NCBI C++ ToolKit
Classes | Public Types | Public Member Functions | List of all members
CSequenceIStream Class Referenceabstract

Search Toolkit Book for CSequenceIStream

Class used to abstract reading nucleotide sequences from various sources. More...

#include <algo/blast/dbindex/sequence_istream.hpp>

+ Inheritance diagram for CSequenceIStream:

Classes

struct  CSeqData
 Type containing the sequence itself along with the masking information. More...
 
class  CSequenceIStream_Exception
 Class representing error conditions in the sequence stream. More...
 

Public Types

typedef CSeqData TSeqData
 Public alias for sequence info data type. More...
 
typedef TSeqData::TMask TMask
 Public alias for type containing masking info. More...
 
typedef Uint4 TStreamPos
 Type used to represent positions within a sequence stream. More...
 

Public Member Functions

virtual ~CSequenceIStream ()
 Object destructor. More...
 
virtual CRef< TSeqDatanext ()=0
 Extract the next sequence from the stream. More...
 
virtual void putback ()=0
 Roll back to the start of the previousely read sequence. More...
 

Detailed Description

Class used to abstract reading nucleotide sequences from various sources.

Definition at line 50 of file sequence_istream.hpp.

Member Typedef Documentation

◆ TMask

Public alias for type containing masking info.

Definition at line 114 of file sequence_istream.hpp.

◆ TSeqData

Public alias for sequence info data type.

Definition at line 113 of file sequence_istream.hpp.

◆ TStreamPos

Type used to represent positions within a sequence stream.

Definition at line 115 of file sequence_istream.hpp.

Constructor & Destructor Documentation

◆ ~CSequenceIStream()

virtual CSequenceIStream::~CSequenceIStream ( )
inlinevirtual

Object destructor.

Definition at line 118 of file sequence_istream.hpp.

Member Function Documentation

◆ next()

virtual CRef< TSeqData > CSequenceIStream::next ( )
pure virtual

Extract the next sequence from the stream.

(To be implemented by derived classes.)

Returns
Smart pointer to the sequence data. The contents of the value is convertible to false if no more sequences are available.

Implemented in CSequenceIStreamFasta, and CSequenceIStreamBlastDB.

Referenced by CSRSearchApplication::Run().

◆ putback()

virtual void CSequenceIStream::putback ( )
pure virtual

Roll back to the start of the previousely read sequence.

(To be implemented by derived classes.). If a derived class does not support this operation it should throw CSequenceIStream_Exception with error code eOpNotSupported.

Implemented in CSequenceIStreamFasta, and CSequenceIStreamBlastDB.


The documentation for this class was generated from the following file:
Modified on Sun Jun 23 05:16:09 2024 by modify_doxy.py rev. 669887