Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Union_of_balls_mesh_3_module< ModuleTraits > Class Template Reference

Module computing a sampling of an input boundary of the union of 3D balls. More...

#include "Union_of_balls_mesh_3_module.hpp"

Static Public Member Functions

static boost::program_options::options_description *& get_options (void)
 Access to the options' description of the module. 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...
 

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...
 

Traits Requirements

typedef ModuleTraits::Union_of_balls_boundary_3 Union_of_balls_boundary_3
 Representation of the boundary of the union of balls. More...
 
typedef SBL::GT::T_Union_of_balls_epsilon_mesh_3< Union_of_balls_boundary_3Sampler
 Construction of the mesh of the union of 3D balls such that any point at the surface of the union of balls has a point of the mesh in its epsilon-neighborhood.
More...
 
typedef Sampler::FT FT
 Number type used for representing coordinates of 3D balls and points.
More...
 
typedef Sampler::Point_3 Point_3
 Representation of a 3D point.
More...
 

Input Accessors

Union_of_balls_boundary_3 *& get_boundary (void)
 Reference to a pointer over the input boundary. More...
 

Output Accessors

const std::vector< Point_3 > & get_sampling (void) const
 Const reference to the output surface area and volume computation. More...
 
std::vector< Point_3 > & get_sampling (void)
 Reference to the output surface area and volume computation. More...
 

Parameters

static void set_epsilon (const FT &epsilon)
 Sets the epsilon value of the sampling. More...
 
static void set_sampling_viewer (const std::string &viewer_name)
 Sets the sampling viewer mode for reporting the sampling. More...
 

Mandatory Requirements

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

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
 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...
 

Detailed Description

template<class ModuleTraits>
class SBL::Modules::T_Union_of_balls_mesh_3_module< ModuleTraits >

Module computing a sampling of an input boundary of the union of 3D balls.

It computes the sampling such that the nearest neighbor of each point of the sampling is under a user defined epsilon distance.

The input is the boundary of the union of 3D balls and can be set using the method SBL::Modules::T_Union_of_balls_mesh_3_module::get_boundary, that returns a reference to a pointer over the input boundary.

The output is a vector of 3D points.

Template Parameters
ModuleTraitsTraits class defining the type SBL::Modules::T_Union_of_balls_mesh_3_module::Union_of_balls_boundary_3

Member Typedef Documentation

◆ FT

typedef Sampler::FT FT

Number type used for representing coordinates of 3D balls and points.

◆ Point_3

Representation of a 3D point.

◆ Sampler

Construction of the mesh of the union of 3D balls such that any point at the surface of the union of balls has a point of the mesh in its epsilon-neighborhood.

...

◆ Union_of_balls_boundary_3

Representation of the boundary of the union of balls.

Representation of the boundary of the union of balls.

  \tparam WeightedAlphaComplex3 A Model of the 3D Weighted \form#2-complex of the CGAL Library.

  \tparam IS_CCW Tag allowing to orientate in CW or CCW the sense of the half-edges.

  \tparam HalfedgeDSBase Base data structure for the boundary of union of balls.

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<>.

◆ check_options()

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

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description<>.

◆ clone()

Self_* clone ( const Self_ *  s) const
inlineinherited

Clones the object using the copy constructor.

◆ get_boundary()

T_Union_of_balls_mesh_3_module< ModuleTraits >::Union_of_balls_boundary_3 *& get_boundary ( void  )
inline

Reference to a pointer over the input boundary.

◆ 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<>.

◆ get_report_mode()

const std::ios_base::openmode get_report_mode ( void  ) const
inlineinherited

Get the report mode to be used when reporting.

◆ get_sampling() [1/2]

const std::vector< typename T_Union_of_balls_mesh_3_module< ModuleTraits >::Point_3 > & get_sampling ( void  ) const
inline

Const reference to the output surface area and volume computation.

◆ get_sampling() [2/2]

std::vector< typename T_Union_of_balls_mesh_3_module< ModuleTraits >::Point_3 > & get_sampling ( void  )
inline

Reference to the output surface area and volume computation.

◆ 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 &  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_epsilon()

void set_epsilon ( const FT epsilon)
inlinestatic

Sets the epsilon value of the sampling.

◆ 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.

◆ set_sampling_viewer()

void set_sampling_viewer ( const std::string &  viewer_name)
inlinestatic

Sets the sampling viewer mode for reporting the sampling.

◆ statistics()

void statistics ( std::ostream &  out)
inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.