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 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 */
