code: 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);
  	}
docs: reads in a nucleotide substitution matrix, if necessary