LocARNA::SparseTraceController Member List

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

consensus_cost(size_type i, size_type j, const std::vector< TraceRange > &trs) const	LocARNA::TraceRange
diag_pos_bef(index_t indexA, index_t indexB, pair_seqpos_t cur_pos_seq, index_t left_endA=std::numeric_limits< index_t >::max(), index_t left_endB=std::numeric_limits< index_t >::max()) const	LocARNA::SparseTraceController	[inline]
get_delta() const	LocARNA::TraceController	[inline]
get_sparse_mapperA() const	LocARNA::SparseTraceController	[inline]
get_sparse_mapperB() const	LocARNA::SparseTraceController	[inline]
idx_after_max_col_idx(index_t indexA, index_t indexB, matidx_t idx_i, index_t left_endB=std::numeric_limits< index_t >::max()) const	LocARNA::SparseTraceController	[inline]
is_valid(size_type i, size_type j) const	LocARNA::TraceController	[inline]
is_valid_idx_pos(index_t idxA, index_t idxB, matpos_t mat_pos) const	LocARNA::SparseTraceController	[inline]
is_valid_match(size_type i, size_type j) const	LocARNA::TraceController	[inline, virtual]
matching_wo_gap(index_t idxA, index_t idxB, const matpos_t &idx_pos_diag, pair_seqpos_t seq_pos_to_be_matched) const	LocARNA::SparseTraceController	[inline]
matpos_t typedef	LocARNA::SparseTraceController
max_col(size_t i) const	LocARNA::TraceRange	[inline]
max_col_	LocARNA::TraceRange	[protected]
min_col(size_t i) const	LocARNA::TraceRange	[inline]
min_col_	LocARNA::TraceRange	[protected]
min_col_idx(index_t indexA, index_t indexB, matidx_t idx_i, index_t left_endB=std::numeric_limits< index_t >::max()) const	LocARNA::SparseTraceController	[inline]
pair_seqpos_t typedef	LocARNA::SparseTraceController
pos_in_seq(index_t idxA, index_t idxB, const matpos_t &cur_pos) const	LocARNA::SparseTraceController	[inline]
pos_unpaired(index_t idxA, index_t idxB, matpos_t pos) const	LocARNA::SparseTraceController	[inline]
print_debug(std::ostream &out) const	LocARNA::TraceRange
remove_common_gaps(const SeqEntry &aliA, const SeqEntry &aliB)	LocARNA::TraceRange	[static]
restrict_by_anchors(const AnchorConstraints &constraints)	LocARNA::TraceController
rows() const	LocARNA::TraceRange	[inline]
SeqEntry typedef	LocARNA::TraceRange
seqentry_pair_t typedef	LocARNA::TraceRange
SparseTraceController(const SparsificationMapper &sparse_mapperA_, const SparsificationMapper &sparse_mapperB_, const TraceController &trace_controller_)	LocARNA::SparseTraceController	[inline]
TraceController(const Sequence &seqA, const Sequence &seqB, const MultipleAlignment *ma, int delta, bool relaxed_merging=false)	LocARNA::TraceController
TraceRange()	LocARNA::TraceRange	[inline, protected]
TraceRange(const SeqEntry &pseqA, const SeqEntry &pseqB, const SeqEntry &aliA, const SeqEntry &aliB, size_type delta)	LocARNA::TraceRange
TraceRange(size_type lenA, size_type lenB, const std::vector< TraceRange > &trs, size_type delta)	LocARNA::TraceRange
~MatchController() (defined in LocARNA::MatchController)	LocARNA::MatchController	[virtual]
~SparseTraceController() (defined in LocARNA::SparseTraceController)	LocARNA::SparseTraceController	[inline, virtual]
~TraceController()	LocARNA::TraceController	[virtual]