Package org.snpeff.reactome

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: