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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alignment__assistant_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/edit/alignment_assistant.cpp Source File

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

: m_TopSeqEntry(seh), m_CmdProcessor(processor)

(parent,

, caption, pos,

, style);

wxFrame::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

Centre(wxBOTH|wxCENTRE_ON_SCREEN);

wxMenuBar *menubar =

wxMenuBar();

wxMenu *file_menu =

wxMenu();

menubar->Append(file_menu,

(

));

wxMenu *export_submenu =

wxMenu();

file_menu->AppendSubMenu(export_submenu,

(

));

export_submenu->Append(interleave_item);

export_submenu->Append(cont_item);

wxMenuItem *close_item =

wxMenuItem(file_menu, wxID_CLOSE,

(

),

(

), wxITEM_NORMAL);

file_menu->Append(close_item);

wxMenu *edit_menu =

wxMenu();

menubar->Append(edit_menu,

(

));

edit_menu->Append(remove_seq_item);

edit_menu->Append(rev_strands_item);

edit_menu->Append(validate_item);

edit_menu->Append(propagate_item);

wxMenu *view_menu =

wxMenu();

menubar->Append(view_menu,

(

));

view_menu->Append(substitute_item);

view_menu->Append(features_item);

wxMenu *feature_menu =

wxMenu();

menubar->Append(feature_menu,

(

));

feature_menu->AppendSubMenu(annotate_seq_submenu,

(

));

wxMenu *annotate_alignment_submenu =

wxMenu();

feature_menu->AppendSubMenu(annotate_alignment_submenu,

(

));

annotate_alignment_submenu->Append(align_cds_item);

annotate_alignment_submenu->Append(align_rna_item);

annotate_alignment_submenu->Append(align_other_item);

wxPanel *Dialog1 =

wxPanel(

,

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

Dialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_LEFT, 0);

itemBoxSizer3->Add(itemButton6, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer3->Add(itemButton7, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_LEFT, 0);

=

wxStaticText( Dialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(Dialog1->ConvertDialogToPixels(wxSize(40, -1)).x, -1), wxNO_BORDER );

itemBoxSizer4->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxLEFT, 5);

wxBoxSizer *BoxSizer =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(BoxSizer, 1, wxGROW, 0);

BoxSizer->Add(

, 1, wxGROW|wxALL, 5);

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL, 0);

itemBoxSizer12->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStatusBar *status = CreateStatusBar();

(!align || align->

(align_ci.GetOriginalSeq_align()) || align->

(*align_ci))

wxStatusBar *status = GetStatusBar();

(pos1 > 0 && pos2 > 0)

->SetLabel(wxEmptyString);

(

.ToLong(&pos))

(

.ToLong(&pos))

vector<string> labels;

labels.push_back(

);

=

;

+= (labels.size() > 1) ?

:

;

report->SetTitle(

(

));

report->Show(

);

vector<vector<pair<TSeqPos,TSeqPos> > > feat_ranges;

vector<pair<string,CSeqFeatData::ESubtype> > feat_types;

vector<CBioseq_Handle::EVectorStrand> feat_strand;

vector<pair<TSeqPos,TSeqPos> > vec;

vec.push_back(pair<TSeqPos,TSeqPos>(feat_start,feat_stop));

feat_types.push_back(pair<string,CSeqFeatData::ESubtype>(

,subtype));

feat_ranges.push_back(vec);

feat_strand.push_back(strand);

(event.IsChecked())

(event.IsChecked())

(sel.first >=0 && sel.second >= 0 && sel.second != sel.first)

(sel.first > sel.second)

(sel.first, sel.second);

interval->

().SetFrom(sel.first);

interval->

().SetTo(sel.second);

interval->

().SetId(*

);

wxWindow* editorWindow = editor->CreateWindow(&edit_dlg);

(edit_dlg.ShowModal() == wxID_OK)

from_align = align_sel.first;

to_align = align_sel.second;

(wxYES != wxMessageBox(

(

),

(

), wxYES_NO | wxNO_DEFAULT | wxICON_QUESTION))

vector<int>

(num_rows, 0);

(sel.first < 0 || sel.second < 0)

from = sel.first;

(start >= from && start +

- 1 <= to)

seqmap_i = seqmap_i.

();

(from > start && from < start+len && to >= start+

-1)

seq_out = seq_in.substr(0, from - start);

(from > start && from < start+

&& to < start+

-1)

seq_out = seq_in.substr(0, from - start) + seq_in.substr(to - start + 1);

(from <= start && to >= start && to < start +

- 1)

seq_out = seq_in.substr(to - start + 1);

->AddCommand(*cmd_bioseq);

already_moved =

;

(from > pos && from < pos + len && to >= pos +

- 1)

new_len = from - pos;

ds->

().push_back(new_len);

already_moved =

;

ds->

()[seg1 * num_rows + dim] = start1;

(from <= pos && to >= pos +

- 1)

already_moved =

;

ds->

()[seg1 * num_rows + dim] = start1;

(from <= pos && to >= pos && to < pos +

- 1)

new_len = pos +

- 1 - to;

ds->

().push_back(new_len);

(from > pos && from < pos + len - 1 && to > pos && to < pos +

- 1)

new_len1 = from - pos;

ds->

().push_back(new_len1);

already_moved =

;

ds->

()[seg1 * num_rows + dim] = start1;

ds->

().push_back(new_len2);

(from < pos && to < pos)

ds->

().push_back(new_len);

ds->

().push_back(new_len);

align->

().SetDenseg(*ds);

->AddCommand(*cmd_align);

(

feat_it(scope, *loc, sel); feat_it; ++feat_it)

new_feat->

(feat_it->GetOriginalFeature());

& feat_loc = feat_it->GetLocation();

modified =

;

removed =

;

->AddCommand(*cmd_del);

((*code_break)->IsSetLoc())

cb_modified =

;

cb_removed =

;

(*code_break)->SetLoc(*cb_loc);

new_feat->

().SetCdregion().ResetFrame();

ac_modified =

;

ac_removed =

;

new_feat->

().SetRna().SetExt().SetTRNA().ResetAnticodon();

new_feat->

().SetRna().SetExt().SetTRNA().SetAnticodon(*ac_loc);

(cmd_change_feat)

->AddCommand(*cmd_change_feat);

new_loc->

(feat_loc);

(feat_start < from && feat_stop >= from && feat_stop <= to)

loc_it.

(from - 1);

(feat_start < from && feat_stop > to)

loc_it.

(feat_stop - (to - from + 1));

(feat_start >= from && feat_start <= to && feat_stop > to)

loc_it.

(to + 1 - (to - from + 1));

loc_it.

(feat_stop - (to - from + 1));

(feat_start >= from && feat_start <= to && feat_stop >= from && feat_stop <= to)

(feat_start > to)

loc_it.

(feat_start - (to - from + 1));

loc_it.

(feat_stop - (to - from + 1));

(; graph_ci; ++graph_ci)

g_modified =

;

g_removed =

;

->AddCommand(*delGraph);

( src_data.

() )

step = new_graph->

();

(

pos = feat_start; pos <= feat_stop; pos += step, graph_pos++)

(pos >= from && pos <= to)

( src_data.

() )

new_graph->

(*g_loc);

( src_data.

() )

->AddCommand(*chgGraph);

(sel.first > sel.second)

(sel.first, sel.second);

interval->

().SetFrom(sel.first);

interval->

().SetTo(sel.second);

->SetLocal().SetStr(

);

interval->

().SetId(*

);

(edit_dlg.ShowModal() == wxID_OK)

(sel.first > sel.second)

(sel.first, sel.second);

interval->

().SetFrom(sel.first);

interval->

().SetTo(sel.second);

->SetLocal().SetStr(

);

interval->

().SetId(*

);

(edit_dlg.ShowModal() == wxID_OK)

(sel.first > sel.second)

(sel.first, sel.second);

interval->

().SetFrom(sel.first);

interval->

().SetTo(sel.second);

->SetLocal().SetStr(

);

interval->

().SetId(*

);

(edit_dlg.ShowModal() == wxID_OK)

->Assign(row_id);

new_loc->

(*

);

(new_start < 0 || new_stop < 0)

(new_stop < new_start)

(new_start, new_stop);

loc_it.

(new_stop);

wxMenuBar *menu_bar = GetMenuBar();

wxMenuItem *menu_item = menu_bar->FindItem( event.GetId() );

= menu_item->GetItemLabelText().ToStdString();

=

(

);

wxFileDialog save_file(

,

(

), wxEmptyString, wxEmptyString,

wxFD_SAVE|wxFD_OVERWRITE_PROMPT);

(save_file.ShowModal() == wxID_OK)

wxString path = save_file.GetPath();

( !path.IsEmpty())

wxFileDialog save_file(

,

(

), wxEmptyString, wxEmptyString,

wxFD_SAVE|wxFD_OVERWRITE_PROMPT);

(save_file.ShowModal() == wxID_OK)

wxString path = save_file.GetPath();

( !path.IsEmpty())

options = validator::CValidator::eVal_val_align;

validator::CValidErrorFormat::SetSuppressionRules(

, *errors);

validator::CValidator validator(*objmgr);

description = vit->GetAccnver() +

+ vit->GetErrCode() +

(!description.empty())

+= description +

;

=

;

report->SetTitle(

(

));

report->Show(

);

vector<CConstRef<CSeq_feat>> propagatedFeats;

(

ci(bsh); ci; ++ci) {

propagatedFeats.push_back(ci->GetSeq_feat());

wxWindow* editorWindow = editor->CreateWindow(&edit_dlg);

(edit_dlg.ShowModal() == wxID_OK)

}

(

&e) {}

(exception &e) {}

(wxYES != wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION))

ids.push_back(*id_iter);

CDense_seg::TStarts::const_iterator start_iter;

CDense_seg::TStrands::const_iterator strand_iter;

(

seg = 0; seg<numseg; seg++)

(

=0;

<dim;

++)

starts.push_back(*start_iter);

strands.push_back(*strand_iter);

align->

().SetDenseg().SetIds().swap(ids);

align->

().SetDenseg().RemovePureGapSegs();

wxMessageBox(

(

),

(

), wxOK|wxICON_ERROR);

(wxYES != wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION))

vector<ENa_strand> new_strands(num_rows * num_segs,

);

: m_Loc(align_loc), m_scope(&scope)

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemCBulkCmdPanel1->SetSizer(itemBoxSizer2);

wxFlexGridSizer* itemFlexGridSizer3 =

wxFlexGridSizer(0, 2, 0, 0);

itemBoxSizer2->Add(itemFlexGridSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText8 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText8, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText9 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText9, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText4 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText4, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText6 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText6, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText10 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText10, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton13 =

wxButton( itemCBulkCmdPanel1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton14 =

wxButton( itemCBulkCmdPanel1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxNullBitmap;

(!locations.empty())

(

= 0;

< locations.size(); ++

)

(!seq_loc || !bsh || (seq_loc->

() && !seq_loc->

().

()))

cds->SetData().SetCdregion();

cds->SetComment(cds_comment);

cds->SetData().SetCdregion().SetCode(*

);

cds->SetLocation().Assign(*seq_loc);

(seq_loc->

())

cds->SetData().SetCdregion().SetFrame(objects::CSeqTranslator::FindBestFrame(*cds, bsh.

()));

->SetData().SetProt().SetName().push_back(prot_name);

->SetData().SetProt().SetDesc(prot_desc);

new_gene->SetData().SetGene().SetLocus(gene_symbol);

new_gene->SetData().SetGene().SetDesc(gene_desc);

new_gene->SetLocation().Assign(cds->GetLocation());

new_gene->SetPartial(

);

: m_Loc(align_loc), m_scope(&scope)

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxHORIZONTAL);

itemCBulkCmdPanel1->SetSizer(itemBoxSizer2);

itemBoxSizer2->Add(0, 500, 0, wxALIGN_CENTER_VERTICAL|wxALL, 0);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxVERTICAL);

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticBox* itemStaticBoxSizer5Static =

wxStaticBox(itemCBulkCmdPanel1,

,

(

));

wxStaticBoxSizer* itemStaticBoxSizer5 =

wxStaticBoxSizer(itemStaticBoxSizer5Static, wxVERTICAL);

itemBoxSizer4->Add(itemStaticBoxSizer5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString m_RNATypeStrings;

m_RNATypeStrings.Add(

(

));

m_RNATypeStrings.Add(

(

));

m_RNATypeStrings.Add(

(

));

m_RNATypeStrings.Add(

(

));

m_RNATypeStrings.Add(

(

));

m_RNATypeStrings.Add(

(

));

m_RNATypeStrings.Add(

(

));

->SetStringSelection(

(

));

itemStaticBoxSizer5->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer7 =

wxBoxSizer(wxHORIZONTAL);

itemStaticBoxSizer5->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText8 =

wxStaticText( itemStaticBoxSizer5->GetStaticBox(), wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer7->Add(itemStaticText8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxArrayString m_ncRNAClassStrings;

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer4->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText11 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText13 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer4->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton16 =

wxButton( itemCBulkCmdPanel1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->Add(itemButton16, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton17 =

wxButton( itemCBulkCmdPanel1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->Add(itemButton17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

(vector<string>, it, class_vals) {

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer4->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton13 =

wxButton( itemCBulkCmdPanel1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton14 =

wxButton( itemCBulkCmdPanel1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxNullBitmap;

wxStaticText* itemStaticText11 =

wxStaticText(

, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxTextCtrl(

,

, wxEmptyString, wxDefaultPosition, wxSize(300, -1), 0 );

->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText13 =

wxStaticText(

, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxTextCtrl(

,

, wxEmptyString, wxDefaultPosition, wxSize(300, -1), 0 );

need_layout =

;

(num_items > 4) {

pos = num_items - 1;

need_layout =

;

need_layout =

;

wxArrayString m_NameStrings;

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

m_NameStrings.Add(

(

));

=

wxComboBox(

,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, m_NameStrings, wxCB_DROPDOWN );

need_layout =

;

need_layout =

;

(!buttons_shown) {

need_layout =

;

(buttons_shown) {

need_layout =

;

wxArrayString m_tRNAStrings;

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

m_tRNAStrings.Add(

(

));

=

wxChoice(

,

, wxDefaultPosition, wxDefaultSize, m_tRNAStrings, 0 );

need_layout =

;

=

wxTextCtrl(

,

, wxEmptyString, wxDefaultPosition, wxSize(300, -1), 0 );

need_layout =

;

comment +=

;

comment +=

;

->SetExt().SetTRNA();

= aa.c_str()[0];

->SetExt().SetTRNA().SetAa().SetIupacaa(

);

rna_name =

;

(

= 0;

< locations.size(); ++

)

(!seq_loc || !bsh || (seq_loc->

() && !seq_loc->

().

()))

gene_symbol =

;

gene_desc =

;

rna_ref->

().SetGen();

rna_ref->

().SetGen().SetProduct(rna_name);

rna_ref->

().SetGen().SetClass(ncrna_class);

rna_ref->

().SetName(rna_name);

->SetData().SetRna().Assign(*rna_ref);

->SetComment(comment);

->SetLocation().Assign(*seq_loc);

->SetPartial(

);

new_gene->SetData().SetGene().SetLocus(gene_symbol);

new_gene->SetData().SetGene().SetDesc(gene_desc);

new_gene->SetLocation().Assign(*seq_loc);

new_gene->SetPartial(

);

: m_Loc(align_loc), m_TopSeqEntry(seh), m_scope(&seh.

())

GetSizer()->SetSizeHints(

);

->SetData().SetImp().SetKey(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemCBulkCmdPanel1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_LEFT|wxALL, 5);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxVERTICAL);

itemBoxSizer3->Add(itemBoxSizer4, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText5 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer4->Add(itemStaticText5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString m_FeatureTypeStrings;

itemBoxSizer4->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxFlexGridSizer* itemFlexGridSizer8 =

wxFlexGridSizer(0, 2, 0, 0);

itemBoxSizer2->Add(itemFlexGridSizer8, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText9 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer8->Add(itemStaticText9, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer8->Add(

, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText11 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer8->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer8->Add(

, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText13 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer8->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer8->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer2->Add(500, 0, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton13 =

wxButton( itemCBulkCmdPanel1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton14 =

wxButton( itemCBulkCmdPanel1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

vector<string> listed_feat;

listed_feat.push_back(

);

listed_feat.push_back(

);

existing.

(listed_feat[0]);

existing.

(listed_feat[1]);

(vector<const CFeatListItem *>, feat_it, featlist) {

feat_type = item.

();

[pair<int,int>(feat_type,feat_subtype)] = desc;

(existing.

(desc) == existing.

()) {

listed_feat.push_back(desc);

(

= 0;

< listed_feat.size(); ++

) {

(find(listed_feat.begin(), listed_feat.end(),

) != listed_feat.end()) {

wxNullBitmap;

(

= 0;

< locations.size(); ++

)

(!seq_loc || !bsh || (seq_loc->

() && !seq_loc->

().

()))

feat->SetData().SetImp().SetKey(

);

feat->SetComment(comment);

feat->SetLocation().Assign(*seq_loc);

feat->SetPartial(

);

new_gene->SetData().SetGene().SetLocus(gene_symbol);

new_gene->SetData().SetGene().SetDesc(gene_desc);

new_gene->SetComment(comment);

new_gene->SetLocation().Assign(*seq_loc);

new_gene->SetPartial(

);

feat.SetQual().push_back(q);

&& feat.GetData().GetImp().IsSetKey() && feat.GetData().GetImp().GetKey() ==

)

feat.SetData().SetImp().SetKey(

);

= (*it)->GetVal();

qual = (*it)->GetQual();

(qual ==

)

gene.SetData().SetGene().SetLocus(

);

(qual ==

)

gene.SetData().SetGene().SetLocus_tag(

);

(qual ==

)

gene.SetData().SetGene().SetAllele(

);

gene.SetData().SetGene().SetMaploc(

);

(qual ==

)

gene.SetData().SetGene().SetSyn().push_back(

);

bool IsReverse(ENa_strand s)

ENa_strand Reverse(ENa_strand s)

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

static bool s_IsRNAFeature(int feat_subtype)

static void s_SettRNAProduct(string aa, CRef< CRNA_ref > rna)

#define ID_CALIGN_RNA_ADD_PANEL_COMBOBOX

#define ID_SHOW_FEATURES_ALIGNMENT_ASSISTANT_MENU

#define ID_SHOW_SUBSTITUTE_ALIGNMENT_ASSISTANT_MENU

#define ID_GOTO_ALIGNMENT_ASSISTANT_BUTTON

#define ID_EDIT_REV_STRANDS_ALIGNMENT_ASSISTANT_MENU

#define ID_EDIT_RM_SEQ_ALIGNMENT_ASSISTANT_MENU

#define ID_ALIGNCDSADD_COMMENT

#define SYMBOL_CALIGNCDSADDPANEL_TITLE

#define ID_CALIGN_RNA_ADD_PANEL_TEXTCTRL10

#define ID_ALIGNCDSADD_GENE_DESC

#define ID_EDIT_PROPAGATE_ALIGNMENT_ASSISTANT_MENU

#define SYMBOL_CALIGN_RNA_ADD_PANEL_TITLE

#define ID_ADD_ALIGN_RNA_ALIGNMENT_ASSISTANT_MENU

#define ID_CALIGN_OTHER_ADDPANEL_TEXTCTRL12

#define ID_ALIGNCDSADD_PROTEIN_NAME

#define ID_EXPORT_CONT_ALIGNMENT_ASSISTANT_MENU

#define ID_CLOSE_ALIGNMENT_ASSISTANT_BUTTON

#define ID_CALIGN_OTHER_ADDPANEL_FEATURE_TYPE_LISTBOX

#define ID_EDIT_VALIDATE_ALIGNMENT_ASSISTANT_MENU

#define ID_ALIGNCDSADD_PROTEIN_DESC

#define ID_CALIGN_RNA_ADD_PANEL_BUTTON11

#define ID_ALIGNCDSADD_GENE_NAME

#define ID_ADD_ALIGN_OTHER_ALIGNMENT_ASSISTANT_MENU

#define ID_EXPORT_INTER_ALIGNMENT_ASSISTANT_MENU

#define ID_GOTO_SEQ_ALIGNMENT_ASSISTANT_BUTTON

#define ID_CALIGN_RNA_ADD_PANEL_BUTTON12

#define ID_CALIGN_OTHER_ADDPANEL_TEXTCTRL11

#define ID_CALIGN_OTHER_ADDPANEL_TEXTCTRL14

#define SYMBOL_CALIGN_OTHER_ADDPANEL_TITLE

#define ID_ADD_ALIGN_CDS_ALIGNMENT_ASSISTANT_MENU

#define ID_CALIGN_RNA_ADD_PANEL_CHOICE1

@ eCmdCreateMobileElement

@ eCmdCreateMiscStructure

@ eCmdCreateBiosourceFeat

@ eCmdCreatePrimTranscript

@ eCmdCreateCommentDescriptor

@ eCmdCreatePubFeatureLabeled

@ eCmdCreateTransitPeptide

@ eCmdCreateSecondaryStructure

@ eCmdCreateMiscDifference

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

bool m_create_general_only

void CreateControls()

Creates the controls and sizers.

void AddOneCommand(const objects::CBioseq_Handle &bsh, CRef< CSeq_loc > seq_loc, CRef< CCmdComposite > cmd)

wxTextCtrl * m_GeneDescription

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

~CAlignCDSAddPanel()

Destructor.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxTextCtrl * m_ProteinName

wxTextCtrl * m_GeneSymbol

CAlignCDSAddPanel()

Constructors.

void Init()

Initialises member variables.

wxTextCtrl * m_ProteinDescription

static bool ShowToolTips()

Should we show tooltips?

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

CLocationPanel * m_Location

CRef< CCmdComposite > GetCommand()

wxListBox * m_FeatureType

CGBQualPanel * m_GBQualPanel

CRef< CCmdComposite > GetCommand()

void Init()

Initialises member variables.

CAlignOtherAddPanel()

Constructors.

CLocationPanel * m_Location

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void x_ChangeFeatureType(const string &key)

void x_AddQuals(objects::CSeq_feat &feat)

CSeq_entry_Handle m_TopSeqEntry

void CreateControls()

Creates the controls and sizers.

static bool ShowToolTips()

Should we show tooltips?

CRef< objects::CSeq_feat > m_QualFeat

wxBoxSizer * m_GBQualSizer

~CAlignOtherAddPanel()

Destructor.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void x_AddGeneQuals(objects::CSeq_feat &gene)

void AddOneCommand(const objects::CBioseq_Handle &bsh, CRef< CSeq_loc > seq_loc, CRef< CCmdComposite > cmd)

void OnFeatureTypeListboxSelected(wxCommandEvent &event)

wxEVT_COMMAND_LISTBOX_SELECTED event handler for ID_FEATURE_TYPE_LISTBOX

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void CreateControls()

Creates the controls and sizers.

wxBoxSizer * m_RNANameSizer

CLocationPanel * m_Location

bool x_RemoveGeneFields()

void OnAdd18SToComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON11

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void AddOneCommand(const objects::CBioseq_Handle &bsh, CRef< CSeq_loc > seq_loc, CRef< CCmdComposite > cmd)

wxFlexGridSizer * m_FieldSizer

wxComboBox * m_ncRNAClass

wxBoxSizer * m_ButtonsSizer

CAlignRNAAddPanel()

Constructors.

static bool ShowToolTips()

Should we show tooltips?

objects::CRNA_ref::TType x_GetRnaType()

~CAlignRNAAddPanel()

Destructor.

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void OnSelectRNAType(wxCommandEvent &event)

wxEVT_COMMAND_CHOICE_SELECTED event handler for ID_CHOICE1

void Init()

Initialises member variables.

void OnAdd16StoComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON12

CRef< CCmdComposite > GetCommand()

void OnTarget(wxCommandEvent &event)

CRef< CSeq_align > AdjustAlign(int from, int to, const vector< int > &offset, CRef< CCmdComposite > cmd)

void OnGoTo(wxCommandEvent &event)

void TrimQualityScores(CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > command)

vector< vector< pair< string, CSeqFeatData::ESubtype > > > m_FeatTypes

void OnValidate(wxCommandEvent &event)

void OnExportCont(wxCommandEvent &event)

void IsNucleotide(wxUpdateUIEvent &event)

void AdjustBioseq(CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > cmd)

vector< vector< vector< pair< TSeqPos, TSeqPos > > > > m_FeatRanges

void OnRemoveSeqFromAlign(wxCommandEvent &)

wxMenu * m_target_submenu

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void AdjustFeatureLocations(CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > cmd)

void OnAddAlignCDS(wxCommandEvent &)

void OnFeatures(wxCommandEvent &event)

static bool ShowToolTips()

Should we show tooltips?

void OnExportInter(wxCommandEvent &event)

CPaintAlignment * m_Panel

void IsSelectionAndClean(wxUpdateUIEvent &event)

void OnReverseStrand(wxCommandEvent &)

wxTextCtrl * m_GoTo_TextCtrl

ICommandProccessor * m_CmdProcessor

vector< string > m_Labels

CSeq_entry_Handle m_TopSeqEntry

void OnAddAlignRNA(wxCommandEvent &)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CRef< CSeq_loc > AdjustLoc(const CSeq_loc &feat_loc, int from, int to, bool &modified, bool &removed)

virtual ~CAlignmentAssistant()

Destructor.

void OnAddAlignOther(wxCommandEvent &)

void GetAlignment(CConstRef< CSeq_align > align)

void ReportPos(int pos, const string &label)

void CreateControls()

Creates the controls and sizers.

CSeq_align_Handle m_Alignment

void CreateFeature(wxCommandEvent &event)

void Init()

Initialises member variables.

void OnSubstitute(wxCommandEvent &event)

void TranslateLocations(CRef< CSeq_loc > loc, vector< pair< CRef< CSeq_loc >, CBioseq_Handle > > &locations)

CAlignmentAssistant()

Constructors.

void OnPropagateFeatures(wxCommandEvent &)

bool x_ExecuteCommand(IEditCommand *command)

vector< vector< CBioseq_Handle::EVectorStrand > > m_FeatStrand

void ReportUnresolvedBioseqs(void)

wxTextCtrl * m_GoToSeq_TextCtrl

void ReportRange(int pos1, int pos2, const string &label)

void OnClose(wxCommandEvent &event)

void OnGoToSeq(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Alignment Assistant"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(775, 595), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

static CRef< objects::CSeq_feat > MakeDefaultFeature(objects::CSeqFeatData::ESubtype subtype)

static objects::CSeqFeatData::ESubtype GetFeatTypeFromCmdID(int cmd_id)

const CSeq_id & GetSeq_id(TDim row) const

void SetEditorWindow(wxWindow *editorWindow)

void SetEditor(CIRef< IEditObject > editor)

CFeatListItem - basic configuration data for one "feature" type.

string GetDescription() const

static bool s_IsRarelyUsedOrDiscouragedFeatureType(int subtype)

static wxString GetDialogFilter(EFileType fileType)

virtual bool TransferDataToWindow()

virtual bool TransferDataFromWindow()

void PopulateGBQuals(objects::CSeq_feat &seq_feat)

@Gb_qual.hpp User-defined methods of the data storage class.

void SetText(const wxString &text)

CRef< CInt_fuzz > Negative(TSeqPos n) const

virtual bool TransferDataFromWindow()

CRef< objects::CSeq_loc > GetSeq_loc() const

virtual bool TransferDataToWindow()

int AlignPosToSeqPos(int pos, int row, bool left) const

static string GetSeqTitle(CBioseq_Handle bsh)

pair< int, int > GetSelection(int row)

void SetAlign(CSeq_align_Handle ah)

void EnableSubstitute(bool enable)

void EnableFeatures(bool enable)

pair< int, int > GetAlignSelection(void)

size_t GetTotalLength() const

void UpdateFeatures(const vector< vector< vector< pair< TSeqPos, TSeqPos > > > > &feat_ranges, const vector< vector< pair< string, objects::CSeqFeatData::ESubtype > > > &feat_types, const vector< vector< objects::CBioseq_Handle::EVectorStrand > > &feat_strand)

static vector< string > GetncRNAClassList()

@RNA_ref.hpp User-defined methods of the data storage class.

static EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype)

@ eFeatureLocationAllowed_NucOnly

@ eFeatureLocationAllowed_ProtOnly

ESubtype GetSubtype(void) const

static bool IsRegulatory(ESubtype subtype)

Non-const iterator over CSeqMap (allows to edit the sequence).

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

static CUICommandRegistry & GetInstance()

the main instance associated with the application

wxMenu * CreateMenu(const SwxMenuItemRec *items)

create a menu from a static definition (see WX_*_MENU macros)

static const string & ConvertSeverity(EDiagSev sev)

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

Interface (functor) for object editing.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

CRef< objects::CSeq_entry > CreateTranslatedProteinSequence(CRef< objects::CSeq_feat > cds, objects::CBioseq_Handle nuc_h, bool create_general_only, int *offset=nullptr)

CRef< objects::CSeq_feat > AddProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

static const char si[8][64]

std::ofstream out("events_result.xml")

main entry point for tests

static void cleanup(void)

static const char * str(char *buf, int n)

static const struct type types[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

vector< const objects::CFeatListItem * > GetSortedFeatList(objects::CSeq_entry_Handle seh, size_t max=numeric_limits< size_t >::max())

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

string GetLabel(const CSeq_id &id)

@ eContent

Untagged human-readable accession or the like.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void Rewind(void)

Reset the iterator to the initial state.

void SetFrom(TSeqPos from)

Set the range from position.

void SetTo(TSeqPos to)

Set the range to position.

void Delete(void)

Delete current element, and make iterator to point to the next element.

ENa_strand GetStrand(void) const

Get the location's strand.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

void ResetFuzzTo(void)

Reset fuzz to.

void ResetFuzzFrom(void)

Reset fuzz from.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

void SetStrand(ENa_strand strand)

Set the range strand.

bool HasChanges(void) const

return true of any part was changed since initialization

const CInt_fuzz * GetFuzzFrom(void) const

const CInt_fuzz * GetFuzzTo(void) const

void SetFuzzTo(CInt_fuzz &fuzz)

Change fuzz to values.

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

size_t GetSize(void) const

Get number of ranges.

TRange GetRange(void) const

Get the range.

void SetFuzzFrom(CInt_fuzz &fuzz)

Change fuzz from.

ENa_strand GetStrand(void) const

TSeqPos GetStop(ESeqLocExtremes ext) const

@ fFGL_Content

Include its content if there is any.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsNucleotide(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

const CSeq_align::TSegs & GetSegs(void) const

CConstRef< CSeq_align > GetSeq_align(void) const

Get const reference to current seq-align.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to the seq-annot.

@ eStrand_Plus

Plus strand.

@ eStrand_Minus

Minus strand.

CSeqMap_I & Remove(void)

Remove current segment.

void GetSequence(string &buffer, CSeqUtil::ECoding buffer_coding) const

Get current sequence as a string with the selected encoding.

const CSeq_loc & GetLocation(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

void SetSequence(const string &buffer, CSeqUtil::ECoding buffer_coding, CSeq_data::E_Choice seq_data_coding)

Set sequence data.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

TSeqPos GetLength(void) const

return length of current segment

CSeq_graph_Handle GetSeq_graph_Handle(void) const

Get original graph handle.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

EType

type of RNA feature

void SetExt(TExt &value)

Assign a value to Ext data member.

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

void SetType(TType value)

Assign a value to Type data member.

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

bool IsSetLens(void) const

lengths in ids order within segs Check if a value has been assigned to Lens data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

TLens & SetLens(void)

Assign a value to Lens data member.

bool IsSetNumseg(void) const

number of segments here Check if a value has been assigned to Numseg data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

void ResetSegs(void)

Reset Segs data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< ENa_strand > TStrands

const TLens & GetLens(void) const

Get the Lens member data.

void SetDim(TDim value)

Assign a value to Dim data member.

vector< TSignedSeqPos > TStarts

void SetDim(TDim value)

Assign a value to Dim data member.

vector< CRef< CSeq_id > > TIds

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

bool IsSetStarts(void) const

start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TIds & SetIds(void)

Assign a value to Ids data member.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsSetIds(void) const

sequences in order Check if a value has been assigned to Ids data member.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

const TRna & GetRna(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

@ eFrame_not_set

not set, code uses one

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TMix & GetMix(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

@ e_not_set

No variant selected.

@ e_Empty

to NULL one Seq-id in a collection

bool IsSetComp(void) const

compression (residues/value) Check if a value has been assigned to Comp data member.

bool IsSetLoc(void) const

region this applies to Check if a value has been assigned to Loc data member.

void ResetValues(void)

Reset Values data member.

TValues & SetValues(void)

Assign a value to Values data member.

TByte & SetByte(void)

Select the variant.

const TInt & GetInt(void) const

Get the variant data.

void SetNumval(TNumval value)

Assign a value to Numval data member.

TReal & SetReal(void)

Select the variant.

TInt & SetInt(void)

Select the variant.

const TGraph & GetGraph(void) const

Get the Graph member data.

TValues & SetValues(void)

Assign a value to Values data member.

const TValues & GetValues(void) const

Get the Values member data.

const TByte & GetByte(void) const

Get the variant data.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

const TReal & GetReal(void) const

Get the variant data.

void ResetValues(void)

Reset Values data member.

void ResetLoc(void)

Reset Loc data member.

const TValues & GetValues(void) const

Get the Values member data.

void ResetValues(void)

Reset Values data member.

E_Choice Which(void) const

Which variant is currently selected.

const TValues & GetValues(void) const

Get the Values member data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

TComp GetComp(void) const

Get the Comp member data.

TValues & SetValues(void)

Assign a value to Values data member.

const TSeq & GetSeq(void) const

Get the variant data.

const TInst & GetInst(void) const

Get the Inst member data.

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Iupacaa

IUPAC 1 letter amino acid code.

CMinPanelContainer::OnRestoreWindow EVT_UPDATE_UI_RANGE(eCmdCloseDockPanel, eCmdWindowRestore, CMinPanelContainer::OnUpdateWindowCommand) CMinPanelContainer

void ReportUsage(const wxString &dialog_name)

Report opening & accepting events in the editing package.

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

#define EDIT_EACH_CODEBREAK_ON_CDREGION(Itr, Var)

#define ERASE_CODEBREAK_ON_CDREGION(Itr, Var)

ERASE_CODEBREAK_ON_CDREGION.

ViewerWindowBase::OnEditMenu ViewerWindowBase::OnJustification EVT_MENU(MID_SHOW_GEOM_VLTNS, ViewerWindowBase::OnShowGeomVltns) EVT_MENU(MID_FIND_PATTERN

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

Selector used in CSeqMap methods returning iterators.

#define WX_DEFINE_MENU(name)

New macros for defining menus for use with CUICommandRegistry.

#define WX_SUBMENU(label)

#define WX_MENU_ITEM(cmd)

#define WX_MENU_ITEM_INT(cmd)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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