#include <Modules_collection.hpp>
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void | run (unsigned verbose=0, std::ostream &out=std::cout) |
| Runs the module following the input options. More...
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void | statistics (std::ostream &out) |
| Reports high-level statistics on the module. More...
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std::string | get_name (void) const |
| Returns the name of the package. More...
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boost::program_options::options_description | add_options (void) const |
| Const access to the options' description of the module. More...
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bool | check_options (std::string &message) const |
| Checks that the input options' values are coherent. More...
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std::string | get_output_prefix (void) const |
| Returns a prefix that concatains the input line options used when running the module. More...
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void | report (const std::string &prefix) |
| Reports the output and statistics in output files. More...
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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...
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const std::string & | get_module_instance_name (void) const |
| Get the name of this instance of this module. More...
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void | set_report_mode (std::ios_base::openmode report_mode) |
| Set a report mode, that is open or append modes. More...
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void | set_report_mode (std::ios_base::openmode &report_mode) |
| Set a report mode, that is open or append modes. More...
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const std::ios_base::openmode | get_report_mode (void) const |
| Get the report mode to be used when reporting. More...
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template<class Self_ > |
Self_ * | clone (const Self_ *s) const |
| Clones the object using the copy constructor. More...
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virtual bool | is_logical_module (void) const |
| Checks that this module defines a logical operator. More...
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virtual bool | is_condition_module (void) const |
| Checks that this module defines a condition operator. More...
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virtual bool | operator() (void) |
| Only for condition modules, for returning the predicate value. More...
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◆ Base
◆ Modules_iterator
◆ Self
◆ T_Modules_collection() [1/2]
◆ T_Modules_collection() [2/2]
◆ ~T_Modules_collection()
◆ add_options()
boost::program_options::options_description add_options |
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void |
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const |
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inlinevirtual |
◆ check_filesystem_directory_exists()
void check_filesystem_directory_exists |
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const std::string & |
output_prefix | ) |
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inlineinherited |
To avoid later crash: check filesystem / existence of directory / directory exists.
◆ check_options()
bool check_options |
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std::string & |
message | ) |
const |
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inlinevirtual |
◆ clone()
Self_* clone |
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const Self_ * |
s | ) |
const |
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inlineinherited |
Clones the object using the copy constructor.
◆ delete_options()
static void delete_options |
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void |
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inlinestaticinherited |
◆ get_module() [1/2]
Module* get_module |
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unsigned |
i | ) |
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inline |
◆ get_module() [2/2]
const Module* get_module |
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unsigned |
i | ) |
const |
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inline |
◆ get_module_instance_name()
const std::string& get_module_instance_name |
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void |
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const |
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inlineinherited |
Get the name of this instance of this module.
◆ get_name()
std::string get_name |
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void |
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const |
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inlinevirtual |
Returns the name of the package.
Reimplemented from Module_base.
◆ get_number_of_modules()
unsigned get_number_of_modules |
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void |
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const |
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inline |
◆ get_options()
static boost::program_options::options_description*& get_options |
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void |
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inlinestaticinherited |
Access to the options' description of the module.
◆ get_output_prefix()
std::string get_output_prefix |
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void |
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const |
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inlinevirtual |
◆ get_report_mode()
const std::ios_base::openmode get_report_mode |
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void |
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const |
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inlineinherited |
Get the report mode to be used when reporting.
◆ get_template_module() [1/2]
Module* get_template_module |
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void |
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inline |
◆ get_template_module() [2/2]
const Module* get_template_module |
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void |
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const |
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inline |
◆ has_options()
static bool has_options |
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void |
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inlinestaticinherited |
◆ initialize_options()
static void initialize_options |
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const std::string & |
caption | ) |
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inlinestaticinherited |
◆ is_condition_module()
virtual bool is_condition_module |
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void |
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const |
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inlineprotectedvirtualinherited |
Checks that this module defines a condition operator.
◆ is_logical_module()
virtual bool is_logical_module |
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void |
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const |
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inlineprotectedvirtualinherited |
Checks that this module defines a logical operator.
◆ is_runnable()
virtual bool is_runnable |
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void |
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const |
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inlinevirtualinherited |
Checks that all the input options were set.
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_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_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_RST_MST_D_Family_matching_module< ModuleTraits >, and T_D_Family_matching_module< ModuleTraits, TSolutionComputer >.
◆ modules_begin()
◆ modules_end()
◆ operator()()
virtual bool operator() |
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void |
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inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
◆ report()
void report |
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const std::string & |
prefix | ) |
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inlinevirtual |
Reports the output and statistics in output files.
Reimplemented from Module_base.
◆ run()
void run |
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unsigned |
verbose = 0 , |
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std::ostream & |
out = std::cout |
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) |
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inlinevirtual |
Runs the module following the input options.
Implements Module_base.
◆ set_individual_inputs()
void set_individual_inputs |
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InputIterator |
begin, |
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InputIterator |
end |
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) |
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inline |
◆ set_module_instance_name()
void set_module_instance_name |
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const std::string & |
module_instance_name | ) |
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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 |
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std::ios_base::openmode & |
report_mode | ) |
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inlineinherited |
Set a report mode, that is open or append modes.
◆ set_report_mode() [2/2]
void set_report_mode |
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std::ios_base::openmode |
report_mode | ) |
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inlineinherited |
Set a report mode, that is open or append modes.
◆ statistics()
void statistics |
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std::ostream & |
out | ) |
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inlinevirtual |
Reports high-level statistics on the module.
Reimplemented from Module_base.