Simulation Class Reference

#include <Simulation.h>

Public Member Functions
	Simulation (void)
	~Simulation (void)
void	setup (int, char **)
void	run (void)
void	analysis (void)
Private Member Functions
void	calcModeSetup (void)
void	visModeSetup (void)
void	inputFileCheck (void)
void	simulate (void)
void	load (void)
void	inputGenerator (void)
void	ipause ()
void	print_help ()
void	patterns (void)
Private Attributes
string	ROOTDIR
string	SIMDIR
string	NODESAVGDIR
string	BITSDIR
string	LOGICDIR
string	EXTSDIR
string	DUMP
bool	noOutFiles
int	n
ofstream	visout
ofstream	outBits
ofstream	outInputBits
ofstream	outAvg
ofstream	outDosage
string	visualFile
string	ext
string	bitsFileName
string	inputBitsFileName
string	runName
string	in_specsFile
string	in_logicFile
string	in_patternSpecsFile
string	in_patternNodesFile
string	outputFile
int	seedVal
bool	seed
bool	ND2TT
bool	TT2ND
bool	postPatterns
bool	patternAnal
bool	rand_init
bool	rand_logicMut
bool	rand_nodeInputs
string	iTables
bool	analysisMode
int	mutRate_nodes
int	mutRate_logic
int	cycleSize
string	cmd
string	runDir
string	avgFileName
string	iNodeList
vector< Matrix >	cycles
bool	ptime
int	runStart
int	progStart
bool	visMode
bool	noBits
bool	usePlugins
bool	outputAll
PluginManager	pManager

Detailed Description

LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

DESCRIPTION

The Simulation class is the class which main interacts and runs the program, it checks the flags and makes desicions about which mode to run.

Constructor & Destructor Documentation

Simulation::Simulation ( void )

Simulation constructor that initializs variables

Simulation::~Simulation ( void )

Simulation destructor, currently empty

Member Function Documentation

void Simulation::analysis ( void )

This method runs differnt analysis through the analysis object based upon which analysis flags were used at the command line

void Simulation::calcModeSetup ( void ) [private]

creates the appropriate directories for calc mode

void Simulation::inputFileCheck ( void ) [private]

exits if the nessicary input files have not been provided

void Simulation::inputGenerator ( void ) [private]

Uses the generator class to create a logic or truth table file

void Simulation::ipause ( ) [private]

This function pauses the program, used only in verbose mode

void Simulation::load ( void ) [private]

load; currently unimplimented

void Simulation::patterns ( void ) [private]

void Simulation::print_help ( ) [private]

A help function that lists the flags and their uses

void Simulation::run ( void )

This function calls the differnt modes of ChemChains based upon which flags were used. The different modes are the File Converter, the analysis mode, and the main simulation.

void Simulation::setup	(	int	argc,
		char **	argv
	)

Setup, takes in argv, its length and cycles through argv to initialize flags, it then creates apropriate directories for the Simulation.

void Simulation::simulate ( void ) [private]

This function represents the bulk of the program It creates a Boolean Network in the form of a NodeList and evaluates the network a set number of times, making some analysis throughout.

void Simulation::visModeSetup ( void ) [private]

opens the appropriate file for vis mode