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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCInversionMergeAligner.html below:

NCBI C++ ToolKit: CInversionMergeAligner Class Reference

Search Toolkit Book for CInversionMergeAligner

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

CInversionMergeAligner (int Threshold) string GetName () const TAlignResultsRef GenerateAlignments (objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults) 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...
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

Definition at line 66 of file inversion_merge_aligner.hpp.

◆ CInversionMergeAligner() ◆ GenerateAlignments() ◆ GetName() string CInversionMergeAligner::GetName ( ) const inlinevirtual ◆ s_SortByPctCoverage() bool CInversionMergeAligner::s_SortByPctCoverage ( const CRef< objects::CSeq_align > & A, const CRef< objects::CSeq_align > & B ) static ◆ x_CreateDiscAlignment() CRef< CSeq_align > CInversionMergeAligner::x_CreateDiscAlignment ( const objects::CSeq_align & Dom, const objects::CSeq_align & Non, objects::CScope & Scope ) private

Definition at line 264 of file inversion_merge_aligner.cpp.

References CDense_seg::Assign(), CSerialObject::Assign(), CDense_seg::Compact(), CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::eType_disc, CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), COpenRange< Position >::GetLength(), CDense_seg_Base::GetLens(), CSeq_id_Base::GetLocal(), GetName(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CDense_seg::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CDense_seg_Base::GetStarts(), CObject_id_Base::GetStr(), COpenRange< Position >::IntersectingWith(), CSeq_id_Base::IsLocal(), CRef< C, Locker >::IsNull(), CDense_seg::RemovePureGapSegs(), CSeq_align_set_Base::Set(), CRange_Base::SetFrom(), COpenRange< Position >::SetLength(), CSeq_align::SetNamedScore(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CSeq_align_Base::SetType(), swap(), CDense_seg::TrimEndGaps(), CSeq_align_Base::C_Segs::Which(), x_IsAllGap(), and x_MergeSeqAlignSet().

Referenced by x_RunMerger().

◆ x_HandleSingleStrandMerging() void CInversionMergeAligner::x_HandleSingleStrandMerging ( objects::CSeq_align_set & Source, objects::CSeq_align_set & Results, objects::CScope & Scope ) private ◆ x_IsAllGap() bool CInversionMergeAligner::x_IsAllGap ( const objects::CDense_seg & Denseg ) private ◆ x_MergeSeqAlignSet() CRef< objects::CSeq_align_set > CInversionMergeAligner::x_MergeSeqAlignSet ( const objects::CSeq_align_set & InAligns, objects::CScope & Scope ) private

Definition at line 376 of file inversion_merge_aligner.cpp.

References CDense_seg::Assign(), CDense_seg_Base::CanGetStrands(), CAlignCleanup::Cleanup(), eNa_strand_plus, ERR_POST, Error(), CDense_seg::FillUnaligned(), CAlignCleanup::FillUnaligned(), CSeq_align_set_Base::Get(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetNumseg(), CDense_seg::GetSeqStrand(), CDense_seg_Base::GetStrands(), ITERATE, NON_CONST_ITERATE, Out(), CException::ReportAll(), CDense_seg::Reverse(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStrands(), and CAlignCleanup::SortInputsByScore().

Referenced by x_CreateDiscAlignment(), and x_HandleSingleStrandMerging().

◆ x_RunMerger()

Definition at line 109 of file inversion_merge_aligner.cpp.

References CQuerySet::Get(), CSeq_align_set_Base::Get(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), COpenRange< Position >::IntersectingWith(), CRef< C, Locker >::IsNull(), ITERATE, CSeq_align_set_Base::Set(), x_CreateDiscAlignment(), x_SortAlignSet(), and x_SplitAlignmentsByStrand().

Referenced by GenerateAlignments().

◆ x_SortAlignSet() void CInversionMergeAligner::x_SortAlignSet ( objects::CSeq_align_set & AlignSet ) private ◆ x_SplitAlignmentsByStrand() void CInversionMergeAligner::x_SplitAlignmentsByStrand ( const objects::CSeq_align_set & Source, objects::CSeq_align_set & Pluses, objects::CSeq_align_set & Minuses ) private ◆ m_Threshold int CInversionMergeAligner::m_Threshold private

The documentation for this class was generated from the following files:

include/algo/align/ngalign/inversion_merge_aligner.hpp
src/algo/align/ngalign/inversion_merge_aligner.cpp

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