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CDynProg类 参考

详细描述

Dynamic Programming Class.

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

在文件 DynProg.h76 行定义.

类 CDynProg 继承关系图:
Inheritance graph
[图例]

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_tget_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_tget_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)
 
CSegmentLossget_segment_loss_object ()
 
void long_transition_settings (bool use_long_transitions, int32_t threshold, int32_t max_len)
 
virtual CSGObjectshallow_copy () const
 
virtual CSGObjectdeep_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="", int32_t param_version=Version::get_version_parameter())
 
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter())
 
DynArray< TParameter * > * load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")
 
DynArray< TParameter * > * load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")
 
void map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)
 
void set_global_io (SGIO *io)
 
SGIOget_global_io ()
 
void set_global_parallel (Parallel *parallel)
 
Parallelget_global_parallel ()
 
void set_global_version (Version *version)
 
Versionget_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 bool update_parameter_hash ()
 
virtual bool equals (CSGObject *other, float64_t accuracy=0.0)
 
virtual CSGObjectclone ()
 

Public 属性

SGIOio
 
Parallelparallel
 
Versionversion
 
Parameterm_parameters
 
Parameterm_model_selection_parameters
 
Parameterm_gradient_parameters
 
ParameterMapm_parameter_map
 
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 TParametermigrate (DynArray< TParameter * > *param_base, const SGParamInfo *target)
 
virtual void one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)
 
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_tm_observation_matrix
 
CDynamicArray< int32_t > m_pos
 
int32_t m_seq_len
 
CDynamicArray< int32_t > m_orf_info
 
CDynamicArray< float64_tm_segment_sum_weights
 
CDynamicObjectArray m_plif_list
 
CDynamicArray< char > m_genestr
 
uint16_t *** m_wordstr
 
CDynamicArray< float64_tm_dict_weights
 
CDynamicArray< float64_tm_segment_loss
 
CDynamicArray< int32_t > m_segment_ids
 
CDynamicArray< float64_tm_segment_mask
 
CDynamicArray< int32_t > m_my_state_seq
 
CDynamicArray< int32_t > m_my_pos_seq
 
CDynamicArray< float64_tm_my_scores
 
CDynamicArray< float64_tm_my_losses
 
CSegmentLossm_seg_loss_obj
 
CDynamicArray< float64_tm_scores
 
CDynamicArray< int32_t > m_states
 
CDynamicArray< int32_t > m_positions
 
CSparseFeatures< float64_t > * m_seq_sparse1
 
CSparseFeatures< float64_t > * m_seq_sparse2
 
CPlifMatrixm_plif_matrices
 
CDynamicArray< bool > m_genestr_stop
 
CIntronListm_intron_list
 
int32_t m_num_intron_plifs
 
CDynamicArray< float64_tm_lin_feat
 
float64_tm_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_tm_transition_matrix_a
 
CDynamicArray< float64_tm_transition_matrix_a_deriv
 
CDynamicArray< float64_tm_initial_state_distribution_p
 initial distribution of states 更多...
 
CDynamicArray< float64_tm_initial_state_distribution_p_deriv
 
CDynamicArray< float64_tm_end_state_distribution_q
 distribution of end-states 更多...
 
CDynamicArray< float64_tm_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_svmsnumber of SVMs

在文件 DynProg.cpp45 行定义.

~CDynProg ( )
virtual

在文件 DynProg.cpp141 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_idssegment ids
segment_masksegment mask
mdimension m

在文件 DynProg.cpp814 行定义.

void best_path_set_segment_loss ( SGMatrix< float64_t segment_loss)

set best path segment loss

参数
segment_losssegment loss

在文件 DynProg.cpp797 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_seqstate sequence of the path
my_pos_seqsequence of positions
my_seq_lenlength of state and position sequences
seq_arrayarray of features
max_num_signalsmaximal number of signals

在文件 DynProg.cpp2051 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
dictdictionary of parameters to be built.

在文件 SGObject.cpp1195 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.cpp600 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.cpp1312 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_signalsmaximal number of signals for a single state
use_orfwhether orf shall be used
nbestnumber of best paths (n)
with_lossuse loss
with_multiple_sequences!!!not functional set to false!!!

在文件 DynProg.cpp943 行定义.

void create_word_string ( )

create word string from char* Jonas

在文件 DynProg.cpp360 行定义.

virtual CSGObject* deep_copy ( ) const
virtualinherited

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

在文件 SGObject.h159 行定义.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0 
)
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
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
返回
true if all parameters were equal, false if not

在文件 SGObject.cpp1216 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_fromorf from
orf_toorf to
startstart
last_poslast position
toto

在文件 DynProg.cpp892 行定义.

int32_t find_frame ( const int32_t  from_state)
protected

find frame

参数
from_statefrom 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
columncolumn in matrix 0...N-1
返回
value at position line colum

在文件 DynProg.h445 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
columncolumn in matrix 0...N-1
返回
value at position line colum

在文件 DynProg.h456 行定义.

SGIO * get_global_io ( )
inherited

get the io object

返回
io object

在文件 SGObject.cpp213 行定义.

Parallel * get_global_parallel ( )
inherited

get the parallel object

返回
parallel object

在文件 SGObject.cpp248 行定义.

Version * get_global_version ( )
inherited

get the version object

返回
version object

在文件 SGObject.cpp261 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.h412 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.cpp1099 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_namename of the parameter
返回
description of the parameter

在文件 SGObject.cpp1123 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_namename of model selection parameter
返回
index of model selection parameter with provided name, -1 if there is no such

在文件 SGObject.cpp1136 行定义.

T_STATES get_N ( ) const

access function for number of states N

在文件 DynProg.h327 行定义.

virtual const char* get_name ( ) const
protectedvirtual
返回
object name

实现了 CSGObject.

在文件 DynProg.h565 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.cpp678 行定义.

int32_t get_num_states ( )

get num states

在文件 DynProg.cpp233 行定义.

int32_t get_num_svms ( )

get num svms

在文件 DynProg.cpp190 行定义.

float64_t get_p ( T_STATES  offset) const

access function for probability of initial states

参数
offsetindex 0...N-1
返回
value at offset

在文件 DynProg.h386 行定义.

float64_t get_p_deriv ( T_STATES  offset) const

access function for derivated probability of initial states

参数
offsetindex 0...N-1
返回
value at offset

在文件 DynProg.h396 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_lossesmy losses
seq_lenlength of sequence

在文件 DynProg.cpp876 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_scoresscores
seq_lenlength of sequence

在文件 DynProg.cpp862 行定义.

SGMatrix< int32_t > get_positions ( )

best path get positions

返回
positions positions

在文件 DynProg.cpp852 行定义.

float64_t get_q ( T_STATES  offset) const

access function for probability of end states

参数
offsetindex 0...N-1
返回
value at offset

在文件 DynProg.h366 行定义.

float64_t get_q_deriv ( T_STATES  offset) const

access function for derivated probability of end states

参数
offsetindex 0...N-1
返回
value at offset

在文件 DynProg.h376 行定义.

SGVector< float64_t > get_scores ( )

best path get scores

返回
scores scores

在文件 DynProg.cpp834 行定义.

CSegmentLoss* get_segment_loss_object ( )

get the segment loss object

在文件 DynProg.h469 行定义.

SGMatrix< int32_t > get_states ( )

best path get states

返回
states states

在文件 DynProg.cpp842 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.cpp268 行定义.

void init_mod_words_array ( SGMatrix< int32_t >  p_mod_words_array)

init mod words array

参数
p_mod_words_arraynew mod words array

在文件 DynProg.cpp578 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_poslocal positions of probes
intensitiesintensities of probes
num_probesnumber of probes

在文件 DynProg.cpp238 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
genericset to the type of the generic if returning TRUE
返回
TRUE if a class template.

在文件 SGObject.cpp267 行定义.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile file,
const char *  prefix = "" 
)
inherited

maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)

参数
file_versionparameter version of the file
current_versionversion from which mapping begins (you want to use Version::get_version_parameter() for this in most cases)
filefile to load from
prefixprefix for members
返回
(sorted) array of created TParameter instances with file data

在文件 SGObject.cpp672 行定义.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo param_info,
int32_t  file_version,
CSerializableFile file,
const char *  prefix = "" 
)
inherited

loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned

参数
param_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
返回
new array with TParameter instances with the attached data

在文件 SGObject.cpp513 行定义.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
)
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
filewhere to load from
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
返回
TRUE if done, otherwise FALSE

在文件 SGObject.cpp344 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
ShogunExceptionWill be thrown if an error occurres.

