// USED FOR TESTING
void get_feature_counts (char *sequence, char *structure, double *counter)
// sequence: sequence (input parameter)
// structure: secondary structure in dot-bracket format () and [] (input parameter)
// counter: array where counter[i] is the number of times the i-th feature occurs (output parameter)
{
// create an array of shorts which denotes the index of the base pairs:
// the first base in the sequence has index 1
// pairseq[0] = 0 always;
// pairseq[1] = i where i is the index of the base paired with base 1, etc;
// pairseq[j] = 0 if base j is unpaired;
int size = strlen (structure);
short pairseq[size+1];
detect_original_PKed_pairs_many(structure, pairseq);
// Hosna -- CAN DELETE THIS NEXT COMMENTED OUT PART - it was for my debugging
// It shows an example of how pairseq should look like
/*
short* pairseq = new short[size+1];
pairseq[0] = 0;
pairseq[1] = 6;
pairseq[5] = 10;
pairseq[6] = 1;
pairseq[10] = 5;
pairseq[2] = 0;
pairseq[3] = 0;
pairseq[4] = 0;
pairseq[7] = 0;
pairseq[8] = 0;
pairseq[9] = 0;
*/
ReadInput* R = new ReadInput(size, sequence, pairseq);
printf("DEBUG = After readinput\n");
Stack * s = new Stack(R);
Bands * B = new Bands(R, s);
int printTrace = 0; // by default, don't print energy trace
printf("Seq: %s \n", R->CSequence);
printf("Size: %d \n", R->Size);
for (int i = 1; i <= R->Size; i++) {
printf("%d ", R->Sequence[i]);
}
printf("\n-------------------------------\n Making the Loop Tree\n");
Loop * L = new Loop(0, MaxN+1, R, B, s);
int a, b; //will store the borders of a closed regoin
for (int i = 1; i <= R->Size; i++){
if (R->BasePair(i)>= 0){
if (s->Add(i, a, b)){
//If a closed region is identifed add it to the tree by calling addLoop
L->addLoop(a,b);
};
};
};
L->Print(-1);
printf("-------------------------------\n");
if (DEBUG2)
{
for (int i = 1; i <= R->Size; i++){
if (R->BasePair(i)>= 0){
s->printPrevStack(i);
}
}
printf("\n");
if (L != NULL && L->RightChild != NULL)
printf("L->NumberOfUnpairedInPseudo = %d\n", L->RightChild->NumberOfUnpairedInPseudo);
}
short* secstructure = new short[R->Size+1];
char *csequence = new char[R->Size+2];
csequence[R->Size+1] = '\0';
for (int i = 0; i < R->Size+1; i++) {
secstructure[i] = (short)(R->Sequence[i]);
if (secstructure[i] == -1) secstructure[i] = 0;
csequence[i] = R->CSequence[i];
printf("%d %c %d \n", i, csequence[i], secstructure[i]);
}
// PlotRna(prefix, &sequence[1], &secstructure[1], outPSFile, L->Energy());
// printf("Energy Model The total free energy is %f cal/mol\n", L->Energy());
float totalEnergy = 0;
cout << setw(15) << left << "Energy Model" << setw(25) << left << "Free Energy (kcal/mol)" << setw(40) << left << "Free Energy without Dangling (kcal/mol)" << endl;
printf("--------------------------------------------------------------\n");
if (RE_FLAG)
{
totalEnergy = -L->Energy(RE);
if (no_pk_dangling_ends == 0)
cout << setw(15) << left << "Rivas&Eddy" << setw(25) << left << (totalEnergy - L->EnergyDangling())/1000 << setw(40) << left << totalEnergy/1000 << endl;
else
cout << setw(15) << left << "Rivas&Eddy" << setw(25) << left << totalEnergy/1000 << setw(40) << left << totalEnergy/1000 << endl;
if (printTrace)
L->printEnergyTrace();
cout << endl;
}
if (DP_FLAG) // energy returned in kcal
{
// double *c = new double[R->Size];
double ** quadratic_matrix;
double f = 0;
int reset_c = 0;
int ignore_dangles = no_pk_dangling_ends;
