feat_table.cpp

来自「ncbi源码」· C++ 代码 · 共 469 行

/*
 * ===========================================================================
 * PRODUCTION $Log: feat_table.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 21:00:30  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.34
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: feat_table.cpp,v 1000.3 2004/06/01 21:00:30 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:
 *    CFeatTable -- extends CListPanel to provide feature-specific options.
 */

#include <ncbi_pch.hpp>
#include "feat_table.hpp"
#include <gui/utils/fltk_utils.hpp>
#include <gui/objutils/utils.hpp>

#include <objmgr/feat_ci.hpp>
#include <objects/seqloc/Seq_bond.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>

#include <FL/fl_draw.H>

BEGIN_NCBI_SCOPE



CFeatTable::CFeatTable(int x, int y, int w, int h, const char* label)
    : CTablePanel<CMappedFeat>(x, y, w, h, label)
{
    //
    // set up the actual columns for our internal data
    //

    SetColumn(eTitle,     "Title",     eString,  FL_ALIGN_LEFT,  0.5f);
    SetColumn(eType,      "Type",      eString,  FL_ALIGN_LEFT,  0.15f);
    SetColumn(eFrom,      "From",      eNumeric, FL_ALIGN_RIGHT, 0.1f);
    SetColumn(eTo,        "To",        eNumeric, FL_ALIGN_RIGHT, 0.1f);
    //SetColumn(eIntervals, "Intervals", eString,  FL_ALIGN_LEFT,  0.5f);
    SetColumn(eStrand,    "Strand",    eString,  FL_ALIGN_LEFT,  0.1f);

    // also set up the column types in our set of filters
    m_Filters.SetColType(eTitle,     CFilter::eString);
    m_Filters.SetColType(eType,      CFilter::eString);
    m_Filters.SetColType(eFrom,      CFilter::eNumeric);
    m_Filters.SetColType(eTo,        CFilter::eNumeric);
    //m_Filters.SetColType(eIntervals, CFilter::eString);
    m_Filters.SetColType(eStrand,    CFilter::eString);

    // set the default visible range method
    m_VisibleRangeMethod = eScrollTo;

    /**
    // set the default virtual columns
    // this defines the order in which all the columns appear
    m_VirtCols.push_back(eTitle);
    m_VirtCols.push_back(eType);
    m_VirtCols.push_back(eFrom);
    m_VirtCols.push_back(eTo);
    **/
}


CFeatTable::~CFeatTable()
{
}


void CFeatTable::Update(const CBioseq_Handle& handle)
{
    Clear();

    //
    // here, we just iterate all features and sort out the types ourselves
    //
    CLayoutFeat::TFeatList feats;
    CSeqUtils::GetFeatures(handle, TSeqRange(0, 0),
                           CSeqFeatData::e_not_set, feats);

    int row = 0;
    m_TotalFeats = 0;
    m_FilteredFeats = 0;
    m_InvFeats.clear();
    vector<TSeqRange> intervals;
    Reserve(feats.size(), eMaxCols);
    ITERATE (CLayoutFeat::TFeatList, feat_iter, feats) {
        const CLayoutFeat& feat = **feat_iter;
        const CSeq_loc& loc  = feat.GetLocation();

        // record the range of this feature
        CRange<TSeqPos> range = loc.GetTotalRange();

        // Check if in visible range for the entirely 
        //  contained and intersection methods
        if (!x_InVisibleRange(range)) {
            continue;
        }

        SetCell(row, eFrom, NStr::IntToString(range.GetFrom()));
        SetCell(row, eTo,   NStr::IntToString(range.GetTo()));

        SetCell(row, eType).erase();
        SetCell(row, eTitle).erase();
        feature::GetLabel(feat.GetFeature(),
                          &SetCell(row, eType), feature::eType);

        feature::GetLabel(feat.GetFeature(),
                          &SetCell(row, eTitle), feature::eContent,
                          &handle.GetScope());

        switch (sequence::GetStrand(loc)) {
        case eNa_strand_unknown:
            SetCell(row, eStrand, "?");
            break;
        case eNa_strand_plus:
            SetCell(row, eStrand, "+");
            break;
        case eNa_strand_minus:
            SetCell(row, eStrand, "-");
            break;
        case eNa_strand_both:
            SetCell(row, eStrand, "+-");
            break;
        case eNa_strand_both_rev:
            SetCell(row, eStrand, "+- (rev)");
            break;
        case eNa_strand_other:
            SetCell(row, eStrand, "other");
            break;
        }

        /**
        // extract a list of intervals from this feature
        intervals = feat.GetIntervals();
        string str;
        ITERATE (vector<TSeqRange>, r_iter, intervals) {
            if ( !str.empty() ) {
                str += ", ";
            }
            str += NStr::IntToString(r_iter->GetFrom());
            str += "..";
            str += NStr::IntToString(r_iter->GetTo());
        }
        SetCell(row, eIntervals) = str;
        **/

        // filter this row
        ++m_TotalFeats;
        if (!m_Filters.Filter(GetRow(row))) {
            continue;
        }
        ++m_FilteredFeats;

        SetData(row) = feat.GetMappedFeature();
        CConstRef<CSeq_feat> ref(&feat.GetMappedFeature().GetOriginalFeature());
        m_InvFeats[ref] = row;

        ++row;
    }

    // Check if Visible Range Scroll To method is set
    if (m_VisibleRangeMethod == eScrollTo) {
        x_ScrollToVisibleRange();
    }

    redraw();
}


void CFeatTable::ClearSelections()
{
    select_all_rows(0);
}


void CFeatTable::SelectFeature(const CSeq_feat& feat)
{
    TInvFeatMap::iterator iter = m_InvFeats.find(CConstRef<CSeq_feat>(&feat));
    if (iter == m_InvFeats.end()) {
        return;
    }

    int idx = iter->second;
    select_row(idx);
}

void CFeatTable::SetVisibleRange(const CSeq_loc& loc)
{
    m_VisibleRange = loc.GetTotalRange();
}


int CFeatTable::handle(int event)
{
    switch (event) {
    case FL_PUSH:
        // we ignore events bound to our internal popup state
        // this removes an artifact with selection mode - it protects our
        // selections when we popup our context menu
        if (CFltkEvent::GetProcessedEvent() != CFltkEvent::ePopupState) {
            break;
        }

        //ShowColSelectDlg();
        return 1;

    default:
        break;
    }

    return CTablePanel< CMappedFeat >::handle(event);
}

bool CFeatTable::x_InVisibleRange(TSeqRange range) 
{
    if (m_VisibleRange.Empty()) {
        return true;
    }

    switch (m_VisibleRangeMethod) {
        case eEntirelyContained:
            if (range.GetFrom() < m_VisibleRange.GetFrom() ||
                    range.GetTo()   > m_VisibleRange.GetTo()) {
                return false;
            }
            break;

        case eIntersection:
            if (range.GetTo() < m_VisibleRange.GetFrom() ||
                    range.GetFrom() > m_VisibleRange.GetTo()) {
                return false;
            }
            break;
    }

    return true;
}


void CFeatTable::x_ScrollToVisibleRange()
{
    
    if (m_VisibleRange.Empty()) {
        return;
    }

    size_t table_from = 
        NStr::StringToInt(GetCell(row_position(), eFrom));
    if (table_from < m_VisibleRange.GetFrom()) {
        x_ScrollDownToVisibleRange();
    } else if (table_from > m_VisibleRange.GetFrom()) {
        x_ScrollUpToVisibleRange();
    }
}

void CFeatTable::x_ScrollDownToVisibleRange()
{
    for (size_t i = row_position() + 1;  i < GetRows();  i++) {
        size_t table_from = NStr::StringToInt(GetCell(i, eFrom));

        if (table_from >= m_VisibleRange.GetFrom()) {
            row_position(i);
            return;
        }
    } 
    // set to last row
    row_position(GetRows() - 1);
}


void CFeatTable::x_ScrollUpToVisibleRange()
{

    for (int i = row_position() - 1; i >= 0; i--) {
        size_t table_from = NStr::StringToInt(GetCell(i, eFrom));

        if (table_from < m_VisibleRange.GetFrom()) {
            row_position(i + 1);
            return;
        }
    } 
    // set to first row
    row_position(0);
}


/**
void CFeatTable::get_style(Flv_Style& s, int row, int col)
{
    // do our base class stuff
    CListPanel< CMappedFeat >::get_style(s, row, col);

    if ( row >= 0  &&  (row / 5) % 2 == 1  &&  !row_selected(row)) {
        s.background(fl_rgb_color(220, 220, 220));
    }
}
**/


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: feat_table.cpp,v $
 * Revision 1000.3  2004/06/01 21:00:30  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.34
 *
 * Revision 1.34  2004/05/21 22:27:49  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.33  2004/05/07 15:35:37  dicuccio
 * Fixed unsigned/signed comparison
 *
 * Revision 1.32  2004/05/03 13:30:49  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.31  2004/03/11 17:47:22  dicuccio
 * Use TSeqRange instead of TRange
 *
 * Revision 1.30  2004/01/20 18:17:52  dicuccio
 * Changed to match new API in CTablePanel
 *
 * Revision 1.29  2004/01/06 20:16:19  dicuccio
 * Dropped intervals list (temporarily) - it crowds the view
 *
 * Revision 1.28  2003/12/30 15:03:54  dicuccio
 * Added ability to pass selections into feature table
 *
 * Revision 1.27  2003/12/22 19:32:23  dicuccio
 * Lots of code clean-up.  Changed to match new APIs in IView.  Added first pass
 * at processing selections (not entirely working)
 *
 * Revision 1.26  2003/12/22 18:15:07  friedman
 * Added various visible range methods and the selection of a method
 * through the preference menu selection and dialog.
 *
 * Revision 1.25  2003/12/04 18:14:47  dicuccio
 * Changed to match API change in CTablePanel
 *
 * Revision 1.24  2003/11/19 20:45:28  friedman
 * Added handling a visible range change event
 *
 * Revision 1.23  2003/09/29 15:41:09  dicuccio
 * Deprecated gui/scope.hpp.  Merged gui/core/types.hpp into gui/types.hpp.  Made
 * all menu bars flat (used FL_FLAT_BOX)
 *
 * Revision 1.22  2003/09/04 14:54:23  dicuccio
 * Use IDocument instead of CDocument.  Changed APIs to match changes in IView
 *
 * Revision 1.21  2003/08/18 14:45:50  dicuccio
 * Changed nales: CFeature -> CLayoutFeat; CAlignment -> CLayoutAlign; CGraph ->
 * CLayoutGraph; CProtProduct -> CLayoutProtProd.
 *
 * Revision 1.20  2003/07/31 17:04:34  dicuccio
 * Changed type stored by feature table view - use CMappedFeat instead of CFeatue
 * (less memory consumption)
 *
 * Revision 1.19  2003/07/28 11:51:49  dicuccio
 * Rewrote CTablePanel<> to be more flexible and better contained.  Added standard
 * multicolumn list dialog.  Deprecated use of COutputDlg.
 *
 * Revision 1.18  2003/07/25 13:44:48  dicuccio
 * Replaced Flv_Table with Fl_Table
 *
 * Revision 1.17  2003/07/11 12:38:45  dicuccio
 * Altered feature table to use smarter feature retrieval
 *
 * Revision 1.16  2003/06/02 16:06:24  dicuccio
 * Rearranged src/objects/ subtree.  This includes the following shifts:
 *     - src/objects/asn2asn --> arc/app/asn2asn
 *     - src/objects/testmedline --> src/objects/ncbimime/test
 *     - src/objects/objmgr --> src/objmgr
 *     - src/objects/util --> src/objmgr/util
 *     - src/objects/alnmgr --> src/objtools/alnmgr
 *     - src/objects/flat --> src/objtools/flat
 *     - src/objects/validator --> src/objtools/validator
 *     - src/objects/cddalignview --> src/objtools/cddalignview
 * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
 * replaces the three libmmdb? libs.
 *
 * Revision 1.15  2003/05/19 13:46:51  dicuccio
 * Moved gui/core/plugin/ --> gui/plugin/.  Merged core libraries into
 * libgui_core.so
 *
 * Revision 1.14  2003/05/16 18:50:34  dicuccio
 * Added smarter retrieval of features
 *
 * Revision 1.13  2003/04/19 14:20:00  ucko
 * remaining occurrences of iterate -> ITERATE
 *
 * Revision 1.12  2003/03/21 17:13:59  dicuccio
 * Moved fltk_utils --> gui/utils
 *
 * Revision 1.11  2003/03/11 15:23:30  kuznets
 * iterate -> ITERATE
 *
 * Revision 1.10  2003/03/03 14:58:56  dicuccio
 * Changed to use visible range from the base class.  Added an explicit setter for
 * the visible range
 *
 * Revision 1.9  2003/02/20 19:50:00  dicuccio
 * Created new plugin architecture, based on ASN.1 spec.  Moved GBENCH frameowrk
 * over to use new plugin architecture.
 *
 * Revision 1.8  2003/02/10 18:54:59  dicuccio
 * Fixed compilation issues relating to changes in CFeat_CI API
 *
 * Revision 1.7  2003/01/17 21:08:58  dicuccio
 * Fill in feature strand value
 *
 * Revision 1.6  2003/01/13 13:10:09  dicuccio
 * Namespace clean-up.  Retired namespace gui -> converted all to namespace ncbi.
 * Moved all FLUID-generated code into namespace ncbi.
 *
 * Revision 1.5  2003/01/09 14:50:42  dicuccio
 * Use 'const CBioseq_Handle&' instead of 'CBioseq_Handle&'
 *
 * Revision 1.4  2003/01/08 14:58:47  dicuccio
 * Major overhaul.  Added column selection dialog to base class - moved out of
 * this class.  Added ability to sort columns based on menu selections.  Added
 * ability to filter features based on a wide range of criteria.
 *
 * Revision 1.3  2003/01/03 17:27:44  dicuccio
 * Added ability to select columns for viewing and sorting
 *
 * Revision 1.2  2002/12/30 20:51:10  dicuccio
 * W\Tweaks for compiling on Windows
 *
 * Revision 1.1  2002/12/30 18:49:41  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */