code: 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);
  	}
docs: reads in an amino acid substitution matrix, if necessary