Simulation Core Library

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?


numberOfAssignmentRulesLoops

int numberOfAssignmentRulesLoops
The number of repetitions for the processing of assignment rules


oldY

double[] oldY
Array for saving older Y values


oldY2

double[] oldY2
Array for saving older Y values (when computing delayed values)


containsDelays

boolean containsDelays

Package org.simulator.sedml

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

serialVersionUID: 1L


Generated at March 17 2014
Version 1.4 Revision 453