Package org.snpeff.reactome

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: