Package | Description |
---|---|
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.
|
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. |
Modifier and Type | Class | Description |
---|---|---|
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.
|
Modifier and Type | Class | Description |
---|---|---|
class |
DistribSBasePlugin |
Modifier and Type | Method | Description |
---|---|---|
AbstractSBasePlugin |
DistribSBasePlugin.clone() |
Modifier and Type | Class | Description |
---|---|---|
class |
DynCompartmentPlugin |
|
class |
DynEventPlugin |
|
class |
DynSBasePlugin |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractFBCSBasePlugin |
Represents the basic properties of all
SBasePlugin in the FBC package. |
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. |
Modifier and Type | Class | Description |
---|---|---|
class |
GroupsModelPlugin |
Modifier and Type | Class | Description |
---|---|---|
class |
LayoutModelPlugin |
Modifier and Type | Class | Description |
---|---|---|
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 |
Modifier and Type | Class | Description |
---|---|---|
class |
QualitativeModel |
Deprecated.
use
QualModelPlugin instead. |
class |
QualModelPlugin |
The
QualModelPlugin adds two lists, one for holding
QualitativeSpecies and the other for holding
Transition s. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractRenderPlugin |
|
class |
RenderGraphicalObjectPlugin |
Extends the
GraphicalObject class with an extra attribute. |
class |
RenderLayoutPlugin |
|
class |
RenderListOfLayoutsPlugin |
Modifier and Type | Class | Description |
---|---|---|
class |
ReqSBasePlugin |
Represents the extended
SBase as define in the req package. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractSpatialSBasePlugin |
|
class |
SpatialCompartmentPlugin |
|
class |
SpatialModelPlugin |
|
class |
SpatialParameterPlugin |
|
class |
SpatialReactionPlugin |
|
class |
SpatialSpeciesPlugin |