hit_matrix_pane.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: hit_matrix_pane.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 21:10:58  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: hit_matrix_pane.cpp,v 1000.3 2004/06/01 21:10:58 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:  Andrey Yazhuk
 *
 * File Description:
 *
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbistl.hpp>
#include <corelib/ncbitime.hpp>
#include <gui/widgets/hit_matrix/hit_matrix_pane.hpp>
#include <gui/widgets/hit_matrix/hit_matrix_widget.hpp>

#include <FL/Fl.H>

BEGIN_NCBI_SCOPE

#define AXIS_AREA_W 50
#define AXIS_AREA_H 30

CHitMatrixPane::CHitMatrixPane(int PosX, int PosY, int Width, int Height, const char* Label)
:   CGlPaneWidgetChild(PosX, PosY, Width, Height, Label),
    m_BackColor(0.95f, 1.0f, 0.95f),
    m_pTextFont(NULL),
    m_pSeqFont(NULL),
    m_VertSelHandler(eVert),
    m_BottomRuler(true),
    m_TopRuler(true),
    m_LeftRuler(false),
    m_RightRuler(false),
    m_QueryGraph(false),
    m_SubjectGraph(true)
{
    m_MatrixPane.EnableOffset(true);
    m_SubjectPane.EnableOffset(true);
    m_QueryPane.EnableOffset(true);

    m_Gen.SetIntegerMode(true, true);
    m_Gen.EnableOneBased(true, true);
    m_Grid.EnableIntegerCentering(true);

    m_pTextFont = new CGlBitmapFont(CGlBitmapFont::eHelvetica12);
    m_pSeqFont = new CGlBitmapFont(CGlBitmapFont::eCourier14);    
    m_QueryGraph.SetFonts(m_pTextFont, m_pSeqFont);
    m_SubjectGraph.SetFonts(m_pTextFont, m_pSeqFont);


    //setup Event Handlers
    m_HorzSelHandler.SetHost(static_cast<ISelHandlerHost*>(this));
    x_RegisterHandler(dynamic_cast<IEventHandler*>(&m_HorzSelHandler), fSubjectArea, &m_SubjectPane);

    m_VertSelHandler.SetHost(static_cast<ISelHandlerHost*>(this));
    x_RegisterHandler(dynamic_cast<IEventHandler*>(&m_VertSelHandler), fQueryArea, &m_QueryPane);

    m_MouseZoomHandler.SetHost(static_cast<IMouseZoomHandlerHost*>(this));
    x_RegisterHandler(dynamic_cast<IEventHandler*>(&m_MouseZoomHandler), fMatrixArea, &m_MatrixPane);

    m_Graph.SetHost(static_cast<IHitMatrixGraphHost*>(this));
    x_RegisterHandler(dynamic_cast<IEventHandler*>(&m_Graph), fMatrixArea, &m_MatrixPane);

    /* x_AddHandler(dynamic_cast<IEventHandler*>(this), fDescrArea);
    */
    m_Event.StandardConfig();  
    
    x_Layout();
    x_SetupAxes();
}

void    CHitMatrixPane::x_SetupAxes()
{
    m_TopRuler.SetHorizontal(true, CRuler::eTop);
    m_RightRuler.SetHorizontal(false, CRuler::eRight);
}

TVPPoint CHitMatrixPane::GetPortSize(void)
{
    return TVPPoint(m_rcMatrix.Width(), m_rcMatrix.Height());
}


void CHitMatrixPane::SetWidget(CHitMatrixWidget* pParent)
{
    m_pParent = pParent;
    
    if(m_pParent)   {
        m_MatrixPane = x_GetParent()->GetPort();
    }
}

void    CHitMatrixPane::resize(int x, int y, int w, int h)
{
    CGlPaneWidgetChild::resize(x, y, w, h);
    x_Layout();

    m_MatrixPane.SetViewport(m_rcMatrix);
    
    m_SubjectPane.SetViewport(m_rcBottomSeq);
    x_AdjsutToMasterPane(m_SubjectPane, true, false);
    
    m_QueryPane.SetViewport(m_rcLeftSeq);        
    x_AdjsutToMasterPane(m_QueryPane, false, true);
}

void    CHitMatrixPane::x_Render(void)
{
    glClearColor(m_BackColor.GetRed(), m_BackColor.GetGreen(), m_BackColor.GetBlue(), m_BackColor.GetAlpha());
    glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);    
    
    // optional render background images    
    x_RenderContent();
}

void    CHitMatrixPane::Update()
{    
    _ASSERT(x_GetParent());    
    m_Graph.DeleteGlyphs();

    CHitMatrixDataSource* pDS = x_GetParent()->GetDS();
    if(pDS) {
        CBioseq_Handle q_handle = pDS->GetQueryHandle();
        CBioseq_Handle s_handle = pDS->GetSubjectHandle();
        const CHitMatrixDataSource::THitAdapterCont&   hits = pDS->GetHits();
        for( CHitMatrixDataSource::THitAdapterCont::const_iterator it =
             hits.begin(); it != hits.end(); it++ )   {
            //const CHitDataAdapter* hit = *it;
            //cout << "Q Start " << hit.GetQueryStart() << ", Subj Start " << hit.GetSubjectStart() << endl;
            m_Graph.CreateGlyph(&(*it));
        }
     
        if(m_ColorScoreId)  {
            m_Graph.AssignColorsByScore(m_ColorScoreId);
            m_ColorScoreId.Reset();
        }
        m_SubjectGraph.SetBioseqHandle(s_handle);
        m_QueryGraph.SetBioseqHandle(q_handle);
    } else {
        CBioseq_Handle h_null;
        m_SubjectGraph.SetBioseqHandle(h_null);
        m_QueryGraph.SetBioseqHandle(h_null);
    }
}

void    CHitMatrixPane::ColorByScore(CConstRef<CObject_id> score_id)
{
    m_ColorScoreId = score_id;
    CHitMatrixDataSource* pDS = x_GetParent()->GetDS();
    if(pDS) {
        m_Graph.AssignColorsByScore(score_id);
    }
}

typedef multimap<const CHitDataAdapter*, const CHitElemGlyph*>  THitToElemGlyphMap;

bool    SubjectStartLess(const CHitElemDataAdapter* el1, const CHitElemDataAdapter* el2)
{
    return  el1->GetSubjectStart() < el2->GetSubjectStart();
} 

CConstRef<CSeq_align_set>    CHitMatrixPane::GetSelectedHits() const
{
    const TElemGlyphSet& glyphs = m_Graph.GetSelectedGlyphs();
    
    // build a temporary map
    THitToElemGlyphMap   hit_to_glyph;
    ITERATE( CHitMatrixPane::TElemGlyphSet, it_G, glyphs)   {
        const CHitElemDataAdapter& elem = (*it_G)->GetHitElem();
        const CHitDataAdapter& hit = elem.GetHit();
        hit_to_glyph.insert(THitToElemGlyphMap::value_type(&hit, *it_G));
    }

    // create a new seq-align-set
    CRef<CSeq_align_set>    set(new CSeq_align_set);
    CSeq_align_set::Tdata   ls_rf_aligns = set->Set();

    const CHitDataAdapter*  p_curr_hit = NULL;
    CSeq_align* p_align = NULL;
    CDense_seg* p_denseg = NULL;
    vector<const CHitElemDataAdapter*>    elems;
    
    // iterate by Glyphs
    for( THitToElemGlyphMap::const_iterator it = hit_to_glyph.begin();
            it != hit_to_glyph.end(); )   {
        // for a new Hit create a CSeq_align
        p_curr_hit = it->first;
        p_align = new CSeq_align();            
        p_align->SetType(CSeq_align::eType_partial);

        ls_rf_aligns.push_back(CRef<CSeq_align>(p_align)); // add to set

        CSeq_align::C_Segs& segs = p_align->SetSegs();
        segs.Select(CSeq_align::C_Segs::e_Denseg);
        p_denseg = & segs.SetDenseg();            
        
        // for all elements of the current hit - add to list
        for( ; it != hit_to_glyph.end()  &&  it->first == p_curr_hit; it++ )    {
            const CHitElemDataAdapter& elem = it->second->GetHitElem();
            elems.push_back(&elem);
        }
        int size = elems.size();
        if(size)
            sort(elems.begin(), elems.end(), SubjectStartLess);

        p_denseg->SetDim(2);
        p_denseg->SetNumseg(size);
        p_denseg->SetStarts().resize(2*size);
        p_denseg->SetLens().resize(size);
        p_denseg->SetStrands().resize(size);

        // add elems to denseg
        int i_start = 0, i_len = 0;
        ITERATE(vector<const CHitElemDataAdapter*>, it_e, elems)   {
            const CHitElemDataAdapter* elem  = *it_e;

            p_denseg->SetStarts()[i_start++] = elem->GetSubjectStart();
            p_denseg->SetStarts()[i_start++] = elem->GetQueryStart();
            p_denseg->SetLens()[i_len++] = elem->GetLength();            
        }
        elems.clear();
    }

    return ConstRef<CSeq_align_set>(set);
}

TModelRect  CHitMatrixPane::GetSelectedHitElemsRect() const
{
    const TElemGlyphSet& glyphs = m_Graph.GetSelectedGlyphs();
    bool b_first = true;    
    
    int left, right, top, bottom;
    ITERATE( CHitMatrixPane::TElemGlyphSet, it_G, glyphs)   {
        const CHitElemDataAdapter& elem = (*it_G)->GetHitElem();
        
        int s_from = elem.GetSubjectStart();
        int q_from = elem.GetQueryStart();
        int len = elem.GetLength();
        int s_to = s_from + len;
        int q_to = q_from + len;        
        
        if(q_from > q_to)
            swap(q_from, q_to);
        if(s_from > s_to)   
            swap(s_from, s_to);

        if(b_first) {
            left = s_from;            right = s_to;
            bottom = q_from;          top = q_to;
            b_first = false;
        } else {
            left = min(left, s_from);
            right = max(right, s_to);
            bottom = min(bottom, q_from);
            top = max(top, q_to);