int eseqclusterData::getOTU(float dist,earray<eintarray>& otus,int size)
{
eintarray otuarr;
int i,j;
otuarr.init(size);
for (i=0; i<size; ++i)
otuarr[i]=i;
// point at the seq we merged with
for (i=0; i<mergearr.size() && mergearr[i].dist>=dist; ++i)
otuarr[mergearr[i].y]=mergearr[i].x;
eintarray otuind;
otuind.init(otuarr.size(),-1);
// translate all the merged seq ids to the last seq id of the otu
for (i=0; i<otuarr.size(); ++i){
for (j=otuarr[i]; j!=otuarr[j]; j=otuarr[j]);
otuarr[i]=j;
if (otuind[j]==-1){
otuind[j]=otus.size();
otus.add(eintarray());
}
}
for (i=0; i<otuarr.size(); ++i)
otus[otuind[otuarr[i]]].add(i);
return(otus.size());
}
void finduniq(ebasicarray<INDTYPE>& uniqind,earray<ebasicarray<INDTYPE> >& dupslist)
{
ebasicstrhashof<long> duphash;
ebasicstrhashof<long>::iter it;
if (!ignoreUnique){
duphash.reserve(arr.size());
for (long i=0; i<arr.size(); ++i){
if (i%1000==0)
fprintf(stderr,"\r%li/%li",i,(long)arr.size());
it=duphash.get(arr.values(i));
if (it==duphash.end())
{ uniqind.add(i); duphash.add(arr.values(i),uniqind.size()-1); dupslist.add(ebasicarray<INDTYPE>(i)); }
else
dupslist[it.value()].add(i);
}
fprintf(stderr,"\r%li\n",(long)arr.size());
}else{
uniqind.init(arr.size());
for (long i=0; i<uniqind.size(); ++i)
uniqind[i]=i;
}
cout << endl;
}