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NCBI C++ ToolKit: include/objtools/blast/seqdb_writer/writedb_isam.hpp Source File

max_file_size=0);

AddIds(

oid,

& ids);

AddPig(

oid,

pig);

AddHash(

oid,

);

CanFit(

num);

()

;

eMaxStringLine = 4096,

eIsamNumericType = 0,

x_FlushNumericIndex();

x_FlushStringIndex();

x_AddGis(

oid,

& idlist);

x_AddTraceIds(

oid,

& idlist);

x_AddStringIds(

oid,

& idlist);

x_AddPdb(

oid,

& seqid);

x_AddLocal(

oid,

& seqid);

x_AddPatent(

oid,

& seqid);

x_AddTextId(

oid,

x_AddStringData(oid, s.data(), (

) s.size());

x_AddStringData(oid, s.

(), (

) s.

());

x_AddStringData(

oid,

* s,

);

x_AddString(

oid,

& s,

ver);

x_WriteHeader();

(

= 0;

< s.size();

++) {

max_file_size);

AddIds(

oid,

& ids);

AddPig(

oid,

pig);

AddHash(

oid,

);

CanFit(

num);

ListFiles(vector<string> & files)

;

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CWriteDB_IndexFile class.

virtual void RenameFileIndex(unsigned int num_digits)

void Close()

Close the file, flushing any remaining data to disk.

virtual void x_Flush()=0

This should flush any unwritten data to disk.

virtual void RenameSingle()

Rename this file, disincluding the volume index.

EWriteDBIsamType EIsamType

Type of identifier stored in this ISAM index.

CWriteDB_IsamIndex class.

EWriteDBIsamType EIsamType

Type of identifier stored in this ISAM index.

bool m_UseInt8

Use an Int8 table for numeric IDs.

void x_ToLower(string &s)

Convert a string to lower case in-place.

void x_AddStringData(int oid, const CTempString &s)

Add a string to the string table.

Uint8 m_DataFileSize

Accumulated size of data file.

EIsamType m_Type

Type of identifier indexed here.

CRef< CWriteDB_IsamData > m_DataFile

The data file associated with this index file.

vector< SIdOid > m_NumberTable

Sorted list of numbers.

CWriteDB_PackedSemiTree m_StringSort

Sorted list of strings.

int m_Oid

OID being to which seqid strings are being added.

vector< CRef< CSeq_id > > TIdList

Type used for lists of sequence identifiers.

int m_PageSize

Ratio of samples to data records.

set< string > m_OidStringData

Keep track of string seqids associated with current value of m_Oid.

bool m_Sparse

If true, fewer strings are used.

void x_AddStdString(int oid, const string &s)

Add a string to the string table.

int m_BytesPerElem

Byte (over)estimate per Seq-id.

CRef< CWriteDB_IsamData > m_DFile

Data file, contains one record for each key/oid pair.

CRef< CWriteDB_IsamIndex > m_IFile

Index file, contains meta data and samples of the key/oid pairs.

vector< CRef< CSeq_id > > TIdList

Type used for lists of sequence identifiers.

EWriteDBIsamType EIsamType

Type of identifier stored in this ISAM index.

Packed string data container with sorting and iteration.

bool Empty(const CNcbiOstrstream &src)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const char * data(void) const

Return a pointer to the array represented.

size_type size(void) const

Return the length of the represented array.

#define NCBI_XOBJWRITE_EXPORT

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Element type for numeric tables.

SIdOid(Int8 i, int o)

Construct an object from oid and ident.

int oid() const

Return the oid.

Int8 id() const

Return the numeric identifier.

Code for database files construction.

EWriteDBIsamType

Type of ISAM index.

@ eAcc

Accession (string) Index.

@ ePig

Protein Identifier Group.

USING_SCOPE(objects)

Import definitions from the objects namespace.

vector< CRef< CSeq_id > > TIdList

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