core::sequence::MatrixScoringScheme Member List

This is the complete list of members for core::sequence::MatrixScoringScheme, including all inherited members.

clone() const	core::sequence::MatrixScoringScheme	inlinevirtual
gap_extend() const	core::sequence::ScoringScheme	virtual
gap_extend(Real const gap_extend)	core::sequence::ScoringScheme
gap_open() const	core::sequence::ScoringScheme	virtual
gap_open(Real const gap_open)	core::sequence::ScoringScheme
init_type()	core::sequence::MatrixScoringScheme	inlineprivate
is_good(Real const &num)	core::sequence::ScoringScheme
MatrixScoringScheme()	core::sequence::MatrixScoringScheme	inline
MatrixScoringScheme(Real open, Real extend, utility::file::FileName const &fn)	core::sequence::MatrixScoringScheme	inline
MatrixScoringScheme(Real open, Real extend, utility::vector1< utility::vector1< core::Real > > matrix)	core::sequence::MatrixScoringScheme	inline
read_data(utility::io::izstream &input)	core::sequence::MatrixScoringScheme	virtual
read_from_database(std::string name="BLOSUM62")	core::sequence::MatrixScoringScheme
read_from_file(utility::file::FileName const &fn)	core::sequence::MatrixScoringScheme	virtual
score(SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)	core::sequence::MatrixScoringScheme	virtual
scoring_matrix() const	core::sequence::MatrixScoringScheme
scoring_matrix_	core::sequence::MatrixScoringScheme	private
ScoringScheme()	core::sequence::ScoringScheme
type() const	core::sequence::ScoringScheme
type(std::string new_type)	core::sequence::ScoringScheme
unimplemented_method_error(std::string const &method_name) const	core::sequence::ScoringScheme
values_for_aa(char aa)	core::sequence::MatrixScoringScheme
values_for_aa(core::chemical::AA aa)	core::sequence::MatrixScoringScheme
~MatrixScoringScheme()	core::sequence::MatrixScoringScheme	inlinevirtual
~ScoringScheme()	core::sequence::ScoringScheme	virtual