cafe_commands.cpp File Reference

#include "../config.h"
#include <stdio.h>
#include <time.h>
#include <map>
#include <string>
#include <iostream>
#include <sstream>
#include <fstream>
#include <vector>
#include <iterator>
#include <algorithm>
#include <stdexcept>
#include <stack>
#include "lambda.h"
#include "lambdamu.h"
#include "cafe_commands.h"
#include "reports.h"
#include "pvalue.h"
#include "conditional_distribution.h"
#include "simerror.h"
#include "error_model.h"
#include "log_buffer.h"
#include "Globals.h"
#include "viterbi.h"
#include "gene_family.h"
#include "cross_validator.h"
#include <dirent.h>
#include <sys/stat.h>
#include <utils_string.h>
#include "cafe_shell.h"
#include "cafe.h"

Data Structures
struct	family_args
struct	errormodel_args

Functions
void	cafe_log (pCafeParam param, const char *msg,...)
	Logs the message and parameters in a standard way. More...
void	__cafe_tree_string_gainloss (pString pstr, pPhylogenyNode ptnode)
void	__cafe_tree_string_sum_gainloss (pString pstr, pPhylogenyNode ptnode)
int	__cafe_cmd_extinct_count_zero (pTree pcafe)
void	__hg_print_sim_extinct (pHistogram **phist_sim_n, pHistogram *phist_sim, int r, pHistogram phist_tmp, double *cnt, int num_trials)
pErrorStruct	cafe_shell_create_error_matrix_from_estimate (pErrorMeasure errormeasure)
void	cafe_shell_set_branchlength (pCafeParam param, int max_family_size)
void	set_range_from_family (family_size_range *range, pCafeFamily family)
double	__cafe_best_lambda_search (double *plambda, void *args)
double	__cafe_cluster_lambda_search (double *parameters, void *args)
map< string, cafe_command2 >	get_dispatcher ()
	Holds the list of commands that are available in Cafe. More...
void	get_doubles_array (vector< double > &loc, pArgument parg)
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...
void	set_log_file (Globals &globals, string log_file)
int	cafe_cmd_log (Globals &globals, std::vector< std::string > tokens)
	Log: Sets file to which data is logged More...
void	write_version (ostream &ost)
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...
void	list_commands (std::ostream &ost)
int	cafe_cmd_list (Globals &, std::vector< std::string > tokens)
	List: List all commands available in CAFE More...
void	clear_node_viterbis (pTree ptree, pTreeNode ptnode, va_list ap1)
void	clear_tree_viterbis (pCafeTree ptree)
int	write_family_gainloss (ostream &ofst, std::string family_id, pCafeTree tree1, pCafeTree tree2)
void	prereqs (pCafeParam param, int flags)
vector< Argument >	build_argument_list (vector< string > tokens)
int	cafe_shell_dispatch_command (Globals &globals, char *cmd)
int	cafe_shell_dispatch_commandf (Globals &globals, const char *format,...)
int	get_num_trials (vector< string > args)
void	cafe_shell_prompt (const char *prompt, const char *format,...)
int	set_family_size_interactive (pCafeTree pcafe)
void	verify_directory (string dirname)
int *	get_root_dist (pCafeTree pcafe, pCafeFamily pfamily, int k_value, family_size_range *range)
vector< int >	get_clusters (int parameterized_k_value, int num_families, double *k_weights)
void	write_node_headers (ostream &s1, ostream &s2, pCafeTree pcafe)
void	write_leaves (ostream &ofst, pCafeTree pcafe, int *k, int i, int id, bool evens)
int	cafe_cmd_generate_random_family (Globals &globals, std::vector< std::string > tokens)
	generate_random_family: Generates random families More...
struct load_args	get_load_arguments (vector< Argument > pargs)
void	copy_args_to_param (Globals &globals, struct load_args &args)
bool	endsWith (std::string const &fullString, std::string const &ending)
int	cafe_cmd_load (Globals &globals, std::vector< std::string > tokens)
	Load: Loads families from a family file with a defined format More...
struct family_args	get_family_arguments (vector< Argument > pargs)
int	cafe_cmd_report (Globals &globals, std::vector< std::string > tokens)
	Report: Generates reports in various formats of the calculations completed More...
template<typename T >
void	write_vector (ostream &ost, vector< T > items, string delimiter)
void	write_family (ostream &ost, pCafeFamily family)
int	cafe_cmd_tree (Globals &globals, std::vector< std::string > tokens)
	: The tree to perform calculations on. Must be in Newick format. More...
struct viterbi_args	get_viterbi_arguments (vector< Argument > pargs)
int	to_integer (std::string str)
int	cafe_shell_parse_familysize (pTree pcafe, std::vector< std::string > tokens)
void	run_viterbi_sim (pCafeTree pcafe, pCafeFamily pfamily, roots &roots)
int	init_histograms (int rfsize, roots &roots, int nsamples)
ostream &	operator<< (ostream &os, const Histogram &hist)
struct pvalue_args	get_pvalue_arguments (vector< Argument > pargs)
int	cafe_cmd_pvalue (Globals &globals, std::vector< std::string > tokens)
	PValue: Calculates pvalues More...
lhtest_args	get_lhtest_arguments (vector< Argument > pargs)
std::vector< std::string >	enumerate_directory (std::string dir, std::string ext)
int	cafe_cmd_lhtest (Globals &globals, std::vector< std::string > tokens)
int	cafe_cmd_simerror (Globals &globals, std::vector< std::string > tokens)
errormodel_args	get_errormodel_arguments (vector< Argument > pargs)
int	cafe_cmd_errormodel (Globals &globals, std::vector< std::string > tokens)
	errormodel: allows the user to specify an error distribution. More...
esterror_args	get_esterror_arguments (vector< Argument > pargs)
void	validate (esterror_args args)
int	cafe_cmd_esterror (Globals &globals, std::vector< std::string > tokens)
int	cafe_cmd_noerrormodel (Globals &globals, std::vector< std::string > tokens)
void	tree_set_branch_lengths (pCafeTree pcafe, std::vector< int > lengths)
int	s_to_i (std::string s)
std::string	get_input_file (std::vector< std::string > tokens)
int	cafe_cmd_rootdist (Globals &globals, std::vector< std::string > tokens)
	Specify root family size distribution for simulation. More...
void	log_param_values (std::ostream &ost, Globals &globals)
int	cafe_cmd_seed (Globals &globals, std::vector< std::string > tokens)
	Set the random seed for reproducible results. More...
void	__tree_build_node_list (pTree ptree, pTreeNode ptnode, va_list ap1)
void	__tree_build_prefix_node_list (pTree ptree, pTreeNode ptnode, va_list ap1)
void	__tree_build_postfix_node_list (pTree ptree, pTreeNode ptnode, va_list ap1)
void	tree_traveral_infix (pTree ptree, tree_func_node func,...)
void	tree_build_node_list (pTree ptree)
pTree	__cafe_tree_new (tree_func_node_new new_tree_node_func, int size)
void	cafe_tree_parse_node (pTree ptree, pTreeNode ptnode)
pCafeTree	cafe_tree_new (const char *sztree, family_size_range *range, double lambda, double mu)

Variables
pTree	tmp_lambda_tree
pBirthDeathCacheArray	probability_cache

Function Documentation

double __cafe_best_lambda_search	(	double *	plambda,
		void *	args
	)

double __cafe_cluster_lambda_search	(	double *	parameters,
		void *	args
	)

int __cafe_cmd_extinct_count_zero

(

pTree

pcafe

)

pTree __cafe_tree_new	(	tree_func_node_new	new_tree_node_func,
		int	size
	)

void __cafe_tree_string_gainloss	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

void __cafe_tree_string_sum_gainloss	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

void __hg_print_sim_extinct	(	pHistogram **	phist_sim_n,
		pHistogram *	phist_sim,
		int	r,
		pHistogram	phist_tmp,
		double *	cnt,
		int	num_trials
	)

void __tree_build_node_list	(	pTree	ptree,
		pTreeNode	ptnode,
		va_list	ap1
	)

void __tree_build_postfix_node_list	(	pTree	ptree,
		pTreeNode	ptnode,
		va_list	ap1
	)

void __tree_build_prefix_node_list	(	pTree	ptree,
		pTreeNode	ptnode,
		va_list	ap1
	)

vector<Argument> build_argument_list

(

vector< string >

tokens

)

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

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

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

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

void cafe_log	(	pCafeParam	param,
		const char *	msg,
			...
	)

Logs the message and parameters in a standard way.

If the user has assigned a file for logging, message is written to the file and also to stdout. The stdout write will be suppressed if the param "quiet" flag is set.

pErrorStruct cafe_shell_create_error_matrix_from_estimate

(

pErrorMeasure

errormeasure

)

int cafe_shell_dispatch_command	(	Globals &	globals,
		char *	cmd
	)

int cafe_shell_dispatch_commandf	(	Globals &	globals,
		const char *	format,
			...
	)

int cafe_shell_parse_familysize	(	pTree	pcafe,
		std::vector< std::string >	tokens
	)

void cafe_shell_prompt	(	const char *	prompt,
		const char *	format,
			...
	)

void cafe_shell_set_branchlength	(	pCafeParam	param,
		int	max_family_size
	)

pCafeTree cafe_tree_new	(	const char *	sztree,
		family_size_range *	range,
		double	lambda,
		double	mu
	)

void cafe_tree_parse_node	(	pTree	ptree,
		pTreeNode	ptnode
	)

void clear_node_viterbis	(	pTree	ptree,
		pTreeNode	ptnode,
		va_list	ap1
	)

void clear_tree_viterbis

(

pCafeTree

ptree

)

void copy_args_to_param	(	Globals &	globals,
		struct load_args &	args
	)

bool endsWith	(	std::string const &	fullString,
		std::string const &	ending
	)

std::vector<std::string> enumerate_directory	(	std::string	dir,
		std::string	ext
	)

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

map<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	(	vector< double > &	loc,
		pArgument	parg
	)

errormodel_args get_errormodel_arguments

(

vector< Argument >

pargs

)

esterror_args get_esterror_arguments

(

vector< Argument >

pargs

)

struct family_args get_family_arguments

(

vector< Argument >

pargs

)

std::string get_input_file

(

std::vector< std::string >

tokens

)

lhtest_args get_lhtest_arguments

(

vector< Argument >

pargs

)

struct load_args get_load_arguments

(

vector< Argument >

pargs

)

int get_num_trials

(

vector< string >

args

)

struct pvalue_args get_pvalue_arguments

(

vector< Argument >

pargs

)

int* get_root_dist	(	pCafeTree	pcafe,
		pCafeFamily	pfamily,
		int	k_value,
		family_size_range *	range
	)

struct viterbi_args get_viterbi_arguments

(

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
	)

ostream& operator<<	(	ostream &	os,
		const Histogram &	hist
	)

void prereqs	(	pCafeParam	param,
		int	flags
	)

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

int s_to_i

(

std::string

s

)

int set_family_size_interactive

(

pCafeTree

pcafe

)

void set_log_file	(	Globals &	globals,
		string	log_file
	)

void set_range_from_family	(	family_size_range *	range,
		pCafeFamily	family
	)

int to_integer

(

std::string

str

)

void tree_build_node_list

(

pTree

ptree

)

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

void tree_traveral_infix	(	pTree	ptree,
		tree_func_node	func,
			...
	)

void validate

(

esterror_args

args

)

void verify_directory

(

string

dirname

)

void write_family	(	ostream &	ost,
		pCafeFamily	family
	)

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

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

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

template<typename T >

void write_vector	(	ostream &	ost,
		vector< T >	items,
		string	delimiter
	)

void write_version

(

ostream &

ost

)

Variable Documentation

pBirthDeathCacheArray probability_cache

The variable cafe_param is a global singleton that holds general program state. cafe_param holds pcafe, a CafeTree, and pfamily, a CafeFamily . These are set by the user via the commands "tree" and "load" respectively. When the user calls the command "lambda" calculations are performed on the pcafe and pfamily variables.

pTree tmp_lambda_tree