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

C

c2 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c21 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c3 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c31 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c32 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c4 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c41 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c42 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c43 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c51 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c52 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c53 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c54 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c61 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c62 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c63 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c64 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

c65 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

canExecuteSimulation(Simulation) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor

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

changePriority(double) - Method in class org.simulator.sbml.SBMLEventInProgress

Change the priority.

children - Variable in class org.simulator.sbml.astnode.ASTNodeValue

The ASTNodeObjects of the child nodes of the corresponding ASTNode

clearAssignments() - Method in class org.simulator.math.odes.EventInProgress

Clears all event assignments.

clearRuleObjects() - Method in class org.simulator.sbml.SBMLEventInProgress

Clears the assignment rule objects.

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

clone() - Method in class org.simulator.math.odes.AdamsBashforthSolver

clone() - Method in class org.simulator.math.odes.AdamsMoultonSolver

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

clone() - Method in class org.simulator.math.odes.DormandPrince54Solver

clone() - Method in class org.simulator.math.odes.DormandPrince853Solver

clone() - Method in class org.simulator.math.odes.EulerMethod

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

clone() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver

clone() - Method in class org.simulator.math.odes.HighamHall54Solver

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

clone() - Method in class org.simulator.math.odes.RungeKutta_EventSolver

compartmentIndex - Variable in class org.simulator.sbml.astnode.RuleValue

The index of the compartment of the species (if applicable)

CompartmentOrParameterValue - Class in org.simulator.sbml.astnode

This class computes and stores values of ASTNodes that refer to a compartment or a parameter.

CompartmentOrParameterValue(ASTNodeInterpreter, ASTNode, Symbol, SBMLValueHolder, int) - Constructor for class org.simulator.sbml.astnode.CompartmentOrParameterValue

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

The position of the compartment value of the species in the Y vector of the value holder

compile(double, int, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

compile(double, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

compileBoolean(CallableSBase, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

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

Computes the boolean value if the time has changed and otherwise returns the already computed value

compileDouble(String, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

compileDouble(CallableSBase, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

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

Computes the double value if the time has changed and otherwise returns the already computed value

compileDouble(double) - Method in class org.simulator.sbml.astnode.LocalParameterValue

compileReaction(int) - Method in class org.simulator.sbml.SBMLinterpreter

Returns the current reaction velocity of a specific reaction

compileString(ASTNodeValue) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

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

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

Computes the boolean value of the node.

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

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

Computes the change for a given system at the current time with the current setting for the integration step size.

computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.EulerMethod

computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.FirstOrderSolver

computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.RosenbrockSolver

computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.RungeKutta_EventSolver

computeChange(double, double[], double[]) - Method in class org.simulator.sbml.astnode.StoichiometryValue

Computes the change resulting for the corresponding Species in this reaction at the current time and stores it at the correct position in the changeRate array.

computeDelayedValue(double, String) - Method in class org.simulator.math.odes.AbstractDESSolver

computeDelayedValue(double, String) - Method in interface org.simulator.math.odes.DelayValueHolder

Returns the value for the element with the given id at a time point in the past, where the time gives the amount of time in the past.

computeDelayedValue(double, String) - Method in class org.simulator.sbml.SBMLinterpreter

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

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

Computes the double value of the node.

computeDoubleValue() - Method in class org.simulator.sbml.astnode.CompartmentOrParameterValue

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

computeDoubleValue() - Method in class org.simulator.sbml.astnode.NamedValue

computeDoubleValue() - Method in class org.simulator.sbml.astnode.ReactionValue

computeDoubleValue() - Method in class org.simulator.sbml.astnode.RootFunctionValue

computeDoubleValue() - Method in class org.simulator.sbml.astnode.SpeciesReferenceValue

computeDoubleValue() - Method in class org.simulator.sbml.astnode.SpeciesValue

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

Checks whether or not this MultiTable.Block contains a MultiTable.Block.Column with the given identifier.

containsEventsOrRules() - Method in interface org.simulator.math.odes.DESystem

This method is used to check if this differential equation system contains any events or rules that would require a special treatment by the numerical solver.

containsEventsOrRules() - Method in class org.simulator.sbml.SBMLinterpreter

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

containsFastProcesses() - Method in class org.simulator.sbml.SBMLinterpreter

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

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

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

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

createIntegrator() - Method in class org.simulator.math.odes.AdamsBashforthSolver

createIntegrator() - Method in class org.simulator.math.odes.AdamsMoultonSolver

createIntegrator() - Method in class org.simulator.math.odes.DormandPrince54Solver

createIntegrator() - Method in class org.simulator.math.odes.DormandPrince853Solver

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

initialization function of the integrator

createIntegrator() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver

createIntegrator() - Method in class org.simulator.math.odes.HighamHall54Solver

createMultiTableFromProcessedResults(Output, IProcessedSedMLSimulationResults) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor

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

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

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

This field is necessary to also consider local parameters of the current reaction because it is not possible to access these parameters from the model.