CTrie< Trie > 模板类 参考

详细描述

template<class Trie>
class shogun::CTrie< Trie >

Template class Trie implements a suffix trie, i.e. a tree in which all suffixes up to a certain length are stored.

It is excessively used in the CWeightedDegreeStringKernel and CWeightedDegreePositionStringKernel to construct the whole features space \(\Phi(x)\) and enormously helps here to speed up SVM training and evaluation.

Note that depending on the underlying structure used, a single symbol in the tree requires 20 bytes (DNATrie). It is also used to do the efficient recursion in computing positional oligomer importance matrices (POIMs) where the structure requires * 20+3*8 (POIMTrie) bytes.

Finally note that this tree may use compact internal nodes (for strings that appear without modifications, thus not requiring further branches), which may save a lot of memory on higher degree tries.

在文件 Trie.h 第 136 行定义.

类 CTrie< Trie > 继承关系图:

Public 成员函数
	CTrie ()
	CTrie (int32_t d, bool p_use_compact_terminal_nodes=true)
	CTrie (const CTrie &to_copy)
virtual	~CTrie ()
const CTrie &	operator= (const CTrie &to_copy)
bool	compare_traverse (int32_t node, const CTrie &other, int32_t other_node)
bool	compare (const CTrie &other)
bool	find_node (int32_t node, int32_t *trace, int32_t &trace_len) const
int32_t	find_deepest_node (int32_t start_node, int32_t &deepest_node) const
void	display_node (int32_t node) const
void	destroy ()
void	set_degree (int32_t d)
void	create (int32_t len, bool p_use_compact_terminal_nodes=true)
void	delete_trees (bool p_use_compact_terminal_nodes=true)
void	add_to_trie (int32_t i, int32_t seq_offset, int32_t *vec, float32_t alpha, float64_t *weights, bool degree_times_position_weights)
float64_t	compute_abs_weights_tree (int32_t tree, int32_t depth)
float64_t *	compute_abs_weights (int32_t &len)
float64_t	compute_by_tree_helper (int32_t *vec, int32_t len, int32_t seq_pos, int32_t tree_pos, int32_t weight_pos, float64_t *weights, bool degree_times_position_weights)
void	compute_by_tree_helper (int32_t *vec, int32_t len, int32_t seq_pos, int32_t tree_pos, int32_t weight_pos, float64_t *LevelContrib, float64_t factor, int32_t mkl_stepsize, float64_t *weights, bool degree_times_position_weights)
void	compute_scoring_helper (int32_t tree, int32_t i, int32_t j, float64_t weight, int32_t d, int32_t max_degree, int32_t num_feat, int32_t num_sym, int32_t sym_offset, int32_t offs, float64_t *result)
void	add_example_to_tree_mismatch_recursion (int32_t tree, int32_t i, float64_t alpha, int32_t *vec, int32_t len_rem, int32_t degree_rec, int32_t mismatch_rec, int32_t max_mismatch, float64_t *weights)
void	traverse (int32_t tree, const int32_t p, struct TreeParseInfo info, const int32_t depth, int32_t *const x, const int32_t k)
void	count (const float64_t w, const int32_t depth, const struct TreeParseInfo info, const int32_t p, int32_t *x, const int32_t k)
int32_t	compact_nodes (int32_t start_node, int32_t depth, float64_t *weights)
float64_t	get_cumulative_score (int32_t pos, uint64_t seq, int32_t deg, float64_t *weights)
void	fill_backtracking_table_recursion (Trie *tree, int32_t depth, uint64_t seq, float64_t value, DynArray< ConsensusEntry > *table, float64_t *weights)
void	fill_backtracking_table (int32_t pos, DynArray< ConsensusEntry > *prev, DynArray< ConsensusEntry > *cur, bool cumulative, float64_t *weights)
void	POIMs_extract_W (float64_t *const *const W, const int32_t K)
void	POIMs_precalc_SLR (const float64_t *const distrib)
void	POIMs_get_SLR (const int32_t parentIdx, const int32_t sym, const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
void	POIMs_add_SLR (float64_t *const *const poims, const int32_t K, const int32_t debug)
bool	get_use_compact_terminal_nodes ()
void	set_use_compact_terminal_nodes (bool p_use_compact_terminal_nodes)
int32_t	get_num_used_nodes ()
void	set_position_weights (float64_t *p_position_weights)
int32_t	get_node (bool last_node=false)
void	check_treemem ()
void	set_weights_in_tree (bool weights_in_tree_)
bool	get_weights_in_tree ()
void	POIMs_extract_W_helper (const int32_t nodeIdx, const int32_t depth, const int32_t offset, const int32_t y0, float64_t *const *const W, const int32_t K)
void	POIMs_calc_SLR_helper1 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, int32_t const lastSym, float64_t *S, float64_t *L, float64_t *R)
void	POIMs_calc_SLR_helper2 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
void	POIMs_add_SLR_helper1 (const int32_t nodeIdx, const int32_t depth, const int32_t i, const int32_t y0, float64_t *const *const poims, const int32_t K, const int32_t debug)
void	POIMs_add_SLR_helper2 (float64_t *const *const poims, const int32_t K, const int32_t k, const int32_t i, const int32_t y, const float64_t valW, const float64_t valS, const float64_t valL, const float64_t valR, const int32_t debug)
virtual const char *	get_name () const
template<>
void	POIMs_extract_W_helper (const int32_t nodeIdx, const int32_t depth, const int32_t offset, const int32_t y0, float64_t *const *const W, const int32_t K)
template<>
void	POIMs_extract_W (float64_t *const *const W, const int32_t K)
template<>
void	POIMs_calc_SLR_helper1 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, int32_t const lastSym, float64_t *S, float64_t *L, float64_t *R)
template<>
void	POIMs_calc_SLR_helper2 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
template<>
void	POIMs_precalc_SLR (const float64_t *const distrib)
template<>
void	POIMs_get_SLR (const int32_t parentIdx, const int32_t sym, const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
template<>
void	POIMs_add_SLR_helper2 (float64_t *const *const poims, const int32_t K, const int32_t k, const int32_t i, const int32_t y, const float64_t valW, const float64_t valS, const float64_t valL, const float64_t valR, const int32_t debug)
template<>
void	POIMs_add_SLR_helper1 (const int32_t nodeIdx, const int32_t depth, const int32_t i, const int32_t y0, float64_t *const *const poims, const int32_t K, const int32_t debug)
template<>
void	POIMs_add_SLR (float64_t *const *const poims, const int32_t K, const int32_t debug)
virtual CSGObject *	shallow_copy () const
virtual CSGObject *	deep_copy () const
virtual bool	is_generic (EPrimitiveType *generic) const
template<class T >
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
template<>
void	set_generic ()
void	unset_generic ()
virtual void	print_serializable (const char *prefix="")
virtual bool	save_serializable (CSerializableFile *file, const char *prefix="")
virtual bool	load_serializable (CSerializableFile *file, const char *prefix="")
void	set_global_io (SGIO *io)
SGIO *	get_global_io ()
void	set_global_parallel (Parallel *parallel)
Parallel *	get_global_parallel ()
void	set_global_version (Version *version)
Version *	get_global_version ()
SGStringList< char >	get_modelsel_names ()
void	print_modsel_params ()
char *	get_modsel_param_descr (const char *param_name)
index_t	get_modsel_param_index (const char *param_name)
void	build_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict)
virtual void	update_parameter_hash ()
virtual bool	parameter_hash_changed ()
virtual bool	equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)
virtual CSGObject *	clone ()

Public 属性
int32_t	NUM_SYMS
SGIO *	io
Parallel *	parallel
Version *	version
Parameter *	m_parameters
Parameter *	m_model_selection_parameters
Parameter *	m_gradient_parameters
uint32_t	m_hash

Protected 成员函数
virtual void	load_serializable_pre () throw (ShogunException)
virtual void	load_serializable_post () throw (ShogunException)
virtual void	save_serializable_pre () throw (ShogunException)
virtual void	save_serializable_post () throw (ShogunException)

Protected 属性
int32_t	length
int32_t *	trees
int32_t	degree
float64_t *	position_weights
Trie *	TreeMem
int32_t	TreeMemPtr
int32_t	TreeMemPtrMax
bool	use_compact_terminal_nodes
bool	weights_in_tree
int32_t *	nofsKmers

构造及析构函数说明

CTrie

(

)

default constructor

在文件 Trie.h 第 662 行定义.

CTrie	(	int32_t	d,
		bool	p_use_compact_terminal_nodes = true
	)

constructor

参数

d	degree
p_use_compact_terminal_nodes	if compact terminal nodes shall be used

在文件 Trie.h 第 679 行定义.

CTrie

(

const CTrie< Trie > &

to_copy

)

copy constructor

在文件 Trie.h 第 695 行定义.

~CTrie ( )

virtual

在文件 Trie.h 第 1128 行定义.

成员函数说明

void add_example_to_tree_mismatch_recursion	(	int32_t	tree,
		int32_t	i,
		float64_t	alpha,
		int32_t *	vec,
		int32_t	len_rem,
		int32_t	degree_rec,
		int32_t	mismatch_rec,
		int32_t	max_mismatch,
		float64_t *	weights
	)

add example to tree mismatch recursion

参数

tree	tree
i	i
alpha	alpha
vec	vector
len_rem	length of rem
degree_rec	degree rec
mismatch_rec	mismatch rec
max_mismatch	maximum mismatch
weights	weights

在文件 Trie.h 第 1234 行定义.

void add_to_trie	(	int32_t	i,
		int32_t	seq_offset,
		int32_t *	vec,
		float32_t	alpha,
		float64_t *	weights,
		bool	degree_times_position_weights
	)

add to trie

参数

i	i
seq_offset	sequence offset
vec	vector
alpha	alpha
weights	weights
degree_times_position_weights	if degree times position weights shall be applied

在文件 Trie.h 第 1496 行定义.

void build_gradient_parameter_dictionary ( CMap< TParameter *, CSGObject * > *  dict )

inherited

Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.

参数

dict	dictionary of parameters to be built.

在文件 SGObject.cpp 第 597 行定义.

void check_treemem

(

)

check tree memory usage

在文件 Trie.h 第 518 行定义.

CSGObject * clone ( )

virtualinherited

Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.

返回

an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

在文件 SGObject.cpp 第 714 行定义.

int32_t compact_nodes	(	int32_t	start_node,
		int32_t	depth,
		float64_t *	weights
	)

compact nodes

参数

start_node	start node
depth	depth
weights	weights

在文件 Trie.h 第 814 行定义.

bool compare

(

const CTrie< Trie > &

other

)

compare

参数

other

other trie

返回

if comparison was successful

在文件 Trie.h 第 1010 行定义.

bool compare_traverse	(	int32_t	node,
		const CTrie< Trie > &	other,
		int32_t	other_node
	)

compare traverse

参数

node	node
other	other trie
other_node	other node

返回

if comparison was successful

在文件 Trie.h 第 923 行定义.

float64_t * compute_abs_weights

(

int32_t &

len

)

compute absolute weights

参数

len

length

返回

computed absolute weights

在文件 Trie.h 第 1214 行定义.

float64_t compute_abs_weights_tree	(	int32_t	tree,
		int32_t	depth
	)

compute absolute weights tree

参数

tree	tree to compute for
depth	depth

返回

computed absolute weights tree

在文件 Trie.h 第 1185 行定义.

float64_t compute_by_tree_helper	(	int32_t *	vec,
		int32_t	len,
		int32_t	seq_pos,
		int32_t	tree_pos,
		int32_t	weight_pos,
		float64_t *	weights,
		bool	degree_times_position_weights
	)

compute by tree helper

参数

vec	vector
len	length
seq_pos	sequence position
tree_pos	tree position
weight_pos	weight position
weights
degree_times_position_weights	if degree times position weights shall be applied

返回

a computed value

在文件 Trie.h 第 1722 行定义.

void compute_by_tree_helper	(	int32_t *	vec,
		int32_t	len,
		int32_t	seq_pos,
		int32_t	tree_pos,
		int32_t	weight_pos,
		float64_t *	LevelContrib,
		float64_t	factor,
		int32_t	mkl_stepsize,
		float64_t *	weights,
		bool	degree_times_position_weights
	)

compute by tree helper

参数

vec	vector
len	length
seq_pos	sequence position
tree_pos	tree position
weight_pos	weight position
LevelContrib	level contribution
factor	factor
mkl_stepsize	MKL stepsize
weights
degree_times_position_weights	if degree times position weights shall be applied

在文件 Trie.h 第 1797 行定义.

void compute_scoring_helper	(	int32_t	tree,
		int32_t	i,
		int32_t	j,
		float64_t	weight,
		int32_t	d,
		int32_t	max_degree,
		int32_t	num_feat,
		int32_t	num_sym,
		int32_t	sym_offset,
		int32_t	offs,
		float64_t *	result
	)

compute scoring helper

参数

tree	tree
i	i
j	j
weight	weight
d	degree
max_degree	maximum degree
num_feat	number of features
num_sym	number of symbols
sym_offset	symbol offset
offs	offsets
result	result

在文件 Trie.h 第 1347 行定义.

void count	(	const float64_t	w,
		const int32_t	depth,
		const struct TreeParseInfo	info,
		const int32_t	p,
		int32_t *	x,
		const int32_t	k
	)

count

参数

w	w
depth	depth
info	tree parse info
p	p
x	x
k

在文件 Trie.h 第 1442 行定义.

void create	(	int32_t	len,
		bool	p_use_compact_terminal_nodes = true
	)

create

参数

len	length of new trie
p_use_compact_terminal_nodes	if compact terminal nodes shall be used

在文件 Trie.h 第 1156 行定义.

CSGObject * deep_copy ( ) const

virtualinherited

A deep copy. All the instance variables will also be copied.

在文件 SGObject.cpp 第 198 行定义.

void delete_trees

(

bool

p_use_compact_terminal_nodes = true

)

delete trees

参数

p_use_compact_terminal_nodes

if compact terminal nodes shall be used

在文件 Trie.h 第 1171 行定义.

void destroy

(

)

destroy

在文件 Trie.h 第 1135 行定义.

void display_node

(

int32_t

node

)

const

display node

参数

node	node to display

在文件 Trie.h 第 1064 行定义.

bool equals ( CSGObject *  other, float64_t  accuracy = 0.0, bool  tolerant = false  )

virtualinherited

Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!

May be overwritten but please do with care! Should not be necessary in most cases.

参数

other	object to compare with
accuracy	accuracy to use for comparison (optional)
tolerant	allows linient check on float equality (within accuracy)

返回

true if all parameters were equal, false if not

在文件 SGObject.cpp 第 618 行定义.

void fill_backtracking_table	(	int32_t	pos,
		DynArray< ConsensusEntry > *	prev,
		DynArray< ConsensusEntry > *	cur,
		bool	cumulative,
		float64_t *	weights
	)

fill backtracking table

参数

pos	position
prev	previous concencus entry
cur	current concensus entry
cumulative	if is cumulative
weights	weights

在文件 Trie.h 第 2087 行定义.

void fill_backtracking_table_recursion	(	Trie *	tree,
		int32_t	depth,
		uint64_t	seq,
		float64_t	value,
		DynArray< ConsensusEntry > *	table,
		float64_t *	weights
	)

fill backtracking table recursion

参数

tree	tree
depth	depth
seq	sequence
value	value
table	table of concensus entries
weights	weights

在文件 Trie.h 第 2013 行定义.

int32_t find_deepest_node	(	int32_t	start_node,
		int32_t &	deepest_node
	)		const

find deepest node

参数

start_node	start node
deepest_node	deepest node will be stored in here

返回

depth of deepest node

在文件 Trie.h 第 757 行定义.

bool find_node	(	int32_t	node,
		int32_t *	trace,
		int32_t &	trace_len
	)		const

find node

参数

node	node to find
trace	trace
trace_len	length of trace

在文件 Trie.h 第 1023 行定义.

float64_t get_cumulative_score	(	int32_t	pos,
		uint64_t	seq,
		int32_t	deg,
		float64_t *	weights
	)

get cumulative score

参数

pos	position
seq	sequence
deg	degree
weights	weights

返回

cumulative score

在文件 Trie.h 第 2055 行定义.

SGIO * get_global_io ( )

inherited

get the io object

返回

io object

在文件 SGObject.cpp 第 235 行定义.

Parallel * get_global_parallel ( )

inherited

get the parallel object

返回

parallel object

在文件 SGObject.cpp 第 277 行定义.

Version * get_global_version ( )

inherited

get the version object

返回

version object

在文件 SGObject.cpp 第 290 行定义.

