C++ Species::getPlugin方法代码示例

void TestRoadRunner::testCons1()
{
    ConservationPkgNamespaces *sbmlns = new ConservationPkgNamespaces(3,1,1);

    SBMLDocument doc(sbmlns);

    ConservationDocumentPlugin* docPlugin =
            dynamic_cast<ConservationDocumentPlugin*>(doc.getPlugin("conservation"));

    cout << "document plugin: " << docPlugin << endl;

    Model *m = doc.createModel("foo");

    Parameter *p = m->createParameter();

    ConservedMoietyPlugin *paramPlugin =
            dynamic_cast<ConservedMoietyPlugin*>(p->getPlugin("conservation"));

    cout << "parameter plugin: " << paramPlugin << endl;

    Species *s = m->createSpecies();

    ConservedMoietyPlugin *speciesPlugin =
            dynamic_cast<ConservedMoietyPlugin*>(s->getPlugin("conservation"));

    cout << "species plugin: " << speciesPlugin << endl;



    cout << "its all good" << endl;

}

int 
  FbcToCobraConverter::convert()
{  
  int result = LIBSBML_OPERATION_FAILED;

  if (mDocument == NULL) 
  {
    return LIBSBML_INVALID_OBJECT;
  }

  Model* mModel = mDocument->getModel();
  if (mModel == NULL) 
  {
    return LIBSBML_INVALID_OBJECT;
  }

  FbcModelPlugin *plugin =
    static_cast<FbcModelPlugin*>(mDocument->getModel()->getPlugin("fbc"));

  // if we have don't have a fbc model we cannot do the conversion
  if (plugin == NULL || mDocument->getLevel() != 3)
  {
    return LIBSBML_OPERATION_FAILED;
  }

  // collect information

  Model* model = mDocument->getModel();
  map<const string, int> chargeMap;
  map<const string, string> formulaMap;

  for (unsigned int i = 0; i < model->getNumSpecies(); ++i)
  {
    Species* current = model->getSpecies(i);
    const string& currentId = current->getId();
    FbcSpeciesPlugin *splugin = static_cast<FbcSpeciesPlugin*>(current->getPlugin("fbc"));
    if (splugin == NULL)
      continue;
    if (splugin->isSetCharge())
    {
      chargeMap[currentId] = splugin->getCharge();
    }
    if (splugin->isSetChemicalFormula())
    {
      formulaMap[currentId] = splugin->getChemicalFormula();
    }
  }

  // create KineticLaw
  for (unsigned int i = 0; i < model->getNumReactions(); ++i)
  {
    Reaction* reaction = model->getReaction(i);
    if (reaction == NULL)
      continue;

    createKineticLawForReaction(reaction);

  }

  // update kinetic law from bounds
  for (unsigned int i = 0; i < plugin->getNumFluxBounds(); ++i)
  {
    FluxBound *current = plugin->getFluxBound(i);
    if (current == NULL)
      continue;
    Reaction* reaction = model->getReaction(current->getReaction());
    if (reaction == NULL)
      continue;

    updateKineticLawFromBound(reaction, current);

  }

  setObjectiveCoefficient(plugin, model);

  // disable package
  mDocument->enablePackage("http://www.sbml.org/sbml/level3/version1/fbc/version1", "fbc",false);

  // convert model to L2V1 (as L2V2 is the last model that had charge)
  mDocument->setConversionValidators(AllChecksON & UnitsCheckOFF);
  
  ConversionProperties prop(new SBMLNamespaces(2,1));
  prop.addOption("strict", false, "should validity be preserved");
  prop.addOption("ignorePackages", true, "convert even if packages are used");
  prop.addOption("setLevelAndVersion", true, "convert the document to the given level and version");
  int conversionResult = mDocument->convert(prop);
  if (conversionResult != LIBSBML_OPERATION_SUCCESS)
    return conversionResult;

  // set charge on species
  for (unsigned int i = 0; i < model->getNumSpecies(); ++i)  
  {
    Species* current = model->getSpecies(i);
    const string currentId = current->getId();
    int charge = chargeMap[currentId];

    if (charge != 0)
      current->setCharge(charge);

    const string formula = formulaMap[currentId];
//.........这里部分代码省略.........

END_TEST

START_TEST(test_FbcExtension_read_and_validate_chemicals)
{
  FbcPkgNamespaces *ns = new FbcPkgNamespaces();
  SBMLDocument*doc = new SBMLDocument(ns);
  doc->setPackageRequired("fbc", false);
  Model* model = doc->createModel();
  Compartment* comp = model->createCompartment();
  comp->initDefaults();
  comp->setId("comp");
  comp->setSize(1);
  Species *s = model->createSpecies();
  s->initDefaults();
  s->setId("s1");
  s->setCompartment("comp");
  s->setInitialAmount(1);
  FbcSpeciesPlugin* splugin = static_cast<FbcSpeciesPlugin*>(s->getPlugin("fbc"));
  fail_unless(splugin != NULL);
  
  // valid 
  splugin->setChemicalFormula("H2O");
  doc->checkInternalConsistency();
  fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
  
  // valid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("HO");
  doc->checkInternalConsistency();
  fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // valid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("");
  doc->checkInternalConsistency();
  fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("h1O");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("1hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("_hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("H 2 O");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
  
  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("H*_)(++2 O");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  delete doc;
}

END_TEST

START_TEST(test_FbcExtension_read_L3V1V1_with_wonky_chemicals)
{
  const char* modelString = "<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' level='3' version='1' fbc:required='false'>"
"  <model metaid='xxx' id='yyy' timeUnits='dimensionless'>"
"    <listOfCompartments>"
"      <compartment id='Internal_Species' name='Internal_Species' spatialDimensions='3' size='1' constant='false'/>"
"      <compartment id='External_Species' name='External_Species' spatialDimensions='3' size='1' constant='false'/>"
"    </listOfCompartments>"
"    <listOfSpecies>"
"      <species metaid='meta_B1' id='B1' name='Protein component' compartment='Internal_Species' initialConcentration='0' hasOnlySubstanceUnits='false' boundaryCondition='false' constant='false' fbc:chemicalFormula='PROTEIN COMPONENT'>"
"        <notes>"
"          <html:p>chemFormula: Protein component</html:p>"
"        </notes>"
"        <annotation>"
"          <listOfKeyValueData xmlns='http://pysces.sourceforge.net/KeyValueData'>"
"            <data id='chemFormula' type='string' value='Protein component'/>"
"          </listOfKeyValueData>"
"        </annotation>"
"      </species>"
"      <species metaid='meta_B2' id='B2' name='DNA component' compartment='Internal_Species' initialConcentration='0' hasOnlySubstanceUnits='false' boundaryCondition='false' constant='false' fbc:chemicalFormula='DNA COMPONENT'>"
"        <notes>"
"          <html:p>chemFormula: DNA component</html:p>"
"        </notes>"
"        <annotation>"
"          <listOfKeyValueData xmlns='http://pysces.sourceforge.net/KeyValueData'>"
"            <data id='chemFormula' type='string' value='DNA component'/>"
"          </listOfKeyValueData>"
"        </annotation>"
"      </species>"
"    </listOfSpecies>"
"    <listOfReactions>"
"      <reaction metaid='meta_R00192' id='R00192' name='R106' reversible='false' fast='false'>"
"        <notes>"
"          <html:p>EC Number: 3.3.1.1</html:p>"
"          <html:p>GENE ASSOCIATION: sll1234</html:p>"
"        </notes>"
"        <annotation>"
"          <listOfKeyValueData xmlns='http://pysces.sourceforge.net/KeyValueData'>"
"            <data id='EC_Number' type='string' value='3.3.1.1'/>"
"            <data id='GENE_ASSOCIATION' type='string' value='sll1234'/>"
"          </listOfKeyValueData>"
"        </annotation>"
"        <listOfReactants>"
"          <speciesReference species='B1' stoichiometry='1' constant='true'/>"
"        </listOfReactants>"
"        <listOfProducts>"
"          <speciesReference species='B2' stoichiometry='1' constant='true'/>"
"        </listOfProducts>"
"      </reaction>"
"    </listOfReactions>"
"    <fbc:listOfFluxBounds>"
"      <fbc:fluxBound fbc:reaction='R00192' fbc:operation='greaterEqual' fbc:value='0'/>"
"      <fbc:fluxBound fbc:reaction='R00192' fbc:operation='lessEqual' fbc:value='999999'/>     "
"    </fbc:listOfFluxBounds>"
"    <fbc:listOfObjectives fbc:activeObjective='obj'>"
"      <fbc:objective fbc:id='obj' fbc:type='maximize'>"
"        <fbc:listOfFluxObjectives>"
"          <fbc:fluxObjective fbc:reaction='R00192' fbc:coefficient='1'/>"
"        </fbc:listOfFluxObjectives>"
"      </fbc:objective>"
"    </fbc:listOfObjectives>"
"  </model>"
"</sbml>";

  SBMLDocument* doc = readSBMLFromString(modelString);
  doc->checkConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  //convert to cobra just to test
  ConversionProperties prop;
  prop.addOption("convert fbc to cobra", true);
  fail_unless(doc->convert(prop) == LIBSBML_OPERATION_SUCCESS);
  
  // add species with notes 
  Species* testSpecies = doc->getModel()->createSpecies();
  testSpecies->initDefaults();
  testSpecies->setId("testSpecies");
  testSpecies->setNotes(
          "<body xmlns='http://www.w3.org/1999/xhtml'>"
          "  <p>FORMULA: Fe2S2X</p>                   "
          "  <p>CHARGE: -1</p>                        "
          "</body>                                    "
  );
  
  // convert it back
  prop.addOption("convert cobra", true);
  fail_unless(doc->convert(prop) == LIBSBML_OPERATION_SUCCESS);
  
  // check the formula
  Species* tested = doc->getModel()->getSpecies("testSpecies");
  fail_unless(tested != NULL);
  FbcSpeciesPlugin* fbcSpeciesPlugin = dynamic_cast<FbcSpeciesPlugin*>(tested->getPlugin("fbc"));
  fail_unless(fbcSpeciesPlugin != NULL);
  fail_unless(fbcSpeciesPlugin->getCharge() == -1);
  fail_unless(fbcSpeciesPlugin->getChemicalFormula() == "Fe2S2X");
  

//.........这里部分代码省略.........

int main(int argc,char** argv)
{
  int retval = 0;
  SBMLNamespaces sbmlns(3,1,"comp",1);

  // create the document
  SBMLDocument *document = new SBMLDocument(&sbmlns);

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


  // create the main Model
  Model* model=document->createModel();
  
  // Set the submodels
  CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin("comp"));
  Submodel* submod1 = mplugin->createSubmodel();
  submod1->setId("A");
  submod1->setModelRef("ExtMod1");
  Submodel* submod2 = mplugin->createSubmodel();
  submod2->setId("B");
  submod2->setModelRef("ExtMod1");

  // create a replacement compartment
  Compartment* comp=model->createCompartment();
  comp->setSpatialDimensions((unsigned int)3);
  comp->setConstant(true);
  comp->setId("comp");
  comp->setSize(1L);

  //Tell the model that this compartment replaces both of the inside ones.
  CompSBasePlugin* compartplug = static_cast<CompSBasePlugin*>(comp->getPlugin("comp"));
  ReplacedElement re;
  re.setIdRef("comp");
  re.setSubmodelRef("A");
  compartplug->addReplacedElement(&re);
  re.setSubmodelRef("B");
  compartplug->addReplacedElement(&re);

  // create a replacement species
  Species* 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.
  CompSBasePlugin* spp = static_cast<CompSBasePlugin*>(spec->getPlugin("comp"));
  re.setIdRef("S");
  re.setSubmodelRef("A");
  spp->addReplacedElement(&re);
  re.setSubmodelRef("B");
  spp->addReplacedElement(&re);

  writeSBMLToFile(document,"eg-import-external.xml");
  writeSBMLToFile(document,"spec_example2.xml");
  delete document;
  document = readSBMLFromFile("spec_example2.xml");
  if (document == NULL)
  {
    cout << "Error reading back in file." << endl;
    retval = -1;
  }
  else
  {
    document->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
    document->checkConsistency();
    if (document->getErrorLog()->getNumFailsWithSeverity(2) > 0
        || document->getErrorLog()->getNumFailsWithSeverity(3) > 0)
    {
      stringstream errorstream;
      document->printErrors(errorstream);
      cout << "Errors encoutered when round-tripping  SBML file: \n"
           <<  errorstream.str() << endl;
      retval = -1;
    }
    writeSBMLToFile(document, "spec_example2_rt.xml");
    delete document;
  }
#ifdef WIN32
  if (retval != 0)
  {
    cout << "(Press any key to exit.)" << endl;
    _getch();
  }
#endif
  return retval;
}

void readSpatialSBML() {
	SBMLDocument *document2 = readSBML("spatial_example0.xml");
  
	Model *model2 = document2->getModel();
	Compartment *comp;
	SpatialCompartmentPlugin* cplugin;
	RequiredElementsSBasePlugin* reqplugin;
	for (unsigned int i = 0; i < model2->getNumCompartments(); i++) {
		comp = model2->getCompartment(i);
		cout << "Compartment" << i << ": "  << comp->getId() << endl;
		reqplugin = static_cast<RequiredElementsSBasePlugin*>(comp->getPlugin("req"));
		if (!reqplugin->getMathOverridden().empty()) {
			cout << "Comp" << i << "  req mathOverridden: "  << reqplugin->getMathOverridden() << endl;
		}
		cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
		if (cplugin->getCompartmentMapping()->isSetSpatialId()) {
			cout << "Comp" << i << "  CMSpId: "  << cplugin->getCompartmentMapping()->getSpatialId() << endl;
			cout << "Comp" << i << "  CM_Comp: "  << cplugin->getCompartmentMapping()->getCompartment() << endl;
			cout << "Comp" << i << "  CM_DType: "  << cplugin->getCompartmentMapping()->getDomainType() << endl;
			cout << "Comp" << i << "  CM_UnitSz: "  << cplugin->getCompartmentMapping()->getUnitSize() << endl;
		}
	}

	Species *sp;
	SpatialSpeciesRxnPlugin* srplugin;
	for (unsigned int i = 0; i < model2->getNumSpecies(); i++) {
		sp = model2->getSpecies(i);
		cout << "Species" << i << ": "      << sp->getId()      << endl;
		srplugin = static_cast<SpatialSpeciesRxnPlugin*>(sp->getPlugin("spatial"));
		if (srplugin->getIsSpatial()) {
			cout << "species" << i << "  isSpatial: "  << srplugin->getIsSpatial() << endl;
		}
	}

	Parameter *param;
	SpatialParameterPlugin* pplugin;
	for (unsigned int i = 0; i < model2->getNumParameters(); i++) {
		param = model2->getParameter(i);
		cout << "Parameter" << i << ": "  << param->getId() << endl;
		reqplugin = static_cast<RequiredElementsSBasePlugin*>(param->getPlugin("req"));
		if (!reqplugin->getMathOverridden().empty()) {
			cout << "Parameter" << i << "  req mathOverridden: "  << reqplugin->getMathOverridden() << endl;
		}
		pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
		if (pplugin->getSpatialSymbolReference()->isSetSpatialId()) {
			cout << "Parameter" << i << "  SpRefId: "  << pplugin->getSpatialSymbolReference()->getSpatialId() << endl;
			cout << "Parameter" << i << "  SpRefType: "  << pplugin->getSpatialSymbolReference()->getType() << endl;
		}
		if (pplugin->getDiffusionCoefficient()->isSetVariable()) {
			cout << "Diff_" << i << "  SpeciesVarId: "  << pplugin->getDiffusionCoefficient()->getVariable() << endl;
			cout << "Diff_" << i << "  SpCoordIndex: "  << pplugin->getDiffusionCoefficient()->getCoordinateIndex() << endl;
		}
		if (pplugin->getAdvectionCoefficient()->isSetVariable()) {
			cout << "Adv_" << i << "  SpeciesVarId: "  << pplugin->getAdvectionCoefficient()->getVariable() << endl;
			cout << "Adv_" << i << "  SpCoordIndex: "  << pplugin->getAdvectionCoefficient()->getCoordinateIndex() << endl;
		}
		if (pplugin->getBoundaryCondition()->isSetVariable()) {
			cout << "BC_" << i << "  SpeciesVarId: "  << pplugin->getBoundaryCondition()->getVariable() << endl;
			cout << "BC_" << i << "  SpCoordBoundary: "  << pplugin->getBoundaryCondition()->getCoordinateBoundary() << endl;
			cout << "BC_" << i << "  SpBoundaryType: "  << pplugin->getBoundaryCondition()->getType() << endl;
		}
	}

	Reaction *rxn;
	for (unsigned int i = 0; i < model2->getNumReactions(); i++) {
		rxn = model2->getReaction(i);
		cout << "Reaction" << i << ": "      << rxn->getId()      << endl;
		srplugin = static_cast<SpatialSpeciesRxnPlugin*>(rxn->getPlugin("spatial"));
		if (srplugin->getIsLocal()) {
			cout << "rxn" << i << "  isLocal: "  << srplugin->getIsLocal() << endl;
		}
	}

	Rule *rule;
	for (unsigned int i = 0; i < model2->getNumRules(); i++) {
		rule = model2->getRule(i);
		cout << "Rule" << i << ": "      << rule->getVariable()      << endl;
	}

	//
	// Get a SpatialModelPlugin object plugged in the model object.
	//
	// The type of the returned value of SBase::getPlugin() function is 
	// SBasePlugin*, and thus the value needs to be cast for the 
	// corresponding derived class.
	//
	SpatialModelPlugin* mplugin2;
	mplugin2 = static_cast<SpatialModelPlugin*>(model2->getPlugin("spatial"));
	cout << "URI: "      << mplugin2->getURI()      << endl;
	cout << "prefix: "      << mplugin2->getPrefix()      << endl;

	// get a Geometry object via SpatialModelPlugin object.
	Geometry* geometry2 = mplugin2->getGeometry();
	cout << "Geometry coordSystem: "      << geometry2->getCoordinateSystem()      << endl;
    
	// get a CoordComponent object via the Geometry object.	
	CoordinateComponent* coordComp = geometry2->getCoordinateComponent(0);
	std::cout << "CoordComponent spatialId: " << coordComp->getSpatialId() << std::endl;
	std::cout << "CoordComponent compType: " << coordComp->getComponentType() << std::endl;
	std::cout << "CoordComponent sbmlUnit: " << coordComp->getSbmlUnit() << std::endl;
//.........这里部分代码省略.........

LIBSBML_CPP_NAMESPACE_USE

int
main (int argc, char* argv[])
{
  SBMLNamespaces sbmlns(3,1,"multi",1);

  // create the document

  SBMLDocument *document = new SBMLDocument(&sbmlns);

  // set the required attribute to true
  MultiSBMLDocumentPlugin * docPlug = 
    static_cast<MultiSBMLDocumentPlugin*>(document->getPlugin("multi"));
  docPlug->setRequired(true);


  // create the Model

  Model* model=document->createModel();

  // create the compartments

  Compartment * c = model->createCompartment();
  c->setId("membrane");
  c->setConstant(true);

  // set the multi attribute isType via the compartmentPlugin
  MultiCompartmentPlugin * compPlug = 
    static_cast<MultiCompartmentPlugin*>(c->getPlugin("multi"));
  compPlug->setIsType(true);

  // create the speciesTypes

  MultiModelPlugin * modelPlug = 
    static_cast<MultiModelPlugin*>(model->getPlugin("multi"));

  MultiSpeciesType * st = modelPlug->createMultiSpeciesType();
  st->setId("stX");
  st->setCompartment("membrane");

  // create species
  Species *s = model->createSpecies();
  s->setId("s1");
  s->setCompartment("membrane");
  s->setBoundaryCondition(false);
  s->setHasOnlySubstanceUnits(false);
  s->setConstant(false);

  // set the multi attribute speciesType via the compartmentPlugin
  MultiSpeciesPlugin * spPlug = 
    static_cast<MultiSpeciesPlugin*>(s->getPlugin("multi"));
  spPlug->setSpeciesType("stX");

  // create species feature
  SpeciesFeature *sf = spPlug->createSpeciesFeature();
  sf->setSpeciesFeatureType("a");
  sf->setOccur(1);
  sf->setComponent("b");

  SpeciesFeatureValue *sfv = sf->createSpeciesFeatureValue();
  sfv->setValue("c");

  // create a subListOfSpeciesFeatures
  SubListOfSpeciesFeatures* subloSF = spPlug->createSubListOfSpeciesFeatures();
  subloSF->setRelation(Relation_fromString("and"));

  // add speciesFeatures to the subList
  SpeciesFeature *sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a1");
  sf1->setOccur(1);
  sf1->setComponent("b1");

  SpeciesFeatureValue *sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c1");

  subloSF->appendAndOwn(sf1);

  sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a2");
  sf1->setOccur(1);
  sf1->setComponent("b2");

  sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c2");

  subloSF->appendAndOwn(sf1);

  // create a second subListOfSpeciesfeatures
  subloSF = spPlug->createSubListOfSpeciesFeatures();
  subloSF->setRelation(Relation_fromString("or"));

  sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a3");
  sf1->setOccur(1);
  sf1->setComponent("b3");

  sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c3");

//.........这里部分代码省略.........

void readSpatialSBML() {
	SBMLDocument *document2 = readSBML("spatial_example2.xml");
  
	Model *model2 = document2->getModel();
	Compartment *comp;
	SpatialCompartmentPlugin* cplugin;
	for (unsigned int i = 0; i < model2->getNumCompartments(); i++) {
		comp = model2->getCompartment(i);
		cout << "Compartment" << i << ": "  << comp->getId() << endl;
		cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
		if (cplugin->getCompartmentMapping()->isSetId()) {
			cout << "Comp" << i << "  CMSpId: "  << cplugin->getCompartmentMapping()->getId() << endl;
			cout << "Comp" << i << "  CM_DType: "  << cplugin->getCompartmentMapping()->getDomainType() << endl;
			cout << "Comp" << i << "  CM_UnitSz: "  << cplugin->getCompartmentMapping()->getUnitSize() << endl;
		}
	}

	Species *sp;
	SpatialSpeciesPlugin* srplugin;
	for (unsigned int i = 0; i < model2->getNumSpecies(); i++) {
		sp = model2->getSpecies(i);
		cout << "Species" << i << ": "      << sp->getId()      << endl;
		srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
		if (srplugin->getIsSpatial()) {
			cout << "species" << i << "  isSpatial: "  << srplugin->getIsSpatial() << endl;
		}
	}

	Parameter *param;
	SpatialParameterPlugin* pplugin;
	for (unsigned int i = 0; i < model2->getNumParameters(); i++) {
		param = model2->getParameter(i);
		cout << "Parameter" << i << ": "  << param->getId() << endl;
		pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
		if (pplugin->isSetSpatialSymbolReference()) {
			cout << "Parameter" << i << "  SpRefId: "  << pplugin->getSpatialSymbolReference()->getSpatialRef() << endl;
		}
		if (pplugin->isSetDiffusionCoefficient()) {
			cout << "Diff_" << i << "  SpeciesVarId: "  << pplugin->getDiffusionCoefficient()->getVariable() << endl;
			cout << "Diff_" << i << "  Type: "  << DiffusionKind_toString(pplugin->getDiffusionCoefficient()->getType()) << endl;
      for (unsigned int j = 0; j < pplugin->getDiffusionCoefficient()->getNumCoordinateReferences(); ++j)
        cout << "Diff_" << i << "  SpCoordIndex  " << j << " : " << CoordinateKind_toString(pplugin->getDiffusionCoefficient()->getCoordinateReference(j) ->getCoordinate()) << endl;
		}
		if (pplugin->isSetAdvectionCoefficient()) {
			cout << "Adv_" << i << "  SpeciesVarId: "  << pplugin->getAdvectionCoefficient()->getVariable() << endl;
			cout << "Adv_" << i << "  SpCoordIndex: "  << CoordinateKind_toString(pplugin->getAdvectionCoefficient()->getCoordinate()) << endl;
		}
		if (pplugin->isSetBoundaryCondition()) {
			cout << "BC_" << i << "  SpeciesVarId: "  << pplugin->getBoundaryCondition()->getVariable() << endl;
			cout << "BC_" << i << "  SpCoordBoundary: "  << pplugin->getBoundaryCondition()->getCoordinateBoundary() << endl;
			cout << "BC_" << i << "  SpBoundaryType: "  << pplugin->getBoundaryCondition()->getType() << endl;
		}
	}

	Reaction *rxn;
	SpatialReactionPlugin* rplugin;
	for (unsigned int i = 0; i < model2->getNumReactions(); i++) {
		rxn = model2->getReaction(i);
		cout << "Reaction" << i << ": "      << rxn->getId()      << endl;
		rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial"));
		if (rplugin->getIsLocal()) {
			cout << "rxn" << i << "  isLocal: "  << rplugin->getIsLocal() << endl;
		}
	}

	Rule *rule;
	for (unsigned int i = 0; i < model2->getNumRules(); i++) {
		rule = model2->getRule(i);
		cout << "Rule" << i << ": "      << rule->getVariable()      << endl;
	}

	//
	// Get a SpatialModelPlugin object plugged in the model object.
	//
	// The type of the returned value of SBase::getPlugin() function is 
	// SBasePlugin*, and thus the value needs to be cast for the 
	// corresponding derived class.
	//
	SpatialModelPlugin* mplugin2;
	mplugin2 = static_cast<SpatialModelPlugin*>(model2->getPlugin("spatial"));
	cout << "URI: "      << mplugin2->getURI()      << endl;
	cout << "prefix: "      << mplugin2->getPrefix()      << endl;

	// get a Geometry object via SpatialModelPlugin object.
	Geometry* geometry2 = mplugin2->getGeometry();
	cout << "Geometry coordSystem: "      << geometry2->getCoordinateSystem()      << endl;
    
	// get a CoordComponent object via the Geometry object.	
	CoordinateComponent* coordComp = geometry2->getCoordinateComponent(0);
	std::cout << "CoordComponent Id: " << coordComp->getId() << std::endl;
  std::cout << "CoordComponent type: " << CoordinateKind_toString( coordComp->getType()) << std::endl;
	std::cout << "CoordComponent sbmlUnit: " << coordComp->getUnit() << std::endl;
  if (coordComp->isSetBoundaryMin())
  {
  Boundary* minX = coordComp->getBoundaryMin();
	std::cout << "minX name: " << minX->getId() << std::endl;
	std::cout << "minX value: " << minX->getValue() << std::endl;
  }
  if (coordComp->isSetBoundaryMax())
  {
//.........这里部分代码省略.........

END_TEST


START_TEST (test_SpatialExtension_read_L3V1V1_defaultNS)
{
    string file = TestDataDirectory;
    file += "/read_L3V1V1_defaultNS.xml";

    SBMLDocument *document = readSBMLFromFile(file.c_str());
    string sbmlDoc = writeSBMLToStdString(document);
    Model *model = document->getModel();

    //document->printErrors();

    fail_unless(model != NULL);
    //fail_unless(document->getNumErrors() == 0);

    // model : compartment
    fail_unless(model->getNumCompartments() == 1);

    Compartment *comp = model->getCompartment(0);

    // compartment : compartmentMapping
    SpatialCompartmentPlugin* cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
    fail_unless(cplugin != NULL);

    CompartmentMapping *cMapping = cplugin->getCompartmentMapping();
    if (cMapping->isSetId()) {
        fail_unless(cMapping->getId()		 == "compMap1");
        fail_unless(cMapping->getDomainType()	 == "dtype1");
        fail_unless(cMapping->getUnitSize()		 == 1);
    }

    // model : species 1
    fail_unless(model->getNumSpecies() == 2);

    Species *sp = model->getSpecies(0);

    SpatialSpeciesPlugin* srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
    fail_unless(srplugin != NULL);
    fail_unless(srplugin->getIsSpatial() == true);

    // model : species 2
    sp = model->getSpecies(1);
    srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
    fail_unless(srplugin != NULL);
    fail_unless(srplugin->getIsSpatial() == true);

    // model : parameters (species diffusion, advection coeffs, species boundary conditions, coordinate components from Geometry
    fail_unless(model->getNumParameters() == 5);



    // parameter 0 : diffusionCoefficient
    Parameter *param = model->getParameter(0);
    SpatialParameterPlugin* pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
    fail_unless(pplugin != NULL);
    fail_unless(pplugin->isSpatialParameter() == true);
    fail_unless(pplugin->getType() == SBML_SPATIAL_DIFFUSIONCOEFFICIENT);
    DiffusionCoefficient *diffCoeff = pplugin->getDiffusionCoefficient();
    fail_unless(diffCoeff->getVariable()		== "ATPc");
    fail_unless(diffCoeff->isSetCoordinateReference1());
    fail_unless(diffCoeff->getCoordinateReference1() == SPATIAL_COORDINATEKIND_CARTESIAN_X);

    // parameter 1 : advectionCoefficient
    param = model->getParameter(1);
    pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
    fail_unless(pplugin != NULL);
    fail_unless(pplugin->isSpatialParameter() == true);
    fail_unless(pplugin->getType() == SBML_SPATIAL_ADVECTIONCOEFFICIENT);
    AdvectionCoefficient *advCoeff = pplugin->getAdvectionCoefficient();
    fail_unless(advCoeff->getVariable()		== "ATPc");
    fail_unless(advCoeff->getCoordinate() == SPATIAL_COORDINATEKIND_CARTESIAN_X);

    // parameter 2 : boundaryCondition X
    param = model->getParameter(2);
    pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
    fail_unless(pplugin != NULL);
    fail_unless(pplugin->isSpatialParameter() == true);
    fail_unless(pplugin->getType() == SBML_SPATIAL_BOUNDARYCONDITION);
    BoundaryCondition *bc = pplugin->getBoundaryCondition();
    fail_unless(bc->getVariable()		   == "ATPc");
    fail_unless(bc->getCoordinateBoundary() == "Xmin");
    fail_unless(bc->getType() == SPATIAL_BOUNDARYKIND_DIRICHLET);

    // parameter 3 : SpatialSymbolReference (coordinateComponent from geometry)
    param = model->getParameter(3);
    pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
    fail_unless(pplugin != NULL);
    SpatialSymbolReference *spSymRef = pplugin->getSpatialSymbolReference();
    fail_unless(spSymRef->getSpatialRef() == "coordComp1");

    // model : reaction
    fail_unless(model->getNumReactions() == 1);

    Reaction *rxn = model->getReaction(0);
    SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial"));
    fail_unless(rplugin != NULL);
    fail_unless(rplugin->getIsLocal() == true);

//.........这里部分代码省略.........