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 tests_1() {
const int TSTRL = 128;
char tdata[2048];
char tstr[TSTRL];
int fc = 0;
bool ok = false;
djs_tok_t res, r3;
int aryLen = 0;
loadFile(tdata,"inputs/example.json");
djs_tok_t whole = djs_createFrom(tdata);
fc += eT(ok = djs_findNamed(&whole, "this", &res));
fc += eT(ok = djs_getStr(&res,tstr,TSTRL));
fc += eS(tstr,"that");
fc += eT(ok = djs_findNamed(&whole,"other",&res));
djs_tok_t res2;
fc += eT(ok = djs_findNamed(&res,"this",&res2));
fc += eT(ok = djs_getStr(&res2,tstr,TSTRL));
fc += eS(tstr,"notthat");
fc += eT(ok = djs_findNamed(&res,"smelly",&res2));
bool smelly = false;
fc += eT(ok = djs_getBool(&res2,&smelly));
fc += eT(smelly);
fc += eT(ok = djs_findNamed(&res,"ugly",&res2));
bool ugly = true;
fc += eT(ok = djs_getBool(&res2,&ugly));
fc += eF(ugly);
fc += eT(ok = djs_findNamed(&whole,"boo",&res));
fc += eI(aryLen = djs_getLength(&res),6);
bool intables[] = { true, true, false, true, false, true };
int tvals[] = { 11, 222, -1, 3333, -1, 55 };
for (int i=0;i<aryLen;i++) {
djs_tok_t r2;
fc += eT(ok = djs_findIndex(&res,i,&r2));
int ival;
fc += eI(djs_getInt(&r2,&ival),intables[i]);
if (intables[i]) {
fc += eI(ival, tvals[i]);
}
}
fc += eT(ok = djs_findNamed(&whole,"poop",&res));
fc += eT(ok = djs_findIndex(&res,2,&r3));
fc += eT(ok = djs_getStr(&r3,tstr,TSTRL));
fc += eS(tstr,
"{ \"in\": 2, \"st\": 333333, \"rs\": [ 3,3,3,3,3,3 ] }");
if (fc) {
printf("---- FAIL with %d errors ----\n",fc);
}
return fc;
};
int tests_3() {
const int TSTRL = 128;
char tdata[2048];
char tstr[TSTRL];
int fc = 0;
bool ok = false;
djs_tok_t res;
loadFile(tdata,"inputs/ex2.json");
djs_tok_t w2 = djs_createFrom(tdata);
djs_showTok(&w2,TEST_DEBUG);
const char *digits[] = {
"one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "ten"
};
const int ivals[] = { 1, 2, 3, 4, 5, 6, 7, 8, 9, -10 };
const char *svals[] = { "1", "2", "3", "4", "5", "6", "7", "8", "9", "[ 10 ]" };
fc += eT(djs_valid(&w2));
for (int i=0;i<10;i++) {
fc += eT(ok = djs_findNamed(&w2,digits[i],&res));
fc += eT(ok = djs_getStr(&res,tstr,TSTRL));
fc += eS(tstr,svals[i]);
int ival = 42;
fc += eI(djs_getInt(&res,&ival),(ivals[i] > 0));
fc += (ivals[i] > 0) ? eI(ivals[i], ival) : 42;
}
return fc;
}
int tests_4() {
const int TSTRL = 128;
char tdata[2048];
char tstr[TSTRL];
int fc = 0;
bool ok = false;
djs_tok_t res;
loadFile(tdata,"inputs/ex3.json");
djs_tok_t w2 = djs_createFrom(tdata);
djs_showTok(&w2,TEST_DEBUG);
const char *svals[] = {
"this",
"is",
"a",
"thing",
"with,commas,n'stuff,",
"and single quotes '",
"and escped double quotes -- singly \\\"",
"and in pairs \\\"ding\\\""
};
fc += eT(djs_valid(&w2));
for (int i=0;i<8;i++) {
fc += eT(ok = djs_findIndex(&w2,i,&res));
fc += eT(ok = djs_getStr(&res,tstr,TSTRL));
fc += eS(tstr,svals[i]);
}
return fc;
}
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;
}
//Shel: Function for scoring a node (recursive)
int ScoreNode(TreeNode* node, int* RNA, nndb_constants* param, int length){
int result;
result = 0;
int *pairedChildren;
pairedChildren = NULL;
int numPairedChildren;
numPairedChildren = 0;
int i;
for (i = 0 ; i < node->numChildren ; i++){
// find location and number of paired children
//and add scores of associated loops
if ((node->children[i])->isPair) {
//Manoj: Changed the code to generate warnings in case of pairing in structure which are not valid
/*Base lb = (node->children[i])->lowBase.base;
char lbChar;
if(lb==1)lbChar='A';else if(lb==2)lbChar='C';else if(lb==4)lbChar='G';else if(lb==8)lbChar='U';else lbChar="X";
Base hb = (node->children[i])->highBase.base;
char hbChar;
if(hb==1)hbChar='A';else if(hb==2)hbChar='C';else if(hb==4)hbChar='G';else if(hb==8)hbChar='U';else hbChar="X";
printf("CHECKING: bases %d and %d (%c%c) if they can pair!\n",(node->children[i])->lowBase.index, (node->children[i])->highBase.index,lbChar, hbChar);*/
if(!canPair((node->children[i])->lowBase.base, (node->children[i])->highBase.base)){
Base lb = (node->children[i])->lowBase.base;
char lbChar;
if(lb==1)lbChar='A';else if(lb==2)lbChar='C';else if(lb==4)lbChar='G';else if(lb==8)lbChar='U';else lbChar='X';
Base hb = (node->children[i])->highBase.base;
char hbChar;
if(hb==1)hbChar='A';else if(hb==2)hbChar='C';else if(hb==4)hbChar='G';else if(hb==8)hbChar='U';else hbChar='X';
printf("WARNING: bases %d and %d (%c%c) can't pair; structure cannot be scored. Exiting.\n",(node->children[i])->lowBase.index, (node->children[i])->highBase.index,lbChar, hbChar);
exit(-1);
//continue;
}
//printf("Yes they can pair\n");
result += ScoreNode(node->children[i], RNA, param, length);
numPairedChildren += 1;
pairedChildren = realloc(pairedChildren, sizeof(int) * numPairedChildren);
pairedChildren[numPairedChildren - 1] = i;
}
}
if (node->lowBase.index != 0)
{
if (numPairedChildren == 0) // must be a hairpin
{
int energy = eH(node->lowBase.index,node->highBase.index, RNA, param);
result += energy;
if(printOn2)printf("%d \t %d: Hairpin Loop with energy %.2f\n", node->lowBase.index, node->highBase.index, (double)energy/100);
}
else if (numPairedChildren == 1) // must be stack, bulge, or internal
{
if (node->numChildren == 1) // must be stack
{
int energy = eS(node->lowBase.index, node->highBase.index, RNA, param);
result += energy;
if(printOn2)printf("%d \t %d: Stacked pair with energy %.2f\n", node->lowBase.index, node->highBase.index, (double)energy/100);
}
else
{ // must be bulge or internal
int energy = eL(node->lowBase.index, node->highBase.index,
node->children[pairedChildren[0]]->lowBase.index,
node->children[pairedChildren[0]]->highBase.index,
RNA, param);
result += energy;
if(printOn2)printf("%d \t %d: Bulge or Inernal Loop with energy %.2f\n", node->lowBase.index, node->highBase.index, (double)energy/100);
}
}
else // must be a multi-loop
{
int energy = eM(node, pairedChildren, numPairedChildren, RNA, param);
result += energy;
if(printOn2)printf("%d \t %d: Multi-loop with energy %.2f\n", node->lowBase.index, node->highBase.index, (double)energy/100);
}
}
else { // must be external
int energy = eE(node, pairedChildren, numPairedChildren, RNA, param, length);
result += energy;
if(printOn2)printf("%d \t %d: External loop with energy %.2f\n", node->lowBase.index, node->highBase.index, (double)energy/100);
}
return result;
}
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];
}
