_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 | |
print(const string &file) 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 | |
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] |