Package org.snpeff.reactome.events
Class Reaction
java.lang.Object
org.snpeff.reactome.Entity
org.snpeff.reactome.events.Event
org.snpeff.reactome.events.Reaction
- All Implemented Interfaces:
Comparable<Entity>
- Direct Known Subclasses:
BlackBoxEvent
,CatalystActivity
,Complex
,Depolymerisation
,Pathway
,Polymerisation
A reaction
- Author:
- pcingola
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Nested Class Summary
Nested ClassesNested classes/interfaces inherited from class org.snpeff.reactome.Entity
Entity.TransferFunction
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final double
protected HashMap<Entity,
Reaction.RegulationType> Fields inherited from class org.snpeff.reactome.Entity
BETA, compartment, debug, fixedOutput, geneIds, id, name, output, TRANSFER_FUNCTION, weight
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
void
void
void
addRegulator
(Entity e, String type) void
addRegulator
(Entity e, Reaction.RegulationType type) double
Calculate entities.boolean
void
Scale weights so that they add to 1toString()
protected double
transferFunction
(double h, double inCat, double inRegPos, double inRegNeg, double inRegReq) Transfer functionMethods inherited from class org.snpeff.reactome.Entity
addGeneId, calc, compareTo, getCompartment, getGeneIds, getId, getName, getOutput, getWeight, hasOutput, isFixed, reset, setCompartment, setFixedOutput, setWeight, toStringSimple, transferFunction
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Field Details
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MAX_WEIGHT_SUM
public static final double MAX_WEIGHT_SUM- See Also:
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inputs
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outputs
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catalyst
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regulator
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Constructor Details
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Reaction
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Method Details
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addCatalyst
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addInput
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addOutput
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addRegulator
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addRegulator
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calc
Calculate entities. Make sure we don't calculate twice (keep 'doneEntities' set up to date) -
getCatalyst
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getInputs
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getOutputs
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getRegulator
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isReaction
public boolean isReaction()- Overrides:
isReaction
in classEntity
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scaleWeights
public void scaleWeights()Scale weights so that they add to 1 -
toString
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toString
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transferFunction
protected double transferFunction(double h, double inCat, double inRegPos, double inRegNeg, double inRegReq) Transfer function- Parameters:
h
-- Returns:
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