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CSplitQueryBlk Class Reference

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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< intGetQueryContexts (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...
 
SSplitQueryBlkGetCStruct () 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...
 
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 Member Functions

 CSplitQueryBlk (const CSplitQueryBlk &rhs)
 Do not allow copy-construction. More...
 
CSplitQueryBlkoperator= (const CSplitQueryBlk &rhs)
 Do not allow assignment operator. More...
 

Private Attributes

SSplitQueryBlkm_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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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.

Constructor & Destructor Documentation

CSplitQueryBlk::CSplitQueryBlk ( const CSplitQueryBlk rhs)
private

Do not allow copy-construction.

Member Function Documentation

CSplitQueryBlk& CSplitQueryBlk::operator= ( const CSplitQueryBlk rhs)
private

Do not allow assignment operator.

Friends And Related Function Documentation

ostream& operator<< ( ostream &  out,
const CSplitQueryBlk rhs 
)
friend

Print this object so that its contents can be directly used to update split_query.ini (for unit testing)

Parameters
outstream to print this object [in|out]
rhsobject to print [in]

Definition at line 219 of file split_query_blk.cpp.

Member Data Documentation

SSplitQueryBlk* CSplitQueryBlk::m_SplitQueryBlk
private

The documentation for this class was generated from the following files:
Modified on Mon Apr 23 11:44:24 2018 by modify_doxy.py rev. 546573