#include "cafe.h"
#include <stdlib.h>
#include <math.h>
#include <mathfunc.h>
#include <chooseln_cache.h>
#include "time.h"

Functions
void	__phylogeny_free_node (pTree ptree, pTreeNode ptnode, va_list ap1)

pTreeNode	cafe_tree_new_empty_node (pTree ptree)

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

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

void	cafe_tree_free (pCafeTree pcafe)

void	cafe_tree_string_name (pString pstr, pPhylogenyNode ptnode)

void	cafe_tree_string_familysize_lambda (pString pstr, pPhylogenyNode ptnode)

void	cafe_tree_string_familysize (pString pstr, pPhylogenyNode ptnode)

void	cafe_tree_string_lambda (pString pstr, pPhylogenyNode ptnode)

void	cafe_tree_string_id (pString pstr, pPhylogenyNode pnode)

pString	cafe_tree_string_with_familysize_lambda (pCafeTree pcafe)

pString	cafe_tree_string_with_lambda (pCafeTree pcafe)

pString	cafe_tree_string_with_familysize (pCafeTree pcafe)

pString	cafe_tree_string_with_id (pCafeTree pcafe)

pString	cafe_tree_string (pCafeTree pcafe)

void	cafe_tree_string_print (pCafeTree pcafe)

double	cafe_tree_mp_remark (pString pstr, pTree ptree, pMetapostConfig pmc, va_list ap1)

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	initialize_leaf_likelihoods (pTree ptree, pTreeNode ptnode)
	Set likelihood to 1 for actual value, 0 otherwise, or copy values from an existing errormodel Copies likelihood values from an errormodel if one exists, otherwise sets all likelihoods to 0 except for familysize, which is set to 1. More...

void	compute_viterbis (pCafeNode node, int k, double *factors, int rootfamilysize_start, int rootfamilysize_end, int familysize_start, int familysize_end)

void	compute_child_factor (pCafeTree pcafe, pCafeNode child, family_size_range range, double factors)

void	compute_internal_node_likelihood (pTree ptree, pTreeNode ptnode)

void	free_probabilities (struct probabilities *probs)

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

void	compute_node_likelihoods_recursive (pTree ptree, pTreeNode ptnode)

void	compute_tree_likelihoods (pCafeTree pcafe)

double *	get_likelihoods (const pCafeTree pcafe)

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	get_keys_from_node (pCafeNode pcnode, pArrayList arr, int num_lambdas)

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

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

void	cafe_tree_set_birthdeath (pCafeTree pcafe, int max_family_size)

void	cafe_tree_node_copy (pTreeNode psrc, pTreeNode pdest)

void	__cafe_tree_copy_new_fill (pCafeTree psrc, pCafeTree pdest)

pCafeTree	cafe_tree_copy (pCafeTree psrc)

pCafeTree	cafe_tree_split (pCafeTree pcafe, int idx)

void	__cafe_tree_node_random_familysize (pTree ptree, pTreeNode pnode, va_list ap1)

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

void	initialize_leaf_likelihood_clustered (pTree ptree, pTreeNode ptnode)

void	compute_internal_node_likelihood_clustered (pTree ptree, pTreeNode ptnode)

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

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

void	cafe_tree_node_free_clustered_likelihoods (pCafeParam param)

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

Variables
pBirthDeathCacheArray	probability_cache

struct chooseln_cache	cache
	A cache of values of chooseln. More...

Function Documentation

void __cafe_tree_copy_new_fill	(	pCafeTree	psrc,
		pCafeTree	pdest
	)

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

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

void __cafe_tree_node_random_familysize	(	pTree	ptree,
		pTreeNode	pnode,
		va_list	ap1
	)

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

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

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

pCafeTree cafe_tree_copy ( pCafeTree psrc )

void cafe_tree_free ( pCafeTree pcafe )

double cafe_tree_mp_remark	(	pString	pstr,
		pTree	ptree,
		pMetapostConfig	pmc,
		va_list	ap1
	)

pTreeNode cafe_tree_new_empty_node ( pTree ptree )

void cafe_tree_node_copy	(	pTreeNode	psrc,
		pTreeNode	pdest
	)

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_birthdeath	(	pCafeTree	pcafe,
		int	max_family_size
	)

Set each node's birthdeath matrix based on its values of branchlength, lambdas, and mus

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_familysize	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

void cafe_tree_string_familysize_lambda	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

void cafe_tree_string_id	(	pString	pstr,
		pPhylogenyNode	pnode
	)

void cafe_tree_string_lambda	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

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 compute_child_factor	(	pCafeTree	pcafe,
		pCafeNode	child,
		family_size_range *	range,
		double *	factors
	)

void compute_internal_node_likelihood	(	pTree	ptree,
		pTreeNode	ptnode
	)

void compute_internal_node_likelihood_clustered	(	pTree	ptree,
		pTreeNode	ptnode
	)

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

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

void compute_node_likelihoods_recursive	(	pTree	ptree,
		pTreeNode	ptnode
	)

void compute_tree_likelihoods ( pCafeTree pcafe )

void compute_viterbis	(	pCafeNode	node,
		int	k,
		double *	factors,
		int	rootfamilysize_start,
		int	rootfamilysize_end,
		int	familysize_start,
		int	familysize_end
	)

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

void free_probabilities ( struct probabilities * probs )

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

void get_keys_from_node	(	pCafeNode	pcnode,
		pArrayList	arr,
		int	num_lambdas
	)

double* get_likelihoods ( const pCafeTree pcafe )

void initialize_leaf_likelihood_clustered	(	pTree	ptree,
		pTreeNode	ptnode
	)

void initialize_leaf_likelihoods	(	pTree	ptree,
		pTreeNode	ptnode
	)

Set likelihood to 1 for actual value, 0 otherwise, or copy values from an existing errormodel Copies likelihood values from an errormodel if one exists, otherwise sets all likelihoods to 0 except for familysize, which is set to 1.

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 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.

Variable Documentation

struct chooseln_cache cache

A cache of values of chooseln.

Chooseln evaluates the natural logarithm of Gamma(n+1)/(Gamma(k+1)*Gamma(n-k+1)) The cache holds values for integer values of n and k. It does not appear to be threadsafe.

P(X(t) = c | X(0) = s) = {j=0}^{(s,c)} {s}{j}{s+c-j-1}{s-1} ^{s+c-2j}(1-2)^j

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.

Functions

Variables

Function Documentation

Variable Documentation