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
Ordering
  1. Alphabetic
  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
  1. Hide All
  2. Show All
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

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