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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.sbml.
EventInProcess
The event has been aborted between trigger and execution.
aborted(double)
- Method in class org.simulator.sbml.
EventInProcessWithDelay
abs(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
abs(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
abs(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
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.sbml.
EventInProcess
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(AssignmentRuleObject)
- Method in class org.simulator.sbml.
EventInProcess
Adds the math of an assignment rule as an AssignmentRuleObject.
addValues(Double[], double)
- Method in class org.simulator.sbml.
EventInProcess
The event associated with this class has been triggered.
addValues(Double[], double)
- Method in class org.simulator.sbml.
EventInProcessWithDelay
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.
ASTNodeObject
Flag that tells whether a calculation of the value has already been done (important in the case of constant values)
and(List<ASTNodeObject>, int, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
and(List<ASTNode>)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
and(List<ASTNode>)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arccos(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arccos(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arccos(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arccosh(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arccosh(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arccosh(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arccot(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arccot(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arccot(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arccoth(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arccoth(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arccoth(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arccsc(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arccsc(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arccsc(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arccsch(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arccsch(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arccsch(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arcsec(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arcsec(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arcsec(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arcsech(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arcsech(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arcsech(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arcsin(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arcsin(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arcsin(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arcsinh(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arcsinh(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arcsinh(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arctan(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arctan(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arctan(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
arctanh(ASTNodeObject, double)
- Method in class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
arctanh(ASTNode)
- Method in class org.simulator.sbml.
ASTNodeInterpreter
arctanh(ASTNode)
- Method in class org.simulator.sbml.
EfficientASTNodeInterpreter
argumentValues
- Variable in class org.simulator.sbml.astnode.
FunctionValue
The current values of the function arguments.
AssignmentRuleObject
- Class in
org.simulator.sbml.astnode
This class can compute and store the value of an AssignmentRule together with the variable of the rule.
AssignmentRuleObject(ASTNodeObject, int)
- Constructor for class org.simulator.sbml.astnode.
AssignmentRuleObject
AssignmentRuleObject(ASTNodeObject, String, Map<String, Double>)
- Constructor for class org.simulator.sbml.astnode.
AssignmentRuleObject
Constructor for rules that refer to a species reference
AssignmentRuleObject(ASTNodeObject, int, Species, int, boolean, ValueHolder)
- Constructor for class org.simulator.sbml.astnode.
AssignmentRuleObject
Constructor for rules that refer to a species
assignments
- Variable in class org.simulator.sbml.
EventInProcess
ASTNodeInterpreter
- Class in
org.simulator.sbml
This class is an implementation of an ASTNodeCompiler.
ASTNodeInterpreter(ValueHolder)
- Constructor for class org.simulator.sbml.
ASTNodeInterpreter
Constructs an interpreter with a special value holder.
ASTNodeInterpreterWithTime
- Class in
org.simulator.sbml.astnode
This class is an efficient ASTNodeInterpreter that takes the time of the calculation into account.
ASTNodeInterpreterWithTime(ValueHolder)
- Constructor for class org.simulator.sbml.astnode.
ASTNodeInterpreterWithTime
ASTNodeObject
- 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.
ASTNodeObject(ASTNodeInterpreterWithTime, ASTNode)
- Constructor for class org.simulator.sbml.astnode.
ASTNodeObject
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