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NCBI C++ ToolKit: CCachedSeqDataForRemote Class Reference
Search Toolkit Book for CCachedSeqDataForRemote
This class defines a "bundle" of elements to cache which are then returned by CRemoteBlastDbAdapter. More...
#include "remote_blastdb_adapter.hpp"
(Private to src/objtools/data_loaders/blastdb.)
CCachedSeqDataForRemote () Default constructor, needed to insert objects in std::map. More...
void SetLength (TSeqPos length, bool use_fixed_size_slices) Sets the length of the sequence data for a given Bioseq. More...
TSeqPos GetLength () const Retrieve the sequence length. More...
void SetIdList (const IBlastDbAdapter::TSeqIdList &idlist) Sets the Seq-id's associated with a given sequence param idlist IDs to assign to this object [in]. More...
IBlastDbAdapter::TSeqIdList GetIdList () const Retrieve the Seq-id's associated with a given sequence. More...
void SetBioseq (CRef< CBioseq > bioseq) Set the Bioseq associated with a given sequence. More...
CRef< CBioseq > GetBioseq () const Retrieve the Bioseq associated with a given sequence. More...
bool IsValid () Returns true if this object has been properly initialized and it's ready to be used. More...
bool HasSequenceData (int begin, int end) Returns true if the requested range has sequence data already. More...
CRef< CSeq_data > & GetSeqDataChunk (int begin, int end) Access the sequence data chunk for a given starting and ending offset. More...
CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const
This class defines a "bundle" of elements to cache which are then returned by CRemoteBlastDbAdapter.
The actual data for this object comes from the remote BLAST databases accessed by the blast4 server.
Definition at line 47 of file remote_blastdb_adapter.hpp.
◆ CCachedSeqDataForRemote() CCachedSeqDataForRemote::CCachedSeqDataForRemote ( ) inline ◆ GetBioseq() CRef<CBioseq> CCachedSeqDataForRemote::GetBioseq ( void ) const inline ◆ GetIdList() ◆ GetLength() TSeqPos CCachedSeqDataForRemote::GetLength ( void ) const inline ◆ GetSeqDataChunk() ◆ HasSequenceData() bool CCachedSeqDataForRemote::HasSequenceData ( int begin, int end ) inline ◆ ilog2() Int4 CCachedSeqDataForRemote::ilog2 ( Int4 x ) inlineprivate ◆ IsValid() bool CCachedSeqDataForRemote::IsValid ( void ) inline ◆ SetBioseq() void CCachedSeqDataForRemote::SetBioseq ( CRef< CBioseq > bioseq ) inline ◆ SetIdList() ◆ SetLength() void CCachedSeqDataForRemote::SetLength ( TSeqPos length, bool use_fixed_size_slices ) inline ◆ x_CalculateNumberOfSlices() TSeqPos CCachedSeqDataForRemote::x_CalculateNumberOfSlices ( ) inlineprivate ◆ m_Bioseq ◆ m_IdList ◆ m_Length TSeqPos CCachedSeqDataForRemote::m_Length private ◆ m_SeqDataVector vector< CRef<CSeq_data> > CCachedSeqDataForRemote::m_SeqDataVector private ◆ m_UseFixedSizeSlices bool CCachedSeqDataForRemote::m_UseFixedSizeSlices private
Determines whether sequences should be fetched in fixed size slices or in incrementally larger sizes.
Definition at line 135 of file remote_blastdb_adapter.hpp.
The documentation for this class was generated from the following file:
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