test.cpp File Reference

#include "../config.h"
#include <stdexcept>
#include <vector>
#include <string>
#include <sstream>
#include <iostream>
#include <math.h>
#include <algorithm>
#include <queue>
#include "gene_family.h"
#include <utils_string.h>
#include <cafe_shell.h>
#include <tree.h>
#include <cafe.h>
#include <chooseln_cache.h>
#include <cafe_commands.h>
#include <lambda.h>
#include <reports.h>
#include <likelihood_ratio.h>
#include <pvalue.h>
#include <branch_cutting.h>
#include <conditional_distribution.h>
#include <simerror.h>
#include <error_model.h>
#include <Globals.h>
#include <viterbi.h>
#include "CppUTest/TestHarness.h"
#include "CppUTest/CommandLineTestRunner.h"

Functions
void	show_sizes (FILE *, pCafeTree pcafe, family_size_range *range, pCafeFamilyItem pitem, int i)
void	phylogeny_lambda_parse_func (pTree ptree, pTreeNode ptnode)
	TEST_GROUP (FirstTestGroup)
	TEST_GROUP (LikelihoodRatio)
	TEST_GROUP (TreeTests)
	TEST_GROUP (PValueTests)
	TEST (TreeTests, node_set_birthdeath_matrix)
	TEST (TreeTests, cafe_tree_clustered_likelihood)
	TEST (TreeTests, node_set_birthdeath_matrix2)
	TEST (TreeTests, thousand_node_tree_to_string_and_back)
	TEST (FirstTestGroup, TestStringSplitter)
	TEST (FirstTestGroup, Tokenize)
	TEST (TreeTests, TestCafeTree)
	TEST (FirstTestGroup, TestShellDispatcher)
	TEST (FirstTestGroup, TestShowSizes)
	TEST (FirstTestGroup, TestPhylogenyLoadFromString)
void	build_matrix (square_matrix &m)
	TEST (TreeTests, compute_internal_node_likelihood)
pCafeTree	create_small_tree (family_size_range &range)
	TEST (TreeTests, compute_tree_likelihood)
	TEST (TreeTests, add_key)
	TEST (TreeTests, add_key_skips_matching_keys)
	TEST (FirstTestGroup, compute_likelihoods)
	TEST (FirstTestGroup, compute_posterior)
	TEST (FirstTestGroup, cafe_tree_p_values)
	TEST (FirstTestGroup, cafe_set_prior_rfsize_empirical)
	TEST (FirstTestGroup, cafe_set_prior_rfsize_poisson_lambda)
	TEST (FirstTestGroup, list_commands)
void	store_node_id (pTree ptree, pTreeNode ptnode, va_list ap1)
	TEST (FirstTestGroup, tree_traversal_prefix)
	TEST (FirstTestGroup, tree_traversal_infix)
	TEST (FirstTestGroup, tree_traversal_postfix)
	TEST (TreeTests, cafe_tree_random_probabilities)
	TEST (FirstTestGroup, cafe_tree_new_empty_node)
	TEST (FirstTestGroup, chooseln_cache)
	TEST (FirstTestGroup, birthdeath_rate_with_log_alpha)
	TEST (FirstTestGroup, birthdeath_likelihood_with_s_c)
	TEST (FirstTestGroup, square_matrix_resize)
	TEST (FirstTestGroup, square_matrix_multiply)
	TEST (FirstTestGroup, compute_birthdeath_rates)
	TEST (FirstTestGroup, compute_birthdeath_rates2)
std::ostream &	operator<< (std::ostream &ost, square_matrix &matrix)
	TEST (FirstTestGroup, compute_birthdeath_rates_without_mu)
	TEST (FirstTestGroup, clear_tree_viterbis)
int	get_family_size (pTree ptree, int id)
	TEST (FirstTestGroup, cafe_tree_random_familysize)
	TEST (FirstTestGroup, cafe_tree_random_familysize__must_be_less_than_cache_size)
	TEST (FirstTestGroup, reset_birthdeath_cache)
	TEST (FirstTestGroup, birthdeath_cache_get_matrix_ignores_fractional_branch_lengths)
	TEST (FirstTestGroup, get_num_trials)
	TEST (FirstTestGroup, viterbi_sum_probabilities)
	TEST (FirstTestGroup, initialize_leaf_likelihoods)
	TEST (FirstTestGroup, initialize_leaf_likelihoods_clustered)
	TEST (FirstTestGroup, get_clusters)
	TEST (FirstTestGroup, write_node_headers)
	TEST (FirstTestGroup, write_version)
	TEST (FirstTestGroup, compute_viterbis)
void	set_familysize_to_node_times_three (pTree ptree, pTreeNode pnode, va_list ap1)
	TEST (FirstTestGroup, write_leaves)
	TEST (FirstTestGroup, run_viterbi_sim)
	TEST (FirstTestGroup, init_histograms)
	TEST (FirstTestGroup, init_family_size)
	TEST (FirstTestGroup, cafe_tree_set_parameters)
	TEST (FirstTestGroup, cut_branch)
	TEST (FirstTestGroup, conditional_distribution)
	TEST (FirstTestGroup, set_size_for_split)
	TEST (FirstTestGroup, compute_cutpvalues)
	TEST (FirstTestGroup, simulate_misclassification)
	TEST (FirstTestGroup, get_random)
	TEST (FirstTestGroup, tree_set_branch_lengths)
	TEST (FirstTestGroup, initialize_k_bd_no_lambda)
	TEST (FirstTestGroup, initialize_k_bd_with_lambda)
	TEST (FirstTestGroup, globals_Clear__clears_probability_cache)
	TEST (FirstTestGroup, input_values_randomize__with_k)
	TEST (FirstTestGroup, input_values_randomize__without_k)
	TEST (FirstTestGroup, set_birth_death_probabilities3)
	TEST (FirstTestGroup, initialize_k_weights)
double	my_pvalue (double v, std::vector< double > &conddist)
	TEST (PValueTests, pvalue3)
	TEST (PValueTests, pvalue2)
	TEST (PValueTests, pvalue)
	TEST (PValueTests, pvalues_for_family)
	TEST (PValueTests, read_pvalues)
	TEST (LikelihoodRatio, cafe_likelihood_ratio_test)
	TEST (LikelihoodRatio, likelihood_ratio_report)
	TEST (LikelihoodRatio, update_branchlength)
	TEST (FirstTestGroup, sync_sanity_check_passes)
	TEST (FirstTestGroup, viterbi_max_p)
int	main (int ac, char **av)

Variables
pCafeParam	cafe_param
	Holds the global program state that user commands act on. More...
pBirthDeathCacheArray	probability_cache
struct chooseln_cache	cache
	A cache of values of chooseln. More...

Function Documentation

void build_matrix

(

square_matrix &

m

)

pCafeTree create_small_tree

(

family_size_range &

range

)

int get_family_size	(	pTree	ptree,
		int	id
	)

int main	(	int	ac,
		char **	av
	)

double my_pvalue	(	double	v,
		std::vector< double > &	conddist
	)

std::ostream& operator<<	(	std::ostream &	ost,
		square_matrix &	matrix
	)

void phylogeny_lambda_parse_func	(	pTree	ptree,
		pTreeNode	ptnode
	)

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

void show_sizes	(	FILE *	,
		pCafeTree	pcafe,
		family_size_range *	range,
		pCafeFamilyItem	pitem,
		int	i
	)

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

TEST	(	TreeTests	,
		node_set_birthdeath_matrix
	)

TEST	(	TreeTests	,
		cafe_tree_clustered_likelihood
	)

TEST	(	TreeTests	,
		node_set_birthdeath_matrix2
	)

TEST	(	TreeTests	,
		thousand_node_tree_to_string_and_back
	)

TEST	(	FirstTestGroup	,
		TestStringSplitter
	)

TEST	(	FirstTestGroup	,
		Tokenize
	)

TEST	(	TreeTests	,
		TestCafeTree
	)

TEST	(	FirstTestGroup	,
		TestShellDispatcher
	)

TEST	(	FirstTestGroup	,
		TestShowSizes
	)

TEST	(	FirstTestGroup	,
		TestPhylogenyLoadFromString
	)

TEST	(	TreeTests	,
		compute_internal_node_likelihood
	)

TEST	(	TreeTests	,
		compute_tree_likelihood
	)

TEST	(	TreeTests	,
		add_key
	)

TEST	(	TreeTests	,
		add_key_skips_matching_keys
	)

TEST	(	FirstTestGroup	,
		compute_likelihoods
	)

TEST	(	FirstTestGroup	,
		compute_posterior
	)

TEST	(	FirstTestGroup	,
		cafe_tree_p_values
	)

TEST	(	FirstTestGroup	,
		cafe_set_prior_rfsize_empirical
	)

TEST	(	FirstTestGroup	,
		cafe_set_prior_rfsize_poisson_lambda
	)

TEST	(	FirstTestGroup	,
		list_commands
	)

TEST	(	FirstTestGroup	,
		tree_traversal_prefix
	)

TEST	(	FirstTestGroup	,
		tree_traversal_infix
	)

TEST	(	FirstTestGroup	,
		tree_traversal_postfix
	)

TEST	(	TreeTests	,
		cafe_tree_random_probabilities
	)

TEST	(	FirstTestGroup	,
		cafe_tree_new_empty_node
	)

TEST	(	FirstTestGroup	,
		chooseln_cache
	)

TEST	(	FirstTestGroup	,
		birthdeath_rate_with_log_alpha
	)

TEST	(	FirstTestGroup	,
		birthdeath_likelihood_with_s_c
	)

TEST	(	FirstTestGroup	,
		square_matrix_resize
	)

TEST	(	FirstTestGroup	,
		square_matrix_multiply
	)

TEST	(	FirstTestGroup	,
		compute_birthdeath_rates
	)

TEST	(	FirstTestGroup	,
		compute_birthdeath_rates2
	)

TEST	(	FirstTestGroup	,
		compute_birthdeath_rates_without_mu
	)

TEST	(	FirstTestGroup	,
		clear_tree_viterbis
	)

TEST	(	FirstTestGroup	,
		cafe_tree_random_familysize
	)

TEST	(	FirstTestGroup	,
		cafe_tree_random_familysize__must_be_less_than_cache_size
	)

TEST	(	FirstTestGroup	,
		reset_birthdeath_cache
	)

TEST	(	FirstTestGroup	,
		birthdeath_cache_get_matrix_ignores_fractional_branch_lengths
	)

TEST	(	FirstTestGroup	,
		get_num_trials
	)

TEST	(	FirstTestGroup	,
		viterbi_sum_probabilities
	)

TEST	(	FirstTestGroup	,
		initialize_leaf_likelihoods
	)

TEST	(	FirstTestGroup	,
		initialize_leaf_likelihoods_clustered
	)

TEST	(	FirstTestGroup	,
		get_clusters
	)

TEST	(	FirstTestGroup	,
		write_node_headers
	)

TEST	(	FirstTestGroup	,
		write_version
	)

TEST	(	FirstTestGroup	,
		compute_viterbis
	)

TEST	(	FirstTestGroup	,
		write_leaves
	)

TEST	(	FirstTestGroup	,
		run_viterbi_sim
	)

TEST	(	FirstTestGroup	,
		init_histograms
	)

TEST	(	FirstTestGroup	,
		init_family_size
	)

TEST	(	FirstTestGroup	,
		cafe_tree_set_parameters
	)

TEST	(	FirstTestGroup	,
		cut_branch
	)

TEST	(	FirstTestGroup	,
		conditional_distribution
	)

TEST	(	FirstTestGroup	,
		set_size_for_split
	)

TEST	(	FirstTestGroup	,
		compute_cutpvalues
	)

TEST	(	FirstTestGroup	,
		simulate_misclassification
	)

TEST	(	FirstTestGroup	,
		get_random
	)

TEST	(	FirstTestGroup	,
		tree_set_branch_lengths
	)

TEST	(	FirstTestGroup	,
		initialize_k_bd_no_lambda
	)

TEST	(	FirstTestGroup	,
		initialize_k_bd_with_lambda
	)

TEST	(	FirstTestGroup	,
		globals_Clear__clears_probability_cache
	)

TEST	(	FirstTestGroup	,
		input_values_randomize__with_k
	)

TEST	(	FirstTestGroup	,
		input_values_randomize__without_k
	)

TEST	(	FirstTestGroup	,
		set_birth_death_probabilities3
	)

TEST	(	FirstTestGroup	,
		initialize_k_weights
	)

TEST	(	PValueTests	,
		pvalue3
	)

TEST	(	PValueTests	,
		pvalue2
	)

TEST	(	PValueTests	,
		pvalue
	)

TEST	(	PValueTests	,
		pvalues_for_family
	)

TEST	(	PValueTests	,
		read_pvalues
	)

TEST	(	LikelihoodRatio	,
		cafe_likelihood_ratio_test
	)

TEST	(	LikelihoodRatio	,
		likelihood_ratio_report
	)

TEST	(	LikelihoodRatio	,
		update_branchlength
	)

TEST	(	FirstTestGroup	,
		sync_sanity_check_passes
	)

TEST	(	FirstTestGroup	,
		viterbi_max_p
	)

TEST_GROUP

(

FirstTestGroup

)

TEST_GROUP

(

LikelihoodRatio

)

TEST_GROUP

(

TreeTests

)

TEST_GROUP

(

PValueTests

)

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

pCafeParam cafe_param

Holds the global program state that user commands act on.

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.