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.

Public Member Functions
virtual boost::program_options::options_description	add_options (void)
	Virtual method for adding options to the module.

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module.

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.

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

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

Data Management
const Data_vector &	get_all_data (void) const
	Access to all the containers of spheres (const).
Data_vector &	get_all_data (void)
	Access to all the containers of spheres.
unsigned	get_number_of_data (void) const
	Number of containers of spheres.
const SerializedData &	get_data (unsigned i) const
	ith container of spheres corresponding to the ith input file (const).
SerializedData &	get_data (unsigned i)
	ith container of spheres corresponding to the ith input file.
const SerializedData &	get_data (void) const
	Container of spheres (use only if one input file was provided) (const).
SerializedData &	get_data (void)
	Container of spheres (use only if one input file was provided).
const std::vector< SecondaryData * > &	get_secondary_data (void) const
	Container of spheres (use only if one input file was provided) (const).
std::vector< SecondaryData * > &	get_secondary_data (void)
	Container of spheres (use only if one input file was provided).
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.
void	statistics (std::ostream &out) const
	Print high level statistics on the loaded spheres.

Requirements
virtual std::string	get_name (void) const
	Return the name of the class itself.

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

SecondaryArchive	Type of the secondary archive where the full data are stored.
SecondaryData	Type of the data fully stored in the secondary archive.
SerializedData	Type of the data serialized in the archive.

Member Typedef Documentation

Data_vector

template<class SecondaryArchive, class SecondaryData, class SerializedData>

typedef std::vector<SerializedData> Data_vector

List of serialized data.

Constructor & Destructor Documentation

T_Multiple_archives_xml_archive_file_loader()

template<class SecondaryArchive, class SecondaryData, class SerializedData>

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()

template<class Dummy = void>

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

inlinevirtualinherited

Virtual method for adding options to the module.

Reimplemented in T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Biomolecule_representation_loader< Protein_representation, Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Biomolecule_representation_loader< Protein_representation_FIAT, Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Biomolecule_representation_loader< Protein_representation_FIT, Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Biomolecule_representation_loader< Protein_representation_HIAT, Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Biomolecule_representation_loader< Protein_representation_HIT, Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Conformation_loader< Conformation_builder_ >, T_Conformation_loader< Conformation >, T_Conformation_loader< Conformation_builder >, T_Conformation_loader< SBL::CSB::T_Conformation_builder_cartesian_default< Conformation > >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< Covalent_structure_builder >, T_Molecular_covalent_structure_loader< Default_molecular_covalent_structure_builder_martini >, T_Molecular_covalent_structure_loader< MCS_builder_biomols >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIT >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader_from_MOL< Covalent_structure >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, 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_system_loader< Molecular_system >, T_Molecular_system_loader< Particle_traits::Molecular_system >, T_Molecular_system_loader< Traits::Particle_traits::Molecular_system >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< Traits::FT >, T_Numbers_file_loader< Traits::Point >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Primitive_labels_loader< Label_traits >, T_Primitive_labels_loader< Partner_label_traits, Mediator_label_traits, Extra_label_traits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Protein_representation_loader< Protein_representation >, T_Protein_representation_loader< Protein_representation, MCS_loader_biomols >, T_Protein_representation_loader< Protein_representation, Molecular_covalent_structure_loader >, T_Protein_representation_loader< Protein_representation_FIAT, MCS_loader_biomols_FIAT >, T_Protein_representation_loader< Protein_representation_FIT, MCS_loader_biomols_FIT >, T_Protein_representation_loader< Protein_representation_HIAT, MCS_loader_biomols_HIAT >, T_Protein_representation_loader< Protein_representation_HIT, MCS_loader_biomols_HIT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Traits::Graph, Traits::NT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Particle_annotator_collector< Name_and_radius_annotator, Dynamic_annotator >, T_Particle_annotator_collector< Name_annotator, Radius_annotator >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader< K::Point_d >, T_Points_d_file_loader< Traits::Point >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< typename Base::FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Spheres_3_file_loader< CGAL::Weighted_point_3< K >, K::Point_3 >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_sequences_module< Module_traits >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< Module_traits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< Traits, Alignment_engine >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< Module_traits >, T_Alpha_complex_of_molecular_model_module< Traits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< Module_traits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Buried_surface_area_without_label_module< Module_traits >, T_Cluster_engine_module< ModuleTraits >, T_Cluster_engine_module< Traits >, T_Earth_mover_distance_module< ModuleTraits >, T_Earth_mover_distance_module< Traits >, T_Molecular_interfaces_module< ModuleTraits >, T_Molecular_interfaces_module< Module_traits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< Traits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Morse_theory_based_analyzer_module< ModuleTraits, Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, 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_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_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< Traits >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_RMSD_comb_edge_weighted_module< Module_traits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Spatial_search_module< Traits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< Traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_3_module< Module_traits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_boundary_patch_shelling_3_module< Module_traits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_mesh_3_module< Module_traits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, and T_Union_of_balls_surface_volume_3_module< Traits >.

check_options()

template<class SecondaryArchive, class SecondaryData, class SerializedData>

bool check_options ( std::string & message ) const

inlineoverridevirtual

Check that the parsed options are valid for this loader.

Reimplemented from T_Module_option_description< Dummy >.

get_all_data() [1/2]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

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]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

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]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

SerializedData & get_data ( unsigned i )

inline

ith container of spheres corresponding to the ith input file.

get_data() [2/4]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

const SerializedData & get_data ( unsigned i ) const

inline

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

get_data() [3/4]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

SerializedData & get_data ( void )

inline

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

get_data() [4/4]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

const SerializedData & get_data ( void ) const

inline

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

get_name()

virtual std::string get_name ( void ) const

inlinevirtualinherited

Return the name of the class itself.

Reimplemented in T_Archive_file_loader< InputArchive, SerializedData >, T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >, T_Biomolecule_representation_loader< Protein_representation, Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Biomolecule_representation_loader< Protein_representation_FIAT, Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Biomolecule_representation_loader< Protein_representation_FIT, Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Biomolecule_representation_loader< Protein_representation_HIAT, Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Biomolecule_representation_loader< Protein_representation_HIT, Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Conformation_loader< Conformation_builder_ >, T_Conformation_loader< Conformation >, T_Conformation_loader< Conformation_builder >, T_Conformation_loader< SBL::CSB::T_Conformation_builder_cartesian_default< Conformation > >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< Covalent_structure_builder >, T_Molecular_covalent_structure_loader< Default_molecular_covalent_structure_builder_martini >, T_Molecular_covalent_structure_loader< MCS_builder_biomols >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_FIT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIAT >, T_Molecular_covalent_structure_loader< MCS_builder_biomols_HIT >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader_from_MOL< Covalent_structure >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, 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_system_loader< Molecular_system >, T_Molecular_system_loader< Particle_traits::Molecular_system >, T_Molecular_system_loader< Traits::Particle_traits::Molecular_system >, T_Nucleic_acid_representation_loader< NucleicAcidRepresentation, MCSLoader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation, Molecular_covalent_structure_loader >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIAT, MCS_loader_biomols_FIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_FIT, MCS_loader_biomols_FIT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIAT, MCS_loader_biomols_HIAT >, T_Nucleic_acid_representation_loader< Nucleic_acid_representation_HIT, MCS_loader_biomols_HIT >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< FT, Tag >, T_Numbers_file_loader< Traits::FT >, T_Numbers_file_loader< Traits::Point >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Primitive_labels_loader< Label_traits >, T_Primitive_labels_loader< Partner_label_traits, Mediator_label_traits, Extra_label_traits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Protein_representation_loader< ProteinRepresentation, MCSLoader >, T_Protein_representation_loader< Protein_representation >, T_Protein_representation_loader< Protein_representation, MCS_loader_biomols >, T_Protein_representation_loader< Protein_representation, Molecular_covalent_structure_loader >, T_Protein_representation_loader< Protein_representation_FIAT, MCS_loader_biomols_FIAT >, T_Protein_representation_loader< Protein_representation_FIT, MCS_loader_biomols_FIT >, T_Protein_representation_loader< Protein_representation_HIAT, MCS_loader_biomols_HIAT >, T_Protein_representation_loader< Protein_representation_HIT, MCS_loader_biomols_HIT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, No_particle_annotator, T_Domain_annotator_for_particles< Annotations >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Traits::Graph, Traits::NT >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Particle_annotator_collector< Name_and_radius_annotator, Dynamic_annotator >, T_Particle_annotator_collector< Name_annotator, Radius_annotator >, T_Points_d_file_loader< PointD >, T_Points_d_file_loader< K::Point_d >, T_Points_d_file_loader< Traits::Point >, T_Points_d_file_loader_generic< PointD, PointD_filler >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Radius_annotator_for_particles_with_annotated_name< typename Base::FT >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Spheres_3_file_loader< CGAL::Weighted_point_3< K >, K::Point_3 >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, and T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >.

get_number_of_data()

template<class SecondaryArchive, class SecondaryData, class SerializedData>

unsigned get_number_of_data ( void ) const

inline

Number of containers of spheres.

get_options()

template<class Dummy = void>

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

inlinestaticinherited

Access to the options' description of the module.

get_output_prefix()

template<class SecondaryArchive, class SecondaryData, class SerializedData>

std::string get_output_prefix ( void ) const

inlineoverridevirtual

Access to the output prefix of this loader.

Reimplemented from T_Module_option_description< Dummy >.

get_secondary_data() [1/2]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

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

inline

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

get_secondary_data() [2/2]

template<class SecondaryArchive, class SecondaryData, class SerializedData>

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

inline

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

load()

template<class SecondaryArchive, class SecondaryData, class SerializedData>

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()

template<class SecondaryArchive, class SecondaryData, class SerializedData>

void statistics ( std::ostream & out ) const

inline

Print high level statistics on the loaded spheres.