void MetabolicNetworkTools::fillStoichiometricMatrix(boost::numeric::ublas::mapped_matrix<double>& matrix, 
00180                                                        std::map<std::string, unsigned int>& rowLabels, 
00181                                                        std::map<std::string, unsigned int>& colLabels)
00182   {
00183     std::map< Molecule_sptr, std::vector<Reaction_sptr > > molRxnMap =         		
		MN.useTools).connectMetabolitesToReactions();
00184     
00185     typedef std::map<std::string, unsigned int> MNMapType; // map for metabolite names ->  rxn no.
00186     MNMapType mnMap;
00187     unsigned int metNo = molRxnMap.size();
00188     unsigned int rxnNo = this->MN.size();
00189     matrix.resize(metNo, rxnNo, false);
00190 
00191     const std::vector<Reaction_sptr> & reactions = this->MN.getReactions();
00192 
00193     std::pair<MNMapType::iterator, bool> inserted;
00194     for (unsigned int reactionNo = 0; reactionNo < reactions.size(); ++reactionNo) {
00195       colLabels[reactions[reactionNo]->getName()] = reactionNo;
00196       // process educts
00197       SetOfMolecules_sptr edPr = reactions[reactionNo]->getEducts();
00198       for (unsigned int k = 0; k < edPr->size(); ++k) {
00199         
00200         const std::string& molName = edPr->getMolecule(k)->getName();
00201         MNMapType::iterator iter = mnMap.find(molName);
00202         if (iter == mnMap.end()) {
00203           rowLabels[molName] = mnMap.size();
00204           inserted = mnMap.insert(std::pair<std::string, unsigned int>(molName, mnMap.size()));
00205           iter = inserted.first;
00206         }
00207         matrix(iter->second, reactionNo) = -edPr->getStoich(k);
00208 
00209       }
00210       
00211       // process products
00212       edPr = reactions[reactionNo]->getProducts();
00213       for (unsigned int k = 0; k < edPr->size(); ++k) {
00214         
00215         const std::string& molName = edPr->getMolecule(k)->getName();
00216         MNMapType::iterator iter = mnMap.find(molName);
00217         if (iter == mnMap.end()) {
00218           rowLabels[molName] = mnMap.size();
00219           inserted = mnMap.insert(std::pair<std::string, unsigned int>(molName, mnMap.size()));
00220           iter = inserted.first;
00221         }
00222         matrix(iter->second, reactionNo) = edPr->getStoich(k);
00223 
00224       }
00225 
00226     }
00227       
00228   }