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CDeltaBlastArgs Class Reference

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Argument class to collect options specific to DELTA-BLAST. More...

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

+ Inheritance diagram for CDeltaBlastArgs:
+ Collaboration diagram for CDeltaBlastArgs:

Public Member Functions

 CDeltaBlastArgs (void)
 Constructor. More...
 
virtual ~CDeltaBlastArgs ()
 Our virtual destructor. More...
 
virtual void SetArgumentDescriptions (CArgDescriptions &arg_desc)
 Interface method,. More...
 
virtual void ExtractAlgorithmOptions (const CArgs &cmd_line_args, CBlastOptions &options)
 Interface method,. More...
 
CRef< CSearchDatabaseGetDomainDatabase (void)
 Get domain database. More...
 
bool GetShowDomainHits (void) const
 Get show domain hits option value. More...
 
- Public Member Functions inherited from IBlastCmdLineArgs
virtual ~IBlastCmdLineArgs ()
 Our virtual destructor. 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
 

Private Member Functions

 CDeltaBlastArgs (const CDeltaBlastArgs &rhs)
 Prohibit copy constructor. More...
 
CDeltaBlastArgsoperator= (const CDeltaBlastArgs &rhs)
 Prohibit assignment operator. More...
 

Private Attributes

CRef< CSearchDatabasem_DomainDb
 Conserved Domain Database. More...
 
bool m_ShowDomainHits
 Is printing CDD hits requested. 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...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Argument class to collect options specific to DELTA-BLAST.

Definition at line 718 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CDeltaBlastArgs() [1/2]

CDeltaBlastArgs::CDeltaBlastArgs ( void  )
inline

Constructor.

Definition at line 723 of file blast_args.hpp.

◆ ~CDeltaBlastArgs()

virtual CDeltaBlastArgs::~CDeltaBlastArgs ( )
inlinevirtual

Our virtual destructor.

Definition at line 726 of file blast_args.hpp.

◆ CDeltaBlastArgs() [2/2]

CDeltaBlastArgs::CDeltaBlastArgs ( const CDeltaBlastArgs rhs)
private

Prohibit copy constructor.

Member Function Documentation

◆ ExtractAlgorithmOptions()

void CDeltaBlastArgs::ExtractAlgorithmOptions ( const CArgs cmd_line_args,
CBlastOptions options 
)
virtual

◆ GetDomainDatabase()

CRef<CSearchDatabase> CDeltaBlastArgs::GetDomainDatabase ( void  )
inline

Get domain database.

Definition at line 735 of file blast_args.hpp.

References m_DomainDb.

◆ GetShowDomainHits()

bool CDeltaBlastArgs::GetShowDomainHits ( void  ) const
inline

Get show domain hits option value.

Definition at line 739 of file blast_args.hpp.

References m_ShowDomainHits.

◆ operator=()

CDeltaBlastArgs& CDeltaBlastArgs::operator= ( const CDeltaBlastArgs rhs)
private

Prohibit assignment operator.

◆ SetArgumentDescriptions()

void CDeltaBlastArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

Member Data Documentation

◆ m_DomainDb

CRef<CSearchDatabase> CDeltaBlastArgs::m_DomainDb
private

Conserved Domain Database.

Definition at line 750 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetDomainDatabase().

◆ m_ShowDomainHits

bool CDeltaBlastArgs::m_ShowDomainHits
private

Is printing CDD hits requested.

Definition at line 753 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetShowDomainHits().


The documentation for this class was generated from the following files:
Modified on Mon Jun 24 05:22:00 2024 by modify_doxy.py rev. 669887