viterbi.cpp File Reference

#include <iostream>
#include <algorithm>
#include "viterbi.h"
#include "Globals.h"
#include "pvalue.h"
#include <family.h>
#include "cafe.h"
#include <pthread.h>

Functions
void	viterbi_parameters_init (viterbi_parameters *viterbi, int nnodes, int nrows)
void	viterbi_set_max_pvalue (viterbi_parameters *viterbi, int index, const std::vector< double > &values)
void	viterbi_sum_probabilities (viterbi_parameters *viterbi, pCafeTree pcafe, pCafeFamilyItem pitem)
void	familysize_sanity_check (pTree ptree)
void	viterbi_section (pCafeFamily pcf, double pvalue, int num_random_samples, viterbi_parameters *viterbi, int i, pCafeTree pcafe, double *cP, std::vector< std::vector< double > > *pCD)
void *	__cafe_viterbi_thread_func (void *ptr)
void	cafe_viterbi (Globals &globals, viterbi_parameters &viterbi, std::vector< std::vector< double > > *pCD)
void	cafe_viterbi_print (pCafeParam param, viterbi_parameters &viterbi)
void	__cafe_tree_node_compute_viterbi (pTree ptree, pTreeNode ptnode, va_list ap1)
void	__cafe_tree_node_backtrack_viterbi (pTree ptree, pTreeNode ptnode, va_list ap1)
void	__cafe_tree_node_compute_clustered_viterbi (pTree ptree, pTreeNode ptnode, va_list ap1)
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	viterbi_family_print (pCafeTree pcafe, pCafeFamily pfamily, int idx)

Variables
struct chooseln_cache	cache
	A cache of values of chooseln. More...
pthread_mutex_t	mutex_cafe_viterbi = PTHREAD_MUTEX_INITIALIZER

Function Documentation

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

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

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

void* __cafe_viterbi_thread_func

(

void *

ptr

)

void cafe_tree_clustered_viterbi	(	pCafeTree	pcafe,
		int	num_likelihoods
	)

void cafe_tree_viterbi

(

pCafeTree

pcafe

)

void cafe_tree_viterbi_posterior	(	pCafeTree	pcafe,
		pCafeParam	param
	)

void cafe_viterbi	(	Globals &	globals,
		viterbi_parameters &	viterbi,
		std::vector< std::vector< double > > *	pCD
	)

void cafe_viterbi_print	(	pCafeParam	param,
		viterbi_parameters &	viterbi
	)

void familysize_sanity_check

(

pTree

ptree

)

void viterbi_family_print	(	pCafeTree	pcafe,
		pCafeFamily	pfamily,
		int	idx
	)

void viterbi_parameters_init	(	viterbi_parameters *	viterbi,
		int	nnodes,
		int	nrows
	)

void viterbi_section	(	pCafeFamily	pcf,
		double	pvalue,
		int	num_random_samples,
		viterbi_parameters *	viterbi,
		int	i,
		pCafeTree	pcafe,
		double *	cP,
		std::vector< std::vector< double > > *	pCD
	)

void viterbi_set_max_pvalue	(	viterbi_parameters *	viterbi,
		int	index,
		const std::vector< double > &	values
	)

void viterbi_sum_probabilities	(	viterbi_parameters *	viterbi,
		pCafeTree	pcafe,
		pCafeFamilyItem	pitem
	)

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

pthread_mutex_t mutex_cafe_viterbi = PTHREAD_MUTEX_INITIALIZER