features_panel_ir.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: features_panel_ir.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 21:12:35  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.19
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: features_panel_ir.cpp,v 1000.3 2004/06/01 21:12:35 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/seq_graphic/features_panel_ir.hpp>

#include <algorithm>
#include <ctype.h>
#include <math.h>



#include <objmgr/scope.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/alnmgr/alnmix.hpp>

#include <serial/iterator.hpp>
#include <util/sequtil/sequtil_manip.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);



const TModelUnit kPixPerBase4Sequence = 8.0f; // at this point sequence will fit
const int        kLabelsMaxWidth      = 90;   // width of a feature label small


//const TSeqPos    kGenesOverviewZoom  = 150;  // 150 bp per pixel


CFeaturesPanelIR::CFeaturesPanelIR()
{
}


CFeaturesPanelIR::~CFeaturesPanelIR()
{
}


void CFeaturesPanelIR::SetHandle(const CBioseq_Handle& handle)
{
    m_Handle = handle;
    if (m_RenderPolicy) {
        m_RenderPolicy->SetHandle(handle);
    }

    if (m_LayoutPolicy) {
        m_LayoutPolicy->SetHandle(handle);
    }
}


void CFeaturesPanelIR::SetRenderPolicy(IPolicy* policy)
{
    m_RenderPolicy.Reset(policy);
    if (m_RenderPolicy) {
        m_RenderPolicy->SetConfig(m_ConfigSettings);
        m_RenderPolicy->SetHandle(m_Handle);
    }
}


void CFeaturesPanelIR::SetLayoutPolicy(ILayoutPolicy* policy)
{
    m_LayoutPolicy.Reset(policy);
    if (m_LayoutPolicy) {
        m_LayoutPolicy->SetConfig(m_ConfigSettings);
        m_LayoutPolicy->SetHandle(m_Handle);
    }
}


void CFeaturesPanelIR::SetConfig(CSeqGraphicConfig* config)
{
    m_ConfigSettings = config;
    if (m_RenderPolicy) {
        m_RenderPolicy->SetConfig(config);
    }
    if (m_LayoutPolicy) {
        m_LayoutPolicy->SetConfig(config);
    }
}


TModelUnit CFeaturesPanelIR::GetHeight(CGlPane& pane)
{
    m_LayoutPolicy->PrepareData(pane, m_PackedObjects);

    m_RowCount = 0;
    pane.OpenOrtho();
    x_MainObjectIterator(pane, IPolicy::eCalcObjectRows);
    pane.Close();

    return (m_RowCount + 5);// * m_RenderPolicy->GetOneRowHeight();
}


void CFeaturesPanelIR::Render(CGlPane& pane)
{    
    pane.OpenOrtho();

    glBegin(GL_LINES);
    x_DrawXGrid(pane);
    glEnd();


    m_ConfigSettings->GetElementColor(CSeqGraphicColorConfig::eGridHorizontal);
    x_MainObjectIterator(pane, IPolicy::eDrawObjectGrid);

    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_MainObjectIterator(pane, IPolicy::eDrawObjectQuads);
    x_MainObjectIterator(pane, IPolicy::eDrawObjectLines);
    x_MainObjectIterator(pane, IPolicy::eDrawObjectLabel);

    glDisable(GL_BLEND);
    glDisable(GL_LINE_SMOOTH);
    glLineWidth(1.0f);

    pane.Close();
}




TVPRect CFeaturesPanelIR::GetVPRect()
{
    TVPRect rc(0, 0, 0, 0);
    return rc;
}


