void traceW(int j) {
int done = 0, i;
int wim1, flag = 1 ;
if (j == 0 || j == 1)
return;
for (i = 1; i < j && !done; i++) {
if (j-i < TURN) continue;
wim1 = MIN(0, W[i-1]);
flag = 1;
if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0;
if (g_unamode||g_mismatch) {
if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
traceV(i, j - 1);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
traceV(i + 1, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00);
total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1));
traceV(i + 1, j - 1);
if (flag ) traceW(i - 1);
break;
}
} else if (g_dangles == 2) {
int e_dangles = 0;
if (i>1) e_dangles += Ed3(j,i,i-1);
if (j<length) e_dangles += Ed5(j,i,j+1);
if ((W[j] == V(i,j) + auPenalty(i, j) + e_dangles + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i, j) + e_dangles)/100.00);
total_ex += (auPenalty(i, j) + e_dangles);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
}
} else if (g_dangles == 0) {
if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
}
} else { // default
if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
traceV(i, j - 1);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
traceV(i + 1, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
traceV(i + 1, j - 1);
if (flag ) traceW(i - 1);
break;
}
}
}
if (W[j] == W[j - 1] && !done) traceW(j-1);
//if (!done) {
// fprintf(stderr, "ERROR: W(%d) could not be traced\n", j);
//}
return;
}
int traceVM(int i, int j) {
int done = 0;
int eVM = 0;
if (g_unamode||g_mismatch) {
if (VM(i,j) == WMPrime[i+1][j - 1] + Ea + Eb + auPenalty(i, j) ) {
done = 1;
eVM += traceWMPrime(i + 1, j - 1);
} else if (VM(i,j) == WMPrime[i + 2][j - 1] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ec && canSS(i+1) ) {
done = 1;
eVM += traceWMPrime(i + 2, j - 1);
}
else if ( VM(i,j) == WMPrime[i + 1][j - 2] + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1) + Ec && canSS(j-1)) {
done = 1;
eVM += traceWMPrime(i + 1, j - 2);
}
else if (V(i,j) == WMPrime[i + 2][j - 2] + Ea + Eb + auPenalty(i,j) + Estackm(i,j) + 2*Ec && canSS(i+1) && canSS(j-1) ) {
done = 1;
eVM += traceWMPrime(i + 2, j - 2);
}
} else if (g_dangles == 2) {
if (V(i,j) == WMPrime[i + 1][j - 1] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1) && canSS(i+1) && canSS(j-1) ) {
done = 1;
eVM += traceWMPrime(i + 1, j - 1);
}
} else if (g_dangles == 0) {
if (VM(i,j) == WMPrime[i+1][j - 1] + Ea + Eb + auPenalty(i, j) ) {
done = 1;
eVM += traceWMPrime(i + 1, j - 1);
}
} else {
if (VM(i,j) == WMPrime[i+1][j - 1] + Ea + Eb + auPenalty(i, j) ) {
done = 1;
eVM += traceWMPrime(i + 1, j - 1);
} else if (VM(i,j) == WMPrime[i + 2][j - 1] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ec && canSS(i+1) ) {
done = 1;
eVM += traceWMPrime(i + 2, j - 1);
}
else if ( VM(i,j) == WMPrime[i + 1][j - 2] + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1) + Ec && canSS(j-1)) {
done = 1;
eVM += traceWMPrime(i + 1, j - 2);
} else if (V(i,j) == WMPrime[i + 2][j - 2] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1) + 2*Ec && canSS(i+1) && canSS(j-1) ) {
done = 1;
eVM += traceWMPrime(i + 2, j - 2);
}
}
if(!done) {
fprintf(stderr, "ERROR: VM(%d,%d) could not be traced\n", i,j);
}
return eVM;
}
int traceWM(int i, int j) {
assert(i < j);
int done=0, eWM=0;
if (!done && WM(i,j) == WMPrime[i][j]) {
eWM += traceWMPrime(i,j);
done = 1;
}
if (!done){
if (g_unamode||g_mismatch) {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) {
eWM += traceV(i, j);
done = 1;
} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) {
eWM += traceV(i + 1, j);
done = 1;
} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) {
done = 1;
eWM += traceV(i, j - 1);
} else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
done = 1;
