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()
{
/* 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 */