T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences > Class Template Reference

Module which computes a pairwise alignment of two sequences Module which computes a pairwise alignment of two sequences. More...

#include "Alignment_sequences_module.hpp"

Public Types
typedef T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >	Self
typedef SBL::Modules::Module_base	Base
typedef ModuleTraits::Sequence	Sequence
typedef ModuleTraits::FT	FT
typedef AlignmentEngineSequences	Alignment_engine
	Base engine for making alignments between structures and sequences. Base engine for making alignments between structures and sequences. More...
typedef Alignment_engine::Aligner_algorithm	Aligner_algorithm
	Core algorithm performing the alignment. More...
typedef Alignment_engine::Alignment_unit	Sequence_unit
	Type for a unit (e.g residue or nucleotid) More...
typedef Alignment_engine::Alignment_type	Alignment_type
	Representation of an alignment as a sequence of aligned units. More...
typedef Alignment_engine::Sequence_length_type	Sequence_length_type
	Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages. More...

Public Member Functions
virtual std::string	get_output_prefix (void) const
	Returns a prefix that concatains the input line options used when running the module. More...

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module. More...
static bool	has_options (void)
static void	delete_options (void)
static void	initialize_options (const std::string &caption)

Input Accessors and modifiers
Sequence *&	get_first_sequence (void)
Sequence *&	get_second_sequence (void)
const Alignment_type &	get_alignment (void) const
Aligner_algorithm &	get_aligner_algorithm (void)
const Aligner_algorithm &	get_aligner_algorithm (void) const
Alignment_engine *&	get_alignment_engine (void)
const Alignment_engine *	get_alignment_engine (void) const

Mandatory Requirements
void	run (unsigned verbose, std::ostream &out)
	Runs the module following the input options. More...
bool	is_runnable (void) const
	Checks that all the input options were set. More...
void	statistics (std::ostream &out)
	Reports high-level statistics on the module. More...
boost::program_options::options_description	add_options () const
	Virtual method for adding options to the module. More...
std::string	get_name (void) const
	Returns the name of the package. More...

Optional Requirements
bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. More...
void	report (const std::string &prefix)
	Reports the output and statistics in output files. More...

Modules Management
void	set_module_instance_name (const std::string &module_instance_name)
	Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules. More...
const std::string &	get_module_instance_name (void) const
	Get the name of this instance of this module. More...
void	set_report_mode (std::ios_base::openmode report_mode)
	Set a report mode, that is open or append modes. More...
void	set_report_mode (std::ios_base::openmode &report_mode)
	Set a report mode, that is open or append modes. More...
const std::ios_base::openmode	get_report_mode (void) const
	Get the report mode to be used when reporting. More...

Optional Requirements
void	check_filesystem_directory_exists (const std::string &output_prefix)
	To avoid later crash: check filesystem / existence of directory / directory exists. More...

Others
template<class Self_ >
Self_ *	clone (const Self_ *s) const
	Clones the object using the copy constructor. More...
virtual bool	is_logical_module (void) const
	Checks that this module defines a logical operator. More...
virtual bool	is_condition_module (void) const
	Checks that this module defines a condition operator. More...
virtual bool	operator() (void)
	Only for condition modules, for returning the predicate value. More...
virtual bool	is_modules_collection (void) const
	Checks that this module defines a collection of modules. More...

Detailed Description

template<class ModuleTraits, class AlignmentEngineSequences = SBL::CSB::T_Alignment_engine_sequences_seqan<typename ModuleTraits::Sequence>>
class SBL::Modules::T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >

Module which computes a pairwise alignment of two sequences Module which computes a pairwise alignment of two sequences.

Member Typedef Documentation

Aligner_algorithm

typedef Alignment_engine::Aligner_algorithm Aligner_algorithm

Core algorithm performing the alignment.

Alignment_engine

typedef AlignmentEngineSequences Alignment_engine

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.

Alignment_type

typedef Alignment_engine::Alignment_type Alignment_type

Representation of an alignment as a sequence of aligned units.

Base

typedef SBL::Modules::Module_base Base

FT

typedef ModuleTraits::FT FT

Self

typedef T_Alignment_sequences_module<ModuleTraits, AlignmentEngineSequences> Self

Sequence

typedef ModuleTraits::Sequence Sequence

Sequence_length_type

typedef Alignment_engine::Sequence_length_type Sequence_length_type

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

Sequence_unit

typedef Alignment_engine::Alignment_unit Sequence_unit

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

Member Function Documentation

add_options()

boost::program_options::options_description add_options ( void  ) const

inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

check_filesystem_directory_exists()

void check_filesystem_directory_exists ( const std::string &  output_prefix )

inlineinherited

To avoid later crash: check filesystem / existence of directory / directory exists.

check_options()

bool check_options ( std::string &  message ) const

inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

clone()

Self_* clone ( const Self_ *  s ) const

inlineinherited

Clones the object using the copy constructor.

delete_options()

static void delete_options ( void  )

inlinestaticinherited

get_aligner_algorithm() [1/2]

T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Aligner_algorithm & get_aligner_algorithm ( void  )

inline

get_aligner_algorithm() [2/2]

const T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Aligner_algorithm & get_aligner_algorithm ( void  ) const

inline

get_alignment()

const T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Alignment_type & get_alignment ( void  ) const

inline

get_alignment_engine() [1/2]

T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Alignment_engine *& get_alignment_engine ( void  )

inline

get_alignment_engine() [2/2]

const T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Alignment_engine * get_alignment_engine ( void  ) const

inline

get_first_sequence()

T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Sequence *& get_first_sequence ( void  )

inline

get_module_instance_name()

const std::string& get_module_instance_name ( void  ) const

inlineinherited

Get the name of this instance of this module.

get_name()

std::string get_name ( void  ) const

inlinevirtual

Returns the name of the package.

Reimplemented from Module_base.

get_options()

static boost::program_options::options_description*& get_options ( void  )

inlinestaticinherited

Access to the options' description of the module.

get_output_prefix()

virtual std::string get_output_prefix ( void  ) const

inlinevirtualinherited

Returns a prefix that concatains the input line options used when running the module.

Reimplemented in T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Weights_file_loader< FT >, T_Graph_loader< GraphType, FT >, T_Stop_criterion_module< ModuleTraits >, T_Sample_selector_module< ModuleTraits >, T_Sample_extender_module< ModuleTraits >, T_Exploration_parameters_update_module< ModuleTraits >, T_Exploration_parameters_with_layers< NumberType, Distance >, T_Exploration_parameters_default< NumberType, Distance >, T_Acceptance_test_module< ModuleTraits >, T_Graph_loader< GraphType, FT >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Weighted_points_d_loader< PointD, WeightType >, T_Sequences_loader< FT >, T_Graph_loader< Graph >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_Point_cloud_hausdorff_distance_d_module< ModuleTraits >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, T_Graph_loader< GraphType, FT >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< ModuleTraits::Nearest_neighbors_graph, ModuleTraits::Morse_function, ModuleTraits::Distance_graph_function >::Morse_Smale_Witten_chain_complex >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Molecular_interfaces_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Module_condition< void, Predicate >, T_Module_condition< Module, Predicate >, T_Module_based_workflow< Dummy >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_Earth_mover_distance_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Points_d_file_loader< PointD >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, No_particle_annotator, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, Space_filling_model_loader, Conformations_loader, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Domain_annotator_for_particles< Annotations >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Numbers_file_loader< FT, Tag >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, T_Clustering_loader< Graph, Clustering >, T_Archive_file_loader< InputArchive, SerializedData >, and T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >.

get_report_mode()

const std::ios_base::openmode get_report_mode ( void  ) const

inlineinherited

Get the report mode to be used when reporting.

get_second_sequence()

T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >::Sequence *& get_second_sequence ( void  )

inline

has_options()

static bool has_options ( void  )

inlinestaticinherited

initialize_options()

static void initialize_options ( const std::string &  caption )

inlinestaticinherited

is_condition_module()

virtual bool is_condition_module ( void  ) const

inlineprotectedvirtualinherited

Checks that this module defines a condition operator.

is_logical_module()

virtual bool is_logical_module ( void  ) const

inlineprotectedvirtualinherited

Checks that this module defines a logical operator.

is_modules_collection()

virtual bool is_modules_collection ( void  ) const

inlineprotectedvirtualinherited

Checks that this module defines a collection of modules.

is_runnable()

bool is_runnable ( void  ) const

inlinevirtual

Checks that all the input options were set.

Reimplemented from Module_base.

operator()()

virtual bool operator() ( void  )

inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

report()

void report ( const std::string &  prefix )

inlinevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

run()

void run ( unsigned  verbose, std::ostream &  out  )

inlinevirtual

Runs the module following the input options.

Implements Module_base.

set_module_instance_name()

void set_module_instance_name ( const std::string &  module_instance_name )

inlineinherited

Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules.

set_report_mode() [1/2]

void set_report_mode ( std::ios_base::openmode &  report_mode )

inlineinherited

Set a report mode, that is open or append modes.

set_report_mode() [2/2]

void set_report_mode ( std::ios_base::openmode  report_mode )

inlineinherited

Set a report mode, that is open or append modes.

statistics()

void statistics ( std::ostream &  out )

inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.