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pseudo_loop.cpp
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#include "pseudo_loop.h"
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <iostream>
#include <math.h>
#include "constants.h"
#include "h_struct.h"
#include "externs.h"
#include "h_externs.h"
#include "h_common.h"
#include "s_hairpin_loop.h"
#include "s_stacked_pair.h"
#include "VM_final.h"
#include "V_final.h"
#include "s_specific_functions.h"
// Ian Wark July 19 2017
// constant that defines what fres[i].pair will be compared against (>=) for impossible cases
// set to -1 because >= 0 means there is already a base pair there,
// and -1 means restricted struture says there is no base pair there.
#define FRES_RESTRICTED_MIN -1
pseudo_loop::pseudo_loop(char *seq, char* restricted, V_final *V, s_hairpin_loop *H, s_stacked_pair *S, s_internal_loop *VBI, VM_final *VM)
{
this->sequence = seq;
this->restricted = restricted;
this->V = V;
this->H = H;
this->S = S;
this->VBI = VBI;
this->VM = VM;
allocate_space();
if (debug){
printf("an object of pseudo_loop was successfully created! \n");
}
}
void pseudo_loop::allocate_space()
{
int i;
nb_nucleotides = strlen(sequence);
needs_computation = 0; // Hosna, March 14, 2012 I need to remove this variable!! to make everything a lot faster
index = new int [nb_nucleotides];
int total_length = (nb_nucleotides *(nb_nucleotides+1))/2;
index[0] = 0;
for (int i=1; i < nb_nucleotides; i++)
index[i] = index[i-1]+nb_nucleotides-i+1;
WI = new int [total_length];
if (WI == NULL) giveup ("Cannot allocate memory", "energy");
for (i=0; i < total_length; i++) WI[i] = 0; // if i == j -> p_up
weakly_closed = new int[total_length];
if (weakly_closed == NULL) giveup ("Cannot allocate memory", "weakly_closed");
for (i=0; i < total_length; i++) weakly_closed[i] = 0;
not_paired_all = new int[total_length];
if (not_paired_all == NULL) giveup ("Cannot allocate memory", "not_paired_all");
for (i=0; i < total_length; i++) not_paired_all[i] = 0;
VP = new int[total_length];
if (VP == NULL) giveup ("Cannot allocate memory", "VP");
for (i=0; i < total_length; i++) VP[i] = INF;
WMB = new int[total_length];
if (WMB == NULL) giveup ("Cannot allocate memory", "WMB");
for (i=0; i < total_length; i++) WMB[i] = INF;
WMBP = new int[total_length];
if (WMBP == NULL) giveup("Cannot allocate memory","WMBP");
for (i=0; i < total_length; i++) WMBP[i] = INF;
WIP = new int[total_length];
if (WIP == NULL) giveup ("Cannot allocate memory", "WIP");
for (i=0; i < total_length; i++) WIP[i] = INF;
VPP = new int[total_length];
if (VPP == NULL) giveup ("Cannot allocate memory", "VPP");
for (i=0; i < total_length; i++) VPP[i] = INF;
BE = new int[total_length];
if (BE == NULL) giveup ("Cannot allocate memory", "BE");
for (i=0; i < total_length; i++) BE[i] = 0; //check
border_bs = new int*[nb_nucleotides];
for(i = 0; i < nb_nucleotides; i++) border_bs[i] = new int[nb_nucleotides];
border_bps = new int*[nb_nucleotides];
for(i = 0; i < nb_nucleotides; i++) border_bps[i] = new int[nb_nucleotides];
int_sequence = new int[nb_nucleotides];
if (int_sequence == NULL) giveup ("Cannot allocate memory", "energy");
for (i=0; i < nb_nucleotides; i++) int_sequence[i] = nuc_to_int(sequence[i]);
}
pseudo_loop::~pseudo_loop()
{
delete [] WI;
delete [] WIP;
delete [] VP;
delete [] VPP;
delete [] WMB;
delete [] WMBP;
delete [] BE;
delete [] weakly_closed;
delete [] not_paired_all;
// Ian Wark July 21 2017
// border_bs is array of arrays
// need to delete sub arrays as well
for(int i = 0; i < nb_nucleotides; i++) {
delete [] border_bs[i];
delete [] border_bps[i];
}
delete [] border_bs;
delete [] border_bps;
delete [] index;
delete [] int_sequence;
}
void pseudo_loop::set_features(h_str_features *f){
fres = f;
}
int pseudo_loop::is_weakly_closed(int i, int j){
// base case: if i > j then the region is weakly closed
if (i>j){
return 1;
}
int ij = index[i]+j-i;
if (weakly_closed[ij] == 1)
return 1;
return 0;
}
int pseudo_loop::is_empty_region(int i, int j){
//base case: if i> j then the region is empty
if (i>j){
return 1;
}
int ij = index[i]+j-i;
if (not_paired_all[ij] == 1){
return 1;
}
return 0;
}
void pseudo_loop::initialize(){
int i, j;
//Hosna: before going further, we should fill up the weakly closed array
detect_weakly_closed(fres, weakly_closed, nb_nucleotides, index);
detect_not_paired_all(fres, not_paired_all, nb_nucleotides, index);
detect_border_bs(fres,border_bs, nb_nucleotides);
detect_border_bps(fres,border_bps, nb_nucleotides);
//testing to see if all the structures were found correctly
// if (debug){
// for (i=0; i < nb_nucleotides; i++){
//if (fres[i].pair != -1 && fres[i].pair != -2)
// if(debug)
// printf ("%d pairs %d, is in arc %d, and has type %c\n", i, fres[i].pair, fres[i].arc, fres[i].type);
// }
// for (i = 0; i < nb_nucleotides; i++){
// int j;
// for (j = i; j < nb_nucleotides; j++){
// int ij = index[i]+j -i;
// if (weakly_closed[ij] == 1){
// printf("region [%d,%d] is weakly closed. \n", i, j);
// }
// else{
// printf("region [%d,%d] is NOT weakly closed. \n", i, j);
// }
// if (not_paired_all[ij] == 1){::compute_WI
// printf("region [%d,%d] is EMPTY \n",i,j);
// }
//checking WI, VP and WMB to see if they have been initialized correctly
// if (debug)
// if(WI[ij] != 0){
// printf("WI[%d,%d] NOT initialized correctly!\n",i,j);
// }
// if(VP[ij] != 0){
// printf("VP[%d,%d] NOT initialized correctly!\n",i,j);
// }
// if(WMB[ij] != 0){
// printf("WMB[%d,%d] NOT initialized correctly!\n",i,j);
// }
// }
// }
// }
// printf("WMB was initialized successfully! \n");
}
void pseudo_loop::compute_energies(int i, int j)
{
// Hosna, April 18th, 2007
// based on discussion with Anne, we changed WMB to case 2 and WMBP(containing the rest of the recurrences)
// if(debug){
// printf("calculating VP(%d,%d) \n",i,j);
// }
compute_VP(i,j,fres); // Hosna, March 14, 2012, changed the positionof computing VP from after BE to befor WMBP
// if(debug){
// printf("calculating WMBP(%d,%d) \n",i,j);
// }::compute_WI
compute_WMBP(i,j,fres);
// if(debug){
// printf("calculating WMB(%d,%d) \n",i,j);
// }
compute_WMB(i,j,fres);
// if(debug){
// printf("calculating WI(%d,%d) \n",i,j);
// }
compute_WI(i,j,fres);
// if(debug){
// printf("calculating WIP(%d,%d) \n",i,j);
// }
compute_WIP(i,j,fres);
// if(debug){
// printf("calculating VPP(%d,%d) \n",i,j);
// }
compute_VPP(i,j,fres);
// if(debug){
// printf("calculating BE(%d,%d) \n",i,j);
// }
compute_BE(fres[j].pair,j,fres[i].pair,i,fres);
// if (debug){
// printf("WI(%d,%d) = %d \n", i,j, get_WI(i,j));
// printf("WIP(%d,%d) = %d \n", i,j, get_WIP(i,j));
// printf("VPP(%d,%d) = %d \n", i,j, get_VPP(i,j));
// printf("BE(%d,%d,%d,%d) = %d \n", i,fres[i].pair,j,fres[j].pair, get_BE(i,fres[i].pair,j,fres[j].pair));
// printf("VP(%d,%d) = %d \n", i,j, get_VP(i,j));
// printf("WMBP(%d,%d) = %d \n", i,j, get_WMBP(i,j));
// printf("WMB(%d,%d) = %d \n", i,j, get_WMB(i,j));
// }
}
//AP
void pseudo_loop::compute_energies_emodel(int i, int j, std::vector<energy_model> *energy_models)
{
/*
// Ian Wark and Kevin July 20 2017
// i and j cannot be X
if (int_sequence[i] == X || int_sequence[j] == X )
return;
*/
// Hosna, April 18th, 2007
// based on discussion with Anne, we changed WMB to case 2 and WMBP(containing the rest of the recurrences)
// Hosna, March 14, 2012, changed the position of computing VP from after BE to before WMBP
compute_VP_emodel(i,j,fres, energy_models);
compute_WMBP(i,j,fres);
compute_WMB(i,j,fres);
compute_WI(i,j,fres);
compute_WIP(i,j,fres);
compute_VPP(i,j,fres);
compute_BE_emodel(fres[j].pair,j,fres[i].pair,i,fres,energy_models);
}
void pseudo_loop::compute_WI(int i, int j , h_str_features *fres){
int min = INF, m1 = INF, m2= INF, m3= INF;
int ij = index[i]+j-i;
if (WI[ij] != 0){ //calculated before
// if (debug)
// {
// printf("WI(%d,%d) was calculated before ==> WI(%d,%d) = %d \n",i,j,i,j,get_WI(i,j));
// }
return;
}
//Kevin and Mahyar, Nov 30, 2017
if(int_sequence[i] == X && int_sequence[j] == X){
WI[ij] = START_HYBRID_PENALTY;
return;
}
//14 Aug 2017 kevin and Mahyar
//
if(int_sequence[i] == X || int_sequence[j] == X){
int new_ij = -1;
if(int_sequence[i] == X){
i++;
while(int_sequence[i] == X){
i++;
}
}
if(int_sequence[j] == X){
j--;
while(int_sequence[j] == X){
j--;
}
}
if(i > j){
WI[ij] = 0;
return;
}
//Mahyar and Kevin, Nov 30 2017 , changed from 0 to Pup + START_HYBRID_PENALTY
if(i == j){
WI[ij] = PUP_penalty + START_HYBRID_PENALTY;
return;
}
new_ij = index[i] + j -i;
//Mahyar and Kevin, Nov 16 2017
WI[ij] = WI[new_ij] + START_HYBRID_PENALTY;
return;
}
//base cases
// if [i,j] is not weakly closed then WI[i,j] = INF
if (is_weakly_closed(i,j) == 0){
WI[ij] = INF;
// if (debug)
// {
// printf("[%d,%d] is not weakly closed ==> WI(%d,%d) = %d \n",i,j,i,j,get_WI(i,j));
// }
return;
}
// branch 4, one base
if (i == j){
WI[ij] = PUP_penalty;
// if (debug){
// printf("i ==j => WI[%d,%d]= %d \n",i,j,WI[ij]);
// }
return;
}
// Hosna: Feb 12, 2007
// changed this part to see if it works better
// Hosna: Feb 16, 2007:
// we don't need to check to see if i and j are inside an arc
// because they are not in an arc in G but they will be in an arc in G'
if (fres[i].arc != fres[j].arc){
WI[ij] = INF;
// if (debug){
// printf("i and j not in the same arc => WI[%d,%d]= %d \n",i,j,WI[ij]);
// }
return;
}
// Hosna: July 2nd, 2007
// in branch 1 of WI, we can have a case like
// ((..))((...))
// such that both i and j are paired but we can chop them
// branch 1:compute_WI
// if (fres[i].pair < 0 && fres[j].pair < 0)
// {
int t;
for (t = i; t< j; t++){
//Mahyar and Kevin, Nov 16, 2017
if (int_sequence[t] == X){
continue;
}
int wi_1 = get_WI(i,t);
int wi_2 = get_WI(t+1,j);
int energy = wi_1 + wi_2;
m1 = (m1 > energy)? energy : m1;
// if (debug_WI){
// printf("WI branch 1: WI[%d,%d] = %d and WI[%d,%d] = %d => energy = %d and m1 = %d \n",i,t,wi_1,(t+1),j,wi_2,energy, m1);
// }
}
// if (debug){
// printf("WI(%d,%d) branch 1: m1 = %d\n",i,j,m1);
// }
// }
// Ian Wark July 19 2017
// fres[i].pair < 0 changed to fres[i].pair < FRES_RESTRICTED_MIN (which equals -1 at time of writing)
// otherwise it will create pairs in spots where the restricted structure says there should be no pairs
// branch 2:
if ((fres[i].pair == j && fres[j].pair == i)||(fres[i].pair < FRES_RESTRICTED_MIN && fres[j].pair < 0)){
// Hosna, April 16th, 2007
// changed back to see if it will work fine
// Hosna: April 19th, 2007
// I think we should call the restricted version
int v_ener = (i>j)? INF: V->get_energy(i,j);
m2 = v_ener + PPS_penalty;
// if (debug){
// printf("WI(%d,%d) branch 2: m2 = %d\n",i,j,m2);
// }
}
// branch 3:
// Hosna: April 20, 2007
// removed the penalty of PPS
// Hosna: July 5th, 2007
// Anne said we should put PPS back
// change PSM to PSP
// if (debug && i == 6 && j == 15){newi newj
// printf("WI(6,15) is calling WMB \n");
// }
m3 = get_WMB(i,j) + PSP_penalty + PPS_penalty;
// if (debug){
// printf("WI(%d,%d) branch 3: m3 = %d\n",i,j,m3);
// }
min = MIN(m1,MIN(m2,m3));
WI[ij] = min;
// if (debug ){
// printf("WI[%d,%d]: m1 = %d, m2 = %d and m3 = %d ==> min = %d \n",i,j,m1,m2,m3,WI[ij]);
// }
}
void pseudo_loop::compute_WI_pkonly(int i, int j , h_str_features *fres){
int min = INF, m1 = INF, m2= INF, m3= INF;
int ij = index[i]+j-i;
if (WI[ij] != 0){ //calculated before
return;
}
//base cases
// if [i,j] is not weakly closed then WI[i,j] = INF
if (is_weakly_closed(i,j) == 0){
WI[ij] = INF;
return;
}
// branch 4, one base
if (i == j){
WI[ij] = PUP_penalty;
return;
}
if (fres[i].arc != fres[j].arc){
WI[ij] = INF;
return;
}
// branch 1:
int t;
for (t = i; t< j; t++){
int wi_1 = get_WI(i,t);
int wi_2 = get_WI(t+1,j);
int energy = wi_1 + wi_2;
m1 = (m1 > energy)? energy : m1;
}
// branch 2:
if (fres[i].pair == j && fres[j].pair == i){
int v_ener = (i>j)? INF: V->get_energy(i,j);
m2 = v_ener + PPS_penalty;
}
// branch 3:
m3 = get_WMB(i,j) + PSP_penalty + PPS_penalty;
min = MIN(m1,MIN(m2,m3));
WI[ij] = min;
}
//AP
void pseudo_loop::compute_VP_emodel(int i, int j, h_str_features *fres, std::vector<energy_model> *energy_models){
int ij = index[i]+j-i;
if (VP[ij] != INF){//has been calculated before
// if (debug)
// {
// printf("VP(%d,%d) was calculated before ==> VP(%d,%d) = %d \n",i,j,i,j,VP[ij]);
// }
return;
}
// Ian Wark July 19 2017
// fres[i].pair >= 0 changed to fres[i].pair >= FRES_RESTRICTED_MIN (which equals -1 at time of writing)
// otherwise it will create pairs in spots where the restricted structure says there should be no pairs
if (i == j || weakly_closed[ij] == 1
|| fres[i].pair >= FRES_RESTRICTED_MIN || fres[j].pair >= FRES_RESTRICTED_MIN
|| can_pair(int_sequence[i],int_sequence[j]) != 1) {
VP[ij] = INF;
return;
}
else{
// base cases:
// a) i == j => VP[ij] = INF
// b) [i,j] is a weakly_closed region => VP[ij] = INF
// c) i or j is paired in original structure => VP[ij] = INF
int m1 = INF, m2 = INF, m3 = INF, m4= INF, m5 = INF, m6 = INF, m7 = INF, m8 = INF; //different branches
//branchs:
// 1) inArc(i) and NOT_inArc(j)
// WI(i+1)(B'(i,j)-1)+WI(B(i,j)+1)(j-1)
// Hosna April 9th, 2007
// need to check the borders as they may be negative
if(fres[i].arc > -1 && fres[j].arc < fres[i].arc && get_Bp(i,j) >= 0 && get_Bp(i,j)< nb_nucleotides && get_B(i,j) >= 0 && get_B(i,j) < nb_nucleotides && get_bp(i,j) < 0){
int Bp_i = get_Bp(i,j);
int B_i = get_B(i,j);
int WI_ipus1_BPminus = get_WI(i+1,Bp_i - 1) ;
int WI_Bplus_jminus = get_WI(B_i + 1,j-1);
m1 = WI_ipus1_BPminus + WI_Bplus_jminus;
// if(debug){
// printf("VP[%d,%d] branch 1: WI(%d+1)(BP(%d)-1) = %d and WI(B(%d)+1)(%d-1) = %d => m1 = %d \n",i,j,i,i,WI_ipus1_BPminus,i,j,WI_Bplus_jminus, m1);
// }
}
// 2) NOT_inArc(i) and inArc(j)
// WI(i+1)(b(i,j)-1)+WI(b'(i,j)+1)(j-1)
// Hosna April 9th, 2007
// checking the borders as they may be negative
if (fres[i].arc < fres[j].arc && fres[j].arc > -1 && get_b(i,j)>= 0 && get_b(i,j) < nb_nucleotides && get_bp(i,j) >= 0 && get_bp(i,j) < nb_nucleotides && get_Bp(i,j) < 0){
int b_i = get_b(i,j);
int bp_i = get_bp(i,j);
int WI_i_plus_b_minus = get_WI(i+1,b_i - 1);
int WI_bp_plus_j_minus = get_WI(bp_i + 1,j-1);
m2 = WI_i_plus_b_minus + WI_bp_plus_j_minus;
// if(debug){
// printf("VP[%d,%d] branch 2: WI(%d+1)(b(%d)-1) = %d and WI(bp(%d)+1)(%d-1) = %d => m2 = %d \n",i,j,i,i,WI_i_plus_b_minus,i,j,WI_bp_plus_j_minus, m2);
// }
}
// 3) inArc(i) and inArc(j)
// WI(i+1)(B'(i,j)-1)+WI(B(i,j)+1)(b(i,j)-1)+WI(b'(i,j)+1)(j-1)
// Hosna April 9th, 2007
// checking the borders as they may be negative
if(fres[i].arc > -1 && fres[j].arc > -1 && get_Bp(i,j) >= 0 && get_Bp(i,j) < nb_nucleotides && get_B(i,j) >= 0 && get_B(i,j) < nb_nucleotides && get_b(i,j) >= 0 && get_b(i,j) < nb_nucleotides && get_bp(i,j)>= 0 && get_bp(i,j) < nb_nucleotides){
int Bp_i = get_Bp(i,j);
int B_i = get_B(i,j);
int b_i = get_b(i,j);
int bp_i = get_bp(i,j);
int WI_i_plus_Bp_minus = get_WI(i+1,Bp_i - 1);
int WI_B_plus_b_minus = get_WI(B_i + 1,b_i - 1);
int WI_bp_plus_j_minus = get_WI(bp_i +1,j - 1);
m3 = WI_i_plus_Bp_minus + WI_B_plus_b_minus + WI_bp_plus_j_minus;
// if(debug){
// printf("VP[%d,%d] branch 3: WI(%d+1)(B'(%d)-1) = %d, WI(B(%d)+1)(b(%d)-1) = %d and WI(b'(%d)+1)(%d-1) = %d => m3 = %d \n",i,j,i,i, WI_i_plus_Bp_minus,i,i,WI_B_plus_b_minus,i,j,WI_bp_plus_j_minus, m3);
// }
}
// 4) NOT_paired(i+1) and NOT_paired(j-1) and they can pair together
// e_stP(i,i+1,j-1,j) + VP(i+1)(j-1)
if(fres[i+1].pair < 0 && fres[j-1].pair < 0 && can_pair(int_sequence[i+1],int_sequence[j-1])){
//AP
for (auto &model : *energy_models) {
model.energy_value = get_e_stP_emodel(i,j,&model) + get_VP(i+1,j-1);
}
m4 = emodel_energy_function (i, j, energy_models);
// if (debug){
// printf("VP[%d,%d] branch 4: S->get_energy(%d,%d) = %d and VP[%d,%d] = %d so m4 = %d\n", i,j,i,j, S->get_energy(i,j,int_sequence), i+1, j-1, get_VP(i+1,j-1), m4);
// }
}
// 5) NOT_paired(r) and NOT_paired(rp)
// VP(i,j) = e_intP(i,ip,jp,j) + VP(ip,jp)
int ip, jp;
int max_borders;
// Hosna, April 6th, 2007
// whenever we use get_borders we have to check for the correct values
int min_borders = 0; // what if both are negative
if (get_Bp(i,j)> 0 && get_Bp(i,j) < nb_nucleotides && get_b(i,j) >0 && get_b(i,j) < nb_nucleotides){
min_borders = MIN(get_Bp(i,j),get_b(i,j));
}else if (get_b(i,j) > 0 && get_b(i,j) < nb_nucleotides && (get_Bp(i,j) < 0 || get_Bp(i,j) > nb_nucleotides)){
min_borders = get_b(i,j);
}else if (get_Bp(i,j) > 0 && get_Bp(i,j) < nb_nucleotides && (get_b(i,j) < 0 || get_b(i,j) > nb_nucleotides)){
min_borders = get_Bp(i,j);
}
// printf("B'(%d,%d) = %d, b(%d,%d) = %d, min_borders = %d\n",i,j,get_Bp(i,j),i,j,get_b(i,j), min_borders);
for (ip = i+1; ip < min_borders; ip++){
//Mahyar and Kevin, Nov 16, 2017
if (int_sequence[ip] == X){
continue;
}
// Hosna: April 20, 2007
// i and ip and j and jp should be in the same arc
// also it should be the case that [i+1,ip-1] && [jp+1,j-1] are empty regions
if (fres[ip].pair < 0 && (fres[i].arc == fres[ip].arc) && is_empty_region(i+1,ip-1) == 1){
// Hosna, April 6th, 2007
// whenever we use get_borders we have to check for the correct values
max_borders= 0;
if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides){
max_borders = MAX(get_bp(i,j),get_B(i,j));
}else if (get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides && (get_bp(i,j) < 0 || get_bp(i,j) > nb_nucleotides)){
max_borders = get_B(i,j);
}else if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && (get_B(i,j) < 0 || get_B(i,j) > nb_nucleotides)){
max_borders = get_bp(i,j);
}
// printf("b'(%d,%d) = %d, B(%d,%d) = %d, max_borders = %d\n",i,j,get_bp(i,j),i,j,get_B(i,j), max_borders);
for (jp = max_borders+1; jp < j ; jp++){
//Mahyar and Kevin, Nov 16, 2017
if (int_sequence[jp] == X){
continue;
}
if (fres[jp].pair < 0 && can_pair(int_sequence[ip],int_sequence[jp]) && is_empty_region(jp+1,j-1) == 1){
// Hosna: April 20, 2007
// i and ip and j and jp should be in the same arc
if (fres[j].arc == fres[jp].arc ){
//AP
for (auto &model : *energy_models) {
model.energy_value = get_e_intP_emodel(i,ip,jp,j,&model) + get_VP(ip,jp);
}
int temp = emodel_energy_function (i, j, energy_models);
// if (debug){
// printf("VP(%d,%d) branch 5: e_intP(%d,%d,%d,%d) = %d, VP(%d,%d) = %d, temp = %d \n",i,j,i,ip,jp,j,get_e_intP(i,ip,jp,j),ip,jp,get_VP(ip,jp),temp);
// }
// printf("m5 = %d \n", m5);
if (m5 > temp){
m5 = temp;
}
}
}
}
}
}
// 6) VP(i,j) = WIP(i+1,r-1) + VPP(r,j-1)
int r;
// Hosna April 9th, 2007
// checking the borders as they may be negative numbers
int min_Bp_j = j;
if (get_Bp(i,j) > 0 && get_Bp(i,j) < nb_nucleotides && get_Bp(i,j) < min_Bp_j){
min_Bp_j = get_Bp(i,j);
}
for (r = i+1; r < min_Bp_j ; r++){
//Mahyar and Kevin, Nov 16, 2017
if (int_sequence[r] == X){
continue;
}
if (fres[r].pair < 0){
// Hosna: July 5th, 2007
// After meeting with Anne and Cristina --> ap should have 2* bp to consider the biggest and the one that crosses
// in a multiloop that spans a band
int tmp = get_WIP(i+1,r-1) + get_VPP(r,j-1) + ap_penalty + 2*bp_penalty;
// if (debug)
// {
// printf("VP(%d,%d) branch 6: WIP(%d,%d) = %d, VPP(%d,%d) = %d ==> tmp = %d and m6 = %d \n",i,j,i+1,r-1,get_WIP(i+1,r-1),r,j-1,get_VPP(r,j-1),tmp,m6);
// }
if (tmp < m6){
m6 = tmp;
}
}
}
// 7) VP(i,j) = VPP(i+1,r) + WIP(r+1,j-1)
// Hosna April 9th, 2007
// checking the borders as they may be negative numbers
int max_i_bp = i;
if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && get_bp(i,j) > max_i_bp){
max_i_bp = get_bp(i,j);
}
for (r = max_i_bp+1; r < j ; r++){
//Mahyar and Kevin, Nov 16, 2017
if (int_sequence[r] == X){
continue;
}
if (fres[r].pair < 0){
// Hosna: July 5th, 2007
// After meeting with Anne and Cristina --> ap should have 2* bp to consider the biggest and the one that crosses
// in a multiloop that spans a band
int tmp = get_VPP(i+1,r) + get_WIP(r+1,j-1)+ ap_penalty + 2* bp_penalty;
// if (debug)
// {
// printf("VP(%d,%d) branch 7: VPP(%d,%d) = %d, WIP(%d,%d) = %d ==> tmp = %d and m7 = %d \n",i,j,i+1,r,get_VPP(i+1,r),r+1,j-1,get_WIP(r+1,j-1),tmp,m7);
// }
if (tmp < m7){
m7 = tmp;
}
}
}
// Hosna: June 29, 2007
// As case 6 and 7 handle what we wanted from case 8, then I think we don't need this any more
// // Hosna: April 20, 2007
// // based on the discussion with Anne, we decided we need another case for VP
// // which is like case 5 with the difference that it can have some structure
// // between [i+1,ip-1] and [jp+1,j-1]
//
// // 8) VP(i,j) = WI(i+1,ip-1) + VP(ip,jp) + WI(jp+1,j-1) + P_ps + ap_penalty
// // Hosna, April 6th, 2007
// // whenever we use get_borders we have to check for the correct values
// if (get_Bp(i,j)> 0 && get_Bp(i,j) < nb_nucleotides && get_b(i,j) >0 && get_b(i,j) < nb_nucleotides){
// min_borders = MIN(get_Bp(i,j),get_b(i,j));
// }else if (get_b(i,j) > 0 && get_b(i,j) < nb_nucleotides && (get_Bp(i,j) < 0 || get_Bp(i,j) > nb_nucleotides)){
