scalation.dynamics

SSA

Related Doc: package dynamics

class SSA extends Error

The SSA class implements the Gillespie Stochastic Simulation Algorithm (SSA).

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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
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  3. final def ==(arg0: Any): Boolean

    Definition Classes
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  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
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  9. def clone(): AnyRef

    Attributes
    protected[java.lang]
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    @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

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  14. def finalize(): Unit

    Attributes
    protected[java.lang]
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    @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
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  18. final def isInstanceOf[T0]: Boolean

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  19. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  20. final def notify(): Unit

    Definition Classes
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  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
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    @throws( ... )

  27. final def wait(arg0: Long, arg1: Int): Unit

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    @throws( ... )

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

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