Packages

t

sessl.pssalib

Observation

trait Observation extends Experiment with AbstractObservation

Observe results by working with files created in the temporary directory. Invokes the analyzer binary to create CSV files from the results.

Linear Supertypes
AbstractObservation, TrajectoryOperations, Experiment, SBMLFileManipulation, DynamicSimulationRuns, AbstractExperiment, CSVInput, SupportStoppingConditions, SupportReplicationConditions, SupportRNGSetup, SupportSimulatorConfiguration, SupportModelConfiguration, BasicExperimentConfiguration, StopOnError, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. Observation
  2. AbstractObservation
  3. TrajectoryOperations
  4. Experiment
  5. SBMLFileManipulation
  6. DynamicSimulationRuns
  7. AbstractExperiment
  8. CSVInput
  9. SupportStoppingConditions
  10. SupportReplicationConditions
  11. SupportRNGSetup
  12. SupportSimulatorConfiguration
  13. SupportModelConfiguration
  14. BasicExperimentConfiguration
  15. StopOnError
  16. ExperimentConfiguration
  17. Logging
  18. StrictLogging
  19. AnyRef
  20. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Type Members

  1. implicit class ObservableName extends AnyRef
    Definition Classes
    AbstractObservation
  2. type RunOutput = Unit
    Definition Classes
    Experiment → DynamicSimulationRuns
  3. implicit class TrajectoryIterOps[T] extends AnyRef
    Definition Classes
    TrajectoryOperations
  4. 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 additionalOptions: Seq[String]
    Attributes
    protected
    Definition Classes
    Observation → Experiment
  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() @HotSpotIntrinsicCandidate() @throws( ... )
  19. def collectExperimentResultsAspects(): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  20. def collectReplicationsResults(assignID: Int): ObservationReplicationsResultsAspect
    Definition Classes
    AbstractObservation
  21. def collectReplicationsResultsAspects(assignId: Int): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  22. def collectResults(runID: Int, removeData: Boolean = false): ObservationRunResultsAspect
    Definition Classes
    Observation → AbstractObservation
  23. def collectRunResultsAspects(runId: Int): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  24. def configs(configs: Config*): Unit
    Definition Classes
    SupportModelConfiguration
  25. def configure(): Unit
    Definition Classes
    AbstractExperiment → ExperimentConfiguration
  26. def designFromCSV(file: File): Unit
    Definition Classes
    CSVInput
  27. def designFromCSV(uri: URI): Unit
    Definition Classes
    CSVInput
  28. def designFromCSV(fileName: String): Unit
    Definition Classes
    CSVInput
  29. def dirForRun(runId: Int): File
    Attributes
    protected
    Definition Classes
    Experiment
  30. def enoughReplications(replicationCondition: ReplicationCondition, finishedRuns: List[RunResults]): Boolean
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  31. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  32. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  33. def executeExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    Experiment → AbstractExperiment
  34. val executionMode: SimulatorExecutionOption
    Definition Classes
    SupportSimulatorConfiguration
  35. val executor: ExecutorService
    Attributes
    protected
    Definition Classes
    Experiment
  36. val expStartTime: LocalDateTime
    Definition Classes
    AbstractExperiment
  37. final def experimentDone(): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  38. def fail(t: Throwable): Nothing
    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() @HotSpotIntrinsicCandidate()
  44. def getOrElseUpdate[T](name: String, obs: ⇒ Observable[T]): Observable[T]
    Attributes
    protected
    Definition Classes
    AbstractObservation
  45. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  46. def isDone: Boolean
    Definition Classes
    BasicExperimentConfiguration
  47. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  48. def isObservationTimingDefined: Boolean
    Definition Classes
    AbstractObservation
  49. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  50. implicit def lookupObservable[T](name: String): Observable[T]
    Definition Classes
    AbstractObservation
  51. def minReplicationNumber(replicationCondition: ReplicationCondition, finishedRuns: List[RunResults]): Int
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  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. def overrideParamValues(doc: SBMLDocument, values: Map[String, Double]): Unit
    Definition Classes
    SBMLFileManipulation
  66. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  67. def processOutput(runId: Int, runOutput: RunOutput): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  68. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  69. def readFile(path: String): SBMLDocument
    Definition Classes
    SBMLFileManipulation
  70. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  71. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  72. def replicationCondition_=(rc: ReplicationCondition): Unit
    Definition Classes
    SupportReplicationConditions
  73. def replications: Int
    Definition Classes
    SupportReplicationConditions
  74. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  75. def replications_=(reps: Int): Unit
    Definition Classes
    SupportReplicationConditions
  76. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  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. lazy val sim: PSSALibSimulator
    Attributes
    protected
    Definition Classes
    Experiment
  84. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  85. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  86. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  87. final def startBlocking(): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  88. def startSimulationRun(runId: Int, assignment: Map[String, AnyRef]): Future[Unit]
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  89. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  90. def stopCondition_=(sc: StoppingCondition): Unit
    Definition Classes
    SupportStoppingConditions
  91. def stopOnError: Boolean
    Definition Classes
    StopOnError
  92. def stopOnError_=(stop: Boolean): Unit
    Definition Classes
    StopOnError
  93. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  94. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  95. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  96. implicit def stringToObservable(varName: String): Observable[Double]
  97. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  98. val theBatchSize: Option[Int]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  99. def toString(): String
    Definition Classes
    AnyRef → Any
  100. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  101. def variableAssignments: Seq[Map[String, AnyRef]]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  102. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  103. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  104. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  105. def withExperimentResult(f: (ObservationExperimentResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  106. def withReplicationsResult(f: (ObservationReplicationsResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  107. def withRunResult(f: (ObservationRunResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  108. def writeFile(doc: SBMLDocument, directory: File): File
    Definition Classes
    SBMLFileManipulation

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 AbstractObservation

Inherited from TrajectoryOperations

Inherited from Experiment

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 StopOnError

Inherited from ExperimentConfiguration

Inherited from Logging

Inherited from StrictLogging

Inherited from AnyRef

Inherited from Any

Ungrouped