roadrunner  2.6.0
Fast simulator for SBML models
Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]
 Crrllvm::ASTNodeCodeGenAll of the LLVM IR generation is handled here
 Crrllvm::ASTNodeCodeGenScalarTicketUsed in LoadSymbolResolverBase::loadReactionRate when resolving a kinetic law
 Crrllvm::ASTNodeFactoryManages a set of ASTNodes
 Crrllvm::CodeGenBase class for code generation
 Crrllvm::CodeGenBase< FunctionPtrType >Convenience class to pull the vars out of a context, and store them as ivars
 Crrllvm::CodeGenBase< EvalConversionFactorCodeGen_FunctionPtr >
 Crrllvm::CodeGenBase< EvalInitialConditions_FunctionPtr >
 Crrllvm::CodeGenBase< EvalRateRuleRates_FunctionPtr >
 Crrllvm::CodeGenBase< EvalReactionRates_FunctionPtr >
 Crrllvm::CodeGenBase< EvalVolatileStoichCodeGen_FunctionPtr >
 Crrllvm::CodeGenBase< EventCodeGenBase_FunctionPtr >
 Crrllvm::CodeGenBase< GetEventValueCodeGenBase_FunctionPtr >
 Crrllvm::CodeGenBase< GetInitialValueCodeGenBase_FunctionPtr >
 Crrllvm::CodeGenBase< GetPiecewiseTriggerCodeGen_FunctionPtr >
 Crrllvm::CodeGenBase< GetValueCodeGenBase_FunctionPtr >
 Crrllvm::CodeGenBase< SetValueCodeGenBase_FunctionPtr >
 Crr::CompiledModelGeneratorBoth compiled model generators (C and CSharp) share a lot of functionality, so implement that here
 Crr::CompiledModelStateSaves the 'state' of a Model
 Crr::CompilerInterface to manipulate 'compiler' settings
 Crr::ConfigRead or store default values
 Crrllvm::SymbolForest::ConstIteratorSyntatically the same as a std::map<std::string, const libsbml::ASTNode*>::const_iterator
 Crr::DictionaryThis class is frozen, no new features A dictionary interface that objects can implement
 Cstd::disjunction
 Crr::Event
 Crrllvm::EventThe Event class, which mirrors an SBML Event
 Crr::EventListenerNotifies the user of SBML events
 Crrllvm::EventPredicateStruct to check the event ID number of an event ID
 Crrllvm::EventQueueWhen events are queued to execute, but have not yet executed
 Cstd::exception
 Crr::ExecutableModelBase class for all code generation systems; allows compiling and evaluating the model
 Crr::ExecutableModelFactoryA factory class to create ExecutableModel objects
 Crr::IntegratorListenerIntegratorListener listens for integrator events
 Crr::isValidVariantType< T, ALL_T >Generic type checking mechanism for membership of type T in variant ALL_T
 Crrllvm::JitSuperclass of all Jit types
 Crrllvm::JitFactoryUse the options in LoadSBMLOptions.ModelGeneratorOpt or fall back on the global Config settings to create a Jit
 Crrllvm::LLVMModelDataA data structure that is that allows data to be exchanged with running SBML models
 Crrllvm::LLVMModelDataIRBuilderTestingTesting class
 Crrllvm::LLVMModelDataSymbolsStores the names of all the symbols in the sbml model and thier indexes in the ModelData arrays
 Crrllvm::LLVMModelGeneratorGeneral concepts:
 Crrllvm::LoadSymbolResolverLLVM load instruction class
 Crr::LoggerThe roadrunner logger
 Crr::LoggingBufferPoco LogStream dumps to the log when a newline i.e
 Cstd::map
 Cls::Matrix
 Crr::Matrix3D< IndexType, DataType >A basic local 3D version of the Matrix class, based on initializer_list
 Crrllvm::ModelDataIRBuilderThe model data IR builder
 Crrllvm::ModelGeneratorContextAll LLVM code generating objects basically need at a minimum three things to operate:
 Crrllvm::ModelResourceProvider
 Crr::ModelSharedLibraryAccess an actual compiled shared library (.so, .dll or .dylib) that was compiled by a ModelGenerator and provides access to the exported C functions
 Crr::ModelSymbols
 CMTRand_int32
 Crr::NOMSupportMethods to query various information from an SBML document
 Cllvm::ObjectCache
 Crr::PendingAssignmentHolds a handle to a block of memory allocated by the model, the model is also responsible for freeing this block
 Crr::Random
 Crrllvm::RandomDefine and collect ways to generate random values and values from random distributions
 Crrllvm::LLVMModelSymbols::ReactionSymbolsHold the symbols that belong to a reactions
 Crr::RegistrableHandles constructing a solver and contains meta information about it
 Crr::RegistrationFactoryConstructs new integrators
 Crr::RoadRunnerThe main RoadRunner class
 Crr::RoadRunnerDataUsed for simulation output, and provides a wrapper around 2D matrix data
 Crr::RoadRunnerImplImplemention class, hide all details here
 Crr::RoadRunnerMapHash table designed for storing RoadRunner models
 Crr::RoadRunnerOptionsA set of options that determine how the top level RoadRunner class should behave
 CRRCDataStructure for the result type from the simulate calls. The client is responsible for freeing the RRCDataPtr
 CRRComplexStructure for a complex number
 CRRComplexMatrixStructure for a simple complex Matrix type
 CRRComplexVectorStructure for a simple complex Vector type
 CRRDoubleMatrixStructure for a simple double Matrix type
 CRRListA list type, stores int, double, strings and lists
 CRRListItemA single list element type
 Crr::RRRule
 CRRStringArrayStructure for a simple vector of strings
 CRRVectorStructure for a simple vector of doubles
 Cstd::runtime_error
 Crr::SBMLReaderRead an sbml document from either disk, a remote url, or as a std::string
 Crr::SBMLSymbol
 Crr::SBMLSymbolDependencies
 Clibsbml::SBMLVisitor
 Crr::Scanner
 Crr::SelectionRecordWay to find sbml model elements using the RoadRunner syntax
 Crr::SettingStore a roadrunner option (or setting) as a Variant type
 Crr::SimulateOptionsThis class is frozen, no new features RoadRunner simulation options
 CSModelDataA data structure that is that allows data to be exchanged with running SBML models
 Crr::sort_pred
 Crr::SortByPriority
 Crrllvm::LLVMModelDataSymbols::SpeciesReferenceInfoInfo about an entry in the stoich matrix
 Crrllvm::StoreSymbolResolverLLVM store symbol class
 Crr::StringBuilder
 Crr::StringList
 Crr::StringListContainer
 Crr::SVDThe routine computes the singular value decomposition (SVD) of a real m-by-n matrix
 Crr::SymbolAn SBML species definition
 Crrllvm::SymbolForestSimilar to a symbol table, except instead of a name / value, we have a name / tree, where the tree is the root of an ASTNode tree
 Crr::Token
 Crr::VariantA basic type to hold a variety of data types
 Crr::VariantImpl
 Cstd::vector