Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > Member List

This is the complete list of members for T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >, including all inherited members.

align()T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
align(unsigned verbose, std::ostream &out)T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
Aligned_pair typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Aligner_algorithm typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
ALIGNMENT_SEQUENCE_LENGTH enum valueT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Alignment_type typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Alignment_unit typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Alignment_unit_name typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Alignment_unit_rep typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
get_aligner(void) constT_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) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
get_first_sos(void) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
get_identity_percentage(Sequence_length_type type=ALIGNMENT_SEQUENCE_LENGTH) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
get_score(void) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
get_score(void)T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
get_second_sos(void) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
get_similarity_percentage(Sequence_length_type type=ALIGNMENT_SEQUENCE_LENGTH) constT_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) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
LARGEST_SEQUENCE_LENGTH enum valueT_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 valueT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Name_pair typedefT_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) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
print_txt_alignment(std::ostream &out) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
Score_type typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Self typedefT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Sequence_length_type enum nameT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
Sequence_or_structure typedefT_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 valueT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >
statistics(std::ostream &out, Sequence_length_type type) constT_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >inline
Substitution_matrix typedefT_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