A RetroSearch Logo

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

Search Query:

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

NCBI C++ ToolKit: CAlignmentAssistant Class Reference

Search Toolkit Book for CAlignmentAssistant

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

  CAlignmentAssistant ()   Constructors. More...
    CAlignmentAssistant (wxWindow *parent, CSeq_entry_Handle seh, ICommandProccessor *processor, CConstRef< CSeq_align > align=CConstRef< CSeq_align >(NULL), wxWindowID id=wxID_ANY, const wxString &caption=_("Alignment Assistant"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(775, 595), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)   bool  Create (wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Alignment Assistant"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(775, 595), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)   Creation. More...
  virtual  ~CAlignmentAssistant ()   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...
  void  OnClose (wxCommandEvent &event)   void  OnGoTo (wxCommandEvent &event)   void  OnGoToSeq (wxCommandEvent &event)   void  OnFeatures (wxCommandEvent &event)   void  OnSubstitute (wxCommandEvent &event)   void  ReportPos (int pos, const string &label)   void  ReportRange (int pos1, int pos2, const string &label)   void  IsSelectionAndClean (wxUpdateUIEvent &event)   void  IsNucleotide (wxUpdateUIEvent &event)   void  CreateFeature (wxCommandEvent &event)   void  OnTarget (wxCommandEvent &event)   void  OnExportInter (wxCommandEvent &event)   void  OnExportCont (wxCommandEvent &event)   void  OnValidate (wxCommandEvent &event)   void  OnPropagateFeatures (wxCommandEvent &)   void  OnRemoveSeqFromAlign (wxCommandEvent &)   void  OnReverseStrand (wxCommandEvent &)   void  OnAddAlignCDS (wxCommandEvent &)   void  OnAddAlignRNA (wxCommandEvent &)   void  OnAddAlignOther (wxCommandEvent &)   void  TranslateLocations (CRef< CSeq_loc > loc, vector< pair< CRef< CSeq_loc >, CBioseq_Handle > > &locations)   void  DeleteSelection ()    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...
  void  GetFeatures ()   void  GetAlignment (CConstRef< CSeq_align > align)   bool  x_ExecuteCommand (IEditCommand *command)   void  ReportUnresolvedBioseqs (void)   void  AdjustBioseq (CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > cmd)   CRef< CSeq_align >  AdjustAlign (int from, int to, const vector< int > &offset, CRef< CCmdComposite > cmd)   void  AdjustFeatureLocations (CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > cmd)   CRef< CSeq_loc >  AdjustLoc (const CSeq_loc &feat_loc, int from, int to, bool &modified, bool &removed)   void  TrimQualityScores (CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > command)    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  

Definition at line 99 of file alignment_assistant.hpp.

◆ CAlignmentAssistant() [1/2] static CAlignmentAssistant::CAlignmentAssistant ( ) ◆ CAlignmentAssistant() [2/2] ◆ ~CAlignmentAssistant() CAlignmentAssistant::~CAlignmentAssistant ( ) virtual ◆ AdjustAlign()

Definition at line 904 of file alignment_assistant.cpp.

References CSerialObject::Assign(), cmd, eNa_strand_minus, CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CDense_seg_Base::IsSetStrands(), ITERATE, len, m_Alignment, offset, CSeq_align_Base::ResetSegs(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and si.

Referenced by DeleteSelection().

◆ AdjustBioseq()

Definition at line 831 of file alignment_assistant.cpp.

References CScope::AddTopLevelSeqEntry(), cmd, copy(), CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeqMap::fFindData, CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), CSeqMap_CI::GetLength(), CSeq_entry_Base::GetSeq(), CSeq_entry_Handle::GetSeq(), CBioseq_Handle::GetSeq_entry_Handle(), CSeqMap_I::GetSequence(), CBioseq_Handle::IsNa(), len, CSeqMap_I::Remove(), SSeqMapSelector::SetFlags(), and CSeqMap_I::SetSequence().

Referenced by DeleteSelection().

◆ AdjustFeatureLocations()

Definition at line 1143 of file alignment_assistant.cpp.

