SHOGUN
4.1.0
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Dynamic Programming Class.
Structure and Function collection. This Class implements a Dynamic Programming functions.
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="", 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) |
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 |
ParameterMap * | m_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 TParameter * | migrate (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) |
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] |
CDynProg | ( | int32_t | p_num_svms = 8 | ) |
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virtual |
在文件 DynProg.cpp 第 142 行定义.
void best_path_set_segment_ids_mask | ( | int32_t * | segment_ids, |
float64_t * | segment_mask, | ||
int32_t | m | ||
) |
set best path segmend ids mask
segment_ids | segment ids |
segment_mask | segment mask |
m | dimension m |
在文件 DynProg.cpp 第 815 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
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.
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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.
dict | dictionary of parameters to be built. |
在文件 SGObject.cpp 第 1244 行定义.
bool check_svm_arrays | ( | ) |
check SVM arrays call this function to check consistency
在文件 DynProg.cpp 第 601 行定义.
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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.
在文件 SGObject.cpp 第 1361 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
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.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
在文件 SGObject.cpp 第 200 行定义.
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.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
在文件 SGObject.cpp 第 1265 行定义.
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protected |
extend orf
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.
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protected |
find frame
from_state | from state |
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inherited |
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inherited |
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inherited |
float64_t* get_lin_feat | ( | int32_t & | dim1, |
int32_t & | dim2 | ||
) |
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inherited |
在文件 SGObject.cpp 第 1136 行定义.
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
在文件 SGObject.cpp 第 1160 行定义.
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inherited |
Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
在文件 SGObject.cpp 第 1173 行定义.
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protectedvirtual |
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
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.
void get_path_losses | ( | float64_t ** | my_losses, |
int32_t * | seq_len | ||
) |
get path losses
best_path_trans_deriv result retrieval functions
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
my_scores | scores |
seq_len | length of sequence |
在文件 DynProg.cpp 第 863 行定义.
SGMatrix< int32_t > get_positions | ( | ) |
CSegmentLoss* get_segment_loss_object | ( | ) |
SGMatrix< int32_t > get_states | ( | ) |
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
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 | ) |
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
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.
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virtualinherited |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
在文件 SGObject.cpp 第 298 行定义.
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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)
file_version | parameter version of the file |
current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
file | file to load from |
prefix | prefix for members |
在文件 SGObject.cpp 第 705 行定义.
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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
param_info | information of parameter |
file_version | parameter version of the file, must be <= provided parameter version |
file | file to load from |
prefix | prefix for members |
在文件 SGObject.cpp 第 546 行定义.
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virtualinherited |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
file | where to load from |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
在文件 SGObject.cpp 第 375 行定义.
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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.
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 1063 行定义.
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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.
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 1058 行定义.
void long_transition_settings | ( | bool | use_long_transitions, |
int32_t | threshold, | ||
int32_t | max_len | ||
) |
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protected |
lookup content SVM values
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.
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protected |
lookup tiling Plif values
from_state | from state |
to_state | to state |
len | length |
svm_values | SVM values |
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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
param_base | set of TParameter instances that are mapped to the provided target parameter infos |
base_version | version of the parameter base |
target_param_infos | set of SGParamInfo instances that specify the target parameter base |
在文件 SGObject.cpp 第 743 行定义.
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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
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
在文件 SGObject.cpp 第 950 行定义.
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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)
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
replacement | (used as output) here the TParameter instance which is returned by migration is created into |
to_migrate | the only source that is used for migration |
old_name | with this parameter, a name change may be specified |
在文件 SGObject.cpp 第 890 行定义.
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virtualinherited |
在文件 SGObject.cpp 第 264 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
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.
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inherited |
prints all parameter registered for model selection and their type
在文件 SGObject.cpp 第 1112 行定义.
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virtualinherited |
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protected |
raw intensities interval query
from_pos | from position |
to_pos | to position |
intensities | intensities |
type | type |
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
num_new_feat | number of new rows to add |
在文件 DynProg.cpp 第 279 行定义.
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virtualinherited |
Save this object to file.
file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
在文件 SGObject.cpp 第 316 行定义.
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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.
ShogunException | will be thrown if an error occurs. |
被 CKernel 重载.
在文件 SGObject.cpp 第 1073 行定义.
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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.
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 1068 行定义.
void set_a_id | ( | SGMatrix< int32_t > | a | ) |
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
seg_path | seg path |
在文件 DynProg.cpp 第 684 行定义.
void set_gene_string | ( | SGVector< char > | genestr | ) |
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在文件 SGObject.cpp 第 42 行定义.
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在文件 SGObject.cpp 第 47 行定义.
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在文件 SGObject.cpp 第 52 行定义.
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在文件 SGObject.cpp 第 57 行定义.
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在文件 SGObject.cpp 第 62 行定义.
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在文件 SGObject.cpp 第 67 行定义.
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在文件 SGObject.cpp 第 72 行定义.
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在文件 SGObject.cpp 第 77 行定义.
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在文件 SGObject.cpp 第 82 行定义.
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在文件 SGObject.cpp 第 87 行定义.
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在文件 SGObject.cpp 第 92 行定义.
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在文件 SGObject.cpp 第 97 行定义.
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在文件 SGObject.cpp 第 102 行定义.
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在文件 SGObject.cpp 第 107 行定义.
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在文件 SGObject.cpp 第 112 行定义.
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set generic type to T
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void set_intron_list | ( | CIntronList * | intron_list, |
int32_t | num_plifs | ||
) |
void set_lin_feat | ( | float64_t * | p_lin_feat, |
int32_t | p_num_svms, | ||
int32_t | p_seq_len | ||
) |
void set_my_pos_seq | ( | int32_t * | my_pos_seq | ) |
void set_my_state_seq | ( | int32_t * | my_state_seq | ) |
void set_num_states | ( | int32_t | N | ) |
void set_orf_info | ( | SGMatrix< int32_t > | orf_info | ) |
set best path orf info only for compute_nbest_paths
orf_info | the orf info |
在文件 DynProg.cpp 第 723 行定义.
void set_plif_matrices | ( | CPlifMatrix * | pm | ) |
void set_pos | ( | SGVector< int32_t > | pos | ) |
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.
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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 194 行定义.
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inherited |
unset generic type
this has to be called in classes specializing a template class
在文件 SGObject.cpp 第 305 行定义.
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Updates the hash of current parameter combination
在文件 SGObject.cpp 第 250 行定义.
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io
在文件 SGObject.h 第 496 行定义.
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parameters wrt which we can compute gradients
在文件 SGObject.h 第 511 行定义.
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Hash of parameter values
在文件 SGObject.h 第 517 行定义.
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model selection parameters
在文件 SGObject.h 第 508 行定义.
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map for different parameter versions
在文件 SGObject.h 第 514 行定义.
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parameters
在文件 SGObject.h 第 505 行定义.
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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
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parallel
在文件 SGObject.h 第 499 行定义.
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version
在文件 SGObject.h 第 502 行定义.
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