C++ KineticLaw::createParameter方法代码示例

END_TEST


START_TEST ( test_KineticLaw_parent_NULL )
{
    Reaction * r = new Reaction(2, 4);
    KineticLaw *kl = r->createKineticLaw();
    Parameter *p = kl->createParameter();

    fail_unless(r == kl->getParentSBMLObject());
    fail_unless(r == p->getAncestorOfType(SBML_REACTION));
    fail_unless(kl == p->getAncestorOfType(SBML_KINETIC_LAW));

    KineticLaw *kl1 = kl->clone();

    fail_unless(kl1->getParentSBMLObject() == NULL);
    fail_unless(kl1->getParameter(0)->getAncestorOfType(SBML_REACTION) == NULL);
    fail_unless(kl1 == kl1->getParameter(0)->getAncestorOfType(SBML_KINETIC_LAW));

    delete r;
}

//.........这里部分代码省略.........
   //              <ci> ES </ci>
   //            </apply>
   //          </apply>
   //        </apply>
   //
   //--------------------------------------------

   ASTNode* astMath = new ASTNode(AST_TIMES);
   astMath->addChild(astCytosol);
   astMath->addChild(astMinus);

   //---------------------------------------------
   //
   // set the Math element
   //
   //------------------------------------------------

   kl->setMath(astMath);

  // KineticLaw::setMath(const ASTNode*) sets the math of the KineticLaw object
  // to a copy of the given ASTNode, and thus basically the caller should delete 
  // the original ASTNode object if the caller has the ownership of the object to 
  // avoid memory leak.

   delete astMath;


  //---------------------------------------------------------------------------
  // Creates local Parameter objects inside the KineticLaw object.
  //---------------------------------------------------------------------------

  // Creates a Parameter ("kon")

  Parameter* para = kl->createParameter();
  para->setId("kon");
  para->setValue(1000000);
  para->setUnits("litre_per_mole_per_second");

  // Creates a Parameter ("koff")

  para = kl->createParameter();
  para->setId("koff");
  para->setValue(0.2);
  para->setUnits("per_second");


  //---------------------------------------------------------------------------
  // (Reaction2) Creates a Reaction object ("vcat") .
  //---------------------------------------------------------------------------
  
  reaction = model->createReaction();
  reaction->setId("vcat");
  reaction->setReversible(false);

  //---------------------------------------------------------------------------
  // Creates Reactant objects inside the Reaction object ("vcat"). 
  //---------------------------------------------------------------------------

  // (Reactant1) Creates a Reactant object that references Species "ES" in the
  // model.

  spr = reaction->createReactant();
  spr->setSpecies("ES");

  //---------------------------------------------------------------------------
  // Creates a Product object inside the Reaction object ("vcat"). 

//.........这里部分代码省略.........
  	sp->setId("_void_");
	sp->setInitialAmount(0);
	sp->setBoundaryCondition(true);
	sp->setConstant(true);
	all_sp.push_back(sp);
	//model.addSpecies(species[size]);


	// SET SYNTHESIS AND DEGRADATION REACTIONS FOR EVERY GENE
	for (int i=0; i<size; i++) {
		//::logging::log::emit<Info>() << ::logging::log::dec << i <<
		//::logging::log::endl;
		
		// the ID of gene i
//			String currentGeneID = nodeIds_.get(i);
		string currentGeneID = (nodes_.at(i)).getLabel();
		// The modifiers (regulators) of gene i
		std::vector<std::string> inputGenes = (nodes_.at(i)).getInputGenes();
		
		// SYNTHESIS REACTION
		std::string reactionId = currentGeneID + "_synthesis";
		Reaction *reaction = model->createReaction();
		KineticLaw *kineticLaw = reaction->createKineticLaw();
		SpeciesReference *spr;
		ModifierSpeciesReference *msr;
		reaction->setId(reactionId);
		reaction->setReversible (false);
		spr = reaction->createReactant();
  		spr->setSpecies(sp->getId());
  		spr = reaction->createProduct();
  		spr->setSpecies((all_sp.at(i))->getId());
		
		std::stringstream ss;
		ss << inputGenes.size();
		//::logging::log::emit<Debug>() << "node = " << nodes_.at(i).getLabel().c_str() << " #inputs = " << ss.str().c_str() << ::logging::log::endl;
		
		for (unsigned int r=0; r<inputGenes.size(); r++) {// set gene modifiers
//				reaction.addModifier(species[inputIndexes.get(r)]);
			//log.log(Level.INFO, "i = " + size);
			msr = reaction->createModifier();
			msr->setSpecies((all_sp.at(getIndexOfNode(inputGenes.at(r))))->getId());
		}

		//std::vector<RegulatoryModule> modules = (nodes_.at(i)).getRegulatoryModules();
		//log.log(Level.INFO, "size = " + modules.size());
		std::map<std::string, double> *params = new std::map<std::string, double>();
		(nodes_.at(i)).compileParameters(*params);
		
		//char buf[256];
		//sprintf(buf, "%f", nodes_.at(i).getDelta());
		//::logging::log::emit<Info>() << buf << ::logging::log::endl;
		//::logging::log::emit<Info>() << ::logging::log::dec << nodes_.at(i).getAlpha().size() <<
		//		::logging::log::endl;
		
		Parameter *para;
		// save gene parameters (note, the first param is the degradation rate)
		std::map<std::string, double>::iterator p = params->begin();
		//p++;
		for (; p!=params->end(); p++) {
			//if (p == params->begin()) {
			//	p++;
			//	continue;
			//}
			//::logging::log::emit<Info>() << p->first.c_str() <<
			//	::logging::log::endl;
			if (p->first != "delta") {
				para = kineticLaw->createParameter();
				para->setId(p->first);
				para->setValue(p->second);
			}
		}
		reaction->setKineticLaw(kineticLaw);
		model->addReaction(reaction);

		// DEGRADATION REACTION
		reaction = model->createReaction();
		kineticLaw = reaction->createKineticLaw();
		reactionId = currentGeneID + "_degradation";
		reaction->setId(reactionId);
		reaction->setReversible(false);
		spr = reaction->createReactant();
  		spr->setSpecies((all_sp.at(i))->getId());
  		spr = reaction->createProduct();
  		spr->setSpecies(sp->getId());

		para = kineticLaw->createParameter();
		std::map<std::string,double>::iterator it = params->find("delta");
		para->setId(it->first);
		para->setValue(it->second);
		
		reaction->setKineticLaw (kineticLaw);
		model->addReaction (reaction);
	}
	
	// PRINT FILE
	SBMLWriter sbmlWriter;
	sbmlWriter.writeSBML(sbmlDoc, filename);
	
	delete sbmlDoc;
}