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

A

a21 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a31 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a32 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a41 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a42 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a43 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a51 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a52 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a53 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

a54 - Static variable in class org.simulator.math.odes.RosenbrockSolver

Constants for solving

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

The event has been aborted between trigger and execution.

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

About - Class in org.simulator

This class displays a short about message for this library.

About() - Constructor for class org.simulator.About

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

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

Default absolute allowable vectorial tolerance.

AbstractDESSolver - Class in org.simulator.math.odes

This Class represents an abstract solver for event-driven DES

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

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

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

Clone constructor.

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

Initialize with given integration step size.

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

Initialize with given step size and a flag whether or not negative values should be allowed.

AdamsBashforthSolver - Class in org.simulator.math.odes

This class is a wrapper for the Adams-Bashforth solver in the Apache Math Library.

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

default constructor

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

Clone constructor

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

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

AdamsMoultonSolver - Class in org.simulator.math.odes

This class is a wrapper for the Adams-Moulton solver in the Apache Math Library.

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

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

clone constructor

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

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

AdaptiveStepsizeIntegrator - Class in org.simulator.math.odes

This is an abstract class for solvers with adaptive stepsizes and given relative and absolute tolerances.

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

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

clone constructor

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

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

addAssignment(int, double) - Method in class org.simulator.math.odes.EventInProgress

Adds an event assignment.

addBlock(String[]) - Method in class org.simulator.math.odes.MultiTable

Creates a new MultiTable.Block and adds it to this object.

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

Adds the given ConstraintListener to this interpreter's list of listeners.

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

Compute additional result values

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

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

Add PropertyChangedListener to this Solver

addRuleObject(AssignmentRuleValue) - Method in class org.simulator.sbml.SBMLEventInProgress

Adds the math of an assignment rule as an AssignmentRuleObject.

addValues(Double[], double) - Method in class org.simulator.math.odes.EventInProgress

The event associated with this class has been triggered.

addValues(Double[], double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay

ALF - Static variable in class org.simulator.math.MatrixOperations

Ensures sufficient decrease in function value

AlgebraicRuleConverter - Class in org.simulator.sbml

This class converts the algebraic rules of a model to assignment rules based on the given matching.

AlgebraicRuleConverter(Map<SBase, SBase>, Model) - Constructor for class org.simulator.sbml.AlgebraicRuleConverter

Creates a new AlgebraicRuleConverter for the given matching and model

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

Flag that tells whether a calculation of the value has already been done (important in the case of constant values)

and(ASTNodeValue[], int, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

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

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

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

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

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

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

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

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

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

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

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

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

argumentValues - Variable in class org.simulator.sbml.astnode.FunctionValue

The current values of the function arguments.

ArithmeticMean - Class in org.simulator.math

Class that computes the arithmetic mean of the given column distances.

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

AssignmentRuleValue - Class in org.simulator.sbml.astnode

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

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

AssignmentRuleValue(ASTNodeValue, String, Map<String, Double>) - Constructor for class org.simulator.sbml.astnode.AssignmentRuleValue

Constructor for rules that refer to a species reference

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

Constructor for rules that refer to a species

assignments - Variable in class org.simulator.math.odes.EventInProgress

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

The event assignments

ASTNodeInterpreter - Class in org.simulator.sbml.astnode

This class is an efficient ASTNodeInterpreter that takes the time of the calculation into account.

ASTNodeInterpreter(SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.ASTNodeInterpreter

ASTNodeValue - Class in org.simulator.sbml.astnode

This class can compute and store the interpreted value (double or boolean) of an ASTNode at the current time.

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