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

Packages that use Entity

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

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

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

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

Entity

ExperimentalFormImpl.getExperimentalFormEntity()

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

java.util.Set<Entity>

InteractionImpl.getParticipant()

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

void	MolecularInteractionImpl.addParticipant(Entity participant)
void	InteractionImpl.addParticipant(Entity aParticipant)
void	InteractionImpl.removeParticipant(Entity aParticipant)
void	ExperimentalFormImpl.setExperimentalFormEntity(Entity experimentalFormEntity)

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

protected void

InteractionImpl.setParticipant(java.util.Set<Entity> participant)

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

Subinterfaces of Entity 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	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	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

Entity

ExperimentalForm.getExperimentalFormEntity()

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

java.util.Set<Entity>

Interaction.getParticipant() The entities that participate in this interaction.

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

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)