Generic manager for reading arguments of the program and run the calculations More...

#include <Morse_theory_based_analyzer_module.hpp>

Public Types
typedef T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >	Self

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::Nearest_neighbors_graph	Nearest_neighbors_graph

typedef ModuleTraits::Morse_function	Morse_function

typedef ModuleTraits::Distance_graph_function	Distance_graph_function

Other Types
typedef SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< Nearest_neighbors_graph, Morse_function >	Morse_Smale_Witten_chain_complex_builder

typedef SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< Nearest_neighbors_graph, Morse_function, Distance_graph_function >	Morse_Smale_Witten_chain_complex_builder_normalized

typedef Morse_Smale_Witten_chain_complex_builder::Morse_Smale_Witten_chain_complex	Morse_Smale_Witten_chain_complex

typedef T_Morse_theory_based_analyzer_module< ModuleTraits, Morse_Smale_Witten_chain_complex >	Base

Other Types
typedef SBL::GT::T_Morse_theory_based_analyzer< Morse_Smale_Witten_chain_complex >	Morse_theory_based_analyzer

typedef Morse_theory_based_analyzer::Point	Point

typedef Morse_theory_based_analyzer::FT	FT

typedef Morse_theory_based_analyzer::Persistence_diagram	Persistence_diagram

typedef std::vector< std::pair< FT, FT > >	Persistence_intervals_container

typedef Morse_theory_based_analyzer::Disconnectivity_forest	Disconnectivity_forest

typedef Morse_theory_based_analyzer::Stable_manifold_partition	Stable_manifold_partition

typedef Morse_theory_based_analyzer::Sublevelsets_connected_components	Sublevelsets_connected_components

Input Accessors
Nearest_neighbors_graph *&	get_nearest_neighbors_graph (void)

Morse_function *&	get_Morse_function (void)

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...

std::string	get_name (void) const
	Returns the name of the package. More...

Optional Requirements
void	report (const std::string &prefix)
	Reports the output and statistics in output files. More...

boost::program_options::options_description	add_options () const
	Virtual method for adding options to the module. More...

Input Accessors
Morse_Smale_Witten_chain_complex *&	get_Morse_Smale_Witten_chain_complex (void)

static const std::string &	get_Morse_Smale_Witten_chain_complex_filename (void)

Output Accessors
const Morse_theory_based_analyzer &	get_Morse_theory_based_analyzer (void) const

Morse_theory_based_analyzer &	get_Morse_theory_based_analyzer (void)

Mandatory Requirements
void	statistics (std::ostream &out)
	Reports high-level statistics on the module. More...

Optional Requirements
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...

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 bool &	get_show_diagrams (void)

Detailed Description

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

Generic manager for reading arguments of the program and run the calculations

Template Parameters

ModuleTraits Model of a traits class defining the types used in the manager (see T_Conformational_clustering_traits).

Member Typedef Documentation

◆ Base

typedef T_Morse_theory_based_analyzer_module<ModuleTraits, Morse_Smale_Witten_chain_complex> Base

◆ Disconnectivity_forest

typedef Morse_theory_based_analyzer::Disconnectivity_forest Disconnectivity_forest

inherited

◆ Distance_graph_function

typedef ModuleTraits::Distance_graph_function Distance_graph_function

◆ FT

typedef Morse_theory_based_analyzer::FT FT

inherited

◆ Morse_function

typedef ModuleTraits::Morse_function Morse_function

◆ Morse_Smale_Witten_chain_complex

typedef Morse_Smale_Witten_chain_complex_builder::Morse_Smale_Witten_chain_complex Morse_Smale_Witten_chain_complex

◆ Morse_Smale_Witten_chain_complex_builder

typedef SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder<Nearest_neighbors_graph, Morse_function> Morse_Smale_Witten_chain_complex_builder

◆ Morse_Smale_Witten_chain_complex_builder_normalized

typedef SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder<Nearest_neighbors_graph, Morse_function, Distance_graph_function> Morse_Smale_Witten_chain_complex_builder_normalized

◆ Morse_theory_based_analyzer

typedef SBL::GT::T_Morse_theory_based_analyzer<Morse_Smale_Witten_chain_complex> Morse_theory_based_analyzer

inherited

◆ Nearest_neighbors_graph

typedef ModuleTraits::Nearest_neighbors_graph Nearest_neighbors_graph

◆ Persistence_diagram

typedef Morse_theory_based_analyzer::Persistence_diagram Persistence_diagram

inherited

◆ Persistence_intervals_container

typedef std::vector<std::pair<FT, FT> > Persistence_intervals_container

inherited

◆ Point

typedef Morse_theory_based_analyzer::Point Point

inherited

◆ Self

typedef T_Morse_theory_based_analyzer_for_NNG_module<ModuleTraits> Self

◆ Stable_manifold_partition

typedef Morse_theory_based_analyzer::Stable_manifold_partition Stable_manifold_partition

inherited

◆ Sublevelsets_connected_components

typedef Morse_theory_based_analyzer::Sublevelsets_connected_components Sublevelsets_connected_components

inherited

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< Dummy >.

◆ check_filesystem_directory_exists()

void check_filesystem_directory_exists ( const std::string & output_prefix )

inlineinherited

To avoid later crash: check filesystem / existence of directory / directory exists.

◆ check_options()

bool check_options ( std::string & message ) const

inlinevirtualinherited

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

◆ clone()

Self_* clone ( const Self_ * s ) const

inlineinherited

Clones the object using the copy constructor.

◆ delete_options()

static void delete_options ( void )

inlinestaticinherited

◆ get_module_instance_name()

const std::string& get_module_instance_name ( void ) const

inlineinherited

Get the name of this instance of this module.

◆ get_Morse_function()

T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >::Morse_function *& get_Morse_function ( void )

inline

◆ get_Morse_Smale_Witten_chain_complex()

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 *& get_Morse_Smale_Witten_chain_complex ( void )

inlineinherited

◆ get_Morse_Smale_Witten_chain_complex_filename()

const std::string & get_Morse_Smale_Witten_chain_complex_filename ( void )

inlinestaticprotectedinherited

◆ get_Morse_theory_based_analyzer() [1/2]

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 >::Morse_theory_based_analyzer & get_Morse_theory_based_analyzer ( void )

inlineinherited

◆ get_Morse_theory_based_analyzer() [2/2]

const 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 >::Morse_theory_based_analyzer & get_Morse_theory_based_analyzer ( void ) const

inlineinherited

◆ get_name()

std::string get_name ( void ) const

inlinevirtual

Returns the name of the package.

Reimplemented from Module_base.

◆ get_nearest_neighbors_graph()

T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >::Nearest_neighbors_graph *& get_nearest_neighbors_graph ( void )

inline

◆ 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

inlinevirtualinherited

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ get_report_mode()

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

inlineinherited

Get the report mode to be used when reporting.

◆ get_show_diagrams()

bool & get_show_diagrams ( void )

inlinestaticinherited

◆ has_options()

static bool has_options ( void )

inlinestaticinherited

◆ initialize_options()

static void initialize_options ( const std::string & caption )

inlinestaticinherited

◆ 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_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.

◆ statistics()

void statistics ( std::ostream & out )

inlinevirtualinherited

Reports high-level statistics on the module.

Reimplemented from Module_base.

Public Types

Static Public Member Functions

Traits Requirements

Other Types

Other Types

Input Accessors

Mandatory Requirements

Optional Requirements

Input Accessors

Output Accessors

Mandatory Requirements

Optional Requirements

Modules Management

Optional Requirements

Others

Parameters

Detailed Description

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

Member Typedef Documentation

◆ Base

◆ Disconnectivity_forest

◆ Distance_graph_function

◆ FT

◆ Morse_function

◆ Morse_Smale_Witten_chain_complex

◆ Morse_Smale_Witten_chain_complex_builder

◆ Morse_Smale_Witten_chain_complex_builder_normalized

◆ Morse_theory_based_analyzer

◆ Nearest_neighbors_graph

◆ Persistence_diagram

◆ Persistence_intervals_container

◆ Point

◆ Self

◆ Stable_manifold_partition

◆ Sublevelsets_connected_components

Member Function Documentation

◆ add_options()

◆ check_filesystem_directory_exists()

◆ check_options()

◆ clone()

◆ delete_options()

◆ get_module_instance_name()

◆ get_Morse_function()

◆ get_Morse_Smale_Witten_chain_complex()

◆ get_Morse_Smale_Witten_chain_complex_filename()

◆ get_Morse_theory_based_analyzer() [1/2]

◆ get_Morse_theory_based_analyzer() [2/2]

◆ get_name()

◆ get_nearest_neighbors_graph()

◆ get_options()

◆ get_output_prefix()

◆ get_report_mode()

◆ get_show_diagrams()

◆ has_options()

◆ initialize_options()

◆ is_condition_module()

◆ is_logical_module()

◆ is_modules_collection()

◆ is_runnable()

◆ operator()()

◆ report()

◆ run()

◆ set_module_instance_name()

◆ set_report_mode() [1/2]

◆ set_report_mode() [2/2]

◆ statistics()

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