feat_table.cpp
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- /*
- * ===========================================================================
- * 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
- * WTweaks for compiling on Windows
- *
- * Revision 1.1 2002/12/30 18:49:41 dicuccio
- * Initial revision
- *
- * ===========================================================================
- */