Modifier and Type | Method | Description |
---|---|---|
SBasePlugin |
AbstractSBase.createPlugin(java.lang.String nameOrUri) |
|
SBasePlugin |
SBase.createPlugin(java.lang.String nameOrUri) |
Creates a new
SBasePlugin for the given package name or URI
and adds it to this SBase . |
SBasePlugin |
AbstractSBase.getExtension(java.lang.String nameOrUri) |
|
SBasePlugin |
SBase.getExtension(java.lang.String nameOrUri) |
Returns the
SBasePlugin extension object which matches this package
name or URI. |
SBasePlugin |
AbstractSBase.getPlugin(java.lang.String nameOrUri) |
|
SBasePlugin |
SBase.getPlugin(java.lang.String nameOrUri) |
Returns an
SBasePlugin for an SBML Level 3 package extension
with the given package name or URI. |
Modifier and Type | Method | Description |
---|---|---|
java.util.Map<java.lang.String,SBasePlugin> |
AbstractSBase.getExtensionPackages() |
|
java.util.Map<java.lang.String,SBasePlugin> |
SBase.getExtensionPackages() |
Returns the map containing all the
SBasePlugin extension objects
of this SBase . |
Modifier and Type | Method | Description |
---|---|---|
void |
AbstractSBase.addExtension(java.lang.String nameOrUri,
SBasePlugin sbasePlugin) |
|
void |
SBase.addExtension(java.lang.String nameOrUri,
SBasePlugin sbasePlugin) |
Adds a
SBasePlugin extension object to this SBase . |
void |
AbstractSBase.addPlugin(java.lang.String nameOrUri,
SBasePlugin sbasePlugin) |
|
void |
SBase.addPlugin(java.lang.String nameOrUri,
SBasePlugin sbasePlugin) |
Adds a
SBasePlugin extension object to this SBase . |
static java.lang.String |
LevelVersionError.packageVersionMismatchMessage(SBasePlugin element1,
SBase element2) |
Creates an error message showing the different package versions of the given SBase elements.
|
Constructor | Description |
---|---|
LevelVersionError(SBasePlugin element1,
SBase element2) |
|
PropertyUndefinedError(java.lang.String property,
SBasePlugin sbasePlugin) |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractSBasePlugin |
Modifier and Type | Method | Description |
---|---|---|
abstract SBasePlugin |
AbstractSBasePlugin.clone() |
|
SBasePlugin |
SBasePlugin.clone() |
Creates a new instance of
SBasePlugin from this SBasePlugin . |
Constructor | Description |
---|---|
AbstractSBasePlugin(SBasePlugin plugin) |
This method will need to be further tested
|
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 | 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 |
Modifier and Type | Method | Description |
---|---|---|
SBasePlugin |
ArraysParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
CompParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
DistribParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
DynParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
FBCParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
GroupsParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
L3LayoutParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
LayoutParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
MultiParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
PackageParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
QualParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
RenderParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
ReqParser.createPluginFor(SBase sbase) |
|
SBasePlugin |
SpatialParser.createPluginFor(SBase sbase) |