Uses of Interface
fr.ens.biologie.genomique.eoulsan.core.Step

Packages that use Step

Package	Description
fr.ens.biologie.genomique.eoulsan.core	This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.schedulers	This package contains classes for schedulers.
fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters	This package contains classes for cluster schedulers.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
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.ui	This package contains Eoulsan user interface classes.

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

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

Modifier and Type	Method	Description
Step	StepConfigurationContext.getCurrentStep()	Get the current step.
Step	Workflow.getDesignStep()	Get the design step of the workflow.
Step	Workflow.getFirstStep()	Get the first step of the workflow (after generator steps).
Step	Workflow.getRootStep()	Get the first steps of the workflow.

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

Modifier and Type	Method	Description
Set<Step>	AbstractPort.getLinkedSteps()
Set<Step>	Port.getLinkedSteps()	Get the steps linked to this port.
Set<Step>	Workflow.getSteps()	Get the steps of the workflow.

Uses of Step in fr.ens.biologie.genomique.eoulsan.core.schedulers

Methods in fr.ens.biologie.genomique.eoulsan.core.schedulers that return Step

Modifier and Type	Method	Description
protected Step	AbstractTaskScheduler.getStep(int contextId)	Get the step related to a context.
protected Step	AbstractTaskScheduler.getStep(TaskContextImpl context)	Get the step related to a context.

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

Modifier and Type	Method	Description
StepResult	AbstractTaskScheduler.getResult(Step step)
StepResult	ClusterCombinedTaskScheduler.getResult(Step step)
StepResult	CombinedTaskScheduler.getResult(Step step)
StepResult	TaskScheduler.getResult(Step step)	Get the result related to a step.
StepStatus	AbstractTaskScheduler.getStatus(Step step)
StepStatus	ClusterCombinedTaskScheduler.getStatus(Step step)
StepStatus	CombinedTaskScheduler.getStatus(Step step)
StepStatus	TaskScheduler.getStatus(Step step)	Get the status related to a step.
int	AbstractTaskScheduler.getTaskDoneCount(Step step)
int	ClusterCombinedTaskScheduler.getTaskDoneCount(Step step)
int	CombinedTaskScheduler.getTaskDoneCount(Step step)
int	TaskScheduler.getTaskDoneCount(Step step)	Get the count of done task contexts of a step.
int	AbstractTaskScheduler.getTaskRunningCount(Step step)
int	ClusterCombinedTaskScheduler.getTaskRunningCount(Step step)
int	CombinedTaskScheduler.getTaskRunningCount(Step step)
int	TaskScheduler.getTaskRunningCount(Step step)	Get the count of running task contexts of a step.
int	AbstractTaskScheduler.getTaskSubmittedCount(Step step)
int	ClusterCombinedTaskScheduler.getTaskSubmittedCount(Step step)
int	CombinedTaskScheduler.getTaskSubmittedCount(Step step)
int	TaskScheduler.getTaskSubmittedCount(Step step)	Get the count of submitted task contexts of a step.
void	AbstractTaskScheduler.submit(Step step, TaskContextImpl context)
void	AbstractTaskScheduler.submit(Step step, Set<TaskContextImpl> contexts)
void	ClusterCombinedTaskScheduler.submit(Step step, TaskContextImpl context)
void	ClusterCombinedTaskScheduler.submit(Step step, Set<TaskContextImpl> contexts)
void	CombinedTaskScheduler.submit(Step step, TaskContextImpl context)
void	CombinedTaskScheduler.submit(Step step, Set<TaskContextImpl> contexts)
void	HadoopCompatibleTaskScheduler.submit(Step step, TaskContextImpl context)
void	MonoThreadTaskScheduler.submit(Step step, TaskContextImpl context)
void	MultiThreadTaskScheduler.submit(Step step, TaskContextImpl context)
void	TaskScheduler.submit(Step step, TaskContextImpl context)	Submit a context to execute.
void	TaskScheduler.submit(Step step, Set<TaskContextImpl> contexts)	Submit contexts to execute.
void	AbstractTaskScheduler.waitEndOfTasks(Step step)
void	ClusterCombinedTaskScheduler.waitEndOfTasks(Step step)
void	CombinedTaskScheduler.waitEndOfTasks(Step step)
void	TaskScheduler.waitEndOfTasks(Step step)	Wait the end of the task contexts.

Uses of Step in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters

Methods in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters with parameters of type Step

Modifier and Type	Method	Description
void	AbstractClusterTaskScheduler.submit(Step step, TaskContextImpl context)

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

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

Modifier and Type	Class	Description
class	AbstractStep	This class define a step of the workflow.
class	CommandStep	This class define a step based on a Command object (workflow file).

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

Modifier and Type	Method	Description
protected Step	AbstractWorkflow.getCheckerStep()	Get checker step.
Step	StepConfigurationContextImpl.getCurrentStep()
Step	TaskContextImpl.getCurrentStep()
Step	AbstractWorkflow.getDesignStep()
Step	AbstractWorkflow.getFirstStep()
Step	AbstractWorkflow.getRootStep()
Step	UIStepEvent.getStep()	Get the step.

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

Modifier and Type	Method	Description
Set<Step>	AbstractWorkflow.getSteps()

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

Modifier and Type	Method	Description
Module	StepInstances.getModule(Step step)	Get a module instance.
Module	StepInstances.getModule(Step step, String moduleName, String moduleVersion)	Get a step instance.
static String	StepOutputDataFile.newStandardFilename(Step step, String portName, DataFormat format, Sample sample, int fileIndex, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create a standard filename.
void	StepObserver.notifyStepState(Step step, int terminatedTasks, int submittedTasks, double progress)	The progress of the step has been changed.
void	StepObserver.notifyStepState(Step step, int contextId, String contextName, double progress)	The progress of the step for a sample has been changed.
void	StepObserver.notifyStepState(Step step, Step.StepState stepState)	The status of the step has been changed.
void	StepObserver.notifyStepState(Step step, String note)	The note of the step has been changed.
void	StepObserver.notifyTaskDone(Step step, int contextId)	Notify that a task has been done.
void	StepObserver.notifyTaskRunning(Step step, int contextId)	Notify that a task is running.
void	StepObserver.notifyTaskSubmitted(Step step, int contextId)	Notify that a task has been submitted.
void	StepInstances.registerStep(Step step, Module module)	Register a step instance.
void	StepInstances.removeStep(Step step)	Remove a step instance.

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

Constructor	Description
UITaskEvent(Step step, fr.ens.biologie.genomique.eoulsan.core.workflow.UITaskEvent.TaskStatusMessage status, int contextId)	Constructor.

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

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

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

Uses of Step in fr.ens.biologie.genomique.eoulsan.ui

Methods in fr.ens.biologie.genomique.eoulsan.ui with parameters of type Step

Modifier and Type	Method	Description
void	BasicUI.notifyStepState(Step step, int terminatedTasks, int submittedTasks, double progress)
void	BasicUI.notifyStepState(Step step, int contextId, String contextName, double progress)
void	BasicUI.notifyStepState(Step step, Step.StepState stepState)
void	BasicUI.notifyStepState(Step step, String note)
void	LanternaUI.notifyStepState(Step step, int terminatedTasks, int submittedTasks, double progress)
void	LanternaUI.notifyStepState(Step step, int contextId, String contextName, double progress)
void	LanternaUI.notifyStepState(Step step, Step.StepState stepState)
void	LanternaUI.notifyStepState(Step step, String note)
void	NoUI.notifyStepState(Step step, int terminatedTasks, int submittedTasks, double progress)
void	NoUI.notifyStepState(Step step, int contextId, String contextName, double progress)
void	NoUI.notifyStepState(Step step, Step.StepState stepState)
void	NoUI.notifyStepState(Step step, String note)
void	BasicUI.notifyTaskDone(Step step, int contextId)
void	LanternaUI.notifyTaskDone(Step step, int contextId)
void	NoUI.notifyTaskDone(Step step, int contextId)
void	BasicUI.notifyTaskRunning(Step step, int contextId)
void	LanternaUI.notifyTaskRunning(Step step, int contextId)
void	NoUI.notifyTaskRunning(Step step, int contextId)
void	BasicUI.notifyTaskSubmitted(Step step, int contextId)
void	LanternaUI.notifyTaskSubmitted(Step step, int contextId)
void	NoUI.notifyTaskSubmitted(Step step, int contextId)