NCBI C++ ToolKit
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CBlastSequenceSource Class Reference

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#include <algo/align/splign/compart_matching.hpp>

+ Inheritance diagram for CBlastSequenceSource:
+ Collaboration diagram for CBlastSequenceSource:

Public Member Functions

 CBlastSequenceSource (const string &db)
 
virtual ~CBlastSequenceSource (void)
 
virtual Uint8 GetTotalLength (void)
 
virtual int GetNumSeqs (void)
 
virtual bool GetNext (void)
 
virtual int GetSeqLength (int idx)
 
virtual void SetMemoryBound (Uint8)
 
virtual int GetSeq (int idx, const char **buffer)
 
virtual void RetSequence (const char **buffer)
 
virtual CConstRef< CSeq_idGetSeqID (int idx)
 
virtual int GetSeq (const char **buffer)
 
virtual int GetSeq (int idx, const char **buffer)
 
virtual int GetSeqLength (int idx)
 
virtual int GetSeqLength (void)
 
virtual CConstRef< CSeq_idGetSeqID (int idx)
 
virtual CConstRef< CSeq_idGetSeqID ()
 
- Public Member Functions inherited from ISequenceSource
virtual void ResetIndex (void)
 
virtual int GetCurrentIndex ()
 
virtual int GetSeq (const char **buffer)
 
virtual ~ISequenceSource (void)
 

Protected Attributes

CRef< CSeqDBm_seqdb
 
- Protected Attributes inherited from ISequenceSource
int m_idx
 
vector< char > m_seq
 

Static Protected Attributes

static vector< CSeq_id_Handles_ids
 

Private Member Functions

virtual const vector< CSeq_id_Handle > & GetIds (void) const
 
virtual CBioseq_Handle GetSequence (const CSeq_id_Handle &)
 

Detailed Description

Definition at line 108 of file compart_matching.hpp.

Constructor & Destructor Documentation

◆ CBlastSequenceSource()

CBlastSequenceSource::CBlastSequenceSource ( const string db)
inline

Definition at line 119 of file compart_matching.hpp.

◆ ~CBlastSequenceSource()

virtual CBlastSequenceSource::~CBlastSequenceSource ( void  )
inlinevirtual

Definition at line 120 of file compart_matching.hpp.

Member Function Documentation

◆ GetIds()

virtual const vector<CSeq_id_Handle>& CBlastSequenceSource::GetIds ( void  ) const
inlineprivatevirtual

Implements ISequenceSource.

Definition at line 111 of file compart_matching.hpp.

References s_ids.

◆ GetNext()

virtual bool CBlastSequenceSource::GetNext ( void  )
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 124 of file compart_matching.hpp.

References CSeqDB::CheckOrFindOID(), ISequenceSource::m_idx, and m_seqdb.

◆ GetNumSeqs()

virtual int CBlastSequenceSource::GetNumSeqs ( void  )
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 123 of file compart_matching.hpp.

References CSeqDB::GetNumSeqs(), and m_seqdb.

◆ GetSeq() [1/3]

virtual int ISequenceSource::GetSeq ( void  )
inline

Definition at line 84 of file compart_matching.hpp.

References buffer, ISequenceSource::GetSeq(), and ISequenceSource::m_idx.

◆ GetSeq() [2/3]

virtual int ISequenceSource::GetSeq ( void  )
inline

◆ GetSeq() [3/3]

virtual int CBlastSequenceSource::GetSeq ( int  idx,
const char **  buffer 
)
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 130 of file compart_matching.hpp.

References buffer, CSeqDB::GetSequence(), and m_seqdb.

◆ GetSeqID() [1/3]

virtual CConstRef<CSeq_id> ISequenceSource::GetSeqID ( void  )
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 98 of file compart_matching.hpp.

References ISequenceSource::GetSeqID(), and ISequenceSource::m_idx.

◆ GetSeqID() [2/3]

virtual CConstRef<CSeq_id> ISequenceSource::GetSeqID ( void  )
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 97 of file compart_matching.hpp.

References ISequenceSource::GetIds().

◆ GetSeqID() [3/3]

virtual CConstRef<CSeq_id> CBlastSequenceSource::GetSeqID ( int  idx)
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 132 of file compart_matching.hpp.

References CSeqDB::GetSeqIDs(), and m_seqdb.

◆ GetSeqLength() [1/3]

virtual int ISequenceSource::GetSeqLength ( void  )
inlinevirtual

◆ GetSeqLength() [2/3]

virtual int CBlastSequenceSource::GetSeqLength ( int  idx)
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 128 of file compart_matching.hpp.

References CSeqDB::GetSeqLength(), and m_seqdb.

◆ GetSeqLength() [3/3]

virtual int ISequenceSource::GetSeqLength ( void  )
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 82 of file compart_matching.hpp.

References ISequenceSource::GetSeqLength(), and ISequenceSource::m_idx.

◆ GetSequence()

virtual CBioseq_Handle CBlastSequenceSource::GetSequence ( const CSeq_id_Handle )
inlineprivatevirtual

Implements ISequenceSource.

Definition at line 112 of file compart_matching.hpp.

◆ GetTotalLength()

virtual Uint8 CBlastSequenceSource::GetTotalLength ( void  )
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 122 of file compart_matching.hpp.

References CSeqDB::GetTotalLength(), and m_seqdb.

◆ RetSequence()

virtual void CBlastSequenceSource::RetSequence ( const char **  buffer)
inlinevirtual

Reimplemented from ISequenceSource.

Definition at line 131 of file compart_matching.hpp.

References buffer, m_seqdb, and CSeqDB::RetSequence().

◆ SetMemoryBound()

virtual void CBlastSequenceSource::SetMemoryBound ( Uint8  )
inlinevirtual

Definition at line 129 of file compart_matching.hpp.

Member Data Documentation

◆ m_seqdb

CRef<CSeqDB> CBlastSequenceSource::m_seqdb
protected

◆ s_ids

vector< CSeq_id_Handle > CBlastSequenceSource::s_ids
staticprotected

Definition at line 136 of file compart_matching.hpp.

Referenced by GetIds().


The documentation for this class was generated from the following files:
Modified on Sat May 18 11:36:03 2024 by modify_doxy.py rev. 669887