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

#include <subst_weight_matrix.hh>

Public Types

typedef short WeightType

Public Member Functions

 SubstWeightMatrix ()
WeightType GetWeight (char aa_one, char aa_two) 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 41 of file subst_weight_matrix.hh.


Member Typedef Documentation

typedef short WeightType

Definition at line 44 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 50 of file subst_weight_matrix.hh.


Member Function Documentation

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 58 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 71 of file subst_weight_matrix.hh.


Field Documentation

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

Definition at line 45 of file subst_weight_matrix.hh.


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