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NCBI C++ ToolKit: include/gui/widgets/edit/alignment_assistant.hpp Source File

28 #ifndef _ALIGNMENT_ASSISTANT_H_ 29 #define _ALIGNMENT_ASSISTANT_H_ 48 #include <wx/bmpbuttn.h> 49 #include <wx/textctrl.h> 51 #include <wx/dialog.h> 52 #include <wx/radiobut.h> 53 #include <wx/checkbox.h> 54 #include <wx/choice.h> 56 #include <wx/combobox.h> 57 #include <wx/listbox.h> 76 #define ID_CALIGNMENT_ASSISTANT wxID_ANY 77 #define SYMBOL_CALIGNMENT_ASSISTANT_STYLE wxMINIMIZE_BOX | wxMAXIMIZE_BOX |wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 78 #define SYMBOL_CALIGNMENT_ASSISTANT_TITLE _("Alignment Assistant"

)

79 #define SYMBOL_CALIGNMENT_ASSISTANT_IDNAME ID_CALIGNMENT_ASSISTANT 80 #define SYMBOL_CALIGNMENT_ASSISTANT_SIZE wxSize(775,595) 81 #define SYMBOL_CALIGNMENT_ASSISTANT_POSITION wxDefaultPosition 83 #define ID_CLOSE_ALIGNMENT_ASSISTANT_BUTTON 11501 84 #define ID_GOTO_ALIGNMENT_ASSISTANT_BUTTON 11502 85 #define ID_GOTO_SEQ_ALIGNMENT_ASSISTANT_BUTTON 11503 86 #define ID_EDIT_RM_SEQ_ALIGNMENT_ASSISTANT_MENU 11504 87 #define ID_EDIT_REV_STRANDS_ALIGNMENT_ASSISTANT_MENU 11505 88 #define ID_EDIT_VALIDATE_ALIGNMENT_ASSISTANT_MENU 11506 89 #define ID_EDIT_PROPAGATE_ALIGNMENT_ASSISTANT_MENU 11507 90 #define ID_EXPORT_INTER_ALIGNMENT_ASSISTANT_MENU 11508 91 #define ID_EXPORT_CONT_ALIGNMENT_ASSISTANT_MENU 11509 92 #define ID_EXPORT_TEXT_ALIGNMENT_ASSISTANT_MENU 11510 93 #define ID_SHOW_SUBSTITUTE_ALIGNMENT_ASSISTANT_MENU 11511 94 #define ID_SHOW_FEATURES_ALIGNMENT_ASSISTANT_MENU 11512 95 #define ID_ADD_ALIGN_CDS_ALIGNMENT_ASSISTANT_MENU 11513 96 #define ID_ADD_ALIGN_RNA_ALIGNMENT_ASSISTANT_MENU 11514 97 #define ID_ADD_ALIGN_OTHER_ALIGNMENT_ASSISTANT_MENU 11515 102

DECLARE_EVENT_TABLE()

120 void

CreateControls();

123

wxBitmap GetBitmapResource(

const

wxString& name );

126

wxIcon GetIconResource(

const

wxString& name );

129 static bool

ShowToolTips();

131 void

OnClose( wxCommandEvent& event );

132 void

OnGoTo( wxCommandEvent& event );

133 void

OnGoToSeq( wxCommandEvent& event );

134 void

OnFeatures( wxCommandEvent& event );

135 void

OnSubstitute( wxCommandEvent& event );

136 void

ReportPos(

int

pos,

const string

label

);

137 void

ReportRange(

int

pos1,

int

pos2,

const string

label

);

138 void

IsSelectionAndClean(wxUpdateUIEvent &event);

139 void

IsNucleotide(wxUpdateUIEvent &event);

140 void

CreateFeature ( wxCommandEvent& event);

141 void

OnTarget( wxCommandEvent& event);

142 void

OnExportInter( wxCommandEvent& event);

143 void

OnExportCont( wxCommandEvent& event);

144 void

OnValidate( wxCommandEvent& event);

145 void

OnPropagateFeatures(wxCommandEvent&

);

146 void

OnRemoveSeqFromAlign(wxCommandEvent&

);

147 void

OnReverseStrand(wxCommandEvent&

);

148 void

OnAddAlignCDS(wxCommandEvent&

);

149 void

OnAddAlignRNA(wxCommandEvent&

);

