Index (Systems Biology Simulation Core Library (SBSCL) 1.5 API)

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(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.
AbstractDESSolver(AbstractDESSolver) - Constructor for class org.simulator.math.odes.AbstractDESSolver: Clone constructor.
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(double) - Constructor for class org.simulator.math.odes.AdamsBashforthSolver
AdamsBashforthSolver(double, boolean) - Constructor for class org.simulator.math.odes.AdamsBashforthSolver
AdamsBashforthSolver(AdamsBashforthSolver) - Constructor for class org.simulator.math.odes.AdamsBashforthSolver: Clone constructor
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(double) - Constructor for class org.simulator.math.odes.AdamsMoultonSolver
AdamsMoultonSolver(double, boolean) - Constructor for class org.simulator.math.odes.AdamsMoultonSolver
AdamsMoultonSolver(AdamsMoultonSolver) - Constructor for class org.simulator.math.odes.AdamsMoultonSolver: clone constructor
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(double) - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator
AdaptiveStepsizeIntegrator(double, boolean) - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator
AdaptiveStepsizeIntegrator(AdaptiveStepsizeIntegrator) - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator: clone constructor
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
AddMetaInfo - Class in org.simulator.sbml: This class contains static methods to add meta information to a model inside SBMLDocument.
AddMetaInfo() - Constructor for class org.simulator.sbml.AddMetaInfo
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, int, Species, int, boolean, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.AssignmentRuleValue: Constructor for rules that refer to a species
AssignmentRuleValue(ASTNodeValue, String, Map<String, Double>) - Constructor for class org.simulator.sbml.astnode.AssignmentRuleValue: Constructor for rules that refer to a species reference
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

B

balance(double[][]) - Static method in class org.simulator.math.MatrixOperations: Given a matrix a[1..n][1..n], this routine replaces it by a balanced matrix with identical eigenvalues.
BiomodelsExample - Class in org.simulator.examples: This class can test the simulation of all models from BioModels database.
BiomodelsExample() - Constructor for class org.simulator.examples.BiomodelsExample
booleanValue - Variable in class org.simulator.sbml.astnode.ASTNodeValue: Boolean value of the node (if the type of the value is boolean)

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
canExecuteSimulation(Simulation) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor
ceiling(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
changePriority(double) - Method in class org.simulator.sbml.SBMLEventInProgress: Change the priority.
children - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The ASTNodeObjects of the child nodes of the corresponding ASTNode
clearAssignments() - Method in class org.simulator.math.odes.EventInProgress: Clears all event assignments.
clearRuleObjects() - Method in class org.simulator.sbml.SBMLEventInProgress: 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
clonedSolver - Variable in class org.simulator.math.odes.AbstractDESSolver: A cloned version of this object
close() - Method in class org.simulator.omex.OMEXArchive: Since we directly work with zip archive, it needs to be closed after use
COBRAsolver - Class in org.simulator.fba: This solver implementation only accepts SBML models with FBC package versions 1 or 2.
COBRAsolver(SBMLDocument) - Constructor for class org.simulator.fba.COBRAsolver: Initializes the linear program and all data structures based on the definitions in the given SBMLDocument.
COBRAsolverExample - Class in org.simulator.examples: A simple test class to demonstrate the capabilities of the FBA implementation in Simulation Core Library.
COBRAsolverExample(File) - Constructor for class org.simulator.examples.COBRAsolverExample
compartmentIndex - Variable in class org.simulator.sbml.astnode.RuleValue: 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(ASTNodeInterpreter, ASTNode, Symbol, SBMLValueHolder, 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
CompExample - Class in org.simulator.examples: A simple program that performs a simulation of SBML files containing hierarchical models.
CompExample() - Constructor for class org.simulator.examples.CompExample
compile(double, int, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compile(double, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileBoolean(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Computes the boolean value if the time has changed and otherwise returns the already computed value
compileBoolean(CallableSBase, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileDouble(double) - Method in class org.simulator.sbml.astnode.StoichiometryValue: Computes the value of the stoichiometry at the current time if it has not been computed yet or is not constant.
compileDouble(double, double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Computes the double value if the time has changed and otherwise returns the already computed value
compileDouble(double, double) - Method in class org.simulator.sbml.astnode.LocalParameterValue
compileDouble(String, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileDouble(CallableSBase, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileReaction(int) - Method in class org.simulator.sbml.SBMLinterpreter
compileString(ASTNode) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileString(ASTNodeValue) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
CompSimulator - Class in org.simulator.comp: Class for simulating comp models.
CompSimulator(File) - Constructor for class org.simulator.comp.CompSimulator
computeBooleanValue() - Method in class org.simulator.sbml.astnode.ASTNodeValue: 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
computeDelayedValue(double, String, DESystem, double[], int) - Method in class org.simulator.math.odes.AbstractDESSolver
computeDelayedValue(double, String, DESystem, double[], int) - Method in interface org.simulator.math.odes.DelayValueHolder: Returns the value for the element with the given id at a time point in the past, where the time gives the amount of time in the past.
computeDelayedValue(double, String, DESystem, double[], int) - Method in class org.simulator.sbml.SBMLinterpreter
computeDerivatives(double, double[], double[]) - Method in class org.simulator.sbml.SBMLinterpreter
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Computes the double value of the node.
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.CompartmentOrParameterValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.DivideValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.FunctionValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.IntegerValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.MinusValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.NamedValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.PlusValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.PowerValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.ReactionValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.RootFunctionValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.SpeciesReferenceValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.SpeciesValue
computeDoubleValue(double) - Method in class org.simulator.sbml.astnode.TimesValue
computeMean(double...) - Method in class org.simulator.math.ArithmeticMean
computeMean(double...) - Method in class org.simulator.math.DistanceSum
computeMean(double...) - Method in class org.simulator.math.MeanFunction: Computes the overall distance
computeMean(Iterable<? extends Number>) - Method in class org.simulator.math.MeanFunction: Computes the overall distance
computeMean(List<Double>) - Method in class org.simulator.math.MeanFunction: Computes the overall distance
computeSteadyState(FastProcessDESystem, double[], double) - Method in class org.simulator.math.odes.AbstractDESSolver
ConstraintEvent - Class in org.simulator.sbml: This class represents the violation of a Constraint during simulation.
ConstraintEvent(Constraint, double) - Constructor for class org.simulator.sbml.ConstraintEvent: Creates a new ConstraintEvent for the given Constraint and the given point in time.
ConstraintExample - Class in org.simulator.examples: This class tests the ConstraintListener interface implementation SimpleConstraintListener by evaluating a simple test model that contains a Constraint.
ConstraintExample() - Constructor for class org.simulator.examples.ConstraintExample
ConstraintListener - Interface in org.simulator.sbml: A listener interface that allows the processing of Constraints that triggered during simulation.
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: This method is used to check if this differential equation system contains any events or rules that would require a special treatment by the numerical solver.
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
containsSBMLModel() - Method in class org.simulator.omex.OMEXArchive
containsSEDMLDescp() - Method in class org.simulator.omex.OMEXArchive
convert(Model, String) - Method in class org.simulator.io.CSVImporter: Function for importing a file and adapting the data to the current model
cos(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
cosh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
cot(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
coth(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
csch(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
CSVImporter - Class in org.simulator.io: This class is for importing CSV files.
CSVImporter() - Constructor for class org.simulator.io.CSVImporter
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.

D

d1 - Static variable in class org.simulator.math.odes.RosenbrockSolver
d2 - Static variable in class org.simulator.math.odes.RosenbrockSolver
d3 - Static variable in class org.simulator.math.odes.RosenbrockSolver
d4 - Static variable in class org.simulator.math.odes.RosenbrockSolver
defaultValue - Variable in class org.simulator.math.QualityMeasure: The return value of the distance function in cases where the distance cannot be computed.
delay(ASTNodeValue, ASTNodeValue, String, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
DelayedDESystem - Interface in org.simulator.math.odes: This interface describes a differential equation system containing values with a delay function.
delayObject - Variable in class org.simulator.sbml.SBMLEventInProgress: The delay math of the event
DelayValueHolder - Interface in org.simulator.math.odes: This interface describes a value holder that can compute values with delay.
denominator - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The denominator of the corresponding ASTNode
DESSolver - Interface in org.simulator.math.odes: A DESSolver provides algorithm for the numerical simulation of given DESystems.
DESystem - Interface in org.simulator.math.odes: A differential equation system describes how to compute the rate of change at a given state of the system.
distance(MultiTable.Block.Column, MultiTable.Block.Column) - Method in class org.simulator.math.QualityMeasure: Returns the distance of the two vectors x and y where the currently set root is used.
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.N_Metric
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.PearsonCorrelation
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.QualityMeasure: Returns the distance of the two vectors x and y with the given root.
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.Relative_N_Metric
distance(MultiTable, MultiTable) - Method in class org.simulator.math.QualityMeasure
DistanceSum - Class in org.simulator.math: Sets the overall distance to the sum of the column distances.
DistanceSum() - Constructor for class org.simulator.math.DistanceSum
distanceToZero(MultiTable.Block.Column, double) - Method in class org.simulator.math.N_Metric
DivideValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a division object.
DivideValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.DivideValue
DormandPrince54Solver - Class in org.simulator.math.odes: This class is a wrapper for the Dormand-Prince-54 solver in the Apache Math Library.
DormandPrince54Solver() - Constructor for class org.simulator.math.odes.DormandPrince54Solver: default constructor
DormandPrince54Solver(double) - Constructor for class org.simulator.math.odes.DormandPrince54Solver
DormandPrince54Solver(double, boolean) - Constructor for class org.simulator.math.odes.DormandPrince54Solver
DormandPrince54Solver(DormandPrince54Solver) - Constructor for class org.simulator.math.odes.DormandPrince54Solver: clone constructor
DormandPrince853Solver - Class in org.simulator.math.odes: This class is a wrapper for the Dormand-Prince-853 solver in the Apache Math Library.
DormandPrince853Solver() - Constructor for class org.simulator.math.odes.DormandPrince853Solver: default constructor
DormandPrince853Solver(double) - Constructor for class org.simulator.math.odes.DormandPrince853Solver
DormandPrince853Solver(double, boolean) - Constructor for class org.simulator.math.odes.DormandPrince853Solver
DormandPrince853Solver(DormandPrince853Solver) - Constructor for class org.simulator.math.odes.DormandPrince853Solver: clone constructor
doubleValue - Variable in class org.simulator.sbml.astnode.ASTNodeValue: Double value of the node (if the type of the value is double)

E

elmhes(double[][]) - Static method in class org.simulator.math.MatrixOperations: Reduces a[1..n][1..n] to upper Hessenberg form
EPS - Static variable in class org.simulator.math.MatrixOperations: Approximate square root of the JVM precision
eq(ASTNodeValue, ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
EuclideanDistance - Class in org.simulator.math: Class for computation of the Euclidean distance of two vectors.
EuclideanDistance() - Constructor for class org.simulator.math.EuclideanDistance: Initializes a new object
EulerMethod - Class in org.simulator.math.odes: In this class the Euler method for integration a differential equation system is implemented.
EulerMethod() - Constructor for class org.simulator.math.odes.EulerMethod: default constructor
EulerMethod(double) - Constructor for class org.simulator.math.odes.EulerMethod
EulerMethod(double, boolean) - Constructor for class org.simulator.math.odes.EulerMethod
EulerMethod(EulerMethod) - Constructor for class org.simulator.math.odes.EulerMethod: clone constructor
evaluationBlock - Variable in class org.simulator.sbml.astnode.FunctionValue: The value of the evaluation block of the function stored in an ASTNodeObject.
EventDESystem - Interface in org.simulator.math.odes: This class represents an event-driven differential equation system
EventInProgress - Class in org.simulator.math.odes: This class represents a compilation of the values and execution times during simulation concerning events.
EventInProgress(boolean) - Constructor for class org.simulator.math.odes.EventInProgress: Creates a new EventInProcess with the given boolean value indicating whether or not it can fire at the initial time point.
eventOccurred(double, double[], boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
execTimes - Variable in class org.simulator.math.odes.EventInProgress
executed(double) - Method in class org.simulator.math.odes.EventInProgress: The event associated with this class has been executed therefore reset some values.
executed(double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay
executeSedML(InputStream) - Method in class org.simulator.sedml.SEDMLWriter
executeSimulation(String, OneStep) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor
executeSimulation(String, Simulation, Map<String, double[]>, int) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor
executeSimulation(String, SteadyState) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor
executeSimulation(String, UniformTimeCourse) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: This method performs the actual simulation, using the model and simulation configuration that are passed in as arguments.It runs UniformTimeCourse simulation
ExecutionException - Exception in org.simulator.sedml: Runtime exception indicating that SED-ML execution has failed.
ExecutionException(String) - Constructor for exception org.simulator.sedml.ExecutionException
exp(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
exponent - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The exponent of the corresponding ASTNode
extractArchive(File) - Method in class org.simulator.omex.OMEXArchive: A simple method to uncompress combine archives at desired location

F

fac1 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)
fac2 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)
factorial(double) - Static method in class org.simulator.math.Mathematics: This method computes the factorial! function.
factorial(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
FastProcessDESystem - Interface in org.simulator.math.odes: This interface describes differential equation systems with fast processes.
FileModelResolver - Class in org.simulator.sedml: This resolver will resolve relative URIs with no scheme, i.e., relative URIs to files.
For example:
"Myfile.xml" a/b/c/d.xml URIs specified with the 'file' schema will not be resolved unless the path is absolute.
FileModelResolver(String) - Constructor for class org.simulator.sedml.FileModelResolver
filter(double[]) - Method in class org.simulator.math.odes.MultiTable: Creates a multi block table only containing the values for the given timepoints (if available)
fired - Variable in class org.simulator.math.odes.EventInProgress
fired(double) - Method in class org.simulator.math.odes.EventInProgress: Associated event has triggered therefore current value of fired to true
firePropertyChange(double, double) - Method in class org.simulator.math.odes.AbstractDESSolver
firePropertyChange(double, double) - Method in interface org.simulator.math.odes.DESSolver: Tell each listener that property value changed.
FirstOrderSolver - Class in org.simulator.math.odes: This class is the superclass of the wrapper classes for the solvers of the Apache Math Library.
FirstOrderSolver() - Constructor for class org.simulator.math.odes.FirstOrderSolver: default constructor
FirstOrderSolver(double) - Constructor for class org.simulator.math.odes.FirstOrderSolver
FirstOrderSolver(double, boolean) - Constructor for class org.simulator.math.odes.FirstOrderSolver
FirstOrderSolver(FirstOrderSolver) - Constructor for class org.simulator.math.odes.FirstOrderSolver: clone constructor
floor(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
frac(int, int) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
frac(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionBoolean(String, List<ASTNodeValue>) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionBoolean(ASTNodeValue, List<String>, ASTNodeValue[], double[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionDouble(String, List<ASTNodeValue>, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionDouble(ASTNodeValue, List<String>, ASTNodeValue[], int, double[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
FunctionValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to the application of a FunctionDefinition.
FunctionValue(ASTNodeInterpreter, ASTNode, List<ASTNode>) - Constructor for class org.simulator.sbml.astnode.FunctionValue

G

g(double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
gam - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
geq(ASTNodeValue, ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
getAbsTol() - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
getAdditionalValueCount() - Method in interface org.simulator.math.odes.RichDESystem: Gives the number of intermediate results that are computed by this class.
getAdditionalValueCount() - Method in class org.simulator.sbml.SBMLinterpreter
getAdditionalValueIds() - Method in interface org.simulator.math.odes.RichDESystem: This provides the column/row identifiers of all intermediate results: one identifier per result.
getAdditionalValueIds() - Method in class org.simulator.sbml.SBMLinterpreter
getAdditionalValues(double, double[]) - Method in interface org.simulator.math.odes.RichDESystem: Computes and/or delivers the intermediate results at the given time and for the given results from the previous time step.
getAdditionalValues(double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter
getArgumentValues() - Method in class org.simulator.sbml.astnode.FunctionValue: Returns the values of the arguments.
getAssignmentRules() - Method in class org.simulator.sbml.AlgebraicRuleConverter: Creates a list an assignment rule for every algebraic rule in the given model
getAssignments() - Method in class org.simulator.math.odes.EventInProgress: Returns all event assignments as a map.
getBlock(int) - Method in class org.simulator.math.odes.MultiTable
getBlockCount() - Method in class org.simulator.math.odes.MultiTable
getColumn(int) - Method in class org.simulator.math.odes.MultiTable.Block: Grants access to the specified column.
getColumn(int) - Method in class org.simulator.math.odes.MultiTable
getColumn(String) - Method in class org.simulator.math.odes.MultiTable.Block: Provides access to the MultiTable.Block.Column corresponding to the given identifier.
getColumn(String) - Method in class org.simulator.math.odes.MultiTable: Returns the column corresponding to the given identifier.
getColumnClass(int) - Method in class org.simulator.math.odes.MultiTable
getColumnCount() - Method in class org.simulator.math.odes.MultiTable.Block
getColumnCount() - Method in class org.simulator.math.odes.MultiTable
getColumnDistances(MultiTable, MultiTable) - Method in class org.simulator.math.QualityMeasure: Computes the distance of two matrices as the sum of the distances of each row.
getColumnHeaders() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getColumnIdentifier(int) - Method in class org.simulator.math.odes.MultiTable.Block
getColumnIdentifier(int) - Method in class org.simulator.math.odes.MultiTable
getColumnIndex(String) - Method in class org.simulator.math.odes.MultiTable: Returns the index of a column for a given identifier.
getColumnName() - Method in class org.simulator.math.odes.MultiTable.Block.Column: Returns the human-readable name for this column if there is any, otherwise this will return the same value as MultiTable.Block.Column.getId().
getColumnName(int) - Method in class org.simulator.math.odes.MultiTable.Block
getColumnName(int) - Method in class org.simulator.math.odes.MultiTable
getColumnNames() - Method in class org.simulator.math.odes.MultiTable.Block
getConstant() - Method in class org.simulator.sbml.astnode.ASTNodeValue
getConstant() - Method in class org.simulator.sbml.astnode.IntegerValue
getConstraintListenerCount() - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentCompartmentSize(String) - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentCompartmentSize(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the size of the compartment with the given id.
getCurrentCompartmentValueOf(String) - Method in class org.simulator.sbml.SBMLinterpreter: Checks if the given symbol id refers to a Species and returns the value of its Compartment or 1d otherwise
getCurrentCompartmentValueOf(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the size of the compartment of the species with the given id.
getCurrentParameterValue(String) - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentParameterValue(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the value of the parameter with the given id.
getCurrentSpeciesValue(String) - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentSpeciesValue(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the value of the species with the given id.
getCurrentStoichiometry(String) - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentStoichiometry(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the value of the stoichiometry of the species reference with the given id.
getCurrentTime() - Method in class org.simulator.sbml.SBMLinterpreter: Returns the timepoint where the simulation is currently situated
getCurrentTime() - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the current simulation time.
getCurrentValueOf(int) - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentValueOf(int) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the current value of the Y vector at the given position.
getCurrentValueOf(String) - Method in class org.simulator.sbml.SBMLinterpreter
getCurrentValueOf(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the current value of the SBase with the given id.
getData() - Method in class org.simulator.math.odes.MultiTable.Block
getData() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getDataByColumnId(String) - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getDataByColumnIndex(int) - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getDefaultValue() - Method in class org.simulator.math.QualityMeasure: Returns the default value that is returned by the distance function in cases in which the computation of the distance is not possible.
getDelayObject() - Method in class org.simulator.sbml.SBMLEventInProgress
getDimension() - Method in class org.simulator.sbml.SBMLinterpreter
getDoc() - Method in class org.simulator.comp.CompSimulator
getDocFlat() - Method in class org.simulator.comp.CompSimulator
getEventCount() - Method in interface org.simulator.math.odes.EventDESystem: Counts the number of events in this system.
getEventCount() - Method in class org.simulator.sbml.SBMLinterpreter
getFileEntries() - Method in class org.simulator.omex.OMEXArchive
getFireStatus(double) - Method in class org.simulator.math.odes.EventInProgress: Returns a boolean value indication if the associated event has recently been triggered / fired
getId() - Method in class org.simulator.math.odes.MultiTable.Block.Column: Delivers the MultiTable.Block.Column identifier of this particular column.
getIdentifiers() - Method in interface org.simulator.math.odes.DESystem: Delivers an array of Strings that describe the content of each dimension of the resulting array of this DESystem.
getIdentifiers() - Method in class org.simulator.math.odes.MultiTable.Block
getIdentifiers() - Method in class org.simulator.sbml.SBMLinterpreter
getIndex() - Method in class org.simulator.sbml.astnode.RuleValue: Returns the index of the variable in the Y vector of the value holder.
getIndex(String) - Method in class org.simulator.sbml.astnode.FunctionValue: Returns the index of a specific argument.
getIndexByColumnID(String) - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getInitialValues() - Method in class org.simulator.sbml.SBMLinterpreter: Returns the initial values of the model to be simulated.
getIntegrator() - Method in class org.simulator.math.odes.FirstOrderSolver
getKiSAOterm() - Method in class org.simulator.math.odes.AdamsBashforthSolver
getKiSAOterm() - Method in class org.simulator.math.odes.AdamsMoultonSolver
getKiSAOterm() - Method in interface org.simulator.math.odes.DESSolver: For details about the Kinetic Simulation Algorithm Ontology (KiSAO) see http://biomodels.net/kisao/.
getKiSAOterm() - Method in class org.simulator.math.odes.DormandPrince54Solver
getKiSAOterm() - Method in class org.simulator.math.odes.DormandPrince853Solver
getKiSAOterm() - Method in class org.simulator.math.odes.EulerMethod
getKiSAOterm() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver
getKiSAOterm() - Method in class org.simulator.math.odes.HighamHall54Solver
getKiSAOterm() - Method in class org.simulator.math.odes.RosenbrockSolver
getKiSAOterm() - Method in class org.simulator.math.odes.RungeKutta_EventSolver
getLastTimeExecuted() - Method in class org.simulator.math.odes.EventInProgress: Returns the last time the event has been executed.
getLastTimeFired() - Method in class org.simulator.math.odes.EventInProgress: Returns the last time the event has been fired.
getMappings() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getMath() - Method in class org.simulator.sbml.astnode.AssignmentRuleValue
getMeanFunction() - Method in class org.simulator.math.QualityMeasure
getModel() - Method in class org.simulator.sbml.SBMLinterpreter: Returns the model that is used by this object.
getModelXMLFor(URI) - Method in class org.simulator.sedml.FileModelResolver: Makes a best effort to read an XML based model and return it as a String based upon the URI.
getMultiTable() - Method in class org.simulator.sedml.MultTableSEDMLWrapper: Gets the underlying MultiTable wrapped by this class.
getName() - Method in class org.simulator.math.odes.AbstractDESSolver: This gives a human-readable name of this solver that can be displayed in a graphical user interface.
getName() - Method in class org.simulator.math.odes.AdamsBashforthSolver
getName() - Method in class org.simulator.math.odes.AdamsMoultonSolver
getName() - Method in class org.simulator.math.odes.DormandPrince54Solver
getName() - Method in class org.simulator.math.odes.DormandPrince853Solver
getName() - Method in class org.simulator.math.odes.EulerMethod
getName() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver
getName() - Method in class org.simulator.math.odes.HighamHall54Solver
getName() - Method in class org.simulator.math.odes.MultiTable.Block.Column
getName() - Method in class org.simulator.math.odes.MultiTable.Block
getName() - Method in class org.simulator.math.odes.MultiTable: Gives this MultiTable's name.
getName() - Method in class org.simulator.math.odes.RosenbrockSolver
getName() - Method in class org.simulator.math.odes.RungeKutta_EventSolver
getName() - Method in class org.simulator.sbml.astnode.ASTNodeValue: Returns the name of the corresponding ASTNode.
getNextEventAssignments(double, double, double[]) - Method in interface org.simulator.math.odes.EventDESystem: Returns a list with event assignments for the events triggered either by the time t or by the concentrations of the species stored in Y.
getNextEventAssignments(double, double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter
getNode() - Method in class org.simulator.sbml.astnode.ASTNodeValue
getNoDerivatives() - Method in interface org.simulator.math.odes.EventDESystem
getNoDerivatives() - Method in class org.simulator.sbml.SBMLinterpreter
getNumBlocks() - Method in class org.simulator.math.odes.MultiTable
getNumColumns() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getNumDataRows() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getNumEquations() - Method in class org.simulator.math.odes.RosenbrockSolver
getNumEventAssignments() - Method in class org.simulator.sbml.SBMLEventInProgress
getObjetiveValue() - Method in class org.simulator.fba.COBRAsolver: Returns the objective value of the current solution.
getParameterCount() - Method in interface org.simulator.math.odes.ParameterizedDESystem: Gives the number of parameters in the ParameterizedDESystem.
getParameterCount() - Method in class org.simulator.sbml.SBMLinterpreter: This method tells you the complete number of parameters within the model.
getParameterIdentifiers() - Method in interface org.simulator.math.odes.ParameterizedDESystem: It is assumed that each parameter value in the system is associated with a unique identifier, which can be used to address it in numerical calculations.
getParameterValues() - Method in interface org.simulator.math.odes.ParameterizedDESystem: This method allows you to access all current values of the parameters within the ParameterizedDESystem in form of a double array.
getPersistent() - Method in class org.simulator.sbml.SBMLEventInProgress
getPositionOfParameters() - Method in class org.simulator.sbml.SBMLinterpreter
getPositiveValueCount() - Method in interface org.simulator.math.odes.DESystem
getPositiveValueCount() - Method in class org.simulator.sbml.SBMLinterpreter
getPriority() - Method in class org.simulator.sbml.SBMLEventInProgress: Return the priority of the associated event.
getPriorityObject() - Method in class org.simulator.sbml.SBMLEventInProgress
getProcessedResult() - Method in class org.simulator.sedml.ProcessSedMLResults
getRelTol() - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
getRoot() - Method in class org.simulator.math.N_Metric: Returns the n of the metric.
getRow(int) - Method in class org.simulator.math.odes.MultiTable.Block: Delivers the given row of the data matrix as an array of doubles only, i.e., no time points.
getRowCount() - Method in class org.simulator.math.odes.MultiTable.Block.Column: Gives the number of rows in this MultiTable.Block.Column.
getRowCount() - Method in class org.simulator.math.odes.MultiTable.Block
getRowCount() - Method in class org.simulator.math.odes.MultiTable
getRuleCount() - Method in interface org.simulator.math.odes.EventDESystem: Counts the number of rules to be evaluated in each time point.
getRuleCount() - Method in class org.simulator.sbml.SBMLinterpreter
getRuleObjects() - Method in class org.simulator.sbml.SBMLEventInProgress
getSEDMLDescp() - Method in class org.simulator.omex.OMEXArchive
getSerialversionuid() - Static method in class org.simulator.math.odes.AbstractDESSolver
getSerialversionuid() - Static method in class org.simulator.math.odes.MultiTable
getSource() - Method in class org.simulator.sbml.ConstraintEvent
getSpeciesReferenceID() - Method in class org.simulator.sbml.astnode.AssignmentRuleValue: Returns the id of the species reference (if present), null otherwise.
getStepSize() - Method in class org.simulator.math.odes.AbstractDESSolver
getStepSize() - Method in interface org.simulator.math.odes.DESSolver: Obtain the currently set integration step size.
getStoichiometry() - Method in class org.simulator.sbml.astnode.StoichiometryValue
getStoichiometrySet() - Method in class org.simulator.sbml.astnode.StoichiometryValue
getTime() - Method in class org.simulator.math.odes.EventInProgress: Return the next time of execution of the associated event.
getTime() - Method in class org.simulator.sbml.astnode.ASTNodeValue
getTime() - Method in class org.simulator.sbml.ConstraintEvent
getTimeName() - Method in class org.simulator.math.odes.MultiTable: The column identifier for the first column, i.e., the time column.
getTimePoint(int) - Method in class org.simulator.math.odes.MultiTable: Returns the time value at the given index position.
getTimePoints() - Method in class org.simulator.math.odes.MultiTable.Block: Access to the time points of the overall table.
getTimePoints() - Method in class org.simulator.math.odes.MultiTable
getTriggerObject() - Method in class org.simulator.sbml.SBMLEventInProgress
getUseValuesFromTriggerTime() - Method in class org.simulator.sbml.SBMLEventInProgress: Returns true if the values of the assignments are calculated at the trigger time of the event, otherwise false.
getValue() - Method in class org.simulator.sbml.astnode.RuleValue: Returns the value of the rule.
getValue(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Returns the value as an object (double or boolean)
getValue(int) - Method in class org.simulator.math.odes.MultiTable.Block.Column: Access to the given row in this column.
getValue(String) - Method in class org.simulator.fba.COBRAsolver: Returns the solution value for the Reaction variable with the given identifier.
getValueAt(int, int) - Method in class org.simulator.math.odes.MultiTable.Block
getValueAt(int, int) - Method in class org.simulator.math.odes.MultiTable
getValues() - Method in class org.simulator.fba.COBRAsolver: Returns solution values for an array of Reaction variables.
getValues() - Method in class org.simulator.math.odes.EventInProgress: Return the values used in the next execution of the associated event.
GraggBulirschStoerSolver - Class in org.simulator.math.odes: This class is a wrapper for the Gragg-Bulirsch-Stoer solver in the Apache Math Library.
GraggBulirschStoerSolver() - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver: default constructor
GraggBulirschStoerSolver(double) - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver
GraggBulirschStoerSolver(double, boolean) - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver
GraggBulirschStoerSolver(GraggBulirschStoerSolver) - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver: clone constructor
gt(ASTNodeValue, ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

H

hasExecutionTime() - Method in class org.simulator.math.odes.EventInProgress: Returns true if the event is supposed to be executed at some time.
hasMoreAssignments(double) - Method in class org.simulator.math.odes.EventInProgress: Checks if this event has still assignments to perform for the given point in time
hasOnlySubstanceUnits - Variable in class org.simulator.sbml.astnode.RuleValue: The hasOnlySubstanceUnits attribute of the species (if applicable)
hasOnlySubstanceUnits - Variable in class org.simulator.sbml.astnode.SpeciesValue: The hasOnlySubstanceUnits attribute of the species
hasSolverEventProcessing() - Method in class org.simulator.math.odes.AbstractDESSolver
hasSolverEventProcessing() - Method in class org.simulator.math.odes.EulerMethod
hasSolverEventProcessing() - Method in class org.simulator.math.odes.FirstOrderSolver
hasSolverEventProcessing() - Method in class org.simulator.math.odes.RosenbrockSolver
hasSolverEventProcessing() - Method in class org.simulator.math.odes.RungeKutta_EventSolver
hasZeroSpatialDimensions - Variable in class org.simulator.sbml.astnode.RuleValue: This flag is true if the variable is a species and its compartment has no spatial dimensions
HighamHall54Solver - Class in org.simulator.math.odes: This class is a wrapper for the Higham-Hall-54 solver in the Apache Math Library.
HighamHall54Solver() - Constructor for class org.simulator.math.odes.HighamHall54Solver: default constructor
HighamHall54Solver(double) - Constructor for class org.simulator.math.odes.HighamHall54Solver
HighamHall54Solver(double, boolean) - Constructor for class org.simulator.math.odes.HighamHall54Solver
HighamHall54Solver(HighamHall54Solver) - Constructor for class org.simulator.math.odes.HighamHall54Solver: clone constructor
hqr(double[][], double[], double[]) - Static method in class org.simulator.math.MatrixOperations: Finds all eigenvalues of an upper Hessenberg matrix a[1..n][1..n].

I

id - Variable in class org.simulator.sbml.astnode.CompartmentOrParameterValue: The id of the compartment or parameter.
id - Variable in class org.simulator.sbml.astnode.SpeciesValue: The id of the species
inBetweenSteps(double, double, double) - Method in class org.simulator.math.odes.AbstractDESSolver: Computes the number of necessary steps between two time steps.
index - Variable in class org.simulator.sbml.astnode.RuleValue: The index of the variable in the Y vector of the value holder
indexMap - Variable in class org.simulator.sbml.astnode.FunctionValue: A map for storing the indexes of the arguments in the array argumentValues.
init() - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
init(boolean) - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
init(boolean, double, double, double) - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
init(boolean, double, double, double, Map<String, Boolean>) - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
initialValues - Variable in class org.simulator.sbml.SBMLinterpreter: An array, which stores all computed initial values of the model.
initResultMatrix(DESystem, double[], double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
initResultMatrix(DESystem, double[], double, double) - Method in class org.simulator.math.odes.AbstractDESSolver
initResultMatrix(DESystem, double[], double, int) - Method in class org.simulator.math.odes.AbstractDESSolver
IntegerValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of an integer node.
IntegerValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.IntegerValue
integrator - Variable in class org.simulator.math.odes.FirstOrderSolver: The integrator used.
interpreter - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The interpreter for calculating the value
isAmount - Variable in class org.simulator.sbml.astnode.SpeciesValue: Is the Y value of the species referring to an amount?
isCellEditable(int, int) - Method in class org.simulator.math.odes.MultiTable
isConstant - Variable in class org.simulator.sbml.astnode.ASTNodeValue: Flag that is true if the value of the ASTNode is constant.
isDouble - Variable in class org.simulator.sbml.astnode.ASTNodeValue: Flag that is true if the value has double as type and false if the value is boolean
isIncludeIntermediates() - Method in class org.simulator.math.odes.AbstractDESSolver
isIncludeIntermediates() - Method in interface org.simulator.math.odes.DESSolver: If this method returns true, intermediate results that may originate from a RichDESystem are included into the MultiTable that contains the result of a numerical integration.
isInfinite - Variable in class org.simulator.sbml.astnode.ASTNodeValue: Flag that is true if the value is positive/negative infinity
isName() - Method in class org.simulator.sbml.astnode.ASTNodeValue: Returns true if the corresponding ASTNode is of type name.
isNonnegative() - Method in class org.simulator.math.odes.AbstractDESSolver
isSetData() - Method in class org.simulator.math.odes.MultiTable.Block: Checks whether or not a data matrix has been defined in this object
isSetInitialAmount - Variable in class org.simulator.sbml.astnode.RuleValue: The isSetInitialAmount attribute of the species (if applicable)
isSetInitialConcentration - Variable in class org.simulator.sbml.astnode.RuleValue: The isSetInitialConcentration attribute of the species (if applicable)
isSetInitialConcentration - Variable in class org.simulator.sbml.astnode.SpeciesValue: Has the species an initial concentration set?
isSetTimePoints() - Method in class org.simulator.math.odes.MultiTable: Checks whether an array of time points has been set for this object.
isSpecies - Variable in class org.simulator.sbml.astnode.RuleValue: Flag that is true if the variable is referring to a species, otherwise false
isUnstable() - Method in class org.simulator.math.odes.AbstractDESSolver
isUnstable() - Method in interface org.simulator.math.odes.DESSolver: Method to check whether the solution of the numerical integration procedure contains Double.NaN values.
iterator() - Method in class org.simulator.math.odes.MultiTable.Block.Column
iterator() - Method in class org.simulator.math.odes.MultiTable

K

kHelp - Variable in class org.simulator.math.odes.RungeKutta_EventSolver: Helper variable for the k values.
kineticLawUserObject - Variable in class org.simulator.sbml.astnode.ReactionValue: The object hat refers to the kinetic law of the reaction
kVals - Variable in class org.simulator.math.odes.RungeKutta_EventSolver: Stores temporary results for the fourth-order Runge-Kutta method.

L

lambdaBoolean(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
lambdaDouble(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
lastTimeExecuted - Variable in class org.simulator.math.odes.EventInProgress
lastTimeFired - Variable in class org.simulator.math.odes.EventInProgress
lastTimeRecovered - Variable in class org.simulator.math.odes.EventInProgress
leftChild - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The ASTNodeObject of the left child of the corresponding ASTNode
leq(ASTNodeValue, ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
ln(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
LocalParameterValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a LocalParameter.
LocalParameterValue(ASTNodeInterpreter, ASTNode, LocalParameter) - Constructor for class org.simulator.sbml.astnode.LocalParameterValue
log(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
log(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
logger - Static variable in class org.simulator.sbml.astnode.ASTNodeInterpreter: A logger.
logger - Static variable in class org.simulator.sbml.astnode.ASTNodeValue: A Logger for this class.
lp - Variable in class org.simulator.sbml.astnode.LocalParameterValue: The corresponding local parameter
lt(ASTNodeValue, ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
lubksb(double[][], int[], double[]) - Static method in class org.simulator.math.MatrixOperations: Solves the set of n linear equations AX = B.
ludcmp(double[][], int[]) - Static method in class org.simulator.math.MatrixOperations: Given a matrix a[1..n][1..n], this routine replaces it by the LU decomposition of a rowwise permutation of itself.

M

main(String[]) - Static method in class org.simulator.About
main(String[]) - Static method in class org.simulator.examples.BiomodelsExample: * Input: directory with models (containing the biomodels), first model to be simulated, last model to be simulated,
main(String[]) - Static method in class org.simulator.examples.COBRAsolverExample: Simple test function that reads and solves an SBML file in a flux balance constraints framework.
main(String[]) - Static method in class org.simulator.examples.CompExample: Starts a simulation at the command line.
main(String[]) - Static method in class org.simulator.examples.ConstraintExample
main(String[]) - Static method in class org.simulator.examples.OMEXExample
main(String[]) - Static method in class org.simulator.examples.SEDMLExample
main(String[]) - Static method in class org.simulator.examples.SimulatorExample: Starts a simulation at the command line.
ManhattanDistance - Class in org.simulator.math: Class for computation of the Manhattan distance of two vectors.
ManhattanDistance() - Constructor for class org.simulator.math.ManhattanDistance: Initializes a new distance object
mantissa - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The mantissa of the corresponding ASTNode
math - Variable in class org.simulator.sbml.astnode.FunctionValue: The math of the function definition.
Mathematics - Class in org.simulator.math: This class contains a collection of mathematical functions like the faculty, logarithms and several trigonometric functions.
Mathematics() - Constructor for class org.simulator.math.Mathematics
MatrixException() - Constructor for exception org.simulator.math.MatrixOperations.MatrixException: Constructor for MatrixException
MatrixException(String) - Constructor for exception org.simulator.math.MatrixOperations.MatrixException: Constructor for MatrixException with message
MatrixOperations - Class in org.simulator.math: Class used to perform matrix operations, focusing on finding vector solutions to the vector equation F(x) = 0.
MatrixOperations() - Constructor for class org.simulator.math.MatrixOperations
MatrixOperations.MatrixException - Exception in org.simulator.math: This exception is thrown when errors in the computation of matrix-related solutions, their eigenvalues or eigenvectors.
meanFunction - Variable in class org.simulator.math.QualityMeasure
MeanFunction - Class in org.simulator.math: In this class functions for the computation of an overall distance based on the distance values determined for each column of a table are defined.
MeanFunction() - Constructor for class org.simulator.math.MeanFunction
metric - Variable in class org.simulator.math.Relative_N_Metric: The metric the relative distance is based on.
min(int, int, int) - Static method in class org.simulator.math.Mathematics: This just computes the minimum of three integer values.
minus(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
MinusValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a minus node.
MinusValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.MinusValue
model - Variable in class org.simulator.sbml.SBMLinterpreter: The model to be simulated.
MODEL_ID - Static variable in class org.simulator.sbml.AddMetaInfo: string constant for (Sub-)Model id
MultiTable - Class in org.simulator.math.odes: This data structure contains the an array of sorted time points and a matrix organized in one column per quantity for which data (measurement or simulation) are gathered.
MultiTable() - Constructor for class org.simulator.math.odes.MultiTable: Constructs an empty MultiTable object.
MultiTable(double[], double[][], String[]) - Constructor for class org.simulator.math.odes.MultiTable: Constructs a data object for the given values.
MultiTable(double[], double[][], String[], String[]) - Constructor for class org.simulator.math.odes.MultiTable
MultiTable.Block - Class in org.simulator.math.odes: A MultiTable.Block is a data structure with a two-dimensional double array of actual data together with identifiers for each column.
MultiTable.Block.Column - Class in org.simulator.math.odes: A column of the MultiTable.Block matrix.
MultTableSEDMLWrapper - Class in org.simulator.sedml: This class adapts the native results to an interface that the SED-ML processor can use to post-process results.
MultTableSEDMLWrapper(MultiTable) - Constructor for class org.simulator.sedml.MultTableSEDMLWrapper

N

N_Metric - Class in org.simulator.math: An implementation of an n-metric.
N_Metric() - Constructor for class org.simulator.math.N_Metric: Constructs a new NMetric with a default root of two.
N_Metric(double) - Constructor for class org.simulator.math.N_Metric: Constructs a new NMetric with a customized root.
name - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The name of the corresponding ASTNode
NamedValue - Class in org.simulator.sbml.astnode: This class computes and stores values of variables occurring in a function.
NamedValue(ASTNodeInterpreter, ASTNode, FunctionValue) - Constructor for class org.simulator.sbml.astnode.NamedValue
neq(ASTNodeValue, ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
node - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The ASTNode this object is referring to
nodeObject - Variable in class org.simulator.sbml.astnode.RuleValue: Object that refers to the math of the rule
nodeType - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The node type of the corresponding ASTNode
not(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
numChildren - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The number of children of the corresponding ASTNode
numerator - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The numerator of the corresponding ASTNode

O

OMEXArchive - Class in org.simulator.omex
OMEXArchive(File) - Constructor for class org.simulator.omex.OMEXArchive
OMEXExample - Class in org.simulator.examples
OMEXExample() - Constructor for class org.simulator.examples.OMEXExample
or(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
org.simulator - package org.simulator: This package simply contains a default main program to display very basic licensing terms and other information.
org.simulator.comp - package org.simulator.comp
org.simulator.examples - package org.simulator.examples
org.simulator.fba - package org.simulator.fba: This package contains an implementation of flux balance analysis for COBRA models.
org.simulator.io - package org.simulator.io: Import and export of files.
org.simulator.math - package org.simulator.math: Classes that contain several mathematical operations.
org.simulator.math.odes - package org.simulator.math.odes: The various solver classes that are all derived from AbstractDESSolver.
org.simulator.omex - package org.simulator.omex
org.simulator.plot - package org.simulator.plot
org.simulator.sbml - package org.simulator.sbml: Classes for storing and interpreting an SBML model.
org.simulator.sbml.astnode - package org.simulator.sbml.astnode: Classes for efficient numerical treatment of equations in form of abstract syntax trees.
org.simulator.sedml - package org.simulator.sedml: Classes for reading and executing SED-ML files.
ORIG_ID - Static variable in class org.simulator.sbml.AddMetaInfo: string constant for SBase id of original model

P

ParameterizedDESystem - Interface in org.simulator.math.odes: This class defines a differential equation system that contains parameters whose values influence its behavior.
PearsonCorrelation - Class in org.simulator.math: Implementation of the Pearson correlation.
PearsonCorrelation() - Constructor for class org.simulator.math.PearsonCorrelation: Default constructor.
PearsonCorrelation(double) - Constructor for class org.simulator.math.PearsonCorrelation: Constructor, which allows setting the parameter value for default value.
persistent - Variable in class org.simulator.sbml.SBMLEventInProgress: The persistent attribute of the event
piecewise(ASTNodeValue[], double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
PlotMultiTable - Class in org.simulator.plot: This class adds output data-plot support to SBSCL
PlotMultiTable(MultiTable) - Constructor for class org.simulator.plot.PlotMultiTable
PlotMultiTable(MultiTable, String) - Constructor for class org.simulator.plot.PlotMultiTable: Initializes the JFreeChart and dataSet for the chart using MultiTable
PlotProcessedSedmlResults - Class in org.simulator.plot: This class adds output data-plot support to SBSCL
PlotProcessedSedmlResults(IProcessedSedMLSimulationResults, String) - Constructor for class org.simulator.plot.PlotProcessedSedmlResults: Initializes the JFreeChart and dataSet for the chart using IProcessedSedMLSimulationResults
PlotProcessedSedmlResults(IProcessedSedMLSimulationResults, List<Curve>, String) - Constructor for class org.simulator.plot.PlotProcessedSedmlResults
plus(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
PlusValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a plus node.
PlusValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.PlusValue
position - Variable in class org.simulator.sbml.astnode.CompartmentOrParameterValue: The position of the current compartment/parameter value in the Y vector of the value holder
position - Variable in class org.simulator.sbml.astnode.SpeciesValue: The position of the species value in the Y vector of the value holder
pow(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
PowerValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a power expression.
PowerValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.PowerValue
priority - Variable in class org.simulator.sbml.SBMLEventInProgress: The priority of the event
priorityObject - Variable in class org.simulator.sbml.SBMLEventInProgress: The priority math of the event
process(Map<AbstractTask, List<IRawSedmlSimulationResults>>) - Method in class org.simulator.sedml.ProcessSedMLResults: This method modifies jlibsedml's process method to support dataGenerators for repeatedTasks.
processAssignmentRules(double, double[]) - Method in interface org.simulator.math.odes.EventDESystem: Calculates the changes or assignments that are defined by all rules in the system at the given simulation time point.
processAssignmentRules(double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter
processAssignmentVariable(double) - Method in class org.simulator.sbml.astnode.RuleValue: Calculates the math of the rule and returns the new value of the variable.
processEvents(EventDESystem, double, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Processes sudden changes in the system due to events in the EDES
processEventsAndRules(boolean, DESystem, double, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Function for processing the events and rules at a certain time step.
processInitialAssignments(double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter: Processes the initial assignments
processRule(double[], double[], double) - Method in class org.simulator.sbml.astnode.RateRuleValue: Processes the rule and saves the new value of the corresponding variable in the changeRate vector.
processRule(double[], double, boolean) - Method in class org.simulator.sbml.astnode.AssignmentRuleValue: Processes the rule and saves the new value of the corresponding variable in the Y vector if changeY is set to true.
processRules(double, double[], double[], boolean) - Method in class org.simulator.sbml.SBMLinterpreter: Processes the rules
processRules(EventDESystem, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Function for processing the rules at a certain time step.
ProcessSedMLResults - Class in org.simulator.sedml: Processes raw simulation results according to instructions specified in the DataGenerator elements specified in the output.
ProcessSedMLResults(SedML, Output) - Constructor for class org.simulator.sedml.ProcessSedMLResults
processSimulationResults(Output, Map<AbstractTask, List<IRawSedmlSimulationResults>>) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: Process raw data from simulations and return a output MultiTable which contains wanted Output
processVelocities(double[], double) - Method in class org.simulator.sbml.SBMLinterpreter: This method computes the multiplication of the stoichiometric matrix of the given model system with the reaction velocities vector passed to this method.
processViolation(ConstraintEvent) - Method in interface org.simulator.sbml.ConstraintListener: Processes the given ConstraintEvent.
processViolation(ConstraintEvent) - Method in class org.simulator.sbml.SimpleConstraintListener
PROGRESS - Static variable in class org.simulator.math.odes.AbstractDESSolver: Key used when informing listeners about progress by this solver.
putOrigId(SBMLDocument) - Static method in class org.simulator.sbml.AddMetaInfo: A static method which add id information of each element to userObjects map which is an element of AbstractTreeNode SBML class to store extra information
PWR - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)

Q

QualityMeasure - Class in org.simulator.math: This class is the basis of various implementations of distance functions.
QualityMeasure() - Constructor for class org.simulator.math.QualityMeasure: Default constructor.
QualityMeasure(double) - Constructor for class org.simulator.math.QualityMeasure: Constructor, which allows setting the parameter value for default value.
QualityMeasure(double, MeanFunction) - Constructor for class org.simulator.math.QualityMeasure: Constructor, which allows setting the parameter values for QualityMeasure.meanFunction and QualityMeasure.defaultValue.

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, List<Integer>, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.RateRuleValue: Constructor for a rule with a compartment as variable
RateRuleValue(ASTNodeValue, int, Species, int, boolean, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.RateRuleValue: Constructor for a rule with a species 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() - Method in class org.simulator.sbml.astnode.StoichiometryValue: Refreshes the stoichiometry.
refresh(boolean) - Method in class org.simulator.math.odes.EventInProgress
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.math.odes.EventInProgress: Refreshes the status of the event regarding the current time.
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(int) - Method in class org.simulator.sbml.SBMLinterpreter: Removes the ConstraintListener with the given index from this interpreter.
removeConstraintListener(ConstraintListener) - Method in class org.simulator.sbml.SBMLinterpreter: Removes the given ConstraintListener 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(double, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
root(ASTNodeValue, 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.
run() - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: This method is a wrapper to the runSimulations method from AbstractSedmlExecutor to add additional support for repeatedTasks.
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

S

s - Variable in class org.simulator.sbml.astnode.SpeciesValue: The corresponding species
SAFETY - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)
saveExperimentToSEDML(double, double, double, AbstractDESSolver, Model, URI, OutputStream) - Method in class org.simulator.sedml.SEDMLWriter: Given a configured simulation, will write to SED-ML using the specified OutputStream.
savePlot(String, String) - Method in class org.simulator.plot.PlotProcessedSedmlResults: Helper function that can save the generated plot (simulationPath sedml file) as a PNG image with fileName in the results folder
sb - Variable in class org.simulator.sbml.astnode.CompartmentOrParameterValue: The compartment or parameter the corresponding ASTNode is referring to
SBMLEventInProgress - Class in org.simulator.sbml: This class represents a compilation of all information calculated during simulation concerning events in SBML.
SBMLEventInProgress(boolean) - Constructor for class org.simulator.sbml.SBMLEventInProgress: Creates a new EventInProcess with the given boolean value indicating whether or not it can fire at the initial time point.
SBMLEventInProgressWithDelay - Class in org.simulator.sbml: This class represents a compilation of all information calculated during simulation concerning events in SBML.
SBMLEventInProgressWithDelay(boolean) - Constructor for class org.simulator.sbml.SBMLEventInProgressWithDelay: Creates a new SBMLEventInProcessWithDelay with the given boolean value indicating whether or not it can fire at time point 0d.
SBMLinterpreter - Class in org.simulator.sbml: This differential equation system (DESystem) takes a model in SBML format and maps it to a data structure that is understood by the AbstractDESSolver.
SBMLinterpreter(Model) - Constructor for class org.simulator.sbml.SBMLinterpreter: This constructs a new DESystem for the given SBML Model.
SBMLinterpreter(Model, double, double, double) - Constructor for class org.simulator.sbml.SBMLinterpreter
SBMLinterpreter(Model, double, double, double, Map<String, Boolean>) - Constructor for class org.simulator.sbml.SBMLinterpreter: Creates a new SBMLinterpreter
SBMLValueHolder - Interface in org.simulator.sbml: A SBMLValueHolder is necessary to provide the current values for Compartments, Species, Parameters, and SpeciesReferences at simulation time.
scale(double, double[]) - Static method in class org.simulator.math.Mathematics: Scales a vector with the given scalar.
sec(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
sech(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
SEDMLExample - Class in org.simulator.examples: This test class shows how a SED-ML file can be interpreted and executed using SBML Simulator Core solvers.
SEDMLExample() - Constructor for class org.simulator.examples.SEDMLExample
SedMLSBMLSimulatorExecutor - Class in org.simulator.sedml: This class extends an abstract class from jlibsedml, which provides various support functions such as retrieving models, applying changes to models, working out what tasks need to be executed to achieve an Output, and post-processing of results.
SedMLSBMLSimulatorExecutor(SedML, Output, String) - Constructor for class org.simulator.sedml.SedMLSBMLSimulatorExecutor
SedMLSBMLSimulatorExecutor(SedML, Output, Map<String, Boolean>, String) - Constructor for class org.simulator.sedml.SedMLSBMLSimulatorExecutor
SEDMLWriter - Class in org.simulator.sedml: Writes a simulation configuration to SED-ML for export and sharing.
Usage:
SEDMLWriter() - Constructor for class org.simulator.sedml.SEDMLWriter
setAbsTol(double) - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
setColumnNames(String[]) - Method in class org.simulator.math.odes.MultiTable.Block
setComment(String) - Method in class org.simulator.sedml.SEDMLWriter: Set an optional human-readable comment to be added to the SED-ML file.
setData(double[][]) - Method in class org.simulator.math.odes.MultiTable.Block
setDefaultValue(double) - Method in class org.simulator.math.QualityMeasure: Set the value to be returned by the distance function in cases, in which no distance can be computed.
setDefaultValue(double) - Method in class org.simulator.math.Relative_N_Metric
setDelayObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the math of the delay to a specific ASTNodeObject.
setDelaysIncluded(boolean) - Method in interface org.simulator.math.odes.DESystem
setDelaysIncluded(boolean) - Method in class org.simulator.sbml.SBMLinterpreter
setFastProcessComputation(boolean) - Method in interface org.simulator.math.odes.FastProcessDESystem
setFastProcessComputation(boolean) - Method in class org.simulator.sbml.SBMLinterpreter
setIdentifiers(String[]) - Method in class org.simulator.math.odes.MultiTable.Block
setIncludeIntermediates(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
setIncludeIntermediates(boolean) - Method in interface org.simulator.math.odes.DESSolver: Allows switching whether or not intermediate results should be included into the MultiTable of the result.
setIsArchive(ArchiveComponents) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: Enables models to be retrieved from a SED-ML archive format.
This method must be called before AbstractSedmlExecutor.runSimulations() is called, if a SED-ML archive is to be used as a model source.
setMath(ASTNode) - Method in class org.simulator.sbml.astnode.FunctionValue: Sets the math and evaluation block of the function definition.
setMeanFunction(MeanFunction) - Method in class org.simulator.math.QualityMeasure
setName(String) - Method in class org.simulator.math.odes.MultiTable.Block
setName(String) - Method in class org.simulator.math.odes.MultiTable: Sets the name of this MultiTable.
setNonnegative(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
setParameters(double[]) - Method in interface org.simulator.math.odes.ParameterizedDESystem: With this method it is possible to change the values of particular parameters.
setParameters(double[]) - Method in class org.simulator.sbml.SBMLinterpreter: This method allows us to set the parameters of the model to the specified values in the given array.
setPersistent(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the persistent flag of the event.
setPriorityObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the math of the priority to a specific ASTNodeObject.
setRelTol(double) - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
setRoot(double) - Method in class org.simulator.math.EuclideanDistance
setRoot(double) - Method in class org.simulator.math.ManhattanDistance
setRoot(double) - Method in class org.simulator.math.N_Metric: Sets the root.
setRoot(double) - Method in class org.simulator.math.Relative_N_Metric: Sets the root
setRoot(double) - Method in class org.simulator.math.RelativeEuclideanDistance
setRoot(double) - Method in class org.simulator.math.RelativeManhattanDistance
setRowData(int, double[]) - Method in class org.simulator.math.odes.MultiTable.Block: Sets the given array as the new row in the given position of the data matrix, but requires that the number of values in the array equal the number of columns in the matrix.
setStepSize(double) - Method in class org.simulator.math.odes.AbstractDESSolver
setStepSize(double) - Method in interface org.simulator.math.odes.DESSolver: Set the integration step size.
setStepSize(double) - Method in class org.simulator.math.odes.FirstOrderSolver
setTime(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue
setTimeName(String) - Method in class org.simulator.math.odes.MultiTable: Set the name of the time column
setTimePoints(double[]) - Method in class org.simulator.math.odes.MultiTable
setTriggerObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the math of the trigger to a specific ASTNodeObject.
setUnstableFlag(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
setUseValuesFromTriggerTime(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the useValuesFromTriggerTime value of the event.
setValue(double, int) - Method in class org.simulator.math.odes.MultiTable.Block.Column: Change the entry at the given row in this MultiTable.Block.Column.
setValueAt(Double, int, int) - Method in class org.simulator.math.odes.MultiTable
setValueAt(Object, int, int) - Method in class org.simulator.math.odes.MultiTable.Block
sign(double, double) - Static method in class org.simulator.math.MatrixOperations: Returns the value of a or |a| with the same sign as b
SimpleConstraintListener - Class in org.simulator.sbml: This class represents a simple listener implementation to process the violation of Constraints during simulation by logging the violation event in form of a warning.
SimpleConstraintListener() - Constructor for class org.simulator.sbml.SimpleConstraintListener
SimulatorExample - Class in org.simulator.examples: A simple program that performs a simulation of a model.
SimulatorExample() - Constructor for class org.simulator.examples.SimulatorExample
sin(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
sinh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
solve() - Method in class org.simulator.fba.COBRAsolver: Solves the linear program that is defined in the SBMLDocument with which this solver was initialized.
solve(double, double) - Method in class org.simulator.comp.CompSimulator
solve(double, double, DESSolver) - Method in class org.simulator.comp.CompSimulator
solve(File) - Method in class org.simulator.examples.COBRAsolverExample
solve(DESystem, double[], double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
solve(DESystem, double[], double[]) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double, double) - Method in class org.simulator.math.odes.AbstractDESSolver
solve(DESystem, double[], double, double) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system
solve(DESystem, double[], double, double, int) - Method in class org.simulator.math.odes.AbstractDESSolver
solve(DESystem, double[], double, double, int) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, MultiTable.Block, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
solve(DESystem, MultiTable.Block, double[]) - Method in interface org.simulator.math.odes.DESSolver: Solves the given DESystem using new initial conditions in each time step.
SpeciesReferenceValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a SpeciesReference.
SpeciesReferenceValue(ASTNodeInterpreter, ASTNode, SpeciesReference, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.SpeciesReferenceValue
SpeciesValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a Species.
SpeciesValue(ASTNodeInterpreter, ASTNode, Species, SBMLValueHolder, int, int, String, boolean, boolean) - Constructor for class org.simulator.sbml.astnode.SpeciesValue
sqrt(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
steadystate(DESystem, double[], double) - Method in class org.simulator.math.odes.AbstractDESSolver
step(DESystem) - Method in class org.simulator.math.odes.RosenbrockSolver: This function tries to make a time step.
stoichiometricCoefHash - Variable in class org.simulator.sbml.SBMLinterpreter: This Map saves the current stoichiometric coefficients for those SpeciesReference objects that are a target to an Assignment .
StoichiometryValue - Class in org.simulator.sbml.astnode: Computes for a SpeciesReference with a stoichiometry occuring in some Reaction the stoichiometry.
StoichiometryValue(SpeciesReference, int, Map<String, Double>, double[], ASTNodeValue) - Constructor for class org.simulator.sbml.astnode.StoichiometryValue
STPMX - Static variable in class org.simulator.math.MatrixOperations: Scaled maximum step length allowed in line searches
supportsLanguage(String) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor
svMult(double, double[], double[]) - Static method in class org.simulator.math.Mathematics: Multiplies (scales) every element of the array v with s in place.
svvAddAndScale(double, double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Add vectors scaled: res[i] = s*(v[i] + w[i])
svvAddScaled(double, double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Add vectors scaled: res[i] = s*v[i] + w[i]
swap(double, double) - Static method in class org.simulator.math.Mathematics: Swaps a and b if a is greater then b.
symbolTime() - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

