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core::sequence::DPScoringScheme Class Reference

#include <DPScoringScheme.hh>

Inheritance diagram for core::sequence::DPScoringScheme:
Inheritance graph
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Public Member Functions

 DPScoringScheme (Real open=-4, Real extend=-1)
 ctor More...
 
ScoringSchemeOP clone () const override
 clone method. More...
 
 ~DPScoringScheme () override=default
 dtor More...
 
Real score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2) override
 
- Public Member Functions inherited from core::sequence::ScoringScheme
 ScoringScheme ()
 ctor More...
 
 ~ScoringScheme () override
 dtor More...
 
virtual void read_from_file (utility::file::FileName const &)
 Initialize from a file. 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...
 
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)
 

Constructor & Destructor Documentation

core::sequence::DPScoringScheme::DPScoringScheme ( Real  open = -4,
Real  extend = -1 
)
inline
core::sequence::DPScoringScheme::~DPScoringScheme ( )
overridedefault

dtor

Member Function Documentation

ScoringSchemeOP core::sequence::DPScoringScheme::clone ( ) const
inlineoverridevirtual
Real core::sequence::DPScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
Size  pos1,
Size  pos2 
)
overridevirtual

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