public void test_SBMLDocument_setModel2()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(1, 2);
m1.createCompartment();
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_LEVEL_MISMATCH);
assertTrue(d.getModel() == null);
d = null;
}
public void test_SBMLDocument_setLevelAndVersion()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 2);
d.setModel(m1);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
d = null;
}
public void test_SBMLDocument_createWith()
{
SBMLDocument d = new SBMLDocument(1, 2);
assertTrue(d.getTypeCode() == libsbml.SBML_DOCUMENT);
assertTrue(d.getNotes() == null);
assertTrue(d.getAnnotation() == null);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
assertTrue(d.getNumErrors() == 0);
d = null;
}
public void test_SBMLConvert_convertToL3_event()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
Event e = m.createEvent();
Event e1;
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
e1 = m.getEvent(0);
assertTrue(e1.hasRequiredAttributes() == true);
d = null;
}
public TwoStepTertiaryModel(string tertDocName, SBMLDocument tertDoc,
List <PrimaryModelWData> primModels, List <string> secDocNames,
List <SBMLDocument> secDocs)
{
this.tertDocName = tertDocName;
this.tertDoc = tertDoc;
this.primModels = primModels;
this.secDocNames = secDocNames;
this.secDocs = secDocs;
}
public static void Main(String[] args)
{
if (!SBMLExtensionRegistry.isPackageEnabled("comp"))
{
Console.WriteLine("This copy of libSBML does not contain the 'comp' extension");
Console.WriteLine("Unable to proceed with the resolver example the model.");
Environment.Exit(2);
}
// create custom resolver
CustomResolver resolver = new CustomResolver();
// add the resolver and store its index, so we can free it later.
int index = SBMLResolverRegistry.getInstance().addResolver(resolver);
// create a new document with comp enabled
SBMLDocument doc = new SBMLDocument(new CompPkgNamespaces());
// get a hold of a plugin object
CompSBMLDocumentPlugin plugin = (CompSBMLDocumentPlugin)doc.getPlugin("comp");
// create an external model definition
ExternalModelDefinition external = plugin.createExternalModelDefinition();
// set the source to the URI
external.setSource("http://www.ebi.ac.uk/biomodels-main/download?mid=BMID000000063853");
// resolve the model
Model model = external.getReferencedModel();
if (model == null)
{
Console.Error.WriteLine("couldn't resolve");
Environment.Exit(2);
}
// model is ready to be used now, however, only as long and the document
// holding the external model definition is still alive and referenced
Console.WriteLine("Model id: " + model.getId());
Console.WriteLine("# species: " + model.getNumSpecies());
Console.WriteLine("# reactions: " + model.getNumReactions());
// now that we are done get rid of the resolver
SBMLResolverRegistry.getInstance().removeResolver(index);
// also clear the resolver instance, just to be sure that it has
// no more references to the C# resolver
SBMLResolverRegistry.deleteResolerRegistryInstance();
// finally we can get rid of the C# resolver
resolver = null;
}
static void testCreateSBML()
{
SBMLDocument d = new SBMLDocument(defLevel, defVersion);
Model m = d.createModel();
m.setId("testmodel");
Compartment c1 = m.createCompartment();
Compartment c2 = m.createCompartment();
c1.setId("c1");
c2.setId("c2");
Species s1 = m.createSpecies();
Species s2 = m.createSpecies();
string id1 = "s1";
string id2 = "s2";
// strings with non-ASCII characters (multibyte characters)
string n1 = "γ-lyase";
string n2 = "β-synthase";
s1.setId(id1);
s1.setName(n1);
s1.setCompartment("c1");
s2.setId(id2);
s2.setName(n2);
s2.setCompartment("c2");
string file = "test2.xml";
try
{
if (libsbml.writeSBML(d, file) == 0)
{
ERR("[CreateSBML] Error: cannot write " + file);
}
else
{
OK();
}
}
catch (Exception e)
{
ERR("[CreateSBML] (" + file + ") Error: Exception thrown : " + e.Message);
}
testReadSBMLFromFile(file);
}
private static void TestKineticLaw(int level, int version)
{
var doc = new SBMLDocument(level, version);
var model = doc.createModel();
var reaction = model.createReaction();
reaction.initDefaults();
reaction.createKineticLaw();
PrintLineNumbers(level,
version,
doc, "KineticLaw");
}
public void test_FunctionDefinition_parent_NULL()
{
SBMLDocument d = new SBMLDocument();
Model m = d.createModel();
FunctionDefinition c = m.createFunctionDefinition();
FunctionDefinition c1 = c.clone();
d = null;
assertTrue(c1.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getParentSBMLObject() == null);
assertEquals(c1.getSBMLDocument(), null);
c1 = null;
}
public void test_Species_parent_NULL()
{
SBMLDocument d = new SBMLDocument();
Model m = d.createModel();
Species c = m.createSpecies();
Species c1 = c.clone();
d = null;
assertTrue(c1.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getParentSBMLObject() == null);
assertEquals(c1.getSBMLDocument(), null);
c1 = null;
}
public OneStepTertiaryModel(string tertDocName, SBMLDocument tertDoc,
List <string> secDocNames, List <SBMLDocument> secDocs,
List <string> dataDocNames, List <NuMLDocument> dataDocs)
{
this.tertDocName = tertDocName;
this.tertDoc = tertDoc;
this.secDocNames = secDocNames;
this.secDocs = secDocs;
this.dataDocNames = dataDocNames;
this.dataDocs = dataDocs;
}
static SBMLDocument testReadSBMLFromString(string file)
{
if (!File.Exists(file))
{
ERR("[ReadSBMLFromString] Error: (" + file + ") : No such file or directory.");
return(null);
}
StreamReader oReader = new StreamReader(file);
string sSBML = oReader.ReadToEnd();
SBMLDocument d = libsbml.readSBMLFromString(sSBML);
if (d == null)
{
ERR("[ReadSBMLFromString] Error: (" + file + ") SBMLDocument is null.");
return(null);
}
if (d.getModel() == null)
{
for (int i = 0; i < d.getNumErrors(); i++)
{
ERR("[ReadSBMLFromString] Error: (" + file + ") : " + d.getError(i).getMessage());
}
return(null);
}
else if (d.getNumErrors() > 0)
{
bool iserror = false;
for (int i = 0; i < d.getNumErrors(); i++)
{
long severity = d.getError(i).getSeverity();
if ((severity == libsbml.LIBSBML_SEV_ERROR) ||
(severity == libsbml.LIBSBML_SEV_FATAL)
)
{
iserror = true;
ERR("[ReadSBMLFromString] Error: (" + file + ") : " + d.getError(i).getMessage());
}
}
if (iserror)
{
return(null);
}
}
OK();
return(d);
}
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);
}
private static void TestSpeciesReference(int level, int version)
{
var doc = new SBMLDocument(level, version);
var model = doc.createModel();
var reaction = model.createReaction();
reaction.initDefaults();
var sr = reaction.createReactant();
PrintLineNumbers(level,
version,
doc, "SpeciesReference");
}
public void test_SBMLDocument_copyConstructor()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(2, 1, false);
assertTrue(o1.getLevel() == 2);
assertTrue(o1.getVersion() == 1);
SBMLDocument o2 = new SBMLDocument(o1);
assertTrue(o2.getLevel() == 2);
assertTrue(o2.getVersion() == 1);
o2 = null;
o1 = null;
}
public void test_SBMLConvert_convertToL3_reactant()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
SpeciesReference sr1;
sr.setSpecies("s");
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
sr1 = m.getReaction(0).getReactant(0);
assertTrue(sr1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_parameter()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Parameter p = m.createParameter();
Parameter p1;
p.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
p1 = m.getParameter(0);
assertTrue(p1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_compartment()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
Compartment c1;
c.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
c1 = m.getCompartment(0);
assertTrue(c1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_reaction()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Reaction r = m.createReaction();
r.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
Reaction r1 = m.getReaction(0);
assertTrue(r1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL2_SBMLDocument()
{
SBMLDocument d = new SBMLDocument(1, 2);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
assertTrue(d.setLevelAndVersion(2, 2, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 2);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 3);
d = null;
}
public void test_RDFAnnotation_testMissingMetaId()
{
SBMLDocument doc = new SBMLDocument ( 3,1 );
Model model = doc.createModel();
assertTrue( model != null );
model.setId("test1");
CVTerm term = new CVTerm ( libsbml.MODEL_QUALIFIER );
term.addResource("testResource");
term.setModelQualifierType(libsbml.BQM_IS);
model.setMetaId("t1");
model.addCVTerm(term);
model.setMetaId("");
string test = model.toSBML();
assertTrue( test == "<model id=\"test1\"/>" );
}
public void test_SBMLConvert_convertToL3_species()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Species s = m.createSpecies();
Species s1;
s.setId(sid);
s.setCompartment("comp");
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
s1 = m.getSpecies(0);
assertTrue(s1.hasRequiredAttributes() == true);
d = null;
}
private static void TestLocalParameter(int level, int version)
{
var doc = new SBMLDocument(level, version);
var model = doc.createModel();
var reaction = model.createReaction();
reaction.initDefaults();
var law = reaction.createKineticLaw();
law.createParameter();
PrintLineNumbers(level,
version,
doc, "LocalParameter");
}
public void test_SBMLDocument_assignmentOperator()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(2, 1, false);
assertTrue(o1.getLevel() == 2);
assertTrue(o1.getVersion() == 1);
SBMLDocument o2 = new SBMLDocument();
o2 = o1;
assertTrue(o2.getLevel() == 2);
assertTrue(o2.getVersion() == 1);
o2 = null;
o1 = null;
}
public void Initialize(Model sbmlModel, SBMLDocument sbmlDoc)
{
Level = (int)sbmlDoc.getLevel();
Version = (int)sbmlDoc.getVersion();
SaveSpeciesReferences(sbmlModel);
if (sbmlModel.isSetConversionFactor())
{
ConversionFactor = sbmlModel.getConversionFactor();
}
if (sbmlModel.isSetSBOTerm())
{
SboTerm = sbmlModel.getSBOTerm();
}
}
public void test_SBMLConvert_convertFromL3_priority()
{
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
Event e = m.createEvent();
Priority p = e.createPriority();
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.setLevelAndVersion(2, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(2, 4, false) == true);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
}
private static void TestStoichiometryMath(int level, int version)
{
var doc = new SBMLDocument(level, version);
var model = doc.createModel();
var reaction = model.createReaction();
reaction.initDefaults();
var sr = reaction.createReactant();
sr.createStoichiometryMath();
PrintLineNumbers(level,
version,
doc, "StoichiometryMath");
}
public void test_SBMLConvert_invalidLevelVersion()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits("volume");
assertTrue(d.setLevelAndVersion(1, 3, true) == false);
assertTrue(d.setLevelAndVersion(2, 7, true) == false);
assertTrue(d.setLevelAndVersion(3, 5, true) == false);
assertTrue(d.setLevelAndVersion(4, 1, true) == false);
}
/// <summary>
/// The program is to be invoked with one argument, the input file.
/// </summary>
/// <param name="args">command line arguments</param>
/// <returns>0 in case of no errors</returns>
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("{0}Usage: getAllElementsWithNotes filename{0}{0}", Environment.NewLine);
return(1);
}
string filename = args[0];
// read the document
long start = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBMLFromFile(filename);
long stop = DateTime.Now.Ticks;
Console.WriteLine();
Console.WriteLine(" filename: {0}", filename);
Console.WriteLine(" read time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
// stop in case of serious errors
long errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (errors > 0)
{
Console.WriteLine(" error(s): {0}", errors);
document.printErrors();
return((int)errors);
}
// create the filter we want to use
var filter = new NotesFilter();
// get a list of all elements with notes
start = DateTime.Now.Ticks;
Console.WriteLine(" searching ......:");
SBaseList allElements = document.getListOfAllElements(filter);
stop = DateTime.Now.Ticks;
Console.WriteLine(" search time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
Console.WriteLine();
Console.WriteLine(" elements with notes: {0}", allElements.getSize());
Console.WriteLine();
// if we got here all went well ...
return(0);
}
private static void TestPriority(int level, int version)
{
var doc = new SBMLDocument(level, version);
var model = doc.createModel();
var element = model.createEvent();
if (element == null)
{
return;
}
element.createPriority();
PrintLineNumbers(level,
version,
doc, "Priority");
}
