rr::ModelGenerator Class Reference

#include <rrModelGenerator.h>

Public Types
enum	ModelGeneratorOptions {   CONSERVED_MOIETIES = (0x1 << 0), RECOMPILE = (0x1 << 1), READ_ONLY = (0x1 << 2), MUTABLE_INITIAL_CONDITIONS = (0x1 << 3),   OPTIMIZE_GVN = (0x1 << 4), OPTIMIZE_CFG_SIMPLIFICATION = (0x1 << 5), OPTIMIZE_INSTRUCTION_COMBINING = (0x1 << 6), OPTIMIZE_DEAD_INST_ELIMINATION = (0x1 << 7),   OPTIMIZE_DEAD_CODE_ELIMINATION = (0x1 << 8), OPTIMIZE_INSTRUCTION_SIMPLIFIER = (0x1 << 9), OPTIMIZE }

Public Member Functions
virtual bool	setTemporaryDirectory (const std::string &path)=0
virtual std::string	getTemporaryDirectory ()=0
virtual ExecutableModel *	createModel (const std::string &sbml, unsigned int options)=0
virtual Compiler *	getCompiler ()=0
virtual bool	setCompiler (const std::string &compiler)=0
virtual	~ModelGenerator ()

Detailed Description

The interface which generates executable models from sbml source. This can have different concrete implementations such as compiler based generators, JIT'ed or interpreter based ones.

Member Enumeration Documentation

enum rr::ModelGenerator::ModelGeneratorOptions

Enumerator
CONSERVED_MOIETIES	perform conservation analysis. This causes a re-ordering of the species, so results generated with this flag enabled can not be compared index wise to results generated otherwise. currently only implemented with the C code generating model
RECOMPILE	Should the model be recompiled? The LLVM ModelGenerator maintins a hash table of currently running models. If this flag is NOT set, then the generator will look to see if there is already a running instance of the given model and use the generated code from that one. If only a single instance of a model is run, there is no need to cache the models, and this can safetly be enabled, realizing some performance gains.
READ_ONLY	If this is set, then a read-only model is generated. A read-only model can be simulated, but no code is generated to set model values, i.e. parameters, amounts, values, etc... It takes a finite amount of time to generate the model value setting functions, and if they are not needed, one may see some performance gains, especially in very large models.
MUTABLE_INITIAL_CONDITIONS	Generate accessor functions to allow changing of initial conditions.
OPTIMIZE_GVN	GVN - This pass performs global value numbering and redundant load elimination cotemporaneously.
OPTIMIZE_CFG_SIMPLIFICATION	CFGSimplification - Merge basic blocks, eliminate unreachable blocks, simplify terminator instructions, etc...
OPTIMIZE_INSTRUCTION_COMBINING	InstructionCombining - Combine instructions to form fewer, simple instructions. This pass does not modify the CFG, and has a tendency to make instructions dead, so a subsequent DCE pass is useful.
OPTIMIZE_DEAD_INST_ELIMINATION	DeadInstElimination - This pass quickly removes trivially dead instructions without modifying the CFG of the function. It is a BasicBlockPass, so it runs efficiently when queued next to other BasicBlockPass's.
OPTIMIZE_DEAD_CODE_ELIMINATION	DeadCodeElimination - This pass is more powerful than DeadInstElimination, because it is worklist driven that can potentially revisit instructions when their other instructions become dead, to eliminate chains of dead computations.
OPTIMIZE_INSTRUCTION_SIMPLIFIER	InstructionSimplifier - Remove redundant instructions.
OPTIMIZE	all optimizations, use to check if bit mask has any optimizations.

Constructor & Destructor Documentation

virtual rr::ModelGenerator::~ModelGenerator ( )

inlinevirtual

public dtor, one can and most certainly delete an object of this class.

Member Function Documentation

virtual ExecutableModel* rr::ModelGenerator::createModel ( const std::string &  sbml, unsigned int  options  )

pure virtual

Create an executable model from an sbml string.

Parameters

sbml	a string containging the contents of an sbml doc.
options	a bitfield containing items from the ModelGeneratorOptions enumeration.

virtual Compiler* rr::ModelGenerator::getCompiler ( )

pure virtual

Get the compiler object that the model generator is using to 'compile' sbml. Certain model generators may be interpreters, in this case, the Compiler interface should still be sufficiently general to manipulate interpreters as well.

virtual std::string rr::ModelGenerator::getTemporaryDirectory ( )

pure virtual

certain model generators, such as the compiler based ones generate files such as shared libraries. This specifies the location where they are stored.

virtual bool rr::ModelGenerator::setCompiler ( const std::string &  compiler )

pure virtual

Set the name of the compiler to use. In the case of source code generating model generators, this is the exectuable name of the external compiler, i.e. 'gcc', 'icc', etc... For JITing generators, this may have no effect.

virtual bool rr::ModelGenerator::setTemporaryDirectory ( const std::string &  path )

pure virtual

certain model generators, such as the compiler based ones generate files such as shared libraries. This specifies the location where they are stored.

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The documentation for this class was generated from the following file:

• rrModelGenerator.h