T_Module_condition< Module, Predicate > Class Template Reference

Condition module for selecting one of two possible outflows. More...

#include <Module_condition.hpp>

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.

Optional Requirements
bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent.
std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module.
void	report (const std::string &prefix) override
	Reports the output and statistics in output files.

Mandatory Requirements
void	run (unsigned verbose, std::ostream &out) override
	Runs the module following the input options.
bool	is_runnable (void) const override
	Checks that all the input options were set.
void	statistics (std::ostream &out) override
	Reports high-level statistics on the module.
std::string	get_name (void) const override
	Returns the name of the package.

Modules Management
void	set_module_instance_name (const std::string &module_instance_name)
	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.
const std::string &	get_module_instance_name (void) const
	Get the name of this instance of this module.
void	set_report_mode (std::ios_base::openmode report_mode)
	Set a report mode, that is open or append modes.
void	set_report_mode (std::ios_base::openmode &report_mode)
	Set a report mode, that is open or append modes.
const std::ios_base::openmode	get_report_mode (void) const
	Get the report mode to be used when reporting.

Optional Requirements
void	check_filesystem_directory_exists (const std::string &output_prefix)
	To avoid later crash: check filesystem / existence of directory / directory exists.

Others
template<class Self_>
Self_ *	clone (const Self_ *s) const
	Clones the object using the copy constructor.
virtual bool	is_logical_module (void) const
	Checks that this module defines a logical operator.
virtual bool	is_modules_collection (void) const
	Checks that this module defines a collection of modules.

Detailed Description

template<class Module, class Predicate>
class SBL::Modules::T_Module_condition< Module, Predicate >

Condition module for selecting one of two possible outflows.

Requirements are...

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_filesystem_directory_exists()

void check_filesystem_directory_exists ( const std::string & output_prefix )

inlineinherited

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

check_options()

template<class Predicate>

bool check_options ( std::string & message ) const

inlineoverridevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

clone()

template<class Self_>

Self_ * clone ( const Self_ * s ) const

inlineinherited

Clones the object using the copy constructor.

get_module_instance_name()

const std::string & get_module_instance_name ( void ) const

inlineinherited

Get the name of this instance of this module.

get_name()

template<class Predicate>

std::string get_name ( void ) const

inlineoverridevirtual

Returns the name of the package.

Reimplemented from Module_base.

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 Predicate>

std::string get_output_prefix ( void ) const

inlineoverridevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

get_report_mode()

const std::ios_base::openmode get_report_mode ( void ) const

inlineinherited

Get the report mode to be used when reporting.

is_logical_module()

virtual bool is_logical_module ( void ) const

inlineprotectedvirtualinherited

Checks that this module defines a logical operator.

is_modules_collection()

virtual bool is_modules_collection ( void ) const

inlineprotectedvirtualinherited

Checks that this module defines a collection of modules.

is_runnable()

template<class Predicate>

bool is_runnable ( void ) const

inlineoverridevirtual

Checks that all the input options were set.

Reimplemented from Module_base.

report()

template<class Predicate>

void report ( const std::string & prefix )

inlineoverridevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

run()

template<class Predicate>

void run ( unsigned verbose, std::ostream & out )

inlineoverridevirtual

Runs the module following the input options.

Implements Module_base.

set_module_instance_name()

void set_module_instance_name ( const std::string & module_instance_name )

inlineinherited

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_report_mode() [1/2]

void set_report_mode ( std::ios_base::openmode & report_mode )

inlineinherited

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

set_report_mode() [2/2]

void set_report_mode ( std::ios_base::openmode report_mode )

inlineinherited

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

statistics()

template<class Predicate>

void statistics ( std::ostream & out )

inlineoverridevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.