Inheritance diagram for core::sequence::DPScoringScheme:

Collaboration diagram for core::sequence::DPScoringScheme:

Public Member Functions
	DPScoringScheme (Real open=-4, Real extend=-1)
	ctor More...

ScoringSchemeOP	clone () const
	clone method. More...

virtual	~DPScoringScheme ()
	dtor More...

virtual Real	score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)

Public Member Functions inherited from core::sequence::ScoringScheme
	ScoringScheme ()
	ctor More...

virtual	~ScoringScheme ()
	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)