/*
# 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.
*/

#include <iostream>
#include <cmath>
#include <fstream>
#include <cstdlib>
#include <iomanip>
#include <cstring>
using namespace std;
#define maxlength 35000
#define maxnseqs 201
#define maxpairs 200

// Function declarations.
double calc_prob_col(double weight[][64], double nuc[][4], 
		     int sequences[][maxnseqs], int base0[3], 
		     int codonpos[][2], int seqid0[2], int model, 
		     int expnmuts, int aa2aa[64], double Vfix);
int readsequence(char seq[128], int gsequences[][maxnseqs], int seqid);
int readorfs(char cpos[128], int codonpos[][2], int length, int circular,
	     int posid);
int checkgaps(int lookup[][maxnseqs], int codonpos[][2], int nseq0, int seqid,
	      int pos);
int test_stop(double weight[][64], int sequences[][maxnseqs], int base0[3], 
	      int codonpos[][2], int seqid0[2], int pos);
int stopcodon(int aa2aa[64], int sequences[][maxnseqs], int base0[2], 
	      int codonpos[][2], int seqid, int pos);
int calc_nuc(double nuc[][4], double ttt, double nucB1[][4], double nucB2[][4],
	     double nucD[][4]);

int main(int argc, char* argv[])
{
  if (2 != argc) {
    cerr << "Aborting: need setup file; use '" << argv[0] << " setupfile'.\n";
    exit(EXIT_FAILURE);
  }

  //---------------------------------------------------------------------------
  // Variable declarations.

  int i, j, k, lines, nseq, nseqs, nseq0, temp95, temp98, temp99; 
  int aa2aa[64], j1[2], j2[2], j3[2], jcid[2], seqid, seqid0[2], basex[2];
  int maxiter, niter, wholeseq, range1, range2, tttobs, model, circular;
  int base1, base2, base, base0[3], gsequences[maxlength+10][maxnseqs];
  int sequences[maxlength+10][maxnseqs], codonpos[maxlength+10][2], pos2[7][7];
  int lookup[maxlength+10][maxnseqs], degnseq[maxnseqs], N0NsNnsum, npairs, np;
  int ntotal[maxnseqs], nmuts[maxnseqs], nmuts2[maxnseqs], norfs, test;
  int nuccount[maxnseqs], stopcount[maxnseqs][2], gapcount[maxnseqs];
  int N0synnon[3][maxnseqs], N123[3][maxnseqs][2], flag[maxnseqs][2];
  int ntree[maxlength+10];
  double score[20][20], weight[64][64], codon[64],  nucB1[4][4], nucB2[4][4];
  double nucA[4][4], nucD[4][4], nuc[4][4], nuc0[4][4], nuc1[4][4];
  double testA[4][4], tempA[4][4], epsilon, logepsilon, temp96, temp97;
  double ttt, tttmin, tttmax, tttfit, fitmuts, expmuts, lambda, lambdasum;
  double ettt[2], enmuts[2], emtx[2][maxnseqs], tttx[2][maxnseqs], Vfix;
  double N123r[3][maxnseqs], N0NsNn[3][maxnseqs], treesum[maxlength+10][3];
  char aa[20], aa2codon[64], seq[128], temp, temp2[128];

  int verbose = 0;

  tttmin = 0.0;    // pairwise sequence divergence fitting params
  tttmax = 10.0;   //    "        "         "         "      "
  tttfit = 0.01;   //    "        "         "         "      "
  maxiter = 40;    //    "        "         "         "      "
  tttobs = 1;      // use observed number of mutations
  lambda = 0;      // only used if tttobs = 0
  Vfix = 1.;       // nonsynonymous:synonymous scaling
  epsilon = 0.001; // writes log of all mut probs < epsilon

  if (verbose) {
    cout << "\n";
  }

  for (i = 0; i < maxlength+10; ++i) {
    treesum[i][0] = treesum[i][1] = treesum[i][2] = 0.;
    ntree[i] = 0;
  }
  lambdasum = 0.;

  //---------------------------------------------------------------------------
  // Setup parameters.

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

  // Read in setup parameters.
  setupfile >> wholeseq;
  if (0 == wholeseq || 2 == wholeseq) {
    setupfile >> range1;
    setupfile >> range2;
  }
  setupfile.ignore(1000, '\n');
  setupfile >> circular;
  setupfile.ignore(1000, '\n');
  setupfile.close();

  //---------------------------------------------------------------------------
  // Amino acid, nucleotide and codon weight matrices.

  // Number of lines in 20 x 20 amino acid weight matrix.
  ifstream matrixfile("aa.dat");
  if (!matrixfile) {
    cerr << "Aborting: can't find file 'aa.dat'.\n";
    exit(EXIT_FAILURE);
  }
  lines = 0;
  while (matrixfile.ignore(1000, '\n')) {
    ++lines;
  }
  matrixfile.clear();
  matrixfile.seekg(0);
  
  // Read amino acid weight matrix.
  temp = '#';
  while ('#' == temp) {
    matrixfile.get(temp);
    if ('#' == temp) {
      matrixfile.ignore(1000, '\n');
    }
  }
  for (j = 0; j < 20; ++j) {
    matrixfile >> aa[j];
  }
  matrixfile.ignore(1000, '\n');
  for (i = 0; i < 20; ++i) { 
    for (j = 0; j <= i; ++j) {
      matrixfile >> score[i][j];
    }
    matrixfile.ignore(1000, '\n');
  }
  matrixfile.close();  
  
  // Fill in other half of weight matrix.
  for (i = 0; i < 20; ++i) { 
    for (j = i + 1; j < 20; ++j) {
      score[i][j] = score[j][i];
    }
  }
  
  // Check no values greater than corresponding values on the diagonal.
  for (i = 0; i < 20; ++i) {
    for (k = 0; k < 20; ++k) {
      if (score[i][k] > score[i][i] || score[i][k] > score[k][k]) {
	cerr << "Aborting: scoring matrix value at " << i+1 << ", " << k+1 
	     << " is greater than value on diagonal.\n";
	exit(EXIT_FAILURE);
      }
    }
  }

  // Check no negative values.
  for (i = 0; i < 20; ++i) {
    for (k = 0; k < 20; ++k) {
      if (score[i][k] < 0.) {
	cerr << "Aborting: scoring matrix value at " << i+1 << ", " << k+1 
	     << " is negative.\n";
	exit(EXIT_FAILURE);
      }
    }
  }

  // Read codon to amino acid table.
  ifstream aa2codonfile("aa2codon.dat");
  if (!aa2codonfile) {
    cerr << "Aborting: can't find file 'aa2codon.dat'.\n";
    exit(EXIT_FAILURE);
  }
  for (i = 0; i < 64; ++i) {
    aa2codonfile.get(aa2codon[i]);
    aa2codonfile.ignore(1000, '\n');
  }
  aa2codonfile.close();
  
  // Lookup table connecting aa2codon[64] and aa[20] (aa[20] is the 
  //  order in  which the amino acids appear in the weight matrix).
  for (i = 0; i < 64; ++i) {
    aa2aa[i] = 99;                            // for STOP codons
    for (j = 0; j < 20; ++j) {
      if (aa2codon[i] == aa[j]) {
	aa2aa[i] = j;
      }
    }
  }
  
  // Paste weights into 64 x 64 matrix; set stop codons = 1, 0.  Weight 
  //   is for row i -> column j.
  for (i = 0; i < 64; ++i) {
    for (j = 0; j < 64; ++j) {
      if (99 == aa2aa[i] && 99 == aa2aa[j]) {
	weight[i][j] = 1.;
      } else if (99 == aa2aa[i]) {
	weight[i][j] = 0.;
      } else if (99 == aa2aa[j]) {
	weight[i][j] = 0.;
      } else {
	weight[i][j] = score[aa2aa[i]][aa2aa[j]];
      }
    }
  }

  // Read 4 x 4 diagonalized nucleotide mutation matrix. Order is UCAG; 
  //  row i -> column k.  Four matrices in input file: A, B, D, B^{-1}, where
  //  A = B.D.B^{-1} and D is diagonal.  A itself isn't actually used.
  ifstream nucfile("nuc.dat");
  if (!nucfile) {
    cerr << "Aborting: can't find file 'nuc.dat'.\n";
    exit(EXIT_FAILURE);
  }
  for (i = 0; i < 4; ++i) {
    for (k = 0; k < 4; ++k) {
      nucfile >> nucA[i][k];
    }
    nucfile.ignore(1000, '\n');
  }
  nucfile.ignore(1000, '\n');
  for (i = 0; i < 4; ++i) {
    for (k = 0; k < 4; ++k) {
      nucfile >> nucB1[i][k];
    }
    nucfile.ignore(1000, '\n');
  }
  nucfile.ignore(1000, '\n');
  for (i = 0; i < 4; ++i) {
    for (k = 0; k < 4; ++k) {
      nucfile >> nucD[i][k];
    }
    nucfile.ignore(1000, '\n');
  }
  nucfile.ignore(1000, '\n');
  for (i = 0; i < 4; ++i) {
    for (k = 0; k < 4; ++k) {
      nucfile >> nucB2[i][k];
    }
    nucfile.ignore(1000, '\n');
  }
  nucfile.ignore(1000, '\n');
  nucfile.close();

  // Check B.D.B{^-1}.
  for (i = 0; i < 4; ++i) {
    for (j = 0; j < 4; ++j) {
      tempA[i][j] = nucB1[i][j]*nucD[j][j];
    }
  }
  for (i = 0; i < 4; ++i) {
    for (j = 0; j < 4; ++j) {
      testA[i][j] = 0.;
      for (k = 0; k < 4; ++k) {
	testA[i][j] += tempA[i][k]*nucB2[k][j];
      }
    }
  }
  if (verbose) {
    cout << "Product B D B^{-1}\n";
    for (i = 0; i < 4; ++i) {
      cout << "   ";
      for (j = 0; j < 4; ++j) {
	cout << testA[i][j] << " ";
      }
      cout << "\n";
    }
    cout << "\n";
  }
  for (i = 0; i < 4; ++i) {
    for (k = 0; k < 4; ++k) {
      if (i == k) {
	if (testA[i][k] > 0.) {
	  cerr << "Aborting: nucleotide matrix value at " << i+1 << ", " 
	       << k+1 << " is positive.\n";
	  exit(EXIT_FAILURE);
	}
      } else {
	if (testA[i][k] < 0.) {
	  cerr << "Aborting: nucleotide matrix value at " << i+1 << ", " 
	       << k+1 << " is negative.\n";
	  exit(EXIT_FAILURE);
	}
      }
    }
  }

  // Read codon usage table (scaling unimportant; set all values equal if you
  //   don't want to use codon usage weights).
  ifstream codonfile("codon.dat");
  if (!codonfile) {
    cerr << "Aborting: can't find file 'codon.dat'.\n";
    exit(EXIT_FAILURE);
  }
  for (i = 0; i < 64; ++i) {
    codonfile.getline(temp2, 128, ' ');
    codonfile >> codon[i];
    codonfile.ignore(1000, '\n');
  }
  codonfile.close();
  for (i = 0; i < 64; ++i) {
    if (codon[i] < 0.) {
      cerr << "Aborting: codon usage table value at " << i+1 
	   << " is negative.\n";
      exit(EXIT_FAILURE);
    }
  }

  // Apply codon usage weighting.
  for (i = 0; i < 64; ++i) {
    for (j = 0; j < 64; ++j) {
      weight[i][j] *= codon[j];
    }
  }

  //---------------------------------------------------------------------------
  // Miscellaneous stuff.

  // Fitting parameters for ttt (evolutionary time).
  if (tttmin < 0.) {
    tttmin = 0.;
  }
  if (tttmax < tttmin) {
    tttmax = tttmin;
  }
  if (tttfit <= 0 || tttfit > 1.) {
    tttfit = 1.;
  }

  // Check epsilon.
  if (epsilon <= 0) {
    cerr << "\nRequire epsilon > 0.  Adjusting to 0.001.\n";
    epsilon = 0.001;
  }
  logepsilon = log(epsilon);

  // MLE/STOPs/gaps/glitches logfiles.
  ofstream logfile1("mlogd_out.MLElog");
  if (!logfile1) {
    cerr << "Failed to open log file 'mlogd_out.MLElog'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream logfile2("mlogd_out.stoplog");
  if (!logfile2) {
    cerr << "Failed to open log file 'mlogd_out.stoplog'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream logfile3("mlogd_out.gaplog");
  if (!logfile3) {
    cerr << "Failed to open log file 'mlogd_out.gaplog'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream logfile4("mlogd_out.glitches");
  if (!logfile4) {
    cerr << "Failed to open log file 'mlogd_out.glitches'.\n";
    exit(EXIT_FAILURE);
  }

  //---------------------------------------------------------------------------
  // Input sequences (msa - with gaps).  First sequence in seqs.dat is 
  //   reference sequence.

  // Number of sequences in sequences file.
  ifstream sequencesfile("seqs.dat");
  if (!sequencesfile) {
    cerr << "Aborting: can't find file 'seqs.dat'.\n";
    exit(EXIT_FAILURE);
  }
  nseqs = -1;
  while (sequencesfile.ignore(1000, '\n')) {
    ++nseqs;
  }
  sequencesfile.clear();
  sequencesfile.seekg(0);
  if (nseqs > maxnseqs) {
    cerr << "Aborting: too many sequence in file 'seqs.dat'.\n"
	 << "Maximum is " << maxnseqs << "\n";
    exit(EXIT_FAILURE);
  }

  // Read sequences.
  for (seqid = 0; seqid < nseqs; ++seqid) {
    sequencesfile.getline(seq, 128, '\n');
    nseq = readsequence(seq, gsequences, seqid);
    if (verbose) {
      cout << "Read " << seq << ", length = " << nseq << ".\n";
    }
    if (0 == seqid) {
      nseq0 = nseq;
    } else if (nseq != nseq0) {
      cerr << "Aborting: gapped sequences of differing length.\n";
      exit(EXIT_FAILURE);
    }
  }
  sequencesfile.close();

  // Degap sequences and make lookup table connecting input alignment 
  //   sequence coords to degapped coords.
  for (seqid = 0; seqid < nseqs; ++seqid) {
    degnseq[seqid] = 0;                      // degapped sequence lengths
    for (i = 0; i < nseq0; ++i) {
      if (9 != gsequences[i][seqid]) {       // not a gap
	sequences[degnseq[seqid]][seqid] = gsequences[i][seqid];
	lookup[i][seqid] = degnseq[seqid];
	++degnseq[seqid];
      } else {
	lookup[i][seqid] = -1;               // gap
      }
    }
    if (verbose) {
      cout << "Degapped sequence " << seqid << "; length = " << degnseq[seqid] 
	   << ".\n";
    }
  }

  //---------------------------------------------------------------------------
  // Codon position files (for degapped reference sequence).  For each 
  //   nucleotide position: 0 = non-coding; 1/2/3 = 1st/2nd/3rd positions in 
  //   a forward read direction codon; 4/5/6 = 1st/2nd/3rd positions in a 
  //   reverse (complementary strand) read direction codon.  codonpos[][0] 
  //   gives null model.  codonpos[][1] gives alternative model.  
  //   codonpos[][0] + codonpos[][1] may be non-coding, single-coding (in
  //   null or alternative), double-coding or a mixture, depending on sequence 
  //   position.  Programme calculates the likelihood ratio of null to 
  //   alternative model.
  norfs = readorfs("orfs.1", codonpos, degnseq[0], circular, 0);
  if (verbose) {
    cout << "Read 'orfs.1', containing " << norfs << " ORFs.\n";
  }
  norfs = readorfs("orfs.2", codonpos, degnseq[0], circular, 1);
  if (verbose) {
    cout << "Read 'orfs.2', containing " << norfs << " ORFs.\n";
  }

  //---------------------------------------------------------------------------
  // Find range boundaries (in degapped reference sequence).
  if (0 == wholeseq || 2 == wholeseq) {
    range1 -= 1; range2 -= 1; // since indices start at 0
    if (range1 > range2) {    // make range1 < range2
      temp95 = range1;
      range1 = range2;
      range2 = temp95;
    }
    if (range2 > degnseq[0] - 1) {
      range2 = degnseq[0] - 1;
    }
    if (range1 < 0) {
      range1 = 0;
    }
  } else {                    // whole sequence
    range1 = 0;
    range2 = degnseq[0] - 1;
  }

  // Find corresponding boundaries in alignment coords
  if (0 == wholeseq || 2 == wholeseq) {
    for (base = 0; base < nseq0; ++base) {
      if (lookup[base][0] == range1) {  // base in degapped refseq or -1 if gap
	base1 = base;  // note if whole refseq, still removes leading gaps
      }
      if (lookup[base][0] == range2) {  // base in degapped refseq or -1 if gap
	base2 = base;  // note if whole refseq, still removes leading gaps
      }
    }
  } else {                    // whole sequence
    base1 = 0;
    base2 = nseq0 - 1;
  }

  //---------------------------------------------------------------------------

  // Check for gaps not in groups of 3 in coding sequences
  // Note - have to do this before changing ambiguous nt to -1.
  for (seqid = 0; seqid < nseqs; ++seqid) {
    test = checkgaps(lookup, codonpos, nseq0, seqid, 0);
  }
  for (seqid = 0; seqid < nseqs; ++seqid) {
    test = checkgaps(lookup, codonpos, nseq0, seqid, 1);
  }

  // Change lookup[][] entries for ambiguous nt to -1.
  for (seqid = 0; seqid < nseqs; ++seqid) {
    for (i = 0; i < nseq0; ++i) {
      if (5 == sequences[lookup[i][seqid]][seqid]) {
	lookup[i][seqid] = -1;  // ambiguous nt
      }
    }
  }

  //---------------------------------------------------------------------------
  //If (circular), then shift data in sequences[][seqid] and codonpos[][2]
  //  by +2.  Append the last two nt to the beginning and the first 2 nt to
  //  the end.  Then correct lookup[][seqid] by adding +2 to each entry (except
  //  for '-1's).  Note that base1, base2, lookup[][seqid] are in msa coords, 
  //  which are unchanged; range1 and range2 are in refseq coords; hereafter 
  //  they are used just for pos2 calculation; therefore need to adjust.
  //  not used again so are left as they are.  It is impossible for 
  //  lookup[][seqid] to reference the 4 nt added to each sequence in 
  //  sequences[][seqid].  They are only there to be used as neighbouring nt in
  //  codons in the subroutines test_stop and calc_prob_col.

  //If (!circular), if the first nt of seq_i is aligned to a N2 or N3 nt in 
  //  refseq, or the last nt of seq_i is aligned to a N1 or N2 nt in 
  //  refseq, then you may end up references out-of-bounds in
  //  sequences[][seqid].  Avoid this by padding all seqs with 2 nt at 
  //  either end.  For non-circular sequences, use 'N's - which will result
  //  in any codon incorporating them being skipped, but at least you don't 
  //  reference out-of-bounds.

  for (seqid = 0; seqid < nseqs; ++seqid) {     // update values in lookup[][]
    for (i = 0; i < nseq0; ++i) {
      if (-1 != lookup[i][seqid]) {
	lookup[i][seqid] += 2;
      }
    }
  }
  for (seqid = 0; seqid < nseqs; ++seqid) {     // shift sequences[][] by +2
    for (i = degnseq[seqid]+1; i >= 2; --i) {
      sequences[i][seqid] = sequences[i-2][seqid];
    }
    if (circular) {             // circularize
      sequences[1][seqid] = sequences[degnseq[seqid]+1][seqid];
      sequences[0][seqid] = sequences[degnseq[seqid]][seqid];
      sequences[degnseq[seqid]+3][seqid] = sequences[3][seqid] ;
      sequences[degnseq[seqid]+2][seqid] = sequences[2][seqid];
    } else {                    // pad ends with 'N's
      sequences[1][seqid] = sequences[0][seqid] 
	= sequences[degnseq[seqid]+3][seqid] 
	= sequences[degnseq[seqid]+2][seqid] = 5;
    }
  }
  for (k = 0; k < 2; ++k) {     // shift codonpos[][] by +2
    for (i = degnseq[0]+1; i >= 2; --i) {
      codonpos[i][k] = codonpos[i-2][k];
    }
    if (circular) {             // circularize
      codonpos[1][k] = codonpos[degnseq[0]+1][k];
      codonpos[0][k] = codonpos[degnseq[0]][k];
      codonpos[degnseq[0]+3][k] = codonpos[3][k] ;
      codonpos[degnseq[0]+2][k] = codonpos[2][k];
    } else {                    // pad ends with '0's
      codonpos[1][k] = codonpos[0][k] = codonpos[degnseq[0]+3][k] 
	= codonpos[degnseq[0]+2][k] = 0;
    }
  }
  range1 += 2;
  range2 += 2;

  //---------------------------------------------------------------------------
  // Write out logs of all stops in null and alternative model ORFs in each 
  //   sequence.  Also log of all gaps (and ambiguous nt).
  // Note that codons containing ambiguous nt are assumed not to be stops.

  ofstream posfile1("mlogd_out.stoppos1");
  if (!posfile1) {
    cerr << "Failed to open log file 'mlogd_out.stoppos1'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream posfile2("mlogd_out.stoppos2");
  if (!posfile2) {
    cerr << "Failed to open log file 'mlogd_out.stoppos2'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream posfile3("mlogd_out.gappos");
  if (!posfile3) {
    cerr << "Failed to open log file 'mlogd_out.gappos'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream posfile4("mlogd_out.startpos1");
  if (!posfile4) {
    cerr << "Failed to open log file 'mlogd_out.startpos1'.\n";
    exit(EXIT_FAILURE);
  }
  ofstream posfile5("mlogd_out.startpos2");
  if (!posfile5) {
    cerr << "Failed to open log file 'mlogd_out.startpos2'.\n";
    exit(EXIT_FAILURE);
  }
  for (seqid = 0; seqid < nseqs; ++seqid) { 
    for (base = 0; base < nseq0; ++base) {
      basex[0] = lookup[base][0];     // base in degapped reference sequence
      basex[1] = lookup[base][seqid]; // base in degapped sequence
      if (-1 != basex[1] && -1 != basex[0]) {  // not gapped or ambiguous nt
	// Note stops/starts that overlap a reference sequence gap will not 
	//   be annotated.
	temp98 = stopcodon(aa2aa, sequences, basex, codonpos, seqid, 0);
	temp99 = stopcodon(aa2aa, sequences, basex, codonpos, seqid, 1);
	if (0 == temp98) { 
	  posfile1 << seqid+1 << " " << base+1 << "\n";
	}
	if (0 == temp99) { 
	  posfile2 << seqid+1 << " " << base+1 << "\n";
	}
	if (4 == temp98) { 
	  posfile4 << seqid+1 << " " << base+1 << "\n";
	}
	if (4 == temp99) { 
	  posfile5 << seqid+1 << " " << base+1 << "\n";
	}
      } else {                  // gap or ambiguous nt
	if (-1 == basex[1]) {   // gap or ambiguous nt in the non-ref seq
	  posfile3 << seqid+1 << " " << base+1 << "\n";
	}
      }
    }
  }
  posfile1.close();
  posfile2.close();
  posfile3.close();
  posfile4.close();
  posfile5.close();

  //---------------------------------------------------------------------------
  // If using 'Only use nt within query CDS(s)', mask all nt that are not
  //   annotated as CDSs in the alternate model.
  if (2 == wholeseq) {
    for (base = 0; base < nseq0; ++base) {
      base0[2] = lookup[base][0];         // base in degapped refseq
      if (-1 != base0[2]) {               // not gapped or ambiguous nt
	if (0 == codonpos[base0[2]][1]) { // non-coding in alt model
	  lookup[base][0] = -1;
	}
      }
    }
  }

  //---------------------------------------------------------------------------
  // Number of pairs in pairs file.
  ifstream pairsfile("pairs.dat");
  if (!pairsfile) {
    cerr << "Aborting: can't find file 'pairs.dat'.\n";
    exit(EXIT_FAILURE);
  }
  npairs = -1;
  while (pairsfile.ignore(1000, '\n')) {
    ++npairs;
  }
  pairsfile.clear();
  pairsfile.seekg(0);
  if (npairs > maxpairs) {
    cerr << "Aborting: too many sequence pairs in file 'pairs.dat'.\n"
	 << "Maximum is " << maxpairs << "\n";
    exit(EXIT_FAILURE);
  }

  //---------------------------------------------------------------------------
  // Step through sequence pairs.

