void help(const char *letters)
{
/* display help information */
char input[100];
printf("\n\nR Rearrange a tree by moving a node or group\n");
printf("# Show the states of the next %s that doesn't fit tree\n", letters);
printf("+ Show the states of the next %s\n", letters);
printf("- ... of the previous %s\n", letters);
printf("S Show the states of a given %s\n", letters);
printf(". redisplay the same tree again\n");
printf("T Try all possible positions of a node or group\n");
printf("U Undo the most recent rearrangement\n");
printf("W Write tree to a file\n");
printf("O select an Outgroup for the tree\n");
printf("F Flip (rotate) branches at a node\n");
printf("H Move viewing window to the left\n");
printf("J Move viewing window downward\n");
printf("K Move viewing window upward\n");
printf("L Move viewing window to the right\n");
printf("C show only one Clade (subtree) (useful if tree is too big)\n");
printf("? Help (this screen)\n");
printf("Q (Quit) Exit from program\n");
printf("X Exit from program\n\n\n");
printf("TO CONTINUE, PRESS ON THE Return OR Enter KEY");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
getstryng(input);
} /* help */
void makedists()
{
/* compute distance matrix */
long i, j;
double v;
if (progress) {
printf("Distances calculated for species\n");
#ifdef WIN32
phyFillScreenColor();
#endif
}
for (i = 0; i < spp; i++)
d[i][i] = 0.0;
for (i = 1; i < spp; i++) {
if (progress) {
printf(" ");
for (j = 0; j < nmlngth; j++)
putchar(nayme[i - 1][j]);
printf(" ");
}
for (j = i + 1; j <= spp; j++) {
makev(i, j, &v);
d[i - 1][j - 1] = v;
d[j - 1][i - 1] = v;
if (progress)
putchar('.');
}
if (progress) {
putchar('\n');
#ifdef WIN32
phyFillScreenColor();
#endif
}
}
if (progress) {
printf(" ");
for (j = 0; j < nmlngth; j++)
putchar(nayme[spp - 1][j]);
putchar('\n');
#ifdef WIN32
phyFillScreenColor();
#endif
}
} /* makedists */
void bootwrite()
{ /* does bootstrapping and writes out data sets */
long i, j, rr, repdiv10;
if (!(bootstrap || jackknife || permute || ild || lockhart))
reps = 1;
repdiv10 = reps / 10;
if (repdiv10 < 1)
repdiv10 = 1;
if (progress)
putchar('\n');
for (rr = 1; rr <= (reps); rr++) {
for (i = 0; i < spp; i++)
for (j = 0; j < maxnewsites; j++)
charorder[i][j] = j;
if(rr==1)
firstrep = true;
else
firstrep = false;
if (ild) {
charpermute(0, maxnewsites);
for (i = 1; i < spp; i++)
for (j = 0; j < maxnewsites; j++)
charorder[i][j] = charorder[0][j];
}
if (lockhart)
for (i = 0; i < spp; i++)
charpermute(i, maxnewsites);
bootweights();
if (!justwts || permute || ild || lockhart)
writedata();
if (justwts && !(permute || ild || lockhart))
writeweights();
if (categories)
writecategories();
if (factors)
writefactors();
if (mixture)
writeauxdata(mixdata, outmixfile);
if (ancvar)
writeauxdata(ancdata, outancfile);
if (progress && (bootstrap || jackknife || permute || ild || lockhart)
&& ((reps < 10) || rr % repdiv10 == 0)) {
printf("completed replicate number %4ld\n", rr);
#ifdef WIN32
phyFillScreenColor();
#endif
}
}
if (progress) {
if (justwts)
printf("\nOutput weights written to file \"%s\"\n\n", outweightfilename);
else
printf("\nOutput written to file \"%s\"\n\n", outfilename);
}
} /* bootwrite */
void treeoptions(boolean waswritten, Char *ch, FILE **outtree,
Char *outtreename, Char *progname)
{ /* interactively get options for writing a tree */
char input[100];
if (waswritten) {
printf("\nTree file already was open.\n");
printf(" A Add to this tree to tree file\n");
