3.6.3 Sequence Alignment (Needleman-Wunsch)

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/*

Given two strings, determine their minimum-cost alignment. An alignment of two strings is a
transformation of both strings by inserting gap characters `_` in some way to make the final lengths
equal. The total cost of an alignment given a `gap_cost` (insertion or deletion cost) and a
`sub_cost` (substitution, i.e. mismatch cost) is `gap_cost` times the number of inserted gaps, plus
`sub_cost` times the number of indices at which the two aligned strings differ.

- `align_sequences(s1, s2, gap_cost, sub_cost)` returns a pair of aligned strings for strings `s1`
  and `s2`, using a classic dynamic programming approach. This implementation first computes
  `dp[i][j]` (the cost of aligning the length $i$ prefix of `s1` with the length $j$ prefix of `s2`)
  before following the path backwards to construct the answer. For `gap_cost = sub_cost = 1`,
  `dp[n][m]` will be the Levenshtein edit distance, where $n$ and $m$ are the lengths of `s1` and
  `s2`, respectively.
- `hirschberg_align_sequences(s1, s2, gap_cost, sub_cost)` returns the sequence alignment of strings
  `s1` and `s2` using the more memory efficient Hirschberg's algorithm.

Time Complexity:
- O(n*m) per call to `align_sequences(s1, s2)` as well as `hirschberg_align_sequences(s1, s2)`,
  where $n$ and $m$ are the lengths of `s1` and `s2`, respectively.

Space Complexity:
- O(n*m) auxiliary heap space for `align_sequences(s1, s2)`, where $n$ and $m$ are the lengths of
  `s1` and `s2`, respectively.
- O(log(max(n, m))) auxiliary stack space and O(min(n, m)) auxiliary heap space for
  `hirschberg_align_sequences(s1, s2)`, where $n$ and $m$ are the lengths of `s1` and `s2`,
  respectively.

*/

#include <algorithm>
#include <string>
#include <utility>
#include <vector>
using std::string;

std::pair<string, string> align_sequences(
    const string &s1, const string &s2, int gap_cost = 1, int sub_cost = 1
) {
  int n = static_cast<int>(s1.size()), m = static_cast<int>(s2.size());
  std::vector<std::vector<int>> dp(n + 1, std::vector<int>(m + 1, 0));
  for (int i = 0; i <= n; i++) {
    dp[i][0] = i * gap_cost;
  }
  for (int j = 0; j <= m; j++) {
    dp[0][j] = j * gap_cost;
  }
  for (int i = 1; i <= n; i++) {
    for (int j = 1; j <= m; j++) {
      dp[i][j] = (s1[i - 1] == s2[j - 1]) ? dp[i - 1][j - 1]
                                          : std::min(
                                                dp[i - 1][j - 1] + sub_cost,
                                                std::min(dp[i - 1][j], dp[i][j - 1]) + gap_cost
                                            );
    }
  }
  string res1, res2;
  int i = n, j = m;
  while (i > 0 && j > 0) {
    if (s1[i - 1] == s2[j - 1] || dp[i][j] == dp[i - 1][j - 1] + sub_cost) {
      res1 += s1[--i];
      res2 += s2[--j];
    } else if (dp[i][j] == dp[i - 1][j] + gap_cost) {
      res1 += s1[--i];
      res2 += '_';
    } else if (dp[i][j] == dp[i][j - 1] + gap_cost) {
      res1 += '_';
      res2 += s2[--j];
    }
  }
  while (i > 0 || j > 0) {
    res1 += (i > 0) ? s1[--i] : '_';
    res2 += (j > 0) ? s2[--j] : '_';
  }
  std::reverse(res1.begin(), res1.end());
  std::reverse(res2.begin(), res2.end());
  return {res1, res2};
}

template<class It>
std::vector<int> row_cost(It lo1, It hi1, It lo2, It hi2, int gap_cost, int sub_cost) {
  std::vector<int> res(std::distance(lo2, hi2) + 1), prev(res);
  for (It it1 = lo1; it1 != hi1; ++it1) {
    res.swap(prev);
    int i = 0;
    for (It it2 = lo2; it2 != hi2; ++it2) {
      res[i + 1] = (*it1 == *it2) ? prev[i] : std::min(prev[i] + sub_cost, res[i] + gap_cost);
      i++;
    }
  }
  return res;
}

template<class It>
void hirschberg_rec(
    It lo1, It hi1, It lo2, It hi2, string *res1, string *res2, int gap_cost, int sub_cost
) {
  if (lo1 == hi1) {
    for (It it2 = lo2; it2 != hi2; ++it2) {
      *res1 += '_';
      *res2 += *it2;
    }
    return;
  }
  if (lo1 + 1 == hi1) {
    It pos = std::find(lo2, hi2, *lo1);
    bool insert = (pos == hi2) && (gap_cost * (hi2 - lo2 + 1) < sub_cost);
    if (lo2 == hi2 || insert) {
      *res1 += *lo1;
      *res2 += '_';
    }
    for (It it2 = lo2; it2 != hi2; ++it2) {
      *res1 += (pos == it2 || (!insert && it2 == lo2)) ? *lo1 : '_';
      *res2 += *it2;
    }
    return;
  }
  It mid1 = lo1 + (hi1 - lo1) / 2;
  std::reverse_iterator<It> rlo1(hi1), rmid1(mid1), rlo2(hi2), rhi2(lo2);
  std::vector<int> fwd = row_cost(lo1, mid1, lo2, hi2, gap_cost, sub_cost);
  std::vector<int> rev = row_cost(rlo1, rmid1, rlo2, rhi2, gap_cost, sub_cost);
  It mid2 = lo2;
  int mincost = -1;
  for (int i = 0, j = static_cast<int>(rev.size()) - 1; i < static_cast<int>(fwd.size());
       i++, j--) {
    if (mincost < 0 || fwd[i] + rev[j] < mincost) {
      mincost = fwd[i] + rev[j];
      mid2 = lo2 + i;
    }
  }
  hirschberg_rec(lo1, mid1, lo2, mid2, res1, res2, gap_cost, sub_cost);
  hirschberg_rec(mid1, hi1, mid2, hi2, res1, res2, gap_cost, sub_cost);
}

std::pair<string, string> hirschberg_align_sequences(
    const string &s1, const string &s2, int gap_cost = 1, int sub_cost = 1
) {
  if (s1.size() < s2.size()) {
    return hirschberg_align_sequences(s2, s1, gap_cost, sub_cost);
  }
  string res1, res2;
  hirschberg_rec(s1.begin(), s1.end(), s2.begin(), s2.end(), &res1, &res2, gap_cost, sub_cost);
  return {res1, res2};
}

/*** Example Usage ***/

#include <cassert>

int main() {
  assert(
      align_sequences("AGGGCT", "AGGCA", 2, 3) == (std::pair<string, string>{"AGGGCT", "A_GGCA"})
  );
  assert(
      hirschberg_align_sequences("AGGGCT", "AGGCA", 2, 3) ==
      (std::pair<string, string>{"AGGGCT", "A_GGCA"})
  );
  return 0;
}