Serialized Form

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
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.util.Map<K,V> declaredNamespaces
```
      Contains all the namespaces declared on the XML node with their prefixes.
    - extensions
```
java.util.SortedMap<K,V> extensions
```
      Map containing the SBML extension object of additional packages with the appropriate name space of the package.
    - ignoredExtensions
```
java.util.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 java.lang.Comparable<? super L>,V extends java.lang.Comparable<? super V>> lv
```
      Level and version of the SBML component. Matches the level XML attribute of an SBML node.
    - metaId
```
java.lang.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.
    - sboTerm
```
int sboTerm
```
      sbo term of the SBML component. Matches the sboTerm XML attribute of an element in a SBML file.
    - elementNamespace
```
java.lang.String elementNamespace
```
      the namespace which this SBase element belong to.
- Class org.sbml.jsbml.AbstractTreeNode extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8629109724566600238L
  - Serialized Fields
    - listOfListeners
```
java.util.List<E> listOfListeners
```
      List of listeners for this component
    - parent
```
javax.swing.tree.TreeNode parent
```
      The parent element of this Annotation.
    - userObjects
```
java.util.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
```
java.lang.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
```
java.util.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
```
java.lang.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
```
java.lang.String id
```
      Possible attributes for a MathML element
    - style
```
java.lang.String style
```
      Possible attributes for a MathML element
    - className
```
java.lang.String className
```
      Possible attributes for a MathML element
    - encoding
```
java.lang.String encoding
```
      Possible attributes for a MathML element
    - 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
```
java.util.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
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.lang.String outsideID
```
      Deprecated.
      
      Represents the outside XML attribute of a compartment element. It matches a compartment id in the model instance.
    - spatialDimensions
```
java.lang.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
```
java.lang.String email
```
      email of the creator
    - familyName
```
java.lang.String familyName
```
      Family name of the creator
    - givenName
```
java.lang.String givenName
```
      Given name of the creator
    - organisation
```
java.lang.String organisation
```
      Organisation name of the creator.
    - otherAttributes
```
java.util.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
```
java.util.List<E> resourceURIs
```
      Contains all the MIRIAM URI associated with the qualifier of this CVTerm instance.
    - 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
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.lang.String id
```
      Represents the "id" attribute of a functionDefinition element.
    - name
```
java.lang.String name
```
      Represents the "name" attribute of a functionDefinition element.
- Class org.sbml.jsbml.History extends AnnotationElement implements Serializable
  
  serialVersionUID:
  
  -1699117162462037149L
  - Serialized Fields
    - creation
```
java.util.Date creation
```
      Date of creation
    - listOfCreators
```
java.util.List<E> listOfCreators
```
      Contains all the Creator instances of this History.
    - listOfModification
```
java.util.List<E> listOfModification
```
      Contains all the modified date instances of this History.
    - modified
```
java.util.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
```
java.lang.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
```
java.util.Map<K,V> mapOfLocalParameters
```
      For internal computation: a mapping between their identifiers and the LocalParameters in KineticLaws themselves:
    - substanceUnitsID
```
java.lang.String substanceUnitsID
```
      Deprecated.
      
      Represents the 'substanceUnits' XML attribute of this KineticLaw.
    - timeUnitsID
```
java.lang.String timeUnitsID
```
      Deprecated.
      
      Represents the 'timeUnits' XML attribute of this KineticLaw.
    - unitsID
```
java.lang.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
```
java.util.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
```
java.lang.String areaUnitsID
```
      Represents the 'areaUnits' XML attribute of a model element.
    - conversionFactorID
```
java.lang.String conversionFactorID
```
      Represents the 'conversionFactor' XML attribute of a model element.
    - extentUnitsID
```
java.lang.String extentUnitsID
```
      Represents the 'extentUnits' XML attribute of a model element.
    - lengthUnitsID
```
java.lang.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
```
java.util.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
```
java.util.Map<K,V> mapOfLocalParameters
```
      A mapping between the identifiers of LocalParameters and the containing Reaction objects.
    - mapOfUniqueNamedSBases
```
java.util.Map<K,V> mapOfUniqueNamedSBases
```
      For internal computation: a mapping between their identifiers and the UniqueNamedSBases in Models themselves:
    - mapOfUnitDefinitions
```
java.util.Map<K,V> mapOfUnitDefinitions
```
      A mapping between their identifiers and associated UnitDefinition objects.
    - substanceUnitsID
```
java.lang.String substanceUnitsID
```
      Represents the 'substanceUnits' XML attribute of a model element.
    - timeUnitsID
```
java.lang.String timeUnitsID
```
      Represents the 'timeUnits' XML attribute of a model element.
    - volumeUnitsID
```
java.lang.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
```
java.lang.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
```
java.lang.String compartmentID
```
      Represents the 'compartment' XML attribute of a reaction element.
    - fast
```
java.lang.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
```
java.lang.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
```
java.util.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
```
java.util.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
```
java.util.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
```
java.util.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
```
java.lang.String category
```
    - code
```
int code
```
    - excerpt
```
java.lang.String excerpt
```
    - column
```
int column
```
    - line
```
int line
```
    - message
```
Message message
```
    - shortmessage
```
Message shortmessage
```
    - detail
```
Detail detail
```
    - severity
```
java.lang.String severity
```
    - packageName
```
java.lang.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
```
java.lang.String shortMessage
```
    - type
```
SBMLException.Type type
```
- Class org.sbml.jsbml.SBMLReader extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3313609137341424804L
- Class org.sbml.jsbml.SBMLTypeUndefinedException extends SBMLError implements Serializable
  
