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the refactoring is causing some issues with how the equations become
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you need to look at my refactoring functions and see if I can avoid situations I don't want
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@skeating
skeating committed Dec 22, 2024
1 parent 30eb874 commit 7ec9f90
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Showing 9 changed files with 240 additions and 45 deletions.
27 changes: 17 additions & 10 deletions src/sbml/conversion/ExpressionAnalyser.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ LIBSBML_CPP_NAMESPACE_BEGIN

bool compareExpressions(SubstitutionValues_t* values1, SubstitutionValues_t* values2)
{
if (values1->type >= values2->type)
if (values1->type <= values2->type)
return true;
return false;
}
Expand Down Expand Up @@ -160,9 +160,9 @@ ExpressionAnalyser::setModel(Model* model)
return LIBSBML_OPERATION_SUCCESS;
}

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

// need to actually address the expressions in the correct order
Expand Down Expand Up @@ -202,7 +202,7 @@ void ExpressionAnalyser::substituteParametersForExpressions(List* hiddenSpecies)
}
}

void ExpressionAnalyser::substituteParameters(List* hiddenSpecies, SubstitutionValues_t* exp)
void ExpressionAnalyser::substituteParameters(SubstitutionValues_t* exp)
{
for (unsigned int j = 0; j < mODEs.size(); j++)
{
Expand All @@ -219,7 +219,7 @@ void ExpressionAnalyser::substituteParameters(List* hiddenSpecies, SubstitutionV
exp->z_value = zName;
mNewVarCount++;
// replaceExpressionWithNewParameter(odeRHS, exp);
// addParametersAndRateRules(hiddenSpecies, exp);
// addParametersAndRateRules(exp);
}
//cout << "ode in main: " << SBML_formulaToL3String(odeRHS) << endl;
}
Expand Down Expand Up @@ -502,6 +502,12 @@ ExpressionAnalyser::printSubstitutionValues(const SubstitutionValues_t* values)
else
cout << "current: NULL" << endl;
cout << "odeIndex: " << values->odeIndex << endl;
cout << "levelInExpression: " << values->levelInExpression << endl;
}

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

SubstitutionValues_t* ExpressionAnalyser::createBlankSubstitutionValues()
Expand Down Expand Up @@ -713,7 +719,7 @@ ExpressionAnalyser::analyse(bool minusXPlusYOnly)
value->levelInExpression = currentNode.first;
if (shouldAddExpression(value, currentNode))
{
//printSubstitutionValues(value);
printSubstitutionValues(value);
mExpressions.push_back(value);
}
}
Expand All @@ -728,7 +734,7 @@ void ExpressionAnalyser::orderExpressions()
}

void
ExpressionAnalyser::detectHiddenSpecies(List * hiddenSpecies)
ExpressionAnalyser::detectHiddenSpecies()
{
// find -x+y and replace with y-x
// actually don't have to do this if we decompose the AST
Expand All @@ -748,7 +754,8 @@ ExpressionAnalyser::detectHiddenSpecies(List * hiddenSpecies)
//{
// cout << mODEs[odeIndex].first << ": " << SBML_formulaToL3String(mODEs[odeIndex].second) << endl;
//}
substituteParametersForExpressions(hiddenSpecies);
orderExpressions();
substituteParametersForExpressions();
}

/*
Expand Down Expand Up @@ -809,7 +816,7 @@ ExpressionAnalyser::getUniqueNewParameterName()


void
ExpressionAnalyser::addParametersAndRateRules(List* hiddenSpecies, SubstitutionValues_t* exp)
ExpressionAnalyser::addParametersAndRateRules(SubstitutionValues_t* exp)
{
if (exp->z_value.empty()) return;
//for (unsigned int i = 0; i < mExpressions.size(); i++)
Expand Down Expand Up @@ -892,7 +899,7 @@ ExpressionAnalyser::addParametersAndRateRules(List* hiddenSpecies, SubstitutionV
zParam->setId(exp->z_value);
zParam->setConstant(false);
zParam->setValue(SBMLTransforms::evaluateASTNode(zNode, mModel));
hiddenSpecies->add(zParam);
mHiddenSpecies->add(zParam);

delete zNode;
delete math; //its children dxdt and minus1 deleted as part of this.
Expand Down
11 changes: 6 additions & 5 deletions src/sbml/conversion/ExpressionAnalyser.h
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Original file line number Diff line number Diff line change
Expand Up @@ -157,13 +157,13 @@ class LIBSBML_EXTERN ExpressionAnalyser
*/
int setModel(Model* m);


List* getHiddenSpecies();
SubstitutionValues_t* createBlankSubstitutionValues();
unsigned int getNumExpressions();
SubstitutionValues_t* getExpression(unsigned int index);


void detectHiddenSpecies(List * hiddenSpecies);
void detectHiddenSpecies();

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

Expand All @@ -174,7 +174,7 @@ class LIBSBML_EXTERN ExpressionAnalyser
void printSubstitutionValues(const SubstitutionValues_t* values1);
bool areIdenticalSubstitutionValues(SubstitutionValues_t* values1, SubstitutionValues_t* values2);

void substituteParametersForExpressions(List* hiddenSpecies);
void substituteParametersForExpressions();

/*
* identify instances of - x + y within formula and create expressions
Expand All @@ -200,7 +200,7 @@ class LIBSBML_EXTERN ExpressionAnalyser
bool matchesType(SubstitutionValues_t* values1, SubstitutionValues_t* values2);


void substituteParameters(List* hiddenSpecies, SubstitutionValues_t* values);
void substituteParameters(SubstitutionValues_t* values);

SubstitutionValues_t* getSubstitutionValuesByType(ExpressionType_t type, size_t index = 0);

Expand All @@ -223,7 +223,7 @@ class LIBSBML_EXTERN ExpressionAnalyser
* ALSO NEED TO TAKE THE MATCHING OF THE ODES OUT OF THE COMPARISON OF EXPRESSIONS
* AND CHECK THAT THE MATCHES VARIABLES INCLUDES ALL THE VARIABLES
*/
void addParametersAndRateRules(List* hiddenSpecies, SubstitutionValues_t* exp = NULL);
void addParametersAndRateRules(SubstitutionValues_t* exp = NULL);

void replaceExpressionInNodeWithNode(ASTNode* node, ASTNode* replaced, ASTNode* replacement);

Expand Down Expand Up @@ -335,3 +335,4 @@ LIBSBML_CPP_NAMESPACE_END
#endif /* !SWIG */
#endif /* ExpressionAnalyser_h */


7 changes: 3 additions & 4 deletions src/sbml/conversion/SBMLRateRuleConverter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -880,12 +880,11 @@ SBMLRateRuleConverter::populateODEinfo()
ExpressionAnalyser *ea = new ExpressionAnalyser(model, mODEs);


List hiddenSpecies;
ea->detectHiddenSpecies(&hiddenSpecies);
ea->detectHiddenSpecies();
// add all hidden species to the model
for (unsigned int hs=0; hs < hiddenSpecies.getSize(); hs++)
for (unsigned int hs=0; hs < (*ea->getHiddenSpecies()).getSize(); hs++)
{
Parameter* hidden = (Parameter*) hiddenSpecies.get(hs);
Parameter* hidden = (Parameter*) (*ea->getHiddenSpecies()).get(hs);
addODEPair(hidden->getId(), model);
}
cout << "After\n";
Expand Down
54 changes: 49 additions & 5 deletions src/sbml/conversion/test/TestExpressionAnalyser.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -488,11 +488,11 @@ END_TEST
START_TEST(test_order_expressions_1)
{
RateRule* rr = d->getModel()->createRateRule();
rr->setVariable("b");
rr->setVariable("a");
rr->setMath(SBML_parseFormula("k - x + w - y"));

RateRule* rrr = d->getModel()->createRateRule();
rrr->setVariable("a");
rrr->setVariable("b");
rrr->setMath(SBML_parseFormula("k-x-y"));
converter->populateInitialODEinfo();
ExpressionAnalyser* analyser = new ExpressionAnalyser(m, converter->getOdePairs());
Expand All @@ -503,9 +503,9 @@ START_TEST(test_order_expressions_1)

fail_unless(analyser->getNumExpressions() == 2);
SubstitutionValues_t* value = analyser->getExpression(0);
//fail_unless(value->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y);
fail_unless(value->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y);
SubstitutionValues_t* value1 = analyser->getExpression(1);
//fail_unless(value1->type == TYPE_K_MINUS_X_MINUS_Y);
fail_unless(value1->type == TYPE_K_MINUS_X_MINUS_Y);

analyser->orderExpressions();
fail_unless(analyser->getNumExpressions() == 2);
Expand All @@ -516,6 +516,49 @@ START_TEST(test_order_expressions_1)
}
END_TEST

START_TEST(test_order_expressions_2)
{
ConversionProperties props;
props.addOption("inferReactions", true);

SBMLRateRuleConverter* converter = new SBMLRateRuleConverter();
converter->setProperties(&props);

std::string filename(TestDataDirectory);
filename += "mraterules5.xml";


SBMLDocument* d = readSBMLFromFile(filename.c_str());
Model* model = d->getModel();
fail_unless(model != NULL);
fail_unless(model->getNumParameters() == 2);

converter->setDocument(d);
converter->populateInitialODEinfo();
converter->populateInitialODEinfo();
ExpressionAnalyser* analyser = new ExpressionAnalyser(model, converter->getOdePairs());

fail_unless(analyser->getNumExpressions() == 0);

analyser->analyse();

fail_unless(analyser->getNumExpressions() == 2);
SubstitutionValues_t* value = analyser->getExpression(0);
fail_unless(value->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y);
SubstitutionValues_t* value1 = analyser->getExpression(1);
fail_unless(value1->type == TYPE_K_MINUS_X_MINUS_Y);

analyser->orderExpressions();
fail_unless(analyser->getNumExpressions() == 2);
SubstitutionValues_t* value2 = analyser->getExpression(0);
fail_unless(value2->type == TYPE_K_MINUS_X_MINUS_Y);
SubstitutionValues_t* value3 = analyser->getExpression(1);
fail_unless(value3->type == TYPE_K_MINUS_X_PLUS_W_MINUS_Y);

delete converter;
delete d;
}
END_TEST

START_TEST(test_reorder_minusXplusYIteratively_simple)
{
Expand Down Expand Up @@ -757,7 +800,7 @@ Suite *suite = suite_create("ExpressionAnalyser");

if (testing)
{
tcase_add_test(tcase, test_order_expressions_1);
tcase_add_test(tcase, test_order_expressions_2);
}
else
{
Expand All @@ -772,6 +815,7 @@ Suite *suite = suite_create("ExpressionAnalyser");
tcase_add_test(tcase, test_analyse_1_two_terms); //(k+v-x-y)+(k-x)
tcase_add_test(tcase, test_analyse_1_different); //k+v-x-y
tcase_add_test(tcase, test_reorder_minusXplusYIteratively_simple);
tcase_add_test(tcase, test_order_expressions_1);
//tcase_add_test(tcase, test_order_of_replacements1);
//tcase_add_test(tcase, test_order_of_replacements2);

Expand Down
37 changes: 19 additions & 18 deletions src/sbml/conversion/test/test-data/mraterules5.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,58 +5,59 @@
<compartment metaid="COPASI1" id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="c" name="c" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false"/>

<species id="a" name="a" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false"/>
<species id="b" name="b" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<species id="c" name="c" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k" value="2.1"/>
<parameter id="v" value="2.1" constant="false"/>
</listOfParameters>
<listOfRules>
<rateRule variable="c">
<rateRule variable="a">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<apply>
<times/>
<cn> 1 </cn>
<cn> -1 </cn>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<ci> k </ci>
<ci> v </ci>
</apply>
<ci> a </ci>
</apply>
<ci> b </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="a">
<rateRule variable="b">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> c </ci>
</math>
</rateRule>
<rateRule variable="c">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> -1 </cn>
<cn> 1 </cn>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<ci> k </ci>
<ci> v </ci>
</apply>
<ci> a </ci>
</apply>
<ci> b </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="b">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> c </ci>
</math>
</rateRule>
</listOfRules>
</listOfRules>
</model>
</sbml>
13 changes: 13 additions & 0 deletions src/sbml/math/ASTNode.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1139,6 +1139,7 @@ ASTNode::getListOfNodesWithLevel() const

fillListOfNodesWithLevel((ASTNodePredicate)ASTNode_isOperator, vector_pairs, 0);
fillListOfNodesWithLevel((ASTNodePredicate)ASTNode_isName, vector_pairs, 0);
fillListOfNodesWithLevel((ASTNodePredicate)ASTNode_isNumber, vector_pairs, 0);

return vector_pairs;
}
Expand Down Expand Up @@ -4719,6 +4720,18 @@ ASTNode::unsetDeclaredNamespaces()

/** @cond doxygenIgnored */

LIBSBML_EXTERN
void
printNodeLevels(ASTNodeLevels vector_pairs)
{
ASTNodeLevels::iterator it;
for (it = vector_pairs.begin(); it != vector_pairs.end(); it++)
{
cout << "level:" << it->first << " " << SBML_formulaToL3String(it->second) << endl;
}
}


LIBSBML_EXTERN
ASTNode_t *
ASTNode_create (void)
Expand Down
9 changes: 7 additions & 2 deletions src/sbml/math/ASTNode.h
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,6 @@ typedef ASTNodeLevels::iterator ASTNodeLevelsIterator;

#endif // !SWIG


class List;
class ASTBasePlugin;
class ExtendedMathList;
Expand Down Expand Up @@ -2373,7 +2372,6 @@ setValue(value, 0);
/** @endcond */


protected:

friend class SBMLRateRuleConverter;

Expand Down Expand Up @@ -2448,6 +2446,8 @@ setValue(value, 0);
*/
void convertRootToPower();

protected:

/*
* returns derivativeof particular function
* i.e. derivativePlus gets a function A + B and returns d(A+B)/dx
Expand Down Expand Up @@ -2562,6 +2562,11 @@ LIBSBML_CPP_NAMESPACE_END
#ifndef SWIG

LIBSBML_CPP_NAMESPACE_BEGIN
LIBSBML_EXTERN
void
printNodeLevels(ASTNodeLevels vector_pairs);


BEGIN_C_DECLS


Expand Down
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