private static SubstitutionMatrix < AminoAcidCompound > getAminoAcidMatrix ( String file ) { if ( ! aminoAcidMatrices . containsKey ( file ) ) { aminoAcidMatrices . put ( file , new SimpleSubstitutionMatrix < AminoAcidCompound > ( AminoAcidCompoundSet . getAminoAcidCompoundSet ( ) , getReader ( file ) , file ) ) ; } return aminoAcidMatrices . get ( file ) ; }
reads in an amino acid substitution matrix if necessary