qualifiers.cpp

来自「ncbi源码」· C++ 代码 · 共 730 行 · 第 1/2 页

    if ( s_IsNote(flags) ) {
        m_Suffix = (m_Value->GetSubtype() == COrgMod::eSubtype_other ? &kEOL : &kSemicolon);
        if ( name != "orgmod_note" ) {
            x_AddFQ(q, "note", name + ": " + subname);
        } else {
            x_AddFQ(q, "note", subname);
        }
    } else {
        x_AddFQ(q, name, subname);
    }
}


void CFlatOrganelleQVal::Format(TFlatQuals& q, const string& name,
                              CBioseqContext&, IFlatQVal::TFlags) const
{
    const string& organelle
        = CBioSource::GetTypeInfo_enum_EGenome()->FindName(m_Value, true);

    switch (m_Value) {
    case CBioSource::eGenome_chloroplast: case CBioSource::eGenome_chromoplast:
    case CBioSource::eGenome_cyanelle:    case CBioSource::eGenome_apicoplast:
    case CBioSource::eGenome_leucoplast:  case CBioSource::eGenome_proplastid:
        x_AddFQ(q, name, "plastid:" + organelle);
        break;

    case CBioSource::eGenome_kinetoplast:
        x_AddFQ(q, name, "mitochondrion:kinetoplast");
        break;

    case CBioSource::eGenome_mitochondrion: case CBioSource::eGenome_plastid:
    case CBioSource::eGenome_nucleomorph:
        x_AddFQ(q, name, organelle);
        break;

    case CBioSource::eGenome_macronuclear: case CBioSource::eGenome_proviral:
    case CBioSource::eGenome_virion:
        x_AddFQ(q, organelle, kEmptyStr, CFormatQual::eEmpty);
        break;

    case CBioSource::eGenome_plasmid: case CBioSource::eGenome_transposon:
        x_AddFQ(q, organelle, kEmptyStr);
        break;

    case CBioSource::eGenome_insertion_seq:
        x_AddFQ(q, "insertion_seq", kEmptyStr);
        break;

    default:
        break;
    }
    
}


void CFlatPubSetQVal::Format(TFlatQuals& q, const string& name,
                           CBioseqContext& ctx, IFlatQVal::TFlags) const
{
    ITERATE (vector< CRef<CReferenceItem> >, it, ctx.GetReferences()) {
        if ((*it)->Matches(*m_Value)) {
            x_AddFQ(q, name, '[' + NStr::IntToString((*it)->GetSerial()) + ']',
                    CFormatQual::eUnquoted);
        }
    }
}


void CFlatSeqIdQVal::Format(TFlatQuals& q, const string& name,
                          CBioseqContext& ctx, IFlatQVal::TFlags) const
{
    // XXX - add link in HTML mode
    string id_str;
    if ( m_Value->IsGi() ) {
        if ( m_GiPrefix ) {
            id_str = "GI:";
        }
        m_Value->GetLabel(&id_str, CSeq_id::eContent);
    } else {
        id_str = m_Value->GetSeqIdString(true);
    }
    x_AddFQ(q, name, id_str);
}


void CFlatSubSourceQVal::Format(TFlatQuals& q, const string& name,
                              CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
    string subname = m_Value->CanGetName() ? m_Value->GetName() : kEmptyStr;
    if ( s_StringIsJustQuotes(subname) ) {
        subname = kEmptyStr;
    }

    if ( s_IsNote(flags) ) {
        bool note = false;
        if ( m_Value->GetSubtype() == CSubSource::eSubtype_other ) {
            m_Suffix = &kEOL;
            note = true;
        } else {
            m_Suffix = &kSemicolon;
        }

        x_AddFQ(q, "note", note ? subname : name + ": " + subname);
    } else {
        CSubSource::TSubtype subtype = m_Value->GetSubtype();
        if ( subtype == CSubSource::eSubtype_germline            ||
             subtype == CSubSource::eSubtype_rearranged          ||
             subtype == CSubSource::eSubtype_transgenic          ||
             subtype == CSubSource::eSubtype_environmental_sample ) {
            x_AddFQ(q, name, kEmptyStr, CFormatQual::eEmpty);
        } else {
            x_AddFQ(q, name, subname);
        }
    }
}


void CFlatXrefQVal::Format(TFlatQuals& q, const string& name,
                         CBioseqContext& ctx, IFlatQVal::TFlags flags) const
{
    // XXX - add link in HTML mode?
    ITERATE (TXref, it, m_Value) {
        if ( !m_Quals.Empty()  &&  x_XrefInGeneXref(**it) ) {
            continue;
        }
        string s((*it)->GetDb());
        const CObject_id& id = (*it)->GetTag();
        switch ( id.Which() ) {
        case CObject_id::e_Id:
            s += ':' + NStr::IntToString(id.GetId());
            break;
        case CObject_id::e_Str:
            s += ':' + id.GetStr();
            break;
        default:
            break;
        }
        x_AddFQ(q, name, s);
    }
}


bool CFlatXrefQVal::x_XrefInGeneXref(const CDbtag& dbtag) const
{
    if ( !m_Quals->HasQual(eFQ_gene_xref) ) {
        return false;
    }

    typedef TQuals::const_iterator TQCI;
    pair<TQCI, TQCI> gxrefs = m_Quals->GetQuals(eFQ_gene_xref);
    for ( TQCI it = gxrefs.first; it != gxrefs.second; ++it ) {
        const CFlatXrefQVal* xrefqv =
            dynamic_cast<const CFlatXrefQVal*>(it->second.GetPointerOrNull());
        if ( xrefqv != 0 ) {
            ITERATE (TXref, dbt, xrefqv->m_Value) {
                if ( dbtag.Match(**dbt) ) {
                    return true;
                }
            }
        }
    }
    return false;
}