printf(" R Replace tree file contents by this tree\n");
printf(" F Write out tree to a different tree file\n");
printf(" N Do Not write out this tree\n");
do {
printf("Which should we do? ");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
getstryng(input);
*ch = input[0];
uppercase(ch);
} while (*ch != 'A' && *ch != 'R' && *ch != 'N' && *ch != 'F');
}
if (*ch == 'F') {
outtreename[0] = '\0';
while (outtreename[0] =='\0') {
printf("Please enter a tree file name>");
#ifdef MAC
fixmacfile(outtreename);
#endif
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
getstryng(outtreename);
}
FClose(*outtree);
}
if (*ch == 'R' || *ch == 'A' || *ch == 'F' || !waswritten) {
openfile(outtree,outtreename,"output tree file",
(*ch == 'A' && waswritten) ? "a" : "w",
progname,outtreename);
}
} /* treeoptions */
void inpnum(long *n, boolean *success)
{
/* used by dnamove, dolmove, move, & retree */
int fields;
char line[100];
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
getstryng(line);
*n = atof(line);
fields = sscanf(line,"%ld",n);
*success = (fields == 1);
} /* inpnum */
void addtraverse(node2 *a, node2 *b, node2 *c, long *m, long *n,
valptr valyew, placeptr place)
{
/* traverse all places to add b */
if (done)
return;
if ((*m) <= 2 || !(noroot && (a == root || a == root->next->back))) {
add3(a, b, c, &root, treenode);
(*n)++;
evaluate(root);
examined++;
if (examined == howoften) {
examined = 0;
mults++;
if (mults == howmanny)
done = true;
if (progress) {
printf("%6ld", mults);
if (bestyet >= 0)
printf("%18.5f", bestyet);
else
printf(" - ");
printf("%17ld%20.2f\n", nextree - 1, fracdone * 100);
#ifdef WIN32
phyFillScreenColor();
#endif
}
}
valyew[(*n) - 1] = like;
place[(*n) - 1] = a->index;
re_move3(&b, &c, &root, treenode);
}
if (!a->tip) {
addtraverse(a->next->back, b, c, m,n,valyew,place);
addtraverse(a->next->next->back, b, c, m,n,valyew,place);
}
} /* addtraverse */
void maketree()
{
/* contruct the tree */
long nextsp,numtrees;
boolean succeeded=false;
long i, j, which;
if (usertree) {
inputdata(replicates, printdata, lower, upper, x, reps);
setuptree(&curtree, nonodes2);
for (which = 1; which <= spp; which++)
setuptipf(which, &curtree);
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
openfile(&intree,INTREE,"input tree file","r",progname,intreename);
fscanf(intree, "%ld%*[^\n]", &numtrees);
getc(intree);
if (numtrees > MAXNUMTREES) {
printf("\nERROR: number of input trees is read incorrectly from %s\n",
intreename);
exxit(-1);
}
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
fprintf(outfile, ":\n\n");
}
first = true;
which = 1;
while (which <= numtrees) {
treeread2 (intree, &curtree.start, curtree.nodep,
lengths, &trweight, &goteof, intreename, "Fitch",
&haslengths, &spp);
nums = spp;
curtree.start = curtree.nodep[outgrno - 1]->back;
treevaluate();
printree(&curtree, curtree.start, treeprint, false, false);
summarize(numtrees);
which++;
}
FClose(intree);
} else {
if (jumb == 1) {
inputdata(replicates, printdata, lower, upper, x, reps);
setuptree(&curtree, nonodes2);
setuptree(&priortree, nonodes2);
setuptree(&bestree, nonodes2);
if (njumble > 1) setuptree(&bestree2, nonodes2);
}
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
nextsp = 3;
buildsimpletree(&curtree, nextsp);
curtree.start = curtree.nodep[enterorder[0] - 1]->back;
if (jumb == 1) numtrees = 1;
nextsp = 4;
if (progress) {
printf("Adding species:\n");
writename(0, 3, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
while (nextsp <= spp) {
nums = nextsp;
buildnewtip(enterorder[nextsp - 1], &curtree, nextsp);
copy_(&curtree, &priortree);
bestree.likelihood = -99999.0;
addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back,
curtree.start, true, &numtrees,&succeeded);
copy_(&bestree, &curtree);
if (progress) {
writename(nextsp - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
if (global && nextsp == spp) {
if (progress) {
printf("Doing global rearrangements\n");
printf(" !");
for (j = 1; j <= (spp - 2); j++)
putchar('-');
printf("!\n");
printf(" ");
}
}
succeeded = true;
while (succeeded) {
succeeded = false;
rearrange(curtree.start,
&numtrees,&nextsp,&succeeded);
if (global && ((nextsp) == spp) && progress)
printf("\n ");
}
if (global && nextsp == spp) {
putc('\n', outfile);
if (progress)
putchar('\n');
}
if (njumble > 1) {
if (jumb == 1 && nextsp == spp)
copy_(&bestree, &bestree2);
else if (nextsp == spp) {
if (bestree2.likelihood < bestree.likelihood)
copy_(&bestree, &bestree2);
}
}
if (nextsp == spp && jumb == njumble) {
if (njumble > 1) copy_(&bestree2, &curtree);
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(&curtree, curtree.start, treeprint, true, false);
summarize(numtrees);
}
nextsp++;
}
}
if (jumb == njumble && progress) {
printf("\nOutput written to output file\n\n");
if (trout) {
printf("Tree also written onto file\n");
putchar('\n');
}
}
} /* maketree */
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 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 */
void jointree()
{
/* calculate the tree */
long nc, nextnode, mini=0, minj=0, i, j, ia, ja, ii, jj, nude, iter;
double fotu2, total, tmin, dio, djo, bi, bj, bk, dmin=0, da;
long el[3];
vector av;
intvector oc;
/* for Y. Ina speedups */
double *R;
R = (double *)calloc(spp,sizeof(double));
for (i = 0; i <= spp - 2; i++) {
for (j = i + 1; j < spp; j++) {
da = (x[i][j] + x[j][i]) / 2.0;
x[i][j] = da;
x[j][i] = da;
}
}
/* First initialization */
fotu2 = spp - 2.0;
nextnode = spp + 1;
av = (vector)Malloc(spp*sizeof(double));
oc = (intvector)Malloc(spp*sizeof(long));
for (i = 0; i < spp; i++) {
av[i] = 0.0;
oc[i] = 1;
}
/* Enter the main cycle */
if (njoin)
iter = spp - 3;
else
iter = spp - 1;
for (nc = 1; nc <= iter; nc++) {
for (j = 2; j <= spp; j++) {
for (i = 0; i <= j - 2; i++)
x[j - 1][i] = x[i][j - 1];
}
tmin = 99999.0;
/* Compute sij and minimize */
if (njoin) { /* Y. Ina */
for (i = 0; i < spp; i++) { /* Y. Ina */
R[i] = 0.0; /* Y. Ina */
} /* Y. Ina */
for (ja = 2; ja <= spp; ja++) { /* Y. Ina */
jj = enterorder[ja - 1]; /* Y. Ina */
if (cluster[jj - 1] != NULL) { /* Y. Ina */
for (ia = 0; ia <= ja - 2; ia++) { /* Y. Ina */
ii = enterorder[ia]; /* Y. Ina */
if (cluster[ii - 1] != NULL) { /* Y. Ina */
R[ii - 1] += x[ii - 1][jj - 1]; /* Y. Ina */
R[jj - 1] += x[ii - 1][jj - 1]; /* Y. Ina */
} /* Y. Ina */
} /* Y. Ina */
} /* Y. Ina */
} /* Y. Ina */
} /* Y. Ina */
for (ja = 2; ja <= spp; ja++) {
jj = enterorder[ja - 1];
if (cluster[jj - 1] != NULL) {
for (ia = 0; ia <= ja - 2; ia++) {
ii = enterorder[ia];
if (cluster[ii - 1] != NULL) {
if (njoin) {
/* diq = 0.0;
djq = 0.0;
dij = x[ii - 1][jj - 1];
for (i = 0; i < spp; i++) {
diq += x[i][ii - 1];
djq += x[i][jj - 1];
}
total = fotu2 * dij - diq - djq; */ /* deleted by Y. Ina */
total = fotu2 * x[ii - 1][jj - 1] - R[ii - 1] - R[jj - 1]; /* Y. Ina */
} else
total = x[ii - 1][jj - 1];
if (total < tmin) {
tmin = total;
mini = ii;
minj = jj;
}
}
}
}
}
/* compute lengths and print */
if (njoin) {
dio = 0.0;
djo = 0.0;
for (i = 0; i < spp; i++) {
