_array_seq | PrimarySequenceSet< Sequence > | [protected] |
_coder | PrimaryCount | [protected] |
_coder_in | PrimaryCount | [protected] |
_count | PrimaryCount | [protected] |
_count_ok | PrimaryCount | [protected] |
_length_max | PrimarySequenceSet< Sequence > | [protected] |
_nb_seq | PrimarySequenceSet< Sequence > | [protected] |
_nbinv | PrimaryCount | [protected] |
_nbvalue | PrimaryCount | [protected] |
_nmodal | PrimarySequenceSet< Sequence > | [protected] |
_order | PrimaryCount | [protected] |
_phase | PrimaryCount | [protected] |
_total_length | PrimarySequenceSet< Sequence > | [protected] |
_transl | PrimarySequenceSet< Sequence > | [protected] |
clear_count() const | PrimaryCount | |
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_coder() const | PrimaryCount | [inline] |
get_count(short p=0) const | PrimaryCount | [inline] |
get_jump() const | PrimaryCount | [inline] |
get_p_count() const | PrimaryCount | [inline] |
get_sequence(int i) const | PrimarySequenceSet< Sequence > | [inline] |
get_translator() const | PrimarySequenceSet< Sequence > | [inline] |
init_count() const | PrimaryCount | [protected] |
is_count_ok() const | PrimaryCount | [inline] |
null_count() const | PrimaryCount | |
operator()(int i) const | PrimarySequenceSet< Sequence > | [inline] |
PrimarySequenceSet() | PrimarySequenceSet< Sequence > | [inline] |
SequenceSet(const string &seq_list_file, const string &alpha_file, short order, int nbseq=BUFFERSEQ) | SequenceSet | |
SequenceSet(const string &seq_list_file, short mode, const string &line2parse, bool case_sensitivity, short order, int nbseq=BUFFERSEQ) | SequenceSet | |
tell_alphabet_size() const | PrimarySequenceSet< Sequence > | [inline] |
tell_file_name(int i) const | PrimarySequenceSet< Sequence > | [inline] |
tell_jump() const | PrimaryCount | [inline] |
tell_length() const | PrimarySequenceSet< Sequence > | [inline, virtual] |
tell_length_max() const | PrimarySequenceSet< Sequence > | [inline] |
tell_length_seq(int i) const | PrimarySequenceSet< Sequence > | [inline] |
tell_nb_inv() const | PrimarySequenceSet< Sequence > | [inline] |
tell_nb_sequence() const | PrimarySequenceSet< Sequence > | [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_phase() const | PrimaryCount | [inline] |
tell_seq_name(int i) const | PrimarySequenceSet< Sequence > | [inline] |
weight_matrix(double **wmat) const | PrimarySequenceSet< Sequence > | [inline] |
~PrimaryCount() | PrimaryCount | [inline, virtual] |
~PrimarySequenceSet() | PrimarySequenceSet< Sequence > | [inline, virtual] |