id1_fetch.cpp

ncbi源码

        return s + string(m_Width - s.size(), ' ');
    }
    SIZE_TYPE Width()  const { return m_Width; }
    size_t    Height() const { return m_Strings.size(); }
 
private:
    SIZE_TYPE      m_Width;
    vector<string> m_Strings;
};


void CId1FetchApp::WriteHistoryTable(const CID1server_back& id1_reply)
{
    CTextColumn gis, dates, dbs, numbers;
    gis.Add("GI").Add("--");
    dates.Add("Loaded").Add("------");
    dbs.Add("DB").Add("--");
    numbers.Add("Retrieval No.").Add("-------------");
    for (CTypeConstIterator<CSeq_hist_rec> it = ConstBegin(id1_reply);
         it;  ++it) {
        int    gi = 0;
        string dbname, number;

        if ( it->GetDate().IsStr() ) {
            dates.Add(it->GetDate().GetStr());
        } else {
            CNcbiOstrstream oss;
            const CDate_std& date = it->GetDate().GetStd();
            oss << setfill('0') << setw(2) << date.GetMonth() << '/'
                << setw(2) << date.GetDay() << '/' << date.GetYear();
            dates.Add(CNcbiOstrstreamToString(oss));
        }

        ITERATE (CSeq_hist_rec::TIds, it2, it->GetIds()) {
            if ( (*it2)->IsGi() ) {
                gi = (*it2)->GetGi();
            } else if ( (*it2)->IsGeneral() ) {
                dbname = (*it2)->GetGeneral().GetDb();
                const CObject_id& tag = (*it2)->GetGeneral().GetTag();
                if ( tag.IsStr() ) {
                    number = tag.GetStr();
                } else {
                    number = NStr::IntToString(tag.GetId());
                }
            }
        }

        gis.Add(NStr::IntToString(gi));
        dbs.Add(dbname);
        numbers.Add(number);
    }

    for (unsigned int n = 0;  n < gis.Height();  n++) {
        *m_OutputFile << gis.Get(n) << "  " << dates.Get(n) << "  "
                      << dbs.Get(n) << "  " << numbers.Get(n) << NcbiEndl;
    }
}



void CId1FetchApp::WriteQualityScores(CBioseq_Handle& handle)
{   
    /* Test case:
     * /net/ncbi/ncbi/ftp/genbank/quality_scores/gbvrt.qscore.gz
     *  GI 13508865: gotseqentry.set.annot.data.graph
     *  >AL590146.2 Phrap Quality (Length:121086, Min: 31, Max: 99)
     *   99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
     *   ...
     */
    string id = FindBestChoice(handle.GetBioseqCore()->GetId(), CSeq_id::Score)
        ->GetSeqIdString(true);
    
    for (CGraph_CI it(handle, 0, 0);  it;  ++it) {
        string title = it->GetTitle();
        if (title.find("uality") == NPOS) {
            continue;
        }

        const CByte_graph& data = it->GetGraph().GetByte();
        *m_OutputFile << '>' << id << ' ' << title
                      << " (Length: " << it->GetNumval()
                      << ", Min: " << data.GetMin()
                      << ", Max: " << data.GetMax() << ')' << NcbiEndl;
        for (SIZE_TYPE n = 0;  n < data.GetValues().size();  ++n) {
            *m_OutputFile << setw(3) << static_cast<int>(data.GetValues()[n]);
            if (n % 20 == 19) {
                *m_OutputFile << NcbiEndl;
            }
        }
    }
}

END_NCBI_SCOPE



/////////////////////////////////////////////////////////////////////////////
//  MAIN
//

USING_NCBI_SCOPE;

int main(int argc, const char* argv[]) 
{
    return CId1FetchApp().AppMain(argc, argv);
}

