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NCBI C++ ToolKit: src/gui/core/document.cpp Source File

, m_UndoManager(new

(x_GetUndoSize(), this))

, m_AssemblyInitialized(

)

, m_UndoManager(new

(x_GetUndoSize(), this))

, m_AssemblyInitialized(

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s =

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TViews::iterator it = std::find(

.begin(),

.end(), ref);

max_index =

(max_index, it->second);

unique_ptr<CNcbiIfstream> istr;

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unique_ptr<CNcbiIstream> is;

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is.reset(http_str.release());

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path = _fname.substr(pos, _fname.length() - pos);

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[

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fileName(fname.ToUTF8());

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<< fileName <<

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serialization_success =

;

wxString serialized_fname;

serialized_fname = fname;

(

= 1; ; ++

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( !::wxFileExists(

) ) {

serialized_fname =

;

(std::exception& e) {

<<

<< e.what());

serialization_success =

;

(serialization_success) {

is->Skip(CGBProject::GetTypeInfo());

is->Skip(CGBProject_ver2::GetTypeInfo());

(std::exception& e) {

<<

<< e.what());

serialization_success =

;

( !serialization_success ) {

::wxRemoveFile(serialized_fname);

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+= fname.ToUTF8();

( ::wxFileExists(fname) ) {

+=

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+=

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+=

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wxString backup_fname = fname +

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(::wxFileExists(backup_fname))

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(::wxFileExists(fname))

::wxRenameFile(fname,backup_fname);

}

(::wxFileExists(fname)) {

::wxRemoveFile(fname);

::wxRenameFile(serialized_fname, fname);

undoSize = -1;

(undoSize == -1) {

undoSize = view.

(

, undoSize);

(

exception&) {

(

)undoSize;

handles->Attach(scope, item);

(vector<IProjectItemExtension*>, it, clients) {

extName =

;

(*it)->ProjectItemAttached(item, doc, srvLocator);

}

(

+ extName +

);

(vector<IProjectItemExtension*>, it, clients) {

extName =

;

(*it)->ProjectItemDetached(item, doc, srvLocator);

}

(

+ extName +

);

(TViews::iterator it =

.begin(); it !=

.end(); ++it) {

(*it)->GetMainObject(

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(TConstScopedObjects::const_iterator it2 =

.begin(); it2 !=

.end(); ++it2) {

*

= it2->object.GetPointer();

viewToDelete.

(*it);

objToView[object] = it->GetPointer();

(!objToView.

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(it2 != objToView.

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viewToDelete.

(it2->second);

(!item)

;

vector<CProjectItem*> items;

items.push_back(item);

removed =

;

(

= 0;

< items.size(); ++

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(!item)

;

= item->

();

vector<CProjectItem*> items;

items.push_back(item);

vector<CProjectItem*> items;

items.push_back(item);

(

= 0;

< items.size(); ++

) {

(!item)

;

vector<IProjectItemExtension*> clients;

(!clients.empty()) {

vector<CProjectItem*> enabled;

(

= 0;

< items.size(); ++

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vector<IProjectItemExtension*> clients;

(!clients.empty()) {

enabled.push_back(item);

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: enabled)

(

));

((*it).GetPointer() == &adapter) {

((*it).GetPointer() == &adapter) {

(

= 0;

< items.size(); ++

) {

(

!= uniqueLabel) {

(

& d : annot.

().Set()) {

(d->GetName() ==

)

d->SetName(uniqueLabel);

adapter->

(*job);

projName =

;

objects::CProjectDescr& descr = GetDescr();

projName = descr.GetTitle();

=

+ projName +

;

(task_srv) task_srv->

(*task);

(!folderName.empty()) {

.SetTitle(folderName);

.SetComment(folderName);

folder = new_folder;

folder = &topFolder;

(

= 0;

< items.size(); ++

)

AddItem(*items[

], *folder);

& s = (*iter)->GetLabel();

& loader_type = loader->GetLoader_type();

(data_source != 0) {

loader_name = data_source->

(loader->GetData());

loaded =

;

(curr_name == loader_name) {

= loader->GetLabel();

(

!= uniqueLabel)

loader->SetLabel(uniqueLabel);

AddDataLoader(*loader);

vector<IProjectItemExtension*> clients;

(!clients.empty()) {

(

= 0;

< items.size(); ++

)

(m_Project->IsSetDataLoaders()) {

TDataLoaders& loaders = m_Project->SetDataLoaders();

((*iter)->GetLabel() == loader.

()) {

loaders.erase(iter);

srv->GetDataSources(data_sources);

(

= 0;

< data_sources.size(); ++

) {

(data_source == 0)

(loader_name.empty()) {

(loader_name_field)

(loader_name.empty()) {

(data_source == 0)

(loader_name.empty())

}

(

+ loader.

() +

);

TDataLoaders& loaders = m_Project->SetDataLoaders();

TDataLoaders& loaders = m_Project->SetDataLoaders();

vector<IProjectItemExtension*> clients;

(!it->IsEnabled())

(!clients.empty()) {

.push_back(it->second);

(

= 0;

<

.size(); ++

) {

gis[

].first->SetItem().SetId().

(*seqId);

(!it->CanGetItem() || !it->GetItem().IsId())

;

& seqId = it->GetItem().GetId();

(!seqId.

())

;

(gis.size() >= 2000) {

(gis.size() > 0) {

vector<IProjectItemExtension*> clients;

(!clients.empty()) {

(

= 0;

< views.size();

++) {

(!smartFile.empty()) {

wxFileName(wxString::FromUTF8(smartFile.c_str())).GetPath();

wxEmptyString;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

std::invoke_result< _Fty, ICanceled & >::type GUI_AsyncExec(_Fty &&_Fnarg, const wxString &msg=wxT("Accessing network..."))

const string & GetFolderName() const

vector< CRef< CProjectItem > > m_Items

vector< CRef< CProjectItem > > & GetProjectItems()

CAddItemsData(const string &folderName, vector< CRef< CProjectItem > > &items, const CGBDocument::TLoaders &loaders)

const CGBDocument::TLoaders & GetLoaders() const

CGBDocument::TLoaders m_Loaders

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CAppJob - default implementation of IAppJob that could be used as a base class.

CAppTaskService - Application Task Service.

virtual string x_GetJobName() const

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

CAttachProjectItemsJob(CAddItemsData &data, CScope &scope)

virtual ~CAttachProjectItemsJob()

CRef< CAddItemsData > m_Data

virtual CRef< CObject > GetResult()

Returns the Job Result.

CRef< CAppJobError > m_Error

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

void Detach(objects::CScope &scope)

CConn_FtpStream specialization (ctor) for download.

This stream exchanges data with an HTTP server located at the URL: http[s]://host[:port]/path[?...

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

CRef< CGBDocument > m_Document

CDocLoadingJob(CGBDocument &doc, const wxString &path)

void SetFileName(const wxString &filename)

TViews & x_GetViews(void)

void Save(const wxString &abs_path)

void x_ProjectViewsChanged()

void ProjectItemsChanged()

bool RemoveProjectItems(const vector< objects::CProjectItem * > &items)

friend class CDocLoadingJob

void DetachProjectItem(objects::CProjectItem *item)

CIRef< IAppJob > m_LoadJob

virtual void OnJobResult(CObject *result, CJobAdapter &adapter)

string GetDefaultAssembly() const

bool DetachDataLoader(objects::CLoaderDescriptor &loader)

friend class CAddItemsData

bool LoadFile(const wxString &fname, ICanceled *canceledCallback)

void x_DetachView(IProjectView *view)

detach a view from the current document

TViewToIndex m_ViewToIndex

static size_t x_GetUndoSize()

void x_AddItems(const string &folderName, vector< CRef< objects::CProjectItem > > &items, const TLoaders &loaders)

void AttachProjectItems(const vector< objects::CProjectItem * > &items)

IDataLoaderProvider * x_GetDataSourceByType(const string &type)

void ReplaceGiSeqIds(ICanceled *canceled)

virtual void OnJobFailed(const string &, CJobAdapter &adapter)

virtual void CreateProjectScope()

wxString GetWorkDir() const

bool RemoveDataLoader(objects::CLoaderDescriptor &loader)

void x_RemoveAllViews(bool reset_hist_async)

virtual const TViews & GetViews(void) const

Retrieve the existing views for this class.

void x_CloseProjectItemViews(objects::CProjectItem &item)

void x_ProjectUpdateLabel()

void x_AttachDataLoaders()

void UnloadProject(bool reset_hist_async=true)

void x_ClearAssembly() const

CProjectService * m_Service

pointer to the service that manages the document

IAppJob * CreateLoadJob(const wxString &fileName)

void x_AttachProjectItems()

void AddItems(const string &folderName, vector< CRef< objects::CProjectItem > > &items, const TLoaders &loaders)

CGBDocument(CProjectService *srv)

CGBDocument.

void x_DetachDataLoaders()

bool AttachDataLoader(objects::CLoaderDescriptor &loader)

void x_SaveFile(const wxString &fname, ESerialDataFormat fmt, bool keep_backups)

wxString GetFileName() const

void ProjectStateChanged()

void x_AssignViewIndex(IProjectView *view)

void DetachProjectItems(const vector< objects::CProjectItem * > &items)

void x_AttachView(IProjectView *view)

Attach a view to the current document.

vector< TLoaderRef > TLoaders

vector< CIRef< IProjectView > > TViews

bool RemoveProjectItem(objects::CProjectItem *item)

void x_DetachProjectItems()

void x_InitializeAssembly() const

bool m_AssemblyInitialized

virtual void x_FireViewEvent(IProjectView &view, CViewEvent::EEventType type)

TViews m_Views

Views attached to this project.

string m_AssemblyAccession

list< CRef< CJobAdapter > > m_JobAdapters

virtual void x_FireProjectChanged(TEvent::EEventSubtype subtype)

void ViewLabelChanged(IProjectView &view)

void AttachProjectItem(objects::CProjectItem *item)

void Save(CNcbiOstream &ostr, ESerialDataFormat fmt) const

Serialize to a stream in a given format.

bool Load(CNcbiIstream &istr, ICanceled *canceledCallback)

force a project to be loaded from an external stream

string GetAccession() const

Retrieve the accession for this assembly.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

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

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

Base class to build jobs with cancel functionality.

NULL stream writer for test serialization.

ERW_Result Write(const void *buf, size_t count, size_t *bytes_written)

Write up to "count" bytes from the buffer pointed to by the "buf" argument onto the output device.

ERW_Result Flush()

Flush pending data (if any) down to the output device.

const CProjectFolder * FindProjectItemFolder(CProjectItem::TId id) const

bool RemoveChildItem(CProjectItem &child_item)

const CProjectItem * GetProjectItem(CProjectItem::TId id) const

CProjectFolder * FindChildFolderByTitle(const string &title)

void AddChildFolder(CProjectFolder &child_folder)

CObject * GetUserObject()

const CSerialObject * GetObject() const

retrieve the object pointed to as a CObject*

void SetUserObject(CObject *object)

bool IsEnabled(void) const

enabled flag

CProjectService - a service providing API for operations with Workspaces and Projects.

IServiceLocator * GetServiceLocator()

void RemoveProjectView(IProjectView &view)

removes the view from View manager Service and disconnects it from the project

CProjectTreePanel - a window that represents Project View.

void ProjectUpdateLabel(CGBDocument &doc)

void ProjectViewsChanged(CGBDocument &doc)

void ProjectUpdateItems(CGBDocument &doc)

void ProjectStateChanged(CGBDocument &doc)

void UpdateViewLabel(CGBDocument &doc, IProjectView &view)

CProjectTreeView - a system view that displays Project Tree.

virtual wxWindow * GetWindow()

returns a pointer to the wxWindow representing the client

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

Base class for all serializable objects.

Template class for iteration on objects of class C (non-medifiable version)

Template class for iteration on objects of class C.

vector< TUIDataSourceRef > TUIDataSourceVec

CUniqueLabelGenerator Modifies the given label so that it becomes unique in the given set of labels b...

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

@ eViewReleased

a view has been initialized and ready

Interface for testing cancellation request in a long lasting operation.

IDataLoaderProvider - an interface representing a Data Source.

IExtension IExtension interface represents an abstract pluggable component.

IGBProject - abstract interface for a project used by CGBProjectHandle.

list< CRef< CLoaderDescriptor > > TDataLoaders

virtual EProjectVersion GetVersion() const =0

retrieve this project's version; this is fixed per subclass

class IProjectView defines the abstract interface for views observing projects.

virtual void SetAsyncDestroy(bool reset_hist_async)=0

Set async destruction mode.

virtual void DestroyView()=0

disconnects view from the project and associated data

IServiceLocator - an abstract mechanism for locating services.

IViewManagerService IViewManagerService manages views in Workbench.

virtual void SaveSettingsAtProject(objects::CGBProjectHandle &project) const =0

virtual string GetClientLabel(IWMClient::ELabel ltype=IWMClient::eDefault) const =0

returns the client label (name) to be displayed in UI

A very basic data-write interface.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define LOG_POST(message)

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

void Error(CExceptionArgs_Base &args)

#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.

void Info(CExceptionArgs_Base &args)

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

static string GetTmpName(ETmpFileCreationMode mode=eTmpFileGetName)

Get temporary file name.

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

void AddTask(IAppTask &task)

Add a task to the queue.

vector< CIRef< IView > > TViews

virtual void GetViews(TViews &views)=0

get all registered views

virtual void RemoveFromWorkbench(IView &view)=0

disconnects view from services and removes from the Workbench

virtual string AddDataLoader(const objects::CUser_object &obj)=0

Add a new data loader to object manager.

virtual string GetLoaderName(const objects::CUser_object &obj) const =0

Get the data loader's name based on input object.

virtual void RemoveListener(CEventHandler *listener)

Remove a listener.

