org.biopax.paxtools.impl.level3

Class ControlImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

org.biopax.paxtools.impl.level3.NamedImpl

org.biopax.paxtools.impl.level3.EntityImpl

org.biopax.paxtools.impl.level3.ProcessImpl

org.biopax.paxtools.impl.level3.InteractionImpl

org.biopax.paxtools.impl.level3.ControlImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Control, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable

Direct Known Subclasses:

CatalysisImpl, ModulationImpl, TemplateReactionRegulationImpl

@Entity
 @Indexed
public class ControlImpl
extends InteractionImpl
implements Control

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
ControlImpl()

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.
protected boolean	checkControlled(Process Controlled)
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.
Class<? extends Control>	getModelInterface() This method returns the actual model interface that a class implements.
protected Set<Pathway>	getPathwayController()
protected Set<PhysicalEntity>	getPeController()
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.
protected void	setControlled(Set<Process> controlled)
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.
protected void	setPathwayController(Set<Pathway> pathwayController)
protected void	setPeController(Set<PhysicalEntity> peController)

Methods inherited from class org.biopax.paxtools.impl.level3.InteractionImpl

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant, setInteractionType, setParticipant

Methods inherited from class org.biopax.paxtools.impl.level3.ProcessImpl

getControlledOf, getPathwayComponentOf, getStepProcessOf, setControlledOf, setPathwayComponentOf, setStepProcessOf

Methods inherited from class org.biopax.paxtools.impl.level3.EntityImpl

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, semanticallyEquivalent, setAvailability, setDataSource, setEvidence, setParticipantOf

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, getXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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, getRDFId, isEquivalent

Constructor Detail

ControlImpl

public ControlImpl()

Method Detail

getModelInterface

public Class<? extends Control> 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 InteractionImpl

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getControlType

public ControlType getControlType()

Description copied from interface: Control

Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.

Specified by:

getControlType in interface Control

Returns:

control type

setControlType

public void setControlType(ControlType ControlType)

Description copied from interface: Control

Sets the controlType BioPAX property value, which fefines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.

Specified by:

setControlType in interface Control

Parameters:

ControlType - new control type value

getControlled

public Set<Process> getControlled()

Description copied from interface: Control

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.

Specified by:

getControlled in interface Control

Returns:

The entity that is controlled

setControlled

protected void setControlled(Set<Process> controlled)

addControlled

public void addControlled(Process controlled)

Description copied from interface: Control

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.

Specified by:

addControlled in interface Control

Parameters:

controlled - The entity that is controlled

removeControlled

public void removeControlled(Process controlled)

Description copied from interface: Control

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.

Specified by:

removeControlled in interface Control

Parameters:

controlled - The entity that is controlled

getController

public Set<Controller> getController()

Description copied from interface: Control

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.

Specified by:

getController in interface Control

Returns:

The controlling entity

addController

public void addController(Controller controller)

Description copied from interface: Control

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.

Specified by:

addController in interface Control

Parameters:

controller - The controlling entity

removeController

public void removeController(Controller controller)

Description copied from interface: Control

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.

Specified by:

removeController in interface Control

Parameters:

controller - The controlling entity

checkControlled

protected boolean checkControlled(Process Controlled)

getPathwayController

protected Set<Pathway> getPathwayController()

setPathwayController

protected void setPathwayController(Set<Pathway> pathwayController)

getPeController

protected Set<PhysicalEntity> getPeController()

setPeController

protected void setPeController(Set<PhysicalEntity> peController)