NCBI C++ ToolKit
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CMakeProfileDBApp Class Reference

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+ Inheritance diagram for CMakeProfileDBApp:
+ Collaboration diagram for CMakeProfileDBApp:

Classes

class  CRPS_DbInfo
 

Public Member Functions

 CMakeProfileDBApp (void)
 @inheritDoc More...
 
 ~CMakeProfileDBApp ()
 
- 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 Types

enum  op_mode { op_rps , op_cobalt , op_delta , op_invalid }
 
enum  CheckInputScoremat_RV { sm_valid_has_pssm , sm_valid_freq_only , sm_invalid }
 
enum  { eUndefined = -1 , eFalse , eTrue }
 

Private Member Functions

virtual void Init ()
 @inheritDoc More...
 
virtual int Run ()
 @inheritDoc More...
 
CheckInputScoremat_RV x_CheckInputScoremat (const CPssmWithParameters &pssm_w_parameters, const string &filename)
 
void x_SetupArgDescriptions (void)
 
void x_InitProgramParameters (void)
 
vector< stringx_GetSMPFilenames (void)
 
void x_InitOutputDb (CRPS_DbInfo &rpsDBInfo)
 
void x_InitRPSDbInfo (CRPS_DbInfo &rpsDBInfo, Int4 vol, Int4 num_files)
 
void x_UpdateRPSDbInfo (CRPS_DbInfo &rpsDbInfo, const CPssmWithParameters &pssm_p)
 
void x_RPSAddFirstSequence (CRPS_DbInfo &rpsDbInfo, CPssmWithParameters &pssm_w_parameters, bool freq_only)
 
void x_RPSUpdateLookup (CRPS_DbInfo &rpsDbInfo, Int4 seq_size)
 
void x_RPSUpdateStatistics (CRPS_DbInfo &rpsDbInfo, CPssmWithParameters &seq, Int4 seq_size)
 
void x_FillInRPSDbParameters (CRPS_DbInfo &rpsDbInfo, CPssmWithParameters &pssm_p)
 
void x_RPSUpdatePSSM (CRPS_DbInfo &rpsDbInfo, const CPssm &pssm, Int4 seq_index, Int4 seq_size)
 
void x_RPS_DbClose (CRPS_DbInfo &rpsDbInfo)
 
void x_UpdateCobalt (CRPS_DbInfo &rpsDbInfo, const CPssmWithParameters &pssm_p, Int4 seq_size)
 
bool x_CheckDelta (const CPssm &pssm, Int4 seq_size, const string &filename)
 
bool x_ValidateCd (const list< double > &freqs, const list< double > &observ, unsigned int alphabet_size)
 
void x_WrapUpDelta (CRPS_DbInfo &rpsDbInfo, CTmpFile &tmp_obsr_file, CTmpFile &tmp_freq_file, list< Int4 > &FreqOffsets, list< Int4 > &ObsrOffsets, Int4 CurrFreqOffset, Int4 CurrObsrOffset)
 
vector< stringx_CreateDeltaList (void)
 
void x_UpdateFreqRatios (CRPS_DbInfo &rpsDbInfo, const CPssmWithParameters &pssm_p, Int4 seq_index, Int4 seq_size)
 
void x_UpdateDelta (CRPS_DbInfo &rpsDbInfo, vector< string > &smpFilenames)
 
bool x_IsUpdateFreqRatios (const CPssm &p)
 
void x_MakeVol (Int4 vol, vector< string > &smps)
 
int x_Run (void)
 
void x_AddCmdOptions (void)
 
void x_CreateAliasFile (void)
 

Private Attributes

CNcbiOstreamm_LogFile
 
CNcbiIstreamm_InPssmList
 
string m_Title
 
double m_WordDefaultScoreThreshold
 
string m_OutDbName
 
string m_OutDbType
 
bool m_CreateIndexFile
 
int m_GapOpenPenalty
 
int m_GapExtPenalty
 
double m_PssmScaleFactor
 
string m_Matrix
 
op_mode m_op_mode
 
bool m_binary_scoremat
 
int m_MaxSmpFilesPerVol
 
int m_NumOfVols
 
EBlastDbVersion m_DbVer
 
CRef< CTaxIdSetm_Taxids
 
bool m_UserTaxIds
 
bool m_Done
 
double m_ObsrvThreshold
 
bool m_ExcludeInvalid
 
int m_UpdateFreqRatios
 
bool m_UseModelThreshold
 
vector< stringm_VolNames
 
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...
 
