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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) - 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.
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) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arccosh(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arccot(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arccoth(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arccsc(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arccsch(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arcsec(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arcsech(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arcsin(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arcsinh(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arctan(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
 
arctanh(ASTNodeValue, 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
 

Generated December 13 2012
A B C D E F G H I K L M N O P Q R S T U V X Y Z