Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/edit__sequence_8cpp_source.html below:

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

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

: m_loc(loc), m_scope(&scope), m_start(start), m_readonly_timer(this,

)

(parent,

, caption, pos,

, style);

( wxWindow* parent, wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

wxFrame::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

Centre(wxBOTH|wxCENTRE_ON_SCREEN);

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

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;

SetPosition(wxPoint(pos_x,pos_y));

wxMenuBar *menubar =

wxMenuBar();

wxMenu *menu =

wxMenu();

menubar->Append(menu,

(

));

wxMenu *translate_menu =

wxMenu();

menu->AppendSubMenu(translate_menu,

(

));

wxMenuItem *revcomp_item =

wxMenuItem(menu,

,

(

),

(

), wxITEM_CHECK);

menu->Append(revcomp_item);

wxMenuItem *features_item =

wxMenuItem(menu,

,

(

),

(

), wxITEM_CHECK);

menu->Append(features_item);

wxMenuItem * onthefly_item =

wxMenuItem(menu,

,

(

),

(

), wxITEM_CHECK);

menu->Append(onthefly_item);

wxMenuItem * mismatch_item =

wxMenuItem(menu,

,

(

),

(

), wxITEM_CHECK);

menu->Append(mismatch_item);

wxMenu *menu2 =

wxMenu();

menubar->Append(menu2,

(

));

wxMenuItem *cut_item =

wxMenuItem(menu2,

,

(

),

(

), wxITEM_NORMAL);

menu2->Append(cut_item);

wxMenuItem *copy_item =

wxMenuItem(menu2,

,

(

),

(

), wxITEM_NORMAL);

menu2->Append(copy_item);

wxMenuItem *paste_item =

wxMenuItem(menu2,

,

(

),

(

), wxITEM_NORMAL);

menu2->Append(paste_item);

wxMenuItem *find_item =

wxMenuItem(menu2,

,

(

),

(

), wxITEM_NORMAL);

menu2->Append(find_item);

menubar->Append(menu3,

(

));

menubar->Append(menu3,

(

));

wxPanel *Dialog1 =

wxPanel(

,

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

Dialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

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

wxButton* itemButton6 =

wxButton( Dialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText8 =

wxStaticText( Dialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(itemStaticText8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxStaticText( Dialog1, wxID_STATIC,

(

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

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton7 =

wxButton( Dialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

=

wxTextCtrl( Dialog1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxLEFT|wxTOP|wxBOTTOM, 5);

->SetValidator( wxTextValidator( wxFILTER_NUMERIC ) );

wxStaticText* rangeDash =

wxStaticText( Dialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(rangeDash, 0, wxALIGN_CENTER_VERTICAL|wxTOP|wxBOTTOM, 5);

=

wxTextCtrl( Dialog1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxRIGHT|wxTOP|wxBOTTOM, 5);

->SetValidator( wxTextValidator( wxFILTER_NUMERIC ) );

vector<bool> read_only;

seq_len.push_back(

);

read_only.push_back(

);

read_only.push_back(

);

seq_len.push_back(

(seq.size()));

read_only.push_back(

);

allowed_char_set =

;

allowed_char_set =

;

wxBoxSizer *BoxSizer =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(BoxSizer, 1, wxGROW|wxALL, 5);

=

(Dialog1, seq, seq_len,

,

,

,

,

,

, allowed_char_set,

, read_only,

,

);

BoxSizer->Add(

, 1, wxGROW|wxALL, 5);

features_item->Check();

mismatch_item->Check();

=

wxStaticText( Dialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxTOP|wxBOTTOM|wxRESERVE_SPACE_EVEN_IF_HIDDEN, 5);

=

wxStaticText( Dialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxTOP|wxBOTTOM|wxRESERVE_SPACE_EVEN_IF_HIDDEN, 5);

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

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

itemBoxSizer12->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton13 =

wxButton( Dialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

wxButton* itemButton14 =

wxButton( Dialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

wxHyperlinkCtrl* itemHyperlinkCtrl =

wxHyperlinkCtrl( Dialog1, wxID_HELP,

(

),

(

), wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

itemHyperlinkCtrl->SetForegroundColour(wxColour(192, 192, 192));

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

&

= *(it->GetSeqId());

(

.IsGenbank() &&

.GetGenbank().IsSetAccession())

accession =

.GetGenbank().GetAccession();

(

.IsLocal() &&

.GetLocal().IsStr())

=

.GetLocal().GetStr();

(!accession.empty())

(!

.empty())

modified =

;

removed =

;

seq_out = seq.substr(start,seq_len[

]);

(seq_in != seq_out)

(!seq_out.empty())

seqmap_i = seqmap_i.

();

start += seq_len[

];

vector<int>::iterator seq_len_i = seq_len.begin();

vector<bool>::iterator read_only_i = read_only.begin();

(seq_len_i != seq_len.end() && read_only_i != read_only.end())

seq_len_i = seq_len.erase(seq_len_i);

read_only_i = read_only.erase(read_only_i);

answer = wxMessageBox (

(

),

(

), wxYES_NO | wxICON_QUESTION);

(pos1 > 0 && pos2 > 0)

(

.ToLong(&pos))

(!

.IsEmpty())

(val1.ToLong(&pos1) && val2.ToLong(&pos2) && pos1 > 0 && pos2 > 0 && pos2 > pos1 && pos1 <= seq_len && pos2 <= seq_len)

->

(

(pos1),

(pos2));

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

(event.IsChecked())

* seq_id = loc.GetId();

vector<pair<TSeqPos,TSeqPos> > vec;

CSeq_loc& feat_loc = feat_it->

();

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

(strand == objects::CBioseq_Handle::eStrand_Minus && !prot_seq.empty())

reverse(prot_seq.begin(), prot_seq.end());

(

.empty())

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

,subtype));

(

feat_ci(prot_bsh); feat_ci; ++feat_ci)

vector<pair<TSeqPos,TSeqPos> > vec;

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

feat_it(scope, *loc, sel);

CSeq_loc& feat_loc = feat_it->

();

new_loc->

(feat_loc);

(feat_start != new_start)

(feat_stop != new_stop)

loc_it.

(new_stop);

(

feat_ci(prot_bsh); feat_ci; ++feat_ci)

(feat_start != new_start)

(feat_stop != new_stop)

loc_it.

(new_stop);

new_feat->

(feat_ci->GetOriginalFeature());

(event.IsChecked())

(event.IsChecked())

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

interval->

().SetFrom(sel.first);

interval->

().SetTo(sel.second);

interval->

().SetId(*

);

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

(edit_dlg.ShowModal() == wxID_OK)

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

interval->

().SetFrom(sel.first);

interval->

().SetTo(sel.second);

interval->

().SetId(*

);

regulatory_class;

(evt.GetId())

(!regulatory_class.empty())

q->

(

);

q->

(regulatory_class);

feat->

().push_back(q);

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

(edit_dlg.ShowModal() == wxID_OK)

create_general_only =

;

(!vec_tse.empty())

(

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

: m_Panel(panel), m_is_nucleotide(is_nucleotide)

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxStaticText* itemStaticText3 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(itemStaticText3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

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

itemBoxSizer4->Add(

, 1, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxStaticText( itemDialog1, wxID_STATIC, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticBox* itemStaticBoxSizer7Static =

wxStaticBox(itemDialog1,

,

(

));

wxStaticBoxSizer* itemStaticBoxSizer7 =

wxStaticBoxSizer(itemStaticBoxSizer7Static, wxVERTICAL);

itemBoxSizer2->Add(itemStaticBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer8 =

wxBoxSizer(wxHORIZONTAL);

itemStaticBoxSizer7->Add(itemBoxSizer8, 0, wxALIGN_LEFT|wxALL, 5);

=

wxRadioButton( itemStaticBoxSizer7->GetStaticBox(),

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->SetValue(

);

itemBoxSizer8->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer8->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer11 =

wxBoxSizer(wxHORIZONTAL);

itemStaticBoxSizer7->Add(itemBoxSizer11, 0, wxALIGN_LEFT|wxALL, 5);

itemBoxSizer11->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxArrayString m_FrameChoiceStrings;

m_FrameChoiceStrings.Add(

(

));

m_FrameChoiceStrings.Add(

(

));

m_FrameChoiceStrings.Add(

(

));

m_FrameChoiceStrings.Add(

(

));

m_FrameChoiceStrings.Add(

(

));

m_FrameChoiceStrings.Add(

(

));

m_FrameChoiceStrings.Add(

(

));

itemBoxSizer11->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer14 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer14, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

itemBoxSizer14->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer14->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton17 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer14->Add(itemButton17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemStaticBoxSizer7Static->Hide();

wxNullBitmap;

(sel != wxNOT_FOUND)

(!

->GetValue() && choice ==

)

(

=0;

<

.length();

++)

(

->GetValue())

(pos !=

&& pos <str->

())

pos_actual = pos;

(!

->GetValue())

(choice ==

|| choice ==

|| choice ==

)

pos_actual =

->size() - pos_actual - 1 - (

.size() - 1);

(choice ==

)

(choice ==

)

(choice ==

)

(choice ==

)

(choice ==

)

(!

->GetValue())

(

j = 0; j < length; j++)

highlights.

(

((*it)+j));

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

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

@ eCmdCreateRegulatory_ribosome_binding_site

@ eCmdCreateMobileElement

@ eCmdCreateMiscStructure

@ eCmdCreateBiosourceFeat

@ eCmdCreatePrimTranscript

@ eCmdCreateRegulatory_promoter

@ eCmdCreateRegulatory_riboswitch

@ eCmdCreateCodingRegion_ext

@ eCmdCreateCommentDescriptor

@ eCmdCreatePubFeatureLabeled

@ eCmdCreateRegulatory_enhancer

@ eCmdCreateTransitPeptide

@ eCmdCreateSecondaryStructure

@ eCmdCreateRegulatory_terminator

@ eCmdCreateMiscDifference

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

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

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

void GetLabel(string *label, ELabelType type, bool worst=false) const

void AddCommand(IEditCommand &command)

void SetEditorWindow(wxWindow *editorWindow)

void SetEditor(CIRef< IEditObject > editor)

wxMenuItem * m_translate_item2

void IsSelectionAndClean(wxUpdateUIEvent &event)

void OnTranslate(wxCommandEvent &event)

void OnRevTranslate2(wxCommandEvent &event)

wxMenuItem * m_translate_item_none

void OnTranslateAll(wxCommandEvent &event)

static bool ShowToolTips()

Should we show tooltips?

void OnTranslate1(wxCommandEvent &event)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void OnMismatch(wxCommandEvent &event)

void ReportRange(int pos1, int pos2)

wxStaticText * m_readonly_warning

wxMenuItem * m_translate_item_everything

wxMenuItem * m_translate_item1

void IsNucleotide(wxUpdateUIEvent &event)

void CreateControls()

Creates the controls and sizers.

wxTextCtrl * m_GoTo_TextCtrl

void OnRevTranslateAll(wxCommandEvent &event)

void OnPaste(wxCommandEvent &event)

void OnTranslate2(wxCommandEvent &event)

void OnTranslateEverything(wxCommandEvent &event)

void IsClipboard(wxUpdateUIEvent &event)

wxMenuItem * m_translate_item_all

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

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

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

void OnReadOnlyTimer(wxTimerEvent &event)

virtual ~CEditSequence()

Destructor.

wxMenuItem * m_revtranslate_item2

virtual void SaveSettings() const

CEditSequence()

Constructors.

void OnTranslateNone(wxCommandEvent &event)

virtual void SetRegistryPath(const string &reg_path)

void OnFeatures(wxCommandEvent &event)

vector< CBioseq_Handle::EVectorStrand > m_FeatStrand

void AdjustProtFeatureLocations(CRef< CCmdComposite > composite, const CSeq_feat &old_cds, const CSeq_feat &cds, int i, const CSeq_id *seq_id, TSeqPos seq_start)

void CreateRegulatory(wxCommandEvent &event)

void Init()

Initialises member variables.

wxMenuItem * m_translate_item

vector< bool > m_Feat5Partial

void GetProteinFeatures(CBioseq_Handle prot_bsh, int i, const CSeq_id *seq_id, const CSeq_feat &old_cds, TSeqPos seq_start)

void GetFeatures(const CSeq_loc &loc, CScope &scope)

wxMenuItem * m_revtranslate_item

void OnGoTo(wxCommandEvent &event)

CSeq_entry_Handle m_edited_seh

void CreateFeature(wxCommandEvent &event)

vector< int > m_FeatFrames

wxButton * m_CommitButton

void OnRevTranslate1(wxCommandEvent &event)

wxButton * m_RetranslateButton

void OnRevTranslate(wxCommandEvent &event)

void OnRetranslate(wxCommandEvent &event)

virtual void LoadSettings()

vector< CRef< CGenetic_code > > m_GeneticCode

bool x_ExecuteCommand(IEditCommand *command)

IUndoManager * m_UndoManager

void OnCopy(wxCommandEvent &event)

void OnComplement(wxCommandEvent &event)

vector< string > m_RealProt

void ShowReadOnlyWarning()

unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > m_ProtFeatRanges

void OnFind(wxCommandEvent &event)

void AdjustFeatureLocations(CRef< CCmdComposite > composite)

void OnCut(wxCommandEvent &event)

void EnableCommit(bool enable)

wxMenuItem * m_revtranslate_item_all

wxStaticText * m_commit_warning

void OnRange(wxCommandEvent &event)

void OnOnTheFly(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Edit Sequence"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(704, 504), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void IsSelection(wxUpdateUIEvent &event)

void OnClose(wxCommandEvent &event)

void OnAccept(wxCommandEvent &event)

void OnCancel(wxCommandEvent &event)

wxMenuItem * m_revtranslate_item1

void OnChange(wxCommandEvent &event)

void CreateControls()

Creates the controls and sizers.

static bool ShowToolTips()

Should we show tooltips?

set< int >::iterator m_CurrentPos

void OnPrev(wxCommandEvent &event)

void FindMatchPositions(const string &choice)

void OnDismiss(wxCommandEvent &event)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CFindEditSequence()

Constructors.

wxRadioButton * m_TransFrame

void OnClose(wxCloseEvent &event)

~CFindEditSequence()

Destructor.

void Init()

Initialises member variables.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void OnNext(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=29000, const wxString &caption=_("find"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

wxStaticText * m_ItemOfText

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

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

set< int > & SetHighlights()

void EnableRevTranslation1(bool enable)

void EnableOnTheFly(bool enable)

void OnCut(wxCommandEvent &event)

vector< int > & GetSeqLen()

string * GetFindString(bool is_nuc, bool is_revcomp, const string &choice)

pair< int, int > GetSelection()

TSeqPos GetProtFeatureStart(int i, int k, int j)

void EnableMismatch(bool enable)

vector< bool > & GetReadOnly()

void EnableComplement(bool enable)

void UpdateFeatures(const vector< vector< pair< TSeqPos, TSeqPos > > > &feat_ranges, const vector< pair< string, objects::CSeqFeatData::ESubtype > > &feat_types, const vector< objects::CBioseq_Handle::EVectorStrand > &feat_strand, const vector< int > &feat_frames, const vector< CRef< objects::CGenetic_code > > &genetic_code, const vector< bool > &feat_partial5, const vector< string > &real_prot, const unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > &prot_feat_ranges)

void OnPaste(wxCommandEvent &event)

void EnableTranslation1(bool enable)

void SetRange(int pos1, int pos2)

void OnCopy(wxCommandEvent &event)

void EnableRevTranslation(bool enable)

void EnableTranslation2(bool enable)

void EnableTranslation(bool enable)

void Search(const string &val)

void EnableRevTranslation2(bool enable)

void SetClean(bool clean)

TSeqPos GetFeatureStop(int i, int j)

TSeqPos GetProtFeatureStop(int i, int k, int j)

void EnableFeatures(bool enable)

TSeqPos GetFeatureStart(int i, int j)

void GetLabel(string *label) const

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

void Set(const string &key, int val)

access a named key at this level, with no recursion

static EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype)

@ eFeatureLocationAllowed_NucOnly

@ eFeatureLocationAllowed_ProtOnly

ESubtype GetSubtype(void) const

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

namespace ncbi::objects::

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)

Undo/Redo interface for editing operations.

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

Interface (functor) for object editing.

virtual bool RequestExclusiveEdit(wxWindow *window, const string &descr)=0

virtual bool ReleaseExclusiveEdit(wxWindow *window)=0

virtual void Undo(wxWindow *window=0)=0

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

static const char * kFramePosX

static const char * kFrameHeight

const char * kExclusiveEditDescr

static const char * kFramePosY

static const char * kFrameWidth

#define ID_ACCEPT_EDSEQ_BUTTON

#define ID_TRANSFRAME_FIND_EDIT_SEQ

#define READONLY_TIMER_ID

#define ID_SHOW_ONTHEFLY_EDSEQ_MENU

#define ID_EDIT_CUT_EDSEQ_MENU

#define ID_EDIT_PASTE_EDSEQ_MENU

#define ID_SHOW_TRANSLATE_NONE_EDSEQ_MENU

#define ID_DISMISS_FIND_EDIT_SEQ

#define ID_SHOW_TRANSLATE_EVERYTHING_EDSEQ_MENU

#define ID_TEXTCTRL_FIND_EDIT_SEQ

#define ID_CLOSE_EDSEQ_BUTTON

#define ID_SHOW_TRANSLATE2_EDSEQ_MENU

#define ID_SHOW_REVTRANSLATE_EDSEQ_MENU

#define ID_SHOW_REVTRANSLATE2_EDSEQ_MENU

#define ID_SHOW_REVCOMP_EDSEQ_MENU

#define ID_SHOW_REVTRANSLATE1_EDSEQ_MENU

#define ID_GOTO_EDSEQ_BUTTON

#define ID_NUC_FIND_EDIT_SEQ

#define ID_SHOW_FEATURES_EDSEQ_MENU

#define ID_SHOW_MISMATCH_EDSEQ_MENU

#define ID_RANGE_EDSEQ_BUTTON

#define ID_RETRANSLATE_EDSEQ_BUTTON

#define ID_PREV_FIND_EDIT_SEQ

#define ID_SHOW_REVTRANSLATE_ALL_EDSEQ_MENU

#define ID_EDIT_COPY_EDSEQ_MENU

#define ID_NEXT_FIND_EDIT_SEQ

#define ID_REVCOMP_FIND_EDIT_SEQ

#define ID_EDIT_FIND_EDSEQ_MENU

#define ID_SHOW_TRANSLATE1_EDSEQ_MENU

#define ID_CANCEL_EDSEQ_BUTTON

#define ID_SHOW_TRANSLATE_EDSEQ_MENU

#define ID_FRAMECHOICE_FIND_EDIT_SEQ

#define ID_SHOW_TRANSLATE_ALL_EDSEQ_MENU

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

string GetLabel(const CSeq_id &id)

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

return constructed CSeq_loc with all changes

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.

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.

bool HasChanges(void) const

return true of any part was changed since initialization

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.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

@ fFGL_Content

Include its content if there is any.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

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.

void GetAllTSEs(TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

vector< CSeq_entry_Handle > TTSE_Handles

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

bool IsNucleotide(void) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

bool IsSetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

bool IsProtein(void) const

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.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeqFeatData::ESubtype GetFeatSubtype(void) const

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,...

bool IsPlainFeat(void) const

Check if this is plain feature.

const TId & GetId(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eStrand_Plus

Plus strand.

@ eStrand_Minus

Minus strand.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

const CSeq_loc & GetProduct(void) const

CSeqMap::ESegmentType GetType(void) const

TSeqPos GetLength(void) const

return length of current segment

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

@ eSeqData

real sequence data

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Convert int to string.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetQual(const TQual &value)

Assign a value to Qual data member.

bool IsSetData(void) const

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

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TCode & GetCode(void) const

Get the Code member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

void SetVal(const TVal &value)

Assign a value to Val data member.

const TProt & GetProt(void) const

Get the variant data.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetFrame(void) const

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

@ eFrame_three

reading frame

bool IsNull(void) const

Check if variant Null is selected.

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 GenericPointer< typename T::ValueType > T2 value

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

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

Selector used in CSeqMap methods returning iterators.

#define WX_MENU_ITEM_EXT(cmd)

#define WX_DEFINE_MENU(name)

New macros for defining menus for use with CUICommandRegistry.

#define WX_SUBMENU_EXT(label)

#define WX_SUBMENU_INT(label)

#define WX_MENU_ITEM_INT(cmd)

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

CRef< CCmdComposite > GetRetranslateCDSCommand(objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)

wxString ToWxString(const string &s)

wxRect GetScreenRect(const wxWindow &win)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4