public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getNumErrors() > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] Echoed {0} to {1}", inputFile, outputFile);
}
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) ));
}
public static void Main(String[] args)
{
if (args.Length < 2 || args.Length > 3)
{
Console.WriteLine("Usage: FlattenModel [-p] input-filename output-filename");
Console.WriteLine(" -p : list unused ports");
Environment.Exit(2);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
bool leavePorts = false;
SBMLDocument doc;
if (args.Length == 2)
{
doc = reader.readSBML(args[0]);
}
else
{
doc = reader.readSBML(args[1]);
leavePorts = true;
}
if (doc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
doc.printErrors();
}
else
{
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to flatten */
props.addOption("flatten comp", true, "flatten comp");
/* add an option to leave ports if the user has requested this */
props.addOption("leavePorts", leavePorts, "unused ports should be listed in the flattened model");
/* perform the conversion */
int result = doc.convert(props);
if (result != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine("conversion failed ... ({0})", result);
doc.printErrors();
Environment.Exit(3);
}
if (args.Length == 2)
{
writer.writeSBML(doc, args[1]);
}
else
{
writer.writeSBML(doc, args[2]);
}
}
}
public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
var now = DateTime.Now.Ticks;
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
Console.WriteLine("Read {0} in {1}", inputFile, new TimeSpan(DateTime.Now.Ticks - now).TotalMilliseconds);
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to convert a model with
L3 FBC to L2 with COBRA annotation */
props.addOption("convert fbc to cobra", true, "Convert FBC model to Cobra model");
now = DateTime.Now.Ticks;
/* perform the conversion */
int result = sbmlDoc.convert(props);
if (result != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] converted to FBC from {0} and wrote to {1} (in {2} msec)", inputFile, outputFile, new TimeSpan(DateTime.Now.Ticks - now).TotalMilliseconds);
}
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 static void Main(string[] args)
{
if (args.Length != 3)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename package-to-strip output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string packageToStrip = args[1];
string outputFile = args[2];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to strip a given package */
props.addOption("stripPackage", true, "Strip SBML Level 3 package constructs from the model");
/* add an option with the package we want to remove */
props.addOption("package", packageToStrip, "Name of the SBML Level 3 package to be stripped");
/* perform the conversion */
if (sbmlDoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] Stripped package '{0}' from {1} and wrote to {2}", packageToStrip, inputFile, outputFile);
}
public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filenameoutput-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to promote parameters */
props.addOption("promoteLocalParameters", true, "Promotes all Local Parameters to Global ones");
/* perform the conversion */
if (sbmlDoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] promoted paramters from {0} and wrote to {1}", inputFile, outputFile);
}
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 == 2 );
assertTrue( d.getError(0).getErrorId() == 10214 );
assertTrue( d.getError(1).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 test_read_MathML_2()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
FunctionDefinition fd;
InitialAssignment ia;
Rule r;
string filename = "../../sbml/math/test/test-data/";
filename += "mathML_2-invalid.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 == null );
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_QUALIFIER_LOGBASE);
//assertTrue( child1.getNumChildren() == 1 );
//assertTrue( child2.getType() == libsbml.AST_NAME );
//assertTrue( child2.getNumChildren() == 0 );
//assertTrue(( "x" == libsbml.formulaToString(child2) ));
//child2 = child1.getChild(0);
//assertTrue(child2.getType() == libsbml.AST_REAL);
//assertTrue(child2.getNumChildren() == 0);
//assertTrue(("3" == libsbml.formulaToString(child2)));
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;
}
internal static HandleRef getCPtr(SBMLReader obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
internal static HandleRef getCPtrAndDisown(SBMLReader obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
internal static HandleRef getCPtr(SBMLReader obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void test_read_MathML_1()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
FunctionDefinition fd;
InitialAssignment ia;
Rule r;
KineticLaw kl;
string filename = "../../sbml/math/test/test-data/";
filename += "mathML_1-invalid.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 == null );
d = null;
}
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;
Event e;
Trigger t;
Priority pr;
string filename = "../../sbml/test/test-data/";
filename += "l3v1-new-invalid.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() == "" );
e = m.getEvent(0);
t = e.getTrigger();
assertEquals( true, t.isSetPersistent() );
assertTrue( t.getPersistent() == false );
assertEquals( true, t.isSetInitialValue() );
assertTrue( t.getInitialValue() == false );
assertEquals( true, e.isSetPriority() );
pr = e.getPriority();
assertTrue( pr != null );
assertEquals( true, pr.isSetMath() );
e = m.getEvent(1);
assertEquals( false, e.isSetPriority() );
t = e.getTrigger();
assertEquals( false, (t.isSetPersistent()) );
assertEquals( false, (t.isSetInitialValue()) );
d = null;
}
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_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;
}
