Serialized Form (JSBML 1.1 API Specification)

Package org.sbml.jsbml
- Class org.sbml.jsbml.AbstractMathContainer extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -6630349025482311163L
  - Serialized Fields
    - math
```
ASTNode math
```
      The math formula as an abstract syntax tree.
- Class org.sbml.jsbml.AbstractNamedSBase extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -9186483076164094500L
  - Serialized Fields
    - id
```
String id
```
      id of the SBML component (can be optional depending on the level and version). Matches the id attribute of an element in a SBML file.
    - name
```
String name
```
      name of the SBML component (can be optional depending on the level and version). Matches the name attribute of an element in a SBML file.
- Class org.sbml.jsbml.AbstractNamedSBaseWithUnit extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  3611229078069091891L
  - Serialized Fields
    - unitsID
```
String unitsID
```
      The unit attribute of this variable.
- Class org.sbml.jsbml.AbstractSBase extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  8781459818293592636L
  - Serialized Fields
    - annotation
```
Annotation annotation
```
      Annotations of the SBML component. Matches the annotation XML node in a SBML file.
    - declaredNamespaces
```
Map<K,V> declaredNamespaces
```
      Contains all the namespaces declared on the XML node with their prefixes.
    - elementNamespace
```
String elementNamespace
```
      the namespace which this SBase element belong to.
    - extensions
```
SortedMap<K,V> extensions
```
      Map containing the SBML extension object of additional packages with the appropriate name space of the package.
    - ignoredExtensions
```
SortedMap<K,V> ignoredExtensions
```
      Map containing the ignored package objects.
      Package are considered ignored if JSBML does not support this package or support the package but not the associated namespace.
    - ignoredXMLElements
```
XMLNode ignoredXMLElements
```
      Contains the unknown XML attributes or elements.
    - lv
```
ValuePair<L extends Comparable<? super L>,V extends Comparable<? super V>> lv
```
      Level and version of the SBML component. Matches the level XML attribute of an SBML node.
    - metaId
```
String metaId
```
      metaid of the SBML component. Matches the metaid XML attribute of an element in a SBML file.
    - notesXMLNode
```
XMLNode notesXMLNode
```
      notes of the SBML component. Matches the notes XML node in a SBML file.
    - packageName
```
String packageName
```
      the name of the package which this SBase element belong to, 'core' by default.
    - packageVersion
```
int packageVersion
```
      the version of the package which this SBase element belong to, '0' by default for core.
    - sboTerm
```
int sboTerm
```
      sbo term of the SBML component. Matches the sboTerm XML attribute of an element in a SBML file.
- Class org.sbml.jsbml.AbstractTreeNode extends Object implements Serializable
  
  serialVersionUID:
  
  8629109724566600238L
  - Serialized Fields
    - listOfListeners
```
List<E> listOfListeners
```
      List of listeners for this component
    - parent
```
TreeNode parent
```
      The parent element of this Annotation.
    - userObjects
```
Map<K,V> userObjects
```
      Any kind of Object that can be stored in addition to all other features of this AbstractTreeNode in form of key-value pairs. Note that things stored here will not be written to SBML files. This only provides a possibility to attach some in-memory information to derived classes.
- Class org.sbml.jsbml.AlgebraicRule extends Rule implements Serializable
  
  serialVersionUID:
  
  -3952858495318158175L
- Class org.sbml.jsbml.Annotation extends AnnotationElement implements Serializable
  
  serialVersionUID:
  
  2127495202258145900L
  - Serialized Fields
    - about
```
String about
```
      matches the about XML attribute of an annotation element in a SBML file.
    - history
```
History history
```
      The ModelHistory which represents the history section of a RDF annotation
    - listOfCVTerms
```
List<E> listOfCVTerms
```
      contains all the CVTerm of the RDF annotation
    - nonRDFannotation
```
XMLNode nonRDFannotation
```
      contains all the remaining annotation not mapped to Objects.
- Class org.sbml.jsbml.AnnotationElement extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  495755171215798027L
- Class org.sbml.jsbml.AssignmentRule extends ExplicitRule implements Serializable
  
  serialVersionUID:
  
  683172080347613789L
- Class org.sbml.jsbml.ASTNode extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  -1391327698196553142L
  - Serialized Fields
    - definitionURL
```
String definitionURL
```
      The value of the definitionURL for csymbol element. Level 3 extensions can create new csymbol element that we would not necessary be aware of, so we need to store the attribute value.
    - denominator
```
int denominator
```
    - exponent
```
int exponent
```
    - id
```
String id
```
      Possible attributes for a MathML element
    - style
```
String style
```
    - className
```
String className
```
    - encoding
```
String encoding
```
    - isSetNumberType
```
boolean isSetNumberType
```
      Tells if the type attribute of the cn element was set and we need to write it back or if it is set to the default (REAL).
    - listOfNodes
```
List<E> listOfNodes
```
      Child nodes.
    - mantissa
```
double mantissa
```
      The part of a number in scientific format (with an E) that is on the left side of the E (the prefix of the number). For instance, in the number 3.5E-2.7 the mantissa is 3.5.
    - name
```
String name
```
      If no NamedSBase object exists or can be identified when ASTNode.setName(String) is called, the given name is stored in this field.
    - numerator
```
int numerator
```
      This value stores the numerator if this.isRational() is true, or the value of an integer if this.isInteger() is true.
    - parentSBMLObject
```
MathContainer parentSBMLObject
```
      The container that holds this ASTNode.
    - type
```
ASTNode.Type type
```
      The type of this ASTNode.
    - unitId
```
String unitId
```
      Since Level 3 SBML allows to equip numbers with unit identifiers. In this case a reference to an identifier of a UnitDefinition in the model can be stored here.
    - variable
```
CallableSBase variable
```
      A direct pointer to a referenced variable. This can save a lot of computation time because it will then not be necessary to query the corresponding model again and again for this variable.
- Class org.sbml.jsbml.Compartment extends Symbol implements Serializable
  
  serialVersionUID:
  
  -1117854029388326636L
  - Serialized Fields
    - compartmentTypeID
```
String compartmentTypeID
```
      Deprecated.
      
      Represents the compartmentType XML attribute of a compartment element. It matches a compartmentType id in the model.
    - isSetSpatialDimensions
```
boolean isSetSpatialDimensions
```
      Helper variable to check if spatial dimensions has been set by the user.
    - outsideID
```
String outsideID
```
      Deprecated.
      
      Represents the outside XML attribute of a compartment element. It matches a compartment id in the model instance.
    - spatialDimensions
```
Double spatialDimensions
```
      Represents the spatialDimensions XML attribute of a compartment element.
- Class org.sbml.jsbml.CompartmentType extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -2894837299868213399L
- Class org.sbml.jsbml.Constraint extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  7396734926596485200L
  - Serialized Fields
    - message
```
XMLNode message
```
      Represents the subnode message of a constraint element.
- Class org.sbml.jsbml.Creator extends AnnotationElement implements Serializable
  
  serialVersionUID:
  
  -3403463908044292946L
  - Serialized Fields
    - email
```
String email
```
      email of the creator
    - familyName
```
String familyName
```
      Family name of the creator
    - givenName
```
String givenName
```
      Given name of the creator
    - organisation
```
String organisation
```
      Organisation name of the creator.
    - otherAttributes
```
Map<K,V> otherAttributes
```
      Holding any additional vCard elements. This is a quick and dirty solution as the vCard can contain many elements that have sub-elements. TODO: use an XMLNode to hold all the additional informations
- Class org.sbml.jsbml.CVTerm extends AnnotationElement implements Serializable
  
  serialVersionUID:
  
  -3648054739091227113L
  - Serialized Fields
    - qualifier
```
CVTerm.Qualifier qualifier
```
      Represents the MIRIAM qualifier node in the annotation node of a SBML component.
    - resourceURIs
```
List<E> resourceURIs
```
      Contains all the MIRIAM URI associated with the qualifier of this CVTerm instance.
    - listOfNestedCVTerms
```
List<E> listOfNestedCVTerms
```
      Contains all the CVTerm that qualifies this CVTerm. Since SBML level 2 version 5 (and future SBML L3V2), the annotations can be recursive.
    - type
```
CVTerm.Type type
```
      Represents the type of MIRIAM qualifier for this CVTerm. It depends on the name space in the SBML file, it can be a model qualifier or a biological qualifier.
- Class org.sbml.jsbml.Delay extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  -1578051749680028593L
- Class org.sbml.jsbml.Event extends AbstractNamedSBaseWithUnit implements Serializable
  
  serialVersionUID:
  
  5282750820355199194L
  - Serialized Fields
    - delay
```
Delay delay
```
      Represents the delay sub-element of an event element.
    - isSetUseValuesFromTriggerTime
```
boolean isSetUseValuesFromTriggerTime
```
    - listOfEventAssignments
```
ListOf<T extends SBase> listOfEventAssignments
```
      Represents the listOfEventAssignments sub-element of an event element.
    - priority
```
Priority priority
```
      Represents the priority sub-element of an event.
    - trigger
```
Trigger trigger
```
      Represents the trigger sub-element of an event element.
    - useValuesFromTriggerTime
```
Boolean useValuesFromTriggerTime
```
      Represents the 'useValuesFromTriggerTime' XML attribute of an event element.
- Class org.sbml.jsbml.EventAssignment extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  -263409745456083049L
  - Serialized Fields
    - variableID
```
String variableID
```
      Represents the 'variable' XML attribute of an eventAssignment element.
- Class org.sbml.jsbml.ExplicitRule extends Rule implements Serializable
  
  serialVersionUID:
  
  7458241628289830621L
  - Serialized Fields
    - unitsID
```
String unitsID
```
      Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
      
      Represents the 'units' XML attribute of a ParameterRule.
    - variableID
```
String variableID
```
      Represents the id of a Variable. Matches the variable XML attribute of an assignmentRule or rateRule element.
- Class org.sbml.jsbml.FunctionDefinition extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  5103621145642898899L
  - Serialized Fields
    - id
```
String id
```
      Represents the "id" attribute of a functionDefinition element.
    - name
```
String name
```
      Represents the "name" attribute of a functionDefinition element.
- Class org.sbml.jsbml.History extends AnnotationElement implements Serializable
  
  serialVersionUID:
  
  -1699117162462037149L
  - Serialized Fields
    - creation
```
Date creation
```
      Date of creation
    - listOfCreators
```
List<E> listOfCreators
```
      Contains all the Creator instances of this History.
    - listOfModification
```
List<E> listOfModification
```
      Contains all the modified date instances of this History.
    - modified
```
Date modified
```
      Last date of modification
- Class org.sbml.jsbml.IdentifierException extends SBMLException implements Serializable
  
  serialVersionUID:
  
  3203848126194894206L
- Class org.sbml.jsbml.InitialAssignment extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  2798071640186792089L
  - Serialized Fields
    - variableID
```
String variableID
```
      Represents the 'symbol' XML attribute of an initialAssignmnent element.
- Class org.sbml.jsbml.KineticLaw extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  7528194464711501708L
  - Serialized Fields
    - listOfLocalParameters
```
ListOf<T extends SBase> listOfLocalParameters
```
      Represents the listOfLocalParameters or listOfParameters sub-element of a kineticLaw element.
    - mapOfLocalParameters
```
Map<K,V> mapOfLocalParameters
```
      For internal computation: a mapping between their identifiers and the LocalParameters in KineticLaws themselves:
    - substanceUnitsID
```
String substanceUnitsID
```
      Deprecated.
      
      Represents the 'substanceUnits' XML attribute of this KineticLaw.
    - timeUnitsID
```
String timeUnitsID
```
      Deprecated.
      
      Represents the 'timeUnits' XML attribute of this KineticLaw.
    - unitsID
```
String unitsID
```
      Deprecated.
      
      In case that a variant of substance per time is set, this will memorize the identifier of the corresponding element in the Model.
- Class org.sbml.jsbml.LevelVersionError extends SBMLError implements Serializable
  
  serialVersionUID:
  
  -5549251465153191735L
- Class org.sbml.jsbml.ListOf extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  5757549697766609627L
  - Serialized Fields
    - listOf
```
List<E> listOf
```
      list containing all the SBase elements of this object.
    - listType
```
ListOf.Type listType
```
      name of the list at it appears in the SBMLFile. By default, it is SBaseListType.none.
- Class org.sbml.jsbml.LocalParameter extends QuantityWithUnit implements Serializable
  
  serialVersionUID:
  
  57994535283502018L
  - Serialized Fields
    - isExplicitlySetConstant
```
boolean isExplicitlySetConstant
```
      This field memorizes whether this LocalParameter has been explicitly set to be constant. All instances of LocalParameter are constant by definition, however, in earlier versions of SBML (before Level 3) it was possible to explicitly state that a LocalParameter is constant. Therefore, a special field has become necessary to reflect this property.
- Class org.sbml.jsbml.Model extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  5256379371231860049L
  - Serialized Fields
    - areaUnitsID
```
String areaUnitsID
```
      Represents the 'areaUnits' XML attribute of a model element.
    - conversionFactorID
```
String conversionFactorID
```
      Represents the 'conversionFactor' XML attribute of a model element.
    - extentUnitsID
```
String extentUnitsID
```
      Represents the 'extentUnits' XML attribute of a model element.
    - lengthUnitsID
```
String lengthUnitsID
```
      Represents the 'lengthUnits' XML attribute of a model element.
    - listOfCompartments
```
ListOf<T extends SBase> listOfCompartments
```
      Represents the listOfCompartments subnode of a model element.
    - listOfCompartmentTypes
```
ListOf<T extends SBase> listOfCompartmentTypes
```
      Deprecated. only valid in SBML Level 2 for Versions 2 through 4.
      
      Represents the listOfCompartmentTypes subnode of a model element.
    - listOfConstraints
```
ListOf<T extends SBase> listOfConstraints
```
      Represents the listOfConstraints subnode of a model element.
    - listOfEvents
```
ListOf<T extends SBase> listOfEvents
```
      Represents the listOfEvents subnode of a model element.
    - listOfFunctionDefinitions
```
ListOf<T extends SBase> listOfFunctionDefinitions
```
      Represents the listOfFunctionDefinitions subnode of a model element.
    - listOfInitialAssignments
```
ListOf<T extends SBase> listOfInitialAssignments
```
      Represents the listOfInitialAssignments subnode of a model element.
    - listOfParameters
```
ListOf<T extends SBase> listOfParameters
```
      Represents the listOfParameters subnode of a model element.
    - listOfPredefinedUnitDefinitions
```
List<E> listOfPredefinedUnitDefinitions
```
      Represents the list of predefined UnitDefinitions for a given SBML level and version.
    - listOfReactions
```
ListOf<T extends SBase> listOfReactions
```
      Represents the listOfReactions subnode of a model element.
    - listOfRules
```
ListOf<T extends SBase> listOfRules
```
      Represents the listOfRules subnode of a model element.
    - listOfSpecies
```
ListOf<T extends SBase> listOfSpecies
```
      Represents the listOfSpecies subnode of a model element.
    - listOfSpeciesTypes
```
ListOf<T extends SBase> listOfSpeciesTypes
```
      Deprecated. only valid in SBML Level 2 for Versions 2 through 4.
      
      Represents the listOfSpeciesTypes subnode of a model element.
    - listOfUnitDefinitions
```
ListOf<T extends SBase> listOfUnitDefinitions
```
      Represents the listOfUnitDefinitions sub-node of a model element.
    - mapOfLocalParameters
```
Map<K,V> mapOfLocalParameters
```
      A mapping between the identifiers of LocalParameters and the containing Reaction objects.
    - mapOfUniqueNamedSBases
```
Map<K,V> mapOfUniqueNamedSBases
```
      For internal computation: a mapping between their identifiers and the UniqueNamedSBases in Models themselves:
    - mapOfUnitDefinitions
```
Map<K,V> mapOfUnitDefinitions
```
      A mapping between their identifiers and associated UnitDefinition objects.
    - substanceUnitsID
```
String substanceUnitsID
```
      Represents the 'substanceUnits' XML attribute of a model element.
    - timeUnitsID
```
String timeUnitsID
```
      Represents the 'timeUnits' XML attribute of a model element.
    - volumeUnitsID
```
String volumeUnitsID
```
      Represents the 'volumeUnits' XML attribute of a model element.
- Class org.sbml.jsbml.ModifierSpeciesReference extends SimpleSpeciesReference implements Serializable
  
  serialVersionUID:
  
  6033910247622532704L
- Class org.sbml.jsbml.Parameter extends Symbol implements Serializable
  
  serialVersionUID:
  
  3300762892435768291L
- Class org.sbml.jsbml.Priority extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  391689890391156873L
- Class org.sbml.jsbml.PropertyException extends SBMLError implements Serializable
  
  serialVersionUID:
  
  -3416620362835594659L
- Class org.sbml.jsbml.PropertyNotAvailableException extends PropertyException implements Serializable
  
  serialVersionUID:
  
  3030431702957624218L
- Class org.sbml.jsbml.PropertyUndefinedError extends PropertyException implements Serializable
  
  serialVersionUID:
  
  2990146647017147195L
- Class org.sbml.jsbml.QuantityWithUnit extends AbstractNamedSBaseWithUnit implements Serializable
  
  serialVersionUID:
  
  -9088772458214208160L
  - Serialized Fields
    - isSetValue
```
boolean isSetValue
```
      a boolean to help knowing is the value as been set by the user or is the default one.
    - value
```
Double value
```
      The size, initial amount or concentration, or the actual value of this variable.
- Class org.sbml.jsbml.RateRule extends ExplicitRule implements Serializable
  
  serialVersionUID:
  
  -1631920547145001765L
- Class org.sbml.jsbml.Reaction extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  1385417662249487643L
  - Serialized Fields
    - compartmentID
```
String compartmentID
```
      Represents the 'compartment' XML attribute of a reaction element.
    - fast
```
Boolean fast
```
      Represents the 'fast' XML attribute of a reaction element.
    - isSetFast
```
boolean isSetFast
```
      Checks whether the Reaction.fast attribute has been set by using a default or by changing its value.
    - isSetReversible
```
boolean isSetReversible
```
      Checks whether the Reaction.reversible attribute has been set by using a default or by changing its value.
    - kineticLaw
```
KineticLaw kineticLaw
```
      Represents the 'kineticLaw' XML subNode of a reaction element.
    - listOfModifiers
```
ListOf<T extends SBase> listOfModifiers
```
      Represents the 'listOfModifiers' XML subNode of a reaction element.
    - listOfProducts
```
ListOf<T extends SBase> listOfProducts
```
      Represents the 'listOfProducts' XML subNode of a reaction element.
    - listOfReactants
```
ListOf<T extends SBase> listOfReactants
```
      Represents the 'listOfReactants' XML subNode of a reaction element.
    - reversible
```
Boolean reversible
```
      Represents the 'reversible' XML attribute of a reaction element.
- Class org.sbml.jsbml.Rule extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  -8151628772496225902L
- Class org.sbml.jsbml.SBMLDocument extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -3927709655186844513L
  - Serialized Fields
    - checkConsistencyParameters
```
Map<K,V> checkConsistencyParameters
```
      Contains all the parameter to validate the SBML document
    - listOfErrors
```
SBMLErrorLog listOfErrors
```
      Memorizes all SBMLError when parsing the file containing this document.
    - mappingFromMetaId2SBase
```
Map<K,V> mappingFromMetaId2SBase
```
      Stores all the meta identifiers within this SBMLDocument to avoid the creation of multiple identical meta identifiers. These identifiers have to be unique within the document.
    - model
```
Model model
```
      Represents the 'model' XML subnode of a SBML file.
    - enabledPackageMap
```
Map<K,V> enabledPackageMap
```
      Stores a package namespace associated with it's status. The status being: enabled if the Boolean is true, disable otherwise
    - SBMLDocumentAttributes
```
Map<K,V> SBMLDocumentAttributes
```
      Contains all the XML attributes of the sbml XML node.
- Class org.sbml.jsbml.SBMLError extends XMLException implements Serializable
  
  serialVersionUID:
  
  -6071833473902680630L
  - Serialized Fields
    - category
```
String category
```
    - code
```
int code
```
    - excerpt
```
String excerpt
```
    - column
```
int column
```
    - line
```
int line
```
    - message
```
Message message
```
    - shortmessage
```
Message shortmessage
```
    - detail
```
Detail detail
```
    - severity
```
String severity
```
    - packageName
```
String packageName
```
- Class org.sbml.jsbml.SBMLException extends XMLException implements Serializable
  
  serialVersionUID:
  
  7680394947436628860L
  - Serialized Fields
    - category
```
SBMLException.Category category
```
      The category of this exception.
    - code
```
SBMLException.Code code
```
    - shortMessage
```
String shortMessage
```
    - type
```
SBMLException.Type type
```
- Class org.sbml.jsbml.SBMLReader extends Object implements Serializable
  
  serialVersionUID:
  
  -3313609137341424804L
- Class org.sbml.jsbml.SBMLTypeUndefinedException extends SBMLError implements Serializable
  
  serialVersionUID:
  
  -6120311866715719809L
- Class org.sbml.jsbml.SBMLWriter extends Object implements Serializable
  
  serialVersionUID:
  
  7320725236081166704L
  - Serialized Fields
    - programName
```
String programName
```
      The name of the program that has been used to create an SBML String representation (possibly in a File) with the help of JSBML.
    - programVersion
```
String programVersion
```
      The version of the program using JSBML to serialize a model in an SBML String or File.
    - sbmlWriter
```
SBMLWriter sbmlWriter
```
      The actual writer.
- Class org.sbml.jsbml.SimpleSpeciesReference extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -504780573593345060L
  - Serialized Fields
    - speciesID
```
String speciesID
```
      Represents the 'species' XML attribute.
- Class org.sbml.jsbml.Species extends Symbol implements Serializable
  
  serialVersionUID:
  
  4427015656530890393L
  - Serialized Fields
    - amount
```
boolean amount
```
      True means initial amount is set. False means that an initial concentration is set.
    - boundaryCondition
```
Boolean boundaryCondition
```
      Represents the 'boundaryCondition' attribute of a Species element.
    - charge
```
Integer charge
```
      Deprecated.
      
