C++ Species::getInitialAmount方法代码示例

bool getSetValue(string id, Model* model, const set<string>& tests, double& setValue) 
{
  SBase* element = model->getElementBySId(id);
  if (element==NULL) return false;
  Compartment* comp = static_cast<Compartment*>(element);
  Species* species = static_cast<Species*>(element);
  Parameter* param = static_cast<Parameter*>(element);
  Reaction* rxn = static_cast<Reaction*>(element);
  SpeciesReference* sr= static_cast<SpeciesReference*>(element);
  switch(element->getTypeCode()) {
  case SBML_COMPARTMENT:
    if (comp->isSetSize()) {
      setValue = comp->getSize();
      return true;
    }
    break;
  case SBML_SPECIES:
    if (species->isSetInitialAmount()) {
      setValue = species->getInitialAmount();
      if (tests.find("Concentration") != tests.end()) {
        comp = model->getCompartment(species->getCompartment());
        if (comp->isSetSize()) {
          setValue = setValue/comp->getSize();
        }
      }
      return true;
    }
    if (species->isSetInitialConcentration()) {
      setValue = species->getInitialConcentration();
      if (tests.find("Amount") != tests.end()) {
        comp = model->getCompartment(species->getCompartment());
        if (comp->isSetSize()) {
          setValue = setValue*comp->getSize();
        }
      }
      return true;
    }
    break;
  case SBML_PARAMETER:
    if (param->isSetValue()) {
      setValue = param->getValue();
      return true;
    }
    break;
  case SBML_REACTION:
    return false; //We'd have to calculate the math here, which I'm not going to do.
  case SBML_SPECIES_REFERENCE:
    if (sr->isSetStoichiometry()) {
      setValue = sr->getStoichiometry();
      return true;
    }
    break;
  default:
    assert(false); //Uncaught type!
    return false;
    break;
  }
  return false;
}

/* create MOLECULE */
map< string,Id > SbmlReader::createMolecule( map< string,Id > &idMap )
{	
	map<string,Id>molMap;
	static const Cinfo* moleculeCinfo = initMoleculeCinfo();
	static const Finfo* modeFinfo = moleculeCinfo->findFinfo( "mode" );
	static const Finfo* nInitFinfo = moleculeCinfo->findFinfo( "nInit" );	
	static const Cinfo* kincomptCinfo = initKinComptCinfo();
	static const Finfo* dimensionFinfo = kincomptCinfo->findFinfo( "numDimensions" );
	static const Finfo* sizeFinfo = kincomptCinfo->findFinfo( "size" );
	int num_species = model_->getNumSpecies();
	//cout << "num species: " << num_species << endl;
	for ( int sindex = 0; sindex < num_species; sindex++ )
	{
		Species* s = model_->getSpecies(sindex);
		if (!s){
			//cout << "species " << sindex << " is nul" << endl;
			continue;
		}
		std::string compt = "";		
		if ( s->isSetCompartment() )		
			compt = s->getCompartment();
		if (compt.length()< 1){
			cout << "compt is empty for species "<< sindex << endl;
			continue;
		}
		string id = s->getId();
		//cout<<"species is :"<<id<<endl;
		if (id.length() < 1){
			continue;
		}
		/*std::string name = "";
		if ( s->isSetName() ){
			name = s->getName();
		}*/ 
		Id comptEl = idMap[compt];
		molecule_ = Neutral::create( "Molecule",id,comptEl,Id::scratchId() );//create Molecule
		molMap[id] = comptEl; 
		elmtMap_[id] = Eref( molecule_ );
		//printNotes(s);
		UnitDefinition * ud = s->getDerivedUnitDefinition();
		assert(ud != NULL);
		/*string udef = UnitDefinition::printUnits(ud);
		//cout << "species unit :" << udef << endl;*/
		double initvalue =0.0;
		if ( s->isSetInitialConcentration() )
			initvalue = s->getInitialConcentration();
		else if ( s->isSetInitialAmount() )
			initvalue = s->getInitialAmount() ;
		else {
			cout << "Invalid SBML: Either initialConcentration or initialAmount must be set." << endl;
			return molMap;
		}
		double transvalue = transformUnits(1,ud);
		//cout << "initAmount: " << initvalue << endl;
		transvalue *= initvalue;
		//cout << "transvalue: " << transvalue << endl;
		unsigned int dimension;
        	get< unsigned int >( comptEl.eref(), dimensionFinfo,dimension );
		bool initconc = s->isSetInitialConcentration();
		if ( dimension > 0 &&  initconc) { 
			double size;
			get< double > (comptEl.eref(),sizeFinfo,size); 		
			transvalue *= size;	
		}
		::set< double >( molecule_, nInitFinfo, transvalue ); //initialAmount 	
		bool cons=s->getConstant(); 
		bool bcondition = s->getBoundaryCondition();
		if (cons){
			::set< int >( molecule_,modeFinfo,4 );
			//cout << "set constant 4" << endl;
		}else if (bcondition) {
			::set< int >( molecule_,modeFinfo,1 );
			//cout << "set constant 1" << endl;
		}else {
			::set< int >( molecule_,modeFinfo,0 );
			//cout << "set constant 0" << endl;	
		}
	}
	return molMap;
}

/* create MOLECULE  */
const SbmlReader::sbmlStr_mooseId SbmlReader::createMolecule( map< string,Id > &comptSidMIdMap) {
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    map< string, Id >molSidcmptMIdMap;
    double transvalue = 0.0;
    int num_species = model_->getNumSpecies();

    if (num_species == 0) {
        baseId = Id();
        errorFlag_ = true;
        return molSidcmptMIdMap;
    }

    for ( int sindex = 0; sindex < num_species; sindex++ ) {
        Species* spe = model_->getSpecies(sindex);
        if (!spe) {
            continue;
        }
        std::string compt = "";
        if ( spe->isSetCompartment() ) {
            compt = spe->getCompartment();
        }
        if (compt.length()< 1) {
            //cout << "compt is empty for species "<< sindex << endl;
            continue;
        }
        string id = spe->getId();
        if (id.length() < 1) {
            continue;
        }
        std::string name = "";
        if ( spe->isSetName() ) {
            name = spe->getName();
            name = nameString(name);
        }
        if (name.empty())
            name = id;

        double initvalue =0.0;
        if ( spe->isSetInitialConcentration() )
            initvalue = spe->getInitialConcentration();
        else if ( spe->isSetInitialAmount() )
            initvalue = spe->getInitialAmount() ;
        else {
            unsigned int nr = model_->getNumRules();
            bool found = false;
            for ( unsigned int r = 0; r < nr; r++ ) {
                Rule * rule = model_->getRule(r);
                bool assignRule = rule->isAssignment();
                if ( assignRule ) {
                    string rule_variable = rule->getVariable();
                    if (rule_variable.compare(id) == 0) {
                        found = true;
                        break;
                    }
                }
            }
            if (found == false) {
                cout << "Invalid SBML: Either initialConcentration or initialAmount must be set or it should be found in assignmentRule but non happening for " << spe->getName() <<endl;
                return molSidcmptMIdMap;
            }
        }
        Id comptEl = comptSidMIdMap[compt];
        Id meshEntry = Neutral::child( comptEl.eref(), "mesh" );
        bool constant = spe->getConstant();
        bool boundaryCondition = spe->getBoundaryCondition();
        if (boundaryCondition == true)
            cout << "Pools having BoundaryCondition true " << name <<endl;
        Id pool;
        //If constant is true then its equivalent to BuffPool in moose
        if (constant == true)
            //if( (boundaryCondition == true) && (constant==false))
            pool = shell->doCreate("BufPool",comptEl,name,1);
        else
            pool = shell->doCreate("Pool", comptEl, name ,1);
        molSidcmptMIdMap[id] = comptEl;
        //Map to Molecule SBML id to Moose Id
        molSidMIdMap_[id] = pool;

        //shell->doAddMsg( "OneToOne",pool, "mesh", meshEntry, "mesh" );
        bool bcondition = spe->getBoundaryCondition();
        if ( constant == true && bcondition == false)
            cout <<"The species "<< name << " should not appear in reactant or product as per sbml Rules"<< endl;

        unsigned int spatialDimen =Field< unsigned int >::get( comptEl, "numDimensions");

        UnitDefinition * ud = spe->getDerivedUnitDefinition();
        assert(ud != NULL);
        bool hasonlySubUnit = spe->getHasOnlySubstanceUnits();

        //double v = Field< double >::get( comptEl.path(), "volume" );
        transvalue = transformUnits(1,ud,"substance",hasonlySubUnit);
        if (hasonlySubUnit) {
            // In Moose, no. of molecules (nInit) and unit is "item"
            if (spatialDimen > 0 && spe->isSetInitialAmount() ) {
                //transvalue *= initvalue;
                initvalue *=transvalue;
                Field < double> :: set( pool, "nInit", initvalue);
            }
        } else {
//.........这里部分代码省略.........