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
idx_vec_t typedef (defined in LocARNA::TraceRange)	LocARNA::TraceRange	protected
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	inlinevirtual
lenA_	LocARNA::TraceRange	protected
lenB_	LocARNA::TraceRange	protected
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=std::cerr) const	LocARNA::TraceRange
remove_common_gaps(const SeqEntry &aliA, const SeqEntry &aliB)	LocARNA::TraceRange	static
restrict_by_anchors(const AnchorConstraints &constraints)	LocARNA::TraceController
restrict_by_trace_probabilities(const TraceProbs &trace_probs, double min_prob)	LocARNA::TraceController
reverse() const	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(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
TraceRange(size_t lenA, size_t lenB)	LocARNA::TraceRange	inlineprotected
~MatchController() (defined in LocARNA::MatchController)	LocARNA::MatchController	virtual
~SparseTraceController() (defined in LocARNA::SparseTraceController)	LocARNA::SparseTraceController	inlinevirtual
~TraceController()	LocARNA::TraceController	virtual