Serialized Form

Package org.simulator.math

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

Package org.simulator.math.odes

Class org.simulator.math.odes.AbstractDESSolver extends java.lang.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

java.util.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.AdaptiveStepsizeIntegrator extends AbstractDESSolver implements Serializable

serialVersionUID: -5411228466445964211L

Serialized Fields

absTol

double absTol

Default absolute allowable vectorial tolerance.

relTol

double relTol

Default relative allowable vectorial tolerance.

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 AdaptiveStepsizeIntegrator implements Serializable

serialVersionUID: -2671266540106066022L

Serialized Fields

integrationResult

double[] integrationResult

The result of the integration.

integrator

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

The integrator used.

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 javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID: 1853070398348919488L

Serialized Fields

listOfBlocks

java.util.List<E> listOfBlocks

A list of actual data

name

java.lang.String name

timeName

java.lang.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 javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID: -6797479340761921075L

Serialized Fields

blockName

java.lang.String blockName

The optional name of the block.

columnNames

java.lang.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

java.lang.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

java.util.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 AdaptiveStepsizeIntegrator implements Serializable

serialVersionUID: -3446213991016212781L

Serialized Fields

hMax

double hMax

maximum stepsize

hMin

double hMin

minimum stepsize

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 java.lang.Object implements Serializable

serialVersionUID: 3453063382705340995L

Serialized Fields

algebraicRules

java.util.List<E> algebraicRules

Contains a list of all algebraic rules transformed to assignment rules for further processing

compartmentHash

java.util.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

java.util.HashSet<E> priorities

This set stores the priorities of the currently processed events.

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

java.util.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

java.util.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

java.lang.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

java.util.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

java.util.List<E> runningEvents

Stores the indices of the events triggered for the current point in time.

delayedEvents

java.util.List<E> delayedEvents

Stores the indices of the events triggered for a future point in time.

nodeInterpreter

EfficientASTNodeInterpreter nodeInterpreter

Node interpreter for interpreting MathML objects.

speciesMap

java.util.Map<K,V> speciesMap

Map for faster access to species.

inConcentration

java.util.Set<E> inConcentration

Species with the unit given in mol/volume for which it has to be considered that the change rate should always be only in mol/time

kineticLawRoots

java.util.List<E> kineticLawRoots

List of kinetic laws given as ASTNodeObjects

nodes

java.util.List<E> nodes

List of all occuring ASTNodes

nodeInterpreterWithTime

ASTNodeInterpreterWithTime nodeInterpreterWithTime

Node interpreter taking the time into consideration

stoichiometries

java.util.List<E> stoichiometries

List of all occuring stoichiometries

stoichiometriesSize

int stoichiometriesSize

Size of the list of stoichiometries (for time-saving)

reactionFast

boolean[] reactionFast

Array that stores which reactions are fast

reactionReversible

boolean[] reactionReversible

Array that stores which reactions are reversible

assignmentRulesRoots

java.util.List<E> assignmentRulesRoots

List of the assignment rules (as AssignmentRuleObjects)

rateRulesRoots

java.util.List<E> rateRulesRoots

List of the rate rules (as RateRuleObjects)

astNodeTime

double astNodeTime

Current time for the ASTNode processing (not equal to the simulation time!)

delayValueHolder

DelayValueHolder delayValueHolder

Value holder for computation of delayed values

highOrderEvents

java.util.List<E> highOrderEvents

List which is used for choosing the next event to process

conversionFactors

double[] conversionFactors

Array of the conversionFactors given (default value: 1)

modelHasEvents

boolean modelHasEvents

Flag which stores whether the model contains any events

nRateRules

int nRateRules

Number of rate rules

nAssignmentRules

int nAssignmentRules

Number of assignment rules

nConstraints

int nConstraints

Number of constraints

initialAssignmentRoots

java.util.List<E> initialAssignmentRoots

List of the initial assignments (as AssignmentRuleObjects)

noDerivatives

boolean noDerivatives

Flag which is true if no changes (in rate rules and kinetic laws) are occuring in the model