int traceWM(int i, int j) {
int done;
int h1, h;
int eWM = 0;
done = 0;
h1 = 0;
if (i >= j)
return 0;
else {
for (h = i; h < j && !done; h++) {
int aa = WM(i,h) + WM(h + 1,j);
if (aa == WM(i,j)) {
done = 1;
h1 = h;
break;
}
}
if (h1 != 0) {
eWM += traceWM(i, h);
eWM += traceWM(h + 1, j);
} else {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb) {
done = 1;
structure[i] = j;
structure[j] = i;
eWM += traceV(i, j);
} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && check_base(i)) {
done = 1;
eWM += traceV(i + 1, j);
structure[i + 1] = j;
structure[j] = i + 1;
} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && check_base(j) ) {
done = 1;
eWM += traceV(i, j - 1);
structure[i] = j - 1;
structure[j - 1] = i;
} 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 && check_base(i) && check_base(j)) {
done = 1;
eWM += traceV(i + 1, j - 1);
structure[i + 1] = j - 1;
structure[j - 1] = i + 1;
} else if (WM(i,j) == WM(i + 1,j) + Ec && check_base(i)) {
done = 1;
eWM += traceWM(i + 1, j);
} else if (WM(i,j) == WM(i,j - 1) + Ec && check_base(j)) {
done = 1;
eWM += traceWM(i, j - 1);
}
}
}
return eWM;
}
int traceWMPrime(int i, int j) {
int done=0, h, energy=0;
for (h = i; h < j && !done; h++) {
if (WM(i,h) + WM(h + 1,j) == WMPrime(i,j)) {
energy += traceWM(i, h);
energy += traceWM(h + 1, j);
done = 1;
break;
}
}
return energy;
}
int traceVM(int i, int j) {
int done;
int h;
int A_temp;
int eVM = 0;
done = 0;
int VMij = VM(i,j);
for (h = i + 2; h <= j - 1 && !done; h++) {
A_temp = WM(i+1,h-1) + WM(h,j - 1) + Ea + Eb + auPenalty(i, j);
if (A_temp == VMij) {
done = 1;
eVM += traceWM(i + 1, h - 1);
eVM += traceWM(h, j - 1);
break;
}
}
if (check_base(i+1)) {
for (h = i + 3; h <= j - 1 && !done; h++) {
A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1);
if (A_temp == VMij) {
done = 1;
eVM += traceWM(i + 2, h - 1);
eVM += traceWM(h, j - 1);
break;
}
}
}
if (check_base(j-1)) {
for (h = i + 2; h <= j - 2 && !done; h++) {
A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
if (A_temp == VMij) {
done = 1;
eVM += traceWM(i + 1, h - 1);
eVM += traceWM(h, j - 2);
break;
}
}
}
if (check_base(i+1)&&check_base(j-1)) {
for (h = i + 3; h <= j - 2 && !done; h++) {
A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
if (A_temp == VMij) {
done = 1;
eVM += traceWM(i + 2, h - 1);
eVM += traceWM(h, j - 2);
break;
}
}
}
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;
}
