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CEditSequence Class Reference

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#include <gui/widgets/edit/edit_sequence.hpp>

+ Inheritance diagram for CEditSequence:
+ Collaboration diagram for CEditSequence:

Public Member Functions

 CEditSequence ()
 Constructors. More...
 
 CEditSequence (wxWindow *parent, const CSeq_loc *loc, CScope &scope, ICommandProccessor *processor, int start=0, 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)
 
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. More...
 
virtual ~CEditSequence ()
 Destructor. More...
 
void Init ()
 Initialises member variables. More...
 
void CreateControls ()
 Creates the controls and sizers. More...
 
wxBitmap GetBitmapResource (const wxString &name)
 Retrieves bitmap resources. More...
 
wxIcon GetIconResource (const wxString &name)
 Retrieves icon resources. More...
 
virtual void SetRegistryPath (const string &reg_path)
 
virtual void LoadSettings ()
 
virtual void SaveSettings () const
 
void OnClose (wxCommandEvent &event)
 
void OnCancel (wxCommandEvent &event)
 
void OnAccept (wxCommandEvent &event)
 
void OnGoTo (wxCommandEvent &event)
 
void OnRange (wxCommandEvent &event)
 
void OnFind (wxCommandEvent &event)
 
void OnTranslate (wxCommandEvent &event)
 
void OnTranslate1 (wxCommandEvent &event)
 
void OnTranslate2 (wxCommandEvent &event)
 
void OnTranslateAll (wxCommandEvent &event)
 
void OnRevTranslate (wxCommandEvent &event)
 
void OnRevTranslate1 (wxCommandEvent &event)
 
void OnRevTranslate2 (wxCommandEvent &event)
 
void OnRevTranslateAll (wxCommandEvent &event)
 
void OnTranslateEverything (wxCommandEvent &event)
 
void OnTranslateNone (wxCommandEvent &event)
 
void OnOnTheFly (wxCommandEvent &event)
 
void OnMismatch (wxCommandEvent &event)
 
void OnComplement (wxCommandEvent &event)
 
void OnFeatures (wxCommandEvent &event)
 
void OnCopy (wxCommandEvent &event)
 
void OnCut (wxCommandEvent &event)
 
void OnPaste (wxCommandEvent &event)
 
void GetSequence ()
 
void ReportPos (int pos)
 
void ReportRange (int pos1, int pos2)
 
void IsClipboard (wxUpdateUIEvent &event)
 
void IsSelection (wxUpdateUIEvent &event)
 
void IsSelectionAndClean (wxUpdateUIEvent &event)
 
void IsNucleotide (wxUpdateUIEvent &event)
 
void CreateFeature (wxCommandEvent &event)
 
void CreateRegulatory (wxCommandEvent &event)
 
void EnableCommit (bool enable)
 
void OnRetranslate (wxCommandEvent &event)
 
void ShowReadOnlyWarning ()
 
void OnReadOnlyTimer (wxTimerEvent &event)
 
- Public Member Functions inherited from CEventHandler
 CEventHandler ()
 CEventHandler. More...
 
virtual ~CEventHandler ()
 
virtual void AddListener (CEventHandler *listener, int pool_name=ePool_Default)
 Add a listener. More...
 
virtual void RemoveListener (CEventHandler *listener)
 Remove a listener. More...
 
virtual void RemoveAllListeners (void)
 
virtual bool HasListener (CEventHandler *listener, int pool_name=ePool_Default) const
 returns "true" if the given listener belongs to the specified pool More...
 
virtual const TListeners * GetListeners (int pool_name=ePool_Default) const
 returns a set of listeners fro the specified pool More...
 
virtual bool OnEvent (CEvent *evt)
 Processes en event. Returns "true" if event has been processed. More...
 
virtual bool Dispatch (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
 Dispatches an event to the listeners (but does not handle it). More...
 
virtual bool Send (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
 Sends an event synchronously. More...
 
virtual bool Send (CEvent *evt, int pool_name)
 
void Post (CRef< CEvent > evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
 Handles an event asynchronously (process and/or dispatch). More...
 

Static Public Member Functions

static bool ShowToolTips ()
 Should we show tooltips? More...
 
- Static Public Member Functions inherited from CEventHandler
static bool HandlePostRequest ()
 
static void ClearPostQueue ()
 erases all events from the queue More...
 
static void DestroyPostQueue ()
 

Private Member Functions

void GetFeatures (const CSeq_loc &loc, CScope &scope)
 
void GetProteinFeatures (CBioseq_Handle prot_bsh, int i, const CSeq_id *seq_id, const CSeq_feat &old_cds, TSeqPos seq_start)
 
void AdjustFeatureLocations (CRef< CCmdComposite > composite)
 
void AdjustProtFeatureLocations (CRef< CCmdComposite > composite, const CSeq_feat &old_cds, const CSeq_feat &cds, int i, const CSeq_id *seq_id, TSeqPos seq_start)
 
string GetSeqTitle ()
 
bool x_ExecuteCommand (IEditCommand *command)
 

