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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gb__ui__data__source_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence/gb_ui_data_source.cpp Source File

72 #include <wx/filename.h> 113

m_SrvLocator(

NULL

),

125  return "genbank_data_source"

;

131  return "GenBank Data Source"

;

149  if

(items.size() != 1 || workbench ==

NULL

) {

165

wxMenu* menu =

new

wxMenu;

166

menu->Append(wxID_SEPARATOR,

wxT

(

"Top Actions"

));

169

contrib.first = menu;

202  "attempt to open already open data source"

);

216  registry

.GetReadView(

"GBENCH.Services.ObjectManager"

);

221  int

priority = view.

GetInt

(

"Priority"

, 99);

226  if

(

sizeof

(

void

*) == 8)

227

system_cache_path.append(

wxT

(

"64"

));

231  if

( !wxFileName::DirExists(system_cache_path) ) {

232  if

( !wxFileName::Mkdir(system_cache_path) ) {

234

<< system_cache_path.ToUTF8() <<

"); caching will be disabled"

);

236  LOG_POST

(

Info

<<

"Created cache path: "

<< system_cache_path.ToUTF8());

240  const string

ts_key =

"GBENCH.Application.LastRunBuildStamp"

;

241  const string

st_build_date = __DATE__

"."

__TIME__;

243  bool

cache_reset = (last_run_build_date != st_build_date);

246  if

(cache_reset ||

registry

.

GetBool

(

"GBENCH.Application.CrashDetected"

,

false

)) {

247

::wxRemoveFile(wxFileName(system_cache_path,

wxT

(

"cache_ids.db"

)).GetFullPath());

248

::wxRemoveFile(wxFileName(system_cache_path,

wxT

(

"cache_blobs.db"

)).GetFullPath());

249

wxFileName vdb_cache_path =

wxFileName::DirName

(system_cache_path + wxFileName::GetPathSeparator() +

"vdb"

);

250

vdb_cache_path.Rmdir(wxPATH_RMDIR_RECURSIVE);

251

vdb_cache_path.Mkdir(wxS_DIR_DEFAULT, wxPATH_MKDIR_FULL);

257  int

cache_age = view.

GetInt

(

"CacheAge"

, 5);

258  if

(cache_age == 0) {

263  int

id_resolution_time = view.

GetInt

(

"IdResolutionTime"

, 24);

264  if

(id_resolution_time > 24 * 3) {

265

id_resolution_time = 24 * 3;

268

wxString objmgr_config_path =

270  wxT

(

"<std>/etc/gbench-objmgr.ini"

));

272  if

(objmgr_config_path.empty()) {

281

reg.

Set

(

"genbank/cache/id_cache/sqlite3"

,

"database"

,

282

cache_path +

"/cache_ids.db"

);

283

reg.

Set

(

"genbank/cache/id_cache/sqlite3"

,

"cache_age"

,

285

reg.

Set

(

"genbank/cache/blob_cache/sqlite3"

,

"database"

,

286

cache_path +

"/cache_blobs.db"

);

287

reg.

Set

(

"genbank/cache/blob_cache/sqlite3"

,

"cache_age"

,

301  msg

=

"An error occurred while creating the GenBank connection\n("

;

305  catch

(std::exception& e) {

306  msg

=

"An error occurred while creating the GenBank connection\n("

;

311  if

( !

msg

.empty() ) {

319  LOG_POST

(

Info

<<

"Registered GenBank Data Source - "

<<

t

<<

" sec"

);

332  LOG_POST

(

Info

<<

"Registered VDBGraph, WGS and SNP data sources - "

<<

t

<<

" sec"

);

348  bool

revoked =

m_ObjMgr

->RevokeDataLoader(

"GBLOADER"

);

357  catch

(std::exception&)

367  LOG_POST

(

Error

<<

"CGenBankUIDataSource::ShutDownService(): " 368  "object manager still referenced"

);

409

: m_Descr(

"GenBank Connection"

,

""

)

413  wxT

(

"gb_data_source.png"

));

437  static string

ext_id(

"genbank_data_source_type"

);

452

: m_SrvLocator(

NULL

),

453

m_ParentWindow(

NULL

),

456

m_OptionPanel(

NULL

),

457

m_ProjectSelPanel(

NULL

)

524  return

action ==

eNext

;

557  if

(action ==

eBack

) {

560

}

else if

(action ==

eNext

) {

581

loader.

Reset

( chain );

User-defined methods of the data storage class.

static void COpenDialog(IWorkbench *workbench, const string &loader_label=NcbiEmptyString, const vector< wxString > &filenames=vector< wxString >())

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const SLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

virtual void CloseCache(void)=0

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CGenBankDSEvtHandler - wxEvtHandler-derived adapter for GenBank data source.

CGenBankDSEvtHandler(IWorkbench *workbench)

void OnLoadFromGenBank(wxCommandEvent &event)

CGenBankUIDataSourceType.

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.

CProjectSelectorPanel - a panel that allows the user to specify how the project items created by a pl...

virtual bool TransferDataFromWindow()

void SetProjectService(CProjectService *service)

void GetParams(SProjectSelectorParams &params) const

virtual bool TransferDataToWindow()

void SetParams(const SProjectSelectorParams &params)

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

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

CProjectSelectOptions - describes how new Project Items shall be added to a workspace.

static wxString ResolvePath(const wxString &path, const wxString &rel_name)

Utility function to hide the platform specifics of locating our standard directories and files.

static wxString ResolvePathExisting(const wxString &path, const wxString &delim=wxT(","))

Utility function to hide the platform specifics of locating our standard directories.

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

static CUICommandRegistry & GetInstance()

the main instance associated with the application

wxMenuItem * AppendMenuItem(wxMenu &menu, TCmdID cmd_id) const

pair< wxMenu *, wxEvtHandler * > TContribution

Contribution consists of a Menu object and event handler.

IServiceLocator - an abstract mechanism for locating services.

IUIDataSourceType - defines a type of a Data Source, can serve as a Data Source factory.

IUIDataSource - an interface representing a Data Source.

IUIObject - object that provides basic properties often required in a UI object.

IWorkbench is the central interface in the application framework.

virtual int GetType() const =0

const TData & GetData() const

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

string DirName(const string &path)

static const char * kProjectParamsTag

static const char * kGenBankLoadOption

static const char * kGB_DS_Icon

CGenBankUIDataSource.

static const char * kAppExpCmdExtPoint

#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)

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)

CIRef< T > GetServiceByType()

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

void SaveMruAccessions(const string &regPath)

virtual void EditProperties()

void SaveSettings(const string &regPath)

CGenBankLoadOptionPanel * m_OptionPanel

SProjectSelectorParams m_ProjectParams

virtual const IUIObject & GetDescr()

returns UI description of the type (label, icon etc.)

virtual bool IsOpen()

a Data source needs to be open before use and closed after.

virtual void SetServiceLocator(IServiceLocator *locator)

virtual void CleanUI()

CleanUI() is called after the host finished using the manager.

virtual bool CanDo(EAction action)

Indicates whether given transition is possible in the current state.

IServiceLocator * m_SrvLocator

virtual void InitUI()

Initializes the Manager before using it in UI.

virtual IExplorerItemCmdContributor::TContribution GetMenu(wxTreeCtrl &treeCtrl, PT::TItems &items)

for the given set of items returns a contribution

CProjectSelectorPanel * m_ProjectSelPanel

virtual void SetRegistryPath(const string &path)

virtual wxEvtHandler * CreateEvtHandler()

const vector< string > & GetNAs() const

virtual bool DoTransition(EAction action)

Performs transition if possible and returns true, otherwise the function shall warn the user about th...

virtual const IUIObject & GetDescr()

returns UI description of the object (label, icon etc.)

virtual IUIToolManager * GetLoadManager()

virtual bool AutoCreateDefaultDataSource()

returns "true" if this type needs to create a default instance of the Data Source at start-up

virtual int GetDefaultCommand()

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

CRef< objects::CObjectManager > m_ObjMgr

virtual void LoadSettings()

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual string GetExtensionIdentifier() const

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

IServiceLocator * m_SrvLocator

virtual bool Open()

Prepares Data Source for use, any initialization that can be potentially time-consuming or may requir...

virtual void SaveSettings() const

virtual bool IsCompletedState()

Manager goes into "Complete" state when "Finish" button is pressed and all input data is gatherred an...

virtual IUIDataSource * CreateDataSource()

factory method; create an Data Source instance

CGenBankUILoadManager()

CGenBankUILoadManager.

virtual bool IsFinalState()

True if Tool Manager has reached its final state, i.e.

virtual IAppTask * GetTask()

Once parameters are gathered and validated this function is called to produce the final Task object t...

wxWindow * m_ParentWindow

void Add(IObjectLoader *loader)

const vector< string > & GetGenomicAccessions() const

virtual IUIDataSourceType & GetType() const

virtual const IUIObject & GetDescriptor() const

Returns the object describing this tool (UI meta data).

virtual wxPanel * GetCurrentPanel()

Return the panel corresponding to the current state of Tool Manager.

CGenBankUIDataSourceType()

CGenBankUIDataSourceType.

virtual string GetExtensionIdentifier() const

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

virtual void SetServiceLocator(IServiceLocator *srv_locator)

Sets / unsets Service Locator.

virtual void SetParentWindow(wxWindow *parent)

CRef< CGenBankUIDataSourceType > m_Type

void LoadSettings(const string &regPath)

static CIRef< IExtensionRegistry > GetInstance()

provides access to the Singleton

virtual void SetLogEvent(const string &log_event)

virtual const string & GetLabel() const

const TParamTree * GetTree() const

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

string GetName(void) const

void SetLoaderOptions(const string &loader_name, EIsDefault is_default, TPriority priority=kPriority_Default)

Update loader's default-ness and priority.

CDataLoader * RegisterDataLoader(TPluginManagerParamTree *params=0, const string &driver_name=kEmptyStr)

Add data loader using plugin manager.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool ReferencedOnlyOnce(void) const THROWS_NONE

Check if object is referenced only once.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

IRWRegistry * Read(CNcbiIstream &is, TFlags flags=0, const string &path=kEmptyStr)

Read and parse the stream "is", and merge its content with current Registry entries.

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

Defines process management classes.

Defines a portable execute class.

NetCache ICache client specs.

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

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

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

void LoadSettings(CRegistryReadView &view, const string &section)

bool m_CreateFolder

package in a single item

void ToLoadingOptions(CSelectProjectOptions &options)

void SaveSettings(CRegistryWriteView &view, const string &section) const

wxFileArtProvider * GetDefaultFileArtProvider()

wxString ToWxString(const string &s)

wxString FnToWxString(const string &s)

string FnToStdString(const wxString &s)


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