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

typedef short WeightType

Definition at line 41 of file subst_weight_matrix.hh.

Member Enumeration Documentation

enum Preset

Enumerator
BLOSUM45
BLOSUM62
BLOSUM80
BLOSUM100
IDENTITY
MATCH
NUC44

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 54 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 77 of file subst_weight_matrix.hh.

WeightType GetMinWeight ( ) const

inline

Get the minimal substitution weight of the matrix.

Definition at line 74 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 64 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 83 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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The documentation for this class was generated from the following file:

• build-2.6/stage/include/ost/seq/alg/subst_weight_matrix.hh