Class Reactome

  • All Implemented Interfaces:
    java.lang.Iterable<Entity>

    public class Reactome
    extends java.lang.Object
    implements java.lang.Iterable<Entity>
    Load reactome data from TXT files
    Author:
    pcingola
    • Constructor Detail

      • Reactome

        public Reactome()
    • Method Detail

      • main

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

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

        public Monitor getMonitor()
      • getMonitorTrace

        public Monitor getMonitorTrace()
      • iterator

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

        public void load​(java.lang.String dirName,
                         java.lang.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​(java.lang.String geneIdsFile)
        Load Gene IDs data, then map geneIDs <-> Entities
        Parameters:
        geneIdsFile -
      • loadMap

        protected void loadMap​(java.lang.String name,
                               java.lang.String fileName,
                               java.util.HashMap<java.lang.String,​java.lang.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,
                           java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • toStringDetails

        public java.lang.String toStringDetails()
        Show details
        Returns: