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NCBI C++ ToolKit: src/gui/widgets/seq/text_panel.cpp Source File

33 #include <wx/choice.h> 34 #include <wx/stattext.h> 35 #include <wx/checkbox.h> 36 #include <wx/textctrl.h> 37 #include <wx/button.h> 38 #include <wx/bmpbuttn.h> 39 #include <wx/choice.h> 40 #include <wx/bitmap.h> 42 #include <wx/msgdlg.h> 43 #include <wx/filedlg.h> 44 #include <wx/dcclient.h> 45 #include <wx/settings.h> 101

IMPLEMENT_DYNAMIC_CLASS(

CTextPanel

, wxPanel )

137

: m_bVector(bVector), m_Pos(0) {}

142

m_bVector.set(m_Pos, expandItem.

IsExpanded

());

178 case

0: pointSize = 8;

break

;

179 case

2: pointSize = 12;

break

;

180 case

3: pointSize = 14;

break

;

183 #ifdef __WXOSX_COCOA__ 184 float

mult =

GetDisplayPPI

().y / (float)wxGetDisplayPPI().y;

185

pointSize = (

int

)(pointSize*mult + .5);

188 return

wxFont(pointSize, wxFONTFAMILY_MODERN, wxFONTSTYLE_NORMAL, wxFONTWEIGHT_NORMAL);

214

Create(parent,

id

, pos,

size

, style);

295

SetExtraStyle(wxWS_EX_VALIDATE_RECURSIVELY);

309 m_TextWindow

->SetBackgroundColour(wxSystemSettings::GetColour(wxSYS_COLOUR_WINDOW));

331 static bool

sImagesRegistered =

false

;

332 if

(!sImagesRegistered) {

336

sImagesRegistered =

true

;

340

wxAuiToolBar* toolbar =

nullptr

;

344

toolbar = (wxAuiToolBar*)pane.window;

347 if

(ctrl) ctrl->Destroy();

358 if

(ctrl) ctrl->Destroy();

361

toolbar->ClearTools();

364

toolbar =

new

wxAuiToolBar(

this

wxID_ANY

, wxDefaultPosition,

365

wxDefaultSize, wxAUI_TB_HORIZONTAL | wxBORDER_NONE);

371 strings

.Add(

(

"Do not match case"

));

375 if

(m_FindMode < 0 || m_FindMode >= (

int

)

m_FindModeCtrl

->GetCount())

383

wxMenu* menu =

new

wxMenu();

384

menu->Append(wxID_COPY,

(

"&Copy"

));

385

menu->Append(wxID_PASTE,

(

"&Paste"

));

390

toolbar->AddTool(

ID_TB_SearchButton

wxT

(

"Search"

), wxArtProvider::GetBitmap(

wxT

(

"text_panel::search"

)),

wxT

(

"Search"

));

392

toolbar->AddSeparator();

393

toolbar->AddTool(

ID_TB_Options

wxT

(

"Options"

), wxArtProvider::GetBitmap(

wxT

(

"text_panel::options"

)),

wxT

(

"Options"

));

396

toolbar->AddSeparator();

402

toolbar->AddStretchSpacer();

417

.LeftDockable(

false

)

418

.RightDockable(

false

)

419

.BottomDockable(

false

)

424

.DestroyOnClose(

true

)

427

pane.BestSize(toolbar->GetClientSize());

437

objs.push_back(scoped_object);

468

}

catch

(

const

exception& e) {

482 if

(

data

.IsEntrys()) {

485

seq_entry = *

entries

.begin();

514 else if

(bioseq_set) {

550 if

m_SO

)

return

;

561 if

(

data

.IsEntrys()) {

569

submitBlock = &seq_submit->

GetSub

();

571

}

else if

(!seq_feat) {

575 if

(!seq_feat && !seh)

595

formatter->SetContext(*

ctx

);

637

wxClientDC dc(

this

);

638

wxFont font(

context

.GetFontDesc());

646 "&Expand All\tCtrl+E"

650 "Command expands(opens) all of a FlatFile view"

);

651

wxAcceleratorEntry accelerator(wxACCEL_CTRL,

'E'

kExpandAll

);

656

vector<IEditorFactory*> factories;

659 ITERATE

(vector<IEditorFactory*>, it, factories) {

660

(*it)->RegisterCommands(cmd_reg, provider);

668

vector<IEditorFactory*> factories;

671 ITERATE

(vector<IEditorFactory*>, it, factories) {

684 if

m_SO

)

return

;

701 if

m_SO

)

return

;

718 if

m_SO

)

return

;

768

root->SetDeleteChildren(

false

);

773 for

(

size_t i

= 0;

< root->GetItemCount(); ++

) {

804

root->UpdatePositions();

848

.LeftDockable(

false

)

849

.RightDockable(

false

)

850

.BottomDockable(

false

)

855

.DestroyOnClose(

true

)

924 return

seq_id || seq_loc || seq_feat || seq_entry || bioseq || bioseq_set;

937

}

NCBI_CATCH

(

"CTextPanel::CanShowFastA()"

);

1043 else if

(seq_id || seq_loc || seq_entry || bioseq || bioseq_set)

1063

GetSizer()->Layout();

1071 if

(widget ==

NULL

)

1074 const

wxString caption =

wxT

(

"Find Text"

);

1077 if

(

text

.empty()) {

1078

wxMessageBox(

wxT

(

"Search string is empty."

), caption, wxOK | wxICON_EXCLAMATION);

1082 bool

found =

false

;

1093

wxMessageBox(

wxT

(

"Search string not found."

), caption, wxOK | wxICON_EXCLAMATION);

1111 if

(dlg.ShowModal() == wxID_OK) {

1135

vector<pair<CBioseq_Handle, string> > handles(

m_FlatFileSeqs

.size());

1139

vector<ITextItem*> items;

1141 bool

loaded =

true

;

1145

errMsg =

"No nucleotide sequences."

;

1160

errMsg =

"No sequences."

;

1171 string

selSeq = seqName;

1176 if

(dlg.ShowModal() != wxID_OK)

1182

errMsg =

"Sequence '"

+ selSeq +

"' not found."

;

1204 if

(items.empty()) {

1224 if

(seq_submit && seq_submit->

IsSetSub

())

1225

submitBlock = &seq_submit->

GetSub

();

1256 for

(

size_t i

= 0;

< seqCount; ++

) {

1271 for

(

size_t i

= (

size_t

)listStart;

min

(seqCount, (

size_t

)listStart +

kMaxSeqNumber

); ++

)

1278 size_t

selection = 0;

1284

selection = seqIndex - listStart + 2;

1291 if

(!pane.IsOk())

return

;

1292

wxAuiToolBar* toolbar =

dynamic_cast<

wxAuiToolBar*

>

(pane.window);

1293 if

(!toolbar)

return

;

1297

item->SetMinSize(wxDefaultSize);

1300

pane.BestSize(toolbar->GetSize());

1312 if

(s.m_Handle == h) {

1321 if

(seq.empty())

return false

;

1365 if

(

objects

.size() != 1)

return false

;

1397 string str

(

"failed to retrieve sequence for id "

);

1407

wxString viewTypeString;

1412 if

(seq_id || seq_loc || seq_feat || seq_entry || bioseq || bioseq_set) {

1419 if

(seq_feat !=

NULL

)

1431

viewTypeString =

pszASN

;

1447

viewTypeString =

pszASN

;

1455

TransferDataToWindow();

1468 if

(!widget)

return

;

1479 if

(!widget)

return

;

1511 if

(!widget)

return

;

1538 i

.m_Item->Traverse(trv);

User-defined methods of the data storage class.

void InsertItems(size_t index, ITextItem *const *items, size_t count, bool updatePositions=true)

void SetDeleteChildren(bool val)

virtual void SetRegistryPath(const string &path)

virtual void Toggle(CTextPanelContext *context, bool update)

virtual bool IsExpanded() const

CTextItem * GetExpandedItem()

static void RegisterCommands(CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)

static CFlatItemFormatter * New(CFlatFileConfig::TFormat format)

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.

