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NCBI C++ ToolKit: CSeq_align_Mapper_Base Class Reference

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Class used to map seq-alignments. More...

#include <objects/seq/seq_align_mapper_base.hpp>

  CSeq_align_Mapper_Base (const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper)     ~CSeq_align_Mapper_Base (void)   void  Convert (void)   Map the whole alignment through the linked seq-loc mapper. More...
  void  Convert (size_t row)   Map a single row of the alignment through the linked seq-loc mapper. More...
  CRef< CSeq_align >  GetDstAlign (void) const   Create mapped alignment. More...
  size_t  GetDim (void) const   Some of the following methods use only the first segment to get information about rows. More...
  const CSeq_id_Handle &  GetRowId (size_t idx) const   Get seq-id for the given row. More...
  const TSegments &  GetSegments () const   Get parsed segments. More...
    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   SAlignment_Segment &  x_PushSeg (int len, size_t dim, ENa_strand strand=eNa_strand_unknown)   void  x_Init (const TDendiag &diags)   void  x_Init (const CDense_seg &denseg)   void  x_Init (const TStd &sseg)   void  x_Init (const CPacked_seg &pseg)   void  x_Init (const CSeq_align_set &align_set)   void  x_Init (const CSpliced_seg &spliced)   void  x_Init (const CSparse_seg &sparse)   void  x_ConvertAlign (size_t *row)   void  x_ConvertRow (size_t row)   CSeq_id_Handle  x_ConvertSegment (TSegments::iterator &seg_it, size_t row)   void  x_FillKnownStrands (TStrands &strands) const   void  x_GetDstDendiag (CRef< CSeq_align > &dst) const   void  x_GetDstDenseg (CRef< CSeq_align > &dst) const   void  x_GetDstStd (CRef< CSeq_align > &dst) const   void  x_GetDstPacked (CRef< CSeq_align > &dst) const   void  x_GetDstDisc (CRef< CSeq_align > &dst) const   void  x_GetDstSpliced (CRef< CSeq_align > &dst) const   void  x_GetDstSparse (CRef< CSeq_align > &dst) const   bool  x_GetDstExon (CSpliced_seg &spliced, TSegments::const_iterator &seg, CSeq_id_Handle &gen_id, CSeq_id_Handle &prod_id, ENa_strand &gen_strand, ENa_strand &prod_strand, bool &last_exon_partial, const CSeq_id_Handle &last_gen_id, const CSeq_id_Handle &last_prod_id) const   void  x_PushExonPart (CRef< CSpliced_exon_chunk > &last_part, CSpliced_exon_chunk::E_Choice part_type, int part_len, CSpliced_exon &exon) const   void  x_ConvToDstDisc (CRef< CSeq_align > &dst) const   ssize_t  x_GetPartialDenseg (CRef< CSeq_align > &dst, size_t start_seg) const   void  x_GetDstSplicedSubAlign (CSpliced_seg &spliced, const CSeq_align_Mapper_Base &sub_align, bool &last_exon_partial, CSeq_id_Handle &gen_id, CSeq_id_Handle &last_gen_id, bool &single_gen_id, ENa_strand &gen_strand, bool &single_gen_str, CSeq_id_Handle &prod_id, CSeq_id_Handle &last_prod_id, bool &single_prod_id, ENa_strand &prod_strand, bool &single_prod_str, bool &partial) const   bool  x_HaveMixedSeqTypes (void) const   bool  x_HaveMixedStrand (void) const   bool  x_IsEmpty (void) const  

Class used to map seq-alignments.

Parses, maps and generates alignments. Does not contain mapping information and can be used only with an instance of CSeq_loc_Mapper_Base class. The seq-loc mapper is also used to retrieve information about types of sequences.

Definition at line 128 of file seq_align_mapper_base.hpp.

◆ TDendiag ◆ TScores ◆ TScoresGroups ◆ TSegments ◆ TStd ◆ TStrands ◆ TSubAligns ◆ EAlignFlags ◆ CSeq_align_Mapper_Base() [1/2] ◆ ~CSeq_align_Mapper_Base() ◆ CSeq_align_Mapper_Base() [2/2] ◆ Convert() [1/2] void CSeq_align_Mapper_Base::Convert ( size_t  row ) ◆ Convert() [2/2] void CSeq_align_Mapper_Base::Convert ( void  ) ◆ CreateSubAlign() [1/2] ◆ CreateSubAlign() [2/2] ◆ GetDim() size_t CSeq_align_Mapper_Base::GetDim ( void  ) const inline

Some of the following methods use only the first segment to get information about rows.

They do not check if this information is consistent through all segments, but it should be. Get maximal number of rows in the alignment's segments.

Definition at line 151 of file seq_align_mapper_base.hpp.

References m_Dim.

◆ GetDstAlign()

Create mapped alignment.

Definition at line 2894 of file seq_align_mapper_base.cpp.

References CSerialObject::Assign(), CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, eAlign_Normal, CSeq_loc_Mapper_Base::fMixedAlignsAsSpliced, CSeq_align_Base::GetBounds(), CSeq_align_Base::GetDim(), CSeq_align_Base::GetExt(), CSeq_align_Base::GetId(), CSeq_align_Base::GetSegs(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSeq_align_Base::GetType(), CSeq_align_Base::IsSetBounds(), CSeq_align_Base::IsSetDim(), CSeq_align_Base::IsSetExt(), CSeq_align_Base::IsSetId(), kInvalidSeqPos, m_AlignFlags, m_AlignScores, m_DstAlign, SAlignment_Segment::SAlignment_Row::m_Id, m_LocMapper, m_OrigAlign, m_Segs, SAlignment_Segment::SAlignment_Row::m_Start, NCBI_THROW, r(), row, CSeq_align_Base::SetBounds(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetExt(), CSeq_align_Base::SetId(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetType(), CSeq_align_Base::C_Segs::Which(), x_ConvToDstDisc(), x_GetDstDendiag(), x_GetDstDenseg(), x_GetDstDisc(), x_GetDstPacked(), x_GetDstSparse(), x_GetDstSpliced(), x_GetDstStd(), x_HaveMixedSeqTypes(), x_IsEmpty(), and CSeq_loc_Mapper_Base::x_IsSetMiscFlag().

Referenced by CSeq_loc_Conversion_Set::Convert().

◆ GetLocMapper() ◆ GetMaxDim() size_t CSeq_align_Mapper_Base::GetMaxDim ( void  ) const inlineprotected ◆ GetRowId()

Get seq-id for the given row.

Throw exception if the row does not exist. The function uses row id from the first segment. Other segments may have different id for the same row.

Definition at line 3072 of file seq_align_mapper_base.cpp.

References m_Segs, and NCBI_THROW.

◆ GetSegments()

Get parsed segments.

There is no storage for the original set of segments - it's modified during the mapping to produce mapped alignment.

Definition at line 384 of file seq_align_mapper_base.hpp.

◆ InitExon()

Definition at line 689 of file seq_align_mapper_base.cpp.

References SAlignment_Segment::AddRow(), CProduct_pos::AsSeqPos(), CSpliced_exon_chunk_Base::e_Match, eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSplicedRow_Gen, CSeq_loc_Mapper_Base::eSplicedRow_Prod, CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_id(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_exon_Base::GetScores(), CSpliced_exon_chunk_Base::IsGenomic_ins(), CSpliced_exon_chunk_Base::IsProduct_ins(), IsReverse(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetParts(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), CSpliced_exon_Base::IsSetScores(), ITERATE, m_Dim, m_HaveStrands, m_OrigExon, SAlignment_Segment::m_PartType, m_SegsScores, CConstRef< C, Locker >::Reset(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), Warning(), CSpliced_exon_chunk_Base::Which(), and x_PushSeg().

◆ x_ConvertAlign() void CSeq_align_Mapper_Base::x_ConvertAlign ( size_t *  row ) private ◆ x_ConvertRow() void CSeq_align_Mapper_Base::x_ConvertRow ( size_t  row ) private ◆ x_ConvertSegment() CSeq_id_Handle CSeq_align_Mapper_Base::x_ConvertSegment ( TSegments::iterator &  seg_it, size_t  row  ) private

Definition at line 1002 of file seq_align_mapper_base.cpp.

References CRangeMapBase< Traits >::begin(), SAlignment_Segment::CopyRow(), dr, eAlign_MultiId, eAlign_Normal, CRangeMapBase< Traits >::empty(), eNa_strand_unknown, map_checker< Container >::end(), CSeq_loc_Mapper_Base::fCheckStrand, CSeq_loc_Mapper_Base::fErrorOnPartial, map_checker< Container >::find(), CRange_Base::GetFrom(), CMappingRanges::GetIdMap(), IsReverse(), ITERATE, kInvalidSeqPos, m_AlignFlags, SAlignment_Segment::m_GroupIdx, SAlignment_Segment::m_HaveStrands, m_HaveStrands, SAlignment_Segment::SAlignment_Row::m_Id, SAlignment_Segment::SAlignment_Row::m_IsSetStrand, SAlignment_Segment::m_Len, m_LocMapper, CSeq_loc_Mapper_Base::m_Mappings, SAlignment_Segment::m_PartType, SAlignment_Segment::m_Rows, SAlignment_Segment::m_Scores, SAlignment_Segment::m_ScoresGroupIdx, m_Segs, SAlignment_Segment::SAlignment_Row::m_Start, SAlignment_Segment::SAlignment_Row::m_Strand, NCBI_THROW, r(), row, SAlignment_Segment::SAlignment_Row::SameStrand(), SAlignment_Segment::SAlignment_Row::SetMapped(), ct::sort(), CSeq_loc_Mapper_Base::x_GetPrimaryId(), x_InsertSeg(), x_InvalidateScores(), and CSeq_loc_Mapper_Base::x_IsSetMiscFlag().

Referenced by x_ConvertRow().

◆ x_ConvToDstDisc() void CSeq_align_Mapper_Base::x_ConvToDstDisc ( CRef< CSeq_align > &  dst ) const private ◆ x_FillKnownStrands() void CSeq_align_Mapper_Base::x_FillKnownStrands ( TStrands &  strands ) const private ◆ x_GetDstDendiag() void CSeq_align_Mapper_Base::x_GetDstDendiag ( CRef< CSeq_align > &  dst ) const private

Definition at line 1274 of file seq_align_mapper_base.cpp.

References CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, kInvalidSeqPos, SAlignment_Segment::m_HaveStrands, m_LocMapper, SAlignment_Segment::m_Rows, SAlignment_Segment::m_Scores, m_Segs, NCBI_THROW, row, CSeq_align_Base::SetSegs(), and x_FillKnownStrands().

Referenced by GetDstAlign().

◆ x_GetDstDenseg() void CSeq_align_Mapper_Base::x_GetDstDenseg ( CRef< CSeq_align > &  dst ) const private

Definition at line 1331 of file seq_align_mapper_base.cpp.

References _ASSERT, eAlign_MultiDim, eNa_strand_plus, eNa_strand_unknown, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, kInvalidSeqPos, m_AlignFlags, m_HaveStrands, m_LocMapper, m_Segs, m_SegsScores, NCBI_THROW, r(), row, CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetScores(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and x_FillKnownStrands().

Referenced by GetDstAlign().

◆ x_GetDstDisc() void CSeq_align_Mapper_Base::x_GetDstDisc ( CRef< CSeq_align > &  dst ) const private ◆ x_GetDstExon()

Definition at line 1718 of file seq_align_mapper_base.cpp.

References _ASSERT, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_not_set, CSpliced_exon_chunk_Base::e_Product_ins, eNa_strand_unknown, CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CSeq_loc_Mapper_Base::eSplicedRow_Gen, CSeq_loc_Mapper_Base::eSplicedRow_Prod, CSpliced_exon_Base::GetAcceptor_before_exon(), CSpliced_exon_Base::GetDonor_after_exon(), CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetExt(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_exon_Base::GetProduct_start(), CSpliced_seg_Base::GetProduct_type(), SAlignment_Segment::SAlignment_Row::GetSegStart(), CSeq_id_Handle::GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), IsExonGap(), CProduct_pos_Base::IsProtpos(), IsReverse(), CSpliced_exon_Base::IsSetAcceptor_before_exon(), CSpliced_exon_Base::IsSetDonor_after_exon(), CSpliced_exon_Base::IsSetExt(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetProduct_type(), SAlignment_Segment::SAlignment_Row::m_Id, SAlignment_Segment::SAlignment_Row::m_IsSetStrand, m_LocMapper, SAlignment_Segment::SAlignment_Row::m_Mapped, m_OrigExon, m_Segs, m_SegsScores, SAlignment_Segment::SAlignment_Row::m_Strand, NCBI_THROW, CSpliced_exon_Base::ResetAcceptor_before_exon(), CSpliced_exon_Base::ResetDonor_after_exon(), CSpliced_seg_Base::SetExons(), CSpliced_exon_Base::SetPartial(), CSpliced_seg_Base::SetProduct_type(), and x_PushExonPart().

