SSeqLoc blast_sseq_loc_from_fasta::make(const char* fasta_str, std::size_t s, ENa_strand strand,
std::size_t from, std::size_t to, bool get_lcase_mask) {
std::istringstream is(fasta_str);
TSeqLocVector vec = BLASTGetSeqLocFromStream(is, *_objmngr, strand, from, to, &_counter, get_lcase_mask);
if (s < 0 ) {
throw std::runtime_error("Only non negative sequence selections are allowed.");
}
if (vec.size() <= s ) {
throw std::runtime_error("Could not read requested sequence from fasta file.");
}
return vec[s];
}
CQueryFactoryInfo::CQueryFactoryInfo(const TSeqLocVector& subj_seqs,
EBlastProgramType program)
: m_IsProt(Blast_SubjectIsProtein(program) ? true : false), m_MaxLength(0),
m_MinLength(1), m_AvgLength(0), m_QuerySource(0), m_NumSeqs(subj_seqs.size())
{
// Fix subject location for tblast[nx].
if (Blast_SubjectIsTranslated(program))
{
TSeqLocVector temp_slv;
vector<Int2> strand_v;
ITERATE(TSeqLocVector, iter, subj_seqs)
{
strand_v.push_back((Int2) (*iter).seqloc->GetStrand());
CRef<CSeq_loc> sl(new CSeq_loc);
sl->Assign(*((*iter).seqloc));
sl->SetStrand(eNa_strand_both);
if ((*iter).mask)
{
CRef<CSeq_loc> mask_sl(new CSeq_loc);
mask_sl->Assign(*((*iter).mask));
SSeqLoc sseq_loc(*sl, *((*iter).scope), *mask_sl);
temp_slv.push_back(sseq_loc);
}
else
{
SSeqLoc sseq_loc(*sl, *((*iter).scope));
temp_slv.push_back(sseq_loc);
}
}
SetupSubjects(temp_slv, program, &m_SeqBlkVector, &m_MaxLength);
int index=0;
ITERATE(vector<Int2>, s_iter, strand_v)
{
m_SeqBlkVector[index++]->subject_strand = *s_iter;
}
}