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

P

persistent - Variable in class org.simulator.sbml.SBMLEventInProgress

piecewise(List<ASTNodeValue>, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

plus(List<ASTNodeValue>, int, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

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) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

priority - Variable in class org.simulator.sbml.SBMLEventInProgress

priorityObject - Variable in class org.simulator.sbml.SBMLEventInProgress

processAssignmentRules(double, double[]) - Method in interface org.simulator.math.odes.EventDESystem

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, 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.

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.

processRules(EventDESystem, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver

Function for processing the rules at a certain time step.

processRules(double, double[], double[], boolean) - Method in class org.simulator.sbml.SBMLinterpreter

Processes the rules

processSimulationResults(Output, Map<Task, IRawSedmlSimulationResults>) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor

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.

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)