NCBI C++ ToolKit
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Search Toolkit Book for CSplitQueryBlk
Wrapper class around SSplitQueryBlk structure. More...
#include "split_query_blk.hpp"
(Private to src/algo/blast/api
.)
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... | |
Wrapper class around SSplitQueryBlk structure.
Definition at line 53 of file split_query_blk.hpp.