Beispiel #1
0
void pairing_submenu()
{
  /* this allows the user to select a different tree pairing scheme. */
  long loopcount;
  boolean done = false;
  Char    ch;

  loopcount = 0;
  while (!done) {
    cleerhome();
    printf ("Tree Pairing Submenu:\n");
    printf (" A     Distances between adjacent pairs in tree file.\n");
    printf (" P     Distances between all possible pairs in tree file.\n");
    printf (" C     Distances between corresponding pairs in one tree file and another.\n");
    printf (" L     Distances between all pairs in one tree file and another.\n");

    printf ("\n Choose one: (A,P,C,L)\n");
      
    fflush(stdout);
    scanf("%c%*[^\n]", &ch);
    getchar();
    uppercase(&ch);

    if (strchr("APCL", ch) != NULL) {
      switch (ch) {
        case 'A':
          tree_pairing = ADJACENT_PAIRS;
          break;
              
        case 'P':
          tree_pairing = ALL_IN_FIRST;
          break;

        case 'C':
          tree_pairing = CORR_IN_1_AND_2;
          break;
              
        case 'L':
          tree_pairing = ALL_IN_1_AND_2;
          break;
      }
      output_submenu();
      done = true;
    }
    countup(&loopcount, 10);
  }
}  /* pairing_submenu */
Beispiel #2
0
void getoptions()
{ /* interactively set options */
  long inseed0, loopcount;
  Char ch;
  boolean done;

  fprintf(outfile, "\nContinuous character Maximum Likelihood");
  fprintf(outfile, " method version %s\n\n",VERSION);
  putchar('\n');
  global = false;
  jumble = false;
  njumble = 1;
  lengths = false;
  outgrno = 1;
  outgropt = false;
  all = false;
  contchars = false;
  trout = true;
  usertree = false;
  printdata = false;
  progress = true;
  treeprint = true;
  loopcount = 0;
  do {
    cleerhome();
    printf("\nContinuous character Maximum Likelihood");
    printf(" method version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  U                       Search for best tree?  %s\n",
           (usertree ? "No, use user trees in input" : "Yes"));
    if (usertree) {
      printf("  L                Use lengths from user trees?%s\n",
             (lengths ? "  Yes" : "  No"));
    }
    printf("  C  Gene frequencies or continuous characters?  %s\n",
           (contchars ? "Continuous characters" : "Gene frequencies"));
    if (!contchars)
      printf("  A   Input file has all alleles at each locus?  %s\n",
             (all ? "Yes" : "No, one allele missing at each"));
    printf("  O                              Outgroup root?  %s %ld\n",
           (outgropt ? "Yes, at species number" :
                       "No, use as outgroup species"),outgrno);
    if (!usertree) {
      printf("  G                      Global rearrangements?  %s\n",
             (global ? "Yes" : "No"));
      printf("  J           Randomize input order of species?");
      if (jumble)
        printf("  Yes (seed=%8ld,%3ld times)\n", inseed0, njumble);
      else
        printf("  No. Use input order\n");
    }
    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 out the data at start of run  %s\n",
           (printdata ? "Yes" : "No"));
    printf("  2        Print indications of progress of run  %s\n",
           (progress ? "Yes" : "No"));
    printf("  3                              Print out tree  %s\n",
           (treeprint ? "Yes" : "No"));
    printf("  4             Write out trees onto tree file?  %s\n",
           (trout ? "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);
    done = (ch == 'Y');
    if (!done) {
      if (((!usertree) && (strchr("JOUGACM12340", ch) != NULL))
          || (usertree && ((strchr("LOUACM12340", ch) != NULL)))){
        switch (ch) {

        case 'A':
          if (!contchars)
            all = !all;
          break;

        case 'C':
          contchars = !contchars;
          break;

        case 'G':
          global = !global;
          break;

        case 'J':
          jumble = !jumble;
          if (jumble)
            initjumble(&inseed, &inseed0, seed, &njumble);
          else njumble = 1;
          break;

         case 'L':
           lengths = !lengths;
           break;

        case 'O':
          outgropt = !outgropt;
          if (outgropt)
            initoutgroup(&outgrno, spp);
          break;

        case 'U':
          usertree = !usertree;
          break;

        case 'M':
          mulsets = !mulsets;
          if (mulsets)
            initdatasets(&datasets);
          break;

        case '0':
          initterminal(&ibmpc, &ansi);
          break;

        case '1':
          printdata = !printdata;
          break;

