NCBI C++ ToolKit
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CSeqDbSeqInfoSrc Class Reference

Search Toolkit Book for CSeqDbSeqInfoSrc

Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a BLAST database. More...

#include <algo/blast/api/seqinfosrc_seqdb.hpp>

+ Inheritance diagram for CSeqDbSeqInfoSrc:
+ Collaboration diagram for CSeqDbSeqInfoSrc:

Public Member Functions

 CSeqDbSeqInfoSrc (const string &dbname, bool is_protein)
 Constructor: includes initializing the CSeqDB object. More...
 
 CSeqDbSeqInfoSrc (ncbi::CSeqDB *seqdb)
 Constructor from an already existing CSeqDB object. More...
 
virtual ~CSeqDbSeqInfoSrc ()
 Our destructor. More...
 
void SetFilteringAlgorithmId (int algo_id)
 Sets the filtering algorithm ID used in the search. More...
 
virtual list< CRef< objects::CSeq_id > > GetId (Uint4 oid) const
 Retrieve a sequence identifier given its ordinal number. More...
 
virtual CConstRef< objects::CSeq_loc > GetSeqLoc (Uint4 oid) const
 Method to retrieve the sequence location given its ordinal number. More...
 
virtual Uint4 GetLength (Uint4 oid) const
 Retrieve sequence length given its ordinal number. More...
 
virtual size_t Size () const
 Returns the size of the underlying container of sequences. More...
 
virtual bool HasGiList () const
 Returns true if the subject is restricted by a GI list. More...
 
virtual bool GetMasks (Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const
 Retrieves the subject masks for the corresponding index. More...
 
virtual bool GetMasks (Uint4 index, const vector< TSeqRange > &target_ranges, TMaskedSubjRegions &retval) const
 Retrieves the subject masks for the corresponding index. More...
 
virtual bool CanReturnPartialSequence () const
 Return true if the implementation can return anything besides a seq-loc for the entire sequence. More...
 
- Public Member Functions inherited from IBlastSeqInfoSrc
virtual ~IBlastSeqInfoSrc ()
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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...
 
- Public Member Functions inherited from CDebugDumpable
 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
 

Private Attributes

CRef< CSeqDBm_iSeqDb
 BLAST database object. More...
 
int m_FilteringAlgoId
 Filtering algorithm ID used with these subjects, use -1 if not applicable. More...
 

Friends

class CBlastTracebackSearch
 Friend declaration so that this class can access the CSeqDB object to enable partial subject sequence fetching. More...
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a BLAST database.

Definition at line 52 of file seqinfosrc_seqdb.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:24:31 2024 by modify_doxy.py rev. 669887