public void TestAll()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_BIOMD0000000003);
Model sbmlModel = document.getModel();
// Set FunctionDefinition
ASTNode math = libsbml.libsbml.parseFormula("V0 * 5");
FunctionDefinition fd = sbmlModel.createFunctionDefinition();
fd.setId("FD");
fd.setName("FD");
fd.setMath(math);
// Set Event
Event ev = sbmlModel.createEvent();
ev.setId("Event");
ev.setName("Event");
ev.setTrigger(new Trigger(2,3));
EventAssignment ea = ev.createEventAssignment();
ea.setId("Assignment");
ea.setName("Assignment");
// Set Initial Amount
InitialAssignment ia = sbmlModel.createInitialAssignment();
ia.setSymbol("M1");
ia.setMath(math);
// Set UnitDefinition
UnitDefinition ud = sbmlModel.createUnitDefinition();
ud.setId("UD");
ud.setName("UD");
Unit unit = ud.createUnit();
unit.setId("Unit");
unit.setName("Unit");
//
SBML_Model model = new SBML_Model(sbmlModel);
}
public void test_SBMLTransforms_replaceFD()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
ASTNode ast;
FunctionDefinition fd;
ListOfFunctionDefinitions lofd;
string filename = "../../sbml/test/test-data/";
filename += "multiple-functions.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
m = d.getModel();
assertTrue( m.getNumFunctionDefinitions() == 2 );
d.expandFunctionDefinitions();
assertTrue( d.getModel().getNumFunctionDefinitions() == 0 );
ast = d.getModel().getReaction(0).getKineticLaw().getMath();
assertTrue(( "S1 * p * compartmentOne / t" == libsbml.formulaToString(ast) ));
ast = d.getModel().getReaction(1).getKineticLaw().getMath();
assertTrue(( "S1 * p * compartmentOne / t" == libsbml.formulaToString(ast) ));
ast = d.getModel().getReaction(2).getKineticLaw().getMath();
assertTrue(( "S1 * p * compartmentOne / t" == libsbml.formulaToString(ast) ));
}
internal static HandleRef getCPtrAndDisown(SBMLReader obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return(ptr);
}
public void test_read_l2v4_new()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
Compartment c;
Event e;
Trigger trigger;
EventAssignment ea;
ASTNode ast;
string filename = "../../sbml/test/test-data/";
filename += "l2v4-new.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
m = d.getModel();
assertTrue( m != null );
assertTrue( m.getId() == "l2v4_all" );
assertTrue( m.getNumCompartments() == 1 );
c = m.getCompartment(0);
assertTrue( c != null );
assertTrue( c.getId() == "a" );
assertTrue( c.getSize() == 1 );
assertEquals( false, c.getConstant() );
assertTrue( m.getNumEvents() == 1 );
e = m.getEvent(0);
assertTrue( e != null );
assertEquals( true, e.getUseValuesFromTriggerTime() );
assertEquals( true, e.isSetTrigger() );
trigger = e.getTrigger();
assertTrue( trigger != null );
ast = trigger.getMath();
assertTrue(( "lt(x, 3)" == libsbml.formulaToString(ast) ));
assertTrue( e.getNumEventAssignments() == 1 );
ea = e.getEventAssignment(0);
assertTrue( ea != null );
assertTrue( ea.getVariable() == "a" );
ast = ea.getMath();
assertTrue(( "x * p3" == libsbml.formulaToString(ast) ));
d = null;
}
public void test_consistency_checks()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
long errors;
string filename = "../../sbml/test/test-data/";
filename += "inconsistent.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
errors = d.checkConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 10301 );
d.getErrorLog().clearLog();
d.setConsistencyChecks(libsbml.LIBSBML_CAT_IDENTIFIER_CONSISTENCY,false);
errors = d.checkConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 20612 );
d.getErrorLog().clearLog();
d.setConsistencyChecks(libsbml.LIBSBML_CAT_GENERAL_CONSISTENCY,false);
errors = d.checkConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 10701 );
d.getErrorLog().clearLog();
d.setConsistencyChecks(libsbml.LIBSBML_CAT_SBO_CONSISTENCY,false);
errors = d.checkConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 10214 );
d.getErrorLog().clearLog();
d.setConsistencyChecks(libsbml.LIBSBML_CAT_MATHML_CONSISTENCY,false);
errors = d.checkConsistency();
assertTrue( errors == 3 );
assertTrue( d.getError(0).getErrorId() == 99505 );
assertTrue( d.getError(1).getErrorId() == 99505 );
assertTrue( d.getError(2).getErrorId() == 80701 );
d.getErrorLog().clearLog();
d.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY,false);
errors = d.checkConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_SBMLTransforms_replaceIA()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
ASTNode ast;
FunctionDefinition fd;
ListOfFunctionDefinitions lofd;
string filename = "../../sbml/test/test-data/";
filename += "initialAssignments.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
m = d.getModel();
assertTrue( m.getNumInitialAssignments() == 2 );
assertEquals( false, (m.getCompartment(0).isSetSize()) );
assertTrue( m.getParameter(1).getValue() == 2 );
d.expandInitialAssignments();
assertTrue( d.getModel().getNumInitialAssignments() == 0 );
assertEquals( true, d.getModel().getCompartment(0).isSetSize() );
assertTrue( d.getModel().getCompartment(0).getSize() == 25.0 );
assertTrue( m.getParameter(1).getValue() == 50 );
}
public void TestSBML_Parameter()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Parameter p = new SBML_Parameter(model);
ParameterStruct ps = new ParameterStruct();
// getParameterID
ps.ID = "Test1";
string id = p.getParameterID(ps);
Assert.AreEqual("/SBMLParameter:Test1", id, "getParameterID returns unexpected value.");
try
{
ps.ID = "";
id = p.getParameterID(ps);
}
catch (Exception)
{
}
model.Level = 1;
ps.Name = "Test2";
id = p.getParameterID(ps);
Assert.AreEqual("/SBMLParameter:Test2", id, "getParameterID returns unexpected value.");
try
{
ps.Name = "";
id = p.getParameterID(ps);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = p.getParameterID(ps);
}
catch (Exception)
{
}
}
internal static HandleRef getCPtr(SBMLReader obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
public void test_read_l3v1_new()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
UnitDefinition ud;
Unit u;
Compartment c;
Species s;
Parameter p;
Reaction r;
SpeciesReference sr;
KineticLaw kl;
LocalParameter lp;
string filename = "../../sbml/test/test-data/";
filename += "l3v1-new.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
assertTrue( d.getLevel() == 3 );
assertTrue( d.getVersion() == 1 );
m = d.getModel();
assertTrue( m != null );
assertEquals( true, m.isSetSubstanceUnits() );
assertEquals( true, m.isSetTimeUnits() );
assertEquals( true, m.isSetVolumeUnits() );
assertEquals( true, m.isSetLengthUnits() );
assertEquals( true, m.isSetAreaUnits() );
assertEquals( true, m.isSetExtentUnits() );
assertEquals( true, m.isSetConversionFactor() );
assertTrue( m.getSubstanceUnits() == "mole" );
assertTrue( m.getTimeUnits() == "second" );
assertTrue( m.getVolumeUnits() == "litre" );
assertTrue( m.getLengthUnits() == "metre" );
assertTrue( m.getAreaUnits() == "metre" );
assertTrue( m.getExtentUnits() == "mole" );
assertTrue( m.getConversionFactor() == "p" );
assertTrue( m.getNumUnitDefinitions() == 2 );
ud = m.getUnitDefinition(0);
assertTrue( ud.getNumUnits() == 1 );
u = ud.getUnit(0);
assertEquals( false, u.isSetExponent() );
assertEquals( false, u.isSetScale() );
assertEquals( false, u.isSetMultiplier() );
assertEquals( true, isnan(u.getExponentAsDouble()) );
assertTrue( u.getScale() == SBML_INT_MAX );
assertEquals( true, isnan(u.getMultiplier()) );
ud = m.getUnitDefinition(1);
assertTrue( ud.getNumUnits() == 3 );
u = ud.getUnit(0);
assertEquals( true, u.isSetExponent() );
assertEquals( true, u.isSetScale() );
assertEquals( true, u.isSetMultiplier() );
assertTrue( u.getExponent() == -1 );
assertTrue( u.getExponentAsDouble() == -1 );
assertTrue( u.getScale() == 2 );
assertTrue( u.getMultiplier() == 1.3 );
u = ud.getUnit(1);
assertEquals( true, u.isSetExponent() );
assertEquals( true, u.isSetScale() );
assertEquals( true, u.isSetMultiplier() );
assertTrue( u.getExponentAsDouble() == 1.5 );
assertTrue( u.getScale() == 10 );
assertTrue( u.getMultiplier() == 0.5 );
u = ud.getUnit(2);
assertEquals( true, u.isSetExponent() );
assertEquals( true, u.isSetScale() );
assertEquals( true, u.isSetMultiplier() );
assertTrue( u.getExponent() == 1 );
assertTrue( u.getScale() == 0 );
assertTrue( u.getMultiplier() == 1 );
assertTrue( m.getNumCompartments() == 3 );
c = m.getCompartment(0);
assertEquals( true, c.isSetSize() );
assertEquals( true, c.isSetSpatialDimensions() );
assertEquals( true, c.isSetConstant() );
assertTrue( c.getId() == "comp" );
assertTrue( c.getSize() == 1e-14 );
assertTrue( c.getSpatialDimensions() == 3 );
assertTrue( c.getSpatialDimensionsAsDouble() == 3 );
assertTrue( c.getUnits() == "litre" );
assertTrue( c.getConstant() == true );
c = m.getCompartment(1);
assertEquals( false, c.isSetSize() );
assertEquals( false, c.isSetSpatialDimensions() );
assertEquals( true, c.isSetConstant() );
assertTrue( c.getId() == "comp1" );
assertEquals( true, isnan(c.getSize()) );
assertEquals( true, isnan(c.getSpatialDimensionsAsDouble()) );
assertTrue( c.getConstant() == false );
c = m.getCompartment(2);
assertEquals( false, c.isSetSize() );
assertEquals( true, c.isSetSpatialDimensions() );
assertEquals( false, c.isSetConstant() );
assertTrue( c.getId() == "comp2" );
assertTrue( c.getSpatialDimensionsAsDouble() == 4.6 );
assertTrue( m.getNumSpecies() == 2 );
s = m.getSpecies(0);
assertTrue( s.getId() == "ES" );
assertTrue( s.getCompartment() == "comp" );
assertEquals( true, s.isSetConversionFactor() );
assertTrue( s.getConversionFactor() == "p" );
assertEquals( true, s.isSetBoundaryCondition() );
assertTrue( s.getBoundaryCondition() == false );
assertEquals( true, s.isSetHasOnlySubstanceUnits() );
assertTrue( s.getHasOnlySubstanceUnits() == false );
assertEquals( true, s.isSetSubstanceUnits() );
assertTrue( s.getSubstanceUnits() == "mole" );
assertEquals( true, s.isSetConstant() );
assertTrue( s.getConstant() == false );
assertEquals( true, s.isSetInitialAmount() );
assertTrue( s.getInitialAmount() == 0 );
assertEquals( false, s.isSetInitialConcentration() );
assertEquals( true, isnan(s.getInitialConcentration()) );
s = m.getSpecies(1);
assertTrue( s.getId() == "P" );
assertTrue( s.getCompartment() == "comp" );
assertEquals( false, s.isSetConversionFactor() );
assertTrue( s.getConversionFactor() == "" );
assertEquals( false, s.isSetBoundaryCondition() );
assertEquals( false, s.isSetHasOnlySubstanceUnits() );
assertEquals( false, s.isSetSubstanceUnits() );
assertTrue( s.getSubstanceUnits() == "" );
assertEquals( false, s.isSetConstant() );
assertEquals( false, s.isSetInitialAmount() );
assertEquals( true, isnan(s.getInitialAmount()) );
assertEquals( false, s.isSetInitialConcentration() );
assertEquals( true, isnan(s.getInitialConcentration()) );
assertTrue( m.getNumParameters() == 3 );
p = m.getParameter(0);
assertTrue( p.getId() == "Keq" );
assertEquals( true, p.isSetValue() );
assertTrue( p.getValue() == 2.5 );
assertEquals( true, p.isSetUnits() );
assertTrue( p.getUnits() == "dimensionless" );
assertEquals( true, p.isSetConstant() );
assertTrue( p.getConstant() == true );
p = m.getParameter(1);
assertTrue( p.getId() == "Keq1" );
assertEquals( false, p.isSetValue() );
assertEquals( true, isnan(p.getValue()) );
assertEquals( false, p.isSetUnits() );
assertTrue( p.getUnits() == "" );
assertEquals( true, p.isSetConstant() );
assertTrue( p.getConstant() == false );
p = m.getParameter(2);
assertTrue( p.getId() == "Keq2" );
assertEquals( false, p.isSetValue() );
assertEquals( true, isnan(p.getValue()) );
assertEquals( false, p.isSetUnits() );
assertTrue( p.getUnits() == "" );
assertEquals( false, p.isSetConstant() );
assertTrue( m.getNumReactions() == 3 );
r = m.getReaction(0);
assertEquals( true, r.isSetFast() );
assertTrue( r.getFast() == false );
assertEquals( true, r.isSetReversible() );
assertTrue( r.getReversible() == false );
assertEquals( true, r.isSetCompartment() );
assertTrue( r.getCompartment() == "comp" );
sr = r.getReactant(0);
assertEquals( true, sr.isSetConstant() );
assertTrue( sr.getConstant() == true );
assertEquals( true, sr.isSetStoichiometry() );
assertTrue( sr.getStoichiometry() == 1 );
sr = r.getProduct(0);
assertEquals( true, sr.isSetConstant() );
assertTrue( sr.getConstant() == false );
assertEquals( false, sr.isSetStoichiometry() );
assertEquals( true, isnan(sr.getStoichiometry()) );
kl = r.getKineticLaw();
assertTrue( kl.getNumLocalParameters() == 2 );
assertTrue( kl.getNumParameters() == 2 );
p = kl.getParameter(0);
assertEquals( true, p.isSetUnits() );
assertTrue( p.getUnits() == "per_second" );
assertEquals( true, p.isSetValue() );
assertTrue( p.getValue() == 0.1 );
lp = kl.getLocalParameter(0);
assertEquals( true, lp.isSetUnits() );
assertTrue( lp.getUnits() == "per_second" );
assertEquals( true, lp.isSetValue() );
assertTrue( lp.getValue() == 0.1 );
lp = kl.getLocalParameter(1);
assertEquals( false, lp.isSetUnits() );
assertTrue( lp.getUnits() == "" );
assertEquals( false, lp.isSetValue() );
assertEquals( true, isnan(lp.getValue()) );
r = m.getReaction(1);
assertEquals( true, r.isSetFast() );
assertTrue( r.getFast() == true );
assertEquals( true, r.isSetReversible() );
assertTrue( r.getReversible() == true );
assertEquals( false, r.isSetCompartment() );
assertTrue( r.getCompartment() == "" );
sr = r.getReactant(0);
assertEquals( false, sr.isSetConstant() );
r = m.getReaction(2);
assertEquals( false, r.isSetFast() );
assertEquals( false, r.isSetReversible() );
assertEquals( false, r.isSetCompartment() );
assertTrue( r.getCompartment() == "" );
d = null;
}
public void test_read_l2v3_all()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
