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NCBI C++ ToolKit: include/algo/blast/api/uniform_search.hpp Source File

( GetErrCode() ) {

eConfigErr:

;

eMemErr:

;

eInternal:

;

& entrez_query);

SetDatabaseName(

&

);

GetDatabaseName()

;

SetMoleculeType(EMoleculeType mol_type);

EMoleculeType GetMoleculeType()

;

GetMoleculeType() == eBlastDbIsProtein;

SetEntrezQueryLimitation(

& entrez_query);

GetEntrezQueryLimitation()

;

TGiList GetGiListLimitation()

;

TGiList GetNegativeGiListLimitation()

;

SetFilteringAlgorithm(

&filt_algorithm,

GetFilteringAlgorithm()

;

GetFilteringAlgorithmKey()

;

x_TranslateFilteringAlgorithm()

;

x_InitializeDb()

;

x_ValidateMaskingAlgorithm()

;

ESubjectMaskingType

Define the possible subject masking types.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definition of classes which constitute the results of running a BLAST search.

Definitions of special type used in BLAST.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

Experimental interface (since this does not provide a full interface to PSI-BLAST)

Single Iteration Blast Database Search.

Single Iteration Search of Sequence(s) Against Blast Database(s)

int m_FilteringAlgorithmId

virtual void SetSubject(CConstRef< CSearchDatabase > subject)=0

Set the subject database(s) to search.

bool m_NeedsFilteringTranslation

virtual void SetOptions(CRef< CBlastOptionsHandle > options)=0

Configure the search.

string m_EntrezQueryLimitation

entrez query

string m_FilteringAlgorithmString

filtering to apply to database sequences

virtual CRef< ISeqSearch > GetSeqSearch()=0

Create a new search object with a sequence-based query.

CRef< CSeqDBGiList > m_GiList

gi list

virtual void SetQuery(CRef< objects::CPssmWithParameters > pssm)=0

Set the queries to search.

virtual CRef< CBlastOptionsHandle > GetOptions(EProgram program)=0

Create a CBlastOptionsHandle.

virtual void SetQueryFactory(CRef< IQueryFactory > query_factory)=0

Set the queries to search.

bool IsProtein() const

Determine whether this database contains protein sequences or not.

string m_DbName

database name

EMoleculeType m_MolType

molecule type

vector< TGi > TGiList

Define a list of gis.

virtual const char * GetErrCodeString() const override

Get a message describing the situation leading to the throw.

virtual CRef< CSearchResultSet > Run()=0

Run the search to completion.

virtual ~ISeqSearch()

Destructor.

CRef< CSeqDBGiList > m_NegativeGiList

negative gi list

ESubjectMaskingType m_MaskType

virtual CRef< IPssmSearch > GetPssmSearch()=0

Create a new search object with a pssm-based query.

NCBI_EXCEPTION_DEFAULT(CSearchException, CException)

Include standard NCBI exception behavior.

EMoleculeType

Molecule of the BLAST database.

EErrCode

Errors are classified into one of two types.

@ eBlastDbIsProtein

protein

@ eMemErr

Memory allocation failed.

@ eConfigErr

Argument validation failed.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#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.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Defines BLAST database access classes.

Defines exception class and several constants for SeqDB.

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