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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
 
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
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, 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.
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.
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)

Generated at April 19 2013
Version 1.3 Revision 424
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