ChainStatsVisitor(int nodes, int longest) : counts_(nodes)
{
for(CountVector::iterator it=counts_.begin(); it!=counts_.end(); ++it)
{
it->resize(longest);
}
}
virtual bool process (size_t partId, const typename Kmer<span>::Type& kmer, const CountVector& count, CountNumber sum)
{
// get a mutex
LocalSynchronizer sync (synchro);
// output kmer and counts
cout << kmer.toString(kmerSize) << " ";
for (size_t i=0; i<count.size(); i++) { cout << count[i] << " "; }
cout << endl;
return true;
}
// We refine the 'process' method
virtual bool process (size_t partId, const typename Kmer<span>::Type& kmer, const CountVector& count, CountNumber sum)
{
// We try each possible pair (i,j) through the 'i' and 'j' loops
for (size_t i=0; i<count.size(); i++)
{
if (_range.includes(count[i]) == true)
{
for (size_t j=i; j<count.size(); j++)
{
if (_range.includes(count[j]) == true)
{
// Both 'i' and 'j' banks hold the current kmer with an abundance in the correct range
// so we increase the number of common kmers for this pair (i,j)
_countTotal [offset(i,j)] ++;
}
}
}
}
return true;
}
void print() const
{
Rprintf("Chain position counts\n");
for(CountVector::size_type node=0; node<counts_.size(); ++node)
{
CountVector::const_reference v = counts_[node];
Rprintf("[%d] ", node);
for(CountVector::value_type::size_type pos=0; pos!=v.size(); ++pos)
{
Rprintf("%d:%lu, ", pos, v[pos]);
}
Rprintf("\n");
}
}
