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NCBI C++ ToolKit: src/algo/blast/blastinput/blast_scope_src.cpp Source File

m_UseFixedSizeSlices =

;

m_UseBlastDbs = (options & eUseBlastDbDataLoader) ?

:

;

m_UseGenbank = (options & eUseGenbankDataLoader) ?

:

;

m_BlastDbName.assign(

);

m_IsLoadingProteins = load_proteins;

x_LoadBlastDbDataLoaderConfig(

);

kDataLoadersConfig(

);

& kLoaders =

.

(

, kDataLoadersConfig);

kProtBlastDbLoaderConfig(

);

kNuclBlastDbLoaderConfig(

);

? kProtBlastDbLoaderConfig

: kNuclBlastDbLoaderConfig;

: m_Config(load_proteins)

<<

);

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().find(

) !=

) {

(

<<

<< e.

() <<

);

<<

);

<<

<< e.

());

(

<<

<< e.

() <<

);

(db_handle.

()) {

<<

);

}

(

exception& e) {

<<

<< e.what() <<

);

<<

);

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<< e.

());

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=

;

blastdb_loader_priority =

blastdb_loader_priority);

!(*

== rhs);

static const string kPrefixThread

Data loader implementation that uses the blast databases remotely.

static int s_CountBlastDbDataLoaders()

Counts the number of BLAST database data loaders registered in the object manager.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

EDbType

Describes the type of blast database to use.

@ eNucleotide

nucleotide database

@ eProtein

protein database

void AddDataLoaders(CRef< objects::CScope > scope)

Add the data loader configured in the object to the provided scope.

CBlastScopeSource(bool load_proteins=true, CObjectManager *objmgr=NULL)

Constructor which only registers the Genbank data loader.

static const int kGenbankLoaderPriority

Data loader priority for Genbank data loader.

string m_GbLoaderName

Name of the Genbank data loader.

string m_BlastDbLoaderName

Name of the BLAST database data loader.

static const int kBlastDbLoaderPriority

Data loader priority for BLAST database data loader (if multiple BLAST database data loaders are regi...

CRef< objects::CObjectManager > m_ObjMgr

Our reference to the object manager.

SDataLoaderConfig m_Config

The configuration for this object.

void x_InitGenbankDataLoader()

Initialize the Genbank data loader.

void x_InitBlastDatabaseDataLoader(const string &dbname, EDbType dbtype)

Initializes the BLAST database data loader.

CRef< objects::CScope > NewScope()

Create a new, properly configured CScope.

void RevokeBlastDbDataLoader()

Removes the BLAST database data loader from the object manager.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static CNcbiApplication * Instance(void)

Singleton method.

void SetPreopenConnection(bool preopen=true)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

const string & GetDBNameList() const

Get list of database names.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

TLoader * GetLoader(void) const

Get pointer to the loader.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void GetRegisteredNames(TRegisteredNames &names)

Get names of all registered data loaders.

vector< string > TRegisteredNames

bool RevokeDataLoader(CDataLoader &loader)

Revoke previously registered data loader.

@ kPriority_NotSet

Deprecated: use kPriority_Default instead.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

virtual bool HasEntry(const string &section, const string &name=kEmptyStr, TFlags flags=0) const

#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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Uint4 GetSequenceType(const CBioseq_Handle &bsh)

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

static SLJIT_INLINE sljit_ins nr(sljit_gpr dst, sljit_gpr src)

Configuration structure for the CBlastScopeSource.

bool operator!=(const SDataLoaderConfig &rhs) const

Inequality operator.

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)

void x_LoadDataLoadersConfig(const CNcbiRegistry &registry)

Load the DATA_LOADERS configuration value from the config file.

static const char * kDefaultNucleotideBlastDb

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

bool operator==(const SDataLoaderConfig &rhs) const

Equality operator.

bool m_UseBlastDbs

Use the BLAST database data loaders.

bool m_UseFixedSizeSlices

Argument to configure BLAST database data loader.

void x_LoadBlastDbDataLoaderConfig(const CNcbiRegistry &registry)

Load the BLAST database configured to search for the blastdb DATA_LOADERS option from the config file...

EConfigOpts

Configuration options for the BlastScopeSource.

bool m_IsLoadingProteins

Is this intended to load protein sequences.

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