ASTNode math
java.lang.String unitsID
Annotation annotation
java.util.Map<K,V> declaredNamespaces
java.lang.String elementNamespace
java.util.SortedMap<K,V> extensions
Map
containing the SBML extension object of additional packages
with the appropriate name space of the package.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.
XMLNode ignoredXMLElements
ValuePair<L extends java.lang.Comparable<? super L>,V extends java.lang.Comparable<? super V>> lv
java.lang.String metaId
XMLNode notesXMLNode
java.lang.String packageName
int packageVersion
int sboTerm
java.lang.String id
java.lang.String name
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- - If any of the usual Input/Output related exceptions occur.java.lang.ClassNotFoundException
- - If the class of a serialized object cannot be found.Serializable
javax.swing.tree.TreeNode parent
Annotation
.java.util.Map<K,V> userObjects
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.java.lang.String about
History history
java.util.List<E> listOfCVTerms
XMLNode nonRDFannotation
java.lang.String definitionURL
int denominator
int exponent
java.lang.String id
java.lang.String style
java.lang.String className
java.lang.String encoding
java.util.List<E> semanticsAnnotationList
boolean isSetNumberType
java.util.List<E> listOfNodes
double mantissa
java.lang.String name
ASTNode.setName(String)
is called, the given name is stored in this
field.int numerator
true
, or the
value of an integer if this.isInteger() is true
.MathContainer parentSBMLObject
ASTNode.Type type
java.lang.String unitId
UnitDefinition
in the
model can be stored here.CallableSBase variable
java.util.SortedMap<K,V> plugins
Map
containing the ASTNode plugin object of additional packages
with the appropriate name of the package.java.lang.String compartmentTypeID
boolean isSetSpatialDimensions
java.lang.String outsideID
java.lang.Double spatialDimensions
XMLNode message
java.lang.String email
java.lang.String familyName
java.lang.String givenName
java.lang.String organisation
java.util.Map<K,V> otherAttributes
CVTerm.Qualifier qualifier
java.lang.String unknownQualifierName
java.util.List<E> resourceURIs
CVTerm
instance.java.util.List<E> listOfNestedCVTerms
CVTerm.Type type
CVTerm
. It
depends on the name space in the SBML file, it can be a model qualifier
or a biological qualifier.Delay delay
boolean isSetUseValuesFromTriggerTime
ListOf<T extends SBase> listOfEventAssignments
Priority priority
Trigger trigger
java.lang.Boolean useValuesFromTriggerTime
java.lang.String variableID
java.lang.String unitsID
Parameter
s.
In this case this AssignmentRule
represents the SBML
element ParameterRule.java.lang.String variableID
Variable
. Matches the variable XML
attribute of an assignmentRule or rateRule element.java.util.Date creation
java.util.List<E> listOfCreators
java.util.List<E> listOfModification
History
.java.util.Date modified
java.lang.String variableID
ListOf<T extends SBase> listOfLocalParameters
java.util.Map<K,V> mapOfLocalParameters
LocalParameter
s in KineticLaw
s themselves:java.lang.String substanceUnitsID
java.lang.String timeUnitsID
java.lang.String unitsID
Model
.java.util.List<E> listOf
ListOf.Type listType
java.lang.String otherListName
ListOf.Type.other
.boolean isExplicitlySetConstant
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.java.lang.String areaUnitsID
java.lang.String conversionFactorID
java.lang.String extentUnitsID
java.lang.String lengthUnitsID
ListOf<T extends SBase> listOfCompartments
ListOf<T extends SBase> listOfCompartmentTypes
ListOf<T extends SBase> listOfConstraints
ListOf<T extends SBase> listOfEvents
ListOf<T extends SBase> listOfFunctionDefinitions
ListOf<T extends SBase> listOfInitialAssignments
ListOf<T extends SBase> listOfParameters
java.util.List<E> listOfPredefinedUnitDefinitions
ListOf<T extends SBase> listOfReactions
ListOf<T extends SBase> listOfRules
ListOf<T extends SBase> listOfSpecies
ListOf<T extends SBase> listOfSpeciesTypes
ListOf<T extends SBase> listOfUnitDefinitions
java.util.Map<K,V> mapOfLocalParameters
LocalParameter
s and the
containing Reaction
objects.java.util.Map<K,V> mapOfUniqueNamedSBases
java.util.Map<K,V> mapOfUnitDefinitions
UnitDefinition
objects.java.lang.String substanceUnitsID
java.lang.String timeUnitsID
java.lang.String volumeUnitsID
boolean isSetValue
java.lang.Double value
java.lang.String compartmentID
java.lang.Boolean fast
boolean isSetFast
Reaction.fast
attribute has been set by using a default or
by changing its value.boolean isSetReversible
Reaction.reversible
attribute has been set by using a default or
by changing its value.KineticLaw kineticLaw
ListOf<T extends SBase> listOfModifiers
ListOf<T extends SBase> listOfProducts
ListOf<T extends SBase> listOfReactants
java.lang.Boolean reversible
java.util.Map<K,V> checkConsistencyParameters
SBMLErrorLog listOfErrors
SBMLError
when parsing the file containing this
document.java.util.Map<K,V> mappingFromMetaId2SBase
SBMLDocument
to avoid
the creation of multiple identical meta identifiers. These identifiers
have to be unique within the document.Model model
java.util.Map<K,V> enabledPackageMap
java.util.Map<K,V> SBMLDocumentAttributes
SBMLException.Category category
SBMLException.Code code
java.lang.String shortMessage
SBMLException.Type type
java.lang.String programName
String
representation (possibly in a File
) with the help
of JSBML.java.lang.String programVersion
String
or File
.SBMLWriter sbmlWriter
java.lang.String speciesID
boolean amount
java.lang.Boolean boundaryCondition
java.lang.Integer charge
java.lang.String compartmentID
java.lang.String conversionFactorID
java.lang.Boolean hasOnlySubstanceUnits
boolean isSetBoundaryCondition
boolean isSetCharge
boolean isSetHasOnlySubstanceUnits
java.lang.String spatialSizeUnitsID
java.lang.String speciesTypeID
java.lang.Boolean constant
java.lang.Integer denominator
boolean isSetConstant
boolean isSetDenominator
boolean isSetStoichiometry
java.lang.Double stoichiometry
StoichiometryMath stoichiometryMath
java.lang.Boolean constant
boolean isSetConstant
java.lang.Boolean initialValue
java.lang.Boolean persistent
java.lang.Double exponent
boolean isSetExponent
boolean isSetMultiplier
boolean isSetOffset
boolean isSetScale
Unit.Kind kind
java.lang.Double multiplier
java.lang.Double offset
java.lang.Integer scale
ASTNode extendedASTNode
int packageVersion
java.lang.String elementNamespace
SBase extendedSBase
int packageVersion
java.lang.String elementNamespace
MathContainer parentSBMLObject
AbstractASTNode
.boolean strict
ASTNode.Type type
java.lang.String id
java.lang.String style
java.lang.String mathMLClass
java.lang.String definitionURL
java.lang.String name
ASTCiFunctionNode
.java.lang.String refId
java.lang.String definitionURL
java.lang.String refId
ASTCiNumberNode
.java.lang.Object number
java.lang.String units
java.lang.String variable
java.lang.String definitionURL
java.lang.String encoding
java.lang.String name
ASTCSymbolAvogadroNode
.java.lang.String name
java.lang.String definitionURL
java.lang.String encoding
java.lang.String encoding
java.lang.String definitionURL
java.lang.String name
ASTCSymbolTimeNode
.java.util.List<E> listOfNodes
java.lang.String name
ASTFunction
.Token currentToken
int[][] expectedTokenSequences
java.lang.String[] tokenImage
java.lang.String eol
int kind
int beginLine
int beginColumn
int endLine
int endColumn
java.lang.String image
Token next
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.Token specialToken
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
.int errorCode
org.biojava.nbio.ontology.Triple triple
org.biojava.nbio.ontology.Triple
.Token currentToken
int[][] expectedTokenSequences
java.lang.String[] tokenImage
java.lang.String eol
int kind
int beginLine
int beginColumn
int endLine
int endColumn
java.lang.String image
Token next
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.Token specialToken
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
.int errorCode
java.lang.String elementName
java.lang.Object l
java.lang.Object v
java.lang.Object userObject
javax.swing.tree.TreeNode previousParent
TreeNodeRemovedEvent.getSource()
) before the deletion.java.util.ArrayList<E> attributeNames
java.util.ArrayList<E> attributeValues
java.util.Map<K,V> namespaces
java.util.List<E> childElements
XMLAttributes attributes
java.lang.StringBuilder characters
long column
boolean isEndElement
boolean isEOF
boolean isStartElement
boolean isText
long line
XMLNamespaces namespaces
XMLTriple triple
java.lang.String name
java.lang.String prefix
java.lang.String namespaceURI