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 */
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 */
void getoptions()
{
/* interactively set options */
long i;
long inseed0 = 0;
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;
for(;;) {
printf(ansi ? "\033[2J\033[H" : "\n");
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) {
do {
printf("Random number seed (must be odd)?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%ld%*[^\n]", &inseed);
getchar();
} while (!(inseed & 1));
inseed0 = inseed;
for (i = 0; i <= 5; i++)
seed[i] = 0;
i = 0;
do {
seed[i] = inseed & 63;
inseed /= 64;
i++;
} while (inseed != 0);
}
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);
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");
}
} /* getoptions */
int
main(int argc, char *argv[])
{
/* *INDENT-OFF* */
static MENU mainmenu[] = {
{ "Exit", 0 },
{ "Test of cursor movements", tst_movements },
{ "Test of screen features", tst_screen },
{ "Test of character sets", tst_characters },
{ "Test of double-sized characters", tst_doublesize },
{ "Test of keyboard", tst_keyboard },
{ "Test of terminal reports", tst_reports },
{ "Test of VT52 mode", tst_vt52 },
{ "Test of VT102 features (Insert/Delete Char/Line)", tst_insdel },
{ "Test of known bugs", tst_bugs },
{ "Test of reset and self-test", tst_rst },
{ "Test non-VT100 (e.g., VT220, XTERM) terminals", tst_nonvt100 },
{ "Modify test-parameters", tst_setup },
{ "", 0 }
};
/* *INDENT-ON* */
while (argc-- > 1) {
const char *opt = *++argv;
if (*opt == '-') {
while (*++opt != '\0') {
switch (*opt) {
case 'f':
if (!*++opt) {
if (argc-- < 1)
usage();
opt = *++argv;
}
setup_softchars(opt);
opt = "?";
break;
case 'l':
enable_logging();
break;
case 'p':
use_padding = TRUE;
break;
case 's':
slow_motion = TRUE;
break;
case '8':
output_8bits = TRUE;
break;
default:
usage();
}
}
} else {
/*
* Allow user to specify geometry of terminal to accommodate quasi-VT100
* terminals such as Linux console and xterm.
*/
char *p = argv[0];
char *q;
int values[3], n, m;
for (n = 0; n < 3; n++) {
if (!*p)
break;
if ((m = (int) strtol(p, &q, 10)) > 0) {
values[n] = m;
p = q;
if (*p)
p++;
} else {
break;
}
}
switch (n) {
case 3:
max_cols = values[2];
/* FALLTHRU */
case 2:
min_cols = values[1];
/* FALLTHRU */
case 1:
max_lines = values[0];
break;
}
if ((max_cols < min_cols) || (n == 0)) {
usage();
}
}
}
#ifdef UNIX
initterminal(setjmp(intrenv));
signal(SIGINT, onbrk);
signal(SIGTERM, onterm);
reading = FALSE;
#else
initterminal(0);
#endif
do {
vt_clear(2);
__(title(0), printf("VT100 test program, version %d.%d", RELEASE, PATCHLEVEL));
#ifdef PATCH_DATE
if (PATCH_DATE)
printf(" (%d)", PATCH_DATE);
#endif
title(1);
if (max_lines != 24
|| min_cols != 80
|| max_cols != 132)
printf("Screen size %dx%d (%d max) ", max_lines, min_cols, max_cols);
if (tty_speed != DEFAULT_SPEED)
printf("Line speed %dbd ", tty_speed);
if (use_padding)
printf(" (padded)");
__(title(2), println("Choose test type:"));
} while (menu(mainmenu));
bye();
return EXIT_SUCCESS;
}
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 */
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 */
/* 10 */ smallnumber c ;
c = curmod ;
if ( jobname == 0 )
openlogfile () ;
while ( inputptr > 0 ) if ( ( curinput .indexfield > 15 ) )
endtokenlist () ;
else endfilereading () ;
while ( loopptr != 0 ) stopiteration () ;
while ( openparens > 0 ) {
print ( 1078 ) ;
decr ( openparens ) ;
}
while ( condptr != 0 ) {
printnl ( 1079 ) ;
printcmdmod ( 2 , curif ) ;
if ( ifline != 0 )
{
print ( 1080 ) ;
printint ( ifline ) ;
}
print ( 1081 ) ;
ifline = mem [condptr + 1 ].cint ;
curif = mem [condptr ].hhfield .b1 ;
loopptr = condptr ;
condptr = mem [condptr ].hhfield .v.RH ;
freenode ( loopptr , 2 ) ;
}
if ( history != 0 ) {
if ( ( ( history == 1 ) || ( interaction < 3 ) ) ) {
if ( selector == 3 )
{
selector = 1 ;
printnl ( 1082 ) ;
selector = 3 ;
}
}
}
if ( c == 1 )
{
;
#ifdef INIMF
if ( iniversion )
{
storebasefile () ;
goto lab10 ;
}
#endif /* INIMF */
printnl ( 1083 ) ;
goto lab10 ;
}
lab10: ;
}
#ifdef INIMF
void
initprim ( void )
{
primitive ( 409 , 41 , 1 ) ;
primitive ( 410 , 41 , 2 ) ;
primitive ( 411 , 41 , 3 ) ;
primitive ( 412 , 41 , 4 ) ;
primitive ( 413 , 41 , 5 ) ;
primitive ( 414 , 41 , 6 ) ;
primitive ( 415 , 41 , 7 ) ;
primitive ( 416 , 41 , 8 ) ;
primitive ( 417 , 41 , 9 ) ;
primitive ( 418 , 41 , 10 ) ;
primitive ( 419 , 41 , 11 ) ;
primitive ( 420 , 41 , 12 ) ;
primitive ( 421 , 41 , 13 ) ;
primitive ( 422 , 41 , 14 ) ;
primitive ( 423 , 41 , 15 ) ;
primitive ( 424 , 41 , 16 ) ;
primitive ( 425 , 41 , 17 ) ;
primitive ( 426 , 41 , 18 ) ;
primitive ( 427 , 41 , 19 ) ;
primitive ( 428 , 41 , 20 ) ;
primitive ( 429 , 41 , 21 ) ;
primitive ( 430 , 41 , 22 ) ;
primitive ( 431 , 41 , 23 ) ;
primitive ( 432 , 41 , 24 ) ;
primitive ( 433 , 41 , 25 ) ;
primitive ( 434 , 41 , 26 ) ;
primitive ( 435 , 41 , 27 ) ;
primitive ( 436 , 41 , 28 ) ;
primitive ( 437 , 41 , 29 ) ;
primitive ( 438 , 41 , 30 ) ;
primitive ( 439 , 41 , 31 ) ;
primitive ( 440 , 41 , 32 ) ;
primitive ( 441 , 41 , 33 ) ;
primitive ( 442 , 41 , 34 ) ;
primitive ( 443 , 41 , 35 ) ;
primitive ( 444 , 41 , 36 ) ;
primitive ( 445 , 41 , 37 ) ;
primitive ( 446 , 41 , 38 ) ;
primitive ( 447 , 41 , 39 ) ;
primitive ( 448 , 41 , 40 ) ;
primitive ( 449 , 41 , 41 ) ;
primitive ( 408 , 48 , 0 ) ;
primitive ( 91 , 64 , 0 ) ;
eqtb [9760 ]= eqtb [cursym ];
primitive ( 93 , 65 , 0 ) ;
primitive ( 125 , 66 , 0 ) ;
primitive ( 123 , 47 , 0 ) ;
primitive ( 58 , 82 , 0 ) ;
eqtb [9762 ]= eqtb [cursym ];
primitive ( 459 , 81 , 0 ) ;
primitive ( 460 , 80 , 0 ) ;
primitive ( 461 , 78 , 0 ) ;
primitive ( 44 , 83 , 0 ) ;
primitive ( 59 , 84 , 0 ) ;
eqtb [9763 ]= eqtb [cursym ];
primitive ( 92 , 7 , 0 ) ;
primitive ( 462 , 19 , 0 ) ;
primitive ( 463 , 73 , 0 ) ;
