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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/mhfile_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/proteinkmer/mhfile.cpp Source File

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59 string

errmsg =

m_IndexName

".pki has zero length"

;

67 string

errmsg =

m_IndexName

".pkd has zero length"

;

77 if

(hits.size() < numHashes)

78

hits.resize(numHashes);

84 for

(

int

index=0; index<numHashes; index++)

90 for

(

int

index=0; index<numHashes; index++)

96 for

(

int

index=0; index<numHashes; index++)

122 for

(

int i

=1;

<=num;

++)

123

badMers.push_back(

array

[

]);

142

subject_oid =

array

[num_hashes];

158 inline unsigned char

uint32_t * x_GetMinHits32(int oid, int &subjectOid) const

void GetBadMers(vector< int > &badMers) const

Overrepresented KMERs.

uint32_t * GetMinHits(int oid) const

int GetNumHashes(void) const

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

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

uint32_t * GetRandomNumbers(void) const

int GetDataWidth(void) const

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

CMinHashFile(const string &indexname)

parameterized constructor

unique_ptr< CMemoryFile > m_MmappedData

unsigned char * GetKValues(void) const

LSH points for Buhler approach.

Int8 m_DataFileSize

m_MmappedData File size

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

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#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.

#define KMER_RANDOM_NUM_OFFSET

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