Package org.biojava.nbio.core.alignment.matrices
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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 directoryScaledSubstitutionMatrix 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 oneCompound
in a sequence for another.SubstitutionMatrixHelper Static utility to access substitution matrices that come bundled with BioJava.