org.snpeff.reactome.events.Pathway

All Implemented Interfaces:: Comparable<Entity>, Iterable<Event>

public class Pathway extends Reaction implements Iterable<Event>

A Reactome pathway

Author:: pcingola

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.reactome.events.Reaction
Reaction.RegulationType

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

Fields inherited from class org.snpeff.reactome.events.Reaction
catalyst, inputs, MAX_WEIGHT_SUM, outputs, 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

Pathway(int id, String name)
Method Summary

Modifier and Type

Method

Description

void

add(Event e)

boolean

contains(Object o)

boolean

isEmpty()

Iterator<Event>

iterator()

int

size()

String

toString()

String

toString(int tabs, HashSet<Entity> done)

Methods inherited from class org.snpeff.reactome.events.Reaction
addCatalyst, addInput, addOutput, addRegulator, addRegulator, calc, getCatalyst, getInputs, getOutputs, getRegulator, isReaction, scaleWeights, transferFunction

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- Pathway
  
  public Pathway(int id, String name)
Method Details
- add
  
  public void add(Event e)
- contains
  
  public boolean contains(Object o)
- isEmpty
  
  public boolean isEmpty()
- iterator
  
  public Iterator<Event> iterator()
  
  Specified by:
  
  iterator in interface Iterable<Event>
- size
  
  public int size()
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Reaction
- toString
  
  public String toString(int tabs, HashSet<Entity> done)
  
  Overrides:
  
  toString in class Reaction

Class Pathway

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.reactome.events.Reaction

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

Field Summary

Fields inherited from class org.snpeff.reactome.events.Reaction

Fields inherited from class org.snpeff.reactome.Entity

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.reactome.events.Reaction

Methods inherited from class org.snpeff.reactome.Entity

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Details

Pathway

Method Details

add

contains

isEmpty

iterator

size

toString

toString