Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
core::sequence::CompositeScoringScheme Class Reference

#include <CompositeScoringScheme.hh>

Inheritance diagram for core::sequence::CompositeScoringScheme:
Inheritance graph
[legend]

Public Member Functions

 CompositeScoringScheme ()
 
 CompositeScoringScheme (Real gap_open_in, Real gap_extend_in, utility::vector1< ScoringSchemeOP > schemes)
 ctor More...
 
ScoringSchemeOP clone () const override
 clone method. More...
 
utility::vector1< ScoringSchemeOPscoring_schemes () const
 
Size count () const
 
void add_scoring_scheme (ScoringSchemeOP scheme)
 
 ~CompositeScoringScheme () override=default
 dtor More...
 
void read_from_file (utility::file::FileName const &fn) override
 Initialize from a file. More...
 
Real score (SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2) override
 
- Public Member Functions inherited from core::sequence::ScoringScheme
 ScoringScheme ()
 ctor More...
 
 ~ScoringScheme () override
 dtor More...
 
virtual void read_data (utility::io::izstream &)
 
virtual Real gap_open () const
 Gets the gap opening penalty. More...
 
virtual Real gap_extend () const
 Gets the gap extension penalty. More...
 
void gap_open (Real const gap_open)
 Sets the gap opening penalty. More...
 
void gap_extend (Real const gap_extend)
 Sets the gap extension penalty. More...
 
std::string type () const
 getters for type, which is a unique string name for this object. More...
 
void type (std::string new_type)
 getters for type, which is a unique string name for this object. More...
 
virtual Real score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)=0
 
void unimplemented_method_error (std::string const &method_name) const
 Utility method for producing useful error messages and exiting from program. Declared const which is funny, because exiting the program certainly changes the state of this object! This might be replaced with exception handling if we ever start using those. More...
 
bool is_good (Real const &num)
 

Private Attributes

utility::vector1< ScoringSchemeOPscoring_schemes_
 

Constructor & Destructor Documentation

core::sequence::CompositeScoringScheme::CompositeScoringScheme ( )
inline
core::sequence::CompositeScoringScheme::CompositeScoringScheme ( Real  gap_open_in,
Real  gap_extend_in,
utility::vector1< ScoringSchemeOP schemes 
)
inline
core::sequence::CompositeScoringScheme::~CompositeScoringScheme ( )
overridedefault

dtor

Member Function Documentation

void core::sequence::CompositeScoringScheme::add_scoring_scheme ( ScoringSchemeOP  scheme)

References scoring_schemes_.

ScoringSchemeOP core::sequence::CompositeScoringScheme::clone ( ) const
inlineoverridevirtual
Size core::sequence::CompositeScoringScheme::count ( ) const
inline

References scoring_schemes_.

Referenced by score().

void core::sequence::CompositeScoringScheme::read_from_file ( utility::file::FileName const &  )
overridevirtual

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

Real core::sequence::CompositeScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
core::Size  pos1,
core::Size  pos2 
)
override
utility::vector1< ScoringSchemeOP > core::sequence::CompositeScoringScheme::scoring_schemes ( ) const
inline

References scoring_schemes_.

Referenced by clone().

Member Data Documentation

utility::vector1< ScoringSchemeOP > core::sequence::CompositeScoringScheme::scoring_schemes_
private

The documentation for this class was generated from the following files: