gene_family.cpp File Reference

#include <sstream>
#include <fstream>
#include <algorithm>
#include <iostream>
#include <stdexcept>
#include "gene_family.h"
#include <tree.h>
#include "cafe.h"

Data Structures
class	my_ctype

Functions
void	__cafe_famliy_check_the_pattern (pCafeFamily pcf)
	Sets ref on the family meaning an index to a lower numbered family with the same species count for each species. More...
vector< string >	tokenize (string s, int flags)
vector< string >	string_split (string line, char delimiter)
pCafeFamily	cafe_family_init (const std::vector< std::string > &species_list)
void	cafe_family_free (pCafeFamily pcf)
int	to_int (std::string s)
std::istream &	operator>> (std::istream &ist, gene_family &fam)
pCafeFamily	load_gene_families (std::istream &ist, char separator, int max_size)
void	cafe_family_add_item (pCafeFamily pcf, const gene_family &gf)
void	cafe_family_item_free (pCafeFamilyItem pitem)
void	cafe_family_filter (pCafeParam param)
int	log_cluster_membership (pCafeFamily pcf, int k_value, double **p_z_membership, std::ostream &log)
void	cafe_family_reset_maxlh (pCafeFamily pcf)
int	cafe_family_get_index (pCafeFamily pcf, const char *szid)

Variables
pCafeParam	cafe_param
	Holds the global program state that user commands act on. More...

Function Documentation

void __cafe_famliy_check_the_pattern

(

pCafeFamily

pcf

)

Sets ref on the family meaning an index to a lower numbered family with the same species count for each species.

void cafe_family_add_item	(	pCafeFamily	pcf,
		const gene_family &	gf
	)

Data array is assumes to contain a description, an identifier, and a set of integers giving the family size in species order

void cafe_family_filter

(

pCafeParam

param

)

void cafe_family_free

(

pCafeFamily

pcf

)

int cafe_family_get_index	(	pCafeFamily	pcf,
		const char *	szid
	)

pCafeFamily cafe_family_init

(

const std::vector< std::string > &

species_list

)

void cafe_family_item_free

(

pCafeFamilyItem

pitem

)

void cafe_family_reset_maxlh

(

pCafeFamily

pcf

)

pCafeFamily load_gene_families	(	std::istream &	ist,
		char	separator,
		int	max_size
	)

int log_cluster_membership	(	pCafeFamily	pcf,
		int	k_value,
		double **	p_z_membership,
		std::ostream &	log
	)

std::istream& operator>>	(	std::istream &	ist,
		gene_family &	fam
	)

vector<string> string_split	(	string	line,
		char	delimiter
	)

int to_int

(

std::string

s

)

vector<string> tokenize	(	string	s,
		int	flags
	)

Variable Documentation

pCafeParam cafe_param

Holds the global program state that user commands act on.