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)
{
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_GetMultipleObjects_noLocalParameters()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase rxn = d.getElementBySId("J0");
assertTrue(rxn != null);
SBase obj = rxn.getElementBySId("x");
assertTrue(obj == null);
obj = rxn.getElementByMetaId("meta28");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER);
d = null;
}
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 void test_SBMLTransforms_replaceIA_species()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
Model m;
ASTNode ast;
FunctionDefinition fd;
ListOfFunctionDefinitions lofd;
string filename = "../../sbml/test/test-data/";
filename += "initialAssignments_species.xml";
d = reader.readSBML(filename);
if (d == null);
{
}
m = d.getModel();
assertTrue( m.getNumInitialAssignments() == 3 );
assertTrue( m.getParameter(1).getValue() == 0.75 );
assertEquals( false, (m.getParameter(2).isSetValue()) );
assertEquals( true, m.getSpecies(2).isSetInitialAmount() );
assertTrue( m.getSpecies(2).getInitialAmount() == 2 );
d.expandInitialAssignments();
assertTrue( d.getModel().getNumInitialAssignments() == 0 );
assertTrue( m.getParameter(1).getValue() == 3 );
assertEquals( true, m.getParameter(2).isSetValue() );
assertTrue( m.getParameter(2).getValue() == 0.75 );
assertEquals( false, (m.getSpecies(2).isSetInitialAmount()) );
assertTrue( m.getSpecies(2).getInitialConcentration() == 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);
}
/// <summary>
/// Initializes and returns a new binary model based on an SBML file.
/// </summary>
/// <param name="filePath">The SBML file path</param>
/// <returns>A new <see cref="BinaryModel" /> instance initialized from <paramref name="filePath" /></returns>
public BinaryModel ReadFromSbmlFile(string filePath)
{
var reader = new SBMLReader();
var sbmlDoc = reader.readSBML(filePath);
var sbmlModel = sbmlDoc.getModel();
Console.WriteLine("Initializing boolean model");
var binaryModel = new BinaryModel();
InitFromSbmlQualModel(binaryModel, sbmlModel);
return(binaryModel);
}
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 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 == 4);
assertTrue(d.getError(0).getErrorId() == 99505);
assertTrue(d.getError(1).getErrorId() == 99505);
assertTrue(d.getError(2).getErrorId() == 99505);
assertTrue(d.getError(3).getErrorId() == 80701);
d.getErrorLog().clearLog();
d.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
errors = d.checkConsistency();
assertTrue(errors == 0);
d = null;
}
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 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_GetMultipleObjects_allElements()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBaseList list = d.getListOfAllElements();
assertTrue(list.getSize() == 37);
d = null;
}
public void test_GetMultipleObjects_getId()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase obj = d.getElementBySId("no_id");
assertTrue(obj == null);
obj = d.getElementBySId("");
assertTrue(obj == null);
obj = d.getElementBySId("find_id");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_MODEL);
obj = d.getElementBySId("func1");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION);
obj = d.getElementBySId("comp");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_COMPARTMENT);
obj = d.getElementBySId("b");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_SPECIES);
obj = d.getElementBySId("x");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_PARAMETER);
obj = d.getElementBySId("J0");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_REACTION);
obj = d.getElementBySId("E0");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT);
d = null;
}
public void test_GetMultipleObjects_noUnits()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase obj = d.getElementBySId("volume");
assertTrue(obj == null);
obj = d.getElementByMetaId("meta30");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_UNIT_DEFINITION);
d = null;
}
public void test_GetMultipleObjects_noAssignments()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "assignments-invalid.xml";
d = reader.readSBML(filename);
if (d.getModel() == null)
{
;
}
{
}
SBase obj = d.getElementBySId("ia");
assertTrue(obj == null);
obj = d.getElementByMetaId("ia_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
obj = d.getElementBySId("ar");
assertTrue(obj == null);
obj = d.getElementByMetaId("ar_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE);
obj = d.getElementBySId("rr");
assertTrue(obj == null);
obj = d.getElementByMetaId("rr_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_RATE_RULE);
obj = d.getElementBySId("ea");
assertTrue(obj == null);
obj = d.getElementByMetaId("ea_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
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_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_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_GetMultipleObjects_getMetaId()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase obj = d.getElementByMetaId("no_id");
assertTrue(obj == null);
obj = d.getElementByMetaId("");
assertTrue(obj == null);
obj = d.getElementByMetaId("meta1");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_DOCUMENT);
obj = d.getElementByMetaId("meta2");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_MODEL);
obj = d.getElementByMetaId("meta3");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_COMPARTMENT);
obj = d.getElementByMetaId("meta4");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_COMPARTMENT);
obj = d.getElementByMetaId("meta5");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_SPECIES);
obj = d.getElementByMetaId("meta6");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_SPECIES);
obj = d.getElementByMetaId("meta7");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_REACTION);
obj = d.getElementByMetaId("meta8");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_REACTION);
obj = d.getElementByMetaId("meta9");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_SPECIES_REFERENCE);
obj = d.getElementByMetaId("meta10");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE);
obj = d.getElementByMetaId("meta11");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_KINETIC_LAW);
obj = d.getElementByMetaId("meta12");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_EVENT);
obj = d.getElementByMetaId("meta13");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT);
obj = d.getElementByMetaId("meta14");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_TRIGGER);
obj = d.getElementByMetaId("meta15");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
obj = d.getElementByMetaId("meta16");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
obj = d.getElementByMetaId("meta17");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_DELAY);
obj = d.getElementByMetaId("meta18");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_PARAMETER);
obj = d.getElementByMetaId("meta19");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_PRIORITY);
obj = d.getElementByMetaId("meta20");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_FUNCTION_DEFINITION);
obj = d.getElementByMetaId("meta21");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION);
obj = d.getElementByMetaId("meta22");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
obj = d.getElementByMetaId("meta23");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
obj = d.getElementByMetaId("meta24");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_RULE);
obj = d.getElementByMetaId("meta25");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_RATE_RULE);
obj = d.getElementByMetaId("meta26");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE);
obj = d.getElementByMetaId("meta27");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_LOCAL_PARAMETER);
obj = d.getElementByMetaId("meta28");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER);
obj = d.getElementByMetaId("meta29");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_UNIT_DEFINITION);
obj = d.getElementByMetaId("meta30");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_UNIT_DEFINITION);
obj = d.getElementByMetaId("meta31");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_UNIT);
obj = d.getElementByMetaId("meta32");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_UNIT);
obj = d.getElementByMetaId("meta33");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_PARAMETER);
obj = d.getElementByMetaId("meta34");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE);
obj = d.getElementByMetaId("meta35");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE);
d = null;
}
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_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;
}
