![]() |
Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
|
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 |
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... | |
Application's module instantiating the eartyh mover distance algorithm.
Application's module instantiating the eartyh mover distance algorithm.
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). |
struct SBL::Modules::T_Earth_mover_distance_module::Transportation_plans |
Class Members | ||
---|---|---|
Transportation_plan_with_cc | cc | |
Transportation_plan_with_cc | cc_sym | |
Transportation_plan | wcc | |
Transportation_plan | wcc_sym |
typedef SBL::Modules::Module_base Base |
typedef SBL::CADS::T_Earth_mover_distance_connectivity_constraints_checker<EMD_WCC_engine> Earth_mover_distance_checker |
typedef SBL::CADS::T_Earth_mover_distance_with_connectivity_constraints<EMD_vertices_accessor, EMD_distance> EMD_CC_engine |
typedef ModuleTraits::EMD_distance EMD_distance |
typedef ModuleTraits::EMD_vertices_accessor EMD_vertices_accessor |
typedef EMD_vertices_accessor::Index_type Index_type |
typedef T_Earth_mover_distance_module<ModuleTraits> Self |
typedef EMD_vertices_accessor::Vertex_rep Vertex_rep |
typedef EMD_vertices_accessor::Vertices_container Vertices_container |
typedef EMD_vertices_accessor::Vertices_iterator Vertices_iterator |
|
inline |
Constructs the module.
|
inline |
Constructs the module.
|
inlinevirtual |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
|
inlineinherited |
To avoid later crash: check filesystem / existence of directory / directory exists.
|
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 >.
|
inlineinherited |
Clones the object using the copy constructor.
|
inlinestaticinherited |
|
inline |
|
inlineinherited |
Get the name of this instance of this module.
|
inlinevirtual |
Returns the name of the package.
Reimplemented from Module_base.
|
inlinestaticinherited |
Access to the options' description of the module.
|
inlinevirtual |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented from T_Module_option_description< Dummy >.
|
inlineinherited |
Get the report mode to be used when reporting.
|
inline |
|
inline |
Access to the transportation plans.
|
inline |
Const access to the transportation plans.
|
inlinestaticinherited |
|
inlinestaticinherited |
|
inlineprotectedvirtualinherited |
Checks that this module defines a condition operator.
|
inlineprotectedvirtualinherited |
Checks that this module defines a logical operator.
|
inlineprotectedvirtualinherited |
Checks that this module defines a collection of modules.
|
inlinevirtual |
Checks that all the input options were set.
Reimplemented from Module_base.
|
inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
|
inlinevirtual |
Reports the output and statistics in output files.
Reimplemented from Module_base.
|
inlinevirtual |
Runs the module following the input options.
Implements Module_base.
|
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.
|
inlineinherited |
Set a report mode, that is open or append modes.
|
inlineinherited |
Set a report mode, that is open or append modes.
|
inlinevirtual |
Reports high-level statistics on the module.
Reimplemented from Module_base.