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
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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
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Visibility
  1. Public
  2. All

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 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 finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  35. def finishExperiment(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  36. val fixedReplications: Option[Int]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  37. val fixedStopTime: Option[Double]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  38. lazy val fixedVariables: Map[String, Any]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  39. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  40. def getFinishedRunsForAssignment(assignmentId: Int): List[RunResults]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  41. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  42. def isDone: Boolean
    Definition Classes
    BasicExperimentConfiguration
  43. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  44. def isObservationTimingDefined: Boolean
    Definition Classes
    AbstractObservation
  45. def issueRuns(assignmentId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  46. val logger: Logger
    Attributes
    protected
    Definition Classes
    StrictLogging
  47. def minReplicationNumber(assignmentId: Int, replicationCondition: ReplicationCondition): Int
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  48. def model: String
    Definition Classes
    SupportModelConfiguration
  49. val modelLocation: Option[String]
    Attributes
    protected[this]
    Definition Classes
    SupportModelConfiguration
  50. def model_=(modelString: String): Unit
    Definition Classes
    SupportModelConfiguration
  51. def model_=(modelURI: URI): Unit
    Definition Classes
    SupportModelConfiguration
  52. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  53. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  54. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  55. lazy val observationTimes: List[Double]
    Definition Classes
    AbstractObservation
  56. def observe(binds: DataElemBinding*): Unit
    Definition Classes
    AbstractObservation
  57. final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit
    Definition Classes
    AbstractObservation
  58. final def observeAt(observationTimes: Double*): Unit
    Definition Classes
    AbstractObservation
  59. def onFinishedExperiment(): Unit
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  60. def onFinishedRun(runId: Int): Unit
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  61. def overrideParamValues(doc: SBMLDocument, values: Map[String, Double]): Unit
    Definition Classes
    SBMLFileManipulation
  62. final def prepare(): Unit
    Attributes
    protected[sessl]
    Definition Classes
    AbstractExperiment
  63. val randomNumberGenerator: Option[RNG]
    Attributes
    protected[sessl]
    Definition Classes
    SupportRNGSetup
  64. def readFile(path: String): SBMLDocument
    Definition Classes
    SBMLFileManipulation
  65. val repCondition: Option[ReplicationCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportReplicationConditions
  66. def replicationCondition: ReplicationCondition
    Definition Classes
    SupportReplicationConditions
  67. def replicationCondition_=(rc: ReplicationCondition): Unit
    Definition Classes
    SupportReplicationConditions
  68. def replications: Int
    Definition Classes
    SupportReplicationConditions
  69. final def replicationsDone(assignId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  70. def replications_=(reps: Int): Unit
    Definition Classes
    SupportReplicationConditions
  71. def results: ExperimentResults
    Definition Classes
    BasicExperimentConfiguration
  72. lazy val reverseVariableBindings: Map[String, String]
    Definition Classes
    AbstractObservation
  73. def rng: RNG
    Definition Classes
    SupportRNGSetup
  74. def rng_=(rand: RNG): Unit
    Definition Classes
    SupportRNGSetup
  75. def runAssignment(runId: Int): Int
    Attributes
    protected
    Definition Classes
    BasicExperimentConfiguration
  76. final def runDone(runId: Int): Unit
    Definition Classes
    BasicExperimentConfiguration → ExperimentConfiguration
  77. def runResultsToObservationRunResultsAspects(results: List[RunResults]): List[ObservationRunResultsAspect]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  78. def scan(variablesToScan: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  79. def set(variablesToSet: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  80. lazy val sim: PSSALibSimulator
    Attributes
    protected
    Definition Classes
    Experiment
  81. def simulator: Simulator
    Definition Classes
    SupportSimulatorConfiguration
  82. def simulator_=(s: Simulator): ListBuffer[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  83. val simulators: AlgorithmSet[Simulator]
    Definition Classes
    SupportSimulatorConfiguration
  84. def startSimulationRun(runId: Int, assignmentId: Int): Boolean
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  85. def stopCondition: StoppingCondition
    Definition Classes
    SupportStoppingConditions
  86. def stopCondition_=(sc: StoppingCondition): Unit
    Definition Classes
    SupportStoppingConditions
  87. def stopTime: Double
    Definition Classes
    SupportStoppingConditions
  88. def stopTime_=(time: Double): Unit
    Definition Classes
    SupportStoppingConditions
  89. val stoppingCondition: Option[StoppingCondition]
    Attributes
    protected[sessl]
    Definition Classes
    SupportStoppingConditions
  90. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  91. val theBatchSize: Option[Int]
    Attributes
    protected
    Definition Classes
    DynamicSimulationRuns
  92. def toString(): String
    Definition Classes
    AnyRef → Any
  93. def uniformRandomSampling(num: Int, vars: Variable[_]*): Unit
    Definition Classes
    SupportModelConfiguration
  94. def variableAssignments: List[Map[String, Any]]
    Attributes
    protected
    Definition Classes
    Experiment → DynamicSimulationRuns
  95. def variableBindings: Map[String, Set[String]]
    Definition Classes
    AbstractObservation
  96. lazy val variablesToScan: List[Variable[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  97. lazy val variablesToSet: List[VarSingleVal[_]]
    Attributes
    protected
    Definition Classes
    SupportModelConfiguration
  98. def varsToBeObserved: Set[String]
    Definition Classes
    AbstractObservation
  99. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  100. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  101. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  102. def withExperimentResult(f: (ObservationExperimentResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  103. def withReplicationsResult(f: (ObservationReplicationsResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  104. def withRunResult(f: (ObservationRunResultsAspect) ⇒ Unit): Unit
    Definition Classes
    AbstractObservation
  105. def writeFile(doc: SBMLDocument, directory: File): File
    Definition Classes
    SBMLFileManipulation

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