lds_loader.cpp

来自「ncbi源码」· C++ 代码 · 共 567 行 · 第 1/2 页

    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    if (!m_DbHolder) {
        NcbiMessageBox("Local data storage is not configured.",  
                       eDialog_Ok,
                       eIcon_Stop,
                       "Error");

        reply.SetStatus(eMessageStatus_ignored);
        return;
    }

    CLDS_Database* db = m_DbHolder->GetDefaultDatabase();

    if (!db) {
        NcbiMessageBox("Local data storage is not configured.",  
                       eDialog_Ok,
                       eIcon_Stop,
                       "Error");
        reply.SetStatus(eMessageStatus_ignored);
        return;
    }
        
    CLdsSearchDlg dlg(m_DbHolder);
    if (dlg.Show() == eOK) {
        Fl_Browser* lst = dlg.m_List;
        SLDS_TablesCollection& tables = db->GetTables();

        CLDS_Query query(tables);

        CLDS_Set obj_read; // list of objects already loaded

        for (int i = 1;  i <= lst->size();  ++i) {
            int selected = lst->selected(i);

            if (selected) {
                void* data = lst->data(i);
                int id;
                ::memcpy(&id, &data, sizeof(id));

                if (!id) {
                    continue;
                }
                
                CLDS_Query::SObjectDescr descr = 
                  query.GetObjectDescr(db->GetObjTypeMap(), id, true);

                // check if object is already loaded
                if (LDS_SetTest(obj_read, descr.id)) {
                    continue;
                }
                x_Load(descr, db, &obj_read, reply);
            }
        } // for

        if (obj_read.size() == 0) {
            NcbiMessageBox("Failed to find local sequence(s).",  
                           eDialog_Ok,
                           eIcon_Stop,
                           "Error");
        }
    }

    reply.SetStatus(eMessageStatus_success);
}


bool CDataPlugin_LDSLoader::x_Load(const CLDS_Query::SObjectDescr& obj_descr,
                         CLDS_Database* db,
                         CLDS_Set* obj_read,
                         CPluginReply& reply)
{
    try {

        if (obj_descr.type_str == "Seq-entry" ||
            obj_descr.type_str == "Bioseq" ||
            obj_descr.format == CFormatGuess::eFasta) {
            return x_LoadLDS_BioTSE(obj_descr.id, db, obj_read, reply);
        } 
        else {
            if (obj_descr.type_str == "Seq-annot" ||
                obj_descr.type_str == "Seq-align") {
                return x_LoadLDS_Annot(obj_descr, db, obj_read, reply);
            }
        }
    
    }
    catch (CLDS_Exception& ex)
    {
        ERR_POST("failed to read object: " << ex.what());            
    }
    return false;
}


bool CDataPlugin_LDSLoader::x_LoadLDS_BioTSE(int object_id, 
                                   CLDS_Database* db,
                                   CLDS_Set* obj_read,
                                   CPluginReply& reply)
{
    SLDS_TablesCollection& tables = db->GetTables();

    CRef<CSeq_entry> entry = 
        LDS_LoadTSE(tables, db->GetObjTypeMap(), object_id);

    if (!entry) {
        _TRACE("failed to read LDS object id=" << object_id);
        return false;
    }

    obj_read->insert(object_id);

    string dl_name = "LDS_dataloader_";
    dl_name.append(db->GetAlias());

    CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
    scope->AddDataLoader(dl_name);
    scope->AddTopLevelSeqEntry(*entry);
    scope->AddDefaults();
    IDocument* doc =
        CDocManager::CreateDocument(*scope, *entry);
    reply.AddObject(*doc);
    CDocManager::UpdateAllViews();

    /**
    CBioseq_Handle handle =
        CSeqUtils::CreateBioseqHandle(*scope, *entry);
    if (handle) {
        scope->AddDefaults();
        IDocument* doc =
            CDocManager::CreateDocument(*scope,
                                        *CSeqUtils::GetBestId(*entry));
        reply.AddObject(*doc);
        CDocManager::UpdateAllViews();
    }
    **/
    return true;
}


bool CDataPlugin_LDSLoader::x_LoadLDS_Annot(const CLDS_Query::SObjectDescr& obj_descr, 
                                  CLDS_Database* db,
                                  CLDS_Set* obj_read,
                                  CPluginReply& reply)
{
    SLDS_TablesCollection& tables = db->GetTables();

    CRef<CSeq_annot> annot = LDS_LoadAnnot(tables, obj_descr);

    if (!annot) {
        _TRACE("failed to read LDS annotation id=" << obj_descr.id);
        return false;
    }

    obj_read->insert(obj_descr.id);

    string dl_name = "LDS_dataloader_";
    dl_name.append(db->GetAlias());

    CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
    scope->AddDataLoader(dl_name);
    scope->AddDefaults();

    IDocument* doc = CDocManager::CreateDocument(*scope, *annot);
    reply.AddObject(*doc);
    CDocManager::UpdateAllViews();

    return true;
}



END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: lds_loader.cpp,v $
 * Revision 1000.5  2004/06/01 20:58:08  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.31
 *
 * Revision 1.31  2004/05/25 17:21:59  dicuccio
 * Modified class names.  Fonts to 12 point
 *
 * Revision 1.30  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.29  2004/05/03 13:05:43  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.28  2004/03/23 13:39:07  dicuccio
 * Load objects as seq-entry, not seq-id
 *
 * Revision 1.27  2004/03/16 15:59:50  vasilche
 * Removed warning about unused exception variable
 *
 * Revision 1.26  2003/11/24 15:45:38  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.25  2003/11/18 17:49:02  dicuccio
 * Added standard processing of return values
 *
 * Revision 1.24  2003/11/06 20:12:15  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.23  2003/11/05 13:30:45  kuznets
 * Fixed application crash when there is no LDS instances configured in the
 * system. (Search command). Put a warning pop up dialog.
 *
 * Revision 1.22  2003/11/04 17:49:25  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.21  2003/10/29 16:25:07  kuznets
 * Added support for LDS aliases.
 *
 * Revision 1.20  2003/10/28 14:21:01  kuznets
 * Chages to lds loader to support multiple LDS databases
 *
 * Revision 1.19  2003/10/09 19:20:53  kuznets
 * Added message box if Load or Search fails to find anything
 *
 * Revision 1.18  2003/10/08 18:20:42  kuznets
 * Reflecting changes in LDS library
 *
 * Revision 1.17  2003/10/07 13:47:05  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.16  2003/10/03 18:55:52  kuznets
 * Added search time logging for CDataPlugin_LDSLoader::Load command
 *
 * Revision 1.15  2003/09/04 14:51:43  dicuccio
 * Use IDocument instead of CDocument
 *
 * Revision 1.14  2003/08/19 14:38:01  kuznets
 * Added non default LDS dataloader to all created scopes.
 *
 * Revision 1.13  2003/08/08 15:28:53  kuznets
 * Corrected documents list update when we open new views.
 *
 * Revision 1.12  2003/08/07 20:31:35  kuznets
 * Implemented document opening based on lds_search_dlg selection
 *
 * Revision 1.11  2003/08/05 17:16:25  kuznets
 * Changes to improve code reuse between loaders + CLDS_Database passed as the
 * construction parameter to the lds search dialog
 *
 * Revision 1.10  2003/07/31 20:44:32  kuznets
 * LDS Plugin uses CDataStore to get the LDS database object.
 *
 * Revision 1.9  2003/07/30 14:04:58  kuznets
 * Improved "gi|" search similar to genbank loader plugin
 *
 * Revision 1.8  2003/07/29 20:06:07  kuznets
 * "Search All" option added to Load command
 *
 * Revision 1.7  2003/07/15 17:57:08  kuznets
 * Added annotaion/alignment search capabilities
 *
 * Revision 1.6  2003/07/14 11:17:03  shomrat
 * Plugin messageing system related changes
 *
 * Revision 1.5  2003/07/09 20:59:12  kuznets
 * Added new lds plugin argument "search_all". Works as a boolean flag
 * indicating that search should include both seaquences and annotations.
 *
 * Revision 1.4  2003/07/01 19:29:14  kuznets
 * Open command implementation
 *
 * Revision 1.3  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 1.2  2003/06/20 14:52:57  dicuccio
 * Revised plugin registration - moved GetInfo() into the plugin handler
 *
 * Revision 1.1  2003/06/17 20:16:09  kuznets
 * Initial revision.
 *
 *
 * ===========================================================================
 */