setConsistencyChecks() 공개 메소드

public setConsistencyChecks ( int category, bool apply ) : void
category int
apply bool
리턴 void
예제 #1
0
        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;
        }
예제 #2
0
        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);

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

            //Define the 'simple' model
            var mod1 = compdoc.createModelDefinition();
            mod1.setId("simple");
            var comp = mod1.createCompartment();
            comp.setSpatialDimensions(3);
            comp.setConstant(true);
            comp.setId("comp");
            comp.setSize(1L);

            var spec = new Species(sbmlns);
            //We have to construct it this way because we get the comp plugin from it later.
            spec.setCompartment("comp");
            spec.setHasOnlySubstanceUnits(false);
            spec.setConstant(false);
            spec.setBoundaryCondition(false);
            spec.setId("S");
            spec.setInitialConcentration(5);
            mod1.addSpecies(spec);
            spec.setId("D");
            spec.setInitialConcentration(10);
            mod1.addSpecies(spec);

            var rxn = new Reaction(3, 1);
            rxn.setReversible(true);
            rxn.setFast(false);
            rxn.setId("J0");

            var sr = new SpeciesReference(3, 1);
            sr.setConstant(true);
            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;
        }
예제 #3
0
        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;
        }
예제 #4
0
        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;
        }