C++ SpeciesReference::isSetStoichiometryMath方法代码示例

void checkSpeciesRefs(Model* model, ListOfSpeciesReferences* losr, set<string>& components, set<string>& tests,  const map<string, vector<double> >& results)
{
  for (unsigned int rp=0; rp<losr->size(); rp++) {
    SpeciesReference* sr = static_cast<SpeciesReference*>(losr->get(rp));
    if (sr->isSetStoichiometry() && sr->getStoichiometry() != 1) {
      tests.insert("NonUnityStoichiometry");
    }
    if (sr->isSetStoichiometryMath()) {
      tests.insert("NonUnityStoichiometry");
      components.insert("StoichiometryMath");
      if (variesIn(sr->getStoichiometryMath()->getMath(), model, results)) {
        tests.insert("AssignedVariableStoichiometry");
      }
      else {
        tests.insert("AssignedConstantStoichiometry");
      }
    }
    else if (sr->isSetId()) {
      double initialResult = 1;
      if (results.find(sr->getId()) != results.end()) {
        tests.insert("SpeciesReferenceOutput");
      }
      if (variesIn(sr->getId(), model, results)) {
        tests.insert("AssignedVariableStoichiometry");
        tests.insert("NonUnityStoichiometry");
      }
      else if (initialOverriddenIn(sr->getId(), model, results, tests)) {
        tests.insert("AssignedConstantStoichiometry");
        if (getInitialResultFor(sr->getId(), results, initialResult)) {
          if (initialResult != 1) {
            tests.insert("NonUnityStoichiometry");
          }
        }
        else {
          //Don't know what the actual initial result is, so we'll assume it's not 1.0.
          tests.insert("NonUnityStoichiometry");
        }
      }
      if (initialOverriddenIn(sr->getId(), model, results, tests)) {
        tests.insert("InitialValueReassigned");
      }
      if (foundInMath(sr->getId(), model)) {
        tests.insert("SpeciesReferenceInMath");
      }
    }
  }
}

void
Model::convertStoichiometryMath()
{
  unsigned int n, j;
  Reaction * r;
  SpeciesReference *sr;
  unsigned int idCount = 0;
  char newid[15];
  std::string id;

  for (n = 0; n < getNumReactions(); n++)
  {
    r = getReaction(n);
    for (j = 0; j < r->getNumReactants(); j++)
    {
      sr = r->getReactant(j);
      if (sr->isSetStoichiometryMath())
      {
        if (!sr->isSetId())
        {
          sprintf(newid, "generatedId_%u", idCount);
          id.assign(newid);
          sr->setId(id);
          idCount++;
        }
        else
        {
          id = sr->getId();
        }
        sr->setConstant(false);

        AssignmentRule * ar = createAssignmentRule();
        ar->setVariable(id);
        if (sr->getStoichiometryMath()->isSetMath())
        {
          ar->setMath(sr->getStoichiometryMath()->getMath());
        }
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      sr = r->getProduct(j);
      if (sr->isSetStoichiometryMath())
      {
        if (!sr->isSetId())
        {
          sprintf(newid, "generatedId_%u", idCount);
          id.assign(newid);
          sr->setId(id);
          idCount++;
        }
        else
        {
          id = sr->getId();
        }

        sr->setConstant(false);
        AssignmentRule * ar = createAssignmentRule();
        ar->setVariable(id);
        if (sr->getStoichiometryMath()->isSetMath())
        {
          ar->setMath(sr->getStoichiometryMath()->getMath());
        }
      }
    }
  }
}

void dealWithAssigningL1Stoichiometry(Model & m, bool l2)
{
  //char newid[15];
  std::string id;

  for (unsigned int i = 0; i < m.getNumReactions(); i++)
  {
    Reaction *r = m.getReaction(i);
    unsigned int j;

