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Public Member Functions | Private Attributes | List of all members
core::sequence::ScoringScheme Class Referenceabstract

#include <ScoringScheme.hh>

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

 ScoringScheme ()
 ctor More...
 
 ~ScoringScheme () override
 dtor More...
 
virtual ScoringSchemeOP clone () const =0
 clone method. 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...
 
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 gap_open_
 
Real gap_extend_
 
std::string type_
 

Constructor & Destructor Documentation

core::sequence::ScoringScheme::ScoringScheme ( )
default

ctor

core::sequence::ScoringScheme::~ScoringScheme ( )
overridedefault

dtor

Member Function Documentation

virtual ScoringSchemeOP core::sequence::ScoringScheme::clone ( ) const
pure virtual
Real core::sequence::ScoringScheme::gap_extend ( ) const
virtual
void core::sequence::ScoringScheme::gap_extend ( Real const  gap_extend)

Sets the gap extension penalty.

References gap_extend(), and gap_extend_.

Real core::sequence::ScoringScheme::gap_open ( ) const
virtual
void core::sequence::ScoringScheme::gap_open ( Real const  gap_open)

Sets the gap opening penalty.

References gap_open(), and gap_open_.

bool core::sequence::ScoringScheme::is_good ( Real const &  num)
void core::sequence::ScoringScheme::read_data ( utility::io::izstream &  )
virtual
void core::sequence::ScoringScheme::read_from_file ( utility::file::FileName const &  )
virtual
virtual Real core::sequence::ScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
Size  pos1,
Size  pos2 
)
pure virtual
std::string core::sequence::ScoringScheme::type ( ) const
void core::sequence::ScoringScheme::type ( std::string  new_type)

getters for type, which is a unique string name for this object.

References type_.

void core::sequence::ScoringScheme::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.

References type().

Referenced by read_data(), and read_from_file().

Member Data Documentation

Real core::sequence::ScoringScheme::gap_extend_
private

Referenced by gap_extend().

Real core::sequence::ScoringScheme::gap_open_
private

Referenced by gap_open().

std::string core::sequence::ScoringScheme::type_
private

Referenced by type().


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