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_internal_consistency_check_99902()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Compartment c = new Compartment(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
c.setCompartmentType("hh");
c.setId("c");
m.addCompartment(c);
errors = d.checkInternalConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 10103 );
d = null;
}
public void test_SBMLConvert_convertFromL3()
{
SBMLDocument d = new SBMLDocument(3,1);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits( "volume");
assertTrue( d.setLevelAndVersion(1,1,true) == false );
assertTrue( d.setLevelAndVersion(1,2,true) == false );
assertTrue( d.setLevelAndVersion(2,1,true) == false );
assertTrue( d.setLevelAndVersion(2,2,true) == false );
assertTrue( d.setLevelAndVersion(2,3,true) == false );
assertTrue( d.setLevelAndVersion(2,4,true) == false );
assertTrue( d.setLevelAndVersion(3,1,true) == true );
}
public void test_internal_consistency_check_99903()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Compartment c = new Compartment(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
c.setConstant(true);
c.setId("c");
m.addCompartment(c);
Rule r = m.createAssignmentRule();
r.setVariable("c");
r.setFormula("2*3");
errors = d.checkInternalConsistency();
assertTrue( errors == 3 );
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_internal_consistency_check_99911_react()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
Reaction r = new Reaction(2,4);
d.setLevelAndVersion(2,1,false);
r.setId("r");
r.setSBOTerm(2);
m.addReaction(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99911_param()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
Parameter p = new Parameter(2,4);
d.setLevelAndVersion(2,1,false);
p.setId("p");
p.setSBOTerm(2);
m.addParameter(p);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99904_rule_rate()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Rule r = new RateRule(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
c.setConstant(false);
r.setVariable("cc");
r.setFormula("2");
r.setMetaId("mmm");
m.addRule(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99921()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
SpeciesReference sr = new SpeciesReference(2,4);
d.setLevelAndVersion(2,1,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
Reaction r = m.createReaction();
r.setId("r");
s.setCompartment("c");
sr.setSpecies("s");
sr.setName("mmm");
r.addReactant(sr);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99919()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setId("s");
s.setCompartment("c");
s.setHasOnlySubstanceUnits(true);
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99915_alg()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
Rule r = new AlgebraicRule(2,4);
d.setLevelAndVersion(2,1,false);
r.setUnits("kk");
m.addRule(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99912()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
FunctionDefinition fd = new FunctionDefinition(2,4);
Model m = d.createModel();
d.setLevelAndVersion(1,2,false);
Compartment c = m.createCompartment();
c.setId("cc");
c.setConstant(false);
m.addFunctionDefinition(fd);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99909()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Constraint ct = new Constraint(2,4);
Model m = d.createModel();
d.setLevelAndVersion(2,1,false);
m.addConstraint(ct);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99905_unitdef()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
UnitDefinition u = new UnitDefinition(2,4);
d.setLevelAndVersion(2,2,false);
Model m = d.createModel();
u.setId("ud");
u.setSBOTerm(9);
u.createUnit();
m.addUnitDefinition(u);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99905_trigger()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Trigger trigger = new Trigger(2,4);
Event e = new Event(2,4);
Model m = d.createModel();
d.setLevelAndVersion(2,2,false);
trigger.setSBOTerm(5);
e.setTrigger(trigger);
m.addEvent(e);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99905_stoichmath()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
StoichiometryMath sm = new StoichiometryMath(2,4);
Model m = d.createModel();
d.setLevelAndVersion(2,2,false);
Species s = m.createSpecies();
s.setId("s");
Compartment c = m.createCompartment();
c.setId("c");
s.setCompartment("c");
Reaction r = m.createReaction();
r.setId("r");
SpeciesReference sr = r.createProduct();
sr.setSpecies("s");
sm.setSBOTerm(5);
sr.setStoichiometryMath(sm);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99905_st()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
SpeciesType ct = new SpeciesType(2,4);
Model m = d.createModel();
d.setLevelAndVersion(2,2,false);
ct.setId("st");
ct.setSBOTerm(5);
m.addSpeciesType(ct);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99904_unitdef()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
UnitDefinition u = new UnitDefinition(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
u.setId("ud");
u.setMetaId("mmm");
u.createUnit();
m.addUnitDefinition(u);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99911_rule_rate()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
Parameter p = m.createParameter();
p.setId("p");
p.setConstant(false);
Rule r = new RateRule(2,4);
d.setLevelAndVersion(2,1,false);
r.setVariable("p");
r.setSBOTerm(2);
m.addRule(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99911_ea()
{
SBMLDocument d = new SBMLDocument(2,4);
d.setLevelAndVersion(2,1,false);
long errors;
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
Event e = m.createEvent();
EventAssignment ea = new EventAssignment(2,4);
ea.setVariable("c");
ea.setSBOTerm(2);
e.addEventAssignment(ea);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99911_event()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Event e = new Event(2,4);
Model m = d.createModel();
d.setLevelAndVersion(2,1,false);
e.setSBOTerm(2);
m.addEvent(e);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99913()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
InitialAssignment ia = new InitialAssignment(2,4);
Model m = d.createModel();
d.setLevelAndVersion(1,2,false);
Compartment c = m.createCompartment();
c.setId("cc");
c.setConstant(false);
m.addInitialAssignment(ia);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99904_param()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Parameter p = new Parameter(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
p.setId("p");
p.setMetaId("mmm");
m.addParameter(p);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99915_rate()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
RateRule r = m.createRateRule();
r.setL1TypeCode(libsbml.SBML_SPECIES_CONCENTRATION_RULE);
r.setFormula("2");
r.setVariable("c");
r.setUnits("mmm");
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99911_fd()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
FunctionDefinition fd = new FunctionDefinition(2,4);
d.setLevelAndVersion(2,1,false);
fd.setId("fd");
fd.setSBOTerm(2);
m.addFunctionDefinition(fd);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99903_localparam()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Parameter p = new Parameter(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
Reaction r = m.createReaction();
r.setId("r");
KineticLaw kl = r.createKineticLaw();
kl.setFormula("2");
p.setId("p");
p.setConstant(false);
kl.addParameter(p);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99911_kl()
{
SBMLDocument d = new SBMLDocument(2,4);
d.setLevelAndVersion(2,1,false);
long errors;
Model m = d.createModel();
Reaction r = m.createReaction();
r.setId("r");
KineticLaw kl = new KineticLaw(2,4);
kl.setSBOTerm(2);
Parameter p = kl.createParameter();
p.setId("p");
r.setKineticLaw(kl);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
static void testCreateSBML()
{
SBMLDocument d = new SBMLDocument(defLevel,defVersion);
Model m = d.createModel();
m.setId("testmodel");
Compartment c1 = m.createCompartment();
Compartment c2 = m.createCompartment();
c1.setId("c1");
c2.setId("c2");
Species s1 = m.createSpecies();
Species s2 = m.createSpecies();
string id1 = "s1";
string id2 = "s2";
// strings with non-ASCII characters (multibyte characters)
string n1 = "γ-lyase";
string n2 = "β-synthase";
s1.setId(id1);
s1.setName(n1);
s1.setCompartment("c1");
s2.setId(id2);
s2.setName(n2);
s2.setCompartment("c2");
string file = "test2.xml";
try
{
if ( libsbml.writeSBML(d, file) == 0)
{
ERR("[CreateSBML] Error: cannot write " + file);
}
else
{
OK();
}
}
catch (Exception e)
{
ERR("[CreateSBML] (" + file + ") Error: Exception thrown : " + e.Message);
}
testReadSBMLFromFile(file);
}
public void test_internal_consistency_check_99904_react()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Reaction r = new Reaction(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
r.setId("r");
r.setMetaId("mmm");
m.addReaction(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}