NCBI C++ ToolKit
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CMaskBDBReader Class Reference

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Class for reading sequences from BLAST databases. More...

#include <objtools/seqmasks_io/mask_bdb_reader.hpp>

+ Inheritance diagram for CMaskBDBReader:
+ Collaboration diagram for CMaskBDBReader:

Public Member Functions

 CMaskBDBReader (const string &dbname, bool is_nucl=true)
 Object constructor. More...
virtual ~CMaskBDBReader ()
 Object destructor. More...
virtual CRef< objects::CSeq_entry > GetNextSequence ()
 Read next sequence from the database. More...
- Public Member Functions inherited from CMaskReader
 CMaskReader (CNcbiIstream &newInputStream)
 Object constructor. More...
virtual ~CMaskReader ()
 Object destructor. More...

Private Attributes

CRef< CSeqDBseqdb_
 BLAST database object. More...
CSeqDB::TOID oid_
 Current OID (to be read). More...

Additional Inherited Members

- Protected Attributes inherited from CMaskReader

Detailed Description

Class for reading sequences from BLAST databases.

Definition at line 45 of file mask_bdb_reader.hpp.

Constructor & Destructor Documentation

◆ CMaskBDBReader()

CMaskBDBReader::CMaskBDBReader ( const string dbname,
bool  is_nucl = true 

Object constructor.

dbnameBLAST database to read data from.

Definition at line 55 of file mask_bdb_reader.hpp.

◆ ~CMaskBDBReader()

virtual CMaskBDBReader::~CMaskBDBReader ( )

Object destructor.

Definition at line 67 of file mask_bdb_reader.hpp.

Member Function Documentation

◆ GetNextSequence()

CRef< CSeq_entry > CMaskBDBReader::GetNextSequence ( )

Read next sequence from the database.

pointer (reference counting) to the object containing information about the sequence, or CRef( NULL ) if end of file is reached.

Implements CMaskReader.

Definition at line 44 of file mask_bdb_reader.cpp.

References CSeqDB::GetBioseq(), CRef< C, Locker >::NotEmpty(), oid_, CRef< C, Locker >::Reset(), seqdb_, and CSeq_entry_Base::SetSeq().

Member Data Documentation

◆ oid_

CSeqDB::TOID CMaskBDBReader::oid_

Current OID (to be read).

Definition at line 82 of file mask_bdb_reader.hpp.

Referenced by GetNextSequence().

◆ seqdb_

CRef< CSeqDB > CMaskBDBReader::seqdb_

BLAST database object.

Definition at line 81 of file mask_bdb_reader.hpp.

Referenced by GetNextSequence().

The documentation for this class was generated from the following files:
Modified on Tue Apr 16 20:13:49 2024 by rev. 669887