T_Earth_mover_distance_module< ModuleTraits > Class Template Reference

Application's module instantiating the eartyh mover distance algorithm. More...

#include <Earth_mover_distance_module.hpp>

Classes
struct	Transportation_plans

Public Types
typedef T_Earth_mover_distance_module< ModuleTraits >	Self
typedef SBL::Modules::Module_base	Base

Public Member Functions
virtual bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. 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)

Traits Requirements
typedef ModuleTraits::EMD_distance	EMD_distance
typedef ModuleTraits::EMD_vertices_accessor	EMD_vertices_accessor
typedef EMD_vertices_accessor::Vertices_container	Vertices_container
typedef EMD_vertices_accessor::Vertex_rep	Vertex_rep
typedef EMD_vertices_accessor::Index_type	Index_type
typedef EMD_vertices_accessor::Vertices_iterator	Vertices_iterator

Output Types
typedef SBL::CADS::T_Earth_mover_distance< EMD_vertices_accessor, EMD_distance >	EMD_WCC_engine
typedef SBL::CADS::T_Earth_mover_distance_with_connectivity_constraints< EMD_vertices_accessor, EMD_distance >	EMD_CC_engine
typedef EMD_WCC_engine::Transportation_plan	Transportation_plan
typedef EMD_CC_engine::Transportation_plan	Transportation_plan_with_cc
typedef SBL::CADS::T_Earth_mover_distance_connectivity_constraints_checker< EMD_WCC_engine >	Earth_mover_distance_checker

Constructors
	T_Earth_mover_distance_module (void)
	Constructs the module. More...
	T_Earth_mover_distance_module (const Self &other)
	Constructs the module. More...

Input Accessors
Vertices_container *&	get_source (void)
Vertices_container *&	get_demand (void)

Output Accessors
const Transportation_plans &	get_transportation_plans (void) const
	Const access to the transportation plans. More...
Transportation_plans &	get_transportation_plans (void)
	Access to the transportation plans. More...

Mandatory Requirements
boost::program_options::options_description	add_options (void) const
	Virtual method for adding options to the module. More...
void	run (unsigned verbose, std::ostream &out)
	Runs the module following the input options. More...
bool	is_runnable (void) const
	Checks that all the input options were set. More...
void	statistics (std::ostream &out)
	Reports high-level statistics on the module. More...
std::string	get_name (void) const
	Returns the name of the package. More...

Optional Requirements
std::string	get_output_prefix (void) const
	Returns a prefix that concatains the input line options used when running the module. More...
void	report (const std::string &prefix)
	Reports the output and statistics in output files. More...

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

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

Others
template<class Self_ >
Self_ *	clone (const Self_ *s) const
	Clones the object using the copy constructor. More...
virtual bool	is_logical_module (void) const
	Checks that this module defines a logical operator. More...
virtual bool	is_condition_module (void) const
	Checks that this module defines a condition operator. More...
virtual bool	operator() (void)
	Only for condition modules, for returning the predicate value. More...
virtual bool	is_modules_collection (void) const
	Checks that this module defines a collection of modules. More...

Detailed Description

template<class ModuleTraits>
class SBL::Modules::T_Earth_mover_distance_module< ModuleTraits >

Application's module instantiating the eartyh mover distance algorithm.

Application's module instantiating the eartyh mover distance algorithm.

Template Parameters

ModuleTraits

Traits class defining the types required by this module : the EMD_distance parameter is a distance functor between two input points, and the EMD_vertices_accessor is a class defining accessors for the vertices of the input data structures (see SBL::CADS::T_Earth_mover_distance_vertices_accessor_vector or SBL::CADS::T_Earth_mover_distance_vertices_accessor_graph).

