NCBI C++ ToolKit
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CVDBBlastnApp Class Reference

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CVDBBlastnApp. More...

+ Inheritance diagram for CVDBBlastnApp:
+ Collaboration diagram for CVDBBlastnApp:

Public Member Functions

 CVDBBlastnApp ()
 Constructor, sets up the version info. More...
 
 ~CVDBBlastnApp ()
 
- 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...
 
const CNcbiArgumentsGetArguments (void) const
 Get the application's cached unprocessed command-line arguments. More...
 
virtual const CArgsGetArgs (void) const
 Get parsed command line arguments. More...
 
const CNcbiEnvironmentGetEnvironment (void) const
 Get the application's cached environment. More...
 
CNcbiEnvironmentSetEnvironment (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 CNcbiRegistryGetConfig (void) const
 Get the application's cached configuration parameters (read-only). More...
 
CNcbiRegistryGetConfig (void)
 
const stringGetConfigPath (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 stringGetProgramDisplayName (void) const
 Get the application's "display" name. More...
 
const stringGetProgramExecutablePath (EFollowLinks follow_links=eIgnoreLinks) const
 Get the application's executable path. More...
 
CVersionInfo GetVersion (void) const
 Get the program version information. More...
 
const CVersionAPIGetFullVersion (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 (void)
 Initialize the application. More...
 
virtual int Run (void)
 Run the application. More...
 
virtual void Exit (void)
 Cleanup on application exit. More...
 
void x_SetupLocalVDBSearch ()
 
void x_FillVDBInfo (CBlastFormatUtil::SDbInfo &vecDbInfo)
 
CRef< CScopex_GetScope (void)
 
void x_GetFullVDBPaths (void)
 

Private Attributes

string m_dbAllNames
 
CLocalVDBBlast::SLocalVDBStruct m_localVDBStruct
 
CRef< CBlastnVdbAppArgsm_CmdLineArgs
 This application's command line arguments. More...
 
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 CNcbiApplicationInstance (void)
 Singleton method. More...
 
- Static Public Member Functions inherited from CNcbiApplicationAPI
static CNcbiApplicationAPIInstance (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 CArgDescriptionsGetArgDescriptions (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...
 
CNcbiRegistryGetRWConfig (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...
 
IPhoneHomePolicyGetPhoneHomePolicy () const
 Return pointer to current Phone Home Policy or NULL. More...
 
- Static Protected Member Functions inherited from CNcbiApplicationAPI
static CRWLockGetInstanceLock (void)
 
static string FindProgramExecutablePath (int argc, const char *const *argv, string *real_path=0)
 Find the application's executable file. More...
 

Detailed Description

CVDBBlastnApp.

Blastn application that searches the SRA databases.

Definition at line 78 of file blastn_vdb.cpp.

Constructor & Destructor Documentation

◆ CVDBBlastnApp()

CVDBBlastnApp::CVDBBlastnApp ( )

◆ ~CVDBBlastnApp()

CVDBBlastnApp::~CVDBBlastnApp ( )

Member Function Documentation

◆ Exit()

void CVDBBlastnApp::Exit ( void  )
privatevirtual

Cleanup on application exit.

Reimplemented from CNcbiApplicationAPI.

Definition at line 340 of file blastn_vdb.cpp.

References SetDiagStream().

◆ Init()

void CVDBBlastnApp::Init ( void  )
privatevirtual

◆ Run()

int CVDBBlastnApp::Run ( void  )
privatevirtual

Run the application.

Implements CNcbiApplicationAPI.

Definition at line 176 of file blastn_vdb.cpp.

References abort(), CBlastUsageReport::AddParam(), CFormattingArgs::ArchiveFormatRequested(), BLAST_SRA_ENGINE_ERROR, BLAST_SRA_EXIT_SUCCESS, BLAST_SRA_INPUT_ERROR, BLAST_SRA_UNKNOWN_ERROR, CDebugDumpable::DebugDumpText(), CFormattingArgs::DisplayHtmlOutput(), eDiag_Warning, CBlastUsageReport::eExitStatus, CBlastUsageReport::eNumThreads, CBlastUsageReport::eProgram, CBlastAppArgs::ExecuteRemotely(), CArgs::Exist(), CNcbiApplicationAPI::GetArgs(), CNcbiApplicationAPI::GetArguments(), CBatchSizeMixer::GetBatchSize(), GetCmdlineArgs(), CFormattingArgs::GetCustomOutputFormatSpec(), CBlastFormat::GetDbTotalLength(), CFormattingArgs::GetFormattedOutputChoice(), CBlastAppArgs::GetFormattingArgs(), CBlastAppArgs::GetInputStream(), CFormattingArgs::GetLineLength(), CException::GetMsg(), CFormattingArgs::GetNumAlignments(), CFormattingArgs::GetNumDescriptions(), CLocalVDBBlast::GetNumExtensions(), CBlastAppArgs::GetNumThreads(), CBlastOptionsHandle::GetOptions(), CBlastAppArgs::GetOutputStream(), CQueryOptionsArgs::GetParseDeflines(), CBlastOptions::GetProgram(), CBlastnVdbAppArgs::GetQueryBatchSize(), CBlastAppArgs::GetQueryOptionsArgs(), CQueryOptionsArgs::GetRange(), CQueryOptionsArgs::GetStrand(), GetVDBScope(), input(), ITERATE, kArgDb, kArgIncludeFilteredReads, kArgOutput, CBlastFormat::LogBlastSearchInfo(), LogQueryInfo(), m_CmdLineArgs, m_dbAllNames, m_localVDBStruct, m_UsageReport, NCBI_THROW, NcbiCerr, SDataLoaderConfig::OptimizeForWholeLargeSequenceRetrieval(), CBlastFormat::PrintEpilog(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintProlog(), CBlastAppArgs::ProduceDebugOutput(), CQueryOptionsArgs::QueryIsProtein(), RecoverSearchStrategy(), CVDBBlastUtil::ReleaseVDBManager(), CRef< C, Locker >::Reset(), CBlastFormat::ResetScopeHistory(), result, CLocalVDBBlast::Run(), SaveSearchStrategy(), CBlastFormat::SetBaseFile(), SetDiagPostLevel(), SetDiagPostPrefix(), CBlastFormat::SetLineLength(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), CBlastInputSourceConfig::SetQueryLocalIdMode(), CBlastFormat::SetQueryRange(), CBatchSizeMixer::SetTargetHits(), CVDBBlastUtil::SetupVDBManager(), CFormattingArgs::ShowGis(), SplitQuery_GetChunkSize(), CQueryOptionsArgs::UseLowercaseMasks(), UseXInclude(), CException::what(), CBlastFormat::WriteArchive(), x_FillVDBInfo(), x_GetFullVDBPaths(), and x_SetupLocalVDBSearch().

◆ x_FillVDBInfo()

void CVDBBlastnApp::x_FillVDBInfo ( CBlastFormatUtil::SDbInfo &  vecDbInfo)
private

◆ x_GetFullVDBPaths()

void CVDBBlastnApp::x_GetFullVDBPaths ( void  )
private

◆ x_GetScope()

CRef<CScope> CVDBBlastnApp::x_GetScope ( void  )
private

◆ x_SetupLocalVDBSearch()

void CVDBBlastnApp::x_SetupLocalVDBSearch ( )
private

Member Data Documentation

◆ m_CmdLineArgs

CRef<CBlastnVdbAppArgs> CVDBBlastnApp::m_CmdLineArgs
private

This application's command line arguments.

Definition at line 105 of file blastn_vdb.cpp.

Referenced by Init(), Run(), and x_GetFullVDBPaths().

◆ m_dbAllNames

string CVDBBlastnApp::m_dbAllNames
private

Definition at line 101 of file blastn_vdb.cpp.

Referenced by Run(), x_FillVDBInfo(), x_GetFullVDBPaths(), and x_SetupLocalVDBSearch().

◆ m_localVDBStruct

CLocalVDBBlast::SLocalVDBStruct CVDBBlastnApp::m_localVDBStruct
private

Definition at line 102 of file blastn_vdb.cpp.

Referenced by Run(), x_FillVDBInfo(), and x_SetupLocalVDBSearch().

◆ m_StopWatch

CStopWatch CVDBBlastnApp::m_StopWatch
private

Definition at line 107 of file blastn_vdb.cpp.

Referenced by CVDBBlastnApp(), and ~CVDBBlastnApp().

◆ m_UsageReport

CBlastUsageReport CVDBBlastnApp::m_UsageReport
private

Definition at line 106 of file blastn_vdb.cpp.

Referenced by CVDBBlastnApp(), Run(), and ~CVDBBlastnApp().


The documentation for this class was generated from the following file:
Modified on Mon Jun 24 05:19:25 2024 by modify_doxy.py rev. 669887