Package org.biojava.nbio.core.alignment.matrices
package org.biojava.nbio.core.alignment.matrices
-
ClassDescriptionFactory class to get Providers for substitution matrices the are provided by the AAINDEX database.The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directoryThe 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
Compoundin a sequence for another.Static utility to access substitution matrices that come bundled with BioJava.