Loader_base Class Reference

Base loader from which any loader should inherit. More...

#include <Loader_base.hpp>

Public Member Functions
virtual boost::program_options::options_description	add_options (void) const
	Virtual method for adding options to the module. More...
virtual bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. More...
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...

Requirements
virtual bool	load (unsigned verbose, std::ostream &out)
	Loads the data. More...
virtual std::string	get_name (void) const
	Return the name of the class itself. More...

Management
void	set_loader_instance_name (const std::string &loader_instance_name)
const std::string &	get_loader_instance_name (void) const

Detailed Description

Base loader from which any loader should inherit.

Requirements are...

Member Function Documentation

add_options()

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

inlinevirtualinherited

Virtual method for adding options to the module.

Reimplemented in T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Molecular_interfaces_module< ModuleTraits >, T_Exploration_parameters_with_layers< NumberType, Distance >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Space_filling_model_shelling_diagram_comparison_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< GraphType, GetWeight >::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_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Exploration_parameters_update_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Earth_mover_distance_module< ModuleTraits >, T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Acceptance_test_module< ModuleTraits >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Sample_selector_module< ModuleTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Numbers_file_loader< FT, Tag >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Cluster_engine_module< ModuleTraits >, T_Weights_file_loader< FT >, T_Archive_file_loader< InputArchive, SerializedData >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Exploration_parameters_default< NumberType, Distance >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Points_d_file_loader< PointD >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Domain_annotator_for_particles< Annotations >, T_Iterative_alignment_module< ModuleTraits >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, and T_Graph_loader< Graph >.

check_options()

virtual bool check_options ( std::string &  message ) const

inlinevirtualinherited

Checks that the input options' values are coherent.

Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Molecular_interfaces_module< ModuleTraits >, T_Module_based_workflow< Dummy >, T_Module_based_workflow<>, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, 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< GraphType, GetWeight >::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_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, T_Exploration_parameters_update_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, T_Acceptance_test_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Sample_selector_module< ModuleTraits >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Cluster_engine_module< ModuleTraits >, T_Exploration_parameters_default< NumberType, Distance >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Archive_file_loader< InputArchive, SerializedData >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Domain_annotator_for_particles< Annotations >, T_Graph_loader< GraphType, FT >, T_Module_condition< Module, Predicate >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Weights_file_loader< FT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Points_d_file_loader< PointD >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Numbers_file_loader< FT, Tag >, T_Graph_loader< Graph >, and No_particle_annotator.

get_name()

virtual std::string get_name ( void  ) const

inlinevirtual

Return the name of the class itself.

Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Exploration_parameters_default< NumberType, Distance >, T_Archive_file_loader< InputArchive, SerializedData >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< GraphType, FT >, T_Sequences_loader< FT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Points_d_file_loader< PointD >, T_Weights_file_loader< FT >, T_Numbers_file_loader< FT, Tag >, T_Graph_loader< Graph >, and No_particle_annotator.

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

load()

virtual bool load ( unsigned  verbose, std::ostream &  out  )

inlinevirtual

Loads the data.

Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Archive_file_loader< InputArchive, SerializedData >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Weights_file_loader< FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_Points_d_file_loader< PointD >, T_Numbers_file_loader< FT, Tag >, T_Domain_annotator_for_particles< Annotations >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Exploration_parameters_default< NumberType, Distance >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< Graph >, and No_particle_annotator.