NCBI C++ ToolKit
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CBlastKmerOptions Class Reference

Search Toolkit Book for CBlastKmerOptions

Class of optiosn for the KMEr search. More...

#include <algo/blast/proteinkmer/blastkmeroptions.hpp>

+ Inheritance diagram for CBlastKmerOptions:
+ Collaboration diagram for CBlastKmerOptions:

Public Member Functions

 CBlastKmerOptions ()
 Constructor. More...
 
 ~CBlastKmerOptions ()
 Destructor. More...
 
bool Validate () const
 Checks that options are valid. More...
 
double GetThresh () const
 Get the threshold. More...
 
void SetThresh (double thresh)
 Set the threshold. More...
 
int GetMinHits () const
 Get the number of LSH hits to initiate the calculation of the Jaccard distance. More...
 
void SetMinHits (int minhits)
 Set the minimum number of LSH hits to initiate a calculation of the Jaccard distance. More...
 
int GetNumTargetSeqs () const
 Gets the number of matches (subject sequences) to return. More...
 
void SetNumTargetSeqs (int matches)
 Sets the number of matches (subject sequences) to return. 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 Attributes

double m_Thresh
 value of the threshold More...
 
int m_MinHits
 Value of number of LSH hits to initiate the calculation of the Jaccard distance. More...
 
int m_NumTargetSeqs
 Number of matches to return. 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

Class of optiosn for the KMEr search.

Definition at line 46 of file blastkmeroptions.hpp.

Constructor & Destructor Documentation

◆ CBlastKmerOptions()

CBlastKmerOptions::CBlastKmerOptions ( )

Constructor.

Definition at line 38 of file blastkmeroptions.cpp.

◆ ~CBlastKmerOptions()

CBlastKmerOptions::~CBlastKmerOptions ( )
inline

Destructor.

Definition at line 53 of file blastkmeroptions.hpp.

Member Function Documentation

◆ GetMinHits()

int CBlastKmerOptions::GetMinHits ( void  ) const
inline

Get the number of LSH hits to initiate the calculation of the Jaccard distance.

Returning zero means CBlastKmer chooses a value based upon the alphabet.

Returns
integer

Definition at line 72 of file blastkmeroptions.hpp.

References m_MinHits.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmer::x_RunKmerFile().

◆ GetNumTargetSeqs()

int CBlastKmerOptions::GetNumTargetSeqs ( ) const
inline

Gets the number of matches (subject sequences) to return.

Returns
integer

Definition at line 83 of file blastkmeroptions.hpp.

References m_NumTargetSeqs.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmer::x_SearchMultipleQueries().

◆ GetThresh()

double CBlastKmerOptions::GetThresh ( ) const
inline

Get the threshold.

Returns
double between 0 and 1.

Definition at line 60 of file blastkmeroptions.hpp.

References m_Thresh.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmer::x_RunKmerFile().

◆ SetMinHits()

void CBlastKmerOptions::SetMinHits ( int  minhits)
inline

Set the minimum number of LSH hits to initiate a calculation of the Jaccard distance.

Setting to zero permits CBlastKmer to choose a value based upon the alphabet.

Definition at line 78 of file blastkmeroptions.hpp.

References m_MinHits.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmerSearch::Run().

◆ SetNumTargetSeqs()

void CBlastKmerOptions::SetNumTargetSeqs ( int  matches)
inline

Sets the number of matches (subject sequences) to return.

Zero indicates all.

Parameters
numinteger

Definition at line 88 of file blastkmeroptions.hpp.

References m_NumTargetSeqs.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmerSearch::Run().

◆ SetThresh()

void CBlastKmerOptions::SetThresh ( double  thresh)
inline

Set the threshold.

1 means (nearly) identical matches. the closer to zero, the lower the identity of the matches is likely to be.

Definition at line 66 of file blastkmeroptions.hpp.

References m_Thresh.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmerSearch::Run().

◆ Validate()

bool CBlastKmerOptions::Validate ( void  ) const

Checks that options are valid.

Definition at line 46 of file blastkmeroptions.cpp.

References m_MinHits, and m_NumTargetSeqs.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmer::CBlastKmer().

Member Data Documentation

◆ m_MinHits

int CBlastKmerOptions::m_MinHits
private

Value of number of LSH hits to initiate the calculation of the Jaccard distance.

Definition at line 97 of file blastkmeroptions.hpp.

Referenced by GetMinHits(), SetMinHits(), and Validate().

◆ m_NumTargetSeqs

int CBlastKmerOptions::m_NumTargetSeqs
private

Number of matches to return.

Definition at line 100 of file blastkmeroptions.hpp.

Referenced by GetNumTargetSeqs(), SetNumTargetSeqs(), and Validate().

◆ m_Thresh

double CBlastKmerOptions::m_Thresh
private

value of the threshold

Definition at line 93 of file blastkmeroptions.hpp.

Referenced by GetThresh(), and SetThresh().


The documentation for this class was generated from the following files:
Modified on Sun May 19 04:48:28 2024 by modify_doxy.py rev. 669887