Simulation Core Library
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, 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(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
 
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.
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
 
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(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
 

Generated at March 17 2014
Version 1.4 Revision 453
A B C D E F G H I K L M N O P Q R S T U V X Y Z