Package org.snpeff.reactome.events
Class Reaction
- java.lang.Object
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- org.snpeff.reactome.Entity
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- org.snpeff.reactome.events.Event
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- org.snpeff.reactome.events.Reaction
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- All Implemented Interfaces:
java.lang.Comparable<Entity>
- Direct Known Subclasses:
BlackBoxEvent
,CatalystActivity
,Complex
,Depolymerisation
,Pathway
,Polymerisation
public class Reaction extends Event
A reaction- Author:
- pcingola
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Reaction.RegulationType
Reaction regulation types-
Nested classes/interfaces inherited from class org.snpeff.reactome.Entity
Entity.TransferFunction
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Field Summary
Fields Modifier and Type Field Description protected java.util.HashSet<Entity>
catalyst
protected java.util.HashMap<Entity,java.lang.Double>
inputs
static double
MAX_WEIGHT_SUM
protected java.util.HashSet<Entity>
outputs
protected java.util.HashMap<Entity,Reaction.RegulationType>
regulator
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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 Constructor Description Reaction(int id, java.lang.String name)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCatalyst(Entity e)
void
addInput(Entity e)
void
addOutput(Entity e)
void
addRegulator(Entity e, java.lang.String type)
void
addRegulator(Entity e, Reaction.RegulationType type)
double
calc(java.util.HashSet<Entity> doneEntities)
Calculate entities.java.util.HashSet<Entity>
getCatalyst()
java.util.Collection<Entity>
getInputs()
java.util.HashSet<Entity>
getOutputs()
java.util.HashMap<Entity,Reaction.RegulationType>
getRegulator()
boolean
isReaction()
void
scaleWeights()
Scale weights so that they add to 1java.lang.String
toString()
java.lang.String
toString(int tabs, java.util.HashSet<Entity> done)
protected double
transferFunction(double h, double inCat, double inRegPos, double inRegNeg, double inRegReq)
Transfer function-
Methods 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 Detail
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MAX_WEIGHT_SUM
public static final double MAX_WEIGHT_SUM
- See Also:
- Constant Field Values
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inputs
protected java.util.HashMap<Entity,java.lang.Double> inputs
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outputs
protected java.util.HashSet<Entity> outputs
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catalyst
protected java.util.HashSet<Entity> catalyst
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regulator
protected java.util.HashMap<Entity,Reaction.RegulationType> regulator
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Method Detail
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addCatalyst
public void addCatalyst(Entity e)
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addInput
public void addInput(Entity e)
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addOutput
public void addOutput(Entity e)
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addRegulator
public void addRegulator(Entity e, Reaction.RegulationType type)
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addRegulator
public void addRegulator(Entity e, java.lang.String type)
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calc
public double calc(java.util.HashSet<Entity> doneEntities)
Calculate entities. Make sure we don't calculate twice (keep 'doneEntities' set up to date)
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getCatalyst
public java.util.HashSet<Entity> getCatalyst()
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getInputs
public java.util.Collection<Entity> getInputs()
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getOutputs
public java.util.HashSet<Entity> getOutputs()
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getRegulator
public java.util.HashMap<Entity,Reaction.RegulationType> 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
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toString
public java.lang.String toString(int tabs, java.util.HashSet<Entity> done)
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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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