int traceVBI(int i, int j) {
int VBIij;
int ip, jp;
int ifinal, jfinal;
ifinal = 0;
jfinal = 0;
for (ip = i + 1; ip < j - 1; ip++) {
for (jp = ip + 1; jp < j; jp++) {
VBIij = eL(i, j, ip, jp)+ V(ip,jp);
if (VBIij == VBI(i,j) || forcePair(ip,jp)){
ifinal = ip;
jfinal = jp;
break;
}
}
if (jp != j) break;
}
if (print_energy_decompose==1) fprintf(energy_decompose_outfile, " %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
total_en += eL(i, j, ifinal, jfinal);
return traceV(ifinal, jfinal);
}
int traceV(int i, int j) {
int a, b, c, d, Vij;
if (j-i < TURN) return INFINITY_;
a = canHairpin(i,j)?eH(i, j):INFINITY_;
b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1):INFINITY_;
c = canStack(i,j)?VBI(i,j):INFINITY_;
d = canStack(i,j)?VM(i,j):INFINITY_;
Vij = V(i,j);
structure[i] = j;
structure[j] = i;
if (Vij == a ) {
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d Hairpin %12.2f\n", i, j, eH(i, j)/100.00);
total_en += eH(i,j);
return Vij;
} else if (Vij == b) {
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d Stack %12.2f\n", i, j, eS(i, j)/100.00);
total_en += eS(i,j);
traceV(i + 1, j - 1);
return Vij;
} else if (Vij == c) {
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d IntLoop ", i, j);
traceVBI(i, j);
return Vij;
} else if (Vij == d) {
int eVM = traceVM(i, j);
if (print_energy_decompose ==1) fprintf(energy_decompose_outfile, "i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
total_en += (Vij-eVM);
return Vij;
}
return 0;
}
int traceVBI(int i, int j) {
int VBIij_temp;
int ip, jp, el, v;
int ifinal, jfinal;
ifinal = 0;
jfinal = 0;
for (ip = i + 1; ip < j - 1; ip++) {
for (jp = ip + 1; jp < j; jp++) {
if (check_iloop(i,j,ip,jp)) continue;
el = eL(i, j, ip, jp);
v = V(ip, jp);
VBIij_temp = el + v;
if (VBIij_temp == VBI(i,j)) {
ifinal = ip;
jfinal = jp;
break;
}
}
if (jp != j)
break;
}
structure[ifinal] = jfinal;
structure[jfinal] = ifinal;
if (verbose==1)
printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
total_en += eL(i, j, ifinal, jfinal);
int eVI = traceV(ifinal, jfinal);
return eVI ;
}
int traceV(int i, int j) {
int a, b, c, d, Vij;
if (j-i < TURN) return INFINITY_;
a = eH(i, j);
b = eS(i, j) + V(i + 1, j - 1);
if (eS(i, j) == 0) b = INFINITY_;
c = VBI(i,j);
d = VM(i,j);
Vij = MIN(MIN(a, b), MIN(c, d));
if (Vij == a && Vij != b && Vij != c && Vij != d) {
if (verbose == 1)
printf("i %5d j %5d Hairpin %12.2f\n", i, j, eH(i, j)/100.00);
total_en += eH(i,j);
return Vij;
} else if (Vij == b) {
if (verbose == 1)
printf("i %5d j %5d Stack %12.2f\n", i, j, eS(i, j)/100.00);
total_en += eS(i,j);
structure[i + 1] = j - 1;
structure[j - 1] = i + 1;
traceV(i + 1, j - 1);
return Vij;
} else if (Vij == c) {
if (verbose == 1)
printf("i %5d j %5d IntLoop ", i, j);
traceVBI(i, j);
return Vij;
} else if (Vij == d && Vij != a && Vij != b && Vij != c) {
int eVM = traceVM(i, j);
if (verbose ==1)
printf("i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
total_en += (Vij-eVM);
return Vij;
}
return 0;
}
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];
}