cross_panel_ir.cpp

来自「ncbi源码」· C++ 代码 · 共 401 行

/*
 * ===========================================================================
 * PRODUCTION $Log: cross_panel_ir.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 21:06:37  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: cross_panel_ir.cpp,v 1000.1 2004/06/01 21:06:37 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
 *
 */


#include <ncbi_pch.hpp>
#include <gui/widgets/aln_crossaln/cross_panel_ir.hpp>
#include <objmgr/seq_vector.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/opengl/glcolortable.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


const TModelUnit   kSeqMapBarHeight = 3.0f;

CCrossPanelIR::CCrossPanelIR()
    : m_Font_Bitmap9x15(CGlBitmapFont::eBitmap9x15)
{
    m_OneCharWidth = int( m_Font_Bitmap9x15.TextWidth("A") );
}


CCrossPanelIR::~CCrossPanelIR()
{
}


void CCrossPanelIR::SetProportions(TModelUnit k, TModelUnit dx)
{
    m_K = k;
    m_Dx = dx;
}


void CCrossPanelIR::SetShifts(TModelUnit sh1, TModelUnit sh2)
{
    m_Sh1 = sh1;
    m_Sh2 = sh2;
}


void CCrossPanelIR::SetDataSource(CCrossAlnDataSource* ds)
{
    m_DS = ds;
}


void CCrossPanelIR::Render(CGlPane& pane)
{
    const TModelRect& rcV = pane.GetVisibleRect();
    
    m_OffsetX = pane.GetOffsetX();
    m_OffsetY = pane.GetOffsetY();
        
    pane.OpenOrtho();
    
    // 1) Draw Black bars
    CBioseq_Handle hndl1 = m_DS->GetQueryHandle();
    CBioseq_Handle hndl2 = m_DS->GetSubjectHandle();
    
    TSeqPos s1 = hndl1.GetSeqVector(CBioseq_Handle::eCoding_Iupac).size();
    TSeqPos s2 = hndl2.GetSeqVector(CBioseq_Handle::eCoding_Iupac).size();

    TModelUnit x1 = x_Seq2Lim1(0);  // Convert from sequence to limits
    TModelUnit x2 = x_Seq2Lim1(s1);
    
    TModelUnit xx1 = x_Seq2Lim2(0);
    TModelUnit xx2 = x_Seq2Lim2(s2);

    glColor3f(0.07f, 0.07f, 0.07f);
    glBegin(GL_QUADS);
        glVertex2f(x1, rcV.Top() + 5 - m_OffsetY);
        glVertex2f(x2, rcV.Top() + 5 - m_OffsetY);
        glVertex2f(x2, rcV.Top() + 17 - m_OffsetY);
        glVertex2f(x1, rcV.Top() + 17 - m_OffsetY);
    
        glVertex2f(xx1, rcV.Bottom() - 5 - m_OffsetY);
        glVertex2f(xx2, rcV.Bottom() - 5 - m_OffsetY);
        glVertex2f(xx2, rcV.Bottom() - 18 - m_OffsetY);
        glVertex2f(xx1, rcV.Bottom() - 18 - m_OffsetY);
    glEnd();
    

    // 2) Draw cross alignment lines
    glEnable(GL_BLEND);
    glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
    glEnable(GL_LINE_SMOOTH);
    glHint(GL_LINE_SMOOTH_HINT, GL_NICEST);
    glLineWidth(1.5f);

    x_DrawCrossAlignment(pane, GL_QUADS    );  // Draw our quads
    x_DrawCrossAlignment(pane, GL_LINE_LOOP);  // Draw the outline

    // 3) Draw two Sequences
    bool seq_fit1 = x_IsSeqLettersFit1(pane);
    bool seq_fit2 = x_IsSeqLettersFit2(pane);
    
    GLfloat y1 = rcV.Top() + m_Font_Bitmap9x15.TextHeight() + 5;
    GLfloat y2 = rcV.Bottom() - m_Font_Bitmap9x15.TextHeight() + 3;

    
    TModelUnit one1 = pane.UnProjectWidth(m_OneCharWidth);
    TModelUnit add1 = (1.0f - one1) / 2.0f;
    
    TModelUnit one2 = pane.UnProjectWidth(m_OneCharWidth) / m_K;
    TModelUnit add2 = (1.0f - one2) / 2.0f;
    
