Class Reactome

java.lang.Object
org.snpeff.reactome.Reactome
All Implemented Interfaces:
Iterable<Entity>

public class Reactome extends Object implements Iterable<Entity>
Load reactome data from TXT files
Author:
pcingola
  • Field Details

  • Constructor Details

    • Reactome

      public Reactome()
  • Method Details

    • main

      public static void main(String[] args)
      Main
      Parameters:
      args -
    • add

      public void add(Entity entity, String geneId)
      Add an entity <-> geneId
      Parameters:
      entity -
      geneId -
    • getMonitor

      public Monitor getMonitor()
    • getMonitorTrace

      public Monitor getMonitorTrace()
    • iterator

      public Iterator<Entity> iterator()
      Specified by:
      iterator in interface Iterable<Entity>
    • load

      public void load(String dirName, String geneIdsFile)
    • loadCatalystActivity

      protected void loadCatalystActivity()
      Load catalyst activity to molecule mapping
    • loadComplex2HasComponent

      protected void loadComplex2HasComponent()
      Load complexes
      Parameters:
      name -
      fileName -
      map -
    • loadDatabaseObjects

      protected void loadDatabaseObjects()
      Load objects table (populate objectType and objectName maps)
    • loadGeneIds

      public void loadGeneIds(String geneIdsFile)
      Load Gene IDs data, then map geneIDs <-> Entities
      Parameters:
      geneIdsFile -
    • loadMap

      protected void loadMap(String name, String fileName, HashMap<String,String> map)
      Load a two-column file into a Hash
      Parameters:
      name -
      fileName -
      map -
    • loadPathway2HasEvent

      protected void loadPathway2HasEvent()
      Load pathway events
      Parameters:
      name -
      fileName -
      map -
    • loadPhysicalEntity2Compartment

      protected void loadPhysicalEntity2Compartment()
      Load compartment information
      Parameters:
      name -
      fileName -
      map -
    • loadReactionlikeEvent2CatalystActivity

      protected void loadReactionlikeEvent2CatalystActivity()
      Load reaction catalyst
      Parameters:
      name -
      fileName -
      map -
    • loadReactionlikeEvent2Input

      protected void loadReactionlikeEvent2Input()
      Load reaction inputs
      Parameters:
      name -
      fileName -
      map -
    • loadReactionlikeEvent2Output

      protected void loadReactionlikeEvent2Output()
      Load reaction outputs
      Parameters:
      name -
      fileName -
      map -
    • loadRegulation

      protected void loadRegulation()
      Load reaction regulation
      Parameters:
      name -
      fileName -
      map -
    • reset

      public void reset()
      Reset all nodes in the circuit
    • run

      public boolean run(Gtex gtex, String nameMatch)
      Run all experiments on gtex
      Parameters:
      gtex -
      Returns:
    • run

      public boolean run(GtexExperiment gtexExperiment)
      Run some simulations
      Parameters:
      gtex -
      gtexExperiment -
    • setMonitorTrace

      public void setMonitorTrace(Monitor monitorTrace)
    • setVerbose

      public void setVerbose(boolean verbose)
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • toStringDetails

      public String toStringDetails()
      Show details
      Returns: