Rosetta 3.4
Public Member Functions
core::sequence::MatrixScoringScheme Class Reference

#include <MatrixScoringScheme.hh>

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List of all members.

Public Member Functions

 MatrixScoringScheme ()
 MatrixScoringScheme (Real open, Real extend, utility::file::FileName const &fn)
 ctor
 MatrixScoringScheme (Real open, Real extend, utility::vector1< utility::vector1< core::Real > > matrix)
ScoringSchemeOP clone () const
 returns owning pointer to a new object with a deep copy of this object's values.
virtual ~MatrixScoringScheme ()
 dtor
void read_from_database (std::string name="BLOSUM62")
 Read an alignment matrix from the given database filename using the NCBI BLOSUM format for matrices.
void read_from_file (utility::file::FileName const &fn)
 Read an alignment matrix from the given filename using the NCBI BLOSUM format for matrices.
void read_data (utility::io::izstream &input)
utility::vector1< Realvalues_for_aa (char aa)
 Get the values for amino acid aa, in Rosetta aa order.
utility::vector1< Realvalues_for_aa (core::chemical::AA aa)
 Get the values for amino acid aa, in Rosetta aa order.
utility::vector1
< utility::vector1< Real > > 
scoring_matrix () const
virtual Real score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)

Constructor & Destructor Documentation

core::sequence::MatrixScoringScheme::MatrixScoringScheme ( ) [inline]
core::sequence::MatrixScoringScheme::MatrixScoringScheme ( Real  open,
Real  extend,
utility::file::FileName const &  fn 
) [inline]
core::sequence::MatrixScoringScheme::MatrixScoringScheme ( Real  open,
Real  extend,
utility::vector1< utility::vector1< core::Real > >  matrix 
) [inline]
virtual core::sequence::MatrixScoringScheme::~MatrixScoringScheme ( ) [inline, virtual]

dtor


Member Function Documentation

ScoringSchemeOP core::sequence::MatrixScoringScheme::clone ( ) const [inline, virtual]

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(), MatrixScoringScheme(), and scoring_matrix().

void core::sequence::MatrixScoringScheme::read_data ( utility::io::izstream &  input) [virtual]
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) [virtual]
Real core::sequence::MatrixScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
Size  pos1,
Size  pos2 
) [virtual]
utility::vector1< utility::vector1< Real > > core::sequence::MatrixScoringScheme::scoring_matrix ( ) const
utility::vector1< Real > core::sequence::MatrixScoringScheme::values_for_aa ( core::chemical::AA  aa)

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

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

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