dbsource_item.cpp

来自「ncbi源码」· C++ 代码 · 共 523 行 · 第 1/2 页

    switch (sp.GetClass()) {
    case CSP_block::eClass_standard:
        m_DBSource.push_back("class: standard.");
        break;
    case CSP_block::eClass_prelim:
        m_DBSource.push_back("class: preliminary.");
        break;
    default:
        break;
    }
    // laid out slightly differently from the C version, but I think that's
    // a bug in the latter (which runs some things together)
    if (sp.CanGetExtra_acc()  &&  !sp.GetExtra_acc().empty() ) {
        m_DBSource.push_back("extra_accessions:"
                             + NStr::Join(sp.GetExtra_acc(), ","));
    }
    if (sp.GetImeth()) {
        m_DBSource.push_back("seq starts with Met");
    }
    if (sp.CanGetPlasnm()  &&  !sp.GetPlasnm().empty() ) {
        m_DBSource.push_back("plasmid:" + NStr::Join(sp.GetPlasnm(), ","));
    }
    if (sp.CanGetCreated()) {
        string s("created: ");
        sp.GetCreated().GetDate(&s, "%3N %D %Y");
        m_DBSource.push_back(s + '.');
    }
    if (sp.CanGetSequpd()) {
        string s("sequence updated: ");
        sp.GetSequpd().GetDate(&s, "%3N %D %Y");
        m_DBSource.push_back(s + '.');
    }
    if (sp.CanGetAnnotupd()) {
        string s("annotation updated: ");
        sp.GetAnnotupd().GetDate(&s, "%3N %D %Y");
        m_DBSource.push_back(s + '.');
    }
    if (sp.CanGetSeqref()  &&  !sp.GetSeqref().empty() ) {
        list<string> xrefs;
        ITERATE (CSP_block::TSeqref, it, sp.GetSeqref()) {
            const char* s = 0;
            switch ((*it)->Which()) {
            case CSeq_id::e_Genbank:  s = "genbank accession ";          break;
            case CSeq_id::e_Embl:     s = "embl accession ";             break;
            case CSeq_id::e_Pir:      s = "pir locus ";                  break;
            case CSeq_id::e_Swissprot: s = "swissprot accession ";       break;
            case CSeq_id::e_Gi:       s = "gi: ";                        break;
            case CSeq_id::e_Ddbj:     s = "ddbj accession ";             break;
            case CSeq_id::e_Prf:      s = "prf accession ";              break;
            case CSeq_id::e_Pdb:      s = "pdb accession ";              break;
            case CSeq_id::e_Tpg:   s = "genbank third party accession "; break;
            case CSeq_id::e_Tpe:      s = "embl third party accession "; break;
            case CSeq_id::e_Tpd:      s = "ddbj third party accession "; break;
            default:                  break;
            }
            if ( s ) {
                string acc = (*it)->GetSeqIdString(true);
                xrefs.push_back(s + acc);
            }
        }
        if ( !xrefs.empty() ) {
            m_DBSource.push_back("xrefs: " + NStr::Join(xrefs, ", "));
        }
    }
    if (sp.CanGetDbref()  &&  !sp.GetDbref().empty() ) {
        list<string> xrefs;
        ITERATE (CSP_block::TDbref, it, sp.GetDbref()) {
            const CObject_id& tag = (*it)->GetTag();
            string id = (tag.IsStr() ? tag.GetStr()
                                     : NStr::IntToString(tag.GetId()));
            if ((*it)->GetDb() == "MIM") {
                xrefs.push_back
                    ("MIM <a href=\""
                     "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=" + id
                     + "\">" + id + "</a>");
            } else {
                xrefs.push_back((*it)->GetDb() + id); // no space(!)
            }
        }
        m_DBSource.push_back
            ("xrefs (non-sequence databases): " + NStr::Join(xrefs, ", "));
    }
}


void CDBSourceItem::x_AddPRFBlock(CBioseqContext& ctx)
{
    CSeqdesc_CI dsc(ctx.GetHandle(), CSeqdesc::e_Prf);
    if ( !dsc ) {
        return;
    }

    x_SetObject(*dsc);

    const CPRF_block& prf = dsc->GetPrf();
    if (prf.CanGetExtra_src()) {
        const CPRF_ExtraSrc& es = prf.GetExtra_src();
        if (es.CanGetHost()) {
            m_DBSource.push_back("host: " + es.GetHost());
        }
        if (es.CanGetPart()) {
            m_DBSource.push_back("part: " + es.GetPart());
        }
        if (es.CanGetState()) {
            m_DBSource.push_back("state: " + es.GetState());
        }
        if (es.CanGetStrain()) {
            m_DBSource.push_back("strain: " + es.GetStrain());
        }
        if (es.CanGetTaxon()) {
            m_DBSource.push_back("taxonomy: " + es.GetTaxon());
        }
    }
    NON_CONST_ITERATE (list<string>, it, m_DBSource) {
        *it += (&*it == &m_DBSource.back() ? '.' : ';');
    }
}