primitive ( 464 , 60 , 0 ) ;
primitive ( 465 , 33 , 0 ) ;
bgloc = cursym ;
primitive ( 466 , 58 , 0 ) ;
primitive ( 467 , 20 , 0 ) ;
primitive ( 468 , 61 , 0 ) ;
primitive ( 469 , 28 , 0 ) ;
primitive ( 470 , 12 , 0 ) ;
primitive ( 453 , 85 , 0 ) ;
eqtb [9767 ]= eqtb [cursym ];
egloc = cursym ;
primitive ( 471 , 27 , 0 ) ;
primitive ( 472 , 6 , 0 ) ;
primitive ( 473 , 10 , 0 ) ;
primitive ( 474 , 71 , 0 ) ;
primitive ( 475 , 74 , 0 ) ;
primitive ( 476 , 14 , 0 ) ;
primitive ( 477 , 15 , 0 ) ;
primitive ( 478 , 16 , 0 ) ;
primitive ( 479 , 70 , 0 ) ;
primitive ( 480 , 29 , 0 ) ;
primitive ( 481 , 25 , 0 ) ;
primitive ( 482 , 9 , 0 ) ;
primitive ( 483 , 13 , 0 ) ;
primitive ( 484 , 8 , 0 ) ;
primitive ( 485 , 18 , 0 ) ;
primitive ( 486 , 79 , 0 ) ;
primitive ( 487 , 75 , 0 ) ;
primitive ( 488 , 36 , 0 ) ;
primitive ( 489 , 59 , 0 ) ;
primitive ( 490 , 72 , 0 ) ;
primitive ( 491 , 76 , 0 ) ;
primitive ( 656 , 17 , 1 ) ;
primitive ( 657 , 17 , 2 ) ;
primitive ( 658 , 17 , 54 ) ;
primitive ( 659 , 17 , 45 ) ;
primitive ( 660 , 17 , 50 ) ;
primitive ( 454 , 17 , 0 ) ;
eqtb [9765 ]= eqtb [cursym ];
primitive ( 661 , 4 , 9770 ) ;
primitive ( 662 , 4 , 9920 ) ;
primitive ( 663 , 4 , 1 ) ;
primitive ( 455 , 4 , 0 ) ;
eqtb [9764 ]= eqtb [cursym ];
primitive ( 664 , 62 , 0 ) ;
primitive ( 665 , 62 , 1 ) ;
primitive ( 64 , 62 , 2 ) ;
primitive ( 666 , 62 , 3 ) ;
primitive ( 677 , 57 , 9770 ) ;
primitive ( 678 , 57 , 9920 ) ;
primitive ( 679 , 57 , 10070 ) ;
primitive ( 680 , 57 , 1 ) ;
primitive ( 681 , 57 , 2 ) ;
primitive ( 682 , 57 , 3 ) ;
primitive ( 692 , 3 , 0 ) ;
primitive ( 618 , 3 , 1 ) ;
primitive ( 719 , 1 , 1 ) ;
primitive ( 452 , 2 , 2 ) ;
eqtb [9766 ]= eqtb [cursym ];
primitive ( 720 , 2 , 3 ) ;
primitive ( 721 , 2 , 4 ) ;
primitive ( 347 , 34 , 30 ) ;
primitive ( 348 , 34 , 31 ) ;
primitive ( 349 , 34 , 32 ) ;
primitive ( 350 , 34 , 33 ) ;
primitive ( 351 , 34 , 34 ) ;
primitive ( 352 , 34 , 35 ) ;
primitive ( 353 , 34 , 36 ) ;
primitive ( 354 , 34 , 37 ) ;
primitive ( 355 , 35 , 38 ) ;
primitive ( 356 , 35 , 39 ) ;
primitive ( 357 , 35 , 40 ) ;
primitive ( 358 , 35 , 41 ) ;
primitive ( 359 , 35 , 42 ) ;
primitive ( 360 , 35 , 43 ) ;
primitive ( 361 , 35 , 44 ) ;
primitive ( 362 , 35 , 45 ) ;
primitive ( 363 , 35 , 46 ) ;
primitive ( 364 , 35 , 47 ) ;
primitive ( 365 , 35 , 48 ) ;
primitive ( 366 , 35 , 49 ) ;
primitive ( 367 , 35 , 50 ) ;
primitive ( 368 , 35 , 51 ) ;
primitive ( 369 , 35 , 52 ) ;
primitive ( 370 , 35 , 53 ) ;
primitive ( 371 , 35 , 54 ) ;
primitive ( 372 , 35 , 55 ) ;
primitive ( 373 , 35 , 56 ) ;
primitive ( 374 , 35 , 57 ) ;
primitive ( 375 , 35 , 58 ) ;
primitive ( 376 , 35 , 59 ) ;
primitive ( 377 , 35 , 60 ) ;
primitive ( 378 , 35 , 61 ) ;
primitive ( 379 , 35 , 62 ) ;
primitive ( 380 , 35 , 63 ) ;
primitive ( 381 , 35 , 64 ) ;
primitive ( 382 , 35 , 65 ) ;
primitive ( 383 , 35 , 66 ) ;
primitive ( 384 , 35 , 67 ) ;
primitive ( 385 , 37 , 68 ) ;
primitive ( 43 , 44 , 69 ) ;
primitive ( 45 , 44 , 70 ) ;
primitive ( 42 , 56 , 71 ) ;
primitive ( 47 , 55 , 72 ) ;
eqtb [9761 ]= eqtb [cursym ];
primitive ( 386 , 46 , 73 ) ;
primitive ( 310 , 46 , 74 ) ;
primitive ( 388 , 53 , 76 ) ;
primitive ( 387 , 46 , 75 ) ;
primitive ( 60 , 51 , 77 ) ;
primitive ( 389 , 51 , 78 ) ;
primitive ( 62 , 51 , 79 ) ;
primitive ( 390 , 51 , 80 ) ;
primitive ( 61 , 52 , 81 ) ;
primitive ( 391 , 51 , 82 ) ;
primitive ( 401 , 38 , 94 ) ;
primitive ( 402 , 38 , 95 ) ;
primitive ( 403 , 38 , 96 ) ;
primitive ( 404 , 38 , 97 ) ;
primitive ( 405 , 38 , 98 ) ;
primitive ( 406 , 38 , 99 ) ;
primitive ( 407 , 38 , 100 ) ;
primitive ( 38 , 49 , 83 ) ;
primitive ( 392 , 56 , 84 ) ;
primitive ( 393 , 56 , 85 ) ;
primitive ( 394 , 56 , 86 ) ;
primitive ( 395 , 56 , 87 ) ;
primitive ( 396 , 56 , 88 ) ;
primitive ( 397 , 56 , 89 ) ;
primitive ( 398 , 56 , 90 ) ;
primitive ( 399 , 56 , 91 ) ;
primitive ( 400 , 46 , 92 ) ;
primitive ( 340 , 31 , 15 ) ;
primitive ( 326 , 31 , 4 ) ;
primitive ( 324 , 31 , 2 ) ;
primitive ( 331 , 31 , 9 ) ;
primitive ( 328 , 31 , 6 ) ;
primitive ( 333 , 31 , 11 ) ;
primitive ( 335 , 31 , 13 ) ;
primitive ( 336 , 31 , 14 ) ;
primitive ( 913 , 86 , 0 ) ;
primitive ( 914 , 86 , 1 ) ;
primitive ( 273 , 24 , 0 ) ;
primitive ( 274 , 24 , 1 ) ;
primitive ( 275 , 24 , 2 ) ;
primitive ( 920 , 24 , 3 ) ;
primitive ( 921 , 22 , 0 ) ;
primitive ( 922 , 22 , 1 ) ;
primitive ( 936 , 23 , 0 ) ;
primitive ( 937 , 23 , 1 ) ;
primitive ( 938 , 23 , 2 ) ;
primitive ( 939 , 23 , 3 ) ;
primitive ( 940 , 23 , 4 ) ;
primitive ( 957 , 69 , 1 ) ;
primitive ( 958 , 69 , 0 ) ;
primitive ( 959 , 69 , 2 ) ;
primitive ( 960 , 67 , 6 ) ;
primitive ( 961 , 67 , 16 ) ;
primitive ( 962 , 68 , 0 ) ;
primitive ( 963 , 68 , 1 ) ;
primitive ( 993 , 26 , 0 ) ;
primitive ( 994 , 26 , 1 ) ;
primitive ( 995 , 26 , 2 ) ;
primitive ( 1005 , 21 , 0 ) ;
primitive ( 1006 , 21 , 1 ) ;
primitive ( 1007 , 21 , 2 ) ;
primitive ( 1008 , 21 , 3 ) ;
primitive ( 1009 , 21 , 4 ) ;
primitive ( 1027 , 77 , 0 ) ;
primitive ( 1028 , 77 , 1 ) ;
primitive ( 1029 , 77 , 5 ) ;
primitive ( 1030 , 77 , 2 ) ;
primitive ( 1031 , 77 , 6 ) ;
primitive ( 1032 , 77 , 3 ) ;
primitive ( 1033 , 77 , 7 ) ;
primitive ( 1034 , 77 , 11 ) ;
primitive ( 1035 , 77 , 128 ) ;
primitive ( 1060 , 30 , 4 ) ;
primitive ( 1061 , 30 , 16 ) ;
}
void
inittab ( void )
{
integer k ;
rover = 23 ;
mem [rover ].hhfield .v.RH = 268435455L ;
mem [rover ].hhfield .lhfield = 1000 ;
mem [rover + 1 ].hhfield .lhfield = rover ;
mem [rover + 1 ].hhfield .v.RH = rover ;
lomemmax = rover + 1000 ;
mem [lomemmax ].hhfield .v.RH = 0 ;
mem [lomemmax ].hhfield .lhfield = 0 ;
{register integer for_end; k = memtop - 2 ;for_end = memtop ; if ( k <=
for_end) do
mem [k ]= mem [lomemmax ];
while ( k++ < for_end ) ;}
avail = 0 ;
memend = memtop ;
himemmin = memtop - 2 ;
varused = 23 ;
dynused = memtop + 1 - himemmin ;
intname [1 ]= 409 ;
intname [2 ]= 410 ;
intname [3 ]= 411 ;
intname [4 ]= 412 ;
intname [5 ]= 413 ;
intname [6 ]= 414 ;
intname [7 ]= 415 ;
intname [8 ]= 416 ;
intname [9 ]= 417 ;
intname [10 ]= 418 ;
intname [11 ]= 419 ;
intname [12 ]= 420 ;
intname [13 ]= 421 ;
intname [14 ]= 422 ;
intname [15 ]= 423 ;
intname [16 ]= 424 ;
intname [17 ]= 425 ;
intname [18 ]= 426 ;
intname [19 ]= 427 ;
intname [20 ]= 428 ;
intname [21 ]= 429 ;
intname [22 ]= 430 ;
intname [23 ]= 431 ;
intname [24 ]= 432 ;
intname [25 ]= 433 ;
intname [26 ]= 434 ;
intname [27 ]= 435 ;
intname [28 ]= 436 ;
intname [29 ]= 437 ;
intname [30 ]= 438 ;
intname [31 ]= 439 ;
intname [32 ]= 440 ;
intname [33 ]= 441 ;
intname [34 ]= 442 ;
intname [35 ]= 443 ;
intname [36 ]= 444 ;
intname [37 ]= 445 ;
intname [38 ]= 446 ;
intname [39 ]= 447 ;
intname [40 ]= 448 ;
intname [41 ]= 449 ;
hashused = 9757 ;
stcount = 0 ;
hash [9768 ].v.RH = 451 ;
hash [9766 ].v.RH = 452 ;
hash [9767 ].v.RH = 453 ;
hash [9765 ].v.RH = 454 ;
hash [9764 ].v.RH = 455 ;
hash [9763 ].v.RH = 59 ;
hash [9762 ].v.RH = 58 ;
hash [9761 ].v.RH = 47 ;
hash [9760 ].v.RH = 91 ;
hash [9759 ].v.RH = 41 ;
hash [9757 ].v.RH = 456 ;
eqtb [9759 ].lhfield = 63 ;
mem [19 ].hhfield .lhfield = 9770 ;
mem [19 ].hhfield .v.RH = 0 ;
mem [memtop ].hhfield .lhfield = 268435455L ;
mem [3 ].hhfield .lhfield = 0 ;
mem [3 ].hhfield .v.RH = 0 ;
mem [4 ].hhfield .lhfield = 1 ;
mem [4 ].hhfield .v.RH = 0 ;
{register integer for_end; k = 5 ;for_end = 11 ; if ( k <= for_end) do
mem [k ]= mem [4 ];
while ( k++ < for_end ) ;}
mem [12 ].cint = 0 ;
mem [0 ].hhfield .v.RH = 0 ;
mem [0 ].hhfield .lhfield = 0 ;
mem [1 ].cint = 0 ;
mem [2 ].cint = 0 ;
serialno = 0 ;
mem [13 ].hhfield .v.RH = 13 ;
mem [14 ].hhfield .lhfield = 13 ;
mem [13 ].hhfield .lhfield = 0 ;
mem [14 ].hhfield .v.RH = 0 ;
mem [21 ].hhfield .b1 = 0 ;
mem [21 ].hhfield .v.RH = 9768 ;
eqtb [9768 ].v.RH = 21 ;
eqtb [9768 ].lhfield = 42 ;
eqtb [9758 ].lhfield = 92 ;
hash [9758 ].v.RH = 736 ;
mem [17 ].hhfield .b1 = 11 ;
mem [20 ].cint = 1073741824L ;
mem [16 ].cint = 0 ;
mem [15 ].hhfield .lhfield = 0 ;
if ( iniversion )
baseident = 1070 ;
}
#endif /* INIMF */
void mainbody( void ) {
bounddefault = 250000L ;
boundname = "main_memory" ;
setupboundvariable ( addressof ( mainmemory ) , boundname , bounddefault ) ;
bounddefault = 3000 ;
boundname = "buf_size" ;
setupboundvariable ( addressof ( bufsize ) , boundname , bounddefault ) ;
bounddefault = 79 ;
boundname = "error_line" ;
setupboundvariable ( addressof ( errorline ) , boundname , bounddefault ) ;
bounddefault = 50 ;
boundname = "half_error_line" ;
setupboundvariable ( addressof ( halferrorline ) , boundname , bounddefault
) ;
bounddefault = 79 ;
boundname = "max_print_line" ;
setupboundvariable ( addressof ( maxprintline ) , boundname , bounddefault )
;
bounddefault = 768 ;
boundname = "screen_width" ;
