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

Type Members

  1. implicit class ObservableName extends AnyRef
    Definition Classes
    AbstractObservation

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
    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 dirForRun(runId: Int): File
    Attributes
    protected
    Definition Classes
    Experiment
  27. def enoughReplications(assignmentId: Int, replicationCondition: ReplicationCondition): Boolean
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  28. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  29. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  30. def executeExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    Experiment → AbstractExperiment
  31. val executionMode: SimulatorExecutionOption
    Definition Classes
    SupportSimulatorConfiguration
  32. val executor: ExecutorService
    Attributes
    protected
    Definition Classes
    Experiment
  33. final def experimentDone(): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  34. def fail(t: Throwable): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  35. def finish: Future[Boolean]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  36. def finishExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  37. val fixedReplications: Option[Int]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  38. val fixedStopTime: Option[Double]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  39. lazy val fixedVariables: Map[String, Any]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  40. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  41. def getFinishedRunsForAssignment(assignmentId: Int): List[RunResults]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  42. def getOrElseUpdate[T](name: String, obs: ⇒ Observable[T]): Observable[T]
    Attributes
    protected
    Definition Classes
    AbstractObservation
  43. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  44. def isDone: Boolean
    Definition Classes
    BasicExperimentConfiguration
  45. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  46. def isObservationTimingDefined: Boolean
    Definition Classes
    AbstractObservation
  47. def issueRuns(assignmentId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  48. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  49. implicit def lookupObservable[T](name: String): Observable[T]
    Definition Classes
    AbstractObservation
  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. def namedObservables: Map[String, Observable[_]]
    Definition Classes
    AbstractObservation
  56. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  57. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  58. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  59. def observables: Set[Observable[_]]
    Definition Classes
    AbstractObservation
  60. lazy val observationTimes: List[Double]
    Definition Classes
    AbstractObservation
  61. def observe[T](obs: Observable[T], obss: Observable[_]*): Observable[T]
    Definition Classes
    AbstractObservation
  62. final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit
    Definition Classes
    AbstractObservation
  63. final def observeAt(observationTimes: Double*): Unit
    Definition Classes
    AbstractObservation
  64. def onFinishedExperiment(): Unit
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  65. def onFinishedRun(runId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  66. def overrideParamValues(doc: SBMLDocument, values: Map[String, Double]): Unit
    Definition Classes
    SBMLFileManipulation
  67. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  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 runResultsToObservationRunResultsAspects(results: List[RunResults]): List[ObservationRunResultsAspect]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  82. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  83. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  84. lazy val sim: PSSALibSimulator
    Attributes
    protected
    Definition Classes
    Experiment
  85. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  86. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  87. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  88. def startSimulationRun(runId: Int, assignmentId: Int): Boolean
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  89. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  90. def stopCondition_=(sc: StoppingCondition): Unit
    Definition Classes
    SupportStoppingConditions
  91. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  92. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  93. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  94. implicit def stringToObservable(varName: String): Observable[Double]
  95. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  96. val theBatchSize: Option[Int]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  97. def toString(): String
    Definition Classes
    AnyRef → Any
  98. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  99. def variableAssignments: List[Map[String, Any]]
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  100. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  101. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  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 Experiment

Inherited from SBMLFileManipulation

Inherited from DynamicSimulationRuns

Inherited from AbstractExperiment

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