C# libsbmlcs.SpeciesReference类代码示例

 public void setUp()
 {
     SR = new  SpeciesReference(3,1);
       if (SR == null);
       {
       }
 }

 public void setUp()
 {
     sr = new  SpeciesReference(2,4);
       if (sr == null);
       {
       }
 }

 public void test_SpeciesReference_setDenominator2()
 {
     SpeciesReference c = new  SpeciesReference(2,2);
       int i = c.setDenominator(4);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( c.getDenominator() == 4 );
       c = null;
 }

 public void test_Reaction_addReactant()
 {
     SpeciesReference sr = new  SpeciesReference(2,4);
       sr.setSpecies( "s");
       R.addReactant(sr);
       assertTrue( R.getNumReactants() == 1 );
       assertTrue( R.getNumProducts() == 0 );
       assertTrue( R.getNumModifiers() == 0 );
       sr = null;
 }

 public void test_Reaction_addProduct2()
 {
     Reaction m = new  Reaction(2,2);
       SpeciesReference p = new  SpeciesReference(2,1);
       p.setSpecies( "k");
       int i = m.addProduct(p);
       assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
       assertTrue( m.getNumProducts() == 0 );
       p = null;
       m = null;
 }

 public void test_SpeciesReference_createWithNS()
 {
     XMLNamespaces xmlns = new  XMLNamespaces();
       xmlns.add( "http://www.sbml.org", "testsbml");
       SBMLNamespaces sbmlns = new  SBMLNamespaces(2,1);
       sbmlns.addNamespaces(xmlns);
       SpeciesReference object1 = new  SpeciesReference(sbmlns);
       assertTrue( object1.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE );
       assertTrue( object1.getMetaId() == "" );
       assertTrue( object1.getNotes() == null );
       assertTrue( object1.getAnnotation() == null );
       assertTrue( object1.getLevel() == 2 );
       assertTrue( object1.getVersion() == 1 );
       assertTrue( object1.getNamespaces() != null );
       assertTrue( object1.getNamespaces().getLength() == 2 );
       object1 = null;
 }

 public void test_Reaction_addProduct1()
 {
     Reaction m = new  Reaction(2,2);
       SpeciesReference p = new  SpeciesReference(2,2);
       SpeciesReference p1 = new  SpeciesReference(2,2);
       p1.setSpecies( "k");
       p1.setId( "k1");
       int i = m.addProduct(p);
       assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
       p.setSpecies( "k");
       p.setId( "k1");
       i = m.addProduct(p);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertTrue( m.getNumProducts() == 1 );
       i = m.addProduct(p1);
       assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
       assertTrue( m.getNumProducts() == 1 );
       p = null;
       p1 = null;
       m = null;
 }

 public void test_Reaction_addReactant3()
 {
     Reaction m = new  Reaction(2,2);
       SpeciesReference p = new  SpeciesReference(1,2);
       p.setSpecies( "k");
       int i = m.addReactant(p);
       assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
       assertTrue( m.getNumReactants() == 0 );
       p = null;
       m = null;
 }

 public void test_SpeciesReference()
 {
     SpeciesReference sr = new SpeciesReference(2,4);
       assertEquals( true, sr.hasRequiredElements() );
       sr = null;
 }

 internal static HandleRef getCPtr(SpeciesReference obj)
 {
     return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
 }

 public void test_internal_consistency_check_99921()
 {
     SBMLDocument d = new SBMLDocument(2,4);
       long errors;
       SpeciesReference sr = new SpeciesReference(2,4);
       d.setLevelAndVersion(2,1,false);
       Model m = d.createModel();
       Compartment c = m.createCompartment();
       c.setId("c");
       Species s = m.createSpecies();
       s.setId("s");
       Reaction r = m.createReaction();
       r.setId("r");
       s.setCompartment("c");
       sr.setSpecies("s");
       sr.setName("mmm");
       r.addReactant(sr);
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 21101 );
       d = null;
 }

 /**
    * Adds a given SpeciesReference object as a product in this Reaction.
    *
    * The SpeciesReference instance in @p sr is copied.
    *
    * @param sr a SpeciesReference object referring to a Species in the
    * enclosing Model
    *
    *
  * @return integer value indicating success/failure of the
  * function.  @if clike The value is drawn from the
  * enumeration #OperationReturnValues_t. @endif The possible values
  * returned by this function are:
  * @li @link libsbml#LIBSBML_OPERATION_SUCCESS [email protected]
    * @li @link libsbml#LIBSBML_LEVEL_MISMATCH [email protected]
    * @li @link libsbml#LIBSBML_VERSION_MISMATCH [email protected]
    * @li @link libsbml#LIBSBML_OPERATION_FAILED [email protected]
    *
    *
  * @note This method should be used with some caution.  The fact that this
  * method @em copies the object passed to it means that the caller will be
  * left holding a physically different object instance than the one contained
  * inside this object.  Changes made to the original object instance (such as
  * resetting attribute values) will <em>not affect the instance in this
  * object</em>.  In addition, the caller should make sure to free the
  * original object if it is no longer being used, or else a memory leak will
  * result.  Please see other methods on this class (particularly a
  * corresponding method whose name begins with the word <code>create</code>)
  * for alternatives that do not lead to these issues.
  *
  *
    *
    * @see createProduct()
    */
 public int addProduct(SpeciesReference sr)
 {
     int ret = libsbmlPINVOKE.Reaction_addProduct__SWIG_0(swigCPtr, SpeciesReference.getCPtr(sr));
     return ret;
 }

        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");
//.........这里部分代码省略.........

        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;
        }

 public void test_SpeciesReference()
 {
     SpeciesReference sr = new SpeciesReference(2,4);
       assertEquals( false, (sr.hasRequiredAttributes()) );
       sr.setSpecies("sr");
       assertEquals( true, sr.hasRequiredAttributes() );
       sr = null;
 }