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 T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData > Self
 
typedef SBL::IO::T_Multiple_archives_serialization_xml_iarchive< SecondaryData, SecondaryArchive > Input_archive
 
typedef SBL::IO::Loader_base Base
 
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...
 
static bool has_options (void)
 
static void delete_options (void)
 
static void initialize_options (const std::string &caption)
 

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...
 

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
 

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.

Template Parameters
SecondaryArchiveType of the secondary archive where the full data are stored.
SecondaryDataType of the data fully stored in the secondary archive.
SerializedDataType of the data serialized in the archive.

Member Typedef Documentation

◆ Base

◆ Data_vector

typedef std::vector<SerializedData> Data_vector

List of serialized data.

◆ Input_archive

◆ Self

typedef T_Multiple_archives_xml_archive_file_loader<SecondaryArchive, SecondaryData, SerializedData> Self

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_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_Force_field_atomic_traits< TForceFieldFunctionTraits >::Potential_energy_parameters_loader, 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_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_RST_MST_D_Family_matching_module< ModuleTraits >, 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_interfaces_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Earth_mover_distance_module< ModuleTraits >, T_D_Family_matching_module< ModuleTraits, TSolutionComputer >, 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 >, 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 >, Tripeptide_constraints_loader_from_pdb, 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_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 >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >, T_Iterative_alignment_module< ModuleTraits >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, T_Subdomain_comparator_module< ModuleTraits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, and T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >.

◆ 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< Dummy >.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_all_data() [1/2]

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_all_data() [2/2]

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_data() [1/4]

SerializedData & get_data ( unsigned  i)
inline

ith container of spheres corresponding to the ith input file.

◆ get_data() [2/4]

const SerializedData & get_data ( unsigned  i) const
inline

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

◆ get_data() [3/4]

SerializedData & get_data ( void  )
inline

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

◆ get_data() [4/4]

const SerializedData & get_data ( void  ) const
inline

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

◆ get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const
inlineinherited

◆ get_name()

virtual std::string get_name ( void  ) const
inlinevirtualinherited

Return the name of the class itself.

Reimplemented in T_Weights_file_loader< FT >, T_Graph_loader< GraphType, FT >, T_Exploration_parameters_with_layers< NumberType, Distance >, T_Exploration_parameters_default< NumberType, Distance >, T_Graph_loader< GraphType, FT >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Weighted_points_d_loader< PointD, WeightType >, T_Sequences_loader< FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, 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_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_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< Dummy >.

◆ get_secondary_data() [1/2]

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

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

◆ get_secondary_data() [2/2]

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

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

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

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

◆ 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.

◆ set_loader_instance_name()

void set_loader_instance_name ( const std::string &  loader_instance_name)
inlineinherited

◆ statistics()

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

Print high level statistics on the loaded spheres.