| align() | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| align(unsigned verbose, std::ostream &out) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| Aligned_pair typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Aligner_algorithm typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| ALIGNMENT_SEQUENCE_LENGTH enum value | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Alignment_type typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Alignment_unit typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Alignment_unit_name typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Alignment_unit_rep typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| get_aligner(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_aligner(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_alignment(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_alignment(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_first_sos(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_identity_percentage(Sequence_length_type type=ALIGNMENT_SEQUENCE_LENGTH) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_score(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_score(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_second_sos(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_similarity_percentage(Sequence_length_type type=ALIGNMENT_SEQUENCE_LENGTH) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_substitution_matrix(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_substitution_score(const Alignment_unit_name &p, const Alignment_unit_name &q) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| LARGEST_SEQUENCE_LENGTH enum value | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| load_substitution_matrix(const std::string &matrix_filename, unsigned nb_units_names) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| MEAN_SEQUENCE_LENGTH enum value | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Name_pair typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| operator<<(std::ostream &out, const Sequence_length_type &length_type) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | friend |
| operator>>(std::istream &in, Sequence_length_type &length_type) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | friend |
| print_alignment(std::ostream &out) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| print_txt_alignment(std::ostream &out) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| Score_type typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Self typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Sequence_length_type enum name | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| Sequence_or_structure typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| set_blosum_30(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_blosum_45(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_blosum_62(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_blosum_80(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_pam_120(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_pam_200(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_pam_250(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_pam_40(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_standard_substitution_matrix(SBL::CSB::Alignment_substitution_matrix_type matrix_type) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_substitution_matrix(const Substitution_matrix &matrix) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| set_vtml_200(void) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| SMALLEST_SEQUENCE_LENGTH enum value | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| statistics(std::ostream &out, Sequence_length_type type) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| Substitution_matrix typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| T_Alignment_engine(const SequenceOrStructure &sos_1, const SequenceOrStructure &sos_2, const AlignerAlgorithm &aligner=AlignerAlgorithm(), std::ostream &log=std::cout, unsigned verbose=0) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
1.9.1