eWM += traceV(i + 1, j - 1);
}
} else if (g_dangles == 2) {
int energy = V(i,j) + auPenalty(i, j) + Eb;
energy += (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
/*if (j<len)*/ energy += Ed5(j,i,j+1);
if (WM(i,j) == energy && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
eWM += traceV(i, j);
done = 1;
}
} else if (g_dangles == 0) {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) {
eWM += traceV(i, j);
done = 1;
}
} else {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) {
eWM += traceV(i, j);
done = 1;
} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) {
eWM += traceV(i + 1, j);
done = 1;
} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) {
eWM += traceV(i, j - 1);
done = 1;
} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
eWM += traceV(i + 1, j - 1);
done = 1;
}
}
}
if (!done){
if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) {
done = 1;
eWM += traceWM(i + 1, j);
} else if (WM(i,j) == WM(i,j - 1) + Ec && canSS(j)) {
done = 1;
eWM += traceWM(i, j - 1);
}
}
if(!done) {
fprintf(stderr, "ERROR: WM(%d,%d) could not be traced\n", i,j);
}
return eWM;
}
int calculate(int len, int nThreads) {
int b, i, j;
#ifdef _OPENMP
if (nThreads>0) omp_set_num_threads(nThreads);
#endif
#ifdef _OPENMP
#pragma omp parallel
#pragma omp master
fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
#endif
for (b = TURN+1; b <= len-1; b++) {
#ifdef _OPENMP
#pragma omp parallel for private (i,j) schedule(guided)
#endif
for (i = 1; i <= len - b; i++) {
j = i + b;
int flag = 0, newWM = INFINITY_;
if (canPair(RNA[i], RNA[j])) {
flag = 1;
int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
if (j-i > 6) { // Internal Loop BEGIN
int p=0, q=0;
int VBIij = INFINITY_;
for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
int minq = j-i+p-MAXLOOP-2;
if (minq < p+1+TURN) minq = p+1+TURN;
int maxq = (p==i+1)?(j-2):(j-1);
for (q = minq; q <= maxq; q++) {
if (!canPair(RNA[p], RNA[q])) continue;
if (!canILoop(i,j,p,q)) continue;
VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
}
}
VBI(i,j) = VBIij;
V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
} // Internal Loop END
if (j-i > 10) { // Multi Loop BEGIN
int h;
int VMij, VMijd, VMidj, VMidjd;
VMij = VMijd = VMidj = VMidjd = INFINITY_;
for (h = i+TURN+1; h <= j-1-TURN; h++) {
VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1));
VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));
VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));
VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));
}
int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
VMij = MIN(VMij, (VMijd + d3 +Ec));
VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec));
VMij = VMij + Ea + Eb + auPenalty(i,j);
VM(i,j) = canStack(i,j)?VMij:INFINITY_;
} // Multi Loop END
V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
}
else V(i,j) = INFINITY_;
if (j-i > 4) { // WM BEGIN
int h;
for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
//ZS: This sum corresponds to when i,j are NOT paired with each other.
//So we need to make sure only terms where i,j aren't pairing are considered.
newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
}
newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM);
newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle
newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
WMU(i,j) = WML(i,j) = newWM;
} // WM END
}
}
for (j = TURN+2; j <= len; j++) {
int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
Wj = INFINITY_;
for (i = 1; i < j-TURN; i++) {
Wij = Widjd = Wijd = Widj = INFINITY_;
Wim1 = MIN(0, W[i-1]);
Wij = V(i, j) + auPenalty(i, j) + Wim1;
Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj);
}
W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
}
return W[len];
}