C++ KineticLaw::getParameter方法代码示例

void
Model::convertParametersToLocals(unsigned int level, unsigned int version)
{
  for (unsigned int i = 0; i < getNumReactions(); i++)
  {
    Reaction *r = getReaction(i);
    if (r->isSetKineticLaw())
    {
      KineticLaw *kl = r->getKineticLaw();
      for (unsigned int j = 0; j < kl->getNumParameters(); j++)
      {
        LocalParameter *lp = new LocalParameter(level, version);
        (*lp) = *(kl->getParameter(j));
        kl->addLocalParameter(lp);
      }
    }
  }
}

END_TEST


START_TEST ( test_KineticLaw_Parameter_parent_create_model )
{
    Model *m = new Model(2, 4);
    Reaction *r = m->createReaction();
    KineticLaw* kl = m->createKineticLaw();
    Parameter * p = m->createKineticLawParameter();

    fail_unless(kl->getNumParameters() == 1);

    ListOfParameters *lop = kl->getListOfParameters();

    fail_unless(r == kl->getParentSBMLObject());
    fail_unless(kl == lop->getParentSBMLObject());
    fail_unless(lop == p->getParentSBMLObject());
    fail_unless(lop == kl->getParameter(0)->getParentSBMLObject());

    delete kl;
}

int
main (int argc, char* argv[])
{
  if (argc != 2)
  {
    cout << endl << "Usage: printNotes filename" << endl << endl;
    return 1;
  }

  unsigned int i,j;
  const char* filename   = argv[1];
  SBMLDocument* document;
  SBMLReader reader;

  document = reader.readSBML(filename);

  unsigned int errors = document->getNumErrors();

  cout << endl;
  cout << "filename: " << filename << endl;
  cout << endl;

  if(errors > 0)
  {
    document->printErrors(cerr);
    delete document;

    return errors;
  }

  /* Model */

  Model* m = document->getModel();
  printNotes(m);

  for(i=0; i < m->getNumReactions(); i++)
  {
    Reaction* re = m->getReaction(i);
    printNotes(re);

    /* SpeciesReference (Reacatant) */

    for(j=0; j < re->getNumReactants(); j++)
    {
      SpeciesReference* rt = re->getReactant(j);
      if (rt->isSetNotes()) cout << "   ";
      printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
    }

    /* SpeciesReference (Product) */

    for(j=0; j < re->getNumProducts(); j++)
    {
      SpeciesReference* rt = re->getProduct(j);
      if (rt->isSetNotes()) cout << "   ";
      printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
    }

    /* ModifierSpeciesReference (Modifier) */

    for(j=0; j < re->getNumModifiers(); j++)
    {
      ModifierSpeciesReference* md = re->getModifier(j);
      if (md->isSetNotes()) cout << "   ";
      printNotes(md, (md->isSetSpecies() ? md->getSpecies() : std::string("")) );
    }

    /* Kineticlaw */

    if(re->isSetKineticLaw())
    {
      KineticLaw* kl = re->getKineticLaw();
      if (kl->isSetNotes()) cout << "   ";
      printNotes(kl);

      /* Parameter */

      for(j=0; j < kl->getNumParameters(); j++)
      {
        Parameter* pa = kl->getParameter(j);
        if (pa->isSetNotes()) cout << "      ";
        printNotes(pa);
      }
    }

  }

  /* Species */

  for(i=0; i < m->getNumSpecies(); i++)
  {
    Species* sp = m->getSpecies(i);
    printNotes(sp);
  }

  /* Compartment */

  for(i=0; i < m->getNumCompartments(); i++)
  {
    Compartment* sp = m->getCompartment(i);
//.........这里部分代码省略.........

/** 
 * Load a gene network from an SBML file. Overrides Structure.load(). Format must
 * be equal GeneNetwork.SBML. Note, the SBML file must be in the exact same format
 * as the SBML files produced by writeSBML(). In particular, we assume that reactions are listed
 * *ordered* as we do in writeSBML().
 * @param filename URL to the file describing the network to load
 * @param format File format (GML, DOT, etc.)
 * @throws IOException 
 */
void GeneNetwork::load_sbml(const char *filename) {
	SBMLDocument* document;
  	SBMLReader reader;

  	document = reader.readSBML(filename);

  	unsigned int errors = document->getNumErrors();
	if (errors > 0) {
        std::cerr << "Failed to open file " << filename << std::endl;
        exit(1);
    }

	Model *m = document->getModel();

	// -----------------------------------------
	// Set the network size and create the genes
	// do not count the species _void_
	int size = m->getNumSpecies() - 1;
	ListOfSpecies *species = m->getListOfSpecies();
	
	for (int g=0; g < size; g++) {
		if (species->get(g)->getId() != "_void_") {
			//HillGene hg = new HillGene(this);
			//hg.setLabel(species.get(g).getId());
			HillGene *n = new HillGene(species->get(g)->getId());
			//n.setLabel(species->get(g)->getId());
			nodes_.push_back(*n);
			delete n;
		}
	}
	
	x_ = Vec_DP(nodes_.size());
	x_ = 0;
	y_ = Vec_DP(nodes_.size());
	y_ = 0;
	
	//vector<string> parameterNames; // the names of the parameters
	//vector<double> parameterValues; // the values of the parameters
	std::map<std::string, double> params;
	std::vector<std::string> inputNodes; // the indexes of the inputs
	HillGene src, tgt;
	Parameter *param;
	
	// 2 loops for one gene: both synthesis and degradation reactions
	// (we assume that reactions are listed *ordered* as we do in writeSBML())
	//int counter = 0;
	for (unsigned int i=0; i < m->getNumReactions(); i++) {
		Reaction *re = m->getReaction(i);
		std::string id = re->getId();
		
		std::stringstream ss;
		ss << i;
		//::logging::log::emit<Debug>() << id.c_str() <<
		//		::logging::log::endl;
	
		tgt = nodes_.at(getIndexOfNode(getGeneReactantId(id)));
		//tgt->setLabel(getGeneReactantId(*re));
      	//SpeciesReference *rt = re->getReactant(0);
      	//Node *tgt = new HillGene();
      	//tgt->setLabel(rt->getSpecies());
      	//ListOfSpeciesReferences *modifiers = re->getListOfModifiers();

    	for (unsigned int j=0; j < re->getNumModifiers(); j++) {
      		ModifierSpeciesReference *md = re->getModifier(j);
      		src = nodes_.at(getIndexOfNode(md->getSpecies()));      		
      		inputNodes.push_back(src.getLabel());
      		
            // set output genes
            std::vector<std::string> outputs = src.getOutputGenes();
            outputs.push_back(tgt.getLabel());
            src.setOutputGenes(outputs);
      		
            // The edge type is unknown for now, it is initialized later
      		Edge *e = new Edge(&src, &tgt, "+-");
			edges_.push_back(*e);
			//delete src;
			delete e;
		}

      	KineticLaw *kl = re->getKineticLaw();
      		
      	for(unsigned int j=0; j < kl->getNumParameters(); j++) {
        	param = kl->getParameter(j);
			params[param->getId()] = param->getValue();
			//char buf[256];
      		//sprintf(buf, "%s\t%f", param->getId().c_str(), param->getValue());
			//::logging::log::emit<Info>() << buf <<	::logging::log::endl;
		}
		
		//::logging::log::emit<Info>() << ::logging::log::dec << params.size() <<
		//		::logging::log::endl;
//.........这里部分代码省略.........

//.........这里部分代码省略.........
          if (pSBase->isSetId())
            {
              id = pSBase->getId();

              if (ids.find(id) == ids.end())
                {
                  ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
                }
              else
                {
                  CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
                }
            }

          if (pSBase->isSetMetaId())
            {
              id = pSBase->getMetaId();

              if (metaIds.find(id) == metaIds.end())
                {
                  metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
                }
              else
                {
                  CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
                }
            }

          // each parameter
          unsigned int i, iMax = pModel->getListOfParameters()->size();

          for (i = 0; i < iMax; ++i)
            {
              pSBase = pModel->getParameter(i);
              assert(pSBase != NULL);

              if (pSBase->isSetId())
                {
                  id = pSBase->getId();

                  if (ids.find(id) == ids.end())
                    {
                      ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
                    }
                  else
                    {
                      CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
                    }
                }

              if (pSBase->isSetMetaId())
                {
                  id = pSBase->getMetaId();

                  if (metaIds.find(id) == metaIds.end())
                    {
                      metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
                    }
                  else
                    {
                      CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
                    }
                }
            }
        }