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NCBI C++ ToolKit: include/algo/blast/proteinkmer/mhfile.hpp Source File

( GetErrCode() ) {

eArgErr:

;

eFileEmpty:

;

(

)

{

m_Data->rows_per_band;}

(

)

{

(m_Data->dataWidth == 0 ? 4 : m_Data->dataWidth);}

GetBadMers(vector<int> &badMers)

;

GetMinHits(

oid,

& subjectOid, vector<uint32_t>& hits)

;

()

{

(m_DataFileSize/(GetDataWidth()*GetNumHashes()+4));}

* x_GetMinHits32(

oid,

& subjectOid)

;

* x_GetMinHits16(

oid,

& subjectOid)

;

* x_GetMinHits8(

oid,

& subjectOid)

;

Declares the BLAST exception class.

Defines to provide correct exporting from BLAST DLL in Windows.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

void GetRandomNumbers(uint32_t *a, uint32_t *b, int numHashes)

Get the random numbers for the hash function.

void GetKValues(vector< vector< int > > &kvector, int k_value, int l_value, int array_size)

Function to get the k sites to compare for Buhler LSH.

@ eArgErr

Argument validation failed.

@ eFileEmpty

Zero length files.

virtual const char * GetErrCodeString() const override

Get a message describing the situation leading to the throw.

NCBI_EXCEPTION_DEFAULT(CMinHashException, CException)

Include standard NCBI exception behavior.

Access data in Minhash files.

int GetLSHSize(void) const

int GetNumSignatures() const

Returns the number of hash arrays.

uint32_t * GetMinHits(int oid) const

int GetNumHashes(void) const

Returns the number of values in an array of hashes (probably 32)

uint64_t * GetLSHArray(void) const

string m_IndexName

Name of the index file.

unsigned char * m_MinHitsData

Pointer to start of min-hits arrays.

int GetVersion(void) const

unique_ptr< CMemoryFile > m_MmappedIndex

MinHashIndexHeader * m_Data

int GetNumSeqs(void) const

int GetDataWidth(void) const

unique_ptr< CMemoryFile > m_MmappedData

uint64_t GetLSHMatchEnd(void) const

int GetChunkSize(void) const

Get number of letters in a chunk (version 3 or higher)

int GetKmerSize(void) const

Returns the length of the KMER.

int GetSegStatus(void) const

int GetAlphabet(void) const

One of two alphabets from Shiryev et al.

int * GetHits(uint64_t offset) const

Int8 m_DataFileSize

m_MmappedData File size

int GetLSHStart(void) const

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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