family.h File Reference

#include <tree.h>
#include <birthdeath.h>
#include "input_values.h"

Go to the source code of this file.

Data Structures
struct	family_size_range
struct	CafeTree
struct	ErrorStruct
struct	probabilities
struct	CafeNode
struct	CafeFamily
	Structure representing a matrix of values of family sizes. More...
struct	tagCafeParam
	Singleton structure that holds all of the global data that Cafe acts on. More...

Macros
#define	FAMILYSIZEMAX   1000

Typedefs
typedef CafeTree *	pCafeTree
typedef ErrorStruct *	pErrorStruct
typedef CafeNode *	pCafeNode
typedef CafeFamily *	pCafeFamily
typedef struct tagCafeParam	CafeParam
typedef CafeParam *	pCafeParam
typedef void(*	param_func )(pCafeParam param, double *parameters)

Enumerations
enum	OPTIMIZER_INIT_TYPE { UNKNOWN, DO_NOTHING, LAMBDA_ONLY, LAMBDA_MU }

Functions
void	free_probabilities (struct probabilities *probs)
void	init_family_size (family_size_range *fs, int max)
void	copy_range_to_tree (pCafeTree tree, family_size_range *range)
void	cafe_shell_set_lambdas (pCafeParam param, double *lambda)
void	thread_run_with_arraylist (int numthreads, void *(*run)(void *), pArrayList pal)
void	cafe_tree_set_birthdeath (pCafeTree pcafe, int max_family_size)

Macro Definition Documentation

#define FAMILYSIZEMAX   1000

Typedef Documentation

typedef struct tagCafeParam CafeParam

typedef void(* param_func)(pCafeParam param, double *parameters)

typedef CafeFamily* pCafeFamily

typedef CafeNode* pCafeNode

typedef CafeParam* pCafeParam

typedef CafeTree* pCafeTree

typedef ErrorStruct* pErrorStruct

Enumeration Type Documentation

enum OPTIMIZER_INIT_TYPE

Enumerator
UNKNOWN
DO_NOTHING
LAMBDA_ONLY
LAMBDA_MU

Function Documentation

void cafe_shell_set_lambdas	(	pCafeParam	param,
		double *	lambda
	)

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 copy_range_to_tree	(	pCafeTree	tree,
		family_size_range *	range
	)

void free_probabilities

(

struct probabilities *

probs

)

void init_family_size	(	family_size_range *	fs,
		int	max
	)

void thread_run_with_arraylist	(	int	numthreads,
		void *(*)(void *)	run,
		pArrayList	pal
	)