TModelRect CFeaturesPanelIR::GetModelRect()
{
    TModelRect rc(0, 0);
    rc.SetSize(0, m_RowCount + 5);// * m_RenderPolicy->GetOneRowHeight());
    return rc;
}



bool CFeaturesPanelIR::x_IsSeqLettersFit(CGlPane& pane) const
{
    return pane.GetScaleX() <= 1.0f / kPixPerBase4Sequence;
}



const CLayoutObject*
CFeaturesPanelIR::HitTest(CGlPane& pane, int x, int y)
{
    pane.OpenOrtho();
    m_LastClick = pane.UnProject(x, y);
    pane.Close();
    m_RenderPolicy->SetHitPoint(m_LastClick);

    const CLayoutObject* obj = x_MainObjectIterator(pane, IPolicy::eObjectHitTest);
    return obj;
}


void CFeaturesPanelIR::GetTooltip(const CLayoutObject* obj, string* title) const
{
    m_RenderPolicy->GetTitle(obj, title, CLabel::eTooltipDetailed);
}


void CFeaturesPanelIR::GetHTMLActiveAreas(CGlPane& pane,
                                          IPolicy::TAreaVector* p_areas)
{
    m_RenderPolicy->SetActiveArea(p_areas);

    x_MainObjectIterator(pane, IPolicy::eGetHTMLAreas);
}


const CLayoutObject* 
CFeaturesPanelIR::x_MainObjectIterator(CGlPane& pane,
                                       IPolicy::EObj_IterMode mode)
{
    glLineWidth(1.0f);

    switch (mode) {
    case IPolicy::eDrawObjectLines:
    case IPolicy::eDrawObjectGrid:
        glBegin(GL_LINES);
        break;

    case IPolicy::eDrawObjectQuads:
        glBegin(GL_QUADS);
        break;
    default:
        break;
    }

    TModelUnit row = 0.0f;
    vector<CLayoutFeat::TFeatList> leaves;
    ITERATE (CLayout::TLayout, row_iter, m_PackedObjects.GetLayout()) {
        TModelUnit new_row = row;
        ITERATE (CLayout::TLayoutRow, obj_iter, *row_iter) {
            TModelUnit temp_row = row;
            const CLayoutObject* obj = *obj_iter;

            const CLayoutFeat* curr_feat =
                dynamic_cast<const CLayoutFeat*>(obj);

            bool selected = x_IsObjectSelected(obj);

            // First, decompose into a vector of leaves suitable for
            // rendering.  we do this in an odd way - we exclude the current
            // feature and only examine its kids.
            leaves.clear();
            if (curr_feat) {
                ITERATE (CLayoutFeat::TFeatList, kid_iter,
                         curr_feat->GetChildren()) {
                    x_DecomposeToLeaves(*kid_iter, leaves);
                }
            }

            // render the current feature
            if (m_RenderPolicy->ProcessObject(pane, *obj_iter, temp_row,
                                              mode, selected)) {
                return *obj_iter;
            }

            temp_row += m_RenderPolicy->GetRowHeight(pane, *obj_iter, selected);

            // now, render all the leaf arrays
            ITERATE (vector<CLayoutFeat::TFeatList>, leaf_iter, leaves) {
                ITERATE (CLayoutFeat::TFeatList, iter, *leaf_iter) {
                    bool selected = x_IsObjectSelected(iter->GetPointer());
                    if (m_RenderPolicy->ProcessObject(pane, *iter, temp_row,
                                                      mode, selected)) {
                        return *iter;
                    }
                    temp_row += m_RenderPolicy->GetRowHeight(pane, *iter, selected);
                }
            }  // leaf arrays
            new_row = max (new_row, temp_row);
        } // top features
        row = new_row;
    } // row iterator

    switch (mode) {
    case IPolicy::eDrawObjectLines:
    case IPolicy::eDrawObjectQuads:
    case IPolicy::eDrawObjectGrid:
        glEnd();
        break;

    case IPolicy::eCalcObjectRows:
        m_RowCount = row;  // save number of rows
        break;
    default:
        break;
    }

