Packages

c

sessl.pssalib

Experiment

class Experiment extends AbstractExperiment with DynamicSimulationRuns with SBMLFileManipulation

A PSSALib experiment gets executed by invoking the native binary (which must be installed separately). To configure the model with parameter values, the SBML model file is copied and modified before it becomes the input for the simulator. A temporary directory is created for these model file copies. The individual simulation runs are started in Futures to enable concurrency.

Linear Supertypes
SBMLFileManipulation, DynamicSimulationRuns, AbstractExperiment, CSVInput, SupportStoppingConditions, SupportReplicationConditions, SupportRNGSetup, SupportSimulatorConfiguration, SupportModelConfiguration, BasicExperimentConfiguration, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
Known Subclasses
Observation, ParallelExecution
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. Experiment
  2. SBMLFileManipulation
  3. DynamicSimulationRuns
  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()

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 additionalOptions: Seq[String]
    Attributes
    protected
  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
    Attributes
    protected
    Definition Classes
    Experiment → AbstractExperiment
  14. def batchSize: Int
    Definition Classes
    DynamicSimulationRuns
  15. def batchSize_=(b: Int): Unit
    Definition Classes
    DynamicSimulationRuns
  16. def checkAndGetReplicationCondition(): ReplicationCondition
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  17. def checkAndGetStoppingCondition(): StoppingCondition
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  18. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  19. def collectExperimentResultsAspects(): Unit
    Attributes
    protected
    Definition Classes
    ExperimentConfiguration
  20. def collectReplicationsResultsAspects(assignId: Int): Unit
    Attributes
    protected
    Definition Classes
    ExperimentConfiguration
  21. def collectRunResultsAspects(runId: Int): Unit
    Attributes
    protected
    Definition Classes
    ExperimentConfiguration
  22. def configs(configs: Config*): Unit
    Definition Classes
    SupportModelConfiguration
  23. def configure(): Unit
    Definition Classes
    AbstractExperiment → ExperimentConfiguration
  24. def designFromCSV(file: File): Unit
    Definition Classes
    CSVInput
  25. def designFromCSV(uri: URI): Unit
    Definition Classes
    CSVInput
  26. def designFromCSV(fileName: String): Unit
    Definition Classes
    CSVInput
  27. def dirForRun(runId: Int): File
    Attributes
    protected
  28. def enoughReplications(assignmentId: Int, replicationCondition: ReplicationCondition): Boolean
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  29. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  30. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  31. def executeExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    Experiment → AbstractExperiment
  32. val executionMode: SimulatorExecutionOption
    Definition Classes
    SupportSimulatorConfiguration
  33. val executor: ExecutorService
    Attributes
    protected
  34. val expStartTime: Instant
    Definition Classes
    AbstractExperiment
  35. final def experimentDone(): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  36. def fail(t: Throwable): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  37. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  38. def finish: Future[Boolean]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  39. def finishExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  40. val fixedReplications: Option[Int]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  41. val fixedStopTime: Option[Double]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  42. lazy val fixedVariables: Map[String, Any]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  43. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  44. def getFinishedRunsForAssignment(assignmentId: Int): List[RunResults]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  45. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  46. def isDone: Boolean
    Definition Classes
    BasicExperimentConfiguration
  47. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  48. def issueRuns(assignmentId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  49. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  50. def minReplicationNumber(assignmentId: Int, replicationCondition: ReplicationCondition): Int
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  51. def model: String
    Definition Classes
    SupportModelConfiguration
  52. val modelLocation: Option[String]
    Attributes
    protected[this]
    Definition Classes
    SupportModelConfiguration
  53. def model_=(modelString: String): Unit
    Definition Classes
    SupportModelConfiguration
  54. def model_=(modelURI: URI): Unit
    Definition Classes
    SupportModelConfiguration
  55. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  56. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  57. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  58. def onFinishedExperiment(): Unit
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  59. def onFinishedRun(runId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  60. def overrideParamValues(doc: SBMLDocument, values: Map[String, Double]): Unit
    Definition Classes
    SBMLFileManipulation
  61. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  62. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  63. def readFile(path: String): SBMLDocument
    Definition Classes
    SBMLFileManipulation
  64. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  65. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  66. def replicationCondition_=(rc: ReplicationCondition): Unit
    Definition Classes
    SupportReplicationConditions
  67. def replications: Int
    Definition Classes
    SupportReplicationConditions
  68. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  69. def replications_=(reps: Int): Unit
    Definition Classes
    SupportReplicationConditions
  70. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  71. def rng: RNG
    Definition Classes
    SupportRNGSetup
  72. def rng_=(rand: RNG): Unit
    Definition Classes
    SupportRNGSetup
  73. def runAssignment(runId: Int): Int
    Attributes
    protected
    Definition Classes
    BasicExperimentConfiguration
  74. final def runDone(runId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  75. def runResultsToObservationRunResultsAspects(results: List[RunResults]): List[ObservationRunResultsAspect]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  76. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  77. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  78. lazy val sim: PSSALibSimulator
    Attributes
    protected
  79. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  80. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  81. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  82. def startSimulationRun(runId: Int, assignmentId: Int): Boolean
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  83. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  84. def stopCondition_=(sc: StoppingCondition): Unit
    Definition Classes
    SupportStoppingConditions
  85. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  86. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  87. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  88. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  89. val theBatchSize: Option[Int]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  90. def toString(): String
    Definition Classes
    AnyRef → Any
  91. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  92. def variableAssignments: List[Map[String, Any]]
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  93. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  94. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  95. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  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. def writeFile(doc: SBMLDocument, directory: File): File
    Definition Classes
    SBMLFileManipulation

Inherited from SBMLFileManipulation

Inherited from DynamicSimulationRuns

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