Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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 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...
 

Input Accessors and modifiers

Sequence *& get_first_sequence (void)
 
Sequence *& get_second_sequence (void)
 
const Alignment_typeget_alignment (void) const
 
Aligner_algorithmget_aligner_algorithm (void)
 
const Aligner_algorithmget_aligner_algorithm (void) const
 
Alignment_engine *& get_alignment_engine (void)
 
const Alignment_engineget_alignment_engine (void) const
 

Mandatory Requirements

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

Optional Requirements

bool check_options (std::string &message) const override
 Checks that the input options' values are coherent. More...
 
void report (const std::string &prefix) override
 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
SequenceOrStructureRepresentation 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.
AlignerAlgorithmBase 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
FTNumber 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.

◆ 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  )
inlineoverridevirtual

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
inlineoverridevirtual

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.

◆ 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
inlineoverridevirtual

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_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_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Module_condition< Module, Predicate >, T_Module_based_workflow< Dummy >, 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_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Protein_representation_loader< Protein_representation_ >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Numbers_file_loader< FT, Tag >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Molecular_system_loader< Molecular_system_ >, T_Molecular_system_loader< Molecular_system >, T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< typename Protein_representation_::Polypeptide_chain::Molecular_covalent_structure > >, T_Conformation_loader< Conformation_builder_ >, T_Archive_file_loader< InputArchive, SerializedData >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, No_particle_annotator, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Domain_annotator_for_particles< Annotations >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, and T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >.

◆ get_report_mode()

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

Get the report mode to be used when reporting.

◆ 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
inlineoverridevirtual

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)
inlineoverridevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

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

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)
inlineoverridevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.