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Version 4.0.0 |
#include <seqpp/PrimaryCount.h>
Inheritance diagram for PrimaryCount:
Public Member Functions | |
virtual | ~PrimaryCount () |
destructor | |
void | clear_count () const |
clear the count | |
void | null_count () const |
put all counts down to 0 | |
short | tell_order () const |
returns the markovian order | |
int | tell_nb_value () const |
returns the nber of codes/words taking into interest | |
long | tell_jump () const |
returns the jump to the codes of _order+1 letters | |
long * | get_jump () const |
returns the vector of the jumps to the codes of i letters, 0<i<=order+2 | |
Coder & | get_coder () const |
allows a const access to the coder | |
bool | is_count_ok () const |
checks if the count is available | |
unsigned long ** | get_p_count () const |
get the total count, in the phased case | |
unsigned long * | get_count (short p=0) const |
get the total count in a phase p, or in the unphased case | |
short | tell_phase () const |
returns nb of phase | |
void | count_p_occurencies (short phase, short initial_phase, unsigned long beg, unsigned long end) const |
Phased count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0. | |
void | count_p_occurencies (unsigned long **extern_count, short phase, short initial_phase, unsigned long beg, unsigned long end) const |
Phased extern count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0. | |
void | count_p_occurencies (unsigned long **extern_count, short phase, short initial_phase=0) const |
Phased extern count the number of occurencies of all the nbvalue codes in the whole sequence. | |
void | count_p_occurencies (short phase, short initial_phase=0) const |
Phased count the number of occurencies of all the nbvalue codes in the whole sequence. | |
void | count_occurencies (unsigned long beg, unsigned long end) const |
Extern count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0. | |
void | count_occurencies () const |
Count the number of occurencies of all the nbvalue codes in the whole sequence. | |
unsigned long | tell_p_occurencies (long code, short numphase) const |
extract the number of occurencies of code in phase | |
unsigned long | tell_occurencies (long code) const |
extract the number of occurencies of obs | |
Protected Member Functions | |
void | init_count () const |
initialize the count | |
virtual unsigned long | tell_max_count () const =0 |
return the max length for the count | |
virtual void | compute_count (unsigned long **extern_count, short phase, short initial_phase, unsigned long beg, unsigned long end) const =0 |
compute the count | |
Protected Attributes | |
short | _order |
Order of the model. | |
long | _nbvalue |
nber of codes/words taking into interest | |
short | _nbinv |
number of invalid negative code | |
Coder * | _coder |
markovian coder associated to the order of the sequence | |
bool | _coder_in |
true if _coder is build in the class | |
unsigned long ** | _count |
count of each code/word, even invalid (-1) | |
bool | _count_ok |
if the count is available | |
short | _phase |
phase for the count |
This object is based on integer codes to store words as required for a markov modelling (see Sequence). The words are coded in alphabet_size base, coding the 1-token words, then the 2-tokens words, the 3-tokens words... Let call jump(i) the first code of a i-tokens words, a PrimaryCount object is designed to count all words:
(example with alphabet AGCT and order=2) 0 first word ( 0 -> A) .. .. 1-token words (from A to T) .. jump(1) (4 -> AA) .. .. 2-tokens words (from AA to TT) .. jump(2) (20 -> AAA) .. .. 3-tokens words (from AAA to TTT) .. .. .. last word (TTT) jump(order+1) (64 -> /end)
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Extern count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0.
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Phased count the number of occurencies of all the nbvalue codes in the whole sequence.
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Phased extern count the number of occurencies of all the nbvalue codes in the whole sequence.
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Phased extern count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0.
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Phased count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0.
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get the total count in a phase p, or in the unphased case
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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin |