void
TestExtension::init()
{
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
return;
}
TestExtension testExtension;
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
SBaseExtensionPoint sbmldocExtPoint("core",SBML_DOCUMENT);
SBaseExtensionPoint modelExtPoint("core",SBML_MODEL);
SBasePluginCreator<SBMLDocumentPlugin, TestExtension> sbmldocPluginCreator(sbmldocExtPoint,packageURIs);
SBasePluginCreator<TestModelPlugin, TestExtension> modelPluginCreator(modelExtPoint,packageURIs);
testExtension.addSBasePluginCreator(&sbmldocPluginCreator);
testExtension.addSBasePluginCreator(&modelPluginCreator);
int result = SBMLExtensionRegistry::getInstance().addExtension(&testExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] TestExtension::init() failed." << std::endl;
}
}
/*
* Initialization function of req extension module which is automatically invoked
* by SBMLExtensionRegister class before main() function invoked.
*/
void
ReqExtension::init()
{
//----------------------------------------------------------------
//
// 1. Check if the req package has already been registered
//
//----------------------------------------------------------------
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
// do nothing
return;
}
//----------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object
//
//----------------------------------------------------------------
ReqExtension reqExtension;
//----------------------------------------------------------------
//
// 3. Creates the SBasePlugins required by this package
//
//----------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
SBaseExtensionPoint sbmldocExtPoint("core", SBML_DOCUMENT);
SBaseExtensionPoint sbaseExtPoint("all", SBML_GENERIC_SBASE);
SBasePluginCreator<ReqSBMLDocumentPlugin, ReqExtension> sbmldocPluginCreator(sbmldocExtPoint, packageURIs);
SBasePluginCreator<ReqSBasePlugin, ReqExtension> sbasePluginCreator(sbaseExtPoint, packageURIs);
//----------------------------------------------------------------
//
// 4. Adds the creator objects to the extension
//
//----------------------------------------------------------------
reqExtension.addSBasePluginCreator(&sbmldocPluginCreator);
reqExtension.addSBasePluginCreator(&sbasePluginCreator);
//----------------------------------------------------------------
//
// 5. Register the object with the registry
//
//----------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&reqExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] ReqExtension::init() failed." << std::endl;
}
}
SBMLNamespaces*
TestExtension::getSBMLExtensionNamespaces(const std::string &uri) const
{
TestPkgNamespaces* pkgns = NULL;
if ( uri == getXmlnsL3V1V1())
{
pkgns = new TestPkgNamespaces(3,1,1);
}
return pkgns;
}
unsigned int
TestExtension::getPackageVersion(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 1;
}
return 0;
}
/*
* Returns an SBMLExtensionNamespaces<class SBMLExtensionType> object
* (e.g. SBMLExtensionNamespaces<GroupsExtension> whose alias type is
* GroupsPkgNamespaces) corresponding to the given uri.
* NULL will be returned if the given uri is not defined in the corresponding package.
*
* (NOTICE) Package developers MUST OVERRIDE this pure virtual function in their derived class.
*
*/
SBMLNamespaces*
GroupsExtension::getSBMLExtensionNamespaces(const std::string &uri) const
{
GroupsPkgNamespaces* pkgns = 0;
if ( uri == getXmlnsL3V1V1())
{
pkgns = new GroupsPkgNamespaces(3,1,1);
}
return pkgns;
}
/*
* Returns the SBML version with the given URI of this package.
*
* (NOTICE) Package developers MUST OVERRIDE this pure virtual function in their derived class.
*
*/
unsigned int
GroupsExtension::getVersion(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 1;
}
return 0;
}
unsigned int
TestExtension::getLevel(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 3;
}
return 0;
}
/*
* Returns the SBML level with the given URI of this package.
*/
unsigned int
LayoutExtension::getLevel(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 3;
}
else if (uri == getXmlnsL2())
{
return 2;
}
return 0;
}
/*
* Returns the package version with the given URI of this package.
*/
unsigned int
LayoutExtension::getPackageVersion(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 1;
}
else if (uri == getXmlnsL2())
{
//
// (NOTE) This should be harmless but may cause some problem.
//
return 1;
}
return 0;
}
/*
* Returns an SBMLExtensionNamespaces<class SBMLExtensionType> object
* (e.g. SBMLExtensionNamespaces<LayoutExtension> whose alias type is
* LayoutPkgNamespaces) corresponding to the given uri.
* Null will be returned if the given uri is not defined in the corresponding package.
*/
SBMLNamespaces*
LayoutExtension::getSBMLExtensionNamespaces(const std::string &uri) const
{
LayoutPkgNamespaces* pkgns = NULL;
if ( uri == getXmlnsL3V1V1())
{
pkgns = new LayoutPkgNamespaces(3,1,1);
}
else if ( uri == getXmlnsL2())
{
//
// (NOTE) This should be harmless but may cause some problem.
//
pkgns = new LayoutPkgNamespaces(2);
}
return pkgns;
}
/*
* Returns the SBML version with the given URI of this package.
*/
unsigned int
LayoutExtension::getVersion(const std::string &uri) const
{
if (uri == getXmlnsL3V1V1())
{
return 1;
}
else if (uri == getXmlnsL2())
{
//
// (NOTE) This may cause unexpected behaviour.
//
/* which indeed it does */
return 1;
}
return 0;
}
const std::string&
TestExtension::getURI(unsigned int sbmlLevel, unsigned int sbmlVersion, unsigned int pkgVersion) const
{
if (sbmlLevel == 3)
{
if (sbmlVersion == 1)
{
if (pkgVersion == 1)
{
return getXmlnsL3V1V1();
}
}
}
static std::string empty = "";
return empty;
}
/*
*
* Initialization function of groups extension module which is automatically invoked
* by SBMLExtensionRegister class before main() function invoked.
*
*/
void
GroupsExtension::init()
{
//-------------------------------------------------------------------------
//
// 1. Checks if the groups pacakge has already been registered.
//
//-------------------------------------------------------------------------
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
// do nothing;
return;
}
//-------------------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object.
//
//-------------------------------------------------------------------------
GroupsExtension groupsExtension;
//-------------------------------------------------------------------------------------
//
// 3. Creates SBasePluginCreatorBase derived objects required for this
// extension. The derived classes can be instantiated by using the following
// template class.
//
// temaplate<class SBasePluginType> class SBasePluginCreator
//
// The constructor of the creator class has two arguments:
//
// (1) SBaseExtensionPoint : extension point to which the plugin object connected
// (2) std::vector<std::string> : a std::vector object that contains a list of URI
// (package versions) supported by the plugin object.
//
// For example, two plugin objects (plugged in SBMLDocument and Model elements) are
// required for the groups extension.
//
// Since only 'required' attribute is used in SBMLDocument by the groups package, existing
// SBMLDocumentPluginNotRequired class can be used as-is for the plugin.
//
// Since the lists of supported package versions (currently only L3V1-groups-V1 supported )
// are equal in the both plugin objects, the same vector object is given to each
// constructor.
//
//---------------------------------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
SBaseExtensionPoint sbmldocExtPoint("core",SBML_DOCUMENT);
SBaseExtensionPoint modelExtPoint("core",SBML_MODEL);
SBasePluginCreator<GroupsSBMLDocumentPlugin, GroupsExtension> sbmldocPluginCreator(sbmldocExtPoint, packageURIs);
SBasePluginCreator<GroupsModelPlugin, GroupsExtension> modelPluginCreator(modelExtPoint,packageURIs);
//--------------------------------------------------------------------------------------
//
// 3. Adds the above SBasePluginCreatorBase derived objects to the SBMLExtension derived object.
//
//--------------------------------------------------------------------------------------
groupsExtension.addSBasePluginCreator(&sbmldocPluginCreator);
groupsExtension.addSBasePluginCreator(&modelPluginCreator);
//-------------------------------------------------------------------------
//
// 4. Registers the SBMLExtension derived object to SBMLExtensionRegistry
//
//-------------------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&groupsExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] GroupsExtension::init() failed." << std::endl;
}
}
/*
* Initialization function of multi extension module which is automatically invoked
* by SBMLExtensionRegister class before main() function invoked.
*/
void
MultiExtension::init()
{
//----------------------------------------------------------------
//
// 1. Check if the multi package has already been registered
//
//----------------------------------------------------------------
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
// do nothing
return;
}
//----------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object
//
//----------------------------------------------------------------
MultiExtension multiExtension;
//----------------------------------------------------------------
//
// 3. Creates the SBasePlugins required by this package
//
//----------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
SBaseExtensionPoint sbmldocExtPoint("core", SBML_DOCUMENT);
SBaseExtensionPoint modelExtPoint("core", SBML_MODEL);
SBaseExtensionPoint compartmentExtPoint("core", SBML_COMPARTMENT);
SBaseExtensionPoint speciesExtPoint("core", SBML_SPECIES);
SBaseExtensionPoint reactionExtPoint("core", SBML_REACTION);
SBaseExtensionPoint simplespeciesreferenceExtPoint("core", SBML_MODIFIER_SPECIES_REFERENCE);
SBaseExtensionPoint speciesreferenceExtPoint("core", SBML_SPECIES_REFERENCE);
SBasePluginCreator<MultiSBMLDocumentPlugin, MultiExtension> sbmldocPluginCreator(sbmldocExtPoint, packageURIs);
SBasePluginCreator<MultiModelPlugin, MultiExtension> modelPluginCreator(modelExtPoint, packageURIs);
SBasePluginCreator<MultiCompartmentPlugin, MultiExtension> compartmentPluginCreator(compartmentExtPoint, packageURIs);
SBasePluginCreator<MultiSpeciesPlugin, MultiExtension> speciesPluginCreator(speciesExtPoint, packageURIs);
SBasePluginCreator<MultiReactionPlugin, MultiExtension> reactionPluginCreator(reactionExtPoint, packageURIs);
SBasePluginCreator<MultiSimpleSpeciesReferencePlugin, MultiExtension> simplespeciesreferencePluginCreator(simplespeciesreferenceExtPoint, packageURIs);
SBasePluginCreator<MultiSpeciesReferencePlugin, MultiExtension> speciesreferencePluginCreator(speciesreferenceExtPoint, packageURIs);
//----------------------------------------------------------------
//
// 4. Adds the creator objects to the extension
//
//----------------------------------------------------------------
multiExtension.addSBasePluginCreator(&sbmldocPluginCreator);
multiExtension.addSBasePluginCreator(&modelPluginCreator);
multiExtension.addSBasePluginCreator(&compartmentPluginCreator);
multiExtension.addSBasePluginCreator(&speciesPluginCreator);
multiExtension.addSBasePluginCreator(&reactionPluginCreator);
multiExtension.addSBasePluginCreator(&simplespeciesreferencePluginCreator);
multiExtension.addSBasePluginCreator(&speciesreferencePluginCreator);
multiExtension.setASTBasePlugin(new MultiASTPlugin(getXmlnsL3V1V1()));
//----------------------------------------------------------------
//
// 5. Register the object with the registry
//
//----------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&multiExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] MultiExtension::init() failed." << std::endl;
}
}
/*
* Initialization function of spatial extension module which is automatically invoked
* by SBMLExtensionRegister class before main() function invoked.
*/
void
SpatialExtension::init()
{
//----------------------------------------------------------------
//
// 1. Check if the spatial package has already been registered
//
//----------------------------------------------------------------
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
// do nothing
return;
}
//----------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object
//
//----------------------------------------------------------------
SpatialExtension spatialExtension;
//----------------------------------------------------------------
//
// 3. Creates the SBasePlugins required by this package
//
//----------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
SBaseExtensionPoint sbmldocExtPoint("core", SBML_DOCUMENT);
SBaseExtensionPoint modelExtPoint("core", SBML_MODEL);
SBaseExtensionPoint compartmentExtPoint("core", SBML_COMPARTMENT);
SBaseExtensionPoint speciesExtPoint("core", SBML_SPECIES);
SBaseExtensionPoint parameterExtPoint("core", SBML_PARAMETER);
SBaseExtensionPoint reactionExtPoint("core", SBML_REACTION);
SBasePluginCreator<SpatialSBMLDocumentPlugin, SpatialExtension> sbmldocPluginCreator(sbmldocExtPoint, packageURIs);
SBasePluginCreator<SpatialModelPlugin, SpatialExtension> modelPluginCreator(modelExtPoint, packageURIs);
SBasePluginCreator<SpatialCompartmentPlugin, SpatialExtension> compartmentPluginCreator(compartmentExtPoint, packageURIs);
SBasePluginCreator<SpatialSpeciesPlugin, SpatialExtension> speciesPluginCreator(speciesExtPoint, packageURIs);
SBasePluginCreator<SpatialParameterPlugin, SpatialExtension> parameterPluginCreator(parameterExtPoint, packageURIs);
SBasePluginCreator<SpatialReactionPlugin, SpatialExtension> reactionPluginCreator(reactionExtPoint, packageURIs);
//----------------------------------------------------------------
//
// 4. Adds the creator objects to the extension
//
//----------------------------------------------------------------
spatialExtension.addSBasePluginCreator(&sbmldocPluginCreator);
spatialExtension.addSBasePluginCreator(&modelPluginCreator);
spatialExtension.addSBasePluginCreator(&compartmentPluginCreator);
spatialExtension.addSBasePluginCreator(&speciesPluginCreator);
spatialExtension.addSBasePluginCreator(¶meterPluginCreator);
spatialExtension.addSBasePluginCreator(&reactionPluginCreator);
//----------------------------------------------------------------
//
// 5. Register the object with the registry
//
//----------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&spatialExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] SpatialExtension::init() failed." << std::endl;
}
}
/*
*
* Initialization function of layout extension module which is automatically invoked
* by SBMLExtensionRegister class before main() function invoked.
*
*/
void
LayoutExtension::init()
{
//-------------------------------------------------------------------------
//
// 1. Checks if the layout package has already been registered.
//
//-------------------------------------------------------------------------
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
// do nothing;
return;
}
//-------------------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object.
//
//-------------------------------------------------------------------------
LayoutExtension layoutExtension;
//-------------------------------------------------------------------------------------
//
// 3. Creates SBasePluginCreatorBase derived objects required for this extension.
// The derived classes can be instantiated by using the following template class.
//
// temaplate<class SBasePluginType> class SBasePluginCreator
//
// The constructor of the creator class has two arguments:
//
// (1) SBaseExtensionPoint : extension point to which the plugin object connected
// (2) std::vector<std::string> : a std::vector object that contains a list of URI
// (package versions) supported by the plugin object.
//
// For example, three plugin classes (plugged in SBMLDocument, Model, and SpeciesReference)
// are required for the layout extension (The plugin class for SpeciesReference is required
// only for SBML Level 2) .
//
//---------------------------------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
packageURIs.push_back(getXmlnsL2());
//
// LayoutSpeciesReferencePlugin is used only for SBML Level 2
//
std::vector<std::string> L2packageURI;
L2packageURI.push_back(getXmlnsL2());
SBaseExtensionPoint sbmldocExtPoint("core",SBML_DOCUMENT);
SBaseExtensionPoint modelExtPoint("core",SBML_MODEL);
SBaseExtensionPoint sprExtPoint("core",SBML_SPECIES_REFERENCE);
SBaseExtensionPoint msprExtPoint("core",SBML_MODIFIER_SPECIES_REFERENCE);
SBasePluginCreator<LayoutSBMLDocumentPlugin, LayoutExtension> sbmldocPluginCreator(sbmldocExtPoint, packageURIs);
SBasePluginCreator<LayoutModelPlugin, LayoutExtension> modelPluginCreator(modelExtPoint,packageURIs);
SBasePluginCreator<LayoutSpeciesReferencePlugin, LayoutExtension> sprPluginCreator(sprExtPoint,L2packageURI);
SBasePluginCreator<LayoutSpeciesReferencePlugin, LayoutExtension> msprPluginCreator(msprExtPoint,L2packageURI);
//------------------------------------------------------------------------------------------
//
// 4. Adds the above SBasePluginCreatorBase derived objects to the SBMLExtension derived object.
//
//------------------------------------------------------------------------------------------
layoutExtension.addSBasePluginCreator(&sbmldocPluginCreator);
layoutExtension.addSBasePluginCreator(&modelPluginCreator);
layoutExtension.addSBasePluginCreator(&sprPluginCreator);
layoutExtension.addSBasePluginCreator(&msprPluginCreator);
//-------------------------------------------------------------------------
//
// 5. Registers the SBMLExtension derived object to SBMLExtensionRegistry
//
//-------------------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&layoutExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] LayoutExtension::init() failed." << std::endl;
}
}
/*
*
* Initialization function of groups extension module which is automatically invoked
* by SBMLExtensionRegister class before main() function invoked.
