Serialized Form


Package org.simulator.math

Class org.simulator.math.MatrixOperations.MatrixException extends Exception implements Serializable


Package org.simulator.math.odes

Class org.simulator.math.odes.AbstractDESSolver extends Object implements Serializable

serialVersionUID: 1859418461410763939L

Serialized Fields

includeIntermediates

boolean includeIntermediates
Switches the inclusion of intermediate results on or off. This feature is important if the given DESystem is an instance of RichDESystem. Setting this switch to false speeds up the computation and lowers the memory consumption.


intervalFactor

double intervalFactor
factor describing an interval for the progress of a certain simulation intervalFactor = 100 / (endTime - startTime)


listenerList

List<E> listenerList
List of PropertyChangeListeners (for threading purpose)


nonnegative

boolean nonnegative
Flag to indicate whether or not negative values within the solution should be set to zero.


stepSize

double stepSize
The integration step size.


unstableFlag

boolean unstableFlag
Flag to indicate whether at some time point during the simulation NaN values occur within the solution.


data

MultiTable data

Class org.simulator.math.odes.AdamsBashforthSolver extends FirstOrderSolver implements Serializable

serialVersionUID: -2601862472447650296L

Class org.simulator.math.odes.AdamsMoultonSolver extends FirstOrderSolver implements Serializable

serialVersionUID: -2601862472447650296L

Class org.simulator.math.odes.DormandPrince54Solver extends FirstOrderSolver implements Serializable

serialVersionUID: -2601862472447650296L

Class org.simulator.math.odes.DormandPrince853Solver extends FirstOrderSolver implements Serializable

serialVersionUID: -2601862472447650296L

Class org.simulator.math.odes.EulerMethod extends AbstractDESSolver implements Serializable

serialVersionUID: 9094797527506196715L

Class org.simulator.math.odes.FirstOrderSolver extends AbstractDESSolver implements Serializable

serialVersionUID: 1L

Serialized Fields

integrationResult

double[] integrationResult

integrator

org.apache.commons.math.ode.AbstractIntegrator integrator

Class org.simulator.math.odes.GraggBulirschStoerSolver extends FirstOrderSolver implements Serializable

serialVersionUID: -2601862472447650296L

Class org.simulator.math.odes.HighamHall54Solver extends FirstOrderSolver implements Serializable

serialVersionUID: -2601862472447650296L

Class org.simulator.math.odes.MultiTable extends AbstractTableModel implements Serializable

serialVersionUID: 1853070398348919488L

Serialized Fields

listOfBlocks

List<E> listOfBlocks
A list of actual data


name

String name

timeName

String timeName
The name of the time column. Default is the English word "Time".


timePoints

double[] timePoints
The array to gather the time points in this data structure. This array must be sorted.

Class org.simulator.math.odes.MultiTable.Block extends AbstractTableModel implements Serializable

serialVersionUID: -6797479340761921075L

Serialized Fields

blockName

String blockName
The optional name of the block.


columnNames

String[] columnNames
Human-readable names that are used to display the name of a column.


data

double[][] data
The matrix of actual data. Must have an equal number of rows as the time points array.


identifiers

String[] identifiers
These are the column names for all columns in the data matrix. This array does not include the name for the time column.


idHash

Hashtable<K,V> idHash
This Hashtable memorizes the column indices of all identifiers.


parent

MultiTable parent
Pointer to the containing table.

Class org.simulator.math.odes.RosenbrockSolver extends AbstractDESSolver implements Serializable

serialVersionUID: -3446213991016212781L

Serialized Fields

hMax

double hMax
maximum stepsize


hMin

double hMin
minimum stepsize


absTol

double absTol
absolute tolerance


relTol

double relTol
relative tolerance


t

double t
the current value of the independent variable


h

double h
the current step size


sk

double sk
factor for calculating error value used in adjusting step size


hAdap

double hAdap
factor used for adjusting the step size, divide current step size by hAdap to get new step size


numEqn

int numEqn
The number of equations


y

double[] y
the current values of the dependent variables


oldY

double[] oldY
Saving of older values of y.


f1

double[] f1
arrays to store derivative evaluations and intermediate steps


f2

double[] f2
arrays to store derivative evaluations and intermediate steps


f3

double[] f3
arrays to store derivative evaluations and intermediate steps


f4

double[] f4
arrays to store derivative evaluations and intermediate steps


f5

double[] f5
arrays to store derivative evaluations and intermediate steps


f6

double[] f6
arrays to store derivative evaluations and intermediate steps


k1

double[] k1
arrays to store derivative evaluations and intermediate steps


k2

double[] k2
arrays to store derivative evaluations and intermediate steps


k3

double[] k3
arrays to store derivative evaluations and intermediate steps


k4

double[] k4
arrays to store derivative evaluations and intermediate steps


k5

double[] k5
arrays to store derivative evaluations and intermediate steps


yNew

double[] yNew
array that is y with approximated errors added on, used for comparing y to y+yerr


