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CKBlastpArgs Class Reference

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Argument class to collect options specific to KBLASTP. More...

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

+ Inheritance diagram for CKBlastpArgs:
+ Collaboration diagram for CKBlastpArgs:

Public Member Functions

 CKBlastpArgs (void)
 Constructor. More...
 
virtual ~CKBlastpArgs ()
 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...
 
double GetJaccardDistance (void)
 Get the Jaccard distance. More...
 
int GetMinHits (void)
 Get the minimum number of LSH matches. More...
 
string GetDatabase (void)
 The database. More...
 
int GetCandidateSeqs (void)
 Number of candidate sequences to attempt with BLASTP. 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

 CKBlastpArgs (const CKBlastpArgs &rhs)
 Prohibit copy constructor. More...
 
CKBlastpArgsoperator= (const CKBlastpArgs &rhs)
 Prohibit assignment operator. More...
 

Private Attributes

double m_JDistance
 Jaccard distance. More...
 
int m_MinHits
 Minimum number of hits in LSH phase. More...
 
string m_DbIndex
 Database/index. More...
 
int m_CandidateSeqs
 Number of candidate sequences to try BLAST on. 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 KBLASTP.

Definition at line 669 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CKBlastpArgs() [1/2]

CKBlastpArgs::CKBlastpArgs ( void  )
inline

Constructor.

Definition at line 674 of file blast_args.hpp.

◆ ~CKBlastpArgs()

virtual CKBlastpArgs::~CKBlastpArgs ( )
inlinevirtual

Our virtual destructor.

Definition at line 677 of file blast_args.hpp.

◆ CKBlastpArgs() [2/2]

CKBlastpArgs::CKBlastpArgs ( const CKBlastpArgs rhs)
private

Prohibit copy constructor.

Member Function Documentation

◆ ExtractAlgorithmOptions()

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

◆ GetCandidateSeqs()

int CKBlastpArgs::GetCandidateSeqs ( void  )
inline

Number of candidate sequences to attempt with BLASTP.

Definition at line 696 of file blast_args.hpp.

References m_CandidateSeqs.

◆ GetDatabase()

string CKBlastpArgs::GetDatabase ( void  )
inline

The database.

Definition at line 693 of file blast_args.hpp.

References m_DbIndex.

◆ GetJaccardDistance()

double CKBlastpArgs::GetJaccardDistance ( void  )
inline

Get the Jaccard distance.

Definition at line 687 of file blast_args.hpp.

References m_JDistance.

◆ GetMinHits()

int CKBlastpArgs::GetMinHits ( void  )
inline

Get the minimum number of LSH matches.

Definition at line 690 of file blast_args.hpp.

References m_MinHits.

◆ operator=()

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

Prohibit assignment operator.

◆ SetArgumentDescriptions()

void CKBlastpArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

Member Data Documentation

◆ m_CandidateSeqs

int CKBlastpArgs::m_CandidateSeqs
private

Number of candidate sequences to try BLAST on.

Definition at line 714 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetCandidateSeqs().

◆ m_DbIndex

string CKBlastpArgs::m_DbIndex
private

Database/index.

Definition at line 711 of file blast_args.hpp.

Referenced by GetDatabase().

◆ m_JDistance

double CKBlastpArgs::m_JDistance
private

Jaccard distance.

Definition at line 705 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetJaccardDistance().

◆ m_MinHits

int CKBlastpArgs::m_MinHits
private

Minimum number of hits in LSH phase.

Definition at line 708 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetMinHits().


The documentation for this class was generated from the following files:
Modified on Thu Feb 29 12:17:12 2024 by modify_doxy.py rev. 669887