int ignore_AU = 0; // 0 = do include AU penalties
if (DEBUG)
printf("Before call to Energy for DP model\n");
totalEnergy = -L->Energy(DP, quadratic_matrix, counter, f, reset_c, ignore_dangles);
if (DEBUG)
printf("After call to Energy for DP model\n");
cout << setw(15) << left << "Dirks&Pierce" << setw(25) << left << totalEnergy - L->EnergyDangling(DP, quadratic_matrix,counter,f,reset_c,ignore_dangles,ignore_AU) << setw(40) << left << totalEnergy << endl;
if (printTrace)
L->printEnergyTrace();
}
printf("\n");
printf("PARAMETER TUNING\n");
printf("Ps Psm Psp Pb Pup Pps a b c stP intP a_p b_p c_p\n");
cout << g_count_Ps << " " << g_count_Psm << " " << g_count_Psp << " " << g_count_Pb << " " << g_count_Pup << " " <<
g_count_Pps << " " << g_count_a << " " << g_count_b << " " << g_count_c << " " << g_count_stP << " " <<
g_count_intP << " " << g_count_a_p << " " << g_count_b_p << " " << g_count_c_p << endl;
// counter[0] = g_count_Ps;
// counter[1] = g_count_Psm;
// counter[2] = g_count_Psp;
// counter[3] = g_count_Pb;
// counter[4] = g_count_Pup;
// counter[5] = g_count_Pps;
// counter[6] = g_count_a;
// counter[7] = g_count_b;
// counter[8] = g_count_c;
// counter[9] = g_count_stP;
// counter[10] = g_count_intP;
// counter[11] = g_count_a_p;
// counter[12] = g_count_b_p;
// counter[13] = g_count_c_p;
}
// USED FOR PARAMETER TUNING (CC2006b energy model)
// returns the free energy (in kcal/mol) of sequence folded into structure
double free_energy_PK_CC2006b(char *sequence, char *structure)
// sequence: sequence (input parameter)
// structure: secondary structure in dot-bracket format () and [] (input parameter)
{
// create an array of shorts which denotes the index of the base pairs:
// the first base in the sequence has index 1
// pairseq[0] = 0 always;
// pairseq[1] = i where i is the index of the base paired with base 1, etc;
// pairseq[j] = 0 if base j is unpaired;
int size = strlen (structure);
short pairseq[size+1];
detect_original_PKed_pairs_many(structure, pairseq);
ReadInput* R = new ReadInput(size, sequence, pairseq);
// printf("DEBUG = After readinput\n");
Stack * s = new Stack(R);
Bands * B = new Bands(R, s);
int printTrace = 0; // by default, don't print energy trace
if (DEBUG)
{
printf("Seq: %s \n", R->CSequence);
printf("Size: %d \n", R->Size);
for (int i = 1; i <= R->Size; i++) {
printf("%d ", R->Sequence[i]);
}
printf("\n-------------------------------\n Making the Loop Tree\n");
}
Loop * L = new Loop(0, MaxN+1, R, B, s);
int a, b; //will store the borders of a closed regoin
for (int i = 1; i <= R->Size; i++){
if (R->BasePair(i)>= 0){
if (s->Add(i, a, b)){
//If a closed region is identifed add it to the tree by calling addLoop
L->addLoop(a,b);
};
};
};
L->countNumberOfChildren(); // set number of children for the top loop
if (DEBUG)
{
L->Print(-1);
printf("-------------------------------\n");
}
if (DEBUG2)
{
for (int i = 1; i <= R->Size; i++){
if (R->BasePair(i)>= 0){
s->printPrevStack(i);
}
}
printf("\n");
if (L != NULL && L->RightChild != NULL)
printf("L->NumberOfUnpairedInPseudo = %d\n", L->RightChild->NumberOfUnpairedInPseudo);
}
short* secstructure = new short[R->Size+1];
char *csequence = new char[R->Size+2];
csequence[R->Size+1] = '\0';
for (int i = 0; i < R->Size+1; i++) {
secstructure[i] = (short)(R->Sequence[i]);
if (secstructure[i] == -1) secstructure[i] = 0;
