Access data in Minhash files. More...

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

Inheritance diagram for CMinHashFile:

Collaboration diagram for CMinHashFile:

Public Member Functions
	CMinHashFile (const string &indexname)
	parameterized constructor More...

int	GetVersion (void) const

int	GetNumSeqs (void) const

int	GetNumHashes (void) const
	Returns the number of values in an array of hashes (probably 32) More...

int	GetSegStatus (void) const

int	GetKmerSize (void) const
	Returns the length of the KMER. More...

int	GetRows (void) const

int	GetDataWidth (void) const

int	GetAlphabet (void) const
	One of two alphabets from Shiryev et al. More...

int	GetLSHSize (void) const

int	GetLSHStart (void) const

uint64_t	GetLSHMatchEnd (void) const

int	GetChunkSize (void) const
	Get number of letters in a chunk (version 3 or higher) More...

uint32_t *	GetRandomNumbers (void) const

void	GetBadMers (vector< int > &badMers) const
	Overrepresented KMERs. More...

unsigned char *	GetKValues (void) const
	LSH points for Buhler approach. More...

uint64_t *	GetLSHArray (void) const

int *	GetHits (uint64_t offset) const

uint32_t *	GetMinHits (int oid) const

void	GetMinHits (int oid, int &subjectOid, vector< uint32_t > &hits) const
	Gets the database OID and vector of hash values for entry given by oid. More...

int	GetNumSignatures () const
	Returns the number of hash arrays. 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 Member Functions
uint32_t *	x_GetMinHits32 (int oid, int &subjectOid) const

uint16_t *	x_GetMinHits16 (int oid, int &subjectOid) const

unsigned char *	x_GetMinHits8 (int oid, int &subjectOid) const

void	x_Init ()

Private Attributes
unique_ptr< CMemoryFile >	m_MmappedIndex

unique_ptr< CMemoryFile >	m_MmappedData

MinHashIndexHeader *	m_Data

unsigned char *	m_MinHitsData
	Pointer to start of min-hits arrays. More...

Int8	m_DataFileSize
	m_MmappedData File size More...

string	m_IndexName
	Name of the index file. 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...