Definition at line 45 of file DynProg.h.
Public Member Functions | |
CDynProg (INT p_num_svms=8) | |
~CDynProg () | |
DREAL | best_path_no_b (INT max_iter, INT &best_iter, INT *my_path) |
void | best_path_no_b_trans (INT max_iter, INT &max_best_iter, SHORT nbest, DREAL *prob_nbest, INT *my_paths) |
void | set_num_states (INT p_N) |
INT | get_num_states () |
INT | get_num_svms () |
void | init_content_svm_value_array (const INT seq_len) |
void | init_tiling_data (DREAL *probe_pos, DREAL *intensities, const INT num_probes, const INT seq_len) |
void | precompute_tiling_plifs (CPlif **PEN, const INT num_penalties, const INT seq_len, const INT *pos) |
void | set_p_vector (DREAL *p, INT N) |
void | set_q_vector (DREAL *q, INT N) |
void | set_a (DREAL *a, INT M, INT N) |
void | set_a_id (INT *a, INT M, INT N) |
void | set_a_trans_matrix (DREAL *a_trans, INT num_trans, INT N) |
void | init_svm_arrays (INT p_num_degrees, INT p_num_svms) |
void | init_word_degree_array (INT *p_word_degree_array, INT num_elem) |
void | init_cum_num_words_array (INT *p_cum_num_words_array, INT num_elem) |
void | init_num_words_array (INT *p_num_words_array, INT num_elem) |
void | init_mod_words_array (INT *p_mod_words_array, INT num_elem, INT num_columns) |
void | init_sign_words_array (bool *p_sign_words_array, INT num_elem) |
void | init_string_words_array (INT *p_string_words_array, INT num_elem) |
bool | check_svm_arrays () |
void | best_path_set_seq (DREAL *seq, INT N, INT seq_len) |
void | best_path_set_seq3d (DREAL *seq, INT p_N, INT seq_len, INT max_num_signals) |
void | best_path_set_pos (INT *pos, INT seq_len) |
void | best_path_set_orf_info (INT *orf_info, INT m, INT n) |
void | best_path_set_segment_sum_weights (DREAL *segment_sum_weights, INT num_states, INT seq_len) |
void | best_path_set_plif_list (CDynamicArray< CPlifBase * > *plifs) |
void | best_path_set_plif_id_matrix (INT *plif_id_matrix, INT m, INT n) |
void | best_path_set_plif_state_signal_matrix (INT *plif_id_matrix, INT m, INT n) |
void | best_path_set_genestr (CHAR *genestr, INT genestr_len, INT genestr_num) |
void | best_path_set_my_state_seq (INT *my_state_seq, INT seq_len) |
void | best_path_set_my_pos_seq (INT *my_pos_seq, INT seq_len) |
void | best_path_set_single_genestr (CHAR *genestr, INT genestr_len) |
void | best_path_set_dict_weights (DREAL *dictionary_weights, INT dict_len, INT n) |
void | best_path_set_segment_loss (DREAL *segment_loss, INT num_segment_id1, INT num_segment_id2) |
void | best_path_set_segment_ids_mask (INT *segment_ids, DREAL *segment_mask, INT m) |
void | best_path_call (INT nbest, bool use_orf) |
void | best_path_deriv_call () |
void | best_path_2struct_call (INT nbest) |
void | best_path_simple_call (INT nbest) |
void | best_path_deriv_call (INT nbest) |
void | best_path_get_scores (DREAL **scores, INT *n) |
void | best_path_get_states (INT **states, INT *m, INT *n) |
void | best_path_get_positions (INT **positions, INT *m, INT *n) |
void | best_path_get_losses (DREAL **my_losses, INT *seq_len) |
template<short int nbest, bool with_loss, bool with_multiple_sequences> | |
void | best_path_trans (const DREAL *seq, INT seq_len, const INT *pos, const INT *orf_info, CPlifBase **PLif_matrix, CPlifBase **Plif_state_signals, INT max_num_signals, INT genestr_num, DREAL *prob_nbest, INT *my_state_seq, INT *my_pos_seq, bool use_orf) |
void | best_path_trans_deriv (INT *my_state_seq, INT *my_pos_seq, DREAL *my_scores, DREAL *my_losses, INT my_seq_len, const DREAL *seq_array, INT seq_len, const INT *pos, CPlifBase **Plif_matrix, CPlifBase **Plif_state_signals, INT max_num_signals, INT genestr_num) |
void | best_path_2struct (const DREAL *seq, INT seq_len, const INT *pos, CPlifBase **Plif_matrix, const char *genestr, INT genestr_len, SHORT nbest, DREAL *prob_nbest, INT *my_state_seq, INT *my_pos_seq, DREAL *dictionary_weights, INT dict_len, DREAL *segment_sum_weights) |
void | best_path_trans_simple (const DREAL *seq, INT seq_len, SHORT nbest, DREAL *prob_nbest, INT *my_state_seq) |
T_STATES | get_N () const |
access function for number of states N | |
void | set_q (T_STATES offset, DREAL value) |
void | set_p (T_STATES offset, DREAL value) |
void | set_a (T_STATES line_, T_STATES column, DREAL value) |
DREAL | get_q (T_STATES offset) const |
DREAL | get_q_deriv (T_STATES offset) const |
DREAL | get_p (T_STATES offset) const |
DREAL | get_p_deriv (T_STATES offset) const |
void | precompute_content_values (WORD ***wordstr, const INT *pos, const INT num_cand_pos, const INT genestr_len, DREAL *dictionary_weights, INT dict_len) |
void | create_word_string (const CHAR *genestr, INT genestr_num, INT genestr_len, WORD ***wordstr) |
void | precompute_stop_codons (const CHAR *genestr, INT genestr_len) |
void | set_genestr_len (INT genestr_len) |
DREAL | get_a (T_STATES line_, T_STATES column) const |
DREAL | get_a_deriv (T_STATES line_, T_STATES column) const |
Static Public Attributes | |
static CParallel | parallel |
static CIO | io |
static CVersion | version |
Protected Member Functions | |
void | lookup_content_svm_values (const INT from_state, const INT to_state, const INT from_pos, const INT to_pos, DREAL *svm_values, INT frame) |
void | lookup_tiling_plif_values (const INT from_state, const INT to_state, const INT len, DREAL *svm_values) |
INT | find_frame (const INT from_state) |
INT | raw_intensities_interval_query (const INT from_pos, const INT to_pos, DREAL *intensities) |
void | translate_from_single_order (WORD *obs, INT sequence_length, INT start, INT order, INT max_val=2) |
void | reset_svm_value (INT pos, INT &last_svm_pos, DREAL *svm_value) |
void | extend_svm_value (WORD *wordstr, INT pos, INT &last_svm_pos, DREAL *svm_value) |
void | reset_segment_sum_value (INT num_states, INT pos, INT &last_segment_sum_pos, DREAL *segment_sum_value) |
void | extend_segment_sum_value (DREAL *segment_sum_weights, INT seqlen, INT num_states, INT pos, INT &last_segment_sum_pos, DREAL *segment_sum_value) |
void | init_svm_values (struct svm_values_struct &svs, INT start_pos, INT seqlen, INT howmuchlookback) |
void | clear_svm_values (struct svm_values_struct &svs) |
void | find_svm_values_till_pos (WORD ***wordstr, const INT *pos, INT t_end, struct svm_values_struct &svs) |
void | find_svm_values_till_pos (WORD **wordstr, const INT *pos, INT t_end, struct svm_values_struct &svs) |
void | update_svm_values_till_pos (WORD ***wordstr, const INT *pos, INT t_end, INT prev_t_end, struct svm_values_struct &svs) |
bool | extend_orf (INT orf_from, INT orf_to, INT start, INT &last_pos, INT to) |
void | init_segment_loss (struct segment_loss_struct &loss, INT seqlen, INT howmuchlookback) |
void | clear_segment_loss (struct segment_loss_struct &loss) |
DREAL | extend_segment_loss (struct segment_loss_struct &loss, const INT *pos_array, INT segment_id, INT pos, INT &last_pos, DREAL &last_value) |
void | find_segment_loss_till_pos (const INT *pos, INT t_end, CArray< INT > &segment_ids, CArray< DREAL > &segment_mask, struct segment_loss_struct &loss) |
Protected Attributes | |
CArray2< DREAL > | dict_weights |
DREAL * | dict_weights_array |
INT | num_degrees |
INT | num_svms |
INT | num_strings |
CArray< INT > | word_degree |
CArray< INT > | cum_num_words |
INT * | cum_num_words_array |
CArray< INT > | num_words |
INT * | num_words_array |
CArray2< INT > | mod_words |
INT * | mod_words_array |
CArray< bool > | sign_words |
bool * | sign_words_array |
CArray< INT > | string_words |
INT * | string_words_array |
CArray< INT > | svm_pos_start |
CArray< INT > | num_unique_words |
bool | svm_arrays_clean |
INT | num_svms_single |
INT | word_degree_single |
INT | cum_num_words_single |
INT | num_words_single |
CArray< bool > | word_used_single |
CArray< DREAL > | svm_value_unnormalized_single |
INT | num_unique_words_single |
INT | max_a_id |
INT | m_step |
INT | m_call |
CArray3< DREAL > | m_seq |
CArray< INT > | m_pos |
CArray2< INT > | m_orf_info |
CArray2< DREAL > | m_segment_sum_weights |
CArray< CPlifBase * > | m_plif_list |
CArray2< CPlifBase * > | m_PEN |
CArray2< CPlifBase * > | m_PEN_state_signals |
CArray2< CHAR > | m_genestr |
CArray2< DREAL > | m_dict_weights |
CArray3< DREAL > | m_segment_loss |
CArray< INT > | m_segment_ids |
CArray< DREAL > | m_segment_mask |
CArray< INT > | m_my_state_seq |
CArray< INT > | m_my_pos_seq |
CArray< DREAL > | m_my_scores |
CArray< DREAL > | m_my_losses |
CArray< DREAL > | m_scores |
CArray2< INT > | m_states |
CArray2< INT > | m_positions |
CArray< bool > | m_genestr_stop |
CArray2< DREAL > | m_precomputed_svm_values |
CArray2< DREAL > | m_precomputed_tiling_values |
DREAL * | m_raw_intensities |
INT * | m_probe_pos |
INT | m_num_probes |
bool | m_use_tiling |
INT | m_genestr_len |
model specific variables. | |
these are p,q,a,b,N,M etc | |
INT | N |
number of states | |
CArray2< INT > | transition_matrix_a_id |
transition matrix | |
CArray2< DREAL > | transition_matrix_a |
CArray2< DREAL > | transition_matrix_a_deriv |
CArray< DREAL > | initial_state_distribution_p |
initial distribution of states | |
CArray< DREAL > | initial_state_distribution_p_deriv |
CArray< DREAL > | end_state_distribution_q |
distribution of end-states | |
CArray< DREAL > | end_state_distribution_q_deriv |
Classes | |
struct | segment_loss_struct |
struct | svm_values_struct |
CDynProg::CDynProg | ( | INT | p_num_svms = 8 |
) |
CDynProg::~CDynProg | ( | ) |
Definition at line 144 of file DynProg.cpp.
best path no b
max_iter | max iter | |
best_iter | best iter | |
my_path | my path |
Definition at line 1056 of file DynProg.cpp.
void CDynProg::best_path_no_b_trans | ( | INT | max_iter, | |
INT & | max_best_iter, | |||
SHORT | nbest, | |||
DREAL * | prob_nbest, | |||
INT * | my_paths | |||
) |
best path no b transition
max_iter | max iter | |
max_best_iter | max best iter | |
nbest | nbest | |
prob_nbest | prob_nbest | |
my_paths | my paths |
Definition at line 1140 of file DynProg.cpp.
void CDynProg::set_num_states | ( | INT | p_N | ) |
set number of states use this to set N first
p_N | new N |
Definition at line 209 of file DynProg.cpp.
INT CDynProg::get_num_states | ( | ) |
get num states
Definition at line 225 of file DynProg.cpp.
INT CDynProg::get_num_svms | ( | ) |
get num svms
Definition at line 187 of file DynProg.cpp.
void CDynProg::init_content_svm_value_array | ( | const INT | seq_len | ) |
init CArray for precomputed content svm values with size seq_len x num_svms
seq_len,: | number of candidate positions |
Definition at line 241 of file DynProg.cpp.
void CDynProg::init_tiling_data | ( | DREAL * | probe_pos, | |
DREAL * | intensities, | |||
const INT | num_probes, | |||
const INT | seq_len | |||
) |
init CArray 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 | |
seq_len,: | number of candidate positions |
Definition at line 229 of file DynProg.cpp.
void CDynProg::precompute_tiling_plifs | ( | CPlif ** | PEN, | |
const INT | num_penalties, | |||
const INT | seq_len, | |||
const INT * | pos | |||
) |
precompute tiling Plifs
PEN | Plif PEN | |
num_penalties | number of penalties | |
seq_len | sequence length | |
pos | pos |
Definition at line 245 of file DynProg.cpp.
set vector p
p | new vector p | |
N | size of vector p |
Definition at line 376 of file DynProg.cpp.
set vector q
q | new vector q | |
N | size of vector q |
Definition at line 385 of file DynProg.cpp.
set matrix a
a | new matrix a | |
M | dimension M of matrix a | |
N | dimension N of matrix a |
Definition at line 391 of file DynProg.cpp.
set a id
a | new a id (identity?) | |
M | dimension M of matrix a | |
N | dimension N of matrix a |
Definition at line 399 of file DynProg.cpp.
set a transition matrix
a_trans | transition matrix a | |
num_trans | number of transitions | |
N | dimension N of matrix a |
Definition at line 410 of file DynProg.cpp.
init SVM arrays
p_num_degrees | number of degrees | |
p_num_svms | number of SVMs |
Definition at line 505 of file DynProg.cpp.
init word degree array
p_word_degree_array | new word degree array | |
num_elem | number of array elements |
Definition at line 523 of file DynProg.cpp.
init cum num words array
p_cum_num_words_array | new cum num words array | |
num_elem | number of array elements |
Definition at line 536 of file DynProg.cpp.
init num words array
p_num_words_array | new num words array | |
num_elem | number of array elements |
Definition at line 548 of file DynProg.cpp.
init mod words array
p_mod_words_array | new mod words array | |
num_elem | number of array elements | |
num_columns | number of columns |
Definition at line 563 of file DynProg.cpp.
void CDynProg::init_sign_words_array | ( | bool * | p_sign_words_array, | |
INT | num_elem | |||
) |
init sign words array
p_sign_words_array | new sign words array | |
num_elem | number of array elements |
Definition at line 583 of file DynProg.cpp.
init string words array
p_string_words_array | new string words array | |
num_elem | number of array elements |
Definition at line 593 of file DynProg.cpp.
bool CDynProg::check_svm_arrays | ( | ) |
check SVM arrays call this function to check consistency
Definition at line 603 of file DynProg.cpp.
set best path seq
seq | the sequence | |
N | dimension N | |
seq_len | length of sequence |
Definition at line 659 of file DynProg.cpp.
set best path seq3d
seq | the 3D sequence | |
p_N | dimension N | |
seq_len | length of sequence | |
max_num_signals | maximal number of signals |
Definition at line 678 of file DynProg.cpp.
set best path pos
pos | the position | |
seq_len | length of sequence |
Definition at line 697 of file DynProg.cpp.
set best path orf info only for best_path_trans
orf_info | the orf info | |
m | dimension m | |
n | dimension n |
Definition at line 710 of file DynProg.cpp.
void CDynProg::best_path_set_segment_sum_weights | ( | DREAL * | segment_sum_weights, | |
INT | num_states, | |||
INT | seq_len | |||
) |
set best path segment sum weights only for best_path_2struct
segment_sum_weights | segment sum weights | |
num_states | number of states | |
seq_len | length of sequence |
Definition at line 725 of file DynProg.cpp.
void CDynProg::best_path_set_plif_list | ( | CDynamicArray< CPlifBase * > * | plifs | ) |
set best path plif id(entity?) matrix
plif_id_matrix | plif id matrix | |
m | dimension m of matrix | |
n | dimension n of matrix |
Definition at line 755 of file DynProg.cpp.
set best path plif state signal matrix
plif_id_matrix | plif id matrix | |
m | dimension m of matrix | |
n | dimension n of matrix |
Definition at line 779 of file DynProg.cpp.
set best path genesstr
genestr | gene string | |
genestr_len | length of gene string | |
genestr_num | number of gene strings, typically 1 |
Definition at line 806 of file DynProg.cpp.
set best path my state sequence
my_state_seq | my state sequence | |
seq_len | length of sequence |
Definition at line 820 of file DynProg.cpp.
set best path my position sequence
my_pos_seq | my position sequence | |
seq_len | length of sequence |
Definition at line 828 of file DynProg.cpp.
set best path dict weights
dictionary_weights | dictionary weights | |
dict_len | length of dictionary weights | |
n | dimension n |
Definition at line 836 of file DynProg.cpp.
void CDynProg::best_path_set_segment_loss | ( | DREAL * | segment_loss, | |
INT | num_segment_id1, | |||
INT | num_segment_id2 | |||
) |
set best path segment loss
segment_loss | segment loss | |
num_segment_id1 | number of segment id1 | |
num_segment_id2 | number of segment id2 |
Definition at line 857 of file DynProg.cpp.
set best path segmend ids mask
segment_ids | segment ids | |
segment_mask | segment mask | |
m | dimension m |
Definition at line 872 of file DynProg.cpp.
void CDynProg::best_path_call | ( | INT | nbest, | |
bool | use_orf | |||
) |
best path call
nbest | nbest | |
use_orf | whether to use orf |
Definition at line 885 of file DynProg.cpp.
void CDynProg::best_path_deriv_call | ( | ) |
best path derivative call
Definition at line 923 of file DynProg.cpp.
void CDynProg::best_path_2struct_call | ( | INT | nbest | ) |
void CDynProg::best_path_simple_call | ( | INT | nbest | ) |
void CDynProg::best_path_deriv_call | ( | INT | nbest | ) |
best path get scores
scores | scores | |
n | dimension n |
Definition at line 1004 of file DynProg.cpp.
best path get states
states | states | |
m | dimension m | |
n | dimension n |
Definition at line 1022 of file DynProg.cpp.
best path get positions
positions | positions | |
m | dimension m | |
n | dimension n |
Definition at line 1034 of file DynProg.cpp.
get best path losses
my_losses | my losses | |
seq_len | length of sequence |
Definition at line 1046 of file DynProg.cpp.
void CDynProg::best_path_trans | ( | const DREAL * | seq, | |
INT | seq_len, | |||
const INT * | pos, | |||
const INT * | orf_info, | |||
CPlifBase ** | PLif_matrix, | |||
CPlifBase ** | Plif_state_signals, | |||
INT | max_num_signals, | |||
INT | genestr_num, | |||
DREAL * | prob_nbest, | |||
INT * | my_state_seq, | |||
INT * | my_pos_seq, | |||
bool | use_orf | |||
) |
best path trans
seq | sequence | |
seq_len | length of sequence | |
pos | position | |
orf_info | orf info | |
PLif_matrix | Plif matrix | |
Plif_state_signals | Plif state signals | |
max_num_signals | maximal number of signals | |
genestr_num | number of gene strings | |
prob_nbest | prob nbest | |
my_state_seq | my state seq | |
my_pos_seq | my pos seq | |
use_orf | whether orf shall be used |
Definition at line 2242 of file DynProg.cpp.
void CDynProg::best_path_trans_deriv | ( | INT * | my_state_seq, | |
INT * | my_pos_seq, | |||
DREAL * | my_scores, | |||
DREAL * | my_losses, | |||
INT | my_seq_len, | |||
const DREAL * | seq_array, | |||
INT | seq_len, | |||
const INT * | pos, | |||
CPlifBase ** | Plif_matrix, | |||
CPlifBase ** | Plif_state_signals, | |||
INT | max_num_signals, | |||
INT | genestr_num | |||
) |
best path trans derivative
my_state_seq | my state seq | |
my_pos_seq | my pos seq | |
my_scores | my scores | |
my_losses | my losses | |
my_seq_len | my sequence length | |
seq_array | sequence array | |
seq_len | length of sequence | |
pos | position | |
Plif_matrix | Plif matrix | |
Plif_state_signals | Plif state signals | |
max_num_signals | maximal number of signals | |
genestr_num | number of gene strings |
Definition at line 2894 of file DynProg.cpp.
void CDynProg::best_path_2struct | ( | const DREAL * | seq, | |
INT | seq_len, | |||
const INT * | pos, | |||
CPlifBase ** | Plif_matrix, | |||
const char * | genestr, | |||
INT | genestr_len, | |||
SHORT | nbest, | |||
DREAL * | prob_nbest, | |||
INT * | my_state_seq, | |||
INT * | my_pos_seq, | |||
DREAL * | dictionary_weights, | |||
INT | dict_len, | |||
DREAL * | segment_sum_weights | |||
) |
best path 2struct
seq | sequence | |
seq_len | length of sequence | |
pos | position | |
Plif_matrix | Plif matrix | |
genestr | gene string | |
genestr_len | length of gene string | |
nbest | nbest | |
prob_nbest | prob(ability?) nbest | |
my_state_seq | my state seq | |
my_pos_seq | my pos seq | |
dictionary_weights | dictionary weights | |
dict_len | length of dictionary weights | |
segment_sum_weights | segment sum weights |
Definition at line 1388 of file DynProg.cpp.
void CDynProg::best_path_trans_simple | ( | const DREAL * | seq, | |
INT | seq_len, | |||
SHORT | nbest, | |||
DREAL * | prob_nbest, | |||
INT * | my_state_seq | |||
) |
best path trans simple
seq | sequence | |
seq_len | length of sequence | |
nbest | nbest | |
prob_nbest | prob(ability?) nbest | |
my_state_seq | my state seq |
Definition at line 3141 of file DynProg.cpp.
T_STATES CDynProg::get_N | ( | ) | const |
void CDynProg::precompute_content_values | ( | WORD *** | wordstr, | |
const INT * | pos, | |||
const INT | num_cand_pos, | |||
const INT | genestr_len, | |||
DREAL * | dictionary_weights, | |||
INT | dict_len | |||
) |
create array of precomputed content svm values Jonas
wordstr | word strings | |
pos | position | |
num_cand_pos | number of cand position | |
genestr_len | length of gene string | |
dictionary_weights | dictionary weights | |
dict_len | lenght of dictionary |
Definition at line 326 of file DynProg.cpp.
void CDynProg::create_word_string | ( | const CHAR * | genestr, | |
INT | genestr_num, | |||
INT | genestr_len, | |||
WORD *** | wordstr | |||
) |
create word string from char* Jonas
genestr | gene string | |
genestr_num | number of gene string | |
genestr_len | length of gene string | |
wordstr | word strings |
Definition at line 297 of file DynProg.cpp.
precompute stop codons
genestr | gene string | |
genestr_len | length of gene string |
Definition at line 191 of file DynProg.cpp.
void CDynProg::set_genestr_len | ( | INT | genestr_len | ) |
set genestr len
genestr_len | length of gene string |
Definition at line 183 of file DynProg.cpp.
find frame
from_state | from state |
void CDynProg::translate_from_single_order | ( | WORD * | obs, | |
INT | sequence_length, | |||
INT | start, | |||
INT | order, | |||
INT | max_val = 2 | |||
) | [protected] |
translate from single order
obs | observation matrix | |
sequence_length | length of sequence | |
start | start | |
order | order | |
max_val | maximum number of bits, e.g. 2 for DNA |
Definition at line 1287 of file DynProg.cpp.
reset SVM value
pos | position | |
last_svm_pos | last SVM position | |
svm_value | value to set |
Definition at line 1320 of file DynProg.cpp.
void CDynProg::extend_svm_value | ( | WORD * | wordstr, | |
INT | pos, | |||
INT & | last_svm_pos, | |||
DREAL * | svm_value | |||
) | [protected] |
extend SVM value
wordstr | word string | |
pos | position | |
last_svm_pos | lsat SVM position | |
svm_value | value to set |
Definition at line 1332 of file DynProg.cpp.
void CDynProg::reset_segment_sum_value | ( | INT | num_states, | |
INT | pos, | |||
INT & | last_segment_sum_pos, | |||
DREAL * | segment_sum_value | |||
) | [protected] |
reset segment sum value
num_states | number of states | |
pos | position | |
last_segment_sum_pos | last segment sum position | |
segment_sum_value | value to set |
Definition at line 1367 of file DynProg.cpp.
void CDynProg::extend_segment_sum_value | ( | DREAL * | segment_sum_weights, | |
INT | seqlen, | |||
INT | num_states, | |||
INT | pos, | |||
INT & | last_segment_sum_pos, | |||
DREAL * | segment_sum_value | |||
) | [protected] |
extend segment sum value
segment_sum_weights | segment sum weights | |
seqlen | length of sequence | |
num_states | number of states | |
pos | position | |
last_segment_sum_pos | last segment sum position | |
segment_sum_value | value to set |
Definition at line 1375 of file DynProg.cpp.
void CDynProg::init_svm_values | ( | struct svm_values_struct & | svs, | |
INT | start_pos, | |||
INT | seqlen, | |||
INT | howmuchlookback | |||
) | [protected] |
init SVM values
svs | SVM values | |
start_pos | start position | |
seqlen | length of sequence | |
howmuchlookback | how far to look back |
Definition at line 1882 of file DynProg.cpp.
void CDynProg::clear_svm_values | ( | struct svm_values_struct & | svs | ) | [protected] |
void CDynProg::find_svm_values_till_pos | ( | WORD *** | wordstr, | |
const INT * | pos, | |||
INT | t_end, | |||
struct svm_values_struct & | svs | |||
) | [protected] |
find SVM values till position (swig compatible?)
wordstr | word string | |
pos | position | |
t_end | t end | |
svs | SVM values |
Definition at line 1989 of file DynProg.cpp.
void CDynProg::find_svm_values_till_pos | ( | WORD ** | wordstr, | |
const INT * | pos, | |||
INT | t_end, | |||
struct svm_values_struct & | svs | |||
) | [protected] |
find SVM values till position
wordstr | word string | |
pos | position | |
t_end | t end | |
svs | SVM values |
Definition at line 2102 of file DynProg.cpp.
void CDynProg::update_svm_values_till_pos | ( | WORD *** | wordstr, | |
const INT * | pos, | |||
INT | t_end, | |||
INT | prev_t_end, | |||
struct svm_values_struct & | svs | |||
) | [protected] |
update SVM values till position
wordstr | word string | |
pos | position | |
t_end | t end | |
prev_t_end | previous t end | |
svs | SVM values |
bool CDynProg::extend_orf | ( | INT | orf_from, | |
INT | orf_to, | |||
INT | start, | |||
INT & | last_pos, | |||
INT | to | |||
) | [protected] |
extend orf
orf_from | orf from | |
orf_to | orf to | |
start | start | |
last_pos | last position | |
to | to |
Definition at line 2205 of file DynProg.cpp.
void CDynProg::init_segment_loss | ( | struct segment_loss_struct & | loss, | |
INT | seqlen, | |||
INT | howmuchlookback | |||
) | [protected] |
init segment loss
loss | segment loss to init | |
seqlen | length of sequence | |
howmuchlookback | how far to look back |
Definition at line 1700 of file DynProg.cpp.
void CDynProg::clear_segment_loss | ( | struct segment_loss_struct & | loss | ) | [protected] |
clear segment loss
loss | segment loss to clear |
Definition at line 1735 of file DynProg.cpp.
DREAL CDynProg::extend_segment_loss | ( | struct segment_loss_struct & | loss, | |
const INT * | pos_array, | |||
INT | segment_id, | |||
INT | pos, | |||
INT & | last_pos, | |||
DREAL & | last_value | |||
) | [protected] |
extend segment loss
loss | segment loss to extend | |
pos_array | position array | |
segment_id | ID of segment | |
pos | position | |
last_pos | last position | |
last_value | last value |
Definition at line 1756 of file DynProg.cpp.
void CDynProg::find_segment_loss_till_pos | ( | const INT * | pos, | |
INT | t_end, | |||
CArray< INT > & | segment_ids, | |||
CArray< DREAL > & | segment_mask, | |||
struct segment_loss_struct & | loss | |||
) | [protected] |
find segment loss till pos
pos | position | |
t_end | t end | |
segment_ids | segment IDs | |
segment_mask | segmend mask | |
loss | segment loss |
Definition at line 1821 of file DynProg.cpp.
INT CDynProg::N [protected] |
CArray2<INT> CDynProg::transition_matrix_a_id [protected] |
CArray2<DREAL> CDynProg::transition_matrix_a [protected] |
CArray2<DREAL> CDynProg::transition_matrix_a_deriv [protected] |
CArray<DREAL> CDynProg::initial_state_distribution_p [protected] |
CArray<DREAL> CDynProg::initial_state_distribution_p_deriv [protected] |
CArray<DREAL> CDynProg::end_state_distribution_q [protected] |
CArray<DREAL> CDynProg::end_state_distribution_q_deriv [protected] |
CArray2<DREAL> CDynProg::dict_weights [protected] |
DREAL* CDynProg::dict_weights_array [protected] |
INT CDynProg::num_degrees [protected] |
INT CDynProg::num_svms [protected] |
INT CDynProg::num_strings [protected] |
CArray<INT> CDynProg::word_degree [protected] |
CArray<INT> CDynProg::cum_num_words [protected] |
INT* CDynProg::cum_num_words_array [protected] |
CArray<INT> CDynProg::num_words [protected] |
INT* CDynProg::num_words_array [protected] |
CArray2<INT> CDynProg::mod_words [protected] |
INT* CDynProg::mod_words_array [protected] |
CArray<bool> CDynProg::sign_words [protected] |
bool* CDynProg::sign_words_array [protected] |
CArray<INT> CDynProg::string_words [protected] |
INT* CDynProg::string_words_array [protected] |
CArray<INT> CDynProg::svm_pos_start [protected] |
CArray<INT> CDynProg::num_unique_words [protected] |
bool CDynProg::svm_arrays_clean [protected] |
INT CDynProg::num_svms_single [protected] |
INT CDynProg::word_degree_single [protected] |
INT CDynProg::cum_num_words_single [protected] |
INT CDynProg::num_words_single [protected] |
CArray<bool> CDynProg::word_used_single [protected] |
CArray<DREAL> CDynProg::svm_value_unnormalized_single [protected] |
INT CDynProg::num_unique_words_single [protected] |
INT CDynProg::max_a_id [protected] |
INT CDynProg::m_step [protected] |
INT CDynProg::m_call [protected] |
CArray3<DREAL> CDynProg::m_seq [protected] |
CArray<INT> CDynProg::m_pos [protected] |
CArray2<INT> CDynProg::m_orf_info [protected] |
CArray2<DREAL> CDynProg::m_segment_sum_weights [protected] |
CArray<CPlifBase*> CDynProg::m_plif_list [protected] |
CArray2<CPlifBase*> CDynProg::m_PEN [protected] |
CArray2<CPlifBase*> CDynProg::m_PEN_state_signals [protected] |
CArray2<CHAR> CDynProg::m_genestr [protected] |
CArray2<DREAL> CDynProg::m_dict_weights [protected] |
CArray3<DREAL> CDynProg::m_segment_loss [protected] |
CArray<INT> CDynProg::m_segment_ids [protected] |
CArray<DREAL> CDynProg::m_segment_mask [protected] |
CArray<INT> CDynProg::m_my_state_seq [protected] |
CArray<INT> CDynProg::m_my_pos_seq [protected] |
CArray<DREAL> CDynProg::m_my_scores [protected] |
CArray<DREAL> CDynProg::m_my_losses [protected] |
CArray<DREAL> CDynProg::m_scores [protected] |
CArray2<INT> CDynProg::m_states [protected] |
CArray2<INT> CDynProg::m_positions [protected] |
CArray<bool> CDynProg::m_genestr_stop [protected] |
CArray2<DREAL> CDynProg::m_precomputed_svm_values [protected] |
CArray2<DREAL> CDynProg::m_precomputed_tiling_values [protected] |
DREAL* CDynProg::m_raw_intensities [protected] |
INT* CDynProg::m_probe_pos [protected] |
INT CDynProg::m_num_probes [protected] |
bool CDynProg::m_use_tiling [protected] |
INT CDynProg::m_genestr_len [protected] |
CParallel CSGObject::parallel [static, inherited] |
Definition at line 105 of file SGObject.h.
CIO CSGObject::io [static, inherited] |
Definition at line 106 of file SGObject.h.
CVersion CSGObject::version [static, inherited] |
Definition at line 107 of file SGObject.h.