Private Attributes

IUndoManager * m_UndoManager
 
CPaintSequence * m_Panel
 
CSeq_entry_Handle m_seh
 
CSeq_entry_Handle m_edited_seh
 
vector< vector< pair< TSeqPos, TSeqPos > > > m_FeatRanges
 
vector< pair< string, CSeqFeatData::ESubtype > > m_FeatTypes
 
unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > m_ProtFeatRanges
 
vector< int > m_FeatFrames
 
vector< bool > m_Feat5Partial
 
vector< CRef< CGenetic_code > > m_GeneticCode
 
bool m_modified
 
wxStaticText * m_Pos
 
wxStaticText * m_RangeLabel
 
wxStaticText * m_Range
 
wxTextCtrl * m_GoTo_TextCtrl
 
wxTextCtrl * m_RangeFrom
 
wxTextCtrl * m_RangeTo
 
wxMenuItem * m_translate_item
 
wxMenuItem * m_translate_item1
 
wxMenuItem * m_translate_item2
 
wxMenuItem * m_translate_item_all
 
wxMenuItem * m_revtranslate_item
 
wxMenuItem * m_revtranslate_item1
 
wxMenuItem * m_revtranslate_item2
 
wxMenuItem * m_revtranslate_item_all
 
wxMenuItem * m_translate_item_everything
 
wxMenuItem * m_translate_item_none
 
wxButton * m_CommitButton
 
wxButton * m_RetranslateButton
 
wxStaticText * m_commit_warning
 
wxStaticText * m_readonly_warning
 
wxTimer m_readonly_timer
 
vector< string > m_RealProt
 
vector< CBioseq_Handle::EVectorStrand > m_FeatStrand
 
bool m_is_nucleotide
 
unsigned int m_NumCmds
 
const CSeq_loc * m_loc
 
CScope * m_scope
 
int m_start
 
string m_RegPath
 

Additional Inherited Members

- Public Types inherited from CEventHandler
enum  EDispatch { eDispatch_SelfOnly , eDispatch_AllHandlers , eDispatch_FirstHandler , eDispatch_Default = eDispatch_AllHandlers }
 enum controlling dispatching strategies More...
 
enum  EPoolName {
  ePool_Default = 0 , ePool_Parent , ePool_Child , ePool_Sibling ,
  ePool_NextAvailable
}
 Identifiers for standard pools. More...
 
typedef vector< CEventHandler * > TListeners
 
typedef map< int, TListeners > TPools
 
typedef list< AutoPtr< SPostRequest > > TPostRequests
 
typedef std::map< CEventHandler *, int > THandlerToCount
 
typedef void(* FOnPostCallback) ()
 
- Protected Member Functions inherited from CEventHandler
virtual const SEvtMap * GetEventMap () const
 
void x_DeclareDead ()
 Removes itself unavailable for async event delivery. More...
 
void x_AddListenerToPool (CEventHandler *listener, int pool_name)
 
- Protected Attributes inherited from CEventHandler
TPools m_Pools
 
- Static Protected Attributes inherited from CEventHandler
static const SEvtMap sm_EvtMap
 

Detailed Description

Definition at line 105 of file edit_sequence.hpp.

Constructor & Destructor Documentation

◆ CEditSequence() [1/2]

static CEditSequence::CEditSequence ( )

Constructors.

CEditSequence event table definition

CEditSequence constructors

Definition at line 359 of file edit_sequence.cpp.

References Init().

◆ CEditSequence() [2/2]

CEditSequence::CEditSequence ( wxWindow *  parent,
const CSeq_loc *  loc,
CScope &  scope,
ICommandProccessor *  processor,
int  start = 0,
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 
)

Definition at line 367 of file edit_sequence.cpp.

References Create(), Init(), CPaintSequence::InitPanel(), LoadSettings(), m_is_nucleotide, m_Panel, m_UndoManager, NEditingStats::ReportUsage(), SetRegistryPath(), and ncbi::grid::netcache::search::fields::size.

◆ ~CEditSequence()

CEditSequence::~CEditSequence ( )
virtual

Destructor.

CEditSequence destructor

Definition at line 407 of file edit_sequence.cpp.

References m_NumCmds, m_seh, m_UndoManager, IUndoManager::ReleaseExclusiveEdit(), and SaveSettings().

Member Function Documentation

◆ AdjustFeatureLocations()

void CEditSequence::AdjustFeatureLocations ( CRef< CCmdComposite >  composite)
private

Definition at line 1327 of file edit_sequence.cpp.

References CCmdComposite::AddCommand(), AdjustProtFeatureLocations(), CSeq_loc::Assign(), CSerialObject::Assign(), cmd, CSeq_loc_I::Delete(), eExtreme_Positional, CSeqFeatData::eSubtype_cdregion, CSeqTranslator::FindBestFrame(), CSeq_feat_Base::GetData(), CPaintSequence::GetFeatureStart(), CPaintSequence::GetFeatureStop(), CRange_Base::GetFrom(), CSeq_loc::GetId(), CMappedFeat::GetLocation(), CMappedFeat::GetOriginalFeature(), CSeq_loc_CI::GetRange(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq(), CMappedFeat::GetSeq_feat_Handle(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStart(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeq_loc_I::HasChanges(), i, CSeq_loc_CI::IsEmpty(), CSeq_loc_Base::IsNull(), IsSameBioseq(), CSeq_feat_Base::IsSetData(), m_edited_seh, m_Panel, m_ProtFeatRanges, m_seh, CSeq_loc_I::MakeSeq_loc(), max(), CSeq_feat_Base::SetData(), CSeq_loc_I::SetFrom(), CSeq_feat_Base::SetLocation(), and CSeq_loc_I::SetTo().

Referenced by OnAccept().

◆ AdjustProtFeatureLocations()

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

Definition at line 1418 of file edit_sequence.cpp.

References CCmdComposite::AddCommand(), CSerialObject::Assign(), cmd, CSeq_loc_I::Delete(), CSeq_loc_Mapper_Base::eLocationToProduct, CSeq_loc_Mapper_Base::eProductToLocation, CSeqFeatData::eSubtype_prot, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetFeatSubtype(), CRange_Base::GetFrom(), CSeq_feat_Base::GetProduct(), CPaintSequence::GetProtFeatureStart(), CPaintSequence::GetProtFeatureStop(), CSeq_loc_CI::GetRange(), CSeq_entry_Handle::GetScope(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSize(), CRange_Base::GetTo(), CSeq_loc_I::HasChanges(), i, CSeq_loc_CI::IsEmpty(), CSeq_loc_Base::IsNull(), CSeq_feat_Handle::IsPlainFeat(), IsSameBioseq(), m_Panel, m_seh, CSeq_loc_I::MakeSeq_loc(), CSeq_loc_Mapper_Base::Map(), max(), CSeq_loc_I::SetFrom(), CSeq_feat_Base::SetLocation(), CSeq_loc_Mapper_Base::SetMergeAbutting(), and CSeq_loc_I::SetTo().

Referenced by AdjustFeatureLocations().

◆ Create()

bool CEditSequence::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.

Definition at line 385 of file edit_sequence.cpp.

References CreateControls(), and ncbi::grid::netcache::search::fields::size.

Referenced by CEditSequence().

◆ CreateControls()

void CEditSequence::CreateControls ( )

Creates the controls and sizers.

Control creation for CEditSequence

Definition at line 495 of file edit_sequence.cpp.

References _, CUICommandRegistry::CreateMenu(), CBioseq_Handle::eCoding_Iupac, CPaintSequence::EnableFeatures(), CPaintSequence::EnableMismatch(), CSeqMap::eSeqData, eUnknown, CSeqMap::fDefaultFlags, CBioseq_Handle::GetBioseqLength(), CUICommandRegistry::GetInstance(), CSeqMap_CI::GetLength(), CSeq_entry_Handle::GetSeq(), GetSeqTitle(), GetSequence(), CSeqMap_CI::GetType(), ID_ACCEPT_EDSEQ_BUTTON, ID_CANCEL_EDSEQ_BUTTON, ID_CLOSE_EDSEQ_BUTTON, ID_EDIT_COPY_EDSEQ_MENU, ID_EDIT_CUT_EDSEQ_MENU, ID_EDIT_FIND_EDSEQ_MENU, ID_EDIT_PASTE_EDSEQ_MENU, ID_GOTO_EDSEQ_BUTTON, ID_RANGE_EDSEQ_BUTTON, ID_RETRANSLATE_EDSEQ_BUTTON, ID_SHOW_FEATURES_EDSEQ_MENU, ID_SHOW_MISMATCH_EDSEQ_MENU, ID_SHOW_ONTHEFLY_EDSEQ_MENU, ID_SHOW_REVCOMP_EDSEQ_MENU, ID_SHOW_REVTRANSLATE1_EDSEQ_MENU, ID_SHOW_REVTRANSLATE2_EDSEQ_MENU, ID_SHOW_REVTRANSLATE_ALL_EDSEQ_MENU, ID_SHOW_REVTRANSLATE_EDSEQ_MENU, ID_SHOW_TRANSLATE1_EDSEQ_MENU, ID_SHOW_TRANSLATE2_EDSEQ_MENU, ID_SHOW_TRANSLATE_ALL_EDSEQ_MENU, ID_SHOW_TRANSLATE_EDSEQ_MENU, ID_SHOW_TRANSLATE_EVERYTHING_EDSEQ_MENU, ID_SHOW_TRANSLATE_NONE_EDSEQ_MENU, CBioseq_Handle::IsNucleotide(), CSeqMap_CI::IsValid(), len, m_commit_warning, m_CommitButton, m_Feat5Partial, m_FeatFrames, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GeneticCode, m_GoTo_TextCtrl, m_is_nucleotide, m_Panel, m_Pos, m_ProtFeatRanges, m_RangeFrom, m_RangeTo, m_readonly_warning, m_RealProt, m_RetranslateButton, m_revtranslate_item, m_revtranslate_item1, m_revtranslate_item2, m_revtranslate_item_all, m_seh, m_start, m_translate_item, m_translate_item1, m_translate_item2, m_translate_item_all, m_translate_item_everything, m_translate_item_none, NCBI_THROW, RunningInsideNCBI(), SSeqMapSelector::SetFlags(), SetTitle(), wxID_ANY, and wxT.

Referenced by Create().

◆ CreateFeature()

void CEditSequence::CreateFeature ( wxCommandEvent &  event)

Definition at line 1588 of file edit_sequence.cpp.

References CSeq_loc::Assign(), cmd, CBioseqEditor::GetFeatTypeFromCmdID(), GetFeatures(), CSeq_loc::GetId(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_entry_Handle::GetScope(), CPaintSequence::GetSelection(), CSeq_entry_Handle::GetSeq(), m_Feat5Partial, m_FeatFrames, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GeneticCode, m_Panel, m_ProtFeatRanges, m_RealProt, m_seh, CBioseqEditor::MakeDefaultFeature(), NULL, CEditObjViewDlgModal::SetEditor(), CEditObjViewDlgModal::SetEditorWindow(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CPaintSequence::UpdateFeatures(), and x_ExecuteCommand().

◆ CreateRegulatory()

void CEditSequence::CreateRegulatory ( wxCommandEvent &  event)

Definition at line 1627 of file edit_sequence.cpp.

References CSeq_loc::Assign(), cmd, eCmdCreateRegulatory_enhancer, eCmdCreateRegulatory_promoter, eCmdCreateRegulatory_ribosome_binding_site, eCmdCreateRegulatory_riboswitch, eCmdCreateRegulatory_terminator, CSeqFeatData::eSubtype_regulatory, GetFeatures(), CSeq_loc::GetId(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_entry_Handle::GetScope(), CPaintSequence::GetSelection(), CSeq_entry_Handle::GetSeq(), m_Feat5Partial, m_FeatFrames, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GeneticCode, m_Panel, m_ProtFeatRanges, m_RealProt, m_seh, CBioseqEditor::MakeDefaultFeature(), NULL, CEditObjViewDlgModal::SetEditor(), CEditObjViewDlgModal::SetEditorWindow(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CGb_qual_Base::SetVal(), CPaintSequence::UpdateFeatures(), and x_ExecuteCommand().

◆ EnableCommit()

void CEditSequence::EnableCommit ( bool  enable)

Definition at line 707 of file edit_sequence.cpp.

References m_commit_warning, m_CommitButton, and m_RetranslateButton.

Referenced by CPaintSequence::SetClean().

◆ GetBitmapResource()

wxBitmap CEditSequence::GetBitmapResource ( const wxString &  name)

Retrieves bitmap resources.

Get bitmap resources

Definition at line 762 of file edit_sequence.cpp.

◆ GetFeatures()

void CEditSequence::GetFeatures ( const CSeq_loc &  loc,
CScope &  scope 
)
private

Definition at line 1206 of file edit_sequence.cpp.

References CSeqFeatData_Base::e_Prot, CBioseq_Handle::eCoding_Iupac, CSeq_loc_CI::eEmpty_Skip, eExtreme_Positional, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eNa_strand_minus, CSeq_loc_CI::eOrder_Positional, CBioseq_Handle::eStrand_Minus, CBioseq_Handle::eStrand_Plus, CSeqFeatData::eSubtype_cdregion, fFGL_Content, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetData(), CCdregion_Base::GetFrame(), CRange_Base::GetFrom(), GetLabel(), CProt_ref::GetLabel(), CMappedFeat::GetLocation(), CMappedFeat::GetOriginalFeature(), CMappedFeat::GetProduct(), CSeqFeatData_Base::GetProt(), GetProteinFeatures(), CSeq_feat_Handle::GetScope(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeqFeatData_Base::IsCdregion(), CBioseq_Handle::IsProtein(), IsSameBioseq(), CCdregion_Base::IsSetCode(), CSeq_feat_Base::IsSetData(), CCdregion_Base::IsSetFrame(), CSeq_feat_Handle::IsSetProduct(), label, m_Feat5Partial, m_FeatFrames, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GeneticCode, m_ProtFeatRanges, and m_RealProt.

Referenced by CreateFeature(), CreateRegulatory(), GetSequence(), and OnRetranslate().

◆ GetIconResource()

wxIcon CEditSequence::GetIconResource ( const wxString &  name)

Retrieves icon resources.

Get icon resources

Definition at line 773 of file edit_sequence.cpp.

◆ GetProteinFeatures()

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

Definition at line 1297 of file edit_sequence.cpp.

References CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional, CSeq_loc_Mapper_Base::eProductToLocation, CSeqFeatData::eSubtype_prot, CSeq_feat_Handle::GetFeatSubtype(), CRange_Base::GetFrom(), CSeq_feat_Handle::GetLocation(), CBioseq_Handle::GetScope(), CRange_Base::GetTo(), i, CSeq_feat_Handle::IsPlainFeat(), IsSameBioseq(), m_ProtFeatRanges, CSeq_loc_Mapper_Base::Map(), and CSeq_loc_Mapper_Base::SetMergeAbutting().

Referenced by GetFeatures().

◆ GetSeqTitle()

string CEditSequence::GetSeqTitle ( )
private

Definition at line 685 of file edit_sequence.cpp.

References CBioseq::eContent, CBioseq_Handle::GetBioseqCore(), CBioseq_Handle::GetId(), CBioseq::GetLabel(), CSeq_entry_Handle::GetSeq(), label, local, and m_seh.

Referenced by CreateControls().

◆ GetSequence()

void CEditSequence::GetSequence ( void  )

Definition at line 726 of file edit_sequence.cpp.

References CScope::AddTopLevelSeqEntry(), copy(), eUnknown, CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), GetFeatures(), CObjectManager::GetInstance(), CSeq_entry_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_entry_Handle::IsSeq(), m_edited_seh, m_loc, m_scope, m_seh, and NCBI_THROW.

Referenced by CreateControls().

◆ Init()

void CEditSequence::Init ( void  )

Initialises member variables.

Member initialisation

Definition at line 477 of file edit_sequence.cpp.

References m_commit_warning, m_GoTo_TextCtrl, m_modified, m_NumCmds, m_Panel, m_Pos, m_RangeFrom, m_RangeTo, m_readonly_warning, and NULL.

Referenced by CEditSequence().

◆ IsClipboard()

void CEditSequence::IsClipboard ( wxUpdateUIEvent &  event)

Definition at line 1561 of file edit_sequence.cpp.

References CPaintSequence::IsClipboard(), m_Panel, and m_seh.

◆ IsNucleotide()

void CEditSequence::IsNucleotide ( wxUpdateUIEvent &  event)

Definition at line 1571 of file edit_sequence.cpp.

References m_is_nucleotide, and m_seh.

◆ IsSelection()

void CEditSequence::IsSelection ( wxUpdateUIEvent &  event)

Definition at line 1566 of file edit_sequence.cpp.

References CPaintSequence::IsSelection(), m_Panel, and m_seh.

◆ IsSelectionAndClean()

void CEditSequence::IsSelectionAndClean ( wxUpdateUIEvent &  event)

Definition at line 1576 of file edit_sequence.cpp.

References CSeqFeatData::AllowedFeatureLocation(), CSeqFeatData::eFeatureLocationAllowed_NucOnly, CSeqFeatData::eFeatureLocationAllowed_ProtOnly, CPaintSequence::GetClean(), CBioseqEditor::GetFeatTypeFromCmdID(), CPaintSequence::IsSelection(), m_is_nucleotide, m_Panel, and m_seh.

◆ LoadSettings()

void CEditSequence::LoadSettings ( )
virtual

Definition at line 442 of file edit_sequence.cpp.

References CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), i, kFrameHeight, kFramePosX, kFramePosY, kFrameWidth, and m_RegPath.

Referenced by CEditSequence().

◆ OnAccept()

void CEditSequence::OnAccept ( wxCommandEvent &  event)

Definition at line 780 of file edit_sequence.cpp.

References CCmdComposite::AddCommand(), AdjustFeatureLocations(), cmd, CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeqMap::fDefaultFlags, CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Base::GetInst(), CPaintSequence::GetReadOnly(), CPaintSequence::GetSeq(), CSeq_entry_Base::GetSeq(), CSeq_entry_Handle::GetSeq(), CPaintSequence::GetSeqLen(), CSeqMap_I::GetSequence(), i, m_edited_seh, m_is_nucleotide, m_Panel, m_seh, CSeqMap_I::Remove(), CPaintSequence::SetClean(), SSeqMapSelector::SetFlags(), CSeqMap_I::SetSequence(), and x_ExecuteCommand().

◆ OnCancel()

void CEditSequence::OnCancel ( wxCommandEvent &  event)

Definition at line 867 of file edit_sequence.cpp.

References IUndoManager::CanUndo(), m_NumCmds, m_seh, m_UndoManager, IUndoManager::ReleaseExclusiveEdit(), and IUndoManager::Undo().

◆ OnClose()

void CEditSequence::OnClose ( wxCommandEvent &  event)

Definition at line 855 of file edit_sequence.cpp.

References CPaintSequence::GetClean(), m_Panel, and ToWxString().

◆ OnComplement()

void CEditSequence::OnComplement ( wxCommandEvent &  event)

Definition at line 1191 of file edit_sequence.cpp.

References CPaintSequence::EnableComplement(), m_Panel, and CPaintSequence::UpdateData().

◆ OnCopy()

void CEditSequence::OnCopy ( wxCommandEvent &  event)

Definition at line 1543 of file edit_sequence.cpp.

References m_Panel, and CPaintSequence::OnCopy().

◆ OnCut()

void CEditSequence::OnCut ( wxCommandEvent &  event)

Definition at line 1549 of file edit_sequence.cpp.

References m_Panel, and CPaintSequence::OnCut().

◆ OnFeatures()

void CEditSequence::OnFeatures ( wxCommandEvent &  event)

Definition at line 1515 of file edit_sequence.cpp.

References CPaintSequence::EnableFeatures(), and m_Panel.

◆ OnFind()

void CEditSequence::OnFind ( wxCommandEvent &  event)

Definition at line 933 of file edit_sequence.cpp.

References m_is_nucleotide, and m_Panel.

◆ OnGoTo()

void CEditSequence::OnGoTo ( wxCommandEvent &  event)

Definition at line 904 of file edit_sequence.cpp.

References m_GoTo_TextCtrl, m_Panel, CPaintSequence::Search(), CPaintSequence::SetPos(), and val.

◆ OnMismatch()

void CEditSequence::OnMismatch ( wxCommandEvent &  event)

Definition at line 1529 of file edit_sequence.cpp.

References CPaintSequence::EnableMismatch(), and m_Panel.

◆ OnOnTheFly()

void CEditSequence::OnOnTheFly ( wxCommandEvent &  event)

Definition at line 1176 of file edit_sequence.cpp.

References CPaintSequence::EnableOnTheFly(), m_Panel, and CPaintSequence::UpdateData().

◆ OnPaste()

void CEditSequence::OnPaste ( wxCommandEvent &  event)

Definition at line 1555 of file edit_sequence.cpp.

References m_Panel, and CPaintSequence::OnPaste().

◆ OnRange()

void CEditSequence::OnRange ( wxCommandEvent &  event)

Definition at line 920 of file edit_sequence.cpp.

References CPaintSequence::GetLength(), m_Panel, m_RangeFrom, m_RangeTo, and CPaintSequence::SetRange().

◆ OnReadOnlyTimer()

void CEditSequence::OnReadOnlyTimer ( wxTimerEvent &  event)

Definition at line 721 of file edit_sequence.cpp.

References m_readonly_warning.

◆ OnRetranslate()

void CEditSequence::OnRetranslate ( wxCommandEvent &  event)

Definition at line 1685 of file edit_sequence.cpp.

References cmd, CScope::eAllTSEs, CSeqFeatData::eSubtype_cdregion, CScope::GetAllTSEs(), GetFeatures(), CBioseq_Handle::GetRangeSeq_loc(), GetRetranslateCDSCommand(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq(), IsGeneralIdProtPresent(), m_Feat5Partial, m_FeatFrames, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GeneticCode, m_Panel, m_ProtFeatRanges, m_RealProt, m_seh, offset, CPaintSequence::UpdateFeatures(), and x_ExecuteCommand().

◆ OnRevTranslate()

void CEditSequence::OnRevTranslate ( wxCommandEvent &  event)

Definition at line 1020 of file edit_sequence.cpp.

References CPaintSequence::EnableRevTranslation(), m_Panel, m_revtranslate_item_all, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnRevTranslate1()

void CEditSequence::OnRevTranslate1 ( wxCommandEvent &  event)

Definition at line 1038 of file edit_sequence.cpp.

References CPaintSequence::EnableRevTranslation1(), m_Panel, m_revtranslate_item_all, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnRevTranslate2()

void CEditSequence::OnRevTranslate2 ( wxCommandEvent &  event)

Definition at line 1056 of file edit_sequence.cpp.

References CPaintSequence::EnableRevTranslation2(), m_Panel, m_revtranslate_item_all, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnRevTranslateAll()

void CEditSequence::OnRevTranslateAll ( wxCommandEvent &  event)

Definition at line 1074 of file edit_sequence.cpp.

References CPaintSequence::EnableRevTranslation(), CPaintSequence::EnableRevTranslation1(), CPaintSequence::EnableRevTranslation2(), m_Panel, m_revtranslate_item, m_revtranslate_item1, m_revtranslate_item2, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnTranslate()

void CEditSequence::OnTranslate ( wxCommandEvent &  event)

Definition at line 939 of file edit_sequence.cpp.

References CPaintSequence::EnableTranslation(), m_Panel, m_translate_item_all, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnTranslate1()

void CEditSequence::OnTranslate1 ( wxCommandEvent &  event)

Definition at line 957 of file edit_sequence.cpp.

References CPaintSequence::EnableTranslation1(), m_Panel, m_translate_item_all, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnTranslate2()

void CEditSequence::OnTranslate2 ( wxCommandEvent &  event)

Definition at line 975 of file edit_sequence.cpp.

References CPaintSequence::EnableTranslation2(), m_Panel, m_translate_item_all, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnTranslateAll()

void CEditSequence::OnTranslateAll ( wxCommandEvent &  event)

Definition at line 993 of file edit_sequence.cpp.

References CPaintSequence::EnableTranslation(), CPaintSequence::EnableTranslation1(), CPaintSequence::EnableTranslation2(), m_Panel, m_translate_item, m_translate_item1, m_translate_item2, m_translate_item_everything, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnTranslateEverything()

void CEditSequence::OnTranslateEverything ( wxCommandEvent &  event)

Definition at line 1101 of file edit_sequence.cpp.

References CPaintSequence::EnableRevTranslation(), CPaintSequence::EnableRevTranslation1(), CPaintSequence::EnableRevTranslation2(), CPaintSequence::EnableTranslation(), CPaintSequence::EnableTranslation1(), CPaintSequence::EnableTranslation2(), m_Panel, m_revtranslate_item, m_revtranslate_item1, m_revtranslate_item2, m_revtranslate_item_all, m_translate_item, m_translate_item1, m_translate_item2, m_translate_item_all, m_translate_item_none, and CPaintSequence::UpdateData().

◆ OnTranslateNone()

void CEditSequence::OnTranslateNone ( wxCommandEvent &  event)

Definition at line 1148 of file edit_sequence.cpp.

References CPaintSequence::EnableRevTranslation(), CPaintSequence::EnableRevTranslation1(), CPaintSequence::EnableRevTranslation2(), CPaintSequence::EnableTranslation(), CPaintSequence::EnableTranslation1(), CPaintSequence::EnableTranslation2(), m_Panel, m_revtranslate_item, m_revtranslate_item1, m_revtranslate_item2, m_revtranslate_item_all, m_translate_item, m_translate_item1, m_translate_item2, m_translate_item_all, and m_translate_item_everything.

◆ ReportPos()

void CEditSequence::ReportPos ( int  pos)

Definition at line 884 of file edit_sequence.cpp.

References NStr::IntToString(), m_Pos, and ToWxString().

Referenced by CPaintSequence::OnPaint(), and CPaintSequence::SetStartPos().

◆ ReportRange()

void CEditSequence::ReportRange ( int  pos1,
int  pos2 
)

Definition at line 889 of file edit_sequence.cpp.

References NStr::IntToString(), m_RangeFrom, m_RangeTo, and ToWxString().

Referenced by CPaintSequence::OnPaint().

◆ SaveSettings()

void CEditSequence::SaveSettings ( ) const
virtual

Definition at line 427 of file edit_sequence.cpp.

References CGuiRegistry::GetInstance(), GetScreenRect(), CGuiRegistry::GetWriteView(), kFrameHeight, kFramePosX, kFramePosY, kFrameWidth, m_RegPath, and CRegistryWriteView::Set().

Referenced by ~CEditSequence().

◆ SetRegistryPath()

void CEditSequence::SetRegistryPath ( const string &  reg_path)
virtual

Definition at line 422 of file edit_sequence.cpp.

References m_RegPath.

Referenced by CEditSequence().

◆ ShowReadOnlyWarning()

void CEditSequence::ShowReadOnlyWarning ( )

Definition at line 714 of file edit_sequence.cpp.

References m_readonly_timer, and m_readonly_warning.

Referenced by CPaintSequence::CutSelection(), CPaintSequence::DeleteChar(), CPaintSequence::InsertChar(), and CPaintSequence::OnPaste().

◆ ShowToolTips()

bool CEditSequence::ShowToolTips ( )
static

Should we show tooltips?

Should we show tooltips?

Definition at line 753 of file edit_sequence.cpp.

◆ x_ExecuteCommand()

bool CEditSequence::x_ExecuteCommand ( IEditCommand *  command)
private

Definition at line 1504 of file edit_sequence.cpp.

References command, ICommandProccessor::Execute(), kExclusiveEditDescr, m_NumCmds, m_seh, m_UndoManager, and IUndoManager::RequestExclusiveEdit().

Referenced by CreateFeature(), CreateRegulatory(), OnAccept(), and OnRetranslate().

Member Data Documentation

◆ m_commit_warning

wxStaticText* CEditSequence::m_commit_warning
private

Definition at line 207 of file edit_sequence.hpp.

Referenced by CreateControls(), EnableCommit(), and Init().

◆ m_CommitButton

wxButton* CEditSequence::m_CommitButton
private

Definition at line 205 of file edit_sequence.hpp.

Referenced by CreateControls(), and EnableCommit().

◆ m_edited_seh

CSeq_entry_Handle CEditSequence::m_edited_seh
private

Definition at line 188 of file edit_sequence.hpp.

Referenced by AdjustFeatureLocations(), GetSequence(), and OnAccept().

◆ m_Feat5Partial

vector<bool> CEditSequence::m_Feat5Partial
private

Definition at line 193 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_FeatFrames

vector<int> CEditSequence::m_FeatFrames
private

Definition at line 192 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_FeatRanges

vector<vector<pair<TSeqPos,TSeqPos> > > CEditSequence::m_FeatRanges
private

Definition at line 189 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_FeatStrand

vector<CBioseq_Handle::EVectorStrand> CEditSequence::m_FeatStrand
private

Definition at line 211 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_FeatTypes

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

Definition at line 190 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_GeneticCode

vector< CRef<CGenetic_code> > CEditSequence::m_GeneticCode
private

Definition at line 194 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_GoTo_TextCtrl

wxTextCtrl* CEditSequence::m_GoTo_TextCtrl
private

Definition at line 199 of file edit_sequence.hpp.

Referenced by CreateControls(), Init(), and OnGoTo().

◆ m_is_nucleotide

bool CEditSequence::m_is_nucleotide
private

Definition at line 212 of file edit_sequence.hpp.

Referenced by CEditSequence(), CreateControls(), IsNucleotide(), IsSelectionAndClean(), OnAccept(), and OnFind().

◆ m_loc

const CSeq_loc* CEditSequence::m_loc
private

Definition at line 214 of file edit_sequence.hpp.

Referenced by GetSequence().

◆ m_modified

bool CEditSequence::m_modified
private

Definition at line 195 of file edit_sequence.hpp.

Referenced by Init().

◆ m_NumCmds

unsigned int CEditSequence::m_NumCmds
private

Definition at line 213 of file edit_sequence.hpp.

Referenced by Init(), OnCancel(), x_ExecuteCommand(), and ~CEditSequence().

◆ m_Panel

CPaintSequence* CEditSequence::m_Panel
private

Definition at line 187 of file edit_sequence.hpp.

Referenced by AdjustFeatureLocations(), AdjustProtFeatureLocations(), CEditSequence(), CreateControls(), CreateFeature(), CreateRegulatory(), Init(), IsClipboard(), IsSelection(), IsSelectionAndClean(), OnAccept(), OnClose(), OnComplement(), OnCopy(), OnCut(), OnFeatures(), OnFind(), OnGoTo(), OnMismatch(), OnOnTheFly(), OnPaste(), OnRange(), OnRetranslate(), OnRevTranslate(), OnRevTranslate1(), OnRevTranslate2(), OnRevTranslateAll(), OnTranslate(), OnTranslate1(), OnTranslate2(), OnTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_Pos

wxStaticText* CEditSequence::m_Pos
private

Definition at line 196 of file edit_sequence.hpp.

Referenced by CreateControls(), Init(), and ReportPos().

◆ m_ProtFeatRanges

unordered_map<int, vector<vector<pair<TSeqPos,TSeqPos> > > > CEditSequence::m_ProtFeatRanges
private

Definition at line 191 of file edit_sequence.hpp.

Referenced by AdjustFeatureLocations(), CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), GetProteinFeatures(), and OnRetranslate().

◆ m_Range

wxStaticText* CEditSequence::m_Range
private

Definition at line 198 of file edit_sequence.hpp.

◆ m_RangeFrom

wxTextCtrl* CEditSequence::m_RangeFrom
private

Definition at line 200 of file edit_sequence.hpp.

Referenced by CreateControls(), Init(), OnRange(), and ReportRange().

◆ m_RangeLabel

wxStaticText* CEditSequence::m_RangeLabel
private

Definition at line 197 of file edit_sequence.hpp.

◆ m_RangeTo

wxTextCtrl* CEditSequence::m_RangeTo
private

Definition at line 201 of file edit_sequence.hpp.

Referenced by CreateControls(), Init(), OnRange(), and ReportRange().

◆ m_readonly_timer

wxTimer CEditSequence::m_readonly_timer
private

Definition at line 209 of file edit_sequence.hpp.

Referenced by ShowReadOnlyWarning().

◆ m_readonly_warning

wxStaticText* CEditSequence::m_readonly_warning
private

Definition at line 208 of file edit_sequence.hpp.

Referenced by CreateControls(), Init(), OnReadOnlyTimer(), and ShowReadOnlyWarning().

◆ m_RealProt

vector<string> CEditSequence::m_RealProt
private

Definition at line 210 of file edit_sequence.hpp.

Referenced by CreateControls(), CreateFeature(), CreateRegulatory(), GetFeatures(), and OnRetranslate().

◆ m_RegPath

string CEditSequence::m_RegPath
private

Definition at line 217 of file edit_sequence.hpp.

Referenced by LoadSettings(), SaveSettings(), and SetRegistryPath().

◆ m_RetranslateButton

wxButton* CEditSequence::m_RetranslateButton
private

Definition at line 206 of file edit_sequence.hpp.

Referenced by CreateControls(), and EnableCommit().

◆ m_revtranslate_item

wxMenuItem* CEditSequence::m_revtranslate_item
private

Definition at line 203 of file edit_sequence.hpp.

Referenced by CreateControls(), OnRevTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_revtranslate_item1

wxMenuItem * CEditSequence::m_revtranslate_item1
private

Definition at line 203 of file edit_sequence.hpp.

Referenced by CreateControls(), OnRevTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_revtranslate_item2

wxMenuItem * CEditSequence::m_revtranslate_item2
private

Definition at line 203 of file edit_sequence.hpp.

Referenced by CreateControls(), OnRevTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_revtranslate_item_all

wxMenuItem * CEditSequence::m_revtranslate_item_all
private

Definition at line 203 of file edit_sequence.hpp.

Referenced by CreateControls(), OnRevTranslate(), OnRevTranslate1(), OnRevTranslate2(), OnTranslateEverything(), and OnTranslateNone().

◆ m_scope

CScope* CEditSequence::m_scope
private

Definition at line 215 of file edit_sequence.hpp.

Referenced by GetSequence().

◆ m_seh

CSeq_entry_Handle CEditSequence::m_seh
private

Definition at line 188 of file edit_sequence.hpp.

Referenced by AdjustFeatureLocations(), AdjustProtFeatureLocations(), CreateControls(), CreateFeature(), CreateRegulatory(), GetSeqTitle(), GetSequence(), IsClipboard(), IsNucleotide(), IsSelection(), IsSelectionAndClean(), OnAccept(), OnCancel(), OnRetranslate(), x_ExecuteCommand(), and ~CEditSequence().

◆ m_start

int CEditSequence::m_start
private

Definition at line 216 of file edit_sequence.hpp.

Referenced by CreateControls().

◆ m_translate_item

wxMenuItem* CEditSequence::m_translate_item
private

Definition at line 202 of file edit_sequence.hpp.

Referenced by CreateControls(), OnTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_translate_item1

wxMenuItem * CEditSequence::m_translate_item1
private

Definition at line 202 of file edit_sequence.hpp.

Referenced by CreateControls(), OnTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_translate_item2

wxMenuItem * CEditSequence::m_translate_item2
private

Definition at line 202 of file edit_sequence.hpp.

Referenced by CreateControls(), OnTranslateAll(), OnTranslateEverything(), and OnTranslateNone().

◆ m_translate_item_all

wxMenuItem * CEditSequence::m_translate_item_all
private

Definition at line 202 of file edit_sequence.hpp.

Referenced by CreateControls(), OnTranslate(), OnTranslate1(), OnTranslate2(), OnTranslateEverything(), and OnTranslateNone().

◆ m_translate_item_everything

wxMenuItem* CEditSequence::m_translate_item_everything
private

Definition at line 204 of file edit_sequence.hpp.

Referenced by CreateControls(), OnRevTranslate(), OnRevTranslate1(), OnRevTranslate2(), OnRevTranslateAll(), OnTranslate(), OnTranslate1(), OnTranslate2(), OnTranslateAll(), and OnTranslateNone().

◆ m_translate_item_none

wxMenuItem * CEditSequence::m_translate_item_none
private

Definition at line 204 of file edit_sequence.hpp.

Referenced by CreateControls(), OnRevTranslate(), OnRevTranslate1(), OnRevTranslate2(), OnRevTranslateAll(), OnTranslate(), OnTranslate1(), OnTranslate2(), OnTranslateAll(), and OnTranslateEverything().

◆ m_UndoManager

IUndoManager* CEditSequence::m_UndoManager
private

Definition at line 186 of file edit_sequence.hpp.

Referenced by CEditSequence(), OnCancel(), x_ExecuteCommand(), and ~CEditSequence().

The documentation for this class was generated from the following files:
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Modified on Tue Dec 05 02:22:45 2023 by modify_doxy.py rev. 669887