file_export.cpp

来自「ncbi源码」· C++ 代码 · 共 293 行

/*
 * ===========================================================================
 * PRODUCTION $Log: file_export.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:57:30  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.14
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: file_export.cpp,v 1000.5 2004/06/01 20:57:30 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:  Mike DiCuccio
 *
 * File Description:
 *    CDataPlugin_FileExport - load sequence information from a file.
 */

#include <ncbi_pch.hpp>
#include "file_export.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 <objects/seqset/Seq_entry.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objtools/flat/flat_gbseq_formatter.hpp>
#include <objtools/flat/flat_gff_formatter.hpp>
#include <objtools/flat/flat_table_formatter.hpp>
#include <serial/objostrasn.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


static const string sc_text_str  ("Text ASN.1");
static const string sc_binary_str("Binary ASN.1");
static const string sc_xml_str   ("full XML");
static const string sc_gbseq_str ("GBSeq XML");
static const string sc_fasta_str ("FastA");
static const string sc_flat_str  ("GenBank/EMBL/DDBJ Flat-File");
static const string sc_gff_str   ("GFF/GTF");
static const string sc_table_str ("Sequin 5-column Feature Table");


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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CDataPlugin_FileExport",
                 "File", "File import / export plugin", "");

    // command info
    CPluginCommandSet& cmds     = info.SetCommands();
    CPluginCommand& save_args   = cmds.AddDataCommand(eDataCommand_save);
    save_args.AddArgument("file", "File name", CPluginArg::eFile);
    save_args.AddArgument("document", "Document", CPluginArg::eDocument);
    save_args.AddArgument("fmt", "Format", CPluginArg::eString);
    save_args.SetConstraint("fmt",
                            (*CPluginValueConstraint::CreateSet(),
                             sc_text_str,
                             sc_binary_str,
                             sc_xml_str,
                             sc_gbseq_str,
                             sc_fasta_str,
                             sc_flat_str,
                             sc_gff_str,
                             sc_table_str
                             ));
}


//
// Save()
// Save the information in a given document into a file
//
void CDataPlugin_FileExport::Save(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    IDocument* doc = const_cast<IDocument*> (&args["document"].AsDocument());
    if ( !doc ) {
        reply.SetStatus(eMessageStatus_failed);
        return;
    }

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

    try {
        string fmt_str = args["fmt"].AsString();

        // find out what object to serialize
        // in general, we serialize precisely what the document contains
        // the exception to this is that we dereference any seq-id
        // to its largest component (= top-level seq-entry)
        CConstRef<CSerialObject> obj
            (dynamic_cast<const CSerialObject*> (doc->GetObject()));
        if (obj.GetPointer()  &&
            obj->GetThisTypeInfo() == CSeq_id::GetTypeInfo()) {
            const CSeq_id& id =
                dynamic_cast<const CSeq_id&>(*doc->GetObject());
            CBioseq_Handle handle = doc->GetScope().GetBioseqHandle(id);
            obj.Reset(&handle.GetTopLevelSeqEntry());
        }

        //
        // format handling
        //

        ESerialDataFormat fmt = eSerial_None;
        if (fmt_str == sc_text_str) {
            // ASN.1 text
            fmt = eSerial_AsnText;
        } else if (fmt_str == sc_binary_str) {
            // ASN.1 binary
            fmt = eSerial_AsnBinary;
        } else if (fmt_str == sc_xml_str) {
            // XML
            fmt = eSerial_Xml;
        } else if (fmt_str == sc_fasta_str) {

            //
            // FastA - alternate format
            //
            CScope& scope = doc->GetScope();
            CNcbiOfstream ostr(fname.c_str());
            CFastaOstream fasta_ostr(ostr);
            CObjectConverter::TObjList objs;
            CObjectConverter::Convert(scope, *obj, CSeq_entry::GetTypeInfo(),
                                      objs);

            ITERATE (CObjectConverter::TObjList, iter, objs) {
                const CSeq_entry& entry =
                    dynamic_cast<const CSeq_entry&> (**iter);
                CBioseq_CI bioseq_iter(scope, entry);
                for ( ;  bioseq_iter;  ++bioseq_iter) {
                    fasta_ostr.Write(*bioseq_iter);
                }
            }

        } else {

            //
            // Flat-File - alternate format
            //
            // should bring up a second dialog box rather than hardcoding
            // parameters
            CScope& scope = doc->GetScope();
            CNcbiOfstream ostr(fname.c_str());
            CFlatTextOStream ftos(ostr);
            auto_ptr<CObjectOStream> oos;
            auto_ptr<IFlatFormatter> ff;

            IFlatFormatter::EMode mode = IFlatFormatter::eMode_GBench;

            if (fmt_str == sc_flat_str) {
                ff.reset(CFlatTextFormatter::New(ftos, scope, mode,
                                                 IFlatFormatter::eDB_NCBI));
            } else if (fmt_str == sc_table_str) {
                ff.reset(new CFlatTableFormatter(ftos, scope));
            } else if (fmt_str == sc_gff_str) {
                ff.reset(new CFlatGFFFormatter(ftos, scope, mode,
                                               CFlatGFFFormatter::fGTFCompat));
            } else if (fmt_str == sc_gbseq_str) {
                oos.reset(CObjectOStream::Open(eSerial_Xml, ostr));
                ff.reset(new CFlatGBSeqFormatter(*oos, scope, mode));
            }

            CObjectConverter::TObjList objs;
            CObjectConverter::Convert(scope, *obj,
                                      CSeq_entry::GetTypeInfo(), objs);
            ITERATE (CObjectConverter::TObjList, iter, objs) {
                ff->Format(dynamic_cast<const CSeq_entry&>(**iter), *ff);
            }

        }

        //
        // generic handler - use object ostreams
        if ( fmt != eSerial_None ) {
            auto_ptr<CObjectOStream> os(CObjectOStream::Open(fmt, fname));
            os->Write(obj, obj->GetThisTypeInfo());
        }

        reply.SetStatus(eMessageStatus_success);
    }
    catch (CException& e) {
        string msg("Failed to save file:\n");
        msg += e.GetMsg();
        NcbiMessageBox(msg);
        reply.SetStatus(eMessageStatus_failed);
    }
#ifndef _DEBUG
    catch (...) {
        NcbiMessageBox("Failed to save file:\nUnknown error\n");
        reply.SetStatus(eMessageStatus_failed);
    }
#endif
}



END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: file_export.cpp,v $
 * Revision 1000.5  2004/06/01 20:57:30  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.14
 *
 * Revision 1.14  2004/05/25 17:21:59  dicuccio
 * Modified class names.  Fonts to 12 point
 *
 * Revision 1.13  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.12  2004/03/11 17:42:01  dicuccio
 * Dropped unneeded #includes
 *
 * Revision 1.11  2004/01/27 18:45:31  dicuccio
 * Added missing header files
 *
 * Revision 1.10  2004/01/21 12:38:19  dicuccio
 * redesigned CObjectCOnverter API to eliminate temporary object creation
 *
 * Revision 1.9  2004/01/13 20:38:16  dicuccio
 * Use the filename provided by the plugin arg dialog
 *
 * Revision 1.8  2003/12/31 20:29:31  dicuccio
 * Turned on use of file type arguments.  Fixed issues relating to importation of
 * items into scopes - can now import anything.
 *
 * Revision 1.7  2003/12/05 13:07:52  dicuccio
 * Split management interface into a separate plugin.  Fixed linker error
 * introduced with status bar
 *
 * Revision 1.6  2003/11/24 15:45:33  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.5  2003/11/06 20:12:14  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.4  2003/11/04 17:49:24  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.3  2003/10/09 16:11:07  ucko
 * Added types mediated by the flat-file generator: GBSeq, GenBank,
 * GFF/GTF, and Sequin feature table.
 *
 * Revision 1.2  2003/10/07 13:47:05  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.1  2003/09/16 14:06:48  dicuccio
 * Initial revision - split from CFileLoader
 *
 * ===========================================================================
 */