      Represents the 'charge' attribute of a Species element.
    - compartmentID
```
String compartmentID
```
      Represents the 'compartment' attribute of a Species element.
    - conversionFactorID
```
String conversionFactorID
```
      Represents the 'conversionFactor' attribute of a Species element.
    - hasOnlySubstanceUnits
```
Boolean hasOnlySubstanceUnits
```
      Represents the 'hasOnlySubstanceUnits' attribute of a Species element.
    - isSetBoundaryCondition
```
boolean isSetBoundaryCondition
```
    - isSetCharge
```
boolean isSetCharge
```
      Boolean value to test if the charge has been set.
    - isSetHasOnlySubstanceUnits
```
boolean isSetHasOnlySubstanceUnits
```
    - spatialSizeUnitsID
```
String spatialSizeUnitsID
```
      Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
      
      Represents the 'spatialSizeUnits' attribute of a Species element.
    - speciesTypeID
```
String speciesTypeID
```
      Deprecated.
      
      Represents the 'speciesType' attribute of a Species element.
- Class org.sbml.jsbml.SpeciesReference extends SimpleSpeciesReference implements Serializable
  
  serialVersionUID:
  
  4400834403773787677L
  - Serialized Fields
    - constant
```
Boolean constant
```
      Represents the 'constant' XML attribute of this SpeciesReference.
    - denominator
```
Integer denominator
```
      Represents the 'denominator' XML attribute of this SpeciesReference.
    - isSetConstant
```
boolean isSetConstant
```
    - isSetDenominator
```
boolean isSetDenominator
```
      Boolean value to know if the SpeciesReference denominator has been set.
    - isSetStoichiometry
```
boolean isSetStoichiometry
```
    - stoichiometry
```
Double stoichiometry
```
      Represents the 'stoichiometry' XML attribute of this SpeciesReference.
    - stoichiometryMath
```
StoichiometryMath stoichiometryMath
```
      Deprecated.
      
      Contains the MathML expression for the stoichiometry of this SpeciesReference.
- Class org.sbml.jsbml.SpeciesType extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  7341517738480127866L
- Class org.sbml.jsbml.StoichiometryMath extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  -7070065639669486763L
- Class org.sbml.jsbml.Symbol extends QuantityWithUnit implements Serializable
  
  serialVersionUID:
  
  3061467418198640109L
  - Serialized Fields
    - constant
```
Boolean constant
```
      The constant attribute of this variable.
    - isSetConstant
```
boolean isSetConstant
```
- Class org.sbml.jsbml.Trigger extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  -6964409168614117235L
  - Serialized Fields
    - initialValue
```
Boolean initialValue
```
    - persistent
```
Boolean persistent
```
- Class org.sbml.jsbml.Unit extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -6335465287728562136L
  - Serialized Fields
    - exponent
```
Double exponent
```
      Represents the 'exponent' XML attribute of an unit element.
    - isSetExponent
```
boolean isSetExponent
```
    - isSetMultiplier
```
boolean isSetMultiplier
```
    - isSetOffset
```
boolean isSetOffset
```
    - isSetScale
```
boolean isSetScale
```
    - kind
```
Unit.Kind kind
```
      Represents the 'kind' XML attribute of an unit element.
    - multiplier
```
Double multiplier
```
      Represents the 'multiplier' XML attribute of an unit element.
    - offset
```
Double offset
```
      Deprecated. the offset attribute should no longer be used.
      
      Represents the 'offset' XML attribute of an unit element.
    - scale
```
Integer scale
```
      Represents the 'scale' XML attribute of an unit element.
- Class org.sbml.jsbml.UnitDefinition extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -4705380036260408123L
  - Serialized Fields
    - listOfUnits
```
ListOf<T extends SBase> listOfUnits
```
      Represents the 'listOfUnit' XML sub-element of a UnitDefinition.
Package org.sbml.jsbml.ext
- Class org.sbml.jsbml.ext.AbstractSBasePlugin extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  3741496965840142920L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - extendedSBase
```
SBase extendedSBase
```
    - packageVersion
```
int packageVersion
```
    - elementNamespace
```
String elementNamespace
```
Package org.sbml.jsbml.ext.arrays
- Class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -5467877915615614247L
  - Serialized Fields
    - mapOfDimensions
```
Map<K,V> mapOfDimensions
```
      Maps between the Dimension identifiers and themselves.
    - listOfIndices
```
ListOf<T extends SBase> listOfIndices
```
    - listOfDimensions
```
ListOf<T extends SBase> listOfDimensions
```
- Class org.sbml.jsbml.ext.arrays.Dimension extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -2930232424549376654L
  - Serialized Fields
    - size
```
String size
```
      Indicates the size of the dimension. Should be a valid id to a Parameter object.
    - arrayDimension
```
int arrayDimension
```
      Indicates which array dimension this object refers to.
    - isSetArrayDimension
```
boolean isSetArrayDimension
```
      Indicates if the arrayDimension field has a value.
- Class org.sbml.jsbml.ext.arrays.Index extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  2277400816974157871L
  - Serialized Fields
    - referencedAttribute
```
String referencedAttribute
```
    - arrayDimension
```
int arrayDimension
```
    - isSetArrayDimension
```
boolean isSetArrayDimension
```
Package org.sbml.jsbml.ext.comp
- Class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef extends SBaseRef implements Serializable
  
  serialVersionUID:
  
  -7590217205832827913L
  - Serialized Fields
    - id
```
String id
```
      id of the SBML component (can be optional depending on the level and version). Matches the id attribute of an element in a SBML file.
    - name
```
String name
```
      name of the SBML component (can be optional depending on the level and version). Matches the name attribute of an element in a SBML file.
- Class org.sbml.jsbml.ext.comp.CompModelPlugin extends CompSBasePlugin implements Serializable
  
  serialVersionUID:
  
  7104644706063096211L
  - Serialized Fields
    - listOfPorts
```
ListOf<T extends SBase> listOfPorts
```
    - listOfSubmodels
```
ListOf<T extends SBase> listOfSubmodels
```
    - mapOfPorts
```
Map<K,V> mapOfPorts
```
      Maps between the Port identifiers and themselves.
- Class org.sbml.jsbml.ext.comp.CompSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  3364911411091523856L
  - Serialized Fields
    - listOfReplacedElements
```
ListOf<T extends SBase> listOfReplacedElements
```
    - replacedBy
```
ReplacedBy replacedBy
```
- Class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin extends CompSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -6693188330172643491L
  - Serialized Fields
    - listOfModelDefinitions
```
ListOf<T extends SBase> listOfModelDefinitions
```
    - listOfExternalModelDefinitions
```
ListOf<T extends SBase> listOfExternalModelDefinitions
```
- Class org.sbml.jsbml.ext.comp.Deletion extends AbstractNamedSBaseRef implements Serializable
  
  serialVersionUID:
  
  -568486978934971953L
- Class org.sbml.jsbml.ext.comp.ExternalModelDefinition extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  2005205309846284624L
  - Serialized Fields
    - source
```
String source
```
    - modelRef
```
String modelRef
```
    - md5
```
String md5
```
- Class org.sbml.jsbml.ext.comp.ModelDefinition extends Model implements Serializable
  
  serialVersionUID:
  
  11908580298395050L
- Class org.sbml.jsbml.ext.comp.Port extends AbstractNamedSBaseRef implements Serializable
  
  serialVersionUID:
  
  -301236222127386488L
- Class org.sbml.jsbml.ext.comp.ReplacedBy extends SBaseRef implements Serializable
  
  serialVersionUID:
  
  -7067666288732978615L
  - Serialized Fields
    - submodelRef
```
String submodelRef
```
- Class org.sbml.jsbml.ext.comp.ReplacedElement extends SBaseRef implements Serializable
  
  serialVersionUID:
  
  -1222530387127803035L
  - Serialized Fields
    - submodelRef
```
String submodelRef
```
    - deletion
```
String deletion
```
    - conversionFactor
```
String conversionFactor
```
- Class org.sbml.jsbml.ext.comp.SBaseRef extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -4434500961448381830L
  - Serialized Fields
    - portRef
```
String portRef
```
      This attribute is used to refer to a port identifier, in the case when the reference being constructed with the SBaseRef is intended to refer to a port on a submodel. The namespace of the PortSIdRef value is the set of identifiers of type PortSId defined in the submodel, not the parent model.
    - idRef
```
String idRef
```
      This attribute is used to refer to a regular identifier (i.e., the value of an id attribute on some other object), in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the SIdRef value is the set of identifiers of type SId defined in the submodel, not the parent model.
    - unitRef
```
String unitRef
```
      This attribute is used to refer to the identifier of a UnitDefinition object. The namespace of the UnitSIdRef value is the set of unit identifiers defined in the submodel, not the parent model.
    - metaIdRef
```
String metaIdRef
```
      This attribute is used to refer to a metaid attribute value on some other object, in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the metaIdRef value is the entire document in which the referenced model resides
    - sBaseRef
```
SBaseRef sBaseRef
```
      An SBaseRef object may have up to one subcomponent named sBaseRef. This permits recursive structures to be constructed so that objects inside submodels can be referenced.
- Class org.sbml.jsbml.ext.comp.Submodel extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -2588930216065448311L
  - Serialized Fields
    - modelRef
```
String modelRef
```
    - timeConversionFactor
```
String timeConversionFactor
```
    - extentConversionFactor
```
String extentConversionFactor
```
    - listOfDeletions
```
ListOf<T extends SBase> listOfDeletions
```
Package org.sbml.jsbml.ext.distrib
- Class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  8759855933212983388L
  - Serialized Fields
    - drawFromDistribution
```
DrawFromDistribution drawFromDistribution
```
- Class org.sbml.jsbml.ext.distrib.DistribInput extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -5444621543802854220L
  - Serialized Fields
    - index
```
Integer index
```
- Class org.sbml.jsbml.ext.distrib.DistribSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -1732369832900356125L
  - Serialized Fields
    - uncertainty
```
Uncertainty uncertainty
```
- Class org.sbml.jsbml.ext.distrib.DrawFromDistribution extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7217922005569440580L
  - Serialized Fields
    - listOfDistribInputs
```
ListOf<T extends SBase> listOfDistribInputs
```
    - uncertML
```
XMLNode uncertML
```
    - mapOfDistribInputs
```
Map<K,V> mapOfDistribInputs
```
      Maps between the DistribInput identifiers and themselves.
- Class org.sbml.jsbml.ext.distrib.Uncertainty extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -904719821379100471L
  - Serialized Fields
    - uncertML
```
XMLNode uncertML
```
Package org.sbml.jsbml.ext.dyn
- Class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin extends DynSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -3432424478606541965L
  - Serialized Fields
    - listOfSpatialComponents
```
ListOf<T extends SBase> listOfSpatialComponents
```
      List of spatial components which describe compartment in space
- Class org.sbml.jsbml.ext.dyn.DynElement extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  2706393074014198836L
  - Serialized Fields
    - idRef
```
String idRef
```
      Id reference of model component
    - metaIdRef
```
String metaIdRef
```
      metaId reference of model component
- Class org.sbml.jsbml.ext.dyn.DynEventPlugin extends DynSBasePlugin implements Serializable
  
  serialVersionUID:
  
  3183158090508499169L
  - Serialized Fields
    - applyToAll
```
Boolean applyToAll
```
      Indicates whether all model components are affected by the dynEvent
    - listOfDynElements
```
ListOf<T extends SBase> listOfDynElements
```
      List of model components affected by the dynEvent
- Class org.sbml.jsbml.ext.dyn.DynSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  3120251908117414039L
  - Serialized Fields
    - cboTerm
```
Term cboTerm
```
      Cell Behavior Ontology Term associated with SBase object
- Class org.sbml.jsbml.ext.dyn.SpatialComponent extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  3081752496996673423L
  - Serialized Fields
    - spatialIndex
```
SpatialKind spatialIndex
```
      Identifies individual components of spatial location, orientation or force vector of an object
    - variable
```
String variable
```
      Stores the Id of a variable element defined in the model
Package org.sbml.jsbml.ext.fbc
- Class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  4959025739069449677L
- Class org.sbml.jsbml.ext.fbc.And extends LogicalOperator implements Serializable
  
  serialVersionUID:
  
  5964208695186298385L
- Class org.sbml.jsbml.ext.fbc.FBCModelPlugin extends AbstractFBCSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -7451190347195219863L
  - Serialized Fields
    - listOfFluxBounds
```
ListOf<T extends SBase> listOfFluxBounds
```
      Deprecated. Only defined in FBC version 1.
    - listOfGeneProducts
```
ListOf<T extends SBase> listOfGeneProducts
```
      Introduced to FBC in version 2.
    - listOfObjectives
```
ListOfObjectives listOfObjectives
```
    - strict
```
Boolean strict
```
      The mandatory attribute strict is used to apply an additional set of restrictions to the model. The strict attribute ensures that the Flux Balance Constraints package can be used to encode legacy FBA models expressible as Linear Programs (LP's) with software that is unable to analyze arbitrary mathematical expressions.
- Class org.sbml.jsbml.ext.fbc.FBCReactionPlugin extends AbstractFBCSBasePlugin implements Serializable
  
  serialVersionUID:
  
  8382172559018633373L
  - Serialized Fields
    - geneProductAssociation
```
GeneProductAssociation geneProductAssociation
```
    - lowerFluxBound
```
String lowerFluxBound
```
      A reference to a global parameter in the model for the lower bound of the reaction.
    - upperFluxBound
```
String upperFluxBound
```
      A reference to a global parameter in the model for the upper bound of the reaction.
- Class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin extends AbstractFBCSBasePlugin implements Serializable
  
  serialVersionUID:
  
  923773407400143272L
  - Serialized Fields
    - charge
```
int charge
```
    - chemicalFormula
```
String chemicalFormula
```
    - isSetCharge
```
boolean isSetCharge
```
- Class org.sbml.jsbml.ext.fbc.FluxBound extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8885319163985464653L
  - Serialized Fields
    - isSetValue
```
boolean isSetValue
```
      Deprecated.
    - operation
```
FluxBound.Operation operation
```
      Deprecated.
    - reaction
```
String reaction
```
      Deprecated.
    - value
```
Double value
```
      Deprecated.
- Class org.sbml.jsbml.ext.fbc.FluxObjective extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  246449689493121713L
  - Serialized Fields
    - coefficient
```
double coefficient
```
    - isSetCoefficient
```
boolean isSetCoefficient
```
    - reaction
```
String reaction
```
- Class org.sbml.jsbml.ext.fbc.GeneProduct extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -6117717488126260095L
  - Serialized Fields
    - label
```
String label
```
    - associatedSpecies
```
String associatedSpecies
```
- Class org.sbml.jsbml.ext.fbc.GeneProductAssociation extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  3080178338645314056L
  - Serialized Fields
    - association
```
Association association
```
- Class org.sbml.jsbml.ext.fbc.GeneProductRef extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -2978063936433918607L
  - Serialized Fields
    - geneProduct
```
String geneProduct
```
- Class org.sbml.jsbml.ext.fbc.ListOfObjectives extends ListOf<Objective> implements Serializable
  
  serialVersionUID:
  
  8684683156123793632L
  - Serialized Fields
    - activeObjective
```
String activeObjective
```
- Class org.sbml.jsbml.ext.fbc.LogicalOperator extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  7724258767809732147L
  - Serialized Fields
    - listOfAssociations
```
List<E> listOfAssociations
```
- Class org.sbml.jsbml.ext.fbc.Objective extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -3466570440778373634L
  - Serialized Fields
    - listOfFluxObjectives
```
ListOf<T extends SBase> listOfFluxObjectives
```
    - type
```
Objective.Type type
```
- Class org.sbml.jsbml.ext.fbc.Or extends LogicalOperator implements Serializable
  
  serialVersionUID:
  
  -4558397941057530943L
Package org.sbml.jsbml.ext.groups
- Class org.sbml.jsbml.ext.groups.Group extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  2361503116934849753L
  - Serialized Fields
    - kind
```
Group.Kind kind
```
      This attribute is used to indicate the nature of the group
    - listOfMembers
```
ListOf<T extends SBase> listOfMembers
```
- Class org.sbml.jsbml.ext.groups.GroupsModelPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  3334444867660252255L
  - Serialized Fields
    - listOfGroups
```
ListOf<T extends SBase> listOfGroups
```
- Class org.sbml.jsbml.ext.groups.ListOfMemberConstraint extends ListOf<MemberConstraint> implements Serializable
  
  serialVersionUID:
  
  -6306206652658549671L
  - Serialized Fields
    - id
```
String id
```
      Deprecated.
      
      id of the SBML component (can be optional depending on the level and version). Matches the id attribute of an element in a SBML file.
    - name
```
String name
```
      Deprecated.
      
      name of the SBML component (can be optional depending on the level and version). Matches the name attribute of an element in a SBML file.
    - membersShareType
```
boolean membersShareType
```
      Deprecated.
    - isSetMembersShareType
```
boolean isSetMembersShareType
```
      Deprecated.
- Class org.sbml.jsbml.ext.groups.Member extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  1726020714284762330L
  - Serialized Fields
    - idRef
```
String idRef
```
    - metaIdRef
```
String metaIdRef
```
- Class org.sbml.jsbml.ext.groups.MemberConstraint extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -5785868406244137379L
  - Serialized Fields
    - identicalAttribute
```
String identicalAttribute
```
      Deprecated.
    - distinctAttribute
```
String distinctAttribute
```
      Deprecated.
Package org.sbml.jsbml.ext.layout
- Class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph extends GraphicalObject implements Serializable
  
  serialVersionUID:
  
  3542638384361924654L
  - Serialized Fields
    - reference
```
String reference
```
      The identifier of the NamedSBase represented by this GraphicalObject.
- Class org.sbml.jsbml.ext.layout.BoundingBox extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -6371039558611201798L
  - Serialized Fields
    - dimensions
```
Dimensions dimensions
```
    - position
```
Point position
```
- Class org.sbml.jsbml.ext.layout.CompartmentGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  -831178362695634919L
  - Serialized Fields
    - order
```
Double order
```
- Class org.sbml.jsbml.ext.layout.CubicBezier extends LineSegment implements Serializable
  
  serialVersionUID:
  
  -6747242964512145076L
  - Serialized Fields
    - basePoint1
```
Point basePoint1
```
    - basePoint2
```
Point basePoint2
```
- Class org.sbml.jsbml.ext.layout.Curve extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -5435135643993920570L
  - Serialized Fields
    - listOfCurveSegments
```
ListOf<T extends SBase> listOfCurveSegments
```
- Class org.sbml.jsbml.ext.layout.CurveSegment extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -5085246314333062152L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - type
```
CurveSegment.Type type
```
- Class org.sbml.jsbml.ext.layout.Dimensions extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -6114634391235520057L
  - Serialized Fields
    - depth
```
double depth
```
    - height
```
double height
```
    - width
```
double width
```
- Class org.sbml.jsbml.ext.layout.GeneralGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  8770691813350594995L
  - Serialized Fields
    - curve
```
Curve curve
```
    - listOfReferenceGlyphs
```
ListOf<T extends SBase> listOfReferenceGlyphs
```
    - listOfSubGlyphs
```
ListOf<T extends SBase> listOfSubGlyphs
```
- Class org.sbml.jsbml.ext.layout.GraphicalObject extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  7587814013754302901L
  - Serialized Fields
    - boundingBox
```
BoundingBox boundingBox
```
    - metaidRef
```
String metaidRef
```
- Class org.sbml.jsbml.ext.layout.Layout extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  8866612784809904674L
  - Serialized Fields
    - dimensions
```
Dimensions dimensions
```
    - listOfAdditionalGraphicalObjects
```
ListOf<T extends SBase> listOfAdditionalGraphicalObjects
```
    - listOfCompartmentGlyphs
```
ListOf<T extends SBase> listOfCompartmentGlyphs
```
    - listOfReactionGlyphs
```
ListOf<T extends SBase> listOfReactionGlyphs
```
    - listOfSpeciesGlyphs
```
ListOf<T extends SBase> listOfSpeciesGlyphs
```
    - listOfTextGlyphs
```
ListOf<T extends SBase> listOfTextGlyphs
```
- Class org.sbml.jsbml.ext.layout.LayoutModelPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  4507170457817702658L
  - Serialized Fields
    - listOfLayouts
```
ListOf<T extends SBase> listOfLayouts
```
- Class org.sbml.jsbml.ext.layout.LineSegment extends CurveSegment implements Serializable
  
  serialVersionUID:
  
  -5085246314333062152L
  - Serialized Fields
    - end
```
Point end
```
    - start
```
Point start
```
- Class org.sbml.jsbml.ext.layout.Point extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -7464572763198848890L
  - Serialized Fields
    - x
```
double x
```
      the x coordinate
    - y
```
double y
```
      the y coordinate
    - z
```
double z
```
      the z coordinate
    - xmlElementName
```
String xmlElementName
```
      The name to be used when writing this point to XML.
- Class org.sbml.jsbml.ext.layout.ReactionGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  8770691813350594995L
  - Serialized Fields
    - curve
```
Curve curve
```
    - listOfSpeciesReferencesGlyphs
```
ListOf<T extends SBase> listOfSpeciesReferencesGlyphs
```
- Class org.sbml.jsbml.ext.layout.ReferenceGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  -8810905237933499989L
  - Serialized Fields
    - curve
```
Curve curve
```
    - role
```
String role
```
    - glyph
```
String glyph
```
- Class org.sbml.jsbml.ext.layout.SpeciesGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  1077785483575936434L
- Class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  -8810905237933499989L
  - Serialized Fields
    - curve
```
Curve curve
```
    - role
```
SpeciesReferenceRole role
```
    - speciesGlyph
```
String speciesGlyph
```
- Class org.sbml.jsbml.ext.layout.TextGlyph extends AbstractReferenceGlyph implements Serializable
  
  serialVersionUID:
  
  -2582985174711830815L
  - Serialized Fields
    - graphicalObject
```
String graphicalObject
```
    - text
```
String text
```
Package org.sbml.jsbml.ext.multi
- Class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType extends SpeciesType implements Serializable
  
  serialVersionUID:
  
  290729813426543362L
- Class org.sbml.jsbml.ext.multi.CompartmentReference extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  6455311889725292763L
  - Serialized Fields
    - compartment
```
String compartment
```
- Class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  798520971474589902L
  - Serialized Fields
    - speciesTypeComponentIndex
```
String speciesTypeComponentIndex
```
- Class org.sbml.jsbml.ext.multi.InSpeciesTypeBond extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8781651881389720582L
  - Serialized Fields
    - bindingSite1
```
String bindingSite1
```
    - bindingSite2
```
String bindingSite2
```
- Class org.sbml.jsbml.ext.multi.IntraSpeciesReaction extends Reaction implements Serializable
  
  serialVersionUID:
  
