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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bdbloader_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/data_loaders/blastdb/bdbloader.hpp Source File

1 #ifndef OBJTOOLS_DATA_LOADERS_BLASTDB___BDBLOADER__HPP 2 #define OBJTOOLS_DATA_LOADERS_BLASTDB___BDBLOADER__HPP 67 bool

use_fixed_size_slices =

true

);

70 bool

use_fixed_size_slices =

true

);

81 const string

dbname

"nr"

83 bool

use_fixed_size_slices =

true

89 bool

use_fixed_size_slices =

true

93 static string

GetLoaderNameFromArgs(

const SBlastDbParam

& param);

106 virtual

TTSE_LockSet GetRecords(

const CSeq_id_Handle

& idh, EChoice choice);

108 virtual void

GetChunk(TChunk chunk);

111 virtual void

GetTaxIds(

const

TIds& ids, TLoaded& loaded, TTaxIds& ret);

113 virtual void

GetSequenceLengths(

const

TIds& ids, TLoaded& loaded,

114

TSequenceLengths& ret);

116 virtual void

GetSequenceTypes(

const

TIds& ids, TLoaded& loaded,

117

TSequenceTypes& ret);

140 virtual bool

CanGetBlobById()

const

;

152 virtual

TTSE_Lock GetBlobById(

const

TBlobId& blob_id);

178 typedef

pair<TBioseqId, TBioseq_setId>

TPlace

;

199 int

x_GetOid(

const TBlobId

& blob_id)

const

;

void NCBI_EntryPoint_DataLoader_BlastDb(CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)

const string kDataLoader_BlastDb_DriverName

const string kCFParam_BlastDb_DbName

void NCBI_EntryPoint_xloader_blastdb(CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)

const string kCFParam_BlastDb_DbType

Interface definition of IBlastDbAdapter.

limited_size_map< CSeq_id_Handle, int > TIdMap

A mapping from sequence identifier to blob ids.

CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam > TMaker

static string GetLoaderNameFromArgs(const string &dbname="nr", const EDbType dbtype=eUnknown)

CRef< IBlastDbAdapter > m_BlastDb

The sequence database.

TIdMap m_Ids

ID to OID translation.

SRegisterLoaderInfo< CBlastDbDataLoader > TRegisterLoaderInfo

string m_DBName

Blast database name.

EDbType m_DBType

Is this database protein or nucleotide?

int TBioseq_setId

TPlace is a Seq-id or an integer id, this data loader uses the former.

CBlastDbDataLoader()

Default (no-op) constructor.

CBlastDbDataLoader & operator=(const CBlastDbDataLoader &)

Prevent automatic assignment operator generation.

EDbType

Describes the type of blast database to use.

pair< TBioseqId, TBioseq_setId > TPlace

CBlastDbDataLoader(const CBlastDbDataLoader &)

Prevent automatic copy constructor generation.

bool m_UseFixedSizeSlices

Configuration value specified to the CCachedSequence.

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

static unsigned char depth[2 *(256+1+29)+1]

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

EIsDefault

Flag defining if the data loader is included in the "default" group.

@ kPriority_NotSet

Deprecated: use kPriority_Default instead.

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

#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 NCBI_XLOADER_BLASTDB_EXPORT

EMol

molecule class in living organism

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Generic map with size limited by some number.

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

Return a (corrected) set of flags identifying the sequence type.

CRef< objects::CObjectManager > om

CRef< CSeqDB > m_BlastDbHandle

bool m_UseFixedSizeSlices

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