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 void test_SBMLConvertStrict_convertNonStrictUnits()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
Parameter p = m.createParameter();
p.setId("p");
p.setUnits("mole");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("c");
ar.setMath(math);
assertTrue(d.setLevelAndVersion(2, 1, 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, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
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_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 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_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_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 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>
/// Converts a SBML document to the latest version (3.1) that is supported.
/// </summary>
private void convertSBML(SBMLDocument sbmlDoc)
{
var latestLevel = SBMLDocument.getDefaultLevel();
var latestVersion = SBMLDocument.getDefaultVersion();
if (sbmlDoc.getLevel() == latestLevel || sbmlDoc.getVersion() == latestVersion)
{
return;
}
var success = sbmlDoc.setLevelAndVersion(latestLevel, latestVersion);
if (!success)
{
throw new MoBiException(SBMLConstants.CouldNotConvertToActualLevel(latestLevel, latestVersion,
sbmlDoc.getLevel(), sbmlDoc.getVersion()));
}
}
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_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 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_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 test_SBMLConvert_addModifiersToReaction()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Reaction r = m.createReaction();
KineticLaw kl = r.createKineticLaw();
kl.setFormula("k1*S1*S2*S3*S4*S5");
SimpleSpeciesReference ssr1;
SimpleSpeciesReference ssr2;
Species s1 = m.createSpecies();
s1.setId("S1");
Species s2 = m.createSpecies();
s2.setId("S2");
Species s3 = m.createSpecies();
s3.setId("S3");
Species s4 = m.createSpecies();
s4.setId("S4");
Species s5 = m.createSpecies();
s5.setId("S5");
SpeciesReference sr1 = r.createReactant();
SpeciesReference sr2 = r.createReactant();
SpeciesReference sr3 = r.createProduct();
sr1.setSpecies("S1");
sr2.setSpecies("S2");
sr3.setSpecies("S5");
assertTrue(r.getNumModifiers() == 0);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
assertTrue(m.getReaction(0).getNumModifiers() == 2);
ssr1 = m.getReaction(0).getModifier(0);
ssr2 = m.getReaction(0).getModifier(1);
assertTrue(("S3" == ssr1.getSpecies()));
assertTrue(("S4" == ssr2.getSpecies()));
d = null;
}
public static int Main(string[] args)
{
int latestLevel = (int)SBMLDocument.getDefaultLevel();
int latestVersion = (int)SBMLDocument.getDefaultVersion();
if (args.Length != 2)
{
Console.Write("Usage: convertSBML input-filename output-filename" + Environment.NewLine
+ "This program will attempt to convert a model either to" + Environment.NewLine
+ "SBML Level " + latestLevel + " Version " + latestVersion
+ " (if the model is not already) or, if " + Environment.NewLine
+ "the model is already expressed in Level " + latestLevel
+ " Version " + latestVersion + ", this" + Environment.NewLine
+ "program will attempt to convert the model to Level 1 Version 2."
+ Environment.NewLine);
return(1);
}
string inputFile = args[0];
string outputFile = args[1];
SBMLDocument document = libsbml.readSBML(inputFile);
long errors = document.getNumErrors();
if (errors > 0)
{
Console.Error.Write("Encountered the following SBML errors:" + Environment.NewLine);
document.printErrors();
Console.Error.Write("Conversion skipped. Please correct the problems above first."
+ Environment.NewLine);
return((int)errors);
}
/**
* If the given model is not already L2v4, assume that the user wants to
* convert it to the latest release of SBML (which is L2v4 currently).
* If the model is already L2v4, assume that the user wants to attempt to
* convert it down to Level 1 (specifically L1v2).
*/
int olevel = (int)document.getLevel();
int oversion = (int)document.getVersion();
bool success;
if (olevel < latestLevel || oversion < latestVersion)
{
Console.Write("Attempting to convert Level " + olevel + " Version " + oversion
+ " model to Level " + latestLevel
+ " Version " + latestVersion + "." + Environment.NewLine);
success = document.setLevelAndVersion(latestLevel, latestVersion);
}
else
{
Console.Write("Attempting to convert Level " + olevel + " Version " + oversion
+ " model to Level 1 Version 2." + Environment.NewLine);
success = document.setLevelAndVersion(1, 2);
}
errors = document.getNumErrors();
if (!success)
{
Console.Error.Write("Unable to perform conversion due to the following:" + Environment.NewLine);
document.printErrors();
Console.Write(Environment.NewLine);
Console.Write("Conversion skipped. Either libSBML does not (yet)" + Environment.NewLine
+ "have the ability to convert this model or (automatic)" + Environment.NewLine
+ "conversion is not possible in this case." + Environment.NewLine);
return((int)errors);
}
else if (errors > 0)
{
Console.Write("Information may have been lost in conversion; but a valid model ");
Console.Write("was produced by the conversion.\nThe following information ");
Console.Write("was provided:\n");
document.printErrors();
libsbml.writeSBML(document, outputFile);
}
else
{
Console.Write("Conversion completed." + Environment.NewLine);
libsbml.writeSBML(document, outputFile);
}
return(0);
}
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 != 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);
}