Interface Module

    • Method Detail

      • getName

        String getName()
        Get the name of the module.
        Returns:
        the name of the module
      • getDescription

        String getDescription()
        Get the description of the module
        Returns:
        the description of the module
      • getVersion

        fr.ens.biologie.genomique.kenetre.util.Version getVersion()
        Get version of the Module.
        Returns:
        a Version object with the version of the Module
      • getRequiredEoulsanVersion

        fr.ens.biologie.genomique.kenetre.util.Version getRequiredEoulsanVersion()
        Get the required Version of the application to run the Module.
        Returns:
        a Version object with the required version of the Module
      • getInputPorts

        InputPorts getInputPorts()
        Get the input data format.
        Returns:
        a set with DataFormat or null if the module does not any need input format
      • getOutputPorts

        OutputPorts getOutputPorts()
        Get the output data format.
        Returns:
        an set with DataFormat or null if the module does not produce any output data
      • getRequirements

        Set<Requirement> getRequirements()
        Get the requirements of the module.
        Returns:
        a set with the requirements of the module
      • getChecker

        Checker getChecker()
        Get the checker for the module
        Returns:
        the checker for the module
      • configure

        void configure​(StepConfigurationContext context,
                       Set<Parameter> stepParameters)
                throws EoulsanException
        Set the parameters of the step to configure the module.
        Parameters:
        context - configuration context. The context can be null for generator steps
        stepParameters - parameters of the step
        Throws:
        EoulsanException - if a parameter is invalid
      • execute

        TaskResult execute​(TaskContext context,
                           TaskStatus status)
        Execute a task step.
        Parameters:
        context - Execution context
        status - of the task
      • getParallelizationMode

        ParallelizationMode getParallelizationMode()
        Get the parallelization mode of the module.
        Returns:
        a ParallelizationMode enum