Commands that are available in CAFE

Functions
int	cafe_cmd_echo (Globals &globals, std::vector< std::string > tokens)
	Echoes test to the log file. More...
int	cafe_cmd_date (Globals &globals, std::vector< std::string > tokens)
	Date: Writes the current date and time to log file More...
int	cafe_cmd_exit (Globals &globals, std::vector< std::string > tokens)
	Exit: Close files, release memory and exit application More...
int	cafe_cmd_log (Globals &globals, std::vector< std::string > tokens)
	Log: Sets file to which data is logged More...
int	cafe_cmd_version (Globals &globals, std::vector< std::string > tokens)
	Version: Prints CAFE version and date of build More...
int	cafe_cmd_source (Globals &globals, std::vector< std::string > tokens)
	Source: Executes a series of commands from a CAFE command file More...
int	cafe_cmd_list (Globals &, std::vector< std::string > tokens)
	List: List all commands available in CAFE More...
int	cafe_cmd_generate_random_family (Globals &globals, std::vector< std::string > tokens)
	generate_random_family: Generates random families More...
int	cafe_cmd_load (Globals &globals, std::vector< std::string > tokens)
	Load: Loads families from a family file with a defined format More...
int	cafe_cmd_report (Globals &globals, std::vector< std::string > tokens)
	Report: Generates reports in various formats of the calculations completed More...
int	cafe_cmd_tree (Globals &globals, std::vector< std::string > tokens)
	: The tree to perform calculations on. Must be in Newick format. More...
int	cafe_cmd_pvalue (Globals &globals, std::vector< std::string > tokens)
	PValue: Calculates pvalues More...
int	cafe_cmd_errormodel (Globals &globals, std::vector< std::string > tokens)
	errormodel: allows the user to specify an error distribution. More...
int	cafe_cmd_rootdist (Globals &globals, std::vector< std::string > tokens)
	Specify root family size distribution for simulation. More...
int	cafe_cmd_seed (Globals &globals, std::vector< std::string > tokens)
	Set the random seed for reproducible results. More...

Detailed Description

Function Documentation

int cafe_cmd_date	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Date: Writes the current date and time to log file

int cafe_cmd_echo	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Echoes test to the log file.

Echo

int cafe_cmd_errormodel	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

errormodel: allows the user to specify an error distribution.

int cafe_cmd_exit	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Exit: Close files, release memory and exit application

int cafe_cmd_generate_random_family	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

generate_random_family: Generates random families

int cafe_cmd_list	(	Globals &	,
		std::vector< std::string >	tokens
	)

List: List all commands available in CAFE

int cafe_cmd_load	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Load: Loads families from a family file with a defined format

Takes six arguments: -t, -r, -p, -l, -i, and -filter

-filter ensures that there is at least one copy at the root (using parsimony) for each family.

int cafe_cmd_log	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Log: Sets file to which data is logged

With no arguments, writes the current log file to stdout

with the argument "stdout" the current log file is closed and log data goes to stdout

int cafe_cmd_pvalue	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

PValue: Calculates pvalues

int cafe_cmd_report	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Report: Generates reports in various formats of the calculations completed

int cafe_cmd_rootdist	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Specify root family size distribution for simulation.

Arguments: -i input file.

int cafe_cmd_seed	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Set the random seed for reproducible results.

int cafe_cmd_source	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Source: Executes a series of commands from a CAFE command file

int cafe_cmd_tree	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

: The tree to perform calculations on. Must be in Newick format.

int cafe_cmd_version	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

Version: Prints CAFE version and date of build