ICanceled * x_GetICanceled()

CRef< CAppJobError > m_Error

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

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

string MakeUniqueLabel(const string &label) const

after considering all existing labels produces a modified unique version of the original label

CAppJobDispatcher::TJobID GetJobId() const

virtual string GetExtensionIdentifier() const =0

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual bool IsCanceled() const override

static void SetLabelByData(objects::CProjectItem &item, objects::CScope *scope=NULL)

void AddExistingLabel(const string &label)

adds an existing label

void Post(CRef< CEvent > evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)

Handles an event asynchronously (process and/or dispatch).

EJobState

Job states (describe FSM)

virtual void AddListener(CEventHandler *listener, int pool_name=ePool_Default)

Add a listener.

vector< SConstScopedObject > TConstScopedObjects

virtual bool Send(CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)

Sends an event synchronously.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

TSeq_id_Handles GetAccVers(const TSeq_id_Handles &idhs, TGetFlags flags=0)

Get accession.version Seq-id Returns null CSeq_id_Handles for sequences that aren't found or don't ha...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

int TPriority

priority type and special value for added objects

void RemoveDataLoader(const string &loader_name, EActionIfLocked action=eThrowIfLocked)

Revoke data loader from the scope.

vector< CSeq_id_Handle > TSeq_id_Handles

Bulk retrieval methods Common argument typedef - vector of requested ids.

@ kPriority_Default

Use default priority for added data.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual bool IsCanceled(void) const =0

ERW_Result

Result codes for I/O operations.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

bool NcbiStreamCopy(CNcbiOstream &os, CNcbiIstream &is)

Copy the entire contents of stream "is" to stream "os".

@ eRW_Success

Everything is okay, I/O completed.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

@ eCurrent

Use current time. See also CCurrentTime.

static const char label[]

bool IsSetLabel(void) const

user-defined label Check if a value has been assigned to Label data member.

void SetDisabled(TDisabled value)

Assign a value to Disabled data member.

void SetLabel(const TLabel &value)

Assign a value to Label data member.

void SetData(TData &value)

Assign a value to Data data member.

TId GetId(void) const

Get the Id member data.

void SetEnabled(TEnabled value)

Assign a value to Enabled data member.

const TLabel & GetLabel(void) const

Get the Label member data.

const TLoader_type & GetLoader_type(void) const

Get the Loader_type member data.

const TLabel & GetLabel(void) const

Get the Label member data.

TEnabled GetEnabled(void) const

Get the Enabled member data.

bool IsSetPriority(void) const

loader priority used in object manager Check if a value has been assigned to Priority data member.

bool IsAnnot(void) const

Check if variant Annot is selected.

const TItem & GetItem(void) const

Get the Item member data.

void SetInfo(TInfo &value)

Assign a value to Info data member.

void SetItem(TItem &value)

Assign a value to Item data member.

TPriority GetPriority(void) const

Get the Priority member data.

const TData & GetData(void) const

Get the Data member data.

const TFilename & GetFilename(void) const

Get the Filename member data.

TFilename & SetFilename(void)

Assign a value to Filename data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsGi(void) const

Check if variant Gi is selected.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

USING_SCOPE(objects)

specific supported project versions

static void s_AttachProjectItem(CProjectItem &item, CScope &scope)

vector< pair< CProjectItem *, CSeq_id_Handle > > TGiProjectItems

static const char * kLoaderName

static void s_ReplaceGIs(TGiProjectItems &gis, CScope &scope)

static CProjectTreePanel * s_FindProjectTreePanel(IServiceLocator *serviceLocator)

static void s_CallExtensionProjectItemDetached(CGBDocument &doc, vector< IProjectItemExtension * > &clients, CProjectItem &item, IServiceLocator *srvLocator)

static void s_CallExtensionProjectItemAttached(CGBDocument &doc, vector< IProjectItemExtension * > &clients, CProjectItem &item, IServiceLocator *srvLocator)

static void s_DetachProjectItem(CProjectItem &item, CScope &scope)

CProject * GetProject(wxTreeCtrl &treeCtrl, const CItem &item)

std::istream & in(std::istream &in_, double &x_)

#define EXT_POINT__PROJECT_ITEM_EXTENSION

Reader-writer based streams.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

STempFileLocker(const string &tmp_name)

string ToStdString(const wxString &s)

wxString FnToWxString(const string &s)

string FnToStdString(const wxString &s)

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