Uses of Class
org.biojava.bio.alignment.SubstitutionMatrix

Packages that use SubstitutionMatrix

org.biojava.bio.alignment

Classes to generate and describe sequence alignments.

Uses of SubstitutionMatrix in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as SubstitutionMatrix

protected SubstitutionMatrix

NeedlemanWunsch.subMatrix

Methods in org.biojava.bio.alignment that return SubstitutionMatrix

SubstitutionMatrix

SubstitutionMatrix.normalizeMatrix() With this method you can get a "normalized" SubstitutionMatrix object; however, since this implementation uses an int matrix, the normalized matrix will be scaled by ten.

Methods in org.biojava.bio.alignment with parameters of type SubstitutionMatrix

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

Constructors in org.biojava.bio.alignment with parameters of type SubstitutionMatrix

NeedlemanWunsch(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.

SmithWaterman(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object.