setupboundvariable ( addressof ( screenwidth ) , boundname , bounddefault )
;
bounddefault = 1024 ;
boundname = "screen_depth" ;
setupboundvariable ( addressof ( screendepth ) , boundname , bounddefault )
;
bounddefault = 16384 ;
boundname = "gf_buf_size" ;
setupboundvariable ( addressof ( gfbufsize ) , boundname , bounddefault ) ;
if ( errorline > 255 )
errorline = 255 ;
if ( screenwidth > 32767 )
screenwidth = 32767 ;
if ( screendepth > 32767 )
screendepth = 32767 ;
{
if ( mainmemory < infmainmemory )
mainmemory = infmainmemory ;
else if ( mainmemory > supmainmemory )
mainmemory = supmainmemory ;
}
memtop = 0 + mainmemory - 1 ;
memmax = memtop ;
{
if ( bufsize < infbufsize )
bufsize = infbufsize ;
else if ( bufsize > supbufsize )
bufsize = supbufsize ;
}
buffer = xmallocarray ( ASCIIcode , bufsize ) ;
rowtransition = xmallocarray ( screencol , screenwidth ) ;
gfbuf = xmallocarray ( eightbits , gfbufsize ) ;
sourcefilenamestack = xmallocarray ( strnumber , 15 ) ;
fullsourcefilenamestack = xmallocarray ( strnumber , 15 ) ;
#ifdef INIMF
if ( iniversion )
{
mem = xmallocarray ( memoryword , memtop + 1 ) ;
}
#endif /* INIMF */
mfluabeginprogram () ;
history = 3 ;
if ( readyalready == 314159L )
goto lab1 ;
bad = 0 ;
if ( ( halferrorline < 30 ) || ( halferrorline > errorline - 15 ) )
bad = 1 ;
if ( maxprintline < 60 )
bad = 2 ;
if ( gfbufsize % 8 != 0 )
bad = 3 ;
if ( 1100 > memtop )
bad = 4 ;
if ( 7919 > 9500 )
bad = 5 ;
if ( headersize % 4 != 0 )
bad = 6 ;
if ( ( ligtablesize < 255 ) || ( ligtablesize > 32510 ) )
bad = 7 ;
#ifdef INIMF
if ( memmax != memtop )
bad = 10 ;
#endif /* INIMF */
if ( memmax < memtop )
bad = 10 ;
if ( ( 0 > 0 ) || ( 255 < 127 ) )
bad = 11 ;
if ( ( 0 > 0 ) || ( 268435455L < 32767 ) )
bad = 12 ;
if ( ( 0 < 0 ) || ( 255 > 268435455L ) )
bad = 13 ;
if ( ( 0 < 0 ) || ( memmax >= 268435455L ) )
bad = 14 ;
if ( maxstrings > 268435455L )
bad = 15 ;
if ( bufsize > 268435455L )
bad = 16 ;
if ( ( 255 < 255 ) || ( 268435455L < 65535L ) )
bad = 17 ;
if ( 9769 + maxinternal > 268435455L )
bad = 21 ;
if ( 10220 > 268435455L )
bad = 22 ;
if ( 15 * 11 > bistacksize )
bad = 31 ;
if ( 20 + 17 * 45 > bistacksize )
bad = 32 ;
if ( basedefaultlength > maxint )
bad = 41 ;
if ( bad > 0 )
{
fprintf ( stdout , "%s%s%ld\n", "Ouch---my internal constants have been clobbered!" , "---case " , (long)bad ) ;
goto lab9999 ;
}
initialize () ;
#ifdef INIMF
if ( iniversion )
{
if ( ! getstringsstarted () )
goto lab9999 ;
inittab () ;
initprim () ;
initstrptr = strptr ;
initpoolptr = poolptr ;
maxstrptr = strptr ;
maxpoolptr = poolptr ;
fixdateandtime () ;
}
#endif /* INIMF */
readyalready = 314159L ;
mfluaPREstartofMF () ;
lab1: selector = 1 ;
tally = 0 ;
termoffset = 0 ;
fileoffset = 0 ;
fprintf ( stdout , "%s%s", "This is MFLua, Version 2.7182818" , "-0.5" ) ;
Fputs ( stdout , versionstring ) ;
if ( baseident == 0 )
fprintf ( stdout , "%s%s%c\n", " (preloaded base=" , dumpname , ')' ) ;
else {
slowprint ( baseident ) ;
println () ;
}
if ( translatefilename )
{
putc ( '(' , stdout );
fputs ( translatefilename , stdout ) ;
{ putc ( ')' , stdout ); putc ( '\n', stdout ); }
}
fflush ( stdout ) ;
jobname = 0 ;
logopened = false ;
outputfilename = 0 ;
{
{
inputptr = 0 ;
maxinstack = 0 ;
inopen = 0 ;
openparens = 0 ;
maxbufstack = 0 ;
paramptr = 0 ;
maxparamstack = 0 ;
first = 1 ;
curinput .startfield = 1 ;
curinput .indexfield = 0 ;
line = 0 ;
curinput .namefield = 0 ;
forceeof = false ;
if ( ! initterminal () )
goto lab9999 ;
curinput .limitfield = last ;
first = last + 1 ;
}
scannerstatus = 0 ;
if ( ( baseident == 0 ) || ( buffer [curinput .locfield ]== 38 ) )
{
if ( baseident != 0 )
initialize () ;
if ( ! openbasefile () )
goto lab9999 ;
if ( ! loadbasefile () )
{
wclose ( basefile ) ;
goto lab9999 ;
}
wclose ( basefile ) ;
while ( ( curinput .locfield < curinput .limitfield ) && ( buffer [
curinput .locfield ]== 32 ) ) incr ( curinput .locfield ) ;
}
buffer [curinput .limitfield ]= 37 ;
fixdateandtime () ;
initrandoms ( ( internal [17 ]/ 65536L ) + internal [16 ]) ;
if ( interaction == 0 )
selector = 0 ;
else selector = 1 ;
if ( curinput .locfield < curinput .limitfield ) {
if ( buffer [curinput .locfield ]!= 92 )
startinput () ;
}
}
history = 0 ;
mfluainitialize () ;
if ( startsym > 0 )
{
cursym = startsym ;
backinput () ;
}
mfluaPREmaincontrol () ;
maincontrol () ;
mfluaPOSTmaincontrol () ;
finalcleanup () ;
mfluaPOSTfinalcleanup () ;
closefilesandterminate () ;
lab9999: {
fflush ( stdout ) ;
readyalready = 0 ;
if ( ( history != 0 ) && ( history != 1 ) )
uexit ( 1 ) ;
else uexit ( 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 */
void getoptions()
{
/* interactively set options */
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;
for (;;) {
printf("%s", (ansi ? ("\033[2J\033[H") : "\n"));
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"));
if (!restsites)
printf(" N Original or modified Nei/Li model? %s\n",
(neili ? "Original" : "Modified"));
if (restsites || !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");
#ifdef WIN32
phyFillScreenColor();
#endif
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 (restsites || !neili)
gama = !gama;
break;
case 'N':
if (!restsites)
neili = !neili;
break;
case 'T':
if (restsites || !neili)
initratio(&ttratio);
break;
case 'S':
do {
printf("New Sitelength?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%lf%*[^\n]", &sitelength);
getchar();
if (sitelength < 1.0)
printf("BAD RESTRICTION SITE LENGTH: %f\n", sitelength);
} 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");
}
if (gama) {
do {
printf(
"\nCoefficient of variation of substitution rate among sites (must be positive)?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%lf%*[^\n]", &cvi);
getchar();
} 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 */
