genbank_formatter.cpp

来自「ncbi源码」· C++ 代码 · 共 757 行 · 第 1/2 页

    Wrap(l, "AUTHORS", auth, eSubp);
}


void CGenbankFormatter::x_Consortium
(list<string>& l,
 const CReferenceItem& ref,
 CBioseqContext& ctx) const
{
    Wrap(l, "CONSRTM", ref.GetConsortium(), eSubp);
}


void CGenbankFormatter::x_Title
(list<string>& l,
 const CReferenceItem& ref,
 CBioseqContext& ctx) const
{
    string title = ref.GetTitle();

    if ( NStr::EndsWith(title, ".") ) {
        title.erase(title.length() - 1);
    }
    
    Wrap(l, "TITLE",   title,   eSubp);
}


void CGenbankFormatter::x_Journal
(list<string>& l,
 const CReferenceItem& ref,
 CBioseqContext& ctx) const
{
    string journal;
    x_FormatRefJournal(journal, ref);
    Wrap(l, "JOURNAL", journal, eSubp);
}


void CGenbankFormatter::x_Medline
(list<string>& l,
 const CReferenceItem& ref,
 CBioseqContext& ctx) const
{
    if ( ref.GetMUID() != 0 ) {
        Wrap(l, GetWidth(), "MEDLINE", NStr::IntToString(ref.GetMUID()), eSubp);
    }
}


void CGenbankFormatter::x_Pubmed
(list<string>& l,
 const CReferenceItem& ref,
 CBioseqContext& ctx) const
{
    if ( ref.GetPMID() != 0 ) {
        Wrap(l, " PUBMED", NStr::IntToString(ref.GetPMID()), eSubp);
    }
}


void CGenbankFormatter::x_Remark
(list<string>& l,
 const CReferenceItem& ref,
 CBioseqContext& ctx) const
{
    Wrap(l, "REMARK", ref.GetRemark(), eSubp);
}


///////////////////////////////////////////////////////////////////////////
//
// COMMENT


void CGenbankFormatter::FormatComment
(const CCommentItem& comment,
 IFlatTextOStream& text_os)
{
    list<string> l;

    if ( !comment.IsFirst() ) {
        Wrap(l, kEmptyStr, comment.GetComment(), eSubp);
    } else {
        Wrap(l, "COMMENT", comment.GetComment());
    }

    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// FEATURES

// Fetures Header

void CGenbankFormatter::FormatFeatHeader
(const CFeatHeaderItem& fh,
 IFlatTextOStream& text_os)
{
    list<string> l;

    Wrap(l, "FEATURES", "Location/Qualifiers", eFeatHead);

    text_os.AddParagraph(l);
}


void CGenbankFormatter::FormatFeature
(const CFeatureItemBase& f,
 IFlatTextOStream& text_os)
{ 
    CConstRef<CFlatFeature> feat = f.Format();
    list<string>        l;
    Wrap(l, feat->GetKey(), feat->GetLoc().GetString(), eFeat);
    ITERATE (vector<CRef<CFormatQual> >, it, feat->GetQuals()) {
        string qual = '/' + (*it)->GetName(), value = (*it)->GetValue();
        switch ((*it)->GetStyle()) {
        case CFormatQual::eEmpty:
            value = qual;
            qual.erase();
            break;
        case CFormatQual::eQuoted:
            qual += "=\"";  value += '"';
            break;
        case CFormatQual::eUnquoted:
            qual += '=';
            break;
        }
        // Call NStr::Wrap directly to avoid unwanted line breaks right
        // before the start of the value (in /translation, e.g.)
        NStr::Wrap(value, GetWidth(), l,
                   /*DoHTML() ? NStr::fWrap_HTMLPre : */0, GetFeatIndent(),
                   GetFeatIndent() + qual);
    }
    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// BASE COUNT

void CGenbankFormatter::FormatBasecount
(const CBaseCountItem& bc,
 IFlatTextOStream& text_os)
{
    list<string> l;

    CNcbiOstrstream bc_line;

    bc_line.setf(IOS_BASE::right, IOS_BASE::adjustfield);
    bc_line
        << setw(7) << bc.GetA() << " a"
        << setw(7) << bc.GetC() << " c"
        << setw(7) << bc.GetG() << " g"
        << setw(7) << bc.GetT() << " t";
    if ( bc.GetOther() > 0 ) {
        bc_line << setw(7) << bc.GetOther() << " others";
    }
    Wrap(l, "BASE COUNT", CNcbiOstrstreamToString(bc_line));
    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// SEQUENCE

void CGenbankFormatter::FormatSequence
(const CSequenceItem& seq,
 IFlatTextOStream& text_os)
{
    list<string> l;
    CNcbiOstrstream seq_line;

    const CSeqVector& vec = seq.GetSequence();

    TSeqPos base_count = seq.GetFrom();
    CSeqVector::const_iterator iter = vec.begin();
    while ( iter ) {
        seq_line.setf(IOS_BASE::right, IOS_BASE::adjustfield);
        seq_line << setw(9) << base_count;
        for ( TSeqPos count = 0; count < 60  &&  iter; ++count, ++iter, ++base_count ) {
            if ( count % 10 == 0 ) {
                seq_line << ' ';
            }
            seq_line << (char)tolower(*iter);
        }
        seq_line << '\n';
    }

    NStr::Split(CNcbiOstrstreamToString(seq_line), "\n", l);
    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// DBSOURCE

void CGenbankFormatter::FormatDBSource
(const CDBSourceItem& dbs,
 IFlatTextOStream& text_os)
{
    list<string> l;

    if ( !dbs.GetDBSource().empty() ) {
        string tag = "DBSOURCE";
        ITERATE (list<string>, it, dbs.GetDBSource()) {
            Wrap(l, tag, *it);
            tag.erase();
        }
        if ( !l.empty() ) {
            text_os.AddParagraph(l);
        }
    }        
}


///////////////////////////////////////////////////////////////////////////
//
// WGS

void CGenbankFormatter::FormatWGS
(const CWGSItem& wgs,
 IFlatTextOStream& text_os)
{
    string tag;

    switch ( wgs.GetType() ) {
    case CWGSItem::eWGS_Projects:
        tag = "WGS";
        break;

    case CWGSItem::eWGS_ScaffoldList:
        tag = "WGS_SCAFLD";
        break;

    case CWGSItem::eWGS_ContigList:
        tag = "WGS_CONTIG";
        break;

    default:
        return;
    }

    list<string> l;
    if ( wgs.GetFirstID() == wgs.GetLastID() ) {
        Wrap(l, tag, wgs.GetFirstID());
    } else {
        Wrap(l, tag, wgs.GetFirstID() + "-" + wgs.GetLastID());
    }
    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// PRIMARY

void CGenbankFormatter::FormatPrimary
(const CPrimaryItem& primary,
 IFlatTextOStream& text_os)
{
    list<string> l;

    Wrap(l, "PRIMARY", primary.GetString());

    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// GENOME

void CGenbankFormatter::FormatGenome
(const CGenomeItem& genome,
 IFlatTextOStream& text_os)
{
    // !!!
}


///////////////////////////////////////////////////////////////////////////
//
// CONTIG

void CGenbankFormatter::FormatContig
(const CContigItem& contig,
 IFlatTextOStream& text_os)
{
    list<string> l;
    string assembly = CFlatSeqLoc(contig.GetLoc(), *contig.GetContext(), 
        CFlatSeqLoc::eType_assembly).GetString();
    Wrap(l, "CONTIG", assembly);
    text_os.AddParagraph(l);
}


///////////////////////////////////////////////////////////////////////////
//
// ORIGIN

void CGenbankFormatter::FormatOrigin
(const COriginItem& origin,
 IFlatTextOStream& text_os)
{
    list<string> l;
    if ( origin.GetOrigin().empty() ) {
        l.push_back("ORIGIN      ");
    } else {
        Wrap(l, "ORIGIN", origin.GetOrigin());
    }
    text_os.AddParagraph(l);
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: genbank_formatter.cpp,v $
* Revision 1000.2  2004/06/01 19:44:37  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.14
*
* Revision 1.14  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.13  2004/05/06 17:53:12  shomrat
* CFlatQual -> CFormatQual
*
* Revision 1.12  2004/04/22 15:59:59  shomrat
* Changes in context
*
* Revision 1.11  2004/04/13 16:47:53  shomrat
* Journal formatting moved to base class
*
* Revision 1.10  2004/03/26 17:25:36  shomrat
* fixes to reference formatting
*
* Revision 1.9  2004/03/18 15:40:28  shomrat
* Fixes to COMMENT formatting
*
* Revision 1.8  2004/03/10 21:29:01  shomrat
* Fix VERSION formatting when empty
*
* Revision 1.7  2004/03/05 18:46:05  shomrat
* fixed formatting of empty qualifier
*
* Revision 1.6  2004/02/19 18:13:12  shomrat
* Added formatting of Contig and Origin
*
* Revision 1.5  2004/01/14 16:16:39  shomrat
* removed const; using ctrl_items
*
* Revision 1.4  2003/12/19 00:14:44  ucko
* Eliminate remaining uses of LEFT and RIGHT manipulators.
*
* Revision 1.3  2003/12/18 21:23:41  ucko
* Avoid using LEFT and RIGHT manipulators lacking in GCC 2.9x.
*
* Revision 1.2  2003/12/18 17:43:34  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:22:12  shomrat
* Initial Revision (adapted from flat lib)
*
*
* ===========================================================================
*/