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.

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
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.
Set<Process>	getControlled() The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
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) Sets the controlType BioPAX property value, which fefines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.

Methods inherited from interface org.biopax.paxtools.model.level3.Interaction

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getUri, isEquivalent

Method Detail

getControlled

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

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