csequence[i] = R->CSequence[i];
if (DEBUG)
printf("%d %c %d \n", i, csequence[i], secstructure[i]);
}
// PlotRna(prefix, &sequence[1], &secstructure[1], outPSFile, L->Energy());
// printf("Energy Model The total free energy is %f cal/mol\n", L->Energy());
float totalEnergy = 0;
if (DEBUG)
{
cout << setw(15) << left << "Energy Model" << setw(25) << left << "Free Energy (kcal/mol)" << setw(40) << left << "Free Energy without Dangling (kcal/mol)" << endl;
printf("--------------------------------------------------------------\n");
}
// energy returned in kcal
totalEnergy = -L->Energy(CC2006b)/1000;
float totalEnergyDang = -L->EnergyDangling()/1000;
if (DEBUG)
cout << setw(15) << left << "Cao&Chen(b)" << setw(25) << left << totalEnergy + totalEnergyDang << setw(40) << left << totalEnergy << endl;
// L->printEnergyTrace();
// if (no_pk_dangling_ends == 0)
return totalEnergy + totalEnergyDang;
// else
// return totalEnergy;
}
// USED FOR PARAMETER TUNING (DP energy model)
double get_feature_counts_quadratic_PK_DP (char *sequence, char *structure, double **quadratic_matrix, double *counter, double &free_value)
// sequence: sequence (input parameter)
// structure: secondary structure in dot-bracket format () and [] (input parameter)
// counter: array where counter[i] is the number of times the i-th feature occurs (output parameter)
// quadratic_matrix: TODO
// free_value: TODO
// Note: The counter, free_value, and quadratic_matrix are automatically reset before passed onto other functions
{
// create an array of shorts which denotes the index of the base pairs:
// the first base in the sequence has index 1
// pairseq[0] = 0 always;
// pairseq[1] = i where i is the index of the base paired with base 1, etc;
// pairseq[j] = 0 if base j is unpaired;
int size = strlen (structure);
short pairseq[size+1];
detect_original_PKed_pairs_many(structure, pairseq);
// Hosna -- CAN DELETE THIS NEXT COMMENTED OUT PART - it was for my debugging
// It shows an example of how pairseq should look like
/*
short* pairseq = new short[size+1];
pairseq[0] = 0;
pairseq[1] = 6;
pairseq[5] = 10;
pairseq[6] = 1;
pairseq[10] = 5;
pairseq[2] = 0;
pairseq[3] = 0;
pairseq[4] = 0;
pairseq[7] = 0;
pairseq[8] = 0;
pairseq[9] = 0;
*/
ReadInput* R = new ReadInput(size, sequence, pairseq);
// printf("DEBUG = After readinput\n");
Stack * s = new Stack(R);
Bands * B = new Bands(R, s);
int printTrace = 0; // by default, don't print energy trace
if (DEBUG)
{
printf("Seq: %s \n", R->CSequence);
printf("Size: %d \n", R->Size);
for (int i = 1; i <= R->Size; i++) {
printf("%d ", R->Sequence[i]);
}
printf("\n-------------------------------\n Making the Loop Tree\n");
}
Loop * L = new Loop(0, MaxN+1, R, B, s);
int a, b; //will store the borders of a closed regoin
for (int i = 1; i <= R->Size; i++){
if (R->BasePair(i)>= 0){
if (s->Add(i, a, b)){
//If a closed region is identifed add it to the tree by calling addLoop
L->addLoop(a,b);
};
};
};
L->countNumberOfChildren(); // set number of children for the top loop
if (DEBUG)
{
L->Print(-1);
printf("-------------------------------\n");
}
if (DEBUG2)
{
for (int i = 1; i <= R->Size; i++){
if (R->BasePair(i)>= 0){
s->printPrevStack(i);
}
}
printf("\n");
if (L != NULL && L->RightChild != NULL)
printf("L->NumberOfUnpairedInPseudo = %d\n", L->RightChild->NumberOfUnpairedInPseudo);
}
short* secstructure = new short[R->Size+1];
char *csequence = new char[R->Size+2];
csequence[R->Size+1] = '\0';
for (int i = 0; i < R->Size+1; i++) {
secstructure[i] = (short)(R->Sequence[i]);
if (secstructure[i] == -1) secstructure[i] = 0;
csequence[i] = R->CSequence[i];
if (DEBUG)
printf("%d %c %d \n", i, csequence[i], secstructure[i]);
}
// PlotRna(prefix, &sequence[1], &secstructure[1], outPSFile, L->Energy());
// printf("Energy Model The total free energy is %f cal/mol\n", L->Energy());
float totalEnergy = 0;
if (DEBUG)
{
cout << setw(15) << left << "Energy Model" << setw(25) << left << "Free Energy (kcal/mol)" << setw(40) << left << "Free Energy without Dangling (kcal/mol)" << endl;
printf("--------------------------------------------------------------\n");
}
// energy returned in kcal
// PARAMETER TUNING
// clear the counter, quadratic_matrix, and free_value
int num_params = get_num_params_PK_DP();
free_value = 0;
for (int i=0; i < num_params; i++)
{
counter[i] = 0;
for (int j=i; j < num_params; j++)
quadratic_matrix[i][j] = 0;
}
int reset_c = 0;
int ignore_dangles = no_pk_dangling_ends;
int ignore_AU = 0; // 0 = do include AU penalties
totalEnergy = -L->Energy(DP, quadratic_matrix, counter, free_value, reset_c, ignore_dangles);
float totalEnergyDang = -L->EnergyDangling(DP, quadratic_matrix,counter,free_value,reset_c,ignore_dangles,ignore_AU);
// CHECK VALUES OF COUNTER, ETC
//int num_params = get_num_params_PK_DP();
//int num_params_pkfree = get_num_params();
//printf("Free Value: %f\n", free_value);
//printf("Counter Values:\n");
//for (int i = num_params_pkfree; i < num_params; i++)
// printf("c[%d]=%f ", i, counter[i]);
//printf("Some P_matrix Values:\n");
//for (int i = 0; i < num_params/10; i++)
// printf("P[%d][%d]=%f ", num_params_pkfree + structure_type_index_PK("stp")-1, i, quadratic_matrix[i][num_params_pkfree + structure_type_index_PK("stp")-1]);
if (DEBUG)
{
cout << setw(15) << left << "Dirks&Pierce" << setw(25) << left << totalEnergy + totalEnergyDang << setw(40) << left << totalEnergy << endl;
printf("\n");
printf("PARAMETER TUNING\n");
printf("Ps Psm Psp Pb Pup Pps a b c stP intP a_p b_p c_p\n");
cout << g_count_Ps << " " << g_count_Psm << " " << g_count_Psp << " " << g_count_Pb << " " << g_count_Pup << " " <<
g_count_Pps << " " << g_count_a << " " << g_count_b << " " << g_count_c << " " << g_count_stP << " " <<
g_count_intP << " " << g_count_a_p << " " << g_count_b_p << " " << g_count_c_p << endl;
}
// return the free energy:
// - deltaG = x' P x + c' x + f
// - where x is the vector of parameters
// - P is a symmetric matrix of the coefficients for each quadratic term
// - c is a vector of counts for each linear term
// - c' means c transposed
// - f is a constant
return totalEnergy + totalEnergyDang;
//int num_params = get_num_params_PK_DP();
//double * energy_temp1 = new double[num_params];
//double * energy_temp2 = new double[num_params];
//double energy = free_value;
//for (int i = 0; i < num_params; i++)
//{
// energy_temp1[i] = counter[i] * params_all[i];
// for (int j = 0; j < num_params; j++)
// {
// if (i <= j)
// energy_temp2[i] += quadratic_matrix[i][j] * params_all[j];
// else // since only the upper triangle of the matrix is filled out
// energy_temp2[i] += quadratic_matrix[j][i] * params_all[j];
// }
//}
//for (int i = 0; i < num_params; i++)
//{
// energy += params_all[i]*energy_temp2[i] + energy_temp1[i];
//}
//return energy;
}