- 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 175 of file makeprofiledb.cpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
private
Enumerator
eUndefined 
eFalse 
eTrue 

Definition at line 245 of file makeprofiledb.cpp.

◆ CheckInputScoremat_RV

Enumerator
sm_valid_has_pssm 
sm_valid_freq_only 
sm_invalid 

Definition at line 238 of file makeprofiledb.cpp.

◆ op_mode

Enumerator
op_rps 
op_cobalt 
op_delta 
op_invalid 

Definition at line 187 of file makeprofiledb.cpp.

Constructor & Destructor Documentation

◆ CMakeProfileDBApp()

CMakeProfileDBApp::CMakeProfileDBApp ( void  )

◆ ~CMakeProfileDBApp()

CMakeProfileDBApp::~CMakeProfileDBApp ( )

Member Function Documentation

◆ Init()

void CMakeProfileDBApp::Init ( void  )
privatevirtual

@inheritDoc

Reimplemented from CNcbiApplicationAPI.

Definition at line 1331 of file makeprofiledb.cpp.

References x_InitProgramParameters(), and x_SetupArgDescriptions().

◆ Run()

int CMakeProfileDBApp::Run ( void  )
privatevirtual

◆ x_AddCmdOptions()

void CMakeProfileDBApp::x_AddCmdOptions ( void  )
private

◆ x_CheckDelta()

bool CMakeProfileDBApp::x_CheckDelta ( const CPssm pssm,
Int4  seq_size,
const string filename 
)
private

◆ x_CheckInputScoremat()

CMakeProfileDBApp::CheckInputScoremat_RV CMakeProfileDBApp::x_CheckInputScoremat ( const CPssmWithParameters pssm_w_parameters,
const string filename 
)
private

◆ x_CreateAliasFile()

void CMakeProfileDBApp::x_CreateAliasFile ( void  )
private

◆ x_CreateDeltaList()

vector< string > CMakeProfileDBApp::x_CreateDeltaList ( void  )
private

◆ x_FillInRPSDbParameters()

void CMakeProfileDBApp::x_FillInRPSDbParameters ( CRPS_DbInfo rpsDbInfo,
CPssmWithParameters pssm_p 
)
private

◆ x_GetSMPFilenames()

vector< string > CMakeProfileDBApp::x_GetSMPFilenames ( void  )
private

◆ x_InitOutputDb()

void CMakeProfileDBApp::x_InitOutputDb ( CRPS_DbInfo rpsDBInfo)
private

◆ x_InitProgramParameters()

void CMakeProfileDBApp::x_InitProgramParameters ( void  )
private

◆ x_InitRPSDbInfo()

void CMakeProfileDBApp::x_InitRPSDbInfo ( CRPS_DbInfo rpsDBInfo,
Int4  vol,
Int4  num_files 
)
private

◆ x_IsUpdateFreqRatios()

bool CMakeProfileDBApp::x_IsUpdateFreqRatios ( const CPssm p)
private

◆ x_MakeVol()

void CMakeProfileDBApp::x_MakeVol ( Int4  vol,
vector< string > &  smps 
)
private

Definition at line 1393 of file makeprofiledb.cpp.

References _ASSERT, CWriteDB::AddSequence(), CTaxIdSet::AddTaxId(), CMakeProfileDBApp::CRPS_DbInfo::aux_file, CWriteDB::Close(), CMakeProfileDBApp::CRPS_DbInfo::curr_seq_offset, CMakeProfileDBApp::CRPS_DbInfo::db_name, CMakeDbPosMatrix::Delete(), CWriteDB::ExtractBioseqDeflines(), f(), CTaxIdSet::FixTaxId(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CPssm_Base::GetFinalData(), CBioseq::GetFirstId(), CPssmFinalData_Base::GetKappa(), CPssmWithParameters_Base::GetPssm(), CPssm_Base::GetQuery(), CPssm::GetQueryLength(), CPssmFinalData_Base::GetScalingFactor(), CSeq_entry_Base::GetSeq(), CPssmFinalData_Base::GetWordScoreThreshold(), CBioseq_Base::IsSetDescr(), CPssmFinalData_Base::IsSetScalingFactor(), CPssmFinalData_Base::IsSetWordScoreThreshold(), CMakeProfileDBApp::CRPS_DbInfo::lookup, m_binary_scoremat, m_op_mode, m_Taxids, m_UseModelThreshold, m_UserTaxIds, m_VolNames, m_WordDefaultScoreThreshold, MSerial_AsnBinary, MSerial_AsnText, NCBI_THROW, NULL, CMakeProfileDBApp::CRPS_DbInfo::num_seqs, op_cobalt, op_delta, CMakeProfileDBApp::CRPS_DbInfo::output_db, CMakeProfileDBApp::CRPS_DbInfo::pos_matrix, s_GenerateBlastDefline(), s_HasDefline(), CMakeProfileDBApp::CRPS_DbInfo::scale_factor, CWriteDB::SetDeflines(), sm_invalid, sm_valid_freq_only, BlastAaLookupTable::threshold, x_CheckInputScoremat(), x_FillInRPSDbParameters(), x_InitOutputDb(), x_InitRPSDbInfo(), x_RPS_DbClose(), x_RPSAddFirstSequence(), x_RPSUpdateLookup(), x_RPSUpdatePSSM(), x_RPSUpdateStatistics(), x_UpdateCobalt(), x_UpdateDelta(), and x_UpdateFreqRatios().

