class Experiment extends AbstractExperiment with SBMLSimResultHandling

Encapsulates the SBMLsimulator (see http://www.ra.cs.uni-tuebingen.de/software/SBMLsimulator). As only the core is provided at Sourceforge (http://sourceforge.net/projects/sbml-simulator/), this will be integrated (i.e., no functionality to set up experiments via the GUI is reused here).

Linear Supertypes
SBMLSimResultHandling, ResultHandling, AbstractExperiment, CSVInput, SupportStoppingConditions, SupportReplicationConditions, SupportRNGSetup, SupportSimulatorConfiguration, SupportModelConfiguration, BasicExperimentConfiguration, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
Known Subclasses
SimpleTestExperiment
Ordering
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  2. By Inheritance
Inherited
  1. Experiment
  2. SBMLSimResultHandling
  3. ResultHandling
  4. AbstractExperiment
  5. CSVInput
  6. SupportStoppingConditions
  7. SupportReplicationConditions
  8. SupportRNGSetup
  9. SupportSimulatorConfiguration
  10. SupportModelConfiguration
  11. BasicExperimentConfiguration
  12. ExperimentConfiguration
  13. Logging
  14. StrictLogging
  15. AnyRef
  16. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Experiment()

Type Members

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

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

  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.

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 afterExperiment(f: (ExperimentResults) ⇒ Unit): ListBuffer[(ExperimentResults) ⇒ Unit]
    Definition Classes
    BasicExperimentConfiguration
  9. def afterReplications(f: (ReplicationsResults) ⇒ Unit): ListBuffer[(ReplicationsResults) ⇒ Unit]
    Definition Classes
    BasicExperimentConfiguration
  10. def afterRun(f: (RunResults) ⇒ Unit): ListBuffer[(RunResults) ⇒ Unit]
    Definition Classes
    BasicExperimentConfiguration
  11. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  12. def basicConfiguration(): Unit
    Definition Classes
    Experiment → AbstractExperiment
  13. def checkAndGetReplicationCondition(): ReplicationCondition
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  14. def checkAndGetStoppingCondition(): StoppingCondition
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  15. def checkResultHandlingCorrectness(methodName: String): Unit
    Definition Classes
    ResultHandling
  16. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  17. def collectExperimentResultsAspects(): Unit
    Attributes
    protected
    Definition Classes
    ExperimentConfiguration
  18. def collectReplicationsResultsAspects(assignId: Int): Unit
    Attributes
    protected
    Definition Classes
    ExperimentConfiguration
  19. def collectRunResultsAspects(runId: Int): Unit
    Attributes
    protected
    Definition Classes
    ExperimentConfiguration
  20. def configs(configs: Config*): Unit
    Definition Classes
    SupportModelConfiguration
  21. def configure(): Unit
    Definition Classes
    AbstractExperiment → ExperimentConfiguration
  22. def configureModelLocation(): Unit

    Configure model location.

  23. def configureSimulatorSetup(): Unit

    Configure simulator setup.

  24. 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.

    Attributes
    protected[sessl.sbmlsim]
    Definition Classes
    SBMLSimResultHandling
  25. def designFromCSV(file: File): Unit
    Definition Classes
    CSVInput
  26. def designFromCSV(uri: URI): Unit
    Definition Classes
    CSVInput
  27. def designFromCSV(fileName: String): Unit
    Definition Classes
    CSVInput
  28. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  29. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  30. def executeExperiment(): Unit

    Executes experiment

    Executes experiment

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

    Executes a job.

    Executes a job.

    Attributes
    protected[sessl.sbmlsim]
  32. def executeJobs(jobs: List[JobDescription]): List[Unit]

    Executes the given list of jobs.

  33. val executionMode: SimulatorExecutionOption
    Definition Classes
    SupportSimulatorConfiguration
  34. val expStartTime: Instant
    Definition Classes
    AbstractExperiment
  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. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  46. def model: String
    Definition Classes
    SupportModelConfiguration
  47. val modelLocation: Option[String]
    Attributes
    protected[this]
    Definition Classes
    SupportModelConfiguration
  48. def model_=(modelString: String): Unit
    Definition Classes
    SupportModelConfiguration
  49. def model_=(modelURI: URI): Unit
    Definition Classes
    SupportModelConfiguration
  50. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  51. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  52. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  53. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  54. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  55. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  56. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  57. def replicationCondition_=(rc: ReplicationCondition): Nothing
    Definition Classes
    Experiment → SupportReplicationConditions
  58. def replications: Int
    Definition Classes
    SupportReplicationConditions
  59. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  60. def replications_=(reps: Int): Nothing
    Definition Classes
    Experiment → SupportReplicationConditions
  61. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  62. def resultsHandlingIsCalled(): Unit
    Attributes
    protected
    Definition Classes
    ResultHandling
  63. def rng: RNG
    Definition Classes
    SupportRNGSetup
  64. def rng_=(rand: RNG): Unit
    Definition Classes
    SupportRNGSetup
  65. def runAssignment(runId: Int): Int
    Attributes
    protected
    Definition Classes
    BasicExperimentConfiguration
  66. final def runDone(runId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  67. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  68. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  69. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  70. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  71. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  72. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  73. def stopCondition_=(sc: StoppingCondition): Nothing
    Definition Classes
    Experiment → SupportStoppingConditions
  74. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  75. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  76. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  77. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  78. def toString(): String
    Definition Classes
    AnyRef → Any
  79. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  80. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  81. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  82. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  83. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  84. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )

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