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W_final.cpp
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W_final.cpp
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#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "pseudo_loop.h"
#include "V_final.h"
#include "W_final.h"
#include "constants.h"
#include "h_struct.h"
#include "externs.h"
#include "h_externs.h"
#include "h_common.h"
//kevin
#include "simfold.h"
#include "params.h"
#include "structs.h"
#include "common.h"
#define debug 0
// Hosna June 20th, 2007
// calls the constructor for s_min_folding
// to create all the matrixes required for simfold
// and then calls allocate_space in here to allocate
// space for WMB and V_final
W_final::W_final(char *seq, char *res):s_min_folding(seq,res)
{
this->nb_nucleotides = strlen(seq);
// Ian Wark July 21 2017
// we don't need this, this is done in s_min_folding
/*
this->int_sequence = new int[this->nb_nucleotides];
if (int_sequence == NULL) giveup ("Cannot allocate memory", "W_final");
int i;
for (i=0; i < this->nb_nucleotides; i++) int_sequence[i] = nuc_to_int(seq[i]);
*/
space_allocation();
}
W_final::W_final(char *seq, char *res, std::vector<energy_model> *energy_models):s_min_folding(seq,res,energy_models)
{
this->nb_nucleotides = strlen(seq);
// Ian Wark July 21 2017
// we don't need this, this is done in s_min_folding
/*
this->int_sequence = new int[this->nb_nucleotides];
if (int_sequence == NULL) giveup ("Cannot allocate memory", "W_final");
int i;
for (i=0; i < this->nb_nucleotides; i++) int_sequence[i] = nuc_to_int(seq[i]);
*/
space_allocation();
}
W_final::~W_final()
{
delete vm;
delete v;
delete WMB;
// Ian Wark July 21 2017
// we don't need this, this is done in s_min_folding
//delete [] int_sequence;
}
// Hosna June 20th, 2007
// allocates space for WMB object and V_final
void W_final::space_allocation(){
// Hosna June 20th, 2007
vm = new VM_final(this->int_sequence,this->nb_nucleotides);
if (vm == NULL) giveup ("Cannot allocate memory", "W_final");
if (debug){
printf("nb_nucleotides = %d \n",this->nb_nucleotides);
}
// Hosna June 20th, 2007
// I don't think we need the following line
//vm->set_energy_matrix(s_min_folding::V);
// Hosna June 20th, 2007
v = new V_final(nb_nucleotides);
if (v == NULL) giveup ("Cannot allocate memory", "W_final");
//s_min_folding::V, s_min_folding::H, s_min_folding::S, s_min_folding::VBI, vm);
v->setloops(this->V,vm);
// Hosna: June 20th 2007
WMB = new pseudo_loop (sequence,restricted,v,this->H,this->S,this->VBI,vm);
if (WMB == NULL) giveup ("Cannot allocate memory", "W_final");
// Hosna: June 20th 2007
vm->set_V_matrix(v);
vm->set_WMB_matrix(WMB);
}
double W_final::hfold_pkonly(){
double energy;
int i, j;
h_str_features *h_fres;
if ((h_fres = new h_str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "h_str_features");
// detect the structure features
detect_h_structure_features (restricted, h_fres);
WMB->set_features(h_fres);
WMB->initialize();
str_features *fres;
if ((fres = new str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "str_features");
// detect the structure features
detect_structure_features (restricted, fres);
// Hosna: June 28, 2007
// set the features for checking
v->set_features(fres);
// Hosna: July 2nd, 2007
// set the VM matrix for VM_final
vm->set_VM_matrix(VM);
// TODO:
// I think I shoud fill simfold tables here, before filling the HFold tables
// Hosna, March 8, 2012
// 1) fill all th ematrices simfold needs (i.e. pk free ones)
// This is done similar to s_min_folding::fold_sequence_restricted()
for (j=0; j < nb_nucleotides; j++)
{
for (i=0; i<j; i++)
{
// V(i,j) = infinity if i restricted or j restricted and pair of i is not j
if ((fres[i].pair > -1 && fres[i].pair !=j) || (fres[j].pair > -1 && fres[j].pair != i))
continue;
if (fres[i].pair == -1 || fres[j].pair == -1) // i or j MUST be unpaired
continue;
V->compute_energy_restricted_pkonly (i, j, fres); // in s_energy_matrix in simfold package
}
// if I put this before V calculation, WM(i,j) cannot be calculated, because it returns infinity
VM->compute_energy_WM_restricted_pkonly (j, fres); // added April 18, 2012
}
for (j=0; j < nb_nucleotides; j++)
{
// Hosna, March 19, 2012
for (i =j; i >= 0; i--)//for (i=0; i<=j; i++)
{
WMB->compute_energies(i,j);
vm->WM_compute_energy(i,j);
}
}
// end of addition at March 8, 2012, Hosna
for (j= 1; j < nb_nucleotides; j++)
{
this->compute_W_restricted_pkonly(j,fres);
}
energy = this->W[nb_nucleotides-1]/100.0;
// printf("energy = %f \n", energy);
// backtrack
// first add (0,n-1) on the stack
stack_interval = new seq_interval;
stack_interval->i = 0;
stack_interval->j = nb_nucleotides - 1;
stack_interval->energy = W[nb_nucleotides-1];
stack_interval->type = FREE;
stack_interval->next = NULL;
seq_interval *cur_interval = stack_interval;
while ( cur_interval != NULL)
{
stack_interval = stack_interval->next;
backtrack_restricted_pkonly (cur_interval, fres); // added April 30, 2012 Hosna
delete cur_interval; // this should make up for the new in the insert_node
cur_interval = stack_interval;
}
if (debug)
{
print_result ();
}
delete [] h_fres;
delete [] fres;
return energy;
}
double W_final::hfold(){
double energy;
int i, j;
h_str_features *h_fres;
if ((h_fres = new h_str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "h_str_features");
// detect the structure features
detect_h_structure_features (restricted, h_fres);
WMB->set_features(h_fres);
WMB->initialize();
str_features *fres;
if ((fres = new str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "str_features");
// detect the structure features
detect_structure_features (restricted, fres);
// Hosna: June 28, 2007
// set the features for checking
v->set_features(fres);
// Hosna: July 2nd, 2007
// set the VM matrix for VM_final
vm->set_VM_matrix(VM);
// TODO:
// I think I shoud fill simfold tables here, before filling the HFold tables
// Hosna, March 8, 2012
// 1) fill all th ematrices simfold needs (i.e. pk free ones)
// This is done similar to s_min_folding::fold_sequence_restricted()
for (j=0; j < nb_nucleotides; j++)
{
for (i=0; i<j; i++)
{
// V(i,j) = infinity if i restricted or j restricted and pair of i is not j
if ((fres[i].pair > -1 && fres[i].pair !=j) || (fres[j].pair > -1 && fres[j].pair != i))
continue;
if (fres[i].pair == -1 || fres[j].pair == -1) // i or j MUST be unpaired
continue;
V->compute_energy_restricted (i, j, fres);
}
// if I put this before V calculation, WM(i,j) cannot be calculated, because it returns infinity
VM->compute_energy_WM_restricted (j, fres);
// test V values
/*
for (i=0; i<j; i++)
{
if (fres[i].pair ==j && fres[j].pair ==i){
printf("---->> V(%d,%d) = %d \n",i,j, V->get_energy(i,j));
}
}
*/
}
for (j=0; j < nb_nucleotides; j++)
{
for (i =j; i >= 0; i--)//for (i=0; i<=j; i++)
{
WMB->compute_energies(i,j);
vm->WM_compute_energy(i,j);
// if (debug){
// printf("WM_final(%d,%d) = %d \n",i,j,vm->get_energy_WM(i,j));
// }
}
}
// end of addition at March 8, 2012, Hosna
for (j= 1; j < nb_nucleotides; j++)
{
this->compute_W_restricted(j,fres);
}
energy = this->W[nb_nucleotides-1]/100.0;
// printf("energy = %f \n", energy);
// backtrack
// first add (0,n-1) on the stack
stack_interval = new seq_interval;
stack_interval->i = 0;
stack_interval->j = nb_nucleotides - 1;
stack_interval->energy = W[nb_nucleotides-1];
stack_interval->type = FREE;
stack_interval->next = NULL;
seq_interval *cur_interval = stack_interval;
while ( cur_interval != NULL)
{
stack_interval = stack_interval->next;
backtrack_restricted (cur_interval, fres);
delete cur_interval; // this should make up for the new in the insert_node
cur_interval = stack_interval;
}
if (debug)
{
print_result ();
}
delete [] h_fres;
delete [] fres;
return energy;
}
//AP
double W_final::hfold_emodel() { //kevin debug
int KEVIN_DEBUG = 0;
double energy;
int i, j;
h_str_features *h_fres;
if ((h_fres = new h_str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "h_str_features");
// detect the structure features
detect_h_structure_features (restricted, h_fres);
WMB->set_features(h_fres);
WMB->initialize();
str_features *fres;
if ((fres = new str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "str_features");
// detect the structure features
detect_structure_features (restricted, fres);
// Hosna: June 28, 2007
// set the features for checking
v->set_features(fres);
// Hosna: July 2nd, 2007
// set the VM matrix for VM_final
vm->set_VM_matrix(VM);
// TODO:
// I think I shoud fill simfold tables here, before filling the HFold tables
// Hosna, March 8, 2012
// 1) fill all th ematrices simfold needs (i.e. pk free ones)
// This is done similar to s_min_folding::fold_sequence_restricted()
for (j=1; j < nb_nucleotides; j++)
{
for (i=0; i<j; i++)
{
// V(i,j) = infinity if i restricted or j restricted and pair of i is not j
if ((fres[i].pair > -1 && fres[i].pair !=j) || (fres[j].pair > -1 && fres[j].pair != i))
continue;
if (fres[i].pair == -1 || fres[j].pair == -1) // i or j MUST be unpaired
continue;
//16 Aug 2017 kevin
//added fourth argument to check if ij is weakly closed
V->compute_energy_restricted_emodel (i, j, fres,WMB->is_weakly_closed(i,j));
}
// if I put this before V calculation, WM(i,j) cannot be calculated, because it returns infinity
VM->compute_energy_WM_restricted_emodel (j, fres, energy_models);
// test V values
/*
for (i=0; i<j; i++)
{
if (fres[i].pair ==j && fres[j].pair ==i){
printf("---->> V(%d,%d) = %d \n",i,j, V->get_energy(i,j));
}
}
*/
}
for (j=1; j < nb_nucleotides; j++) {
for (i =j; i >= 0; i--) {//for (i=0; i<=j; i++) {
WMB->compute_energies_emodel(i,j,energy_models); // TODO need to check this one
vm->WM_compute_energy(i,j);
}
}
//exit(999);
// end of addition at March 8, 2012, Hosna
for (j= 1; j < nb_nucleotides; j++) {
this->compute_W_restricted_emodel(j,fres);
}
if(KEVIN_DEBUG){
//printf("fres:\n");
//for (i=0; i < nb_nucleotides; i++){printf("%c i=%d f_type=%c f_pair=%d\n",restricted[i],i,fres[i].type, fres[i].pair);} //kevin debug
printf("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W1:\n");
for (i=0; i < nb_nucleotides; i++){printf("%c i=%d W=%d\n",restricted[i],i,W[i]);} //kevin debug
}
// backtrack
// first add (0,n-1) on the stack
stack_interval = new seq_interval;
stack_interval->i = 0;
stack_interval->j = nb_nucleotides - 1;
stack_interval->energy = W[nb_nucleotides-1];
stack_interval->type = FREE;
stack_interval->next = NULL;
seq_interval *cur_interval = stack_interval;
/*
//kevin debug
if(KEVIN_DEBUG){
printf("before backtrack_restricted_emodel\nstructure: %s\n",structure);
for (i=0; i < nb_nucleotides; i++){printf("%c i=%d f_type=%c f_pair=%d\n",restricted[i],i,fres[i].type, fres[i].pair);} //kevin debug
}
*/
//printf("before backtrack\n");
while ( cur_interval != NULL) {
stack_interval = stack_interval->next;
backtrack_restricted_emodel (cur_interval, fres); // TODO do we need to check this one?
delete cur_interval; // this should make up for the new in the insert_node
cur_interval = stack_interval;
}
//printf("end of backtrack\n");
// The energy calculation is now placed after backtrack is run because we need the contents of f[] (aka typedef struct minimum_fold) in order to determine if the final structure is pseudoknoted or not. If it is then we add the start_hybrid_penalty to our final energy and divide it by 100.
energy = this->W[nb_nucleotides-1]; //nb_nucleotides-1
// Ian Wark and Kevin July 20 2017
// We don't need this anymore. It is now in s_energy_matrix::compute_energy_restricted_emodel after calculating hairpin
/*
for (i = 0; i < linker_pos; i++) {
if (f[i].pair > linker_pos+linker_length-1) {
energy += start_hybrid_penalty;
break;
}
}
*/
energy /= 100.0;
if (debug)
{
print_result ();
}
delete [] h_fres;
delete [] fres;
if(is_invalid_restriction(restricted,structure)){
fprintf(stderr,"ERROR!!! There is something wrong with the structure, doesn't match restricted\n");
fprintf(stderr," %s\n %s\n %s\t%.2lf\n", sequence, restricted, structure, energy);
fprintf(stderr,"ERROR!!! There is something wrong with the structure, doesn't match restricted\n");
exit(11);
}
return energy;
}
//kevin 18 July
double W_final::call_simfold_emodel(){
double energy;
int i, j;
//16 Aug 2017 kevin
//added this block so we can use WMB->weakly closed in V->compute_energy_restricted_emodel
h_str_features *h_fres;
if ((h_fres = new h_str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "h_str_features");
// detect the structure features
detect_h_structure_features (restricted, h_fres);
WMB->set_features(h_fres);
WMB->initialize();
str_features *fres;
if ((fres = new str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "str_features");
// detect the structure features
detect_structure_features (restricted, fres);
/*
for (i=0; i < nb_nucleotides; i++)
if (fres[i].pair != -1)
printf ("%d pairs %d, type %c\n", i, fres[i].pair, fres[i].type);
*/
for (j=1; j < nb_nucleotides; j++)
{
for (i=0; i<j; i++)
{
// V(i,j) = infinity if i restricted or j restricted and pair of i is not j
if ((fres[i].pair > -1 && fres[i].pair !=j) || (fres[j].pair > -1 && fres[j].pair != i))
continue;
if (fres[i].pair == -1 || fres[j].pair == -1) // i or j MUST be unpaired
continue;
//16 Aug 2017 kevin
//added fourth argument to check if ij is weakly closed
V->compute_energy_restricted_emodel (i, j, fres,WMB->is_weakly_closed(i,j));
}
// if I put this before V calculation, WM(i,j) cannot be calculated, because it returns infinity
VM->compute_energy_WM_restricted_emodel (j, fres, energy_models);
}
for (j=1; j < nb_nucleotides; j++)
{
compute_W_restricted_simfold_emodel (j, fres);
}
energy = W[nb_nucleotides-1]/100.0;
if (debug)
{
for (j=1; j < nb_nucleotides; j++)
{
printf ("W(%d) = %d\n", j, W[j]);
}
}
// backtrack
// first add (0,n-1) on the stack
stack_interval = new seq_interval;
stack_interval->i = 0;
stack_interval->j = nb_nucleotides - 1;
stack_interval->energy = W[nb_nucleotides-1];
stack_interval->type = FREE;
stack_interval->next = NULL;
seq_interval *cur_interval = stack_interval;
while ( cur_interval != NULL)
{
stack_interval = stack_interval->next;
backtrack_restricted_simfold_emodel (cur_interval, fres);
delete cur_interval; // this should make up for the new in the insert_node
cur_interval = stack_interval;
}
if (debug)
{
print_result ();
}
delete [] fres;
delete [] h_fres;
if(is_invalid_restriction(restricted,structure)){
fprintf(stderr,"ERROR!!! There is something wrong with the structure, doesn't match restricted\n");
fprintf(stderr," %s\n %s\n %s\t%.2lf\n", sequence, restricted, structure, energy);
fprintf(stderr,"ERROR!!! There is something wrong with the structure, doesn't match restricted\n");
exit(11);
}
return energy;
}
/*
void W_final::call_simfold_emodel(){
//kevin todo change theese to be actually multi model
char config_file[200];
strcpy (config_file, "./simfold/params/multirnafold.conf");
double temperature;
temperature = 37;
int dna_or_rna;
dna_or_rna = RNA;
init_data ("./simfold", config_file, dna_or_rna, temperature);
fill_data_structures_with_new_parameters ("./simfold/params/turner_parameters_fm363_constrdangles.txt");
fill_data_structures_with_new_parameters ("./simfold/params/parameters_DP09_chopped.txt");
double energy = simfold_restricted (sequence, restricted, structure);
//printf("%s %s %s\n",sequence, restricted, structure);
}
*/
//AP
double W_final::hfold_pkonly_emodel(){
double energy;
int i, j;
h_str_features *h_fres;
if ((h_fres = new h_str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "h_str_features");
// detect the structure features
detect_h_structure_features (restricted, h_fres);
WMB->set_features(h_fres);
WMB->initialize();
str_features *fres;
if ((fres = new str_features[nb_nucleotides]) == NULL) giveup ("Cannot allocate memory", "str_features");
// detect the structure features
detect_structure_features (restricted, fres);
// Hosna: June 28, 2007
// set the features for checking
v->set_features(fres);
// Hosna: July 2nd, 2007
// set the VM matrix for VM_final
vm->set_VM_matrix(VM);
// TODO:
// I think I shoud fill simfold tables here, before filling the HFold tables
// Hosna, March 8, 2012
// 1) fill all th ematrices simfold needs (i.e. pk free ones)
// This is done similar to s_min_folding::fold_sequence_restricted()
for (j=1; j < nb_nucleotides; j++) {
for (i=0; i<j; i++) {
//printf("%d %d is cross model: %d\n",i,j,is_cross_model(i,j));
// V(i,j) = infinity if i restricted or j restricted and pair of i is not j
if ((fres[i].pair > -1 && fres[i].pair !=j) || (fres[j].pair > -1 && fres[j].pair != i))
continue;
if (fres[i].pair == -1 || fres[j].pair == -1) // i or j MUST be unpaired
continue;
//16 Aug 2017 kevin
//added fourth argument to check if ij is weakly closed
V->compute_energy_restricted_pkonly_emodel (i, j, fres,WMB->is_weakly_closed(i,j));
}
// if I put this before V calculation, WM(i,j) cannot be calculated, because it returns infinity
VM->compute_energy_WM_restricted_pkonly_emodel (j, fres, energy_models);
}
for (j=1; j < nb_nucleotides; j++) {
// Hosna, March 19, 2012
for (i =j; i >= 0; i--) {
//
WMB->compute_energies_emodel(i,j,energy_models);
vm->WM_compute_energy(i,j);
}
}
// end of addition at March 8, 2012, Hosna
for (j= 1; j < nb_nucleotides; j++)
{
this->compute_W_restricted_pkonly_emodel(j,fres);
}
// backtrack
// first add (0,n-1) on the stack
stack_interval = new seq_interval;
stack_interval->i = 0;
stack_interval->j = nb_nucleotides - 1;
stack_interval->energy = W[nb_nucleotides-1];
stack_interval->type = FREE;
stack_interval->next = NULL;
seq_interval *cur_interval = stack_interval;
// energy = this->W[nb_nucleotides-1];
while ( cur_interval != NULL)
{
stack_interval = stack_interval->next;
backtrack_restricted_pkonly_emodel (cur_interval, fres);//TODO
delete cur_interval; // this should make up for the new in the insert_node
cur_interval = stack_interval;
}
// The energy calculation is now placed after backtrack is run because we need the contents of f[] (aka typedef struct minimum_fold) in order to determine if the final structure is pseudoknoted or not. If it is then we add the start_hybrid_penalty to our final energy and divide it by 100.
energy = this->W[nb_nucleotides-1];
// Ian Wark and Kevin July 20 2017
// We don't need this anymore. It is now in s_energy_matrix::compute_energy_restricted_pkonly_emodel after calculating hairpin
/*
for (i = 0; i < linker_pos; i++) {
if (f[i].pair > linker_pos+linker_length-1) {
energy += start_hybrid_penalty;
break;
}
}
*/
energy /= 100.0;
delete [] h_fres;
delete [] fres;
if(is_invalid_restriction(restricted,structure)){
fprintf(stderr,"ERROR!!! There is something wrong with the structure, doesn't match restricted\n");
fprintf(stderr," %s\n %s\n %s\t%.2lf\n", sequence, restricted, structure, energy);
fprintf(stderr,"ERROR!!! There is something wrong with the structure, doesn't match restricted\n");
exit(11);
}
return energy;
}
void W_final::return_structure(char *structure){
strcpy (structure, this->structure);
//s_min_folding::return_structure(structure);
}
void W_final::compute_W_restricted (int j, str_features *fres)
// compute W(j)
{
int m1, m2, m3;
int must_choose_this_branch;
m1 = W[j-1];
m2 = compute_W_br2_restricted (j, fres, must_choose_this_branch);
m3 = compute_W_br3_restricted (j, fres);
if (WMB->is_weakly_closed(0,j) < 0){
W[j] = INF;
return;
}
if (must_choose_this_branch)
{
W[j] = MIN(m2,m3);
}
else
{
W[j] = MIN(m1,MIN(m2,m3));
}
}
//AP
void W_final::compute_W_restricted_emodel (int j, str_features *fres)
// compute W(j)
{
int m1 = W[j-1];
int m2, m3;
int must_choose_this_branch = 0;
//AP. This was moved to be checked before the m2 and m3 calculation to save time. Previously it was after the calculation.
if (WMB->is_weakly_closed(0,j) < 0){
W[j] = INF;
return;
}
m2 = compute_W_br2_restricted_emodel (j, fres, must_choose_this_branch);
m3 = compute_W_br3_restricted (j, fres); // TODO ian does this need an emodel?
if (must_choose_this_branch) {
W[j] = MIN(m2,m3);
} else {
W[j] = MIN(m1,MIN(m2,m3));
}
}
//AP
//Kevin July 24 2017
void W_final::compute_W_restricted_simfold_emodel (int j, str_features *fres)
// compute W(j)
{
int m1 = W[j-1];
int m2;
int must_choose_this_branch = 0;
m2 = compute_W_br2_restricted_simfold_emodel (j, fres, must_choose_this_branch);
if (must_choose_this_branch) {
W[j] = m2;
} else {
W[j] = MIN(m1,m2);
}
}
//AP
void W_final::compute_W_restricted_pkonly_emodel (int j, str_features *fres)
// compute W(j)
{
int m1 = W[j-1];
int m2, m3;
int must_choose_this_branch = 0;
//AP. This was moved to be checked before the m2 and m3 calculation to save time. Previously it was after the calculation.
if (WMB->is_weakly_closed(0,j) < 0){
W[j] = INF;
return;
}
m2 = compute_W_br2_restricted_pkonly_emodel (j, fres, must_choose_this_branch);
m3 = compute_W_br3_restricted (j, fres);
if (must_choose_this_branch) {
W[j] = MIN(m2,m3);
} else {
W[j] = MIN(m1,MIN(m2,m3));
}
}
void W_final::compute_W_restricted_pkonly (int j, str_features *fres)
// compute W(j)
{
int m1, m2, m3;
int must_choose_this_branch;
m1 = W[j-1];
m2 = compute_W_br2_restricted_pkonly (j, fres, must_choose_this_branch);
m3 = compute_W_br3_restricted (j, fres);
if (WMB->is_weakly_closed(0,j) < 0){
W[j] = INF;
return;
}
if (must_choose_this_branch)
{
W[j] = MIN(m2,m3);
}
else
{
W[j] = MIN(m1,MIN(m2,m3));
}
}
int W_final::compute_W_br2_restricted (int j, str_features *fres, int &must_choose_this_branch)
{
int min = INF, tmp, energy_ij = INF, acc;
int i;
int chosen = 0;
int best_i = 0;
must_choose_this_branch = 0;
for (i=0; i<=j-1; i++) // TURN shouldn't be there
{
// don't allow pairing with restricted i's
// added Jan 28, 2006
// We don't need to make sure i and j don't have to pair with something else,
// because that would be INF - done in fold_sequence_restricted
acc = (i-1>0) ? W[i-1]: 0;
energy_ij = v->get_energy(i,j);
if (energy_ij < INF)
{
tmp = energy_ij + AU_penalty (int_sequence[i],int_sequence[j]) + acc;
if (tmp < min)
{
min = tmp;
chosen = 21; best_i = i;
if (fres[i].pair == j){
must_choose_this_branch = 1;
}
else must_choose_this_branch = 0;
}
}
// I have to condition on fres[i].pair <= -1 to make sure that i can be unpaired
if (fres[i].pair <= -1 && i+1 < j)
{
energy_ij = v->get_energy(i+1,j);
if (energy_ij < INF)
{
tmp = energy_ij + AU_penalty (int_sequence[i+1],int_sequence[j]) + acc;
PARAMTYPE dan = dangle_bot [int_sequence[j]]
[int_sequence[i+1]]
[int_sequence[i]];
//Hosna, March 27, 2012
// dangle is INF if the bases are non-canonical and \leq 0 otherwise
// to accommodate non-canonical base pairing in input structure I add the MIN
if (fres[i+1].pair == j && fres[j].pair==i+1){
dan = MIN(0,dan);
}
tmp += dan;
if (tmp < min)
{
min = tmp;
chosen = 22; best_i = i;
if (fres[i+1].pair == j){
must_choose_this_branch = 1;
