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core::sequence::CompositeScoringScheme Class Reference

#include <CompositeScoringScheme.hh>

Inheritance diagram for core::sequence::CompositeScoringScheme:
Inheritance graph
Collaboration diagram for core::sequence::CompositeScoringScheme:
Collaboration graph

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< ScoringSchemeOPscoring_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< ScoringSchemeOPscoring_schemes_

Constructor & Destructor Documentation

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


Member Function Documentation

void core::sequence::CompositeScoringScheme::add_scoring_scheme ( ScoringSchemeOP  scheme)

References scoring_schemes_.

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

References scoring_schemes_.

Referenced by score().

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

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

Real core::sequence::CompositeScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
core::Size  pos1,
core::Size  pos2 
utility::vector1< ScoringSchemeOP > core::sequence::CompositeScoringScheme::scoring_schemes ( ) const

References scoring_schemes_.

Referenced by clone().

Member Data Documentation

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

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