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, ExperimentConfiguration, Logging, StrictLogging, AnyRef, Any
Ordering
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  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. ExperimentConfiguration
  16. Logging
  17. StrictLogging
  18. AnyRef
  19. Any
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Visibility
  1. Public
  2. All

Type Members

  1. implicit class ObservableName extends AnyRef
    Definition Classes
    AbstractObservation
  2. implicit class TrajectoryIterOps[T] extends AnyRef
    Definition Classes
    TrajectoryOperations
  3. 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() @throws( ... )
  19. def collectExperimentResultsAspects(): Unit
    Definition Classes
    AbstractObservation → ExperimentConfiguration
  20. def collectReplicationsResults(assignID: Int): ObservationReplicationsResultsAspect
    Definition Classes
    Observation → 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(assignmentId: Int, 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: Instant
    Definition Classes
    AbstractExperiment
  37. final def experimentDone(): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  38. def fail(t: Throwable): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  39. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  40. def finish: Future[Boolean]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  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. def issueRuns(assignmentId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  52. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  53. implicit def lookupObservable[T](name: String): Observable[T]
    Definition Classes
    AbstractObservation
  54. def minReplicationNumber(assignmentId: Int, replicationCondition: ReplicationCondition, finishedRuns: List[RunResults]): Int
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  55. def model: String
    Definition Classes
    SupportModelConfiguration
  56. val modelLocation: Option[String]
    Attributes
    protected[this]
    Definition Classes
    SupportModelConfiguration
  57. def model_=(modelString: String): Unit
    Definition Classes
    SupportModelConfiguration
  58. def model_=(modelURI: URI): Unit
    Definition Classes
    SupportModelConfiguration
  59. def namedObservables: Map[String, Observable[_]]
    Definition Classes
    AbstractObservation
  60. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  61. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  62. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  63. def observables: Set[Observable[_]]
    Definition Classes
    AbstractObservation
  64. lazy val observationTimes: Vector[Double]
    Definition Classes
    AbstractObservation
  65. def observe[T](obs: Observable[T], obss: Observable[_]*): Observable[T]
    Definition Classes
    AbstractObservation
  66. final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit
    Definition Classes
    AbstractObservation
  67. final def observeAt(observationTimes: Double*): Unit
    Definition Classes
    AbstractObservation
  68. def onFinishedExperiment(): Unit
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  69. def onFinishedRun(runId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  70. def overrideParamValues(doc: SBMLDocument, values: Map[String, Double]): Unit
    Definition Classes
    SBMLFileManipulation
  71. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  72. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  73. def readFile(path: String): SBMLDocument
    Definition Classes
    SBMLFileManipulation
  74. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  75. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  76. def replicationCondition_=(rc: ReplicationCondition): Unit
    Definition Classes
    SupportReplicationConditions
  77. def replications: Int
    Definition Classes
    SupportReplicationConditions
  78. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  79. def replications_=(reps: Int): Unit
    Definition Classes
    SupportReplicationConditions
  80. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  81. def rng: RNG
    Definition Classes
    SupportRNGSetup
  82. def rng_=(rand: RNG): Unit
    Definition Classes
    SupportRNGSetup
  83. def runAssignment(runId: Int): Int
    Attributes
    protected
    Definition Classes
    BasicExperimentConfiguration
  84. final def runDone(runId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  85. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  86. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  87. lazy val sim: PSSALibSimulator
    Attributes
    protected
    Definition Classes
    Experiment
  88. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  89. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  90. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  91. def startSimulationRun(runId: Int, assignmentId: Int): Boolean
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  92. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  93. def stopCondition_=(sc: StoppingCondition): Unit
    Definition Classes
    SupportStoppingConditions
  94. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  95. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  96. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  97. implicit def stringToObservable(varName: String): Observable[Double]
  98. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  99. val theBatchSize: Option[Int]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  100. def toString(): String
    Definition Classes
    AnyRef → Any
  101. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  102. def variableAssignments: List[Map[String, Any]]
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  103. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  104. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  105. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  106. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  107. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  108. def withExperimentResult(f: (ObservationExperimentResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  109. def withReplicationsResult(f: (ObservationReplicationsResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  110. def withRunResult(f: (ObservationRunResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  111. def writeFile(doc: SBMLDocument, directory: File): File
    Definition Classes
    SBMLFileManipulation

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 ExperimentConfiguration

Inherited from Logging

Inherited from StrictLogging

Inherited from AnyRef

Inherited from Any

Ungrouped