dlg_blastpoll.cpp

来自「ncbi源码」· C++ 代码 · 共 422 行

/*
 * ===========================================================================
 * PRODUCTION $Log: dlg_blastpoll.cpp,v $
 * PRODUCTION Revision 1000.6  2004/06/01 20:54:21  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.13
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: dlg_blastpoll.cpp,v 1000.6 2004/06/01 20:54:21 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.
*
* ===========================================================================
*
* Author:  Cliff Clausen, Michael DiCuccio
*
* File Description:
*   !!! PUT YOUR DESCRIPTION HERE !!!
*
* ===========================================================================
*/

#include <ncbi_pch.hpp>
#include "dlg_blastpoll.hpp"
#include "blast_poll_table.hpp"

#include <gui/core/plugin_utils.hpp>
#include <gui/utils/fltk_utils.hpp>

#include <algo/blast/api/remote_blast.hpp>

#include <objects/seq/Seq_annot.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Dense_seg.hpp>

#include "blast_rid_cache.hpp"



BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

#include "dlg_blastpoll_.cpp"



CBlastPollDlg::CBlastPollDlg()
{
    m_Window.reset(x_CreateWindow());
    m_PollPending = false;

    m_RidCache.Reset(new CBlastRidCache());
}


void CBlastPollDlg::x_OnPollNow()
{
    // Loop through poll list
    for (size_t i = 0;  i < m_Table->GetRows();  ++i) {
        CBlastPollItem& item = *m_Table->SetData(i);
        if ( !item.m_Active ) {
            continue;
        }

        CTime now(CTime::eCurrent);

        // Get blast results for this rid, if ready
        string msg;
        item.m_Errors = !x_Poll(item);
        item.m_LastPollTime = now;
        m_Table->UpdateItem(i, item);
    }
}


void CBlastPollDlg::x_OnActiveToggle()
{
    for (size_t i = 0;  i < m_Table->GetRows();  ++i) {
        if ( !m_Table->IsRowSelected(i) ) {
            continue;
        }

        if (m_Table->GetData(i)->m_Active) {
            m_Table->DeactivateItem(i);
        } else {
            m_Table->ActivateItem(i);
        }
    }
}


void CBlastPollDlg::x_OnRemove()
{
    m_Table->RemoveSelected();
}


void CBlastPollDlg::x_OnUp()
{
    for (size_t i = 0;  i < m_Table->GetRows();  ++i) {
        if ( !m_Table->IsRowSelected(i) ) {
            continue;
        }

        m_Table->MoveUp(i);
    }
}


void CBlastPollDlg::x_OnDown()
{
    for (size_t i = 0;  i < m_Table->GetRows();  ++i) {
        if ( !m_Table->IsRowSelected(i) ) {
            continue;
        }

        m_Table->MoveDown(i);

        // we need to increment as the next item is the one we just moved.
        ++i;
    }
}


static void s_pollTimeout(void *data)
{
    CBlastPollDlg *dlg = static_cast<CBlastPollDlg*>(data);
    if (dlg) {
        dlg->Poll();
        Fl::repeat_timeout(1.0f, s_pollTimeout, data);
    }
}


void CBlastPollDlg::StartPoll()
{
    if (!m_PollPending) {
        Fl::add_timeout(1.0f, s_pollTimeout, this);
        m_PollPending = true;
    }
}


void CBlastPollDlg::StopPoll()
{
    Fl::remove_timeout(s_pollTimeout);
    m_PollPending = false;
}


void CBlastPollDlg::Poll()
{
    // Loop through poll list
    for (size_t i = 0;  i < m_Table->GetRows();  ++i) {
        CBlastPollItem& item = *m_Table->SetData(i);
        if ( !item.m_Active ) {
            continue;
        }

        CTime now(CTime::eCurrent);
        size_t secs = now.DiffSecond(item.m_LastPollTime);
        if (secs < 30) {
            continue;
        }

        // Get blast results for this rid, if ready
        string msg;
        item.m_Errors = !x_Poll(item);
        item.m_LastPollTime = now;
        m_Table->UpdateItem(i, item);
    }

    CTime now(CTime::eCurrent);
    m_CurrTimeStr = now.AsString("h:m:s");
    m_CurrTime->label(m_CurrTimeStr.c_str());
}


bool CBlastPollDlg::x_Poll(CBlastPollItem& item)
{
    CFltkCursorGuard WAIT;

    string rid = item.m_Rid;
    CRef<CSeq_annot> annot;

    // check our cache first
    annot = m_RidCache->GetRID(rid);
    if ( !annot ) {
        blast::CRemoteBlast rb(rid);
        if (rb.CheckDone()) {
            // Get the alignment, remap, and wrap it in a CSeq_annot
            CRef<CSeq_align_set> results(rb.GetAlignments());

            // Remap the alignments
            if ( item.m_QueryLoc ) {
                CTypeIterator<CDense_seg> ds_iter(*results);
                for ( ;  ds_iter;  ++ds_iter) {
                    ds_iter->RemapToLoc(0, *item.m_QueryLoc);
                }
            }

            annot.Reset(new CSeq_annot);
            annot->SetData().SetAlign() = results->Set();
    
            // name defines how the object manager sees this annotation
            annot->AddName("NetBLAST Results");

            // 'title' defines how the user sees this
            annot->AddTitle("NetBLAST Results, RID: " + rid);

            // set our creation date
            annot->SetCreateDate(CTime(CTime::eCurrent));

            // save our results in the cache
            m_RidCache->AddRID(rid, *annot);
        }
    }

    if (annot) {

        //
        // got results
        //

        item.m_Active = false;
        item.m_Status = "Retrieved";

        // save the annot
        item.m_Results = annot;

        // Attach seq_annot to document
        if ( item.m_Document ) {
            const IDocument &cdoc = 
                dynamic_cast<const IDocument&>(*item.m_Document);
            const_cast<IDocument&>(cdoc).AttachAnnot(*annot);
            const_cast<IDocument&>(cdoc).UpdateAllViews();
        } else {
            CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
            scope->AddDefaults();
            item.m_Document = CDocManager::CreateDocument(*scope, *annot);
            CDocManager::UpdateAllViews();
        }
    }
    
    return true;
}    


void CBlastPollDlg::Add(const CPluginCommand& args)
{
    string rid;
    if (!args.HasArgument("RID")) {
        return;
    }
    rid = args["RID"].AsString();

    if ( !rid.empty()  &&  !m_Table->HasRid(rid)) {

        CRef<CBlastPollItem> item(new CBlastPollItem());
        if ( !args.HasArgument("query_loc")  ||
             !CPluginUtils::IsValid(args["query_loc"])) {
            item->m_Document.Reset();
            item->m_Descr = rid;
        } else {
            item->m_Document = args["query_loc"].GetDocument();
            item->m_QueryLoc = dynamic_cast<const CSeq_loc*>
                (args["query_loc"].GetObject());

            if (!item->m_Document.IsNull()) {
                item->m_Descr = item->m_Document->GetShortTitle();
            } else {
                item->m_Descr = rid;
            }
        }
        if ( args.HasArgument("prog") ) {
            item->m_Descr += " - " + args["prog"].AsString();
        }
        item->m_Rid = rid;
        item->m_Active = true;
        item->m_Errors = false;
        item->m_Status = "Polling";
        item->m_Errors = !x_Poll(*item);
        item->m_SubmitTime   = CTime(CTime::eCurrent);
        item->m_LastPollTime = item->m_SubmitTime;

        // Add rid to poll list
        m_Table->AddItem(*item);
        m_InputRid->value("");
    }
}


void CBlastPollDlg::x_OnAdd()
{
    const char *rid = m_InputRid->value();

    CRef<CBlastPollItem> item(new CBlastPollItem());
    item->m_Document = NULL;
    item->m_Descr = rid;
    item->m_Rid = rid;
    item->m_Active = true;
    item->m_Errors = false;
    item->m_Status = "Polling";

    m_Table->AddItem(*item);
}



END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: dlg_blastpoll.cpp,v $
* Revision 1000.6  2004/06/01 20:54:21  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.13
*
* Revision 1.13  2004/05/21 22:27:46  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.12  2004/04/22 12:22:08  dicuccio
* Added BLAST RID caching.  Added better formatting for BLAST results
*
* Revision 1.11  2004/04/16 14:41:55  dicuccio
* Use CRemoteBlast to poll for results
*
* Revision 1.10  2004/04/07 12:53:11  dicuccio
* m_document -> m_Document.  Store CSeq_align_set in results
*
* Revision 1.9  2004/03/05 17:32:14  dicuccio
* Large-scale clean-up to blast code.  Reorganized blast polling dialog to be
* multi-column; standardized options for BLAST network submissions; changed
* plugin to accept multiple locations for submission and create a submission for
* each
*
* Revision 1.8  2004/02/18 19:02:36  jcherry
* Query is now a Seq-loc, to which alignments get remapped
*
* Revision 1.7  2003/11/18 13:20:11  clausen
* Fixes to remove g++ warnings
*
* Revision 1.6  2003/11/17 16:24:19  clausen
* Added m_Descr
*
* Revision 1.5  2003/11/04 17:49:22  dicuccio
* Changed calling parameters for plugins - pass CPluginMessage instead of paired
* CPluginCommand/CPluginReply
*
* Revision 1.4  2003/10/31 22:56:36  ucko
* Move include of idocument.hpp to header to precede use in CConstRef<>
*
* Revision 1.3  2003/10/31 17:32:08  clausen
* Switched from passing scope to passing document
*
* Revision 1.2  2003/10/27 17:47:04  dicuccio
* Removed dead #includes
*
* Revision 1.1  2003/10/24 12:49:21  dicuccio
* Moved files from algo/net_blast
*
* Revision 1.12  2003/10/24 12:23:41  clausen
* Fixed fltk blocking
*
* Revision 1.11  2003/10/17 16:35:40  dicuccio
* Better handling of optional scope parameter
*
* Revision 1.10  2003/10/07 13:47:04  dicuccio
* Renamed CPluginURL* to CPluginValue*
*
* Revision 1.9  2003/09/04 14:05:25  dicuccio
* Use IDocument instead of IDocument
*
* Revision 1.8  2003/07/23 19:14:09  dicuccio
* Moved logic for validating plugin arguments into CPluginUtils.
*
* Revision 1.7  2003/07/14 11:14:11  shomrat
* Plugin messageing system related changes
*
* Revision 1.6  2003/07/10 13:06:20  dicuccio
* Fixed compilation issues for gcc-3.3: restructured callback mechanism, replaced
* multiple parallel arrays with an array of classes.
*
* Revision 1.5  2003/06/25 17:02:57  dicuccio
* Split CPluginHandle into a handle (pointer-to-implementation) and
* implementation file.  Lots of #include file clean-ups.
*
* Revision 1.4  2003/06/20 19:45:19  dicuccio
* Fixed bizarre compile error related to namespaces on MSVC
*
* Revision 1.3  2003/06/13 12:07:41  clausen
* GUI changes
*
* Revision 1.2  2003/06/04 19:39:56  ucko
* Use new paths to OM headers (the forwarding headers break on WorkShop);
* add missing public domain notice and CVS log.
*
*
* ===========================================================================
*/