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W_final.cpp
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#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <stack>
#include <list>
#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"
// 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):s_min_folding(seq)
{
this->nb_nucleotides = strlen(seq);
// Ian Wark July 21 2017
// we don't need this, this is done in s_min_folding
//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 P;
}
// allocates space for P object and V_final
void W_final::space_allocation(){
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);
}
v = new V_final(nb_nucleotides);
if (v == NULL) giveup ("Cannot allocate memory", "W_final");
v->setloops(this->V,vm);
P = new pseudo_loop (sequence,v,this->H,this->S,this->VBI,vm);
if (P == NULL) giveup ("Cannot allocate memory", "W_final");
vm->set_V_matrix(v);
vm->set_P_matrix(P);
}
double W_final::knotty(){
double energy=INF;
int i=0, j=0;
// set the VM matrix for VM_final
vm->set_VM_matrix(VM);
// 1) fill all the matrices 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 =j; i >= 0; i--)//for (i=0; i<=j; i++)
{
V->compute_energy(i, j);
//std::cout << "i :" << i << " j: " << j << " V->energy: " << V->get_energy(i,j) << std::endl;
//if (debug){
// printf("W_final line 90: V(%d,%d) type %c and V_final(%d,%d) type %c \n",i,j, V->get_type(i,j),i,j,v->get_type (i,j));
//}
}
// if I put this before V calculation, WM(i,j) cannot be calculated, because it returns infinity
VM->compute_energy_WM(j);
}
//printf("W_final::knotty() done with V matrices!\n");
for(i=nb_nucleotides; i>=0; i--)
//for (j=0; j < nb_nucleotides; j++)
{
//printf("i:%d\n",i);
//P->arrays_reset(i);
for(j=i; j<nb_nucleotides; j++)
//for (i =j; i >= 0; i--)//for (i=0; i<=j; i++)
{
P->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));
// }
// if (debug){
// printf("W_final line 111: V(%d,%d) type %c \n",i,j, v->get_type (i,j));
// }
}
P->gc_trace_arrows(i);
P->compactify();
}
for (j= 1; j < nb_nucleotides; j++)
{
this->compute_W(j);
}
energy = this->W[nb_nucleotides-1]/100.0;
//printf("energy = %f \n", energy);
// print candidate list and trace arrow info, if applicable
if (P->sparsify) {
if (P->print_cl_info == 1) {
P->print_CL_sizes();
}
else
if (P->print_cl_info == 2)
P->print_CL_sizes_verbose();
if (P->print_ta_info == 1)
P->print_ta_sizes();
else
if (P->print_ta_info == 2)
P->print_ta_sizes_verbose();
}
//printf("after print stuff\n");
// auto t1 = Clock::now();
// 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 = nullptr;
seq_interval *cur_interval = stack_interval;
while ( cur_interval != NULL)
{
//std::cout << "cur_interval i:" << cur_interval->i;
//std::cout << " j:" << cur_interval->j << " energy:" << cur_interval->energy;
//std::cout << " type:" << cur_interval->type << std::endl;
stack_interval = stack_interval->next;
// printf("stack_interval = stack_interval->next\n");
// if (stack_interval != NULL) {
// std::cout << "stack_interval i:" << stack_interval->i;
// std::cout << " j:" << stack_interval->j << " energy:" << stack_interval->energy;
// std::cout << " type:" << stack_interval->type << std::endl;
// } else
// printf("stack_interval == null\n");
backtrack(cur_interval);
// printf("backtrack(cur_interval) \n");
delete cur_interval; // this should make up for the new in the insert_node
// printf("delete cur_interval \n");
cur_interval = stack_interval;
// printf("cur_interval = stack_interval;\n\n");
}
if(debug){
printf("Backtrack DONE successfully! \n");
}
// Hosna: Feb 18, 2014
// after the backtrack is done, now we can fill the structure array with the help of minimum_fold array, f
fill_structure();
if (debug)
{
print_result ();
}
delete stack_interval;
return energy;
}
void W_final::return_structure(char *structure){
strcpy (structure, this->structure);
//s_min_folding::return_structure(structure);
}
void W_final::compute_W(int j)
// compute W(j)
{
int m1, m2, m3;
m1 = W[j-1];
m2 = compute_W_br2(j);
m3 = compute_W_br3(j);
W[j] = MIN(m1,MIN(m2,m3));
if (debug){
int branch=-1;
if (W[j] == m1) {
branch =1;
}else if (W[j]== m2){
branch =2;
}else{
branch =3;
}
if (j==22){
printf("W(22) = %d coming from branch %d\n",W[j],branch);
}
}
}
int W_final::compute_W_br2(int j)
{
int min_energy= INF, tmp, energy_ij = INF, acc;
int i;
int chosen = 0;
int best_i = 0;
for (i=0; i<=j-1; i++)
{
// 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 + acc+ AU_penalty (int_sequence[i],int_sequence[j]);
if (tmp < min_energy)
{
min_energy = tmp;
chosen = 21; best_i = i;
}
}
energy_ij = v->get_energy(i+1,j);
if (energy_ij < INF)
{
tmp = energy_ij + acc + AU_penalty (int_sequence[i+1],int_sequence[j]);
PARAMTYPE dan = dangle_bot [int_sequence[j]]
[int_sequence[i+1]]
[int_sequence[i]];
tmp += dan;
if (tmp < min_energy)
{
min_energy = tmp;
chosen = 22; best_i = i;
}
}
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 + acc +AU_pen;
PARAMTYPE dan = dangle_top [int_sequence [j-1]]
[int_sequence [i]]
[int_sequence [j]];
tmp += dan;
if (tmp < min_energy)
{
min_energy = tmp;
chosen = 23; best_i = i;
}
}
energy_ij = v->get_energy(i+1,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + acc +AU_penalty (int_sequence[i+1],int_sequence[j-1]);
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]];
tmp += dan_bot;
tmp += dan_top;
if (tmp < min_energy)
{
min_energy = tmp;
chosen = 24; best_i = i;
}
}
}
if (debug){
printf ("W(%d), branch 2, Chosen=%d, best_i=%d\n", j, chosen, best_i);
}
return min_energy;
}
int W_final::compute_W_br3(int j){
int min_energy = INF, tmp, energy_ij = INF, acc=INF;
int i=-1;
// int chosen = 0;
// int best_i = 0;
for (i=0; i<=j-1; i++) // TURN shouldn't be there
{
// We only chop W to W + P when the bases before P are free
//if (i == 0){
// 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 = P->get_energy(i,j);
if (energy_ij < INF)
{
tmp = energy_ij + PS_penalty + acc;
if (tmp < min_energy)
{
min_energy = tmp;
// chosen = 31;
// best_i = i;
}
}
energy_ij = P->get_energy(i+1,j);
if (energy_ij < INF)
{
tmp = energy_ij + acc + PS_penalty;
//tmp += dangle_bot [int_sequence[j]]
// [int_sequence[i+1]]
// [int_sequence[i]];
if (tmp < min_energy)
{
min_energy = tmp;
// chosen = 32;
// best_i = i;
}
}
energy_ij = P->get_energy(i,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + acc +PS_penalty ;
