コード例 #1
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;
}
コード例 #2
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;
}
コード例 #3
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 */
コード例 #4
0
int main(int argc, Char *argv[])
{
  boolean canbeplotted;
  boolean wasplotted = false;
#ifdef MAC
  OSErr retcode;
  FInfo  fndrinfo;
#ifdef OSX_CARBON
  FSRef fileRef;
  FSSpec fileSpec;
#endif
#ifdef __MWERKS__
  SIOUXSetTitle("\pPHYLIP:  Drawtree");
#endif
  argv[0] = "Drawgram";
#endif

  grbg = NULL;
  progname = argv[0];

#ifndef X_DISPLAY_MISSING
  nargc=1;
  nargv=argv;
#endif
  
  init(argc, argv);
  emboss_getoptions("fdrawgram",argc,argv);

  setup_environment(argv, &canbeplotted);

  user_loop(&canbeplotted);
  if (!((previewer == winpreview || previewer == xpreview || previewer == mac)
        && (winaction == quitnow))) {
    
    previewing = false;
    initplotter(spp,fontname);
    numlines = dotmatrix ? ((long)floor(yunitspercm * ysize + 0.5)/strpdeep) : 1;
    if (plotter != ibm)
      printf("\nWriting plot file ...\n");
    drawit(fontname,&xoffset,&yoffset,numlines,root);
    finishplotter();
    FClose(plotfile);
    wasplotted = true;
    printf("\nPlot written to file \"%s\"\n\n", pltfilename);
  }
  FClose(intree);
#ifdef MAC
  if (plotter == pict && wasplotted){
#ifdef OSX_CARBON
    FSPathMakeRef((unsigned char *)pltfilename, &fileRef, NULL);
    FSGetCatalogInfo(&fileRef, kFSCatInfoNone, NULL, NULL, &fileSpec, NULL);
    FSpGetFInfo(&fileSpec, &fndrinfo);
    fndrinfo.fdType='PICT';
    fndrinfo.fdCreator='MDRW';
    FSpSetFInfo(&fileSpec, &fndrinfo);
#else
    retcode=GetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
    fndrinfo.fdType='PICT';
    fndrinfo.fdCreator='MDRW';
    retcode=SetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
#endif
  }
  if (plotter == lw && wasplotted){
#ifdef OSX_CARBON
    FSPathMakeRef((unsigned char *)pltfilename, &fileRef, NULL);
    FSGetCatalogInfo(&fileRef, kFSCatInfoNone, NULL, NULL, &fileSpec, NULL);
    FSpGetFInfo(&fileSpec, &fndrinfo);
    fndrinfo.fdType='TEXT';
    FSpSetFInfo(&fileSpec, &fndrinfo);
#else
    retcode=GetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
    fndrinfo.fdType='TEXT';
    retcode=SetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
#endif
  }
#endif
  printf("Done.\n\n");

#ifdef WIN32
  phyRestoreConsoleAttributes();
#endif

  embExit();
  return 0;
}
コード例 #5
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 */