Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData > Class Template Reference

Loader for one or more multiple archives xml archive files. More...

#include "Multiple_archives_xml_archive_file_loader.hpp"

Public Types

typedef std::vector< SerializedData > Data_vector
 List of serialized data. More...
 

Public Member Functions

virtual boost::program_options::options_description add_options (void) const
 Virtual method for adding options to 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 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
 

Constructors

 T_Multiple_archives_xml_archive_file_loader (const std::string &tag, const std::string &sec_helper="Secondary archive file name", const std::string &sec_option_name="secondary-archive", const std::string &helper="", const std::string &option_name="")
 Default constructor. More...
 

Options Descriptions

bool check_options (std::string &message) const
 Check that the parsed options are valid for this loader. More...
 

Output Prefix

std::string get_output_prefix (void) const
 Access to the output prefix of this loader. More...
 

Data Management

const Data_vectorget_all_data (void) const
 Access to all the containers of spheres (const). More...
 
Data_vectorget_all_data (void)
 Access to all the containers of spheres. More...
 
unsigned get_number_of_data (void) const
 Number of containers of spheres. More...
 
const SerializedData & get_data (unsigned i) const
 ith container of spheres corresponding to the ith input file (const). More...
 
SerializedData & get_data (unsigned i)
 ith container of spheres corresponding to the ith input file. More...
 
const SerializedData & get_data (void) const
 Container of spheres (use only if one input file was provided) (const). More...
 
SerializedData & get_data (void)
 Container of spheres (use only if one input file was provided). More...
 
const std::vector< SecondaryData * > & get_secondary_data (void) const
 Container of spheres (use only if one input file was provided) (const). More...
 
std::vector< SecondaryData * > & get_secondary_data (void)
 Container of spheres (use only if one input file was provided). More...
 
bool load (unsigned verbose=false, std::ostream &out=std::cout)
 Once the command line options were parsed, build the containers of spheres from the input files. More...
 
void statistics (std::ostream &out) const
 Print high level statistics on the loaded spheres. More...
 

Detailed Description

template<class SecondaryArchive, class SecondaryData, class SerializedData>
class SBL::IO::T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >

Loader for one or more multiple archives xml archive files.

Loader for one or more multiple archives xml archive files.

   \tparam SecondaryArchive Type of the secondary archive where the full data are stored.

   \tparam SecondaryData Type of the data fully stored in the secondary archive.

   \tparam SerializedData Type of the data serialized in the archive.   

Member Typedef Documentation

◆ Data_vector

typedef std::vector<SerializedData> Data_vector

List of serialized data.

Constructor & Destructor Documentation

◆ T_Multiple_archives_xml_archive_file_loader()

T_Multiple_archives_xml_archive_file_loader ( const std::string &  tag,
const std::string &  sec_helper = "Secondary archive file name",
const std::string &  sec_option_name = "secondary-archive",
const std::string &  helper = "",
const std::string &  option_name = "" 
)
inline

Default constructor.

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_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_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Molecular_interfaces_module< ModuleTraits >, 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_Correlated_motions_by_domain_module< ModuleTraits >, 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_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Buried_surface_area_with_labels_module< ModuleTraits >, 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()

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

Check that the parsed options are valid for this loader.

Reimplemented from T_Module_option_description<>.

◆ get_all_data() [1/2]

const T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >::Data_vector & get_all_data ( void  ) const
inline

Access to all the containers of spheres (const).

◆ get_all_data() [2/2]

T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >::Data_vector & get_all_data ( void  )
inline

Access to all the containers of spheres.

◆ get_data() [1/4]

const SerializedData & get_data ( unsigned  i) const
inline

ith container of spheres corresponding to the ith input file (const).

◆ get_data() [2/4]

SerializedData & get_data ( unsigned  i)
inline

ith container of spheres corresponding to the ith input file.

◆ get_data() [3/4]

const SerializedData & get_data ( void  ) const
inline

Container of spheres (use only if one input file was provided) (const).

◆ get_data() [4/4]

SerializedData & get_data ( void  )
inline

Container of spheres (use only if one input file was provided).

◆ get_name()

virtual std::string get_name ( void  ) const
inlinevirtualinherited

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_number_of_data()

unsigned get_number_of_data ( void  ) const
inline

Number of containers of spheres.

◆ get_options()

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

Access to the options' description of the module.

◆ get_output_prefix()

std::string get_output_prefix ( void  ) const
inlinevirtual

Access to the output prefix of this loader.

Reimplemented from T_Module_option_description<>.

◆ get_secondary_data() [1/2]

const std::vector< SecondaryData > & get_secondary_data ( void  ) const
inline

Container of spheres (use only if one input file was provided) (const).

◆ get_secondary_data() [2/2]

std::vector< SecondaryData > & get_secondary_data ( void  )
inline

Container of spheres (use only if one input file was provided).

◆ load()

bool load ( unsigned  verbose = false,
std::ostream &  out = std::cout 
)
inlinevirtual

Once the command line options were parsed, build the containers of spheres from the input files.

Reimplemented from Loader_base.

◆ statistics()

void statistics ( std::ostream &  out) const
inline

Print high level statistics on the loaded spheres.