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...

CObject &	operator= (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< Uint8 >	TCounter
	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

num integer

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:

include/algo/blast/proteinkmer/blastkmeroptions.hpp
src/algo/blast/proteinkmer/blastkmeroptions.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBlastKmerOptions()

◆ ~CBlastKmerOptions()

Member Function Documentation

◆ GetMinHits()

◆ GetNumTargetSeqs()

◆ GetThresh()

◆ SetMinHits()

◆ SetNumTargetSeqs()

◆ SetThresh()

◆ Validate()

Member Data Documentation

◆ m_MinHits

◆ m_NumTargetSeqs

◆ m_Thresh