/* insertions move set*/
PRIVATE int
insertions(Encoded *Enc, struct_en *str, struct_en *minim){
int cnt = 0;
short *pt = str->structure;
int len = pt[0];
int i,j;
for (i=1; i<=len; i++) {
if (pt[i]==0) {
for (j=i+1; j<=len; j++) {
/* end if found closing bracket*/
if (pt[j]!=0 && pt[j]<j) break; /*')'*/
if (pt[j]!=0 && pt[j]>j) { /*'('*/
j = pt[j];
continue;
}
/* if conditions are met, do insert*/
if (try_insert(pt, Enc->seq, i, j)) {
Enc->bp_left=i;
Enc->bp_right=j;
if (Enc->noLP) {
/* if lone bases occur, try inserting one another base*/
if (lone_base(pt, i) || lone_base(pt, j)) {
/* inside*/
if (try_insert(pt, Enc->seq, i+1, j-1)) {
Enc->bp_left2=i+1;
Enc->bp_right2=j-1;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
} else /*outside*/
if (try_insert(pt, Enc->seq, i-1, j+1)) {
Enc->bp_left2=i-1;
Enc->bp_right2=j+1;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
} else {
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
} else {
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
}
}
}
}
return cnt;
}
// insertions move set
int insertions(encoded &enc, int &deepest, short *min_pt, degen °, bool verbose)
{
int cnt = 0;
short *pt = enc.pt;
int len = pt[0];
for (int i=1; i<=len; i++) {
if (pt[i]==0) {
for (int j=i+1; j<=len; j++) {
// end if found closing bracket
if (pt[j]!=0 && pt[j]<j) break; //')'
if (pt[j]!=0 && pt[j]>j) { //'('
j = pt[j];
continue;
}
// if conditions are met, do insert
if (try_insert(pt, enc.seq, i, j)) {
enc.bp_left=i;
enc.bp_right=j;
if (deg.opt->noLP) {
// if lone bases occur, try inserting one another base
if (lone_base(pt, i) || lone_base(pt, j)) {
// inside
if (try_insert(pt, enc.seq, i+1, j-1)) {
enc.bp_left2=i+1;
enc.bp_right2=j-1;
cnt += update_deepest(enc, deepest, min_pt, deg, verbose);
// in case useFirst is on and structure is found, end
if (deg.opt->first && cnt > 0) return cnt;
} else //outside
if (try_insert(pt, enc.seq, i-1, j+1)) {
enc.bp_left2=i-1;
enc.bp_right2=j+1;
cnt += update_deepest(enc, deepest, min_pt, deg, verbose);
// in case useFirst is on and structure is found, end
if (deg.opt->first && cnt > 0) return cnt;
}
} else {
cnt += update_deepest(enc, deepest, min_pt, deg, verbose);
// in case useFirst is on and structure is found, end
if (deg.opt->first && cnt > 0) return cnt;
}
} else {
cnt += update_deepest(enc, deepest, min_pt, deg, verbose);
// in case useFirst is on and structure is found, end
if (deg.opt->first && cnt > 0) return cnt;
}
}
}
}
}
return cnt;
}
/* insertions move set*/
PRIVATE int
insertions(Encoded *Enc, struct_en *str, struct_en *minim){
int cnt = 0;
short *pt = str->structure;
int len = pt[0];
int i,j;
if (Enc->verbose_lvl>1) { fprintf(stderr, " "); print_str(stderr, str->structure); fprintf(stderr, " %5d Insertions:\n", str->energy); }
for (i=1; i<=len; i++) {
if (pt[i]==0) {
for (j=i+1; j<=len; j++) {
/* end if found closing bracket*/
if (pt[j]!=0 && pt[j]<j) break; /*')'*/
if (pt[j]!=0 && pt[j]>j) { /*'('*/
j = pt[j];
continue;
}
/* if conditions are met, do insert*/
if (try_insert(pt, Enc->seq, i, j)) {
Enc->bp_left=i;
Enc->bp_right=j;
if (Enc->noLP) {
/* if lone bases occur, try inserting one another base*/
if (lone_base(pt, i, j)) {
/* try only inside insert -- not to repeat structures*/
if (try_insert(pt, Enc->seq, i+1, j-1)) {
/* but now, check if this second insert does not extend the stem */
if (pt[i+2] != 0 && pt[i+2] == pt[j-2]) continue;
Enc->bp_left2=i+1;
Enc->bp_right2=j-1;
} else continue;
}
}
// finally insert:
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
}
}
}
return cnt;
}
void insert(T const& v)
{
maybe_enlarge();
T* idx = lookup(v.key());
if(idx)
idx->assign_value(v);
else
{
while(!try_insert(v))
enlarge();
}
}
void rehash(std::vector<T>& e)
{
deleted = 0; // There will be no deleted elements afterwards
try_insert:
elems = 0;
for(std::size_t i = 0; i < e.size(); ++i)
{
if(e[i].is_filled()
&& !try_insert(e[i]))
{
// We need to make the table larger
tsize = next_prime(tsize + 1);
t.assign(tsize, T());
goto try_insert;
}
}
}
