NCBI C++ ToolKit
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CBlastSeqVectorFromCSeq_data Class Reference

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Implementation of the IBlastSeqVector interface which obtains data from a CSeq_data object. More...

#include "bioseq_extract_data_priv.hpp"
(Private to src/algo/blast/api.)

+ Inheritance diagram for CBlastSeqVectorFromCSeq_data:
+ Collaboration diagram for CBlastSeqVectorFromCSeq_data:

Public Member Functions

 CBlastSeqVectorFromCSeq_data (const objects::CSeq_data &seq_data, TSeqPos length)
 Parametrized constructor. More...
 
virtual void SetCoding (objects::CSeq_data::E_Choice c)
 @inheritDoc More...
 
virtual Uint1 operator[] (TSeqPos pos) const
 @inheritDoc More...
 
virtual SBlastSequence GetCompressedPlusStrand ()
 @inheritDoc More...
 
- Public Member Functions inherited from IBlastSeqVector
virtual ~IBlastSeqVector ()
 Our no-op virtual destructor. More...
 
TSeqPos size () const
 Returns the length of the sequence data (in the case of nucleotides, only one strand) More...
 
virtual void GetStrandData (objects::ENa_strand strand, unsigned char *buf)
 Retrieve strand data in one chunk. More...
 
void SetPlusStrand ()
 For nucleotide sequences this instructs the implementation to convert its representation to be that of the plus strand. More...
 
void SetMinusStrand ()
 For nucleotide sequences this instructs the implementation to convert its representation to be that of the minus strand. More...
 
objects::ENa_strand GetStrand () const
 Accessor for the strand currently set. More...
 

Protected Member Functions

virtual TSeqPos x_Size () const
 @inheritDoc More...
 
virtual void x_SetPlusStrand ()
 @inheritDoc More...
 
virtual void x_SetMinusStrand ()
 @inheritDoc More...
 

Private Member Functions

void x_ComplementData ()
 Complements the data in m_SequenceData in place. More...
 
CSeqUtil::ECoding x_Encoding_CSeq_data2CSeqUtil (objects::CSeq_data::E_Choice c)
 Auxiliary function to map the description of the encoding in CSeq_data::EChoice to CSeqUtil::ECoding. More...
 

Private Attributes

vector< char > m_SequenceData
 Container for the actual sequence data. More...
 
CSeqUtil::ECoding m_Encoding
 Encoding used in the data above. More...
 

Additional Inherited Members

- Protected Attributes inherited from IBlastSeqVector
objects::ENa_strand m_Strand
 Maintains the state of the strand currently saved by the implementation of this class. More...
 

Detailed Description

Implementation of the IBlastSeqVector interface which obtains data from a CSeq_data object.

Definition at line 66 of file bioseq_extract_data_priv.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:40:13 2024 by modify_doxy.py rev. 669887