  7164677471117306392L
- Class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  4526455581462978178L
  - Serialized Fields
    - compartmentType
```
String compartmentType
```
    - isType
```
Boolean isType
```
    - listOfCompartmentReferences
```
ListOf<T extends SBase> listOfCompartmentReferences
```
- Class org.sbml.jsbml.ext.multi.MultiModelPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -2875299722787282885L
  - Serialized Fields
    - listOfSpeciesTypes
```
ListOf<T extends SBase> listOfSpeciesTypes
```
- Class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - compartmentReference
```
String compartmentReference
```
- Class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -5396837209115412420L
  - Serialized Fields
    - listOfOutwardBindingSites
```
ListOf<T extends SBase> listOfOutwardBindingSites
```
    - listOfSpeciesFeatures
```
ListOf<T extends SBase> listOfSpeciesFeatures
```
    - speciesType
```
String speciesType
```
- Class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin extends MultiSimpleSpeciesReferencePlugin implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - listOfSpeciesTypeComponentMapInProducts
```
ListOf<T extends SBase> listOfSpeciesTypeComponentMapInProducts
```
- Class org.sbml.jsbml.ext.multi.OutwardBindingSite extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  2368487517657386175L
  - Serialized Fields
    - bindingStatus
```
BindingStatus bindingStatus
```
    - component
```
String component
```
- Class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8059031235221209834L
  - Serialized Fields
    - numericValue
```
String numericValue
```
- Class org.sbml.jsbml.ext.multi.SpeciesFeature extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - speciesFeatureType
```
String speciesFeatureType
```
    - occur
```
Integer occur
```
    - component
```
String component
```
    - listOfSpeciesFeatureValues
```
ListOf<T extends SBase> listOfSpeciesFeatureValues
```
- Class org.sbml.jsbml.ext.multi.SpeciesFeatureChange extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - reactantSpeciesFeature
```
String reactantSpeciesFeature
```
    - productSpeciesFeature
```
String productSpeciesFeature
```
- Class org.sbml.jsbml.ext.multi.SpeciesFeatureType extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -1796119514784158560L
  - Serialized Fields
    - listOfPossibleSpeciesFeatureValues
```
ListOf<T extends SBase> listOfPossibleSpeciesFeatureValues
```
    - occur
```
Integer occur
```
- Class org.sbml.jsbml.ext.multi.SpeciesFeatureValue extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
String value
```
- Class org.sbml.jsbml.ext.multi.SpeciesType extends SpeciesType implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - compartment
```
String compartment
```
    - listOfInSpeciesTypeBonds
```
ListOf<T extends SBase> listOfInSpeciesTypeBonds
```
    - listOfSpeciesFeatureTypes
```
ListOf<T extends SBase> listOfSpeciesFeatureTypes
```
    - listOfSpeciesTypeComponentIndexes
```
ListOf<T extends SBase> listOfSpeciesTypeComponentIndexes
```
    - listOfSpeciesTypeInstances
```
ListOf<T extends SBase> listOfSpeciesTypeInstances
```
- Class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  8707971676849587247L
  - Serialized Fields
    - component
```
String component
```
    - identifyingParent
```
String identifyingParent
```
- Class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - reactant
```
String reactant
```
    - reactantComponent
```
String reactantComponent
```
    - productComponent
```
String productComponent
```
    - listOfSpeciesFeatureChanges
```
ListOf<T extends SBase> listOfSpeciesFeatureChanges
```
- Class org.sbml.jsbml.ext.multi.SpeciesTypeInstance extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  1775590492963078468L
  - Serialized Fields
    - speciesType
```
String speciesType
```
    - compartmentReference
```
String compartmentReference
```
Package org.sbml.jsbml.ext.qual
- Class org.sbml.jsbml.ext.qual.FunctionTerm extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  -3456373304133826017L
  - Serialized Fields
    - resultLevel
```
Integer resultLevel
```
    - defaultTerm
```
boolean defaultTerm
```
- Class org.sbml.jsbml.ext.qual.Input extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -3370025650545068132L
  - Serialized Fields
    - qualitativeSpecies
```
String qualitativeSpecies
```
    - transitionEffect
```
InputTransitionEffect transitionEffect
```
    - thresholdLevel
```
Integer thresholdLevel
```
    - sign
```
Sign sign
```
- Class org.sbml.jsbml.ext.qual.Output extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -6392002023918667156L
  - Serialized Fields
    - qualitativeSpecies
```
String qualitativeSpecies
```
    - transitionEffect
```
OutputTransitionEffect transitionEffect
```
    - outputLevel
```
Integer outputLevel
```
- Class org.sbml.jsbml.ext.qual.QualConstants extends PropertyChangeEvent implements Serializable
  
  serialVersionUID:
  
  944717095818356337L
- Class org.sbml.jsbml.ext.qual.QualitativeModel extends QualModelPlugin implements Serializable
  
  serialVersionUID:
  
  -2167310699373978921L
- Class org.sbml.jsbml.ext.qual.QualitativeSpecies extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -6048861420699176889L
  - Serialized Fields
    - compartment
```
String compartment
```
    - constant
```
Boolean constant
```
    - initialLevel
```
Integer initialLevel
```
    - maxLevel
```
Integer maxLevel
```
- Class org.sbml.jsbml.ext.qual.QualModelPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  1861588578911387944L
  - Serialized Fields
    - listOfQualitativeSpecies
```
ListOf<T extends SBase> listOfQualitativeSpecies
```
    - listOfTransitions
```
ListOf<T extends SBase> listOfTransitions
```
- Class org.sbml.jsbml.ext.qual.Transition extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  8343744362262634585L
  - Serialized Fields
    - listOfFunctionTerms
```
ListOf<T extends SBase> listOfFunctionTerms
```
    - listOfInputs
```
ListOf<T extends SBase> listOfInputs
```
    - listOfOutputs
```
ListOf<T extends SBase> listOfOutputs
```
Package org.sbml.jsbml.ext.render
- Class org.sbml.jsbml.ext.render.AbstractRenderPlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -4225426173177528441L
  - Serialized Fields
    - versionMajor
```
Short versionMajor
```
    - versionMinor
```
Short versionMinor
```
    - renderInformation
```
GlobalRenderInformation renderInformation
```
- Class org.sbml.jsbml.ext.render.ColorDefinition extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  8904459123022343452L
  - Serialized Fields
    - value
```
Color value
```
- Class org.sbml.jsbml.ext.render.Ellipse extends GraphicalPrimitive2D implements Serializable
  
  serialVersionUID:
  
  -7679215241987476130L
  - Serialized Fields
    - cx
```
Double cx
```
    - cy
```
Double cy
```
    - cz
```
Double cz
```
    - rx
```
Double rx
```
    - ry
```
Double ry
```
    - absoluteCx
```
Boolean absoluteCx
```
    - absoluteCy
```
Boolean absoluteCy
```
    - absoluteCz
```
Boolean absoluteCz
```
    - absoluteRx
```
Boolean absoluteRx
```
    - absoluteRy
```
Boolean absoluteRy
```
- Class org.sbml.jsbml.ext.render.GlobalRenderInformation extends RenderInformationBase implements Serializable
  
  serialVersionUID:
  
  855680727119080659L
  - Serialized Fields
    - listOfStyles
```
ListOf<T extends SBase> listOfStyles
```
- Class org.sbml.jsbml.ext.render.GradientBase extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -3921074024567604440L
  - Serialized Fields
    - spreadMethod
```
org.sbml.jsbml.ext.render.GradientBase.Spread spreadMethod
```
    - listOfGradientStops
```
ListOf<T extends SBase> listOfGradientStops
```
- Class org.sbml.jsbml.ext.render.GradientStop extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  7400974339251884133L
  - Serialized Fields
    - offset
```
Double offset
```
    - stopColor
```
String stopColor
```
- Class org.sbml.jsbml.ext.render.GraphicalPrimitive1D extends Transformation2D implements Serializable
  
  serialVersionUID:
  
  3705246334810811216L
  - Serialized Fields
    - stroke
```
String stroke
```
    - strokeDashArray
```
Short[] strokeDashArray
```
    - strokeWidth
```
Double strokeWidth
```
- Class org.sbml.jsbml.ext.render.GraphicalPrimitive2D extends GraphicalPrimitive1D implements Serializable
  
  serialVersionUID:
  
  -5666416071124784541L
  - Serialized Fields
    - fill
```
String fill
```
    - fillRule
```
GraphicalPrimitive2D.FillRule fillRule
```
- Class org.sbml.jsbml.ext.render.Image extends Transformation2D implements Serializable
  
  serialVersionUID:
  
  6031110715160806863L
  - Serialized Fields
    - x
```
Double x
```
    - y
```
Double y
```
    - z
```
Double z
```
    - width
```
Double width
```
    - height
```
Double height
```
    - absoluteX
```
Boolean absoluteX
```
    - absoluteY
```
Boolean absoluteY
```
    - absoluteZ
```
Boolean absoluteZ
```
    - absoluteWidth
```
Boolean absoluteWidth
```
    - absoluteHeight
```
Boolean absoluteHeight
```
    - href
```
String href
```
- Class org.sbml.jsbml.ext.render.LinearGradient extends GradientBase implements Serializable
  
  serialVersionUID:
  
  825789189989621388L
  - Serialized Fields
    - x1
```
Double x1
```
    - y1
```
Double y1
```
    - z1
```
Double z1
```
    - x2
```
Double x2
```
    - y2
```
Double y2
```
    - z2
```
Double z2
```
- Class org.sbml.jsbml.ext.render.LineEnding extends GraphicalPrimitive2D implements Serializable
  
  serialVersionUID:
  
  938880502591638386L
  - Serialized Fields
    - enableRotationMapping
```
Boolean enableRotationMapping
```
    - boundingBox
```
BoundingBox boundingBox
```
    - group
```
RenderGroup group
```
- Class org.sbml.jsbml.ext.render.LocalRenderInformation extends RenderInformationBase implements Serializable
  
  serialVersionUID:
  
  -8056565578647428405L
  - Serialized Fields
    - listOfLocalStyles
```
ListOf<T extends SBase> listOfLocalStyles
```
- Class org.sbml.jsbml.ext.render.LocalStyle extends Style implements Serializable
  
  serialVersionUID:
  
  4976081641247006722L
  - Serialized Fields
    - idList
```
String[] idList
```
- Class org.sbml.jsbml.ext.render.Polygon extends GraphicalPrimitive2D implements Serializable
  
  serialVersionUID:
  
  9207043017589271103L
  - Serialized Fields
    - listOfElements
```
ListOf<T extends SBase> listOfElements
```
- Class org.sbml.jsbml.ext.render.RadialGradient extends GradientBase implements Serializable
  
  serialVersionUID:
  
  -6976786676644704255L
  - Serialized Fields
    - absoluteCx
```
Boolean absoluteCx
```
    - absoluteCy
```
Boolean absoluteCy
```
    - absoluteCz
```
Boolean absoluteCz
```
    - absoluteR
```
Boolean absoluteR
```
    - absoluteFx
```
Boolean absoluteFx
```
    - absoluteFy
```
Boolean absoluteFy
```
    - absoluteFz
```
Boolean absoluteFz
```
    - cx
```
Double cx
```
    - cy
```
Double cy
```
    - cz
```
Double cz
```
    - r
```
Double r
```
    - fx
```
Double fx
```
    - fy
```
Double fy
```
    - fz
```
Double fz
```
- Class org.sbml.jsbml.ext.render.Rectangle extends GraphicalPrimitive2D implements Serializable
  
  serialVersionUID:
  
  -4314411828208615411L
  - Serialized Fields
    - x
```
Double x
```
    - y
```
Double y
```
    - z
```
Double z
```
    - width
```
Double width
```
    - height
```
Double height
```
    - absoluteX
```
Boolean absoluteX
```
    - absoluteY
```
Boolean absoluteY
```
    - absoluteZ
```
Boolean absoluteZ
```
    - absoluteWidth
```
Boolean absoluteWidth
```
    - absoluteHeight
```
Boolean absoluteHeight
```
    - rx
```
Double rx
```
    - ry
```
Double ry
```
    - absoluteRx
```
Boolean absoluteRx
```
    - absoluteRy
```
Boolean absoluteRy
```
- Class org.sbml.jsbml.ext.render.RenderCubicBezier extends RenderPoint implements Serializable
  
  serialVersionUID:
  
  -2426257418589249467L
  - Serialized Fields
    - absoluteX1
```
Boolean absoluteX1
```
    - absoluteY1
```
Boolean absoluteY1
```
    - absoluteZ1
```
Boolean absoluteZ1
```
    - absoluteX2
```
Boolean absoluteX2
```
    - absoluteY2
```
