, 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] |