org.biopax.paxtools.model.level3
Interface Control
- All Superinterfaces:
- BioPAXElement, java.lang.Cloneable, Entity, Interaction, Level3Element, Named, Observable, Process, java.io.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 Summary |
void |
addControlled(Process controlled)
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. |
void |
addController(Controller controller)
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. |
java.util.Set<Process> |
getControlled()
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. |
java.util.Set<Controller> |
getController()
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. |
ControlType |
getControlType()
Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities. |
void |
removeControlled(Process controlled)
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. |
void |
removeController(Controller controller)
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. |
void |
setControlType(ControlType controlType)
|
getControlled
java.util.Set<Process> getControlled()
- 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)
- 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)
- 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
java.util.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:
setControlType
void setControlType(ControlType controlType)
Copyright © 2011 BioPAX. All Rights Reserved.