Rosetta Core  2014.35
Public Member Functions | Private Attributes | List of all members
core::sequence::SimpleScoringScheme Class Reference

#include <SimpleScoringScheme.hh>

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
 clone method. More...
 
virtual ~SimpleScoringScheme ()
 dtor More...
 
virtual void read_from_file (utility::file::FileName const &fn)
 Initialize from a file. More...
 
Real match_score () const
 
Real mismatch_score () const
 
virtual Real score (SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2)
 
- Public Member Functions inherited from core::sequence::ScoringScheme
 ScoringScheme ()
 ctor More...
 
virtual ~ScoringScheme ()
 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 
)
inline
virtual core::sequence::SimpleScoringScheme::~SimpleScoringScheme ( )
inlinevirtual

dtor

Member Function Documentation

ScoringSchemeOP core::sequence::SimpleScoringScheme::clone ( ) const
inlinevirtual
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 &  )
virtual

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

References utility_exit_with_message.

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

Member Data Documentation

Real core::sequence::SimpleScoringScheme::match_score_
private

Referenced by match_score(), and score().

Real core::sequence::SimpleScoringScheme::mismatch_score_
private

Referenced by mismatch_score(), and score().


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