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NCBI C++ ToolKit: include/objtools/data_loaders/asn_cache/dump_asn_index.hpp Source File

1 #ifndef DUMP_ASN_INDEX_HPP__ 2 #define DUMP_ASN_INDEX_HPP__ 82 inline

std::ostream &

operator<<

( std::ostream & the_stream,

85  return

the_stream << the_sat_satkey_range.

AsString

();

89 inline bool operator==

(

const

ncbi::SSatSatKey& this_one,

const

ncbi::SSatSatKey& other_one )

91  return

( this_one.m_Sat == other_one.m_Sat )

92

&& (this_one.m_SatKey== other_one.m_SatKey );

102

,

size_t

max_bad_blob_count = 0

103

,

unsigned int

thread_count = 1

124  const CTime

& timestamp,

149  void x_CreateBlob

(

const

objects::CSeq_entry & entry,

const CTime

& timestamp );

User-defined methods of the data storage class.

This is a simple BDB structure holding information about a given accession and its indexed location.

objects::CCache_blob m_CacheBlob

CTempStopWatch< EIsInstantiated > m_BuildIndexEntrySW

CTempStopWatch< EIsInstantiated > m_DumpSW

size_t GetBadBlobCount() const

std::vector< SSatSatKey > GetBadBlobList() const

void x_BuildIndexAndSeqIdInfo(const objects::CSeq_entry &entry)

CDumpASNIndex(const std::string &root_dir_path, SSatSatKeyRange sat_id, size_t max_bad_blob_count=0, unsigned int thread_count=1)

std::vector< SSatSatKey > m_BadBlobList

std::string m_RootDirPath

const std::string & GetRootDir()

bool IsBusyIndexing() const

void DumpBlob(const CRef< objects::CSeq_entry > entry, const CTime &timestamp, SSatSatKey blob_id)

CTempStopWatch< EIsInstantiated > m_CreateBlobSW

Uint4 x_GetTaxId(const objects::CBioseq &bio_seq)

CSeqIdChunkFile m_SeqIdChunkFile

unsigned int m_ThreadCount

CTempStopWatch< EIsInstantiated > m_WriteBlobSW

void x_CreateBlob(const objects::CSeq_entry &entry, const CTime &timestamp)

Include a standard set of the NCBI C++ Toolkit most basic headers.

const Uint2 kMinorVersion

std::ostream & operator<<(std::ostream &the_stream, const SSatSatKeyRange &the_sat_satkey_range)

bool operator==(const ncbi::SSatSatKey &this_one, const ncbi::SSatSatKey &other_one)

const Uint2 kMajorVersion

void SetCacheSize(unsigned int cache_size)

Set Berkeley DB memory cache size for the file (default is 256K).

void Open(const string &filename, EOpenMode open_mode, bool support_dirty_read=false, unsigned rec_len=0)

Open file with specified access mode.

@ eReadWriteCreate

read-write, create if it doesn't exist

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned 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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

SSatSatKeyRange(Uint2 sat, Uint4 sat_key_start, Uint4 sat_key_end)

SSatSatKey(Uint2 sat, Uint4 sat_key)

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