| Aligned_pair typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Alignment_type typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Alignment_unit typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Alignment_unit_name typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Alignment_unit_rep typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Conformation typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Distance_difference_matrix typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| get_first_sos(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| get_second_sos(void) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| load_substitution_matrix(const std::string &matrix_filename, unsigned nb_units_names) | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| Matrix_function typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Name_pair typedef | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | |
| print_alignment_dot(std::ostream &out) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| print_alignment_txt(std::ostream &out) const | T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > | inline |
| Score_type typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| Sequence_length_type typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| 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 |
| Substitution_matrix typedef | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | |
| 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 |
| T_Alignment_engine_structures(const StructureType &struct_1, const StructureType &struct_2, const T_Aligner_structure_apurva_wrapper< StructureType > &aligner=T_Aligner_structure_apurva_wrapper< StructureType >()) | T_Alignment_engine_structures< StructureType, T_Aligner_structure_apurva_wrapper< StructureType >, double > | inline |
| T_Alignment_engine_structures_apurva(const StructureType &struct_1, const StructureType &struct_2, const Aligner_algorithm &aligner=Aligner_algorithm()) | T_Alignment_engine_structures_apurva< StructureType, FT, MolecularDistance > | inline |
1.9.1