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

Class AbstractExpressionModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
All Implemented Interfaces:
Module
Direct Known Subclasses:
ExpressionHadoopModule, ExpressionLocalModule
public abstract class AbstractExpressionModule extends AbstractModule
This abstract class define and parse arguments for the expression module.
Since:
1.0
Author:
Laurent Jourdren, Maria Bernard, Claire Wallon

  • Field Details

    • MODULE_NAME

      public static final String MODULE_NAME
      Module name.
      See Also:

    • COUNTER_PARAMETER_NAME

      public static final String COUNTER_PARAMETER_NAME
      Constant for counter parameter name.
      See Also:

    • FEATURES_FILE_FORMAT_PARAMETER_NAME

      public static final String FEATURES_FILE_FORMAT_PARAMETER_NAME
      Constant for file format parameter name.
      See Also:

    • OUTPUT_FILE_FORMAT_PARAMETER_NAME

      public static final String OUTPUT_FILE_FORMAT_PARAMETER_NAME
      Constant for output file format parameter name.
      See Also:

  • Constructor Details

    • AbstractExpressionModule

      public AbstractExpressionModule()

  • Method Details

    • getName

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

    • getDescription

      public String getDescription()
      Description copied from interface: Module
      Get the description of the module
      Specified by:
      getDescription in interface Module
      Overrides:
      getDescription in class AbstractModule
      Returns:
      the description 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