PUBLIC int
move_adaptive(char *string,
short *ptable,
short *s,
short *s1,
int verbosity_level){
srand(time(NULL));
Encoded enc;
enc.seq = string;
enc.s0 = s;
enc.s1 = s1;
/* moves*/
enc.bp_left=0;
enc.bp_right=0;
enc.bp_left2=0;
enc.bp_right2=0;
/* options*/
enc.noLP=0;
enc.verbose_lvl=verbosity_level;
enc.first=1;
enc.shift=0;
/* degeneracy*/
enc.begin_unpr=0;
enc.begin_pr=0;
enc.end_unpr=0;
enc.end_pr=0;
enc.current_en=0;
// function
enc.funct=NULL;
// allocate memory for moves
enc.moves_from = (int*) space(ptable[0]*ptable[0]*sizeof(int));
enc.moves_to = (int*) space(ptable[0]*ptable[0]*sizeof(int));
int i;
for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;
struct_en str;
str.structure = allocopy(ptable);
str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);
while (move_rset(&enc, &str)!=0) {
free_degen(&enc);
}
free_degen(&enc);
copy_arr(ptable, str.structure);
free(str.structure);
free(enc.moves_from);
free(enc.moves_to);
return str.energy;
}
PUBLIC int
move_first( char *string,
short *ptable,
short *s,
short *s1,
int verbosity_level,
int shifts,
int noLP){
cnt_move = 0;
Encoded enc;
enc.seq = string;
enc.s0 = s;
enc.s1 = s1;
/* moves*/
enc.bp_left=0;
enc.bp_right=0;
enc.bp_left2=0;
enc.bp_right2=0;
/* options*/
enc.noLP=noLP;
enc.verbose_lvl=verbosity_level;
enc.first=1;
enc.shift=shifts;
/* degeneracy*/
enc.begin_unpr=0;
enc.begin_pr=0;
enc.end_unpr=0;
enc.end_pr=0;
enc.current_en=0;
/* function */
enc.funct=NULL;
int i;
for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;
struct_en str;
str.structure = allocopy(ptable);
str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);
while (move_set(&enc, &str)!=0) {
free_degen(&enc);
}
free_degen(&enc);
copy_arr(ptable, str.structure);
free(str.structure);
return str.energy;
}
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;
}
/* move to deepest (or first) neighbour*/
PRIVATE int
move_set(Encoded *Enc, struct_en *str){
/* count how many times called*/
cnt_move++;
/* 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 MS:\n "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }
/* if using first dont do all of them*/
bool end = false;
/* insertions*/
if (!end) cnt += insertions(Enc, str, &min);
if (Enc->first && cnt>0) end = true;
if (Enc->verbose_lvl>1) fprintf(stderr, "\n");
/* deletions*/
if (!end) cnt += deletions(Enc, str, &min);
if (Enc->first && cnt>0) end = true;
/* shifts (only if enabled + noLP disabled)*/
if (!end && Enc->shift && !Enc->noLP) {
cnt += shifts(Enc, str, &min);
if (Enc->first && cnt>0) end = true;
}
/* if degeneracy occurs, solve it!*/
if (!end && (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_set(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 ((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);
}
if (Enc->verbose_lvl>1 && !(Enc->first)) { fprintf(stderr, "\n end of MS:\n "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }
return cnt;
}
/* done with all structures along the way to deepest*/
PRIVATE int
update_deepest(Encoded *Enc, struct_en *str, struct_en *min){
/* apply move + get its energy*/
int tmp_en;
tmp_en = str->energy + energy_of_move_pt(str->structure, Enc->s0, Enc->s1, Enc->bp_left, Enc->bp_right);
do_move(str->structure, Enc->bp_left, Enc->bp_right);
if (Enc->bp_left2 != 0) {
tmp_en += energy_of_move_pt(str->structure, Enc->s0, Enc->s1, Enc->bp_left2, Enc->bp_right2);
do_move(str->structure, Enc->bp_left2, Enc->bp_right2);
}
int last_en = str->energy;
str->energy = tmp_en;
/* use f_point if we have it */
if (Enc->funct) {
int end = Enc->funct(str, min);
/* undo moves */
if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);
do_move(str->structure, -Enc->bp_left, -Enc->bp_right);
str->energy = last_en;
Enc->bp_left=0;
Enc->bp_right=0;
Enc->bp_left2=0;
Enc->bp_right2=0;
return (end?1:0);
}
if (Enc->verbose_lvl>1) { fprintf(stderr, " "); print_str(stderr, str->structure); fprintf(stderr, " %d\n", tmp_en); }
/* better deepest*/
if (tmp_en < min->energy) {
min->energy = tmp_en;
copy_arr(min->structure, str->structure);
/* delete degeneracy*/
free_degen(Enc);
/* undo moves*/
if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);
do_move(str->structure, -Enc->bp_left, -Enc->bp_right);
str->energy = last_en;
Enc->bp_left=0;
Enc->bp_right=0;
Enc->bp_left2=0;
Enc->bp_right2=0;
return 1;
}
/* degeneracy*/
if ((str->energy == min->energy) && (Enc->current_en == min->energy)) {
int found = 0;
int i;
for (i=Enc->begin_pr; i<Enc->end_pr; i++) {
if (equals(Enc->processed[i], str->structure)) {
found = 1;
break;
}
}
for (i=Enc->begin_unpr; !found && i<Enc->end_unpr; i++) {
if (equals(Enc->unprocessed[i], str->structure)) {
found = 1;
break;
}
}
if (!found) {
/* print_stren(stderr, str); // fprintf(stderr, " %6.2f\n", str->energy); */
Enc->unprocessed[Enc->end_unpr]=allocopy(str->structure);
Enc->end_unpr++;
}
}
/* undo moves*/
if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);
do_move(str->structure, -Enc->bp_left, -Enc->bp_right);
str->energy = last_en;
Enc->bp_left=0;
Enc->bp_right=0;
Enc->bp_left2=0;
Enc->bp_right2=0;
return 0;
}
