CSeq_align_Mapper_Base Class Reference

Search Toolkit Book for CSeq_align_Mapper_Base

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

#include <objects/seq/seq_align_mapper_base.hpp>

Inheritance diagram for CSeq_align_Mapper_Base:

Collaboration diagram for CSeq_align_Mapper_Base:

Public Types
typedef CSeq_align::C_Segs::TDendiag	TDendiag
typedef CSeq_align::C_Segs::TStd	TStd
typedef list< SAlignment_Segment >	TSegments
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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	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...
Public Member Functions inherited from CObject
	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...
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

Protected Types
enum	EAlignFlags { eAlign_Normal , eAlign_Empty , eAlign_MultiId , eAlign_MultiDim }
typedef vector< CRef< CSeq_align_Mapper_Base > >	TSubAligns

Protected Member Functions
	CSeq_align_Mapper_Base (CSeq_loc_Mapper_Base &loc_mapper)
CSeq_loc_Mapper_Base &	GetLocMapper (void) const
size_t	GetMaxDim (void) const
	Get max number of rows of all segments. More...
virtual CSeq_align_Mapper_Base *	CreateSubAlign (const CSeq_align &align)
virtual CSeq_align_Mapper_Base *	CreateSubAlign (const CSpliced_seg &spliced, const CSpliced_exon &exon)
void	InitExon (const CSpliced_seg &spliced, const CSpliced_exon &exon)
void	x_Init (const CSeq_align &align)
SAlignment_Segment &	x_InsertSeg (TSegments::iterator &where, int len, size_t dim, bool reverse)
void	x_InvalidateScores (SAlignment_Segment *seg=NULL)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CRef< CSeq_align >	m_DstAlign
TSubAligns	m_SubAligns
TSegments	m_Segs
EAlignFlags	m_AlignFlags

Private Types
typedef vector< ENa_strand >	TStrands
typedef SAlignment_Segment::TScores	TScores
typedef vector< TScores >	TScoresGroups

Private Member Functions
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

Private Attributes
CSeq_loc_Mapper_Base &	m_LocMapper
CConstRef< CSeq_align >	m_OrigAlign
CConstRef< CSpliced_exon >	m_OrigExon
bool	m_HaveStrands
size_t	m_Dim
TScores	m_AlignScores
TScores	m_SegsScores
TScoresGroups	m_GroupScores
bool	m_ScoresInvalidated

Additional Inherited Members
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)
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...

Detailed Description

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.

Member Typedef Documentation

TDendiag

typedef CSeq_align::C_Segs::TDendiag CSeq_align_Mapper_Base::TDendiag

Definition at line 131 of file seq_align_mapper_base.hpp.

TScores

typedef SAlignment_Segment::TScores CSeq_align_Mapper_Base::TScores

private

Definition at line 314 of file seq_align_mapper_base.hpp.

TScoresGroups

typedef vector<TScores> CSeq_align_Mapper_Base::TScoresGroups

private

Definition at line 315 of file seq_align_mapper_base.hpp.

TSegments

typedef list<SAlignment_Segment> CSeq_align_Mapper_Base::TSegments

Definition at line 157 of file seq_align_mapper_base.hpp.

TStd

typedef CSeq_align::C_Segs::TStd CSeq_align_Mapper_Base::TStd

Definition at line 132 of file seq_align_mapper_base.hpp.

TStrands

typedef vector<ENa_strand> CSeq_align_Mapper_Base::TStrands

private

Definition at line 234 of file seq_align_mapper_base.hpp.

TSubAligns

typedef vector< CRef<CSeq_align_Mapper_Base> > CSeq_align_Mapper_Base::TSubAligns

protected

Definition at line 330 of file seq_align_mapper_base.hpp.

Member Enumeration Documentation

EAlignFlags

enum CSeq_align_Mapper_Base::EAlignFlags

protected

Enumerator
eAlign_Normal
eAlign_Empty
eAlign_MultiId
eAlign_MultiDim

Definition at line 335 of file seq_align_mapper_base.hpp.

Constructor & Destructor Documentation

CSeq_align_Mapper_Base() [1/2]

CSeq_align_Mapper_Base::CSeq_align_Mapper_Base	(	const CSeq_align &	align,
		CSeq_loc_Mapper_Base &	loc_mapper
	)

Definition at line 135 of file seq_align_mapper_base.cpp.

References x_Init().

Referenced by CreateSubAlign().

~CSeq_align_Mapper_Base()

CSeq_align_Mapper_Base::~CSeq_align_Mapper_Base

(

void

)

Definition at line 150 of file seq_align_mapper_base.cpp.

CSeq_align_Mapper_Base() [2/2]

CSeq_align_Mapper_Base::CSeq_align_Mapper_Base ( CSeq_loc_Mapper_Base &  loc_mapper )

protected

Definition at line 121 of file seq_align_mapper_base.cpp.

Member Function Documentation

Convert() [1/2]

void CSeq_align_Mapper_Base::Convert

(

size_t

row

)

Map a single row of the alignment through the linked seq-loc mapper.

Definition at line 930 of file seq_align_mapper_base.cpp.

References m_DstAlign, m_SubAligns, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), x_ConvertAlign(), and x_InvalidateScores().

Convert() [2/2]

void CSeq_align_Mapper_Base::Convert

(

void

)

Map the whole alignment through the linked seq-loc mapper.

Definition at line 904 of file seq_align_mapper_base.cpp.

References m_DstAlign, m_SubAligns, NON_CONST_ITERATE, NULL, CRef< C, Locker >::Reset(), x_ConvertAlign(), and x_InvalidateScores().

Referenced by CSeq_align_Mapper::Convert().

CreateSubAlign() [1/2]

CSeq_align_Mapper_Base * CSeq_align_Mapper_Base::CreateSubAlign ( const CSeq_align &  align )

protectedvirtual

Reimplemented in CSeq_align_Mapper.

Definition at line 3053 of file seq_align_mapper_base.cpp.

References CSeq_align_Mapper_Base(), and m_LocMapper.

Referenced by x_Init().

CreateSubAlign() [2/2]

CSeq_align_Mapper_Base * CSeq_align_Mapper_Base::CreateSubAlign ( const CSpliced_seg &  spliced, const CSpliced_exon &  exon  )

protectedvirtual

Reimplemented in CSeq_align_Mapper.

Definition at line 3061 of file seq_align_mapper_base.cpp.

References CSeq_align_Mapper_Base(), and m_LocMapper.

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()

CRef< CSeq_align > CSeq_align_Mapper_Base::GetDstAlign

(

void

)

const

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(), 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()

CSeq_loc_Mapper_Base& CSeq_align_Mapper_Base::GetLocMapper ( void  ) const

inlineprotected

Definition at line 168 of file seq_align_mapper_base.hpp.

References m_LocMapper.

Referenced by CSeq_align_Mapper::CreateSubAlign().

GetMaxDim()

size_t CSeq_align_Mapper_Base::GetMaxDim ( void  ) const

inlineprotected

Get max number of rows of all segments.

Definition at line 392 of file seq_align_mapper_base.hpp.

Referenced by CSeq_align_Mapper::x_ConvertAlignCvt().

GetRowId()

const CSeq_id_Handle & CSeq_align_Mapper_Base::GetRowId

(

size_t

idx

)

const

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()

const CSeq_align_Mapper_Base::TSegments & CSeq_align_Mapper_Base::GetSegments ( void  ) const

inline

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()

void CSeq_align_Mapper_Base::InitExon ( const CSpliced_seg &  spliced, const CSpliced_exon &  exon  )

protected

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

Definition at line 950 of file seq_align_mapper_base.cpp.

References m_Dim, m_Segs, and x_ConvertRow().

Referenced by Convert().

x_ConvertRow()

void CSeq_align_Mapper_Base::x_ConvertRow ( size_t  row )

private

Definition at line 966 of file seq_align_mapper_base.cpp.

References eAlign_MultiDim, eAlign_MultiId, eAlign_Normal, m_AlignFlags, m_Segs, and x_ConvertSegment().

Referenced by x_ConvertAlign().

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(), 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

Definition at line 2793 of file seq_align_mapper_base.cpp.

References m_Segs, CSeq_align_Base::SetSegs(), and x_GetPartialDenseg().

Referenced by GetDstAlign().

x_FillKnownStrands()

void CSeq_align_Mapper_Base::x_FillKnownStrands ( TStrands &  strands ) const

private

Definition at line 1242 of file seq_align_mapper_base.cpp.

References eAlign_MultiDim, eNa_strand_plus, eNa_strand_unknown, ITERATE, m_AlignFlags, and m_Segs.

Referenced by x_GetDstDendiag(), x_GetDstDenseg(), x_GetDstPacked(), and x_GetPartialDenseg().

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, 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_id_Handle::GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, kInvalidSeqPos, m_AlignFlags, m_HaveStrands, SAlignment_Segment::SAlignment_Row::m_Id, m_LocMapper, m_Segs, m_SegsScores, SAlignment_Segment::SAlignment_Row::m_Start, NCBI_THROW, r(), 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

Definition at line 1643 of file seq_align_mapper_base.cpp.

References ITERATE, m_SubAligns, and CSeq_align_Base::SetSegs().

Referenced by GetDstAlign().

x_GetDstExon()

bool CSeq_align_Mapper_Base::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

private

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_id_Handle::GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, kInvalidSeqPos, m_AlignFlags, m_HaveStrands, SAlignment_Segment::SAlignment_Row::m_Id, m_LocMapper, m_Segs, m_SegsScores, SAlignment_Segment::SAlignment_Row::m_Start, r(), 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(), 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

Definition at line 2162 of file seq_align_mapper_base.cpp.

References eNa_strand_unknown, m_Segs, and x_GetDstExon().

Referenced by x_GetDstSpliced().

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, CSeq_loc::SetEmpty(), CSeq_loc::SetInt(), CSeq_align_Base::SetSegs(), and swap().

Referenced by GetDstAlign().

x_GetPartialDenseg()

ssize_t CSeq_align_Mapper_Base::x_GetPartialDenseg ( CRef< CSeq_align > &  dst, size_t  start_seg  ) const

private

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, SAlignment_Segment::SAlignment_Row::GetSegStart(), GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), i, IsReverse(), ITERATE, kInvalidSeqPos, m_HaveStrands, SAlignment_Segment::SAlignment_Row::m_Id, SAlignment_Segment::SAlignment_Row::m_IsSetStrand, m_LocMapper, SAlignment_Segment::m_Rows, m_Segs, SAlignment_Segment::SAlignment_Row::m_Strand, r(), CRef< C, Locker >::Reset(), 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

Definition at line 2812 of file seq_align_mapper_base.cpp.

References CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, m_LocMapper, and m_Segs.

Referenced by GetDstAlign().

x_HaveMixedStrand()

bool CSeq_align_Mapper_Base::x_HaveMixedStrand ( void  ) const

private

Definition at line 2835 of file seq_align_mapper_base.cpp.

References eNa_strand_unknown, SAlignment_Segment::SAlignment_Row::GetSegStart(), ITERATE, SAlignment_Segment::SAlignment_Row::m_IsSetStrand, m_Segs, SAlignment_Segment::SAlignment_Row::m_Strand, r(), and SameOrientation().

x_Init() [1/8]

void CSeq_align_Mapper_Base::x_Init ( const CDense_seg &  denseg )

private

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, CSeq_loc_Mapper_Base::SetSeqTypeById(), Warning(), and x_PushSeg().

x_Init() [2/8]

void CSeq_align_Mapper_Base::x_Init ( const CPacked_seg &  pseg )

private

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, Warning(), and x_PushSeg().

x_Init() [3/8]

void CSeq_align_Mapper_Base::x_Init ( const CSeq_align &  align )

protected

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]

void CSeq_align_Mapper_Base::x_Init ( const CSeq_align_set &  align_set )

private

Definition at line 677 of file seq_align_mapper_base.cpp.

References CreateSubAlign(), CSeq_align_set_Base::Get(), ITERATE, m_SubAligns, and Ref().

x_Init() [5/8]

void CSeq_align_Mapper_Base::x_Init ( const CSparse_seg &  sparse )

private

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_align_Base::GetFirst_id(), CSparse_align_Base::GetFirst_starts(), CSparse_align_Base::GetLens(), CSparse_align_Base::GetNumseg(), CSparse_seg_Base::GetRow_scores(), CSparse_seg_Base::GetRows(), CSparse_align_Base::GetSecond_id(), CSparse_align_Base::GetSecond_starts(), CSparse_align_Base::GetSecond_strands(), CSparse_align_Base::GetSeg_scores(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSparse_seg_Base::IsSetRow_scores(), CSparse_align_Base::IsSetSecond_strands(), CSparse_align_Base::IsSetSeg_scores(), m_Dim, m_GroupScores, m_HaveStrands, m_LocMapper, SAlignment_Segment::m_ScoresGroupIdx, m_SegsScores, min(), NCBI_THROW, Warning(), and x_PushSeg().

x_Init() [6/8]

void CSeq_align_Mapper_Base::x_Init ( const CSpliced_seg &  spliced )

private

Definition at line 810 of file seq_align_mapper_base.cpp.

References CreateSubAlign(), CSpliced_seg_Base::GetExons(), ITERATE, m_SubAligns, and Ref().

x_Init() [7/8]

void CSeq_align_Mapper_Base::x_Init ( const TDendiag &  diags )

private

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, 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()

SAlignment_Segment & CSeq_align_Mapper_Base::x_InsertSeg ( TSegments::iterator &  where, int  len, size_t  dim, bool  reverse  )

protected

Definition at line 240 of file seq_align_mapper_base.cpp.

References len, and m_Segs.

Referenced by x_ConvertSegment(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

x_InvalidateScores()

void CSeq_align_Mapper_Base::x_InvalidateScores ( SAlignment_Segment *  seg = NULL )

protected

Definition at line 3082 of file seq_align_mapper_base.cpp.

References m_AlignScores, SAlignment_Segment::m_Scores, SAlignment_Segment::m_ScoresGroupIdx, m_ScoresInvalidated, and m_SegsScores.

Referenced by Convert(), x_ConvertSegment(), and CSeq_align_Mapper::x_ConvertSegmentCvt().

x_IsEmpty()

bool CSeq_align_Mapper_Base::x_IsEmpty ( void  ) const

private

Definition at line 2867 of file seq_align_mapper_base.cpp.

References ITERATE, kInvalidSeqPos, m_Segs, and m_SubAligns.

Referenced by GetDstAlign().

x_PushExonPart()

void CSeq_align_Mapper_Base::x_PushExonPart ( CRef< CSpliced_exon_chunk > &  last_part, CSpliced_exon_chunk::E_Choice  part_type, int  part_len, CSpliced_exon &  exon  ) const

private

Definition at line 1688 of file seq_align_mapper_base.cpp.

References CRef< C, Locker >::Reset(), SetPartLength(), and CSpliced_exon_Base::SetParts().

Referenced by x_GetDstExon().

x_PushSeg()

SAlignment_Segment & CSeq_align_Mapper_Base::x_PushSeg ( int  len, size_t  dim, ENa_strand  strand = eNa_strand_unknown  )

private

Definition at line 220 of file seq_align_mapper_base.cpp.

References IsReverse(), len, and m_Segs.

Referenced by InitExon(), and x_Init().

Member Data Documentation

m_AlignFlags

EAlignFlags CSeq_align_Mapper_Base::m_AlignFlags

protected

Definition at line 345 of file seq_align_mapper_base.hpp.

Referenced by GetDstAlign(), x_ConvertRow(), CSeq_align_Mapper::x_ConvertRowCvt(), x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), x_FillKnownStrands(), x_GetDstDenseg(), x_GetDstPacked(), and x_Init().

m_AlignScores

TScores CSeq_align_Mapper_Base::m_AlignScores

private

Definition at line 318 of file seq_align_mapper_base.hpp.

Referenced by GetDstAlign(), x_Init(), and x_InvalidateScores().

m_Dim

size_t CSeq_align_Mapper_Base::m_Dim

private

Definition at line 311 of file seq_align_mapper_base.hpp.

Referenced by GetDim(), InitExon(), x_ConvertAlign(), and x_Init().

m_DstAlign

CRef<CSeq_align> CSeq_align_Mapper_Base::m_DstAlign

mutableprotected

Definition at line 342 of file seq_align_mapper_base.hpp.

Referenced by CSeq_align_Mapper::Convert(), Convert(), and GetDstAlign().

m_GroupScores

TScoresGroups CSeq_align_Mapper_Base::m_GroupScores

private

Definition at line 322 of file seq_align_mapper_base.hpp.

Referenced by x_GetDstSparse(), and x_Init().

m_HaveStrands

bool CSeq_align_Mapper_Base::m_HaveStrands

private

Definition at line 309 of file seq_align_mapper_base.hpp.

Referenced by InitExon(), x_ConvertSegment(), x_GetDstDenseg(), x_GetDstPacked(), x_GetPartialDenseg(), and x_Init().

m_LocMapper

CSeq_loc_Mapper_Base& CSeq_align_Mapper_Base::m_LocMapper

private

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

CConstRef<CSeq_align> CSeq_align_Mapper_Base::m_OrigAlign

private

Definition at line 305 of file seq_align_mapper_base.hpp.

Referenced by GetDstAlign(), x_GetDstSpliced(), and x_Init().

m_OrigExon

CConstRef<CSpliced_exon> CSeq_align_Mapper_Base::m_OrigExon

private

Definition at line 307 of file seq_align_mapper_base.hpp.

Referenced by InitExon(), and x_GetDstExon().

m_ScoresInvalidated

bool CSeq_align_Mapper_Base::m_ScoresInvalidated

private

Definition at line 325 of file seq_align_mapper_base.hpp.

Referenced by x_InvalidateScores().

m_Segs

TSegments CSeq_align_Mapper_Base::m_Segs

mutableprotected

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

Definition at line 320 of file seq_align_mapper_base.hpp.

Referenced by InitExon(), x_GetDstDenseg(), x_GetDstExon(), x_GetDstPacked(), x_GetDstSparse(), x_Init(), and x_InvalidateScores().

m_SubAligns

TSubAligns CSeq_align_Mapper_Base::m_SubAligns

protected

Definition at line 343 of file seq_align_mapper_base.hpp.

Referenced by CSeq_align_Mapper::Convert(), Convert(), x_GetDstDisc(), x_GetDstSpliced(), x_Init(), and x_IsEmpty().

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

• include/objects/seq/seq_align_mapper_base.hpp
• src/objects/seq/seq_align_mapper_base.cpp