tandemRepeat static method

List<List<int>> tandemRepeat(FastaRecord record, int unitLen, int minRepeat)

(en) Search for tandem repeats (short sequence repeats).

(ja) タンデムリピート（短い配列の反復）を検索します。

• seq : Sequence data.
• unitLen : The length of the arrays that make up the repeats.
• minRepeat : Specifies the minimum number of iterations to find. Value must be 2 or greater.

Returns : [repeatStartPosition, repeatEndPosition,...]

Implementation

static List<List<int>> tandemRepeat(
    FastaRecord record, int unitLen, int minRepeat) {
  List<List<int>> r = [];
  late String pattern;
  for (int i = 0; i <= record.length() - unitLen * minRepeat; i++) {
    pattern = record.seq.substring(i, i + unitLen);
    int repeatCount = 0;
    for (int j = 1; j * unitLen + i <= record.length() - unitLen; j++) {
      if (record.seq.substring(i + j * unitLen, i + (j + 1) * unitLen) ==
          pattern) {
        repeatCount++;
      } else {
        break;
      }
    }
    if (repeatCount >= minRepeat - 1) {
      r.add([i, i + unitLen * (repeatCount + 1)]);
    }
  }
  return r;
}