NCBI C++ ToolKit
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Search Toolkit Book for CBlastQuerySourceOM
Implements the object manager dependant version of the IBlastQuerySource. More...
#include "blast_objmgr_priv.hpp"
(Private to src/algo/blast/api
.)
Public Member Functions | |
CBlastQuerySourceOM (TSeqLocVector &v, EBlastProgramType prog) | |
Constructor which takes a TSeqLocVector. More... | |
CBlastQuerySourceOM (TSeqLocVector &v, const CBlastOptions *opts) | |
Constructor which takes a TSeqLocVector. More... | |
CBlastQuerySourceOM (CBlastQueryVector &v, EBlastProgramType prog) | |
Constructor which takes a CBlastQueryVector. More... | |
CBlastQuerySourceOM (CBlastQueryVector &v, const CBlastOptions *opts) | |
Constructor which takes a CBlastQueryVector. More... | |
virtual | ~CBlastQuerySourceOM () |
dtor which determines if the internal pointer to its data should be deleted or not. More... | |
virtual objects::ENa_strand | GetStrand (int i) const |
Return strand for a sequence. More... | |
virtual CConstRef< objects::CSeq_loc > | GetMask (int i) |
Return the filtered (masked) regions for a sequence. More... | |
virtual TMaskedQueryRegions | GetMaskedRegions (int i) |
Return the filtered (masked) regions for a sequence. More... | |
virtual CConstRef< objects::CSeq_loc > | GetSeqLoc (int i) const |
Return the CSeq_loc associated with a sequence. More... | |
virtual const objects::CSeq_id * | GetSeqId (int index) const |
Return the sequence identifier associated with a sequence. More... | |
virtual Uint4 | GetGeneticCodeId (int index) const |
Retrieve the genetic code associated with a sequence. More... | |
virtual SBlastSequence | GetBlastSequence (int i, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, string *warnings=0) const |
Return the sequence data for a sequence. More... | |
virtual TSeqPos | GetLength (int i) const |
Return the length of a sequence. More... | |
virtual TSeqPos | Size () const |
Return the number of elements in the sequence container. More... | |
virtual string | GetTitle (int index) const |
Return the title of a sequence. More... | |
virtual bool | IsFirstOfAPair (int index) const |
Is this sequence followed by a mate (for mapping short reads) More... | |
virtual int | GetSegmentInfo (int index) const |
Get segment information (for mapping paired short reads) More... | |
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virtual | ~IBlastQuerySource () |
Our no-op virtual destructor. More... | |
bool | Empty () const |
Returns true if the container is empty, else false. More... | |
virtual SBlastSequence | GetBlastSequence (int index, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, std::string *warnings=0) const =0 |
Return the sequence data for a sequence. More... | |
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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... | |
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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 |
Protected Attributes | |
CRef< CBlastQueryVector > | m_QueryVector |
Reference to input CBlastQueryVector (or empty if not used) More... | |
TSeqLocVector * | m_TSeqLocVector |
Reference to input TSeqLocVector (or NULL if not used) More... | |
bool | m_OwnTSeqLocVector |
flag to determine if the member above should or not be deleted in the destructor More... | |
const CBlastOptions * | m_Options |
BLAST algorithm options. More... | |
Private Member Functions | |
void | x_CalculateMasks () |
Performs filtering on the query sequences to calculate the masked locations. More... | |
void | x_AutoDetectGeneticCodes (void) |
Tries to extract the genetic code using the CScope, if it succeeds, it supercedes what's specified in the {SSeqLoc,CBlastSearchQuery}::genetic_code_id field. More... | |
Private Attributes | |
bool | m_CalculatedMasks |
this flag allows for lazy initialization of the masking locations More... | |
EBlastProgramType | m_Program |
BLAST program variable. More... | |
Additional Inherited Members | |
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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... | |
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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... | |
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static void | EnableDebugDump (bool on) |
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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... | |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Implements the object manager dependant version of the IBlastQuerySource.
Definition at line 63 of file blast_objmgr_priv.hpp.