C++ Species::setHasOnlySubstanceUnits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);
}

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.........

void
Model::assignRequiredValues()
{
  // when converting to L3 some attributes which have default values in L1/L2
  // but are required in L3 are not present or set
  unsigned int i, n;

  if (getNumUnitDefinitions() > 0)
  {
    for (i = 0; i < getNumUnitDefinitions(); i++)
    {
      for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
      {
        Unit *u = getUnitDefinition(i)->getUnit(n);
        if (!u->isSetExponent())
          u->setExponent(1.0);
        if (!u->isSetScale())
          u->setScale(0);
        if (!u->isSetMultiplier())
          u->setMultiplier(1.0);
      }
    }
  }
  
  if (getNumCompartments() > 0)
  {
    for (i = 0; i < getNumCompartments(); i++)
    {
      Compartment *c = getCompartment(i);
      c->setConstant(c->getConstant());
    }
  }
  if (getNumSpecies() > 0)
  {
    for (i = 0; i < getNumSpecies(); i++)
    {
      Species * s = getSpecies(i);
      s->setBoundaryCondition(s->getBoundaryCondition());
      s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
      s->setConstant(s->getConstant());
    }
  }
  if (getNumParameters() > 0)
  {
    for (i = 0; i < getNumParameters(); i++)
    {
      Parameter * p = getParameter(i);
      p->setConstant(p->getConstant());
    }
  }
  if (getNumReactions() > 0)
  {
    for (i = 0; i < getNumReactions(); i++)
    {
      Reaction * r = getReaction(i);
      r->setFast(r->getFast());
      r->setReversible(r->getReversible());
      if (r->getNumReactants() > 0)
      {
        for (n = 0; n < r->getNumReactants(); n++)
        {
          SpeciesReference *sr = r->getReactant(n);
          if (sr->isSetStoichiometryMath())
          {
            sr->setConstant(false);
          }
          else
          {
            sr->setConstant(true);
          }
        }
      }
      if (r->getNumProducts() > 0)
      {
        for (n = 0; n < r->getNumProducts(); n++)
        {
          SpeciesReference *sr = r->getProduct(n);
          if (sr->isSetStoichiometryMath())
          {
            sr->setConstant(false);
          }
          else
          {
            sr->setConstant(true);
          }
        }
      }
    }
  }
  if (getNumEvents() > 0)
  {
    for (i = 0; i < getNumEvents(); i++)
    {
      Event * e = getEvent(i);
      e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());

      if (e->isSetTrigger())
      {
        Trigger *t = e->getTrigger();
        t->setPersistent(true);
//.........这里部分代码省略.........

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[])
{
  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.........

//.........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){

//
// 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.........