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CInversionMergeAligner Class Reference

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

+ Inheritance diagram for CInversionMergeAligner:
+ Collaboration diagram for CInversionMergeAligner:

Public Member Functions

 CInversionMergeAligner (int Threshold)
string GetName () const
TAlignResultsRef GenerateAlignments (objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults)
- 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 bool s_SortByPctCoverage (const CRef< objects::CSeq_align > &A, const CRef< objects::CSeq_align > &B)
- 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 Member Functions

void x_RunMerger (objects::CScope &Scope, CQuerySet &QueryAligns, TAlignResultsRef Results)
void x_SortAlignSet (objects::CSeq_align_set &AlignSet)
void x_SplitAlignmentsByStrand (const objects::CSeq_align_set &Source, objects::CSeq_align_set &Pluses, objects::CSeq_align_set &Minuses)
void x_HandleSingleStrandMerging (objects::CSeq_align_set &Source, objects::CSeq_align_set &Results, objects::CScope &Scope)
CRef< objects::CSeq_align > x_CreateDiscAlignment (const objects::CSeq_align &Dom, const objects::CSeq_align &Non, objects::CScope &Scope)
CRef< objects::CSeq_align_set > x_MergeSeqAlignSet (const objects::CSeq_align_set &InAligns, objects::CScope &Scope)
bool x_IsAllGap (const objects::CDense_seg &Denseg)

Private Attributes

int m_Threshold

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 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 66 of file inversion_merge_aligner.hpp.

Constructor & Destructor Documentation

◆ CInversionMergeAligner()

CInversionMergeAligner::CInversionMergeAligner ( int  Threshold)

Definition at line 70 of file inversion_merge_aligner.hpp.

Member Function Documentation

◆ GenerateAlignments()

TAlignResultsRef CInversionMergeAligner::GenerateAlignments ( objects::CScope &  Scope,
ISequenceSet QuerySet,
ISequenceSet SubjectSet,
TAlignResultsRef  AccumResults 

Implements IAlignmentFactory.

Definition at line 65 of file inversion_merge_aligner.cpp.

References _TRACE, m_Threshold, NON_CONST_ITERATE, and x_RunMerger().

◆ GetName()

string CInversionMergeAligner::GetName ( ) const

Implements IAlignmentFactory.

Definition at line 72 of file inversion_merge_aligner.hpp.

Referenced by x_CreateDiscAlignment().

◆ s_SortByPctCoverage()

bool CInversionMergeAligner::s_SortByPctCoverage ( const CRef< objects::CSeq_align > &  A,
const CRef< objects::CSeq_align > &  B 

Definition at line 87 of file inversion_merge_aligner.cpp.

References CSeq_align::GetNamedScore().

Referenced by x_SortAlignSet().

◆ x_CreateDiscAlignment()

CRef< CSeq_align > CInversionMergeAligner::x_CreateDiscAlignment ( const objects::CSeq_align &  Dom,
const objects::CSeq_align &  Non,
objects::CScope &  Scope 

◆ x_HandleSingleStrandMerging()

void CInversionMergeAligner::x_HandleSingleStrandMerging ( objects::CSeq_align_set &  Source,
objects::CSeq_align_set &  Results,
objects::CScope &  Scope 

◆ x_IsAllGap()

bool CInversionMergeAligner::x_IsAllGap ( const objects::CDense_seg &  Denseg)

◆ x_MergeSeqAlignSet()

CRef< objects::CSeq_align_set > CInversionMergeAligner::x_MergeSeqAlignSet ( const objects::CSeq_align_set &  InAligns,
objects::CScope &  Scope 

◆ x_RunMerger()

void CInversionMergeAligner::x_RunMerger ( objects::CScope &  Scope,
CQuerySet QueryAligns,
TAlignResultsRef  Results 

◆ x_SortAlignSet()

void CInversionMergeAligner::x_SortAlignSet ( objects::CSeq_align_set &  AlignSet)

◆ x_SplitAlignmentsByStrand()

void CInversionMergeAligner::x_SplitAlignmentsByStrand ( const objects::CSeq_align_set &  Source,
objects::CSeq_align_set &  Pluses,
objects::CSeq_align_set &  Minuses 

Member Data Documentation

◆ m_Threshold

int CInversionMergeAligner::m_Threshold

Definition at line 87 of file inversion_merge_aligner.hpp.

Referenced by GenerateAlignments().

The documentation for this class was generated from the following files:
Modified on Tue May 21 10:59:47 2024 by rev. 669887