void eseqclustersingle::init(INDTYPE count,const estr& ofilename,const estr& seqsfile,const earray<ebasicarray<INDTYPE> >& dupslist) {
ofile.open(ofilename,"w");
ofile.write("# seqsfile: "+seqsfile+"\n");
ofile.write("# OTU_count Merge_distance Merged_OTU_id1 Merged_OTU_id2\n");
long i,j;
mergecount=0;
scount.reserve(count);
scluster.reserve(count);
smerge.reserve(count);
incluster.reserve(count);
for (i=0; i<count; ++i){
scount.add(1);
scluster.add(i);
smerge.add(-1);
incluster.add(list<INDTYPE>());
incluster[i].push_back(i);
}
for (i=0; i<dupslist.size(); ++i){
for (j=1; j<dupslist[i].size(); ++j){
++mergecount;
ofile.write(estr(scluster.size()-mergecount)+" 1.0 "+dupslist[i][0]+" "+dupslist[i][j]+"\n");
clusterData.mergearr.add(eseqdist(dupslist[i][0],dupslist[i][j],1.0));
}
}
cout << "# initializing cluster with: "<< count<< " seqs" << endl;
}
void eseqclusterData::load(const efile& f,int _count)
{
count=_count;
mergearr.clear();
estr line;
estrarray parts;
while (f.readln(line)){
if (line.len()==0 || line[0]=='#') continue;
parts=line.explode(" ");
if (parts.size()==3){
mergearr.add(eseqdist(parts[1].i(),parts[2].i(),parts[0].f()));
}else if (parts.size()==4){
mergearr.add(eseqdist(parts[2].i(),parts[3].i(),parts[1].f()));
}else
ldie("fields in line different than 3: "+line);
}
}
void eseqclusteravg::init(INDTYPE count,const estr& filename,const estr& seqsfile,const earray<ebasicarray<INDTYPE> >& dupslist,float _thres,float (_fdist)(const estr&,const estr&,int),estrarray& _seqarr,int _seqlen)
{
thres=_thres;
seqarr=&_seqarr;
seqlen=_seqlen;
fdist=_fdist;
ofile.open(filename,"w");
ofile.write("# seqsfile: "+seqsfile+"\n");
ofile.write("# OTU_count Merge_distance Merged_OTU_id1 Merged_OTU_id2\n");
long i,j;
incmaxdist=1.0;
incmaxit=smatrix.end();
cf=0;
lastdist=0.0;
scount.reserve(count);
scluster.reserve(count);
smerge.reserve(count);
inter.reserve(count);
incluster.reserve(count);
mergecount=0;
for (i=0; i<count; ++i){
scount.add(1);
scluster.add(i);
smerge.add(-1);
incluster.add(list<INDTYPE>());
incluster[i].push_back(i);
inter.add(list<INDTYPE>());
}
for (i=0; i<dupslist.size(); ++i){
for (j=1; j<dupslist[i].size(); ++j){
++mergecount;
ofile.write(estr(scluster.size()-mergecount)+" 1.0 "+dupslist[i][0]+" "+dupslist[i][j]+"\n");
clusterData.mergearr.add(eseqdist(dupslist[i][0],dupslist[i][j],1.0));
}
}
cout << "# initializing cluster with: "<< count<< " seqs" << endl;
cout << "# initializing smatrix with: " << (long)(count)*(long)(count)/20000l/2l<< " elements" << endl;
smatrix.reserve((long)(count)*(long)(count)/20000l/2l);
// cout << "# smatrix._hashitems = " << smatrix._hashitems << endl;
}
void eseqclustersingle::merge(INDTYPE x,INDTYPE y,float dist)
{
if (x==y) return;
ldieif(scount[x]==0 || scount[y]==0,"also should not happen");
clusterData.mergearr.add(eseqdist(x,y,dist));
smerge[x]=x;
smerge[y]=x;
scount[x]+=scount[y];
scount[y]=0;
list<INDTYPE>::iterator it;
for (it=incluster[y].begin(); it!=incluster[y].end(); ++it){
scluster[*it]=x;
incluster[x].push_back(*it);
}
++mergecount;
// cout << scluster.size()-mergecount << " " << dist << " " << x << " " << y << endl;
ofile.write(estr(scluster.size()-mergecount)+" "+dist+" "+x+" "+y+"\n");
}
void eseqclusteravg::merge(const eseqdistCount& sdist)
{
ldieif(sdist.x==sdist.y,"should not happen!");
ldieif(scount[sdist.x]==0 || scount[sdist.y]==0,"also should not happen");
clusterData.mergearr.add(eseqdist(sdist.x,sdist.y,sdist.dist));
smerge[sdist.x]=sdist.x;
smerge[sdist.y]=sdist.x;
scount[sdist.x]+=scount[sdist.y];
scount[sdist.y]=0;
list<INDTYPE>::iterator it;
for (it=incluster[sdist.y].begin(); it!=incluster[sdist.y].end(); ++it){
scluster[*it]=sdist.x;
incluster[sdist.x].push_back(*it);
}
eseqdistCount tmpdist,tmpdist2;
// estr tmpstr,tmpstr2;
tmpdist.x=sdist.x;
tmpdist2.x=sdist.y;
INDTYPE i,j;
for (it=inter[sdist.y].begin(); it!=inter[sdist.y].end(); ++it){
j=scluster[*it];
if (sdist.x==j || sdist.y==j) continue;
tmpdist.y=j;
tmpdist2.y=j;
// xy2estr(x,j,tmpstr);
// xy2estr(y,j,tmpstr2);
eseqdistavghash::iter tmpit2=smatrix.get(tmpdist2);
if(tmpit2==smatrix.end()) continue;
eseqdistavghash::iter tmpit=smatrix.get(tmpdist);
if (tmpit!=smatrix.end()){
/*
if (scount[tmpit->x]*scount[tmpit->y]==tmpit->count+tmpit2->count){
if((tmpit->dist*tmpit->count+tmpit2->dist*tmpit2->count)/(tmpit->count+tmpit2->count)>sdist.dist){
cout << "sdist.dist: " << sdist.dist << " tmpit: " << *tmpit << " tmpit2: " << *tmpit2 << " sdist: " << sdist << " scount[x]: " << scount[sdist.x] << " scount[y]: " << scount[sdist.y] << " scount[j]: "<< scount[j] << endl;;
exit(-1);
}
}
*/
tmpit->dist=((double)tmpit->dist*tmpit->count+(double)tmpit2->dist*tmpit2->count)/(double)(tmpit->count+tmpit2->count);
tmpit->count+=tmpit2->count;
}else{
tmpdist.dist=tmpit2->dist;
tmpdist.count=tmpit2->count;
smatrix.add(tmpdist,tmpdist);
inter[sdist.x].push_back(j);
tmpit=smatrix.get(tmpdist);
}
// make sure to add merged neighbors which are complete to the complete list
lassert(scount[tmpit->x]==0 || scount[tmpit->y]==0);
if (scount[tmpit->x]*scount[tmpit->y]==tmpit->count){
// ldieif(tmpit->dist>sdist.dist,"sdist.dist: "+estr(sdist.dist)+" tmpit.dist: "+tmpit->dist+" tmpit.count: "+tmpit->count);
completemerges.insert(*tmpit);
if (tmpit == incmaxit)
incmaxit=smatrix.end();
}
if (tmpit2==incmaxit)
incmaxit=smatrix.end();
smatrix.erase(tmpit2);
}
++mergecount;
}