  serialVersionUID:
  
  -6120311866715719809L
- Class org.sbml.jsbml.SBMLWriter extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  7320725236081166704L
  - Serialized Fields
    - programName
```
java.lang.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
```
java.lang.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.SBO.Term extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2753964994128680208L
  - Serialized Fields
    - id
```
java.lang.String id
```
      The base properties of this SBO.Term.
    - name
```
java.lang.String name
```
      The base properties of this SBO.Term.
    - def
```
java.lang.String def
```
      The base properties of this SBO.Term.
    - term
```
org.biojava3.ontology.Term term
```
      The underlying BioJava org.biojava.ontology.Term.
- Class org.sbml.jsbml.SBO.Triple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  7289048361260650338L
  - Serialized Fields
    - triple
```
org.biojava3.ontology.Triple triple
```
      The BioJava org.biojava.ontology.Triple.
- Class org.sbml.jsbml.SimpleSpeciesReference extends AbstractNamedSBase implements Serializable
  
  serialVersionUID:
  
  -504780573593345060L
  - Serialized Fields
    - speciesID
```
java.lang.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
```
java.lang.Boolean boundaryCondition
```
      Represents the 'boundaryCondition' attribute of a Species element.
    - charge
```
java.lang.Integer charge
```
      Deprecated.
      
      Represents the 'charge' attribute of a Species element.
    - compartmentID
```
java.lang.String compartmentID
```
      Represents the 'compartment' attribute of a Species element.
    - conversionFactorID
```
java.lang.String conversionFactorID
```
      Represents the 'conversionFactor' attribute of a Species element.
    - hasOnlySubstanceUnits
```
java.lang.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
```
java.lang.String spatialSizeUnitsID
```
      Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
      