        case '2':
          progress = !progress;
          break;

        case '3':
          treeprint = !treeprint;
          break;

        case '4':
          trout = !trout;
          break;
        }
      } else
        printf("Not a possible option!\n");
    }
    countup(&loopcount, 100);
  } while (!done);
}  /* getoptions */
Beispiel #3
0
void getoptions()
{
  /* interactively set options */
  long inseed0=0;
  Char ch;
  boolean done=false;

  putchar('\n');
  minev = false;
  global = false;
  jumble = false;
  njumble = 1;
  lengths = false;
  lower = false;
  negallowed = false;
  outgrno = 1;
  outgropt = false;
  power = 2.0;
  replicates = false;
  trout = true;
  upper = false;
  usertree = false;
  printdata = false;
  progress = true;
  treeprint = true;
  do {
    cleerhome();
    printf("\nFitch-Margoliash method version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  D      Method (F-M, Minimum Evolution)?  %s\n",
	     (minev ? "Minimum Evolution" : "Fitch-Margoliash"));
    printf("  U                 Search for best tree?  %s\n",
	   (usertree ? "No, use user trees in input file" : "Yes"));
    if (usertree) {
      printf("  N          Use lengths from user trees?  %s\n",
	     (lengths ? "Yes" : "No"));
    }
    printf("  P                                Power?%9.5f\n",power);
    printf("  -      Negative branch lengths allowed?  %s\n",
	   negallowed ? "Yes" : "No");
    printf("  O                        Outgroup root?");
    if (outgropt)
      printf("  Yes, at species number%3ld\n", outgrno);
    else
      printf("  No, use as outgroup species%3ld\n", outgrno);
    printf("  L         Lower-triangular data matrix?");
    if (lower)
      printf("  Yes\n");
    else
      printf("  No\n");
    printf("  R         Upper-triangular data matrix?");
    if (upper)
      printf("  Yes\n");
    else
      printf("  No\n");
    printf("  S                        Subreplicates?");
    if (replicates)
      printf("  Yes\n");
    else
      printf("  No\n");
    if (!usertree) {
      printf("  G                Global rearrangements?");
      if (global)
        printf("  Yes\n");
      else
        printf("  No\n");
      printf("  J     Randomize input order of species?");
      if (jumble)
        printf("  Yes (seed =%8ld,%3ld times)\n", inseed0, njumble);
      else
        printf("  No. Use input order\n");
    }
    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)?");
    if (ibmpc)
      printf("  IBM PC\n");
    if (ansi)
      printf("  ANSI\n");
    if (!(ibmpc || ansi))
      printf("  (none)\n");
    printf("  1    Print out the data at start of run");
    if (printdata)
      printf("  Yes\n");
    else
      printf("  No\n");
    printf("  2  Print indications of progress of run");
    if (progress)
      printf("  Yes\n");
    else
      printf("  No\n");
    printf("  3                        Print out tree");
    if (treeprint)
      printf("  Yes\n");
    else
      printf("  No\n");
    printf("  4       Write out trees onto tree file?");
    if (trout)
      printf("  Yes\n");
    else
      printf("  No\n");
    printf(
   "\n  Y to accept these or type the letter for one to change\n");
#ifdef WIN32
    phyFillScreenColor();
#endif
    scanf("%c%*[^\n]", &ch);
    getchar();
    uppercase(&ch);
    done = (ch == 'Y');
   if (!done) {
      if (strchr("DJOUNPG-LRSM01234",ch) != NULL) {
        switch (ch) {

        case 'D':
          minev = !minev;
          if (minev && (!negallowed))
            negallowed = true;
          break;

        case '-':
          negallowed = !negallowed;
          break;

        case 'G':
          global = !global;
          break;

        case 'J':
          jumble = !jumble;
          if (jumble)
	    initjumble(&inseed, &inseed0, seed, &njumble);
          else njumble = 1;
          break;

        case 'L':
          lower = !lower;
          break;

 	case 'N':
 	  lengths = !lengths;
 	  break;

        case 'O':
          outgropt = !outgropt;
          if (outgropt)
	    initoutgroup(&outgrno, spp);
          break;

        case 'P':
          initpower(&power);
          break;

        case 'R':
          upper = !upper;
          break;

        case 'S':
          replicates = !replicates;
          break;

        case 'U':
          usertree = !usertree;
          break;

        case 'M':
          mulsets = !mulsets;
          if (mulsets)
	    initdatasets(&datasets);
          break;

        case '0':
	  initterminal(&ibmpc, &ansi);
          break;

        case '1':
          printdata = !printdata;
          break;

        case '2':
          progress = !progress;
          break;

        case '3':
          treeprint = !treeprint;
          break;

        case '4':
          trout = !trout;
          break;
        }
      } else
        printf("Not a possible option!\n");
    }
  } while (!done);
}  /* getoptions */
Beispiel #4
0
void getoptions()
{
    /* interactively set options */
    long loopcount, loopcount2;
    Char ch, ch2;

    fprintf(outfile, "\nPenny algorithm, version %s\n",VERSION);
    fprintf(outfile, " branch-and-bound to find all");
    fprintf(outfile, " most parsimonious trees\n\n");
    howoften = often;
    howmanny = many;
    outgrno = 1;
    outgropt = false;
    simple = true;
    thresh = false;
    threshold = spp;
    trout = true;
    weights = false;
    justwts = false;
    ancvar = false;
    allsokal = false;
    allwagner = true;
    mixture = false;
    printdata = false;
    progress = true;
    treeprint = true;
    stepbox = false;
    ancseq = false;
    loopcount = 0;
    for(;;) {
        cleerhome();
        printf("\nPenny algorithm, version %s\n",VERSION);
        printf(" branch-and-bound to find all most parsimonious trees\n\n");
        printf("Settings for this run:\n");
        printf("  X                     Use Mixed method?  %s\n",
               mixture ? "Yes" : "No");
        printf("  P                     Parsimony method?  %s\n",
               (allwagner && !mixture)  ? "Wagner"       :
               (!(allwagner || mixture)) ? "Camin-Sokal"  : "(methods in mixture)");
        printf("  F        How often to report, in trees:%5ld\n",howoften);
        printf("  H        How many groups of%5ld trees:%6ld\n",howoften,howmanny);
        printf("  O                        Outgroup root?");
        if (outgropt)
            printf("  Yes, at species number%3ld\n", outgrno);
        else
            printf("  No, use as outgroup species%3ld\n", outgrno);
        printf("  S           Branch and bound is simple?  %s\n",
               simple ? "Yes" : "No. reconsiders order of species");
        printf("  T              Use Threshold parsimony?");
        if (thresh)
            printf("  Yes, count steps up to%4.1f per char.\n", threshold);
        else
            printf("  No, use ordinary parsimony\n");
        printf("  A   Use ancestral states in input file?  %s\n",
               ancvar ? "Yes" : "No");
        printf("  W                       Sites weighted?  %s\n",
               (weights ? "Yes" : "No"));
        printf("  M           Analyze multiple data sets?");
        if (mulsets)
            printf("  Yes, %2ld %s\n", msets,
                   (justwts ? "sets of weights" : "data sets"));
        else
            printf("  No\n");
        printf("  0   Terminal type (IBM PC, ANSI, none)?  %s\n",
               ibmpc ? "IBM PC" : ansi  ? "ANSI" : "(none)");
        printf("  1    Print out the data at start of run  %s\n",
               printdata ? "Yes" : "No");
        printf("  2  Print indications of progress of run  %s\n",
               progress ? "Yes" : "No");
        printf("  3                        Print out tree  %s\n",
               treeprint ? "Yes" : "No");
        printf("  4     Print out steps in each character  %s\n",
               stepbox ? "Yes" : "No");
        printf("  5     Print states at all nodes of tree  %s\n",
               ancseq ? "Yes" : "No");
        printf("  6       Write out trees onto tree file?  %s\n",
               trout ? "Yes" : "No");
        if(weights && justwts) {
            printf(
                "WARNING:  W option and Multiple Weights options are both on.  ");
            printf(
                "The W menu option is unnecessary and has no additional effect. \n");
        }
        printf("\nAre these settings correct?");
        printf(" (type Y or the letter for one to change)\n");
#ifdef WIN32
        phyFillScreenColor();
#endif
        scanf("%c%*[^\n]", &ch);
        getchar();
        uppercase(&ch);
        if (ch == 'Y')
            break;
        if (strchr("WHFSOMPATX1234560",ch) != NULL) {
            switch (ch) {

            case 'X':
                mixture = !mixture;
                break;

            case 'P':
                allwagner = !allwagner;
                break;

            case 'A':
                ancvar = !ancvar;
                break;

            case 'H':
                inithowmany(&howmanny, howoften);
                break;

            case 'F':
                inithowoften(&howoften);
                break;

            case 'S':
                simple = !simple;
                break;

            case 'O':
                outgropt = !outgropt;
                if (outgropt)
                    initoutgroup(&outgrno, spp);
                else outgrno = 1;
                break;

            case 'T':
                thresh = !thresh;
                if (thresh)
                    initthreshold(&threshold);
                break;

            case 'W':
                weights = !weights;
                break;

            case 'M':
                mulsets = !mulsets;
                if (mulsets) {
                    printf("Multiple data sets or multiple weights?");
                    loopcount2 = 0;
                    do {
                        printf(" (type D or W)\n");
#ifdef WIN32
                        phyFillScreenColor();
#endif
                        scanf("%c%*[^\n]", &ch2);
                        getchar();
                        if (ch2 == '\n')
                            ch2 = ' ';
                        uppercase(&ch2);
                        countup(&loopcount2, 10);
                    } while ((ch2 != 'W') && (ch2 != 'D'));
                    justwts = (ch2 == 'W');
                    if (justwts)
                        justweights(&msets);
                    else
                        initdatasets(&msets);
                }
                break;

            case '0':
                initterminal(&ibmpc, &ansi);
                break;

            case '1':
                printdata = !printdata;
                break;

            case '2':
                progress = !progress;
                break;

            case '3':
                treeprint = !treeprint;
                break;

            case '4':
                stepbox = !stepbox;
                break;

            case '5':
                ancseq = !ancseq;
                break;

            case '6':
                trout = !trout;
                break;
            }
        } else
            printf("Not a possible option!\n");
        countup(&loopcount, 100);
    }
    allsokal = (!allwagner && !mixture);
}  /* getoptions */
Beispiel #5
0
void getoptions()
{
  /* interactively set options */
  long reps0;
  long inseed, inseed0, loopcount, loopcount2;
  Char ch;
  boolean done1;

  data = seqs;
  seq = dna;
  bootstrap = true;
  jackknife = false;
  permute = false;
  ild = false;
  lockhart = false;
  blocksize = 1;
  regular = true;
  fracsample = 1.0;
  all = false;
  reps = 100;
  weights = false;
  mixture = false;
  ancvar = false;
  categories = false;
  justwts = false;
  printdata = false;
  dotdiff = true;
  progress = true;
  interleaved = true;
  xml = false;
  nexus = false;
  factors = false;
  loopcount = 0;
  for (;;) {
    cleerhome();
    printf("\nBootstrapping algorithm, version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  D      Sequence, Morph, Rest., Gene Freqs?  %s\n",
           (data == seqs       ) ? "Molecular sequences"      :
           (data == morphology ) ? "Discrete Morphology"      :
           (data == restsites)   ? "Restriction Sites"        :
           (data == genefreqs)   ? "Gene Frequencies" : "");
    if (data == restsites)
      printf("  E                       Number of enzymes?  %s\n",
             enzymes ? "Present in input file" :
                       "Not present in input file");
    if (data == genefreqs)
      printf("  A       All alleles present at each locus?  %s\n",
             all ? "Yes" : "No, one absent at each locus");
    if ((!lockhart) && (data == morphology))
      printf("  F                 Use factors information?  %s\n",
           factors ? "Yes" : "No");

    printf("  J  Bootstrap, Jackknife, Permute, Rewrite?  %s\n",
           regular && jackknife ? "Delete-half jackknife" :
           (!regular) && jackknife ? "Delete-fraction jackknife" :
           permute   ? "Permute species for each character" :
           ild ? "Permute character order" :
           lockhart ? "Permute within species" :
           regular && bootstrap ? "Bootstrap" :
           (!regular) && bootstrap ? "Partial bootstrap" :
           rewrite ? "Rewrite data" : "(unknown)" );
    