Referenced by x_Run().

◆ x_RPS_DbClose()

void CMakeProfileDBApp::x_RPS_DbClose ( CRPS_DbInfo rpsDbInfo)
private

◆ x_RPSAddFirstSequence()

void CMakeProfileDBApp::x_RPSAddFirstSequence ( CRPS_DbInfo rpsDbInfo,
CPssmWithParameters pssm_w_parameters,
bool  freq_only 
)
private

◆ x_RPSUpdateLookup()

void CMakeProfileDBApp::x_RPSUpdateLookup ( CRPS_DbInfo rpsDbInfo,
Int4  seq_size 
)
private

◆ x_RPSUpdatePSSM()

void CMakeProfileDBApp::x_RPSUpdatePSSM ( CRPS_DbInfo rpsDbInfo,
const CPssm pssm,
Int4  seq_index,
Int4  seq_size 
)
private

◆ x_RPSUpdateStatistics()

void CMakeProfileDBApp::x_RPSUpdateStatistics ( CRPS_DbInfo rpsDbInfo,
CPssmWithParameters seq,
Int4  seq_size 
)
private

◆ x_Run()

int CMakeProfileDBApp::x_Run ( void  )
private

◆ x_SetupArgDescriptions()

void CMakeProfileDBApp::x_SetupArgDescriptions ( void  )
private

◆ x_UpdateCobalt()

void CMakeProfileDBApp::x_UpdateCobalt ( CRPS_DbInfo rpsDbInfo,
const CPssmWithParameters pssm_p,
Int4  seq_size 
)
private

◆ x_UpdateDelta()

void CMakeProfileDBApp::x_UpdateDelta ( CRPS_DbInfo rpsDbInfo,
vector< string > &  smpFilenames 
)
private

◆ x_UpdateFreqRatios()

void CMakeProfileDBApp::x_UpdateFreqRatios ( CRPS_DbInfo rpsDbInfo,
const CPssmWithParameters pssm_p,
Int4  seq_index,
Int4  seq_size 
)
private

◆ x_UpdateRPSDbInfo()

void CMakeProfileDBApp::x_UpdateRPSDbInfo ( CRPS_DbInfo rpsDbInfo,
const CPssmWithParameters pssm_p 
)
private

◆ x_ValidateCd()

bool CMakeProfileDBApp::x_ValidateCd ( const list< double > &  freqs,
const list< double > &  observ,
unsigned int  alphabet_size 
)
private

Definition at line 1742 of file makeprofiledb.cpp.

References fabs, ITERATE, kEpsylon, and NCBI_THROW.

Referenced by x_CheckDelta().

◆ x_WrapUpDelta()

void CMakeProfileDBApp::x_WrapUpDelta ( CRPS_DbInfo rpsDbInfo,
CTmpFile tmp_obsr_file,
CTmpFile tmp_freq_file,
list< Int4 > &  FreqOffsets,
list< Int4 > &  ObsrOffsets,
Int4  CurrFreqOffset,
Int4  CurrObsrOffset 
)
private

Member Data Documentation

◆ m_binary_scoremat

bool CMakeProfileDBApp::m_binary_scoremat
private

◆ m_CreateIndexFile

bool CMakeProfileDBApp::m_CreateIndexFile
private

Definition at line 289 of file makeprofiledb.cpp.

Referenced by x_InitOutputDb(), and x_InitProgramParameters().

◆ m_DbVer

EBlastDbVersion CMakeProfileDBApp::m_DbVer
private

Definition at line 299 of file makeprofiledb.cpp.

Referenced by x_InitOutputDb(), and x_InitProgramParameters().

