NCBI C++ ToolKit
|
Search Toolkit Book for CBlastSequenceSource
#include <algo/align/splign/compart_matching.hpp>
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_id > | GetSeqID (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_id > | GetSeqID (int idx) |
virtual CConstRef< CSeq_id > | GetSeqID () |
![]() | |
virtual void | ResetIndex (void) |
virtual int | GetCurrentIndex () |
virtual int | GetSeq (const char **buffer) |
virtual | ~ISequenceSource (void) |
Protected Attributes | |
CRef< CSeqDB > | m_seqdb |
![]() | |
int | m_idx |
vector< char > | m_seq |
Static Protected Attributes | |
static CSafeStatic< vector< CSeq_id_Handle > > | s_ids |
Private Member Functions | |
virtual const vector< CSeq_id_Handle > & | GetIds (void) const |
virtual CBioseq_Handle | GetSequence (const CSeq_id_Handle &) |
Definition at line 108 of file compart_matching.hpp.
Definition at line 119 of file compart_matching.hpp.
|
inlinevirtual |
Definition at line 120 of file compart_matching.hpp.
|
inlineprivatevirtual |
Implements ISequenceSource.
Definition at line 111 of file compart_matching.hpp.
References CSafeStatic< T, Callbacks >::Get(), and s_ids.
|
inlinevirtual |
Reimplemented from ISequenceSource.
Definition at line 124 of file compart_matching.hpp.
References CSeqDB::CheckOrFindOID(), ISequenceSource::m_idx, and m_seqdb.
|
inlinevirtual |
Reimplemented from ISequenceSource.
Definition at line 123 of file compart_matching.hpp.
References CSeqDB::GetNumSeqs(), and m_seqdb.
|
inline |
Definition at line 84 of file compart_matching.hpp.
References buffer, ISequenceSource::GetSeq(), and ISequenceSource::m_idx.
|
inline |
Definition at line 85 of file compart_matching.hpp.
References buffer, copy(), CSeq_data_Base::e_Ncbi2na, ISequenceSource::GetIds(), CSeqVector::GetPackedSeqData(), ISequenceSource::GetSequence(), CBioseq_Handle::GetSeqVector(), ISequenceSource::m_seq, CSeqVector::SetCoding(), CSeqVector::SetRandomizeAmbiguities(), and CSeqVector::size().
Reimplemented from ISequenceSource.
Definition at line 130 of file compart_matching.hpp.
References buffer, CSeqDB::GetSequence(), and m_seqdb.
Reimplemented from ISequenceSource.
Definition at line 98 of file compart_matching.hpp.
References ISequenceSource::GetSeqID(), and ISequenceSource::m_idx.
Reimplemented from ISequenceSource.
Definition at line 97 of file compart_matching.hpp.
References ISequenceSource::GetIds().
Reimplemented from ISequenceSource.
Definition at line 132 of file compart_matching.hpp.
References CSeqDB::GetSeqIDs(), and m_seqdb.
|
inlinevirtual |
Reimplemented from ISequenceSource.
Definition at line 81 of file compart_matching.hpp.
References CBioseq_Handle::eCoding_Iupac, ISequenceSource::GetIds(), ISequenceSource::GetSequence(), CBioseq_Handle::GetSeqVector(), and CSeqVector::size().
Reimplemented from ISequenceSource.
Definition at line 128 of file compart_matching.hpp.
References CSeqDB::GetSeqLength(), and m_seqdb.
|
inlinevirtual |
Reimplemented from ISequenceSource.
Definition at line 82 of file compart_matching.hpp.
References ISequenceSource::GetSeqLength(), and ISequenceSource::m_idx.
|
inlineprivatevirtual |
Implements ISequenceSource.
Definition at line 112 of file compart_matching.hpp.
|
inlinevirtual |
Reimplemented from ISequenceSource.
Definition at line 122 of file compart_matching.hpp.
References CSeqDB::GetTotalLength(), and m_seqdb.
|
inlinevirtual |
Reimplemented from ISequenceSource.
Definition at line 131 of file compart_matching.hpp.
References buffer, m_seqdb, and CSeqDB::RetSequence().
|
inlinevirtual |
Definition at line 129 of file compart_matching.hpp.
Definition at line 135 of file compart_matching.hpp.
Referenced by GetNext(), GetNumSeqs(), GetSeq(), GetSeqID(), GetSeqLength(), GetTotalLength(), and RetSequence().
|
staticprotected |
Definition at line 136 of file compart_matching.hpp.
Referenced by GetIds().