    return NULL;
}



//
// recursive function to extract a set of paths from the root of a given tree
// to each of the leaves.
//
void CFeaturesPanelIR::x_DecomposeToLeaves(const CLayoutFeat* feat,
                                           vector<CLayoutFeat::TFeatList>& leaves)
{
    CLayoutFeat::TFeatList leaf;
    x_DecomposeToLeaves(feat, leaves, leaf);
}


void CFeaturesPanelIR::x_DecomposeToLeaves(const CLayoutFeat* feat,
                                           vector<CLayoutFeat::TFeatList>& leaves,
                                           CLayoutFeat::TFeatList& leaf)
{
    leaf.push_back(CRef<CLayoutFeat>(const_cast<CLayoutFeat*>(feat)));
    if (feat->GetChildren().size()) {
        ITERATE (CLayoutFeat::TFeatList, iter, feat->GetChildren()) {
            CLayoutFeat::TFeatList sub_leaf(leaf);
            x_DecomposeToLeaves(*iter, leaves, sub_leaf);
        }
    } else {
        leaves.push_back(leaf);
    }
}


void CFeaturesPanelIR::x_DrawXGrid(CGlPane& pane) const
{
    if ( x_IsSeqLettersFit(pane) ) {
        const TModelRect& rc = pane.GetVisibleRect();

        m_ConfigSettings->GetElementColor(
                                          CSeqGraphicColorConfig::eGridVertical);

        TModelUnit x = rc.Left() - (int)(rc.Left()) % 3;
        TModelUnit x_end = rc.Right() + (int)(rc.Right()) % 3;

        for (;  x <= x_end;  x += 3) 
        {
            glVertex2d(x - pane.GetOffsetX(), rc.Top()    - pane.GetOffsetY() );
            glVertex2d(x - pane.GetOffsetX(), rc.Bottom() - pane.GetOffsetY() );
        }
    }
}




// Selections
void CFeaturesPanelIR::SetSelectedObjects(TConstObjects* objs)
{
    m_SelectedObjects = objs;
}


bool CFeaturesPanelIR::x_IsObjectSelected(const CLayoutObject* obj) const
{
    // Make sure we iterate through all selected objects
    bool found = false;
    ITERATE (TConstObjects, iter, *m_SelectedObjects) {
        try {
            const CObject* tmp = *iter;
            if (obj->HasObject(tmp))
                found = true;
        }
        catch (...) {
        }
    }
    return found;
}



END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: features_panel_ir.cpp,v $
 * Revision 1000.3  2004/06/01 21:12:35  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.19
 *
 * Revision 1.19  2004/05/21 22:27:55  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.18  2004/05/14 15:57:11  lebedev
 * Optional argument to specify the type of title/tooltip added
 *
 * Revision 1.17  2004/04/22 18:15:57  lebedev
 * Slightly changed how the layout objects get selected
 *
 * Revision 1.16  2004/04/16 14:52:19  dicuccio
 * Pass params as raw pointers, not CRef<>
 *
 * Revision 1.15  2004/04/15 13:02:13  lebedev
 * HitTesting for LayoutObjects changed
 *
 * Revision 1.14  2004/04/14 11:25:48  lebedev
 * Added rendering of Mate Pairs.
 *
 * Revision 1.13  2004/04/06 13:43:07  dicuccio
 * Formatting changes.  Folded long lines, removed trailing white space
 *
 * Revision 1.12  2004/03/31 16:08:58  lebedev
 * Methods to get HTML active areas added.
 *
 * Revision 1.11  2004/03/30 13:58:37  lebedev
 * Use elements colors from configuration instead of setting colors directly.
 *
 * Revision 1.10  2004/03/23 12:33:56  lebedev
 * Made sequence and histograms bars a layout objects in the object panel.
 * Made segment map a number of layout objects. Get rid of fixed size rows in
 * the object panel.
 *
 * Revision 1.9  2004/03/11 17:53:06  dicuccio
 * Deprecated typedefs TPosition, TDimension, TIndex, TColor.  Use TSeqRange
 * instead of TRange
 *
 * Revision 1.8  2004/02/24 14:45:25  lebedev
 * Better implementation of main rendering loop. Code clean-up.
 *
 * Revision 1.7  2004/02/13 18:14:33  lebedev
 * Make use of new ILayoutPolicy interface
 *
 * Revision 1.6  2004/01/27 16:14:19  lebedev
 * Changed stored selection from CLayoutObject to CObject
 *
 * Revision 1.5  2004/01/20 19:42:44  rsmith
 * make SetConfig, SetPolicy and SetHandle safer.
 *
 * Revision 1.4  2004/01/16 13:40:15  lebedev
 * Tooltips added
 *
 * Revision 1.3  2004/01/05 19:13:53  dicuccio
 * Use a more optimal mechanism for rendering grid
 *
 * Revision 1.2  2003/12/31 20:30:21  dicuccio
 * Wrap call to CLayoutObject::GetObject() in try/catch to avoide a catastrophic
 * exception
 *
 * Revision 1.1  2003/12/22 12:58:59  lebedev
 * Files renamed
 *
 * Revision 1.21  2003/12/16 18:56:38  lebedev
 * Introduced Rendering Policies for feature panels
 *
 * Revision 1.20  2003/12/09 12:32:43  lebedev
 * Trim gene names in overview mode to fit in columns. 
 * Option to show feature names in detailed mode
 *
 * Revision 1.19  2003/11/17 21:05:39  yazhuk
 * Updated CGlBitmapFont::Truncate() calls to conform with the new argument set
 *
 * Revision 1.18  2003/11/13 19:11:06  lebedev
 * Objects selection reorganized. One row ofset bug in selection fixed
 *
 * Revision 1.17  2003/11/13 14:26:14  lebedev
 * Do not reverse the sequence for neg. strand CDSs (just complement)
 *
 * Revision 1.16  2003/11/10 18:47:07  ucko
 * Adjust for const-correctness.
 *
 * Revision 1.15  2003/11/10 17:01:38  lebedev
 * Display of SeqGraphs and named SeqAnnots added
 *
 * Revision 1.14  2003/11/04 17:50:00  dicuccio
 * Fixed compiler warning on MSVC
 *
 * Revision 1.13  2003/11/04 17:00:39  lebedev
 * Reverse and Compliment the sequence displayed under CDSs and Proteins on
 * negative strand
 *
 * Revision 1.12  2003/11/04 13:55:14  dicuccio
 * Fixed compiler warning on MSVC
 *
 * Revision 1.11  2003/10/30 13:21:59  lebedev
 * Display of master sequence under selected CDSs and Proteins added
 *
 * Revision 1.10  2003/10/28 19:01:43  dicuccio
 * Fixed compilation errors.  Pass CBioseq_Handle by const-ref and store as
 * value, not as pointer
 *
 * Revision 1.9  2003/10/28 15:29:07  lebedev
 * Use new configuration library
 *
 * Revision 1.8  2003/10/24 13:22:27  lebedev
 * Re-enable display of proteins
 *
 * Revision 1.7  2003/10/22 18:31:38  lebedev
 * Zoom that follows mouse added
 *
 * Revision 1.6  2003/10/21 12:59:51  lebedev
 * Rendering of alignments changed
 *
 * Revision 1.5  2003/10/20 16:31:24  lebedev
 * Offset IRenderable panels to bypass OpenGL matrices precision loss on
 * big sequences.
 *
 * Revision 1.4  2003/10/15 19:27:16  ucko
 * Fix test for the presence of a product to compile....
 *
 * Revision 1.3  2003/10/15 18:26:55  dicuccio
 * Reformatted code.  Added '*' to indicate features with products
 *
 * Revision 1.2  2003/10/09 18:02:02  lebedev
 * Compilation error fixed
 *
 * Revision 1.1  2003/10/09 16:27:41  lebedev
 * Initial revision
 *
 * ===========================================================================
 */