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CBlastAligner Class Reference

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#include <algo/align/ngalign/blast_aligner.hpp>

+ Inheritance diagram for CBlastAligner:
+ Collaboration diagram for CBlastAligner:

Public Types

typedef CRef< blast::CBlastOptionsHandle > TBlastOptionsRef
 
typedef CRef< CBlastAlignerTBlastAlignerRef
 
- 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...
 

Public Member Functions

 CBlastAligner (blast::CBlastOptionsHandle &Options, int Threshold)
 
 CBlastAligner (const string &Params, int Threshold)
 
string GetName () const
 
TAlignResultsRef GenerateAlignments (objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults)
 
void SetSoftFiltering (int Filter)
 
void SetSoftFiltering (const string &Filter)
 
void SetUseNegativeGiList (bool Use)
 
void SetInterruptCallback (TInterruptFnPtr fnptr=NULL, void *user_data=NULL)
 
- 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
 

Static Public Member Functions

static list< TBlastAlignerRefCreateBlastAligners (list< TBlastOptionsRef > &Options, int Threshold)
 
static list< TBlastAlignerRefCreateBlastAligners (const list< string > &Params, int Threshold)
 
- 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)
 

Private Attributes

CRef< blast::CBlastOptionsHandle > m_BlastOptions
 
int m_Threshold
 
string m_Filter
 
bool m_UseNegativeGiList
 
TInterruptFnPtr m_InterruptFunc
 
void * m_InterruptData
 

Additional Inherited Members

- 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

Definition at line 86 of file blast_aligner.hpp.

Member Typedef Documentation

◆ TBlastAlignerRef

Definition at line 111 of file blast_aligner.hpp.

◆ TBlastOptionsRef

typedef CRef<blast::CBlastOptionsHandle> CBlastAligner::TBlastOptionsRef

Definition at line 110 of file blast_aligner.hpp.

Constructor & Destructor Documentation

◆ CBlastAligner() [1/2]

CBlastAligner::CBlastAligner ( blast::CBlastOptionsHandle &  Options,
int  Threshold 
)
inline

Definition at line 89 of file blast_aligner.hpp.

Referenced by CreateBlastAligners().

◆ CBlastAligner() [2/2]

CBlastAligner::CBlastAligner ( const string Params,
int  Threshold 
)
inline

Definition at line 93 of file blast_aligner.hpp.

Member Function Documentation

◆ CreateBlastAligners() [1/2]

list< CBlastAligner::TBlastAlignerRef > CBlastAligner::CreateBlastAligners ( const list< string > &  Params,
int  Threshold 
)
static

◆ CreateBlastAligners() [2/2]

list< CBlastAligner::TBlastAlignerRef > CBlastAligner::CreateBlastAligners ( list< TBlastOptionsRef > &  Options,
int  Threshold 
)
static

Definition at line 340 of file blast_aligner.cpp.

References CBlastAligner(), NON_CONST_ITERATE, and CRef< C, Locker >::Reset().

Referenced by CreateBlastAligners().

◆ GenerateAlignments()

TAlignResultsRef CBlastAligner::GenerateAlignments ( objects::CScope &  Scope,
ISequenceSet QuerySet,
ISequenceSet SubjectSet,
TAlignResultsRef  AccumResults 
)
virtual

◆ GetName()

string CBlastAligner::GetName ( ) const
inlinevirtual

Implements IAlignmentFactory.

Definition at line 99 of file blast_aligner.hpp.

Referenced by GenerateAlignments().

◆ SetInterruptCallback()

void CBlastAligner::SetInterruptCallback ( TInterruptFnPtr  fnptr = NULL,
void *  user_data = NULL 
)
inline

Definition at line 116 of file blast_aligner.hpp.

References m_InterruptData, and m_InterruptFunc.

Referenced by CFindOverlapJob::x_PrepareAligner().

◆ SetSoftFiltering() [1/2]

void CBlastAligner::SetSoftFiltering ( const string Filter)
inline

Definition at line 107 of file blast_aligner.hpp.

References Filter(), and m_Filter.

◆ SetSoftFiltering() [2/2]

void CBlastAligner::SetSoftFiltering ( int  Filter)
inline

Definition at line 106 of file blast_aligner.hpp.

References Filter(), and m_Filter.

◆ SetUseNegativeGiList()

void CBlastAligner::SetUseNegativeGiList ( bool  Use)
inline

Definition at line 108 of file blast_aligner.hpp.

References m_UseNegativeGiList.

Member Data Documentation

◆ m_BlastOptions

CRef<blast::CBlastOptionsHandle> CBlastAligner::m_BlastOptions
private

Definition at line 123 of file blast_aligner.hpp.

Referenced by GenerateAlignments().

◆ m_Filter

string CBlastAligner::m_Filter
private

Definition at line 125 of file blast_aligner.hpp.

Referenced by GenerateAlignments(), and SetSoftFiltering().

◆ m_InterruptData

void* CBlastAligner::m_InterruptData
private

Definition at line 129 of file blast_aligner.hpp.

Referenced by GenerateAlignments(), and SetInterruptCallback().

◆ m_InterruptFunc

TInterruptFnPtr CBlastAligner::m_InterruptFunc
private

Definition at line 128 of file blast_aligner.hpp.

Referenced by GenerateAlignments(), and SetInterruptCallback().

◆ m_Threshold

int CBlastAligner::m_Threshold
private

Definition at line 124 of file blast_aligner.hpp.

Referenced by GenerateAlignments().

◆ m_UseNegativeGiList

bool CBlastAligner::m_UseNegativeGiList
private

Definition at line 126 of file blast_aligner.hpp.

Referenced by GenerateAlignments(), and SetUseNegativeGiList().


The documentation for this class was generated from the following files:
Modified on Mon May 27 04:38:47 2024 by modify_doxy.py rev. 669887