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

Packages that use SubstitutionMatrix
org.biojava.bio.alignment: Classes to generate and describe sequence alignments.
org.biojava.bio.structure.io: Input and Output of Structures

Uses of SubstitutionMatrix in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as SubstitutionMatrix
`protected SubstitutionMatrix` `NeedlemanWunsch.subMatrix` A matrix with the size length(alphabet) times length(alphabet)

Methods in org.biojava.bio.alignment that return SubstitutionMatrix
`static SubstitutionMatrix` `SubstitutionMatrix.getSubstitutionMatrix(BufferedReader reader)` This constructor can be used to guess the alphabet of this substitution matrix.
`SubstitutionMatrix` `SubstitutionMatrix.normalizeMatrix()` With this method you can get a “normalized” `SubstitutionMatrix` object; however, since this implementation uses an short 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(short match, short replace, short insert, short delete, short 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(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix matrix)` Constructs the new SmithWaterman alignment object.

Uses of SubstitutionMatrix in org.biojava.bio.structure.io

Methods in org.biojava.bio.structure.io that return SubstitutionMatrix
`static SubstitutionMatrix` `SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet)`