Crrllvm::ASTNodeCodeGen | All of the LLVM IR generation is handled here |
Crrllvm::ASTNodeCodeGenScalarTicket | Used in LoadSymbolResolverBase::loadReactionRate when resolving a kinetic law |
Crrllvm::ASTNodeFactory | Manages a set of ASTNodes |
Crrllvm::CodeGen | Base class for code generation |
►Crrllvm::CodeGenBase< FunctionPtrType > | Convenience class to pull the vars out of a context, and store them as ivars |
►Crrllvm::GetEventValueCodeGenBase< GetEventTriggerCodeGen, GetEventTriggerCodeGen_FunctionPtr > | |
Crrllvm::GetEventTriggerCodeGen | Get the trigger of an SBML Event |
►Crrllvm::CodeGenBase< EvalConversionFactorCodeGen_FunctionPtr > | |
Crrllvm::EvalConversionFactorCodeGen | Evaluate conversion factors, which change the units of species objects in SBML |
►Crrllvm::CodeGenBase< EvalInitialConditions_FunctionPtr > | |
Crrllvm::EvalInitialConditionsCodeGen | Generates a function called 'modeldata_initialvalues_set', which evaluates all of the initial conditions specified in the sbml model (initial values, initial assigments, etc...) and stores these values in the appropriate fields in the LLVMModelData structure |
►Crrllvm::CodeGenBase< EvalRateRuleRates_FunctionPtr > | |
Crrllvm::EvalRateRuleRatesCodeGen | Evaluate the current model state and store the results in ModelData.reactionRates |
►Crrllvm::CodeGenBase< EvalReactionRates_FunctionPtr > | |
Crrllvm::EvalReactionRatesCodeGen | Evaluate the current model state and store the results in ModelData.reactionRates |
►Crrllvm::CodeGenBase< EvalVolatileStoichCodeGen_FunctionPtr > | |
Crrllvm::EvalVolatileStoichCodeGen | Evaluate 'volatile stoichiometries', or, stoichiometries that can change over the course of a simulation |
►Crrllvm::CodeGenBase< EventCodeGenBase_FunctionPtr > | |
►Crrllvm::EventCodeGenBase< EventTriggerCodeGen > | |
Crrllvm::EventTriggerCodeGen | The trigger of an SBML Event |
►Crrllvm::EventCodeGenBase< EventAssignCodeGen > | |
Crrllvm::EventAssignCodeGen | Evaluate SBML Event Assignments (which execute after the event is triggered) |
Crrllvm::EventCodeGenBase< Derived > | Base class for evaluating various types of SBML events |
►Crrllvm::CodeGenBase< GetEventValueCodeGenBase_FunctionPtr > | |
►Crrllvm::GetEventValueCodeGenBase< GetEventDelayCodeGen > | |
Crrllvm::GetEventDelayCodeGen | Get the delay of an SBML Event |
►Crrllvm::GetEventValueCodeGenBase< GetEventPriorityCodeGen > | |
Crrllvm::GetEventPriorityCodeGen | Get the priority of an SBML Event |
Crrllvm::GetEventValueCodeGenBase< Derived, FunctionPtrType > | Base class for getting event values |
►Crrllvm::CodeGenBase< GetInitialValueCodeGenBase_FunctionPtr > | |
►Crrllvm::GetInitialValueCodeGenBase< GetFloatingSpeciesInitAmountCodeGen, true > | |
Crrllvm::GetFloatingSpeciesInitAmountCodeGen | Get the initial amount of a floating species |
►Crrllvm::GetInitialValueCodeGenBase< GetBoundarySpeciesInitAmountCodeGen, true > | |
Crrllvm::GetBoundarySpeciesInitAmountCodeGen | Get the initial amount of a boundary species |
►Crrllvm::GetInitialValueCodeGenBase< GetBoundarySpeciesInitConcentrationCodeGen, false > | |
Crrllvm::GetBoundarySpeciesInitConcentrationCodeGen | Get the initial concentration of a boundary species |
►Crrllvm::GetInitialValueCodeGenBase< GetFloatingSpeciesInitConcentrationCodeGen, false > | |
Crrllvm::GetFloatingSpeciesInitConcentrationCodeGen | Get the initial concentration of a floating species |
►Crrllvm::GetInitialValueCodeGenBase< GetCompartmentInitVolumeCodeGen, false > | |
Crrllvm::GetCompartmentInitVolumeCodeGen | Get the initial volume of a compartment |
►Crrllvm::GetInitialValueCodeGenBase< GetGlobalParameterInitValueCodeGen, false > | |
Crrllvm::GetGlobalParameterInitValueCodeGen | Get the initial value of a parameter |
Crrllvm::GetInitialValueCodeGenBase< Derived, substanceUnits > | Base class for getting the initial value of an element |
►Crrllvm::CodeGenBase< GetPiecewiseTriggerCodeGen_FunctionPtr > | |
Crrllvm::GetPiecewiseTriggerCodeGen | Class for getting piecewise trigger values |
►Crrllvm::CodeGenBase< GetValueCodeGenBase_FunctionPtr > | |
►Crrllvm::GetValueCodeGenBase< GetFloatingSpeciesConcentrationCodeGen, false > | |
Crrllvm::GetFloatingSpeciesConcentrationCodeGen | Get the current concentration of a floating species |
►Crrllvm::GetValueCodeGenBase< GetBoundarySpeciesAmountCodeGen, true > | |
Crrllvm::GetBoundarySpeciesAmountCodeGen | Get the current amount of a boundary species |
►Crrllvm::GetValueCodeGenBase< GetFloatingSpeciesAmountCodeGen, true > | |
Crrllvm::GetFloatingSpeciesAmountCodeGen | Get the current amount of a floating species |
►Crrllvm::GetValueCodeGenBase< GetCompartmentVolumeCodeGen, false > | |
Crrllvm::GetCompartmentVolumeCodeGen | Get the current volume of a compartment |
►Crrllvm::GetValueCodeGenBase< GetBoundarySpeciesConcentrationCodeGen, false > | |
Crrllvm::GetBoundarySpeciesConcentrationCodeGen | Get the current concentration of a boundary species |
►Crrllvm::GetValueCodeGenBase< GetGlobalParameterCodeGen, false > | |
Crrllvm::GetGlobalParameterCodeGen | Get the current value of a parameter |
Crrllvm::GetValueCodeGenBase< Derived, substanceUnits > | Base class for getting the current value of an element |
►Crrllvm::CodeGenBase< SetValueCodeGenBase_FunctionPtr > | |
Crrllvm::SetValueCodeGenBase< Derived, substanceUnits > | Base class for setting values |
►Crr::CompiledModelGenerator | Both compiled model generators (C and CSharp) share a lot of functionality, so implement that here |
Crr::CModelGenerator | Generate executable SBML models by generating and compiling C source code into shared libraries with an external C compiler |
Crr::CompiledModelState | Saves the 'state' of a Model |
►Crr::Compiler | Interface to manipulate 'compiler' settings |
Crr::CCompiler | Compiler class for the C based model system |
Crrllvm::LLVMCompiler | Class LLVMCompiler |
Crr::Config | Read or store default values |
Crrllvm::SymbolForest::ConstIterator | Syntatically the same as a std::map<std::string, const libsbml::ASTNode*>::const_iterator |
►Crr::Dictionary | This class is frozen, no new features A dictionary interface that objects can implement |
►Crr::BasicDictionary | This class is frozen, no new features Basic implementation of the Dictionary interface which uses a std unordered std::map to store the values |
Crr::LoadSBMLOptions | Options for loading SBML into RoadRunner |
►Cstd::disjunction | |
Crr::isValidVariantType< T, std::variant< ALL_T... > > | |
Crr::Event | |
Crrllvm::Event | The Event class, which mirrors an SBML Event |
Crr::EventListener | Notifies the user of SBML events |
Crrllvm::EventPredicate | Struct to check the event ID number of an event ID |
Crrllvm::EventQueue | When events are queued to execute, but have not yet executed |
►Cstd::exception | |
Crr::EventListenerException | |
►Crr::Exception | The RoadRunner exception class |
Crr::CVODEException | Exception class for scanners |
Crr::CoreException | Generic exception class |
Crr::DidNotConvergeException | Exception class for scanners |
Crr::InvalidKeyException | Exception class for scanners |
Crr::KinsolException | Exception class for scanners |
Crr::NLEQException | Exception class for scanners |
Crr::NOMException | Exception class for scanners |
Crr::NotImplementedException | Exception class for scanners |
Crr::NullPointerException | Exception class for scanners |
Crr::ScannerException | Exception class for scanners |
Crr::UninitializedValueException | Thrown whenever an uninitialized value is encountered, see https://github.com/sys-bio/roadrunner/issues/180 |
►Crr::ExecutableModel | Base class for all code generation systems; allows compiling and evaluating the model |
Crr::CompiledExecutableModel | Both the CModelGenerator and the CSharpModelGenerator use the same paradigm of producing source code, calling a external compiler and loadig the resulting shared library |
Crrllvm::LLVMExecutableModel | LLVM executable model |
Crr::ExecutableModelFactory | A factory class to create ExecutableModel objects |
Crr::IntegratorListener | IntegratorListener listens for integrator events |
Crr::isValidVariantType< T, ALL_T > | Generic type checking mechanism for membership of type T in variant ALL_T |
►Crrllvm::Jit | Superclass of all Jit types |
Crrllvm::LLJit | Thin layer around the llvm::orc::LLJit |
Crrllvm::JitFactory | Use the options in LoadSBMLOptions.ModelGeneratorOpt or fall back on the global Config settings to create a Jit |
Crrllvm::LLVMModelData | A data structure that is that allows data to be exchanged with running SBML models |
Crrllvm::LLVMModelDataIRBuilderTesting | Testing class |
Crrllvm::LLVMModelDataSymbols | Stores the names of all the symbols in the sbml model and thier indexes in the ModelData arrays |
Crrllvm::LLVMModelGenerator | General concepts: |
►Crrllvm::LoadSymbolResolver | LLVM load instruction class |
Crrllvm::FunctionResolver | Not thread safe – but perfectly fine if stack allocated |
Crrllvm::KineticLawParameterResolver | Sorts out local parameters in a kinetic law |
►Crrllvm::LoadSymbolResolverBase | Provide common sbml model functionality to three kinds of resolvers |
Crrllvm::SBMLInitialValueSymbolResolver | Pulls values from the original sbml document |
Crr::Logger | The roadrunner logger |
Crr::LoggingBuffer | Poco LogStream dumps to the log when a newline i.e |
►Cstd::map | |
Crr::IntStringHashTable | |
Crr::StringSymbolHashTable | |
►Cls::Matrix | |
Crr::Matrix< T > | A basic local matrix class, based on the libstruct version |
Crr::Matrix3D< IndexType, DataType > | A basic local 3D version of the Matrix class, based on initializer_list |
Crrllvm::ModelDataIRBuilder | The model data IR builder |
Crrllvm::ModelGeneratorContext | All LLVM code generating objects basically need at a minimum three things to operate: |
Crrllvm::ModelResourceProvider | |
Crr::ModelSharedLibrary | Access 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 | |
CMTRand | |
CMTRand53 | |
CMTRand_closed | |
CMTRand_open | |
Crr::NOMSupport | Methods to query various information from an SBML document |
►Cllvm::ObjectCache | |
Crrllvm::SBMLModelObjectCache | Stores SBML model as object files for later use |
Crr::PendingAssignment | Holds a handle to a block of memory allocated by the model, the model is also responsible for freeing this block |
Crr::Random | |
Crrllvm::Random | Define and collect ways to generate random values and values from random distributions |
Crrllvm::LLVMModelSymbols::ReactionSymbols | Hold the symbols that belong to a reactions |
►Crr::Registrable | Handles constructing a solver and contains meta information about it |
►Crr::Solver | Base class for all integrators and steady state solvers |
►Crr::Integrator | Integrator is an abstract base class that provides an interface to specific integrator class implementations |
Crr::CVODEIntegrator | A RoadRunner integrator based on CVODE; serves as RoadRunner's main integrator for ODEs |
Crr::EulerIntegrator | An example class intended to show how to create an Integrator |
Crr::GillespieIntegrator | RoadRunner's implementation of the Gillespie SSA |
Crr::RK45Integrator | A Runge-Kutta Fehlberg method for roadrunner |
Crr::RK4Integrator | A super basic 4'th order fixed step integrator |
►Crr::SensitivitySolver | Generic interface for all SensitivitySolvers |
Crr::SteadyStateSensitivitySolver | Genetic interface for sensitivity solvers that solve for steady state before computing model sensitivities |
►Crr::TimeSeriesSensitivitySolver | Generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point |
Crr::ForwardSensitivitySolver | Time based sensivitity solver |
►Crr::SteadyStateSolver | SteadyStateSolver is an abstract base class that provides an interface to specific steady-state solver class implementations |
►Crr::KinsolSteadyStateSolver | Base class to steady state solvers from the Sundials package |
Crr::FixedPointIteration | Implementation of the fixed point iteration form of the kinsol steady state solver |
►Crr::NewtonIteration | Implementation of the newton iteration form of the kinsol steady state solver |
Crr::BasicNewtonIteration | Solve for steady state using Kinsol's implementation of Newton Iteration |
Crr::LinesearchNewtonIteration | Solve for steady state using Kinsol's implementation of Newton Iteration with linesearch globalization |
Crr::NLEQSolver | Base class for NLEQ type steady state solvers |
►Crr::SteadyStateSolverDecorator | The base class Decorator follows the same interface as other SteadyStateSolvers |
Crr::PresimulationDecorator | Wrapper class to change the solve() method of SteadyStateSolver types |
Crr::PresimulationProgramDecorator | Wrapper class to change the solve() method of SteadyStateSolver types |
►Crr::RegistrationFactory | Constructs new integrators |
Crr::IntegratorFactory | Constructs new integrators |
Crr::SensitivitySolverFactory | Constructs new integrators |
Crr::SteadyStateSolverFactory | Constructs new integrators |
Crr::RoadRunner | The main RoadRunner class |
Crr::RoadRunnerData | Used for simulation output, and provides a wrapper around 2D matrix data |
Crr::RoadRunnerImpl | Implemention class, hide all details here |
Crr::RoadRunnerMap | Hash table designed for storing RoadRunner models |
Crr::RoadRunnerOptions | A set of options that determine how the top level RoadRunner class should behave |
CRRCData | Structure for the result type from the simulate calls. The client is responsible for freeing the RRCDataPtr |
CRRComplex | Structure for a complex number |
CRRComplexMatrix | Structure for a simple complex Matrix type |
CRRComplexVector | Structure for a simple complex Vector type |
CRRDoubleMatrix | Structure for a simple double Matrix type |
CRRList | A list type, stores int, double, strings and lists |
CRRListItem | A single list element type |
Crr::RRRule | |
CRRStringArray | Structure for a simple vector of strings |
CRRVector | Structure for a simple vector of doubles |
►Cstd::runtime_error | |
Crr::IntegratorException | The exception class thrown by the Integrator |
Crr::SBMLReader | Read an sbml document from either disk, a remote url, or as a std::string |
Crr::SBMLSymbol | |
Crr::SBMLSymbolDependencies | |
►Clibsbml::SBMLVisitor | |
Crrllvm::AssignmentRuleEvaluator | Attaches to an existing symbol forest and applies any asigment rule found in the model to the forest |
Crrllvm::LLVMModelSymbols | Hold all the un-evaluated symbolic inforamtion in the model |
Crr::Scanner | |
Crr::SelectionRecord | Way to find sbml model elements using the RoadRunner syntax |
Crr::Setting | Store a roadrunner option (or setting) as a Variant type |
Crr::SimulateOptions | This class is frozen, no new features RoadRunner simulation options |
CSModelData | A data structure that is that allows data to be exchanged with running SBML models |
Crr::sort_pred | |
Crr::SortByPriority | |
Crrllvm::LLVMModelDataSymbols::SpeciesReferenceInfo | Info about an entry in the stoich matrix |
Crrllvm::StoreSymbolResolver | LLVM store symbol class |
►Crr::StringBuilder | |
Crr::CodeBuilder | |
Crr::StringList | |
Crr::StringListContainer | |
Crr::SVD | The routine computes the singular value decomposition (SVD) of a real m-by-n matrix |
Crr::Symbol | An SBML species definition |
Crrllvm::SymbolForest | Similar 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::Variant | A basic type to hold a variety of data types |
Crr::VariantImpl | |
►Cstd::vector | |
Crr::SymbolList | |