public void test_SBMLConvertStrict_convertNonStrictSBO()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c");
c.setConstant(false);
(c).setSBOTerm(64);
assertTrue( d.setLevelAndVersion(2,3,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(2,2,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(2,1,true) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
Compartment c1 = d.getModel().getCompartment(0);
assertTrue( (c1).getSBOTerm() == -1 );
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( d.getLevel() == 1 );
assertTrue( d.getVersion() == 2 );
Compartment c2 = d.getModel().getCompartment(0);
assertTrue( (c2).getSBOTerm() == -1 );
d = null;
}
public void test_SBMLDocument_createWith()
{
SBMLDocument d = new SBMLDocument(1,2);
assertTrue( d.getTypeCode() == libsbml.SBML_DOCUMENT );
assertTrue( d.getNotes() == null );
assertTrue( d.getAnnotation() == null );
assertTrue( d.getLevel() == 1 );
assertTrue( d.getVersion() == 2 );
assertTrue( d.getNumErrors() == 0 );
d = null;
}
public void test_SBMLConvertStrict_convertL1ParamRule()
{
SBMLDocument d = new SBMLDocument(1,2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c");
Parameter p = m.createParameter();
p.setId( "p");
Parameter p1 = m.createParameter();
p1.setId( "p1");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable( "p1");
ar.setMath(math);
ar.setUnits( "mole");
assertTrue( d.setLevelAndVersion(2,1,true) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
Rule r1 = d.getModel().getRule(0);
assertTrue( r1.getUnits() == "" );
d = null;
}
public void test_SBMLConvert_addModifiersToReaction()
{
SBMLDocument d = new SBMLDocument(1,2);
Model m = d.createModel();
Reaction r = m.createReaction();
KineticLaw kl = r.createKineticLaw();
kl.setFormula( "k1*S1*S2*S3*S4*S5");
SimpleSpeciesReference ssr1;
SimpleSpeciesReference ssr2;
Species s1 = m.createSpecies();
s1.setId( "S1" );
Species s2 = m.createSpecies();
s2.setId( "S2");
Species s3 = m.createSpecies();
s3.setId( "S3");
Species s4 = m.createSpecies();
s4.setId( "S4");
Species s5 = m.createSpecies();
s5.setId( "S5");
SpeciesReference sr1 = r.createReactant();
SpeciesReference sr2 = r.createReactant();
SpeciesReference sr3 = r.createProduct();
sr1.setSpecies( "S1");
sr2.setSpecies( "S2");
sr3.setSpecies( "S5");
assertTrue( r.getNumModifiers() == 0 );
assertTrue( d.setLevelAndVersion(2,1,false) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
assertTrue( m.getReaction(0).getNumModifiers() == 2 );
ssr1 = m.getReaction(0).getModifier(0);
ssr2 = m.getReaction(0).getModifier(1);
assertTrue(( "S3" == ssr1.getSpecies() ));
assertTrue(( "S4" == ssr2.getSpecies() ));
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictUnits()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c");
c.setConstant(false);
Parameter p = m.createParameter();
p.setId( "p");
p.setUnits( "mole");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable( "c");
ar.setMath(math);
assertTrue( d.setLevelAndVersion(2,1,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(2,2,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(2,3,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(1,2,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
d = null;
}
public void test_SBMLConvertStrict_convertToL1()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = d.createModel();
(m).setMetaId( "_m");
Compartment c = m.createCompartment();
c.setId( "c");
(c).setSBOTerm(240);
Species s = m.createSpecies();
s.setId( "s");
s.setCompartment( "c");
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( d.getLevel() == 1 );
assertTrue( d.getVersion() == 2 );
Model m1 = d.getModel();
assertTrue( (m1).getMetaId() == "" );
Compartment c1 = m1.getCompartment(0);
assertTrue( (c1).getSBOTerm() == -1 );
Species s1 = m1.getSpecies(0);
assertTrue( s1.getHasOnlySubstanceUnits() == false );
d = null;
}
public void test_SBMLConvert_convertToL2_SBMLDocument()
{
SBMLDocument d = new SBMLDocument(1,2);
assertTrue( d.setLevelAndVersion(2,1,false) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
assertTrue( d.setLevelAndVersion(2,2,false) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 2 );
assertTrue( d.setLevelAndVersion(2,3,false) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 3 );
d = null;
}
public void test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string annotation = "<rdf/>\n<rdf/>";
int i = (m).setAnnotation(annotation);
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
assertTrue( (m).getAnnotation().getNumChildren() == 2 );
assertTrue( d.setLevelAndVersion(2,4,true) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
m = d.getModel();
assertTrue( (m).getAnnotation().getNumChildren() == 1 );
d = null;
}
public void test_ReadSBML_SBML()
{
string s = wrapXML("<sbml level='1' version='1'> </sbml>");
D = libsbml.readSBMLFromString(s);
assertTrue( D.getLevel() == 1 );
assertTrue( D.getVersion() == 1 );
}
public void test_SBMLDocument_copyConstructor()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(2,1,false);
assertTrue( o1.getLevel() == 2 );
assertTrue( o1.getVersion() == 1 );
SBMLDocument o2 = new SBMLDocument(o1);
assertTrue( o2.getLevel() == 2 );
assertTrue( o2.getVersion() == 1 );
o2 = null;
o1 = 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_SBMLDocument_assignmentOperator()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(2,1,false);
assertTrue( o1.getLevel() == 2 );
assertTrue( o1.getVersion() == 1 );
SBMLDocument o2 = new SBMLDocument();
o2 = o1;
assertTrue( o2.getLevel() == 2 );
assertTrue( o2.getVersion() == 1 );
o2 = null;
o1 = null;
}