SGStringList< char > get_modelsel_names ( )

inherited

返回

vector of names of all parameters which are registered for model selection

在文件 SGObject.cpp 第 498 行定义.

char * get_modsel_param_descr ( const char *  param_name )

inherited

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

参数

param_name

name of the parameter

返回

description of the parameter

在文件 SGObject.cpp 第 522 行定义.

index_t get_modsel_param_index ( const char *  param_name )

inherited

Returns index of model selection parameter with provided index

参数

param_name

name of model selection parameter

返回

index of model selection parameter with provided name, -1 if there is no such

在文件 SGObject.cpp 第 535 行定义.

virtual const char* get_name ( ) const

virtual

返回

object name

实现了 CSGObject.

在文件 Trie.h 第 629 行定义.

int32_t get_node

(

bool

last_node = false

)

get node

返回

node

在文件 Trie.h 第 494 行定义.

int32_t get_num_used_nodes

(

)

get number of used nodes

返回

number of used nodes

在文件 Trie.h 第 476 行定义.

bool get_use_compact_terminal_nodes

(

)

get use compact terminal nodes

返回

if compact terminal nodes are used

在文件 Trie.h 第 456 行定义.

bool get_weights_in_tree

(

)

get weights in tree

返回

if weights are in tree

在文件 Trie.h 第 542 行定义.

bool is_generic ( EPrimitiveType *  generic ) const

virtualinherited

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

参数

generic

set to the type of the generic if returning TRUE

返回

TRUE if a class template.

在文件 SGObject.cpp 第 296 行定义.

bool load_serializable ( CSerializableFile *  file, const char *  prefix = ""  )

virtualinherited

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

参数

file	where to load from
prefix	prefix for members

返回

TRUE if done, otherwise FALSE

在文件 SGObject.cpp 第 369 行定义.

void load_serializable_post ( ) throw ( ShogunException )

protectedvirtualinherited

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

异常

ShogunException

will be thrown if an error occurs.

被 CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel , 以及 CExponentialKernel 重载.

在文件 SGObject.cpp 第 426 行定义.

void load_serializable_pre ( ) throw ( ShogunException )

protectedvirtualinherited

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.

异常

ShogunException

will be thrown if an error occurs.

被 CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.

在文件 SGObject.cpp 第 421 行定义.

const CTrie< Trie > & operator=

(

const CTrie< Trie > &

to_copy

)

overload operator =

在文件 Trie.h 第 723 行定义.

bool parameter_hash_changed ( )

virtualinherited

返回

whether parameter combination has changed since last update

在文件 SGObject.cpp 第 262 行定义.

void POIMs_add_SLR	(	float64_t *const *const	poims,
		const int32_t	K,
		const int32_t	debug
	)

在文件 Trie.cpp 第 412 行定义.

void POIMs_add_SLR	(	float64_t *const *const	poims,
		const int32_t	K,
		const int32_t	debug
	)

POIMs add SLR

参数

poims	POIMs
K	K
debug	debug level

void POIMs_add_SLR_helper1	(	const int32_t	nodeIdx,
		const int32_t	depth,
		const int32_t	i,
		const int32_t	y0,
		float64_t *const *const	poims,
		const int32_t	K,
		const int32_t	debug
	)

在文件 Trie.cpp 第 355 行定义.

void POIMs_add_SLR_helper1	(	const int32_t	nodeIdx,
		const int32_t	depth,
		const int32_t	i,
		const int32_t	y0,
		float64_t *const *const	poims,
		const int32_t	K,
		const int32_t	debug
	)

POIMs add SLR helper 1

参数

nodeIdx	node index
depth	depth
i	i
y0	y0
poims	POIMs
K	K
debug	debug level

void POIMs_add_SLR_helper2	(	float64_t *const *const	poims,
		const int32_t	K,
		const int32_t	k,
		const int32_t	i,
		const int32_t	y,
		const float64_t	valW,
		const float64_t	valS,
		const float64_t	valL,
		const float64_t	valR,
		const int32_t	debug
	)

在文件 Trie.cpp 第 294 行定义.

void POIMs_add_SLR_helper2	(	float64_t *const *const	poims,
		const int32_t	K,
		const int32_t	k,
		const int32_t	i,
		const int32_t	y,
		const float64_t	valW,
		const float64_t	valS,
		const float64_t	valL,
		const float64_t	valR,
		const int32_t	debug
	)

