void gthclusterSAstoPGLs(GtArray *pgls, GthSACollection *sa_collection)
{
GtUword forwardgen_file_num, /* the genomic file number of the
current forward cluster */
forwardmaxright, /* the maximal right position of the
current forward cluster */
forward_currentPGLindex, /* the current forward PGL index */
reversegen_file_num, /* the genomic file number of the
current reverse cluster */
reversemaxright, /* the maximal right position of the
current reverse cluster */
reverse_currentPGLindex; /* the current reverse PGL index */
GthSACollectionIterator *iterator;
GthSA *sa;
gt_assert(sa_collection);
/* init */
forwardgen_file_num = GT_UNDEF_UWORD;
forwardmaxright = GT_UNDEF_UWORD;
forward_currentPGLindex = GT_UNDEF_UWORD;
reversegen_file_num = GT_UNDEF_UWORD;
reversemaxright = GT_UNDEF_UWORD;
reverse_currentPGLindex = GT_UNDEF_UWORD;
/* cluster the SAs */
iterator = gth_sa_collection_iterator_new(sa_collection);
while ((sa = gth_sa_collection_iterator_next(iterator))) {
if (gth_sa_gen_strand_forward(sa)) {
saveSAtoPGLs(&forwardgen_file_num, &forwardmaxright,
&forward_currentPGLindex, pgls, sa);
}
else {
saveSAtoPGLs(&reversegen_file_num, &reversemaxright,
&reverse_currentPGLindex, pgls, sa);
}
}
gth_sa_collection_iterator_delete(iterator);
/* cluster is consistent */
gt_assert(cluster_is_consistent(pgls));
}
void gthcalcSAdistributions(bool exondistri, bool introndistri,
GtDiscDistri *exondistribution,
GtDiscDistri *introndistribution,
GthSACollection *sa_collection)
{
GthSACollectionIterator *iterator;
GthSA *sa;
gt_assert(sa_collection);
/* calculate distribution, if necessary */
if (exondistri || introndistri) {
iterator = gth_sa_collection_iterator_new(sa_collection);
while ((sa = gth_sa_collection_iterator_next(iterator))) {
if (exondistri)
addSAtoexondistribution(exondistribution, sa);
if (introndistri)
addSAtointrondistribution(introndistribution, sa);
}
gth_sa_collection_iterator_delete(iterator);
}
}
