C++ (Cpp) seqloc Examples

Example #1

File: test_objmgr.cpp Project: DmitrySigaev/ncbi

SSeqLoc* 
CTestObjMgr::CreateEmptySSeqLoc(CSeq_id& id)
{
    CRef<CSeq_loc> seqloc(new CSeq_loc());
    CRef<CScope> scope(new CScope(GetObjMgr()));
    scope->AddDefaults();

    seqloc->SetEmpty(id);

    return new SSeqLoc(seqloc, scope);
}

Example #2

File: test_objmgr.cpp Project: DmitrySigaev/ncbi

SSeqLoc*
CTestObjMgr::CreateSSeqLoc(CSeq_id& id, ENa_strand strand)
{
    CRef<CSeq_loc> seqloc(new CSeq_loc());
    CRef<CScope> scope(new CScope(GetObjMgr()));
    scope->AddDefaults();

    seqloc->SetInt().SetFrom(0);
    seqloc->SetInt().SetTo(sequence::GetLength(id, scope)-1);
    seqloc->SetInt().SetStrand(strand);
    seqloc->SetInt().SetId().Assign(id);

    return new SSeqLoc(seqloc, scope);
}

Example #3

File: test_objmgr.cpp Project: DmitrySigaev/ncbi

SSeqLoc*
CTestObjMgr::CreateSSeqLoc(CSeq_id& id, 
                           pair<TSeqPos, TSeqPos> range,
                           ENa_strand strand)
{
    CRef<CSeq_loc> seqloc(new CSeq_loc());
    CRef<CScope> scope(new CScope(GetObjMgr()));
    scope->AddDefaults();

    seqloc->SetInt().SetFrom(range.first);
    seqloc->SetInt().SetTo(range.second);
    seqloc->SetInt().SetStrand(strand);
    seqloc->SetInt().SetId().Assign(id);

    return new SSeqLoc(seqloc, scope);
}

Example #4

File: test_objmgr.cpp Project: DmitrySigaev/ncbi

CRef<ncbi::blast::CBlastSearchQuery>
CTestObjMgr::CreateBlastSearchQuery(CSeq_id& id, ENa_strand strand)
{
    CRef<CSeq_loc> seqloc(new CSeq_loc());
    CRef<CScope> scope(new CScope(GetObjMgr()));
    scope->AddDefaults();
    
    seqloc->SetInt().SetFrom(0);
    seqloc->SetInt().SetTo(sequence::GetLength(id, scope)-1);
    seqloc->SetInt().SetStrand(strand);
    seqloc->SetInt().SetId().Assign(id);
    
    TMaskedQueryRegions mqr;
    
    CRef<CBlastSearchQuery>
        bsq(new CBlastSearchQuery(*seqloc, *scope, mqr));
    
    return bsq;
}

Example #5

File: cobalt_test_util.cpp Project: jackgopack4/pico-blast

int ReadFastaQueries(const string& filename,
                      vector< CRef<objects::CSeq_loc> >& seqs,
                      CRef<objects::CScope>& scope,
                      bool parse_deflines /* = false*/,
                      objects::CSeqIdGenerator* id_generator /* = NULL*/)
{
    seqs.clear();
    CNcbiIfstream instream(filename.c_str());
    if (!instream) {
        return -1;
    }

    CStreamLineReader line_reader(instream);
    CFastaReader::TFlags flags =  CFastaReader::fAssumeProt |
        CFastaReader::fForceType;
    
    if (!parse_deflines) {
        flags |= CFastaReader::fNoParseID;
    }

    CFastaReader fasta_reader(line_reader, flags);

    if (id_generator) {
        fasta_reader.SetIDGenerator(*id_generator);
    }

    scope->AddDefaults();
    while (!line_reader.AtEOF()) {

        CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();

        if (entry == 0) {
            return -1;
        }
        scope->AddTopLevelSeqEntry(*entry);
        CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
        CRef<CSeq_loc> seqloc(new CSeq_loc());
        seqloc->SetWhole().Assign(*itr->GetId().front());
        seqs.push_back(seqloc);
    }

    return 0;
}