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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 

boolean includeIntermediates
DESystem
is an instance of
RichDESystem
. Setting this switch to false speeds up the
computation and lowers the memory consumption.
double intervalFactor
List<E> listenerList
List
of PropertyChangeListener
s (for threading purpose)
boolean nonnegative
double stepSize
boolean unstableFlag
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 

double absTol
double relTol
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 

double[] integrationResult
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 

List<E> listOfBlocks
String name
String timeName
double[] timePoints
Class org.simulator.math.odes.MultiTable.Block extends AbstractTableModel implements Serializable 

serialVersionUID: 6797479340761921075L
Serialized Fields 

String blockName
String[] columnNames
double[][] data
String[] identifiers
Hashtable<K,V> idHash
Hashtable
memorizes the column indices of all
identifiers.
MultiTable parent
Class org.simulator.math.odes.RosenbrockSolver extends AdaptiveStepsizeIntegrator implements Serializable 

serialVersionUID: 3446213991016212781L
Serialized Fields 

double hMax
double hMin
double t
double h
double sk
double hAdap
int numEqn
double[] y
double[] oldY
double[] f1
double[] f2
double[] f3
double[] f4
double[] f5
double[] f6
double[] k1
double[] k2
double[] k3
double[] k4
double[] k5
double[] yNew
double[] yerr
double[] yTemp
double[] ya
double[] yb
double[] g0
double[] g1
double[] g2
double[] g1x
double[] g2x
double[] DFDX
int[] indx
double[][] JAC
double[][] FAC
double[][] I
boolean stop
double[] timePoints
boolean[] ignoreNaN
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 

List<E> algebraicRules
Map<K,V> compartmentHash
Reaction currentReaction
double currentTime
SBMLEventInProgress[] events
SBMLEventInProgress
that is used
to handle event processing during simulation
HashSet<E> priorities
double[] initialValues
List<E>[] listOfContraintsViolations
Model model
Map<K,V> symbolHash
Compartment
s, Species
, global
Parameter
s, and, if necessary, SpeciesReference
s in
RateRule
s to an value object which contains the position in the
SBMLinterpreter.Y
vector
String[] symbolIdentifiers
double[] v
Map<K,V> stoichiometricCoefHash
Map
saves the current stoichiometric coefficients for those
SpeciesReference
objects that are a target to an Assignment
.
double[] Y
boolean isProcessingFastReactions
boolean hasFastReactions
List<E> runningEvents
List<E> delayedEvents
Map<K,V> speciesMap
Set<E> inConcentration
List<E> kineticLawRoots
List<E> constraintRoots
List<E> nodes
ASTNodeInterpreter nodeInterpreter
List<E> stoichiometries
int stoichiometriesSize
boolean[] reactionFast
boolean[] reactionReversible
List<E> assignmentRulesRoots
List<E> rateRulesRoots
double astNodeTime
DelayValueHolder delayValueHolder
List<E> highOrderEvents
double[] conversionFactors
boolean modelHasEvents
int nRateRules
int nAssignmentRules
int nConstraints
List<E> initialAssignmentRoots
boolean noDerivatives
Package org.simulator.sedml 

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

serialVersionUID: 1L


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