详细描述

Dynamic Programming Class.

Structure and Function collection. This Class implements a Dynamic Programming functions.

在文件 DynProg.h 第 74 行定义.

类 CDynProg 继承关系图:

Public 成员函数
	CDynProg (int32_t p_num_svms=8)

virtual	~CDynProg ()

void	set_num_states (int32_t N)

int32_t	get_num_states ()

int32_t	get_num_svms ()

void	init_content_svm_value_array (const int32_t p_num_svms)

void	init_tiling_data (int32_t probe_pos, float64_t intensities, const int32_t num_probes)

void	precompute_tiling_plifs (CPlif *PEN, const int32_t tiling_plif_ids, const int32_t num_tiling_plifs)

void	resize_lin_feat (int32_t num_new_feat)

void	set_p_vector (SGVector< float64_t > p)

void	set_q_vector (SGVector< float64_t > q)

void	set_a (SGMatrix< float64_t > a)

void	set_a_id (SGMatrix< int32_t > a)

void	set_a_trans_matrix (SGMatrix< float64_t > a_trans)

void	init_mod_words_array (SGMatrix< int32_t > p_mod_words_array)

bool	check_svm_arrays ()

void	set_observation_matrix (SGNDArray< float64_t > seq)

int32_t	get_num_positions ()

void	set_content_type_array (SGMatrix< float64_t > seg_path)

void	set_pos (SGVector< int32_t > pos)

void	set_orf_info (SGMatrix< int32_t > orf_info)

void	set_gene_string (SGVector< char > genestr)

void	set_dict_weights (SGMatrix< float64_t > dictionary_weights)

void	best_path_set_segment_loss (SGMatrix< float64_t > segment_loss)

void	best_path_set_segment_ids_mask (int32_t segment_ids, float64_t segment_mask, int32_t m)

void	set_sparse_features (CSparseFeatures< float64_t > seq_sparse1, CSparseFeatures< float64_t > seq_sparse2)

void	set_plif_matrices (CPlifMatrix *pm)

SGVector< float64_t >	get_scores ()

SGMatrix< int32_t >	get_states ()

SGMatrix< int32_t >	get_positions ()

void	compute_nbest_paths (int32_t max_num_signals, bool use_orf, int16_t nbest, bool with_loss, bool with_multiple_sequences)

void	best_path_trans_deriv (int32_t my_state_seq, int32_t my_pos_seq, int32_t my_seq_len, const float64_t *seq_array, int32_t max_num_signals)

void	set_my_state_seq (int32_t *my_state_seq)

void	set_my_pos_seq (int32_t *my_pos_seq)

void	get_path_scores (float64_t *my_scores, int32_t seq_len)

void	get_path_losses (float64_t *my_losses, int32_t seq_len)

T_STATES	get_N () const
	access function for number of states N 更多...

void	set_q (T_STATES offset, float64_t value)

void	set_p (T_STATES offset, float64_t value)

void	set_a (T_STATES line_, T_STATES column, float64_t value)

float64_t	get_q (T_STATES offset) const

float64_t	get_q_deriv (T_STATES offset) const

float64_t	get_p (T_STATES offset) const

float64_t	get_p_deriv (T_STATES offset) const

void	precompute_content_values ()

float64_t *	get_lin_feat (int32_t &dim1, int32_t &dim2)

void	set_lin_feat (float64_t *p_lin_feat, int32_t p_num_svms, int32_t p_seq_len)

void	create_word_string ()

void	precompute_stop_codons ()

float64_t	get_a (T_STATES line_, T_STATES column) const

float64_t	get_a_deriv (T_STATES line_, T_STATES column) const

void	set_intron_list (CIntronList *intron_list, int32_t num_plifs)

CSegmentLoss *	get_segment_loss_object ()

void	long_transition_settings (bool use_long_transitions, int32_t threshold, int32_t max_len)

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
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
void	lookup_content_svm_values (const int32_t from_state, const int32_t to_state, const int32_t from_pos, const int32_t to_pos, float64_t *svm_values, int32_t frame)

void	lookup_tiling_plif_values (const int32_t from_state, const int32_t to_state, const int32_t len, float64_t *svm_values)

int32_t	find_frame (const int32_t from_state)

int32_t	raw_intensities_interval_query (const int32_t from_pos, const int32_t to_pos, float64_t *intensities, int32_t type)

bool	extend_orf (int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos, int32_t to)

virtual const char *	get_name () const

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	m_num_degrees

int32_t	m_num_svms

CDynamicArray< int32_t >	m_word_degree

CDynamicArray< int32_t >	m_cum_num_words

int32_t *	m_cum_num_words_array

CDynamicArray< int32_t >	m_num_words

int32_t *	m_num_words_array

CDynamicArray< int32_t >	m_mod_words

int32_t *	m_mod_words_array

CDynamicArray< bool >	m_sign_words

bool *	m_sign_words_array

CDynamicArray< int32_t >	m_string_words

int32_t *	m_string_words_array

CDynamicArray< int32_t >	m_num_unique_words

bool	m_svm_arrays_clean

int32_t	m_max_a_id

CDynamicArray< float64_t >	m_observation_matrix

CDynamicArray< int32_t >	m_pos

int32_t	m_seq_len

CDynamicArray< int32_t >	m_orf_info

CDynamicArray< float64_t >	m_segment_sum_weights

CDynamicObjectArray	m_plif_list

CDynamicArray< char >	m_genestr

uint16_t ***	m_wordstr

CDynamicArray< float64_t >	m_dict_weights

CDynamicArray< float64_t >	m_segment_loss

CDynamicArray< int32_t >	m_segment_ids

CDynamicArray< float64_t >	m_segment_mask

CDynamicArray< int32_t >	m_my_state_seq

CDynamicArray< int32_t >	m_my_pos_seq

CDynamicArray< float64_t >	m_my_scores

CDynamicArray< float64_t >	m_my_losses

CSegmentLoss *	m_seg_loss_obj

CDynamicArray< float64_t >	m_scores

CDynamicArray< int32_t >	m_states

CDynamicArray< int32_t >	m_positions

CSparseFeatures< float64_t > *	m_seq_sparse1

CSparseFeatures< float64_t > *	m_seq_sparse2

CPlifMatrix *	m_plif_matrices

CDynamicArray< bool >	m_genestr_stop

CIntronList *	m_intron_list

int32_t	m_num_intron_plifs

CDynamicArray< float64_t >	m_lin_feat

float64_t *	m_raw_intensities

int32_t *	m_probe_pos

int32_t *	m_num_probes_cum

int32_t *	m_num_lin_feat_plifs_cum

int32_t	m_num_raw_data

bool	m_long_transitions

int32_t	m_long_transition_threshold

model specific variables.
these are p,q,a,b,N,M etc
int32_t	m_N
	number of states 更多...

CDynamicArray< int32_t >	m_transition_matrix_a_id
	transition matrix 更多...

CDynamicArray< float64_t >	m_transition_matrix_a

CDynamicArray< float64_t >	m_transition_matrix_a_deriv

CDynamicArray< float64_t >	m_initial_state_distribution_p
	initial distribution of states 更多...

CDynamicArray< float64_t >	m_initial_state_distribution_p_deriv

CDynamicArray< float64_t >	m_end_state_distribution_q
	distribution of end-states 更多...

CDynamicArray< float64_t >	m_end_state_distribution_q_deriv

静态 Protected 属性
static int32_t	word_degree_default [4] ={3,4,5,6}

static int32_t	cum_num_words_default [5] ={0,64,320,1344,5440}

static int32_t	frame_plifs [3] ={4,5,6}

static int32_t	num_words_default [4] = {64,256,1024,4096}

static int32_t	mod_words_default [32]

static bool	sign_words_default [16]

static int32_t	string_words_default [16]

构造及析构函数说明

CDynProg ( int32_t p_num_svms = 8 )

constructor

参数

p_num_svms number of SVMs

在文件 DynProg.cpp 第 46 行定义.

~CDynProg ( )

virtual

在文件 DynProg.cpp 第 142 行定义.

成员函数说明

void best_path_set_segment_ids_mask	(	int32_t *	segment_ids,
		float64_t *	segment_mask,
		int32_t	m
	)

set best path segmend ids mask

参数

segment_ids	segment ids
segment_mask	segment mask
m	dimension m

在文件 DynProg.cpp 第 815 行定义.

void best_path_set_segment_loss ( SGMatrix< float64_t > segment_loss )

set best path segment loss

参数

segment_loss segment loss

在文件 DynProg.cpp 第 798 行定义.

void best_path_trans_deriv	(	int32_t *	my_state_seq,
		int32_t *	my_pos_seq,
		int32_t	my_seq_len,
		const float64_t *	seq_array,
		int32_t	max_num_signals
	)

given a path though the state model and the corresponding positions compute the features. This can be seen as the derivative of the score (output of dynamic program) with respect to the parameters

参数

my_state_seq	state sequence of the path
my_pos_seq	sequence of positions
my_seq_len	length of state and position sequences
seq_array	array of features
max_num_signals	maximal number of signals

在文件 DynProg.cpp 第 2052 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.

bool check_svm_arrays ( )

check SVM arrays call this function to check consistency

返回: whether arrays are ok

在文件 DynProg.cpp 第 601 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.

void compute_nbest_paths	(	int32_t	max_num_signals,
		bool	use_orf,
		int16_t	nbest,
		bool	with_loss,
		bool	with_multiple_sequences
	)

run the viterbi algorithm to compute the n best viterbi paths

参数

max_num_signals	maximal number of signals for a single state
use_orf	whether orf shall be used
nbest	number of best paths (n)
with_loss	use loss
with_multiple_sequences	!!!not functional set to false!!!

在文件 DynProg.cpp 第 944 行定义.

void create_word_string ( )

create word string from char* Jonas

在文件 DynProg.cpp 第 361 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.

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.

bool extend_orf	(	int32_t	orf_from,
		int32_t	orf_to,
		int32_t	start,
		int32_t &	last_pos,
		int32_t	to
	)

protected

extend orf

参数

orf_from	orf from
orf_to	orf to
start	start
last_pos	last position
to	to

在文件 DynProg.cpp 第 893 行定义.

int32_t find_frame ( const int32_t from_state )

protected

find frame

参数

from_state from state

float64_t get_a	(	T_STATES	line_,
		T_STATES	column
	)		const

access function for matrix a

参数

line_	row in matrix 0...N-1
column	column in matrix 0...N-1

返回: value at position line colum

在文件 DynProg.h 第 443 行定义.

float64_t get_a_deriv	(	T_STATES	line_,
		T_STATES	column
	)		const

access function for matrix a derivated

参数

line_	row in matrix 0...N-1
column	column in matrix 0...N-1

返回: value at position line colum

在文件 DynProg.h 第 454 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.

float64_t* get_lin_feat	(	int32_t &	dim1,
		int32_t &	dim2
	)

return array of precomputed linear features like content predictions and PLiFed tiling array data Jonas

返回: lin_feat_array

在文件 DynProg.h 第 410 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.

T_STATES get_N ( ) const

access function for number of states N

在文件 DynProg.h 第 325 行定义.

virtual const char* get_name ( ) const

protectedvirtual

返回: object name

实现了 CSGObject.

在文件 DynProg.h 第 563 行定义.

int32_t get_num_positions ( )

get number of positions; the dynamic program is sparse encoded and this function gives the number of positions that can actually be part of a predicted path

返回: number of positions

在文件 DynProg.cpp 第 679 行定义.

int32_t get_num_states ( )

get num states

在文件 DynProg.cpp 第 234 行定义.

int32_t get_num_svms ( )

get num svms

在文件 DynProg.cpp 第 191 行定义.

float64_t get_p ( T_STATES offset ) const

access function for probability of initial states

参数

offset index 0...N-1

返回: value at offset

在文件 DynProg.h 第 384 行定义.

float64_t get_p_deriv ( T_STATES offset ) const

access function for derivated probability of initial states

参数

offset index 0...N-1

返回: value at offset

在文件 DynProg.h 第 394 行定义.

void get_path_losses	(	float64_t **	my_losses,
		int32_t *	seq_len
	)

get path losses

best_path_trans_deriv result retrieval functions

参数

my_losses	my losses
seq_len	length of sequence

在文件 DynProg.cpp 第 877 行定义.

void get_path_scores	(	float64_t **	my_scores,
		int32_t *	seq_len
	)

get path scores

best_path_trans_deriv result retrieval functions

参数

my_scores	scores
seq_len	length of sequence

在文件 DynProg.cpp 第 863 行定义.

SGMatrix< int32_t > get_positions ( )

best path get positions

返回: positions positions

在文件 DynProg.cpp 第 853 行定义.

float64_t get_q ( T_STATES offset ) const

access function for probability of end states

参数

offset index 0...N-1

返回: value at offset

在文件 DynProg.h 第 364 行定义.

float64_t get_q_deriv ( T_STATES offset ) const

access function for derivated probability of end states

参数

offset index 0...N-1

返回: value at offset

在文件 DynProg.h 第 374 行定义.

SGVector< float64_t > get_scores ( )

best path get scores

返回: scores scores

在文件 DynProg.cpp 第 835 行定义.

CSegmentLoss* get_segment_loss_object ( )

get the segment loss object

在文件 DynProg.h 第 467 行定义.

SGMatrix< int32_t > get_states ( )

best path get states

返回: states states

在文件 DynProg.cpp 第 843 行定义.

void init_content_svm_value_array ( const int32_t p_num_svms )

init CDynamicArray for precomputed content svm values with size seq_len x num_svms

参数

p_num_svms number of svm weight vectors for content prediction

在文件 DynProg.cpp 第 269 行定义.

void init_mod_words_array ( SGMatrix< int32_t > p_mod_words_array )

init mod words array

参数

p_mod_words_array new mod words array

在文件 DynProg.cpp 第 579 行定义.

void init_tiling_data	(	int32_t *	probe_pos,
		float64_t *	intensities,
		const int32_t	num_probes
	)

init CDynamicArray for precomputed tiling intensitie-plif-values with size seq_len x num_svms

参数

probe_pos	local positions of probes
intensities	intensities of probes
num_probes	number of probes

在文件 DynProg.cpp 第 239 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.

void long_transition_settings	(	bool	use_long_transitions,
		int32_t	threshold,
		int32_t	max_len
	)

settings for long transition handling

参数

use_long_transitions	use the long transition approximation
threshold	use long transition for segments larger than
max_len	allow transitions up to

在文件 DynProg.h 第 478 行定义.

void lookup_content_svm_values	(	const int32_t	from_state,
		const int32_t	to_state,
		const int32_t	from_pos,
		const int32_t	to_pos,
		float64_t *	svm_values,
		int32_t	frame
	)

protected

lookup content SVM values

参数

from_state	from state
to_state	to state
from_pos	from position
to_pos	to position
svm_values	SVM values
frame	frame

在文件 DynProg.cpp 第 2482 行定义.

void lookup_tiling_plif_values	(	const int32_t	from_state,
		const int32_t	to_state,
		const int32_t	len,
		float64_t *	svm_values
	)

protected

lookup tiling Plif values

参数

from_state	from state
to_state	to state
len	length
svm_values	SVM values

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 precompute_content_values ( )

create array of precomputed content svm values

在文件 DynProg.cpp 第 392 行定义.

void precompute_stop_codons ( )

precompute stop codons

在文件 DynProg.cpp 第 196 行定义.

void precompute_tiling_plifs	(	CPlif **	PEN,
		const int32_t *	tiling_plif_ids,
		const int32_t	num_tiling_plifs
	)

precompute tiling Plifs

参数

PEN	Plif PEN
tiling_plif_ids	tiling plif id's
num_tiling_plifs	number of tiling plifs

在文件 DynProg.cpp 第 312 行定义.

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.

int32_t raw_intensities_interval_query	(	const int32_t	from_pos,
		const int32_t	to_pos,
		float64_t *	intensities,
		int32_t	type
	)

protected

raw intensities interval query

参数

from_pos	from position
to_pos	to position
intensities	intensities
type	type

返回: an integer

在文件 DynProg.cpp 第 2456 行定义.

void resize_lin_feat ( int32_t num_new_feat )

append rows to linear features array

参数

num_new_feat number of new rows to add

在文件 DynProg.cpp 第 279 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_a ( SGMatrix< float64_t > a )

set matrix a

参数

a	new matrix a

在文件 DynProg.cpp 第 457 行定义.

void set_a	(	T_STATES	line_,
		T_STATES	column,
		float64_t	value
	)

access function for matrix a

参数

line_	row in matrix 0...N-1
column	column in matrix 0...N-1
value	value to be set

在文件 DynProg.h 第 354 行定义.

void set_a_id ( SGMatrix< int32_t > a )

set a id

参数

a new a id

在文件 DynProg.cpp 第 465 行定义.

void set_a_trans_matrix ( SGMatrix< float64_t > a_trans )

set a transition matrix

参数

a_trans transition matrix a

在文件 DynProg.cpp 第 478 行定义.

void set_content_type_array ( SGMatrix< float64_t > seg_path )

set an array of length #(candidate positions) which specifies the content type of each pos and a mask that determines to which extend the loss should be applied to this position; this is a way to encode label confidence via weights between zero and one

参数

seg_path seg path

在文件 DynProg.cpp 第 684 行定义.

void set_dict_weights ( SGMatrix< float64_t > dictionary_weights )

set best path dict weights

参数

dictionary_weights dictionary weights

在文件 DynProg.cpp 第 779 行定义.

void set_gene_string ( SGVector< char > genestr )

set best path genesstr

参数

genestr gene string

在文件 DynProg.cpp 第 755 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_intron_list	(	CIntronList *	intron_list,
		int32_t	num_plifs
	)

set intron list

参数

intron_list
num_plifs	number of intron plifs

在文件 DynProg.cpp 第 2535 行定义.

void set_lin_feat	(	float64_t *	p_lin_feat,
		int32_t	p_num_svms,
		int32_t	p_seq_len
	)

set your own array of precomputed linear features like content predictions and PLiFed tiling array data Jonas

参数

p_lin_feat	array of features
p_num_svms	number of tracks
p_seq_len	number of candidate positions

在文件 DynProg.h 第 423 行定义.

void set_my_pos_seq ( int32_t * my_pos_seq )

set best path my position sequence

参数

my_pos_seq my position sequence

在文件 DynProg.cpp 第 771 行定义.

void set_my_state_seq ( int32_t * my_state_seq )

set best path my state sequence

参数

my_state_seq my state sequence

在文件 DynProg.cpp 第 763 行定义.

void set_num_states ( int32_t N )

set number of states use this to set N first

参数

N new N

在文件 DynProg.cpp 第 219 行定义.

void set_observation_matrix ( SGNDArray< float64_t > seq )

set best path seq

参数

seq	signal features

在文件 DynProg.cpp 第 657 行定义.

void set_orf_info ( SGMatrix< int32_t > orf_info )

set best path orf info only for compute_nbest_paths

参数

orf_info the orf info

在文件 DynProg.cpp 第 723 行定义.

void set_p	(	T_STATES	offset,
		float64_t	value
	)

access function for probability of first state

参数

offset	index 0...N-1
value	value to be set

在文件 DynProg.h 第 343 行定义.

void set_p_vector ( SGVector< float64_t > p )

set vector p

参数

p	new vector p

在文件 DynProg.cpp 第 442 行定义.

void set_plif_matrices ( CPlifMatrix * pm )

set plif matrices

参数

pm	plif matrix object

在文件 DynProg.cpp 第 746 行定义.

void set_pos ( SGVector< int32_t > pos )

set best path pos

参数

pos	the position vector

在文件 DynProg.cpp 第 717 行定义.

void set_q	(	T_STATES	offset,
		float64_t	value
	)

access function for probability of end states

参数

offset	index 0...N-1
value	value to be set

在文件 DynProg.h 第 334 行定义.

void set_q_vector ( SGVector< float64_t > q )

set vector q

参数

q	new vector q

在文件 DynProg.cpp 第 450 行定义.

void set_sparse_features	(	CSparseFeatures< float64_t > *	seq_sparse1,
		CSparseFeatures< float64_t > *	seq_sparse2
	)

set sparse feature matrices

在文件 DynProg.cpp 第 732 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 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 cum_num_words_default ={0,64,320,1344,5440}

staticprotected

default values storing the cumulative sum of the number of kmers that exist for the different degrees e.g. matlab spoken: cumsum(4.^[3 4 5 6])

在文件 DynProg.h 第 771 行定义.

int32_t frame_plifs ={4,5,6}

staticprotected

default values defining which of the plif are the frame specific plifs

在文件 DynProg.h 第 775 行定义.

SGIO* io

inherited

io

在文件 SGObject.h 第 369 行定义.

CDynamicArray<int32_t> m_cum_num_words

protected

cum num words

在文件 DynProg.h 第 628 行定义.

int32_t* m_cum_num_words_array

protected

cum num words array

在文件 DynProg.h 第 630 行定义.

CDynamicArray<float64_t> m_dict_weights

protected

dict weights

在文件 DynProg.h 第 688 行定义.

CDynamicArray<float64_t> m_end_state_distribution_q

protected

distribution of end-states

在文件 DynProg.h 第 615 行定义.

CDynamicArray<float64_t> m_end_state_distribution_q_deriv

protected

在文件 DynProg.h 第 616 行定义.

