Package org.biopax.paxtools.impl.level3

Class BiochemicalPathwayStepImpl

java.lang.Object
org.biopax.paxtools.impl.BioPAXElementImpl
org.biopax.paxtools.impl.level3.L3ElementImpl
org.biopax.paxtools.impl.level3.PathwayStepImpl
org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, BiochemicalPathwayStep, Level3Element, Observable, PathwayStep, UtilityClass
public class BiochemicalPathwayStepImpl extends PathwayStepImpl implements BiochemicalPathwayStep
See Also:

  • Constructor Details

    • BiochemicalPathwayStepImpl

      public BiochemicalPathwayStepImpl()

  • Method Details

    • getModelInterface

      public Class<? extends BiochemicalPathwayStep> getModelInterface()
      Description copied from interface: BioPAXElement
      This method returns the actual model interface that a class implements.
      Specified by:
      getModelInterface in interface BioPAXElement
      Overrides:
      getModelInterface in class PathwayStepImpl
      Returns:
      an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

    • getStepConversion

      public Conversion getStepConversion()
      Description copied from interface: BiochemicalPathwayStep
      This method returns the central conversion of this BiochemicalPathwayStep. The returned conversion is also stepProcess of this PathwayStep. The step direction defines the direction of this conversion. The conversion must be reversible.
      Specified by:
      getStepConversion in interface BiochemicalPathwayStep
      Returns:
      The central conversion that take place at this step of the biochemical pathway.

    • setStepConversion

      public void setStepConversion(Conversion highLander)
      Description copied from interface: BiochemicalPathwayStep
      This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion. Old step conversion is also removed from the stepProcess list.
      Specified by:
      setStepConversion in interface BiochemicalPathwayStep
      Parameters:
      highLander - the Conversion interaction of this biological pathway step

    • addStepProcess

      public void addStepProcess(Process process)
      Specified by:
      addStepProcess in interface PathwayStep
      Overrides:
      addStepProcess in class PathwayStepImpl

    • getStepDirection

      public StepDirection getStepDirection()
      Description copied from interface: BiochemicalPathwayStep
      This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.
      Specified by:
      getStepDirection in interface BiochemicalPathwayStep
      Returns:
      Direction of the conversion in this particular pathway context.

    • setStepDirection

      public void setStepDirection(StepDirection newSTEP_DIRECTION)
      Description copied from interface: BiochemicalPathwayStep
      This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.
      Specified by:
      setStepDirection in interface BiochemicalPathwayStep
      Parameters:
      newSTEP_DIRECTION - Direction of the conversion in this particular pathway context.

    • getStepProcess

      public Set<Process> getStepProcess()
      Specified by:
      getStepProcess in interface PathwayStep
      Overrides:
      getStepProcess in class PathwayStepImpl