ASTNode math
java.lang.String unitsID
Annotation annotation
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> declaredNamespaces
java.lang.String elementNamespace
java.util.SortedMap<K extends java.lang.Object,V extends java.lang.Object> extensions
Map
containing the SBML extension object of additional packages
with the appropriate name space of the package.java.lang.String id
java.util.SortedMap<K extends java.lang.Object,V extends java.lang.Object> 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
java.lang.String name
XMLNode notesXMLNode
java.lang.String packageName
int packageVersion
int sboTerm
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 extends java.lang.Object,V extends java.lang.Object> 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 extends java.lang.Object> listOfCVTerms
XMLNode nonRDFannotation
java.lang.String className
java.lang.String definitionURL
int denominator
java.lang.String encoding
int exponent
java.lang.String id
boolean isSetNumberType
java.util.List<E extends java.lang.Object> 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
java.util.SortedMap<K extends java.lang.Object,V extends java.lang.Object> plugins
Map
containing the ASTNode plugin object of additional packages
with the appropriate name of the package.java.util.List<E extends java.lang.Object> semanticsAnnotationList
java.lang.String style
ASTNode.Type type
java.lang.String unitId
UnitDefinition
in the
model can be stored here.CallableSBase variable
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 extends java.lang.Object,V extends java.lang.Object> otherAttributes
java.util.List<E extends java.lang.Object> listOfNestedCVTerms
CVTerm.Qualifier qualifier
java.util.List<E extends java.lang.Object> resourceURIs
CVTerm
instance.CVTerm.Type type
CVTerm
. It
depends on the name space in the SBML file, it can be a model qualifier
or a biological qualifier.java.lang.String unknownQualifierName
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 extends java.lang.Object> listOfCreators
java.util.List<E extends java.lang.Object> listOfModification
History
.java.util.Date modified
java.lang.String variableID
ListOf<T extends SBase> listOfLocalParameters
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> mapOfLocalParameters
LocalParameter
s in KineticLaw
s themselves:java.lang.String substanceUnitsID
java.lang.String timeUnitsID
java.lang.String unitsID
Model
.java.util.List<E extends java.lang.Object> 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 extends java.lang.Object> 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 extends java.lang.Object,V extends java.lang.Object> mapOfLocalParameters
LocalParameter
s and the
containing Reaction
objects.java.util.Map<K extends java.lang.Object,V extends java.lang.Object> mapOfUniqueNamedSBases
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> 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 extends java.lang.Object,V extends java.lang.Object> checkConsistencyParameters
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> enabledPackageMap
SBMLErrorLog listOfErrors
SBMLError
when parsing the file containing this
document.java.lang.String locationURI
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> 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 extends java.lang.Object,V extends java.lang.Object> SBMLDocumentAttributes
java.lang.String category
int code
int column
Detail detail
java.lang.String excerpt
int line
Message message
java.lang.String packageName
java.lang.String severity
Message shortmessage
SBase source
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
org.w3c.tidy.Tidy userTidy
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
java.lang.String elementNamespace
ASTNode extendedASTNode
int packageVersion
java.lang.String elementNamespace
SBase extendedSBase
int packageVersion
int arrayDimension
boolean isSetArrayDimension
java.lang.String size
int arrayDimension
boolean isSetArrayDimension
java.lang.String referencedAttribute
ListOf<T extends SBase> listOfReplacedElements
ReplacedBy replacedBy
java.lang.String md5
java.lang.String modelRef
java.lang.String source
java.lang.String submodelRef
java.lang.String conversionFactor
java.lang.String deletion
java.lang.String submodelRef
java.lang.String idRef
java.lang.String metaIdRef
java.lang.String portRef
SBaseRef sBaseRef
java.lang.String unitRef
java.lang.String definitionURL
ListOf<T extends SBase> listOfUncertParameters
ASTNode math
UncertParameter.Type type
java.lang.String units
java.lang.Double value
java.lang.String var
java.lang.Double valueLower
java.lang.Double valueUpper
java.lang.String varLower
java.lang.String varUpper
java.lang.String idRef
java.lang.String metaIdRef
Term cboTerm
SpatialKind spatialIndex
java.lang.String variable
ListOf<T extends SBase> listOfFluxBounds
ListOf<T extends SBase> listOfGeneProducts
ListOfObjectives listOfObjectives
java.lang.Boolean strict
GeneProductAssociation geneProductAssociation
java.lang.String lowerFluxBound
java.lang.String upperFluxBound
int charge
java.lang.String chemicalFormula
boolean isSetCharge
boolean isSetValue
FluxBound.Operation operation
java.lang.String reaction
java.lang.Double value
double coefficient
boolean isSetCoefficient
java.lang.String reaction
java.lang.String associatedSpecies
java.lang.String label
Association association
java.lang.String geneProduct
java.lang.String activeObjective
java.util.List<E extends java.lang.Object> listOfAssociations
ListOf<T extends SBase> listOfFluxObjectives
Objective.Type type
Group.Kind kind
ListOfMembers listOfMembers
boolean isSetMembersShareType
boolean membersShareType
java.lang.String idRef
java.lang.String metaIdRef
java.lang.String distinctAttribute
java.lang.String identicalAttribute
java.lang.String reference
NamedSBase
represented by this
GraphicalObject
.Dimensions dimensions
Point position
java.lang.Double order
CurveSegment.Type type
java.lang.Double depth
java.lang.Double height
java.lang.Double width
BoundingBox boundingBox
java.lang.String metaidRef
Dimensions dimensions
ListOf<T extends SBase> listOfAdditionalGraphicalObjects
ListOf<T extends SBase> listOfCompartmentGlyphs
ListOf<T extends SBase> listOfReactionGlyphs
ListOf<T extends SBase> listOfSpeciesGlyphs
ListOf<T extends SBase> listOfTextGlyphs
java.lang.Double x
java.lang.String xmlElementName
java.lang.Double y
java.lang.Double z
Curve curve
java.lang.String glyph
java.lang.String role
Curve curve
SpeciesReferenceRole role
java.lang.String speciesGlyph
java.lang.String graphicalObject
java.lang.String text
java.lang.String compartment
java.lang.String bindingSite1
java.lang.String bindingSite2
RepresentationType representationType
java.lang.String speciesReference
java.lang.String compartmentReference
java.lang.String compartment
ListOf<T extends SBase> listOfInSpeciesTypeBonds
ListOf<T extends SBase> listOfSpeciesFeatureTypes
ListOf<T extends SBase> listOfSpeciesTypeComponentIndexes
ListOf<T extends SBase> listOfSpeciesTypeInstances
BindingStatus bindingStatus
java.lang.String component
java.lang.String numericValue
java.lang.String value
java.lang.String component
java.lang.String identifyingParent
java.lang.String productComponent
java.lang.String reactant
java.lang.String reactantComponent
java.lang.String compartmentReference
java.lang.String speciesType
java.lang.String component
Relation relation
boolean defaultTerm
java.lang.Integer resultLevel
java.lang.String qualitativeSpecies
Sign sign
java.lang.Integer thresholdLevel
InputTransitionEffect transitionEffect
java.lang.Integer outputLevel
java.lang.String qualitativeSpecies
OutputTransitionEffect transitionEffect
java.lang.String compartment
java.lang.Boolean constant
java.lang.Integer initialLevel
java.lang.Integer maxLevel
GlobalRenderInformation renderInformation
java.awt.Color value
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> attributes
RelAbsVector cx
RelAbsVector cy
RelAbsVector cz
java.lang.Double ratio
RelAbsVector rx
RelAbsVector ry
ListOf<T extends SBase> listOfGradientStops
GradientBase.Spread spreadMethod
RelAbsVector offset
java.lang.String stopColor
java.lang.String stroke
ColorDefinition
java.util.List<E extends java.lang.Object> strokeDashArray
java.lang.Double strokeWidth
java.lang.String fill
ColorDefinition
's
id, or a GradientBase
's id; or "none"GraphicalPrimitive2D.FillRule fillRule
RelAbsVector height
java.lang.String href
RelAbsVector width
RelAbsVector x
RelAbsVector y
RelAbsVector z
RelAbsVector x1
RelAbsVector x2
RelAbsVector y1
RelAbsVector y2
RelAbsVector z1
RelAbsVector z2
BoundingBox boundingBox
java.lang.Boolean enableRotationMapping
RenderGroup group
DefaultValues defaultValues
java.lang.Short versionMajor
java.lang.Short versionMinor
java.util.List<E extends java.lang.Object> idList
RelAbsVector cx
RelAbsVector cy
RelAbsVector cz
RelAbsVector fx
RelAbsVector fy
RelAbsVector fz
RelAbsVector r
RelAbsVector height
java.lang.Double ratio
RelAbsVector rx
RelAbsVector ry
RelAbsVector width
RelAbsVector x
RelAbsVector y
RelAbsVector z
java.lang.Double absolute
java.lang.Double relative
RelAbsVector x1
RelAbsVector x2
RelAbsVector y1
RelAbsVector y2
RelAbsVector z1
RelAbsVector z2
RenderCurveSegment.Type type
java.lang.String objectRole
java.lang.String endHead
java.lang.String fontFamily
java.lang.Short fontSize
java.lang.Boolean fontStyleItalic
java.lang.Boolean fontWeightBold
ListOf<T extends SBase> listOfElements
java.lang.String startHead
HTextAnchor textAnchor
VTextAnchor vTextAnchor
java.awt.Color backgroundColor
ListOf<T extends SBase> listOfColorDefinitions
ListOf<T extends SBase> listOfGradientDefinitions
ListOf<T extends SBase> listOfLineEndings
java.lang.String programName
java.lang.String programVersion
java.lang.String referenceRenderInformation
ListOfLocalRenderInformation listOfLocalRenderInformation
ListOfGlobalRenderInformation listOfGlobalRenderInformation
RelAbsVector x
RelAbsVector y
RelAbsVector z
RenderGroup group
java.util.List<E extends java.lang.Object> roleList
java.util.List<E extends java.lang.Object> typeList
java.lang.String fontFamily
RelAbsVector fontSize
java.lang.Boolean fontStyleItalic
java.lang.Boolean fontWeightBold
java.lang.String text
HTextAnchor textAnchor
VTextAnchor vTextAnchor
RelAbsVector x
RelAbsVector y
RelAbsVector z
java.lang.Double[] transform
java.lang.String changedBy
java.lang.Boolean viableWithoutChange
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
.java.lang.String domain1
java.lang.String domain2
CoordinateKind coordinate
java.lang.String domainType
FunctionKind functionType
java.lang.Integer ordinal
java.lang.String elementName
java.lang.Double value
java.lang.String boundaryDomainType
java.lang.String coordinateBoundary
BoundaryConditionKind type
java.lang.String domainType
java.lang.Double unitSize
Boundary boundaryMaximum
Boundary boundaryMinimum
CoordinateKind type
java.lang.String unit
CoordinateKind coordinate
TransformationComponent forwardTransformation
TransformationComponent reverseTransformation
CSGNode csgNode
java.lang.String domainType
java.lang.Integer ordinal
PrimitiveKind primitiveType
java.lang.String csgObjectRef
java.lang.Double rotateAngleInRadians
java.lang.Double rotateAxisX
java.lang.Double rotateAxisY
java.lang.Double rotateAxisZ
java.lang.Double scaleX
java.lang.Double scaleY
java.lang.Double scaleZ
java.lang.String complementA
java.lang.String complementB
ListOf<T extends SBase> listOfCSGNodes
SetOperation operationType
CSGNode csgNode
java.lang.Double translateX
java.lang.Double translateY
java.lang.Double translateZ
CoordinateKind coordinateReference1
CoordinateKind coordinateReference2
DiffusionKind diffusionKind
java.lang.Integer spatialDimensions
GeometryKind coordinateSystem
ListOf<T extends SBase> listOfAdjacentDomains
ListOf<T extends SBase> listOfCoordinateComponents
ListOf<T extends SBase> listOfDomains
ListOf<T extends SBase> listOfDomainTypes
ListOf<T extends SBase> listOfGeometryDefinitions
ListOf<T extends SBase> listOfSampledFields
java.lang.Boolean isActive
java.lang.Double coord1
java.lang.Double coord2
java.lang.Double coord3
java.lang.String geometryDefinition
java.lang.Integer ordinal
java.lang.String spatialRef
java.lang.String variable
ListOf<T extends SBase> listOfParametricObjects
SpatialPoints spatialPoints
CompressionKind compression
DataKind dataType
java.lang.String domainType
java.lang.String pointIndex
java.lang.Integer pointIndexLength
PolygonKind polygonType
java.lang.Integer[] pointIndex
CompressionKind compression
XMLNode data
DataKind dataType
InterpolationKind interpolation
java.lang.Integer numSamples1
java.lang.Integer numSamples2
java.lang.Integer numSamples3
java.lang.String samples
java.lang.Integer samplesLength
java.lang.String domainType
java.lang.Double maxValue
java.lang.Double minValue
java.lang.Double sampledValue
CompartmentMapping compartmentMapping
Geometry geometry
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> spatialIdMap
ParameterType param
java.lang.String arrayData
java.lang.Integer arrayDataLength
CompressionKind compression
DataKind dataType
java.lang.Boolean isLocal
java.lang.Boolean spatial
java.lang.Double[] components
java.lang.Integer componentsLength
java.lang.String id
java.lang.String mathMLClass
MathContainer parentSBMLObject
AbstractASTNode
.boolean strict
java.lang.String style
ASTNode.Type type
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 definitionURL
java.lang.String encoding
java.lang.String name
java.lang.String definitionURL
java.lang.String encoding
java.lang.String name
ASTCSymbolTimeNode
.java.util.List<E extends java.lang.Object> listOfNodes
java.lang.String name
ASTFunction
.Token currentToken
java.lang.String eol
int[][] expectedTokenSequences
java.lang.String[] tokenImage
int beginColumn
int beginLine
int endColumn
int endLine
java.lang.String image
int kind
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
Triple
.Token currentToken
java.lang.String eol
int[][] expectedTokenSequences
java.lang.String[] tokenImage
int beginColumn
int beginLine
int endColumn
int endLine
java.lang.String image
int kind
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 extends java.lang.Object> attributeNames
java.util.ArrayList<E extends java.lang.Object> attributeValues
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> namespaces
java.util.List<E extends java.lang.Object> 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 namespaceURI
java.lang.String prefix