References AdjustLoc(), CSerialObject::Assign(), cmd, EDIT_EACH_CODEBREAK_ON_CDREGION, eExtreme_Biological, ERASE_CODEBREAK_ON_CDREGION, CTrna_ext_Base::GetAnticodon(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CBioseq_Handle::GetRangeSeq_loc(), CSeqFeatData_Base::GetRna(), CBioseq_Handle::GetScope(), CSeq_loc::GetStart(), CRNA_ref_Base::C_Ext::GetTRNA(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsRna(), CTrna_ext_Base::IsSetAnticodon(), CSeq_feat_Base::IsSetData(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::C_Ext::IsTRNA(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by DeleteSelection().

◆ AdjustLoc()

Definition at line 1223 of file alignment_assistant.cpp.

References CSeq_loc::Assign(), CSeq_loc_I::Delete(), eExtreme_Positional, CRange_Base::GetFrom(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CRange_Base::GetTo(), CSeq_loc_I::HasChanges(), CSeq_loc_I::MakeSeq_loc(), CSeq_loc_CI::Rewind(), CSeq_loc_I::SetFrom(), and CSeq_loc_I::SetTo().

Referenced by AdjustFeatureLocations(), and TrimQualityScores().

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

Creates the controls and sizers.

Control creation for CAlignmentAssistant

Definition at line 341 of file alignment_assistant.cpp.

References _, CUICommandRegistry::CreateMenu(), CUICommandRegistry::GetInstance(), i, ID_ADD_ALIGN_CDS_ALIGNMENT_ASSISTANT_MENU, ID_ADD_ALIGN_OTHER_ALIGNMENT_ASSISTANT_MENU, ID_ADD_ALIGN_RNA_ALIGNMENT_ASSISTANT_MENU, ID_CLOSE_ALIGNMENT_ASSISTANT_BUTTON, ID_EDIT_PROPAGATE_ALIGNMENT_ASSISTANT_MENU, ID_EDIT_REV_STRANDS_ALIGNMENT_ASSISTANT_MENU, ID_EDIT_RM_SEQ_ALIGNMENT_ASSISTANT_MENU, ID_EDIT_VALIDATE_ALIGNMENT_ASSISTANT_MENU, ID_EXPORT_CONT_ALIGNMENT_ASSISTANT_MENU, ID_EXPORT_INTER_ALIGNMENT_ASSISTANT_MENU, ID_GOTO_ALIGNMENT_ASSISTANT_BUTTON, ID_GOTO_SEQ_ALIGNMENT_ASSISTANT_BUTTON, ID_SHOW_FEATURES_ALIGNMENT_ASSISTANT_MENU, ID_SHOW_SUBSTITUTE_ALIGNMENT_ASSISTANT_MENU, m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GoTo_TextCtrl, m_GoToSeq_TextCtrl, m_Labels, m_Panel, m_Range, m_target_submenu, OnTarget(), wxID_ANY, and wxT.

Referenced by Create().

◆ CreateFeature() void CAlignmentAssistant::CreateFeature ( wxCommandEvent &  event )

Definition at line 724 of file alignment_assistant.cpp.

References CSeq_loc::Assign(), cmd, eNa_strand_minus, CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CBioseqEditor::GetFeatTypeFromCmdID(), GetFeatures(), CSeq_loc::GetId(), CBioseq_Handle::GetRangeSeq_loc(), CPaintAlignment::GetRow(), CBioseq_Handle::GetScope(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CPaintAlignment::GetSelection(), CBioseq_Handle::GetSeq_entry_Handle(), CDense_seg::GetSeq_id(), CPaintAlignment::GetVisibleRow(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, m_TopSeqEntry, CBioseqEditor::MakeDefaultFeature(), NULL, row, CEditObjViewDlgModal::SetEditor(), CEditObjViewDlgModal::SetEditorWindow(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

◆ DeleteSelection() void CAlignmentAssistant::DeleteSelection ( )

Definition at line 776 of file alignment_assistant.cpp.

