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

Packages that use Entity

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 Entity in org.biopax.paxtools.impl.level3

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

Modifier and Type	Class	Description
class	BiochemicalReactionImpl
class	CatalysisImpl
class	ComplexAssemblyImpl
class	ComplexImpl
class	ControlImpl
class	ConversionImpl
class	DegradationImpl
class	DnaImpl
class	DnaRegionImpl
class	EntityImpl
class	GeneImpl
class	GeneticInteractionImpl
class	InteractionImpl
class	ModulationImpl
class	MolecularInteractionImpl
class	NucleicAcidImpl
class	PathwayImpl
class	PhysicalEntityImpl
class	ProcessImpl
class	ProteinImpl
class	RnaImpl
class	RnaRegionImpl
class	SimplePhysicalEntityImpl
class	SmallMoleculeImpl
class	TemplateReactionImpl
class	TemplateReactionRegulationImpl
class	TransportImpl
class	TransportWithBiochemicalReactionImpl

Methods in org.biopax.paxtools.impl.level3 that return Entity

Modifier and Type	Method	Description
Entity	ExperimentalFormImpl.getExperimentalFormEntity()

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

Modifier and Type	Method	Description
Set<Entity>	InteractionImpl.getParticipant()

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

Modifier and Type	Method	Description
void	GeneticInteractionImpl.addParticipant(Entity aParticipant)
void	InteractionImpl.addParticipant(Entity aParticipant)
void	MolecularInteractionImpl.addParticipant(Entity participant)
void	InteractionImpl.removeParticipant(Entity aParticipant)
void	ExperimentalFormImpl.setExperimentalFormEntity(Entity experimentalFormEntity)

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

Modifier and Type	Method	Description
protected void	InteractionImpl.setParticipant(Set<Entity> participant)

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

Subinterfaces of Entity 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	Complex	Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
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	Controller	This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
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	Dna	Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
interface	DnaRegion	Definition: A region on a DNA molecule.
interface	Gene	Definition: A continuant that encodes information that can be inherited through replication.
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	NucleicAcid	Tagger interface for DNA and RNA
interface	Pathway
interface	PhysicalEntity
interface	Process	Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
interface	Protein
interface	Rna
interface	RnaRegion	Definition: A region on a RNA molecule.
interface	SequenceEntity	Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
interface	SimplePhysicalEntity	Tagger interface for non-complex physical entities
interface	SmallMolecule
interface	TemplateReaction
interface	TemplateReactionRegulation
interface	Transport
interface	TransportWithBiochemicalReaction

Methods in org.biopax.paxtools.model.level3 that return Entity

Modifier and Type	Method	Description
Entity	ExperimentalForm.getExperimentalFormEntity()

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

Modifier and Type	Method	Description
Set<Entity>	Interaction.getParticipant()	The entities that participate in this interaction.

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

Modifier and Type	Method	Description
void	Interaction.addParticipant(Entity participant)	The entities that participate in this interaction.
void	Interaction.removeParticipant(Entity participant)	The entities that participate in this interaction.
void	ExperimentalForm.setExperimentalFormEntity(Entity newPARTICIPANT)