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SparseDP.h
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// This program is implemented Sparse Dynamic Programming algorithm described in David Eppstein paper
// Author: Jingwen Ren
#ifndef SPARSE_DP_
#define SPARSE_DP_
#include <iostream>
#include <string>
#include <utility>
#include <algorithm> // lower_bound
#include <numeric> //floor
#include <cmath>
#include <set>
#include <iterator>
#include <assert.h>
#include <chrono> // generate random number
#include <random> // generate random number
#include <type_traits>
#include "SubProblem.h"
#include "Sorting.h"
#include "SubRountine.h"
#include "Fragment_Info.h"
#include "Info.h"
// #include "overload.h"
#include "DivideSubByRow1.h"
#include "DivideSubByCol1.h"
#include "DivideSubByRow2.h"
#include "DivideSubByCol2.h"
#include "Point.h"
#include "TupleOps.h"
#include "Options.h"
#include "Clustering.h"
#include "Read.h"
#include "Chain.h"
using std::cerr;
using std::cout;
using std::endl;
using std::iota;
void clear(vector<Point> &H1, vector<unsigned int> &H2, StackOfSubProblems &SubR1, StackOfSubProblems &SubC1, StackOfSubProblems &SubR2,
StackOfSubProblems &SubC2, vector<Fragment_Info> &Value, vector<info> &Row, vector<info> &Col) {
SubR1.clear();
SubC1.clear();
SubR2.clear();
SubC2.clear();
Value.clear();
Row.clear();
Col.clear();
H1.clear();
H2.clear();
}
template <typename Tup>
void ComputeMatchStart(vector<int> & MatchNum, int & totalMatch, const vector<Tup *> & FragInput, SplitChain & inputChain){
totalMatch = FragInput[inputChain[0]]->size();
for (int c = 1; c < inputChain.size(); c++) {
totalMatch += FragInput[inputChain[c]]->size();
MatchNum[c] = FragInput[inputChain[c - 1]]->size();
}
for (int c = 1; c < MatchNum.size(); c++) {
MatchNum[c] = MatchNum[c-1] + MatchNum[c];
}
}
template <typename Tup>
void ComputeMatchStart(vector<int> & MatchNum, int & totalMatch, const vector<Tup> & FragInput, SplitChain & inputChain){
totalMatch = FragInput[inputChain[0]].size();
for (int c = 1; c < inputChain.size(); c++) {
totalMatch += FragInput[inputChain[c]].size();
MatchNum[c] = FragInput[inputChain[c - 1]].size();
}
for (int c = 1; c < MatchNum.size(); c++) {
MatchNum[c] = MatchNum[c-1] + MatchNum[c];
}
}
void
insertPointsPair(vector<Point> & H1, unsigned int frag_num, GenomePos qs, GenomePos ts, int length, int &clusterNum, int Pair, int strand) {
if (Pair == 0) {
//
// Insert pair s1 and e1;
//
Point s1;
H1.push_back(s1);
H1.back().ind = 1; // start
H1.back().inv = 1; // forward direction
H1.back().frag_num = frag_num;
H1.back().se.first = qs;
H1.back().se.second = ts;
H1.back().orient = strand; // forward strand
H1.back().clusterNum = clusterNum;
// H1.back().matchstartNum = matchstartNum;
// insert end point e1 into H1
Point e1;
H1.push_back(e1);
H1.back().ind = 0; // end
H1.back().inv = 1; // forward direction
H1.back().frag_num = frag_num;
H1.back().se.first = qs + length;
H1.back().se.second = ts + length;
H1.back().orient = strand;
H1.back().clusterNum = clusterNum;
// H1.back().matchstartNum = matchstartNum;
}
else {
//
// Insert pair s2 and e2;
//
Point s2;
H1.push_back(s2);
H1.back().ind = 1; // start
H1.back().inv = 0; // backward direction
H1.back().frag_num = frag_num;
H1.back().se.first = qs;
H1.back().se.second = ts + length; //// TODO(Jingwen): fix this "-1" in the other SparseDP
H1.back().orient = strand; // reversed strand
H1.back().clusterNum = clusterNum;
// H1.back().matchstartNum = matchstartNum;
// insert end point e2 into H1
Point e2;
H1.push_back(e2);
H1.back().ind = 0; // end
H1.back().inv = 0; // backward direction
H1.back().frag_num = frag_num;
H1.back().se.first = qs + length;
// assert(ts != 0); // IF this happens, just delete all the "-1" in the section of inserting points;
H1.back().se.second = ts;
H1.back().orient = strand; // reversed strand
H1.back().clusterNum = clusterNum;
// H1.back().matchstartNum = matchstartNum;
}
}
void
PassValueToD1 (unsigned int i, vector<Fragment_Info> & Value, const vector<Point> & H1, StackOfSubProblems & SubR1, StackOfSubProblems & SubC1, long int & ForwardDiag) {
// If all the subproblems B which contain the point H1[i] have been processed, then we can pass the value of the point H1[i] to the D array for every subproblem A
assert (Value[i].counter_B_R1 == 0 and Value[i].counter_B_C1 == 0);
//cerr << "pass the value! Process the SubProblem A of the point " << H1[i] << endl;
//cerr << "Value[" << i << "].SS_A_R1: " << Value[i].SS_A_R1 << " Value[" << i << "].SS_A_C1: " << Value[i].SS_A_C1 << "\n";
//cerr << "-------------Solve SS_A_R1-----------------------" << endl;
unsigned int u;
for (unsigned int tt = 0; tt < Value[i].SS_A_R1.size(); ++tt) {
unsigned int u = Value[i].SS_A_R1[Value[i].SS_A_R1.size() - 1 - tt];
//cerr << "u: " << u << "\n";
if (SubR1[u].Ei.empty()) {
//cerr << "SubR1[" << u << "].Ei is empty" << endl;
continue;
}
else {
vector<unsigned int>::iterator it = Lower_Bound<vector<unsigned int>::iterator, long int>(SubR1[u].D.begin(), SubR1[u].D.end(), ForwardDiag, SubR1[u].Di);
/*
for (unsigned int q = *it; q < SubR1[u].Di.size(); ++q) {
--SubR1[u].counter_D[q];
}
*/
//cerr << "SubR1[" << u << "].Di: " << SubR1[u].Di << endl;
//cerr << "The index of this point in D array: " << *it << "\n";
//cerr << "SubR1[u].Dv[" << *it << "]: " << SubR1[u].Dv[*it] << " SubR1[u].Dp[" << *it << "]: " << SubR1[u].Dp[*it] << "\n";
//cerr << "Update the D array Now\n";
//cerr << "SubR1[u].Dv[" << *it << "]: " << SubR1[u].Dv[*it] << " Value[" << i << "].val: " << Value[i].val << endl;
if (SubR1[u].Dv[*it] < Value[i].val) { // TODO(Jingwen) < or <= ????
