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

R

r - Variable in class org.simulator.sbml.astnode.ReactionValue

The corresponding reaction

randomInt(int, int) - Static method in class org.simulator.math.RNG

Generates a random integer between first and second input value.

RateRuleValue - Class in org.simulator.sbml.astnode

This class can compute and store the value of a rate rule together with the variable of the rule.

RateRuleValue(ASTNodeValue, int) - Constructor for class org.simulator.sbml.astnode.RateRuleValue

RateRuleValue(ASTNodeValue, int, Species, int, boolean, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.RateRuleValue

Constructor for a rule with a species as variable

RateRuleValue(ASTNodeValue, int, List<Integer>, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.RateRuleValue

Constructor for a rule with a compartment as variable

ReactionValue - Class in org.simulator.sbml.astnode

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

ReactionValue(ASTNodeInterpreter, ASTNode, Reaction) - Constructor for class org.simulator.sbml.astnode.ReactionValue

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

The real value of the corresponding ASTNode

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

The trigger of the associated event has made a transition from true to false, so the event can be triggered again.

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

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

Refreshes the status of the event regarding the current time.

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

Refreshes the stoichiometry.

refresh(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress

refresh(boolean) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay

refresh(double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay

registerDelayValueHolder(DelayValueHolder) - Method in interface org.simulator.math.odes.DelayedDESystem

registerDelayValueHolder(DelayValueHolder) - Method in class org.simulator.sbml.SBMLinterpreter

Relative_N_Metric - Class in org.simulator.math

Computes the relative distance of two vectors based on the N_Metric distance.

Relative_N_Metric() - Constructor for class org.simulator.math.Relative_N_Metric

Default constructor

Relative_N_Metric(double) - Constructor for class org.simulator.math.Relative_N_Metric

Initialization with a certain n

Relative_N_Metric(N_Metric) - Constructor for class org.simulator.math.Relative_N_Metric

Initialization with a given N_Metric

RelativeEuclideanDistance - Class in org.simulator.math

Class for computation of the relative Euclidean distance of two vectors.

RelativeEuclideanDistance() - Constructor for class org.simulator.math.RelativeEuclideanDistance

Initializes a new instance

RelativeManhattanDistance - Class in org.simulator.math

Class for computation of the relative Manhattan distance of two vectors.

RelativeManhattanDistance() - Constructor for class org.simulator.math.RelativeManhattanDistance

Initializes a new instance.

RelativeSquaredError - Class in org.simulator.math

An implementation of the relative squared error with a default value to avoid division by zero.

RelativeSquaredError() - Constructor for class org.simulator.math.RelativeSquaredError

Constructs a new RelativeSquaredError.

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

the minimum acceptable value of relTol - attempts to obtain higher accuracy than this are usually very expensive

relTol - Variable in class org.simulator.math.odes.AdaptiveStepsizeIntegrator

Default relative allowable vectorial tolerance.

removeBlock(int) - Method in class org.simulator.math.odes.MultiTable

Removes the MultiTable.Block with the given index from this data structure.

removeConstraintListener(ConstraintListener) - Method in class org.simulator.sbml.SBMLinterpreter

Removes the given ConstraintListener from this interpreter.

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

Removes the ConstraintListener with the given index from this interpreter.

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

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

remove PropertyChangedListener to this Solver

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

Initialize with default integration step size and non-negative attribute true.

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

Resets the node

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

RichDESystem - Interface in org.simulator.math.odes

A RichDESystem is a DESystem that provides additional information besides the pure rate of change during its evaluation.

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

The ASTNodeObject of the right child of the corresponding ASTNode

RNG - Class in org.simulator.math

A Random Number Generator.

RNG() - Constructor for class org.simulator.math.RNG

root - Variable in class org.simulator.math.N_Metric

The n of the metric.

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

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

RootFunctionValue - Class in org.simulator.sbml.astnode

This class computes and stores values of ASTNodes that refer to a root function.

RootFunctionValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.RootFunctionValue

RosenbrockSolver - Class in org.simulator.math.odes

An implementation of Rosenbrock's method to approximate ODE solutions.

RosenbrockSolver() - Constructor for class org.simulator.math.odes.RosenbrockSolver

default constructor

RosenbrockSolver(int, double) - Constructor for class org.simulator.math.odes.RosenbrockSolver

RosenbrockSolver(RosenbrockSolver) - Constructor for class org.simulator.math.odes.RosenbrockSolver

clone constructor

ruleObjects - Variable in class org.simulator.sbml.SBMLEventInProgress

The assignment rules of the event

RuleValue - Class in org.simulator.sbml.astnode

This class can compute and store the value of a rule together with the variable of the rule.

RuleValue(ASTNodeValue, int) - Constructor for class org.simulator.sbml.astnode.RuleValue

RuleValue(ASTNodeValue, int, Species, int, boolean, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.RuleValue

Constructor for rules that refer to a species.

RungeKutta_EventSolver - Class in org.simulator.math.odes

Runge-Kutta method.

RungeKutta_EventSolver() - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver

default constructor

RungeKutta_EventSolver(double) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver

RungeKutta_EventSolver(double, boolean) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver

RungeKutta_EventSolver(RungeKutta_EventSolver) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver

clone constructor