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so in fixing one thing I've broken another
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@skeating
skeating committed Jan 28, 2025
1 parent 1018c4c commit c4a131d
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Showing 3 changed files with 171 additions and 83 deletions.
80 changes: 39 additions & 41 deletions src/sbml/conversion/ExpressionAnalyser.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,8 @@ ExpressionAnalyser::ExpressionAnalyser()
mODEs (),
mNewVarName("newVar"),
mNewVarCount(1),
mHiddenSpecies (NULL)
mHiddenSpecies (NULL),
mHiddenNodes (NULL)
{
}

Expand All @@ -82,7 +83,8 @@ ExpressionAnalyser::ExpressionAnalyser(Model * m, pairODEs odes)
mODEs(odes),
mNewVarName("newVar"),
mNewVarCount(1),
mHiddenSpecies(NULL)
mHiddenSpecies(NULL),
mHiddenNodes(NULL)
{
SBMLTransforms::mapComponentValues(mModel);
mModel->populateAllElementIdList();
Expand All @@ -93,7 +95,8 @@ ExpressionAnalyser::ExpressionAnalyser(const ExpressionAnalyser& orig) :
mODEs(orig.mODEs),
mNewVarName(orig.mNewVarName),
mNewVarCount(orig.mNewVarCount),
mHiddenSpecies(orig.mHiddenSpecies)
mHiddenSpecies(orig.mHiddenSpecies),
mHiddenNodes(orig.mHiddenNodes)
{
SBMLTransforms::mapComponentValues(mModel);
mModel->populateAllElementIdList();
Expand All @@ -112,6 +115,7 @@ ExpressionAnalyser::operator=(const ExpressionAnalyser& rhs)
mNewVarName = rhs.mNewVarName;
mNewVarCount = rhs.mNewVarCount;
mHiddenSpecies = rhs.mHiddenSpecies;
mHiddenNodes = rhs.mHiddenNodes;
}
SBMLTransforms::mapComponentValues(mModel);
mModel->populateAllElementIdList();
Expand All @@ -134,6 +138,7 @@ ExpressionAnalyser::~ExpressionAnalyser ()
// note the odes are owned by the converter
SBMLTransforms::clearComponentValues(mModel);
mHiddenSpecies = NULL;
mHiddenNodes = NULL;
if (mExpressions.size() > 0)
{
mExpressions.clear();
Expand All @@ -144,8 +149,8 @@ void ExpressionAnalyser::identifyHiddenSpeciesWithinExpressions()
{
if (mExpressions.empty())
return;
if (mHiddenSpecies == NULL)
mHiddenSpecies = new List();
if (mHiddenNodes == NULL)
mHiddenNodes = new List();

// need to actually address the expressions in the correct order
// replace k-x-y first with newParam type=TYPE_K_MINUS_X_MINUS_Y
Expand Down Expand Up @@ -238,32 +243,9 @@ void ExpressionAnalyser::identifyHiddenSpeciesWithinExpressions()
addNewParameterPlusVOrW(exp, "v");
}
}
//else if (exp->type == TYPE_K_PLUS_V_MINUS_X)
//{
// if (mExpressions[j - 1]->type == TYPE_K_MINUS_X)
// {
// // here we are dealing with the fact that we have k+v-x and k-x
//// need to check whether they have the same values for k,x
// if (matchesK(mExpressions[j - 1], exp) &&
// matchesXValue(mExpressions[j - 1], exp))
// {
// // the values are the same so we can use the same new parameter
// addPreviousParameterPlusVOrW(exp, mExpressions[j - 1], "v");
// }
// else
// {
// // if the type before was not k-x then we need to create a new parameter
// addNewParameterPlusVOrW(exp, "v");
// }
//}
//else
//{
// // if the type before was not k-x then we need to create a new parameter
// // because it doesn't matter what it was.
// addNewParameterPlusVOrW(exp, "v");
//}
}
}
}
substituteNodes();
}

void ExpressionAnalyser::substituteParameters(SubstitutionValues_t* exp)
Expand Down Expand Up @@ -337,7 +319,7 @@ void ExpressionAnalyser::addSingleNewParameter(SubstitutionValues_t* exp)
ASTNode* z = new ASTNode(AST_NAME);
z->setName(zName.c_str());
exp->z_expression = z->deepCopy();
mHiddenSpecies->add(z);
mHiddenNodes->add(z);
delete z;

}
Expand All @@ -354,7 +336,7 @@ void ExpressionAnalyser::addNewParameterPlusVOrW(SubstitutionValues_t* exp, std:
replacement->addChild(z);
replacement->addChild(var);
exp->z_expression = replacement->deepCopy();
mHiddenSpecies->add(z);
mHiddenNodes->add(z);
delete replacement;
}

Expand All @@ -373,6 +355,7 @@ void ExpressionAnalyser::addPreviousParameterPlusVOrW(SubstitutionValues_t* exp,
}



/*
* Check whether two SubstitutionValues_t match the values that we expect if we need to add them
* based on the type of the SubstitutionValues_t
Expand Down Expand Up @@ -517,12 +500,6 @@ bool ExpressionAnalyser::matchesDydtExpression(SubstitutionValues_t* values1, Su
values1->dydt_expression->exactlyEqual(*(values2->dydt_expression)) == true);
}

bool ExpressionAnalyser::matchesCurrentNode(SubstitutionValues_t* values1, SubstitutionValues_t* values2)
{
return (values1->current != NULL && values2->current != NULL &&
values1->current->exactlyEqual(*(values2->current)) == true);
}

bool ExpressionAnalyser::matchesType(SubstitutionValues_t* values1, SubstitutionValues_t* values2)
{
return values1->type == values2->type;
Expand Down Expand Up @@ -667,6 +644,17 @@ ExpressionAnalyser::getODEFor(std::string name)
zero->setValue(0.0);
return zero->deepCopy();
}

ASTNode*
ExpressionAnalyser::getODE(unsigned int odeIndex)
{
if (odeIndex < mODEs.size())
{
return mODEs.at(odeIndex).second;
}
return nullptr;
}

void
ExpressionAnalyser::analyse()
{
Expand Down Expand Up @@ -731,9 +719,9 @@ ExpressionAnalyser::replaceExpressionInNodeWithNode(ASTNode* node, ASTNode* repl
{
return;
}
//cout << "node: " << SBML_formulaToL3String(node) << endl;
//cout << "with: " << SBML_formulaToL3String(replaced) << endl;
//cout << "by: " << SBML_formulaToL3String(replacement) << endl;
cout << "node: " << SBML_formulaToL3String(node) << endl;
cout << "with: " << SBML_formulaToL3String(replaced) << endl;
cout << "by: " << SBML_formulaToL3String(replacement) << endl;
// we might be replcing the whole node
if (node == replaced)
{
Expand Down Expand Up @@ -773,6 +761,16 @@ ExpressionAnalyser::getUniqueNewParameterName()
return mNewVarName + std::to_string(mNewVarCount);
}

void ExpressionAnalyser::substituteNodes()
{
for (unsigned int i = 0; i < mExpressions.size(); i++)
{
SubstitutionValues_t* exp = mExpressions.at(i);
replaceExpressionInNodeWithNode(exp->current, exp->z_expression, getODE(exp->odeIndex)); //getODEFor(exp->current);
cout << "node: " << SBML_formulaToL3String(getODE(exp->odeIndex)) << endl;
}
}


void
ExpressionAnalyser::addParametersAndRateRules(SubstitutionValues_t* exp)
Expand Down
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