Compartment c;
CompartmentType ct;
Species s;
Parameter p;
AssignmentRule ar;
Reaction r;
SpeciesReference sr;
KineticLaw kl;
UnitDefinition ud;
Constraint con;
Event e;
Delay delay;
Trigger trigger;
EventAssignment ea;
FunctionDefinition fd;
InitialAssignment ia;
AlgebraicRule alg;
RateRule rr;
SpeciesType st;
StoichiometryMath stoich;
Unit u;
ListOfEvents loe;
Event e1;
ListOfEventAssignments loea;
EventAssignment ea1;
ListOfFunctionDefinitions lofd;
FunctionDefinition fd1;
ListOfParameters lop;
Parameter p1;
ListOfSpeciesTypes lost;
SpeciesType st1;
ListOfUnitDefinitions loud;
UnitDefinition ud1;
ListOfUnits lou;
Unit u1;
ASTNode ast;
string filename = "../../sbml/test/test-data/";
filename += "l2v3-all.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 3 );
m = d.getModel();
assertTrue( m != null );
assertTrue( m.getId() == "l2v3_all" );
assertTrue( m.getNumCompartments() == 1 );
c = m.getCompartment(0);
assertTrue( c != null );
assertTrue( c.getId() == "a" );
assertEquals(c.getCompartmentType(), "hh");
assertTrue( c.getSBOTerm() == 236 );
assertTrue( c.getSBOTermID() == "SBO:0000236" );
assertTrue( c.getSize() == 2.3 );
assertTrue( m.getNumCompartmentTypes() == 1 );
ct = m.getCompartmentType(0);
assertTrue( ct != null );
assertTrue( ct.getId() == "hh" );
assertTrue( ct.getSBOTerm() == 236 );
assertTrue( ct.getSBOTermID() == "SBO:0000236" );
assertTrue( m.getNumSpeciesTypes() == 1 );
st = m.getSpeciesType(0);
assertTrue( st != null );
assertTrue( st.getId() == "gg" );
assertTrue( st.getName() == "dd" );
assertTrue( st.getSBOTerm() == 236 );
assertTrue( st.getSBOTermID() == "SBO:0000236" );
lost = m.getListOfSpeciesTypes();
st1 = lost.get(0);
assertTrue( st1 == st );
st1 = lost.get("gg");
assertTrue( st1 == st );
assertTrue( m.getNumConstraints() == 1 );
con = m.getConstraint(0);
assertTrue( con != null );
ast = con.getMath();
assertTrue(( "lt(x, 3)" == libsbml.formulaToString(ast) ));
assertTrue( m.getNumEvents() == 1 );
e = m.getEvent(0);
assertTrue( e != null );
assertTrue( e.getId() == "e1" );
assertTrue( e.getSBOTerm() == 231 );
assertTrue( e.getSBOTermID() == "SBO:0000231" );
assertEquals( true, e.isSetDelay() );
delay = e.getDelay();
assertTrue( delay != null );
assertTrue( delay.getSBOTerm() == 64 );
assertTrue( delay.getSBOTermID() == "SBO:0000064" );
ast = delay.getMath();
assertTrue(( "p + 3" == libsbml.formulaToString(ast) ));
assertEquals( true, e.isSetTrigger() );
trigger = e.getTrigger();
assertTrue( trigger != null );
assertTrue( trigger.getSBOTerm() == 64 );
assertTrue( trigger.getSBOTermID() == "SBO:0000064" );
ast = trigger.getMath();
assertTrue(( "lt(x, 3)" == libsbml.formulaToString(ast) ));
loe = m.getListOfEvents();
e1 = loe.get(0);
assertTrue( e1 == e );
e1 = loe.get("e1");
assertTrue( e1 == e );
assertTrue( e.getNumEventAssignments() == 1 );
ea = e.getEventAssignment(0);
assertTrue( ea != null );
assertTrue( ea.getVariable() == "a" );
assertTrue( ea.getSBOTerm() == 64 );
assertTrue( ea.getSBOTermID() == "SBO:0000064" );
ast = ea.getMath();
assertTrue(( "x * p3" == libsbml.formulaToString(ast) ));
loea = e.getListOfEventAssignments();
ea1 = loea.get(0);
assertTrue( ea1 == ea );
ea1 = loea.get("a");
assertTrue( ea1 == ea );
assertTrue( m.getNumFunctionDefinitions() == 1 );
fd = m.getFunctionDefinition(0);
assertTrue( fd != null );
assertTrue( fd.getId() == "fd" );
assertTrue( fd.getSBOTerm() == 64 );
assertTrue( fd.getSBOTermID() == "SBO:0000064" );
ast = fd.getMath();
assertTrue(( "lambda(x, pow(x, 3))" == libsbml.formulaToString(ast) ));
lofd = m.getListOfFunctionDefinitions();
fd1 = lofd.get(0);
assertTrue( fd1 == fd );
fd1 = lofd.get("fd");
assertTrue( fd1 == fd );
assertTrue( m.getNumInitialAssignments() == 1 );
ia = m.getInitialAssignment(0);
assertTrue( ia != null );
assertTrue( ia.getSymbol() == "p1" );
ast = ia.getMath();
assertTrue(( "x * p3" == libsbml.formulaToString(ast) ));
assertTrue( m.getNumRules() == 3 );
alg = (AlgebraicRule) m.getRule(0);
assertTrue( alg != null );
assertTrue( alg.getSBOTerm() == 64 );
assertTrue( alg.getSBOTermID() == "SBO:0000064" );
ast = alg.getMath();
assertTrue(( "pow(x, 3)" == libsbml.formulaToString(ast) ));
ar = (AssignmentRule) m.getRule(1);
assertTrue( ar != null );
assertTrue( ar.getVariable() == "p2" );
assertTrue( ar.getSBOTerm() == 64 );
assertTrue( ar.getSBOTermID() == "SBO:0000064" );
ast = ar.getMath();
assertTrue(( "x * p3" == libsbml.formulaToString(ast) ));
rr = (RateRule) m.getRule(2);
assertTrue( rr != null );
assertTrue( rr.getVariable() == "p3" );
assertTrue( rr.getSBOTerm() == 64 );
assertTrue( rr.getSBOTermID() == "SBO:0000064" );
ast = rr.getMath();
assertTrue(( "p1 / p" == libsbml.formulaToString(ast) ));
assertTrue( m.getNumSpecies() == 1 );
s = m.getSpecies(0);
assertTrue( s != null );
assertTrue( s.getId() == "s" );
assertEquals(s.getSpeciesType(), "gg");
assertTrue( s.getCompartment() == "a" );
assertTrue( s.getSBOTerm() == 236 );
assertTrue( s.getSBOTermID() == "SBO:0000236" );
assertEquals( true, s.isSetInitialAmount() );
assertEquals( false, s.isSetInitialConcentration() );
assertTrue( s.getInitialAmount() == 0 );
assertTrue( m.getNumReactions() == 1 );
r = m.getReaction(0);
assertTrue( r != null );
assertTrue( r.getId() == "r" );
assertEquals( false, r.getReversible() );
assertEquals( true, r.getFast() );
assertEquals( true, r.isSetKineticLaw() );
kl = r.getKineticLaw();
assertTrue( kl != null );
assertEquals( true, kl.isSetMath() );
ast = kl.getMath();
assertTrue(( "s * k / p" == libsbml.formulaToString(ast) ));
assertTrue( kl.getNumParameters() == 2 );
p = kl.getParameter(0);
assertTrue( p != null );
assertTrue( p.getId() == "k" );
assertTrue( p.getUnits() == "litre" );
assertTrue( p.getValue() == 9 );
ud = p.getDerivedUnitDefinition();
assertTrue( ud.getNumUnits() == 1 );
assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE );
assertTrue( ud.getUnit(0).getExponent() == 1 );
lop = kl.getListOfParameters();
p1 = lop.get(0);
assertTrue( p1 == p );
p1 = lop.get("k");
assertTrue( p1 == p );
p = kl.getParameter(1);
assertTrue( p != null );
assertTrue( p.getId() == "k1" );
assertTrue( p.getUnits() == "ud1" );
assertTrue( p.getValue() == 9 );
ud = p.getDerivedUnitDefinition();
assertTrue( ud.getNumUnits() == 1 );
assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_MOLE );
assertTrue( ud.getUnit(0).getExponent() == 1 );
assertTrue( r.getNumReactants() == 1 );
assertTrue( r.getNumProducts() == 0 );
assertTrue( r.getNumModifiers() == 0 );
sr = r.getReactant(0);
assertTrue( sr != null );
assertTrue( sr.getSpecies() == "s" );
assertTrue( sr.getSBOTerm() == 11 );
assertTrue( sr.getSBOTermID() == "SBO:0000011" );
stoich = sr.getStoichiometryMath();
assertTrue( stoich != null );
assertTrue( stoich.getSBOTerm() == 64 );
