Package org.biopax.paxtools.model.level3

Interface Control

All Superinterfaces:
BioPAXElement, Cloneable, Entity, Interaction, Level3Element, Named, Observable, Process, Serializable, XReferrable
All Known Subinterfaces:
Catalysis, Modulation, TemplateReactionRegulation
All Known Implementing Classes:
CatalysisImpl, ControlImpl, ModulationImpl, TemplateReactionRegulationImpl
public interface Control extends Interaction
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e. pathway or interaction. Usage: Conceptually, physical entities are involved in interactions (or events) and the events are controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction, called "Activity Flow" representation, that can be ambiguous without context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a Biochemical Reaction in which the substrate is phosphorylated. Subclasses of control define types specific to the biological process that is being controlled and should be used instead of the generic "control" class when applicable. A control can potentially have multiple controllers. This acts as a logical AND, i.e. both controllers are needed to regulate the controlled event. Alternatively multiple controllers can control the same event and this acts as a logical OR, i.e. any one of them is sufficient to regulate the controlled event. Using this structure it is possible to describe arbitrary control logic using BioPAX. Rationale: Control can be temporally non-atomic, for example a pathway can control another pathway in BioPAX. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism.

  • Method Details

    • getControlled

      Set<Process> getControlled()
      Deprecated.
      should return one Process or null; see also deprecated addControlled(Process)
      The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. Controlled is a sub-property of participants.
      Returns:
      The entity that is controlled

    • addControlled

      void addControlled(Process controlled)
      Deprecated.
      violates OWL functional property restriction; should be: setControlled(process)
      The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. Controlled is a sub-property of participants.
      Parameters:
      controlled - The entity that is controlled

    • removeControlled

      void removeControlled(Process controlled)
      Deprecated.
      was a mistake; see also deprecated addControlled(Process)
      The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. Controlled is a sub-property of participants.
      Parameters:
      controlled - The entity that is controlled

    • getController

      Set<Controller> getController()
      The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. Controller is a sub-property of participants.
      Returns:
      The controlling entity

    • addController

      void addController(Controller controller)
      The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. Controller is a sub-property of participants.
      Parameters:
      controller - The controlling entity

    • removeController

      void removeController(Controller controller)
      The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. Controller is a sub-property of participants.
      Parameters:
      controller - The controlling entity

    • getControlType

      ControlType getControlType()
      Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.
      Returns:
      control type

    • setControlType

      void setControlType(ControlType controlType)
      Sets the controlType BioPAX property value, which fefines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.
      Parameters:
      controlType - new control type value