#include <MatrixScoringScheme.hh>

Inheritance diagram for core::sequence::MatrixScoringScheme:

Public Member Functions
	MatrixScoringScheme ()

	MatrixScoringScheme (Real open, Real extend, utility::file::FileName const &fn)
	ctor More...

	MatrixScoringScheme (Real open, Real extend, utility::vector1< utility::vector1< core::Real > > matrix)

ScoringSchemeOP	clone () const override
	returns owning pointer to a new object with a deep copy of this object's values. More...

	~MatrixScoringScheme () override=default
	dtor More...

void	read_from_database (std::string name="BLOSUM62")
	Read an alignment matrix from the given database filename using the NCBI BLOSUM format for matrices. More...

void	read_from_file (utility::file::FileName const &fn) override
	Read an alignment matrix from the given filename using the NCBI BLOSUM format for matrices. More...

void	read_data (utility::io::izstream &input) override

utility::vector1< Real >	values_for_aa (char aa)
	Get the values for amino acid aa, in Rosetta aa order. More...

utility::vector1< Real >	values_for_aa (core::chemical::AA aa)
	Get the values for amino acid aa, in Rosetta aa order. More...

utility::vector1 < utility::vector1< Real > >	scoring_matrix () const

Real	score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2) override

Public Member Functions inherited from core::sequence::ScoringScheme
	ScoringScheme ()
	ctor More...

	~ScoringScheme () override
	dtor More...

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...

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 Member Functions
void	init_type ()

Private Attributes
utility::vector1 < utility::vector1< Real > >	scoring_matrix_

Constructor & Destructor Documentation

core::sequence::MatrixScoringScheme::MatrixScoringScheme ( )

inline

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

core::sequence::MatrixScoringScheme::MatrixScoringScheme	(	Real	open,
		Real	extend,
		utility::file::FileName const &	fn
	)

inline

ctor

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

core::sequence::MatrixScoringScheme::MatrixScoringScheme	(	Real	open,
		Real	extend,
		utility::vector1< utility::vector1< core::Real > >	matrix
	)

inline

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

core::sequence::MatrixScoringScheme::~MatrixScoringScheme ( )

overridedefault

dtor

Member Function Documentation

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

inlineoverridevirtual

returns owning pointer to a new object with a deep copy of this object's values.

Implements core::sequence::ScoringScheme.

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

void core::sequence::MatrixScoringScheme::init_type ( )

inlineprivate

References core::sequence::ScoringScheme::type().

Referenced by MatrixScoringScheme().

void core::sequence::MatrixScoringScheme::read_data ( utility::io::izstream & input )

overridevirtual

Reimplemented from core::sequence::ScoringScheme.

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::sequence::end, core::chemical::num_aa_types, core::chemical::oneletter_code_specifies_aa(), protocols::forge::methods::order(), score(), and scoring_matrix_.

Referenced by read_from_file().

void core::sequence::MatrixScoringScheme::read_from_database ( std::string name = "BLOSUM62" )

Read an alignment matrix from the given database filename using the NCBI BLOSUM format for matrices.

References read_from_file().

Referenced by core::sequence::SequenceProfile::generate_from_sequence().

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

overridevirtual

Read an alignment matrix from the given filename using the NCBI BLOSUM format for matrices.

Reimplemented from core::sequence::ScoringScheme.

References read_data().

Referenced by MatrixScoringScheme(), protocols::frag_picker::scores::ProfileScoreBlosum62::ProfileScoreBlosum62(), protocols::frag_picker::scores::ProfileScoreSubMatrix::ProfileScoreSubMatrix(), and read_from_database().

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

overridevirtual

Implements core::sequence::ScoringScheme.

References core::chemical::aa_from_oneletter_code(), core::chemical::aa_unk, scoring_matrix_, and core::sequence::tr().

Referenced by read_data().

utility::vector1< utility::vector1< Real > > core::sequence::MatrixScoringScheme::scoring_matrix ( ) const

References scoring_matrix_.

Referenced by clone(), protocols::frag_picker::scores::ProfileScoreBlosum62::ProfileScoreBlosum62(), and protocols::frag_picker::scores::ProfileScoreSubMatrix::ProfileScoreSubMatrix().

utility::vector1< Real > core::sequence::MatrixScoringScheme::values_for_aa ( char aa )

Get the values for amino acid aa, in Rosetta aa order.

References core::chemical::aa_ala, core::chemical::aa_from_oneletter_code(), core::chemical::oneletter_code_specifies_aa(), and scoring_matrix_.

Referenced by core::sequence::SequenceProfile::generate_from_sequence().

utility::vector1< Real > core::sequence::MatrixScoringScheme::values_for_aa ( core::chemical::AA aa )

Get the values for amino acid aa, in Rosetta aa order.

References protocols::cluster::calibur::aa, and scoring_matrix_.

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::sequence::MatrixScoringScheme::scoring_matrix_

private

Referenced by read_data(), score(), scoring_matrix(), and values_for_aa().

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

src/core/sequence/MatrixScoringScheme.hh
src/core/sequence/MatrixScoringScheme.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation