PrimaryCount Class Reference

Abstract class designed for the (coded)word count. More...

#include <seqpp/PrimaryCount.h>

Inheritance diagram for PrimaryCount:

List of all members.

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

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Detailed Description

Abstract class designed for the (coded)word 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)

The count can also be phased.

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Member Function Documentation

unsigned long* PrimaryCount::get_count

(

short

p = 0

)

const [inline]

get the total count in a phase p, or in the unphased case

Parameters:

p

selected phase, default 0 if unphased case.

References _count.

Referenced by PMarkov::PMarkov().

void PrimaryCount::count_p_occurencies	(	short	phase,
		short	initial_phase,
		unsigned long	beg,
		unsigned long	end
	)			const [inline]

Phased count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0.

Parameters:

	phase	phase
	initial_phase	phase of the first element of associated sequence
	beg	the sub-sequence [beg...
	end	the sub-sequence ...end]

References _count, and compute_count().

Referenced by count_occurencies(), count_p_occurencies(), PhasedMarkov::log_likelihood(), PhasedMarkov::PhasedMarkov(), and PhasedPMarkov::PhasedPMarkov().

void PrimaryCount::count_p_occurencies	(	unsigned long **	extern_count,
		short	phase,
		short	initial_phase,
		unsigned long	beg,
		unsigned long	end
	)			const [inline]

Phased extern count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0.

Parameters:

	extern_count	extern count storage
	phase	phase
	initial_phase	phase of the first element of associated sequence
	beg	the sub-sequence [beg...
	end	the sub-sequence ...end]

References compute_count().

void PrimaryCount::count_p_occurencies	(	unsigned long **	extern_count,
		short	phase,
		short	initial_phase = 0
	)			const [inline]

Phased extern count the number of occurencies of all the nbvalue codes in the whole sequence.

Parameters:

	extern_count	extern count storage
	phase	phase
	initial_phase	phase of the first element of associated sequence

References count_p_occurencies().

void PrimaryCount::count_p_occurencies	(	short	phase,
		short	initial_phase = 0
	)			const [inline]

Phased count the number of occurencies of all the nbvalue codes in the whole sequence.

Parameters:

	phase	phase
	initial_phase	phase of the first element of associated sequence

References count_p_occurencies().

void PrimaryCount::count_occurencies	(	unsigned long	beg,
		unsigned long	end
	)			const [inline]

Extern count the number of occurencies of all the nbvalue codes (in the sub-sequence [beg...end])... beware: beg>=0 but not >0.

Parameters:

	beg	the sub-sequence [beg...
	end	the sub-sequence ...end]

References count_p_occurencies().

Referenced by PMarkov::PMarkov().

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

• PrimaryCount.h
• PrimaryCount.cc