43 #include "../Alphabet/AlphabetTools.h" 51 BLOSUM50::BLOSUM50() :
52 distanceMatrix_(20, 20),
55 #include "__BLOSUM50MatrixCode" 61 size_t stateIndex1 = alpha_->getStateIndex(state1);
62 size_t stateIndex2 = alpha_->getStateIndex(state2);
63 return distanceMatrix_(stateIndex1, stateIndex2);
69 return distanceMatrix_(
70 static_cast<size_t>(alpha_->charToInt(state1)),
71 static_cast<size_t>(alpha_->charToInt(state2)));
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
LinearMatrix< double > distanceMatrix_
An alphabet exception thrown when trying to specify a bad int to the alphabet.
LinearMatrix< double > * getIndexMatrix() const