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@skeating
skeating committed Dec 28, 2024
1 parent 62f3daa commit 6a03580
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Showing 4 changed files with 217 additions and 305 deletions.
211 changes: 106 additions & 105 deletions src/sbml/conversion/ExpressionAnalyser.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -123,18 +123,23 @@ ExpressionAnalyser::clone() const
* Destroy this object.
*/
ExpressionAnalyser::~ExpressionAnalyser ()
{
for (std::vector<std::pair<std::string, ASTNode*> >::iterator it = mODEs.begin(); it != mODEs.end(); ++it)
{
if (it->second != NULL)
{
delete it->second;
it->second = NULL;
}
}
mODEs.clear();
{
// these are owned by the converter
//for (std::vector<std::pair<std::string, ASTNode*> >::iterator it = mODEs.begin(); it != mODEs.end(); ++it)
//{
// if (it->second != NULL)
// {
// delete it->second;
// it->second = NULL;
// }
//}
//mODEs.clear();
SBMLTransforms::clearComponentValues(mModel);
mHiddenSpecies = NULL;
if (mExpressions.size() > 0)
{
mExpressions.clear();
}
}

/*
Expand All @@ -156,13 +161,13 @@ ExpressionAnalyser::setModel(Model* model)
{
SBMLTransforms::clearComponentValues(mModel);
mModel = model;
SBMLTransforms::mapComponentValues(model);
SBMLTransforms::mapComponentValues(mModel);
return LIBSBML_OPERATION_SUCCESS;
}

void ExpressionAnalyser::substituteParametersForExpressions()
{
if (mHiddenSpecies == NULL || mExpressions.empty())
if (mExpressions.empty())
return;

// need to actually address the expressions in the correct order
Expand All @@ -184,6 +189,10 @@ void ExpressionAnalyser::substituteParametersForExpressions()
std::string zName = getUniqueNewParameterName();
exp->z_value = zName;
mNewVarCount++;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(zName.c_str());
exp->z_expression = z->deepCopy();
delete z;
}
else if (j > 0 &&
exp->type == TYPE_K_PLUS_V_MINUS_X_MINUS_Y &&
Expand Down Expand Up @@ -366,16 +375,13 @@ bool ExpressionAnalyser::parentExpressionExists(SubstitutionValues_t* current, S
switch (current->type)
{
case TYPE_K_MINUS_X_MINUS_Y:
parentExists = parentExists && mightAdd->type == TYPE_K_MINUS_X;
parentExists = mightAdd->type == TYPE_K_MINUS_X;
break;
case TYPE_K_PLUS_V_MINUS_X_MINUS_Y:
switch (mightAdd->type)
{
case TYPE_K_PLUS_V_MINUS_X:
parentExists = parentExists && matchesVExpression(current, mightAdd);
break;
case TYPE_K_MINUS_X:
parentExists = true;
parentExists = matchesVExpression(current, mightAdd);
break;
default:
parentExists = false;
Expand All @@ -388,9 +394,6 @@ bool ExpressionAnalyser::parentExpressionExists(SubstitutionValues_t* current, S
case TYPE_K_MINUS_X:
parentExists = true;
break;
case TYPE_K_MINUS_X_MINUS_Y:
parentExists = parentExists && matchesYValue(current, mightAdd);
break;
default:
parentExists = false;
break;
Expand Down Expand Up @@ -633,78 +636,76 @@ ExpressionAnalyser::getODEFor(std::string name)
return zero->deepCopy();
}

//-//ExpressionAnalyser::detect_minusXPlusYOnly()
//{
// for (unsigned int odeIndex = 0; odeIndex < mODEs.size(); odeIndex++)
// {
// std::pair<std::string, ASTNode*> ode = mODEs.at(odeIndex);
// ASTNode* odeRHS = ode.second;
// //odeRHS->decompose();
// odeRHS->reduceToBinary();
// odeRHS->decompose();
// List* operators = odeRHS->getListOfNodes((ASTNodePredicate)ASTNode_isOperator);
// ListIterator it = operators->begin();
//
// while (it != operators->end())
// {
// ASTNode* currentNode = (ASTNode*)*it;
// cout << "current node in not -x+y analyze: " << SBML_formulaToL3String(currentNode) << endl;
// if (currentNode->getType() != AST_PLUS)
// {
// it++;
// continue;
// }
// SubstitutionValues_t* value = createBlankSubstitutionValues();
// unsigned int numChildren = currentNode->getNumChildren();
// ASTNode* rightChild = currentNode->getRightChild();
// ASTNode* leftChild = currentNode->getLeftChild();
// // -x+y node binary; plus; left child type minus; rightchild var/const
// // +
// // - y
// // x
// if (numChildren != 2 || rightChild->getType() != AST_NAME
// || leftChild->getType() != AST_MINUS
// || leftChild->getNumChildren() != 1)
// {
// it++;
// continue;
// }
//
// // if we get to this point, the only thing left to check is
// // whether the ->left->right grandchild (the x in -x+y) is a variable species.
// if (isVariableSpeciesOrParameter(leftChild->getChild(0)))
// {
// value->x_value = leftChild->getChild(0)->getName();
// value->y_value = rightChild->getName();
// value->dydt_expression = getODEFor(rightChild->getName());
// value->dxdt_expression = getODEFor(leftChild->getChild(0)->getName());
// value->type = TYPE_MINUS_X_PLUS_Y;
// value->current = currentNode;
// value->odeIndex = odeIndex;
// //if (shouldAddExpression(value))
// ////{
// // printSubstitutionValues(value);
// // mExpressions.push_back(value);
// //}
//
// }
//
// it++;
// }
// }
//
//}
void
ExpressionAnalyser::detect_minusXPlusYOnly()
{
for (unsigned int odeIndex = 0; odeIndex < mODEs.size(); odeIndex++)
{
std::pair<std::string, ASTNode*> ode = mODEs.at(odeIndex);
ASTNode* odeRHS = ode.second;
//odeRHS->decompose();
odeRHS->reduceToBinary();
odeRHS->decompose();
List* operators = odeRHS->getListOfNodes((ASTNodePredicate)ASTNode_isOperator);
ListIterator it = operators->begin();

while (it != operators->end())
{
ASTNode* currentNode = (ASTNode*)*it;
cout << "current node in not -x+y analyze: " << SBML_formulaToL3String(currentNode) << endl;
if (currentNode->getType() != AST_PLUS)
{
it++;
continue;
}
SubstitutionValues_t* value = createBlankSubstitutionValues();
unsigned int numChildren = currentNode->getNumChildren();
ASTNode* rightChild = currentNode->getRightChild();
ASTNode* leftChild = currentNode->getLeftChild();
// -x+y node binary; plus; left child type minus; rightchild var/const
// +
// - y
// x
if (numChildren != 2 || rightChild->getType() != AST_NAME
|| leftChild->getType() != AST_MINUS
|| leftChild->getNumChildren() != 1)
{
it++;
continue;
}

// if we get to this point, the only thing left to check is
// whether the ->left->right grandchild (the x in -x+y) is a variable species.
if (isVariableSpeciesOrParameter(leftChild->getChild(0)))
{
value->x_value = leftChild->getChild(0)->getName();
value->y_value = rightChild->getName();
value->dydt_expression = getODEFor(rightChild->getName());
value->dxdt_expression = getODEFor(leftChild->getChild(0)->getName());
value->type = TYPE_MINUS_X_PLUS_Y;
value->current = currentNode;
value->odeIndex = odeIndex;
//if (shouldAddExpression(value))
////{
// printSubstitutionValues(value);
// mExpressions.push_back(value);
//}

}

it++;
}
}

}
void
ExpressionAnalyser::analyse(bool minusXPlusYOnly)
ExpressionAnalyser::analyse()
{
for (unsigned int odeIndex = 0; odeIndex < mODEs.size(); odeIndex++)
{
std::pair<std::string, ASTNode*> ode = mODEs.at(odeIndex);
ASTNode* odeRHS = ode.second;
odeRHS->decompose();
odeRHS->reduceToBinary();
ASTNodeLevels operators = odeRHS->getListOfNodesWithLevel();
odeRHS->refactor();
ASTNodeLevels operators = odeRHS->getListOfNodesWithLevel(true);
ASTNodeLevelsIterator it = operators.begin();

while (it != operators.end())
Expand All @@ -719,7 +720,7 @@ ExpressionAnalyser::analyse(bool minusXPlusYOnly)
value->levelInExpression = currentNode.first;
if (shouldAddExpression(value, currentNode))
{
printSubstitutionValues(value);
//printSubstitutionValues(value);
mExpressions.push_back(value);
}
}
Expand Down Expand Up @@ -1229,24 +1230,24 @@ bool ExpressionAnalyser::isNumericalConstantOrConstantParameter(ASTNode* node, b
* Reorder any instance of - x + y with y - x in the set of ODEs.
* Fages Algorithm 3.1 Step 1
*/
void ExpressionAnalyser::reorderMinusXPlusYIteratively()
{
for (unsigned int i = 0; i < mExpressions.size(); i++)
{
SubstitutionValues_t* exp = mExpressions.at(i);
if (exp->type != TYPE_MINUS_X_PLUS_Y)
continue;
ASTNode* ode = (mODEs.at(exp->odeIndex)).second;
ASTNode* replacement = new ASTNode(AST_MINUS);
ASTNode* y = new ASTNode(AST_NAME);
y->setName((exp->y_value).c_str());
ASTNode* x = new ASTNode(AST_NAME);
x->setName((exp->x_value).c_str());
replacement->addChild(y);
replacement->addChild(x);
replaceExpressionInNodeWithNode(ode, exp->current, replacement);
}
}
//void ExpressionAnalyser::reorderMinusXPlusYIteratively()
//{
// for (unsigned int i = 0; i < mExpressions.size(); i++)
// {
// SubstitutionValues_t* exp = mExpressions.at(i);
// if (exp->type != TYPE_MINUS_X_PLUS_Y)
// continue;
// ASTNode* ode = (mODEs.at(exp->odeIndex)).second;
// ASTNode* replacement = new ASTNode(AST_MINUS);
// ASTNode* y = new ASTNode(AST_NAME);
// y->setName((exp->y_value).c_str());
// ASTNode* x = new ASTNode(AST_NAME);
// x->setName((exp->x_value).c_str());
// replacement->addChild(y);
// replacement->addChild(x);
// replaceExpressionInNodeWithNode(ode, exp->current, replacement);
// }
//}

std::pair<ASTNode*, int> ExpressionAnalyser::getParentNode(const ASTNode* child, const ASTNode* root)
{
Expand Down
6 changes: 3 additions & 3 deletions src/sbml/conversion/ExpressionAnalyser.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@ class LIBSBML_EXTERN ExpressionAnalyser

bool analyseNode(ASTNode* node, SubstitutionValues_t* value);

void analyse(bool minusXPlusYOnly = false);
void analyse();

void orderExpressions();

Expand All @@ -180,9 +180,9 @@ class LIBSBML_EXTERN ExpressionAnalyser
* identify instances of - x + y within formula and create expressions
*
*/
void detect_minusXPlusYOnly();
//void detect_minusXPlusYOnly();

void reorderMinusXPlusYIteratively();
//void reorderMinusXPlusYIteratively();

private:
/** @cond doxygenLibsbmlInternal */
Expand Down
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