void CDBSourceItem::x_AddPDBBlock(CBioseqContext& ctx)
{
    CSeqdesc_CI dsc(ctx.GetHandle(), CSeqdesc::e_Pdb);
    if ( !dsc ) {
        return;
    }

    x_SetObject(*dsc);

    const CPDB_block& pdb = dsc->GetPdb();
    {{
        string s("deposition: ");
        DateToString(pdb.GetDeposition(), s);
        m_DBSource.push_back(s);
    }}
    m_DBSource.push_back("class: " + pdb.GetClass());
    if (!pdb.GetSource().empty() ) {
        m_DBSource.push_back("source: " + NStr::Join(pdb.GetSource(), ", "));
    }
    if (pdb.CanGetExp_method()) {
        m_DBSource.push_back("Exp. method: " + pdb.GetExp_method());
    }
    if (pdb.CanGetReplace()) {
        const CPDB_replace& rep = pdb.GetReplace();
        if ( !rep.GetIds().empty() ) {
            m_DBSource.push_back
                ("ids replaced: " + NStr::Join(pdb.GetSource(), ", "));
        }
        string s("replacement date: ");
        DateToString(rep.GetDate(), s);
        m_DBSource.push_back(s);
    }
    NON_CONST_ITERATE (list<string>, it, m_DBSource) {
        *it += (&*it == &m_DBSource.back() ? '.' : ';');
    }
}


string CDBSourceItem::x_FormatDBSourceID(const CSeq_id& id) {
    switch ( id.Which() ) {
    case CSeq_id::e_Local:
        {{
            const CObject_id& oi = id.GetLocal();
            return (oi.IsStr() ? oi.GetStr() : NStr::IntToString(oi.GetId()));
        }}
    case CSeq_id::e_Gi:
        {{
            return "gi: " + NStr::IntToString(id.GetGi());
        }}
    case CSeq_id::e_Pdb:
        {{
            const CPDB_seq_id& pdb = id.GetPdb();
            string s("pdb: "), sep;
            if ( !pdb.GetMol().Get().empty() ) {
                s += "molecule " + pdb.GetMol().Get();
                sep = ",";
            }
            if (pdb.GetChain() > 0) {
                s += sep + "chain " + NStr::IntToString(pdb.GetChain());
                sep = ",";
            }
            if (pdb.CanGetRel()) {
                s += sep + "release ";
                DateToString(pdb.GetRel(), s);
                sep = ",";
            }
            return s;
        }}
    default:
        {{
            const CTextseq_id* tsid = id.GetTextseq_Id();
            if ( !tsid ) {
                return kEmptyStr;
            }
            string s, sep, comma;
            switch (id.Which()) {
            case CSeq_id::e_Embl:       s = "embl ";        comma = ",";  break;
            case CSeq_id::e_Other:      s = "REFSEQ: ";                   break;
            case CSeq_id::e_Swissprot:  s = "swissprot: ";  comma = ",";  break;
            case CSeq_id::e_Pir:        s = "pir: ";                      break;
            case CSeq_id::e_Prf:        s = "prf: ";                      break;
            default:                    break;
            }
            if ( tsid->CanGetName() ) {
                s += "locus " + tsid->GetName();
                sep = " ";
            } else {
                comma.erase();
            }
            if (tsid->CanGetAccession()) {
                string acc = tsid->GetAccession();
                if (tsid->CanGetVersion()) {
                    acc += '.' + NStr::IntToString(tsid->GetVersion());
                }
                s += comma + sep + "accession " + acc;
                sep = " ";
            }
            if (tsid->CanGetRelease()) {
                s += sep + "release " + tsid->GetRelease();
            }
            if (id.IsSwissprot()) {
                s += ';';
            }
            return s;
        }}
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: dbsource_item.cpp,v $
* Revision 1000.1  2004/06/01 19:44:02  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
*
* Revision 1.6  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.5  2004/04/22 15:55:04  shomrat
* Changes in context
*
* Revision 1.4  2004/03/25 20:36:31  shomrat
* Use handles
*
* Revision 1.3  2004/03/16 19:07:25  vasilche
* Use CConstRef<CSeq_id> to store returned CConstRef<CSeq_id>.
*
* Revision 1.2  2003/12/18 17:43:32  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:19:33  shomrat
* Initial Revision (adapted from flat lib)
*
*
* ===========================================================================
*/