lambda_tests.cpp File Reference

#include <stdexcept>
#include <sstream>
#include <fstream>
#include <iostream>
#include <map>
#include "CppUTest/TestHarness.h"
#include "CppUTest/CommandLineTestRunner.h"
#include "cafe_commands.h"
#include "lambda.h"
#include "lambdamu.h"
#include "Globals.h"
#include <gene_family.h>
#include "cafe.h"
#include <cafe_shell.h>

Functions
void	cafe_shell_set_lambda (pCafeParam param, double *parameters)
int	__cafe_cmd_lambda_tree (pCafeParam param, char *arg1, char *arg2)
int	lambda_cmd_helper (Globals &globals)
	TEST_GROUP (LambdaTests)
	TEST (LambdaTests, cafe_cmd_lambda_fails_without_tree)
	TEST (LambdaTests, cafe_cmd_lambda_fails_without_load)
	TEST (LambdaTests, PrepareCafeParam)
	TEST (LambdaTests, TestCmdLambda)
	TEST (LambdaTests, TestLambdaTree)
	TEST (LambdaTests, Test_arguments)
	TEST (LambdaTests, Test_l_argument)
	TEST (LambdaTests, Test_p_argument)
	TEST (LambdaTests, Test_r_argument)
	TEST (LambdaTests, set_all_lambdas)
	TEST (LambdaTests, initialize_params_and_k_weights)
	TEST (LambdaTests, set_parameters)
void	mock_set_params (pCafeParam param, double *parameters)
	TEST (LambdaTests, lambda_set)
	TEST (LambdaTests, lambda_args__validate_parameter_count)
	TEST (LambdaTests, lambdamu_args__validate_parameter_count)
	TEST (LambdaTests, lambdamu_set)
	TEST (LambdaTests, lambdamu_set_without_lambda_tree)
	TEST (LambdaTests, lambdamu_set_with_k_weights)
	TEST (LambdaTests, lambdamu_set_with_k_weights_and_tree)
	TEST (LambdaTests, best_lambda_by_fminsearch)
	TEST (LambdaTests, best_lambda_mu_by_fminsearch)
	TEST (LambdaTests, get_posterior)
	TEST (LambdaTests, find_poisson_lambda)
	TEST (LambdaTests, get_posterior2)
	TEST (LambdaTests, collect_leaf_sizes)

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

Function Documentation

int __cafe_cmd_lambda_tree	(	pCafeParam	param,
		char *	arg1,
		char *	arg2
	)

void cafe_shell_set_lambda	(	pCafeParam	param,
		double *	parameters
	)

int lambda_cmd_helper

(

Globals &

globals

)

void mock_set_params	(	pCafeParam	param,
		double *	parameters
	)

TEST	(	LambdaTests	,
		cafe_cmd_lambda_fails_without_tree
	)

TEST	(	LambdaTests	,
		cafe_cmd_lambda_fails_without_load
	)

TEST	(	LambdaTests	,
		PrepareCafeParam
	)

TEST	(	LambdaTests	,
		TestCmdLambda
	)

TEST	(	LambdaTests	,
		TestLambdaTree
	)

TEST	(	LambdaTests	,
		Test_arguments
	)

TEST	(	LambdaTests	,
		Test_l_argument
	)

TEST	(	LambdaTests	,
		Test_p_argument
	)

TEST	(	LambdaTests	,
		Test_r_argument
	)

TEST	(	LambdaTests	,
		set_all_lambdas
	)

TEST	(	LambdaTests	,
		initialize_params_and_k_weights
	)

TEST	(	LambdaTests	,
		set_parameters
	)

TEST	(	LambdaTests	,
		lambda_set
	)

TEST	(	LambdaTests	,
		lambda_args__validate_parameter_count
	)

TEST	(	LambdaTests	,
		lambdamu_args__validate_parameter_count
	)

TEST	(	LambdaTests	,
		lambdamu_set
	)

TEST	(	LambdaTests	,
		lambdamu_set_without_lambda_tree
	)

TEST	(	LambdaTests	,
		lambdamu_set_with_k_weights
	)

TEST	(	LambdaTests	,
		lambdamu_set_with_k_weights_and_tree
	)

TEST	(	LambdaTests	,
		best_lambda_by_fminsearch
	)

TEST	(	LambdaTests	,
		best_lambda_mu_by_fminsearch
	)

TEST	(	LambdaTests	,
		get_posterior
	)

TEST	(	LambdaTests	,
		find_poisson_lambda
	)

TEST	(	LambdaTests	,
		get_posterior2
	)

TEST	(	LambdaTests	,
		collect_leaf_sizes
	)

TEST_GROUP

(

LambdaTests

)

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.