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CBlastAppArgs Class Referenceabstract

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Base command line argument class for a generic BLAST command line binary. More...

#include <algo/blast/blastinput/blast_args.hpp>

+ Inheritance diagram for CBlastAppArgs:
+ Collaboration diagram for CBlastAppArgs:

Public Member Functions

 CBlastAppArgs ()
 Default constructor. More...
 
virtual ~CBlastAppArgs ()
 Our virtual destructor. More...
 
CArgDescriptionsSetCommandLine ()
 Set the command line arguments. More...
 
string GetTask () const
 Get the task for this object. More...
 
void SetTask (const string &task)
 Set the task for this object. More...
 
CRef< CBlastOptionsHandleSetOptions (const CArgs &args)
 Extract the command line arguments into a CBlastOptionsHandle object. More...
 
CRef< CBlastOptionsHandleSetOptionsForSavedStrategy (const CArgs &args)
 Combine the command line arguments into a CBlastOptions object recovered from saved search strategy. More...
 
void SetOptionsHandle (CRef< CBlastOptionsHandle > opts_hndl)
 Setter for the BLAST options handle, this is used if the options are recovered from a saved BLAST search strategy. More...
 
CRef< CBlastDatabaseArgsGetBlastDatabaseArgs () const
 Get the BLAST database arguments. More...
 
void SetBlastDatabaseArgs (CRef< CBlastDatabaseArgs > args)
 Set the BLAST database arguments. More...
 
CRef< CQueryOptionsArgsGetQueryOptionsArgs () const
 Get the options for the query sequence(s) More...
 
CRef< CFormattingArgsGetFormattingArgs () const
 Get the formatting options. More...
 
size_t GetNumThreads () const
 Get the number of threads to spawn. More...
 
int GetMTMode () const
 
virtual CNcbiIstreamGetInputStream ()
 Get the input stream. More...
 
virtual CNcbiOstreamGetOutputStream ()
 Get the output stream. More...
 
void SetInputStream (CRef< CTmpFile > input_file)
 Set the input stream to a temporary input file (needed when importing a search strategy) More...
 
CNcbiIstreamGetImportSearchStrategyStream (const CArgs &args)
 Get the input stream for the search strategy. More...
 
CNcbiOstreamGetExportSearchStrategyStream (const CArgs &args)
 Get the output stream for the search strategy. More...
 
bool ExecuteRemotely () const
 Determine whether the search should be executed remotely or not. More...
 
bool ProduceDebugRemoteOutput () const
 Return whether debug (verbose) output should be produced on remote searches (only available when compiled with _DEBUG) More...
 
bool ProduceDebugOutput () const
 Return whether debug (verbose) output should be produced on remote searches (only available when compiled with _DEBUG) More...
 
virtual int GetQueryBatchSize () const =0
 Get the query batch size. More...
 
string GetClientId () const
 Retrieve the client ID for remote requests. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Protected Member Functions

virtual CRef< CBlastOptionsHandlex_CreateOptionsHandle (CBlastOptions::EAPILocality locality, const CArgs &args)=0
 Create the options handle based on the command line arguments. More...
 
CRef< CBlastOptionsHandlex_CreateOptionsHandleWithTask (CBlastOptions::EAPILocality locality, const string &task)
 Creates the BLAST options handle based on the task argument. More...
 
void x_IssueWarningsForIgnoredOptions (const CArgs &args)
 Issue warnings when recovering from a search strategy (command line applications only) More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

TBlastCmdLineArgs m_Args
 Set of command line argument objects. More...
 
CRef< CQueryOptionsArgsm_QueryOptsArgs
 query options object More...
 
CRef< CBlastDatabaseArgsm_BlastDbArgs
 database/subject object More...
 
CRef< CFormattingArgsm_FormattingArgs
 formatting options More...
 
CRef< CMTArgsm_MTArgs
 multi-threaded options More...
 
CRef< CRemoteArgsm_RemoteArgs
 remote vs. local execution options More...
 
CRef< CStdCmdLineArgsm_StdCmdLineArgs
 standard command line arguments class More...
 
CRef< CSearchStrategyArgsm_SearchStrategyArgs
 arguments for dealing with search strategies More...
 
CRef< CDebugArgsm_DebugArgs
 Debugging arguments. More...
 
CRef< CHspFilteringArgsm_HspFilteringArgs
 HSP filtering arguments. More...
 
CRef< CBlastOptionsHandlem_OptsHandle
 The BLAST options handle, only non-NULL if assigned via SetOptionsHandle, i.e. More...
 
string m_Task
 Task specified in the command line. More...
 
string m_ClientId
 Client ID used for remote BLAST submissions, must be populated by subclasses. More...
 
bool m_IsUngapped
 Is this application being run ungapped. More...
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Detailed Description

Base command line argument class for a generic BLAST command line binary.

Definition at line 1401 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CBlastAppArgs()

CBlastAppArgs::CBlastAppArgs ( )

Default constructor.

Definition at line 3550 of file blast_args.cpp.

References m_Args, m_IsUngapped, m_SearchStrategyArgs, and CRef< C, Locker >::Reset().

◆ ~CBlastAppArgs()

virtual CBlastAppArgs::~CBlastAppArgs ( )
inlinevirtual

Our virtual destructor.

Definition at line 1407 of file blast_args.hpp.

Member Function Documentation

◆ ExecuteRemotely()

bool CBlastAppArgs::ExecuteRemotely ( ) const
inline

◆ GetBlastDatabaseArgs()

CRef<CBlastDatabaseArgs> CBlastAppArgs::GetBlastDatabaseArgs ( ) const
inline

◆ GetClientId()

string CBlastAppArgs::GetClientId ( ) const
inline

◆ GetExportSearchStrategyStream()

CNcbiOstream* CBlastAppArgs::GetExportSearchStrategyStream ( const CArgs args)
inline

Get the output stream for the search strategy.

Definition at line 1482 of file blast_args.hpp.

References CSearchStrategyArgs::GetExportStream(), and m_SearchStrategyArgs.

Referenced by SetOptions().

◆ GetFormattingArgs()

CRef<CFormattingArgs> CBlastAppArgs::GetFormattingArgs ( ) const
inline

◆ GetImportSearchStrategyStream()

CNcbiIstream* CBlastAppArgs::GetImportSearchStrategyStream ( const CArgs args)
inline

Get the input stream for the search strategy.

Definition at line 1478 of file blast_args.hpp.

References CSearchStrategyArgs::GetImportStream(), and m_SearchStrategyArgs.

◆ GetInputStream()

CNcbiIstream & CBlastAppArgs::GetInputStream ( )
virtual

◆ GetMTMode()

int CBlastAppArgs::GetMTMode ( ) const
inline

◆ GetNumThreads()

size_t CBlastAppArgs::GetNumThreads ( ) const
inline

◆ GetOutputStream()

CNcbiOstream & CBlastAppArgs::GetOutputStream ( )
virtual

◆ GetQueryBatchSize()

virtual int CBlastAppArgs::GetQueryBatchSize ( ) const
pure virtual

◆ GetQueryOptionsArgs()

CRef<CQueryOptionsArgs> CBlastAppArgs::GetQueryOptionsArgs ( ) const
inline

◆ GetTask()

string CBlastAppArgs::GetTask ( ) const
inline

◆ ProduceDebugOutput()

bool CBlastAppArgs::ProduceDebugOutput ( ) const
inline

◆ ProduceDebugRemoteOutput()

bool CBlastAppArgs::ProduceDebugRemoteOutput ( ) const
inline

◆ SetBlastDatabaseArgs()

void CBlastAppArgs::SetBlastDatabaseArgs ( CRef< CBlastDatabaseArgs args)
inline

Set the BLAST database arguments.

Definition at line 1441 of file blast_args.hpp.

References m_BlastDbArgs.

◆ SetCommandLine()

CArgDescriptions * CBlastAppArgs::SetCommandLine ( )

◆ SetInputStream()

void CBlastAppArgs::SetInputStream ( CRef< CTmpFile input_file)
inline

Set the input stream to a temporary input file (needed when importing a search strategy)

Parameters
input_filetemporary input file to read [in]

Definition at line 1473 of file blast_args.hpp.

References input_file, m_StdCmdLineArgs, and CStdCmdLineArgs::SetInputStream().

◆ SetOptions()

CRef< CBlastOptionsHandle > CBlastAppArgs::SetOptions ( const CArgs args)

◆ SetOptionsForSavedStrategy()

CRef< CBlastOptionsHandle > CBlastAppArgs::SetOptionsForSavedStrategy ( const CArgs args)

◆ SetOptionsHandle()

void CBlastAppArgs::SetOptionsHandle ( CRef< CBlastOptionsHandle opts_hndl)
inline

Setter for the BLAST options handle, this is used if the options are recovered from a saved BLAST search strategy.

Definition at line 1432 of file blast_args.hpp.

References m_OptsHandle.

◆ SetTask()

void CBlastAppArgs::SetTask ( const string task)

Set the task for this object.

Parameters
tasktask name to set [in]

Definition at line 3622 of file blast_args.cpp.

References m_Task, and ThrowIfInvalidTask().

Referenced by CBlastnVdbAppArgs::CBlastnVdbAppArgs(), CRPSBlastAppArgs::CRPSBlastAppArgs(), CBlastnVdbAppArgs::x_CreateOptionsHandle(), and x_CreateOptionsHandleWithTask().

◆ x_CreateOptionsHandle()

virtual CRef<CBlastOptionsHandle> CBlastAppArgs::x_CreateOptionsHandle ( CBlastOptions::EAPILocality  locality,
const CArgs args 
)
protectedpure virtual

Create the options handle based on the command line arguments.

Parameters
localitywhether the search will be executed locally or remotely [in]
argscommand line arguments [in]

Implemented in CTblastnVdbAppArgs, CBlastnVdbAppArgs, CTblastxAppArgs, CTblastnNodeArgs, CTblastnAppArgs, CRPSTBlastnNodeArgs, CRPSTBlastnAppArgs, CRPSBlastNodeArgs, CRPSBlastAppArgs, CRMBlastnAppArgs, CPsiBlastAppArgs, CMagicBlastAppArgs, CKBlastpAppArgs, CIgBlastpAppArgs, CIgBlastnAppArgs, CDeltaBlastAppArgs, CBlastxNodeArgs, CBlastxAppArgs, CBlastpNodeArgs, CBlastpAppArgs, CBlastnNodeArgs, and CBlastnAppArgs.

Referenced by SetOptions().

◆ x_CreateOptionsHandleWithTask()

CRef< CBlastOptionsHandle > CBlastAppArgs::x_CreateOptionsHandleWithTask ( CBlastOptions::EAPILocality  locality,
const string task 
)
protected

Creates the BLAST options handle based on the task argument.

Parameters
localitywhether the search will be executed locally or remotely [in]
taskprogram-specific BLAST named parameter set [in]

Definition at line 3666 of file blast_args.cpp.

References _ASSERT, CBlastOptionsFactory::CreateTask(), GetTask(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), and SetTask().

Referenced by CBlastnAppArgs::x_CreateOptionsHandle(), CBlastpAppArgs::x_CreateOptionsHandle(), CBlastxAppArgs::x_CreateOptionsHandle(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CIgBlastpAppArgs::x_CreateOptionsHandle(), CRMBlastnAppArgs::x_CreateOptionsHandle(), and CTblastnAppArgs::x_CreateOptionsHandle().

◆ x_IssueWarningsForIgnoredOptions()

void CBlastAppArgs::x_IssueWarningsForIgnoredOptions ( const CArgs args)
protected

Issue warnings when recovering from a search strategy (command line applications only)

Definition at line 3678 of file blast_args.cpp.

References a, BLAST_EXPECT_VALUE, BLAST_GAP_TRIGGER_NUCL, BLAST_GAP_TRIGGER_PROT, BLAST_GENETIC_CODE, Blast_ProgramIsRpsBlast(), Blast_QueryIsProtein(), NStr::DoubleToString(), map_checker< Container >::end(), set< Key, Compare >::end(), ERR_POST, NStr::Find(), map_checker< Container >::find(), set< Key, Compare >::find(), CArgs::GetAll(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), set< Key, Compare >::insert(), NStr::IntToString(), ITERATE, kArgCompBasedStats, kArgDb, kArgDbGeneticCode, kArgDbHardMask, kArgDbSize, kArgDbSoftMask, kArgDustFiltering, kArgEntrezQuery, kArgEvalue, kArgGapTrigger, kArgIndexName, kArgInputSearchStrategy, kArgLookupTableMaskingOnly, kArgMaskLevel, kArgMaxIntronLength, kArgMaxTargetSequences, kArgNumAlignments, kArgNumDescriptions, kArgNumThreads, kArgOffDiagonalRange, kArgOldStyleIndex, kArgOutput, kArgOutputFormat, kArgParseDeflines, kArgPSIInclusionEThreshold, kArgPSINumIterations, kArgPSIPseudocount, kArgQuery, kArgQueryGeneticCode, kArgQueryLocation, kArgRemote, kArgSegFiltering, kArgStrand, kArgSubject, kArgSubjectLocation, kArgUseIndex, kArgUseLCaseMasking, kDfltArgCompBasedStats, kDfltArgCompBasedStatsDelta, kDfltArgDustFiltering, kDfltArgLookupTableMaskingOnlyNucl, kDfltArgLookupTableMaskingOnlyProt, kDfltArgMaskLevel, kDfltArgMaxIntronLength, kDfltArgNoFiltering, kDfltArgOldStyleIndex, kDfltArgPSINumIterations, kDfltArgSegFiltering, kDfltOffDiagonalRange, kTask, m_OptsHandle, m_Task, NPOS, prog, PSI_INCLUSION_ETHRESH, PSI_PSEUDO_COUNT_CONST, and Warning().

Referenced by SetOptionsForSavedStrategy().

Member Data Documentation

◆ m_Args

TBlastCmdLineArgs CBlastAppArgs::m_Args
protected

◆ m_BlastDbArgs

CRef<CBlastDatabaseArgs> CBlastAppArgs::m_BlastDbArgs
protected

◆ m_ClientId

string CBlastAppArgs::m_ClientId
protected

Client ID used for remote BLAST submissions, must be populated by subclasses.

Definition at line 1540 of file blast_args.hpp.

Referenced by CBlastnVdbAppArgs::CBlastnVdbAppArgs(), CIgBlastnAppArgs::CIgBlastnAppArgs(), CIgBlastpAppArgs::CIgBlastpAppArgs(), CRPSBlastAppArgs::CRPSBlastAppArgs(), and GetClientId().

◆ m_DebugArgs

CRef<CDebugArgs> CBlastAppArgs::m_DebugArgs
protected

◆ m_FormattingArgs

CRef<CFormattingArgs> CBlastAppArgs::m_FormattingArgs
protected

◆ m_HspFilteringArgs

CRef<CHspFilteringArgs> CBlastAppArgs::m_HspFilteringArgs
protected

HSP filtering arguments.

Definition at line 1532 of file blast_args.hpp.

Referenced by CBlastnVdbAppArgs::CBlastnVdbAppArgs().

◆ m_IsUngapped

bool CBlastAppArgs::m_IsUngapped
protected

◆ m_MTArgs

CRef<CMTArgs> CBlastAppArgs::m_MTArgs
protected

◆ m_OptsHandle

CRef<CBlastOptionsHandle> CBlastAppArgs::m_OptsHandle
protected

The BLAST options handle, only non-NULL if assigned via SetOptionsHandle, i.e.

: from a saved search strategy

Definition at line 1535 of file blast_args.hpp.

Referenced by SetOptions(), SetOptionsForSavedStrategy(), SetOptionsHandle(), and x_IssueWarningsForIgnoredOptions().

◆ m_QueryOptsArgs

CRef<CQueryOptionsArgs> CBlastAppArgs::m_QueryOptsArgs
protected

◆ m_RemoteArgs

CRef<CRemoteArgs> CBlastAppArgs::m_RemoteArgs
protected

◆ m_SearchStrategyArgs

CRef<CSearchStrategyArgs> CBlastAppArgs::m_SearchStrategyArgs
protected

◆ m_StdCmdLineArgs

CRef<CStdCmdLineArgs> CBlastAppArgs::m_StdCmdLineArgs
protected

◆ m_Task

string CBlastAppArgs::m_Task
protected

Task specified in the command line.

Definition at line 1537 of file blast_args.hpp.

Referenced by GetTask(), SetTask(), and x_IssueWarningsForIgnoredOptions().


The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:40:36 2024 by modify_doxy.py rev. 669887