Search Toolkit Book for CIndexedDb_Old
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 int | MinIndexWordSize () |
| Get the minimum acceptable word size to use with indexed search. 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... | |
| 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... | |
| 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::TSeqNum > | TSeqMap |
| 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< string > | index_names_ |
| List of index volume names. More... | |
| CRef< CDbIndex > | index_ |
| 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< Uint8 > | TCounter |
| 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< CIndexedDb > | Index_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< CBlastSeqLocWrap > | locs_wrap_ |
| Current set of unmasked query locations. More... | |
Detailed Description
Index wrapper for old style MegaBLAST indexing functionality.
Definition at line 209 of file blast_dbindex.cpp.
The documentation for this class was generated from the following file:
- src/algo/blast/api/blast_dbindex.cpp
