| public setLevelAndVersion ( long level, long version ) : bool | ||
| level | long | |
| version | long | |
| return | bool | |
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_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 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_SBMLConvert_convertToL3_reaction()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
string sid = "C";
Reaction r = m.createReaction();
r.setId(sid);
assertTrue( d.setLevelAndVersion(3,1,false) == true );
Reaction r1 = m.getReaction(0);
assertTrue( r1.hasRequiredAttributes() == true );
d = null;
}
public void test_SBMLConvert_convertToL3_species()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
string sid = "C";
Species s = m.createSpecies();
Species s1;
s.setId(sid);
s.setCompartment( "comp");
assertTrue( d.setLevelAndVersion(3,1,false) == true );
s1 = m.getSpecies(0);
assertTrue( s1.hasRequiredAttributes() == true );
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_convertFromL3_modelUnits()
{
UnitDefinition ud;
SBMLDocument d = new SBMLDocument(3,1);
Model m = d.createModel();
m.setVolumeUnits( "litre");
assertTrue( m.getNumUnitDefinitions() == 0 );
assertTrue( d.setLevelAndVersion(1,2,false) == true );
m = d.getModel();
assertTrue( m.getNumUnitDefinitions() == 1 );
ud = m.getUnitDefinition(0);
assertTrue(( "volume" == ud.getId() ));
assertTrue( ud.getNumUnits() == 1 );
assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE );
}
public void test_SBMLConvert_convertToL3_unit()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
string sid = "C";
UnitDefinition ud = m.createUnitDefinition();
ud.setId(sid);
Unit u = ud.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
assertTrue( d.setLevelAndVersion(3,1,false) == true );
Unit u1 = m.getUnitDefinition(0).getUnit(0);
assertTrue( u1.hasRequiredAttributes() == true );
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.setConstant(true);
c.setSpatialDimensions(3.4);
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_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_convertToL3_compartment()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
Compartment c1;
c.setId(sid);
assertTrue( d.setLevelAndVersion(3,1,false) == true );
c1 = m.getCompartment(0);
assertTrue( c1.hasRequiredAttributes() == true );
d = null;
}
public void test_SBMLConvert_convertToL1_Species_Concentration()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2,1);
Species s = new Species(2,1);
c.setId(sid);
c.setSize(1.2);
m.addCompartment(c);
s.setId( "s" );
s.setCompartment(sid);
s.setInitialConcentration(2.34);
m.addSpecies(s);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
Species s1 = m.getSpecies(0);
assertTrue( s1 != null );
assertTrue(( "C" == s1.getCompartment() ));
assertTrue( m.getCompartment( "C").getSize() == 1.2 );
assertTrue( s1.getInitialConcentration() == 2.34 );
assertTrue( s1.isSetInitialConcentration() == true );
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_SBMLConvert_convertToL1_Species_Amount()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2,4);
Species s = new Species(2,4);
c.setId(sid);
m.addCompartment(c);
s.setCompartment(sid);
s.setInitialAmount(2.34);
m.addSpecies(s);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( s.getInitialAmount() == 2.34 );
d = null;
}
public void test_SBMLConvert_convertFromL3_priority()
{
SBMLDocument d = new SBMLDocument(3,1);
Model m = d.createModel();
Event e = m.createEvent();
Priority p = e.createPriority();
assertTrue( d.setLevelAndVersion(1,1,false) == false );
assertTrue( d.setLevelAndVersion(1,2,false) == false );
assertTrue( d.setLevelAndVersion(2,1,false) == true );
assertTrue( d.setLevelAndVersion(2,2,false) == true );
assertTrue( d.setLevelAndVersion(2,3,false) == true );
assertTrue( d.setLevelAndVersion(2,4,false) == true );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
}
public void test_SBMLConvert_convertFromL3_persistent()
{
SBMLDocument d = new SBMLDocument(3,1);
Model m = d.createModel();
Event e = m.createEvent();
Trigger t = e.createTrigger();
t.setPersistent(false);
assertTrue( d.setLevelAndVersion(1,1,false) == false );
assertTrue( d.setLevelAndVersion(1,2,false) == false );
assertTrue( d.setLevelAndVersion(2,1,false) == false );
assertTrue( d.setLevelAndVersion(2,2,false) == false );
assertTrue( d.setLevelAndVersion(2,3,false) == false );
assertTrue( d.setLevelAndVersion(2,4,false) == false );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
}
public void test_SBMLConvert_convertToL3_stoichiometryMath()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c" );
Species s = m.createSpecies();
s.setId( "s");
s.setCompartment( "c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies( "s");
StoichiometryMath sm = sr.createStoichiometryMath();
ASTNode ast = libsbml.parseFormula("c*2");
sm.setMath(ast);
assertTrue( m.getNumRules() == 0 );
assertTrue( sr.isSetId() == false );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
m = d.getModel();
r = m.getReaction(0);
sr = r.getReactant(0);
assertTrue( m.getNumRules() == 1 );
assertTrue( sr.isSetId() == true );
Rule rule = m.getRule(0);
assertTrue(( rule.getVariable() == sr.getId() ));
d = null;
}
public void test_SBMLConvert_convertToL3_defaultUnits()
{
SBMLDocument d = new SBMLDocument(1,2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits( "volume");
assertTrue( m.getNumUnitDefinitions() == 0 );
assertTrue( d.setLevelAndVersion(3,1,true) == true );
assertTrue( m.getNumUnitDefinitions() == 2 );
UnitDefinition ud = m.getUnitDefinition(0);
assertTrue( ud != null );
assertTrue(( "volume" == ud.getId() ));
assertTrue( ud.getNumUnits() == 1 );
Unit u = ud.getUnit(0);
assertTrue( u.getKind() == libsbml.UNIT_KIND_LITRE );
assertTrue( u.getExponent() == 1 );
assertTrue( u.getMultiplier() == 1 );
assertTrue( u.getScale() == 0 );
ud = m.getUnitDefinition(1);
assertTrue( ud != null );
assertTrue(( "time" == ud.getId() ));
assertTrue( ud.getNumUnits() == 1 );
u = ud.getUnit(0);
assertTrue( u.getKind() == libsbml.UNIT_KIND_SECOND );
assertTrue( u.getExponent() == 1 );
assertTrue( u.getMultiplier() == 1 );
assertTrue( u.getScale() == 0 );
assertTrue(( "time" == m.getTimeUnits() ));
d = null;
}
public void test_SBMLConvert_convertToL3_trigger()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
Event e = m.createEvent();
Trigger t = e.createTrigger();
Trigger t1;
assertTrue( d.setLevelAndVersion(3,1,false) == true );
t1 = m.getEvent(0).getTrigger();
assertTrue( t1.hasRequiredAttributes() == true );
d = null;
}
public void test_internal_consistency_check_99904_species()
{
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.setCompartment("c");
s.setId("s");
s.setMetaId("mmm");
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_SBMLConvert_invalidLevelVersion()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits( "volume");
assertTrue( d.setLevelAndVersion(1,3,true) == false );
assertTrue( d.setLevelAndVersion(2,5,true) == false );
assertTrue( d.setLevelAndVersion(3,2,true) == false );
assertTrue( d.setLevelAndVersion(4,1,true) == false );
}
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_SBMLConvert_convertFromL3_conversionFactor()
{
SBMLDocument d = new SBMLDocument(3,1);
Model m = d.createModel();
string sid = "P";
m.setConversionFactor(sid);
Parameter c = m.createParameter();
c.setId(sid);
c.setConstant(true);
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_SBMLConvert_convertToL3_reactant()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
SpeciesReference sr1;
sr.setSpecies( "s" );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
sr1 = m.getReaction(0).getReactant(0);
assertTrue( sr1.hasRequiredAttributes() == true );
d = null;
}
public void test_SBMLConvert_convertToL3_localParameters()
{
SBMLDocument d = new SBMLDocument(1,2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c" );
Species s = m.createSpecies();
s.setId( "s");
s.setCompartment( "c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies( "s");
KineticLaw kl = r.createKineticLaw();
kl.setFormula( "s*k");
Parameter p = kl.createParameter();
p.setId( "k");
assertTrue( kl.getNumLocalParameters() == 0 );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
m = d.getModel();
r = m.getReaction(0);
kl = r.getKineticLaw();
assertTrue( kl.getNumLocalParameters() == 1 );
LocalParameter lp = kl.getLocalParameter(0);
d = null;
}
public void setUp()
{
D = new SBMLDocument();
D.setLevelAndVersion(3,1,false);
S = 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_SBMLConvert_convertToL3_parameter()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m = d.createModel();
string sid = "C";
Parameter p = m.createParameter();
Parameter p1;
p.setId(sid);
assertTrue( d.setLevelAndVersion(3,1,false) == true );
p1 = m.getParameter(0);
assertTrue( p1.hasRequiredAttributes() == true );
d = null;
}