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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__scope__src_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/blast/blastinput/blast_scope_src.hpp Source File

1 #ifndef ALGO_BLAST_BLASTINPUT___BLAST_SCOPE_SRC__HPP 2 #define ALGO_BLAST_BLASTINPUT___BLAST_SCOPE_SRC__HPP 68 

eUseBlastDbDataLoader = (0x1 << 0),

70 

eUseGenbankDataLoader = (0x1 << 1),

72 

eUseNoDataLoaders = (0x1 << 2),

73  eDefault

= (eUseBlastDbDataLoader | eUseGenbankDataLoader)

83

x_Init(options,

kEmptyStr

, load_proteins);

96

x_Init(options,

dbname

, protein_data);

107

m_UseFixedSizeSlices = !

value

;

190  void

RevokeBlastDbDataLoader();

209  void

x_InitBlastDatabaseDataLoader(

const string

&

dbname

,

EDbType

dbtype);

212  void

x_InitBlastDatabaseDataLoader(

CRef<CSeqDB>

db_handle);

214  void

x_InitGenbankDataLoader();

219  static const int

kBlastDbLoaderPriority = 80;

221  static const int

kGenbankLoaderPriority = 99;

Data loader implementation that uses the blast databases.

Defines to provide correct exporting from BLAST DLL in Windows.

EDbType

Describes the type of blast database to use.

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

string m_GbLoaderName

Name of the Genbank data loader.

string GetBlastDbLoaderName() const

Retrieves the BLAST database data loader name initialized by this instance.

string m_BlastDbLoaderName

Name of the BLAST database data loader.

CRef< objects::CObjectManager > m_ObjMgr

Our reference to the object manager.

SDataLoaderConfig m_Config

The configuration for this object.

CBlastDbDataLoader::EDbType EDbType

Convenience typedef.

bool operator==(const CEquivRange &A, const CEquivRange &B)

#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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_BLASTINPUT_EXPORT

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const GenericPointer< typename T::ValueType > T2 value

Configuration structure for the CBlastScopeSource.

bool m_UseGenbank

Use the Genbank data loader.

static const char * kDefaultProteinBlastDb

Default protein BLAST database to use for the BLAST DB data loaders.

string m_BlastDbName

Name of the BLAST database to use (non-empty if m_UseBlastDbs is true)

bool UseDataLoaders() const

Determine whether either of the data loaders should be used.

static const char * kDefaultNucleotideBlastDb

Default nucleotide BLAST database to use for the BLAST DB data loaders.

SDataLoaderConfig(bool load_proteins, EConfigOpts options=eDefault)

Constructor which relies on the configuration file to set the BLAST database to use.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

bool m_UseBlastDbs

Use the BLAST database data loaders.

bool m_UseFixedSizeSlices

Argument to configure BLAST database data loader.

EConfigOpts

Configuration options for the BlastScopeSource.

bool m_IsLoadingProteins

Is this intended to load protein sequences.

SDataLoaderConfig(const string &dbname, bool protein_data, EConfigOpts options=eDefault)

Constructor which allows the specification of a BLAST database to use to initialize the BLAST DB data...

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