Uses of Class
blinAlignment.SubstitutionMatrix

Uses of SubstitutionMatrix in blinAlignment

Methods in blinAlignment with parameters of type SubstitutionMatrix

void	PairwiseAlignment.setSubstitutionMatrix(SubstitutionMatrix matrix) Sets the substitution matrix to be used to the specified one.

Constructors in blinAlignment with parameters of type SubstitutionMatrix

PairwiseAlignment(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix subMat)
Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.