Uses of Class
org.snpeff.reactome.Entity
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Packages that use Entity Package Description org.snpeff.reactome org.snpeff.reactome.events -
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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 <-> geneIdint
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)
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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 eventclass
CatalystActivity
A catalyst activity eventclass
Complex
A Reactome complex (a bunch of molecules or complexesclass
Depolymerisation
A depolymerization eventclass
Event
A reactome event (any generic event, from pathways to polymerizations)class
Pathway
A Reactome pathwayclass
Polymerisation
A polymerization eventclass
Reaction
A reactionFields 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)
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