NCBI C++ ToolKit
Public Member Functions | Protected Attributes | Private Member Functions | List of all members
ISequenceSource Class Referenceabstract

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

+ Inheritance diagram for ISequenceSource:
+ Collaboration diagram for ISequenceSource:

Public Member Functions

virtual Uint8 GetTotalLength (void)
 
virtual int GetNumSeqs (void)
 
virtual void ResetIndex (void)
 
virtual bool GetNext (void)
 
virtual int GetCurrentIndex ()
 
virtual int GetSeqLength (int idx)
 
virtual int GetSeqLength (void)
 
virtual int GetSeq (const char **buffer)
 
virtual int GetSeq (int idx, const char **buffer)
 
virtual void RetSequence (const char **)
 
virtual CConstRef< CSeq_idGetSeqID (int idx)
 
virtual CConstRef< CSeq_idGetSeqID ()
 
virtual ~ISequenceSource (void)
 

Protected Attributes

int m_idx
 
vector< char > m_seq
 

Private Member Functions

virtual const vector< CSeq_id_Handle > & GetIds (void) const =0
 
virtual CBioseq_Handle GetSequence (const CSeq_id_Handle &)=0
 

Detailed Description

Definition at line 57 of file compart_matching.hpp.

Constructor & Destructor Documentation

◆ ~ISequenceSource()

virtual ISequenceSource::~ISequenceSource ( void  )
inlinevirtual

Definition at line 101 of file compart_matching.hpp.

Member Function Documentation

◆ GetCurrentIndex()

virtual int ISequenceSource::GetCurrentIndex ( )
inlinevirtual

Definition at line 80 of file compart_matching.hpp.

References m_idx.

Referenced by CElementaryMatching::x_CreateRemapData().

◆ GetIds()

virtual const vector<CSeq_id_Handle>& ISequenceSource::GetIds ( void  ) const
privatepure virtual

◆ GetNext()

virtual bool ISequenceSource::GetNext ( void  )
inlinevirtual

◆ GetNumSeqs()

virtual int ISequenceSource::GetNumSeqs ( void  )
inlinevirtual

Reimplemented in CBlastSequenceSource.

Definition at line 73 of file compart_matching.hpp.

References GetIds().

Referenced by GetTotalLength(), and CElementaryMatching::x_CreateRemapData().

◆ GetSeq() [1/2]

virtual int ISequenceSource::GetSeq ( const char **  buffer)
inlinevirtual

◆ GetSeq() [2/2]

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

Reimplemented in CBlastSequenceSource.

Definition at line 85 of file compart_matching.hpp.

◆ GetSeqID() [1/2]

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

Reimplemented in CBlastSequenceSource, and CBlastSequenceSource.

Definition at line 98 of file compart_matching.hpp.

Referenced by CBlastSequenceSource::GetSeqID().

◆ GetSeqID() [2/2]

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

◆ GetSeqLength() [1/2]

virtual int ISequenceSource::GetSeqLength ( int  idx)
inlinevirtual

Reimplemented in CBlastSequenceSource.

Definition at line 81 of file compart_matching.hpp.

Referenced by CElementaryMatching::x_CreateRemapData().

◆ GetSeqLength() [2/2]

virtual int ISequenceSource::GetSeqLength ( void  )
inlinevirtual

Reimplemented in CBlastSequenceSource, and CBlastSequenceSource.

Definition at line 82 of file compart_matching.hpp.

Referenced by CBlastSequenceSource::GetSeqLength(), and GetTotalLength().

◆ GetSequence()

virtual CBioseq_Handle ISequenceSource::GetSequence ( const CSeq_id_Handle )
privatepure virtual

◆ GetTotalLength()

virtual Uint8 ISequenceSource::GetTotalLength ( void  )
inlinevirtual

Reimplemented in CBlastSequenceSource.

Definition at line 66 of file compart_matching.hpp.

References GetNumSeqs(), GetSeqLength(), and i.

Referenced by CElementaryMatching::x_CreateIndex().

◆ ResetIndex()

virtual void ISequenceSource::ResetIndex ( void  )
inlinevirtual

◆ RetSequence()

virtual void ISequenceSource::RetSequence ( const char **  )
inlinevirtual

Member Data Documentation

◆ m_idx

int ISequenceSource::m_idx
protected

◆ m_seq

vector<char> ISequenceSource::m_seq
protected

Definition at line 104 of file compart_matching.hpp.

Referenced by CBlastSequenceSource::GetSeq().


The documentation for this class was generated from the following file:
Modified on Sun May 19 04:47:06 2024 by modify_doxy.py rev. 669887