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HalfLocalSequenceAlignment Member List

This is the complete list of members for HalfLocalSequenceAlignment, including all inherited members.
_alignment_results (defined in SequenceAlignment)SequenceAlignment [protected]
_gap_panelty (defined in SequenceAlignment)SequenceAlignment [protected]
_match_panelty (defined in SequenceAlignment)SequenceAlignment [protected]
_mismatch_panelty (defined in SequenceAlignment)SequenceAlignment [protected]
_neutral_panelty (defined in SequenceAlignment)SequenceAlignment [protected]
_query_sequence (defined in SequenceAlignment)SequenceAlignment [protected]
_target_sequence (defined in SequenceAlignment)SequenceAlignment [protected]
align(const std::string &query, const std::string &target) (defined in SequenceAlignment)SequenceAlignment
DIRECTION enum name (defined in SequenceAlignment)SequenceAlignment [protected]
find_alignment_starting_point(ssize_t &new_query_index, ssize_t &new_target_index) const (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment
find_optimal_alignment() (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [virtual]
find_optimal_alignment_from_point(const size_t query_start, const size_t target_start) const (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment
FROM_LEFT enum value (defined in SequenceAlignment)SequenceAlignment [protected]
FROM_NOWHERE enum value (defined in SequenceAlignment)SequenceAlignment [protected]
FROM_UPPER enum value (defined in SequenceAlignment)SequenceAlignment [protected]
FROM_UPPER_LEFT enum value (defined in SequenceAlignment)SequenceAlignment [protected]
gap_panelty() const (defined in SequenceAlignment)SequenceAlignment [inline]
highest_scored_query_index (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [protected]
highest_scored_target_index (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [protected]
match(const size_t query_index, const size_t target_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
match_matrix (defined in SequenceAlignment)SequenceAlignment [protected]
match_panelty() const (defined in SequenceAlignment)SequenceAlignment [inline]
match_value(const char q, const char t) const (defined in SequenceAlignment)SequenceAlignment [inline]
matrix_height() const (defined in SequenceAlignment)SequenceAlignment [inline]
matrix_width() const (defined in SequenceAlignment)SequenceAlignment [inline]
mismatch_panelty() const (defined in SequenceAlignment)SequenceAlignment [inline]
neutral_panelty() const (defined in SequenceAlignment)SequenceAlignment [inline]
nucleotide_match_score(const size_t query_index, const size_t target_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
origin(const size_t query_index, const size_t target_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
origin_matrix (defined in SequenceAlignment)SequenceAlignment [protected]
populate_match_matrix() (defined in SequenceAlignment)SequenceAlignment [protected]
populate_matrix() (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [virtual]
post_process() (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [virtual]
print_matrix(std::ostream &strm=std::cout) const (defined in SequenceAlignment)SequenceAlignment
query_border (defined in SequenceAlignment)SequenceAlignment [protected]
query_nucleotide(size_t query_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
query_sequence() const (defined in SequenceAlignment)SequenceAlignment [inline]
reset_alignment_results() (defined in SequenceAlignment)SequenceAlignment [protected, virtual]
reset_matrix(size_t width, size_t height) (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [virtual]
resize_matrix(size_t width, size_t height) (defined in SequenceAlignment)SequenceAlignment [protected]
results() const (defined in SequenceAlignment)SequenceAlignment [inline]
safe_score(const ssize_t query_index, const ssize_t target_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
score(const size_t query_index, const size_t target_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
score_matrix (defined in SequenceAlignment)SequenceAlignment [protected]
score_type typedef (defined in SequenceAlignment)SequenceAlignment [protected]
SequenceAlignment() (defined in SequenceAlignment)SequenceAlignment
set_sequences(const std::string &_query, const std::string &target) (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment [virtual]
starting_point_close_to_end_of_sequences(const size_t query_index, const size_t target_index) const (defined in HalfLocalSequenceAlignment)HalfLocalSequenceAlignment
target_border (defined in SequenceAlignment)SequenceAlignment [protected]
target_nucleotide(size_t target_index) const (defined in SequenceAlignment)SequenceAlignment [inline]
target_sequence() const (defined in SequenceAlignment)SequenceAlignment [inline]
~SequenceAlignment() (defined in SequenceAlignment)SequenceAlignment [inline, virtual]

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