Uses of Interface
org.simulator.math.odes.DESystem

Packages that use DESystem

Package	Description
org.simulator.math.odes	The various solver classes that are all derived from AbstractDESSolver.
org.simulator.sbml	Classes for storing and interpreting an SBML model.

Uses of DESystem in org.simulator.math.odes

Subinterfaces of DESystem in org.simulator.math.odes

Modifier and Type	Interface	Description
interface	DelayedDESystem	This interface describes a differential equation system containing values with a delay function.
interface	EventDESystem	This class represents an event-driven differential equation system
interface	FastProcessDESystem	This interface describes differential equation systems with fast processes.
interface	ParameterizedDESystem	This class defines a differential equation system that contains parameters whose values influence its behavior.
interface	RichDESystem	A RichDESystem is a DESystem that provides additional information besides the pure rate of change during its evaluation.

Methods in org.simulator.math.odes with parameters of type DESystem

Modifier and Type	Method	Description
protected double[]	AbstractDESSolver.additionalResults(DESystem DES, double t, double[] yTemp, MultiTable data, int rowIndex)	Compute additional result values
abstract double[]	AbstractDESSolver.computeChange(DESystem DES, double[] y, double t, double stepSize, double[] change, boolean steadyState)	Computes the change for a given system at the current time with the current setting for the integration step size.
double[]	EulerMethod.computeChange(DESystem DES, double[] yPrev, double t, double stepSize, double[] change, boolean steadyState)
double[]	FirstOrderSolver.computeChange(DESystem DES, double[] y, double t, double stepSize, double[] change, boolean steadyState)
double[]	RosenbrockSolver.computeChange(DESystem DES, double[] y2, double time, double currentStepSize, double[] change, boolean steadyState)
double[]	RungeKutta_EventSolver.computeChange(DESystem DES, double[] yTemp, double t, double h, double[] change, boolean steadyState)
double	AbstractDESSolver.computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex)
double	DelayValueHolder.computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex)	Returns the value for the element with the given id at a time point in the past, where the time gives the amount of time in the past.
protected MultiTable	AbstractDESSolver.initResultMatrix(DESystem DES, double[] initialValues, double[] timePoints)
protected MultiTable	AbstractDESSolver.initResultMatrix(DESystem DES, double[] initialValues, double timeBegin, double timeEnd)
protected MultiTable	AbstractDESSolver.initResultMatrix(DESystem DES, double[] initialValues, double timeBegin, int numSteps)
boolean	AbstractDESSolver.processEventsAndRules(boolean forceProcessing, DESystem DES, double t, double previousTime, double[] yTemp)	Function for processing the events and rules at a certain time step.
MultiTable	AbstractDESSolver.solve(DESystem DES, double[] initialValues, double[] timePoints)
MultiTable	AbstractDESSolver.solve(DESystem DES, double[] initialValues, double timeBegin, double timeEnd)
MultiTable	AbstractDESSolver.solve(DESystem DES, double[] initialValues, double x, double h, int steps)
MultiTable	AbstractDESSolver.solve(DESystem DES, MultiTable.Block initConditions, double[] initialValues)
MultiTable	DESSolver.solve(DESystem DES, double[] initialValues, double[] timepoints)	Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
MultiTable	DESSolver.solve(DESystem DES, double[] initialValues, double timeBegin, double timeEnd)	Solves the given differential equation system
MultiTable	DESSolver.solve(DESystem DES, double[] initialValues, double x, double h, int steps)	Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
MultiTable	DESSolver.solve(DESystem DES, MultiTable.Block timeSeriesInitConditions, double[] initialValues)	Solves the given DESystem using new initial conditions in each time step.
MultiTable	AbstractDESSolver.steadystate(DESystem DES, double[] initialValues, double maxSteps)
double	RosenbrockSolver.step(DESystem DES)	This function tries to make a time step.

Uses of DESystem in org.simulator.sbml

Classes in org.simulator.sbml that implement DESystem

Modifier and Type	Class	Description
class	SBMLinterpreter	This differential equation system (DESystem) takes a model in SBML format and maps it to a data structure that is understood by the AbstractDESSolver.

Methods in org.simulator.sbml with parameters of type DESystem

Modifier and Type	Method	Description
double	SBMLinterpreter.computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex)