Packages

class SSA extends Error

The SSA class implements the Gillespie Stochastic Simulation Algorithm 'SSA'.

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Visibility
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Instance Constructors

  1. new SSA(c: MatrixI, r: MatrixI, z: MatrixI, x: MatrixD, t0: Double = 0.0)

    c

    the matrix giving sub-volume connectivity

    r

    the matrix indicating which the reactions that are active in each sub-volume

    z

    the matrix giving stoichiometry for all reactions

    x

    the matrix giving species population per volume

    t0

    the start time for the simulation

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. val L: Int
  5. val R: Int
  6. val S: Int
  7. val a: Array[VectorD]
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  10. val cut: (Double, Double, Double)
  11. val e: IndexedSeq[Int]
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  14. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  15. final def flaw(method: String, message: String): Unit
    Definition Classes
    Error
  16. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  17. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  20. final def notify(): Unit
    Definition Classes
    AnyRef
  21. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  22. def simulate(tf: Double): Unit

  23. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  24. var t: Double
  25. def toString(): String

    Definition Classes
    SSA → AnyRef → Any
  26. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  27. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Error

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