#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`
	)