A B C D E F G H I K L M N O P Q 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, 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

clonedSolver - Variable in class org.simulator.math.odes.AbstractDESSolver

A cloned version of this object

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

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

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

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

Computes the value of the stoichiometry at the current time if it has not been computed yet or is not constant.

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

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

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

computeDelayedValue(double, String, DESystem, double[], int) - 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, DESystem, double[], int) - Method in class org.simulator.sbml.SBMLinterpreter

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

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

Computes the double value of the node.

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

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

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

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

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

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

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

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

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

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

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

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

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

computeMean(double...) - Method in class org.simulator.math.ArithmeticMean

computeMean(double...) - Method in class org.simulator.math.DistanceSum

computeMean(double...) - Method in class org.simulator.math.MeanFunction

Computes the overall distance

computeMean(List<Double>) - Method in class org.simulator.math.MeanFunction

Computes the overall distance

computeMean(Iterable<? extends Number>) - Method in class org.simulator.math.MeanFunction

Computes the overall distance

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

ConstraintEvent - Class in org.simulator.sbml

This class represents the violation of a Constraint during simulation.

ConstraintEvent(Constraint, double) - Constructor for class org.simulator.sbml.ConstraintEvent

Creates a new ConstraintEvent for the given Constraint and the given point in time.

ConstraintListener - Interface in org.simulator.sbml

A listener interface that allows the processing of Constraints that triggered during simulation.

ConstraintTest - Class in org.simulator.sbml

This class tests the ConstraintListener interface implementation SimpleConstraintListener by evaluating a simple test model that contains a Constraint.

ConstraintTest() - Constructor for class org.simulator.sbml.ConstraintTest

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

convert(Model, String) - Method in class org.simulator.io.CSVImporter

Function for importing a file and adapting the data to the current model

convertAbsoluteFilePathToURI(String) - Static method in class org.simulator.SBMLTestSuiteRunner

Converts spaces to %20 Converts \ to /

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

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

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

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

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

CSVImporter - Class in org.simulator.io

This class is for importing CSV files.

CSVImporter() - Constructor for class org.simulator.io.CSVImporter

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.