}
else must_choose_this_branch = 0;
}
}
}
// I have to condition on fres[j].pair <= -1 to make sure that j can be unpaired
if (fres[j].pair <= -1 && i < j-1)
{
energy_ij = v->get_energy(i,j-1);
if (energy_ij < INF)
{
PARAMTYPE AU_pen=AU_penalty (int_sequence[i],int_sequence[j-1]);
tmp = energy_ij + AU_pen+ acc;
PARAMTYPE dan = dangle_top [int_sequence [j-1]]
[int_sequence [i]]
[int_sequence [j]];
//Hosna, March 27, 2012
// dangle is INF if the bases are non-canonical and \leq 0 otherwise
// to accommodate non-canonical base pairing in input structure I add the MIN
if (fres[i].pair == j-1 && fres[j-1].pair==i){
dan = MIN(0,dan);
}
tmp += dan;
if (tmp < min)
{
min = tmp;
chosen = 23; best_i = i;
if (fres[i].pair == j-1){
must_choose_this_branch = 1;
}
else must_choose_this_branch = 0;
}
}
}
if (fres[i].pair <= -1 && fres[j].pair <= -1 && i+1 < j-1)
{
energy_ij = v->get_energy(i+1,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + AU_penalty (int_sequence[i+1],int_sequence[j-1]) + acc;
PARAMTYPE dan_bot = dangle_bot [int_sequence[j-1]]
[int_sequence[i+1]]
[int_sequence[i]];
PARAMTYPE dan_top = dangle_top [int_sequence [j-1]]
[int_sequence [i+1]]
[int_sequence [j]];
//Hosna, March 27, 2012
// dangle is INF if the bases are non-canonical and \leq 0 otherwise
// to accommodate non-canonical base pairing in input structure I add the MIN
if (fres[i+1].pair == j-1 && fres[j-1].pair==i+1){
dan_bot = MIN(0,dan_bot);
dan_top = MIN(0,dan_top);
}
tmp += dan_bot;
tmp += dan_top;
if (tmp < min)
{
min = tmp;
chosen = 24; best_i = i;
if (fres[i+1].pair == j-1){
must_choose_this_branch = 1;
}
else must_choose_this_branch = 0;
}
}
}
}
//printf ("Chosen=%d, best_i=%d\n", chosen, best_i);
return min;
}
//kevin
int W_final::compute_W_br2_restricted_simfold_emodel (int j, str_features *fres, int &must_choose_this_branch) {
int min = INF, tmp, energy_ij = INF, acc;
int i;
int chosen = 0;
int best_i = 0;
energy_model *model;
//Mahyar and Hosna Nov 20 2017
//j cannot devides the X, since it is inclusive,
//if j points to leftmost X it devides the X and is not acceptable
if ((int_sequence[j-1] == X && int_sequence[j+1] == X) || (int_sequence[j] == X && int_sequence[j-1] != X))
return INF;
must_choose_this_branch = 0;
for (i=0; i<=j-1; i++) {
// don't allow pairing with restricted i's
// added Jan 28, 2006
//AP
//if (int_sequence[i] == X || int_sequence[j] == X || int_sequence[i+1] == X || int_sequence[j+1] == X || int_sequence[i-1] == X || int_sequence[j-1] == X)
// continue;
// Ian Wark and Kevin July 20 2017
// If i is X it cannot be paired
// i is done here because it needs to be in the for
if (int_sequence[i] == X)
continue;
for (auto &energy_model : *energy_models) {
model = &energy_model;
model->energy_value = min;
// We don't need to make sure i and j don't have to pair with something else,
// because that would be INF - done in fold_sequence_restricted
acc = (i-1>0) ? W[i-1]: 0;
energy_ij = V->get_energy(i,j);
/*
if (energy_ij != INF && j == 23) {//if (energy_ij != INF && j == 165) {
acc = (i-1>0) ? W[i-1]: 0;
}
*/