POIMs add SLR helper 2

参数

poims	POIMs
K	K
k	k
i	i
y	y
valW	value W
valS	value S
valL	value L
valR	value R
debug	debug level

void POIMs_calc_SLR_helper1	(	const float64_t *const	distrib,
		const int32_t	i,
		const int32_t	nodeIdx,
		int32_t	left_tries_idx[4],
		const int32_t	depth,
		int32_t const	lastSym,
		float64_t *	S,
		float64_t *	L,
		float64_t *	R
	)

在文件 Trie.cpp 第 74 行定义.

void POIMs_calc_SLR_helper1	(	const float64_t *const	distrib,
		const int32_t	i,
		const int32_t	nodeIdx,
		int32_t	left_tries_idx[4],
		const int32_t	depth,
		int32_t const	lastSym,
		float64_t *	S,
		float64_t *	L,
		float64_t *	R
	)

POIMs calc SLR helper

参数

distrib	distribution
i	i
nodeIdx	node index
left_tries_idx	left tries index
depth	depth
lastSym	last symbol
S	S
L	L
R	R

void POIMs_calc_SLR_helper2	(	const float64_t *const	distrib,
		const int32_t	i,
		const int32_t	nodeIdx,
		int32_t	left_tries_idx[4],
		const int32_t	depth,
		float64_t *	S,
		float64_t *	L,
		float64_t *	R
	)

在文件 Trie.cpp 第 134 行定义.

void POIMs_calc_SLR_helper2	(	const float64_t *const	distrib,
		const int32_t	i,
		const int32_t	nodeIdx,
		int32_t	left_tries_idx[4],
		const int32_t	depth,
		float64_t *	S,
		float64_t *	L,
		float64_t *	R
	)

POIMs calc SLR helper 2

参数

distrib	distribution
i	i
nodeIdx	node index
left_tries_idx	left tries index
depth	depth
S	S
L	L
R	R

void POIMs_extract_W	(	float64_t *const *const	W,
		const int32_t	K
	)

在文件 Trie.cpp 第 60 行定义.

void POIMs_extract_W	(	float64_t *const *const	W,
		const int32_t	K
	)

POIMs extract W

参数

W	W
K	K

void POIMs_extract_W_helper	(	const int32_t	nodeIdx,
		const int32_t	depth,
		const int32_t	offset,
		const int32_t	y0,
		float64_t *const *const	W,
		const int32_t	K
	)

在文件 Trie.cpp 第 19 行定义.

void POIMs_extract_W_helper	(	const int32_t	nodeIdx,
		const int32_t	depth,
		const int32_t	offset,
		const int32_t	y0,
		float64_t *const *const	W,
		const int32_t	K
	)

POIMs extract W helper

参数

nodeIdx	node index
depth	depth
offset	offset
y0	y0
W	W
K	K

void POIMs_get_SLR	(	const int32_t	parentIdx,
		const int32_t	sym,
		const int32_t	depth,
		float64_t *	S,
		float64_t *	L,
		float64_t *	R
	)

在文件 Trie.cpp 第 272 行定义.

void POIMs_get_SLR	(	const int32_t	parentIdx,
		const int32_t	sym,
		const int32_t	depth,
		float64_t *	S,
		float64_t *	L,
		float64_t *	R
	)

POIMs get SLR

参数

parentIdx	parent index
sym	symbol
depth	depth
S	will point to S
L	will point to L
R	will point to R

void POIMs_precalc_SLR

(

const float64_t *const

distrib

)

在文件 Trie.cpp 第 245 行定义.

void POIMs_precalc_SLR

(

const float64_t *const

distrib

)

POIMs precalc SLR

参数

distrib

distribution

void print_modsel_params ( )

inherited

prints all parameter registered for model selection and their type

在文件 SGObject.cpp 第 474 行定义.

void print_serializable ( const char *  prefix = "" )

virtualinherited

prints registered parameters out

参数

prefix

prefix for members

在文件 SGObject.cpp 第 308 行定义.

bool save_serializable ( CSerializableFile *  file, const char *  prefix = ""  )

virtualinherited

Save this object to file.

参数

file	where to save the object; will be closed during returning if PREFIX is an empty string.
prefix	prefix for members

返回

TRUE if done, otherwise FALSE

在文件 SGObject.cpp 第 314 行定义.

void save_serializable_post ( ) throw ( ShogunException )

protectedvirtualinherited

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.

异常

ShogunException

will be thrown if an error occurs.

被 CKernel 重载.

在文件 SGObject.cpp 第 436 行定义.

void save_serializable_pre ( ) throw ( ShogunException )

protectedvirtualinherited

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.

异常

ShogunException

will be thrown if an error occurs.

被 CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.

在文件 SGObject.cpp 第 431 行定义.

void set_degree

(

int32_t

d

)

set degree

参数

d	new degree

在文件 Trie.h 第 1150 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 41 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 46 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 51 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 56 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 61 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 66 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 71 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 76 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 81 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 86 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 91 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 96 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 101 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 106 行定义.

void set_generic ( )

inherited

在文件 SGObject.cpp 第 111 行定义.

void set_generic ( )

inherited

set generic type to T

void set_global_io ( SGIO *  io )

inherited

set the io object

参数

io	io object to use

在文件 SGObject.cpp 第 228 行定义.

void set_global_parallel ( Parallel *  parallel )

inherited

set the parallel object

参数

parallel

parallel object to use

在文件 SGObject.cpp 第 241 行定义.

void set_global_version ( Version *  version )

inherited

set the version object

参数

version

version object to use

在文件 SGObject.cpp 第 283 行定义.

void set_position_weights

(

float64_t *

p_position_weights

)

set position weights

参数

p_position_weights

new position weights

在文件 Trie.h 第 485 行定义.

void set_use_compact_terminal_nodes

(

bool

p_use_compact_terminal_nodes

)

set use compact terminal nodes

参数

p_use_compact_terminal_nodes

if compact terminal nodes shall be used

在文件 Trie.h 第 466 行定义.

void set_weights_in_tree

(

bool

weights_in_tree_

)

set weights in tree

参数

weights_in_tree_

if weights shall be in tree

在文件 Trie.h 第 533 行定义.

CSGObject * shallow_copy ( ) const

virtualinherited

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

被 CGaussianKernel 重载.

在文件 SGObject.cpp 第 192 行定义.

void traverse	(	int32_t	tree,
		const int32_t	p,
		struct TreeParseInfo	info,
		const int32_t	depth,
		int32_t *const	x,
		const int32_t	k
	)

traverse

参数

tree	tree
p	p
info	tree parse info
depth	depth
x	x
k	k

在文件 Trie.h 第 1392 行定义.

void unset_generic ( )

inherited

unset generic type

this has to be called in classes specializing a template class

在文件 SGObject.cpp 第 303 行定义.

void update_parameter_hash ( )

virtualinherited

Updates the hash of current parameter combination

在文件 SGObject.cpp 第 248 行定义.

类成员变量说明

int32_t degree

protected

degree

在文件 Trie.h 第 642 行定义.

SGIO* io

inherited

io

在文件 SGObject.h 第 369 行定义.

int32_t length

protected

length

在文件 Trie.h 第 637 行定义.

Parameter* m_gradient_parameters

inherited

parameters wrt which we can compute gradients

在文件 SGObject.h 第 384 行定义.

uint32_t m_hash

inherited

Hash of parameter values

在文件 SGObject.h 第 387 行定义.

Parameter* m_model_selection_parameters

inherited

model selection parameters

在文件 SGObject.h 第 381 行定义.

Parameter* m_parameters

inherited

parameters

在文件 SGObject.h 第 378 行定义.

int32_t* nofsKmers

protected

nofsKmers

在文件 Trie.h 第 659 行定义.

int32_t NUM_SYMS

number of symbols

在文件 Trie.h 第 633 行定义.

Parallel* parallel

inherited

parallel

在文件 SGObject.h 第 372 行定义.

float64_t* position_weights

protected

position weights

在文件 Trie.h 第 644 行定义.

Trie* TreeMem

protected

tree memory

在文件 Trie.h 第 647 行定义.

int32_t TreeMemPtr

protected

tree memory pointer

在文件 Trie.h 第 649 行定义.

int32_t TreeMemPtrMax

protected

tree memory pointer maximum

在文件 Trie.h 第 651 行定义.

int32_t* trees

protected

trees

在文件 Trie.h 第 639 行定义.

bool use_compact_terminal_nodes

protected

if compact terminal nodes are used

在文件 Trie.h 第 653 行定义.

Version* version

inherited

version

在文件 SGObject.h 第 375 行定义.

bool weights_in_tree

protected

if weights are in tree

在文件 Trie.h 第 656 行定义.

---

该类的文档由以下文件生成:

• Trie.h