CTrie< Trie > Class Template Reference

Inheritance diagram for CTrie< Trie >:

[legend]

List of all members.

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Detailed Description

template<class Trie>
class CTrie< Trie >

class Trie

Definition at line 134 of file Trie.h.

Public Member Functions
	CTrie (INT d, bool p_use_compact_terminal_nodes=true)
	CTrie (const CTrie &to_copy)
	~CTrie ()
const CTrie &	operator= (const CTrie &to_copy)
bool	compare_traverse (INT node, const CTrie &other, INT other_node)
bool	compare (const CTrie &other)
bool	find_node (INT node, INT *trace, INT &trace_len) const
INT	find_deepest_node (INT start_node, INT &deepest_node) const
void	display_node (INT node) const
void	destroy ()
void	set_degree (INT d)
void	create (INT len, bool p_use_compact_terminal_nodes=true)
void	delete_trees (bool p_use_compact_terminal_nodes=true)
void	add_to_trie (int i, INT seq_offset, INT *vec, float alpha, DREAL *weights, bool degree_times_position_weights)
DREAL	compute_abs_weights_tree (INT tree, INT depth)
DREAL *	compute_abs_weights (int &len)
DREAL	compute_by_tree_helper (INT *vec, INT len, INT seq_pos, INT tree_pos, INT weight_pos, DREAL *weights, bool degree_times_position_weights)
void	compute_by_tree_helper (INT *vec, INT len, INT seq_pos, INT tree_pos, INT weight_pos, DREAL *LevelContrib, DREAL factor, INT mkl_stepsize, DREAL *weights, bool degree_times_position_weights)
void	compute_scoring_helper (INT tree, INT i, INT j, DREAL weight, INT d, INT max_degree, INT num_feat, INT num_sym, INT sym_offset, INT offs, DREAL *result)
void	add_example_to_tree_mismatch_recursion (INT tree, INT i, DREAL alpha, INT *vec, INT len_rem, INT degree_rec, INT mismatch_rec, INT max_mismatch, DREAL *weights)
void	traverse (INT tree, const INT p, struct TreeParseInfo info, const INT depth, INT *const x, const INT k)
void	count (const DREAL w, const INT depth, const struct TreeParseInfo info, const INT p, INT *x, const INT k)
INT	compact_nodes (INT start_node, INT depth, DREAL *weights)
DREAL	get_cumulative_score (INT pos, ULONG seq, INT deg, DREAL *weights)
void	fill_backtracking_table_recursion (Trie *tree, INT depth, ULONG seq, DREAL value, CDynamicArray< ConsensusEntry > *table, DREAL *weights)
void	fill_backtracking_table (INT pos, CDynamicArray< ConsensusEntry > *prev, CDynamicArray< ConsensusEntry > *cur, bool cumulative, DREAL *weights)
void	POIMs_extract_W (DREAL *const *const W, const INT K)
void	POIMs_precalc_SLR (const DREAL *const distrib)
void	POIMs_get_SLR (const INT parentIdx, const INT sym, const int depth, DREAL *S, DREAL *L, DREAL *R)
void	POIMs_add_SLR (DREAL *const *const poims, const INT K, const INT debug)
bool	get_use_compact_terminal_nodes ()
void	set_use_compact_terminal_nodes (bool p_use_compact_terminal_nodes)
INT	get_num_used_nodes ()
void	set_position_weights (const DREAL *p_position_weights)
INT	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 INT nodeIdx, const int depth, const INT offset, const INT y0, DREAL *const *const W, const INT K)
void	POIMs_calc_SLR_helper1 (const DREAL *const distrib, const INT i, const INT nodeIdx, INT left_tries_idx[4], const int depth, INT const lastSym, DREAL *S, DREAL *L, DREAL *R)
void	POIMs_calc_SLR_helper2 (const DREAL *const distrib, const INT i, const INT nodeIdx, INT left_tries_idx[4], const int depth, DREAL *S, DREAL *L, DREAL *R)
void	POIMs_add_SLR_helper1 (const INT nodeIdx, const int depth, const INT i, const INT y0, DREAL *const *const poims, const INT K, const INT debug)
void	POIMs_add_SLR_helper2 (DREAL *const *const poims, const int K, const int k, const INT i, const INT y, const DREAL valW, const DREAL valS, const DREAL valL, const DREAL valR, const INT debug)
Public Attributes
INT	NUM_SYMS
Static Public Attributes
static CParallel	parallel
static CIO	io
static CVersion	version
Protected Attributes
INT	length
INT *	trees
INT	degree
DREAL const *	position_weights
Trie *	TreeMem
INT	TreeMemPtr
INT	TreeMemPtrMax
bool	use_compact_terminal_nodes
bool	weights_in_tree
INT *	nofsKmers

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Constructor & Destructor Documentation

template<class Trie>

CTrie< Trie >::CTrie	(	INT	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 586 of file Trie.h.

template<class Trie>

CTrie< Trie >::CTrie

(

const CTrie< Trie > &

to_copy

)

copy constructor

Definition at line 602 of file Trie.h.

template<class Trie>

CTrie< Trie >::~CTrie

(

)

Definition at line 1031 of file Trie.h.

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Member Function Documentation

template<class Trie>

const CTrie< Trie > & CTrie< Trie >::operator=

(

const CTrie< Trie > &

to_copy

)

overload operator =

Definition at line 630 of file Trie.h.

template<class Trie>

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

compare traverse

Parameters:

	node	node
	other	other trie
	other_node	other node

Returns:

if comparison was successful

Definition at line 828 of file Trie.h.

template<class Trie>

bool CTrie< Trie >::compare

(

const CTrie< Trie > &

other

)

compare

Parameters:

other

other trie

Returns:

if comparison was successful

Definition at line 914 of file Trie.h.

template<class Trie>

bool CTrie< Trie >::find_node	(	INT	node,
		INT *	trace,
		INT &	trace_len
	)			const

find node

Parameters:

	node	node to find
	trace	trace
	trace_len	length of trace

Definition at line 927 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::find_deepest_node	(	INT	start_node,
		INT &	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 664 of file Trie.h.

template<class Trie>

void CTrie< Trie >::display_node

(

INT

node

)

const

display node

Parameters:

node

node to display

Definition at line 967 of file Trie.h.

template<class Trie>

void CTrie< Trie >::destroy

(

)

destroy

Definition at line 1038 of file Trie.h.

template<class Trie>

void CTrie< Trie >::set_degree

(

INT

d

)

set degree

Parameters:

d

new degree

Definition at line 1053 of file Trie.h.

template<class Trie>

void CTrie< Trie >::create	(	INT	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 1059 of file Trie.h.

template<class Trie>

void CTrie< Trie >::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 1073 of file Trie.h.

template<class Trie>

void CTrie< Trie >::add_to_trie	(	int	i,
		INT	seq_offset,
		INT *	vec,
		float	alpha,
		DREAL *	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 1389 of file Trie.h.

template<class Trie>

DREAL CTrie< Trie >::compute_abs_weights_tree	(	INT	tree,
		INT	depth
	)

compute absolute weights tree

Parameters:

	tree	tree to compute for
	depth	depth

Returns:

computed absolute weights tree

Definition at line 1086 of file Trie.h.

template<class Trie>

DREAL * CTrie< Trie >::compute_abs_weights

(

int &

len

)

compute absolute weights

Parameters:

len

length

Returns:

computed absolute weights

Definition at line 1115 of file Trie.h.

template<class Trie>

DREAL CTrie< Trie >::compute_by_tree_helper	(	INT *	vec,
		INT	len,
		INT	seq_pos,
		INT	tree_pos,
		INT	weight_pos,
		DREAL *	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 1613 of file Trie.h.

template<class Trie>

void CTrie< Trie >::compute_by_tree_helper	(	INT *	vec,
		INT	len,
		INT	seq_pos,
		INT	tree_pos,
		INT	weight_pos,
		DREAL *	LevelContrib,
		DREAL	factor,
		INT	mkl_stepsize,
		DREAL *	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 1688 of file Trie.h.

template<class Trie>

void CTrie< Trie >::compute_scoring_helper	(	INT	tree,
		INT	i,
		INT	j,
		DREAL	weight,
		INT	d,
		INT	max_degree,
		INT	num_feat,
		INT	num_sym,
		INT	sym_offset,
		INT	offs,
		DREAL *	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 1247 of file Trie.h.

template<class Trie>

void CTrie< Trie >::add_example_to_tree_mismatch_recursion	(	INT	tree,
		INT	i,
		DREAL	alpha,
		INT *	vec,
		INT	len_rem,
		INT	degree_rec,
		INT	mismatch_rec,
		INT	max_mismatch,
		DREAL *	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 1135 of file Trie.h.

template<class Trie>

void CTrie< Trie >::traverse	(	INT	tree,
		const INT	p,
		struct TreeParseInfo	info,
		const INT	depth,
		INT *const	x,
		const INT	k
	)

traverse

Parameters:

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

Definition at line 1289 of file Trie.h.

template<class Trie>

void CTrie< Trie >::count	(	const DREAL	w,
		const INT	depth,
		const struct TreeParseInfo	info,
		const INT	p,
		INT *	x,
		const INT	k
	)

count

Parameters:

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

Definition at line 1337 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::compact_nodes	(	INT	start_node,
		INT	depth,
		DREAL *	weights
	)

compact nodes

Parameters:

	start_node	start node
	depth	depth
	weights	weights

Definition at line 720 of file Trie.h.

template<class Trie>

DREAL CTrie< Trie >::get_cumulative_score	(	INT	pos,
		ULONG	seq,
		INT	deg,
		DREAL *	weights
	)

get cumulative score

Parameters:

	pos	position
	seq	sequence
	deg	degree
	weights	weights

Returns:

cumulative score

Definition at line 1946 of file Trie.h.

template<class Trie>

void CTrie< Trie >::fill_backtracking_table_recursion	(	Trie *	tree,
		INT	depth,
		ULONG	seq,
		DREAL	value,
		CDynamicArray< ConsensusEntry > *	table,
		DREAL *	weights
	)

fill backtracking table recursion

Parameters:

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

Definition at line 1906 of file Trie.h.

template<class Trie>

void CTrie< Trie >::fill_backtracking_table	(	INT	pos,
		CDynamicArray< ConsensusEntry > *	prev,
		CDynamicArray< ConsensusEntry > *	cur,
		bool	cumulative,
		DREAL *	weights
	)

fill backtracking table

Parameters:

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

Definition at line 1977 of file Trie.h.

template<class Trie>

void CTrie< Trie >::POIMs_extract_W	(	DREAL *const *const	W,
		const INT	K
	)

POIMs extract W

Parameters:

	W	W
	K	K

template<class Trie>

void CTrie< Trie >::POIMs_precalc_SLR

(

const DREAL *const

distrib

)

POIMs precalc SLR

Parameters:

distrib

distribution

template<class Trie>

void CTrie< Trie >::POIMs_get_SLR	(	const INT	parentIdx,
		const INT	sym,
		const int	depth,
		DREAL *	S,
		DREAL *	L,
		DREAL *	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

template<class Trie>

void CTrie< Trie >::POIMs_add_SLR	(	DREAL *const *const	poims,
		const INT	K,
		const INT	debug
	)

POIMs add SLR

Parameters:

	poims	POIMs
	K	K
	debug	debug level

template<class Trie>

bool CTrie< Trie >::get_use_compact_terminal_nodes

(

)

get use compact terminal nodes

Returns:

if compact terminal nodes are used

Definition at line 398 of file Trie.h.

template<class Trie>

void CTrie< Trie >::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 408 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::get_num_used_nodes

(

)

get number of used nodes

Returns:

number of used nodes

Definition at line 417 of file Trie.h.

template<class Trie>

void CTrie< Trie >::set_position_weights

(

const DREAL *

p_position_weights

)

set position weights

Parameters:

p_position_weights

new position weights

Definition at line 426 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::get_node

(

bool

last_node = false

)

get node

Returns:

node

Definition at line 435 of file Trie.h.

template<class Trie>

void CTrie< Trie >::check_treemem

(

)

check tree memory usage

Definition at line 459 of file Trie.h.

template<class Trie>

void CTrie< Trie >::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 476 of file Trie.h.

template<class Trie>

bool CTrie< Trie >::get_weights_in_tree

(

)

get weights in tree

Returns:

if weights are in tree

Definition at line 485 of file Trie.h.

template<class Trie>

void CTrie< Trie >::POIMs_extract_W_helper	(	const INT	nodeIdx,
		const int	depth,
		const INT	offset,
		const INT	y0,
		DREAL *const *const	W,
		const INT	K
	)

POIMs extract W helper

Parameters:

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

template<class Trie>

void CTrie< Trie >::POIMs_calc_SLR_helper1	(	const DREAL *const	distrib,
		const INT	i,
		const INT	nodeIdx,
		INT	left_tries_idx[4],
		const int	depth,
		INT const	lastSym,
		DREAL *	S,
		DREAL *	L,
		DREAL *	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

template<class Trie>

void CTrie< Trie >::POIMs_calc_SLR_helper2	(	const DREAL *const	distrib,
		const INT	i,
		const INT	nodeIdx,
		INT	left_tries_idx[4],
		const int	depth,
		DREAL *	S,
		DREAL *	L,
		DREAL *	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

template<class Trie>

void CTrie< Trie >::POIMs_add_SLR_helper1	(	const INT	nodeIdx,
		const int	depth,
		const INT	i,
		const INT	y0,
		DREAL *const *const	poims,
		const INT	K,
		const INT	debug
	)

POIMs add SLR helper 1

Parameters:

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

template<class Trie>

void CTrie< Trie >::POIMs_add_SLR_helper2	(	DREAL *const *const	poims,
		const int	K,
		const int	k,
		const INT	i,
		const INT	y,
		const DREAL	valW,
		const DREAL	valS,
		const DREAL	valL,
		const DREAL	valR,
		const INT	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

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Member Data Documentation

template<class Trie>

INT CTrie< Trie >::NUM_SYMS

number of symbols

Definition at line 556 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::length [protected]

length

Definition at line 560 of file Trie.h.

template<class Trie>

INT* CTrie< Trie >::trees [protected]

trees

Definition at line 562 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::degree [protected]

degree

Definition at line 565 of file Trie.h.

template<class Trie>

DREAL const* CTrie< Trie >::position_weights [protected]

position weights

Definition at line 567 of file Trie.h.

template<class Trie>

Trie* CTrie< Trie >::TreeMem [protected]

tree memory

Definition at line 570 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::TreeMemPtr [protected]

tree memory pointer

Definition at line 572 of file Trie.h.

template<class Trie>

INT CTrie< Trie >::TreeMemPtrMax [protected]

tree memory pointer maximum

Definition at line 574 of file Trie.h.

template<class Trie>

bool CTrie< Trie >::use_compact_terminal_nodes [protected]

if compact terminal nodes are used

Definition at line 576 of file Trie.h.

template<class Trie>

bool CTrie< Trie >::weights_in_tree [protected]

if weights are in tree

Definition at line 579 of file Trie.h.

template<class Trie>

INT* CTrie< Trie >::nofsKmers [protected]

nofsKmers

Definition at line 582 of file Trie.h.

CParallel CSGObject::parallel [static, inherited]

Definition at line 105 of file SGObject.h.

CIO CSGObject::io [static, inherited]

Definition at line 106 of file SGObject.h.

CVersion CSGObject::version [static, inherited]

Definition at line 107 of file SGObject.h.

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

• Trie.h