public void test_SBMLDocument_setModel()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m1 = new Model(2, 4);
Model m2 = new Model(2, 4);
Model mout;
assertTrue(d.getModel() == null);
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
mout = d.getModel();
assertTrue(mout != null);
assertTrue(mout != m1);
i = d.setModel(d.getModel());
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
mout = d.getModel();
assertTrue(mout != null);
assertTrue(mout != m1);
i = d.setModel(m2);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
mout = d.getModel();
assertTrue(mout != null);
assertTrue(mout != m2);
d = null;
}
public void test_SBMLDocument_clone()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(1, 1, false);
Model m = new Model(1, 1);
m.createCompartment();
m.createSpecies();
m.createReaction();
m.setId("foo");
o1.setModel(m);
assertTrue(o1.getLevel() == 1);
assertTrue(o1.getVersion() == 1);
assertTrue(o1.getModel().getId() == "foo");
assertTrue(o1.getModel().getLevel() == 1);
assertTrue(o1.getModel().getVersion() == 1);
assertTrue(o1.getModel().getSBMLDocument() == o1);
SBMLDocument o2 = o1.clone();
assertTrue(o2.getLevel() == 1);
assertTrue(o2.getVersion() == 1);
assertTrue(o2.getModel().getId() == "foo");
assertTrue(o2.getModel().getLevel() == 1);
assertTrue(o2.getModel().getVersion() == 1);
assertTrue(o2.getModel().getSBMLDocument() == o2);
o2 = null;
o1 = null;
}
public void test_Model_parent_add()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = new Model(2, 4);
d.setModel(m);
assertTrue(d == d.getModel().getParentSBMLObject());
d = null;
}
public void test_Model_ancestor_add()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = new Model(2, 4);
d.setModel(m);
assertTrue(d == d.getModel().getAncestorOfType(libsbml.SBML_DOCUMENT));
d = null;
}
public void test_SBMLDocument_setModel3()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 2);
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(d.getModel() != null);
d = null;
}
public void test_SBMLDocument_setModel1()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 1);
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_VERSION_MISMATCH);
assertTrue(d.getModel() == null);
d = null;
}
public void test_SBMLDocument_setModel2()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(1, 2);
m1.createCompartment();
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_LEVEL_MISMATCH);
assertTrue(d.getModel() == null);
d = null;
}
public void test_SBMLDocument_setLevelAndVersion()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 2);
d.setModel(m1);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
d = null;
}
public void test_SBMLDocument_setLevelAndVersion_Error()
{
SBMLDocument d = new SBMLDocument();
d.setLevelAndVersion(2, 1, true);
Model m1 = new Model(2, 1);
Unit u = new Unit(2, 1);
u.setKind(libsbml.UnitKind_forName("mole"));
u.setOffset(3.2);
UnitDefinition ud = new UnitDefinition(2, 1);
ud.setId("ud");
ud.addUnit(u);
m1.addUnitDefinition(ud);
d.setModel(m1);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.setLevelAndVersion(1, 1, true) == false);
d = null;
}
public static void Main(string[] args)
{
Model model = new Model(3, 1);
Compartment compartment = new Compartment(3, 1);
compartment.setId("cheese");
compartment.setName("french-cheese");
model.addCompartment(compartment);
Species species = new Species(3, 1);
species.setId("salmonella");
species.setName("german-salmonella");
model.addSpecies(species);
SBMLDocument doc = new SBMLDocument(3, 1);
doc.setModel(model);
Console.Write(new SBMLWriter().writeSBMLToString(doc));
}
public void test_create_l1v1_units()
{
SBMLDocument d;
Model m;
Compartment c;
KineticLaw kl;
Parameter p;
Reaction r;
Species s;
SpeciesReference sr;
Unit u;
UnitDefinition ud;
d = new SBMLDocument();
m = new Model(2, 4);
d.setModel(m);
ud = m.createUnitDefinition();
ud.setName("substance");
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
u.setScale(-3);
ud = m.createUnitDefinition();
ud.setName("mls");
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
u.setScale(-3);
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_LITER);
u.setExponent(-1);
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_SECOND);
u.setExponent(-1);
c = m.createCompartment();
c.setName("cell");
s = m.createSpecies();
s.setName("x0");
s.setCompartment("cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName("x1");
s.setCompartment("cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName("s1");
s.setCompartment("cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName("s2");
s.setCompartment("cell");
s.setInitialAmount(1);
p = m.createParameter();
p.setName("vm");
p.setUnits("mls");
p.setValue(2);
p = m.createParameter();
p.setName("km");
p.setValue(2);
r = m.createReaction();
r.setName("v1");
sr = m.createReactant();
sr.setSpecies("x0");
sr = m.createProduct();
sr.setSpecies("s1");
kl = m.createKineticLaw();
kl.setFormula("(vm * s1)/(km + s1)");
r = m.createReaction();
r.setName("v2");
sr = m.createReactant();
sr.setSpecies("s1");
sr = m.createProduct();
sr.setSpecies("s2");
kl = m.createKineticLaw();
kl.setFormula("(vm * s2)/(km + s2)");
r = m.createReaction();
r.setName("v3");
sr = m.createReactant();
sr.setSpecies("s2");
sr = m.createProduct();
sr.setSpecies("x1");
kl = m.createKineticLaw();
kl.setFormula("(vm * s1)/(km + s1)");
d = null;
}
public static void Main(string[] args)
{
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "layout") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"layout",1,"LAYOUT");
//
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "layout", 1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a layout package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("layout",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(LayoutExtension::XmlnsL3V1V1,"layout");
//
// (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,
// and package version
//
// LayoutPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// set the "required" attribute of layout package to "true"
document.setPkgRequired("layout", true);
// create the Model
Model model = document.createModel();
model.setId("TestModel");
document.setModel(model);
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("Compartment_1");
compartment.setConstant(true);
// create the Species
Species species1 = model.createSpecies();
species1.setId("Species_1");
species1.setCompartment(compartment.getId());
species1.setHasOnlySubstanceUnits(false);
species1.setBoundaryCondition(false);
species1.setConstant(false);
Species species2 = model.createSpecies();
species2.setId("Species_2");
species2.setCompartment(compartment.getId());
species2.setHasOnlySubstanceUnits(false);
species2.setBoundaryCondition(false);
species2.setConstant(false);
// create the Reactions
Reaction reaction1 = model.createReaction();
reaction1.setId("Reaction_1");
reaction1.setReversible(false);
reaction1.setFast(false);
SpeciesReference reference1 = reaction1.createReactant();
reference1.setSpecies(species1.getId());
reference1.setId("SpeciesReference_1");
reference1.setConstant(false);
SpeciesReference reference2 = reaction1.createProduct();
reference2.setSpecies(species2.getId());
reference2.setId("SpeciesReference_2");
reference2.setConstant(false);
Reaction reaction2 = model.createReaction();
reaction2.setId("Reaction_2");
reaction2.setReversible(false);
reaction2.setFast(false);
SpeciesReference reference3 = reaction2.createReactant();
reference3.setSpecies(species2.getId());
reference3.setId("SpeciesReference_3");
reference3.setConstant(false);
SpeciesReference reference4 = reaction2.createProduct();
reference4.setSpecies(species1.getId());
reference4.setId("SpeciesReference_4");
reference4.setConstant(false);
// create the Layout
//
// set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
//
LayoutPkgNamespaces layoutns = new LayoutPkgNamespaces(3, 1, 1);
//
// Get a LayoutModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
LayoutModelPlugin mplugin = (LayoutModelPlugin)(model.getPlugin("layout"));
if (mplugin == null)
{
Console.Error.WriteLine("[Fatal Error] Layout Extension Level " + layoutns.getLevel() + " Version " + layoutns.getVersion() + " package version " + layoutns.getPackageVersion() + " is not registered.");
Environment.Exit(1);
}
//
// Creates a Layout object via LayoutModelPlugin object.
//
Layout layout = mplugin.createLayout();
layout.setId("Layout_1");
Dimensions dim = new Dimensions(layoutns, 400.0, 220.0);
layout.setDimensions(dim);
// create the CompartmentGlyph
CompartmentGlyph compartmentGlyph = layout.createCompartmentGlyph();
compartmentGlyph.setId("CompartmentGlyph_1");
compartmentGlyph.setCompartmentId(compartment.getId());
BoundingBox bb = new BoundingBox(layoutns, "bb1", 5, 5, 390, 210);
compartmentGlyph.setBoundingBox(bb);
// create the SpeciesGlyphs
SpeciesGlyph speciesGlyph1 = layout.createSpeciesGlyph();
speciesGlyph1.setId("SpeciesGlyph_1");
