getPositions static method

List<int> getPositions(NucleotideSequence seq, NucleotideSequence target, bool compareOnlyBase, { bool fuzzyComp = false, })

(en) Returns a list of the indices of the beginning of the pattern where the specified pattern occurs.

(ja) 指定したパターンが出現する、パターンの先頭のインデックスをリストで返します。

• seq : The sequence data.
• target : The target pattern.
• compareOnlyBase : If true, compare only Nucleotide.base. If false, compare also Nucleotide.infoKey.
• fuzzyComp : If true, Can contain m, r, w, s, y, k, v, h, d, b, n. If true, t and u are searched as the same.

Implementation

static List<int> getPositions(
    NucleotideSequence seq, NucleotideSequence target, bool compareOnlyBase,
    {bool fuzzyComp = false}) {
  List<int> r = [];
  for (int i = 0; i <= seq.length() - target.length(); i++) {
    if (compareOnlyBase) {
      if (UtilCompareNucleotide.compareBase(
          seq.subSeqNonInfo(i, i + target.length()), target, fuzzyComp)) {
        r.add(i);
      }
    } else {
      if (UtilCompareNucleotide.compare(
          seq.subSeq(i, i + target.length()), target, fuzzyComp)) {
        r.add(i);
      }
    }
  }
  return r;
}