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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Module computing a sampling of an input boundary of the union of 3D balls. Module computing a sampling of an input boundary of the union of 3D balls. More...
#include "Union_of_balls_mesh_3_module.hpp"
Public Types | |
typedef T_Union_of_balls_mesh_3_module< ModuleTraits > | Self |
typedef SBL::Modules::Module_base | Base |
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::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_3 > | 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. 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... | |
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... | |
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... | |
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... | |
Module computing a sampling of an input boundary of the union of 3D balls. 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.
ModuleTraits | Traits class defining the type SBL::Modules::T_Union_of_balls_mesh_3_module::Union_of_balls_boundary_3 |
typedef SBL::Modules::Module_base Base |
typedef Sampler::FT FT |
Number type used for representing coordinates of 3D balls and points.
typedef Sampler::Point_3 Point_3 |
Representation of a 3D point.
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.
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typedef T_Union_of_balls_mesh_3_module<ModuleTraits> Self |
typedef ModuleTraits:: Union_of_balls_boundary_3 Union_of_balls_boundary_3 |
Representation of the boundary of the union of balls.
Representation of the boundary of the union of balls.
WeightedAlphaComplex3 | A Model of the 3D Weighted ![]() |
IS_CCW | Tag allowing to orientate in CW or CCW the sense of the half-edges. |
HalfedgeDSBase | Base data structure for the boundary of union of balls. |
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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 |
Checks 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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inline |
Reference to a pointer over the input boundary.
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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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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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inlineinherited |
Get the report mode to be used when reporting.
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inline |
Reference to the output surface area and volume computation.
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inline |
Const reference to the output surface area and volume computation.
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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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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 |
Reports the output and statistics in output files.
Reimplemented from Module_base.
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inlinevirtual |
Runs the module following the input options.
Implements Module_base.
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inlinestatic |
Sets the epsilon value of the sampling.
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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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inlinestatic |
Sets the sampling viewer mode for reporting the sampling.
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inlinevirtual |
Reports high-level statistics on the module.
Reimplemented from Module_base.