public void test_SBMLDocument_clone()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(1, 1, false);
Model m = new Model(1, 1);
m.createCompartment();
m.createSpecies();
m.createReaction();
m.setId("foo");
o1.setModel(m);
assertTrue(o1.getLevel() == 1);
assertTrue(o1.getVersion() == 1);
assertTrue(o1.getModel().getId() == "foo");
assertTrue(o1.getModel().getLevel() == 1);
assertTrue(o1.getModel().getVersion() == 1);
assertTrue(o1.getModel().getSBMLDocument() == o1);
SBMLDocument o2 = o1.clone();
assertTrue(o2.getLevel() == 1);
assertTrue(o2.getVersion() == 1);
assertTrue(o2.getModel().getId() == "foo");
assertTrue(o2.getModel().getLevel() == 1);
assertTrue(o2.getModel().getVersion() == 1);
assertTrue(o2.getModel().getSBMLDocument() == o2);
o2 = null;
o1 = null;
}
public void test_SBMLDocument_setModel()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m1 = new Model(2, 4);
Model m2 = new Model(2, 4);
Model mout;
assertTrue(d.getModel() == null);
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
mout = d.getModel();
assertTrue(mout != null);
assertTrue(mout != m1);
i = d.setModel(d.getModel());
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
mout = d.getModel();
assertTrue(mout != null);
assertTrue(mout != m1);
i = d.setModel(m2);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
mout = d.getModel();
assertTrue(mout != null);
assertTrue(mout != m2);
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictSBO()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
(c).setSBOTerm(64);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Compartment c1 = d.getModel().getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Compartment c2 = d.getModel().getCompartment(0);
assertTrue((c2).getSBOTerm() == -1);
d = null;
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine("Usage: inlineInitialAssignments filename outFile");
return(1);
}
string filename = args[0];
string outFile = args[1];
long current = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
document.printErrors();
return(1);
}
var model = document.getModel();
SBMLTransforms.expandInitialAssignments(model);
libsbml.writeSBML(document, outFile);
return(0);
}
public void test_SBMLConvertStrict_convertL1ParamRule()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Parameter p = m.createParameter();
p.setId("p");
Parameter p1 = m.createParameter();
p1.setId("p1");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("p1");
ar.setMath(math);
ar.setUnits("mole");
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Rule r1 = d.getModel().getRule(0);
assertTrue(r1.getUnits() == "");
d = null;
}
public void test_SBMLConvert_convertToL3_stoichiometryMath()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
StoichiometryMath sm = sr.createStoichiometryMath();
ASTNode ast = libsbml.parseFormula("c*2");
sm.setMath(ast);
assertTrue(m.getNumRules() == 0);
assertTrue(sr.isSetId() == false);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
sr = r.getReactant(0);
assertTrue(m.getNumRules() == 1);
assertTrue(sr.isSetId() == true);
Rule rule = m.getRule(0);
assertTrue((rule.getVariable() == sr.getId()));
d = null;
}
public void test_SBMLConvert_convertToL3_localParameters()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
KineticLaw kl = r.createKineticLaw();
kl.setFormula("s*k");
Parameter p = kl.createParameter();
p.setId("k");
assertTrue(kl.getNumLocalParameters() == 0);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
kl = r.getKineticLaw();
assertTrue(kl.getNumLocalParameters() == 1);
LocalParameter lp = kl.getLocalParameter(0);
d = null;
}
public void setUp()
{
string filename = "../../sbml/annotation/test/test-data/annotation.xml";
d = libsbml.readSBML(filename);
m = d.getModel();
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.Write(Environment.NewLine + "Usage: printMath filename" + Environment.NewLine + Environment.NewLine);
return(1);
}
string filename = args[0];
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors() > 0)
{
Console.Error.Write("Encountered the following SBML errors:" + Environment.NewLine);
document.printErrors(new OStream(OStream.CERR));
return(1);
}
Model model = document.getModel();
if (model == null)
{
Console.Write("No model present." + Environment.NewLine);
return(1);
}
printMath(model);
Console.WriteLine();
return(0);
}
public void test_SBMLConvertStrict_convertToL1()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
(m).setMetaId("_m");
Compartment c = m.createCompartment();
c.setId("c");
(c).setSBOTerm(240);
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Model m1 = d.getModel();
assertTrue((m1).getMetaId() == "");
Compartment c1 = m1.getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
Species s1 = m1.getSpecies(0);
assertTrue(s1.getHasOnlySubstanceUnits() == false);
d = null;
}
public static int Main(string[] args)
{
if (args.Length != 4)
{
Console.WriteLine("Usage: replaceOneFD filename functionDefinitionId reactionId outfile");
return(1);
}
string filename = args[0];
string outFile = args[3];
string functionDefinitionId = args[1];
string reactionId = args[2];
long current = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
document.printErrors();
return(1);
}
var model = document.getModel();
var functionDefinition = model.getFunctionDefinition(functionDefinitionId);
if (functionDefinition == null)
{
Console.WriteLine();
Console.WriteLine("No functiondefinition with the given id can be found.");
return(1);
}
var reaction = model.getReaction(reactionId);
if (reaction == null)
{
Console.WriteLine();
Console.WriteLine("No reaction with the given id can be found.");
return(1);
}
if (!reaction.isSetKineticLaw() || !reaction.getKineticLaw().isSetMath())
{
Console.WriteLine();
Console.WriteLine("The reaction has no math set. ");
return(1);
}
// Until here it was all setup, all we needed was an ASTNode, in which we wanted to
// replace calls to a function definition, with the function definitions content.
//
SBMLTransforms.replaceFD(reaction.getKineticLaw().getMath(), functionDefinition);
// finally write to file
libsbml.writeSBML(document, outFile);
return(0);
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.Write(Environment.NewLine + "Usage: printSBML filename" + Environment.NewLine + Environment.NewLine);
return(1);
}
string filename = args[0];
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors() > 0)
{
Console.WriteLine("Encountered the following SBML errors:" + Environment.NewLine);
document.printErrors();
return(1);
}
int level = (int)document.getLevel();
int version = (int)document.getVersion();
Console.Write(Environment.NewLine
+ "File: " + filename
+ " (Level " + level + ", version " + version + ")" + Environment.NewLine);
Model model = document.getModel();
if (model == null)
{
Console.Write("No model present." + Environment.NewLine);
return(1);
}
Console.Write(" "
+ (level == 1 ? "name: " : " id: ")
+ (model.isSetId() ? model.getId() : "(empty)") + Environment.NewLine);
if (model.isSetSBOTerm())
{
Console.Write(" model sboTerm: " + model.getSBOTerm() + Environment.NewLine);
}
Console.Write("functionDefinitions: " + model.getNumFunctionDefinitions() + Environment.NewLine);
Console.Write(" unitDefinitions: " + model.getNumUnitDefinitions() + Environment.NewLine);
Console.Write(" compartmentTypes: " + model.getNumCompartmentTypes() + Environment.NewLine);
Console.Write(" specieTypes: " + model.getNumSpeciesTypes() + Environment.NewLine);
Console.Write(" compartments: " + model.getNumCompartments() + Environment.NewLine);
Console.Write(" species: " + model.getNumSpecies() + Environment.NewLine);
Console.Write(" parameters: " + model.getNumParameters() + Environment.NewLine);
Console.Write(" initialAssignments: " + model.getNumInitialAssignments() + Environment.NewLine);
Console.Write(" rules: " + model.getNumRules() + Environment.NewLine);
Console.Write(" constraints: " + model.getNumConstraints() + Environment.NewLine);
Console.Write(" reactions: " + model.getNumReactions() + Environment.NewLine);
Console.Write(" events: " + model.getNumEvents() + Environment.NewLine);
Console.Write(Environment.NewLine);
return(0);
}
/// <summary>
/// The program is to be invoked with two arguments, the input and output 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 != 2)
{
Console.WriteLine("{0}Usage: setIdFromNames filename output{0}{0}", Environment.NewLine);
return(1);
}
string filename = args[0];
string output = args[1];
// 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);
}
// get a list of all elements, as we will need to know all identifiers
// so that we don't create duplicates.
SBaseList allElements = document.getListOfAllElements();
// get a list of all ids
var allIds = getAllIds(allElements);
// create the transformer with the ids
var trans = new SetIdFromNames(allIds);
// rename the identifiers (using the elements we already gathered before)
start = DateTime.Now.Ticks;
document.getModel().renameIDs(allElements, trans);
stop = DateTime.Now.Ticks;
Console.WriteLine(" rename time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
// write to file
start = DateTime.Now.Ticks;
libsbml.writeSBMLToFile(document, output);
stop = DateTime.Now.Ticks;
Console.WriteLine(" write time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
Console.WriteLine();
// if we got here all went well ...
return(0);
}
public void test_Model_parent_add()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = new Model(2, 4);
d.setModel(m);
assertTrue(d == d.getModel().getParentSBMLObject());
d = null;
}
public void test_Model_ancestor_add()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = new Model(2, 4);
d.setModel(m);
assertTrue(d == d.getModel().getAncestorOfType(libsbml.SBML_DOCUMENT));
d = null;
}
public void test_SBMLDocument_setModel3()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 2);
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(d.getModel() != null);
d = null;
}
public void test_SBMLDocument_setModel1()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 1);
int i = d.setModel(m1);
assertTrue(i == libsbml.LIBSBML_VERSION_MISMATCH);
assertTrue(d.getModel() == null);
d = null;
}
public void test_Model_ancestor_create()
{
SBMLDocument d = new SBMLDocument();
Model m = d.createModel();
assertTrue(m.getAncestorOfType(libsbml.SBML_DOCUMENT) == d);
Model obj = d.getModel();
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == d);
d = null;
}
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;
}
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 void test_SBMLConvert_convertFromL3_modelUnits()
{
UnitDefinition ud;
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
m.setVolumeUnits("litre");
assertTrue(m.getNumUnitDefinitions() == 0);
assertTrue(d.setLevelAndVersion(2, 4, false) == true);
m = d.getModel();
assertTrue(m.getNumUnitDefinitions() == 1);
ud = m.getUnitDefinition(0);
assertTrue(("volume" == ud.getId()));
assertTrue(ud.getNumUnits() == 1);
assertTrue(ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE);
}
public static int Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("Usage: evaluateCustomMath formula [model containing values]");
return(1);
}
string formula = args[0];
string filename = args.Length == 2 ? args[1] : null;
var math = libsbml.parseFormula(formula);
if (math == null)
{
Console.WriteLine("Invalid formula, aborting.");
return(1);
}
SBMLDocument doc = null;
if (filename != null)
{
doc = libsbml.readSBML(filename);
if (doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
doc.printErrors();
return(1);
}
// the following maps a list of ids to their corresponding model values
// this makes it possible to evaluate expressions involving SIds.
SBMLTransforms.mapComponentValues(doc.getModel());
}
else
{
// create dummy document
doc = new SBMLDocument(3, 1);
}
var result = SBMLTransforms.evaluateASTNode(math, doc.getModel());
Console.WriteLine("{0} = {1}", formula, result);
return(0);
}
public void test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string annotation = "<rdf/>\n<rdf/>";
int i = (m).setAnnotation(annotation);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
assertTrue((m).getAnnotation().getNumChildren() == 2);
assertTrue(d.setLevelAndVersion(2, 4, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
m = d.getModel();
assertTrue((m).getAnnotation().getNumChildren() == 1);
d = null;
}
public void test_WriteL3SBML_Reaction_full()
{
string expected = "<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n" +
" <listOfReactants>\n" +
" <speciesReference species=\"x0\"/>\n" +
" </listOfReactants>\n" +
" <listOfProducts>\n" +
" <speciesReference species=\"s1\"/>\n" +
" </listOfProducts>\n" +
" <listOfModifiers>\n" +
" <modifierSpeciesReference species=\"m1\"/>\n" +
" </listOfModifiers>\n" +
" <kineticLaw>\n" +
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" +
" <apply>\n" +
" <divide/>\n" +
" <apply>\n" +
" <times/>\n" +
" <ci> vm </ci>\n" +
" <ci> s1 </ci>\n" +
" </apply>\n" +
" <apply>\n" +
" <plus/>\n" +
" <ci> km </ci>\n" +
" <ci> s1 </ci>\n" +
" </apply>\n" +
" </apply>\n" +
" </math>\n" +
" </kineticLaw>\n" +
"</reaction>";
D.createModel();
Reaction r = D.getModel().createReaction();
r.setId("v1");
r.setReversible(true);
r.setFast(false);
r.createReactant().setSpecies("x0");
r.createProduct().setSpecies("s1");
r.createModifier().setSpecies("m1");
r.createKineticLaw().setFormula("(vm * s1)/(km + s1)");
assertEquals(true, equals(expected, r.toSBML()));
}
static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("usage: printMulti sbml-file");
return;
}
SBMLDocument document = libsbml.readSBMLFromFile(args[0]);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
document.printErrors();
return;
}
Model model = document.getModel();
// print multi model information
printModelInfo(model);
// print multi compartment information
for (int i = 0; i < model.getNumCompartments(); ++i)
{
printCompartmentInfo(model.getCompartment(i));
}
// print multi species information
for (int i = 0; i < model.getNumSpecies(); ++i)
{
printSpeciesInfo(model.getSpecies(i));
}
// print multi reaction information
for (int i = 0; i < model.getNumReactions(); ++i)
{
printReactionInfo(model.getReaction(i));
}
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
Console.WriteLine(" Adds controlled vocabulary term to a species");
Console.WriteLine();
return(2);
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0)
{
Console.WriteLine("Read Error(s):");
d.printErrors();
Console.WriteLine("Correct the above and re-run.");
}
else
{
long n = d.getModel().getNumSpecies();
if (n <= 0)
{
Console.WriteLine("Model has no species.\n Cannot add CV terms\n");
}
else
{
Species s = d.getModel().getSpecies(0);
/* check that the species has a metaid
* no CVTerms will be added if there is no metaid to reference
*/
if (!s.isSetMetaId())
{
s.setMetaId("metaid_0000052");
}
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
cv1.addResource("urn:miriam:obo.go:GO%3A0005764");
s.addCVTerm(cv1);
// now create the additional annotation
//<rdf:Statement>
// <rdf:subject rdf:resource="#metaid_0000052"/>
// <rdf:predicate rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
// <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
// <bqbiol:isDescribedBy>
// <rdf:Bag>
// <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
// <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
// </rdf:Bag>
// </bqbiol:isDescribedBy>
//</rdf:Statement>
/* attributes */
XMLAttributes blank_att = new XMLAttributes();
XMLAttributes resource_att = new XMLAttributes();
/* create the outer statement node */
XMLTriple statement_triple = new XMLTriple("Statement",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken statement_token = new XMLToken(statement_triple, blank_att);
XMLNode statement = new XMLNode(statement_token);
/*create the subject node */
XMLTriple subject_triple = new XMLTriple("subject",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "#" + s.getMetaId());
XMLToken subject_token = new XMLToken(subject_triple, resource_att);
XMLNode subject = new XMLNode(subject_token);
/*create the predicate node */
XMLTriple predicate_triple = new XMLTriple("predicate",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource",
"http://biomodels.net/biology-qualifiers/occursIn");
XMLToken predicate_token = new XMLToken(predicate_triple, resource_att);
XMLNode predicate = new XMLNode(predicate_token);
/*create the object node */
XMLTriple object_triple = new XMLTriple("object",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764");
XMLToken object_token = new XMLToken(object_triple, resource_att);
XMLNode object_ = new XMLNode(object_token);
/* create the bqbiol node */
XMLTriple bqbiol_triple = new XMLTriple("isDescribedBy",
"http://biomodels.net/biology-qualifiers/",
"bqbiol");
XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);
XMLNode bqbiol = new XMLNode(bqbiol_token);
/* create the bag node */
XMLTriple bag_triple = new XMLTriple("Bag",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken bag_token = new XMLToken(bag_triple, blank_att);
XMLNode bag = new XMLNode(bag_token);
/* create each li node and add to the bag */
XMLTriple li_triple = new XMLTriple("li",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004");
XMLToken li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
XMLNode li = new XMLNode(li_token);
bag.addChild(li);
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
li = new XMLNode(li_token);
bag.addChild(li);
/* add the bag to bqbiol */
bqbiol.addChild(bag);
/* add subject, predicate, object and bqbiol to statement */
statement.addChild(subject);
statement.addChild(predicate);
statement.addChild(object_);
statement.addChild(bqbiol);
/* create a top-level RDF element
* this will ensure correct merging
*/
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
xmlns.add("http://purl.org/dc/terms/", "dcterms");
xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");
XMLTriple RDF_triple = new XMLTriple("RDF",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);
XMLNode annotation = new XMLNode(RDF_token);
/* add the staement node to the RDF node */
annotation.addChild(statement);
s.appendAnnotation(annotation);
libsbml.writeSBML(d, args[1]);
}
}
return((int)errors);
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine(" Usage: printRenderInformation <input file> \n" +
" prints a summary of the render information object.");
return(1);
}
string inputFile = args[0];
SBMLDocument doc = libsbml.readSBMLFromFile(inputFile);
Console.WriteLine("Using libSBML: {0} supporting packages for:", libsbml.getLibSBMLDottedVersion());
for (int i = 0; i < SBMLExtensionRegistry.getNumRegisteredPackages(); ++i)
{
Console.WriteLine("\t {0}", SBMLExtensionRegistry.getRegisteredPackageName(i));
}
Console.WriteLine("\nThe document is: level {0}, version {1}", doc.getLevel(), doc.getVersion());
for (int i = 0; i < doc.getNumPlugins(); ++i)
{
Console.WriteLine(" doc uses package: {0}", doc.getPlugin(i).getElementNamespace());
}
Console.WriteLine("\n");
long numErrors = doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (numErrors > 0)
{
Console.WriteLine("Encountered errors while reading the file. ");
Console.WriteLine("Please correct the following errors and try again.");
doc.printErrors();
return(2);
}
Model model = doc.getModel();
LayoutModelPlugin plugin = (LayoutModelPlugin)model.getPlugin("layout");
if (plugin == null || plugin.getNumLayouts() == 0)
{
Console.WriteLine("The loaded model contains no layout information, please add these first.");
return(3);
}
RenderListOfLayoutsPlugin lolPlugin = (RenderListOfLayoutsPlugin)plugin.getListOfLayouts().getPlugin("render");
if (lolPlugin != null && lolPlugin.getNumGlobalRenderInformationObjects() > 0)
{
Console.WriteLine("The loaded model contains global Render information: ");
for (int i = 0; i < lolPlugin.getNumGlobalRenderInformationObjects(); ++i)
{
GlobalRenderInformation info = lolPlugin.getRenderInformation(i);
print_render_info(info);
}
}
Layout layout = plugin.getLayout(0);
RenderLayoutPlugin rPlugin = (RenderLayoutPlugin)layout.getPlugin("render");
if (rPlugin != null && rPlugin.getNumLocalRenderInformationObjects() > 0)
{
Console.WriteLine("The loaded model contains local Render information. ");
// here we would do the same as above for the local render information ...
for (int i = 0; i < rPlugin.getNumLocalRenderInformationObjects(); ++i)
{
LocalRenderInformation info = rPlugin.getRenderInformation(i);
print_render_info(info);
}
}
return(0);
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Usage: printUnits filename");
return(1);
}
string filename = args[0];
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors() > 0)
{
Console.Error.WriteLine("Encountered the following SBML errors:");
document.printErrors();
return(1);
}
Model model = document.getModel();
if (model == null)
{
Console.WriteLine("No model present.");
return(1);
}
int i, j;
for (i = 0; i < model.getNumSpecies(); i++)
{
Species s = model.getSpecies(i);
Console.WriteLine("Species " + i + ": "
+ UnitDefinition.printUnits(s.getDerivedUnitDefinition()));
}
for (i = 0; i < model.getNumCompartments(); i++)
{
Compartment c = model.getCompartment(i);
Console.WriteLine("Compartment " + i + ": "
+ UnitDefinition.printUnits(c.getDerivedUnitDefinition()))
;
}
for (i = 0; i < model.getNumParameters(); i++)
{
Parameter p = model.getParameter(i);
Console.WriteLine("Parameter " + i + ": "
+ UnitDefinition.printUnits(p.getDerivedUnitDefinition()))
;
}
for (i = 0; i < model.getNumInitialAssignments(); i++)
{
InitialAssignment ia = model.getInitialAssignment(i);
Console.WriteLine("InitialAssignment " + i + ": "
+ UnitDefinition.printUnits(ia.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((ia.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (i = 0; i < model.getNumEvents(); i++)
{
Event e = model.getEvent(i);
Console.WriteLine("Event " + i + ": ");
if (e.isSetDelay())
{
Console.WriteLine("Delay: "
+ UnitDefinition.printUnits(e.getDelay().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((e.getDelay().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (j = 0; j < e.getNumEventAssignments(); j++)
{
EventAssignment ea = e.getEventAssignment(j);
Console.WriteLine("EventAssignment " + j + ": "
+ UnitDefinition.printUnits(ea.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((ea.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
for (i = 0; i < model.getNumReactions(); i++)
{
Reaction r = model.getReaction(i);
Console.WriteLine("Reaction " + i + ": ");
if (r.isSetKineticLaw())
{
Console.WriteLine("Kinetic Law: "
+ UnitDefinition.printUnits(r.getKineticLaw().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((r.getKineticLaw().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (j = 0; j < r.getNumReactants(); j++)
{
SpeciesReference sr = r.getReactant(j);
if (sr.isSetStoichiometryMath())
{
Console.WriteLine("Reactant stoichiometryMath" + j + ": "
+ UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((sr.getStoichiometryMath().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
for (j = 0; j < r.getNumProducts(); j++)
{
SpeciesReference sr = r.getProduct(j);
if (sr.isSetStoichiometryMath())
{
Console.WriteLine("Product stoichiometryMath" + j + ": "
+ UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((sr.getStoichiometryMath().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
}
for (i = 0; i < model.getNumRules(); i++)
{
Rule r = model.getRule(i);
Console.WriteLine("Rule " + i + ": "
+ UnitDefinition.printUnits(r.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((r.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
return(0);
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine(" Usage: addRenderInformation <input file> <output file> \n" +
" Adds a render information object to the input file");
return(1);
}
string inputFile = args[0];
string outputFile = args[1];
SBMLDocument doc = libsbml.readSBMLFromFile(inputFile);
long numErrors = doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (numErrors > 0)
{
Console.WriteLine("Encountered errors while reading the file. ");
Console.WriteLine("Please correct the following errors and try again.");
doc.printErrors();
return(2);
}
Model model = doc.getModel();
LayoutModelPlugin plugin = (LayoutModelPlugin)model.getPlugin("layout");
if (plugin == null || plugin.getNumLayouts() == 0)
{
Console.WriteLine("The loaded model contains no layout information, please add these first.");
return(3);
}
RenderListOfLayoutsPlugin lolPlugin = (RenderListOfLayoutsPlugin)plugin.getListOfLayouts().getPlugin("render");
if (lolPlugin != null && lolPlugin.getNumGlobalRenderInformationObjects() > 0)
{
Console.WriteLine("The loaded model contains global Render information. ");
}
// add render information to the first layout
Layout layout = plugin.getLayout(0);
RenderLayoutPlugin rPlugin = (RenderLayoutPlugin)layout.getPlugin("render");
if (rPlugin != null && rPlugin.getNumLocalRenderInformationObjects() > 0)
{
Console.WriteLine("The loaded model contains local Render information. ");
}
else
{
string uri = doc.getLevel() == 2 ? RenderExtension.getXmlnsL2() : RenderExtension.getXmlnsL3V1V1();
// enable render package
doc.enablePackage(uri, "render", true);
doc.setPackageRequired("render", false);
rPlugin = (RenderLayoutPlugin)layout.getPlugin("render");
addRenderInformation(rPlugin);
libsbml.writeSBMLToFile(doc, outputFile);
}
return(0);
}