/*
tmp += dangle_top [int_sequence [j-1]]
[int_sequence [i]]
[int_sequence [j]];
*/
if (tmp < min_energy)
{
min_energy = tmp;
// chosen = 33;
// best_i = i;
}
}
energy_ij = P->get_energy(i+1,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + acc +PS_penalty;
/*
tmp += dangle_bot [int_sequence[j-1]]
[int_sequence[i+1]]
[int_sequence[i]];
tmp += dangle_top [int_sequence [j-1]]
[int_sequence [i+1]]
[int_sequence [j]];
*/
if (tmp < min_energy)
{
min_energy = tmp;
// chosen = 34;
// best_i = i;
}
}
//}
}
//printf ("Chosen=%d, best_i=%d\n", chosen, best_i);
return min_energy;
}
void W_final::backtrack(seq_interval *cur_interval){
char type;
//Hosna, March 8, 2012
// changing nested if to switch for optimality
switch (cur_interval->type){
case LOOP:
{
int i = cur_interval->i;
int j = cur_interval->j;
if (i >= j)
return;
f[i].pair = j;
f[j].pair = i;
structure[i] = '(';
structure[j] = ')';
type = v->get_type (i,j);
if (debug)
printf ("\t(%d,%d) LOOP - type %c\n", i,j,type);
// Hosna, March 8, 2012
// changing nested ifs to switch for optimality
switch (type){
case STACK:
//if (type == STACK)
{
f[i].type = STACK;
f[j].type = STACK;
if (i+1 < j-1)
this->insert_node(i+1,j-1, LOOP);
//insert_node (i+1, j-1, LOOP);
else
{
printf ("NOT GOOD STACK, i=%d, j=%d\n", i, j);
exit (1);
}
}
break;
case HAIRP:
//else if (type == HAIRP)
{
f[i].type = HAIRP;
f[j].type = HAIRP;
}
break;
case INTER:
//else if (type == INTER)
{
f[i].type = INTER;
f[j].type = INTER;
// detect the other closing pair
int ip, jp, best_ip = -1, best_jp = -1, minq;
int tmp, min_energy = INF;
for (ip = i+1; ip <= MIN(j-2,i+MAXLOOP+1); ip++)
{
// Hosna, August 28, 2012
// TODO: cannot understand why we have the following calculations, as it makes the following case be missed!
// GACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUC
// (____(_____((__(_______)__))_______________________________)____)
// 0....5....1....5....2....5....3....5....4....5....5....5....6...4
// in this example int(5,59,11,27) is falsely missed and is equal to INF
// So I am changing it to the be jp=ip+1; jp<j; jp++ instead
//minq = MAX (j-i+ip-MAXLOOP-2, ip+1); // without TURN
minq = ip+1;
for (jp = minq; jp < j; jp++)
{
tmp = VBI->get_energy_str (i,j,ip,jp);
if (tmp < min_energy)
{
min_energy = tmp;
best_ip = ip;
best_jp = jp;
}
}
}
if (best_ip < best_jp)
insert_node (best_ip, best_jp, LOOP);
else
{
printf ("NOT GOOD INTER, i=%d, j=%d, best_ip=%d, best_jp=%d\n", i, j, best_ip, best_jp);
exit (1);
}
}
break;
case MULTI:
//else if (type == MULTI)
{
f[i].type = MULTI;
f[j].type = MULTI;
int k, best_k = -1, best_row = -1;
int tmp= INF, min_energy = INF;
for (k = i+TURN+1; k <= j-TURN-2; k++)
{
tmp = vm->get_energy_WM (i+1,k) + vm->get_energy_WM (k+1, j-1);
if (tmp < min_energy)
{
min_energy = tmp;
best_k = k;
best_row = 1;
}
tmp = vm->get_energy_WM (i+2,k) + vm->get_energy_WM (k+1, j-1) +
dangle_top [int_sequence[i]][int_sequence[j]][int_sequence[i+1]] +
misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_k = k;
best_row = 2;
}
tmp = vm->get_energy_WM (i+1,k) + vm->get_energy_WM (k+1, j-2) +
dangle_bot [int_sequence[i]][int_sequence[j]][int_sequence[j-1]] +
misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_k = k;
best_row = 3;
}
tmp = vm->get_energy_WM (i+2,k) + vm->get_energy_WM (k+1, j-2) +
dangle_top [int_sequence[i]][int_sequence[j]][int_sequence[i+1]] +
dangle_bot [int_sequence[i]][int_sequence[j]][int_sequence[j-1]] +
2*misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_k = k;
best_row = 4;
}
// Hosna: June 28, 2007
// the last branch of VM, which is WMB_(i+1),(j-1)
// Hosna: July 5th, 2007
// add a b_penalty to this case to match the previous cases
tmp = P->get_energy(i+1,j-1)+ a_penalty + PSM_penalty+ b_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 5;
}
}
switch (best_row)
{
case 1:
// printf("M_WM(%d,%d) branch 1: pushing M_WM(%d,%d) and M_WM(%d,%d) \n", i,j,i+1,best_k,best_k+1,j-1);
insert_node (i+1, best_k, M_WM);
insert_node (best_k+1, j-1, M_WM);
break;
case 2:
// printf("M_WM(%d,%d) branch 2: pushing M_WM(%d,%d) and M_WM(%d,%d) \n", i,j,i+2,best_k,best_k+1,j-1);
insert_node (i+2, best_k, M_WM);
insert_node (best_k+1, j-1, M_WM);
break;
case 3:
// printf("M_WM(%d,%d) branch 3: pushing M_WM(%d,%d) and M_WM(%d,%d) \n", i,j,i+1,best_k,best_k+1,j-2);
insert_node (i+1, best_k, M_WM);
insert_node (best_k+1, j-2, M_WM);
break;
case 4:
// printf("M_WM(%d,%d) branch 4: pushing M_WM(%d,%d) and M_WM(%d,%d) \n", i,j,i+2,best_k,best_k+1,j-2);
insert_node (i+2, best_k, M_WM);
insert_node (best_k+1, j-2, M_WM);
break;
// Hosna: June 28, 2007
// the last branch of VM, which is WMB_(i+1),(j-1)
case 5:
//printf("M_WM(%d,%d) branch 3: pushing P_WMB(%d,%d)\n", i,j,i+1,j-1);
insert_node(i+1,j-1, P_P);
break;
}
}
break;
}
}
break;
case FREE:
{
int j = cur_interval->j;
if (j==0) return;
int min_energy=INF, tmp=INF, best_row=-1, i=-1, best_i=-1, acc=INF, energy_ij=INF;
if (debug)
printf ("\t(0,%d) FREE\n", j);
tmp = W[j-1];
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 0;
}
for (i=0; i<=j-1; i++) // no TURN
{
acc = (i-1>0) ? W[i-1] : 0;
energy_ij = v->get_energy(i,j);
if (energy_ij < INF)
{
tmp = energy_ij + acc + AU_penalty (int_sequence[i],int_sequence[j]);
if (tmp < min_energy)
{
min_energy = tmp;
best_i = i;
best_row = 1;
}
}
energy_ij = v->get_energy(i+1,j);
if (energy_ij < INF)
{
tmp = energy_ij + acc +AU_penalty (int_sequence[i+1],int_sequence[j]);
tmp += dangle_bot [int_sequence[j]]
[int_sequence[i+1]]
[int_sequence[i]];
if (tmp < min_energy)
{
min_energy = tmp;
best_i = i;
best_row = 2;
}
}
energy_ij = v->get_energy(i,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + acc +AU_penalty (int_sequence[i],int_sequence[j-1]);
tmp += dangle_top [int_sequence[j-1]]
[int_sequence[i]]
[int_sequence[j]];
if (tmp < min_energy)
{
min_energy = tmp;
best_i = i;
best_row = 3;
}
}
energy_ij = v->get_energy(i+1,j-1);
if (energy_ij > 0)
{
tmp = energy_ij + acc + AU_penalty (int_sequence[i+1],int_sequence[j-1]);
tmp += dangle_bot [int_sequence[j-1]]
[int_sequence[i+1]]
[int_sequence[i]];
tmp += dangle_top [int_sequence[j-1]]
[int_sequence[i+1]]
[int_sequence[j]];
if (tmp < min_energy)
{
min_energy = tmp;
best_i = i;
best_row = 4;
}
}
}
for (i=0; i<=j-1; i++)
{
acc = (i-1>0) ? W[i-1]: 0;
energy_ij = P->get_energy(i,j);
if (energy_ij < INF)
{
tmp = energy_ij + acc + PS_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 5;
best_i = i;
}
}
energy_ij = P->get_energy(i+1,j);
if (energy_ij < INF)
{
tmp = energy_ij + acc +PS_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 6;
best_i = i;
}
}
energy_ij = P->get_energy(i,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + acc + PS_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 7;
best_i = i;
}
}
energy_ij = P->get_energy(i+1,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + acc +PS_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 8;
best_i = i;
}
}
}
switch (best_row)
{
case 0:
if (debug)
printf("W(%d) case 0: inserting Free (0,%d)\n",j,j-1);
insert_node (0, j-1, FREE); break;
case 1:
if (debug)
printf("W(%d) case 1: inserting Loop(%d,%d) and Free (0,%d)\n",j,best_i,j,best_i-1);
insert_node (best_i, j, LOOP);
if (best_i-1 > 0) // it was TURN instead of 0 - not sure if TURN shouldn't be here
insert_node (0, best_i-1, FREE);
break;
case 2:
if (debug)
printf("W(%d) case 2: inserting Loop(%d,%d) and Free (0,%d)\n",j,best_i+1,j,best_i);
insert_node (best_i+1, j, LOOP);
if (best_i >= 0)// Hosna, March 26, 2012, was best_i-1 instead of best_i
insert_node (0, best_i, FREE);
break;
case 3:
if (debug)
printf("W(%d) case 3: inserting Loop(%d,%d) and Free (0,%d)\n",j,best_i,j-1,best_i-1);
insert_node (best_i, j-1, LOOP);
if (best_i-1 > 0)
insert_node (0, best_i-1, FREE);
break;
case 4:
if (debug)
printf("W(%d) case 4: inserting Loop(%d,%d) and Free (0,%d)\n",j,best_i+1,j-1,best_i);
insert_node (best_i+1, j-1, LOOP);
if (best_i >= 0) // Hosna, March 26, 2012, was best_i-1 instead of best_i
insert_node (0, best_i, FREE);
break;
// Hosna: June 28, 2007
// the last branch of W, which is P_i,j
case 5:
if (debug)
printf("W(%d) case 5: inserting P(%d,%d) and Free (0,%d)\n",j,best_i,j,best_i-1);
insert_node (best_i, j, P_P);
if (best_i-1 > 0) // it was TURN instead of 0 - not sure if TURN shouldn't be here
insert_node (0, best_i-1, FREE);
break;
case 6:
if (debug)
printf("W(%d) case 6: inserting P(%d,%d) and Free (0,%d)\n",j,best_i+1,j,best_i);
insert_node (best_i+1, j, P_P);
if (best_i >= 0) // Hosna, March 26, 2012, was best_i-1 instead of best_i
insert_node (0, best_i, FREE);
break;
case 7:
if (debug)
printf("W(%d) case 7: inserting P(%d,%d) and Free (0,%d)\n",j,best_i,j-1,best_i-1);
insert_node (best_i, j-1, P_P);
if (best_i-1 > 0)
insert_node (0, best_i-1, FREE);
break;
case 8:
if (debug)
printf("W(%d) case 8: inserting P(%d,%d) and Free (0,%d)\n",j,best_i+1,j-1,best_i);
insert_node (best_i+1, j-1, P_P);
if (best_i >= 0) // Hosna, March 26, 2012, was best_i-1 instead of best_i
insert_node (0, best_i, FREE);
break;
}
}
break;
case M_WM:
// else if(cur_interval->type == M_WM)
{
int i = cur_interval->i;
int j = cur_interval->j;
int tmp, min_energy = INF;
int best_k=-1, best_row;
if (debug)
printf ("\t (%d,%d) M_WM\n", i,j);
tmp = v->get_energy(i,j) +
AU_penalty (int_sequence[i], int_sequence[j]) +
misc.multi_helix_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 1;
}
tmp = v->get_energy(i+1,j) +
AU_penalty (int_sequence[i+1], int_sequence[j]) +
dangle_bot [int_sequence[j]]
[int_sequence[i+1]]
[int_sequence[i]] +
misc.multi_helix_penalty +
misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 2;
}
tmp = v->get_energy(i,j-1) +
AU_penalty (int_sequence[i], int_sequence[j-1]) +
dangle_top [int_sequence[j-1]]
[int_sequence[i]]
[int_sequence[j]] +
misc.multi_helix_penalty +
misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 3;
}
tmp = v->get_energy(i+1,j-1) +
AU_penalty (int_sequence[i+1], int_sequence[j-1]) +
dangle_bot [int_sequence[j-1]]
[int_sequence[i+1]]
[int_sequence[i]] +
dangle_top [int_sequence[j-1]]
[int_sequence[i+1]]
[int_sequence[j]] +
misc.multi_helix_penalty +
2*misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 4;
}
tmp = vm->get_energy_WM (i+1,j) + misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 5;
}
tmp = vm->get_energy_WM (i,j-1) + misc.multi_free_base_penalty;
if (tmp < min_energy)
{
min_energy = tmp;
best_row = 6;
}
for (int k=i; k < j; k++)
{
tmp = vm->get_energy_WM (i, k) + vm->get_energy_WM (k+1, j);
if (tmp < min_energy)
{
min_energy = tmp;
best_k = k;
best_row = 7;
}
}
// the last branch of WM, which is P_i,j
tmp = P->get_energy(i,j)+PSM_penalty;
if (tmp < min_energy){
min_energy = tmp;
best_row = 8;
}
switch (best_row)
{
case 1: insert_node (i, j, LOOP); break;
case 2: insert_node (i+1, j, LOOP); break;
case 3: insert_node (i, j-1, LOOP); break;
case 4: insert_node (i+1, j-1, LOOP); break;
case 5:
if (j-i-1 > 0)
insert_node (i+1, j, M_WM);
break;
case 6:
if (j-1-i > 0)
insert_node (i, j-1, M_WM);
break;
case 7:
if (best_k-i > 0)
insert_node (i, best_k, M_WM);
if (j-best_k-1 > 0)
insert_node (best_k+1, j, M_WM);
break;
// the last branch of WM, which is P_i,j
case 8:
printf("insert_node(%d,%d,%c)\n",i,j,P_P);
insert_node(i,j,P_P);
break;
}
}
break;
// Pseudo loop stuff
case P_P: ;
case P_PK: ;
case P_WB: ;
case P_WBP: ;
case P_WP: ;
case P_WPP: ;
case P_PL: ;
case P_PR: ;
case P_PM: ;
case P_PO: ;
case P_PfromL: ;
case P_PfromR: ;
case P_PfromM: ;
case P_PfromO: ;
case P_PLiloop: ;
case P_PRiloop: ;
case P_PMiloop: ;
case P_POiloop: ;
case P_PLmloop: ;
case P_PLmloop1: ;
case P_PLmloop0: ;
case P_PRmloop: ;
case P_PRmloop1: ;
case P_PRmloop0: ;
case P_PMmloop: ;
case P_PMmloop1: ;
case P_PMmloop0: ;
case P_POmloop: ;
case P_POmloop1: ;
case P_POmloop0: ;
p_backtrack(cur_interval); break;
default:
printf("Should not be here!\n");
}
}
// helper fucntion in W_final::backtrack for calling any of the pseudo loop backtracking
void W_final::p_backtrack(seq_interval* cur_interval) {
P->set_stack_interval(stack_interval);
// Hosna, Feb 18, 2014
// removed structure in pseudoloop backtrack, see pseudoloop.cpp for detail
//P->back_track(structure,f,cur_interval);
P->back_track(f,cur_interval);
stack_interval = P->get_stack_interval();
//structure = P->get_structure();
f = P->get_minimum_fold();
}
//Hosna, Feb 19, 2014
//the algorithm I have in mind is something like this:
/*
for (int i = 0; i < nb_nucleotides; i++){
if (i < f[i].pair){
for (int j= 0; j < num_bands; j++){
if(f[i].pair < band[j]->end){ // i.e. i.pair[i] is nested in the band
structure[i] = band[j]->open;
structure[j] = band[j]->close;
isInABand=1;
}
}
if (!isInABand){