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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)
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Generated at April 19 2013
Version 1.3 Revision 424
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