SubR1[u].Dv[*it] = Value[i].val;
SubR1[u].Dp[*it] = i;
//cerr << "Updated! SubR1[" << u << "].Dv[*it]: " << SubR1[u].Dv[*it] << " SubR1[" << u << "].Dp[*it]: " << SubR1[u].Dp[*it] << endl;
}
//else{cerr <<"Not Updated!" << endl;}
}
//cerr << endl;
}
//cerr << "----------Solve SS_A_C1-----------" << endl;
for (unsigned int tt = 0; tt < Value[i].SS_A_C1.size(); ++tt) {
unsigned int u = Value[i].SS_A_C1[Value[i].SS_A_C1.size() - 1 - tt];
//cerr << "u: " << u << "\n";
if (SubC1[u].Ei.empty()) {
//cerr << "SubC1[" << u << "].Ei is empty" << endl;
continue;
}
else {
vector<unsigned int>::reverse_iterator it = Lower_Bound<vector<unsigned int>::reverse_iterator, long int>(SubC1[u].D.rbegin(), SubC1[u].D.rend(), ForwardDiag, SubC1[u].Di);
/*
for (unsigned int q = *it; q < SubC1[u].Di.size(); ++q) {
--SubC1[u].counter_D[q];
}
*/
//cerr << "SubC1[" << u << "].Di: " << SubC1[u].Di << endl;
//cerr << "The index of this point in D array: " << *it << "\n";
//cerr << "SubC1[u].Dv[" << *it << "]: " << SubC1[u].Dv[*it] << " SubC1[u].Dp[" << *it << "]: " << SubC1[u].Dp[*it] << "\n";
//cerr << "Update the D array Now\n";
//cerr << "SubC1[u].Dv[*it]: " << SubC1[u].Dv[*it] << " Value[i].val: " << Value[i].val << endl;
if (SubC1[u].Dv[*it] < Value[i].val) {
SubC1[u].Dv[*it] = Value[i].val;
SubC1[u].Dp[*it] = i;
//cerr << "Updated! SubC1[" << u << "].Dv[*it]: " << SubC1[u].Dv[*it] << " SubC1[" << u << "].Dp[*it]: " << SubC1[u].Dp[*it] << endl;
}
//cerr <<"Not Updated!" << endl;
}
//cerr << endl;
}
//cerr << endl << endl;
}
void
PassValueToD2 (unsigned int i, vector<Fragment_Info> & Value, const vector<Point> & H1, StackOfSubProblems & SubR2, StackOfSubProblems & SubC2, long int & BackDiag) {
// If all the subproblems B which contain the point H1[i] have been processed, then we can pass the value of the point H1[i] to the D array for every subproblem A
assert (Value[i].counter_B_R2 == 0 and Value[i].counter_B_C2 == 0);
//cerr << "pass the value! Process the SubProblem A of the point " << H1[i] << endl;
//cerr << "Value[" << i << "].SS_A_R2: " << Value[i].SS_A_R2 << " Value[" << i << "].SS_A_C2: " << Value[i].SS_A_C2 << "\n";
//cerr << "-------------Solve SS_A_R2-----------------------" << endl;
unsigned int u;
for (unsigned int tt = 0; tt < Value[i].SS_A_R2.size(); ++tt) {
unsigned int u = Value[i].SS_A_R2[Value[i].SS_A_R2.size() - 1 - tt];
//cerr << "u: " << u << "\n";
if (SubR2[u].Ei.empty()) {
//cerr << "SubR2[" << u << "].Ei is empty" << endl;
continue;
}
else {
vector<unsigned int>::reverse_iterator it = Lower_Bound<vector<unsigned int>::reverse_iterator, long int>(SubR2[u].D.rbegin(), SubR2[u].D.rend(), BackDiag, SubR2[u].Di);
/*
for (unsigned int q = *it; q < SubR2[u].Di.size(); ++q) {
--SubR2[u].counter_D[q];
}
*/
//cerr << "SubR2[" << u << "].Di: " << SubR2[u].Di << endl;
//cerr << "The index of this point in D array: " << *it << "\n";
//cerr << "SubR2[u].Dv[" << *it << "]: " << SubR2[u].Dv[*it] << " SubR2[u].Dp[" << *it << "]: " << SubR2[u].Dp[*it] << "\n";
//cerr << "Update the D array Now\n";
//cerr << "SubR2[u].Dv[" << *it << "]: " << SubR2[u].Dv[*it] << " Value[" << i << "].val: " << Value[i].val << endl;
if (SubR2[u].Dv[*it] < Value[i].val) { // TODO(Jingwen) < or <= ????
SubR2[u].Dv[*it] = Value[i].val;
SubR2[u].Dp[*it] = i;
//cerr << "Updated! SubR2[" << u << "].Dv[*it]: " << SubR2[u].Dv[*it] << " SubR2[" << u << "].Dp[*it]: " << SubR2[u].Dp[*it] << endl;
}
//else{cerr <<"Not Updated!" << endl;}
}
//cerr << endl;
}
//cerr << "----------Solve SS_A_C2-----------" << endl;
for (unsigned int tt = 0; tt < Value[i].SS_A_C2.size(); ++tt) {
unsigned int u = Value[i].SS_A_C2[Value[i].SS_A_C2.size() - 1 - tt];
//cerr << "u: " << u << "\n";
if (SubC2[u].Ei.empty()) {
//cerr << "SubC2[" << u << "].Ei is empty" << endl;
continue;
}
else {
vector<unsigned int>::iterator it = Lower_Bound<vector<unsigned int>::iterator, long int>(SubC2[u].D.begin(), SubC2[u].D.end(), BackDiag, SubC2[u].Di);
/*
for (unsigned int q = *it; q < SubC2[u].Di.size(); ++q) {
--SubC2[u].counter_D[q];
}
*/
//cerr << "SubC2[" << u << "].Di: " << SubC2[u].Di << endl;
//cerr << "The index of this point in D array: " << *it << "\n";
//cerr << "SubC2[u].Dv[" << *it << "]: " << SubC2[u].Dv[*it] << " SubC2[u].Dp[" << *it << "]: " << SubC2[u].Dp[*it] << "\n";
//cerr << "Update the D array Now\n";
//cerr << "SubC2[u].Dv[*it]: " << SubC2[u].Dv[*it] << " Value[i].val: " << Value[i].val << endl;
if (SubC2[u].Dv[*it] < Value[i].val) {
SubC2[u].Dv[*it] = Value[i].val;
SubC2[u].Dp[*it] = i;
//cerr << "Updated! SubC2[" << u << "].Dv[*it]: " << SubC2[u].Dv[*it] << " SubC2[" << u << "].Dp[*it]: " << SubC2[u].Dp[*it] << endl;
}
//cerr <<"Not Updated!" << endl;
}
//cerr << endl;
}
//cerr << endl << endl;
}
//
// Each fragment has different length, so we need to pass FragInput to this function
// This function is for splitCluster
//
template<typename Tup>
void ProcessPoint (const vector<Point> & H1, vector<info> & V, StackOfSubProblems & SubR1, StackOfSubProblems & SubC1,
StackOfSubProblems & SubR2, StackOfSubProblems & SubC2, vector<Fragment_Info> & Value, const Options & opts,
const vector<float> & LookUpTable, const vector<Tup> & FragInput, float & rate) { // vector<ClusterCoordinates> & FragInput
bool step_sdp = 0;
for (unsigned int i = 0; i < H1.size(); ++i) { // process points by row
long int ForwardDiag = (long int)(H1[i].se.second) - (long int)(H1[i].se.first);
long int BackDiag = (long int)(H1[i].se.second) + (long int)(H1[i].se.first);
//cerr << "\n\n\n\nprocessing point " << H1[H3[i]] << endl;
//cerr << "the Value[" << H1[H3[i]].frag_num << "] of this point: " << Value[H1[H3[i]].frag_num] << "\n";
unsigned int ii = H1[i].frag_num;
if (H1[i].ind == 1 and H1[i].inv == 1) { // H1[i] is a start point s1
//cerr << "----------------------------------------this is a start point (s1) ------------------------------------" << endl;
//cerr << "dealing with the subproblem B first. Solve Value[" << H1[i].frag_num << "].SS_B_R1 and SS_B_C1" << endl;
//cerr <<"----------------Solve SS_B_R1 -------------------" << endl;
//
// For each subproblem B_R1 that point H1[i] is in, get Ev[ForwardDiag] and update Value[H1[i]].frag_num].val
//
for (unsigned int k = 0; k < Value[ii].SS_B_R1.size(); ++k) {
unsigned int j = Value[ii].SS_B_R1[Value[ii].SS_B_R1.size() - 1 - k];
//cerr << "Solving SubR1[" << j << "]: " << SubR1[j]<< "\n";
// If subproblem SubR1[j] is a leaf case, then
if (SubR1[j].Di.empty()) {
//cerr << "SubR1[" << j << "] is a leaf case or non-leaf case but Di is empty" << "\n";
assert(Value[ii].counter_B_R1 != 0);
--Value[ii].counter_B_R1;
continue;
}
else {
// Then subproblem SubR1[j] is non-leaf case. find the index of the point in E array
vector<unsigned int>::iterator t = Lower_Bound<vector<unsigned int>::iterator,long int>(SubR1[j].E.begin(), SubR1[j].E.end(), ForwardDiag, SubR1[j].Ei);
//cerr << "SubR1[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubR1[" << j << "].Ei: " << SubR1[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubR1[j].Eb[*t] == -1) {
//cerr << "SubR1[" << j << "] is a non-leaf case but there is no forward diag smaller than the current in D array" << endl;
assert(Value[ii].counter_B_R1 != 0);
--Value[ii].counter_B_R1;
continue;
}
else {
//assert(SubR1[j].counter_D[SubR1[j].Eb[*t]] == 0);
//cerr << "SubR1[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already." << endl;
//cerr << "Start to compute the maximization structure.\n";
SubR1[j].now = SubR1[j].Eb[*t];
Maximization (SubR1[j].now, SubR1[j].last, SubR1[j].Di, SubR1[j].Ei, SubR1[j].Dv, SubR1[j].Db, SubR1[j].Block, SubR1[j].S_1, LookUpTable, opts, step_sdp); // TODO(Jingwen) anything change for SubC????
SubR1[j].last = SubR1[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores the index in Ei that ForwardDiag is in
unsigned int i2; // i2 stores the index in Di which is the best candidate for ForwardDiag
FindValueInBlock(ForwardDiag, SubR1[j].S_1, SubR1[j].Ei, SubR1[j].Block, i1, i2);
//cerr << "the index in Ei that ForwardDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for ForwardDiag ---- i2: " << i2 << "\n";
SubR1[j].Ev[i1] = SubR1[j].Dv[i2] + w(SubR1[j].Di[i2], SubR1[j].Ei[i1], LookUpTable, opts, step_sdp) + FragInput[ii].Val*rate;
//min(FragInput[ii].qEnd - FragInput[ii].qStart, FragInput[ii].tEnd - FragInput[ii].tStart) * rate;
SubR1[j].Ep[i1] = i2;
//cerr << "SubR1[" << j << "].Ev[" << i1 << "]: " << SubR1[j].Ev[i1] << ", SubR1[" << j << "].Ep[" << i1 << "]: " << SubR1[j].Ep[i1] << "\n";
// Update the value of this point
//TODO(Jingwen): if this point is a s1 of a reverse orientated anchor, only update the value when SubR1[j].Dp[Ep[i1]] points to a forward orientated anchor
//TODO(Jingwen): only for debug
assert(Value[ii].orient == H1[i].orient);
int p = SubR1[j].Dp[SubR1[j].Ep[i1]];
// if the current anchor is reverse oriented and the previous anchor is also reverse oriented, then do not update Value[ii]
// Otherwise update Value[ii]
//if (! (Value[ii].orient == 0 and Value[p].orient == 0)) {
if (Value[ii].val < SubR1[j].Ev[i1]) {
Value[ii].val = SubR1[j].Ev[i1];
Value[ii].prev_sub = SubR1[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 1; // the best value comes from row subproblem
Value[ii].inv = 1; // the best value comes from SubR1
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
//}
assert(Value[ii].counter_B_R1 != 0);
--Value[ii].counter_B_R1;
//cerr << "Do not update the value of this point\n";
}
}
}
//cerr << endl << endl;
//cerr << "--------------Solve SS_B_C1 ----------------" << endl;
// For each subproblem B_C1 that point H1[i] is in, get Ev[H1[i].first - H1[i].second] and update Value[H1[i]].val
for (unsigned int k = 0; k < Value[ii].SS_B_C1.size(); ++k) {
unsigned int j = Value[ii].SS_B_C1[Value[ii].SS_B_C1.size() - 1 - k];
//cerr << "SubC1[" << j << "]: " << SubC1[j]<< "\n";
// If subproblem SubC1[j] is a leaf case, then
if (SubC1[j].Di.empty()) {
//cerr << "SubC1[" << j << "] is a leaf case or it's a non-leaf case with an empty Di" << "\n";
assert(Value[ii].counter_B_C1 != 0);
--Value[ii].counter_B_C1;
continue;
}
else {
// find the index of this point in E array
vector<unsigned int>::reverse_iterator t = Lower_Bound<vector<unsigned int>::reverse_iterator,long int>(SubC1[j].E.rbegin(), SubC1[j].E.rend(), ForwardDiag, SubC1[j].Ei);
//cerr << "SubC1[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubC1[" << j << "].Ei: " << SubC1[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubC1[j].Eb[*t] == -1) {
//cerr << "SubC1[" << j << "] is a non-leaf case but there is no forward diag larger than the current\n ";
assert(Value[ii].counter_B_C1 != 0);
--Value[ii].counter_B_C1;
continue;
}
else {
//assert(SubC1[j].counter_D[SubC1[j].Eb[*t]] == 0);
//cerr << "SubC1[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already.\n";
//cerr << "Start to compute the maximization structure.\n";
SubC1[j].now = SubC1[j].Eb[*t];
Maximization (SubC1[j].now, SubC1[j].last, SubC1[j].Di, SubC1[j].Ei, SubC1[j].Dv, SubC1[j].Db, SubC1[j].Block, SubC1[j].S_1, LookUpTable, opts, step_sdp);
SubC1[j].last = SubC1[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores the index in Ei that ForwardDiag is in
unsigned int i2; // i2 stores the index in Di which is the best candidate for ForwardDiag
FindValueInBlock(ForwardDiag, SubC1[j].S_1, SubC1[j].Ei, SubC1[j].Block, i1, i2);
//cerr << "the index in Ei that ForwardDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for ForwardDiag ---- i2: " << i2 << "\n";
// SubC1[j].Ev[i1] = SubC1[j].Dv[i2] + w(SubC1[j].Di[i2], SubC1[j].Ei[i1], LookUpTable, opts) + opts.globalK;
// SubC1[j].Ep[i1] = i2;
SubC1[j].Ev[i1] = SubC1[j].Dv[i2] + w(SubC1[j].Di[i2], SubC1[j].Ei[i1], LookUpTable, opts, step_sdp) + FragInput[ii].Val*rate;
//min(FragInput[ii].qEnd - FragInput[ii].qStart, FragInput[ii].tEnd - FragInput[ii].tStart) * rate;
SubC1[j].Ep[i1] = i2;
//cerr << "SubC1[" << j << "].Ev[" << i1 << "]: " << SubC1[j].Ev[i1] << ", SubC1[" << j << "].Ep[" << i1 << "]: " << SubC1[j].Ep[i1] << "\n";
// Update the value of this point
//TODO(Jingwen): if this point is a s1 of a reverse orientated anchor, only update the value when SubR1[j].Dp[Ep[i1]] points to a forward orientated anchor
//TODO(Jingwen): Only for debug
assert(Value[ii].orient == H1[i].orient);
int p = SubC1[j].Dp[SubC1[j].Ep[i1]];
//
// If the current anchor is reverse oriented and the previous anchor is also reverse oriented, then do not update Value[ii]
// Otherwise update Value[ii]
//if (! (Value[ii].orient == 0 and Value[p].orient == 0)) {
if (Value[ii].val < SubC1[j].Ev[i1]) {
Value[ii].val = SubC1[j].Ev[i1];
Value[ii].prev_sub = SubC1[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 0; // the best value comes from col subproblem
Value[ii].inv = 1; // the best value comes from SubC1
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
//}
assert(Value[ii].counter_B_C1 != 0);
--Value[ii].counter_B_C1;
//cerr << "Do not update the value of this point\n";
}
}
}
}
else if (H1[i].ind == 1 and H1[i].inv == 0) { // H1[i] is a start point s2
//cerr << "----------------------------------------this is a start point (s2) ------------------------------------" << endl;
//cerr << "dealing with the subproblem B first. Solve Value[" << H1[i].frag_num << "].SS_B_R2 and SS_B_C2" << endl;
//cerr <<"----------------Solve SS_B_R2 -------------------" << endl;
// For each subproblem B_R2 that point H1[i] is in, get Ev[BackDiag] and update Value[H1[i]].frag_num].val
for (unsigned int k = 0; k < Value[ii].SS_B_R2.size(); ++k) {
unsigned int j = Value[ii].SS_B_R2[Value[ii].SS_B_R2.size() - 1 - k];
//cerr << "Solving SubR2[" << j << "]: " << SubR2[j]<< "\n";
// If subproblem SubR2[j] is a leaf case, then
if (SubR2[j].Di.empty()) {
//cerr << "SubR2[" << j << "] is a leaf case or non-leaf case but Di is empty" << "\n";
assert(Value[ii].counter_B_R2 != 0);
--Value[ii].counter_B_R2;
continue;
}
else {
// Then subproblem SubR2[j] is non-leaf case. find the index of the point in E array
vector<unsigned int>::reverse_iterator t = Lower_Bound<vector<unsigned int>::reverse_iterator,long int>(SubR2[j].E.rbegin(), SubR2[j].E.rend(), BackDiag, SubR2[j].Ei);
//cerr << "SubR2[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubR2[" << j << "].Ei: " << SubR2[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubR2[j].Eb[*t] == -1) {
//cerr << "SubR2[" << j << "] is a non-leaf case but there is no back diag larger than the current" << endl;
assert(Value[ii].counter_B_R2 != 0);
--Value[ii].counter_B_R2;
continue;
}
else {
//assert(SubR2[j].counter_D[SubR2[j].Eb[*t]] == 0);
//cerr << "SubR2[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already." << endl;
//cerr << "Start to compute the maximization structure.\n";
SubR2[j].now = SubR2[j].Eb[*t];
Maximization (SubR2[j].now, SubR2[j].last, SubR2[j].Di, SubR2[j].Ei, SubR2[j].Dv, SubR2[j].Db, SubR2[j].Block, SubR2[j].S_1, LookUpTable, opts, step_sdp); // TODO(Jingwen) anything change for SubC????
