view_crossalign.cpp

来自「ncbi源码」· C++ 代码 · 共 347 行

/*
 * ===========================================================================
 * PRODUCTION $Log: view_crossalign.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:59:09  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.36
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: view_crossalign.cpp,v 1000.5 2004/06/01 20:59:09 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:  Vlad Lebedev
 *
 * File Description:
 *    User-modifiable implementation file for extension 
 *    of Cross Alignment viewer
 */

#include <ncbi_pch.hpp>
#include "view_crossalign.hpp"

#include <gui/core/plugin_utils.hpp>
#include <gui/core/version.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginValue.hpp>
#include <gui/objutils/utils.hpp>
#include <objmgr/util/sequence.hpp>


BEGIN_NCBI_SCOPE

// We include the generated _.cpp file here.  This avoids a nasty bug in some
// versions of gcc in which inline functions are not intantiated.
#include "view_crossalign_.cpp"


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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlnCrossAlignView",
                 "Cross Alignment Viewer",
                 "Cross Alignment Viewer", "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddViewCommand(eViewCommand_new_view);
    args.AddArgument("alignments", "Alignments to merge and render",
                     CSeq_annot::GetTypeInfo(),
                     CPluginArg::TData::e_Single);
    args.SetConstraint("alignments",
                       *CPluginValueConstraint::CreateAnnotType
                       (CSeq_annot::TData::e_Align));
}


CAlnCrossAlignView::CAlnCrossAlignView(const CPluginMessage& msg,
                                       const string& pool_name)
    : CAlnView()
{
    m_Window.reset(x_CreateWindow());

    // set our core components
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    const CPluginArg& arg = args["alignments"];

    // extract the alignments from the argument
    const CSeq_annot* annot =
        dynamic_cast<const CSeq_annot*>(arg.GetObject());
    const IDocument* doc = arg.GetDocument();

    if (annot  &&  doc) {
        m_AnnotData.Reset(annot);
        x_SetDocument(*doc);
    }
}




void CAlnCrossAlignView::OnDocumentChanged()
{
    if (!m_Document) {
        return;
    }

    SetTitle(m_Document->GetShortTitle() + ": " + GetTitle());

    // create our datasource
    m_DataSource.Reset(
            new CCrossAlnDataSource(*m_AnnotData, m_Document->GetScope()));

    CCrossAlnDataSource::TIdRefCont all_ids =  m_DataSource->GetSeqIDs();

    // choosing sequences to display
    m_SeqChoice1->clear();
    m_SeqChoice2->clear();
    
    if(all_ids.size() >1 )  {
        CCrossAlnDataSource::TIdRefCont::const_iterator  it = all_ids.begin();
        CConstRef<CSeq_id>   s_id(*it);
        CConstRef<CSeq_id>   q_id(*(++it));
        m_DataSource->SelectIds(s_id, q_id);

        m_AlnWidget->SetDataSource(m_DataSource.GetPointer());
        
        int i_q = -1, i_s = -1; 
        for(unsigned int i = 0; i < all_ids.size(); i++ ) {
            CConstRef<CSeq_id> id = all_ids[i];
            if(id->Match(*q_id)) {
                i_q = i;
            }
            if(id->Match(*s_id)) {
                i_s = i;
            }
        
            CBioseq_Handle handle = m_Document->GetScope().GetBioseqHandle(*id);
            const CSeq_id& best_id =
                sequence::GetId(handle, sequence::eGetId_Best);

            string str;
            best_id.GetLabel(&str);
            m_SeqChoice1->add(str.c_str());
            m_SeqChoice2->add(str.c_str());
        }
        m_SeqChoice1->value(i_q);
        m_SeqChoice2->value(i_s);
    }    
}



void CAlnCrossAlignView::x_OnSelectionChanged()
{
    int idx1 = m_SeqChoice1->value();
    int idx2 = m_SeqChoice2->value();
    
    CCrossAlnDataSource::TIdRefCont all_ids =  m_DataSource->GetSeqIDs();

    m_DataSource->SelectIds(all_ids[idx1], all_ids[idx2]);                
    m_AlnWidget->Update();
}

void CAlnCrossAlignView::x_OnFitToWindow()
{
    m_AlnWidget->FitToWindow();
}

void CAlnCrossAlignView::x_OnZoomToSequence()
{
    m_AlnWidget->ZoomToSequence();
}

void CAlnCrossAlignView::x_OnShowMismatches()
{
    //bool show = m_Menu->mvalue()->value() ? true : false;
    //m_AlnWidget->ShowSequenceAsDots(show);
}

const string& CAlnCrossAlignView::GetTitle(void) const
{
    static string s_str("Cross Alignment View");
    return s_str;
}