  if (verbose) {
    cout << "\nWorking...";
  }

  for (np = 0; np < npairs; ++np) {
    pairsfile >> seqid0[0];
    pairsfile >> seqid0[1];
    pairsfile.ignore(1000, '\n');
    seqid0[0] -= 1;           // since sequence indices start from 0
    seqid0[1] -= 1;           // since sequence indices start from 0
    flag[0][np] = 0;   // for failure of ttt fitting to converge (null model)
    flag[1][np] = 0;   // for failure of ttt fitting to converge (alt model)
    nmuts[np] = 0;     // number of point differences, inc stop <-> nonstop
    nmuts2[np] = 0;    // ditto but not including stop <-> nonstop
    nuccount[np] = 0;  // non-gap, not stop <-> nonstop, in both sequences
    gapcount[np] = 0;  // gaps in one or both sequences
    ntotal[np] = 0;    // non-gap in both sequences
    stopcount[np][0] = 0; // stop <-> nonstop in null model
    stopcount[np][1] = 0; // stop <-> nonstop in alternative model
    N123[0][np][0] = N123[1][np][0] = N123[2][np][0] = 0;
    N123[0][np][1] = N123[1][np][1] = N123[2][np][1] = 0;
    // Any ambiguous nt codes are treated as gaps (skipped over for most 
    //   statistics, written to log and plot files as gaps, counted as part of 
    //   gapcount).  However they are not stripped out in the gap-stripping, so
    //   CDSs are not put out-of-frame.  If an ambiguous nt code is part of a 
    //   codon being referenced for a neighbouring nt, then test_stop will 
    //   return a 0 (zero-probability transition) and the nt will be logged 
    //   along with the zero-probability transitions.  The subroutine
    //   calc_prob_col is never referenced unless test_stop != 0 so shouldn't 
    //   cause any problems.
    for (base = base1; base <= base2; ++base) {
      base0[0] = lookup[base][seqid0[0]]; // base in degapped seq1
      base0[1] = lookup[base][seqid0[1]]; // base in degapped seq2
      base0[2] = lookup[base][0];         // base in degapped refseq
      if (-1 != base0[0] && -1 != base0[1] && -1 != base0[2]) { // not gapped
	ntotal[np] += 1; 
	if (1 == codonpos[base0[2]][0] || 
	    4 == codonpos[base0[2]][0]) {
	  N123[0][np][1] += 1;
	} else if (2 == codonpos[base0[2]][0] || 
		   5 == codonpos[base0[2]][0]) {
	  N123[1][np][1] += 1;
	} else if (3 == codonpos[base0[2]][0] || 
		   6 == codonpos[base0[2]][0]) {
	  N123[2][np][1] += 1;
	} else if (0 != codonpos[base0[2]][0]) {
	  cerr << "Can't get here! (016)\n";
	  exit(EXIT_FAILURE); 
	}
	if (sequences[base0[0]][seqid0[0]] != sequences[base0[1]][seqid0[1]]) {
	  nmuts[np] += 1;
	  if (1 == codonpos[base0[2]][0] || 
	      4 == codonpos[base0[2]][0]) {
	    N123[0][np][0] += 1;
	  } else if (2 == codonpos[base0[2]][0] || 
		     5 == codonpos[base0[2]][0]) {
	    N123[1][np][0] += 1;
	  } else if (3 == codonpos[base0[2]][0] || 
		     6 == codonpos[base0[2]][0]) {
	    N123[2][np][0] += 1;
	  } else if (0 != codonpos[base0[2]][0]) {
	    cerr << "Can't get here! (016)\n";
	    exit(EXIT_FAILURE); 
	  }
	}
	temp98 = test_stop(weight, sequences, base0, codonpos, seqid0, 0);
	temp99 = test_stop(weight, sequences, base0, codonpos, seqid0, 1);
	if (temp98 && temp99) { // not stop <-> non-stop in both models
	  nuccount[np] += 1;
	  if (sequences[base0[0]][seqid0[0]] != 
	      sequences[base0[1]][seqid0[1]]) {
	    nmuts2[np] += 1;
	  }
	} else {
	  if (!temp98) { 
	    stopcount[np][0] += 1; 
	    logfile2 << seqid0[0]+1 << " " << seqid0[1]+1 << " " << base+1 
		     << " 0\n";
	  }
	  if (!temp99) { 
	    stopcount[np][1] += 1; 
	    logfile2 << seqid0[0]+1 << " " << seqid0[1]+1 << " " << base+1 
		     << " 1\n";
	  }
	}
      } else {                  // gaps in one or both sequences
	gapcount[np] += 1;
	logfile3 << seqid0[0]+1 << " " << seqid0[1]+1 << " " << base+1 << "\n";
      }
    }
    for (k = 0; k < 3; ++k) {
      if (0 != N123[k][np][1]) {
	N123r[k][np] = float(N123[k][np][0])/float(N123[k][np][1]);
      } else {
	N123r[k][np] = 0.;
      }
    }
    if (0 != ntotal[np]) {
      lambdasum += float(nmuts[np])/float(ntotal[np]);
    } else {
      lambdasum += 0.;
    }

    if (tttobs) {
      fitmuts = float(nmuts2[np]);          // fit exp#muts to obs#muts
    } else {
      fitmuts = float(nuccount[np])*lambda; // fit exp#muts to lambda*#nucs
    }

    // Find ttt value giving closest match between expected # muts and
    //   fitmuts.  Use bisection method -> since nmuts increases monotonically
    //   with ttt.  Stop when abs(exp#muts - fitmuts) < tttfit.  Take
    //   best guess and flag, if number of iterations exceeds maxiter or if 
    //   fitmuts is outside range allowed by tttmin--tttmax.  Note fitmuts
    //   skips muts in gaps or stops <-> non-stops, since these are skipped by
    //   MLOGD.

    for (model = 0; model < 2; ++model) {  // null and alternative models

      if (0. == fitmuts) {

	tttx[model][np] = 0.;
	
      } else {

	ettt[0] = tttmin;
	ettt[1] = tttmax;

	// Calculate exp#muts for ettt[].
	for (k = 0; k < 2; ++k) {
	  test = calc_nuc(nuc, ettt[k], nucB1, nucB2, nucD);
	  enmuts[k] = 0.;
	  for (base = base1; base <= base2; ++base) {
	    base0[0] = lookup[base][seqid0[0]]; // base in degapped seq1
	    base0[1] = lookup[base][seqid0[1]]; // base in degapped seq2
	    base0[2] = lookup[base][0];         // base in degapped refseq
	    if (-1 != base0[0] && -1 != base0[1] && -1 != base0[2]) {
	      temp98 = test_stop(weight,sequences,base0,codonpos,seqid0,0);
	      temp99 = test_stop(weight,sequences,base0,codonpos,seqid0,1);
	      if (temp98 && temp99) {  // only if not stop <-> non-stop
		enmuts[k] += calc_prob_col(weight, nuc, sequences, base0, 
					   codonpos, seqid0, model, 1, aa2aa, 
					   Vfix);
	      }
	    }
	  }
	}

	// Check tttmin--tttmax range is sufficient.
	if ((enmuts[0] - tttfit) > fitmuts) {
	  cerr << "Fitting number of mutations (" << fitmuts << ") outside "
	       << "that allowed by given t range.  Sequences " << seqid0[0]+1
	       << " and " << seqid0[1]+1 << ".\n";
	  tttx[model][np] = tttmin;
	  flag[model][np] = 1;
	} else if (enmuts[1] < fitmuts) {
	  cerr << "Fitting number of mutations (" << fitmuts << ") outside "
	       << "that allowed by given t range.  Sequences " << seqid0[0]+1
	       << " and " << seqid0[1]+1 << ".\n";
	  tttx[model][np] = tttmax;
	  flag[model][np] = 1;
	} else {

	  // Iterate on ttt.
	  niter = 0;
	  while (abs(enmuts[0] - fitmuts) > tttfit) {
	
	    niter++;
	    if (niter > maxiter) {
	      cerr << "Iteration on t failed to converge in " << maxiter 
		   << " iterations.  Sequences " << seqid0[0]+1
		   << " and " << seqid0[1]+1 << ".\n";
	      flag[model][np] = 1;
	      break;
	    }
	
	    // Bisector.
	    ttt = 0.5 * (ettt[0] + ettt[1]);
	
	    // Calculate expected number of mutations at bisector.
	    test = calc_nuc(nuc, ttt, nucB1, nucB2, nucD);
	    expmuts = 0.;
	    for (base = base1; base <= base2; ++base) {
	      base0[0] = lookup[base][seqid0[0]]; // base in degapped seq1
	      base0[1] = lookup[base][seqid0[1]]; // base in degapped seq2
	      base0[2] = lookup[base][0];         // base in degapped refseq
	      if (-1 != base0[0] && -1 != base0[1] && -1 != base0[2]) {
		temp98 = test_stop(weight,sequences,base0,codonpos,seqid0,0);
		temp99 = test_stop(weight,sequences,base0,codonpos,seqid0,1);
		if (temp98 && temp99) {  // only if not stop <-> non-stop
		  expmuts += calc_prob_col(weight, nuc, sequences, base0, 
					   codonpos, seqid0, model, 1, aa2aa, 
					   Vfix);
		}
	      }
	    }

	    // Reassign ettt[] and enmuts[].
	    if (fitmuts > expmuts) {
	      ettt[0] = ttt;
	      enmuts[0] = expmuts;
	    } else {
	      ettt[1] = ttt;
	      enmuts[1] = expmuts;
	    }
	    
	  } // exit while loop when converged
         
	  tttx[model][np] = ettt[0];

	} // close if/else for fitmuts outside/within allowed ttt range
      }   // close if/else for fitmuts ==/!= 0
    }     // close loop over model = 0/1

    // Calculate nucleotide matrices for best ttt values.
    test = calc_nuc(nuc0, tttx[0][np], nucB1, nucB2, nucD);
    test = calc_nuc(nuc1, tttx[1][np], nucB1, nucB2, nucD);