SubR2[j].last = SubR2[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores the index in Ei that BackDiag is in
unsigned int i2; // i2 stores the index in Di which is the best candidate for BackDiag
FindValueInBlock(BackDiag, SubR2[j].S_1, SubR2[j].Ei, SubR2[j].Block, i1, i2);
//cerr << "the index in Ei that BackDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for BackDiag ---- i2: " << i2 << "\n";
SubR2[j].Ev[i1] = SubR2[j].Dv[i2] + w(SubR2[j].Di[i2], SubR2[j].Ei[i1], LookUpTable, opts, step_sdp) + FragInput[ii].Val*rate;
//min(FragInput[ii].qEnd - FragInput[ii].qStart, FragInput[ii].tEnd - FragInput[ii].tStart) * rate;
SubR2[j].Ep[i1] = i2;
//cerr << "SubR2[" << j << "].Ev[" << i1 << "]: " << SubR2[j].Ev[i1] << ", SubR2[" << j << "].Ep[" << i1 << "]: " << SubR2[j].Ep[i1] << "\n";
// Update the value of this point
if (Value[ii].val < SubR2[j].Ev[i1]) {
Value[ii].val = SubR2[j].Ev[i1];
Value[ii].prev_sub = SubR2[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 1; // the best value comes from row subproblem
Value[ii].inv = 0; // the best value comes from SubR2
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
assert(Value[ii].counter_B_R2 != 0);
--Value[ii].counter_B_R2;
//cerr << "Do not update the value of this point\n";
}
}
}
//cerr << endl << endl;
//cerr << "--------------Solve SS_B_C2 ----------------" << endl;
// For each subproblem B_C2 that point H1[i] is in, get Ev[H1[i].first - H1[i].second] and update Value[H1[i]].val
for (unsigned int k = 0; k < Value[ii].SS_B_C2.size(); ++k) {
//cerr << "k: " << k << endl;
unsigned int j = Value[ii].SS_B_C2[Value[ii].SS_B_C2.size() - 1 - k];
//cerr << "j: " << j << endl;
//cerr << "SubC2[" << j << "]: " << SubC2[j]<< "\n";
// If subproblem SubC2[j] is a leaf case, then
if (SubC2[j].Di.empty()) {
//cerr << "SubC2[" << j << "] is a leaf case or it's a non-leaf case with an empty Di" << "\n";
assert(Value[ii].counter_B_C2 != 0);
--Value[ii].counter_B_C2;
continue;
}
else {
// find the index of this point in E array
vector<unsigned int>::iterator t = Lower_Bound<vector<unsigned int>::iterator,long int>(SubC2[j].E.begin(), SubC2[j].E.end(), BackDiag, SubC2[j].Ei);
//cerr << "SubC2[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubC2[" << j << "].Ei: " << SubC2[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubC2[j].Eb[*t] == -1) {
//cerr << "SubC2[" << j << "] is a non-leaf case but there is no forward diag larger than the current\n ";
assert(Value[ii].counter_B_C2 != 0);
--Value[ii].counter_B_C2;
continue;
}
else {
//assert(SubC2[j].counter_D[SubC2[j].Eb[*t]] == 0);
//cerr << "SubC2[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already.\n";
//cerr << "Start to compute the maximization structure.\n";
SubC2[j].now = SubC2[j].Eb[*t];
Maximization (SubC2[j].now, SubC2[j].last, SubC2[j].Di, SubC2[j].Ei, SubC2[j].Dv, SubC2[j].Db, SubC2[j].Block, SubC2[j].S_1, LookUpTable, opts, step_sdp);
SubC2[j].last = SubC2[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores
unsigned int i2;
FindValueInBlock(BackDiag, SubC2[j].S_1, SubC2[j].Ei, SubC2[j].Block, i1, i2);
//cerr << "the index in Ei that ForwardDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for ForwardDiag ---- i2: " << i2 << "\n";
SubC2[j].Ev[i1] = SubC2[j].Dv[i2] + w(SubC2[j].Di[i2], SubC2[j].Ei[i1], LookUpTable, opts, step_sdp) + FragInput[ii].Val*rate;
//min(FragInput[ii].qEnd - FragInput[ii].qStart, FragInput[ii].tEnd - FragInput[ii].tStart) * rate;
SubC2[j].Ep[i1] = i2;
//cerr << "SubC2[" << j << "].Ev[" << i1 << "]: " << SubC2[j].Ev[i1] << ", SubC2[" << j << "].Ep[" << i1 << "]: " << SubC2[j].Ep[i1] << "\n";
// Update the value of this point
if (Value[ii].val < SubC2[j].Ev[i1]) {
Value[ii].val = SubC2[j].Ev[i1];
Value[ii].prev_sub = SubC2[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 0; // the best value comes from col subproblem
Value[ii].inv = 0; // the best value comes from SubC2
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
assert(Value[ii].counter_B_C2 != 0);
--Value[ii].counter_B_C2;
//cerr << "Do not update the value of this point\n";
}
}
}
}
else if (H1[i].ind == 0 and H1[i].inv == 1) { // H1[i] is an end point (e1)
//cerr << "---------------------------------This is an end point (e1) --------------------------------"<< endl;
//cerr << "Pass the value Value[ii].val to SS_A_R1 and SS_A_C1" << endl;
// If all the subproblems B that the point H1[i] is in are already processed, then Value[H1[i]].val is ready
// For each subproblem A that the point H1[i] is in, Pass the Value[H1[i]].val to the D array
PassValueToD1(ii, Value, H1, SubR1, SubC1, ForwardDiag);
}
else { // H1[i] is an end point (e2)
//cerr << "---------------------------------This is an end point (e2) --------------------------------"<< endl;
//cerr << "Pass the value Value[ii].val to SS_A_R2 and SS_A_C2" << endl;
// If all the subproblems B that the point H1[i] is in are already processed, then Value[H1[i]].val is ready
// For each subproblem A that the point H1[i] is in, Pass the Value[H1[i]].val to the D array
PassValueToD2(ii, Value, H1, SubR2, SubC2, BackDiag);
}
}
}
//
// Each fragment has different length, so we need to pass vector<Cluster> vt to the function
// This function is for ExtendClusters;
//
template<typename Tup>
void ProcessPoint (const vector<Point> & H1, vector<info> & V, StackOfSubProblems & SubR1, StackOfSubProblems & SubC1,
StackOfSubProblems & SubR2, StackOfSubProblems & SubC2, vector<Fragment_Info> & Value, const Options & opts,
const vector<float> & LookUpTable, const vector<Tup*> &FragInput, float rate) { // vector<ClusterCoordinates> & FragInput
bool step_sdp = 1;
for (unsigned int i = 0; i < H1.size(); ++i) { // process points by row
long int ForwardDiag = (long int)(H1[i].se.second) - (long int)(H1[i].se.first);
long int BackDiag = (long int)(H1[i].se.second) + (long int)(H1[i].se.first);
//cerr << "\n\n\n\nprocessing point " << H1[H3[i]] << endl;
//cerr << "the Value[" << H1[H3[i]].frag_num << "] of this point: " << Value[H1[H3[i]].frag_num] << "\n";
unsigned int ii = H1[i].frag_num;
// int mi = H1[i].matchstartNum;
int fi = H1[i].clusterNum;
int ms = FragInput[fi]->matchStart;
if (H1[i].ind == 1 and H1[i].inv == 1) { // H1[i] is a start point s1
//cerr << "----------------------------------------this is a start point (s1) ------------------------------------" << endl;
//cerr << "dealing with the subproblem B first. Solve Value[" << H1[i].frag_num << "].SS_B_R1 and SS_B_C1" << endl;
//cerr <<"----------------Solve SS_B_R1 -------------------" << endl;
//
// For each subproblem B_R1 that point H1[i] is in, get Ev[ForwardDiag] and update Value[H1[i]].frag_num].val
//
for (unsigned int k = 0; k < Value[ii].SS_B_R1.size(); ++k) {
unsigned int j = Value[ii].SS_B_R1[Value[ii].SS_B_R1.size() - 1 - k];
//cerr << "Solving SubR1[" << j << "]: " << SubR1[j]<< "\n";
// If subproblem SubR1[j] is a leaf case, then
if (SubR1[j].Di.empty()) {
//cerr << "SubR1[" << j << "] is a leaf case or non-leaf case but Di is empty" << "\n";
assert(Value[ii].counter_B_R1 != 0);
--Value[ii].counter_B_R1;
continue;
}
else {
// Then subproblem SubR1[j] is non-leaf case. find the index of the point in E array
vector<unsigned int>::iterator t = Lower_Bound<vector<unsigned int>::iterator,long int>(SubR1[j].E.begin(), SubR1[j].E.end(), ForwardDiag, SubR1[j].Ei);
//cerr << "SubR1[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubR1[" << j << "].Ei: " << SubR1[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubR1[j].Eb[*t] == -1) {
//cerr << "SubR1[" << j << "] is a non-leaf case but there is no forward diag smaller than the current in D array" << endl;
assert(Value[ii].counter_B_R1 != 0);
--Value[ii].counter_B_R1;
continue;
}
else {
//assert(SubR1[j].counter_D[SubR1[j].Eb[*t]] == 0);
//cerr << "SubR1[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already." << endl;
//cerr << "Start to compute the maximization structure.\n";
SubR1[j].now = SubR1[j].Eb[*t];
Maximization (SubR1[j].now, SubR1[j].last, SubR1[j].Di, SubR1[j].Ei, SubR1[j].Dv, SubR1[j].Db, SubR1[j].Block, SubR1[j].S_1, LookUpTable, opts, step_sdp); // TODO(Jingwen) anything change for SubC????
SubR1[j].last = SubR1[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores the index in Ei that ForwardDiag is in
unsigned int i2; // i2 stores the index in Di which is the best candidate for ForwardDiag
FindValueInBlock(ForwardDiag, SubR1[j].S_1, SubR1[j].Ei, SubR1[j].Block, i1, i2);
//cerr << "the index in Ei that ForwardDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for ForwardDiag ---- i2: " << i2 << "\n";
SubR1[j].Ev[i1] = SubR1[j].Dv[i2] + w(SubR1[j].Di[i2], SubR1[j].Ei[i1], LookUpTable, opts, step_sdp) +
rate * FragInput[fi]->length(ii - ms);
//FragInput[inputChain[mi]]->matchesLengths[ii - MatchStart[mi]];
SubR1[j].Ep[i1] = i2;
//cerr << "SubR1[" << j << "].Ev[" << i1 << "]: " << SubR1[j].Ev[i1] << ", SubR1[" << j << "].Ep[" << i1 << "]: " << SubR1[j].Ep[i1] << "\n";
// Update the value of this point
//TODO(Jingwen): if this point is a s1 of a reverse orientated anchor, only update the value when SubR1[j].Dp[Ep[i1]] points to a forward orientated anchor
//TODO(Jingwen): only for debug
assert(Value[ii].orient == H1[i].orient);
int p = SubR1[j].Dp[SubR1[j].Ep[i1]];
// if the current anchor is reverse oriented and the previous anchor is also reverse oriented, then do not update Value[ii]
// Otherwise update Value[ii]
//if (! (Value[ii].orient == 0 and Value[p].orient == 0)) {
if (Value[ii].val < SubR1[j].Ev[i1]) {
Value[ii].val = SubR1[j].Ev[i1];
Value[ii].prev_sub = SubR1[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 1; // the best value comes from row subproblem
Value[ii].inv = 1; // the best value comes from SubR1
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
//}
assert(Value[ii].counter_B_R1 != 0);
--Value[ii].counter_B_R1;
//cerr << "Do not update the value of this point\n";
}
}
}
//cerr << endl << endl;
//cerr << "--------------Solve SS_B_C1 ----------------" << endl;
// For each subproblem B_C1 that point H1[i] is in, get Ev[H1[i].first - H1[i].second] and update Value[H1[i]].val
for (unsigned int k = 0; k < Value[ii].SS_B_C1.size(); ++k) {
unsigned int j = Value[ii].SS_B_C1[Value[ii].SS_B_C1.size() - 1 - k];
//cerr << "SubC1[" << j << "]: " << SubC1[j]<< "\n";
// If subproblem SubC1[j] is a leaf case, then
if (SubC1[j].Di.empty()) {
//cerr << "SubC1[" << j << "] is a leaf case or it's a non-leaf case with an empty Di" << "\n";
assert(Value[ii].counter_B_C1 != 0);
--Value[ii].counter_B_C1;
continue;
}
else {
// find the index of this point in E array
vector<unsigned int>::reverse_iterator t = Lower_Bound<vector<unsigned int>::reverse_iterator,long int>(SubC1[j].E.rbegin(), SubC1[j].E.rend(), ForwardDiag, SubC1[j].Ei);
//cerr << "SubC1[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubC1[" << j << "].Ei: " << SubC1[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubC1[j].Eb[*t] == -1) {
//cerr << "SubC1[" << j << "] is a non-leaf case but there is no forward diag larger than the current\n ";
assert(Value[ii].counter_B_C1 != 0);
--Value[ii].counter_B_C1;
continue;
}
else {
//assert(SubC1[j].counter_D[SubC1[j].Eb[*t]] == 0);
//cerr << "SubC1[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already.\n";
//cerr << "Start to compute the maximization structure.\n";
SubC1[j].now = SubC1[j].Eb[*t];
Maximization (SubC1[j].now, SubC1[j].last, SubC1[j].Di, SubC1[j].Ei, SubC1[j].Dv, SubC1[j].Db, SubC1[j].Block, SubC1[j].S_1, LookUpTable, opts, step_sdp);
SubC1[j].last = SubC1[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores the index in Ei that ForwardDiag is in
unsigned int i2; // i2 stores the index in Di which is the best candidate for ForwardDiag
FindValueInBlock(ForwardDiag, SubC1[j].S_1, SubC1[j].Ei, SubC1[j].Block, i1, i2);
//cerr << "the index in Ei that ForwardDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for ForwardDiag ---- i2: " << i2 << "\n";
// SubC1[j].Ev[i1] = SubC1[j].Dv[i2] + w(SubC1[j].Di[i2], SubC1[j].Ei[i1], LookUpTable, opts) + opts.globalK;
// SubC1[j].Ep[i1] = i2;
SubC1[j].Ev[i1] = SubC1[j].Dv[i2] + w(SubC1[j].Di[i2], SubC1[j].Ei[i1], LookUpTable, opts, step_sdp) +
rate * FragInput[fi]->length(ii - ms);
//FragInput[inputChain[mi]]->matchesLengths[ii - MatchStart[mi]];
SubC1[j].Ep[i1] = i2;
//cerr << "SubC1[" << j << "].Ev[" << i1 << "]: " << SubC1[j].Ev[i1] << ", SubC1[" << j << "].Ep[" << i1 << "]: " << SubC1[j].Ep[i1] << "\n";
// Update the value of this point
//TODO(Jingwen): if this point is a s1 of a reverse orientated anchor, only update the value when SubR1[j].Dp[Ep[i1]] points to a forward orientated anchor
//TODO(Jingwen): Only for debug
assert(Value[ii].orient == H1[i].orient);
int p = SubC1[j].Dp[SubC1[j].Ep[i1]];
//
// If the current anchor is reverse oriented and the previous anchor is also reverse oriented, then do not update Value[ii]
// Otherwise update Value[ii]
//if (! (Value[ii].orient == 0 and Value[p].orient == 0)) {
if (Value[ii].val < SubC1[j].Ev[i1]) {
Value[ii].val = SubC1[j].Ev[i1];
Value[ii].prev_sub = SubC1[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 0; // the best value comes from col subproblem
Value[ii].inv = 1; // the best value comes from SubC1
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
//}
assert(Value[ii].counter_B_C1 != 0);
--Value[ii].counter_B_C1;
//cerr << "Do not update the value of this point\n";
}
}
}
}
else if (H1[i].ind == 1 and H1[i].inv == 0) { // H1[i] is a start point s2
//cerr << "----------------------------------------this is a start point (s2) ------------------------------------" << endl;
//cerr << "dealing with the subproblem B first. Solve Value[" << H1[i].frag_num << "].SS_B_R2 and SS_B_C2" << endl;
//cerr <<"----------------Solve SS_B_R2 -------------------" << endl;
// For each subproblem B_R2 that point H1[i] is in, get Ev[BackDiag] and update Value[H1[i]].frag_num].val
for (unsigned int k = 0; k < Value[ii].SS_B_R2.size(); ++k) {
unsigned int j = Value[ii].SS_B_R2[Value[ii].SS_B_R2.size() - 1 - k];
//cerr << "Solving SubR2[" << j << "]: " << SubR2[j]<< "\n";
// If subproblem SubR2[j] is a leaf case, then
if (SubR2[j].Di.empty()) {
//cerr << "SubR2[" << j << "] is a leaf case or non-leaf case but Di is empty" << "\n";
assert(Value[ii].counter_B_R2 > 0);
--Value[ii].counter_B_R2;
continue;
}
else {
// Then subproblem SubR2[j] is non-leaf case. find the index of the point in E array
vector<unsigned int>::reverse_iterator t = Lower_Bound<vector<unsigned int>::reverse_iterator,long int>(SubR2[j].E.rbegin(), SubR2[j].E.rend(), BackDiag, SubR2[j].Ei);
//cerr << "SubR2[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubR2[" << j << "].Ei: " << SubR2[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubR2[j].Eb[*t] == -1) {
//cerr << "SubR2[" << j << "] is a non-leaf case but there is no back diag larger than the current" << endl;
assert(Value[ii].counter_B_R2 > 0);
--Value[ii].counter_B_R2;
continue;
}
else {
//assert(SubR2[j].counter_D[SubR2[j].Eb[*t]] == 0);
//cerr << "SubR2[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already." << endl;
//cerr << "Start to compute the maximization structure.\n";
SubR2[j].now = SubR2[j].Eb[*t];
Maximization (SubR2[j].now, SubR2[j].last, SubR2[j].Di, SubR2[j].Ei, SubR2[j].Dv, SubR2[j].Db, SubR2[j].Block, SubR2[j].S_1, LookUpTable, opts, step_sdp); // TODO(Jingwen) anything change for SubC????
