T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT > Class Template Reference

Base engine for making alignments between structures and sequences. Base engine for making alignments between structures and sequences. More...

#include <Alignment_engine.hpp>

Classes
class	Is_lower_name_pair
	Predicate for comparing two pairs whatever the order of Alignment_unit_rep in each pair. More...
class	Matrix_function
	Functor for the substitution matrix. Is imposed the following properties: (i) symmetry, (ii) undefined values are 0. Thus, it is just enough to specify non null values on only one triangle of the matrix. More...

Public Types
enum	Sequence_length_type
	Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages. More...
typedef SequenceOrStructure	Sequence_or_structure
	Type for representing the sequences or the structures to align.
typedef AlignerAlgorithm	Aligner_algorithm
	Core algorithm performing the alignment.
typedef SequenceOrStructure::Alignment_unit	Alignment_unit
	Type for a unit (e.g residue or nucleotid)
typedef SequenceOrStructure::Alignment_unit_name	Alignment_unit_name
	Representation of the name of a unit.
typedef SequenceOrStructure::Alignment_unit_rep	Alignment_unit_rep
	Representation of a unit for index purposes.
typedef AlignerAlgorithm::Score_type	Score_type
	Representation of the score of the algorithm.
typedef std::pair< Alignment_unit_rep, Alignment_unit_rep >	Aligned_pair
	Representation of two aligned units.
typedef std::vector< Aligned_pair >	Alignment_type
	Representation of an alignment as a sequence of aligned units.
typedef std::pair< Alignment_unit_name, Alignment_unit_name >	Name_pair
	Representation of two unit names.
typedef std::map< Name_pair, FT, Is_lower_name_pair >	Substitution_matrix
	Representation of the storage of values of the subtitution matrix.

Constructors
	T_Alignment_engine (const SequenceOrStructure &sos_1, const SequenceOrStructure &sos_2, const AlignerAlgorithm &aligner=AlignerAlgorithm(), std::ostream &log=std::cout, unsigned verbose=0)
	Constructor initializing the input sos and possibly the aligner algorithm.

Accessors
const SequenceOrStructure &	get_first_sos (void) const
	Returns the first sequence or structure of the alignment.
const SequenceOrStructure &	get_second_sos (void) const
	Returns the second sequence or structure of the alignment.

Analysis
void	set_substitution_matrix (const Substitution_matrix &matrix)
	The input is a map from pairs of Alignment_unit_name to the associated score. Note that by construction, it is enough to specify non null values on a half of the matrix, diagonal excluded.
void	load_substitution_matrix (const std::string &matrix_filename, unsigned nb_units_names)
	Loads directly the substitution matrix from a file of the format : Alignment_unit_name Alignment_unit_name Value. If duplicated values, the last one is taken.
void	set_blosum_30 (void)
	Set the current matrix as the BLOSUM30 matrix as defined in Seqan 2.0.
void	set_blosum_45 (void)
	Set the current matrix as the BLOSUM45 matrix as defined in Seqan 2.0.
void	set_blosum_62 (void)
	Set the current matrix as the BLOSUM62 matrix as defined in Seqan 2.0.
void	set_blosum_80 (void)
	Set the current matrix as the BLOSUM80 matrix as defined in Seqan 2.0.
void	set_pam_40 (void)
	Set the current matrix as the PAM40 matrix as defined in Seqan 2.0.
void	set_pam_120 (void)
	Set the current matrix as the PAM120 matrix as defined in Seqan 2.0.
void	set_pam_200 (void)
	Set the current matrix as the PAM200 matrix as defined in Seqan 2.0.
void	set_pam_250 (void)
	Set the current matrix as the PAM250 matrix as defined in Seqan 2.0.
void	set_vtml_200 (void)
	Set the current matrix as the VTML200 matrix as defined in Seqan 2.0.
void	set_standard_substitution_matrix (SBL::CSB::Alignment_substitution_matrix_type matrix_type)
	Set the current matrix as one of the standard substitution matrices.
void	print_alignment_txt (std::ostream &out) const
	Print the alignment in txt format.
void	print_alignment_dot (std::ostream &out) const
	Print the alignment as a dot graph.

Detailed Description

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>
class SBL::CSB::T_Alignment_engine< SequenceOrStructure, AlignerAlgorithm, FT >

Base engine for making alignments between structures and sequences. Base engine for making alignments between structures and sequences.

It provides a generic interface for wrapping existing algorithms aligning pairs of sequences or structures. It is designed such that it provides all common statistics to both type of algorithms. For a data structure that is more specific to structural alignments, see the class T_Alignement_engine_for_structures

Template Parameters

SequenceOrStructure	Representation of a sequence or structure (sos) : it requires in particular to define the type Alignment_unit for the base representation of a residue or a nucleotid to align, the type Alignment_unit_name for the representation of the name of the unit (e.g ALA), Alignment_unit_rep for indexing the units in the sos, the method get_name() to return the name of the unit, size() to return the length of the sequence, and the operator [Alignment_unit_rep] for accessing to the corresponding unit of the sos.
AlignerAlgorithm	Base functor for the algorithm that makes the alignment between the two input sos : it requires to define a type Score_type for the score (e.g a double, or a pair of doubles if two scores are required), to take two input sos and an output iterator over pairs of Alignment_unit_rep for the output alignment, and to return the score of the algorithm
FT	Number type representation used for all statistics except the algorithm score.

