Packages

c

sessl.util.test.sbmlsim

SimpleTestExperiment

class SimpleTestExperiment extends Experiment with ParallelExecution with Observation

Simple test experiment.

Linear Supertypes
Observation, SimpleObservation, AbstractObservation, TrajectoryOperations, ParallelExecution, AbstractParallelExecution, Experiment, SBMLSimResultHandling, ResultHandling, AbstractExperiment, CSVInput, SupportStoppingConditions, SupportReplicationConditions, SupportRNGSetup, SupportSimulatorConfiguration, SupportModelConfiguration, BasicExperimentConfiguration, StopOnError, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
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  2. By Inheritance
Inherited
  1. SimpleTestExperiment
  2. Observation
  3. SimpleObservation
  4. AbstractObservation
  5. TrajectoryOperations
  6. ParallelExecution
  7. AbstractParallelExecution
  8. Experiment
  9. SBMLSimResultHandling
  10. ResultHandling
  11. AbstractExperiment
  12. CSVInput
  13. SupportStoppingConditions
  14. SupportReplicationConditions
  15. SupportRNGSetup
  16. SupportSimulatorConfiguration
  17. SupportModelConfiguration
  18. BasicExperimentConfiguration
  19. StopOnError
  20. ExperimentConfiguration
  21. Logging
  22. StrictLogging
  23. AnyRef
  24. 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
  3. implicit class ObservableName extends AnyRef
    Definition Classes
    AbstractObservation
  4. implicit class TrajectoryIterOps[T] extends AnyRef
    Definition Classes
    TrajectoryOperations
  5. implicit class TrajectoryOps[T] extends AnyRef
    Definition Classes
    TrajectoryOperations

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[T](runID: Int, observable: Observable[T], value: TimeStampedData[T]): 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() @HotSpotIntrinsicCandidate() @throws( ... )
  18. def collectExperimentResultsAspects(): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  19. def collectReplicationsResults(assignID: Int): ObservationReplicationsResultsAspect
    Definition Classes
    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. def designFromCSV(file: File): Unit
    Definition Classes
    CSVInput
  30. def designFromCSV(uri: URI): Unit
    Definition Classes
    CSVInput
  31. def designFromCSV(fileName: String): Unit
    Definition Classes
    CSVInput
  32. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  33. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  34. def executeExperiment(): Unit

    Executes experiment

    Executes experiment

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

    Executes a job.

    Executes a job.

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

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @Deprecated @deprecated @throws( classOf[java.lang.Throwable] )
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from Observation

Inherited from SimpleObservation

Inherited from AbstractObservation

Inherited from TrajectoryOperations

Inherited from ParallelExecution

Inherited from AbstractParallelExecution

Inherited from Experiment

Inherited from SBMLSimResultHandling

Inherited from ResultHandling

Inherited from AbstractExperiment

Inherited from CSVInput

Inherited from SupportStoppingConditions

Inherited from SupportReplicationConditions

Inherited from SupportRNGSetup

Inherited from SupportSimulatorConfiguration

Inherited from SupportModelConfiguration

Inherited from BasicExperimentConfiguration

Inherited from StopOnError

Inherited from ExperimentConfiguration

Inherited from Logging

Inherited from StrictLogging

Inherited from AnyRef

Inherited from Any

Ungrouped