#include <ScoringScheme.hh>

Public Member Functions
	ScoringScheme ()
	ctor More...

virtual	~ScoringScheme ()
	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 ( )

ctor

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

virtual

dtor

Member Function Documentation

virtual ScoringSchemeOP core::sequence::ScoringScheme::clone ( ) const

pure virtual

clone method.

Implemented in core::sequence::MatrixScoringScheme, core::sequence::PairScoringScheme, core::sequence::ProfSimScoringScheme, core::sequence::CompositeScoringScheme, core::sequence::SimpleScoringScheme, core::sequence::DPScoringScheme, core::sequence::L1ScoringScheme, core::sequence::CompassScoringScheme, and core::sequence::ChemicalShiftScoringScheme.

Real core::sequence::ScoringScheme::gap_extend ( ) const

virtual

Gets the gap extension penalty.

References gap_extend_.

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

Gets the gap opening penalty.

References gap_open_.

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 )

Referenced by core::sequence::ChemicalShiftScoringScheme::score(), core::sequence::L1ScoringScheme::score(), and core::sequence::DPScoringScheme::score().

void core::sequence::ScoringScheme::read_data ( utility::io::izstream & )

virtual

Reimplemented in core::sequence::MatrixScoringScheme.

References unimplemented_method_error().

void core::sequence::ScoringScheme::read_from_file ( utility::file::FileName const & )

virtual

Initialize from a file.

Reimplemented in core::sequence::MatrixScoringScheme, core::sequence::PairScoringScheme, core::sequence::CompositeScoringScheme, and core::sequence::SimpleScoringScheme.

References unimplemented_method_error().

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

pure virtual

Implemented in core::sequence::MatrixScoringScheme, core::sequence::ProfSimScoringScheme, core::sequence::DPScoringScheme, core::sequence::L1ScoringScheme, core::sequence::CompassScoringScheme, and core::sequence::ChemicalShiftScoringScheme.

std::string core::sequence::ScoringScheme::type ( ) const

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

References type_.

Referenced by core::sequence::ChemicalShiftScoringScheme::ChemicalShiftScoringScheme(), core::sequence::CompassScoringScheme::CompassScoringScheme(), core::sequence::CompositeScoringScheme::CompositeScoringScheme(), core::sequence::DPScoringScheme::DPScoringScheme(), core::sequence::MatrixScoringScheme::init_type(), core::sequence::L1ScoringScheme::L1ScoringScheme(), core::sequence::PairScoringScheme::PairScoringScheme(), core::sequence::ProfSimScoringScheme::ProfSimScoringScheme(), core::sequence::SimpleScoringScheme::SimpleScoringScheme(), and unimplemented_method_error().

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(), and utility_exit_with_message.

Referenced by read_data(), and read_from_file().