◆ m_Done

bool CMakeProfileDBApp::m_Done
private

Definition at line 302 of file makeprofiledb.cpp.

Referenced by x_Run(), and ~CMakeProfileDBApp().

◆ m_ExcludeInvalid

bool CMakeProfileDBApp::m_ExcludeInvalid
private

Definition at line 306 of file makeprofiledb.cpp.

Referenced by x_CheckDelta(), and x_InitProgramParameters().

◆ m_GapExtPenalty

int CMakeProfileDBApp::m_GapExtPenalty
private

Definition at line 291 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_InitRPSDbInfo().

◆ m_GapOpenPenalty

int CMakeProfileDBApp::m_GapOpenPenalty
private

Definition at line 290 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_InitRPSDbInfo().

◆ m_InPssmList

CNcbiIstream* CMakeProfileDBApp::m_InPssmList
private

Definition at line 284 of file makeprofiledb.cpp.

Referenced by x_GetSMPFilenames(), and x_InitProgramParameters().

◆ m_LogFile

CNcbiOstream* CMakeProfileDBApp::m_LogFile
private

Definition at line 283 of file makeprofiledb.cpp.

Referenced by x_CheckDelta(), x_InitProgramParameters(), and x_Run().

◆ m_Matrix

string CMakeProfileDBApp::m_Matrix
private

Definition at line 293 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_InitRPSDbInfo().

◆ m_MaxSmpFilesPerVol

int CMakeProfileDBApp::m_MaxSmpFilesPerVol
private

Definition at line 296 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_Run().

◆ m_NumOfVols

int CMakeProfileDBApp::m_NumOfVols
private

Definition at line 297 of file makeprofiledb.cpp.

Referenced by x_Run().

◆ m_ObsrvThreshold

double CMakeProfileDBApp::m_ObsrvThreshold
private

Definition at line 305 of file makeprofiledb.cpp.

Referenced by x_CheckDelta(), and x_InitProgramParameters().

◆ m_op_mode

op_mode CMakeProfileDBApp::m_op_mode
private

◆ m_OutDbName

string CMakeProfileDBApp::m_OutDbName
private

◆ m_OutDbType

string CMakeProfileDBApp::m_OutDbType
private

Definition at line 288 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters().

◆ m_PssmScaleFactor

double CMakeProfileDBApp::m_PssmScaleFactor
private

Definition at line 292 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_InitRPSDbInfo().

◆ m_StopWatch

CStopWatch CMakeProfileDBApp::m_StopWatch
private

Definition at line 313 of file makeprofiledb.cpp.

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

◆ m_Taxids

CRef<CTaxIdSet> CMakeProfileDBApp::m_Taxids
private

Definition at line 300 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_MakeVol().

◆ m_Title

string CMakeProfileDBApp::m_Title
private

Definition at line 285 of file makeprofiledb.cpp.

Referenced by x_CreateAliasFile(), x_InitOutputDb(), and x_InitProgramParameters().

◆ m_UpdateFreqRatios

int CMakeProfileDBApp::m_UpdateFreqRatios
private

Definition at line 308 of file makeprofiledb.cpp.

Referenced by x_CheckInputScoremat(), x_RPS_DbClose(), and x_UpdateFreqRatios().

◆ m_UsageReport

CBlastUsageReport CMakeProfileDBApp::m_UsageReport
private

Definition at line 312 of file makeprofiledb.cpp.

Referenced by CMakeProfileDBApp(), Run(), x_AddCmdOptions(), and ~CMakeProfileDBApp().

◆ m_UseModelThreshold

bool CMakeProfileDBApp::m_UseModelThreshold
private

Definition at line 309 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), x_MakeVol(), and x_RPSAddFirstSequence().

◆ m_UserTaxIds

bool CMakeProfileDBApp::m_UserTaxIds
private

Definition at line 301 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), and x_MakeVol().

◆ m_VolNames

vector<string> CMakeProfileDBApp::m_VolNames
private

Definition at line 311 of file makeprofiledb.cpp.

Referenced by x_CreateAliasFile(), x_MakeVol(), x_Run(), and ~CMakeProfileDBApp().

◆ m_WordDefaultScoreThreshold

double CMakeProfileDBApp::m_WordDefaultScoreThreshold
private

Definition at line 286 of file makeprofiledb.cpp.

Referenced by x_InitProgramParameters(), x_MakeVol(), and x_RPSAddFirstSequence().


The documentation for this class was generated from the following file:
Modified on Mon Mar 04 05:13:09 2024 by modify_doxy.py rev. 669887