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CIndexedDb_Old Class Reference

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Index wrapper for old style MegaBLAST indexing functionality. More...

+ Inheritance diagram for CIndexedDb_Old:
+ Collaboration diagram for CIndexedDb_Old:

Public Member Functions

 CIndexedDb_Old (const string &indexname)
 Object constructor. More...
 
virtual int CheckOid (Int4 oid, Int4 *)
 Check whether any results were reported for a given subject sequence. More...
 
virtual void EndSearchIndication (Int4)
 Not used. More...
 
virtual void DoPreSearch (BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
 Wrapper around PreSearch(). More...
 
virtual unsigned long GetResults (CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const
 Return results corresponding to a given subject sequence and chunk. More...
 
- Public Member Functions inherited from CIndexedDb
virtual ~CIndexedDb ()
 Object destructor. More...
 
void SetQueryInfo (CRef< CBlastSeqLocWrap > locs_wrap)
 Set the current set of unmasked query segments. More...
 
- 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 Types

typedef vector< CConstRef< CDbIndex::CSearchResults > > TResultSet
 Type used to represent collections of search result sets. More...
 
typedef vector< CDbIndex::TSeqNumTSeqMap
 Type used to map loaded indices to subject ids. More...
 

Private Member Functions

TSeqMap::size_type LocateIndex (CDbIndex::TSeqNum oid) const
 Find an index corresponding to the given subject id. More...
 
void PreSearch (BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
 Invoke the seed search procedure on each of the loaded indices. More...
 

Private Attributes

TResultSet results_
 Set of result sets, one per loaded index. More...
 
TSeqMap seqmap_
 For each element of indices_ with index i seqmap_[i] contains one plus the last oid of that database index. More...
 
vector< stringindex_names_
 List of index volume names. More...
 
CRef< CDbIndexindex_
 Currently loaded index. 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 CIndexedDb
static CRef< CIndexedDbIndex_Set_Instance
 Shared representation of currently loaded index volumes. More...
 
- 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...
 
- Protected Attributes inherited from CIndexedDb
CRef< CBlastSeqLocWraplocs_wrap_
 Current set of unmasked query locations. More...
 

Detailed Description

Index wrapper for old style MegaBLAST indexing functionality.

Definition at line 210 of file blast_dbindex.cpp.


The documentation for this class was generated from the following file:
Modified on Fri Jan 05 07:24:08 2024 by modify_doxy.py rev. 669887