genome_layoutpolicy.cpp

来自「ncbi源码」· C++ 代码 · 共 207 行

/*
 * ===========================================================================
 * PRODUCTION $Log: genome_layoutpolicy.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 21:12:39  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: genome_layoutpolicy.cpp,v 1000.1 2004/06/01 21:12:39 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:
 *
 */


#include <ncbi_pch.hpp>
#include <gui/widgets/seq_graphic/genome_layoutpolicy.hpp>

#include <gui/objutils/feature.hpp>
#include <gui/objutils/comment.hpp>
#include <gui/objutils/alignment.hpp>
#include <gui/objutils/feat_pack.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/feat_label.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);



CGenomeLayoutPolicy::CGenomeLayoutPolicy()
{
}



void CGenomeLayoutPolicy::PrepareData(CGlPane& pane, CLayout& lay_objects)
{
    pane.OpenOrtho();

    if (x_IsOverviewMode(pane)) {
        x_PrepareGenomeView(pane, lay_objects);
    } else {
        x_PrepareDetailedView(pane, lay_objects);    
    }
    
    pane.Close();
}

void CGenomeLayoutPolicy::x_PrepareGenomeView(CGlPane& pane, CLayout& lay_objects)
{
    TModelRect rcV = pane.GetVisibleRect();
    TSeqRange range( TSeqPos(rcV.Left()), TSeqPos(rcV.Right()) );
    
    lay_objects.Clear();
    
    C2DLayoutEngine engine;
    engine.SetMinDist( x_GetMinSpacing(pane) );
        
    CLayout temporary;
    CLayoutFeat::TFeatList feats;
    CLayoutFeat::TFeatList land_marks;
    CLayoutEngine::TObjects objs;
    
    lay_objects.Clear();
    engine.Layout(objs, lay_objects);
    
    // Add Segment Map
    x_AddSeqSegmentMap(pane, lay_objects, range);
    // Add feature profile histograms
    x_AddHistograms(pane, lay_objects, range);
    
    // All Genes
    CSeqUtils::GetFeatures(m_Handle, range, CSeqFeatData::e_Gene, feats);
    
    // Landmark Genes
    CSeqUtils::GetLandmarkFeatures(m_Handle, range, 150, land_marks);

    // Comments for All Genes
    string str = "All Genes: " + NStr::UIntToString(feats.size());
    CRef<CLayoutObject> comment1(new CLayoutComment(str));
    objs.push_back(comment1);
    engine.Layout(objs, temporary);
    lay_objects.Append(temporary);
        
    if (land_marks.size() < feats.size()) {
        objs.clear();
        NON_CONST_ITERATE (CLayoutFeat::TFeatList, iter, feats) {
            (*iter)->HideLabels();  // hide labels for all genes
            CRef<CLayoutObject> obj(*iter);
            objs.push_back(obj);
        }

        engine.Layout(objs, temporary);
        lay_objects.Append(temporary);
    }

    // Comments for Landmark Genes
    if (land_marks.size() < feats.size()) {
        objs.clear();
        temporary.Clear();
        str  = "Landmark Genes: " + NStr::UIntToString(land_marks.size());
        
        CRef<CLayoutObject> comment2(new CLayoutComment(str));
        objs.push_back(comment2);
        engine.Layout(objs, temporary);
        lay_objects.Append(temporary);
    }

    objs.clear();
    SAnnotSelector sel =
        CSeqUtils::GetAnnotSelector(CSeqFeatData::eSubtype_mRNA);
    NON_CONST_ITERATE (CLayoutFeat::TFeatList, iter, land_marks) {
        CLayoutFeat& feat = **iter;
        TSeqRange range = feat.GetMappedFeature().GetLocation().GetTotalRange();

        CRef<CLayoutObject> gene_obj(*iter);
        objs.push_back(gene_obj);

        CLayoutFeat::TFeatList feats_tmp;
        CSeqUtils::GetFeatures(m_Handle, range, sel, feats_tmp);
        
        if (feats_tmp.size() > 1) {  // Add a pack of features
            CRef<CLayoutFeatPack> pack(new CLayoutFeatPack(feats_tmp));
            CRef<CLayoutObject> obj(pack);
            objs.push_back(obj);
        } else if (feats_tmp.size() == 1) {  // Just add mRNA
            CRef<CLayoutObject> rna_obj(feats_tmp[0]);
            objs.push_back(rna_obj);        
        }
    }
    
    temporary.Clear();
    engine.Layout(objs, temporary);
    
    lay_objects.Append(temporary);
}







END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: genome_layoutpolicy.cpp,v $
 * Revision 1000.1  2004/06/01 21:12:39  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
 *
 * Revision 1.7  2004/05/21 22:27:55  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.6  2004/05/03 13:23:58  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.5  2004/04/07 13:11:28  dicuccio
 * Use proper annotation selector for retrieving mRNA features
 *
 * Revision 1.4  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 1.3  2004/03/11 17:53:06  dicuccio
 * Deprecated typedefs TPosition, TDimension, TIndex, TColor.  Use TSeqRange instead of TRange
 *
 * Revision 1.2  2004/03/02 15:29:14  lebedev
 * Switch to detailed mode if reached certain number of
 * genes in visible range.
 *
 * Revision 1.1  2004/02/24 14:43:49  lebedev
 * Initial revision
 *
 * ===========================================================================
 */