// min_borders = get_b(i,j);
// }else if (get_Bp(i,j) > 0 && get_Bp(i,j) < nb_nucleotides && (get_b(i,j) < 0 || get_b(i,j) > nb_nucleotides)){
// min_borders = get_Bp(i,j);
// }
// for (ip = i+1; ip < min_borders; ip++){
// // Hosna: April 20, 2007
// // i and ip and j and jp should be in the same arc
// if (fres[ip].pair < 0 && (fres[i].arc == fres[ip].arc)){
// // Hosna, April 6th, 2007
// // whenever we use get_borders we have to check for the correct values
// int max_borders= 0;
// if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides){
// max_borders = MAX(get_bp(i,j),get_B(i,j));
// }else if (get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides && (get_bp(i,j) < 0 || get_bp(i,j) > nb_nucleotides)){
// max_borders = get_B(i,j);
// }else if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && (get_B(i,j) < 0 || get_B(i,j) > nb_nucleotides)){
// max_borders = get_bp(i,j);
// }
// for (jp = max_borders+1; jp < j ; jp++){
// if (fres[jp].pair < 0 && can_pair(int_sequence[ip],int_sequence[jp])){
// // Hosna: April 20, 2007
// // i and ip and j and jp should be in the same arc
// if (fres[j].arc == fres[jp].arc){
// int temp = get_WI(i+1,ip-1) + get_VP(ip,jp) + get_WI(jp+1,j-1) + PPS_penalty + ap_penalty;
// if (m8 > temp){
// m8 = temp;
// }
// }
// }
// }
// }
// }
//finding the min energy
int min = MIN(MIN(m1,m8),MIN(m2,m3));
min = (min > MIN(m4,m5))? MIN(m4,m5) : min;
min = (min > MIN(m6,m7))? MIN(m6,m7) : min;
// if (debug ){
// printf("VP[%d,%d]: m1 = %d, m2 = %d, m3 = %d, m4 = %d, m5 = %d, m6 = %d, m7 = %d and min = %d \n",i,j,m1,m2,m3,m4,m5,m6,m7,min);
// }
VP[ij] = min;
}
}
void pseudo_loop::compute_VP(int i, int j, h_str_features *fres){
int ij = index[i]+j-i;
if (VP[ij] != INF){//has been calculated before
// if (debug)
// {
// printf("VP(%d,%d) was calculated before ==> VP(%d,%d) = %d \n",i,j,i,j,VP[ij]);
// }
return;
}
// Ian Wark July 19 2017
// fres[i].pair >= 0 changed to fres[i].pair >= FRES_RESTRICTED_MIN (which equals -1 at time of writing)
// otherwise it will create pairs in spots where the restricted structure says there should be no pairs
// base cases:
// a) i == j => VP[ij] = INF
// b) [i,j] is a weakly_closed region => VP[ij] = INF
// c) i or j is paired in original structure => VP[ij] = INF
if (i == j || weakly_closed[ij] == 1
|| fres[i].pair >= FRES_RESTRICTED_MIN || fres[j].pair >= FRES_RESTRICTED_MIN
|| can_pair(int_sequence[i],int_sequence[j]) != 1) {
VP[ij] = INF;
// if (debug){
// printf("VP[%d,%d] = %d and can_pair(%d,%d) = %d\n", i,j, VP[ij],int_sequence[i],int_sequence[j],can_pair(int_sequence[i],int_sequence[j]));
// }
return;
}
else{
int m1 = INF, m2 = INF, m3 = INF, m4= INF, m5 = INF, m6 = INF, m7 = INF, m8 = INF; //different branches
//branchs:
// 1) inArc(i) and NOT_inArc(j)
// WI(i+1)(B'(i,j)-1)+WI(B(i,j)+1)(j-1)
// Hosna April 9th, 2007
// need to check the borders as they may be negative
if(fres[i].arc > -1 && fres[j].arc < fres[i].arc && get_Bp(i,j) >= 0 && get_Bp(i,j)< nb_nucleotides && get_B(i,j) >= 0 && get_B(i,j) < nb_nucleotides && get_bp(i,j) < 0){
int Bp_i = get_Bp(i,j);
int B_i = get_B(i,j);
int WI_ipus1_BPminus = get_WI(i+1,Bp_i - 1) ;
int WI_Bplus_jminus = get_WI(B_i + 1,j-1);
m1 = WI_ipus1_BPminus + WI_Bplus_jminus;
// if(debug){
// printf("VP[%d,%d] branch 1: WI(%d+1)(BP(%d)-1) = %d and WI(B(%d)+1)(%d-1) = %d => m1 = %d \n",i,j,i,i,WI_ipus1_BPminus,i,j,WI_Bplus_jminus, m1);
// }
}
// 2) NOT_inArc(i) and inArc(j)
// WI(i+1)(b(i,j)-1)+WI(b'(i,j)+1)(j-1)
// Hosna April 9th, 2007
// checking the borders as they may be negative
if (fres[i].arc < fres[j].arc && fres[j].arc > -1 && get_b(i,j)>= 0 && get_b(i,j) < nb_nucleotides && get_bp(i,j) >= 0 && get_bp(i,j) < nb_nucleotides && get_Bp(i,j) < 0){
int b_i = get_b(i,j);
int bp_i = get_bp(i,j);
int WI_i_plus_b_minus = get_WI(i+1,b_i - 1);
int WI_bp_plus_j_minus = get_WI(bp_i + 1,j-1);
m2 = WI_i_plus_b_minus + WI_bp_plus_j_minus;
// if(debug){
// printf("VP[%d,%d] branch 2: WI(%d+1)(b(%d)-1) = %d and WI(bp(%d)+1)(%d-1) = %d => m2 = %d \n",i,j,i,i,WI_i_plus_b_minus,i,j,WI_bp_plus_j_minus, m2);
// }
}
// 3) inArc(i) and inArc(j)
// WI(i+1)(B'(i,j)-1)+WI(B(i,j)+1)(b(i,j)-1)+WI(b'(i,j)+1)(j-1)
// Hosna April 9th, 2007
// checking the borders as they may be negative
if(fres[i].arc > -1 && fres[j].arc > -1 && get_Bp(i,j) >= 0 && get_Bp(i,j) < nb_nucleotides && get_B(i,j) >= 0 && get_B(i,j) < nb_nucleotides && get_b(i,j) >= 0 && get_b(i,j) < nb_nucleotides && get_bp(i,j)>= 0 && get_bp(i,j) < nb_nucleotides){
int Bp_i = get_Bp(i,j);
int B_i = get_B(i,j);
int b_i = get_b(i,j);
int bp_i = get_bp(i,j);
int WI_i_plus_Bp_minus = get_WI(i+1,Bp_i - 1);
int WI_B_plus_b_minus = get_WI(B_i + 1,b_i - 1);
int WI_bp_plus_j_minus = get_WI(bp_i +1,j - 1);
m3 = WI_i_plus_Bp_minus + WI_B_plus_b_minus + WI_bp_plus_j_minus;
// if(debug){
// printf("VP[%d,%d] branch 3: WI(%d+1)(B'(%d)-1) = %d, WI(B(%d)+1)(b(%d)-1) = %d and WI(b'(%d)+1)(%d-1) = %d => m3 = %d \n",i,j,i,i, WI_i_plus_Bp_minus,i,i,WI_B_plus_b_minus,i,j,WI_bp_plus_j_minus, m3);
// }
}
// 4) NOT_paired(i+1) and NOT_paired(j-1) and they can pair together
// e_stP(i,i+1,j-1,j) + VP(i+1)(j-1)
if(fres[i+1].pair < 0 && fres[j-1].pair < 0 && can_pair(int_sequence[i+1],int_sequence[j-1])){
m4 = get_e_stP(i,j)+ get_VP(i+1,j-1);
// if (debug){
// printf("VP[%d,%d] branch 4: S->get_energy(%d,%d) = %d and VP[%d,%d] = %d so m4 = %d\n", i,j,i,j, S->get_energy(i,j,int_sequence), i+1, j-1, get_VP(i+1,j-1), m4);
// }
}
// 5) NOT_paired(r) and NOT_paired(rp)
// VP(i,j) = e_intP(i,ip,jp,j) + VP(ip,jp)
int ip, jp;
int max_borders;
// Hosna, April 6th, 2007
// whenever we use get_borders we have to check for the correct values
int min_borders = 0; // what if both are negative
if (get_Bp(i,j)> 0 && get_Bp(i,j) < nb_nucleotides && get_b(i,j) >0 && get_b(i,j) < nb_nucleotides){
min_borders = MIN(get_Bp(i,j),get_b(i,j));
}else if (get_b(i,j) > 0 && get_b(i,j) < nb_nucleotides && (get_Bp(i,j) < 0 || get_Bp(i,j) > nb_nucleotides)){
min_borders = get_b(i,j);
}else if (get_Bp(i,j) > 0 && get_Bp(i,j) < nb_nucleotides && (get_b(i,j) < 0 || get_b(i,j) > nb_nucleotides)){
min_borders = get_Bp(i,j);
}
// printf("B'(%d,%d) = %d, b(%d,%d) = %d, min_borders = %d\n",i,j,get_Bp(i,j),i,j,get_b(i,j), min_borders);
for (ip = i+1; ip < min_borders; ip++){
// Hosna: April 20, 2007
// i and ip and j and jp should be in the same arc
// also it should be the case that [i+1,ip-1] && [jp+1,j-1] are empty regions
if (fres[ip].pair < 0 && (fres[i].arc == fres[ip].arc) && is_empty_region(i+1,ip-1) == 1){
// Hosna, April 6th, 2007
// whenever we use get_borders we have to check for the correct values
max_borders= 0;
if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides){
max_borders = MAX(get_bp(i,j),get_B(i,j));
}else if (get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides && (get_bp(i,j) < 0 || get_bp(i,j) > nb_nucleotides)){
max_borders = get_B(i,j);
}else if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && (get_B(i,j) < 0 || get_B(i,j) > nb_nucleotides)){
max_borders = get_bp(i,j);
}
// printf("b'(%d,%d) = %d, B(%d,%d) = %d, max_borders = %d\n",i,j,get_bp(i,j),i,j,get_B(i,j), max_borders);
for (jp = max_borders+1; jp < j ; jp++){
if (fres[jp].pair < 0 && can_pair(int_sequence[ip],int_sequence[jp]) && is_empty_region(jp+1,j-1) == 1){
// Hosna: April 20, 2007
// i and ip and j and jp should be in the same arc
if (fres[j].arc == fres[jp].arc ){
int temp = get_e_intP(i,ip,jp,j) + get_VP(ip,jp);
// if (debug){
// printf("VP(%d,%d) branch 5: e_intP(%d,%d,%d,%d) = %d, VP(%d,%d) = %d, temp = %d \n",i,j,i,ip,jp,j,get_e_intP(i,ip,jp,j),ip,jp,get_VP(ip,jp),temp);
// }
// printf("m5 = %d \n", m5);
if (m5 > temp){
m5 = temp;
}
}
}
}
}
}
// 6) VP(i,j) = WIP(i+1,r-1) + VPP(r,j-1)
int r;
// Hosna April 9th, 2007
// checking the borders as they may be negative numbers
int min_Bp_j = j;
if (get_Bp(i,j) > 0 && get_Bp(i,j) < nb_nucleotides && get_Bp(i,j) < min_Bp_j){
min_Bp_j = get_Bp(i,j);
}
for (r = i+1; r < min_Bp_j ; r++){
if (fres[r].pair < 0){
// Hosna: July 5th, 2007
// After meeting with Anne and Cristina --> ap should have 2* bp to consider the biggest and the one that crosses
// in a multiloop that spans a band
int tmp = get_WIP(i+1,r-1) + get_VPP(r,j-1) + ap_penalty + 2*bp_penalty;
// if (debug)
// {
// printf("VP(%d,%d) branch 6: WIP(%d,%d) = %d, VPP(%d,%d) = %d ==> tmp = %d and m6 = %d \n",i,j,i+1,r-1,get_WIP(i+1,r-1),r,j-1,get_VPP(r,j-1),tmp,m6);
// }
if (tmp < m6){
m6 = tmp;
}
}
}
// 7) VP(i,j) = VPP(i+1,r) + WIP(r+1,j-1)
// Hosna April 9th, 2007
// checking the borders as they may be negative numbers
int max_i_bp = i;
if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && get_bp(i,j) > max_i_bp){
max_i_bp = get_bp(i,j);
}
for (r = max_i_bp+1; r < j ; r++){
if (fres[r].pair < 0){
// Hosna: July 5th, 2007
// After meeting with Anne and Cristina --> ap should have 2* bp to consider the biggest and the one that crosses
// in a multiloop that spans a band
int tmp = get_VPP(i+1,r) + get_WIP(r+1,j-1)+ ap_penalty + 2* bp_penalty;
// if (debug)
// {
// printf("VP(%d,%d) branch 7: VPP(%d,%d) = %d, WIP(%d,%d) = %d ==> tmp = %d and m7 = %d \n",i,j,i+1,r,get_VPP(i+1,r),r+1,j-1,get_WIP(r+1,j-1),tmp,m7);
// }
if (tmp < m7){
m7 = tmp;
}
}
}
// Hosna: June 29, 2007
// As case 6 and 7 handle what we wanted from case 8, then I think we don't need this any more
// // Hosna: April 20, 2007
// // based on the discussion with Anne, we decided we need another case for VP
// // which is like case 5 with the difference that it can have some structure
// // between [i+1,ip-1] and [jp+1,j-1]
//
// // 8) VP(i,j) = WI(i+1,ip-1) + VP(ip,jp) + WI(jp+1,j-1) + P_ps + ap_penalty
// // Hosna, April 6th, 2007
// // whenever we use get_borders we have to check for the correct values
// if (get_Bp(i,j)> 0 && get_Bp(i,j) < nb_nucleotides && get_b(i,j) >0 && get_b(i,j) < nb_nucleotides){
// min_borders = MIN(get_Bp(i,j),get_b(i,j));
// }else if (get_b(i,j) > 0 && get_b(i,j) < nb_nucleotides && (get_Bp(i,j) < 0 || get_Bp(i,j) > nb_nucleotides)){
// min_borders = get_b(i,j);
// }else if (get_Bp(i,j) > 0 && get_Bp(i,j) < nb_nucleotides && (get_b(i,j) < 0 || get_b(i,j) > nb_nucleotides)){
// min_borders = get_Bp(i,j);
// }
// for (ip = i+1; ip < min_borders; ip++){
// // Hosna: April 20, 2007
// // i and ip and j and jp should be in the same arc
// if (fres[ip].pair < 0 && (fres[i].arc == fres[ip].arc)){
// // Hosna, April 6th, 2007
// // whenever we use get_borders we have to check for the correct values
// int max_borders= 0;
// if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides){
// max_borders = MAX(get_bp(i,j),get_B(i,j));
// }else if (get_B(i,j) > 0 && get_B(i,j) < nb_nucleotides && (get_bp(i,j) < 0 || get_bp(i,j) > nb_nucleotides)){
// max_borders = get_B(i,j);
// }else if (get_bp(i,j) > 0 && get_bp(i,j) < nb_nucleotides && (get_B(i,j) < 0 || get_B(i,j) > nb_nucleotides)){
// max_borders = get_bp(i,j);
// }
// for (jp = max_borders+1; jp < j ; jp++){
// if (fres[jp].pair < 0 && can_pair(int_sequence[ip],int_sequence[jp])){
// // Hosna: April 20, 2007
// // i and ip and j and jp should be in the same arc
// if (fres[j].arc == fres[jp].arc){
// int temp = get_WI(i+1,ip-1) + get_VP(ip,jp) + get_WI(jp+1,j-1) + PPS_penalty + ap_penalty;
// if (m8 > temp){
// m8 = temp;
// }
// }
// }
// }
// }
// }