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
CNcbiOstream *	m_OutputFile

CID1Client	m_ID1Client

CEntrez2Client	m_E2Client

CRef< CObjectManager >	m_ObjMgr

CRef< CScope >	m_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 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...

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...

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

Definition at line 696 of file id1_fetch.cpp.

References CID1Client_Base::AskGetgi(), data, ctll::empty(), INVALID_GI, kEmptyStr, m_ID1Client, NPOS, NStr::Split(), NStr::StringToInt(), and THROW_TRACE_ARGS.

Referenced by Run().

◆ LookUpGI()

bool CId1FetchApp::LookUpGI ( TGi gi )

private

Definition at line 422 of file id1_fetch.cpp.

References CScope::AddTopLevelSeqEntry(), CEntrez2Client_Base::AskGet_docsum(), CID1Client_Base::AskGetgihist(), CID1Client_Base::AskGetgirev(), ConstBegin(), CFlatFileConfig::eMode_Entrez, ERR_FATAL, ERR_POST, eSerial_AsnBinary, eSerial_AsnText, eSerial_None, eSerial_Xml, SAnnotSelector::ExcludeNamedAnnots(), CFastaOstream::fAssembleParts, CFastaOstream::fInstantiateGaps, format, CFlatFileGenerator::Generate(), CNcbiApplicationAPI::GetArgs(), CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Base::GetId(), CConstRef< C, Locker >::GetPointer(), CSerialObject::GetThisTypeInfo(), CBioseq_Handle::GetTopLevelEntry(), CEntrez2_id_list::GetUidIterator(), GI_TO, lt, m_E2Client, m_ID1Client, m_OutputFile, m_Scope, NcbiEndl, CConstRef< C, Locker >::NotEmpty(), CObjectOStream::Open(), out(), CEntrez2_id_list::PackUids(), CScope::ResetDataAndHistory(), CEntrez2_id_list::Resize(), CFlatFileGenerator::SetAnnotSelector(), CEntrez2_id_list_Base::SetDb(), CFlatFileConfig::SetFormatGenbank(), CSeq_id_Base::SetGi(), CFlatFileConfig::SetHideSNPFeatures(), CFlatFileConfig::SetMode(), CFlatFileConfig::SetShowContigFeatures(), CFlatFileConfig::SetShowContigSources(), CFlatFileConfig::SetViewProt(), WriteFastaIDs(), WriteHistoryTable(), and WriteQualityScores().

Referenced by Run().

◆ LookUpRawSeqID()

TGi CId1FetchApp::LookUpRawSeqID ( const string & s )

private

Definition at line 681 of file id1_fetch.cpp.

References CID1Client_Base::AskGetgi(), CSeq_id::fParse_AnyRaw, CSeq_id::fParse_NoFASTA, INVALID_GI, and m_ID1Client.

Referenced by Run().

◆ Run() [1/2]

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.

Definition at line 267 of file id1_fetch.cpp.

References CScope::AddDefaults(), CEntrez2Client_Base::AskEval_boolean(), eDiag_Info, eDPF_All, ctll::empty(), ERR_POST, CNcbiApplicationAPI::GetArgs(), CObjectManager::GetInstance(), GI_FROM, LookUpFastaSeqID(), LookUpFlatSeqID(), LookUpGI(), LookUpRawSeqID(), m_E2Client, m_ID1Client, m_ObjMgr, m_OutputFile, m_ResetDiagStream, m_Scope, NCBI_THROW, NcbiStreamToString(), NPOS, query, CGBDataLoader::RegisterInObjectManager(), s_IsControl(), STimeoutTag::sec, CID1Client::SetAllowDeadEntries(), CEntrez2Client_Base::SetDefaultRequest(), SetDiagPostFlag(), SetDiagPostLevel(), SetDiagStream(), CEntrez2_eval_boolean_Base::SetQuery(), CEntrez2_eval_boolean_Base::SetReturn_UIDs(), CRPCClient< TRequest, TReply >::SetTimeout(), CEntrez2_request_Base::SetTool(), str(), STimeoutTag::usec, and ZERO_GI.

◆ 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

Definition at line 766 of file id1_fetch.cpp.

References CTextColumn::Add(), ConstBegin(), dbname(), CTextColumn::Get(), CDate_std::GetDate(), CDate_std_Base::GetDay(), CDate_std_Base::GetMonth(), CDate_std_Base::GetYear(), CTextColumn::Height(), NStr::IntToString(), ITERATE, m_OutputFile, n, NcbiEndl, number, NStr::NumericToString(), tag, and ZERO_GI.

Referenced by LookUpGI().

◆ WriteQualityScores()

void CId1FetchApp::WriteQualityScores ( CBioseq_Handle & handle )

private

Definition at line 815 of file id1_fetch.cpp.

References data, FindBestChoice(), CBioseq_Handle::GetBioseqCore(), CBioseq_Base::GetId(), NPOS, and CSeq_id::Score().

Referenced by LookUpGI().

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:

src/app/id1_fetch/id1_fetch.cpp
src/app/id1_fetch/id1_fetch_simple.cpp

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ Exit() [1/2]

◆ Exit() [2/2]

◆ Init() [1/2]

◆ Init() [2/2]

◆ LookUpFastaSeqID()

◆ LookUpFlatSeqID()

◆ LookUpGI()

◆ LookUpRawSeqID()

◆ Run() [1/2]

◆ Run() [2/2]

◆ WriteFastaIDs()

◆ WriteHistoryTable()

◆ WriteQualityScores()

Member Data Documentation

◆ m_E2Client

◆ m_ID1Client

◆ m_ObjMgr

◆ m_OutputFile

◆ m_ResetDiagStream

◆ m_Scope