lm_sbml_import.cpp File Reference

#include <iostream>
#include <string>
#include <vector>
#include <map>
#include <memory>
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <sys/stat.h>
#include <sbml/SBMLTypes.h>
#include "core/Exceptions.h"
#include "ReactionModel.pb.h"
#include "io/SimulationFile.h"
#include "core/Print.h"
#include "lptf/Profile.h"
#include "core/util.h"

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Classes
class	Exception
	Base class for exceptions. More...
class	SimulationFile
	A representation of the simulation that is used to input or output from an HDF5 file. More...

Functions
void	parseArguments (int argc, char **argv)
void	printUsage (int argc, char **argv)
void	importSBMLModel (SimulationFile *lmFile, string sbmlFilename)
void	importSBMLModelL3V1 (ReactionModel *lmModel, Model *sbmlModel)
void	importSBMLModelL3V1Kinetics (uint reactionIndex, KineticLaw *kinetics, ReactionModel *lmModel, uint *D, map< string, uint > &speciesIndices, uint numberReactions, vector< string > &globalParameters, map< string, double > &globalParameterValues)
bool	isFirstOrderReaction (const ASTNode *root, vector< string > &parameters)
void	importFirstOrderReaction (const ASTNode *root, vector< string > &parameters, map< string, double > &parameterValues, uint reactionIndex, uint numberReactions, ReactionModel *lmModel, uint *D, map< string, uint > &speciesIndices)
bool	isSecondOrderReaction (const ASTNode *root, vector< string > &parameters)
void	importSecondOrderReaction (const ASTNode *root, vector< string > &parameters, map< string, double > &parameterValues, uint reactionIndex, uint numberReactions, ReactionModel *lmModel, uint *D, map< string, uint > &speciesIndices)
bool	isSecondOrderSelfReaction (const ASTNode *root, vector< string > &parameters)
void	importSecondOrderSelfReaction (const ASTNode *root, vector< string > &parameters, map< string, double > &parameterValues, uint reactionIndex, uint numberReactions, ReactionModel *lmModel, uint *D, map< string, uint > &speciesIndices)
int	main (int argc, char **argv)
void	getSpeciesUsedInExpression (vector< string > &speciesUsed, const ASTNode *node, vector< string > &parameters)
void	getOperatorsUsedInExpression (vector< string > &speciesUsed, const ASTNode *node)
const ASTNode *	getFirstExpressionOfType (const ASTNode *node, ASTNodeType_t type)
double	calculateMultiplierInExpression (const ASTNode *node, map< string, double > &parameterValues, bool ignoreSpeciesMinusOne=false)

Variables
string	function = ""
string	outputFilename = ""
string	inputFilename = ""
map< string, double >	userParameterValues
	PROF_ALLOC

Function Documentation

calculateMultiplierInExpression()

double calculateMultiplierInExpression	(	const ASTNode *	node,
		map< string, double > &	parameterValues,
		bool	ignoreSpeciesMinusOne = false )

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getFirstExpressionOfType()

const ASTNode * getFirstExpressionOfType	(	const ASTNode *	node,
		ASTNodeType_t	type )

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getOperatorsUsedInExpression()

void getOperatorsUsedInExpression	(	vector< string > &	speciesUsed,
		const ASTNode *	node )

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getSpeciesUsedInExpression()

void getSpeciesUsedInExpression	(	vector< string > &	speciesUsed,
		const ASTNode *	node,
		vector< string > &	parameters )

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importFirstOrderReaction()

void importFirstOrderReaction	(	const ASTNode *	root,
		vector< string > &	parameters,
		map< string, double > &	parameterValues,
		uint	reactionIndex,
		uint	numberReactions,
		ReactionModel *	lmModel,
		uint *	D,
		map< string, uint > &	speciesIndices )

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importSBMLModel()

void importSBMLModel	(	SimulationFile *	lmFile,
		string	sbmlFilename )

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importSBMLModelL3V1()

void importSBMLModelL3V1	(	ReactionModel *	lmModel,
		Model *	sbmlModel )

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importSBMLModelL3V1Kinetics()

void importSBMLModelL3V1Kinetics	(	uint	reactionIndex,
		KineticLaw *	kinetics,
		ReactionModel *	lmModel,
		uint *	D,
		map< string, uint > &	speciesIndices,
		uint	numberReactions,
		vector< string > &	globalParameters,
		map< string, double > &	globalParameterValues )

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importSecondOrderReaction()

void importSecondOrderReaction	(	const ASTNode *	root,
		vector< string > &	parameters,
		map< string, double > &	parameterValues,
		uint	reactionIndex,
		uint	numberReactions,
		ReactionModel *	lmModel,
		uint *	D,
		map< string, uint > &	speciesIndices )

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importSecondOrderSelfReaction()

void importSecondOrderSelfReaction	(	const ASTNode *	root,
		vector< string > &	parameters,
		map< string, double > &	parameterValues,
		uint	reactionIndex,
		uint	numberReactions,
		ReactionModel *	lmModel,
		uint *	D,
		map< string, uint > &	speciesIndices )

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isFirstOrderReaction()

bool isFirstOrderReaction	(	const ASTNode *	root,
		vector< string > &	parameters )

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isSecondOrderReaction()

bool isSecondOrderReaction	(	const ASTNode *	root,
		vector< string > &	parameters )

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isSecondOrderSelfReaction()

bool isSecondOrderSelfReaction	(	const ASTNode *	root,
		vector< string > &	parameters )

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main()

int main	(	int	argc,
		char **	argv )

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parseArguments()

void parseArguments	(	int	argc,
		char **	argv )

Parses the command line arguments.

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printUsage()

void printUsage	(	int	argc,
		char **	argv )

Prints the usage for the program.

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Variable Documentation

function

string function = ""

The function being performed.

inputFilename

string inputFilename = ""

The sbml file to import the model from.

outputFilename

string outputFilename = ""

The lm file to output the model into.

PROF_ALLOC

PROF_ALLOC

userParameterValues

map<string, double> userParameterValues

Parameters specified by the user.