A B C D E F G H I J 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
ceiling(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
ceiling(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
ceiling(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
changePriority(double) - Method in class org.simulator.sbml.EventInProcess
Change the priority.
checkSolution(double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
Checks whether or not the given current state contains Double.NaN values.
checkSolution(double[], double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
Checks whether or not the given current state contains Double.NaN values.
children - Variable in class org.simulator.sbml.astnode.ASTNodeObject
The ASTNodeObjects of the child nodes of the corresponding ASTNode
clearAssignments() - Method in class org.simulator.sbml.EventInProcess
Clears all event assignments.
clearRuleObjects() - Method in class org.simulator.sbml.EventInProcess
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.RuleObject
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(ASTNodeInterpreterWithTime, ASTNode, Symbol, ValueHolder, 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.ASTNodeInterpreterWithTime
 
compile(double, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
compile(CallableSBase) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
compile(Compartment) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
compile(double, int, String) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
compile(double, String) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
compile(int, String) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
compile(String) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
compile(CallableSBase) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
compile(Compartment) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
compile(double, int, String) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
compile(double, String) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
compile(int, String) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
compile(String) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
compileBoolean(CallableSBase, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
compileBoolean(double) - Method in class org.simulator.sbml.astnode.ASTNodeObject
Computes the boolean value if the time has changed and otherwise returns the already computed value
compileBoolean(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
Compiles an ASTNode to a boolean value.
compileBoolean(double) - Method in class org.simulator.sbml.SpecialASTNodeValue
Compiles the ASTNode at the current time to a boolean value.
compileDouble(String, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
compileDouble(CallableSBase, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
compileDouble(double) - Method in class org.simulator.sbml.astnode.ASTNodeObject
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
 
compileDouble(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
Compiles an ASTNode to a double value.
compileDouble(double) - Method in class org.simulator.sbml.SpecialASTNodeValue
Compiles the ASTNode at the current time to a double value.
compileString(ASTNodeObject) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
compileString(ASTNode) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
computeBooleanValue() - Method in class org.simulator.sbml.astnode.ASTNodeObject
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.StoichiometryObject
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
 
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.ASTNodeObject
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
 
computeNextState(DESystem, double, double, double[], double[], double[], boolean, boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
 
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
 
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(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
cos(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
cos(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
cosh(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
cosh(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
cosh(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
cot(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
cot(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
cot(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
coth(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
coth(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
coth(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
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
 
csc(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
csc(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
csc(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
csch(ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
csch(ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
csch(ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
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.

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