SimpleTestExperiment

Instance Constructors

new SimpleTestExperiment()

Type Members

type AssignmentDescription = (Map[String, Any], Int)

Describes a variable assignment (first element) and its id (second element).
Describes a variable assignment (first element) and its id (second element).

Definition Classes
Experiment
type JobDescription = ((AssignmentDescription, BasicSBMLSimSimulator, Boolean), Int)

Describes a job with a an id as second element and a triple (variable assignment, simulator-setup,flag-replications-done) as a first element.
Describes a job with a an id as second element and a triple (variable assignment, simulator-setup,flag-replications-done) as a first element.

Definition Classes
Experiment

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def addAssignmentForRun(runId: Int, assignId: Int, assignment: VariableAssignment): Unit

Definition Classes
BasicExperimentConfiguration
def addExperimentResultsAspect(a: ExperimentResultsAspect): Unit

Definition Classes
BasicExperimentConfiguration
def addReplicationsResultsAspect(assignmentId: Int, a: ReplicationsResultsAspect): Unit

Definition Classes
BasicExperimentConfiguration
def addRunResultsAspect(runId: Int, a: RunResultsAspect): Unit

Definition Classes
BasicExperimentConfiguration
def addValueFor(runID: Int, internalName: String, value: TimeStampedData): Unit

Attributes
protected[sessl]
Definition Classes
SimpleObservation
def afterExperiment(f: (ExperimentResults) ⇒ Unit): ListBuffer[(ExperimentResults) ⇒ Unit]

Definition Classes
BasicExperimentConfiguration
def afterReplications(f: (ReplicationsResults) ⇒ Unit): ListBuffer[(ReplicationsResults) ⇒ Unit]

Definition Classes
BasicExperimentConfiguration
def afterRun(f: (RunResults) ⇒ Unit): ListBuffer[(RunResults) ⇒ Unit]

Definition Classes
BasicExperimentConfiguration
final def asInstanceOf[T0]: T0

Definition Classes
Any
def basicConfiguration(): Unit

Definition Classes
Experiment → AbstractExperiment
def checkAndGetReplicationCondition(): ReplicationCondition

Attributes
protected[sessl]
Definition Classes
SupportReplicationConditions
def checkAndGetStoppingCondition(): StoppingCondition

Attributes
protected[sessl]
Definition Classes
SupportStoppingConditions
def checkResultHandlingCorrectness(methodName: String): Unit

Definition Classes
ResultHandling
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def collectExperimentResultsAspects(): Unit

Definition Classes
AbstractObservation → ExperimentConfiguration
def collectReplicationsResults(assignId: Int): ObservationReplicationsResultsAspect

Definition Classes
SimpleObservation → AbstractObservation
def collectReplicationsResultsAspects(assignId: Int): Unit

Definition Classes
AbstractObservation → ExperimentConfiguration
def collectResults(runId: Int, removeData: Boolean): ObservationRunResultsAspect

Definition Classes
SimpleObservation → AbstractObservation
def collectRunResultsAspects(runId: Int): Unit

Definition Classes
AbstractObservation → ExperimentConfiguration
def configure(): Unit

Definition Classes
AbstractParallelExecution → ExperimentConfiguration
def configureModelLocation(): Unit

Configure model location.
Configure model location.

Definition Classes
Experiment
def configureParallelExecution(threads: Int): Unit

Definition Classes
ParallelExecution → AbstractParallelExecution
def configureSimulatorSetup(): Unit

Configure simulator setup.
Configure simulator setup.

Definition Classes
Experiment
def considerResults(runId: Int, assignmentId: Int, results: MultiTable): Unit

Method to be overridden to extract data from the results.
Method to be overridden to extract data from the results. They use a lot of memory, so the results of each run will be discarded after calling this method.

Definition Classes
Observation → SBMLSimResultHandling
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def executeExperiment(): Unit

Executes experiment
Executes experiment

Definition Classes
Experiment → AbstractExperiment
final def executeJob(jobDesc: JobDescription): Unit

Executes a job.
Executes a job.

Attributes
protected[sessl.sbmlsim]
Definition Classes
Experiment
def executeJobs(jobs: List[JobDescription]): List[Unit]

Definition Classes
ParallelExecution
var executionMode: SimulatorExecutionOption

Definition Classes
SupportSimulatorConfiguration
final def experimentDone(): Unit

Definition Classes
BasicExperimentConfiguration → ExperimentConfiguration
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
def finishExperiment(): Unit

Attributes
protected[sessl]
Definition Classes
AbstractExperiment
var fixedReplications: Option[Int]

Attributes
protected[sessl]
Definition Classes
SupportReplicationConditions
var fixedStopTime: Option[Double]

Attributes
protected[sessl]
Definition Classes
SupportStoppingConditions
lazy val fixedVariables: Map[String, AnyRef]

Attributes
protected
Definition Classes
SupportModelConfiguration
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

Definition Classes
AnyRef → Any
def isDone: Boolean

Definition Classes
BasicExperimentConfiguration
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isObservationTimingDefined: Boolean

Definition Classes
AbstractObservation
val logger: Logger

Attributes
protected
Definition Classes
StrictLogging
def model: String

Definition Classes
SupportModelConfiguration
var modelLocation: Option[String]

Attributes
protected[this]
Definition Classes
SupportModelConfiguration
def model_=(modelString: String): Unit

Definition Classes
SupportModelConfiguration
def model_=(modelURI: URI): Unit

Definition Classes
SupportModelConfiguration
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
lazy val observationTimes: List[Double]

Definition Classes
AbstractObservation
def observe(binds: DataElemBinding*): Unit

Definition Classes
AbstractObservation
final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit

Definition Classes
AbstractObservation
final def observeAt(observationTimes: Double*): Unit

Definition Classes
AbstractObservation
var parallelThreads: Int

Definition Classes
AbstractParallelExecution
final def prepare(): Unit

Attributes
protected[sessl]
Definition Classes
AbstractExperiment
var randomNumberGenerator: Option[RNG]

Attributes
protected[sessl]
Definition Classes
SupportRNGSetup
var repCondition: Option[ReplicationCondition]

Attributes
protected[sessl]
Definition Classes
SupportReplicationConditions
def replicationCondition: ReplicationCondition

Definition Classes
SupportReplicationConditions
def replicationCondition_=(rc: ReplicationCondition): Nothing

Definition Classes
Experiment → SupportReplicationConditions
def replications: Int

Definition Classes
SupportReplicationConditions
final def replicationsDone(assignId: Int): Unit

Definition Classes
BasicExperimentConfiguration → ExperimentConfiguration
def replications_=(reps: Int): Nothing

Definition Classes
Experiment → SupportReplicationConditions
def results: ExperimentResults

Definition Classes
BasicExperimentConfiguration
def resultsHandlingIsCalled(): Unit

Attributes
protected
Definition Classes
ResultHandling
lazy val reverseVariableBindings: Map[String, String]

Definition Classes
AbstractObservation
def rng: RNG

Definition Classes
SupportRNGSetup
def rng_=(rand: RNG): Unit

Definition Classes
SupportRNGSetup
final def runDone(runId: Int): Unit

Definition Classes
BasicExperimentConfiguration → ExperimentConfiguration
def scan(variablesToScan: Variable*): ListBuffer[Variable]

Definition Classes
SupportModelConfiguration
def set(variablesToSet: Variable*): Unit

Definition Classes
SupportModelConfiguration
def simulator: Simulator

Definition Classes
SupportSimulatorConfiguration
def simulator_=(s: Simulator): ListBuffer[Simulator]

Definition Classes
SupportSimulatorConfiguration
val simulators: AlgorithmSet[Simulator]

Definition Classes
SupportSimulatorConfiguration
def stopCondition: StoppingCondition

Definition Classes
SupportStoppingConditions
def stopCondition_=(sc: StoppingCondition): Nothing

Definition Classes
Experiment → SupportStoppingConditions
def stopTime: Double

Definition Classes
SupportStoppingConditions
def stopTime_=(time: Double): Unit

Definition Classes
SupportStoppingConditions
var stoppingCondition: Option[StoppingCondition]

Attributes
protected[sessl]
Definition Classes
SupportStoppingConditions
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
def variableBindings: Map[String, Set[String]]

Definition Classes
AbstractObservation
lazy val variablesToScan: List[Variable]

Attributes
protected
Definition Classes
SupportModelConfiguration
lazy val variablesToSet: List[VarSingleVal]

Attributes
protected
Definition Classes
SupportModelConfiguration
def varsToBeObserved: Set[String]

Definition Classes
AbstractObservation
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
def withExperimentResult(f: (ObservationExperimentResultsAspect) ⇒ Unit): ListBuffer[(ExperimentResults) ⇒ Unit]

Definition Classes
AbstractObservation
def withReplicationsResult(f: (ObservationReplicationsResultsAspect) ⇒ Unit): ListBuffer[(ReplicationsResults) ⇒ Unit]

Definition Classes
AbstractObservation
def withRunResult(f: (ObservationRunResultsAspect) ⇒ Unit): ListBuffer[(RunResults) ⇒ Unit]

Definition Classes
AbstractObservation

Related Doc: package sbmlsim

class SimpleTestExperiment extends Experiment with ParallelExecution with Observation

Instance Constructors

new SimpleTestExperiment()

Type Members

type AssignmentDescription = (Map[String, Any], Int)

type JobDescription = ((AssignmentDescription, BasicSBMLSimSimulator, Boolean), Int)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def addAssignmentForRun(runId: Int, assignId: Int, assignment: VariableAssignment): Unit

def addExperimentResultsAspect(a: ExperimentResultsAspect): Unit

def addReplicationsResultsAspect(assignmentId: Int, a: ReplicationsResultsAspect): Unit

def addRunResultsAspect(runId: Int, a: RunResultsAspect): Unit

def addValueFor(runID: Int, internalName: String, value: TimeStampedData): Unit

def afterExperiment(f: (ExperimentResults) ⇒ Unit): ListBuffer[(ExperimentResults) ⇒ Unit]

def afterReplications(f: (ReplicationsResults) ⇒ Unit): ListBuffer[(ReplicationsResults) ⇒ Unit]

def afterRun(f: (RunResults) ⇒ Unit): ListBuffer[(RunResults) ⇒ Unit]

final def asInstanceOf[T0]: T0

def basicConfiguration(): Unit

def checkAndGetReplicationCondition(): ReplicationCondition

def checkAndGetStoppingCondition(): StoppingCondition

def checkResultHandlingCorrectness(methodName: String): Unit

def clone(): AnyRef

def collectExperimentResultsAspects(): Unit

def collectReplicationsResults(assignId: Int): ObservationReplicationsResultsAspect

def collectReplicationsResultsAspects(assignId: Int): Unit

def collectResults(runId: Int, removeData: Boolean): ObservationRunResultsAspect

def collectRunResultsAspects(runId: Int): Unit

def configure(): Unit

def configureModelLocation(): Unit

def configureParallelExecution(threads: Int): Unit

def configureSimulatorSetup(): Unit

def considerResults(runId: Int, assignmentId: Int, results: MultiTable): Unit

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def executeExperiment(): Unit

final def executeJob(jobDesc: JobDescription): Unit

def executeJobs(jobs: List[JobDescription]): List[Unit]

var executionMode: SimulatorExecutionOption

final def experimentDone(): Unit

def finalize(): Unit

def finishExperiment(): Unit

var fixedReplications: Option[Int]

var fixedStopTime: Option[Double]

lazy val fixedVariables: Map[String, AnyRef]

final def getClass(): Class[_]

def hashCode(): Int

def isDone: Boolean

final def isInstanceOf[T0]: Boolean

def isObservationTimingDefined: Boolean

val logger: Logger

def model: String

var modelLocation: Option[String]

def model_=(modelString: String): Unit

def model_=(modelURI: URI): Unit

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

lazy val observationTimes: List[Double]

def observe(binds: DataElemBinding*): Unit

final def observeAt[T <: AnyVal](r: ValueRange[T])(implicit n: Numeric[T]): Unit

final def observeAt(observationTimes: Double*): Unit

var parallelThreads: Int

final def prepare(): Unit

var randomNumberGenerator: Option[RNG]

var repCondition: Option[ReplicationCondition]

def replicationCondition: ReplicationCondition

def replicationCondition_=(rc: ReplicationCondition): Nothing

def replications: Int

final def replicationsDone(assignId: Int): Unit

def replications_=(reps: Int): Nothing

def results: ExperimentResults

def resultsHandlingIsCalled(): Unit

lazy val reverseVariableBindings: Map[String, String]

def rng: RNG

def rng_=(rand: RNG): Unit

final def runDone(runId: Int): Unit