VALUE
rb_struct_alloc_noinit(VALUE klass)
{
return struct_alloc(klass);
}
static struct loop *construct_loop(int ibase)
/*
* Starting at residue ibase, recursively constructs the loop containing
* said base and all deeper bases.
*/
{
int i,mate;
struct loop *retloop,*lp;
struct connection *cp;
struct region *rp;
struct radloop *rlp;
retloop = &loops[loop_count++];
retloop->nconnection = 0;
retloop->connections = (struct connection **) vrna_alloc(sizeof(struct connection *));
retloop->depth = 0;
retloop->number = loop_count;
retloop->radius = 0.0;
for (rlp = rlphead; rlp; rlp = rlp->next)
if (rlp->loopnumber == loop_count) retloop->radius = rlp->radius;
i = ibase;
do {
if ((mate = bases[i].mate) != 0) {
rp = bases[i].region;
if (!bases[rp->start1].extracted) {
if (i == rp->start1) {
bases[rp->start1].extracted = true;
bases[rp->end1].extracted = true;
bases[rp->start2].extracted = true;
bases[rp->end2].extracted = true;
lp = construct_loop(rp->end1 < nbase ? rp->end1+1 : 0);
}
else if (i == rp->start2){
bases[rp->start2].extracted = true;
bases[rp->end2].extracted = true;
bases[rp->start1].extracted = true;
bases[rp->end1].extracted = true;
lp = construct_loop(rp->end2 < nbase ? rp->end2+1 : 0);
}
else {
fprintf(stderr, "naview: Error detected in construct_loop. i = %d not found in region table.\n",i);
exit(FATAL_ERROR);
}
retloop->connections = (struct connection **)
realloc(retloop->connections,
(++retloop->nconnection+1) *
sizeof(struct connection *));
retloop->connections[retloop->nconnection-1] = cp =
struct_alloc(connection);
retloop->connections[retloop->nconnection] = NULL;
cp->loop = lp;
cp->region = rp;
if (i == rp->start1) {
cp->start = rp->start1;
cp->end = rp->end2;
}
else {
cp->start = rp->start2;
cp->end = rp->end1;
}
cp->extruded = false;
cp->broken = false;
lp->connections = (struct connection **)
realloc(lp->connections,
(++lp->nconnection+1) *
sizeof(struct connection *));
lp->connections[lp->nconnection-1] = cp =
struct_alloc(connection);
lp->connections[lp->nconnection] = NULL;
cp->loop = retloop;
cp->region = rp;
if (i == rp->start1) {
cp->start = rp->start2;
cp->end = rp->end1;
}
else {
cp->start = rp->start1;
cp->end = rp->end2;
}
cp->extruded = false;
cp->broken = false;
}
i = mate;
}
if (++i > nbase) i = 0;
}
while (i != ibase);
return retloop;
}
