CDynProg Class Reference

Inheritance diagram for CDynProg:

Inheritance graph
[legend]

List of all members.


Detailed Description

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

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< DREALdict_weights
DREALdict_weights_array
INT num_degrees
INT num_svms
INT num_strings
CArray< INTword_degree
CArray< INTcum_num_words
INTcum_num_words_array
CArray< INTnum_words
INTnum_words_array
CArray2< INTmod_words
INTmod_words_array
CArray< bool > sign_words
bool * sign_words_array
CArray< INTstring_words
INTstring_words_array
CArray< INTsvm_pos_start
CArray< INTnum_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< DREALsvm_value_unnormalized_single
INT num_unique_words_single
INT max_a_id
INT m_step
INT m_call
CArray3< DREALm_seq
CArray< INTm_pos
CArray2< INTm_orf_info
CArray2< DREALm_segment_sum_weights
CArray< CPlifBase * > m_plif_list
CArray2< CPlifBase * > m_PEN
CArray2< CPlifBase * > m_PEN_state_signals
CArray2< CHARm_genestr
CArray2< DREALm_dict_weights
CArray3< DREALm_segment_loss
CArray< INTm_segment_ids
CArray< DREALm_segment_mask
CArray< INTm_my_state_seq
CArray< INTm_my_pos_seq
CArray< DREALm_my_scores
CArray< DREALm_my_losses
CArray< DREALm_scores
CArray2< INTm_states
CArray2< INTm_positions
CArray< bool > m_genestr_stop
CArray2< DREALm_precomputed_svm_values
CArray2< DREALm_precomputed_tiling_values
DREALm_raw_intensities
INTm_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< INTtransition_matrix_a_id
 transition matrix
CArray2< DREALtransition_matrix_a
CArray2< DREALtransition_matrix_a_deriv
CArray< DREALinitial_state_distribution_p
 initial distribution of states
CArray< DREALinitial_state_distribution_p_deriv
CArray< DREALend_state_distribution_q
 distribution of end-states
CArray< DREALend_state_distribution_q_deriv

Classes

struct  segment_loss_struct
struct  svm_values_struct

Constructor & Destructor Documentation

CDynProg::CDynProg ( INT  p_num_svms = 8  ) 

constructor

Parameters:
p_num_svms number of SVMs

Definition at line 77 of file DynProg.cpp.

CDynProg::~CDynProg (  ) 

Definition at line 144 of file DynProg.cpp.


Member Function Documentation

DREAL CDynProg::best_path_no_b ( INT  max_iter,
INT best_iter,
INT my_path 
)

best path no b

Parameters:
max_iter max iter
best_iter best iter
my_path my path
Returns:
best path no b

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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
PEN Plif PEN
num_penalties number of penalties
seq_len sequence length
pos pos

Definition at line 245 of file DynProg.cpp.

void CDynProg::set_p_vector ( DREAL p,
INT  N 
)

set vector p

Parameters:
p new vector p
N size of vector p

Definition at line 376 of file DynProg.cpp.

void CDynProg::set_q_vector ( DREAL q,
INT  N 
)

set vector q

Parameters:
q new vector q
N size of vector q

Definition at line 385 of file DynProg.cpp.

void CDynProg::set_a ( DREAL a,
INT  M,
INT  N 
)

set matrix a

Parameters:
a new matrix a
M dimension M of matrix a
N dimension N of matrix a

Definition at line 391 of file DynProg.cpp.

void CDynProg::set_a_id ( INT a,
INT  M,
INT  N 
)

set a id

Parameters:
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.

void CDynProg::set_a_trans_matrix ( DREAL a_trans,
INT  num_trans,
INT  N 
)

set a transition matrix

Parameters:
a_trans transition matrix a
num_trans number of transitions
N dimension N of matrix a

Definition at line 410 of file DynProg.cpp.

void CDynProg::init_svm_arrays ( INT  p_num_degrees,
INT  p_num_svms 
)

init SVM arrays

Parameters:
p_num_degrees number of degrees
p_num_svms number of SVMs

Definition at line 505 of file DynProg.cpp.

void CDynProg::init_word_degree_array ( INT p_word_degree_array,
INT  num_elem 
)

init word degree array

Parameters:
p_word_degree_array new word degree array
num_elem number of array elements

Definition at line 523 of file DynProg.cpp.

void CDynProg::init_cum_num_words_array ( INT p_cum_num_words_array,
INT  num_elem 
)

init cum num words array

Parameters:
p_cum_num_words_array new cum num words array
num_elem number of array elements

Definition at line 536 of file DynProg.cpp.

void CDynProg::init_num_words_array ( INT p_num_words_array,
INT  num_elem 
)

init num words array

Parameters:
p_num_words_array new num words array
num_elem number of array elements

Definition at line 548 of file DynProg.cpp.

void CDynProg::init_mod_words_array ( INT p_mod_words_array,
INT  num_elem,
INT  num_columns 
)

init mod words array

Parameters:
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

Parameters:
p_sign_words_array new sign words array
num_elem number of array elements

Definition at line 583 of file DynProg.cpp.

void CDynProg::init_string_words_array ( INT p_string_words_array,
INT  num_elem 
)

init string words array

Parameters:
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

Returns:
whether arrays are ok

Definition at line 603 of file DynProg.cpp.

void CDynProg::best_path_set_seq ( DREAL seq,
INT  N,
INT  seq_len 
)

set best path seq

Parameters:
seq the sequence
N dimension N
seq_len length of sequence

Definition at line 659 of file DynProg.cpp.

void CDynProg::best_path_set_seq3d ( DREAL seq,
INT  p_N,
INT  seq_len,
INT  max_num_signals 
)

set best path seq3d

Parameters:
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.

void CDynProg::best_path_set_pos ( INT pos,
INT  seq_len 
)

set best path pos

Parameters:
pos the position
seq_len length of sequence

Definition at line 697 of file DynProg.cpp.

void CDynProg::best_path_set_orf_info ( INT orf_info,
INT  m,
INT  n 
)

set best path orf info only for best_path_trans

Parameters:
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

Parameters:
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 list

Parameters:
plifs list of Plifs

Definition at line 741 of file DynProg.cpp.

void CDynProg::best_path_set_plif_id_matrix ( INT plif_id_matrix,
INT  m,
INT  n 
)

set best path plif id(entity?) matrix

Parameters:
plif_id_matrix plif id matrix
m dimension m of matrix
n dimension n of matrix

Definition at line 755 of file DynProg.cpp.

void CDynProg::best_path_set_plif_state_signal_matrix ( INT plif_id_matrix,
INT  m,
INT  n 
)

set best path plif state signal matrix

Parameters:
plif_id_matrix plif id matrix
m dimension m of matrix
n dimension n of matrix

Definition at line 779 of file DynProg.cpp.

void CDynProg::best_path_set_genestr ( CHAR genestr,
INT  genestr_len,
INT  genestr_num 
)

set best path genesstr

Parameters:
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.

void CDynProg::best_path_set_my_state_seq ( INT my_state_seq,
INT  seq_len 
)

set best path my state sequence

Parameters:
my_state_seq my state sequence
seq_len length of sequence

Definition at line 820 of file DynProg.cpp.

void CDynProg::best_path_set_my_pos_seq ( INT my_pos_seq,
INT  seq_len 
)

set best path my position sequence

Parameters:
my_pos_seq my position sequence
seq_len length of sequence

Definition at line 828 of file DynProg.cpp.

void CDynProg::best_path_set_single_genestr ( CHAR genestr,
INT  genestr_len 
)

set best path single gene string

Parameters:
genestr gene string
genestr_len length of gene string

Definition at line 329 of file DynProg.h.

void CDynProg::best_path_set_dict_weights ( DREAL dictionary_weights,
INT  dict_len,
INT  n 
)

set best path dict weights

Parameters:
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

Parameters:
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.

void CDynProg::best_path_set_segment_ids_mask ( INT segment_ids,
DREAL segment_mask,
INT  m 
)

set best path segmend ids mask

Parameters:
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

Parameters:
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  ) 

best path 2struct call

Parameters:
nbest nbest

Definition at line 946 of file DynProg.cpp.

void CDynProg::best_path_simple_call ( INT  nbest  ) 

best path simple call

Parameters:
nbest nbest

Definition at line 972 of file DynProg.cpp.

void CDynProg::best_path_deriv_call ( INT  nbest  ) 

best path derivative call

Parameters:
nbest nbest

Definition at line 992 of file DynProg.cpp.

void CDynProg::best_path_get_scores ( DREAL **  scores,
INT n 
)

best path get scores

Parameters:
scores scores
n dimension n

Definition at line 1004 of file DynProg.cpp.

void CDynProg::best_path_get_states ( INT **  states,
INT m,
INT n 
)

best path get states

Parameters:
states states
m dimension m
n dimension n

Definition at line 1022 of file DynProg.cpp.

void CDynProg::best_path_get_positions ( INT **  positions,
INT m,
INT n 
)

best path get positions

Parameters:
positions positions
m dimension m
n dimension n

Definition at line 1034 of file DynProg.cpp.

void CDynProg::best_path_get_losses ( DREAL **  my_losses,
INT seq_len 
)

get best path losses

Parameters:
my_losses my losses
seq_len length of sequence

Definition at line 1046 of file DynProg.cpp.

template<short int nbest, bool with_loss, bool with_multiple_sequences>
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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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

access function for number of states N

Definition at line 501 of file DynProg.h.

void CDynProg::set_q ( T_STATES  offset,
DREAL  value 
)

access function for probability of end states

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

Definition at line 510 of file DynProg.h.

void CDynProg::set_p ( T_STATES  offset,
DREAL  value 
)

access function for probability of first state

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

Definition at line 519 of file DynProg.h.

void CDynProg::set_a ( T_STATES  line_,
T_STATES  column,
DREAL  value 
)

access function for matrix a

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

Definition at line 530 of file DynProg.h.

DREAL CDynProg::get_q ( T_STATES  offset  )  const

access function for probability of end states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 540 of file DynProg.h.

DREAL CDynProg::get_q_deriv ( T_STATES  offset  )  const

access function for derivated probability of end states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 550 of file DynProg.h.

DREAL CDynProg::get_p ( T_STATES  offset  )  const

access function for probability of initial states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 560 of file DynProg.h.

DREAL CDynProg::get_p_deriv ( T_STATES  offset  )  const

access function for derivated probability of initial states

Parameters:
offset index 0...N-1
Returns:
value at offset

Definition at line 570 of file DynProg.h.

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

Parameters:
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

Parameters:
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.

void CDynProg::precompute_stop_codons ( const CHAR genestr,
INT  genestr_len 
)

precompute stop codons

Parameters:
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

Parameters:
genestr_len length of gene string

Definition at line 183 of file DynProg.cpp.

DREAL CDynProg::get_a ( T_STATES  line_,
T_STATES  column 
) const

access function for matrix a

Parameters:
line_ row in matrix 0...N-1
column column in matrix 0...N-1
Returns:
value at position line colum

Definition at line 619 of file DynProg.h.

DREAL CDynProg::get_a_deriv ( T_STATES  line_,
T_STATES  column 
) const

access function for matrix a derivated

Parameters:
line_ row in matrix 0...N-1
column column in matrix 0...N-1
Returns:
value at position line colum

Definition at line 630 of file DynProg.h.

void CDynProg::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 
) [protected]

lookup content SVM values

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

Definition at line 1053 of file DynProg.h.

void CDynProg::lookup_tiling_plif_values ( const INT  from_state,
const INT  to_state,
const INT  len,
DREAL svm_values 
) [protected]

lookup tiling Plif values

Parameters:
from_state from state
to_state to state
len length
svm_values SVM values

Definition at line 1077 of file DynProg.h.

INT CDynProg::find_frame ( const INT  from_state  )  [protected]

find frame

Parameters:
from_state from state

INT CDynProg::raw_intensities_interval_query ( const INT  from_pos,
const INT  to_pos,
DREAL intensities 
) [protected]

raw intensities interval query

Parameters:
from_pos from position
to_pos to position
intensities intensities
Returns:
an integer

Definition at line 1026 of file DynProg.h.

void CDynProg::translate_from_single_order ( WORD obs,
INT  sequence_length,
INT  start,
INT  order,
INT  max_val = 2 
) [protected]

translate from single order

Parameters:
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.

void CDynProg::reset_svm_value ( INT  pos,
INT last_svm_pos,
DREAL svm_value 
) [protected]

reset SVM value

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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]

clear SVM values

Parameters:
svs SVM values

Definition at line 1953 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 (swig compatible?)

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
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

Parameters:
loss segment loss to extend
pos_array position array
segment_id ID of segment
pos position
last_pos last position
last_value last value
Returns:
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

Parameters:
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.


Member Data Documentation

INT CDynProg::N [protected]

number of states

Definition at line 871 of file DynProg.h.

transition matrix

Definition at line 874 of file DynProg.h.

Definition at line 875 of file DynProg.h.

Definition at line 876 of file DynProg.h.

initial distribution of states

Definition at line 879 of file DynProg.h.

Definition at line 880 of file DynProg.h.

distribution of end-states

Definition at line 883 of file DynProg.h.

Definition at line 884 of file DynProg.h.

dict weights

Definition at line 889 of file DynProg.h.

dict weights array

Definition at line 891 of file DynProg.h.

number of degress

Definition at line 894 of file DynProg.h.

INT CDynProg::num_svms [protected]

number of SVMs

Definition at line 896 of file DynProg.h.

number of strings

Definition at line 898 of file DynProg.h.

word degree

Definition at line 901 of file DynProg.h.

cum num words

Definition at line 903 of file DynProg.h.

cum num words array

Definition at line 905 of file DynProg.h.

num words

Definition at line 907 of file DynProg.h.

num words array

Definition at line 909 of file DynProg.h.

mod words

Definition at line 911 of file DynProg.h.

mod words array

Definition at line 913 of file DynProg.h.

CArray<bool> CDynProg::sign_words [protected]

sign words

Definition at line 915 of file DynProg.h.

bool* CDynProg::sign_words_array [protected]

sign words array

Definition at line 917 of file DynProg.h.

string words

Definition at line 919 of file DynProg.h.

string words array

Definition at line 921 of file DynProg.h.

SVM start position

Definition at line 927 of file DynProg.h.

number of unique words

Definition at line 929 of file DynProg.h.

bool CDynProg::svm_arrays_clean [protected]

SVM arrays clean

Definition at line 931 of file DynProg.h.

number of SVMs single

Definition at line 934 of file DynProg.h.

word degree single

Definition at line 936 of file DynProg.h.

cum num words single

Definition at line 938 of file DynProg.h.

num words single

Definition at line 940 of file DynProg.h.

word used single

Definition at line 943 of file DynProg.h.

SVM value unnormalised single

Definition at line 945 of file DynProg.h.

number of unique words single

Definition at line 947 of file DynProg.h.

INT CDynProg::max_a_id [protected]

max a id

Definition at line 950 of file DynProg.h.

INT CDynProg::m_step [protected]

m step

Definition at line 954 of file DynProg.h.

INT CDynProg::m_call [protected]

m call

Definition at line 956 of file DynProg.h.

m sequence

Definition at line 960 of file DynProg.h.

CArray<INT> CDynProg::m_pos [protected]

m position

Definition at line 962 of file DynProg.h.

m orf info

Definition at line 964 of file DynProg.h.

m segment sum weights

Definition at line 966 of file DynProg.h.

m Plif list

Definition at line 968 of file DynProg.h.

m PEN

Definition at line 970 of file DynProg.h.

m PEN state signals

Definition at line 972 of file DynProg.h.

m genestr

Definition at line 974 of file DynProg.h.

m dict weights

Definition at line 976 of file DynProg.h.

m segment loss

Definition at line 978 of file DynProg.h.

m segment IDs

Definition at line 980 of file DynProg.h.

m segment mask

Definition at line 982 of file DynProg.h.

m my state seq

Definition at line 984 of file DynProg.h.

m my position sequence

Definition at line 986 of file DynProg.h.

m my scores

Definition at line 988 of file DynProg.h.

m my losses

Definition at line 990 of file DynProg.h.

m scores

Definition at line 994 of file DynProg.h.

m states

Definition at line 996 of file DynProg.h.

m positions

Definition at line 998 of file DynProg.h.

CArray<bool> CDynProg::m_genestr_stop [protected]

storeage of stop codons array of size length(sequence)

Definition at line 1003 of file DynProg.h.

array for storage of content svm values Jonas

Definition at line 1009 of file DynProg.h.

precomputed tiling values

Definition at line 1012 of file DynProg.h.

raw intensities

Definition at line 1015 of file DynProg.h.

INT* CDynProg::m_probe_pos [protected]

prope position

Definition at line 1017 of file DynProg.h.

number of probes

Definition at line 1019 of file DynProg.h.

bool CDynProg::m_use_tiling [protected]

use tiling

Definition at line 1021 of file DynProg.h.

length of gene string

Definition at line 1023 of file DynProg.h.

CParallel CSGObject::parallel [static, inherited]

Definition at line 105 of file SGObject.h.

CIO CSGObject::io [static, inherited]

Definition at line 106 of file SGObject.h.

CVersion CSGObject::version [static, inherited]

Definition at line 107 of file SGObject.h.


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

SHOGUN Machine Learning Toolbox - Documentation