/* 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;
}
PRIVATE int
move_rset(Encoded *Enc, struct_en *str){
/* count better neighbours*/
int cnt = 0;
/* deepest descent*/
struct_en min;
min.structure = allocopy(str->structure);
min.energy = str->energy;
Enc->current_en = str->energy;
if (Enc->verbose_lvl>0) { fprintf(stderr, " start of MR:\n "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }
// construct and permute possible moves
construct_moves(Enc, str->structure);
/* find first lower one*/
int i;
for (i=0; i<Enc->num_moves; i++) {
Enc->bp_left = Enc->moves_from[i];
Enc->bp_right = Enc->moves_to[i];
cnt = update_deepest(Enc, str, &min);
if (cnt) break;
}
/* if degeneracy occurs, solve it!*/
if (deal_deg && !cnt && (Enc->end_unpr - Enc->begin_unpr)>0) {
Enc->processed[Enc->end_pr] = str->structure;
Enc->end_pr++;
str->structure = Enc->unprocessed[Enc->begin_unpr];
Enc->unprocessed[Enc->begin_unpr]=NULL;
Enc->begin_unpr++;
cnt += move_rset(Enc, str);
} else {
/* write output to str*/
copy_arr(str->structure, min.structure);
str->energy = min.energy;
}
/* release minimal*/
free(min.structure);
/* resolve degeneracy in local minima*/
if (deal_deg && (Enc->end_pr - Enc->begin_pr)>0) {
Enc->processed[Enc->end_pr]=str->structure;
Enc->end_pr++;
int min = find_min(Enc->processed, Enc->begin_pr, Enc->end_pr);
short *tmp = Enc->processed[min];
Enc->processed[min] = Enc->processed[Enc->begin_pr];
Enc->processed[Enc->begin_pr] = tmp;
str->structure = Enc->processed[Enc->begin_pr];
Enc->begin_pr++;
free_degen(Enc);
}
return cnt;
}
/* deletions move set*/
PRIVATE int
deletions(Encoded *Enc, struct_en *str, struct_en *minim){
int cnt = 0;
short *pt = str->structure;
int len = pt[0];
int i;
for (i=1; i<=len; i++) {
if (pt[i]>pt[pt[i]]) { /* '('*/
Enc->bp_left=-i;
Enc->bp_right=-pt[i];
/*if nolp enabled, make (maybe) 2nd delete*/
if (Enc->noLP) {
int lone = -1;
if (lone_base(pt, i-1)) lone=i-1;
else if (lone_base(pt, i+1)) lone=i+1;
else if (lone_base(pt, pt[i]-1)) lone=pt[i]-1;
else if (lone_base(pt, pt[i]+1)) lone=pt[i]+1;
/* check*/
if (lone != -1 && (pt[lone]==0 || pt[pt[lone]]==0)) {
fprintf(stderr, "WARNING: pt[%d(or %d)]!=\'.\'", lone, pt[lone]);
}
if (lone != -1) {
Enc->bp_left2=-lone-1;
Enc->bp_right2=-pt[lone]-1;
}
if (!lone_base(pt, pt[lone]-1) && !lone_base(pt, pt[lone]+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 { /* nolp not enabled*/
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;
}
// deletions move set
int deletions(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]>pt[pt[i]]) { // '('
enc.bp_left=-i;
enc.bp_right=-pt[i];
//if nolp enabled, make (maybe) 2nd delete
if (deg.opt->noLP) {
int lone = -1;
if (lone_base(pt, i-1)) lone=i-1;
else if (lone_base(pt, i+1)) lone=i+1;
else if (lone_base(pt, pt[i]-1)) lone=pt[i]-1;
else if (lone_base(pt, pt[i]+1)) lone=pt[i]+1;
// check
if (lone != -1 && (pt[lone]==0 || pt[pt[lone]]==0)) {
fprintf(stderr, "WARNING: pt[%d(or %d)]!=\'.\'", lone, pt[lone]);
}
if (lone != -1) {
enc.bp_left2=-lone-1;
enc.bp_right2=-pt[lone]-1;
}
if (!lone_base(pt, pt[lone]-1) && !lone_base(pt, pt[lone]+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 { // nolp not enabled
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;
}
/* deletions move set*/
PRIVATE int
deletions(Encoded *Enc, struct_en *str, struct_en *minim){
int cnt = 0;
short *pt = str->structure;
int len = pt[0];
int i;
if (Enc->verbose_lvl>1) { fprintf(stderr, " "); print_str(stderr, str->structure); fprintf(stderr, " %5d Deletions:\n", str->energy); }
for (i=1; i<=len; i++) {
if (pt[i]>pt[pt[i]]) { /* '('*/
Enc->bp_left=-i;
Enc->bp_right=-pt[i];
/*if nolp enabled, make (maybe) 2nd delete*/
if (Enc->noLP) {
/* is there a pair around? */
bool inside_pair = exists_base(pt, i+1, pt[i]-1);
bool outside_pair = exists_base(pt, i-1, pt[i]+1);
/* we would destroy 1/2 bpairs from inside a stack*/
if (inside_pair && outside_pair) continue;
/* check if we are in noLP space */
if (!inside_pair && !outside_pair) {
fprintf(stderr, "WRONG!!!! %d %d\n", i, pt[i]);
}
/* and make a delete or double delete if necessary, double delete do only from one side*/
if (inside_pair) {
if (!exists_base(pt, i+2, pt[i]-2)) {
Enc->bp_left2=-(i+1);
Enc->bp_right2=-(pt[i]-1);
}
} else if (outside_pair) {
if (!exists_base(pt, i-2, pt[i]+2)) {
continue;
}
}
}
/* finally the delete */
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*/
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;
}
/*shift move set*/
PRIVATE int
shifts(Encoded *Enc, struct_en *str, struct_en *minim){
int cnt = 0;
int brack_num = 0;
short *pt = str->structure;
int len = pt[0];
int i, k;
for (i=1; i<=len; i++) {
if (pt[i]!=0 && pt[i]>i) { /*'('*/
int j=pt[i];
/* outer switch left*/
if (Enc->verbose_lvl>1) fprintf(stderr, "%2d bracket %2d position, outer switch left\n", brack_num+1, i);
for (k=i-1; k>0; k--) {
if (pt[k]!=0 && pt[k]>k/*'('*/) break;
if (pt[k]!=0 && pt[k]<k/*')'*/) {
k = pt[k];
continue;
}
/* checks*/
if (pt[k]!=0) {
fprintf(stderr, "WARNING: \'%c\'should be \'.\' at pos %d!\n", pt[k], k);
}
/* switch (i,j) to (k,j)*/
if (j-k>MINGAP && compat(Enc->seq[k-1], Enc->seq[j-1])) {
Enc->bp_left=-i;
Enc->bp_right=-j;
Enc->bp_left2=k;
Enc->bp_right2=j;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
/* switch (i,j) to (k,i)*/
if (i-k>MINGAP && compat(Enc->seq[i-1], Enc->seq[k-1])) {
Enc->bp_left=-i;
Enc->bp_right=-j;
Enc->bp_left2=k;
Enc->bp_right2=i;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
}
/* outer switch right*/
if (Enc->verbose_lvl>1) fprintf(stderr, "%2d bracket %2d position, outer switch right\n", brack_num+1, i);
for (k=j+1; k<=len; k++) {
if (pt[k]!=0 && pt[k]<k/*')'*/) break;
if (pt[k]!=0 && pt[k]>k/*'('*/) {
k = pt[k];
continue;
}
/* check*/
if (pt[k]!=0) {
fprintf(stderr, "WARNING: \'%c\'should be \'.\' at pos %d!\n", pt[k], k);
}
/* switch (i,j) to (i,k)*/
if (k-i>MINGAP && compat(Enc->seq[i-1], Enc->seq[k-1])) {
Enc->bp_left=-i;
Enc->bp_right=-j;
Enc->bp_left2=i;
Enc->bp_right2=k;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
/* switch (i,j) to (j,k)*/
if (k-j>MINGAP && compat(Enc->seq[j-1], Enc->seq[k-1])) {
Enc->bp_left=-i;
Enc->bp_right=-j;
Enc->bp_left2=j;
Enc->bp_right2=k;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
}
if (Enc->verbose_lvl>1) fprintf(stderr, "%2d bracket %2d position, inner switch\n", brack_num+1, i);
/* inner switch*/
for (k=i+1; k<j; k++) {
/* jump to end of the sub-bracketing*/
if (pt[k]!=0 && pt[k]>k/*'('*/) {
k=pt[k];
continue;
}
/* left switch (i,j) to (k,j)*/
if (j-k>MINGAP && compat(Enc->seq[k-1], Enc->seq[j-1])) {
Enc->bp_left=-i;
Enc->bp_right=-j;
Enc->bp_left2=k;
Enc->bp_right2=j;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
/* right switch (i,j) to (i,k)*/
if (k-i>MINGAP && compat(Enc->seq[i-1], Enc->seq[k-1])) {
Enc->bp_left=-i;
Enc->bp_right=-j;
Enc->bp_left2=i;
Enc->bp_right2=k;
cnt += update_deepest(Enc, str, minim);
/* in case useFirst is on and structure is found, end*/
if (Enc->first && cnt > 0) return cnt;
}
} /* end inner switch for*/
brack_num++;
} /* end if (pt[i]=='(')*/
} /* end for in switches*/
return cnt;
}
//shift move set
int shifts(encoded &enc, int &deepest, short *min_pt, degen °, bool verbose)
{
int cnt = 0;
int brack_num = 0;
short *pt = enc.pt;
int len = pt[0];
for (int i=1; i<=len; i++) {
if (pt[i]!=0 && pt[i]>i) { //'('
int j=pt[i];
// outer switch left
if (verbose) fprintf(stderr, "%2d bracket %2d position, outer switch left\n", brack_num+1, i);
for (int k=i-1; k>0; k--) {
if (pt[k]!=0 && pt[k]>k/*'('*/) break;
if (pt[k]!=0 && pt[k]<k/*')'*/) {
k = pt[k];
continue;
}
// checks
if (pt[k]!=0) {
fprintf(stderr, "WARNING: \'%c\'should be \'.\' at pos %d!\n", pt[k], k);
}
// switch (i,j) to (k,j)
if (j-k>MINGAP && compat(enc.seq[k-1], enc.seq[j-1])) {
enc.bp_left=-i;
enc.bp_right=-j;
enc.bp_left2=k;
enc.bp_right2=j;
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;
}
// switch (i,j) to (k,i)
if (i-k>MINGAP && compat(enc.seq[i-1], enc.seq[k-1])) {
enc.bp_left=-i;
enc.bp_right=-j;
enc.bp_left2=k;
enc.bp_right2=i;
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;
}
}
// outer switch right
if (verbose) fprintf(stderr, "%2d bracket %2d position, outer switch right\n", brack_num+1, i);
for (int k=j+1; k<=len; k++) {
if (pt[k]!=0 && pt[k]<k/*')'*/) break;
if (pt[k]!=0 && pt[k]>k/*'('*/) {
k = pt[k];
continue;
}
// check
if (pt[k]!=0) {
fprintf(stderr, "WARNING: \'%c\'should be \'.\' at pos %d!\n", pt[k], k);
}
// switch (i,j) to (i,k)
if (k-i>MINGAP && compat(enc.seq[i-1], enc.seq[k-1])) {
enc.bp_left=-i;
enc.bp_right=-j;
enc.bp_left2=i;
enc.bp_right2=k;
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;
}
// switch (i,j) to (j,k)
if (k-j>MINGAP && compat(enc.seq[j-1], enc.seq[k-1])) {
enc.bp_left=-i;
enc.bp_right=-j;
enc.bp_left2=j;
enc.bp_right2=k;
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;
}
}
if (verbose) fprintf(stderr, "%2d bracket %2d position, inner switch\n", brack_num+1, i);
// inner switch
for (int k=i+1; k<j; k++) {
// jump to end of the sub-bracketing
if (pt[k]!=0 && pt[k]>k/*'('*/) {
k=pt[k];
continue;
}
// left switch (i,j) to (k,j)
if (j-k>MINGAP && compat(enc.seq[k-1], enc.seq[j-1])) {
enc.bp_left=-i;
enc.bp_right=-j;
enc.bp_left2=k;
enc.bp_right2=j;
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;
}
// right switch (i,j) to (i,k)
if (k-i>MINGAP && compat(enc.seq[i-1], enc.seq[k-1])) {
enc.bp_left=-i;
enc.bp_right=-j;
enc.bp_left2=i;
enc.bp_right2=k;
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;
}
} // end inner switch for
brack_num++;
} // end if (pt[i]=='(')
} // end for in switches
return cnt;
}