---

Class Documentation

SBL::Modules::T_Earth_mover_distance_module::Transportation_plans

struct SBL::Modules::T_Earth_mover_distance_module::Transportation_plans

template<class ModuleTraits>
struct SBL::Modules::T_Earth_mover_distance_module< ModuleTraits >::Transportation_plans

Class Members
Transportation_plan_with_cc	cc
Transportation_plan_with_cc	cc_sym
Transportation_plan	wcc
Transportation_plan	wcc_sym

Member Typedef Documentation

Base

typedef SBL::Modules::Module_base Base

Earth_mover_distance_checker

typedef SBL::CADS::T_Earth_mover_distance_connectivity_constraints_checker<EMD_WCC_engine> Earth_mover_distance_checker

EMD_CC_engine

typedef SBL::CADS::T_Earth_mover_distance_with_connectivity_constraints<EMD_vertices_accessor, EMD_distance> EMD_CC_engine

EMD_distance

typedef ModuleTraits::EMD_distance EMD_distance

EMD_vertices_accessor

typedef ModuleTraits::EMD_vertices_accessor EMD_vertices_accessor

EMD_WCC_engine

typedef SBL::CADS::T_Earth_mover_distance<EMD_vertices_accessor, EMD_distance> EMD_WCC_engine

Index_type

typedef EMD_vertices_accessor::Index_type Index_type

Self

typedef T_Earth_mover_distance_module<ModuleTraits> Self

Transportation_plan

typedef EMD_WCC_engine::Transportation_plan Transportation_plan

Transportation_plan_with_cc

typedef EMD_CC_engine::Transportation_plan Transportation_plan_with_cc

Vertex_rep

typedef EMD_vertices_accessor::Vertex_rep Vertex_rep

Vertices_container

typedef EMD_vertices_accessor::Vertices_container Vertices_container

Vertices_iterator

typedef EMD_vertices_accessor::Vertices_iterator Vertices_iterator

Constructor & Destructor Documentation

T_Earth_mover_distance_module() [1/2]

T_Earth_mover_distance_module ( void  )

inline

Constructs the module.

T_Earth_mover_distance_module() [2/2]

T_Earth_mover_distance_module ( const Self &  other )

inline

Constructs the module.

Member Function Documentation

add_options()

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

inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

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()

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

inlinevirtualinherited

Checks that the input options' values are coherent.

Reimplemented in 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_structure_classifier_module< ModuleTraits >, T_Molecular_interfaces_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Module_condition< void, Predicate >, T_Module_condition< Module, Predicate >, T_Module_based_workflow< Dummy >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_D_Family_matching_module< ModuleTraits, TSolutionComputer >, T_Cluster_engine_module< ModuleTraits >, 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_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, 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_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_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_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, 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 >, and T_Archive_file_loader< InputArchive, SerializedData >.

clone()

Self_* clone ( const Self_ *  s ) const

inlineinherited

Clones the object using the copy constructor.

delete_options()

static void delete_options ( void  )

inlinestaticinherited

get_demand()

T_Earth_mover_distance_module< ModuleTraits >::Vertices_container *& get_demand ( void  )

inline

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()

std::string get_name ( void  ) const

inlinevirtual

Returns the name of the package.

Reimplemented from Module_base.

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

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.

get_source()

T_Earth_mover_distance_module< ModuleTraits >::Vertices_container *& get_source ( void  )

inline

get_transportation_plans() [1/2]

T_Earth_mover_distance_module< ModuleTraits >::Transportation_plans & get_transportation_plans ( void  )

inline

Access to the transportation plans.

get_transportation_plans() [2/2]

const T_Earth_mover_distance_module< ModuleTraits >::Transportation_plans & get_transportation_plans ( void  ) const

inline

Const access to the transportation plans.

has_options()

static bool has_options ( void  )

inlinestaticinherited

initialize_options()

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

inlinestaticinherited

is_condition_module()

virtual bool is_condition_module ( void  ) const

inlineprotectedvirtualinherited

Checks that this module defines a condition operator.

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()

bool is_runnable ( void  ) const

inlinevirtual

Checks that all the input options were set.

Reimplemented from Module_base.

operator()()

virtual bool operator() ( void  )

inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

report()

void report ( const std::string &  output_prefix )

inlinevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

run()

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

inlinevirtual

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()

void statistics ( std::ostream &  out )

inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.