bool
LayoutExtension::isInUse(SBMLDocument *doc) const
{
if (doc == NULL || doc->getModel() == NULL) return false;
LayoutModelPlugin* plugin = (LayoutModelPlugin*)doc->getModel()->getPlugin("layout");
if (plugin == NULL) return false;
return (plugin->getNumLayouts() > 0);
}
void convertLayoutToL2()
{
if (_doc == NULL || _doc->getModel() == NULL)
return;
layoutNsUri = "http://projects.eml.org/bcb/sbml/level2";
layoutNs = new LayoutPkgNamespaces(2, 1);
#ifdef LIBSBML_HAS_PACKAGE_RENDER
foundRenderElements = false;
renderNsUri = "http://projects.eml.org/bcb/sbml/render/level2";
renderNs = new RenderPkgNamespaces(2, 1);
#endif
LayoutModelPlugin* plugin
= (LayoutModelPlugin*)_doc->getModel()->getPlugin("layout");
if (plugin == NULL)
return;
ConversionProperties prop(new SBMLNamespaces(2, 4));
prop.addOption("strict", false);
prop.addOption("setLevelAndVersion", true);
prop.addOption("ignorePackages", true);
if (_doc->convert(prop) != LIBSBML_OPERATION_SUCCESS)
{
cout << "Conversion failed!" << endl;
_doc->printErrors();
exit(2);
}
plugin->setElementNamespace(layoutNsUri);
SBMLDocumentPlugin *docPlugin = (SBMLDocumentPlugin*)_doc->getPlugin("layout");
if (docPlugin != NULL)
docPlugin->setElementNamespace(layoutNsUri);
updateNs(plugin->getListOfLayouts());
_doc->getSBMLNamespaces()->removePackageNamespace(3, 1, "layout", 1);
#ifdef LIBSBML_HAS_PACKAGE_RENDER
SBMLDocumentPlugin *rdocPlugin = (SBMLDocumentPlugin*)_doc->getPlugin("render");
if (rdocPlugin!= NULL)
rdocPlugin->setElementNamespace(renderNsUri);
_doc->getSBMLNamespaces()->removePackageNamespace(3, 1, "render", 1);
#endif
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc, char** argv){
if (argc != 2)
{
cout << endl << "Usage: addLayout input-filename"
<< endl << endl;
return 2;
}
SBMLDocument *d = readSBML(argv[1]);
if ( d->getNumErrors() > 0)
{
d->printErrors();
}
else
{
// enable the layout package
// note layout in L2 uses a different namespace than L3
if (d->getLevel() == 2)
{
d->enablePackage(LayoutExtension::getXmlnsL2(), "layout", true);
}
else if (d->getLevel() == 3)
{
d->enablePackage(LayoutExtension::getXmlnsL3V1V1(), "layout", true);
}
// get the model plugin
Model * model = d->getModel();
LayoutModelPlugin* mplugin
= static_cast<LayoutModelPlugin*>(model->getPlugin("layout"));
// create the Layout
LayoutPkgNamespaces layoutns(d->getLevel(), d->getVersion());
Layout* layout = mplugin->createLayout();
layout->setId("Layout_1");
Dimensions dim(&layoutns, 400.0, 220.0);
layout->setDimensions(&dim);
// write out the model
writeSBML(d, "added-layout.xml");
}
}
void convertLayoutToL3()
{
if (_doc == NULL || _doc->getModel() == NULL)
return;
layoutNsUri = "http://www.sbml.org/sbml/level3/version1/layout/version1";
layoutNs = new LayoutPkgNamespaces(3, 1, 1);
#ifdef CONVERT_RENDER
renderNsUri = "http://www.sbml.org/sbml/level3/version1/render/version1";
renderNs = new RenderPkgNamespaces(3, 1, 1);
#endif
LayoutModelPlugin* plugin = (LayoutModelPlugin*)_doc->getModel()->getPlugin("layout");
if (plugin == NULL)
return;
ConversionProperties prop(new SBMLNamespaces(3, 1));
prop.addOption("strict", false);
prop.addOption("setLevelAndVersion", true);
prop.addOption("ignorePackages", true);
_doc->convert(prop);
plugin->setElementNamespace(layoutNsUri);
SBMLDocumentPlugin *docPlugin = (SBMLDocumentPlugin*)_doc->getPlugin("layout");
if (docPlugin != NULL)
docPlugin->setElementNamespace(layoutNsUri);
updateNs(plugin->getListOfLayouts());
_doc->getSBMLNamespaces()->addPackageNamespace("layout", 1);
_doc->setPackageRequired("layout", false);
#ifdef CONVERT_RENDER
SBMLDocumentPlugin *rdocPlugin = (SBMLDocumentPlugin*)_doc->getPlugin("render");
if (rdocPlugin != NULL)
rdocPlugin->setElementNamespace(renderNsUri);
_doc->getSBMLNamespaces()->addPackageNamespace("render", 1);
_doc->setPackageRequired("render", false);
#endif
}
END_TEST
START_TEST ( test_RenderExtension_writeL3Render )
{
RenderPkgNamespaces renderns;
LayoutPkgNamespaces layoutns;
SBMLDocument doc(3,1);
doc.enablePackage(layoutns.getURI(), "layout", true);
doc.enablePackage(renderns.getURI(), "render", true);
Model* model = doc.createModel();
LayoutModelPlugin *lPlugin = (LayoutModelPlugin*)model->getPlugin("layout");
fail_unless(lPlugin != NULL);
Layout* layout = lPlugin->createLayout();
Dimensions dim(&layoutns, 100,100 );
layout->setDimensions(&dim);
GraphicalObject* additional = layout->createAdditionalGraphicalObject();
additional->setId("go1");
BoundingBox bb(&layoutns, "bb1", 10, 10, 90, 90);
additional->setBoundingBox(&bb);
RenderLayoutPlugin *rPlugin = (RenderLayoutPlugin*)layout->getPlugin("render");
fail_unless(rPlugin != NULL);
LocalRenderInformation* local = rPlugin->createLocalRenderInformation();
ColorDefinition *black = local->createColorDefinition();
black->setId("black");
black->setColorValue("#000000");
LocalStyle *lStyle = local->createStyle("style_go1");
lStyle->addId("go1");
RenderGroup* group = lStyle->getGroup();
group->setStroke("black");
std::string sbml = writeSBMLToStdString(&doc);
fail_unless (sbml.length() != 0);
}
bool
RenderExtension::isInUse(SBMLDocument *doc) const
{
if (doc == NULL || doc->getModel() == NULL) return false;
LayoutModelPlugin* plugin = (LayoutModelPlugin*)doc->getModel()->getPlugin("layout");
if (plugin == NULL || plugin->getNumLayouts() == 0) return false;
RenderListOfLayoutsPlugin* lolPlugin = (RenderListOfLayoutsPlugin*) plugin->getListOfLayouts()->getPlugin("render");
if (lolPlugin != NULL && lolPlugin->getNumGlobalRenderInformationObjects() > 0) return true;
for(int i = 0; i < plugin->getNumLayouts(); i++)
{
Layout* layout = plugin->getLayout(i);
RenderLayoutPlugin* rPlugin = (RenderLayoutPlugin*)layout->getPlugin("render");
if (rPlugin != NULL && rPlugin->getNumLocalRenderInformationObjects() > 0) return true;
}
return false;
}
/**
* This method tries to import CellDesigner annotations.
*/
void DataModelGUI::importCellDesigner()
{
// add code to check for CellDesigner annotations
// ask the user if the annotations should be imported
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
if (pDataModel != NULL)
{
SBMLDocument* pSBMLDocument = pDataModel->getCurrentSBMLDocument();
if (pSBMLDocument != NULL &&
pSBMLDocument->getModel() != NULL &&
pSBMLDocument->getModel()->getAnnotation() != NULL)
{
// check for the CellDesigner namespace
std::pair<bool, std::string> foundNamespace = CCellDesignerImporter::findCellDesignerNamespace(pSBMLDocument);
if (foundNamespace.first == true)
{
const XMLNode* pAnno = CCellDesignerImporter::findCellDesignerAnnotation(pSBMLDocument, pSBMLDocument->getModel()->getAnnotation());
// first we check if there are supported cell designer annotations
if (pAnno != NULL)
{
// check if the file contains the correct version
double version = CCellDesignerImporter::determineVersion(pAnno);
if (version < 4.0)
{
CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
}
else
{
bool importCD = false;
#if LIBSBML_VERSION >= 50400
// if we don't have a layout import it!
LayoutModelPlugin* mplugin = (LayoutModelPlugin*)pSBMLDocument->getModel()->getPlugin("layout");
if (mplugin == NULL || (mplugin != NULL && mplugin->getNumLayouts() == 0))
importCD = true;
#endif
// ask the user if the CellDesigner annotation should be imported
if (importCD || CQMessageBox::question(NULL, "CellDesigner import", "A CellDesigner diagram was found in this file.\nDo you want to import the diagram?" , QMessageBox::Yes | QMessageBox::No , QMessageBox::No) == QMessageBox::Yes)
{
// do the import
CCellDesignerImporter cd_importer(pSBMLDocument);
if (cd_importer.getLayout() == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "Sorry, CellDesigner annotations could not be importet.");
}
else
{
// now we have to import the created layout
// create the model map
std::string s1, s2;
std::map<std::string, std::string> modelmap;
std::map<CCopasiObject*, SBase*>::const_iterator it;
std::map<CCopasiObject*, SBase*>::const_iterator itEnd = pDataModel->getCopasi2SBMLMap().end();
for (it = pDataModel->getCopasi2SBMLMap().begin(); it != itEnd; ++it)
{
s1 = SBMLUtils::getIdFromSBase(it->second);
if (it->first)
{
s2 = it->first->getKey();
}
else
{
s2 = "";
}
if ((s1 != "") && (s2 != ""))
{
modelmap[s1] = s2;
}
}
// the layout map and the id to key map can be empty
std::map<std::string, std::string> layoutmap;
std::map<std::string, std::string> idToKeyMap;
#ifdef USE_CRENDER_EXTENSION
CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap, idToKeyMap);
#else
CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap);
#endif /* USE_CRENDER_EXTENSION */
// add the layout to the DataModel
if (pLayout != NULL && pDataModel->getListOfLayouts() != NULL)
{
// the addLayout methods expects a map as the second argument which currently is
// ignored, so we just pass an empty one
// TODO maybe the methods actually expects one of the maps above (layoutmap or idToKeyMap), but
// TODO this is not documented in CListOfLayouts
std::map<std::string, std::string> tmp;
pDataModel->getListOfLayouts()->addLayout(pLayout, tmp);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "Sorry, Layout from CellDesigner annotations could not be created.");
}
}
}
}
}
else
{
CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
}
}
}
}
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc, char** argv)
{
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name.
//
SBMLNamespaces sbmlns(2, 3);
sbmlns.addNamespace(LayoutExtension::getXmlnsL2(), "layout");
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with the following other style.
//
// (2) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class
// for layout package. The class is basically used for createing an
// SBase derived objects belonging to the layout package) with the
// given SBML level, version. (Package version is not required by
// Layout extension of SBML Level 2)
//
// LayoutPkgNamespaces sbmlns(2, 3);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// create the Model
Model* model = document->createModel();
model->setId("TestModel_with_modifiers");
document->setModel(model);
// create the Layout
LayoutPkgNamespaces layoutns(2, 3);
LayoutModelPlugin* mplugin
= static_cast<LayoutModelPlugin*>(model->getPlugin("layout"));
Layout* layout = mplugin->createLayout();
layout->setId("Layout_1");
Dimensions dim(&layoutns, 400.0, 230.0);
layout->setDimensions(&dim);
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("Yeast");
// create the CompartmentGlyph
CompartmentGlyph* compartmentGlyph = layout->createCompartmentGlyph();
compartmentGlyph->setId("CompartmentGlyph_1");
compartmentGlyph->setCompartmentId(compartment->getId());
BoundingBox bb(&layoutns, "bb1", 5, 5, 390, 220);
compartmentGlyph->setBoundingBox(&bb);
// create the Species, SpeciesGlyphs and associated TextGlyphs
// Glucose
Species* species_Gluc = model->createSpecies();
species_Gluc->setId("Glucose");
species_Gluc->setCompartment(compartment->getId());
SpeciesGlyph* glyph_Gluc = layout->createSpeciesGlyph();
glyph_Gluc->setId("SpeciesGlyph_Glucose");
glyph_Gluc->setSpeciesId(species_Gluc->getId());
bb = BoundingBox(&layoutns, "bb2", 105, 20, 130, 20);
glyph_Gluc->setBoundingBox(&bb);
TextGlyph* tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_Glucose");
bb = BoundingBox(&layoutns, "bbA", 115, 20, 110, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_Gluc->getId());
tGlyph->setGraphicalObjectId(glyph_Gluc->getId());
// Glucose-6-phosphate
Species* species_G6P = model->createSpecies();
species_G6P->setId("Glucose_hyphen_6_hyphen_phosphate");
