cafe_commands.h File Reference

#include <vector>
#include <string>
#include <map>
#include <iosfwd>
#include <stdexcept>
#include "family.h"
#include "cafe_shell.h"

Go to the source code of this file.

Data Structures
struct	Argument
struct	load_args
struct	viterbi_args
struct	pvalue_args
struct	lhtest_args
struct	esterror_args
struct	roots
class	io_error

Macros
#define	MAKE_FN_NAME(x)   int cafe_cmd_##x (Globals& globals, std::vector<std::string>)
#define	COMMAND(signal)   MAKE_FN_NAME(signal)

Typedefs
typedef Argument *	pArgument
typedef int(*	cafe_command2 )(Globals &globals, std::vector< std::string >)

Functions
	COMMAND (accuracy)
	COMMAND (branchlength)
	COMMAND (cvfamily)
	COMMAND (cvspecies)
	COMMAND (date)
	COMMAND (echo)
	COMMAND (errormodel)
	COMMAND (esterror)
	COMMAND (exit)
	COMMAND (extinct)
	COMMAND (family)
	COMMAND (gainloss)
	COMMAND (generate_random_family)
	COMMAND (lambdamu)
	COMMAND (lhtest)
	COMMAND (list)
	COMMAND (load)
	COMMAND (log)
	COMMAND (noerrormodel)
	COMMAND (print_param)
	COMMAND (pvalue)
	COMMAND (retrieve)
	COMMAND (rootdist)
	COMMAND (save)
	COMMAND (score)
	COMMAND (seed)
	COMMAND (simerror)
	COMMAND (simextinct)
	COMMAND (source)
	COMMAND (tree)
	COMMAND (version)
	COMMAND (viterbi)
std::map< std::string, cafe_command2 >	get_dispatcher ()
	Holds the list of commands that are available in Cafe. More...
int	cafe_shell_dispatch_command (Globals &globals, char *cmd)
void	list_commands (std::ostream &ost)
std::vector< Argument >	build_argument_list (std::vector< std::string > tokens)
void	clear_tree_viterbis (pCafeTree psum)
int	get_num_trials (std::vector< std::string > args)
int	write_family_gainloss (std::ostream &ofst, std::string family_id, pCafeTree tree1, pCafeTree tree2)
std::vector< int >	get_clusters (int parameterized_k_value, int num_families, double *k_weights)
void	write_node_headers (std::ostream &s1, std::ostream &s2, pCafeTree pcafe)
void	write_leaves (std::ostream &ofst, pCafeTree pcafe, int *k, int i, int id, bool evens)
void	write_version (std::ostream &ost)
void	write_family (std::ostream &ost, pCafeFamily family)
void	viterbi_write (std::ostream &ost, pCafeTree pcafe, pCafeFamily pfamily)
void	tree_set_branch_lengths (pCafeTree pcafe, std::vector< int > lengths)
load_args	get_load_arguments (std::vector< Argument > pargs)
viterbi_args	get_viterbi_arguments (std::vector< Argument > pargs)
pvalue_args	get_pvalue_arguments (std::vector< Argument > pargs)
lhtest_args	get_lhtest_arguments (std::vector< Argument > pargs)
esterror_args	get_esterror_arguments (std::vector< Argument > pargs)
void	validate (esterror_args args)
void	run_viterbi_sim (pCafeTree pcafe, pCafeFamily pfamily, roots &roots)
int	init_histograms (int rfsize, roots &roots, int nsamples)
void	get_doubles_array (std::vector< double > &loc, pArgument parg)
void	log_param_values (std::ostream &ost, Globals &globals)
void	prereqs (pCafeParam param, int flags)

Variables
const int	REQUIRES_FAMILY = 0x01
const int	REQUIRES_TREE = 0x02
const int	REQUIRES_LAMBDA = 0x04
const int	REQUIRES_ERRORMODEL = 0x08

Macro Definition Documentation

#define COMMAND

(

signal

)

MAKE_FN_NAME(signal)

#define MAKE_FN_NAME

(

x

)

int cafe_cmd_##x (Globals& globals, std::vector<std::string>)