*
*/
void
RenderExtension::init()
{
//-------------------------------------------------------------------------
//
// 1. Checks if the groups pacakge has already been registered.
//
//-------------------------------------------------------------------------
if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
{
// do nothing;
return;
}
//-------------------------------------------------------------------------
//
// 2. Creates an SBMLExtension derived object.
//
//-------------------------------------------------------------------------
RenderExtension renderExtension;
//-------------------------------------------------------------------------------------
//
// 3. Creates SBasePluginCreatorBase derived objects required for this
// extension. The derived classes can be instantiated by using the following
// template class.
//
// temaplate<class SBasePluginType> class SBasePluginCreator
//
// The constructor of the creator class has two arguments:
//
// (1) SBaseExtensionPoint : extension point to which the plugin object connected
// (2) std::vector<std::string> : a std::vector object that contains a list of URI
// (package versions) supported by the plugin object.
//
// For example, two plugin objects (plugged in SBMLDocument and Model elements) are
// required for the groups extension.
//
// Since only 'required' attribute is used in SBMLDocument by the groups package, existing
// SBMLDocumentPluginNotRequired class can be used as-is for the plugin.
//
// Since the lists of supported package versions (currently only L3V1-groups-V1 supported )
// are equal in the both plugin objects, the same vector object is given to each
// constructor.
//
//---------------------------------------------------------------------------------------
std::vector<std::string> packageURIs;
packageURIs.push_back(getXmlnsL3V1V1());
packageURIs.push_back(getXmlnsL2());
//
// LayoutSpeciesReferencePlugin is used only for SBML Level 2
//
std::vector<std::string> L2packageURI;
L2packageURI.push_back(getXmlnsL2());
SBaseExtensionPoint sbmldocExtPoint("core",SBML_DOCUMENT);
SBaseExtensionPoint layoutExtPoint("layout",SBML_LAYOUT_LAYOUT);
SBaseExtensionPoint layoutGOExtPoint("layout",SBML_LAYOUT_GRAPHICALOBJECT);
SBaseExtensionPoint clayoutExtPoint("core",SBML_LAYOUT_LAYOUT);
SBaseExtensionPoint listOfLayoutsExtPoint("layout", SBML_LIST_OF);
SBasePluginCreator<RenderSBMLDocumentPlugin, RenderExtension> sbmldocPluginCreator(sbmldocExtPoint,packageURIs);
SBasePluginCreator<RenderLayoutPlugin, RenderExtension> layoutPluginCreator(layoutExtPoint,packageURIs);
SBasePluginCreator<RenderLayoutPlugin, RenderExtension> clayoutPluginCreator(clayoutExtPoint,packageURIs);
SBasePluginCreator<RenderListOfLayoutsPlugin, RenderExtension> lolPluginCreator(listOfLayoutsExtPoint,packageURIs);
SBasePluginCreator<RenderGraphicalObjectPlugin, RenderExtension> goPluginCreator(layoutGOExtPoint,packageURIs);
//--------------------------------------------------------------------------------------
//
// 3. Adds the above SBasePluginCreatorBase derived objects to the SBMLExtension derived object.
//
//--------------------------------------------------------------------------------------
renderExtension.addSBasePluginCreator(&sbmldocPluginCreator);
renderExtension.addSBasePluginCreator(&layoutPluginCreator);
renderExtension.addSBasePluginCreator(&clayoutPluginCreator);
renderExtension.addSBasePluginCreator(&lolPluginCreator);
renderExtension.addSBasePluginCreator(&goPluginCreator);
//-------------------------------------------------------------------------
//
// 4. Registers the SBMLExtension derived object to SBMLExtensionRegistry
//
//-------------------------------------------------------------------------
int result = SBMLExtensionRegistry::getInstance().addExtension(&renderExtension);
if (result != LIBSBML_OPERATION_SUCCESS)
{
std::cerr << "[Error] RenderExtension::init() failed." << std::endl;
}
// add converter to registry;
RenderLayoutConverter rlc;
SBMLConverterRegistry::getInstance().addConverter(&rlc);
}