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...

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.

The documentation for this class was generated from the following files:

Public Member Functions