SubstWeightMatrix Class Reference

position-independet substitution weight matrix More...

#include <subst_weight_matrix.hh>

Public Types

enum  Preset { BLOSUM45 = 0, BLOSUM62 = 1, BLOSUM80 = 2, BLOSUM100 = 3 }
typedef short WeightType

Public Member Functions

 SubstWeightMatrix ()
void AssignPreset (Preset p)
WeightType GetWeight (char aa_one, char aa_two) const
WeightType GetMinWeight () const
WeightType GetMaxWeight () const
void SetWeight (char aa_one, char aa_two, WeightType weight)

Static Public Attributes

static const int ALPHABET_SIZE = 'Z'-'A'+1

Detailed Description

position-independet substitution weight matrix

Definition at line 38 of file subst_weight_matrix.hh.


Member Typedef Documentation

typedef short WeightType

Definition at line 41 of file subst_weight_matrix.hh.


Member Enumeration Documentation

enum Preset
Enumerator:
BLOSUM45 
BLOSUM62 
BLOSUM80 
BLOSUM100 

Definition at line 43 of file subst_weight_matrix.hh.


Constructor & Destructor Documentation

SubstWeightMatrix (  )  [inline]

Initialize substitution matrix with zero.

In order to get a useful substitution weight matrix, use SetWeight(). Alternatively you may want to load the substitution from an info group.

Definition at line 51 of file subst_weight_matrix.hh.


Member Function Documentation

void AssignPreset ( Preset  p  ) 
WeightType GetMaxWeight (  )  const [inline]

Get the maximal substitution weight of the matrix.

Definition at line 74 of file subst_weight_matrix.hh.

WeightType GetMinWeight (  )  const [inline]

Get the minimal substitution weight of the matrix.

Definition at line 71 of file subst_weight_matrix.hh.

WeightType GetWeight ( char  aa_one,
char  aa_two 
) const [inline]

Get the substitution weight between two amino acids.

If the amino acid single letter code is unknown (e.g. '?') a weight of 0 is returned

Definition at line 61 of file subst_weight_matrix.hh.

void SetWeight ( char  aa_one,
char  aa_two,
WeightType  weight 
) [inline]

Set the substitution weight between two amino acids.

The weight is only set if the amino acid single letter code is known (e.g. no weight is set for '?')

Definition at line 80 of file subst_weight_matrix.hh.


Field Documentation

const int ALPHABET_SIZE = 'Z'-'A'+1 [static]

Definition at line 42 of file subst_weight_matrix.hh.


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