/// Constructor
CMultiSeqInfo::CMultiSeqInfo(TSeqLocVector& seq_vector,
EBlastProgramType program,
bool dbscan_mode)
{
m_ibIsProt = Blast_SubjectIsProtein(program) ? true : false;
m_DbScanMode = dbscan_mode;
m_iTotalLength=0;
// Fix subject location for tblast[nx].
if (Blast_SubjectIsTranslated(program))
{
TSeqLocVector temp_slv;
vector<Int2> strand_v;
ITERATE(TSeqLocVector, iter, seq_vector)
{
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_ivSeqBlkVec, &m_iMaxLength);
int index=0;
ITERATE(vector<Int2>, s_iter, strand_v)
{
m_ivSeqBlkVec[index++]->subject_strand = *s_iter;
}
}
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;
}
}