yerr

double[] yerr
array that holds approximate errors in the values in y


yTemp

double[] yTemp
helper array to hold intermediate values


ya

double[] ya
helper array to hold intermediate values


yb

double[] yb
helper array to hold intermediate values


g0

double[] g0
helper array to hold intermediate values


g1

double[] g1
helper array to hold intermediate values


g2

double[] g2
helper array to hold intermediate values


g1x

double[] g1x
helper array to hold intermediate values


g2x

double[] g2x
helper array to hold intermediate values


DFDX

double[] DFDX
helper array to hold intermediate values


indx

int[] indx
helper array to hold intermediate values


JAC

double[][] JAC
helper array to hold intermediate values


FAC

double[][] FAC
helper array to hold intermediate values


I

double[][] I
helper array to hold intermediate values


stop

boolean stop
Keep track whether the thread is killed or not


timePoints

double[] timePoints

ignoreNaN

boolean[] ignoreNaN
NaNs that are set before the calculation are ignored.

Class org.simulator.math.odes.RungeKutta_EventSolver extends AbstractDESSolver implements Serializable

serialVersionUID: -2034495479346567501L


Package org.simulator.sbml

Class org.simulator.sbml.SBMLinterpreter extends Object implements Serializable

serialVersionUID: 3453063382705340995L

Serialized Fields

algebraicRules

List<E> algebraicRules
Contains a list of all algebraic rules transformed to assignment rules for further processing


compartmentHash

Map<K,V> compartmentHash
Hashes the id of all species located in a compartment to the position of their compartment in the Y vector. When a species has no compartment, it is hashed to null.


currentReaction

org.sbml.jsbml.Reaction currentReaction
This field is necessary to also consider local parameters of the current reaction because it is not possible to access these parameters from the model. Hence we have to memorize an additional reference to the Reaction and thus to the list of these parameters.


currentTime

double currentTime
Holds the current time of the simulation


events

EventInProcess[] events
This array stores for every event an object of EventInProcess that is used to handel event processing during simulation


priorities

HashSet<E> priorities

initialValues

double[] initialValues
An array, which stores all computed initial values of the model. If this model does not contain initial assignments, the initial values will only be taken once from the information stored in the model. Otherwise they have to be computed again as soon as the parameter values of this model are changed, because the parameters may influence the return values of the initial assignments.


listOfContraintsViolations

List<E>[] listOfContraintsViolations
An array, which stores for each constraint the list of times, in which the constraint was violated during the simulation.


model

org.sbml.jsbml.Model model
The model to be simulated.


symbolHash

Map<K,V> symbolHash
Hashes the id of all Compartments, Species, global Parameters, and, if necessary, SpeciesReferences in RateRules to an value object which contains the position in the SBMLinterpreter.Y vector


symbolIdentifiers

String[] symbolIdentifiers
An array of strings that memorizes at each position the identifier of the corresponding element in the Y array.


v

double[] v
An array of the velocities of each reaction within the model system. Holding this globally saves many new memory allocations during simulation time.


stoichiometricCoefHash

Map<K,V> stoichiometricCoefHash
This Map saves the current stoichiometric coefficients for those SpeciesReference objects that are a target to an Assignment .


Y

double[] Y
An array of the current concentration of each species within the model system.


isProcessingFastReactions

boolean isProcessingFastReactions
A boolean indicating whether the solver is currently processing fast reactions or not


hasFastReactions

boolean hasFastReactions
A boolean indicating whether a model has fast reactions or not.


runningEvents

List<E> runningEvents
Stores the indices of the events triggered for the current point in time.


delayedEvents

List<E> delayedEvents
Stores the indices of the events triggered for a future point in time.


nodeInterpreter

EfficientASTNodeInterpreter nodeInterpreter

speciesMap

Map<K,V> speciesMap

inConcentration

Set<E> inConcentration

level

int level

kineticLawRoots

List<E> kineticLawRoots

nodes

List<E> nodes

nodeInterpreterWithTime

ASTNodeInterpreterWithTime nodeInterpreterWithTime

stoichiometries

List<E> stoichiometries

stoichiometriesSize

int stoichiometriesSize

reactionFast

boolean[] reactionFast

reactionReversible

boolean[] reactionReversible

assignmentRulesRoots

List<E> assignmentRulesRoots

rateRulesRoots

List<E> rateRulesRoots

astNodeTime

double astNodeTime

delayValueHolder

DelayValueHolder delayValueHolder

highOrderEvents

List<E> highOrderEvents

conversionFactors

double[] conversionFactors

modelHasEvents

boolean modelHasEvents

nRateRules

int nRateRules

nAssignmentRules

int nAssignmentRules

nConstraints

int nConstraints

initialAssignmentRoots

List<E> initialAssignmentRoots

noDerivatives

boolean noDerivatives