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NCBI C++ ToolKit: CSparseAlignment Class Reference

Search Toolkit Book for CSparseAlignment

CSparseAlignment - an alignment based on CSparse_seg and CAlingRangeCollection classes rather than on CDense_seg. More...

#include <gui/objutils/sparse_alignment.hpp>

CSparseAlignment () CSparseAlignment. More...
virtual ~CSparseAlignment () void Init (const objects::CSeq_id &master_id, vector< SAlignedSeq * > &aln_seqs, objects::CScope &scope) void Clear () void SetGapChar (TResidue gap_char) CRef< objects::CScope > GetScope () TNumrow GetNumRows () const TARange GetAlnRange () const returns number of rows in the alignment More...
const TAlignColl & GetAlignCollection (TNumrow row) bool IsSetAnchor () const TNumrow GetAnchor () const const objects::CSeq_id & GetSeqId (TNumrow row) const TSignedSeqPos GetSeqAlnStart (TNumrow row) const TSignedSeqPos GetSeqAlnStop (TNumrow row) const TSignedRange GetSeqAlnRange (TNumrow row) const TSeqPos GetSeqStart (TNumrow row) const TSeqPos GetSeqStop (TNumrow row) const IAlnExplorer::TRange GetSeqRange (TNumrow row) const bool IsPositiveStrand (TNumrow row) const bool IsNegativeStrand (TNumrow row) const TSignedSeqPos GetAlnPosFromSeqPos (TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const TSignedSeqPos GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const string & GetSeqString (TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to) const string & GetSeqString (TNumrow row, string &buffer, const IAlnExplorer::TRange &seq_rng) const string & GetAlnSeqString (TNumrow row, string &buffer, const TSignedRange &aln_rng) const const objects::CBioseq_Handle & GetBioseqHandle (TNumrow row) const virtual IAlnSegmentIterator * CreateSegmentIterator (TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) 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

CSparseAlignment - an alignment based on CSparse_seg and CAlingRangeCollection classes rather than on CDense_seg.

Assumptions: master is always specified in CSparse-seg and has a Seq-id we display it always anchored chaning anchor is not supported

Definition at line 59 of file sparse_alignment.hpp.

◆ TAlignColl ◆ TAlignRange ◆ TARange ◆ TNumrow ◆ TPos ◆ TResidue ◆ TRows ◆ TSignedRange ◆ CSparseAlignment() CSparseAlignment::CSparseAlignment ( ) ◆ ~CSparseAlignment() ◆ Clear() void CSparseAlignment::Clear ( void ) ◆ CreateSegmentIterator() ◆ GetAlignCollection() ◆ GetAlnPosFromSeqPos() ◆ GetAlnRange() ◆ GetAlnSeqString()

Definition at line 317 of file sparse_alignment.cpp.

References _ASSERT, buffer, CBioseq_Handle::eCoding_Iupac, IAlnSegmentIterator::eSkipGaps, CBioseq_Handle::eStrand_Minus, CBioseq_Handle::eStrand_Plus, IAlnSegment::GetAlnRange(), GetBioseqHandle(), CAlignRangeCollection< TAlnRange >::GetFirstFrom(), CAlignRangeCollection< TAlnRange >::GetFirstTo(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), IAlnSegment::GetRange(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CRange_Base::GetTo(), int, len, m_GapChar, m_Rows, max(), min(), positive(), r(), row, ncbi::grid::netcache::search::fields::size, CSeqVector::size(), and x_AssertRowValid().

◆ GetAnchor() ◆ GetBioseqHandle() ◆ GetNumRows() ◆ GetScope() CRef< CScope > CSparseAlignment::GetScope ( void ) ◆ GetSeqAlnRange() ◆ GetSeqAlnStart() ◆ GetSeqAlnStop() ◆ GetSeqId() ◆ GetSeqPosFromAlnPos() ◆ GetSeqRange() ◆ GetSeqStart() ◆ GetSeqStop() ◆ GetSeqString() [1/2] ◆ GetSeqString() [2/2]

Definition at line 281 of file sparse_alignment.cpp.

References buffer, CBioseq_Handle::eCoding_Iupac, CBioseq_Handle::eStrand_Minus, CBioseq_Handle::eStrand_Plus, GetBioseqHandle(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), m_GapChar, m_Rows, positive(), row, ncbi::grid::netcache::search::fields::size, CSeqVector::size(), and x_AssertRowValid().

Referenced by GetSeqString().

◆ Init() void CSparseAlignment::Init ( const objects::CSeq_id & master_id, vector< SAlignedSeq * > & aln_seqs, objects::CScope & scope )

Definition at line 74 of file sparse_alignment.cpp.

References Clear(), COpenRange< Position >::CombineWith(), CAlignRangeCollection< TAlnRange >::GetFirstRange(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), i, CAlignRangeCollection< TAlnRange >::insert(), SAlignedSeq::m_AlignColl, CSparseAlignment::SRowRec::m_AlignedSeq, m_AlnRange, m_MasterId, m_Rows, m_Scope, SAlignedSeq::m_SecondRange, SAlignedSeq::m_SeqId, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), and CRange_Base::SetFrom().

Referenced by BuildSparseAlignment().

◆ IsNegativeStrand() bool CSparseAlignment::IsNegativeStrand ( TNumrow row ) const ◆ IsPositiveStrand() bool CSparseAlignment::IsPositiveStrand ( TNumrow row ) const ◆ IsSetAnchor() ◆ SetGapChar() void CSparseAlignment::SetGapChar ( TResidue gap_char ) ◆ x_AssertRowValid() void CSparseAlignment::x_AssertRowValid ( TNumrow row ) const protected

Definition at line 411 of file sparse_alignment.cpp.

References _ASSERT, m_Rows, and row.

Referenced by CreateSegmentIterator(), GetAlnPosFromSeqPos(), GetAlnSeqString(), GetBioseqHandle(), GetSeqAlnRange(), GetSeqAlnStart(), GetSeqAlnStop(), GetSeqId(), GetSeqPosFromAlnPos(), GetSeqRange(), GetSeqStart(), GetSeqStop(), GetSeqString(), IsNegativeStrand(), and IsPositiveStrand().

◆ m_AlnRange TARange CSparseAlignment::m_AlnRange protected ◆ m_GapChar ◆ m_MasterId CConstRef<objects::CSeq_id> CSparseAlignment::m_MasterId protected ◆ m_Rows TRows CSparseAlignment::m_Rows mutableprotected

Definition at line 141 of file sparse_alignment.hpp.

Referenced by Clear(), CreateSegmentIterator(), GetAlignCollection(), GetAlnPosFromSeqPos(), GetAlnSeqString(), GetAnchor(), GetBioseqHandle(), GetNumRows(), GetSeqAlnRange(), GetSeqAlnStart(), GetSeqAlnStop(), GetSeqId(), GetSeqPosFromAlnPos(), GetSeqRange(), GetSeqStart(), GetSeqStop(), GetSeqString(), Init(), IsNegativeStrand(), IsPositiveStrand(), and x_AssertRowValid().

◆ m_Scope CRef<objects::CScope> CSparseAlignment::m_Scope mutableprotected

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

include/gui/objutils/sparse_alignment.hpp
src/gui/objutils/sparse_alignment.cpp

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