Serialized Form (Systems Biology Simulation Core Library (SBSCL) 2.1 API)

Package fern.analysis
- Class fern.analysis.IntQueue extends cern.colt.list.IntArrayList implements Serializable
  
  serialVersionUID:
  
  1L
- Class fern.analysis.IntStack extends cern.colt.list.IntArrayList implements Serializable
  
  serialVersionUID:
  
  1L
Package fern.network
- Class fern.network.FeatureNotSupportedException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package fern.tools.gnuplot
- Class fern.tools.gnuplot.GnuPlot extends JFrame implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - img
```
BufferedImage img
```
    - commands
```
List<E> commands
```
    - axes
```
List<E> axes
```
    - clearedAxes
```
List<E> clearedAxes
```
    - defaultStyle
```
String defaultStyle
```
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.MaxAbsDistance extends QualityMeasure implements Serializable
- Class org.simulator.math.MaxDivergenceTolerance extends QualityMeasure implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - metric
```
MaxAbsDistance metric
```
      The metric the relative distance is based on
    - absTol
```
double absTol
```
      Absolute tolerance for the reaction
    - relTol
```
double relTol
```
      Relative tolerance for the reaction
- 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.RelativeMaxDistance extends QualityMeasure implements Serializable
  - Serialized Fields
    - metric
```
MaxAbsDistance metric
```
      The metric the relative distance is based on
- 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
```
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 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.plot
- Class org.simulator.plot.PlotMultiTable extends org.jfree.ui.ApplicationFrame implements Serializable
  - Serialized Fields
    - species
```
MultiTable species
```
    - data
```
org.jfree.data.category.DefaultCategoryDataset data
```
    - title
```
String title
```
- Class org.simulator.plot.PlotProcessedSedmlResults extends org.jfree.ui.ApplicationFrame implements Serializable
  - Serialized Fields
    - species
```
org.jlibsedml.execution.IProcessedSedMLSimulationResults species
```
    - graphData
```
org.jfree.data.xy.XYSeriesCollection graphData
```
    - title
```
String title
```
    - curves
```
List<E> curves
```
    - lineChart
```
org.jfree.chart.JFreeChart lineChart
```
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.EquationSystem extends Object implements Serializable
  - 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
```
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.
    - changeRate
```
double[] changeRate
```
      An array that stores derivatives of each species in the model system at current time.
    - 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 EquationSystem.Y vector
    - constantHash
```
Map<K,V> constantHash
```
      Hashes the id of all Compartments, Species, global Parameters, and, if necessary, SpeciesReferences in RateRules to an boolean object which contains whether it is constant or not
    - 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 state variables within the model including species and parameters.
    - 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)
    - rateRuleHash
```
Map<K,V> rateRuleHash
```
      Map for getting the raterule index (in the rateRulesRoots ArrayList) of particular id
    - 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) occur 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
```
    - latestTimePoint
```
double latestTimePoint
```
      The value of the latest time point
    - previousTimePoint
```
double previousTimePoint
```
      The value of the previous time point
    - latestTimePointResult
```
double[] latestTimePointResult
```
      An array of the concentration of each species at latest processed time point within the model system.
- Class org.simulator.sbml.SBMLinterpreter extends EquationSystem implements Serializable
  
  serialVersionUID:
  
  3453063382705340995L
Package org.simulator.sedml
- Class org.simulator.sedml.ExecutionException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L

Serialized Form

Package fern.analysis

Class fern.analysis.IntQueue extends cern.colt.list.IntArrayList implements Serializable

Class fern.analysis.IntStack extends cern.colt.list.IntArrayList implements Serializable

Package fern.network

Class fern.network.FeatureNotSupportedException extends Exception implements Serializable

Package fern.tools.gnuplot

Class fern.tools.gnuplot.GnuPlot extends JFrame implements Serializable

Serialized Fields

img

commands

axes

clearedAxes

defaultStyle

Package org.simulator.math

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

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

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

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

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

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

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

Serialized Fields

metric

absTol

relTol

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

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

Serialized Fields

root

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

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

Serialized Fields

defaultValue

meanFunction

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

Serialized Fields

defaultNaN

metric

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

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

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

Serialized Fields

metric

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

Package org.simulator.math.odes

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

Serialized Fields

includeIntermediates

intervalFactor

listenerList

nonnegative

stepSize

unstableFlag

data

clonedSolver

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

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

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

Serialized Fields

absTol

relTol

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

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

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

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

Serialized Fields

integrationResult

integrator

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

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

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

Serialized Fields

listOfBlocks

name

timeName

timePoints

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

Serialized Fields

blockName