/* ******************************************* */
DBL_TYPE ExplHairpin( int i, int j, int seq[], int seqlength, int **etaN) {
//this version disallows nicks here
DBL_TYPE energy = 0;
int index;
int nNicks = 0;
index = EtaNIndex(i+0.5, j-0.5, seqlength);
nNicks = etaN[ index][0];
if( nNicks >= 1) return 0;
if( nNicks == 0 && j-i <= 3) {
return 0;
}
if( nNicks == 0) {
energy = HairpinEnergy( i, j, seq);
}
if( energy == NAD_INFINITY) {
return 0.0;
}
return EXP_FUNC( -energy/( kB*TEMP_K) );
}
void CapR::CalcHairpinProbability(vector<double> &hairpin_probability){
for(int x = 1; x <=_seq_length;x++){
double temp = 0.0;
int type = 0;
bool flag = 0;
double h_energy = 0.0;
for(int i = max(1,x-_maximal_span);i<x ;i++){
for(int j = x+1; j<=min(i+_maximal_span,_seq_length);j++){
type = BP_pair[_int_sequence[i]][_int_sequence[j]];
if(_Beta_stemend[i][j-i-1] != -INF){
h_energy = _Beta_stemend[i][j-i-1] + HairpinEnergy(type, i,j);
temp = flag == 1 ? logsumexp(temp, h_energy) : h_energy;
flag = 1;
}
}
}
if(flag == 1){
hairpin_probability[x-1] = exp(temp-_Alpha_outer[_seq_length]);
}else{
hairpin_probability[x-1] = 0.0;
}
}
}
void CapR::CalcInsideVariable(){
for (int j =TURN+1; j <= _seq_length; j++){
for (int i=j-TURN; i >= max(0,j-_maximal_span-1); i--){
//Alpha_stem
int type = BP_pair[_int_sequence[i+1]][_int_sequence[j]];
int type2 = BP_pair[_int_sequence[i+2]][_int_sequence[j-1]];
double temp = 0; bool flag = 0;
if (type != 0) {
type2 = rtype[type2];
if(_Alpha_stem[i+1][j-i-2] != -INF){
//Stem¨Stem
if(type2 != 0){
temp = _Alpha_stem[i+1][j-i-2]+ LoopEnergy(type, type2,i+1,j,i+2,j-1);
}
flag = 1;
}
if(_Alpha_stemend[i+1][j-i-2] != -INF){
//Stem¨StemEnd
temp = flag == 1 ? logsumexp(temp,_Alpha_stemend[i+1][j-i-2]) : _Alpha_stemend[i+1][j-i-2];
flag = 1;
}
_Alpha_stem[i][j-i] = flag == 0 ? -INF : temp;
}else{
_Alpha_stem[i][j-i] = -INF;
}
//Alpha_multiBif
temp = 0; flag = 0;
for (int k=i+1; k<=j-1; k++){
if(_Alpha_multi1[i][k-i] != -INF && _Alpha_multi2[k][j-k] != -INF){
temp = flag == 0 ? _Alpha_multi1[i][k-i]+_Alpha_multi2[k][j-k] : logsumexp(temp,_Alpha_multi1[i][k-i]+_Alpha_multi2[k][j-k]);
flag = 1;
}
}
_Alpha_multibif[i][j-i] = flag == 0 ? -INF : temp;
//Alpha_multi2
temp = 0; flag = 0;
if (type != 0) {
if(_Alpha_stem[i][j-i] != -INF){
temp = _Alpha_stem[i][j-i]+MLintern+CalcDangleEnergy(type,i,j);
flag = 1;
}
}
if(_Alpha_multi2[i][j-i-1] != -INF){
_Alpha_multi2[i][j-i] = _Alpha_multi2[i][j-i-1]+MLbase;
if(flag == 1){
_Alpha_multi2[i][j-i] = logsumexp(temp,_Alpha_multi2[i][j-i]);
}
}else{
_Alpha_multi2[i][j-i] = flag == 0 ? -INF : temp;
}
//Alpha_multi1
if(_Alpha_multi2[i][j-i] != -INF && _Alpha_multibif[i][j-i] != -INF){
_Alpha_multi1[i][j-i] = logsumexp(_Alpha_multi2[i][j-i],_Alpha_multibif[i][j-i]);
}else if(_Alpha_multi2[i][j-i] == -INF){
_Alpha_multi1[i][j-i] = _Alpha_multibif[i][j-i];
}else if(_Alpha_multibif[i][j-i] == -INF){
_Alpha_multi1[i][j-i] = _Alpha_multi2[i][j-i];
}else{
_Alpha_multi1[i][j-i] = -INF;
}
//Alpha_multi
flag = 0;
if(_Alpha_multi[i+1][j-i-1] != -INF){
_Alpha_multi[i][j-i] = _Alpha_multi[i+1][j-i-1]+MLbase;
flag = 1;
}
if(flag == 1){
if(_Alpha_multibif[i][j-i] != -INF){
_Alpha_multi[i][j-i] = logsumexp(_Alpha_multi[i][j-i],_Alpha_multibif[i][j-i]);
}
}else{
_Alpha_multi[i][j-i] = _Alpha_multibif[i][j-i];
}
//Alpha_stemend
if(j != _seq_length){
temp = 0;
type = BP_pair[_int_sequence[i]][_int_sequence[j+1]];
if (type!=0) {
//StemEnd¨sn
temp = HairpinEnergy(type, i,j+1);
//StemEnd¨sm_Stem_sn
for (int p =i; p <= min(i+MAXLOOP,j-TURN-2); p++) {
int u1 = p-i;
for (int q=max(p+TURN+2,j-MAXLOOP+u1); q<=j; q++) {
type2 = BP_pair[_int_sequence[p+1]][_int_sequence[q]];
if(_Alpha_stem[p][q-p] != -INF){
if (type2 != 0 && !(p == i && q == j)) {
type2 = rtype[type2];
temp = logsumexp(temp,_Alpha_stem[p][q-p]+LoopEnergy(type, type2,i,j+1,p+1,q));
}
}
}
}
//StemEnd¨Multi
int tt = rtype[type];
temp = logsumexp(temp,_Alpha_multi[i][j-i]+MLclosing+MLintern+dangle3[tt][_int_sequence[i+1]]+dangle5[tt][_int_sequence[j]]);
_Alpha_stemend[i][j-i] = temp;
}else{
_Alpha_stemend[i][j-i] = -INF;
}
}
}
}
//Alpha_Outer
for(int i = 1;i <= _seq_length;i++){
double temp = _Alpha_outer[i-1];
for(int p = max(0,i-_maximal_span-1); p <i;p++){
if(_Alpha_stem[p][i-p] != -INF){
int type = BP_pair[_int_sequence[p+1]][_int_sequence[i]];
double ao = _Alpha_stem[p][i-p]+CalcDangleEnergy(type,p,i);
temp = logsumexp(temp,ao+_Alpha_outer[p]);
}
}
_Alpha_outer[i] = temp;
}
}