void ctgJoiner(asmMerge & merge,asmMerge & merge1,fastaSeq & hybrid, fastaSeq & pbOnly, fastaSeq & merged)
{
string name,subseq,subseqR,indexL1,indexL2,seqHolder;
vector<int> v1;
//entry by michel
// tempRef_st initalized and moved at second for-loop
int begin_insrt = 1;
for(map<string,vector<string> >::iterator it = merge1.lseq.begin(); it!=merge1.lseq.end();it++) // merge1.lseq is container for the contig names
{
name = it->first;
begin_insrt = 1;
for(unsigned int i=0;i<merge1.lseq[name].size();i++)
{
int q1_f = 0,q1_last = 0,q2_f = 0,q2_last = 0,r1_f = 0,r1_last = 0,r2_f = 0,r2_last = 0,tempRef_st = 0;
if( i ==0 && (find(merge.q_name.begin(),merge.q_name.end(),merge1.lseq[name][i])!=merge.q_name.end()))//if first element is query
{
indexL2 = merge1.rseq[name][i]; // index name coresponding to the query element
q2_f = merge.q_st[indexL2][0];
q2_last = merge.q_end[indexL2][merge.q_end[indexL2].size()-1];
if(q2_f > merge.q_end[indexL2][0]) // if query is reverse oriented
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(q2_f); //take q_f to the end of the sequence
}
if(q2_f < merge.q_end[indexL2][0]) // if query is forward oriented
{
if(merge.sideInfo[indexL2] == 'R')
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(0,q2_last);
if(merge1.lseq[name][i] != merge1.lseq[name][merge1.lseq[name].size()-1]) //if the first and last element are not same
{
begin_insrt = -1; // this is experimental
}
}
if((merge.sideInfo[indexL2] == 'L') || (merge1.lseq[name][0] == merge1.lseq[name][merge1.lseq[name].size()-1]))
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(0,q2_f);
}
}
}
if(i == 0 && (find(merge.r_name.begin(),merge.r_name.end(),merge1.lseq[name][i]) != merge.r_name.end())) // if first element is reference
{
indexL2 = merge1.rseq[name][i];
r2_last = merge.ref_end[indexL2][merge.ref_end[indexL2].size()-1];
r2_f = merge.ref_st[indexL2][0];
if(merge1.lseq[name][i] == name)
{
subseq = pbOnly.seq[merge1.lseq[name][i]].substr(0,r2_last);
}
if(merge1.lseq[name][i] != name)
{
if((merge.Ori[name][i] == 1) && (merge.Ori[name][i+1] == -1) && (merge.sideInfoQ[merge1.rseq[name][i]]=='R'))
{
subseq = pbOnly.seq[merge1.lseq[name][i]].substr(0,r2_last);
}
if(merge.Ori[name][i] == merge.Ori[name][i+1])
{
subseq = pbOnly.seq[merge1.lseq[name][i]].substr(0,r2_last);
}
if((merge.Ori[name][i] == 1) && (merge.Ori[name][i+1] == -1) && (merge.sideInfoQ[merge1.rseq[name][i]]=='L'))
{
subseq = pbOnly.seq[merge1.lseq[name][i]].substr(r2_f,(merge.ref_len[indexL2] - r2_f));
begin_insrt = -1;
}
}
}
if(i > 0 && (find(merge.q_name.begin(),merge.q_name.end(),merge1.lseq[name][i])!=merge.q_name.end())) // if the element is query
{
indexL1 = merge1.rseq[name][i-1];
q1_f = merge.q_st[indexL1][0];
q1_last = merge.q_end[indexL1][merge.q_end[indexL1].size()-1];
if(i != (merge1.lseq[name].size()-1)) //if it isn't the last element
{
indexL2 = merge1.rseq[name][i];
q2_f = merge.q_st[indexL2][0];
q2_last = merge.q_end[indexL2][merge.q_end[indexL2].size() -1];
if(chkOvl(q1_f,q1_last,q2_f,q2_last) == 0) //alignments are non-overlapping
{
v1 = minD(q1_f,q1_last,q2_f,q2_last);
int cheatF = min(v1[0],v1[1]);
int cheatR = max(v1[0],v1[1]);
subseq = hybrid.seq[merge1.lseq[name][i]].substr(cheatF,(cheatR-cheatF));
}
if(chkOvl(q1_f,q1_last,q2_f,q2_last) == 1) // if alignments are overlapping
{
tempRef_st = mapQonRef(indexL1,indexL2,merge);
subseq = ""; // may be add a single base if this causes segfault for revcom
}
}
if( i == (merge1.lseq[name].size()-1)) // if this is the last element
{
if(merge.q_st[merge1.rseq[name][i-1]][0] > merge.q_end[merge1.rseq[name][i-1]][0]) // last element uses (i-1) th index. if query reverse oriented
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(0,q1_last);
if((i>1) && (merge1.lseq[name][i] == merge1.lseq[name][i-2])) //if two queries for the reference are same
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(q1_f,(merge.q_len[merge1.rseq[name][i-1]] - q1_f));
}
