Detailed Description

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.

Definition at line 136 of file Trie.h.

Inheritance diagram for CTrie< Trie >:

[legend]

Public Member Functions
	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)

bool	has (const std::string &name) const

template<typename T >
bool	has (const Tag< T > &tag) const

template<typename T , typename U = void>
bool	has (const std::string &name) const

template<typename T >
void	set (const Tag< T > &_tag, const T &value)

template<typename T , typename U = void>
void	set (const std::string &name, const T &value)

template<typename T >
T	get (const Tag< T > &_tag) const

template<typename T , typename U = void>
T	get (const std::string &name) const

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 Attributes
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 Member Functions
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)

template<typename T >
void	register_param (Tag< T > &_tag, const T &value)

template<typename T >
void	register_param (const std::string &name, const T &value)

Protected Attributes
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

Constructor & Destructor Documentation

CTrie ( )

default constructor

Definition at line 662 of file Trie.h.

CTrie	(	int32_t	d,
		bool	p_use_compact_terminal_nodes = `true`
	)

constructor

Parameters

d	degree
p_use_compact_terminal_nodes	if compact terminal nodes shall be used

Definition at line 679 of file Trie.h.

CTrie ( const CTrie< Trie > & to_copy )

copy constructor

Definition at line 695 of file Trie.h.

~CTrie ( )

virtual

Definition at line 1128 of file Trie.h.

Member Function Documentation

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

Parameters

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

Definition at line 1234 of file Trie.h.

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

Parameters

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

Definition at line 1496 of file Trie.h.

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.

Parameters

dict	dictionary of parameters to be built.

Definition at line 630 of file SGObject.cpp.

void check_treemem ( )

check tree memory usage

Definition at line 518 of file Trie.h.

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.

Returns: 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

Definition at line 747 of file SGObject.cpp.

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

compact nodes

Parameters

start_node	start node
depth	depth
weights	weights

Definition at line 814 of file Trie.h.

bool compare ( const CTrie< Trie > & other )

compare

Parameters

other other trie

Returns: if comparison was successful

Definition at line 1010 of file Trie.h.

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

compare traverse

Parameters

node	node
other	other trie
other_node	other node

Returns: if comparison was successful

Definition at line 923 of file Trie.h.

float64_t * compute_abs_weights ( int32_t & len )

compute absolute weights

Parameters

len length

Returns: computed absolute weights

Definition at line 1214 of file Trie.h.

float64_t compute_abs_weights_tree	(	int32_t	tree,
		int32_t	depth
	)

compute absolute weights tree

Parameters

tree	tree to compute for
depth	depth

Returns: computed absolute weights tree

Definition at line 1185 of file Trie.h.

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

Parameters

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

Returns: a computed value

Definition at line 1722 of file Trie.h.

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

Parameters

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

Definition at line 1797 of file Trie.h.

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

Parameters

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

Definition at line 1347 of file Trie.h.

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

Parameters

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

Definition at line 1442 of file Trie.h.

void create	(	int32_t	len,
		bool	p_use_compact_terminal_nodes = `true`
	)

create

Parameters

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

Definition at line 1156 of file Trie.h.

CSGObject * deep_copy ( ) const

virtualinherited

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

Definition at line 231 of file SGObject.cpp.

void delete_trees ( bool p_use_compact_terminal_nodes = true )

delete trees

Parameters

p_use_compact_terminal_nodes if compact terminal nodes shall be used

Definition at line 1171 of file Trie.h.

void destroy ( )

destroy

Definition at line 1135 of file Trie.h.

void display_node ( int32_t node ) const

display node

Parameters

node	node to display

Definition at line 1064 of file Trie.h.

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.

Parameters

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

Returns: true if all parameters were equal, false if not

Definition at line 651 of file SGObject.cpp.

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

fill backtracking table

Parameters

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

Definition at line 2087 of file Trie.h.

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

Parameters

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

Definition at line 2013 of file Trie.h.

int32_t find_deepest_node	(	int32_t	start_node,
		int32_t &	deepest_node
	)		const

find deepest node

Parameters

start_node	start node
deepest_node	deepest node will be stored in here

Returns: depth of deepest node

Definition at line 757 of file Trie.h.

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

find node

Parameters

node	node to find
trace	trace
trace_len	length of trace

Definition at line 1023 of file Trie.h.

T get ( const Tag< T > & _tag ) const

inherited

Getter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter

Returns: value of the parameter identified by the input tag

Definition at line 367 of file SGObject.h.

T get ( const std::string & name ) const

inherited

Getter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter

Returns: value of the parameter corresponding to the input name and type

Definition at line 388 of file SGObject.h.

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

get cumulative score

Parameters

pos	position
seq	sequence
deg	degree
weights	weights

Returns: cumulative score

Definition at line 2055 of file Trie.h.

SGIO * get_global_io ( )

inherited

get the io object

Returns: io object

Definition at line 268 of file SGObject.cpp.

Parallel * get_global_parallel ( )

inherited

get the parallel object

Returns: parallel object

Definition at line 310 of file SGObject.cpp.

Version * get_global_version ( )

inherited

get the version object

Returns: version object

Definition at line 323 of file SGObject.cpp.

SGStringList< char > get_modelsel_names ( )

inherited

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

Definition at line 531 of file SGObject.cpp.

char * get_modsel_param_descr ( const char * param_name )

inherited

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

Parameters

param_name name of the parameter

Returns: description of the parameter

Definition at line 555 of file SGObject.cpp.

index_t get_modsel_param_index ( const char * param_name )

inherited

Returns index of model selection parameter with provided index

Parameters

param_name name of model selection parameter

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

Definition at line 568 of file SGObject.cpp.

virtual const char* get_name ( ) const

virtual

Returns: object name

Implements CSGObject.

Definition at line 629 of file Trie.h.

int32_t get_node ( bool last_node = false )

get node

Returns: node

Definition at line 494 of file Trie.h.

int32_t get_num_used_nodes ( )

get number of used nodes

Returns: number of used nodes

Definition at line 476 of file Trie.h.

bool get_use_compact_terminal_nodes ( )

get use compact terminal nodes

Returns: if compact terminal nodes are used

Definition at line 456 of file Trie.h.

bool get_weights_in_tree ( )

get weights in tree

Returns: if weights are in tree

Definition at line 542 of file Trie.h.

bool has ( const std::string & name ) const

inherited

Checks if object has a class parameter identified by a name.

Parameters

name	name of the parameter

Returns: true if the parameter exists with the input name

Definition at line 289 of file SGObject.h.

bool has ( const Tag< T > & tag ) const

inherited

Checks if object has a class parameter identified by a Tag.

Parameters

tag	tag of the parameter containing name and type information

Returns: true if the parameter exists with the input tag

Definition at line 301 of file SGObject.h.

bool has ( const std::string & name ) const

inherited

Checks if a type exists for a class parameter identified by a name.

Parameters

name	name of the parameter

Returns: true if the parameter exists with the input name and type

Definition at line 312 of file SGObject.h.

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.

Parameters

generic set to the type of the generic if returning TRUE

Returns: TRUE if a class template.

Definition at line 329 of file SGObject.cpp.

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!

Parameters

file	where to load from
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 402 of file SGObject.cpp.

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.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 459 of file SGObject.cpp.

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.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 454 of file SGObject.cpp.

const CTrie< Trie > & operator= ( const CTrie< Trie > & to_copy )

overload operator =

Definition at line 723 of file Trie.h.

bool parameter_hash_changed ( )

virtualinherited

Returns: whether parameter combination has changed since last update

Definition at line 295 of file SGObject.cpp.

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

Definition at line 412 of file Trie.cpp.

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

POIMs add SLR

Parameters

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
	)

Definition at line 355 of file Trie.cpp.

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

Parameters

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
	)

Definition at line 294 of file Trie.cpp.

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

Parameters

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
	)

Definition at line 74 of file Trie.cpp.

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

Parameters

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
	)

Definition at line 134 of file Trie.cpp.

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

Parameters

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
	)

Definition at line 60 of file Trie.cpp.

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

POIMs extract W

Parameters

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
	)

Definition at line 19 of file Trie.cpp.

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

Parameters

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
	)

Definition at line 272 of file Trie.cpp.

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

Parameters

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 )

Definition at line 245 of file Trie.cpp.

void POIMs_precalc_SLR ( const float64_t *const distrib )

POIMs precalc SLR

Parameters

distrib distribution

void print_modsel_params ( )

inherited

prints all parameter registered for model selection and their type

Definition at line 507 of file SGObject.cpp.

void print_serializable ( const char * prefix = "" )

virtualinherited

prints registered parameters out

Parameters

prefix prefix for members

Definition at line 341 of file SGObject.cpp.

void register_param	(	Tag< T > &	_tag,
		const T &	value
	)

protectedinherited

Registers a class parameter which is identified by a tag. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 439 of file SGObject.h.

void register_param	(	const std::string &	name,
		const T &	value
	)

protectedinherited

Registers a class parameter which is identified by a name. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 452 of file SGObject.h.

