public String addError(
String str, double insertionRate, double deletionRate, double substitutionRate) {
if (insertionRate < 0.0 || deletionRate < 0.0 || substitutionRate < 0.0)
throw new MhapRuntimeException("Error rate cannot be negative.");
if (insertionRate + deletionRate + substitutionRate > 1.00001)
throw new MhapRuntimeException("Error rate must be less than or equal to 1.0.");
double errorRate = insertionRate + deletionRate + substitutionRate;
// use a linked list for insertions
LinkedList<Character> modifiedSequence = new LinkedList<>();
for (char a : str.toCharArray()) modifiedSequence.add(a);
// now mutate
ListIterator<Character> iter = modifiedSequence.listIterator();
while (iter.hasNext()) {
char i = iter.next();
if (randGenerator.nextDouble() < errorRate) {
double errorType = randGenerator.nextDouble();
if (errorType < substitutionRate) { // mismatch
// switch base
iter.set(getRandomBase(i));
i++;
} else if (errorType < insertionRate + substitutionRate) { // insert
iter.previous();
iter.add(getRandomBase(null));
} else { // delete
iter.remove();
}
} else {
// i++;
}
}
StringBuilder returnedString = new StringBuilder(modifiedSequence.size());
for (char c : modifiedSequence) returnedString.append(c);
return returnedString.toString();
}
/**
* Generate a random value from this distribution.
*
* @param rng random number generator
* @return random value from this distribution
*/
public double generate(MersenneTwisterFast rng) {
try {
return gammaDist.inverseCumulativeProbability(rng.nextDouble());
} catch (MathException e) {
System.out.println(e.getMessage());
e.printStackTrace();
System.exit(-1);
}
return -1d;
}