entrez_search_dlg.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: entrez_search_dlg.cpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 21:27:00  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: entrez_search_dlg.cpp,v 1000.0 2004/06/01 21:27:00 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:
 *    CEntrezSearchDlg -- search Entrez databases for sequence information
 */

#include <ncbi_pch.hpp>
#include "entrez_search_dlg.hpp"
#include "entrez_record_table.hpp"

#include <gui/core/version.hpp>
#include <gui/core/doc_manager.hpp>
#include <gui/utils/message_box.hpp>
#include <gui/utils/fltk_utils.hpp>

#include <objects/entrez2/entrez2_client.hpp>
#include <objects/entrez2/Entrez2_info.hpp>
#include <objects/entrez2/Entrez2_eval_boolean.hpp>
#include <objects/entrez2/Entrez2_boolean_reply.hpp>
#include <objects/entrez2/Entrez2_boolean_exp.hpp>
#include <objects/entrez2/Entrez2_boolean_element.hpp>
#include <objects/entrez2/Entrez2_id_list.hpp>
#include <objects/entrez2/Entrez2_docsum.hpp>
#include <objects/entrez2/Entrez2_docsum_list.hpp>
#include <objects/entrez2/Entrez2_docsum_data.hpp>
#include <objects/entrez2/Entrez2_db_id.hpp>
#include <objects/entrez2/Entrez2_limits.hpp>
#include <objmgr/util/sequence.hpp>

#include <gui/plugin/PluginMessage.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginArg.hpp>
#include <gui/plugin/PluginValue.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/core/plugin_handle.hpp>
#include <gui/core/plugin_registry.hpp>
#include <gui/objutils/label.hpp>

#include <serial/serial.hpp>
#include <serial/objostr.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


#include "entrez_search_dlg_.cpp"

CEntrezSearchDlg::CEntrezSearchDlg()
    : m_Start(0)
    , m_Visible(10)
    , m_Length(0)
{
    m_Window.reset(x_CreateWindow());
    CenterOnActive();

    // retrieve our list of databases
    list<string> dbs;
    m_Table->GetDatabases(dbs);
    int default_idx = 0;
    ITERATE (list<string>, iter, dbs) {
        int idx = m_DB->add(iter->c_str());
        if (*iter == "Nucleotide") {
            default_idx = idx;
        }
    }
    m_DB->value(default_idx);
    m_Table->SetDatabase(m_DB->text(default_idx));
    m_Table->SetReporter(m_StatusBar);
    m_StatusBar->PushMessage("Ready");
}


void CEntrezSearchDlg::SetQuery(const string& str)
{
    m_QueryStr->value(str.c_str());
    x_OnChangeTerms();
}


void CEntrezSearchDlg::SetDB(const string& str)
{
    for (int i = 0;  i < m_DB->size();  ++i) {
        const char* ptr = m_DB->text(i);
        if (ptr  &&  str == ptr) {
            m_DB->value(i);
            x_OnChangeDB();
            break;
        }
    }
}


void CEntrezSearchDlg::x_OnPrevious()
{
    if (m_Visible > 0  &&  m_Start > 0) {
        m_Start  = max(0, m_Start - m_Visible);
        x_OnSearch();
    }
}


void CEntrezSearchDlg::x_OnNext()
{
    if (m_Visible > 0  &&  (m_Start + m_Visible < m_Length)) {
        m_Start = min(m_Length - m_Visible, m_Start + m_Visible);
        m_Start = max(0, m_Start);
        x_OnSearch();
    }
}


void CEntrezSearchDlg::x_OnLoad()
{
    CStatusBarGuard GUARD(*m_StatusBar, "Loading accessions...");
    m_Table->OnNewDocument();

#if 0
    CPluginArg::TValues value_list;


    // this is a hack to get the nice GUI effect we want
    // we simply create a new default scope and use it to load our sequences
    CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
    scope->AddDefaults();

    try {
        // gather our docsums and prepare to do the docsum -> seqid conversion
        CEntrez2_docsum_list docsums;
        for (size_t i = 0;  i < m_Table->GetRows();  ++i) {
            if ( !m_Table->IsRowSelected(i) ) {
                continue;
            }

            CRef<CEntrez2_docsum> ref = m_Table->GetData(i);
            docsums.SetList().push_back(ref);
        }
        docsums.SetCount(docsums.GetList().size());

        // retrieve our handler and get our IDs.
        const char* p = m_DB->text();
        if ( !p ) {
            throw runtime_error("No database chosen.");
        }
        IEntrezDBHandler& handler = m_DbManager.GetHandler(p);
        IEntrezDBHandler::TIds ids = handler.GetSeqIds(docsums);

        // force loading to make a nice GUI statement...
        size_t idx = 0;
        ITERATE (IEntrezDBHandler::TIds, iter, ids) {
            string str;
            try {
                CBioseq_Handle handle = scope->GetBioseqHandle(**iter);
                if (handle) {
                    str = "Loaded sequence ";

                    string id_str;
                    CLabel::GetLabel(**iter, &id_str, CLabel::eDefault, scope);
                    str += id_str;

                    CRef<CPluginValue> value(new CPluginValue());
                    value->SetString(id_str);
                    value_list.push_back(value);
                }
            }
            catch (CException& e) {
                str = "Failed to load sequence ";
                CLabel::GetLabel(**iter, &str, CLabel::eDefault);
                str += ": " + e.GetMsg();
            }
            catch (...) {
            }

            if (str.empty()) {
                str = "Failed to load sequence ";
                CLabel::GetLabel(**iter, &str, CLabel::eDefault);
            }

            m_StatusBar->SetMessage(str);

            ++idx;
            m_StatusBar->SetPctCompleted(100 * idx / ids.size());
        }
    }
    catch (CException& e) {
        string str("Can't load accessions:\n");
        str += e.GetMsg();
        NcbiMessageBox(str);
    }
    catch (std::exception& e) {
        string str("Can't load accessions:\n");
        str += e.what();
        NcbiMessageBox(str);
    }
    catch (...) {
    }

    if (value_list.size() != 0) {
        CPluginHandle ph =
            CPluginRegistry::GetPlugin("CDataPlugin_GenbankLoader");
        if (ph) {
            CRef<CPluginMessage> msg = ph.CreateMessage(eDataCommand_load);
            CPluginArg& arg = msg->SetRequest().SetCommand()["acc"];
            arg.SetList(value_list);

            CPluginUtils::CallPlugin(*msg);
        }
    }

    m_StatusBar->SetPctCompleted(0);
#endif
}


void CEntrezSearchDlg::x_OnChangeTerms()
{
    m_Start = 0;
    x_OnSearch();
}