Example #1
0
void Submodel::convertCSymbols(ASTNode*& math, const ASTNode* tcfdiv, const ASTNode* tcftimes)
{
  if (tcfdiv==NULL) return;
  if (math->getType()==AST_NAME_TIME) {
    ASTNode* div = tcfdiv->deepCopy();
    div->insertChild(0, math);
    math = div;
    return;
  }
  for (unsigned int ch=0; ch<math->getNumChildren(); ch++) {
    ASTNode* child = math->getChild(ch);
    convertCSymbols(child, tcfdiv, tcftimes);
    if (child != math->getChild(ch)) {
      math->removeChild(ch);
      math->insertChild(ch, child);
    }
  }
  if (math->getType()==AST_FUNCTION_DELAY) {
    if (math->getNumChildren() != 2) return;
    ASTNode* timechild = math->getChild(1);
    ASTNode* newtime = tcftimes->deepCopy();
    newtime->addChild(timechild);
    math->removeChild(1);
    math->addChild(newtime);
  }
}
Example #2
0
int Submodel::convertTimeAndExtentWith(const ASTNode* tcf, const ASTNode* xcf, const ASTNode* klmod)
{
  if (tcf==NULL && xcf==NULL) return LIBSBML_OPERATION_SUCCESS;
  Model* model = getInstantiation();
  if (model==NULL) {
    //getInstantiation sets its own error messages.
    return LIBSBML_OPERATION_FAILED;
  }
  ASTNode* tcftimes = NULL;
  ASTNode* tcfdiv = NULL;
  if (tcf != NULL) {
    tcftimes = new ASTNode(AST_TIMES);
    tcftimes->addChild(tcf->deepCopy());
    tcfdiv = new ASTNode(AST_DIVIDE);
    tcfdiv->addChild(tcf->deepCopy());
  }
  ASTNode* rxndivide = NULL;
  if (klmod != NULL) {
    rxndivide = new ASTNode(AST_DIVIDE);
    ASTNode rxnref(AST_NAME);
    rxndivide->addChild(rxnref.deepCopy());
    rxndivide->addChild(klmod->deepCopy());
  }
  List* allelements = model->getAllElements();
  for (unsigned int el=0; el<allelements->getSize(); el++) {
    SBase* element = static_cast<SBase*>(allelements->get(el));
    assert(element != NULL);
    ASTNode* ast1 = NULL;
    ASTNode* ast2 = NULL;
    Constraint* constraint = NULL;
    Delay* delay = NULL;
    EventAssignment* ea = NULL;
    InitialAssignment* ia = NULL;
    KineticLaw* kl = NULL;
    Priority* priority = NULL;
    RateRule* rrule = NULL;
    Rule* rule = NULL;
    Submodel* submodel = NULL;
    Trigger* trigger = NULL;
    string cf = "";
    //Reaction math will be converted below, in the bits with the kinetic law.  But because of that, we need to handle references *to* the reaction:  even if it has no kinetic law, the units have changed, and this needs to be reflected by the flattening routine.
    if (rxndivide != NULL && element->getTypeCode()==SBML_REACTION && element->isSetId()) {
      rxndivide->getChild(0)->setName(element->getId().c_str());
      for (unsigned int sube=0; sube<allelements->getSize(); sube++) {
        SBase* subelement = static_cast<SBase*>(allelements->get(sube));
        subelement->replaceSIDWithFunction(element->getId(), rxndivide);
      }
    }

    //Submodels need their timeConversionFactor and extentConversionFactor attributes converted.  We're moving top-down, so all we need to do here is fix the conversion factor attributes themselves, pointing them to new parameters if need be.
    if ((tcf !=NULL || xcf != NULL) && element->getTypeCode()==SBML_COMP_SUBMODEL) {
      submodel = static_cast<Submodel*>(element);
      if (tcf != NULL) {
        if (submodel->isSetTimeConversionFactor()) {
          createNewConversionFactor(cf, tcf, submodel->getTimeConversionFactor(), model);
          submodel->setTimeConversionFactor(cf);
        }
        else {
          submodel->setTimeConversionFactor(tcf->getName());
        }
      }
      if (xcf != NULL) {
        if (submodel->isSetExtentConversionFactor()) {
          createNewConversionFactor(cf, xcf, submodel->getExtentConversionFactor(), model);
          submodel->setExtentConversionFactor(cf);
        }
        else {
          submodel->setExtentConversionFactor(xcf->getName());
        }
      }
    }
    if (tcf==NULL) {
      if (klmod !=NULL && element->getTypeCode()==SBML_KINETIC_LAW) {
        kl = static_cast<KineticLaw*>(element);
        if (kl->isSetMath()) {
          ast1 = new ASTNode(AST_TIMES);
          ast1->addChild(klmod->deepCopy());
          ast1->addChild(kl->getMath()->deepCopy());
          kl->setMath(ast1);
          delete ast1;
        }
      }
    }
    else {
      // All math 'time' and 'delay' csymbols must still be converted.
      // Also, several constructs are modified directly.
      switch(element->getTypeCode()) {
        //This would be a WHOLE LOT SIMPLER if there was a 'hasMath' class in libsbml.  But even so, it would have to
        // handle the kinetic laws, rate rules, and delays separately.
      case SBML_KINETIC_LAW:
        //Kinetic laws are multiplied by 'klmod'.
        kl = static_cast<KineticLaw*>(element);
        ast1 = kl->getMath()->deepCopy();
        convertCSymbols(ast1, tcfdiv, tcftimes);
        if (klmod !=NULL) {
          kl = static_cast<KineticLaw*>(element);
          if (kl->isSetMath()) {
            ast2 = new ASTNode(AST_TIMES);
            ast2->addChild(klmod->deepCopy());
            ast2->addChild(ast1);
            kl->setMath(ast2);
            delete ast2;
          }
        }
        else {
          kl->setMath(ast1);
          delete ast1;
        }
        break;
      case SBML_DELAY:
        //Delays are multiplied by the time conversion factor.
        delay = static_cast<Delay*>(element);
        if (delay->isSetMath()) {
          ast1 = delay->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          tcftimes->addChild(ast1);
          delay->setMath(tcftimes);
          tcftimes->removeChild(1);
        }
        break;
      case SBML_RATE_RULE:
        //Rate rules are divided by the time conversion factor.
        rrule = static_cast<RateRule*>(element);
        if (rrule->isSetMath()) {
          ast1 = rrule->getMath()->deepCopy();
          tcfdiv->insertChild(0, rrule->getMath()->deepCopy());
          rrule->setMath(tcfdiv);
          tcfdiv->removeChild(0);
        }
        //Fall through to:
      case SBML_ASSIGNMENT_RULE:
      case SBML_ALGEBRAIC_RULE:
        //Rules in general need csymbols converted.
        rule = static_cast<Rule*>(element);
        if (rule->isSetMath()) {
          ast1 = rule->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          rule->setMath(ast1);
          delete ast1;
        }
        break;
      case SBML_EVENT_ASSIGNMENT:
        //Event assignments need csymbols converted.
        ea = static_cast<EventAssignment*>(element);
        if (ea->isSetMath()) {
          ast1 = ea->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          ea->setMath(ast1);
          delete ast1;
        }
        break;
      case SBML_INITIAL_ASSIGNMENT:
        //Initial assignments need csymbols converted.
        ia = static_cast<InitialAssignment*>(element);
        if (ia->isSetMath()) {
          ast1 = ia->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          ia->setMath(ast1);
          delete ast1;
        }
        break;
      case SBML_CONSTRAINT:
        //Constraints need csymbols converted.
        constraint = static_cast<Constraint*>(element);
        if (constraint->isSetMath()) {
          ast1 = constraint->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          constraint->setMath(ast1);
          delete ast1;
        }
        break;
      case SBML_PRIORITY:
        //Priorities need csymbols converted.
        priority = static_cast<Priority*>(element);
        if (priority->isSetMath()) {
          ast1 = priority->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          priority->setMath(ast1);
          delete ast1;
        }
        break;
      case SBML_TRIGGER:
        //Triggers need csymbols converted.
        trigger = static_cast<Trigger*>(element);
        if (trigger->isSetMath()) {
          ast1 = trigger->getMath()->deepCopy();
          convertCSymbols(ast1, tcfdiv, tcftimes);
          trigger->setMath(ast1);
          delete ast1;
        }
        break;
      default:
        //Do nothing!  If we wanted to call a plugin routine, this would be the place.  The only other alternative is to #ifdef some code in here that deals with the math-containing package objects explicitly.  Which might be the best option, all told.
        break;
      }
    }
  }

  delete allelements;

  return LIBSBML_OPERATION_SUCCESS;
}