46 for (i = 0; i < imax; ++i)
56 if (!reaction)
return ret;
79 if (dynamic_cast<const CMassAction*>(reaction->
getFunction()))
return ret;
88 for (i = 0; i < imax; ++i)
95 for (j = 0; j < jmax; ++j)
118 for (i = 0; i < imax; ++i)
124 for (j = 0; j < jmax; ++j)
145 for (i = 0; i < imax; ++i)
152 for (j = 0; j < jmax; ++j)
175 for (i = 0; i < imax; ++i)
198 for (j = 0; j < jmax; ++j)
218 for (j = 0; j < jmax; ++j)
238 for (j = 0; j < jmax; ++j)
260 for (j = 0; j < jmax; ++j)
272 for (j = 0; j < jmax; ++j)
292 for (j = 0; j < jmax; ++j)
341 #define WRITE(__level, __text) os << CFunctionAnalyzer::write(__level, rt, __text, "");
348 if (rt) os <<
"<h2>";
352 if (rt) os <<
"</h2>";
359 "This means that checking the kinetic function will be less strict.");
362 os <<
CFunctionAnalyzer::write(3, rt,
"The reversibility of the reaction and the kinetic function doesn't match.",
"");
367 for (i = 0; i < imax; ++i)
371 +
"\" is not mapped to a corresponding function parameter.",
"");
376 for (i = 0; i < imax; ++i)
380 +
"\" is not mapped to a corresponding function parameter.",
"");
385 for (i = 0; i < imax; ++i)
389 +
"\" is not mapped to a corresponding function parameter.",
"");
394 for (i = 0; i < imax; ++i)
398 +
"\" which should be mapped to a metabolite is mapped to something else.",
"");
403 for (i = 0; i < imax; ++i)
407 +
"\" is not mapped to a substrate of the reaction.",
"");
412 for (i = 0; i < imax; ++i)
416 +
"\" is not mapped to a product of the reaction.",
"");
421 for (i = 0; i < imax; ++i)
425 +
"\" is not mapped to a modifier of the reaction.",
"");
430 for (i = 0; i < imax; ++i)
434 +
"\" is not mapped to local parameter or a global value.",
"");
439 for (i = 0; i < imax; ++i)
443 +
"\" is not mapped to a compartment.",
"");
448 for (i = 0; i < imax; ++i)
452 +
"\" is not correctly handled as model time.",
"");
457 for (i = 0; i < imax; ++i)
461 +
"\" is marked as \"variable\". Not sure what this means.",
"");
465 std::ostringstream tmpss;
484 for (i = 0; i < imax; ++i)
bool mReversibilityMismatch
std::vector< std::string > mChemEqProds
CFunctionAnalyzer::Result mFunctionResult
const std::string & getObjectName() const
const CCopasiVectorN< CModelValue > & getModelValues() const
virtual size_t size() const
std::vector< std::string > mFunctionParametersProds
std::vector< std::string > mFunctionParametersVol
std::string mReactionName
void checkModel(const CModel *model)
std::vector< std::string > mFunctionParametersSubs
bool writeResult(std::ostream &os, bool rt, bool verbose) const
size_t getTotSteps() const
virtual const std::string & getKey() const
const CCopasiVector< CChemEqElement > & getProducts() const
const CFunction * getFunction() const
const CFunctionParameters & getFunctionParameters() const
const TriLogic & isReversible() const
virtual const std::string & getKey() const
static std::string write(int level, bool rt, const std::string &text, const std::string &longText)
std::vector< std::string > mFunctionParametersMods
std::vector< std::string > mFunctionParametersTime
CCopasiParameter * getParameter(const std::string &name)
const CCopasiVector< CChemEqElement > & getSubstrates() const
const std::string & getKey() const
bool isReversible() const
CModelAnalyzer(const CModel *model)
CCopasiVectorNS< CCompartment > & getCompartments()
std::vector< std::string > mChemEqSubs
std::vector< std::string > mFunctionParametersVar
static CKeyFactory * getKeyFactory()
const CCopasiVector< CChemEqElement > & getModifiers() const
const CCopasiParameterGroup & getParameters() const
std::vector< std::string > mNotMetabolite
CCopasiVectorNS< CReaction > & getReactions()
std::vector< ReactionResult > mReactionResults
bool mKineticUnspecifiedReversibility
const std::vector< std::vector< std::string > > & getParameterMappings() const
ReactionResult checkReaction(const CReaction *reaction)
std::vector< std::string > mFunctionParametersParams
void writeReport(std::ostream &os, bool rt, bool verbose) const
const CChemEq & getChemEq() const
bool writeResult(std::ostream &os, bool rt, bool verbose) const
std::vector< std::string > mChemEqMods