Region *Region_create(gint query_start, gint target_start,
gint query_length, gint target_length) {
register Region *region = g_new(Region, 1);
region->ref_count = 1;
region->query_start = query_start;
region->target_start = target_start;
region->query_length = query_length;
region->target_length = target_length;
g_assert(Region_is_valid(region));
return region;
}
void Region_init_static(Region *region,
gint query_start, gint target_start,
gint query_length, gint target_length) {
region->ref_count = -1;
region->query_start = query_start;
region->target_start = target_start;
region->query_length = query_length;
region->target_length = target_length;
g_assert(Region_is_valid(region));
return;
}
static Region *Optimal_find_region(Optimal *optimal, Region *region,
gpointer user_data, C4_Score threshold,
SubOpt *subopt, C4_Score *region_score){
register Region *alignment_region;
register Viterbi_Data *vd;
register C4_Score score;
g_assert(optimal->type & Optimal_Type_REDUCED_SPACE);
if(!optimal->find_region) /* Must be a global model */
return Region_share(region); /* Already know region */
g_assert(optimal->find_region);
vd = Viterbi_Data_create(optimal->find_region, region);
score = Viterbi_calculate(optimal->find_region, region,
vd, user_data, subopt);
if(score < threshold)
return NULL;
alignment_region = Region_share(vd->alignment_region);
(*region_score) = score;
g_assert(Region_is_valid(alignment_region));
g_assert(Region_is_within(region, alignment_region));
Viterbi_Data_destroy(vd);
return alignment_region;
}
