C++ Species::setInitialAmount方法代码示例

END_TEST

START_TEST ( test_Species_L1 )
{
  Species* s = new Species(1, 2);
  
  fail_unless (!(s->hasRequiredAttributes()));

  s->setId("s");

  fail_unless (!(s->hasRequiredAttributes()));

  s->setCompartment("c");

  fail_unless (!(s->hasRequiredAttributes()));

  s->setInitialAmount(2);

  fail_unless (s->hasRequiredAttributes());

  delete s;
}

END_TEST


START_TEST (test_WriteL3SBML_Species)
{
  const char* expected = 
    "<species id=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\""
    " substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\""
    " boundaryCondition=\"true\" constant=\"true\"/>";


  Species *s = D->createModel()->createSpecies();
  s->setId("Ca2");
  s->setCompartment("cell");
  s->setInitialAmount(0.7);
  s->setUnits("mole");
  s->setBoundaryCondition(true);
  s->setHasOnlySubstanceUnits(false);
  s->setConstant(true);

  char* sbml = s->toSBML();
  fail_unless( equals(expected, sbml) );
  safe_free(sbml);
}

//.........这里部分代码省略.........
  
  // Temporary pointer (reused more than once below).
  
  Species *sp;

  //---------------------------------------------------------------------------
  // (Species1) Creates a Species object ("ES")
  //---------------------------------------------------------------------------

  // Create the Species objects inside the Model object. 

  sp = model->createSpecies();
  sp->setId("ES");
  sp->setName("ES");

  // Sets the "compartment" attribute of the Species object to identify the 
  // compartment in which the Species object is located.

  sp->setCompartment(compName);

  // Sets the "initialAmount" attribute of the Species object.
  //
  //  In SBML, the units of a Species object's initial quantity are
  //  determined by two attributes, "substanceUnits" and
  //  "hasOnlySubstanceUnits", and the "spatialDimensions" attribute
  //  of the Compartment object ("cytosol") in which the species
  //  object is located.  Here, we are using the default values for
  //  "substanceUnits" (which is "mole") and "hasOnlySubstanceUnits"
  //  (which is "false").  The compartment in which the species is
  //  located uses volume units of liters, so the units of these
  //  species (when the species appear in numerical formulas in the
  //  model) will be moles/liters.  
  //
  sp->setInitialAmount(0);

  //---------------------------------------------------------------------------
  // (Species2) Creates a Species object ("P")
  //---------------------------------------------------------------------------

  sp = model->createSpecies();
  sp->setCompartment(compName);
  sp->setId("P");
  sp->setName("P");
  sp->setInitialAmount(0);

  //---------------------------------------------------------------------------
  // (Species3) Creates a Species object ("S")
  //---------------------------------------------------------------------------

  sp = model->createSpecies();
  sp->setCompartment(compName);
  sp->setId("S");
  sp->setName("S");
  sp->setInitialAmount(1e-20);

  //---------------------------------------------------------------------------
  // (Species4) Creates a Species object ("E")
  //---------------------------------------------------------------------------

  sp = model->createSpecies();
  sp->setCompartment(compName);
  sp->setId("E");
  sp->setName("E");
  sp->setInitialAmount(5e-21);

  

END_TEST

START_TEST(test_FbcExtension_read_and_validate_chemicals)
{
  FbcPkgNamespaces *ns = new FbcPkgNamespaces();
  SBMLDocument*doc = new SBMLDocument(ns);
  doc->setPackageRequired("fbc", false);
  Model* model = doc->createModel();
  Compartment* comp = model->createCompartment();
  comp->initDefaults();
  comp->setId("comp");
  comp->setSize(1);
  Species *s = model->createSpecies();
  s->initDefaults();
  s->setId("s1");
  s->setCompartment("comp");
  s->setInitialAmount(1);
  FbcSpeciesPlugin* splugin = static_cast<FbcSpeciesPlugin*>(s->getPlugin("fbc"));
  fail_unless(splugin != NULL);
  
  // valid 
  splugin->setChemicalFormula("H2O");
  doc->checkInternalConsistency();
  fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
  
  // valid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("HO");
  doc->checkInternalConsistency();
  fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // valid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("");
  doc->checkInternalConsistency();
  fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("h1O");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("1hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("_hO");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("H 2 O");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
  
  // invalid
  doc->getErrorLog()->clearLog();
  splugin->setChemicalFormula("H*_)(++2 O");
  doc->checkInternalConsistency();
  fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));

  delete doc;
}

/**
 * Save the gene network to an SBML file. If the argument is null, use the network id.
 * @param filename URL to the file describing the network to load
 * @throws IOException
 */
void GeneNetwork::writeSBML(const char *filename) {
			
	ofstream data_file(filename); 
    if (!data_file.is_open()) {
        std::cerr << "Failed to open file " << filename << std::endl;
        exit(1);
    }
    data_file.close();
			
	::logging::log::emit<Info>() << "Writing file " << filename <<
		::logging::log::endl;
	
	SBMLDocument *sbmlDoc = new SBMLDocument(3, 1);

	Model *model = sbmlDoc->createModel();
	model->setId(id_);
	//model.getNotes ().add (comment_); // save network description
	
	int size = getSize();
	
	Compartment *comp = model->createCompartment();
  	comp->setId("cell");
	comp->setSize(1);

	std::vector<Species*> all_sp;
	Species *sp;

	for (int s=0; s < size; s++) { // save gene as species
//			species[s] = new Species(nodeIds_.get(s), nodeIds_.get(s));
		sp = model->createSpecies();
  		sp->setCompartment("cell");
  		sp->setId((nodes_.at(s)).getLabel());
  		all_sp.push_back(sp);
		//species[s].setInitialAmount(?); // maybe save the wild-type steady state?
		//model.addSpecies(species[s]);
	}
	
	// create the void species
	sp = model->createSpecies();
  	sp->setCompartment("cell");
  	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;
//.........这里部分代码省略.........

void Module::CreateSBMLModel()
{
  Model* sbmlmod = m_sbml.createModel();
  sbmlmod->setId(m_modulename);
  sbmlmod->setName(m_modulename);
  sbmlmod->setNotes("<body xmlns=\"http://www.w3.org/1999/xhtml\"><p> Originally created by libAntimony " VERSION_STRING " (using libSBML " LIBSBML_DOTTED_VERSION ") </p></body>");
  char cc = g_registry.GetCC();
  //User-defined functions
  for (size_t uf=0; uf<g_registry.GetNumUserFunctions(); uf++) {
    const UserFunction* userfunction = g_registry.GetNthUserFunction(uf);
    assert(userfunction != NULL);
    FunctionDefinition* fd = sbmlmod->createFunctionDefinition();
    fd->setId(userfunction->GetModuleName());
    ASTNode* math = parseStringToASTNode(userfunction->ToSBMLString());
    fd->setMath(math);
    delete math;
  }
  //Compartments
  Compartment* defaultCompartment = sbmlmod->createCompartment();
  defaultCompartment->setId(DEFAULTCOMP);
  defaultCompartment->setConstant(true);
  defaultCompartment->setSize(1);
  defaultCompartment->setSBOTerm(410); //The 'implicit compartment'
  size_t numcomps = GetNumVariablesOfType(allCompartments);
  for (size_t comp=0; comp<numcomps; comp++) {
    const Variable* compartment = GetNthVariableOfType(allCompartments, comp);
    Compartment* sbmlcomp = sbmlmod->createCompartment();
    sbmlcomp->setId(compartment->GetNameDelimitedBy(cc));
    if (compartment->GetDisplayName() != "") {
      sbmlcomp->setName(compartment->GetDisplayName());
    }
    sbmlcomp->setConstant(compartment->GetIsConst());
    formula_type ftype = compartment->GetFormulaType();
    assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE);
    if (ftype != formulaINITIAL) {
      sbmlcomp->setConstant(false);
    }
    const Formula* formula = compartment->GetFormula();
    if (formula->IsDouble()) {
      sbmlcomp->setSize(atof(formula->ToSBMLString().c_str()));
    }
    SetAssignmentFor(sbmlmod, compartment);
  }

  //Species
  size_t numspecies = GetNumVariablesOfType(allSpecies);
  for (size_t spec=0; spec < numspecies; spec++) {
    const Variable* species = GetNthVariableOfType(allSpecies, spec);
    Species* sbmlspecies = sbmlmod->createSpecies();
    sbmlspecies->setId(species->GetNameDelimitedBy(cc));
    if (species->GetDisplayName() != "") {
      sbmlspecies->setName(species->GetDisplayName());
    }
    sbmlspecies->setConstant(false); //There's no need to try to distinguish between const and var for species.
    if (species->GetIsConst()) {
      sbmlspecies->setBoundaryCondition(true);
    }
    else {
      sbmlspecies->setBoundaryCondition(false);
    }
    const Variable* compartment = species->GetCompartment();
    if (compartment == NULL) {
      sbmlspecies->setCompartment(defaultCompartment->getId());
    }
    else {
      sbmlspecies->setCompartment(compartment->GetNameDelimitedBy(cc));
    }
    const Formula* formula = species->GetFormula();
    if (formula->IsDouble()) {
      sbmlspecies->setInitialConcentration(atof(formula->ToSBMLString().c_str()));
    }
    else if (formula->IsAmountIn(species->GetCompartment())) {
      sbmlspecies->setInitialAmount(formula->ToAmount());
    }
    SetAssignmentFor(sbmlmod, species);
  }

  //Formulas
  size_t numforms = GetNumVariablesOfType(allFormulas);
  for (size_t form=0; form < numforms; form++) {
    const Variable* formvar = GetNthVariableOfType(allFormulas, form);
    const Formula*  formula = formvar->GetFormula();
    Parameter* param = sbmlmod->createParameter();
    param->setId(formvar->GetNameDelimitedBy(cc));
    if (formvar->GetDisplayName() != "") {
      param->setName(formvar->GetDisplayName());
    }
    param->setConstant(formvar->GetIsConst());
    if (formula->IsDouble()) {
      param->setValue(atof(formula->ToSBMLString().c_str()));
    }
    SetAssignmentFor(sbmlmod, formvar);
    formula_type ftype = formvar->GetFormulaType();
    assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE);
    if (ftype != formulaINITIAL) {
      param->setConstant(false);
    }
  }

  //Reactions
//.........这里部分代码省略.........