NCBI C++ ToolKit
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CAlnBuildApp Class Reference

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+ Inheritance diagram for CAlnBuildApp:
+ Collaboration diagram for CAlnBuildApp:

Public Member Functions

virtual void Init (void)
 Initialize the application. More...
virtual int Run (void)
 Run the application. More...
CScopeGetScope (void) const
void LoadInputAlns (void)
bool InsertAln (const CSeq_align *aln)
void ReportTime (const string &msg)
void PrintAnchoredAln (const CAnchoredAln &anchored_aln)
- 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 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 Attributes

CRef< CObjectManagerm_ObjMgr
CRef< CScopem_Scope
CAlnContainer m_AlnContainer
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

Definition at line 70 of file aln_build_app.cpp.

Member Function Documentation

◆ GetScope()

CScope & CAlnBuildApp::GetScope ( void  ) const

◆ Init()

void CAlnBuildApp::Init ( void  )

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 93 of file aln_build_app.cpp.

References CArgDescriptions::eBoolean, CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eOutputFile, and CArgDescriptions::eString.

◆ InsertAln()

bool CAlnBuildApp::InsertAln ( const CSeq_align aln)

Definition at line 77 of file aln_build_app.cpp.

References CSeq_align::Validate().

Referenced by LoadInputAlns().

◆ LoadInputAlns()

void CAlnBuildApp::LoadInputAlns ( void  )

◆ PrintAnchoredAln()

void CAlnBuildApp::PrintAnchoredAln ( const CAnchoredAln anchored_aln)

◆ ReportTime()

void CAlnBuildApp::ReportTime ( const string msg)

Definition at line 236 of file aln_build_app.cpp.

References CTimeSpan::eSSP_Millisecond.

◆ Run()

int CAlnBuildApp::Run ( void  )

Member Data Documentation

◆ m_AlnContainer

CAlnContainer CAlnBuildApp::m_AlnContainer

Definition at line 88 of file aln_build_app.cpp.

◆ m_ObjMgr

CRef<CObjectManager> CAlnBuildApp::m_ObjMgr

Definition at line 86 of file aln_build_app.cpp.

◆ m_Scope

CRef<CScope> CAlnBuildApp::m_Scope

Definition at line 87 of file aln_build_app.cpp.

◆ m_StopWatch

CStopWatch CAlnBuildApp::m_StopWatch

Definition at line 89 of file aln_build_app.cpp.

The documentation for this class was generated from the following file:
Modified on Tue Jun 18 13:32:54 2024 by rev. 669887