      Represents the 'spatialSizeUnits' attribute of a Species element.
    - speciesTypeID
```
java.lang.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
```
java.lang.Boolean constant
```
      Represents the 'constant' XML attribute of this SpeciesReference.
    - denominator
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.lang.Boolean initialValue
```
    - persistent
```
java.lang.Boolean persistent
```
- Class org.sbml.jsbml.Unit extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -6335465287728562136L
  - Serialized Fields
    - exponent
```
java.lang.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
```
java.lang.Double multiplier
```
      Represents the 'multiplier' XML attribute of an unit element.
    - offset
```
java.lang.Double offset
```
      Deprecated. the offset attribute should no longer be used.
      
      Represents the 'offset' XML attribute of an unit element.
    - scale
```
java.lang.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
    - extendedSBase
```
SBase extendedSBase
```
    - packageVersion
```
int packageVersion
```
Package org.sbml.jsbml.math
- Class org.sbml.jsbml.math.AbstractASTCSymbolNode extends AbstractASTNode implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
      name attribute for MathML element
    - definitionURL
```
java.lang.String definitionURL
```
      definitionURL attribute for MathML element
    - encodingURL
```
java.lang.String encodingURL
```
      encodingURL attribute for MathML element
- Class org.sbml.jsbml.math.AbstractASTNode extends AbstractTreeNode implements Serializable
  - 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 number 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
- Class org.sbml.jsbml.math.ASTArithmeticNode extends ASTFunction implements Serializable
- Class org.sbml.jsbml.math.ASTBinaryFunctionNode extends ASTFunction implements Serializable
- Class org.sbml.jsbml.math.ASTCiFunctionNode extends ASTFunction implements Serializable
  - Serialized Fields
    - definitionURL
```
java.lang.String definitionURL
```
      definitionURL attribute for MathML element
    - name
```
java.lang.String name
```
      name attribute for MathML element
- Class org.sbml.jsbml.math.ASTCiNumberNode extends ASTNumber implements Serializable
  - Serialized Fields
    - definitionURL
```
java.lang.String definitionURL
```
      definitionURL attribute for MathML element
    - name
```
java.lang.String name
```
      name attribute for MathML element
- Class org.sbml.jsbml.math.ASTCnExponentialNode extends ASTCnNumberNode implements Serializable
  - Serialized Fields
    - exponent
```
java.lang.Integer exponent
```
      The exponent value of this node
    - mantissa
```
java.lang.Double mantissa
```
      The mantissa value of this node
- Class org.sbml.jsbml.math.ASTCnIntegerNode extends ASTCnNumberNode implements Serializable
  - Serialized Fields
    - value
```
java.lang.Integer value
```
      The value of this node
- Class org.sbml.jsbml.math.ASTCnNumberNode extends ASTNumber implements Serializable
  - Serialized Fields
    - base
```
java.lang.Double base
```
      Numerical base for MathML element
    - units
```
java.lang.String units
```
      units attribute for MathML element
- Class org.sbml.jsbml.math.ASTCnRationalNode extends ASTCnNumberNode implements Serializable
  - Serialized Fields
    - numerator
```
java.lang.Integer numerator
```
      The numerator of this rational number
    - denominator
```
java.lang.Integer denominator
```
      The denominator of this rational number
- Class org.sbml.jsbml.math.ASTCnRealNode extends ASTCnNumberNode implements Serializable
  - Serialized Fields
    - value
```
java.lang.Double value
```
      The value of this node
- Class org.sbml.jsbml.math.ASTConstantNumber extends ASTNumber implements Serializable
  - Serialized Fields
    - value
```
java.lang.Double value
```
      This variable stores the value of the constant number
- Class org.sbml.jsbml.math.ASTCSymbolAvogadroNode extends ASTConstantNumber implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
      name attribute for MathML element
    - definitionURL
```
java.lang.String definitionURL
```
      definitionURL attribute for MathML element
    - encodingURL
```
java.lang.String encodingURL
```
      encodingURL attribute for MathML element
- Class org.sbml.jsbml.math.ASTCSymbolDelayNode extends ASTBinaryFunctionNode implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
      name attribute for MathML element
    - definitionURL
```
java.lang.String definitionURL
```
      definitionURL attribute for MathML element
    - encodingURL
```
java.lang.String encodingURL
```
      encodingURL attribute for MathML element
- Class org.sbml.jsbml.math.ASTCSymbolTimeNode extends ASTCiNumberNode implements Serializable
  - Serialized Fields
    - encodingURL
```
java.lang.String encodingURL
```
      The encodingURL of this csymbol element
- Class org.sbml.jsbml.math.ASTDivideFunction extends ASTBinaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTFunction extends AbstractASTNode implements Serializable
  - Serialized Fields
    - listOfNodes
```
java.util.List<E> listOfNodes
```
      Child nodes.
    - parentSBMLObject
```
MathContainer parentSBMLObject
```
      The container that holds this ASTFunctionNode.
- Class org.sbml.jsbml.math.ASTHyperbolicNode extends ASTUnaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTLambdaFunctionNode extends ASTFunction implements Serializable
  - Serialized Fields
    - numBvars
```
java.lang.Integer numBvars
```
      The number of MathML bvar elements inside this lambda function
- Class org.sbml.jsbml.math.ASTLogarithmNode extends ASTBinaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTLogicalOperatorNode extends ASTFunction implements Serializable
- Class org.sbml.jsbml.math.ASTNumber extends AbstractASTNode implements Serializable
- Class org.sbml.jsbml.math.ASTPiecewiseFunctionNode extends ASTFunction implements Serializable
  - Serialized Fields
    - numPiece
```
java.lang.Integer numPiece
```
      The number of piece elements associated with this MathML piecewise element
    - hasOtherwise
```
boolean hasOtherwise
```
      True iff piecewise element contains an otherwise element
- Class org.sbml.jsbml.math.ASTPowerNode extends ASTBinaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTQualifierNode extends ASTFunction implements Serializable
- Class org.sbml.jsbml.math.ASTRelationNode extends ASTFunction implements Serializable
- Class org.sbml.jsbml.math.ASTSqrtNode extends ASTUnaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTTimesNode extends ASTBinaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTTrigonometricNode extends ASTUnaryFunctionNode implements Serializable
- Class org.sbml.jsbml.math.ASTUnaryFunctionNode extends ASTFunction implements Serializable
Package org.sbml.jsbml.text.parser
- Class org.sbml.jsbml.text.parser.ParseException extends java.lang.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
```
java.lang.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
```
java.lang.String eol
```
      The end of line string for this machine.
- Class org.sbml.jsbml.text.parser.Token extends java.lang.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
```
java.lang.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 java.lang.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
```
java.lang.String elementName
```
- Class org.sbml.jsbml.util.NotImplementedException extends java.lang.Error implements Serializable
  
