#include "cafe.h"
#include <stdlib.h>
#include <stdio.h>
#include <mathfunc.h>
#include <memalloc.h>
#include <utils.h>

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...

int	cafe_family_split_cvfiles_byfamily (pCafeParam param, int cv_fold)

void	cafe_family_split_cvfiles_byspecies (pCafeParam param)

int	cafe_family_set_species_index (pCafeFamily pcf, pCafeTree pcafe)
	Synchronize a family and tree together. More...

int	cafe_family_get_species_index (pCafeFamily pcf, char *speciesname)

int	sync_sanity_check (pCafeFamily pcf, pCafeTree pcafe)

void	cafe_family_set_size (pCafeFamily pcf, pCafeFamilyItem pitem, pCafeTree pcafe)
	Copy sizes of an individual gene family into the tree. More...

void	cafe_family_set_size_with_family_forced (pCafeFamily pcf, int idx, pCafeTree pcafe)

void	cafe_family_set_size_with_family (pCafeFamily pcf, int idx, pCafeTree pcafe)

void	cafe_family_set_truesize_with_family (pCafeFamily pcf, int idx, pCafeTree pcafe)

void	cafe_family_set_size_by_species (char *speciesname, int size, pCafeTree pcafe)

void	init_family_size (family_size_range *fs, int max)

Macro Definition Documentation

#define E_INCONSISTENT_SIZE 2

#define E_NOT_SYNCHRONIZED 1

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.

int cafe_family_get_species_index	(	pCafeFamily	pcf,
		char *	speciesname
	)

Copy sizes of an individual gene family into the tree.

Takes the given gene family and copies the size of the family in the species into the tree node that corresponds to that species

Side effect is to set the familysize member for each node in the tree, but since that is a convenience variable it shouldn't make any difference

void cafe_family_set_size_by_species	(	char *	speciesname,
		int	size,
		pCafeTree	pcafe
	)

void cafe_family_set_size_with_family	(	pCafeFamily	pcf,
		int	idx,
		pCafeTree	pcafe
	)

void cafe_family_set_size_with_family_forced	(	pCafeFamily	pcf,
		int	idx,
		pCafeTree	pcafe
	)

int cafe_family_set_species_index	(	pCafeFamily	pcf,
		pCafeTree	pcafe
	)

Synchronize a family and tree together.

Sets the value of index in pcf to the node index in the tree of the leaf with the matching species ID.

Returns: 0 on success, or -1 if there is a species in the tree with no matching species in the family

void cafe_family_set_truesize_with_family	(	pCafeFamily	pcf,
		int	idx,
		pCafeTree	pcafe
	)

int cafe_family_split_cvfiles_byfamily	(	pCafeParam	param,
		int	cv_fold
	)

void cafe_family_split_cvfiles_byspecies ( pCafeParam param )