flat_reference.cpp

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    }
    if (gen.IsSetSerial_number()  &&  !m_Serial) {
        m_Serial = gen.GetSerial_number();
    }
    if (gen.IsSetTitle()  &&  m_Title.empty()) {
        m_Title = gen.GetTitle();
    }
    if (gen.IsSetPmid()) {
        m_PMIDs.insert(gen.GetPmid());
    }
}


void CFlatReference::x_Init(const CCit_sub& sub, const CFlatContext& /* ctx */)
{
    m_Category = eSubmission;
    x_AddAuthors(sub.GetAuthors());
    if (sub.GetAuthors().IsSetAffil()) {
        s_FormatAffil(sub.GetAuthors().GetAffil(), m_Journal);
    }
    if (sub.IsSetDate()) {
        m_Date = &sub.GetDate();
    } else {
        // complain?
        if (sub.IsSetImp()) {
            m_Date = &sub.GetImp().GetDate();
        }
    }
}


void CFlatReference::x_Init(const CMedline_entry& mle, const CFlatContext& ctx)
{
    m_Category = ePublished;
    if (mle.IsSetUid()) {
        m_MUIDs.insert(mle.GetUid());
    }
    m_Date = &mle.GetEm();
    if (mle.IsSetPmid()) {
        m_PMIDs.insert(mle.GetPmid());
    }
    x_Init(mle.GetCit(), ctx);
}


void CFlatReference::x_Init(const CCit_art& art, const CFlatContext& ctx)
{
    if (art.IsSetTitle()  &&  !art.GetTitle().Get().empty() ) {
        m_Title = art.GetTitle().GetTitle();
    }
    if (art.IsSetAuthors()) {
        x_AddAuthors(art.GetAuthors());
    }
    switch (art.GetFrom().Which()) {
    case CCit_art::C_From::e_Journal:
        x_Init(art.GetFrom().GetJournal(), ctx);
        break;
    case CCit_art::C_From::e_Book:
        x_Init(art.GetFrom().GetBook(), ctx);
        break;
    case CCit_art::C_From::e_Proc:
        x_Init(art.GetFrom().GetProc().GetBook(), ctx);
        break;
    default:
        break;
    }
    if (art.IsSetIds()) {
        ITERATE (CArticleIdSet::Tdata, it, art.GetIds().Get()) {
            switch ((*it)->Which()) {
            case CArticleId::e_Pubmed:
                m_PMIDs.insert((*it)->GetPubmed());
                break;
            case CArticleId::e_Medline:
                m_MUIDs.insert((*it)->GetMedline());
                break;
            default:
                break;
            }
        }
    }
}


void CFlatReference::x_Init(const CCit_jour& jour, const CFlatContext& ctx)
{
    x_SetJournal(jour.GetTitle(), ctx);
    x_AddImprint(jour.GetImp(), ctx);
}


void CFlatReference::x_Init(const CCit_book& book, const CFlatContext& ctx)
{
    // XXX -- should add more stuff to m_Journal (exactly what depends on
    // the format and whether this is for an article)
    if ( !book.GetTitle().Get().empty() ) {
        m_Journal = book.GetTitle().GetTitle();
    }
    if (m_Authors.empty()) {
        x_AddAuthors(book.GetAuthors());
    }
    x_AddImprint(book.GetImp(), ctx);
}


void CFlatReference::x_Init(const CCit_pat& pat, const CFlatContext& ctx)
{
    m_Title = pat.GetTitle();
    x_AddAuthors(pat.GetAuthors());
    int seqid = 0;
    ITERATE (CBioseq::TId, it, ctx.GetHandle().GetBioseqCore()->GetId()) {
        if ((*it)->IsPatent()) {
            seqid = (*it)->GetPatent().GetSeqid();
        }
    }
    // XXX - same for EMBL?
    if (pat.IsSetNumber()) {
        m_Category = ePublished;
        m_Journal = "Patent: " + pat.GetCountry() + ' ' + pat.GetNumber()
            + '-' + pat.GetDoc_type() + ' ' + NStr::IntToString(seqid);
        if (pat.IsSetDate_issue()) {
            ctx.GetFormatter().FormatDate(pat.GetDate_issue(), m_Journal);
        }
        m_Journal += ';';
    } else {
        // ...
    }
}


void CFlatReference::x_Init(const CCit_let& man, const CFlatContext& ctx)
{
    x_Init(man.GetCit(), ctx);
    if (man.IsSetType()  &&  man.GetType() == CCit_let::eType_thesis) {
        const CImprint& imp = man.GetCit().GetImp();
        m_Journal = "Thesis (";
        imp.GetDate().GetDate(&m_Journal, "%Y");
        m_Journal += ')';
        if (imp.IsSetPrepub()
            &&  imp.GetPrepub() == CImprint::ePrepub_in_press) {
            m_Journal += ", In press";
        }
        if (imp.IsSetPub()) {
            string affil;
            s_FormatAffil(imp.GetPub(), affil);
            replace(affil.begin(), affil.end(), '\"', '\'');
            m_Journal += ' ' + affil;
        }
    }
}


static string& s_FixMedlineName(string& s)
{
    SIZE_TYPE space = s.find(' ');
    if (space) {
        s[space] = ',';
        for (SIZE_TYPE i = space + 1;  i < s.size();  ++i) {
            if (s[i] == ' ') {
                break;
            } else if (isupper(s[i])) {
                s.insert(++i, 1, ',');
            }
        }
    }
    return s;
}


void CFlatReference::x_AddAuthors(const CAuth_list& auth)
{
    typedef CAuth_list::C_Names TNames;
    const TNames& names = auth.GetNames();
    switch (names.Which()) {
    case TNames::e_Std:
        ITERATE (TNames::TStd, it, names.GetStd()) {
            const CPerson_id& name = (*it)->GetName();
            switch (name.Which()) {
            case CPerson_id::e_Name:
            {
                const CName_std& ns = name.GetName();
                string           s  = ns.GetLast();
                if (ns.IsSetInitials()) {
                    s += ',' + ns.GetInitials();
                } else if (ns.IsSetFirst()) {
                    s += ',' + ns.GetFirst()[0] + '.';
                    if (ns.IsSetMiddle()) {
                        s += ns.GetMiddle()[0] + '.';
                    }
                }
                // suffix?
                m_Authors.push_back(s);
                break;
            }
            case CPerson_id::e_Ml:
            {
                string s = name.GetMl();
                m_Authors.push_back(s_FixMedlineName(s));
                break;
            }
            case CPerson_id::e_Str:
                m_Authors.push_back(name.GetStr());
                break;
            case CPerson_id::e_Consortium:
                m_Consortium = name.GetConsortium();
                break;
            default:
                // complain?
                break;
            }
        }
        break;

    case TNames::e_Ml:
        ITERATE (TNames::TMl, it, names.GetMl()) {
            string s = *it;
            m_Authors.push_back(s_FixMedlineName(s));
        }
        break;

    case TNames::e_Str:
        m_Authors.insert(m_Authors.end(),
                         names.GetStr().begin(), names.GetStr().end());
        break;

    default:
        break;
    }
}


void CFlatReference::x_SetJournal(const CTitle& title, const CFlatContext& ctx)
{
    ITERATE (CTitle::Tdata, it, title.Get()) {
        if ((*it)->IsIso_jta()) {
            m_Journal = (*it)->GetIso_jta();
            return;
        }
    }
    if (ctx.GetFormatter().GetMode() == IFlatFormatter::eMode_Release) {
        // complain
    } else if ( !title.Get().empty() ) {
        m_Journal = title.GetTitle();
    }
}


void CFlatReference::x_AddImprint(const CImprint& imp, const CFlatContext& ctx)
{
    if ( !m_Date ) {
        m_Date.Reset(&imp.GetDate());
    }
    if (imp.IsSetVolume()) {
        // add part-sup?
        m_Volume = imp.GetVolume();
    }
    if (imp.IsSetIssue()) {
        // add part-supi?
        m_Issue = imp.GetIssue();
    }
    if (imp.IsSetPages()) {
        m_Pages = imp.GetPages();
        // Restore redundant leading digits of the second number if needed
        SIZE_TYPE digits1 = m_Pages.find_first_not_of("0123456789");
        if (digits1 != 0) {
            SIZE_TYPE hyphen = m_Pages.find('-', digits1);
            if (hyphen != NPOS) {
                SIZE_TYPE digits2 = m_Pages.find_first_not_of("0123456789",
                                                              hyphen + 1);
                digits2 -= hyphen + 1;
                if (digits2 < digits1) {
                    // lengths of the tail portions
                    SIZE_TYPE len1 = hyphen + digits2 - digits1;
                    SIZE_TYPE len2 = m_Pages.size() - hyphen - 1;
                    int x = NStr::strncasecmp(&m_Pages[digits1 - digits2],
                                              &m_Pages[hyphen + 1],
                                              min(len1, len2));
                    if (x > 0  ||  (x == 0  &&  len1 >= len2)) {
                        // complain?
                    } else {
                        m_Pages.insert(hyphen + 1, m_Pages, 0,
                                       digits1 - digits2);
                    }
                }
            }
        }
    }
    if (imp.IsSetPrepub()  &&  imp.GetPrepub() != CImprint::ePrepub_in_press) {
        m_Category = eUnpublished;
    } else {
        m_Category = ePublished;
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: flat_reference.cpp,v $
* Revision 1000.2  2004/06/01 19:43:28  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11
*
* Revision 1.11  2004/05/21 21:42:53  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.10  2003/12/02 19:22:17  ucko
* Properly detect unpublished references, and give them a pseudo-journal
* of Unpublished.
*
* Revision 1.9  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 1.8  2003/04/24 16:15:58  vasilche
* Added missing includes and forward class declarations.
*
* Revision 1.7  2003/04/09 20:03:11  ucko
* Fix unsafe assumptions in CFlatReference::Matches.
*
* Revision 1.6  2003/03/28 17:46:21  dicuccio
* Added missing include for CAnnotObject_Info because MSVC gets confused
* otherwise....
*
* Revision 1.5  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 1.4  2003/03/11 15:37:51  kuznets
* iterate -> ITERATE
*
* Revision 1.3  2003/03/10 22:06:04  ucko
* Explicitly call NotEmpty to avoid a bogus MSVC error.
* Fix a typo that interpreted some MUIDs as PMIDs.
*
* Revision 1.2  2003/03/10 20:18:16  ucko
* Fix broken call to string::insert (caught by Compaq's compiler).
*
* Revision 1.1  2003/03/10 16:39:09  ucko
* Initial check-in of new flat-file generator
*
*
* ===========================================================================
*/