Core algorithm performing the alignment.

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.

Representation of an alignment as a sequence of aligned units.

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

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

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

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

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

Clones the object using the copy constructor.

Get the name of this instance of this module.

Returns the name of the package.

Reimplemented from Module_base.

Access to the options' description of the module.

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 the report mode to be used when reporting.

Checks that this module defines a condition operator.

Checks that this module defines a logical operator.

Checks that this module defines a collection of modules.

Checks that all the input options were set.

Reimplemented from Module_base.

Only for condition modules, for returning the predicate value.

Reports the output and statistics in output files.

Reimplemented from Module_base.

Runs the module following the input options.

Implements Module_base.

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 a report mode, that is open or append modes.

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

Reports high-level statistics on the module.

Reimplemented from Module_base.