Search Toolkit Book for CSplitQueryBlk
Wrapper class around SSplitQueryBlk structure. More...
#include "split_query_blk.hpp"
(Private to src/algo/blast/api.)
Inheritance diagram for CSplitQueryBlk:
Collaboration diagram for CSplitQueryBlk:
Public Member Functions | |
| CSplitQueryBlk (Uint4 num_chunks, bool gapped_merge=true) | |
| Constructor for wrapper class for SSplitQueryBlk. More... | |
| ~CSplitQueryBlk () | |
| Destructor. More... | |
| size_t | GetNumChunks () const |
| Retrieve the number of chunks. More... | |
| size_t | GetNumQueriesForChunk (size_t chunk_num) const |
| Get the number of queries in a given chunk. More... | |
| vector< size_t > | GetQueryIndices (size_t chunk_num) const |
| Get the indices of the queries contained in a given chunk. More... | |
| vector< int > | GetQueryContexts (size_t chunk_num) const |
| Get the contexts of the queries contained in a given chunk. More... | |
| vector< size_t > | GetContextOffsets (size_t chunk_num) const |
| Get the context offsets (corrections) of the queries contained in a given chunk. More... | |
| TChunkRange | GetChunkBounds (size_t chunk_num) const |
| Get the boundaries of a chunk in the concatenated query. More... | |
| void | SetChunkBounds (size_t chunk_num, const TChunkRange &chunk_range) |
| Set the boundaries of a chunk in the concatenated query. More... | |
| void | AddQueryToChunk (size_t chunk_num, Int4 query_index) |
| Adds a query index to a given chunk. More... | |
| void | AddContextToChunk (size_t chunk_num, Int4 context_index) |
| Adds a query context to a given chunk. More... | |
| void | AddContextOffsetToChunk (size_t chunk_num, Int4 context_offset) |
| Adds a context offset (correction) to a given chunk. More... | |
| SSplitQueryBlk * | GetCStruct () const |
| Returns the C structure managed by objects of this class. More... | |
| void | SetChunkOverlapSize (size_t size) |
| Sets the size (# of bases/residues) of overlap between query chunks. More... | |
| size_t | GetChunkOverlapSize () const |
| Gets the size (# of bases/residues) of overlap between query chunks. 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 Member Functions | |
| CSplitQueryBlk (const CSplitQueryBlk &rhs) | |
| Do not allow copy-construction. More... | |
| CSplitQueryBlk & | operator= (const CSplitQueryBlk &rhs) |
| Do not allow assignment operator. More... | |
Private Attributes | |
| SSplitQueryBlk * | m_SplitQueryBlk |
| The structure this object manages. More... | |
Friends | |
| ostream & | operator<< (ostream &out, const CSplitQueryBlk &rhs) |
| Print this object so that its contents can be directly used to update split_query.ini (for unit testing) 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 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
Wrapper class around SSplitQueryBlk structure.
Definition at line 53 of file split_query_blk.hpp.
The documentation for this class was generated from the following files:
- src/algo/blast/api/split_query_blk.hpp
- src/algo/blast/api/split_query_blk.cpp