if(merge1.lseq[name][i] == merge1.lseq[name][0]) //if first element and last elements are same
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(0,q1_last);
}
}
if(merge.q_st[merge1.rseq[name][i-1]][0] < merge.q_end[merge1.rseq[name][i-1]][0]) // if query is forward oriented
{
if(merge.sideInfo[merge1.rseq[name][i-1]] == 'L')
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(0,q1_f);
}
if(merge.sideInfo[merge1.rseq[name][i-1]] == 'R')
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(q1_last);
}
if(merge1.lseq[name][i] == merge1.lseq[name][0]) //if first element and last elements are same
{
subseq = hybrid.seq[merge1.lseq[name][i]].substr(q1_last);
}
}
}
if(merge.Ori[name][i] == -1)
{
subseqR = revCom(subseq); // if needs to be reverse complemented
subseq = subseqR;
}
}
if(i>0 && (find(merge.r_name.begin(),merge.r_name.end(),merge1.lseq[name][i]) != merge.r_name.end())) // if the element is reference
{
indexL1 = merge1.rseq[name][i-1];
r1_f = merge.ref_st[indexL1][0];
r1_last = merge.ref_end[indexL1][merge.ref_end[indexL1].size()-1];
if(i != (merge1.lseq[name].size()-1)) // if this is not the last element
{
indexL2 = merge1.rseq[name][i];
r2_f = merge.ref_st[indexL2][0];
r2_last = merge.ref_end[indexL2][merge.ref_end[indexL2].size()-1];
if(tempRef_st != 0)
{
r1_f = tempRef_st;
//r1_last = tempRef_st; //transfer the number so that it is used in case of an overlap;
//v1 = maxD(r1_last,r1_last,r2_f,r2_last);//CHANGED
}
v1 = maxD(r1_f,r1_last,r2_f,r2_last); // maximum distance between coords from the two alignments
r1_f = min(v1[0],v1[1]);
r2_last = max(v1[0],v1[1]);
subseq = pbOnly.seq[merge1.lseq[name][i]].substr(r1_f,(r2_last - r1_f));
tempRef_st = 0; //reset tempRef_st
if((i<2)&&(merge.Ori[name][i] == -1)) // && (name == merge1.lseq[name][i]) this was inside earlier
{
begin_insrt = -1;
}
if((i>1)&&(merge.Ori[name][i] == -1) && (name == merge1.lseq[name][i]) && (merge.Ori[name][i-2] == 1)) // if the preceding reference is of different sign
{
begin_insrt = -1;
}
}
//if(i == (merge1.lseq[name].size()-1))
else
{
if((merge.Ori[name][i] == -1) && (name == merge1.lseq[name][i]))
{
begin_insrt = -1;
}
if(tempRef_st != 0)
{
r1_f = tempRef_st; //transfer the number so that it is used in case of an overlap;
tempRef_st = 0; //reset tempRef
}
const std::string& s = pbOnly.seq[merge1.lseq[name][i]];
subseq = s.substr(r1_f,(merge.ref_len[indexL1] - r1_f)); // error here
}
if(merge.Ori[name][i] == -1)
{
subseqR = revCom(subseq);
subseq = subseqR;
}
}
if(begin_insrt == -1)
{
subseq.append(seqHolder);
seqHolder = subseq;
}
if(begin_insrt == 1)
{
seqHolder.append(subseq);
}
}
merged.seq[name] = seqHolder;
seqHolder.clear();
}
}
//TSP 본체
int travel(int start, const int W[][13], int P[][4096], int b[], int D[][MAX_BINT]){
//반복 변수
int i, j, k;
//D가 되는 개수 변수, 주소 변수
int cnt=0, index=0;
//부분집합을 표현하는 비트
int bitS=0;
//임시 D값 저장 배열, 임시 최단 거리 주소 저장 배열
int temp[12]={MAX,MAX,MAX,MAX,MAX,MAX,MAX,MAX,MAX,MAX,MAX,MAX},
indexP[12]={0,};
//출발점 제외한 나머지 거리에서 도착점까지 최단 경로 저장
for(i=1;i<=CITYCOUNT;++i)
if(i!=start)
D[i][0]=W[i][start];
//부분집합 1~10개의 경우 계산
for(k=1;k<=CITYCOUNT-2;++k){
//개수에 맞는 최초부분집합 계산
bitS=0;
for(j=0;j<=k;++j){
b[j]=1;
bitS |= (int)pow(2.0, j);
}
b[start-1]=0;
bitS ^= (int)pow(2.0, start-1);
while(1){
for(j=1;j<=CITYCOUNT;++j){
//부분집합 A, 출발점에 포함되면 넘어감
if((bitS & (1<<(j-1)))>0)
continue;
//A인 경우에 D행렬, P행렬의 일부 계산
for(i=1, cnt=0;cnt<k;++i){
if((bitS & (1<<(i-1)))>0){
temp[cnt]=W[j][i]+D[i][bitS^(1<<i)];
indexP[cnt]=i;
++cnt;
}
}
D[j][bitS]=minD(temp, cnt, &index);
P[j][bitS]=indexP[index];
}
//비트수 검사하여 개수 맞으면 계속 진행, 범위 초과시 종료
while(1){
++bitS;
//범위 초과시 반복 종료
if(bitS>4095)
break;
//개수 일치 시 반복 종료
else if(checkBit(bitS)==k)
break;
}
//범위 초과 시 구문 종료
if(bitS>4095)
break;
}
}
//출발 제외한 나머지 경로 거칠 때 경우 계산
bitS=4095;
bitS^=(int)pow(2.0, start-1);
for(i=1, cnt=0;cnt<CITYCOUNT-1;++i){
if((bitS & (1<<(i-1)))>0){
temp[cnt]=W[start][i]+D[i][bitS^(1<<j)];
indexP[cnt]=i;
++cnt;
}
}
D[start][bitS]=minD(temp,cnt,&index);
P[start][bitS]=indexP[index];
return D[start][bitS];
}
