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_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 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_internal_consistency_check_99904_model()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
d.setLevelAndVersion(1,2,false);
Model m = new Model(2,4);
Compartment c = m.createCompartment();
c.setId("cc");
m.setMetaId("mmm");
d.setModel(m);
errors = d.checkInternalConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 20201 );
d = null;
}
public void test_internal_consistency_check_99911_model()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
d.setLevelAndVersion(2,1,false);
Model m = new Model(2,4);
m.setSBOTerm(2);
d.setModel(m);
errors = d.checkInternalConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 20201 );
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 ...");
}
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 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_setModel2()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m1 = new Model(1,2);
int i = d.setModel(m1);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( d.getModel() == null );
d = null;
}
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;
}