/**
* Copy constructor.
*/
SpeciesReferenceGlyph::SpeciesReferenceGlyph(const SpeciesReferenceGlyph& source) :
GraphicalObject(source)
{
this->mSpeciesReference=source.getSpeciesReferenceId();
this->mSpeciesGlyph=source.getSpeciesGlyphId();
this->mRole=source.getRole();
this->mCurve=*source.getCurve();
}
/*
* Copy constructor.
*/
SpeciesReferenceGlyph::SpeciesReferenceGlyph(const SpeciesReferenceGlyph& source) :
GraphicalObject(source)
{
this->mSpeciesReference=source.getSpeciesReferenceId();
this->mSpeciesGlyph=source.getSpeciesGlyphId();
this->mRole=source.getRole();
this->mCurve=*source.getCurve();
this->mCurveExplicitlySet = source.mCurveExplicitlySet;
connectToChild();
}
CLMetabReferenceGlyph::CLMetabReferenceGlyph(const SpeciesReferenceGlyph & sbml,
const std::map<std::string, std::string> & modelmap,
std::map<std::string, std::string> & layoutmap,
const CCopasiContainer * pParent)
: CLGlyphWithCurve(sbml, modelmap, layoutmap, pParent),
mMetabGlyphKey(), //initialized in the body below
mRole((Role)sbml.getRole())
{
//get the copasi key corresponding to the sbml id for the species reference
if (sbml.getSpeciesReferenceId() != "")
{
std::map<std::string, std::string>::const_iterator it = modelmap.find(sbml.getSpeciesReferenceId());
if (it != modelmap.end())
setModelObjectKey(it->second);
}
//get the copasi key corresponding to the sbml id for the species glyph
if (sbml.getSpeciesGlyphId() != "")
{
std::map<std::string, std::string>::const_iterator it = layoutmap.find(sbml.getSpeciesGlyphId());
if (it != layoutmap.end())
mMetabGlyphKey = it->second;
}
//curve
if (sbml.getCurve())
{
CLCurve copy(*sbml.getCurve());
mCurve = copy;
}
}
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;
}