C++ (Cpp) pVariant示例

示例#1

文件： vcf_reader.cpp 项目： swuecho/igblast

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantIns(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();

    CRef<CVariation_ref> pVariant(new CVariation_ref);
    {{
        string insertion(data.m_Alt[index]);
        CRef<CSeq_literal> pLiteral(new CSeq_literal);
        pLiteral->SetSeq_data().SetIupacna().Set(insertion);
        pLiteral->SetLength(insertion.size());
        CRef<CDelta_item> pItem(new CDelta_item);
        pItem->SetAction(CDelta_item::eAction_ins_before);
        pItem->SetSeq().SetLiteral(*pLiteral); 
        CVariation_inst& instance =  pVariant->SetData().SetInstance();
        instance.SetType(CVariation_inst::eType_ins);
        instance.SetDelta().push_back(pItem);       
    }}
    variants.push_back(pVariant);
    return true;
}

示例#2

文件： vcf_reader.cpp 项目： swuecho/igblast

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDelins(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();

    CRef<CVariation_ref> pVariant(new CVariation_ref);
    {{
        string insertion(data.m_Alt[index]);
        CRef<CSeq_literal> pLiteral(new CSeq_literal);
        pLiteral->SetSeq_data().SetIupacna().Set(insertion);
        pLiteral->SetLength(insertion.size());
        CRef<CDelta_item> pItem(new CDelta_item);
        pItem->SetSeq().SetLiteral(*pLiteral); 
        CVariation_inst& instance =  pVariant->SetData().SetInstance();


        //Let's try to smartly set the Type.

        if( data.m_Alt[index].size() == 1 && data.m_strRef.size() == 1) {
          instance.SetType(CVariation_inst::eType_snv);
        } else {
          instance.SetType(CVariation_inst::eType_delins);
        }


        instance.SetDelta().push_back(pItem);       
    }}
    variants.push_back(pVariant);
    return true;
}

示例#3

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDel(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();

    CRef<CVariation_ref> pVariant(new CVariation_ref);
    {{
        //pVariant->SetData().SetNote("DEL");
        pVariant->SetDeletion();
        CVariation_inst& instance =  pVariant->SetData().SetInstance();
        CRef<CDelta_item> pItem(new CDelta_item);
        pItem->SetAction(CDelta_item::eAction_del_at);
        pItem->SetSeq().SetThis();
        instance.SetDelta().push_back(pItem);
    }}
    variants.push_back(pVariant);

    CRef<CVariation_ref> pIdentity(new CVariation_ref);
    {{
        //pIdentity->SetData().SetNote("IDENTITY");
        vector<string> variant;
        variant.push_back(data.m_strRef);
        pIdentity->SetSNV(variant, CVariation_ref::eSeqType_na);
        CVariation_inst& instance =  pIdentity->SetData().SetInstance();
        instance.SetType(CVariation_inst::eType_identity);
        instance.SetObservation(CVariation_inst::eObservation_asserted);
    }}
    variants.push_back(pIdentity);
    return true;
}

示例#4

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantSnv(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();

    CRef<CVariation_ref> pVariant(new CVariation_ref);
    {{
        vector<string> variant;
        variant.push_back(data.m_Alt[index]);
        pVariant->SetSNV(variant, CVariation_ref::eSeqType_na);
    }}
    variants.push_back(pVariant);

    CRef<CVariation_ref> pIdentity(new CVariation_ref);
    {{
        vector<string> variant;
        variant.push_back(data.m_strRef);
        pIdentity->SetSNV(variant, CVariation_ref::eSeqType_na);
        CVariation_inst& instance =  pIdentity->SetData().SetInstance();
        instance.SetType(CVariation_inst::eType_identity);
        instance.SetObservation(CVariation_inst::eObservation_asserted);
    }}
    variants.push_back(pIdentity);

    return true;
}

示例#5

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariationAlleles(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    if (data.IsSnv(index)) {
        return xAssignVariantSnv(data, index, pFeature);
    }
    if (data.IsDel(index)) {
        return xAssignVariantDel(data, index, pFeature);
    }
    if (data.IsIns(index)) {
        return xAssignVariantIns(data, index, pFeature);
    }
    if (data.IsDelins(index)) {
        return xAssignVariantDelins(data, index, pFeature);
    }
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
    CRef<CVariation_ref> pVariant(new CVariation_ref);
    string note("Warning: Could not place variation for record \"" + 
        NStr::Replace(data.m_strLine.substr(0, 40), "\t", "  "));
    if (data.m_strLine.size() > 40) {
        note += "...";
    }
    note += "\". Offending values: ref=\"" + data.m_strRef + 
        "\", alt=\"" + data.m_Alt[index] + "\"";
    pVariant->SetData().SetNote(note);
    variants.push_back(pVariant);
    return true;
}

示例#6

文件： vcf_reader.cpp 项目： swuecho/igblast

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantMnv(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();

    CRef<CVariation_ref> pVariant(new CVariation_ref);
    {{
        vector<string> variant;
        variant.push_back(data.m_Alt[index]);
        pVariant->SetMNP(variant, CVariation_ref::eSeqType_na);
    }}
    variants.push_back(pVariant);
    return true;
}

示例#7

文件： vcf_reader.cpp 项目： swuecho/igblast

//  ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDel(
    const CVcfData& data,
    unsigned int index,
    CRef<CSeq_feat> pFeature )
//  ----------------------------------------------------------------------------
{
    CVariation_ref::TData::TSet::TVariations& variants =
        pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();

    CRef<CVariation_ref> pVariant(new CVariation_ref);
    {{
        //pVariant->SetData().SetNote("DEL");
        pVariant->SetDeletion();
        CVariation_inst& instance =  pVariant->SetData().SetInstance();
        CRef<CDelta_item> pItem(new CDelta_item);
        pItem->SetAction(CDelta_item::eAction_del_at);
        pItem->SetSeq().SetThis();
        instance.SetDelta().push_back(pItem);
    }}
    variants.push_back(pVariant);
    return true;
}