Uses of Class
org.snpeff.reactome.Entity

Packages that use Entity

Package	Description
org.snpeff.reactome
org.snpeff.reactome.events

Uses of Entity in org.snpeff.reactome

Subclasses of Entity in org.snpeff.reactome

Modifier and Type	Class	Description
class	Compartment	A Reactome compartment (a part of a cell)

Methods in org.snpeff.reactome that return types with arguments of type Entity

Modifier and Type	Method	Description
java.util.Iterator<Entity>	Reactome.iterator()

Methods in org.snpeff.reactome with parameters of type Entity

Modifier and Type	Method	Description
void	Monitor.add(Entity e)
void	Reactome.add(Entity entity, java.lang.String geneId)	Add an entity <-> geneId
int	Entity.compareTo(Entity e)

Method parameters in org.snpeff.reactome with type arguments of type Entity

Modifier and Type	Method	Description
double	Entity.calc(java.util.HashSet<Entity> doneEntities)	Calculate entities.
java.lang.String	Entity.toString(int tabs, java.util.HashSet<Entity> done)

Uses of Entity in org.snpeff.reactome.events

Subclasses of Entity in org.snpeff.reactome.events

Modifier and Type	Class	Description
class	BlackBoxEvent	A black box event
class	CatalystActivity	A catalyst activity event
class	Complex	A Reactome complex (a bunch of molecules or complexes
class	Depolymerisation	A depolymerization event
class	Event	A reactome event (any generic event, from pathways to polymerizations)
class	Pathway	A Reactome pathway
class	Polymerisation	A polymerization event
class	Reaction	A reaction

Fields in org.snpeff.reactome.events with type parameters of type Entity

Modifier and Type	Field	Description
protected java.util.HashSet<Entity>	Reaction.catalyst
protected java.util.HashMap<Entity,java.lang.Double>	Reaction.inputs
protected java.util.HashSet<Entity>	Reaction.outputs
protected java.util.HashMap<Entity,Reaction.RegulationType>	Reaction.regulator

Methods in org.snpeff.reactome.events that return types with arguments of type Entity

Modifier and Type	Method	Description
java.util.HashSet<Entity>	Reaction.getCatalyst()
java.util.Collection<Entity>	Reaction.getInputs()
java.util.HashSet<Entity>	Reaction.getOutputs()
java.util.HashMap<Entity,Reaction.RegulationType>	Reaction.getRegulator()
java.util.Iterator<Entity>	Complex.iterator()

Methods in org.snpeff.reactome.events with parameters of type Entity

Modifier and Type	Method	Description
void	Complex.add(Entity e)
void	Reaction.addCatalyst(Entity e)
void	Reaction.addInput(Entity e)
void	Reaction.addOutput(Entity e)
void	Reaction.addRegulator(Entity e, java.lang.String type)
void	Reaction.addRegulator(Entity e, Reaction.RegulationType type)

Method parameters in org.snpeff.reactome.events with type arguments of type Entity

Modifier and Type	Method	Description
double	Reaction.calc(java.util.HashSet<Entity> doneEntities)	Calculate entities.
java.lang.String	Complex.toString(int tabs, java.util.HashSet<Entity> done)
java.lang.String	Pathway.toString(int tabs, java.util.HashSet<Entity> done)
java.lang.String	Reaction.toString(int tabs, java.util.HashSet<Entity> done)