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

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

access a named key at this level, with no recursion

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

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

void Set(const string &key, int val)

access a named key at this level, with no recursion

const bm::bvector & m_bVector

virtual bool ProcessItem(CTextItem &)

CRestoreTreeTraverser(CTextPanelContext &context, const bm::bvector<> &bVector)

virtual bool ProcessItem(CExpandItem &expandItem)

CTextPanelContext & m_Context

CRichTextCtrl - a wrapper for wxRichTextCtrl that handles additional keyboard events (such as Clipboa...

void SetContextMenu(wxMenu *contextMenu)

virtual bool ProcessItem(CExpandItem &expandItem)

virtual bool ProcessItem(CTextItem &)

CSaveTreeTraverser(bm::bvector<> &bVector)

string GetSequenceId() const

namespace ncbi::objects::

Base class for all serializable objects.

void LoadXml(CTextPanelContext *context, const CSerialObject &so, objects::CScope &scope)

void LoadFasta(CTextPanelContext *context, const vector< pair< objects::CBioseq_Handle, string > > &handles)

void GetFlatFileSeqs(objects::CSeq_entry_Handle &h, const objects::CSubmit_block *submitBlock, const objects::CSeq_loc *seq_loc, objects::CFlatFileConfig::EStyle style)

void LoadAsn(CTextPanelContext *context, const CSerialObject &so, objects::CScope &scope)

void LoadFlatFile(CTextPanelContext *context, const vector< pair< objects::CBioseq_Handle, string > > &handles, const SFlatFileParams &params)

bool MakeObjectVisible(const CObject &object)

void SetMainItem(ITextItem *item, CTextPanelContext *context)

ITextItem * GetRootItem()

CTextPanelContext * GetContext()

void ReportError(const string &report)

bool FindText(const wxString &text, bool matchCase, bool forward)

bool FindSequence(const wxString &text)

virtual bool SetFont(const wxFont &font)

virtual void SetHost(IGuiWidgetHost *host)

IGuiWidgetHost implementation.

CTextPanelContext * x_CreateFastaContext()

CTextPanelContext * x_CreateAsnContext(const CSerialObject &so)

virtual bool SetPosition(const string &seq, const CObject *object)

CTextPanelContext * x_CreateFlatFileContext(bool createEditor=true)

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void Init()

Initialises member variables.

CTextItemPanel * m_TextWindow

void OnContextMenu(wxContextMenuEvent &event)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

virtual void SetSelectedObjects(const TConstObjects &objects)

bool m_ShowComponentFeats

CTextPanelContext * x_CreateXmlContext(const CSerialObject &so)

void SetInitialViewType(const string &type)

void CreateControls()

Creates the controls and sizers.

IGuiWidgetHost * m_WidgetHost

virtual void DataChanging()

void GetMainObjects(TConstScopedObjects &objs)

static void RegisterCommands(CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)

static bool ShowToolTips()

Should we show tooltips?

virtual void GetSelectedObjects(TConstObjects &objects) const

void OnFindModeSelected(wxCommandEvent &event)

void OnSequenceSelected(wxCommandEvent &event)

vector< CFlatFileSeq > m_FlatFileSeqs

void x_CreateMainToolbar()

static void SetTextBackground(const wxColor &color)

bool x_SelectFlatFileSequence(const string &seqName)

bool CanShowFlatFile() const

CRichTextCtrl * m_FindTextCtrl

CConstRef< CObject > m_PositionOnLoad

CRef< CTextDataSource > m_DataSource

ICommandProccessor * m_CmdProccessor

void OnFindNextClick(wxCommandEvent &event)

~CTextPanel()

Destructor.

static wxWindow * CreateForm(wxWindow *parent)

void x_InitContext(CTextPanelContext &context)

wxAuiManager m_AuiManager

CConstRef< CSerialObject > m_SO

CTextItemPanel * GetWidget() const

void SetFontSize(int value)

CRef< objects::CScope > m_Scope

void OnOptionsClick(wxCommandEvent &event)

map< string, bm::bvector<> > m_TreeState

bool GetShowASNPathToRoot() const

wxChoice * m_FindModeCtrl

wxChoice * m_SequenceList

void AddExtensionToolbar(wxAuiToolBar &toolbar, const wxString &name)

void x_UpdateViewType(const wxString &type)

virtual void GetActiveObjects(vector< TConstScopedObjects > &objects)

bool GetShowASNTypes() const

virtual void SetUndoManager(ICommandProccessor *cmdProccessor)

CIRef< IBioseqEditor > x_CreateEditor()

void SequenceListLoaded(const vector< CFlatFileSeq > &sequenceList)

virtual bool InitWidget(TConstScopedObjects &objects)

friend class CAsnViewContext

bool CanShowFastA() const

CIRef< IMenuContributor > GetMenuContributor()

CTextPanel()

Constructors.

virtual void DataChanged()

virtual const CObject * GetOrigObject() const

void DataLoaded(shared_ptr< CRootTextItem > root, shared_ptr< CTextPanelContext > context)

void OnSearchTermCtrlEnter(wxCommandEvent &event)

bool ObjectIsFeature() const

static wxFont GetFont(int size)

CUICommandRegistry is a centralized registry where all application commands should be registered.

int RegisterCommand(CUICommand *cmd)

assumes ownership of the given object returns a command id (useful when registry is used for auto id ...

void AddAccelerator(const wxAcceleratorEntry &entry)

Undo/Redo interface for editing operations.

virtual bool Traverse(ICompositeTraverser &)=0

const_iterator end() const

const_iterator find(const key_type &key) const

virtual void RegisterFileAlias(const wxArtID &anId, const wxArtClient &aClient, const wxSize &aSize, const wxString &aName, long aType=wxBITMAP_TYPE_ANY, int anIndex=-1)

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

const int kFastaTextOffset

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

static const char *const strings[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

TValue Get(void) const THROWS_NONE

Get atomic counter value.

#define LOG_POST(message)

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

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

CRef< objects::CScope > scope

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

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

vector< CConstRef< CObject > > TConstObjects

CConstRef< CObject > object

vector< SConstScopedObject > TConstScopedObjects

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Return a handle for the top-level seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CConstRef< CSeq_entry > GetSeq_entryCore(void) const

Get const reference to the seq-entry.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

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

list< CRef< CSeq_entry > > TEntrys

const TData & GetData(void) const

Get the Data member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

unsigned int

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

#define EXT_POINT__EDITOR_FACTORY

static void text(MDB_val *v)

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

const GenericPointer< typename T::ValueType > T2 value

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

CConstRef< objects::CSeq_loc > m_SeqLoc

objects::CFlatFileConfig::EMode m_Mode

bool m_ShowComponentFeats

CConstRef< objects::CSubmit_block > m_SeqSubmit

objects::CFlatFileConfig::EStyle m_Style

CAtomicCounter_WithAutoInit gITextItemCount

static const wxChar * pszFlatFile

static const wxChar * pszMainToolbar

static wxColor m_BackgroundColor

static const char * kFeatureMode

static const char * kViewTypeSeq

static const char * kViewTypeFeat

static const char * kMoreSequences

static const char * kAllSequences

static const char * kFFHideSTS

static CSeq_entry_Handle GetSeqEntryHandle(CScope &scope, const CSerialObject &so)

static const char * kShowSequence

static const wxChar * pszASN

const size_t kMaxSeqNumber

static const char * kViewTypeGeneric

static const char * kFontSize

static const char * kFlatFileMode

static const wxChar * pszFastA

static const char * kASNShowPathToRoot

static CFlatFileConfig::EMode s_FFMode(int val)

static const wxChar * pszSequenceToolbar

static CFlatFileConfig::EStyle s_FFStyle(bool showSequence)

static const char * kFindMode

static const char * kOpenExpanded

static const char * kFFHideVariations

static const char * kTextViewPath

static const char * kAllNucleotides

static const char * kFlatFileSequence

static bool s_BackgroundColorSet

static const wxChar * pszXML

static const CSeq_entry * GetSeqEntryFromSeqSubmit(const CSerialObject *so)

static const char * kASNShowTypes

static CS_CONTEXT * context

static wxAcceleratorEntry entries[3]

wxFileArtProvider * GetDefaultFileArtProvider()

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

wxSize GetDisplayPPI()

Mac always seems to return 72 for screen PPI so use wx function for non-mac and on mac divide the dis...

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