Exemplo n.º 1
0
int main(int argc, Char *argv[])
{  /* Read in sequences or frequencies and bootstrap or jackknife them */
#ifdef MAC
  argc = 1;                /* macsetup("SeqBoot","");                */
  argv[0] = "SeqBoot";
#endif
  init(argc,argv);
  openfile(&infile, INFILE, "input file", "r", argv[0], infilename);
  ibmpc = IBMCRT;
  ansi = ANSICRT;
  doinput(argc, argv);
  bootwrite();
  
  freenewer();
  freenew();
  freerest();

  if (nodep)
    matrix_char_delete(nodep, spp);
  if (nodef)
    matrix_double_delete(nodef, spp);

  FClose(infile);
  if (factors) {
    FClose(factfile);
    FClose(outfactfile);
  }
  if (weights)
    FClose(weightfile);
  if (categories) {
    FClose(catfile);
    FClose(outcatfile);
  }
  if(mixture)
    FClose(outmixfile);
  if(ancvar)
    FClose(outancfile);
  if (justwts && !permute) {
    FClose(outweightfile);
  }
  else
    FClose(outfile);
#ifdef MAC
  fixmacfile(outfilename);
  if (justwts && !permute)
    fixmacfile(outweightfilename);
  if (categories)
    fixmacfile(outcatfilename);
  if (mixture)
    fixmacfile(outmixfilename);
#endif
  printf("Done.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}
Exemplo n.º 2
0
int main(int argc, Char *argv[])
{
  int i;
#ifdef MAC
  argc = 1;		/* macsetup("Fitch","");	*/
  argv[0]="Fitch";
#endif
#ifdef WIN32
  phySetConsoleAttributes();
  phyClearScreen();
#endif
  strcpy(progname,argv[0]);
  openfile(&infile,INFILE,"input file","r",argv[0],infilename);
  openfile(&outfile,OUTFILE,"output file","w",argv[0],outfilename);

  ibmpc = IBMCRT;
  ansi = ANSICRT;
  mulsets = false;
  datasets = 1;
  firstset = true;
  doinit();
  if (trout)
    openfile(&outtree,OUTTREE,"output tree file","w",argv[0],outtreename);
  for (i=0;i<spp;++i){
    enterorder[i]=0;}
  for (ith = 1; ith <= datasets; ith++) {
    if (datasets > 1) {
      fprintf(outfile, "Data set # %ld:\n\n",ith);
      if (progress)
        printf("\nData set # %ld:\n\n",ith);
    }
    fitch_getinput();
    for (jumb = 1; jumb <= njumble; jumb++)
        maketree();
    firstset = false;
    if (eoln(infile)) {
      fscanf(infile, "%*[^\n]");
      getc(infile);
    }
  }
  if (trout)
    FClose(outtree);
  FClose(outfile);
  FClose(infile);
#ifdef MAC
  fixmacfile(outfilename);
  fixmacfile(outtreename);
#endif
  printf("Done.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}
Exemplo n.º 3
0
int main(int argc, Char *argv[])
{  /* main program */
  long i;

#ifdef MAC
  argc = 1;                /* macsetup("Contml","");                */
  argv[0] = "Contml";
#endif
  init(argc, argv);
  emboss_getoptions("fcontml", argc, argv);
  progname = argv[0];

  ibmpc = IBMCRT;
  ansi = ANSICRT;
  firstset = true;
  doinit();

  for (ith = 1; ith <= datasets; ith++) {
    getinput();
    if (ith == 1)
      firstset = false;
    if (datasets > 1) {
      fprintf(outfile, "Data set # %ld:\n\n", ith);
      if (progress)
        printf("\nData set # %ld:\n", ith);
    }
    for (jumb = 1; jumb <= njumble; jumb++)
      maketree();
    if (usertree)
      for (i = 0; i < MAXSHIMOTREES; i++)
        free(l0gf[i]);
  }
  FClose(outfile);
  FClose(outtree);
#ifdef MAC
  fixmacfile(outfilename);
  fixmacfile(outtreename);
#endif
  printf("\nDone.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  ajPhyloFreqDel(&phylofreq);
  ajPhyloTreeDelarray(&phylotrees);

  ajFileClose(&embossoutfile);
  ajFileClose(&embossouttree);

  embExit();
  return 0;
}
Exemplo n.º 4
0
int main(int argc, Char *argv[])
{  /* main program */
  long i;

#ifdef MAC
  argc = 1;                /* macsetup("Contml","");                */
  argv[0] = "Contml";
#endif
  init(argc, argv);
  progname = argv[0];
  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();
  if (trout)
    openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
  for (ith = 1; ith <= datasets; ith++) {
    getinput();
    if (ith == 1)
      firstset = false;
    if (datasets > 1) {
      fprintf(outfile, "Data set # %ld:\n\n", ith);
      if (progress)
        printf("\nData set # %ld:\n", ith);
    }
    for (jumb = 1; jumb <= njumble; jumb++)
      maketree();
    if (usertree)
      for (i = 0; i < MAXSHIMOTREES; i++)
        free(l0gf[i]);
  }
  FClose(outfile);
  FClose(outtree);
  FClose(infile);
#ifdef MAC
  fixmacfile(outfilename);
  fixmacfile(outtreename);
#endif
  printf("\nDone.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}
Exemplo n.º 5
0
int main(int argc, Char *argv[])
{  /* main program */
#ifdef MAC
  argc = 1;		/* macsetup("Neighbor","");		*/
  argv[0] = "Neighbor";
#endif
#ifdef WIN32
  phySetConsoleAttributes();
  phyClearScreen();
#endif
  openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
  openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);
  ibmpc = IBMCRT;
  ansi = ANSICRT;
  mulsets = false;
  datasets = 1;
  doinit();
  if (trout)
    openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
  ith = 1;
  while (ith <= datasets) {
    if (datasets > 1) {
      fprintf(outfile, "Data set # %ld:\n",ith);
      if (progress)
        printf("Data set # %ld:\n",ith);
    }
    getinput();
    maketree();
    if (eoln(infile)) {
      fscanf(infile, "%*[^\n]");
      getc(infile);
    }
    ith++;
  }
  FClose(infile);
  FClose(outfile);
  FClose(outtree);
#ifdef MAC
  fixmacfile(outfilename);
  fixmacfile(outtreename);
#endif
  printf("Done.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}
Exemplo n.º 6
0
int main(int argc, Char *argv[])
{  /* Read in sequences or frequencies and bootstrap or jackknife them */
#ifdef MAC
  argc = 1;                /* macsetup("SeqBoot","");                */
  argv[0] = "SeqBoot";
#endif
  init(argc,argv);
  emboss_getoptions("ffreqboot", argc, argv);
  ibmpc = IBMCRT;
  ansi = ANSICRT;
  doinput(argc, argv);
  bootwrite();
  FClose(infile);
  if (weights)
    FClose(weightfile);
  if (categories) {
    FClose(catfile);
    FClose(outcatfile);
  }
  if(mixture)
    FClose(outmixfile);
  if(ancvar)
    FClose(outancfile);
  if (justwts && !permute) {
    FClose(outweightfile);
  }
  else
    FClose(outfile);
#ifdef MAC
  fixmacfile(outfilename);
  if (justwts && !permute)
    fixmacfile(outweightfilename);
  if (categories)
    fixmacfile(outcatfilename);
  if (mixture)
    fixmacfile(outmixfilename);
#endif
  printf("Done.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  embExit();
  return 0;
}
Exemplo n.º 7
0
void treeoptions(boolean waswritten, Char *ch, FILE **outtree,
                 Char *outtreename, Char *progname)
{   /* interactively get options for writing a tree */
    char input[100];

    if (waswritten) {
        printf("\nTree file already was open.\n");
        printf("   A   Add to this tree to tree file\n");
        printf("   R   Replace tree file contents by this tree\n");
        printf("   F   Write out tree to a different tree file\n");
        printf("   N   Do Not write out this tree\n");
        do {
            printf("Which should we do? ");
#ifdef WIN32
            phyFillScreenColor();
#endif
            fflush(stdout);
            getstryng(input);
            *ch  = input[0];
            uppercase(ch);
        } while (*ch != 'A' && *ch != 'R' && *ch != 'N' && *ch != 'F');
    }
    if (*ch == 'F') {
        outtreename[0] = '\0';
        while (outtreename[0] =='\0') {
            printf("Please enter a tree file name>");
#ifdef MAC
            fixmacfile(outtreename);
#endif
#ifdef WIN32
            phyFillScreenColor();
#endif
            fflush(stdout);
            getstryng(outtreename);
        }
        FClose(*outtree);
    }
    if (*ch == 'R' || *ch == 'A' || *ch == 'F' || !waswritten) {
        openfile(outtree,outtreename,"output tree file",
                 (*ch == 'A' && waswritten) ? "a" : "w",
                 progname,outtreename);
    }
}  /* treeoptions */
Exemplo n.º 8
0
int main(int argc, Char *argv[])
{  /* distances from restriction sites or fragments */
#ifdef MAC
  argc = 1;		/* macsetup("Restdist",""); */
  argv[0] = "Restdist";
#endif
#ifdef WIN32
  phySetConsoleAttributes();
  phyClearScreen();
#endif
  strcpy(progname,argv[0]);
  openfile(&infile,INFILE,"input data file","r",argv[0],infilename);
  openfile(&outfile,OUTFILE,"output file","w",argv[0],outfilename);
  ibmpc = IBMCRT;
  ansi = ANSICRT;
  mulsets = false;
  datasets = 1;
  firstset = true;
  doinit();
  for (ith = 1; ith <= datasets; ith++) {
    getinput();
    if (ith == 1)
      firstset = false;
    if (datasets > 1 && progress)
      printf("\nData set # %ld:\n\n",ith);
    makedists();
    writedists();
  }
  FClose(infile);
  FClose(outfile);
#ifdef MAC
  fixmacfile(outfilename);
#endif
  printf("Done.\n\n");
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  return 0;
}  /* distances from restriction sites or fragments */
Exemplo n.º 9
0
int main(int argc, Char *argv[])
{  /* Dollo or polymorphism parsimony by uphill search */
#ifdef MAC
  argc = 1;           /* macsetup("Dollop","");  */
  argv[0] = "Dollop";
#endif
  init(argc, argv);
  emboss_getoptions("fdollop", argc, argv);
  /* reads in spp, chars, and the data. Then calls maketree to
     construct the tree */
  progname = argv[0];

  ibmpc = IBMCRT;
  ansi = ANSICRT;
  garbage = NULL;

  firstset = true;
  bits = 8*sizeof(long) - 1;
  doinit();
 
  if (dollo)
      fprintf(outfile, "Dollo");
  else
      fprintf(outfile, "Polymorphism");
  fprintf(outfile, " parsimony method\n\n");
  if (printdata && justwts)
      fprintf(outfile, "%2ld species, %3ld  characters\n\n", spp, chars);

  for (ith = 1; ith <= (msets); ith++) {
    if (msets > 1 && !justwts) {
      fprintf(outfile, "Data set # %ld:\n\n",ith);
      if (progress)
        printf("\nData set # %ld:\n",ith);
    }
    if (justwts){
        fprintf(outfile, "Weights set # %ld:\n\n", ith);
        if (progress)
            printf("\nWeights set # %ld:\n\n", ith);
    }
    if (printdata && !justwts)
        fprintf(outfile, "%2ld species, %3ld  characters\n\n", spp, chars);
    doinput();
    if (ith == 1)
      firstset = false;
    for (jumb = 1; jumb <= njumble; jumb++)
      maketree();
  }
  /* this would be an appropriate place to deallocate memory, including these items:
  */
  free(steps);
  FClose(infile);
  FClose(outfile);
  FClose(outtree);
#ifdef MAC
  fixmacfile(outfilename);
  fixmacfile(outtreename);
#endif
#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif
  embExit();
  return 0;
}  /* Dollo or polymorphism parsimony by uphill search */
Exemplo n.º 10
0
int main(int argc, Char *argv[])
{   /* Penny's branch-and-bound method */
    /* Reads in the number of species, number of characters,
      options and data.  Then finds all most parsimonious trees */
#ifdef MAC
    argc = 1;                /* macsetup("Penny","");                */
    argv[0] = "Penny";
#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;
    msets = 1;
    firstset = true;
    garbage = NULL;
    bits = 8*sizeof(long) - 1;
    doinit();
    if (weights || justwts)
        openfile(&weightfile,WEIGHTFILE,"weights file","r",argv[0],weightfilename);
    if (trout)
        openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
    if(ancvar)
        openfile(&ancfile,ANCFILE,"ancestors file", "r",argv[0],ancfilename);
    if(mixture)
        openfile(&mixfile,MIXFILE,"mixture file", "r",argv[0],mixfilename);

    for (ith = 1; ith <= msets; ith++) {
        if(firstset) {
            if (allsokal && !mixture)
                fprintf(outfile, "Camin-Sokal parsimony method\n\n");
            if (allwagner && !mixture)
                fprintf(outfile, "Wagner parsimony method\n\n");
        }
        doinput();
        if (msets > 1 && !justwts) {
            fprintf(outfile, "Data set # %ld:\n\n",ith);
            if (progress)
                printf("\nData set # %ld:\n",ith);
        }
        if (justwts) {
            if(firstset && mixture && printdata)
                printmixture(outfile, wagner);
            fprintf(outfile, "Weights set # %ld:\n\n", ith);
            if (progress)
                printf("\nWeights set # %ld:\n\n", ith);
        }
        else if (mixture && printdata)
            printmixture(outfile, wagner);
        if (printdata) {
            if (weights || justwts)
                printweights(outfile, 0, chars, weight, "Characters");
            if (ancvar)
                printancestors(outfile, anczero, ancone);
        }
        if (ith == 1)
            firstset = false;
        maketree();
    }
    FClose(infile);
    FClose(outfile);
    FClose(outtree);
#ifdef MAC
    fixmacfile(outfilename);
    fixmacfile(outtreename);
#endif
#ifdef WIN32
    phyRestoreConsoleAttributes();
#endif
    return 0;
}  /* Penny's branch-and-bound method */
Exemplo n.º 11
0
int main(int argc, Char *argv[])
{  
  pattern_elm  ***pattern_array;
  long tip_count = 0;
  double ln_maxgrp;
  double ln_maxgrp1;
  double ln_maxgrp2;
  node * p;