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

virtualinherited

Save this object to file.

Parameters

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

Returns: TRUE if done, otherwise FALSE

Definition at line 347 of file SGObject.cpp.

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.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel.

Definition at line 469 of file SGObject.cpp.

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.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 464 of file SGObject.cpp.

void set	(	const Tag< T > &	_tag,
		const T &	value
	)

inherited

Setter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 328 of file SGObject.h.

void set	(	const std::string &	name,
		const T &	value
	)

inherited

Setter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 354 of file SGObject.h.

void set_degree ( int32_t d )

set degree

Parameters

d	new degree

Definition at line 1150 of file Trie.h.

void set_generic ( )

inherited

Definition at line 74 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 79 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 84 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 89 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 94 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 99 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 104 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 109 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 114 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 119 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 124 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 129 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 134 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 139 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 144 of file SGObject.cpp.

void set_generic ( )

inherited

set generic type to T

void set_global_io ( SGIO * io )

inherited

set the io object

Parameters

io	io object to use

Definition at line 261 of file SGObject.cpp.

void set_global_parallel ( Parallel * parallel )

inherited

set the parallel object

Parameters

parallel parallel object to use

Definition at line 274 of file SGObject.cpp.

void set_global_version ( Version * version )

inherited

set the version object

Parameters

version version object to use

Definition at line 316 of file SGObject.cpp.

void set_position_weights ( float64_t * p_position_weights )

set position weights

Parameters

p_position_weights new position weights

Definition at line 485 of file Trie.h.

void set_use_compact_terminal_nodes ( bool p_use_compact_terminal_nodes )

set use compact terminal nodes

Parameters

p_use_compact_terminal_nodes if compact terminal nodes shall be used

Definition at line 466 of file Trie.h.

void set_weights_in_tree ( bool weights_in_tree_ )

set weights in tree

Parameters

weights_in_tree_ if weights shall be in tree

Definition at line 533 of file Trie.h.

CSGObject * shallow_copy ( ) const

virtualinherited

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

Reimplemented in CGaussianKernel.

Definition at line 225 of file SGObject.cpp.

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

Parameters

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

Definition at line 1392 of file Trie.h.

void unset_generic ( )

inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 336 of file SGObject.cpp.

void update_parameter_hash ( )

virtualinherited

Updates the hash of current parameter combination

Definition at line 281 of file SGObject.cpp.

Member Data Documentation

int32_t degree

protected

degree

Definition at line 642 of file Trie.h.

SGIO* io

inherited

io

Definition at line 537 of file SGObject.h.

int32_t length

protected

length

Definition at line 637 of file Trie.h.

Parameter* m_gradient_parameters

inherited

parameters wrt which we can compute gradients

Definition at line 552 of file SGObject.h.

uint32_t m_hash

inherited

Hash of parameter values

Definition at line 555 of file SGObject.h.

Parameter* m_model_selection_parameters

inherited

model selection parameters

Definition at line 549 of file SGObject.h.

Parameter* m_parameters

inherited

parameters

Definition at line 546 of file SGObject.h.

int32_t* nofsKmers

protected

nofsKmers

Definition at line 659 of file Trie.h.

int32_t NUM_SYMS

number of symbols

Definition at line 633 of file Trie.h.

Parallel* parallel

inherited

parallel

Definition at line 540 of file SGObject.h.

float64_t* position_weights

protected

position weights

Definition at line 644 of file Trie.h.

Trie* TreeMem

protected

tree memory

Definition at line 647 of file Trie.h.

int32_t TreeMemPtr

protected

tree memory pointer

Definition at line 649 of file Trie.h.

int32_t TreeMemPtrMax

protected

tree memory pointer maximum

Definition at line 651 of file Trie.h.

int32_t* trees

protected

trees

Definition at line 639 of file Trie.h.

bool use_compact_terminal_nodes

protected

if compact terminal nodes are used

Definition at line 653 of file Trie.h.

Version* version

inherited

version

Definition at line 543 of file SGObject.h.

bool weights_in_tree

protected

if weights are in tree

Definition at line 656 of file Trie.h.

The documentation for this class was generated from the following file:

Trie.h

Detailed Description

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

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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