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Public Member Functions | Private Attributes | List of all members
core::sequence::SimpleScoringScheme Class Reference

#include <SimpleScoringScheme.hh>

Inheritance diagram for core::sequence::SimpleScoringScheme:
Inheritance graph

Public Member Functions

 SimpleScoringScheme (Real match_score=4, Real mismatch_score=1, Real gap_open_in=-4, Real gap_extend_in=-1)
 ctor More...
ScoringSchemeOP clone () const override
 clone method. More...
 ~SimpleScoringScheme () override=default
 dtor More...
void read_from_file (utility::file::FileName const &fn) override
 Initialize from a file. More...
Real match_score () const
Real mismatch_score () const
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

Real match_score_
Real mismatch_score_

Constructor & Destructor Documentation

core::sequence::SimpleScoringScheme::SimpleScoringScheme ( Real  match_score = 4,
Real  mismatch_score = 1,
Real  gap_open_in = -4,
Real  gap_extend_in = -1 
core::sequence::SimpleScoringScheme::~SimpleScoringScheme ( )


Member Function Documentation

ScoringSchemeOP core::sequence::SimpleScoringScheme::clone ( ) const
Real core::sequence::SimpleScoringScheme::match_score ( ) const

References match_score_.

Referenced by clone().

Real core::sequence::SimpleScoringScheme::mismatch_score ( ) const

References mismatch_score_.

Referenced by clone().

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

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

Real core::sequence::SimpleScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
core::Size  pos1,
core::Size  pos2 

References match_score_, and mismatch_score_.

Member Data Documentation

Real core::sequence::SimpleScoringScheme::match_score_

Referenced by match_score(), and score().

Real core::sequence::SimpleScoringScheme::mismatch_score_

Referenced by mismatch_score(), and score().

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