file_loader.cpp

来自「ncbi源码」· C++ 代码 · 共 1,097 行 · 第 1/3 页

}


//
// x_Load() - load a given record into a document
//
void CDataPlugin_FileLoader::x_Load(CBioseq_set& bioseq_set, IDocument* doc,
                         CPluginReply& reply)
{
    CObjectConverter::TObjList objs;
    CRef<CScope> scope;
    if (doc) {
        scope = &doc->GetScope();
    } else {
        scope = (new CScope(CDocManager::GetObjectManager()));
        scope->AddDefaults();
    }
    CObjectConverter::Convert(*scope, bioseq_set,
                              CSeq_entry::GetTypeInfo(), objs);
    NON_CONST_ITERATE (CObjectConverter::TObjList, iter, objs) {
        CSeq_entry& entry =
            const_cast<CSeq_entry&>(dynamic_cast<const CSeq_entry&>(**iter));
        x_Load(entry, doc, reply);
    }
}


//
// x_Load() - load a given record into a document
//
void CDataPlugin_FileLoader::x_Load(CBioseq& bioseq, IDocument* doc,
                         CPluginReply& reply)
{
    CObjectConverter::TObjList objs;
    CRef<CScope> scope;
    if (doc) {
        scope = &doc->GetScope();
    } else {
        scope = (new CScope(CDocManager::GetObjectManager()));
        scope->AddDefaults();
    }
    CObjectConverter::Convert(*scope, bioseq,
                              CSeq_entry::GetTypeInfo(), objs);
    ITERATE (CObjectConverter::TObjList, iter, objs) {
        CSeq_entry& entry =
            const_cast<CSeq_entry&>(dynamic_cast<const CSeq_entry&>(**iter));
        x_Load(entry, doc, reply);
    }
}


//
// x_Load() - load a given record into a document
// This version adds a given annotation to the current record, or creates a new
// one as needed.
//
void CDataPlugin_FileLoader::x_Load(CSeq_annot& annot, IDocument* doc,
                         CPluginReply& reply)
{
    try {
        if (doc) {
            doc->AttachAnnot(annot);
            doc->PostDocumentChanged();
            reply.SetStatus(eMessageStatus_success);
            LOG_POST(Info << "Imported and attached Seq-annot");
        } else {
            CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
            scope->AddDefaults();
            IDocument* doc = CDocManager::CreateDocument(*scope, annot);
            reply.AddObject(*doc);
            reply.SetStatus(eMessageStatus_success);
            LOG_POST(Info << "Imported Seq-annot");
        }
    }
    catch (CDocException& e) {
        LOG_POST(Error << "Error loading annotation: " << e.what());
    }
}


//
// x_Load() - load a given record into a document
//
void CDataPlugin_FileLoader::x_Load(CSeq_submit& submit, IDocument* doc,
                         CPluginReply& reply)
{
    CRef<CScope> scope;
    if (doc) {
        scope.Reset(&doc->GetScope());
    } else {
        scope.Reset(new CScope(CDocManager::GetObjectManager()));
        scope->AddDefaults();
    }

    // a seq-submit may contain multiple records

    // first, Seq-entries
    if (submit.GetData().IsEntrys()) {
        NON_CONST_ITERATE (CSeq_submit::C_Data::TEntrys, iter,
                           submit.SetData().SetEntrys()) {
            scope->AddTopLevelSeqEntry(**iter);
        }
    }

    // next, Seq-annots
    if (submit.GetData().IsAnnots()) {
        CObjectConverter::TObjList entries;
        NON_CONST_ITERATE (CSeq_submit::C_Data::TAnnots, iter,
                           submit.SetData().SetAnnots()) {
            CObjectConverter::Convert(*scope, **iter,
                                      CSeq_entry::GetTypeInfo(), entries);
        }

        ITERATE (CObjectConverter::TObjList, iter, entries) {
            const CSeq_entry& entry = dynamic_cast<const CSeq_entry&>(**iter);
            scope->AddTopLevelSeqEntry(const_cast<CSeq_entry&>(entry));
        }
    }

    if ( !doc ) {
        doc = CDocManager::CreateDocument(*scope, submit);
        reply.AddObject(*doc);
    } else {
        reply.AddObject(*doc, submit);
    }
    reply.SetStatus(eMessageStatus_success);
    LOG_POST(Info << "Imported Seq-submit");
}



END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: file_loader.cpp,v $
 * Revision 1000.6  2004/06/01 20:57:37  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.67
 *
 * Revision 1.67  2004/05/25 17:21:59  dicuccio
 * Modified class names.  Fonts to 12 point
 *
 * Revision 1.66  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.65  2004/05/18 11:22:34  friedman
 * Add recently loaded documents to the MRU list.
 *
 * Revision 1.64  2004/05/03 13:05:42  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.63  2004/04/14 21:04:11  jcherry
 * Open file in binary mode so binary asn.1 works
 *
 * Revision 1.62  2004/04/09 18:37:26  dicuccio
 * Added default resolvers to scopre for seq-submit
 *
 * Revision 1.61  2004/04/05 14:27:10  dicuccio
 * Added check to make sure the file exists before opening.  Added support for
 * seq-align-set conversions
 *
 * Revision 1.60  2004/03/29 20:06:35  jcherry
 * Don't try to get scope from null document pointer
 *
 * Revision 1.59  2004/03/24 22:13:36  ucko
 * Use the correct type (CT_POS_TYPE rather than int) for tellg's return value.
 *
 * Revision 1.58  2004/03/23 22:09:01  jcherry
 * Isolate stream operations from file stuff
 *
 * Revision 1.57  2004/03/23 13:38:47  dicuccio
 * Cleaned up use of convert function - use standard object conversion routines
 *
 * Revision 1.56  2004/03/22 15:14:27  jcherry
 * Added short synonyms for file type strings
 *
 * Revision 1.55  2004/03/16 15:59:50  vasilche
 * Removed warning about unused exception variable
 *
 * Revision 1.54  2004/03/11 17:42:01  dicuccio
 * Dropped unneeded #includes
 *
 * Revision 1.53  2004/03/09 22:12:50  jcherry
 * Catch std::exception when reading Newick
 *
 * Revision 1.52  2004/03/01 22:55:56  jcherry
 * Use string rather than char* for format names (find was comparing
 * pointer values)
 *
 * Revision 1.51  2004/03/01 21:42:39  dicuccio
 * Use correct exception class for alignment reader
 *
 * Revision 1.50  2004/03/01 15:12:04  dicuccio
 * Added support for CLUSTAL alignments.  Added handling of type specification in
 * plugin args.  Added support for Newic format phylogenetic trees.
 *
 * Revision 1.49  2004/01/27 18:45:32  dicuccio
 * Added missing header files
 *
 * Revision 1.48  2004/01/21 12:38:19  dicuccio
 * redesigned CObjectCOnverter API to eliminate temporary object creation
 *
 * Revision 1.47  2004/01/06 20:48:17  dicuccio
 * Moved CFltkCursorGuard into CPlugin::Execute() - broadly applied to all plugins
 *
 * Revision 1.46  2004/01/06 20:15:53  dicuccio
 * Use CFltkCursorGuard on load / import / search
 *
 * Revision 1.45  2004/01/06 17:19:09  rsmith
 * Took out class specifier (CSniffReader::) within class definition.
 *
 * Revision 1.44  2004/01/05 15:02:57  kuznets
 * Bug fix: implemented Reset() function to correctly restore after a
 * failed try.
 *
 * Revision 1.43  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 1.42  2003/12/22 19:29:35  dicuccio
 * Updated to macth API changes in IDocument - UpdateAllViews() goes away
 *
 * Revision 1.41  2003/11/24 15:45:33  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.40  2003/11/18 17:49:01  dicuccio
 * Added standard processing of return values
 *
 * Revision 1.39  2003/11/06 20:12:15  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.38  2003/11/04 17:49:24  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.37  2003/10/10 17:17:28  dicuccio
 * Added Import() method - split out from Load()
 *
 * Revision 1.36  2003/10/07 13:47:05  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.35  2003/09/16 14:07:28  dicuccio
 * Removed Save function - split into separate plugin class
 *
 * Revision 1.34  2003/09/04 14:51:01  dicuccio
 * Use IDocument instead of CDocument
 *
 * Revision 1.33  2003/07/25 14:59:05  kuznets
 * Improved diagnostics when Open/Create document throws an exception.
 *
 * Revision 1.32  2003/07/23 19:14:09  dicuccio
 * Moved logic for validating plugin arguments into CPluginUtils.
 *
 * Revision 1.31  2003/07/21 19:33:27  dicuccio
