Version 4.1.5

SequenceSet Member List

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

_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()	SequenceSet	[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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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin

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