species_G6P->setCompartment(compartment->getId());
SpeciesGlyph* glyph_G6P = layout->createSpeciesGlyph();
glyph_G6P->setId("SpeciesGlyph_G6P");
glyph_G6P->setSpeciesId(species_G6P->getId());
bb = BoundingBox(&layoutns, "bb5", 50, 190, 270, 20);
glyph_G6P->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_G6P");
bb = BoundingBox(&layoutns, "bbD", 60, 190, 250, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_G6P->getId());
tGlyph->setGraphicalObjectId(glyph_G6P->getId());
// ATP
Species* species_ATP = model->createSpecies();
species_ATP->setId("ATP");
species_ATP->setCompartment(compartment->getId());
SpeciesGlyph* glyph_ATP = layout->createSpeciesGlyph();
glyph_ATP->setId("SpeciesGlyph_ATP");
glyph_ATP->setSpeciesId(species_ATP->getId());
bb = BoundingBox(&layoutns, "bb3", 270, 70, 80, 20);
glyph_ATP->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_ATP");
bb = BoundingBox(&layoutns, "bbB", 280, 70, 60, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_ATP->getId());
tGlyph->setGraphicalObjectId(glyph_ATP->getId());
// ADP
Species* species_ADP = model->createSpecies();
species_ADP->setId("ADP");
species_ADP->setCompartment(compartment->getId());
SpeciesGlyph* glyph_ADP = layout->createSpeciesGlyph();
glyph_ADP->setId("glyph_ADP");
glyph_ADP->setSpeciesId(species_ADP->getId());
bb = BoundingBox(&layoutns, "bb4", 270, 140, 80, 20);
glyph_ADP->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_ADP");
bb = BoundingBox(&layoutns, "bbC", 280, 140, 60, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_ADP->getId());
tGlyph->setGraphicalObjectId(glyph_ADP->getId());
// Phosphate
Species* species_Pi = model->createSpecies();
species_Pi->setId("Pi");
species_Pi->setCompartment(compartment->getId());
SpeciesGlyph* glyph_Pi = layout->createSpeciesGlyph();
glyph_Pi->setId("SpeciesGlyph_Pi");
glyph_Pi->setSpeciesId(species_Pi->getId());
bb = BoundingBox(&layoutns, "bb6", 50, 100, 60, 20);
glyph_Pi->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_PI");
bb = BoundingBox(&layoutns, "bbE", 60, 100, 40, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_Pi->getId());
tGlyph->setGraphicalObjectId(glyph_Pi->getId());
// create the Reaction
Reaction* reaction_Hexokinase = model->createReaction();
reaction_Hexokinase->setId("Hexokinase");
reaction_Hexokinase->setReversible(false);
ReactionGlyph* glyph_Hexokinase = layout->createReactionGlyph();
glyph_Hexokinase->setId("glyph_Hexokinase");
glyph_Hexokinase->setReactionId(reaction_Hexokinase->getId());
Curve* curve_Hexokinase = glyph_Hexokinase->getCurve();
LineSegment* ls = curve_Hexokinase->createLineSegment();
Point p(&layoutns, 170, 100);
ls->setStart(&p);
p = Point(&layoutns, 170, 130);
ls->setEnd(&p);
// create the species reference for glucose
SpeciesReference* reference_Gluc = reaction_Hexokinase->createReactant();
reference_Gluc->setSpecies(species_Gluc->getId());
reference_Gluc->setId("SpeciesReference_Glucose");
// create species reference glyph for glucose
SpeciesReferenceGlyph* speciesReferenceGlyph
= glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_Glucose");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_Gluc->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_Gluc->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_SUBSTRATE);
ls = speciesReferenceGlyph->createLineSegment();
p = Point(&layoutns, 170, 100);
ls->setStart(&p);
p = Point(&layoutns, 170, 50);
ls->setEnd(&p);
// create species reference for ATP
SpeciesReference* reference_ATP
= reaction_Hexokinase->createReactant();
reference_ATP->setSpecies(species_ATP->getId());
reference_ATP->setId("SpeciesReference_ATP");
// create the species reference glyph for ATP
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_ATP");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_ATP->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_ATP->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_SIDESUBSTRATE);
CubicBezier* cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 170, 100);
cb->setStart(&p);
p = Point(&layoutns, 170, 80);
cb->setBasePoint1(&p);
p = Point(&layoutns, 170, 80);
cb->setBasePoint2(&p);
p = Point(&layoutns, 260, 80);
cb->setEnd(&p);
// create species reference for G6P
SpeciesReference* reference_G6P = reaction_Hexokinase->createProduct();
reference_G6P->setSpecies(species_G6P->getId());
reference_G6P->setId("SpeciesReference_G6P");
// create species reference for G6P as product
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_G6P_1");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_G6P->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_G6P->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_PRODUCT);
ls = speciesReferenceGlyph->createLineSegment();
p = Point(&layoutns, 170, 130);
ls->setStart(&p);
p = Point(&layoutns, 170, 180);
ls->setEnd(&p);
// create species reference for ADP
SpeciesReference* reference_ADP = reaction_Hexokinase->createProduct();
reference_ADP->setSpecies(species_ADP->getId());
reference_ADP->setId("SpeciesReference_ADP");
// create the species reference glyph for ADP
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_ADP");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_ADP->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_ADP->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_SIDEPRODUCT);
cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 170, 130);
cb->setStart(&p);
p = Point(&layoutns, 170, 150);
cb->setBasePoint1(&p);
p = Point(&layoutns, 170, 150);
cb->setBasePoint2(&p);
p = Point(&layoutns, 260, 150);
cb->setEnd(&p);
// create modifier species reference for glucose-6-phosphate
ModifierSpeciesReference* reference_G6P_2
= reaction_Hexokinase->createModifier();
reference_G6P_2->setSpecies(species_G6P->getId());
reference_G6P_2->setId("ModifierSpeciesReference_G6P");
reaction_Hexokinase->addModifier(reference_G6P_2);
// create species reference glyph for G6P as a modifier
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_G6P_2");
speciesReferenceGlyph->setSpeciesReferenceId(reference_G6P_2->getId());
speciesReferenceGlyph->setSpeciesGlyphId(glyph_G6P->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_INHIBITOR);
cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 45, 200);
cb->setStart(&p);
p = Point(&layoutns, 0, 200);
cb->setBasePoint1(&p);
p = Point(&layoutns, 0, 120);
cb->setBasePoint2(&p);
p = Point(&layoutns, 165, 120);
cb->setEnd(&p);
// create modifier species reference for phosphate
ModifierSpeciesReference* reference_Pi = reaction_Hexokinase->createModifier();
reference_Pi->setSpecies(species_Pi->getId());
reference_Pi->setId("ModifierSpeciesReference_Pi");
reaction_Hexokinase->addModifier(reference_Pi);
// create the species reference glyph for Phosphate
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_PI");
speciesReferenceGlyph->setSpeciesReferenceId(reference_Pi->getId());
speciesReferenceGlyph->setSpeciesGlyphId(glyph_Pi->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_ACTIVATOR);
cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 115, 110);
cb->setStart(&p);
p = Point(&layoutns, 140, 110);
cb->setBasePoint1(&p);
p = Point(&layoutns, 140, 110);
cb->setBasePoint2(&p);
p = Point(&layoutns, 165, 110);
cb->setEnd(&p);
// write model to file
writeSBML(document, "layout_example3_L2.xml");
delete document;
}
END_TEST
START_TEST ( test_RenderExtension_gradient )
{
RenderPkgNamespaces renderns;
LayoutPkgNamespaces layoutns;
SBMLDocument doc(3,1);
doc.enablePackage(layoutns.getURI(), "layout", true);
doc.enablePackage(renderns.getURI(), "render", true);
Model* model = doc.createModel();
LayoutModelPlugin *lPlugin = (LayoutModelPlugin*)model->getPlugin("layout");
fail_unless(lPlugin != NULL);
Layout* layout = lPlugin->createLayout();
Dimensions dim(&layoutns, 100,100 );
layout->setDimensions(&dim);
GraphicalObject* additional = layout->createAdditionalGraphicalObject();
additional->setId("go1");
BoundingBox bb(&layoutns, "bb1", 10, 10, 90, 90);
additional->setBoundingBox(&bb);
RenderGraphicalObjectPlugin* goPlugin = (RenderGraphicalObjectPlugin*)additional->getPlugin("render");
fail_unless(goPlugin != NULL);
goPlugin->setObjectRole("myRole");
RenderLayoutPlugin *rPlugin = (RenderLayoutPlugin*)layout->getPlugin("render");
fail_unless(rPlugin != NULL);
LocalRenderInformation* local = rPlugin->createLocalRenderInformation();
ColorDefinition *black = local->createColorDefinition();
black->setId("black");
black->setColorValue("#000000");
ColorDefinition *grey = local->createColorDefinition();
grey->setId("grey");
grey->setColorValue("#F0F0F0");
LinearGradient* gradient = local->createLinearGradientDefinition();
gradient->setId("test");
gradient->setPoint1(RelAbsVector(), RelAbsVector());
gradient->setPoint2(RelAbsVector(0,100), RelAbsVector(0,100));
GradientStop *stop = gradient->createGradientStop();
stop->setOffset(RelAbsVector());
stop->setStopColor("white");
stop = gradient->createGradientStop();
stop->setOffset(RelAbsVector(0, 100));
stop->setStopColor("silver");
std::string smodel = writeSBMLToStdString(&doc);
fail_unless( stop->getStopColor() == "silver" );
}
