Version 4.1.5

Sequence Member List

This is the complete list of members for Sequence, including all inherited members.

_coder	PrimaryCount	[protected]
_coder_in	PrimaryCount	[protected]
_count	PrimaryCount	[protected]
_count_ok	PrimaryCount	[protected]
_ipos	PrimarySequence	[protected]
_length	PrimarySequence	[protected]
_name	PrimarySequence	[protected]
_name_file	PrimarySequence	[protected]
_nbinv	PrimaryCount	[protected]
_nbvalue	PrimaryCount	[protected]
_nmodal	PrimarySequence	[protected]
_obs	PrimarySequence	[protected]
_order	PrimaryCount	[protected]
_phase	PrimaryCount	[protected]
_sizecode	PrimarySequence	[protected]
_transl	PrimarySequence	[protected]
clear_count() const	PrimaryCount
compute_count(unsigned long **extern_count, short phase, short initial_phase, unsigned long beg, unsigned long end) const	Sequence	[protected, virtual]
count_occurencies(unsigned long beg, unsigned long end) const	PrimaryCount	[inline]
count_occurencies() const	PrimaryCount	[inline]
count_p_occurencies(short phase, short initial_phase, unsigned long beg, unsigned long end) const	PrimaryCount	[inline]
count_p_occurencies(unsigned long **extern_count, short phase, short initial_phase, unsigned long beg, unsigned long end) const	PrimaryCount	[inline]
count_p_occurencies(unsigned long **extern_count, short phase, short initial_phase=0) const	PrimaryCount	[inline]
count_p_occurencies(short phase, short initial_phase=0) const	PrimaryCount	[inline]
get_code() const	Sequence	[inline]
get_coder() const	PrimaryCount	[inline]
get_count(short p=0) const	PrimaryCount	[inline]
get_jump() const	PrimaryCount	[inline]
get_p_count() const	PrimaryCount	[inline]
init_count() const	PrimaryCount	[protected]
is_count_ok() const	PrimaryCount	[inline]
null_count() const	PrimaryCount
operator()(unsigned long pos) const	Sequence	[inline]
print(const string &file, ios_base::openmode mode=ios::out) const	PrimarySequence
ref_translator() const	PrimarySequence	[inline]
seq() const	Sequence	[inline]
Sequence(ifstream &ifile, short order, const Translator &transl, Coder &coder, const string &name_file="noname")	Sequence
Sequence(short order, unsigned long length, const Translator &transl)	Sequence
Sequence(const string &name_file, short order, const Translator &transl)	Sequence
Sequence(const Sequence &seq)	Sequence
Sequence(const Sequence &seq, short order)	Sequence
set_pos(unsigned long t)	PrimarySequence	[inline]
simule(const double *m_trans, const double *v_init, const gsl_rng *r)	Sequence
simule(const double *m_trans, const gsl_rng *r)	Sequence	[inline]
simule(unsigned long position, double *proba, const gsl_rng *r)	Sequence
simule_phased(short phase, const double **m_trans, const double *v_init, const gsl_rng *r)	Sequence
strseq() const	PrimarySequence
tell_alphabet_size() const	PrimarySequence	[inline]
tell_code(unsigned long pos) const	Sequence	[inline]
tell_code() const	Sequence	[inline]
tell_file_name() const	PrimarySequence	[inline]
tell_int(unsigned long pos) const	Sequence	[virtual]
PrimarySequence::tell_int()	PrimarySequence	[inline]
tell_int_compl(unsigned long pos) const	PrimarySequence	[inline]
tell_int_compl() const	PrimarySequence	[inline]
tell_jump() const	PrimaryCount	[inline]
tell_label(unsigned long pos) const	PrimarySequence	[inline]
tell_labels(unsigned long beg, unsigned long stop) const	PrimarySequence
tell_length() const	PrimarySequence	[inline, virtual]
tell_max_count() const	Sequence	[inline, protected, virtual]
tell_nb_inv() const	PrimarySequence	[inline]
tell_nb_value() const	PrimaryCount	[inline]
tell_occurencies(long code) const	PrimaryCount	[inline]
tell_order() const	PrimaryCount	[inline]
tell_p_occurencies(long code, short numphase) const	PrimaryCount
tell_pattern(unsigned long pos) const	PrimarySequence	[inline]
tell_pattern_compl(unsigned long pos)	PrimarySequence	[inline]
tell_patterns(unsigned long beg, unsigned long stop) const	PrimarySequence
tell_phase() const	PrimaryCount	[inline]
tell_pos()	PrimarySequence	[inline]
tell_seq_name() const	PrimarySequence	[inline]
~PrimaryCount()	PrimaryCount	[inline, virtual]
~PrimarySequence()=0	PrimarySequence	[pure virtual]
~Sequence()	Sequence	[virtual]

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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin

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