void CapR::CalcLogSumBulgeAndInternalProbability(vector<double> &bulge_probability, vector<double> &internal_probability){
double probability = 0;
double temp = 0;
int type = 0;
int type2 = 0;
vector<bool> b_flag_array; b_flag_array.resize(_seq_length,0);
vector<bool> i_flag_array; i_flag_array.resize(_seq_length,0);
for(int i = 1; i<_seq_length-TURN-2;i++){
for(int j = i+TURN+3; j<=min(i+_maximal_span,_seq_length);j++){
type = BP_pair[_int_sequence[i]][_int_sequence[j]];
if (type!=0) {
for (int p =i+1; p <= min(i+MAXLOOP+1,j-TURN-2); p++) {
int u1 = p-i-1;
for (int q=max(p+TURN+1,j-MAXLOOP+u1-1); q<j; q++) {
type2 = BP_pair[_int_sequence[p]][_int_sequence[q]];
if (type2 != 0 && !(p == i+1 && q == j-1)) {
type2 = rtype[type2];
if(_Beta_stemend[i][j-i-1] != -INF && _Alpha_stem[p-1][q-p+1] != -INF){
temp = _Beta_stemend[i][j-i-1] + LoopEnergy(type, type2,i,j,p,q)+_Alpha_stem[p-1][q-p+1];
for(int k = i+1; k <= p-1;k++){
if(j == q+1){
bulge_probability[k-1] = b_flag_array[k-1] == 1 ? logsumexp(bulge_probability[k-1], temp) : temp;
b_flag_array[k-1] = 1;
}else{
internal_probability[k-1] = i_flag_array[k-1] == 1 ? logsumexp(internal_probability[k-1], temp) : temp;
i_flag_array[k-1] = 1;
}
}
for(int k = q+1; k <= j-1;k++){
if(i == p-1){
bulge_probability[k-1] = b_flag_array[k-1] == 1 ? logsumexp(bulge_probability[k-1], temp) : temp;
b_flag_array[k-1] = 1;
}else{
internal_probability[k-1] = i_flag_array[k-1] == 1 ? logsumexp(internal_probability[k-1], temp) : temp;
i_flag_array[k-1] = 1;
}
}
}
}
}
}
}
}
}
for(int i=0;i<_seq_length;i++){
if(b_flag_array[i]==1){
bulge_probability[i] = exp(bulge_probability[i]-_Alpha_outer[_seq_length]);
}
if(i_flag_array[i]==1){
internal_probability[i] = exp(internal_probability[i]-_Alpha_outer[_seq_length]);
}
}
}
PRIVATE char *backtrack(int i, int j) {
/* backtrack structure going backwards from i, and forwards from j
return structure in bracket notation with & as separator */
int k, l, type, type2, E, traced, i0, j0;
char *st1, *st2, *struc;
st1 = (char *) space(sizeof(char)*(n1+1));
st2 = (char *) space(sizeof(char)*(n2+1));
i0=MIN2(i+1,n1); j0=MAX2(j-1,1);
while (i>0 && j<=n2) {
E = c[i][j]; traced=0;
st1[i-1] = '(';
st2[j-1] = ')';
type = pair[S1[i]][S2[j]];
if (!type) nrerror("backtrack failed in fold duplex");
for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {
for (l=j+1; l<=n2; l++) {
int LE;
if (i-k+l-j-2>MAXLOOP) break;
type2 = pair[S1[k]][S2[l]];
if (!type2) continue;
LE = LoopEnergy(i-k-1, l-j-1, type2, rtype[type],
SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1]);
if (E == c[k][l]+LE) {
traced=1;
i=k; j=l;
break;
}
}
if (traced) break;
}
if (!traced) {
if (i>1) E -= P->dangle5[type][SS1[i-1]];
if (j<n2) E -= P->dangle3[type][SS2[j+1]];
if (type>2) E -= P->TerminalAU;
if (E != P->DuplexInit) {
nrerror("backtrack failed in fold duplex");
} else break;
}
}
if (i>1) i--;
if (j<n2) j++;
struc = (char *) space(i0-i+1+j-j0+1+2);
for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';
for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';
strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&");
strcat(struc, st2+j0-1);
/* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j); */
free(st1); free(st2);
return struc;
}
void CapR::CalcBulgeAndInternalProbability(vector<double> &bulge_probability, vector<double> &internal_probability){
double temp = 0;
int type = 0;
int type2 = 0;
for(int i = 1; i<_seq_length-TURN-2;i++){
for(int j = i+TURN+3; j<=min(i+_maximal_span,_seq_length);j++){
type = BP_pair[_int_sequence[i]][_int_sequence[j]];
if (type!=0) {
for (int p =i+1; p <= min(i+MAXLOOP+1,j-TURN-2); p++) {
int u1 = p-i-1;
for (int q=max(p+TURN+1,j-MAXLOOP+u1-1); q<j; q++) {
type2 = BP_pair[_int_sequence[p]][_int_sequence[q]];
if (type2 != 0 && !(p == i+1 && q == j-1)) {
type2 = rtype[type2];
if(_Beta_stemend[i][j-i-1] != -INF && _Alpha_stem[p-1][q-p+1] != -INF){
temp = exp(_Beta_stemend[i][j-i-1] + LoopEnergy(type, type2,i,j,p,q)+_Alpha_stem[p-1][q-p+1]);
for(int k = i+1; k <= p-1;k++){
if(j == q+1){
bulge_probability[k-1] += temp;
}else{
internal_probability[k-1] += temp;
}
}
for(int k = q+1; k <= j-1;k++){
if(i == p-1){
bulge_probability[k-1] += temp;
}else{
internal_probability[k-1] += temp;
}
}
}
}
}
}
}
}
}
for(int i=0;i<_seq_length;i++){
if(bulge_probability[i] != 0){
bulge_probability[i] /= exp(_Alpha_outer[_seq_length]);
}
if(internal_probability[i] != 0){
internal_probability[i] /= exp(_Alpha_outer[_seq_length]);
}
}
}
PRIVATE int fill_arrays(const char *string) {
/* fill "c", "fML" and "f5" arrays and return optimal energy */
int i, j, k, length, energy;
int decomp, new_fML, max_separation;
int no_close, type, type_2, tt;
int bonus=0;
length = (int) strlen(string);
max_separation = (int) ((1.-LOCALITY)*(double)(length-2)); /* not in use */
for (j=1; j<=length; j++) {
Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;
}
for (j = 1; j<=length; j++)
for (i=(j>TURN?(j-TURN):1); i<j; i++) {
c[indx[j]+i] = fML[indx[j]+i] = INF;
if (uniq_ML) fM1[indx[j]+i] = INF;
}
if (length <= TURN) return 0;
for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */
for (j = i+TURN+1; j <= length; j++) {
int p, q, ij;
ij = indx[j]+i;
bonus = 0;
type = ptype[ij];
/* enforcing structure constraints */
if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;
if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;
if ((BP[i]==-4)||(BP[j]==-4)) type=0;
no_close = (((type==3)||(type==4))&&no_closingGU&&(bonus==0));
if (j-i-1 > max_separation) type = 0; /* forces locality degree */
if (type) { /* we have a pair */
int new_c=0, stackEnergy=INF;
/* hairpin ----------------------------------------------*/
if (no_close) new_c = FORBIDDEN;
else
new_c = HairpinE(j-i-1, type, S1[i+1], S1[j-1], string+i-1);
/*--------------------------------------------------------
check for elementary structures involving more than one
closing pair.
--------------------------------------------------------*/
for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1) ; p++) {
int minq = j-i+p-MAXLOOP-2;
if (minq<p+1+TURN) minq = p+1+TURN;
for (q = minq; q < j; q++) {
type_2 = ptype[indx[q]+p];
if (type_2==0) continue;
type_2 = rtype[type_2];
if (no_closingGU)
if (no_close||(type_2==3)||(type_2==4))
if ((p>i+1)||(q<j-1)) continue; /* continue unless stack */
#if 1
energy = LoopEnergy(p-i-1, j-q-1, type, type_2,
S1[i+1], S1[j-1], S1[p-1], S1[q+1]);
#else
/* duplicated code is faster than function call */
#endif
new_c = MIN2(energy+c[indx[q]+p], new_c);
if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */
} /* end q-loop */
} /* end p-loop */
/* multi-loop decomposition ------------------------*/
if (!no_close) {
int MLenergy;
decomp = DMLi1[j-1];
if (dangles) {
int d3=0, d5=0;
tt = rtype[type];
d3 = P->dangle3[tt][S1[i+1]];
d5 = P->dangle5[tt][S1[j-1]];
if (dangles==2) /* double dangles */
decomp += d5 + d3;
else { /* normal dangles */
decomp = MIN2(DMLi2[j-1]+d3+P->MLbase, decomp);
decomp = MIN2(DMLi1[j-2]+d5+P->MLbase, decomp);
decomp = MIN2(DMLi2[j-2]+d5+d3+2*P->MLbase, decomp);
}
}
MLenergy = P->MLclosing+P->MLintern[type]+decomp;
new_c = MLenergy < new_c ? MLenergy : new_c;
}
/* coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1) */
if (dangles==3) {
decomp = INF;
for (k = i+2+TURN; k < j-2-TURN; k++) {
type_2 = ptype[indx[k]+i+1]; type_2 = rtype[type_2];
if (type_2)
decomp = MIN2(decomp, c[indx[k]+i+1]+P->stack[type][type_2]+
fML[indx[j-1]+k+1]);
type_2 = ptype[indx[j-1]+k+1]; type_2 = rtype[type_2];
if (type_2)
decomp = MIN2(decomp, c[indx[j-1]+k+1]+P->stack[type][type_2]+
fML[indx[k]+i+1]);
}
/* no TermAU penalty if coax stack */
decomp += 2*P->MLintern[1] + P->MLclosing;
new_c = MIN2(new_c, decomp);
}
new_c = MIN2(new_c, cc1[j-1]+stackEnergy);
cc[j] = new_c + bonus;
if (noLonelyPairs)
c[ij] = cc1[j-1]+stackEnergy+bonus;
else
c[ij] = cc[j];
} /* end >> if (pair) << */
else c[ij] = INF;
/* done with c[i,j], now compute fML[i,j] */
/* free ends ? -----------------------------------------*/
new_fML = fML[ij+1]+P->MLbase;
new_fML = MIN2(fML[indx[j-1]+i]+P->MLbase, new_fML);
energy = c[ij]+P->MLintern[type];
if (dangles==2) { /* double dangles */
energy += (i==1) ? /* works also for circfold */
P->dangle5[type][S1[length]] : P->dangle5[type][S1[i-1]];
/* if (j<length) */ energy += P->dangle3[type][S1[j+1]];
}
new_fML = MIN2(energy, new_fML);
if (uniq_ML)
fM1[ij] = MIN2(fM1[indx[j-1]+i] + P->MLbase, energy);
if (dangles%2==1) { /* normal dangles */
tt = ptype[ij+1]; /* i+1,j */
new_fML = MIN2(c[ij+1]+P->dangle5[tt][S1[i]]
+P->MLintern[tt]+P->MLbase,new_fML);
tt = ptype[indx[j-1]+i];
new_fML = MIN2(c[indx[j-1]+i]+P->dangle3[tt][S1[j]]
+P->MLintern[tt]+P->MLbase, new_fML);
tt = ptype[indx[j-1]+i+1];
new_fML = MIN2(c[indx[j-1]+i+1]+P->dangle5[tt][S1[i]]+
P->dangle3[tt][S1[j]]+P->MLintern[tt]+2*P->MLbase, new_fML);
}
/* modular decomposition -------------------------------*/
for (decomp = INF, k = i+1+TURN; k <= j-2-TURN; k++)
decomp = MIN2(decomp, Fmi[k]+fML[indx[j]+k+1]);
DMLi[j] = decomp; /* store for use in ML decompositon */
new_fML = MIN2(new_fML,decomp);
/* coaxial stacking */
if (dangles==3) {
/* additional ML decomposition as two coaxially stacked helices */
for (decomp = INF, k = i+1+TURN; k <= j-2-TURN; k++) {
type = ptype[indx[k]+i]; type = rtype[type];
type_2 = ptype[indx[j]+k+1]; type_2 = rtype[type_2];
if (type && type_2)
decomp = MIN2(decomp,
c[indx[k]+i]+c[indx[j]+k+1]+P->stack[type][type_2]);
}
decomp += 2*P->MLintern[1]; /* no TermAU penalty if coax stack */
#if 0
/* This is needed for Y shaped ML loops with coax stacking of
interior pairts, but backtracking will fail if activated */
DMLi[j] = MIN2(DMLi[j], decomp);
DMLi[j] = MIN2(DMLi[j], DMLi[j-1]+P->MLbase);
DMLi[j] = MIN2(DMLi[j], DMLi1[j]+P->MLbase);
new_fML = MIN2(new_fML, DMLi[j]);
#endif
new_fML = MIN2(new_fML, decomp);
}
fML[ij] = Fmi[j] = new_fML; /* substring energy */
}
{
int *FF; /* rotate the auxilliary arrays */
FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;
FF = cc1; cc1=cc; cc=FF;
for (j=1; j<=length; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }
}
}
/* calculate energies of 5' and 3' fragments */
f5[TURN+1]=0;
for (j=TURN+2; j<=length; j++) {
f5[j] = f5[j-1];
type=ptype[indx[j]+1];
if (type) {
energy = c[indx[j]+1];
if (type>2) energy += P->TerminalAU;
if ((dangles==2)&&(j<length)) /* double dangles */
energy += P->dangle3[type][S1[j+1]];
f5[j] = MIN2(f5[j], energy);
}
type=ptype[indx[j-1]+1];
if ((type)&&(dangles%2==1)) {
energy = c[indx[j-1]+1]+P->dangle3[type][S1[j]];
if (type>2) energy += P->TerminalAU;
f5[j] = MIN2(f5[j], energy);
}
for (i=j-TURN-1; i>1; i--) {
type = ptype[indx[j]+i];
if (type) {
energy = f5[i-1]+c[indx[j]+i];
if (type>2) energy += P->TerminalAU;
if (dangles==2) {
energy += P->dangle5[type][S1[i-1]];
if (j<length) energy += P->dangle3[type][S1[j+1]];
}
f5[j] = MIN2(f5[j], energy);
if (dangles%2==1) {
energy = f5[i-2]+c[indx[j]+i]+P->dangle5[type][S1[i-1]];
if (type>2) energy += P->TerminalAU;
f5[j] = MIN2(f5[j], energy);
}
}
type = ptype[indx[j-1]+i];
if ((type)&&(dangles%2==1)) {
energy = c[indx[j-1]+i]+P->dangle3[type][S1[j]];
if (type>2) energy += P->TerminalAU;
f5[j] = MIN2(f5[j], f5[i-1]+energy);
f5[j] = MIN2(f5[j], f5[i-2]+energy+P->dangle5[type][S1[i-1]]);
}
}
}
return f5[length];
}
void CapR::CalcInsideVariable(){
for (int j =TURN+1; j <= _seq_length; j++){
for (int i=j-TURN; i >= max(0,j-_maximal_span-1); i--){
//Alpha_stem
int type = BP_pair[_int_sequence[i+1]][_int_sequence[j]];
