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.

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.

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.

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.

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: