySingularityEnabled() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Is Docker features are enabled using singularity.
isDockerConnectionDefined() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if a Docker connection has been set.
isDockerMountNFSRoots() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if when use Docker, NFS roots must been mounted instead of file paths.
isDoneState() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState: Test if the state is a done state.
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
isEmpty() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Test if the object is empty
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
isEmpty() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Test if the number of the elements of the data is equals to 0.
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
isEmpty() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Test if there is no metadata.
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
isEndOfStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager: Test if this is the end of the step.
isException() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Test if an exception has been thrown.
isExistingDirectoryFile(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a directory exists
isFile(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
isFilenameValid(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a filename is valid.
isFilenameValid(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a filename is valid.
isFilenameValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a filename is valid.
isFinalState() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState: Test if the state is a final state.
isFormatPrefixValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a format prefix id is valid.
isGenerator() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Test if a generator is available for this DataFormat.
isGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
isGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
isGenerator(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a module contain the @Generator annotation.
isGTFInputFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule: Test if GTF input format must be used.
isHadoopCompatible() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Test if the execution mode is compatible with Hadoop mode.
isHadoopJarMode() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
isHadoopJarMode() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Test if the action can be executed in hadoop Jar mode.
isHadoopJarMode() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
isHadoopMode() - Method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode: Test if Eoulsan is in an Hadoop mode.
isHadoopProtocolMode() - Method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode: Test if Hadoop protocols can be used in the current Eoulsan mode.
isHidden() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
isHidden() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Test if the action must be hidden from the list of available actions.
isHidden() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
isImmutable() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Test if the object immutable.
isInstallable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
isInstallable() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Test if the requirement is installable.
isKeepRServeFiles() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if save.r.keep.files is true
isList() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
isList() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Test if the port requires a list as value.
isList() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
isList() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
isList() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Test if the data is a list.
isLocalCompatible() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Test if the excution mode is compatible with local mode.
isLocalFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Test if the DataFile use the defaultProtocol.
isMayNotExist() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
isMerger() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Test if a merger class is available for this DataFormat.
isMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
isMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
isNoLog(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a module contain the @NoLog annotation.
isNoObserverRegistered() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Test if observers has been registered
isNoOutputDirectory(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a module contain the @NoOutputDirectory annotation.
isNoTokenToReceive() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager: Test if there is no token to be received by the token manager.
isObfuscateDesign() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if design must be obfuscated
isObfuscateDesignRemoveReplicateInfo() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if replicate information must be removed from design.
isOneFilePerAnalysis() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Test if there is only one file for this DataType per analysis.
isOneFilePerAnalysis() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
isOneFilePerAnalysis() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
isOptional() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Checks if is optional.
isOptional() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
isOptional() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Test if the requirement is optional.
isPairedData(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule: Check if a SAM file contains paired-end data.
isPairedEnd() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Test if the data is paired end data.
isPairedEnd() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Test if the step works in pair end mode.
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement: Test if the parameter value is valid
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
isPortNameValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a port name is valid.
isPrintStackTrace() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test is the debug mode is enabled.
isReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the reference.
isReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
isReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the reference.
isReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
isRequiredInWorkingDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.InputPort: Test if input data of the port is required in the working directory.
isRequiredInWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
isRequiresAllPreviousSteps(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a module contain the @RequiresPreviousStep annotation.
isRequiresPreviousStep(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a module contain the @RequiresPreviousStep annotation.
isReuseStepInstance(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a module contain the @ReuseStepInstance annotation.
isRServeServerEnabled() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if RServe is enabled.
isRunning() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
isRuntime() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime: Test if an instance of the runtime is set.
isSameLocalPath(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Check if two file have the same local path
isSAMOutputFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule: Test if SAM output format must be used.
isSaveRscripts() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if save.r.script is true
isSaveWorkflowImage() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if an image of the workflow must be saved.
isSendResultMail() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if an email must be sent at the end of the analysis.
isService(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement: Checks if the value has been set (is not the default value).
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: Test if the value has been set (if not the default value)
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
isSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if a setting key exists.
isSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Test if the step must be skipped
isSkip() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
isSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the skip option.
isSkip() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
isSkipped(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Test if an experiement is skipped.
isSplitable(JobContext, Path) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
isSplitable(JobContext, Path) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
isSplitter() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Test if a splitter class is available for this DataFormat.
isSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
isSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
isStarted() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
isStarted() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager: Test if the thread for the token is started.
isStepIdValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if a step id is valid.
isStepSkipped(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Test if the step is skipped.
isStopped() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
isSuccess() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Test the result of the step is successful.
isSuccess() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Test if the step result is a success.
isSuccess() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
isSuccess() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent: Test if the event is a success.
isSymbolicLink() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Test if the file is a symbolic link.
isTechnicalReplicates(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Test if there is Technical replicates into rRepTechGroup field.
isTerminal(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils: Test if a step contain the @Terminal annotation.
isTerminalStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Test if the step is a terminal step.
isUseBundledBinaries() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Test if the bundled binaries must be used to perform the step.
isUseOldEoulsanResultFormat() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if Eoulsan result files must be written using the old format.
isUserDefinedTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if the temporary directory File has been defined by user.
isUseStandardExternalModules() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Test if standard external modules must be used.
isWorking() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
isWorkingState() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState: Test if the state is a working state.
ITERATE - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
iterator() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts

J

JarRepack - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to repackage a jar file.
JarRepack(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.JarRepack: Public constructor.
JOB_ID_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Job id constant name.
JOB_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Logs path constant name.
JOB_UUID_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Job UUID constant name.

K

keySet() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the keys of the entries.
keySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
keySet() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the keys of the metadata
keySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
keySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata

L

LANG_ENVIRONMENT_VARIABLE - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
LanternaUI - Class in fr.ens.biologie.genomique.eoulsan.ui: This class define an UI using Lanterna library.
LanternaUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
LATIN1_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: Latin1 charset.
LATIN1_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: Latin1 file encoding.
LAUNCH_MODE_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Launch mode property.
LAUNCH_SCRIPT_PATH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Launch script path.
LIBS_TO_HADOOP_REPACK_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The name of the system property that contains the list of libraries to repack for hadoop mode.
LICENSE_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Licence text.
LinuxCpuInfo - Class in fr.ens.biologie.genomique.eoulsan.util: Get information about processor on Linux systems.
LinuxCpuInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Public constructor.
LinuxInfo - Class in fr.ens.biologie.genomique.eoulsan.util: This class define a linux info file parser.
LinuxInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo
LinuxMemInfo - Class in fr.ens.biologie.genomique.eoulsan.util: Get information about memory on Linux systems
LinuxMemInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo: Public constructor.
list() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: List the content of a directory.
list() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
list(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: List a directory.
list(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
list(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
listFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: List files on Rserve server.
listPathsByPrefix(Path, String, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Return a list of the file of a path
listPathsByPrefix(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Return a list of the file of a path
listPathsBySuffix(Path, String, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Return a list of the file of a path
listPathsBySuffix(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Return a list of the file of a path
load(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Load a resource.
loadAllResources() - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
loadAllResources() - Method in interface fr.ens.biologie.genomique.eoulsan.util.ResourceLoader: Load all available resources.
loadImage(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Load an image.
loadMetadata(Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Set the metadata of a data from the metadata storage.
loadMetadata(Data, List<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Set the metadata of a data from the metadata storage.
loadModule(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry: Load a module.
loadPreResults(File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Load pre result file.
loadPreResults(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Load pre-result file.
loadResources(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
loadResources(String) - Method in interface fr.ens.biologie.genomique.eoulsan.util.ResourceLoader: Load a resource.
loadSAMHeaders(JobContext) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils: Load SAM headers.
loadSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Load application options.
loadSettings(File) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Load application options.
loadTranslator(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils: Create a translator annotation from a link file.
loadTranslator(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils: Create a translator annotation from an additional annotation file and a link file.
LOCAL - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
LOCAL - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
LOCAL - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
LOCAL_ONLY - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
LOCAL_THREADS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
LocalEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan: This class define the Runtime to execute low level IO operation for Eoulsan in local mode.
LocalOnly - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a plug-in class as usable in local mode only.
LocalUploadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This class define a Step for local mode file uploading.
LocalUploadModule(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule: Public constructor.
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
lock() - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.Locker: Wait the token and then lock the resource.
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
Locker - Interface in fr.ens.biologie.genomique.eoulsan.util.locker: This interface define an interface for the global execution locker.
LockerUtils - Class in fr.ens.biologie.genomique.eoulsan.util.locker: Utility class for the locker classes.
LockerUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.LockerUtils
log(Level, Infos.Info) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Log a list of Info.
log(Level, List<Infos.Info>) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Log a list of Info.
LOG_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Log extension.
LOG_FILENAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Eoulsan log filename.
LOG_FORMATTER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Format of the log.
LOG_LEVEL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The log level of the application.
logConfig(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Log a CONFIG message using getLogger().config().
logEndTime(Process, String, long) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Log the time of execution of a process.
logFiner(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Log a FINER message using getLogger().finer().
logFinest(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Log a FINEST message using getLogger().finest().
logHadoopSysInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopInfo
logInfo(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Log an INFO message using getLogger().info().
logPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Create the log path.
logSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Add all the settings to the log.
logSevere(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Log an SEVERE message using getLogger().severe().
logWarning(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Log an WARNING message using getLogger().warning().
LOW_QUAL_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
LRT - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest

M

MACS2_RMODEL - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats: MACS 2 R model format.
MACS2Module - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This class defines the macs2 peak-calling step.
MACS2Module() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
mailInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with email configuration informations.
main(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.Main: Main method of the program.
main(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker: Main method.
Main - Class in fr.ens.biologie.genomique.eoulsan: This class is the main class.
MainCLI - Class in fr.ens.biologie.genomique.eoulsan: Main class in local mode.
MainCLI(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.MainCLI: Constructor.
MainHadoop - Class in fr.ens.biologie.genomique.eoulsan: Main class in Hadoop mode.
MainHadoop(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.MainHadoop: Constructor.
makeOptions() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create options for command line
makeOptions() - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI: Create options for command line
makeReport(HTMLReportArchive) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper: 'key': offset of the beginning of the line from the beginning of the TFQ file.
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper: 'key': offset of the beginning of the line from the beginning of the alignment file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper: 'key': offset of the beginning of the line from the beginning of the alignment file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper: 'key': offset of the beginning of the line from the beginning of the TFQ file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper: 'key': offset of the beginning of the line from the beginning of the TFQ file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper: 'key': offset of the beginning of the line from the beginning of the SAM file if data are in single-end mode or in TSAM file if data are in paired-end mode.
MAPPER_ARGUMENTS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAPPER_DOCKER_IMAGE_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAPPER_FLAVOR_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAPPER_INDEX_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
MAPPER_INDEX_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAPPER_NAME_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAPPER_RESULT_BED - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BED format.
MAPPER_RESULTS_BAM - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BAM results data format.
MAPPER_RESULTS_INDEX_BAI - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BAM index results data format.
MAPPER_RESULTS_LOG - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Mapper log file format.
MAPPER_RESULTS_SAM - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: SAM results data format.
MAPPER_VERSION_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAPPER_WRITING_ERRORS - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
MapperIndexDataFormat - Class in fr.ens.biologie.genomique.eoulsan.data: This class define a DataFormat from an XML file.
MapperIndexDataFormat(Mapper) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat: Public constructor.
MapperIndexDataFormat(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat: Public constructor.
MapperInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for mapper reports.
MapperInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
MappingCounters - Enum in fr.ens.biologie.genomique.eoulsan.modules.mapping: This enum define the names of the counters of the steps of this package.
MapReduceUtils - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class contains utility method to easily manipulate the new Hadoop MapReduce API.
markSupported() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
MatrixToCellRangerMatrixModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell: This class define a class that allow to create a Cell Ranger matrix from an existing matrix file.
MatrixToCellRangerMatrixModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
MAX_LINE_LENGTH - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
MAX_LOCAL_THREADS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MAX_READS_TO_CHECK - Static variable in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
MaxByteInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class allow to create an InputStream that can read a maximum of byte from another InputStream.
MaxByteInputStream(InputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream: Public constructor
MAXIMUM - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
maxValueLength() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info: Get the maximal length of the values
MEAN - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
memInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with memory informations.
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
merge(Iterator<DataFile>, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger: Merger data.
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
MergeInputRepLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq: This class merges SAM files of input of the same experiment.
MergeInputRepLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
mergeInto(OutputStream, Path, String, String, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
mergeInto(OutputStream, Path, String, String, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils: Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
MergePeaksModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This class defines the peak merging step.
MergePeaksModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
Merger - Interface in fr.ens.biologie.genomique.eoulsan.splitermergers: This interface define a splitter.
MergerModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a generic merger module.
MergerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
mergeSAMInto(Path, Path, String, String, SAMFormat, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.
mergeSAMInto(Path, Path, String, String, SAMFormat, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils: Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.
Metadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines common methods for metadata.
MINIMAL_JAVA_VERSION_REQUIRED - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Minimal java version required by Eoulsan.
MINIMAP2_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Minimap2 index data format.
Minimap2IndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class define a module that generate a Minimap2 mapper index.
Minimap2IndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
MISSING_MATES_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
mkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create a directory with the path of the DataFile.
mkdir(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create a directory.
mkdir(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
mkdir(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
mkdirs() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create a directory and its parents if not exists with the path of the DataFile.
mkdirs(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create a directory and its parents if not exists.
mkdirs(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
mkdirs(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
mkdirs(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create a directory.
MODEL_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Module - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a Module.
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule: Module name.
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule: Module name.
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
ModuleRegistry - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a registry for modules.
Modules - Class in fr.ens.biologie.genomique.eoulsan.core: This class contains useful methods for writing Step classes.
ModulesAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action that show the list of available formats.
ModulesAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
modulesAndFormatsInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with modules and format informations.
ModuleService - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class allow to get a Step object from a class in the classpath.
MonoThreadTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class define a mono thread scheduler.
MonoThreadTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
move(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Move file from a path to another path.
move(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Move file from a path to another path.
MULTIQC_REPORT_HTML - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: MultiQC HTML report format.
MultiQCModule - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a module for MultiQC.
MultiQCModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
MultiThreadTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class define a muti thread scheduler.
MultiThreadTaskScheduler(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler: Constructor.

N

name() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
name() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
name() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
NAME_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
Naming - Class in fr.ens.biologie.genomique.eoulsan.core: This class contains methods to validate workflow object names.
needAdditionalRecordAfterSplit() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
newDataPath(DataPath, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
newDataPath(DataPath, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
newDataPath(DataPath, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
newDataPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
newDataPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
newDataPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
newDockerRequirement(String) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement: Create a new docker image as mandatory requirement.
newDockerRequirement(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement: Create a new docker image requirement.
newEoulsanException(ToolInfo, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Create an EoulsanException.
newEoulsanException(ToolInfo, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Create an EoulsanException.
newEoulsanRuntime(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime: Public constructor, initialize the runtime.
newEoulsanRuntime(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime: Public constructor, initialize the runtime.
newGenericCounter(String, String, long) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
newJobContext(Configuration, JobID) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil: Creates JobContext from a JobConf and jobId using the correct constructor for based on Hadoop version.
newPathRequirement(String) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement: Create a new mandatory executable requirement.
newPathRequirement(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement: Create a new executable requirement.
newPathWithOtherExtension(Path, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create a new path with the same parent directory and basename but without another extension.
newRExecutor(RExecutorFactory.Mode, String, String, File, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory: Create a new instance of RExecutor.
newRserveRequirement(String) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement: Create a new mandatory Rserve requirement.
newRserveRequirement(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement: Create a new Rserve requirement.
newServer(Set<Ticket>, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
newService(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
newSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter: Create a new SimpleProcess that will be use to launch the command.
newSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
newStandardFilename(Step, String, DataFormat, Sample, int, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Create a standard filename.
newTaskAttemptContext(Configuration, TaskAttemptID) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil: Creates TaskAttempContext from a JobConf and jobId using the correct constructor for based on Hadoop version.
newToolElement(ToolInfo, Element) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElementFactory: Gets the instance tool element.
newToolElement(ToolInfo, Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElementFactory: Gets the instance tool element.
next() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
next() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
nextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream: Get the next InputStream to concatenate
nextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream
nextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.PathConcatInputStream
nextKeyValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
nextKeyValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
nextKeyValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
nextKeyValue(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
NO - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
NO_HDFS_DOWNLOAD - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule: Key in the settings to use to disable the downloads.
noInputPort() - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Create the ports with no ports.
NoLog - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that requires no log.
NONE - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
NoOutputDirectory - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that requires no output directory.
noOutputPort() - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Create the ports with no ports.
Normalization - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class create and launch an R script to compute normalisation of expression data
Normalization(RExecutor, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Public constructor.
NORMALIZATION_FUNCTIONS - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
NormalizationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class define the module for normalization
NormalizationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
NOT_ALIGNED_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
NOT_NEEDED - fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
NOT_UNIQUE_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
notifyStepState(Step, int, int, double) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: The progress of the step has been changed.
notifyStepState(Step, int, int, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyStepState(Step, int, int, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyStepState(Step, int, int, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyStepState(Step, int, String, double) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: The progress of the step for a sample has been changed.
notifyStepState(Step, int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyStepState(Step, int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyStepState(Step, int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyStepState(Step, Step.StepState) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: The status of the step has been changed.
notifyStepState(Step, Step.StepState) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyStepState(Step, Step.StepState) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyStepState(Step, Step.StepState) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyStepState(Step, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: The note of the step has been changed.
notifyStepState(Step, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyStepState(Step, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyStepState(Step, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyTaskDone(Step, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: Notify that a task has been done.
notifyTaskDone(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyTaskDone(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyTaskDone(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyTaskRunning(Step, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: Notify that a task is running.
notifyTaskRunning(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyTaskRunning(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyTaskRunning(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyTaskSubmitted(Step, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: Notify that a task has been submitted.
notifyTaskSubmitted(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyTaskSubmitted(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyTaskSubmitted(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
notifyWorkflowSuccess(boolean, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver: Notify the success of the workflow.
notifyWorkflowSuccess(boolean, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
notifyWorkflowSuccess(boolean, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
notifyWorkflowSuccess(boolean, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
NoUI - Class in fr.ens.biologie.genomique.eoulsan.ui: This class define an UI that do nothing.
NoUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.NoUI
nullToEmpty(Collection<E>) - Static method in class fr.ens.biologie.genomique.eoulsan.util.CollectionUtils: Return an empty collection if the input collection is null;

O

obfuscate(Design, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Remove optional description fields and obfuscate condition field.
OBFUSCATE_DESIGN_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Obfuscate design default.
OBFUSCATE_DESIGN_REMOVE_REPLICATE_INFO_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Remove design replicate info when obfuscate design default.
onResized(Terminal, TerminalSize) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
open() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create an InputStream for the DataFile.
open() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
openConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
openConnection() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Open the connection.
openConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
openDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Open the design file.
openFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Open a file to read on Rserve server.
openParamFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Open the Workflow file.
OPERATOR_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
OPTIONAL_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
OTHER_LOG_FILENAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Other log filename.
OtherLogConfigurator - Class in fr.ens.biologie.genomique.eoulsan: This class allow to configure non Eoulsan log using Log4J.
OtherLogConfigurator() - Constructor for class fr.ens.biologie.genomique.eoulsan.OtherLogConfigurator
OUTPUT_COMPRESSION_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
OUTPUT_FILE_FORMAT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
OUTPUT_FILTERED_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
OUTPUT_FILTERED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
OUTPUT_MAPPING_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
OUTPUT_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Output path constant name.
OUTPUT_PRETREATMENT_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
OUTPUT_TREE_TYPE_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Output tree type.
OutputPort - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define an output port of a step.
outputPortName - Variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser.StepOutputPort
OutputPorts - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a group of output ports.
OutputPortsBuilder - Class in fr.ens.biologie.genomique.eoulsan.core: This class allow to easily create input ports for a step.
OutputPortsBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
OWN_PARALLELIZATION - fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode

P

PAIRED_END_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
PairedEndFastqToTfq - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class allow to convert two FASTQ file in one TFQ file.
PairedEndFastqToTfq() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq
PairedEndFastqToTfq.FastqPairedEndReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define the reducer required to convert FASTQ files into TFQ file.
ParallelizationMode - Enum in fr.ens.biologie.genomique.eoulsan.core: This enum define the parallelization modes of a step.
Parameter - Class in fr.ens.biologie.genomique.eoulsan.core: This class define a parameter.
Parameter(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.Parameter: Public constructor.
PARAMETER_PREFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The prefix of the parameters of the application.
PARAMETRIC - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
PARAMETRIC - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
PARENT_ID_NOT_FOUND_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
PARENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
parse() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Parse the workflow file.
parse() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo
parse(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create a FileNaming object from a DataFile object.
parse(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create a FileNaming object from a File object.
parse(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create a FileNaming object from a filename.
parse(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput: This method define a parser for the values of the "discardoutput" attribute of the Eoulsan workflow.
parse(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode: Parse a mode name and returns the mode.
parseRExecutorParameter(StepConfigurationContext, Set<Parameter>, Set<Requirement>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration: Parse the step parameter and create a configured RExecutor object.
PARTIALLY_DONE - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
partitionInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with Docker configuration informations.
patchFastQC() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher: Patch FastQC for hadoop mode.
PathConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define an InputStream that concatenate path in an InputStream.
PathConcatInputStream(List<Path>, Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.PathConcatInputStream: Constructor.
PathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define an abstract class for DataProtocols based on the Hadoop framework Path object.
PathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol: Constructor.
PathRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define a executable requirement.
PathRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
PathUtils - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: This class define utility method to manipulate the Hadoop Path object.
PathUtils.PrefixPathFilter - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: Simple PathFilter to filter Paths with their beginning
PathUtils.SuffixPathFilter - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop: Simple PathFilter to filter Paths with their suffix
PausableThreadPoolExecutor - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class define a Pausable thread pool executor.
PausableThreadPoolExecutor(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor: public constructor.
pause() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
pause() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor: Pause the executor.
PBSProTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a PBSPro cluster scheduler using a Bpipe script.
PBSProTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.PBSProTaskScheduler: Constructor.
PEAK - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats: Peak format data format.
PEAK_XLS - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats: Peaks XLS format.
PER_CONDITION - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
POOLED - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
Port - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a port of a step.
Ports<E extends Port> - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a group of ports.
PORTS_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
PrefixPathFilter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter: Public constructor.
PrefixPathFilter(String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter: Public constructor.
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
preprocess(TaskContext, Data, File) - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor: Preprocess data.
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
PreTreatmentExpressionMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: This class define a mapper for the pretreatment of paired-end data before the expression estimation step.
PreTreatmentExpressionMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
PreTreatmentExpressionReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: This class define a reducer for the pretreatment of paired-end data before the expression estimation step.
PreTreatmentExpressionReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer
PreTreatmentMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.
PreTreatmentMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
PreTreatmentReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define a reducer for the pretreatment of paired-end data before the reads filtering step.
PreTreatmentReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentReducer
PRINT_STACK_TRACE_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Print stack trace default.
printWarning(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print warning.
printWrapped(PrintStream, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
printWrapped(PrintStream, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
printWrapped(PrintStream, String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
process(WatchedEvent) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
process(WatchedEvent) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
PROCESS - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
ProcessRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define a standard RExecutor using a system process.
ProcessRExecutor(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Constructor.
processSequence(Sequence) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
ProcessThreadErrOutput(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
ProcessThreadOutput(InputStream, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler.ProcessThreadOutput: Constructor.
ProcessUtils - Class in fr.ens.biologie.genomique.eoulsan.util: Utility class for launching external process.
ProcessUtils.ProcessResult - Class in fr.ens.biologie.genomique.eoulsan.util
ProcessUtils.ProcessThreadErrOutput - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to fetch standard error of the process, without printing
Progress - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface allow to set the progress of a task.
ProgressCounterInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class implements a FilterInputStream that inform Hadoop of the progress of task using counters.
ProgressCounterInputStream(InputStream, Counter) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
ProgressCounterOutputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class implements an OutputStream that inform Hadoop of the progress of task using counters.
ProgressCounterOutputStream(OutputStream, Counter) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol: Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol: Protocol name.
publish(LogRecord) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
put(MapperInstance, GenomeDescription, Map<String, String>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Put the index archive in the storage.
putData(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create an OutputStream from the source.
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
putData(DataFile, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Copy data from a source to a destination source
putData(DataFile, DataFileMetadata) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create an OutputStream from the source.
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Put a file for the analysis.
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
putFile(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Put a file from the RServer.
putFile(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Put a file from the RServer.
putInputFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
putInputFile(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Put a file for the analysis.
putInputFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
putInputFile(DataFile, String) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Put a file.
PYTHON_VARIABLES_DICT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: The Constant INSTANCE_NAME.

R

raisesError() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
raisesWarning() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
rAndRserveInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with R and Rserve configuration informations.
RATIO - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
rawCopy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles: Copy a file.
rawCreate() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create an OutputStream for the DataFile.
rawCreate() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
rawOpen() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create an InputStream for the DataFile.
rawOpen() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
rConnection - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
rConnection - Variable in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
read() - Method in interface fr.ens.biologie.genomique.eoulsan.design.io.DesignReader: Read the design.
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
read(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
read(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
read(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
read(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Read a step result file.
read(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Read a step result file.
readAndCheckDesign(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Read and Check design
readLine(Text, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
READS_FASTQ - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Reads fastq data format.
READS_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
READS_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
READS_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
READS_REJECTED_BY_FILTERS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
READS_TFQ - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Reads tfq data format.
ReadsChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a checker on FASTQ files.
ReadsChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
ReadsFilterHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class is the main class for the filter reads program in hadoop mode.
ReadsFilterHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
ReadsFilterLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for reads filtering.
ReadsFilterLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsFilterLocalModule
ReadsFilterMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class defines a read filter mapper.
ReadsFilterMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
ReadsMapperHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define an mapper module in Hadoop mode.
ReadsMapperHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
ReadsMapperLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for reads mapping.
ReadsMapperLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
ReadsMapperMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class defines a generic mapper for reads mapping.
ReadsMapperMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
readStaticScript(String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Read a static part of the generated script.
READY - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
reduce(Text, Iterable<LongWritable>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionReducer: 'key': annotation identifier of the feature (gene, mRNA, exon...).
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer: 'key': the identifier of the aligned read without the integer indicating the member of the pair.
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq.FastqPairedEndReducer
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentReducer: 'key': the identifier of the read without the integer indicating the member of the pair.
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterReducer: 'key': identifier of the aligned read, without the integer indicating the pair member if data are in paired-end mode.
REFERENCE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
REFERENCE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
REFERENCE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
referenceValueToInt(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Convert a reference value to an integer.
register(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Register a step of the workflow.
register(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Register a DataFormat.
register(DataFormat[]) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Register DataFormats.
register(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus: Register an listener object.
registerInputAndOutputPorts(Module) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
registerStep(Step, Module) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Register a step instance.
registerThreadGroupLogger(ThreadGroup, Logger) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Register a logger for a thread group.
reload() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry: Reload the list of available modules.
reload() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Reload the list of the available data types.
reload() - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader
reload() - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
reload() - Method in interface fr.ens.biologie.genomique.eoulsan.util.ResourceLoader: Reload the list of available resources.
remove(EmergencyStopTask) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks: Remove an emergency task.
remove(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
remove(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Remove the value according the key.
remove(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
remove(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
removeAllFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Remove all the files of the working directory.
removedParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for removed parameters.
removedParameter(String, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for removed parameters.
removeExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Remove the experiment.
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Remove a file of the analysis.
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Remove a file on the RServer.
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
removeHadoopJobEmergencyStopTask(ClusterTaskScheduler, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask: Remove a cluster Job to the EmergencyStopTasks.
removeHadoopJobEmergencyStopTask(Job) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask: Remove an Hadoop Job to the EmergencyStopTasks.
removeInputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
removeInputFiles() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Remove input files.
removeKey(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Remove a entry.
removeNamespace(String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Remove the namespace from the name of a variable.
removeObserver(StepObserver) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Remove a listener.
removeResourcePath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Add a resource path.
removeSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Remove the sample.
removeSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
removeSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
removeSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Remove the sample.
removeStep(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Remove a step instance.
removeThreadGroupLogger(ThreadGroup) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Remove a logger for a thread group.
rename(DataFile, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Rename a file.
rename(DataFile, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
rename(DataFile, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
renamedParameter(StepConfigurationContext, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters that has been renamed.
renamedParameter(StepConfigurationContext, Parameter, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters that has been renamed.
renamedParameter(String, Parameter, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters that has been renamed.
renameTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Rename the DataFile.
REP_TECH_GROUP_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
REP_TECH_GROUP_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
repack() - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJarRepackager: Repackage the jar application only if the repackaged file does not exist.
repack(File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJarRepackager: Repackage the jar application.
replaceLocalPathBySymlinks(Design, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Replace the local paths in the design by paths to symbolic links in a directory.
replaceRtgNA(List<String>, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Replace na values in RepTechGroup list to avoid pooling error.
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
Requirement - Interface in fr.ens.biologie.genomique.eoulsan.requirements: This interface define a requirement for an Eoulsan Step.
REQUIREMENT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
REQUIREMENT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
REQUIREMENT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
RequirementInstallerModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class allow to install a requirement.
RequirementInstallerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
RequirementService - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define a service for requirements.
RequiresAllPreviousSteps - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that requires the all the previous step in the workflow file.
RequiresPreviousStep - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that requires the previous step in the workflow file.
reset() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
reset() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
resolveClass(ObjectStreamClass) - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream
ResourceLoader<S> - Interface in fr.ens.biologie.genomique.eoulsan.util: This interface define a resource loader.
resume() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
resume() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor: Resume the executor.
ReuseModuleInstance - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a module class that can reuse a module instance for each task.
RExecutor - Interface in fr.ens.biologie.genomique.eoulsan.util.r: This interface define how to prepare, launch and retrieve data of a R analysis.
REXECUTOR_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
REXECUTOR_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
REXECUTOR_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
RExecutorFactory - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define a factory to create RExecutor objects.
RExecutorFactory() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory
RExecutorFactory.Mode - Enum in fr.ens.biologie.genomique.eoulsan.util.r: Define a enum for the mode of RExecutor.
RmDupLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq: This class removes PCR duplicates from a SAM file.
RmDupLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
RModuleCommonConfiguration - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class define common methods used for the configuration of the step of the package.
RModuleCommonConfiguration() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
ROOT_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
RSConnection - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define an enhanced connection to RServe.
RSConnection() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Default constructor.
RSConnection(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Public constructor.
RSCRIPT_EXECUTABLE - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
RSERVE - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
RSERVE_SERVER_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
RserveRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define a Rserve server requirement.
RserveRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
RserveRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define a RServe RExecutor.
RserveRExecutor(File, File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor: Public constructor.
RSingleCellExperimentCreatorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell: This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.
RSingleCellExperimentCreatorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler.ProcessThreadOutput
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Run the task context.
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
run() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
run(TaskContext, Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Run normalisation step
run(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp: This is the main driver for recursively copying directories across file systems.
runDEseq2(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2: Method to run DESeq2.
RUNNING - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
runRExecutor(TaskContext, Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Execute Rnw script.
runWithException(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp: This is the main driver for recursively copying directories across file systems.

S

SAM2BAMHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define a module for converting SAM files into BAM.
SAM2BAMHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
SAM2BAMLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for converting SAM files into BAM.
SAM2BAMLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2BAMLocalModule
SAM2FASTQLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for converting SAM files into FASTQ.
SAM2FASTQLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2FASTQLocalModule
SAMFilterHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define a filter alignment step in Hadoop mode.
SAMFilterHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
SAMFilterLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a Step for alignments filtering.
SAMFilterLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAMFilterLocalModule
SAMFilterMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class defines a mapper for alignment filtering.
SAMFilterMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
SAMFilterReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define a reducer for alignments filtering.
SAMFilterReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterReducer
SAMHeaderHadoopUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.
SAMHeaderHadoopUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils
SAMHeaderHadoopUtils.SAMHeaderWriter - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class allow to save the SAM header read by a mapper.
SAMHeaderWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter: Constructor.
SAMInputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define an InputFormat for SAM files for the Hadoop MapReduce framework.
SAMInputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
SAMMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for SAM files.
SAMMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
SAMOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a SAM output format.
SAMOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMOutputFormat
Sample - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines a sample.
SAMPLE_ID_FIELD - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Sample Id field.
SAMPLE_ID_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
SAMPLE_NAME_FIELD - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Sample Name field.
SAMPLE_NAME_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
SAMPLE_NUMBER_FIELD - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Sample Name field.
SAMPLE_NUMBER_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
SampleMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the sample metadata.
SAMRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordReader for SAM files for the Hadoop MapReduce framework.
SAMRecordReader(TaskAttemptContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader: Public constructor.
SAMRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordWriter for SAM files.
SAMRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter: Public constructor.
SAMSequenceFile - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class define a SequenceFile for SAM files.
SAMSequenceFile(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile: Public constructor.
SAMSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for SAM files.
SAMSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
SAVE_WORKFLOW_IMAGE_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Save workflow image.
saveConfigurationFiles() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Save configuration files.
saveConfigurationFiles() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow
saveDotFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Workflow2Graphviz: Convert and save the workflow as a Graphviz file.
saveFinalResults(File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Save the final results.
saveFinalResults(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Save the final results.
saveImageFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Workflow2Graphviz: Convert and save the workflow as an image file.
saveMetaData(Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Save metadata of a Data object.
saveSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Save application options.
saveSettings(File) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Save application options.
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.PBSProTaskScheduler
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.SLURMTaskScheduler
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TORQUETaskScheduler
SelectParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a select tool element parameter.
SelectParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement: Instantiates a new select tool element parameter.
SelectParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement: Instantiates a new select tool element parameter.
sendMail(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
sendTokens(TaskContextImpl, TaskResultImpl) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Send tokens for a serialized task result.
SEP - Static variable in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: The Constant SEP.
separator - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFile: The separator char ('/') as a String.
separatorChar - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFile: The separator char ('/').
SERIAL_NUMBER_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
SerializableStopwatch - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
SerializableStopwatch() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
serialize(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Serialize the TaskContext object.
serialize(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Serialize the TaskResult object.
serialize(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Serialize the TaskContext object.
serialize(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Serialize the TaskResult object.
serialize(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Serialize the TaskContext object.
serialize(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Serialize the TaskResult object.
serializeOutputData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Serialize output data.
serializeOutputData(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Serialize output data.
serializeOutputData(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Serialize output data.
set(Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set several field of the object from a Data object.
set(DataMetadata) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: The the entries of the metadata with the entries of another metadata object.
set(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Set a metadata entry.
set(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
set(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Set the value according the key.
set(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
set(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
set(String, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
set(String, List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Set the value as a list according the key.
set(String, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
set(String, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
setAdditionalAnnotationFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Set the additional annotation file.
setAdditionalAnnotationFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
setAdditionalAnnotationHypertextLinksPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the additional annotation hypertext links path.
setAdditionalAnnotationStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the additional annotation storage path.
setArgv0Class(Class<?>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
setAWSAccessKey(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the AWS access key.
setAWSSecretKey(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the AWS secret key.
setBuildContrast(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the buildContrast DEseq2 option.
setBuildContrast(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setBypassPlatformChecking(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if the platform checking must be avoided.
setClusterSchedulerName(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the name of the cluster scheduler.
setCommandArgs(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Override the commandArg() R function.
setCommandLine(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Set the context command line.
setCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
setComment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the comment.
setComparisons(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the comparisons DEseq2 option.
setComparisons(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setCompression(CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the compression
setCondition(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Set the condition.
setCondition(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
setCondition(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the condition.
setCondition(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
setConf(Configuration) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
setContextName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Set the context name.
setContextName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
setContrast(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the contrast DEseq2 option.
setContrast(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setContrastFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the contrastFile DEseq2 option.
setContrastFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setCounters(Reporter, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Set the context counters.
setCounters(Reporter, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
setDataFile(Data, int, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Change the DataFile in a Data object
setDataFile(Data, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils: Change the DataFile in a Data object
setDataFile(Data, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Change the DataFile in a Data object
setDataFiles(Data, List<DataFile>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils: Change the DataFiles in a Data object
setDataFiles(Data, List<DataFile>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Change the DataFiles in a Data object
setDataFormatPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the format path.
setDataFormatPaths(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the data format paths
setDataMetadata(Data, Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Set the metadata of a data object from the information of another data object.
setDataMetadata(Data, Collection<Data>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils: Set the metadata of a data object from the information of another data object.
setDataMetadata(Data, Collection<Data>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Set the metadata of a data object from the information of another data object.
setDataMetaData(Data, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils: Set the metadata of a data object from the information of a Sample object from a Design.
setDataMetaData(Data, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Set the metadata of a data object from the information of a Sample object from a Design.
setDataName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the data name.
setDataPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the data directory path.
setDate(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the date.
setDebug(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the debug setting.
setDefaultClusterMemoryRequired(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the default memory required for the steps in cluster mode.
setDefaultFastqFormat(FastqFormat) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Fastq format default value.
setDefaultLocale() - Static method in class fr.ens.biologie.genomique.eoulsan.Globals: Set the default Local of the application
setDescription(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Set the context description.
setDescription(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
setDescription(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the description.
setDesignFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Set the design file.
setDesignFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the designFile DEseq2 option.
setDesignFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setDesignPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the design file path.
setDockerBackEnd(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Docker URI.
setDockerBySingularityEnabled(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Enable Docker features using Singularity
setDockerConnectionURI(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Docker URI.
setDockerMountNFSRoots(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if when use Docker, NFS roots must been mounted instead of file paths.
setDockerSingularityStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Docker singularity storage path.
setElementValue(ToolElement, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Set the tool element value.
setExecutablesTempDirectory(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the temporary directory for executables.
setFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Set the FASTQ format of the data.
setFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the fastq format.
setFileIndex(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the file index.
setForceStepInstanceReuse(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Force the TaskRunner to reuse the original step instance when execute the task.
setFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the format.
setFormatter(Formatter) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
setGalaxyToolPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Galaxy tool path.
setGalaxyToolsPaths(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Galaxy tools paths
setGenomeDescStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the genome description storage path.
setGenomeFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Set the genome file.
setGenomeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
setGenomeMapperIndexStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the genome index storage path.
setGenomeStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the genome storage path.
setGffFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Set the gff file.
setGffFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
setGFFStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the GFF storage path.
setGtfFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Set the gff file.
setGtfFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
setGTFStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the GTF storage path.
setHadoopLogLevel(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the Hadoop log level.
setHadoopWorkingPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the local working path.
setHeaderMergerSortOrder(Configuration, SAMFileHeader.SortOrder) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
setImmutable() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Set the object immutable.
setInstallable(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
setJarFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Set the jar file.
setJobDescription(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set job description.
setJobEnvironment(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set job environment.
setJobPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the job path
setKeepRServeFiles(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if save Rscripts is true
setLevel(Level) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
setLocalThreadsNumber(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the number of threads to use in local mode.
setLocalWorkingPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the local working path.
setLoggerName(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Set the logger name.
setMode(AbstractEoulsanRuntime.EoulsanExecMode) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime: Set the cluster mode.
setModel(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the model DEseq2 option.
setModel(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Set the design name.
setName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Set the name of the experiment.
setName(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
setName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Set the sample name.
setName(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
setNote(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set the note.
setObfuscateDesign(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if the design must be obfuscated
setObfuscateRemoveDesignInfo(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if the replicate information must be removed from the design.
setOperator(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the operator.
setOptionnal(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
setOutputPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the output path
setOutputTreeType(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the output tree type.
setPairedEnd(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Set single-end/paired-end data type.
setPart(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the part number.
setPortName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the port name.
setPrintStackTrace(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the print stack trace setting.
setProgress(double) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Set the progress of the processing.
setProgress(double) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set the progress of a step.
setProgress(double) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
setProgress(int, int, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Set the progress of the processing.
setProgress(int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set the progress of a step.
setProgress(int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
setProgressMessage(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Set the progress message.
setProgressMessage(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
setReads(List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the reads.
setReference(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Set the reference.
setReference(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
setReference(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
setReference(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the reference option.
setReference(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Set the reference.
setReference(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
setReference(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the reference.
setReference(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setReference(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
setRepTechGroup(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Set the ReptechGroup.
setRepTechGroup(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
setRepTechGroup(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the ReptechGroup.
setRepTechGroup(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
setResultMail(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the mail address for eoulsan results.
setRServeServerEnabled(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if RServe is enabled.
setRServeServerName(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the RServe server name.
setSampleId(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Set the sample id related to the data
setSampleName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Set the sample name related to the data.
setSampleNumber(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the sample number related to the data.
setSampleNumber(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Set the sample number related to the data
setSaveRscript(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if save Rscripts is true
setSaveWorkflowImage(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if an image of the workflow must be saved.
setSendResultMail(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if an email must be sent at the end of the analysis.
setSerialNumber(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the serial number.
setSetting(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set a setting value.
setSetting(String, String, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set a setting value.
setSettings(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the values of the settings with another Settings object.
setSkip(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Set the skip option.
setSkip(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
setSMTPHost(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the SMTP server host.
setStepId(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Set the step id.
setTaskDone(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set task done.
setTaskPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the task path
setTaskProgress(int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set the progress of a task.
setTaskProgress(int, String, int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set the progress of a task.
setTaskRunning(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set task running.
setTaskSubmitted(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Set task submitted.
setTempDirectory(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the temporary directory.
setTemporaryPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the temporary directory path.
Settings - Class in fr.ens.biologie.genomique.eoulsan: This class define a settings class.
setUIName(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the UI name.
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
setup(Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer
setup(Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentReducer
setup(Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterReducer
setUseOldEoulsanResultFormat(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if Eoulsan result files must be written using the old format.
setUseStandardExternalModules(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set if standard external modules must be used.
setUUID(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Set the UUID.
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
setValue(String) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Sets the value.
setValues(Map<String, Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: Set the values.
setWorkflowFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Set the workflow file.
setWorkflowPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Set the workflow file path.
setWorking(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
setZooKeeperConnectString(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the ZooKeeper connect string.
setZooKeeperDefaultPort(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the ZooKeeper default port.
setZooKeeperSessionTimeout(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Set the ZooKeeper session timeout.
sh(List<String>) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command.
sh(List<String>, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command.
ShellModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a module that execute a shell command.
ShellModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
showAndLogErrorMessage(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Show and log an error message.
showDesign(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Show a design
showErrorMessageAndExit(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Show a message and then exit.
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction: Show the information on stdout
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction: Show the information on stdout
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
showMessageAndExit(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Show a message and then exit.
SimpleInputPort - Class in fr.ens.biologie.genomique.eoulsan.core: This class define an input port of a step.
SimpleInputPort(String, boolean, DataFormat, EnumSet<CompressionType>, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort: Constructor.
SimpleInputPort(String, DataFormat, EnumSet<CompressionType>, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort: Constructor.
SimpleInputPorts - Class in fr.ens.biologie.genomique.eoulsan.core: This class define a class that handles a set of input ports.
SimpleOutputPort - Class in fr.ens.biologie.genomique.eoulsan.core: This class define an output port of a step.
SimpleOutputPort(String, boolean, DataFormat, CompressionType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort: Constructor.
SimpleOutputPort(String, DataFormat, CompressionType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort: Constructor.
SimpleOutputPorts - Class in fr.ens.biologie.genomique.eoulsan.core: This class define a class that contains several output ports.
SINGLE_CELL_EXPERMIMENT_RDS - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: R single cell experiment.
singleInputPort(DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Convenient method to create the ports with only one port.
singleInputPort(String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Convenient method to create the ports with only one port.
singleOutputPort(DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Convenient method to create the ports with only one port.
singleOutputPort(String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Convenient method to create the ports with only one port.
size() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
size() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get the number of ports in the object.
size() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
size() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the size of the data.
size() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
size() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the number of metadata.
size() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
size() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
skip(long) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
SKIP_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
SLURMTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a SLURM cluster scheduler using a Bpipe script.
SLURMTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.SLURMTaskScheduler: Constructor.
softwareInfos(Main) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with Eoulsan software informations.
Splice2BEDModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for converting SAM files into BED.
Splice2BEDModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.Splice2BEDModule
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
split(DataFile, Iterator<DataFile>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter: Split data.
splitByChromosomes(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter: Split BAM file by chromosomes.
splitByChromosomes(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter: Split SAM file by chromosomes.
Splitter - Interface in fr.ens.biologie.genomique.eoulsan.splitermergers: This interface define a splitter.
SplitterModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a generic splitter module.
SplitterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
STANDARD - fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
STANDARD_EXTERNAL_MODULES_ENABLED_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Enable standard external modules.
STANDARD_EXTERNAL_MODULES_ENABLED_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
STANDARD_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
STAR_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: STAR index data format.
STARIndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class define a module that generate a STAR mapper index.
STARIndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
start() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Start the scheduler.
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
statusJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
statusJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Get the status of a job.
StatusResult(ClusterTaskScheduler.StatusValue) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult: Constructor.
StatusResult(ClusterTaskScheduler.StatusValue, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult: Constructor.
STD_OUTPUT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default standard output state.
Step - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a step of the workflow.
STEP_LOG_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Step log extension.
STEP_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
STEP_OUTPUT_DIRECTORY_SUFFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Step output directory suffix.
STEP_RESULT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Step result extension.
STEP_RESULT_OLD_FORMAT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Old step result format extension.
Step.DiscardOutput - Enum in fr.ens.biologie.genomique.eoulsan.core: This enum define the value of the discard output attribute of the step tag in the Eoulsan workflow file.
Step.StepState - Enum in fr.ens.biologie.genomique.eoulsan.core: This enum define the states of the steps.
Step.StepType - Enum in fr.ens.biologie.genomique.eoulsan.core: This enum define the type of step.
StepConfigurationContext - Interface in fr.ens.biologie.genomique.eoulsan.core
StepConfigurationContextImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a concrete implementation of the configuration context of a step.
stepId - Variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser.StepOutputPort
StepInstances - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class store module instances and avoid storing this instance in Step objects that are serialized.
StepObserver - Interface in fr.ens.biologie.genomique.eoulsan.core.workflow: This interface define workflow step events
StepObserverRegistry - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class allow to relay workflow step events to other observers.
StepOutputDataFile - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define an output file of workflow set.
StepOutputDataFile(StepOutputPort, Sample) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Constructor.
StepOutputDataFile(StepOutputPort, Sample, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Constructor.
StepOutputPort(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser.StepOutputPort
StepResult - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a step result.
StepResult(AbstractStep) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Constructor.
StepStateDependencies - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class allow to store the step state and its dependencies.
StepStateDependencies(AbstractStep) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Constructor.
stepStateEvent(StepStateEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Listen StepState events.
stepStateEvent(StepStateEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Handle step state change events.
stepStateEvent(StepStateEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Listen StepState events.
StepStatus - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a step status.
StepStatus(AbstractStep) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
stop() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Stop the scheduler.
stop() - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTask: Execute the stop task.
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks: Stop all the tasks.
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
stop() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
stopJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
stopJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Stop a job.
StorageDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This abstract class define a storage protocol.
StorageDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
storageInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with storage informations.
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
submit(Step, TaskContextImpl) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Submit a context to execute.
submit(Step, Set<TaskContextImpl>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
submit(Step, Set<TaskContextImpl>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
submit(Step, Set<TaskContextImpl>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
submit(Step, Set<TaskContextImpl>) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Submit contexts to execute.
submit(Runnable, T, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor: Submit a task.
submitAndWaitForJob(Job, String, int, TaskStatus, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.MapReduceUtils: Wait the completion of a job.
submitJob(String, List<String>, File, int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
submitJob(String, List<String>, File, int, int, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Submit a job.
SUCCESS - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
SuffixPathFilter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter: Public constructor.
SuffixPathFilter(String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter: Public constructor.
symlink(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create a symbolic link that target is the current file.
symlink(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create a symbolic link that target is the current file.
symlink(DataFile, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create a symbolic link.
symlink(DataFile, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
symlinkOrCopy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles: Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.
symlinkOrCopy(DataFile, DataFile, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles: Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.
symlinkOrCopy(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
sysInfoLog() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Log system information.
sysInfoLog() - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
system(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command.
SYSTEM_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: The system default charset.
SYSTEM_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: The system default charset.
systemInfos() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with system informations.

T

TAG_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement: The Constant TAG_NAME.
TARGET_CREATION - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
TASK_CONTEXT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task context extension.
TASK_DATA_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task output data extension.
TASK_DONE_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task done extension.
TASK_JOB_ID - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task jobb id extension.
TASK_LOG_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task done extension.
TASK_RESULT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task result extension.
TASK_STDERR_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task stderr extension.
TASK_STDOUT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Task stdout extension.
TaskContext - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define the context of a step.
TaskContextImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a task context.
TaskResult - Interface in fr.ens.biologie.genomique.eoulsan.core: This class define the result of a step.
TaskResultImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a result for a task context.
TaskResultImpl(TaskContextImpl, Date, Date, long, Throwable, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
TaskRunner - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class allow to run a task context.
TaskRunner(TaskContextImpl) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Constructor.
TaskRunner(TaskContextImpl, StepStatus) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Constructor.
TaskScheduler - Interface in fr.ens.biologie.genomique.eoulsan.core.schedulers: This interface define a task scheduler.
TaskSchedulerFactory - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class define a factory for TaskScheduler that can create only one instance.
TaskSerializationUtils - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class contains utility methods for serialization, deserialization and execution of Task objects.
TaskSerializationUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils
TaskStatus - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a step status.
TaskStatusImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a task status.
TechnicalReplicateMergerModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a merger module for technical replicates.
TechnicalReplicateMergerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
TEMP_PREFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The prefix for temporary files.
Terminal - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that is a terminal step.
TERMINAL_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
TerminalModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a terminal task that do nothing.
TerminalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
TextParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a text tool element parameter.
TextParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement: Instantiates a new text tool element parameter.
TextParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement: Instantiates a new text tool element parameter.
TGCCTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a TGCC cluster scheduler.
TGCCTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
throwExitCodeException(int, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Throw an IOException if the exit code of a process is not equals to 0.
Ticket - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a ticket for the TicketLocker.
Ticket() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
Ticket(int, long, long, long, String, long, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
Ticket(Ticket) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
Ticket(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
TicketLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a global locker using RMI messaging.
TicketLocker(String, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker: Public constructor.
TicketLocker(String, int, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker: Public constructor.
TicketScheduler - Interface in fr.ens.biologie.genomique.eoulsan.util.locker: Define the rmi interface for the TicketSchedulerServer.
TicketSchedulerServer - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a server for the scheduler.
toAbsoluteDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Convert the the DataFile to a absolute DataFile.
toDESeq2Value() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType: Convert the enum name into DESeq2 value.
toDESeq2Value() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType: Convert the enum name into DESeq2 value.
toDESeq2Value() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
toEoulsanLogV1() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get a representation of the result in the old Eoulsan format.
toFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Convert the DataFile object to File object if the underlying protocol allow it.
toFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
toJSON() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Convert the object to JSON
tokenEvent(Token) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
TokenManager - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a token manager for a step.
TokenManagerRegistry - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class store all the TokenManager instances.
ToolElement - Interface in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: The ToolElement interface.
ToolElementFactory - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a factory for ToolElement objects.
ToolElementFactory() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElementFactory
ToolExecutor - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: The class define an executor on tool set in XML file.
ToolExecutor(TaskContext, ToolInfo, String, Set<File>) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutor: Constructor a new galaxy tool executor.
ToolExecutorResult - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: The class define a result on execution tool.
ToolExecutorResult(List<String>, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Public constructor, command line can not be null or empty
ToolExecutorResult(List<String>, Throwable) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Public constructor, command line can not be null or empty
ToolInfo - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: The class define a tool data which contains all data extracted from XML file.
toPath() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Convert the DataFile object to Path object if the underlying protocol allow it.
toRealDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Convert the the DataFile to a DataFile where all the indirection has been solved.
TORQUETaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a TORQUE cluster scheduler using a Bpipe script.
TORQUETaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TORQUETaskScheduler: Constructor.
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIEvent
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
toString() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
toString() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
toString() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
toString() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
toString() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
toString() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
toString() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
toString() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
TOTAL_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
TOTAL_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
toUri() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Convert the DataFile object to an URI.
toValidName(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Naming: Convert a string to a valid name string that can be used for step id or data name.
toXML() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Convert the object in XML.
TrackHubModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq: This class construct TrackHub for genome browser visualization.
TrackHubModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
tryLock(long, TimeUnit) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement: The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement: The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement: The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement: The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement: The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement: The Constant TYPE.

U

UI - Interface in fr.ens.biologie.genomique.eoulsan.ui: This interface define how UI is informed of The workflow changes.
UI_NAME_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default UI name.
UIEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define an abstract UIEvent
UIEvent() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.UIEvent
UIService - Class in fr.ens.biologie.genomique.eoulsan.ui: This class define a service to retrieve a UI.
uiStepEvent(UIStepEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Handle UI step events.
UIStepEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a UI step event.
uiTaskEvent(UITaskEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Handle UI task events.
UITaskEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a UI task event.
UITaskEvent(Step, UITaskEvent.TaskStatusMessage, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.UITaskEvent: Constructor.
uiWorkflowEvent(UIWorkflowEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Handle UI workflow events.
UIWorkflowEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a UI workflow event.
UIWorkflowEvent(boolean, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent: Constructor.
uk.ac.babraham.FastQC.Report - package uk.ac.babraham.FastQC.Report
UNKNOWN - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
unknownParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for unknown parameters.
unknownParameter(String, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for unknown parameters.
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
unlock() - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.Locker: Unlock the resource.
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
UNMAP_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
UNMAP_READS_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Unmap reads results data format.
UNMAPPED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
UnmodifiableData - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define an unmodifiable data
unmodifiableDesign(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignFactory: Create an unmodifiable wrapper around an existing design.
UnmodifiableExperiment - Class in fr.ens.biologie.genomique.eoulsan.design
UnmodifiableExperiment(Experiment) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
UnmodifiableExperimentMetadata - Class in fr.ens.biologie.genomique.eoulsan.design
UnmodifiableExperimentSampleMetadata - Class in fr.ens.biologie.genomique.eoulsan.design
UnmodifiableExperimentSampleMetadata(ExperimentSampleMetadata) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
unregister(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus: Unregister an listener object.
UNUSED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
unZipPathToLocalFile(Path, File, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Unzip a zip file on local file system.
unZipPathToLocalFile(Path, File, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Unzip a zip file on local file system.
updateLastActiveTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
UploadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This class define a abstract module class for files uploading.
UploadModule(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule: Public constructor.
URLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define an abstract class for DataProtocols based on the URL class.
URLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
USE_BUNDLED_BINARIES_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
USE_OLD_EOULSAN_RESULT_FORMAT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Write results using old Eoulsan format.
USED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
UTF8_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: UTF-8 charset.
UTF8_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: UTF-8 file encoding.
Utils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
Utils() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
UUID_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata

V

valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode: Returns the enum constant of this type with the specified name.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
VAR_CMD_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: The Constant VAR_CMD_NAME.
VERSION_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Version constant name.

W

waitEndOfTasks(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
waitEndOfTasks(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
waitEndOfTasks(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
waitEndOfTasks(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Wait the end of the task contexts.
waitForCompletion(Job, int) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.MapReduceUtils: Wait for job completion.
WAITING - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
WAITING - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
waitRandom(int) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Wait a random number of milliseconds.
waitUntilExecutableRunning(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Wait the end of the execution of all the instance of an executable.
WALD - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Application Website url.
WELCOME_MSG - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The welcome message.
WORK_FILENAME_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
Workflow - Interface in fr.ens.biologie.genomique.eoulsan.core: This interface define a Workflow.
WORKFLOW_COPY_FILENAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
WORKFLOW_FILE_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Parameters file path constant name.
Workflow2Graphviz - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: Convert a Workflow to Graphviz
Workflow2Graphviz(AbstractWorkflow, DataFile, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.Workflow2Graphviz: Public constructor.
WorkflowContext - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define the context implementation.
WorkflowDataUtils - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define an utility on data object.
WorkflowEventBus - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a single for the event bus.
WorkflowFileNaming - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class contains methods to create workflow data file names.
WORKING - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
write(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
write(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
write(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
write(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
write(int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
write(int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
write(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Write the result.
write(Design) - Method in interface fr.ens.biologie.genomique.eoulsan.design.io.DesignWriter
write(Design) - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter
write(Design) - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter
write(OutputStream, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Write the result.
write(Text, LongWritable) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter
write(Text, Text) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter
write(Text, Text) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter
writeIfHeaderLine(JobContext, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter: Write the line to the SAM header file if the line is a SAM header.
writeLog(File, long, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Write log data.
writeLog(OutputStream, long, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Write log data.
writerFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
writerFile(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Write a file.
writerFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
writeStringAsFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Write a file to the RServer.

X

XMLDataFormat - Class in fr.ens.biologie.genomique.eoulsan.data: This class define a DataFormat from an XML file.
XMLDataFormat(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat: Public constructor.

Z

ZOOKEEPER_DEFAULT_PORT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: ZooKeeper default port.
ZOOKEEPER_SESSION_TIMEOUT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: ZooKeeper default session timeout.
ZooKeeperLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class implements a locker using Zookeeper.
ZooKeeperLocker(String, int, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker: Public constructor.
ZooKeeperLocker(String, int, String, String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker: Public constructor.

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