    if (bootstrap || jackknife) {
      printf("  %%    Regular or altered sampling fraction?  ");
      if (regular)
        printf("regular\n");
      else {
        if (fabs(fracsample*100 - (int)(fracsample*100)) > 0.01) {
          printf("%.1f%% sampled\n", 100.0*fracsample);
        } else { 
          printf("%.0f%% sampled\n", 100.0*fracsample);
        }
      }
    }
    if ((data == seqs) && rewrite) {
      printf("  P     PHYLIP, NEXUS, or XML output format?  %s\n",
           nexus ? "NEXUS" : xml ? "XML" : "PHYLIP");
      if (xml || ((data == seqs) && nexus)) {
        printf("  S             Type of molecular sequences?  " );
        switch (seq) {
          case (dna) : printf("DNA\n"); break;
          case (rna) : printf("RNA\n"); break;
          case (protein) : printf("Protein\n"); break;
        }
      }
    }
    if ((data == morphology) && rewrite)
      printf("  P           PHYLIP or NEXUS output format?  %s\n",
                                         nexus ? "NEXUS" : "PHYLIP");
    if (bootstrap) {
      if (blocksize > 1)
      printf("  B      Block size for block-bootstrapping?  %ld\n", blocksize);
      else
        printf("  B      Block size for block-bootstrapping?  %ld (regular bootstrap)\n", blocksize);
    }
    if (!rewrite)
      printf("  R                     How many replicates?  %ld\n", reps);
    if (jackknife || bootstrap || permute || ild) {
      printf("  W              Read weights of characters?  %s\n",
          (weights ? "Yes" : "No"));
      if (data == morphology) {
        printf("  X                       Read mixture file?  %s\n",
               (mixture ? "Yes" : "No"));
        printf("  N                     Read ancestors file?  %s\n",
               (ancvar ? "Yes" : "No"));
      }
      if (data == seqs)
        printf("  C                Read categories of sites?  %s\n",
          (categories ? "Yes" : "No"));
      if ((!permute)) {
        printf("  S     Write out data sets or just weights?  %s\n",
          (justwts ? "Just weights" : "Data sets"));
      }
    }
    if (data == seqs || data == restsites)
      printf("  I             Input sequences interleaved?  %s\n",
             interleaved ? "Yes" : "No, sequential");
    printf("  0      Terminal type (IBM PC, ANSI, none)?  %s\n",
           ibmpc ? "IBM PC" : ansi  ? "ANSI" : "(none)");
    printf("  1       Print out the data at start of run  %s\n",
           printdata ? "Yes" : "No");
    if (printdata)
      printf("  .     Use dot-differencing to display them  %s\n",
           dotdiff ? "Yes" : "No");
    printf("  2     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 (
        (bootstrap && (strchr("ABCDEFSJPRWXNI%1.20",ch) != NULL)) ||
        (jackknife && (strchr("ACDEFSJPRWXNI%1.20",ch) != NULL)) ||
        (permute && (strchr("ACDEFSJPRWXNI%1.20",ch) != NULL)) ||
        ((ild || lockhart) && (strchr("ACDESJPRXNI%1.20",ch) != NULL)) ||
        ((!(bootstrap || jackknife || permute || ild || lockhart)) &&
         ((!xml) && (strchr("ADEFJPI1.20",ch) != NULL))) ||
        (((data == morphology) || (data == seqs))
         && (nexus || xml) && (strchr("ADEFJPSI1.20",ch) != NULL))
        ) {
      switch (ch) {
        
      case 'D':
        if (data == genefreqs)
          data = seqs;
        else
          data = (datatype)((long)data + 1);
        break;
        
      case 'A':
        all = !all;
        break;
        
      case 'E':
        enzymes = !enzymes;
        break;
        
    case 'J':
      if (bootstrap) {
        bootstrap = false;
        jackknife = true;
      } else if (jackknife) {
        jackknife = false;
        permute = true;
      } else if (permute) {
        permute = false;
        ild = true;
      } else if (ild) {
        ild = false;
        lockhart = true;
      } else if (lockhart) {
        lockhart = false;
        rewrite = true;
      } else if (rewrite) {
        rewrite = false;
        bootstrap = true;
      } else {
        assert(0); /* Shouldn't happen */
        bootstrap
          = true;
        jackknife = permute = ild = lockhart = rewrite
          = false;
      }
      break;
        
      case '%':
        regular = !regular;
        if (!regular) {
          loopcount2 = 0;
          do {
            printf("Samples as percentage of");
            if ((data == seqs) || (data == restsites))
              printf(" sites?\n");
            if (data == morphology)
            printf(" characters?\n");
            if (data == genefreqs)
              printf(" loci?\n");
            fflush(stdout);
            scanf("%lf%*[^\n]", &fracsample);
            getchar();
            done1 = (fracsample > 0.0);
            if (!done1) {
              printf("BAD NUMBER: must be positive\n");
            }
            fracsample = fracsample/100.0;
            countup(&loopcount2, 10);
          } while (done1 != true);
        }
        break;

      case 'P':
        if (data == seqs) {
          if (!xml && !nexus)
            nexus = true;
          else {
            if (nexus) {
              nexus = false;
              xml = true;
              }
            else xml = false;
            }
          }
        if (data == morphology) {
          nexus = !nexus;
          xml = false;
          }
        break;
        
      case 'S':
        if(!rewrite){
          justwts = !justwts;          
        } else {
          switch (seq) {
          case (dna): seq = rna; break;
          case (rna): seq = protein; break;
          case (protein): seq = dna; break;
          }
        }
        break;
        
      case 'B':
        loopcount2 = 0;
        do {
          printf("Block size?\n");
#ifdef WIN32
          phyFillScreenColor();
#endif
          fflush(stdout);
          scanf("%ld%*[^\n]", &blocksize);
          getchar();
          done1 = (blocksize > 0);
          if (!done1) {
            printf("BAD NUMBER: must be positive\n");
          }
          countup(&loopcount2, 10);
        } while (done1 != true);
        break;

      case 'R':
        reps0 = reps;
        loopcount2 = 0;
        do {
          printf("Number of replicates?\n");
#ifdef WIN32
          phyFillScreenColor();
#endif
          fflush(stdout);
          scanf("%ld%*[^\n]", &reps);
          getchar();
          done1 = (reps > 0);
          if (!done1) {
            printf("BAD NUMBER: must be positive\n");
            reps = reps0;
          }
          countup(&loopcount2, 10);
        } while (done1 != true);
        break;

      case 'W':
        weights = !weights;
        break;

      case 'X':
        mixture = !mixture;
        break;

      case 'N':
        ancvar = !ancvar;
        break;

      case 'C':
        categories = !categories;
        break;

      case 'F':
        factors = !factors;
        break;

      case 'I':
        interleaved = !interleaved;
        break;
        
      case '0':
        initterminal(&ibmpc, &ansi);
        break;
        
      case '1':
        printdata = !printdata;
        break;
        
      case '.':
        dotdiff = !dotdiff;
        break;
        
      case '2':
        progress = !progress;
        break;
      }
    } else
      printf("Not a possible option!\n");
    countup(&loopcount, 100);
  }
  if (bootstrap || jackknife) {
    if (jackknife && regular)
      fracsample = 0.5;
    if (bootstrap && regular)
      fracsample = 1.0;
  }
  if (!rewrite)
    initseed(&inseed, &inseed0, seed);

  /* These warnings only appear when user has changed an option that
   * subsequently became inapplicable */
  if (factors && lockhart) {
    printf("Warning: Cannot use factors when permuting within species.\n");
    factors = false;
  }
  if (data != seqs) {
    if (xml) {
      printf("warning: XML output not available for this type of data\n");
      xml = false;
    }
    if (categories) {
      printf("warning: cannot use categories file with this type of data\n");
      categories = false;
    }
  }
  if (data != morphology) {
    if (mixture) {
      printf("warning: cannot use mixture file with this type of data\n");
      mixture = false;
    }
    if (ancvar) {
      printf("warning: cannot use ancestors file with this type of data\n");
      ancvar = false;
    }
  }
}  /* getoptions */
Beispiel #6
0
void getoptions()
{
  /* interactively set options */
  long inseed0 = 0, loopcount;
  Char ch;

  fprintf(outfile, "\nNeighbor-Joining/UPGMA method version %s\n\n",VERSION);
  putchar('\n');
  jumble = false;
  lower = false;
  outgrno = 1;
  outgropt = false;
  replicates = false;
  trout = true;
  upper = false;
  printdata = false;
  progress = true;
  treeprint = true;
  njoin = true;
  loopcount = 0;
  for(;;) {
    cleerhome();
    printf("\nNeighbor-Joining/UPGMA method version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  N       Neighbor-joining or UPGMA tree?  %s\n",
           (njoin ? "Neighbor-joining" : "UPGMA"));
    if (njoin) {
      printf("  O                        Outgroup root?");
      if (outgropt)
        printf("  Yes, at species number%3ld\n", outgrno);
      else
        printf("  No, use as outgroup species%3ld\n", outgrno);
    }
    printf("  L         Lower-triangular data matrix?  %s\n",
           (lower ? "Yes" : "No"));
    printf("  R         Upper-triangular data matrix?  %s\n",
           (upper ? "Yes" : "No"));
    printf("  S                        Subreplicates?  %s\n",
           (replicates ? "Yes" : "No"));
    printf("  J     Randomize input order of species?");
    if (jumble)
      printf("  Yes (random number seed =%8ld)\n", inseed0);
    else
      printf("  No. Use input order\n");
    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 out the data at start of run  %s\n",
           (printdata ? "Yes" : "No"));
    printf("  2  Print indications of progress of run  %s\n",
           (progress ? "Yes" : "No"));
    printf("  3                        Print out tree  %s\n",
           (treeprint ? "Yes" : "No"));
    printf("  4       Write out trees onto tree file?  %s\n",
           (trout ? "Yes" : "No"));
    printf("\n\n  Y to accept these or type the letter for one to change\n");
#ifdef WIN32
    phyFillScreenColor();
#endif
    scanf("%c%*[^\n]", &ch);
    getchar();
    if (ch == '\n')
      ch = ' ';
    uppercase(&ch);
    if  (ch == 'Y')
      break;
    if (strchr("NJOULRSM01234",ch) != NULL){
      switch (ch) {
        
      case 'J':
        jumble = !jumble;
         if (jumble)
          initseed(&inseed, &inseed0, seed);
        break;
        
      case 'L':
        lower = !lower;
        break;
        
      case 'O':
        outgropt = !outgropt;
        if (outgropt)
          initoutgroup(&outgrno, spp);
        else
          outgrno = 1;
        break;
        
      case 'R':
        upper = !upper;
        break;
        
      case 'S':
        replicates = !replicates;
        break;
        
      case 'N':
        njoin = !njoin;
        break;
        
      case 'M':
        mulsets = !mulsets;
        if (mulsets)
          initdatasets(&datasets);
        jumble = true;
         if (jumble)
          initseed(&inseed, &inseed0, seed);
        break;
        
      case '0':
        initterminal(&ibmpc, &ansi);
        break;
        
      case '1':
        printdata = !printdata;
        break;
        
      case '2':
        progress = !progress;
        break;
        
      case '3':
        treeprint = !treeprint;
        break;
        
      case '4':
        trout = !trout;
        break;
      }
    } else
      printf("Not a possible option!\n");
    countup(&loopcount, 100);
  }
}  /* getoptions */
Beispiel #7
0
void getoptions()
{
  /* interactively set options */
  long loopcount;
  Char ch;
  boolean done, gotopt;
  char input[100];

  how = arb;
  usertree = false;
  goteof = false;
  thresh = false;
  threshold = spp;
  weights = false;
  ancvar = false;
  factors = false;
  dollo = true;
  loopcount = 0;
  do {
    cleerhome();
    printf("\nInteractive Dollo or polymorphism parsimony,");
    printf(" version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  P                        Parsimony method?");
    printf("  %s\n",(dollo ? "Dollo" : "Polymorphism"));
    printf("  A                    Use ancestral states?  %s\n",
           ancvar ? "Yes" : "No");
    printf("  F                 Use factors information?  %s\n",
           factors ? "Yes" : "No");
    printf("  W                          Sites weighted?  %s\n",
           (weights ? "Yes" : "No"));
    printf("  T                 Use Threshold parsimony?");
    if (thresh)
      printf("  Yes, count steps up to%4.1f\n", threshold);
    else
      printf("  No, use ordinary parsimony\n");
    printf("  A      Use ancestral states in input file?");
    printf("  %s\n",(ancvar ? "Yes" : "No"));
    printf("  U Initial tree (arbitrary, user, specify)?");
    printf("  %s\n",(how == arb) ? "Arbitrary" :
                    (how == use) ? "User tree from tree file" :
                                   "Tree you specify");
    printf("  0      Graphics type (IBM PC, ANSI, none)?  %s\n",
           ibmpc ? "IBM PC" : ansi  ? "ANSI"   : "(none)");
    printf("  L               Number of lines on screen?%4ld\n",screenlines);
    printf("  S                Width of terminal screen?%4ld\n",screenwidth);
    printf(
      "\n\nAre these settings correct? (type Y or the letter for one to change)\n");
#ifdef WIN32
    phyFillScreenColor();
#endif
    getstryng(input);
    ch = input[0];
    uppercase(&ch);
    done = (ch == 'Y');
    gotopt = (strchr("SFTPULA0W",ch) != NULL) ? true : false;
    if (gotopt) {
      switch (ch) {

      case 'A':
        ancvar = !ancvar;
        break;

      case 'F':
        factors = !factors;
        break;

      case 'W':
        weights = !weights;
        break;
        
      case 'P':
        dollo = !dollo;
        break;

      case 'T':
        thresh = !thresh;
        if (thresh)
          initthreshold(&threshold);
        break;

      case 'U':
        if (how == arb)
          how = use;
        else if (how == use)
            how = spec;
          else
            how = arb;
        break;

      case '0':
        initterminal(&ibmpc, &ansi);
        break;

      case 'L':
        initnumlines(&screenlines);
        break;

      case 'S':
        screenwidth = readlong("Width of terminal screen (in characters)?\n");
      }
    }
    else  
      printf("Not a possible option!\n");
    countup(&loopcount, 100);
  } while (!done);
  if (scrollinc < screenwidth / 2.0)
    hscroll = scrollinc;
  else
    hscroll = screenwidth / 2;
  if (scrollinc < screenlines / 2.0)
    vscroll = scrollinc;
  else
    vscroll = screenlines / 2;
}  /* getoptions */
Beispiel #8
0
void getoptions()
{
  /* interactively set options */
  long loopcount, loopcount2;
  Char ch;

  putchar('\n');
  sitelength = 6.0;
  neili = false;
  gama = false;
  cvi = 0.0;
  weights = false;
  lower = false;
  printdata = false;
  progress = true;
  restsites = true;
  interleaved = true;
  ttratio = 2.0;
  loopcount = 0;
  for (;;) {
    cleerhome();
    printf("\nRestriction site or fragment distances, ");
    printf("version %s\n\n",VERSION);
    printf("Settings for this run:\n");
    printf("  R           Restriction sites or fragments?  %s\n",
           (restsites ? "Sites" : "Fragments"));
    printf("  N        Original or modified Nei/Li model?  %s\n",
           (neili ? "Original" : "Modified"));
    if (!neili) {
      printf("  G  Gamma distribution of rates among sites?");
      if (!gama)
        printf("  No\n");
      else
        printf("  Yes\n");
      printf("  T            Transition/transversion ratio?  %f\n", ttratio);
    }
    printf("  S                              Site length? %4.1f\n",sitelength);
    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("  I              Input sequences interleaved?  %s\n",
           (interleaved ? "Yes" : "No, sequential"));
    printf("  0       Terminal type (IBM PC, ANSI, none)?  %s\n",
           ibmpc ? "IBM PC" : ansi  ? "ANSI" : "(none)");
    printf("  1       Print out the data at start of run?  %s\n",
           (printdata ? "Yes" : "No"));
    printf("  2     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");
    fflush(stdout);
    scanf("%c%*[^\n]", &ch);
    getchar();
    if (ch == '\n')
      ch = ' ';
    uppercase(&ch);
    if (ch == 'Y')
      break;
    if (strchr("RDNGTSLMI012",ch) != NULL){
      switch (ch) {
        
      case 'R':
        restsites = !restsites;
        break;
        
      case 'G':
        if (!neili) 
          gama = !gama;
        break;

      case 'N':
        neili = !neili;
        break;

      case 'T':
        if (!neili)
          initratio(&ttratio);
        break;

      case 'S':
        loopcount2 = 0;
        do {
          printf("New Sitelength?\n");
          fflush(stdout);
          scanf("%lf%*[^\n]", &sitelength);
          getchar();
          if (sitelength < 1.0)
            printf("BAD RESTRICTION SITE LENGTH: %f\n", sitelength); 
          countup(&loopcount2, 10);
        } while (sitelength < 1.0);
        break;
        
      case 'L':
        lower = !lower;
        break;

      case 'M':
        mulsets = !mulsets;
        if (mulsets)
          initdatasets(&datasets);
        break;
        
      case 'I':
        interleaved = !interleaved;
        break;
        
      case '0':
        initterminal(&ibmpc, &ansi);
        break;
        
      case '1':
        printdata = !printdata;
        break;
        
      case '2':
        progress = !progress;
        break;
        
      }
    } else
      printf("Not a possible option!\n");
    countup(&loopcount, 100);
  }
  if (gama) {
    loopcount = 0;
    do {
      printf(
"\nCoefficient of variation of substitution rate among sites (must be positive)?\n");
      fflush(stdout);
      scanf("%lf%*[^\n]", &cvi);
      getchar();
      countup(&loopcount, 100);
    } while (cvi <= 0.0);
    cvi = 1.0 / (cvi * cvi);
    printf("\n");
  }
  xi = (ttratio - 0.5)/(ttratio + 0.5);
  xv = 1.0 - xi;
  fracchange = xi*0.5 + xv*0.75;
}  /* getoptions */