Version 4.1.5
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Sequence Member List

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

_coderPrimaryCount [protected]
_coder_inPrimaryCount [protected]
_countPrimaryCount [protected]
_count_okPrimaryCount [protected]
_iposPrimarySequence [protected]
_lengthPrimarySequence [protected]
_namePrimarySequence [protected]
_name_filePrimarySequence [protected]
_nbinvPrimaryCount [protected]
_nbvaluePrimaryCount [protected]
_nmodalPrimarySequence [protected]
_obsPrimarySequence [protected]
_orderPrimaryCount [protected]
_phasePrimaryCount [protected]
_sizecodePrimarySequence [protected]
_translPrimarySequence [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()=0PrimarySequence [pure virtual]
~Sequence()Sequence [virtual]



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