Package org.biojava.nbio.core.alignment.matrices

Interface Summary

Interface	Description
AAIndexProvider

Class Summary

Class	Description
AAindexFactory	Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.
AAIndexFileParser
DefaultAAIndexProvider	The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
ScaledSubstitutionMatrix	The biojava-alignment module represents substitution matrices with short values.
SimpleSubstitutionMatrix<C extends Compound>	Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SubstitutionMatrixHelper	Static utility to access substitution matrices that come bundled with BioJava.