Serialized Form

Package org.simulator.math

Class org.simulator.math.ArithmeticMean extends MeanFunction implements Serializable

serialVersionUID: 1738283911802695133L

Class org.simulator.math.DistanceSum extends MeanFunction implements Serializable

serialVersionUID: 7739137402966833880L

Class org.simulator.math.EuclideanDistance extends N_Metric implements Serializable

serialVersionUID: -2520265250898674233L

Class org.simulator.math.ManhattanDistance extends N_Metric implements Serializable

serialVersionUID: -7863697829237313786L

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

Class org.simulator.math.MeanFunction extends Object implements Serializable

serialVersionUID: -7272984374334773096L

Class org.simulator.math.N_Metric extends QualityMeasure implements Serializable

serialVersionUID: -216525074796086162L

Serialized Fields

root

double root

The n of the metric.

Class org.simulator.math.PearsonCorrelation extends QualityMeasure implements Serializable

serialVersionUID: -493779339080103217L

Class org.simulator.math.QualityMeasure extends Object implements Serializable

serialVersionUID: -1923357284664688319L

Serialized Fields

defaultValue

double defaultValue

The return value of the distance function in cases where the distance cannot be computed.

meanFunction

MeanFunction meanFunction

Class org.simulator.math.Relative_N_Metric extends QualityMeasure implements Serializable

serialVersionUID: 5066304615795368201L

Serialized Fields

defaultNaN

boolean defaultNaN

Is default value NaN? (for faster computation)

metric

N_Metric metric

The metric the relative distance is based on.

Class org.simulator.math.RelativeEuclideanDistance extends Relative_N_Metric implements Serializable

serialVersionUID: -7488743431449082030L

Class org.simulator.math.RelativeManhattanDistance extends Relative_N_Metric implements Serializable

serialVersionUID: -5446188147827736620L

Class org.simulator.math.RelativeSquaredError extends N_Metric implements Serializable

serialVersionUID: 1643317436479699973L

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

clonedSolver

AbstractDESSolver clonedSolver

A cloned version of this object

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

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 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 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.ConstraintEvent extends EventObject implements Serializable

serialVersionUID: -7217087217464285486L

Serialized Fields

violationTime

double violationTime

The point in time, at which a violation occurred.

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

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

SBMLEventInProgress[] events

This array stores for every event an object of SBMLEventInProgress that is used to handle event processing during simulation

priorities

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.

listOfConstraintListeners

List<E> listOfConstraintListeners

A List of ConstraintListener, which deal with violation of Constraints during simulation.

model

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.

speciesMap

Map<K,V> speciesMap

Map for faster access to species.

inConcentration

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

ASTNodeValue[] kineticLawRoots

List of kinetic laws given as ASTNodeObjects

constraintRoots

List<E> constraintRoots

List of constraints given as ASTNodeValue objects

nodes

List<E> nodes

List of all occurring ASTNodes

nodeInterpreter

ASTNodeInterpreter nodeInterpreter

Node interpreter taking the time into consideration

stoichiometryValues

StoichiometryValue[] stoichiometryValues

List of all occuring stoichiometries

reactionFast

boolean[] reactionFast

Array that stores which reactions are fast

reactionReversible

boolean[] reactionReversible

Array that stores which reactions are reversible

assignmentRulesRoots

List<E> assignmentRulesRoots

List of the assignment rules (as AssignmentRuleObjects)

rateRulesRoots

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

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

initialAssignmentRoots

List<E> initialAssignmentRoots

List of the InitialAssignment (as AssignmentRuleValue objects)

noDerivatives

boolean noDerivatives

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

inConcentrationValues

boolean[] inConcentrationValues

Array that shows whether a division by the compartment size is necessary after computation of the derivatives.

compartmentIndexes

int[] compartmentIndexes

Contains the compartment indexes of the species in the Y vector.

stoichiometrySet

boolean[] stoichiometrySet

Are the stoichiometries in the stoichiometry values set?

constantStoichiometry

boolean[] constantStoichiometry

Are the stoichiometries in the stoichiometry values constant?

zeroChange

boolean[] zeroChange

Is the stoichiometry value referring to a species whose value does not change?

isReactant

boolean[] isReactant

Is the stoichiometry value referring to a reactant?

reactionIndex

int[] reactionIndex

The indices of the reactions the stoichiometry values are referring to

speciesIndex

int[] speciesIndex

The species indices of the stoichiometry values

stoichiometry

double[] stoichiometry

The current stoichiometries of the stoichiometry values

isAmount

boolean[] isAmount

Is the SBase in the Y vector an amount?

delaysIncluded

boolean delaysIncluded

Are delays included in the computation?

Package org.simulator.sedml

Class org.simulator.sedml.ExecutionException extends RuntimeException implements Serializable

serialVersionUID: 1L