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Public Types | Public Member Functions | Static Public Attributes
SubstWeightMatrix Class Reference

#include <subst_weight_matrix.hh>

Public Types

enum  Preset {
  BLOSUM45 = 0 , BLOSUM62 = 1 , BLOSUM80 = 2 , BLOSUM100 = 3 ,
  IDENTITY = 4 , MATCH = 5 , NUC44 = 6
}
 
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

◆ WeightType

typedef short WeightType

Definition at line 41 of file subst_weight_matrix.hh.

Member Enumeration Documentation

◆ Preset

enum Preset
Enumerator
BLOSUM45 
BLOSUM62 
BLOSUM80 
BLOSUM100 
IDENTITY 
MATCH 
NUC44 

Definition at line 43 of file subst_weight_matrix.hh.

Constructor & Destructor Documentation

◆ SubstWeightMatrix()

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 54 of file subst_weight_matrix.hh.

Member Function Documentation

◆ AssignPreset()

void AssignPreset ( Preset  p)

◆ GetMaxWeight()

WeightType GetMaxWeight ( ) const
inline

Get the maximal substitution weight of the matrix.

Definition at line 77 of file subst_weight_matrix.hh.

◆ GetMinWeight()

WeightType GetMinWeight ( ) const
inline

Get the minimal substitution weight of the matrix.

Definition at line 74 of file subst_weight_matrix.hh.

◆ GetWeight()

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 64 of file subst_weight_matrix.hh.

◆ SetWeight()

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 83 of file subst_weight_matrix.hh.

Field Documentation

◆ ALPHABET_SIZE

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

Definition at line 42 of file subst_weight_matrix.hh.

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