+ if (isNa != smtrx.isDNA())
+ {
+ throw new InvalidSequenceTypeException(
+ "matrix " + smtrx.getClass().getCanonicalName()
+ + " is not a valid matrix for "
+ + (isNa ? "nucleotide" : "protein") + "sequences");
+ }
+ matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex, smtrx.getMatrix());