/*
* ===========================================================================
*
* ---------------------------------------------------------------------------
* $Log: id1_fetch.cpp,v $
* Revision 1000.2  2004/06/01 18:30:30  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.50
*
* Revision 1.50  2004/05/21 21:41:40  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.49  2004/04/26 20:46:11  ucko
* Fix typo that accidentally introduced an implicit temporary CSeq_id.
*
* Revision 1.48  2004/04/26 16:53:17  ucko
* Don't try to pass temporary CSeq_id objects, even by const reference,
* as CSeq_id has no public copy constructor.
*
* Revision 1.47  2004/01/05 17:59:32  vasilche
* Moved genbank loader and its readers sources to new location in objtools.
* Genbank is now in library libncbi_xloader_genbank.
* Id1 reader is now in library libncbi_xreader_id1.
* OBJMGR_LIBS macro updated correspondingly.
*
* Old headers temporarily will contain redirection to new location
* for compatibility:
* objmgr/gbloader.hpp > objtools/data_loaders/genbank/gbloader.hpp
* objmgr/reader_id1.hpp > objtools/data_loaders/genbank/readers/id1/reader_id1.hpp
*
* Revision 1.46  2003/10/21 13:48:48  grichenk
* Redesigned type aliases in serialization library.
* Fixed the code (removed CRef-s, added explicit
* initializers etc.)
*
* Revision 1.45  2003/06/02 16:06:16  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 1.44  2003/05/13 17:14:17  ucko
* Direct flat output to *m_OutputFile rather than hard-coding cout.
*
* Revision 1.43  2003/04/24 16:17:10  vasilche
* Added '-repeat' option.
* Updated includes.
*
* Revision 1.42  2003/04/09 16:00:15  ucko
* Give all RPC clients unique basenames.
*
* Revision 1.41  2003/04/03 17:45:25  ucko
* Switch to new (differently buggy ;-)) flat-file generator.
* Drop s_SplitString, as NStr::Tokenize does the same thing.
*
* Revision 1.40  2003/03/10 18:48:48  kuznets
* iterate->ITERATE
*
* Revision 1.39  2002/11/13 20:14:51  ucko
* Rework to take advantage of new ID1 and Entrez2 client classes
* generated by datatool
*
* Revision 1.38  2002/08/27 21:41:53  ucko
* Use CFastaOstream rather than custom code.
* Fix spelling of NONEXISTENT.
*
* Revision 1.37  2002/08/14 20:28:02  ucko
* Fix behavior when given a list of IDs.
*
* Revision 1.36  2002/07/11 14:23:48  gouriano
* exceptions replaced by CNcbiException-type ones
*
* Revision 1.35  2002/06/28 17:25:53  grichenk
* +Error message if a GI was not found
*
* Revision 1.34  2002/06/12 16:51:55  lavr
* Take advantage of CONNECT_Init()
*
* Revision 1.33  2002/06/07 16:11:40  ucko
* GetTitle() is now in sequence::.
*
* Revision 1.32  2002/06/06 23:46:24  vakatov
* Use GetTitle() from <objects/util/sequence.hpp>
*
* Revision 1.31  2002/05/06 16:13:46  ucko
* Merge in Andrei Gourianov's changes to use the new OM (thanks!)
* Remove some dead code.
* Don't automatically turn on tracing, even when building with _DEBUG;
* it is always possible to set DIAG_TRACE in the environment instead.
* Move CVS log to end.
*
*
* *** These four entries are from src/app/id1_fetch1/id1_fetch1.cpp ***
* Revision 1.5  2002/05/06 03:31:52  vakatov
* OM/OM1 renaming
*
* Revision 1.4  2002/05/03 21:28:21  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.3  2002/04/10 21:02:21  gouriano
* moved construction of iterators out of "for" loop initialization:
* Sun Workshop compiler does not call destructors of such objects
* in case we use break to exit the loop
*
