#include <family.h>
#include <gmatrix.h>
#include <chooseln_cache.h>

Data Structures
struct	CafeFamilyItem
	Represents a single gene family and the number of members of that family that exist in each species. More...

Macros
#define	E_NOT_SYNCHRONIZED 1

#define	E_INCONSISTENT_SIZE 2

Typedefs
typedef CafeFamilyItem *	pCafeFamilyItem

Enumerations
enum	enumCafeReport { CAFE_REPORT_TEXT = 0, CAFE_REPORT_HTML, CAFE_REPORT_PDF }

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

pTreeNode	cafe_tree_new_empty_node (pTree pcafe)

void	cafe_tree_set_parameters (pCafeTree pcafe, family_size_range *range, double lambda)

pCafeTree	cafe_tree_copy (pCafeTree psrc)

pCafeTree	cafe_tree_split (pCafeTree pcafe, int idx)

void	cafe_tree_free (pCafeTree pcafe)

void	__cafe_tree_free_node (pTree ptree, pTreeNode ptnode, va_list ap)

void	cafe_tree_string_name (pString pstr, pPhylogenyNode ptnode)

pString	cafe_tree_string_with_lambda (pCafeTree pcafe)

pString	cafe_tree_string_with_id (pCafeTree pcafe)

pString	cafe_tree_string (pCafeTree pcafe)

pString	cafe_tree_string_with_familysize_lambda (pCafeTree pcafe)

pString	cafe_tree_string_with_familysize (pCafeTree pcafe)

void	cafe_tree_string_print (pCafeTree pcafe)

void	compute_internal_node_likelihood (pTree ptree, pTreeNode ptnode)

void	compute_tree_likelihoods (pCafeTree pcafe)

double *	get_likelihoods (const pCafeTree pcafe)

void	cafe_tree_node_free_clustered_likelihoods (pCafeParam param)

double **	cafe_tree_clustered_likelihood (pCafeTree pcafe, struct chooseln_cache *ln_cache)

void	cafe_tree_viterbi (pCafeTree pcafe)

void	cafe_tree_clustered_viterbi (pCafeTree pcafe, int num_likelihoods)

void	cafe_tree_viterbi_posterior (pCafeTree pcafe, pCafeParam param)

void	initialize_leaf_likelihood_clustered (pTree ptree, pTreeNode ptnode)

double	cafe_tree_mp_remark (pString str, pTree ptree, pMetapostConfig pmc, va_list ap)

int	cafe_tree_random_familysize (pCafeTree pcafe, int rootFamilysize, int maxFamilySize)

void	node_set_birthdeath_matrix (pCafeNode pcnode, pBirthDeathCacheArray cache, int num_lambdas)
	Initialize node with probability values that it may need. If multiple lambdas are set, k_bd is set to an arraylist of matrices with probability values In this case, values are set up to the value of num_lambdas otherwise the value birthdeath_matrix is used probability values are drawn from the cache argument, which should hold a variety of possible values. More...

void	add_key (pArrayList arr, double branchlength, double lambda, double mu)

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

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)

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)

int	cafe_family_get_index (pCafeFamily pcf, const char *szid)

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

void	cafe_family_filter (pCafeParam param)

void	cafe_family_reset_maxlh (pCafeFamily pcf)

int	cafe_family_split_cvfiles_byfamily (pCafeParam param, int cv_fold)

void	cafe_family_split_cvfiles_byspecies (pCafeParam param)

void	cafe_log (pCafeParam param, const char *msg,...)
	Logs the message and parameters in a standard way. More...

void	reset_birthdeath_cache (pCafeTree tree, int k_value, family_size_range *range)

double *	cafe_best_lambda_by_fminsearch (pCafeParam param, int lambda_len, int k)

double *	cafe_each_best_lambda_by_fminsearch (pCafeParam param, int lambda_len)

void	cafe_lambda_set_default (pCafeParam param, double *lambda)

void	cafe_free_birthdeath_cache (pCafeTree pcafe)

void	cafe_likelihood_ratio_test (pCafeParam param, double *maximumPvalues)

void	input_values_randomize (input_values vals, int lambda_len, int mu_len, int k, int kfix, double max_branch_length, double k_weights)

void	initialize_leaf_likelihoods_for_viterbi (double **matrix, int num_rows, int range, int familysize, int num_cols, pErrorStruct errormodel)
	Initialize matrix values according to the error model or to defaults if familysize < 0, sets the first (range) values of each row to 1, ignoring the others otherwise if errormodel is NULL, initializes all values of each row to 0 except for the one indexed by familysize, which is 1 otherwise, sets each row of matrix to the row of errormatrix indexed by familysize I doubt this function is doing what was intended. More...

void	reset_k_likelihoods (pCafeNode pcnode, int k, int num_factors)

double	cafe_get_clustered_posterior (pCafeParam param, double ML, double MAP, double *prior_rfsize)

int	sync_sanity_check (pCafeFamily pcf, pCafeTree pcafe)

Macro Definition Documentation

#define E_INCONSISTENT_SIZE 2

#define E_NOT_SYNCHRONIZED 1

Typedef Documentation

typedef CafeFamilyItem* pCafeFamilyItem

Enumeration Type Documentation

enum enumCafeReport

Enumerator
CAFE_REPORT_TEXT
CAFE_REPORT_HTML
CAFE_REPORT_PDF

Function Documentation

void __cafe_tree_free_node	(	pTree	ptree,
		pTreeNode	ptnode,
		va_list	ap
	)

void add_key	(	pArrayList	arr,
		double	branchlength,
		double	lambda,
		double	mu
	)

double* cafe_best_lambda_by_fminsearch	(	pCafeParam	param,
		int	lambda_len,
		int	k
	)

double* cafe_each_best_lambda_by_fminsearch	(	pCafeParam	param,
		int	lambda_len
	)

void cafe_family_filter ( pCafeParam param )

int cafe_family_get_index	(	pCafeFamily	pcf,
		const char *	szid
	)

int cafe_family_get_species_index	(	pCafeFamily	pcf,
		char *	speciesname
	)

void cafe_family_reset_maxlh ( pCafeFamily pcf )

void cafe_family_set_size	(	pCafeFamily	pcf,
		pCafeFamilyItem	pitem,
		pCafeTree	pcafe
	)

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 )

void cafe_free_birthdeath_cache ( pCafeTree pcafe )

double cafe_get_clustered_posterior	(	pCafeParam	param,
		double *	ML,
		double *	MAP,
		double *	prior_rfsize
	)

void cafe_lambda_set_default	(	pCafeParam	param,
		double *	lambda
	)

void cafe_likelihood_ratio_test	(	pCafeParam	param,
		double *	maximumPvalues
	)

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.

double** cafe_tree_clustered_likelihood	(	pCafeTree	pcafe,
		struct chooseln_cache *	ln_cache
	)

void cafe_tree_clustered_viterbi	(	pCafeTree	pcafe,
		int	num_likelihoods
	)

pCafeTree cafe_tree_copy ( pCafeTree psrc )

void cafe_tree_free ( pCafeTree pcafe )

double cafe_tree_mp_remark	(	pString	str,
		pTree	ptree,
		pMetapostConfig	pmc,
		va_list	ap
	)

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

pTreeNode cafe_tree_new_empty_node ( pTree pcafe )

void cafe_tree_node_free_clustered_likelihoods ( pCafeParam param )

int cafe_tree_random_familysize	(	pCafeTree	pcafe,
		int	rootFamilysize,
		int	maxFamilySize
	)

Sets the family size of each node to random value between 0 and the tree's pbdc_array maxFamilySize.

void cafe_tree_set_parameters	(	pCafeTree	pcafe,
		family_size_range *	range,
		double	lambda
	)

pCafeTree cafe_tree_split	(	pCafeTree	pcafe,
		int	idx
	)

pString cafe_tree_string ( pCafeTree pcafe )

void cafe_tree_string_name	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

void cafe_tree_string_print ( pCafeTree pcafe )

pString cafe_tree_string_with_familysize ( pCafeTree pcafe )

pString cafe_tree_string_with_familysize_lambda ( pCafeTree pcafe )

pString cafe_tree_string_with_id ( pCafeTree pcafe )

pString cafe_tree_string_with_lambda ( pCafeTree pcafe )

void cafe_tree_viterbi ( pCafeTree pcafe )

void cafe_tree_viterbi_posterior	(	pCafeTree	pcafe,
		pCafeParam	param
	)

void compute_internal_node_likelihood	(	pTree	ptree,
		pTreeNode	ptnode
	)

void compute_tree_likelihoods ( pCafeTree pcafe )

double* get_likelihoods ( const pCafeTree pcafe )

void initialize_leaf_likelihood_clustered	(	pTree	ptree,
		pTreeNode	ptnode
	)

void initialize_leaf_likelihoods_for_viterbi	(	double **	matrix,
		int	num_rows,
		int	range,
		int	familysize,
		int	num_cols,
		pErrorStruct	errormodel
	)

Initialize matrix values according to the error model or to defaults if familysize < 0, sets the first (range) values of each row to 1, ignoring the others otherwise if errormodel is NULL, initializes all values of each row to 0 except for the one indexed by familysize, which is 1 otherwise, sets each row of matrix to the row of errormatrix indexed by familysize I doubt this function is doing what was intended.

void input_values_randomize	(	input_values *	vals,
		int	lambda_len,
		int	mu_len,
		int	k,
		int	kfix,
		double	max_branch_length,
		double *	k_weights
	)

void node_set_birthdeath_matrix	(	pCafeNode	pcnode,
		pBirthDeathCacheArray	cache,
		int	num_lambdas
	)

Initialize node with probability values that it may need. If multiple lambdas are set, k_bd is set to an arraylist of matrices with probability values In this case, values are set up to the value of num_lambdas otherwise the value birthdeath_matrix is used probability values are drawn from the cache argument, which should hold a variety of possible values.

void reset_birthdeath_cache	(	pCafeTree	tree,
		int	k_value,
		family_size_range *	range
	)

void reset_k_likelihoods	(	pCafeNode	pcnode,
		int	k,
		int	num_factors
	)

int sync_sanity_check	(	pCafeFamily	pcf,
		pCafeTree	pcafe
	)

Data Structures

Macros

Typedefs

Enumerations

Functions

Macro Definition Documentation

Typedef Documentation

Enumeration Type Documentation

Function Documentation