ppALIGN API documentation

ProteinScoring Class Reference

#include <scorematrix.hpp>

Inheritance diagram for ProteinScoring:
ScoreMatrix

List of all members.

Public Member Functions

 ProteinScoring (const std::string &name)

Static Public Member Functions

static double GetScale (const std::string &name)

Detailed Description

Integer valued score matrix for proteins.

Definition at line 170 of file scorematrix.hpp.

Constructor & Destructor Documentation

ProteinScoring::ProteinScoring ( const std::string &  name  ) 

Constructor.

Parameters:
name matrix name (e.g. blosum62)

Member Function Documentation

static double ProteinScoring::GetScale ( const std::string &  name  )  [inline, static]

Scale $ \lambda $ of the named score matrix. The scale is defined through: $ s[a][b]= \lambda \log \frac{p(a,b)}{q(a)q(b)} $.

Parameters:
a1 alphabet of the first sequence
a2 alphabet of the second sequence
name name of the protein score matrix

Definition at line 186 of file scorematrix.hpp.

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