dio += x[i][mini - 1];
djo += x[i][minj - 1];
}
dmin = x[mini - 1][minj - 1];
dio = (dio - dmin) / fotu2;
djo = (djo - dmin) / fotu2;
bi = (dmin + dio - djo) * 0.5;
bj = dmin - bi;
bi -= av[mini - 1];
bj -= av[minj - 1];
} else {
bi = x[mini - 1][minj - 1] / 2.0 - av[mini - 1];
bj = x[mini - 1][minj - 1] / 2.0 - av[minj - 1];
av[mini - 1] += bi;
}
if (progress) {
printf("Cycle %3ld: ", iter - nc + 1);
if (njoin)
nodelabel(av[mini - 1] > 0.0);
else
nodelabel(oc[mini - 1] > 1.0);
printf("%3ld (%10.5f) joins ", mini, bi);
if (njoin)
nodelabel(av[minj - 1] > 0.0);
else
nodelabel(oc[minj - 1] > 1.0);
printf("%3ld (%10.5f)\n", minj, bj);
#ifdef WIN32
phyFillScreenColor();
#endif
}
hookup(curtree.nodep[nextnode - 1]->next, cluster[mini - 1]);
hookup(curtree.nodep[nextnode - 1]->next->next, cluster[minj - 1]);
cluster[mini - 1]->v = bi;
cluster[minj - 1]->v = bj;
cluster[mini - 1]->back->v = bi;
cluster[minj - 1]->back->v = bj;
cluster[mini - 1] = curtree.nodep[nextnode - 1];
cluster[minj - 1] = NULL;
nextnode++;
if (njoin)
av[mini - 1] = dmin * 0.5;
/* re-initialization */
fotu2 -= 1.0;
for (j = 0; j < spp; j++) {
if (cluster[j] != NULL) {
if (njoin) {
da = (x[mini - 1][j] + x[minj - 1][j]) * 0.5;
if (mini - j - 1 < 0)
x[mini - 1][j] = da;
if (mini - j - 1 > 0)
x[j][mini - 1] = da;
} else {
da = x[mini - 1][j] * oc[mini - 1] + x[minj - 1][j] * oc[minj - 1];
da /= oc[mini - 1] + oc[minj - 1];
x[mini - 1][j] = da;
x[j][mini - 1] = da;
}
}
}
for (j = 0; j < spp; j++) {
x[minj - 1][j] = 0.0;
x[j][minj - 1] = 0.0;
}
oc[mini - 1] += oc[minj - 1];
}
/* the last cycle */
nude = 1;
for (i = 1; i <= spp; i++) {
if (cluster[i - 1] != NULL) {
el[nude - 1] = i;
nude++;
}
}
if (!njoin) {
curtree.start = cluster[el[0] - 1];
curtree.start->back = NULL;
free(av);
free(oc);
return;
}
bi = (x[el[0] - 1][el[1] - 1] + x[el[0] - 1][el[2] - 1] - x[el[1] - 1]
[el[2] - 1]) * 0.5;
bj = x[el[0] - 1][el[1] - 1] - bi;
bk = x[el[0] - 1][el[2] - 1] - bi;
bi -= av[el[0] - 1];
bj -= av[el[1] - 1];
bk -= av[el[2] - 1];
if (progress) {
printf("last cycle:\n");
putchar(' ');
nodelabel(av[el[0] - 1] > 0.0);
printf("%3ld (%10.5f) joins ", el[0], bi);
nodelabel(av[el[1] - 1] > 0.0);
printf("%3ld (%10.5f) joins ", el[1], bj);
nodelabel(av[el[2] - 1] > 0.0);
printf("%3ld (%10.5f)\n", el[2], bk);
#ifdef WIN32
phyFillScreenColor();
#endif
}
hookup(curtree.nodep[nextnode - 1], cluster[el[0] - 1]);
hookup(curtree.nodep[nextnode - 1]->next, cluster[el[1] - 1]);
hookup(curtree.nodep[nextnode - 1]->next->next, cluster[el[2] - 1]);
cluster[el[0] - 1]->v = bi;
cluster[el[1] - 1]->v = bj;
cluster[el[2] - 1]->v = bk;
cluster[el[0] - 1]->back->v = bi;
cluster[el[1] - 1]->back->v = bj;
cluster[el[2] - 1]->back->v = bk;
curtree.start = cluster[el[0] - 1]->back;
free(av);
free(oc);
} /* jointree */
void makedists()
{
/* compute distance matrix */
long i, j;
double v;
inittable();
for (i = 0; i < endsite; i++)
weightrat[i] = weight[i] * rate[category[alias[i] - 1] - 1];
if (progress) {
printf("Distances calculated for species\n");
#ifdef WIN32
phyFillScreenColor();
#endif
}
for (i = 0; i < spp; i++)
if (similarity)
d[i][i] = 1.0;
else
d[i][i] = 0.0;
baddists = false;
float cur_prog = 0;
int total = (spp*spp / 2) + 1;
float step = (1.0f / total) * 100.0f;
for (i = 1; i < spp; i++) {
if (progress) {
printf(" ");
for (j = 0; j < nmlngth; j++)
putchar(nayme[i - 1][j]);
printf(" ");
}
for (j = i + 1; j <= spp; j++) {
makev(i, j, &v);
v = fabs(v);
if ( baddists == true ) {
v = -1;
baddists = false;
}
d[i - 1][j - 1] = v;
d[j - 1][i - 1] = v;
U2::TaskStateInfo* ts = U2::getTaskInfo();
if (ts->cancelFlag != 0) {
ugene_exit("Task canceled!");
} else if(!U2::isBootstr()){
cur_prog += step;
ts->progress = int (cur_prog);
}
if (progress) {
putchar('.');
fflush(stdout);
}
}
if (progress) {
putchar('\n');
#ifdef WIN32
phyFillScreenColor();
#endif
}
}
if (progress) {
printf(" ");
for (j = 0; j < nmlngth; j++)
putchar(nayme[spp - 1][j]);
putchar('\n');
}
} /* makedists */
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 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 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 maketree()
{
/* constructs a binary tree from the pointers in treenode.
adds each node at location which yields highest "likelihood"
then rearranges the tree for greatest "likelihood" */
long i, j, nextnode;
double gotlike;
node *item, *nufork, *dummy, *p;
char *treestr;
fullset = (1L << (bits + 1)) - (1L << 1);
if (!usertree) {
for (i = 1; i <= (spp); i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
root = treenode[enterorder[0] - 1];
add(treenode[enterorder[0] - 1], treenode[enterorder[1] - 1],
treenode[spp], &root, treenode);
if (progress) {
printf("Adding species:\n");
writename(0, 2, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
lastrearr = false;
for (i = 3; i <= (spp); i++) {
bestyet = -350.0 * spp * chars;
item = treenode[enterorder[i - 1] - 1];
nufork = treenode[spp + i - 2];
addpreorder(root, item, nufork);
add(there, item, nufork, &root, treenode);
like = bestyet;
rearrange(&root);
if (progress) {
writename(i - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
lastrearr = (i == spp);
if (lastrearr) {
if (progress) {
printf("\nDoing global rearrangements\n");
printf(" !");
for (j = 1; j <= (nonodes); j++)
if ( j % (( nonodes / 72 ) + 1 ) == 0 )
putchar('-');
printf("!\n");
#ifdef WIN32
phyFillScreenColor();
#endif
}
bestlike = bestyet;
if (jumb == 1) {
bstlike2 = bestlike;
nextree = 1;
}
do {
if (progress)
printf(" ");
gotlike = bestlike;
for (j = 0; j < (nonodes); j++) {
bestyet = - 350.0 * spp * chars;
item = treenode[j];
if (item != root) {
nufork = treenode[j]->back;
re_move(&item, &nufork, &root, treenode);
there = root;
addpreorder(root, item, nufork);
add(there, item, nufork, &root, treenode);
}
if (progress) {
if ( j % (( nonodes / 72 ) + 1 ) == 0 )
putchar('.');
fflush(stdout);
}
}
if (progress) {
putchar('\n');
#ifdef WIN32
phyFillScreenColor();
#endif
}
} while (bestlike > gotlike);
}
}
if (progress)
putchar('\n');
for (i = spp - 1; i >= 1; i--)
re_move(&treenode[i], &dummy, &root, treenode);
if (jumb == njumble) {
if (treeprint) {
putc('\n', outfile);
if (nextree == 2)
fprintf(outfile, "One most parsimonious tree found:\n");
else
fprintf(outfile, "%6ld trees in all found\n", nextree - 1);
}
if (nextree > maxtrees + 1) {
if (treeprint)
fprintf(outfile, "here are the first%4ld of them\n", (long)maxtrees);
nextree = maxtrees + 1;
}
if (treeprint)
putc('\n', outfile);
for (i = 0; i <= (nextree - 2); i++) {
root = treenode[0];
add(treenode[0], treenode[1], treenode[spp], &root, treenode);
for (j = 3; j <= spp; j++) {
add(treenode[bestrees[i].btree[j - 1] - 1], treenode[j - 1],
treenode[spp + j - 2], &root, treenode);}
evaluate(root);
printree(1.0, treeprint, root);
describe();
for (j = 1; j < (spp); j++)
re_move(&treenode[j], &dummy, &root, treenode);
}
}
} else {
if (numtrees > 2) {
emboss_initseed(inseed, &inseed0, seed);
printf("\n");
}
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
fprintf(outfile, ":\n");
}
names = (boolean *)Malloc(spp*sizeof(boolean));
which = 1;
firsttree = true; /**/
nodep = NULL; /**/
nextnode = 0; /**/
haslengths = 0; /**/
phirst = 0; /**/
zeros = (long *)Malloc(chars*sizeof(long)); /**/
for (i = 0; i < chars; i++) /**/
zeros[i] = 0; /**/
while (which <= numtrees) {
treestr = ajStrGetuniquePtr(&phylotrees[which-1]->Tree);
treeread(&treestr, &root, treenode, &goteof, &firsttree,
nodep, &nextnode, &haslengths,
&grbg, initdollopnode,false,nonodes);
for (i = spp; i < (nonodes); i++) {
p = treenode[i];
for (j = 1; j <= 3; j++) {
p->stateone = (bitptr)Malloc(words*sizeof(long));
p->statezero = (bitptr)Malloc(words*sizeof(long));
p = p->next;
}
} /* debug: see comment at initdollopnode() */
if (treeprint)
fprintf(outfile, "\n\n");
evaluate(root);
printree(1.0, treeprint, root);
describe();
which++;
}
FClose(intree);
fprintf(outfile, "\n\n");
if (numtrees > 1 && chars > 1)
standev(numtrees, minwhich, minsteps, nsteps, fsteps, seed);
free(names);
}
if (jumb == njumble) {
if (progress) {
printf("Output written to file \"%s\"\n\n", outfilename);
if (trout)
printf("Trees also written onto file \"%s\"\n\n", outtreename);
}
if (ancseq)
freegarbage(&garbage);
}
} /* maketree */
void maketree()
{ /* construct the tree */
long i;
if (usertree) {
/* Open in binary: ftell() is broken for UNIX line-endings under WIN32 */
openfile(&intree,INTREE,"input tree file", "rb",progname,intreename);
numtrees = countsemic(&intree);
if(numtrees > MAXSHIMOTREES)
shimotrees = MAXSHIMOTREES;
else
shimotrees = numtrees;
if (numtrees > 2)
initseed(&inseed, &inseed0, seed);
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
putc('\n', outfile);
}
setuptree(&curtree, nonodes2);
for (which = 1; which <= spp; which++)
inittip(which, &curtree);
which = 1;
while (which <= numtrees) {
for (i = 0 ; i < nonodes2 ; i++) {
if ( i > spp) {
/* must do this since not all nodes may be used if an
unrooted tree is read in after a rooted one */
curtree.nodep[i]->back = NULL;
curtree.nodep[i]->next->back = NULL;
curtree.nodep[i]->next->next->back = NULL;
}
else curtree.nodep[i]->back = NULL;
}
treeread2 (intree, &curtree.start, curtree.nodep,
lengths, &trweight, &goteof, &haslengths, &spp,false,nonodes2);
curtree.start = curtree.nodep[outgrno - 1]->back;
treevaluate();
printree();
summarize();
which++;
}
FClose(intree);
if (numtrees > 1 && loci > 1 ) {
weight = (long *)Malloc(loci*sizeof(long));
for (i = 0; i < loci; i++)
weight[i] = 1;
standev2(numtrees, maxwhich, 0, loci-1, maxlogl, l0gl, l0gf, seed);
free(weight);
fprintf(outfile, "\n\n");
}
} else { /* if ( !usertree ) */
if (jumb == 1) {
setuptree(&curtree, nonodes2);
setuptree(&priortree, nonodes2);
setuptree(&bestree, nonodes2);
if (njumble > 1)
setuptree(&bestree2, nonodes2);
}
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
nextsp = 3;
buildsimpletree(&curtree);
curtree.start = curtree.nodep[enterorder[0] - 1]->back;
if (jumb == 1) numtrees = 1;
nextsp = 4;
if (progress) {
printf("Adding species:\n");
writename(0, 3, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
while (nextsp <= spp) {
buildnewtip(enterorder[nextsp - 1], &curtree, nextsp);
copy_(&curtree, &priortree);
bestree.likelihood = -DBL_MAX;
addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back,
curtree.start, true );
copy_(&bestree, &curtree);
if (progress) {
writename(nextsp - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
if (global && nextsp == spp) {
if (progress) {
printf("\nDoing global rearrangements\n");
printf(" !");
for (i = 1; i <= spp - 2; i++)
if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 )
putchar('-');
printf("!\n");
printf(" ");
}
}
succeeded = true;
while (succeeded) {
succeeded = false;
if ( global && nextsp == spp )
globrearrange();
else
rearrange(curtree.start);
if (global && nextsp == spp)
putc('\n', outfile);
}
if (global && nextsp == spp && progress)
putchar('\n');
if (njumble > 1) {
if (jumb == 1 && nextsp == spp)
copy_(&bestree, &bestree2);
else if (nextsp == spp) {
if (bestree2.likelihood < bestree.likelihood)
copy_(&bestree, &bestree2);
}
}
if (nextsp == spp && jumb == njumble) {
if (njumble > 1) copy_(&bestree2, &curtree);
curtree.start = curtree.nodep[outgrno - 1]->back;
printree();
summarize();
}
nextsp++;
}
}
if ( jumb < njumble)
return;
if (progress) {
printf("\nOutput written to file \"%s\"\n", outfilename);
if (trout)
printf("\nTree also written onto file \"%s\"\n", outtreename);
}
freeview(&curtree, nonodes2);
if (!usertree) {
freeview(&bestree, nonodes2);
freeview(&priortree, nonodes2);
}
for (i = 0; i < spp; i++)
free(x[i]);
if (!contchars) {
free(locus);
free(pbar);
}
} /* maketree */
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 maketree()
{
/* tree construction recursively by branch and bound */
long i, j, k;
node2 *dummy;
fullset = (1L << (bits + 1)) - (1L << 1);
if (progress) {
printf("\nHow many\n");
printf("trees looked Approximate\n");
printf("at so far Length of How many percentage\n");
printf("(multiples shortest tree trees this long searched\n");
printf("of %4ld): found so far found so far so far\n",
howoften);
printf("---------- ------------ ------------ ------------\n");
#ifdef WIN32
phyFillScreenColor();
#endif
}
done = false;
mults = 0;
examined = 0;
nextree = 1;
root = treenode[0];
firsttime = true;
for (i = 0; i < (spp); i++)
added[i] = false;
added[0] = true;
order[0] = 1;
k = 2;
fracdone = 0.0;
fracinc = 1.0;
bestyet = -1.0;
addit(k);
if (done) {
if (progress) {
printf("Search broken off! Not guaranteed to\n");
printf(" have found the most parsimonious trees.\n");
}
if (treeprint) {
fprintf(outfile, "Search broken off! Not guaranteed to\n");
fprintf(outfile, " have found the most parsimonious\n");
fprintf(outfile, " trees, but here is what we found:\n");
}
}
if (treeprint) {
fprintf(outfile, "\nrequires a total of %18.3f\n\n", bestyet);
if (nextree == 2)
fprintf(outfile, "One most parsimonious tree found:\n");
else
fprintf(outfile, "%5ld trees in all found\n", nextree - 1);
}
if (nextree > maxtrees + 1) {
if (treeprint)
fprintf(outfile, "here are the first%4ld of them\n", (long)maxtrees);
nextree = maxtrees + 1;
}
if (treeprint)
putc('\n', outfile);
for (i = 0; i < (spp); i++)
added[i] = true;
for (i = 0; i <= (nextree - 2); i++) {
for (j = k; j <= (spp); j++)
add3(treenode[bestrees[i][j - 1] - 1],
treenode[bestorders[i][j - 1] - 1], treenode[spp + j - 2],
&root, treenode);
if (noroot)
reroot(treenode[outgrno - 1]);
didreroot = (outgropt && noroot);
evaluate(root);
printree(treeprint, noroot, didreroot, root);
describe();
for (j = k - 1; j < (spp); j++)
re_move3(&treenode[bestorders[i][j] - 1], &dummy, &root, treenode);
}
if (progress) {
printf("\nOutput written to file \"%s\"\n\n", outfilename);
if (trout)
printf("Trees also written onto file \"%s\"\n\n", outtreename);
}
if (ancseq)
freegarbage(&garbage);
} /* maketree */
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 */