private static SubstitutionMatrix < NucleotideCompound > getNucleotideMatrix ( String file ) { if ( ! nucleotideMatrices . containsKey ( file ) ) { nucleotideMatrices . put ( file , new SimpleSubstitutionMatrix < NucleotideCompound > ( AmbiguityDNACompoundSet . getDNACompoundSet ( ) , getReader ( file ) , file ) ) ; } return nucleotideMatrices . get ( file ) ; }
reads in a nucleotide substitution matrix if necessary