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NCBI C++ ToolKit: CQuerySet Class Reference
Search Toolkit Book for CQuerySet
#include <algo/align/ngalign/result_set.hpp>
CQuerySet (const blast::CSearchResults &Results) CQuerySet (const objects::CSeq_align_set &Results) CQuerySet (CRef< objects::CSeq_align > Alignment) CQuerySet (const blast::CSearchResults &Results, CRef< objects::CGC_Assembly > GenColl, bool AllowDupes=false) CQuerySet (const objects::CSeq_align_set &Results, CRef< objects::CGC_Assembly > GenColl, bool AllowDupes=false) CQuerySet (CRef< objects::CSeq_align > Alignment, CRef< objects::CGC_Assembly > GenColl, bool AllowDupes=false) TAssemblyToSubjectSet & Get () const TAssemblyToSubjectSet & Get () const CRef< objects::CSeq_align_set > ToSeqAlignSet () const CRef< objects::CSeq_align_set > ToBestSeqAlignSet () const CConstRef< objects::CSeq_id > GetQueryId () const void Insert (CRef< CQuerySet > QuerySet) void Insert (const objects::CSeq_align_set &AlignSet) void Insert (CRef< objects::CSeq_align > Alignment) int GetBestRank (const string AssemblyAcc="") const 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 65 of file result_set.hpp.
◆ TAssemblyToSubjectSet ◆ TSubjectToAlignSet ◆ CQuerySet() [1/6] CQuerySet::CQuerySet ( const blast::CSearchResults & Results ) ◆ CQuerySet() [2/6] CQuerySet::CQuerySet ( const objects::CSeq_align_set & Results ) ◆ CQuerySet() [3/6] CQuerySet::CQuerySet ( CRef< objects::CSeq_align > Alignment ) ◆ CQuerySet() [4/6] CQuerySet::CQuerySet ( const blast::CSearchResults & Results, CRef< objects::CGC_Assembly > GenColl, bool AllowDupes = false ) ◆ CQuerySet() [5/6] CQuerySet::CQuerySet ( const objects::CSeq_align_set & Results, CRef< objects::CGC_Assembly > GenColl, bool AllowDupes = false ) ◆ CQuerySet() [6/6] CQuerySet::CQuerySet ( CRef< objects::CSeq_align > Alignment, CRef< objects::CGC_Assembly > GenColl, bool AllowDupes = false ) ◆ Get() [1/2] ◆ Get() [2/2] ◆ GetBestRank() ◆ GetQueryId() CConstRef<objects::CSeq_id> CQuerySet::GetQueryId ( ) const inline ◆ Insert() [1/3] void CQuerySet::Insert ( const objects::CSeq_align_set & AlignSet ) ◆ Insert() [2/3] ◆ Insert() [3/3] void CQuerySet::Insert ( CRef< objects::CSeq_align > Alignment ) ◆ ToBestSeqAlignSet() ◆ ToSeqAlignSet() ◆ x_AlreadyContains() bool CQuerySet::x_AlreadyContains ( const objects::CSeq_align_set & Set, const objects::CSeq_align & New ) const private ◆ x_ContainsAlignment() bool CQuerySet::x_ContainsAlignment ( const objects::CSeq_align & Outer, const objects::CSeq_align & Inner ) const private
Definition at line 395 of file result_set.cpp.
References CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqRange(), CDense_seg_Base::GetStarts(), COpenRange< Position >::IntersectingWith(), COpenRange< Position >::IntersectionWith(), CSeq_align_Base::C_Segs::IsDisc(), ITERATE, m_AllowDupes, CRange_Base::SetFrom(), and COpenRange< Position >::SetLength().
Referenced by x_FilterStrictSubAligns().
◆ x_FilterStrictSubAligns() void CQuerySet::x_FilterStrictSubAligns ( objects::CSeq_align_set & Source ) const private ◆ m_AllowDupes bool CQuerySet::m_AllowDupes private ◆ m_AssemblyMap ◆ m_GenColl ◆ m_QueryId CRef<objects::CSeq_id> CQuerySet::m_QueryId private ◆ m_SubjectMap
The documentation for this class was generated from the following files:
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