  serialVersionUID:
  
  8871684506701754580L
- Class org.sbml.jsbml.util.Pair extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6483695107543561182L
  - Serialized Fields
    - l
```
java.lang.Object l
```
      Left value.
    - v
```
java.lang.Object v
```
      Right value.
- Class org.sbml.jsbml.util.TreeNodeAdapter extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  -6818272462908634740L
  - Serialized Fields
    - userObject
```
java.lang.Object userObject
```
      The object to be wrapped.
- Class org.sbml.jsbml.util.TreeNodeChangeEvent extends java.beans.PropertyChangeEvent implements Serializable
  
  serialVersionUID:
  
  1669574491009205844L
- Class org.sbml.jsbml.util.TreeNodeRemovedEvent extends java.util.EventObject implements Serializable
  
  serialVersionUID:
  
  4860717212990689980L
  - Serialized Fields
    - previosParent
```
javax.swing.tree.TreeNode previosParent
```
      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 java.lang.Comparable<? super L>,V extends java.lang.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 java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -5288546434951201722L
Package org.sbml.jsbml.xml
- Class org.sbml.jsbml.xml.XMLException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  -7347204499480036729L
- Class org.sbml.jsbml.xml.XMLNode extends XMLToken implements Serializable
  
  serialVersionUID:
  
  -7699595383368237593L
  - Serialized Fields
    - childrenElements
```
java.util.List<E> childrenElements
```
- Class org.sbml.jsbml.xml.XMLToken extends AbstractTreeNode implements Serializable
  
  serialVersionUID:
  
  -3501521107595952650L
  - Serialized Fields
    - attributes
```
XMLAttributes attributes
```
    - characters
```
java.lang.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

extensions

ignoredExtensions

ignoredXMLElements

lv

metaId

notesXMLNode

sboTerm

elementNamespace

Class org.sbml.jsbml.AbstractTreeNode extends java.lang.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

type

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

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