void treeoutr(node *p, long *col, tree *curtree)
{
/* write out file with representation of final tree.
* Rooted case. Used in kitsch and neighbor. */
long i, n, w;
Phylip_Char c;
double x;
if (p->tip) {
n = 0;
for (i = 1; i <= nmlngth; i++) {
if (nayme[p->index - 1][i - 1] != ' ')
n = i;
}
for (i = 0; i < n; i++) {
c = nayme[p->index - 1][i];
if (c == ' ')
c = '_';
putc(c, outtree);
}
(*col) += n;
} else {
putc('(', outtree);
(*col)++;
treeoutr(p->next->back,col,curtree);
putc(',', outtree);
(*col)++;
if ((*col) > 55) {
putc('\n', outtree);
(*col) = 0;
}
treeoutr(p->next->next->back,col,curtree);
putc(')', outtree);
(*col)++;
}
x = p->v;
if (x > 0.0)
w = (long)(0.43429448222 * log(x));
else if (x == 0.0)
w = 0;
else
w = (long)(0.43429448222 * log(-x)) + 1;
if (w < 0)
w = 0;
if (p == curtree->root)
fprintf(outtree, ";\n");
else {
// HACK: format using Qt instead of ":%*.5f" which uses system locale radix sign, which can be ","
QString number = QString("%1").arg(x, (int)(w + 7), 'f', 5);
fprintf(outtree, ":%s", number.toStdString().c_str());
(*col) += w + 8;
}
} /* treeoutr */
void treeoutr(node *p, long *col, tree *curtree)
{
/* write out file with representation of final tree.
* Rooted case. Used in kitsch and neighbor. */
long i, n, w;
Char c;
double x;
if (p->tip) {
n = 0;
for (i = 1; i <= nmlngth; i++) {
if (nayme[p->index - 1][i - 1] != ' ')
n = i;
}
for (i = 0; i < n; i++) {
c = nayme[p->index - 1][i];
if (c == ' ')
c = '_';
putc(c, outtree);
}
(*col) += n;
} else {
putc('(', outtree);
(*col)++;
treeoutr(p->next->back,col,curtree);
putc(',', outtree);
(*col)++;
if ((*col) > 55) {
putc('\n', outtree);
(*col) = 0;
}
treeoutr(p->next->next->back,col,curtree);
putc(')', outtree);
(*col)++;
}
x = p->v;
if (x > 0.0)
w = (long)(0.43429448222 * log(x));
else if (x == 0.0)
w = 0;
else
w = (long)(0.43429448222 * log(-x)) + 1;
if (w < 0)
w = 0;
if (p == curtree->root)
fprintf(outtree, ";\n");
else {
fprintf(outtree, ":%*.5f", (int)(w + 7), x);
(*col) += w + 8;
}
} /* treeoutr */
void maketree()
{
/* construct the tree */
long i ;
inputdata(replicates, printdata, lower, upper, x, reps);
/* if (njoin && (spp < 3)) {
mexPrintf("\nERROR: Neighbor-Joining runs must have at least 3 species\n\n");
exxit(-1);
} */
if (progress)
putchar('\n');
if (ith == 1)
setuptree(&curtree, nonodes2 + 1);
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
for (i = 0; i < spp; i++)
cluster[i] = curtree.nodep[i];
jointree();
if (njoin)
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(curtree.start, treeprint, njoin, (boolean)(!njoin));
if (treeprint)
summarize();
if (trout) {
col = 0;
if (njoin)
treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start);
else
curtree.root = curtree.start,
treeoutr(curtree.start,&col,&curtree);
}
if (progress) {
mexPrintf("\nOutput written on file \"%s\"\n\n", outfilename);
if (trout)
mexPrintf("Tree written on file \"%s\"\n\n", outtreename);
}
} /* maketree */
void maketree()
{
/* construct the tree */
long i ;
inputdata(replicates, printdata, lower, upper, x, reps);
if (progress)
putchar('\n');
if (ith == 1)
setuptree(&curtree, nonodes2 + 1);
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
for (i = 0; i < spp; i++)
cluster[i] = curtree.nodep[i];
jointree();
if (outgropt)
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(&curtree, curtree.start->next,
treeprint, njoin, !njoin);
if (treeprint)
summarize();
if (trout) {
col = 0;
if (njoin)
treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start);
else
curtree.root = curtree.start,
treeoutr(curtree.start,&col,&curtree);
}
if (progress) {
printf("\nOutput written on output file\n\n");
if (trout)
printf("Tree written on tree file\n\n");
}
} /* maketree */