#ifdef MAC
  argc = 1;                /* macsetup("Treedist", "");        */
  argv[0] = "Treedist";
#endif
  init(argc, argv);
  emboss_getoptions("ftreedist",argc,argv);

  /* Initialize option-based variables, then ask for changes regarding
     their values. */
 

  ntrees = 0.0;
  lasti  = -1;

  /* read files to determine size of structures we'll be working with */
  countcomma(ajStrGetuniquePtr(&phylotrees[0]->Tree),&tip_count);
  tip_count++; /* countcomma does a raw comma count, tips is one greater */


  /* 
   * EWFIX.BUG.756 -- this section may be killed if a good solution
   * to bug 756 is found
   * 
   * inside cons.c there are several arrays which are allocated
   * to size "maxgrp", the maximum number of groups (sets of
   * tips more closely connected than the rest of the tree) we
   * can see as the code executes.
   *
   * We have two measures we use to determine how much space to
   * allot:
   *  (1) based on the tip count of the trees in the infile
   *  (2) based on total number of trees in infile, and 
   *
   * (1) -- Tip Count Method
   * Since each group is a subset of the set of tips we must
   * represent at most pow(2,tips) different groups. (Technically
   * two fewer since we don't store the empty or complete subsets,
   * but let's keep this simple.
   *
   * (2) -- Total Tree Size Method
   * Each tree we read results in 
   *      singleton groups for each tip, plus
   *      a group for each interior node except the root
   * Since the singleton tips are identical for each tree, this gives
   * a bound of #tips + ( #trees * (# tips - 2 ) )
   *
   *
   * Ignoring small terms where expedient, either of the following should
   * result in an adequate allocation:
   *       pow(2,#tips)
   *       (#trees + 1) * #tips 
   *
   * Since "maxgrp" is a limit on the number of items we'll need to put
   * in a hash, we double it to make space for quick hashing
   *
   * BUT -- all of this has the possibility for overflow, so -- let's
   * make the initial calculations with doubles and then convert
   *
   */

  /* limit chosen to make hash arithmetic work */
  maxgrp = LONG_MAX / 2;
  ln_maxgrp = log((double)maxgrp);

  /* 2 * (#trees + 1) * #tips */
  ln_maxgrp1  = log(2.0 * (double)tip_count * 
                            ((double)trees_in_1 + (double)trees_in_2));

  /* ln only for 2 * pow(2,#tips) */
  ln_maxgrp2 = (double)(1 + tip_count) * log(2.0);

  /* now -- find the smallest of the three */
  if(ln_maxgrp1 < ln_maxgrp)
  {
    maxgrp = 2 * (trees_in_1 + trees_in_2 + 1) * tip_count;
    ln_maxgrp = ln_maxgrp1;
  }
  if(ln_maxgrp2 < ln_maxgrp)
  {
    maxgrp = pow(2,tip_count+1);
  }
   

  /* Read the (first) tree file and put together grouping, order, and
     timesseen */
  read_groups (&pattern_array, trees_in_1 + trees_in_2, tip_count, phylotrees);

  if ((tree_pairing == ADJACENT_PAIRS) ||
      (tree_pairing == ALL_IN_FIRST)) {

    /* Here deal with the adjacent or all-in-first pairing
       difference computation */

    compute_distances (pattern_array, trees_in_1, 0);

   } else if (tree_pairing == NO_PAIRING) {
    /* Compute the consensus tree. */
    putc('\n', outfile);
    /* consensus();         Reserved for future development */
  }

  if (progress)
    printf("\nOutput written to file \"%s\"\n\n", outfilename);

  FClose(outtree);
  FClose(intree);
  FClose(outfile);

  if ((tree_pairing == ALL_IN_1_AND_2) || 
      (tree_pairing == CORR_IN_1_AND_2))
    FClose(intree2);

#ifdef MAC
  fixmacfile(outfilename);
  fixmacfile(outtreename);
#endif

  free_patterns (pattern_array, trees_in_1 + trees_in_2);
  clean_up_final();
  /* clean up grbg */
  p = grbg;
  while (p != NULL) {
     node * r = p;
     p = p->next;
     free(r->nodeset);
     free(r->view);
     free(r);
  }


  printf("Done.\n\n");

  embExit();
  return 0;
}  /* main */