speciesGlyph1.setSpeciesId(species1.getId());
bb = new BoundingBox(layoutns, "bb2", 80, 26, 240, 24);
speciesGlyph1.setBoundingBox(bb);
TextGlyph textGlyph1 = layout.createTextGlyph();
textGlyph1.setId("TextGlyph_01");
bb = new BoundingBox(layoutns, "bbA", 92, 26, 228, 24);
textGlyph1.setBoundingBox(bb);
textGlyph1.setOriginOfTextId(speciesGlyph1.getId());
textGlyph1.setGraphicalObjectId(speciesGlyph1.getId());
SpeciesGlyph speciesGlyph2 = layout.createSpeciesGlyph();
speciesGlyph2.setId("SpeciesGlyph_2");
speciesGlyph2.setSpeciesId(species2.getId());
bb = new BoundingBox(layoutns, "bb3", 80, 170, 240, 24);
speciesGlyph2.setBoundingBox(bb);
TextGlyph textGlyph2 = layout.createTextGlyph();
textGlyph2.setId("TextGlyph_02");
bb = new BoundingBox(layoutns, "bbB", 92, 170, 228, 24);
textGlyph2.setBoundingBox(bb);
textGlyph2.setOriginOfTextId(speciesGlyph2.getId());
textGlyph2.setGraphicalObjectId(speciesGlyph2.getId());
// create the ReactionGlyphs
ReactionGlyph reactionGlyph1 = layout.createReactionGlyph();
reactionGlyph1.setId("ReactionGlyph_1");
reactionGlyph1.setReactionId(reaction1.getId());
Curve reactionCurve1 = reactionGlyph1.getCurve();
LineSegment ls = reactionCurve1.createLineSegment();
Point p = new Point(layoutns, 165, 105);
ls.setStart(p);
p = new Point(layoutns, 165, 115);
ls.setEnd(p);
ReactionGlyph reactionGlyph2 = layout.createReactionGlyph();
reactionGlyph2.setId("ReactionGlyph_1");
reactionGlyph2.setReactionId(reaction2.getId());
Curve reactionCurve2 = reactionGlyph2.getCurve();
ls = reactionCurve2.createLineSegment();
p = new Point(layoutns, 235, 105);
ls.setStart(p);
p = new Point(layoutns, 235, 115);
ls.setEnd(p);
// add the SpeciesReferenceGlyphs
SpeciesReferenceGlyph speciesReferenceGlyph1 = reactionGlyph1.createSpeciesReferenceGlyph();
speciesReferenceGlyph1.setId("SpeciesReferenceGlyph_1");
speciesReferenceGlyph1.setSpeciesGlyphId(speciesGlyph1.getId());
speciesReferenceGlyph1.setSpeciesReferenceId(reference1.getId());
speciesReferenceGlyph1.setRole(libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve1 = speciesReferenceGlyph1.getCurve();
CubicBezier cb = speciesReferenceCurve1.createCubicBezier();
p = new Point(layoutns, 165, 105);
cb.setStart(p);
p = new Point(layoutns, 165, 90);
cb.setBasePoint1(p);
p = new Point(layoutns, 165, 90);
cb.setBasePoint2(p);
p = new Point(layoutns, 195, 60);
cb.setEnd(p);
SpeciesReferenceGlyph speciesReferenceGlyph2 = reactionGlyph1.createSpeciesReferenceGlyph();
speciesReferenceGlyph2.setId("SpeciesReferenceGlyph_2");
speciesReferenceGlyph2.setSpeciesGlyphId(speciesGlyph2.getId());
speciesReferenceGlyph2.setSpeciesReferenceId(reference2.getId());
speciesReferenceGlyph2.setRole(libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve2 = speciesReferenceGlyph2.getCurve();
cb = speciesReferenceCurve2.createCubicBezier();
p = new Point(layoutns, 165, 115);
cb.setStart(p);
p = new Point(layoutns, 165, 130);
cb.setBasePoint1(p);
p = new Point(layoutns, 165, 130);
cb.setBasePoint2(p);
p = new Point(layoutns, 195, 160);
cb.setEnd(p);
SpeciesReferenceGlyph speciesReferenceGlyph3 = reactionGlyph2.createSpeciesReferenceGlyph();
speciesReferenceGlyph3.setId("SpeciesReferenceGlyph_3");
speciesReferenceGlyph3.setSpeciesGlyphId(speciesGlyph2.getId());
speciesReferenceGlyph3.setSpeciesReferenceId(reference3.getId());
speciesReferenceGlyph3.setRole(libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve3 = speciesReferenceGlyph3.getCurve();
cb = speciesReferenceCurve3.createCubicBezier();
p = new Point(layoutns, 235, 115);
cb.setStart(p);
p = new Point(layoutns, 235, 130);
cb.setBasePoint1(p);
p = new Point(layoutns, 235, 130);
cb.setBasePoint2(p);
p = new Point(layoutns, 205, 160);
cb.setEnd(p);
SpeciesReferenceGlyph speciesReferenceGlyph4 = reactionGlyph2.createSpeciesReferenceGlyph();
speciesReferenceGlyph4.setId("SpeciesReferenceGlyph_4");
speciesReferenceGlyph4.setSpeciesGlyphId(speciesGlyph1.getId());
speciesReferenceGlyph4.setSpeciesReferenceId(reference4.getId());
speciesReferenceGlyph4.setRole(libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve4 = speciesReferenceGlyph4.getCurve();
cb = speciesReferenceCurve4.createCubicBezier();
p = new Point(layoutns, 235, 105);
cb.setStart(p);
p = new Point(layoutns, 235, 90);
cb.setBasePoint1(p);
p = new Point(layoutns, 235, 90);
cb.setBasePoint2(p);
p = new Point(layoutns, 205, 60);
cb.setEnd(p);
libsbml.writeSBML(document, "layout_example1_L3-cs.xml");
Console.WriteLine("all done ...");
}