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W_final.cpp
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#include <stdio.h>
#include <math.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"
// 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);
/*
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;
//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;
}
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));
}
}
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;
}
int W_final::compute_W_br2_restricted_pkonly (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 = (fres[j].pair == i && fres[i].pair ==j)? v->get_energy(i,j) : INF; //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
// in the pk_only version we don't add any pseudoknot free base pairs
if (fres[i].pair <= -1 && i+1 < j && fres[i+1].pair ==j && fres[j].pair==i+1)
{
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
// in the pkonly version we don't add any pseudoknot free base pairs
if (fres[j].pair <= -1 && i < j-1 && fres[i].pair ==j-1 && fres[j-1].pair ==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 + 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;
}
}
}
// in the pkonly version we don't add any pseudoknot free base pairs
if (fres[i].pair <= -1 && fres[j].pair <= -1 && i+1 < j-1 && fres[i+1].pair==j-1 && fres[j-1].pair==i+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;
}
int W_final::compute_W_br3_restricted(int j, str_features *fres){
// Hosna June 30, 2007
// The following would not take care of when
// we have some unpaired bases before the start of the WMB
//return WMB->get_energy(0,j) + PS_penalty;
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
// Hosna: July 9, 2007
// We only chop W to W + WMB when the bases before WMB are free
if (i == 0 || (WMB->is_weakly_closed(0,i-1) && WMB->is_weakly_closed(i,j))){
// 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 = WMB->get_energy(i,j);
if (energy_ij < INF)
{
tmp = energy_ij + PS_penalty + acc;
if (tmp < min)
{
min = tmp;
chosen = 31;
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 = WMB->get_energy(i+1,j);
if (energy_ij < INF)
{
tmp = energy_ij + PS_penalty + acc;
// tmp += dangle_bot [int_sequence[j]]
// [int_sequence[i+1]]
// [int_sequence[i]];
if (tmp < min)
{
min = tmp;
chosen = 32;
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 = WMB->get_energy(i,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + PS_penalty + acc;
// tmp += dangle_top [int_sequence [j-1]]
// [int_sequence [i]]
// [int_sequence [j]];
if (tmp < min)
{
min = tmp;
chosen = 33;
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 = WMB->get_energy(i+1,j-1);
if (energy_ij < INF)
{
tmp = energy_ij + PS_penalty + acc;
// 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)
{
min = tmp;
chosen = 34;
best_i = i;
// if (fres[i+1].pair == j-1) must_choose_this_branch = 1;
// else must_choose_this_branch = 0;
}
}
}
}
if (min == -8376) {
int temp = 0;;
}
}
//printf ("Chosen=%d, best_i=%d\n", chosen, best_i);
return min;
}
void W_final::backtrack_restricted(seq_interval *cur_interval, str_features *fres){
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;
// Hosna Jun. 28 2007
// if the pairing is part of original structure, put '(' and ')' in the structure
// otherwise make it '[' and ']'
if (fres[i].pair == j){
structure[i] = '(';
structure[j] = ')';
}else{
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
{
fprintf (stderr, "NOT GOOD RESTR STACK, i=%d, j=%d\n", i, j);
exit (0);
}
}
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, best_jp, minq;
int tmp, min = INF;
for (ip = i+1; ip <= MIN(j-2,i+MAXLOOP+1); ip++)
{
// Hosna, August 28, 2012
// TODO: cannot understand why we have th efollowing 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++)
{
if (exists_restricted (i,ip,fres) || exists_restricted (jp,j,fres))
continue;
//tmp = VBI->get_energy_str (i,j,ip,jp);
// Hosna, March 26, 2012
// modified to accommodate non-canonical base pairing in restricted structure
tmp = VBI->get_energy_str_restricted(i,j,ip,jp,fres);
if (tmp < min)
{
min = tmp;
best_ip = ip;
best_jp = jp;
}
}
}
if (best_ip < best_jp)
insert_node (best_ip, best_jp, LOOP);
else
{
fprintf (stderr, "NOT GOOD RESTR INTER, i=%d, j=%d, best_ip=%d, best_jp=%d\n", i, j, best_ip, best_jp);
exit (0);
}
}
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 = INF;
for (k = i+1; k <= j-1; k++)
{
tmp = vm->get_energy_WM (i+1,k) + vm->get_energy_WM (k+1, j-1);
if (tmp < min)
{
min = tmp;
best_k = k;
best_row = 1;
}
// TODO:
// Hosna, May 1st, 2012
// do I need to check for non-canonical base pairings here as well so the dangle values not be INF??
if (fres[i+1].pair <= -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)
{
min = tmp;
best_k = k;
best_row = 2;
}
}
if (fres[j-1].pair <= -1)
{
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)
{
min = tmp;
best_k = k;
best_row = 3;
}
}
if (fres[i+1].pair <= -1 && fres[j-1].pair <= -1)
{
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)
{
min = 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 = WMB->get_energy(i+1,j-1)+ a_penalty + PSM_penalty+ b_penalty;
if (tmp < min)
{
min = 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_WMB);
break;
}
}
break;
}
}
break;
case FREE:
{
int j = cur_interval->j;
if (j==0) return;
int min = INF, tmp, best_row, i, best_i, acc, energy_ij;
if (debug)
printf ("\t(0,%d) FREE\n", j);
// this case is for j unpaired, so I have to check that.
if (fres[j].pair <= -1)
{
tmp = W[j-1];
if (tmp < min)
{
min = tmp;
best_row = 0;
}
}
for (i=0; i<=j-1; i++) // no TURN
{
// Don't need to make sure i and j don't have to pair with something else
// it's 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;
best_i = i;
best_row = 1;
}
}
if (fres[i].pair <= -1)
{
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;
tmp += dangle_bot [int_sequence[j]]
[int_sequence[i+1]]
[int_sequence[i]];
if (tmp < min)
{
min = tmp;
best_i = i;
best_row = 2;
}
}
}
if (fres[j].pair <= -1)