void CFlatModelEvQVal::Format
(TFlatQuals& q,
 const string& name,
 CBioseqContext& ctx,
 IFlatQVal::TFlags flags) const
{
    const string* method = 0;
    if ( m_Value->HasField("Method") ) {
        const CUser_field& uf = m_Value->GetField("Method");
        if ( uf.GetData().IsStr() ) {
            method = &uf.GetData().GetStr();
        }
    }

    size_t nm = 0;
    if ( m_Value->HasField("mRNA") ) {
        const CUser_field& field = m_Value->GetField("mRNA");
        if ( field.GetData().IsFields() ) {
            ITERATE (CUser_field::C_Data::TFields, it1, field.GetData().GetFields()) {
                const CUser_field& uf = **it1;
                if ( !uf.CanGetData()  ||  !uf.GetData().IsFields() ) {
                    continue;
                }
                ITERATE (CUser_field::C_Data::TFields, it2, uf.GetData().GetFields()) {
                    if ( !(*it2)->CanGetLabel() ) {
                        continue;
                    }
                    const CObject_id& oid = (*it2)->GetLabel();
                    if ( oid.IsStr() ) {
                        if ( oid.GetStr() == "accession" ) {
                            ++nm;
                        }
                    }
                }
            }
        }
    }

    CNcbiOstrstream text;
    text << "Derived by automated computational analysis";
    if ( method != 0  &&  !method->empty() ) {
         text << " using gene prediction method: " << *method;
    }
    text << ".";

    if ( nm > 0 ) {
        text << " Supporting evidence includes similarity to: " << nm << " mRNA";
        if ( nm > 1 ) {
            text << "s";
        }
    }

    x_AddFQ(q, name, CNcbiOstrstreamToString(text));
}


void CFlatGoQVal::Format
(TFlatQuals& q,
 const string& name,
 CBioseqContext& ctx,
 IFlatQVal::TFlags flags) const
{
    _ASSERT(m_Value->GetData().IsFields());
    bool is_ftable = ctx.Config().IsFormatFTable();

    if ( s_IsNote(flags) ) {
        static const string sfx = ";";
        m_Prefix = &kEOL;
        m_Suffix = &sfx;
        x_AddFQ(q, "note", name + ": " + s_GetGOText(*m_Value, is_ftable));
    } else {
        x_AddFQ(q, name, s_GetGOText(*m_Value, is_ftable));
    }
}


void CFlatAnticodonQVal::Format
(TFlatQuals& q,
 const string& name,
 CBioseqContext& ctx,
 IFlatQVal::TFlags flags) const
{
    if ( !m_Anticodon->IsInt()  ||  !m_Aa.empty() ) {
        return;
    }

    CSeq_loc::TRange range = m_Anticodon->GetTotalRange();
    CNcbiOstrstream text;
    text << "(pos:" << range.GetFrom() + 1 << ".." << range.GetTo() + 1
         << ",aa:" << m_Aa << ")";

    x_AddFQ(q, name, CNcbiOstrstreamToString(text), CFormatQual::eUnquoted);
}


void CFlatTrnaCodonsQVal::Format
(TFlatQuals& q,
 const string& name,
 CBioseqContext& ctx,
 IFlatQVal::TFlags flags) const
{
    // !!!
}


void CFlatProductQVal::Format
(TFlatQuals& q,
 const string& n,
 CBioseqContext& ctx,
 TFlags) const
{
    // !!!
    /*
    if ( ctx.DropIllegalQuals() ) {
        if ( !s_LegalQualForFeature(eFQ_product, m_Subtype)
    */
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: qualifiers.cpp,v $
* Revision 1000.1  2004/06/01 19:45:20  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
*
* Revision 1.15  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.14  2004/05/06 17:58:52  shomrat
* CFlatQual -> CFormatQual
*
* Revision 1.13  2004/04/27 15:13:16  shomrat
* fixed SubSource formatting
*
* Revision 1.12  2004/04/22 15:57:06  shomrat
* Changes in context
*
* Revision 1.11  2004/04/07 14:28:44  shomrat
* Fixed GO quals formatting for FTable format
*
* Revision 1.10  2004/03/30 20:32:53  shomrat
* Fixed go and modelev qual formatting
*
* Revision 1.9  2004/03/25 20:46:19  shomrat
* implement CFlatPubSetQVal formatting
*
* Revision 1.8  2004/03/18 15:43:27  shomrat
* Fixes to quals formatting
*
* Revision 1.7  2004/03/08 21:01:44  shomrat
* GI prefix flag for Seq-id quals
*
* Revision 1.6  2004/03/08 15:24:27  dicuccio
* FIxed dereference of string pointer
*
* Revision 1.5  2004/03/05 18:47:32  shomrat
* Added qualifier classes
*
* Revision 1.4  2004/02/11 16:55:38  shomrat
* changes in formatting of OrgMod and SubSource quals
*
* Revision 1.3  2004/01/14 16:18:07  shomrat
* uncomment code
*
* Revision 1.2  2003/12/18 17:43:35  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:24:04  shomrat
* Initial Revision (adapted from flat lib)
*
* Revision 1.4  2003/06/02 16:06:42  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.3  2003/03/21 18:49:17  ucko
* Turn most structs into (accessor-requiring) classes; replace some
* formerly copied fields with pointers to the original data.
*
* Revision 1.2  2003/03/11 15:37:51  kuznets
* iterate -> ITERATE
*
* Revision 1.1  2003/03/10 16:39:09  ucko
* Initial check-in of new flat-file generator
*
*
* ===========================================================================
*/