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SequenceSet Member List

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

_array_seqPrimarySequenceSet< Sequence > [protected]
_coderPrimaryCount [protected]
_coder_inPrimaryCount [protected]
_countPrimaryCount [protected]
_count_okPrimaryCount [protected]
_length_maxPrimarySequenceSet< Sequence > [protected]
_nb_seqPrimarySequenceSet< Sequence > [protected]
_nbinvPrimaryCount [protected]
_nbvaluePrimaryCount [protected]
_nmodalPrimarySequenceSet< Sequence > [protected]
_orderPrimaryCount [protected]
_phasePrimaryCount [protected]
_total_lengthPrimarySequenceSet< Sequence > [protected]
_translPrimarySequenceSet< 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]



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