restrictionSites method

Map<String, List<Map<String, int>>> restrictionSites({ int minSiteLen = 4, int maxSiteLen = 8, })

Returns the restriction sites of this sequence.

Alter the length of the restriction sites by modifying minSiteLen and maxSiteLen.

Implementation

Map<String, List<Map<String, int>>> restrictionSites({
  int minSiteLen = 4,
  int maxSiteLen = 8,
}) {
  // Fetch a reverse complementary sequence to this sequence.
  String revComp = complementary(rev: true);

  // Fetch all possible combinations of this sequence.
  List<String> origSeqCombos = combinations();

  // Fetch only the combinations whose length is equato to or between [minSiteLen] and [maxSiteLen].
  Iterable<String> seqIter =
      origSeqCombos.where((seq) => (seq.length >= minSiteLen) && (seq.length <= maxSiteLen));

  // Fecth only the unique combinations.
  List<String> restSeqs = seqIter.toSet().toList();

  Map<String, List<Map<String, int>>> restSiteSeqs = {};
  List<Map<String, int>> restSiteLocations = [];

  // Loop through each combination.
  for (String restSeq in restSeqs) {
    restSiteLocations = [];
    RegExp regRestExp = RegExp(restSeq);
    // Find all matches between the combination and the reverse complementary sequence.
    Iterable<RegExpMatch> matches = regRestExp.allMatches(revComp);
    // Loop through each match.
    for (RegExpMatch match in matches) {
      int startIdx = this.seq.length - (restSeq.length + match.start);
      int endIdx = startIdx + restSeq.length;
      // Detect palindrome.
      // Check if the sub-sequence matches the current combination.
      if (this.seq.substring(startIdx, endIdx) == restSeq) {
        restSiteLocations.add({kStartIndex: startIdx, kEndIndex: endIdx});
        restSiteSeqs[restSeq] = restSiteLocations;
      }
      ;
    }
  }
  return restSiteSeqs;
}