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


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_module< ModuleTraits, MorseSmaleWittenChainComplex > 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 MorseSmaleWittenChainComplex Morse_Smale_Witten_chain_complex
 

Other Types

typedef SBL::GT::T_Morse_theory_based_analyzer< Morse_Smale_Witten_chain_complexMorse_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
 

Parameters

static bool & get_show_diagrams (void)
 

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_analyzerget_Morse_theory_based_analyzer (void) const
 
Morse_theory_based_analyzerget_Morse_theory_based_analyzer (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...
 
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...
 

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...
 

Detailed Description

template<class ModuleTraits, class MorseSmaleWittenChainComplex = typename ModuleTraits::Morse_Smale_Witten_chain_complex>
class SBL::Modules::T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >


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

Template Parameters
ModuleTraitsModel of a traits class defining the types used in the manager (see T_Conformational_clustering_traits).

Member Typedef Documentation

◆ Base

◆ Disconnectivity_forest

◆ FT

◆ Morse_Smale_Witten_chain_complex

typedef MorseSmaleWittenChainComplex Morse_Smale_Witten_chain_complex

◆ Morse_theory_based_analyzer

◆ Persistence_diagram

◆ Persistence_intervals_container

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

◆ Point

◆ Self

typedef T_Morse_theory_based_analyzer_module<ModuleTraits, MorseSmaleWittenChainComplex> Self

◆ Stable_manifold_partition

◆ Sublevelsets_connected_components

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_options()

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

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_Smale_Witten_chain_complex()

MorseSmaleWittenChainComplex *& get_Morse_Smale_Witten_chain_complex ( void  )
inline

◆ get_Morse_Smale_Witten_chain_complex_filename()

const std::string & get_Morse_Smale_Witten_chain_complex_filename ( void  )
inlinestaticprotected

◆ get_Morse_theory_based_analyzer() [1/2]

T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >::Morse_theory_based_analyzer & get_Morse_theory_based_analyzer ( void  )
inline

◆ get_Morse_theory_based_analyzer() [2/2]

const T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >::Morse_theory_based_analyzer & get_Morse_theory_based_analyzer ( void  ) const
inline

◆ 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< 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  )
inlinestatic

◆ 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)
inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.