//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;
}
cv::Mat permute_e(int nc, int M)
{
cv::Mat eM, eM1, eM2, eM3;
// Permutation of 1 bit error
eM1 = cv::Mat::eye(nc, nc, CV_32FC1);
eM2 = cv::Mat::zeros(1, 1, CV_32FC1);
eM3 = cv::Mat::zeros(1, 1, CV_32FC1);
// Permutation of 2 bit error
if (M > 1)
{
int MeM2 = (nc*(nc - 1)) / 2;
eM2 = cv::Mat::zeros(MeM2, nc, CV_32FC1);
eM2.at<float>(0, 0) = 1;
eM2.at<float>(0, 1) = 1;
int z = 0;
for (int ko = 0; ko <= nc - 3;ko++)
{
for (int ki = 2; ki <= nc - 1 - ko; ki++)
{
z = z + 1;
eM2.at<float>(z, ko + 0) = 1;
eM2.at<float>(z, ki + ko - 1) = 0;
eM2.at<float>(z, ki + ko) = 1;
}
z = z + 1;
eM2.at<float>(z, ko + 1) = 1;
eM2.at<float>(z, ko + 2) = 1;
}
}
if (M>2)
{
int MeM3 = (nc*(nc - 1)*(nc - 2)) / 6;
eM3 = cv::Mat::zeros(MeM3, nc, CV_32FC1);
int arg = 0;
for (int ko = 0; ko <= nc - 3; ko++)
{
for (int km = 0; km <= nc - 3; km++)
{
int idx = nc - 2 - km - ko;
if (idx < 1){break;}
cv::Mat eSub = cv::Mat::zeros(idx, nc, CV_32FC1);
//cv::Mat m1 = cv::Mat::zeros(idx, ko, CV_32FC1);
cv::Mat m2 = cv::Mat::ones(idx, 1, CV_32FC1);
//cv::Mat m3 = cv::Mat::zeros(idx, km, CV_32FC1);
cv::Mat m4 = cv::Mat::ones(idx, 1, CV_32FC1);
cv::Mat m5 = cv::Mat::eye(idx, idx, CV_32FC1);
//m1.copyTo(eSub(cv::Rect(0, 0, m1.cols, m1.rows)));
m2.copyTo(eSub(cv::Rect(ko, 0, m2.cols, m2.rows)));
//m3.copyTo(eSub(cv::Rect(m1.cols + m2.cols, 0, m3.cols, m3.rows)));
m4.copyTo(eSub(cv::Rect(ko + 1 + km, 0, m4.cols, m4.rows)));
m5.copyTo(eSub(cv::Rect(ko + 1 + km + 1, 0, m5.cols, m5.rows)));
eSub.copyTo(eM3(cv::Rect(0, arg, eSub.cols, eSub.rows)));
arg += eSub.rows;
}
}
}
eM = cv::Mat::zeros(eM1.rows + eM2.rows + eM3.rows, nc, CV_32FC1);
eM1.copyTo(eM(cv::Rect(0, 0, eM1.cols, eM1.rows)));
eM2.copyTo(eM(cv::Rect(0, eM1.rows, eM2.cols, eM2.rows)));
eM3.copyTo(eM(cv::Rect(0, eM1.rows + eM2.rows, eM3.cols, eM3.rows)));
return eM;
}
