NCBI C++ ToolKit
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CBlastQuerySourceOM Class Reference

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Implements the object manager dependant version of the IBlastQuerySource. More...

#include "blast_objmgr_priv.hpp"
(Private to src/algo/blast/api.)

+ Inheritance diagram for CBlastQuerySourceOM:
+ Collaboration diagram for CBlastQuerySourceOM:

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...
 
- Public Member Functions inherited from IBlastQuerySource
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...
 
- 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
 

Protected Attributes

CRef< CBlastQueryVectorm_QueryVector
 Reference to input CBlastQueryVector (or empty if not used) More...
 
TSeqLocVectorm_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 CBlastOptionsm_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

- 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< Uint8TCounter
 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

Implements the object manager dependant version of the IBlastQuerySource.

Definition at line 63 of file blast_objmgr_priv.hpp.


The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:08:53 2024 by modify_doxy.py rev. 669887