scalation.dynamics

SSA

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. def flaw(method: String, message: String): Unit

    Show the flaw by printing the error message.

    Show the flaw by printing the error message.

    method

    the method where the error occurred

    message

    the error message

    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
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    @throws( ... )

  28. final def wait(arg0: Long): Unit

    Definition Classes
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    @throws( ... )

Inherited from Error

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