DNA Mutation doesn't handle unknown bases

[Paucey]

From what I understand, DNA Strings will sometimes have "n" in them, to indicate an unknown base. The way DNA Mutation is set up, currently, it doesn't recognize "n" as a possible base, so if it is encountered during the mutation process, it will likely throw an error. There are two options, I think, for how to handle this, and they're both simple to implement:

1. If encountered during mutation, an unknown base will be kept unknown. They wouldn't be considered when looking at what bases to mutate, or,

2. If encountered during mutation, a "n" base will be treated like any other base, and changed to one of the known bases.

For option 1, it could just be a matter of filtering out "n" or "N" when producing the available mutatable positions within the original dnaString:

List<Integer> availablePositions = new ArrayList<>();
for (int i = 0; i < dnaString.length(); i++) {
  char base = dnaString.charAt(i);
  if (base == 'n' || base == 'N') {
    continue; // Skip
  }
  availablePositions.add(i);
}

For option 2, I think it would just be a matter of adding a little filter to the beginning of the getDifferentBase() method to catch them:

if (originalBase == 'n' || originalBase == 'N') { // Unknown base in original DNA sequence
      return BASES[random.nextInt(BASES.length)]; // Randomly choose any known base
}

Which do you think would be the better approach? @VerisimilitudeX

[VerisimilitudeX]

Option 1 sounds good! It’s critical that the N stays there. We can use imputation to determine its value later.