C++ (Cpp) mask_sl Exemples

Exemple #1

Fichier : seqsrc_multiseq.cpp Projet : DmitrySigaev/ncbi

/// 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;
        }
    }

Exemple #2

Fichier : seqsrc_query_factory.cpp Projet : jackgopack4/pico-blast

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;
        }
    }