Uses of Interface
org.biopax.paxtools.model.level3.Process

Packages that use Process

Package	Description
org.biopax.paxtools.impl.level3	This package contains the default implementation for BioPAX Level 3.
org.biopax.paxtools.model.level3	This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.

Uses of Process in org.biopax.paxtools.impl.level3

Classes in org.biopax.paxtools.impl.level3 that implement Process

Modifier and Type	Class	Description
class	BiochemicalReactionImpl
class	CatalysisImpl
class	ComplexAssemblyImpl
class	ControlImpl
class	ConversionImpl
class	DegradationImpl
class	GeneticInteractionImpl
class	InteractionImpl
class	ModulationImpl
class	MolecularInteractionImpl
class	PathwayImpl
class	ProcessImpl
class	TemplateReactionImpl
class	TemplateReactionRegulationImpl
class	TransportImpl
class	TransportWithBiochemicalReactionImpl

Methods in org.biopax.paxtools.impl.level3 that return types with arguments of type Process

Modifier and Type	Method	Description
Set<Process>	ControlImpl.getControlled()
Set<Process>	PathwayImpl.getPathwayComponent()
Set<Process>	BiochemicalPathwayStepImpl.getStepProcess()
Set<Process>	PathwayStepImpl.getStepProcess()

Methods in org.biopax.paxtools.impl.level3 with parameters of type Process

Modifier and Type	Method	Description
void	ControlImpl.addControlled(Process process)
void	PathwayImpl.addPathwayComponent(Process component)
void	BiochemicalPathwayStepImpl.addStepProcess(Process process)
void	PathwayStepImpl.addStepProcess(Process processStep)
protected boolean	CatalysisImpl.checkControlled(Process controlled)
protected boolean	ControlImpl.checkControlled(Process Controlled)
protected boolean	ModulationImpl.checkControlled(Process controlled)
void	ControlImpl.removeControlled(Process controlled)
void	PathwayImpl.removePathwayComponent(Process component)
void	PathwayStepImpl.removeStepProcess(Process processStep)

Uses of Process in org.biopax.paxtools.model.level3

Subinterfaces of Process in org.biopax.paxtools.model.level3

Modifier and Type	Interface	Description
interface	BiochemicalReaction	Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
interface	Catalysis	Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
interface	ComplexAssembly	Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
interface	Control	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
interface	Conversion	Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.
interface	Degradation	Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.
interface	GeneticInteraction	Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
interface	Interaction	Definition: A biological relationship between two or more entities.
interface	Modulation	Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
interface	MolecularInteraction	Definition: An interaction in which at least one participant is a physical entity, e.g.
interface	Pathway
interface	TemplateReaction
interface	TemplateReactionRegulation
interface	Transport
interface	TransportWithBiochemicalReaction

Methods in org.biopax.paxtools.model.level3 that return types with arguments of type Process

Modifier and Type	Method	Description
Set<Process>	Control.getControlled()	Deprecated. should return one Process or null; see also deprecated Control.addControlled(Process)
Set<Process>	Pathway.getPathwayComponent()
Set<Process>	PathwayStep.getStepProcess()

Methods in org.biopax.paxtools.model.level3 with parameters of type Process

Modifier and Type	Method	Description
void	Control.addControlled(Process controlled)	Deprecated. violates OWL functional property restriction; should be: setControlled(process)
void	Pathway.addPathwayComponent(Process components)
void	PathwayStep.addStepProcess(Process newSTEP_INTERACTIONS)
void	Control.removeControlled(Process controlled)	Deprecated. was a mistake; see also deprecated Control.addControlled(Process)
void	Pathway.removePathwayComponent(Process components)
void	PathwayStep.removeStepProcess(Process oldSTEP_INTERACTIONS)