 * Call IDocument::UpdateAllViews() after adding annotations to a document
 *
 * Revision 1.30  2003/07/14 11:16:41  shomrat
 * Plugin messageing system related changes
 *
 * Revision 1.29  2003/07/08 20:17:31  kuznets
 * Improved diagnostics
 *
 * Revision 1.28  2003/06/25 17:02:58  dicuccio
 * Split CPluginHandle into a handle (pointer-to-implementation) and
 * implementation file.  Lots of #include file clean-ups.
 *
 * Revision 1.27  2003/06/23 13:23:13  dicuccio
 * Deprecated seq_utils.[h,c]pp - moved functions into gui.utils/utils.hpp
 *
 * Revision 1.26  2003/06/20 14:52:57  dicuccio
 * Revised plugin registration - moved GetInfo() into the plugin handler
 *
 * Revision 1.25  2003/06/19 16:15:23  dicuccio
 * Check to make sure the argument named 'document' exists before referencing it.
 *
 * Revision 1.24  2003/06/17 19:14:56  dicuccio
 * Cleaned up and re-enabled file importing
 *
 * Revision 1.23  2003/06/16 16:00:44  dicuccio
 * Code clean-up - removed old functions, reformatted.
 *
 * Revision 1.22  2003/06/10 14:59:13  kuznets
 * File opening reimplemented using CObjectsSniffer(obj_sniff.hpp)
 *
 * Revision 1.21  2003/06/04 19:40:37  ucko
 * Update #include for FASTA reader.
 *
 * Revision 1.20  2003/05/19 13:40:44  dicuccio
 * Moved gui/core/plugin/ -> gui/plugin/.  Merged core libraries into libgui_core.
 * Removed old, unused dialog box.
 *
 * Revision 1.19  2003/04/24 16:39:08  dicuccio
 * Updated to reflect changes in plugin API.  Changed location of document marshal
 * from framework to plugin
 *
 * Revision 1.18  2003/04/16 18:25:28  dicuccio
 * Removed older file read mechanism, in favor of a more precise mechanism,
 * especially when reading ASN.1 text or XML
 *
 * Revision 1.17  2003/03/11 15:23:29  kuznets
 * iterate -> ITERATE
 *
 * Revision 1.16  2003/02/28 15:07:21  dicuccio
 * Restored adding of default scope after loading a file
 *
 * Revision 1.15  2003/02/24 13:03:16  dicuccio
 * Renamed classes in plugin spec:
 *     CArgSeg --> CPluginArgSet
 *     CArgument --> CPluginArg
 *     CPluginArgs --> CPluginCommand
 *     CPluginCommands --> CPluginCommandSet
 *
 * Revision 1.14  2003/02/20 19:49:56  dicuccio
 * Created new plugin architecture, based on ASN.1 spec.  Moved GBENCH frameowrk
 * over to use new plugin architecture.
 *
 * Revision 1.13  2003/02/06 18:48:36  dicuccio
 * Made 'catch (...)' conditional for non-debug builds
 *
 * Revision 1.12  2003/02/05 19:55:23  dicuccio
 * Major reworking of handling of files.  Implemented file save.
 *
 * Revision 1.11  2003/01/13 13:10:07  dicuccio
 * Namespace clean-up.  Retired namespace gui -> converted all to namespace ncbi.
 * Moved all FLUID-generated code into namespace ncbi.
 *
 * Revision 1.10  2003/01/10 17:34:56  dicuccio
 * Converted some _TRACE() -> LOG_POST statements (judicious tracking of what a
 * user is trying to load)
 *
 * Revision 1.9  2003/01/03 17:25:13  dicuccio
 * Changed most LOG_POST() -> _TRACE().
 *
 * Revision 1.8  2002/12/30 17:48:28  dicuccio
 * Added mechanism for data loader plugins to announce supported modes of
 * operation (load, import, save currently)
 *
 * Revision 1.7  2002/12/23 13:55:37  dicuccio
 * Set the default scope *after* a file has been retrieved.
 *
 * Revision 1.6  2002/12/12 15:22:20  dicuccio
 * Must always save the scope used to create a CBioseq_Handle.  Removed some
 * extraneous _TRACE() statements.
 *
 * Revision 1.5  2002/12/11 18:55:56  dicuccio
 * Added some additional log tracing during file open
 *
 * Revision 1.4  2002/12/09 20:35:59  dicuccio
 * Large revision to file loading code - added ability to read more object types,
 * added ability to import annotations into current document.
 *
 * Revision 1.3  2002/12/09 13:34:22  dicuccio
 * Fixed file loading (temporarily)
 *
 * Revision 1.2  2002/11/25 22:11:54  dicuccio
 * Fixed minor compilation errors
 *
 * Revision 1.1  2002/11/25 20:51:01  dicuccio
 * Initial revision.
 *
 * ===========================================================================
 */