Member Typedef Documentation

Aligned_pair

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef std::pair<Alignment_unit_rep, Alignment_unit_rep> Aligned_pair

Representation of two aligned units.

Aligner_algorithm

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef AlignerAlgorithm Aligner_algorithm

Core algorithm performing the alignment.

Alignment_type

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef std::vector<Aligned_pair> Alignment_type

Representation of an alignment as a sequence of aligned units.

Alignment_unit

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef SequenceOrStructure::Alignment_unit Alignment_unit

Type for a unit (e.g residue or nucleotid)

Alignment_unit_name

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef SequenceOrStructure::Alignment_unit_name Alignment_unit_name

Representation of the name of a unit.

Alignment_unit_rep

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef SequenceOrStructure::Alignment_unit_rep Alignment_unit_rep

Representation of a unit for index purposes.

Name_pair

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef std::pair<Alignment_unit_name, Alignment_unit_name> Name_pair

Representation of two unit names.

Score_type

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef AlignerAlgorithm::Score_type Score_type

Representation of the score of the algorithm.

Sequence_or_structure

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef SequenceOrStructure Sequence_or_structure

Type for representing the sequences or the structures to align.

Substitution_matrix

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

typedef std::map<Name_pair, FT, Is_lower_name_pair> Substitution_matrix

Representation of the storage of values of the subtitution matrix.

Member Enumeration Documentation

Sequence_length_type

template<class SequenceOrStructure, class AlignerAlgorithm, class FT = double>

enum Sequence_length_type

Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages.

Constructor & Destructor Documentation

T_Alignment_engine()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

T_Alignment_engine ( const SequenceOrStructure & sos_1, const SequenceOrStructure & sos_2, const AlignerAlgorithm & aligner = AlignerAlgorithm(), std::ostream & log = std::cout, unsigned verbose = 0 )

inline

Constructor initializing the input sos and possibly the aligner algorithm.

Member Function Documentation

get_first_sos()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

const SequenceOrStructure & get_first_sos ( void ) const

inline

Returns the first sequence or structure of the alignment.

get_second_sos()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

const SequenceOrStructure & get_second_sos ( void ) const

inline

Returns the second sequence or structure of the alignment.

load_substitution_matrix()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void load_substitution_matrix ( const std::string & matrix_filename, unsigned nb_units_names )

inline

Loads directly the substitution matrix from a file of the format : Alignment_unit_name Alignment_unit_name Value. If duplicated values, the last one is taken.

print_alignment_dot()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void print_alignment_dot ( std::ostream & out ) const

inline

Print the alignment as a dot graph.

print_alignment_txt()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void print_alignment_txt ( std::ostream & out ) const

inline

Print the alignment in txt format.

set_blosum_30()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_blosum_30 ( void )

inline

Set the current matrix as the BLOSUM30 matrix as defined in Seqan 2.0.

set_blosum_45()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_blosum_45 ( void )

inline

Set the current matrix as the BLOSUM45 matrix as defined in Seqan 2.0.

set_blosum_62()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_blosum_62 ( void )

inline

Set the current matrix as the BLOSUM62 matrix as defined in Seqan 2.0.

set_blosum_80()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_blosum_80 ( void )

inline

Set the current matrix as the BLOSUM80 matrix as defined in Seqan 2.0.

set_pam_120()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_pam_120 ( void )

inline

Set the current matrix as the PAM120 matrix as defined in Seqan 2.0.

set_pam_200()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_pam_200 ( void )

inline

Set the current matrix as the PAM200 matrix as defined in Seqan 2.0.

set_pam_250()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_pam_250 ( void )

inline

Set the current matrix as the PAM250 matrix as defined in Seqan 2.0.

set_pam_40()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_pam_40 ( void )

inline

Set the current matrix as the PAM40 matrix as defined in Seqan 2.0.

set_standard_substitution_matrix()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_standard_substitution_matrix ( SBL::CSB::Alignment_substitution_matrix_type matrix_type )

inline

Set the current matrix as one of the standard substitution matrices.

set_substitution_matrix()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_substitution_matrix ( const Substitution_matrix & matrix )

inline

The input is a map from pairs of Alignment_unit_name to the associated score. Note that by construction, it is enough to specify non null values on a half of the matrix, diagonal excluded.

set_vtml_200()

template<class SequenceOrStructure, class AlignerAlgorithm, class FT>

void set_vtml_200 ( void )

inline

Set the current matrix as the VTML200 matrix as defined in Seqan 2.0.