A B C D E F G H I J K L M N O P 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)

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

The compartment or parameter the corresponding ASTNode is referring to

SBMLinterpreter - Class in org.simulator.sbml

This DifferentialEquationSystem 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.

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

Scales a vector with the given scalar.

sec(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime

sec(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter

sec(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter

sech(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime

sech(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter

sech(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter

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

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

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

setDelayObject(ASTNodeObject) - Method in class org.simulator.sbml.EventInProcess

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.

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

Sets the math and evaluation block of the function definition.

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 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.EventInProcess

Sets the persistent flag of the event.

setPriorityObject(ASTNodeObject) - Method in class org.simulator.sbml.EventInProcess

Sets the math of the priority to a specific ASTNodeObject.

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

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.ASTNodeObject

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(ASTNodeObject) - Method in class org.simulator.sbml.EventInProcess

Sets the math of the trigger to a specific ASTNodeObject.

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

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

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(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime

sin(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter

sin(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter

sinh(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime

sinh(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter

sinh(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter

sk - Variable in class org.simulator.math.odes.RosenbrockSolver

factor for calculating error value used in adjusting step size

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.

SpecialASTNodeValue - Class in org.simulator.sbml

Run-time efficient implementation of ASTNodeValue

SpecialASTNodeValue(EfficientASTNodeInterpreter) - Constructor for class org.simulator.sbml.SpecialASTNodeValue

SpeciesReferenceValue - Class in org.simulator.sbml.astnode

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

SpeciesReferenceValue(ASTNodeInterpreterWithTime, ASTNode, SpeciesReference, ValueHolder) - 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(ASTNodeInterpreterWithTime, ASTNode, Species, ValueHolder, int, int, boolean) - Constructor for class org.simulator.sbml.astnode.SpeciesValue

sqrt(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime

sqrt(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter

sqrt(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter

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 .

StoichiometryObject - Class in org.simulator.sbml.astnode

Computes for a species reference with a stoichiometry occuring in some reaction the stoichiometry and the change of the corresponding species that is caused by the reaction.

StoichiometryObject(SpeciesReference, int, int, int, Map<String, Double>, ValueHolder, double[], EfficientASTNodeInterpreter, int, Set<String>, boolean) - Constructor for class org.simulator.sbml.astnode.StoichiometryObject

stop - Variable in class org.simulator.math.odes.RosenbrockSolver

Keep track whether the thread is killed or not

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

Scaled maximum step length allowed in line searches

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.ASTNodeInterpreterWithTime

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

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