Referenced by x_GetDstSplicedSubAlign().

◆ x_GetDstPacked() void CSeq_align_Mapper_Base::x_GetDstPacked ( CRef< CSeq_align > &  dst ) const private

Definition at line 1585 of file seq_align_mapper_base.cpp.

References _ASSERT, eAlign_MultiDim, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, kInvalidSeqPos, m_AlignFlags, m_HaveStrands, m_LocMapper, m_Segs, m_SegsScores, r(), row, CPacked_seg_Base::SetDim(), CPacked_seg_Base::SetIds(), CPacked_seg_Base::SetLens(), CPacked_seg_Base::SetNumseg(), CPacked_seg_Base::SetPresent(), CPacked_seg_Base::SetScores(), CSeq_align_Base::SetSegs(), CPacked_seg_Base::SetStarts(), CPacked_seg_Base::SetStrands(), and x_FillKnownStrands().

Referenced by GetDstAlign().

◆ x_GetDstSparse() void CSeq_align_Mapper_Base::x_GetDstSparse ( CRef< CSeq_align > &  dst ) const private

Definition at line 2498 of file seq_align_mapper_base.cpp.

References eNa_strand_unknown, CSeq_loc_Mapper_Base::eSeq_prot, SAlignment_Segment::SAlignment_Row::GetSegStart(), CSeq_id_Handle::GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), i, IsForward(), ITERATE, m_GroupScores, SAlignment_Segment::SAlignment_Row::m_Id, SAlignment_Segment::SAlignment_Row::m_IsSetStrand, m_LocMapper, m_Segs, m_SegsScores, SAlignment_Segment::SAlignment_Row::m_Strand, NCBI_THROW, Reverse(), CSparse_seg_Base::SetRow_scores(), CSparse_seg_Base::SetRows(), and CSeq_align_Base::SetSegs().

Referenced by GetDstAlign().

◆ x_GetDstSpliced() void CSeq_align_Mapper_Base::x_GetDstSpliced ( CRef< CSeq_align > &  dst ) const private

Definition at line 2236 of file seq_align_mapper_base.cpp.

References _ASSERT, CSeq_loc::Assign(), bounds, CloneContainer(), eNa_strand_unknown, CSpliced_seg_Base::eProduct_type_protein, CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSplicedRow_Gen, CSeq_loc_Mapper_Base::eSplicedRow_Prod, CSeq_loc_Mapper_Base::fTrimSplicedSegs, CSeq_align_Base::GetBounds(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_chunk_Base::GetProduct_ins(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_type(), CSeq_align_Base::GetSegs(), CSeq_id_Handle::GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSeq_align_Base::C_Segs::GetSpliced(), IsExonGap(), CSpliced_exon_chunk_Base::IsGenomic_ins(), CSeq_loc_Base::IsNull(), IsReverse(), CSeq_align_Base::IsSetBounds(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetProduct_strand(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, SAlignment_Segment::SAlignment_Row::m_Id, m_LocMapper, CSeq_loc_Mapper_Base::m_Mappings, m_OrigAlign, m_Segs, m_SubAligns, CSeq_loc_Mapper_Base::Map(), NON_CONST_ITERATE, orig, CSeq_align_Base::SetBounds(), CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetGenomic_id(), CSpliced_seg_Base::SetGenomic_strand(), CSpliced_seg_Base::SetModifiers(), CSpliced_seg_Base::SetPoly_a(), CSpliced_seg_Base::SetProduct_id(), CSpliced_seg_Base::SetProduct_length(), CSpliced_seg_Base::SetProduct_strand(), CSeq_align_Base::SetSegs(), swap(), x_GetDstSplicedSubAlign(), and CSeq_loc_Mapper_Base::x_IsSetMiscFlag().

Referenced by GetDstAlign().

◆ x_GetDstSplicedSubAlign() void CSeq_align_Mapper_Base::x_GetDstSplicedSubAlign ( CSpliced_seg &  spliced, const CSeq_align_Mapper_Base &  sub_align, bool &  last_exon_partial, CSeq_id_Handle &  gen_id, CSeq_id_Handle &  last_gen_id, bool &  single_gen_id, ENa_strand &  gen_strand, bool &  single_gen_str, CSeq_id_Handle &  prod_id, CSeq_id_Handle &  last_prod_id, bool &  single_prod_id, ENa_strand &  prod_strand, bool &  single_prod_str, bool &  partial  ) const private ◆ x_GetDstStd() void CSeq_align_Mapper_Base::x_GetDstStd ( CRef< CSeq_align > &  dst ) const private

Definition at line 1411 of file seq_align_mapper_base.cpp.

References _ASSERT, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::GetSeqTypeById(), IsReverse(), ITERATE, kInvalidSeqPos, m_LocMapper, m_Segs, SAlignment_Segment::SAlignment_Row::m_Start, SAlignment_Segment::SAlignment_Row::m_Strand, row, CSeq_loc::SetEmpty(), CSeq_loc::SetInt(), CSeq_align_Base::SetSegs(), and swap().

Referenced by GetDstAlign().

◆ x_GetPartialDenseg()

Definition at line 2606 of file seq_align_mapper_base.cpp.

References _ASSERT, eNa_strand_plus, eNa_strand_unknown, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_align_Base::eType_partial, GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), i, IsReverse(), ITERATE, kInvalidSeqPos, m_HaveStrands, m_LocMapper, SAlignment_Segment::m_Rows, m_Segs, r(), CRef< C, Locker >::Reset(), row, SameOrientation(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CSeq_align_Base::SetType(), and x_FillKnownStrands().

Referenced by x_ConvToDstDisc().

◆ x_HaveMixedSeqTypes() bool CSeq_align_Mapper_Base::x_HaveMixedSeqTypes ( void  ) const private ◆ x_HaveMixedStrand() bool CSeq_align_Mapper_Base::x_HaveMixedStrand ( void  ) const private ◆ x_Init() [1/8]

Definition at line 327 of file seq_align_mapper_base.cpp.

References SAlignment_Segment::AddRow(), set< Key, Compare >::empty(), eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CDense_seg_Base::GetDim(), CSeq_id_Handle::GetHandle(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetScores(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), set< Key, Compare >::insert(), CDense_seg_Base::IsSetScores(), CDense_seg_Base::IsSetStrands(), ITERATE, m_Dim, m_HaveStrands, SAlignment_Segment::m_Len, m_LocMapper, m_SegsScores, min(), NCBI_THROW, row, CSeq_loc_Mapper_Base::SetSeqTypeById(), Warning(), and x_PushSeg().

◆ x_Init() [2/8]

Definition at line 603 of file seq_align_mapper_base.cpp.

References SAlignment_Segment::AddRow(), eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CPacked_seg_Base::GetDim(), CPacked_seg_Base::GetIds(), CPacked_seg_Base::GetLens(), CPacked_seg_Base::GetNumseg(), CPacked_seg_Base::GetPresent(), CPacked_seg_Base::GetScores(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CPacked_seg_Base::GetStarts(), CPacked_seg_Base::GetStrands(), CPacked_seg_Base::IsSetScores(), CPacked_seg_Base::IsSetStrands(), kInvalidSeqPos, m_Dim, m_HaveStrands, SAlignment_Segment::m_Len, m_LocMapper, m_SegsScores, min(), NCBI_THROW, row, Warning(), and x_PushSeg().

◆ x_Init() [3/8]

Definition at line 181 of file seq_align_mapper_base.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::C_Segs::GetPacked(), CSeq_align_Base::GetScore(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), CSeq_align_Base::IsSetScore(), m_AlignScores, m_OrigAlign, CConstRef< C, Locker >::Reset(), and CSeq_align_Base::C_Segs::Which().

Referenced by CSeq_align_Mapper_Base().

◆ x_Init() [4/8] ◆ x_Init() [5/8]

Definition at line 820 of file seq_align_mapper_base.cpp.

References SAlignment_Segment::AddRow(), eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CSparse_seg_Base::GetRow_scores(), CSparse_seg_Base::GetRows(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSparse_seg_Base::IsSetRow_scores(), m_Dim, m_GroupScores, m_HaveStrands, m_LocMapper, SAlignment_Segment::m_ScoresGroupIdx, m_SegsScores, min(), NCBI_THROW, row, Warning(), and x_PushSeg().

◆ x_Init() [6/8] ◆ x_Init() [7/8]

Definition at line 255 of file seq_align_mapper_base.cpp.

References SAlignment_Segment::AddRow(), eAlign_MultiDim, eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CDense_diag_Base::GetDim(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetLen(), CDense_diag_Base::GetScores(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CDense_diag_Base::GetStarts(), CDense_diag_Base::GetStrands(), CDense_diag_Base::IsSetScores(), CDense_diag_Base::IsSetStrands(), ITERATE, m_AlignFlags, m_Dim, m_HaveStrands, SAlignment_Segment::m_Len, m_LocMapper, SAlignment_Segment::m_Scores, max(), min(), NCBI_THROW, row, Warning(), and x_PushSeg().

◆ x_Init() [8/8] void CSeq_align_Mapper_Base::x_Init ( const TStd &  sseg ) private

Definition at line 412 of file seq_align_mapper_base.cpp.

References _ASSERT, SAlignment_Segment::AddRow(), CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, eAlign_MultiDim, eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CStd_seg_Base::GetDim(), CRange_Base::GetFrom(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CStd_seg_Base::GetIds(), CSeq_loc_Base::GetInt(), COpenRange< Position >::GetLength(), CSeq_loc_Base::GetPnt(), CStd_seg_Base::GetScores(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSeq_loc::GetStrand(), CSeq_loc::GetTotalRange(), int, CStd_seg_Base::IsSetIds(), CStd_seg_Base::IsSetScores(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), CSeq_loc_Base::IsWhole(), ITERATE, kInvalidSeqPos, len, m_AlignFlags, m_Dim, m_HaveStrands, SAlignment_Segment::m_Len, m_LocMapper, SAlignment_Segment::m_Rows, SAlignment_Segment::m_Scores, max(), min(), NCBI_THROW, CSeq_loc_Mapper_Base::SetSeqTypeById(), swap(), Warning(), CSeq_loc_Base::Which(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), and x_PushSeg().

◆ x_InsertSeg() ◆ x_InvalidateScores() ◆ x_IsEmpty() bool CSeq_align_Mapper_Base::x_IsEmpty ( void  ) const private ◆ x_PushExonPart() ◆ x_PushSeg() ◆ m_AlignFlags ◆ m_AlignScores TScores CSeq_align_Mapper_Base::m_AlignScores private ◆ m_Dim size_t CSeq_align_Mapper_Base::m_Dim private ◆ m_DstAlign ◆ m_GroupScores ◆ m_HaveStrands bool CSeq_align_Mapper_Base::m_HaveStrands private ◆ m_LocMapper

Definition at line 303 of file seq_align_mapper_base.hpp.

Referenced by CreateSubAlign(), GetDstAlign(), GetLocMapper(), x_ConvertSegment(), x_GetDstDendiag(), x_GetDstDenseg(), x_GetDstExon(), x_GetDstPacked(), x_GetDstSparse(), x_GetDstSpliced(), x_GetDstStd(), x_GetPartialDenseg(), x_HaveMixedSeqTypes(), and x_Init().

◆ m_OrigAlign ◆ m_OrigExon ◆ m_ScoresInvalidated bool CSeq_align_Mapper_Base::m_ScoresInvalidated private ◆ m_Segs

Definition at line 344 of file seq_align_mapper_base.hpp.

Referenced by GetDstAlign(), GetRowId(), x_ConvertAlign(), x_ConvertRow(), CSeq_align_Mapper::x_ConvertRowCvt(), x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), x_ConvToDstDisc(), x_FillKnownStrands(), x_GetDstDendiag(), x_GetDstDenseg(), x_GetDstExon(), x_GetDstPacked(), x_GetDstSparse(), x_GetDstSpliced(), x_GetDstSplicedSubAlign(), x_GetDstStd(), x_GetPartialDenseg(), x_HaveMixedSeqTypes(), x_HaveMixedStrand(), x_InsertSeg(), x_IsEmpty(), and x_PushSeg().

◆ m_SegsScores TScores CSeq_align_Mapper_Base::m_SegsScores private ◆ m_SubAligns

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

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