user_feat_table_reader.cpp

来自「ncbi源码」· C++ 代码 · 共 238 行

/*
 * ===========================================================================
 * PRODUCTION $Log: user_feat_table_reader.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 20:58:44  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: user_feat_table_reader.cpp,v 1000.3 2004/06/01 20:58:44 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:
 *
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
#include <gui/core/doc_exception.hpp>
#include <gui/core/doc_manager.hpp>
#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/utils/system_path.hpp>
#include <gui/core/version.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/utils/message_box.hpp>

#include <objmgr/object_manager.hpp>
#include <objects/seqset/Seq_entry.hpp>

#include <serial/iterator.hpp>
#include <serial/objostrasn.hpp>
#include <serial/serial.hpp>

#include "user_feat_table_reader.hpp"
#include <objtools/data_loaders/table/user_feature_dload.hpp>
#include <sqlite/sqlite.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CUsrFeatTableReader",
                 "Tabular user features",
                 "Load the contents of a table of user features",
                 "");

    // 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("offset", "Numbering convention in file",
                                   CPluginArg::eString, 
                                   "Start of sequence is 1");
    import_args.SetConstraint("offset", (*CPluginValueConstraint::CreateSet(),
                                          "Start of sequence is 1",
                                          "Start of sequence is 0"));

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

    import_args.AddOptionalArgument("type",
                      "\"type\" of user feature (overrides any in file)",
                       CPluginArg::eString);
}


void CUsrFeatTableReader::Import(CPluginMessage& msg)
{

    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();

    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();

    CUsrFeatDataLoader* loader = NULL;
    TLoaders::iterator iter = m_Loaders.find(fname);
    if (iter != m_Loaders.end()) {
        loader = iter->second;
    }

    string import_name;
    bool delete_file = true;
    if ( !CSQLite::IsValidDB(fname) ) {
        if (NcbiMessageBox("Do you want to save the generated SQL file "
                           "for future use?",
                           eDialog_YesNo, eIcon_Question,
                           "Save SQL File?") == eYes) {
            import_name = fname;
            import_name += ".db";
            delete_file = false;
        }
    } else {
        import_name = fname;
        delete_file = false;
    }

    if (import_name.empty()) {
        import_name = CSystemPath::ResolvePath("<home>", "tmp");
        CDir dir(import_name);
        if ( !dir.Exists() ) {
            dir.Create();
        }
        import_name = CFile::GetTmpNameEx(import_name, "tdb_");
    }

    // figure out parameters
    string offset_string = args["offset"].AsString();
    CUsrFeatDataLoader::EOffset offset;
    if (offset_string == "Start of sequence is 0") {
        offset = CUsrFeatDataLoader::eBeginIsZero;
    } else {
        offset = CUsrFeatDataLoader::eBeginIsOne;
    }

    const CSeq_id* id_to_use = 0;
    if (args["mode"].AsString() == "Use this ID") {
        id_to_use = id;
    }

    string type_string;
    if (args.HasArgument("type")  &&
        CPluginUtils::IsValid(args["type"])) {
        type_string = args["type"].AsString();
    }

    if ( !loader ) {
        try {
            loader = new CUsrFeatDataLoader(fname, import_name,
                                            delete_file, offset,
                                            type_string, id_to_use);
        }
        catch (exception& e) {
            NcbiMessageBox(e.what(), eDialog_Ok, eIcon_Exclamation);
            reply.SetStatus(eMessageStatus_failed);
            return;
        }
        CDocManager::GetObjectManager().RegisterDataLoader(*loader);
        m_Loaders[loader->GetName()] = loader;
    }


    // create our data loader
    CScope& scope = doc->GetScope();
    scope.AddDataLoader(loader->GetName(), 80);

    doc->PostDocumentChanged();

    reply.SetStatus(eMessageStatus_success);
}


END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: user_feat_table_reader.cpp,v $
 * Revision 1000.3  2004/06/01 20:58:44  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  2004/02/17 20:35:28  rsmith
 * moved core/settings.[ch]pp and core/system_path.[ch]pp to config and utils, respectively.
 *
 * Revision 1.7  2004/02/17 15:17:31  jcherry
 * Removed help url in favor of new help system
 *
 * Revision 1.6  2004/02/11 21:01:52  jcherry
 * Use file argument rather than manually launching file chooser
 *
 * Revision 1.5  2004/01/27 18:45:34  dicuccio
 * Added missing header files
 *
 * Revision 1.4  2003/12/22 19:30:11  dicuccio
 * Updated to match change in IDocument - UpdateAllViews() goes away
 *
 * Revision 1.3  2003/11/24 15:45:41  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.2  2003/11/14 21:30:15  jcherry
 * Added url for help
 *
 * Revision 1.1  2003/11/14 19:09:19  jcherry
 * Initial version
 *
 * ===========================================================================
 */