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S

s - Variable in class org.simulator.sbml.astnode.SpeciesValue
 
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
 
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 of EvA2.
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
 
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
 
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
 
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
 
setPriorityObject(ASTNodeObject) - Method in class org.simulator.sbml.EventInProcess
 
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
 
setUnstableFlag(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
 
setUseValuesFromTriggerTime(boolean) - Method in class org.simulator.sbml.EventInProcess
 
setValue(Double) - Method in class org.simulator.math.odes.DESAssignment
 
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
When set to TRUE, includeTimes will make the solver to return a matrix with the first column containing the times.
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 DESystem from the begin time till the end time according to the given step size.
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 DESystem at the given time points using the currently set integration step size and the given initial values.
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
 
SpeciesReferenceValue(ASTNodeInterpreterWithTime, ASTNode, SpeciesReference, ValueHolder) - Constructor for class org.simulator.sbml.astnode.SpeciesReferenceValue
 
SpeciesValue - Class in org.simulator.sbml.astnode
 
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
 
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
 
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
 

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