T_Alignment_engine_sequences_seqan< SequenceType, SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm > Member List

This is the complete list of members for T_Alignment_engine_sequences_seqan< SequenceType, SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm >, including all inherited members.

align(void)	T_Alignment_engine_sequences_seqan< SequenceType, SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm >	inline
Aligned_pair typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
Alignment_type typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
Alignment_unit typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
Alignment_unit_name typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
Alignment_unit_rep typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
get_first_sos(void) const	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
get_second_sos(void) const	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
load_seqan_substitution_matrix(const std::string &matrix_filename)	T_Alignment_engine_sequences_seqan< SequenceType, SeqanSequenceConverter, FreeEndsAlignment, ScoreType, SeqanUnitType, SeqanCustomMatrix, SeqanAlgorithm >	inline
load_substitution_matrix(const std::string &matrix_filename, unsigned nb_units_names)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
Name_pair typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
print_alignment_dot(std::ostream &out) const	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
print_alignment_txt(std::ostream &out) const	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
Score_type typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
Sequence_length_type enum name	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
Sequence_or_structure typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
set_blosum_30(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_blosum_45(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_blosum_62(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_blosum_80(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_pam_120(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_pam_200(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_pam_250(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_pam_40(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_standard_substitution_matrix(SBL::CSB::Alignment_substitution_matrix_type matrix_type)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_substitution_matrix(const Substitution_matrix &matrix)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
set_vtml_200(void)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline
Substitution_matrix typedef	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >
T_Alignment_engine(const SequenceType &sos_1, const SequenceType &sos_2, const T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh > &aligner=T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >(), std::ostream &log=std::cout, unsigned verbose=0)	T_Alignment_engine< SequenceType, T_Aligner_sequence_seqan_wrapper< T_Default_amino_acid_seqan_sequence_converter<>, true, int, seqan::AminoAcid, seqan::CustomAminoAcidMatrix, seqan::Gotoh >, double >	inline