SubR2[j].last = SubR2[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores the index in Ei that BackDiag is in
unsigned int i2; // i2 stores the index in Di which is the best candidate for BackDiag
FindValueInBlock(BackDiag, SubR2[j].S_1, SubR2[j].Ei, SubR2[j].Block, i1, i2);
//cerr << "the index in Ei that BackDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for BackDiag ---- i2: " << i2 << "\n";
SubR2[j].Ev[i1] = SubR2[j].Dv[i2] + w(SubR2[j].Di[i2], SubR2[j].Ei[i1], LookUpTable, opts, step_sdp) +
rate * FragInput[fi]->length(ii - ms);
//FragInput[inputChain[mi]]->matchesLengths[ii - MatchStart[mi]];
SubR2[j].Ep[i1] = i2;
//cerr << "SubR2[" << j << "].Ev[" << i1 << "]: " << SubR2[j].Ev[i1] << ", SubR2[" << j << "].Ep[" << i1 << "]: " << SubR2[j].Ep[i1] << "\n";
// Update the value of this point
if (Value[ii].val < SubR2[j].Ev[i1]) {
Value[ii].val = SubR2[j].Ev[i1];
Value[ii].prev_sub = SubR2[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 1; // the best value comes from row subproblem
Value[ii].inv = 0; // the best value comes from SubR2
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
assert(Value[ii].counter_B_R2 > 0);
--Value[ii].counter_B_R2;
//cerr << "Do not update the value of this point\n";
}
}
}
//cerr << endl << endl;
//cerr << "--------------Solve SS_B_C2 ----------------" << endl;
// For each subproblem B_C2 that point H1[i] is in, get Ev[H1[i].first - H1[i].second] and update Value[H1[i]].val
for (unsigned int k = 0; k < Value[ii].SS_B_C2.size(); ++k) {
//cerr << "k: " << k << endl;
unsigned int j = Value[ii].SS_B_C2[Value[ii].SS_B_C2.size() - 1 - k];
//cerr << "j: " << j << endl;
//cerr << "SubC2[" << j << "]: " << SubC2[j]<< "\n";
// If subproblem SubC2[j] is a leaf case, then
if (SubC2[j].Di.empty()) {
//cerr << "SubC2[" << j << "] is a leaf case or it's a non-leaf case with an empty Di" << "\n";
assert(Value[ii].counter_B_C2 > 0);
--Value[ii].counter_B_C2;
continue;
}
else {
// find the index of this point in E array
vector<unsigned int>::iterator t = Lower_Bound<vector<unsigned int>::iterator,long int>(SubC2[j].E.begin(), SubC2[j].E.end(), BackDiag, SubC2[j].Ei);
//cerr << "SubC2[" << j << "] is a non-leaf case! Find the index of the point in E array" << "/n";
//cerr << "SubC2[" << j << "].Ei: " << SubC2[j].Ei << "/n";
//cerr << "The index of this point in E array: " << *t << "\n";
if (SubC2[j].Eb[*t] == -1) {
//cerr << "SubC2[" << j << "] is a non-leaf case but there is no forward diag larger than the current\n ";
assert(Value[ii].counter_B_C2 > 0);
--Value[ii].counter_B_C2;
continue;
}
else {
//assert(SubC2[j].counter_D[SubC2[j].Eb[*t]] == 0);
//cerr << "SubC2[" << j << "] is a non-leaf case and The part of D array where forward diags are smaller than current is filled out already.\n";
//cerr << "Start to compute the maximization structure.\n";
SubC2[j].now = SubC2[j].Eb[*t];
Maximization (SubC2[j].now, SubC2[j].last, SubC2[j].Di, SubC2[j].Ei, SubC2[j].Dv, SubC2[j].Db, SubC2[j].Block, SubC2[j].S_1, LookUpTable, opts, step_sdp);
SubC2[j].last = SubC2[j].Eb[*t];
//cerr << "retrieve the value from the maximization structure\n";
unsigned int i1 = *t; // i1 stores
unsigned int i2;
FindValueInBlock(BackDiag, SubC2[j].S_1, SubC2[j].Ei, SubC2[j].Block, i1, i2);
//cerr << "the index in Ei that ForwardDiag is in----i1: " << i1 << "\n";
//cerr << "the index in Di which is the best candidate for ForwardDiag ---- i2: " << i2 << "\n";
SubC2[j].Ev[i1] = SubC2[j].Dv[i2] + w(SubC2[j].Di[i2], SubC2[j].Ei[i1], LookUpTable, opts, step_sdp) +
rate * FragInput[fi]->length(ii - ms);
// FragInput[inputChain[mi]]->matchesLengths[ii - MatchStart[mi]];
SubC2[j].Ep[i1] = i2;
//cerr << "SubC2[" << j << "].Ev[" << i1 << "]: " << SubC2[j].Ev[i1] << ", SubC2[" << j << "].Ep[" << i1 << "]: " << SubC2[j].Ep[i1] << "\n";
// Update the value of this point
if (Value[ii].val < SubC2[j].Ev[i1]) {
Value[ii].val = SubC2[j].Ev[i1];
Value[ii].prev_sub = SubC2[j].num;
Value[ii].prev_ind = i1;
Value[ii].prev = 0; // the best value comes from col subproblem
Value[ii].inv = 0; // the best value comes from SubC2
//cerr << "update the value of this point\n";
//cerr << "Value[ii].val: " << Value[ii].val << ", Value[ii].prev_sub: " << Value[ii].prev_sub << ", Value[ii].prev_ind: " << Value[ii].prev_ind <<
//", Value[ii].prev: " << Value[ii].prev << endl;
}
assert(Value[ii].counter_B_C2 > 0);
--Value[ii].counter_B_C2;
//cerr << "Do not update the value of this point\n";
}
}
}
}
else if (H1[i].ind == 0 and H1[i].inv == 1) { // H1[i] is an end point (e1)
//cerr << "---------------------------------This is an end point (e1) --------------------------------"<< endl;
//cerr << "Pass the value Value[ii].val to SS_A_R1 and SS_A_C1" << endl;
// If all the subproblems B that the point H1[i] is in are already processed, then Value[H1[i]].val is ready
// For each subproblem A that the point H1[i] is in, Pass the Value[H1[i]].val to the D array
PassValueToD1(ii, Value, H1, SubR1, SubC1, ForwardDiag);
}
else { // H1[i] is an end point (e2)