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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Module building the boundary of the union of input 3D balls. Module building the boundary of the union of input 3D balls. More...
#include "Union_of_balls_boundary_3_module.hpp"
Public Types | |
typedef T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT > | 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... | |
Other Types | |
typedef Union_of_balls_boundary_3::Weighted_alpha_complex_3 | Alpha_complex |
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Input Accessors | |
Alpha_complex *& | get_alpha_complex (void) |
Reference to a pointer over the input ![]() | |
Output Accessors | |
const Union_of_balls_boundary_3 & | get_boundary (void) const |
Const reference to the output boundary of the union of the input 3D balls. More... | |
Union_of_balls_boundary_3 & | get_boundary (void) |
Reference to the output boundary of the union of the input 3D balls. 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... | |
Module building the boundary of the union of input 3D balls. Module building the boundary of the union of input 3D balls.
The boundary of the union of balls, which consists of spherical polygons bounded by circle arcs themselves bounded by points, is represented using the Halfedge Data Structure of the CGAL library: each spherical cap is represented by a face, each face being possibly bounded by one or more oriented edges called the halfedges. When two faces are adjacent, they share a common edge represented by two halfedges with opposite orientations.
The package Union_of_balls_boundary_3 provides the class SBL::GT::T_Union_of_balls_boundary_3_data_structure< WeightedAlphaComplex3 , bool IS_CCW , HalfedgeDSBase > for representing this halfedge data structure. The first template parameter is the representation of the -complex of the input data. The second parameter is a tag determining the orientation of all the half-edges around a face (by default, the face lies to the left of the bounding half-edges). Finally, the third parameter is the base class for the used halfedge data structure (a base minimal structure is given by default).
The input is the -complex of the input 3D balls and can be set with the method SBL::Modules::T_Union_of_balls_boundary_3_module::get_alpha_complex that returns a reference to a pointer over the input
-complex.
The output boundary is accessible using the method SBL::Modules::T_Union_of_balls_boundary_3_module::get_boundary
ModuleTraits | Traits class defining the types SBL::Modules::T_Union_of_balls_boundary_3_module::Union_of_balls_boundary_3. |
ExactNT | Optional parameter for the exact number type used with the filtered algebraic kernel (CGAL::Gmpq by default). |
typedef Union_of_balls_boundary_3::Weighted_alpha_complex_3 Alpha_complex |
-complex representing the input set of 3D balls.
typedef SBL::Modules::Module_base Base |
typedef T_Union_of_balls_boundary_3_module<ModuleTraits, ExactNT> 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 -complex.
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inline |
Reference to the output boundary of the union of the input 3D balls.
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inline |
Const reference to the output boundary of the union of the input 3D balls.
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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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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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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 |
Reports high-level statistics on the module.
Reimplemented from Module_base.