Class Entity

  • All Implemented Interfaces:
    java.lang.Comparable<Entity>
    Direct Known Subclasses:
    Compartment, Event

    public class Entity
    extends java.lang.Object
    implements java.lang.Comparable<Entity>
    A reactome basic entity (e.g. anything in reactome database derives fro this object)
    Author:
    pcingola
    • Field Detail

      • debug

        public static boolean debug
      • BETA

        public static double BETA
      • id

        protected int id
      • name

        protected java.lang.String name
      • output

        protected double output
      • weight

        protected double weight
      • fixedOutput

        protected double fixedOutput
      • geneIds

        protected java.util.HashSet<java.lang.String> geneIds
    • Constructor Detail

      • Entity

        public Entity​(int id,
                      java.lang.String name)
    • Method Detail

      • addGeneId

        public void addGeneId​(java.lang.String geneId)
        Add a geneId
        Parameters:
        geneId -
      • calc

        public double calc()
      • calc

        public double calc​(java.util.HashSet<Entity> doneEntities)
        Calculate entities. Make sure we don't calculate twice (keep 'doneEntities' set up to date)
        Parameters:
        doneEntities -
        Returns:
      • compareTo

        public int compareTo​(Entity e)
        Specified by:
        compareTo in interface java.lang.Comparable<Entity>
      • getGeneIds

        public java.util.Collection<java.lang.String> getGeneIds()
      • getId

        public int getId()
      • getName

        public java.lang.String getName()
      • getOutput

        public double getOutput()
      • getWeight

        public double getWeight()
      • hasOutput

        public boolean hasOutput()
      • isFixed

        public boolean isFixed()
      • isReaction

        public boolean isReaction()
      • reset

        public void reset()
      • setCompartment

        public void setCompartment​(Compartment compartment)
      • setFixedOutput

        public void setFixedOutput​(double fixedOutput)
      • setWeight

        public void setWeight​(double weight)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • toString

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

        public java.lang.String toStringSimple()
      • transferFunction

        protected double transferFunction​(double x)
        Transfer function
        Parameters:
        x -
        Returns: