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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/editingbtnspanel_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/editingbtnspanel.cpp Source File

(wxPanel* parent, wxWindowID

,

wxString &

,

wxPoint &pos,

wxSize &

,

style) : wxButton(parent,

,

,pos,

,style),

m_OrigId(id), m_Position(pos), m_dragging(

),

m_locked(

),m_removed(

),m_Sizer(parent->GetSizer())

occupied =

;

wxRect

= GetRect();

wxSizerItemList& children =

->GetChildren();

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

(w ==

wxWindow*

(

))

wxRect

= w->GetRect();

(

.Intersects(

))

width = GetRect().GetWidth();

height = GetRect().GetHeight();

wxSizerItemList& children = sizer->GetChildren();

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxRect

(x,y,width,height);

wxWindow* w = (*child)->GetWindow();

(w ==

wxWindow*

(

))

wxRect

= w->GetRect();

(

.GetTop() >

.GetTop())

(

.Intersects(

))

(x+width > sizer->GetContainingWindow()->GetRect().GetWidth() ||

> 2)

(p == wxDefaultPosition)

bottom = panel->GetVirtualSize().y;

(button_bottom > bottom)

panel->SetVirtualSize(panel->GetVirtualSize().x, button_bottom);

wxPoint mouseOnScreen = wxGetMousePosition();

(

.Contains(mouseOnScreen.x,mouseOnScreen.y))

(!IsShownOnScreen())

wxPoint mouseOnScreen = wxGetMousePosition();

(

.Contains(mouseOnScreen.x,mouseOnScreen.y))

wxPoint mouseOnScreen = wxGetMousePosition();

GetPosition(&cx,&cy);

wxRect

= w->GetScreenRect();

(cx >

.GetWidth())

SetPosition( wxPoint(cx, cy) );

= wxPoint(w->CalcUnscrolledPosition(GetPosition()));

bottom = w->GetVirtualSize().y;

(button_bottom > bottom)

w->SetVirtualSize(w->GetVirtualSize().x, button_bottom);

GetPosition(&cx,&cy);

( event.GetKeyCode() )

WXK_LEFT : pos.x--;

(pos); found =

;

;

WXK_RIGHT : pos.x += sdx+1;

(pos); found =

;

;

WXK_UP : pos.y--;

(pos); found =

;

;

WXK_DOWN : pos.y += sdy+1;

(pos); found =

;

;

:

.Skip();

;

(wxPanel* parent, wxWindowID

,

wxString &

=wxEmptyString,

wxPoint &pos=wxDefaultPosition,

wxSize &

=wxDefaultSize,

style=0) :

(parent,id,

,pos,

,style) {}

(wxPanel* parent, wxWindowID

,

subtype,

wxString &

=wxEmptyString,

wxPoint &pos=wxDefaultPosition,

wxSize &

=wxDefaultSize,

style=0) :

(parent,id,

,pos,

,style),

(subtype) {}

(wxPanel* parent, wxWindowID

,

subtype,

wxString &

=wxEmptyString,

wxPoint &pos=wxDefaultPosition,

wxSize &

=wxDefaultSize,

style=0) :

(parent,id,

,pos,

,style),

(subtype) {}

(wxPanel* parent, wxWindowID

,

subtype,

wxString &

=wxEmptyString,

wxPoint &pos=wxDefaultPosition,

wxSize &

=wxDefaultSize,

style=0) :

(parent,id,

,pos,

,style),

(subtype) {}

m_MovingButton =

;

wxWindow*

= GetGrandParent()->GetParent();

(!e)

;

wxSizer* sizer = GetSizer();

wxSizerItemList& children = sizer->GetChildren();

bottom = GetVirtualSize().y;

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

(p.x < 0 || p.y < 0)

button->SetPosition(CalcScrolledPosition(p));

auto_layout = GetAutoLayout();

SetAutoLayout(

);

SetVirtualSize(GetVirtualSize().x, bottom);

SetAutoLayout(auto_layout);

wxPoint p = evt.GetPosition();

wxPoint scrollpos = GetViewStart();

GetScrollPixelsPerUnit(&x,&y);

wxString a_label =

->GetLabel();

wxString b_label =

->GetLabel();

(a_label[0].GetValue() ==

&& b_label[0].GetValue() !=

)

(a_label[0].GetValue() !=

&& b_label[0].GetValue() ==

)

a_label.CmpNoCase(b_label) < 0;

IMPLEMENT_DYNAMIC_CLASS(

, wxScrolledWindow )

(autostart && !m_Instance->ShouldAutoStart())

m_Instance->Destroy();

m_Instance->Show(

);

m_Instance->SetFocus();

(!instance.empty())

title <<

<< instance <<

;

wxFrame::Create( parent,

,

(

), pos,

, style );

GetSizer()->SetSizeHints(

);

wxColour bg_color = wxSystemSettings::GetColour(wxSYS_COLOUR_FRAMEBK);

->SetBackgroundColour(bg_color);

->SetBackgroundColour(bg_color);

->SetBackgroundColour(bg_color);

wxColourDialog dlg(

);

(dlg.ShowModal() == wxID_OK)

= dlg.GetColourData().GetColour();

wxPanel* itemPanel1 =

wxPanel(

,

,wxPoint(0,20),wxSize(600,380));

wxBoxSizer* itemBoxSizer1 =

wxBoxSizer(wxVERTICAL);

itemPanel1->SetSizer(itemBoxSizer1);

itemBoxSizer1->Add(

, 2, wxALL|wxGROW, 0);

->SetVirtualSize(-1, 1500);

->SetVirtualSize(-1, 1500);

->SetVirtualSize(-1, 1500);

=

wxBoxSizer(wxVERTICAL);

=

wxBoxSizer(wxVERTICAL);

=

wxBoxSizer(wxVERTICAL);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALL|wxEXPAND, 0);

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer3, 0, wxALL|wxEXPAND, 0);

itemBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxSearchCtrl( itemPanel1,

,wxEmptyString,wxDefaultPosition,wxDefaultSize,wxTE_PROCESS_ENTER);

itemBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer4, 0, wxALL|wxEXPAND, 0);

wxHyperlinkCtrl* itemHyperLink1 =

wxHyperlinkCtrl(itemPanel1,

,

(

),

(

));

itemHyperLink1->SetVisitedColour(itemHyperLink1->GetNormalColour());

itemBoxSizer4->Add(itemHyperLink1, 0, wxALIGN_CENTER_VERTICAL|wxLEFT|wxRIGHT, 5);

wxHyperlinkCtrl* itemHyperLink2 =

wxHyperlinkCtrl(itemPanel1,

,

(

),

(

));

itemHyperLink2->SetVisitedColour(itemHyperLink2->GetNormalColour());

itemBoxSizer4->Add(itemHyperLink2, 0, wxALIGN_CENTER_VERTICAL|wxLEFT|wxRIGHT, 5);

(wxSizerItemList::iterator child = children1.begin(); child != children1.end(); ++child)

wxWindow* w = (*child)->GetWindow();

wxFrame::TransferDataToWindow();

wxSizerItemList& children = sizer->GetChildren();

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

old =

.GetOldSelection();

current =

.GetSelection();

found =

;

(sel != wxNOT_FOUND)

found = panel->

(evt);

vector<wxSizer*> sizers;

vector<IMovableButton*> buttons;

(

=0;

<sizers.size();

++)

wxSizer *sz = sizers[

];

wxSizerItemList& children = sz->GetChildren();

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

buttons.push_back(button);

(

=0;

<buttons.size();

++)

buttons[

]->DeleteButton();

wxString

=

.GetString().Lower();

(!

.IsEmpty())

(

.Lower().Find(

) == wxNOT_FOUND)

button_id = btn.first;

filename = btn.second;

(report_required)

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

id_to_win[button->

()] = button;

win_id =

->first;

(vector<pair<int,wxPoint> >::const_iterator j =

->second.begin(); j !=

->second.end(); ++j)

x = j->second.x;

y = j->second.y;

button->SetPosition(win->CalcScrolledPosition(p));

action =

;

( !path.empty() ){

( wxFileName::FileExists( path ) ){

(

<< action <<

<< path );

(

<< action <<

<< path );

(

<< action <<

);

(!coords.empty())

(

< coords.size()-3 )

= coords[

];

x = coords[

+1];

y = coords[

+2];

win = coords[

+3];

width = 600,height = 400;

pos_x = 5, pos_y = 5;

(

= 0;

< wxDisplay::GetCount();

++)

wxDisplay display(

);

max_x += display.GetGeometry().GetWidth();

(pos_x + width > max_x) pos_x = wxGetDisplaySize().GetWidth()-width-5;

(pos_x < 0) pos_x = 5;

(pos_y + height > wxGetDisplaySize().GetHeight()) pos_y = wxGetDisplaySize().GetHeight()-height-5;

(pos_y < 0) pos_y = 5;

vector<string> button_names;

vector<string> titles;

(

= 0;

< ids.size();

++)

button_name = button_names[

];

title = titles[

];

(

= ids.size() - 1;

>= 0;

--)

ids.erase(ids.begin() +

);

button_names.erase(button_names.begin() +

);

titles.erase(titles.begin() +

);

vector<wxSizer*> sizers;

(

=0;

<sizers.size();

++)

wxSizer *sz = sizers[

];

wxSizerItemList& children = sz->GetChildren();

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

coords.push_back(button->

());

coords.push_back(col);

coords.push_back(

);

coords.push_back(panel->GetId());

vector<string> button_names;

vector<string> titles;

button_id = btn.first;

filename = btn.second;

ids.push_back(button_id);

button_names.push_back(button_name);

titles.push_back(title);

( !path.empty() ){

(

<<

);

(dlg.ShowModal() == wxID_OK)

wxString button_name = dlg.

();

(filename.empty())

button->AddDynamicMenu();

button->SetRemoved(

);

(report_required)

button->GetPosition(

, &y);

pos =

(

);

vector<wxSizer *> sizers;

vector<IMovableButton *> buttons;

(

= 0;

< sizers.size();

++)

wxSizer *sz = sizers[

];

wxSizerItemList& children = sz->GetChildren();

(wxSizerItemList::iterator child = children.begin(); child != children.end(); ++child)

wxWindow* w = (*child)->GetWindow();

buttons.push_back(btn);

(

=0;

<buttons.size();

++)

buttons[

]->Destroy();

wxWindow* main_window =

;

wxFileDialog asn_save_file(

,

(

), wxEmptyString, wxEmptyString,

wxFD_SAVE|wxFD_OVERWRITE_PROMPT);

(asn_save_file.ShowModal() == wxID_OK)

wxString path = asn_save_file.GetPath();

( !path.empty() )

wxFileDialog asn_save_file(

,

(

), wxEmptyString, wxEmptyString,

wxFD_OPEN|wxFD_FILE_MUST_EXIST);

(asn_save_file.ShowModal() == wxID_OK)

wxString path = asn_save_file.GetPath();

( !path.empty() )

wxNullBitmap;

sel_srv->GetActiveObjects(

);

(!ws)

;

vector<CRef<CSeq_loc> > locs;

(!sel_srv)

locs;

sel_srv->GetCurrentSelection(

);

sel_srv->GetActiveObjects(

);

(

.empty())

locs;

* ptr = it->object.GetPointer();

objects::CSeq_feat* seqfeat =

objects::CSeq_feat*

(ptr);

objects::CSeq_loc* seqloc =

objects::CSeq_loc*

(ptr);

objects::CBioseq* bioseq =

objects::CBioseq*

(ptr);

objects::CSeqdesc* seqdesc =

objects::CSeqdesc*

(ptr);

objects::CPubdesc* pubdesc =

objects::CPubdesc*

(ptr);

objects::CSeq_id* seq_id =

objects::CSeq_id*

(ptr);

(seqfeat->IsSetLocation()) {

loc->

(seqfeat->GetLocation());

locs.push_back(loc);

}

(seq_id) {

new_id->

(*seq_id);

locs.push_back(loc);

}

(seqloc) {

locs.push_back(loc);

}

(bioseq) {

loc->

().SetId().Assign(*(bioseq->GetId().front()));

loc->

().SetFrom(0);

loc->

().SetTo(bioseq->GetLength() - 1);

locs.push_back(loc);

}

(seqdesc) {

loc->

().SetId().Assign(*(bi->

().front().GetSeqId()));

loc->

().SetFrom(0);

locs.push_back(loc);

}

(pubdesc) {

loc->

().SetId().Assign(*(bi->

().front().GetSeqId()));

loc->

().SetFrom(0);

locs.push_back(loc);

found =

;

sel_srv->GetCurrentSelection(

);

sel_srv->GetActiveObjects(

);

wxWindow* main_window =

;

report->Show(

);

wxWindow* main_window =

;

(regpath.empty() || !dlg)

(regpath.empty() || !dlg)

(width >= 0 && height >= 0)

dlg->SetSize(wxSize(width,height));

(pos_x >= 0 && pos_y >= 0) {

(

= 0;

< wxDisplay::GetCount();

++)

wxDisplay display(

);

max_x += display.GetGeometry().GetWidth();

(pos_x + width > max_x) pos_x = wxGetDisplaySize().GetWidth()-width-5;

(pos_y + height > wxGetDisplaySize().GetHeight()) pos_y = wxGetDisplaySize().GetHeight()-height-5;

dlg->SetPosition(wxPoint(pos_x,pos_y));

wxTopLevelWindow* top_win =

wxTopLevelWindow*

(dlg);

wxRect rc = dlg->GetRect();

dlg->Move(rc.GetLeftTop());

vector< CIRef<IFileLoadPanelClientFactory> > file_formats;

(

= 0;

< file_formats.size(); ++

) {

(file_formats[

]->GetFileLoaderId() ==

) {

format_manager.

(file_formats[

]->CreateInstance());

(

== format_manager->GetFileLoaderId()) {

(const_qual_mgr) {

wxTextDataObject

;

(wxTheClipboard->Open())

(wxTheClipboard->IsSupported( wxDF_UNICODETEXT ))

wxTheClipboard->GetData(

);

wxTheClipboard->Close();

(

.GetText().length() == 0) {

wxMessageBox(

);

fname =

.GetFileName();

vector<wxString> fnames;

dlg.SetSize(760, 940);

dlg.Centre(wxBOTH | wxCENTRE_ON_SCREEN);

dlg.SetMinSize(wxSize(760, 750));

(dlg.ShowModal() == wxID_OK) {

tmp_file(fname);

start_all = chrono::steady_clock::now();

diff_all = chrono::steady_clock::now() - start_all;

(

<<

<< chrono::duration_cast<chrono::seconds>(diff_all).

() <<

);

wxWindow* main_window =

;

wxWindow* main_window =

;

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

edit_dlg->Show(

);

wxWindow* main_window =

;

(dlg.ShowModal() == wxID_OK) {

(dlg.ShowModal() == wxID_OK)

(dlg.ShowModal() == wxID_OK) {

wxMessageBox(

,

(

),

wxOK | wxICON_ERROR,

);

wxWindow* main_window =

;

(dlg.ShowModal() == wxID_OK) {

wxMessageBox(

,

(

),

wxOK | wxICON_ERROR,

);

(dlg.ShowModal() == wxID_OK)

wxWindow* main_window =

;

(dlg.ShowModal() == wxID_OK) {

wxMessageBox(

,

(

),

wxOK | wxICON_ERROR,

);

(dlg.ShowModal() == wxID_OK)

ispartial5 =

, ispartial3 =

;

ispartial5 =

, ispartial3 =

;

ispartial5 =

, ispartial3 =

;

wxWindow* main_window =

;

dlg->

(

);

wxWindow* main_window =

;

wxMessageBox(e.

(),

(

), wxOK | wxICON_ERROR,

);

wxMessageBox(e.

(),

(

), wxOK | wxICON_ERROR,

);

vector<string> format_ids;

format_ids.push_back(

);

fileManager->LoadFormats(format_ids);

(

= 0;

< fileManager->GetFormatManagers().

(); ++

) {

(const_qual_mgr) {

vector<CIRef<IOpenObjectsPanelClient> > loadManagers;

dlg.SetSize(760, 940);

dlg.Centre(wxBOTH | wxCENTRE_ON_SCREEN);

dlg.SetMinSize(wxSize(760, 750));

(dlg.ShowModal() == wxID_OK) {

(dlg.ShowModal() == wxID_OK) {

(dlg.ShowModal() == wxID_OK)

->Equals(*second);

(dlg.ShowModal() == wxID_OK) {

vector<CRef<CSeq_loc> > cpy = orig_locs;

vector<CRef<CSeq_loc> >::iterator lit = cpy.begin();

(lit != cpy.end()) {

(!

||

.IsAa()) {

lit = cpy.erase(lit);

stable_sort(cpy.begin(), cpy.end(),

);

cpy.erase(unique(cpy.begin(), cpy.end(),

), cpy.end());

->AddCommand(*subcmd);

(dlg.ShowModal() == wxID_OK)

ispartial5 =

;

ispartial3 =

;

ispartial5 =

;

ispartial3 =

;

ispartial5 =

;

ispartial3 =

;

ispartial5 =

;

ispartial3 =

;

ispartial5 =

;

ispartial3 =

;

show_label =

;

show_label =

;

show_label =

;

show_label =

;

show_label =

;

(dlg.ShowModal() == wxID_OK){

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

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

edit_dlg->Show(

);

wxWindow* main_window =

;

(!macro_dir.DirExists()) {

(!macro_dir.Mkdir(wxS_DIR_DEFAULT, wxPATH_MKDIR_FULL)) {

(

<<

<<

(macro_dir.GetPath().ToUTF8()) <<

);

wxFileName macro_file(macro_dir.GetPath(), filename);

(!macro_file.FileExists()) {

orig_location =

;

(!orig_path.DirExists()) {

wxFileName orig_file(orig_path.GetPath(), filename);

wxFileName dst_file(macro_dir.GetPath(), filename);

(!wxCopyFile(orig_file.GetFullPath(), dst_file.GetFullPath())) {

(

<<

<< filename <<

<<

(macro_dir.GetPath().ToUTF8()) <<

);

(macro_file.GetFullPath().ToUTF8());

username[1024];

(username);

(orig_dir_path.empty() || upd_dir_path.empty()) {

dir(upd_dir_path);

(

& it : files) {

filename = it->GetName();

(lcl_chksum == upd_chksum) {

(lcl_chksum == orig_chksum) {

lcl(lcl_filename);

upd(upd_filename);

(upd.

(

(lcl_dir.GetFullPath().ToUTF8()))) {

(!username.empty()) {

(

<<

<< upd_filename <<

<<

(lcl_dir.GetFullPath().ToUTF8()) <<

);

(!username.empty()) {

title, filename;

add_user_object =

;

(event.GetId()) {

title =

;

add_user_object =

;

title =

;

=

.GetId();

(macros.empty() && filename.empty()) {

wxWindow* main_window =

;

kMacroReport(

);

(wxWindowList, wit, main_window->GetChildren()){

wxWindow* child = *wit;

status =

;

(!macros.empty()) {

(!filename.empty()) {

(!status || report_msg.empty()) {

report_msg.assign(

);

title.append(kMacroReport);

report->Show(

);

vector<string> macro;

add_user_object =

;

resolve_vars =

;

(event.GetId()) {

add_user_object =

;

resolve_vars =

;

=

.GetId();

(macro.empty() && filename.empty()) {

(!macro.empty()) {

(!filename.empty()) {

(dlg.ShowModal() == wxID_OK)

wxWindow* main_window =

;

seqdesc->

().

(*edit::CGenomeAssemblyComment::MakeEmptyUserObject());

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

edit_dlg->Show(

);

new_feat->

().SetProt().AutoFixEC();

new_feat->

().SetProt().RemoveBadEC();

sel_srv->GetActiveObjects(

);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

vector<CBioseq_Handle> bioseqs;

* ptr = it->object.GetPointer();

objects::CBioseq* bioseq =

objects::CBioseq*

(ptr);

bioseqs.push_back(bsh);

objects::CSeq_loc* loc =

objects::CSeq_loc*

(ptr);

bioseqs.push_back(bsh);

(bioseqs.size() == 1)

seh = bioseqs.front().GetSeq_entry_Handle();

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

sel_srv->GetActiveObjects(

);

(

.empty())

;

(dlg.ShowModal() == wxID_OK)

wxWindow* main_window =

;

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

edit_dlg->Show(

);

modified =

;

edited_desc->

(*desc_it);

->AddCommand(*change_molinfo);

edited_object->

(seq_it->GetInst());

->AddCommand(*change_inst);

found =

;

edited_desc->

(*desc_it);

->AddCommand(*change_molinfo);

edited_object->

(seq_it->GetInst());

->AddCommand(*change_inst);

wxWindow* main_window =

;

dlg->

(

);

frame->Show(

);

(!

->GetData().front().object)

sViewType(

);

prjSrv->AddProjectView(sViewType,

->GetData(), 0).GetPointer();

wxWindow* main_window =

;

wxWindow* main_window =

;

sel_srv->GetActiveObjects(

);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

CSeq_loc* loc =

;

CSeq_loc* obj_loc =

CSeq_loc*

(o.object.GetPointer());

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

(!loc->IsWhole())

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

wxWindow* main_window =

;

wxWindow* main_window =

;

wxFileDialog asn_save_file(main_window,

(

),

, wxEmptyString,

wxFD_SAVE|wxFD_OVERWRITE_PROMPT);

(asn_save_file.ShowModal() == wxID_OK)

wxString path = asn_save_file.GetPath();

( !path.IsEmpty())

(dlg.ShowModal() == wxID_OK) {

wxMessageBox(

,

(

),

wxOK | wxICON_ERROR,

);

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

void RemoveTitlesSeqEntry(CSeq_entry_Handle seh, const CSeq_entry &entry, CCmdComposite *composite)

EVT_CHECKBOX(ID_CADJUSTFEATURES_CHECKBOX, CAdjustFeaturesForGaps::OnKnownUnknownSelected) EVT_CHECKBOX(ID_CADJUSTFEATURES_CHECKBOX1

CSeq_entry_Handle GetSeqEntryForSeqdesc(CRef< CScope > scope, const CSeqdesc &seq_desc)

void ConfigureAutodefParamsForBestCombo(SAutodefParams &params, objects::CSeq_entry_Handle seh)

void ConfigureAutodefParamsForID(SAutodefParams &params, objects::CSeq_entry_Handle seh)

unsigned int ConfigureParamsForPrefixCombo(SAutodefParams &params, objects::CSeq_entry_Handle seh)

CRef< CCmdComposite > InstantiateProteinTitles(objects::CSeq_entry_Handle entry)

CRef< CCmdComposite > AutodefSeqEntryNoTitle(objects::CSeq_entry_Handle entry, SAutodefParams *params, bool docsum_only=false)

Checksum and hash calculation classes.

void SetInitParameters(EActionType action_type, EFieldType field_type, const string &field=kEmptyStr, const wxString &title=wxEmptyString)

@ eFieldType_StructuredComment

@ eActionType_RemoveTextOutside

bool apply(objects::CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

wxString GetName() const override

string GetFileName() const

void apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProccessor)

static void ExportDialog(IWorkbench *workbench)

CRef< CCmdComposite > GetCommand()

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

bool apply(objects::CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

void x_TableReaderMacro(bool modal=false)

void ShowSourceOptions(bool show)

void SetParams(SAutodefParams *params)

void PopulateParams(SAutodefParams &params)

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

CRef< CCmdComposite > GetCommand()

void SetEditingType(EEditingType editing_type)

void ChooseFeatureType(objects::CSeqFeatData::ESubtype subtype)

CRef< CCmdComposite > GetCommand()

CRef< CCmdComposite > GetCommand()

CRef< CCmdComposite > GetCommand()

virtual bool OnChar(wxKeyEvent &event)

virtual void OnKeyDown(wxKeyEvent &event)

void SetMovingButton(IMovableButton *btn, bool dragging)

IMovableButton * CreateButton(wxWindow *w, int x, int y)

virtual void onMouseClick(wxMouseEvent &evt)

IMovableButton * m_MovingButton

CChecksum – Checksum calculator.

ncbi::objects::CBioseq_set::EClass GetClass()

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse, bool capitalize_after_colon)

virtual void SetRegistryPath(const string &path)

static CDiscrepancyDlg * OpenDiscrepancyDlg(EReportType type, CScope &scope, IWorkbench *workbench, const wxString &workDir=wxEmptyString)

void SetEditorWindow(wxWindow *editorWindow)

void SetEditor(CIRef< IEditObject > editor)

virtual void SetWorkDir(const wxString &workDir)

virtual void SetUndoManager(ICommandProccessor *cmdProccessor)

void RemoveTextOutsideString(wxCommandEvent &evt)

void AddGSet(wxCommandEvent &event)

void ValidateSeq(wxCommandEvent &event)

void OnSetBackground(wxHyperlinkEvent &event)

void ParseText(wxCommandEvent &evt)

void PrefixHaplotToDefLine(wxCommandEvent &event)

void OnFixOrgModInstitution(wxCommandEvent &event)

void AutodefMisc(wxCommandEvent &evt)

void ApplyDbxrefs(wxCommandEvent &event)

void EditFeatQual(wxCommandEvent &evt)

void Add_rRNA(wxCommandEvent &evt)

void SwapCGPQual(wxCommandEvent &evt)

void AddDefaultMacroButtons()

bool IsLocationSelectedAa()

void RemoveStaticButtons(vector< int > &ids, vector< string > &filenames, vector< string > &button_names, vector< string > &titles)

void TrimOrganismNames(wxCommandEvent &event)

void EditSequence(wxCommandEvent &event)

void Add_gene(wxCommandEvent &evt)

void RemoveUnverified(wxCommandEvent &event)

CSeq_entry_Handle x_GetSelectedSeq()

void RemoveSourceQual(wxCommandEvent &evt)

virtual void LoadSettings()

void AutodefDefaultOptions(wxCommandEvent &evt)

void OnStripAuthorSuffixes(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON13

void RemoveDupFeats(wxCommandEvent &evt)

void OnMergePrimerSets(wxCommandEvent &event)

void RunMacro(wxCommandEvent &event)

void ParseStrainSerotypeFromNames(wxCommandEvent &event)

void RevComp16S(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON24

void OnFixCapitalizationAll(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON4

void OnAddCitSubForUpdate(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON19

void OnRemoveAuthorConsortiums(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON14

void EditFeatureEvidence(wxCommandEvent &evt)

void SaveASN1File(wxCommandEvent &event)

vector< CRef< CSeq_loc > > m_Locations

void OnAppendModToOrg(wxCommandEvent &event)

void ApplyCGPQual(wxCommandEvent &evt)

void OnRemoveAllStructuredComments(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON27

void OnCancelFindButton(wxCommandEvent &event)

void OnRemoveDescriptors(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON25

void OnCallerTool(wxCommandEvent &event)

void ImportFeatureTableClipboard(wxCommandEvent &event)

void ConvertSourceQual(wxCommandEvent &evt)

void TaxFixCleanup(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON11

void ShowAfter(wxWindow *dlg)

void ParseTextFromDefline(wxCommandEvent &evt)

void AddTranslExcept(wxCommandEvent &event)

void OnAssignFeatureIds(wxCommandEvent &event)

void AddNamedrRNALarge(wxCommandEvent &event)

void RunMacroWithReport(wxCommandEvent &event)

virtual void SaveSettings() const

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void RemoveAllFeatures(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON12

void FixupOrganismNames(wxCommandEvent &event)

ICommandProccessor * m_CmdProccessor

void RemoveFeatQual(wxCommandEvent &evt)

void ConvertCGPQual(wxCommandEvent &evt)

void RemoveUnreviewed(wxCommandEvent &event)

void EditPubs(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON2

void ApplyRNAQual(wxCommandEvent &evt)

void RemoveRNAQual(wxCommandEvent &evt)

void SplitStructuredCollections(wxCommandEvent &event)

void AddCDS(wxCommandEvent &event)

void OnAddrRNA16S(wxCommandEvent &event)

void LaunchDesktop(wxCommandEvent &event)

void OnAddStructuredCommentKeyword(wxCommandEvent &event)

void ExtendPartialsConstr(wxCommandEvent &evt)

void PrefixOrgToDefLine(wxCommandEvent &event)

void IllegalQualsToNote(wxCommandEvent &event)

void LowercaseQuals(wxCommandEvent &evt)

void BulkEdit(wxCommandEvent &event)

void OnConvertComment(wxCommandEvent &event)

void ConvertRNAQual(wxCommandEvent &evt)

wxButton * m_exportTabsButton

void AddSequences(wxCommandEvent &event)

void EditSourceQual(wxCommandEvent &evt)

bool IsLocationSelected()

void EditButton(IMovableButton *button)

void MacroEditor(wxCommandEvent &event)

void SegregateSets(wxCommandEvent &event)

void TableReaderFromClipboard(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON10

void BulkEditRNA(wxCommandEvent &event)

void OnAddrRNA23S(wxCommandEvent &event)

void RemoveCGPQual(wxCommandEvent &evt)

void AddMicrosatellite(wxCommandEvent &event)

void StrainToSp(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON26

void OnResetBackground(wxHyperlinkEvent &event)

void OnFixCapitalizationTitles(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON6

void AddNamedrRNASmall(wxCommandEvent &event)

void AddRNA(wxCommandEvent &event)

void PrefixStrainToDefLine(wxCommandEvent &event)

void RetranslateCDS(wxCommandEvent &event)

void EditCGPQual(wxCommandEvent &evt)

void LabelrRNAs(wxCommandEvent &event)

void OnFixCapitalizationAffiliation(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON7

void BulkEditCDS(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON28

void AddNamedrRNA28S(wxCommandEvent &event)

void OnReorderStructuredComment(wxCommandEvent &event)

void EditSubmitBlock(wxCommandEvent &event)

wxButton * m_resetTabsButton

void OnResetTabs(wxCommandEvent &event)

void DiscrepancyReport(wxCommandEvent &event)

wxButton * m_importTabsButton

void OnRemoveGenomeProjectsDB(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON21

void CreateControls()

Creates the controls and sizers.

void EditRNAQual(wxCommandEvent &evt)

void ApplySourceQual(wxCommandEvent &event)

void VectorTrim(wxCommandEvent &event)

void OnFixiInPrimerSeqs(wxCommandEvent &event)

CConstRef< CSeq_submit > m_SeqSubmit

void EditStructField(wxCommandEvent &evt)

void UpdateMultSeqClipboard(wxCommandEvent &event)

void RetranslateCDS_NoStp(wxCommandEvent &event)

void OnRemoveUnpublishedPublications(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON9

void OnFindButton(wxCommandEvent &event)

void OnReorderSequences(wxCommandEvent &event)

void OnAddMacroClick(wxCommandEvent &event)

void UnculTaxTool(wxCommandEvent &event)

objects::CSeq_entry_Handle m_TopSeqEntry

void OnMegaReport(wxCommandEvent &event)

void UpdateSingleSeqClipboard(wxCommandEvent &event)

void RmCultureNotes(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON23

bool Create(wxWindow *parent, wxWindowID id=10020, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(600, 400), long style=wxDEFAULT_FRAME_STYLE)

Creation.

vector< CRef< CSeq_loc > > x_GetSelectedLocations()

void TrimNsTerminal(wxCommandEvent &event)

void RmWrongOrIllegalQuals(wxCommandEvent &event)

void OnParseCollectionDateDayFirst(wxCommandEvent &event)

void x_LockButtons(wxSizer *sizer, bool locked)

map< int, vector< pair< int, wxPoint > > > m_MovableButtonPosition

void OnReverseAuthorNamesClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON1

map< int, string > m_dynamic_buttons_name

void ClickableSortUniqueCount(wxCommandEvent &event)

void BulkEditMiscFeat(wxCommandEvent &event)

void OnRemoveStructuredCommentKeyword(wxCommandEvent &event)

void SetFrameAndPosition()

CEditingBtnsPanel()

Constructors.

void OnRemoveDefLines(wxCommandEvent &event)

void ShowFeatureTable(wxCommandEvent &event)

void CorrectGenes(wxCommandEvent &event)

bool IsLocationSelectedNa()

void RemProtTitles(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON22

void SetPanelsBackgroundColour()

void AddControlRegion(wxCommandEvent &event)

void CreateFeature(wxCommandEvent &evt)

void PrefixListToDefLine(wxCommandEvent &event)

void ExtendPartialsAll(wxCommandEvent &evt)

void ExportTable(wxCommandEvent &evt)

void AutodefOptions(wxCommandEvent &evt)

map< int, string > m_dynamic_buttons_filename

wxSearchCtrl * m_findButton

void AddOtherFeature(wxCommandEvent &event)

void OnRemoveBankitComment(wxCommandEvent &event)

void OnRemoveSequences(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON20

void OnImportBtnClick(wxCommandEvent &event)

void AddStrainSerotypeToNames(wxCommandEvent &event)

void AddIsolSource(wxCommandEvent &evt)

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void ApplyFeatQual(wxCommandEvent &evt)

vector< IMovableButton * > m_all_buttons

void GroupExplode(wxCommandEvent &event)

void OnClickLock(wxCommandEvent &event)

void RemoveTextInsideStr(wxCommandEvent &evt)

void OnAddrRNA18S(wxCommandEvent &event)

void SwapRNAQual(wxCommandEvent &evt)

void ParseLocalIdToSrc(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON3

void SelectTarget(wxCommandEvent &event)

void AutodefNoMods(wxCommandEvent &evt)

void SequesterSets(wxCommandEvent &event)

void OnParseCollectionDateMonthFirst(wxCommandEvent &event)

void PrefixCultivarToDefLine(wxCommandEvent &event)

void RemoveButton(IMovableButton *button)

void RemoveSrcNotes(wxCommandEvent &evt)

void Save(wxCommandEvent &evt)

void OnCountryFixupCap(wxCommandEvent &event)

void ImportFeatureTable(wxCommandEvent &event)

wxButton * m_AddMacroButton

void BarcodeTool(wxCommandEvent &event)

wxBoxSizer * m_SizerRemoved

void TrimNsRich(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON16

void rRNAtoDNA(wxCommandEvent &event)

void RmIllegalQuals(wxCommandEvent &event)

void AutodefRefresh(wxCommandEvent &evt)

void OnExportBtnClick(wxCommandEvent &event)

void AddDefLine(wxCommandEvent &event)

void ConvertFeatures(wxCommandEvent &evt)

void SwapFeatQual(wxCommandEvent &evt)

void MolInfoEdit(wxCommandEvent &evt)

void OnFixCapitalizationAuthors(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON5

void SwapSourceQual(wxCommandEvent &evt)

void AutodefPopset(wxCommandEvent &evt)

void MrnaCds(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON18

static CEditingBtnsPanel * m_Instance

static bool ShowToolTips()

Should we show tooltips?

void FindASN1(wxCommandEvent &evt)

void ECNumberCleanup(wxCommandEvent &evt)

void AutodefId(wxCommandEvent &evt)

void OnSwapPrimerSeqName(wxCommandEvent &event)

void AddNamedrRNA12S(wxCommandEvent &event)

void Add_misc_feat(wxCommandEvent &evt)

void AnnotateDescriptorComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON17

void AddSet(wxCommandEvent &event)

void AddNamedrRNA26S(wxCommandEvent &event)

~CEditingBtnsPanel()

Destructor.

void OnParseComment(wxCommandEvent &event)

CButtonPanel * m_panel_removed

void BulkGeneEdit(wxCommandEvent &event)

void SplitQualifiersAtCommas(wxCommandEvent &event)

void OnRemoveFeatures(wxCommandEvent &event)

void SetTextViewBackgroundColour(const wxColour &color)

void SortUniqueCount(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON8

void CreateDescGenomeAssemblyComment(wxCommandEvent &evt)

virtual bool TransferDataToWindow()

Transfer data to the window.

void Init()

Initialises member variables.

void OnCountryFixupNoCap(wxCommandEvent &event)

void TableReader(wxCommandEvent &event)

void OnChar(wxKeyEvent &evt)

void PrefixCloneToDefLine(wxCommandEvent &event)

void RmWrongQuals(wxCommandEvent &event)

void ConvertCdsToMiscFeat(wxCommandEvent &evt)

void PT_Cleanup(wxCommandEvent &event)

void OnSplitPrimerSets(wxCommandEvent &event)

void ConvertFeatQual(wxCommandEvent &evt)

map< int, string > m_dynamic_buttons_title

void EditFeatureLocation(wxCommandEvent &evt)

virtual void SetRegistryPath(const string &reg_path)

void WrongQualsToNote(wxCommandEvent &event)

void OnNotebookTabChanged(wxBookCtrlEvent &event)

void PrefixIsolateToDefLine(wxCommandEvent &event)

void SaveTable(const wxString &workDir=wxEmptyString)

virtual ~CFeatureMovableButtonAa()

CFeatureMovableButtonAa(wxPanel *parent, wxWindowID id, CSeqFeatData::ESubtype subtype, const wxString &label=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=0)

CFeatureMovableButtonAa()

virtual bool VerifySelection(CEditingBtnsPanel *e)

virtual bool VerifySelection(CEditingBtnsPanel *e)

virtual ~CFeatureMovableButtonNa()

CFeatureMovableButtonNa(wxPanel *parent, wxWindowID id, CSeqFeatData::ESubtype subtype, const wxString &label=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=0)

CFeatureMovableButtonNa()

virtual bool VerifySelection(CEditingBtnsPanel *e)

virtual ~CFeatureMovableButton()

CFeatureMovableButton(wxPanel *parent, wxWindowID id, CSeqFeatData::ESubtype subtype, const wxString &label=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=0)

virtual ~CFeatureSubtypeSelector()

virtual CSeqFeatData::ESubtype GetSubtype()

CSeqFeatData::ESubtype m_Subtype

CFeatureSubtypeSelector()

CFeatureSubtypeSelector(CSeqFeatData::ESubtype subtype)

void SetWorkDir(const wxString &workDir)

static wxString GetDialogFilter(EFileType fileType)

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

wxString GetWorkDir() const

CUndoManager & GetUndoManager()

void SetText(const wxString &text)

void SetRefresh(IRefreshCntrl *refresh)

static void apply(IWorkbench *wb, ICommandProccessor *cmd_processor, CScope &scope)

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

void Write(CNcbiOstream &ostr, int priority=ePriority_Local) const

Write the local policy to a specified stream.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

CRef< CRegistryFile > AddSite(CNcbiIstream &istr, int priority)

Add a site-specific repository.

CIRef< IEditCommand > ImportFeaturesFromClipboard(const wxString &workDir)

CIRef< IEditCommand > ImportFeaturesFromFile(const wxString &workDir=wxEmptyString, const string &format_id=kEmptyStr)

bool apply(objects::CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title, wxWindow *parent)

bool apply(IWorkbench *wb, ICommandProccessor *cmdProcessor, const string &title, CScope &scope)

static CMacroFlowEditor * GetInstance(wxWindow *parent, CRef< IGuiCoreHelper > gui_core_helper, wxWindowID id=15000, const wxString &caption=_("Macro Flow Editor"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(1500, 1000), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCLOSE_BOX)

void OpenScript(const wxString &path, bool recent_scripts, bool allow_empty)

static const char * sm_AutofixWGS

vector< string > TVecMacroNames

static const char * sm_AutofixGB

static TVecMacroNames s_GetMacroSteps(const CTempString &macro_class)

bool ExecuteMacros(const vector< string > &macro_names, CNcbiOstrstream &log, bool add_user_object=false, bool resolve_vars=false)

static const char * sm_AutofixTSA

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

CRef< CCmdComposite > GetCommand()

virtual ~CMovableButton()

virtual bool VerifySelection(CEditingBtnsPanel *e)

CMovableButton(wxPanel *parent, wxWindowID id, const wxString &label=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=0)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void SetManagers(vector< CIRef< IOpenObjectsPanelClient > > &managers)

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse, bool monthFirst)

void SetFromFieldType(EFieldType field_type)

void SetToFieldType(EFieldType field_type)

CRef< CCmdComposite > GetCommand()

void PopulateModifierCombo()

void SetParams(SAutodefParams *params)

CProjectService - a service providing API for operations with Workspaces and Projects.

virtual void SetFilenames(const vector< wxString > &filenames)

initilize the manager with the given filenames

virtual void SetServiceLocator(IServiceLocator *srv_locator)

Sets / unsets Service Locator.

CAttribTableColumnIdPanel * x_GetColumnIdPanel()

void SetTopLevelEntry(CSeq_entry_Handle seq_entry)

class CRegistryReadView provides a nested hierarchical view at a particular key.

int GetInt(const string &key, int default_val=0) const

access a named key at this level, with no recursion

bool GetBool(const string &key, bool default_val=false) const

void GetIntVec(const string &key, vector< int > &val) const

string GetString(const string &key, const string &default_val=kEmptyStr) const

void GetStringVec(const string &key, vector< string > &val) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

bool apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

CRef< CCmdComposite > GetCommand()

static void RemoveDuplicateFeatures(objects::CSeq_entry_Handle tse, ICommandProccessor *processor)

static void RemoveAllFeatures_Ex(CSeq_entry_Handle seh, ICommandProccessor *processor)

bool apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

CRef< CCmdComposite > GetCommand()

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

CRef< CCmdComposite > Apply(objects::CSeq_entry_Handle tse)

bool apply(objects::CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

CRef< CCmdComposite > GetCommand()

virtual bool Show(bool show=1)

Report opening events in dialogs used in the editing package.

@ eRetranslateCDSChooseFrame

@ eRetranslateCDSIgnoreStopExceptEnd

void apply(objects::CSeq_entry_Handle seh, ICommandProccessor *cmdProcessor, string title, ERetranslateMethod method)

bool ApplyToPubdesc(CConstRef< CObject > obj, objects::CSeq_entry_Handle tse, CCmdComposite &composite)

void SetSeqUpdateType(ESeqUpdateType update_type)

void UpdateMultipleSequences(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse, ICommandProccessor *cmdProcessor)

void UpdateSingleSequence(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse, ICommandProccessor *cmdProcessor) const

namespace ncbi::objects::

Base class for all serializable objects.

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse, const string &title)

@ eCommandInfluenza_fixup

@ eCommandTrimOrganismNames

@ eCommandSplitQualsAtCommas

@ eCommandSplitStructuredCollections

@ eCommandInfluenza_parse

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

static wxString ResolvePath(const wxString &path, const wxString &rel_name)

Utility function to hide the platform specifics of locating our standard directories and files.

static void SetDoInference(objects::CUser_object &params, bool val)

static void SetDoAlignment(objects::CUser_object &params, bool val)

static void SetTextBackground(const wxColor &color)

CTextItemPanel * GetWidget() const

bool apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title, wxWindow *parent, const wxString &workDir, const CSequenceAmbigTrimmer::TTrimRuleVec &trim_rules=CSequenceAmbigTrimmer::GetDefaultTrimRules())

static void GetInstance(wxWindow *parent, IWorkbench *workbench, CRef< objects::CUser_object > params, wxWindowID id=17000, const wxString &caption=_("Validation Errors"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(900, 600), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxTAB_TRAVERSAL)

CWorkbench - default implementation of IWorkbench.

static void RmWrongQuals(CSeq_entry_Handle seh, ICommandProccessor *cmd_processor)

static void RmWrongOrIllegalQuals(CSeq_entry_Handle seh, ICommandProccessor *cmd_processor)

static void IllegalQualsToNote(CSeq_entry_Handle seh, ICommandProccessor *cmd_processor)

static void WrongQualsToNote(CSeq_entry_Handle seh, ICommandProccessor *cmd_processor)

static void RmIllegalQuals(CSeq_entry_Handle seh, ICommandProccessor *cmd_processor)

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

virtual string GetFileLoaderId() const =0

void SetScrollPos(wxPoint scrollpos)

wxPoint GetOrigPosition()

virtual void SetDragging(bool dragging)

virtual wxPoint FindUnoccupiedPosition(wxSizer *sizer=NULL)

void CopyButton(wxSizer *sizer, wxPoint p)

void OnPopupClick(wxCommandEvent &evt)

void OnPopupClickUpdate(wxUpdateUIEvent &event)

virtual void OnRightClick(wxContextMenuEvent &evt)

virtual void MoveButton(wxPoint mousePos)

virtual void SetSizers(wxWindow *win_top=NULL, wxSizer *sizer1=NULL, wxSizer *sizer2=NULL, wxSizer *sizer3=NULL, wxSizer *sizer_removed_actual=NULL)

void SetOriginalPosition(wxPoint p)

virtual bool OnChar(wxKeyEvent &event)

virtual bool IsOccupiedPosition()

virtual void onMouseClick(wxCommandEvent &evt)

virtual void SetLocked(bool locked)

virtual bool VerifySelection(CEditingBtnsPanel *e)=0

virtual void OnKeyDown(wxKeyEvent &evt)

virtual void SetRemoved(bool removed)

wxSizer * m_TopSizerRemoved

class IProjectView defines the abstract interface for views observing projects.

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >(nullptr))

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

IViewManagerService IViewManagerService manages views in Workbench.

virtual wxWindow * GetWindow()=0

returns a pointer to the wxWindow representing the client

IWorkbench is the central interface in the application framework.

unsigned int m_MiscFeatRule

CRef< CCmdComposite > GetCommand()

void SetWorkDir(const wxString &workDir)

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

int main(int argc, const char *argv[])

static const char * kFrameDlgHeight

static const char * kFramePosX

static const char * kBGColor

static Uint4 s_GetCheckSumForFile(const string &filename)

static const char * kFrameDlgPosX

static const char * kFrameHeight

static bool EqualLoc(CRef< CSeq_loc > first, CRef< CSeq_loc > second)

static bool comp_buttons(const IMovableButton *a, const IMovableButton *b)

static const char * kBGColorSet

static const char * kSettingsVersion

static const char * kFilenamesArray

static const char * kDynIdsArray

static const char * kAutoStart

#define DIST_BETWEEN_BUTTONS

static const char * kFrameDlgPosY

static const char * kNamesArray

static string s_GetMacroScriptLocation(const string &filename)

static const char * kFrameDlgWidth

static bool CompLoc(CRef< CSeq_loc > first, CRef< CSeq_loc > second)

static const char * kEditingButtonsPanelLayout

static const char * kFramePosY

static const char * kCoordsArray

static const char * kFrameWidth

static const char * kTitlesArray

static string s_GetUsername()

static void s_UpdateMacros()

#define ID_CHECKBOX_AUTOSTART

#define ID_CHECKBOX_COLLAPSE

#define ID_BUTTON_DYNAMIC

#define ID_RESET_BG_COLOR

#define ID_NOTEBOOK_PANEL

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

main entry point for tests

CRef< CCmdComposite > CreateControlRegion(objects::CSeq_entry_Handle entry)

CRef< CCmdComposite > AddNamedrRna(objects::CSeq_entry_Handle entry, string rna_name, bool ispartial5, bool ispartial3)

CRef< CCmdComposite > CreateMicrosatellite(objects::CSeq_entry_Handle entry)

string DirName(const string &path)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void AddFile(const string &file_path)

Update checksum with the file data.

Uint4 GetChecksum(void) const

Return calculated checksum.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

static string ConcatPathEx(const string &first, const string &second)

Concatenate two parts of the path for any OS.

bool CopyToDir(const string &dir, TCopyFlags flags=fCF_Default, size_t buf_size=0) const

Copy the entry to a specified directory.

@ eIfExists_ReturnCurrent

Return reference to current stream, create new one if it does not exists yet.

@ eNoRemove

Do not remove file.

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

vector< CIRef< IView > > TViews

virtual wxFrame * GetMainWindow()

returns a pointer to the main application frame window

virtual void GetViews(TViews &views)=0

get all registered views

objects::CSeq_entry_Handle GetTopSeqEntryFromScopedObject(SConstScopedObject &obj)

objects::CSeq_entry_Handle GetSeqEntryForPubdesc(CRef< objects::CScope > scope, const objects::CPubdesc &pubdesc)

void GetExtensionAsInterface(const string &ext_point_id, vector< CIRef< I > > &interfaces)

GetExtensionAsInterface() is a helper function that extracts all extensions implementing the specifie...

EDialogReturnValue NcbiMessageBox(const string &message, TDialogType type=eDialog_Ok, EDialogIcon icon=eIcon_Exclamation, const string &title="Error", EDialogTextMode text_mode=eRaw)

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

string GetLabel(const CSeq_id &id)

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

Override Assign() to incorporate cache invalidation.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

vector< STrimRule > TTrimRuleVec

Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_c...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

TInst_Length GetInst_Length(void) const

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,...

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TId & GetId(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

const char * CORE_GetUsername(char *buf, size_t bufsize)

Equivalent to CORE_GetUsernameEx(buf, bufsize, eNCBI_UsernameLogin) except that it always returns non...

static const char label[]

bool IsSetData(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

void ResetStrand(void)

Reset Strand data member.

TComment & SetComment(void)

Select the variant.

void SetTopology(TTopology value)

Assign a value to Topology data member.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

TUser & SetUser(void)

Select the variant.

TMolinfo & SetMolinfo(void)

Select the variant.

void SetMol(TMol value)

Assign a value to Mol data member.

@ e_Molinfo

info on the molecule and techniques

@ eMol_na

just a nucleic acid

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

unsigned int

A callback function used to compare two keys in a database.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

Macro engine for macro execution.

Functions used in the DO/DONE section affecting the top seq-entry.

void GetViewObjects(IWorkbench *workbench, TConstScopedObjects &objects)

const TYPE & Get(const CNamedParameterList *param)

void ReportMacroToBeUpdated(const string &username, const string &filename, const string &action)

Report attempt to update a local macro script.

constexpr auto sort(_Init &&init)

const string version

version string

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

static PyObject * Connect(PyObject *self, PyObject *args, PyObject *kwargs)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

bool AddOrgToDefline(objects::CSeq_entry_Handle seh, CCmdComposite *composite)

bool AddModToDefline(objects::CSeq_entry_Handle entry, CCmdComposite *composite, const objects::CAutoDefAvailableModifier &mod, bool show_label)

wxEVT_COMMAND_MENU_SELECTED

static const sljit_gpr r1

#define row(bind, expected)

For example, if bases_to_check is 10 and max_bases_allowed_to_be_ambig is 5, then on each iteration w...

static void SetTitle(CRef< CSeq_entry > entry, string title)

CRef< CCmdComposite > CleanupCommand(objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax)

CRef< CCmdComposite > GetRmCultureNotesCommand(objects::CSeq_entry_Handle seh)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

void CorrectWindowRect(wxTopLevelWindow *win, wxRect &rc)

wxRect GetScreenRect(const wxWindow &win)

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