CDynamicArray<char> m_genestr

protected

a single string (to be segmented)

在文件 DynProg.h 第 671 行定义.

CDynamicArray<bool> m_genestr_stop

protected

storeage of stop codons array of size length(sequence)

在文件 DynProg.h 第 726 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.

CDynamicArray<float64_t> m_initial_state_distribution_p

protected

initial distribution of states

在文件 DynProg.h 第 611 行定义.

CDynamicArray<float64_t> m_initial_state_distribution_p_deriv

protected

在文件 DynProg.h 第 612 行定义.

CIntronList* m_intron_list

protected

administers a list of introns and quality scores and provides functions for fast access

在文件 DynProg.h 第 730 行定义.

CDynamicArray<float64_t> m_lin_feat

protected

array for storage of precomputed linear features linge content svm values or pliffed tiling data Jonas

在文件 DynProg.h 第 739 行定义.

int32_t m_long_transition_threshold

protected

threshold for transitions that are computed the traditional way

在文件 DynProg.h 第 756 行定义.

bool m_long_transitions

protected

use long transition approximation

在文件 DynProg.h 第 753 行定义.

int32_t m_max_a_id

protected

max a id

在文件 DynProg.h 第 655 行定义.

CDynamicArray<int32_t> m_mod_words

protected

mod words

在文件 DynProg.h 第 636 行定义.

int32_t* m_mod_words_array

protected

mod words array

在文件 DynProg.h 第 638 行定义.

Parameter* m_model_selection_parameters

inherited

model selection parameters

在文件 SGObject.h 第 381 行定义.

CDynamicArray<float64_t> m_my_losses

protected

my losses

在文件 DynProg.h 第 702 行定义.

CDynamicArray<int32_t> m_my_pos_seq

protected

my position sequence

在文件 DynProg.h 第 698 行定义.

CDynamicArray<float64_t> m_my_scores

protected

my scores

在文件 DynProg.h 第 700 行定义.

CDynamicArray<int32_t> m_my_state_seq

protected

my state seq

在文件 DynProg.h 第 696 行定义.

int32_t m_N

protected

number of states

在文件 DynProg.h 第 603 行定义.

int32_t m_num_degrees

protected

number of degress

在文件 DynProg.h 第 621 行定义.

int32_t m_num_intron_plifs

protected

number of intron features and plifs

在文件 DynProg.h 第 733 行定义.

int32_t* m_num_lin_feat_plifs_cum

protected

num lin feat plifs cum

在文件 DynProg.h 第 748 行定义.

int32_t* m_num_probes_cum

protected

number of probes

在文件 DynProg.h 第 746 行定义.

int32_t m_num_raw_data

protected

number of additional data tracks like tiling, RNA-Seq, ...

在文件 DynProg.h 第 750 行定义.

int32_t m_num_svms

protected

number of SVMs

在文件 DynProg.h 第 623 行定义.

CDynamicArray<int32_t> m_num_unique_words

protected

SVM start position number of unique words

在文件 DynProg.h 第 651 行定义.

CDynamicArray<int32_t> m_num_words

protected

num words

在文件 DynProg.h 第 632 行定义.

int32_t* m_num_words_array

protected

num words array

在文件 DynProg.h 第 634 行定义.

CDynamicArray<float64_t> m_observation_matrix

protected

sequence

在文件 DynProg.h 第 659 行定义.

CDynamicArray<int32_t> m_orf_info

protected

orf info

在文件 DynProg.h 第 665 行定义.

Parameter* m_parameters

inherited

parameters

在文件 SGObject.h 第 378 行定义.

CDynamicObjectArray m_plif_list

protected

Plif list

在文件 DynProg.h 第 669 行定义.

CPlifMatrix* m_plif_matrices

protected

plif matrices

在文件 DynProg.h 第 721 行定义.

CDynamicArray<int32_t> m_pos

protected

candidate position

在文件 DynProg.h 第 661 行定义.

CDynamicArray<int32_t> m_positions

protected

positions

在文件 DynProg.h 第 714 行定义.

int32_t* m_probe_pos

protected

probe position

在文件 DynProg.h 第 744 行定义.

float64_t* m_raw_intensities

protected

raw intensities

在文件 DynProg.h 第 742 行定义.

CDynamicArray<float64_t> m_scores

protected

scores

在文件 DynProg.h 第 710 行定义.

CSegmentLoss* m_seg_loss_obj

protected

segment loss object containing the functions to compute the segment loss

在文件 DynProg.h 第 706 行定义.

CDynamicArray<int32_t> m_segment_ids

protected

segment IDs

在文件 DynProg.h 第 692 行定义.

CDynamicArray<float64_t> m_segment_loss

protected

segment loss

在文件 DynProg.h 第 690 行定义.

CDynamicArray<float64_t> m_segment_mask

protected

segment mask

在文件 DynProg.h 第 694 行定义.

CDynamicArray<float64_t> m_segment_sum_weights

protected

segment sum weights

在文件 DynProg.h 第 667 行定义.

int32_t m_seq_len

protected

number of candidate positions

在文件 DynProg.h 第 663 行定义.

CSparseFeatures<float64_t>* m_seq_sparse1

protected

sparse feature matrix dim1

在文件 DynProg.h 第 717 行定义.

CSparseFeatures<float64_t>* m_seq_sparse2

protected

sparse feature matrix dim2

在文件 DynProg.h 第 719 行定义.

CDynamicArray<bool> m_sign_words

protected

sign words

在文件 DynProg.h 第 640 行定义.

bool* m_sign_words_array

protected

sign words array

在文件 DynProg.h 第 642 行定义.

CDynamicArray<int32_t> m_states

protected

states

在文件 DynProg.h 第 712 行定义.

CDynamicArray<int32_t> m_string_words

protected

string words

在文件 DynProg.h 第 644 行定义.

int32_t* m_string_words_array

protected

string words array

在文件 DynProg.h 第 646 行定义.

bool m_svm_arrays_clean

protected

SVM arrays clean

在文件 DynProg.h 第 653 行定义.

CDynamicArray<float64_t> m_transition_matrix_a

protected

在文件 DynProg.h 第 607 行定义.

CDynamicArray<float64_t> m_transition_matrix_a_deriv

protected

在文件 DynProg.h 第 608 行定义.

CDynamicArray<int32_t> m_transition_matrix_a_id

protected

transition matrix

在文件 DynProg.h 第 606 行定义.

CDynamicArray<int32_t> m_word_degree

protected

word degree

在文件 DynProg.h 第 626 行定义.

uint16_t*** m_wordstr

protected

wordstr is a vector of L n-gram indices, with wordstr(i) representing a number betweeen 0 and 4095 corresponding to the 6-mer in genestr(i-5:i) pos is a vector of candidate transition positions (it is input to compute_nbest_paths) t_end is some index in pos

svs has been initialized by init_svm_values

At the end of this procedure, svs.svm_values[i+s*svs.seqlen] has the value of the s-th SVM on genestr(pos(t_end-i):pos(t_end)) for every i satisfying pos(t_end)-pos(t_end-i) <= svs.maxlookback

The SVM weights are precomputed in m_dict_weights

在文件 DynProg.h 第 686 行定义.

int32_t mod_words_default

staticprotected

初始值:

= {1,1,1,1,1,1,1,1,
                                    1,1,1,1,1,1,1,1,
                                    0,0,0,0,0,0,0,0,
                                    0,0,0,0,0,0,0,0}

default values

在文件 DynProg.h 第 782 行定义.

int32_t num_words_default = {64,256,1024,4096}

staticprotected

default values like cum_num_words_default but not cumsumed: e.g. 4.^[3 4 5 6]

在文件 DynProg.h 第 779 行定义.

Parallel* parallel

inherited

parallel

在文件 SGObject.h 第 372 行定义.

bool sign_words_default

staticprotected

初始值:

= {true,true,true,true,true,true,true,true,

false,false,false,false,false,false,false,false}

default values

在文件 DynProg.h 第 785 行定义.

int32_t string_words_default

staticprotected

初始值:

= {0,0,0,0,0,0,0,0,

1,1,1,1,1,1,1,1}

default values

在文件 DynProg.h 第 788 行定义.

Version* version

inherited

version

在文件 SGObject.h 第 375 行定义.

int32_t word_degree_default ={3,4,5,6}

staticprotected

maximal length of a long transition Note: is ignored in the current implementation => arbitrarily long transitions can be decodeddefault values defining the k-mer degrees used for content type prediction

在文件 DynProg.h 第 766 行定义.

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详细描述

Public 成员函数

Public 属性

Protected 成员函数

Protected 属性

静态 Protected 属性

构造及析构函数说明

成员函数说明

类成员变量说明