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

Packages that use Process

org.biopax.paxtools.controller
org.biopax.paxtools.impl.level3
org.biopax.paxtools.model.level3

Uses of Process in org.biopax.paxtools.controller

Methods in org.biopax.paxtools.controller with type parameters of type Process

<T extends Process> void

ModelUtils.generateEntityProcessXrefs(java.lang.Class<T> processClass) Creates "process" (membership) relationship xrefs for each child Entity if possible.

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

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

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

java.util.Set<Process>	ControlImpl.getControlled()
java.util.Set<Process>	PathwayImpl.getPathwayComponent()
java.util.Set<Process>	PathwayStepImpl.getStepProcess()

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

void	ControlImpl.addControlled(Process controlled)
void	PathwayImpl.addPathwayComponent(Process component)
void	PathwayStepImpl.addStepProcess(Process processStep)
protected boolean	ModulationImpl.checkControlled(Process controlled)
protected boolean	ControlImpl.checkControlled(Process Controlled)
protected boolean	CatalysisImpl.checkControlled(Process controlled)
void	ControlImpl.removeControlled(Process controlled)
void	PathwayImpl.removePathwayComponent(Process component)
void	PathwayStepImpl.removeStepProcess(Process processStep)

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

protected void	ControlImpl.setControlled(java.util.Set<Process> controlled)
protected void	PathwayImpl.setPathwayComponent(java.util.Set<Process> pathwayComponent)
void	PathwayStepImpl.setStepProcess(java.util.Set<Process> stepProcess)

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

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

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

java.util.Set<Process>	Control.getControlled() The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
java.util.Set<Process>	Pathway.getPathwayComponent()
java.util.Set<Process>	PathwayStep.getStepProcess()

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

void	Control.addControlled(Process controlled) The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
void	Pathway.addPathwayComponent(Process components)
void	PathwayStep.addStepProcess(Process newSTEP_INTERACTIONS)
void	Control.removeControlled(Process controlled) The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
void	Pathway.removePathwayComponent(Process components)
void	PathwayStep.removeStepProcess(Process oldSTEP_INTERACTIONS)