    for (j = 0; j < r->getNumReactants(); j++)
    {
      SpeciesReference *sr = r->getReactant(j);
      // we do not get here unless the stoichiometryMath is an integer
      // or a rational 
      if (l2 == true && sr->isSetStoichiometryMath() == true)
      {
        const ASTNode* ast = sr->getStoichiometryMath()->getMath();
        if (ast->isInteger())
        {
          int num = ast->getInteger();
          sr->setStoichiometry(num);
          sr->setDenominator(1);
        }
        else
        {
          int num = ast->getNumerator();
          int denom = ast->getDenominator();
          sr->setStoichiometry(num);
          sr->setDenominator(denom);
        }
        sr->unsetStoichiometryMath();
      }
      else
      {
        sr->setStoichiometry(sr->getStoichiometry());
        sr->setDenominator(1);
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      SpeciesReference *sr = r->getProduct(j);
      // we do not get here unless the stoichiometryMath is an integer
      // or a rational 
      if (l2 == true && sr->isSetStoichiometryMath() == true)
      {
        const ASTNode* ast = sr->getStoichiometryMath()->getMath();
        if (ast->isInteger())
        {
          int num = ast->getInteger();
          sr->setStoichiometry(num);
          sr->setDenominator(1);
        }
        else
        {
          int num = ast->getNumerator();
          int denom = ast->getDenominator();
          sr->setStoichiometry(num);
          sr->setDenominator(denom);
        }
        sr->unsetStoichiometryMath();
      }
      else
      {
        sr->setStoichiometry(sr->getStoichiometry());
        sr->setDenominator(1);
      }
    }
  }
}

void
Model::assignRequiredValues()
{
  // when converting to L3 some attributes which have default values in L1/L2
  // but are required in L3 are not present or set
  unsigned int i, n;

  if (getNumUnitDefinitions() > 0)
  {
    for (i = 0; i < getNumUnitDefinitions(); i++)
    {
      for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
      {
        Unit *u = getUnitDefinition(i)->getUnit(n);
        if (!u->isSetExponent())
          u->setExponent(1.0);
        if (!u->isSetScale())
          u->setScale(0);
        if (!u->isSetMultiplier())
          u->setMultiplier(1.0);
      }
    }
  }
  
  if (getNumCompartments() > 0)
  {
    for (i = 0; i < getNumCompartments(); i++)
    {
      Compartment *c = getCompartment(i);
      c->setConstant(c->getConstant());
    }
  }
  if (getNumSpecies() > 0)
  {
    for (i = 0; i < getNumSpecies(); i++)
    {
      Species * s = getSpecies(i);
      s->setBoundaryCondition(s->getBoundaryCondition());
      s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
      s->setConstant(s->getConstant());
    }
  }
  if (getNumParameters() > 0)
  {
    for (i = 0; i < getNumParameters(); i++)
    {
      Parameter * p = getParameter(i);
      p->setConstant(p->getConstant());
    }
  }
  if (getNumReactions() > 0)
  {
    for (i = 0; i < getNumReactions(); i++)
    {
      Reaction * r = getReaction(i);
      r->setFast(r->getFast());
      r->setReversible(r->getReversible());
      if (r->getNumReactants() > 0)
      {
        for (n = 0; n < r->getNumReactants(); n++)
        {
          SpeciesReference *sr = r->getReactant(n);
          if (sr->isSetStoichiometryMath())
          {
            sr->setConstant(false);
          }
          else
          {
            sr->setConstant(true);
          }
        }
      }
      if (r->getNumProducts() > 0)
      {
        for (n = 0; n < r->getNumProducts(); n++)
        {
          SpeciesReference *sr = r->getProduct(n);
          if (sr->isSetStoichiometryMath())
          {
            sr->setConstant(false);
          }
          else
          {
            sr->setConstant(true);
          }
        }
      }
    }
  }
  if (getNumEvents() > 0)
  {
    for (i = 0; i < getNumEvents(); i++)
    {
      Event * e = getEvent(i);
      e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());

      if (e->isSetTrigger())
      {
        Trigger *t = e->getTrigger();
        t->setPersistent(true);
//.........这里部分代码省略.........

//.........这里部分代码省略.........
        Compartment *c = model->getCompartment(i);
        cout << "Compartment " << i << ": "
             << UnitDefinition::printUnits(c->getDerivedUnitDefinition())
             << endl;
    }

    for (i = 0; i < model->getNumParameters(); i++)
    {
        Parameter *p = model->getParameter(i);
        cout << "Parameter " << i << ": "
             << UnitDefinition::printUnits(p->getDerivedUnitDefinition())
             << endl;
    }


    for (i = 0; i < model->getNumInitialAssignments(); i++)
    {
        InitialAssignment *ia = model->getInitialAssignment(i);
        cout << "InitialAssignment " << i << ": "
             << UnitDefinition::printUnits(ia->getDerivedUnitDefinition()) << endl;
        cout << "        undeclared units: ";
        cout << (ia->containsUndeclaredUnits() ? "yes\n" : "no\n");
    }

    for (i = 0; i < model->getNumEvents(); i++)
    {
        Event *e = model->getEvent(i);
        cout << "Event " << i << ": " << endl;

        if (e->isSetDelay())
        {
            cout << "Delay: "
                 << UnitDefinition::printUnits(e->getDelay()->getDerivedUnitDefinition()) << endl;
            cout << "        undeclared units: ";
            cout << (e->getDelay()->containsUndeclaredUnits() ? "yes\n" : "no\n");
        }

        for (j = 0; j < e->getNumEventAssignments(); j++)
        {
            EventAssignment *ea = e->getEventAssignment(j);
            cout << "EventAssignment " << j << ": "
                 << UnitDefinition::printUnits(ea->getDerivedUnitDefinition()) << endl;
            cout << "        undeclared units: ";
            cout << (ea->containsUndeclaredUnits() ? "yes\n" : "no\n");
        }
    }

    for (i = 0; i < model->getNumReactions(); i++)
    {
        Reaction *r = model->getReaction(i);

        cout << "Reaction " << i << ": " << endl;

        if (r->isSetKineticLaw())
        {
            cout << "Kinetic Law: "
                 << UnitDefinition::printUnits(r->getKineticLaw()->getDerivedUnitDefinition()) << endl;
            cout << "        undeclared units: ";
            cout << (r->getKineticLaw()->containsUndeclaredUnits() ? "yes\n" : "no\n");
        }

        for (j = 0; j < r->getNumReactants(); j++)
        {
            SpeciesReference *sr = r->getReactant(j);

            if (sr->isSetStoichiometryMath())
            {
                cout << "Reactant stoichiometryMath" << j << ": "
                     << UnitDefinition::printUnits(sr->getStoichiometryMath()->getDerivedUnitDefinition()) << endl;
                cout << "        undeclared units: ";
                cout << (sr->getStoichiometryMath()->containsUndeclaredUnits() ? "yes\n" : "no\n");
            }
        }

        for (j = 0; j < r->getNumProducts(); j++)
        {
            SpeciesReference *sr = r->getProduct(j);

            if (sr->isSetStoichiometryMath())
            {
                cout << "Product stoichiometryMath" << j << ": "
                     << UnitDefinition::printUnits(sr->getStoichiometryMath()->getDerivedUnitDefinition()) << endl;
                cout << "        undeclared units: ";
                cout << (sr->getStoichiometryMath()->containsUndeclaredUnits() ? "yes\n" : "no\n");
            }
        }
    }

    for (i = 0; i < model->getNumRules(); i++)
    {
        Rule *r = model->getRule(i);
        cout << "Rule " << i << ": "
             << UnitDefinition::printUnits(r->getDerivedUnitDefinition()) << endl;
        cout << "        undeclared units: ";
        cout << (r->containsUndeclaredUnits() ? "yes\n" : "no\n");
    }

    delete document;
    return 0;
}