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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Generic manager for reading arguments of the program and run the calculations. More...
#include <Nearest_neighbors_graph_builder_module.hpp>
Classes | |
class | Distance |
Public Types | |
typedef T_Nearest_neighbors_graph_builder_module< ModuleTraits > | Self |
typedef SBL::Modules::Module_base | Base |
typedef ModuleTraits::Nearest_neighbors_graph | Nearest_neighbors_graph |
typedef ModuleTraits::Nearest_neighbors_distance | Nearest_neighbors_distance |
typedef Nearest_neighbors_distance::Point | Point |
typedef Nearest_neighbors_distance::FT | FT |
typedef std::vector< Point > | Points_vector |
typedef ModuleTraits::template Nearest_neighbors_query< Distance > | Nearest_neighbors_query |
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) |
Constructors / Destructors | |
T_Nearest_neighbors_graph_builder_module (void) | |
T_Nearest_neighbors_graph_builder_module (const Self &other) | |
~T_Nearest_neighbors_graph_builder_module (void) | |
Requirements | |
std::string | get_name (void) const |
Returns the name of the package. More... | |
boost::program_options::options_description | add_options (void) const |
Virtual method for adding options to the module. More... | |
bool | check_options (std::string &message) const |
Check that the input options' values are coherent. More... | |
bool | is_runnable (void) const |
Checks that all the input options were set. More... | |
void | run (unsigned verbose, std::ostream &out) |
run the model following the input options. More... | |
void | reset (void) |
std::string | get_output_prefix (void) const |
Returns a prefix that concatains the input line options used when running the module. More... | |
void | statistics (std::ostream &out) |
Report high-level statistics on the module. More... | |
void | report (const std::string &prefix) |
Report the output and statistics in output files. More... | |
Access | |
Points_vector *& | get_points (void) |
Nearest_neighbors_graph & | get_nearest_neighbors_graph (void) |
const Nearest_neighbors_graph & | get_nearest_neighbors_graph (void) const |
Nearest_neighbors_query & | get_nearest_neighbors_query (void) |
const Nearest_neighbors_query & | get_nearest_neighbors_query (void) const |
bool | is_nng_connected (void) const |
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... | |
Generic manager for reading arguments of the program and run the calculations.
ModuleTraits | Model of a traits class defining the types used in the manager (see T_Conformational_clustering_traits). |
ModuleInput | should define points_begin and points_end |
typedef SBL::Modules::Module_base Base |
typedef Nearest_neighbors_distance::FT FT |
typedef ModuleTraits::Nearest_neighbors_distance Nearest_neighbors_distance |
typedef ModuleTraits::Nearest_neighbors_graph Nearest_neighbors_graph |
typedef ModuleTraits::template Nearest_neighbors_query<Distance> Nearest_neighbors_query |
typedef Nearest_neighbors_distance::Point Point |
typedef std::vector<Point> Points_vector |
typedef T_Nearest_neighbors_graph_builder_module<ModuleTraits> Self |
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inline |
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inline |
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inline |
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inlinevirtual |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
To avoid later crash: check filesystem / existence of directory / directory exists.
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inlinevirtual |
Check that the input options' values are coherent.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
Clones the object using the copy constructor.
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inlinestaticinherited |
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inlineinherited |
Get the name of this instance of this module.
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inlinevirtual |
Returns the name of the package.
Reimplemented from Module_base.
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inline |
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inline |
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inline |
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inline |
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inlinestaticinherited |
Access to the options' description of the module.
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inlinevirtual |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented from T_Module_option_description< Dummy >.
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inline |
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inlineinherited |
Get the report mode to be used when reporting.
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inlinestaticinherited |
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inlinestaticinherited |
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inlineprotectedvirtualinherited |
Checks that this module defines a condition operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a logical operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a collection of modules.
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inline |
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inlinevirtual |
Checks that all the input options were set.
Reimplemented from Module_base.
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inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
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inlinevirtual |
Report the output and statistics in output files.
Reimplemented from Module_base.
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inline |
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inlinevirtual |
run the model following the input options.
Implements Module_base.
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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.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlinevirtual |
Report high-level statistics on the module.
Reimplemented from Module_base.