Class Entity

java.lang.Object
org.snpeff.reactome.Entity
All Implemented Interfaces:
Comparable<Entity>
Direct Known Subclasses:
Compartment, Event

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

    • debug

      public static boolean debug
    • TRANSFER_FUNCTION

      public static Entity.TransferFunction TRANSFER_FUNCTION
    • BETA

      public static double BETA
    • id

      protected int id
    • name

      protected String name
    • compartment

      protected Compartment compartment
    • output

      protected double output
    • weight

      protected double weight
    • fixedOutput

      protected double fixedOutput
    • geneIds

      protected HashSet<String> geneIds
  • Constructor Details

    • Entity

      public Entity(int id, String name)
  • Method Details

    • addGeneId

      public void addGeneId(String geneId)
      Add a geneId
      Parameters:
      geneId -
    • calc

      public double calc()
    • calc

      public double calc(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 Comparable<Entity>
    • getCompartment

      public Compartment getCompartment()
    • getGeneIds

      public Collection<String> getGeneIds()
    • getId

      public int getId()
    • getName

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

      public String toString(int tabs, HashSet<Entity> done)
    • toStringSimple

      public String toStringSimple()
    • transferFunction

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