NCBI C++ ToolKit
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CCompositionBasedStatsArgs Class Reference

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Argument class for collecting composition based statistics options. More...

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

+ Inheritance diagram for CCompositionBasedStatsArgs:
+ Collaboration diagram for CCompositionBasedStatsArgs:

Public Member Functions

 CCompositionBasedStatsArgs (bool is_2and3supported=true, const string &default_option=kDfltArgCompBasedStats, const string &zero_option_descr="")
 Constructor. More...
 
virtual void SetArgumentDescriptions (CArgDescriptions &arg_desc)
 Interface method,. More...
 
virtual void ExtractAlgorithmOptions (const CArgs &cmd_line_args, CBlastOptions &options)
 Interface method,. 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
 

Protected Attributes

bool m_Is2and3Supported
 Are options 2 and 3 supported. More...
 
string m_DefaultOpt
 Default option. More...
 
string m_ZeroOptDescr
 Non standard description for option zero. 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 for collecting composition based statistics options.

Definition at line 372 of file blast_args.hpp.

Constructor & Destructor Documentation

CCompositionBasedStatsArgs::CCompositionBasedStatsArgs ( bool  is_2and3supported = true,
const string default_option = kDfltArgCompBasedStats,
const string zero_option_descr = "" 
)
inline

Constructor.

Parameters
is_2and3supportedAre composition based statistics options 2 and 3 supported [in]
default_optionDefault composition based satatistics option [in]
zero_option_descrNon-standard description for composition based statistics option zero [in]

Definition at line 381 of file blast_args.hpp.

Member Function Documentation

void CCompositionBasedStatsArgs::ExtractAlgorithmOptions ( const CArgs cmd_line_args,
CBlastOptions options 
)
virtual
void CCompositionBasedStatsArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

Member Data Documentation

string CCompositionBasedStatsArgs::m_DefaultOpt
protected

Default option.

Definition at line 399 of file blast_args.hpp.

Referenced by SetArgumentDescriptions().

bool CCompositionBasedStatsArgs::m_Is2and3Supported
protected

Are options 2 and 3 supported.

Definition at line 397 of file blast_args.hpp.

Referenced by SetArgumentDescriptions().

string CCompositionBasedStatsArgs::m_ZeroOptDescr
protected

Non standard description for option zero.

Definition at line 401 of file blast_args.hpp.

Referenced by SetArgumentDescriptions().


The documentation for this class was generated from the following files:
Modified on Mon Apr 23 11:40:07 2018 by modify_doxy.py rev. 546573