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< 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

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.

CArray2<INT> CDynProg::transition_matrix_a_id [protected]

transition matrix

Definition at line 874 of file DynProg.h.

CArray2<DREAL> CDynProg::transition_matrix_a [protected]

Definition at line 875 of file DynProg.h.

CArray2<DREAL> CDynProg::transition_matrix_a_deriv [protected]

Definition at line 876 of file DynProg.h.

CArray<DREAL> CDynProg::initial_state_distribution_p [protected]

initial distribution of states

Definition at line 879 of file DynProg.h.

CArray<DREAL> CDynProg::initial_state_distribution_p_deriv [protected]

Definition at line 880 of file DynProg.h.

CArray<DREAL> CDynProg::end_state_distribution_q [protected]

distribution of end-states

Definition at line 883 of file DynProg.h.

CArray<DREAL> CDynProg::end_state_distribution_q_deriv [protected]

Definition at line 884 of file DynProg.h.

CArray2<DREAL> CDynProg::dict_weights [protected]

dict weights

Definition at line 889 of file DynProg.h.

DREAL* CDynProg::dict_weights_array [protected]

dict weights array

Definition at line 891 of file DynProg.h.

INT CDynProg::num_degrees [protected]

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.

INT CDynProg::num_strings [protected]

number of strings

Definition at line 898 of file DynProg.h.

CArray<INT> CDynProg::word_degree [protected]

word degree

Definition at line 901 of file DynProg.h.

CArray<INT> CDynProg::cum_num_words [protected]

cum num words

Definition at line 903 of file DynProg.h.

INT* CDynProg::cum_num_words_array [protected]

cum num words array

Definition at line 905 of file DynProg.h.

CArray<INT> CDynProg::num_words [protected]

num words

Definition at line 907 of file DynProg.h.

INT* CDynProg::num_words_array [protected]

num words array

Definition at line 909 of file DynProg.h.

CArray2<INT> CDynProg::mod_words [protected]

mod words

Definition at line 911 of file DynProg.h.

INT* CDynProg::mod_words_array [protected]

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.

CArray<INT> CDynProg::string_words [protected]

string words

Definition at line 919 of file DynProg.h.

INT* CDynProg::string_words_array [protected]

string words array

Definition at line 921 of file DynProg.h.

CArray<INT> CDynProg::svm_pos_start [protected]

SVM start position

Definition at line 927 of file DynProg.h.

CArray<INT> CDynProg::num_unique_words [protected]

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.

INT CDynProg::num_svms_single [protected]

number of SVMs single

Definition at line 934 of file DynProg.h.

INT CDynProg::word_degree_single [protected]

word degree single

Definition at line 936 of file DynProg.h.

INT CDynProg::cum_num_words_single [protected]

cum num words single

Definition at line 938 of file DynProg.h.

INT CDynProg::num_words_single [protected]

num words single

Definition at line 940 of file DynProg.h.

CArray<bool> CDynProg::word_used_single [protected]

word used single

Definition at line 943 of file DynProg.h.

CArray<DREAL> CDynProg::svm_value_unnormalized_single [protected]

SVM value unnormalised single

Definition at line 945 of file DynProg.h.

INT CDynProg::num_unique_words_single [protected]

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.

CArray3<DREAL> CDynProg::m_seq [protected]

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.

CArray2<INT> CDynProg::m_orf_info [protected]

m orf info

Definition at line 964 of file DynProg.h.

CArray2<DREAL> CDynProg::m_segment_sum_weights [protected]

m segment sum weights

Definition at line 966 of file DynProg.h.

CArray<CPlifBase*> CDynProg::m_plif_list [protected]

m Plif list

Definition at line 968 of file DynProg.h.

CArray2<CPlifBase*> CDynProg::m_PEN [protected]

m PEN

Definition at line 970 of file DynProg.h.

CArray2<CPlifBase*> CDynProg::m_PEN_state_signals [protected]

m PEN state signals

Definition at line 972 of file DynProg.h.

CArray2<CHAR> CDynProg::m_genestr [protected]

m genestr

Definition at line 974 of file DynProg.h.

CArray2<DREAL> CDynProg::m_dict_weights [protected]

m dict weights

Definition at line 976 of file DynProg.h.

CArray3<DREAL> CDynProg::m_segment_loss [protected]

m segment loss

Definition at line 978 of file DynProg.h.

CArray<INT> CDynProg::m_segment_ids [protected]

m segment IDs

Definition at line 980 of file DynProg.h.

CArray<DREAL> CDynProg::m_segment_mask [protected]

m segment mask

Definition at line 982 of file DynProg.h.

CArray<INT> CDynProg::m_my_state_seq [protected]

m my state seq

Definition at line 984 of file DynProg.h.

CArray<INT> CDynProg::m_my_pos_seq [protected]

m my position sequence

Definition at line 986 of file DynProg.h.

CArray<DREAL> CDynProg::m_my_scores [protected]

m my scores

Definition at line 988 of file DynProg.h.

CArray<DREAL> CDynProg::m_my_losses [protected]

m my losses

Definition at line 990 of file DynProg.h.

CArray<DREAL> CDynProg::m_scores [protected]

m scores

Definition at line 994 of file DynProg.h.

CArray2<INT> CDynProg::m_states [protected]

m states

Definition at line 996 of file DynProg.h.

CArray2<INT> CDynProg::m_positions [protected]

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.

CArray2<DREAL> CDynProg::m_precomputed_svm_values [protected]

array for storage of content svm values Jonas

Definition at line 1009 of file DynProg.h.

CArray2<DREAL> CDynProg::m_precomputed_tiling_values [protected]

precomputed tiling values

Definition at line 1012 of file DynProg.h.

DREAL* CDynProg::m_raw_intensities [protected]

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.

INT CDynProg::m_num_probes [protected]

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.

INT CDynProg::m_genestr_len [protected]

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