Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Modules_collection< Module, SetIndividualInput > Class Template Reference

#include <Modules_collection.hpp>

Public Types

typedef T_Modules_collection< Module, SetIndividualInput > Self
 
typedef SBL::Modules::Module_base Base
 
typedef std::vector< Module * >::iterator Modules_iterator
 

Public Member Functions

 T_Modules_collection (void)
 
 T_Modules_collection (const Self &other)
 
virtual ~T_Modules_collection (void)
 

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)
 

Collection Management

Module * get_template_module (void)
 
const Module * get_template_module (void) const
 
unsigned get_number_of_modules (void) const
 
Module * get_module (unsigned i)
 
Modules_iterator modules_begin (void)
 
Modules_iterator modules_end (void)
 
const Module * get_module (unsigned i) const
 
template<class InputIterator >
void set_individual_inputs (InputIterator begin, InputIterator end)
 

Mandatory Requirements

void run (unsigned verbose=0, std::ostream &out=std::cout)
 Runs the module following the input options. 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

boost::program_options::options_description add_options (void) const
 Const access to the options' description of the module. More...
 
bool check_options (std::string &message) const
 Checks that the input options' values are coherent. More...
 
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

virtual bool is_runnable (void) const
 Checks that all the input options were set. 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...
 

Member Typedef Documentation

◆ Base

◆ Modules_iterator

typedef std::vector<Module*>::iterator Modules_iterator

◆ Self

typedef T_Modules_collection<Module, SetIndividualInput> Self

Constructor & Destructor Documentation

◆ T_Modules_collection() [1/2]

T_Modules_collection ( void  )
inline

◆ T_Modules_collection() [2/2]

T_Modules_collection ( const Self other)
inline

◆ ~T_Modules_collection()

virtual ~T_Modules_collection ( void  )
inlinevirtual

Member Function Documentation

◆ add_options()

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

Const access to the options' description of the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ check_options()

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

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

◆ clone()

Self_* clone ( const Self_ *  s) const
inlineinherited

Clones the object using the copy constructor.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_module() [1/2]

Module* get_module ( unsigned  i)
inline

◆ get_module() [2/2]

const Module* get_module ( unsigned  i) const
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_number_of_modules()

unsigned get_number_of_modules ( void  ) const
inline

◆ 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_template_module() [1/2]

Module* get_template_module ( void  )
inline

◆ get_template_module() [2/2]

const Module* get_template_module ( void  ) const
inline

◆ 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_runnable()

virtual bool is_runnable ( void  ) const
inlinevirtualinherited

Checks that all the input options were set.

Reimplemented in T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, 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_Subdomain_comparator_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Sample_selector_module< ModuleTraits >, T_Sample_extender_module< ModuleTraits >, T_Record_new_sample_module< ModuleTraits >, T_Exploration_parameters_update_module< ModuleTraits >, T_Acceptance_test_module< ModuleTraits >, T_Energy_landscape_transition_graph_topology_module< ModuleTraits >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_Point_cloud_hausdorff_distance_d_module< ModuleTraits >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, T_Conformational_ensemble_sampling_diversity_analysis_module< ModuleTraits >, T_Conformational_ensemble_pairwise_distances_module< ModuleTraits >, T_Conformational_ensemble_MST_module< ModuleTraits >, 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_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_vertex_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_NNG_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_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_Earth_mover_distance_module< ModuleTraits >, 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_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_RST_MST_D_Family_matching_module< ModuleTraits >, and T_D_Family_matching_module< ModuleTraits, TSolutionComputer >.

◆ modules_begin()

Modules_iterator modules_begin ( void  )
inline

◆ modules_end()

Modules_iterator modules_end ( void  )
inline

◆ operator()()

virtual bool operator() ( void  )
inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

◆ report()

void report ( const std::string &  prefix)
inlinevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

void run ( unsigned  verbose = 0,
std::ostream &  out = std::cout 
)
inlinevirtual

Runs the module following the input options.

Implements Module_base.

◆ set_individual_inputs()

void set_individual_inputs ( InputIterator  begin,
InputIterator  end 
)
inline

◆ 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.