    //cout << "m_K: " << m_K << "  /  one1: " << one1 << "  /  one2: " << one2 << endl;
    
    char bases[2];
    bases[1] = '\0';
    string seq1, seq2;
    glColor3f(0.55f, 0.55f, 0.55f);

    if (seq_fit1) {  // sequence 1 fit
        TModelUnit l1 = x_Lim2Seq1( rcV.Left () );
        TModelUnit r1 = x_Lim2Seq1( rcV.Right() );

        if (l1 < 0) l1 = 0;
        x_GetSequence(hndl1, l1, r1, seq1);
        
        for (TSeqPos bp = 0;  bp != seq1.length();  bp++) {
            bases[0] = seq1[bp];
            m_Font_Bitmap9x15.TextOut(x_Seq2Lim1(TSeqPos(l1) + bp) + add1,
                                      y1 - m_OffsetY, bases);
        }
    }
    
    if (seq_fit2) {  // sequence 2 fit
        TModelUnit l2 = x_Lim2Seq2( rcV.Left () );
        TModelUnit r2 = x_Lim2Seq2( rcV.Right() );

        if (l2 < 0) l2 = 0;
        x_GetSequence(hndl2, l2, r2, seq2);
        
        for (TSeqPos bp = 0;  bp != seq2.length();  bp++) {
            bases[0] = seq2[bp];
            m_Font_Bitmap9x15.TextOut(x_Seq2Lim2(TSeqPos(l2) + bp) + add2,
                                      y2 - m_OffsetY, bases);
        }
    }

    
    // 4) Highlight mismatches (and draw connection lines)
    if (seq_fit1  ||  seq_fit2) {
        const CCrossAlnDataSource::THitAdapterCont& hits = m_DS->GetHits();        
        ITERATE(CCrossAlnDataSource::THitAdapterCont, iter, hits) {
            for (size_t idx = 0;  idx != (*iter).GetElemsCount();  idx++) {
                CHitElemDataAdapter elem = (*iter).GetElem(idx);
                if (elem.GetQueryStart() < 0  || elem.GetSubjectStart() < 0 ) {
                    continue;
                }
                
                TSeqPos from1 = elem.GetQueryStart();
                TSeqPos from2 = elem.GetSubjectStart();
                TSeqPos to1   = from1 + elem.GetLength();
                TSeqPos to2   = from2 + elem.GetLength();
                //cout << "from1: " << from1 << " : to1: " << to1 << "   /   from2: " << from2 << " : to2: " << to2 << endl;
                
                x_GetSequence(hndl1, from1, to1, seq1);
                x_GetSequence(hndl2, from2, to2, seq2);
    
                GLfloat y1 = rcV.Top() + m_Font_Bitmap9x15.TextHeight() + 5;
                GLfloat y2 = rcV.Bottom() - m_Font_Bitmap9x15.TextHeight() + 3;
                
                TSeqPos bp = 0;
                for (TSeqPos pos = 0;  pos != to1 - from1;  pos++) {
                    GLfloat x1 = x_Seq2Lim1(from1 + pos);
                    GLfloat x2 = x_Seq2Lim2(from2 + pos);
                    
                    // Draw lines to connect mismatches
                    glColor3f(1.0f, 1.0f, 1.0f);  // black
                    
                    if (seq1[bp] != seq2[bp]) {
                        if (seq_fit1  &&  seq_fit2) {
                            glColor4f(1.0f, 0.0f, 0.0f, 0.5f);
                            
                            glBegin(GL_LINES);
                            glVertex2f(x1  , rcV.Top()    + 17 - m_OffsetY);
                            glVertex2f(x2  , rcV.Bottom() - 18 - m_OffsetY);
                            glVertex2f(x1+1, rcV.Top()    + 17 - m_OffsetY);
                            glVertex2f(x2+1, rcV.Bottom() - 18 - m_OffsetY);
                            glEnd();
                        }
                        glColor3f(1.0f, 0.0f, 0.0f);
                    }
                    
                    if (seq_fit1) {
                        bases[0] = seq1[bp];
                        m_Font_Bitmap9x15.TextOut(x1 + add1, 
                                                y1 - m_OffsetY, bases);
                    }
    
                    if (seq_fit2) {
                        bases[0] = seq2[bp];
                        m_Font_Bitmap9x15.TextOut(x2 + add2, 
                                                y2 - m_OffsetY, bases);
                    }
                    bp++;
                } // for: pos
            } // size_t
        } // for: map
    }
    
    glDisable(GL_BLEND);
    glDisable(GL_LINE_SMOOTH);
    glLineWidth(1.0f);

    pane.Close();
}


void CCrossPanelIR::x_DrawCrossAlignment(CGlPane& pane, GLenum shape)
{
    const TModelRect& rcV = pane.GetVisibleRect();

    const CCrossAlnDataSource::THitAdapterCont& hits = m_DS->GetHits();
    int count = 0;
    ITERATE(CCrossAlnDataSource::THitAdapterCont, iter, hits) {
        count += (*iter).GetElemsCount();
    }
    
    CGlColorTable table(count, 0.5f, 0.75f);
    ITERATE(CCrossAlnDataSource::THitAdapterCont, iter, hits) {
        for (size_t idx = 0;  idx != (*iter).GetElemsCount();  idx++) {
            CHitElemDataAdapter elem = (*iter).GetElem(idx);
            if (elem.GetQueryStart() < 0  || elem.GetSubjectStart() < 0 ) {
                continue;
            }
            
            TSeqPos from1 = elem.GetQueryStart();
            TSeqPos from2 = elem.GetSubjectStart();
            TSeqPos to1   = from1 + elem.GetLength();
            TSeqPos to2   = from2 + elem.GetLength();
            
            TModelUnit x_from1 = x_Seq2Lim1(from1);
            TModelUnit x_to1   = x_Seq2Lim1(to1);
    
            TModelUnit x_from2 = x_Seq2Lim2(from2);
            TModelUnit x_to2   = x_Seq2Lim2(to2);
            
            CGlColor color = table.GetColor(idx);
            glColor4f(color.GetRed(), color.GetGreen(), color.GetBlue(), 
                shape == GL_QUADS ? 0.4 : 0.8);
    
            glBegin(shape);
            glVertex2f(x_from1, rcV.Top() + 19 - m_OffsetY);
            glVertex2f(x_to1,   rcV.Top() + 19 - m_OffsetY);
            glVertex2f(x_to2,   rcV.Bottom() - 21 - m_OffsetY);
            glVertex2f(x_from2, rcV.Bottom() - 21 - m_OffsetY);
            glEnd();
        }
    }    
}



void CCrossPanelIR::x_GetSequence(const CBioseq_Handle& handle,
            TModelUnit from, TModelUnit to, string& buffer) const
{
    buffer.erase();
    CSeqVector s_vec =
        handle.GetSeqVector(CBioseq_Handle::eCoding_Iupac);

    s_vec.GetSeqData(TSeqPos(from), TSeqPos(to), buffer);
}





// Convert sequence to limits
TModelUnit CCrossPanelIR::x_Seq2Lim1(TModelUnit seq)
{
    if (m_Dx < 0) return seq - m_Dx - m_OffsetX;
    else return seq - m_OffsetX;
}


TModelUnit CCrossPanelIR::x_Seq2Lim2(TModelUnit seq)
{
    if (m_Dx > 0) return (seq + m_Dx - m_Sh2 ) * m_K + m_Sh1 - m_OffsetX;
    else return (seq - m_Sh2) * m_K + m_Sh1 - m_OffsetX;
}


// Convert limits to sequence
TModelUnit CCrossPanelIR::x_Lim2Seq1(TModelUnit lim)
{
    if (m_Dx < 0) return lim + m_Dx;
    else return lim;
}


TModelUnit CCrossPanelIR::x_Lim2Seq2(TModelUnit lim)
{
    if (m_Dx > 0) return (lim - m_Sh1) / m_K -m_Dx + m_Sh2;
    else return (lim - m_Sh1) / m_K + m_Sh2;
}


bool CCrossPanelIR::x_IsSeqLettersFit1(CGlPane& pane) const
{
    return pane.GetScaleX() <= 1.0f / 8.0f;
}

bool CCrossPanelIR::x_IsSeqLettersFit2(CGlPane& pane) const
{
    return pane.GetScaleX() / m_K <= 1.0f / 8.0f;
}


// IRenderable
TVPRect CCrossPanelIR::GetVPRect()
{
    TVPRect rc(0, 0);
    rc.SetSize(0, 0);
    return rc;
}


TModelRect CCrossPanelIR::GetModelRect()
{
    TModelRect rc(0, 0);
    rc.SetSize(0, 0);
    return rc;
}




    
END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: cross_panel_ir.cpp,v $
 * Revision 1000.1  2004/06/01 21:06:37  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 *
 * Revision 1.6  2004/05/21 22:27:52  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.5  2004/05/03 13:23:57  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.4  2004/03/11 17:50:41  dicuccio
 * Updated typedefs: dropped TDimension, TPosition, TIndex, TColor; use TSeqRange
 * instead of TRange
 *
 * Revision 1.3  2003/12/23 12:59:42  ucko
 * Avoid deque<>::const_iterator::operator->, which fails to compile on
 * GCC 2.95.x due to a typo in its STL implementation. :-/
 *
 * Revision 1.2  2003/12/22 16:51:33  lebedev
 * Use CHitElemDataAdapter to get start/length from datasource
 *
 * Revision 1.1  2003/12/22 13:12:34  lebedev
 * Initial revision
 *
 * ===========================================================================
 */