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, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
Ordering
  1. Alphabetic
  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. ExperimentConfiguration
  20. Logging
  21. StrictLogging
  22. AnyRef
  23. 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
  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() @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. 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: List[JobDescription]): List[Unit]
    Definition Classes
    ParallelExecution
  37. val executionMode: SimulatorExecutionOption
    Definition Classes
    SupportSimulatorConfiguration
  38. val expStartTime: Instant
    Definition Classes
    AbstractExperiment
  39. final def experimentDone(): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  40. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  41. def finishExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  42. val fixedReplications: Option[Int]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  43. val fixedStopTime: Option[Double]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  44. lazy val fixedVariables: Map[String, Any]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  45. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  46. def getOrElseUpdate[T](name: String, obs: ⇒ Observable[T]): Observable[T]
    Attributes
    protected
    Definition Classes
    AbstractObservation
  47. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  48. def isDone: Boolean
    Definition Classes
    BasicExperimentConfiguration
  49. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  50. def isObservationTimingDefined: Boolean
    Definition Classes
    AbstractObservation
  51. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  52. implicit def lookupObservable[T](name: String): Observable[T]
    Definition Classes
    AbstractObservation
  53. def model: String
    Definition Classes
    SupportModelConfiguration
  54. val modelLocation: Option[String]
    Attributes
    protected[this]
    Definition Classes
    SupportModelConfiguration
  55. def model_=(modelString: String): Unit
    Definition Classes
    SupportModelConfiguration
  56. def model_=(modelURI: URI): Unit
    Definition Classes
    SupportModelConfiguration
  57. def namedObservables: Map[String, Observable[_]]
    Definition Classes
    AbstractObservation
  58. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  59. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  60. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  61. def observables: Set[Observable[_]]
    Definition Classes
    AbstractObservation
  62. lazy val observationTimes: Vector[Double]
    Definition Classes
    AbstractObservation
  63. def observe[T](obs: Observable[T], obss: Observable[_]*): Observable[T]
    Definition Classes
    AbstractObservation
  64. final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit
    Definition Classes
    AbstractObservation
  65. final def observeAt(observationTimes: Double*): Unit
    Definition Classes
    AbstractObservation
  66. val parallelThreads: Int
    Definition Classes
    AbstractParallelExecution
  67. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  68. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  69. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  70. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  71. def replicationCondition_=(rc: ReplicationCondition): Nothing
    Definition Classes
    Experiment → SupportReplicationConditions
  72. def replications: Int
    Definition Classes
    SupportReplicationConditions
  73. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  74. def replications_=(reps: Int): Nothing
    Definition Classes
    Experiment → SupportReplicationConditions
  75. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  76. def resultsHandlingIsCalled(): Unit
    Attributes
    protected
    Definition Classes
    ResultHandling
  77. def rng: RNG
    Definition Classes
    SupportRNGSetup
  78. def rng_=(rand: RNG): Unit
    Definition Classes
    SupportRNGSetup
  79. def runAssignment(runId: Int): Int
    Attributes
    protected
    Definition Classes
    BasicExperimentConfiguration
  80. final def runDone(runId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  81. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  82. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  83. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  84. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  85. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  86. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  87. def stopCondition_=(sc: StoppingCondition): Nothing
    Definition Classes
    Experiment → SupportStoppingConditions
  88. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  89. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  90. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  91. implicit def stringToObservable(varName: String): Observable[Double]
    Definition Classes
    Observation
  92. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  93. def toString(): String
    Definition Classes
    AnyRef → Any
  94. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  95. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  96. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  97. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  98. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  99. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  100. def withExperimentResult(f: (ObservationExperimentResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  101. def withReplicationsResult(f: (ObservationReplicationsResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  102. def withRunResult(f: (ObservationRunResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  103. val x: Observable[Double]

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 ExperimentConfiguration

Inherited from Logging

Inherited from StrictLogging

Inherited from AnyRef

Inherited from Any

Ungrouped