void makedists()
{
/* compute distance matrix */
long i, j;
double v;
if (progress)
printf("Distances calculated for species\n");
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');
}
if (progress) {
printf(" ");
for (j = 0; j < nmlngth; j++)
putchar(nayme[spp - 1][j]);
putchar('\n');
}
} /* makedists */
vector sptk_window(vector data, WINDOW_SETTINGS * settings)
{
int fleng = settings->leng,
outl = -1,
normflg = NORMFLG,
i,j;
Window wintype = settings->window_type;
double *x;
vector res;
if (outl < 0)
outl = fleng;
res = makev(data.x);
x = dgetmem(fleng > outl ? fleng : outl);
for(i=0;i<data.x;i+=fleng){
for(j=0;j<fleng;j++) x[j] = data.v[j+i];
window(wintype, x, fleng, normflg);
for(j=0;j<fleng;j++) res.v[j+i] = x[j];
}
return res;
}
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 */