Package fr.ens.biologie.genomique.eoulsan.modules

Class CopyInputDataModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
All Implemented Interfaces:
Module
public class CopyInputDataModule extends AbstractModule
Copy input files of a format in another location or in different compression format.
Since:
2.0
Author:
Laurent Jourdren

  • Field Details

  • Constructor Details

    • CopyInputDataModule

      public CopyInputDataModule()

  • Method Details

    • getName

      public String getName()
      Description copied from interface: Module
      Get the name of the module.
      Returns:
      the name of the module

    • getVersion

      public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
      Description copied from interface: Module
      Get version of the Module.
      Returns:
      a Version object with the version of the Module

    • getInputPorts

      public InputPorts getInputPorts()
      Description copied from interface: Module
      Get the input data format.
      Specified by:
      getInputPorts in interface Module
      Overrides:
      getInputPorts in class AbstractModule
      Returns:
      a set with DataFormat or null if the module does not any need input format

    • getOutputPorts

      public OutputPorts getOutputPorts()
      Description copied from interface: Module
      Get the output data format.
      Specified by:
      getOutputPorts in interface Module
      Overrides:
      getOutputPorts in class AbstractModule
      Returns:
      an set with DataFormat or null if the module does not produce any output data

    • configure

      public void configure(StepConfigurationContext context, Set<Parameter> stepParameters) throws EoulsanException
      Description copied from interface: Module
      Set the parameters of the step to configure the module.
      Specified by:
      configure in interface Module
      Overrides:
      configure in class AbstractModule
      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

      public TaskResult execute(TaskContext context, TaskStatus status)
      Description copied from interface: Module
      Execute a task step.
      Parameters:
      context - Execution context
      status - of the task
      Returns:
      a TaskResult object

    • encodeAllowedCompressionsParameterValue

      public static String encodeAllowedCompressionsParameterValue(EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> outputCompressionAllowed)
      Method to encode an EnumSet of the allowed compressions parameter in a string.
      Parameters:
      outputCompressionAllowed - the EnumSet to encode
      Returns:
      a string with the EnumSet encoded