T

tan(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
tanh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
TEMP_VALUE - Static variable in class org.simulator.sbml.SBMLinterpreter: Key to memorize user objects in ASTNode
testBiomodels(String, int, int) - Static method in class org.simulator.examples.BiomodelsExample: Tests the models of biomodels.org using the RosenbrockSolver as integrator
time - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The time of the last computation
times(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
TimesValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of times nodes.
TimesValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.TimesValue: Initializes a new instance with the interpreter and ASTNode given
TINY - Static variable in class org.simulator.math.MatrixOperations: Extremely small value.
TOLF - Static variable in class org.simulator.math.MatrixOperations: Convergence criterion on function values
TOLMIN - Static variable in class org.simulator.math.MatrixOperations: Criterion deciding whether spurious convergence to a minimum of min
TOLX - Static variable in class org.simulator.math.MatrixOperations: Convergence criterion on delta X
toString() - Method in class org.simulator.math.odes.MultiTable.Block.Column
toString() - Method in class org.simulator.math.odes.MultiTable.Block
toString() - Method in class org.simulator.math.odes.MultiTable
toString(ASTNode) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
triggerObject - Variable in class org.simulator.sbml.SBMLEventInProgress: The trigger of the event
tryAlternateAlgo(Simulation) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor

U

uMinus(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
unitRoundoff() - Method in class org.simulator.math.odes.RosenbrockSolver: Returns an approximation to the error involved with the current arithmetic implementation
units - Variable in class org.simulator.sbml.astnode.ASTNodeValue: The units of the corresponding ASTNode
useValuesFromTriggerTime - Variable in class org.simulator.sbml.SBMLEventInProgress: Are the values used from trigger time?

V

v - Variable in class org.simulator.sbml.SBMLinterpreter: An array of the velocities of each reaction within the model system.
value - Variable in class org.simulator.sbml.astnode.RuleValue: The calculated value of the rul
valueHolder - Variable in class org.simulator.sbml.astnode.CompartmentOrParameterValue: The value holder that stores the current simulation results.
valueHolder - Variable in class org.simulator.sbml.astnode.RuleValue: The value holder that stores the current simulation results
valueHolder - Variable in class org.simulator.sbml.astnode.SpeciesValue: The value holder that stores the current simulation results
values - Variable in class org.simulator.math.odes.EventInProgress
variables - Variable in class org.simulator.sbml.astnode.FunctionValue: The variables of the function
vvAdd(double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Add vectors in place setting res = v1 + v2.
vvAddOffs(double[], int, double[], int, double[], int, int) - Static method in class org.simulator.math.Mathematics: Add vectors in place setting with an offset within the target vector, meaning that res[resOffs+i]=v1[v1Offs+i]+v2[v2Offs+i] for i in length.
vvSub(double[], double[]) - Static method in class org.simulator.math.Mathematics: Subtract vectors returning a new vector c = a - b.
vvSub(double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Subtract vectors returning a new vector c = a - b.

X

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

Y

Y - Variable in class org.simulator.sbml.SBMLinterpreter: An array of the current concentration of each species within the model system.

Z

zeroSpatialDimensions - Variable in class org.simulator.sbml.astnode.SpeciesValue: Has the compartment of the species no spatial dimensions?

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