assertTrue( stoich.getSBOTermID() == "SBO:0000064" );
ast = stoich.getMath();
assertTrue(( "s * p" == libsbml.formulaToString(ast) ));
assertTrue( m.getNumUnitDefinitions() == 1 );
ud = m.getUnitDefinition(0);
assertTrue( ud != null );
assertTrue( ud.getId() == "ud1" );
loud = m.getListOfUnitDefinitions();
ud1 = loud.get(0);
assertTrue( ud1 == ud );
ud1 = loud.get("ud1");
assertTrue( ud1 == ud );
assertTrue( ud.getNumUnits() == 1 );
u = ud.getUnit(0);
assertTrue( u != null );
assertTrue( u.getKind() == libsbml.UNIT_KIND_MOLE );
lou = ud.getListOfUnits();
u1 = lou.get(0);
assertTrue( u1 == u );
d = null;
}
public void test_read_MathML_2()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
FunctionDefinition fd;
InitialAssignment ia;
Rule r;
string filename = "../../math/test/test-data/";
filename += "mathML_2.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
m = d.getModel();
assertTrue( m != null );
assertTrue( m.getNumFunctionDefinitions() == 2 );
assertTrue( m.getNumInitialAssignments() == 1 );
assertTrue( m.getNumRules() == 2 );
fd = m.getFunctionDefinition(0);
ASTNode fd_math = fd.getMath();
assertTrue( fd_math.getType() == libsbml.AST_LAMBDA );
assertTrue( fd_math.getNumChildren() == 1 );
assertTrue(( "lambda()" == libsbml.formulaToString(fd_math) ));
ASTNode child = fd_math.getChild(0);
assertTrue( child.getType() == libsbml.AST_UNKNOWN );
assertTrue( child.getNumChildren() == 0 );
assertTrue(( "" == libsbml.formulaToString(child) ));
fd = m.getFunctionDefinition(1);
ASTNode fd1_math = fd.getMath();
assertTrue( fd1_math.getType() == libsbml.AST_LAMBDA );
assertTrue( fd1_math.getNumChildren() == 2 );
assertTrue(( "lambda(x, piecewise(p, leq(x, 4)))" == libsbml.formulaToString(fd1_math) ));
ASTNode child1 = fd1_math.getRightChild();
assertTrue( child1.getType() == libsbml.AST_FUNCTION_PIECEWISE );
assertTrue( child1.getNumChildren() == 2 );
assertTrue(( "piecewise(p, leq(x, 4))" == libsbml.formulaToString(child1) ));
ASTNode c1 = child1.getChild(0);
assertTrue( c1.getType() == libsbml.AST_NAME );
assertTrue( c1.getNumChildren() == 0 );
assertTrue(( "p" == libsbml.formulaToString(c1) ));
ASTNode c2 = child1.getChild(1);
assertTrue( c2.getType() == libsbml.AST_RELATIONAL_LEQ );
assertTrue( c2.getNumChildren() == 2 );
assertTrue(( "leq(x, 4)" == libsbml.formulaToString(c2) ));
ia = m.getInitialAssignment(0);
ASTNode ia_math = ia.getMath();
assertTrue( ia_math.getType() == libsbml.AST_FUNCTION_PIECEWISE );
assertTrue( ia_math.getNumChildren() == 4 );
assertTrue(( "piecewise(-x, lt(x, 0), 0, eq(x, 0))" == libsbml.formulaToString(ia_math) ));
child1 = ia_math.getChild(0);
ASTNode child2 = ia_math.getChild(1);
ASTNode child3 = ia_math.getChild(2);
ASTNode child4 = ia_math.getChild(3);
assertTrue( child1.getType() == libsbml.AST_MINUS );
assertTrue( child1.getNumChildren() == 1 );
assertTrue(( "-x" == libsbml.formulaToString(child1) ));
assertTrue( child2.getType() == libsbml.AST_RELATIONAL_LT );
assertTrue( child2.getNumChildren() == 2 );
assertTrue(( "lt(x, 0)" == libsbml.formulaToString(child2) ));
assertTrue( child3.getType() == libsbml.AST_REAL );
assertTrue( child3.getNumChildren() == 0 );
assertTrue(( "0" == libsbml.formulaToString(child3) ));
assertTrue( child4.getType() == libsbml.AST_RELATIONAL_EQ );
assertTrue( child4.getNumChildren() == 2 );
assertTrue(( "eq(x, 0)" == libsbml.formulaToString(child4) ));
r = m.getRule(0);
ASTNode r_math = r.getMath();
assertTrue( r_math.getType() == libsbml.AST_CONSTANT_TRUE );
assertTrue( r_math.getNumChildren() == 0 );
assertTrue(( "true" == libsbml.formulaToString(r_math) ));
r = m.getRule(1);
ASTNode r1_math = r.getMath();
assertTrue( r1_math.getType() == libsbml.AST_FUNCTION_LOG );
assertTrue( r1_math.getNumChildren() == 2 );
assertTrue(( "log(3, x)" == libsbml.formulaToString(r1_math) ));
child1 = r1_math.getChild(0);
child2 = r1_math.getChild(1);
assertTrue( child1.getType() == libsbml.AST_REAL );
assertTrue( child1.getNumChildren() == 0 );
assertTrue(( "3" == libsbml.formulaToString(child1) ));
assertTrue( child2.getType() == libsbml.AST_NAME );
assertTrue( child2.getNumChildren() == 0 );
assertTrue(( "x" == libsbml.formulaToString(child2) ));
d = null;
}
public void TestSBML_Species()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Compartment sc = new SBML_Compartment(model);
SBML_Species species = new SBML_Species(model);
// getConstant
SpeciesStruct ss = new SpeciesStruct();
int i = species.getConstant(ss);
Assert.AreEqual(0, i, "getConstant returns unexpected value.");
ss.Constant = true;
i = species.getConstant(ss);
Assert.AreEqual(1, i, "getConstant returns unexpected value.");
model.Level = 1;
i = species.getConstant(ss);
Assert.AreEqual(0, i, "getConstant returns unexpected value.");
ss.BoundaryCondition = true;
i = species.getConstant(ss);
Assert.AreEqual(1, i, "getConstant returns unexpected value.");
try
{
model.Level = 0;
i = species.getConstant(ss);
}
catch (Exception)
{
}
// getSpeciesValue
double d = species.getSpeciesValue(ss);
Assert.AreEqual(0.0, d, "getSpeciesValue returns unexpected value.");
model.Level = 2;
ss.InitialAmount = double.NaN;
ss.Compartment = "cell";
d = species.getSpeciesValue(ss);
Assert.AreEqual(0.0, d, "getSpeciesValue returns unexpected value.");
try
{
ss.InitialConcentration = double.NaN;
d = species.getSpeciesValue(ss);
}
catch (Exception)
{
}
// getSpeciesID
ss.ID = "Test1";
string id = species.getSpeciesID(ss);
Assert.AreEqual("/cell:Test1", id, "getSpeciesID returns unexpected value.");
try
{
model.Level = 1;
ss.Name = "Test2";
id = species.getSpeciesID(ss);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = species.getSpeciesID(ss);
}
catch (Exception)
{
}
try
{
model.Level = 2;
ss.Compartment = "";
id = species.getSpeciesID(ss);
}
catch (Exception)
{
}
}
public void test_read_l2v1_assignment()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
Compartment c;
Species s;
Parameter p;
AssignmentRule ar;
Reaction r;
SpeciesReference sr;
KineticLaw kl;
UnitDefinition ud;
Reaction r1;
ListOfCompartments loc;
Compartment c1;
ListOfRules lor;
AssignmentRule ar1;
ListOfParameters lop;
Parameter p1;
ListOfSpecies los;
Species s1;
string filename = "../../sbml/test/test-data/";
filename += "l2v1-assignment.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
m = d.getModel();
assertTrue( m != null );
assertTrue( m.getNumCompartments() == 1 );
c = m.getCompartment(0);
assertTrue( c != null );
assertTrue( c.getId() == "cell" );
ud = c.getDerivedUnitDefinition();
assertTrue( ud.getNumUnits() == 1 );
assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE );
loc = m.getListOfCompartments();
c1 = loc.get(0);
assertTrue( c1 == c );
c1 = loc.get("cell");
assertTrue( c1 == c );
assertTrue( m.getNumSpecies() == 5 );
s = m.getSpecies(0);
assertTrue( s != null );
assertTrue( s.getId() == "X0" );
assertTrue( s.getCompartment() == "cell" );
assertTrue( s.getInitialConcentration() == 1.0 );
los = m.getListOfSpecies();
s1 = los.get(0);
assertTrue( s1 == s );
s1 = los.get("X0");
assertTrue( s1 == s );
s = m.getSpecies(1);
assertTrue( s != null );
assertTrue( s.getId() == "X1" );
assertTrue( s.getCompartment() == "cell" );
assertTrue( s.getInitialConcentration() == 0.0 );
s = m.getSpecies(2);
assertTrue( s != null );
assertTrue( s.getId() == "T" );
assertTrue( s.getCompartment() == "cell" );
assertTrue( s.getInitialConcentration() == 0.0 );
s = m.getSpecies(3);
assertTrue( s != null );
assertTrue( s.getId() == "S1" );
assertTrue( s.getCompartment() == "cell" );
assertTrue( s.getInitialConcentration() == 0.0 );
s = m.getSpecies(4);
assertTrue( s != null );
assertTrue( s.getId() == "S2" );
assertTrue( s.getCompartment() == "cell" );
assertTrue( s.getInitialConcentration() == 0.0 );
assertTrue( m.getNumParameters() == 1 );
p = m.getParameter(0);
assertTrue( p != null );
assertTrue( p.getId() == "Keq" );
assertTrue( p.getValue() == 2.5 );
lop = m.getListOfParameters();
p1 = lop.get(0);
assertTrue( p1 == p );
p1 = lop.get("Keq");
assertTrue( p1 == p );
ud = p.getDerivedUnitDefinition();
assertTrue( ud.getNumUnits() == 0 );
assertTrue( m.getNumRules() == 2 );
ar = (AssignmentRule) m.getRule(0);
assertTrue( ar != null );
assertTrue( ar.getVariable() == "S1" );
assertTrue( ar.getFormula() == "T / (1 + Keq)" );
ud = ar.getDerivedUnitDefinition();
assertTrue( ud.getNumUnits() == 2 );
assertTrue( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_MOLE );
assertTrue( ud.getUnit(0).getExponent() == 1 );
assertTrue( ud.getUnit(1).getKind() == libsbml.UNIT_KIND_LITRE );
assertTrue( ud.getUnit(1).getExponent() == -1 );
assertTrue( ar.containsUndeclaredUnits() == true );
lor = m.getListOfRules();
ar1 = (AssignmentRule) lor.get(0);
assertTrue( ar1 == ar );
ar1 = (AssignmentRule) lor.get("S1");
assertTrue( ar1 == ar );
ar = (AssignmentRule) m.getRule(1);
assertTrue( ar != null );
assertTrue( ar.getVariable() == "S2" );
assertTrue( ar.getFormula() == "Keq * S1" );
assertTrue( m.getNumReactions() == 2 );
r = m.getReaction(0);
assertTrue( r != null );
assertTrue( r.getId() == "in" );
assertTrue( r.getNumReactants() == 1 );
assertTrue( r.getNumProducts() == 1 );
sr = r.getReactant(0);
assertTrue( sr != null );
assertTrue( sr.getSpecies() == "X0" );
sr = r.getProduct(0);
assertTrue( sr != null );
assertTrue( sr.getSpecies() == "T" );
kl = r.getKineticLaw();
assertTrue( kl != null );
assertTrue( kl.getFormula() == "k1 * X0" );
assertTrue( kl.getNumParameters() == 1 );
r1 = (Reaction) kl.getParentSBMLObject();
assertTrue( r1 != null );
assertTrue( r1.getId() == "in" );
assertTrue( r1.getNumReactants() == 1 );
assertTrue( r1.getNumProducts() == 1 );
p = kl.getParameter(0);
assertTrue( p != null );
assertTrue( p.getId() == "k1" );
assertTrue( p.getValue() == 0.1 );
kl = (KineticLaw) p.getParentSBMLObject().getParentSBMLObject();
assertTrue( kl != null );
assertTrue( kl.getFormula() == "k1 * X0" );
assertTrue( kl.getNumParameters() == 1 );
r = m.getReaction(1);
assertTrue( r != null );
assertTrue( r.getId() == "out" );
assertTrue( r.getNumReactants() == 1 );
assertTrue( r.getNumProducts() == 1 );
sr = r.getReactant(0);
assertTrue( sr != null );
assertTrue( sr.getSpecies() == "T" );
sr = r.getProduct(0);
assertTrue( sr != null );
assertTrue( sr.getSpecies() == "X1" );
kl = r.getKineticLaw();
assertTrue( kl != null );
assertTrue( kl.getFormula() == "k2 * T" );
assertTrue( kl.getNumParameters() == 1 );
p = kl.getParameter(0);
assertTrue( p != null );
assertTrue( p.getId() == "k2" );
assertTrue( p.getValue() == 0.15 );
d = null;
}
internal static HandleRef getCPtrAndDisown(SBMLReader obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
public void TestSBML_Model()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
// getSpeciesReferenceID
SpeciesStruct ss = new SpeciesStruct();
ss.Compartment = "cell";
ss.ID = "Test1";
ss.Name = "Test1";
string id;
try
{
id = model.getSpeciesReferenceID(ss.ID);
}
catch (Exception)
{
}
model.SpeciesList.Add(ss);
id = model.getSpeciesReferenceID(ss.ID);
Assert.AreEqual("/cell:Test1", id, "getEventID returns unexpected value.");
try
{
model.Level = 1;
id = model.getSpeciesReferenceID(ss.ID);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = model.getSpeciesReferenceID(ss.ID);
}
catch (Exception)
{
}
// setFunctionDefinitionToDictionary
FunctionDefinitionStruct ud = new FunctionDefinitionStruct();
ud.ID = "Function";
ud.Name = "Function";
ud.Formula = "1 * 2";
model.FunctionDefinitionList.Add(ud);
Type type = model.GetType();
MethodInfo info1 = type.GetMethod("setFunctionDefinitionToDictionary", BindingFlags.NonPublic | BindingFlags.Instance);
info1.Invoke(model, new object[] { });
// getNewUnitValue
MethodInfo info2 = type.GetMethod("getNewUnitValue", BindingFlags.NonPublic | BindingFlags.Instance);
UnitStruct unit = new UnitStruct("Kind", 2, 1, 0.5, 3);
double value = (double)info2.Invoke(model, new object[] { unit });
Assert.AreEqual(28.0d, value, "getNewUnitValue returns unexpected value.");
// convertUnit
model.Level = 2;
value = model.convertUnit("test", 0.1d);
Assert.AreEqual(0.1d, value, "convertUnit returns unexpected value.");
value = model.convertUnit("substance", 1.0d);
Assert.AreEqual(1.0d, value, "convertUnit returns unexpected value.");
model.Level = 1;
value = model.convertUnit("test", 0.1d);
Assert.AreEqual(0.1d, value, "convertUnit returns unexpected value.");
value = model.convertUnit("minute", 1.0d);
Assert.AreEqual(60.0d, value, "convertUnit returns unexpected value.");
try
{
model.Level = 0;
model.convertUnit("test", 0.1d);
}
catch (Exception)
{
}
// getPath
string path;
try
{
path = model.getPath("");
}
catch (Exception)
{
}
path = model.getPath("default");
Assert.AreEqual("/", path, "getPath returns unexpected value.");
}
public void TestSBML_Event()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Event e = new SBML_Event(model);
EventStruct es = new EventStruct();
es.ID = "Test1";
string id = e.getEventID(es);
Assert.AreEqual("Process:/:Test1", id, "getEventID returns unexpected value.");
model.Level = 1;
es.Name = "Test2";
id = e.getEventID(es);
Assert.AreEqual("Process:/:Test2", id, "getEventID returns unexpected value.");
model.Level = 0;
id = e.getEventID(es);
Assert.AreEqual("Process:/:Event0", id, "getEventID returns unexpected value.");
}
public void TestSBML_Compartment()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Compartment c = new SBML_Compartment(model);
CompartmentStruct cs = new CompartmentStruct();
try
{
c.getCompartmentID(cs);
}
catch (Exception)
{
}
string id;
cs.Outside = "";
cs.ID = "Test1";
id = c.getCompartmentID(cs);
Assert.AreEqual("System:/:Test1", id, "getCompartmentID returns unexpected value.");
try
{
model.Level = 1;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
model.Level = 2;
cs.Outside = "cell";
id = c.getCompartmentID(cs);
Assert.AreEqual("System:/cell:Test1", id, "getCompartmentID returns unexpected value.");
try
{
model.Level = 1;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
// GetModuleType
Type type = c.GetType();
MethodInfo info1 = type.GetMethod("setSizeToDictionary", BindingFlags.NonPublic | BindingFlags.Instance);
MethodInfo info2 = type.GetMethod("setUnitToDictionary", BindingFlags.NonPublic | BindingFlags.Instance);
try
{
info1.Invoke(c, new object[] { cs });
}
catch (Exception)
{
}
try
{
info2.Invoke(c, new object[] { cs });
}
catch (Exception)
{
}
model.Level = 1;
cs.Volume = double.NaN;
cs.Name = "Test1";
info1.Invoke(c, new object[] { cs });
info2.Invoke(c, new object[] { cs });
// getOutsideSize
model.Level = 2;
MethodInfo info3 = type.GetMethod("getOutsideSize", BindingFlags.NonPublic | BindingFlags.Instance);
double size;
size = (double)info3.Invoke(c, new object[] { "" });
Assert.AreEqual(1.0d, size, "getOutsideSize returns unexpected value.");
size = (double)info3.Invoke(c, new object[] { "cell" });
Assert.AreEqual(1.0d, size, "getOutsideSize returns unexpected value.");
// getOutsideUnit
MethodInfo info4 = type.GetMethod("getOutsideUnit", BindingFlags.NonPublic | BindingFlags.Instance);
string unit;
unit = (string)info4.Invoke(c, new object[] { "" });
Assert.AreEqual("", unit, "getCompartmentSize returns unexpected value.");
unit = (string)info4.Invoke(c, new object[] { "cell" });
Assert.AreEqual("", unit, "getCompartmentSize returns unexpected value.");
// getCompartmentSize
size = c.getCompartmentSize(cs);
Assert.AreEqual(1.0d, size, "getCompartmentSize returns unexpected value.");
model.Level = 1;
size = c.getCompartmentSize(cs);
Assert.AreEqual(1.0d, size, "getCompartmentSize returns unexpected value.");
try
{
model.Level = 0;
size = c.getCompartmentSize(cs);
}
catch (Exception)
{
}
// getCompartmentUnit
model.Level = 2;
id = c.getCompartmentUnit(cs);
Assert.AreEqual(null, id, "getCompartmentUnit returns unexpected value.");
model.Level = 1;
id = c.getCompartmentUnit(cs);
Assert.AreEqual(null, id, "getCompartmentUnit returns unexpected value.");
try
{
model.Level = 0;
id = c.getCompartmentUnit(cs);
}
catch (Exception)
{
}
}
public void test_read_l2v2_newComponents()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
Compartment c;
CompartmentType ct;
Species s;
Parameter p;
Reaction r;
SpeciesReference sr;
KineticLaw kl;
Constraint con;
InitialAssignment ia;
SpeciesType st;
ListOfCompartmentTypes loct;
CompartmentType ct1;
ListOfConstraints locon;
Constraint con1;
ListOfInitialAssignments loia;
InitialAssignment ia1;
ListOfReactions lor;
Reaction r1;
ListOfSpeciesReferences losr;
SpeciesReference sr1;
ASTNode ast;
string filename = "../../sbml/test/test-data/";
filename += "l2v2-newComponents.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 2 );
m = d.getModel();
assertTrue( m != null );
assertTrue( m.getId() == "l2v2_newComponents" );
assertTrue( m.getSBOTerm() == 4 );
assertTrue( m.getSBOTermID() == "SBO:0000004" );
assertTrue( m.getNumCompartments() == 2 );
c = m.getCompartment(0);
assertTrue( c != null );
assertTrue( c.getId() == "cell" );
assertEquals(c.getCompartmentType(), "mitochondria");
assertTrue( c.getOutside() == "m" );
assertTrue( c.getSBOTerm() == -1 );
assertTrue( c.getSBOTermID() == "" );
c = m.getCompartment(1);
assertTrue( c != null );
assertTrue( c.getId() == "m" );
assertEquals(c.getCompartmentType(), "mitochondria");
assertTrue( m.getNumCompartmentTypes() == 1 );
ct = m.getCompartmentType(0);
assertTrue( ct != null );
assertTrue( ct.getId() == "mitochondria" );
loct = m.getListOfCompartmentTypes();
ct1 = loct.get(0);
assertTrue( ct1 == ct );
ct1 = loct.get("mitochondria");
assertTrue( ct1 == ct );
assertTrue( m.getNumSpeciesTypes() == 1 );
st = m.getSpeciesType(0);
assertTrue( st != null );
assertTrue( st.getId() == "Glucose" );
assertTrue( m.getNumSpecies() == 2 );
s = m.getSpecies(0);
assertTrue( s != null );
assertTrue( s.getId() == "X0" );
assertEquals(s.getSpeciesType(), "Glucose");
assertTrue( s.getCompartment() == "cell" );
assertEquals( false, s.isSetInitialAmount() );
assertEquals( false, s.isSetInitialConcentration() );
s = m.getSpecies(1);
assertTrue( s != null );
assertTrue( s.getId() == "X1" );
assertEquals( false, s.isSetSpeciesType() );
assertTrue( s.getCompartment() == "cell" );
assertTrue( s.getInitialConcentration() == 0.013 );
assertEquals( false, s.isSetInitialAmount() );
assertEquals( true, s.isSetInitialConcentration() );
assertTrue( m.getNumParameters() == 1 );
p = m.getParameter(0);
assertTrue( p != null );
assertTrue( p.getId() == "y" );
assertTrue( p.getValue() == 2 );
assertTrue( p.getUnits() == "dimensionless" );
assertTrue( p.getId() == "y" );
assertTrue( p.getSBOTerm() == 2 );
assertTrue( p.getSBOTermID() == "SBO:0000002" );
assertTrue( m.getNumConstraints() == 1 );
con = m.getConstraint(0);
assertTrue( con != null );
assertTrue( con.getSBOTerm() == 64 );
assertTrue( con.getSBOTermID() == "SBO:0000064" );
ast = con.getMath();
assertTrue(( "lt(1, cell)" == libsbml.formulaToString(ast) ));
locon = m.getListOfConstraints();
con1 = locon.get(0);
assertTrue( con1 == con );
assertTrue( m.getNumInitialAssignments() == 1 );
ia = m.getInitialAssignment(0);
assertTrue( ia != null );
assertTrue( ia.getSBOTerm() == 64 );
assertTrue( ia.getSBOTermID() == "SBO:0000064" );
assertTrue( ia.getSymbol() == "X0" );
ast = ia.getMath();
assertTrue(( "y * X1" == libsbml.formulaToString(ast) ));
loia = m.getListOfInitialAssignments();
ia1 = loia.get(0);
assertTrue( ia1 == ia );
ia1 = loia.get("X0");
assertTrue( ia1 == ia );
assertTrue( m.getNumReactions() == 1 );
r = m.getReaction(0);
assertTrue( r != null );
assertTrue( r.getSBOTerm() == 231 );
assertTrue( r.getSBOTermID() == "SBO:0000231" );
assertTrue( r.getId() == "in" );
lor = m.getListOfReactions();
r1 = lor.get(0);
assertTrue( r1 == r );
r1 = lor.get("in");
assertTrue( r1 == r );
assertEquals( true, r.isSetKineticLaw() );
kl = r.getKineticLaw();
assertTrue( kl != null );
assertTrue( kl.getSBOTerm() == 1 );
assertTrue( kl.getSBOTermID() == "SBO:0000001" );
assertEquals( true, kl.isSetMath() );
ast = kl.getMath();
assertTrue(( "v * X0 / t" == libsbml.formulaToString(ast) ));
assertTrue( kl.getNumParameters() == 2 );
p = kl.getParameter(0);
assertTrue( p != null );
assertTrue( p.getSBOTerm() == 2 );
assertTrue( p.getSBOTermID() == "SBO:0000002" );
assertTrue( p.getId() == "v" );
assertTrue( p.getUnits() == "litre" );
assertTrue( r.getNumReactants() == 1 );
assertTrue( r.getNumProducts() == 0 );
assertTrue( r.getNumModifiers() == 0 );
sr = r.getReactant(0);
assertTrue( sr != null );
assertTrue( sr.getName() == "sarah" );
assertTrue( sr.getId() == "me" );
assertTrue( sr.getSpecies() == "X0" );
losr = r.getListOfReactants();
sr1 = (SpeciesReference) losr.get(0);
assertTrue( sr1 == sr );
sr1 = (SpeciesReference) losr.get("me");
assertTrue( sr1 == sr );
d = null;
}
public void test_read_MathML_1()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
FunctionDefinition fd;
InitialAssignment ia;
Rule r;
KineticLaw kl;
string filename = "../../math/test/test-data/";
filename += "mathML_1.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
m = d.getModel();
assertTrue( m != null );
assertTrue( m.getNumFunctionDefinitions() == 2 );
assertTrue( m.getNumInitialAssignments() == 1 );
assertTrue( m.getNumRules() == 2 );
assertTrue( m.getNumReactions() == 1 );
fd = m.getFunctionDefinition(0);
ASTNode fd_math = fd.getMath();
assertTrue( fd_math.getType() == libsbml.AST_LAMBDA );
assertTrue( fd_math.getNumChildren() == 2 );
assertTrue(( "lambda(x, )" == libsbml.formulaToString(fd_math) ));
assertTrue( fd_math.getParentSBMLObject() == fd );
ASTNode child = fd_math.getRightChild();
assertTrue( child.getType() == libsbml.AST_UNKNOWN );
assertTrue( child.getNumChildren() == 0 );
assertTrue(( "" == libsbml.formulaToString(child) ));
fd = m.getFunctionDefinition(1);
ASTNode fd1_math = fd.getMath();
assertTrue( fd1_math.getType() == libsbml.AST_LAMBDA );
assertTrue( fd1_math.getNumChildren() == 2 );
assertTrue(( "lambda(x, true)" == libsbml.formulaToString(fd1_math) ));
assertTrue( fd1_math.getParentSBMLObject() == fd );
ASTNode child1 = fd1_math.getRightChild();
assertTrue( child1.getType() == libsbml.AST_CONSTANT_TRUE );
assertTrue( child1.getNumChildren() == 0 );
assertTrue(( "true" == libsbml.formulaToString(child1) ));
ia = m.getInitialAssignment(0);
ASTNode ia_math = ia.getMath();
assertTrue( ia_math.getType() == libsbml.AST_UNKNOWN );
assertTrue( ia_math.getNumChildren() == 0 );
assertTrue(( "" == libsbml.formulaToString(ia_math) ));
assertTrue( ia_math.getParentSBMLObject() == ia );
r = m.getRule(0);
ASTNode r_math = r.getMath();
assertTrue( r_math.getType() == libsbml.AST_CONSTANT_TRUE );
assertTrue( r_math.getNumChildren() == 0 );
assertTrue(( "true" == libsbml.formulaToString(r_math) ));
assertTrue( r_math.getParentSBMLObject() == r );
r = m.getRule(1);
ASTNode r1_math = r.getMath();
assertTrue( r1_math.getType() == libsbml.AST_REAL );
assertTrue( r1_math.getNumChildren() == 0 );
assertTrue(( "INF" == libsbml.formulaToString(r1_math) ));
assertTrue( r1_math.getParentSBMLObject() == r );
kl = m.getReaction(0).getKineticLaw();
ASTNode kl_math = kl.getMath();
assertTrue( kl_math.getType() == libsbml.AST_REAL );
assertTrue( kl_math.getNumChildren() == 0 );
assertTrue(( "4.5" == libsbml.formulaToString(kl_math) ));
assertTrue( kl_math.getParentSBMLObject() == kl );
d = null;
}
internal static HandleRef getCPtr(SBMLReader obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void TestSBML_Reaction()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Reaction reaction = new SBML_Reaction(model);
}
/// <summary>
///
/// </summary>
/// <param name="filename"></param>
public static EcellModel Convert(string filename)
{
if (!File.Exists(filename))
throw new EcellException(string.Format(MessageResources.ErrFindFile, filename));
string sbml = File.ReadAllText(filename);
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBMLFromString(sbml);
Model model = document.getModel();
if (model == null)
{
throw new EcellException(string.Format("{0} has no model.", filename));
}
SBML_Model theModel = new SBML_Model(model);
SBML_Compartment theCompartment = new SBML_Compartment(theModel);
SBML_Parameter theParameter = new SBML_Parameter( theModel );
SBML_Species theSpecies = new SBML_Species( theModel );
SBML_Rule theRule = new SBML_Rule( theModel );
SBML_Reaction theReaction = new SBML_Reaction(theModel);
SBML_Event theEvent = new SBML_Event(theModel);
document.Dispose();
//Eml eml = new Eml(null);
string modelId = Path.GetFileNameWithoutExtension(filename);
EcellModel modelObject = (EcellModel)EcellObject.CreateObject(modelId, "", Constants.xpathModel, "", new List<EcellData>());
// Set Layer
List<EcellLayer> layers = new List<EcellLayer>();
layers.Add(new EcellLayer(SbmlConstant.GlobalParameters, true));
modelObject.Layers = layers;
//
// Set Stepper.
//
EcellObject stepper = EcellObject.CreateObject(modelId, "DE", EcellObject.STEPPER, "FixedODE1Stepper", new List<EcellData>());
modelObject.Children.Add(stepper);
//
// Set Compartment ( System ).
//
EcellSystem rootSystem = (EcellSystem)EcellObject.CreateObject(modelId, "/", EcellObject.SYSTEM, EcellObject.SYSTEM, new List<EcellData>());
rootSystem.SetEcellValue("StepperID", new EcellValue("DE"));
rootSystem.SetEcellValue("Name", new EcellValue("Default"));
modelObject.Children.Add(rootSystem);
EcellSystem system = rootSystem;
foreach (CompartmentStruct aCompartment in theModel.CompartmentList)
{
// getPath
string aPath = "";
if ( theModel.Level == 1 )
aPath = theModel.getPath( aCompartment.Name );
else if ( theModel.Level == 2 )
aPath = theModel.getPath( aCompartment.ID );
// setFullID
if( aPath != "/" )
{
system = (EcellSystem)EcellObject.CreateObject(modelId, aPath, EcellObject.SYSTEM, EcellObject.SYSTEM, new List<EcellData>());
modelObject.Children.Add(system);
}
// setStepper
system.SetEcellValue("StepperID", new EcellValue("DE"));
// setName( default = [] )
if (theModel.Level == 2)
if (aCompartment.Name != "")
system.SetEcellValue("Name", new EcellValue(aCompartment.Name));
// setDimensions( default = 3 )
EcellObject dimension = EcellObject.CreateObject(modelId, aPath + ":Dimensions", EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
dimension.SetEcellValue("Value", new EcellValue((int)aCompartment.SpatialDimension));
system.Children.Add(dimension);
// setSIZE
EcellObject size = EcellObject.CreateObject(modelId, aPath + ":SIZE", EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
size.SetEcellValue("Value", new EcellValue((double)theCompartment.getCompartmentSize(aCompartment)));
system.Children.Add(size);
}
// Set GlobalParameter ( Variable )
if ( theModel.ParameterList.Count > 0)
{
foreach(ParameterStruct aParameter in theModel.ParameterList)
{
// setFullID
string parameterKey = theParameter.getParameterID( aParameter );
EcellObject parameter = EcellObject.CreateObject(modelId, parameterKey, EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
// Set Layer
parameter.Layer = SbmlConstant.GlobalParameters;
// setName
if ( aParameter.Name != "" )
parameter.SetEcellValue("Name", new EcellValue(aParameter.Name));
// setValue
parameter.SetEcellValue("Value", new EcellValue(aParameter.Value));
// setFixed ( default = 1 )
if ( aParameter.Constant)
parameter.SetEcellValue("Fixed", new EcellValue(1));
// set to system.
rootSystem.Children.Add(parameter);
}
}
// Set Species ( Variable )
foreach(SpeciesStruct aSpecies in theModel.SpeciesList)
{
// Create
string aSpeciesID = theSpecies.getSpeciesID( aSpecies );
EcellObject variable = EcellObject.CreateObject(modelId, aSpeciesID, EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
// setName
if( theModel.Level == 2 )
if ( aSpecies.Name != "" )
variable.SetEcellValue("Name", new EcellValue(aSpecies.Name));
// setValue
variable.SetEcellValue("Value", new EcellValue(theSpecies.getSpeciesValue( aSpecies )));
// setFixed
variable.SetEcellValue("Fixed", new EcellValue(theSpecies.getConstant( aSpecies )));
// add
modelObject.AddEntity(variable);
}
// Set Rule ( Process )
if ( theModel.RuleList.Count > 0)
{
// make Rule System
string aSystemKey = "/SBMLRule";
system = (EcellSystem)EcellObject.CreateObject(modelId, aSystemKey, EcellObject.SYSTEM, EcellObject.SYSTEM, new List<EcellData>());
system.SetEcellValue("Name", new EcellValue("System for SBML Rule"));
system.SetEcellValue("StepperID", new EcellValue("DE"));
modelObject.Children.Add(system);
foreach(RuleStruct aRule in theModel.RuleList)
{
theRule.initialize();
// setFullID
string aRuleID = theRule.getRuleID();
EcellObject process = EcellObject.CreateObject(modelId, aRuleID, EcellObject.PROCESS, EcellObject.PROCESS, new List<EcellData>());
modelObject.AddEntity(process);
// Algebraic Rule
if ( aRule.RuleType == libsbml.libsbml.SBML_ALGEBRAIC_RULE )
{
process.Classname = "ExpressionAlgebraicProcess";
}
// Assignment Rule
else if (aRule.RuleType == libsbml.libsbml.SBML_ASSIGNMENT_RULE ||
aRule.RuleType == libsbml.libsbml.SBML_SPECIES_CONCENTRATION_RULE ||
aRule.RuleType == libsbml.libsbml.SBML_COMPARTMENT_VOLUME_RULE ||
aRule.RuleType == libsbml.libsbml.SBML_PARAMETER_RULE)
{
process.Classname = "ExpressionAssignmentProcess";
int aVariableType = theRule.getVariableType( aRule.Variable );
if (aVariableType == libsbml.libsbml.SBML_SPECIES)
theRule.setSpeciesToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_PARAMETER)
theRule.setParameterToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_COMPARTMENT)
theRule.setCompartmentToVariableReference( aRule.Variable, 1 );
else
throw new EcellException("Variable type must be Species, Parameter, or Compartment");
}
// Rate Rule
else if (aRule.RuleType == libsbml.libsbml.SBML_RATE_RULE)
{
process.Classname = "ExpressionFluxProcess";
int aVariableType = theRule.getVariableType( aRule.Variable );
if (aVariableType == libsbml.libsbml.SBML_SPECIES)
theRule.setSpeciesToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_PARAMETER)
theRule.setParameterToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_COMPARTMENT)
theRule.setCompartmentToVariableReference( aRule.Variable, 1 );
else
throw new EcellException("Variable type must be Species, Parameter, or Compartment");
}
else
throw new EcellException(" The type of Rule must be Algebraic, Assignment or Rate Rule");
// convert SBML formula to E-Cell formula
string convertedFormula = theRule.convertRuleFormula( aRule.Formula );
// set Expression Property
process.SetEcellValue("Expression", new EcellValue(convertedFormula));
// setVariableReferenceList
process.SetEcellValue("VariableReferenceList", new EcellValue(theRule.GetVariableReferenceList()));
}
}
// Set Reaction ( Process )
foreach(ReactionStruct aReaction in theModel.ReactionList)
{
theReaction.initialize();
// setFullID
string aReactionID = theReaction.getReactionID( aReaction );
EcellProcess process = (EcellProcess)EcellObject.CreateObject(modelId, aReactionID, EcellObject.PROCESS, "ExpressionFluxProcess", new List<EcellData>());
// setName
if ( theModel.Level == 2 )
if( aReaction.Name != "" )
process.SetEcellValue("Name",new EcellValue(aReaction.Name));
// setSubstrate
foreach(ReactantStruct aSubstrate in aReaction.Reactants)
{
string name = "S" + theReaction.SubstrateNumber.ToString();
string aSubstrateID = theModel.getSpeciesReferenceID( aSubstrate.Species );
if ( aSubstrateID == null )
throw new EcellException("Species "+aSubstrate.Species+" not found");
if ( aSubstrate.Denominator != 1 )
throw new EcellException("Stoichiometry Error : E-Cell System can't set a floating Stoichiometry");
int coefficient = -1 * theReaction.getStoichiometry(aSubstrate.Species, aSubstrate.Stoichiometry );
VariableReferenceStruct aSubstrateList = new VariableReferenceStruct(name, "Variable:" + aSubstrateID, coefficient);
theReaction.VariableReferenceList.Add( aSubstrateList );
theReaction.SubstrateNumber = theReaction.SubstrateNumber + 1;
}
// setProduct
foreach(ProductStruct aProduct in aReaction.Products)
{
string name = 'P' + theReaction.ProductNumber.ToString();
string aProductID = theModel.getSpeciesReferenceID( aProduct.Species );
if ( aProductID == "" )
throw new EcellException("Species "+aProduct.Species+" not found");
if ( aProduct.Denominator != 1 )
throw new EcellException("Stoichiometry Error : E-Cell System can't set a floating Stoichiometry");
int coefficient = 1 * theReaction.getStoichiometry(aProduct.Species, aProduct.Stoichiometry );
VariableReferenceStruct aProductList = new VariableReferenceStruct(name, "Variable:" + aProductID, coefficient);
theReaction.VariableReferenceList.Add( aProductList );
theReaction.ProductNumber = theReaction.ProductNumber + 1;
}
// setCatalyst
foreach(string aModifier in aReaction.Modifiers)
{
string name = "C" + theReaction.ModifierNumber.ToString();
string aModifierID = theModel.getSpeciesReferenceID( aModifier );
if ( aModifierID == "" )
throw new EcellException("Species "+aModifier+" not found");
VariableReferenceStruct aModifierList = new VariableReferenceStruct(name, "Variable:" + aModifierID, 0);
theReaction.VariableReferenceList.Add( aModifierList );
theReaction.ModifierNumber = theReaction.ModifierNumber + 1;
}
// setProperty
foreach(KineticLawStruct kineticLaw in aReaction.KineticLaws)
{
foreach(ParameterStruct aParameter in kineticLaw.Parameters)
{
if (theModel.Level == 1)
process.SetEcellValue(aParameter.Name, new EcellValue(aParameter.Value));
else if (theModel.Level == 2)
process.SetEcellValue(aParameter.ID, new EcellValue(aParameter.Value));
}
// set "Expression" Property
// convert SBML format formula to E-Cell format formula
if( kineticLaw.Formula != "" )
{
string anExpression = theReaction.convertKineticLawFormula( kineticLaw.Formula );
// set Expression Property for ExpressionFluxProcess
process.SetEcellValue("Expression", new EcellValue(anExpression));
// setVariableReferenceList
process.SetEcellValue("VariableReferenceList", new EcellValue(theReaction.GetVariableReferenceList()));
}
}
// Set Parent System.
string sysKey = process.ParentSystemID;
foreach (EcellReference er in process.ReferenceList)
{
if (er.Coefficient == -1)
sysKey = er.Key.Split(':')[0];
}
foreach (EcellReference er in process.ReferenceList)
{
if (er.Coefficient == 1)
sysKey = er.Key.Split(':')[0];
}
process.Key = sysKey + ":" + process.LocalID;
// Update EntityPath.
foreach (EcellData data in process.Value)
{
data.EntityPath = process.FullID + ":" + data.Name;
}
modelObject.AddEntity(process);
}
return modelObject;
}
public void TestSBML_Rule()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_BIOMD0000000003);
Model sbmlModel = document.getModel();
SBML_Model model = new SBML_Model(sbmlModel);
SBML_Compartment sc = new SBML_Compartment(model);
SBML_Species species = new SBML_Species(model);
SBML_Rule rule = new SBML_Rule(model);
}