Boolean absoluteY2
```
    - absoluteZ2
```
Boolean absoluteZ2
```
    - x1
```
Double x1
```
    - y1
```
Double y1
```
    - z1
```
Double z1
```
    - x2
```
Double x2
```
    - y2
```
Double y2
```
    - z2
```
Double z2
```
- Class org.sbml.jsbml.ext.render.RenderCurve extends GraphicalPrimitive1D implements Serializable
  
  serialVersionUID:
  
  -1941713884972334826L
  - Serialized Fields
    - startHead
```
String startHead
```
    - endHead
```
String endHead
```
    - listOfElements
```
ListOf<T extends SBase> listOfElements
```
- Class org.sbml.jsbml.ext.render.RenderGroup extends GraphicalPrimitive2D implements Serializable
  
  serialVersionUID:
  
  2302368129571619877L
  - Serialized Fields
    - id
```
String id
```
    - fontFamily
```
FontFamily fontFamily
```
    - fontSize
```
Short fontSize
```
    - fontWeightBold
```
Boolean fontWeightBold
```
    - fontStyleItalic
```
Boolean fontStyleItalic
```
    - textAnchor
```
TextAnchor textAnchor
```
    - vTextAnchor
```
VTextAnchor vTextAnchor
```
    - startHead
```
String startHead
```
    - endHead
```
String endHead
```
    - listOfElements
```
ListOf<T extends SBase> listOfElements
```
- Class org.sbml.jsbml.ext.render.RenderInformationBase extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -9096154126197866584L
  - Serialized Fields
    - programName
```
String programName
```
    - programVersion
```
String programVersion
```
    - referenceRenderInformation
```
String referenceRenderInformation
```
    - backgroundColor
```
Color backgroundColor
```
    - listOfColorDefinitions
```
ListOf<T extends SBase> listOfColorDefinitions
```
    - listOfGradientDefinitions
```
ListOf<T extends SBase> listOfGradientDefinitions
```
    - listOfLineEndings
```
ListOf<T extends SBase> listOfLineEndings
```
- Class org.sbml.jsbml.ext.render.RenderLayoutPlugin extends AbstractRenderPlugin implements Serializable
  
  serialVersionUID:
  
  6636572993878851570L
  - Serialized Fields
    - listOfLocalRenderInformation
```
ListOf<T extends SBase> listOfLocalRenderInformation
```
- Class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin extends AbstractRenderPlugin implements Serializable
  
  serialVersionUID:
  
  -4727110538908666931L
  - Serialized Fields
    - listOfGlobalRenderInformation
```
ListOf<T extends SBase> listOfGlobalRenderInformation
```
- Class org.sbml.jsbml.ext.render.RenderPoint extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  6792387139122188270L
  - Serialized Fields
    - absoluteX
```
Boolean absoluteX
```
    - absoluteY
```
Boolean absoluteY
```
    - absoluteZ
```
Boolean absoluteZ
```
    - x
```
Double x
```
    - y
```
Double y
```
    - z
```
Double z
```
- Class org.sbml.jsbml.ext.render.Style extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -4660813321564690910L
  - Serialized Fields
    - group
```
RenderGroup group
```
    - roleList
```
String[] roleList
```
    - typeList
```
String[] typeList
```
- Class org.sbml.jsbml.ext.render.Text extends GraphicalPrimitive1D implements Serializable
  
  serialVersionUID:
  
  -7468181076596795203L
  - Serialized Fields
    - absoluteX
```
Boolean absoluteX
```
    - absoluteY
```
Boolean absoluteY
```
    - absoluteZ
```
Boolean absoluteZ
```
    - fontFamily
```
FontFamily fontFamily
```
    - fontSize
```
Short fontSize
```
    - fontWeightBold
```
Boolean fontWeightBold
```
    - fontStyleItalic
```
Boolean fontStyleItalic
```
    - textAnchor
```
TextAnchor textAnchor
```
    - vTextAnchor
```
VTextAnchor vTextAnchor
```
    - x
```
Double x
```
    - y
```
Double y
```
    - z
```
Double z
```
- Class org.sbml.jsbml.ext.render.Transformation extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  1845276761656867150L
  - Serialized Fields
    - transform
```
Double[] transform
```
- Class org.sbml.jsbml.ext.render.Transformation2D extends Transformation implements Serializable
  
  serialVersionUID:
  
  -1737694519381619398L
  - Serialized Fields
    - transform
```
Double[] transform
```
Package org.sbml.jsbml.ext.req
- Class org.sbml.jsbml.ext.req.ChangedMath extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  2446721938903003641L
  - Serialized Fields
    - viableWithoutChange
```
Boolean viableWithoutChange
```
      The viableWithoutChange attribute is required, and is of type boolean. The attribute should be used to indicate whether an interpreter that does not understand the package from the changedBy attribute would have an interpretable version of the mathematics for the given component in a model. This can be established using two criteria: “Complete” and “Workable”. Obviously, if the math being interpreted is incomplete, the viableWithoutChange attribute must be false. If the math is complete, then whether the solution is “workable” requires a judgment call on the part of the modeler: if the modeler feels that the alternative version makes sense in an alternative context, they may set the attribute value to true; conversely, if they feel that the resulting model component makes no sense, even if technically “complete”, then they should set the attribute value to false.
    - changedBy
```
String changedBy
```
      The changedBy attribute is required, and is of type string. The attribute must be set to the namespace URI of the SBML Level 3 package that redefines or alters the mathematical semantics of the parent object. In other words, if the mathematical semantics of a given component C in a model is changed by the use of a Level 3 package P, then C can be given a ChangedMath child, and its attribute changedBy should be P's namespace URI.
- Class org.sbml.jsbml.ext.req.ReqSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -8899476363934112466L
  - Serialized Fields
    - listOfChangedMaths
```
ListOf<T extends SBase> listOfChangedMaths
```
Package org.sbml.jsbml.ext.spatial
- Class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -1814806955800042477L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialId
```
String spatialId
```
- Class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -75143209163226722L
- Class org.sbml.jsbml.ext.spatial.AdjacentDomains extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  1600690320824551145L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domain1
```
String domain1
```
    - domain2
```
String domain2
```
- Class org.sbml.jsbml.ext.spatial.AdvectionCoefficient extends ParameterType implements Serializable
  
  serialVersionUID:
  
  8982184068116596444L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - coordinate
```
CoordinateKind coordinate
```
- Class org.sbml.jsbml.ext.spatial.AnalyticGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -6680739495215471035L
  - Serialized Fields
    - listOfAnalyticVolumes
```
ListOf<T extends SBase> listOfAnalyticVolumes
```
- Class org.sbml.jsbml.ext.spatial.AnalyticVolume extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  1757917501241390228L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialId
```
String spatialId
```
    - domainType
```
String domainType
```
    - functionType
```
FunctionKind functionType
```
    - ordinal
```
Integer ordinal
```
- Class org.sbml.jsbml.ext.spatial.Boundary extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -5283759970799753982L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - value
```
Double value
```
- Class org.sbml.jsbml.ext.spatial.BoundaryCondition extends ParameterType implements Serializable
  
  serialVersionUID:
  
  -6986768113234565819L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - boundaryDomainType
```
String boundaryDomainType
```
    - coordinateBoundary
```
String coordinateBoundary
```
    - type
```
BoundaryConditionKind type
```
- Class org.sbml.jsbml.ext.spatial.CompartmentMapping extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -4623759168043277022L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - unitSize
```
Double unitSize
```
- Class org.sbml.jsbml.ext.spatial.CoordinateComponent extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -3561130269969678307L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - type
```
CoordinateKind type
```
    - boundaryMaximum
```
Boundary boundaryMaximum
```
    - boundaryMinimum
```
Boundary boundaryMinimum
```
    - unit
```
String unit
```
- Class org.sbml.jsbml.ext.spatial.CoordinateReference extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7651871640808157489L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      Deprecated.
      
      A Logger for this class.
    - coordinate
```
CoordinateKind coordinate
```
      Deprecated.
- Class org.sbml.jsbml.ext.spatial.CSGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -3162376343741365280L
  - Serialized Fields
    - listOfCSGObjects
```
ListOf<T extends SBase> listOfCSGObjects
```
- Class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  1247170964151052926L
  - Serialized Fields
    - forwardTransformation
```
TransformationComponent forwardTransformation
```
    - reverseTransformation
```
TransformationComponent reverseTransformation
```
- Class org.sbml.jsbml.ext.spatial.CSGNode extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  5499821335582691196L
- Class org.sbml.jsbml.ext.spatial.CSGObject extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  1385748485171648666L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - ordinal
```
Integer ordinal
```
    - csgNode
```
CSGNode csgNode
```
- Class org.sbml.jsbml.ext.spatial.CSGPrimitive extends CSGNode implements Serializable
  
  serialVersionUID:
  
  -6783804853380306509L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - primitiveType
```
PrimitiveKind primitiveType
```
- Class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive extends CSGNode implements Serializable
  
  serialVersionUID:
  
  303742063326104808L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - csgObjectRef
```
String csgObjectRef
```
- Class org.sbml.jsbml.ext.spatial.CSGRotation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  -4799604235135248586L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - rotateAxisX
```
Double rotateAxisX
```
    - rotateAxisY
```
Double rotateAxisY
```
    - rotateAxisZ
```
Double rotateAxisZ
```
    - rotateAngleInRadians
```
Double rotateAngleInRadians
```
- Class org.sbml.jsbml.ext.spatial.CSGScale extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  7021488698800177528L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - scaleX
```
Double scaleX
```
    - scaleY
```
Double scaleY
```
    - scaleZ
```
Double scaleZ
```
- Class org.sbml.jsbml.ext.spatial.CSGSetOperator extends CSGNode implements Serializable
  
  serialVersionUID:
  
  3448308755493169761L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - operationType
```
SetOperation operationType
```
    - complementA
```
String complementA
```
    - complementB
```
String complementB
```
    - listOfCSGNodes
```
ListOf<T extends SBase> listOfCSGNodes
```
- Class org.sbml.jsbml.ext.spatial.CSGTransformation extends CSGNode implements Serializable
  
  serialVersionUID:
  
  5388780141573233538L
  - Serialized Fields
    - csgNode
```
CSGNode csgNode
```
- Class org.sbml.jsbml.ext.spatial.CSGTranslation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  7030963917812170311L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - translateX
```
Double translateX
```
    - translateY
```
Double translateY
```
    - translateZ
```
Double translateZ
```
- Class org.sbml.jsbml.ext.spatial.DiffusionCoefficient extends ParameterType implements Serializable
  
  serialVersionUID:
  
  1233063375698575897L
  - Serialized Fields
    - diffusionKind
```
DiffusionKind diffusionKind
```
    - coordinateReference1
```
CoordinateKind coordinateReference1
```
    - coordinateReference2
```
CoordinateKind coordinateReference2
```
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
- Class org.sbml.jsbml.ext.spatial.Domain extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  7959434109047369076L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - listOfInteriorPoints
```
