gene_family.h File Reference

#include <vector>
#include <string>
#include <iosfwd>
#include "cafe.h"
#include "family.h"

Go to the source code of this file.

Data Structures
struct	gene_family

Functions
std::vector< std::string >	tokenize (std::string s, int flags)
pCafeFamily	cafe_family_init (const std::vector< std::string > &species_list)
pCafeFamily	load_gene_families (std::istream &ist, char separator, int max_size)
void	cafe_family_free (pCafeFamily pcf)
std::istream &	operator>> (std::istream &ist, gene_family &fam)
void	cafe_family_add_item (pCafeFamily pcf, const gene_family &gf)
void	cafe_family_item_free (pCafeFamilyItem pitem)
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
const int	REGULAR_WHITESPACE = 0
const int	COMMA_AS_WHITESPACE = 1

Function Documentation

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_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
	)

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

Variable Documentation

const int COMMA_AS_WHITESPACE = 1

const int REGULAR_WHITESPACE = 0