Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class AbstractStep

java.lang.Object
fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
All Implemented Interfaces:
Step, Serializable
Direct Known Subclasses:
CommandStep
public abstract class AbstractStep extends Object implements Step
This class define a step of the workflow. This class must be extended by a class to be able to work with a specific workflow file format.
Since:
2.0
Author:
Laurent Jourdren
See Also:

  • Method Details

    • getWorkflow

      public Workflow getWorkflow()
      Description copied from interface: Step
      Get the workflow of the step.
      Specified by:
      getWorkflow in interface Step
      Returns:
      the workflow of the step

    • getNumber

      public int getNumber()
      Description copied from interface: Step
      Get the unique numerical identifier of the step.
      Specified by:
      getNumber in interface Step
      Returns:
      the number of the step

    • getId

      public String getId()
      Description copied from interface: Step
      Get step id.
      Specified by:
      getId in interface Step
      Returns:
      the step id

    • getStepVersion

      public String getStepVersion()
      Description copied from interface: Step
      Get the step version required by user.
      Specified by:
      getStepVersion in interface Step
      Returns:
      a string with the version of the step required by the user

    • isSkip

      public boolean isSkip()
      Description copied from interface: Step
      Test if the step must be skipped
      Specified by:
      isSkip in interface Step
      Returns:
      true if the step must be skipped

    • getType

      public Step.StepType getType()
      Description copied from interface: Step
      Get the type of the step.
      Specified by:
      getType in interface Step
      Returns:
      the type of the step;

    • getModule

      public Module getModule()
      Get the underlying Module object.
      Returns:
      the Module object

    • getEoulsanMode

      public ExecutionMode getEoulsanMode()
      Get the Eoulsan mode of the step.
      Returns:
      an EoulsanMode enum

    • getModuleName

      public String getModuleName()
      Description copied from interface: Step
      Get the module name.
      Specified by:
      getModuleName in interface Step
      Returns:
      the module object

    • getState

      public Step.StepState getState()
      Description copied from interface: Step
      Get the state of the step.
      Specified by:
      getState in interface Step
      Returns:
      the state of the step

    • getParameters

      public Set<Parameter> getParameters()
      Description copied from interface: Step
      Get the parameter of the step.
      Specified by:
      getParameters in interface Step
      Returns:
      a Set with the parameters of the step

    • getInputPorts

      public InputPorts getInputPorts()
      Description copied from interface: Step
      Get the input ports of the step.
      Specified by:
      getInputPorts in interface Step
      Returns:
      the input ports of the step

    • getOutputPorts

      public OutputPorts getOutputPorts()
      Description copied from interface: Step
      Get the output ports of the step.
      Specified by:
      getOutputPorts in interface Step
      Returns:
      the output ports of the step

    • getRequiredMemory

      public int getRequiredMemory()
      Description copied from interface: Step
      Get the required memory for the step.
      Specified by:
      getRequiredMemory in interface Step
      Returns:
      the required memory of the step in MB or -1 if the default setting must be used

    • getRequiredProcessors

      public int getRequiredProcessors()
      Description copied from interface: Step
      Get the required processors for the step.
      Specified by:
      getRequiredProcessors in interface Step
      Returns:
      the required processors count for the step in MB or -1 if the default setting must be used

    • getChecker

      public Checker getChecker()
      Description copied from interface: Step
      Get Checker.
      Specified by:
      getChecker in interface Step
      Returns:
      the checker for the step

    • getStepOutputDirectory

      public DataFile getStepOutputDirectory()
      Get step output directory (where output file of the step will be written).
      Returns:
      the output directory

    • getParallelizationMode

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

    • getDiscardOutput

      public Step.DiscardOutput getDiscardOutput()
      Get the discard output value.
      Returns:
      the discard output value