#include <ScoringScheme.hh>

Inheritance diagram for core::sequence::ScoringScheme:

Collaboration diagram for core::sequence::ScoringScheme:

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_

Detailed Description

Definition at line 41 of file ScoringScheme.hh.

Constructor & Destructor Documentation

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

ctor

Definition at line 33 of file ScoringScheme.cc.

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

virtual

dtor

Definition at line 36 of file ScoringScheme.cc.

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.

Definition at line 55 of file ScoringScheme.cc.

References gap_extend_.

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

Sets the gap extension penalty.

Definition at line 65 of file ScoringScheme.cc.

References gap_extend(), and gap_extend_.

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

virtual

Gets the gap opening penalty.

Definition at line 50 of file ScoringScheme.cc.

References gap_open_.

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

Sets the gap opening penalty.

Definition at line 60 of file ScoringScheme.cc.

References gap_open(), and gap_open_.

bool core::sequence::ScoringScheme::is_good ( Real const & num)

Definition at line 92 of file ScoringScheme.cc.

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.

Definition at line 45 of file ScoringScheme.cc.

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.

Definition at line 39 of file ScoringScheme.cc.

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.

Definition at line 70 of file ScoringScheme.cc.

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.

Definition at line 75 of file ScoringScheme.cc.

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.

Definition at line 83 of file ScoringScheme.cc.

References type().

Referenced by read_data(), and read_from_file().

Member Data Documentation

Real core::sequence::ScoringScheme::gap_extend_

private

Definition at line 96 of file ScoringScheme.hh.

Referenced by gap_extend().

Real core::sequence::ScoringScheme::gap_open_

private

Definition at line 95 of file ScoringScheme.hh.

Referenced by gap_open().

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

private

Definition at line 97 of file ScoringScheme.hh.

Referenced by type().

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

src/core/sequence/ScoringScheme.hh
src/core/sequence/ScoringScheme.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation