/*
# Copyright (C) 2005 Andrew E Firth, University of Otago, Dunedin, 
# New Zealand, aef(at)sanger.otago.ac.nz
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License (version 2) as
# published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA.
*/

// Programming for making running means of columns 4 and 5 in input logfile.
// Command line input: file name and halfwindow size n (window is 2n + 1).
// Leaves columns 1, 2 and 3 unchanged.  
// Assumes input file is in nucleotide order.
// To skip gaps (etc) just miss those nucleotides out of the input file.

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

int main(int argc, char* argv[])
{
  if (4 != argc) {
    cerr << "Aborting; use '" << argv[0] 
	 << " logfile window_half_size circular'.\n";
    exit(EXIT_FAILURE);
  }

  int verbose = 0;

  int j, k, nlines, col1[maxlength], col2[maxlength], col3[maxlength];
  int n, hfw, circular;
  double col4[maxlength], col5[maxlength], sum1, sum2;

  hfw = atoi(argv[2]);
  circular = atoi(argv[3]);

  // Initialize arrays
  for (k = 0; k < maxlength; ++k) {
    col1[k] = col2[k] = col3[k] = 0;
    col4[k] = col5[k] = 0.;
  }

  // Open log file.
  ifstream logfile(argv[1]); 
  if (!logfile) {
    cerr << "Aborting: can't find log file '" << argv[1] << "'.\n";
    exit(EXIT_FAILURE);
  }

  // Number of lines in log file
  nlines = -1;
  while (logfile.ignore(1000, '\n')) {
    ++nlines;
  }
  logfile.clear();
  logfile.seekg(0);
  if (verbose) {
    cout << "There are " << nlines << " data lines.\n\n";
  }

  // Read in logfile
  for (k = 0; k < nlines; ++k) {
    logfile >> col1[k];
    logfile >> col2[k];
    logfile >> col3[k];
    logfile >> col4[k];
    logfile >> col5[k];
    logfile.ignore(1000, '\n');
  }

  // Running mean
  for (k = 0; k < nlines; ++k) {
    sum1 = sum2 = 0.;
    n = 0;
    for (j = k - hfw; j <= k + hfw; ++j) { 
      if (!circular && j >= 0 && j < nlines || circular) {
	sum1 += col4[(j+nlines)%nlines];
	sum2 += col5[(j+nlines)%nlines];
	n += 1;
      }
    }
    if (0 != n) {
      cout << col1[k] << " " << col2[k] << " " << col3[k] << " " 
	   << sum1/float(n) << " " << sum2/float(n) 
	   << "\n";
    } else {
      cout << col1[k] << " " << col2[k] << " " << col3[k] << " " 
	   << 0 << " " << 0 << "\n";
    }
  }

}