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;
}
public static int Main(string[] args)
{
int retval = 0;
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create a replacement parameter
Parameter parameter = model.createParameter();
parameter.setId("x");
parameter.setConstant(true);
// create a parameter to be a conversion factor
Parameter param2 = model.createParameter();
param2.setId("x_conv");
param2.setMetaId("_110013");
param2.setConstant(true);
// create a parameter to be a conversion factor
Parameter param3 = model.createParameter();
param3.setId("lcf");
param3.setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin splugin = (CompSBasePlugin)(parameter.getPlugin("comp"));
// Add a replaced element.
ReplacedElement rep1 = splugin.createReplacedElement();
int rv = rep1.setSubmodelRef("submod1");
rv = rep1.setConversionFactor("x_conv");
rv = rep1.setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2 = new ReplacedElement();
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin.addReplacedElement(rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef sbr5 = rep2.createSBaseRef();
sbr5.setIdRef("submodelG");
SBaseRef sbr6 = sbr5.createSBaseRef();
sbr6.setIdRef("buriedElement");
splugin.addReplacedElement(rep2);
// Create a submodel
CompModelPlugin mplugin = (CompModelPlugin)(model.getPlugin("comp"));
CompSBMLDocumentPlugin compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
ModelDefinition moddef1 = compdoc.createModelDefinition();
moddef1.setId("Mod1");
Parameter m1param1 = moddef1.createParameter();
m1param1.setId("param1");
m1param1.setConstant(true);
Parameter m1param2 = moddef1.createParameter();
m1param2.setId("param2");
m1param2.setConstant(false);
m1param2.setValue(3.2);
ModelDefinition moddef2 = new ModelDefinition();
moddef2.setId("Mod2");
Parameter subparam2 = moddef2.createParameter();
subparam2.setId("subparam2");
subparam2.setConstant(false);
compdoc.addModelDefinition(moddef2);
ExternalModelDefinition extmod1 = compdoc.createExternalModelDefinition();
extmod1.setId("ExtMod1");
extmod1.setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2 = new ExternalModelDefinition();
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc.addExternalModelDefinition(extmod2);
Submodel submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("Mod1");
Deletion del1 = submod1.createDeletion();
del1.setId("deletionA");
del1.setIdRef("param2");
Submodel submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2 = new Deletion();
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef sbr = del2.createSBaseRef();
sbr.setIdRef("element5");
rv = submod2.addDeletion(del2);
Deletion del3 = new Deletion();
del3.setIdRef("submodG");
SBaseRef sbr2 = new SBaseRef();
sbr2.setIdRef("subsubmodQ");
SBaseRef subsbr = sbr2.createSBaseRef();
subsbr.setPortRef("toBdel");
del3.setSBaseRef(sbr2);
submod2.addDeletion(del3);
mplugin.addSubmodel(submod2);
Port port1 = mplugin.createPort();
port1.setId("port1");
port1.setMetaIdRef("_110013");
Port port2 = new Port();
port2.setId("port2");
port2.setIdRef("x");
mplugin.addPort(port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(sbr2);
mplugin.addPort(port2);
libsbml.writeSBMLToFile(document, "comp_example1.xml");
document = libsbml.readSBMLFromFile("comp_example1.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
OStringStream stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "comp_example1_rt.xml");
}
return(retval);
}
public static int Main(string[] args)
{
int retval = 0;
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create a replacement parameter
Parameter parameter = model.createParameter();
parameter.setId("x");
parameter.setConstant(true);
// create a parameter to be a conversion factor
Parameter param2 = model.createParameter();
param2.setId("x_conv");
param2.setMetaId("_110013");
param2.setConstant(true);
// create a parameter to be a conversion factor
Parameter param3 = model.createParameter();
param3.setId("lcf");
param3.setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin splugin = (CompSBasePlugin) (parameter.getPlugin("comp"));
// Add a replaced element.
ReplacedElement rep1 = splugin.createReplacedElement();
int rv = rep1.setSubmodelRef("submod1");
rv = rep1.setConversionFactor("x_conv");
rv = rep1.setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2 = new ReplacedElement();
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin.addReplacedElement(rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef sbr5 = rep2.createSBaseRef();
sbr5.setIdRef("submodelG");
SBaseRef sbr6 = sbr5.createSBaseRef();
sbr6.setIdRef("buriedElement");
splugin.addReplacedElement(rep2);
// Create a submodel
CompModelPlugin mplugin = (CompModelPlugin) (model.getPlugin("comp"));
CompSBMLDocumentPlugin compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
compdoc.setRequired(true);
ModelDefinition moddef1 = compdoc.createModelDefinition();
moddef1.setId("Mod1");
Parameter m1param1 = moddef1.createParameter();
m1param1.setId("param1");
m1param1.setConstant(true);
Parameter m1param2 = moddef1.createParameter();
m1param2.setId("param2");
m1param2.setConstant(false);
m1param2.setValue(3.2);
ModelDefinition moddef2 = new ModelDefinition();
moddef2.setId("Mod2");
Parameter subparam2 = moddef2.createParameter();
subparam2.setId("subparam2");
subparam2.setConstant(false);
compdoc.addModelDefinition(moddef2);
ExternalModelDefinition extmod1 = compdoc.createExternalModelDefinition();
extmod1.setId("ExtMod1");
extmod1.setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2 = new ExternalModelDefinition();
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc.addExternalModelDefinition(extmod2);
Submodel submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("Mod1");
Deletion del1 = submod1.createDeletion();
del1.setId("deletionA");
del1.setIdRef("param2");
Submodel submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2 = new Deletion();
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef sbr = del2.createSBaseRef();
sbr.setIdRef("element5");
rv = submod2.addDeletion(del2);
Deletion del3 = new Deletion();
del3.setIdRef("submodG");
SBaseRef sbr2 = new SBaseRef();
sbr2.setIdRef("subsubmodQ");
SBaseRef subsbr = sbr2.createSBaseRef();
subsbr.setPortRef("toBdel");
del3.setSBaseRef(sbr2);
submod2.addDeletion(del3);
mplugin.addSubmodel(submod2);
Port port1 = mplugin.createPort();
port1.setId("port1");
port1.setMetaIdRef("_110013");
Port port2 = new Port();
port2.setId("port2");
port2.setIdRef("x");
mplugin.addPort(port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(sbr2);
mplugin.addPort(port2);
libsbml.writeSBMLToFile(document, "comp_example1.xml");
document = libsbml.readSBMLFromFile("comp_example1.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
OStringStream stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "comp_example1_rt.xml");
}
return retval;
}