150 void

OnAddAlignOther(wxCommandEvent&

);

152 void

DeleteSelection();

157 void

ReportUnresolvedBioseqs(

void

);

171

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

m_FeatTypes

;

189 #define ID_CALIGNCDSADDPANEL wxID_ANY 190 #define ID_ALIGNCDSADD_PROTEIN_NAME wxID_ANY 191 #define ID_ALIGNCDSADD_PROTEIN_DESC wxID_ANY 192 #define ID_ALIGNCDSADD_GENE_NAME wxID_ANY 193 #define ID_ALIGNCDSADD_GENE_DESC wxID_ANY 194 #define ID_ALIGNCDSADD_COMMENT wxID_ANY 195 #define ID_WINDOW wxID_ANY 196 #define SYMBOL_CALIGNCDSADDPANEL_STYLE wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 197 #define SYMBOL_CALIGNCDSADDPANEL_TITLE _("Add CDS to Alignment"

)

198 #define SYMBOL_CALIGNCDSADDPANEL_IDNAME ID_CALIGNCDSADDPANEL 199 #define SYMBOL_CALIGNCDSADDPANEL_SIZE wxDefaultSize 200 #define SYMBOL_CALIGNCDSADDPANEL_POSITION wxDefaultPosition 212

DECLARE_EVENT_TABLE()

271 #define ID_CALIGN_RNA_ADD_PANEL wxID_ANY 272 #define ID_CALIGN_RNA_ADD_PANEL_CHOICE1 11601 273 #define ID_CALIGN_RNA_ADD_PANEL_COMBOBOX wxID_ANY 274 #define ID_CALIGN_RNA_ADD_PANEL_TEXTCTRL10 wxID_ANY 275 #define ID_CALIGN_RNA_ADD_PANEL_BUTTON11 11602 276 #define ID_CALIGN_RNA_ADD_PANEL_BUTTON12 11603 277 #define ID_CALIGN_RNA_ADD_PANEL_WINDOW1 wxID_ANY 278 #define SYMBOL_CALIGN_RNA_ADD_PANEL_STYLE wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 279 #define SYMBOL_CALIGN_RNA_ADD_PANEL_TITLE _("Add RNA to Alignment"

)

280 #define SYMBOL_CALIGN_RNA_ADD_PANEL_IDNAME ID_CALIGN_RNA_ADD_PANEL 281 #define SYMBOL_CALIGN_RNA_ADD_PANEL_SIZE wxDefaultSize 282 #define SYMBOL_CALIGN_RNA_ADD_PANEL_POSITION wxDefaultPosition 293

DECLARE_EVENT_TABLE()

372 #define ID_CALIGN_OTHER_ADDPANEL wxID_ANY 373 #define ID_CALIGN_OTHER_ADDPANEL_FEATURE_TYPE_LISTBOX 11701 374 #define ID_CALIGN_OTHER_ADDPANEL_TEXTCTRL11 wxID_ANY 375 #define ID_CALIGN_OTHER_ADDPANEL_TEXTCTRL12 wxID_ANY 376 #define ID_CALIGN_OTHER_ADDPANEL_TEXTCTRL14 wxID_ANY 377 #define ID_CALIGN_OTHER_ADDPANEL_WINDOW1 wxID_ANY 378 #define SYMBOL_CALIGN_OTHER_ADDPANEL_STYLE wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 379 #define SYMBOL_CALIGN_OTHER_ADDPANEL_TITLE _("Add Other Feature to Alignment"

)

380 #define SYMBOL_CALIGN_OTHER_ADDPANEL_IDNAME ID_CALIGN_OTHER_ADDPANEL 381 #define SYMBOL_CALIGN_OTHER_ADDPANEL_SIZE wxDefaultSize 382 #define SYMBOL_CALIGN_OTHER_ADDPANEL_POSITION wxDefaultPosition 393

DECLARE_EVENT_TABLE()

#define SYMBOL_CALIGN_OTHER_ADDPANEL_STYLE

#define SYMBOL_CALIGN_RNA_ADD_PANEL_IDNAME

#define SYMBOL_CALIGN_RNA_ADD_PANEL_POSITION

#define SYMBOL_CALIGNMENT_ASSISTANT_TITLE

#define SYMBOL_CALIGN_RNA_ADD_PANEL_SIZE

USING_SCOPE(ncbi::objects)

#define SYMBOL_CALIGNMENT_ASSISTANT_POSITION

#define SYMBOL_CALIGNMENT_ASSISTANT_SIZE

#define SYMBOL_CALIGNCDSADDPANEL_IDNAME

#define SYMBOL_CALIGNCDSADDPANEL_STYLE

#define SYMBOL_CALIGNMENT_ASSISTANT_STYLE

#define SYMBOL_CALIGNMENT_ASSISTANT_IDNAME

#define SYMBOL_CALIGN_OTHER_ADDPANEL_SIZE

#define SYMBOL_CALIGN_RNA_ADD_PANEL_STYLE

#define SYMBOL_CALIGN_OTHER_ADDPANEL_POSITION

#define SYMBOL_CALIGN_OTHER_ADDPANEL_IDNAME

#define SYMBOL_CALIGNCDSADDPANEL_SIZE

#define SYMBOL_CALIGNCDSADDPANEL_POSITION

bool m_create_general_only

void CreateControls()

Creates the controls and sizers.

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

wxTextCtrl * m_GeneDescription

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

~CAlignCDSAddPanel()

Destructor.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxTextCtrl * m_ProteinName

wxTextCtrl * m_GeneSymbol

CAlignCDSAddPanel()

Constructors.

void Init()

Initialises member variables.

wxTextCtrl * m_ProteinDescription

static bool ShowToolTips()

Should we show tooltips?

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

Creation.

CLocationPanel * m_Location

CRef< CCmdComposite > GetCommand()

wxListBox * m_FeatureType

CGBQualPanel * m_GBQualPanel

CRef< CCmdComposite > GetCommand()

void Init()

Initialises member variables.

CAlignOtherAddPanel()

Constructors.

CLocationPanel * m_Location

Creation.

void x_ChangeFeatureType(const string &key)

void x_AddQuals(objects::CSeq_feat &feat)

CSeq_entry_Handle m_TopSeqEntry

void CreateControls()

Creates the controls and sizers.

static bool ShowToolTips()

Should we show tooltips?

CRef< objects::CSeq_feat > m_QualFeat

wxBoxSizer * m_GBQualSizer

~CAlignOtherAddPanel()

Destructor.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void x_AddGeneQuals(objects::CSeq_feat &gene)

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

void OnFeatureTypeListboxSelected(wxCommandEvent &event)

wxEVT_COMMAND_LISTBOX_SELECTED event handler for ID_FEATURE_TYPE_LISTBOX

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void CreateControls()

Creates the controls and sizers.

wxBoxSizer * m_RNANameSizer

CLocationPanel * m_Location

bool x_RemoveGeneFields()

void OnAdd18SToComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON11

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

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

wxFlexGridSizer * m_FieldSizer

wxComboBox * m_ncRNAClass

wxBoxSizer * m_ButtonsSizer

CAlignRNAAddPanel()

Constructors.

static bool ShowToolTips()

Should we show tooltips?

objects::CRNA_ref::TType x_GetRnaType()

~CAlignRNAAddPanel()

Destructor.

Creation.

void OnSelectRNAType(wxCommandEvent &event)

wxEVT_COMMAND_CHOICE_SELECTED event handler for ID_CHOICE1

void Init()

Initialises member variables.

void OnAdd16StoComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON12

CRef< CCmdComposite > GetCommand()

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

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

wxMenu * m_target_submenu

CPaintAlignment * m_Panel

wxTextCtrl * m_GoTo_TextCtrl

ICommandProccessor * m_CmdProcessor

vector< string > m_Labels

CSeq_entry_Handle m_TopSeqEntry

CSeq_align_Handle m_Alignment

vector< vector< CBioseq_Handle::EVectorStrand > > m_FeatStrand

wxTextCtrl * m_GoToSeq_TextCtrl

Undo/Redo interface for editing operations.

Interface (functor) for object editing.

void AdjustFeatureLocations(const map< objects::CBioseq_Handle, vector< SGap >> &map_gaps, CRef< CCmdComposite > composite, bool split_gene_locations, bool break_features, bool keep_gap_length, bool create_general_only, objects::CObject_id::TId &max_feat_id, map< objects::CObject_id::TId, objects::CObject_id::TId > &old_to_new, bool create_xref_map)

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_EDIT_EXPORT

static const char label[]

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

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

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