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it's a very good place save
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@skeating
skeating committed Jan 20, 2025
1 parent 17a80dd commit 9231b69
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Showing 3 changed files with 648 additions and 82 deletions.
274 changes: 197 additions & 77 deletions src/sbml/conversion/ExpressionAnalyser.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,8 @@ void ExpressionAnalyser::substituteParametersForExpressions()
{
if (mExpressions.empty())
return;
if (mHiddenSpecies == NULL)
mHiddenSpecies = 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 All @@ -194,71 +196,147 @@ void ExpressionAnalyser::substituteParametersForExpressions()
// and cannot rely on any other expression
if (j == 0)
{
std::string zName = getUniqueNewParameterName();
exp->z_value = zName;
mNewVarCount++;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(zName.c_str());
if (exp->type == TYPE_K_MINUS_X_MINUS_Y ||
exp->type == TYPE_K_MINUS_X)
{
// we have a value for k-x-y or k-x
exp->z_expression = z->deepCopy();
delete z;
addSingleNewParameter(exp);
}
else if (exp->type == TYPE_K_PLUS_V_MINUS_X_MINUS_Y ||
exp->type == TYPE_K_PLUS_V_MINUS_X)
{
// we have a value for k+v-x-y and no value for k-x-y
// we have a value for k+v-x and no value for k-x
ASTNode* replacement = new ASTNode(AST_PLUS);
ASTNode* v = exp->v_expression->deepCopy();
replacement->addChild(z);
replacement->addChild(v);
exp->z_expression = replacement->deepCopy();
delete replacement;
addNewParameterPlusVOrW(exp);
}
else if (exp->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y)
{
// we have a value for k-x+w-y and no value for k-x-y
ASTNode* replacement = new ASTNode(AST_PLUS);
ASTNode* w = exp->w_expression->deepCopy();
replacement->addChild(z);
replacement->addChild(w);
exp->z_expression = replacement->deepCopy();
delete replacement;
addNewParameterPlusVOrW(exp, "w");
}
}
else
else // j > 0 so not the first expression
{
std::string zName = getUniqueNewParameterName();
exp->z_value = zName;
mNewVarCount++;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(zName.c_str());
if (exp->type == TYPE_K_MINUS_X_MINUS_Y ||
exp->type == TYPE_K_MINUS_X)
if (exp->type == TYPE_K_MINUS_X_MINUS_Y)
{
// we have a different value for k-x-y or k-x
exp->z_expression = z->deepCopy();
delete z;
// we have a different value for k-x-y
// we know this because the expressions are in order and k-x-y is always first
// and the code that decides whether to add the expression well have checked that it is not identical
// so we if we have an expression of this type but is not first then it must be
// k-x-y but with a different value
addSingleNewParameter(exp);
}
else if (exp->type == TYPE_K_MINUS_X)
{
// k-x will always be replaced by a new variable
addSingleNewParameter(exp);
}
else if (exp->type == TYPE_K_PLUS_V_MINUS_X_MINUS_Y)
{
// we need to know what type of expression has come before
// deal with the case where the previous expression was the same type
if (mExpressions[j - 1]->type == TYPE_K_PLUS_V_MINUS_X_MINUS_Y)
{
// here we are dealing with the fact that we have k+v-x-y and k+v-x-a
// so we have two different expressions of the same type
// need to create a new parameter
addNewParameterPlusVOrW(exp);
}
else if (mExpressions[j - 1]->type == TYPE_K_MINUS_X_MINUS_Y)
{
// here we are dealing with the fact that we have k+v-x-y and k-x-y
// need to check whether they have the same values for k,x,y
if (matchesK(mExpressions[j - 1], exp) &&
matchesXValue(mExpressions[j - 1], exp) &&
matchesYValue(mExpressions[j - 1], exp))
{
// the values are the same so we can use the same new parameter
exp->z_value = mExpressions[j - 1]->z_value;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(mExpressions[j - 1]->z_value.c_str());
ASTNode* replacement = new ASTNode(AST_PLUS);
ASTNode* v = exp->v_expression->deepCopy();
replacement->addChild(z);
replacement->addChild(v);
exp->z_expression = replacement->deepCopy();
delete replacement;
}
else
{
addNewParameterPlusVOrW(exp);
}
}
}
else if (exp->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y)
{
// we need to know what type of expression has come before
// deal with the case where the previous expression was the same type
if (mExpressions[j - 1]->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y)
{
// here we are dealing with the fact that we have k-x+w-y and k-x+w-a
// so we have two different expressions of the same time
// need to create a new parameter
addNewParameterPlusVOrW(exp, "w");
}
else if (mExpressions[j - 1]->type == TYPE_K_MINUS_X_MINUS_Y)
{
// here we are dealing with the fact that we have k-x+w-y and k-x-y
// need to check whether they have the same values for k,x,y
if (matchesK(mExpressions[j - 1], exp) &&
matchesXValue(mExpressions[j - 1], exp) &&
matchesYValue(mExpressions[j - 1], exp))
{
// the values are the same so we can use the same new parameter
exp->z_value = mExpressions[j - 1]->z_value;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(mExpressions[j - 1]->z_value.c_str());
ASTNode* replacement = new ASTNode(AST_PLUS);
ASTNode* w = exp->w_expression->deepCopy();
replacement->addChild(z);
replacement->addChild(w);
exp->z_expression = replacement->deepCopy();
delete replacement;
}
else
{
addNewParameterPlusVOrW(exp, "w");
}
}
}
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,y
if (matchesK(mExpressions[j - 1], exp) &&
matchesXValue(mExpressions[j - 1], exp))
{
// the values are the same so we can use the same new parameter
exp->z_value = mExpressions[j - 1]->z_value;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(mExpressions[j - 1]->z_value.c_str());
ASTNode* replacement = new ASTNode(AST_PLUS);
ASTNode* v = exp->v_expression->deepCopy();
replacement->addChild(z);
replacement->addChild(v);
exp->z_expression = replacement->deepCopy();
delete replacement;
}
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");
}
}

}
//else if (j > 0 &&
// exp->type == TYPE_K_PLUS_V_MINUS_X_MINUS_Y &&
// exp->z_expression == NULL)
//{
// // we have a value for k-x-y
// ASTNode* replacement = new ASTNode(AST_PLUS);
// ASTNode* z = new ASTNode(AST_NAME);
// z->setName(mExpressions[j - 1]->z_value.c_str());
// ASTNode* v = exp->v_expression->deepCopy();
// replacement->addChild(z);
// replacement->addChild(v);
// exp->z_expression = replacement->deepCopy();

//}
}
}

Expand Down Expand Up @@ -307,6 +385,43 @@ SubstitutionValues_t* ExpressionAnalyser::getSubstitutionValuesByType(Expression
return NULL;
}

void ExpressionAnalyser::addSingleNewParameter(SubstitutionValues_t* exp)
{
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();
mHiddenSpecies->add(z);
delete z;

}

void ExpressionAnalyser::addNewParameterPlusVOrW(SubstitutionValues_t* exp, std::string vOrW)
{
ASTNode* var = NULL;
if (vOrW == "v")
{
var = exp->v_expression->deepCopy();
}
else
{
var = exp->w_expression->deepCopy();
}
std::string zName = getUniqueNewParameterName();
exp->z_value = zName;
mNewVarCount++;
ASTNode* z = new ASTNode(AST_NAME);
z->setName(zName.c_str());
ASTNode* replacement = new ASTNode(AST_PLUS);
replacement->addChild(z);
replacement->addChild(var);
exp->z_expression = replacement->deepCopy();
mHiddenSpecies->add(z);
delete replacement;
}

/*
* Check whether two SubstitutionValues_t are identical.
*/
Expand Down Expand Up @@ -525,45 +640,50 @@ bool ExpressionAnalyser::matchesType(SubstitutionValues_t* values1, Substitution
void
ExpressionAnalyser::printSubstitutionValues(const SubstitutionValues_t* values)
{
cout << "k_value: " << values->k_value << endl;
cout << "k_real_value: " << values->k_real_value << endl;
cout << "x_value: " << values->x_value << endl;
cout << "y_value: " << values->y_value << endl;
cout << "z_value: " << values->z_value << endl;
if (values->dxdt_expression != NULL)
cout << "dxdt_expression: " << SBML_formulaToL3String(values->dxdt_expression) << " " << values->dxdt_expression << endl;
else
cout << "dxdt_expression: NULL" << endl;
if (values->dydt_expression != NULL)
cout << "dydt_expression: " << SBML_formulaToL3String(values->dydt_expression) << " " << values->dydt_expression << endl;
else
cout << "dydt_expression: NULL" << endl;
if (values->v_expression != NULL)
cout << "v_expression: " << SBML_formulaToL3String(values->v_expression) << " " << values->v_expression << endl;
else
cout << "v_expression: NULL" << endl;
if (values->w_expression != NULL)
cout << "w_expression: " << SBML_formulaToL3String(values->w_expression) << " " << values->w_expression << endl;
else
cout << "w_expression: NULL" << endl;
if (values->z_expression != NULL)
cout << "z_expression: " << SBML_formulaToL3String(values->z_expression) << " " << values->z_expression << endl;
else
cout << "z_expression: NULL" << endl;
cout << "type: " << values->type << endl;
if (values->current != NULL)
cout << "current: " << SBML_formulaToL3String(values->current) << " " << values->current << endl;
else
cout << "current: NULL" << endl;
cout << "odeIndex: " << values->odeIndex << endl;
cout << "levelInExpression: " << values->levelInExpression << endl;
// cout << "k_value: " << values->k_value << endl;
// cout << "k_real_value: " << values->k_real_value << endl;
// cout << "x_value: " << values->x_value << endl;
// cout << "y_value: " << values->y_value << endl;
// cout << "z_value: " << values->z_value << endl;
// if (values->dxdt_expression != NULL)
// cout << "dxdt_expression: " << SBML_formulaToL3String(values->dxdt_expression) << " " << values->dxdt_expression << endl;
// else
// cout << "dxdt_expression: NULL" << endl;
// if (values->dydt_expression != NULL)
// cout << "dydt_expression: " << SBML_formulaToL3String(values->dydt_expression) << " " << values->dydt_expression << endl;
// else
// cout << "dydt_expression: NULL" << endl;
// if (values->v_expression != NULL)
// cout << "v_expression: " << SBML_formulaToL3String(values->v_expression) << " " << values->v_expression << endl;
// else
// cout << "v_expression: NULL" << endl;
// if (values->w_expression != NULL)
// cout << "w_expression: " << SBML_formulaToL3String(values->w_expression) << " " << values->w_expression << endl;
// else
// cout << "w_expression: NULL" << endl;
// if (values->z_expression != NULL)
// cout << "z_expression: " << SBML_formulaToL3String(values->z_expression) << " " << values->z_expression << endl;
// else
// cout << "z_expression: NULL" << endl;
// cout << "type: " << values->type << endl;
// if (values->current != NULL)
// cout << "current: " << SBML_formulaToL3String(values->current) << " " << values->current << endl;
// else
// cout << "current: NULL" << endl;
// cout << "odeIndex: " << values->odeIndex << endl;
// cout << "levelInExpression: " << values->levelInExpression << endl;
}

List* ExpressionAnalyser::getHiddenSpecies()
{
return mHiddenSpecies;
}

unsigned int ExpressionAnalyser::getNumHiddenSpecies()
{
return mHiddenSpecies->getSize();
}

SubstitutionValues_t* ExpressionAnalyser::createBlankSubstitutionValues()
{
SubstitutionValues_t* values = new SubstitutionValues_t;
Expand Down
6 changes: 4 additions & 2 deletions src/sbml/conversion/ExpressionAnalyser.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -157,6 +157,8 @@ class LIBSBML_EXTERN ExpressionAnalyser
int setModel(Model* m);

List* getHiddenSpecies();

unsigned int getNumHiddenSpecies();
SubstitutionValues_t* createBlankSubstitutionValues();
unsigned int getNumExpressions();
SubstitutionValues_t* getExpression(unsigned int index);
Expand Down Expand Up @@ -208,9 +210,9 @@ class LIBSBML_EXTERN ExpressionAnalyser

// functions that represents steps of algo 3.1

void addSingleNewParameter(SubstitutionValues_t* exp);



void addNewParameterPlusVOrW(SubstitutionValues_t* exp, std::string var = "v");
/*
* Return the ODE for the given variable
* or an ASTNode representing zero if there is no time derivative
Expand Down
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