bulk_miscfeat_edit.cpp

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/*  $Id: bulk_miscfeat_edit.cpp 47479 2023-05-02 13:24:02Z ucko $
 * ===========================================================================
 *
 *                            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:  Andrea Asztalos, based on a file written by Igor Filippov
 */
#include <ncbi_pch.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqtable/seq_table_exception.hpp>
#include <objmgr/feat_ci.hpp>
 
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/packages/pkg_sequence_edit/string_constraint_select.hpp>
#include <gui/packages/pkg_sequence_edit/apply_edit_convert_panel.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_miscfeat_edit.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
 
IMPLEMENT_DYNAMIC_CLASS(CBulkMiscFeat, wxDialog )
 
BEGIN_EVENT_TABLE(CBulkMiscFeat, wxDialog )
 
    EVT_BUTTON( wxID_OK, CBulkMiscFeat::OnClickOk )
 
    EVT_BUTTON( wxID_CANCEL, CBulkMiscFeat::OnClickCancel )
 
 
END_EVENT_TABLE()
 
CBulkMiscFeat::CBulkMiscFeat()
{
    Init();
}
 
CBulkMiscFeat::CBulkMiscFeat( wxWindow* parent, CSeq_entry_Handle seh,  IWorkbench* workbench, 
    CConstRef<CSeq_submit> seqSubmit, wxWindowID id, const wxString& caption, const wxPoint& pos, 
    const wxSize& size, long style )
{
    this->m_Workbench = workbench;
    this->m_SeqSubmit = seqSubmit;
 
    CFeat_CI fi(seh, SAnnotSelector(CSeqFeatData::eSubtype_misc_feature));           
    for ( ; fi ; ++fi ) {
        m_FeatHandles.push_back(fi->GetSeq_feat_Handle());
    }
 
    Init();
    Create(parent, id, caption, pos, size, style);
}
 
CBulkMiscFeat::CBulkMiscFeat( wxWindow* parent, const vector<CSeq_feat_Handle> &feat_handles, 
    IWorkbench* workbench, wxWindowID id, const wxString& caption, const wxPoint& pos, 
    const wxSize& size, long style )
    : m_FeatHandles(feat_handles)
{
    this->m_Workbench = workbench;
 
    Init();
    Create(parent, id, caption, pos, size, style);
}
 
 
bool CBulkMiscFeat::Create( wxWindow* parent, wxWindowID id, const wxString& caption, 
    const wxPoint& pos, const wxSize& size, long style )
{
    SetExtraStyle(wxWS_EX_BLOCK_EVENTS);
    SetLayoutAdaptationMode(wxDIALOG_ADAPTATION_MODE_ENABLED);
    wxDialog::Create( parent, id, caption, pos, size, style );
 
    CreateControls();
    if (GetSizer())
    {
        GetSizer()->SetSizeHints(this);
    }
    Centre();
    return true;
}
 
/*!
 * Member initialisation
 */
 
void CBulkMiscFeat::Init()
{
    m_Grid = nullptr;
    m_AecrPanel = nullptr;
    m_GridPanel = nullptr;
}
 
 
void CBulkMiscFeat::CreateControls()
{    
    CBulkMiscFeat* itemDialog1 = this;
 
    wxBoxSizer* itemBoxSizer2 = new wxBoxSizer(wxVERTICAL);
    itemDialog1->SetSizer(itemBoxSizer2);
 
    wxBoxSizer* itemBoxSizer3 = new wxBoxSizer(wxHORIZONTAL);
    itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);
    
    wxArrayString itemChoiceStrings, itemChoiceStringsWritable;
 
    string error_msg = "No Misc features were found";
    if (m_FeatHandles.empty()) {
        wxMessageBox(ToWxString(error_msg), wxT("Error"), wxOK | wxICON_ERROR);
        NCBI_THROW( CException, eUnknown, error_msg );
    }
 
    CRef<CSeq_table> values_table = GetValuesTableFromSeqEntry();
    if (values_table->GetNum_rows() < 1) {
        wxMessageBox(ToWxString(error_msg), wxT("Error"), wxOK | wxICON_ERROR);
        NCBI_THROW( CException, eUnknown, error_msg );
    }
 
    CRef<CSeq_table> choices = GetChoices(values_table);
    int glyph_col = GetCollapsible();
    m_GridPanel = new CSeqTableGridPanel(this, values_table, choices, glyph_col);
    itemBoxSizer3->Add(m_GridPanel, 0, wxALIGN_TOP|wxALL, 5);
    
    m_Grid = m_GridPanel->GetGrid();
    CSeqTableGrid *gridAdapter = new CSeqTableGrid(values_table);
    m_Grid->SetTable(gridAdapter, true);
    m_Grid->AutoSizeColumns();
    
    int l_height = m_Grid->GetColLabelSize();
    m_Grid->SetColLabelSize( 2 * l_height );
    m_GridPanel->SetColumnSizesAndChoices();
    
    int pos = 0;
    for (auto&& it: values_table->GetColumns()) {
        if (pos > 0)  {
            if (it->IsSetHeader() && it->GetHeader().IsSetTitle()) {
                string title = it->GetHeader().GetTitle();
                if (!title.empty()) {
                    itemChoiceStrings.Add(wxString(title));
                    if (!IsReadOnlyColumn(title)) 
                        itemChoiceStringsWritable.Add(wxString(title));
                }
                if (IsReadOnlyColumn(title)) 
                    m_GridPanel->MakeColumnReadOnly(pos - 1, true);
            } 
        }
        ++pos;
    }
    
    if (glyph_col >= 0 && glyph_col+1 < m_Grid->GetNumberCols()) {
        m_GridPanel->InitColumnCollapse(glyph_col+1);  
    }
    
    CStringConstraintSelect *itemStringConstraintPanel = new CStringConstraintSelect( itemDialog1, m_GridPanel, itemChoiceStrings, wxID_ANY, wxDefaultPosition, wxDefaultSize, 0 );
    itemBoxSizer2->Add(itemStringConstraintPanel, 0, wxALIGN_CENTER_HORIZONTAL|wxALL|wxFIXED_MINSIZE, 0);
    
    m_AecrPanel = new CApplyEditconvertPanel( itemDialog1, m_GridPanel, itemChoiceStringsWritable, 0, true, wxID_ANY, wxDefaultPosition, wxSize(1046, 219));
    itemBoxSizer2->Add(m_AecrPanel, 0, wxALIGN_CENTER_HORIZONTAL|wxALL|wxFIXED_MINSIZE, 1);
 
    wxBoxSizer* itemBoxSizer13 = new wxBoxSizer(wxHORIZONTAL);
    itemBoxSizer2->Add(itemBoxSizer13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);
 
    wxButton* itemButton14 = new wxButton( itemDialog1, wxID_OK, _("Accept"), wxDefaultPosition, wxDefaultSize, 0 );
    itemBoxSizer13->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);
 
    wxButton* itemButton15 = new wxButton( itemDialog1, wxID_CANCEL, _("Cancel"), wxDefaultPosition, wxDefaultSize, 0 );
    itemBoxSizer13->Add(itemButton15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);
}
 
 
CRef<CSeq_table> CBulkMiscFeat::GetValuesTableFromSeqEntry()
{
    CRef<CSeqTable_column> id_col(new CSeqTable_column());
    id_col->SetHeader().SetField_id(CSeqTable_column_info::eField_id_location_id);
    id_col->SetHeader().SetTitle(kSequenceIdColLabel);
 
    CRef<CSeqTable_column> expand_col(new CSeqTable_column());
    expand_col->SetHeader().SetTitle("");
    expand_col->SetHeader().SetField_name("expand");
    expand_col->SetData().SetString();
 
    CRef<CSeqTable_column> comment_col(new CSeqTable_column());
    comment_col->SetHeader().SetTitle("comment");
    comment_col->SetHeader().SetField_name("comment");
    comment_col->SetData().SetString();
 
    CRef<CSeqTable_column> loc_col(new CSeqTable_column());
    loc_col->SetHeader().SetTitle("location");
    loc_col->SetHeader().SetField_name("location");
    loc_col->SetData().SetString();
 
    // bogus column to include last, otherwise deletion of the previous column will not work
    CRef<CSeqTable_column> bogus_col(new CSeqTable_column());
    bogus_col->SetHeader().SetTitle("");
    bogus_col->SetHeader().SetField_name("");
    bogus_col->SetData().SetString();
 
    CRef<CSeq_table> table(new CSeq_table());  
    table->SetColumns().push_back(id_col);
    table->SetColumns().push_back(expand_col);
    table->SetColumns().push_back(comment_col);
    table->SetColumns().push_back(loc_col);
 
    CRef<CFeatureSeqTableColumnBase> partial_start_feat_col = CFeatureSeqTableColumnBaseFactory::Create(kPartialStart);
    CRef<CSeqTable_column> partial_start_col = AddStringColumnToTable(table, kPartialStart);
    partial_start_col->SetHeader().SetField_name(kPartialStart);
 
    CRef<CFeatureSeqTableColumnBase> partial_stop_feat_col = CFeatureSeqTableColumnBaseFactory::Create(kPartialStop);
    CRef<CSeqTable_column> partial_stop_col = AddStringColumnToTable(table, kPartialStop);
    partial_stop_col->SetHeader().SetField_name(kPartialStop);
 
    table->SetColumns().push_back(bogus_col);
 
    size_t row = 0;
    for (vector<CSeq_feat_Handle>::iterator fi = m_FeatHandles.begin(); fi != m_FeatHandles.end() ; ++fi )     {
        string loc,comment;
        
        const CSeq_feat &feat = *fi->GetOriginalSeq_feat();
 
        if (feat.IsSetComment())
            comment = feat.GetComment();
        if (feat.IsSetLocation())
            feat.GetLocation().GetLabel(&loc);
 
        CRef<CSeq_id> id(new CSeq_id());
        id->SetLocal().SetId(static_cast<CObject_id::TId>(row));
        id_col->SetData().SetId().push_back(id);
        expand_col->SetData().SetString().push_back("");
        comment_col->SetData().SetString().push_back(comment);
        loc_col->SetData().SetString().push_back(loc);
 
        AddValueToColumn(partial_start_col, partial_start_feat_col->GetFromFeat(feat), row);
        AddValueToColumn(partial_stop_col, partial_stop_feat_col->GetFromFeat(feat), row);
        bogus_col->SetData().SetString().push_back("");
        row++;
    }
    
    table->SetNum_rows(static_cast<CSeq_table::TNum_rows>(row));
    return table;
}
 
 
CRef<CCmdComposite> CBulkMiscFeat::GetCommandFromValuesTable(CRef<CSeq_table> values_table)
{
     CRef<CCmdComposite> cmd(new CCmdComposite("Bulk Mic Feature Edit"));
     CRef<CFeatureSeqTableColumnBase> partial_start_feat_col = CFeatureSeqTableColumnBaseFactory::Create(kPartialStart);
     CRef<CFeatureSeqTableColumnBase> partial_stop_feat_col = CFeatureSeqTableColumnBaseFactory::Create(kPartialStop);
     
     m_Modified = false;
     size_t row = 0;
     for ( vector<CSeq_feat_Handle>::iterator fi = m_FeatHandles.begin(); fi != m_FeatHandles.end() ; ++fi ) {
         const CSeq_feat &feat =  *fi->GetOriginalSeq_feat();
         CRef<CSeq_feat> new_feat(new CSeq_feat());
         new_feat->Assign(feat);
 
         string loc,comment;
         bool modified = false;
         if (feat.IsSetComment())
             comment = feat.GetComment();
         if (feat.IsSetLocation())
             feat.GetLocation().GetLabel(&loc);
 
         string new_comment;
         try {
             if (row <  values_table->GetColumn("comment").GetData().GetString().size())
                 new_comment = values_table->GetColumn("comment").GetData().GetString()[row];
         } catch(const CSeqTableException&) {}
     
         if (new_comment != comment) {
             if (new_comment.empty())
                 new_feat->ResetComment();
             else
                 new_feat->SetComment() = new_comment;
             modified = true;
         }
 
         string partial_start_val = partial_start_feat_col->GetFromFeat(feat);
         string new_partial_start_val;
         try {
             if (row <  values_table->GetColumn(kPartialStart).GetData().GetString().size())
                 new_partial_start_val = values_table->GetColumn(kPartialStart).GetData().GetString()[row];
         } catch(const CSeqTableException&) {}
     
         if (new_partial_start_val != partial_start_val) {
             if (new_partial_start_val.empty())
                 partial_start_feat_col->ClearInFeature(*new_feat);
             else
                 partial_start_feat_col->AddToFeature(*new_feat, new_partial_start_val, edit::eExistingText_replace_old);
             modified = true;
         }
         
         string partial_stop_val = partial_stop_feat_col->GetFromFeat(feat);
         string new_partial_stop_val;
         try {
             if (row <  values_table->GetColumn(kPartialStop).GetData().GetString().size())
                 new_partial_stop_val = values_table->GetColumn(kPartialStop).GetData().GetString()[row];
         } catch(const CSeqTableException&) {}
     
         if (new_partial_stop_val != partial_stop_val) {
             if (new_partial_stop_val.empty())
                 partial_stop_feat_col->ClearInFeature(*new_feat);
             else
                 partial_stop_feat_col->AddToFeature(*new_feat, new_partial_stop_val, edit::eExistingText_replace_old);
             modified = true;
         }
 
         if (modified)
             cmd->AddCommand(*CRef<CCmdChangeSeq_feat>(new CCmdChangeSeq_feat(*fi,*new_feat)));
         m_Modified |= modified;
         row++;
    }            
 
    return cmd;  
}
 
 
CRef<CCmdComposite> CBulkMiscFeat::GetCommand()
{
    CRef<CSeq_table> values_table = m_GridPanel->GetValuesTable();
    return GetCommandFromValuesTable(values_table);
}
 
string CBulkMiscFeat::GetErrorMessage()
{
    return "Invalid operation in Bulk Misc Feature Edit";
}
 
 
/*!
 * Should we show tooltips?
 */
 
bool CBulkMiscFeat::ShowToolTips()
{
    return true;
}
 
/*!
 * Get bitmap resources
 */
 
wxBitmap CBulkMiscFeat::GetBitmapResource( const wxString& name )
{
    // Bitmap retrieval
////@begin CBulkGene bitmap retrieval
    wxUnusedVar(name);
    return wxNullBitmap;
////@end CBulkGene bitmap retrieval
}
 
/*!
 * Get icon resources
 */
 
wxIcon CBulkMiscFeat::GetIconResource( const wxString& name )
{
    // Icon retrieval
////@begin CBulkGene icon retrieval
    wxUnusedVar(name);
    return wxNullIcon;
////@end CBulkGene icon retrieval
}
 
/*!
 * wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON
 */
 
void CBulkMiscFeat::OnClickOk( wxCommandEvent& event )
{
    event.Skip(); 
}
 
/*!
 * wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON1
 */
 
void CBulkMiscFeat::OnClickCancel( wxCommandEvent& event )
{
    bool modified = m_GridPanel->GetModified() | m_AecrPanel->GetModified();
    if (modified) {
        wxMessageDialog dlg(this,_("Discard modifications?"), _("Attention"),wxOK|wxCANCEL|wxCENTRE);
        if (dlg.ShowModal() == wxID_OK) {
            event.Skip();
        }
    }
    else
        event.Skip();
}
 
const CObject* CBulkMiscFeat::RowToScopedObjects(int row, TConstScopedObjects &objects,  CBioseq_Handle &bsh)
{
    objects.clear();
    const CObject* obj = nullptr;
 
    if (row < m_FeatHandles.size()) {
        if (m_FeatHandles[row].GetOriginalSeq_feat()->IsSetLocation()) {
            bsh = m_FeatHandles[row].GetScope().GetBioseqHandle(m_FeatHandles[row].GetOriginalSeq_feat()->GetLocation());
            if (bsh) {
                if (m_SeqSubmit)
                    objects.push_back(SConstScopedObject(m_SeqSubmit,&bsh.GetScope()));
                else
                    objects.push_back(SConstScopedObject(bsh.GetTopLevelEntry().GetCompleteSeq_entry(),&bsh.GetScope()));                
                obj = bsh.GetBioseqCore().GetPointer();
            }
        }
    }
    return obj;
}
 
 
END_NCBI_SCOPE