* Revision 1.2  2002/04/10 16:07:30  gouriano
* corrected data output in different formats
*
* Revision 1.1  2002/04/04 16:31:36  gouriano
* id1_fetch1 - modified version of id1_fetch, which uses objmgr1
*
* Revision 1.29  2002/03/11 21:52:05  lavr
* Print complete debug and trace information when compiled with _DEBUG
*
* Revision 1.28  2002/01/16 22:14:00  ucko
* Removed CRef<> argument from choice variant setter, updated sources to
* use references instead of CRef<>s
*
* Revision 1.27  2001/12/07 21:15:16  ucko
* Remove duplicate includes.
*
* Revision 1.26  2001/12/07 21:11:01  grichenk
* Fixed includes to work with the updated datatool
*
* Revision 1.25  2001/12/07 21:03:47  ucko
* Add #includes required by new datatool version.
*
* Revision 1.24  2001/11/16 16:06:45  ucko
* Handle new Entrez docsum interface properly.
*
* Revision 1.23  2001/10/26 14:49:16  ucko
* Restructured to avoid CRefs as arguments.
*
* Revision 1.22  2001/10/23 20:05:12  ucko
* Request ASCII from CSeq_vector.
*
* Revision 1.21  2001/10/17 21:17:53  ucko
* Seq_vector now properly starts from zero rather than one; adjust code
* that uses it accordingly.
*
* Revision 1.20  2001/10/12 19:32:58  ucko
* move BREAK to a central location; move CBioseq::GetTitle to object manager
*
* Revision 1.19  2001/10/12 15:34:01  ucko
* Edit in-source version of CVS log to avoid end-of-comment marker.  (Oops.)
*
* Revision 1.18  2001/10/12 15:29:08  ucko
* Drop {src,include}/objects/util/asciiseqdata.* in favor of CSeq_vector.
* Rewrite GenBank output code to take fuller advantage of the object manager.
*
* Revision 1.17  2001/10/10 16:02:53  ucko
* Clean up includes.
*
* Revision 1.16  2001/10/04 19:11:56  ucko
* Centralize (rudimentary) code to get a sequence's title.
*
* Revision 1.15  2001/09/25 20:31:13  ucko
* Work around bug in Workshop's handling of declarations in for-loop
* initializers.
*
* Revision 1.14  2001/09/25 20:12:02  ucko
* More cleanups from Denis.
* Put utility code in the objects namespace.
* Moved utility code to {src,include}/objects/util (to become libxobjutil).
* Moved static members of CGenbankWriter to above their first use.
*
* Revision 1.13  2001/09/25 13:26:36  lavr
* CConn_ServiceStream() - arguments adjusted
*
* Revision 1.12  2001/09/24 03:22:09  vakatov
* Un-#include <cstdlib> and <cctype> which break IRIX/MIPSpro compilation and
* apparently are not needed after all
*
* Revision 1.11  2001/09/21 22:38:59  ucko
* Cope with new Entrez interface; fix MSVC build.
*
* Revision 1.10  2001/09/05 16:25:56  ucko
* Adapted to latest revision of object manager interface.
*
* Revision 1.9  2001/09/05 14:44:37  ucko
* Use NStr::IntToString instead of Stringify.
*
* Revision 1.8  2001/09/04 16:20:53  ucko
* Dramatically fleshed out id1_fetch
*
* Revision 1.7  2001/07/19 19:40:20  lavr
* Typo fixed
*
* Revision 1.6  2001/06/01 18:43:44  vakatov
* Comment out excessive debug/trace printout
*
* Revision 1.5  2001/05/16 17:55:37  grichenk
* Redesigned support for non-blocking stream read operations
*
* Revision 1.4  2001/05/11 20:41:16  grichenk
* Added support for non-blocking stream reading
*
* Revision 1.3  2001/05/11 14:06:45  grichenk
* The first working revision
*
* Revision 1.2  2001/04/13 14:09:34  grichenk
* Next debug version, still not working
*
* Revision 1.1  2001/04/10 22:39:04  vakatov
* Initial revision.
* Compiles and links, but apparently is not working yet.
*
* ===========================================================================
*/