view_multialign.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: view_multialign.cpp,v $
 * PRODUCTION Revision 1000.6  2004/06/01 20:59:28  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.51
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: view_multialign.cpp,v 1000.6 2004/06/01 20:59:28 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:
 *    User-modifiable implementation file for extension of Multiple Alignment
 *    viewer for GBENCH
 */

#include <ncbi_pch.hpp>
#include "view_multialign.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 <objects/seqset/Seq_entry.hpp>
#include <objtools/alnmgr/alnmix.hpp>
#include <objtools/alnmgr/alnvec.hpp>

#include <gui/widgets/aln_multiple/align_row.hpp>
#include <gui/widgets/aln_multiple/alnvec_multi_ds.hpp>
#include <gui/widgets/aln_multiple/align_row.hpp>

#include <serial/iterator.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_multialign_.cpp"

DEFINE_MENU(Menu)
    SUBMENU("Display")
        MENU_ITEM(eCmdZoomIn, "Zoom In")
        MENU_ITEM(eCmdZoomOut, "Zoom Out")
        MENU_ITEM(eCmdZoomAll, "Zoom All")
        MENU_ITEM(eCmdZoomSeq, "Zoom to Sequence")
        MENU_ITEM(eCmdZoomSel, "Zoom Selection")
        MENU_SEPARATOR()
        MENU_ITEM(eCmdSetSelMaster , "Set Selected as Master")
        MENU_ITEM(eCmdSetConsMaster, "Set Consensus as Master")
        MENU_ITEM(eCmdUnsetMaster, "Unset Master")
        MENU_SEPARATOR()
        MENU_ITEM(eCmdHideSelected, "Hide Selected Rows")
	    MENU_ITEM(eCmdShowAll, "Show All Rows")
        MENU_SEPARATOR()
        MENU_ITEM(eCmdMoveSelectedUp, "Move Selected Items Up")
    END_SUBMENU()
    SUBMENU("Selection")
        MENU_ITEM(eCmdResetSelection, "Reset Selection")
        MENU_SEPARATOR()
        MENU_ITEM(eCmdMarkSelected, "Mark Selected")
        MENU_ITEM(eCmdUnMarkSelected, "UnMark Selected")
        MENU_ITEM(eCmdUnMarkAll, "UnMark All")
        MENU_SEPARATOR()
        MENU_ITEM(eCmdMoveSelectedUp, "Move Selected Items Up")
    END_SUBMENU()
    SUBMENU("View")
    END_SUBMENU()
    SUBMENU("Tools")
    END_SUBMENU()    
    SUBMENU("&Help")
    END_SUBMENU()
END_MENU()

// Events map
EVENT_MAP_RX_BEGIN(CAlnMultiView)
    EVENT_ACCEPT(CViewEvent::eSelectionChanged,  OnSelChangedEvent)
EVENT_MAP_RX_END

//
// standard plugin announcement boilerplate
//
void CAlnMultiView::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlnMultiView",
                 "Multiple Alignment Viewer",
                 "Multiple 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_Array);
    args.SetConstraint("alignments",
                       *CPluginValueConstraint::CreateAnnotType
                       (CSeq_annot::TData::e_Align));
}


CAlnMultiView::CAlnMultiView(const CPluginMessage& msg, const string& pool_name)
    : CAlnView()
{
    m_Window.reset(x_CreateWindow());
    m_AlnWidget->Create();
    m_AlnWidget->SetListener(this);

    // Setup menu and command handling
    m_Menu->SetItems(Menu);
    m_Menu->SetCmdTarget(static_cast<CCommandTarget*>(this));
    AddChildCmdTarget(static_cast<CCommandTarget*>(m_AlnWidget));

    m_StyleCatalog.SetDefaultStyle(new CAlnVecRowDisplayStyle());
    m_StyleCatalog.SetWidgetStyle(m_AlnWidget->GetDisplayStyle());

    m_AlnWidget->SetStyleCatalog(&m_StyleCatalog);

    // set our core components
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    plugin_args::TAnnotList aligns;
    GetArgValue(args["alignments"], aligns);
    CRef<CSeq_annot> annot(new CSeq_annot());
    const IDocument* doc = NULL;

    ITERATE (plugin_args::TAnnotList, iter, aligns) {
        doc = iter->first;
        annot->SetData().SetAlign()
            .insert(annot->SetData().SetAlign().end(),
                    iter->second->GetData().GetAlign().begin(),
                    iter->second->GetData().GetAlign().end());
    }

    // extract the alignments from the argument

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

    // create the view menu manager
    m_ViewMenuMgr.reset(new CViewMenuMgr(m_Menu, "View", this, pool_name));
    m_AlgoMenuMgr.reset(new CAlgoMenuMgr(m_Menu, "Tools", this));
}

BEGIN_CMD_MAP(CAlnMultiView, CAlnView)
    ON_COMMAND(eCmdResetSelection,  &CAlnMultiView::OnResetSelection)
    ON_COMMAND(eCmdSetConsMaster,   &CAlnMultiView::OnMakeConsensusRowMaster)    
    ON_COMMAND(eCmdMarkSelected,    &CAlnMultiView::OnMarkSelected)
    ON_COMMAND(eCmdUnMarkAll,       &CAlnMultiView::OnUnMarkAll)
END_CMD_MAP()

void CAlnMultiView::OnDocumentChanged()
{
    if (m_Document) {
        SetTitle(m_Document->GetShortTitle() + ": " + GetTitle());

        // create our alignment manager
        m_DataSource.Reset(new CAlnVecMultiDataSource());
        m_DataSource->Init(*m_AnnotData, m_Document->GetScope());

        m_AlnWidget->SetDataSource(m_DataSource);

        SetSelBuffer().Clear();
        SetSelBuffer().AddSelection(GetDocument(), *m_AnnotData);

        m_ViewMenuMgr->AddActiveViews(m_Document);
        m_ViewMenuMgr->AddNewViews();//   (GetSelBuffer());
        m_AlgoMenuMgr->AddAlgoMenu();//   (GetSelBuffer());
    }
}

void CAlnMultiView::OnSelectionChanged(const CSelectionBuffer& buf)
{
    if (m_Document) {
        if ( !GetSelBuffer() ) {
            SetSelBuffer().AddSelection(GetDocument(), *m_AnnotData);
        }

        m_ViewMenuMgr->AddActiveViews(m_Document);
        m_ViewMenuMgr->AddNewViews();//   (GetSelBuffer());
        m_AlgoMenuMgr->AddAlgoMenu();//   (GetSelBuffer());
    }
}


void CAlnMultiView::OnVisibleRangeChanged(const CSeq_loc& loc)
{
}

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

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

void CAlnMultiView::x_OnHelp()
{
}

void CAlnMultiView::OnResetSelection()
{
    if (m_AlnWidget) {
        m_AlnWidget->OnResetSelection();
    }

    SetSelBuffer().Clear();
    SetSelBuffer().AddSelection(GetDocument(), *m_AnnotData);

    m_ViewMenuMgr->AddActiveViews(m_Document);
    m_ViewMenuMgr->AddNewViews();//   (GetSelBuffer());
    m_AlgoMenuMgr->AddAlgoMenu();//   (GetSelBuffer());
}


void CAlnMultiView::OnMakeConsensusRowMaster()
{
    if (m_DataSource.GetPointer()  &&  m_AlnWidget) {
        IAlnMultiDataSource::TNumrow row = m_DataSource->GetConsensusRow();
        
        if(row == -1)   { // create it
            m_DataSource->CreateConsensus();
            row = m_DataSource->GetConsensusRow();
        }

        m_DataSource->SetAnchor(row); //last row - consensus

        m_AlnWidget->SetDataSource(m_DataSource);
        //m_AlnWidget->MakeConsensusRowMaster();
        //m_AlnWidget->redraw();
    }
}

void CAlnMultiView::OnMarkSelected(void)
{
    if (m_AlnWidget) {
        m_AlnWidget->OnMarkSelected();

        // fill our selection buffer
        SetSelBuffer().Clear();

        // GetMarks() returns marked locations
        CAlnMultiWidget::TPSeqLocList locs;
        m_AlnWidget->GetMarks(locs);
        ITERATE (CAlnMultiWidget::TPSeqLocList, iter, locs) {
            SetSelBuffer().AddSelection(GetDocument(), **iter);
        }

        /**
        // GetSelection() returns selections in alignment coordinates
        const CAlnMultiWidget::TRangeColl& range_coll = m_AlnWidget->GetSelection();