void CAlnCrossAlignView::x_OnFileClose()
{
    Hide();
}


void CAlnCrossAlignView::x_OnHelp()
{
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: view_crossalign.cpp,v $
 * Revision 1000.5  2004/06/01 20:59:09  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.36
 *
 * Revision 1.36  2004/05/21 22:27:49  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.35  2004/05/03 13:30:17  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.34  2004/04/07 13:05:10  dicuccio
 * Changed view API - require CPluginMessage instead of CPluginArgSet
 *
 * Revision 1.33  2004/03/05 17:37:11  dicuccio
 * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
 *
 * Revision 1.32  2003/12/22 19:33:13  dicuccio
 * Lots of changes.  Changed to match new APIs in IView.  Added better handling of messages received from other views
 *
 * Revision 1.31  2003/12/22 16:50:07  lebedev
 * Do not use ViewMenuManager (no menu present)
 *
 * Revision 1.30  2003/12/22 13:28:21  lebedev
 * Plugin updated to use new CrossAlignment Widget
 *
 * Revision 1.29  2003/11/24 15:45:42  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.28  2003/11/19 20:45:26  friedman
 * Added handling a visible range change event
 *
 * Revision 1.27  2003/11/04 12:51:27  friedman
 * Added event message pool callbacks for the document all-view message pool.
 *
 * Revision 1.26  2003/10/27 20:03:26  dicuccio
 * Rearranged Update() to be consistent
 *
 * Revision 1.25  2003/10/07 13:47:06  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.24  2003/09/24 18:26:46  dicuccio
 * Large clean-ups to alignment viewers.  Reimplemented data sources and alignment
 * generation mechanism to be more generic.
 *
 * Revision 1.23  2003/09/04 14:54:21  dicuccio
 * Use IDocument instead of CDocument.  Changed APIs to match changes in IView
 *
 * Revision 1.22  2003/07/22 15:32:16  dicuccio
 * Changed to make use of new API in plugin_utils.hpp - GetArgValue()
 *
 * Revision 1.21  2003/06/26 15:33:41  dicuccio
 * Moved GetURLValue() from PluginURL.hpp to plugin_utils.hpp.  Fixed compilation
 * errors relating to missing #includes
 *
 * Revision 1.20  2003/06/25 17:02:59  dicuccio
 * Split CPluginHandle into a handle (pointer-to-implementation) and
 * implementation file.  Lots of #include file clean-ups.
 *
 * Revision 1.19  2003/06/23 13:23:13  dicuccio
 * Deprecated seq_utils.[h,c]pp - moved functions into gui.utils/utils.hpp
 *
 * Revision 1.18  2003/06/20 14:53:52  dicuccio
 * Revised plugin registration - moved GetInfo() into the plugin handler
 *
 * Revision 1.17  2003/06/02 16:06:22  dicuccio
 * Rearranged src/objects/ subtree.  This includes the following shifts:
 *     - src/objects/asn2asn --> arc/app/asn2asn
 *     - src/objects/testmedline --> src/objects/ncbimime/test
 *     - src/objects/objmgr --> src/objmgr
 *     - src/objects/util --> src/objmgr/util
 *     - src/objects/alnmgr --> src/objtools/alnmgr
 *     - src/objects/flat --> src/objtools/flat
 *     - src/objects/validator --> src/objtools/validator
 *     - src/objects/cddalignview --> src/objtools/cddalignview
 * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
 * replaces the three libmmdb? libs.
 *
 * Revision 1.16  2003/05/22 18:50:04  dicuccio
 * Standardized construction, argument specification for all alignment views
 *
 * Revision 1.15  2003/05/19 13:43:32  dicuccio
 * Moved gui/core/plugin --> gui/plugin/.  Merged core libraries into libgui_core
 *
 * Revision 1.14  2003/04/24 16:40:38  dicuccio
 * Updated to reflect changes in plugin API.  Added new common alignment view base
 * class - handles notions of creating alignment manager in a standard way
 *
 * Revision 1.13  2003/03/17 14:54:14  dicuccio
 * Changed base class CView - added member variable for FLTK gui component for
 * child windows, which is now maintained via an auto_ptr<>.  Eliminated
 * Show()/Hide() as a pure virtual requirement.
 *
 * Revision 1.12  2003/03/07 13:35:59  dicuccio
 * Fixed titles in drop-down menu for sequence selection
 *
 * Revision 1.11  2003/03/04 20:08:36  lebedev
 * Prepare Cross Alignment Viewer for MDI
 *
 * Revision 1.10  2003/03/03 18:31:22  dicuccio
 * Deprecated CAlnUtils::GetTitle() in favor of sequence::GetTitle()
 *
 * Revision 1.9  2003/02/20 19:49:58  dicuccio
 * Created new plugin architecture, based on ASN.1 spec.  Moved GBENCH frameowrk
 * over to use new plugin architecture.
 *
 * Revision 1.8  2003/01/17 18:38:49  lebedev
 * Menu item to hide matching sequence letters added
 *
 * Revision 1.7  2003/01/15 21:35:43  lebedev
 * Zoom to Sequence menu item added
 *
 * Revision 1.6  2003/01/13 13:10:08  dicuccio
 * Namespace clean-up.  Retired namespace gui -> converted all to namespace ncbi.
 * Moved all FLUID-generated code into namespace ncbi.
 *
 * Revision 1.5  2003/01/09 14:50:41  dicuccio
 * Use 'const CBioseq_Handle&' instead of 'CBioseq_Handle&'
 *
 * Revision 1.4  2002/12/20 19:52:21  dicuccio
 * Cnaged TRange::SetFrom()/TRange::SetTo() --> TRange::Set()
 *
 * Revision 1.3  2002/12/20 19:22:51  dicuccio
 * Lots of changes to the menus.  Standardized the menu syntax across all views.
 * Changed to use new dynamic menu managers.
 *
 * Revision 1.2  2002/12/13 13:18:52  dicuccio
 * Added work-around for inlining problems in some versions of gcc: directly
 * include a FLUID-generated '*_.cpp' file in the corresponding '*.cpp' and
 * remove this file from the build.  Thanks Aaron!
 *
 * Revision 1.1  2002/12/05 19:07:20  lebedev
 * Initial revision
 *
 * ===========================================================================
 */