org.snpeff.reactome.events.Reaction

All Implemented Interfaces:: 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 enum

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 HashSet<Entity>

catalyst

protected HashMap<Entity,Double>

inputs

static final double

MAX_WEIGHT_SUM

protected HashSet<Entity>

outputs

protected 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, 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, String type)

void

addRegulator(Entity e, Reaction.RegulationType type)

double

calc(HashSet<Entity> doneEntities)

Calculate entities.

HashSet<Entity>

getCatalyst()

Collection<Entity>

getInputs()

HashSet<Entity>

getOutputs()

HashMap<Entity,Reaction.RegulationType>

getRegulator()

boolean

isReaction()

void

scaleWeights()

Scale weights so that they add to 1

String

toString()

String

toString(int tabs, 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 Details
- MAX_WEIGHT_SUM
  
  public static final double MAX_WEIGHT_SUM
  See Also:
  
  Constant Field Values
- inputs
  
  protected HashMap<Entity,Double> inputs
- outputs
  
  protected HashSet<Entity> outputs
- catalyst
  
  protected HashSet<Entity> catalyst
- regulator
  
  protected HashMap<Entity,Reaction.RegulationType> regulator
Constructor Details
- Reaction
  
  public Reaction(int id, String name)
Method Details
- 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, String type)
- calc
  
  public double calc(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 HashSet<Entity> getCatalyst()
- getInputs
  
  public Collection<Entity> getInputs()
- getOutputs
  
  public HashSet<Entity> getOutputs()
- getRegulator
  
  public 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 String toString()
  
  Overrides:
  
  toString in class Entity
- toString
  
  public String toString(int tabs, 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:

Class Reaction

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.reactome.Entity

Field Summary

Fields inherited from class org.snpeff.reactome.Entity

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.reactome.Entity

Methods inherited from class java.lang.Object

Field Details

MAX_WEIGHT_SUM

inputs

outputs

catalyst

regulator

Constructor Details

Reaction

Method Details

addCatalyst

addInput

addOutput

addRegulator

addRegulator

calc

getCatalyst

getInputs

getOutputs

getRegulator

isReaction

scaleWeights

toString

toString

transferFunction