C++ Species::setCompartment方法代码示例

END_TEST


START_TEST (test_WriteL3SBML_Species_conversionFactor)
{
  const char* expected = 
    "<species id=\"Ca2\" compartment=\"cell\""
    " hasOnlySubstanceUnits=\"false\""
    " boundaryCondition=\"true\" constant=\"true\""
    " conversionFactor=\"p\"/>";

  const char* expected1 = 
    "<species id=\"Ca2\" compartment=\"cell\""
    " hasOnlySubstanceUnits=\"false\""
    " boundaryCondition=\"true\" constant=\"true\"/>";

  Species *s = D->createModel()->createSpecies();
  s->setId("Ca2");
  s->setCompartment("cell");
  s->setBoundaryCondition(true);
  s->setHasOnlySubstanceUnits(false);
  s->setConstant(true);
  s->setConversionFactor("p");

  char* sbml = s->toSBML();
  fail_unless( equals(expected, sbml) );
  safe_free(sbml);

  s->unsetConversionFactor();

  sbml = s->toSBML();
  fail_unless( equals(expected1, sbml) );
  safe_free(sbml);
}

END_TEST

START_TEST ( test_Species )
{
  Species* s = new Species(2, 4);
  
  fail_unless (!(s->hasRequiredAttributes()));

  s->setId("s");

  fail_unless (!(s->hasRequiredAttributes()));

  s->setCompartment("c");

  fail_unless (s->hasRequiredAttributes());

  delete s;
}

END_TEST



START_TEST ( test_Species_parent_add )
{
    Species *ia = new Species(2, 4);
    ia->setId("s");
    ia->setCompartment("c");
    Model *m = new Model(2, 4);

    m->addSpecies(ia);

    delete ia;

    ListOf *lo = m->getListOfSpecies();

    fail_unless(lo == m->getSpecies(0)->getParentSBMLObject());
    fail_unless(m == lo->getParentSBMLObject());
}

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;
}

LIBSBML_CPP_NAMESPACE_USE

int main(int argc,char** argv)
{
  
  DynPkgNamespaces sbmlns;

  // create the document

  SBMLDocument *document = new SBMLDocument(&sbmlns);
  document->setPackageRequired("dyn", true);

  // create the Model

  Model* model=document->createModel();
  model->setId("singleCell");

  // create the Compartment

  Compartment* compartment = model->createCompartment();
  compartment->setId("Extracellular");
  compartment->setConstant(true);
  compartment->setSize(8000000);
  compartment->setSpatialDimensions(3.0);

  compartment = model->createCompartment();
  compartment->setId("PlasmaMembrane");
  compartment->setConstant(true);
  compartment->setSize(314);
  compartment->setSpatialDimensions(2.0);

  compartment = model->createCompartment();
  compartment->setId("Cytosol");
  compartment->setConstant(true);
  compartment->setSize(523);
  compartment->setSpatialDimensions(3.0);

  // create the Species

  Species* species = model->createSpecies();
  species->setId("C_EC");
  species->setCompartment("Extracellular");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("RTR_M");
  species->setCompartment("PlasmaMembrane");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("RCC_M");
  species->setCompartment("PlasmaMembrane");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("A_C");
  species->setCompartment("Cytosol");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("AA_C");
  species->setCompartment("Cytosol");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("T");
  species->setCompartment("Cytosol");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setInitialConcentration(10);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("S");
  species->setCompartment("Cytosol");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setInitialConcentration(5);
  species->setHasOnlySubstanceUnits(false);

  // create the Reactions

  Reaction* reaction = model->createReaction();
  reaction->setId("r1");
  reaction->setReversible(true);
  reaction->setFast(false);
  reaction->setCompartment("Extracellular");
  
  SpeciesReference* reactant = reaction->createReactant();
  reactant->setSpecies("RTR_M");
//.........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;
}

LIBSBML_CPP_NAMESPACE_USE

int main(int argc,char** argv){

//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "groups") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
//    SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
//

SBMLNamespaces sbmlns(3,1,"groups",1);

//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced 
//         with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
//     adds a groups package namespace to the object. 
//
//         SBMLNamespaces sbmlns(3,1);
//         sbmlns.addPkgNamespace("groups",1);
//
//          OR
//
//         SBMLNamespaces sbmlns(3,1);
//         sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
//
// (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
//     groups package. The class is basically used for createing an SBase derived
//     objects defined in the groups package) with the given SBML level, version, 
//     and package version
//
//        GroupsPkgNamespaces sbmlns(3,1,1);
//     


// create the document

SBMLDocument *document = new SBMLDocument(&sbmlns);

// create the Model

Model* model=document->createModel();

// create the Compartment

Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);

compartment=model->createCompartment();
compartment->setId("mitochon");
compartment->setConstant(true);

// create the Species

Species* species = model->createSpecies();
species->setId("ATPc");
species->setCompartment("cytosol");
species->setInitialConcentration(1);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);

species = model->createSpecies();
species->setId("ATPm");
species->setCompartment("mitochon");
species->setInitialConcentration(2);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);

// create the Groups

//
// Get a GroupsModelPlugin 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 casted for the corresponding derived class. 
//
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));

//
// Creates a Group object via GroupsModelPlugin object.
//
Group* group = mplugin->createGroup();

group->setId("ATP");
group->setKind(GROUP_KIND_CLASSIFICATION);
group->setSBOTerm("SBO:0000252");

Member* member = group->createMember();
member->setIdRef("ATPc");

member = group->createMember();
//.........这里部分代码省略.........

//.........这里部分代码省略.........
 
  // Sets the "size" attribute of the Compartment object.
  //
  // We are not setting the units on the compartment size explicitly, so
  // the units of this Compartment object will be the default SBML units of
  // volume, which are liters.
  //
  comp->setSize(1e-14);


  //---------------------------------------------------------------------------
  //
  // Creates Species objects inside the Model object. 
  //
  //---------------------------------------------------------------------------
  
  // Temporary pointer (reused more than once below).
  
  Species *sp;

  //---------------------------------------------------------------------------
  // (Species1) Creates a Species object ("ES")
  //---------------------------------------------------------------------------

  // Create the Species objects inside the Model object. 

  sp = model->createSpecies();
  sp->setId("ES");
  sp->setName("ES");

  // Sets the "compartment" attribute of the Species object to identify the 
  // compartment in which the Species object is located.

  sp->setCompartment(compName);

  // Sets the "initialAmount" attribute of the Species object.
  //
  //  In SBML, the units of a Species object's initial quantity are
  //  determined by two attributes, "substanceUnits" and
  //  "hasOnlySubstanceUnits", and the "spatialDimensions" attribute
  //  of the Compartment object ("cytosol") in which the species
  //  object is located.  Here, we are using the default values for
  //  "substanceUnits" (which is "mole") and "hasOnlySubstanceUnits"
  //  (which is "false").  The compartment in which the species is
  //  located uses volume units of liters, so the units of these
  //  species (when the species appear in numerical formulas in the
  //  model) will be moles/liters.  
  //
  sp->setInitialAmount(0);

  //---------------------------------------------------------------------------
  // (Species2) Creates a Species object ("P")
  //---------------------------------------------------------------------------

  sp = model->createSpecies();
  sp->setCompartment(compName);
  sp->setId("P");
  sp->setName("P");
  sp->setInitialAmount(0);

  //---------------------------------------------------------------------------
  // (Species3) Creates a Species object ("S")
  //---------------------------------------------------------------------------

  sp = model->createSpecies();
  sp->setCompartment(compName);

END_TEST

START_TEST(test_FbcExtension_create_and_write_L3V1V1)
{
  FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 1);

  // create the document

  SBMLDocument *document = new SBMLDocument(sbmlns);
  delete sbmlns;

  // create the Model

  Model* model = document->createModel();

  // create the Compartment

  Compartment* compartment = model->createCompartment();
  compartment->setId("compartment");
  compartment->setConstant(true);
  compartment->setSize(1);

  // create the Species

  Species* species = model->createSpecies();
  species->setId("Node1");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);

  species = model->createSpecies();
  species->setId("Node2");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);

  Reaction* reaction = model->createReaction();
  reaction->setId("J0");
  reaction->setReversible(false);
  SpeciesReference* reactant = reaction->createReactant();
  reactant->setSpecies("Node0");
  reactant->setStoichiometry(1);
  SpeciesReference* product = reaction->createProduct();
  product->setSpecies("Node1");
  product->setStoichiometry(1);

  // use fbc

  FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));

  fail_unless(mplugin != NULL);

  FluxBound* bound = mplugin->createFluxBound();

  bound->setId("bound1");
  bound->setReaction("J0");
  bound->setOperation("equal");
  bound->setValue(10);

  Objective* objective = mplugin->createObjective();
  objective->setId("obj1");
  objective->setType("maximize");

  FluxObjective* fluxObjective = objective->createFluxObjective();
  fluxObjective->setReaction("J0");
  fluxObjective->setCoefficient(1);

  string s1 = writeSBMLToStdString(document);

  // check clone()

  SBMLDocument* document2 = document->clone();
  string s2 = writeSBMLToStdString(document2);
  fail_unless(s1 == s2);

  // check operator=

  Model m = *(document->getModel());
  document2->setModel(&m);
  s2 = writeSBMLToStdString(document2);

  fail_unless(s1 == s2);
  delete document2;

  delete document;
}

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 Module::CreateSBMLModel()
{
  Model* sbmlmod = m_sbml.createModel();
  sbmlmod->setId(m_modulename);
  sbmlmod->setName(m_modulename);
  sbmlmod->setNotes("<body xmlns=\"http://www.w3.org/1999/xhtml\"><p> Originally created by libAntimony " VERSION_STRING " (using libSBML " LIBSBML_DOTTED_VERSION ") </p></body>");
  char cc = g_registry.GetCC();
  //User-defined functions
  for (size_t uf=0; uf<g_registry.GetNumUserFunctions(); uf++) {
    const UserFunction* userfunction = g_registry.GetNthUserFunction(uf);
    assert(userfunction != NULL);
    FunctionDefinition* fd = sbmlmod->createFunctionDefinition();
    fd->setId(userfunction->GetModuleName());
    ASTNode* math = parseStringToASTNode(userfunction->ToSBMLString());
    fd->setMath(math);
    delete math;
  }
  //Compartments
  Compartment* defaultCompartment = sbmlmod->createCompartment();
  defaultCompartment->setId(DEFAULTCOMP);
  defaultCompartment->setConstant(true);
  defaultCompartment->setSize(1);
  defaultCompartment->setSBOTerm(410); //The 'implicit compartment'
  size_t numcomps = GetNumVariablesOfType(allCompartments);
  for (size_t comp=0; comp<numcomps; comp++) {
    const Variable* compartment = GetNthVariableOfType(allCompartments, comp);
    Compartment* sbmlcomp = sbmlmod->createCompartment();
    sbmlcomp->setId(compartment->GetNameDelimitedBy(cc));
    if (compartment->GetDisplayName() != "") {
      sbmlcomp->setName(compartment->GetDisplayName());
    }
    sbmlcomp->setConstant(compartment->GetIsConst());
    formula_type ftype = compartment->GetFormulaType();
    assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE);
    if (ftype != formulaINITIAL) {
      sbmlcomp->setConstant(false);
    }
    const Formula* formula = compartment->GetFormula();
    if (formula->IsDouble()) {
      sbmlcomp->setSize(atof(formula->ToSBMLString().c_str()));
    }
    SetAssignmentFor(sbmlmod, compartment);
  }

  //Species
  size_t numspecies = GetNumVariablesOfType(allSpecies);
  for (size_t spec=0; spec < numspecies; spec++) {
    const Variable* species = GetNthVariableOfType(allSpecies, spec);
    Species* sbmlspecies = sbmlmod->createSpecies();
    sbmlspecies->setId(species->GetNameDelimitedBy(cc));
    if (species->GetDisplayName() != "") {
      sbmlspecies->setName(species->GetDisplayName());
    }
    sbmlspecies->setConstant(false); //There's no need to try to distinguish between const and var for species.
    if (species->GetIsConst()) {
      sbmlspecies->setBoundaryCondition(true);
    }
    else {
      sbmlspecies->setBoundaryCondition(false);
    }
    const Variable* compartment = species->GetCompartment();
    if (compartment == NULL) {
      sbmlspecies->setCompartment(defaultCompartment->getId());
    }
    else {
      sbmlspecies->setCompartment(compartment->GetNameDelimitedBy(cc));
    }
    const Formula* formula = species->GetFormula();
    if (formula->IsDouble()) {
      sbmlspecies->setInitialConcentration(atof(formula->ToSBMLString().c_str()));
    }
    else if (formula->IsAmountIn(species->GetCompartment())) {
      sbmlspecies->setInitialAmount(formula->ToAmount());
    }
    SetAssignmentFor(sbmlmod, species);
  }

  //Formulas
  size_t numforms = GetNumVariablesOfType(allFormulas);
  for (size_t form=0; form < numforms; form++) {
    const Variable* formvar = GetNthVariableOfType(allFormulas, form);
    const Formula*  formula = formvar->GetFormula();
    Parameter* param = sbmlmod->createParameter();
    param->setId(formvar->GetNameDelimitedBy(cc));
    if (formvar->GetDisplayName() != "") {
      param->setName(formvar->GetDisplayName());
    }
    param->setConstant(formvar->GetIsConst());
    if (formula->IsDouble()) {
      param->setValue(atof(formula->ToSBMLString().c_str()));
    }
    SetAssignmentFor(sbmlmod, formvar);
    formula_type ftype = formvar->GetFormulaType();
    assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE);
    if (ftype != formulaINITIAL) {
      param->setConstant(false);
    }
  }

  //Reactions
//.........这里部分代码省略.........

//.........这里部分代码省略.........
  param->setValue(2);

  param = model->createParameter();
  param->initDefaults();
  param->setId("q4_Y");
  param->setValue(2);

  // create SubModels

  CompModelPlugin* mplugin =
    static_cast<CompModelPlugin*>(model->getPlugin("comp"));

  Submodel* submodel = mplugin->createSubmodel();
  submodel->setId("GRID_1_1_cell");
  submodel->setModelRef("Cell");

  submodel = mplugin->createSubmodel();
  submodel->setId("GRID_1_2_cell");
  submodel->setModelRef("Cell");

  submodel = mplugin->createSubmodel();
  submodel->setId("GRID_2_1_cell");
  submodel->setModelRef("Cell");

  submodel = mplugin->createSubmodel();
  submodel->setId("GRID_2_2_cell");
  submodel->setModelRef("Cell");

  // create the ModelDefinition

  CompSBMLDocumentPlugin* dplugin =
    static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
  
  ModelDefinition* mdef = dplugin->createModelDefinition();
  mdef->setId("Cell");

  compartment = mdef->createCompartment();
  compartment->initDefaults();
  compartment->setId("C");
  compartment->setSpatialDimensions(2.0);
  compartment->setSize(1.0);

  Species* species = mdef->createSpecies();
  species->setId("R");
  species->setCompartment("C");
  species->setHasOnlySubstanceUnits(false);
  species->setBoundaryCondition(false);
  species->setConstant(false);

  species = mdef->createSpecies();
  species->setId("S");
  species->setCompartment("C");
  species->setHasOnlySubstanceUnits(false);
  species->setBoundaryCondition(false);
  species->setConstant(false);

  Reaction* reaction = mdef->createReaction();
  reaction->setId("Degradation_R");
  reaction->setReversible(false);
  reaction->setFast(false);
  reaction->setCompartment("C");

  SpeciesReference* reactant = reaction->createReactant();  
  reactant->setSpecies("R");
  reactant->setStoichiometry(1);
  reactant->setConstant(true);
  
  reaction = mdef->createReaction();
  reaction->setId("Degradation_S");
  reaction->setReversible(false);
  reaction->setFast(false);
  reaction->setCompartment("C");

  reactant = reaction->createReactant();
  reactant->setSpecies("S");
  reactant->setStoichiometry(1);
  reactant->setConstant(true);
  document->checkConsistency();

  Event* event = mdef->createEvent();
  event->setId("event0");
  event->setUseValuesFromTriggerTime(false);

  DynEventPlugin* eplugin =
    static_cast<DynEventPlugin*>(event->getPlugin("dyn"));
  eplugin->setApplyToAll(true);
  eplugin->setCboTerm("http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDivision");

  Trigger* trigger = event->createTrigger();
  trigger->setInitialValue(false);
  trigger->setPersistent(false);
  trigger->setMath(SBML_parseFormula("true"));

  if (document->getNumErrors(LIBSBML_SEV_ERROR) > 0)
    document->printErrors();

  writeSBML(document,"dyn_example2.xml");
  delete document;

}

LIBSBML_CPP_NAMESPACE_USE

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

  // create the document

  SBMLDocument *document = new SBMLDocument(&sbmlns);
  document->setPackageRequired("fbc", false);

  // create the Model

  Model* model=document->createModel();

  // create the Compartment

  Compartment* compartment = model->createCompartment();
  compartment->setId("compartment");
  compartment->setConstant(true);
  compartment->setSize(1);

  // create the Species

  Species* species = model->createSpecies();
  species->setId("Node1");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node2");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node3");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node4");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node5");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node6");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node7");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node8");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node0");
  species->setCompartment("compartment");
  species->setBoundaryCondition(true);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  species = model->createSpecies();
  species->setId("Node9");
  species->setCompartment("compartment");
  species->setBoundaryCondition(true);
  species->setConstant(false);
  species->setHasOnlySubstanceUnits(false);

  Reaction* reaction = model->createReaction();
  reaction->setId("J0");
  reaction->setReversible(false);
  reaction->setFast(false);
  SpeciesReference* reactant = reaction->createReactant();
  reactant->setSpecies("Node0");
//.........这里部分代码省略.........

/**
 *
 * Creates an SBML model represented in "7.8 Example involving function definitions"
 * in the SBML Level 2 Version 4 Specification.
 *
 */
SBMLDocument* createExampleInvolvingFunctionDefinitions()
{
  const unsigned int level   = Level;
  const unsigned int version = Version;

  //---------------------------------------------------------------------------
  //
  // Creates an SBMLDocument object 
  //
  //---------------------------------------------------------------------------

  SBMLDocument* sbmlDoc = new SBMLDocument(level,version);

  //---------------------------------------------------------------------------
  //
  // Creates a Model object inside the SBMLDocument object. 
  //
  //---------------------------------------------------------------------------

  Model* model = sbmlDoc->createModel();
  model->setId("functionExample");

  //---------------------------------------------------------------------------
  //
  // Creates a FunctionDefinition object inside the Model object. 
  //
  //---------------------------------------------------------------------------

  FunctionDefinition* fdef = model->createFunctionDefinition();
  fdef->setId("f");

  // Sets a math (ASTNode object) to the FunctionDefinition object.

  string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
                         "  <lambda>"
                         "    <bvar>"
                         "      <ci> x </ci>"
                         "    </bvar>"
                         "    <apply>"
                         "      <times/>"
                         "      <ci> x </ci>"
                         "      <cn> 2 </cn>"
                         "    </apply>"
                         "  </lambda>"
                         "</math>";

  ASTNode* astMath = readMathMLFromString(mathXMLString.c_str());
  fdef->setMath(astMath);
  delete astMath;


  //---------------------------------------------------------------------------
  //
  // Creates a Compartment object inside the Model object. 
  //
  //---------------------------------------------------------------------------

  Compartment* comp;
  const string compName = "compartmentOne";

  // Creates a Compartment object ("compartmentOne")

  comp = model->createCompartment();
  comp->setId(compName);
 
  // Sets the "size" attribute of the Compartment object.
  //
  //   The units of this Compartment object is the default SBML 
  //   units of volume (litre), and thus we don't have to explicitly invoke 
  //   setUnits("litre") function to set the default units.
  //
  comp->setSize(1);


  //---------------------------------------------------------------------------
  //
  // Creates Species objects inside the Model object. 
  //
  //---------------------------------------------------------------------------
  
  Species* sp;

  //---------------------------------------------------------------------------
  // (Species1) Creates a Species object ("S1")
  //---------------------------------------------------------------------------

  sp = model->createSpecies();
  sp->setId("S1");

  // Sets the "compartment" attribute of the Species object to identify the 
  // compartnet in which the Species object located.

  sp->setCompartment(compName);

//.........这里部分代码省略.........

END_TEST

START_TEST(test_FbcExtension_create_and_write_new_geneassociation
)
{
  FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2);

  // create the document

  SBMLDocument document(sbmlns);
  document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
  document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false);

  // create the Model

  Model* model = document.createModel();

  // create the Compartment

  Compartment* compartment = model->createCompartment();
  compartment->setId("compartment");
  compartment->setConstant(true);
  compartment->setSize(1);

  // create the Species

  Species* species = model->createSpecies();
  species->setId("Node1");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);

  species = model->createSpecies();
  species->setId("Node2");
  species->setCompartment("compartment");
  species->setBoundaryCondition(false);

  Reaction* reaction = model->createReaction();
  reaction->setId("J0");
  reaction->setReversible(false);
  SpeciesReference* reactant = reaction->createReactant();
  reactant->setSpecies("Node0");
  reactant->setStoichiometry(1);
  SpeciesReference* product = reaction->createProduct();
  product->setSpecies("Node1");
  product->setStoichiometry(1);

  // use fbc

  FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));

  fail_unless(mplugin != NULL);

  FluxBound* bound = mplugin->createFluxBound();

  bound->setId("bound1");
  bound->setReaction("J0");
  bound->setOperation("equal");
  bound->setValue(10);

  Objective* objective = mplugin->createObjective();
  objective->setId("obj1");
  objective->setType("maximize");

  FluxObjective* fluxObjective = objective->createFluxObjective();
  fluxObjective->setReaction("J0");
  fluxObjective->setCoefficient(1);

  FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc"));
  fail_unless(rplug != NULL);

  GeneProductAssociation * ga = rplug->createGeneProductAssociation();
  ga->setId("ga1");
  ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
  fail_unless(ga->getAssociation() != NULL);

  fail_unless(mplugin->getNumGeneProducts() == 5);

  ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
  fail_unless(ga->getAssociation() != NULL);

  fail_unless(mplugin->getNumGeneProducts() == 5);


  delete sbmlns;

}