    // Calculate likelihoods for best ttt values.
    emtx[0][np] = emtx[1][np] = 0.;
      
    for (base = base1; base <= base2; ++base) {
      base0[0] = lookup[base][seqid0[0]]; // base in degapped seq1
      base0[1] = lookup[base][seqid0[1]]; // base in degapped seq2
      base0[2] = lookup[base][0];         // base in degapped refseq
      if (-1 != base0[0] && -1 != base0[1] && -1 != base0[2]) {
	temp98 = test_stop(weight, sequences, base0, codonpos, seqid0, 0);
	temp99 = test_stop(weight, sequences, base0, codonpos, seqid0, 1);
	if (temp98 && temp99) {    // only if not stop <-> non-stop
	  temp96 = calc_prob_col(weight, nuc0, sequences, base0, 
				 codonpos, seqid0, 0, 0, aa2aa, Vfix);
	  temp97 = calc_prob_col(weight, nuc1, sequences, base0, 
				 codonpos, seqid0, 1, 0, aa2aa, Vfix);
	  emtx[0][np] += temp96;
	  emtx[1][np] += temp97;
	  logfile1 << seqid0[0]+1 << " " << seqid0[1]+1 << " " << base+1 
		   << " " << temp96 << " " << temp97 << "\n";
	  if (0 != ntotal[np]) {
	    treesum[base][0] += float(nmuts[np])/float(ntotal[np]);
	  } else {
	    treesum[base][0] += 0.;
	  }
	  treesum[base][1] += temp96;
	  treesum[base][2] += temp97;
	  ntree[base] += 1;
	  if (temp96 < logepsilon) {
	    logfile4 << seqid0[0]+1 << " " << seqid0[1]+1 << " " << base+1 
		     << " 0 " << temp96 << "\n";
	  }
	  if (temp97 < logepsilon) {
	    logfile4 << seqid0[0]+1 << " " << seqid0[1]+1 << " " << base+1 
		     << " 1 " << temp97 << "\n";
	  }
	}
      }
    }
    if (0 != nuccount[np]) {
      emtx[0][np] /= nuccount[np]; 
      emtx[1][np] /= nuccount[np]; 
    } else {
      emtx[0][np] = 0.; 
      emtx[1][np] = 0.; 
    }

    // Calculate N_identical, N_synonomous, N_nonsynonomous
    N0synnon[0][np] = 0; // N_identical
    N0synnon[1][np] = 0; // N_synonomous
    N0synnon[2][np] = 0; // N_nonsynonomous

    for (base = base1; base <= base2; ++base) {
      base0[0] = lookup[base][seqid0[0]]; // base in degapped seq1
      base0[1] = lookup[base][seqid0[1]]; // base in degapped seq2
      base0[2] = lookup[base][0];         // base in degapped refseq
      if (-1 != base0[0] && -1 != base0[1] && -1 != base0[2]) {
	if (0 != codonpos[base0[2]][0]) {      // coding in primary frame
	  for (k = 0; k < 2; ++k) {
	    if (1 == codonpos[base0[2]][0]) {
	      j1[k] = sequences[base0[k]][seqid0[k]];
	      j2[k] = sequences[base0[k]+1][seqid0[k]];
	      j3[k] = sequences[base0[k]+2][seqid0[k]];
	    } else if (2 == codonpos[base0[2]][0]) {
	      j1[k] = sequences[base0[k]-1][seqid0[k]];
	      j2[k] = sequences[base0[k]][seqid0[k]];
	      j3[k] = sequences[base0[k]+1][seqid0[k]];
	    } else if (3 == codonpos[base0[2]][0]) {
	      j1[k] = sequences[base0[k]-2][seqid0[k]];
	      j2[k] = sequences[base0[k]-1][seqid0[k]];
	      j3[k] = sequences[base0[k]][seqid0[k]];
	    } else if (6 == codonpos[base0[2]][0]) {
	      j3[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	      j2[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
	      j1[k] = (sequences[base0[k]+2][seqid0[k]] + 2) % 4;
	    } else if (5 == codonpos[base0[2]][0]) {
	      j3[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
	      j2[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	      j1[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
	    } else if (4 == codonpos[base0[2]][0]) {
	      j3[k] = (sequences[base0[k]-2][seqid0[k]] + 2) % 4;
	      j2[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
	      j1[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	    } else {
	      cerr << "Can't get here! (004)\n";
	      exit(EXIT_FAILURE); 
	    }
	    jcid[k] = 16 * j1[k] + 4 * j2[k] + j3[k];              
	  }
	  if (jcid[0] == jcid[1]) {
	    N0synnon[0][np] += 1;
	  } else if (aa2aa[jcid[0]] == aa2aa[jcid[1]]) {
	    N0synnon[1][np] += 1;
	  } else {
	    N0synnon[2][np] += 1;
	  }
	}
      }
    }

    N0NsNnsum = N0synnon[0][np]+N0synnon[1][np]+N0synnon[2][np];
    for (k = 0; k < 3; ++k) {
      if (0 != N0NsNnsum) {
	N0NsNn[k][np] = float(N0synnon[k][np]) / float(N0NsNnsum);
      } else {
	N0NsNn[k][np] = 0.;
      }
    }

  } // finish loop over sequences pairs

  logfile1.close();
  logfile2.close();
  logfile3.close();
  logfile4.close();
  pairsfile.close();

  //---------------------------------------------------------------------------
  // Write statistics to file.
  
  ofstream outputfile("mlogd_out.dat");
  if (!outputfile) {
    cerr << "Failed to open output file 'mlogd_out.dat'.\n";
    exit(EXIT_FAILURE);
  }
  outputfile << setprecision(3);
  for (np = 0; np < npairs; ++np) {
    outputfile << setw(6) << tttx[0][np] << " "
               << setw(6) << tttx[1][np] << " "
               << setw(8) << emtx[0][np] << " "
               << setw(8) << emtx[1][np] << " "
               << setw(6) << nuccount[np] << " "
               << setw(5) << stopcount[np][0] << " "
               << setw(5) << stopcount[np][1] << " "
               << setw(6) << gapcount[np] << " "
               << setw(9) << N0NsNn[0][np] << " "
               << setw(9) << N0NsNn[1][np] << " "
               << setw(9) << N0NsNn[2][np] << " "
               << setw(6) << ntotal[np] << " "
               << setw(6) << nmuts[np] << " "
               << setw(6) << nmuts2[np] << " "
               << setw(9) << N123r[0][np] << " "
               << setw(9) << N123r[1][np] << " "
               << setw(9) << N123r[2][np] << " "
	       << setw(4) << flag[0][np] << " "
	       << setw(4) << flag[1][np] << "\n";
   }
  outputfile.close();
  
  ofstream treesumfile("mlogd_out.treesum");
  if (!treesumfile) {
    cerr << "Failed to open output file 'mlogd_out.treesum'.\n";
    exit(EXIT_FAILURE);
  }
  for (base = 0; base < nseq0; ++base) {
    treesumfile << base+1 << " "
		<< ntree[base] << " "
		<< treesum[base][0] << " "
		<< treesum[base][1] << " "
		<< treesum[base][2] << " ";
    if (-1 == lookup[base][0]) {
      treesumfile << "-\n";
    } else {
      if (0 == sequences[lookup[base][0]][0]) {
	treesumfile << "U\n";
      } else if (1 == sequences[lookup[base][0]][0]) {
	treesumfile << "C\n";
      } else if (2 == sequences[lookup[base][0]][0]) {
	treesumfile << "A\n";
      } else if (3 == sequences[lookup[base][0]][0]) {
	treesumfile << "G\n";
      } else if (9 == sequences[lookup[base][0]][0]) {
	treesumfile << "-\n";
      } else if (5 == sequences[lookup[base][0]][0]) {
	treesumfile << "N\n";
      } else {
	cerr << "Can't get here! (006)\n";
	exit(EXIT_FAILURE); 
      }
    }
  }
  treesumfile.close();

  //---------------------------------------------------------------------------
  // Write out some stats.

  ofstream infofile("mlogd_out.info");
  if (!infofile) {
    cerr << "Failed to open log file 'mlogd_out.info'.\n";
    exit(EXIT_FAILURE);
  }
  infofile << nseq0 << " " << base1+1 << " " << base2+1 << "\n";
  infofile << lambdasum << "\n";

  // Find frame from codonpos[][], within range.
  for (j = 0; j < 7; ++j) {
    for (k = 0; k < 7; ++k) {
      pos2[j][k] = 0;
    }
  }
  //  for (i = range1; i <= range2; ++i) {
  //    pos2[codonpos[i][0]][codonpos[i][1]] += 1;
  //  }
  for (base = base1; base <= base2; ++base) {
    base0[2] = lookup[base][0]; // base in degapped refseq
    if (-1 != base0[2]) {       // not gapped
      pos2[codonpos[base0[2]][0]][codonpos[base0[2]][1]] += 1;
    }
  }
  for (j = 0; j < 7; ++j) {
    for (k = 0; k < 7; ++k) {
      if (pos2[j][k] > 0) {
	infofile << j << " " << k << " " << pos2[j][k] << "\n";
      }
    }
  }
  infofile.close();

  if (verbose) {
    cout << "\n\nFinished.\n";
  }
  
  return(0);
}

//-----------------------------------------------------------------------------
// expnmuts = 0: returns log(prob) for a given nucleotide mutation in a given
//   sequence pair.  
// expnmuts = 1: returns expected number of mutations (in the range 0-1) for a 
//   given nucleotide site in a given sequence pair at a given divergence ttt.

double calc_prob_col(double weight[][64], double nuc[][4], 
		     int sequences[][maxnseqs], int base0[3], 
		     int codonpos[][2], int seqid0[2], int model, 
		     int expnmuts, int aa2aa[64], double Vfix)

{
  int jn[2], j1[2], j2[2], j3[2], jcid[2], k, kn, k1, k2, k3, kcid;
  int c1[2], c2[2], c3[2], ccid[2];
  double sum, prob_col[4];
  
  // base0[0,1,2] are locations of the nucleotide in
  //   sequences[][seqid1,seqid2,0]; codonpos[][0,1] correspond to the refseq 
  //   and should be referenced with base0[2].  Assumed that in general this 
  //   will be the correct codonpos for the non-refseqs also.  Gaps have been 
  //   stripped out in codonpos[][] and sequences[][].

  jn[0] = sequences[base0[0]][seqid0[0]]; // nucleotide in seq1
  jn[1] = sequences[base0[1]][seqid0[1]]; // nucleotide in seq2
 
  if ((0 == codonpos[base0[2]][0] && 0 == model) ||
      (0 == codonpos[base0[2]][0] && 0 == codonpos[base0[2]][1] 
       && 1 == model)) {              // use non-coding model
    sum = 0.;
    for (kn = 0; kn < 4; ++kn) {
      prob_col[kn] = nuc[jn[0]][kn];
      sum += prob_col[kn];
    }
    
  } else {                            // single or double coding model

    if (0 != codonpos[base0[2]][0]) { // coding in pos.1
      // Find primary frame codon containing the nucleotide in seq1 and seq2
      for (k = 0; k < 2; ++k) {
	if (1 == codonpos[base0[2]][0]) {
	  j1[k] = sequences[base0[k]][seqid0[k]];
	  j2[k] = sequences[base0[k]+1][seqid0[k]];
	  j3[k] = sequences[base0[k]+2][seqid0[k]];
	} else if (2 == codonpos[base0[2]][0]) {
	  j1[k] = sequences[base0[k]-1][seqid0[k]];
	  j2[k] = sequences[base0[k]][seqid0[k]];
	  j3[k] = sequences[base0[k]+1][seqid0[k]];
	} else if (3 == codonpos[base0[2]][0]) {
	  j1[k] = sequences[base0[k]-2][seqid0[k]];
	  j2[k] = sequences[base0[k]-1][seqid0[k]];
	  j3[k] = sequences[base0[k]][seqid0[k]];
	} else if (6 == codonpos[base0[2]][0]) {
	  j3[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	  j2[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
	  j1[k] = (sequences[base0[k]+2][seqid0[k]] + 2) % 4;
	} else if (5 == codonpos[base0[2]][0]) {
	  j3[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
	  j2[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	  j1[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
	} else if (4 == codonpos[base0[2]][0]) {
	  j3[k] = (sequences[base0[k]-2][seqid0[k]] + 2) % 4;
	  j2[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
	  j1[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	} else {
	  cerr << "Can't get here! (006)\n";
	  exit(EXIT_FAILURE); 
	}
	jcid[k] = 16 * j1[k] + 4 * j2[k] + j3[k];              
      }
    }

    if (0 != codonpos[base0[2]][1] && 1 == model) { // coding in pos.2
      // Find secondary frame codon containing the nucleotide in seq1 and seq2 
      for (k = 0; k < 2; ++k) {
	if (1 == codonpos[base0[2]][1]) {
	  c1[k] = sequences[base0[k]][seqid0[k]];
	  c2[k] = sequences[base0[k]+1][seqid0[k]];
	  c3[k] = sequences[base0[k]+2][seqid0[k]];
	} else if (2 == codonpos[base0[2]][1]) {
	  c1[k] = sequences[base0[k]-1][seqid0[k]];
	  c2[k] = sequences[base0[k]][seqid0[k]];
	  c3[k] = sequences[base0[k]+1][seqid0[k]];
	} else if (3 == codonpos[base0[2]][1]) {
	  c1[k] = sequences[base0[k]-2][seqid0[k]];
	  c2[k] = sequences[base0[k]-1][seqid0[k]];
	  c3[k] = sequences[base0[k]][seqid0[k]];
	} else if (6 == codonpos[base0[2]][1]) {
	  c3[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	  c2[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
	  c1[k] = (sequences[base0[k]+2][seqid0[k]] + 2) % 4;
	} else if (5 == codonpos[base0[2]][1]) {
	  c3[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
	  c2[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	  c1[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
	} else if (4 == codonpos[base0[2]][1]) {
	  c3[k] = (sequences[base0[k]-2][seqid0[k]] + 2) % 4;
	  c2[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
	  c1[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
	} else {
	  cerr << "Can't get here! (008)\n";
	  exit(EXIT_FAILURE); 
	}
	ccid[k] = 16 * c1[k] + 4 * c2[k] + c3[k];              
      }
    }

    sum = 0.;
    for (kn = 0; kn < 4; ++kn) { // possible point mutations at that position

      // Weight for nucleotide mutation.
      prob_col[kn] = nuc[jn[0]][kn];

      if (0 != codonpos[base0[2]][0]) {      // coding in pos.1
	k1 = j1[1]; k2 = j2[1]; k3 = j3[1];  // codon in seq2
	if (1 == codonpos[base0[2]][0]) {    // new codon in seq2
	  k1 = kn;
	} else if (2 == codonpos[base0[2]][0]) {
	  k2 = kn;
	} else if (3 == codonpos[base0[2]][0]) {
	  k3 = kn;
	} else if (6 == codonpos[base0[2]][0]) {
	  k3 = (kn + 2) % 4;
	} else if (5 == codonpos[base0[2]][0]) {
	  k2 = (kn + 2) % 4;
	} else if (4 == codonpos[base0[2]][0]) {
	  k1 = (kn + 2) % 4;
	} else {
	  cerr << "Can't get here! (009)\n";
	  exit(EXIT_FAILURE); 
	}
	kcid = 16 * k1 + 4 * k2 + k3;
	// Amino acid acceptability (new nucleotide kn in seq2 context, 
	//   compared with old nucleotide in seq1 context).
	prob_col[kn] *= weight[jcid[0]][kcid];
	if (aa2aa[kcid] != aa2aa[jcid[0]]) {
	  prob_col[kn] *= Vfix; // nonsynonymous:synonymous scaling
	}
      }

      if (0 != codonpos[base0[2]][1] && 1 == model) { // coding in pos.2
	k1 = c1[1]; k2 = c2[1]; k3 = c3[1];           // codon in seq2
	if (1 == codonpos[base0[2]][1]) {             // new codon in seq2
	  k1 = kn;
	} else if (2 == codonpos[base0[2]][1]) {
	  k2 = kn;
	} else if (3 == codonpos[base0[2]][1]) {
	  k3 = kn;
	} else if (6 == codonpos[base0[2]][1]) {
	  k3 = (kn + 2) % 4;
	} else if (5 == codonpos[base0[2]][1]) {
	  k2 = (kn + 2) % 4;
	} else if (4 == codonpos[base0[2]][1]) {
	  k1 = (kn + 2) % 4;
	} else {
	  cerr << "Can't get here! (010)\n";
	  exit(EXIT_FAILURE); 
	}
	kcid = 16 * k1 + 4 * k2 + k3;
	// Amino acid acceptability (new nucleotide kn in seq2 context, 
	//   compared with old nucleotide in seq1 context).
	prob_col[kn] *= weight[ccid[0]][kcid];
	if (aa2aa[kcid] != aa2aa[ccid[0]]) {
	  prob_col[kn] *= Vfix; // nonsynonymous:synonymous scaling
	}
      }

      sum += prob_col[kn];
    }
  }

  if (0. == sum) {
    // This can occassionally occur, e.g. seq1 codon CAA, seq2 codon UAC, 
    //   mutating N3; for ttt ~ 0, prob_col[U] = prob_col[C] = prob_col[G] = 0,
    //   and prob_col[A] = 0 since UAG is a stop codon.  Once ttt has converged
    //   on the best fit ttt, this probelm shouldn't occur.
    if (expnmuts) {  // return exp # muts at this site for pairwise distance
      return(0);
    } else {  // return log(prob) for nuc mutation from seq1 to seq2
      return(-100);
    }
  }

  // Normalize probs so that sum = 1.
  for (kn = 0; kn < 4; ++kn) {
    prob_col[kn] /= sum;  
  }
  if (prob_col[0] > 1.01 || prob_col[0] < -0.01||
      prob_col[1] > 1.01 || prob_col[1] < -0.01||
      prob_col[2] > 1.01 || prob_col[2] < -0.01||
      prob_col[3] > 1.01 || prob_col[3] < -0.01) {
    cerr << "Error: invalid probability value; possible rounding error:\n   " 
	 << prob_col[0] << " " << prob_col[1] << " "
	 << prob_col[2] << " " << prob_col[3] << " " << sum << "\n";
  } 
  
  if (expnmuts) {  // return exp # muts at this site for pairwise distance
    return(1. - prob_col[jn[0]]);
  } else {  // return log(prob) for nuc mutation from seq1 to seq2
    if (prob_col[jn[1]] > 0) {
      return(log(prob_col[jn[1]]));
    } else {
      cerr << "Error: unexpected zero-probability mutation (e.g. stop codon "
	   << "to non-stop). (002)\n";
      exit(EXIT_FAILURE);
    }
  }

}

//-----------------------------------------------------------------------------

int readsequence(char seq[128], int gsequences[][maxnseqs], int seqid)

{
  int i, k, nlines, nseq;
  char seqline[1000], inputseq[maxlength+10];

  ifstream sequence(seq);
  if (!sequence) {
    cerr << "Aborting: can't find file '" << seq << "'.\n";
    exit(EXIT_FAILURE);
  }
  nlines = -1;
  while (sequence.ignore(1000, '\n')) {
    ++nlines;
  }
  sequence.clear();
  sequence.seekg(0);
  sequence.ignore(1000, '\n');
  for (i = 0; i < nlines; ++i) {
    sequence.getline(seqline, 1000, '\n');
    if (0 == i) {
      strcpy(inputseq, seqline);
    } else {
      strcat(inputseq, seqline);
    }
  }
  sequence.close();
  for (i = 0; ; ++i) {
    if (inputseq[i] == 'U' || inputseq[i] == 'u') {
      gsequences[i][seqid] = 0;
    } else if (inputseq[i] == 'T' || inputseq[i] == 't') {
      gsequences[i][seqid] = 0;
    } else if (inputseq[i] == 'C' || inputseq[i] == 'c') {
      gsequences[i][seqid] = 1;
    } else if (inputseq[i] == 'A' || inputseq[i] == 'a') {
      gsequences[i][seqid] = 2;
    } else if (inputseq[i] == 'G' || inputseq[i] == 'g') {
      gsequences[i][seqid] = 3;
    } else if (inputseq[i] == '-' || inputseq[i] == '.') {
      gsequences[i][seqid] = 9;
    } else if (inputseq[i] == '\0') {      
      nseq = i;
      break;
    } else {
      if (inputseq[i] == 'M' || inputseq[i] == 'm' ||
	  inputseq[i] == 'R' || inputseq[i] == 'r' ||
	  inputseq[i] == 'W' || inputseq[i] == 'w' ||
	  inputseq[i] == 'V' || inputseq[i] == 'v' ||
	  inputseq[i] == 'H' || inputseq[i] == 'h' ||
	  inputseq[i] == 'D' || inputseq[i] == 'd' ||
	  inputseq[i] == 'B' || inputseq[i] == 'b' ||
	  inputseq[i] == 'S' || inputseq[i] == 's' ||
	  inputseq[i] == 'Y' || inputseq[i] == 'y' ||
	  inputseq[i] == 'K' || inputseq[i] == 'k' ||
	  inputseq[i] == 'N' || inputseq[i] == 'n' ||
	  inputseq[i] == 'X' || inputseq[i] == 'x') {
	gsequences[i][seqid] = 5; // ambiguous nt
	cerr << "Warning: sequence " << seq << ", ambiguous nt '" 
	     << inputseq[i] << "', at " << i+1 << ".\n";
      } else {
	cerr << "Aborting: sequence " << seq << ", unknown nucleotide '" 
	     << inputseq[i] << "', at " << i+1 << ".\n";
	exit(EXIT_FAILURE);
      }
    }
  }
  return(nseq);
  
}

//-----------------------------------------------------------------------------
// Note that if there are overlapping ORFs in the same frame (e.g. alternative 
//   start points) then only one is counted at any nt.
// Note that if there are overlapping ORFs in different frames, then only the
//   first one is counted in the overlap regions.
// Note that the alternate model can repeat the null model CDS, in which case
//   you're comparing a CDS versus two copies of the same CDS.  

int readorfs(char cpos[128], int codonpos[][2], int length, int circular, 
 int posid)

{  

  int i, j, k, orf1, orf2, nseg, count, norfs, test;

  test = 1; // for warning message for overlapping ORFs 

  for (i = 0; i < length; ++i) {
    codonpos[i][posid] = 0;
  }

  // Work through ORF list.
  ifstream orffile(cpos);
  if (!orffile) {
    cerr << "Aborting: can't find file '" << cpos << "'.\n";
    exit(EXIT_FAILURE);
  }
  norfs = -1;
  while (orffile.ignore(1000, '\n')) {
    ++norfs;
  }
  orffile.clear();
  orffile.seekg(0);

  for (i = 0; i < norfs; ++i) {
    count = 0;
    orffile >> nseg;
    nseg /= 2;
    for (k = 0; k < nseg; ++k) {
      orffile >> orf1;
      orffile >> orf2;
      if (orf1<1||orf2<1||orf1>length||orf2>length) {
	cerr << "Aborting: ORF " << i+1 << " in " << cpos
	     << ", endpoints outside sequence range.\n";
	exit(EXIT_FAILURE);
      }

      // Since arrays start at 0 rather than 1.
      orf1--;
      orf2--;

      // Enter 1,2,3 (forward) or 4,5,6 (reverse) into codonpos[][]
      if (orf1 < orf2) { // forward frame
	for (j = orf1; j <= orf2; ++j) {
	  // blank codons overlapping joins except for circular genomes
	  if (!((j==orf2&&count+1!=3)||(j==orf2-1&&count+1==1)||
		(j==orf1&&count+1!=1)||(j==orf1+1&&count+1==3))||
	      (circular&&(j==length-1||j==length-2||j==0||j==1))){
	    if (0 == codonpos[j][posid]) {
	      codonpos[j][posid] = count+1;
	    } else {
	      if (test) {
		cerr << "Warning: " << cpos << " has overlapping ORFs. "
		     << "Only the first will be used in overlap regions.\n";
		test = 0;
	      }
	    }
	  }
	  count = (count+1)%3;
	}
      } else { // reverse frame
	for (j = orf1; j >= orf2; --j) {
	  // blank codons overlapping joins except for circular genomes
	  if (!((j==orf2&&count+1!=3)||(j==orf2+1&&count+1==1)||
		(j==orf1&&count+1!=1)||(j==orf1-1&&count+1==3))||
	      (circular&&(j==length-1||j==length-2||j==0||j==1))){
	    if (0 == codonpos[j][posid]) {
	      codonpos[j][posid] = count+4;
	    } else {
	      if (test) {
		cerr << "Warning: " << cpos << " has overlapping ORFs. "
		     << "Only the first will be used in overlap regions.\n";
		test = 0;
	      }
	    } 
	  }
	  count = (count+1)%3;
	}
      }
    }
    if (0 != count%3) {
      cerr << "Warning: number of nucleotides in ORF " << i+1 << " in " 
	   << cpos << " not a multiple of 3.\n";
    }  
    orffile.ignore(1000, '\n');
  }
  orffile.close();

  return(norfs);

}

//-----------------------------------------------------------------------------
// Check input aligned sequences for gaps occurring not in multiples of 3
//   within coding regions (in null model if pos = 0 and in alternative model 
//   if pos = 1).  Output a warning if any problem.

int checkgaps(int lookup[][maxnseqs], int codonpos[][2], int nseq0, int seqid, 
	      int pos)

{
  int i, cdstest, gaptest, count;

  cdstest = 0;  // 0 -> in a non-coding region; 1 -> in a coding region
  gaptest = 0;  // 0 -> in a non-gapped region; 1 -> in a gapped region

  for (i = 0; i < nseq0; ++i) {
    if (!cdstest) {                  // non-coding region
      if (-1 != lookup[i][seqid]) {  // not a gap in seq seqid
	if (0 != codonpos[lookup[i][0]][pos]) {  
	  cdstest = 1;               // switch to coding region
	}
      }
    } else {                         // coding-region
      if (gaptest) {                 // gapped region
	if (-1 == lookup[i][seqid]) {    // a gap in seq seqid
	  count += 1;
	} else if (0 == codonpos[lookup[i][0]][pos]) {
	  cdstest = 0;               // switch to non-coding region
	  gaptest = 0;               // switch to non-gapped region
	} else {
	  gaptest = 0;               // switch to non-gapped region
	  if (0 != count % 3) {
	    if (0 == pos) {
	      cerr << "Warning: gap within null model coding region not"
		   << " a multiple of three nt;\n  sequence " << seqid+1 
		   << ", sequence coords " << lookup[i][seqid] 
		   << ", alignment coords " << i << ".\n";
	    } else {
	      cerr << "Warning: gap within alternative model coding region not"
		   << " a multiple of three nt;\n  sequence " << seqid+1 
		   << ", sequence coords " << lookup[i][seqid] 
		   << ", alignment coords " << i << ".\n";
	    }
	  }
	}
      } else {                       // not a gapped region
	if (-1 == lookup[i][seqid]) {
	  gaptest = 1;               // switch to gapped region
	  count = 1;
	} else if (0 == codonpos[lookup[i][0]][pos]) {
	  cdstest = 0;               // switch to non-coding region
	}
      }
    }
  }

  return(0);
}

//-----------------------------------------------------------------------------
// Tests for stop <-> non-stop transitions between a sequence pair, in
//  null (pos = 0) or alternative (pos = 1) models.  Actually checks for any 
//  transitions which have zero probability in the amino acid x CUT 
//  substitution matrix.  These are skipped over when calculating MLOGD (sice 
//  log(0) is undefined) and recorded in the stoplog file.

int test_stop(double weight[][64], int sequences[][maxnseqs], int base0[3], 
	      int codonpos[][2], int seqid0[2], int pos)

{
  int k, j1[2], j2[2], j3[2], jcid[2], k1, k2, k3;

  if (0 == codonpos[base0[2]][pos]) {
    return(2);   // allowed transition, non-coding
  }
  
  for (k = 0; k < 2; ++k) {

    if (1 == codonpos[base0[2]][pos] || 6 == codonpos[base0[2]][pos]) {
      k1 = sequences[base0[k]][seqid0[k]];
      k2 = sequences[base0[k]+1][seqid0[k]];
      k3 = sequences[base0[k]+2][seqid0[k]];
    } else if (2 == codonpos[base0[2]][pos] || 5 == codonpos[base0[2]][pos]) {
      k1 = sequences[base0[k]-1][seqid0[k]];
      k2 = sequences[base0[k]][seqid0[k]];
      k3 = sequences[base0[k]+1][seqid0[k]];
    } else if (3 == codonpos[base0[2]][pos] || 4  == codonpos[base0[2]][pos]) {
      k1 = sequences[base0[k]-2][seqid0[k]];
      k2 = sequences[base0[k]-1][seqid0[k]];
      k3 = sequences[base0[k]][seqid0[k]];
    }
    if (5 == k1 || 5 == k2 || 5 == k3) {
      return(0);  // codon contains an ambiguous nt code
    }

    if (1 == codonpos[base0[2]][pos]) {
      j1[k] = sequences[base0[k]][seqid0[k]];
      j2[k] = sequences[base0[k]+1][seqid0[k]];
      j3[k] = sequences[base0[k]+2][seqid0[k]];
    } else if (2 == codonpos[base0[2]][pos]) {
      j1[k] = sequences[base0[k]-1][seqid0[k]];
      j2[k] = sequences[base0[k]][seqid0[k]];
      j3[k] = sequences[base0[k]+1][seqid0[k]];
    } else if (3 == codonpos[base0[2]][pos]) {
      j1[k] = sequences[base0[k]-2][seqid0[k]];
      j2[k] = sequences[base0[k]-1][seqid0[k]];
      j3[k] = sequences[base0[k]][seqid0[k]];
    } else if (6 == codonpos[base0[2]][pos]) {
      j3[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
      j2[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
      j1[k] = (sequences[base0[k]+2][seqid0[k]] + 2) % 4;
    } else if (5 == codonpos[base0[2]][pos]) {
      j3[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
      j2[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
      j1[k] = (sequences[base0[k]+1][seqid0[k]] + 2) % 4;
    } else if (4 == codonpos[base0[2]][pos]) {
      j3[k] = (sequences[base0[k]-2][seqid0[k]] + 2) % 4;
      j2[k] = (sequences[base0[k]-1][seqid0[k]] + 2) % 4;
      j1[k] = (sequences[base0[k]][seqid0[k]] + 2) % 4;
    } else {
      cerr << "Can't get here! (012)\n";
      exit(EXIT_FAILURE); 
    }
    jcid[k] = 16 * j1[k] + 4 * j2[k] + j3[k];              
  }
  
  if (0 == weight[jcid[0]][jcid[1]]) {
    return(0);   // zero probability transition
  } else { 
    return(1);   // allowed transition
  } 

}

//-----------------------------------------------------------------------------
// Makes 4x4 nucleotide P matrix for a given t.
 
int calc_nuc(double nuc[][4], double ttt, double nucB1[][4], double nucB2[][4],
	     double nucD[][4])

{
  int ni, nj, nk;
  double tempA[4][4];

  for (ni = 0; ni < 4; ++ni) {
    for (nj = 0; nj < 4; ++nj) {
      tempA[ni][nj] = nucB1[ni][nj]*exp(ttt*nucD[nj][nj]);
    }
  }
  for (ni = 0; ni < 4; ++ni) {
    for (nj = 0; nj < 4; ++nj) {
      nuc[ni][nj] = 0.;
      for (nk = 0; nk < 4; ++nk) {
	nuc[ni][nj] += tempA[ni][nk]*nucB2[nk][nj];
      }
      if (nuc[ni][nj] < 0.) { 
	nuc[ni][nj] = 0.; // in case of rounding errors
      }
    }
  }
  return(0);

}

//-----------------------------------------------------------------------------
// Tests for stop codons in a sequence, in null (pos = 0) or alternative 
//   (pos = 1) models.  base0[0] is the refseq base (to find codon position),
//   base0[1] is the sequence base.
// Returns
//    0 -> stop codon
//    1 -> not a stop or start
//    2 -> non-coding (therefore not a stop)
//    3 -> codon contains an ambiguous nt code
//    4 -> start codon

int stopcodon(int aa2aa[64], int sequences[][maxnseqs], int base0[2], 
	      int codonpos[][2], int seqid, int pos)

{
  int j1, j2, j3, jcid, k1, k2, k3;

  if (0 == codonpos[base0[0]][pos]) {
    return(2);   // non-coding (therefore not a stop)
  }
  
  if (1 == codonpos[base0[0]][pos] || 6 == codonpos[base0[0]][pos]) {
    k1 = sequences[base0[1]][seqid];
    k2 = sequences[base0[1]+1][seqid];
    k3 = sequences[base0[1]+2][seqid];
  } else if (2 == codonpos[base0[0]][pos] || 5 == codonpos[base0[0]][pos]) {
    k1 = sequences[base0[1]-1][seqid];
    k2 = sequences[base0[1]][seqid];
    k3 = sequences[base0[1]+1][seqid];
  } else if (3 == codonpos[base0[0]][pos] || 4  == codonpos[base0[0]][pos]) {
    k1 = sequences[base0[1]-2][seqid];
    k2 = sequences[base0[1]-1][seqid];
    k3 = sequences[base0[1]][seqid];
  }
  if (5 == k1 || 5 == k2 || 5 == k3) {
    return(3);  // codon contains an ambiguous nt code
  }

  if (1 == codonpos[base0[0]][pos]) {
    j1 = sequences[base0[1]][seqid];
    j2 = sequences[base0[1]+1][seqid];
    j3 = sequences[base0[1]+2][seqid];
  } else if (2 == codonpos[base0[0]][pos]) {
    j1 = sequences[base0[1]-1][seqid];
    j2 = sequences[base0[1]][seqid];
    j3 = sequences[base0[1]+1][seqid];
  } else if (3 == codonpos[base0[0]][pos]) {
    j1 = sequences[base0[1]-2][seqid];
    j2 = sequences[base0[1]-1][seqid];
    j3 = sequences[base0[1]][seqid];
  } else if (6 == codonpos[base0[0]][pos]) {
    j3 = (sequences[base0[1]][seqid] + 2) % 4;
    j2 = (sequences[base0[1]+1][seqid] + 2) % 4;
    j1 = (sequences[base0[1]+2][seqid] + 2) % 4;
  } else if (5 == codonpos[base0[0]][pos]) {
    j3 = (sequences[base0[1]-1][seqid] + 2) % 4;
    j2 = (sequences[base0[1]][seqid] + 2) % 4;
    j1 = (sequences[base0[1]+1][seqid] + 2) % 4;
  } else if (4 == codonpos[base0[0]][pos]) {
    j3 = (sequences[base0[1]-2][seqid] + 2) % 4;
    j2 = (sequences[base0[1]-1][seqid] + 2) % 4;
    j1 = (sequences[base0[1]][seqid] + 2) % 4;
  } else {
    cerr << "Can't get here! (012)\n";
    exit(EXIT_FAILURE); 
  }
  jcid = 16 * j1 + 4 * j2 + j3;              
  
  if (99 == aa2aa[jcid]) {
    return(0);   // stop codon
  } else if (35 == jcid) { 
    return(4);   // start codon
  } else { 
    return(1);   // not a stop
  } 

}