int main(void)
{
// read lines, get sorted nodes
Time *nodes = read();
find_overlap( nodes );
return 0;
}
int CReadBlastApp::simple_overlaps()
{
int nabsent=0;
int saved_m_verbosity_threshold = m_verbosity_threshold;
// m_verbosity_threshold = 300;
if(PrintDetails()) NcbiCerr << "simple_overlaps starts: " << NcbiEndl;
TSimpleSeqs& seqs=m_simple_seqs; // now calculated in CopyGenestoforgotthename
TSimpleSeqs::iterator first_user_in_range = seqs.begin();
TSimpleSeqs::iterator first_user_non_in_range = seqs.begin();
TSimpleSeqs::iterator first_ext_in_range = m_extRNAtable2.begin();
TSimpleSeqs::iterator first_ext_non_in_range = m_extRNAtable2.begin();
TSimpleSeqs::iterator seq = seqs.begin();
NON_CONST_ITERATE(TSimpleSeqs, ext_rna, m_extRNAtable2)
{
int from, to;
from = ext_rna->exons[0].from;
to = ext_rna->exons[ext_rna->exons.size()-1].to;
ENa_strand strand = ext_rna->exons[0].strand;
int range_scale = to - from;
int max_distance = get_max_distance(range_scale);
string type2 = ext_rna->name;
string ext_rna_range = printed_range(ext_rna);
if(PrintDetails()) NcbiCerr << "simple_overlaps[" << type2 << "[" << ext_rna_range << "]" << "]" << NcbiEndl;
// find BEST overlap, not good enough here
TSimpleSeqs best_seq;
find_overlap(seq, ext_rna, seqs, best_seq); // this will slide seq along seqs
bool absent = true;
string diag_name = ext_rna->name;
// for buffer
int n_user_neighbors=0; int n_ext_neighbors = 0; string bufferstr="";
NON_CONST_ITERATE(TSimpleSeqs, seq2, best_seq)
{
int overlap=0;
overlaps(ext_rna, seq2, overlap);
strstream seq2_range_stream;
string seq2_range = printed_range(seq2);
if(PrintDetails()) NcbiCerr << "simple_overlaps"
<< "[" << type2
<< "[" << ext_rna_range << "]"
<< "[" << seq2_range << "]"
<< "]"
<< ". "
<< "Overlap = " << overlap
<< NcbiEndl;
if(PrintDetails()) NcbiCerr << "ext_rna->type = " << ext_rna->type << NcbiEndl;
if(PrintDetails()) NcbiCerr << "seq2->type = " << seq2->type << NcbiEndl;
if(PrintDetails()) NcbiCerr << "strand = " << int(strand) << NcbiEndl;
if(PrintDetails()) NcbiCerr << "seq2->exons[0].strand = " << int(seq2->exons[0].strand) << NcbiEndl;
absent = absent && (!overlap || ext_rna->type != seq2->type); // Absent
bool bad_strand = (overlap>0 && ext_rna->type == seq2->type && strand != seq2->exons[0].strand); // BadStrand
if(!bad_strand) continue;
string diag_name2 = seq2->name;
int from2, to2;
from2 = seq2->exons[0].from;
to2 = seq2->exons[seq2->exons.size()-1].to;
bool undef_strand = seq2->exons[0].strand == eNa_strand_unknown;
if(!bufferstr.size())
{
if(PrintDetails())
{
if(first_user_in_range==seqs.end())
{
NcbiCerr << "simple_overlaps: first_user_in_range is already at the end" << NcbiEndl;
}
else
{
NcbiCerr << "simple_overlaps: first_user_in_range = " << printed_range(first_user_in_range) << NcbiEndl;
}
}
ugly_simple_overlaps_call(n_user_neighbors, n_ext_neighbors,
ext_rna, first_user_in_range, first_user_non_in_range, seqs, max_distance,
first_ext_in_range, first_ext_non_in_range, bufferstr);
}
strstream misc_feat;
string seq_range = printed_range(seq);
EProblem trnaStrandProblem = undef_strand ? eTRNAUndefStrand : eTRNABadStrand;
misc_feat << "RNA does not match strand for feature located at " << seq_range << NcbiEndl;
misc_feat << '\0';
// this goes to the misc_feat, has to be original location, and name, corrected strand
problemStr problem = {trnaStrandProblem, bufferstr, misc_feat.str(), "", "", from2, to2, strand};
m_diag[diag_name2].problems.push_back(problem);
if(PrintDetails()) NcbiCerr << "simple_overlaps: adding problem:" << "\t"
<< diag_name << "\t"
<< "eTRNABadStrand" << "\t"
<< bufferstr << "\t"
<< NcbiEndl;
// this goes to the log, has to be new
problemStr problem2 = {trnaStrandProblem, bufferstr, "", "", "", from, to, strand};
m_diag[diag_name].problems.push_back(problem2);
} // best_Seq iteration NON_CONST_ITERATE(TSimpleSeqs, seq2, best_seq)
