Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext |
The base package for all SBML extensions.
|
org.sbml.jsbml.ext.arrays | |
org.sbml.jsbml.ext.comp |
Provides classes for the
Hierarchical Model Composition package.
|
org.sbml.jsbml.ext.distrib | |
org.sbml.jsbml.ext.dyn |
Provides classes for the
Dynamic Structures package.
|
org.sbml.jsbml.ext.fbc |
Provides classes for the
Flux Balance Constraints package (FBC).
|
org.sbml.jsbml.ext.groups |
Provides classes for the Groups
package.
|
org.sbml.jsbml.ext.layout |
Provides classes for the Layout
package.
|
org.sbml.jsbml.ext.multi |
Provides classes for the Multi package.
|
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.ext.render |
Provides classes for the render package, see the specification at sbml.org.
|
org.sbml.jsbml.ext.req | |
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.math | |
org.sbml.jsbml.util |
A collection of handy utilities when working with JSBML classes,
such as classes for String manipulation or mathematical operations.
|
org.sbml.jsbml.validator.offline.constraints.helper | |
org.sbml.jsbml.xml |
This package provides classes and methods to deal with SBML in form of XML
elements, i.e., here you can find parsers and writers for SBML and also
elements to define XML nodes to be used for notes or annotations.
|
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
class |
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
class |
AbstractNamedSBaseWithUnit |
This simple implementation of the interfaces
NamedSBaseWithDerivedUnit and SBaseWithUnit defines elements
that can be addressed by their identifier and are or can be associated with a
defined Unit or UnitDefinition . |
class |
AbstractSBase |
The base class for each
SBase component. |
class |
AlgebraicRule |
Represents the algebraicRule XML element of a SBML file.
|
class |
Annotation |
An Annotation represents the annotations of an
SBase element. |
class |
AnnotationElement |
A common super class for all those elements that can be part of an
Annotation . |
class |
AssignmentRule |
Represents the assignmentRule XML element of a SBML file.
|
class |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
class |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
class |
CompartmentType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
class |
Constraint |
Represents the constraint XML element of a SBML file.
|
class |
Creator |
|
class |
CVTerm |
Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
of a SBML component.
|
class |
Delay |
Represents the delay subnode of an event element.
|
class |
Event |
Represents the event XML element of a SBML file.
|
class |
EventAssignment |
Represents the eventAssignment XML element of a SBML file.
|
class |
ExplicitRule |
An explicit
Rule is a rule that explicitly declares its variable
element. |
class |
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
class |
History |
|
class |
InitialAssignment |
Represents the initialAssignment XML element of a SBML file.
|
class |
KineticLaw |
Represents the kineticLaw XML element of a SBML file.
|
class |
ListOf<T extends SBase> |
This list implementation is a Java
List that extends
AbstractSBase . |
class |
LocalParameter |
A local parameter can only be used to specify a constant within a
KineticLaw . |
class |
Model |
JSBML implementation of SBML's
Model construct. |
class |
ModifierSpeciesReference |
Represents the modifierSpeciesReference XML element of a SBML file.
|
class |
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
class |
Priority |
This class represents the priority element in SBML.
|
class |
QuantityWithUnit |
This object represents an element with identifier and name, a value, and a
defined unit.
|
class |
RateRule |
Represents the rateRule XML element of a SBML file.
|
class |
Reaction |
Represents the reaction XML element of a SBML file.
|
class |
Rule |
|
class |
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
class |
SimpleSpeciesReference |
The base class of
SpeciesReference and
ModifierSpeciesReference . |
class |
Species |
Represents the species XML element of a SBML file.
|
class |
SpeciesReference |
Represents the speciesReference XML element of a SBML file.
|
class |
SpeciesType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
class |
StoichiometryMath |
Deprecated.
Since SBML Level 3 Version 1 use
AssignmentRule with
instances of SpeciesReference as Variable
instead. |
class |
Symbol |
|
class |
Trigger |
Represents the trigger XML element of a SBML file.
|
class |
Unit |
Represents the unit XML element of a SBML file.
|
class |
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractASTNodePlugin |
|
class |
AbstractSBasePlugin |
Modifier and Type | Class | Description |
---|---|---|
class |
ArraysSBasePlugin |
The
ArraysSBasePlugin class extends the SBase class by adding
an optional ListOfDimension s child and a single optional
Index child. |
class |
Dimension |
|
class |
Index |
The
Index is used to referenced an arrayed element specified in
an attribute. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractNamedSBaseRef |
This abstract class is used by Deletion and Port classes.
|
class |
CompModelPlugin |
|
class |
CompSBasePlugin |
Extends the
SBase class by adding an optional ListOfReplacedElement s child and a single optional ReplacedBy child. |
class |
CompSBMLDocumentPlugin |
Allows SBML documents to contain more than one model.
|
class |
Deletion |
Defines a deletion operation to
be applied when a submodel instantiates a model definition.
|
class |
ExternalModelDefinition |
The
ExternalModelDefinition objects are model definitions - in and of
themselves, they are definitions of the models but not uses of those models. |
class |
ModelDefinition |
Holder class for model definitions, which are
Model s. |
class |
Port |
|
class |
ReplacedBy |
Indicates when the parent object is to be replaced by another object.
|
class |
ReplacedElement |
Points to a submodel object that should be considered "replaced".
|
class |
SBaseRef |
Contains the machinery for constructing references to specific components
within enclosed models or even within external models located in other files.
|
class |
Submodel |
Submodel s are instantiations of models contained within other models. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractDistribSBase |
|
class |
DistribSBasePlugin |
|
class |
Uncertainty |
The
Uncertainty class is a collection of zero or more statistical measures related to the uncertainty of the parent
SBML element. |
class |
UncertParameter |
Defines one uncertainty statistic about the parent element.
|
class |
UncertSpan |
The
UncertSpan class defines a span of values that define an uncertainty statistic such as confidence interval or
range. |
Modifier and Type | Class | Description |
---|---|---|
class |
DynCompartmentPlugin |
|
class |
DynElement |
|
class |
DynEventPlugin |
|
class |
DynSBasePlugin |
|
class |
SpatialComponent |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractFBCSBasePlugin |
Represents the basic properties of all
SBasePlugin in the FBC package. |
class |
And |
This class represents a set of two or more associations that are related in an order independent ‘and’
relationship.
|
class |
FBCModelPlugin |
FBCModelPlugin is the extended Model class for the FBC package. |
class |
FBCReactionPlugin |
Extends the SBML Level 3 Version 1 Core
Reaction class with the addition of a
new optional element GeneProductAssociation as well as two optional attributes lowerFluxBound and
upperFluxBound. |
class |
FBCSpeciesPlugin |
Extends the SBML core
Species class with the additional
attributes charge and chemicalFormula. |
class |
FluxBound |
Deprecated.
Only defined in FBC Version 1.
|
class |
FluxObjective |
The
FluxObjective class is a relatively simple container for a model
variable weighted by a signed linear coefficient. |
class |
GeneProduct |
Defines a single gene product.
|
class |
GeneProductAssociation |
Contains a single
Association . |
class |
GeneProductRef |
References a
GeneProduct . |
class |
ListOfObjectives |
ListOfObjectives adds an additional required attribute: 'activeObjective'. |
class |
LogicalOperator |
Represents a collection of genes in a logical expression.
|
class |
Objective |
An integral component in a complete description of a steady-state model is the so-called
'objective function' which generally consists of a linear combination of model variables
(fluxes) and a sense (direction).
|
class |
Or |
This class represents a set of two or more associations that are related in an order independent ‘and’
relationship.
|
Modifier and Type | Class | Description |
---|---|---|
class |
Group |
|
class |
GroupsModelPlugin |
|
class |
ListOfMemberConstraint |
Deprecated.
This class was removed from the specifications as of version 0.7
(2015-11-24) as no software wanted to implement support for it.
It might be added back in a future version of the specifications
if somebody want to implement it.
|
class |
ListOfMembers |
|
class |
Member |
|
class |
MemberConstraint |
Deprecated.
This class was removed from the specifications as of version 0.7
(2015-11-24) as no software wanted to implement support for it.
It might be added back in a future version of the specifications
if somebody want to implement it.
|
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractReferenceGlyph |
Abstract super class for all kinds of glyphs that graphically represent an
instance of
NamedSBase . |
class |
BoundingBox |
The
BoundingBox class specifies the required elements position and dimension. |
class |
CompartmentGlyph |
The
CompartmentGlyph class is derived from GraphicalObject
and inherits its attributes. |
class |
CubicBezier |
Represents smooth curves in the
Layout package. |
class |
Curve |
|
class |
CurveSegment |
Parent class to
LineSegment and CubicBezier . |
class |
Dimensions |
A
Dimensions is specified via the required attributes width,
height and an optional attribute depth, all of which are of type double. |
class |
GeneralGlyph |
The
GeneralGlyph is used to facilitate the representation of elements
other than Compartment , Species
and Reaction and thus
can be used for the display of relationships of Rule
or
elements defined by other SBML packages. |
class |
GraphicalObject |
All the more specific layout elements (
CompartmentGlyph , GeneralGlyph ,
SpeciesGlyph , ReactionGlyph , ReferenceGlyph , TextGlyph ,
and SpeciesReferenceGlyph ) are derived from the class GraphicalObject . |
class |
Layout |
|
class |
LayoutModelPlugin |
|
class |
LineSegment |
The
LineSegment class consists of the mandatory attribute xsi:type and two child
elements of type Point . |
class |
Point |
The representation of a point in the "layout" package.
|
class |
ReactionGlyph |
Analogous to how a
Reaction object has to at least have one reactant
or product, the ReactionGlyph has to at least have one
SpeciesReferenceGlyph stored in the
ReactionGlyph.listOfSpeciesReferenceGlyphs . |
class |
ReferenceGlyph |
The
ReferenceGlyph element describes the graphical connection between
an arbitrary GraphicalObject (or derived element) and a
GeneralGlyph (which would be an arrow or some curve in most cases). |
class |
SpeciesGlyph |
The
SpeciesGlyph class has an optional species attribute, in
addition to to the attributes from GraphicalObject . |
class |
SpeciesReferenceGlyph |
The
SpeciesReferenceGlyph class describes the graphical connection
between a SpeciesGlyph and a ReactionGlyph (which would be
an arrow or some curve in most cases). |
class |
TextGlyph |
The
TextGlyph class describes the position and dimension of text labels. |
Modifier and Type | Class | Description |
---|---|---|
class |
BindingSiteSpeciesType |
A
BindingSiteSpeciesType object is a binding site, and therefore its instance can further define the bindingStatus
attribute and can participate a binding internally and explicitly in an InSpeciesTypeBond object, or externally and
implicitly defined by an OutwardBindingSite object. |
class |
CompartmentReference |
|
class |
InSpeciesTypeBond |
Defines a bond existing within a
MultiSpeciesType . |
class |
IntraSpeciesReaction |
|
class |
MultiASTNodePlugin |
|
class |
MultiCompartmentPlugin |
|
class |
MultiModelPlugin |
In order to encode the structures needed to define and use multistate and multi-component
complexes, the element model is extended to be linked to a list of
MultiSpeciesType s. |
class |
MultiSimpleSpeciesReferencePlugin |
|
class |
MultiSpeciesPlugin |
A species in the Multi package is extended from a pool to a
template or pattern which multiple pools may map to.
|
class |
MultiSpeciesReferencePlugin |
|
class |
MultiSpeciesType |
The element MultiSpeciesType, which is part of SBML Level 2 Version 4 specification, is not part
of SBML Level 3 Version 1 Core any more.
|
class |
OutwardBindingSite |
A binding site not involved in any
InSpeciesTypeBond object in the MultiSpeciesType referenced by a Species is
an outwardBindingSite. |
class |
PossibleSpeciesFeatureValue |
Each state feature (
SpeciesFeatureType ) also requires the definition of all
the possible values it can take. |
class |
SpeciesFeature |
Defines the state of a component in a species by selecting values from
the listOfPossibleSpeciesFeatureValues of the referenced
SpeciesFeatureType . |
class |
SpeciesFeatureType |
A species type (
MultiSpeciesType ) can carry any number of features
(SpeciesFeatureType ), which are characteristic properties specific
for this type of species (Species ). |
class |
SpeciesFeatureValue |
|
class |
SpeciesTypeComponentIndex |
Provides a way to identify or index a component within a
MultiSpeciesType . |
class |
SpeciesTypeComponentMapInProduct |
A speciesTypeComponentMapInProduct defines the mapping between a component in a reactant and a component
in a product.
