SCompartmentData(const CSeq_align_set &compartment)
: num_alignments(compartment.Get().size())
{
CSeq_align align;
align.SetSegs().SetDisc(const_cast<CSeq_align_set &>(compartment));
query_range = align.GetSeqRange(0);
subject_range = align.GetSeqRange(1);
}
static void s_MergeAlignSet(CSeq_align_set & final_set, const CSeq_align_set & input_set)
{
CSeq_align_set::Tdata & final_list = final_set.Set();
const CSeq_align_set::Tdata & input_list = input_set.Get();
CSeq_align_set::Tdata::const_iterator input_it = input_list.begin();
CSeq_align_set::Tdata::iterator final_it = final_list.begin();
while(input_it != input_list.end())
{
double final_evalue;
double input_evalue;
(*final_it)->GetNamedScore(CSeq_align::eScore_EValue, final_evalue);
(*input_it)->GetNamedScore(CSeq_align::eScore_EValue, input_evalue);
if(input_evalue == final_evalue)
{
//Pulling a trick here to keep the program flow simple
//Replace the final evalue with input bitscore and vice versa
(*final_it)->GetNamedScore(CSeq_align::eScore_BitScore, input_evalue);
(*input_it)->GetNamedScore(CSeq_align::eScore_BitScore, final_evalue);
}
if(input_evalue < final_evalue)
{
CSeq_align_set::Tdata::const_iterator start_input_it = input_it;
while(1)
{
const CSeq_id & id_prev = (*input_it)->GetSeq_id(1);
input_it++;
if(input_it == input_list.end())
{
break;
}
if(! id_prev.Match((*input_it)->GetSeq_id(1)))
{
break;
}
}
final_list.insert(final_it, start_input_it, input_it);
}
else
{
while(1)
{
const CSeq_id & id_prev = (*final_it)->GetSeq_id(1);
final_it++;
if(final_it == final_list.end())
{
break;
}
if(! id_prev.Match((*final_it)->GetSeq_id(1)))
{
break;
}
}
if(final_it == final_list.end())
{
final_list.insert(final_it, input_it, input_list.end());
break;
}
}
}
}