int type2 = BP_pair[_int_sequence[i+2]][_int_sequence[j-1]];
double temp = 0; bool flag = 0;
if (type != 0) {
type2 = rtype[type2];
if(_Alpha_stem[i+1][j-i-2] != -INF){
//Stem¨Stem
if(type2 != 0){
temp = _Alpha_stem[i+1][j-i-2]+ LoopEnergy(type, type2,i+1,j,i+2,j-1);
}
flag = 1;
}
if(_Alpha_stemend[i+1][j-i-2] != -INF){
//Stem¨StemEnd
temp = flag == 1 ? logsumexp(temp,_Alpha_stemend[i+1][j-i-2]) : _Alpha_stemend[i+1][j-i-2];
flag = 1;
}
_Alpha_stem[i][j-i] = flag == 0 ? -INF : temp;
}else{
_Alpha_stem[i][j-i] = -INF;
}
//Alpha_multiBif
temp = 0; flag = 0;
for (int k=i+1; k<=j-1; k++){
if(_Alpha_multi1[i][k-i] != -INF && _Alpha_multi2[k][j-k] != -INF){
temp = flag == 0 ? _Alpha_multi1[i][k-i]+_Alpha_multi2[k][j-k] : logsumexp(temp,_Alpha_multi1[i][k-i]+_Alpha_multi2[k][j-k]);
flag = 1;
}
}
_Alpha_multibif[i][j-i] = flag == 0 ? -INF : temp;
//Alpha_multi2
temp = 0; flag = 0;
if (type != 0) {
if(_Alpha_stem[i][j-i] != -INF){
temp = _Alpha_stem[i][j-i]+MLintern+CalcDangleEnergy(type,i,j);
flag = 1;
}
}
if(_Alpha_multi2[i][j-i-1] != -INF){
_Alpha_multi2[i][j-i] = _Alpha_multi2[i][j-i-1]+MLbase;
if(flag == 1){
_Alpha_multi2[i][j-i] = logsumexp(temp,_Alpha_multi2[i][j-i]);
}
}else{
_Alpha_multi2[i][j-i] = flag == 0 ? -INF : temp;
}
//Alpha_multi1
if(_Alpha_multi2[i][j-i] != -INF && _Alpha_multibif[i][j-i] != -INF){
_Alpha_multi1[i][j-i] = logsumexp(_Alpha_multi2[i][j-i],_Alpha_multibif[i][j-i]);
}else if(_Alpha_multi2[i][j-i] == -INF){
_Alpha_multi1[i][j-i] = _Alpha_multibif[i][j-i];
}else if(_Alpha_multibif[i][j-i] == -INF){
_Alpha_multi1[i][j-i] = _Alpha_multi2[i][j-i];
}else{
_Alpha_multi1[i][j-i] = -INF;
}
//Alpha_multi
flag = 0;
if(_Alpha_multi[i+1][j-i-1] != -INF){
_Alpha_multi[i][j-i] = _Alpha_multi[i+1][j-i-1]+MLbase;
flag = 1;
}
if(flag == 1){
if(_Alpha_multibif[i][j-i] != -INF){
_Alpha_multi[i][j-i] = logsumexp(_Alpha_multi[i][j-i],_Alpha_multibif[i][j-i]);
}
}else{
_Alpha_multi[i][j-i] = _Alpha_multibif[i][j-i];
}
//Alpha_stemend
if(j != _seq_length){
temp = 0;
type = BP_pair[_int_sequence[i]][_int_sequence[j+1]];
if (type!=0) {
//StemEnd¨sn
temp = HairpinEnergy(type, i,j+1);
//StemEnd¨sm_Stem_sn
for (int p =i; p <= min(i+MAXLOOP,j-TURN-2); p++) {
int u1 = p-i;
for (int q=max(p+TURN+2,j-MAXLOOP+u1); q<=j; q++) {
type2 = BP_pair[_int_sequence[p+1]][_int_sequence[q]];
if(_Alpha_stem[p][q-p] != -INF){
if (type2 != 0 && !(p == i && q == j)) {
type2 = rtype[type2];
temp = logsumexp(temp,_Alpha_stem[p][q-p]+LoopEnergy(type, type2,i,j+1,p+1,q));
}
}
}
}
//StemEnd¨Multi
int tt = rtype[type];
temp = logsumexp(temp,_Alpha_multi[i][j-i]+MLclosing+MLintern+dangle3[tt][_int_sequence[i+1]]+dangle5[tt][_int_sequence[j]]);
_Alpha_stemend[i][j-i] = temp;
}else{
_Alpha_stemend[i][j-i] = -INF;
}
}
}
}
//Alpha_Outer
for(int i = 1;i <= _seq_length;i++){
double temp = _Alpha_outer[i-1];
for(int p = max(0,i-_maximal_span-1); p <i;p++){
if(_Alpha_stem[p][i-p] != -INF){
int type = BP_pair[_int_sequence[p+1]][_int_sequence[i]];
double ao = _Alpha_stem[p][i-p]+CalcDangleEnergy(type,p,i);
temp = logsumexp(temp,ao+_Alpha_outer[p]);
}
}
_Alpha_outer[i] = temp;
}
}
void CapR::CalcOutsideVariable(){
//Beta_outer
for(int i = _seq_length-1;i >= 0;i--){
double temp = _Beta_outer[i+1];
for(int p = i+1; p <= min(i+_maximal_span+1,_seq_length);p++){
if(_Alpha_stem[i][p-i] != -INF){
int type = BP_pair[_int_sequence[i+1]][_int_sequence[p]];
double bo = _Alpha_stem[i][p-i] + CalcDangleEnergy(type,i,p);
temp = logsumexp(temp,bo+_Beta_outer[p]);
}
}
_Beta_outer[i] = temp;
}
for (int q=_seq_length; q>=TURN+1; q--) {
for (int p=max(0,q-_maximal_span-1); p<= q-TURN; p++) {
int type = 0;
int type2 = 0;
double temp = 0; bool flag = 0;
if(p != 0 && q != _seq_length){
//Beta_stemend
_Beta_stemend[p][q-p] = q-p >= _maximal_span ? -INF : _Beta_stem[p-1][q-p+2];
//Beta_Multi
flag = 0;
if(q-p+1 <= _maximal_span+1){
if(_Beta_multi[p-1][q-p+1] != -INF){
temp = _Beta_multi[p-1][q-p+1] + MLbase;
flag = 1;
}
}
type = BP_pair[_int_sequence[p]][_int_sequence[q+1]];
int tt = rtype[type];
if(flag == 1){
if(_Beta_stemend[p][q-p] != -INF){
temp = logsumexp(temp,_Beta_stemend[p][q-p]+MLclosing+MLintern+ dangle3[tt][_int_sequence[p+1]]+dangle5[tt][_int_sequence[q]]);
}
}else{
if(_Beta_stemend[p][q-p] != -INF){
temp = _Beta_stemend[p][q-p]+MLclosing+MLintern+dangle3[tt][_int_sequence[p+1]]+dangle5[tt][_int_sequence[q]];
}else{
temp = -INF;
}
}
_Beta_multi[p][q-p] = temp;
//Beta_Multi1
temp = 0; flag = 0;
for(int k = q+1 ; k<= min(_seq_length,p+_maximal_span);k++){
if(_Beta_multibif[p][k-p] != -INF && _Alpha_multi2[q][k-q] != -INF){
temp = flag == 0 ? _Beta_multibif[p][k-p]+_Alpha_multi2[q][k-q] : logsumexp(temp,_Beta_multibif[p][k-p]+_Alpha_multi2[q][k-q]) ;
flag = 1;
}
}
_Beta_multi1[p][q-p] = flag == 1 ? temp: -INF;
//Beta_Multi2
temp = 0; flag = 0;
if(_Beta_multi1[p][q-p] != -INF){
temp = _Beta_multi1[p][q-p];
flag = 1;
}
if(q-p <= _maximal_span){
if(_Beta_multi2[p][q-p+1] != -INF){
temp = flag == 1 ? logsumexp(temp,_Beta_multi2[p][q-p+1]+MLbase) : _Beta_multi2[p][q-p+1]+MLbase;
flag = 1;
}
}
for(int k = max(0,q-_maximal_span); k < p ;k++){
if(_Beta_multibif[k][q-k] != -INF && _Alpha_multi1[k][p-k] != -INF){
temp = flag == 0 ? _Beta_multibif[k][q-k]+_Alpha_multi1[k][p-k] : logsumexp(temp,_Beta_multibif[k][q-k]+_Alpha_multi1[k][p-k]);
flag = 1;
}
}
_Beta_multi2[p][q-p] = flag == 0 ? -INF : temp;
//Beta_multibif
if(_Beta_multi1[p][q-p] != -INF && _Beta_multi[p][q-p] != -INF){
_Beta_multibif[p][q-p] = logsumexp(_Beta_multi1[p][q-p],_Beta_multi[p][q-p]);
}else if(_Beta_multi[p][q-p] == -INF){
_Beta_multibif[p][q-p] = _Beta_multi1[p][q-p];
}else if(_Beta_multi1[p][q-p] == -INF){
_Beta_multibif[p][q-p] = _Beta_multi[p][q-p];
}else{
_Beta_multibif[p][q-p] = -INF;
}
}
//Beta_stem
type2 = BP_pair[_int_sequence[p+1]][_int_sequence[q]];
if(type2 != 0){
temp = _Alpha_outer[p]+_Beta_outer[q]+CalcDangleEnergy(type2,p,q);
type2 = rtype[type2];
for (int i=max(1,p-MAXLOOP); i<=p; i++){
for (int j=q; j<=min(q+ MAXLOOP -p+i,_seq_length-1); j++) {
type = BP_pair[_int_sequence[i]][_int_sequence[j+1]];
if (type != 0 && !(i == p && j == q)) {
if(j-i <= _maximal_span+1 && _Beta_stemend[i][j-i] != -INF){
temp = logsumexp(temp,_Beta_stemend[i][j-i]+LoopEnergy(type,type2,i,j+1,p+1,q));
}
}
}
}
if(p != 0 && q != _seq_length){
type = BP_pair[_int_sequence[p]][_int_sequence[q+1]];
if(type != 0){
if(q-p+2 <= _maximal_span+1 && _Beta_stem[p-1][q-p+2] != -INF){
temp = logsumexp(temp,_Beta_stem[p-1][q-p+2]+LoopEnergy(type,type2,p,q+1,p+1,q));
}
}
}
_Beta_stem[p][q-p] = temp;
if(_Beta_multi2[p][q-p] != -INF){
type2 = rtype[type2];
temp = _Beta_multi2[p][q-p] + MLintern + CalcDangleEnergy(type2,p,q);
_Beta_stem[p][q-p] = logsumexp(temp,_Beta_stem[p][q-p]);
}
}else{
_Beta_stem[p][q-p] = -INF;
}
}
}
}
duplexT duplexfold(const char *s1, const char *s2) {
int i, j, l1, Emin=INF, i_min=0, j_min=0;
char *struc;
duplexT mfe;
n1 = (int) strlen(s1);
n2 = (int) strlen(s2);
if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {
update_fold_params(); P = scale_parameters();
make_pair_matrix();
}
c = (int **) space(sizeof(int *) * (n1+1));
for (i=1; i<=n1; i++) c[i] = (int *) space(sizeof(int) * (n2+1));
encode_seq(s1, s2);
for (i=1; i<=n1; i++) {
for (j=n2; j>0; j--) {
int type, type2, E, k,l;
type = pair[S1[i]][S2[j]];
c[i][j] = type ? P->DuplexInit : INF;
if (!type) continue;
if (i>1) c[i][j] += P->dangle5[type][SS1[i-1]];
if (j<n2) c[i][j] += P->dangle3[type][SS2[j+1]];
if (type>2) c[i][j] += P->TerminalAU;
for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {
for (l=j+1; l<=n2; l++) {
if (i-k+l-j-2>MAXLOOP) break;
type2 = pair[S1[k]][S2[l]];
if (!type2) continue;
E = LoopEnergy(i-k-1, l-j-1, type2, rtype[type],
SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1]);
c[i][j] = MIN2(c[i][j], c[k][l]+E);
}
}
E = c[i][j];
if (i<n1) E += P->dangle3[rtype[type]][SS1[i+1]];
if (j>1) E += P->dangle5[rtype[type]][SS2[j-1]];
if (type>2) E += P->TerminalAU;
if (E<Emin) {
Emin=E; i_min=i; j_min=j;
}
}
}
struc = backtrack(i_min, j_min);
if (i_min<n1) i_min++;
if (j_min>1 ) j_min--;
l1 = strchr(struc, '&')-struc;
/*
printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", struc, i_min+1-l1, i_min,
j_min, j_min+strlen(struc)-l1-2, Emin*0.01);
*/
mfe.i = i_min;
mfe.j = j_min;
mfe.energy = (float) Emin/100.;
mfe.structure = struc;
if (!delay_free) {
for (i=1; i<=n1; i++) free(c[i]);
free(c);
free(S1); free(S2); free(SS1); free(SS2);
}
return mfe;
}