scalation.dynamics

SSA

class SSA extends Error

This 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: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

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    Any

  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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

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  6. val L: Int

  7. val R: Int

  8. val S: Int

  9. val a: Array[VectorD]

  10. final def asInstanceOf[T0]: T0

    Definition Classes
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  11. def clone(): AnyRef

    Attributes
    protected[lang]
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    @throws()

  12. val cut: (Double, Double, Double)

  13. val e: IndexedSeq[Int]

  14. final def eq(arg0: AnyRef): Boolean

    Definition Classes
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  15. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  16. def finalize(): Unit

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    protected[lang]
    Definition Classes
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    @throws()

  17. 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

  18. final def getClass(): java.lang.Class[_]

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  19. def hashCode(): Int

    Definition Classes
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  20. final def isInstanceOf[T0]: Boolean

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

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  22. final def notify(): Unit

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  23. final def notifyAll(): Unit

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  24. def simulate(tf: Double): Unit

  25. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
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  26. var t: Double

  27. def toString(): String

    Definition Classes
    SSA → AnyRef → Any

  28. final def wait(): Unit

    Definition Classes
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    @throws()

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

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    @throws()

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

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Inherited from Error

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