phylip.c

一个神经网络工具箱

{
  /* go to new line if i is a multiple of j, indent k spaces */
  long m;

  if ((i - 1) % j != 0 || i <= 1)
    return;
  putc('\n', filename);
  for (m = 1; m <= k; m++)
    putc(' ', filename);
}  /* newline */

void inputnumbersold(long *spp, long *chars, long *nonodes, long n)
{
  /* input the numbers of species and of characters */

  if (fscanf(infile, "%ld%ld", spp, chars) != 2 || *spp <= 0 || *chars <= 0) {
    printf(
    "ERROR: Unable to read the number of species or characters in data set\n");
    printf(
      "The input file is incorrect (perhaps it was not saved text only).\n");
  }
  *nonodes = *spp * 2 - n;
}  /* inputnumbersold */



void inputnumbers(long *spp, long *chars, long *nonodes, long n)
{
  /* input the numbers of species and of characters */

  if (fscanf(infile, "%ld%ld", spp, chars) != 2 || *spp <= 0 || *chars <= 0) {
    printf(
    "ERROR: Unable to read the number of species or characters in data set\n");
    printf(
      "The input file is incorrect (perhaps it was not saved text only).\n");
  }
  fscanf(infile, "%*[^\n]");
  *nonodes = *spp * 2 - n;
}  /* inputnumbers */


void inputnumbers2(long *spp, long *nonodes, long n)
{
  /* read species number */

  if (fscanf(infile, "%ld", spp) != 1 || *spp <= 0) {
    printf("ERROR: Unable to read the number of species in data set\n");
    printf(
      "The input file is incorrect (perhaps it was not saved text only).\n");
  }
  fscanf(infile, "%*[^\n]");
  fprintf(outfile, "\n%4ld Populations\n", *spp);
  *nonodes = *spp * 2 - n;
}  /* inputnumbers2 */


void inputnumbers3(long *spp, long *chars)
{
  /* input the numbers of species and of characters */

  if (fscanf(infile, "%ld%ld", spp, chars) != 2 || *spp <= 0 || *chars <= 0) {
    printf(
    "ERROR: Unable to read the number of species or characters in data set\n");
    printf(
       "The input file is incorrect (perhaps it was not saved text only).\n");
    exxit(-1);
  }
}  /* inputnumbers3 */


void samenumsp(long *chars, long ith)
{
  /* check if spp is same as the first set in other data sets */
  long cursp, curchs;

  if (eoln(infile)) 
    scan_eoln(infile);
  fscanf(infile, "%ld%ld", &cursp, &curchs);
  if (cursp != spp) {
    printf(
         "\n\nERROR: Inconsistent number of species in data set %ld\n\n", ith);
    exxit(-1);
  }
  *chars = curchs;
} /* samenumsp */


void samenumsp2(long ith)
{
  /* check if spp is same as the first set in other data sets */
  long cursp;

  if (eoln(infile)) 
    scan_eoln(infile);
  if (fscanf(infile, "%ld", &cursp) != 1) {
    printf("\n\nERROR: Unable to read number of species in data set %ld\n",
      ith);
    printf(
      "The input file is incorrect (perhaps it was not saved text only).\n");
    exxit(-1);
  }
  if (cursp != spp) {
    printf(
      "\n\nERROR: Inconsistent number of species in data set %ld\n\n", ith);
    exxit(-1);
  }
} /* samenumsp2 */


void readoptions(long *extranum, const char *options)
{ /* read option characters from input file */
  Char ch;

  while (!(eoln(infile))) {
    ch = gettc(infile);
    uppercase(&ch);
    if (strchr(options, ch) != NULL)
     (* extranum)++;
    else if (!(ch == ' ' || ch == '\t')) {
      printf("BAD OPTION CHARACTER: %c\n", ch);
      exxit(-1);
    }
  }
  scan_eoln(infile);
}  /* readoptions */


void matchoptions(Char *ch, const char *options)
{  /* match option characters to those in auxiliary options line */

  *ch = gettc(infile);
  uppercase(ch);
  if (strchr(options, *ch) == NULL) {
    printf("ERROR: Incorrect auxiliary options line");
    printf(" which starts with %c\n", *ch);
    exxit(-1);
  }
}  /* matchoptions */


void inputweightsold(long chars, steptr weight, boolean *weights)
{
  Char ch;
  int i;

  for (i = 1; i < nmlngth ; i++)
    getc(infile);
 
  for (i = 0; i < chars; i++) {
    do {
      if (eoln(infile)) 
        scan_eoln(infile);
      ch = gettc(infile);
      if (ch == '\n')
        ch = ' ';
    } while (ch == ' ');
    weight[i] = 1;
    if (isdigit(ch))
      weight[i] = ch - '0';
    else if (isalpha(ch)) {
      uppercase(&ch);
      weight[i] = ch - 'A' + 10;
    } else {
      printf("\n\nERROR: Bad weight character: %c\n\n", ch);
      exxit(-1);
    }
  }
  scan_eoln(infile);
  *weights = true;
} /*inputweightsold*/

void inputweights(long chars, steptr weight, boolean *weights)
{
  /* input the character weights, 0-9 and A-Z for weights 0 - 35 */
  Char ch;
  long i;

  for (i = 0; i < chars; i++) {
    do {
      if (eoln(weightfile)) 
        scan_eoln(weightfile);
      ch = gettc(weightfile);
      if (ch == '\n')
        ch = ' ';
    } while (ch == ' ');
    weight[i] = 1;
    if (isdigit(ch))
      weight[i] = ch - '0';
    else if (isalpha(ch)) {
      uppercase(&ch);
      weight[i] = ch - 'A' + 10;
    } else {
      printf("\n\nERROR: Bad weight character: %c\n\n", ch);
      exxit(-1);
    }
  }
  scan_eoln(weightfile);
  *weights = true;
}  /* inputweights */


void inputweights2(long a, long b, long *weightsum,
        steptr weight, boolean *weights, const char *prog)
{
  /* input the character weights, 0 or 1 */
  Char ch;
  long i;

  *weightsum = 0;
  for (i = a; i < b; i++) {
    do {
      if (eoln(weightfile))
        scan_eoln(weightfile);
      ch = gettc(weightfile);
    } while (ch == ' ');
    weight[i] = 1;
    if (ch == '0' || ch == '1')
      weight[i] = ch - '0';
    else {
      printf("\n\nERROR: Bad weight character: %c -- ", ch);
      printf("weights in %s must be 0 or 1\n", prog);
      exxit(-1);
    }
    *weightsum += weight[i];
  }
  *weights = true;
  scan_eoln(weightfile);
}  /* inputweights2 */


void printweights(FILE *filename, long inc, long chars,
        steptr weight, const char *letters)
{
  /* print out the weights of sites */
  long i, j;
  boolean letterweights;

  letterweights = false;
  for (i = 0; i < chars; i++)
    if (weight[i] > 9)
      letterweights = true;
  fprintf(filename, "\n    %s are weighted as follows:",letters);
  if (letterweights)
    fprintf(filename, " (A = 10, B = 11, etc.)\n");
  else
    putc('\n', filename);
  for (i = 0; i < chars; i++) {
    if (i % 60 == 0) {
      putc('\n', filename);
      for (j = 1; j <= nmlngth + 3; j++)
        putc(' ', filename);
    }
    if (weight[i+inc] < 10)
      fprintf(filename, "%ld", weight[i + inc]);
    else
      fprintf(filename, "%c", 'A'-10+(int)weight[i + inc]);
    if ((i+1) % 5 == 0 && (i+1) % 60 != 0)
      putc(' ', filename);
  }
  fprintf(filename, "\n\n");
}  /* printweights */


void inputcategs(long a, long b, steptr category, long categs,const char *prog)
{
  /* input the categories, 1-9 */
  Char ch;
  long i;

  for (i = a; i < b; i++) {
    do {
      if (eoln(catfile)) 
        scan_eoln(catfile);
      ch = gettc(catfile);
    } while (ch == ' ');
    if ((ch >= '1') && (ch <= ('0'+categs)))
      category[i] = ch - '0';
    else {
      printf("\n\nERROR: Bad category character: %c", ch);
      printf(" -- categories in %s are currently 1-%ld\n", prog, categs);
      exxit(-1);
    }
  }
  scan_eoln(catfile);
}  /* inputcategs */


void printcategs(FILE *filename, long chars, steptr category,
                 const char *letters)
{
  /* print out the sitewise categories */
  long i, j;

  fprintf(filename, "\n    %s are:\n",letters);
  for (i = 0; i < chars; i++) {
    if (i % 60 == 0) {
      putc('\n', filename);
      for (j = 1; j <= nmlngth + 3; j++)
        putc(' ', filename);
    }
    fprintf(filename, "%ld", category[i]);
    if ((i+1) % 10 == 0 && (i+1) % 60 != 0)
      putc(' ', filename);
  }
  fprintf(filename, "\n\n");
}  /* printcategs */


void inputfactors(long chars, Char *factor, boolean *factors)
{
  /* reads the factor symbols */
  long i;

  for (i = 1; i < nmlngth; i++)
    gettc(infile);
  for (i = 0; i < (chars); i++) {
    if (eoln(infile)) 
      scan_eoln(infile);
    factor[i] = gettc(infile);
    if (factor[i] == '\n')
      factor[i] = ' ';
  }
  scan_eoln(infile);
  *factors = true;
}  /* inputfactors */

void inputfactorsnew(long chars, Char *factor, boolean *factors)
{
  /* reads the factor symbols */
  long i;

  for (i = 0; i < (chars); i++) {
    if (eoln(factfile)) 
      scan_eoln(factfile);
    factor[i] = gettc(factfile);
    if (factor[i] == '\n')
      factor[i] = ' ';
  }
  scan_eoln(factfile);
  *factors = true;
}  /* inputfactorsnew */

void printfactors(FILE *filename, long chars, Char *factor, const char *letters)
{
  /* print out list of factor symbols */
  long i;

  fprintf(filename, "Factors%s:\n\n", letters);
  for (i = 1; i <= nmlngth - 5; i++)
    putc(' ', filename);
  for (i = 1; i <= (chars); i++) {
    newline(filename, i, 55, nmlngth + 3);
    putc(factor[i - 1], filename);
    if (i % 5 == 0)
      putc(' ', filename);
  }
  putc('\n', filename);
}  /* printfactors */


void headings(long chars, const char *letters1, const char *letters2)
{
  long i, j;

  putc('\n', outfile);
  j = nmlngth + (chars + (chars - 1) / 10) / 2 - 5;
  if (j < nmlngth - 1)
    j = nmlngth - 1;
  if (j > 37)
    j = 37;
  fprintf(outfile, "Name");
  for (i = 1; i <= j; i++)
    putc(' ', outfile);
  fprintf(outfile, "%s\n", letters1);
  fprintf(outfile, "----");
  for (i = 1; i <= j; i++)
    putc(' ', outfile);
  fprintf(outfile, "%s\n\n", letters2);
}  /* headings */


void initname(long i)
{
  /* read in species name */
  long j;

  for (j = 0; j < nmlngth; j++) {
    if (eoff(infile) | eoln(infile)){
      printf("\n\nERROR: end-of-line or end-of-file");
      printf(" in the middle of species name for species %ld\n\n", i+1);
      exxit(-1);
    }
    nayme[i][j] = gettc(infile);
    if ((nayme[i][j] == '(') || (nayme[i][j] == ')') || (nayme[i][j] == ':')
        || (nayme[i][j] == ',') || (nayme[i][j] == ';') || (nayme[i][j] == '[')
        || (nayme[i][j] == ']')) {
      printf("\nERROR: Species name may not contain characters ( ) : ; , [ ] \n");
      printf("       In name of species number %ld there is character %c\n\n",
              i+1, nayme[i][j]);
      exxit(-1);
    }
  }
} /* initname */


void findtree(boolean *found,long *pos,long nextree,long *place,bestelm *bestrees)
{
  /* finds tree given by array place in array bestrees by binary search */
  /* used by dnacomp, dnapars, dollop, mix, & protpars */
  long i, lower, upper;
  boolean below, done;

  below = false;
  lower = 1;
  upper = nextree - 1;
  (*found) = false;
  while (!(*found) && lower <= upper) {
    (*pos) = (lower + upper) / 2;
    i = 3;
    done = false;
    while (!done) {
      done = (i > spp);
      if (!done)
        done = (place[i - 1] != bestrees[(*pos) - 1].btree[i - 1]);
      if (!done)
        i++;
    }
    (*found) = (i > spp);
    if (*found)
      break;
    below = (place[i - 1] <  bestrees[(*pos )- 1].btree[i - 1]);
    if (below)
      upper = (*pos) - 1;
    else
      lower = (*pos) + 1;
  }
  if (!(*found) && !below)
    (*pos)++;
}  /* findtree */


void addtree(long pos,long *nextree,boolean collapse,long *place,bestelm *bestrees)
{
  /* puts tree from array place in its proper position in array bestrees */
  /* used by dnacomp, dnapars, dollop, mix, & protpars */
  long i;

  for (i = *nextree - 1; i >= pos; i--){
    memcpy(bestrees[i].btree, bestrees[i - 1].btree, spp * sizeof(long));
    bestrees[i].gloreange = bestrees[i - 1].gloreange;
    bestrees[i - 1].gloreange = false;
    bestrees[i].locreange = bestrees[i - 1].locreange;
    bestrees[i - 1].locreange = false;
    bestrees[i].collapse = bestrees[i - 1].collapse;
  }
  for (i = 0; i < spp; i++)
    bestrees[pos - 1].btree[i] = place[i];
    bestrees[pos - 1].collapse = collapse;
  (*nextree)++;
}  /* addtree */


long findunrearranged(bestelm *bestrees, long nextree, boolean glob)
{
  /* finds bestree with either global or local field false */
  long i;

  if (glob) {
    for (i = 0; i < nextree - 1; i++)
      if (!bestrees[i].gloreange)
        return i;
  } else {
    for (i = 0; i < nextree - 1; i++)
      if (!bestrees[i].locreange)
        return i;
  }
  return -1;
} /* findunrearranged */


boolean torearrange(bestelm *bestrees, long nextree)
{ /* sees if any best tree is yet to be rearranged */

  if (findunrearranged(bestrees, nextree, true) >= 0)
    return true;
  else if (findunrearranged(bestrees, nextree, false) >= 0)
    return true;
  else
    return false;
} /* torearrange */


void reducebestrees(bestelm *bestrees, long *nextree)
{
  /* finds best trees with collapsible branches and deletes them */
  long i, j;

  i = 0;
  j = *nextree - 2;
  do {
    while (!bestrees[i].collapse && i < *nextree - 1) i++;
    while (bestrees[j].collapse && j >= 0) j--;
    if (i < j) {
      memcpy(bestrees[i].btree, bestrees[j].btree, spp * sizeof(long));
      bestrees[i].gloreange = bestrees[j].gloreange;
      bestrees[i].locreange = bestrees[j].locreange;
      bestrees[i].collapse = false;
      bestrees[j].collapse = true;
    }
  } while (i < j);
  *nextree = i + 1;