Packages

c

sessl.util.test.sbmlsim

SimpleTestExperiment

class SimpleTestExperiment extends Experiment with ParallelExecution with Observation

Simple test experiment.

Linear Supertypes
Observation, SimpleObservation, AbstractObservation, ParallelExecution, AbstractParallelExecution, Experiment, SBMLSimResultHandling, ResultHandling, AbstractExperiment, SupportStoppingConditions, SupportReplicationConditions, SupportRNGSetup, SupportSimulatorConfiguration, SupportModelConfiguration, BasicExperimentConfiguration, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
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  2. By Inheritance
Inherited
  1. SimpleTestExperiment
  2. Observation
  3. SimpleObservation
  4. AbstractObservation
  5. ParallelExecution
  6. AbstractParallelExecution
  7. Experiment
  8. SBMLSimResultHandling
  9. ResultHandling
  10. AbstractExperiment
  11. SupportStoppingConditions
  12. SupportReplicationConditions
  13. SupportRNGSetup
  14. SupportSimulatorConfiguration
  15. SupportModelConfiguration
  16. BasicExperimentConfiguration
  17. ExperimentConfiguration
  18. Logging
  19. StrictLogging
  20. AnyRef
  21. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new SimpleTestExperiment()

Type Members

  1. type AssignmentDescription = (Map[String, Any], Int)

    Describes a variable assignment (first element) and its id (second element).

    Describes a variable assignment (first element) and its id (second element).

    Definition Classes
    Experiment
  2. type JobDescription = ((AssignmentDescription, BasicSBMLSimSimulator, Boolean), Int)

    Describes a job with a an id as second element and a triple (variable assignment, simulator-setup,flag-replications-done) as a first element.

    Describes a job with a an id as second element and a triple (variable assignment, simulator-setup,flag-replications-done) as a first element.

    Definition Classes
    Experiment

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. def addAssignmentForRun(runId: Int, assignId: Int, assignment: VariableAssignment): Unit
    Definition Classes
    BasicExperimentConfiguration
  5. def addExperimentResultsAspect(a: ExperimentResultsAspect): Unit
    Definition Classes
    BasicExperimentConfiguration
  6. def addReplicationsResultsAspect(assignmentId: Int, a: ReplicationsResultsAspect): Unit
    Definition Classes
    BasicExperimentConfiguration
  7. def addRunResultsAspect(runId: Int, a: RunResultsAspect): Unit
    Definition Classes
    BasicExperimentConfiguration
  8. def addValueFor(runID: Int, internalName: String, value: TimeStampedData[_]): Unit
    Attributes
    protected[sessl]
    Definition Classes
    SimpleObservation
  9. def afterExperiment(f: (ExperimentResults) ⇒ Unit): ListBuffer[(ExperimentResults) ⇒ Unit]
    Definition Classes
    BasicExperimentConfiguration
  10. def afterReplications(f: (ReplicationsResults) ⇒ Unit): ListBuffer[(ReplicationsResults) ⇒ Unit]
    Definition Classes
    BasicExperimentConfiguration
  11. def afterRun(f: (RunResults) ⇒ Unit): ListBuffer[(RunResults) ⇒ Unit]
    Definition Classes
    BasicExperimentConfiguration
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. def basicConfiguration(): Unit
    Definition Classes
    Experiment → AbstractExperiment
  14. def checkAndGetReplicationCondition(): ReplicationCondition
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  15. def checkAndGetStoppingCondition(): StoppingCondition
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  16. def checkResultHandlingCorrectness(methodName: String): Unit
    Definition Classes
    ResultHandling
  17. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  18. def collectExperimentResultsAspects(): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  19. def collectReplicationsResults(assignId: Int): ObservationReplicationsResultsAspect
    Definition Classes
    SimpleObservation → AbstractObservation
  20. def collectReplicationsResultsAspects(assignId: Int): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  21. def collectResults(runId: Int, removeData: Boolean): ObservationRunResultsAspect
    Definition Classes
    SimpleObservation → AbstractObservation
  22. def collectRunResultsAspects(runId: Int): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  23. def configs(configs: Config*): Unit
    Definition Classes
    SupportModelConfiguration
  24. def configure(): Unit
    Definition Classes
    AbstractParallelExecution → ExperimentConfiguration
  25. def configureModelLocation(): Unit

    Configure model location.

    Configure model location.

    Definition Classes
    Experiment
  26. def configureParallelExecution(threads: Int): Unit
    Definition Classes
    ParallelExecution → AbstractParallelExecution
  27. def configureSimulatorSetup(): Unit

    Configure simulator setup.

    Configure simulator setup.

    Definition Classes
    Experiment
  28. def considerResults(runId: Int, assignmentId: Int, results: MultiTable): Unit

    Method to be overridden to extract data from the results.

    Method to be overridden to extract data from the results. They use a lot of memory, so the results of each run will be discarded after calling this method.

    Definition Classes
    Observation → SBMLSimResultHandling
  29. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  30. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  31. def executeExperiment(): Unit

    Executes experiment

    Executes experiment

    Definition Classes
    Experiment → AbstractExperiment
  32. final def executeJob(jobDesc: JobDescription): Unit

    Executes a job.

    Executes a job.

    Attributes
    protected[sessl.sbmlsim]
    Definition Classes
    Experiment
  33. def executeJobs(jobs: List[JobDescription]): List[Unit]
    Definition Classes
    ParallelExecution
  34. val executionMode: SimulatorExecutionOption
    Definition Classes
    SupportSimulatorConfiguration
  35. final def experimentDone(): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  36. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  37. def finishExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  38. val fixedReplications: Option[Int]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  39. val fixedStopTime: Option[Double]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  40. lazy val fixedVariables: Map[String, Any]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  41. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  42. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  43. def isDone: Boolean
    Definition Classes
    BasicExperimentConfiguration
  44. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  45. def isObservationTimingDefined: Boolean
    Definition Classes
    AbstractObservation
  46. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  47. def model: String
    Definition Classes
    SupportModelConfiguration
  48. val modelLocation: Option[String]
    Attributes
    protected[this]
    Definition Classes
    SupportModelConfiguration
  49. def model_=(modelString: String): Unit
    Definition Classes
    SupportModelConfiguration
  50. def model_=(modelURI: URI): Unit
    Definition Classes
    SupportModelConfiguration
  51. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  52. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  53. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  54. lazy val observationTimes: List[Double]
    Definition Classes
    AbstractObservation
  55. def observe(binds: DataElemBinding*): Unit
    Definition Classes
    AbstractObservation
  56. final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit
    Definition Classes
    AbstractObservation
  57. final def observeAt(observationTimes: Double*): Unit
    Definition Classes
    AbstractObservation
  58. val parallelThreads: Int
    Definition Classes
    AbstractParallelExecution
  59. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  60. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  61. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  62. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  63. def replicationCondition_=(rc: ReplicationCondition): Nothing
    Definition Classes
    Experiment → SupportReplicationConditions
  64. def replications: Int
    Definition Classes
    SupportReplicationConditions
  65. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  66. def replications_=(reps: Int): Nothing
    Definition Classes
    Experiment → SupportReplicationConditions
  67. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  68. def resultsHandlingIsCalled(): Unit
    Attributes
    protected
    Definition Classes
    ResultHandling
  69. lazy val reverseVariableBindings: Map[String, String]
    Definition Classes
    AbstractObservation
  70. def rng: RNG
    Definition Classes
    SupportRNGSetup
  71. def rng_=(rand: RNG): Unit
    Definition Classes
    SupportRNGSetup
  72. def runAssignment(runId: Int): Int
    Attributes
    protected
    Definition Classes
    BasicExperimentConfiguration
  73. final def runDone(runId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  74. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  75. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  76. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  77. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  78. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  79. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  80. def stopCondition_=(sc: StoppingCondition): Nothing
    Definition Classes
    Experiment → SupportStoppingConditions
  81. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  82. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  83. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  84. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  85. def toString(): String
    Definition Classes
    AnyRef → Any
  86. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  87. def variableBindings: Map[String, Set[String]]
    Definition Classes
    AbstractObservation
  88. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  89. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  90. def varsToBeObserved: Set[String]
    Definition Classes
    AbstractObservation
  91. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  92. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  93. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  94. def withExperimentResult(f: (ObservationExperimentResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  95. def withReplicationsResult(f: (ObservationReplicationsResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  96. def withRunResult(f: (ObservationRunResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation

Inherited from Observation

Inherited from SimpleObservation

Inherited from AbstractObservation

Inherited from ParallelExecution

Inherited from AbstractParallelExecution

Inherited from Experiment

Inherited from SBMLSimResultHandling

Inherited from ResultHandling

Inherited from AbstractExperiment

Inherited from SupportStoppingConditions

Inherited from SupportReplicationConditions

Inherited from SupportRNGSetup

Inherited from SupportSimulatorConfiguration

Inherited from SupportModelConfiguration

Inherited from BasicExperimentConfiguration

Inherited from ExperimentConfiguration

Inherited from Logging

Inherited from StrictLogging

Inherited from AnyRef

Inherited from Any

Ungrouped