LocARNA::EPM Member List

This is the complete list of members for LocARNA::EPM, including all inherited members.

add(seqpos_t posA, seqpos_t posB, char c)	LocARNA::EPM	[inline]
add_am(const Arc &a, const Arc &b)	LocARNA::EPM	[inline]
am_begin() const	LocARNA::EPM	[inline]
am_end() const	LocARNA::EPM	[inline]
Arc typedef	LocARNA::EPM
ArcIdx typedef	LocARNA::EPM
begin() const	LocARNA::EPM	[inline]
clear_am_to_do()	LocARNA::EPM	[inline]
el_pat_vec typedef	LocARNA::EPM
end() const	LocARNA::EPM	[inline]
EPM()	LocARNA::EPM	[inline]
get_am(PairArcIdxVec::size_type idx) const	LocARNA::EPM	[inline]
get_cur_pos() const	LocARNA::EPM	[inline]
get_first_insertion() const	LocARNA::EPM	[inline]
get_max_tol_left() const	LocARNA::EPM	[inline]
get_score() const	LocARNA::EPM	[inline]
get_state() const	LocARNA::EPM	[inline]
includes(const EPM &epm_to_test) const	LocARNA::EPM	[inline]
includes_am(const EPM &epm_to_test) const	LocARNA::EPM	[inline]
insert_epm(const EPM &epm_to_insert)	LocARNA::EPM	[inline]
is_invalid() const	LocARNA::EPM	[inline]
last_matched_pos()	LocARNA::EPM	[inline]
matpos_t typedef	LocARNA::EPM
next_arcmatch()	LocARNA::EPM	[inline]
number_of_am()	LocARNA::EPM	[inline]
overwrite(seqpos_t posA, seqpos_t posB, char c, pat_vec_t::size_type pos)	LocARNA::EPM	[inline]
pair_seqpos_t typedef	LocARNA::EPM
PairArcIdx typedef	LocARNA::EPM
PairArcIdxVec typedef	LocARNA::EPM
pat_vec_at(pat_vec_t::size_type idx) const	LocARNA::EPM	[inline]
pat_vec_size() const	LocARNA::EPM	[inline]
pat_vec_t typedef	LocARNA::EPM
print_epm(std::ostream &out, bool verbose) const	LocARNA::EPM	[inline]
seqpos_t typedef	LocARNA::EPM
set_cur_pos(const matpos_t &cur_pos_)	LocARNA::EPM	[inline]
set_first_insertion(bool first_insertion_)	LocARNA::EPM	[inline]
set_invalid()	LocARNA::EPM	[inline]
set_max_tol_left(score_t tol)	LocARNA::EPM	[inline]
set_score(score_t score_)	LocARNA::EPM	[inline]
set_state(int state_)	LocARNA::EPM	[inline]
sort_am_to_do()	LocARNA::EPM	[inline]
sort_patVec()	LocARNA::EPM	[inline]
store_am(const Arc &a, const Arc &b)	LocARNA::EPM	[inline]
~EPM()	LocARNA::EPM	[inline, virtual]