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NCBI C++ ToolKit: CMinHashFile Class Reference
Search Toolkit Book for CMinHashFile
Access data in Minhash files. More...
#include <algo/blast/proteinkmer/mhfile.hpp>
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...
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...
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
Access data in Minhash files.
Definition at line 108 of file mhfile.hpp.
◆ CMinHashFile() CMinHashFile::CMinHashFile ( const string & indexname ) ◆ GetAlphabet() int CMinHashFile::GetAlphabet ( void ) const inline ◆ GetBadMers() void CMinHashFile::GetBadMers ( vector< int > & badMers ) const ◆ GetChunkSize() int CMinHashFile::GetChunkSize ( void ) const inline ◆ GetDataWidth() int CMinHashFile::GetDataWidth ( void ) const inline ◆ GetHits() ◆ GetKmerSize() int CMinHashFile::GetKmerSize ( void ) const inline ◆ GetKValues() unsigned char * CMinHashFile::GetKValues ( void ) const ◆ GetLSHArray() uint64_t* CMinHashFile::GetLSHArray ( void ) const inline ◆ GetLSHMatchEnd() uint64_t CMinHashFile::GetLSHMatchEnd ( void ) const inline ◆ GetLSHSize() int CMinHashFile::GetLSHSize ( void ) const inline ◆ GetLSHStart() int CMinHashFile::GetLSHStart ( void ) const inline ◆ GetMinHits() [1/2] ◆ GetMinHits() [2/2] void CMinHashFile::GetMinHits ( int oid, int & subjectOid, vector< uint32_t > & hits ) const ◆ GetNumHashes() int CMinHashFile::GetNumHashes ( void ) const inline
Returns the number of values in an array of hashes (probably 32)
Definition at line 118 of file mhfile.hpp.
References m_Data, and MinHashIndexHeader::num_hashes.
Referenced by BOOST_AUTO_TEST_CASE(), GetKValues(), GetMinHits(), GetNumSignatures(), CBlastKmer::Run(), s_BlastKmerVerifyVolume(), x_GetMinHits16(), x_GetMinHits32(), x_GetMinHits8(), and CBlastKmer::x_RunKmerFile().
◆ GetNumSeqs() int CMinHashFile::GetNumSeqs ( void ) const inline ◆ GetNumSignatures() int CMinHashFile::GetNumSignatures ( ) const inline ◆ GetRandomNumbers() uint32_t * CMinHashFile::GetRandomNumbers ( void ) const ◆ GetRows() int CMinHashFile::GetRows ( void ) const inline ◆ GetSegStatus() int CMinHashFile::GetSegStatus ( void ) const inline ◆ GetVersion() int CMinHashFile::GetVersion ( void ) const inline ◆ x_GetMinHits16() uint16_t * CMinHashFile::x_GetMinHits16 ( int oid, int & subjectOid ) const inlineprivate ◆ x_GetMinHits32() uint32_t * CMinHashFile::x_GetMinHits32 ( int oid, int & subjectOid ) const inlineprivate ◆ x_GetMinHits8() unsigned char * CMinHashFile::x_GetMinHits8 ( int oid, int & subjectOid ) const inlineprivate ◆ x_Init() void CMinHashFile::x_Init ( void ) private ◆ m_Data
Definition at line 180 of file mhfile.hpp.
Referenced by GetAlphabet(), GetChunkSize(), GetDataWidth(), GetKmerSize(), GetLSHMatchEnd(), GetLSHSize(), GetLSHStart(), GetNumHashes(), GetNumSeqs(), GetRows(), GetSegStatus(), GetVersion(), and x_Init().
◆ m_DataFileSize Int8 CMinHashFile::m_DataFileSize private ◆ m_IndexName string CMinHashFile::m_IndexName private ◆ m_MinHitsData unsigned char* CMinHashFile::m_MinHitsData private ◆ m_MmappedData ◆ m_MmappedIndex
The documentation for this class was generated from the following files:
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