getting there

src/sbml/conversion/ExpressionAnalyser.cpp

@@ -245,7 +245,7 @@ void ExpressionAnalyser::identifyHiddenSpeciesWithinExpressions()
             }
         }
     }
-    substituteNodes();
+    //substituteNodes();
 }
 
 void ExpressionAnalyser::substituteParameters(SubstitutionValues_t* exp)
@@ -691,7 +691,7 @@ void ExpressionAnalyser::orderExpressions()
 }
 
 void
-ExpressionAnalyser::detectHiddenSpecies()
+ExpressionAnalyser::detectHiddenSpecies(bool testing)
 {
   mExpressions.clear();
 
@@ -703,6 +703,10 @@ ExpressionAnalyser::detectHiddenSpecies()
   //}
   orderExpressions();
   identifyHiddenSpeciesWithinExpressions();
+  if (!testing)
+  {
+      substituteNodes();
+  }
 }
 
 /*
@@ -766,8 +770,9 @@ 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);
+    replaceExpressionInNodeWithNode(getODE(exp->odeIndex), exp->current, exp->z_expression); //getODEFor(exp->current);
     cout << "node: " << SBML_formulaToL3String(getODE(exp->odeIndex)) << endl;
+    addParametersAndRateRules(exp);
   }
 }
 
@@ -776,6 +781,7 @@ void
 ExpressionAnalyser::addParametersAndRateRules(SubstitutionValues_t* exp)
 {
     if (exp->z_value.empty()) return;
+    if (mHiddenSpecies == NULL) mHiddenSpecies = new List();
   //for (unsigned int i = 0; i < mExpressions.size(); i++)
   //{
   //  SubstitutionValues_t *exp = mExpressions.at(i);
@@ -947,6 +953,14 @@ ExpressionAnalyser::replaceExpressionWithNewParameter(ASTNode* ode, Substitution
   }
 }
 
+unsigned int ExpressionAnalyser::getNumHiddenNodes()
+{   
+    if (mHiddenNodes == NULL)
+        return 0;
+    else
+        return mHiddenNodes->getSize();
+}
+
 
 /*
 * Have we already created a parameter for this expression

src/sbml/conversion/ExpressionAnalyser.h

@@ -155,13 +155,16 @@ class LIBSBML_EXTERN ExpressionAnalyser
     */
     unsigned int getNumHiddenSpecies();
 
+    unsigned int getNumHiddenNodes();
+
+
     // need a function to get hidden species by index
     // TODO
 
     /**
     * Function to work through all the expressions and detect hidden species
     */
-    void detectHiddenSpecies();
+    void detectHiddenSpecies(bool testing = false);
 
     /**
     * Function to create a blank substitution value
@@ -407,7 +410,6 @@ class LIBSBML_EXTERN ExpressionAnalyser
 
     void replaceExpressionWithNewParameter(ASTNode* ode, SubstitutionValues_t* exp);
 
-
     // member variables populated during analysis
     pairODEs mODEs;
 

src/sbml/conversion/SBMLRateRuleConverter.cpp

@@ -881,6 +881,7 @@ SBMLRateRuleConverter::populateODEinfo()
 
 
   ea->detectHiddenSpecies();
+
   // add all hidden species to the model
   for (unsigned int hs=0; hs < ea->getNumHiddenSpecies(); hs++)
   {