command_tests.cpp File Reference

#include <stdexcept>
#include <vector>
#include <string>
#include <sstream>
#include <map>
#include "CppUTest/TestHarness.h"
#include "CppUTest/CommandLineTestRunner.h"
#include "cafe_commands.h"
#include "reports.h"
#include "Globals.h"
#include "viterbi.h"
#include "gene_family.h"
#include "cafe.h"

Functions
	TEST_GROUP (CommandTests)
	TEST (CommandTests, command_list)
	TEST (CommandTests, Test_cafe_cmd_source_prereqs)
	TEST (CommandTests, cafe_cmd_generate_random_family)
	TEST (CommandTests, cafe_cmd_date)
	TEST (CommandTests, cafe_cmd_echo)
	TEST (CommandTests, cafe_cmd_exit)
	TEST (CommandTests, cafe_command_report_prereqs)
void	assert_gainloss_exception (Globals &globals, std::string expected)
	TEST (CommandTests, cafe_cmd_gainloss_exceptions)
	TEST (CommandTests, cafe_cmd_log)
	TEST (CommandTests, get_load_arguments)
	TEST (CommandTests, get_load_arguments_filter_and_max_size)
	TEST (CommandTests, cafe_cmd_load)
	TEST (CommandTests, cafe_cmd_save)
	TEST (CommandTests, cafe_cmd_tree)
	TEST (CommandTests, cafe_cmd_tree_syncs_family_if_loaded)
	TEST (CommandTests, cafe_cmd_tree_missing_branch_length)
void	prepare_viterbi (CafeParam &param)
	TEST (CommandTests, cafe_cmd_viterbi_id_not_existing)
	TEST (CommandTests, cafe_cmd_viterbi_family_out_of_range)
	TEST (CommandTests, cafe_cmd_viterbi_args)
	TEST (CommandTests, viterbi_write)
	TEST (CommandTests, get_pvalue_arguments)
	TEST (CommandTests, get_lhtest_arguments)
	TEST (CommandTests, cafe_cmd_lhtest)
	TEST (CommandTests, cafe_cmd_esterror)
	TEST (CommandTests, validate_esterror)
	TEST (CommandTests, cafe_cmd_seed)

Variables
struct chooseln_cache	cache
	A cache of values of chooseln. More...
pBirthDeathCacheArray	probability_cache

Function Documentation

void assert_gainloss_exception	(	Globals &	globals,
		std::string	expected
	)

void prepare_viterbi

(

CafeParam &

param

)

TEST	(	CommandTests	,
		command_list
	)

TEST	(	CommandTests	,
		Test_cafe_cmd_source_prereqs
	)

TEST	(	CommandTests	,
		cafe_cmd_generate_random_family
	)

TEST	(	CommandTests	,
		cafe_cmd_date
	)

TEST	(	CommandTests	,
		cafe_cmd_echo
	)

TEST	(	CommandTests	,
		cafe_cmd_exit
	)

TEST	(	CommandTests	,
		cafe_command_report_prereqs
	)

TEST	(	CommandTests	,
		cafe_cmd_gainloss_exceptions
	)

TEST	(	CommandTests	,
		cafe_cmd_log
	)

TEST	(	CommandTests	,
		get_load_arguments
	)

TEST	(	CommandTests	,
		get_load_arguments_filter_and_max_size
	)

TEST	(	CommandTests	,
		cafe_cmd_load
	)

TEST	(	CommandTests	,
		cafe_cmd_save
	)

TEST	(	CommandTests	,
		cafe_cmd_tree
	)

TEST	(	CommandTests	,
		cafe_cmd_tree_syncs_family_if_loaded
	)

TEST	(	CommandTests	,
		cafe_cmd_tree_missing_branch_length
	)

TEST	(	CommandTests	,
		cafe_cmd_viterbi_id_not_existing
	)

TEST	(	CommandTests	,
		cafe_cmd_viterbi_family_out_of_range
	)

TEST	(	CommandTests	,
		cafe_cmd_viterbi_args
	)

TEST	(	CommandTests	,
		viterbi_write
	)

TEST	(	CommandTests	,
		get_pvalue_arguments
	)

TEST	(	CommandTests	,
		get_lhtest_arguments
	)

TEST	(	CommandTests	,
		cafe_cmd_lhtest
	)

TEST	(	CommandTests	,
		cafe_cmd_esterror
	)

TEST	(	CommandTests	,
		validate_esterror
	)

TEST	(	CommandTests	,
		cafe_cmd_seed
	)

TEST_GROUP

(

CommandTests

)

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.