OpenStructure
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#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 |
position-independet substitution weight matrix
Definition at line 38 of file subst_weight_matrix.hh.
typedef short WeightType |
Definition at line 41 of file subst_weight_matrix.hh.
enum Preset |
Enumerator | |
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BLOSUM45 | |
BLOSUM62 | |
BLOSUM80 | |
BLOSUM100 |
Definition at line 43 of file subst_weight_matrix.hh.
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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.
void AssignPreset | ( | Preset | p | ) |
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inline |
Get the maximal substitution weight of the matrix.
Definition at line 74 of file subst_weight_matrix.hh.
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Get the minimal substitution weight of the matrix.
Definition at line 71 of file subst_weight_matrix.hh.
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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.
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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.
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static |
Definition at line 42 of file subst_weight_matrix.hh.