A B C D E F G H I K L M N O P Q R S T U V X Y Z

S

s - Variable in class org.simulator.sbml.astnode.SpeciesValue

The corresponding species

SAFETY - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants used to adapt the stepsize according to the error in the last step (see rodas.f)

saveExperimentToSEDML(double, double, double, AbstractDESSolver, Model, URI, OutputStream) - Method in class org.simulator.sedml.SEDMLWriter

Given a configured simulation, will write to SED-ML using the specified OutputStream.

sb - Variable in class org.simulator.sbml.astnode.CompartmentOrParameterValue

The compartment or parameter the corresponding ASTNode is referring to

SBMLEventInProgress - Class in org.simulator.sbml

This class represents a compilation of all information calculated during simulation concerning events in SBML.

SBMLEventInProgress(boolean) - Constructor for class org.simulator.sbml.SBMLEventInProgress

Creates a new EventInProcess with the given boolean value indicating whether or not it can fire at the initial time point.

SBMLEventInProgressWithDelay - Class in org.simulator.sbml

This class represents a compilation of all information calculated during simulation concerning events in SBML.

SBMLEventInProgressWithDelay(boolean) - Constructor for class org.simulator.sbml.SBMLEventInProgressWithDelay

Creates a new SBMLEventInProcessWithDelay with the given boolean value indicating whether or not it can fire at time point 0d.

SBMLinterpreter - Class in org.simulator.sbml

This differential equation system (DESystem) takes a model in SBML format and maps it to a data structure that is understood by the AbstractDESSolver.

SBMLinterpreter(Model) - Constructor for class org.simulator.sbml.SBMLinterpreter

This constructs a new DESystem for the given SBML Model.

SBMLinterpreter(Model, double, double, double) - Constructor for class org.simulator.sbml.SBMLinterpreter

SBMLinterpreter(Model, double, double, double, Map<String, Boolean>) - Constructor for class org.simulator.sbml.SBMLinterpreter

Creates a new SBMLinterpreter

SBMLTestSuiteRunner - Class in org.simulator

This class can test the simulation of all models from the SBML test suite.

SBMLTestSuiteRunner() - Constructor for class org.simulator.SBMLTestSuiteRunner

SBMLTestSuiteRunner.Options - Enum in org.simulator

Commannd-line options for this test program.

SBMLTestSuiteWrapper - Class in org.simulator

SBMLTestSuiteWrapper() - Constructor for class org.simulator.SBMLTestSuiteWrapper

SBMLValueHolder - Interface in org.simulator.sbml

A SBMLValueHolder is necessary to provide the current values for Compartments, Species, Parameters, and SpeciesReferences at simulation time.

scale(double, double[]) - Static method in class org.simulator.math.Mathematics

Scales a vector with the given scalar.

sec(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

sech(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

SEDMLExecutor - Class in org.simulator.sedml

Facade class to provide a jlibsedml-independent means to execute a SEDML file.

SEDMLExecutor() - Constructor for class org.simulator.sedml.SEDMLExecutor

SEDMLExecutorTest - Class in org.simulator.sedml

This test class shows how a SED-ML file can be interpreted and executed using SBML Simulator Core solvers.

SEDMLExecutorTest() - Constructor for class org.simulator.sedml.SEDMLExecutorTest

SedMLSBMLSimulatorExecutor - Class in org.simulator.sedml

This class extends an abstract class from jlibsedml, which provides various support functions such as retrieving models, applying changes to models, working out what tasks need to be executed to achieve an Output, and post-processing of results.

SedMLSBMLSimulatorExecutor(SedML, Output) - Constructor for class org.simulator.sedml.SedMLSBMLSimulatorExecutor

SedMLSBMLSimulatorExecutor(SedML, Output, Map<String, Boolean>) - Constructor for class org.simulator.sedml.SedMLSBMLSimulatorExecutor

SEDMLWriter - Class in org.simulator.sedml

Writes a simulation configuration to SED-ML for export and sharing.

SEDMLWriter() - Constructor for class org.simulator.sedml.SEDMLWriter

SEDMLWriterTest - Class in org.simulator.sedml

Tests the SEDMLWriter

SEDMLWriterTest() - Constructor for class org.simulator.sedml.SEDMLWriterTest

setAbsTol(double) - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator

setColumnNames(String[]) - Method in class org.simulator.math.odes.MultiTable.Block

setComment(String) - Method in class org.simulator.sedml.SEDMLWriter

Set an optional human-readable comment to be added to the SED-ML file.

setData(double[][]) - Method in class org.simulator.math.odes.MultiTable.Block

setDefaultValue(double) - Method in class org.simulator.math.QualityMeasure

Set the value to be returned by the distance function in cases, in which no distance can be computed.

setDefaultValue(double) - Method in class org.simulator.math.Relative_N_Metric

setDelayObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress

Sets the math of the delay to a specific ASTNodeObject.

setFastProcessComputation(boolean) - Method in interface org.simulator.math.odes.FastProcessDESystem

setFastProcessComputation(boolean) - Method in class org.simulator.sbml.SBMLinterpreter

setIdentifiers(String[]) - Method in class org.simulator.math.odes.MultiTable.Block

setIncludeIntermediates(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver

setIncludeIntermediates(boolean) - Method in interface org.simulator.math.odes.DESSolver

Allows switching whether or not intermediate results should be included into the MultiTable of the result.

setIsArchive(ArchiveComponents) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor

Enables models to be retrieved from a SED-ML archive format.

setMath(ASTNode) - Method in class org.simulator.sbml.astnode.FunctionValue

Sets the math and evaluation block of the function definition.

setMeanFunction(MeanFunction) - Method in class org.simulator.math.QualityMeasure

setName(String) - Method in class org.simulator.math.odes.MultiTable.Block

setName(String) - Method in class org.simulator.math.odes.MultiTable

Sets the name of this MultiTable.

setNonnegative(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver

setParameters(double[]) - Method in interface org.simulator.math.odes.ParameterizedDESystem

With this method it is possible to change the values of particular parameters.

setParameters(double[]) - Method in class org.simulator.sbml.SBMLinterpreter

This method allows us to set the parameters of the model to the specified values in the given array.

setPersistent(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress

Sets the persistent flag of the event.

setPriorityObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress

Sets the math of the priority to a specific ASTNodeObject.

setRelTol(double) - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator

setRoot(double) - Method in class org.simulator.math.EuclideanDistance

setRoot(double) - Method in class org.simulator.math.ManhattanDistance

setRoot(double) - Method in class org.simulator.math.N_Metric

Sets the root.

setRoot(double) - Method in class org.simulator.math.Relative_N_Metric

Sets the root

setRoot(double) - Method in class org.simulator.math.RelativeEuclideanDistance

setRoot(double) - Method in class org.simulator.math.RelativeManhattanDistance

setRowData(int, double[]) - Method in class org.simulator.math.odes.MultiTable.Block

Sets the given array as the new row in the given position of the data matrix, but requires that the number of values in the array equal the number of columns in the matrix.

setStepSize(double) - Method in class org.simulator.math.odes.AbstractDESSolver

setStepSize(double) - Method in interface org.simulator.math.odes.DESSolver

Set the integration step size.

setStepSize(double) - Method in class org.simulator.math.odes.FirstOrderSolver

setTime(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue

setTimeName(String) - Method in class org.simulator.math.odes.MultiTable

Set the name of the time column

setTimePoints(double[]) - Method in class org.simulator.math.odes.MultiTable

setTriggerObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress

Sets the math of the trigger to a specific ASTNodeObject.

setUnstableFlag(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver

setUp() - Method in class org.simulator.sedml.SEDMLExecutorTest

setUp() - Method in class org.simulator.sedml.SEDMLWriterTest

setUseValuesFromTriggerTime(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress

Sets the useValuesFromTriggerTime value of the event.

setValue(double, int) - Method in class org.simulator.math.odes.MultiTable.Block.Column

Change the entry at the given row in this MultiTable.Block.Column.

setValueAt(Object, int, int) - Method in class org.simulator.math.odes.MultiTable.Block

setValueAt(Object, int, int) - Method in class org.simulator.math.odes.MultiTable

sign(double, double) - Static method in class org.simulator.math.MatrixOperations

Returns the value of a or |a| with the same sign as b

SimulatorTest - Class in org.simulator

A simple program that performs a simulation of a model.

SimulatorTest() - Constructor for class org.simulator.SimulatorTest

sin(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

sinh(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

solve(DESystem, double[], double, double) - Method in class org.simulator.math.odes.AbstractDESSolver

solve(DESystem, double[], double, double, int) - Method in class org.simulator.math.odes.AbstractDESSolver

solve(DESystem, double[], double[]) - Method in class org.simulator.math.odes.AbstractDESSolver

solve(DESystem, MultiTable.Block, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver

solve(DESystem, double[], double, double) - Method in interface org.simulator.math.odes.DESSolver

Solves the given differential equation system

solve(DESystem, double[], double, double, int) - Method in interface org.simulator.math.odes.DESSolver

Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.

solve(DESystem, double[], double[]) - Method in interface org.simulator.math.odes.DESSolver

Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.

solve(DESystem, MultiTable.Block, double[]) - Method in interface org.simulator.math.odes.DESSolver

Solves the given DESystem using new initial conditions in each time step.

SpeciesReferenceValue - Class in org.simulator.sbml.astnode

This class computes and stores values of ASTNodes that refer to a species reference.

SpeciesReferenceValue(ASTNodeInterpreter, ASTNode, SpeciesReference, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.SpeciesReferenceValue

SpeciesValue - Class in org.simulator.sbml.astnode

This class computes and stores values of ASTNodes that refer to a species.

SpeciesValue(ASTNodeInterpreter, ASTNode, Species, SBMLValueHolder, int, int, boolean, boolean) - Constructor for class org.simulator.sbml.astnode.SpeciesValue

sqrt(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

statisticForSolvers(String, int, int) - Static method in class org.simulator.SBMLTestSuiteRunner

Computes a statistic for the SBML test suite testing all provided integrators

step(DESystem) - Method in class org.simulator.math.odes.RosenbrockSolver

This function tries to make a time step.

stoichiometricCoefHash - Variable in class org.simulator.sbml.SBMLinterpreter

This Map saves the current stoichiometric coefficients for those SpeciesReference objects that are a target to an Assignment .

StoichiometryValue - Class in org.simulator.sbml.astnode

Computes for a SpeciesReference with a stoichiometry occuring in some Reaction the stoichiometry.

StoichiometryValue(SpeciesReference, int, Map<String, Double>, double[], ASTNodeValue) - Constructor for class org.simulator.sbml.astnode.StoichiometryValue

STPMX - Static variable in class org.simulator.math.MatrixOperations

Scaled maximum step length allowed in line searches

supportsLanguage(String) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor

svMult(double, double[], double[]) - Static method in class org.simulator.math.Mathematics

Multiplies (scales) every element of the array v with s in place.

svvAddAndScale(double, double[], double[], double[]) - Static method in class org.simulator.math.Mathematics

Add vectors scaled: res[i] = s*(v[i] + w[i])

svvAddScaled(double, double[], double[], double[]) - Static method in class org.simulator.math.Mathematics

Add vectors scaled: res[i] = s*v[i] + w[i]

swap(double, double) - Static method in class org.simulator.math.Mathematics

Swaps a and b if a is greater then b.

symbolTime(String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter