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G

g(double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
 
g0 - Variable in class org.simulator.math.odes.RosenbrockSolver
helper array to hold intermediate values
g1 - Variable in class org.simulator.math.odes.RosenbrockSolver
helper array to hold intermediate values
g1x - Variable in class org.simulator.math.odes.RosenbrockSolver
helper array to hold intermediate values
g2 - Variable in class org.simulator.math.odes.RosenbrockSolver
helper array to hold intermediate values
g2x - Variable in class org.simulator.math.odes.RosenbrockSolver
helper array to hold intermediate values
gam - Static variable in class org.simulator.math.odes.RosenbrockSolver
Constants for solving
geq(ASTNodeObject, ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
geq(ASTNode, ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
geq(ASTNode, ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
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
 
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.sbml.EventInProcess
 
getASTNodeInterpreter() - Method in class org.simulator.sbml.SBMLinterpreter
 
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
 
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.ASTNodeObject
 
getConstantAvogadro(String) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getConstantAvogadro(String) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
getConstantE() - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getConstantE() - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
getConstantFalse() - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getConstantFalse() - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
getConstantPi() - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getConstantPi() - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
getConstantTrue() - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getConstantTrue() - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
getCurrentCompartmentSize(String) - Method in class org.simulator.sbml.SBMLinterpreter
 
getCurrentCompartmentSize(String) - Method in interface org.simulator.sbml.ValueHolder
 
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.ValueHolder
 
getCurrentParameterValue(String) - Method in class org.simulator.sbml.SBMLinterpreter
 
getCurrentParameterValue(String) - Method in interface org.simulator.sbml.ValueHolder
 
getCurrentSpeciesValue(String) - Method in class org.simulator.sbml.SBMLinterpreter
 
getCurrentSpeciesValue(String) - Method in interface org.simulator.sbml.ValueHolder
 
getCurrentStoichiometry(String) - Method in class org.simulator.sbml.SBMLinterpreter
 
getCurrentStoichiometry(String) - Method in interface org.simulator.sbml.ValueHolder
 
getCurrentTime() - Method in class org.simulator.sbml.SBMLinterpreter
Returns the timepoint where the simulation is currently situated
getCurrentTime() - Method in interface org.simulator.sbml.ValueHolder
 
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.ValueHolder
 
getCurrentValueOf(int) - Method in interface org.simulator.sbml.ValueHolder
 
getData() - Method in class org.simulator.math.odes.MultiTable.Block
 
getDelayObject() - Method in class org.simulator.sbml.EventInProcess
 
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
 
getEventNumber() - Method in class org.simulator.math.odes.DESAssignment
 
getFireStatus(double) - Method in class org.simulator.sbml.EventInProcess
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.math.odes.DESAssignment
 
getIndex(String) - Method in class org.simulator.sbml.astnode.FunctionValue
 
getIndex() - Method in class org.simulator.sbml.astnode.RuleObject
 
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
 
getLastTimeExecuted() - Method in class org.simulator.sbml.EventInProcess
 
getLastTimeFired() - Method in class org.simulator.sbml.EventInProcess
 
getModel() - Method in class org.simulator.sbml.SBMLinterpreter
Returns the model that is used by this object.
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.ASTNodeObject
 
getNegativeInfinity() - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getNegativeInfinity() - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
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
 
getNoDerivatives() - Method in interface org.simulator.math.odes.EventDESystem
 
getNoDerivatives() - Method in class org.simulator.sbml.SBMLinterpreter
 
getNumAdditionalValues() - Method in interface org.simulator.math.odes.RichDESystem
Gives the number of intermediate results that are computed by this class.
getNumAdditionalValues() - Method in class org.simulator.sbml.SBMLinterpreter
 
getNumBlocks() - Method in class org.simulator.math.odes.MultiTable
 
getNumEquations() - Method in class org.simulator.math.odes.RosenbrockSolver
 
getNumEventAssignments() - Method in class org.simulator.sbml.EventInProcess
 
getNumPositiveValues() - Method in interface org.simulator.math.odes.DESystem
 
getNumPositiveValues() - Method in class org.simulator.sbml.SBMLinterpreter
 
getParameterCount() - Method in class org.simulator.sbml.SBMLinterpreter
This method tells you the complete number of parameters within the model.
getPersistent() - Method in class org.simulator.sbml.EventInProcess
 
getPositionOfParameters() - Method in class org.simulator.sbml.SBMLinterpreter
 
getPositiveInfinity() - Method in class org.simulator.sbml.ASTNodeInterpreter
 
getPositiveInfinity() - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
getPriority() - Method in class org.simulator.sbml.EventInProcess
Return the priority of the associated event.
getPriorityObject() - Method in class org.simulator.sbml.EventInProcess
 
getProcessTime() - Method in class org.simulator.math.odes.DESAssignment
 
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.EventInProcess
 
getSerialversionuid() - Static method in class org.simulator.math.odes.AbstractDESSolver
 
getSerialversionuid() - Static method in class org.simulator.math.odes.MultiTable
 
getSpeciesIndex() - Method in class org.simulator.sbml.astnode.StoichiometryObject
 
getSpeciesReferenceID() - Method in class org.simulator.sbml.astnode.AssignmentRuleObject
 
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.
getTime() - Method in class org.simulator.sbml.astnode.ASTNodeObject
 
getTime() - Method in class org.simulator.sbml.EventInProcess
Return the next time of execution of the associated event.
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.EventInProcess
 
getUseValuesFromTriggerTime() - Method in class org.simulator.sbml.EventInProcess
 
getValue() - Method in class org.simulator.math.odes.DESAssignment
 
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.ASTNodeObject
 
getValue() - Method in class org.simulator.sbml.astnode.RuleObject
 
getValue() - Method in class org.simulator.sbml.SpecialASTNodeValue
 
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.sbml.EventInProcess
Return the values used in the next execution of the associated event.
GraggBulirschStoerSolver - Class in org.simulator.math.odes
 
GraggBulirschStoerSolver() - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver
 
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
 
gt(ASTNodeObject, ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
gt(ASTNode, ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
gt(ASTNode, ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 

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