void CFunction::load(CReadConfig & configBuffer,
CReadConfig::Mode mode)
{
// cleanup();
C_INT32 Type;
mode = CReadConfig::SEARCH;
configBuffer.getVariable("User-defined", "C_INT32", &Type, mode);
switch (Type)
{
case 1:
setType(UserDefined);
break;
default:
fatalError();
}
configBuffer.getVariable("Reversible", "C_INT32", &mReversible);
mode = CReadConfig::SEARCH;
std::string tmp;
configBuffer.getVariable("FunctionName", "string", &tmp, mode);
setObjectName(tmp);
configBuffer.getVariable("Description", "string", &tmp);
setInfix(tmp);
// For older file version the parameters have to be build from information
// dependend on the function type. Luckilly, only user defined functions are
// the only ones occuring in those files.
}
CMassAction::CMassAction(const TriLogic & reversible,
const CCopasiContainer * pParent):
CFunction((reversible == TriTrue) ?
"Mass action (reversible)" :
"Mass action (irreversible)",
pParent,
CFunction::MassAction)
{
CONSTRUCTOR_TRACE;
if (reversible != TriFalse && reversible != TriTrue)
CCopasiMessage(CCopasiMessage::ERROR, MCMassAction + 1);
if (reversible == TriTrue)
setInfix(Infix[0]);
else
setInfix(Infix[1]);
}
// This is only used when reading Gepasi Files
void CKinFunction::createParameters()
{
CCopasiVectorN < CFunctionParameter > Substrates;
CCopasiVectorN < CFunctionParameter > Products;
CCopasiVectorN < CFunctionParameter > Modifiers;
CCopasiVectorN < CFunctionParameter > Parameters;
CCopasiVectorN < CFunctionParameter > Volumes;
size_t i, imax = mNodes.size();
CFunctionParameter *pParameter;
for (i = 0; i < imax; i++)
{
if (mNodes[i]->getType() == N_IDENTIFIER)
{
// We need to check that we have no reserved name.
const char *Reserved[] =
{"pi", "exponentiale", "true", "false", "infinity", "nan",
"PI", "EXPONENTIALE", "TRUE", "FALSE", "INFINITY", "NAN"
};
std::string Name = mNodes[i]->getName();
size_t j, jmax = 12;
for (j = 0; j < jmax; j++)
if (Name == Reserved[j]) break;
if (j != jmax)
{
// It is save to prepend the identifyer with '_' since this is not allowed in
// Gepasi but within COPASI.
std::string OldName = Name;
Name = "_" + Name;
// We have to replace the corresponding CEvaluationNodes to reflect the change.
std::vector< CEvaluationNode * >::iterator it = mpNodeList->begin();
std::vector< CEvaluationNode * >::iterator end = mpNodeList->end();
for (; it != end; ++it)
if (((*it)->getType() & 0xFF000000) == CEvaluationNode::CONSTANT &&
(*it)->getData() == OldName)
(*it)->setData(Name);
// The Infix has changed we need to update it.
setInfix(mpRoot->buildInfix());
}
pParameter = new CFunctionParameter(Name);
pParameter->setType(CFunctionParameter::FLOAT64);
switch (mNodes[i]->getSubtype())
{
case N_SUBSTRATE:
pParameter->setUsage(CFunctionParameter::SUBSTRATE);
if (Substrates.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Substrates.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_PRODUCT:
pParameter->setUsage(CFunctionParameter::PRODUCT);
if (Products.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Products.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_MODIFIER:
pParameter->setUsage(CFunctionParameter::MODIFIER);
if (Modifiers.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Modifiers.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_KCONSTANT:
case N_NOP:
pParameter->setUsage(CFunctionParameter::PARAMETER);
if (Parameters.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Parameters.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_VOLUME:
pParameter->setUsage(CFunctionParameter::VOLUME);
if (Volumes.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Volumes.add(pParameter, false);
else
pdelete(pParameter);
break;
default:
pdelete(pParameter);
fatalError();
}
}
}
getVariables().cleanup();
imax = Substrates.size();
for (i = 0; i < imax; i++)
getVariables().add(Substrates[i], true);
Substrates.cleanup();
imax = Products.size();
for (i = 0; i < imax; i++)
getVariables().add(Products[i], true);
Products.cleanup();
imax = Modifiers.size();
for (i = 0; i < imax; i++)
getVariables().add(Modifiers[i], true);
Modifiers.cleanup();
imax = Parameters.size();
for (i = 0; i < imax; i++)
getVariables().add(Parameters[i], true);
Parameters.cleanup();
imax = Volumes.size();
for (i = 0; i < imax; i++)
getVariables().add(Volumes[i], true);
Volumes.cleanup();
}