ListOf<T extends SBase> listOfInteriorPoints
```
- Class org.sbml.jsbml.ext.spatial.DomainType extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -1429902642364213170L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialDimensions
```
Integer spatialDimensions
```
- Class org.sbml.jsbml.ext.spatial.Geometry extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  9115597691155572976L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - listOfCoordinateComponents
```
ListOf<T extends SBase> listOfCoordinateComponents
```
    - listOfDomainTypes
```
ListOf<T extends SBase> listOfDomainTypes
```
    - listOfDomains
```
ListOf<T extends SBase> listOfDomains
```
    - listOfAdjacentDomains
```
ListOf<T extends SBase> listOfAdjacentDomains
```
    - listOfGeometryDefinitions
```
ListOf<T extends SBase> listOfGeometryDefinitions
```
    - listOfSampledFields
```
ListOf<T extends SBase> listOfSampledFields
```
    - coordinateSystem
```
GeometryKind coordinateSystem
```
- Class org.sbml.jsbml.ext.spatial.GeometryDefinition extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  211166389798247646L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - isActive
```
Boolean isActive
```
- Class org.sbml.jsbml.ext.spatial.InteriorPoint extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  5525511951071345435L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - coord1
```
Double coord1
```
    - coord2
```
Double coord2
```
    - coord3
```
Double coord3
```
- Class org.sbml.jsbml.ext.spatial.MixedGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -7544034155315224945L
  - Serialized Fields
    - listOfGeometryDefinitions
```
ListOf<T extends SBase> listOfGeometryDefinitions
```
    - listOfOrdinalMappings
```
ListOf<T extends SBase> listOfOrdinalMappings
```
- Class org.sbml.jsbml.ext.spatial.OrdinalMapping extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7174553771288567408L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - geometryDefinition
```
String geometryDefinition
```
    - ordinal
```
Integer ordinal
```
- Class org.sbml.jsbml.ext.spatial.ParameterType extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  1359841900912406174L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spId
```
String spId
```
      Refers to SpIdRef in the documentation
    - speciesRef
```
String speciesRef
```
      Refers to species object that the parameter is associated with
- Class org.sbml.jsbml.ext.spatial.ParametricGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  5947368889263003716L
  - Serialized Fields
    - spatialPoints
```
SpatialPoints spatialPoints
```
    - listOfParametricObjects
```
ListOf<T extends SBase> listOfParametricObjects
```
- Class org.sbml.jsbml.ext.spatial.ParametricObject extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8093810090391511545L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - polygonType
```
PolygonKind polygonType
```
    - domainType
```
String domainType
```
    - compression
```
CompressionKind compression
```
    - pointIndex
```
String pointIndex
```
    - pointIndexLength
```
Integer pointIndexLength
```
    - dataType
```
DataKind dataType
```
- Class org.sbml.jsbml.ext.spatial.PolygonObject extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -4878021358939009394L
  - Serialized Fields
    - pointIndex
```
Integer[] pointIndex
```
      Deprecated.
- Class org.sbml.jsbml.ext.spatial.SampledField extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  4345673559248715940L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - numSamples1
```
Integer numSamples1
```
    - numSamples2
```
Integer numSamples2
```
    - numSamples3
```
Integer numSamples3
```
    - interpolation
```
InterpolationKind interpolation
```
    - compression
```
CompressionKind compression
```
    - samples
```
String samples
```
    - samplesLength
```
Integer samplesLength
```
    - dataType
```
DataKind dataType
```
    - data
```
XMLNode data
```
- Class org.sbml.jsbml.ext.spatial.SampledFieldGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -1541677165317653439L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - listOfSampledVolumes
```
ListOf<T extends SBase> listOfSampledVolumes
```
    - sampledField
```
String sampledField
```
- Class org.sbml.jsbml.ext.spatial.SampledVolume extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8253664900275697978L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - sampledValue
```
Double sampledValue
```
    - minValue
```
Double minValue
```
    - maxValue
```
Double maxValue
```
- Class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  1363097365327594433L
  - Serialized Fields
    - compartmentMapping
```
CompartmentMapping compartmentMapping
```
- Class org.sbml.jsbml.ext.spatial.SpatialModelPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  8449591192464040411L
  - Serialized Fields
    - geometry
```
Geometry geometry
```
    - spatialIdMap
```
HashMap<K,V> spatialIdMap
```
- Class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -3766260342134204275L
  - Serialized Fields
    - param
```
ParameterType param
```
- Class org.sbml.jsbml.ext.spatial.SpatialPoints extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -3467717442431545263L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - compression
```
CompressionKind compression
```
    - arrayDataLength
```
Integer arrayDataLength
```
    - dataType
```
DataKind dataType
```
    - arrayData
```
String arrayData
```
- Class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -2154884901226244123L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - isLocal
```
Boolean isLocal
```
- Class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  1636970127352490380L
  - Serialized Fields
    - spatial
```
Boolean spatial
```
- Class org.sbml.jsbml.ext.spatial.SpatialSymbolReference extends ParameterType implements Serializable
  
  serialVersionUID:
  
  -8906622500258765056L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialRef
```
String spatialRef
```
- Class org.sbml.jsbml.ext.spatial.TransformationComponent extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -2905551100912455549L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - components
```
Double[] components
```
    - componentsLength
```
Integer componentsLength
```
Package org.sbml.jsbml.math
- Class org.sbml.jsbml.math.AbstractASTNode extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  -3581414034848792129L
  - Serialized Fields
    - parentSBMLObject
```
MathContainer parentSBMLObject
```
      The container that holds this AbstractASTNode.
    - strict
```
boolean strict
```
      Specifies strictness. When true, ASTUnaryFunction and ASTBinaryFunction nodes can only contain the specified # of children. When false, there is a bit of leeway (i.e. ASTUnaryFunction can contain more than one child) (not recommended).
    - type
```
ASTNode.Type type
```
      The type of this node
    - id
```
String id
```
      The style of this MathML element
    - style
```
String style
```
      The style of this MathML element
    - mathMLClass
```
String mathMLClass
```
      class attribute for MathML element
- Class org.sbml.jsbml.math.ASTArithmeticOperatorNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  -7712374792704509306L
- Class org.sbml.jsbml.math.ASTBinaryFunctionNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  -4036869111918452252L
- Class org.sbml.jsbml.math.ASTBoolean extends AbstractASTNode implements Serializable
  
  serialVersionUID:
  
  7734825161484457512L
- Class org.sbml.jsbml.math.ASTCiFunctionNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  -3672567229521583280L
  - Serialized Fields
    - definitionURL
```
String definitionURL
```
      definitionURL attribute for MathML element
    - name
```
String name
```
      The name of the MathML element represented by this ASTCiFunctionNode.
    - refId
```
String refId
```
      refId attribute for MathML element
- Class org.sbml.jsbml.math.ASTCiNumberNode extends ASTNumber implements Serializable
  
  serialVersionUID:
  
  -6842905005458975038L
  - Serialized Fields
    - definitionURL
```
String definitionURL
```
      definitionURL attribute for MathML element
    - refId
```
String refId
```
      The name of the MathML element represented by this ASTCiNumberNode.
- Class org.sbml.jsbml.math.ASTCnExponentialNode extends ASTCnNumberNode<ValuePair<Integer,Double>> implements Serializable
  
  serialVersionUID:
  
  2454959490592406140L
- Class org.sbml.jsbml.math.ASTCnIntegerNode extends ASTCnNumberNode<Integer> implements Serializable
  
  serialVersionUID:
  
  5478874063299110266L
- Class org.sbml.jsbml.math.ASTCnNumberNode extends ASTNumber implements Serializable
  
  serialVersionUID:
  
  5649353555778706414L
  - Serialized Fields
    - number
```
Object number
```
      Numerical base for MathML element
    - units
```
String units
```
      units attribute for MathML element
    - variable
```
String variable
```
      variable attribute for MathML element
- Class org.sbml.jsbml.math.ASTCnRationalNode extends ASTCnNumberNode<ValuePair<Integer,Integer>> implements Serializable
  
  serialVersionUID:
  
  -6844137576018089451L
- Class org.sbml.jsbml.math.ASTCnRealNode extends ASTCnNumberNode<Double> implements Serializable
  
  serialVersionUID:
  
  6142072741733701867L
- Class org.sbml.jsbml.math.ASTConstantNumber extends ASTNumber implements Serializable
  
  serialVersionUID:
  
  -6872240196225149289L
- Class org.sbml.jsbml.math.ASTCSymbolAvogadroNode extends ASTConstantNumber implements Serializable
  
  serialVersionUID:
  
  8877555355478243825L
  - Serialized Fields
    - definitionURL
```
String definitionURL
```
      definitionURL attribute for MathML element
    - encoding
```
String encoding
```
      encodingURL attribute for MathML element
    - name
```
String name
```
      The name of the MathML element represented by this ASTCSymbolAvogadroNode.
- Class org.sbml.jsbml.math.ASTCSymbolDelayNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  -5565842362242854303L
  - Serialized Fields
    - name
```
String name
```
      name attribute for MathML element
    - definitionURL
```
String definitionURL
```
      definitionURL attribute for MathML element
    - encoding
```
String encoding
```
      encoding attribute for MathML element
- Class org.sbml.jsbml.math.ASTCSymbolTimeNode extends ASTNumber implements Serializable
  
  serialVersionUID:
  
  3788959657360296692L
  - Serialized Fields
    - encoding
```
String encoding
```
      The encoding of this csymbol element
    - definitionURL
```
String definitionURL
```
      definitionURL attribute for MathML element
    - name
```
String name
```
      The name of the MathML element represented by this ASTCSymbolTimeNode.
- Class org.sbml.jsbml.math.ASTDivideNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  -3326276752533782545L
- Class org.sbml.jsbml.math.ASTFunction extends AbstractASTNode implements Serializable
  
  serialVersionUID:
  
  -6517879717740815227L
  - Serialized Fields
    - listOfNodes
```
List<E> listOfNodes
```
      Child nodes.
    - name
```
String name
```
      The name of the MathML element represented by this ASTFunction.
- Class org.sbml.jsbml.math.ASTHyperbolicNode extends ASTUnaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  -3473804919513699915L
- Class org.sbml.jsbml.math.ASTLambdaFunctionNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  3189146748998908918L
- Class org.sbml.jsbml.math.ASTLogarithmNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  5350043898749220594L
- Class org.sbml.jsbml.math.ASTLogicalOperatorNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  -4435213506053944443L
- Class org.sbml.jsbml.math.ASTMinusNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  652890680815928656L
- Class org.sbml.jsbml.math.ASTNumber extends AbstractASTNode implements Serializable
  
  serialVersionUID:
  
  -5149881530966539809L
- Class org.sbml.jsbml.math.ASTPiecewiseFunctionNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  -8915335867694118907L
- Class org.sbml.jsbml.math.ASTPlusNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  -2608955943324026802L
- Class org.sbml.jsbml.math.ASTPowerNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  460517738739696555L
- Class org.sbml.jsbml.math.ASTQualifierNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  6765565477557495208L
- Class org.sbml.jsbml.math.ASTRelationalOperatorNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  5739652236362075869L
- Class org.sbml.jsbml.math.ASTRootNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  -8803559492792642628L
- Class org.sbml.jsbml.math.ASTTimesNode extends ASTBinaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  6946535893613905831L
- Class org.sbml.jsbml.math.ASTTrigonometricNode extends ASTUnaryFunctionNode implements Serializable
  
  serialVersionUID:
  
  8375728473620884311L
- Class org.sbml.jsbml.math.ASTUnaryFunctionNode extends ASTFunction implements Serializable
  
  serialVersionUID:
  
  -8088831456874690229L
- Class org.sbml.jsbml.math.ASTUnknown extends Object implements Serializable
  
  serialVersionUID:
  
  7504401136695608469L
Package org.sbml.jsbml.math.compiler
- Class org.sbml.jsbml.math.compiler.UnitException extends SBMLException implements Serializable
  
  serialVersionUID:
  
  -5630929507888356877L
Package org.sbml.jsbml.math.parser
- Class org.sbml.jsbml.math.parser.ParseException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentToken
```
Token currentToken
```
      This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.
    - expectedTokenSequences
```
int[][] expectedTokenSequences
```
      Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.
    - tokenImage
```
String[] tokenImage
```
      This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.
    - eol
```
String eol
```
      The end of line string for this machine.
- Class org.sbml.jsbml.math.parser.Token extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - kind
```
int kind
```
      An integer that describes the kind of this token. This numbering system is determined by JavaCCParser, and a table of these numbers is stored in the file ...Constants.java.
    - beginLine
```
int beginLine
```
      The line number of the first character of this Token.
    - beginColumn
```
int beginColumn
```
      The column number of the first character of this Token.
    - endLine
```
int endLine
```
      The line number of the last character of this Token.
    - endColumn
```
int endColumn
```
      The column number of the last character of this Token.
    - image
```
String image
```
      The string image of the token.
    - next
```
Token next
```
      A reference to the next regular (non-special) token from the input stream. If this is the last token from the input stream, or if the token manager has not read tokens beyond this one, this field is set to null. This is true only if this token is also a regular token. Otherwise, see below for a description of the contents of this field.
    - specialToken
```
Token specialToken
```
      This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token. If there are no such special tokens, this field is set to null. When there are more than one such special token, this field refers to the last of these special tokens, which in turn refers to the next previous special token through its specialToken field, and so on until the first special token (whose specialToken field is null). The next fields of special tokens refer to other special tokens that immediately follow it (without an intervening regular token). If there is no such token, this field is null.
- Class org.sbml.jsbml.math.parser.TokenMgrError extends Error implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - errorCode
```
int errorCode
```
      Indicates the reason why the exception is thrown. It will have one of the above 4 values.
Package org.sbml.jsbml.ontology
- Class org.sbml.jsbml.ontology.Term extends Object implements Serializable
  
  serialVersionUID:
  
  -2753964994128680208L
  - Serialized Fields
    - id
```
String id
```
      The base properties of this Term.
    - name
```
String name
```
      The base properties of this Term.
    - def
```
String def
```
      The base properties of this Term.
    - term
```
org.biojava3.ontology.Term term
```
      The underlying BioJava Term.
- Class org.sbml.jsbml.ontology.Triple extends Object implements Serializable
  
  serialVersionUID:
  
  7289048361260650338L
  - Serialized Fields
    - triple
```
org.biojava3.ontology.Triple triple
```
      The BioJava Triple.
Package org.sbml.jsbml.text.parser
- Class org.sbml.jsbml.text.parser.ParseException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentToken
```
Token currentToken
```
      This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.
    - expectedTokenSequences
```
int[][] expectedTokenSequences
```
      Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.
    - tokenImage
```
String[] tokenImage
```
      This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.
    - eol
```
String eol
```
      The end of line string for this machine.
- Class org.sbml.jsbml.text.parser.Token extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - kind
```
int kind
```
      An integer that describes the kind of this token. This numbering system is determined by JavaCCParser, and a table of these numbers is stored in the file ...Constants.java.
    - beginLine
```
int beginLine
```
      The line number of the first character of this Token.
    - beginColumn
```
int beginColumn
```
      The column number of the first character of this Token.
    - endLine
```
int endLine
```
      The line number of the last character of this Token.
    - endColumn
```
int endColumn
```
      The column number of the last character of this Token.
    - image
```
String image
```
      The string image of the token.
    - next
```
Token next
```
      A reference to the next regular (non-special) token from the input stream. If this is the last token from the input stream, or if the token manager has not read tokens beyond this one, this field is set to null. This is true only if this token is also a regular token. Otherwise, see below for a description of the contents of this field.
    - specialToken
```
Token specialToken
```
      This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token. If there are no such special tokens, this field is set to null. When there are more than one such special token, this field refers to the last of these special tokens, which in turn refers to the next previous special token through its specialToken field, and so on until the first special token (whose specialToken field is null). The next fields of special tokens refer to other special tokens that immediately follow it (without an intervening regular token). If there is no such token, this field is null.
- Class org.sbml.jsbml.text.parser.TokenMgrError extends Error implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - errorCode
```
int errorCode
```
      Indicates the reason why the exception is thrown. It will have one of the above 4 values.
Package org.sbml.jsbml.util
- Class org.sbml.jsbml.util.ListOfWithName extends ListOf<T extends SBase> implements Serializable
  
  serialVersionUID:
  
  -1585956493391213596L
  - Serialized Fields
    - elementName
```
String elementName
```
- Class org.sbml.jsbml.util.NotImplementedException extends Error implements Serializable
  
  serialVersionUID:
  
  8871684506701754580L
- Class org.sbml.jsbml.util.Pair extends Object implements Serializable
  
  serialVersionUID:
  
  6483695107543561182L
  - Serialized Fields
    - l
```
Object l
```
      Left value.
    - v
```
Object v
```
      Right value.
- Class org.sbml.jsbml.util.TreeNodeAdapter extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  -6818272462908634740L
  - Serialized Fields
    - userObject
```
Object userObject
```
      The object to be wrapped.
- Class org.sbml.jsbml.util.TreeNodeChangeEvent extends PropertyChangeEvent implements Serializable
  
  serialVersionUID:
  
  1669574491009205844L
- Class org.sbml.jsbml.util.TreeNodeRemovedEvent extends EventObject implements Serializable
  
  serialVersionUID:
  
  4860717212990689980L
  - Serialized Fields
    - previousParent
```
TreeNode previousParent
```
      The previous parent node in the tree, i.e., the node that was the parent of the deleted node (see TreeNodeRemovedEvent.getSource()) before the deletion.
- Class org.sbml.jsbml.util.ValuePair extends Pair<L extends Comparable<? super L>,V extends Comparable<? super V>> implements Serializable
  
  serialVersionUID:
  
  -4230267902609475128L
Package org.sbml.jsbml.util.compilers
- Class org.sbml.jsbml.util.compilers.UnitException extends SBMLException implements Serializable
  
  serialVersionUID:
  
  -5630929507888356877L
Package org.sbml.jsbml.validator
- Class org.sbml.jsbml.validator.ModelOverdeterminedException extends Exception implements Serializable
  
  serialVersionUID:
  
  -5288546434951201722L
Package org.sbml.jsbml.xml
- Class org.sbml.jsbml.xml.XMLException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -7347204499480036729L
- Class org.sbml.jsbml.xml.XMLNode extends XMLToken implements Serializable
  
  serialVersionUID:
  
  -7699595383368237593L
  - Serialized Fields
    - childElements
```
List<E> childElements
```
- Class org.sbml.jsbml.xml.XMLToken extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  -3501521107595952650L
  - Serialized Fields
    - attributes
```
XMLAttributes attributes
```
    - characters
```
StringBuilder characters
```
    - column
```
long column
```
    - isEndElement
```
boolean isEndElement
```
    - isEOF
```
boolean isEOF
```
    - isStartElement
```
boolean isStartElement
```
    - isText
```
boolean isText
```
    - line
```
long line
```
    - namespaces
```
XMLNamespaces namespaces
```
    - triple
```
XMLTriple triple
```
      the XMLTripe (name, uri and prefix) of this XML element.

Serialized Form

Package org.sbml.jsbml

Class org.sbml.jsbml.AbstractMathContainer extends AbstractSBase implements Serializable

Serialized Fields

math

Class org.sbml.jsbml.AbstractNamedSBase extends AbstractSBase implements Serializable

Serialized Fields

id

name

Class org.sbml.jsbml.AbstractNamedSBaseWithUnit extends AbstractNamedSBase implements Serializable

Serialized Fields

unitsID

Class org.sbml.jsbml.AbstractSBase extends AbstractTreeNode implements Serializable

Serialized Fields

annotation

declaredNamespaces

elementNamespace

extensions

ignoredExtensions

ignoredXMLElements

lv

metaId

notesXMLNode

packageName

packageVersion

sboTerm

Class org.sbml.jsbml.AbstractTreeNode extends Object implements Serializable

Serialized Fields

listOfListeners

parent

userObjects

Class org.sbml.jsbml.AlgebraicRule extends Rule implements Serializable

Class org.sbml.jsbml.Annotation extends AnnotationElement implements Serializable

Serialized Fields

about

history

listOfCVTerms

nonRDFannotation

Class org.sbml.jsbml.AnnotationElement extends AbstractTreeNode implements Serializable

Class org.sbml.jsbml.AssignmentRule extends ExplicitRule implements Serializable

Class org.sbml.jsbml.ASTNode extends AbstractTreeNode implements Serializable

Serialized Fields

definitionURL

denominator

exponent

id

style

className

encoding

isSetNumberType

listOfNodes

mantissa

name

numerator

parentSBMLObject

type

unitId

variable

Class org.sbml.jsbml.Compartment extends Symbol implements Serializable

Serialized Fields

compartmentTypeID

isSetSpatialDimensions

outsideID

spatialDimensions

Class org.sbml.jsbml.CompartmentType extends AbstractNamedSBase implements Serializable

Class org.sbml.jsbml.Constraint extends AbstractMathContainer implements Serializable

Serialized Fields

message

Class org.sbml.jsbml.Creator extends AnnotationElement implements Serializable

Serialized Fields

email

familyName

givenName

organisation

otherAttributes

Class org.sbml.jsbml.CVTerm extends AnnotationElement implements Serializable

Serialized Fields

qualifier

resourceURIs

listOfNestedCVTerms