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

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(String) - Method in class org.simulator.math.odes.MultiTable.Block

Provides access to the MultiTable.Block.Column corresponding to the given identifier.

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

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.Block, MultiTable.Block) - 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

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(String) - Method in class org.simulator.sbml.SBMLinterpreter

getCurrentValueOf(int) - 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.

getCurrentValueOf(int) - Method in interface org.simulator.sbml.SBMLValueHolder

Returns the current value of the Y vector at the given position.

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

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

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(String) - Method in class org.simulator.sbml.astnode.FunctionValue

Returns the index of a specific argument.

getIndex() - Method in class org.simulator.sbml.astnode.RuleValue

Returns the index of the variable in the Y vector of the value holder.

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

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.

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

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

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

getSerialversionuid() - Static method in class org.simulator.math.odes.AbstractDESSolver

getSerialversionuid() - Static method in class org.simulator.math.odes.MultiTable

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

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

Access to the given row in this column.

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

Returns the value as an object (double or boolean)

getValue() - Method in class org.simulator.sbml.astnode.RuleValue

Returns the value of the rule.

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.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