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

在文件 SGObject.cpp1028 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
ShogunExceptionWill be thrown if an error occurres.

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

在文件 SGObject.cpp1023 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_transitionsuse the long transition approximation
thresholduse long transition for segments larger than
max_lenallow transitions up to

在文件 DynProg.h480 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_statefrom state
to_stateto state
from_posfrom position
to_posto position
svm_valuesSVM values
frameframe

在文件 DynProg.cpp2481 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_statefrom state
to_stateto state
lenlength
svm_valuesSVM values
void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
)
inherited

Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match

参数
param_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset of SGParamInfo instances that specify the target parameter base

在文件 SGObject.cpp710 行定义.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
)
protectedvirtualinherited

creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.

If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass

参数
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
返回
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

在文件 SGObject.cpp917 行定义.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
)
protectedvirtualinherited

This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)

参数
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith this parameter, a name change may be specified

在文件 SGObject.cpp857 行定义.

void precompute_content_values ( )

create array of precomputed content svm values

在文件 DynProg.cpp391 行定义.

void precompute_stop_codons ( )

precompute stop codons

在文件 DynProg.cpp195 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
PENPlif PEN
tiling_plif_idstiling plif id's
num_tiling_plifsnumber of tiling plifs

在文件 DynProg.cpp311 行定义.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

在文件 SGObject.cpp1075 行定义.

void print_serializable ( const char *  prefix = "")
virtualinherited

prints registered parameters out

参数
prefixprefix for members

在文件 SGObject.cpp279 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_posfrom position
to_posto position
intensitiesintensities
typetype
返回
an integer

在文件 DynProg.cpp2455 行定义.

void resize_lin_feat ( int32_t  num_new_feat)

append rows to linear features array

参数
num_new_featnumber of new rows to add

在文件 DynProg.cpp278 行定义.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
)
virtualinherited

Save this object to file.

参数
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
返回
TRUE if done, otherwise FALSE

在文件 SGObject.cpp285 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
ShogunExceptionWill be thrown if an error occurres.

CKernel 重载.

在文件 SGObject.cpp1038 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
ShogunExceptionWill be thrown if an error occurres.

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.cpp1033 行定义.

void set_a ( SGMatrix< float64_t a)

set matrix a

参数
anew matrix a

在文件 DynProg.cpp456 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
columncolumn in matrix 0...N-1
valuevalue to be set

在文件 DynProg.h356 行定义.

void set_a_id ( SGMatrix< int32_t >  a)

set a id

参数
anew a id

在文件 DynProg.cpp464 行定义.

void set_a_trans_matrix ( SGMatrix< float64_t a_trans)

set a transition matrix

参数
a_transtransition matrix a

在文件 DynProg.cpp477 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_pathseg path

在文件 DynProg.cpp683 行定义.

void set_dict_weights ( SGMatrix< float64_t dictionary_weights)

set best path dict weights

参数
dictionary_weightsdictionary weights

在文件 DynProg.cpp778 行定义.

void set_gene_string ( SGVector< char >  genestr)

set best path genesstr

参数
genestrgene string

在文件 DynProg.cpp754 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp40 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp45 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp50 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp55 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp60 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp65 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp70 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp75 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp80 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp85 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp90 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp95 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp100 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp105 行定义.

void set_generic ( )
inherited

在文件 SGObject.cpp110 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
ioio object to use

在文件 SGObject.cpp206 行定义.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

参数
parallelparallel object to use

在文件 SGObject.cpp219 行定义.

void set_global_version ( Version version)
inherited

set the version object

参数
versionversion object to use

在文件 SGObject.cpp254 行定义.

void set_intron_list ( CIntronList intron_list,
int32_t  num_plifs 
)

set intron list

参数
intron_list
num_plifsnumber of intron plifs

在文件 DynProg.cpp2534 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_featarray of features
p_num_svmsnumber of tracks
p_seq_lennumber of candidate positions

在文件 DynProg.h425 行定义.

void set_my_pos_seq ( int32_t *  my_pos_seq)

set best path my position sequence

参数
my_pos_seqmy position sequence

在文件 DynProg.cpp770 行定义.

void set_my_state_seq ( int32_t *  my_state_seq)

set best path my state sequence

参数
my_state_seqmy state sequence

在文件 DynProg.cpp762 行定义.

void set_num_states ( int32_t  N)

set number of states use this to set N first

参数
Nnew N

在文件 DynProg.cpp218 行定义.

void set_observation_matrix ( SGNDArray< float64_t seq)

set best path seq

参数
seqsignal features

在文件 DynProg.cpp656 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_infothe orf info

在文件 DynProg.cpp722 行定义.

void set_p ( T_STATES  offset,
float64_t  value 
)

access function for probability of first state

参数
offsetindex 0...N-1
valuevalue to be set

在文件 DynProg.h345 行定义.

void set_p_vector ( SGVector< float64_t p)

set vector p

参数
pnew vector p

在文件 DynProg.cpp441 行定义.

void set_plif_matrices ( CPlifMatrix pm)

set plif matrices

参数
pmplif matrix object

在文件 DynProg.cpp745 行定义.

void set_pos ( SGVector< int32_t >  pos)

set best path pos

参数
posthe position vector

在文件 DynProg.cpp716 行定义.

void set_q ( T_STATES  offset,
float64_t  value 
)

access function for probability of end states

参数
offsetindex 0...N-1
valuevalue to be set

在文件 DynProg.h336 行定义.

void set_q_vector ( SGVector< float64_t q)

set vector q

参数
qnew vector q

在文件 DynProg.cpp449 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.cpp731 行定义.

virtual CSGObject* shallow_copy ( ) const
virtualinherited

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

CGaussianKernel 重载.

在文件 SGObject.h150 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.cpp274 行定义.

bool update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination.

返回
bool if parameter combination has changed since last update.

在文件 SGObject.cpp226 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.h773 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.h777 行定义.

SGIO* io
inherited

io

在文件 SGObject.h513 行定义.

CDynamicArray<int32_t> m_cum_num_words
protected

cum num words

在文件 DynProg.h630 行定义.

int32_t* m_cum_num_words_array
protected

cum num words array

在文件 DynProg.h632 行定义.

CDynamicArray<float64_t> m_dict_weights
protected

dict weights

在文件 DynProg.h690 行定义.

CDynamicArray<float64_t> m_end_state_distribution_q
protected

distribution of end-states

在文件 DynProg.h617 行定义.

CDynamicArray<float64_t> m_end_state_distribution_q_deriv
protected

在文件 DynProg.h618 行定义.

CDynamicArray<char> m_genestr
protected

a single string (to be segmented)

在文件 DynProg.h673 行定义.

CDynamicArray<bool> m_genestr_stop
protected

storeage of stop codons array of size length(sequence)

在文件 DynProg.h728 行定义.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

在文件 SGObject.h528 行定义.

uint32_t m_hash
inherited

Hash of parameter values

在文件 SGObject.h534 行定义.

CDynamicArray<float64_t> m_initial_state_distribution_p
protected

initial distribution of states

在文件 DynProg.h613 行定义.

CDynamicArray<float64_t> m_initial_state_distribution_p_deriv
protected

在文件 DynProg.h614 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.h732 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.h741 行定义.

int32_t m_long_transition_threshold
protected

threshold for transitions that are computed the traditional way

在文件 DynProg.h758 行定义.

bool m_long_transitions
protected

use long transition approximation

在文件 DynProg.h755 行定义.

int32_t m_max_a_id
protected

max a id

在文件 DynProg.h657 行定义.

CDynamicArray<int32_t> m_mod_words
protected

mod words

在文件 DynProg.h638 行定义.

int32_t* m_mod_words_array
protected

mod words array

在文件 DynProg.h640 行定义.

Parameter* m_model_selection_parameters
inherited

model selection parameters

在文件 SGObject.h525 行定义.

CDynamicArray<float64_t> m_my_losses
protected

my losses

在文件 DynProg.h704 行定义.

CDynamicArray<int32_t> m_my_pos_seq
protected

my position sequence

在文件 DynProg.h700 行定义.

CDynamicArray<float64_t> m_my_scores
protected

my scores

在文件 DynProg.h702 行定义.

CDynamicArray<int32_t> m_my_state_seq
protected

my state seq

在文件 DynProg.h698 行定义.

int32_t m_N
protected

number of states

在文件 DynProg.h605 行定义.

int32_t m_num_degrees
protected

number of degress

在文件 DynProg.h623 行定义.

int32_t m_num_intron_plifs
protected

number of intron features and plifs

在文件 DynProg.h735 行定义.

int32_t* m_num_lin_feat_plifs_cum
protected

num lin feat plifs cum

在文件 DynProg.h750 行定义.

int32_t* m_num_probes_cum
protected

number of probes

在文件 DynProg.h748 行定义.

int32_t m_num_raw_data
protected

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

在文件 DynProg.h752 行定义.

int32_t m_num_svms
protected

number of SVMs

在文件 DynProg.h625 行定义.

CDynamicArray<int32_t> m_num_unique_words
protected

SVM start position number of unique words

在文件 DynProg.h653 行定义.

CDynamicArray<int32_t> m_num_words
protected

num words

在文件 DynProg.h634 行定义.

int32_t* m_num_words_array
protected

num words array

在文件 DynProg.h636 行定义.

CDynamicArray<float64_t> m_observation_matrix
protected

sequence

在文件 DynProg.h661 行定义.

CDynamicArray<int32_t> m_orf_info
protected

orf info

在文件 DynProg.h667 行定义.

ParameterMap* m_parameter_map
inherited

map for different parameter versions

在文件 SGObject.h531 行定义.

Parameter* m_parameters
inherited

parameters

在文件 SGObject.h522 行定义.

CDynamicObjectArray m_plif_list
protected

Plif list

在文件 DynProg.h671 行定义.

CPlifMatrix* m_plif_matrices
protected

plif matrices

在文件 DynProg.h723 行定义.

CDynamicArray<int32_t> m_pos
protected

candidate position

在文件 DynProg.h663 行定义.

CDynamicArray<int32_t> m_positions
protected

positions

在文件 DynProg.h716 行定义.

int32_t* m_probe_pos
protected

probe position

在文件 DynProg.h746 行定义.

float64_t* m_raw_intensities
protected

raw intensities

在文件 DynProg.h744 行定义.

CDynamicArray<float64_t> m_scores
protected

scores

在文件 DynProg.h712 行定义.

CSegmentLoss* m_seg_loss_obj
protected

segment loss object containing the functions to compute the segment loss

在文件 DynProg.h708 行定义.

CDynamicArray<int32_t> m_segment_ids
protected

segment IDs

在文件 DynProg.h694 行定义.

CDynamicArray<float64_t> m_segment_loss
protected

segment loss

在文件 DynProg.h692 行定义.

CDynamicArray<float64_t> m_segment_mask
protected

segment mask

在文件 DynProg.h696 行定义.

CDynamicArray<float64_t> m_segment_sum_weights
protected

segment sum weights

在文件 DynProg.h669 行定义.

int32_t m_seq_len
protected

number of candidate positions

在文件 DynProg.h665 行定义.

CSparseFeatures<float64_t>* m_seq_sparse1
protected

sparse feature matrix dim1

在文件 DynProg.h719 行定义.

CSparseFeatures<float64_t>* m_seq_sparse2
protected

sparse feature matrix dim2

在文件 DynProg.h721 行定义.

CDynamicArray<bool> m_sign_words
protected

sign words

在文件 DynProg.h642 行定义.

bool* m_sign_words_array
protected

sign words array

在文件 DynProg.h644 行定义.

CDynamicArray<int32_t> m_states
protected

states

在文件 DynProg.h714 行定义.

CDynamicArray<int32_t> m_string_words
protected

string words

在文件 DynProg.h646 行定义.

int32_t* m_string_words_array
protected

string words array

在文件 DynProg.h648 行定义.

bool m_svm_arrays_clean
protected

SVM arrays clean

在文件 DynProg.h655 行定义.

CDynamicArray<float64_t> m_transition_matrix_a
protected

在文件 DynProg.h609 行定义.

CDynamicArray<float64_t> m_transition_matrix_a_deriv
protected

在文件 DynProg.h610 行定义.

CDynamicArray<int32_t> m_transition_matrix_a_id
protected

transition matrix

在文件 DynProg.h608 行定义.

CDynamicArray<int32_t> m_word_degree
protected

word degree

在文件 DynProg.h628 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.h688 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.h784 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.h781 行定义.

Parallel* parallel
inherited

parallel

在文件 SGObject.h516 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.h787 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.h790 行定义.

Version* version
inherited

version

在文件 SGObject.h519 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.h768 行定义.


该类的文档由以下文件生成:

SHOGUN Machine Learning Toolbox - Documentation