References _, AdjustAlign(), AdjustBioseq(), AdjustFeatureLocations(), cmd, GetAlignment(), CPaintAlignment::GetAlignSelection(), CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CPaintAlignment::GetSelection(), CDense_seg::GetSeq_id(), CPaintAlignment::GetTotalLength(), CPaintAlignment::IsSelection(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, m_TopSeqEntry, offset, row, CPaintAlignment::SetAlign(), swap(), TrimQualityScores(), CPaintAlignment::UpdateFeatures(), wxT, and x_ExecuteCommand().

Referenced by CPaintAlignment::OnKeyDown().

◆ GetAlignment() ◆ GetBitmapResource() wxBitmap CAlignmentAssistant::GetBitmapResource ( const wxString &  name ) ◆ GetFeatures() void CAlignmentAssistant::GetFeatures ( ) private

Definition at line 598 of file alignment_assistant.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_loc_CI::eEmpty_Skip, eExtreme_Positional, eNa_strand_minus, CSeq_loc_CI::eOrder_Positional, CBioseq_Handle::eStrand_Minus, CBioseq_Handle::eStrand_Plus, fFGL_Content, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), GetLabel(), CMappedFeat::GetLocation(), CDense_seg_Base::GetNumseg(), CMappedFeat::GetOriginalFeature(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CDense_seg::GetSeq_id(), CPaintAlignment::GetSeqTitle(), CSeq_loc::GetStart(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CBioseq_Handle::IsNucleotide(), CSeq_feat_Base::IsSetData(), CDense_seg_Base::IsSetDim(), CDense_seg_Base::IsSetIds(), CDense_seg_Base::IsSetLens(), CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetStarts(), label, m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_is_nucleotide, m_Labels, row, and CSeq_align_Base::C_Segs::Which().

Referenced by CreateFeature(), GetAlignment(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), and OnPropagateFeatures().

◆ GetIconResource() wxIcon CAlignmentAssistant::GetIconResource ( const wxString &  name ) ◆ Init() void CAlignmentAssistant::Init ( void  ) ◆ IsNucleotide() void CAlignmentAssistant::IsNucleotide ( wxUpdateUIEvent &  event ) ◆ IsSelectionAndClean() void CAlignmentAssistant::IsSelectionAndClean ( wxUpdateUIEvent &  event ) ◆ OnAddAlignCDS() void CAlignmentAssistant::OnAddAlignCDS ( wxCommandEvent &  )

Definition at line 1426 of file alignment_assistant.cpp.

References cmd, eNa_strand_minus, CPaintAlignment::GetAlignSelection(), CAlignCDSAddPanel::GetCommand(), GetFeatures(), CSeq_entry_Handle::GetScope(), i, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_TopSeqEntry, CSeq_loc::SetInt(), str(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

◆ OnAddAlignOther() void CAlignmentAssistant::OnAddAlignOther ( wxCommandEvent &  )

Definition at line 1506 of file alignment_assistant.cpp.

References cmd, eNa_strand_minus, CPaintAlignment::GetAlignSelection(), CAlignOtherAddPanel::GetCommand(), GetFeatures(), i, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_TopSeqEntry, CSeq_loc::SetInt(), str(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

◆ OnAddAlignRNA() void CAlignmentAssistant::OnAddAlignRNA ( wxCommandEvent &  )

Definition at line 1466 of file alignment_assistant.cpp.

References cmd, eNa_strand_minus, CPaintAlignment::GetAlignSelection(), CAlignRNAAddPanel::GetCommand(), GetFeatures(), CSeq_entry_Handle::GetScope(), i, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_TopSeqEntry, CSeq_loc::SetInt(), str(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

◆ OnClose() ◆ OnExportCont() void CAlignmentAssistant::OnExportCont ( wxCommandEvent &  event ) ◆ OnExportInter() void CAlignmentAssistant::OnExportInter ( wxCommandEvent &  event ) ◆ OnFeatures() void CAlignmentAssistant::OnFeatures ( wxCommandEvent &  event ) ◆ OnGoTo() void CAlignmentAssistant::OnGoTo ( wxCommandEvent &  event ) ◆ OnGoToSeq() void CAlignmentAssistant::OnGoToSeq ( wxCommandEvent &  event ) ◆ OnPropagateFeatures() void CAlignmentAssistant::OnPropagateFeatures ( wxCommandEvent &  )

Definition at line 1707 of file alignment_assistant.cpp.

References cmd, CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), GetFeatures(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CDense_seg::GetSeq_id(), CPaintAlignment::GetTarget(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, NULL, row, CEditObjViewDlgModal::SetEditor(), CEditObjViewDlgModal::SetEditorWindow(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

◆ OnRemoveSeqFromAlign() void CAlignmentAssistant::OnRemoveSeqFromAlign ( wxCommandEvent &  )

Definition at line 1748 of file alignment_assistant.cpp.

References _, CSerialObject::Assign(), cmd, GetAlignment(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CSeq_align_Handle::GetSeq_align(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CPaintAlignment::GetTarget(), i, CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetStarts(), CDense_seg_Base::IsSetStrands(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_target_submenu, CPaintAlignment::RefreshWithScroll(), row, CPaintAlignment::SetAlign(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), CPaintAlignment::UpdateFeatures(), wxT, and x_ExecuteCommand().

◆ OnReverseStrand() void CAlignmentAssistant::OnReverseStrand ( wxCommandEvent &  )

Definition at line 1838 of file alignment_assistant.cpp.

References _, CSerialObject::Assign(), cmd, eNa_strand_minus, eNa_strand_plus, GetAlignment(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSeq_align(), CDense_seg::GetSeq_id(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CPaintAlignment::GetTarget(), CDense_seg_Base::IsSetStrands(), len, m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, CPaintAlignment::RefreshWithScroll(), row, CPaintAlignment::SetAlign(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CPaintAlignment::UpdateFeatures(), wxT, and x_ExecuteCommand().

◆ OnSubstitute() void CAlignmentAssistant::OnSubstitute ( wxCommandEvent &  event ) ◆ OnTarget() void CAlignmentAssistant::OnTarget ( wxCommandEvent &  event ) ◆ OnValidate() void CAlignmentAssistant::OnValidate ( wxCommandEvent &  event )

Definition at line 1677 of file alignment_assistant.cpp.

References CValidErrItem::ConvertSeverity(), CSeq_align_Handle::GetAnnot(), CSeq_entry_Handle::GetCompleteSeq_entry(), CObjectManager::GetInstance(), m_Alignment, m_TopSeqEntry, msg(), NULL, CGenericReportDlg::SetText(), ToWxString(), and wxT.

◆ ReportPos() ◆ ReportRange() ◆ ReportUnresolvedBioseqs() void CAlignmentAssistant::ReportUnresolvedBioseqs ( void  ) private

Definition at line 559 of file alignment_assistant.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_id::eContent, CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetNumseg(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CDense_seg::GetSeq_id(), CDense_seg_Base::IsSetDim(), CDense_seg_Base::IsSetIds(), CDense_seg_Base::IsSetLens(), CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetStarts(), NStr::Join(), label, m_Alignment, msg(), row, CGenericReportDlg::SetText(), ToWxString(), CSeq_align_Base::C_Segs::Which(), and wxT.

Referenced by CAlignmentAssistant().

◆ ShowToolTips() bool CAlignmentAssistant::ShowToolTips ( ) static ◆ TranslateLocations()

Definition at line 1546 of file alignment_assistant.cpp.

References CPaintAlignment::AlignPosToSeqPos(), CSeq_loc::Assign(), CSerialObject::Assign(), CSeq_loc_I::Delete(), CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, eExtreme_Positional, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), CSeq_loc_CI::GetFuzzFrom(), CSeq_loc_CI::GetFuzzTo(), CSeq_loc_CI::GetRange(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), CDense_seg::GetSeq_id(), CSeq_align::GetSeqStrand(), CSeq_loc::GetStart(), CSeq_loc_CI::GetStrand(), CRange_Base::GetTo(), CSeq_loc_CI::IsEmpty(), IsReverse(), m_Alignment, m_Panel, CSeq_loc_I::MakeSeq_loc(), CInt_fuzz::Negative(), CRef< C, Locker >::Reset(), CSeq_loc_I::ResetFuzzFrom(), CSeq_loc_I::ResetFuzzTo(), Reverse(), row, CSeq_loc_I::SetFrom(), CSeq_loc_I::SetFuzzFrom(), CSeq_loc_I::SetFuzzTo(), CSeq_loc::SetId(), CSeq_loc_I::SetStrand(), CSeq_loc_I::SetTo(), swap(), and CSeq_loc_Base::Which().

Referenced by CAlignCDSAddPanel::GetCommand(), CAlignRNAAddPanel::GetCommand(), and CAlignOtherAddPanel::GetCommand().

◆ TrimQualityScores()

Definition at line 1307 of file alignment_assistant.cpp.

References AdjustLoc(), CSerialObject::Assign(), command, CSeq_graph_Base::C_Graph::e_Byte, CSeq_annot_Base::C_Data::e_Graph, CSeq_graph_Base::C_Graph::e_Int, CSeq_graph_Base::C_Graph::e_Real, CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional, CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetComp(), CRange_Base::GetFrom(), CSeq_graph_Base::GetGraph(), CSeq_graph_Base::C_Graph::GetInt(), CSeq_graph_Base::GetLoc(), CMappedGraph::GetOriginalGraph(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_graph_Base::C_Graph::GetReal(), CMappedGraph::GetSeq_graph_Handle(), CRange_Base::GetTo(), CByte_graph_Base::GetValues(), CInt_graph_Base::GetValues(), CReal_graph_Base::GetValues(), CSeq_graph_Base::IsSetComp(), CSeq_graph_Base::IsSetLoc(), CSeq_graph_Base::ResetLoc(), CByte_graph_Base::ResetValues(), CInt_graph_Base::ResetValues(), CReal_graph_Base::ResetValues(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::C_Graph::SetInt(), CSeq_graph_Base::SetLoc(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::C_Graph::SetReal(), CByte_graph_Base::SetValues(), CInt_graph_Base::SetValues(), CReal_graph_Base::SetValues(), and CSeq_graph_Base::C_Graph::Which().

Referenced by DeleteSelection().

◆ x_ExecuteCommand()

Definition at line 666 of file alignment_assistant.cpp.

References command, ICommandProccessor::Execute(), m_CmdProcessor, and m_TopSeqEntry.

Referenced by CreateFeature(), DeleteSelection(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), and OnReverseStrand().

◆ m_Alignment

Definition at line 166 of file alignment_assistant.hpp.

Referenced by AdjustAlign(), CreateControls(), CreateFeature(), DeleteSelection(), GetAlignment(), GetFeatures(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), OnReverseStrand(), OnValidate(), ReportUnresolvedBioseqs(), and TranslateLocations().

◆ m_CmdProcessor ◆ m_FeatRanges vector<vector<vector<pair<TSeqPos,TSeqPos> > > > CAlignmentAssistant::m_FeatRanges private ◆ m_FeatStrand ◆ m_FeatTypes ◆ m_GoTo_TextCtrl wxTextCtrl* CAlignmentAssistant::m_GoTo_TextCtrl private ◆ m_GoToSeq_TextCtrl wxTextCtrl* CAlignmentAssistant::m_GoToSeq_TextCtrl private ◆ m_is_nucleotide bool CAlignmentAssistant::m_is_nucleotide private ◆ m_Labels vector<string> CAlignmentAssistant::m_Labels private ◆ m_Panel

Definition at line 168 of file alignment_assistant.hpp.

Referenced by CreateControls(), CreateFeature(), DeleteSelection(), Init(), IsSelectionAndClean(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnExportCont(), OnExportInter(), OnFeatures(), OnGoTo(), OnGoToSeq(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), OnReverseStrand(), OnSubstitute(), OnTarget(), and TranslateLocations().

◆ m_Range wxStaticText* CAlignmentAssistant::m_Range private ◆ m_target_submenu wxMenu* CAlignmentAssistant::m_target_submenu private ◆ m_TopSeqEntry

The documentation for this class was generated from the following files:

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