five_column_reader.cpp

来自「ncbi源码」· C++ 代码 · 共 203 行

/*
 * ===========================================================================
 * PRODUCTION $Log: five_column_reader.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:58:38  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: five_column_reader.cpp,v 1000.5 2004/06/01 20:58:38 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors: Josh Cherry
 *
 * File Description:   Plugin to load five-column feature table
 */


#include <ncbi_pch.hpp>
#include "five_column_reader.hpp"
#include <objtools/readers/readfeat.hpp>

#include <gui/core/idocument.hpp>
#include <gui/core/version.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginValue.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>

#include <objects/general/Int_fuzz.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_loc.hpp>

#include <corelib/ncbistd.hpp>
#include <objmgr/util/feature.hpp>
#include <serial/objostr.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


void CFiveColumnReader::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CFiveColumnReader",
                 "Five-column feature table",
                 "Load the contents of a five-column feature table",
                 "");

    // command info
    CPluginCommandSet& cmds     = info.SetCommands();
    CPluginCommand& import_args = cmds.AddDataCommand(eDataCommand_import);
    import_args.AddArgument("id", "ID",
                            CSeq_id::GetTypeInfo(),
                            CPluginArg::TData::e_Single);

    import_args.AddArgument("fname", "File to load", CPluginArg::eFile);
    import_args.AddDefaultArgument("mode", "Accession to use",
                                   CPluginArg::eString,
                                   "Use this ID");
    import_args.SetConstraint("mode", (*CPluginValueConstraint::CreateSet(),
                                       "Use this ID",
                                       "Get accession from file"));
}


void CFiveColumnReader::Import(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    reply.SetStatus(eMessageStatus_failed);
    LOG_POST(Info << "CFiveColumnReader::Load: start point.");

    const CPluginArg& arg = args["id"];
    IDocument* doc = const_cast<IDocument*>(arg.GetDocument());
    const CSeq_id* id = dynamic_cast<const CSeq_id*>(arg.GetObject());

    const string& fname = args["fname"].AsString();

    try {
        _TRACE("CFiveColumnReader::Load: reading file...");

        CNcbiIfstream is(fname.c_str());
        CRef<CSeq_annot> annot;
        if (args["mode"].AsString() == "Get accession from file") {
            annot = CFeature_table_reader::ReadSequinFeatureTable(is);
        } else {
            // use the id we're handed

            // may need to throw away the first line of file
            // (this allows use of a file that does have a
            // ">Features" line)
            string first;
            getline(is, first);
            if (!(first[0] == '>')) {
                // it's not a ">" line, so rewind the file
                is.seekg(0);
            }
            string id_string = id->GetSeqIdString();
            annot = CFeature_table_reader
                ::ReadSequinFeatureTable(is, id_string, fname);
        }

            
        // this is not the same 'name' that's filled in by
        // ReadSequinFeatureTable, which is within a desc
        annot->SetName(fname);
        string comment = string("Annotations loaded from file ")
            + fname;
        annot->AddComment(comment);

        // save the object in the reply for framework processing
        reply.AddObject(*doc, *annot);
        reply.AddAction(CPluginReplyAction::e_Add_to_document);
        reply.SetStatus(eMessageStatus_success);
    }

    catch (CException& e) {
        LOG_POST(Info << "failed to read five-column file: " << e.what());
        _TRACE("failed to read five-column file: " << e.what() );
    }
#ifndef _DEBUG
    catch (...) {
        _TRACE("failed to read five-column file: unknown error");
    }
#endif
}


END_NCBI_SCOPE


/*
 * =====================================================================
 * $Log: five_column_reader.cpp,v $
 * Revision 1000.5  2004/06/01 20:58:38  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 *
 * Revision 1.9  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.8  2004/02/13 15:11:28  mjohnson
 * Removed hardcoded plugin help URL
 *
 * Revision 1.7  2004/02/11 21:01:52  jcherry
 * Use file argument rather than manually launching file chooser
 *
 * Revision 1.6  2003/11/24 15:45:39  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.5  2003/11/18 17:49:26  dicuccio
 * Added standard processing of return values
 *
 * Revision 1.4  2003/11/14 00:20:30  jcherry
 * Added url for help
 *
 * Revision 1.3  2003/11/06 20:12:15  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.2  2003/11/04 17:49:25  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.1  2003/11/03 14:58:36  jcherry
 * Initial version
 *
 * =====================================================================
 */