|
class |
SpeciesTypeInstance |
Provides a way to construct
MultiSpeciesType s and Species with multiple components. |
class |
SubListOfSpeciesFeature |
Allows to regroup a set of
SpeciesFeature that have a specific Relation between them. |
Modifier and Type | Class | Description |
---|---|---|
class |
FunctionTerm |
Each
FunctionTerm is also associated with a result and in addition to a Boolean
function inside a Math element that can be used to set the conditions under which this term
is selected. |
class |
Input |
|
class |
Output |
Each
Output refers to a QualitativeSpecies that participates
in (is affected by) the corresponding Transition . |
class |
QualitativeModel |
Deprecated.
use
QualModelPlugin instead. |
class |
QualitativeSpecies |
Similarly to the
Species in SBML, the components of qualitative
models refer to pools of entities that are considered indistinguishable and
are each located in a specific Compartment . |
class |
QualModelPlugin |
The
QualModelPlugin adds two lists, one for holding
QualitativeSpecies and the other for holding
Transition s. |
class |
Transition |
A
Transition defines the changes in level associated with the QualitativeSpecies
that occur when a Transition is enabled. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractRenderPlugin |
|
class |
ColorDefinition |
|
class |
DefaultValues |
Encodes default values within the containing
ListOfGlobalRenderInformation or
ListOfLocalRenderInformation . |
class |
Ellipse |
Encodes an ellipse.
|
class |
GlobalRenderInformation |
|
class |
GradientBase |
|
class |
GradientStop |
|
class |
GraphicalPrimitive1D |
|
class |
GraphicalPrimitive2D |
|
class |
Image |
|
class |
LinearGradient |
|
class |
LineEnding |
|
class |
ListOfGlobalRenderInformation |
Derives from the
ListOf class and contains one or more objects of type GlobalRenderInformation . |
class |
ListOfLocalRenderInformation |
Derives from the
ListOf class and contains one or more objects of type LocalRenderInformation . |
class |
ListOfRenderInformation<T extends RenderInformationBase> |
Derives from the
ListOf class and contains one or more objects of type RenderInformationBase . |
class |
LocalRenderInformation |
|
class |
LocalStyle |
|
class |
Polygon |
|
class |
RadialGradient |
|
class |
Rectangle |
|
class |
RelAbsVector |
Implements the RelAbsVector-datatype defined in the render-specification:
A RelAbsVector encodes a single number as a combination of an absolute and a
relative part: "a + r%", where the relative part is with respect to some
surrounding space (like a boundingBox).
This implementation deviates from the one in libSBML in that the support for ,Coordinate' get/set/isSet is reduced |
class |
RenderCubicBezier |
|
class |
RenderCurve |
Implements the curve concept from the SBML render extension.
|
class |
RenderCurveSegment |
Parent class to
RenderPoint and RenderCubicBezier . |
class |
RenderGraphicalObjectPlugin |
Extends the
GraphicalObject class with an extra attribute. |
class |
RenderGroup |
The
RenderGroup class from the SBML render extension is used to group graphical primitives together
to create composite representations from simple primitives. |
class |
RenderInformationBase |
|
class |
RenderLayoutPlugin |
|
class |
RenderListOfLayoutsPlugin |
|
class |
RenderPoint |
|
class |
Style |
|
class |
Text |
|
class |
Transformation |
|
class |
Transformation2D |
Modifier and Type | Class | Description |
---|---|---|
class |
ChangedMath |
Declares which package has modified the value or the mathematical meaning of
an
SBase and in which way. |
class |
ReqSBasePlugin |
Represents the extended
SBase as define in the req package. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractASTNode |
A node in the Abstract Syntax Tree (AST) representation
of a mathematical expression.
|
class |
ASTArithmeticOperatorNode |
An Abstract Syntax Tree (AST) node representing an arithmetic
operator in a mathematical expression.
|
class |
ASTBinaryFunctionNode |
An Abstract Syntax Tree (AST) node representing a function with two
parameters
|
class |
ASTBoolean |
An Abstract Syntax Tree (AST) node representing a boolean
|
class |
ASTCiFunctionNode |
An Abstract Syntax Tree (AST) node representing a MathML ci element
in a mathematical expression.
|
class |
ASTCiNumberNode |
An Abstract Syntax Tree (AST) node representing a MathML ci element
in a mathematical expression.
|
class |
ASTCnExponentialNode |
An Abstract Syntax Tree (AST) node representing an exponent
in a mathematical expression
|
class |
ASTCnIntegerNode |
An Abstract Syntax Tree (AST) node representing an Integer
in a mathematical expression
|
class |
ASTCnNumberNode<T> |
An Abstract Syntax Tree (AST) node representing a MathML cn element in a
mathematical expression. cn elements are used to specify actual numerical
constants.
|
class |
ASTCnRationalNode |
An Abstract Syntax Tree (AST) node representing a rational number
in a mathematical expression
|
class |
ASTCnRealNode |
An Abstract Syntax Tree (AST) node representing a real number
in a mathematical expression
|
class |
ASTConstantNumber |
An Abstract Syntax Tree (AST) node representing a constant number
in a mathematical expression.
|
class |
ASTCSymbolAvogadroNode |
An Abstract Syntax Tree (AST) node representing avogadro's number
|
class |
ASTCSymbolDelayNode |
An Abstract Syntax Tree (AST) node representing the delay function
|
class |
ASTCSymbolTimeNode |
An Abstract Syntax Tree (AST) node representing the time function
|
class |
ASTDivideNode |
An Abstract Syntax Tree (AST) node representing the divide function
|
class |
ASTFunction |
An Abstract Syntax Tree (AST) node representing a function
in a mathematical expression.
|
class |
ASTHyperbolicNode |
An Abstract Syntax Tree (AST) node representing a hyperbolic function
|
class |
ASTLambdaFunctionNode |
An Abstract Syntax Tree (AST) node representing a lambda function
in a mathematical expression.
|
class |
ASTLogarithmNode |
An Abstract Syntax Tree (AST) node representing the logarithm function
|
class |
ASTLogicalOperatorNode |
An Abstract Syntax Tree (AST) node representing a logical operator
in a mathematical expression.
|
class |
ASTMinusNode |
An Abstract Syntax Tree (AST) node representing the minus operator
|
class |
ASTNumber |
An Abstract Syntax Tree (AST) node representing a number
in a mathematical expression.
|
class |
ASTPiecewiseFunctionNode |
An Abstract Syntax Tree (AST) node representing a MathML piecewise
element in a mathematical expression.
|
class |
ASTPlusNode |
An Abstract Syntax Tree (AST) node representing the plus operator
|
class |
ASTPowerNode |
An Abstract Syntax Tree (AST) node representing the power function
|
class |
ASTQualifierNode |
An Abstract Syntax Tree (AST) node representing a MathML qualifier element
in a mathematical expression.
|
class |
ASTRelationalOperatorNode |
An Abstract Syntax Tree (AST) node representing a relational
operator in a mathematical expression.
|
class |
ASTRootNode |
An Abstract Syntax Tree (AST) node representing a root function
|
class |
ASTTimesNode |
An Abstract Syntax Tree (AST) node representing the times operator
|
class |
ASTTrigonometricNode |
An Abstract Syntax Tree (AST) node representing a trigonometric function
|
class |
ASTUnaryFunctionNode |
An Abstract Syntax Tree (AST) node representing a function with only one
parameter
|
Modifier and Type | Class | Description |
---|---|---|
class |
ListOfWithName<T extends SBase> |
Deprecated.
since JSBML 1.2 and the introduction of
ListOf.setOtherListName(String) , this class is not necessary any more. |
class |
TreeNodeAdapter |
This class is a wrapper element for any
Object that should be linked
into a tree data structure as represented by AbstractTreeNode , but
that might by itself not be an instance of TreeNode , i.e., not
compatible with the remaining tree data structure. |
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
ValidationTools.checkInvalidAttribute(ValidationContext ctx,
AbstractTreeNode treeNode,
java.lang.String attributeName) |
Checks if the given
SBase contains an attribute in the invalid XML user object. |
static java.lang.String |
ValidationTools.checkUnknowndAttribute(ValidationContext ctx,
AbstractTreeNode treeNode,
java.lang.String attributeName) |
Checks if the given
SBase contains an attribute in the unknown XML user object. |
Modifier and Type | Class | Description |
---|---|---|
class |
XMLNode |
Representation of a node in an XML document tree.
|
class |
XMLToken |
Representation of a token in an XML stream.
|