Typedef Documentation

typedef int(* cafe_command2)(Globals &globals, std::vector< std::string >)

typedef Argument* pArgument

Function Documentation

std::vector<Argument> build_argument_list

(

std::vector< std::string >

tokens

)

int cafe_shell_dispatch_command	(	Globals &	globals,
		char *	cmd
	)

void clear_tree_viterbis

(

pCafeTree

psum

)

COMMAND

(

accuracy

)

COMMAND

(

branchlength

)

COMMAND

(

cvfamily

)

COMMAND

(

cvspecies

)

COMMAND

(

date

)

COMMAND

(

echo

)

COMMAND

(

errormodel

)

COMMAND

(

esterror

)

COMMAND

(

exit

)

COMMAND

(

extinct

)

COMMAND

(

family

)

COMMAND

(

gainloss

)

COMMAND

(

generate_random_family

)

COMMAND

(

lambdamu

)

COMMAND

(

lhtest

)

COMMAND

(

list

)

COMMAND

(

load

)

COMMAND

(

log

)

COMMAND

(

noerrormodel

)

COMMAND

(

print_param

)

COMMAND

(

pvalue

)

COMMAND

(

retrieve

)

COMMAND

(

rootdist

)

COMMAND

(

save

)

COMMAND

(

score

)

COMMAND

(

seed

)

COMMAND

(

simerror

)

COMMAND

(

simextinct

)

COMMAND

(

source

)

COMMAND

(

tree

)

COMMAND

(

version

)

COMMAND

(

viterbi

)

std::vector<int> get_clusters	(	int	parameterized_k_value,
		int	num_families,
		double *	k_weights
	)

std::map<std::string, cafe_command2> get_dispatcher

(

)

Holds the list of commands that are available in Cafe.

Each element consists of a command and the function that is called to handle that command. Functions include cafe_cmd_lambda, #cafe_cmd_family, cafe_cmd_tree, etc.

void get_doubles_array	(	std::vector< double > &	loc,
		pArgument	parg
	)

esterror_args get_esterror_arguments

(

std::vector< Argument >

pargs

)

lhtest_args get_lhtest_arguments

(

std::vector< Argument >

pargs

)

load_args get_load_arguments

(

std::vector< Argument >

pargs

)

int get_num_trials

(

std::vector< std::string >

args

)

pvalue_args get_pvalue_arguments

(

std::vector< Argument >

pargs

)

viterbi_args get_viterbi_arguments

(

std::vector< Argument >

pargs

)

int init_histograms	(	int	rfsize,
		roots &	roots,
		int	nsamples
	)

void list_commands

(

std::ostream &

ost

)

void log_param_values	(	std::ostream &	ost,
		Globals &	globals
	)

void prereqs	(	pCafeParam	param,
		int	flags
	)

void run_viterbi_sim	(	pCafeTree	pcafe,
		pCafeFamily	pfamily,
		roots &	roots
	)

void tree_set_branch_lengths	(	pCafeTree	pcafe,
		std::vector< int >	lengths
	)

void validate

(

esterror_args

args

)

void viterbi_write	(	std::ostream &	ost,
		pCafeTree	pcafe,
		pCafeFamily	pfamily
	)

void write_family	(	std::ostream &	ost,
		pCafeFamily	family
	)

int write_family_gainloss	(	std::ostream &	ofst,
		std::string	family_id,
		pCafeTree	tree1,
		pCafeTree	tree2
	)

void write_leaves	(	std::ostream &	ofst,
		pCafeTree	pcafe,
		int *	k,
		int	i,
		int	id,
		bool	evens
	)

void write_node_headers	(	std::ostream &	s1,
		std::ostream &	s2,
		pCafeTree	pcafe
	)

void write_version

(

std::ostream &

ost

)

Variable Documentation

const int REQUIRES_ERRORMODEL = 0x08

const int REQUIRES_FAMILY = 0x01

const int REQUIRES_LAMBDA = 0x04

const int REQUIRES_TREE = 0x02