roadrunner
2.6.0
Fast simulator for SBML models
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Both compiled model generators (C and CSharp) share a lot of functionality, so implement that here. More...
#include <rrCompiledModelGenerator.h>
Protected Member Functions | |
std::string | substituteTerms (const std::string &reactionName, const std::string &inputEquation, bool bFixAmounts) |
std::string | substituteTerms (const int &numReactions, const std::string &reactionName, const std::string &equation) |
virtual std::string | convertUserFunctionExpression (const std::string &equation)=0 |
virtual void | substituteEquation (const std::string &reactionName, Scanner &s, CodeBuilder &sb)=0 |
virtual void | substituteWords (const std::string &reactionName, bool bFixAmounts, Scanner &s, CodeBuilder &sb)=0 |
virtual void | substituteToken (const std::string &reactionName, bool bFixAmounts, Scanner &s, CodeBuilder &sb)=0 |
virtual std::string | findSymbol (const std::string &varName)=0 |
virtual void | writeComputeAllRatesOfChange (CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0 |
virtual void | writeComputeConservedTotals (CodeBuilder &sb, const int &numFloatingSpecies, const int &numDependentSpecies)=0 |
virtual void | writeUpdateDependentSpecies (CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0 |
virtual void | writeUserDefinedFunctions (CodeBuilder &sb)=0 |
virtual void | writeResetEvents (CodeBuilder &sb, const int &numEvents)=0 |
virtual void | writeSetConcentration (CodeBuilder &sb)=0 |
virtual void | writeGetConcentration (CodeBuilder &sb)=0 |
virtual void | writeConvertToAmounts (CodeBuilder &sb)=0 |
virtual void | writeConvertToConcentrations (CodeBuilder &sb)=0 |
virtual void | writeProperties (CodeBuilder &sb)=0 |
virtual void | writeAccessors (CodeBuilder &sb)=0 |
virtual void | writeOutVariables (CodeBuilder &sb)=0 |
virtual void | writeClassHeader (CodeBuilder &sb)=0 |
virtual void | writeTestConstraints (CodeBuilder &sb)=0 |
virtual void | writeEvalInitialAssignments (CodeBuilder &sb, const int &numReactions)=0 |
virtual int | writeComputeRules (CodeBuilder &sb, const int &numReactions)=0 |
virtual void | writeComputeReactionRates (CodeBuilder &sb, const int &numReactions)=0 |
virtual void | writeEvalEvents (CodeBuilder &sb, const int &numEvents, const int &numFloatingSpecies)=0 |
virtual void | writeEvalModel (CodeBuilder &sb, const int &numReactions, const int &numIndependentSpecies, const int &numFloatingSpecies, const int &numOfRules)=0 |
virtual void | writeEventAssignments (CodeBuilder &sb, const int &numReactions, const int &numEvents)=0 |
virtual void | writeSetParameterValues (CodeBuilder &sb, const int &numReactions)=0 |
virtual void | writeSetCompartmentVolumes (CodeBuilder &sb)=0 |
virtual void | writeSetBoundaryConditions (CodeBuilder &sb)=0 |
virtual void | writeSetInitialConditions (CodeBuilder &sb, const int &numFloatingSpecies)=0 |
virtual std::string | convertCompartmentToC (const std::string &compartmentName)=0 |
virtual std::string | convertSpeciesToBc (const std::string &speciesName)=0 |
virtual std::string | convertSpeciesToY (const std::string &speciesName)=0 |
virtual std::string | convertSymbolToC (const std::string &compartmentName)=0 |
virtual std::string | convertSymbolToGP (const std::string ¶meterName)=0 |
void | reset () |
int | numAdditionalRates () |
virtual std::string | getInfo () |
get various information about the model in a user displayable format. | |
ls::DoubleMatrix * | initializeL0 (int &nrRows, int &nrCols) |
bool | expressionContainsSymbol (ASTNode *ast, const std::string &symbol) |
bool | expressionContainsSymbol (const std::string &expression, const std::string &symbol) |
const Symbol * | getSpecies (const std::string &id) |
int | readGlobalParameters () |
void | readLocalParameters (const int &numReactions, std::vector< int > &localParameterDimensions, int &totalLocalParmeters) |
int | readCompartments () |
std::string | writeDouble (const double &value, const std::string &format="%G") |
Static Protected Member Functions | |
static ASTNode * | cleanEquation (ASTNode *ast) |
creates a new AST node | |
static std::string | cleanEquation (const std::string &equation) |
Protected Attributes | |
ls::LibStructural * | mLibStruct |
Refernce to libstruct library this are set by createModel, and for the time being remain after createModel completes. | |
NOMSupport * | mNOM |
Object that provide some wrappers and new "NOM" functions. More... | |
bool | mComputeAndAssignConsevationLaws |
const std::string | mFixAmountCompartments |
StringList | mWarnings |
ModelSymbols | ms |
hold all the symbolic (AKA metadata) information in the model The idea is that all the memebers of this class will be const, and the entire thing will be created anew each time createModel is called. More... | |
Both compiled model generators (C and CSharp) share a lot of functionality, so implement that here.
|
protected |
Object that provide some wrappers and new "NOM" functions.
this are set by createModel, and for the time being remain after createModel completes.
|
protected |
hold all the symbolic (AKA metadata) information in the model The idea is that all the memebers of this class will be const, and the entire thing will be created anew each time createModel is called.
This thing will creted in one shot, then all the code building will access it.