ppALIGN API documentation

ScoreMatrix Class Reference

#include <scorematrix.hpp>

Inheritance diagram for ScoreMatrix:
ProteinScoring

List of all members.

Public Member Functions

 ScoreMatrix (const Alphabet &a1, const Alphabet &a2)
 ScoreMatrix (const Alphabet &a1, const Alphabet &a2, int match, int mismatch)
 ScoreMatrix (const Alphabet &a1, const Alphabet &a2, const std::string &name)
const Alphabet & GetAlphabet1 () const
const Alphabet & GetAlphabet2 () const
double GetScale (const Frequencies &freq1, const Frequencies &freq2) const
double GetScale (const Sequence &seq1, const Sequence &seq2) const

Static Public Member Functions

static double GetScale (const Alphabet &a1, const Alphabet &a2, const std::string name)

Detailed Description

Integer valued score matrix.

Examples:

freescore.cpp.

Definition at line 31 of file scorematrix.hpp.

Constructor & Destructor Documentation

ScoreMatrix::ScoreMatrix ( const Alphabet &  a1,
const Alphabet &  a2 
) [inline]

Construct a score matrix.

Parameters:
a1 alphabet for the first index
a2 alphabet for the second index

Definition at line 41 of file scorematrix.hpp.

ScoreMatrix::ScoreMatrix ( const Alphabet &  a1,
const Alphabet &  a2,
int  match,
int  mismatch 
) [inline]

Construct a score matrix and initalize.

Parameters:
a1 alphabet for the first index
a2 alphabet for the second index
match set diagonal (i==j) values to match
mismatch set off-diagonal (i!=j) values to mismatch

Definition at line 62 of file scorematrix.hpp.

ScoreMatrix::ScoreMatrix ( const Alphabet &  a1,
const Alphabet &  a2,
const std::string &  name 
)

Construct a score matrix by name or by file. If name is not a valid matrix name, try to open a file and read the data from that.

Member Function Documentation

const Alphabet& ScoreMatrix::GetAlphabet1 (  )  const [inline]

Alphabetbet.

Returns:
underlying alphabet of the first sequence.

Definition at line 88 of file scorematrix.hpp.

const Alphabet& ScoreMatrix::GetAlphabet2 (  )  const [inline]

Alphabetbet.

Returns:
underlying alphabet of the second sequence.

Definition at line 96 of file scorematrix.hpp.

double ScoreMatrix::GetScale ( const Sequence &  seq1,
const Sequence &  seq2 
) const

Estimate scale from input sequences. If &GetAlphabet1()==&GetAlphabet2() the background frequencies q(a) are estimated from both sequences and $ \lambda $ is determined as the root of

\[ \sum_{a,b} q(a) q(b) e^{s[a][b])/\lambda} = 1 \]

If &GetAlphabet1()!=&GetAlphabet2() the background frequencies are determined for both sequences separtely q_1(a) and q_2 and $ \lambda $ is determined as the root of

\[ \sum_{a,b} q_1(a) q_2(b) e^{s[a][b])/\lambda} = 1 \]

Parameters:
seq1 
seq2 
double ScoreMatrix::GetScale ( const Frequencies &  freq1,
const Frequencies &  freq2 
) const

Determine scale of the score matrix. The scale is defined through $ s[a][b]= \lambda \log \frac{p(a,b)}{q(a)q(b)} $. It is estimated by the unique solution of the equation

\[ \sum_{a,b} freq1[a] freq2[b] e^{s[a][b])/\lambda} = 1 \]

Parameters:
freq1 background frequencies (assumed to be normalized)
freq2 background frequencies (assumed to be normalized)
static double ScoreMatrix::GetScale ( const Alphabet &  a1,
const Alphabet &  a2,
const std::string  name 
) [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)} $.

The scales of the blosum matrices are:

  • blosum30 : 1/5 bit $ \lambda = 5 / \log(2) $
  • blosum35-blosum40 : 1/4 bit,$ \lambda = 4 / \log(2) $
  • blosum45-blosum55: 1/3 bit,$ \lambda = 3 / \log(2) $
  • blosum60-blosum100: 1/2 bit,$ \lambda = 2 / \log(2) $

The scales of the pam matrices are:

  • pam10-pam160 1/2 bit,
  • pam170-pam260 1/3 bit,
  • pam270-pam340 1/4 bit,
  • pam350-pam400 1/5 bit,
  • pam410-pam460 1/6 bit,
  • pam470-pam500 1/7 bit
Parameters:
a1 alphabet of the first sequence
a2 alphabet of the second sequence
name name of the score matrix
Examples:
freescore.cpp.
The documentation for this class was generated from the following file: