This is the complete list of members for vg::MatrixAlignmentScorer, including all inherited members.

alignment_score_partition_function(double lambda, const double matrix[16], const double nt_freqs[4])	vg::AlignmentScorer	privatestatic
EditAlignmentScorer(int8_t match=default_match, int8_t mismatch=default_mismatch, int8_t gap_open=default_gap_open, int8_t gap_extension=default_gap_extension, int8_t full_length_bonus=default_full_length_bonus)	vg::EditAlignmentScorer
full_length_bonus	vg::EditAlignmentScorer
gap_extension	vg::EditAlignmentScorer
gap_open	vg::EditAlignmentScorer
get_log_base() const override	vg::MatrixAlignmentScorer	virtual
log_base	vg::MatrixAlignmentScorer	protected
longest_detectable_gap(const Alignment &alignment, const std::string::const_iterator &read_pos) const	vg::EditAlignmentScorer
longest_detectable_gap(size_t read_length, size_t read_pos) const	vg::EditAlignmentScorer
longest_detectable_gap(const Alignment &alignment) const	vg::EditAlignmentScorer
longest_detectable_gap(size_t read_length) const	vg::EditAlignmentScorer
match	vg::EditAlignmentScorer
MatrixAlignmentScorer(const int8_t *score_matrix_4x4=default_score_matrix, int8_t gap_open=default_gap_open, int8_t gap_extension=default_gap_extension, int8_t full_length_bonus=default_full_length_bonus, double gc_content=default_gc_content)	vg::MatrixAlignmentScorer
MatrixAlignmentScorer(const MatrixAlignmentScorer &)=delete	vg::MatrixAlignmentScorer
mismatch	vg::EditAlignmentScorer
nt_table	vg::MatrixAlignmentScorer
operator=(const MatrixAlignmentScorer &)=delete	vg::MatrixAlignmentScorer
recover_log_base(const double matrix[16], double gc_content, double tol=1e-12)	vg::AlignmentScorer	protectedstatic
remove_bonuses(const Alignment &aln, bool pinned=false, bool pin_left=false) const	vg::EditAlignmentScorer	virtual
score_alignment(const Alignment &aln) const override	vg::EditAlignmentScorer	virtual
score_contiguous_alignment(const Alignment &aln, bool allow_left_bonus=true, bool allow_right_bonus=true) const	vg::EditAlignmentScorer	virtual
score_discontiguous_alignment(const Alignment &aln, const std::function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool allow_left_bonus=true, bool allow_right_bonus=true) const	vg::EditAlignmentScorer	virtual
score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const override	vg::MatrixAlignmentScorer	virtual
score_exact_match(const std::string &sequence, const std::string &base_quality) const override	vg::MatrixAlignmentScorer	virtual
score_exact_match(std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const override	vg::MatrixAlignmentScorer	virtual
score_exact_match(const std::string &sequence) const	vg::MatrixAlignmentScorer
score_exact_match(std::string::const_iterator seq_begin, std::string::const_iterator seq_end) const	vg::MatrixAlignmentScorer
score_full_length_bonus(bool left_side, std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const override	vg::MatrixAlignmentScorer	virtual
score_full_length_bonus(bool left_side, const Alignment &alignment) const override	vg::MatrixAlignmentScorer	virtual
score_gap(size_t gap_length) const	vg::EditAlignmentScorer	virtual
score_matrix	vg::MatrixAlignmentScorer
score_mismatch(std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const override	vg::MatrixAlignmentScorer	virtual
score_mismatch(size_t length) const	vg::MatrixAlignmentScorer
score_partial_alignment(const Alignment &alignment, const HandleGraph &graph, const path_t &path, std::string::const_iterator seq_begin, bool no_read_end_scoring=false) const override	vg::MatrixAlignmentScorer	virtual
verify_valid_log_odds_score_matrix(const double matrix[16], const double nt_freqs[4])	vg::AlignmentScorer	privatestatic
~AlignmentScorer()=default	vg::AlignmentScorer	virtual
~MatrixAlignmentScorer() override	vg::MatrixAlignmentScorer