// This software is Copyright (C) 2005 by Andrew Firth, University of Otago, 
// Dunedin, New Zealand. All rights reserved.

// Whereas ntadjust.cxx adjusts coords in the ungapped sequence to coords in
//   the gapped sequence, this programme adjusts coords in the gapped sequence 
//   to coords in the ungapped sequence.

#include <iostream>
#include <cmath>
#include <fstream>
#include <cstdlib>
#include <iomanip>
#include <cstring>
using namespace std;
#define maxlength 50000

int main(int argc, char* argv[])
{

  int i, nlines, seq1g[maxlength], nseq1, count;
  char name[1000], inputseq1[maxlength], seqline[1000];
  int orf1g = atoi(argv[2]);

  if (3 != argc) {
    cerr << "Usage '" << argv[0] << " gapped_sequence coordinate'.\n";
    exit(EXIT_FAILURE);
  }

  // Initialize arrays.
  for (i = 0; i < maxlength; ++i) {
    seq1g[i] = 9;
  }

  // Read initial sequence files.  ('U' or 'T' = 0, 'C' = 1, 'A' = 2, 'G' = 3, 
  // unfilled part of array = 9, gaps ('-' and '.') = 8.  utcga also accepted.
  // Also accepts standard ambiguous nt codes.  Aborts if any other characters.
  ifstream sequence1(argv[1]);
  if (!sequence1) {
    cerr << "Aborting: can't find file '" << argv[1] << "'.\n";
    exit(EXIT_FAILURE);
  }
  nlines = 0;
  while (sequence1.ignore(1000, '\n')) { ++nlines; }
  sequence1.clear(); sequence1.seekg(0);
  sequence1.getline(name, 1000, '\n');
  for (i = 0; i < nlines - 1; ++i) {
    sequence1.getline(seqline, 1000, '\n');
    if (0 == i) { strcpy(inputseq1, seqline); } 
    else { strcat(inputseq1, seqline); }
  }
  sequence1.close();
  for (i = 0; ; ++i) {
    if (inputseq1[i] == 'U' || inputseq1[i] == 'u') { seq1g[i] = 0; }
    else if (inputseq1[i] == 'T' || inputseq1[i] == 't') { seq1g[i] = 0; }
    else if (inputseq1[i] == 'C' || inputseq1[i] == 'c') { seq1g[i] = 1; }
    else if (inputseq1[i] == 'A' || inputseq1[i] == 'a') { seq1g[i] = 2; }
    else if (inputseq1[i] == 'G' || inputseq1[i] == 'g') { seq1g[i] = 3; }
    else if (inputseq1[i] == '.' || inputseq1[i] == '-') { seq1g[i] = 8; }
    else if (inputseq1[i] == 'M' || inputseq1[i] == 'm' ||
	     inputseq1[i] == 'R' || inputseq1[i] == 'r' ||
	     inputseq1[i] == 'W' || inputseq1[i] == 'w' ||
	     inputseq1[i] == 'V' || inputseq1[i] == 'v' ||
	     inputseq1[i] == 'H' || inputseq1[i] == 'h' ||
	     inputseq1[i] == 'D' || inputseq1[i] == 'd' ||
	     inputseq1[i] == 'B' || inputseq1[i] == 'b' ||
	     inputseq1[i] == 'S' || inputseq1[i] == 's' ||
	     inputseq1[i] == 'Y' || inputseq1[i] == 'y' ||
	     inputseq1[i] == 'K' || inputseq1[i] == 'k' ||
	     inputseq1[i] == 'N' || inputseq1[i] == 'n' ||
	     inputseq1[i] == 'X' || inputseq1[i] == 'x') { seq1g[i] = 5; }
    else if (inputseq1[i] == '\0') { nseq1 = i; break; } 
    else {
      cerr << "\nAborting: unknown nucleotide '" << inputseq1[i] 
	   << "' at position " << i << " in original sequence.\n";
      exit(EXIT_FAILURE);
    }
  }
  
  //Adjust orf1g for introduced gaps.
  count = 0;    //Counts number of gaps up to orf1g
  orf1g -= 1;   //Since C++ starts arrays from 0
  for (i = 0; i <= orf1g; ++i) {
    if (seq1g[i] > 6) {
      count++;
    }
  }
  orf1g += 1;   //Since C++ starts arrays from 0
  orf1g -= count;


  cout << orf1g << "\n";
  
}