Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName > Class Template Reference

Model of ParticleAnnotator for attributing any annotation to a particle. More...

#include <Generic_annotator.hpp>

Public Types

typedef T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName > Self
 
typedef SBL::IO::Loader_base Base
 

Public Member Functions

 T_Generic_annotator (void)
 
 ~T_Generic_annotator (void)
 
SetAnnotation & get_annotations_setter (void)
 
bool set_options (boost::program_options::options_description &options) const
 
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...
 
bool load (unsigned verbose, std::ostream &out)
 Loads the data. More...
 
Baseget_annotator (const std::string &name)
 
std::string get_name (void) const
 Return the name of the class itself. More...
 
template<class Particle >
void operator() (Particle &p) const
 

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)
 

Management

void set_loader_instance_name (const std::string &loader_instance_name)
 
const std::string & get_loader_instance_name (void) const
 

Detailed Description

template<class KeyType, class AnnotationType, class MakeKey, class SetAnnotation, class GetOptionName = Get_annotator_option_name_default, class GetOptionHelp = Get_annotator_option_help_default, class GetOptionDisplayName = Get_annotator_option_display_name_default>
class SBL::Models::T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >

Model of ParticleAnnotator for attributing any annotation to a particle.

It loads the annotations from a file into a map: the format of the file should be, at each line, the key foloowing by the annotation. The key should be a loadable value that alows a given particle to recognize its annotation.

Template Parameters
KeyTypeType of the key of an annotation.
AnnotationTypeType of the annotation.
MakeKeyFunctor taking a particle as input and returning its key.
SetAnnotationFunctor taking a particle and its annotation as input and setting the annotation of the particle.

Member Typedef Documentation

◆ Base

◆ Self

typedef T_Generic_annotator<KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName> Self

Constructor & Destructor Documentation

◆ T_Generic_annotator()

T_Generic_annotator ( void  )
inline

◆ ~T_Generic_annotator()

~T_Generic_annotator ( void  )
inline

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 >.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_annotations_setter()

SetAnnotation& get_annotations_setter ( void  )
inline

◆ get_annotator()

Base* get_annotator ( const std::string &  name)
inline

◆ get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const
inlineinherited

◆ get_name()

std::string get_name ( void  ) const
inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_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 >.

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

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

◆ load()

bool load ( unsigned  verbose,
std::ostream &  out 
)
inlinevirtual

Loads the data.

Reimplemented from Loader_base.

◆ operator()()

void operator() ( Particle &  p) const
inline

◆ set_loader_instance_name()

void set_loader_instance_name ( const std::string &  loader_instance_name)
inlineinherited

◆ set_options()

bool set_options ( boost::program_options::options_description &  options) const
inline