/* build the global (flat) graph of the universe. this is 'flat'
in the sense that there is one data structure for the entire graph
(not 'flat' in the sense of flat edges within the same level.)
*/
static rank_t *globalize(Agraph_t *user, Agraph_t *topmodel)
{
rank_t *globrank;
int minr,maxr,r;
/* setup bookkeeping */
interclusterpaths(user, topmodel);
/* allocate global ranks */
minr = GD_minrank(topmodel);
maxr = GD_maxrank(topmodel);
globrank = T_array(minr,maxr,sizeof(rank_t));
countup(user,globrank);
for (r = minr; r <= maxr; r++) {
globrank[r].v = N_NEW(globrank[r].n+1,Agnode_t*); /* NIL at end */
globrank[r].n = 0; /* reset it */
}
/* installation */
for (r = minr; r <= maxr; r++)
installglob(user,topmodel,globrank,r);
removejunk(user, topmodel);
reconnect(user, topmodel);
/* optimization */
return globrank;
}
void output_submenu()
{
/* this allows the user to select a different output of distances scheme. */
long loopcount;
boolean done = false;
Char ch;
if (tree_pairing == NO_PAIRING)
return;
loopcount = 0;
while (!done) {
printf ("\nDistances output options:\n");
if ((tree_pairing == ALL_IN_1_AND_2) ||
(tree_pairing == ALL_IN_FIRST))
printf (" F Full matrix.\n");
printf (" V One pair per line, verbose.\n");
printf (" S One pair per line, sparse.\n");
if ((tree_pairing == ALL_IN_1_AND_2) ||
(tree_pairing == ALL_IN_FIRST))
printf ("\n Choose one: (F,V,S)\n");
else
printf ("\n Choose one: (V,S)\n");
fflush(stdout);
scanf("%c%*[^\n]", &ch);
getchar();
uppercase(&ch);
if (strchr("FVS", ch) != NULL) {
switch (ch) {
case 'F':
if ((tree_pairing == ALL_IN_1_AND_2) ||
(tree_pairing == ALL_IN_FIRST))
output_scheme = FULL_MATRIX;
else
/* If this can't be a full matrix... */
continue;
break;
case 'V':
output_scheme = VERBOSE;
break;
case 'S':
output_scheme = SPARSE;
break;
}
done = true;
}
countup(&loopcount, 10);
}
} /* output_submenu */
static void do_launch_program()
{
int num = 1;
launch_cfg_t lc;
/*
* Control flow:
* - Do the startup led blinks.
* - Read the launch config switches.
* - Store launch config
* - Light the launch config leds.
* - Wait for launch button to be pressed
* - Do countdown
* - Activate launch transistors per the launch config.
*/
do_startup_blinky();
g_launch_cfg = get_launch_cfg();
set_launch_cfg_leds(g_launch_cfg);
while (1) {
/*
* poll for launch cfg change or launch button press
*/
lc = get_launch_cfg();
set_launch_cfg_leds(lc);
/*
* Is a human pressing the launch button?
*/
if ((PINC & (1 << PINC3)) == 0) {
break;
}
delay_ms(300);
}
num = countdown(9, 900);
if (!num) {
do_launch();
num = countup(0, 900);
} else {
blink(num, 900);
}
}
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 */
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 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 inseed0=0, loopcount;
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;
loopcount = 0;
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);
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);
} while (!done);
if (lower && upper) {
printf("ERROR: Data matrix cannot be both uppeR and Lower triangular\n");
exxit(-1);
}
} /* 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 */
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 */
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 */
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 */
