#include "phylip.h"

/* version 3.696.
   Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.

   Copyright (c) 1993-2014, Joseph Felsenstein
   All rights reserved.

   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice,
      this list of conditions and the following disclaimer in the documentation
      and/or other materials provided with the distribution.

   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
   AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
   IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
   ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
   LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
   CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
   SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
   INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
   CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
   POSSIBILITY OF SUCH DAMAGE.
*/


#define epsilong         0.02 /* a small number                            */

#ifndef OLDC
/* function prototypes */
void   getoptions(void);
void   allocrest(void);
void   doinit(void);
void   getalleles(void);
void   inputdata(void);
void   getinput(void);
void   makedists(void);
void   writedists(void);
void   freerest(void);
void   freex(void);
/* function prototypes */
#endif



Char infilename[FNMLNGTH], outfilename[FNMLNGTH];
long loci, totalleles, df, datasets, ith;
long nonodes;
long *alleles;
phenotype3 *x;
double **d;
boolean all, cavalli, lower, nei, reynolds,  mulsets,
               firstset, progress;

void getoptions()
{
  /* interactively set options */
  long loopcount;
  Char ch;

  all = false;
  cavalli = false;
  lower = false;
  nei = true;
  reynolds = false;
  lower = false;
  progress = true;
  loopcount = 0;
  for (;;) {
    cleerhome();
    printf("\nGenetic Distance Matrix program, version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  A   Input file contains all alleles at each locus?  %s\n",
           all ? "Yes" : "One omitted at each locus");
    printf("  N                        Use Nei genetic distance?  %s\n",
           nei ? "Yes" : "No");
    printf("  C                Use Cavalli-Sforza chord measure?  %s\n",
           cavalli ? "Yes" : "No");
    printf("  R                   Use Reynolds genetic distance?  %s\n",
           reynolds ? "Yes" : "No");
    printf("  L                         Form of distance matrix?  %s\n",
           lower ? "Lower-triangular" : "Square");
    printf("  M                      Analyze multiple data sets?");
    if (mulsets)
      printf("  Yes, %2ld sets\n", datasets);
    else
      printf("  No\n");
    printf("  0              Terminal type (IBM PC, ANSI, none)?  %s\n",
           ibmpc ? "IBM PC" : ansi  ? "ANSI" : "(none)");
    printf("  1            Print indications of progress of run?  %s\n",
           progress ? "Yes" : "No");
    printf("\n  Y to accept these or type the letter for one to change\n");
#ifdef WIN32
    phyFillScreenColor();
#endif
    fflush(stdout);
    scanf("%c%*[^\n]", &ch);
    getchar();
    uppercase(&ch);
    if (ch == 'Y')
      break;
    if (strchr("ACNMRL01", ch) != NULL) {
      switch (ch) {
        
      case 'A':
        all = !all;
        break;
        
      case 'C':
        cavalli = true;
        nei = false;
        reynolds = false;
        break;
        
      case 'N':
        cavalli = false;
        nei = true;
        reynolds = false;
        break;
        
      case 'R':
        reynolds = true;
        cavalli = false;
        nei = false;
        break;
        
      case 'L':
        lower = !lower;
        break;
        
      case 'M':
        mulsets = !mulsets;
        if (mulsets)
          initdatasets(&datasets);
        break;
        
      case '0':
        initterminal(&ibmpc, &ansi);
        break;
        
      case '1':
        progress = !progress;
        break;
      }
    } else
      printf("Not a possible option!\n");
    countup(&loopcount, 100);
  }
  putchar('\n');
}  /* getoptions */


void allocrest()
{
  long i;

  x = (phenotype3 *)Malloc(spp*sizeof(phenotype3));
  d = (double **)Malloc(spp*sizeof(double *));
  for (i = 0; i < (spp); i++)
    d[i] = (double *)Malloc(spp*sizeof(double));
  alleles = (long *)Malloc(loci*sizeof(long));
  nayme = (naym *)Malloc(spp*sizeof(naym));
}  /* allocrest */


void freerest()
{
  long i;

  for (i = 0; i < (spp); i++)
    free(d[i]);
  free(d);
  free(alleles);
  free(nayme);
}  /* freerest */


void freex()
{
  long i;

  for (i = 0; i < (spp); i++)
    free(x[i]);
  free(x);
}

void doinit()
{
  /* initializes variables */

  inputnumbers(&spp, &loci, &nonodes, 1);
  getoptions();
}  /* doinit */


void getalleles()
{
  long i;

  if (!firstset) {
    samenumsp(&loci, ith);
    free(alleles);
    alleles = (long *)Malloc(loci*sizeof(long));
  }
  totalleles = 0;
  scan_eoln(infile);
  for (i = 0; i < loci; i++) {
    if (eoln(infile))
      scan_eoln(infile);
    fscanf(infile, "%ld", &alleles[i]);
    totalleles += alleles[i];
  }
  df = totalleles - loci;
}  /* getalleles */


void inputdata()
{
  /* read allele frequencies */
  long i, j, k, m, m1, n;
  double sum;

  for (i = 0; i < spp; i++)
    x[i] = (phenotype3)Malloc(totalleles*sizeof(double));
  for (i = 1; i <= (spp); i++) {
    scan_eoln(infile);
    initname(i-1);
    m = 1;
    for (j = 1; j <= loci; j++) {
      sum = 0.0;
      if (all)
        n = alleles[j - 1];
      else
        n = alleles[j - 1] - 1;
      for (k = 1; k <= n; k++) {
        if (eoln(infile)) 
          scan_eoln(infile);
        fscanf(infile, "%lf", &x[i - 1][m - 1]);
        sum += x[i - 1][m - 1];
        if (x[i - 1][m - 1] < 0.0) {
          printf("\n\nERROR: Locus %ld in species %ld: an allele", j, i);
          printf(" frequency is negative\n\n");
          exxit(-1);
        }
        m++;
      }
      if (all && fabs(sum - 1.0) > epsilong) {
        printf(
     "\n\nERROR: Locus %ld in species %ld: frequencies do not add up to 1\n\n",
               j, i);
        for (m1 = 1; m1 <= n; m1 += 1) {
          if (m1 == 1)
            printf("%f", x[i-1][m-n+m1-2]);
          else {
            if ((m1 % 8) == 1)
              printf("\n");
            printf("+%f", x[i-1][m-n+m1-2]);
            }
          }
        printf(" = %f\n\n", sum);
        exxit(-1);
      }
      if (!all) {
        x[i - 1][m - 1] = 1.0 - sum;
        if (x[i-1][m-1] < -epsilong) {
          printf("\n\nERROR: Locus %ld in species %ld: ",j,i);
          printf("frequencies add up to more than 1\n\n");
          for (m1 = 1; m1 <= n; m1 += 1) {
            if (m1 == 1)
              printf("%f", x[i-1][m-n+m1-2]);
            else {
              if ((m1 % 8) == 1)
                printf("\n");
              printf("+%f", x[i-1][m-n+m1-2]);
              }
            }
          printf(" = %f\n\n", sum);
          exxit(-1);
        }
        m++;
      }
    }
  }
}  /* inputdata */


void getinput()
{
  /* read the input data */
  getalleles();
  inputdata();
}  /* getinput */


void makedists()
{
  long i, j, k;
  double s, s1, s2, s3, f;
  double TEMP;

  if (progress)
    printf("Distances calculated for species\n");
  for (i = 0; i < spp; i++)
    d[i][i] = 0.0;
  for (i = 1; i <= spp; i++) {
    if (progress) {
#ifdef WIN32
      phyFillScreenColor();
#endif
      printf("    ");
      for (j = 0; j < nmlngth; j++)
        putchar(nayme[i - 1][j]);
      printf("   ");
    }
    for (j = 0; j <= i - 2; j++) { /* ignore the diagonal */
      if (cavalli) {
        s = 0.0;
        for (k = 0; k < (totalleles); k++) {
          f = x[i - 1][k] * x[j][k];
          if (f > 0.0)
            s += sqrt(f);
        }
        d[i - 1][j] = 4 * (loci - s) / df;
      }
      if (nei) {
        s1 = 0.0;
        s2 = 0.0;
        s3 = 0.0;
        for (k = 0; k < (totalleles); k++) {
          s1 += x[i - 1][k] * x[j][k];
          TEMP = x[i - 1][k];
          s2 += TEMP * TEMP;
          TEMP = x[j][k];
          s3 += TEMP * TEMP;
        }
        if (s1 <= 1.0e-20) {
          d[i - 1][j] = -1.0;
          printf("\nWARNING: INFINITE DISTANCE BETWEEN SPECIES ");
          printf("%ld AND %ld; -1.0 WAS WRITTEN\n", i, j);
        } else
          d[i - 1][j] = fabs(-log(s1 / sqrt(s2 * s3)));
      }
      if (reynolds) {
        s1 = 0.0;
        s2 = 0.0;
        for (k = 0; k < totalleles; k++) {
          TEMP = x[i - 1][k] - x[j][k];
          s1 += TEMP * TEMP;
          s2 += x[i - 1][k] * x[j][k];
        }
        d[i - 1][j] = s1 / (loci * 2 - 2 * s2);
      }
      if (progress) {
        putchar('.');
        fflush(stdout);
      }
      d[j][i - 1] = d[i - 1][j];
    }
    if (progress) {
      putchar('\n');
      fflush(stdout);
    }
  }
  if (progress) {
    putchar('\n');
    fflush(stdout);
  }
}  /* makedists */


void writedists()
{
  long i, j, k;

  fprintf(outfile, "%5ld\n", spp);
  for (i = 0; i < (spp); i++) {
    for (j = 0; j < nmlngth; j++)
      putc(nayme[i][j], outfile);
    if (lower)
      k = i;
    else
      k = spp;
    for (j = 1; j <= k; j++) {
      if (d[i][j-1] < 100.0)
        fprintf(outfile, "%10.6f", d[i][j-1]);
      else if (d[i][j-1] < 1000.0)
        fprintf(outfile, " %10.6f", d[i][j-1]);
        else
          fprintf(outfile, " %11.6f", d[i][j-1]);
      if ((j + 1) % 7 == 0 && j < k)
        putc('\n', outfile);
    }
    putc('\n', outfile);
  }
  if (progress)
    printf("Distances written to file \"%s\"\n\n", outfilename);
}  /* writedists */


int main(int argc, Char *argv[])
{  /* main program */
#ifdef MAC
  argc = 1;                /* macsetup("Gendist","");                */
  argv[0] = "Gendist";
#endif
  init(argc, argv);
  openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
  openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);

  ibmpc = IBMCRT;
  ansi = ANSICRT;
  mulsets = false;
  firstset = true;
  datasets = 1;
  doinit();
  for (ith = 1; ith <= (datasets); ith++) {
    allocrest();
    getinput();
    firstset = false;
    if ((datasets > 1) && progress)
      printf("\nData set # %ld:\n\n",ith);
    makedists();
    writedists();
    freerest();
    freex();
  }
  FClose(infile);
  FClose(outfile);
#ifdef MAC
  fixmacfile(outfilename);
#endif
  printf("Done.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}