agp_reader.cpp

来自「ncbi源码」· C++ 代码 · 共 209 行

/*
 * ===========================================================================
 * PRODUCTION $Log: agp_reader.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 20:57:21  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: agp_reader.cpp,v 1000.1 2004/06/01 20:57:21 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:
 *    CDataPlugin_AgpReader - load information from an agp file
 */

#include <ncbi_pch.hpp>
#include "agp_reader.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/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 <gui/objutils/utils.hpp>

#include <objects/general/Object_id.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Seq_descr.hpp>

#include <objtools/readers/agp_read.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

static const string sc_separate = "Load each sequence as a separate document";
static const string sc_together = "Group all sequences in a single document";

//
// factory implementations
//

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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CDataPlugin_AgpReader",
                 "AGP File", "Read a file in AGP format",
                 "");

    // command info
    CPluginCommandSet& cmds     = info.SetCommands();
    CPluginCommand& load_args   = cmds.AddDataCommand(eDataCommand_load);

    load_args.AddArgument("fname", "File to load", CPluginArg::eFile);
    load_args.AddDefaultArgument("mode", "Treatment of multiple sequences",
                                 CPluginArg::eString, sc_separate);
    load_args.SetConstraint("mode", (*CPluginValueConstraint::CreateSet(),
                                     sc_separate, sc_together));
}


//
// Default ctor
//
CDataPlugin_AgpReader::CDataPlugin_AgpReader()
{
}


//
// One and only dtor
//
CDataPlugin_AgpReader::~CDataPlugin_AgpReader()
{
}


//
// Load()
// This is a pure virtual requirement and is the main plugin hook.
//
void CDataPlugin_AgpReader::Load(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    const string& fname = args["fname"].AsString();

    try {
        CNcbiIfstream istr(fname.c_str());

        if (args["mode"].AsString() == sc_separate) {
            vector<CRef<CSeq_entry> > entries;
            AgpRead(istr, entries);
            
            NON_CONST_ITERATE(vector<CRef<CSeq_entry> >, iter, entries) {
                CRef<CSeq_entry> &entry = *iter;
                CRef<CScope> 
                    scope(new CScope(CDocManager::GetObjectManager()));
                scope->AddTopLevelSeqEntry(*entry);
                scope->AddDefaults();
                IDocument* doc = CDocManager::CreateDocument(*scope, *entry);
                reply.AddObject(*doc);
            }
        } else if (args["mode"].AsString() == sc_together) {
            CRef<CBioseq_set> bioseq_set = AgpRead(istr);

            CRef<CSeqdesc> title(new CSeqdesc);
            title->SetTitle(string("Sequences from file ") + fname);
            bioseq_set->SetDescr().Set().push_back(title);

            CRef<CSeq_entry> entry(new CSeq_entry);
            entry->SetSet(*bioseq_set);
            CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
            scope->AddTopLevelSeqEntry(*entry);
            scope->AddDefaults();
            IDocument* doc = CDocManager::CreateDocument(*scope, *entry);
            reply.AddObject(*doc);
        } else {
            throw runtime_error(string("invalid load mode: ")
                                + args["mode"].AsString());
        }
        reply.SetStatus(eMessageStatus_success);
    }
    catch (exception& _DEBUG_ARG(e)) {
        _TRACE("failed to read agp: " << e.what());
    }
    catch (...) {
        _TRACE("failed to read agp: unknown error");
    }

}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: agp_reader.cpp,v $
 * Revision 1000.1  2004/06/01 20:57:21  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 *
 * Revision 1.10  2004/05/25 17:21:59  dicuccio
 * Modified class names.  Fonts to 12 point
 *
 * Revision 1.9  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.8  2004/05/03 13:05:42  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.7  2004/03/16 15:59:50  vasilche
 * Removed warning about unused exception variable
 *
 * Revision 1.6  2004/02/17 15:17:31  jcherry
 * Removed help url in favor of new help system
 *
 * Revision 1.5  2004/02/11 21:01:51  jcherry
 * Use file argument rather than manually launching file chooser
 *
 * Revision 1.4  2004/01/27 18:45:31  dicuccio
 * Added missing header files
 *
 * Revision 1.3  2003/12/10 15:09:32  dicuccio
 * Changed menu item - capitalize AGP
 *
 * Revision 1.2  2003/12/09 21:33:54  jcherry
 * Added url for help
 *
 * Revision 1.1  2003/12/09 00:20:09  jcherry
 * Initial version
 *
 * ===========================================================================
 */