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:

java.lang.Comparable<Entity>

Direct Known Subclasses:

BlackBoxEvent, CatalystActivity, Complex, Depolymerisation, Pathway, Polymerisation

public class Reaction
extends Event

A reaction

Author:

pcingola

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

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

Fields inherited from class org.snpeff.reactome.Entity

BETA, compartment, debug, fixedOutput, geneIds, id, name, output, TRANSFER_FUNCTION, weight

Constructor Summary

Constructors

Constructor	Description
Reaction(int id, java.lang.String name)

Method Summary

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 1
java.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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

MAX_WEIGHT_SUM

public static final double MAX_WEIGHT_SUM

See Also:

Constant Field Values

inputs

protected java.util.HashMap<Entity,java.lang.Double> inputs

outputs

protected java.util.HashSet<Entity> outputs

catalyst

protected java.util.HashSet<Entity> catalyst

regulator

protected java.util.HashMap<Entity,Reaction.RegulationType> regulator

Constructor Detail

Reaction

public Reaction(int id,
                java.lang.String name)

Method Detail

addCatalyst

public void addCatalyst(Entity e)

addInput

public void addInput(Entity e)

addOutput

public void addOutput(Entity e)

addRegulator

public void addRegulator(Entity e,
                         Reaction.RegulationType type)

addRegulator

public void addRegulator(Entity e,
                         java.lang.String type)

calc

public double calc(java.util.HashSet<Entity> doneEntities)

Calculate entities. Make sure we don't calculate twice (keep 'doneEntities' set up to date)

Overrides:

calc in class Entity

Parameters:

doneEntities -

Returns:

getCatalyst

public java.util.HashSet<Entity> getCatalyst()

getInputs

public java.util.Collection<Entity> getInputs()

getOutputs

public java.util.HashSet<Entity> getOutputs()

getRegulator

public java.util.HashMap<Entity,Reaction.RegulationType> getRegulator()

isReaction

public boolean isReaction()

Overrides:

isReaction in class Entity

scaleWeights

public void scaleWeights()

Scale weights so that they add to 1

toString

public java.lang.String toString()

Overrides:

toString in class Entity

toString

public java.lang.String toString(int tabs,
                                 java.util.HashSet<Entity> done)

Overrides:

toString in class Entity

transferFunction

protected double transferFunction(double h,
                                  double inCat,
                                  double inRegPos,
                                  double inRegNeg,
                                  double inRegReq)

Transfer function

Parameters:

h -

Returns: