C# SBMLDocument.checkConsistency方法代码示例

    //===============================================================================
    //
    //
    // Helper functions for writing/validating the given SBML documents.
    //
    //
    //===============================================================================
    /**
     *
     *  Validates the given SBMLDocument.
     *
     *   This function is based on validateSBML.cpp implemented by
     *   Sarah Keating, Ben Bornstein, and Michael Hucka.
     *
     */
    private static bool validateExampleSBML(SBMLDocument sbmlDoc)
    {
        if (sbmlDoc == null)
        {
            Console.Error.WriteLine("validateExampleSBML: given a null SBML Document");
            return false;
        }

        string consistencyMessages = "";
        string validationMessages = "";
        bool noProblems = true;
        int numCheckFailures = 0;
        int numConsistencyErrors = 0;
        int numConsistencyWarnings = 0;
        int numValidationErrors = 0;
        int numValidationWarnings = 0;

        // LibSBML 3.3 is lenient when generating models from scratch using the
        // API for creating objects.  Once the whole model is done and before it
        // gets written out, it's important to check that the whole model is in
        // fact complete, consistent and valid.

        numCheckFailures = (int)sbmlDoc.checkInternalConsistency();
        if (numCheckFailures > 0)
        {
            noProblems = false;
            for (int i = 0;
            i < numCheckFailures;
            i++)
            {
                SBMLError sbmlErr = sbmlDoc.getError(i);
                if (sbmlErr.isFatal() || sbmlErr.isError())
                {
                    ++numConsistencyErrors;
                }
                else
                {
                    ++numConsistencyWarnings;
                }
            }
            consistencyMessages = sbmlDoc.getErrorLog().toString();
        }

        // If the internal checks fail, it makes little sense to attempt
        // further validation, because the model may be too compromised to
        // be properly interpreted.

        if (numConsistencyErrors > 0)
        {
            consistencyMessages += "Further validation aborted.";
        }
        else
        {
            numCheckFailures = (int)sbmlDoc.checkConsistency();
            if (numCheckFailures > 0)
            {
                noProblems = false;
                for (int i = 0;
                i < numCheckFailures;
                i++)
                {
                    SBMLError sbmlErr = sbmlDoc.getError(i);
                    if (sbmlErr.isFatal() || sbmlErr.isError())
                    {
                        ++numValidationErrors;
                    }
                    else
                    {
                        ++numValidationWarnings;
                    }
                }

                validationMessages = sbmlDoc.getErrorLog().toString();
            }
        }

        if (noProblems)
            return true;
        else
        {
            if (numConsistencyErrors > 0)
            {
                Console.WriteLine("ERROR: encountered " + numConsistencyErrors
                + " consistency error" + (numConsistencyErrors == 1 ? "" : "s")
                + " in model '" + sbmlDoc.getModel().getId() + "'.");
//.........这里部分代码省略.........

        private static int Main(string[] args)
        {
            var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);

            // create the document
            var document = new SBMLDocument(sbmlns);

            //Define the external model definitions
            var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
            compdoc.setRequired(true);
            var extmod = compdoc.createExternalModelDefinition();
            extmod.setId("ExtMod1");
            extmod.setSource("enzyme_model.xml");
            extmod.setModelRef("enzyme");

            // create the main Model
            var model = document.createModel();

            // Set the submodels
            var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
            var submod1 = mplugin.createSubmodel();
            submod1.setId("A");
            submod1.setModelRef("ExtMod1");
            var submod2 = mplugin.createSubmodel();
            submod2.setId("B");
            submod2.setModelRef("ExtMod1");

            // create a replacement compartment
            var comp = model.createCompartment();
            comp.setSpatialDimensions(3);
            comp.setConstant(true);
            comp.setId("comp");
            comp.setSize(1L);

            //Tell the model that this compartment replaces both of the inside ones.
            var compartplug = (CompSBasePlugin)(comp.getPlugin("comp"));
            var re = new ReplacedElement();
            re.setIdRef("comp");
            re.setSubmodelRef("A");
            compartplug.addReplacedElement(re);
            re.setSubmodelRef("B");
            compartplug.addReplacedElement(re);

            // create a replacement species
            var spec = model.createSpecies();
            spec.setCompartment("comp");
            spec.setHasOnlySubstanceUnits(false);
            spec.setConstant(false);
            spec.setBoundaryCondition(false);
            spec.setId("S");

            //Tell the model that this species replaces both of the inside ones.
            var spp = (CompSBasePlugin)(spec.getPlugin("comp"));
            re.setIdRef("S");
            re.setSubmodelRef("A");
            spp.addReplacedElement(re);
            re.setSubmodelRef("B");
            spp.addReplacedElement(re);

            libsbml.writeSBMLToFile(document, "spec_example2.xml");
            document = libsbml.readSBMLFromFile("spec_example2.xml");
            if (document == null)
            {
                Console.WriteLine("Error reading back in file.");
                return -1;
            }
            else
            {
                document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
                document.checkConsistency();
                if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
                    document.getErrorLog().getNumFailsWithSeverity(3) > 0)
                {
                    var stream = new OStringStream();
                    document.printErrors(stream);
                    Console.WriteLine("Errors encoutered when round-tripping  SBML file: \n" +
                                      stream.str());
                    return -1;
                }
                libsbml.writeSBMLToFile(document, "spec_example2_rt.xml");
            }

            return 0;
        }

 public void test_ReadSBML_FunctionDefinition_OnlyBVars()
 {
     FunctionDefinition fd;
       SBMLError error;
       int numErrors;
       ASTNode math;
       string formula;
       string s = wrapSBML_L2v1("<listOfFunctionDefinitions>" +
     "  <functionDefinition id='invalid'>" +
     "    <math xmlns='http://www.w3.org/1998/Math/MathML'>" +
     "      <lambda>" +
     "        <bvar><ci> x </ci></bvar>" +
     "        <bvar><ci> y </ci></bvar>" +
     "        <bvar><ci> z </ci></bvar>" +
     "      </lambda>" +
     "    </math>" +
     "  </functionDefinition>" +
     "</listOfFunctionDefinitions>");
       D = libsbml.readSBMLFromString(s);
       M = D.getModel();
       D.checkInternalConsistency();
       D.checkConsistency();
       numErrors = (int)D.getNumErrors();
       assertTrue( numErrors == 1 );
       error = D.getError(0);
       int errorId = (int)error.getErrorId();
       assertTrue( errorId == libsbml.NoBodyInFunctionDef );
       assertTrue( M.getNumFunctionDefinitions() == 1 );
       fd = M.getFunctionDefinition(0);
       assertTrue( fd != null );
       assertEquals( true, fd.isSetId() );
       assertEquals( false, fd.isSetName() );
       assertTrue((  "invalid"   == fd.getId() ));
       assertTrue( fd.getBody() == null );
       assertEquals( true, fd.isSetMath() );
       math = fd.getMath();
       formula = libsbml.formulaToString(math);
       assertTrue( formula != null );
       assertTrue((  "lambda(x, y, z)" == formula ));
 }

//.........这里部分代码省略.........
            sr.setStoichiometry(1);
            sr.setSpecies("S");
            rxn.addReactant(sr);
            sr.setSpecies("D");
            rxn.addProduct(sr);

            mod1.addReaction(rxn);

            var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
            var port = new Port();
            port.setId("S_port");
            port.setIdRef("S");
            mod1plug.addPort(port);

            var port2 = mod1plug.createPort();
            port2.setId("D_port");
            port2.setIdRef("D");

            port.setId("comp_port");
            port.setIdRef("comp");
            mod1plug.addPort(port);

            port.setId("J0_port");
            port.setIdRef("J0");
            mod1plug.addPort(port);

            // create the Model
            var model = document.createModel();
            model.setId("complexified");

            // Set the submodels
            var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
            var submod1 = mplugin.createSubmodel();
            submod1.setId("A");
            submod1.setModelRef("ExtMod1");
            var submod2 = mplugin.createSubmodel();
            submod2.setId("B");
            submod2.setModelRef("simple");
            var del = submod2.createDeletion();
            del.setPortRef("J0_port");

            // Synchronize the compartments
            var mcomp = model.createCompartment();
            mcomp.setSpatialDimensions(3);
            mcomp.setConstant(true);
            mcomp.setId("comp");
            mcomp.setSize(1L);
            var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
            var re = new ReplacedElement();
            re.setIdRef("comp");
            re.setSubmodelRef("A");
            compartplug.addReplacedElement(re);
            re.setSubmodelRef("B");
            re.unsetIdRef();
            re.setPortRef("comp_port");
            compartplug.addReplacedElement(re);

            //Synchronize the species
            spec.setId("S");
            spec.setInitialConcentration(5);
            var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
            var sre = specplug.createReplacedElement();
            sre.setSubmodelRef("A");
            sre.setIdRef("S");
            var sre2 = specplug.createReplacedElement();
            sre2.setSubmodelRef("B");
            sre2.setPortRef("S_port");
            model.addSpecies(spec);

            spec.setId("D");
            spec.setInitialConcentration(10);
            sre.setIdRef("D");
            sre2.setPortRef("D_port");
            model.addSpecies(spec);

            libsbml.writeSBMLToFile(document, "spec_example3.xml");
            document = libsbml.readSBMLFromFile("spec_example3.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)
                {
                    var stream = new OStringStream();
                    document.printErrors(stream);
                    Console.WriteLine("Errors encoutered when round-tripping  SBML file: \n" +
                                      stream.str());
                    retval = -1;
                }
                libsbml.writeSBMLToFile(document, "spec_example3_rt.xml");
            }
            return retval;
        }

        private static int Main(string[] args)
        {
            var retval = 0;
            var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);

            // create the document
            var document = new SBMLDocument(sbmlns);

            //Create our submodel
            var compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
            compdoc.setRequired(true);
            var mod1 = compdoc.createModelDefinition();
            mod1.setId("enzyme");
            mod1.setName("enzyme");
            var comp = mod1.createCompartment();
            comp.setSpatialDimensions(3);
            comp.setConstant(true);
            comp.setId("comp");
            comp.setSize(1L);
            var spec = new Species(3, 1);
            spec.setCompartment("comp");
            spec.setHasOnlySubstanceUnits(false);
            spec.setConstant(false);
            spec.setBoundaryCondition(false);
            spec.setId("S");
            mod1.addSpecies(spec);
            spec.setId("E");
            mod1.addSpecies(spec);
            spec.setId("D");
            mod1.addSpecies(spec);
            spec.setId("ES");
            mod1.addSpecies(spec);
            var rxn = new Reaction(3, 1);
            rxn.setReversible(true);
            rxn.setFast(false);
            var rxn2 = new Reaction(rxn);
            rxn.setId("J0");
            rxn2.setId("J1");
            var sr = new SpeciesReference(3, 1);
            sr.setConstant(true);
            sr.setStoichiometry(1);
            sr.setSpecies("S");
            rxn.addReactant(sr);
            sr.setSpecies("E");
            rxn.addReactant(sr);
            rxn2.addProduct(sr);
            sr.setSpecies("ES");
            rxn.addProduct(sr);
            rxn2.addReactant(sr);
            sr.setSpecies("D");
            rxn2.addProduct(sr);

            mod1.addReaction(rxn);
            mod1.addReaction(rxn2);

            // create the Model
            var model = document.createModel();
            model.setId("aggregate");

            // Create a submodel
            var mplugin = (CompModelPlugin) (model.getPlugin("comp"));
            var submod1 = mplugin.createSubmodel();
            submod1.setId("submod1");
            submod1.setModelRef("enzyme");

            var submod2 = new Submodel();
            submod2.setId("submod2");
            submod2.setModelRef("enzyme");
            mplugin.addSubmodel(submod2);

            libsbml.writeSBMLToFile(document, "enzyme_model.xml");
            document = libsbml.readSBMLFromFile("enzyme_model.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)
                {
                    var stream = new OStringStream();
                    document.printErrors(stream);
                    Console.WriteLine("Errors encoutered when round-tripping  SBML file: \n" +
                                      stream.str());
                    retval = -1;
                }
                libsbml.writeSBMLToFile(document, "enzyme_model_rt.xml");
            }
            return retval;
        }