static void gthinitfragments(GtFragment *fragments,
GtUword *num_of_fragments,
GthMatch *storematchtab,
GtUword numofmatches,
GtUword rare,
double fragweightfactor)
{
GthMatch *mptr;
GtFragment *fragmentptr;
GtWord tmp, largestdim1 = 0, largestdim2 = 0;
GtDiscDistri *startpointdistri = NULL;
/* init number of fragments */
*num_of_fragments = 0;
if (rare)
startpointdistri = gt_disc_distri_new();
for (mptr = storematchtab; mptr < storematchtab + numofmatches; mptr++) {
/* first dimension */
tmp = mptr->Storepositionreference + mptr->Storelengthreference - 1;
if (largestdim1 < tmp)
largestdim1 = tmp;
/* second dimension */
tmp = mptr->Storepositiongenomic + mptr->Storelengthgenomic - 1;
if (largestdim2 < tmp)
largestdim2 = tmp;
}
for (mptr = storematchtab, fragmentptr = fragments;
mptr < storematchtab + numofmatches;
mptr++) {
if (rare)
gt_disc_distri_add(startpointdistri, mptr->Storepositionreference);
if ((!rare ||
gt_disc_distri_get(startpointdistri, mptr->Storepositionreference)
<= rare) &&
(mptr == storematchtab || /* is the first match */
!gth_matches_are_equal(mptr, mptr-1))) { /* or is different from last
one */
fragmentptr->weight = (GtWord) (fragweightfactor *
(double) abs(mptr->Storescore));
fragmentptr->startpos1 = mptr->Storepositionreference;
fragmentptr->endpos1 = mptr->Storepositionreference
+ mptr->Storelengthreference - 1;
fragmentptr->startpos2 = mptr->Storepositiongenomic;
fragmentptr->endpos2 = mptr->Storepositiongenomic
+ mptr->Storelengthgenomic - 1;
fragmentptr++;
(*num_of_fragments)++;
}
}
gt_disc_distri_delete(startpointdistri);
gt_assert(*num_of_fragments <= numofmatches);
}
int gt_disc_distri_unit_test(GtError *err)
{
GtDiscDistri *d;
int had_err = 0;
gt_error_check(err);
d = gt_disc_distri_new();
ensure(had_err, gt_disc_distri_get(d, 0) == 0);
ensure(had_err, gt_disc_distri_get(d, 100) == 0);
if (!had_err) {
gt_disc_distri_add(d, 0);
gt_disc_distri_add_multi(d, 100, 256);
}
ensure(had_err, gt_disc_distri_get(d, 0) == 1);
ensure(had_err, gt_disc_distri_get(d, 100) == 256);
gt_disc_distri_delete(d);
return had_err;
}
