## 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.