core::sequence::PairScoringScheme Class Reference

#include <PairScoringScheme.hh>

Inheritance diagram for core::sequence::PairScoringScheme:

Public Member Functions
	PairScoringScheme ()
	PairScoringScheme (Real gap_open_in, Real gap_extend_in, utility::vector1< utility::vector1< core::Real > > pairs)
	ctor More...
ScoringSchemeOP	clone () const override
	clone method. More...
utility::vector1 < utility::vector1< core::Real > >	pairs () const
void	add_scored_pair (core::Size const res1, core::Size const res2, core::Real const score)
	~PairScoringScheme () override=default
	dtor More...
void	read_from_file (utility::file::FileName const &fn) override
	Initialize from a file. More...
Real	score (SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2) override
Public Member Functions inherited from core::sequence::ScoringScheme
	ScoringScheme ()
	ctor More...
	~ScoringScheme () override
	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
utility::vector1 < utility::vector1< core::Real > >	pairs_

Constructor & Destructor Documentation

core::sequence::PairScoringScheme::PairScoringScheme ( )

inline

References core::sequence::ScoringScheme::gap_extend(), core::sequence::ScoringScheme::gap_open(), and core::sequence::ScoringScheme::type().

core::sequence::PairScoringScheme::PairScoringScheme ( Real  gap_open_in, Real  gap_extend_in, utility::vector1< utility::vector1< core::Real > >  pairs  )

inline

ctor

References core::sequence::ScoringScheme::gap_extend(), core::sequence::ScoringScheme::gap_open(), and core::sequence::ScoringScheme::type().

core::sequence::PairScoringScheme::~PairScoringScheme ( )

overridedefault

dtor

Member Function Documentation

void core::sequence::PairScoringScheme::add_scored_pair ( core::Size const  res1, core::Size const  res2, core::Real const  score  )

inline

References pairs_, and score().

ScoringSchemeOP core::sequence::PairScoringScheme::clone ( ) const

inlineoverridevirtual

clone method.

Implements core::sequence::ScoringScheme.

References core::sequence::ScoringScheme::gap_extend(), core::sequence::ScoringScheme::gap_open(), and pairs().

utility::vector1< utility::vector1< core::Real > > core::sequence::PairScoringScheme::pairs ( ) const

inline

References pairs_.

Referenced by clone().

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

overridevirtual

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

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

override

References pairs_.

Referenced by add_scored_pair().

Member Data Documentation

utility::vector1< utility::vector1< core::Real > > core::sequence::PairScoringScheme::pairs_

private

Referenced by add_scored_pair(), pairs(), and score().

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

• src/core/sequence/PairScoringScheme.hh
• src/core/sequence/PairScoringScheme.cc