Search Toolkit Book for CBlastVdbCmdApp

The application class. More...

Inheritance diagram for CBlastVdbCmdApp:

Collaboration diagram for CBlastVdbCmdApp:

Public Member Functions
	CBlastVdbCmdApp ()
	@inheritDoc More...

	~CBlastVdbCmdApp ()

Public Member Functions inherited from CNcbiApplication
virtual	~CNcbiApplication (void)
	Destructor. More...

	CNcbiApplication (const SBuildInfo &build_info=NCBI_SBUILDINFO_DEFAULT())
	Constructor. More...

Public Member Functions inherited from CNcbiApplicationAPI
	CNcbiApplicationAPI (const SBuildInfo &build_info)
	Constructor. More...

virtual	~CNcbiApplicationAPI (void)
	Destructor. More...

int	AppMain (int argc, const char const argv, const char const envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)
	Main function (entry point) for the NCBI application. More...

virtual int	DryRun (void)
	Test run the application. More...

virtual void	Exit (void)
	Cleanup on application exit. More...

const CNcbiArguments &	GetArguments (void) const
	Get the application's cached unprocessed command-line arguments. More...

virtual const CArgs &	GetArgs (void) const
	Get parsed command line arguments. More...

const CNcbiEnvironment &	GetEnvironment (void) const
	Get the application's cached environment. More...

CNcbiEnvironment &	SetEnvironment (void)
	Get a non-const copy of the application's cached environment. More...

void	SetEnvironment (const string &name, const string &value)
	Set a specified environment variable by name. More...

bool	HasLoadedConfig (void) const
	Check if the config file has been loaded. More...

bool	FinishedLoadingConfig (void) const
	Check if the application has finished loading config file (successfully or not). More...

const CNcbiRegistry &	GetConfig (void) const
	Get the application's cached configuration parameters (read-only). More...

CNcbiRegistry &	GetConfig (void)

const string &	GetConfigPath (void) const
	Get the full path to the configuration file (if any) we ended up using. More...

bool	ReloadConfig (CMetaRegistry::TFlags flags=CMetaRegistry::fReloadIfChanged, IRegistry::TFlags reg_flags=IRegistry::fWithNcbirc)
	Reload the configuration file. More...

SIZE_TYPE	FlushDiag (CNcbiOstream *os, bool close_diag=false)
	Flush the in-memory diagnostic stream (for "eDS_ToMemory" case only). More...

const string &	GetProgramDisplayName (void) const
	Get the application's "display" name. More...

const string &	GetProgramExecutablePath (EFollowLinks follow_links=eIgnoreLinks) const
	Get the application's executable path. More...

CVersionInfo	GetVersion (void) const
	Get the program version information. More...

const CVersionAPI &	GetFullVersion (void) const
	Get the program version information. More...

bool	IsDryRun (void) const
	Check if it is a test run. More...

virtual bool	SetupDiag_AppSpecific (void)
	Setup application specific diagnostic stream. More...

template<class TFunc >
void	AddOnExitAction (TFunc func)
	Add callback to be executed from CNcbiApplicationAPI destructor. More...

Private Member Functions
virtual void	Init ()
	@inheritDoc More...

virtual int	Run ()
	@inheritDoc More...

void	x_InitApplicationData ()
	Initializes the application's data members. More...

CRef< CVDBBlastUtil >	x_GetVDBBlastUtil (bool isCSRA)
	Get vdb util. More...

int	x_PrintBlastDatabaseInformation ()
	Prints the BLAST database information (e.g. More...

int	x_ProcessSearchRequest ()
	Processes all requests except printing the BLAST database information. More...

int	x_PrintVDBPaths (bool recursive)
	Print vdb paths. More...

void	x_GetFullPaths ()
	Resolve vdb paths. More...

vector< string >	x_GetQueries ()
	Retrieve the queries from the command line arguments. More...

string	x_FormatRuntime (const CStopWatch &sw) const

void	x_AddCmdOptions ()

Private Attributes
string	m_allDbs

string	m_origDbs

bool	m_isRef

bool	m_includeFilteredReads

CBlastUsageReport	m_UsageReport

CStopWatch	m_StopWatch

Additional Inherited Members
Public Types inherited from CNcbiApplicationAPI
enum	EAppNameType { eBaseName , eFullName , eRealName }

Static Public Member Functions inherited from CNcbiApplication
static CNcbiApplication *	Instance (void)
	Singleton method. More...

Static Public Member Functions inherited from CNcbiApplicationAPI
static CNcbiApplicationAPI *	Instance (void)
	Singleton method. More...

static CNcbiApplicationGuard	InstanceGuard (void)
	Singleton method. More...

static SSystemMutex &	GetInstanceMutex (void)
	Mutex for application singleton object. More...

static string	GetAppName (EAppNameType name_type=eBaseName, int argc=0, const char const argv=NULL)

Protected Types inherited from CNcbiApplicationAPI
enum	EPreparseArgs { ePreparse_Continue , ePreparse_Exit }
	Result of PreparseArgs() More...

enum	EDisableArgDesc { fDisableStdArgs = 0x01 }
	Disable argument descriptions. More...

enum	EHideStdArgs { fHideLogfile = CArgDescriptions::fHideLogfile , fHideConffile = CArgDescriptions::fHideConffile , fHideVersion = CArgDescriptions::fHideVersion , fHideFullVersion = CArgDescriptions::fHideFullVersion , fHideDryRun = CArgDescriptions::fHideDryRun , fHideHelp = CArgDescriptions::fHideHelp , fHideFullHelp = CArgDescriptions::fHideFullHelp , fHideXmlHelp = CArgDescriptions::fHideXmlHelp , fHideAll = CArgDescriptions::fHideAll }
	Which standard flag's descriptions should not be displayed in the usage message. More...

enum	EStdioSetup { fNoSyncWithStdio = 0x01 , fDefault_CinBufferSize = 0x02 , fBinaryCin = 0x04 , fBinaryCout = 0x08 , fDefault_SyncWithStdio = 0x00 }
	Flags to adjust standard I/O streams' behaviour. More...

enum	EExitMode { eNoExits , eExceptionalExits , eAllExits }
	When to return a user-set exit code. More...

enum	EAppFlags { fSkipSafeStaticDestroy = 1 << 0 }

typedef int	TDisableArgDesc
	Binary OR of "EDisableArgDesc". More...

typedef int	THideStdArgs
	Binary OR of "EHideStdArgs". More...

typedef int	TStdioSetupFlags
	Binary OR of "EStdioSetup". More...

typedef int	TAppFlags

Protected Member Functions inherited from CNcbiApplicationAPI
virtual EPreparseArgs	PreparseArgs (int argc, const char const argv)
	Check the command line arguments before parsing them. More...

void	DisableArgDescriptions (TDisableArgDesc disable=fDisableStdArgs)

void	HideStdArgs (THideStdArgs hide_mask)
	Set the hide mask for the Hide Std Flags. More...

void	SetStdioFlags (TStdioSetupFlags stdio_flags)
	Adjust the behavior of standard I/O streams. More...

void	SetVersion (const CVersionInfo &version)
	Set the version number for the program. More...

void	SetVersion (const CVersionInfo &version, const SBuildInfo &build_info)

void	SetVersionByBuild (int major)

void	SetFullVersion (CRef< CVersionAPI > version)
	Set version data for the program. More...

virtual void	SetupArgDescriptions (CArgDescriptions *arg_desc)
	Setup the command line argument descriptions. More...

const CArgDescriptions *	GetArgDescriptions (void) const
	Get argument descriptions (set by SetupArgDescriptions) More...

bool	SetupDiag (EAppDiagStream diag)
	Setup the application diagnostic stream. More...

virtual bool	LoadConfig (CNcbiRegistry &reg, const string *conf, CNcbiRegistry::TFlags reg_flags)
	Load settings from the configuration file to the registry. More...

virtual bool	LoadConfig (CNcbiRegistry &reg, const string *conf)
	Load settings from the configuration file to the registry. More...

CNcbiRegistry &	GetRWConfig (void)
	Get the application's cached configuration parameters, accessible for read-write for an application's internal use only. More...

void	SetProgramDisplayName (const string &app_name)
	Set program's display name. More...

virtual void	AppStart (void)
	Method to be called before application start. More...

virtual void	AppStop (int exit_code)
	Method to be called before application exit. More...

void	SetExitCode (int exit_code, EExitMode when=eExceptionalExits)
	Force the program to return a specific exit code later, either when it exits due to an exception or unconditionally. More...

void	SetAppFlags (TAppFlags flags)

void	ExecuteOnExitActions ()
	Should only be called from the destructors of classes derived from CNcbiApplicationAPI - if it is necessary to access their data members and virtual methods; or to dynamic_cast<> from the base app class. More...

void	SetPhoneHomePolicy (IPhoneHomePolicy *policy, ENcbiOwnership ownership=eNoOwnership)
	Set Phone Home Policy. More...

IPhoneHomePolicy *	GetPhoneHomePolicy () const
	Return pointer to current Phone Home Policy or NULL. More...

Static Protected Member Functions inherited from CNcbiApplicationAPI
static CRWLock &	GetInstanceLock (void)

static string	FindProgramExecutablePath (int argc, const char const argv, string *real_path=0)
	Find the application's executable file. More...