NCBI C++ ToolKit
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CId1FetchApp Class Reference

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+ Inheritance diagram for CId1FetchApp:
+ Collaboration diagram for CId1FetchApp:

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...
 
bool LookUpGI (TGi gi)
 
TGi LookUpFastaSeqID (const string &s)
 
TGi LookUpRawSeqID (const string &s)
 
TGi LookUpFlatSeqID (const string &s)
 
void WriteFastaIDs (const list< CRef< CSeq_id > > &ids)
 
void WriteHistoryTable (const CID1server_back &id1_reply)
 
void WriteQualityScores (CBioseq_Handle &handle)
 
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...
 

Private Attributes

CNcbiOstreamm_OutputFile
 
CID1Client m_ID1Client
 
CEntrez2Client m_E2Client
 
CRef< CObjectManagerm_ObjMgr
 
CRef< CScopem_Scope
 
bool m_ResetDiagStream = false
 

Additional Inherited Members

- Public Types inherited from CNcbiApplicationAPI
enum  EAppNameType { eBaseName , eFullName , eRealName }
 
- 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...
 
- 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

Definition at line 94 of file id1_fetch.cpp.

Member Function Documentation

◆ Exit() [1/2]

void CId1FetchApp::Exit ( void  )
privatevirtual

Cleanup on application exit.

Perform cleanup before exiting. The default behavior of this is "do nothing". If you have special cleanup logic that needs to be performed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 666 of file id1_fetch.cpp.

References m_ResetDiagStream, and SetDiagStream().

◆ Exit() [2/2]

virtual void CId1FetchApp::Exit ( void  )
privatevirtual

Cleanup on application exit.

Perform cleanup before exiting. The default behavior of this is "do nothing". If you have special cleanup logic that needs to be performed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

◆ Init() [1/2]

void CId1FetchApp::Init ( void  )
privatevirtual

Initialize the application.

The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 120 of file id1_fetch.cpp.

References CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eIntId, CArgDescriptions::eOutputFile, CArgDescriptions::eString, CArgDescriptions::fBinary, CArgDescriptions::fPreOpen, CNcbiApplicationAPI::GetArguments(), kMax_I8, kMax_Int, and CNcbiApplicationAPI::SetupArgDescriptions().

◆ Init() [2/2]

virtual void CId1FetchApp::Init ( void  )
privatevirtual

Initialize the application.

The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

◆ LookUpFastaSeqID()

TGi CId1FetchApp::LookUpFastaSeqID ( const string s)
private

Definition at line 674 of file id1_fetch.cpp.

References CID1Client_Base::AskGetgi(), and m_ID1Client.

Referenced by Run().

◆ LookUpFlatSeqID()

TGi CId1FetchApp::LookUpFlatSeqID ( const string s)
private

◆ LookUpGI()

bool CId1FetchApp::LookUpGI ( TGi  gi)
private

◆ LookUpRawSeqID()

TGi CId1FetchApp::LookUpRawSeqID ( const string s)
private

◆ Run() [1/2]

int CId1FetchApp::Run ( void  )
privatevirtual

◆ Run() [2/2]

virtual int CId1FetchApp::Run ( void  )
privatevirtual

Run the application.

It is defined as a pure virtual method – so you must(!) supply the Run() method to implement the application-specific logic.

Returns
Exit code.

Implements CNcbiApplicationAPI.

◆ WriteFastaIDs()

void CId1FetchApp::WriteFastaIDs ( const list< CRef< CSeq_id > > &  ids)
private

Definition at line 731 of file id1_fetch.cpp.

References ITERATE, and m_OutputFile.

Referenced by LookUpGI().

◆ WriteHistoryTable()

void CId1FetchApp::WriteHistoryTable ( const CID1server_back id1_reply)
private

◆ WriteQualityScores()

void CId1FetchApp::WriteQualityScores ( CBioseq_Handle handle)
private

Member Data Documentation

◆ m_E2Client

CEntrez2Client CId1FetchApp::m_E2Client
private

Definition at line 113 of file id1_fetch.cpp.

Referenced by LookUpGI(), and Run().

◆ m_ID1Client

CID1Client CId1FetchApp::m_ID1Client
private

Definition at line 112 of file id1_fetch.cpp.

Referenced by LookUpFastaSeqID(), LookUpFlatSeqID(), LookUpGI(), LookUpRawSeqID(), and Run().

◆ m_ObjMgr

CRef<CObjectManager> CId1FetchApp::m_ObjMgr
private

Definition at line 114 of file id1_fetch.cpp.

Referenced by Run().

◆ m_OutputFile

CNcbiOstream* CId1FetchApp::m_OutputFile
private

Definition at line 111 of file id1_fetch.cpp.

Referenced by LookUpGI(), Run(), WriteFastaIDs(), and WriteHistoryTable().

◆ m_ResetDiagStream

bool CId1FetchApp::m_ResetDiagStream = false
private

Definition at line 116 of file id1_fetch.cpp.

Referenced by Exit(), and Run().

◆ m_Scope

CRef<CScope> CId1FetchApp::m_Scope
private

Definition at line 115 of file id1_fetch.cpp.

Referenced by LookUpGI(), and Run().


The documentation for this class was generated from the following files:
Modified on Thu Jun 13 17:33:04 2024 by modify_doxy.py rev. 669887