core::sequence::CompositeScoringScheme Class Reference

#include <CompositeScoringScheme.hh>

Inheritance diagram for core::sequence::CompositeScoringScheme:

Collaboration diagram for core::sequence::CompositeScoringScheme:

Public Member Functions
	CompositeScoringScheme ()
	CompositeScoringScheme (Real gap_open_in, Real gap_extend_in, utility::vector1< ScoringSchemeOP > schemes)
	ctor More...
ScoringSchemeOP	clone () const
	clone method. More...
utility::vector1< ScoringSchemeOP >	scoring_schemes () const
Size	count () const
void	add_scoring_scheme (ScoringSchemeOP scheme)
virtual	~CompositeScoringScheme ()
	dtor More...
virtual void	read_from_file (utility::file::FileName const &fn)
	Initialize from a file. More...
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
utility::vector1< ScoringSchemeOP >	scoring_schemes_

Detailed Description

Definition at line 29 of file CompositeScoringScheme.hh.

Constructor & Destructor Documentation

core::sequence::CompositeScoringScheme::CompositeScoringScheme ( )

inline

Definition at line 32 of file CompositeScoringScheme.hh.

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

Referenced by clone().

core::sequence::CompositeScoringScheme::CompositeScoringScheme ( Real  gap_open_in, Real  gap_extend_in, utility::vector1< ScoringSchemeOP >  schemes  )

inline

ctor

Definition at line 39 of file CompositeScoringScheme.hh.

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

virtual core::sequence::CompositeScoringScheme::~CompositeScoringScheme ( )

inlinevirtual

dtor

Definition at line 72 of file CompositeScoringScheme.hh.

Member Function Documentation

void core::sequence::CompositeScoringScheme::add_scoring_scheme

(

ScoringSchemeOP

scheme)

Definition at line 40 of file CompositeScoringScheme.cc.

References scoring_schemes_.

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

inlinevirtual

clone method.

Implements core::sequence::ScoringScheme.

Definition at line 51 of file CompositeScoringScheme.hh.

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

Size core::sequence::CompositeScoringScheme::count ( ) const

inline

Definition at line 65 of file CompositeScoringScheme.hh.

References scoring_schemes_.

Referenced by score().

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

virtual

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

Definition at line 36 of file CompositeScoringScheme.cc.

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

virtual

Definition at line 44 of file CompositeScoringScheme.cc.

References count(), scoring_schemes_, and core::scoring::total_score.

utility::vector1< ScoringSchemeOP > core::sequence::CompositeScoringScheme::scoring_schemes ( ) const

inline

Definition at line 61 of file CompositeScoringScheme.hh.

References scoring_schemes_.

Referenced by clone().

Member Data Documentation

utility::vector1< ScoringSchemeOP > core::sequence::CompositeScoringScheme::scoring_schemes_

private

Definition at line 79 of file CompositeScoringScheme.hh.

Referenced by add_scoring_scheme(), count(), score(), and scoring_schemes().

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

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